bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial modeling algorithms for reactions and transport (SMART) in biological cells
Authors: Francis Emmet A. , Laughlin Justin , Dokken Jørgen S. , Finsberg Henrik , Lee Christopher T. , Rognes Marie E. , Rangamani Padmini 
Published: May 2024

ABSTRACTBiological cells rely on precise spatiotemporal coordination of biochemical reactions to control their many functions. Such cell signaling networks have been a common focus for mathematical models, but they remain challenging to simulate, particularly in realistic cell geometries. Herein, we present our software, Spatial Modeling Algorithms for Reaction and Transport (SMART), a package that takes in high-level user specifications about cell signaling networks and molecular transport, and then assembles and solves the associated mathematical and computational systems. SMART uses state-of-the-art finite element analysis, via the FEniCS Project software, to efficiently and accurately resolve cell signaling events over discretized cellular and subcellular geometries. We demonstrate its application to several different biological systems, including YAP/TAZ mechanotransduction, calcium signaling in neurons and cardiomyocytes, and ATP generation in mitochondria. Throughout, we utilize experimentally-derived realistic cellular geometries represented by well-conditioned tetrahedral meshes. These scenarios demonstrate the applicability, flexibility, accuracy and efficiency of SMART across a range of temporal and spatial scales.
Performance comparison of ten state-of-the-art machine learning algorithms for outcome prediction modeling of radiation-induced toxicity
Authors: Salazar Ramon M. , Nair Saurabh S. , Leone Alexandra O. , Xu Ting , Mumme Raymond P. , Duryea Jack D. , De Brian , Corrigan Kelsey L. , Rooney Michael K. , Ning Matthew S. , Das Prajnan , Holliday Emma B. , Liao Zhongxing , Court Laurence E. , Niedzielski Joshua S. 
Published: May 2024

AbstractPurposeTo evaluate the efficacy of prominent machine learning algorithms in predicting normal tissue complication probability utilizing clinical data obtained from two distinct disease sites, and to create a software tool that facilitates the automatic determination of the optimal algorithm to model any given labeled dataset.Methods and MaterialsWe obtained 3 sets of radiation toxicity data (478 patients) from our clinic, gastrointestinal toxicity (GIT), radiation pneumonitis (RP), and radiation esophagitis (RE). These data comprised clinicopathological and dosimetric information for patients diagnosed with non-small cell lung cancer and anal squamous cell carcinoma. Each dataset was modeled using ten commonly employed machine learning algorithms (elastic net, LASSO, random forest, regression forest, support vector machine, XGBoost, k-nearest- neighbors, neural network, Bayesian-LASSO, and Bayesian neural network) by randomly dividing the dataset into a training and test set. The training set was used to create and tune the model, and the test set served to assess it by calculating performance metrics. This process was repeated 100 times by each algorithm for each dataset. Figures were generated to visually compare the performance of the algorithms. A graphical user interface was developed to automate this whole process.ResultsLASSO achieved the highest area under the precision-recall curve (AUPRC) (0.807±0.067) for RE, random forest for GIT (0.726±0.096), and the neural network for RP (0.878±0.060). Area-under-the-curve was 0.754±0.069, 0.889±0.043, and 0.905±0.045, respectively. The graphical user interface was used to compare all algorithms for each dataset automatically. When averaging AUPRC across all toxicities, Bayesian-LASSO was the best model.ConclusionOur results show that there is no best algorithm for all datasets. Therefore, it is important to compare multiple algorithms when training an outcome prediction model on a new dataset. The graphical user interface created for this study automatically compares the performance of these ten algorithms for any dataset.
Targeted Sequencing of CTX-M Alleles in Seattle Area Wastewater
Authors: Ong Angelo Q. , Philo Sarah E. , Taylor Anysiah , Hu Ruohan , Meschke John Scott , Fuhrmeister Erica R. 
Published: May 2024

AbstractExtended-spectrum-beta-lactamases (ESBLs) are a growing group of antimicrobial resistance (AMR) enzymes that can result in severe clinical outcomes. The CTX-M gene, which encodes for ESBLs in bacteria, confers resistance to third generation cephalosporins and is of high clinical concern. We developed a targeted, long-read sequencing method utilizing unique molecular identifiers to generate accurate, full length CTX-M gene sequences from wastewater. We characterized CTX-M in 36 samples from three Seattle area wastewater treatment plants from April 2020 to March 2021. We identified a core community of alleles that persisted across time and treatment plant. The CTX-M-15 containing protein variant (CTX-M-15/216/28) was detected in all but three samples and made up, at most, 30% of detected CTX-M alleles. We observed significant diversity across the CTX-M gene at the nucleic acid level, although most nucleotide mutations were synonymous - resulting in two to three amino acid variants across 19 loci. By average relative abundance, 23% of protein variants were novel, defined as those not represented in the CARD database. This method provides information (full length gene sequences) that cannot be obtained through other culture-independent methods. This flexible approach can be expanded to additional targets and implemented in settings where AMR surveillance is a priority, such as hospital wastewater.
Percutaneous rheolytic thrombectomy of thrombosed arteriovenous dialysis access using the AngioJet catheter- A Systematic Review
Authors: Lee Quinncy , Ho Dominic Lap Hin , Ng Jun Jie , Choong Andrew MTL 
Published: May 2024

AbstractIntroductionThe endovascular removal of thrombi in occluded arteriovenous (AV) access sites has been increasingly accepted by surgeons as an alternative to surgical thrombectomy and revision [1,2]. This systematic review documents the experiences and outcomes of using the AngioJet Rheolytic Thrombectomy Device for salvaging thrombosed arteriovenous fistulas (AVFs) or grafts (AVGs).MethodsElectronic databases, such as PubMed, Embase, and the Cochrane Library, were searched from their establishment until May 2024. Initially, 549 articles were reviewed for potential inclusion, and only 10 studies fulfilled our inclusion criteria. Our final dataset included 771 patients who underwent 996 thrombectomies to treat 338 thrombosed AVFs and 457 AVGs.ResultsThe demographics, technical and procedural success, patency rates, and complications were evaluated to examine the effectiveness and safety of AngioJet thrombectomy. The mean primary patency rates at 3, 6, and 12 months were 64.09 ± 10.12, 50.36 ± 11.73, and 40.81 ± 15.13 (p < 0.05). The mean assisted primary patency rates at 3, 6, and 12 months were 75.37 ± 13.98, 59.58 ± 14.26 and 40.88 ± 18.81 (p < 0.05). Finally, the mean secondary patency rates at 3, 6, and 12 months were 84.03 ± 8.38, 77.93 ± 9.07, and 65.81 ± 12.12 (p < 0.05). A total of 92 complications were recorded; most were minor complications, thereby being transient and self-limiting. Additionally, 5 total deaths were reported; however, all were not considered related to the AngioJet device.DiscussionOur study deemed devices such as AngioJet efficacious in performing pharmacomechanical thrombectomies, as promising results in terms of safeness and effectiveness to re-establish patency in occluded AVFs and AVGs have been reported.
Streamlining Marker-less Allelic Replacement inStreptococcus pneumoniaeThrough a Single Transformation Step Strategy: easyJanus
Authors: Chembilikandy Vipin , D’Mello Adonis , Tettelin Hervé , Martínez Eriel , Orihuela Carlos J. 
Published: May 2024

ABSTRACTThe ability to genetically manipulate bacteria is a staple of modern molecular microbiology. Since the 2000’s, marker-less mutants ofStreptococcus pneumoniae(Spn) have been made by allelic-exchange predominantly using thekanR-rpsLcassette known as “Janus”. The conventional Janus protocol involves two transformation steps using multiple PCR-assembled products containing the Janus cassette and the target gene’s flanking DNA. We present an innovative strategy to achieve marker-less allelic replacement through a single transformation step. Our approach involves the integration of an additional gene downstream region upstream of the Janus cassette, resulting in a modified genetic arrangement. This single modification reduced the number of required PCR fragments from five to four, lowered the number of assembly reactions from two to one, and simplified the transformation process to a single step. To validate the efficacy of our approach, we implemented this strategy to delete inSpnserotype 4 strain TIGR4 the virulence genepspA, the entire capsular polysaccharide synthesis locuscps4, and to introduce a single nucleotide replacement into the chromosome. Notably, beyond streamlining the procedure, our method markedly reduced false positives typically encountered during negative selection with streptomycin when employing the traditional Janus protocol. Furthermore, and as consequence of reducing the amount of exogenous DNA required for construct synthesis, we show that our new method is amendable to the use of commercially available synthetic DNA for construct creation, further reducing the work needed to obtain a mutant. Our streamlined strategy, termed easyJanus, substantially expedites the genetic manipulation ofSpnfacilitating future research endeavors.IMPORTANCEWe introduce a groundbreaking strategy aimed at streamlining the process for marker-less allelic replacement inStreptococcus pneumoniae, a Gram-positive bacterium and leading cause of pneumonia, meningitis, and ear infections. Our approach involves a modified genetic arrangement of the Janus cassette to facilitate self-excision during the segregation step. Since this new method reduces the amount of exogenous DNA required, it is highly amendable to the use of synthetic DNA for construction of the mutagenic construct. Our streamlined strategy, called easyJanus, offers significant time and cost savings, while concurrently enhancing the efficiency of obtaining marker-less allelic replacement inS. pneumoniae.
Mucin-induced surface dispersal ofStaphylococcus aureusandStaphylococcus epidermidisvia quorum sensing-dependent and independent mechanisms
Authors: Jacob Kristin M. , Hernandez-Villamizar Santiago , Hammer Neal D. , Reguera Gemma 
Published: May 2024

AbstractNasopharyngeal carriage of staphylococci spreads potentially pathogenic strains into (peri)oral regions and increases the chance of cross-infections. Some laboratory strains can also move rapidly on hydrated agar surfaces, but the biological relevance of these observations is not clear. Using soft-agar (0.3% w/v) plate assays, we demonstrate the rapid surface dispersal of (peri)oral isolates ofStaphylococcus aureusandStaphylococcus epidermidisand closely related laboratory strains in the presence of mucin glycoproteins. Mucin-induced dispersal was a stepwise process initiated by the passive spreading of the growing colonies followed by their rapid branching (dendrites) from the colony edge. Although most spreading strains used mucin as a growth substrate, dispersal was primarily dependent on the lubricating and hydrating properties of the mucins. UsingS. aureusJE2 as a genetically tractable representative, we demonstrate that mucin-induced dendritic dispersal, but not colony spreading, is facilitated by the secretion of surfactant-active Phenol-Soluble Modulins (PSMs) in a process regulated by theagrquorum sensing system. Furthermore, the dendritic dispersal ofS. aureusJE2 colonies was further stimulated in the presence of surfactant-active supernatants recovered from the most robust (peri)oral spreaders ofS. aureusandS. epidermidis. These findings suggest complementary roles for lubricating mucins and staphylococcal PSMs in the active dispersal of potentially pathogenic strains from perioral to respiratory mucosae, where gel-forming, hydrating mucins abound. They also highlight the impact that interspecies interactions have on the co-dispersal ofS. aureuswith other perioral bacteria, heightening the risk of polymicrobial infections and the severity of the clinical outcomes.ImportanceDespite lacking classical motility machinery, nasopharyngeal staphylococci spread rapidly in (peri)oral and respiratory mucosa and cause cross-infections. We describe laboratory conditions for the reproducible study of staphylococcal dispersal on mucosa-like surfaces and the identification of two dispersal stages (colony spreading and dendritic expansion) stimulated by mucin glycoproteins. The mucin type mattered, as dispersal required the surfactant activity and hydration provided by some mucin glycoproteins. While colony spreading was a passive mode of dispersal lubricated by the mucins, the more rapid and invasive form of dendritic expansion ofStaphylococcus aureusandStaphylococcus epidermidisrequired additional lubrication by surfactant-active peptides (phenol-soluble modulins) secreted at high cell densities through quorum sensing. These results highlight a hitherto unknown role for gel-forming mucins in the dispersal of staphylococcal strains associated with cross-infections and point at perioral regions as overlooked sources of carriage and infection by staphylococci.
Polyomavirus ALTOs, but not MTs, downregulate viral early gene expression by activating the NF-κB pathway
Authors: Salisbury Nicholas J. H. , Amonkar Supriya , Landazuri Vinueza Joselyn , Carter Joseph J. , Roman Ann , Galloway Denise A. 
Published: May 2024

AbstractPolyomaviruses are small, circular dsDNA viruses that can cause cancer. Alternative splicing of polyomavirus early transcripts generates large and small tumor antigens (LT, ST) that play essential roles in viral replication and tumorigenesis. Some polyomaviruses also express middle tumor antigens (MTs) orAlternateLT ORFs (ALTOs), which are evolutionarily related but have distinct gene structures. MTs are a splice variant of the early transcript whereas ALTOs are overprinted on the second exon of the LT transcript in an alternate reading frame and are translated via an alternative start codon. Merkel cell polyomavirus (MCPyV), the only human polyomavirus that causes cancer, encodes an ALTO but its role in the viral lifecycle and tumorigenesis has remained elusive. Here, we show MCPyV ALTO acts as a tumor suppressor and is silenced in Merkel cell carcinoma (MCC). Rescuing ALTO in MCC cells induces growth arrest and activates NF-κB signaling. ALTO activates NF-κB by binding SQSTM1 and TRAF2&3 via twoN-TerminalActivatingRegions (NTAR1+2), resembling Epstein-Barr virus (EBV) Latent Membrane Protein 1 (LMP1).. Following activation, NF-κB dimers bind the MCPyV non-coding control region (NCCR) and downregulate early transcription. Beyond MCPyV, NTAR motifs are conserved in other polyomavirus ALTOs, which activate NF-κB signaling, but are lacking in MTs that do not. Furthermore, polyomavirus ALTOs downregulate their respective viral early transcription in an NF-κB and NTAR dependent manner. Our findings suggest that ALTOs evolved to suppress viral replication and promote viral latency and that MCPyV ALTO must be silenced for MCC to develop.
Skeletal muscle myosin heavy chain protein fragmentation as a potential marker of protein degradation in response to resistance training and disuse atrophy
Authors: Plotkin Daniel L. , Mattingly Madison L. , Anglin Derick A. , Michel J. Max , Godwin Joshua S. , McIntosh Mason C. , Bergamasco João G. A. , Scarpelli Maíra C. , Angleri Vitor , Taylor Lemuel W. , Willoughby Darryn S. , Mobley C. Brooks , Kavazis Andreas N. , Ugrinowitsch Carlos , Libardi Cleiton A. , Roberts Michael D. 
Published: May 2024

ABSTRACTWe sought to examine how resistance exercise (RE), cycling exercise, and disuse atrophy affect myosin heavy chain (MyHC) protein fragmentation in humans. In the first study (1boutRE), younger adult men (n=8; 5±2 years of RE experience) performed a lower body RE bout with vastus lateralis (VL) biopsies obtained immediately before, 3-, and 6-hours post-exercise. In the second study (10weekRT), VL biopsies were obtained in untrained younger adults (n=36, 18 men and 18 women) before and 24 hours (24h) after their first/naïve RE bout. These participants also engaged in 10 weeks (24 sessions) of resistance training and donated VL biopsies before and 24h after their last RE bout. VL biopsies were also examined from a third acute cycling study (n=7) and a fourth study involving two weeks of leg immobilization (n=20, 15 men and 5 women) to determine how MyHC fragmentation was affected. In the 1boutRE study, the fragmentation of all MyHC isoforms (MyHCTotal) increased 3 hours post-RE (∼ +200%, p=0.018) and returned to pre-exercise levels by 6 hours post-RE. Immunoprecipitation of MyHCTotalrevealed ubiquitination levels remained unaffected at the 3- and 6-hour post-RE time points. Interestingly, a greater increase in magnitude for MyHC type IIa versus I isoform fragmentation occurred 3-hours post-RE (8.6±6.3-fold versus 2.1±0.7-fold, p=0.018). In all 10weekRT participants, the first/naïve and last RE bouts increased MyHCTotalfragmentation 24h post-RE (+65% and +36%, respectively; p<0.001); however, the last RE bout response was attenuated compared to the first bout (p=0.045). The first/naïve bout response was significantly elevated in females only (p<0.001), albeit females also demonstrated a last bout attenuation response (p=0.002). Although an acute cycling bout did not alter MyHCTotalfragmentation, ∼8% VL atrophy with two weeks of leg immobilization led to robust MyHCTotalfragmentation (+108%, p<0.001), and no sex-based differences were observed. In summary, RE and disuse atrophy increase MyHC protein fragmentation. A dampened response with 10 weeks of resistance training, and more refined responses in well-trained men, suggest this is an adaptive process. Given the null polyubiquitination IP findings, more research is needed to determine how MyHC fragments are processed. Moreover, further research is needed to determine how aging and disease-associated muscle atrophy affect these outcomes, and whether MyHC fragmentation is a viable surrogate for muscle protein turnover rates.
A hierarchy of processing complexity and timescales for natural sounds in human auditory cortex
Authors: Rupp Kyle M. , Hect Jasmine L. , Harford Emily E. , Holt Lori L. , Ghuman Avniel Singh , Abel Taylor J. 
Published: May 2024

AbstractEfficient behavior is supported by humans’ ability to rapidly recognize acoustically distinct sounds as members of a common category. Within auditory cortex, there are critical unanswered questions regarding the organization and dynamics of sound categorization. Here, we performed intracerebral recordings in the context of epilepsy surgery as 20 patient-participants listened to natural sounds. We built encoding models to predict neural responses using features of these sounds extracted from different layers within a sound-categorization deep neural network (DNN). This approach yielded highly accurate models of neural responses throughout auditory cortex. The complexity of a cortical site’s representation (measured by the depth of the DNN layer that produced the best model) was closely related to its anatomical location, with shallow, middle, and deep layers of the DNN associated with core (primary auditory cortex), lateral belt, and parabelt regions, respectively. Smoothly varying gradients of representational complexity also existed within these regions, with complexity increasing along a posteromedial-to-anterolateral direction in core and lateral belt, and along posterior-to-anterior and dorsal-to-ventral dimensions in parabelt. When we estimated the time window over which each recording site integrates information, we found shorter integration windows in core relative to lateral belt and parabelt. Lastly, we found a relationship between the length of the integration window and the complexity of information processing within core (but not lateral belt or parabelt). These findings suggest hierarchies of timescales and processing complexity, and their interrelationship, represent a functional organizational principle of the auditory stream that underlies our perception of complex, abstract auditory information.
Single-cell transcriptomics reveal individual and synergistic effects of Trisomy 21 and GATA1s on hematopoiesis
Authors: Takasaki Kaoru , Wafula Eric K. , Kumar Sara S. , Smith David , Sit Ying Ting , Gagne Alyssa L. , French Deborah L. , Thom Christopher S. , Chou Stella T. 
Published: May 2024

AbstractTrisomy 21 (T21), or Down syndrome (DS), is associated with baseline macrocytic erythrocytosis, thrombocytopenia, and neutrophilia, as well as transient abnormal myelopoiesis (TAM) and myeloid leukemia of DS (ML-DS). TAM and ML-DS blasts both arise from an aberrant megakaryocyte-erythroid progenitor and exclusively express GATA1s, the truncated isoform ofGATA1, while germlineGATA1smutations in a non-T21 context lead to congenital cytopenia(s) without a leukemic predisposition. This suggests that T21 and GATA1s both perturb hematopoiesis in multipotent progenitors, but studying their individual effects is challenging due to limited access to relevant human progenitor populations. To dissect individual developmental impacts, we used single-cell RNA-sequencing to interrogate hematopoietic progenitor cells (HPCs) from isogenic human induced pluripotent stem cells differing only by chromosome 21 and/orGATA1status. The transcriptomes of these HPCs revealed significant heterogeneity and lineage skew dictated by T21 and/or GATA1s. T21 and GATA1s each disrupted temporal regulation of lineage-specific transcriptional programs and specifically perturbed cell cycle genes. Trajectory inference revealed that GATA1s nearly eliminated erythropoiesis, slowed MK maturation, and promoted myelopoiesis in the euploid context, while in T21 cells, GATA1s competed with the enhanced erythropoiesis and impaired megakaryopoiesis driven by T21 to promote production of immature erythrocytes, MKs, and myeloid cells. The use of isogenic cells revealed distinct transcriptional programs that can be attributed specifically to T21 and GATA1s, and how they independently and synergistically result in HPC proliferation at the expense of maturation, consistent with a pro-leukemic phenotype.
SspA is a transcriptional regulator of CRISPR adaptation inE. coli
Authors: Lopez Santiago C. , Lee Yumie , Zhang Karen , Shipman Seth L. 
Published: May 2024

ABSTRACTThe CRISPR integrases Cas1-Cas2 create immunological memories of viral infection by storing phage-derived DNA in CRISPR arrays, a process known as CRISPR adaptation. A number of host factors have been shown to influence adaptation, but the full pathway from infection to a fully integrated, phage-derived sequences in the array remains incomplete. Here, we deploy a new CRISPRi-based screen to identify putative host factors that participate in CRISPR adaptation in theE. coliType I-E system. Our screen uncovers a novel host factor, SspA, which transcriptionally regulates CRISPR adaptation. One target of SspA is H-NS, a known repressor of CRISPR interference proteins, but we find that the role of SspA on adaptation is not H-NS-dependent. We propose a new model of CRISPR-Cas defense that includes independent cellular control of adaptation and interference by SspA.