bluuebunny/crossref_metadata_2025_split huggingface dataset:
Perioperative methadone for posterior spinal fusion in adolescents: Results from a double‐blind randomized‐controlled trial
Authors: Fons Roger A. , Hainsworth Keri R. , Michlig Johanna , Jablonski Megan , Czarnecki Michelle L. , Weisman Steven J. 
Published: January 2024

AbstractBackgroundPosterior spinal fusion is the most common surgical procedure performed for correction of adolescent idiopathic scoliosis in the United States. Intraoperative methadone has been shown to improve pain control in adult patients undergoing complex spine surgery, and current pediatric studies show encouraging results; however, prospective randomized‐controlled trials are lacking in the pediatric literature.AimsWe conducted a single‐center double‐blind randomized‐controlled trial to compare intraoperative use of methadone to morphine in pediatric patients undergoing posterior spinal fusion.MethodsA total of 47 adolescents undergoing posterior spinal fusion were randomized (stratified by sex) to either a methadone (n = 25) or morphine (n = 22) group. The primary outcome was postoperative opioid consumption. Secondary outcomes included postoperative pain severity, opioid‐related side effects, and ratio of patient‐controlled analgesia injections: attempts as a behavioral index of uncontrolled pain.ResultsPatients in the methadone group consumed less total opioid postoperatively (median [interquartile range], 0.3 mg/kg [0.1, 0.5]) than patients in the morphine group (0.3 mg/kg [0.2, 0.6]), median difference [95% confidence interval] −0.07 [−0.2 to 0.02]; (p = .026). Despite the lower amount of opioid used postoperatively, pain scores for the methadone group (3.5 [3.0, 4.3]) were not significantly different from those in the morphine group (4.0 [3.2, 5.0]; p = .250). Groups did not differ on opioid‐related side effects.ConclusionsA two‐dose intraoperative methadone regimen resulted in decreased opioid consumption compared to morphine. Although the clinical significance of these results may be limited, the analgesic equipoise without increased opioid‐related side effects and potential for a lower incidence of chronic pain may tip the balance in favor of routine methadone use for adolescents undergoing posterior spinal fusion.
A precise balance of TETRASPANIN1/TORNADO2 activity is required for vascular proliferation and ground tissue patterning in Arabidopsis
Authors: Konstantinova Nataliia , Mor Eliana , Verhelst Eline , Nolf Jonah , Vereecken Kenzo , Wang Feng , Van Damme Daniel , De Rybel Bert , Glanc Matouš 
Published: January 2024

AbstractThe molecular mechanisms guiding oriented cell divisions in the root vascular tissues of Arabidopsis thaliana are still poorly characterised. By overlapping bulk and single‐cell transcriptomic datasets, we unveiled TETRASPANIN1 (TET1) as a putative regulator in this process. TET1 is expressed in root vascular cells, and loss‐of‐function mutants contain fewer vascular cell files. We further generated and characterised a CRISPR deletion mutant and showed, unlike previously described mutants, that the full knock out is additionally missing endodermal cells in a stochastic way. Finally, we show that HA‐tagged versions of TET1 are functional in contrast to fluorescent TET1 translational fusions. Immunostaining using HA‐TET1 lines complementing the mutant phenotype suggested a dual plasma membrane and intracellular localisation in the root vasculature and a polar membrane localisation in the young cortex, endodermal and initial cells. Taken together, we show that TET1 is involved in both vascular proliferation and ground tissue patterning. Our initial results pave the way for future work to decipher its precise mode of action.
On the expectations of equivariant matrix‐valued functions of Wishart and inverse Wishart matrices
Authors: Hillier Grant , Kan Raymond M. 
Published: January 2024

AbstractMany matrix‐valued functions of an Wishart matrix , , say, are homogeneous of degree in , and are equivariant under the conjugate action of the orthogonal group , that is, , . It is easy to see that the expectation of such a function is itself homogeneous of degree in , the covariance matrix, and are also equivariant under the action of on . The space of such homogeneous, equivariant, matrix‐valued functions is spanned by elements of the type , where and, for each , varies over the partitions of , and denotes the power‐sum symmetric function indexed by . In the analogous case where is replaced by , these elements are replaced by . In this paper, we derive recurrence relations and analytical expressions for the expectations of such functions. Our results provide highly efficient methods for the computation of all such moments.
Trans health training objectives: A scoping review
Authors: Ahmad Tehmina , Robinson Lilian , Uleryk Elizabeth , Yu Catherine 
Published: January 2024

AbstractBackgroundTransgender individuals are discriminated against in health care environments and consistently experience poorer health outcomes than their cisgender counterparts. Enhancing physician training in transgender‐specific health is critical to closing the transgender health gap.MethodsWe conducted a scoping review to identify transgender health training objectives in Internal Medicine and Internal Medicine Subspecialty residency programmes in Canada and the United States. A systematic search was conducted from 1946 to 15 February 2022. Studies were eligible for inclusion if they were written in English, included transgender training objectives, and were aimed at resident physicians in Internal Medicine or Internal Medicine Subspecialty training programmes in Canada or the United States.FindingsWe found 4048 papers, of which 11 were included for analysis. Transgender health training objectives were synthesised into five themes, including (1) terminology, physiology, and gender presentation, (2) gender‐affirming care and communication, (3) hormonal and surgical management, (4) routine health management and maintenance, and (5) equity, diversity, and inclusion in clinical care. The majority of objectives pertained to equity, diversity, and inclusion in clinical care, namely, respectful communication and non‐judgemental care of transgender patients.DiscussionOur findings provide a comprehensive overview of published transgender health objectives in Canada and the United States and highlight existing gaps in postgraduate medical education for Internal Medicine and Subspecialty programmes.ConclusionsWe argue a need for standardisation of transgender‐related residency training and suggest that postgraduate Internal Medicine programmes can utilise this review as a framework to begin enhancing transgender health education for their residents.
An Experimental Study on the Accuracy of Cumulative Damage Models in Gear Tooth Bending Fatigue
Authors: Anichowski Gabriel , Damm Riley , Kahraman Ahmet , Hong Isaac 
Published: January 2024

Abstract
Tooth bending fatigue failure is a primary design concern for gear designers in power transmission applications. Fracture of a gear tooth in operation results in overload conditions to adjacent teeth, which cascades into potential failure. Total loss of power transmission usually occurs within seconds of the primary failure. While standard constant stress amplitude fatigue evaluations are common to experimentally determine probabilistic stress–life (PSN) relationships, they do not directly measure the fatigue lives under complex, non-constant amplitude loading scenarios applied to gears in most applications. Various cumulative damage models exist to estimate fatigue life under duty cycle loading, but their accuracy is both material and stress state dependent. Most models are validated under only uniaxial stress states and for limited materials. There is a void of experimental data that would enable the evaluation of the accuracy of cumulative damage models for gear tooth bending fatigue in typical cases of carburized gear steels. This research study conducts a standard fatigue evaluation along with two sets of dual stress amplitude single tooth bending fatigue tests to empirically determine the effects of multi-stage loading. Various cumulative damage fatigue models are then employed to estimate the fatigue lives of the dual stress amplitude specimens, and the accuracy of each model is assessed.
Transposition mechanism of IS
Apl1
—the determinant of colistin resistance dissemination
Authors: Li Wei , He Zhien , Di Wei , Xu Weifeng , Li Yujie , Sun Baolin 
Published: January 2024

ABSTRACT

Multidrug-resistant
Enterobacteriaceae
, a prominent family of gram-negative pathogenic bacteria, causes a wide range of severe diseases. Strains carrying the mobile colistin resistance (
mcr-1
) gene show resistance to polymyxin, the last line of defense against multidrug-resistant gram-negative bacteria. However, the transmission of
mcr-1
is not well understood. In this study, genomes of
mcr-1
-positive strains were obtained from the NCBI database, revealing their widespread distribution in China. We also showed that IS
Apl1
, a crucial factor in
mcr-1
transmission, is capable of self-transposition. Moreover, the self-cyclization of IS
Apl1
is mediated by its own encoded transposase. The electrophoretic mobility shift assay experiment validated that the transposase can bind to the inverted repeats (IRs) on both ends, facilitating the cyclization of IS
Apl1
. Through knockout or shortening of IRs at both ends of IS
Apl1
, we demonstrated that the cyclization of IS
Apl1
is dependent on the sequences of the IRs at both ends. Simultaneously, altering the ATCG content of the bases at both ends of IS
Apl1
can impact the excision rate by modifying the binding ability between IRs and ISAPL1. Finally, we showed that heat-unstable nucleoid protein (HU) can inhibit IS
Apl1
transposition by binding to the IRs and preventing ISAPL1 binding and expression. In conclusion, the regulation of IS
Apl1
-self-circling is predominantly controlled by the inverted repeat (IR) sequence and the HU protein. This molecular mechanism deepens our comprehension of
mcr-1
dissemination.
sRNA molecules participate in hyperosmotic stress response regulation in
Sphingomonas melonis
TY
Authors: Wang Xiaoyu , Wang Lvjing , Wang Yihan , Fu Xueni , Wang Xuejun , Wu Hao , Wang Haixia , Lu Zhenmei 
Published: January 2024

ABSTRACT

Drought and salinity are ubiquitous environmental factors that pose hyperosmotic threats to microorganisms and impair their efficiency in performing environmental functions. However, bacteria have developed various responses and regulatory systems to cope with these abiotic challenges. Posttranscriptional regulation plays vital roles in regulating gene expression and cellular homeostasis, as hyperosmotic stress conditions can lead to the induction of specific small RNA molecules (sRNAs) that participate in stress response regulation. Here, we report a candidate functional sRNA landscape of
Sphingomonas melonis
TY under hyperosmotic stress, and 18 sRNAs were found with a clear response to hyperosmotic stress. These findings will help in the comprehensive analysis of sRNA regulation in
Sphingomonas
species. Weighted correlation network analysis revealed a 263 nucleotide sRNA, SNC251, which was transcribed from its own promoter and showed the most significant correlation with hyperosmotic response factors. Deletion of
snc251
affected biofilm formation and multiple cellular processes, including ribosome-related pathways, aromatic compound degradation, and the nicotine degradation capacity of
S. melonis
TY, while overexpression of SNC251 facilitated biofilm formation by TY under hyperosmotic stress. Two genes involved in the TonB system were further verified to be activated by SNC251, which also indicated that SNC251 is a
trans
-acting sRNA. Briefly, this research reports a landscape of sRNAs participating in the hyperosmotic stress response in
S. melonis
and reveals a novel sRNA, SNC251, which contributes to the
S. melonis
TY biofilm formation and thus enhances its hyperosmotic stress response ability.

IMPORTANCE

Sphingomonas
species play a vital role in plant defense and pollutant degradation and survive extensively under drought or salinity. Previous studies have focused on the transcriptional and translational responses of
Sphingomonas
under hyperosmotic stress, but the posttranscriptional regulation of small RNA molecules (sRNAs) is also crucial for quickly modulating cellular processes to adapt dynamically to osmotic environments. In addition, the current knowledge of sRNAs in
Sphingomonas
is extremely scarce. This research revealed a novel sRNA landscape of
Sphingomonas melonis
and will greatly enhance our understanding of sRNAs’ acting mechanisms in the hyperosmotic stress response.
Listeria monocytogenes
utilizes glutathione and limited inorganic sulfur compounds as sources of essential cysteine
Authors: Berude John C. , Kennouche Paul , Reniere Michelle L. , Portnoy Daniel A. 
Published: January 2024

ABSTRACT

Listeria monocytogenes
(
Lm
) is a Gram-positive facultative intracellular pathogen that leads a biphasic lifecycle, transitioning its metabolism and selectively inducing virulence genes when it encounters mammalian hosts. Virulence gene expression is controlled by the master virulence regulator PrfA, which is allosterically activated by the host- and bacterially derived glutathione (GSH). The amino acid cysteine is the rate-limiting substrate for GSH synthesis in bacteria and is essential for bacterial growth. Unlike many bacteria,
Lm
is auxotrophic for cysteine and must import exogenous cysteine for growth and virulence. GSH is enriched in the host cytoplasm, and previous work suggests that
Lm
utilizes exogenous GSH for PrfA activation. Despite these observations, the import mechanism(s) for GSH remains elusive. Analysis of known GSH importers predicted a homologous importer in
Lm
comprised of the Ctp ABC transporter and the OppDF ATPases of the Opp oligopeptide importer. Here, we demonstrated that the Ctp complex is a high-affinity GSH/GSSG importer that is required for
Lm
growth at physiologically relevant concentrations. Furthermore, we demonstrated that OppDF is required for GSH/GSSG import in an Opp-independent manner. These data support a model where Ctp and OppDF form a unique complex for GSH/GSSG import that supports growth and pathogenesis. In addition, we show that
Lm
utilizes the inorganic sulfur sources thiosulfate and H
2
S for growth in a CysK-dependent manner in the absence of other cysteine sources. These findings suggest a pathoadaptive role for partial cysteine auxotrophy in
Lm
, where locally high GSH/GSSG or inorganic sulfur concentrations may signal arrival to distinct host niches.
Fitness benefits of a synonymous substitution in an ancient EF-Tu gene depend on the genetic background
Authors: McGrath Kaitlyn M. , Russell Steven J. , Fer Evrim , Garmendia Eva , Hosgel Ali , Baltrus David A. , Kaçar Betül 
Published: January 2024

ABSTRACT

Synonymous mutations are changes to DNA sequence, which occur within translated genes but which do not affect the protein sequence. Although often referred to as silent mutations, evidence suggests that synonymous mutations can affect gene expression, mRNA stability, and even translation efficiency. A collection of both experimental and bioinformatic data has shown that synonymous mutations can impact cell phenotype, yet less is known about the molecular mechanisms and potential of beneficial or adaptive effects of such changes within evolved populations. Here, we report a beneficial synonymous mutation acquired via experimental evolution in an essential gene variant encoding the translation elongation factor protein EF-Tu. We demonstrate that this particular synonymous mutation increases EF-Tu mRNA and protein levels as well as global polysome abundance on RNA transcripts. Although presence of the synonymous mutation is clearly causative of such changes, we also demonstrate that fitness benefits are highly contingent on other potentiating mutations present within the genetic background in which the mutation arose. Our results underscore the importance of beneficial synonymous mutations, especially those that affect levels of proteins that are key for cellular processes.

IMPORTANCE

This study explores the degree to which synonymous mutations in essential genes can influence adaptation in bacteria. An experimental system whereby an
Escherichia coli
strain harboring an engineered translation protein elongation factor-Tu (EF-Tu) was subjected to laboratory evolution. We find that a synonymous mutation acquired on the gene encoding for EF-Tu is conditionally beneficial for bacterial fitness. Our findings provide insight into the importance of the genetic background when a synonymous substitution is favored by natural selection and how such changes have the potential to impact evolution when critical cellular processes are involved.
Mycobacterial FtsEX-RipC interaction is required for normal growth and cell morphology in rifampicin and low ionic strength conditions
Authors: Samuels Veneshley , Mulelu Andani E. , Ndlovu Hlumani , Marakalala Mohlopheni J. 
Published: January 2024

ABSTRACT

Tuberculosis, a lung disease caused by
Mycobacterium tuberculosis
(
Mtb
), remains a major global health problem ranking as the second leading cause of death from a single infectious agent. One of the major factors contributing toward
Mtb’s
success as a pathogen is its unique cell wall and its ability to counteract various arms of the host’s immune response. A recent genome-scale study profiled a list of candidate genes that are predicted to be essential for
Mtb
survival of host-mediated responses. One candidate was FtsEX, a protein complex composed of an ATP-binding domain, FtsE, and a transmembrane domain, FtsX. FtsEX functions through interaction with a periplasmic hydrolase, RipC. Homologs of FtsEX exist in other bacteria and have been linked with playing a key role in regulating peptidoglycan hydrolysis during cell elongation and division. Here, we report on
Mycobacterium smegmatis,
FtsE, FtsX, and RipC and their protective roles in stressful conditions. We demonstrate that the individual genes of FtsEX complex and RipC are not essential for survival in normal growth conditions but conditionally essential in low-salt media and antibiotic-treated media. Growth defects in these conditions were characterized by short and bulgy cells as well as elongated filamentous cells. Our results suggest that FtsE, FtsX, and RipC are required for both normal cell elongation and division and ultimately for survival in stressful conditions.

IMPORTANCE

Mycobacterial cell growth and division are coordinated with regulated peptidoglycan hydrolysis. Understanding cell wall gene complexes that govern normal cell division and elongation will aid in the development of tools to disarm the ability of mycobacteria to survive immune-like and antibiotic stresses. We combined genetic analyses and scanning electron microscopy to analyze morphological changes of mycobacterial FtsEX and RipC mutants in stressful conditions. We demonstrate that FtsE, FtsX, FtsEX, and RipC are conditionally required for the survival of
Mycobacterium smegmatis
during rifampicin treatment and in low-salt conditions. Growth defects in these conditions were characterized by short and bulgy cells as well as elongated filamentous cells. We also show that the FtsEX-RipC interaction is essential for the survival of
M. smegmatis
in rifampicin. Our results suggest that FtsE, FtsX, and RipC are required for normal cell wall regulation and ultimately for survival in stressful conditions.
Development and evaluation of three automated media pooling and molecular diagnostic systems for the detection of SARS-CoV-2
Authors: Matsumura Yasufumi , Noguchi Taro , Shinohara Koh , Yamamoto Masaki , Nagao Miki 
Published: January 2024

ABSTRACT

Pooled testing combined with molecular diagnostics for the detection of SARS-CoV-2 is a promising method that can increase testing capacities and save costs. However, pooled testing is also associated with the risks of decreased test sensitivity and specificity. To perform reliable pooled testing, we developed and validated three automated media pooling and molecular diagnostic systems. These pooling systems (geneLEAD-PS, Panther-PS, and Biomek-PS) comprised existing automated molecular detection platforms, corresponding automated media pooling devices, and laboratory information management systems. Analytical sensitivity analysis and mock sample evaluation were performed, and the obtained data were used to determine the sizes of the pool for the validation study. In the validation study, a total of 2,448, 3,228, and 6,420 upper respiratory samples were used for geneLEAD-PS, Panther-PS, and Biomek-PS, respectively, and the diagnostic performances were compared with the reference RT‒PCR assay. A pool size of 6 for geneLEAD-PS and a pool size of 4 for Panther-PS and Biomek-PS were selected for the validation studies. All three systems showed high positive percent agreement values of ≥90.5% and negative percent agreement values of ≥99.8% for any specimen type. Pooled testing resulted in a 65%–71% reduction in cost per sample. The testing capacities of geneLEAD-PS, Panther-PS, and Biomek-PS were 144 samples in 3 hours, 384 samples in 5.5 hours, and 376 samples in 4 hours, respectively. The developed pooling systems showed robust diagnostic performances and will increase the testing capacities of molecular diagnostic tests while saving costs and may contribute to infection control of COVID-19.

IMPORTANCE
During the COVID-19 pandemic, there have been surges in demand for accurate molecular diagnostic testing and laboratory supply shortages. Pooled testing combined with highly sensitive molecular testing, which entails mixing multiple samples as a single sample, is a promising approach to increase testing capacities while reducing the use of consumables. However, pooled testing is associated with risks that compromise diagnostic performance, such as false negatives due to dilution of positive samples or false positives due to cross-contamination. To perform reliable pooled testing, three different pooling systems (an automated pooling device, an automated molecular detection platform, and a laboratory information management system) were developed to accurately interpret pooled testing results. These three systems were validated using multiple clinical samples and showed high concordance with individual testing. The developed pooling systems will contribute to increasing reliable molecular testing capacities while using fewer consumables and saving costs.