bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unveiling Chemotherapy’s Impact on Lung Cancer through Single-Cell Transcriptomics
Authors: Sayad Saed , Hiatt Mark , Mustafa Hazem 
Published: July 2024

AbstractBackgroundLung adenocarcinoma (LUAD) is the most common subtype of non-small cell lung cancer (NSCLC) and frequently affects non-smokers, especially women. It is characterized by a complex genetic profile and interactions with its microenvironment, which contribute to its aggressive and adaptable nature. Early symptoms are often subtle, leading to late diagnoses. Treatment approaches have advanced with targeted therapies and immunotherapy supplementing traditional chemotherapy and radiation. Despite these advancements, the prognosis remains variable, highlighting the need for continued research into new treatment strategies to improve outcomes.MethodIn this study, we employed Single-cell RNA Sequencing (scRNA-seq) to comprehensively analyze the impact of chemotherapy on lung adenocarcinoma at the individual cell level. By comparing before and after treatment samples, we assessed the differential expression of genes and pathways, revealing insights into how different cell types within the tumour respond to chemotherapy. This approach enabled us to pinpoint specific mechanisms of drug resistance and highlight potential therapeutic targets for overcoming these challenges.ResultsOur analysis uncovered substantial changes in gene expression between primary tumour cells and metastatic cells following chemotherapy. Notably, we observed that 45 pathways were shared between the top 50 upregulated pathways in the primary tumour and the top 50 downregulated pathways in the metastatic tumour post-chemotherapy. Conversely, there was no overlap between the top 50 downregulated pathways in the primary tumour and the top 50 upregulated pathways in the metastatic tumour after chemotherapy. This suggests that chemotherapy effectively downregulated the major upregulated pathways but did not upregulate the key downregulated pathways in metastatic tumours.ConclusionsIntegrating single-cell transcriptomics into LUAD research offers detailed insights into the tumour’s response to chemotherapy and its interaction with the immune system. This approach enhances our understanding of LUAD and aids in developing targeted and effective treatments. Based on our analysis, we hypothesize that combining chemotherapy with drugs designed to upregulate the downregulated pathways in primary tumour cells could significantly enhance treatment efficacy and improve patient outcomes.
Extracting the Sample Size From Randomized Controlled Trials in Explainable Fashion Using Natural Language Processing
Authors: Windisch Paul , Dennstädt Fabio , Koechli Carole , Förster Robert , Schröder Christina , Aebersold Daniel M. , Zwahlen Daniel R. 
Published: July 2024

BackgroundExtracting the sample size from randomized controlled trials (RCTs) remains a challenge to developing better search functionalities or automating systematic reviews. Most current approaches rely on the sample size being explicitly mentioned in the abstract.Methods847 RCTs from high-impact medical journals were tagged with six different entities that could indicate the sample size. A named entity recognition (NER) model was trained to extract the entities and then deployed on a test set of 150 RCTs. The entities’ performance in predicting the actual number of trial participants who were randomized was assessed and possible combinations of the entities were evaluated to create predictive models.ResultsThe most accurate model could make predictions for 64.7% of trials in the test set, and the resulting predictions were within 10% of the ground truth in 96.9% of cases. A less strict model could make a prediction for 96.0% of trials, and its predictions were within 10% of the ground truth in 88.2% of cases.ConclusionTraining a named entity recognition model to predict the sample size from randomized controlled trials is feasible, not only if the sample size is explicitly mentioned but also if the sample size can be calculated, e.g., by adding up the number of patients in each arm.
Genetic co-occurrence networks identify polymorphisms within ontologies highly associated with preeclampsia
Authors: Obersterescu Andreea , Cox Brian J. 
Published: July 2024

AbstractPolygenic diseases require the co-occurrence of multiple risk variants to initiate a pathology. An example is preeclampsia, a hypertensive disease of pregnancy with no known cure or therapy other than the often-preterm delivery of the neonate and placenta. Preeclampsia is challenging to predict due to symptomatic and outcome heterogeneity. Transcriptomic and genetic analysis suggests that this is a multi-syndromic and multigenic disease. Previous research applications of traditional GWAS methods to preeclampsia identified only a few alleles with marginal differences between cases and controls. We seek to identify genetic networks related to the pathophysiology of preeclampsia as potential avenues of therapeutic investigation and early genetic testing. We created a novel systems biology-based method that identifies networks of co-occurring SNPs associated with a trait or disease. The co-occurring pairs are assembled into higher-order associations using network graphs. We validated our method using simulation modelling and tested it against maternal genetic data of a previously assessed preeclampsia cohort. The genetic co-occurrence network identified SNPs in or near genes with ontological enrichment for VEGF, immunological and hormonal pathways, among others with known physiological disruption in preeclampsia. Our findings suggests that preeclampsia is caused by relatively common alleles (<5%) that accumulate in unfavorable combinations.
NETosis is an important component of chronic inflammation in patients with heart failure
Authors: Kostin Sawa , Richter Manfred , Krizanic Florian , Sasko Benjamin , Kelesidis Theodoros , Pagonas Nikolaos 
Published: July 2024

AbstractBackground and aimWe have previously demonstrated that heart failure (HF) is characterized by low-grade myocardial inflammation. However, the role of neutrophils (N), neutrophil extracellular traps (NETs) and neutrophil cell death by NETosis in the myocardium of patients with HF remains largely unknown. The present study investigated the number of neutrophils (N) and their proportion undergoing NETosis and developing NETs in HF.MethodsWe used quantitative confocal microscopy and NETosis markers in the left ventricular biopsies obtained from 5 control and from patients with HF due to dilated (DCM, n=7), inflammatory (infCMP, n=7) and ischemic cardiomyopathy (ICM, n=7). We used immunolabeling for CD45, CD66b and CD11b for (N) and citrullinated histone3 (citH3), peptidylarginine deiminase-4 (PAD-4), neutrophil elastase (NE) and myeoloperoxidase (MPO) for NETosis. These proteins were also investigated by quantitative fluorescence intensity analysis, Western blot and quantitative polymerase chain reaction (qPCR).ResultsCompared to control, the number of N was increased 3-4 times in HF. We found that using a single marker for NETosemarkers, 43.2% of N in DCM, 46.7% in ICM and 57.3% in infCMP experienced NETosis. The use of double labeling (NE with CitH3) showed that 55.6% of N developed NETosis in DCM, 57.9% in ICM and 79.4% in infCMP. The difference between the N who underwent NETosis in infCMP and those in DCM was statistically different (p<0.01). The proportion of N who developed NETosis or formed NETs in control tissue was less than 5% and differed significantly from that in HF patients, regardless of etiology (p<0.01). These results were confirmed by quantitative fluorescence analysis, Western blot and qPCR.ConclusionsThis is the first study to show the occurrence of NETosis in human heartsin situindicating that NETosis is an important component of low-grade myocardial inflammation in HF.What is new?Low-grade myocardial inflammation is a typical feature of heart failure and neutrophil cell death (NETosis) is an important component of this pathological process.What are the clinical implications?Preventing excessive neutrophil activation and inhibiting the major components involved in the NETosis program (neutrophil elastase, myeloperoxidase and peptidylarginine deiminase-4) are perspective targets for the treatment of HF.
Triton-X 100-treated virus-based ELLA demonstrates discordant antigenic evolution of influenza B virus haemagglutinin and neuraminidase
Authors: Do Thi H. T. , Wille Michelle , Wheatley Adam K. , Koutsakos Marios 
Published: July 2024

AbstractNeuraminidase (NA)-specific antibodies have been associated with protection against influenza and thus NA is considered a promising target for next-generation vaccines against influenza A (IAV) and B viruses (IBV). NA inhibition (NI) by antibodies is typically assessed using an enzyme-linked lectin assay (ELLA). However, ELLA can be confounded by anti- hemagglutinin (anti-HA) antibodies that block NA by steric hindrance (termed HA interference). While strategies have been employed to overcome HA interference for IAV, similar approaches have not been assessed for IBV. We found HA interference is common in ELLA using IBV, rendering the technique unreliable. Anti-HA antibodies were not completely depleted from sera by HA-expressing cell lines and this approach was of limited utility. In contrast, we find that treatment of virions with Triton-X 100, but not Tween-20 or ether, efficiently separates the HA and NA components and overcomes interference caused by anti-HA antibodies. We also characterise a panel of recombinant IBV NA proteins that further validated the results from Triton-X 100-treated virus-based ELLA. Using these reagents and assays we demonstrate discordant antigenic evolution between IBV NA and HA over the last 80 years. This optimized ELLA protocol will facilitate further in-depth serological surveys of IBV immunity as well as antigenic characterisation of the IBV NA on a larger scale.ImportanceInfluenza B viruses contribute to annual epidemics and may cause severe disease, especially in children. Consequently, several approaches are being explored to improve vaccine efficacy, including the addition of neuraminidase. Antigen selection and assessment of serological responses will require a reliable serological assay to specifically quantify Neuraminidase inhibition. While such assays have been assessed for influenza A viruses, this has not been done of influenza B viruses. Our study identifies a readily applicable strategy to measure inhibitory activity of neuraminidase-specific antibodies against influenza B virus without interference from anti-hemagglutinin antibodies. This will aid broader serological assessment of influenza B virus-specific antibodies and antigenic characterisation of the influenza B virus neuraminidase.
Environmental controls on crenarchaeol distributions in hydrothermal springs
Authors: Calhoun Amanda N. , Blewett Jerome , Colman Daniel R. , Amenabar Maximiliano J. , Harris Carolynn M. , Boyd Eric S. , Pearson Ann , Leavitt William D. 
Published: July 2024

AbstractThermophilic archaea synthesize cellular membranes composed primarily of isoprenoid glycerol dibiphytanyl glycerol tetraethers (iGDGTs). Cells can adjust the structure of iGDGTs by increasing the number of cyclopentyl rings to enhance lipid packing, thereby decreasing membrane permeability and fluidity to maintain cellular function at high temperature and/or acidic pH. Certain archaea synthesize an iGDGT, crenarchaeol, with four cyclopentyl rings and a unique cyclohexyl ring, the function of which is unknown. Structural modeling suggests the cyclohexyl ring may increase membrane fluidity, potentially representing an adaptation that allowed thermophiles to radiate into cooler environments. To begin to investigate this hypothesis, iGDGT abundance was quantified in forty-one hydrothermal springs in Yellowstone National Park (YNP), USA, and contextualized within a compilation of global hydrothermal spring iGDGTs with pH values of 1.1 to 10.1 and temperatures of 16.3 to 95 °C. pH most strongly correlated with both crenarchaeol abundance and the number of cyclopentyl rings per iGDGT. Crenarchaeol abundance exhibited a nonlinear relationship with both pH and temperature, with highest abundances at pH 7.4 and 46 °C, then decreasing in abundance above and below these values. These observations support the hypothesis that crenarchaeol’s cyclohexyl ring facilitated the adaptation of thermophilic and acidophilic archaea to lower temperature and higher pH niches, enabling their radiation into the marine realm.ImportanceArchaea change the composition of their membrane lipids to alter the fluidity of their membranes to protect cellular functions from environmental stressors. Some archaea produce a lipid, crenarchaeol, with a unique six-membered ring, the effect of which on archaeal membrane dynamics remains unknown. In this study, we identify pH as the most important geochemical variable for archaeal membrane response in Yellowstone National Park hot springs. In addition, the lipid distributions we find support the hypothesis that crenarchaeol facilitated the archaeal evolutionary transition from hot and acidic to cool and neutral waters. We contextualize these findings in a literature compilation that spans the globe.
N-Glycosylation of MRS2 balances aerobic and anaerobic energy production by reducing rapid mitochondrial Mg2+influx in conditions of high glucose or impaired respiratory chain function
Authors: Peng Min , Mathew Neal D. , Anderson Vernon E. , Falk Marni J. , Nakamaru-Ogiso Eiko 
Published: July 2024

ABSTRACTN-linked glycoproteins function in numerous biological processes, modulating enzyme activities as well as protein folding, stability, oligomerization, and trafficking. WhileN-glycosylation of mitochondrial proteins has been detected by untargeted MS-analyses, the physiological existence and roles of mitochondrial proteinN-linked glycosylation remain under debate. Here, we report that MRS2, a mitochondrial inner membrane protein that functions as the high flux magnesium transporter, isN-glycosylated to various extents depending on cellular bioenergetic status. BothN-glycosylated and unglycosylated isoforms were consistently detected in mitochondria isolated from mouse liver, rat and mouse liver fibroblast cells (BRL 3A and AFT024, respectively) as well as human skin fibroblast cells. Immunoblotting of MRS2 showed it was bound to, and required stringent elution conditions to remove from, lectin affinity columns with covalently bound concanavalin A orLens culinarisagglutinin. Following peptide:N-glycosidase F (PNGase F) digestion of the stringently eluted proteins, the higher MrMRS2 bands gel-shifted to lower Mrand loss of lectin affinity was seen. BRL 3A cells treated with two differentN-linked glycosylation inhibitors, tunicamycin or 6-diazo-5-oxo-L-norleucine, resulted in decreased intensity or loss of the higher MrMRS2 isoform. To investigate the possible functional role of MRS2N-glycosylation, we measured rapid Mg2+influx capacity in intact mitochondria isolated from BRL 3A cells in control media or following treatment with tunicamycin or 6-diazo-5-oxo-L-norleucine. Interestingly, rapid Mg2+influx capacity increased in mitochondria isolated from BRL 3A cells treated with eitherN-glycosylation inhibitor. Forcing reliance on mitochondrial respiration by treatment with either galactose media or the glycolytic inhibitor 2-deoxyglucose or by minimizing glucose concentration similarly reduced theN-glycosylated isoform of MRS2, with a correlated concomitant increase in rapid Mg2+influx capacity. Conversely, inhibiting mitochondrial energy production in BRL 3A cells with either rotenone or oligomycin resulted in an increased fraction ofN-glycosylated MRS2, with decreased rapid Mg2+influx capacity. Collectively, these data provide strong evidence that MRS2N-glycosylation is directly involved in the regulation of mitochondrial matrix Mg2+, dynamically communicating relative cellular nutrient status and bioenergetic capacity by serving as a physiologic brake on the influx of mitochondrial matrix Mg2+under conditions of glucose excess or mitochondrial bioenergetic impairment.
Comprehensive deletion scan of anti-CRISPR AcrIIA4 reveals essential and dispensable domains for Cas9 inhibition
Authors: Iturralde Annette B , Weller Cory A , Sadhu Meru J 
Published: July 2024

AbstractDelineating a protein’s essential and dispensable domains provides critical insight into how it carries out its function. Here, we developed a high-throughput method to synthesize and test the functionality of all possible in-frame and continuous deletions in a gene of interest, enabling rapid and unbiased determination of protein domain importance. Our approach generates precise deletions using a CRISPR library framework that is free from constraints of gRNA target site availability and efficacy. We applied our method to AcrIIA4, a phage-encoded anti-CRISPR protein that robustly inhibits SpCas9. Extensive structural characterization has shown that AcrIIA4 physically occupies the DNA-binding interfaces of several SpCas9 domains; nonetheless, the importance of each AcrIIA4 interaction for SpCas9 inhibition is unknown. We used our approach to determine the essential and dispensable regions of AcrIIA4. Surprisingly, not all contacts with SpCas9 were required, and in particular, we found that the AcrIIA4 loop that inserts into SpCas9’s RuvC catalytic domain can be deleted. Our results show that AcrIIA4 inhibits SpCas9 primarily by blocking PAM binding, and that its interaction with the SpCas9 catalytic domain is inessential.
A magnesium transporter CorA ofMycobacterium smegmatisenhances the tolerance of structurally unrelated antibiotics in the host cells
Authors: Chatterjee Debasmita , Daya Manasi A R , Rastogi Sumit Kumar , Panda Aditya Prasad , Biju Bayomi , Bhattacharyya Debleena , Ghosh Anindya Sundar 
Published: July 2024

ABSTRACTIon transporters or channels are involved in maintaining metal homeostasis in bacterial cells by aiding the movement of metal ions across the cell, which might also facilitate the export of antimicrobials. Ubiquitous magnesium transporter, CorA ofMycobacterium smegmatisis well known for its role in maintaining magnesium homeostasis. However, little is known about its involvement in exerting antimicrobial resistance. Here, with the help of molecular genetics,in vivoandin silicostudies we tried to envisage the role of CorA ofM. smegmatisin antimicrobial resistance ofM. smegmatisandE. coli. Expression ofcorAinM. smegmatisandE. coliincreased the tolerance of the host cells towards various structurally unrelated antibiotics and anti-tubercular drugs. In addition, a significantly lower accumulation of norfloxacin and ofloxacin by the host cells expressingcorAfurther indicated its role in enhancing the efflux pump activity. Moreover, the presence of a sub-inhibitory concentration of Mg2+resulted in increased low-level tolerance towards the tested drugs. Furthermore, CorA enhanced the biofilm-forming ability of cells expressing it. Overall, we speculate that magnesium transporter CorA facilitates multi-drug efflux activity of the host cells where Mg2+might act as a facilitator in the process.IMPORTANCEMagnesium acts as a co-factor for various biochemical and physiological reactions, such as protein synthesis, cell membrane integrity, nucleic acid synthesis, etc. Metal transporters maintain metal homeostasis by regulating the uptake, efflux, or transportation of metals in certain necessary cellular compartments. In bacteria, magnesium ion (Mg2+) is mainly supplied by the CorA protein which is a ubiquitous family of transport proteins and extensively studied inE. coliandSalmonella sp. However, little is known about the functional relationship of metal transporters ofMycobacterium spwith extrusion of antibiotics, and their involvement in stress tolerance. Here, we report CorA (MSMEG_5056), a magnesium transporter ofMycobacterium smegmatisin influencing the extrusion of multiple structurally unrelated classes of drugs and enhancing the biofilm formation ofE. coliandMycobacterium smegmatis.Abstract FigureGraphical Abstract:Hypothetical model of Antibiotic export by CorA.Antibiotics bind to the closed state of the protein (left). During the transition to the open state (right), the to-and-fro motion between multiple open states drives the efflux of the antibiotic while facilitating the import of Mg2+. The colors of the models correspond to the chain ID. The bottom views of both the closed and open states are shown in the rectangular box, with the color indicated by their respective chain IDs.
Acute BRCAness Induction and AR Signaling Blockage through CDK12/7/9 Degradation Enhances PARP Inhibitor Sensitivity in Prostate Cancer
Authors: Gui Fu , Jiang Baishan , Jiang Jie , He Zhixiang , Tsujino Takuya , Takai Tomoaki , Arai Seiji , Pana Celine , Köllermann Jens , Bradshaw Gary Andrew , Eisert Robyn , Kalocsay Marian , Fassl Anne , Balk Steven P , Kibel Adam S. , Jia Li 
Published: July 2024

AbstractCurrent treatments for advanced prostate cancer (PCa) primarily target the androgen receptor (AR) pathway. However, the emergence of castration-resistant prostate cancer (CRPC) and resistance to AR pathway inhibitors (APSIs) remains ongoing challenges. Here, we present BSJ-5-63, a novel proteolysis-targeting chimera (PROTAC) targeting cyclin-dependent kinases (CDKs) CDK12, CDK7, and CDK9, offering a multi-pronged approach to CRPC therapy. BSJ-5-63 degrades CDK12, diminishing BRCA1 and BRCA2 expression and inducing a sustained “BRCAness” state. This sensitizes cancer cells to PARP inhibitors (PARPis) regardless of their homologous recombination repair (HRR) status. Furthermore, CDK7 and CDK9 degradation attenuates AR signaling, enhancing its therapeutic efficacy. Preclinical studies, including bothin vitroandin vivoCRPC models, demonstrate that BSJ-5-63 exerts potent anti-tumor activity in both AR-positive and AR-negative setting. This study introduces BSJ-5-63 as a promising therapeutic agent that addresses both DNA repair and AR signaling mechanisms, with potential benefits for a board patient population.
Measurements of low-energy nuclear recoil quenching factors for Na and I recoils in the NaI(Tl) scintillator
Authors: Lee S. H. , Joo H. W. , Kim H. J. , Kim K. W. , Kim S. K. , Kim Y. D. , Ko Y. J. , Lee H. S. , Lee J. Y. , Park H. S. , Yoon Y. S. 
Published: July 2024

Elastic scattering off nuclei in target detectors, involving interactions with dark matter and coherent elastic neutrino nuclear recoil (CEνNS), results in the deposition of low energy within the nuclei, dissipating rapidly through a combination of heat and ionization. The primary energy loss mechanism for nuclear recoil is heat, leading to consistently smaller measurable scintillation signals compared to electron recoils of the same energy. The nuclear recoil quenching factor (QF), representing the ratio of scintillation light yield produced by nuclear recoil to that of electron recoil at the same energy, is a critical parameter for understanding dark matter and neutrino interactions with nuclei. The low energy QF of NaI(Tl) crystals, commonly employed in dark matter searches and CEνNS measurements, is of substantial importance. Previous low energy QF measurements were constrained by contamination from photomultiplier tube (PMT)-induced noise, resulting in an observed light yield of approximately 15 photoelectrons per keVee (kilo-electron-volt electron-equivalent energy) and nuclear recoil energy above 5 keVnr (kilo-electron-volt nuclear recoil energy). Through enhanced crystal encapsulation, an increased light yield of around 26 photoelectrons per keVee is achieved. This improvement enables the measurement of the nuclear recoil QF for sodium nuclei at an energy of 3.8±0.6keVnr with a QF of 11.2±1.7%. Furthermore, a re-evaluation of previously reported QF results is conducted, incorporating enhancements in low energy events based on waveform simulation. The outcomes are generally consistent with various recent QF measurements for sodium and iodine.

Published by the American Physical Society
2024