bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving Hi-C contact matrices using genome graphs
Authors: Shen Yihang , Yu Lingge , Qiu Yutong , Zhang Tianyu , Kingsford Carl 
Published: November 2023

AbstractThree-dimensional chromosome structure plays an important role in fundamental genomic functions. Hi-C, a high-throughput, sequencing-based technique, has drastically expanded our comprehension of 3D chromosome structures. The first step of Hi-C analysis pipeline involves mapping sequencing reads from Hi-C to linear reference genomes. However, the linear reference genome does not incorporate genetic variation information, which can lead to incorrect read alignments, especially when analyzing samples with substantial genomic differences from the reference such as cancer samples. Using genome graphs as the reference facilitates more accurate mapping of reads, however, new algorithms are required for inferring linear genomes from Hi-C reads mapped on genome graphs and constructing corresponding Hi-C contact matrices, which is a prerequisite for the subsequent steps of the Hi-C analysis such as identifying topologically associated domains and calling chromatin loops. We introduce the problem of genome sequence inference from Hi-C data mediated by genome graphs. We formalize this problem, show the hardness of solving this problem, and introduce a novel heuristic algorithm specifically tailored to this problem. We provide a theoretical analysis to evaluate the efficacy of our algorithm. Finally, our empirical experiments indicate that the linear genomes inferred from our method lead to the creation of improved Hi-C contact matrices. These enhanced matrices show a reduction in erroneous patterns caused by structural variations and are more effective in accurately capturing the structures of topologically associated domains.
Unraveling Shared Pathways: A Comprehensive Systematic Review of Common Fiber Tracts in Amyotrophic Lateral Sclerosis and Frontotemporal Dementia using Diffusion Tensor Imaging
Authors: Alruwaili Ashwag Rafea S , Devine Matthew , Mccombe Pamela 
Published: November 2023

AbstractThis systematic review evaluated MRI studies of fibre tract abnormalities in patients with amyotrophic lateral sclerosis (ALS) and/or fronto-temporal dementia (FTD). After searching 5 databases, 63 papers met inclusion criteria reporting 1674 patients and 1411 healthy controls. The papers studied a range of fibre tracts. Techniques used included overall comparisons and regions of interest. All papers reported results of fractional anisotropy (FA) and some also reported other DTI metrics. In ALS, the hallmark feature of cortico-spinal tracts (CST) involvement is consistently found, while in FTD the only part of the motor tracts that was found to show changes is the corona radiata (CR). The review also highlighted overlapping abnormalities between ALS and FTD, suggesting that these conditions exist on a spectrum. Both ALS and FTD exhibited CST abnormalities, with extra-motor involvement in the cingulum and the CC. Many tracts including the corpus callosum (CC) and cingulum (Cg), the superior longitudinal fasciculus (SLF) and inferior fronto-occiptal fasciculus (IFOF), were abnormal in both ALS and FTD. The integrity of specific white matter tracts, such as the uncinated fasciculus (uncF), forceps minor, and callosal radiation, appeared critical for cognitive functions related to Theory of Mind, cognitive control, and emotion recognition.There was, however, extramotor involvement in ALS.
Glial ferritin maintains neural stem cells via transporting iron required for self-renewal inDrosophila
Authors: Ma Zhixin , Wang Wenshu , Yang Xiaojing , Rui Menglong , Wang Su 
Published: November 2023

AbstractStem cell niche is critical for regulating the behavior of stem cells. Drosophila neural stem cells (Neuroblasts, NBs) are encased by glial niche cells closely, but it still remains unclear whether glial niche cells can regulate the self-renewal and differentiation of NBs. Here we show that ferritin produced by glia, cooperates with Zip13 to transport iron into NBs for the energy production, which is essential to the self-renewal and proliferation of NBs. The knockdown of glial ferritin encoding genes causes energy shortage in NBs via downregulating aconitase activity and NAD+level, which leads to the low proliferation and premature differentiation of NBs mediated by Prospero entering nuclei. More importantly, ferritin is a potential target for tumor suppression. In addition, the level of glial ferritin production is affected by the status of NBs, establishing a bicellular iron homeostasis. In this study, we demonstrate that glial cells are indispensable to maintain the self-renewal of NBs, unveiling a novel role of the NB glial niche during brain development.
The Determinants of Malnutrition Among Adolescent Girls: A Systematic Review
Authors: Hameed Abdul Rahman , Ghaffari Mohtasham , Fung Teresa T. , Daneshzad Elnaz , Ghaffari Mohtasham , Mousavi Sayed Hamid , Azadbakht Leila 
Published: November 2023

AbstractBackgroundMalnutrition, encompassing deficiencies, excesses, or imbalances in energy and nutrient intake, continues to be a critical global issue. Adolescent girls, with their pivotal role as potential future mothers, are particularly susceptible to the challenges of malnutrition. The vulnerability of this group emanates from factors including inadequate nutritional intake and a lack of essential nutritional knowledge. This comprehensive systematic review strives to meticulously scrutinize the impact of environmental and behavioral determinants on malnutrition among adolescent girls in educational settings.MethodsAdhering rigorously to the guidelines stipulated by the Preferred Reporting Items for Systematic Review and Meta-Analysis, an exhaustive literature search was conducted up to April 9th, 2023, across esteemed databases such as PubMed, Web of Science, and Google Scholar. Employing a refined search strategy incorporating Boolean operators, the search query (“Malnutrition” [Major]) AND “Adolescent” [MeSH] was deployed. Inclusivity criteria comprised original cross-sectional and case-control studies that comprehensively investigated the determinants of malnutrition among adolescent girls. This review places notable emphasis on studies published between 2013 and 2023, ensuring a contemporary and nuanced analysis of this critical subject matter.ResultsThe initial search resulted in 2438 articles. Twenty studies fully met the inclusion criteria. Most studies found that socioeconomic status, dietary patterns and their role, cultural and social norms, education and knowledge, early marriage and pregnancy, access to healthcare, and food security are the main key determinants of malnutrition among adolescent girls.ConclusionThe complex issue of malnutrition among adolescent girls, identifies various factors contributing to it, including social, economic, cultural, and individual factors. To combat malnutrition effectively, a holistic approach is needed, focusing on education, gender equality, and improved healthcare access, rather than just providing more food. This requires collaboration among policymakers, healthcare professionals, and local communities to raise awareness, empower economically, and remove healthcare barriers. By uniting these efforts, we can loosen the grip of malnutrition on adolescent girls and pave the way for their robust development and a brighter future.
Lung-Kidney Axis in Cystic Fibrosis: Early Urinary Markers of Kidney Injury Correlate with Neutrophil Activation and Worse Lung Function
Authors: Rosner Grace M. , Goswami Himanshu B. , Sessions Katherine , Mendyka Lindsay K. , Kerin Brenna , Vlasac Irma , Mellinger Diane , Gwilt Lorraine , Hampton Thomas H. , Graber Martha , Ashare Alix , Harris William T. , Christensen Brock , Stanton Bruce A. , Swiatecka-Urban Agnieszka , Skopelja-Gardner Sladjana 
Published: November 2023

AbstractBackgroundAdult people with cystic fibrosis (PwCF) have a higher risk of end-stage kidney disease than the general population. The nature and mechanism of kidney disease in CF are unknown. This study quantifies urinary kidney injury markers and examines the hypothesis that neutrophil activation and lung infection are associated with early kidney injury in CF.MethodsUrinary total protein, albumin, and markers of kidney injury and neutrophil activation, normalized to creatinine, as well as urinary immune cells, were quantified in CF (n = 48) and healthy (n = 33) cohorts. Infection burden and chronicity were defined by sputum culture and serum titers of anti-bacterial antibodies.ResultsPwCF had increased urinary protein levels, consisting of low-molecular-weight tubular injury markers, independent of glomerular filtration rate (eGFR). This finding suggests subclinical renal injury processes. Urinary analysis of the CF cohort identified different associations of urinary injury markers with aminoglycoside exposure, lung function, and neutrophil activation. High urinary KIM-1 levels and increased prevalence of neutrophils among urine immune cells correlated with decreased lung function in PwCF. The relationship between tubular injury and decreased lung function was most prominent in patients harboring chronicPseudomonas aeruginosainfection.ConclusionsIncreased urinary tubular injury markers in PwCF suggest early subclinical renal injury not readily detected by eGFR. The strong association of high urinary KIM-1 and neutrophils with diminished lung function and highPseudomonas aeruginosaburden suggests that pulmonary disease may contribute to renal injury in CF.
The cross-sectional correlation between the oxidative balance score and cardiometabolic risk factors and its potential correlation with longitudinal mortality in patients with cardiometabolic risk factors
Authors: Lai Qiancheng , Ye Liu , Luo Jun , Zhang Cheng , Shao Yue 
Published: November 2023

AbstractBackgroundThis study sought to analyze the correlation between oxidative balance score (OBS) and cardiometabolic risk factors (CMRFs) and mortality in individuals with CMRFs.MethodsData were chosen from the National Health and Nutrition Examination Survey. The survey-weighted multivariable logistic regression models were implemented to explore the relationship between OBS and the risk of CMRFs. Then, Cox proportional hazard models were employed to estimate the impact of OBS on mortality in individuals with CMRFs.ResultsFollowing multivariate adjustment, the subjects in the highest quartile exhibited a 46% reduction in the risk of CMRFs, a 33% reduction in the risk of diabetes, a 31% reduction in the risk of hypertension, and a 36% reduction in the risk of hyperlipidemia, compared with those in the lowest quartile. Furthermore, each 1-unit increase in OBS was remarkably negatively correlated with the prevalence of CMRFs, diabetes, hypertension, and hyperlipidemia. The correlation between OBS and CMFRs was found to be mediated by serum γ-glutamyltransferase (GGT) and white blood cells (WBC), and the mediation effect of GGT levels and WBC, accounting for 6.90% and 11.51%, respectively. Lastly, the multivariate Cox regression model revealed that elevated OBS, irrespective of whether it was treated as a categorical or continuous variable, exhibited a significant association with decreased mortality from all causes, cardiovascular disease, and cancer.ConclusionsAn increased OBS might reflect a lower risk of CMRFs and a favorable prognosis for individuals with CMRFs. Moreover, WBC and GGT may play a potential mediating role between OBS and CMRFs.What is new?An elevated OBS was correlated with a reduced risk of developing CMRFs. Furthermore, WBC and GGT could act as mediators in this association.An increased OBS might indicate a positive prognosis for individuals with CMRFs.What are the clinical implications?OBS might serve as a valuable tool to guide the general population toward adopting healthy diets and positive lifestyle patterns in order to mitigate the risk of CMRFs and enhance the prognosis of CMRFs individuals with CMRFs.
Prognostic Implications of Right Ventricular Dysfunction in Degenerative Mitral Regurgitation
Authors: Bohbot Yohann , Essayagh Benjamin , Benfari Giovanni , Bax Jeroen J. , Le Tourneau Thierry , Topilsky Yan , Antoine Clemence , Rusinaru Dan , Grigioni Francesco , Ajmone Marsan Nina , van Wijngaarden Aniek , Hochstadt Aviram , Roussel Jean Christian , Thapa Prabin , Michelena Hector I , Enriquez-Sarano Maurice , Tribouilloy Christophe 
Published: November 2023

ABSTRACTBackgroundThe prevalence and impact of right ventricular dysfunction (RVD) in degenerative mitral regurgitation (DMR) is unknown. We aimed to determine whether RVD assessed by echocardiography in routine clinical practice is independently associated with survival in patients with DMR.MethodsWe used data from the Mitral Regurgitation International DAtabase-Quantitative (MIDA-Q) which included patients with isolated DMR due to mitral valve prolapse from January 2003 to January 2020 from 5 tertiary centers across North America, Europe, and the Middle East. A cohort of 4,379 (mean age: 67 years, 64.6% males, follow-up:5.3[3.3-8.2]years) consecutive patients with significant (≥moderate) DMR was included and long-term survival was analyzed.ResultsRVD, identified in 584(13.3%) patients, was associated with reduced 10-year survival (49±3%vs.67±1%;p<0.001), overall and in all subgroups of patients, even after comprehensive adjustment including left ventricular dilatation and dysfunction, DMR severity, pulmonary pressures and surgery (adjusted HR[95%CI]=1.55[1.31-1.84];p<0.001). This excess mortality was observed under medical management (adjusted HR[95%CI]=1.39[1.12-1.72];p=0.003) and after surgical correction of mitral regurgitation (adjusted HR[95%CI]=1.56[1.08-2.27];p=0.019). Patients with RVD undergoing surgery within 3 months of diagnosis experienced a better 10-year survival (73±4% vs. 38±4%;p<0.001), even after adjustment (adjusted HR[95%CI]=0.53[0.35-0.81];p=0.003)despite an increase of 1-month post-operative mortality (5% vs 2.2% for patients without RVD;p<0.001).ConclusionsRVD is observed in 13.3% of significant DMR and exhibits a powerful and independent association with excess mortality partially attenuated by mitral surgery. Therefore, assessment of right ventricular systolic function should be included in routine DMR evaluation and in the clinical decision-making process.
Structural alterations in a rumination-related network in patients with major depressive disorder
Authors: Cheng Paul Z. , Lee Hsin-Chien , Lane Timothy J. , Hsu Tzu-Yu , Duncan Niall W. 
Published: November 2023

AbstractRumination is a common symptom in major depressive disorder (MDD) and has been linked to risk for that disorder, its prognosis, and relapse likelihood. Previous work has linked individual differences in rumination to structural properties in a variety of brain regions. Some of these regions, such as the dorsolateral prefrontal cortex (dlPFC), have also been highlighted as being altered in MDD, suggesting a connection between structural changes and ruminative symptoms. Although informative, such localised relations have some limitations in the context of a network view of the brain. To further investigate rumination-related structural changes in depression and to situate these within potential functional networks, we acquired structural data from patients with MDD (n = 32) and controls (n = 69). Analysis of cortical grey-matter identified group differences in the dlPFC that were, however, not related to rumination. Instead, rumination was correlated with grey-matter properties in the right precuneus. Using normative functional connectivity analysis on a large independent sample, we show that these two regions are interconnected. It was further shown that the rumination-related precuneus region is highly connected with networks associated with processes such as executive function, autobiographical memory, and visual perception. Notably, each of these processes has been connected to rumination. These results suggest that rumination in depression may be linked to focal structural changes that disrupt a distributed functional network.
Distinct expression patterns of Hedgehog signaling components In mouse gustatory system during postnatal tongue development and adult homeostasis
Authors: Kumari Archana , Franks Nicole E. , Li Libo , Audu Gabrielle , Liskowicz Sarah , Johnson John D. , Mistretta Charlotte M. , Allen Benjamin L. 
Published: November 2023

AbstractIt is well established that the Hedgehog (HH) pathway regulates embryonic development of anterior tongue taste fungiform papilla (FP) and the posterior circumvallate (CVP) and foliate (FOP) taste papillae, and taste organ maintenance and regeneration in adults. However, there are knowledge gaps in determining HH signaling regulation in postnatal taste organ differentiation and maturation. Importantly, the HH transcription factors GLI1, GLI2 and GLI3 have not been investigated in early postnatal stages; and, the receptors PTCH1, GAS1, CDON and HHIP, required to either drive HH pathway activation or antagonism, remain unexplored. UsinglacZreporter mouse models, we mapped expression of the HH ligand SHH, receptors, and transcription factors in FP, CVP and FOP in early and late postnatal and adult stages. In adults we also studied the soft palate, and the geniculate and trigeminal ganglia which extend afferent fibers to the anterior tongue.ShhandGas1are the only components that were consistently expressed within taste buds of all three papillae and the soft palate. In the first postnatal week, we observed a broad expression of HH signaling components in FP and adjacent, non-taste filiform (FILIF) papillae in epithelium or stroma and tongue muscles. Remarkably, we observed elimination ofGli1in FILIF andGas1in muscles, and downregulation ofPtch1in lingual epithelium and ofCdon,Gas1andHhipin stroma from late postnatal stage. Further, HH receptor expression patterns in CVP and FOP epithelium differed from anterior FP. Among all the components, only known positive regulators of HH signaling, SHH,Ptch1,Gli1andGli2, were expressed in the ganglia. Our studies emphasize differential regulation of HH signaling in distinct postnatal developmental periods and in anterior versus posterior taste organs, and lay the foundation for functional studies to understand the roles of numerous HH signaling components in postnatal tongue development.
Herbicidal Quassinoids Isolated fromAilanthus altissimaLeaves
Authors: Kim Young Sook , Moon Surk-Sik , Choi Jung Sup 
Published: November 2023

ABSTRACTBioassay-guided fractionation of the methanolic extract ofAilanthus altissimaleaves led to the isolation of one new quassinoid, named 6-α-tigloyloxyailanthone (3), and three known quassinoids, ailanthone (1), 13, 18-dehydroglaucarubinone (2), and 6-α-tigloyloxychaparrinone (4) by a series of chromatographic methods. The structures of the isolates were established by one-dimensional (1D) and 2D-nuclear magnetic resonance (NMR) analysis along with high-resolution time-of-flight mass spectrometry (HRTOFMS) and chemical methods. In addition, herbicidal activity against five grassy weeds and five broad-leaf weeds was evaluated.
Frommeccassette tordhA: a keyDehalobactergenomic neighborhood in a chloroform and dichloromethane–transforming microbial consortium
Authors: Bulka Olivia , Picott Katherine , Mahadevan Radhakrishnan , Edwards Elizabeth A. 
Published: November 2023

AbstractChloroform (CF) and dichloromethane (DCM) are groundwater contaminants of concern due to their high toxicity and inhibition of important biogeochemical processes such as methanogenesis. Anaerobic biotransformation of CF and DCM has been well documented but typically independently of one another. CF is the electron acceptor for certain organohalide-respiring bacteria that use reductive dehalogenases (RDases) to dechlorinate CF to DCM. In contrast, known DCM-degraders use DCM as their electron donor, which is oxidized using a series of methyltransferases and associated proteins encoded by themeccassette to facilitate the entry of DCM to the Wood-Ljungdahl pathway. The SC05 culture is an enrichment culture sold commercially for bioaugmentation, that transforms CF via DCM to CO2. This culture has the unique ability to dechlorinate CF to DCM using electron equivalents provided by the oxidation of DCM to CO2. Here we use metagenomic and metaproteomic analysis to identify the functional genes involved in each of these transformations. Though 91 metagenome-assembled genomes were assembled, the genes for an RDase—namedacdA—and a completemeccassette were found to be encoded on a single contig belonging toDehalobacter. AcdA and critical Mec proteins were also highly expressed by the culture. Heterologously-expressed AcdA dechlorinated CF and other chloroalkanes but had 100-fold lower activity on DCM. Overall, the high expression of Mec proteins and the activity of AcdA suggest aDehalobactercapable of dechlorination of CF to DCM, and subsequent mineralization of DCM using themeccassette.ImportanceChloroform (CF) and dichloromethane (DCM) are regulated groundwater contaminants. A cost-effective approach to remove these pollutants from contaminated groundwater is to employ microbes that transform CF and DCM as part of their metabolism, thus depleting the contamination as the microbes continue to grow. In this work, we investigate bioaugmentation culture SC05, a mixed microbial consortium that effectively and simultaneously degrades both CF and DCM coupled to the growth ofDehalobacter. We identified the functional genes responsible for the transformation of CF and DCM in SC05. These genetic biomarkers provide a means to monitor the remediation process in the field.
Modeling the effect of spatial structure on solid tumor evolution and ctDNA composition
Authors: Rachman Thomas , Bartlett David , Laframboise William , Wagner Patrick , Schwartz Russell , Carja Oana 
Published: November 2023

AbstractCirculating tumor DNA (ctDNA) monitoring, while sufficiently advanced to reflect tumor evolution in real time and inform on cancer diagnosis, treatment, and prognosis, mainly relies on DNA that originates from cell death via apoptosis or necrosis. In solid tumors, chemotherapy and immune infiltration can induce spatially variable rates of cell death, with the potential to bias and distort the clonal composition of ctDNA. Using a stochastic evolutionary model of boundary-driven growth, we study how elevated cell death on the edge of a tumor can simultaneously impact driver mutation accumulation and the representation of tumor clones and mutation detectability in ctDNA. We describe conditions in which invasive clones end up over-represented in ctDNA, clonal diversity can appear elevated in the blood, and spatial bias in shedding can inflate subclonal variant allele frequencies (VAFs). Additionally, we find that tumors that are mostly quiescent can display similar biases, but are far less detectable, and the extent of perceptible spatial bias strongly depends on sequence detection limits. Overall, we show that spatially structured shedding might cause liquid biopsies to provide highly biased profiles of tumor state. While this may enable more sensitive detection of expanding clones, it could also increase the risk of targeting a subclonal variant for treatment. Our results indicate that the effects and clinical consequences of spatially variable cell death on ctDNA composition present an important area for future work.