bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bayesian Multi-Study Non-Negative Matrix Factorization for Mutational Signatures
Authors: Grabski Isabella N. , Trippa Lorenzo , Parmigiani Giovanni 
Published: March 2023

AbstractMutational signatures shed insight into the range of mutational processes giving rise to tumors and allow a better understanding of cancer origin. They are typically identified from high-throughput sequencing data of cancer genomes using non-negative matrix factorization (NMF), and many such techniques have been developed towards this aim. However, it is often of particular interest to compare mutational signatures across multiple conditions, e.g. to understand which signatures are present across different treatments, or to identify signatures that are shared or specific across cancer types. Existing techniques within the NMF context only allow decomposition within a single dataset, so that integrating results across multiple conditions requires running separate analyses on each dataset, followed by subjective and manual comparisons of the identified signatures. To address this issue, we propose a Bayesian multi-study NMF method that jointly decomposes multiple studies or conditions to identify signatures that are common, specific, or partially shared by any subset. We propose two models: a “discovery-only” model that estimates de novo signatures in a completely unsupervised manner, and a “recovery-discovery” model that builds informative priors from previously known signatures to both update the estimates of these signatures and identify any novel signatures. We then further extend these models to estimate the effects of sample-level covariates on the exposures to each signature, enforcing sparsity through a non-local spike-and-slab prior. We demonstrate our approach on a range of simulations, and apply our method to colorectal cancer samples to show its utility.
Competence for transcellular infection in the root cortex involves a post-replicative, cell-cycle exit decision inMedicago truncatula
Authors: Batzenschlager Morgane , Lace Beatrice , Zhang Ning , Su Chao , Egli Sabrina , Krohn Pascal , Salfeld Jule , Ditengou Franck Anicet , Laux Thomas , Ott Thomas 
Published: March 2023

ABSTRACTDuring root nodule symbiosis (RNS), cell-division activity is re-initiated and sustained in the root cortex to create a hospitable cellular niche. Such temporary and spatially confined site is required to render host cells compatible with the intracellular progression of rhizobia. Although it has been suggested that early infection events might involve a pre-mitotic cell-cycle arrest, this process has not been dissected with cellular resolution. Here, we show that a dual-colour Medicago histone reporter robustly identifies cells with different mitotic or endoreduplication activities in the root cortex. By imaging deep root tissues, we found that a confined trajectory of cortical cells that are transcellularly passed by infection threads are in a stage of the cell-cycle that is distinct from directly adjacent cells. Distinctive features of infected cells include nuclear widening and large-scale chromatin rearrangements consistent with a cell-cycle exit prior to differentiation. Using a combination of fluorescent reporters demarcating cell-cycle phase progression, we confirmed that a reduced proliferation potential and modulating the G2/M transition, a process possibly controlled by the NF-YA1 transcription factor, mark the success of rhizobial delivery to nodule cells.
Design and implementation of suspended drop crystallization
Authors: Gillman Cody , Nicolas William J. , Martynowycz Michael W. , Gonen Tamir 
Published: March 2023

AbstractWe have developed a novel crystal growth method known as suspended drop crystallization. Unlike traditional methods, this technique involves mixing protein and precipitant directly on an electron microscopy grid without any additional support layers. The grid is then suspended within a crystallization chamber which we designed, allowing for vapor diffusion to occur from both sides of the drop. A UV transparent window above and below the grid enables the monitoring of crystal growth via light, UV, or fluorescence microscopy. Once crystals have formed, the grid can be removed and utilized for x-ray crystallography or microcrystal electron diffraction (MicroED) directly without having to manipulate the crystals. To demonstrate the efficacy of this method, we grew crystals of the enzyme proteinase K and determined its structure by MicroED following FIB/SEM milling to render the sample thin enough for cryoEM. Suspended drop crystallization overcomes many of the challenges associated with sample preparation, providing an alternative workflow for crystals embedded in viscous media, sensitive to mechanical stress, and/or suffering from preferred orientation on EM grids.
KGETCDA: an efficient representation learning framework based on knowledge graph encoder from transformer for predicting circRNA-disease associations
Authors: Wu Jinyang , Ning Zhiwei , Ding Yidong , Wang Ying , Peng Qinke , Fu Laiyi 
Published: March 2023

ABSTRACTRecent studies have demonstrated the significant role that circRNA plays in the progression of human diseases. Identifying circRNA-disease associations (CDA) in an efficient manner can offer crucial insights into disease diagnosis. While traditional biological experiments can be time-consuming and labor-intensive, computational methods have emerged as a viable alternative in recent years. However, these methods are often limited by data sparsity and their inability to explore high-order information. In this paper, we introduce a novel method named Knowledge Graph Encoder from Transformer for predicting CDA (KGETCDA). Specifically, KGETCDA first integrates more than 10 databases to construct a large heterogeneous non-coding RNA dataset, which contains multiple relationships between circRNA, miRNA, lncRNA and disease. Then, a biological knowledge graph is created based on this dataset and Transformer-based knowledge representation learning and attentive propagation layers are applied to obtain high-quality embeddings with accurately captured high-order interaction information. Finally, multilayer perceptron is utilized to predict the matching scores of CDA based on their embeddings. Our empirical results demonstrate that KGETCDA significantly outperforms other state-of-the-art models. To enhance user experience, we have developed an interactive web-based platform named HNRBase that allows users to visualize, download data and make predictions using KGETCDA with ease.
Molecular Evidence of Internal Carbon-Driven Partial Denitrification Annamox (PdNA) in a mainstream Pilot A-B System Coupled with Side-stream EBPR treating municipal wastewater
Authors: Kang Da , Han IL , Lee Jangho , McCullough Kester , Li Guangyu , Wang Dongqi , Klaus Stephanie , Zheng Ping , Srinivasan Varun , Bott Charles , Gu April Z. 
Published: March 2023

AbstractAchieving mainstream short-cut nitrogen removal via nitrite has been a carbon and energy-efficient goal which wastewater engineers are dedicated to explore. This study applied a novel pilot-scale A-B-S2EBPR system process integrated with sidestream enhanced biological phosphorus removal) to achieve the nitrite accumulation and downstream anammox for treating municipal wastewater. Nitrite accumulated to 5.5 ± 0.3 mg N/L in the intermittently aerated tanks of B-stage with the nitrite accumulation ratio (NAR) of 79.1 ± 6.5%. The final effluent concentration and removal efficiency of total inorganic nitrogen (TIN) were 4.6 ± 1.8 mg N/L and 84.9 ± 5.6%, respectively. Batch nitrification/denitrification activity tests and functional gene abundance of ammonium oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) suggested that the nitrite accumulation was mostly caused by partial denitrification without NOB- selection. The unique features of S2EBPR (longer anaerobic HRT/SRT, lower ORPs, high and more complex VFAs etc.) seemed to impact the nitrogen microbial communities: the conventional AOB kept at a very low level of 0.13 ± 0.13% during the operation period, and the dominant candidate internal carbon-accumulating heterotrophic genera ofAcinetobacter(17.8 ± 15.5)% andComamonadaceae(6.7 ± 3.4%) were highly enriched. Furthermore, the single-cell Raman spectroscopy-based intracellular polymer analysis revealed the dominate microorganisms that could utilize polyhydroxyalkanoates (PHA) as the potential internal carbon source to drive partial denitrification. This study provides insights and a new direction for implementing the mainstream PdNA short-cut nitrogen removal via incorporating S2EBPR into sustainable A-B process.
Maternal Infection with Group B Streptococcus Correlates Inversely with Preeclampsia in Pregnant African American Women
Authors: Kwon Keun Soo , Cheng Tzu Hsuan , Zhou Jordan , Cai Huchong , Lee Sharon , Velickovic Ivan , Dalloul Mudar , Wlody David , Zhang Ming 
Published: March 2023

AbstractObjectivePreeclampsia is more prevalent in African American women than other races. GBS colonization rate in African American women is the highest among different races. We hypothesized there is an association between GBS colonization and preeclampsia among pregnant African American women.Study DesignWe evaluated the relationship between GBS colonization and preeclampsia in 11,766 patients’ records (93% were African Americans patients) between 2010 and 2017.ResultsThe preeclampsia rate of GBS colonized patients (2.6%) was 59% less than that of GBS-negative patients (6.3%). This inverse correlation was independently significant after adjusting for other potential risk factors for preeclampsia: chronic hypertension, gestational diabetes mellitus and diabetes mellitus and other covariates. Further analysis among the patients without these risk factors also confirmed that the preeclampsia rate of GBS colonized patients (2.6%) was 55% less than that of GBS negative patients (5.7%). Similarly, patients with HSV+ or HIV+ had lower incidence of preeclampsia than those with HSV- or HIV-.ConclusionsThe unexpected finding of an inverse relationship between GBS colonization and preeclampsia suggests that the maternal immune response to GBS infection may be beneficial in reducing preeclampsia among African American patients.
The meaning and role of the functional-organic distinction: a study of clinicians in psychiatry and neurology services
Authors: Chesterfield Alice , Harvey Jordan , Hendrie Callum , Wilkinson Sam , San Juan Norha Vera , Bell Vaughan 
Published: March 2023

AbstractAimsThe functional-organic distinction attempts to differentiate disorders with diagnosable biological causes from those without and is a central axis on which diagnoses, medical specialities, and services are organised. Previous studies report poor agreement between clinicians regarding the meanings of the terms and some of the conditions to which they apply, while noting the value-laden implications of relevant diagnoses. Consequently, we aimed to understand how clinicians working in psychiatry and neurology services navigate the functional-organic distinction in their work.MethodTwenty clinicians (10 physicians, 10 psychologists) working in psychiatry and neurology services participated in semi-structured interviews that were analysed applying a constructivist grounded theory approach.ResultsThe distinction was described as often incongruent with how clinicians conceptualise patients’ problems. Organic factors were considered to be objective, unambiguously identifiable, and clearly causative, whereas functional causes were invisible and to be hypothesised through thinking and conversation. Contextual factors – including cultural assumptions, service demands, patient needs, and colleagues’ views – were key in how the distinction was deployed in practice. The distinction was considered theoretically unsatisfactory, eventually to be superseded, but clinical decision-making required it to be used strategically. This included helping communicate medical problems, navigating services, hiding meaning by making psychological explanations more palatable, tackling stigma, giving hope, and giving access to illness identity. Clinicians cited moral issues at individual and societal levels as integral to the conceptual basis and deployment of the functional-organic distinction and described actively navigating these as part of their work.ConclusionsThere is a considerable distance between the status of the functional-organic distinction as a sound theoretical concept generalisable across conditions and its role as a gatekeeping tool within the structures of healthcare. Ambiguity and contradictions were considered as both obstacles and benefits when deployed in practice and strategic considerations were important in deciding which to lean on.
Metabolic regulation of misfolded protein import into mitochondria
Authors: Wang Yuhao , Ruan Linhao , Zhu Jin , Zhang Xi , Chang Alexander Chih-Chieh , Tomaszewski Alexis , Li Rong 
Published: March 2023

AbstractMitochondria are the cellular energy hub and central target of metabolic regulation. Mitochondria also facilitate proteostasis through pathways such as the ‘mitochondria as guardian in cytosol’ (MAGIC) whereby cytosolic misfolded proteins (MPs) are imported into and degraded inside mitochondria. In this study, a genome-wide screen in yeast uncovered that Snf1, the yeast AMP-activated protein kinase (AMPK), inhibits the import of MPs into mitochondria while promoting mitochondrial biogenesis under glucose starvation. We show that this inhibition requires a downstream transcription factor regulating mitochondrial gene expression and is likely to be conferred through substrate competition and mitochondrial import channel selectivity. We further show that Snf1/AMPK activation protects mitochondrial fitness in yeast and human cells under stress induced by MPs such as those associated with neurodegenerative diseases.
Mycobacterium ulceransnot detected by PCR on human skin in Buruli ulcer endemic areas of south eastern Australia
Authors: Velink Anita , Porter Jessica L. , Stinear Timothy P , Johnson Paul D. R. 
Published: March 2023

AbstractIntroductionMycobacterium ulcerans(MU) causes Buruli ulcer (BU), a geographically restricted infection that can result in skin loss, contracture, and permanent scarring. Lesion-location maps compiled from more than 640 cases in south eastern Australia suggest biting insects are likely involved in transmission, but it is unclear whether MU is brought by insects to their target or if MU is already on the skin and inoculation is an opportunistic event that need not be insect dependent.MethodsWe validated a PCR swab detection assay and defined its dynamic range using laboratory culturedM. ulceransand fresh pigskin. We invited volunteers in Buruli-endemic and non-endemic areas to sample their skin surfaces with self-collected skin swabs tested by IS2404 quantitative PCR.ResultsPigskin validation experiments established a limit-of-detection of 0.06 CFU/cm2at a qPCR cycle threshold (Ct) of 35. Fifty-seven volunteers returned their self-collected kits of 4 swabs (bilateral ankles, calves, wrists, forearms), 10 from control areas and 47 from endemic areas. Collection was timed to coincide with the known peak-transmission period of Buruli. All swabs from human volunteers tested negative (Ct ≥35).ConclusionsM. ulceranswas not detected on the skin of humans from highly BU endemic areas.Author SummaryBuruli ulcer (BU) incidence is increasing in temperate south eastern Australia. We have yet to develop public health programs to assist people avoid BU partly because the precise mode of transmission is contentious. Recent research has shown that environmental contamination withM. ulcerans(the cause of BU) is widespread in endemic areas as a result of faecal shedding from infected possums that live close to humans, although direct human-possum contact is rare. We investigated the possibility that the skin of humans in endemic areas could become transiently contaminated withM. ulceranswhile outdoors. If this were the case then BU prevention programs could be developed around skin protection and regular washing/showering. To study this possibility, we developed a sensitive skin swab PCR-assay that we tested using a pigskin laboratory model so we could be confident in our results. We asked volunteers to collect their own skin swabs after spending at least 4 hours outside during the known period of peak Buruli transmission. Fifty seven volunteers returned swab sets for testing. Our results were negative. We did not find evidence that humans in our endemic zone haveM. ulceranscontamination on their skin.
Improving magnetic resonance spectroscopy in the brainstem periaqueductal grey using spectral registration
Authors: Sirucek Laura , Zoelch Niklaus , Schweinhardt Petra 
Published: March 2023

AbstractPurposeFunctional understanding of the periaqueductal grey (PAG), a clinically relevant brainstem region, can be advanced using proton magnetic resonance spectroscopy (1H-MRS). However, the PAG’s small size and high levels of physiological noise are methodologically challenging. This study aimed to (1) improve1H-MRS quality in the PAG using spectral registration for frequency and phase error correction, (2) investigate whether spectral registration is particularly useful in cases of greater head motion and (3) examine metabolite quantification using literature-based or individual-based water relaxation times.MethodsSpectra were acquired in 33 healthy volunteers (50.1 years, SD=17.19, 18 females) on a 3T Philipps MR system using a point-resolved spectroscopy sequence optimized with very selective saturation pulses (OVERPRESS) and voxel-based flip angle calibration (effective volume of interest size: 8.8×10.2×12.2 mm3). Spectra were fitted using LCModel and signal-to-noise ratios (SNR), N-acetylaspartate peak linewidths and Cramér-Rao lower bounds (CRLBs) were measured after spectral registration and after minimal frequency alignment.ResultsSpectral registration improved SNR by 5 % (p=0.026, median value post-correction: 18.0) and spectral linewidth by 23 % (p<0.001, 4.3 Hz), and reduced the metabolites’ CRLBs by 1-15 % (p’s<0.026). Correlational analyses revealed smaller SNR improvements with greater head motion (p=0.010) recorded using a markerless motion tracking system. Higher metabolite concentrations were detected using individual-based compared to literature-based water relaxation times (p’s<0.001).ConclusionThis study demonstrates high-quality1H-MRS acquisition in the PAG using spectral registration. This shows promise for future1H-MRS studies in the PAG and possibly also other clinically relevant brain regions with similar methodological challenges.
Selection of processed and packaged potato-based snacks among university students: a cross-sectional study regarding food environment and dietary behavior
Authors: Sattar Saima , Khalid Nauman 
Published: March 2023

PurposePotato-based snacks (PBS) are widely popular among people of all age groups despite known negative health aspects. University students, due to their busy routines and less familiarity with diets are more prone to selecting unhealthy meals and snacks. The study aims to explore the outlook of university students regarding their consumption of processed and packaged PBS in their daily lives and compares gender’s PBS choices with dietary habits and food environment.Design/methodology/approachA total of 122 students from various universities across Pakistan were included in this study. The data were collected using a structured questionnaire and distributed using the snowball method.FindingsThe university students showed a significant difference in their living habits (p = 0.016), where 25.4% of enrolled male students were hostellers as compared to females (14.8%). Significant differences were noticed in choosing PBS that further depends on the familiarity of the product, (p = 0.030), where 9.0% of female students rated familiarity with the product as being important while 20.5% of males responded familiarity as a critical factor. Studying the usual location/point of purchase for a PBS, a significant difference was observed (p = 0.008%) where more male students (27.9%) choose to buy their PBS from a local convenience store as compared to female students (18.9%). Female students (13.1%) would rather choose to buy their PBS on their weekly grocery runs.Originality/valueThis study concluded that female and male students’ attitudes regarding the consumption of PBS were almost the same regardless of environment and brand repute.HighlightsDietary behavioral studies of consumption of PBSThe environment and brand reputation have no impact on the consumption of PBSGender differences have no impact on the selection of PBSAwareness and healthy selection of PBS are critical factors that need to be focused
Increasing the organizational performance of online sellers: the powerful back-end management systems
Authors: Ku Edward C.S. , Chen Chun-Der 
Published: March 2023

PurposeThis study examines how customer-linking capabilities, the flexibility of back-end management systems, strategic agility and the perceived absorptive capacity of e-commerce influence the organizational performance of online sellers.Design/methodology/approachA performance model based on the adaptive structuration theory was employed to test the hypotheses using structural equation modeling (SEM) on a dataset of 325 samples with acceptable responses.FindingsThe results reveal that the customer-linking capability and flexibility of back-end management systems, strategic agility and assimilation of e-commerce activity significantly influence organizational performance in a virtual environment.Originality/valueThe agility of online sellers is becoming increasingly important, and from the perspective of adaptive structuration theory, back-end management systems have been built to manage buyer orders for online sellers.
Exploration of exhaustion in early-career construction professionals in India
Authors: Rastogi Ashish , Singla Harish Kumar 
Published: March 2023

PurposeThe purpose of this study is to examine the effect of job, organizational and personal factors on exhaustion (EXH) in early career construction professionals in India.Design/methodology/approachA survey questionnaire was developed and circulated among early career construction professionals in India. The responses on job, organizational and personal demands (role ambiguity, stakeholder management and work-family conflict respectively) and job, organizational and personal resources (job autonomy (JA), perceived organizational support and emotional intelligence respectively) were sought using standard measures. The valid data (N = 187) thus collected, was analysed using structural equation modelling (SEM).FindingsThe study finds that in terms of demands, stakeholder management and work family conflict have a significant positive effect on EXH. In other words, EXH level increases with the increase in these two. With respect to resources, JA has a negative effect on EXH. This implies that as JA increases, the EXH level goes down.Originality/valueThis study is the first to examine factors causing EXH in early career construction professionals in India. This study is significant on two counts. First, it proposes a comprehensive theoretical model based in job demands-resources (JD-R) theory customized for construction sector. Second, the empirical examination is situated in the Indian context, which remains underexplored despite its economic and demographic significance.