bluuebunny/crossref_metadata_2025_split huggingface dataset:
Magneto-Mechanical Metamaterials: A Perspective
Authors: Sim Jay , Zhao Ruike Renee 
Published: October 2023

Abstract
Magneto-mechanical metamaterials possess unique and tunable properties by adjusting their shape configurations in response to an external magnetic field. Their designs and functionalities are diverse and are utilized in a wide variety of applications, such as highly tunable elastic and electromagnetic wave filters and targeted shape morphing. In this perspective, we examine the general background of magneto-mechanical metamaterials and their diverse applications. The possible future directions in the field are also thoroughly discussed.
Closed-Form Expressions of Shear Correction Factor for Functionally Graded Beams
Authors: Amandeep  , Pathak Anup Kumar , Padhee Srikant Sekhar 
Published: October 2023

Abstract
In this work, closed-form expressions of shear correction factor (SCF) have been derived for beams with functionally graded material (FGM), through variational asymptotic method (VAM). An energy equivalence approach has been adopted between VAM and Timoshenko model, for estimating the SCF. A planar FGM beam has been considered and the calculation for SCF has been carried out. The formulation has been derived in a functional form that permits solutions for a large class of gradation models of FGM. In the limiting case when the material becomes homogeneous the estimated SCF matches exactly with that of the literature, thus validating the solution. A detailed discussion has been carried out on the results and conclusions have been drawn.
Drosophila melanogaster
as an organism model for studying cystic fibrosis and its major associated microbial infections
Authors: Touré Hamadoun , Herrmann Jean-Louis , Szuplewski Sébastien , Girard-Misguich Fabienne 
Published: October 2023

ABSTRACT

Cystic fibrosis (CF) is a human genetic disease caused by mutations in the
cystic fibrosis transmembrane conductance regulator
gene that encodes a chloride channel. The most severe clinical manifestation is associated with chronic pulmonary infections by pathogenic and opportunistic microbes.
Drosophila melanogaster
has become the invertebrate model of choice for modeling microbial infections and studying the induced innate immune response. Here, we review its contribution to the understanding of infections with six major pathogens associated with CF (
Staphylococcus aureus
,
Pseudomonas aeruginosa
,
Burkholderia cepacia
,
Mycobacterium abscessus
,
Streptococcus pneumoniae,
and
Aspergillus fumigatus
) together with the perspectives opened by the recent availability of two CF models in this model organism.
Diet-induced obesity and diabetes enhance mortality and reduce vaccine efficacy for SARS-CoV-2
Authors: Johnson Robert M. , Ardanuy Jeremy , Hammond Holly , Logue James , Jackson Lian , Baracco Lauren , McGrath Marisa , Dillen Carly , Patel Nita , Smith Gale , Frieman Matthew 
Published: October 2023

ABSTRACT
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), emerged in Wuhan, China, in December 2019. As of September 2023, there have been over 770 million confirmed cases of COVID-19, including over 6.9 million deaths. Epidemiologic studies have indicated that comorbidities of obesity and diabetes mellitus are associated with increased morbidity and mortality following SARS-CoV-2 infection. We determined how the comorbidities of obesity and diabetes affect morbidity and mortality following SARS-CoV-2 infection in unvaccinated and adjuvanted spike nanoparticle (NVX-CoV2373) vaccinated mice. We find that obese/diabetic mice infected with SARS-CoV-2 have increased morbidity and mortality compared to age-matched normal mice. Mice that were fed a high-fat diet (HFD) and then vaccinated with NVX-CoV2373 produce equivalent neutralizing antibody titers compared to those fed a normal diet (ND). However, the HFD mice have reduced viral clearance early in infection. Analysis of the inflammatory immune response in HFD mice demonstrates a recruitment of neutrophils that was correlated with increased mortality and reduced clearance of the virus. Depletion of neutrophils in diabetic/obese vaccinated mice reduced disease severity and protected mice from lethality. This model recapitulates the increased disease severity associated with obesity and diabetes in humans with COVID-19 and is an important comorbidity to study with increasing obesity and diabetes across the world.

IMPORTANCE
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has caused a wide spectrum of diseases in the human population, from asymptomatic infections to death. It is important to study the host differences that may alter the pathogenesis of this virus. One clinical finding in coronavirus disease 2019 (COVID-19) patients is that people with obesity or diabetes are at increased risk of severe illness from SARS-CoV-2 infection. We used a high-fat diet model in mice to study the effects of obesity and type 2 diabetes on SARS-CoV-2 infection as well as how these comorbidities alter the response to vaccination. We find that diabetic/obese mice have increased disease after SARS-CoV-2 infection and they have slower clearance of the virus. We find that the lungs of these mice have increased neutrophils and that removing these neutrophils protects diabetic/obese mice from disease. This demonstrates why these diseases have increased risk of severe disease and suggests specific interventions upon infection.
MacP bypass variants of
Streptococcus pneumoniae
PBP2a suggest a conserved mechanism for the activation of bifunctional cell wall synthases
Authors: Midonet Caroline , Bisset Sean , Shlosman Irina , Cava Felipe , Rudner David Z. , Bernhardt Thomas G. 
Published: October 2023

ABSTRACT

The peptidoglycan (PG) layer protects bacteria from osmotic lysis and defines their shape. The class A penicillin-binding proteins (aPBPs) are PG synthases that possess both glycan polymerization and crosslinking activities needed for PG biogenesis. In Gram-negative bacteria, aPBPs require activation by outer membrane lipoproteins, which are thought to stimulate their cognate synthase by inducing conformational changes that promote polymerase function. How aPBPs are controlled in Gram-positive bacteria is less clear. One of the few known regulators is MacP in
Streptococcus pneumoniae
(
Sp
). MacP is required for the activity of
Sp
PBP2a, but its mode of action has been obscure. We therefore selected for PBP2a variants capable of functioning in the absence of MacP. Amino acid substitutions that bypassed the MacP requirement for PBP2a function
in vivo
also activated its polymerase activity
in vitro
. Many of these changes mapped to the interface between the transmembrane (TM) helix and polymerase domain in a model PBP2a structure. This region is conformationally flexible in the experimentally determined structures of aPBPs and undergoes a structural transition upon binding the substrate-mimicking drug moenomycin. Our findings suggest that MacP promotes PG polymerization by altering the TM-polymerase domain interface in PBP2a and that this mechanism for aPBP activation may be broadly conserved. Furthermore,
Sp
cells expressing an activated PBP2a variant displayed heterogeneous shapes, highlighting the importance of proper aPBP regulation in cell morphogenesis.

IMPORTANCE

Class A penicillin-binding proteins (aPBPs) play critical roles in bacterial cell wall biogenesis. As the targets of penicillin, they are among the most important drug targets in history. Although the biochemical activities of these enzymes have been well studied, little is known about how they are regulated in cells to control when and where peptidoglycan is made. In this report, we isolate variants of the
Streptococcus pneumoniae
enzyme PBP2a that function in cells without MacP, a partner normally required for its activity. The amino acid substitutions activate the cell wall synthase activity of PBP2a, and their location in a model structure suggests an activation mechanism for this enzyme that is shared with aPBPs from distantly related organisms with distinct activators.
High-quality full genome assembly of historic
Xylella fastidiosa
strains from ICMP collection using a hybrid sequencing approach
Authors: Kant Pragya , Brohier Natasha , Mann Rachel , Rigano Luciano , Taylor Robert , Wong-Bajracharya Johanna , Chapman Toni A. , Kehoe Monica , Roach Rebecca , Rodoni Brendan , Constable Fiona 
Published: October 2023

ABSTRACT

High-quality complete genomes of five
Xylella fastidiosa
strains were assembled by combining Nanopore and Illumina sequencing data. Among these, International Collection of Micro-organisms from Plants (ICMP) 8731, ICMP 8742 and ICMP 8745 belong to subspecies
fastidiosa
while ICMP 8739 and ICMP 8740 were determined as subspecies
multiplex
. The strains were further classified into sequence types.
Metagenome-assembled genomes from sugarcane mill mud
Authors: Uchimiya Minori , Elliott Leah E. , Derito Christopher M. , Hay Anthony G. 
Published: October 2023

ABSTRACT
The genomes of 11 bacteria and 3 archaea were assembled from metagenomic DNA extracted from sugarcane mill mud. These metagenome-assembled genomes ranged from 1.79 to 6.45 Mb, with 2,263 to 5,551 predicted proteins, 80.65% to 100% genome completeness, and 43.19% to 68.02% G+C content.
Draft genomes of 16
Bartonella henselae
strains from cats in Valdivia, Chile
Authors: Sepulveda Paulina , Stegger Marc , Monti Gustavo , Canales Nivia , Mella Armin , Butaye Patrick , Müller Ananda 
Published: October 2023

ABSTRACT

Bartonella henselae
is a primary zoonotic agent, having cats as asymptomatic reservoirs. In humans, it causes cat scratch disease. Here, we report the whole genome sequences of 16 strains isolated from cats in Valdivia city, Southern Chile. Strains showed little variability in the multilocus sequence typing profiles.
Genome sequences of Phasi Charoen-like phasivirus and Fako virus from
Aedes aegypti
mosquitoes collected in coastal Kenya
Authors: Langat Solomon K. , Kerich Gladys , Cinkovich Stephanie , Johnson Jaree , Ambale Janet , Yalwala Santos , Opot Benjamin , Garges Eric , Ojwang Elly , Eyase Fredrick 
Published: October 2023

ABSTRACT

We report the sequencing of two viruses, Phasi Charoen-like phasivirus (PCLV) and Fako virus (FAKV), which were detected in a pool of
Aedes aegypti
from Kenya. Analysis showed a high similarity of PCLV to publicly available PCLV genomes from Kenya. FAKV showed a high genetic divergence from publicly available FAKV genomes.
Rapid bacteriolysis of
Staphylococcus aureus
by lysin exebacase
Authors: Vila-Farres Xavier , Sauve Karen , Oh Jun , Swift Steven , DeJonge Boudewijn , Ambler Jane E. , Schuch Raymond 
Published: October 2023

ABSTRACT

Lysins (peptidoglycan hydrolases) are promising new protein-based antimicrobial candidates under development to address rising antibiotic resistance encountered among pathogenic bacteria. Exebacase is an antistaphylococcal lysin and the first member of the lysin class to have entered clinical trials in the United States. In this study, the bacteriolytic activity of exebacase was characterized with time-kill assays, turbidity reduction assays, and microscopy. Three methicillin-susceptible
Staphylococcus aureus
and three methicillin-resistant
S. aureus
isolates were tested in time-kill assays over a range of concentrations from 0.25 to 8 × MIC. Exebacase demonstrated a concentration-dependent killing and showed bactericidal activity (≥3 log
10
kill achieved relative to the starting inoculum) within 3 h at 1 × MIC against all strains tested. Dose-dependent lysis by exebacase was, furthermore, observed in the turbidity reduction assay, wherein decreases in initial OD
600
of 50% were observed within ~15 min at concentrations as low as 4 µg/mL. Membrane dissolution, loss of cytoplasmic material, and lysis were confirmed by video and electron microscopy. The demonstrated rapid bacteriolytic effect of exebacase is an important distinguishing feature of this novel modality.

IMPORTANCE

To guide the development of an investigational new antibacterial entity, microbiological data are required to evaluate the killing kinetics against target organism(s). Exebacase is a lysin (peptidoglycan hydrolase) that represents a novel antimicrobial modality based on degradation of the cell wall of
Staphylococcus aureus
. Killing by exebacase was determined in multiple assay formats including time-kill assays, wherein reductions of viability of ≥3 log
10
colony-forming units/mL were observed within 3 h for multiple different isolates tested, consistent with very rapid bactericidal activity. Rapid reductions in optical density were likewise observed in exebacase-treated cultures, which were visually consistent with microscopic observations of rapid lysis. Overall, exebacase provides a novel antimicrobial modality against
S. aureus
, characterized by a rapid cidal and lytic activity.
Population Dynamics and Distribution of the Lake Smelt, a Dwarf Form of the European Smelt Osmerus eperlanus (Osmeridae), and the Black Sea Sprat Clupeonella cultriventris (Clupeidae) while Cohabiting the Rybinsk Reservoir
Authors: Gerasimov Yu. V. , Komarova A. S. , Tarleva A. F. , Solomatin Yu. I. , Bazarov M. I. , Borisenko E. S. 
Published: October 2023

AbstractThe data for a 23-year period (2000–2022) on the population dynamics and distribution of the lake smelt (a form of the European smelt Osmerus eperlanus) and the Black Sea sprat Clupeonella cultriventris in the Rybinsk Reservoir have been summarized. The lake smelt dominated the reservoir pelagial from the 1950s to the mid-1990s. An anomalously low water level in the reservoir in 1996 and abnormal (for this reservoir) water warming in subsequent years led to elimination of the species from the reservoir ichthyofauna in 2002. The Black-Sea sprat invaded the reservoir in the mid-1990s; its population irruption occurred in the early 2000s (during the depressed state of the smelt population). Currently, this species dominates in the pelagial of the reservoir. Since the early 2000s there were noted two periods when the lake smelt was found in practically all parts of the Rybinsk Reservoir and the sprat abundance was also high. However, high water temperatures in 2010 and 2021, as well as low level in 2014, resulted in almost complete disappearance of the lake smelt disappeared. During the periods of cohabitation of the studied species, a significant similarity in the diet of individuals of both species with the size of up to 80 mm has been noted. The larger smelt fed on larger plankton, and in the summer also on fish. Currently, the main limiting factor negatively affecting the recovery of the smelt population in the Rybinsk Reservoir is the abnormal heating of the water column in some years.
Lipid Profile of the Muscle Tissue of Some Mesopelagic Fish Species of the Families Stomiidae and Myctophidae from Different Depths of the Irminger Sea, North Atlantic
Authors: Voronin V. P. , Artemenkov D. V. , Orlov A. M. , Murzina S. A. 
Published: October 2023

AbstractFor the first time the qualitative and quantitative lipid profile (total lipids and polar and nonpolar lipids) of the muscle tissue of six mesopelagic fish species, which are representatives of two deep-sea families widespread in the World Ocean: Stomiidae and Myctophidae were studied. It was found the species specificity of lipid accumulation for the studied fishes, which indicates differences in the mechanisms of compensatory responses. Triacylglycerols are the main form of lipid storage in the studied species. However, an accumulation of cholesterol esters and waxes (lipid characteristic of vertical migrants) has also been recorded inBorostomias antarcticus. The revealed distinctive features of Myctophidae and Stomiatidae, related to the accumulation of cholesterol and variations in the content of different phospholipid fractions, indicate that the fishes of these families use different mechanisms for regulating and maintaining the physicochemical state (permeability and fluidity) of biological membranes under conditions of change in a set of environmental factors (temperature, salinity, hydrostatic pressure, and specific photoperiod) with increase in the habitat depth.
Pulmonary function after lobectomy in children: a systematic review and meta-analysis
Authors: Liu Chenyu , Liu Jie , Yuan Miao , Cheng Kaisheng , Luo Dengke , Zeng Li , Xu Chang 
Published: October 2023

BackgroundThe influence of lobectomy on pulmonary function in children was still controversial. A systematic review and meta-analysis were essential to explore whether pulmonary function was impaired after lobectomy in children.MethodsPubMed, Embase and Web of Science were searched from 1 January 1946 to 1 July 2022. Forced expiratory volume in 1 s (FEV1), forced vital capacity (FVC), FEV1/FVC and total lung capacity were extracted from the studies as the primary analysis indicators. Subgroup analyses were performed between the congenital lung malformation (CLM) group and other diseases group, early surgery and late surgery group (1 year old as the dividing line).ResultsA total of 5302 articles were identified through the search strategy; finally, 10 studies met the inclusion criteria. Through the meta-analysis, we found a mild obstructive ventilatory disorder in children who underwent lobectomy. However, a normal pulmonary function could be found in young children with CLM who underwent lobectomy, and the time of operation had no significant influence on their pulmonary function.ConclusionsThe overall result of pulmonary function after lobectomy in children was good. Surgeons may not need to be excessively concerned about the possibility of lung surgery affecting pulmonary function in children, particularly in patients with CLM.PROSPERO registration numberCRD42022342243.
Efficacy and safety of cosibelimab, an anti-PD-L1 antibody, in metastatic cutaneous squamous cell carcinoma
Authors: Clingan Philip , Ladwa Rahul , Brungs Daniel , Harris Dean Laurence , McGrath Margaret , Arnold Susan , Coward Jermaine , Fourie Samuel , Kurochkin Andriy , Malan Daniel R , Mant Andrew , Sharma Vinay , Shue Hong , Tazbirkova Andrea , Berciano-Guerrero Miguel-Angel , Charoentum Chaiyut , Dalle Stéphane , Dechaphunkul Arunee , Dudnichenko Oleksandr , Koralewski Piotr , Lugowska Iwona , Montaudié Henri , Muñoz-Couselo Eva , Sriuranpong Virote , Oliviero James , Desai Jayesh 
Published: October 2023

BackgroundProgrammed cell death receptor-1 (PD-1)-blocking antibodies are approved to treat metastatic or locally advanced cutaneous squamous cell carcinoma (CSCC) cases ineligible for curative surgery or radiation. Notwithstanding, some patients experience inadequate responses or severe immune-related adverse events (AEs), indicating the need for improved therapies. Cosibelimab is a high-affinity programmed cell death-ligand 1 (PD-L1)-blocking antibody that activates innate and adaptive immunity by blocking PD-L1 interaction with PD-1 and B7-1 receptors. It is an unmodified immunoglobulin G1 subtype with a functional Fc domain capable of inducing antibody-dependent cellular cytotoxicity and complement-dependent cytotoxicity. Here, we present results of the pivotal study of patients with metastatic CSCC from an open-label, multicenter, multiregional, multicohort, phase 1 trial of cosibelimab.MethodsIn this trial, participants with metastatic CSCC received cosibelimab 800 mg intravenously every 2 weeks. Primary endpoint was objective response rate (ORR) by independent central review using Response Evaluation Criteria in Solid Tumors, V.1.1. Secondary endpoints included duration of response (DOR) and safety.ResultsObjective response was observed in 37 of 78 participants (47.4% (95% CI: 36.0% to 59.1%)), with median follow-up of 15.4 months (range: 0.4 to 40.5) as of data cut-off. Median DOR was not reached (range: 1.4+ to 34.1+ months), with response ongoing in 73.0% of participants. Common treatment-emergent AEs (≥15%) were fatigue (26.9%), rash (16.7%), and anemia (15.4%). Eighteen participants (23.1%) experienced immune-related AEs (grade 3: n=2 (2.6%); no grade 4/5). No treatment-related deaths were reported.ConclusionsCosibelimab demonstrated clinically meaningful ORR and DOR and was associated with a manageable safety profile.Trial registration numberNCT03212404.
COVID-19 prognosis in systemic lupus erythematosus compared with rheumatoid arthritis and spondyloarthritis: results from the CONTROL-19 Study by the Italian Society for Rheumatology
Authors: Scirocco Chiara , Ferrigno Sara , Andreoli Laura , Fredi Micaela , Lomater Claudia , Moroni Luca , Mosca Marta , Raffeiner Bernd , Carrara Greta , Landolfi Gianpiero , Rozza Davide , Zanetti Anna , Scirè Carlo Alberto , Sebastiani Gian Domenico 
Published: October 2023

IntroductionData concerning SARS-CoV-2 in patients affected by SLE are contradicting.The aim of this study was to investigate disease-related differences in COVID-19 prognosis of patients affected by rheumatic diseases before vaccination; we tested the hypothesis that patients with SLE may have a different outcome compared with those with rheumatoid arthritis (RA) or spondyloarthritis (SPA).MethodsWe analysed data from the national CONTROL-19 Database with a retrospective, observational design, including rheumatic patients affected by COVID-19. The principal outcome measure was hospitalisation with death or mechanical ventilation. Differences between SLE, RA and SPA were analysed by univariable and multivariable logistic regression models.ResultsWe included 103 patients with SLE (88.2% female, mean age 48.9 years, 50.4% active disease), 524 patients with RA (74.4% female, mean age 60.6 years, 59.7% active disease) and 486 patients with SPA (58.1% female, mean age 53.2 years, 58% active disease).Outcome prevalence was not different between patients with SLE and those with RA (SLE 24.5%, RA 25.6%), while patients with SPA showed a more favourable outcome compared with those with SLE (SPA 15.9%); data from the multivariable analysis confirmed this result.In SLE, age >65 years (OR 17.3, CI 5.51 to 63.16, p<0.001), hypertension (OR 6.2, CI 2.37 to 17.04, p<0.001) and prednisone (PDN) use (OR 3.8, CI 1.43 to 11.39, p=0.01) were associated with severe outcomes, whereas hydroxychloroquine use was found to be protective (OR 0.3, CI 0.14 to 0.91, p=0.03).ConclusionOur data suggest that patients with SLE and RA do not show a different COVID-19 outcome, while patients with SPA have a more favourable disease course compared with those with SLE. Risk of hospitalisation with ventilation or death was associated with age >65 years, hypertension and PDN use in patients with SLE.