bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effectiveness of manipulation of fingers with Dupuytren's contracture 7 days after collagenase clostridial histolyticum injection
Authors: Reynolds Bethany , Tobin Vicky , Smith Julian A , Rozen Warren M , Hunter-Smith David J. 
Published: December 2019

Timing of manipulation of digits after collagenase injection for Dupuytren’s disease varies and often takes place within the first few days post-injection. We prospectively investigated the effectiveness of performing manipulation under local anaesthesia 7 days after injection in 100 patients. Demographic data, passive extension deficit, and patient-reported outcome measures were recorded before collagenase injection. Four to 7 weeks after manipulation, passive extension deficit and patient-reported outcome measures improved significantly without the development of any tendon ruptures. Clinical success was achieved in 41% and clinical improvement in 76% of the patients. Adverse events were reported by 85%. The outcomes were comparable with studies with early manipulation, and demonstrate a safe and effective variation to current protocols. We conclude that delaying manipulation to 7 days after collagenase injection is safe and efficient, which allows for flexibility in clinical appointments without negatively affecting outcome. Level of evidence: III
Prevalence of feline immunodeficiency virus and feline leukaemia virus in domestic cats in Hungary
Authors: Szilasi Anna , Dénes Lilla , Krikó Eszter , Heenemann Kristin , Ertl Reinhard , Mándoki Míra , Vahlenkamp Thomas W , Balka Gyula 
Published: December 2019

Objectives Feline immunodeficiency virus (FIV) and feline leukaemia virus (FeLV) are retroviruses affecting cats worldwide. The objectives of the study were to estimate the prevalence of these retroviruses in domestic cats in Hungary and to characterise the phylogenetic relationships of FIV strains. Methods A total of 335 anticoagulated whole-blood samples obtained from both a healthy and ill cat population were examined for the presence of FIV and FeLV with two methods: ELISA and PCR. Statistical analysis was carried out to analyse the data obtained. Sequencing and phylogenetic analysis of partial polymerase ( pol) gene sequences was performed to describe circulating FIV subtypes. Results Statistical analysis showed 11.8% and 9.9% true prevalence of FeLV and FIV, respectively, with ELISA. The apparent prevalence calculated from the PCR results were 17.3% for FeLV and 13.1% for FIV. Phylogenetic analysis of partial pol gene sequences obtained from 22 FIV strains showed that all observed Hungarian strains belonged to FIV subtype B. The strains were grouped into several monophyletic subgroups reflecting the geographic locations of the origin of the samples. The overall mean genetic similarity between the analysed strains was 98.2%. Conclusions and relevance We report the first thorough overview of the prevalence of FeLV and FIV in Hungary, which is relatively high, and give insight into the genetic diversity of Hungarian strains of FIV.
Israeli Jews from Muslim Countries: Immigrant Associations and Civic Leverage
Authors: Kabalo Paula 
Published: December 2019

This article sheds light on the salient and far-reaching pattern of association-forming among Jewish immigrants from Muslim countries in Israel during the 1950s and 1960s. They were formally established associations that operated by means of representatives and spokespersons and strove to mediate between the population group that they represented and the state authorities that dealt with immigration and its integration. Interestingly, although few of the members or leaders of these entities have lived under democratic regimes, they established organizations that operated on the basis of democratic principles: election of representatives, holding members’ assemblies, and freedom of expression. They articulated their positions publicly and openly and were not deterred from criticizing policymakers, even those in the highest of echelons. The extent of the phenomenon challenges the conventional image in research on immigration to Israel from the Islamic countries—that of a passive, dependent population that has no voice of its own. Additionally, it suggests that the volunteer organizations’ pressure and contacts with the authorities paid off and influenced policymakers’ agendas—leading to an additional assumption that immigrant absorption policy was crafted via exchange and interaction and not solely in a “top-down” manner.
Association of Race/Ethnicity, Stage, and Survival in Oral Cavity Squamous Cell Carcinoma: A SEER Study
Authors: Yu Alison J. , Choi Janet S. , Swanson Mark S. , Kokot Niels C. , Brown Tamara N. , Yan Guofen , Sinha Uttam K. 
Published: December 2019

ObjectiveSurvival differences in oral cancer between black and white patients have been reported, but the contributing factors, especially the role of stage, are incompletely understood. Furthermore, the outcomes for Hispanic and Asian patients have been scarcely examined.Study DesignRetrospective, population‐based national study.SettingSurveillance, Epidemiology, and End Results 18 Custom database (January 1, 2010, to December 31, 2014).Subjects and MethodsIn total, 7630 patients with primary squamous cell carcinoma in the oral cavity were classified as non‐Hispanic white (white), non‐Hispanic black (black), Hispanic, or Asian. Cox regression was used to obtain unadjusted and adjusted hazard ratios (HRs) of 5‐year mortality for race/ethnicity with sequential adjustments for stage and other covariates. Logistic regression was used to examine the relationship between race/ethnicity and stage with adjusted odds ratios (aORs).ResultsThe cohort consisted of 75.0% whites, 7.6% blacks, 9.1% Hispanics, and 8.3% Asians. Compared to whites, the unadjusted HR for all‐cause mortality for blacks was 1.68 (P <. 001), which attenuated to 1.15 (P =. 039) after adjusting for stage and became insignificant after including insurance. The unadjusted HRs for all‐cause mortality were not significant for Hispanics and Asians vs whites. Compared to whites, blacks and Hispanics were more likely to present at later stages (aORs of 2.63 and 1.42, P <. 001, respectively).ConclusionThe greater mortality for blacks vs whites was largely attributable to the higher prevalence of later stages at presentation and being uninsured among blacks. There was no statistically significant difference in mortality for Hispanics vs whites or Asians vs whites.
PTCy ameliorates GVHD by restoring regulatory and effector T-cell homeostasis in recipients with PD-1 blockade
Authors: Ikegawa Shuntaro , Meguri Yusuke , Kondo Takumi , Sugiura Hiroyuki , Sando Yasuhisa , Nakamura Makoto , Iwamoto Miki , Maeda Yoshinobu , Matsuoka Ken-ichi 
Published: December 2019

Key PointsPD-1 blockade exacerbated GVHD by altering the homeostasis of Tregs and effector T cells after HSCT. PTCy ameliorated GVHD after PD-1 blockade by restoring the homeostatic balance of T-cell subsets.
Impact of last lenalidomide dose, duration, and IMiD-free interval in patients with myeloma treated with pomalidomide/dexamethasone
Authors: Kastritis Efstathios , Roussou Maria , Gavriatopoulou Maria , Kanellias Nikolaos , Migkou Magdalini , Eleutherakis-Papaiakovou Evangelos , Ziogas Dimitrios C. , Fotiou Despina , Ntanasis-Stathopoulos Ioannis , Dialoupi Ioanna , Giannouli Stavroula , Tsirigotis Panagiotis , Delimpasi Sossana , Mparmparousi Despina , Spyropoulou-Vlachou Mairylin , Xirokosta Aikaterini , Terpos Evangelos , Dimopoulos Meletios A. 
Published: December 2019

Key Points
There was no significant difference in response rates, PFS, or OS among patients that developed resistance to different lenalidomide doses. Longer duration of prior lenalidomide and a longer lenalidomide-free interval are associated with better outcomes with pomalidomide.
A novel immature natural killer cell subpopulation predicts relapse after cord blood transplantation
Authors: Li Li , Chen Han , Marin David , Xi Yuanxin , Miao Qi , Lv Jiangxing , Banerjee Pinaki Prosad , Shaim Hila , Daher May , Basar Rafet , Imahashi Nobuhiko , Jimenez Juan , Hu Bingqian , Mehta Rohtesh S. , Kerbauy Lucila Nassif , Kaplan Mecit , Mendt Mayela , Ozcan Gonca , Gokdemir Elif , Hernandez Sanabria Mayra , Li Ye , Chen Ken , Wang Jing , Muniz-Feliciano Luis , Zhao Wei-Li , Champlin Richard E. , Shpall Elizabeth J. , Rezvani Katayoun 
Published: December 2019

Key Points
Cytomegalovirus reactivation and interleukin 15 are major contributors to NK cell repertoire diversity and maturation after CBT. An immature NK cell subset characterized by low diversity index and poor effector function was highly predictive of relapse after CBT.
Vedolizumab for prevention of graft-versus-host disease after allogeneic hematopoietic stem cell transplantation
Authors: Chen Yi-Bin , Shah Nirav N. , Renteria Anne S. , Cutler Corey , Jansson Johan , Akbari Mona , Chen Chunlin , Quadri Syed , Parfionovas Andrejus , Devine Steven M. 
Published: December 2019

Key PointsIn adults undergoing allo-HSCT, vedolizumab IV 300 mg was well tolerated and had a low incidence of overall and lower-intestinal aGVHD. These phase 1b data support further evaluation of vedolizumab for the prevention of aGVHD in adults undergoing allo-HSCT.
Port selection based on customer questionnaire: a case study of German port selection
Authors: Lin Yisong , Wang Xuefeng 
Published: December 2019

AbstractA new research idea regarding port selection concerns customer-oriented, rather than product-oriented, thinking. Through investigation and interviews with over 280 active customers in the global shipping industry, port selection criteria were proposed, and an evaluation scheme based on the responses to a questionnaire survey is compared with a scheme based on the weight calculation of the analytic hierarchy process. The results indicate that due to different priorities between customers and container carriers, port selection is sometimes inconsistent. Against the background of deployment of large-scale vessels, over-capacity has become normal in the industry; this study has great practical value for the whole industry.
Longitudinal linear combination test for gene set analysis
Authors: Khodayari Moez Elham , Hajihosseini Morteza , Andrews Jeffrey L. , Dinu Irina 
Published: December 2019

Abstract
Background
Although microarray studies have greatly contributed to recent genetic advances, lack of replication has been a continuing concern in this area. Complex study designs have the potential to address this concern, though they remain undervalued by investigators due to the lack of proper analysis methods. The primary challenge in the analysis of complex microarray study data is handling the correlation structure within data while also dealing with the combination of large number of genetic measurements and small number of subjects that are ubiquitous even in standard microarray studies. Motivated by the lack of available methods for analysis of repeatedly measured phenotypic or transcriptomic data, herein we develop a longitudinal linear combination test (LLCT).

Results
LLCT is a two-step method to analyze multiple longitudinal phenotypes when there is high dimensionality in response and/or explanatory variables. Alternating between calculating within-subjects and between-subjects variations in two steps, LLCT examines if the maximum possible correlation between a linear combination of the time trends and a linear combination of the predictors given by the gene expressions is statistically significant. A generalization of this method can handle family-based study designs when the subjects are not independent. This method is also applicable to time-course microarray, with the ability to identify gene sets that exhibit significantly different expression patterns over time. Based on the results from a simulation study, LLCT outperformed its alternative: pathway analysis via regression. LLCT was shown to be very powerful in the analysis of large gene sets even when the sample size is small.

Conclusions
This self-contained pathway analysis method is applicable to a wide range of longitudinal genomics, proteomics, metabolomics (OMICS) data, allows adjusting for potentially time-dependent covariates and works well with unbalanced and incomplete data. An important potential application of this method could be time-course linkage of OMICS, an attractive possibility for future genetic researchers.
Availability: R package of LLCT is available at: https://github.com/its-likeli-jeff/LLCT
Vertical and horizontal integration of multi-omics data with miodin
Authors: Ulfenborg Benjamin 
Published: December 2019

Abstract
Background
Studies on multiple modalities of omics data such as transcriptomics, genomics and proteomics are growing in popularity, since they allow us to investigate complex mechanisms across molecular layers. It is widely recognized that integrative omics analysis holds the promise to unlock novel and actionable biological insights into health and disease. Integration of multi-omics data remains challenging, however, and requires combination of several software tools and extensive technical expertise to account for the properties of heterogeneous data.

Results
This paper presents the miodin R package, which provides a streamlined workflow-based syntax for multi-omics data analysis. The package allows users to perform analysis of omics data either across experiments on the same samples (vertical integration), or across studies on the same variables (horizontal integration). Workflows have been designed to promote transparent data analysis and reduce the technical expertise required to perform low-level data import and processing.

Conclusions
The miodin package is implemented in R and is freely available for use and extension under the GPL-3 license. Package source, reference documentation and user manual are available at https://gitlab.com/algoromics/miodin.
Aurora A site specific TACC3 phosphorylation regulates astral microtubule assembly by stabilizing γ-tubulin ring complex
Authors: Rajeev Resmi , Singh Puja , Asmita Ananya , Anand Ushma , Manna Tapas K. 
Published: December 2019

Abstract
Background
Astral microtubules emanating from the mitotic centrosomes play pivotal roles in defining cell division axis and tissue morphogenesis. Previous studies have demonstrated that human transforming acidic coiled-coil 3 (TACC3), the most conserved TACC family protein, regulates formation of astral microtubules at centrosomes in vertebrate cells by affecting γ-tubulin ring complex (γ-TuRC) assembly. However, the molecular mechanisms underlying such function were not completely understood.

Results
Here, we show that Aurora A site-specific phosphorylation in TACC3 regulates formation of astral microtubules by stabilizing γ-TuRC assembly in human cells. Mutation of the most conserved Aurora A targeting site, Ser 558 to alanine (S558A) in TACC3 results in robust loss of astral microtubules and disrupts localization of the γ-tubulin ring complex (γ-TuRC) proteins at the spindle poles. Under similar condition, phospho-mimicking S558D mutation retains astral microtubules and the γ-TuRC proteins in a manner similar to control cells expressed with wild type TACC3. Time-lapse imaging reveals that S558A mutation leads to defects in positioning of the spindle-poles and thereby causes delay in metaphase to anaphase transition. Biochemical results determine that the Ser 558- phosphorylated TACC3 interacts with the γ-TuRC proteins and further, S558A mutation impairs the interaction. We further reveal that the mutation affects the assembly of γ-TuRC from the small complex components.

Conclusions
The results demonstrate that TACC3 phosphorylation stabilizes γ- tubulin ring complex assembly and thereby regulates formation of centrosomal asters. They also implicate a potential role of TACC3 phosphorylation in the functional integrity of centrosomes/spindle poles.
Handwriting in children with Attention Deficient Hyperactive Disorder: role of graphology
Authors: Cohen Rony , Cohen-Kroitoru Batia , Halevy Ayelet , Aharoni Sharon , Aizenberg Irena , Shuper Avinoam 
Published: December 2019

AbstractBackgroundHandwriting difficulties are common in children with attention deficient hyperactive disorder (ADHD). The aim of our study was to find distinctive characteristics of handwriting in children with ADHD by using graphology to analyze physical characteristics and patterns, and to evaluate whether graphological analysis is an effective ADHD diagnostic tool for clinicians.MethodThe cohort included 49 children aged 13–18 years attending a tertiary neurology and epilepsy center in 2016–2017; 22 had a previous DSM-IV/V diagnosis of ADHD. The children were asked to write a 10–12-line story in Hebrew on a blank sheet of paper with a blue pen over a 20-min period. The samples were analyzed by a licensed graphologist blinded to the clinical details of the children against a predetermined handwriting profile of individuals with ADHD. Each ADHD characteristic identified in each sample was accorded 1 point, up to a total of 15 points. Patients with a graphology score of 9–15 were considered to have ADHD.ResultsThere were 21 boys (43%) and 28 girls (57%) in the cohort; 15 boys (71.4%) and 7 girls (25%) had a DSM-IV/V diagnosis of ADHD. The mean graphology score was significantly higher in the children who had a DSM-IV/V diagnosis of ADHD than in the children who did not (9.61 + 3.49 vs. 5.79 + 4.01,p = 0.002, respectfully).Using a score of 9 as the cutoff, in the girls, graphology had a specificity of 80% (95% CI 59.2–92.8) and a of sensitivity 71.4% for predicting ADHD.Corresponding values in the boys were 75.0 and 76.2%.ConclusionThe handwriting of children with ADHD has specific characteristics. Graphology may serve as a clinically useful tool in the diagnosis of ADHD.
RETRACTED ARTICLE: Therapeutic effect of nanoliposomal PCSK9 vaccine in a mouse model of atherosclerosis
Authors: Momtazi-Borojeni Amir Abbas , Jaafari Mahmoud Reza , Badiee Ali , Banach Maciej , Sahebkar Amirhossein 
Published: December 2019

Abstract
Background
Proprotein convertase subtilisin/kexin 9 (PCSK9) is an important regulator of low-density lipoprotein receptor (LDLR) and plasma levels of LDL cholesterol (LDL-C). PCSK9 inhibition is an efficient therapeutic approach for the treatment of dyslipidemia. We tested the therapeutic effect of a PCSK9 vaccine on dyslipidemia and atherosclerosis.

Methods
Lipid film hydration method was used to prepare negatively charged nanoliposomes as a vaccine delivery system. An immunogenic peptide called immunogenic fused PCSK9-tetanus (IFPT) was incorporated on the surface of nanoliposomes using DSPE-PEG-maleimide lipid (L-IFPT) and adsorbed to Alhydrogel® (L-IFPTA+). The prepared vaccine formulation (L-IFPTA+) and empty liposomes (negative control) were inoculated four times with bi-weekly intervals in C57BL/6 mice on the background of a severe atherogenic diet and poloxamer 407 (thrice weekly) injection. Antibody titers were evaluated 2 weeks after each vaccination and at the end of the study in vaccinated mice. Effects of anti-PCSK9 vaccination on plasma concentrations of PCSK9 and its interaction with LDLR were determined using ELISA. To evaluate the inflammatory response, interferon-gamma (IFN-γ)- and interleukin (IL)-10-producing splenic cells were assayed using ELISpot analysis.

Results
L-IFPTA+ vaccine induced a high IgG antibody response against PCSK9 peptide in the vaccinated hypercholesterolemic mice. L-IFPTA+-induced antibodies specifically targeted PCSK9 and decreased its plasma consecration by up to 58.5% (− 164.7 ± 9.6 ng/mL, p = 0.0001) compared with the control. PCSK9-LDLR binding assay showed that generated antibodies could inhibit PCSK9-LDLR interaction. The L-IFPTA+ vaccine reduced total cholesterol, LDL-C, and VLDL-C by up to 44.7%, 51.7%, and 19.2%, respectively, after the fourth vaccination booster, compared with the control group at week 8. Long-term studies of vaccinated hypercholesterolemic mice revealed that the L-IFPTA+ vaccine was able to induce a long-lasting humoral immune response against PCSK9 peptide, which was paralleled by a significant decrease of LDL-C by up to 42% over 16 weeks post-prime immunization compared to control. Splenocytes isolated from the vaccinated group showed increased IL-10-producing cells and decreased IFN-γ-producing cells when compared with control and naive mice, suggesting the immune safety of the vaccine.

Conclusions
L-IFPTA+ vaccine could generate long-lasting, functional, and safe PCSK9-specific antibodies in C57BL/6 mice with severe atherosclerosis, which was accompanied by long-term therapeutic effect against hypercholesterolemia and atherosclerosis.
1,25-(OH)2D3/Vitamin D receptor alleviates systemic lupus erythematosus by downregulating Skp2 and upregulating p27
Authors: Liu Dan , Fang Yu-Xuan , Wu Xia , Tan Wei , Zhou Wei , Zhang Yu , Liu Yan-Qing , Li Guo-Qing 
Published: December 2019

Abstract
Background
Recent evidence has suggested that the 1,25(OH)2D3/Vitamin D receptor (VDR) acts to suppress the immune response associated with systemic lupus erythematosus (SLE), a serious multisystem autoimmune disease. Hence, the aim of the current study was to investigate the mechanism by which 1,25-(OH)2D3/VDR influences SLE through regulating the Skp2/p27 signaling pathway.

Methods
Initially, the levels of 1,25(OH)2D3, VDR, Skp2, and p27 were measured in collected renal tissues and peripheral blood. Meanwhile, the levels of inflammatory factors, biochemical indicators (BUN, Cr, anti-nRNP IgG, anti-dsDNA IgG) and urinary protein levels were assayed in in VDRinsert and VDR-knockout mice in response to 1,25(OH)2D3 supplement. In addition, the distribution of splenic immune cells was observed in these mice.

Results
Among the SLE patients, the levels of 1,25(OH)2D3, VDR and p27 were reduced, while the levels of Skp2 were elevated. In addition, the levels of anti-nRNP IgG and anti-dsDNA IgG were increased, suggesting induction of inflammatory responses. Notably, 1,25(OH)2D3/VDR mice had lower concentrations of BUN and Cr, urinary protein levels, precipitation intensity of the immune complex and complement, as well as the levels of anti-nRNP IgG and anti-dsDNA IgG in SLE mice. Additionally, 1,25(OH)2D3 or VDR reduced the degree of the inflammatory response while acting to regulate the distribution of splenic immune cells.

Conclusion
This study indicated that 1,25-(OH)2D3/VDR facilitated the recovery of SLE by downregulating Skp2 and upregulating p27 expression, suggesting the potential of 1,25-(OH)2D3/VDR as a promising target for SLE treatment.
Identification of emerging viral genomes in transcriptomic datasets of alfalfa (Medicago sativa L.)
Authors: Jiang Peng , Shao Jonathan , Nemchinov Lev G. 
Published: December 2019

Abstract
Background
Publicly available transcriptomic datasets have become a valuable tool for the discovery of new pathogens, particularly viruses. In this study, several coding-complete viral genomes previously not found or experimentally confirmed in alfalfa were identified in the plant datasets retrieved from the NCBI Sequence Read Archive.

Methods
Publicly available Medicago spp. transcriptomic datasets were retrieved from the NCBI SRA database. The raw reads were first mapped to the reference genomes of Medicago sativa and Medigago truncatula followed by the alignment of the unmapped reads to the NCBI viral genome database and de novo assembly using the SPAdes tool. When possible, assemblies were experimentally confirmed using 5′/3′ RACE and RT-PCRs.

Results
Twenty three different viruses were identified in the analyzed datasets, of which several represented emerging viruses not reported in alfalfa prior to this study. Among them were two strains of cnidium vein yellowing virus, lychnis mottle virus and Cactus virus X, for which coding-complete genomic sequences were obtained by a de novo assembly.

Conclusions
The results improve our knowledge of the diversity and host range of viruses infecting alfalfa, provide essential tools for their diagnostics and characterization and demonstrate the utility of transcriptomic datasets for the discovery of new pathogens.