bluuebunny/crossref_metadata_2025_split huggingface dataset:
Left Atrial Appendage Closure in Patients with Atrial Fibrillation and Acute Ischemic Stroke Despite Anticoagulation
Authors: Abramovitz Fouks Avia , Yaghi Shadi , Selim Magdy , Gökçal Elif , Das Alvin S. , Rotschild Ofer , Silverman Scott B , Singhal Aneesh B. , Kapur Sunil , Greenberg Steven M. , Gurol M. Edip 
Published: August 2023

AbstractBackgroundThe occurrence of acute ischemic stroke (AIS) while regularly using oral anticoagulants (OAC) is an increasingly recognized problem among nonvalvular atrial fibrillation (NVAF) patients. Due to the high risk of AIS recurrence (reported 5.3-8.9 per 100 patient-years) even when the type of OAC is changed, we aimed to elucidate the potential role of left atrial appendage closure (LAAC) for prevention of recurrent strokes among AIS-despite-OAC patients.MethodsThrough retrospective review of electronic medical records of a single hospital system between January 2015 and October 2021, we collected baseline and follow-up data from consecutive NVAF patients who had AIS despite regular use of OAC per current guidelines and subsequently underwent endovascular LAAC for recurrent stroke prevention. The primary outcome measure was the occurrence of AIS after LAAC, and the safety outcome was symptomatic intracerebral hemorrhage (ICH).ResultsTwenty-nine patients had the endovascular LAAC specifically because of AIS-despite-OAC. The mean age was 73.4 ± 8.7, 13 were female (44.82%). Mean CHA2DS2-VASc score was 5.96 ± 1.32, with an expected AIS risk of 8.44 per 100 patient-years. Fourteen of the patients had two or more past AIS-despite-OAC. After LAAC, 27 patients (93.10%) were discharged on anticoagulant which was discontinued in 17 (58.62%) after transesophageal echocardiogram (TEE) at 6 weeks. Over a mean of 1.75±1.0 years follow-up after LAAC, only one patient had an AIS (incidence rate [IR] 1.97 per 100 patient-years) and one patient had a small ICH (IR 1.97 per 100 patient-years).ConclusionsLAAC in patients who had AIS-despite-OAC demonstrated a low annual rate of recurrent AIS in our cohort (1.97%) compared both to the expected IR based on their CHA2DS2-VASc scores (8.44%) and to the recent large series of AIS-despite-OAC patients treated with OAC/aspirin only (5.3%-8.9%). These findings support randomized trials of LAAC in patients who have AIS-despite-OAC.
Machine learning model interpretations explain T cell receptor binding
Authors: Carter Brandon , Krog Jonathan , Birnbaum Michael E. , Gifford David K. 
Published: August 2023

AbstractT cells mediate immune responses against pathogens and cancer through T cell receptors (TCRs) that recognize foreign peptides presented on the cell surface by Major Histocompatibility Complex (MHC) proteins. TCRs carry enormous diversity and differ across individuals, and mechanisms that determine TCR-pMHC binding are poorly understood. The ability to predict TCR-pMHC interactions would accelerate development of cellular therapeutics to design TCRs that specifically bind to a target of interest. We designed a randomized library of 196TCR CDR3βsequences and experimentally evaluated their affinities for the Tax-A02 peptide-MHC target. We trained ML models that predict TCR binding to Tax-A02 from TCR sequence and used model interpretation to identify TCR sequence features associated with binding. We found these features accurately mirror the true sequence features in our experimental data.
Longer mandible or nose? Co-evolution of feeding organs in early elephantiforms
Authors: Li Chunxiao , Deng Tao , Wang Yang , Sun Fajun , Wolff Burt , Jiangzuo Qigao , Ma Jiao , Xing Luda , Fu Jiao , Zhang Ji , Wang Shi-Qi 
Published: August 2023

AbstractThe long-trunked elephantids underwent a significant evolutionary stage characterized by an exceptionally elongated mandible. The initial elongation and subsequent regression of the long mandible, along with its co-evolution with the trunk, present an intriguing issue that remains incompletely understood. Through comparative functional and eco-morphological investigations, as well as feeding preference analysis, we reconstructed the feeding behavior of major groups of longirostrine elephantiforms. In thePlatybelodonclade, the rapid evolutionary changes observed in the narial region, strongly correlated with mandible and tusk characteristics, suggest a crucial evolutionary transition where feeding function shifted from the mandible to the trunk, allowing proboscideans to expand their niches to more open regions. This functional shift further resulted in elephantids relying solely on their trunks for feeding. Our research provides insights into how unique environmental pressures shape the extreme evolution of organs, particularly in large mammals that developed various peculiar adaptations during the late Cenozoic global cooling trends.
Expanding the Drosophila toolkit for dual control of gene expression
Authors: Zirin Jonathan , Jusiak Barbara , Lopes Raphael , Ewen-Campen Ben , Bosch Justin A. , Risbeck Alexandria , Forman Corey , Villalta Christians , Hu Yanhui , Perrimon Norbert 
Published: August 2023

SummaryThe ability to independently control gene expression in two different tissues in the same animal is emerging as a major need, especially in the context of inter-organ communication studies. This type of study is made possible by technologies combining the GAL4/UAS and a second binary expression system such as the LexA-system or QF-system. Here, we describe a resource of reagents that facilitate combined use of the GAL4/UAS and a second binary system in variousDrosophilatissues. Focusing on genes with well-characterizsed GAL4 expression patterns, we generated a set of more than 40 LexA-GAD and QF2 insertions by CRISPR knock-in and verified their tissue-specificity in larvae. We also built constructs that encode QF2 and LexA-GAD transcription factors in a single vector. Following successful integration of this construct into the fly genome, FLP/FRT recombination is used to isolate fly lines that express only QF2 or LexA-GAD. Finally, using new compatible shRNA vectors, we evaluated both LexA and QF systems forin vivogene knockdown and are generating a library of such RNAi fly lines as a community resource. Together, these LexA and QF system vectors and fly lines will provide a new set of tools for researchers who need to activate or repress two different genes in an orthogonal manner in the same animal.
Sex-specific effects of injury and beta-adrenergic activation on metabolic and inflammatory mediators in a murine model of post-traumatic osteoarthritis
Authors: Komaravolu Ravi K. , Mehta-D’souza Padmaja , Conner Taylor , Allen Madeline , Lumry Jessica , Griffin Timothy M. 
Published: August 2023

AbstractMetabolic processes are intricately linked to the resolution of innate inflammation and tissue repair, two critical steps for treating post-traumatic osteoarthritis (PTOA). Here we used the β-adrenergic receptor (βAR) agonist isoproterenol as a tool to perturb intra-articular metabolism 3.5 weeks after applying a non-invasive single-load compression injury to knees of 12-week-old male and female mice. We examined the acute effects of intra-articular treatment with isoproterenol relative to saline on pain behavior, histology, multiplex gene expression, and synovial fluid metabolomics. Injured knees developed PTOA pathology characterized by heterotopic ossification, loss of tibial and femoral articular cartilage, and infrapatellar fat pad (IFP) atrophy and fibrosis. Isoproterenol modestly increased IFP atrophy and fibrosis, and it also caused sexually dimorphic and injury-dependent effects on IFP and synovium gene expression. In injured joints of female mice, isoproterenol suppressed the upregulation of pro-fibrotic genes and downregulated the expression of adipose tissue genes and pro-inflammatory genes (Adam17,Cd14,Icam1,Csf1r, andCasp1). Injury substantially altered synovial fluid metabolites by increasing amino acids, peptides, sphingolipids, phospholipids, bile acids, and dicarboxylic acids, but these changes were not appreciably altered by isoproterenol. Mechanical allodynia was also not altered by isoproterenol, although isoproterenol downregulated the expression of nociception-associated genes,NgfandTacr1,in injured IFP-synovium of female mice. Overall, these results suggest that βAR activation functions in a sexually dimorphic manner in PTOA joints. The findings support further exploration of therapeutic strategies that target neuro-metabolic signaling pathways for treating PTOA, particularly in women.
The Overexpression of AmpC is Not Required but May Contribute to Imipenem/Relebactam Non-susceptibility
Authors: Freed Shawn , Hanson Nancy D. 
Published: August 2023

AbstractIn the US, carbapenem resistance inPseudomonas aeruginosais strongly linked to the regulation of chromosomal resistance determinants, AmpC and OprD. The β-lactamase AmpC requires overexpression and genetic modifications to be capable of inhibiting imipenem activity. The outer membrane porin OprD can be downregulated or undergo genetic modifications that strongly correlate with imipenem non-susceptibility. Co-administration of imipenem and the β-lactamase inhibitor, relebactam, can lower imipenem MICs and restore susceptibility. However, how this occurs inP. aeruginosaisolates that do not overproduce AmpC or produce a functional OprD for imipenem entry is not understood. Therefore, we investigated whether imipenem could enterP. aeruginosain the absence of OprD and whether any of the chromosomal β-lactamases (AmpC, OXA-51, PIB-1) contributed to imipenem and/or imipenem/relebactam non-susceptibility. This investigation evaluated 17 imipenem non-susceptible clinical isolates and 3 laboratory strains of PAO1, two of which were porin deletion mutants for eitheroprDoropdP. Expression of OXA-50 and PIB-1 RNA was similar to PAO1. However, all 20 isolates exhibited AmpC induction under sub-lethal exposure to imipenem. This occurred in the absence of detectable OprD protein in 18 isolates. Collectively, our data identify that OprD is not the only channel required for imipenem entry and that in many isolates the restored susceptibility to imipenem by imipenem/relebactam was due to the interaction of relebactam on the overexpression of AmpC due to imipenem induction.
Increasing the accuracy of single-molecule data analysis using tMAVEN
Authors: Verma Anjali R. , Ray Korak Kumar , Bodick Maya , Kinz-Thompson Colin D. , Gonzalez Ruben L. 
Published: August 2023

AbstractTime-dependent single-molecule experiments contain rich kinetic information about the functional dynamics of biomolecules. A key step in extracting this information is the application of kinetic models, such as hidden Markov models (HMMs), which characterize the molecular mechanism governing the experimental system. Unfortunately, researchers rarely know the physico-chemical details of this molecular mechanisma priori, which raises questions about how to select the most appropriate kinetic model for a given single-molecule dataset and what consequences arise if the wrong model is chosen. To address these questions, we have developed and used time-seriesModeling,Analysis, andVisualizationENvironment (tMAVEN), a comprehensive, open-source, and extensible software platform. tMAVEN can perform each step of the single-molecule analysis pipeline, from pre-processing to kinetic modeling to plotting, and has been designed to enable the analysis of a single-molecule dataset with multiple types of kinetic models. Using tMAVEN, we have systematically investigated mismatches between kinetic models and molecular mechanisms by analyzing simulated examples of prototypical single-molecule datasets exhibiting common experimental complications, such as molecular heterogeneity, with a series of different types of HMMs. Our results show that no single kinetic modeling strategy is mathematically appropriate for all experimental contexts. Indeed, HMMs only correctly capture the underlying molecular mechanism in the simplest of cases. As such, researchers must modify HMMs using physico-chemical principles to avoid the risk of missing the significant biological and biophysical insights into molecular heterogeneity that their experiments provide. By enabling the facile, side-by-side application of multiple types of kinetic models to individual single-molecule datasets, tMAVEN allows researchers to carefully tailor their modeling approach to match the complexity of the underlying biomolecular dynamics and increase the accuracy of their single-molecule data analyses.Statement of SignificanceThe power of time-dependent single-molecule biophysical experiments lies in their ability to uncover the molecular mechanisms governing experimental systems by computationally applying kinetic models to the data. While many software solutions have been developed to estimate the optimal parameters of such models, the results reported here show that the models themselves are often inherently mismatched with the molecular mechanisms they are being used to analyze. To investigate these mismatches and demonstrate how to best model the kinetics of a molecular mechanism, we have used time-seriesModeling,Analysis, andVisualizationENvironment (tMAVEN), an open-source software platform we have developed that, among other features, enables the analysis of single-molecule datasets using different kinetic models within a single, extensible, and customizable pipeline.
Bacteriophage P22 SieA mediated superinfection exclusion
Authors: Leavitt Justin C. , Woodbury Brianna M. , Gilcrease Eddie B. , Bridges Charles M. , Teschke Carolyn M. , Casjens Sherwood R. 
Published: August 2023

ABSTRACTMany temperate phages encode prophage-expressed functions that interfere with superinfection of the host bacterium by external phages.Salmonellaphage P22 has four such systems that are expressed from the prophage in a lysogen that are encoded by thec2(repressor),gtrABC,sieA, andsieBgenes. Here we report that the P22-encoded SieA protein is the only phage protein required for exclusion by the SieA system, and that it is an inner membrane protein that blocks DNA injection by P22 and its relatives, but has no effect on infection by other tailed phage types. The P22 virion injects its DNA through the host cell membranes and periplasm via a conduit assembled from three “ejection proteins” after their release from the virion. Phage P22 mutants were isolated that overcome the SieA block, and they have amino acid changes in the C-terminal regions of the gene16and20encoded ejection proteins. Three different single amino acid changes in these proteins are required to obtain nearly full resistance to SieA. Hybrid P22 phages that have phage HK620 ejection protein genes are also partially resistant to SieA. There are three sequence types of extant phage-encoded SieA proteins that are less than 30% identical to one another, yet comparison of two of these types found no differences in target specificity. Our data are consistent with a model in which the inner membrane protein SieA interferes with the assembly or function of the periplasmic gp20 and membrane-bound gp16 DNA delivery conduit.HIGHLIGHTSPhage P22 SieA protein blocks DNA injection by P22-like phagesSieA is an inner membrane proteinHybrid P22 phages with phage HK620 ejection proteins partially escape SieA exclusionSieA escape mutants of P22 alter the gp16 and 20 proteins that form the DNA ejection tube.
The α-crystallin chaperones undergo a quasi-ordered co-aggregation process in response to saturating client interaction
Authors: Miller Adam P. , O’Neill Susan E. , Lampi Kirsten J. , Reichow Steve L. 
Published: August 2023

ABSTRACTSmall heat shock proteins (sHSPs) are ATP-independent chaperones vital to cellular proteostasis, preventing protein aggregation events linked to various human diseases including cataract. The α-crystallins, αA-crystallin (αAc) and αB-crystallin (αBc), represent archetypal sHSPs that exhibit complex polydispersed oligomeric assemblies and rapid subunit exchange dynamics. Yet, our understanding of how this plasticity contributes to chaperone function remains poorly understood. This study investigates structural changes in αAc and αBc during client sequestration under varying degree of chaperone saturation. Using biochemical and biophysical analyses combined with single-particle electron microscopy (EM), we examined αAc and αBc in their apo-states and at various stages of client-induced co-aggregation, using lysozyme as a model client. Quantitative single-particle analysis unveiled a continuous spectrum of oligomeric states formed during the co-aggregation process, marked by significant client-triggered expansion and quasi-ordered elongation of the sHSP scaffold. These structural modifications culminated in an apparent amorphous collapse of chaperone-client complexes, resulting in the creation of co-aggregates capable of scattering visible light. Intriguingly, these co-aggregates maintain internal morphological features of highly elongated sHSP scaffolding with striking resemblance to polymeric α-crystallin species isolated from aged lens tissue. This mechanism appears consistent across both αAc and αBc, albeit with varying degrees of susceptibility to client-induced co-aggregation. Importantly, our findings suggest that client-induced co-aggregation follows a distinctive mechanistic and quasi-ordered trajectory, distinct from a purely amorphous process. These insights reshape our understanding of the physiological and pathophysiological co-aggregation processes of sHSPs, carrying potential implications for a pathway toward cataract formation.
Combined PI3K and MAPK inhibition synergizes to suppress PDAC
Authors: Bye Bailey A. , Jack Jarrid , Pierce Alexandra , Walsh R. McKinnon , Eades Austin , Chalise Prabhakar , Olou Appolinaire , VanSaun Michael N. 
Published: August 2023

AbstractOncogenic KRAS mutations are nearly ubiquitous in pancreatic ductal adenocarcinoma (PDAC), yet therapeutic attempts to target KRAS as well as its target MAPK pathway effectors have shown limited success due to the difficulty to pharmacologically target KRAS, inherent drug resistance in PDAC cells, and acquired resistance through activation of alternative mitogenic pathways such JAK-STAT and PI3K-AKT. While KRAS canonically drives the MAPK signaling pathway via RAF-MEK-ERK, it is also known to play a role in PI3K-AKT signaling. Our therapeutic study targeted the PI3K-AKT pathway with the drug Omipalisib (p110α/β/δ/γ and mTORC1/2 inhibitor) in combination with MAPK pathway targeting drug Trametinib (MEK1/2 inhibitor) or SHP099-HCL (SHP099), which is an inhibitor of the KRAS effector SHP2. Western blot analysis demonstrated that application of Trametinib or SHP099 alone selectively blocked ERK phosphorylation (pERK) but failed to suppress phosphorylated AKT (pAKT) and in some instances increased pAKT levels. Conversely, Omipalisib alone successfully inhibited pAKT but failed to suppress pERK. Therefore, we hypothesized that a combination therapeutic comprised of Omipalisib with either Trametinib or SHP099 would inhibit two prominent mitogenic pathways, MEK and PI3K-AKT, to more effectively suppress pancreatic cancer.In vitrostudies demonstrated that both Omipalisib/Trametinib and Omipalisib/SHP099 combination therapeutic strategies were generally more effective than treatment with each drug individually at reducing proliferation, colony formation, and cell migration compared to vehicle controls. Additionally, we found that while combination Omipalisib/SHP099 treatment reduced implanted tumor growthin vivo, the Omipalisib/Trametinib treatment was significantly more effective. Therefore, we additionally tested the Omipalisib/Trametinib combination therapeutic in the highly aggressive PKT (Ptf1acre, LSL-KrasG12D, TGFbR2fl/fl) spontaneous mouse model of PDAC. We subsequently found that PKT mice treated with the Omipalisib/Trametinib combination therapeutic survived significantly longer than mice treated with either drug alone, and more than doubled the mean survival time of vehicle control mice. Altogether, our data support the importance of a dual treatment strategy targeting both MAPK and PI3K-AKT pathways.
SCALiR: a web application for automating absolute quantification of mass spectrometry-based metabolomics data
Authors: Bishop Stephanie L. , Ponce-Alvarez Luis F. , Wacker Soren , Groves Ryan A. , Lewis Ian A. 
Published: August 2023

ABSTRACTMetabolomics is an important approach for studying complex biological systems. Quantitative liquid chromatography-mass spectrometry (LC-MS)-based metabolomics is becoming a mainstream strategy but presents several technical challenges that limit its widespread use. Computing metabolite concentrations using standard curves generated from standard mixtures of known concentrations is a labor-intensive process which is often performed manually. Currently, there are few options for open-source software tools that can automatically calculate metabolite concentrations. Herein, we introduce SCALiR (Standard Curve Application for determining Linear Ranges), a new web-based software tool specifically built for this task, which allows users to automatically transform LC-MS signal data into absolute quantitative data (https://www.lewisresearchgroup.org/software). The algorithm used in SCALiR automatically finds the equation of the line of best fit for each standard curve and uses this equation to calculate compound concentrations from their LC-MS signal. Using a standard mix containing 77 metabolites, we found excellent correlation between the concentrations calculated by SCALiR and the expected concentrations of each compound (R2= 0.99) and that SCALiR reproducibly calculated concentrations of mid-range standards across ten analytical batches (average coefficient of variation 0.091). SCALiR offers users several advantages, including that it (1) is open-source and vendor agnostic; (2) requires only 10 seconds of analysis time to compute concentrations of >75 compounds; (3) facilitates automation of quantitative workflows; and (4) performs deterministic evaluation of compound quantification limits. SCALiR provides the metabolomics community with a simple and rapid tool that enables rigorous and reproducible quantitative metabolomics studies.