bluuebunny/crossref_metadata_2025_split huggingface dataset:
ATG7(2) Interacts With Metabolic Proteins and Regulates Central Energy Metabolism
Authors: Ostacolo Kevin , López García de Lomana Adrián , Larat Clémence , Hjaltalin Valgerdur , Holm Kristrun Yr , Hlynsdóttir Sigríður S. , Soucheray Margaret , Sooman Linda , Rolfsson Ottar , Krogan Nevan J. , Steingrimsson Eirikur , Swaney Danielle L. , Ogmundsdottir Margret H. 
Published: April 2024

ABSTRACTMacroautophagy/autophagy is an essential catabolic process that targets a wide variety of cellular components including proteins, organelles, and pathogens. ATG7, a protein involved in the autophagy process, plays a crucial role in maintaining cellular homeostasis and can contribute to the development of diseases such as cancer. ATG7 initiates autophagy by facilitating the lipidation of the ATG8 proteins in the growing autophagosome membrane. The noncanonical isoform ATG7(2) is unable to perform ATG8 lipidation; however, its cellular regulation and function are unknown. Here, we uncovered a distinct regulation and function of ATG7(2) in contrast with ATG7(1), the canonical isoform. First, affinity‐purification mass spectrometry analysis revealed that ATG7(2) establishes direct protein–protein interactions (PPIs) with metabolic proteins, whereas ATG7(1) primarily interacts with autophagy machinery proteins. Furthermore, we identified that ATG7(2) mediates a decrease in metabolic activity, highlighting a novel splice‐dependent function of this important autophagy protein. Then, we found a divergent expression pattern of ATG7(1) and ATG7(2) across human tissues. Conclusively, our work uncovers the divergent patterns of expression, protein interactions, and function of ATG7(2) in contrast to ATG7(1). These findings suggest a molecular switch between main catabolic processes through isoform‐dependent expression of a key autophagy gene.
Human ST3Gal II and ST6GalNAc IV genes increase human serum‐mediated cytotoxicity to xenogeneic cells
Authors: Choi Hyunju , Song Kwon‐Ho , Kim Hee‐Do , Park Jun‐Young , Lee Young‐Choon , Choi Hee‐Jung , Kim Cheorl‐Ho 
Published: April 2024

AbstractCarbohydrate‐antigens widely existed on glycoproteins and glycosphingolipids of all mammalian cells play a crucial role in self‐defense and immunity. Xeno‐reactive antibodies included in natural human sera play a protecting role in an acute phase‐rejection of xenotransplantation. In this study, we investigated the effect of an alteration of glycosylation‐pattern, caused by human sialyltransferases such as hST3Gal II or hST6GalNAc IV, on human serum mediated cytotoxicity in pig kidney PK15 cells. From LDH cytotoxicity assay, cytotoxicity to human serum was significantly increased in hST3Gal II and hST6GalNAc IV‐transfected PK15 cells, as compared to the control. In the hST6Gal I‐carrying cells, the cytotoxicity to human serum was rather decreased. Moreover, flow cytometry analysis revealed that an alteration of pig glycosylation‐pattern by hST3Gal II or hST6GalNAc IV influences on a binding of human IgM or IgG, respectively, in pig kidney cells, regardless of Gal antigen alteration. Finally, we found that hST6GalNAc IV contributed to increase of terminal disialylated tetrasaccharide structure, disialyl T antigen, as evidenced by increase of the MAL II lectin binding capacity in the hST6GalNAc IV‐transfected PK15 cells, compared with control. Therefore, our results suggest that carbohydrate antigens, such as disialyl T antigen, newly synthesized by the ST3Gal II‐ and ST6GalNAc IV are potentially believed to be new xeno‐reactive elements.
Effects of Leading-Edge Blowing Control and Reduced Frequency on Airfoil Aerodynamic Performances
Authors: Chen Yang , Avital Eldad , Willams John , Santra Srimanta , Seifert Avraham 
Published: April 2024

Abstract
Airfoil leading-edge fluid-blowing control is computationally studied to improve aerodynamic efficiency. The fluid injection momentum coefficient Cμ (the ratio of injection to incoming square velocities times the slot's width to airfoil's half chord length) varies from 0.5% to 5.4%. Both static and dynamic conditions are investigated for a NACA0018 airfoil at low speed and Reynolds number of 250 k based on the airfoil's chord length. The airfoil is dynamically pitched at a reduced frequency (the pitching tangential speed to the freestream speed ratio), varying between 0.0078 and 0.2. Reynolds-averaged Navier–Stokes (RANS) and unsteady RANS (URANS) is used in the simulations as based on the Transition SST and Spalart–Allmaras models, generally achieving good agreement with experimental results in lift and drag coefficients and in the pressure coefficient distributions along the airfoil. It is found that oscillating the airfoil can delay stall, as expected, in dynamic stall (DS). Leading-edge blowing control can also significantly delay stall both in static and dynamic conditions as long as sufficient momentum is applied to the control. On the other hand, for a small Cμ such as 0.5%, the leading-edge control worsens the performance and hastens the appearance of stall in both static and dynamic conditions. The airfoil's oscillation reduces the differences between pitch-up and pitch-down aerodynamic performances. Detailed analysis of vorticity, pressure, velocity, and streamline contours is given to provide plausible explanations and insight to the flow.
Effect of Tip Gap Size on the Tip Flow Structure and Turbulence Generation in a Low Reynolds Number Compressor Cascade
Authors: Shi Lei , Hongwei Ma , Wang Huajie , Wang Tianyou 
Published: April 2024

Abstract
Efficient and compact axial compressors are currently undergoing rapid development for use in microcooling systems and small-scale vehicles. Limited experimental work concentrates on the inner flow field of the compressors working at such low Reynolds numbers (Re∼104). This study examines the vortical structures and the resulting turbulence production in the transitional flow over a C4 compressor blade at a Reynolds number Re of 24,000, with a specific focus on the impact of tip clearance. The particle image velocimetry measurements reveal the tip flow structures in detail, including the tip leakage vortex (TLV) and its induced complex vortical structures. The tip secondary flow at the low Reynolds number can be divided as the tip leakage flow (TLF)/vortex and transitional boundary layer both at the end walls and the blade surfaces. The TLV propagates at the highest spanwise positions and farthest pitchwise positions at the middle tip gap size (τ/C = 3%) for the three tip gap sizes investigated. The tip flow fluctuations decrease from τ/C = 5% to τ/C = 3% and then increase from τ/C = 3% to τ/C = 1%. The spatial distribution, streamwise evolution, and individual Reynolds normal stress components contributing to the turbulent kinetic energy (TKE) are discussed. The primary contributors to the turbulence generation are examined to elucidate the flow mechanism leading to the distinct anisotropic turbulence structure in the tip region with various tip gap sizes.
Difficult-to-treat (DTR)
Pseudomonas aeruginosa
harboring Verona-Integron metallo-β-lactamase (
bla
VIM
): infection management and molecular analysis
Authors: Vega Ana D. , DeRonde Kailynn , Jimenez Adriana , Piazza Michael , Vu Christine , Martinez Octavio , Rojas Laura J. , Marshall Steven , Yasmin Mohamad , Bonomo Robert A. , Abbo Lilian M. 
Published: April 2024

ABSTRACT

Pseudomonas aeruginosa
harboring Verona Integron-encoded metallo-β-lactamase enzymes (VIM-CRPA) have been associated with infection outbreaks in several parts of the world. In the US, however, VIM-CRPA remain rare. Starting in December 2018, we identified a cluster of cases in our institution. Herein, we present our epidemiological investigation and strategies to control/manage these challenging infections. This study was conducted in a large academic healthcare system in Miami, FL, between December 2018 and January 2022. Patients were prospectively identified via rapid molecular diagnostics when cultures revealed carbapenem-resistant
P. aeruginosa
. Alerts were received in real time by the antimicrobial stewardship program and infection prevention teams. Upon alert recognition, a series of interventions were performed as a coordinated effort. A retrospective chart review was conducted to collect patient demographics, antimicrobial therapy, and clinical outcomes. Thirty-nine VIM-CRPA isolates led to infection in 21 patients. The majority were male (76.2%); the median age was 52 years. The majority were mechanically ventilated (
n
= 15/21; 71.4%); 47.6% (
n
= 10/21) received renal replacement therapy at the time of index culture. Respiratory (
n
= 20/39; 51.3%) or bloodstream (
n
= 13/39; 33.3%) were the most common sources. Most infections (
n
= 23/37; 62.2%) were treated with an aztreonam–avibactam regimen. Six patients (28.6%) expired within 30 days of index VIM-CRPA infection. Fourteen isolates were selected for whole genome sequencing. Most of them belonged to ST111 (12/14), and they all carried bla
VIM-2
chromosomally. This report describes the clinical experience treating serious VIM-CRPA infections with either aztreonam–ceftazidime/avibactam or cefiderocol in combination with other agents. The importance of implementing infection prevention strategies to curb VIM-CRPA outbreaks is also demonstrated.
Breaking the habit: isolating nicotine-degrading bacteria in undergraduate microbiology teaching labs
Authors: Mastenbrook J. , Pathak E. , Beaver C. , Stull F. , Koestler B. J. 
Published: April 2024

ABSTRACT

Nicotine is a major alkaloid in tobacco plants and an addictive component of tobacco products. Some bacteria grow on tobacco plants and have evolved the ability to metabolize nicotine. As part of our microbiology teaching lab, we used minimal media with nicotine as the sole carbon source to isolate nicotine-degrading bacteria from tobacco leaves and commercial tobacco products. Students then identified these bacteria using 16S rRNA sequencing and biochemical assays and assessed their ability to catabolize nicotine using UV spectroscopy. Students were able to isolate and identify 14 distinct genera that can metabolize nicotine. This modification of the commonly used unknown project gave students firsthand experience using selective media, and students got the opportunity to work with largely uncharacterized microbes with a real-world connection to public health, which increased student engagement. Students had the opportunity to think critically about why nicotine-degrading microorganisms associate with tobacco plants, why there are different bacteria that use the same specialized metabolism, and how these organisms are isolated from other bacteria using selective media.
Metagenome-assembled genomes of the methanogenic enrichment obtained from drilling fluid wastes stored in permafrost
Authors: Shcherbakova V. A. , Rechkina V. I. , Trubitsyn V. E. 
Published: April 2024

ABSTRACT

We studied methanogenic enrichment (Kha) from spent drilling fluid stored in permafrost, Kharasavey (71°10′50″N 66°51′50″E) gas field located in the western part of the Yamal Peninsula. The metagenome-assembled genomes showed that Kha consists of representatives of
Methanosarcina
,
Methanobacterium
,
Proteinifillum
, and
Synergistetes
genera.
Bacterial and fungal community structures in Hulun Lake are regulated by both stochastic processes and environmental factors
Authors: Shang Yongquan , Wang Xibao , Wu Xiaoyang , Dou Huashan , Wei Qinguo , Wang Qi , Liu Gang , Sun Guolei , Wang Lidong , Zhang Honghai 
Published: April 2024

ABSTRACT

Microorganisms are a crucial component of lake ecosystems and significant contributors to biogeochemical cycles. However, the understanding of how primary microorganism groups (e.g., bacteria and fungi) are distributed and constructed within different lake habitats is lacking. We investigated the bacterial and fungal communities of Hulun Lake using high-throughput sequencing techniques targeting 16S rRNA and Internal Transcribed Spacer 2 genes, including a range of ecological and statistical methodologies. Our findings reveal that environmental factors have high spatial and temporal variability. The composition and community structures vary significantly depending on differences in habitats. Variance partitioning analysis showed that environmental and geographical factors accounted for <20% of the community variation. Canonical correlation analysis showed that among the environmental factors, temperature, pH, and dissolved oxygen had strong control over microbial communities. However, the microbial communities (bacterial and fungal) were primarily controlled by the dispersal limitations of stochastic processes. This study offers fresh perspectives regarding the maintenance mechanism of bacterial and fungal biodiversity in lake ecosystems, especially regarding the responses of microbial communities under identical environmental stress.

IMPORTANCE
Lake ecosystems are an important part of the freshwater ecosystem. Lake microorganisms play an important role in material circulation and energy flow owing to their unique enzymatic and metabolic capacity. In this study, we observed that bacterial and fungal communities varied widely in the water and sediments of Hulun Lake. The primary factor affecting their formation was identified as dispersal limitation during stochastic processes. Environmental and geographical factors accounted for <20% of the variation in bacterial and fungal communities, with pH, temperature, and dissolved oxygen being important environmental factors. Our findings provide new insights into the responses of bacteria and fungi to the environment, shed light on the ecological processes of community building, and deepen our understanding of lake ecosystems. The results of this study provide a reference for lake management and conservation, particularly with respect to monitoring and understanding microbial communities in response to environmental changes.
Maternal and infant outcomes in women with sickle cell disease: a matched cohort study
Authors: Sikdar Oishi , Ambulkar Hemant , Jenkinson Allan , Hedley Catherine , Johns Jemma , Bhat Ravindra , Dassios Theodore , Harris Christopher , Greenough Anne 
Published: April 2024

ObjectiveWomen with sickle cell disease (SCD) have adverse maternal and infant outcomes. Our aim was to determine whether the outcomes of SCD mothers and their infants differed from African or Caribbean women not affected by SCD and whether there were differences between SCD individuals with the haemoglobin SS (HbSS) or haemoglobin SC (HbSC) genotypes. Furthermore, we wished to determine if any differences related to deprivation.DesignA matched cohort study.SettingTertiary perinatal centre in LondonPatients4964 African or Caribbean women without SCD and 148 with SCD.Main outcome measuresMode of delivery, maternal exchange transfusion, birthweight, neonatal unit admission, neonatal death and deprivation indicesResultsSCD women were more likely to be delivered by caesarean section (p<0.001) and had babies of lower birthweight (p<0.001). Their infants were no more likely to be admitted to neonatal intensive care unit or suffer a neonatal death. There were no significant differences between the SCD women and those without SCD in their deprivation index or deprivation decile. The women with the HbSS genotype compared to those with the HbSC genotype were more anaemic (p<0.02), required more exchange transfusions (p<0.001) and were more likely to be delivered by caesarean section (p=0.008). The infant outcomes did not differ significantly between the genotypes.ConclusionsAlthough, the SCD women, particularly those with the HbSS genotype, had greater morbidity, infant morbidity, and mortality was similar in mothers with the HbSS or HbSC genotypes and those without SCD.
Influencing factors of effective lens position in patients with Marfan syndrome and ectopia lentis
Authors: Shen Xin , Chen Zexu , Jia WanNan , Wang Yalei , Chen Tianhui , Sun Yang , Jiang Yongxiang 
Published: April 2024

AimsThe aim of this study was to analyse the effective lens position (ELP) in patients with Marfan syndrome (MFS) and ectopia lentis (EL).MethodsPatients with MFS undergoing lens removal and primary intraocular lens (IOL) implantation were enrolled in the study. The back-calculated ELP was obtained with the vergence formula and compared with the theoretical ELPs. The back-calculated ELP and ELP error were evaluated among demographic and biometric parameters, including axial length (AL), corneal curvature radius (CCR) and white-to-white (WTW).ResultsA total of 292 eyes from 200 patients were included. The back-calculated ELP was lower in patients undergoing scleral-fixated IOL than those receiving in-the-bag IOL implantation (4.54 (IQR 3.65–5.20) mm vs 4.98 (IQR 4.56–5.67) mm, p<0.001). The theoretical ELP of the SRK/T formula exhibited the highest accuracy, with no difference from the back-calculated ELP in patients undergoing in-the-bag IOL implantation (5.11 (IQR 4.83–5.65) mm vs 4.98 (IQR 4.56–5.67) mm, p=0.209). The ELP errors demonstrated significant correlations with refraction prediction error (PE): a 1 mm ELP error led to PE of 2.42D (AL<22 mm), 1.47D (22 mm≤AL<26 mm) and 0.54D (AL≥26 mm). Multivariate analysis revealed significant correlations of ELP with AL (b=0.43, p<0.001), CCR (b=−0.85, p<0.001) and WTW (b=0.41, p=0.004).ConclusionThis study provides novel insights into the origin of PE in patients with MFS and EL and potentially refines existing formulas.
Circulating metabolomic markers in association with overall burden of microvascular complications in type 1 diabetes
Authors: Rotbain Curovic Viktor , Sørland Brede A , Hansen Tine W , Jain Siddhi Y , Sulek Karolina , Mattila Ismo Matias , Frimodt-Moller Marie , Trost Kajetan , Legido-Quigley Cristina , Theilade Simone , Tofte Nete , Winther Signe Abitz , Hansen Christian Stevns , Rossing Peter , Ahluwalia Tarunveer S 
Published: April 2024

IntroductionDiabetic retinopathy (DR), diabetic kidney disease (DKD) and distal symmetric polyneuropathy (DSPN) share common pathophysiology and pose an additive risk of early mortality.Research design and methodsIn adults with type 1 diabetes, 49 metabolites previously associated with either DR or DKD were assessed in relation to presence of DSPN. Metabolites overlapping in significance with presence of all three complications were assessed in relation to microvascular burden severity (additive number of complications—ie, presence of DKD±DR±DSPN) using linear regression models. Subsequently, the same metabolites were assessed with progression to endpoints: soft microvascular events (progression in albuminuria grade, ≥30% estimated glomerular filtration rate (eGFR) decline, or any progression in DR grade), hard microvascular events (progression to proliferative DR, chronic kidney failure, or ≥40% eGFR decline), and hard microvascular or macrovascular events (hard microvascular events, cardiovascular events (myocardial infarction, stroke, or arterial interventions), or cardiovascular mortality), using Cox models. All models were adjusted for sex, baseline age, diabetes duration, systolic blood pressure, HbA1c, body mass index, total cholesterol, smoking, and statin treatment.ResultsThe full cohort investigated consisted of 487 participants. Mean (SD) follow-up was 4.8 (2.9, 5.7) years. Baseline biothesiometry was available in 202 participants, comprising the cross-sectional cohort. Eight metabolites were significantly associated with presence of DR, DKD, and DSPN, and six with additive microvascular burden severity. In the full cohort longitudinal analysis, higher levels of 3,4-dihydroxybutanoic acid (DHBA), 2,4-DHBA, ribonic acid, glycine, and ribitol were associated with development of events in both crude and adjusted models. Adding 3,4-DHBA, ribonic acid, and glycine to a traditional risk factor model improved the discrimination of hard microvascular events.ConclusionsWhile prospective studies directly assessing the predictive ability of these markers are needed, our results strengthen the role of clinical metabolomics in relation to risk assessment of diabetic complications in chronic type 1 diabetes.
Postprogression therapy and confounding for the estimated treatment effect on overall survival in phase III oncology trials
Authors: Sherry Alexander D , Msaouel Pavlos , Lin Timothy A , Abi Jaoude Joseph , Kouzy Ramez , Beck Esther J , Miller Avital M , Passy Adina H , Kupferman Gabrielle S , Koay Eugene J , Fuller Clifton David , Thomas Charles R , McCaw Zachary R , Ludmir Ethan B 
Published: April 2024

ObjectiveEstimations of the treatment effect on overall survival (OS) may be influenced by post-progression therapies (PPTs). It is unclear how often OS analyses account for PPT effects. The purpose of this cross-sectional analysis was to determine the prevalence of OS analyses accounting for PPT effects in phase III oncology trials.Methods and analysisWe screened two-arm, superiority design, phase III, randomised, oncology trials reporting OS from ClinicalTrials.gov. The primary outcome was the frequency of OS analyses adjusting for PPT confounding. Logistic regressions computed ORs for the association between trial-level covariates and the outcome.ResultsA total of 334 phase III trials enrolling 265 310 patients were included, with publications between 2004 and 2020. PPTs were reported in 47% of trials (157 of 334), and an analysis accounting for PPTs was performed in only 12% of trials (N=41). PPT adjustments were often prespecified (N=23, 56%), and appeared to be more likely in cross-over studies (OR 5.04, 95% CI 2.42 to 10.38) and studies with discordant surrogate-OS findings (OR 2.26, 95% CI 1.16 to 4.38). In key subgroup analyses, PPT analyses were infrequent, including 8% of trials among those studying locoregional/first-line therapy and 11% of trials among those powered for OS.ConclusionsAlthough time on PPTs is an important component of OS, PPTs are rarely considered in OS analyses, which may introduce confounding on estimates of the treatment effect on OS. PPTs and methods to account for their effects on OS estimates should be considered at the time of trial design and reporting.