bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adjustable Cortical Fixation Device for Quadriceps Tendon Repair: A Cadaveric Biomechanical Study
Authors: Gould Heath P. , Rate William R. , Abbasi Pooyan , Mistretta Katherine L. , Hammond Jason W. 
Published: January 2021

Background: Adjustable cortical fixation devices have demonstrated utility in orthopaedic applications, such as ankle syndesmosis repair. Purpose: To assess the cyclic gap formation of a quadriceps tendon repair technique using an adjustable cortical fixation device compared with repair with knotless suture anchors and suture tape, a modification of conventional suture anchor repair. Study Design: Controlled laboratory study. Methods: Eight fresh-frozen matched pairs of cadaveric knees were used. Specimens in each pair were randomized to undergo either modified suture anchor repair (control) or adjustable cortical fixation repair. The control repair was performed as previously described. The experimental repair was performed using 2 No. 2 FiberWire sutures placed into the quadriceps tendon in a running locked Krackow configuration and 2 adjustable loop devices passed through transosseous tunnels. The lagging strands of the devices were tensioned to seat the cortical fixation buttons at the inferior patellar pole and then tied to the free Krackow strands at the superior pole to complete the repair. The mean plastic gap (permanent tendon displacement that did not recover with cyclic extension) and mean maximum gap (peak displacement that occurred with cyclic knee flexion and partially recovered with extension) were evaluated during cyclic loading for 500 cycles of full knee extension to 90° of flexion. Results: At all testing intervals, the mean plastic gap was significantly smaller for the cortical fixation group versus the suture anchor group ( P < .02). Similarly, the mean maximum gap was significantly smaller for the cortical fixation specimens at all testing intervals ( P < .01). After cyclic loading, the mean maximum gap was significantly smaller in the cortical fixation group (4.80 ± 1.56 mm) versus the suture anchor group (8.47 ± 1.47 mm; P = < .001). The mean plastic gap was also significantly smaller in the cortical fixation versus the suture anchor group (3.25 ± 1.10 mm vs 6.57 ± 1.62 mm, respectively; P = < .001). Conclusion: Quadriceps tendon repair using an adjustable cortical fixation device demonstrated superior biomechanical properties in cyclic displacement testing compared with repair using the suture anchor technique. Clinical Relevance: These results suggest that an adjustable cortical fixation device is a biomechanically viable alternative for quadriceps tendon repair.
An analysis of heavy metals contamination and estimating the daily intakes of vegetables from Uganda
Authors: Kasozi Keneth Iceland , Otim Eric Oloya , Ninsiima Herbert Izo , Zirintunda Gerald , Tamale Andrew , Ekou Justin , Musoke Grace Henry , Muyinda Robert , Matama Kevin , Mujinya Regan , Matovu Henry , Ssempijja Fred , Eze Ejike Daniel , Atino Mauryn , Udechukwu Bede , Kayima Ronald , Etiang Patrick , Ayikobua Emmanuel Tiyo , Kembabazi Stellamaris , Usman Ibe Michael , Sulaiman Sheu Oluwadare , Natabo Phyllis Candy , Kyeyune Grace Nambatya , Batiha Gaber El-Saber , Otim Ochan 
Published: January 2021

Background: Environmental contamination with elevated levels of copper (Cu), cobalt (Co), iron (Fe), zinc (Zn), lead (Pb), chromium (Cr6+), cadmium (Cd), and nickel (Ni)—all states of which are found in Uganda—raises health risk to the public. Pb, Cr6+, Cd, and Ni for instance are generally considered nonessential to cellular functions, notwithstanding the importance of the oxidative state of the metals in bioavailability. As such, we aimed in this study (i) to evaluate heavy metal concentrations in four vegetables from a typical open-air market in Uganda, (ii) to assess the safety of consuming these vegetables against the World Health Organization (WHO) recommended limits of heavy metals consumption, and (iii) to formulate a model of estimated daily intake (EDI) among consumers in the country. Methods: This was a cross-sectional study conducted in five georeferenced markets of Bushenyi district in January 2020. Amaranthus, cabbages, scarlet eggplants, and tomatoes were collected from open markets, processed, and analyzed by atomic absorption spectrometry. Modeled EDI, principal component (PCA) and cluster analysis (CA) were conducted to identify relationships in the samples. Results: The levels of essential elements in the four vegetables were found to fall from Co > Cu > Fe > Zn. Those of non-essential metals were significantly higher and followed the pattern Cd > Cr > Pb > Ni. The highest EDI values were those of Cu in scarlet eggplants, Zn in amaranthus, Fe in amaranthus, Co in amaranthus, Pb in cabbages, total Cr in scarlet eggplant, Cd in cabbages and tomatoes, and Ni in cabbages. In comparison to international limits, EDIs for Zn, Cu, Co and Fe were low while Ni in cabbages were high. PCA showed high variations in scarlet eggplant and amaranthus. The study vegetables were found to be related with each other, not according to the location of the markets from where they were obtained, but according to their species by CA. Conclusion: The presence of non-essential elements above WHO limits raises policy challenges for the consumption and marketing of vegetables in the study area. Furthermore, low EDIs of essential elements in the vegetables create demand for nutritious foods to promote healthy communities.
Treatment Patterns and Clinical Outcomes for Branch Retinal Vein Occlusion: An 8-Year Experience at a Tertiary Eye Center
Authors: Lee Terry , Robbins Cason B. , Thomas Akshay S. , Fekrat Sharon 
Published: January 2021

Purpose: This work aims to investigate real-world treatment patterns and outcomes in eyes with branch retinal vein occlusion in the antivascular endothelial growth factor (anti-VEGF) era. Methods: A retrospective, nonrandomized, comparative study was conducted on eyes diagnosed with branch retinal vein occlusion at a single tertiary center between 2009 and 2017. Medical history, treatment patterns, and visual acuity outcomes were examined. Subanalysis was performed for eyes that met the eligibility criteria for the BRAVO (Ranibizumab for the Treatment of Macular Edema Following Branch Retinal Vein Occlusion) trial. Results: A total of 315 eyes were included, of which 244 were treatment naive. In all eyes, the most common first treatment was the following: intravitreal bevacizumab (38.4%), aflibercept (15.1%), ranibizumab (8.1%), sectoral scatter laser (6.2%), and triamcinolone (3.1%). At 1 year, treatment-naive eyes had received an average of 2.43 anti-VEGF injections. During follow-up, treatment-naive eyes gained an average of 0.21 Early Treatment Diabetic Retinopathy Study lines. Forty eyes that met BRAVO trial criteria received an average of 5.05 anti-VEGF injections in the first year and gained an average of 1.83 Early Treatment Diabetic Retinopathy Study lines. Conclusions: This real-world cohort received fewer anti-VEGF injections at year 1 and experienced less improvement in visual acuity during the course of treatment than clinical trial participants. Trial-eligible patients received more injections and had greater visual gains than those who would not have been eligible for the trial.
Chest physiotherapy enhances detection ofPseudomonas aeruginosain nonexpectorating children with cystic fibrosis
Authors: Marguet Christophe , Houdouin Véronique , Pin Isabelle , Reix Philippe , Huet Frédéric , Mittaine Marie , Ramel Sophie , Wizla-Derambure Nathalie , Abely Michel , Dalphin Marie-Laure , Fayon Michael , Bihouée Tiphaine , Le Bourgeois Muriel , Deneuville Eric , Corvol Harriet , Laurans Muriel , Couderc Laure , Leroux Evelyne , Lémée Ludovic 
Published: January 2021

Lung damage in cystic fibrosis (CF) is strongly associated with lower airway infections. Early treatment ofPseudomonas aeruginosais recommended. Pathogen detection requires sampling of lower airway secretions, which remains a challenge in nonexpectorating patients. Our hypothesis was that chest physiotherapy would improve the quality of airway secretion samples and increase the rates of pathogens detected in nonexpectorating patients.This prospective multicentre study compared three successive methods for sampling airway secretions applied through the same session: 1) an oropharyngeal swab (OP), 2) a chest physiotherapy session followed by a provoked cough to obtain sputum (CP-SP) and 3) a second oropharyngeal swab collected after chest physiotherapy (CP-OP).Haemophilus influenzae,Staphylococcus aureusandP. aeruginosagrowth cultures were assessed. Accuracy tests and an equivalence test were performed to compare the three successive methods of collection.300 nonexpectorating children with CF were included.P. aeruginosawas detected cumulatively in 56 (18.9%) children, and according to the different collection methods in 28 (9.8%), 37 (12.4%) and 44 (14.7%) children by using OP, CP-OP and CP-SP, respectively. Compared with OP, the increased detection rate was +22% for CP-OP (p=0.029) and +57% for CP-SP (p=0.003). CP-SP had the best positive predictive value (86.3%) and negative predictive value (96.0%) forP. aeruginosacompared with the overall detection.The results of this adequately powered study show differences in the rates of pathogens detected according to the sampling method used. Chest physiotherapy enhanced detection ofP. aeruginosain nonexpectorating children with CF.
Caspase-1/IL-1β represses membrane transport of GluA1 by inhibiting the interaction between Stargazin and GluA1 in Alzheimer’s disease
Authors: Gu Xunhu , Wu Hanjun , Xie Yuqin , Xu Lijun , Liu Xu , Wang Wei 
Published: January 2021

Abstract
Background
Alzheimer's disease is a neurodegenerative disease. Previous study has reported that caspase-1/IL-1β is closely associated with Alzheimer's disease. However, the biological role of caspase-1/IL-1β in Alzheimer's disease has not been fully elucidated. This study aimed to explore the mechanism of action of caspase-1/IL-1β in Alzheimer's disease.

Methods
Mouse hippocampal neurones were treated with Aβ1-42 to induce Alzheimer's disease cell model. APP/PS1 mice and Aβ1-42-induced hippocampal neurones were treated with AC-YVAD-CMK (caspase-1 inhibitor). Spatial learning and memory ability of mice were detected by morris water maze. Flow cytometry, TUNEL staining, Thioflavin S staining and immunohistochemistry were performed to examine apoptosis and senile plaque deposition. Enzyme linked immunosorbent assay and western blot were performed to assess the levels of protein or cytokines. Co-Immunoprecipitation was performed to verify the interaction between Stargazin and GluA1.

Results
AC-YVAD-CMK treatment improved spatial learning and memory ability and reduced senile plaque deposition of APP/PS1 mice. Moreover, AC-YVAD-CMK promoted membrane transport of GluA1 in APP/PS1 mice. In vitro, Aβ1-42-induced hippocampal neurones exhibited an increase in apoptosis and a decrease in the membrane transport of GluA1, which was abolished by AC-YVAD-CMK treatment. In addition, Stargazin interacted with GluA1, which was repressed by caspase-1. Caspase-1/IL-1β inhibited membrane transport of GluA1 by inhibiting the interaction between Stargazin and GluA1.

Conclusions
Our data demonstrate that caspase-1/IL-1β represses membrane transport of GluA1 by inhibiting the interaction between Stargazin in Alzheimer's disease. Thus, caspase-1/IL-1β may be a target for Alzheimer's disease treatment.
Evaluation of genetic structure in European wheat cultivars and advanced breeding lines using high-density genotyping-by-sequencing approach
Authors: Tyrka Mirosław , Mokrzycka Monika , Bakera Beata , Tyrka Dorota , Szeliga Magdalena , Stojałowski Stefan , Matysik Przemysław , Rokicki Michał , Rakoczy-Trojanowska Monika , Krajewski Paweł 
Published: January 2021

Abstract
Background
The genetic diversity and gene pool characteristics must be clarified for efficient genome-wide association studies, genomic selection, and hybrid breeding. The aim of this study was to evaluate the genetic structure of 509 wheat accessions representing registered varieties and advanced breeding lines via the high-density genotyping-by-sequencing approach.

Results
More than 30% of 13,499 SNP markers representing 2162 clusters were mapped to genes, whereas 22.50% of 26,369 silicoDArT markers overlapped with coding sequences and were linked in 3527 blocks. Regarding hexaploidy, perfect sequence matches following BLAST searches were not sufficient for the unequivocal mapping to unique loci. Moreover, allelic variations in homeologous loci interfered with heterozygosity calculations for some markers. Analyses of the major genetic changes over the last 27 years revealed the selection pressure on orthologs of the gibberellin biosynthesis-related GA2 gene and the senescence-associated SAG12 gene. A core collection representing the wheat population was generated for preserving germplasm and optimizing breeding programs.

Conclusions
Our results confirmed considerable differences among wheat subgenomes A, B and D, with D characterized by the lowest diversity but the highest LD. They revealed genomic regions that have been targeted by breeding.
The seasonal changes of the gut microbiome of the population living in traditional lifestyles are represented by characteristic species-level and functional-level SNP enrichment patterns
Authors: Zhu Xue , Qin Jiyue , Tan Chongyang , Ning Kang 
Published: January 2021

Abstract
Background
Most studies investigating human gut microbiome dynamics are conducted on humans living in an urban setting. However, few studies have researched the gut microbiome of the populations living traditional lifestyles. These understudied populations are arguably better subjects in answering human-gut microbiome evolution because of their lower exposure to antibiotics and higher dependence on natural resources. Hadza hunter-gatherers in Tanzania have exhibited high biodiversity and seasonal patterns in their gut microbiome composition at the family level, where some taxa disappear in one season and reappear later. Such seasonal changes have been profiled, but the nucleotide changes remain unexplored at the genome level. Thus, it is still elusive how microbial communities change with seasonal changes at the genome level.

Results
In this study, we performed a strain-level single nucleotide polymorphism (SNP) analysis on 40 Hadza fecal metagenome samples spanning three seasons. With more SNP presented in the wet season, eight prevalent species have significant SNP enrichment with the increasing number of SNP calling by VarScan2, among which only three species have relatively high abundances. Eighty-three genes have the most SNP distributions between the wet season and dry season. Many of these genes are derived from Ruminococcus obeum, and mainly participated in metabolic pathways including carbon metabolism, pyruvate metabolism, and glycolysis.

Conclusions
Eight prevalent species have significant SNP enrichments with the increasing number of SNP, among which only Eubacterium biforme, Eubacterium hallii and Ruminococcus obeum have relatively high species abundances. Many genes in the microbiomes also presented characteristic SNP distributions between the wet season and the dry season. This implies that the seasonal changes might indirectly impact the mutation patterns for specific species and functions for the gut microbiome of the population that lives in traditional lifestyles through changing the diet in wet and dry seasons, indicating the role of these variants in these species’ adaptation to the changing environment and diets.
Inferring time series chromatin states for promoter-enhancer pairs based on Hi-C data
Authors: Miko Henriette , Qiu Yunjiang , Gaertner Bjoern , Sander Maike , Ohler Uwe 
Published: January 2021

Abstract
Background
Co-localized combinations of histone modifications (“chromatin states”) have been shown to correlate with promoter and enhancer activity. Changes in chromatin states over multiple time points (“chromatin state trajectories”) have previously been analyzed at promoter and enhancers separately. With the advent of time series Hi-C data it is now possible to connect promoters and enhancers and to analyze chromatin state trajectories at promoter-enhancer pairs.

Results
We present TimelessFlex, a framework for investigating chromatin state trajectories at promoters and enhancers and at promoter-enhancer pairs based on Hi-C information. TimelessFlex extends our previous approach Timeless, a Bayesian network for clustering multiple histone modification data sets at promoter and enhancer feature regions. We utilize time series ATAC-seq data measuring open chromatin to define promoters and enhancer candidates. We developed an expectation-maximization algorithm to assign promoters and enhancers to each other based on Hi-C interactions and jointly cluster their feature regions into paired chromatin state trajectories.
We find jointly clustered promoter-enhancer pairs showing the same activation patterns on both sides but with a stronger trend at the enhancer side. While the promoter side remains accessible across the time series, the enhancer side becomes dynamically more open towards the gene activation time point. Promoter cluster patterns show strong correlations with gene expression signals, whereas Hi-C signals get only slightly stronger towards activation.
The code of the framework is available at https://github.com/henriettemiko/TimelessFlex.

Conclusions
TimelessFlex clusters time series histone modifications at promoter-enhancer pairs based on Hi-C and it can identify distinct chromatin states at promoter and enhancer feature regions and their changes over time.
Genome-wide characterization of the WAK gene family and expression analysis under plant hormone treatment in cotton
Authors: Dou Lingling , Li Zhifang , Shen Qian , Shi Huiran , Li Huaizhu , Wang Wenbo , Zou Changsong , Shang Haihong , Li Hongbin , Xiao Guanghui 
Published: January 2021

Abstract
Background
Wall-associated kinases (WAK), one of the receptor-like kinases (RLK), function directly in the connection and communication between the plant cell wall and the cytoplasm. WAK genes are highly conserved and have been identified in plants, such as rice, but there is little research on the WAK gene family in cotton.

Results
In the present study, we identified 29 GhWAK genes in Gossypium hirsutum. Phylogenetic analysis showed that cotton WAK proteins can be divided into five clades. The results of synteny and Ka/Ks analysis showed that the GhWAK genes mainly originated from whole genome duplication (WGD) and were then mainly under purifying selection. Transcriptome data and real-time PCR showed that 97% of GhWAK genes highly expressed in cotton fibers and ovules. β-glucuronidase (GUS) staining assays showed that GhWAK5 and GhWAK16 expressed in Arabidopsis leaf trichomes. Fourteen GhWAK genes were found to possess putative gibberellin (GA) response elements in the promoter regions, 13 of which were significantly induced by GA treatment. Ten GhWAK genes contained auxin (IAA) response elements and the expression level of nine GhWAKs significantly increased under auxin treatment.

Conclusions
We provide a preliminary analysis of the WAK gene family in G. hirsutum, which sheds light on the potantial roles of GhWAK genes in cotton fiber cell development. Our data also provides a useful resource for future studies on the functional roles of GhWAK genes.
Genome-wide identification of ubiquitin proteasome subunits as superior reference genes for transcript normalization during receptacle development in strawberry cultivars
Authors: Chen Jianqing , Zhou Jinyu , Hong Yanhong , Li Zekun , Cheng Xiangyu , Zheng Aiying , Zhang Yilin , Song Juanjuan , Xie Guifeng , Chen Changmei , Yuan Meng , Wang Tengyun , Chen Qingxi 
Published: January 2021

Abstract
Background
Gene transcripts that show invariant abundance during development are ideal as reference genes (RGs) for accurate gene expression analyses, such as RNA blot analysis and reverse transcription–quantitative real time PCR (RT-qPCR) analyses. In a genome-wide analysis, we selected three “Commonly used” housekeeping genes (HKGs), fifteen “Traditional” HKGs, and nine novel genes as candidate RGs based on 80 publicly available transcriptome libraries that include data for receptacle development in eight strawberry cultivars.

Results
The results of the multifaceted assessment consistently revealed that expression of the novel RGs showed greater stability compared with that of the “Commonly used” and “Traditional” HKGs in transcriptome and RT-qPCR analyses. Notably, the majority of stably expressed genes were associated with the ubiquitin proteasome system. Among these, two 26 s proteasome subunits, RPT6A and RPN5A, showed superior expression stability and abundance, and are recommended as the optimal RGs combination for normalization of gene expression during strawberry receptacle development.

Conclusion
These findings provide additional useful and reliable RGs as resources for the accurate study of gene expression during receptacle development in strawberry cultivars.
Clinical observations of bone marrow transfusion for promoting bone marrow reconstruction after chemotherapy for AIDS-related lymphoma
Authors: Liu Yixuan , Xie Suhong , Li Lei , Si Yanhui , Zhang Weiwei , Liu Xin , Guo Lin , Liu Baochi , Lu Renquan 
Published: January 2021

Abstract
Background
This study investigates the effect of autologous bone marrow transfusion (BMT) on the reconstruction of both bone marrow and the immune system in patients with AIDS-related lymphoma (ARL).

Methods
A total of 32 patients with ARL participated in this study. Among them, 16 participants were treated with conventional surgery and chemotherapy (control group) and the remaining 16 patients were treated with chemotherapy followed by autologous bone marrow transfusion via a mesenteric vein (8 patients, ABM-MVI group) or a peripheral vein (8 patients, ABM-PI group). Subsequently, peripheral blood and lymphocyte data subsets were detected and documented in all patients.

Results
Before chemotherapy, no significant difference in indicators was observed between three groups of ARL patients. Unexpectedly, 2 weeks after the end of 6 courses of chemotherapy, the ABM-MVI group, and the ABM-PI group yielded an increased level of CD8+T lymphocytes, white blood cells (WBC), and platelet (PLT) in peripheral blood in comparison to the control group. Notably, the number of CD4+T lymphocytes in the ABM-PI group was significantly higher than that in the other two groups. Additionally, no significant difference in haemoglobin levels was observed before and after chemotherapy in both the ABM-MVI and ABM-PI groups, while haemoglobin levels in the control group decreased significantly following chemotherapy.

Conclusions
Autologous bone marrow transfusion after chemotherapy can promote the reconstruction of both bone marrow and the immune system. There was no significant difference in bone marrow recovery and reconstruction between the mesenteric vein transfusion group and the peripheral vein transfusion group.