Clinical and functional spectrum of RAC2-related immunodeficiency.

ABSTRACT: Mutations in the small Rho-family guanosine triphosphate hydrolase RAC2, critical for actin cytoskeleton remodeling and intracellular signal transduction, are associated with neonatal severe combined immunodeficiency (SCID), infantile neutrophilic disorder resembling leukocyte adhesion deficiency (LAD), and later-onset combined immune deficiency (CID). We investigated 54 patients (23 previously reported) from 37 families yielding 15 novel RAC2 missense mutations, including one present only in homozygosity. Data were collected from referring physicians and literature reports with updated clinical information. Patients were grouped by presentation: neonatal SCID (n = 5), infantile LAD-like disease (n = 5), or CID (n = 44). Disease correlated to RAC2 activity: constitutively active RAS-like mutations caused neonatal SCID, dominant-negative mutations caused LAD-like disease, whereas dominant-activating mutations caused CID. Significant T- and B-lymphopenia with low immunoglobulins were seen in most patients; myeloid abnormalities included neutropenia, altered oxidative burst, impaired neutrophil migration, and visible neutrophil macropinosomes. Among 42 patients with CID with clinical data, upper and lower respiratory infections and viral infections were common. Twenty-three distinct RAC2 mutations, including 15 novel variants, were identified. Using heterologous expression systems, we assessed downstream effector functions including superoxide production, p21-activated kinase 1 binding, AKT activation, and protein stability. Confocal microscopy showed altered actin assembly evidenced by membrane ruffling and macropinosomes. Altered protein localization and aggregation were observed. All tested RAC2 mutant proteins exhibited aberrant function; no single assay was sufficient to determine functional consequence. Most mutants produced elevated superoxide; mutations unable to support superoxide formation were associated with bacterial infections. RAC2 mutations cause a spectrum of immune dysfunction, ranging from early onset SCID to later-onset combined immunodeficiencies depending on RAC2 activity. This trial was registered at www.clinicaltrials.gov as #NCT00001355 and #NCT00001467.

Structural, functional, and behavioral insights of dopamine dysfunction revealed by a deletion in SLC6A3.

The human dopamine (DA) transporter (hDAT) mediates clearance of DA. Genetic variants in hDAT have been associated with DA dysfunction, a complication associated with several brain disorders, including autism spectrum disorder (ASD). Here, we investigated the structural and behavioral bases of an ASD-associated in-frame deletion in hDAT at N336 (∆N336). We uncovered that the deletion promoted a previously unobserved conformation of the intracellular gate of the transporter, likely representing the rate-limiting step of the transport process. It is defined by a "half-open and inward-facing" state (HOIF) of the intracellular gate that is stabilized by a network of interactions conserved phylogenetically, as we demonstrated in hDAT by Rosetta molecular modeling and fine-grained simulations, as well as in its bacterial homolog leucine transporter by electron paramagnetic resonance analysis and X-ray crystallography. The stabilization of the HOIF state is associated both with DA dysfunctions demonstrated in isolated brains of Drosophila melanogaster expressing hDAT ∆N336 and with abnormal behaviors observed at high-time resolution. These flies display increased fear, impaired social interactions, and locomotion traits we associate with DA dysfunction and the HOIF state. Together, our results describe how a genetic variation causes DA dysfunction and abnormal behaviors by stabilizing a HOIF state of the transporter.

68Ga-PSMA-PET screening and transponder-guided salvage radiotherapy to the prostate bed alone for biochemical recurrence following prostatectomy: interim outcomes of a phase II trial.

PURPOSE: To evaluate outcomes for men with biochemically recurrent prostate cancer who were selected for transponder-guided salvage radiotherapy (SRT) to the prostate bed alone by 68Ga-labelled prostate-specific membrane antigen positron emission tomography (68Ga-PSMA-PET). METHODS: This is a single-arm, prospective study of men with a prostate-specific antigen (PSA) level rising to 0.1-2.5 ng/mL following radical prostatectomy. Patients were staged with 68Ga-PSMA-PET and those with a negative finding, or a positive finding localised to the prostate bed, continued to SRT only to the prostate bed alone with real-time target-tracking using electromagnetic transponders. The primary endpoint was freedom from biochemical relapse (FFBR, PSA > 0.2 ng/mL from the post-radiotherapy nadir). Secondary endpoints were time to biochemical relapse, toxicity and patient-reported quality of life (QoL). RESULTS: Ninety-two patients (median PSA of 0.18 ng/ml, IQR 0.12-0.36), were screened with 68Ga-PSMA-PET and metastatic disease was found in 20 (21.7%) patients. Sixty-nine of 72 non-metastatic patients elected to proceed with SRT. At the interim (3-year) analysis, 32 (46.4%) patients (95% CI 34.3-58.8%) were FFBR. The median time to biochemical relapse was 16.1 months. The rate of FFBR was 82.4% for ISUP grade-group 2 patients. Rates of grade 2 or higher gastrointestinal and genitourinary toxicity were 0% and 15.2%, respectively. General health and disease-specific QoL remained stable. CONCLUSION: Pre-SRT 68Ga-PSMA-PET scans detect metastatic disease in a proportion of patients at low PSA levels but fail to improve FFBR. Transponder-guided SRT to the prostate bed alone is associated with a favourable toxicity profile and preserved QoL. TRIAL REGISTRATION NUMBER: ACTRN12615001183572, 03/11/2015, retrospectively registered.

Atherosclerotic Cardiovascular Disease in Individuals with Hepatitis C Viral Infection.

PURPOSE OF REVIEW: Hepatitis C virus (HCV) and atherosclerotic cardiovascular disease (ASCVD) are two diseases that affect millions around the globe. Hepatitis C affects more than 70 million individuals globally. ASCVD is commonly encountered and remains the top cause of death worldwide. A link has been identified between HCV and atherosclerosis. RECENT FINDINGS: A review of recent studies which define the association between HCV infection and an increased risk of subclinical ASCVD and experiencing cardiovascular (CV) events. It is now recognized that there is an increased burden of atherosclerosis in individuals infected with HCV that translates into increased cardiovascular events. An increase in the number of diagnosed cases of HCV is expected as screening recommendations for the virus have expanded. Strategies to educate healthcare professionals about this increased CV risk will need to be considered as well as the optimal strategy to lower CV risk in this growing population.

Synaptic, transcriptional and chromatin genes disrupted in autism.

The genetic architecture of autism spectrum disorder involves the interplay of common and rare variants and their impact on hundreds of genes. Using exome sequencing, here we show that analysis of rare coding variation in 3,871 autism cases and 9,937 ancestry-matched or parental controls implicates 22 autosomal genes at a false discovery rate (FDR) < 0.05, plus a set of 107 autosomal genes strongly enriched for those likely to affect risk (FDR < 0.30). These 107 genes, which show unusual evolutionary constraint against mutations, incur de novo loss-of-function mutations in over 5% of autistic subjects. Many of the genes implicated encode proteins for synaptic formation, transcriptional regulation and chromatin-remodelling pathways. These include voltage-gated ion channels regulating the propagation of action potentials, pacemaking and excitability-transcription coupling, as well as histone-modifying enzymes and chromatin remodellers-most prominently those that mediate post-translational lysine methylation/demethylation modifications of histones.

Patterns and rates of exonic de novo mutations in autism spectrum disorders.

Autism spectrum disorders (ASD) are believed to have genetic and environmental origins, yet in only a modest fraction of individuals can specific causes be identified. To identify further genetic risk factors, here we assess the role of de novo mutations in ASD by sequencing the exomes of ASD cases and their parents (n = 175 trios). Fewer than half of the cases (46.3%) carry a missense or nonsense de novo variant, and the overall rate of mutation is only modestly higher than the expected rate. In contrast, the proteins encoded by genes that harboured de novo missense or nonsense mutations showed a higher degree of connectivity among themselves and to previous ASD genes as indexed by protein-protein interaction screens. The small increase in the rate of de novo events, when taken together with the protein interaction results, are consistent with an important but limited role for de novo point mutations in ASD, similar to that documented for de novo copy number variants. Genetic models incorporating these data indicate that most of the observed de novo events are unconnected to ASD; those that do confer risk are distributed across many genes and are incompletely penetrant (that is, not necessarily sufficient for disease). Our results support polygenic models in which spontaneous coding mutations in any of a large number of genes increases risk by 5- to 20-fold. Despite the challenge posed by such models, results from de novo events and a large parallel case-control study provide strong evidence in favour of CHD8 and KATNAL2 as genuine autism risk factors.

Laparoscopic lens fogging: solving a common surgical problem in standard and robotic laparoscopes via a scientific model.

BACKGROUND: Laparoscopic lens fogging (LLF) hampers vision and impedes operative efficiency. Attempts to reduce LLF have led to the development of various anti-fogging fluids and warming devices. Limited literature exists directly comparing these techniques. We constructed a model peritoneum to simulate LLF and to compare the efficacy of various anti-fogging techniques. MATERIALS AND METHODS: Intraperitoneal space was simulated using a suction bag suspended within an 8 L container of water. LLF was induced by varying the temperature and humidity within the model peritoneum. Various anti-fogging techniques were assessed including scope warmers, FREDTM, ResoclearTM, chlorhexidine, betadine and immersion in heated saline. These products were trialled with and without the use of a disposable scope warmer. Vision scores were evaluated by the same investigator for all tests and rated according to a predetermined scale. Fogging was assessed for each product or technique 30 times and a mean vision rating was recorded. RESULTS: All products tested imparted some benefit, but FREDTM performed better than all other techniques. Betadine and ResoclearTM performed no better than the use of a scope warmer alone. Immersion in saline prior to insertion resulted in decreased vision ratings. The robotic scope did not result in LLF within the model. CONCLUSIONS: In standard laparoscopes, the most superior preventative measure was FREDTM utilised on a pre-warmed scope. Despite improvements in LLF with other products FREDTM was better than all other techniques. The robotic laparoscope performed superiorly regarding LLF compared to standard laparoscope.

Quantum State Discrimination Using the Minimum Average Number of Copies.

In the task of discriminating between nonorthogonal quantum states from multiple copies, the key parameters are the error probability and the resources (number of copies) used. Previous studies have considered the task of minimizing the average error probability for fixed resources. Here we introduce a new state discrimination task: minimizing the average resources for a fixed admissible error probability. We show that this new task is not performed optimally by previously known strategies, and derive and experimentally test a detection scheme that performs better.

Erratum: Quantum State Discrimination Using the Minimum Average Number of Copies [Phys. Rev. Lett. 118, 030502 (2017)].

This corrects the article DOI: 10.1103/PhysRevLett.118.030502.

Consensus Genotyper for Exome Sequencing (CGES): improving the quality of exome variant genotypes.

MOTIVATION: The development of cost-effective next-generation sequencing methods has spurred the development of high-throughput bioinformatics tools for detection of sequence variation. With many disparate variant-calling algorithms available, investigators must ask, 'Which method is best for my data?' Machine learning research has shown that so-called ensemble methods that combine the output of multiple models can dramatically improve classifier performance. Here we describe a novel variant-calling approach based on an ensemble of variant-calling algorithms, which we term the Consensus Genotyper for Exome Sequencing (CGES). CGES uses a two-stage voting scheme among four algorithm implementations. While our ensemble method can accept variants generated by any variant-calling algorithm, we used GATK2.8, SAMtools, FreeBayes and Atlas-SNP2 in building CGES because of their performance, widespread adoption and diverse but complementary algorithms. RESULTS: We apply CGES to 132 samples sequenced at the Hudson Alpha Institute for Biotechnology (HAIB, Huntsville, AL) using the Nimblegen Exome Capture and Illumina sequencing technology. Our sample set consisted of 40 complete trios, two families of four, one parent-child duo and two unrelated individuals. CGES yielded the fewest total variant calls (N(CGES) = 139° 897), the highest Ts/Tv ratio (3.02), the lowest Mendelian error rate across all genotypes (0.028%), the highest rediscovery rate from the Exome Variant Server (EVS; 89.3%) and 1000 Genomes (1KG; 84.1%) and the highest positive predictive value (PPV; 96.1%) for a random sample of previously validated de novo variants. We describe these and other quality control (QC) metrics from consensus data and explain how the CGES pipeline can be used to generate call sets of varying quality stringency, including consensus calls present across all four algorithms, calls that are consistent across any three out of four algorithms, calls that are consistent across any two out of four algorithms or a more liberal set of all calls made by any algorithm. AVAILABILITY AND IMPLEMENTATION: To enable accessible, efficient and reproducible analysis, we implement CGES both as a stand-alone command line tool available for download in GitHub and as a set of Galaxy tools and workflows configured to execute on parallel computers. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Whole exome sequencing reveals minimal differences between cell line and whole blood derived DNA.

Two common sources of DNA for whole exome sequencing (WES) are whole blood (WB) and immortalized lymphoblastoid cell line (LCL). However, it is possible that LCLs have a substantially higher rate of mutation than WB, causing concern for their use in sequencing studies. We compared results from paired WB and LCL DNA samples for 16 subjects, using LCLs of low passage number (<5). Using a standard analysis pipeline we detected a large number of discordant genotype calls (approximately 50 per subject) that we segregated into categories of "confidence" based on read-level quality metrics. From these categories and validation by Sanger sequencing, we estimate that the vast majority of the candidate differences were false positives and that our categories were effective in predicting valid sequence differences, including LCLs with putative mosaicism for the non-reference allele (3-4 per exome). These results validate the use of DNA from LCLs of low passage number for exome sequencing.

Corrigendum to "RPN (Radius, Position of tumour, iNvasion of renal sinus) Classification and Nephrometry Scoring System: An Internationally Developed Clinical Classification To Describe the Surgical Difficulty for Renal Masses for Which Robotic Partial Nephrectomy Is Planned" [Eur. Urol. Open Sci. 54 (2023) 33-42].

[This corrects the article DOI: 10.1016/j.euros.2023.05.007.].

An information theory-based approach to characterize drivers of upstream salmon migration.

The migration timing of Pacific salmon in the Columbia River basin is subject to multiple influences related to climate, human water resource management, and lagged effects such as oceanic conditions. We apply an information theory-based approach to analyze drivers of adult Chinook salmon migration within the spring and fall spawning seasons and between years based on salmon counts at dams along the Columbia and Snake Rivers. Time-lagged mutual information and information decomposition measures, which characterize lagged and nonlinear dependencies as reductions in uncertainty, are used to detect interactions between salmon counts and lagged streamflows, air and water temperatures, precipitation, snowpack, climate indices and downstream salmon counts. At a daily timescale, these interdependencies reflect migration timing and show differences between fall and spring run salmon, while dependencies based on variables at an annual resolution reflect long-term predictability. We also highlight several types of joint dependencies where predictability of salmon counts depends on the knowledge of multiple lagged sources. This study illustrates how co-varying human and natural drivers could propagate to influence salmon migration timing or overall returns, and how nonlinear types of dependencies between variables enhance predictability of a target. This information-based framework is broadly applicable to assess driving factors in other types of complex water resources systems or species life cycles.

A Real-Time Dual-Mode High-Frequency Beamformer for Ultrafast and Focused Imaging.

A firmware-based high-frequency beam- former implementing both conventional transmit focused B-mode imaging and diverging wave ultrafast (UF) imaging for Doppler overlay was developed. The beamformer can generate one transmit focused frame with four transmit focal zones (FZs), and 68 UF frames with 16 diverging waves each at a 10-Hz frame rate. The beamformer firmware stores the beamforming delays as a single bit, enabling efficient compression within the internal memory. The beamformer was characterized using a 30-MHz 64-element phased array endoscope. The hybrid system generates a 128 line by 768-pixel focused B-mode image spanning 1.2-12.6 mm axially over a ±32° range of steering angles. In addition, the system generates an UF image that is 64 lines by 384-pixels spanning 3.5-10.8 mm axially over a ±16° angle.

Consideration of Management Techniques for Advanced Hepatocellular Carcinoma With Metastasis to the Right Atrium: A Case Report.

Hepatocellular carcinoma (HCC) is a common form of cancer and the most common form of liver cancer. Multiple etiological factors leading to HCC include hepatitis B and C, diabetes, alcoholic fatty liver disease, and non-alcoholic fatty liver disease. Hepatocellular carcinoma in the late stages may present with tumor burden and thrombi that can extend into the right atrium (RA). This late-stage form of HCC has a poor prognosis. In this case, we present a 63-year-old male who presented to the hospital with acute encephalopathy with bilateral pulmonary emboli and a thrombus secondary to HCC extending into the RA. Clinical trials for non-surgical interventions are ongoing and are needed to treat patients with tumor burden who may be at bleeding risk from tumor resection.

A High-Performance 3-D Imaging Technique Using Simultaneous Azimuth and Elevation Compounding.

A new technique for 3-D imaging with a row-column array (RCA) configuration has been developed. The technique requires an electrostrictive piezoelectric for the active substrate. While the top set of electrodes is connected to RF transmit and receive channels for conventional diverging wave imaging (DWI), the orthogonal bottom set of electrodes is connected to independently controlled variable dc bias channels. By implementing modulated bias patterns compounded across multiple pulses, fine delay control across the bottom elements can be achieved simultaneously with imaging with the top set of electrodes. This resulted in a high-quality two-way focus in both azimuth and elevation. A 20-MHz electrostrictive composite substrate was fabricated, and 64 top ×64 bottom electrodes were patterned and connected to custom beamforming and biasing electronics. The point spread functions were generated in all dimensions, and the -6 dB resolution was measured to be 93 [Formula: see text] axially, [Formula: see text] in the azimuth, and 328 [Formula: see text] in the elevation dimension. This was in good agreement with the simulated resolutions of 80, 273, and 280 [Formula: see text], respectively.

Colocalization and regulated physical association of presynaptic serotonin transporters with A3 adenosine receptors.

Activation of A3 adenosine receptors (A3ARs) rapidly enhances the activity of antidepressant-sensitive serotonin (5-HT) transporters (SERTs) in vitro, ex vivo, and in vivo. A3AR agonist stimulation of SERT activity is lost in A3AR knockout mice. A3AR-stimulated SERT activity is mediated by protein kinase G1 (PKGI)- and p38 mitogen-activated protein kinase (MAPK)-linked pathways that support, respectively, enhanced SERT surface expression and catalytic activation. The mechanisms by which A3ARs target SERTs among other potential effectors is unknown. Here we present evidence that A3ARs are coexpressed with SERT in midbrain serotonergic neurons and form a physical complex in A3AR/hSERT cotransfected cells. Treatment of A3AR/SERT-cotransfected Chinese hamster ovary cells with the A3AR agonist N6-(3-iodobenzyl)-N-methyl-5'-carbamoyladenosine (1 µM, 10 min), conditions previously reported to increase SERT surface expression and 5-HT uptake activity, enhanced the abundance of A3AR/SERT complexes in a PKGI-dependent manner. Cotransfection of SERT with L90V-A3AR, a hyperfunctional coding variant identified in subjects with autism spectrum disorder, resulted in a prolonged recovery of receptor/transporter complexes after A3AR activation. Because PKGI and nitric-oxide synthetase are required for A3AR stimulation of SERT activity, and proteins PKGI and NOS both form complexes with SERT, our findings suggest a mechanism by which signaling pathways coordinating A3AR signaling to SERT can be spatially restricted and regulated, as well as compromised by neuropsychiatric disorders.

Update on malignant pleural mesothelioma.

Malignant pleural mesothelioma is an aggressive cancer principally attributable to asbestos. Although the incidence is now declining in the United States, it will continue to increase worldwide until all nations institute regulations limiting asbestos use and exposure. This is a heterogeneous disease, with three pathological subtypes that yield very different outcomes. Stage is less important than histology in determining prognosis. The biomarkers serum mesothelin-related peptide and osteopontin are being evaluated for screening asbestos-exposed individuals and monitoring disease response. The optimal surgical procedure remains controversial because extrapleural pneumonectomy and pleurectomy/decortication can achieve similar results. The reference chemotherapy regimen, pemetrexed-cisplatin, improves survival and quality of life. Key questions about maintenance therapy and the optimal regimens for elderly and frail patients remain to be answered. Although few other cytotoxic drugs have activity, a surprising number of novel agents are being investigated.

Trying to stomach multiple myeloma: A case report.

We report a case of a 51-year-old male with minimal past medical history who presented to his primary care provider with nausea, vomiting and constipation in the outpatient setting. Concomitantly, he was found to have a renal injury, anemia and lytic lesions which were confirmed to be due to multiple myeloma. After further investigation of the gastrointestinal symptoms, he was diagnosed with gastroparesis. This case represents an unusual presentation of gastroparesis, diagnosed at the same time as multiple myeloma, for which there has yet to be a published association. Here we detail the case, review gastric emptying physiology, the diagnostic criteria for gastroparesis and hypothesize the connection if it might have with multiple myeloma.

A Dual-Frequency Lens-Focused Endoscopic Histotripsy Transducer.

A forward-looking miniature histotripsy transducer has been developed that incorporates an acoustic lens and dual-frequency stacked transducers. An acoustic lens is used to increase the peak negative pressure through focal gain and the dual-frequency transducers are designed to increase peak negative pressure by summing the pressure generated by each transducer individually. Four lens designs, each with an f -number of approximately 1, were evaluated in a PZT5A composite transducer. The finite-element model (FEM) predicted axial beamwidths of 1.61, 2.40, 2.84, and 2.36 mm for the resin conventional, resin Fresnel, silicone conventional, and silicone Fresnel lenses, respectively; the measured axial beamwidths were 1.30, 2.28, 2.71, and 2.11 mm, respectively. Radial beamwidths from the model were between 0.32 and 0.35 mm, while measurements agreed to within 0.2 mm. The measured peak negative was 0.150, 0.124, 0.160, and 0.160 MPa/V for the resin conventional, resin Fresnel, silicone conventional, and silicone Fresnel lenses, respectively. For the dual-frequency device, the 5-MHz (therapy) transducer had a measured peak negative pressure of 0.136 MPa/V for the PZT5A composite and 0.163 MPa/V for the PMN-PT composite. The 1.2-MHz (pump) transducer had a measured peak negative pressure of 0.028 MPa/V. The pump transducer significantly lowered the cavitation threshold of the therapy transducer. The dual-frequency device was tested on an ex vivo rat brain, ablating tissue at up to 4-mm depth, with lesion sizes as small as [Formula: see text].