bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of positive end expiratory pressure on non‐hypoxic apnea time and atelectasis during induction of anesthesia in infant: A randomized controlled trial
Authors: Kim Eun‐Hee , Park Jung‐Bin , Kang Pyoyoon , Ji Sang‐Hwan , Jang Young‐Eun , Lee Ji‐Hyun , Kim Jin‐Tae , Kim Hee‐Soo 
Published: July 2024

AbstractIntroductionThis study aimed to assess the impact of positive‐end‐expiratory pressure (PEEP) on the non‐hypoxic apnea time in infants during anesthesia induction with an inspired oxygen fraction of 0.8.MethodsThis age stratified randomized controlled trial included patients under 1 year of age. Preoxygenation was performed using an inspired oxygen fraction of 0.8 for 2 min. Inspired oxygen fraction of 0.8 was administered via a face mask with volume‐controlled ventilation at a tidal volume of 6 mL.kg−1, with or without 7 cmH2O of PEEP. Tracheal intubation was performed after 3 min of ventilation; however, it was disconnected from the breathing circuit. Ventilation was resumed once the pulse oximetry readings reached 95%. The primary outcome was the non‐hypoxic apnea time, defined as the time from the cessation of ventilation to achieving a pulse oximeter reading of 95%. The secondary outcome measures included the degree of atelectasis assessed by ultrasonography and the presence of gastric air insufflation.ResultsEighty‐four patients were included in the final analysis. In the positive end‐expiratory pressure group, the atelectasis score decreased (17.0 vs. 31.5, p < .001; mean difference and 95% CI of 11.6, 7.5–15.6), while the non‐hypoxic apnea time increased (80.1 s vs. 70.6 s, p = .005; mean difference and 95% CI of −9.4, −16.0 to −2.9), compared to the zero end‐expiratory pressure group, among infants who are 6 months old or younger, not in those aged older than 6 months.DiscussionThe application of positive end‐expiratory pressure reduced the incidence of atelectasis and extended the non‐hypoxic apnea time in infants who are 6 months old or younger. However, it did not affect the incidence of atelectasis nor the non‐hypoxic apnea time in patients aged older than 6 months.
Characterization of the alcohol biomarker phosphatidylethanol in donor whole blood and apheresis red blood cells: Implications for transfusion recipients
Authors: Kinard Theresa N. , Sharma Pragya , Alegria Kathy N. , Langman Loralie J. , Jannetto Paul J. , Snozek Christine L. H. 
Published: July 2024

AbstractIntroductionPhosphatidylethanol (PEth) is a long‐term marker of alcohol consumption used frequently in clinical scenarios such as liver transplant evaluation. Recent cases have demonstrated that packed red blood cell (pRBC) transfusion creates the potential for artificial elevation or decrease of observed PEth concentrations in recipients. Very little is known about the prevalence or stability of PEth in pRBCs.MethodsApheresis and whole‐blood (WB) donations were tested for PEth using liquid chromatography – tandem mass spectrometry with limit of quantitation 10 ng/mL. Units were stored under routine blood bank conditions to evaluate the stability of PEth and the impact of irradiation.ResultsOver 40% of apheresis and WB donors had PEth ≥10 ng/mL (maximum observed 587 ng/mL). As WB units were processed into component pRBCs, PEth concentrations increased and were higher than donor WB levels (EDTA sample) prior to collection (maximum observed 711 ng/mL). Storage for up to 5 weeks post donation resulted in mean 17.3% decrease in PEth‐positive units; in contrast to a prior report, we observed no PEth formation in units with negative (<10 ng/mL) baseline concentrations. Irradiation of pRBCs did not substantially affect PEth concentrations in either PEth‐positive or PEth‐negative units.DiscussionPEth concentrations in healthy blood donors may potentially confound alcohol use or abstinence assessment in pRBC recipients. Transfusion medicine services and clinical practices such as transplantation and behavioral medicine should recognize this phenomenon and collaborate on testing protocols to appropriately interpret PEth in pRBC recipients.
Seroprevalence of human brucellosis in Turkey: A comprehensive meta‐analysis
Authors: Kıran Pınar , Uçku Reyhan 
Published: July 2024

AbstractAimsBrucellosis remains a common zoonotic disease, in developing countries, as well as in Turkey where it is endemic, underdiagnosed, and underreported. The aim of this meta‐analysis was to provide a comprehensive estimate of seroprevalence with a large sample size, covering all regions of Turkey, including both grey literature and published studies.Methods and ResultsA systematic search was performed in MEDLINE (via PubMed), TürkMedline (National Health Sciences‐Periodicals Database), and YÖKSİS database (Higher Education Council Information System) until May 5th, 2023. The quality of the studies was evaluated independently using Joanna Briggs Institute (JBI) critical assessment tool for prevalence studies. A random‐effects model (DerSimion and Laird) was utilized to estimate the overall pooled prevalence. A sensitivity analysis was performed, excluding studies with a high risk of bias. The subgroup analyses and meta‐regression were conducted to explore sources of heterogeneity. Egger test and funnel plot were used to assess publication bias. The meta‐analysis included 30 studies in total published between 1999 and 2021 with 51,560 individuals. In Turkey, the pooled seroprevalence of human brucellosis was estimated to be 4.5% (95% confidence interval [CI]: 3.8%–5.3%). According to the subgroup analysis, a higher seroprevalence was found in rural areas (8.0%, 95% CI: 5.4%–10.7%), high‐risk occupational groups (9.9%, 95% CI: 5.3%–14.6%), and the Central East Anatolia Region (13%, 95% CI: 3.2%–22.8%). The meta‐regression analysis identified living in rural areas and certain geographic regions as significant risk factors associated with higher seroprevalence.ConclusionsThis meta‐analysis revealed a significant burden of human brucellosis in Turkey. The findings highlight the need for public health measures and targeted interventions to reduce the burden of this zoonotic disease, especially in rural areas, high‐risk occupational groups, and the East Anatolia Region.
Metapresence: a tool for accurate species detection in metagenomics based on the genome-wide distribution of mapping reads
Authors: Sanguineti Davide , Zampieri Guido , Treu Laura , Campanaro Stefano 
Published: July 2024

ABSTRACT

Shotgun metagenomics allows comprehensive sampling of the genomic information of microbes in a given environment and is a tool of choice for studying complex microbial systems. Mapping sequencing reads against a set of reference or metagenome-assembled genomes is in principle a simple and powerful approach to define the species-level composition of the microbial community under investigation. However, despite the widespread use of this approach, there is no established way to properly interpret the alignment results, with arbitrary relative abundance thresholds being routinely used to discriminate between present and absent species. Such an approach can be affected by significant biases, especially in the identification of rare species. Therefore, it is important to develop new metrics to overcome these biases. Here, we present Metapresence, a new tool to perform reliable identification of the species in metagenomic samples based on the distribution of mapped reads on the reference genomes. The analysis is based on two metrics describing the breadth of coverage and the genomic distance between consecutive reads. We demonstrate the high precision and wide applicability of the tool using data from various synthetic communities, a real mock community, and the gut microbiome of healthy individuals and antibiotic-associated-diarrhea patients. Overall, our results suggest that the proposed approach has a robust performance in hard-to-analyze microbial communities containing contaminated or closely related genomes in low abundance.

IMPORTANCE
Despite the prevalent use of genome-centric alignment-based methods to characterize microbial community composition, there lacks a standardized approach for accurately identifying the species within a sample. Currently, arbitrary relative abundance thresholds are commonly employed for this purpose. However, due to the inherent complexity of genome structure and biases associated with genome-centric approaches, this practice tends to be imprecise. Notably, it introduces significant biases, particularly in the identification of rare species. The method presented here addresses these limitations and contributes significantly to overcoming inaccuracies in precisely defining community composition, especially when dealing with rare members.
In-hospital areas with distinct maintenance and staff/patient traffic have specific microbiome profiles, functions, and resistomes
Authors: Duller Stefanie , Kumpitsch Christina , Moissl-Eichinger Christine , Wink Lisa , Koskinen Mora Kaisa , Mahnert Alexander 
Published: July 2024

ABSTRACT

Hospitals are subject to strict microbial control. Stringent cleaning and confinement measures in hospitals lead to a decrease in microbial diversity, but an increase in resistance genes. Given the rise of antimicrobial resistances and healthcare-associated infections, understanding the hospital microbiome and its resistome is crucial. This study compared the microbiome and resistome at different levels of confinement (CL) within a single hospital. Using amplicon sequencing, shotgun metagenomics, and genome/plasmid reconstruction, we demonstrate that microbial composition differs in a stable way between the CLs and that the most restrictive confinement level CL1 had the lowest microbial but the highest functional diversity. This CL also exhibited a greater abundance of functions related to virulence, disease, defense, and stress response. Comparison of antibiotic resistance also showed differences among CLs in terms of the selection process and specific mechanisms for antimicrobial/antibiotic resistance. The resistances found in the samples of CL1 were mostly mediated via antibiotic efflux pumps and were mainly located on chromosomes, whereas in the other, less restrictive CL antibiotic resistances were more present on plasmids. This could be of particular importance for patient-related areas (CL2), as the potential spread of antibiotic resistances could be a major concern in this area. Our results show that there are differences in the microbiome and resistome even within a single hospital, reflecting room utilization and confinement. Since restrictive confinement selects for resistant microorganisms, strategies are required to deepen our understanding of dynamic processes of microbiome and resistome within hospital environments.

IMPORTANCE
Effective measures to combat antibiotic resistances and healthcare-associated infections are urgently needed, including optimization of microbial control. However, previous studies have indicated that stringent control can lead to an increase in the resistance capacities of microbiomes on surfaces. This study adds to previous knowledge by focusing on the conditions in a single hospital, resolving the microbiomes and their resistomes in three different confinement levels (CL): operating room, patient-related areas, and non-patient-related areas. We were able to identify stable key taxa; profiled the capacities of taxa, functions, and antimicrobial resistances (AMR); and reconstruct genomes and plasmids in each CL. Our results show that the most restrictive CL indeed had the highest functional diversity, but that resistances were mostly encoded on chromosomes, indicating a lower possibility of resistance spread. However, clever strategies are still required to strike a balance between microbial control and selective pressures in environments where patients need protection.
Physiology, fast and slow: bacterial response to variable resource stoichiometry and dilution rate
Authors: Peoples Logan M. , Isanta-Navarro Jana , Bras Benedicta , Hand Brian K. , Rosenzweig Frank , Elser James J. , Church Matthew J. 
Published: July 2024

ABSTRACT

Microorganisms grow despite imbalances in the availability of nutrients and energy. The biochemical and elemental adjustments that bacteria employ to sustain growth when these resources are suboptimal are not well understood. We assessed how
Pseudomonas putida
KT2440 adjusts its physiology at differing dilution rates (to approximate growth rates) in response to carbon (C), nitrogen (N), and phosphorus (P) stress using chemostats. Cellular elemental and biomolecular pools were variable in response to different limiting resources at a slow dilution rate of 0.12 h
−1
, but these pools were more similar across treatments at a faster rate of 0.48 h
−1
. At slow dilution rates, limitation by P and C appeared to alter cell growth efficiencies as reflected by changes in cellular C quotas and rates of oxygen consumption, both of which were highest under P- and lowest under C- stress. Underlying these phenotypic changes was differential gene expression of terminal oxidases used for ATP generation that allows for increased energy generation efficiency. In all treatments under fast dilution rates, KT2440 formed aggregates and biofilms, a physiological response that hindered an accurate assessment of growth rate, but which could serve as a mechanism that allows cells to remain in conditions where growth is favorable. Our findings highlight the ways that microorganisms dynamically adjust their physiology under different resource supply conditions, with distinct mechanisms depending on the limiting resource at slow growth and convergence toward an aggregative phenotype with similar compositions under conditions that attempt to force fast growth.

IMPORTANCE

All organisms experience suboptimal growth conditions due to low nutrient and energy availability. Their ability to survive and reproduce under such conditions determines their evolutionary fitness. By imposing suboptimal resource ratios under different dilution rates on the model organism
Pseudomonas putida
KT2440, we show that this bacterium dynamically adjusts its elemental composition, morphology, pools of biomolecules, and levels of gene expression. By examining the ability of bacteria to respond to C:N:P imbalance, we can begin to understand how stoichiometric flexibility manifests at the cellular level and impacts the flow of energy and elements through ecosystems.
Evaluation of Xpert point-of-care assays for detection of HIV infection in persons using long-acting cabotegravir for pre-exposure prophylaxis
Authors: Fogel Jessica M. , Piwowar-Manning Estelle , Moser Amber , Hill Tinia , Ahmed Shahnaz , Cummings Vanessa , Mostafa Heba H. , Wang Zhe , Jennings Andrea , Gallardo-Cartagena Jorge A. , Figueroa María Inés , St Clair Marty , Rinehart Alex R. , Adeyeye Adeola , Rooney James F. , Cohen Myron S. , Grinsztejn Beatriz , Landovitz Raphael J. , Eshleman Susan H. ,   On behalf of the HPTN 083 Study Team
Published: July 2024

ABSTRACT

Detection of HIV infection may be challenging in persons using long-acting cabotegravir (CAB-LA) pre-exposure prophylaxis (PrEP) due to viral suppression and reduced/delayed antibody production. We evaluated two point-of-care tests for detecting HIV infection in persons who received CAB-LA in the HPTN 083 trial. Samples were obtained from 12 participants who received CAB-LA and had delayed detection of HIV infection using HIV rapid tests and an antigen/antibody test (52 plasma samples; 18 dried blood spot [DBS] samples). Plasma samples were tested with the Xpert HIV-1 Viral Load XC test (Xpert VL-XC); DBS samples were tested with the total nucleic acid Xpert HIV-1 Qual XC test (Xpert Qual-XC). Results from these assays were compared to results from three reference, laboratory-based, plasma RNA assays (Aptima HIV-1 Qualitative assay [Aptima Qual]; Aptima HIV-1 Quant DX Assay [Aptima Quant]; cobas HIV-1/HIV-2 Qualitative Test [cobas]). HIV RNA was detected with all four plasma assays for all samples with viral loads (VLs) ≥ 200 copies/mL; the number of samples with VLs < 200 copies/mL with HIV RNA detected was: Xpert VL-XC: 19/26 (73.1%); Aptima Qual: 17/26 (65.4%); Aptima Quant: 17/26 (65.4%); and cobas: 12/21 (57.1%). The Xpert Qual-XC assay was positive for all DBS samples with VLs ≥ 200 copies/mL and 1/10 DBS with VLs < 200 copies/mL. The performance of the Xpert VL-XC assay was comparable to the reference assays for detecting HIV infection in these cases. The Xpert Qual-XC assay was less sensitive than plasma-based HIV RNA assays for detecting HIV in the setting of CAB-LA PrEP.

IMPORTANCE
HIV RNA assays can detect HIV infections earlier than HIV rapid tests or Ag/Ab tests in persons using CAB-LA PrEP. Earlier HIV diagnosis could allow for earlier treatment initiation and reduced risk of INSTI resistance. POC tests may help detect HIV infection before CAB-LA administration and may be more accessible than laboratory-based assays in some settings. In this study, the POC Xpert VL-XC assay detected HIV RNA in most samples from individuals who received CAB-LA PrEP and had delayed detection of HIV infection with HIV rapid tests and an Ag/Ab test. The performance of this assay was similar to laboratory-based HIV RNA assays in this cohort. The POC Xpert Qual-XC assay detects both HIV RNA and DNA, with a higher viral load cutoff for RNA detection. This assay was negative for most lower viral load samples and did not offer an advantage for HIV screening in persons using CAB-LA PrEP.
Children and adolescents with primary headaches exhibit altered sensory profiles – a multi-modal investigation
Authors: Pieniak Michal , Höfer Berit , Knipping Jenny , Faria Vanda , Richter Matthias , Schriever Valentin A. , Haehner Antje , Gossrau Gudrun 
Published: July 2024

Abstract
Background
Pediatric headache is an increasing medical problem that has adverse effects on children’s quality of life, academic performance, and social functioning. Children with primary headaches exhibit enhanced sensory sensitivity compared to their healthy peers. However, comprehensive investigations including multimodal sensory sensitivity assessment are lacking. This study aimed to compare sensory sensitivity of children with primary headaches with their healthy peers across multiple sensory domains.

Methods
The study included 172 participants aged 6 to 17 years (M = 13.09, SD = 3.02 years; 120 girls). Of these 80 participants were patients with migraine, 23 were patients with tension-type headache, and 69 were healthy controls. The following sensory measures were obtained: Mechanical Detection Threshold (MDT), Mechanical Pain Threshold (MPT), Mechanical Pain Sensitivity (MPS), detection and pain threshold for Transcutaneous Electrical Nerve Stimulation (TENS), olfactory and intranasal trigeminal detection threshold, and odor identification ability. Sensory sensitivity was compared between groups with a series of Kruskal-Wallis tests. Binomial regression models were used to compare the relative utility of sensory sensitivity measures in classifying participants into patients and healthy controls, as well as into patients with migraine and tension-type headache.

Results
Patients with migraine had lower MPT measured at the forearm than patients with tension-type headaches and healthy controls. MPS was higher in patients with migraine than in healthy controls. All patients with headaches had lower detection threshold of TENS and higher olfactory sensitivity. Healthy controls showed increased intranasal trigeminal sensitivity. Scores in MPS, TENS, and olfactory and trigeminal thresholds were significantly predicting presence of primary headaches. Additionally, scores in MPT, olfactory and trigeminal threshold were positive predictors of type of headache.

Conclusions
Children with primary headaches exhibit different sensory profiles than healthy controls. The obtained results suggest presence of increased overall, multimodal sensitivity in children with primary headaches, what may negatively impact daily functioning and contribute to further pain chronification.

Trial registration
The study was registered in the German Registry of Clinical Trials (DRKS) DRKS00021062.
Design of a two functional permeable reactive barrier for synergistic enzymatic and microbial bioremediation of phenol-contaminated waters: laboratory column evaluation
Authors: Mirdamadian Sayed Hossein , Asad Sedigheh , Dastgheib Seyed Mohammad Mehdi , Moghimi Hamid 
Published: July 2024

AbstractThe present study aimed to develop a system using a combination of enzymatic and microbial degradation techniques for removing phenol from contaminated water. In our prior research, the HRP enzyme extracted from horseradish roots was utilized within a core-shell microcapsule to reduce phenolic shock, serving as a monolayer column. To complete the phenol removal process, a second column containing degrading microorganisms was added to the last column in this research. Phenol-degrading bacteria were isolated from different microbial sources on a phenolic base medium. Additionally, encapsulated calcium peroxide nanoparticles were used to provide dissolved oxygen for the microbial population. Results showed that the both isolated strains, WC1 and CC1, were able to completely remove phenol from the contaminated influent water the range within 5 to 7 days, respectively. Molecular identification showed 99.8% similarity for WC1 isolate to Stenotrophomonas rizophila strain e-p10 and 99.9% similarity for CC1 isolate to Bacillus cereus strain IAM 12,605. The results also indicated that columns using activated sludge as a microbial source had the highest removal rate, with the microbial biofilm completely removing 100% of the 100 mg/L phenol concentration in contaminated influent water after 40 days. Finally, the concurrent use of core-shell microcapsules containing enzymes and capsules containing Stenotrophomonas sp. WC1 strain in two continuous column reactors was able to completely remove phenol from polluted water with a concentration of 500 mg/L for a period of 20 days. The results suggest that a combination of enzymatic and microbial degrading systems can be used as a new system to remove phenol from polluted streams with higher concentrations of phenol by eliminating the shock of phenol on the microbial population.