Protein Set Transformer: A protein-based genome language model to power high diversity viromics.

Exponential increases in microbial and viral genomic data demand transformational advances in scalable, generalizable frameworks for their interpretation. Standard homology-based functional analyses are hindered by the rapid divergence of microbial and especially viral genomes and proteins that significantly decreases the volume of usable data. Here, we present Protein Set Transformer (PST), a protein-based genome language model that models genomes as sets of proteins without considering sparsely available functional labels.

Evolutionary history and origins of Dsr-mediated sulfur oxidation.

Microorganisms play vital roles in sulfur cycling through the oxidation of elemental sulfur and reduction of sulfite. These metabolisms are catalyzed by dissimilatory sulfite reductases (Dsr) functioning in either the reductive or reverse, oxidative direction. Dsr-mediated sulfite reduction is an ancient metabolism proposed to have fueled energy metabolism in some of Earth's earliest microorganisms, whereas sulfur oxidation is believed to have evolved later in association with the widespread availability of oxygen on Earth.

Protein Set Transformer: A protein-based genome language model to power high diversity viromics.

Exponential increases in microbial and viral genomic data demand transformational advances in scalable, generalizable frameworks for their interpretation. Standard homology-based functional analyses are hindered by the rapid divergence of microbial and especially viral genomes and proteins that significantly decreases the volume of usable data. Here, we present Protein Set Transformer (PST), a protein-based genome language model that models genomes as sets of proteins without considering sparsely available functional labels.

Prophage-DB: A comprehensive database to explore diversity, distribution, and ecology of prophages.

Background: Viruses that infect prokaryotes (phages) constitute the most abundant group of biological agents, playing pivotal roles in microbial systems. They are known to impact microbial community dynamics, microbial ecology, and evolution. Efforts to document the diversity, host range, infection dynamics, and effects of bacteriophage infection on host cell metabolism are extremely underexplored.

Systematic genome-wide discovery of host factors governing bacteriophage infectivity.

Bacterial host factors regulate the infection cycle of bacteriophages. Except for some well-studied host factors (e.g.

ViWrap: A modular pipeline to identify, bin, classify, and predict viral-host relationships for viruses from metagenomes.

Viruses are increasingly being recognized as important components of human and environmental microbiomes. However, viruses in microbiomes remain difficult to study because of the difficulty in culturing them and the lack of sufficient model systems. As a result, computational methods for identifying and analyzing uncultivated viral genomes from metagenomes have attracted significant attention.

Spatial and temporal control of lysis by the lambda holin.

The infection cycle of phage λ terminates in lysis mediated by three types of lysis proteins, each disrupting a layer in the bacterial envelope: the S105 holin, the R endolysin, and the Rz/Rz1 spanin complex targeting the inner membrane, cell wall or peptidoglycan, and the outer membrane, respectively. Video microscopy has shown that in most infections, lysis occurs as a sudden, explosive event at a cell pole, such that the initial product is a less refractile ghost that retains rod-shaped morphology. Here, we investigate the molecular basis of polar lysis using time-lapse fluorescence microscopy.

Methionine restriction-induced sulfur deficiency impairs antitumour immunity partially through gut microbiota.

Restriction of methionine (MR), a sulfur-containing essential amino acid, has been reported to repress cancer growth and improve therapeutic responses in several preclinical settings. However, how MR impacts cancer progression in the context of the intact immune system is unknown. Here we report that while inhibiting cancer growth in immunocompromised mice, MR reduces T cell abundance, exacerbates tumour growth and impairs tumour response to immunotherapy in immunocompetent male and female mice.

zol & fai: large-scale targeted detection and evolutionary investigation of gene clusters.

Many universally and conditionally important genes are genomically aggregated within clusters. Here, we introduce fai and zol, which together enable large-scale comparative analysis of different types of gene clusters and mobile-genetic elements (MGEs), such as biosynthetic gene clusters (BGCs) or viruses. Fundamentally, they overcome a current bottleneck to reliably perform comprehensive orthology inference at large scale across broad taxonomic contexts and thousands of genomes.

ViWrap: A modular pipeline to identify, bin, classify, and predict viral-host relationships for viruses from metagenomes.

Viruses are increasingly being recognized as important components of human and environmental microbiomes. However, viruses in microbiomes remain difficult to study because of difficulty in culturing them and the lack of sufficient model systems. As a result, computational methods for identifying and analyzing uncultivated viral genomes from metagenomes have attracted significant attention.

Butyrate Differentiates Permissiveness to Clostridioides difficile Infection and Influences Growth of Diverse C. difficile Isolates.

A disrupted "dysbiotic" gut microbiome engenders susceptibility to the diarrheal pathogen Clostridioides difficile by impacting the metabolic milieu of the gut. Diet, in particular the microbiota-accessible carbohydrates (MACs) found in dietary fiber, is one of the most powerful ways to affect the composition and metabolic output of the gut microbiome. As such, diet is a powerful tool for understanding the biology of C.

Operating Room Fire During Total Knee Arthroplasty Tibial Impaction: A Case Report and Review of the Literature.

A fire in the operating room is a rare but potentially deadly occurrence. We present an operating room fire during an elective total knee arthroplasty with an unclear ignition source. Flames were visualized originating from the excess bone cement while impacting the tibial component.

Phage-encoded cationic antimicrobial peptide required for lysis.

Most phages of Gram-negative hosts encode spanins for disruption of the outer membrane, the last step in host lysis. However, bioinformatic analysis indicates that ∼15% of these phages lack a spanin gene, suggesting they have an alternate way of disrupting the OM. Here, we show that the T7-like coliphage phiKT causes the explosive cell lysis associated with spanin activity despite not encoding spanins.

Complete Genome Sequence of Klebsiella pneumoniae Myophage Muenster.

is associated with antibiotic-resistant nosocomial infections. Here, we present the annotated genome sequence of the jumbo phage Muenster. The Muenster genome sequence (346,937 bp) encodes 6 tRNAs and 561 putative protein-coding genes, including 9 tail fibers, suggesting a genetic mechanism to broaden the host range.

Intra-articular Corticosteroid Injections for Symptomatic Knee Osteoarthritis: What the Orthopaedic Provider Needs to Know.

Intra-articular corticosteroid injections have been used for decades in the management of symptomatic osteoarthritis of the knee and remain a common practice. The pain relief from a steroid injection is thought to work by reducing inflammation within the arthritic knee. Substantial variability remains among providers with regard to the technique used to perform the procedure, including the site of the injection, the medications injected, and the level of sterility.

Special Considerations for Mass Violence Events in Senior Living Facilities: A Case Report on the Pinelake Health and Rehab Center Shooting.

The 2009 Pinelake Health and Rehab Center shooting in Carthage, North Carolina, presents a unique case study for examining the specific considerations for mass violence events in senior living facilities. A variety of factors, including reduced sensory perception, reduced mobility, and cognitive decline, may increase the vulnerability of the populations of senior living facilities during mass violence events. Management of response aspects such as evacuation, relocation, and reunification also require special consideration in the context of mass violence at senior living facilities.

Opening a New Level II Trauma Center Near an Established Level I Trauma Center: Is This Good for Trauma Care?

Objectives: To describe how the initiation and later removal of a provisional level II trauma center (PL2TC) status at a community hospital affected the volume and severity of injured patients seen at an established academic level 1 trauma center (AL1TC).

Methods: Census data including counts of injury ICD-9 codes and patients seen in the emergency department (ED) and trauma center at an AL1TC were collected monthly from January 2010 to October 2014. An interrupted time series analysis was used to model the monthly census data with 2 time interruptions to describe the change in patient volume at the interruptions.

Dynamic time warping and sparse representation classification for birdsong phrase classification using limited training data.

Annotation of phrases in birdsongs can be helpful to behavioral and population studies. To reduce the need for manual annotation, an automated birdsong phrase classification algorithm for limited data is developed. Limited data occur because of limited recordings or the existence of rare phrases.

Structural design principles of complex bird songs: a network-based approach.

Bird songs are acoustic communication signals primarily used in male-male aggression and in male-female attraction. These are often monotonous patterns composed of a few phrases, yet some birds have extremely complex songs with a large phrase repertoire, organized in non-random fashion with discernible patterns. Since structure is typically associated with function, the structures of complex bird songs provide important clues to the evolution of animal communication systems.

Blood transfusion associated with shoulder arthroplasty.

Background: Studies have reported high rates of transfusion in shoulder arthroplasty. This study was conducted to evaluate the rate of transfusion at our institution, to confirm reported risk factors for transfusion, and to look for changes over time.We hypothesized that transfusion rates associated with shoulder arthroplasty at our institution are lower than those recently reported and that the incidence of transfusion is higher in individuals with low preoperative hemoglobin, with revision arthroplasty, and in older individuals.

Involuntary memory chaining versus event cueing: Which is a better indicator of autobiographical memory organisation?

Involuntary memory chains are spontaneous recollections of the past that occur in a sequence. Much like semantic memory priming, this memory phenomenon has provided some insights into the nature of associations in autobiographical memory. The event-cueing procedure (a laboratory-based memory sequencing task) has also provided some insights into the nature of autobiographical memory organisation.

Bird diversity and density in south african forests.

Afromontane woodlands are fairly continuous in eastern Cape Province of southern Africa, but occur as increasingly smaller and more isolated patches towards Cape Town in the southwest. These habitat patches are similar in both vegetation structure and floristic composition. Although bird species numbers in the patches decline three-fold from east to west to 15 species at Table Mountain, total bird density remains roughly constant, and bird density per species increases threefold as species diversity declines by the same factor.