bluuebunny/crossref_metadata_2025_split huggingface dataset:
Time since liver transplant and immunosuppression withdrawal outcomes: Systematic review and individual patient data meta‐analysis
Authors: Appenzeller‐Herzog Christian , Rosat Aurélie , Mathes Tim , Baroja‐Mazo Alberto , Chruscinski Andrzej , Feng Sandy , Herrero Ignacio , Londono Maria‐Carlota , Mazariegos George , Ohe Hidenori , Pons José A. , Sanchez‐Fueyo Alberto , Waki Kayo , Vionnet Julien 
Published: October 2023

AbstractBackground & AimsSuccessful immunosuppression withdrawal (ISW) is possible for a subfraction of liver transplant (LT) recipients but the factors that define the risk of ISW failure are largely unknown. One candidate prognostic factor for ISW success or operational tolerance (OT) is longer time between LT and ISW which we term “pre‐withdrawal time”. To clarify the impact of pre‐withdrawal time span on subsequent ISW success or failure, we conducted a systematic review with meta‐analysis.MethodsWe systematically interrogated the literature for LT recipient ISW studies reporting pre‐withdrawal time. Eligible articles from Embase, Medline, and the Cochrane Central Register of Controlled Trials were used for backward and forward citation searching. Pre‐withdrawal time individual patient data (IPD) was requested from authors. Pooled mean differences and time‐response curves were calculated using random‐effects meta‐analyses.ResultsWe included 17 studies with 691 patients, 15 of which (620 patients) with IPD. Study‐level risk of bias was heterogeneous. Mean pre‐withdrawal time was greater by 427 days [95% confidence interval (CI) 67–788] in OT compared to non‐OT patients. This increase was potentiated to 799 days (95% CI 369–1229) or 1074 days (95% CI 685–1463) when restricting analysis to adult or European study participants. In time‐response meta‐analysis for adult or European ISW candidates, likelihood of OT increased by 7% (95% CI 4–10%) per year after LT (GRADE low‐ and moderate‐certainty of evidence, respectively).ConclusionsOur data support the impact of pre‐withdrawal time in ISW decision‐making for adult and European LT recipients. PROSPERO REGISTRATION: CRD42021272995.
Clinical characteristics and prognosis of hospitalized patients with moderate alcohol‐associated hepatitis
Authors: Gaurnizo‐Ortiz Maria , Nephew Lauren D. , Vilar‐Gomez Eduardo , Kettler Carla D. , Slaven James E. , Ghabril Marwan S. , Desai Archita P. , Orman Eric S. , Chalasani Naga , Gawrieh Samer , Patidar Kavish R. 
Published: October 2023

AbstractBackground and AimsLittle is known about the clinical characteristics and prognosis of hospitalized patients with moderate alcohol‐associated hepatitis (mAH) as compared to severe alcohol‐associated hepatitis (sAH). Therefore, we aimed to describe the clinical characteristics and risk factors associated with mortality in hospitalized mAH patients.MethodsPatients hospitalized with alcohol‐associated hepatitis (AH) from 1 January 2010 to 31 December 2020 at a large US healthcare system [11 hospitals, one liver transplant centre] were retrospectively analysed for outcomes. Primary outcome was 90‐day mortality. AH and mAH were defined according to NIAAA Alcoholic Hepatitis Consortia and Model for End‐stage Liver Disease Score ≤ 20 respectively. Multivariable Cox regression analysis was performed to identify independent risk factors associated with 90‐day mortality.Results1504 AH patients were hospitalized during the study period, of whom 39% (n = 590) had mAH. Compared to sAH patients, mAH patients were older (50 vs. 48 years, p < 0.001) and less likely to have underlying cirrhosis (74% vs. 83%, p < 0.001). There were no differences between the two groups for median alcohol intake g/day (mAH 140.0 vs. sAH 112.0, p = 0.071). The cumulative proportion surviving at 90 days was 88% in mAH versus 62% in sAH (p < 0.001). On multivariable analysis, older age [HR 1.03 (95% CI 1.00–1.06), p = 0.020], corticosteroid use [HR 1.80 (95% CI 1.06–3.06), p = 0.030] and acute kidney injury (AKI) [HR 2.43 (95% CI 1.33–4.47), p = 0.004] were independently associated with 90‐day mortality.ConclusionsmAH carries a 12% mortality rate at 90 days. Age, AKI and corticosteroid use were associated with an increased risk for 90‐day mortality. Avoidance of corticosteroids and strategies to reduce the risk of AKI could improve outcomes in mAH patients.
A marine-derived fatty acid targets the cell membrane of Gram-positive bacteria
Authors: Upender Isha , Yoshida Olivia , Schrecengost Anna , Ranson Hilary , Wu Qihao , Rowley David C. , Kishore Shreya , Cywes Claire , Miller Eric L. , Whalen Kristen E. 
Published: October 2023

ABSTRACT

The rapid evolution of antibiotic resistance is shrinking our stockpile of commercially available antibiotics. Therefore, new antimicrobials with novel mechanisms of action (MoAs) are desperately needed. The free fatty acid, (
Z
)-13-methyltetra-4-decenoic acid ((
Z
)-4C-14:1), isolated from a marine sediment bacterium
Olleya marilimosa
, displays strong inhibition of Gram-positive pathogens with minimal cytotoxic effects to mammalian cells. Here, we applied a combination of experimental approaches to identify the mechanism by which (
Z
)-4C-14:1 kills the Gram-positive bacterium
Bacillus subtilis
. Using quick and cost-effective bacterial cytological profiling (BCP), we established the cytological signatures of 17 antibiotics representing 6 general classes of antibiotic MoAs. We used BCP to demonstrate that while (
Z
)-4C-14:1-treated
B. subtilis
cells display unique morphological features compared to other antibiotic classes, (
Z
)-4C-14:1 mode of action shares substantial overlap with the fast-acting antibiotic colistin specifically in Gram-positive cells and daptomycin, both of which target bacterial permeability by destroying the cell membrane and causing extensive cell surface alterations. To further determine if the cell membrane of
B. subtilis
was the target of (
Z
)-4C-14:1, we used cell membrane- and peptidoglycan-specific diagnostic stains to investigate bacterial permeability. Our results indicate that (
Z
)-4C-14:1 destabilizes the cell membrane by pore formation in Gram-positive bacteria and emphasize the importance of mining the marine environment for naturally occurring antibiotics.

IMPORTANCE

With the lack of new antibiotics in the drug discovery pipeline, coupled with accelerated evolution of antibiotic resistance, new sources of antibiotics that target pathogens of clinical importance are paramount. Here, we use bacterial cytological profiling to identify the mechanism of action of the monounsaturated fatty acid (
Z
)-13-methyltetra-4-decenoic acid isolated from the marine bacterium
Olleya marilimosa
with antibacterial effects against Gram-positive bacteria. The fatty acid antibiotic was found to rapidly destabilize the cell membrane by pore formation and membrane aggregation in
Bacillus subtilis
, suggesting that this fatty acid may be a promising adjuvant used in combination to enhance antibiotic sensitivity.
Identification of host dependency factors involved in SARS-CoV-2 replication organelle formation through proteomics and ultrastructural analysis
Authors: Pahmeier Felix , Lavacca Teresa-Maria , Goellner Sarah , Neufeldt Christopher J. , Prasad Vibhu , Cerikan Berati , Rajasekharan Sreejith , Mizzon Giulia , Haselmann Uta , Funaya Charlotta , Scaturro Pietro , Cortese Mirko , Bartenschlager Ralf 
Published: October 2023

ABSTRACT
Positive-strand RNA viruses subvert the cellular endomembrane system for the generation of distinct compartments termed replication organelles (ROs) that harbor the site where viral RNAs are generated. In this study, we corroborate that the SARS-CoV-2 non-structural proteins 3 and 4 (nsp3 and nsp4) suffice to remodel the endoplasmic reticulum to form double-membrane vesicles similar to ROs observed in viral infection. Cellular membrane alterations induced by nsp3/4 expression were evaluated through electron tomography and confocal microscopy, and nsp3/4-associated host factors were identified using mass spectrometry. The role of these host factors in virus infection was determined using gene silencing, identifying several host proteins involved in the SARS-CoV-2 replication cycle. Combining the gene silencing approach with ultrastructural analysis of nsp3/4-expressing cells, we found that the host dependency factors FAM149B1, CCAR2, and ZC3HAV1 play a role in the formation of double-membrane vesicles in a replication-independent manner.

IMPORTANCE
Remodeling of the cellular endomembrane system by viruses allows for efficient and coordinated replication of the viral genome in distinct subcellular compartments termed replication organelles. As a critical step in the viral life cycle, replication organelle formation is an attractive target for therapeutic intervention, but factors central to this process are only partially understood. In this study, we corroborate that two viral proteins, nsp3 and nsp4, are the major drivers of membrane remodeling in SARS-CoV-2 infection. We further report a number of host cell factors interacting with these viral proteins and supporting the viral replication cycle, some of them by contributing to the formation of the SARS-CoV-2 replication organelle.
MmuPV1 E6 induces cell proliferation and other hallmarks of cancer
Authors: Romero-Masters James C. , Muehlbauer Laura K. , Hayes Mitchell , Grace Miranda , Shishkova Evgenia , Coon Joshua J. , Munger Karl , Lambert Paul F. 
Published: October 2023

ABSTRACT
The E6 protein encoded by the murine papillomavirus (MmuPV1) is essential for MmuPV1-induced skin disease. Our previous work has identified a number of cellular interacting partners of MmuPV1 E6 and E7 through affinity purification/mass spectrometry analysis. These studies revealed that MmuPV1 E6 potently inhibits keratinocyte differentiation through multiple molecular mechanisms including inhibition of NOTCH and TGF-β signaling. Here, we report that MmuPV1 E6 has additional important oncogenic activities when expressed in its natural host cells, mouse keratinocytes, including increasing proliferation, overcoming density-mediated growth arrest, and proliferation under conditions of limited supply of growth factors. Unbiased proteomic/transcriptomic analyses of mouse keratinocytes expressing MmuPV1 E6 substantiated its effect on these cellular processes and divulged that some of these effects may be mediated in part through it upregulating E2F activity. Our analyses also revealed that MmuPV1 E6 may alter other cancer hallmarks including evasion of growth suppressors, inhibition of immune response, resistance to cell death, and alterations in DNA damage response. Collectively, our results suggest that MmuPV1 E6 is a major driver of multiple hallmarks of cancer in MmuPV1’s natural host cells, mouse keratinocytes.

IMPORTANCE
The Mus musculus papillomavirus 1 (MmuPV1) E6 and E7 proteins are required for MmuPV1-induced disease. Our understanding of the activities of MmuPV1 E6 has been based on affinity purification/mass spectrometry studies where cellular interacting partners of MmuPV1 E6 were identified, and these studies revealed that MmuPV1 E6 can inhibit keratinocyte differentiation through multiple mechanisms. We report that MmuPV1 E6 encodes additional activities including the induction of proliferation, resistance to density-mediated growth arrest, and decreased dependence on exogenous growth factors. Proteomic and transcriptomic analyses provided evidence that MmuPV1 E6 increases the expression and steady state levels of a number of cellular proteins that promote cellular proliferation and other hallmarks of cancer. These results indicate that MmuPV1 E6 is a major driver of MmuPV1-induced pathogenesis.
Complete genome sequence of
Lactiplantibacillus plantarum
strain VHProbi P06, isolated from kimchi
Authors: Guo Chaoqun , Cui Hongchang , Wang Qian , Duan Zhi 
Published: October 2023

ABSTRACT

Lactiplantibacillus plantarum
strain VHProbi P06 is a probiotic that was isolated from kimchi soup. Here, we investigate the whole-genome sequence of this strain, which contains a chromosome and seven plasmids.
Genome and characteristics of
Arthrobacter globiformis
AZ cluster phage London
Authors: Beyer Andrea R. , Hatke Hughes Hannah L. , Flowers Jasmae S. , Bullock Jacquelin , Daniels Demesha T. , Drew Makayla , Lee-Mayes Queen , Marshall Brianna M. , Remson Vivica , Thomas Micaelah 
Published: October 2023

ABSTRACT

London is a predicted temperate bacteriophage with siphovirus morphology infecting
Arthrobacter globiformis
NRRL strain B-2880. Sequencing of the genome revealed a length of 43,599 bp comprising 69 predicted open-reading frames and no tRNA genes. It is categorized as a cluster AZ1 phage along with closely related actinobacteriophages Elezi, Eraser, and Niobe.
Complete genome sequence of the
Escherichia coli
phage vB_Ec_Tarrare
Authors: Veilleux Forrest I. , Ayyash Ibrahim , Page Shallee T. 
Published: October 2023

ABSTRACT

We report the isolation, sequencing, and annotation of the novel bacteriophage vB_Ec_Tarrare, which infects the
Escherichia coli
K-12 strain. It was isolated from a bat guano sample collected in Rindge, NH, USA. Its genome is 40,953 base pairs long with 49 putative protein-coding genes and no transfer RNAs.
Cross-sectional evaluation of an asynchronous multiple mini-interview (MMI) in selection to health professions training programmes with 10 principles for fairness built-in
Authors: Callwood Alison , Harris Jenny , Gillam Lee , Roberts Sarah , Kubacki Angela , Christidis Angelos , Tiffin Paul Alexander 
Published: October 2023

ObjectivesWe aimed to explore the psychometric properties of the first known online asynchronous multiple mini-interview (MMI) designed for fairness with subgroup analyses by key characteristics, usability and acceptability.DesignCross-discipline multimethod evaluation.SettingOne UK University.ParticipantsApplicants to nursing, midwifery and paramedic science undergraduate programmes during 2021–2022.Primary, secondary outcome measuresPsychometric properties (internal consistency, construct validity, dimensionality) were assessed using Cronbach’s alpha (α), parallel analysis (PA), Schmid-Leiman transformation and ordinal confirmatory factor analysis (CFA). Usability and acceptability were evaluated using descriptive statistics and conventional content analysis.MethodsThe system was configured in a seven question 4 min MMI. Applicants’ videorecorded their answers which were later assessed by interviewers and scores summed. Applicants and interviewers completed online evaluation questionnaires.ResultsPerformance data from 712 applicants determined good-excellent reliability for the asynchronous MMI (mean α 0.72) with similar results across subgroups (gender, age, disability/support needs, UK/non-UK). PA and factor analysis results suggested there were seven factors relating to the MMI questions with an underlying general factor that explained the variance in observed candidate responses. A CFA testing a seven-factor hierarchical model showed an excellent fit to the data (Confirmatory Fit Index=0.99), Tucker Lewis Index=0.99, root mean square error (RMSE) =0.034). Applicants (n=210) viewed the flexibility, relaxed environment and cost savings advantageous. Interviewers (n=65) reported the system to be intuitive, flexible with >70% time saved compared with face-to-face interviews. Reduced personal communication was cited as the principal disadvantage.ConclusionsWe found that the asynchronous MMI was reliable, time-efficient, fair and acceptable and building fairness in was lost-cost. These novel, insights are applicable across health professions selection internationally informing the future configuration of online interviews to ensure workforces represent the societies they serve.
High temperature Raman spectroscopic analysis of the crystal growth of Bi2ZnOB2O6
Authors: Zhang Ji , Liu Daojun 
Published: October 2023

Micromechanism of crystal growth has received considerable attention as a fundamental subject. However, in situ observation of the crystal growth process remains challenging. In this study, high-temperature Raman spectroscopy has been utilized to investigate the growth pattern of Bi2ZnOB2O6 crystals via in situ exploration of the starting solution structure near the crystal–solution interface. The experimental results show that the solution primarily consists of ZO4 and BO3 units corresponding to 370, 539, 664, and 1293 cm−1 vibration frequencies. These units connect with each other forming longer chains in the area close to the crystal, and they are related to the presence of low-wavenumber vibrations in the Raman spectrum. Furthermore, a loose embryonic structure of the Bi2ZnOB2O6 crystal is observed near the crystal–solution interface owing to the formation of Bi–O bonds. Therefore, this study successfully provides a clear understanding of the formation mechanism of Bi2ZnOB2O6 crystals.
Multiple verdazyl radicals appended to a triarylamine scaffold
Authors: Reiber Sydney , Templeman-Vivian Bennett , Mills Michelle B. , Tremblay Christopher , Leitch David C. , Chernick Erin T. 
Published: October 2023

We report the synthesis of three triphenylamine-based verdazyl radicals. These include a mono, bis, and tris(verdazyl) at the 4-position(s) of the N–Ar groups, containing one, two, and three unpaired electrons, respectively. Each of these compounds is air stable and fully characterized using EPR spectroscopy, high-resolution mass spectrometry, infrared spectroscopy, UV/Vis spectroscopy, and cyclic voltammetry. From the UV/Vis absorbance data, the optical absorbance energy gaps were found to be ∼2.35 eV for all three verdazyl-containing compounds. Cyclic voltammetry was used to estimate the energy levels of the singly occupied molecular orbitals, which are −4.91, −5.12, and −4.98 eV for mono, bis, and tris(verdazyl) compounds, respectively. Spin–spin exchange interactions were observed in the EPR spectra of both the bis and tris(verdazyl)s, leading to additional hyperfine coupling patterns and assignment of the ground states as triplet and quartet, respectively.
Note on Landau–Stanyukovich rule and the similarity parameter of converging shock waves
Authors: Kwang-Hua Chu A. , Qiao Zhiqin , Li Zhi-Hui , Xiao Yingchao 
Published: October 2023

Using similarity methods with general physical assumptions and sufficient mathematical relations, researchers can obtain approximate solutions ready for experimental confirmation. Singh et al. claimed to have analyzed the second-kind self-similar motion of converging cylindrical shock waves in magnetogasdynamics. However, we found the dominated equation (11) and relevant equations of Singh et al. [Chin. Phys. Lett. 28(9) (2011) 094701] as well as the dominated equation (12) and relevant equations of Singh et al. [AIAA J. 48(11) (2010) 2523] being not correct. We show the correct mathematical derivations in details. It seems to us corresponding equations as well as illustrations by Singh et al. are of doubt due to above-mentioned issues. Our results imply the similarity exponent [Formula: see text] obtained by Singh et al. will be close to that for the converging spherical shock waves.
Dual Construct Fixation of the Scaphoid
Authors: SIVAKUMAR Brahman Shankar , LAWSON Richard Dorrien , AN Vincent V. G. , LEDGARD James P. 
Published: October 2023

Dual construct fixation has been increasingly used in complex peri-articular or peri-prosthetic long bone fractures, those with poor bone quality and in revision situations. We describe the utilisation of a screw-plate construct in the setting of a juxta-articular distal pole scaphoid fracture, review the literature and provide recommendations for future use. Level of Evidence: Level V (Therapeutic)
The Role of the Gut Microbiome in Hematological Cancers
Authors: Hussein Najihah , Rajasuriar Reena , Khan Asif M. , Lim Yvonne Ai-Lian , Gan Gin Gin 
Published: October 2023

Abstract
Humans are in a complex symbiotic relationship with a wide range of microbial organisms, including bacteria, viruses, and fungi. The evolution and composition of the human microbiome can be an indicator of how it may affect human health and susceptibility to diseases. Microbiome alteration, termed as dysbiosis, has been linked to the pathogenesis and progression of hematological cancers. A variety of mechanisms, including epithelial barrier disruption, local chronic inflammation response trigger, antigen dis-sequestration, and molecular mimicry, have been proposed to be associated with gut microbiota. Dysbiosis may be induced or worsened by cancer therapies (such as chemotherapy and/or hematopoietic stem cell transplantation) or infection. The use of antibiotics during treatment may also promote dysbiosis, with possible long-term consequences. The aim of this review is to provide a succinct summary of the current knowledge describing the role of the microbiome in hematological cancers, as well as its influence on their therapies. Modulation of the gut microbiome, involving modifying the composition of the beneficial microorganisms in the management and treatment of hematological cancers is also discussed. Additionally discussed are the latest developments in modeling approaches and tools used for computational analyses, interpretation and better understanding of the gut microbiome data.
Quantifying the Environmental Effects on Tropical Cyclone Intensity Change Using a Simple Dynamically Based Dynamical System Model
Authors: Xu Jing , Wang Yuqing , Yang Chi 
Published: October 2023

Abstract
Accurate prediction of tropical cyclone (TC) intensity is quite challenging due to multiple competing processes among the TC internal dynamics and the environment. Most previous studies have evaluated the environmental effects on TC intensity change from both internal dynamics and external influence. This study quantifies the environmental effects on TC intensity change using a simple dynamically based dynamical system (DBDS) model recently developed. In this simple model, the environmental effects are uniquely represented by a ventilation parameter B, which can be expressed as multiplicative of individual ventilation parameters of the corresponding environmental effects. Their individual ventilation parameters imply their relative importance to the bulk environmental ventilation effect and thus to the TC intensity change. Six environmental factors known to affect TC intensity change are evaluated in the DBDS model using machine learning approaches with the best track data for TCs over the North Atlantic, central, eastern, and western North Pacific and the Statistical Hurricane Intensity Prediction Scheme (SHIPS) dataset during 1982–2021. Results show that the deep-layer vertical wind shear (VWS) is the dominant ventilation factor to reduce the intrinsic TC intensification rate or to drive the TC weakening, with its ventilation parameter ranging between 0.5 and 0.8 when environmental VWS between 200 and 850 hPa is larger than 8 m s−1. Other environmental factors are generally secondary, with their respective ventilation parameters over 0.8. An interesting result is the strong dependence of the environmental effects on the stage of TC development.