bluuebunny/crossref_metadata_2025_split huggingface dataset:
Role of Strain-Induced Microscale Compositional Pulling on Optical Properties of High Al Content AlGaN Quantum Wells for Deep-Ultraviolet LED
Authors: Lu Shiqiang , Luo Zongyan , Li Jinchai , Lin Wei , Chen Hangyang , Liu Dayi , Cai Duanjun , Huang Kai , Gao Na , Zhou Yinghui , Li Shuping , Kang Junyong 
Published: January 2022

AbstractA systematic study was carried out for strain-induced microscale compositional pulling effect on the structural and optical properties of high Al content AlGaN multiple quantum wells (MQWs). Investigations reveal that a large tensile strain is introduced during the epitaxial growth of AlGaN MQWs, due to the grain boundary formation, coalescence and growth. The presence of this tensile strain results in the microscale inhomogeneous compositional pulling and Ga segregation, which is further confirmed by the lower formation enthalpy of Ga atom than Al atom on AlGaN slab using first principle simulations. The strain-induced microscale compositional pulling leads to an asymmetrical feature of emission spectra and local variation in emission energy of AlGaN MQWs. Because of a stronger three-dimensional carrier localization, the area of Ga segregation shows a higher emission efficiency compared with the intrinsic area of MQWs, which is benefit for fabricating efficient AlGaN-based deep-ultraviolet light-emitting diode.
1.3 kV Vertical GaN-Based Trench MOSFETs on 4-Inch Free Standing GaN Wafer
Authors: He Wei , Li Jian , Liao Zeliang , Lin Feng , Wu Junye , Wang Bing , Wang Maojun , Liu Nan , Chiu Hsien-Chin , Kuo Hao-Chung , Lin Xinnan , Li Jingbo , Liu Xinke 
Published: January 2022

AbstractIn this work, a vertical gallium nitride (GaN)-based trench MOSFET on 4-inch free-standing GaN substrate is presented with threshold voltage of 3.15 V, specific on-resistance of 1.93 mΩ·cm2, breakdown voltage of 1306 V, and figure of merit of 0.88 GW/cm2. High-quality and stable MOS interface is obtained through two-step process, including simple acid cleaning and a following (NH4)2S passivation. Based on the calibration with experiment, the simulation results of physical model are consistent well with the experiment data in transfer, output, and breakdown characteristic curves, which demonstrate the validity of the simulation data obtained by Silvaco technology computer aided design (Silvaco TCAD). The mechanisms of on-state and breakdown are thoroughly studied using Silvaco TCAD physical model. The device parameters, including n−-GaN drift layer, p-GaN channel layer and gate dielectric layer, are systematically designed for optimization. This comprehensive analysis and optimization on the vertical GaN-based trench MOSFETs provide significant guide for vertical GaN-based high power applications.
Aristotle: stratified causal discovery for omics data
Authors: Mansouri Mehrdad , Khakabimamaghani Sahand , Chindelevitch Leonid , Ester Martin 
Published: January 2022

Abstract
Background
There has been a simultaneous increase in demand and accessibility across genomics, transcriptomics, proteomics and metabolomics data, known as omics data. This has encouraged widespread application of omics data in life sciences, from personalized medicine to the discovery of underlying pathophysiology of diseases. Causal analysis of omics data may provide important insight into the underlying biological mechanisms. Existing causal analysis methods yield promising results when identifying potential general causes of an observed outcome based on omics data. However, they may fail to discover the causes specific to a particular stratum of individuals and missing from others.

Methods
To fill this gap, we introduce the problem of stratified causal discovery and propose a method, Aristotle, for solving it. Aristotle addresses the two challenges intrinsic to omics data: high dimensionality and hidden stratification. It employs existing biological knowledge and a state-of-the-art patient stratification method to tackle the above challenges and applies a quasi-experimental design method to each stratum to find stratum-specific potential causes.

Results
Evaluation based on synthetic data shows better performance for Aristotle in discovering true causes under different conditions compared to existing causal discovery methods. Experiments on a real dataset on Anthracycline Cardiotoxicity indicate that Aristotle’s predictions are consistent with the existing literature. Moreover, Aristotle makes additional predictions that suggest further investigations.
Assigning protein function from domain-function associations using DomFun
Authors: Rojano Elena , Jabato Fernando M. , Perkins James R. , Córdoba-Caballero José , García-Criado Federico , Sillitoe Ian , Orengo Christine , Ranea Juan A. G. , Seoane-Zonjic Pedro 
Published: January 2022

Abstract
Background
Protein function prediction remains a key challenge. Domain composition affects protein function. Here we present DomFun, a Ruby gem that uses associations between protein domains and functions, calculated using multiple indices based on tripartite network analysis. These domain-function associations are combined at the protein level, to generate protein-function predictions.

Results
We analysed 16 tripartite networks connecting homologous superfamily and FunFam domains from CATH-Gene3D with functional annotations from the three Gene Ontology (GO) sub-ontologies, KEGG, and Reactome. We validated the results using the CAFA 3 benchmark platform for GO annotation, finding that out of the multiple association metrics and domain datasets tested, Simpson index for FunFam domain-function associations combined with Stouffer’s method leads to the best performance in almost all scenarios. We also found that using FunFams led to better performance than superfamilies, and better results were found for GO molecular function compared to GO biological process terms. DomFun performed as well as the highest-performing method in certain CAFA 3 evaluation procedures in terms of $$F_{max}$$

F

max

and $$S_{min}$$

S

min

We also implemented our own benchmark procedure, Pathway Prediction Performance (PPP), which can be used to validate function prediction for additional annotations sources, such as KEGG and Reactome. Using PPP, we found similar results to those found with CAFA 3 for GO, moreover we found good performance for the other annotation sources. As with CAFA 3, Simpson index with Stouffer’s method led to the top performance in almost all scenarios.

Conclusions
DomFun shows competitive performance with other methods evaluated in CAFA 3 when predicting proteins function with GO, although results vary depending on the evaluation procedure. Through our own benchmark procedure, PPP, we have shown it can also make accurate predictions for KEGG and Reactome. It performs best when using FunFams, combining Simpson index derived domain-function associations using Stouffer’s method. The tool has been implemented so that it can be easily adapted to incorporate other protein features, such as domain data from other sources, amino acid k-mers and motifs. The DomFun Ruby gem is available from https://rubygems.org/gems/DomFun. Code maintained at https://github.com/ElenaRojano/DomFun. Validation procedure scripts can be found at https://github.com/ElenaRojano/DomFun_project.
Influence of mechanical and TGF-β3 stimulation on the tenogenic differentiation of tonsil-derived mesenchymal stem cells
Authors: Wee Jaeyeon , Kim Hyang , Shin Sang-Jin , Lee Taeyong , Lee Seung Yeol 
Published: January 2022

Abstract
Background
Organogenesis from tonsil-derived mesenchymal cells (TMSCs) has been reported, wherein tenogenic markers are expressed depending on the chemical stimulation during tenogenesis. However, there are insufficient studies on the mechanical strain stimulation for tenogenic cell differentiation of TMSCs, although these cells possess advantages as a cell source for generating tendinous tissue. The purpose of this study was to investigate the effects of mechanical strain and transforming growth factor-beta 3 (TGF-β3) on the tenogenic differentiation of TMSCs and evaluate the expression of tendon-related genes and extracellular matrix (ECM) components, such as collagen.

Results
mRNA expression of tenogenic genes was significantly higher when the mechanical strain was applied than under static conditions. Moreover, mRNA expression of tenogenic genes was significantly higher with TGF-β3 treatment than without. mRNA expression of osteogenic and chondrogenic genes was not significantly different among different mechanical strain intensities. In cells without TGF-β3 treatment, double-stranded DNA concentration decreased, while the amount of normalized collagen increased as the intensity of mechanical strain increased.

Conclusions
Mechanical strain and TGF-β3 have significant effects on TMSC differentiation into tenocytes. Mechanical strain stimulates the differentiation of TMSCs, particularly into tenocytes, and cell differentiation, rather than proliferation. However, a combination of these two did not have a synergistic effect on differentiation. In other words, mechanical loading did not stimulate the differentiation of TMSCs with TGF-β3 supplementation. The effect of mechanical loading with TGF-β3 treatment on TMSC differentiation can be manipulated according to the differentiation stage of TMSCs. Moreover, TMSCs have the potential to be used for cell banking, and compared to other mesenchymal stem cells, they can be procured from patients via less invasive procedures.
Investigating the genomic alteration improved the clinical outcome of aged patients with lung carcinoma
Authors: Chen Sixian , Fu Aizhen , Lu Yuan , Lu Wei , Chen Yongfeng , Hong Shuiqiang , Zhou Suli , Xiang Tianmin , Zhang Zhenzhen , Cai Yongguang 
Published: January 2022

Abstract
Background
Lung carcinoma is a common geriatric disease. The development of genotype-targeted therapies greatly improved the management of lung carcinoma. However, the treatment for old patients can be more complex than that for young individuals.

Results
To investigate the benefits of genetic detection for older patients with lung carcinoma, we explored the genomic profiling of 258 patients with more than 55 years using a targeted next generation sequencing, and some of these patients were treated with targeted therapies based on the results of genomic detection. KRAS codon 61 mutations were found in 15.2% KRAS-mutated patients, which tend to be co-existing with other classical activating mutations other than codons 12/13. Acquired EGFR C797S mutations were identified in 2 cases and ERBB2 amplification was identified in 1 case. All these 3 cases developed resistance to EGFR tyrosine kinase inhibitors and showed expected results of their followed therapies. The median progression-free survival and median overall survival of patients treated with molecular targeted therapies were better than those of patients treated with chemoradiotherapy alone.

Conclusions
Our findings revealed the specific genomic profiles of patients older than 55 years with lung carcinoma and suggested that these old patients have been benefit from the genetic detection, which helped identify druggable mutations and distinguish resistance mechanisms.
Impact of Helicobacter pylori infection on fluid duodenal microbial community structure and microbial metabolic pathways
Authors: Maeda Tadashi , Zai Hiroaki , Fukui Yuto , Kato Yoshifumi , Kumade Eri , Watanabe Toshiyasu , Furusyo Norihiro , Nakajima Hitoshi , Arai Kazuho , Ishii Yoshikazu , Tateda Kazuhiro , Urita Yoshihisa 
Published: January 2022

Abstract
Background
The bioactivities of commensal duodenal microbiota greatly influence the biofunction of hosts. We investigated the role of Helicobacter pylori infection in extra-gastroduodenal diseases by determining the impact of H. pylori infection on the duodenal microbiota. We sequenced 16 S rRNA genes in samples aspirated from the descending duodenum of 47 (male, 20; female, 27) individuals who were screened for gastric cancer. Samples were analysed using 16 S rRNA gene amplicon sequencing, and the LEFSe and Kyoto Encyclopaedia of Genes and Genomes methods were used to determine whether the duodenal microflora and microbial biofunctions were affected using H. pylori infection.

Results
Thirteen and 34 participants tested positive and negative for H. pylori, respectively. We identified 1,404 bacterial operational taxonomic units from 23 phyla and 253 genera. H. pylori infection changed the relative mean abundance of three phyla (Proteobacteria, Actinobacteria, and TM7) and ten genera (Neisseria, Rothia, TM7-3, Leptotrichia, Lachnospiraceae, Megasphaera, F16, Moryella, Filifactor, and Paludibacter). Microbiota features were significantly influenced in H. pylori-positive participants by 12 taxa mostly classified as Gammaproteobacteria. Microbial functional annotation revealed that H. pylori significantly affected 12 microbial metabolic pathways.

Conclusions
H. pylori disrupted normal bacterial communities in the duodenum and changed the biofunctions of commensal microbiota primarily by upregulating specific metabolic pathways. Such upregulation may be involved in the onset of diseases associated with H. pylori infection.
Strategies for discontinuation of proton pump inhibitors (PPIs) in patients with long-term PPI administration: a randomized controlled trial
Authors: Hojo Mariko , Asaoka Daisuke , Shimada Yuji , Nojiri Shuko , Nagahara Akihito 
Published: January 2022

Abstract
Background
Proton pump inhibitors (PPIs), including potassium ion-competitive acid blocker, are widely used worldwide and are often used for long periods of time. However, in recent years, potential side effects associated with long-term PPI use have been reported. Many patients take PPI for a long period of time, even though it is unnecessary, and it is necessary to discontinue PPI administration in such patients. However, sudden discontinuation may cause symptoms to recur and discontinuation may be unsuccessful. A strategy for safe and secure PPI discontinuation has not yet been established. The purpose of this study is to determine whether PPI can be safely discontinued by tapering the PPI dose or by abrupt discontinuation of PPI, and to establish a strategy for safe and secure PPI discontinuation.

Methods
The evaluation will be conducted as a multicenter, randomized, parallel-group clinical trial with five assessment points at the start of the study and 2 weeks, 4 weeks, 6 months, and 12 months after the start of the study. One intervention group is the group in which PPI administration is abruptly discontinued (Group A), and the second group is the group in which the PPI dose is gradually tapered and then PPI administration is discontinued (Group B). The primary outcome and secondary outcome are the proportion of patients who successfully discontinued the PPI at 6 months and at 12 months after the start of the study in groups A and B, respectively.

Discussion
We predict that the proportion of patients who successfully discontinue PPI will be higher in the group in which PPI administration was gradually tapered than in the group in which PPI administration was abruptly discontinued. On the other hand, we expect that many participants will succeed in discontinuing PPI regardless of the discontinuation strategy due to the explanation that discontinuation is necessary.

Trial registration

Japan Registry of Clinical Trials, jRCT1031180383. Registered 20 March 2019, https://jrct.niph.go.jp/latest-detail/jRCT1031180383.
A patient with granulomatous amoebic encephalitis caused by Balamuthia mandrillaris survived with two excisions and medication
Authors: Peng Limei , Zhou Quan , Wu Yu , Cao Xiaoli , Lv Zili , Su Minghua , Yu Yachun , Huang Wen 
Published: January 2022

Abstract
Background
Granulomatous amoebic encephalitis (GAE) is a rare central nervous system infection caused by the Balamuthia mandrillaris or Acanthamoeba species. Diagnosis is challenging because of the non-specific clinical presentation, cerebrospinal fluid analysis, and radiological features. There is no effective treatment for GAE to date.

Case presentation
A 54-year-old male was admitted to hospital after experiencing acute onset of numbness and weakness on his left limb. Due to the initial consideration of intracranial tumor, surgical removal of the right parietal lesion was performed. However, the patient had a headache accompanied by diplopia, difficulty walking and a new lesion was found in the left occipital-parietal lobe two weeks after the first operation. High-throughput next-generation sequencing (NGS) detected the presence of high copy reads of the B. mandrillaris genome sequence in the patient’s blood, cerebral spinal fluid (CSF), and brain tissue. Pathological investigation of the brain tissue showed granulomatous changes and amoebic trophozoite scattered around blood vessels under high magnification. The patient was re-operated due to developing progressive confusion caused by subfalcine herniation of the left cerebral hemisphere. The lesions of the right parietal lobe were obviously decreasing in size after the first surgery, and the lesions of the left occipital lobe and the sunfalcine herniation didn’t ameliorate two months after the second surgery. The patient was transferred to local hospital for continuous treatment with sulfamethoxazole and azithromycin. After five months of the second surgery, the patient showed good recovery with mild headache.

Conclusions
This is the first report of a patient with B. mandrillaris encephalitis initially confirmed by NGS and have experienced two excisions, responding favorably to the combination of surgeries and medications. Early surgical resection of intracranial lesions combined with drug treatment may offer the chance of a cure.
Volumetric accuracy of different imaging modalities in acute intracerebral hemorrhage
Authors: Schlunk Frieder , Kuthe Johannes , Harmel Peter , Audebert Heinrich , Hanning Uta , Bohner Georg , Scheel Michael , Kleine Justus , Nawabi Jawed 
Published: January 2022

Abstract
Background
Follow-up imaging in intracerebral hemorrhage is not standardized and radiologists rely on different imaging modalities to determine hematoma growth. This study assesses the volumetric accuracy of different imaging modalities (MRI, CT angiography, postcontrast CT) to measure hematoma size.

Methods
28 patients with acute spontaneous intracerebral hemorrhage referred to a tertiary stroke center were retrospectively included between 2018 and 2019. Inclusion criteria were (1) spontaneous intracerebral hemorrhage (supra- or infratentorial), (2) noncontrast CT imaging performed on admission, (3) follow-up imaging (CT angiography, postcontrast CT, MRI), and (4) absence of hematoma expansion confirmed by a third cranial image within 6 days. Two independent raters manually measured hematoma volume by drawing a region of interest on axial slices of admission noncontrast CT scans as well as on follow-up imaging (CT angiography, postcontrast CT, MRI) using a semi-automated segmentation tool (Visage image viewer; version 7.1.10). Results were compared using Bland–Altman plots.

Results
Mean admission hematoma volume was 18.79 ± 19.86 cc. All interrater and intrarater intraclass correlation coefficients were excellent (1; IQR 0.98–1.00). In comparison to hematoma volume on admission noncontrast CT volumetric measurements were most accurate in patients who received postcontrast CT (bias of − 2.47%, SD 4.67: n = 10), while CT angiography often underestimated hemorrhage volumes (bias of 31.91%, SD 45.54; n = 20). In MRI sequences intracerebral hemorrhage volumes were overestimated in T2* (bias of − 64.37%, SD 21.65; n = 10). FLAIR (bias of 6.05%, SD 35.45; n = 13) and DWI (bias of-14.6%, SD 31.93; n = 12) over- and underestimated hemorrhagic volumes.

Conclusions
Volumetric measurements were most accurate in postcontrast CT while CT angiography and MRI sequences often substantially over- or underestimated hemorrhage volumes.
Vitamin D receptor gene polymorphism predicts left ventricular hypertrophy in maintenance hemodialysis
Authors: Liu Bingman , Yang Qingqing , Zhao Liangyu , Shui Hua , Si Xiaoyun 
Published: January 2022

Abstract
Background
To verify that the single nucleotide polymorphisms (SNP) of vitamin D receptor (VDR) may lead to genetic susceptibility to left ventricular hypertrophy (LVH), the present study was designed to study four SNPs of VDR associated with LVH in maintenance hemodialysis (MHD) patients of Han nationality.

Methods
120 MHD patients were recruited at Department of Nephrology, Zhongnan Hospital of Wuhan University to analyze the expression of genotype, allele and haplotype of Fok I, Bsm I, Apa I and Taq I in blood samples, and to explore their correlation with blood biochemical indexes and ventricular remodeling.

Results
The results showed that the risks of CVD included gender, dialysis time, heart rate, SBP, glycated hemoglobin, calcium, iPTH and CRP concentration. Moreover, LAD, LVDd, LVDs, IVST and LVMI in B allele of Bsm I increased significantly. Fok I, Apa I and Taq I polymorphisms have no significant difference between MHD with LVH and without LVH. Further study showed that VDR expression level decreased significantly in MHD patients with LVH, and the B allele was positively correlated with VDR Expression.

Conclusion
VDR Bsm I gene polymorphism may predict cardiovascular disease risk of MDH patients, and provided theoretical basis for early detection and prevention of cardiovascular complications.
Ranking patients on the kidney transplant waiting list based on fuzzy inference system
Authors: Taherkhani Nasrin , Sepehri Mohammad Mehdi , Khasha Roghaye , Shafaghi Shadi 
Published: January 2022

Abstract
Background
Kidney transplantation is the best treatment for people with End-Stage Renal Disease (ESRD). Kidney allocation is the most important challenge in kidney transplantation process. In this study, a Fuzzy Inference System (FIS) was developed to rank the patients based on kidney allocation factors. The main objective was to develop an expert system, which would mimic the expert intuitive thinking and decision-making process in the face of the complexity of kidney allocation.

Methods
In the first stage, kidney allocation factors were identified. Next, Intuitionistic Fuzzy Analytic Hierarchy Process (IF-AHP) has been used to weigh them. The purpose of this stage is to develop a point scoring system for kidney allocation. Fuzzy if-then rules were extracted from the United Network for Organ Sharing (UNOS) dataset by constructing the decision tree, in the second stage. Then, a Multi-Input Single-Output (MISO) Mamdani fuzzy inference system was developed for ranking the patients on the waiting list.

Results
To evaluate the performance of the developed Fuzzy Inference System for Kidney Allocation (FISKA), it was compared with a point scoring system and a filtering system as two common approaches for kidney allocation. The results indicated that FISKA is more acceptable to the experts than the mentioned common methods.

Conclusion
Given the scarcity of donated kidneys and the importance of optimal use of existing kidneys, FISKA can be very useful for improving kidney allocation systems. Countries that decide to change or improve the kidney allocation system can simply use the proposed model. Furthermore, this model is applicable to other organs, including lung, liver, and heart.