bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deciphering reductive dehalogenase specificity through targeted mutagenesis of chloroalkane reductases
Authors: Picott Katherine J. , Bowers Connor M. , Edwards Elizabeth A. 
Published: February 2025

ABSTRACT

Reductive dehalogenases (RDases) are essential in the anaerobic degradation of various organohalide contaminants. This family of enzymes has broad sequence diversity, but high structural conservation. There have been few studies assessing how RDase amino acid sequences affect their substrate selectivity. Here, we focus on two chloroalkane RDases, CfrA and DcrA, which have 95% protein sequence identity but have diverged to have opposite substrate preferences. CfrA dechlorinates chloroform (CF) and 1,1,1-trichloroethane (TCA) but not 1,1-dichloroethane (DCA), while DcrA will dechlorinate 1,1-DCA but not CF or 1,1,1-TCA. We mutated several residues in the active site of CfrA to investigate a change in substrate preference and to identify which wild-type residues contribute the most to substrate specialization. We determined that no individual residue solely dictates substrate discrimination, but both Y80W and F125W mutations were needed to force CfrA to prefer 1,1-DCA as a substrate. When using 1,1,2-TCA as a substrate, CfrA predominately performs hydrogenolysis to 1,2-DCA, yet the introduction of the double mutant changed this preference to dihaloelimination (forming vinyl chloride). We use predictive protein models and substrate docking to predict what interactions are made between the enzyme and substrate to aid in selection. The residues of significance identified in this study are consistent with those identified from chloroethene RDases, suggesting residue locations with a particularly high impact on activity.

IMPORTANCE
Reductive dehalogenases (RDases) play an integral role in the removal of chlorinated solvents from the environment. These enzymes have specificity toward different chlorinated compounds, and it is known that natural variants of highly similar RDases can have distinct activities. How specific differences in protein sequence influence activity is largely unknown. In this study, we demonstrate that mutating a few residues within the active site of CfrA—a chloroform and trichloroethane-specific dehalogenase—changes its substrate preference to dichloroethane. We determine that only two mutations are needed to disrupt the native activity, underscoring the nuances in substrate-structure relationships in RDases. Though we are still far from predicting function from the sequence, this knowledge can give some insight into engineering RDases for new target contaminants.
Colonization or coinfection? A case report of
Mycobacterium avium
complex detected in a patient with pulmonary tuberculosis
Authors: Bui Tina I. , Rowe Jackson , Eberly Allison R. 
Published: February 2025

ABSTRACT

Background

Nontuberculous mycobacteria (NTM) infections have been increasingly reported in the literature; however, isolation of both NTM and
Mycobacterium tuberculosis
complex (MTBC) in respiratory samples may indicate transient NTM colonization rather than true coinfection. Distinguishing between NTM colonization and true infection is necessary for guiding appropriate antimicrobial treatment regimen.

Case Summary

Here, we describe a case of a 41-year-old immunocompetent female with pulmonary tuberculosis in which
Mycobacterium avium
and
Mycobacterium intracellulare
, both members of the
M. avium
complex (MAC), were independently identified with MTBC in two of three sputum cultures using Bruker Biotyper matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). After completing MTBC-targeted therapy, the patient fully returned to her baseline physical activity, and all subsequent cultures were negative for MTBC and MAC.

Conclusion
This case study underscores the challenges in the adjudication of colonization from coinfection in mixed mycobacterial specimens. Although there are microbiological guidelines for diagnosing independent NTM infections and MTBC infections, there is an unmet need for guidance on diagnosing and treating NTM in patients with pulmonary tuberculosis.
Persistent delay in maturation of the developing gut microbiota in infants with cystic fibrosis
Authors: Verster Adrian J. , Salerno Paige , Valls Rebecca , Barrack Kaitlyn , Price Courtney E. , McClure Emily A. , Madan Juliette C. , O’Toole George A. , Sanville Julie L. , Ross Benjamin D. 
Published: February 2025

ABSTRACT

The healthy human infant gut microbiome undergoes stereotypical changes in taxonomic composition between birth and maturation to an adult-like stable state. During this time, extensive communication between microbiota and the host immune system contributes to health status later in life. Although there are many reported associations between microbiota compositional alterations and disease in adults, less is known about how microbiome development is altered in pediatric diseases. One pediatric disease linked to altered gut microbiota composition is cystic fibrosis (CF), a multi-organ genetic disease involving impaired chloride secretion across epithelia and heightened inflammation both in the gut and at other body sites. Here, we use shotgun metagenomics to profile the strain-level composition and developmental dynamics of the infant fecal microbiota from several CF and non-CF longitudinal cohorts spanning from birth to greater than 36 months of life. We identify a set of keystone species that define microbiota development in early life in non-CF infants but are missing or decreased in relative abundance in infants with CF, resulting in a delayed pattern of microbiota maturation, persistent entrenchment in a transitional developmental phase, and subsequent failure to attain an adult-like stable microbiota. Delayed maturation is strongly associated with cumulative antibiotic treatments, and we also detect the increased relative abundance of oral-derived bacteria and higher levels of fungi in infants with CF, features that are associated with decreased gut bacterial density. These findings suggest the potential for future directed therapies targeted at overcoming developmental delays in microbiota maturation for infants with CF.

IMPORTANCE
The human gastrointestinal tract harbors a diversity of microbes that colonize upon birth and collectively contribute to host health throughout life. Infants with the disease cystic fibrosis (CF) harbor altered gut microbiota compared to non-CF counterparts, with lower levels of beneficial bacteria. How this altered population is established in infants with CF and how it develops over the first years of life is not well understood. By leveraging multiple large non-CF infant fecal metagenomic data sets and samples from a CF cohort collected prior to highly effective modulator therapy, we define microbiome maturation in infants up to 3 years of age. Our findings identify conserved age-diagnostic species in the non-CF infant microbiome that are diminished in abundance in CF counterparts that instead exhibit an enrichment of oral-derived bacteria and fungi associated with antibiotic exposure. Together, our study builds toward microbiota-targeted therapy to restore healthy microbiota dynamics in infants with CF.
Abundance of clinically relevant antimicrobial resistance genes in the golden jackal (
Canis aureus
) gut
Authors: Lapid Roi , Motro Yair , Craddock Hillary , Salah Ikram , King Roni , Winner Katherine , Kahila Bar-Gal Gila , Moran-Gilad Jacob 
Published: February 2025

ABSTRACT

The spread of antimicrobial resistance (AMR) is a critical One Health issue. Wildlife could act as reservoirs or vehicles of AMR bacteria (ARBs) and AMR genes (ARGs) but are relatively understudied. We sought to investigate clinically relevant ARGs in golden jackals (
Canis aureus
) thriving near human settlements in Israel. Fecal samples were collected from 111 jackals across four regions over a 10-month period. Various animal and spatio-temporal metadata were collected. Samples were analyzed by quantitative PCR (qPCR) for beta-lactamases (
bla
TEM,
bla
CTX-M15, and
bla
SHV),
qnrS
and
int1
. A subset of samples was subject to shotgun metagenomic sequencing followed by resistome and microbiome analyses. qPCR detected a high prevalence of ARGs, including beta-lactamases (
bla
TEM-1, 96.4%;
bla
CTX-M-15, 51.4%,
bla
SHV, 15.3%), fluoroquinolone resistance (
qnrS
, 87.4%), and class 1 integrons (
Int1
, 94.6%). The
bla
TEM-1 gene was found to be more prevalent in adult jackals compared to younger ones. Metagenomic analysis of a subset of samples revealed a diverse gut microbiome harboring a rich resistome with tetracycline resistance genes being the most prevalent. Metagenome-assembled genome analysis further identified several ARGs associated with clinically relevant bacteria. These findings highlight the potential role of golden jackals as reservoirs for AMR and emphasize the need for ongoing surveillance to better understand AMR transmission dynamics at the wildlife–human interface.

IMPORTANCE
The research highlights the potential role of the golden jackals as reservoirs for antimicrobial resistance (AMR). The high prevalence of clinically relevant AMR genes in these jackals emphasizes the need for ongoing surveillance and monitoring to better understand AMR transmission dynamics at the wildlife–human interface.
Trends in depression and anxiety prevalence by cancer status among US adults: analyses of the 2019-2022 National Health Interview Survey
Authors: Kim Ian , Lee Michelle , Begay Cynthia M , Lee Jonathan , Unger Jennifer 
Published: February 2025

ObjectiveTo examine trends in the prevalence of depression and anxiety during the COVID-19 pandemic among US adult cancer patients and survivors (CPS) in comparison to those of non-CPS (NCPS).Methods and analysisNational Health Interview Survey 2019–2022 data were analysed using spline logistic regression.ResultsA total of 115 664 participants completed the survey (mean age (SD), 52.8 (18.4) years; 54.3% female; 12.6% CPS). The age-adjusted prevalence of depression significantly increased from 26.53% in 2019 to 29.78% in 2022 among CPS, while that of anxiety increased from 24.02% in 2019 to 28.08% in 2022. Throughout the pandemic, there were consistently significant annual increases in the prevalence of both depression and anxiety with CPS experiencing significantly faster rates of increase compared with NCPS (average annual absolute increase 0.72% in NCPS vs 1.08% in CPS, p<0.01 for depression; 0.98% in NCPS vs 1.35% in CPS, p<0.01 for anxiety). Difficulty in social activity engagement emerged as the primary risk factor for both depression (adjusted OR (aOR), 7.38 (95% CI, 7.04 to 7.73), p<0.01) and anxiety disorders (aOR, 7.58 (95% CI, 7.23 to 7.95), p<0.01). Significant interactions were found between difficulty in social engagement and cancer status on the diagnoses of depression (aOR, 0.72 (95% CI, 0.63 to 0.83), p<0.01) and anxiety (aOR, 0.62 (95% CI, 0.55 to 0.70), p<0.01).ConclusionsThe notably higher prevalence and more rapid increase in rates of depression and anxiety disorders among CPS compared with NCPS underscore the disproportionate impact of the COVID-19 pandemic on CPS and the necessity of prioritising mental health support and interventions for this population.
Applying positive end-expiratory pressure before and during endotracheal tube removal versus extubation with concomitant aspiration: protocol for the randomised controlled multicentre EXSUPEEP trial
Authors: Sedillot Nicholas , Kallel Hela , Robine Adrien , Pineda Jose Arturo , Quenot Jean-Pierre , Servant Marion , Levrat Albrice , Damieux-Verdeau Clovis , Mezidi Mehdi , Thibert Nathalie , Bohé Julien , Ballesteros-Calzado Alvaro , Stevic Neven , Mahi Lena , Sigaud Florian , Maisonneuve Margaux , Thiery Guillaume , Prat Paul , Thille Arnaud W , Haouat Safia , Plantefeve Gaetan , Decullier Evelyne , Rabilloud Muriel , Bernon Pauline , Poncelin Yves , Bonnici Julie Catherine 
Published: February 2025

IntroductionThe optimal method for removing the endotracheal tube (ETT) during extubation in the intensive care unit (ICU) remains uncertain. Two methods are described for removing the ETT in ICU, namely the ‘Traditional technique’ with continuous aspiration during cuff deflation and ETT removal; and the ‘PEEP’ method, which consists in applying positive end-expiratory pressure (PEEP) before and during cuff deflation and ETT removal. Our hypothesis is that applying PEEP during extubation in the ICU would improve clinical outcome.Methods and analysisThis is a prospective, multicentre, randomised, open-label, controlled, superiority trial, analysed by intention-to-treat, comparing ETT removal with concomitant suction vs application of PEEP before and during ETT removal. In total, 424 patients will be recruited and randomly assigned in a 1:1 ratio to one of two groups, according to the strategy of ETT removal. The primary outcome is the number of days free from any mechanical ventilation within 28 days following extubation. Secondary outcomes include the reintubation rate up to 7 days after ETT removal, the cumulative duration of non-invasive ventilation up to 7 days following extubation, the rate of acute respiratory failure, the rate of acquired pneumonia during the first 7 days following ETT removal, the length of stay in ICU and in hospital and all-cause mortality at 28 days following ETT removal.Ethics and disseminationThe study was approved by the Ethics Committee ‘CPP Ile de France II’. Patients will be included after providing written informed consent. The results will be submitted for publication in peer-reviewed journals, and in national and international congresses.Trial registration numberNCT05147636.
Incidence and determinants of households’ catastrophic payments for TB care: evidence from a multi-country trial (EXIT-TB project) implemented in East Africa
Authors: Ngadaya Francis Donard , Philbert Doreen , Wilfred Amani , Mshiu Johnson Jeremia , Binyaruka Peter , Mnyambwa Nicholaus P , Kimaro Godfather , Mori Amani Thomas , Wandinga Steve , Mmbaga Blandina T , Kirenga Bruce J , Yimer Getnet , Mfinanga Sayoki , Ngadaya Esther 
Published: February 2025

BackgroundDespite free tuberculosis (TB) services in low-resource settings which are provided under countries’ respective National TB programmes, TB patients incur substantial costs when seeking care. These costs not only act as a barrier to access but also reduce adherence to TB treatment which further affects patients’ health outcomes and poses a financial burden to households. In the context of the EXIT-TB project implementation, we nested a patient cost study aiming at estimating the costs incurred by patients when seeking TB services. In addition, we also assessed the incidence and determinants of catastrophic health expenditure (CHE) among households affected by TB.MethodsA cross-sectional analytical study was carried out in four East African Countries, namely; Tanzania, Kenya, Uganda and Ethiopia alongside EXIT-TB project implementation from 2019 to 2022. Direct and indirect costs incurred by drug-sensitive TB patients were collected after they had received TB services. Costs were considered catastrophic if they exceeded 20% of annual household income. Cost data were collected in each country’s national currency and converted to 2023 US dollars afterwards.ResultsThe mean total cost incurred by patients when seeking TB care were US$130.85, US$97.90, US$84.63 and US$101.60 in Tanzania, Kenya, Uganda and Ethiopia, respectively. Overall, more than half (51.81%) of the TB-affected households experienced CHE due to TB. CHE was high among TB-affected households with poor socioeconomic status. TB patients residing in Ethiopia, households with >5 members, households with TB patients as household heads, unemployed and poor socioeconomic status were among the factors associated with a high incidence of CHE (p<0.05).ConclusionDespite the availability of free TB services in East Africa provided by the respective National TB programmes, more than half of TB-affected households experienced CHE due to TB. Our findings reinforce the need for cost mitigation policies among TB-affected households, particularly the worse offs so as to reduce the incidence of CHE and further impoverishment.
Relative importance and interactions of factors influencing low-value care provision: a factorial survey experiment among Swedish primary care physicians
Authors: Roczniewska Marta , Augustsson Hanna , Ingvarsson Sara , Hedberg Rundgren Emma , Szymański Kamil , von Thiele Schwarz Ulrica , Nilsen Per , Hasson Henna 
Published: February 2025

BackgroundLow-value care (LVC) describes practices that persist in healthcare, despite being ineffective, inefficient or causing harm. Several determinants for the provision of LVC have been identified, but understanding how these factors influence professionals’ decisions, individually and jointly, is a necessary next step to guide deimplementation.MethodsA factorial survey experiment was employed using vignettes that presented hypothetical medical scenarios among 593 Swedish primary care physicians. Each vignette varied systematically by factors such as patient age, patient request for the LVC, physician’s perception of this practice, practice cost to the primary care centre and time taken to deliver it. For each scenario, we measured the reported likelihood of providing the LVC. We collected information on the physician’s worry about missing a serious illness.ResultsPatient requests and physicians’ positive perceptions of the practice were the factors that increased the reported likelihood of providing LVC the most (by 14 and 13 percentage points (pp), respectively). When the LVC was low in cost or not time-consuming, patient requests further boosted the likelihood of provision by 29 and 18 pp. In contrast, credible evidence against the LVC reduced the role of patient requests by 11 pp. Physicians’ fear of missing a serious illness was linked with higher reported probability of providing LVC, and the credibility of the evidence against the LVC reduced the role of this concern.ConclusionsThe findings highlight that patient requests enhance the role of many determinants, while the credibility of evidence diminishes the impact of others. Overall, these findings point to the relevance of increased clinician knowledge about LVC, tools for patient communication and the use of decision support tools to reduce the uncertainty in decision-making.
Successful reperfusion accompanied by symptomatic intracranial hemorrhage (sICH) versus unsuccessful reperfusion without sICH after endovascular stroke thrombectomy: a post-hoc analysis of two randomized trials
Authors: Li Yanling , Fu Yusi , Feng Xinggang , Chen Lve , Luo Shiwei , Jiang Shunfu , Peng Huiyuan , Huang Xianjun , Zhang Wensheng , Huang Yihong , Zhang Min , Luo Genpei , Ge Fukui , Xu Jing , Huang Hanning , Guan Min , Chen Zhenze , Zi Wenjie , Yang Qingwu , Sang Hongfei , Qiu Zhongming , Li Mingchao , Nguyen Thanh N , Zhao Zhenqiang , Li Wei 
Published: February 2025

BackgroundFunctional outcomes in patients with acute ischemic stroke (AIS) with large vessel occlusion (LVO) undergoing endovascular treatment (EVT) with successful reperfusion (expanded Thrombolysis In Cerebral Infarction (eTICI) 2b-3) complicated by symptomatic intracranial hemorrhage (sICH) were compared with patients with unsuccessful reperfusion (eTICI 0–2a) without sICH.MethodsPatients enrolled in this post hoc analysis were from two Chinese multicenter, randomized controlled trials: the DEVT and the RESCUE BT registries. Patients with AIS who underwent EVT were categorized into two groups according to the state of reperfusion: eTICI 2b-3 with sICH and eTICI 0–2a without sICH. The primary outcome was the modified Rankin Scale (mRS) scores at 90 days. The safety outcomes included early neurological deterioration and 90-day mortality.Results161 patients were included in this cohort analysis, among whom 71 experienced eTICI 2b-3 with sICH, and 90 had eTICI 0–2a without sICH. After adjusting for potential confounding factors, patients in the eTICI 2b-3 with sICH group had worse mRS at 90 days compared with those in the eTICI 0–2a without sICH group in the adjusted analysis (median 6 (IQR 4–6) vs median 4 (IQR 3–6); adjusted common OR 0.39, 95% CI 0.17 to 0.66). There were also higher rates of very poor outcome (mRS 5–6, 70.4% vs 42.2%; OR 2.90, 95% CI 1.38 to 6.11), mortality (66.2% vs 32.2%; OR 0.48, 95% CI 0.30 to 0.79), and early neurological deterioration (81.7% vs 40.0%; OR 0.16, 95% CI 0.07 to 0.35) in the eTICI 2b-3 with sICH group versus the eTICI 0–2a without sICH group.ConclusionsSuccessful reperfusion complicated by sICH after EVT was associated with worse outcomes and higher mortality than unsuccessful reperfusion without sICH. These findings emphasize the need for additional efforts in assessing and managing post-EVT-associated sICH to optimize treatment strategies and improve outcomes.Trial registration numberDirect Endovascular Treatment for Large Vessel Occlusion Stroke;https://www.chictr.org.cn; ChiCTR-IOR-17013568.Intravenous Tirofiban Before Endovascular Thrombectomy for Acute Ischemic Stroke;https://www.chictr.org.cn; ChiCTR-INR-17014167.
Prediction of mortality risk in critically ill patients with systemic lupus erythematosus: a machine learning approach using the MIMIC-IV database
Authors: Chen Zhihan , Dai Yunfeng , Chen Yilin , Chen Han , Wu Huiping , Zhang Li 
Published: February 2025

ObjectiveEarly prediction of long-term outcomes in patients with systemic lupus erythematosus (SLE) remains a great challenge in clinical practice. Our study aims to develop and validate predictive models for the mortality risk.MethodsThis observational study identified patients with SLE requiring hospital admission from the Medical Information Mart for Intensive Care (MIMIC-IV) database. We downloaded data from Fujian Provincial Hospital as an external validation set. Variable selection was performed using the Least Absolute Shrinkage and Selection Operator (LASSO) regression. Then, we constructed two predictive models: a traditional nomogram based on logistic regression and a machine learning model employing a stacking ensemble approach. The predictive ability of the models was evaluated by the areas under the receiver operating characteristic curve (AUC) and the calibration curve.ResultsA total of 395 patients and 100 patients were enrolled respectively from MIMIC-IV database and the validation cohort. The LASSO regression identified 18 significant variables. Both models demonstrated good discrimination, with AUCs above 0.8. The machine learning model outperformed the nomogram in terms of precision and specificity, highlighting its potential superiority in risk prediction. The SHapley additive explanations analysis further elucidated the contribution of each variable to the model’s predictions, emphasising the importance of factors such as urine output, age, weight and alanine aminotransferase.ConclusionsThe machine learning model provides a superior tool for predicting mortality risk in patients with SLE, offering a basis for clinical decision-making and potential improvements in patient outcomes.