bluuebunny/crossref_metadata_2025_split huggingface dataset:
Acute isolated posterior cerebral artery stroke treated with mechanical thrombectomy: A single-center experience and review of the literature
Authors: Baig Ammad A , Monteiro Andre , Waqas Muhammad , Cappuzzo Justin M , Siddiqi Manhal , Doane Jacob , Dossani Rimal H , Almayman Faisal , Khawar Wasiq I , Davies Jason M , Snyder Kenneth V , Levy Elad I , Siddiqui Adnan H 
Published: January 2022

Background Acute isolated posterior cerebral artery (PCA) occlusions account for 5–10% of all ischemic events. Due to peculiar patient presentation, the potential benefit of mechanical thrombectomy (MT) remains controversial. We evaluated the safety, feasibility, and effectiveness of MT in our patients and compared our results with the literature review conducted. Methods Charts were reviewed retrospectively for consecutive patients diagnosed with acute PCA stroke who underwent MT. Demographics, procedural, and follow-up details were noted. For the literature review, a systematic search of PubMed, MEDLINE, and EMBASE databases was conducted for the keywords “posterior cerebral artery” and “thrombectomy” for articles published between January 1, 2010 and June 30, 2021. Estimated rates for recanalization, favorable outcomes (modified Rankin Scale [mRS] score 0–2), symptomatic intracerebral hemorrhage (sICH), and mortality were extracted. Results Our cohort included 21 patients. Mean age was 71.2 years (standard deviation [SD] ± 10.2). Median National Institutes of Health Stroke Scale (NIHSS) presentation score was 9 (interquartile range [IQR] 5–15), with visual symptoms reported in 12(57.1%) patients. Overall, final modified thrombolysis in cerebral infarction (mTICI) 2b-3 was achieved in 17 patients (80.9%) with first-pass mTICI 2b-3 attained in 8 (38.1%). Postprocedure sICH occurred in 1 (4.8%) patient. Fifteen (71.4%) patients had a 0–2 mRS score at 90 days. Visual symptoms resolved in 10 of 12(83.3%) patients. Mortality occurred in 2 (9.5%) patients. For the systematic review, cohorts from 4 articles plus ours were included, totaling 222 patients. The estimated rate of successful recanalization was 85.25% (95% confidence interval[CI], 73.05%–97.45%), sICH was 3.60% (95% CI, 1.11%–6.09%), and mortality was 10.51% (95% CI, 5.88%–15.15%). Conclusion The results of our series and systematic review indicate MT as a potentially safe and effective treatment modality for acute PCA stroke. These results also indicate that patient selection and assessment may be the key in obtaining favorable outcomes.
Serum NfL levels in the first five years predict 10-year thalamic fraction in patients with MS
Authors: Lokhande Hrishikesh , Rosso Mattia , Tauhid Shahamat , Chu Renxin , Healy Brian C. , Saxena Shrishti , Barro Christian , Paul Anu , Polgar-Turcsanyi Mariann , Anderson Mark , Glanz Bonnie I. , Kropshofer Harald , Granziera Cristina , Leppert David , Kappos Ludwig , Kuhle Jens , Weiner Howard L. , Bakshi Rohit , Chitnis Tanuja 
Published: January 2022

Background Serum neurofilament light chain (sNfL) levels are associated with relapses, MRI lesions, and brain volume in multiple sclerosis (MS). Objective To explore the value of early serum neurofilament light (sNfL) measures in prognosticating 10-year regional brain volumes in MS. Methods Patients with MS enrolled in the Comprehensive Longitudinal Investigations in MS at Brigham and Women's Hospital (CLIMB) study within five years of disease onset who had annual blood samples from years 1–10 (n = 91) were studied. sNfL was measured with a single molecule array (SIMOA) assay. We quantified global cortical thickness and normalized deep gray matter (DGM) volumes (fractions of the thalamus, caudate, putamen, and globus pallidus) from high-resolution 3 T MRI at 10 years. Correlations between yearly sNfL levels and 10-year MRI outcomes were assessed using linear regression models. Results sNfL levels from years 1 and 2 were associated with 10-year thalamus fraction. Early sNfL levels were not associated with 10-year putamen, globus pallidus or caudate fractions. At 10 years, cortical thickness was not associated with early sNfL levels, but was weakly correlated with total DGM fraction. Conclusions Early sNfL levels correlate with 10-year thalamic volume, supporting its role as a prognostic biomarker in MS.
The CLL comorbidity index in a population-based cohort: a tool for clinical care and research
Authors: Rotbain Emelie C. , Gordon Max J. , Vainer Noomi , Frederiksen Henrik , Hjalgrim Henrik , Danilov Alexey V. , Niemann Carsten U. 
Published: January 2022

Abstract
The chronic lymphocytic leukemia comorbidity index (CLL-CI) is an efficient, CLL-specific tool derived from the Cumulative Illness Rating Scale. The CLL-CI is based on the assessment of the organ systems found to be most strongly associated with event-free survival (EFS) in CLL: vascular, upper gastrointestinal, and endocrine, at the time of initiation of CLL therapy. The CLL-CI categorizes patients into low, intermediate, and high risk groups. In the present study, we have employed the CLL-CI in a population-based cohort comprising 4975 patients with CLL. We demonstrate that CLL-CI retains prognostic significance in this large cohort and is associated with overall survival (OS) and EFS from time of first therapy. Furthermore, CLL-CI associates with OS, EFS, and time to first treatment from diagnosis independently of the CLL International Prognostic Index. These findings support the use of the CLL-CI both in research and in clinical practice.
Successful outcome of pre-engraftment COVID-19 in an HCT patient: impact of targeted therapies and cellular immunity
Authors: Pourhassan Hoda , La Rosa Corinna , Chiuppesi Flavia , Puing Alfredo , Aldoss Ibrahim , Park Yoonsuh , Zhou Qiao , Karpinski Veronica , Faircloth Katelyn , Kaltcheva Teodora , Johnson Daisy , Francisco Sandra Ortega , Zaia John A. , Nakamura Ryotaro , Al Malki Monzr M. , Diamond Don J. , Dadwal Sanjeet Singh , Forman Stephen J. 
Published: January 2022

AbstractCoronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has emerged as a global pandemic that upended existing protocols and practices, including those for allogeneic hematopoietic stem cell transplantation (HCT). Here, we describe the successful clinical course and multiple key interventions administered to an acute lymphoblastic leukemia patient, who tested SARS-CoV-2 positive by reverse transcriptase polymerase chain reaction on day −1 of matched unrelated donor (SARS-CoV-2 immunoglobulin G negative) T-cell-replete HCT. This experience allowed for implementing a virologic and immunomonitoring panel to characterize the impact of SARS-CoV-2 on the recipient’s nascent humoral and cellular immune response. The finding of robust, functional, and persistent levels of SARS-CoV-2-specific T cells, starting early after transplant was unexpected, and in combination with the clinical strategy, may have contributed to the favorable outcome. Additionally, it is plausible that preexisting cross-reactive endemic coronavirus immunity in the allogeneic graft reduced recipient susceptibility to COVID-19 disease. This case supports the critical role that T-cell responses may play in mitigating SARS-CoV-2 infection, even in the context of transplant immunosuppression, in which reconstitution of humoral response is commonly delayed. Interventional approaches to transfer SARS-CoV-2-specific cellular immunity such as HCT donor vaccination and adaptive cellular therapy could be of benefit.
Migraine-relevant sex-dependent activation of mouse meningeal afferents by TRPM3 agonists
Authors: Krivoshein G. , Tolner E. A. , Maagdenberg AMJM van den , Giniatullin R. A. 
Published: January 2022

Abstract
Background
Migraine is a common brain disorder that predominantly affects women. Migraine pain seems mediated by the activation of mechanosensitive channels in meningeal afferents. Given the role of transient receptor potential melastatin 3 (TRPM3) channels in mechanical activation, as well as hormonal regulation, these channels may play a role in the sex difference in migraine. Therefore, we investigated whether nociceptive firing induced by TRPM3 channel agonists in meningeal afferents was different between male and female mice. In addition, we assessed the relative contribution of mechanosensitive TRPM3 channels and that of mechanosensitive Piezo1 channels and transient receptor potential vanilloid 1 (TRPV1) channels to nociceptive firing relevant to migraine in both sexes.

Methods
Ten- to 13-week-old male and female wildtype (WT) C57BL/6 J mice were used. Nociceptive spikes were recorded directly from nerve terminals in the meninges in the hemiskull preparations.

Results
Selective agonists of TRPM3 channels profoundly activated peripheral trigeminal nerve fibres in mouse meninges. A sex difference was observed for nociceptive firing induced by either PregS or CIM0216, both agonists of TRPM3 channels, with the induced firing being particularly prominent for female mice. Application of Yoda1, an agonist of Piezo1 channels, or capsaicin activating TRPV1 channels, although also leading to increased nociceptive firing of meningeal fibres, did not reveal a sex difference. Cluster analyses of spike activities indicated a massive and long-lasting activation of TRPM3 channels with preferential induction of large-amplitude spikes in female mice. Additional spectral analysis revealed ​a dominant contribution of spiking activity in the α- and β-ranges following TRPM3 agonists in female mice.

Conclusions
Together, we revealed a specific mechanosensitive profile of nociceptive firing in females and suggest TRPM3 channels as a potential novel candidate for the generation of migraine pain, with particular relevance to females.
Two genomic regions of a sodium azide induced rice mutant confer broad-spectrum and durable resistance to blast disease
Authors: Lo Kuan-Lin , Chen Yi-Nian , Chiang Min-Yu , Chen Mei-Chun , Panibe Jerome P. , Chiu Chung-Chun , Liu Lu-Wei , Chen Liang-Jwu , Chen Chun-Wei , Li Wen-Hsiung , Wang Chang-Sheng 
Published: January 2022

AbstractRice blast, one of the most destructive epidemic diseases, annually causes severe losses in grain yield worldwide. To manage blast disease, breeding resistant varieties is considered a more economic and environment-friendly strategy than chemical control. For breeding new resistant varieties, natural germplasms with broad-spectrum resistance are valuable resistant donors, but the number is limited. Therefore, artificially induced mutants are an important resource for identifying new broad-spectrum resistant (R) genes/loci. To pursue this approach, we focused on a broad-spectrum blast resistant rice mutant line SA0169, which was previously selected from a sodium azide induced mutation pool of TNG67, an elite japonica variety. We found that SA0169 was completely resistant against the 187 recently collected blast isolates and displayed durable resistance for almost 20 years. Linkage mapping and QTL-seq analysis indicated that a 1.16-Mb region on chromosome 6 (Pi169-6(t)) and a 2.37-Mb region on chromosome 11 (Pi169-11(t)) conferred the blast resistance in SA0169. Sequence analysis and genomic editing study revealed 2 and 7 candidate R genes in Pi169-6(t) and Pi169-11(t), respectively. With the assistance of mapping results, six blast and bacterial blight double resistant lines, which carried Pi169-6(t) and/or Pi169-11(t), were established. The complementation of Pi169-6(t) and Pi169-11(t), like SA0169, showed complete resistance to all tested isolates, suggesting that the combined effects of these two genomic regions largely confer the broad-spectrum resistance of SA0169. The sodium azide induced mutant SA0169 showed broad-spectrum and durable blast resistance. The broad resistance spectrum of SA0169 is contributed by the combined effects of two R regions, Pi169-6(t) and Pi169-11(t). Our study increases the understanding of the genetic basis of the broad-spectrum blast resistance induced by sodium azide mutagenesis, and lays a foundation for breeding new rice varieties with durable resistance against the blast pathogen.
Temperature is not a major factor in the differentiation of gonocytes into ad spermatogonia and fertility outcome in congenitally cryptorchid boys
Authors: Hadziselimovic Faruk 
Published: January 2022

AbstractSpermatogenesis in mammals is a heat-sensitive developmental pathway incompatible with the typical mammalian body temperature of 37 °C. It is thought that this is the reason why the testicles of most mammalian males are outside of the body cavity, in the scrotum, where they function at approximately 33 °C. It has been suggested that the abnormally high temperature environment of cryptorchid testes may lead to impaired testicular development and adult infertility. Here, I summarize the clinical, genetic, and histological evidence that argues against temperature stress and in favor of hypogonadotropic hypogonadism as the underlying cause of adult infertility in cryptorchidism.Patient summary: Infertility and an increased risk of testicular cancer in patients diagnosed with undescended testes are the consequence of a hormonal deficiency rather than temperature-induced cellular damage. Cryptorchidism therefore requires both surgical and hormonal treatment.
Exploring dynamic metabolomics data with multiway data analysis: a simulation study
Authors: Li Lu , Hoefsloot Huub , de Graaf Albert A. , Acar Evrim , Smilde Age K. 
Published: January 2022

Abstract
Background
Analysis of dynamic metabolomics data holds the promise to improve our understanding of underlying mechanisms in metabolism. For example, it may detect changes in metabolism due to the onset of a disease. Dynamic or time-resolved metabolomics data can be arranged as a three-way array with entries organized according to a subjects mode, a metabolites mode and a time mode. While such time-evolving multiway data sets are increasingly collected, revealing the underlying mechanisms and their dynamics from such data remains challenging. For such data, one of the complexities is the presence of a superposition of several sources of variation: induced variation (due to experimental conditions or inborn errors), individual variation, and measurement error. Multiway data analysis (also known as tensor factorizations) has been successfully used in data mining to find the underlying patterns in multiway data. To explore the performance of multiway data analysis methods in terms of revealing the underlying mechanisms in dynamic metabolomics data, simulated data with known ground truth can be studied.

Results
We focus on simulated data arising from different dynamic models of increasing complexity, i.e., a simple linear system, a yeast glycolysis model, and a human cholesterol model. We generate data with induced variation as well as individual variation. Systematic experiments are performed to demonstrate the advantages and limitations of multiway data analysis in analyzing such dynamic metabolomics data and their capacity to disentangle the different sources of variations. We choose to use simulations since we want to understand the capability of multiway data analysis methods which is facilitated by knowing the ground truth.

Conclusion
Our numerical experiments demonstrate that despite the increasing complexity of the studied dynamic metabolic models, tensor factorization methods CANDECOMP/PARAFAC(CP) and Parallel Profiles with Linear Dependences (Paralind) can disentangle the sources of variations and thereby reveal the underlying mechanisms and their dynamics.
A novel nonparametric computational strategy for identifying differential methylation regions
Authors: Sun Xifang , Wang Donglin , Zhu Jiaqiang , Sun Shiquan 
Published: January 2022

Abstract
Background
DNA methylation has long been known as an epigenetic gene silencing mechanism. For a motivating example, the methylomes of cancer and non-cancer cells show a number of methylation differences, indicating that certain features characteristics of cancer cells may be related to methylation characteristics. Robust methods for detecting differentially methylated regions (DMRs) could help scientists narrow down genome regions and even find biologically important regions. Although some statistical methods were developed for detecting DMR, there is no default or strongest method. Fisher’s exact test is direct, but not suitable for data with multiple replications, while regression-based methods usually come with a large number of assumptions. More complicated methods have been proposed, but those methods are often difficult to interpret.

Results
In this paper, we propose a three-step nonparametric kernel smoothing method that is both flexible and straightforward to implement and interpret. The proposed method relies on local quadratic fitting to find the set of equilibrium points (points at which the first derivative is 0) and the corresponding set of confidence windows. Potential regions are further refined using biological criteria, and finally selected based on a Bonferroni adjusted t-test cutoff. Using a comparison of three senescent and three proliferating cell lines to illustrate our method, we were able to identify a total of 1077 DMRs on chromosome 21.

Conclusions
We proposed a completely nonparametric, statistically straightforward, and interpretable method for detecting differentially methylated regions. Compared with existing methods, the non-reliance on model assumptions and the straightforward nature of our method makes it one competitive alternative to the existing statistical methods for defining DMRs.
Using dual-network-analyser for communities detecting in dual networks
Authors: Guzzi Pietro Hiram , Tradigo Giuseppe , Veltri Pierangelo 
Published: January 2022

AbstractBackgroundRepresentations of the relationships among data using networks are widely used in several research fields such as computational biology, medical informatics and social network mining. Recently, complex networks have been introduced to better capture the insights of the modelled scenarios. Among others, dual networks (DNs) consist of mapping information as pairs of networks containing the same set of nodes but with different edges: one, called physical network, has unweighted edges, while the other, called conceptual network, has weighted edges.ResultsWe focus on DNs and we propose a tool to find common subgraphs (aka communities) in DNs with particular properties. The tool, called Dual-Network-Analyser, is based on the identification of communities that induce optimal modular subgraphs in the conceptual network and connected subgraphs in the physical one. It includes the Louvain algorithm applied to the considered case. TheDual-Network-Analysercan be used to study DNs, to find common modular communities. We report results on using the tool to identify communities on synthetic DNs as well as real cases in social networks and biological data.ConclusionThe proposed method has been tested by using synthetic and biological networks. Results demonstrate that it is well able to detect meaningful information from DNs.
RAD gene family analysis in cotton provides some key genes for flowering and stress tolerance in upland cotton G. hirsutum
Authors: Kabir Nosheen , Zhang Xin , Liu Le , Qanmber Ghulam , Zhang Lian , Wang Yu Xuan , Sun Zhuojing , Zhao Na , Wang Gang 
Published: January 2022

Abstract
Background
RADIALIS (RAD), belongs to the MYB gene family and regulates a variety of functions including floral dorsoventral asymmetry in Antirrhinum majus and development of fruit proteins in Solanum lycopersicum. RAD genes contain an SNF2_N superfamily domain. Here, we comprehensively identified 68 RAD genes from six different species including Arabidopsis and five species of cotton.

Results
Phylogenetic analysis classified RAD genes into five groups. Gene structure, protein motifs and conserved amino acid residues indicated that GhRAD genes were highly conserved during the evolutionary process. Chromosomal location information showed that GhRAD genes were distributed unevenly on different chromosomes. Collinearity and selection pressure analysis indicated RAD gene family expansion in G. hirsutum and G. barbadense with purifying selection pressure. Further, various growth and stress related promotor cis-acting elements were observed. Tissue specific expression level indicated that most GhRAD genes were highly expressed in roots and flowers (GhRAD2, GhRAD3, GhRAD4 and GhRAD11). Next, GhRAD genes were regulated by phytohormonal stresses (JA, BL and IAA). Moreover, Ghi-miRN1496, Ghi-miR1440, Ghi-miR2111b, Ghi-miR2950a, Ghi-miR390a, Ghi-miR390b and Ghi-miR7495 were the miRNAs targeting most of GhRAD genes.

Conclusions
Our study revealed that RAD genes are evolutionary conserved and might be involved in different developmental processes and hormonal stress response. Data presented in our study could be used as the basis for future studies of RAD genes in cotton.
Genome-wide association studies for immunoglobulin concentrations in colostrum and serum in Chinese Holstein
Authors: Lin Shan , Ke Cuncun , Liu Lin , Gao Yahui , Xu Lingna , Han Bo , Zhao Yaofeng , Zhang Shengli , Sun Dongxiao 
Published: January 2022

AbstractBackgroundThe early death and health problems of calves caused substantial economic losses in the dairy industry. As the immune system of neonates has not been fully developed, the absorption of maternal immunoglobulin (Ig) from colostrum is essential in protecting newborn calves against common disease organisms in their early life. The overwhelming majority of Ig in bovine whey is transported from the serum. Therefore, Ig concentration in the colostrum and serum of dairy cows are critical traits when estimating the potential disease resistance of its offspring.ResultsColostrum, blood, and hair follicle samples were collected from 588 Chinese Holstein cows within 24 h after calving. The concentration of total IgG, IgG1, IgG2, IgA and IgM in both colostrum and serum were detected via ELISA methods. With GCTA software, genome-wide association studies (GWASs) were performed with 91,620 SNPs genotyped by GeneSeek 150 K (140,668 SNPs) chips. As a result, 1, 5, 1 and 29 significant SNPs were detected associated with the concentrations of colostrum IgG1, IgG2, IgA IgM, and serum IgG2 at the genome-wide level (P < 3.08E–6); 11, 2, 13, 2, 12, 8, 2, 27, 1 and 4 SNPs were found significantly associated with total IgG, IgG1, IgG2, IgA and IgM in colostrum and serum at the suggestive level (P < 6.15E–5). Such SNPs located in or proximate to (±1 Mb) 423 genes, which were functionally implicated in biological processes and pathways, such as immune response, B cell activation, inflammatory response and NF-kappaB signaling pathways. By combining the biological functions and the known QTL data for immune traits in bovine, 14 promising candidate functional genes were identified for immunoglobulin concentrations in colostrum and serum in dairy cattle, they wereFGFR4,FGFR2,NCF1,IKBKG,SORBS3,IGHV1S18,KIT,PTGS2,BAX,GRB2,TAOK1,ICAM1,TGFB1andRAC3.ConclusionsIn this study, we identified 14 candidate genes related to concentrations of immunoglobulins in colostrum and serum in dairy cattle by performing GWASs. Our findings provide a groundwork for unraveling the key genes and causal mutations affecting immunoglobulin concentrations in colostrum and important information for genetic improvement of such traits in dairy cattle.