bluuebunny/crossref_metadata_2025_split huggingface dataset:
The electron transport chain of
Shewanella oneidensis
MR-1 can operate bidirectionally to enable microbial electrosynthesis
Authors: Ford Kathryne C. , TerAvest Michaela A. 
Published: December 2023

ABSTRACT

Extracellular electron transfer is a process by which bacterial cells can exchange electrons with a redox-active material located outside of the cell. In
Shewanella oneidensis
, this process is natively used to facilitate respiration using extracellular electron acceptors such as Fe(III) or an anode. Previously, it was demonstrated that this process can be used to drive the microbial electrosynthesis (MES) of 2,3-butanediol (2,3-BDO) in
S. oneidensis
exogenously expressing butanediol dehydrogenase (BDH). Electrons taken into the cell from a cathode are used to generate NADH, which in turn is used to reduce acetoin to 2,3-BDO via BDH. However, generating NADH via electron uptake from a cathode is energetically unfavorable, so NADH dehydrogenases couple the reaction to proton motive force. We therefore need to maintain the proton gradient across the membrane to sustain NADH production. This work explores accomplishing this task by bidirectional electron transfer, where electrons provided by the cathode go to both NADH formation and oxygen (O
2
) reduction by oxidases. We show that oxidases use trace dissolved oxygen in a microaerobic bioelectrical chemical system (BES), and the translocation of protons across the membrane during O
2
reduction supports 2,3-BDO generation. Interestingly, this process is inhibited by high levels of dissolved oxygen in this system. In an aerated BES, O
2
molecules react with the strong reductant (cathode) to form reactive oxygen species, resulting in cell death.

IMPORTANCE
Microbial electrosynthesis (MES) is increasingly employed for the generation of specialty chemicals, such as biofuels, bioplastics, and cancer therapeutics. For these systems to be viable for industrial scale-up, it is important to understand the energetic requirements of the bacteria to mitigate unnecessary costs. This work demonstrates sustained production of an industrially relevant chemical driven by a cathode. Additionally, it optimizes a previously published system by removing any requirement for phototrophic energy, thereby removing the additional cost of providing a light source. We also demonstrate the severe impact of oxygen intrusion into bioelectrochemical systems, offering insight to future researchers aiming to work in an anaerobic environment. These studies provide insight into both the thermodynamics of electrosynthesis and the importance of the bioelectrochemical systems’ design.
Prisoner's science
Authors: Casadevall Arturo , Fang Ferric 
Published: December 2023

ABSTRACT
Decisions involving cooperation or competition are common in science. Here, we consider three situations frequently encountered in the biomedical sciences, namely, establishing priority, sharing reagents, and selecting a journal for publication, through the lens of the prisoner's dilemma. In each situation, cooperation is the best strategy for scientists and for science.
Formation of a border ischemic zone depends on plasma potassium concentration
Authors: Bernikova Olesya , Durkina Aleksandra , Gonotkov Mikhail , Minnebaeva Elena , Arteyeva Natalia , Azarov Jan 
Published: December 2023

Extracellular potassium concentration might modify electrophysiological properties in the border zone of ischemic myocardium. We evaluated the depolarization and repolarization characteristics across the ischemic–normal border under [K+] variation. Sixty-four-lead epicardial mapping was performed in 26 rats ([K+] 2.3–6.4 mM) in a model of acute ischemia/reperfusion. The animals with [K+] < 4.7 mM (low–normal potassium) had an ischemic zone with ST-segment elevation and activation delay, a border zone with ST-segment elevation and no activation delay, and a normal zone without electrophysiological abnormalities. The animals with [K+] >4.7 mM (normal-high potassium) had only the ischemic and normal zones and no transitional area. Activation–repolarization intervals and local conduction velocities were inversely associated with [K+] in linear regression analysis with adjustment for the zone of myocardium. The reperfusion extrasystolic burden (ESB) was greater in the low–normal as compared to normal-high potassium animals. Ventricular tachycardia/fibrillation incidence did not differ between the groups. In patch-clamp experiments, hypoxia shortened action potential duration at 5.4 mM but not at 1.3 mM of [K+]. IK(ATP) current was lower at 1.3 mM than at 5.4 mM of [K+]. We conclude that the border zone formation in low–normal [K+] was associated with attenuation of IK(ATP) response to hypoxia and increased reperfusion ESB.
A class of rotating metrics in the presence of a scalar field
Authors: Mirza Behrouz , Kangazi Parichehr Kangazian , Sadeghi Fatemeh 
Published: December 2023

AbstractWe consider a class of three parameter static and axially symmetric metrics that reduce to the Janis–Newman–Winicour (JNW) and $$ \gamma $$
γ
-metrics in certain limits of the parameters. We obtain rotating form of the metrics that are asymptotically flat, stationary and axisymmetric. In certain values of the parameters, the solutions represent the rotating JNW metric, rotating $$ \gamma $$
γ
-metric and Bogush–Gal’tsov (BG) metric. The singularities of rotating metrics are investigated. Using the light-ring method, we obtain the quasi normal modes (QNMs) related to rotating metrics in the eikonal limit. Finally, we investigate the precession frequency of a test gyroscope in the presence of the rotating metrics.
A Large-Scale Meta-Analysis Reveals Positive Feedback between Macrophages and T Cells That Sensitizes Tumors to Immunotherapy
Authors: Yang Jing , Liu Qi , Shyr Yu 
Published: December 2023

Abstract

Although considerable efforts have been dedicated to identifying predictive signatures for immune checkpoint inhibitor (ICI) treatment response, current biomarkers suffer from poor generalizability and reproducibility across different studies and cancer types. The integration of large-scale multiomics studies holds great promise for discovering robust biomarkers and shedding light on the mechanisms of immune resistance. In this study, we conducted the most extensive meta-analysis involving 3,037 ICI-treated patients with genetic and/or transcriptomics profiles across 14 types of solid tumor. The comprehensive analysis uncovered both known and novel reliable signatures associated with ICI treatment outcomes. The signatures included tumor mutational burden (TMB), IFNG and PDCD1 expression, and notably, interactions between macrophages and T cells driving their activation and recruitment. Independent data from single-cell RNA sequencing and dynamic transcriptomic profiles during the ICI treatment provided further evidence that enhanced cross-talk between macrophages and T cells contributes to ICI response. A multivariable model based on eight nonredundant signatures significantly outperformed existing models in five independent validation datasets representing various cancer types. Collectively, this study discovered biomarkers predicting ICI response that highlight the contribution of immune cell networks to immunotherapy efficacy and could help guide patient treatment.

Significance:
Identification of robust immunogenomic connections, particularly macrophage T-cell interactions, in a large-scale pan-cancer meta-analysis and development of a predictive model for immunotherapy response that outperformed existing models could facilitate clinical decision-making.
Diet Matters in Breast Cancer Prognosis: Clinical Trial Evidence and Questions
Authors: McTiernan Anne 
Published: December 2023

SummaryDiet and weight matter in breast cancer prognosis. The DIANA-5 randomized controlled trial found no effect of a Mediterranean macrobiotic diet on 5-year breast cancer recurrence, but high adherence was associated with a 41% lower risk of recurrence versus controls. The effects of substantial weight loss on prognosis remain unknown.See related article by Berrino et al., p. 965
ERA5 Precipitation over China: Better Relative Hourly and Daily Distribution than Absolute Values
Authors: Wu Guocan , Lv Pengfei , Mao Yuna , Wang Kaicun 
Published: December 2023

Abstract
The temporal distribution of precipitation is of great importance in water availability and the hydrological cycle. Existing studies, directly comparing observed and simulated precipitation amount and intensity over different temporal intervals, show that reanalyses overestimate precipitation frequency and underestimate precipitation intensity, and therefore cannot characterize extreme precipitations. In this study, relative values of precipitation (i.e., the cumulative fractions of precipitation on different percentiles of wettest hours or days to the annual total) were used to evaluate ERA5 over China during the warm seasons of from 1979 to 2015. We found that ERA5 well reproduced the relative values of daily precipitation to the annual total, although hourly results were less satisfied. The cumulative fractions at the hourly time scale at the 99th, 95th, and 90th percentiles were 15.2% ± 3.4%, 38.7% ± 6.6%, and 54.5% ± 7.4% for the gauge observations, and 9.0% ± 1.7%, 27.2% ± 4.0%, and 41.5% ± 5.0% for ERA5, respectively. ERA5 had excellent agreement with gauge observations at daily time scales: gauge observations were 13.0% ± 3.4%, 32.1% ± 5.1%, and 47.6% ± 5.7%, compared to 11.5% ± 3.7%, 30.7% ± 7.0%, and 46.0% ± 8.8% for ERA5, respectively. This difference was mainly due to the high frequency of hourly precipitation in the reanalyses, which were cancelled out at the daily scale. Gauge observations at the hourly scale showed an increase cumulative fraction at the 99th, 95th, and 90th percentiles (0.07% ± 0.03% decade−1, 0.15% ± 0.03% decade−1, and 0.17% ± 0.03% decade−1, respectively) from 1979 to 2015, but did not show an obvious trend at the daily scale. These tendencies were underestimated at the hourly scale but overestimated at the daily scale in ERA5. The results helped us to characterize the temporal distributions and variations of precipitation, and to deepen our understanding of hydrological processes and reanalyses performance.
Incidental findings on staging rectal MRI: clinical significance and outcomes
Authors: Tang Yen Zhi , Alabousi Abdullah 
Published: December 2023

Background Incidental findings (IFs) are commonly seen in staging rectal magnetic resonance imaging (MRI) scans. Their prevalence and clinical significance have not been previously documented. Purpose To assess the prevalence, clinical significance, and outcomes of incidental findings in MRI scans performed for the staging of rectal cancer. Material and Methods A retrospective study was performed at a tertiary colorectal imaging institution. Consecutive MRI rectal staging scans with correlative pathology confirmed primary rectal cancer between March 2014 and March 2021 were identified. The respective imaging reports were reviewed for IFs, which were classified as high, moderate, and low, according to their clinical significance. Medical records were reviewed to assess the outcomes of the highly significant IFs. Results There were 266 eligible patients (97 women; mean age = 64.2 years) during the study period. A total of 120 (45%) patients did not have any IFs. A total of 238 IFs in 146 (55%) patients were found. There were 21 (9%) IFs of high clinical significance, 122 (51%) of moderate clinical significance, and 95 (40%) of low clinical significance. The prostate and uterus had the most IFs of high clinical significance, two of which were subsequently pathology confirmed as prostate adenocarcinomas. Conclusion IFs were seen in more than half of the staging MRI scans in rectal cancer but less than 10% of these were of high clinical significance. The results of this study highlight the range of potential IFs and can guide future research assessing the potential impact of these IFs on patients and the healthcare system.
Pharmacoeconomic evaluation of stroke and myocardial infarction prevention in hypertensive patients: Markov model based on the ACCOMPLISH trial
Authors: Feng Aozi , Lin Weizhao , Li Li , Zeng Mengnan , Lyu Jun 
Published: December 2023

Objective We evaluated the pharmacoeconomics of amlodipine combined with benazepril and hydrochlorothiazide combined with benazepril in the treatment of hypertension using a Markov model to provide an evidence-based reference for clinical drug use. Methods In this retrospective study, we constructed two types of Markov model using data from the ACCOMPLISH (Avoiding Cardiovascular Events through Combination Therapy in Patients Living with Systolic Hypertension) trial to dynamically simulate the development of hypertension. The models were subjected to rollback analysis and cohort analysis to obtain the cost and effectiveness of the two drug regimens in preventing stroke and myocardial infarction in hypertensive patients. We conducted sensitivity analysis to determine the stability of the results. Results The cost-effectiveness of amlodipine combined with benazepril was 66,196.97 RMB with 6.59 QALYs and that of hydrochlorothiazide combined with benazepril was 74,588.50 RMB with 6.46 QALYs. The incremental cost-effectiveness ratio of hydrochlorothiazide + benazepril was −64,550.23 compared with amlodipine + benazepril. The amlodipine + benazepril regimen was therefore more cost-effective than hydrochlorothiazide combined with benazepril. The sensitivity analysis results showed that the model was robust. Conclusion Compared with the hydrochlorothiazide + benazepril treatment regimen, the amlodipine + benazepril regimen showed greater economic benefits.
Blurred lines: Ethical challenges related to autonomy in home-based care
Authors: Hertzberg Cecilie Knagenhjelm , Heggestad Anne Kari Tolo , Magelssen Morten 
Published: December 2023

Background Home-based care workers mainly work alone in the patient’s home. They encounter a diverse patient population with complex health issues. This inevitably leads to several ethical challenges. Aim The aim is to gain insight into ethical challenges related to patient autonomy in home-based care and how home-based care staff handle such challenges. Research design The study is based on a 9-month fieldwork, including participant observation and interviews in home-based care. Data were analysed with a thematic analysis approach. Participants and research context The study took place within home-based care in three municipalities in Eastern Norway, with six staff members as key informants. Ethical considerations The Norwegian Agency for Shared Services in Education and Research evaluated the study. All participants were competent to consent and signed an informed consent form. Findings A main challenge was that staff found it difficult to respect the patient’s autonomy while at the same time practicing appropriate care. We found two main themes: Autonomy and risk in tension; and strategies to balance autonomy and risk. These were explicated in four sub-themes: Refusing and resisting care; when choosing to live at home becomes risky; sweet-talking and coaxing; and building trust over time. Staff’s threshold for considering the use of coercion appeared to be high. Conclusions Arguably, home-based care staff need improved knowledge of coercion and the legislation regulating it. There is also a need for arenas for ethics reflection and building of competence in balancing ethical values in recurrent ethical problems.
Olecranon fractures: A biomechanical comparison of three tension band wiring fixation methods on bone models
Authors: Calisal Emre , Uğur Levent 
Published: December 2023

Purpose This study aimed to compare the biomechanical pull-out strength of the three different tension band wiring (TBW) methods employed to fix transverse olecranon fractures on bone models. Methods Three different fixation models were created in groups of seven synthetic olecranon fractured bone models. The first technique was fixed the olecranon with the traditional TBW method. The second technique was fixed the olecranon with a large intramedullary screw TBW method. The third technique was fixed the olecranon with the double-screw TBW method. The pull-out force needed for the failure of each specimen under the tensile test device was evaluated, and the results were recorded. Results We found that the lowest average pull out strength was 55.10 N (range: 35.87–65.85 ± 10.17) in the traditional TBW method, the highest pull out strength was 84.28 N (range: 63.67–117 ± 18.87) in the double-screw TBW method. The pull out strength was 70.80 N (range: 52.60–80.95 ± 10.18) in the intramedullary screw TBW method. In terms of ultimate failure loads, there was no significant difference between the intramedullary screw TBW and the double-screw TBW ( p > .05) while there was a significant difference between the traditional TBW and the other two methods ( p < .05). Conclusion The use of screw(s) shows higher biomechanical stability than K-wires in the TBW method. Double-screws fixation gives similar results in terms of the biomechanical load to failure compared to a large intramedullary screw fixation. Both screw methods can be used as stable constructs in clinical practice. Level of Evidence III, biomechanical trial.
Comparative genomics analysis and characterization of Shiga toxin-producing Escherichia coli O157:H7 strains reveal virulence genes, resistance genes, prophages and plasmids
Authors: Naidoo Natalie , Zishiri Oliver T. 
Published: December 2023

AbstractEscherichia coli O157:H7 is a foodborne pathogen that has been linked to global disease outbreaks. These diseases include hemorrhagic colitis and hemolytic uremic syndrome. It is vital to know the features that make this strain pathogenic to understand the development of disease outbreaks. In the current study, a comparative genomic analysis was carried out to determine the presence of structural and functional features of O157:H7 strains obtained from 115 National Center for Biotechnology Information database. These strains of interest were analysed in the following programs: BLAST Ring Image Generator, PlasmidFinder, ResFinder, VirulenceFinder, IslandViewer 4 and PHASTER. Five strains (ECP19–198, ECP19–798, F7508, F8952, H2495) demonstrated a great homology with Sakai because of a few regions missing. Five resistant genes were identified, however, Macrolide-associated resistance gene mdf(A) was commonly found in all genomes. Majority of the strains (97%) were positive for 15 of the virulent genes (espA, espB, espF, espJ, gad, chuA, eae, iss, nleA, nleB, nleC, ompT, tccP, terC and tir). The plasmid analysis demonstrated that the IncF group was the most prevalent in the strains analysed. The prophage and genomic island analysis showed a distribution of bacteriophages and genomic islands respectively. The results indicated that structural and functional features of the many O157:H7 strains differ and may be a result of obtaining mobile genetic elements via horizontal gene transfer. Understanding the evolution of O157:H7 strains pathogenicity in terms of their structural and functional features will enable the development of detection and control of transmission strategies.
Regulatory effect of bacterial melanin on the isoforms of new superoxide-producing associates from rat tissues in rotenone-induced Parkinson’s disease
Authors: Danielyan Margarita , Nebogova Kristina , Simonyan Ruzan , Hovsepyan Anichka , Avetisyan Zubeida , Simonyan Karen , Simonyan Gegham , Khachatryan Vahagn , Karapetyan Kristine 
Published: December 2023

AbstractAccording to recent research, selective neuronal vulnerability in Parkinson’s disease (PD) results from several phenotypic traits, including calcium-dependent, feed-forward control of mitochondrial respiration leading to elevated reactive oxygen species and cytosolic calcium concentration, an extensive axonal arbor, and a reactive neurotransmitter. Therefore, antioxidant therapy is a promising direction in the treatment of PD. In vitro studies have indicated the survival-promoting activity of bacterial melanin (BM) on midbrain dopaminergic neuron cultures. It has been established that BM has a number of protective and anti-inflammatory properties, so there is a high probability of a protective effect of BM in the early stages of PD. In this study, PD was induced through the unilateral intracerebral administration of rotenone followed by bacterial melanin. Tissues (brain, lungs, and small intestine) from the observed groups underwent isolation and purification to extract isoforms of new thermostable superoxide (О2−)-producing associates between NADPH-containing lipoprotein (NLP) and NADPH oxidase-Nox (NLP-Nox). The optical absorption spectral characteristics, specific amounts, stationary concentration of the produced О2−, and the content of NADPH in the observed associates were determined. The optical absorption spectra of the NLP-Nox isoforms in the visible and UV regions in the experimental groups did not differ from those of the control group. However, compared with the control group, the specific content of the total fractions of NLP-Nox isoforms associated with PD groups was higher, especially in the small intestine. These findings suggest that the described changes may represent a novel mechanism for rotenone-induced PD. Furthermore, bacterial melanin demonstrated antioxidant properties and regulated membrane formation in the brain, lung, and small intestine. This regulation occurred by inhibiting the release of new membrane-bound formations (NLP-Nox associates) from these membranes while simultaneously regulating the steady-state concentration of the formed О2−.
Comparative physiological and transcriptomic analysis of two salt-tolerant soybean germplasms response to low phosphorus stress: role of phosphorus uptake and antioxidant capacity
Authors: Zhou Xiu-Wen , Yao Xing-Dong , He De-Xin , Sun He-Xiang , Xie Fu-Ti 
Published: December 2023

Abstract
Background
Phosphorus (P) and salt stress are common abiotic stressors that limit crop growth and development, but the response mechanism of soybean to low phosphorus (LP) and salt (S) combined stress remains unclear.

Results
In this study, two soybean germplasms with similar salt tolerance but contrasting P-efficiency, A74 (salt-tolerant and P-efficient) and A6 (salt-tolerant and P-inefficient), were selected as materials. By combining physiochemical and transcriptional analysis, we aimed to elucidate the mechanism by which soybean maintains high P-efficiency under salt stress. In total, 14,075 differentially expressed genes were identified through pairwise comparison. PageMan analysis subsequently revealed several significantly enriched categories in the LP vs. control (CK) or low phosphorus + salt (LPS) vs. S comparative combination when compared to A6, in the case of A74. These categories included genes involved in mitochondrial electron transport, secondary metabolism, stress, misc, transcription factors and transport. Additionally, weighted correlation network analysis identified two modules that were highly correlated with acid phosphatase and antioxidant enzyme activity. Citrate synthase gene (CS), acyl-coenzyme A oxidase4 gene (ACX), cytokinin dehydrogenase 7 gene (CKXs), and two-component response regulator ARR2 gene (ARR2) were identified as the most central hub genes in these two modules.

Conclusion
In summary, we have pinpointed the gene categories responsible for the LP response variations between the two salt-tolerant germplasms, which are mainly related to antioxidant, and P uptake process. Further, the discovery of the hub genes layed the foundation for further exploration of the molecular mechanism of salt-tolerant and P-efficient in soybean.