bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Iliofemoral Bounce Test: Identifying Hip Capsular Insufficiency
Authors: Bucci Gabriella , McGovern Ryan P. , Singleton Steven B. , Christoforetti John J. 
Published: April 2022

Background: Insufficiency of hip capsular structures has recently gained recognition as a cause of pre-arthritic hip pain, leading to hip joint instability and progressive chondrolabral injury. An accurate evaluation of capsular integrity can help orthopedic surgeons plan capsular management prior to hip arthroscopy. Indications: The proposed iliofemoral bounce test is meant to be applied preoperatively for identification of hip capsular integrity when microinstability is suspected or in the setting of revision hip arthroscopy. Technique Description: After induction of general anesthesia and complete muscle relaxation, the patient is placed in a supine figure-four position by placing the foot of the pathologic hip on the contralateral knee. Two examination techniques are performed: (1) The examiner places one hand on the patient’s contralateral anterior superior iliac spine and applies consecutive downward pressure in a “rocking” manner to the pelvis; (2) the examiner applies a preload and release force to the flexed knee (examined hip), with the contralateral pelvis stabilized, and observes the response of the knee to this loads. Results: Technique 1: The expected physiologic response in a preserved joint is a “bounce” of the contralateral hip (examined hip), evidenced by an up-and-down movement of the knee in response to the rocking movement applied. This movement reflects the integrity and functionality of the hip capsule ligaments’ elastic recoil forces, allowing the hip to remain in a stable state in response to destabilizing forces. In contrast, when capsular insufficiency is present, a lack of bouncing will be observed due to unrestricted external rotation of the hip to constrain the hip joint. Technique 2: In a preserved joint capsule, the knee will return to its preload position, while in capsular insufficiency, no bouncing of the knee will be observed. Discussion/Conclusion: The iliofemoral bounce test is a novel, dynamic, and reproducible examination technique for clinicians to evaluate patient’s true hip capsular integrity and for preoperative identification of the proper capsular management, either with a less invasive capsulotomy or performing a capsular closure, plication or even reconstruction, when necessary.
Mount Mather Creek, British Columbia – a new sodalite-bearing carbohydrothermal breccia deposit including a new Canadian occurrence for the rare minerals edingtonite and quintinite
Authors: Piilonen Paula C. , Poirier Glenn , Rowe Ralph , Mitchell Roger , Robak Chris 
Published: April 2022

AbstractThe Mount Mather Creek sodalite-bearing carbohydrothermal breccia dyke is located ~35 km northwest of Golden, British Columbia, Canada, within the Foreland Belt on the eastern side of the Mississippian-to-Devonian British Columbia Alkaline Province. The dyke occurs in situ on the western side of the Mount Mather Creek gully, cropping out over a distance of ~80 m with a thickness of up to 10 m, intruding a syncline of Middle and Upper Cambrian Chancellor Group carbonate rocks. To date, no parental alkaline complex has been found adjacent or proximal to the dyke. The breccia dyke is flow-banded and matrix-supported and consists of host rock clasts, medium- to coarse-grained, anhedral-to-poikilitic carbonate-rich syenite segregations that occur as veins and pods, and fine-grained banded sodalite plus carbonate fragments in a carbonate-rich matrix. The sodalite-carbonate segregations consist dominantly of sodalite, ferroan dolomite, calcite and microcline, with an extensive suite of trace minerals enriched in rare earth elements (REE), Na, Ba and Sr, including albite, analcime, ancylite-(Ce), chabazite-Na, fluorapatite, baryte, barytocalcite, cancrinite, galena, goethite, gonnardite, harmotome, edingtonite, a potentially new Mg-bearing edingtonite-like mineral, natrolite, nordstrandite, pyrite, quintinite and sphalerite. Alteration of the primary silicate–carbonate assemblage has resulted in a secondary assemblage of hydrothermal or carbohydrothermal REE–Ba–Sr–Na phases including albite, analcime, cancrinite, gonnardite and nordstrandite after sodalite, together with complex intergrowths of ancylite-(Ce), barytocalcite, edingtonite, and a potentially-new Mg-bearing edingtonite-like mineral. Remobilisation of Ba and Sr from barytocalcite resulted in crystallisation of late-stage baryte and Sr-rich calcite. Mount Mather Creek is only the fifth Canadian occurrence of the Ba-zeolite, edingtonite, and the second Canadian occurrence of the rare layered double hydroxide quintinite. The Mount Mather Creek breccia is a carbohydrothermal deposit, the product of a low temperature (<450°C), highly evolved, alkaline, SiO2-undersaturated, Na–Ba–REE–Cl-rich, residual carbonated silicate melt whose parental origins remain unknown.
HGDTI: predicting drug–target interaction by using information aggregation based on heterogeneous graph neural network
Authors: Yu Liyi , Qiu Wangren , Lin Weizhong , Cheng Xiang , Xiao Xuan , Dai Jiexia 
Published: April 2022

Abstract
Background
In research on new drug discovery, the traditional wet experiment has a long period. Predicting drug–target interaction (DTI) in silico can greatly narrow the scope of search of candidate medications. Excellent algorithm model may be more effective in revealing the potential connection between drug and target in the bioinformatics network composed of drugs, proteins and other related data.

Results
In this work, we have developed a heterogeneous graph neural network model, named as HGDTI, which includes a learning phase of network node embedding and a training phase of DTI classification. This method first obtains the molecular fingerprint information of drugs and the pseudo amino acid composition information of proteins, then extracts the initial features of nodes through Bi-LSTM, and uses the attention mechanism to aggregate heterogeneous neighbors. In several comparative experiments, the overall performance of HGDTI significantly outperforms other state-of-the-art DTI prediction models, and the negative sampling technology is employed to further optimize the prediction power of model. In addition, we have proved the robustness of HGDTI through heterogeneous network content reduction tests, and proved the rationality of HGDTI through other comparative experiments. These results indicate that HGDTI can utilize heterogeneous information to capture the embedding of drugs and targets, and provide assistance for drug development.

Conclusions
The HGDTI based on heterogeneous graph neural network model, can utilize heterogeneous information to capture the embedding of drugs and targets, and provide assistance for drug development. For the convenience of related researchers, a user-friendly web-server has been established at http://bioinfo.jcu.edu.cn/hgdti.
GenomicDistributions: fast analysis of genomic intervals with Bioconductor
Authors: Kupkova Kristyna , Mosquera Jose Verdezoto , Smith Jason P. , Stolarczyk Michał , Danehy Tessa L. , Lawson John T. , Xue Bingjie , Stubbs John T. , LeRoy Nathan , Sheffield Nathan C. 
Published: April 2022

AbstractBackgroundEpigenome analysis relies on defined sets of genomic regions output by widely used assays such as ChIP-seq and ATAC-seq. Statistical analysis and visualization of genomic region sets is essential to answer biological questions in gene regulation. As the epigenomics community continues generating data, there will be an increasing need for software tools that can efficiently deal with more abundant and larger genomic region sets. Here, we introduce GenomicDistributions, an R package for fast and easy summarization and visualization of genomic region data.ResultsGenomicDistributions offers a broad selection of functions to calculate properties of genomic region sets, such as feature distances, genomic partition overlaps, and more. GenomicDistributions functions are meticulously optimized for best-in-class speed and generally outperform comparable functions in existing R packages. GenomicDistributions also offers plotting functions that produce editable ggplot objects. All GenomicDistributions functions follow a uniform naming scheme and can handle either single or multiple region set inputs.ConclusionsGenomicDistributions offers a fast and scalable tool for exploratory genomic region set analysis and visualization. GenomicDistributions excels in user-friendliness, flexibility of outputs, breadth of functions, and computational performance. GenomicDistributions is available from Bioconductor (https://bioconductor.org/packages/release/bioc/html/GenomicDistributions.html).
Neural network modeling of differential binding between wild-type and mutant CTCF reveals putative binding preferences for zinc fingers 1–2
Authors: Kaplow Irene M. , Banerjee Abhimanyu , Foo Chuan Sheng 
Published: April 2022

Abstract
Background
Many transcription factors (TFs), such as multi zinc-finger (ZF) TFs, have multiple DNA binding domains (DBDs), and deciphering the DNA binding motifs of individual DBDs is a major challenge. One example of such a TF is CCCTC-binding factor (CTCF), a TF with eleven ZFs that plays a variety of roles in transcriptional regulation, most notably anchoring DNA loops. Previous studies found that CTCF ZFs 3–7 bind CTCF’s core motif and ZFs 9–11 bind a specific upstream motif, but the motifs of ZFs 1–2 have yet to be identified.

Results
We developed a new approach to identifying the binding motifs of individual DBDs of a TF through analyzing chromatin immunoprecipitation sequencing (ChIP-seq) experiments in which a single DBD is mutated: we train a deep convolutional neural network to predict whether wild-type TF binding sites are preserved in the mutant TF dataset and interpret the model. We applied this approach to mouse CTCF ChIP-seq data and identified the known binding preferences of CTCF ZFs 3–11 as well as a putative GAG binding motif for ZF 1. We analyzed other CTCF datasets to provide additional evidence that ZF 1 is associated with binding at the motif we identified, and we found that the presence of the motif for ZF 1 is associated with CTCF ChIP-seq peak strength.

Conclusions
Our approach can be applied to any TF for which in vivo binding data from both the wild-type and mutated versions of the TF are available, and our findings provide new potential insights binding preferences of CTCF’s DBDs.
Whole blood transcriptome profiling identifies candidate genes associated with alopecia in male giant pandas (Ailuropoda melanoleuca)
Authors: Shen Haibo , Li Caiwu , He Ming , Huang Yan , Wang Jing , Luo Jing , Wang Minglei , Yue Bisong , Zhang Xiuyue 
Published: April 2022

AbstractBackgroundThe giant panda (Ailuropoda melanoleuca) is a threatened species endemic to China. Alopecia, characterized by thinning and broken hair, mostly occurs in breeding males. Alopecia significantly affects the health and public image of the giant panda and the cause of alopecia is unclear.ResultsHere, we researched gene expression profiles of four alopecia giant pandas and seven healthy giant pandas. All pandas were approximately ten years old and their blood samples collected during the breeding season. A total of 458 up-regulated DEGs and 211 down-regulated DEGs were identified. KEGG pathway enrichment identified that upregulated genes were enriched in the Notch signaling pathway and downregulated genes were enriched in ribosome, oxidative phosphorylation, and thermogenesis pathways. We obtained 28 hair growth-related DEGs, and identified three hub genesNOTCH1,SMAD3, andTGFB1in PPI analysis. Five hair growth-related signaling pathways were identified with abnormal expression, these were Notch, Wnt, TGF-β, Mapk, and PI3K-Akt. The overexpression ofNOTCH1delays inner root sheath differentiation and results in hair shaft abnormalities. The delayed hair regression was associated with a significant decrease in the expression levels ofTGFB1.ConclusionsOur data confirmed the abnormal expression of several hair-related genes and pathways and identified alopecia candidate genes in the giant panda. Results of this study provide theoretical basis for the establishment of prevention and treatment strategies for giant pandas with alopecia.
Repair-related molecular changes during recovery phase of ischemic stroke in female rats
Authors: Mostajeran Maryam , Edvinsson Lars , Ahnstedt Hilda , Arkelius Kajsa , Ansar Saema 
Published: April 2022

Abstract
Background
Some degree of spontaneous recovery is usually observed after stroke. Experimental studies have provided information about molecular mechanisms underlying this recovery. However, the majority of pre-clinical stroke studies are performed in male rodents, and females are not well studied. This is a clear discrepancy when considering the clinical situation. Thus, it is important to include females in the evaluation of recovery mechanisms for future therapeutic strategies. This study aimed to evaluate spontaneous recovery and molecular mechanisms involved in the recovery phase two weeks after stroke in female rats.

Methods
Transient middle cerebral artery occlusion was induced in female Wistar rats using a filament model. Neurological functions were assessed up to day 14 after stroke. Protein expression of interleukin 10 (IL-10), transforming growth factor (TGF)-β, neuronal specific nuclei protein (NeuN), nestin, tyrosine-protein kinase receptor Tie-2, extracellular signal-regulated kinase (ERK) 1/2, and Akt were evaluated in the peri-infarct and ischemic core compared to contralateral side of the brain at day 14 by western blot. Expression of TGF-β in middle cerebral arteries was evaluated by immunohistochemistry.

Results
Spontaneous recovery after stroke was observed from day 2 to day 14 and was accompanied by a significantly higher expression of nestin, p-Akt, p-ERK1/2 and TGF-β in ischemic regions compared to contralateral side at day 14. In addition, a significantly higher expression of TGF-β was observed in occluded versus non-occluded middle cerebral arteries. The expression of Tie-2 and IL-10 did not differ between the ischemic and contralateral sides.

Conclusion
Spontaneous recovery after ischemic stroke in female rats was coincided by a difference observed in the expression of molecular markers. The alteration of these markers might be of importance to address future therapeutic strategies.
Comparative transcriptomic analysis of two Cucumis melo var. saccharinus germplasms differing in fruit physical and chemical characteristics
Authors: Liang Renfan , Su Yicheng , Qin Xiaojuan , Gao Zhongkui , Fu Zhixin , Qiu Huijun , Lin Xu , Zhu Jinlian 
Published: April 2022

Abstract
Background
Hami melon (Cucumis melo var. saccharinus) is a popular fruit in China because of its excellent taste, which is largely determined by its physicochemical characteristics, including flesh texture, sugar content, aroma, and nutrient composition. However, the mechanisms by which these characteristics are regulated have not yet been determined. In this study, we monitored changes in the fruits of two germplasms that differed in physicochemical characteristics throughout the fruit development period.

Results
Ripe fruit of the bred variety ‘Guimi’ had significantly higher soluble sugar contents than the fruit of the common variety ‘Yaolong.’ Additionally, differences in fruit shape and color between these two germplasms were observed during development. Comparative transcriptome analysis, conducted to identify regulators and pathways underlying the observed differences at corresponding stages of development, revealed a higher number of differentially expressed genes (DEGs) in Guimi than in Yaolong. Moreover, most DEGs detected during early fruit development in Guimi were associated with cell wall biogenesis. Temporal analysis of the identified DEGs revealed similar trends in the enrichment of downregulated genes in both germplasms, although there were differences in the enrichment trends of upregulated genes. Further analyses revealed trends in differential changes in multiple genes involved in cell wall biogenesis and sugar metabolism during fruit ripening.

Conclusions
We identified several genes associated with the ripening of Hami melons, which will provide novel insights into the molecular mechanisms underlying the development of fruit characteristics in these melons.
Genome-wide expression analysis of carboxylesterase (CXE) gene family implies GBCXE49 functional responding to alkaline stress in cotton
Authors: Rui Cun , Peng Fanjia , Fan Yapeng , Zhang Yuexin , Zhang Zhigang , Xu Nan , Zhang Hong , Wang Jing , Li Shengmei , Yang Tao , Malik Waqar Afzal , Lu Xuke , Chen Xiugui , Wang Delong , Chen Chao , Gao Wenwei , Ye Wuwei 
Published: April 2022

Abstract
Background
Carboxylesterase (CXE) is a type of hydrolase with α/β sheet hydrolase activity widely found in animals, plants and microorganisms, which plays an important role in plant growth, development and resistance to stress.

Results
A total of 72, 74, 39, 38 CXE genes were identified in Gossypium barbadense, Gossypium hirsutum, Gossypium raimondii and Gossypium arboreum, respectively. The gene structure and expression pattern were analyzed. The GBCXE genes were divided into 6 subgroups, and the chromosome distribution of members of the family were mapped. Analysis of promoter cis-acting elements showed that most GBCXE genes contain cis-elements related to plant hormones (GA, IAA) or abiotic stress. These 6 genes we screened out were expressed in the root, stem and leaf tissues. Combined with the heat map, GBCXE49 gene was selected for subcellular locate and confirmed that the protein was expressed in the cytoplasm.

Conclusions
The collinearity analysis of the CXE genes of the four cotton species in this family indicated that tandem replication played an indispensable role in the evolution of the CXE gene family. The expression patterns of GBCXE gene under different stress treatments indicated that GBCXE gene may significantly participate in the response to salt and alkaline stress through different mechanisms. Through the virus-induced gene silencing technology (VIGS), it was speculated that GBCXE49 gene was involved in the response to alkaline stress in G. barbadense.
Prevalence and predictors of non-alcoholic liver disease on MRI among patients with Crohn's disease
Authors: Hong Qijin , Shen Jun , Feng Qi , Zheng Qing , Qiao Yuqi 
Published: April 2022

Abstract
Background
It has been documented that Crohn’s disease (CD) patients were prone to develop non-alcoholic liver fatty liver disease (NAFLD) with less metabolic factors. Our purpose is to investigate the prevalence, clinical characteristics and possible indicators for NAFLD in a cohort of Chinese patients with CD.

Methods
Established CD patients who underwent magnetic resonance enterography (MRE) at the gastroenterology unit of our hospital were consecutively enrolled between June 2018 and May 2020. The diagnosis of NAFLD was made by magnetic resonance proton density fat fraction (MR-PDFF) maps. Medical records during hospitalization were collected and examined by univariate and multivariate analyses. Then a predictive model was constructed based on logistic regression analysis to evaluate the risk of developing NAFLD.

Results
A total of 340 CD subjects were enrolled in this study, 83 (24.4%) suffered from NAFLD. Compared with those without NAFLD, patients with NAFLD showed longer disease duration, higher body mass index (BMI), more frequent use of corticosteroid and pronouncedly elevated liver function tests. The comparison showed no difference in terms of prolonged anti tumor necrosis factor-α (TNF-α) use (> 54w). Multivariate analysis demonstrated that BMI, serum transaminase, pre-albumin and disease duration could independently predict hepatic steatosis.

Conclusion
NAFLD is frequent in chronic CD patients, while long term use of anti TNF-α seems to have no impact on the development of NAFLD in this population. The model incorporating duration, serum transaminase and body mass index presented as a clinical nomogram could well predict the risk of NAFLD in patient with CD.
Plasma and fecal zonulin are not altered by a high green leafy vegetable dietary intervention: secondary analysis of a randomized control crossover trial
Authors: Riviere Aaron J. , Smith Kristen S. , Schaberg Megan N. , Greene Michael W. , Frugé Andrew D. 
Published: April 2022

Abstract
Background
Zonulin is observed in animal models to regulate intestinal permeability and influenced by dietary intake, gut microbiota, and inflammation. We conducted a secondary analysis of a randomized controlled crossover trial (NCT03582306) in individuals with a BMI greater than 30 kg/m2 and high habitual red meat intake and low habitual green leafy vegetable (GLV) intake.

Methods
Participants were provided with frozen GLV during the first or last four weeks (immediate or delayed intervention) of the twelve-week trial. Biological and anthropometric measures were taken at the beginning and at each four-week interval. A subset of 20 participants was selected for this secondary analysis of the intestinal permeability and inflammation-related biomarkers: serum and fecal zonulin; serum lipopolysaccharide binding protein (LBP), Alpha-1-acid glycoprotein 1 (ORM-1), tumor necrosis factor α (TNFα), interleukin-6 (IL-6), and C-reactive protein; 8-hydroxy-2'-deoxyguanosine (8OHdG) and plasma Vitamin K1 as a marker of protocol adherence. Nutrient and food group intake from two-24-h dietary recalls collected at each time point were assessed. Fecal microbiota was measured by 16 s rRNA PCR sequencing. Changes in biological markers, dietary factors, and microbial taxa were assessed with Wilcoxon Sign Ranks Tests. Exploratory analyses of the relationship between changes in outcome variables were conducted with Spearman correlations.

Results
No changes in serum and fecal zonulin and serum LBP were observed. Plasma Vitamin K (p = 0.005) increased, while plasma 8OHdG (p = 0.023) decreased during the intervention compared to the control. The only dietary factors that changed significantly were increases during intervention in Vitamin K and Dark GLV (p < 0.001 for both) compared to control. Fecal microbiota did not change significantly across all times points; however, change in serum zonulin was associated with change in Proteobacteria (ρ = − 0.867, p = 0.001) in females and Bifidobacterium (ρ = − 0.838, p = 0.009) and Bacteroidaceae (ρ = 0.871, p = 0.005) in men.

Conclusions
A high GLV dietary intervention increased serum zonulin levels and had no effect on fecal zonulin. Lack of concordance between several inflammation-associated biomarkers and zonulin corroborate recent reports of limited utility of zonulin in obese adults free of lower gastrointestinal disease.
Trial Registration information: https://clinicaltrials.gov/ct2/show/NCT03582306 (NCT03582306) registered on 07/11/2018.