bluuebunny/crossref_metadata_2025_split huggingface dataset:
Muscle fibre typology affects whole‐body metabolic rate during isolated muscle contractions and human locomotion
Authors: Swinnen Wannes , Lievens Eline , Hoogkamer Wouter , De Groote Friedl , Derave Wim , Vanwanseele Benedicte 
Published: March 2024

AbstractThe wide variation in muscle fibre type distribution across individuals, along with the very different energy consumption rates in slow versus fast muscle fibres, suggests that muscle fibre typology contributes to inter‐individual differences in metabolic rate during exercise. However, this has been hard to demonstrate due to the gap between a single muscle fibre and full‐body exercises. We investigated the isolated effect of triceps surae muscle contraction velocity on whole‐body metabolic rate during cyclic contractions in individuals a priori selected for their predominantly slow (n = 11) or fast (n = 10) muscle fibre typology by means of proton magnetic resonance spectroscopy (1H‐MRS). Subsequently, we examined their whole‐body metabolic rate during walking and running at 2 m/s, exercises with comparable metabolic rates but distinct triceps surae muscle force and velocity demands (walking: low force, high velocity; running: high force, low velocity). Increasing triceps surae contraction velocity during cyclic contractions elevated net whole‐body metabolic rate for both typology groups. However, the slow group consumed substantially less net metabolic energy at the slowest contraction velocity, but the metabolic difference between groups diminished at faster velocities. Consistent with the more economic force production during slow contractions, the slow group exhibited lower metabolic rates than the fast group while running, whereas metabolic rates were similar during walking. These findings provide important insights into the influence of muscle fibre typology on whole‐body metabolic rate and emphasize the importance of considering muscle mechanical demands to understand muscle fibre typology related differences in whole‐body metabolic rates.
imageKey points
Muscle fibre typology is often suggested to affect whole‐body metabolic rate, yet convincing in vivo evidence is lacking.
Using isolated plantar flexor muscle contractions in individuals a priori selected for their predominantly slow or fast muscle fibre typology, we demonstrated that having predominantly slow muscle fibres provides a metabolic advantage during slow muscle contractions, but this benefit disappeared at faster contractions.
We extended these results to full‐body exercises, where we demonstrated that higher proportions of slow fibres associated with better economy during running but not when walking.
These findings provide important insights into the influence of muscle fibre typology on whole‐body metabolic rate and emphasize the importance of considering muscle mechanical demands to understand muscle fibre typology related differences in whole‐body metabolic rate.
Vancomycin heteroresistance caused by unstable tandem amplifications of the
vanM
gene cluster on linear conjugative plasmids in a clinical
Enterococcus faecium
Authors: Sun Lingyan , Zhuang Hemu , Chen Mengzhen , Chen Yan , Chen Yiyi , Shi Keren , Yu Yunsong 
Published: March 2024

ABSTRACT

Vancomycin heteroresistance is prone to missed detection and poses a risk of clinical treatment failure. We encountered one clinical
Enterococcus faecium
strain, SRR12, that carried a complete
vanM
gene cluster but was determined as susceptible to vancomycin using the broth microdilution method. However, distinct subcolonies appeared within the clear zone of inhibition in the E-test assay, one of which, named SRR12-v1, showed high-level resistance to vancomycin. SRR12 was confirmed as heteroresistant to vancomycin using population analysis profiling and displayed “revive” growth curves with a lengthy lag phase of over 13 hours when exposed to 2–32 mg/L vancomycin. The resistant subcolony SRR12-v1 was found to carry an identical
vanM
gene cluster to that of SRR12 but a significantly increased
vanM
copy number in the genome. Long-read whole genome sequencing revealed that a one-copy
vanM
gene cluster was located on a pELF1-like linear plasmid in SRR12. In comparison, tandem amplification of the
vanM
gene cluster jointed with IS
1216E
was seated on a linear plasmid in the genome of SRR12-v1. These amplifications of the
vanM
gene cluster were demonstrated as unstable and would decrease accompanied by fitness reversion after serial passaging for 50 generations under increasing vancomycin pressure or without antibiotic pressure but were relatively stable under constant vancomycin pressure. Further,
vanM
resistance in resistant variants was verified to be carried by conjugative plasmids with variable sizes using conjugation assays and S1-pulsed field gel electrophoresis blotting, suggesting the instability/flexibility of
vanM
cluster amplification in the genome and an increased risk of
vanM
resistance dissemination.
Sub-MIC levels of bedaquiline and clofazimine can select
Mycobacterium tuberculosis
mutants with increased MIC
Authors: Villellas Cristina , Stevenaert Frederik , Remmerie Bart , Andries Koen 
Published: March 2024

ABSTRACT

Multidrug-resistant tuberculosis (MDR-TB) patients not cured at the time of stopping treatment are exposed to Minimum Inhibitory Concentration (MIC) and sub-MIC levels for many months after discontinuing bedaquiline (BDQ) or clofazimine (CFZ) treatment.
In vitro
cultures treated with BDQ and CFZ sub-MIC concentrations clearly showed enrichment in the
Rv0678
mutant population, demonstrating that pre-existing
Rv0678
mutants can be selected by sub-MIC concentrations of BDQ and CFZ if not protected by an alternative MDR-TB treatment.
Bacterial hemophilin homologs and their specific type eleven secretor proteins have conserved roles in heme capture and are diversifying as a family
Authors: Grossman Alex S. , Gell David A. , Wu Derek G. , Carper Dana L. , Hettich Robert L. , Goodrich-Blair Heidi 
Published: March 2024

ABSTRACT

Cellular life relies on enzymes that require metals, which must be acquired from extracellular sources. Bacteria utilize surface and secreted proteins to acquire such valuable nutrients from their environment. These include the cargo proteins of the type eleven secretion system (T11SS), which have been connected to host specificity, metal homeostasis, and nutritional immunity evasion. This Sec-dependent, Gram-negative secretion system is encoded by organisms throughout the phylum Proteobacteria, including human pathogens
Neisseria meningitidis, Proteus mirabilis, Acinetobacter baumannii,
and
Haemophilus influenzae
. Experimentally verified T11SS-dependent cargo include
t
ransferrin-
b
inding
p
rotein B (TbpB), the hemophilin homologs
h
eme
r
eceptor
p
rotein C (HrpC),
h
emo
ph
ilin
A
(HphA), the immune evasion protein
f
actor-
H b
inding
p
rotein (fHbp), and the host symbiosis factor
n
ematode
i
ntestinal
l
ocalization protein C (NilC). Here, we examined the specificity of T11SS systems for their cognate cargo proteins using taxonomically distributed homolog pairs of T11SS and hemophilin cargo and explored the ligand binding ability of those hemophilin cargo homologs.
In vivo
expression in
Escherichia coli
of hemophilin homologs revealed that each is secreted in a specific manner by its cognate T11SS protein. Sequence analysis and structural modeling suggest that all hemophilin homologs share an N-terminal ligand-binding domain with the same topology as the ligand-binding domains of the
Haemophilus haemolyticus
heme binding protein (Hpl) and HphA. We term this signature feature of this group of proteins the hemophilin ligand-binding domain. Network analysis of hemophilin homologs revealed five subclusters and representatives from four of these showed variable heme-binding activities, which, combined with sequence-structure variation, suggests that hemophilins are diversifying in function.

IMPORTANCE
The secreted protein hemophilin and its homologs contribute to the survival of several bacterial symbionts within their respective host environments. Here, we compared taxonomically diverse hemophilin homologs and their paired Type 11 secretion systems (T11SS) to determine if heme binding and T11SS secretion are conserved characteristics of this family. We establish the existence of divergent hemophilin sub-families and describe structural features that contribute to distinct ligand-binding behaviors. Furthermore, we demonstrate that T11SS are specific for their cognate hemophilin family cargo proteins. Our work establishes that hemophilin homolog-T11SS pairs are diverging from each other, potentially evolving into novel ligand acquisition systems that provide competitive benefits in host niches.
Diagnostic accuracy of tongue swab testing on two automated tuberculosis diagnostic platforms, Cepheid Xpert MTB/RIF Ultra and Molbio Truenat MTB Ultima
Authors: Wood Rachel C. , Luabeya Angelique K. , Dragovich Rane B. , Olson Alaina M. , Lochner Katherine A. , Weigel Kris M. , Codsi Renée , Mulenga Humphrey , de Vos Margaretha , Kohli Mikashmi , Penn-Nicholson Adam , Hatherill Mark , Cangelosi Gerard A. 
Published: March 2024

ABSTRACT

Tongue dorsum swabbing is a potential alternative to sputum collection for tuberculosis (TB) testing. Previous studies showed that Cepheid Xpert MTB/RIF Ultra (Xpert Ultra) can detect
Mycobacterium tuberculosis
DNA on tongue swabs stored in buffer, with 72% sensitivity and 100% specificity relative to a sputum microbiological reference standard (sputum MRS). The present study evaluated a more convenient sample collection protocol (dry swab storage), combined with streamlined sample processing protocols, for evaluating two commercial TB diagnostic tests: Xpert Ultra and Molbio Truenat MTB Ultima (MTB Ultima). Copan FLOQSwabs were self-collected or collected by study workers from 321 participants in Western Cape, South Africa. All participants had symptoms suggestive of TB, and 245 of them had sputum MRS-confirmed TB (by sputum MGIT culture and/or Xpert Ultra). One tongue swab per participant was tested on Xpert Ultra, and another tongue swab was tested with MTB Ultima. Xpert Ultra was 75.5% sensitive and 100% specific relative to sputum MRS, similar to previous methods that used swabs stored in buffer. MTB Ultima was 71.6% sensitive and 96.9% specific relative to sputum MRS. When sample lysates that were false-negative or invalid by MTB Ultima were frozen, thawed, and re-tested, MTB Ultima sensitivity rose to 79.1%. Both tests were more sensitive with swabs from participants with higher sputum Xpert Ultra semi-quantitative results. Although additional development could improve diagnostic accuracy, these results further support tongue swabs as easy-to-collect samples for TB testing.

IMPORTANCE
Tongue dorsum swabbing is a promising alternative to sputum collection for tuberculosis (TB) testing. Our results lend further support for tongue swabs as exceptionally easy-to-collect samples for high-throughput TB testing.
Evaluation of analyte-specific reagents for the direct detection of
Pneumocystis jirovecii
Authors: Giffen Samantha R. , Stoeppler Elizabeth , Elliott Avian , Miller Melissa B. 
Published: March 2024

ABSTRACT

Pneumocystis jirovecii
pneumonia (PJP) is a serious and sometimes fatal infection occurring in immunocompromised individuals. High-risk patients include those with low CD4 counts due to human immunodeficiency virus infection and transplant recipients. The incidence of PJP is increasing, and rapid detection of PJP is needed to effectively target treatment and improve patient outcomes. A common method used is an immunofluorescent assay (IFA), which has limitations, including labor costs, low sensitivity, and requirement for expert interpretation. This study evaluates the performance of the DiaSorin Molecular
Pneumocystis jirovecii
analyte-specific reagent (ASR) in a laboratory-developed test (LDT) for the direct detection of
P. jirovecii
DNA without prior nucleic acid extraction. Respiratory samples (
n
= 135) previously tested by IFA from 111 patients were included. Using a composite standard of in-house IFA and reference lab PJP PCR, the percent positive agreement for the LDT using the DiaSorin ASR was 97.8% (90/92). The negative percent agreement was 97.7% (42/43). The lower limit of detection of the assay was determined to be 1,200 copies/mL in bronchoalveolar lavage fluid. Analytical specificity was assessed using cultures of oropharyngeal flora and common respiratory bacterial and fungal pathogens. No cross-reactivity was observed. Our study suggests that the DiaSorin
Pneumocystis
ASR accurately detects
P. jirovecii
DNA and demonstrates improved sensitivity compared to the IFA method.

IMPORTANCE
Our study is unique compared to other previously published studies on the DiaSorin analyte-specific reagent (ASR) because we focused on microbiological diagnostic methods commonly used (immunofluorescent assay) as opposed to pathology findings or reference PCR. In addition, in our materials and methods, we describe the protocol for the use of the DiaSorin ASR as a singleplex assay, which will allow other users to evaluate the ASR for clinical use in their lab.
Performance evaluation of machine-assisted interpretation of Gram stains from positive blood cultures
Authors: Walter Christian , Weissert Christoph , Gizewski Eve , Burckhardt Irene , Mannsperger Heiko , Hänselmann Siegfried , Busch Winfried , Zimmermann Stefan , Nolte Oliver 
Published: March 2024

ABSTRACT

Manual microscopy of Gram stains from positive blood cultures (PBCs) is crucial for diagnosing bloodstream infections but remains labor intensive, time consuming, and subjective. This study aimed to evaluate a scan and analysis system that combines fully automated digital microscopy with deep convolutional neural networks (CNNs) to assist the interpretation of Gram stains from PBCs for routine laboratory use. The CNN was trained to classify images of Gram stains based on staining and morphology into seven different classes: background/false-positive, Gram-positive cocci in clusters (GPCCL), Gram-positive cocci in pairs (GPCP), Gram-positive cocci in chains (GPCC), rod-shaped bacilli (RSB), yeasts, and polymicrobial specimens. A total of 1,555 Gram-stained slides of PBCs were scanned, pre-classified, and reviewed by medical professionals. The results of assisted Gram stain interpretation were compared to those of manual microscopy and cultural species identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The comparison of assisted Gram stain interpretation and manual microscopy yielded positive/negative percent agreement values of 95.8%/98.0% (GPCCL), 87.6%/99.3% (GPCP/GPCC), 97.4%/97.8% (RSB), 83.3%/99.3% (yeasts), and 87.0%/98.5% (negative/false positive). The assisted Gram stain interpretation, when compared to MALDI-TOF MS species identification, also yielded similar results. During the analytical performance study, assisted interpretation showed excellent reproducibility and repeatability. Any microorganism in PBCs should be detectable at the determined limit of detection of 10
5
CFU/mL. Although the CNN-based interpretation of Gram stains from PBCs is not yet ready for clinical implementation, it has potential for future integration and advancement.
Draft genome sequences of
Chryseobacterium
sp. MHB01,
Rhodococcus qingshengii
MHB02, and
Agrobacterium tumefaciens
MHB03 isolated from superabsorbent polymer granules inoculated with an arbuscular mycorrhizal fungus
Authors: Abdellatif Lobna , Huynh Amanda , Xu Renlin , Banchini Claudia , Akuma Mercy , Paré Louis , Stefani Franck , Tambong James T. 
Published: March 2024

ABSTRACT

Chryseobacterium
sp. MHB01,
Rhodococcus qingshengii
MHB02, and
Agrobacterium tumefaciens
MHB03 were isolated from superabsorbent polymer granules cultured with an arbuscular mycorrhizal fungus. Whole-genome sequencing of these three strains revealed genome sizes of 4.57 Mb, 7.13 Mb, and 5.49 Mb with G + C contents of 36.9%, 62.5%, and 58.2%, respectively.
The complete genome sequence of probiotic
Lactobacillus acidophilus
ATCC 9224 isolated from sour milk
Authors: Kumar Anand , Rawat Manmeet , Kunde Yuliya A. , Davenport Karen W. , Al-Sadi Rana , Chain Patrick Sam Guy , Ma Thomas Y. 
Published: March 2024

ABSTRACT

We present the complete genome sequence of the probiotic strain
Lactobacillus acidophilus
ATCC 9224. The genome sequence provides a valuable resource for investigating the phylogenetic evolution of this lineage and conducting comparative genomics with other
Lactobacillus
strains and species.
Draft genome sequence of
Neofusicoccum caryigenum
associated with pecan leaf dieback
Authors: Arthur Erin , Jo Young-Ki 
Published: March 2024

ABSTRACT

Pecan leaf dieback caused by
Neofusicoccum caryigenum
is an emerging disease in southeastern United States pecan orchards. In this study, a first draft
N. caryigenum
genome was sequenced and assembled. Genome size was estimated as 42.5 Mbp, and genome completeness was estimated as 97.4%.
Eight complete genome sequences of bacteria isolated from laboratory stock of giant kelp gametophytes
Authors: Tolentino Bernadeth , Nuzhdin Sergey 
Published: March 2024

ABSTRACT

We report whole-genome sequences of eight bacteria isolated from laboratory-kept
Macrocystis pyrifera
gametophytes. The bacterial culture collection is maintained in cryostorage and will be utilized in future applications as inoculants. The genomes were assembled using Oxford Nanopore Technology long-read sequencing.
Genome sequencing of
Pseudomonas aeruginosa
phages; UF_RH7 and UF_RH9
Authors: Hashemi Shahraki Abdolrazagh , Vahed Majid , Mirsaeidi Mehdi 
Published: March 2024

ABSTRACT

We have sequenced the genomes of two lytic phages, UF_RH7 and UF_RH9, which infect
Pseudomonas aeruginosa
. UF_RH7 belongs to
Casjensviridae
family and has a genome length of 58,217 bp and encodes 82 proteins. UF_RH9 belongs to
Caudoviricetes
class and has a genome length of 42,609 bp and encodes 55 proteins.
Draft genome sequencing of
Brucella melitensis
isolated from aborted Iraqi sheep
Authors: Khudhair Yahia I. , Ayyez Hayder Naji , Quiroz-Castañeda Rosa Estela , Martínez-Ocampo Fernando , Ben Said Mourad 
Published: March 2024

ABSTRACT

Brucellosis remains a significant zoonotic disease, with
Brucella melitensis
maintaining endemicity in Middle Eastern nations. This study presents the draft genome sequencing of an Iraqi
B. melitensis
strain, representing a crucial step in monitoring virulence, antimicrobial resistance, and exploring the diversity and evolution of the
Brucella
genus.
A comparative medical genomics approach may facilitate the interpretation of rare missense variation
Authors: Haque Bushra , Guirguis George , Curtis Meredith , Mohsin Hera , Walker Susan , Morrow Michelle M , Costain Gregory 
Published: March 2024

PurposeTo determine the degree to which likely causal missense variants of single-locus traits in domesticated species have features suggestive of pathogenicity in a human genomic context.MethodsWe extracted missense variants from the Online Mendelian Inheritance in Animals database for nine animals (cat, cattle, chicken, dog, goat, horse, pig, rabbit and sheep), mapped coordinates to the human reference genome and annotated variants using genome analysis tools. We also searched a private commercial laboratory database of genetic testing results from >400 000 individuals with suspected rare disorders.ResultsOf 339 variants that were mappable to the same residue and gene in the human genome, 56 had been previously classified with respect to pathogenicity: 31 (55.4%) pathogenic/likely pathogenic, 1 (1.8%) benign/likely benign and 24 (42.9%) uncertain/other. The odds ratio for a pathogenic/likely pathogenic classification in ClinVar was 7.0 (95% CI 4.1 to 12.0, p<0.0001), compared with all other germline missense variants in these same 220 genes. The remaining 283 variants disproportionately had allele frequencies and REVEL scores that supported pathogenicity.ConclusionCross-species comparisons could facilitate the interpretation of rare missense variation. These results provide further support for comparative medical genomics approaches that connect big data initiatives in human and veterinary genetics.
Risk factors for SARS-CoV-2 infection at a UK electricity-generating company: a test-negative design case-control study
Authors: Rutter Charlotte E , van Tongeren Martie , Fletcher Tony , Rhodes Sarah , Chen Yiqun , Hall Ian , Warren Nicholas , Pearce Neil 
Published: March 2024

ObjectivesIdentify workplace risk factors for SARS-CoV-2 infection, using data collected by a UK electricity-generating company.MethodsUsing a test-negative design case-control study, we estimated the OR of infection by job category, site, test reason, sex, vaccination status, vulnerability, site outage and site COVID-19 weekly risk rating, adjusting for age, test date and test type.ResultsFrom an original 80 077 COVID-19 tests, there were 70 646 included in the final analysis. Most exclusions were due to being visitor tests (5030) or tests after an individual first tested positive (2968).Women were less likely to test positive than men (OR=0.71; 95% CI 0.58 to 0.86). Test reason was strongly associated with positivity and although not a cause of infection itself, due to differing test regimes by area, it was a strong confounder for other variables. Compared with routine tests, tests due to symptoms were highest risk (94.99; 78.29 to 115.24), followed by close contact (16.73; 13.80 to 20.29) and broader-defined work contact 2.66 (1.99 to 3.56). After adjustment, we found little difference in risk by job category, but some differences by site with three sites showing substantially lower risks, and one site showing higher risks in the final model.ConclusionsIn general, infection risk was not associated with job category. Vulnerable individuals were at slightly lower risk, tests during outages were higher risk, vaccination showed no evidence of an effect on testing positive, and site COVID-19 risk rating did not show an ordered trend in positivity rates.
Clinical photodynamic therapy: The evolution of photodynamic therapy treatment of head and neck cancer
Authors: Biel Merrill A. 
Published: March 2024

The modern era of photodynamic therapy (PDT) treatment of human cancer began in earnest in 1978, with the publication by Dougherty et al. of the first large series of humans with refractory or recurrent skin cancers successfully treated with PDT using HpD (Photofrin). The first human series of head and neck cancer patients successfully treated with PDT (Photofrin) was published in 1985, by Keller et al. Since that time, numerous clinical investigators around the world have treated thousands of head and neck cancer patients with PDT in clinical trials. These head and neck cancer PDT clinical trials enrolled patients with various stages of disease, and locations of the tumor and were treated using a variety of photosensitizers. Head and neck cancer PDT treatments were performed as the primary treatment with the intent to cure, as a late-stage treatment for palliation of the tumor, or as an adjuvant or neoadjuvant treatment in combination with surgery, radiation, chemotherapy and most recently immunotherapy. Over the past five decades, head and neck cancer PDT has evolved as newer and more targeted photosensitizers became available for clinical use, as well as advances in laser and fiberoptic technologies allowing for the activating light to be successfully and more easily delivered deep into large invasive tumors. In addition, PDT can be accurately delivered using endoscopic, robotic, CT, ultrasound and MRI guidance thereby specifically targeting the tumor and reducing treatment morbidity. Significant progress has been achieved in the ease of use and treatment efficacy of head and neck cancer PDT in various stages of the disease.