bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of interhemispheric functional connectivity with the congenital blindness: interactions between blindness and emotional regulation
Authors: Kang Jiayu , Pan Yicong , Kang Min , zhang Lijuan , Xu Sanhua , Wu Jieli , Shu Huiye , Liao Xulin , Su Ting , Tang Liying , Tan Yehui , Shao Yi 
Published: March 2022

Abstract
Purpose Negative emotions, as an important risk factor, promote the development of many diseases. The study is designed to discuss alterations of interhemispheric functional connectivity (FC) with congenital blindness (CB) subjects by adopting voxel-mirrored homotopic connectivity (VMHC). Based on the alterations in FC, we assessed whether there was an interaction between blindness and emotional regulation. Method VMHC values were collected from 24(males/females = 9/15) subjects with congenital blindness and 24(males/females = 9/15) healthy controls. The gender, age and other information of the healthy controls were closely matched with the disease group. The VMHC values were applied to assess alterations in hemispheric FC between the two groups. Receiver Operating Characteristic (ROC) were applied so as to classify the mean VMHC values of the CB and HC subjects. In addition, an evaluation, which was applied the Pearson Correlation analysis, was employed to compare the correlation between VMHC values of specific brain areas and clinical features of CB subjects. Result The area under curve (AUC) was 0.8750 (P < 0.0001) for bilateral fusiform gyrus (FFG), 0.9670 (P < 0.0001) for bilateral superior occipital gyrus (SOG), 0.9653 (P < 0.0001) for bilateral thalamus (THA) and 0.9462 (P < 0.0001) for bilateral paracentral lobule (PCL). Furthermore, anxiety scores (AS) and depression scores (DS) displayed a positive correlation with the VMHC values of bilateral thalamus (r =− 0.943; P< 0.001 and r = 0.869; P< 0.001) in CB group. Conclusion In the CB group, aberrant interhemispheric FC was observed in specific cerebral regions. These altered VMHC values in the cerebral areas might be potential diagnostic markers of emotional disorders and aberrant brain activities in the CB patients. Humanistic care and necessary psychological treatment for blind patients may be one of the measures to prevent vision from persistent loss in the future. At the same time, the changes of brain function may also provide new ideas for individualized treatment of patients with anxiety, depression and other emotional disorders.
Reduced precipitation limits growth return on plant N in mesic grassland
Authors: Polley H. Wayne , Jones Katherine A. , Kolodziejczyk Chris A. , Fay Philip A. 
Published: March 2022

Abstract
Grassland production is sensitive to both precipitation and plant N accumulation and utilization, such that change in one variable influences grassland response to the second variable. We investigated effects of interannual variation in precipitation on the response of community-level values of relative growth rate (RGR) to two multiplicative components of RGR, nitrogen productivity (NP; rate of change in biomass/plant N) and N concentration ([N]), in two grassland communities in Texas, USA. Communities included a diverse mixture of perennial grass and forb species and monoculture of the perennial C4 grass Panicum virgatum. RGR and its N components were measured at the spatial scale of 7-m diameter circular patches in each community near the spring peak in mixture biomass during each of 5 years. We found that RGR varied substantially among patches and years and between communities. RGR variation was strongly correlated with variation in NP. Precipitation during the 3 months prior to RGR measurement mediated the RGR response to NP by altering the correlation between NP and [N] in both grasslands. Reduced precipitation led to more negative NP-[N] correlation coefficients, which reduced proportional change in RGR per change in NP by as much as 30% even in the absence of a precipitation effect on means of community RGR and NP. Our results highlight an under-appreciated aspect of the pervasive role of precipitation in grassland growth that was mediated via change in plant growth return on accumulated N.
Pediatric esophagogastroduodenoscopy in China: indications, diagnostic yield, and factors associated with findings
Authors: Wang Shengnan , Qiu Xiaoxia , Chen Jingfang , Mei Hong , Yan Haiyan , You Jieyu , Huang Ying 
Published: March 2022

Abstract
Background: Large-scale data on esophagogastroduodenoscopy (EGD) in China are scarce. This study aimed to assess the indications and diagnostic yield of EGD in children and the relationship between factors (such as age, sex, and indications) and diagnostic yield.Methods: We performed a prospective cross-sectional observational study involving patients aged < 18 years who underwent diagnostic EGD. The study was conducted in five children’s hospitals, each in a different city. Demographic features, indications for endoscopy, and endoscopic and histopathological findings were collected. Univariable and multivariable ordinal logistic regression analyses of the relationship between the factors and diagnostic yield were performed.Results: The study included 2268 patients (male/female ratio, 1.3:1) with a median age of 8.68 years. Among the 2268 children, the most frequent indications were abdominal pain in 1954 (86.2%), recurrent vomiting in 706 (31.1%), weight loss in 343 (15.1%), and others. The endoscopic yield was 62.5% and was the highest in patients with dysphagia (90.9%). The histologic yield was 32.4% and was the highest in patients with unexplained anemia (54.6%). On multivariable regression analysis, the endoscopic yield was associated with dysphagia, gastrointestinal (GI) bleeding, and recurrent vomiting, and the histologic yield was associated with weight loss and age. Different groups of patients with abdominal pain had variable probabilities of abnormal endoscopic findings.Conclusions: The most frequent indication of pediatric EGD is abdominal pain, with variable probabilities of abnormal endoscopic findings in different groups. Endoscopic yield and histologic yield are associated with certain alarming features.Trial registration: The trial registration number (TRN): NCT03603093 (ClinicalTrials. gov), Date of registration: July 18th, 2018
Multiple sampling schemes and deep learning improve active learning performance in drug-drug interaction information retrieval analysis from the literature
Authors: Li Lang , Xie Weixin , Fan Kunjie , Zhang Shijun 
Published: March 2022

Abstract
Background: Drug-drug interaction (DDI) information retrieval (IR) is an important natural language process (NLP) task from the PubMed literature. For the first time, active learning (AL) is studied in DDI IR analysis. DDI IR analysis from PubMed abstracts faces the challenges of relatively small positive DDI samples among overwhelmingly large negative samples. Random negative sampling and positive sampling are purposely designed to improve the efficiency of AL analysis. The consistency of random negative sampling and positive sampling is shown in the paper. Results: PubMed abstracts are divided into two pools. Screened pool contains all abstracts that pass the DDI keywords query in PubMed, while unscreened pool includes all the other abstracts. At a prespecified recall rate of 0.95, DDI IR analysis performance is evaluated and compared in precision. In screened pool IR analysis using supporting vector machine (SVM), similarity sampling plus uncertainty sampling improves the precision of AL over uncertainty sampling, from 0.89 to 0.92 respectively. In the unscreened pool IR analysis, the integrated random negative sampling, positive sampling, and similarity sampling improve the IR analysis performance over uncertainty sampling along, from 0.72 to 0.81 respectively. When we change the SVM to a deep learning method, all sampling schemes consistently benefit DDI AL analysis in both screened pool and unscreened pool. Deep learning has significant improvement of precision over SVM, 0.96 vs 0.91 in screened pool, and 0.90 vs 0.81 in the unscreened pool, respectively.Conclusions: By integrating various sampling schemes and deep learning algorithms into AL, the DDI IR analysis from literature is significantly improved. The random negative sampling and positive sampling are highly effective methods in improving AL analysis where the positive and negative samples are extremely imbalanced.
Thermal cracking prediction for a squeeze casting process with an approach of multi-scale and multi-model coupling
Authors: Zhao zhan , LIU Yan , Niu Xiaofeng , GE Tao-tao , ZHANG Ming-yu , ZHOU Wei , LUO Pei-lin 
Published: March 2022

Abstract
The smooth particle hydrodynamics (SPH) method is advantageous in tracking a free surface and a moving interface. This paper uses the SPH method to simulate the filling process of squeeze casting. The simulated temperature field at the end of filling was input into a finite element model (FEM) program to simulate the solidification process after squeeze casting. Due to the existence of a liquid phase, a solid phase, and a two-phase mushy zone in the solidification process after squeeze casting, the deformation behavior in the solidification process was modeled with a thermoelasto–viscoplastic constitutive model representing these different phases. In the RDG thermal cracking criterion based on the principle of dendrite gap complement, there are a strain rate term, a secondary dendritic spacing term, and a pressure term. These terms accurately describe the squeeze casting process. Therefore, the RDG criterion was used to predict thermal cracking. The strain rate term in the RDG criterion was calculated by the FEM. For the calculation of the secondary dendritic spacing, the temperature field during the solidification process is locally refined by the FDM method to complete the transition from the macroscale to the mesoscale; then the refinement results are imported into the phase field method for dendritic growth simulation. The results show that the method based on multi-model coupling has satisfactory prediction accuracy for the thermal cracking in the squeeze casting process. The combination of the phase field method and the RDG criterion provides a new approach to the simulation of thermal cracking defects. The prediction results show that the thermal cracking tendency increases with an increase in strain rate. However, the local position C of the bracket sample had a higher strain rate of 7.15/s, and a lower cooling rate of 2.96 K/s offset the effect of the high strain rate. As a result, a low thermal cracking tendency level of 1.13729 was obtained.
Determinants of ethnic differences in the uptake of child healthcare services in New Zealand: a decomposition analysis
Authors: Lewycka Sonia , Dasgupta Kabir , Plum Alexander , Clark Terryann , Hedges Mary , Pacheco Gail 
Published: March 2022

Abstract
BackgroundThere are persistent ethnic gaps in uptake of child healthcare services in New Zealand (NZ), despite increasing policy to promote equitable access. We examined ethnic differences in the uptake of immunisation and primary healthcare services at different ages and quantified the contribution of relevant explanatory factors, in order to identify potential points of intervention.MethodsWe used data from the Growing Up in New Zealand birth cohort study, including children born between 2009 and 2010. Econometric approaches were used to explore underlying mechanisms behind ethnic differences in service uptake. Multivariable regression was used to adjust for mother, child, household, socioeconomic, mobility, and social factors. Decomposition analysis was used to assess the proportion of each ethnic gap that could be explained, as well as the main drivers behind the explained component. These analyses were repeated for four data time-points.Results6,822 mothers were enrolled during the antenatal survey, and children were followed up at 9-months, 2-years and 4-years. In univariable models, there were ethnic gaps in uptake of immunisation and primary care services. After adjusting for covariates in multivariable models, compared to NZ Europeans, Asian and Pacific children had higher timeliness and completeness of immunisation at all time-points, while indigenous Māori had lower timeliness of first-year vaccines despite high intentions to immunize. Asian and Pacific mothers were less likely to have their first-choice lead maternity caregiver (LMC) than NZ Europeans mothers, and Māori and Asian mothers were less likely to be satisfied with their general practitioner (GP) at 2-years. Healthcare utilisation was strongly influenced by socio-economic, mobility and social factors including ethnic discrimination. In decomposition models comparing Māori to NZ Europeans, the strongest drivers for timely first-year immunisations and GP satisfaction (2-years) were household composition and household income. Gaps between Pacific and NZ Europeans in timely first-year immunisations and choice of maternity carer were largely unexplained by factors included in the models.Conclusions Ethnic gaps in uptake of child healthcare services vary by ethnicity, service, and time-point, and are driven by different factors. Addressing healthcare disparities will require interventions tailored to specific ethnic groups, as well as addressing underlying social determinants and structural racism. Gaps that remain unexplained by our models require further investigation.
Heat Shock Transcription Factor B2b Acts as a Transcriptional Repressor of Vin3, a Gene Induced by Long-term Cold for Flowering
Authors: Lee Ilha , Jeong Goowon , Shin Jinwoo 
Published: March 2022

Abstract
Vernalization, an acceleration of flowering after long-term winter cold, is an intensively studied flowering mechanism in winter annual plants. In Arabidopsis, Polycomb Repressive Complex2 (PRC2)-mediated suppression of the strong floral repressor, FLOWERING LOCUS C (FLC), is critical for vernalization and a PHD finger domain protein, VERNALIZATION INSENSITIVE 3 (VIN3), recruits PRC2 on FLC chromatin. The level of VIN3 was found to gradually increase in proportion to the length of cold period during vernalization. However, how plants finely regulate VIN3 expression according to the cold environment has not been completely elucidated. As a result, we performed EMS mutagenesis using a transgenic line with a minimal promoter of VIN3 fused to the GUS reporter gene, and isolated a mutant, hyperactivation of VIN3 1 (hov1), which showed increased GUS signal and endogenous VIN3 transcript levels. Using positional cloning combined with whole-genome resequencing, we found that hov1 carries a nonsense mutation, leading to a premature stop codon on the HEAT SHOCK TRANSCRIPTION FACTOR B2b (HsfB2b), which encodes a repressive heat shock transcription factor. HsfB2b directly binds to the VIN3 promoter, and HsfB2b overexpression leads to reduced acceleration of flowering after vernalization. Collectively our findings reveal a novel fine-tuning mechanism to repress undesirable vernalization responses.
Experiences of and recommendations on clinical trial design in Alzheimer’s disease from the participant’s point of view
Authors: Ottenhoff Lois , Vijverberg Everard G.B. , Visser Leonie N.C. , Verijp Merike , Prins Niels D. , Flier Wiesje M. van der , Sikkes Sietske A.M. 
Published: March 2022

Abstract
Introduction.
In the context of the development of pharmaceutical interventions, expectations and experiences of participants are essential. Their insights may be particularly helpful to address the challenges of recruiting and retaining participants for Alzheimer’s disease (AD) clinical trials. We examined clinical trial participants’ experiences to optimize trial design in Alzheimer’s disease (AD).
Method.
In this mixed-methods study, we included adults who participated in sponsor-initiated AD trials at Brain Research Center, a clinical trial organization in the Netherlands. Participants (N = 71, age 69 ± 6.5, 54%F, 19 cognitively normal (CN), 19 Mild Cognitive Impairment (MCI) and 33 AD dementia) first completed an online survey. Next, a subsample (N = 12; 8 = CN, 4 = MCI) participated in focus groups to gain in-depth insight into their views on optimizing trial design. Audio recordings from focus group interviews were transcribed verbatim and analysed by thematic content analysis by two independent researchers.
Results.
To benefit future generations was most frequently (34%) reported as a motive for enrolment. The lumbar puncture (40%) and memory assessments (15%) were most often experienced as being of high burden. Structurally receiving individualized test results and smaller chance to get placebo, increased willingness to participate. Two main themes emerged from the focus groups: “trials design”, such as follow-up visit(s) after participating, and “trial center”, including the relevance of a professional and empathic staff.
Conclusion.
Relevant factors include expectation management and careful planning of high burden assessments, provision of individual feedback and prioritizing professionalism and empathy throughout conduct of the trial. Our findings provide insight into participants’ priorities to increase willingness to participate and can be used to optimize trial success.
3-D Printed BCP Blocks with Different Pore Sizes for Regeneration in Rabbit Calvarial Defects
Authors: Seo Young-Wook , Park Jin-Young , Lee Da-Na , Jin Xiang , Cha Jae-Kook , Paik Jeong-Won , Choi Seong-Ho 
Published: March 2022

Abstract
Background
Alveolar ridge augmentation is frequently performed in the deficient alveolar ridge to facilitate the placement of dental implants. Severe resorption of the bony ridge may occur because of aging or periodontal and periapical pathologies. When faced with this situation, a block bone graft might be indicated, since the block bone provides structural stability to the augmented site. The aim of this study was to compare three-dimensionally printed biphasic calcium phosphate (BCP) block bone substitutes with different pore sizes (0.8, 1.0 and 1.2 mm) for regeneration rabbit calvarial defects.
Material & Methods
Four circular defects were formed on the calvaria of ten rabbits. Each defect was randomly allocated to the following study groups: 1) Control group, 2) 0.8 mm group, 3) 1.0 mm group, and 4) 1.2 mm group. All specimens were harvested at 2 and 8 weeks postoperatively, and the samples were analyzed radiographically and histomorphometrically.
Results
Histologically, the BCP blocks remained unresorbed up to 8 weeks, and new bone formation occurred within the porous structure of the blocks. At the early healing period of 2 weeks, histomorphometric analysis revealed significantly greater new bone formation in the BCP groups compared to the control (p < 0.05). However, there were no significant differences between the groups with different pore sizes (p > 0.05). At 8 weeks, only the 1.0 mm group (3.42 ± 0.48 mm2) showed a significantly greater area of new bone compared to the control group (2.26 ± 0.59 mm2) (p < 0.05). Among the BCP block groups, 1.0 mm and 1.2 mm groups exhibited significantly greater area of new bone compared to the 0.8 mm group (3.42 ± 0.48 and 3.04 ± 0.66 vs 1.60 ± 0.70 mm2, respectively).
Conclusions
Within the limitations of this study, 1.0 mm pore diameter of the BCP block bone substitute was the most optimal size for bone regeneration. The BCP block bone substitutes can be applied in bone defects for successful bone regeneration, and further study should be performed in more challenging defect configurations prior to the clinical application.
An integrated cell atlas of the human lung in health and disease
Authors: Luecken Malte , Sikkema Lisa , Strobl Daniel , Zappia Luke , Madissoon Elo , Markov Nikolay , Zaragosi Laure-Emmanuelle , Ansari Meshal , Arguel Marie-Jeanne , Apperloo Leonie , Becavin Christophe , Berg Marijn , Chichelnitskiy Evgeny , Chung Mei-i , Collin Antoine , Gay Aurore , Kashani Baharak Hooshiar , Jain Manu , Kapellos Theodore , Kole Tessa , Mayr Christoph , von Papen Michael , Peter Lance , Ramírez-Suástegui Ciro , Schniering Janine , Taylor Chase , Walzthoeni Thomas , Xu Chuan , Bui Linh , de Donno Carlo , Dony Leander , Guo Minzhe , Gutierrez Austin , Heumos Lukas , Huang Ni , Río Ignacio Ibarra Del , Jackson Nathan , Murthy Preetish Kadur Lakshminarasimha , Lotfollahi Mohammad , Tabib Tracy , Talavera-Lopez Carlos , Travaglini Kyle , Wilbrey-Clark Anna , Worlock Kaylee , Yoshida Masahiro , Desai Tushar , Rozenblatt-Rosen Orit , Falk Christine , Kaminski Naftali , Krasnow Mark , Lafyatis Robert , Nikolic Marko , Powell Joseph , Rajagopal Jay , Seibold Max , Sheppard Dean , Shepherd Douglas , Teichmann Sarah , Tsankov Alexander , Whitsett Jeffrey , Xu Yan , Banovich Nicholas , Barbry Pascal , Duong Thu , Meyer Kerstin , Kropski Jonathan , Pe'er Dana , Schiller Herbert , Tata Purushothama Rao , Schultze Joachim , Berge Maarten van den , Chen Yuexin , Hagood James , Hassan Ahmed , Horvath Peter , Lundeberg Joakim , Leroy Sylvie , Marquette Charles , Pryhuber Gloria , Samakovlis Christos , Sun Xin , Ware Lorraine , Zhang Kun , Misharin Alexander , Nawijn Martijn , Theis Fabian 
Published: March 2022

Abstract
Organ- and body-scale cell atlases have the potential to transform our understanding of human biology. To capture the variability present in the population, these atlases must include diverse demographics such as age and ethnicity from both healthy and diseased individuals. The growth in both size and number of single-cell datasets, combined with recent advances in computational techniques, for the first time makes it possible to generate such comprehensive large-scale atlases through integration of multiple datasets. Here, we present the integrated Human Lung Cell Atlas (HLCA) combining 46 datasets of the human respiratory system into a single atlas spanning over 2.2 million cells from 444 individuals across health and disease. The HLCA contains a consensus re-annotation of published and newly generated datasets, resolving under- or misannotation of 59% of cells in the original datasets. The HLCA enables recovery of rare cell types, provides consensus marker genes for each cell type, and uncovers gene modules associated with demographic covariates and anatomical location within the respiratory system. To facilitate the use of the HLCA as a reference for single-cell lung research and allow rapid analysis of new data, we provide an interactive web portal to project datasets onto the HLCA. Finally, we demonstrate the value of the HLCA reference for interpreting disease-associated changes. Thus, the HLCA outlines a roadmap for the development and use of organ-scale cell atlases within the Human Cell Atlas.
The Histone H2B Arg95 residue links the Pheromone Response Pathway to Rapamycin-Induced G1 Arrest in Yeast
Authors: Sulaiman Abdallah , Ali Reem , Aouida Mustapha , Ramotar Dindial 
Published: March 2022

Abstract
Rapamycin is an immunosuppressant used for treating many types of diseases such as kidney carcinomas. In yeast, rapamycin inhibits the TORC1 kinase signaling pathway causing rapid alteration in gene expression and ultimately cell cycle arrest in G 1 through mechanisms that are not fully understood. Herein, we screened a histone mutant collection and report that one of the mutants, H2B R95A, is strikingly resistant to rapamycin due to a defective cell cycle arrest. We show that the H2B R95A causes defects in the expression of a subset of genes of the pheromone pathway required for α factor-induced G 1 arrest. The expression of the STE5 gene and its encoded scaffold protein Ste5, required for the sequential activation of the MAPKs of the pheromone pathway, is greatly reduced in the H2B R95A mutant. Similar to the H2B R95A mutant, cells devoid of Ste5 are also resistant to rapamycin. Rapamycin-induced G 1 arrest does not involve detectable phosphorylation of the MAPKs, Kss1 and Fus3, as reported for α factor-induced G 1 arrest. However, we observed a sharp induction of the G 1 cyclin Cln2 (~ 3- to 4-fold) in the ste5Δ mutant within 30 mins of exposure to rapamycin. Our data provide a new insight whereby rapamycin signaling via the Torc1 kinase may exploit the pheromone pathway to arrest cells in the G 1 phase.