bluuebunny/crossref_metadata_2025_split huggingface dataset:
Iron-sulfur clusters are involved in post-translational arginylation
Authors: Van Verna , Brown Janae B. , O’Shea Corin R. , Rosenbach Hannah , Mohamed Ijaz , Ejimogu Nna-Emeka , Bui Toan S. , Szalai Veronika A. , Chacón Kelly N. , Span Ingrid , Zhang Fangliang , Smith Aaron T. 
Published: January 2023

AbstractEukaryotic arginylation is an essential post-translational modification that modulates protein stability and regulates protein half-life. Arginylation is catalyzed by a family of enzymes known as the arginyl-tRNA transferases (ATE1s), which are conserved across the eukaryotic domain. Despite their conservation and importance, little is known regarding the structure, mechanism, and regulation of ATE1s. In this work, we show that ATE1s bind a previously undiscovered [Fe-S] cluster that is conserved across evolution. We characterize the nature of this [Fe-S] cluster and find that the presence of the [Fe-S] cluster in ATE1 is linked to its arginylation activity, both in vitro and in vivo, and the initiation of the yeast stress response. Importantly, the ATE1 [Fe-S] cluster is oxygen-sensitive, which could be a molecular mechanism of the N-degron pathway to sense oxidative stress. Taken together, our data provide the framework of a cluster-based paradigm of ATE1 regulatory control.
Quantitative dose-response analysis untangles host bottlenecks to enteric infection
Authors: Campbell Ian W. , Hullahalli Karthik , Turner Jerrold R. , Waldor Matthew K. 
Published: January 2023

AbstractHost bottlenecks prevent many infections before the onset of disease by eliminating invading pathogens. By monitoring the diversity of a barcoded population of the diarrhea causing bacterium Citrobacter rodentium during colonization of its natural host, mice, we determine the number of cells that found the infection by establishing a replicative niche. In female mice the size of the pathogen’s founding population scales with dose and is controlled by a severe yet slow-acting bottleneck. Reducing stomach acid or changing host genotype modestly relaxes the bottleneck without breaking the fractional relationship between dose and founders. In contrast, disrupting the microbiota causes the founding population to no longer scale with the size of the inoculum and allows the pathogen to infect at almost any dose, indicating that the microbiota creates the dominant bottleneck. Further, in the absence of competition with the microbiota, the diversity of the pathogen population slowly contracts as the population is overtaken by bacteria having lost the critical virulence island, the locus of enterocyte effacement (LEE). Collectively, our findings reveal that the mechanisms of protection by colonization bottlenecks are reflected in and can be generally defined by the impact of dose on the pathogen’s founding population.
Next-Generation Morphometry for pathomics-data mining in histopathology
Authors: Hölscher David L. , Bouteldja Nassim , Joodaki Mehdi , Russo Maria L. , Lan Yu-Chia , Sadr Alireza Vafaei , Cheng Mingbo , Tesar Vladimir , Stillfried Saskia V. , Klinkhammer Barbara M. , Barratt Jonathan , Floege Jürgen , Roberts Ian S. D. , Coppo Rosanna , Costa Ivan G. , Bülow Roman D. , Boor Peter 
Published: January 2023

AbstractPathology diagnostics relies on the assessment of morphology by trained experts, which remains subjective and qualitative. Here we developed a framework for large-scale histomorphometry (FLASH) performing deep learning-based semantic segmentation and subsequent large-scale extraction of interpretable, quantitative, morphometric features in non-tumour kidney histology. We use two internal and three external, multi-centre cohorts to analyse over 1000 kidney biopsies and nephrectomies. By associating morphometric features with clinical parameters, we confirm previous concepts and reveal unexpected relations. We show that the extracted features are independent predictors of long-term clinical outcomes in IgA-nephropathy. We introduce single-structure morphometric analysis by applying techniques from single-cell transcriptomics, identifying distinct glomerular populations and morphometric phenotypes along a trajectory of disease progression. Our study provides a concept for Next-generation Morphometry (NGM), enabling comprehensive quantitative pathology data mining, i.e., pathomics.
Coherence protection of spin qubits in hexagonal boron nitride
Authors: Ramsay Andrew J. , Hekmati Reza , Patrickson Charlie J. , Baber Simon , Arvidsson-Shukur David R. M. , Bennett Anthony J. , Luxmoore Isaac J. 
Published: January 2023

AbstractSpin defects in foils of hexagonal boron nitride are an attractive platform for magnetic field imaging, since the probe can be placed in close proximity to the target. However, as a III-V material the electron spin coherence is limited by the nuclear spin environment, with spin echo coherence times of ∽100 ns at room temperature accessible magnetic fields. We use a strong continuous microwave drive with a modulation in order to stabilize a Rabi oscillation, extending the coherence time up to ∽ 4μs, which is close to the 10 μs electron spin lifetime in our sample. We then define a protected qubit basis, and show full control of the protected qubit. The coherence times of a superposition of the protected qubit can be as high as 0.8 μs. This work establishes that boron vacancies in hexagonal boron nitride can have electron spin coherence times that are competitive with typical nitrogen vacancy centres in small nanodiamonds under ambient conditions.
Wearable in-sensor reservoir computing using optoelectronic polymers with through-space charge-transport characteristics for multi-task learning
Authors: Wu Xiaosong , Wang Shaocong , Huang Wei , Dong Yu , Wang Zhongrui , Huang Weiguo 
Published: January 2023

AbstractIn-sensor multi-task learning is not only the key merit of biological visions but also a primary goal of artificial-general-intelligence. However, traditional silicon-vision-chips suffer from large time/energy overheads. Further, training conventional deep-learning models is neither scalable nor affordable on edge-devices. Here, a material-algorithm co-design is proposed to emulate human retina and the affordable learning paradigm. Relying on a bottle-brush-shaped semiconducting p-NDI with efficient exciton-dissociations and through-space charge-transport characteristics, a wearable transistor-based dynamic in-sensor Reservoir-Computing system manifesting excellent separability, fading memory, and echo state property on different tasks is developed. Paired with a ‘readout function’ on memristive organic diodes, the RC recognizes handwritten letters and numbers, and classifies diverse costumes with accuracies of 98.04%, 88.18%, and 91.76%, respectively (higher than all reported organic semiconductors). In addition to 2D images, the spatiotemporal dynamics of RC naturally extract features of event-based videos, classifying 3 types of hand gestures at an accuracy of 98.62%. Further, the computing cost is significantly lower than that of the conventional artificial-neural-networks. This work provides a promising material-algorithm co-design for affordable and highly efficient photonic neuromorphic systems.
Rapid emergence of extensively drug-resistant Shigella sonnei in France
Authors: Lefèvre Sophie , Njamkepo Elisabeth , Feldman Sarah , Ruckly Corinne , Carle Isabelle , Lejay-Collin Monique , Fabre Laëtitia , Yassine Iman , Frézal Lise , Pardos de la Gandara Maria , Fontanet Arnaud , Weill François-Xavier 
Published: January 2023

AbstractShigella sonnei, the main cause of bacillary dysentery in high-income countries, has become increasingly resistant to antibiotics. We monitored the antimicrobial susceptibility of 7121 S. sonnei isolates collected in France between 2005 and 2021. We detected a dramatic increase in the proportion of isolates simultaneously resistant to ciprofloxacin (CIP), third-generation cephalosporins (3GCs) and azithromycin (AZM) from 2015. Our genomic analysis of 164 such extensively drug-resistant (XDR) isolates identified 13 different clusters within CIP-resistant sublineage 3.6.1, which was selected in South Asia ∼15 years ago. AZM resistance was subsequently acquired, principally through IncFII (pKSR100-like) plasmids. The last step in the development of the XDR phenotype involved various extended-spectrum beta-lactamase genes (blaCTX-M-3, blaCTX-M-15, blaCTX-M-27, blaCTX-M-55, and blaCTX-M-134) carried by different plasmids (IncFII, IncI1, IncB/O/K/Z) or even integrated into the chromosome, and encoding resistance to 3GCs. This rapid emergence of XDR S. sonnei, including an international epidemic strain, is alarming, and good laboratory-based surveillance of shigellosis will be crucial for informed decision-making and appropriate public health action.
Stringent response ensures the timely adaptation of bacterial growth to nutrient downshift
Authors: Zhu Manlu , Dai Xiongfeng 
Published: January 2023

AbstractTimely adaptation to nutrient downshift is crucial for bacteria to maintain fitness during feast and famine cycle in the natural niche. However, the molecular mechanism that ensures the timely adaption of bacterial growth to nutrient downshift remains poorly understood. Here, we quantitatively investigated the adaptation of Escherichia coli to various kinds of nutrient downshift. We found that relA deficient strain, which is devoid of stringent response, exhibits a significantly longer growth lag than wild type strain during adapting to both amino acid downshift and carbon downshift. Quantitative proteomics show that increased (p)ppGpp level promotes the growth adaption of bacteria to amino acid downshift via triggering the proteome resource re-allocation from ribosome synthesis to amino acid biosynthesis. Such type of proteome re-allocation is significantly delayed in the relA-deficient strain, which underlies its longer lag than wild type strain during amino acid downshift. During carbon downshift, a lack of stringent response in relA deficient strain leads to disruption of the transcription-translation coordination, thus compromising the transcription processivity and further the timely expression of related catabolic operons for utilizing secondary carbon sources. Our studies shed light on the fundamental strategy of bacteria to maintain fitness under nutrient-fluctuating environments.
Musculoskeletal research in human space flight – unmet needs for the success of crewed deep space exploration
Authors: Liphardt Anna-Maria , Fernandez-Gonzalo Rodrigo , Albracht Kirsten , Rittweger Jörn , Vico Laurence 
Published: January 2023

AbstractBased on the European Space Agency (ESA) Science in Space Environment (SciSpacE) community White Paper “Human Physiology – Musculoskeletal system”, this perspective highlights unmet needs and suggests new avenues for future studies in musculoskeletal research to enable crewed exploration missions. The musculoskeletal system is essential for sustaining physical function and energy metabolism, and the maintenance of health during exploration missions, and consequently mission success, will be tightly linked to musculoskeletal function. Data collection from current space missions from pre-, during-, and post-flight periods would provide important information to understand and ultimately offset musculoskeletal alterations during long-term spaceflight. In addition, understanding the kinetics of the different components of the musculoskeletal system in parallel with a detailed description of the molecular mechanisms driving these alterations appears to be the best approach to address potential musculoskeletal problems that future exploratory-mission crew will face. These research efforts should be accompanied by technical advances in molecular and phenotypic monitoring tools to provide in-flight real-time feedback.
Metabolic changes in bile acids with pregnancy progression and their correlation with perinatal complications in intrahepatic cholestasis of pregnant patients
Authors: Ma Zhixin , Liu Yifeng , Chai Lin , Jin Guochen , Sun Yanni , Zhou Shaomin , Yin Peiyuan , Wang Siwen , Zhu Yuning , Zhang Dan , Lu Shiming , Zhu Bo 
Published: January 2023

AbstractIntrahepatic cholestasis of pregnancy (ICP) is a rare liver disease occurring during pregnancy that is characterized by disordered bile acid (BA) metabolism. It is related to adverse clinical outcomes in both the mother and fetus. Our aim was to evaluate the BA metabolism profiles in different types of ICP and investigate the association between specific BAs and perinatal complications in ICP patients. We consecutively evaluated 95 patients with ICP, in which 53 patients were diagnosed with early-onset ICP (EICP) and 42 patients were diagnosed with late-onset ICP (LICP). Concentrations of 15 BA components were detected using high-performance liquid chromatography tandem mass spectrometry. Clinical information was abstracted from the medical records. The percentage of conjugated bile acids increased in ICP patients. Specifically, taurocholic acid (TCA) accumulated in LICP patients, and glycocholic acid (GCA) predominated in EICP patients. A higher preterm birth incidence was observed among ICP patients. Albumin, total bile acids, total bilirubin and GCA percentage values at ICP diagnosis predicts 83.5% of preterm birth in EICP, and the percentage of TCA in total bile acids at ICP diagnosis predicts 93.2% of preterm birth in LICP. This analysis showed that the BA metabolism profiles of EICP and LICP were distinct. Increased hepatic load was positively correlated with preterm birth in EICP. An elevated TCA percentage in total bile acids provides a biomarker to predict preterm birth in LICP.
Temperature prediction of solar greenhouse based on NARX regression neural network
Authors: Gao Maosheng , Wu Qingli , Li Jianke , Wang Bailing , Zhou Zhongyu , Liu Chunming , Wang Dong 
Published: January 2023

AbstractTemperature has an important influence on plant growth and development. In protected agriculture production, accurate prediction of temperature environment is of great significance. However, due to the time series, nonlinear and multi coupling characteristics of temperature, it is difficult to achieve accurate prediction. We proposed a method for building a solar greenhouse temperature prediction model based on a timeseries analysis, that considers the time series characteristics and dynamic temperature changes in the greenhouse system. The method would predict the temperature of greenhouse, and provide reference for the temperature change law in protected agriculture. A parameter analysis was performed on the nonlinear autoregressive exogenous (NARX) neural network, and a solar greenhouse temperature time series prediction model was established using the NARX regression neural network. The results showed that the proposed model depicted a maximum absolute error of 0.67 °C, and model correlation coefficient of 0.9996. Compared with the wavelet and BP neural networks, the NARX regression neural network accurately predicted and significantly outperformed in the solar greenhouse temperature prediction model. Moreover, the prediction model can accurately predict temperature trends within the solar greenhouse and is pivotal to obtaining precise control of solar greenhouse temperature.
Quantifying the impact of positive stress on companies from online employee reviews
Authors: Šćepanović Sanja , Constantinides Marios , Quercia Daniele , Kim Seunghyun 
Published: January 2023

AbstractWorkplace stress is often considered to be negative, yet lab studies on individuals suggest that not all stress is bad. There are two types of stress: distress refers to harmful stimuli, while eustress refers to healthy, euphoric stimuli that create a sense of fulfillment and achievement. Telling the two types of stress apart is challenging, let alone quantifying their impact across corporations. By leveraging a dataset of 440 K reviews about S &P 500 companies published during twelve successive years, we developed a deep learning framework to extract stress mentions from these reviews. We proposed a new methodology that places each company on a stress-by-rating quadrant (based on its overall stress score and overall rating on the site), and accordingly scores the company to be, on average, either a low stress, passive, negative stress, or positive stress company. We found that (former) employees of positive stress companies tended to describe high-growth and collaborative workplaces in their reviews, and that such companies’ stock evaluations grew, on average, 5.1 times in 10 years (2009–2019) as opposed to the companies of the other three stress types that grew, on average, 3.7 times in the same time period. We also found that the four stress scores aggregated every year—from 2008 to 2020 —closely followed the unemployment rate in the U.S.: a year of positive stress (2008) was rapidly followed by several years of negative stress (2009–2015), which peaked during the Great Recession (2009–2011). These results suggest that automated analyses of the language used by employees on corporate social-networking tools offer yet another way of tracking workplace stress, allowing quantification of its impact on corporations.
Malaria parasite density and detailed qualitative microscopy enhances large-scale profiling of infection endemicity in Nigeria
Authors: Oyibo Wellington , Latham Victoria , Oladipo Oladosu , Ntadom Godwin , Uhomoibhi Perpetua , Ogbulafor Nnenna , Okoronkwo Chukwu , Okoh Festus , Mahmoud Aminu , Shekarau Emmanuel , Oresanya Olusola , Cherima Yakubu Joel , Jalingo Innua , Abba Bintu , Audu Mohammed , Conway David J. 
Published: January 2023

AbstractWith global progress towards malaria reduction stalling, further analysis of epidemiology is required, particularly in countries with the highest burden. National surveys have mostly analysed infection prevalence, while large-scale data on parasite density and different developmental forms rarely available. In Nigeria, the country with the largest burden globally, blood slide microscopy of children up to 5 years of age was conducted in the 2018 National Demographic and Health Survey, and parasite prevalence previously reported. In the current study, malaria parasite density measurements are reported and analysed for 7783 of the children sampled across the 36 states within the six geopolitical zones of the country. Asexual and sexual stages, and infections with different malaria parasite species are analysed. Across all states of Nigeria, there was a positive correlation between mean asexual parasite density within infected individuals and prevalence of infection in the community (Spearman’s rho = 0.39, P = 0.02). Asexual parasite densities were highest in the northern geopolitical zones (geometric means > 2000 μL−1), extending the evidence of exceptionally high infection burden in many areas. Sexual parasite prevalence in each state was highly correlated with asexual parasite prevalence (Spearman’s rho = 0.70, P < 0.001), although sexual parasite densities were low (geometric means < 100 μL−1 in all zones). Infants had lower parasite densities than children above 1 year of age, but there were no differences between male and female children. Most infections were of P. falciparum, which had higher asexual densities but lower sexual parasite densities than P. malariae or P. ovale mono-infections. However, mixed species infections had the highest asexual parasite densities. It is recommended that future large surveys in high burden countries measure parasite densities as well as developmental stages and species, to improve the quality of malaria epidemiology and tracking of future changes.
Influence of mixed ventilation on particulate-gas diffusion and distribution of diesel engine exhaust in fully mechanized excavation face
Authors: Zhou Gang , Yang Yang , Duan Jinjie , Jing Bin , Song Shuzheng , Sun Biao 
Published: January 2023

AbstractTail gas emitted by underground trackless rubber wheel cars poses a serious threat to the health and safety of underground workers. To effectively reduce the tail gas concentration of a comprehensive excavation face, this study adopted a numerical simulation method to investigate the influence of air suction volume Q and distance L between trackless rubber wheel cars and headfaces on the diffusion law of diesel particulate matter, CO, and NOx under long suction and short pressure ventilation. The results showed that under the condition of L = 20 m, the trackless rubber wheel car is closer to the suction air duct. At this point, when Q = 600 m3/min, the tail gas control effect in the roadway is optimum. In addition, under the condition of L = 40 m, the trackless rubber wheel car is in the middle of the roadway. At this point, when Q = 300 m3/min, the tail gas control effect in the roadway is optimum. When L = 60 m and Q = 200 m3/min, the ventilation mode in the roadway is mainly pressure-in ventilation. The high-volume-fraction NOx region and the medium-volume-fraction NOx region under this air volume are small.
Relationship between gut microbiota and nutritional status in patients on peritoneal dialysis
Authors: Tian Na , Yan Yinyin , Chen Na , Xu Siyao , Chu Rui , Wang Mengting , Duan Surong , Ren Hongyan , Song Shuhua , Wang Li , Ma Xiaoqin , Xu Mei , Na Li , Chen Menghua , Li Philip Kam-Tao 
Published: January 2023

AbstractMalnutrition is a common complication in the dialysis population, both hemodialysis and peritoneal dialysis (PD). We report our exploratory study on the characteristics of intestinal microbiota and nutritional status in PD patients. The nutritional status of our PD patients were evaluated, and their feces were collected for 16S rRNA gene V3-V4 regions amplification and high-throughput sequencing. The characteristics and differences of microbiota between the well-nourished (W) and malnourished (M) groups were compared. We studied the genera and the operational taxonomic units (OTUs) within the genus of our patients, initially comparing the malnourished and the well- nourished groups and later on reanalyzing the whole group using these OTUs. At the OTU level, 6 bacteria were significantly correlated with the serum albumin level. The abundances of 2 OTUs (OTU208 Lachnospiraceae_incertae_sedi and OTU4 Bacteroides) were more in W group. Meanwhile, 4 OTUs (OTU225 Akkermansia, OTU87 Megasphaera, OTU31 Peptostreptococcaceae_incertae_sedi and OTU168 Clostridium_sensu_strictu) displayed higher abundance among individuals in M group. Notably, the OTU168 Clostridium_sensu_stricto was the only bacteria that significantly correlated with serum albumin (r = − 0.356, P = 0.05), pre-albumin (r = − 0.399, P = 0.02), and SGA (r = 0.458, P = 0.01). The higher the OTU168 Clostridium_sensu_strictu, the lower serum albumin and pre-albumin and a higher score of SGA signifying a worse nutritional status. Our preliminary findings suggested a relationship between the nutrition status and microbiota in PD patients. Our results provide a basis for further exploration of the interactions between malnutrition and intestinal flora in PD patients with potential interventions using probiotics and prebiotics.