bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cr-pyrope xenocrysts with oxide mineral inclusions from the Chompolo lamprophyres (Aldan shield): Insights into mantle processes beneath the southeastern Siberian craton
Authors: Rezvukhin Dmitriy I. , Nikolenko Evgeny I. , Sharygin Igor S. , Rezvukhina Olga V. , Chervyakovskaya Maria V. , Korsakov Andrey V. 
Published: January 2022

AbstractPyrope xenocrysts (N = 52) with associated inclusions of Ti- and/or Cr-rich oxide minerals from the Aldanskaya dyke and Ogonek diatreme (Chompolo field, southeastern Siberian craton) have been investigated. The majority of xenocrysts are of lherzolitic paragenesis and have concave-upwards (normal) rare earth element (REEN) patterns that increase in concentration from light REE to medium–heavy REE (Group 1). Four Ca-rich (5.7–7.4 wt.% CaO) pyropes are extremely low in Ti, Na and Y and have sinusoidal REEN spectra, thus exhibiting distinct geochemical signatures (Group 2). A peculiar xenocryst, s165, is the only sample to show harzburgitic derivation, whilst demonstrating a normal-to-weakly sinusoidal REEN pattern and the highest Zr (93 ppm) and Sc (471 ppm). Chromite–magnesiochromite, rutile, Mg-ilmenite and crichtonite-group minerals comprise a suite of oxide mineral inclusions in the pyrope xenocrysts. These minerals are characteristically enriched in Cr with 0.6–7.2 wt.% Cr2O3 in rutile, 0.7–3.6 wt.% in Mg-ilmenite and 7.1–18.0 wt.% in the crichtonite-group minerals. Complex titanates of the crichtonite group enriched in large ion lithophile elements (LILE) are high in Al2O3 (0.9–2.2 wt.%), ZrO2 (1.5–5.4 wt.%) and display a trend of compositions from the Ca–Sr-specific varieties to the Ba-dominant species (e.g. lindsleyite). In the pyrope xenocrysts the oxides coexist with silicates (clino- and orthopyroxene and olivine), hydrous silicates (talc, phlogopite and amphibole), carbonate (magnesite), sulfides (pentlandite, chalcopyrite, breakdown products of monosulfide and bornite solid solutions), apatite and graphite. P–T estimates imply the inclusion-bearing pyrope xenocrysts have been derived from low-temperature peridotite assemblages that resided at temperatures of ~600–800°C and a pressure range of ~25–35 kbar in the graphite stability field. Pyrope genesis is linked to the metasomatic enrichment of peridotite protoliths by Ca–Zr–LILE-bearing percolating fluid–melt phases containing significant volatile components. These metasomatic agents are probably volatile-rich melts or supercritical C–O–H–S fluids that were released from a Palaeo-subduction slab.
Congenital anemia reveals distinct targeting mechanisms for master transcription factor GATA1
Authors: Ludwig Leif S. , Lareau Caleb A. , Bao Erik L. , Liu Nan , Utsugisawa Taiju , Tseng Alex M. , Myers Samuel A. , Verboon Jeffrey M. , Ulirsch Jacob C. , Luo Wendy , Muus Christoph , Fiorini Claudia , Olive Meagan E. , Vockley Christopher M. , Munschauer Mathias , Hunter Abigail , Ogura Hiromi , Yamamoto Toshiyuki , Inada Hiroko , Nakagawa Shinichiro , Ohzono Shuichi , Subramanian Vidya , Chiarle Roberto , Glader Bertil , Carr Steven A. , Aryee Martin J. , Kundaje Anshul , Orkin Stuart H. , Regev Aviv , McCavit Timothy L. , Kanno Hitoshi , Sankaran Vijay G. 
Published: January 2022

Abstract
Master regulators, such as the hematopoietic transcription factor (TF) GATA1, play an essential role in orchestrating lineage commitment and differentiation. However, the precise mechanisms by which such TFs regulate transcription through interactions with specific cis-regulatory elements remain incompletely understood. Here, we describe a form of congenital hemolytic anemia caused by missense mutations in an intrinsically disordered region of GATA1, with a poorly understood role in transcriptional regulation. Through integrative functional approaches, we demonstrate that these mutations perturb GATA1 transcriptional activity by partially impairing nuclear localization and selectively altering precise chromatin occupancy by GATA1. These alterations in chromatin occupancy and concordant chromatin accessibility changes alter faithful gene expression, with failure to both effectively silence and activate select genes necessary for effective terminal red cell production. We demonstrate how disease-causing mutations can reveal regulatory mechanisms that enable the faithful genomic targeting of master TFs during cellular differentiation.
Sirolimus plus prednisolone vs sirolimus monotherapy for kaposiform hemangioendothelioma: a randomized clinical trial
Authors: Ji Yi , Chen Siyuan , Zhou Jiangyuan , Yang Kaiying , Zhang Xuepeng , Xiang Bo , Qiu Tong , Gong Xue , Zhang Zixin , Lan Yuru , Hu Fan , Kong Feiteng , Qiu Qingxia , Zhang Yongbo 
Published: January 2022

Abstract
The Kasabach-Merritt phenomenon (KMP) in kaposiform hemangioendothelioma (KHE) is characterized by life-threatening thrombocytopenia and consumptive coagulopathy. This study compared the efficacy and safety of sirolimus plus prednisolone vs sirolimus monotherapy as treatment strategies for KHE with KMP in the largest cohort to date. Participants were randomized to receive either sirolimus in combination with a short course of prednisolone or sirolimus monotherapy for at least 12 months. The primary outcome was defined as achievement of a durable platelet response (platelet count &gt;100 × 109/L) at week 4. Participants completed efficacy assessments 2 years after the initial treatment. At week 4, a durable platelet response was achieved by 35 of 37 patients given sirolimus and prednisolone compared with 24 of 36 patients given sirolimus monotherapy (difference 27.9%; 95% confidence interval, 10.0-44.7). Compared with the sirolimus monotherapy group, the combination treatment group showed improvements in terms of measures of durable platelet responses at all points during the initial 3-week treatment period, median platelet counts during weeks 1 to 4, increased numbers of patients achieving fibrinogen stabilization at week 4, and objective lesion responses at month 12. Patients receiving combination therapy had fewer blood transfusions and a lower total incidence of disease sequelae than patients receiving sirolimus alone. The frequencies of total adverse events and grade 3-4 adverse events during treatment were similar in both groups. The responses seen in patients with KHE with KMP were profound and encouraging, suggesting that sirolimus plus prednisolone should be considered a valid treatment of KHE with KMP. This trial was registered at www.clinicaltrials.gov as #NCT03188068.
Regenerating islet-derived protein 3-α is a prognostic biomarker for gastrointestinal chronic graft-versus-host disease
Authors: DePriest Brittany Paige , Li Hong , Bidgoli Alan , Onstad Lynn , Couriel Daniel , Lee Stephanie J. , Paczesny Sophie 
Published: January 2022

Abstract
Prognostic biomarkers used to identify likelihood of disease progression have not been identified for chronic graft-versus-host disease (cGVHD), the leading cause of late nonrelapse mortality (NRM) in survivors of allogeneic hematopoietic cell transplantation. Gastrointestinal cGVHD (GI-cGVHD) has been particularly challenging to classify. Here, we analyzed 3 proteomics markers (Regenerating islet-derived protein 3-α [Reg3α], C-X-C motif ligand 9 [CXCL9], and Stimulation-2 [ST2]) in 2 independent cohorts of patients with cGVHD totaling 289 patients. Plasma concentrations of Reg3α were significantly increased in patients with GI-cGVHD (P = .0012) compared with those without (P = .01), but plasma concentrations of CXCL9 and ST2 were not. Patients with high Reg3α (≥72 ng/mL) vs low Reg3α had higher NRM (23% vs 11%; P = .015). Because Reg3α has been identified as a lower GI tract marker in acute GVHD, we correlated Reg3α with lower acute-like GI-cGVHD vs classical fibrotic-like esophageal manifestations and found that Reg3α did not differ between the subtypes. No difference was observed between upper GI tract and lower GI tract subtypes. Patients with extremely high Reg3α (≥180 ng/mL) had higher GI scores but not higher scores for the lower GI tract. In a multivariable Cox regression model, patients with high Reg3α were 1.9 times more likely to die without relapse. Our findings demonstrate the utility of Reg3α as a prognostic marker for GI-cGVHD. These data warrant prospective biomarker validation studies.
Indirect comparison of tisagenlecleucel and historical treatments for relapsed/refractory diffuse large B-cell lymphoma
Authors: Maziarz Richard T. , Zhang Jie , Yang Hongbo , Chai Xinglei , Yuan Chengbo , Schwarz Elisabeth , Jakovac Mihael , Martinez-Prieto Marcela , Agarwal Abhijit , Degtyarev Evgeny , Tam Constantine , Salles Gilles 
Published: January 2022

Abstract
No head-to-head trials have compared the efficacy of tisagenlecleucel vs historical treatments for adults with relapsed or refractory diffuse large B-cell lymphoma (r/r DLBCL). This study indirectly compared the overall survival (OS) and overall response rate (ORR) associated with tisagenlecleucel, using data from the JULIET study (Study of Efficacy and Safety of CTL019 in Adult DLBCL Patients; #NCT02445248), vs historical treatments assessed in the CORAL (Collaborative Trial in Relapsed Aggressive Lymphoma) study follow-up population. To assess treatment effects in the treated (full analysis set [FAS]) and enrolled (intention-to-treat [ITT]) study populations, the JULIET FAS vs the CORAL follow-up FAS and JULIET ITT vs CORAL follow-up ITT populations were separately compared. Propensity score weighting using standardized mortality ratio weight (SMRW) and fine stratification weight (FSW) was used to compare OS and ORR, adjusting for baseline confounders. The results indicated that tisagenlecleucel was associated with a lower hazard of death among the FAS (adjusted hazard ratio [95% confidence interval], both FSW and SMRW, 0.44 [0.32, 0.59]) and ITT populations (FSW, 0.60 [0.44, 0.77]; SMRW, 0.57 [0.44, 0.73]; all, P &lt; .001). Median OS was 12.48 months (JULIET) vs 4.34 to 4.40 months (CORAL) for the FAS, and 8.25 (JULIET) months vs 4.04 to 4.86 (CORAL) months for the ITT populations. Tisagenlecleucel was associated with a significantly higher ORR compared with historical treatments among the FAS (adjusted response rate difference [95% confidence interval], both FSW and SMRW, 36% [22%, 0.48%]; P &lt; .001) and among the ITT populations after SMRW adjustment (11% [0%, 22%]; P = .043). This analysis supports that improved response and OS are achieved in patients with r/r DLBCL treated with tisagenlecleucel compared with those treated with alternative historical treatments.
Abnormal lipid droplets accumulation induced cognitive deficits in obstructive sleep apnea syndrome mice via JNK/SREBP/ACC pathway but not through PDP1/PDC pathway
Authors: Li Dongze , Xu Na , Hou Yanyan , Ren Wenjing , Zhang Na , Wang Xi , Sun Yeying , Lu Wenxue , Qu Guiwu , Yu Yan , Lv Changjun , Han Fang 
Published: January 2022

AbstractThe mechanisms of chronic intermittent hypoxia (CIH)-induced cognitive deficits remain unclear. Here, our study found that about 3 months CIH treatment induced lipid droplets (LDs) accumulation in hippocampal nerve and glia cells of C57BL/6 mice, and caused severe neuro damage including neuron lesions, neuroblast (NB) apoptosis and abnormal glial activation. Studies have shown that the neuronal metabolism disorders might contribute to the CIH induced-hippocampal impairment. Mechanistically, the results showed that pyruvate dehydrogenase complex E1ɑ subunit (PDHA1) and the pyruvate dehydrogenase complex (PDC) activator pyruvate dehydrogenase phosphatase 1 (PDP1) did not noticeable change after intermittent hypoxia. Consistent with those results, the level of Acetyl-CoA in hippocampus did not significantly change after CIH exposure. Interestingly, we found that CIH produced large quantities of ROS, which activated the JNK/SREBP/ACC pathway in nerve and glia cells. ACC catalyzed the carboxylation of Acetyl-CoA to malonyl-CoA and then more lipid acids were synthesized, which finally caused aberrant LDs accumulation. Therefore, the JNK/SREBP/ACC pathway played a crucial role in the cognitive deficits caused by LDs accumulation after CIH exposure. Additionally, LDs were peroxidized by the high level of ROS under CIH conditions. Together, lipid metabolic disorders contributed to nerve and glia cells damage, which ultimately caused behavioral dysfunction. An active component ofSalvia miltiorrhiza, SMND-309, dramatically alleviated these injuries and improved cognitive deficits of CIH mice.
Degradome comparison between wild and cultivated rice identifies differential targeting by miRNAs
Authors: Swetha Chenna , Narjala Anushree , Pandit Awadhesh , Tirumalai Varsha , Shivaprasad P. V. 
Published: January 2022

Abstract
Background
Small non-coding (s)RNAs are involved in the negative regulation of gene expression, playing critical roles in genome integrity, development and metabolic pathways. Targeting of RNAs by ribonucleoprotein complexes of sRNAs bound to Argonaute (AGO) proteins results in cleaved RNAs having precise and predictable 5` ends. While tools to study sliced bits of RNAs to confirm the efficiency of sRNA-mediated regulation are available, they are sub-optimal. In this study, we provide an improvised version of a tool with better efficiency to accurately validate sRNA targets.

Results
Here, we improvised the CleaveLand tool to identify additional micro (mi)RNA targets that belong to the same family and also other targets within a specified free energy cut-off. These additional targets were otherwise excluded during the default run. We employed these tools to understand the sRNA targeting efficiency in wild and cultivated rice, sequenced degradome from two rice lines, O. nivara and O. sativa indica Pusa Basmati-1 and analyzed variations in sRNA targeting. Our results indicate the existence of multiple miRNA-mediated targeting differences between domesticated and wild species. For example, Os5NG4 was targeted only in wild rice that might be responsible for the poor secondary wall formation when compared to cultivated rice. We also identified differential mRNA targets of secondary sRNAs that were generated after miRNA-mediated cleavage of primary targets.

Conclusions
We identified many differentially targeted mRNAs between wild and domesticated rice lines. In addition to providing a step-wise guide to generate and analyze degradome datasets, we showed how domestication altered sRNA-mediated cascade silencing during the evolution of indica rice.
Genome-wide high-throughput signal peptide screening via plasmid pUC256E improves protease secretion in Lactiplantibacillus plantarum and Pediococcus acidilactici
Authors: Chen Binbin , Loo Bryan Zong Lin , Cheng Ying Ying , Song Peng , Fan Huan , Latypov Oleg , Kittelmann Sandra 
Published: January 2022

Abstract
Background
Proteases catalyze the hydrolysis of peptide bonds of proteins, thereby improving dietary protein digestibility, nutrient availability, as well as flavor and texture of fermented food and feed products. The lactobacilli Lactiplantibacillus plantarum (formerly Lactobacillus plantarum) and Pediococcus acidilactici are widely used in food and feed fermentations due to their broad metabolic capabilities and safe use. However, extracellular protease activity in these two species is low. Here, we optimized protease expression and secretion in L. plantarum and P. acidilactici via a genetic engineering strategy.

Results
To this end, we first developed a versatile and stable plasmid, pUC256E, which can propagate in both L. plantarum and P. acidilactici. We then confirmed expression and secretion of protease PepG1 as a functional enzyme in both strains with the aid of the previously described L. plantarum-derived signal peptide LP_0373. To further increase secretion of PepG1, we carried out a genome-wide experimental screening of signal peptide functionality. A total of 155 predicted signal peptides originating from L. plantarum and 110 predicted signal peptides from P. acidilactici were expressed and screened for extracellular proteolytic activity in the two different strains, respectively. We identified 12 L. plantarum signal peptides and eight P. acidilactici signal peptides that resulted in improved yield of secreted PepG1. No significant correlation was found between signal peptide sequence properties and its performance with PepG1.

Conclusion
The vector developed here provides a powerful tool for rapid experimental screening of signal peptides in both L. plantarum and P. acidilactici. Moreover, the set of novel signal peptides identified was widely distributed across strains of the same species and even across some closely related species. This indicates their potential applicability also for the secretion of other proteins of interest in other L. plantarum or P. acidilactici host strains. Our findings demonstrate that screening a library of homologous signal peptides is an attractive strategy to identify the optimal signal peptide for the target protein, resulting in improved protein export.
Ultrasonographic assessment of preoperative gastric volume in patients with dyspepsia: a prospective observational study
Authors: Tan Yuming , Wang Xianchun , Yang Han , Pan Chuanlong , Luo Nanbo , Li Junjie , Yang Fang , Bei Yanling , Cahilog Zhen , Chen Qian , Liu Zhiheng , Yang Xinping 
Published: January 2022

Abstract
Background
Patients undergoing gastroenteroscopy during sedation are prone to aspiration, and most patients with dyspepsia have delayed gastric emptying. This study aimed to investigate the feasibility of measuring the gastric antrum cross-sectional area (CSA) to supply a novel clinical diagnostic reference value in patients with dyspepsia.

Methods
Patients with dyspepsia undergoing elective gastroscopy were included. The Perlas qualitative 0–2 grading scale score was determined before the operation. The anteroposterior diameter (D1) and craniocaudal diameter (D2) between gastric antrum serosal surfaces were measured perpendicular to each other in the supine and right lateral decubitus (RLD) positions. CSA values in the supine position and RLD position were determined. Gastric contents were endoscopically suctioned with the volumes measured and noted as actual gastric volume. Multiple regression analysis was used to fit a mathematical model for estimating the gastric volume. Receiver operating characteristic (ROC) curves were constructed to determine the accuracy of RLD CSA to detect gastric volumes of > 0.8 ml/kg.

Results
A total of 117 patients were enrolled and divided into a functional dyspepsia (FD) group and an organic dyspepsia group according to gastroscopy findings. For a gastric volume of > 0.8 ml/kg, cut-off values for FD and organic dyspepsia were 6.7 cm2 and 10.0 cm2, respectively. Two new modified mathematical models were derived to predict an estimated gastric volume for FD and organic dyspepsia: volume = 3.93 × RLD CSA - 0.47 × age; and volume = 6.15 × RLD CSA - 0.61 × age.

Conclusion
We used the cut-off value of the antral area for the fast diagnosis of gastric volumes in patients with dyspepsia, which may assist clinicians in identifying patients at risk of aspiration.

Trial registration
www.chictr.org.cn (CHICTR-DDD-17010871); registered 15 March 2017.
Development of a europium nanoparticles lateral flow immunoassay for NGAL detection in urine and diagnosis of acute kidney injury
Authors: Yin Moli , Nie Yuanwang , Liu Hao , Liu Lei , Tang Lu , Dong Yuan , Hu Chuanmin , Wang Huiyan 
Published: January 2022

AbstractBackgroundAKI is related to severe adverse outcomes and mortality with Coronavirus Disease 2019 (COVID-19) patients, that early diagnosed and intervened is imperative. Neutrophil gelatinase-associated lipocalin (NGAL) is one of the most promising biomarkers for detection of acute kidney injury (AKI), but current detection methods are inadequacy, so more rapid, convenient and accuracy methods are needed to detect NGAL for early diagnosis of AKI. Herein, we established a rapid, reliable and accuracy lateral flow immunoassay (LFIA) based on europium nanoparticles (EU-NPS) for the detection of NGAL in human urine specimens.MethodsA double-antibody sandwich immunofluorescent assay using europium doped nanoparticles was employed and the NGAL monoclonal antibodies (MAbs) conjugate as labels were generated by optimizing electric fusion parameters. Eighty-three urine samples were used to evaluate the clinical application efficiency of this method.ResultsThe quantitative detection range of NGAL in AKI was 1-3000 ng/mL, and the detection sensitization was 0.36 ng/mL. The coefficient of variation (CV) of intra-assay and inter-assay were 2.57-4.98 % and 4.11-7.83 %, respectively. Meanwhile, the correlation coefficient between europium nanoparticles-based lateral fluorescence immunoassays (EU-NPS-LFIA) and ARCHITECT analyzer was significant (R2 = 0.9829,n = 83,p < 0.01).ConclusionsThus, a faster and easier operation quantitative assay of NGAL for AKI has been established, which is very important and meaningful to diagnose the early AKI, suggesting that the assay can provide an early warning of final outcome of disease.
Simple and effective serum biomarkers potential for predicting status epilepticus in anti-N-methyl-D-aspartate receptor encephalitis
Authors: Liu Yingying , Ma Lili , Ma Xiaomeng , Ma Xueying , Li Jing , Li Donghong , Lin Xiuli , Su Zhumin , Chen Xiaohong 
Published: January 2022

Abstract
Background
Patients with anti-N-methyl-D-aspartate receptor (NMDAR) encephalitis who also present with status epilepticus (SE) often have a poor prognosis. The aim of this study is to explore simple and effective predictors for anti-NMDAR encephalitis accompanied with SE.

Methods
We retrospectively analyzed 65 anti-NMDAR encephalitis patients from January 2015 to December 2018 who admitted to the Third Affiliated Hospital of Sun Yat-sen University. Patients were divided into SE group and non-SE groups. Their pre-treatment data and 3-month follow-up data were retrospectively analyzed.

Results
The results showed that compared with the non-SE group, the levels of serum uric acid (UA) and high-density lipoprotein cholesterol (HDL-C) in anti-NMDAR encephalitis patients with SE decreased significantly before treatment. Additionally, the levels of serum UA and HDL-C increased while the level of C-reactive protein (CRP) decreased 3 months after treatment in the SE group. Compared with the non-SE group, the SE patients had higher modified Rankin scale (mRS) scores before (mRS1) and after treatment (mRS2). Serum UA concentrations before treatment showed significantly negative correlations with mRS1 (r = − 0.407, p < 0.01) and mRS2 (r = − 0.458, p < 0.001), while the level of serum CRP before treatment had strong positive correlations with mRS1 (r = 0.304, p < 0.05) and mRS2 (r = 0.301, p < 0.05) in anti-NMDAR encephalitis patients. The receiver operating characteristic curve demonstrated that the combined detection of UA, HDL-C and CRP before treatment had a significantly higher value (the area under the curve = 0.848; 95% confidence interval [CI], 0.74–0.957; p < 0.001) to predict anti-NMDAR encephalitis accompanied with SE than that of single detection.

Conclusions
Hence, the combined detection of serum UA, HDL-C and CRP before treatment may be simple and effective indicators for predicting SE in anti-NMDAR encephalitis, which may be helpful in early stages to remind clinicians to be alert to the emergence of SE.