bluuebunny/crossref_metadata_2025_split huggingface dataset:
Osseous Healing With Nonrigid Suture Fixation in the Arthroscopic Latarjet Procedure
Authors: Weick Jack W. , Kalia Vivek , Pacheco Emily , Jacobson Jon A. , Freehill Michael T. 
Published: November 2020

Background: The Latarjet procedure is a popular means to surgically address anterior glenohumeral joint instability. Although the Latarjet procedure is becoming increasingly common, challenges persist and include postoperative complications secondary to use of the conventional 2 bicortical fixation screws. Recently, a novel surgical technique using a guided surgical approach for graft positioning with nonrigid fixation via a suture suspensory system has been described. Purpose: To evaluate healing rates and stability of the grafts in patients who underwent this new Latarjet technique. Study Design: Case series; Level of evidence, 4. Methods: We retrospectively gathered anonymized computed tomography (CT) data sets from a total of 107 patients who underwent nonrigid suture fixation using a cortical button fixation for anterior glenohumeral instability. Of the 107 patients, 45 had CT scans performed at 2 different time periods. The CT scans of each patient were compared by 2 fellowship-trained musculoskeletal radiologists. Data recorded included age, sex, date of scan, initial graft position on the glenoid, presence and degree of graft migration relative to the equator on follow-up scan, and percentage of osseous healing (as assessed by osseous bridging) on the follow-up scan. Descriptive statistics were calculated to evaluate the average migration and average percentage of healing at both time points. Results: Our population (n = 45) consisted of 38 men (84.4%) and 7 women (15.6%). The mean age was 27.1 ± 1.1 years. The mean time between initial CT scan (2 weeks postoperatively) and follow-up CT scan was 26 ± 2 weeks. On follow-up scan, reviewer 1 found 75.6% of patients had greater than 75% healing, and reviewer 2 found 70.2% of patients had greater than 75% healing. The center of the graft was measured at or below the equator on follow-up examination in 43 of 45 (95.6%) patients by reviewer 1 and 44 of 45 (97.8%) patients by reviewer 2. Conclusion: Based on these findings, nonrigid suture fixation using a cortical button device offers an effective alternative to traditional screw fixation for the Latarjet procedure with a high level of osseous healing and minimal graft migration.
Hematoxylin binds to mutant calreticulin and disrupts its abnormal interaction with thrombopoietin receptor
Authors: Jia Ruochen , Balligand Thomas , Atamanyuk Vasyl , Nivarthi Harini , Xu Erica , Kutzner Leon , Weinzierl Jakob , Nedelec Audrey , Kubicek Stefan , Lesyk Roman , Zagrijtschuk Oleh , Constantinescu Stefan N. , Kralovics Robert 
Published: November 2020

Abstract
Somatic mutations of calreticulin (CALR) have been identified as a main disease driver of myeloproliferative neoplasms, suggesting that development of drugs targeting mutant CALR is of great significance. Site-directed mutagenesis in the N-glycan binding domain (GBD) abolishes the ability of mutant CALR to oncogenically activate the thrombopoietin receptor (MPL). We therefore hypothesized that a small molecule targeting the GBD might inhibit the oncogenicity of the mutant CALR. Using an in silico molecular docking study, we identified candidate binders to the GBD of CALR. Further experimental validation of the hits identified a group of catechols inducing a selective growth inhibitory effect on cells that depend on oncogenic CALR for survival and proliferation. Apoptosis-inducing effects by the compound were significantly higher in the CALR-mutated cells than in CALR wild-type cells. Additionally, knockout or C-terminal truncation of CALR eliminated drug hypersensitivity in CALR-mutated cells. We experimentally confirmed the direct binding of the selected compound to CALR, disruption of the mutant CALR-MPL interaction, inhibition of the JAK2-STAT5 pathway, and reduction at the intracellular level of mutant CALR upon drug treatment. Our data indicate that small molecules targeting the GBD of CALR can selectively kill CALR-mutated cells by disrupting the CALR-MPL interaction and inhibiting oncogenic signaling.
How should we use convalescent plasma therapies for the management of COVID-19?
Authors: Wood Erica M. , Estcourt Lise J. , McQuilten Zoe K. 
Published: November 2020

AbstractConvalescent plasma (CP) from blood donors with antibodies to severe acute respiratory syndrome coronavirus 2 may benefit patients with COVID-19 by providing immediate passive immunity via transfusion or by being used to manufacture hyperimmune immunoglobulin preparations. Optimal product characteristics (including neutralizing antibody titers), transfusion volume, and administration timing remain to be determined. Preliminary COVID-19 CP safety data are encouraging, but establishing the clinical efficacy of CP requires an ongoing international collaborative effort. Preliminary results from large, high-quality randomized trials have recently started to be reported.
LC-N2G: a local consistency approach for nutrigenomics data analysis
Authors: Xu Xiangnan , Solon-Biet Samantha M. , Senior Alistair , Raubenheimer David , Simpson Stephen J. , Fontana Luigi , Mueller Samuel , Yang Jean Y. H. 
Published: November 2020

Abstract
Background
Nutrigenomics aims at understanding the interaction between nutrition and gene information. Due to the complex interactions of nutrients and genes, their relationship exhibits non-linearity. One of the most effective and efficient methods to explore their relationship is the nutritional geometry framework which fits a response surface for the gene expression over two prespecified nutrition variables. However, when the number of nutrients involved is large, it is challenging to find combinations of informative nutrients with respect to a certain gene and to test whether the relationship is stronger than chance. Methods for identifying informative combinations are essential to understanding the relationship between nutrients and genes.

Results
We introduce Local Consistency Nutrition to Graphics (LC-N2G), a novel approach for ranking and identifying combinations of nutrients with gene expression. In LC-N2G, we first propose a model-free quantity called Local Consistency statistic to measure whether there is non-random relationship between combinations of nutrients and gene expression measurements based on (1) the similarity between samples in the nutrient space and (2) their difference in gene expression. Then combinations with small LC are selected and a permutation test is performed to evaluate their significance. Finally, the response surfaces are generated for the subset of significant relationships. Evaluation on simulated data and real data shows the LC-N2G can accurately find combinations that are correlated with gene expression.

Conclusion
The LC-N2G is practically powerful for identifying the informative nutrition variables correlated with gene expression. Therefore, LC-N2G is important in the area of nutrigenomics for understanding the relationship between nutrition and gene expression information.
The MOBSTER R package for tumour subclonal deconvolution from bulk DNA whole-genome sequencing data
Authors: Caravagna Giulio , Sanguinetti Guido , Graham Trevor A. , Sottoriva Andrea 
Published: November 2020

Abstract
Background
The large-scale availability of whole-genome sequencing profiles from bulk DNA sequencing of cancer tissues is fueling the application of evolutionary theory to cancer. From a bulk biopsy, subclonal deconvolution methods are used to determine the composition of cancer subpopulations in the biopsy sample, a fundamental step to determine clonal expansions and their evolutionary trajectories.

Results
In a recent work we have developed a new model-based approach to carry out subclonal deconvolution from the site frequency spectrum of somatic mutations. This new method integrates, for the first time, an explicit model for neutral evolutionary forces that participate in clonal expansions; in that work we have also shown that our method improves largely over competing data-driven methods. In this Software paper we present mobster, an open source R package built around our new deconvolution approach, which provides several functions to plot data and fit models, assess their confidence and compute further evolutionary analyses that relate to subclonal deconvolution.

Conclusions
We present the mobster package for tumour subclonal deconvolution from bulk sequencing, the first approach to integrate Machine Learning and Population Genetics which can explicitly model co-existing neutral and positive selection in cancer. We showcase the analysis of two datasets, one simulated and one from a breast cancer patient, and overview all package functionalities.
Depletion of SNRNP200 inhibits the osteo−/dentinogenic differentiation and cell proliferation potential of stem cells from the apical papilla
Authors: Su Xiaomin , Yang Haoqing , Shi Ruitang , Zhang Chen , Liu Huina , Fan Zhipeng , Zhang Jianpeng 
Published: November 2020

Abstract
Background
Tissue regeneration mediated by mesenchymal stem cells (MSCs) is deemed a desirable way to repair teeth and craniomaxillofacial tissue defects. Nevertheless, the molecular mechanisms about cell proliferation and committed differentiation of MSCs remain obscure. Previous researches have proved that lysine demethylase 2A (KDM2A) performed significant function in the regulation of MSC proliferation and differentiation. SNRNP200, as a co-binding factor of KDM2A, its potential effect in regulating MSCs’ function is still unclear. Therefore, stem cells from the apical papilla (SCAPs) were used to investigate the function of SNRNP200 in this research.

Methods
The alkaline phosphatase (ALP) activity assay, Alizarin Red staining, and osteogenesis-related gene expressions were used to examine osteo−/dentinogenic differentiation potential. Carboxyfluorescein diacetate, succinimidyl ester (CFSE) and cell cycle analysis were applied to detect the cell proliferation. Western blot analysis was used to evaluate the expressions of cell cycle-related proteins.

Results
Depletion of SNRNP200 caused an obvious decrease of ALP activity, mineralization formation and the expressions of osteo−/dentinogenic genes including RUNX2, DSPP, DMP1 and BSP. Meanwhile, CFSE and cell cycle assays revealed that knock-down of SNRNP200 inhibited the cell proliferation and blocked cell cycle at the G2/M and S phase in SCAPs. In addition, it was found that depletion of SNRNP200 up-regulated p21 and p53, and down-regulated the CDK1, CyclinB, CyclinE and CDK2.

Conclusions
Depletion of SNRNP200 repressed osteo−/dentinogenic differentiation potentials and restrained cell proliferation through blocking cell cycle progression at the G2/M and S phase, further revealing that SNRNP200 has crucial effects on preserving the proliferation and differentiation potentials of dental tissue-derived MSCs.
FishDB: an integrated functional genomics database for fishes
Authors: Yang Liandong , Xu Zetan , Zeng Honghui , Sun Ning , Wu Baosheng , Wang Cheng , Bo Jing , Li Lin , Dong Yang , He Shunping 
Published: November 2020

Abstract
Background
Hundreds of genomes and transcriptomes of fish species have been sequenced in recent years. However, fish scholarship currently lacks a comprehensive, integrated, and up-to-date collection of fish genomic data.

Results
Here we present FishDB, the first database for fish multi-level omics data, available online at http://fishdb.ihb.ac.cn. The database contains 233 fish genomes, 201 fish transcriptomes, 5841 fish mitochondrial genomes, 88 fish gene sets, 16,239 miRNAs of 65 fishes, 1,330,692 piRNAs and 4852 lncRNAs of Danio rerio, 59,040 Mb untranslated regions (UTR) of 230 fishes, and 31,918 Mb coding sequences (CDS) of 230 fishes. Among these, we newly generated a total of 11 fish genomes and 53 fish transcriptomes.

Conclusions
This release contains over 410,721.67 Mb sequences and provides search functionality, a BLAST server, JBrowse, and PrimerServer modules.
Current knowledge and perspectives of potential impacts of Salmonella enterica on the profile of the gut microbiota
Authors: Aljahdali Nesreen H. , Sanad Yasser M. , Han Jing , Foley Steven L. 
Published: November 2020

AbstractIn the past decade, the initial studies of the gut microbiota started focusing on the correlation of the composition of the gut microbiota and the health or diseases of the host, and there are extensive literature reviews pertaining to this theme. However, little is known about the association between the microbiota, the host, and pathogenic bacteria, such asSalmonella enterica, which is among the most important foodborne pathogens and identified as the source of multiple outbreaks linked to contaminated foods causing salmonellosis. Secretion systems, flagella, fimbriae, endotoxins, and exotoxins are factors that play the most important roles in the successful infection of the host cell bySalmonella. Infections withS. enterica, which is a threat to human health, can alter the genomic, taxonomic, and functional traits of the gut microbiota. The purpose of this review is to outline the state of knowledge on the impacts ofS. entericaon the intestinal microbiota and highlight the need to identify the gut bacteria that could contribute to salmonellosis.
A longitudinal study on morpho-genetic diversity of pathogenic Rhizoctonia solani from sugar beet and dry beans of western Nebraska
Authors: Das Saurav , Plyler-Harveson T. , Santra Dipak K. , Maharjan Bijesh , Nielson Kathy A. , Harveson Robert M. 
Published: November 2020

Abstract
Background
Root and stem rot caused by Rhizoctonia solani is a serious fungal disease of sugar beet and dry bean production in Nebraska. Rhizoctonia root rot and crown rot in sugar beet and dry bean have reduced the yield significantly and has also created problems in storage. The objective of this study was to analyze morpho-genetic diversity of 38 Rhizoctonia solani isolates from sugar beet and dry bean fields in western Nebraska collected over 10 years. Morphological features and ISSR-based DNA markers were used to study the morphogenetic diversity.

Results
Fungal colonies were morphologically diverse in shapes, aerial hyphae formation, colony, and sclerotia color. Marker analysis using 19 polymorphic ISSR markers showed polymorphic bands ranged from 15 to 28 with molecular weight of 100 bp to 3 kb. Polymorphic loci ranged from 43.26–92.88%. Nei genetic distance within the population ranged from 0.03–0.09 and Shannon diversity index varied from 0.24–0.28. AMOVA analysis based on ΦPT values showed 87% variation within and 13% among the population with statistical significance (p < 0.05). Majority of the isolates from sugar beet showed nearby association within the population. A significant number of isolates showed similarity with isolates of both the crops suggesting their broad pathogenicity. Isolates were grouped into three different clusters in UPGMA based cluster analysis using marker information. Interestingly, there was no geographical correlation among the isolates. Principal component analysis showed randomized distribution of isolates from the same geographical origin. Identities of the isolates were confirmed by both ITS-rDNA sequences and pathogenicity tests.

Conclusion
Identification and categorization of the pathogen will be helpful in designing integrated disease management guidelines for sugar beet and dry beans of mid western America.
The relation of meiotic behaviour to hybridity, polyploidy and apomixis in the Ranunculus auricomus complex (Ranunculaceae)
Authors: Barke Birthe H. , Karbstein Kevin , Daubert Mareike , Hörandl Elvira 
Published: November 2020

AbstractBackgroundHybridization and polyploidization are powerful evolutionary factors that are associated with manifold developmental changes in plants such as irregular progression of meiosis and sporogenesis. The emergence of apomixis, which is asexual reproduction via seeds, is supposed to be connected to these factors and was often regarded as an escape from hybrid sterility. However, the functional trigger of apomixis is still unclear. Recently formed di- and polyploidRanunculushybrids, as well as their parental species were analysed for their modes of mega- and microsporogenesis by microscopy. Chromosomal configurations during male meiosis were screened for abnormalities. Meiotic and developmental abnormalities were documented qualitatively and collected quantitatively for statistical evaluations.ResultsAllopolyploids showed significantly higher frequencies of erroneous microsporogenesis than homoploid hybrid plants. Among diploids, F2hybrids had significantly more disturbed meiosis than F1hybrids and parental plants. Chromosomal aberrations included laggard chromosomes, chromatin bridges and disoriented spindle activities. Failure of megasporogenesis appeared to be much more frequent in than of microsporogenesis is correlated to apomixis onset.ConclusionsResults suggest diverging selective pressures on female and male sporogenesis, with only minor effects of hybridity on microsporogenesis, but fatal effects on the course of megasporogenesis. Hence, pollen development continues without major alterations, while selection will favour apomixis as alternative to the female meiotic pathway. Relation of investigated errors of megasporogenesis with the observed occurrence of apospory inRanunculushybrids identifies disturbed female meiosis as potential elicitor of apomixis in order to rescue these plants from hybrid sterility. Male meiotic disturbance appears to be stronger in neopolyploids than in homoploid hybrids, while disturbances of megasporogenesis were not ploidy-dependent.
Genome-wide transcriptional changes triggered by water deficit on a drought-tolerant common bean cultivar
Authors: Gregorio Jorge Josefat , Villalobos-López Miguel Angel , Chavarría-Alvarado Karen Lizeth , Ríos-Meléndez Selma , López-Meyer Melina , Arroyo-Becerra Analilia 
Published: November 2020

Abstract
Background
Common bean (Phaseolus vulgaris L.) is a relevant crop cultivated over the world, largely in water insufficiency vulnerable areas. Since drought is the main environmental factor restraining worldwide crop production, efforts have been invested to amend drought tolerance in commercial common bean varieties. However, scarce molecular data are available for those cultivars of P. vulgaris with drought tolerance attributes.

Results
As a first approach, Pinto Saltillo (PS), Azufrado Higuera (AH), and Negro Jamapa Plus (NP) were assessed phenotypically and physiologically to determine the outcome in response to drought on these common bean cultivars. Based on this, a Next-generation sequencing approach was applied to PS, which was the most drought-tolerant cultivar to determine the molecular changes at the transcriptional level. The RNA-Seq analysis revealed that numerous PS genes are dynamically modulated by drought. In brief, 1005 differentially expressed genes (DEGs) were identified, from which 645 genes were up-regulated by drought stress, whereas 360 genes were down-regulated. Further analysis showed that the enriched categories of the up-regulated genes in response to drought fit to processes related to carbohydrate metabolism (polysaccharide metabolic processes), particularly genes encoding proteins located within the cell periphery (cell wall dynamics). In the case of down-regulated genes, heat shock-responsive genes, mainly associated with protein folding, chloroplast, and oxidation-reduction processes were identified.

Conclusions
Our findings suggest that secondary cell wall (SCW) properties contribute to P. vulgaris L. drought tolerance through alleviation or mitigation of drought-induced osmotic disturbances, making cultivars more adaptable to such stress. Altogether, the knowledge derived from this study is significant for a forthcoming understanding of the molecular mechanisms involved in drought tolerance on common bean, especially for drought-tolerant cultivars such as PS.
The hunt for efficient, incomplete designs for stepped wedge trials with continuous recruitment and continuous outcome measures
Authors: Hooper Richard , Kasza Jessica , Forbes Andrew 
Published: November 2020

AbstractBackgroundWe consider the design of stepped wedge trials with continuous recruitment and continuous outcome measures. Suppose we recruit from a fixed number of clusters where eligible participants present continuously, and suppose we have fine control over when each cluster crosses to the intervention. Suppose also that we want to minimise the number of participants, leading us to consider “incomplete” designs (i.e. without full recruitment). How can we schedule recruitment and cross-over at different clusters to recruit efficiently while achieving good precision?MethodsThe large number of possible designs can make exhaustive searches impractical. Instead we consider an algorithm using iterative improvements to hunt for an efficient design. At each iteration (starting from a complete design) a single participant – the one with the smallest impact on precision – is removed, and small changes preserving total sample size are made until no further improvement in precision can be found.ResultsStriking patterns emerge. Solutions typically focus recruitment and cross-over on the leading diagonal of the cluster-by-time diagram, but in some scenarios clusters form distinct phases resembling before-and-after designs.ConclusionsThere is much to be learned about optimal design for incomplete stepped wedge trials. Algorithmic searches could offer a practical approach to trial design in complex settings generally.
Authors response to correspondence regarding paper entitled Syphilitic hepatitis: a case report and review of the literature
Authors: Huang Jiaofeng , Wan Bo , Wang Mingfang , Zhu Yueyong , Lin Su 
Published: November 2020

AbstractIn the correspondence from Abdurrahman et al., they raised three main concerns and critiques of our recently published article entitled “Syphilitic hepatitis: a case report and review of the literature”. First question pertains to the timing of dermatology opinion, second regarding the history of sexual exposure, and lastly regarding the treatment duration of syphilitic hepatitis. We thank the authors for their constructive comments and would like to answer these questions in detail.
Infected aortic aneurysm caused by Helicobacter cinaedi: case series and systematic review of the literature
Authors: Matsuo Takahiro , Mori Nobuyoshi , Mizuno Atsushi , Sakurai Aki , Kawai Fujimi , Starkey Jay , Ohkushi Daisuke , Abe Kohei , Yamasaki Manabu , Ito Joji , Yoshino Kunihiko , Mikami Yumiko , Uehara Yuki , Furukawa Keiichi 
Published: November 2020

Abstract
Background
Helicobacter cinaedi is rarely identified as a cause of infected aneurysms; however, the number of reported cases has been increasing over several decades, especially in Japan. We report three cases of aortic aneurysm infected by H. cinaedi that were successfully treated using meropenem plus surgical stent graft replacement or intravascular stenting. Furthermore, we performed a systematic review of the literature regarding aortic aneurysm infected by H. cinaedi.

Case presentation
We present three rare cases of infected aneurysm caused by H. cinaedi in adults. Blood and tissue cultures and 16S rRNA gene sequencing were used for diagnosis. Two patients underwent urgent surgical stent graft replacement, and the other patient underwent intravascular stenting. All three cases were treated successfully with intravenous meropenem for 4 to 6 weeks.

Conclusions
These cases suggest that although aneurysms infected by H. cinaedi are rare, clinicians should be aware of H. cinaedi as a potential causative pathogen, even in immunocompetent patients. Prolonged incubation periods for blood cultures are necessary for the accurate detection of H. cinaedi.