bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel mathematical modelling of Saudi Arabian natural diatomite clay
Authors: Alsawalha Murad , Rao Chintaginjala Venkateswara , Al-Subaie Abeer Mohammed , Haque SK Manirul , Veeraraghavan Vishnu Priya , Surapaneni Krishna Mohan 
Published: September 2019

Abstract

Background: Diatomite is a clay material and a mineral that contains high content of silica and alumina and additional element traces. The characteristics and properties of the Saudi Arabian natural diatomite clay were studied using temperature programmed desorption of pyrrole. The relation between the particular mathematical parameters and the diatomite clay was also investigated, with a mathematical modelling of pyrrole adsorption by means of a regression analysis. Methods: The Polanyi-Wigner equation was computed for the analysis of Saudi Arabian diatomite clay, using temperature programmed desorption (TPD) of pyrrole together with a regression analysis. The correlation and regression analyses were conducted according to the following variables; 1. Temperature versus WLD-Signal- to ascertain the temperature dependence of WLD Signal. 2. Time versus WLD- to determine the time dependence of WLD. 3. 1/Temperature versus lnk to establish both the temperature dependence of the reaction rates and the time dependence of the desorption of pyrrole. Results: The results revealed that a cubic polynomial is the most suitable for the interpretation of the TCD signal of Pyrrole adsorption at a variety of temperature ranges. The findings in this study have determined that Polanyi-Wigner equation for the analysis of natural Saudi Arabian diatomite clay was computed successfully. Conclusion: The proposed equation shown in the current paper serves as the best model in the analysis of natural Saudi Arabian clay in the improvement of accuracy and efficacy of the Pyrrole- TPD. The proposed equation also greatly assists in achieving accurate results when calculating the desorbed amount of pyrrole and as compared to the traditional method, helps set a clear direction and a feedback mechanism for researchers during the investigation of clay samples. Importantly, using the equation can help to develop pyrrole-TPD software which in turn may assist scientists to clearly determine directly desorbed pyrrole amount of the clay samples during the experimental process. The findings conclude that the usefulness of the pyrrole equation can, in future, contribute greatly to the development of TPD-pyrol instrument software. It will also provide better control and quality feedback to investigators in the process of experimental design and during the run in terms of the behavior of clays and their capacity for gas desorption.
Rapid On-Site Evaluation With Telecytology Significantly Reduced Unsatisfactory Rates of Thyroid Fine-Needle Aspiration
Authors: Lin Diana M , Tracht Jessica , Rosenblum Frida , Kouba Erik , Bahl Deepti , Patel Anish , Eltoum Isam-Eldin 
Published: September 2019

AbstractObjectivesWe evaluated telecytology rapid on-site evaluation (ROSE) for thyroid ultrasound-guided fine-needle aspiration. To the best of our knowledge, this study is the first case-control clinical trial of thyroid telecytology.MethodsWe introduced on-site ROSE in our institution’s thyroid clinic for 6 months, followed by telecytology for 12 months. Our institution’s ultrasound clinic, where ROSE is not provided, was used as a control group for each period.ResultsBoth groups had similar initial unsatisfactory rates (thyroid clinic: 8.8%; ultrasound clinic: 8.0%) before the study began. The thyroid clinic’s unsatisfactory rate was significantly reduced to 1.6% after on-site ROSE (P = .001) and to 3.8% after telecytology ROSE (P = .010), with no significant difference between on-site and telecytology ROSE periods (P > .05). The ultrasound clinic’s unsatisfactory rate was unchanged for both periods. Concordance between telecytology ROSE and final adequacy was 97% (κ = 0.699).ConclusionsTelecytology ROSE reduces unsatisfactory rates for ultrasound-guided fine-needle aspiration without compromising patient care.
Clinicopathologic Characterization of Post–Renal Transplantation BK Polyomavirus-Associated Urothelial CarcinomaSingle Institutional Experience
Authors: Chu Ying-Hsia , Zhong Weixiong , Rehrauer William , Pavelec Derek M , Ong Irene M , Arjang Djamali , Patel Sanjay S , Hu Rong 
Published: September 2019

AbstractObjectivesTo review rare cases of BK polyomavirus (BKPyV) associated urologic carcinomas in kidney transplant recipients at one institution and in the literature.MethodsWe describe the clinicopathologic features of BKPyV-associated urologic carcinomas in a single-institution cohort.ResultsAmong 4,772 kidney recipients during 1994 to 2014, 26 (0.5%) and 26 (0.5%) developed posttransplantation urothelial carcinomas (UCs) and renal cell carcinomas (RCCs), respectively, as of 2017. Six (27%) UCs but none of the RCCs expressed large T antigen (TAg). TAg-expressing UCs were high grade with p16 and p53 overexpression (P < .05 compared to TAg-negative UCs). Tumor genome sequencing revealed BKPyV integration and a lack of pathogenic mutations in 50 cancer-relevant genes. Compared to TAg-negative UCs, TAg-expressing UCs more frequently presented at advanced stages (50% T3-T4) with lymph node involvement (50%) and higher UC-specific mortality (50%).ConclusionsPost-renal transplantation BKPyV-associated UCs are aggressive and genetically distinct from most non-BKPyV–related UCs.
Genome organization via loop extrusion, insights from polymer physics models
Authors: Ghosh Surya K , Jost Daniel 
Published: September 2019

Abstract
Understanding how genomes fold and organize is one of the main challenges in modern biology. Recent high-throughput techniques like Hi-C, in combination with cutting-edge polymer physics models, have provided access to precise information on 3D chromosome folding to decipher the mechanisms driving such multi-scale organization. In particular, structural maintenance of chromosome (SMC) proteins play an important role in the local structuration of chromatin, putatively via a loop extrusion process. Here, we review the different polymer physics models that investigate the role of SMCs in the formation of topologically associated domains (TADs) during interphase via the formation of dynamic loops. We describe the main physical ingredients, compare them and discuss their relevance against experimental observations.
Identifying enhancer–promoter interactions with neural network based on pre-trained DNA vectors and attention mechanism
Authors: Hong Zengyan , Zeng Xiangxiang , Wei Leyi , Liu Xiangrong 
Published: September 2019

Abstract

Motivation
Identification of enhancer–promoter interactions (EPIs) is of great significance to human development. However, experimental methods to identify EPIs cost too much in terms of time, manpower and money. Therefore, more and more research efforts are focused on developing computational methods to solve this problem. Unfortunately, most existing computational methods require a variety of genomic data, which are not always available, especially for a new cell line. Therefore, it limits the large-scale practical application of methods. As an alternative, computational methods using sequences only have great genome-scale application prospects.

Results
In this article, we propose a new deep learning method, namely EPIVAN, that enables predicting long-range EPIs using only genomic sequences. To explore the key sequential characteristics, we first use pre-trained DNA vectors to encode enhancers and promoters; afterwards, we use one-dimensional convolution and gated recurrent unit to extract local and global features; lastly, attention mechanism is used to boost the contribution of key features, further improving the performance of EPIVAN. Benchmarking comparisons on six cell lines show that EPIVAN performs better than state-of-the-art predictors. Moreover, we build a general model, which has transfer ability and can be used to predict EPIs in various cell lines.

Availability and implementation
The source code and data are available at: https://github.com/hzy95/EPIVAN.
scDAPA: detection and visualization of dynamic alternative polyadenylation from single cell RNA-seq data
Authors: Ye Congting , Zhou Qian , Wu Xiaohui , Yu Chen , Ji Guoli , Saban Daniel R , Li Qingshun Q 
Published: September 2019

Abstract

Motivation
Alternative polyadenylation (APA) plays a key post-transcriptional regulatory role in mRNA stability and functions in eukaryotes. Single cell RNA-seq (scRNA-seq) is a powerful tool to discover cellular heterogeneity at gene expression level. Given 3′ enriched strategy in library construction, the most commonly used scRNA-seq protocol—10× Genomics enables us to improve the study resolution of APA to the single cell level. However, currently there is no computational tool available for investigating APA profiles from scRNA-seq data.

Results
Here, we present a package scDAPA for detecting and visualizing dynamic APA from scRNA-seq data. Taking bam/sam files and cell cluster labels as inputs, scDAPA detects APA dynamics using a histogram-based method and the Wilcoxon rank-sum test, and visualizes candidate genes with dynamic APA. Benchmarking results demonstrated that scDAPA can effectively identify genes with dynamic APA among different cell groups from scRNA-seq data.

Availability and implementation
The scDAPA package is implemented in Shell and R, and is freely available at https://scdapa.sourceforge.io.

Supplementary information
Supplementary data are available at Bioinformatics online.
Recessive Charcot-Marie-Tooth and multiple sclerosis associated with a variant in MCM3AP
Authors: Sedghi Maryam , Moslemi Ali-Reza , Cabrera-Serrano Macarena , Ansari Behnaz , Ghasemi Majid , Baktashian Mojtaba , Fattahpour Ali , Tajsharghi Homa 
Published: September 2019

Abstract
Variants in MCM3AP, encoding the germinal-centre associated nuclear protein, have been associated with progressive polyneuropathy with or without intellectual disability and ptosis in some cases, and with a complex phenotype with immunodeficiency, skin changes and myelodysplasia. MCM3AP encoded protein functions as an acetyltransferase that acetylates the replication protein, MCM3, and plays a key role in the regulation of DNA replication. In this study, we report a novel variant in MCM3AP (p.Ile954Thr), in a family including three affected individuals with characteristic features of Charcot-Marie-Tooth neuropathy and multiple sclerosis, an inflammatory condition of the central nervous system without known genetic cause. The affected individuals were homozygous for a missense MCM3AP variant, located at the Sac3 domain, which was predicted to affect conserved amino acid likely important for the function of the germinal-centre associated nuclear protein. Our data support further expansion of the clinical spectrum linked to MCM3AP variant and highlight that MCM3AP should be considered in patients with accompaniment of recessive motor axonal Charcot-Marie-Tooth neuropathy and multiple sclerosis.
Epigenetic silencing of microRNA-204 by Helicobacter pylori augments the NF-κB signaling pathway in gastric cancer development and progression
Authors: Chen Peizhan , Guo He , Wu Xuming , Li Jingquan , Duan Xiaohua , Ba Qian , Wang Hui 
Published: September 2019

Abstract
Helicobacter pylori infection induces gastric cancer (GC) development through a progressive cascade; however, the roles of the microRNAs that are involved in the cascade and the underlying mechanisms are still unclear. Here, we found that microRNA-204 was suppressed in gastric mucosal cells in response to H.pylori infection and downregulated in GC tissues due to aberrant methylation of the promoter of its host gene, TRPM3. Helicobacter pylori induced a progressive downregulation of microRNA-204 from superficial gastritis to intestinal metaplasia, with an accompanying increment of the methylated levels of CpG sites in the TRPM3 promoter. With the GC cellular models of AGS, MGC-803 or BGC-823, we found that microRNA-204 suppressed the tumor necrosis factor (TNF)-α-induced activation of NF-κB signaling pathways and, in animal models, inhibited tumor growth and metastasis. The conditional supernatant of microRNA-204 overexpression GC cells led to reduced tube formation of human umbilical vein endothelial cells. A target gene for microRNA-204 was BIRC2, and in GC cells, BIRC2 knockdown recapitulated the biological phenotype of microRNA-204 overexpression. BIRC2 overexpression promoted the metastasis of GC cells and rescued the inhibition activities of microRNA-204 on cell migration and the NF-κB signaling pathway. Moreover, lower microRNA-204 and higher BIRC2 expression levels were associated with a poorer prognosis of GC patients. These results demonstrate that epigenetic silencing of microRNA-204 induced by H.pylori infection augments the NF-κB signaling pathway in H.pylori-induced gastritis and GC, potentially providing novel intervention targets for these diseases.
MicroRNA-204 was epigenetically down-regulated by H. pylori infection in gastric mucosal cells. It led to enhanced BIRC2 expression level and BIRC2/TNF-a/NF-kB signaling pathway activities, which promoted angiogenesis and metastasis of gastric cancer cells.
“My zines, so far, aren't as political as other works I've produced”: Communicative Capitalism Among Queer Feminist Zinesters
Authors: Reynolds Chelsea 
Published: September 2019

AbstractSelf-published zines have been celebrated by some feminist communication scholars for offering an emancipatory outlet for women and queer people. But under the logics of late capitalism, zines cannot reach truly transgressive potentials. This study situates zinester politics within a framework of communicative capitalism: the current era of command individuality and “woke” representational politics. I also historicize zines’ proliferation through punk, do-it-yourself (DIY), and White, feminist communities. Using critical discourse analysis as my analytical approach, I illustrate the interpellation of capitalist ideology in online questionnaires completed by 11 queer, White, feminist zinesters from Chicago. By harnessing a DIY production model, respondents said they resisted mass-mediated expectations of normative sexuality and gender identity, but zinesters also reflect and reify the systems they attempt to transcend.
AMPA Induces NO-Dependent cGMP Signals in Hippocampal and Cortical Neurons via L-Type Voltage-Gated Calcium Channels
Authors: Giesen Jan , Füchtbauer Ernst-Martin , Füchtbauer Annette , Funke Klaus , Koesling Doris , Russwurm Michael 
Published: September 2019

AbstractThe nitric oxide (NO)/cGMP signaling cascade has an established role in synaptic plasticity. However, with conventional methods, the underlying cGMP signals were barely detectable. Here, we set out to confirm the well-known NMDA-induced cGMP increases, to test the impact of AMPA on those signals, and to identify the relevant phosphodiesterases (PDEs) using a more sensitive fluorescence resonance energy transfer (FRET)-based method. Therefore, a “knock-in” mouse was generated that expresses a FRET-based cGMP indicator (cGi-500) allowing detection of cGMP concentrations between 100 nM and 3 μM. Measurements were performed in cultured hippocampal and cortical neurons as well as acute hippocampal slices. In hippocampal and cortical neurons, NMDA elicited cGMP signals half as high as the ones elicited by exogenous NO. Interestingly, AMPA increased cGMP independently of NMDA receptors and dependent on NO synthase (NOS) activation. NMDA- and AMPA-induced cGMP signals were not additive indicating that both pathways converge on the level of NOS. Accordingly, the same PDEs, PDE1 and PDE2, were responsible for degradation of NMDA- as well as AMPA-induced cGMP signals. Mechanistically, AMPAR induced calcium influx through L-type voltage-gated calcium channels leading to NOS and finally NO-sensitive guanylyl cyclase activation. Our results demonstrate that in addition to NMDA also AMPA triggers endogenous NO formation and hence cGMP production.
Typhoid and the Military in the Early 20th Century
Authors: Gradmann Christoph , Harrison Mark , Rasmussen Anne 
Published: September 2019

Abstract

Background
In the decades following the discovery of the bacillus causing typhoid, in 1880, understanding of the disease formerly known as enteric fever was transformed, offering new possibilities for prevention. Gradually, measures that aimed to prevent infection from human carriers were developed, as were inoculations designed to confer immunity against typhoid and paratyphoid fevers. These were initially introduced in European armies that were regularly ravaged by typhoid, especially garrisons stationed in the colonies. This article reviews the research undertaken in the armed forces and the measures that they implemented in the years up to and during the First World War.

Methods
The article is based on an analytical review of scientific literature from the early 19th century, focusing on the United Kingdom, Germany, and France.

Results
The armies of the United Kingdom, Germany, and France undertook important work on the transmission of typhoid in the years between 1890 and 1918. Many preventive measures were introduced to deal with the spread of typhoid but these varied between the 3 countries, depending largely on their political traditions. Inoculation was particularly successful in preventing typhoid and greatly reduced the number of casualties from this disease during the First World War. Despite this, it proved difficult to prevent paratyphoid infection, and debates continued over which vaccines to use and whether or not immunization should be voluntary.

Conclusions
By the end of the First World War, the value of inoculation in preventing the spread of typhoid had been proven. Its successful implementation demonstrates the importance of vaccination as a public health intervention during times of conflict and social upheaval.
Controlled Human Infection With Bordetella pertussis Induces Asymptomatic, Immunizing Colonization
Authors: de Graaf Hans , Ibrahim Muktar , Hill Alison R , Gbesemete Diane , Vaughan Andrew T , Gorringe Andrew , Preston Andrew , Buisman Annemarie M , Faust Saul N , Kester Kent E , Berbers Guy A M , Diavatopoulos Dimitri A , Read Robert C 
Published: September 2019

Abstract

Background
Bordetella pertussis is among the leading causes of vaccine-preventable deaths and morbidity globally. Human asymptomatic carriage as a reservoir for community transmission of infections might be a target of future vaccine strategies, but has not been demonstrated. Our objective was to demonstrate that asymptomatic nasopharyngeal carriage of Bordetella pertussis is inducible in humans and to define the microbiological and immunological features of presymptomatic infection.

Methods
Healthy subjects aged 18–45 years with an antipertussis toxin immunoglobin G (IgG) concentration of &lt;20 international units/ml were inoculated intranasally with nonattenuated, wild-type Bordetella pertussis strain B1917. Safety, colonization, and shedding were monitored over 17 days in an inpatient facility. Colonization was assessed by culture and quantitative polymerase chain reaction. Azithromycin was administered from Day 14. The inoculum dose was escalated, aiming to colonize at least 70% of participants. Immunological responses were measured.

Results
There were 34 participants challenged, in groups of 4 or 5. The dose was gradually escalated from 103 colony-forming units (0% colonized) to 105 colony-forming units (80% colonized). Minor symptoms were reported in a minority of participants. Azithromycin eradicated colonization in 48 hours in 88% of colonized individuals. Antipertussis toxin IgG seroconversion occurred in 9 out of 19 colonized participants and in none of the participants who were not colonized. Nasal wash was a more sensitive method to detect colonization than pernasal swabs. No shedding of Bordetella pertussis was detected in systematically collected environmental samples.

Conclusions
Bordetella pertussis colonization can be deliberately induced and leads to a systemic immune response without causing pertussis symptoms.

Clinical Trials Registration
NCT03751514.
A Survey on Prediction of Suicidal Ideation Using Machine and Ensemble Learning
Authors: Chadha Akshma , Kaushik Baijnath 
Published: September 2019

Abstract
Suicide is a major health issue nowadays and has become one of the highest reason for deaths. There are many negative emotions like anxiety, depression, stress that can lead to suicide. By identifying the individuals having suicidal ideation beforehand, the risk of them completing suicide can be reduced. Social media is increasingly becoming a powerful platform where people around the world are sharing emotions and thoughts. Moreover, this platform in some way is working as a catalyst for invoking and inciting the suicidal ideation. The objective of this proposal is to use social media as a tool that can aid in preventing the same. Data is collected from Twitter, a social networking site using some features that are related to suicidal ideation. The tweets are preprocessed as per the semantics of the identified features and then it is converted into probabilistic values so that it will be suitably used by machine learning and ensemble learning algorithms. Different machine learning algorithms like Bernoulli Naïve Bayes, Multinomial Naïve Bayes, Decision Tree, Logistic Regression, Support Vector Machine were applied on the data to predict and identify trends of suicidal ideation. Further the proposed work is evaluated with some ensemble approaches like Random Forest, AdaBoost, Voting Ensemble to see the improvement.
Epidermal collagenase activity and its induction by 20-hydroxyecdysone in the fiddler crab Uca pugilator
Authors: Toups Erin A. , Zou Enmin 
Published: September 2019

Abstract
The epidermal collagenase activity and its induction by 20- hydroxyecdysone in Uca pugilator were investigated. Zymographic electrophoresis showed four bands of collagenase activity, 16, 19, 22 and 29 kDa in molecular weight, with the former two accounting for 60% and 36%, respectively, of the total collagenase activity. The collagenase activity varies during the molting cycle. Among the molt stages tested, Premolt Stage D0 exhibited the highest epidermal collagenase activity for both the 16 and 19 kDa isoenzymes and, as the molt stage proceeded, the enzymatic activity of these two isoenzymes decreased, with the lowest activity for both found in Premolt Stage D3-4. Injection of 20-hydroxyecdysone significantly induced the activity of the 16 kDa collagenase in the epidermis of Uca pugilator, suggesting that the activity of this isoenzyme is under molting hormone control. Although 20-hydroxyecdysone injection did not result in a statistically significant increase in the activity of the 19 kDa isoenzyme, a tendency of the induction was nonetheless demonstrated. This is the first report on epidermal collagenase activity and its induction by the molting hormone in a crustacean.