Oct4 redox sensitivity potentiates reprogramming and differentiation.

The transcription factor Oct4/Pou5f1 is a component of the regulatory circuitry governing pluripotency and is widely used to induce pluripotency from somatic cells. Here we used domain swapping and mutagenesis to study Oct4's reprogramming ability, identifying a redox-sensitive DNA binding domain, cysteine residue (Cys48), as a key determinant of reprogramming and differentiation. Oct4 Cys48 sensitizes the protein to oxidative inhibition of DNA binding activity and promotes oxidation-mediated protein ubiquitylation. Pou5f1 C48S point mutation has little effect on undifferentiated embryonic stem cells (ESCs) but upon retinoic acid (RA) treatment causes retention of Oct4 expression, deregulated gene expression, and aberrant differentiation. Pou5f1 C48S ESCs also form less differentiated teratomas and contribute poorly to adult somatic tissues. Finally, we describe Pou5f1 C48S (Janky) mice, which in the homozygous condition are severely developmentally restricted after E4.5. Rare animals bypassing this restriction appear normal at birth but are sterile. Collectively, these findings uncover a novel Oct4 redox mechanism involved in both entry into and exit from pluripotency.

Structure and functional determinants of Rad6-Bre1 subunits in the histone H2B ubiquitin-conjugating complex.

The conserved complex of the Rad6 E2 ubiquitin-conjugating enzyme and the Bre1 E3 ubiquitin ligase catalyzes histone H2B monoubiquitination (H2Bub1), which regulates chromatin dynamics during transcription and other nuclear processes. Here, we report a crystal structure of Rad6 and the non-RING domain N-terminal region of Bre1, which shows an asymmetric homodimer of Bre1 contacting a conserved loop on the Rad6 'backside'. This contact is distant from the Rad6 catalytic site and is the location of mutations that impair telomeric silencing in yeast. Mutational analyses validated the importance of this contact for the Rad6-Bre1 interaction, chromatin-binding dynamics, H2Bub1 formation and gene expression. Moreover, the non-RING N-terminal region of Bre1 is sufficient to confer nucleosome binding ability to Rad6 in vitro. Interestingly, Rad6 P43L protein, an interaction interface mutant and equivalent to a cancer mutation in the human homolog, bound Bre1 5-fold more tightly than native Rad6 in vitro, but showed reduced chromatin association of Bre1 and reduced levels of H2Bub1 in vivo. These surprising observations imply conformational transitions of the Rad6-Bre1 complex during its chromatin-associated functional cycle, and reveal the differential effects of specific disease-relevant mutations on the chromatin-bound and unbound states. Overall, our study provides structural insights into Rad6-Bre1 interaction through a novel interface that is important for their biochemical and biological responses.

A toolbox for class I HDACs reveals isoform specific roles in gene regulation and protein acetylation.

The class I histone deacetylases are essential regulators of cell fate decisions in health and disease. While pan- and class-specific HDAC inhibitors are available, these drugs do not allow a comprehensive understanding of individual HDAC function, or the therapeutic potential of isoform-specific targeting. To systematically compare the impact of individual catalytic functions of HDAC1, HDAC2 and HDAC3, we generated human HAP1 cell lines expressing catalytically inactive HDAC enzymes. Using this genetic toolbox we compare the effect of individual HDAC inhibition with the effects of class I specific inhibitors on cell viability, protein acetylation and gene expression. Individual inactivation of HDAC1 or HDAC2 has only mild effects on cell viability, while HDAC3 inactivation or loss results in DNA damage and apoptosis. Inactivation of HDAC1/HDAC2 led to increased acetylation of components of the COREST co-repressor complex, reduced deacetylase activity associated with this complex and derepression of neuronal genes. HDAC3 controls the acetylation of nuclear hormone receptor associated proteins and the expression of nuclear hormone receptor regulated genes. Acetylation of specific histone acetyltransferases and HDACs is sensitive to inactivation of HDAC1/HDAC2. Over a wide range of assays, we determined that in particular HDAC1 or HDAC2 catalytic inactivation mimics class I specific HDAC inhibitors. Importantly, we further demonstrate that catalytic inactivation of HDAC1 or HDAC2 sensitizes cells to specific cancer drugs. In summary, our systematic study revealed isoform-specific roles of HDAC1/2/3 catalytic functions. We suggest that targeted genetic inactivation of particular isoforms effectively mimics pharmacological HDAC inhibition allowing the identification of relevant HDACs as targets for therapeutic intervention.

Exploring the Recent Pioneering Developments of Small Molecules in Antimalarial Drug Armamentarium: A Chemistry Prospective Appraisal.

Malaria is a very destructive and lethal parasitic disease that causes significant mortality worldwide, resulting in the loss of millions of lives annually. It is an infectious disease transmitted by mosquitoes, which is caused by different species of the parasite protozoan belonging to the genus Plasmodium. The uncontrolled intake of antimalarial drugs often employed in clinical settings has resulted in the emergence of numerous strains of plasmodium that are resistant to these drugs, including multidrug-resistant strains. This resistance significantly diminishes the effectiveness of many primary drugs used in the treatment of malaria. Hence, there is an urgent need for developing unique classes of antimalarial drugs that function with distinct mechanisms of action. In this context, the design and development of hybrid compounds that combine pharmacophoric properties from different lead molecules into a single unit gives a unique perspective towards further development of malaria drugs in the next generation. In recent years, the field of medicinal chemistry has made significant efforts resulting in the discovery and synthesis of numerous small novel compounds that exhibit potent antimalarial properties, while also demonstrating reduced toxicity and desirable efficacy. In light of this, we have reviewed the progress of hybrid antimalarial agents from 2021 up to the present. This manuscript presents a comprehensive overview of the latest advancements in the medicinal chemistry pertaining to small molecules, with a specific focus on their potential as antimalarial agents. As possible antimalarial drugs that might target both the dual stage and multi-stage stages of the parasite life cycle, these small hybrid molecules have been studied. This review explores a variety of physiologically active compounds that have been described in the literature in order to lay a strong foundation for the logical design and eventual identification of antimalarial drugs based on lead frameworks.

A framework to identify functional interactors that contribute to disrupted early retinal development in Vsx2 ocular retardation J mice.

BACKGROUND: A goal of developmental genetics is to identify functional interactions that underlie phenotypes caused by mutations. We sought to identify functional interactors of Vsx2, which when mutated, disrupts early retinal development. We utilized the Vsx2 loss-of-function mouse, ocular retardation J (orJ), to assess interactions based on principles of positive and negative epistasis as applied to bulk transcriptome data. This was first tested in vivo with Mitf, a target of Vsx2 repression, and then to cultures of orJ retina treated with inhibitors of Retinoid-X Receptors (RXR) to target Rxrg, an up-regulated gene in the orJ retina, and gamma-Secretase, an enzyme required for Notch signaling, a key mediator of retinal proliferation and neurogenesis. RESULTS: Whereas Mitf exhibited robust positive epistasis with Vsx2, it only partially accounts for the orJ phenotype, suggesting other functional interactors. RXR inhibition yielded minimal evidence for epistasis between Vsx2 and Rxrg. In contrast, gamma-Secretase inhibition caused hundreds of Vsx2-dependent genes associated with proliferation to deviate further from wild-type, providing evidence for convergent negative epistasis with Vsx2 in regulating tissue growth. CONCLUSIONS: Combining in vivo and ex vivo testing with transcriptome analysis revealed quantitative and qualitative characteristics of functional interaction between Vsx2, Mitf, RXR, and gamma-Secretase activities.

Mutations of Rad6 E2 ubiquitin-conjugating enzymes at alanine-126 in helix-3 affect ubiquitination activity and decrease enzyme stability.

Rad6, an E2 ubiquitin-conjugating enzyme conserved from yeast to humans, functions in transcription, genome maintenance, and proteostasis. The contributions of many conserved secondary structures of Rad6 and its human homologs UBE2A and UBE2B to their biological functions are not understood. A mutant RAD6 allele with a missense substitution at alanine-126 (A126) of helix-3 that causes defects in telomeric gene silencing, DNA repair, and protein degradation was reported over 2 decades ago. Here, using a combination of genetics, biochemical, biophysical, and computational approaches, we discovered that helix-3 A126 mutations compromise the ability of Rad6 to ubiquitinate target proteins without disrupting interactions with partner E3 ubiquitin-ligases that are required for their various biological functions in vivo. Explaining the defective in vitro or in vivo ubiquitination activities, molecular dynamics simulations and NMR showed that helix-3 A126 mutations cause local disorder of the catalytic pocket of Rad6 in addition to disorganizing the global structure of the protein to decrease its stability in vivo. We also show that helix-3 A126 mutations deform the structures of UBE2A and UBE2B, the human Rad6 homologs, and compromise the in vitro ubiquitination activity and folding of UBE2B. Providing insights into their ubiquitination defects, we determined helix-3 A126 mutations impair the initial ubiquitin charging and the final discharging steps during substrate ubiquitination by Rad6. In summary, our studies reveal that the conserved helix-3 is a crucial structural constituent that controls the organization of catalytic pockets, enzymatic activities, and biological functions of the Rad6-family E2 ubiquitin-conjugating enzymes.

Optimizing variable flip angles in magnetization-prepared gradient-echo sequences for efficient 3D-T1ρ mapping.

PURPOSE: To optimize the choice of the flip angles of magnetization-prepared gradient-echo sequences for improved accuracy, precision, and speed of 3D-T1ρ mapping. METHODS: We propose a new optimization approach for finding variable flip-angle values that improve magnetization-prepared gradient-echo sequences used for 3D-T1ρ mapping. This new approach can improve the accuracy and SNR, while reducing filtering effects. We demonstrate the concept in the three different versions of the magnetization-prepared gradient-echo sequences that are typically used for 3D-T1ρ mapping and evaluate their performance in model agarose phantoms (n = 4) and healthy volunteers (n = 5) for knee joint imaging. We also tested the optimization with sequence parameters targeting faster acquisitions. RESULTS: Our results show that optimized variable flip angle can improve the accuracy and the precision of the sequences, seen as a reduction of the mean of normalized absolute difference from about 5%-6% to 3%-4% in model phantoms and from 15%-16% to 11%-13% in the knee joint, and improving SNR from about 12-28 to 22-32 in agarose phantoms and about 7-14 to 13-17 in healthy volunteers. The optimization can also compensate for the loss in quality caused by making the sequence faster. This results in sequence configurations that acquire more data per unit of time with SNR and mean of normalized absolute difference measurements close to its slower versions. CONCLUSION: The optimization of the variable flip angle can be used to increase accuracy and precision, and to improve the speed of the typical imaging sequences used for quantitative 3D-T1ρ mapping of the knee joint.

Comparison of a Deep Learning-Accelerated vs. Conventional T2-Weighted Sequence in Biparametric MRI of the Prostate.

BACKGROUND: Demand for prostate MRI is increasing, but scan times remain long even in abbreviated biparametric MRIs (bpMRI). Deep learning can be leveraged to accelerate T2-weighted imaging (T2WI). PURPOSE: To compare conventional bpMRIs (CL-bpMRI) with bpMRIs including a deep learning-accelerated T2WI (DL-bpMRI) in diagnosing prostate cancer. STUDY TYPE: Retrospective. POPULATION: Eighty consecutive men, mean age 66 years (47-84) with suspected prostate cancer or prostate cancer on active surveillance who had a prostate MRI from December 28, 2020 to April 28, 2021 were included. Follow-up included prostate biopsy or stability of prostate-specific antigen (PSA) for 1 year. FIELD STRENGTH AND SEQUENCES: A 3 T MRI. Conventional axial and coronal T2 turbo spin echo (CL-T2), 3-fold deep learning-accelerated axial and coronal T2-weighted sequence (DL-T2), diffusion weighted imaging (DWI) with b = 50 sec/mm2 , 1000 sec/mm2 , calculated b = 1500 sec/mm2 . ASSESSMENT: CL-bpMRI and DL-bpMRI including the same conventional diffusion-weighted imaging (DWI) were presented to three radiologists (blinded to acquisition method) and to a deep learning computer-assisted detection algorithm (DL-CAD). The readers evaluated image quality using a 4-point Likert scale (1 = nondiagnostic, 4 = excellent) and graded lesions using Prostate Imaging Reporting and Data System (PI-RADS) v2.1. DL-CAD identified and assigned lesions of PI-RADS 3 or greater. STATISTICAL TESTS: Quality metrics were compared using Wilcoxon signed rank test, and area under the receiver operating characteristic curve (AUC) were compared using Delong's test. SIGNIFICANCE: P = 0.05. RESULTS: Eighty men were included (age: 66 ± 9 years; 17/80 clinically significant prostate cancer). Overall image quality results by the three readers (CL-T2, DL-T2) are reader 1: 3.72 ± 0.53, 3.89 ± 0.39 (P = 0.99); reader 2: 3.33 ± 0.82, 3.31 ± 0.74 (P = 0.49); reader 3: 3.67 ± 0.63, 3.51 ± 0.62. In the patient-based analysis, the reader results of AUC are (CL-bpMRI, DL-bpMRI): reader 1: 0.77, 0.78 (P = 0.98), reader 2: 0.65, 0.66 (P = 0.99), reader 3: 0.57, 0.60 (P = 0.52). Diagnostic statistics from DL-CAD (CL-bpMRI, DL-bpMRI) are sensitivity (0.71, 0.71, P = 1.00), specificity (0.59, 0.44, P = 0.05), positive predictive value (0.23, 0.24, P = 0.25), negative predictive value (0.88, 0.88, P = 0.48). CONCLUSION: Deep learning-accelerated T2-weighted imaging may potentially be used to decrease acquisition time for bpMRI. EVIDENCE LEVEL: 3. TECHNICAL EFFICACY: Stage 2.

Rapid purification of rabbit immunoglobulins using a single-step, negative-selection chromatography.

Custom polyclonal antibodies raised in rabbits are routinely used in immunoblotting and other protein analysis techniques. Custom rabbit polyclonal antisera are generally purified using immunoaffinity or Protein A-affinity chromatography; however, these methods require harsh elution conditions that can compromise the antigen binding efficacy. We evaluated the utility of Melon™ Gel chromatography for purification of IgG from crude rabbit serum. We show that Melon Gel-purified rabbit IgGs are active and perform well in immunoblotting. In summary, the Melon Gel method is a rapid, one-step, negative-selection approach that can be employed in either preparative or small-scale format to purify IgG from crude rabbit serum without the need for denaturing eluent.

Impact of fat on the apparent T1 value of the liver: assessment by water-only derived T1 mapping.

OBJECTIVES: To determine the impact of fat on the apparent T1 value of the liver using water-only derived T1 mapping. METHODS: 3-T MRI included 2D Look-Locker T1 mapping and proton density fat fraction (PDFF) mapping. T1 values of the liver were compared among T1 maps obtained by in-phase (IP), opposed-phase (OP), and Dixon water sequences using paired t-test. The correlation between T1 values of the liver on each T1 map and PDFF was assessed using Spearman correlation coefficient. The absolute differences between T1 value of the liver on Dixon water images and that on IP or OP images were also correlated with PDFF. RESULTS: One hundred sixty-two patients (median age, 70 [range, 24-91] years, 90 men) were retrospectively evaluated. The T1 values of the liver on each T1 map were significantly different (p < 0.001). The T1 value of the liver on IP images was significantly negatively correlated with PDFF (r = - 0.438), while the T1 value of the liver on OP images was slightly positively correlated with PDFF (r = 0.164). The T1 value of the liver on Dixon water images was slightly negatively correlated with PDFF (r = - 0.171). The absolute differences between T1 value of the liver on Dixon water images and that on IP or OP images were significantly correlated with PDFF (r = 0.606, 0.722; p < 0.001). CONCLUSION: Fat correction for the apparent T1 value by water-only derived T1 maps will be helpful for accurately evaluating the T1 value of the liver. CLINICAL RELEVANCE STATEMENT: Fat-corrected T1 mapping of the liver with the water component only obtained from the 2D Dixon Look-Locker sequence could be useful for accurately evaluating the T1 value of the liver without the impact of fat in daily clinical practice. KEY POINTS: • The T1 values of the liver on the conventional T1 maps are significantly affected by the presence of fat. • The apparent T1 value of the liver on water-only derived T1 maps would be slightly impacted by the presence of fat. • Fat correction for the apparent T1 values is necessary for the accurate assessment of the T1 values of the liver.

Highly sensitive and rapid detection of hypochlorous acid in aqueous media and its bioimaging in live cells and zebrafish using an ESIPT-driven mycophenolic acid-based fluorescent probe.

Excessive production of potent biological oxidants such as HOCl has been implicated in numerous diseases. Thus, it is crucial to develop highly specific and precise methods to detect HOCl in living systems, preferably with molecules that can show a distinct therapeutic effect. Our study introduces the synthesis and application of a highly sensitive fluorescence "turn-on" probe, Myco-OCl, based on the mycophenolic acid scaffold with exceptional water solubility. The ESIPT-driven mechanism enables Myco-OCl to specifically and rapidly detect (<5 s) HOCl with an impressive Stokes shift of 105 nm (λex = 417 nm, λem = 522 nm) and a sub-nanomolar (97.3 nM) detection limit with the detection range of 0 to 50 µM. The potential of Myco-OCl as an excellent biosensor is evident from its successful application for live cell imaging of exogenous and endogenous HOCl. In addition, Myco-OCl enabled us to detect HOCl in a zebrafish inflammatory animal model. These underscore the great potential of Myco-OCl for detecting HOCl in diverse physiological systems. Our findings thus offer a highly promising tool for detecting HOCl in living organisms.

Molecular phylodynamics of fowl adenovirus serotype 11 and 8b from inclusion body hepatitis outbreaks.

Fowl adenovirus (FAdV) serotypes are involved in a variety of clinical manifestations in poultry and has resulted in substantial economic loss to the poultry farmers. Despite the endemicity of Inclusion body hepatitis (IBH) in South Asian countries, including India, its etiology is not well studied. In western India, the rural poultry flocks obtained from the vaccinated parents were experiencing disease outbreaks with substantial economic losses due to heavy outbreaks and mortality. Therefore, the study was conducted to decipher the molecular epidemiology of the FAdV from field outbreaks in western India. A total of 37 commercial broiler poultry flocks and 29 village poultry flocks of western India were visited during 2019 to 2021. Out of these, 19.14% flocks showed incidence of IBH during the age of 15 to 35 days. The mortality ranged from 3.3 percent to 55.28 percent. The samples were subjected for amplification of partial hexon gene covering loop 1 and loop 2. The results revealed 48.28% positivity by PCR. The sequence analysis identified 14 isolates as species D serotype 11 with 0.97 to 0.99% divergence and two as species E serotype 8b with 0.99% divergence. The FAdV-11 isolates showed amino acid substitutions D195N, T399A, N417S, and N496H. The amino acids I188 and N195 were conserved in FAdV-11. The molecular clock in Bayesian methods was used to determine most common ancestor. The isolates MH379249 and MH379248 were determined the most recent common ancestor for FAdV-11 and FAdV-8b isolates. The analysis suggested evolution of 10 FAdV-11 strains in 2012, and four FAdV-11 strains and two FAdV-8b strains in 2018.

Translating AI to Clinical Practice: Overcoming Data Shift with Explainability.

To translate artificial intelligence (AI) algorithms into clinical practice requires generalizability of models to real-world data. One of the main obstacles to generalizability is data shift, a data distribution mismatch between model training and real environments. Explainable AI techniques offer tools to detect and mitigate the data shift problem and develop reliable AI for clinical practice. Most medical AI is trained with datasets gathered from limited environments, such as restricted disease populations and center-dependent acquisition conditions. The data shift that commonly exists in the limited training set often causes a significant performance decrease in the deployment environment. To develop a medical application, it is important to detect potential data shift and its impact on clinical translation. During AI training stages, from premodel analysis to in-model and post hoc explanations, explainability can play a key role in detecting model susceptibility to data shift, which is otherwise hidden because the test data have the same biased distribution as the training data. Performance-based model assessments cannot effectively distinguish the model overfitting to training data bias without enriched test sets from external environments. In the absence of such external data, explainability techniques can aid in translating AI to clinical practice as a tool to detect and mitigate potential failures due to data shift. ©RSNA, 2023 Quiz questions for this article are available in the supplemental material.

Novel fluconazole-resistant zoonotic yeast isolated from mastitis.

A hospital-based cross-sectional study was conducted during 2018-2019 to decipher the prevalence of yeast mastitis. The results indicated a 19.68% prevalence of clinical mastitis in bovines. Among them, 5.51% of samples revealed yeasts constituting 1.09% overall prevalence. Candida albicans was recorded as a significant fungal agent involved in clinical bovine mastitis. We record the association of Kodamaea ohmeri in clinical bovine mastitis. On proteomic and molecular confirmation, K. ohmeri isolates were re-identified from phenotypically identified Candida isolates associated with bovine mastitis. After conventional identification, the yeast isolates were re-identified by MALDI-TOF MS-based proteomic approaches. The D1/D2 domains of 26S-rRNA gene and 5.8S-internal transcribed spacer (ITS) rDNA regions based molecular phylogenetic analysis identified the isolates as K. ohmeri. The isolates were resistant to fluconazole. This study reports the first systemic study of K. ohmeri isolates recovered from bovine clinical mastitis, utilizing conventional, automated, proteomic, and genomic approaches followed by antifungal susceptibility. The findings suggest K. ohmeri as a potent opportunistic emerging pathogen of veterinary and public health concern, need for accurate identification of fungal agents from mycotic mastitis, and use of validated antifungal susceptibility assay because of developing resistance to antimycotic agents. Our findings suggest judicious use of fluconazole and alternative antifungal agents may be considered in case of an outbreak.

The investigation on allelic, genotypic frequencies and gene expression study in coding region of tyrosinase gene in Deoni cattle breed of western India.

An investigation was carried out on Deoni animals of western India to study the allelic and genotypic frequencies in coding region of TYR gene as well as gene expression profile. The animals were grouped according to age, gender, strain and intensity of partial albinism (low, medium and high). The present study revealed that the genotypic frequency of TYR gene across different strains, gender, age group and level of partial albinism was found to be non-significant for both exon-I and exon-II. The AB genotype in Balankya (0.70) was observed highest genotypic frequency followed by Wanera (0.55) and Shewara (0.55) strains. The genotypic frequency of AB and BB genotypes were observed highest in male and female, respectively. In exon-I, genotype frequency of AA genotype was found highest (0.55) in low level of partial albinism. The allelic frequencies in Shewara strain, male and low level of partial albinism were 0.75, 0.63 and 0.73, respectively. However, in exon-II genotype frequency of AB and BB was observed highest (0.70) in Wanera and Balankya strains followed by AA genotype in Shewara (0.50). The highest genotypic frequency of AA (0.87) and BB (0.50) were in male and female, respectively. The genotype frequency of AB genotype was found highest in all level of partial albinism. The allelic frequency was highest (0.85 for B allele) in Wanera strain, male (0.80 for A allele) and high level (0.60 for A allele) of particle albinism. The highly significant (p = 0.002) expression of tyrosinase gene was observed in young animals as compared to adult animals. The TYR gene expression was significantly (p = 0.047) higher in animals with low intensity of partial albinism followed by in the animals with medium and high intensity. Therefore, it is inferred that the TYR gene expression in young animals were high and as compared to the old animals of Deoni cattle breed.

Abdominal T2-Weighted Imaging and T2 Mapping Using a Variable Flip Angle Radial Turbo Spin-Echo Technique.

BACKGROUND: T2 mapping is of great interest in abdominal imaging but current methods are limited by low resolution, slice coverage, motion sensitivity, or lengthy acquisitions. PURPOSE: Develop a radial turbo spin-echo technique with refocusing variable flip angles (RADTSE-VFA) for high spatiotemporal T2 mapping and efficient slice coverage within a breath-hold and compare to the constant flip angle counterpart (RADTSE-CFA). STUDY TYPE: Prospective technical efficacy. SUBJECTS: Testing performed on agarose phantoms and 12 patients. Focal liver lesion classification tested on malignant (N = 24) and benign (N = 11) lesions. FIELD STRENGTH/SEQUENCE: 1.5 T/RADTSE-VFA, RADTSE-CFA. ASSESSMENT: A constrained objective function was used to optimize the refocusing flip angles. Phantom and/or in vivo data were used to assess relative contrast, T2 estimation, specific absorption rate (SAR), and focal liver lesion classification. STATISTICAL TESTS: t-Tests or Mann-Whitney Rank Sum tests were used. RESULTS: Phantom data did not show significant differences in mean relative contrast (P = 0.10) and T2 accuracy (P = 0.99) between RADTSE-VFA and RADTSE-CFA. Adding noise caused T2 overestimation predominantly for RADTSE-CFA and low T2 values. In vivo results did not show significant differences in mean spleen-to-liver (P = 0.62) and kidney-to-liver (P = 0.49) relative contrast between RADTSE-VFA and RADTSE-CFA. Mean T2 values were not significantly different between the two techniques for spleen (T2VFA  = 109.2 ± 12.3 msec; T2CFA  = 110.7 ± 11.1 msec; P = 0.78) and kidney-medulla (T2VFA  = 113.0 ± 8.7 msec; T2CFA  = 114.0 ± 8.6 msec; P = 0.79). Liver T2 was significantly higher for RADTSE-CFA (T2VFA  = 52.6 ± 6.6 msec; T2CFA  = 60.4 ± 8.0 msec) consistent with T2 overestimation in the phantom study. Focal liver lesion classification had comparable T2 distributions for RADTSE-VFA and RADTSE-CFA for malignancies (P = 1.0) and benign lesions (P = 0.39). RADTSE-VFA had significantly lower SAR than RADTSE-CFA increasing slice coverage by 1.5. DATA CONCLUSION: RADTSE-VFA provided noise-robust T2 estimation compared to the constant flip angle counterpart while generating T2-weighted images with comparable contrast. The VFA scheme minimized SAR improving slice efficiency for breath-hold imaging. LEVEL OF EVIDENCE: 2 TECHNICAL EFFICACY STAGE: 1.

Deep Learning Reconstruction Enables Highly Accelerated Biparametric MR Imaging of the Prostate.

BACKGROUND: Early diagnosis and treatment of prostate cancer (PCa) can be curative; however, prostate-specific antigen is a suboptimal screening test for clinically significant PCa. While prostate magnetic resonance imaging (MRI) has demonstrated value for the diagnosis of PCa, the acquisition time is too long for a first-line screening modality. PURPOSE: To accelerate prostate MRI exams, utilizing a variational network (VN) for image reconstruction. STUDY TYPE: Retrospective. SUBJECTS: One hundred and thirteen subjects (train/val/test: 70/13/30) undergoing prostate MRI. FIELD STRENGTH/SEQUENCE: 3.0 T; a T2 turbo spin echo (TSE) T2-weighted image (T2WI) sequence in axial and coronal planes, and axial echo-planar diffusion-weighted imaging (DWI). ASSESSMENT: Four abdominal radiologists evaluated the image quality of VN reconstructions of retrospectively under-sampled biparametric MRIs (bp-MRI), and standard bp-MRI reconstructions for 20 test subjects (studies). The studies included axial and coronal T2WI, DWI B50 seconds/mm2 and B1000 seconds/mm (4-fold T2WI, 3-fold DWI), all of which were evaluated separately for image quality on a Likert scale (1: non-diagnostic to 5: excellent quality). In another 10 test subjects, three readers graded lesions on bp-MRI-which additionally included calculated B1500 seconds/mm2 , and apparent diffusion coefficient map-according to the Prostate Imaging Reporting and Data System (PI-RADS v2.1), for both VN and standard reconstructions. Accuracy of PI-RADS ≥3 for clinically significant cancer was computed. Projected scan time of the retrospectively under-sampled biparametric exam was also computed. STATISTICAL TESTS: One-sided Wilcoxon signed-rank test was used for comparison of image quality. Sensitivity, specificity, positive predictive value, and negative predictive value were calculated for lesion detection and grading. Generalized estimating equation with cluster effect was used to compare differences between standard and VN bp-MRI. A P-value of <0.05 was considered statistically significant. RESULTS: Three of four readers rated no significant difference for overall quality between the standard and VN axial T2WI (Reader 1: 4.00 ± 0.56 (Standard), 3.90 ± 0.64 (VN) P = 0.33; Reader 2: 4.35 ± 0.74 (Standard), 3.80 ± 0.89 (VN) P = 0.003; Reader 3: 4.60 ± 0.50 (Standard), 4.55 ± 0.60 (VN) P = 0.39; Reader 4: 3.65 ± 0.99 (Standard), 3.60 ± 1.00 (VN) P = 0.38). All four readers rated no significant difference for overall quality between standard and VN DWI B1000 seconds/mm2 (Reader 1: 2.25 ± 0.62 (Standard), 2.45 ± 0.75 (VN) P = 0.96; Reader 2: 3.60 ± 0.92 (Standard), 3.55 ± 0.82 (VN) P = 0.40; Reader 3: 3.85 ± 0.72 (Standard), 3.55 ± 0.89 (VN) P = 0.07; Reader 4: 4.70 ± 0.76 (Standard); 4.60 ± 0.73 (VN) P = 0.17) and three of four readers rated no significant difference for overall quality between standard and VN DWI B50 seconds/mm2 (Reader 1: 3.20 ± 0.70 (Standard), 3.40 ± 0.75 (VN) P = 0.98; Reader 2: 2.85 ± 0.81 (Standard), 3.00 ± 0.79 (VN) P = 0.93; Reader 3: 4.45 ± 0.72 (Standard), 4.05 ± 0.69 (VN) P = 0.02; Reader 4: 4.50 ± 0.69 (Standard), 4.45 ± 0.76 (VN) P = 0.50). In the lesion evaluation study, there was no significant difference in the number of PI-RADS ≥3 lesions identified on standard vs. VN bp-MRI (P = 0.92, 0.59, 0.87) with similar sensitivity and specificity for clinically significant cancer. The average scan time of the standard clinical biparametric exam was 11.8 minutes, and this was projected to be 3.2 minutes for the accelerated exam. DATA CONCLUSION: Diagnostic accelerated biparametric prostate MRI exams can be performed using deep learning methods in <4 minutes, potentially enabling rapid screening prostate MRI. LEVEL OF EVIDENCE: 3 TECHNICAL EFFICACY: Stage 5.

Molecular phylodynamics of infectious bursal disease viruses.

The present study was conducted to study the molecular phylodynamics of the Indian field IBDVs. A total of 13 organized commercial poultry farms and 29 village poultry flocks were recruited in the study. The broiler flocks showed 15.25-60.18% mortality, followed by 12.4% in improved native poultry varieties and 5% in indigenous birds. The 664 bp hypervariable VP2 gene fragment of Western and Central Indian vvIBDVs showed 97.14-98.79 and 94.49-96.69% identity to Pakistani and South Indian vvIBDVs, respectively. An isolate was 99.54% identical to the Ventri-Plus vaccine strain, while three IBDVs showed maximum identity with the Georgia strain. Out of 22, 19 strains showed typical vvIBDV amino acid signature, while three strains showed substitutions specific to classical IBDVs. Central Indian vvIBDVs showed conserved substitutions at N212D and E300A, which can be used as a regional marker. Phylogenetic genogrouping placed global IBDVs into seven genogroups based upon virulence and geographical distribution. Nineteen field vvIBDVs were placed in the G3 genogroup, and the other three were grouped with classical IBDVs in G1 genogroup. A nucleotide span from 584 to 1248 covering VP2 hypervariable fragment was found suitable for correct genogrouping of field IBDVs. The Bayesian evolutionary analysis showed tMRCA of the year 2009 for 8 Western Indian vvIBDVs with vvIBDV from Pakistan. Central Indian vvIBDVs were evolved in the year 1991 from BD-3 and PY12 strains of vvIBDVs from Bangladesh and Pondicherry, respectively. An isolate showed evolution in year 2010 from the Nigerian ABIC strain, while three classical strains showed tMRCA of the year 2009 with the Georgia strain as a recent common ancestor.

Antipsychotics for schizophrenia spectrum disorders with catatonic symptoms.

BACKGROUND: Whilst antipsychotics are the mainstay of treatment for schizophrenia spectrum disorders, there have been numerous attempts to identify biomarkers that can predict treatment response. One potential marker may be psychomotor abnormalities, including catatonic symptoms. Early studies suggested that catatonic symptoms predict poor treatment response, whilst anecdotal reports of rare adverse events have been invoked against antipsychotics. The efficacy and safety of antipsychotics in the treatment of this subtype of schizophrenia have rarely been studied in randomised controlled trials (RCTs). OBJECTIVES: To compare the effects of any single antipsychotic medication with another antipsychotic or with other pharmacological agents, electroconvulsive therapy (ECT), other non-pharmacological neuromodulation therapies (e.g. transcranial magnetic stimulation), or placebo for treating positive, negative, and catatonic symptoms in people who have schizophrenia spectrum disorders with catatonic symptoms. SEARCH METHODS: We searched the Cochrane Schizophrenia Group's Study-Based Register of Trials, which is based on CENTRAL, MEDLINE, Embase, CINAHL, PsycINFO, PubMed, ClinicalTrials.gov, the ISRCTN registry, and WHO ICTRP, on 19 September 2021. There were no language, date, document type, or publication status limitations for inclusion of records in the register. We also manually searched reference lists from the included studies, and contacted study authors when relevant. SELECTION CRITERIA: All RCTs comparing any single antipsychotic medication with another antipsychotic or with other pharmacological agents, ECT, other non-pharmacological neuromodulation therapies, or placebo for people who have schizophrenia spectrum disorders with catatonic symptoms. DATA COLLECTION AND ANALYSIS: two review authors independently inspected citations, selected studies, extracted data, and appraised study quality. For binary outcomes, we planned to calculate risk ratios and their 95% confidence intervals (CI) on an intention-to-treat basis. For continuous outcomes, we planned to calculate mean differences between groups and their 95% CI. We assessed risk of bias for the included studies, and created a summary of findings table; however, we did not assess the certainty of the evidence using the GRADE approach because there was no quantitative evidence in the included study. MAIN RESULTS: Out of 53 identified reports, one RCT including 14 hospitalised adults with schizophrenia and catatonic symptoms met the inclusion criteria of the review. The study, which was conducted in India and lasted only three weeks, compared risperidone with ECT in people who did not respond to an initial lorazepam trial.   There were no usable data reported on the primary efficacy outcomes of clinically important changes in positive, negative, or catatonic symptoms. Whilst both study groups improved in catatonia scores on the Bush-Francis Catatonia Rating Scale (BFCRS), the ECT group showed significantly greater improvement at week 3 endpoint (mean +/- estimated standard deviation; 0.68 +/- 4.58; N = 8) than the risperidone group (6.04 +/- 4.58; N = 6; P = 0.035 of a two-way analysis of variance (ANOVA) for repeated measures originally conducted in the trial). Similarly, both groups improved on the Positive and Negative Syndrome Scale (PANSS) scores by week 3, but ECT showed significantly greater improvement in positive symptoms scores compared with risperidone (P = 0.04). However, data on BFCRS scores in the ECT group appeared to be skewed, and mean PANSS scores were not reported, thereby precluding further analyses of both BFCRS and PANSS data according to the protocol.  Although no cases of neuroleptic malignant syndrome were reported, extrapyramidal symptoms as a primary safety outcome were reported in three cases in the risperidone group. Conversely, headache (N = 6), memory loss (N = 4), and a prolonged seizure were reported in people receiving ECT. These adverse effects, which were assessed as specific for antipsychotics and ECT, respectively, were the only adverse effects reported in the study. However, the exact number of participants with adverse events was not clearly reported in both groups, precluding further analysis.  Our results were based only on a single study with a very small sample size, short duration of treatment, unclear or high risk of bias due to unclear randomisation methods, possible imbalance in baseline characteristics, skewed data, and selective reporting. Data on outcomes of general functioning, global state, quality of life, and service use, as well as data on specific phenomenology and duration of catatonic symptoms, were not reported. AUTHORS' CONCLUSIONS: We found only one small, short-term trial suggesting that risperidone may improve catatonic and positive symptoms scale scores amongst people with schizophrenia spectrum disorders and catatonic symptoms, but that ECT may result in greater improvement in the first three weeks of treatment. Due to small sample size, methodological shortcomings and brief duration of the study, as well as risk of bias, the evidence from this review is of very low quality. We are uncertain if these are true effects, limiting any conclusions that can be drawn from the evidence. No cases of neuroleptic malignant syndrome were reported, but we cannot rule out the risk of this or other rare adverse events in larger population samples.  High-quality trials continue to be necessary to differentiate treatments for people with symptoms of catatonia in schizophrenia spectrum disorders. The lack of consensus on the psychopathology of catatonia remains a barrier to defining treatments for people with schizophrenia. Better understanding of the efficacy and safety of antipsychotics may clarify treatment for this unique subtype of schizophrenia.

ANTECEDENTES: Aunque los antipsicóticos son la base del tratamiento de los trastornos del espectro de la esquizofrenia, ha habido numerosos intentos de identificar biomarcadores que puedan predecir la respuesta al tratamiento. Un posible marcador podrían ser las anomalías psicomotoras, incluidos los síntomas catatónicos. Los estudios más antiguos indican que los síntomas catatónicos predicen una respuesta deficiente al tratamiento, mientras que se han alegado informes anecdóticos de eventos adversos poco frecuentes contra los antipsicóticos. La eficacia y la seguridad de los antipsicóticos en el tratamiento de este subtipo de esquizofrenia rara vez se han estudiado en ensayos controlados aleatorizados (ECA). OBJETIVOS: Comparar los efectos de cualquier fármaco antipsicótico único con otro antipsicótico o con otros agentes farmacológicos, terapia electroconvulsiva (TEC), otras terapias de neuromodulación no farmacológicas (p. ej., estimulación magnética transcraneal) o placebo para el tratamiento de los síntomas positivos, negativos y catatónicos en personas que presentan trastornos del espectro de la esquizofrenia con síntomas catatónicos. MÉTODOS DE BÚSQUEDA: El 19 de septiembre de 2021 se realizaron búsquedas en el registro de ensayos basados en estudios del Grupo Cochrane de Esquizofrenia (Cochrane Schizophrenia Group), que se basa en CENTRAL, MEDLINE, Embase, CINAHL, PsycINFO, PubMed, ClinicalTrials.gov, el registro ISRCTN y la ICTRP de la OMS. No hubo limitaciones de idioma, fecha, tipo de documento o estado de publicación para la inclusión de los registros en el registro. También se realizaron búsquedas manuales en las listas de referencias de los estudios incluidos y se estableció contacto con los autores de los estudios cuando fue pertinente. CRITERIOS DE SELECCIÓN: Todos los ECA que compararan cualquier fármaco antipsicótico único con otro antipsicótico o con otros agentes farmacológicos, TEC, otras terapias de neuromodulación no farmacológicas o placebo en personas que presentan trastornos del espectro de la esquizofrenia con síntomas catatónicos. OBTENCIÓN Y ANÁLISIS DE LOS DATOS: Dos autores de la revisión inspeccionaron de forma independiente las citas, seleccionaron los estudios, extrajeron los datos y evaluaron la calidad de los estudios. Para los desenlaces binarios se planeó calcular las razones de riesgos y sus intervalos de confianza (IC) del 95% sobre la base de la intención de tratar. Para los desenlaces continuos se planeó calcular las diferencias de medias entre los grupos y sus IC del 95%. Se evaluó el riesgo de sesgo de los estudios incluidos y se creó una tabla de resumen de los hallazgos. Sin embargo, no se evaluó la certeza de la evidencia mediante el método GRADE porque no hubo evidencia cuantitativa en el estudio incluido. RESULTADOS PRINCIPALES: De los 53 informes identificados, un ECA que incluyó a 14 adultos hospitalizados con esquizofrenia y síntomas catatónicos cumplió con los criterios de inclusión de la revisión. El estudio, realizado en la India y que sólo duró tres semanas, comparó la risperidona con la TEC en personas que no respondieron a una prueba inicial con lorazepam. No se informaron datos utilizables sobre los desenlaces principales de eficacia de cambios clínicamente importantes en los síntomas positivos, negativos o catatónicos. Aunque ambos grupos del estudio mejoraron en las puntuaciones de catatonia en la Bush­Francis Catatonia Rating Scale (BFCRS), el grupo de TEC mostró una mejoría significativamente mayor en el desenlace a las tres semanas (media +/­ desviación estándar estimada; 0,68 +/­ 4,58; n = 8) que el grupo de risperidona (6,04 +/­ 4,58; n = 6; p = 0,035 de un análisis de varianza (ANOVA) de dos vías para medidas repetidas realizado originalmente en el ensayo). Asimismo, ambos grupos mejoraron en las puntuaciones de la Positive and Negative Syndrome Scale (PANSS) a las tres semanas, pero la TEC mostró una mejoría significativamente mayor en las puntuaciones de los síntomas positivos en comparación con la risperidona (p = 0,04). Sin embargo, los datos sobre las puntuaciones de la BFCRS en el grupo de TEC parecieron estar sesgados, y no se informaron las puntuaciones medias de la PANSS, lo que impidió realizar más análisis de los datos de la BFCRS y la PANSS según el protocolo. Aunque no se informaron casos de síndrome neuroléptico maligno, en tres casos del grupo de risperidona se notificaron síntomas extrapiramidales como un desenlace principal de seguridad. Por el contrario, en las personas que recibieron TEC se informó cefalea (n = 6), pérdida de memoria (n = 4) y una convulsión prolongada. Estos efectos adversos, que se evaluaron como específicos de los antipsicóticos y de la TEC, respectivamente, fueron los únicos efectos adversos notificados en el estudio. Sin embargo, el número exacto de participantes con eventos adversos no se informó claramente en ambos grupos, lo que impidió realizar un análisis más profundo. Los resultados de esta revisión se basaron en un solo estudio con un tamaño muestral muy pequeño, una duración corta del tratamiento, un riesgo de sesgo incierto o alto debido a métodos de asignación al azar poco claros, un posible desequilibrio en las características iniciales, datos sesgados y un informe selectivo. No se informaron datos sobre los desenlaces de funcionalidad general, estado global, calidad de vida ni uso de los servicios, así como tampoco datos sobre la fenomenología específica ni la duración de los síntomas catatónicos. CONCLUSIONES DE LOS AUTORES: Solo se encontró un ensayo pequeño, a corto plazo, que indica que la risperidona podría mejorar las puntuaciones de la escala de síntomas catatónicos y positivos entre las personas con trastornos del espectro de la esquizofrenia y síntomas catatónicos, pero que la TEC podría producir una mayor mejoría en las primeras tres semanas de tratamiento. Debido al pequeño tamaño muestral, las deficiencias metodológicas y la breve duración del estudio, así como el riesgo de sesgo, la evidencia de esta revisión es de calidad muy baja. No hay confianza en que estos efectos sean verdaderos, lo que limita cualquier conclusión que se pueda sacar a partir de la evidencia. No se notificaron casos de síndrome neuroléptico maligno, pero no se puede descartar el riesgo de este u otros eventos adversos poco frecuentes en muestras poblacionales más grandes. Aún se necesitan ensayos de calidad alta para diferenciar los tratamientos en las personas con síntomas de catatonia en los trastornos del espectro de la esquizofrenia. La falta de consenso sobre la psicopatología de la catatonia todavía es un obstáculo para definir los tratamientos para las personas con esquizofrenia. Un mejor conocimiento de la eficacia y la seguridad de los antipsicóticos podría aclarar el tratamiento de este subtipo único de esquizofrenia.

The histone H4 basic patch regulates SAGA-mediated H2B deubiquitination and histone acetylation.

Histone H2B monoubiquitylation (H2Bub1) has central functions in multiple DNA-templated processes, including gene transcription, DNA repair, and replication. H2Bub1 also is required for the trans-histone regulation of H3K4 and H3K79 methylation. Although previous studies have elucidated the basic mechanisms that establish and remove H2Bub1, we have only an incomplete understanding of how H2Bub1 is regulated. We report here that the histone H4 basic patch regulates H2Bub1. Yeast cells with arginine-to-alanine mutations in the H4 basic patch (H42RA) exhibited a significant loss of global H2Bub1. H42RA mutant yeast strains also displayed chemotoxin sensitivities similar to, but less severe than, strains containing a complete loss of H2Bub1. We found that the H4 basic patch regulates H2Bub1 levels independently of interactions with chromatin remodelers and separately from its regulation of H3K79 methylation. To measure H2B ubiquitylation and deubiquitination kinetics in vivo, we used a rapid and reversible optogenetic tool, the light-inducible nuclear exporter, to control the subcellular location of the H2Bub1 E3 ligase, Bre1. The ability of Bre1 to ubiquitylate H2B was unaffected in the H42RA mutant. In contrast, H2Bub1 deubiquitination by SAGA-associated Ubp8, but not by Ubp10, increased in the H42RA mutant. Consistent with a function for the H4 basic patch in regulating SAGA deubiquitinase activity, we also detected increased SAGA-mediated histone acetylation in H4 basic patch mutants. Our findings uncover that the H4 basic patch has a regulatory function in SAGA-mediated histone modifications.