bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-cell multi-omic profiling of chromatin conformation and DNA methylation
Authors: Lee Dong-Sung , Luo Chongyuan , Zhou Jingtian , Chandran Sahaana , Rivkin Angeline , Bartlett Anna , Nery Joseph R , Fitzpatrick Conor , O'Connor Carolyn , Dixon Jesse R , Ecker Joseph R 
Published: September 2019

Abstract
The ability to profile epigenomic features in single cells is facilitating the study of the variation in transcription regulation at the single cell level. Single cell methods have also facilitated the generation of cell-type resolved transcriptomic and epigenetic profiles of lineages derived from complex heterogeneous samples. However, integrating different epigenetic features remain challenging, as many current methods profile a single data type at at time. Furthermore, some epigenetic features, such as 3D genome organization, are intrinsically variable between single cells of the same lineage, so it remains unclear how well these methods may resolve cell-types from complex mixtures. Here we describe a method for profiling 3D genome organization and DNA methylation in single cells. This protocol accompanies Lee et al. (Nature Methods 2019) after peer review to aid potential users in applying the method to their own samples.
Molecular evolution and expression of opsin genes in Hydra vulgaris
Authors: Munoz Aide Macias , Murad Rabi , Mortazavi Ali 
Published: September 2019

Abstract
Background The evolution of opsin genes is of great interest because it can provide insight into the evolution of light detection and vision. An interesting group in which to study opsins is Cnidaria because it is a basal phylum sister to Bilateria with much visual diversity within the phylum. Hydra vulgaris ( H. vulgaris ) is a cnidarian with a plethora of genomic resources to characterize the opsin gene family. This eyeless cnidarian has a behavioral reaction to light, but it remains unknown which of its many opsins functions in light detection. Here, we used phylogenetics and RNA-seq to investigate the molecular evolution of opsin genes and their expression in H. vulgaris . We explored where opsin genes are located relative to each other in an improved genome assembly and where they belong in a cnidarian opsin phylogenetic tree. In addition, we used RNA-seq data from different tissues of the H. vulgaris adult body and different time points during regeneration and budding stages to gain insight into their potential functions. Results We identified 45 opsin genes in H. vulgaris , many of which were located near each other suggesting evolution by tandem duplications. Our phylogenetic tree of cnidarian opsin genes supported previous claims that they are evolving by lineage-specific duplications. We identified two H. vulgaris genes ( HvOpA1 and HvOpB1 ) that fall outside of the two commonly determined Hydra groups; these genes possibly have a function in nematocytes and mucous gland cells respectively. We also found opsin genes that have similar expression patterns to phototransduction genes in H. vulgaris . We propose a H. vulgaris phototransduction cascade that has components of both ciliary and rhabdomeric cascades. Conclusions This extensive study provides an in-depth look at the molecular evolution and expression of H. vulgaris opsin genes. The expression data that we have quantified can be used as a springboard for additional studies looking into the specific function of opsin genes in this species. Our phylogeny and expression data are valuable to investigations of opsin gene evolution and cnidarian biology.
The Distribution of Preputial Vessels at Different Severity of Rat Congenital Hypospadias Model
Authors: Lin Defu , Liu Pei , Wang Guannan , Zhang Weiping , Sun Ning 
Published: September 2019

Abstract
Background To reconstruct and analyze the distribution of preputial vessels using micro-computerized tomography (micro-CT) in the finasteride induced congenital hypospadias rat model. Materials and methods Pregnant rats were exposed to finasteride from gestational days 12 to 17. According to the position of the urethral meatus, the pups were divided into normal, mild hypospadias and severe hypospadias groups. Six months after birth, the preputial blood vessels were observed by vascular perfusion with Microfil (a silicone-based polymer) and scanned by micro-CT. CTvox and NRecon were used to reconstruct 3-dimentional(3D) images. A pathological analysis of the specimen was taken to determine the position of Microfil. Results The normal group and the mild hypospadias group had similar preputial image characteristics. At the junction of the inner and outer prepuce, the deep layer vessels of the superficial fascia were transverse distributed and formed a vascular ring-like structure. Among the severe hypospadias group, five had sufficient blood circulation while six had insufficient blood circulation. In the sufficient blood circulation type, the ring-like vessels were found at the junction of the inner and outer prepuce similar to the normal and mild hypospadias group. However, only a small amount of capillary supply to this area in the insufficient type. Conclusion Compares to the traditional techniques, micro-CT improves understanding the 3D structure of the hypospadias preputial vascular. The junction of the inner and outer prepuce with rich blood circulation was suitable to be a vascular pedicle flap.
Reverse Wedge Effect Following Intramedullary Nailing of a Basicervical Trochanteric Fracture Variant Combined with a Mechanically Compromised Greater Trochanter
Authors: Zhang Yu , Hu Jun , Qin Xiaodong , Li Xiang , Hong Guqi 
Published: September 2019

Abstract
Background: To introduce an unreported intraoperative complication in intramedullary nailing (IN) of a trochanteric fracture variant characterized by a basicervical fracture line and coronally disrupted greater trochanter (GT).Materials and Methods : A total of 414 trochanteric fractures (TF) treated with INs from 2013 to 2017 were included. After analysis of intraoperative fluoroscopy, 33 cases, including 21 females and 12 males, with a mean age of 72.5 years (33 to 96 years) were identified for internal rotation of the cephalocervical fragment and inferior opening at the basicervical fracture line caused by nailing a satisfactorily reduced TF. The morphological features of those patients were analyzed on CT scan. On radiograph, the magnitude of the displacement and final femoral neck-shaft angle were measured.Results: CT analysis demonstrated that the basicervical fracture line and the posterolateral fragment (PLF) detached from the GT were the two dominant features of this cohort. They were classified according to the number of main fragments: a 3-fragmentary subgroup containing three consistent fragments (cephalocervical fragment, PLF and distal femoral shaft) and a 4-fragmentary subgroup embracing one additional fragment (lesser trochanter). The four subtypes were as follows: the 3-fragmentary S indicating a small PLF (6 cases), the 3-fragmentary M presenting a moderate PLF (3 cases), the 3-fragmentary L standing for the PLF involving whole lesser trochanter (LT) (4 cases) and the 4-fragmentary GL incorporating separated PLF and LT fragments (20 cases). Geological analysis demonstrated that the majority of the basicervical fracture lines (81.8%) just crossed the center of the piriformis fossa, while the others marginally involved the medial wall of the GT. Postoperatively, the mean width of the inferior opening at the basicervical region was 9.2±4.6 mm. The mean NSA was 135.2±7.8 degrees. The comparison between the 3- and 4-fragmentary subgroups revealed no significant differences in magnitude of displacement and NSA. Conclusion: This unreported intraoperative complication predominantly occurred in the intramedullary nailed basicervical trochanteric fracture variant combined with a PLF from the GT. This secondary displacement was caused by an impingement of the reamer with the superolateral cortex of the cephalocervical fragment and should be addressed during the operation.
Results of surgery using a locking plate for proximal humerus fractures in patients older than 80 years: A retrospective case series
Authors: Shin Won Chul , Kang Suk-Woong , Son Seung Min , Bae Hyuk 
Published: September 2019

Abstract
Background: To evaluate the results of surgical treatment using a locking plate for proximal humeral fractures in patients aged >80 years. Methods: Between September of 2013 and March of 2016, there were 22 patients who received locking plate fixation from proximal humeral fractures over 80 years-old. Among the 22 cases, Clinical, radiological results were analyzed for 19 patients who were able to follow up more than one year. We analyzed bone union, neck-shaft angle, UCLA score, range of motion compared to opposite side and complication. Clinical, radiological results were investigated for medial comminuted fracture or not.Results: All the patients achieved bone union. The mean bone union time was 13.7 weeks, and the mean neck-shaft angle was 126.4. The mean University of California, Los Angeles, shoulder score was 22.4, and score was <28 point in 12 patients. The mean forward flexion, abduction, external rotation, and internal rotation angles were 129.2°, 112.3°, 44.2°, and L2. All motions were significantly different from the normal shoulder motion. A significant difference was found in the loss of neck-shaft angle according to the medial comminuted fracture.Conclusion: In the surgical treatment of proximal humeral fractures in patients aged >80 years, use of a locking plate attained bone union with relatively satisfactory results. However, we considered that prevention of and training for postoperative stiffness are necessary. Other surgical methods should be considered for patients with complex displaced fractures, especially those with medial comminuted fractures.
How feasible is it to abandon statistical significance? A reflection based on a short survey
Authors: Diaz-Quijano Fredi Alexander , Calixto Fernando Morelli , Silva José Mário Nunes da 
Published: September 2019

Abstract
Background : There is a growing trend in using the “statistically significant” term in the scientific literature. However, harsh criticism of this concept motivated the recommendation to withdraw its use of scientific publications. We aimed to validate the support and the feasibility of adherence to this recommendation, among researchers having declared in favor of removing the statistical significance. Methods : We surveyed signatories of an article published that defended this recommendation, to validate their opinion and ask them about how likely they will retire the concept of statistical significance. Results: We obtained 151 responses which confirmed the support for the mentioned publication in aspects such as the adequate interpretation of the p-value, the degree of agreement, and the motivations to sign it. However, there was a wide distribution of answers about how likely are they to use the concept of "statistical significance” in future publications. About 42% declared being neutral, or that would likely use it again. We described arguments referred by several signatories and discussed aspects to be considered in the interpretation of research results. Conclusions : The declared position against the use of statistical significance had had legitimate support from numerous researchers. However, the full application of this recommendation does not seem feasible. The arguments related to the inappropriate use of statistical tests should promote more education among researchers and users of scientific evidence.
Prevalence difference of Helicobacter pylori infection between Tibetan and Han ethnics: A meta-analysis on epidemiologic studies
Authors: Bai Dan , Liu Kai , Wang An-Mo , Duan Si-Yu , Zhang Wei-Han , Bajracharya Pujan Man , Chen Xin-Zu , Hu Jian-Kun 
Published: September 2019

Abstract
Background Helicobacter pylori (Hp) appears worldwide prevalent as a primary carcinogenic pathogen of human gastric cancer. China is a multi-ethnic country, and the prevalence of Hp infection may be diverse among ethnics. This meta-analysis was conducted to compare the prevalence of Hp infection between Tibetan and Han ethnics.Methods The databases, PubMed, Web of Science, Blackwell Journals, CNKI, and Wanfang were searched. Those studies which reported the prevalence of Hp infection between Tibetans and Hans in China were eligible. There were no limitation to Hp detection method, publication language, and observation period. RevMan 5.3 and Stata 12.0 softwares were used for heterogeneity tests and meta-analyses. Meanwhile, subgroup analysis, sensitivity analysis and publication bias evaluation were performed where applicable.Results Totally, 11 studies with 3,826 Tibetans and 19,787 Hans were analyzed. The pooled prevalence of Hp infection were 62.2% and 55.3% among Tibetans and Hans, respectively. Tibetans had higher risk of Hp infection than Hans (OR=1.38, 95% CI 1.05-1.80). In subgroup analysis, those Tibetans with upper gastrointestinal symptoms (OR=1.51, 95% CI 1.06-2.16), inhabiting in Tibet (OR=1.51, 95% CI 1.22-1.87), or in Northwestern region (OR=1.15, 95% CI 1.00-1.31) had significantly higher risk of Hp infection. Additionally, in recent ten years, Hans appeared a decreased risk of Hp infection (OR=1.81, 95% CI 1.42-2.30). Heterogeneity was common, while sensitivity analyses showed partially inconsistent results against main findings.Conclusions This study demonstrated the higher prevalence of Hp infection in Tibetans compared with Hans, especially in recent years, or in the Tibet and the northwest China, as well as symptomatic Tibetans. It suggests tailored strategy and robustness need further consider for Hp screening and eradication among Tibetans.Trial registration: The present systematic review and meta-analysis was registered in the PROSPERO International Prospective Register of Systematic Reviews supported by the National Institute for Health Research of the National Health Service (NHS), UK (registration number: CRD42019121192).
How mHealth can facilitate collaboration in diabetes care: qualitative analysis of co-design workshops
Authors: Bradway Meghan , Morris Rebecca L , Giordanengo Alain , Årsand Eirik 
Published: September 2019

Abstract
Background Individuals with diabetes are using mobile health (mHealth) to make decisions regarding self-management. However, individuals can understand even more about their diabetes by sharing these patient-gathered data (PGD) with health professionals. We conducted experience-based co-design (EBCD) workshops, with the aim of gathering end-users’ needs and expectations for a PGD-sharing system.Methods The first workshop (2017) included patients with Type 2 Diabetes (T2D) (n=4) and general practitioners (GPs) (n=3). The second workshop (2018) included patients with Type 1 Diabetes (T1D) (n=5), diabetes specialists (n=2) and a nurse. The workshops involved two sessions: separate morning sessions for patients and healthcare providers (HCPs), followed by a joint lunch and afternoon session for all participants together. A discussion guide was used to gather input regarding end-users’ expectations for the system. Participants then created and explained their own ideas for a data-sharing system, using paper-prototypes. Workshops were audio recorded, transcribed and translated from Norwegian to English. Inductive thematic analysis was performed.Results The main emergent themes were mHealth technologies’ impacts on end-users, and functionalities of a data-sharing system. Patients and providers agreed that PGD could be used by HCPs to provide more concrete self-management recommendations. Participants made paper-prototypes to explain which data types to gather and display, and how the systems could be used to facilitate shared-decision making. However, all also agreed that a data-sharing system alone was not enough to achieve the full effect of mHealth.Conclusion While seemingly contradictory, these results revealed that by bringing both together in the joint sessions, they were also able to equally elaborate their understanding of realistic limitations and solutions for mHealth integration. These workshops not only demonstrated the value of involving both parties together in co-design, they enabled participants to highlight that mHealth integration requires both validation of the technology as well as research into feasible changes throughout health care education and practice.
Designing of pressure-free filtration system integrating polyvinyl alcohol/chitosan-silver nanoparticle membrane for purification of microbe-containing water
Authors: Taha Tarek H. , Abu-Saied M. A. , Elnouby Mohamed S. , Hashem Mohamed , Alamri Saad , Mostafa Yasser 
Published: September 2019

Abstract
The study is concerned with the designing of a pressure-free filtration system that contains a polyvinyl alcohol (PVA)/chitosan (CS) polymeric membrane integrated with silver nanoparticles (AgNPs) for the purification of microbe-contaminated water. The AgNPs were greenly synthesized using culture filtrate of Bacillus endophyticus. PVA/CS membrane was prepared, integrated with washed and unwashed silver nanoparticles, and their proper integration was characterized using Fourier transform infrared (FTIR) spectroscopy, thermogravimetric analysis (TGA), scanning electron microscopy (SEM), transmission electron microscopy (TEM), particle size analyzer (PSA) and mechanical properties. The membrane was tested against six pathogenic microbes and showed potent antimicrobial activity especially against Klebsiella pneumoniae. A tap water sample was passed through the filtration system and tested for its microbial content before and after filtration. The obtained results showed that the optical densities of the tap water before the treatment and after the passage through the PVA/CS membrane were 1.397 and 1.214, respectively, with almost 88% of the original microbial content. The optical density of the tap water after passage through PVA/CS–washed AgNPs membrane was close to zero. The repeated observations resulting from the obtained optical densities of treated and untreated water refer to the future applicability of the prepared materials and the designed system for the safe purification of microbe-contaminated water for drinking, industrial or pharmaceutical purposes.
Significados de la corrupción en universitarios dominicanos, docentes en formación
Authors: García-Leguizamón Fernando 
Published: September 2019

De manera general, la corrupción se caracteriza como el abuso de un poder encargado, con el fin de obtener un beneficio particular. La gran corrupción ha sido abundantemente abordada desde diferentes perspectivas en las ciencias sociales, pero solo en tiempos relativamente recientes se ha otorgado una mayor importancia al estudio de la pequeña corrupción, la que emerge y se reproduce en prácticas cotidianas que se confunden con la lógica del intercambio privado de favores. Este interés ha implicado la adopción de una mirada culturalista para la comprensión de los significados que en contextos particulares le asignan los sujetos al fenómeno. Siguiendo este camino, nos preguntamos aquí por los significados que un grupo de estudiantes universitarios articulan colectivamente en torno a la corrupción, cuando se encuentran en situaciones sociales de habla. Suponemos que las interacciones lingüísticas que allí ocurren permiten identificar repertorios interpretativos, esto es, recursos culturales compartidos, disponibles para la descripción y la evaluación del fenómeno, recursos con los que los sujetos adoptan frente a la corrupción una posición no exenta de variaciones y tensiones. El acercamiento a estos significados se realizó desde una perspectiva cualitativa, empleando la técnica del grupo focal. La población del estudio son estudiantes de la carrera de educación, en la ciudad de San Pedro de Macorís, en República Dominicana. Identificamos tres de estos repertorios: el de la victimización, el de la aceptación-justificación y el de la superación ética.
Beyond the Cabello-Severini-Winter framework: Making sense of contextuality without sharpness of measurements
Authors: Kunjwal Ravi 
Published: September 2019

We develop a hypergraph-theoretic framework for Spekkens contextuality applied to Kochen-Specker (KS) type scenarios that goes beyond the Cabello-Severini-Winter (CSW) framework. To do this, we add new hypergraph-theoretic ingredients to the CSW framework. We then obtain noise-robust noncontextuality inequalities in this generalized framework by applying the assumption of (Spekkens) noncontextuality to both preparations and measurements. The resulting framework goes beyond the CSW framework in both senses, conceptual and technical. On the conceptual level: 1) as in any treatment based on the generalized notion of noncontextuality à la Spekkens, we relax the assumption of outcome determinism inherent to the Kochen-Specker theorem but retain measurement noncontextuality, besides introducing preparation noncontextuality, 2) we do not require the exclusivity principle -- that pairwise exclusive measurement events must all be mutually exclusive -- as a fundamental constraint on measurement events of interest in an experimental test of contextuality, given that this property is not true of general quantum measurements, and 3) as a result, we do not need to presume that measurement events of interest are ``sharp" (for any definition of sharpness), where this notion of sharpness is meant to imply the exclusivity principle. On the technical level, we go beyond the CSW framework in the following senses: 1) we introduce a source events hypergraph -- besides the measurement events hypergraph usually considered -- and define a new operational quantity Corr that appears in our inequalities, 2) we define a new hypergraph invariant -- the weightedmax-predictability -- that is necessary for our analysis and appears in our inequalities, and 3) our noise-robust noncontextuality inequalities quantify tradeoff relations between three operational quantities -- Corr, R, and p0 -- only one of which (namely, R) corresponds to the Bell-Kochen-Specker functionals appearing in the CSW framework; when Corr=1, the inequalities formally reduce to CSW type bounds on R. Along the way, we also consider in detail the scope of our framework vis-à-vis the CSW framework, particularly the role of Specker's principle in the CSW framework, i.e., what the principle means for an operational theory satisfying it and why we don't impose it in our framework.
Teoria do reconhecimento e interações cotidianas: o caso das lutas dos quilombolas do Pará
Authors: Bargas Janine , Maia Rousiley 
Published: September 2019

Este artigo explora a teoria do reconhecimento, a fim de demonstrar sua pertinência para investigações sobre processos de subjetivação e politização de grupos sociais. Ao focalizar o caso das comunidades quilombolas do Pará, a análise busca responder, de modo situado, como situações históricas de desrespeito a esses grupos sociais, em um processo intersubjetivo que perpassa por distintos processos comunicativos de interação cotidiana, convertem-se em lutas. Acreditamos que os elos construídos nas interações possibilitam o compartilhamento dos sentimentos de injustiça e a promoção de uma interpretação comum sobre os danos sofridos, a partir de percepções geralmente difusas e dispersas na vida social dos sujeitos. A articulação de formas de resistência e agendas concernentes são atadas a essas interpretações.