bluuebunny/crossref_metadata_2025_split huggingface dataset:
Draft genomic sequence for uropathogenic
Staphylococcus saprophyticus
ATCC 49453
Authors: Yang Yishan , Sommers Christopher H. , Liu Yanhong 
Published: February 2024

ABSTRACT

Staphylococcus saprophyticus
, a common contaminant of foods, causes urinary tract infections in humans. Here, we report the draft genomic sequence for
S. saprophyticus
ATCC 49453, which is currently being used in food safety research.
Characterization of the genomic sequence of a circo-like virus and of three chaphamaparvoviruses detected in mute swan (
Cygnus olor
)
Authors: François Sarah , Hill Sarah C. , Perrins Christopher M. , Pybus Oliver G. 
Published: February 2024

ABSTRACT

We report the complete genomes of four ssDNA viruses: a circular replication-associated protein-encoding single-stranded DNA virus belonging to a clade previously detected only in mammals, and three chaphamaparvoviruses, which were detected by viromic surveillance of mute swan (
Cygnus olor
) fecal samples from the United Kingdom.
Complete genome sequence of
Parabacteroides distasonis
strain GP102, isolated from the cecum of a morbid pregnant laboratory guinea pig (
Cavia porcellus
)
Authors: Wang Sharon X. , Summage-West Christine V. , Kim Sung Guk 
Published: February 2024

ABSTRACT

Parabacteroides distasonis
is an anaerobic bacterium with ambivalent health effects.
P. distasonis
strain GP102 was isolated from the cecum content of a morbid pregnant laboratory guinea pig (
Cavia porcellus
). The genome consists of one circular 5.39-Mbp chromosome with a G + C content of 44.79%.
Nanopore adaptive sampling effectively enriches bacterial plasmids
Authors: Ulrich Jens-Uwe , Epping Lennard , Pilz Tanja , Walther Birgit , Stingl Kerstin , Semmler Torsten , Renard Bernhard Y. 
Published: February 2024

ABSTRACT

Bacterial plasmids play a major role in the spread of antibiotic resistance genes. However, their characterization via DNA sequencing suffers from the low abundance of plasmid DNA in those samples. Although sample preparation methods can enrich the proportion of plasmid DNA before sequencing, these methods are expensive and laborious, and they might introduce a bias by enriching only for specific plasmid DNA sequences. Nanopore adaptive sampling could overcome these issues by rejecting uninteresting DNA molecules during the sequencing process. In this study, we assess the application of adaptive sampling for the enrichment of low-abundant plasmids in known bacterial isolates using two different adaptive sampling tools. We show that a significant enrichment can be achieved even on expired flow cells. By applying adaptive sampling, we also improve the quality of
de novo
plasmid assemblies and reduce the sequencing time. However, our experiments also highlight issues with adaptive sampling if target and non-target sequences span similar regions.

IMPORTANCE

Antimicrobial resistance causes millions of deaths every year. Mobile genetic elements like bacterial plasmids are key drivers for the dissemination of antimicrobial resistance genes. This makes the characterization of plasmids via DNA sequencing an important tool for clinical microbiologists. Since plasmids are often underrepresented in bacterial samples, plasmid sequencing can be challenging and laborious. To accelerate the sequencing process, we evaluate nanopore adaptive sampling as an
in silico
method for the enrichment of low-abundant plasmids. Our results show the potential of this cost-efficient method for future plasmid research but also indicate issues that arise from using reference sequences.
Inhibition of SARS-CoV-2 replication by a ssDNA aptamer targeting the nucleocapsid protein
Authors: Huang Yanping , Huang Congcong , Chen Junkai , Chen Siwei , Li Bei , Li Jian , Jin Zhixiong , Zhang Qiwei , Pan Pan , Du Weixing , Liu Long , Liu Zhixin 
Published: February 2024

ABSTRACT

The nucleocapsid protein of SARS-CoV-2 plays significant roles in viral assembly, immune evasion, and viral stability. Due to its immunogenicity, high expression levels during COVID-19, and conservation across viral strains, it represents an attractive target for antiviral treatment. In this study, we identified and characterized a single-stranded DNA aptamer, N-Apt17, which effectively disrupts the liquid-liquid phase separation (LLPS) mediated by the N protein. To enhance the aptamer’s stability, a circular bivalent form, cb-N-Apt17, was designed and evaluated. Our findings demonstrated that cb-N-Apt17 exhibited improved stability, enhanced binding affinity, and superior inhibition of N protein LLPS; thus, it has the potential inhibition ability on viral replication. These results provide valuable evidence supporting the potential of cb-N-Apt17 as a promising candidate for the development of antiviral therapies against COVID-19.

IMPORTANCE

Variants of SARS-CoV-2 pose a significant challenge to currently available COVID-19 vaccines and therapies due to the rapid epitope changes observed in the viral spike protein. However, the nucleocapsid (N) protein of SARS-CoV-2, a highly conserved structural protein, offers promising potential as a target for inhibiting viral replication. The N protein forms complexes with genomic RNA, interacts with other viral structural proteins during virion assembly, and plays a critical role in evading host innate immunity by impairing interferon production during viral infection. In this investigation, we discovered a single-stranded DNA aptamer, designated as N-Apt17, exhibiting remarkable affinity and specificity for the N protein. Notably, N-Apt17 disrupts the liquid-liquid phase separation (LLPS) of the N protein. To enhance the stability and molecular recognition capabilities of N-Apt17, we designed a circular bivalent DNA aptamer termed cb-N-Apt17. In both
in vivo
and
in vitro
experiments, cb-N-Apt17 exhibited increased stability, enhanced binding affinity, and superior LLPS disrupting ability. Thus, our study provides essential proof-of-principle evidence supporting the further development of cb-N-Apt17 as a therapeutic candidate for COVID-19.
Prevalence of vision zero action plans or strategies: USA, 2021
Authors: Webber Bryant J , Whitfield Geoffrey P , Rose Kenneth M , Stowe Ellen W , Zaganjor Hatidza , Ederer David J , Fulton Janet E 
Published: February 2024

BackgroundVision Zero is a strategy to eliminate traffic fatalities and to promote equitable mobility options for all road users. Using a nationally representative survey, we aimed to estimate the prevalence of Vision Zero action plans or strategies in the USA.MethodsMunicipal officials were surveyed in 2021. In this cross-sectional study, we calculated the prevalence of Vision Zero plans or strategies and compared municipalities with adjusted prevalence ratios (PR) to account for region and sociodemographic characteristics.ResultsAmong 1955 municipalities participating in the survey (question-specific response rate: 44.3%), the prevalence of a Vision Zero action plan or strategy was 7.7%; 70.5% respondednoand 21.8%don’t know. Prevalence was 4.8% in small municipalities (1000–2499 residents), 20.3% in medium-large municipalities (50 000–124 999 residents; PR=4.1), and 37.8% in large municipalities (≥125 000 residents; PR=7.6).ConclusionThe prevalence of Vision Zero plans and strategies across the USA is low. Additional adoption of Vision Zero plans and strategies could help address traffic fatalities.
Effects of ingesting beverages containing glycerol and sodium with isomaltulose or sucrose on fluid retention in young adults: a single-blind, randomized crossover trial
Authors: Otsuka Junto , Okamoto Yumi , Enoki Yasuaki , Maejima Daisuke , Fujii Naoto , Kenny Glen P. , Mündel Toby , Cotter James D. , Amano Tatsuro 
Published: February 2024

We evaluated changes in hyperhydration and beverage hydration index (BHI, a composite measure of fluid balance after consuming a test beverage relative to water) during resting, induced by the consumption of beverages containing glycerol and sodium supplemented with fast-absorbing sucrose or slow-absorbing isomaltulose. In a randomized crossover, single-blinded protocol (clinical trials registry: UMIN000042644), 14 young physically active adults (three women) consumed 1 L of beverage containing either 7% glycerol + 0.5% sodium (Gly + Na), Gly + Na plus 7% sucrose (Gly + Na + Suc), Gly + Na plus 7% isomaltulose (Gly + Na + Iso), or water (CON) over a 40 min period. We assessed the change in plasma volume (ΔPV), BHI (calculated from cumulative urine output following consumption of water relative to that of the beverage), and blood glucose and sodium for 180 min after initiating ingestion. Total urine volume was reduced in all beverages containing glycerol and sodium compared to CON (all P ≤ 0.002). The addition of isomaltulose increased BHI by ∼45% (3.43 ± 1.0 vs. 2.50 ± 0.7 for Gly + Na, P = 0.011) whereas sucrose did not (2.6 ± 0.6, P = 0.826). The PV expansion was earliest for Gly + Na (30 min), slower for Gly + Na + Suc (90 min), and slowest for Gly + Na + Iso (120 min) with a concomitant lag in the increase of blood glucose and sodium concentrations. Supplementation of beverages containing glycerol and sodium with isomaltulose but not sucrose enhances BHI from those of glycerol and sodium only under a resting state, likely due to the slow absorption of isomaltulose-derived monosaccharides (i.e., glucose and fructose).
Picturing QCD jets in anisotropic matter: from jet shapes to energy energy correlators
Authors: Barata João , Milhano José Guilherme , Sadofyev Andrey V. 
Published: February 2024

AbstractRecent theoretical developments in the description of jet evolution in the quark gluon plasma have allowed to account for the effects of hydrodynamic gradients in the medium modified jet spectra. These constitute a crucial step towards using jets as tomographic probes of the nuclear matter they traverse. In this work, we complement these studies by providing leading order calculations of widely studied jet observables, taking into account matter anisotropies. We show that the energy distribution inside a jet is pushed towards the direction of the largest matter anisotropy, while the away region is depleted. As a consequence, the jet mass and girth gain a non-trivial azimuthal dependence, with the average value of the distribution increasing along the direction of largest gradients. However, we find that, for these jet shapes, matter anisotropic effects can be potentially suppressed by vacuum Sudakov factors. We argue that the recently proposed measurements of energy correlations within jets do not suffer from such effects, with the azimuthal dependence being visible in a large angular window, regardless of the shape of the distribution.
Mitochondrial and Cytosolic One-Carbon Metabolism Is a Targetable Metabolic Vulnerability in Cisplatin-Resistant Ovarian Cancer
Authors: Wallace-Povirk Adrianne , O'Connor Carrie , Dekhne Aamod S. , Bao Xun , Nayeen Md. Junayed , Schneider Mathew , Katinas Jade M. , Wong-Roushar Jennifer , Kim Seongho , Polin Lisa , Li Jing , Back Jessica B. , Dann Charles E. , Gangjee Aleem , Hou Zhanjun , Matherly Larry H. 
Published: February 2024

Abstract
One-carbon (C1) metabolism is compartmentalized between the cytosol and mitochondria with the mitochondrial C1 pathway as the major source of glycine and C1 units for cellular biosynthesis. Expression of mitochondrial C1 genes including SLC25A32, serine hydroxymethyl transferase (SHMT) 2, 5,10-methylene tetrahydrofolate dehydrogenase 2, and 5,10-methylene tetrahydrofolate dehydrogenase 1-like was significantly elevated in primary epithelial ovarian cancer (EOC) specimens compared with normal ovaries. 5-Substituted pyrrolo[3,2-d]pyrimidine antifolates (AGF347, AGF359, AGF362) inhibited proliferation of cisplatin-sensitive (A2780, CaOV3, IGROV1) and cisplatin-resistant (A2780-E80, SKOV3) EOC cells. In SKOV3 and A2780-E80 cells, colony formation was inhibited. AGF347 induced apoptosis in SKOV3 cells. In IGROV1 cells, AGF347 was transported by folate receptor (FR) α. AGF347 was also transported into IGROV1 and SKOV3 cells by the proton-coupled folate transporter (SLC46A1) and the reduced folate carrier (SLC19A1). AGF347 accumulated to high levels in the cytosol and mitochondria of SKOV3 cells. By targeted metabolomics with [2,3,3–2H]L-serine, AGF347, AGF359, and AGF362 inhibited SHMT2 in the mitochondria. In the cytosol, SHMT1 and de novo purine biosynthesis (i.e., glycinamide ribonucleotide formyltransferase, 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase) were targeted; AGF359 also inhibited thymidylate synthase. Antifolate treatments of SKOV3 cells depleted cellular glycine, mitochondrial NADH and glutathione, and showed synergistic in vitro inhibition toward SKOV3 and A2780-E80 cells when combined with cisplatin. In vivo studies with subcutaneous SKOV3 EOC xenografts in SCID mice confirmed significant antitumor efficacy of AGF347. Collectively, our studies demonstrate a unique metabolic vulnerability in EOC involving mitochondrial and cytosolic C1 metabolism, which offers a promising new platform for therapy.
Gsα Regulates Macrophage Foam Cell Formation During Atherosclerosis
Authors: Ma Chang , Li Yihui , Tian Mi , Deng Qiming , Qin Xiaoteng , Lu Hanlin , Gao Jiangang , Chen Min , Weinstein Lee S. , Zhang Mei , Bu Peili , Yang Jianmin , Zhang Yun , Zhang Cheng , Zhang Wencheng 
Published: February 2024

BACKGROUND:
Many cardiovascular pathologies are induced by signaling through G-protein-coupled receptors via Gsα (G protein stimulatory α subunit) proteins. However, the specific cellular mechanisms that are driven by Gsα and contribute to the development of atherosclerosis remain unclear.

METHODS:

High-throughput screening involving data from single-cell and bulk sequencing were used to explore the expression of Gsα in atherosclerosis. The differentially expression and activity of Gsα were analyzed by immunofluorescence and cAMP measurements. Macrophage-specific Gsα knockout (Mac-Gsα
KO
) mice were generated to study the effect on atherosclerosis. The role of Gsα was determined by transplanting bone marrow and performing assays for foam cell formation, Dil-ox-LDL (oxidized low-density lipoprotein) uptake, chromatin immunoprecipitation, and luciferase reporter assays.

RESULTS:

ScRNA-seq showed elevated
Gnas
in atherosclerotic mouse aorta’s cholesterol metabolism macrophage cluster, while bulk sequencing confirmed increased
GNAS
expression in human plaque macrophage content. A significant upregulation of Gsα and active Gsα occurred in macrophages from human and mouse plaques. Ox-LDL could translocate Gsα from macrophage lipid rafts in short-term and promote
Gnas
transcription through ERK1/2 activation and C/EBPβ phosphorylation via oxidative stress in long-term. Atherosclerotic lesions from Mac-Gsα
KO
mice displayed decreased lipid deposition compared with those from control mice. Additionally, Gsα deficiency alleviated lipid uptake and foam cell formation. Mechanistically, Gsα increased the levels of cAMP and transcriptional activity of the cAMP response element binding protein, which resulted in increased expression of CD36 and SR-A1. In the translational experiments, inhibiting Gsα activation with suramin or cpGN13 reduced lipid uptake, foam cell formation, and the progression of atherosclerotic plaques in mice in vivo.

CONCLUSIONS:
Gsα activation is enhanced during atherosclerotic progression and increases lipid uptake and foam cell formation. The genetic or chemical inactivation of Gsα inhibit the development of atherosclerosis in mice, suggesting that drugs targeting Gsα may be useful in the treatment of atherosclerosis.
How Do Patients and Otolaryngologists Define Dizziness?
Authors: Murphy Brianna L. , Fischer Jakob L. , Tolisano Anthony M. , Navarro Alvaro I. , Trinh Lily , Abuzeid Waleed M. , Humphreys Ian M. , Akbar Nadeem A. , Shah Sharan , Schneider John S. , Riley Charles A. , McCoul Edward D. 
Published: February 2024

Objective: To assess for differences in how patients and otolaryngologists define the term dizziness. Methods: Between June 2020 and December 2022, otolaryngology clinicians and consecutive patients at 5 academic otolaryngology institutions across the United States were asked to define the term “dizziness” by completing a semantics-based questionnaire containing 20 common descriptors of the term within 5 symptom domains (imbalance-related, lightheadedness-related, motion-related, vision-related, and pain-related). The primary outcome was differences between patient and clinician perceptions of dizzy-related symptoms. Secondary outcomes included differences among patient populations by geographic location. Results: Responses were obtained from 271 patients and 31 otolaryngologists. Patients and otolaryngologists selected 7.7 ± 3.5 and 7.1 ± 4.3 symptoms, respectively. Most patients (266, 98.2%) selected from more than 1 domain and 17 (6.3%) patients identified symptoms from all 5 domains. Patients and clinicians were equally likely to define dizziness using terms from the imbalance (difference, −2.3%; 95% CI, −13.2%, 8.6%), lightheadedness (−14.1%; −29.2%, 1.0%), and motion-related (9.4; −0.3, 19.1) domains. Patients were more likely to include terms from the vision-related (23.6%; 10.5, 36.8) and pain-related (18.2%; 10.3%, 26.1%) domains. There were minor variations in how patients defined dizziness based on geographic location. Conclusions: Patients and otolaryngologists commonly described dizziness using symptoms related to imbalance, lightheadedness, and motion. Patients were more likely to use vision or pain-related terms. Understanding of these semantic differences may enable more effective patient-clinician communication.
Meeting the Aerobic and Muscle-Strengthening Physical Activity Guidelines Among Older US Adults, National Health Interview Survey 1998–2018
Authors: Hyde Eric T. , Brown David R. , Webber Bryant J. , Piercy Katrina L. , Omura John D. , Rose Ken , Whitfield Geoffrey P. 
Published: February 2024

The Physical Activity Guidelines for Americans, second edition, recommends older adults participate in ≥150 minutes per week of moderate-intensity equivalent aerobic activity and ≥2 days per week of muscle-strengthening activity. We estimated prevalence and trends of meeting the guidelines among US adults aged ≥65 years from 1998 to 2018. Using the 1998–2018 National Health Interview Survey, we estimated the prevalence of meeting aerobic, muscle-strengthening, and combined physical activity guidelines stratified by age group, sex, race and ethnicity, and education level. Within age groups, we calculated prevalence differences by sociodemographic categories. Prevalence of meeting each guideline increased for all age groups and most sociodemographic subgroups. The increased magnitude of meeting the combined guideline from 1998–2000 to 2016–2018 differed across levels of educational attainment for most age groups. Despite increasing over time, the prevalence among older adults of meeting physical activity guidelines remains low (range for combined guideline: 7.2%–17.2%).
Continuous Versus Intermittent Control Cuff Pressure for Preventing Ventilator-Associated Pneumonia: An Updated Meta-Analysis
Authors: Wu Yanshuo , Li Yanan , Sun Meirong , Bu Jingjing , Zhao Congcong , Hu Zhenjie , Yin Yanling 
Published: February 2024

Objective This study aimed to evaluate the effect of continuous control cuff pressure (CCCP) versus intermittent control cuff pressure (ICCP) for the prevention of ventilator-associated pneumonia (VAP) in critically ill patients. Methods Relevant literature was searched in several databases, including PubMed, Embase, Web of Science, ProQuest, the Cochrane Library, Wanfang Database and China National Knowledge Infrastructure between inception and September 2022. Randomized controlled trials were considered eligible if they compared CCCP with ICCP for the prevention of VAP in critically ill patients. This meta-analysis was performed using the RevMan 5.3 and Trial Sequential Analysis 0.9 software packages. The Grading of Recommendations Assessment, Development and Evaluation (GRADE) framework was used to assess the level of evidence. Results We identified 14 randomized control trials with a total of 2080 patients. Meta-analysis revealed that CCCP was associated with a significantly lower incidence of VAP compared with ICCP (relative risk [RR] = 0.52; 95% confidence interval [CI]: 0.37-0.74; P < 0.001), although considerable heterogeneity was observed ( I2 = 71%). Conducting trial sequential analysis confirmed the finding, and the GRADE level was moderate. Subgroup analysis demonstrated that CCCP combined with subglottic secretion drainage (SSD) had a more significant effect on reducing VAP (RR = 0.39; 95% CI = 0.29-0.52; P < 0.001). The effect of CCCP on ventilator-associated respiratory infection (VARI) incidence was uncertain (RR = 0.81; 95% CI = 0.53-1.24; P = 0.34; I2 = 61%). Additionally, CCCP significantly reduced the duration of mechanical ventilation (MV) (mean difference [MD] = −2.42 days; 95% CI = −4.71-0.12; P = 0.04; I2 = 87%). Descriptive analysis showed that CCCP improved the qualified rate of cuff pressure. However, no significant differences were found in the length of intensive care unit (ICU) stay (MD = 2.42 days; 95% CI = −1.84-6.68; P = 0.27) and ICU mortality (RR = 0.86; 95% CI = 0.74-1.00; P = 0.05). Conclusion Our findings suggest that the combination of CCCP and SSD can reduce the incidence of VAP and the duration of MV and maintain the stability of cuff pressure. A combination of CCCP and SSD applications is suggested for preventing VAP.
Immature Platelet Fraction and Clinical Outcomes in Patients Undergoing Transcatheter Aortic Valve Implantation
Authors: Oppenheim Lee , Loutati Ranel , Marmor David , Perel Nimrod , Tabi Meir , Taha Louay , Dvir Danny , Shuvy Mony , Jubeh Rami , Glikson Michael , Asher Elad 
Published: February 2024

Introduction Immature platelets or reticulated platelets are newly released thrombocytes. They can be identified by their large size and high RNA cytoplasm concentration. Immature platelet fraction (IPF) represents the percentage of immature circulative platelets relative to the total number of platelets. The role of IPF in patients undergoing transcatheter aortic valve implantation (TAVI) is unknown. The aim of the current trial was to assess the levels of IPF in patients undergoing TAVI and correlation with clinical outcomes. Material and Methods Immature platelet fraction levels were measured 3 times in all patients (preprocedure, 1-2 days post-procedure and 1-month post-procedure). Immature platelet fraction measurement was carried out using an autoanalyzer (Sysmex XE-2100). Patients were followed for 12 months. Primary outcomes were defined as complications during hospitalizations, rehospitalization, and mortality. Results Fifty-one patients were included in the study. Mean age was 79.8 (±9.6), and 28 (55%) were women. Twenty-one patients (41%) had complications: Of them, 6 of 21 (29%) occurred during hospitalizations (2—vascular complications; 2—sepsis, 2—implantation of a pacemaker), 9 of 21 (43%) patients were rehospitalized after the index admission, and 6 patients died during the follow-up period. Multivariate Cox regression analysis found that IPF < 7% in at least one of the 3 tests was associated with worse outcomes (hazard ratio 3.42; 95% CI 1.11-10.5, P = .032). Conclusion Immature platelet fraction >7% in patients undergoing TAVI is associated with worse outcomes. Further studies are needed to better understand this phenomenon.