bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cardiac arrhythmias in STEMI patients in ICU: study on occurrence in first 48 h and correlation with age, sex, infarction site, and risk factors
Authors: Alkatib Mahmoud , Alkotyfan Abdul Rahman Naeem , Alshaghel Mohammed Moutaz , Shamiyeh Marwan 
Published: September 2023

Introduction:
Acute myocardial infarction (AMI) is one of the leading causes of death in the developed world. The spread of the disease approaches three million people worldwide, with more than one million deaths in the United States annually. Myocardial ischemia and infarction can lead to electrophysiological and metabolic alterations that result in potentially fatal arrhythmias, some of which may be asymptomatic. About 90% of patients with AMI develop some form of arrhythmia during or immediately after the event, and in 25% of patients, these arrhythmias appear within the first 48 h. The most common cause of death in patients with AMI in pre-hospitalization is ventricular tachycardia/ventricular fibrillation (VT/VF).

Methods:
A cross-sectional study targeting 150 patients with myocardial infarction attending tertiary hospital. According to certain acceptance and exclusion criteria.

Results:
The sample consisted of 150 patients who suffered from heart infarction, the mean age of patients in the sample was 59.41 years with a standard deviation of 11.02 years and range of 28–90. Males constituted the largest portion of patients, with 112 males, that is 75%. The study identified that the anterior wall was the most frequent location for myocardial infarction among patients, with 64% of patients experiencing an infarction in this area. Additionally, ventricular fibrillation was the most commonly occurring arrhythmia, affecting 27% of myocardial infarction patients in the study.

Recommendations:
One of the most important recommendations of our study is the necessity of keeping the patient under observation for at least 48 h after myocardial infarction within the hospital to monitor the ECG (Holter) in order to detect arrhythmias. Detection of arrhythmias in every patient with extensive anterior, lateral, or posterior myocardial infarction. And the need to know and take into account ventricular fibrillation and how to manage it in every patient with a heart infarction. And conducting future studies, including a larger number of patients, to study cardiac arrhythmias more precisely.
Outcomes of Cochlear Implantation in Age Subgroups of Veterans Over 50 Years Old
Authors: Petito Gabrielle T. , Tripathi Siddhant H. , Dhanda Patil Reena 
Published: September 2023

Objective:
This study aimed to determine whether there was a difference in postoperative Arizona Biomedical (AzBio) speech recognition scores in 2 differently aged subgroups of veterans 50 years and older after cochlear implantation (CI).

Study Design:
Retrospective chart review.

Setting:
Tertiary referral center.

Patients:
Seventy-one patients aged 50 to 74 years (younger cohort) were compared with 56 patients aged 75 years and older (older cohort) at the time of CI.

Intervention(s):
Patients underwent therapeutic CI.

Main Outcome Measure(s):
Comparison of AzBio speech recognition test scores in a quiet environment between the 2 differently aged cohorts of veterans 50 years and older.

Results:
Despite no significant differences in preoperative AzBio score between the younger (mean 22.2%) and older cohorts (mean, 17.3%; P > 0.05), when examining the 6- and 12-month postoperative time points, the older cohort had significantly lower mean AzBio scores (50%, 55.8%; P < 0.05) than the younger cohort (69.8%, 71.9%; P < 0.05).

Conclusions:
All patients aged >50 years experienced significant improvement in speech recognition scores following CI, although the cohort of ages 50 to 74 years scored significantly higher in later follow-up visits. These findings suggest that CI should be offered to appropriate candidates, regardless of age, although earlier intervention may be more advantageous.
Vestibular Schwannoma: Long-term Outcome of the Vestibular Function After Stereotactic Radiosurgery
Authors: Anschuetz Lukas , Ermiş Ekin , Gebhart Isabel , Stalder Odile , Raabe Andreas , Mantokoudis Georgios , Caversaccio Marco , Hermann Evelyne , Wagner Franca , Vibert Dominique 
Published: September 2023

Objective:
Evaluation at long term of the impact of the stereotactic surgery (SRS) on the vestibular function in vestibular schwannoma (VS) patients.

Study design and setting:
Retrospective study in a tertiary referral center.

Patients:
Fifty-one VS patients were included (34 females;17 males), aged from 41 to 78 years treated exclusively with SRS.

Intervention:
Vestibular function was assessed before SRS and with median time interval of 14 (FU1) and 25 (FU2) months after treatment. Vestibular evaluation included: history, clinical vestibular examination, videonystagmography, head impulse test (v-HIT) and cervical vestibular evoked myogenic potentials (c-VEMPS).

Results:
Before SRS, caloric testing (Caloric) was impaired in 77%; after treatment, in 92% (FU1) and 77% (FU2). Lateral HIT was decreased in 22% before SRS, in 39% at FU1 and FU2. C-VEMPS were absent in 50% before SRS, in 76% at FU1 and, FU2. Before SRS, no statistically significant association was found between asymptomatic and symptomatic patients with respect to the results of Caloric, v-HIT and c-VEMPS. This lack of association was also seen after SRS, at FU1 and FU2.

Conclusion:
Our study showed that the impairment of the vestibular function might be attributed to the VS itself as well as to the radiation of the inner ear during SRS. The lateral SSC at low frequencies and the saccular function seem to be more involved with the time.
Modeling Cystic Fibrosis Chronic Infection Using Engineered Mucus-like Hydrogels
Authors: O’Brien Courtney L. , Spencer Sarah , Jafari Naeimeh , Huang Andy J. , Scott Alison J. , Cheng Zhenyu , Leung Brendan M. 
Published: September 2023

AbstractThe airway mucus of patients with cystic fibrosis has altered properties which create a microenvironment primed for chronic infections that are difficult to treat. These complex polymicrobial airway infections and corresponding mammalian-microbe interactions are challenging to modelin vitro. Here, we report the development of mucus-like hydrogels with varied compositions and viscoelastic properties reflecting differences between healthy and cystic fibrosis airway mucus. Models of cystic fibrosis and healthy airway microenvironments were created by combining the hydrogels with relevant pathogens, human bronchial epithelial cells, and an antibiotic. Notably, pathogen antibiotic resistance was not solely dependent on the altered properties of the mucus-like hydrogels but was also influenced by culture conditions including microbe species, monomicrobial or polymicrobial culture, and the presence of epithelial cells. Additionally, the cystic fibrosis airway model showed the ability to mimic features characteristic of chronic cystic fibrosis airway infections including sustained polymicrobial growth and increased antibiotic tolerance.
Scale-dependent landscape-biodiversity relationships shape multi-taxa diversity in an oil palm monoculture under restoration
Authors: Cayetano Denver T. , Zemp Delphine Clara , Buchori Damayanti , Fiedler Sebastian , Grass Ingo , Hölscher Dirk , Irawan Bambang , Korol Yevgeniya , Khokthong Watit , Paterno Gustavo Brant , Polle Andrea , Potapov Anton , Sundawati Leti , Tscharntke Teja , Westphal Catrin , Weigelt Patrick , Wiegand Kerstin , Kreft Holger , Guerrero-Ramírez Nathaly R. 
Published: September 2023

ABSTRACTEnhancing biodiversity in monoculture-dominated landscapes is a pressing restoration challenge. Tree islands can enhance biodiversity locally, but the role of scale-dependent processes on local biodiversity remains unclear. Using a multi-scale approach, we explored how scale-dependent processes influence the diversity of seven taxa (woody plants, understory arthropods, birds, herbaceous plants and soil bacteria, fauna, and fungi) within 52 experimental tree islands embedded in an oil palm landscape. We show that local, metacommunity (between islands), and landscape properties shaped above- and below-ground taxa diversity, with the stronger effects on above-ground taxa. The spatial extent that best-predicted diversity ranged from 150 m for woody plants to 700 m for understory arthropods with below-ground taxa responding at large spatial extents. Our results underscore the need for multi-scale approaches to restoration. Additionally, our findings contribute to understanding the complex processes shaping multi-taxa diversity and offer insights for targeted conservation and restoration strategies.
Characterization of SARS-CoV-2 Convalescent Patients’ Serological Repertoire Reveals High Prevalence of Iso–RBD Antibodies
Authors: Curtis Nicholas C. , Shin Seungmin , Hederman Andrew P. , Connor Ruth I. , Wieland-Alter Wendy F. , Ionov Steven , Boylston Jennifer , Rose Josh , Sakharkar Mrunal , Dorman Dana B. , Dessaint John A. , Gwilt Lorraine L. , Crowley Andrew R. , Feldman Jared , Hauser Blake M. , Schmidt Aaron G. , Ashare Alix , Walker Laura M. , Wright Peter F. , Ackerman Margaret E. , Lee Jiwon 
Published: September 2023

AbstractWhile our understanding of SARS-CoV-2 pathogenesis and antibody responses following infection and vaccination has improved tremendously since the outbreak in 2019, the sequence identities and relative abundances of the individual constituent antibody molecules in circulation remain understudied. Using Ig-Seq, we proteomically profiled the serological repertoire specific to the whole ectodomain of SARS-CoV-2 prefusion-stabilized spike (S) as well as to the receptor binding domain (RBD) over a 6-month period in four subjects following SARS-CoV-2 infection before SARS-CoV-2 vaccines were available. In each individual, we identified between 59 and 167 unique IgG clonotypes in serum. To our surprise, we discovered that ∼50% of serum IgG specific for RBD did not recognize prefusion-stabilized S (referred to as iso–RBD antibodies), suggesting that a significant fraction of serum IgG targets epitopes on RBD inaccessible on the prefusion-stabilized conformation of S. On the other hand, the abundance of iso–RBD antibodies in nine individuals who received mRNA-based COVID-19 vaccines encoding prefusion-stabilized S was significantly lower (∼8%). We expressed a panel of 12 monoclonal antibodies (mAbs) that were abundantly present in serum from two SARS-CoV-2 infected individuals, and their binding specificities to prefusion-stabilized S and RBD were all in agreement with the binding specificities assigned based on the proteomics data, including 1 iso–RBD mAb which bound to RBD but not to prefusion-stabilized S. 2 of 12 mAbs demonstrated neutralizing activity, while other mAbs were non-neutralizing. 11 of 12 mAbs also bound to S (B.1.351), but only 1 maintained binding to S (B.1.1.529). This particular mAb binding to S (B.1.1.529) 1) represented an antibody lineage that comprised 43% of the individual’s total S-reactive serum IgG binding titer 6 months post-infection, 2) bound to the S from a related human coronavirus, HKU1, and 3) had a high somatic hypermutation level (10.9%), suggesting that this antibody lineage likely had been elicited previously by pre-pandemic coronavirus and was re-activated following the SARS-CoV-2 infection. All 12 mAbs demonstrated their ability to engage in Fc-mediated effector function activities. Collectively, our study provides a quantitative overview of the serological repertoire following SARS-CoV-2 infection and the significant contribution of iso–RBD antibodies, demonstrating how vaccination strategies involving prefusion-stabilized S may have reduced the elicitation of iso–RBD serum antibodies which are unlikely to contribute to protection.
magpie: a power evaluation method for differential RNA methylation analysis in N6-methyladenosine sequencing
Authors: Guo Zhenxing , Duan Daoyu , Tang Wen , Zhu Julia , Bush William S. , Zhang Liangliang , Zhu Xiaofeng , Jin Fulai , Feng Hao 
Published: September 2023

MotivationRecently, novel biotechnologies to quantify RNA modifications became an increasingly popular choice for researchers who study epitran-scriptome. When studying RNA methylations such as N6-methyladenosine (m6A), researchers need to make several decisions in its experimental design, especially the sample size and a proper statistical power. Due to the complexity and high-throughput nature of m6A sequencing measurements, methods for power calculation and study design are still currently unavailable.ResultsWe propose a statistical power assessment tool,magpie, for power calculation and experimental design for epitranscriptome studies using m6A sequencing data. Our simulation-based power assessment tool will borrow information from real pilot data, and inspect various influential factors including sample size, sequencing depth, effect size, and basal expression ranges. We integrate two modules inmagpie: (i) a flexible and realistic simulator module to synthesize m6A sequencing data based on real data; and (ii) a power assessment module to examine a set of comprehensive evaluation metrics.AvailabilityThe proposed power assessment toolmagpieis publicly available as a R/Bioconductor package at:https://bioconductor.org/packages/magpie/.
Ecological selection of dispersal strategies in metacommunities: impact of landscape features and competitive dynamics
Authors: Khattar Gabriel , Savary Paul , Peres-Neto Pedro R. 
Published: September 2023

AbstractDispersal is simultaneously a cause and a consequence of metacommunity dynamics. While the influence of dispersal on metacommunities is subject of intense research, we still do not understand how species-species and species-environment relationships determine the success of different dispersal strategies in metacommunities. To address this, we employed simulation models considering species with distinct context-dependent dispersal strategies involved in the three stages of dispersal (departure, transience, and settlement). These species were allowed to reach coexistence at the metacommunity scale under various competitive hierarchies and different levels of spatial and temporal environmental variability. By assessing the dispersal strategies of species that persisted and dominated metacommunities, we could understand how metacommunity dynamics impose ecological selection on dispersal. Our simulation model reproduced empirical patterns in species dispersal across different scales, ranging from changes in the success of dispersal strategies caused by local intraspecific and interspecific competition, to observed shifts in dispersal strategies along broad-scale ecological gradients. Additionally, we derived new empirically testable predictions regarding how metacommunity dynamics select for different dispersal strategies. Collectively, our results foster a comprehensive understanding of the factors influencing the success and diversity of dispersal strategies in a large array of ecological contexts.
The role of ion dissolution in metal and metal oxide surface inactivation of SARS-CoV-2
Authors: Hilton Jane , Nanao Yoshiko , Flokstra Machiel , Askari Meisam , Smith Terry K. , Falco Andrea Di , King Phil D.C. , Wahl Peter , Adamson Catherine S 
Published: September 2023

AbstractAntiviral surface coatings are under development to prevent viral fomite transmission from high-traffic touch surfaces in public spaces. Copper’s antiviral properties have been widely documented; but the antiviral mechanism of copper surfaces is not fully understood. We screened a series of metal and metal oxide surfaces for antiviral activity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease (COVID-19). Copper and copper oxide surfaces exhibited superior anti-SARS-CoV-2 activity; however, level of antiviral activity was dependent upon the composition of the carrier solution used to deliver virus inoculum. We demonstrate that copper ions released into solution from test surfaces can mediate virus inactivation, indicating a copper ion dissolution-dependent antiviral mechanism. Level of antiviral activity is, however, not dependent on the amount of copper ions released into solutionper se. Instead, our findings suggest that degree of virus inactivation is dependent upon copper ion complexation with other biomolecules (e.g., proteins/metabolites) in the virus carrier solution that compete with viral components. Although using tissue culture-derived virus inoculum is experimentally convenient to evaluate the antiviral activity of copper-derived test surfaces, we propose that the high organic content of tissue culture medium reduces the availability of “uncomplexed” copper ions to interact with the virus, negatively affecting virus inactivation and hence surface antiviral performance. We propose that laboratory antiviral surface testing should include virus delivered in a physiologically relevant carrier solution (saliva or nasal secretions when testing respiratory viruses) to accurately predict real-life surface antiviral performance when deployed in public spaces.ImportanceThe purpose of evaluating antiviral activity of test surfaces in the laboratory is to identify surfaces that will perform efficiently in preventing fomite transmission when deployed on high-traffic touch surfaces in public spaces. The conventional method in laboratory testing is to use tissue culture-derived virus inoculum, however this study demonstrates that antiviral performance of test copper-containing surfaces is dependent on the composition of the carrier solution in which the virus inoculum is delivered to test surfaces. Therefore, we recommend that laboratory surface testing should include virus delivered in a physiologically relevant carrier solution, to accurately predict real-life test surface performance in public spaces. Understanding the mechanism of virus inactivation is key to future rational design of improved antiviral surfaces. Here, we demonstrate that copper ions released from copper surfaces into small liquid droplets containing SARS-CoV-2, is a mechanism by which the virus that causes COVID-19 can be inactivated.
Fat body glycolysis defects inhibit mTOR and promote distant muscle disorganization through TNF-α/egr and ImpL2 signaling inDrosophilalarvae
Authors: Rodríguez-Vázquez Miriam , Falconi Jennifer , Heron-Milhavet Lisa , Lassus Patrice , Géminard Charles , Djiane Alexandre 
Published: September 2023

SUMMARYThe fat body inDrosophilalarvae serves as a reserve tissue and participates, through its endocrine function, in the regulation of organismal growth and homeostasis. To better understand its role in growth coordination, we induced severe fat body atrophy by knocking down in adipose cells several key enzymes of the glycolytic pathway. Our results show that impairing the last steps of glycolysis led to a drastic shrinkage in adipose cell size and lipid droplets content, and a downregulation of the mTOR pathway. Strikingly, fat body atrophy resulted in the distant disorganization of body wall muscles and the release of muscle-specific proteins in the hemolymph. Molecularly we showed that REPTOR activity was required for fat body atrophy downstream of glycolysis inhibition, and that the effect of fat body atrophy on muscles did not require upd3 secretion, but depended the production of egr/TNF-α and of the insulin pathway inhibitor ImpL2.
Laws of genome nucleotide composition
Authors: Zhang Zhang 
Published: September 2023

AbstractGenome nucleotide composition is of fundamental significance in molecular evolution, genome organization and synthetic biology. Albeit studied for decades, it remains unclear whether there is any theoretical law underlying variable genome nucleotide composition across different species. From the mathematical viewpoint, here we propose three laws of genome nucleotide composition and validate their effectiveness on a large collection of empirical genome sequences across three domains of life. The three laws together provide a unifying framework that is able to unravel the mystery of genome-wide nucleotide composition variation across diverse species, paving the way towards a new era with quantitative insights for deciphering basic principles of life and further advancing theoretical biology.One-Sentence SummaryThe three laws of genome nucleotide composition provide a fundamental framework for molecular evolution, genome organization and synthetic biology.
Protocol for primary human lung organoid-derived air-liquid interfacein vitromodel to study response to SARS-CoV-2
Authors: Castaneda Diana Cadena , Jangra Sonia , Yurieva Marina , Martinek Jan , Callender Megan , Coxe Matthew , Choi Angela , Diego Juan García-Bernalt , Wu Te-Chia , Marches Florentina , Chaussabel Damien , García-Sastre Adolfo , Schotsaert Michael , Williams Adam , Palucka Karolina 
Published: September 2023

SummaryThis article presents a comprehensive protocol for establishing primary human lung organoid-derived air-liquid interface (ALI) cultures from cryopreserved human lung tissue. These cultures serve as a physiologically relevant model to study human airway epitheliumin vitro. The protocol encompasses lung tissue cryostorage, tissue dissociation, lung epithelial organoid generation, and ALI culture differentiation. It also demonstrates SARS-CoV-2 infection in these cultures as an example of their utility. Quality control steps, ALI characterization, and technical readouts for monitoring virus response are included in the study.For additional details on the use and execution of this protocol, please refer to Diana Cadena Castaneda et al (https://doi.org/10.1016/j.isci.2023.107374).HighlightsHuman lung tissue dissection, embedding in OCT blocks, and tissue cryopreservation.Thawing & lung tissue dissociation for lung epithelium organoid generation.Organoid-derived air-liquid-interface cultures for the study of viral infection.Bulk RNA-Seq, flow cytometry, viral titer, and imaging to follow response to virus.Graphical abstract
A biobank-scale test of marginal epistasis reveals genome-wide signals of polygenic epistasis
Authors: Fu Boyang , Pazokitoroudi Ali , Xue Albert , Anand Aakarsh , Anand Prateek , Zaitlen Noah , Sankararaman Sriram 
Published: September 2023

AbstractThe contribution of epistasis (interactions among genes or genetic variants) to human complex trait variation remains poorly understood. Methods that aim to explicitly identify pairs of genetic variants, usually single nucleotide polymorphisms (SNPs), associated with a trait suffer from low power due to the large number of hypotheses tested while also having to deal with the computational problem of searching over a potentially large number of candidate pairs. An alternate approach involves testing whether a single SNP modulates variation in a trait against a polygenic background. While overcoming the limitation of low power, such tests of polygenic or marginal epistasis (ME) are infeasible on Biobank-scale data where hundreds of thousands of individuals are genotyped over millions of SNPs.We present a method to test for ME of a SNP on a trait that is applicable to biobank-scale data. We performed extensive simulations to show that our method provides calibrated tests of ME. We applied our method to test for ME at SNPs that are associated with 53 quantitative traits across ≈ 300 K unrelated white British individuals in the UK Biobank (UKBB). Testing 15, 601 trait-loci associations that were significant in GWAS, we identified 16 trait-loci pairs across 12 traits that demonstrate strong evidence of ME signals (p-value). We further partitioned the significant ME signals across the genome to identify 6 trait-loci pairs with evidence of local (within-chromosome) ME while 15 show evidence of distal (cross-chromosome) ME. Across the 16 trait-loci pairs, we document that the proportion of trait variance explained by ME is about 12x as large as that explained by the GWAS effects on average (range: 0.59 to 43.89). Our results show, for the first time, evidence of interaction effects between individual genetic variants and overall polygenic background modulating complex trait variation.