Automated magnetic resonance imaging-based grading of the lumbar intervertebral disc and facet joints.

Background: Degeneration of both intervertebral discs (IVDs) and facet joints in the lumbar spine has been associated with low back pain, but whether and how IVD/joint degeneration contributes to pain remains an open question. Joint degeneration can be identified by pairing T1 and T2 magnetic resonance imaging (MRI) with analysis techniques such as Pfirrmann grades (IVD degeneration) and Fujiwara scores (facet degeneration). However, these grades are subjective, prompting the need to develop an automated technique to enhance inter-rater reliability. This study introduces an automated convolutional neural network (CNN) technique trained on clinical MRI images of IVD and facet joints obtained from public-access Lumbar Spine MRI Dataset. The primary goal of the automated system is to classify health of lumbar discs and facet joints according to Pfirrmann and Fujiwara grading systems and to enhance inter-rater reliability associated with these grading systems. Methods: Performance of the CNN on both the Pfirrmann and Fujiwara scales was measured by comparing the percent agreement, Pearson's correlation and Fleiss kappa value for results from the classifier to the grades assigned by an expert grader. Results: The CNN demonstrates comparable performance to human graders for both Pfirrmann and Fujiwara grading systems, but with larger errors in Fujiwara grading. The CNN improves the reliability of the Pfirrmann system, aligning with previous findings for IVD assessment. Conclusion: The study highlights the potential of using deep learning in classifying the IVD and facet joint health, and due to the high variability in the Fujiwara scoring system, highlights the need for improved imaging and scoring techniques to evaluate facet joint health. All codes required to use the automatic grading routines described herein are available in the Data Repository for University of Minnesota (DRUM).

One-step syntheses of diaza-dioxa-fenestranes via the sequential (3 + 2) cycloadditions of linear precursors and their structural analyses.

Fenestranes, in which four rings share one carbon atom, have garnered much attention because of their flattened quaternary carbon centers. In addition, the rigid and nonplanar structures of heteroatom-containing fenestranes are attractive scaffolds for pharmaceutical applications. We report one-step syntheses of diaza-dioxa-fenestranes via the sequential (3 + 2) cycloadditions. Our synthesis employs readily synthesizable, nonbranched acyclic allenyl precursors that facilitate sequential cycloaddition reactions. We report the synthesis of 22 heteroatom-containing and differently substituted fenestranes with rings of varying sizes. The prepared diaza-dioxa-fenestranes are subjected to X-ray crystallography and DFT calculations, which suggest that replacing the carbon atoms at the non-bridgehead positions in the fenestrane skeleton with nitrogen and oxygen atoms results in a slight flattening of the quaternary carbon center. Moreover, one of our synthesized c,c-[5.5.5.5]fenestranes containing two isoxazoline rings possesses the flattest quaternary carbon center among previously synthesized heteroatom-containing fenestrane versions.

Seven tesla knee MRI T2*-mapping detects intrasubstance meniscus degeneration in patients with posterior root tears.

Background: Medial meniscus root tears often lead to knee osteoarthritis. The extent of meniscal tissue changes beyond the localized root tear is unknown. Purpose: To evaluate if 7 Tesla 3D T2*-mapping can detect intrasubstance meniscal degeneration in patients with arthroscopically verified medial meniscus posterior root tears (MMPRTs), and assess if tissue changes extend beyond the immediate site of the posterior root tear detected on surface examination by arthroscopy. Methods: In this prospective study we acquired 7 T knee MRIs from patients with MMPRTs and asymptomatic controls. Using a linear mixed model, we compared T2* values between patients and controls, and across different meniscal regions. Patients underwent arthroscopic assessment before MMPRT repair. Changes in pain levels before and after repair were calculated using Knee Injury & Osteoarthritis Outcome Score (KOOS). Pain changes and meniscal extrusion were correlated with T2* using Pearson correlation (r). Results: Twenty patients (mean age 53 ± 8; 16 females) demonstrated significantly higher T2* values across the medial meniscus (anterior horn, posterior body and posterior horn: all P < .001; anterior body: P = .007), and lateral meniscus anterior (P = .024) and posterior (P < .001) horns when compared to the corresponding regions in ten matched controls (mean age 53 ± 12; 8 females). Elevated T2* values were inversely correlated with the change in pain levels before and after repair. All patients had medial meniscal extrusion of ≥2 mm. Arthroscopy did not reveal surface abnormalities in 70% of patients (14 out of 20). Conclusions: Elevated T2* values across both medial and lateral menisci indicate that degenerative changes in patients with MMPRTs extend beyond the immediate vicinity of the posterior root tear. This suggests more widespread meniscal degeneration, often undetected by surface examinations in arthroscopy.

Quasi-Homoepitaxial Growth of Highly Strained Alkali-Metal Ultrathin Films on Kagome Superconductors.

Applying lattice strain to thin films, a critical factor to tailor their properties such as stabilizing a structural phase unstable at ambient pressure, generally necessitates heteroepitaxial growth to control the lattice mismatch with substrate. Therefore, while homoepitaxy, the growth of thin film on a substrate made of the same material, is a useful method to fabricate high-quality thin films, its application to studying strain-induced structural phases is limited. Contrary to this general belief, here the quasi-homoepitaxial growth of Cs and Rb thin films is reported with substantial in-plane compressive strain. This is achieved by utilizing the alkali-metal layer existing in bulk crystal of kagome metals AV3Sb5 (A = Cs and Rb) as a structural template. The angle-resolved photoemission spectroscopy measurements reveal the formation of metallic quantum well states and notable thickness-dependent quasiparticle lifetime. Comparison with density functional theory calculations suggests that the obtained thin films crystalize in the face-centered cubic structure, which is typically stable only under high pressure in bulk crystals. These findings provide a useful approach for synthesizing highly strained thin films by quasi-homoepitaxy, and pave the way for investigating many-body interactions in Fermi liquids with tunable dimensionality.

Seven draft genome sequences of Streptococcus canis strains, revealing reduced penicillin-G susceptibility.

We report seven draft genome sequences of Streptococcus canis strains revealing reduced penicillin-G susceptibility. The genomes measured 2.054-2.385 Mbp, with G+C contents of 38.8%-39.6%. Amino acid substitutions in penicillin-binding proteins were characterized as compared with those of NCTC 12191(T) genome sequence (GenBank accession number NZ_LR134293.1).

Genetic organization of an M protein trans-acting positive regulator (Mga) orthologue and its adjacent M-like protein (SCM) alleles in Streptococcus canis.

OBJECTIVE: The purpose of this study was to identify the M protein trans-acting positive regulator (Mga) orthologue and its adjacent M-like protein (SCM) alleles in Streptococcus canis. RESULTS: Using the 39 SCM allele isolates and polymerase chain reaction-based amplification and sequencing, we obtained the deduced Mga amino acid (AA) sequences. The 22 Mga sequences in whole-genome sequences were obtained by searching the National Collection of Type Cultures 12,191(T) Mga sequence into the database. The percentage identity to the type-strain Mga sequence was examined along with its size. The presence of the Mga-specific motifs was confirmed. Of the 62 strains, we identified 59 Mga sequences with an AA size of 509 (except for four different sizes). Percentage identity ranged from 96.66 to 100% with the confirmed Mga-specific motifs and diverse SCM allele populations. Our findings support the presence of an Mga orthologue and diverse SCM allele populations.

Antimicrobial resistance patterns of Streptococcus uberis isolates from bovine milk in Chiba prefecture, Japan: association between multidrug resistance and clonal complex 996.

Streptococcus uberis is one of major pathogens causing bovine mastitis. However, there is poor information on antimicrobial resistance (AMR) among the Japanese isolates. To provide treatment information for the mastitis caused by S. uberis in Japan, we aimed to clarify AMR patterns of the isolates from bovine milk mainly in Chiba. AMR phenotyping/genotyping [blaZ-erm(A)-erm(B)-mef(A)-linB-lnuD-tet(M)-tet(O)-tet(K)-tet(L)-tet(S)] and multilocus sequence typing were performed to analyze relationships between AMR patterns and clonal complexes (CCs). Resistance to tetracycline-, macrolide-, and lincosamide-classes was mainly associated with possession of tet(O), tet(S), erm(B), linB, and lnuD genes. CC996 was significantly associated with multidrug resistance (P<0.0001). These findings will aid Chiba farm animal clinics in treating bovine mastitis.

Successful treatment of streptococcal toxic shock syndrome complicated by primary peritonitis and bilateral empyema in a healthy young woman: Identification of uncommon clone emm103 and novel sequence type 1363.

Streptococcal toxic shock syndrome (STSS) has a dramatic clinical course and high mortality rate. Here, we report a case of STSS complicated by primary peritonitis and bilateral empyema. A previously healthy young woman was diagnosed with STSS complicated by primary peritonitis and bilateral empyema. Blood culture results on admission were negative. Sever shock, respiratory failure, systemic inflammation, thrombocytopenia, renal failure, ascites, and pleural effusion occurred, mimicking thrombocytopenia, anasarca, fever, reticulin fibrosis/renal failure and organomegaly (TAFRO) syndrome. Retesting blood cultures identified Streptococcus pyogenes. Gram staining of ascites and pleural fluid indicated gram-positive cocci in chains. Antibiotics, immunoglobulins, and surgical intervention led to recovery without complications. Ex-post genotypic analyses showed uncommon emm103.0 (cluster E3) of emm long sequence (784 base) and novel sequence type 1363. STSS diagnosis can be difficult as it mimics other systemic inflammatory diseases. Therefore, it is crucial for clinicians to perform microbiological examinations from infection foci, even if the initial culture is negative.

Imaging Genomics and Multiomics: A Guide for Beginners Starting Radiomics-Based Research.

Radiomics uses advanced mathematical analysis of pixel-level information from radiologic images to extract existing information in traditional imaging algorithms. It is intended to find imaging biomarkers related to the genomics of tumors or disease patterns that improve medical care by advanced detection of tumor response patterns in tumors and to assess prognosis. Radiomics expands the paradigm of medical imaging to help with diagnosis, management of diseases and prognostication, leveraging image features by extracting information that can be used as imaging biomarkers to predict prognosis and response to treatment. Radiogenomics is an emerging area in radiomics that investigates the association between imaging characteristics and gene expression profiles. There are an increasing number of research publications using different radiomics approaches without a clear consensus on which method works best. We aim to describe the workflow of radiomics along with a guide of what to expect when starting a radiomics-based research project.

Draft genome sequence of emm103/ST1363 Streptococcus pyogenes strain AB1, isolated from the blood of a woman with peritonitis and toxic shock syndrome.

We report the draft genome sequence of Streptococcus pyogenes strain AB1 isolated from the blood of a woman with peritonitis-toxic shock syndrome. The genome measured 1.855 Mbp, with a G + C content of 38.3%. Sequences unmapped to the reference genome sequence of M1 SF370 (GenBank accession number AE004092.2) were characterized.

Human Keratinocyte Entry of Noninvasive Streptococcus dysgalactiae Subsp. equisimilis from Humans and Companion Animals: Relatedness with Lancefield Group, Source, Virulence-Associated Genes, and Antimicrobial Resistance Phenotype.

We evaluated the cell invasion ability (CIA) of non-invasive Streptococcus dysgalactiae subsp. equisimilis using human keratinocytes and determined the association of CIA populations with their hosts and microbiological traits. Forty-two isolates from humans and companion animals were selected with host information. In addition to CIA, virulence-associated gene (VAG, spegg-ska-scpA-inlA-sicG-brpA-prtF1-prtF2-lmb-cbp-srtp1-srtp2) profiling, emm genotyping, multilocus sequence typing, and antimicrobial resistance (AMR) phenotyping/genotyping were performed. We designated CIA values higher than the mean of all isolates as high-frequency and those lower than the mean as low-frequency. Differences in the CIA between the different sources and Lancefield groups were assessed. We analyzed the association between high- and low-frequency CIA and VAG, emm genotype, sequence type/clonal complex, and AMR phenotype/genotype. Based on the mean (19.368 colony-forming units/100 cells) of 42 isolates, eight isolates had high-frequency CIA, whereas 34 had low-frequency CIA. We found an association between low-frequency CIA population and group G isolates, as well as a link between high-frequency CIA population and group C isolates. We also observed associations between low-frequency CIA population and oral/respiratory tract origin, ska, scpA, and lmb detection, and the AMR phenotype. Our observations suggest potential associations between high-/low-frequency CIA and the group, source, VAG, and AMR phenotypes.

Moiré-Assisted Realization of Octahedral MoTe2 Monolayer.

A current key challenge in 2D materials is the realization of emergent quantum phenomena in hetero structures via controlling the moiré potential created by the periodicity mismatch between adjacent layers, as highlighted by the discovery of superconductivity in twisted bilayer graphene. Generally, the lattice structure of the original host material remains unchanged even after the moiré superlattice is formed. However, much less attention is paid for the possibility that the moiré potential can also modify the original crystal structure itself. Here, it is demonstrated that octahedral MoTe2 which is unstable in bulk is stabilized in a commensurate MoTe2 /graphene hetero-bilayer due to the moiré potential created between the two layers. It is found that the reconstruction of electronic states via the moiré potential is responsible for this stabilization, as evidenced by the energy-gap opening at the Fermi level observed by angle-resolved photoemission and scanning tunneling spectroscopies. The present results provide a fresh approach to realize novel 2D quantum phases by utilizing the moiré potential.

Phenotypic and Genotypic Traits of Pasteurella multocida subsp. septica Isolates From the Wounds of Two Patients Due to Dog or Cat Biting, 2023.

We describe the phenotypic and genotypic traits of Pasteurella multocida subsp. septica isolates from the dog/cat bite wounds of two patients in 2023. A 79-year-old man with diabetes mellitus and cerebral infarction who was bitten by a dog on his left hand developed deep inflammation under the tendon between his left fourth and fifth fingers. The patient's condition was resolved with antimicrobial treatment and surgical intervention. Another patient, a healthy 49-year-old woman who was bitten by a cat on her left hand, developed superficial inflammation of the left thumb and index finger. The patient's condition improved with antimicrobial treatment without surgical intervention. The isolates from the two patients had similar biochemical properties, and the antimicrobial susceptibility data for both isolates indicated erythromycin resistance. Genotypic analyses revealed clade 2 on the dendrogram of repetitive sequence-based fingerprinting, capsule serogroup cap genotype A, and hsf-1-nanH-pmHAS (virulence-associated genes). Our observations show that the two isolates have similar phenotypic and genotypic traits, regardless of differences in patient background, biting pets, wound inflammation, or the necessity of surgical intervention.

Biotypic and genotypic diversity in Pasteurella canis isolated from host animals and humans: differences in trehalose fermentation and nucleotide sequences encoding trehalose-6-phosphate hydrolase (treC).

The biotypic and genotypic features of Pasteurella canis isolated from dogs, cats, and humans were clarified by repetitive sequence-based fingerprinting and nucleotide sequences encoding trehalose-6-phosphate hydrolase (treC). Thirty P. canis and 48 P. multocida isolates were collected from dogs, cats, and humans to perform biotyping. The genotyping of P. canis by fingerprinting was followed by dendrogram construction. The whole-genome sequences (WGSs) were searched for the enzyme-coding nucleotide sequences around the main and adjacent loci constituting the operon. Full-length nucleotide sequences encoding the enzyme were determined using polymerase chain reaction and direct sequencing. Biotypic results were compared to the dendrogram and nucleotide sequence data. We observed a difference in trehalose fermentation with a positivity rate of 46.7%. Two (A-1/A-2) and three (B-1/B-2/B-3) clades were located on the dendrograms generated based on two repetitive sequence-based fingerprinting techniques, showing no association between trehalose fermentation and the clades. Based on the WGSs, two variants of the gene, namely, a 1,641 bp gene treC and a pseudogene (1,335 bp) of treC with its first 306 nucleotides deleted, were observed. Trehalose-positive isolates harbored treC, whereas trehalose-negative isolates lacked treC with or without the pseudogene. Our observations suggest biotypic and genotypic diversity among the P. canis isolates from animal and human hosts, with respect to trehalose fermentation and treC nucleotide sequences. This is the first report on the diversity of treC nucleotide sequences among these isolates.

Prescribed probiotic usage to prevent Clostridioides difficile infection among older patients receiving antibiotics: A retrospective cohort study.

OBJECTIVES: Clostridioides difficile infection (CDI) is a leading cause of antimicrobial-associated colitis and is a global clinical concern. Probiotics are considered a CDI-preventive measure; however, highly inconsistent data have been previously reported. Thus, we evaluated the CDI-preventive effect of prescribed probiotics in high-risk older patients receiving antibiotics. METHODS: Older patients (aged ≥65 years) admitted to the emergency department who received antibiotics between 2014 and 2017 were enrolled in this single-center retrospective cohort study. Propensity score-matched analysis was used to compare the CDI incidence in patients who took the prescribed probiotics within 2 days of receiving antibiotics for at least 7 days with those who did not. The rates of severe CDI and associated hospital mortality were also evaluated. RESULTS: Among 6148 eligible patients, 221 were included in the prescribed probiotic group. A propensity score-matched (221 matched pairs) well-balanced for patient characteristics was obtained. The incidence of primary nosocomial CDI did not differ significantly between the prescribed and non-prescribed probiotic groups (0% [0/221] vs. 1.0% [2/221], p = 0.156). Of the 6148 eligible patients, 0.5% (30/6148) developed CDI, with a severe CDI rate of 33.3% (10/30). Furthermore, no CDI-associated in-hospital mortality was observed in the study cohort. CONCLUSIONS: The evidence from this study does not support recommendations for the routine use of prescribed probiotics to prevent primary CDI in older patients receiving antibiotics in situations where the CDI is infrequent.

Direct Imaging of Band Structure for Powdered Rhombohedral Boron Monosulfide by Microfocused ARPES.

Boron-based two-dimensional (2D) materials are an excellent platform for nanoelectronics applications. Rhombohedral boron monosulfide (r-BS) is attracting particular attention because of its unique layered crystal structure suitable for exploring various functional properties originating in the 2D nature. However, studies to elucidate its fundamental electronic states have been largely limited because only tiny powdered crystals were available, hindering a precise investigation by spectroscopy such as angle-resolved photoemission spectroscopy (ARPES). Here we report the direct mapping of the band structure with a tiny (∼20 × 20 µm2) r-BS powder crystal by utilizing microfocused ARPES. We found that r-BS is a p-type semiconductor with a band gap of >0.5 eV characterized by the anisotropic in-plane effective mass. The present results demonstrate the high applicability of micro-ARPES to tiny powder crystals and widen an opportunity to access the yet-unexplored electronic states of various novel materials.

Longitudinal 3T MRI T2 * mapping of Juvenile osteochondritis dissecans (JOCD) lesions differentiates operative from non-operative patients-Pilot study.

Juvenile osteochondritis dissecans (JOCD) is an orthopedic joint disorder of children and adolescents that can lead to premature osteoarthritis. Thirteen patients (mean age: 12.3 years, 4 females), 15 JOCD-affected and five contralateral healthy knees, that had a baseline and a follow-up magnetic resonance imaging (MRI) (mean interval of 8.9 months) and were treated nonoperatively during this interval were included. Retrospectively, patients were assigned to operative or nonoperative groups based on their electronic medical records. Volumetric mean T2 * values were calculated within regions of interest (progeny lesion, interface, parent bone) and region matched control bone in healthy contralateral knees and condyles. The normalized percentage difference of T2 * between baseline and follow up MRI in nonoperative patients significantly increased in progeny lesion (-47.8%, p < 0.001), parent bone (-13.9%, p < 0.001), and interface (-32.3%, p = 0.011), whereas the differences in operative patients were nonsignificant and below 11%. In nonoperative patients, the progeny lesion (p < 0.001) and interface T2 * values (p = 0.012) were significantly higher than control bone T2 * at baseline, but not at follow-up (p = 0.219, p = 1.000, respectively). In operative patients, the progeny lesion and interface T2 * values remained significantly elevated compared to the control bone both at baseline (p < 0.001, p < 0.001) and follow-up (p < 0.001, p < 0.001), respectively. Clinical Significance: Longitudinal T2 * mapping differentiated nonhealing from healing JOCD lesions following initial nonoperative treatment, which may assist in prognosis and improve the ability of surgeons to make recommendations regarding operative versus nonoperative treatment.

Biofilm Production Ability of Streptococcus dysgalactiae Subsp. equisimilis: Associations with Host Species, Lancefield Group, Source, Clonal Complex, and Virulence-Associated Genes.

We assessed the biofilm production ability (BPA) of noninvasive Streptococcus dysgalactiae subsp. equisimilis (SDSE) in humans and companion animals and determined the relationship between bacterial populations with BPA and other host and microbiological features. Sixty-four isolates from companion animals and humans were collected along with host information. We measured BPA using crystal violet staining, in addition to emm typing, multilocus sequence typing, antimicrobial resistance (AMR) phenotyping/genotyping, and virulence-associated gene (VAG) detecting (prtF1-prtF2-lmb-cbp-sicG-srtp1-srtp2-brpA). Differences in the BPA of SDSE from different hosts and sources and different Lancefield groups were assessed. We analyzed the associations between populations with and without BPA (strong, moderate, weak, and no biofilm producers) and emm types, sequence types/clonal complexes (CCs), AMR phenotypes/genotypes, and VAG types. Seventeen, twenty-four, and twelve isolates were strong, moderate, and weak biofilm producers, respectively; eleven showed no BPA. There was a difference in the distribution of populations with BPA between human and animal origins and between isolates of groups G and C. We found an association between populations with BPA and the eye and ear source (vs. the pus and skin source). A relationship was observed between the populations with BPA and CC127 (vs. CC17). We observed no association between the populations with BPA and AMR phenotype/genotype. There was an association between the distribution of populations with BPA and srtp1 expression. Our observations suggest potential associations between populations with BPA and the host species, Lancefield group, source, CC, and VAG type.

Virulence-associated Genome Sequences of Pasteurella canis and Unique Toxin Gene Prevalence of P. canis and Pasteurella multocida Isolated from Humans and Companion Animals.

Background: Comparative analysis of virulence factors (VFs) between Pasteurella canis and Pasteurella multocida are lacking, although both cause zoonotic infections. We determined the virulence-associated genome sequence characteristics of P. canis and assessed the toxin gene prevalence unique to P. canis among clinical isolates of P. canis and P. multocida. Methods: We selected 10 P. canis and 16 P. multocida whole-genome sequences (WGSs) from the National Center for Biotechnology database. The VFanalyzer tool was used to estimate P. canis-characteristic VFs. Amino acid sequences of VFs were compared with multiple-aligned sequences. The genome structure containing P. canis-characteristic and adjacent loci was compared to the corresponding P. multocida genome structure. After designing primer sequences and assessing their accuracy, we examined the gene prevalence of the P. canis-characteristic VFs using PCR among clinical isolates of P. multocida and P. canis. Results: Using VFanalyzer, we found virulence-associated cytolethal distending toxin (cdt)A-cdtB-cdtC loci common to all P. canis WGSs that were not found in P. multocida WGSs. Similarities in the multiple alignments of CdtA-CdtB-CdtC amino acid sequences were found among the 10 P. canis WGSs. Shared or similar loci around cdtA-cdtB-cdtC were identified between the P. canis and P. multocida genome structures. The PCR-based cdtA-cdtB-cdtC prevalence differed for P. canis and P. multocida clinical isolates. Conclusions: P. canis-specific cdtA-cdtB-cdtC prevalence was identified among clinical isolates. These three loci may be unique toxin genes and promising targets for the rapid identification of P. canis in clinical settings.

Long non-coding RNA TILR constitutively represses TP53 and apoptosis in lung cancer.

Non-coding RNAs have an integral regulatory role in numerous functions related to lung cancer development. Here, we report identification of a novel lncRNA, termed TP53-inhibiting lncRNA (TILR), which was found to function as a constitutive negative regulator of p53 expression, including activation of downstream genes such as p21 and MDM2, and induction of apoptosis. A proteomic search for TILR-associated proteins revealed an association with PCBP2, while the mid-portion of TILR was found to be required for both PCBP2 and p53 mRNA binding. In addition, depletion of PCBP2 resulted in phenocopied effects of TILR silencing. TILR was also shown to suppress p53 expression in a post-transcriptional manner, as well as via a positive feedback loop involving p53 and Fanconi anemia pathway genes. Taken together, the present findings clearly demonstrate that TILR constitutively inhibits p53 expression in cooperation with PCBP2, thus maintaining p53 transcriptional activity at a level sufficiently low for avoidance of spurious apoptosis induction.