bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mini-XT, a miniaturized tagmentation-based protocol for efficient sequencing of SARS-CoV-2
Authors: Fuchs Marc , Radulescu Clara , Tang Miao , Mahesh Arun , Lavin Deborah , Umbreen Syed , McKenna James , Smyth Mark , McColgan Eilís , Molnar Zoltan , Baxter Chris , Skvortsov Timofey , Singh Aditi , Rogan Fiona , Miskelly Julia , Bridgett Stephen , Fairley Derek , Simpson David A. 
Published: March 2022

Abstract
Background
The COVID-19 pandemic has highlighted the importance of whole genome sequencing (WGS) of SARS-CoV-2 to inform public health policy. By enabling definition of lineages it facilitates tracking of the global spread of the virus. The evolution of new variants can be monitored and knowledge of specific mutations provides insights into the mechanisms through which the virus increases transmissibility or evades immunity. To date almost 1 million SARS-CoV-2 genomes have been sequenced by members of the COVID-19 Genomics UK (COG-UK) Consortium. To achieve similar feats in a more cost-effective and sustainable manner in future, improved high throughput virus sequencing protocols are required. We have therefore developed a miniaturized library preparation protocol with drastically reduced consumable use and costs.

Results
We present the ‘Mini-XT’ miniaturized tagmentation-based library preparation protocol available on protocols.io (10.17504/protocols.io.bvntn5en). SARS-CoV-2 RNA was amplified using the ARTIC nCov-2019 multiplex RT-PCR protocol and purified using a conventional liquid handling system. Acoustic liquid transfer (Echo 525) was employed to reduce reaction volumes and the number of tips required for a Nextera XT library preparation. Sequencing was performed on an Illumina MiSeq. The final version of Mini-XT has been used to sequence 4384 SARS-CoV-2 samples from N. Ireland with a COG-UK QC pass rate of 97.4%. Sequencing quality was comparable and lineage calling consistent for replicate samples processed with full volume Nextera DNA Flex (333 samples) or using nanopore technology (20 samples). SNP calling between Mini-XT and these technologies was consistent and sequences from replicate samples paired together in maximum likelihood phylogenetic trees.

Conclusions
The Mini-XT protocol maintains sequence quality while reducing library preparation reagent volumes eightfold and halving overall tip usage from sample to sequence to provide concomitant cost savings relative to standard protocols. This will enable more efficient high-throughput sequencing of SARS-CoV-2 isolates and future pathogen WGS.
Anti-obesity effects of heat-transformed green tea extract through the activation of adipose tissue thermogenesis
Authors: Im Hyeonyeong , Lee Jaewon , Kim Kyungmin , Son Yeonho , Lee Yun-Hee 
Published: March 2022

Abstract
Background
Adipose tissue thermogenesis is a potential therapeutic target to increase energy expenditure and thereby combat obesity. The aim of the present study was to investigate the thermogenic and anti-obesity effects of heat-transformed green tea extract (HTGT) and enzymatically modified isoquercetin (EMIQ).

Methods
Immortalized brown pre-adipocytes and C3H10T1/2 cells were used for in vitro analyses. A high-fat diet (HFD)-induced obesity mouse model and CIDEA-reporter mice were used for in vivo experiments. The effects of HTGT and EMIQ on mitochondrial metabolism were evaluated by immunoblot, mitochondrial staining, and oxygen consumption rate analyses. In vivo anti-obesity effects of HTGT and EMIQ were measured using indirect calorimetry, body composition analyses, glucose tolerance tests, and histochemical analyses.

Results
Co-treatment with HTGT and EMIQ (50 μg/mL each) for 48 h increased brown adipocyte marker and mitochondrial protein levels (UCP1 and COXIV) in brown adipocytes by 2.9-fold, while the maximal and basal oxygen consumption rates increased by 1.57- and 1.39-fold, respectively. Consistently, HTGT and EMIQ treatment increased the fluorescence intensity of mitochondrial staining in C3H10T1/2 adipocytes by 1.68-fold. The combination of HTGT and EMIQ (100 mg/kg each) increased the expression levels of brown adipocyte markers and mitochondrial proteins in adipose tissue. Two weeks of HTGT and EMIQ treatment (100 mg/kg each) led to a loss of 3% body weight and 7.09% of body fat. Furthermore, the treatment increased energy expenditure by 8.95% and improved glucose tolerance in HFD-fed mice.

Conclusions
The current study demonstrated that HTGT and EMIQ have in vivo anti-obesity effects partly by increasing mitochondrial metabolism in adipocytes. Our findings suggest that a combination of HTGT and EMIQ is a promising therapeutic agent for the treatment of obesity and related metabolic diseases.
Qualitative and quantitative evaluation of thylakoid complexes separated by Blue Native PAGE
Authors: Sárvári Éva , Gellén Gabriella , Sági-Kazár Máté , Schlosser Gitta , Solymosi Katalin , Solti Ádám 
Published: March 2022

AbstractBackgroundBlue Native polyacrylamide gel electrophoresis (BN PAGE) followed by denaturing PAGE is a widely used, convenient and time efficient method to separate thylakoid complexes and study their composition, abundance, and interactions. Previous analyses unravelled multiple monomeric and dimeric/oligomeric thylakoid complexes but, in certain cases, the separation of complexes was not proper. Particularly, the resolution of super- and megacomplexes, which provides important information on functional interactions, still remained challenging.ResultsUsing a detergent mixture of 1% (w/V)n-dodecyl-β-d-maltoside plus 1% (w/V) digitonin for solubilisation and 4.3–8% gel gradients for separation as methodological improvements in BN PAGE, several large photosystem (PS) I containing bands were detected. According to BN(/BN)/SDS PAGE and mass spectrometry analyses, these PSI bands proved to be PSI-NADH dehydrogenase-like megacomplexes more discernible in maize bundle sheath thylakoids, and PSI complexes with different light-harvesting complex (LHC) complements (PSI-LHCII, PSI-LHCII*) more abundant in mesophyll thylakoids of lincomycin treated maize. For quantitative determination of the complexes and their comparison across taxa and physiological conditions, sample volumes applicable to the gel, correct baseline determination of the densitograms, evaluation methods to resolve complexes running together, calculation of their absolute/relative amounts and distribution among their different forms are proposed.ConclusionsHere we report our experience in Blue/Clear-Native polyacrylamide gel electrophoretic separation of thylakoid complexes, their identification, quantitative determination and comparison in different samples. The applied conditions represent a powerful methodology for the analysis of thylakoid mega- and supercomplexes.
Primary immune regulatory disorders: Undiagnosed needles in the haystack?
Authors: Flinn Aisling M. , Gennery Andrew R. 
Published: March 2022

AbstractPrimary Immune Regulatory Disorders (PIRD) describe a group of conditions characterized by loss of normal inflammatory control and immune tolerance mechanisms, with autoimmunity as a predominant clinical feature. PIRD can arise due to defects in the number or function of regulatory T-lymphocytes, defects in the immune mechanisms required to ‘turn off’ inflammation such as in perforin-dependent cytotoxicity or alterations in cytokine signalling pathways. Diagnosis of PIRD is a significant challenge to physicians due to their rarity, complexity, and diversity in clinical manifestations. Many of these individual conditions lack a genotype–phenotype correlation and display incomplete penetrance. However, establishing a diagnosis is integral in optimizing patient management, including the use of individualized treatment approaches. Increasing awareness among physicians is necessary as patients are likely to present to different subspecialties. Due to the rarity of these conditions, worldwide collaboration and data-sharing is essential to improve our knowledge of the clinical spectrum and disease course in PIRD, and to optimize therapeutic strategies including identification of which patients can benefit from hematopoietic stem cell transplant.
3q27.1 microdeletion causes prenatal and postnatal growth restriction and neurodevelopmental abnormalities
Authors: Barua Subit , Pereira Elaine M. , Jobanputra Vaidehi , Anyane-Yeboa Kwame , Levy Brynn , Liao Jun 
Published: March 2022

Abstract
Background
Overlapping microdeletions of chromosome 3q26-3q28 have been reported in eight individuals. The common phenotype observed in these individuals include intrauterine growth restriction, short stature, microcephaly, feeding difficulties, facial dysmorphisms, limb abnormalities and developmental delay. The most striking clinical features shared among all reported cases is prenatal and postnatal growth restriction and neurodevelopmental abnormalities.

Case presentation
We identified two additional individuals with overlapping deletions and shared clinical features by high-resolution SNP oligonucleotide microarray, and refined the smallest region of overlap (SRO) to a 1.2 Mb genomic location in chromosome 3q27.1 by reviewing and comparing all published cases. We evaluated the SRO using ACMG/ClinGen current recommendations for classifying copy number variants (CNVs), and discussed the contribution of the genes deleted in the SRO to the abnormal phenotype observed in these individuals.

Conclusions
This study provides further evidence supporting the existence of a novel 3q27.1 microdeletion syndrome and suggests that haploinsufficiency of potential candidate genes, DVL3, AP2M1, and PARL in the SRO in 3q27.1 is responsible for the phenotype.
HDAC class I inhibitor domatinostat sensitizes pancreatic cancer to chemotherapy by targeting cancer stem cell compartment via FOXM1 modulation
Authors: Roca Maria Serena , Moccia Tania , Iannelli Federica , Testa Cristina , Vitagliano Carlo , Minopoli Michele , Camerlingo Rosa , De Riso Giulia , De Cecio Rossella , Bruzzese Francesca , Conte Mariarosaria , Altucci Lucia , Di Gennaro Elena , Avallone Antonio , Leone Alessandra , Budillon Alfredo 
Published: March 2022

Abstract
Background
Pancreatic ductal adenocarcinoma (PDAC) represents an unmet clinical need due to the very poor prognosis and the lack of effective therapy. Here we investigated the potential of domatinostat (4SC-202), a new class I histone deacetylase (HDAC) inhibitor, currently in clinical development, to sensitize PDAC to first line standard gemcitabine (G)/taxol (T) doublet chemotherapy treatment.

Methods
Synergistic anti-tumor effect of the combined treatment was assessed in PANC1, ASPC1 and PANC28 PDAC cell lines in vitro as well as on tumor spheroids and microtissues, by evaluating combination index (CI), apoptosis, clonogenic capability. The data were confirmed in vivo xenograft models of PANC28 and PANC1 cells in athymic mice. Cancer stem cells (CSC) targeting was studied by mRNA and protein expression of CSC markers, by limiting dilution assay, and by flow cytometric and immunofluorescent evaluation of CSC mitochondrial and cellular oxidative stress. Mechanistic role of forkhead box M1 (FOXM1) and downstream targets was evaluated in FOXM1-overexpressing PDAC cells.

Results
We showed that domatinostat sensitized in vitro and in vivo models of PDAC to chemotherapeutics commonly used in PDAC patients management and particularly to GT doublet, by targeting CSC compartment through the induction of mitochondrial and cellular oxidative stress. Mechanistically, we showed that domatinostat hampers the expression and function of FOXM1, a transcription factor playing a crucial role in stemness, oxidative stress modulation and DNA repair. Domatinostat reduced FOXM1 protein levels by downregulating mRNA expression and inducing proteasome-mediated protein degradation thus preventing nuclear translocation correlated with a reduction of FOXM1 target genes. Furthermore, by overexpressing FOXM1 in PDAC cells we significantly reduced domatinostat-inducing oxidative mitochondrial and cellular stress and abolished GT sensitization, both in adherent and spheroid cells, confirming FOXM1 crucial role in the mechanisms described. Finally, we found a correlation of FOXM1 expression with poor progression free survival in PDAC chemotherapy-treated patients.

Conclusions
Overall, we suggest a novel therapeutic strategy based on domatinostat to improve efficacy and to overcome resistance of commonly used chemotherapeutics in PDAC that warrant further clinical evaluation.
Meiosis-specific cohesin complexes display essential and distinct roles in mitotic embryonic stem cell chromosomes
Authors: Choi Eui-Hwan , Yoon Seobin , Koh Young Eun , Hong Tae Kyung , Do Jeong Tae , Lee Bum-Kyu , Hahn Yoonsoo , Kim Keun P. 
Published: March 2022

AbstractBackgroundCohesin is a chromosome-associated SMC–kleisin complex that mediates sister chromatid cohesion, recombination, and most chromosomal processes during mitosis and meiosis. However, it remains unclear whether meiosis-specific cohesin complexes are functionally active in mitotic chromosomes.ResultsThrough high-resolution 3D-structured illumination microscopy (3D-SIM) and functional analyses, we report multiple biological processes associated with the meiosis-specific cohesin components, α-kleisin REC8 and STAG3, and the distinct loss of function of meiotic cohesin during the cell cycle of embryonic stem cells (ESCs). First, we show that STAG3 is required for the efficient localization of REC8 to the nucleus by interacting with REC8. REC8-STAG3-containing cohesin regulates topological properties of chromosomes and maintains sister chromatid cohesion. Second, REC8-cohesin has additional sister chromatid cohesion roles in concert with mitotic RAD21-cohesin on ESC chromosomes. SIM imaging of REC8 and RAD21 co-staining revealed that the two types of α-kleisin subunits exhibited distinct loading patterns along ESC chromosomes. Third, knockdown of REC8 or RAD21-cohesin not only leads to higher rates of premature sister chromatid separation and delayed replication fork progression, which can cause proliferation and developmental defects, but also enhances chromosome compaction by hyperloading of retinoblastoma protein–condensin complexes from the prophase onward.ConclusionsOur findings indicate that the delicate balance between mitotic and meiotic cohesins may regulate ESC-specific chromosomal organization and the mitotic program.
Foot tapping and unilateral vertical jump performance in athletes after knee surgery: an explorative cross-sectional study
Authors: Kurz Eduard , Schwesig René , Pröger Stefan , Delank Karl-Stefan , Bartels Thomas 
Published: March 2022

AbstractBackgroundGuiding athletes through the rehabilitation process and judging the time at which return to sports can be enabled after anterior cruciate ligament (ACL) injuries are still challenging processes. The purpose of this explorative cross-sectional study was to retrospectively compare unilateral vertical jump as well as vertical foot tapping outcomes in athletes returned to sports after ACL reconstruction (ACLR) with uninjured athletes.MethodsSeven-teen ACLR athletes (male/female: 12/5) were examined 11 (6–23) months after their ACL injury and after return to sport clearance together with 67 uninjured athletes (male/female: 51/16). Seventeen age and stature matched controls were selected from the sample of uninjured athletes. Participants unilaterally performed acyclic (squat jump, SJ; drop jump, DJ) and cyclic (foot tapping, FT) tests. SJ peak power, DJ take-off efficiency (TOE) and FT coefficients (FTC) were compared between ACLR and matched as well as unmatched control groups. Limb symmetry index (LSI) as well as performance score were calculated.ResultsAnalyses of the SJ peak power revealed moderate effects of group (right:P < 0.09, ηp2 = 0.06; left:P < 0.05, ηp2 = 0.08). The TOE was largely affected by group (right:P < 0.01, ηp2 = 0.12; left:P < 0.01, ηp2 = 0.13). No effect of group was found on the FTC (P > 0.8, ηp2 < 0.01). The SJ peak power LSI (r = 0.46,P < 0.07) and TOE LSI (r = 0.38,P = 0.13) were positively associated with the performance score of the ACLR group.ConclusionAlthough already returned to sports, the ACLR group underperformed the matched and unmatched control groups significantly. Unilaterally performed vertical jumps may provide additional information on athletes’ rehabilitation progress and help to manage the rehabilitation process and decisions on potential readiness after ACLR. More attention should be paid to the direction of the LSI results.
Regression-based beam training for UAV mmWave communications
Authors: Zhang Junjie , Zhong Weizhi , Gu Yong , Zhu Qiuming , Zhang Lulu 
Published: March 2022

AbstractFor unmanned aerial vehicle (UAV) millimeter-wave (mmWave) communication systems, efficient and accurate beam training is urgently required to overcome beam misalignment. By taking into account the mmWave propagation environment, a three-dimensional (3D) intelligent beam training strategy that leverages the polynomial regression (PR) model and optimized beam patterns is proposed in this paper. We treat mmWave beam selection as a PR problem. By using machine learning (ML), the regression function is determined. The training dataset applied in the ML method consists of measured power and estimated angles and is obtained by carefully designed beam patterns. Furthermore, a noise suppression method involving the use of a denoising autoencoder (DAE) is developed to overcome the noise sensitivity of the proposed regression model. The numerical simulation results demonstrate that our proposed beam training strategy is capable of obtaining the same precision as an exhaustive search with a shorter time.
Lactobacillus murinus alleviate intestinal ischemia/reperfusion injury through promoting the release of interleukin-10 from M2 macrophages via Toll-like receptor 2 signaling
Authors: Hu Jingjuan , Deng Fan , Zhao Bingcheng , Lin Zebin , Sun Qishun , Yang Xiao , Wu Mei , Qiu Shida , Chen Yu , Yan Zhengzheng , Luo Sidan , Zhao Jin , Liu Weifeng , Li Cai , Liu Ke Xuan 
Published: March 2022

Abstract
Background
Intestinal ischemia/reperfusion (I/R) injury has high morbidity and mortality rates. Gut microbiota is a potential key factor affecting intestinal I/R injury. Populations exhibit different sensitivities to intestinal I/R injury; however, whether this interpopulation difference is related to variation in gut microbiota is unclear. Here, to elucidate the interaction between the gut microbiome and intestinal I/R injury, we performed 16S DNA sequencing on the preoperative feces of C57BL/6 mice and fecal microbiota transplantation (FMT) experiments in germ-free mice. The transwell co-culture system of small intestinal organoids extracted from control mice and macrophages extracted from control mice or Toll-like receptor 2 (TLR2)-deficient mice or interleukin-10 (IL-10)-deficient mice were established separately to explore the potential mechanism of reducing intestinal I/R injury.

Results
Intestinal I/R-sensitive (Sen) and intestinal I/R-resistant (Res) mice were first defined according to different survival outcomes of mice suffering from intestinal I/R. Fecal microbiota composition and diversity prior to intestinal ischemia differed between Sen and Res mice. The relative abundance of Lactobacillus murinus (L. murinus) at the species level was drastically higher in Res than that in Sen mice. Clinically, the abundance of L. murinus in preoperative feces of patients undergoing cardiopulmonary bypass surgery was closely related to the degree of intestinal I/R injury after surgery. Treatment with L. murinus significantly prevented intestinal I/R-induced intestinal injury and improved mouse survival, which depended on macrophages involvement. Further, in vitro experiments indicated that promoting the release of IL-10 from macrophages through TLR2 may be a potential mechanism for L. murinus to reduce intestinal I/R injury.

Conclusion
The gut microbiome is involved in the postoperative outcome of intestinal I/R. Lactobacillus murinus alleviates mice intestinal I/R injury through macrophages, and promoting the release of IL-10 from macrophages through TLR2 may be a potential mechanism for L. murinus to reduce intestinal I/R injury. This study revealed a novel mechanism of intestinal I/R injury and a new therapeutic strategy for clinical practice.
Benefits of mindfulness in academic settings: trait mindfulness has incremental validity over motivational factors in predicting academic affect, cognition, and behavior
Authors: Kuroda Yuji , Yamakawa Osamu , Ito Masayuki 
Published: March 2022

Abstract
Background
Achievement motivation research has established that motivational factors predict academic affect, cognition, and behavior. Recent studies have shown that trait mindfulness might also predict these academic outcomes. However, it remains unclear whether trait mindfulness has incremental validity over motivational factors. We hypothesized that trait mindfulness would explain unique variance in academic outcomes beyond motivational factors, because mindfulness that is characterized by the being mode of mind (i.e., a present-focused, non-striving, and accepting mind mode) would contribute to academic outcomes through unique and effective self-regulatory processes (i.e., bottom-up self-regulation of learning and present-focused, acceptance-based self-regulation of academic stress), which differ from those (i.e., top-down self-regulation of learning and future-focused, change-oriented self-regulation of academic stress) promoted by motivational factors that are characterized by the doing mode of mind (i.e., a goal-oriented, striving, and change-seeking mind mode). We tested the hypothesis by examining four established motivational factors (competence perception, implicit theory of intelligence, achievement goals, and autonomous and controlled academic reasons) and five outcome variables (test anxiety, enjoyment of learning, study strategy, mind-wandering, and help-seeking avoidance) that had been investigated in both the trait mindfulness and achievement motivation literatures.

Methods
One hundred and seventy-five students (104 females) were recruited from undergraduate psychology and cultural studies classes at two universities in Japan. Trait mindfulness was assessed using the Five Facet Mindfulness Questionnaire. The other study variables were assessed using established measures as well. We conducted hierarchical multiple regression analyses to test the hypothesis.

Results
Trait mindfulness predicted four of the five outcome variables (i.e., test anxiety, enjoyment of learning, mind-wandering, and help-seeking avoidance) after controlling for the motivational factors. The acting-with-awareness facet predicted three outcome variables, whereas the other facets predicted one outcome each.

Conclusions
This study supports the incremental validity of trait mindfulness relative to motivational factors, suggesting that not only the doing mode of mind but also the being mode is beneficial for academic learning.