bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hospital factor and prognosis of COVID-19 in New York City, the United States of America: insights from a retrospective cohort study
Authors: Takahashi Mai , Egorova Natalia N. , Iwagami Masao , Kuno Toshiki 
Published: February 2022

Abstract
Background
April 22nd, 2020, New York City (NYC) was the epicenter of the pandemic of Coronavirus disease 2019 (COVID-19) in the US with differences of death rates among its 5 boroughs. We aimed to investigate the difference in mortality associated with hospital factors (teaching versus community hospital) in NYC.

Design
Retrospective cohort study.

Methods
We obtained medical records of 6509 hospitalized patients with laboratory confirmed COVID-19 from the Mount Sinai Health System including 4 teaching hospitals in Manhattan and 2 community hospitals located outside of Manhattan (Queens and Brooklyn) retrospectively. Propensity score analysis using inverse probability of treatment weighting (IPTW) with stabilized weights was performed to adjust for differences in the baseline characteristics of patients initially presenting to teaching or community hospitals, and those who were transferred from community hospitals to teaching hospitals.

Results
Among 6509 patients, 4653 (72.6%) were admitted in teaching hospitals, 1462 (22.8%) were admitted in community hospitals, and 293 (4.6%) were originally admitted in community and then transferred into teaching hospitals. Patients in community hospitals had higher mortality (42.5%) than those in teaching hospitals (17.6%) or those transferred from community to teaching hospitals (23.5%, P < 0.001). After IPTW-adjustment, when compared to patients cared for at teaching hospitals, the hazard ratio (HR) and 95% confidence interval (CI) of mortality were as follows: community hospitals 2.47 (2.03-2.99); transfers 0.80 (0.58-1.09)).

Conclusions
Patients admitted to community hospitals had higher mortality than those admitted to teaching hospitals.
Screens in fly and beetle reveal vastly divergent gene sets required for developmental processes
Authors: Hakeemi Muhammad Salim , Ansari Salim , Teuscher Matthias , Weißkopf Matthias , Großmann Daniela , Kessel Tobias , Dönitz Jürgen , Siemanowski Janna , Wan Xuebin , Schultheis Dorothea , Frasch Manfred , Roth Siegfried , Schoppmeier Michael , Klingler Martin , Bucher Gregor 
Published: February 2022

Abstract
Background
Most of the known genes required for developmental processes have been identified by genetic screens in a few well-studied model organisms, which have been considered representative of related species, and informative—to some degree—for human biology. The fruit fly Drosophila melanogaster is a prime model for insect genetics, and while conservation of many gene functions has been observed among bilaterian animals, a plethora of data show evolutionary divergence of gene function among more closely-related groups, such as within the insects. A quantification of conservation versus divergence of gene functions has been missing, without which it is unclear how representative data from model systems actually are.

Results
Here, we systematically compare the gene sets required for a number of homologous but divergent developmental processes between fly and beetle in order to quantify the difference of the gene sets. To that end, we expanded our RNAi screen in the red flour beetle Tribolium castaneum to cover more than half of the protein-coding genes. Then we compared the gene sets required for four different developmental processes between beetle and fly. We found that around 50% of the gene functions were identified in the screens of both species while for the rest, phenotypes were revealed only in fly (~ 10%) or beetle (~ 40%) reflecting both technical and biological differences. Accordingly, we were able to annotate novel developmental GO terms for 96 genes studied in this work. With this work, we publish the final dataset for the pupal injection screen of the iBeetle screen reaching a coverage of 87% (13,020 genes).

Conclusions
We conclude that the gene sets required for a homologous process diverge more than widely believed. Hence, the insights gained in flies may be less representative for insects or protostomes than previously thought, and work in complementary model systems is required to gain a comprehensive picture. The RNAi screening resources developed in this project, the expanding transgenic toolkit, and our large-scale functional data make T. castaneum an excellent model system in that endeavor.
Capillary microscopy is a potential screening method for connective tissue disease in children with Raynaud’s phenomenon
Authors: Farenhorst Claudette A. , Roon Anniek M. , Gessel Anne I. , Stel Alja J. , Bootsma Hendrika , Armbrust Wineke , Mulder Douwe J. 
Published: February 2022

Abstract
Background
Nailfold capillary microscopy (NCM) is a cornerstone in the diagnosis of Systemic Sclerosis (SSc) in adulthood. Although Raynaud’s phenomenon (RP) is very common in childhood, studies on diagnostic methods to differentiate between primary RP (PRP) and secondary RP (SRP) at a young age are scarce. The aim of this study was to determine the value of NCM in differentiating between PRP and SRP in children and adolescents with RP.

Methods
In this nested case–control study, 83 patients diagnosed with RP and having underwent NCM in childhood were retrospectively included. Based on whether they were diagnosed with a connective tissue disease (CTD) during follow-up, patients were classified as PRP or SRP. NCM was performed by a vascular technician. PRP and SRP patients were compared on demographics, NCM and serology. Variables associated with SRP were included in a multivariate logistic regression model. Predictive values were calculated for NCM, ANA positivity and the combination of NCM and ANA positivity.

Results
At the time of the NCM, the mean age of the RP patients was 15.4 ± 2.3 years. Of these patients, 78.3% were classified as PRP and 21.7% as SRP at mean follow-up of 6.4 ± 3.20 years. CTDs were miscellaneous, with only one patient having developed SSc. Of the NCM parameters, only capillary loss was associated with SRP (p = 0.01). In a multivariate logistic regression model including ANA, capillary loss was not a predictor of SRP. In a model without ANAs, capillary loss was an independent predictor (OR = 3.98, CI 95% 1.22–12.99). Capillary loss had a sensitivity of 44.4% and a specificity of 84.4% for SRP. ANA combined with capillary loss had a sensitivity of 66.7% and a specificity of 85.7%.

Conclusion
Whereas RP in adulthood is most strongly associated with SSc, children with RP seem to be at risk for developing other CTDs with less apparent NCM abnormalities. Of all NCM findings, only capillary loss was predictive for SRP. NCM did not add to the predictive value of ANA screening. However, with a specificity of 84.4% and being non-invasive, NCM shows potential as a screening method for SRP. More research with a larger study population is required before drawing conclusions.
PD-L1 signaling in reactive astrocytes counteracts neuroinflammation and ameliorates neuronal damage after traumatic brain injury
Authors: Gao Xiang , Li Wei , Syed Fahim , Yuan Fang , Li Ping , Yu Qigui 
Published: February 2022

AbstractBackgroundTissue damage and cellular destruction are the major events in traumatic brain injury (TBI), which trigger sterile neuroimmune and neuroinflammatory responses in the brain. While appropriate acute and transient neuroimmune and neuroinflammatory responses facilitate the repair and adaptation of injured brain tissues, prolonged and excessive neuroimmune and neuroinflammatory responses exacerbate brain damage. The mechanisms that control the intensity and duration of neuroimmune and neuroinflammatory responses in TBI largely remain elusive.MethodsWe used the controlled cortical impact (CCI) model of TBI to study the role of immune checkpoints (ICPs), key regulators of immune homeostasis, in the regulation of neuroimmune and neuroinflammatory responses in the brain in vivo.ResultsWe found that de novo expression of PD-L1, a potent inhibitory ICP, was robustly and transiently induced in reactive astrocytes, but not in microglia, neurons, or oligodendrocyte progenitor cells (OPCs). These PD-L1+reactive astrocytes were highly enriched to form a dense zone around the TBI lesion. Blockade of PD-L1 signaling enlarged brain tissue cavity size, increased infiltration of inflammatory Ly-6CHighmonocytes/macrophages (M/Mɸ) but not tissue-repairing Ly-6CLowF4/80+M/Mɸ, and worsened TBI outcomes in mice. PD-L1 gene knockout enhanced production of CCL2 that is best known for its ability to interact with its cognate receptor CCR2 on Ly-6CHighM/Mϕto chemotactically recruit these cells into inflammatory sites. Mechanically, PD-L1 signaling in astrocytes likely exhibits dual inhibitory activities for the prevention of excessive neuroimmune and neuroinflammatory responses to TBI through (1) the PD-1/PD-L1 axis to suppress the activity of brain-infiltrating PD-1+immune cells, such as PD-1+T cells, and (2) PD-L1 intrinsic signaling to regulate the timing and intensity of astrocyte reactions to TBI.ConclusionsPD-L1+astrocytes act as a gatekeeper to the brain to control TBI-related neuroimmune and neuroinflammatory responses, thereby opening a novel avenue to study the role of ICP–neuroimmune axes in the pathophysiology of TBI and other neurological disorders.
Prenatal inflammation causes obesity and abnormal lipid metabolism via impaired energy expenditure in male offspring
Authors: Ni Meng , Zhang Qianqian , Zhao Jiuru , Yao Dongting , Wang Tao , Shen Qianwen , Li Wei , Li Baihe , Ding Xiya , Liu Zhiwei 
Published: February 2022

Abstract
Introduction
Obesity has becoming a global health issue. Fetus exposed to adversity in the uterine are susceptible to unhealth stimulus in adulthood. Prenatal inflammation is related to poor neonatal outcomes like neurodevelopmental impairments and respiratory complications. Recent studies suggested prenatal lipopolysaccharide (LPS) exposure could result in metabolic disorders. Thus, we hypothesized that offspring exposed to prenatal inflammation could develop into metabolic disorder.

Methods
The pregnant C57BL/6J mice were intraperitoneally injected with 50 μg/kg LPS or saline only once at GD15. The male offspring were weighted weekly until sacrificed. Indirect calorimetry and body composition were both performed at 9 and 18 weeks old. At 20 weeks old, mice were fasted overnight before collecting blood samples and liver for metabolomics analysis and RNA sequencing, respectively. Differentially expressed genes were further verified by RT-qPCR and western blotting.

Results
Prenatal inflammation resulted in obesity with increased fat percentage and decreased energy expenditure in middle-age male offspring. Abnormal lipid accumulation, changes of gene expression profile and upregulation of multi-component mechanistic target of rapamycin complex 1 (mTOR)/Peroxisome proliferator-activated receptor-γ pathway was observed in liver, accompanied with decreased bile acids level, unsaturated fatty acids androgens and prostaglandins in serum. Indirect calorimetry showed increased respiratory exchange rate and deceased spontaneous activity at 9 weeks in LPS group. Impaired energy expenditure was also observed at 18 weeks in LPS group.

Conclusion
Prenatal LPS exposure led to obesity and abnormal lipid metabolism through impaired energy expenditure.
CNS endothelial derived extracellular vesicles are biomarkers of active disease in multiple sclerosis
Authors: Mazzucco Michael , Mannheim William , Shetty Samantha V. , Linden Jennifer R. 
Published: February 2022

AbstractBackgroundMultiple sclerosis (MS) is a complex, heterogenous disease characterized by inflammation, demyelination, and blood–brain barrier (BBB) permeability. Currently, active disease is determined by physician confirmed relapse or detection of contrast enhancing lesions via MRI indicative of BBB permeability. However, clinical confirmation of active disease can be cumbersome. As such, disease monitoring in MS could benefit from identification of an easily accessible biomarker of active disease. We believe extracellular vesicles (EV) isolated from plasma are excellent candidates to fulfill this need. Because of the critical role BBB permeability plays in MS pathogenesis and identification of active disease, we sought to identify EV originating from central nervous system (CNS) endothelial as biomarkers of active MS. Because endothelial cells secrete more EV when stimulated or injured, we hypothesized that circulating concentrations of CNS endothelial derived EV will be increased in MS patients with active disease.MethodsTo test this, we developed a novel method to identify EV originating from CNS endothelial cells isolated from patient plasma using flow cytometry. Endothelial derived EV were identified by the absence of lymphocyte or platelet markers CD3 and CD41, respectively, and positive expression of pan-endothelial markers CD31, CD105, or CD144. To determine if endothelial derived EV originated from CNS endothelial cells, EV expressing CD31, CD105, or CD144 were evaluated for expression of the myelin and lymphocyte protein MAL, a protein specifically expressed by CNS endothelial cells compared to endothelial cells of peripheral organs.ResultsQuality control experiments indicate that EV detected using our flow cytometry method are 0.2 to 1 micron in size. Flow cytometry analysis of EV isolated from 20 healthy controls, 16 relapsing–remitting MS (RRMS) patients with active disease not receiving disease modifying therapy, 14 RRMS patients with stable disease not receiving disease modifying therapy, 17 relapsing-RRMS patients with stable disease receiving natalizumab, and 14 RRMS patients with stable disease receiving ocrelizumab revealed a significant increase in the plasma concentration of CNS endothelial derived EV in patients with active disease compared to all other groups (p = 0.001). Conclusions: For the first time, we have identified a method to identify CNS endothelial derived EV in circulation from human blood samples. Results from our pilot study indicate that increased levels of CNS endothelial derived EV may be a biomarker of BBB permeability and active disease in MS.
Development of a split fluorescent protein-based RNA live-cell imaging system to visualize mRNA distribution in plants
Authors: Huang Nien-Chen , Luo Kai-Ren , Yu Tien-Shin 
Published: February 2022

Abstract
Background
RNA live-cell imaging systems have been used to visualize subcellular mRNA distribution in living cells. The RNA-binding protein (RBP)-based RNA imaging system exploits specific RBP and the corresponding RNA recognition sequences to indirectly label mRNAs. Co-expression of fluorescent protein-fused RBP and target mRNA conjugated with corresponding RNA recognition sequences allows for visualizing mRNAs by confocal microscopy. To minimize the background fluorescence in the cytosol, the nuclear localization sequence has been used to sequester the RBP not bound to mRNA in the nucleus. However, strong fluorescence in the nucleus may limit the visualization of nucleus-localized RNA and sometimes may interfere in detecting fluorescence signals in the cytosol, especially in cells with low signal-to-noise ratio.

Results
We eliminated the background fluorescence in the nucleus by using the split fluorescent protein-based approach. We fused two different RBPs with the N- or C-terminus of split fluorescent proteins (FPs). Co-expression of RBPs with the target mRNA conjugated with the corresponding RNA recognition sequences can bring split FPs together to reconstitute functional FPs for visualizing target mRNAs. We optimized the system with minimal background fluorescence and used the imaging system to visualize mRNAs in living plant cells.

Conclusions
We established a background-free RNA live-cell imaging system that provides a platform to visualize subcellular mRNA distribution in living plant cells.
Do clinical guidelines facilitate or impede drivers of treatment in Fabry disease?
Authors: Hughes Derralynn A. , Aguiar Patrício , Lidove Olivier , Nicholls Kathleen , Nowak Albina , Thomas Mark , Torra Roser , Vujkovac Bojan , West Michael L. , Feriozzi Sandro 
Published: February 2022

Abstract
Background
Variable disease progression confounds accurate prognosis in Fabry disease. Evidence supports the long-term benefit of early intervention with disease-specific therapy, but current guidelines recommend treatment initiation based on signs that may present too late to avoid irreversible organ damage. Findings from the ‘PRoposing Early Disease Indicators for Clinical Tracking in Fabry Disease’ (PREDICT-FD) initiative included expert consensus on 27 early indicators of disease progression in Fabry disease and on drivers of and barriers to treatment initiation in Fabry disease. Here, we compared the PREDICT-FD indicators with guidance from the European Fabry Working Group and various national guidelines to identify differences in signs supporting treatment initiation and how guidelines themselves might affect initiation. Finally, anonymized patient histories were reviewed by PREDICT-FD experts to determine whether PREDICT-FD indicators supported earlier treatment than existing guidance.

Results
Current guidelines generally aligned with PREDICT-FD on indicators of renal involvement, but most lacked specificity regarding cardiac indicators. The prognostic significance of neurological indicators such as white matter lesions (excluded by PREDICT-FD) was questioned in some guidelines and excluded from most. Some PREDICT-FD patient-reported signs (e.g., febrile crises) did not feature elsewhere. Key drivers of treatment initiation in PREDICT-FD were: (A) male sex, young age, and clinical findings (e.g., severe pain, organ involvement), (B) improving clinical outcomes and preventing disease progression, and (C) a family history of Fabry disease (especially if outcomes were severe). All guidelines aligned with (A) and several advocated therapy for asymptomatic male patients. There was scant evidence of (B) in current guidance: for example, no countries mandated ancillary symptomatic therapy, and no guidance advocated familial screening with (C) when diagnosis was confirmed. Barriers were misdiagnosis and a lack of biomarkers to inform timing of treatment. Review of patient histories generally found equal or greater support for treatment initiation with PREDICT-FD indicators than with other guidelines and revealed that the same case and guideline criteria often yielded different treatment recommendations.

Conclusions
Wider adoption of PREDICT-FD indicators at a national level could promote earlier treatment in Fabry disease. Clearer, more concise guidance is needed to harmonize treatment initiation in Fabry disease internationally.
Up-regulation of MTHFD2 is associated with clinicopathological characteristics and poor survival in ovarian cancer, possibly by regulating MOB1A signaling
Authors: Cui Xiangrong , Su Huancheng , Yang Jiaolin , Wu Xueqing , Huo Kai , Jing Xuan , Zhang Sanyuan 
Published: February 2022

Abstract
Background
MTHFD2 is a folate-coupled metabolic enzyme, which has been proved to participant in the metabolic reprogramming and tumor cell-sustaining proliferative capacity. However, the function of MTHFD2 in the development of ovarian cancer and its potential molecular mechanisms is still unclear.

Materials and methods
The expression, various mutations, prognosis, and related network signaling pathways of MTHFD2 were analyzed using bioinformatics-related websites, including Oncomine, GEPIA, UCSC, cBioPortal, KM Plotter, TISIDB and TIMER. The prognostic value of MTHFD2 expression was validated by our own ovarian cancer samples using RT-qPCR. The migration ad invasion of ovarian cancer cells were further analyzed by CCK-8 and transwell assay. The Western-blot assay was performed to explore the protein levels of MTHFD2 and MOB1A.

Results
We obtained the following important results. (1) MTHFD2 expression was markedly up-regulated in ovarian cancer than normal samples. (2) Among patients with ovarian cancer, those with higher MTHFD2 expression was associated with lower survival rate. (3) The major mutation type of MTHFD2 in ovarian cancer samples was missense mutation. (4) MTHFD2 knockdown inhibited proliferation, migration, invasion, as well as the expression of MOB1A in vitro.

Conclusion
MTHFD2, as a NAD + -dependent enzyme, accelerated tumor progression by up-regulating MBO1A, suggesting that this protein may be an independent prognostic factor and a potential therapeutic target for future ovarian cancer treatments.
Pregnancy Management in Multiple Sclerosis and Other Demyelinating Diseases
Authors: Bove Riley M. , Houtchens Maria K. 
Published: February 2022

ABSTRACT

PURPOSE OF REVIEW
Multiple sclerosis (MS) and neuromyelitis optica spectrum disorders (NMOSDs) are chronic autoimmune demyelinating conditions of the central nervous system often diagnosed in women of childbearing age. Therefore, safe family planning, pregnancy, and postpartum management are important considerations for many patients with MS or NMOSD.

RECENT FINDINGS
Many patients with MS can safely become pregnant and remain well throughout pregnancy and the postpartum period with guidance from specialists on treatment planning. During pregnancy, women with NMOSD may face some increased risk of both neurologic and obstetric complications. Recent attention has focused on evaluating the safety of pharmacologic agents during pregnancy and breastfeeding. Unfortunately, care disparities remain common in both MS and NMOSD, and recovery of function is often not optimally managed in the postpartum period.

SUMMARY
This article reviews the current state of knowledge on peripartum management in these neurologic conditions and offers practical considerations and case studies. When caring for women with MS and NMOSD of childbearing potential, treatment planning is important to optimize outcomes in both patient and newborn.
DFT Analysis of the Formation of a Titanium n-Butoxide Derivative [[Ti[O(CH2)3CH3]2Cl·OH]2]2 through OH Bridge Formation and Molecular Interactions between Butoxy Groups
Authors: Koike Katsuhiko 
Published: February 2022

Abstract
The structural changes of titanium n-butoxide derivatives in coatings prepared from a mixture of titanium butoxide in concentrated hydrochloric acid, which contains a five-coordinated titanium complex (Ti[O(CH2)3CH3]3Cl·H2O), are investigated using density functional theory calculations. Initially, the complex is stabilized owing to dimer formation through molecular interactions. Subsequently, stabilization occurs due to OH bridge formation upon butanol elimination. The two dimers then unite to form [[Ti[O(CH2)3CH3]2Cl·OH]2]2 owing to the molecular interactions between the butoxy groups.