bluuebunny/crossref_metadata_2025 huggingface dataset:
Nusap1, Melk and L1cam Expression in Cervical Cancer Tissues; Prognostic and Clinicopathological Implications
Authors: Harb Ola A. , Elfeky Mariem A. , Elshafaay Basant Sh , Obaya Ahmed A. , Awd Amr A. , Alkilany Mohamed M. , Gertallah Loay M.
Published: June 2020

Background:

It is important to identify of novel therapeutic targets for cervical carcinoma. Nucleolar and spindle associated protein 1 (NUSAP1) could be able to bind microtubules, and has important role in spindle formation and mitotic progression. Maternal embryonic leucine zipper kinase (MELK) is a cell cycle related conserved protein kinase that is involved in control and regulation of the cell cycle, apoptosis, and carcinogenesis. The L1 cell adhesion molecule (L1-CAM) was discovered as a protein which has an essential role in cell migration and axon guidance in the nervous system.

The Aim of This Study

Is to investigate the tissue protein expression of NUSAP1, MELK and L1CAM in tissues of cervical carcinoma and to detect their prognostic roles.

Methods:

Expression of NUSAP1, MELK and L1CAM was evaluated in sections from 62 cases of cervical carcinoma using immunohistochemistry we followed our patients for 3 years correlate their expression with clinicopathological parameters and patients outcome.

Results:

High levels of NUSAP1, MELK and L1CAM expression was positively related to older age of the patients, high grade of the tumor, lympho-vascular invasion, advanced FIGO stage, poor survival rates and higher recurrence rate after successful therapy (p<0.001). L.N metastases (p=0.002), distant metastases (p=0.003). There are statistically significant positive association between NUSAP1, MELK and L1CAM Phi correlation coefficient= + 0.87 and + 0.721 respectively (p<0.001).

Conclusion:

NUSAP1, MELK and L1CAM are considered markers of poor prognosis in cervical carcinoma cells.
The effect of information literacy instruction on lifelong learning readiness
Authors: Seifi Leili , Habibi Maryam , Ayati Mohsen
Published: June 2020

The purpose of the present study is to examine the effect of information literacy skills instruction on the lifelong learning readiness of users in Iranian public libraries. To this end, 30 active users of two libraries were randomly placed in control and experimental groups. Information literacy skills were taught to the experimental group over one and a half months. The results revealed that information literacy instruction led to a significant increase in readiness for self-directed learning and readiness to overcome deterrents to participation. According to the findings, information literacy skills instruction made a significant difference to the information literacy of users in Iranian public libraries. The results of this study encourage public libraries to plan for the implementation of information literacy instruction in order to make public libraries lifelong learning centres.
Business intelligence in academic libraries in Jordan: Opportunities and challenges
Authors: Hamad Faten , Al-Aamr Razan , Jabbar Sinaria Abdel , Fakhuri Hussam
Published: June 2020

Data plays a major role in helping to understand clearly the changing needs of academic library users, and in helping libraries to innovate their services and procedures accordingly. Data needs to be transformed into information for decision-making and strategic planning. Business intelligence offers powerful analytical tools, such as visualization and data-mining tools, which lead to informed decisions and hence transform the user’s experience, bringing it to a more advanced level. This research investigates the concept of business intelligence from the perceptions of information department staff at academic libraries in Jordan. The opportunities and challenges associated with it are also discussed and explored. As indicated by the results, information department staff agree that business intelligence improves decision-making, helping decision-makers to make the most accurate and timely decisions for the library. The results also indicate that an appropriate infrastructure is important for the successful implementation of business intelligence in academic libraries in Jordan.
The Effect of Undergraduate Major Choices on the Earnings of Sub-Saharan African Immigrant and Native-Born College Graduates
Authors: Seeborg Michael , Ikpebe Ene
Published: June 2020

A very high percentage of sub-Saharan African college-graduate immigrants in the United States have college degrees in science, technology, engineering, and mathematics (STEM) disciplines compared with native-born college graduates. This study uses a pooled cross-section (2013–2018) from the American Community Survey to compare the distribution of undergraduate majors of sub-Saharan African immigrants and native-born college graduates. We estimate ordinary least square (OLS) earnings functions that include detailed college major variables. We find that undergraduate major area of study is a significant predictor of earnings and that there is an overrepresentation of sub-Saharan African immigrants with high-paying undergraduate majors. However, after controlling for human capital differences, college-educated African immigrants have not achieved pay equity with their native-born counterparts.

JEL Classifications: J61, J15, J26, I21
An Opioid Addicted Cosmetic Patient: A Case Report and Review of the Literature for the Management of an Opioid-Dependent Cosmetic Patient
Authors: Wetton Lara , Hodgkinson Darryl
Published: June 2020

There is a large body of literature dedicated to patient selection in plastic surgery. Much of this, however, is dedicated to the recognition of patients with body dysmorphia, those psychologically unfit for surgery, and those who have medical conditions that make the risk of complications unacceptably high. There is, however, little in the way of recognition and management of patients with chronic pain issues. With opioid misuse and dependence on the rise, the likelihood of plastic surgeons encountering patients who have obvious or occult opioid dependence issues has increased. In this case report and review of literature, we aim to present an evidence-based approach to the diagnosis and management of plastic surgery patients with a known opioid dependence.
Respiratory Variation in Carotid Artery Peak Systolic Velocity Is Unable to Predict Fluid Responsiveness in Spontaneously Breathing Critically Ill Patients When Assessed by Novice Physician Sonologists
Authors: Abbasi Adeel , Nayeemuddin Mohammed , Azab Nader , Schick Alexandra , Lopardo Thomas , Phillips Gary S. , Merchant Roland C. , Levy Mitchell M. , Blaivas Michael , Corl Keith A.
Published: June 2020

Background:

Respiratory variation in carotid artery peak systolic velocity (ΔVpeak) assessed by point-of-care ultrasound (POCUS) has been proposed as a noninvasive means to predict fluid responsiveness. We aimed to evaluate the ability of carotid ΔVpeak as assessed by novice physician sonologists to predict fluid responsiveness.

Methods:

This study was conducted in 2 intensive care units. Spontaneously breathing, nonintubated patients with signs of volume depletion were included. Patients with atrial fibrillation/flutter, cardiogenic, obstructive or neurogenic shock, or those for whom further intravenous (IV) fluid administration would be harmful were excluded. Three novice physician sonologists were trained in POCUS assessment of carotid ΔVpeak. They assessed the carotid ΔVpeak in study participants prior to the administration of a 500 mL IV fluid bolus. Fluid responsiveness was defined as a ≥10% increase in cardiac index as measured using bioreactance.

Results:

Eighty-six participants were enrolled, 50 (58.1%) were fluid responders. Carotid ΔVpeak performed poorly at predicting fluid responsiveness. Test characteristics for the optimum carotid ΔVpeak of 8.0% were: area under the receiver operating curve = 0.61 (95% CI: 0.48-0.73), sensitivity = 72.0% (95% CI: 58.3-82.56), specificity = 50.0% (95% CI: 34.5-65.5).

Conclusions:

Novice physician sonologists using POCUS are unable to predict fluid responsiveness using carotid ΔVpeak. Until further research identifies key limiting factors, clinicians should use caution directing IV fluid resuscitation using carotid ΔVpeak.
Characterization of the electrical behavior of a discontinuous hybrid yarn textile made of recycled carbon and PA6 fibers during Joule heating
Authors: Reese Julian , Hoffmann Gerald , Fieres Johannes , Cherif Chokri
Published: June 2020

The Joule heating of carbon fiber-based textiles enables an energy- and cost-efficient processing of carbon fiber reinforced thermoplastic parts. This article introduces a new method to pass direct current into a dry, not pre-consolidated hybrid yarn textile based on recycled carbon fibers and polyamide 6 fibers. The aim is to melt polyamide fibers, subsequently impregnate carbon fibers, and finally consolidate the material to form a composite part in a single process step. To increase the reliability of this technology, the electrical properties and the behavior of the material during the heating process must be thoroughly investigated. It will be addressed how the material is characterized during the process and how the changing resistivity of the textile affects the current flow between the electrodes to generate intrinsic heat. Moreover, a method to determine the effective material resistivity by finite element simulation on the fiber scale based on a CT scan is presented. Thus, a validated material model with respect to the temperature development in the textile based on ρ = ρ (Τ) was established.
Nomenclature for Kidney Function and Disease: Executive Summary and Glossary From a Kidney Disease: Improving Global Outcomes (KDIGO) Consensus Conference
Authors: Levey Andrew S , Eckardt Kai-Uwe , Dorman Nijsje M , Christiansen Stacy L , Cheung Michael , Jadoul Michel , Winkelmayer Wolfgang C
Published: June 2020

This article is being published in Kidney International Reports and reprinted concurrently in several journals. The articles cover identical concepts and wording but vary in minor stylistic and spelling changes, detail, and length of manuscript, in keeping with each journal’s style. Any of these versions may be used in citing this article. Excerpts are adapted with permission of KDIGO and the International Society of Nephrology.
“Hybrid psychology agent”: Overcoming the about/for dichotomy from praxis
Authors: Macías-Gómez-Estern Beatriz
Published: June 2020

I draw on my experience in community development with “othered” groups to present the idea of the “hybrid psychology agent.” This, I contend, is a key figure in overcoming the dichotomies alleged by Indigenous psychologists and confronted by Held (2020). On the one hand, the concept is rooted in hands-on work in multicultural settings. It is also supported by Cultural-Historical research through projects such as Service Learning that connect higher education students with disenfranchised Roma children. On the other hand, the concept follows a critical theory framework where, as implied by Held, a paradigm shift in science is needed. The issue at point is not whether folk Indigenous knowledge should replace so-called objective knowledge, but how the latter should embrace the experience of a more diverse psychological object and subject, mainly through the participation of “othered” people as psychology scientists and practitioners.
Becoming as a possibility of opening the distribution of the research sensible
Authors: Mercieca Daniela , Mercieca Duncan P.
Published: June 2020

This commentary acknowledges Barbara Held’s (2020) idea that knowledge of, from, and for people can create epistemic violence. We look at this through the idea of binaries and how binaries distribute a particular sense in knowledge. We argue that the researcher’s engagement with uncertainty offers possibilities of becoming for the researcher, the researched, and the research process in a way that opens up such binaries and the distribution of the sensible.
Mistaking the subject of violence in scientific psychology
Authors: Olson Rex
Published: June 2020

Barbara Held (2020) claims that critical and Indigenous psychologists are right to point out how scientific psychology has contributed to findings that do undue harm to racial groups, but are wrong to suggest that, due to epistemological violence, scientific psychology cannot provide psychological truths that may inform progressive public policies. She rightly questions the relevance to violence of “for” and “about” findings in being linked to metaphors of “below” and “above” as discussed in Thomas Teo’s work, but then pivots to offer a violent corrective, asserting the importance of objectivity for capturing the situated subjectivity of individuals engaged in the oppressive practice of othering. Despite its promise for socially just consequences, Held offers a psychological science that remains in itself a subject of violence.
Generalizations, concepts, and pseudoconcepts: The subjective content of epistemic violence
Authors: Azeri Siyaves
Published: June 2020

Barbara Held’s article (2020) challenges the “for/about prepositional divide” (p. 349), which is presumed by critical and Indigenous psychologies, at two empirical and epistemological levels. I argue that Held’s critique can be further strengthened empirically, with reference to Lev Vygotsky’s analysis of the relation between spontaneous and scientific concepts, and epistemologically, with reference to Evald Ilyenkov’s treatment of concepts in contrast to mere notions.
Why mainstream research will not end scientific racism in psychology
Authors: Winston Andrew S.
Published: June 2020

Mainstream research on racial essentialization may be valuable in the fight against racism, as Held (2020) suggested. I argue that the production of scientific racism in the literature of psychology is unlikely to be affected by such research. Assertions by psychologists of Black people’s average inferiority in brain size, intelligence, and morality have persisted for over 100 years despite repeated, careful critiques. Recent presentations of these old and discredited claims have sidestepped the fundamental criticism that they rest on essentialized racial categories. The survival of scientific racism in mainstream psychology journals should be understood as a community project with its own Weltanschauung of “racial progress.”
For a knowledge with the other in psychological science
Authors: Gonzalez Ramiro , Silva Guimarães Danilo
Published: June 2020

In our comment on Held (2020) we attempt to deepen her criticism and reflection about epistemic violence while addressing the need for its elimination in psychological science. We acknowledge her argument about the prepositional divisions that emerge between two large groups of psychologies or psychologists (mainstream psychology vs. Indigenous and critical psychologies): from above and from below. In relation to these prepositional problems, we agree that the explanations derived from these divisions in terms of of, for, and about are confusing. However, we consider that Held’s reflections concerning the set of prepositions in the production of knowledge based on “of, from, and for the other” neglect another alternative that is “with the other.” According to this last point, we briefly present Bakhtin’s theoretical notion of co-authorship to argue that generally, epistemic violence is committed by not recognizing the voices of the participants involved. In addition, we use examples of our work with Indigenous communities in Brazil to show that generating knowledge together and with Indigenous peoples is a valid and necessary way to eliminate epistemic violence.
Shaping Mediterranean landscapes: The cultural impact of anthropogenic fires in Tyrrhenian southern Tuscany during the Iron and Middle Ages (800–450 BC / AD 650–1300)
Authors: Buonincontri Mauro Paolo , Pieruccini Pierluigi , Susini Davide , Lubritto Carmine , Ricci Paola , Rey Fabian , Tinner Willy , Colombaroli Daniele , Drescher-Schneider Ruth , Dallai Luisa , Marasco Lorenzo , Poggi Giulio , Bianchi Giovanna , Hodges Richard , Di Pasquale Gaetano
Published: June 2020

Charcoal analysis, applied in sediment facies analysis of the Pecora river palaeochannel (Tyrrhenian southern Tuscany, Italy), detected the occurrence of past fire events in two different fluvial landforms at 800–450 BC and again at AD 650–1300. Taking place in a central Mediterranean district adequately studied through palaeoenvironmental and archaeological research, the investigation determined land changes, time phases and socio-economic driving forces involved in dynamic processes of fire. The fire sequences had purely anthropogenic origins and were linked to forest opening and reduction by local communities. Introduced by the Etruscans, fires dated to 800–450 BC involved mainly the forest cover on the hilly slopes, ensuring agricultural exploitation. From AD 650, fires contributed to Medieval upstream reclamation and vegetation clearing of flat swamplands. From AD 850 to 1050, the use of fire spread over a wider area in the river valley, increasing arable lands. Between AD 1150 and 1300, fires belonged to a regional forest clearance phase. Medieval fire episodes had a paramount importance in shaping and determining the character of the Tuscan Mediterranean landscape. From AD 850, Medieval fire clearing influenced regional vegetation history contributing to the decline of the dominant deciduous Quercus woodland. Open habitats became the new form of a clearly detectable agricultural landscape from AD 950. The use of fire clearing and the resulting landscape changes in the Pecora river valley depended on the political strategies adopted by Medieval authorities and marked, in fact, the progression of a cultural landscape still characterizing central Tyrrhenian Italy.
Walking the Sustainability Talk: If Not Us, Who? If Not Now, When?
Authors: Kanashiro Patricia , Rands Gordon , Starik Mark
Published: June 2020

This essay centers on the personal sustainability behaviors of faculty as related to research, teaching, and service, as well as those behaviors that go far beyond these typical faculty responsibilities. We argue that faculty personal engagement with sustainability can lend credibility to this topic as faculty can set a good example for students, colleagues, and other stakeholders within their respective networks. We draw on the United Nations 17 Sustainable Development Goals to suggest several ideas that faculty could adopt as part of their sustainability plans. Moreover, we offer multiple recommendations as to how faculty might leverage these experiences in the classroom and beyond.
Comprehensive Analysis of a Long Noncoding RNA-Associated Competing Endogenous RNA Network in Wilms Tumor
Authors: Zhang Feng , Zeng Liping , Cai Qinming , Xu Zihao , Liu Ruida , Zhong Haicheng , Mukiibi Robert , Deng Libin , Tang Xiaoli , Xin Hongbo
Published: June 2020

Long noncoding RNA (lncRNA) plays crucial roles in various biological processes of different cancers, especially acting as a competing endogenous RNA (ceRNA). However, the role of lncRNA-mediated ceRNA in Wilms tumor (WT), which is the most common malignant kidney cancer in children, remains unknown. In present study, RNA sequence profiles and clinical data of 125 patients with WT consisting of 119 tumor and 6 normal tissues from Therapeutically Applicable Research To Generate Effective Treatments database were analyzed. A total of 1833 lncRNAs, 156 microRNAs (miRNAs), and 3443 messenger RNAs (mRNAs) were identified as differentially expressed (DE) using “DESeq2” package. The lncRNA-miRNA-mRNA ceRNA regulatory network involving 748 DElncRNAs, 33 DEmiRNAs, and 189 DEmRNAs was constructed based on miRcode, Targetscan, miRTarBase, and miRDB database. Gene Ontology term and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed that DEmRNAs were mainly enriched in cell proliferation-related processes and tumor-related pathways, respectively, and 13 hub genes were identified by a protein–protein interaction network. Survival analysis detected 48 lncRNAs, 7 miRNAs, and 16 mRNAs to have significant impact on the overall survival of patients with WT. Additionally, we found that 6 DElncRNAs with potential prognostic value were correlated with tumor stage ( DENND5B-AS1) and histologic classification ( TMPO-AS1, RP3-523K23.2, RP11-598F7.3, LAMP5-AS1, and AC013275.2) of patients with WT. Our research provides a great insight into understanding the molecular mechanism underlying occurrence and progression of WT, as well as the potential to develop targeted therapies and prognostic biomarkers.
Defining and Teaching Data Journalism: A Typology
Authors: Lewis Norman P.
Published: June 2020

A thematic evaluation of data journalism courses resulted in a typology that parses the field and offers guidance to educators. At the center is pattern detection, preceded by data acquisition and cleaning, and followed by data representation. The typology advances academic understanding by offering a precise conceptualization that distinguishes data journalism from peripheral technologies and identifies coding as a supportive skill. It also enables a fresh definition of data journalism as the primary reliance on numerical evidence as a journalistic tool in detecting patterns, or the visual representation of numerical evidence to enable audiences to discern patterns.
How foreign pressure affects mass mobilization in favor of authoritarian regimes
Authors: Hellmeier Sebastian
Published: June 2020

Authoritarian regimes are frequent targets of international pressure in the form of economic sanctions or threats thereof. Existing research shows that foreign interventions can carry several unintended consequences for politics and the economy in the targeted countries. One of the side effects of such interventions is boosting support for incumbent autocrats. Public demonstrations in support of embattled leaders are one aspect of this dynamic. This article investigates the link between foreign pressure and domestic mobilization in favor of ruling autocrats. It is argued that pressure simultaneously increases regime supporters’ willingness to participate in rallies and the regime’s demand to display and even overstate regime support. Foreign pressure facilitates mobilization as autocrats can fuel nationalist sentiments and frame foreign interventions as an attack on the nation as a whole. At the same time, rallies are a strategic tool to reduce political opportunities for the opposition and to signal resolve to the international community. Empirically, I conduct the first quantitative analysis that evidences the existence of a relationship between international pressure and mobilization in support of incumbent autocrats. Using monthly data on rally events in all authoritarian regimes between 2003 and 2015, I find that sanctions but also threats significantly increase pro-government mobilization. In addition, I show evidence for a moderating role of media freedom in the targeted state, highlighting the importance of how international events are portrayed in national news.
The Role of Ethnography as Ethical and Policy-Relevant Public Scholarship
Authors: Clemens Randall F. , Tierney William G.
Published: June 2020

Amid calls for increased public scholarship, ethnographers occupy precarious positions. They focus on studying underrepresented cultural groups within local contexts and connecting micro and macro levels to understand the impact of social, economic, and political forces. The methodology is particularly well-suited to engage multiple audiences, influence public dialogue, and inform policy issues. And yet, given the current emphasis on experimental and quasi-experimental methods, and the inability of ethnographic findings to generalize, policy makers question the utility of qualitative research. When scholars do translate research for broader audiences, recent examples of best-selling ethnographies demonstrate the increased scrutiny they encounter. The article, as a result, explores the basic characteristics of ethnography and public scholarship. The authors examine issues related to ethnography as ethical and policy-relevant public scholarship. They argue that ethnography serves a valuable role to promote deliberative democracy and social justice; however, to maximize potential and limit unintended consequences, researchers must establish standards and techniques to conduct rigorous and ethical research and identify methods to communicate the merit of such scholarship.
Effect of Chinese Herbal Compound LC09 on Patients With Capecitabine-Associated Hand-Foot Syndrome: A Randomized, Double-Blind, and Parallel-Controlled Trial
Authors: Yu Ran , Wu Xuefeng , Jia Liqun , Lou Yanni
Published: June 2020

Background: LC09 is composed with 5 kinds of traditional Chinese herbal medicines ( Astragalus membranaceus, flowers carthami, lithospermum, geranium wilfordii, and radix angelicae) which are used in China and developed over several thousand years. Aim: To assess the effectiveness and safety of herbal compound LC09 on patients with capecitabine-associated hand-foot syndrome (HFS). Materials and Methods: In this randomized, double-blind, and parallel-controlled study, 156 patients that diagnosed with HFS were randomly assigned to a treatment group (n = 78) or control group (n = 78). Patients were evaluated every week by the National Cancer Institute (NCI) grade and Numerical Rating Scale (NRS) pain scores. The Dermatology Life Quality Index (DLQI) scale and Instrumental Activity of Daily Living (IADL) scale were used to assess the quality of life before the treatment, and at 1 week and after the treatment of 2 cycles. Results: At the baseline, no significant differences were observed between the 2 groups. After treatment, significant differences in NCI grade and NRS pain scores were observed between the 2 groups ( P < .01). In addition, HFS effectiveness rate and pain alleviation rate were significantly higher in the treatment group compared with the control group ( P < .01). Furthermore, the chemotherapy completion rate between 2 groups was significantly different ( P = .002). In addition, no adverse reactions were observed in either LC09 or control group. Conclusion: LC09 can decrease NCI grade and significantly alleviate pain in HFS patients. Besides, it can also increase chemotherapy completion rate.
Annual changes in the prevalence of asthma may be related to air pollution in Fukuoka: 29 years of observation
Authors: Odajima Hiroshi , Kawano Toshiaki , Wakatsuki Masatoshi , Akaminea Yuko , Okabe Koki , Oki Tuyoshi , Matsuzaki Hiroshi , Murakami Yoko , Iwata Mihoko , Taba Naohiko , Motomura Chikako , Honjo Satoshi , Ninomiya Takahito
Published: June 2020

The relationship between the annual changes of the prevalence of bronchial asthma (BA) and that of concentrations of air pollutants has not been reported.

We studied the annual prevalence of BA, remission of BA, and wheeze in children at the same five elementary schools in Fukuoka city, Japan, in October to November from 1988 to 2016 by the same methods using the same questionnaire.

Annual changes in the prevalence of asthma among boys were related to changes in the air concentrations of NO (r=0.708), NO2(r=0.665) suspended particulate matter (SPM) (r=0.803), and smoking rate (r=0.741), but there were no such relationships among girls. Annual changes in the prevalence of wheeze were related to changes of NO, NO2, SPM, and smoking rate among boys and girls (NO: r=0.650, 0.660; NO2: r=0.556, 0.490; SPM: r=0.582, 0.518; smoking rate: r=0.656, 0.593, respectively) (all of the above are significant with p<0.05). There was no relationship between remission of BA and any of the pollutants.

Annual changes in the prevalence of boys' BA and boys' and girls' wheeze among first-grade children (age 6 or 7 years) in Fukuoka were correlated with changes in the concentration of air pollutants (SPM, NO, NO2or smoking rate).

Recent decrease of asthma prevalence in this area might be related to the decreasing tendency of air pollutant concentration. The causal relationship between the two will need to be verified in the future
NASQAR: a web-based platform for high-throughput sequencing data analysis and visualization
Authors: Yousif Ayman , Drou Nizar , Rowe Jillian , Khalfan Mohammed , Gunsalus Kristin C.
Published: June 2020

Background

As high-throughput sequencing applications continue to evolve, the rapid growth in quantity and variety of sequence-based data calls for the development of new software libraries and tools for data analysis and visualization. Often, effective use of these tools requires computational skills beyond those of many researchers. To ease this computational barrier, we have created a dynamic web-based platform, NASQAR (Nucleic Acid SeQuence Analysis Resource).

Results

NASQAR offers a collection of custom and publicly available open-source web applications that make extensive use of a variety of R packages to provide interactive data analysis and visualization. The platform is publicly accessible at http://nasqar.abudhabi.nyu.edu/. Open-source code is on GitHub at https://github.com/nasqar/NASQAR, and the system is also available as a Docker image at https://hub.docker.com/r/aymanm/nasqarall. NASQAR is a collaboration between the core bioinformatics teams of the NYU Abu Dhabi and NYU New York Centers for Genomics and Systems Biology.

Conclusions

NASQAR empowers non-programming experts with a versatile and intuitive toolbox to easily and efficiently explore, analyze, and visualize their Transcriptomics data interactively. Popular tools for a variety of applications are currently available, including Transcriptome Data Preprocessing, RNA-seq Analysis (including Single-cell RNA-seq), Metagenomics, and Gene Enrichment.
Robust principal component analysis for accurate outlier sample detection in RNA-Seq data
Authors: Chen Xiaoying , Zhang Bo , Wang Ting , Bonni Azad , Zhao Guoyan
Published: June 2020

Background

High throughput RNA sequencing is a powerful approach to study gene expression. Due to the complex multiple-steps protocols in data acquisition, extreme deviation of a sample from samples of the same treatment group may occur due to technical variation or true biological differences. The high-dimensionality of the data with few biological replicates make it challenging to accurately detect those samples, and this issue is not well studied in the literature currently. Robust statistics is a family of theories and techniques aim to detect the outliers by first fitting the majority of the data and then flagging data points that deviate from it. Robust statistics have been widely used in multivariate data analysis for outlier detection in chemometrics and engineering. Here we apply robust statistics on RNA-seq data analysis.

Results

We report the use of two robust principal component analysis (rPCA) methods, PcaHubert and PcaGrid, to detect outlier samples in multiple simulated and real biological RNA-seq data sets with positive control outlier samples. PcaGrid achieved 100% sensitivity and 100% specificity in all the tests using positive control outliers with varying degrees of divergence. We applied rPCA methods and classical principal component analysis (cPCA) on an RNA-Seq data set profiling gene expression of the external granule layer in the cerebellum of control and conditional SnoN knockout mice. Both rPCA methods detected the same two outlier samples but cPCA failed to detect any. We performed differentially expressed gene detection before and after outlier removal as well as with and without batch effect modeling. We validated gene expression changes using quantitative reverse transcription PCR and used the result as reference to compare the performance of eight different data analysis strategies. Removing outliers without batch effect modeling performed the best in term of detecting biologically relevant differentially expressed genes.

Conclusions

rPCA implemented in the PcaGrid function is an accurate and objective method to detect outlier samples. It is well suited for high-dimensional data with small sample sizes like RNA-seq data. Outlier removal can significantly improve the performance of differential gene detection and downstream functional analysis.
Genome-wide identification of the class III POD gene family and their expression profiling in grapevine (Vitis vinifera L)
Authors: Xiao Huilin , Wang Chaoping , Khan Nadeem , Chen Mengxia , Fu Weihong , Guan Le , Leng Xiangpeng
Published: June 2020

Background

The class III peroxidases (PODs) are involved in a broad range of physiological activities, such as the formation of lignin, cell wall components, defense against pathogenicity or herbivore, and abiotic stress tolerance. The POD family members have been well-studied and characterized by bioinformatics analysis in several plant species, but no previous genome-wide analysis has been carried out of this gene family in grapevine to date.

Results

We comprehensively identified 47 PODs in the grapevine genome and are further classified into 7 subgroups based on their phylogenetic analysis. Results of motif composition and gene structure organization analysis revealed that PODs in the same subgroup shared similar conjunction while the protein sequences were highly conserved. Intriguingly, the integrated analysis of chromosomal mapping and gene collinearity analysis proposed that both dispersed and tandem duplication events contributed to the expansion of PODs in grapevine. Also, the gene duplication analysis suggested that most of the genes (20) were dispersed followed by (15) tandem, (9) segmental or whole-genome duplication, and (3) proximal, respectively. The evolutionary analysis of PODs, such as Ka/Ks ratio of the 15 duplicated gene pairs were less than 1.00, indicated that most of the gene pairs exhibiting purifying selection and 7 pairs underwent positive selection with value greater than 1.00. The Gene Ontology Enrichment (GO), Kyoto Encyclopedia of Genes Genomics (KEGG) analysis, and cis-elements prediction also revealed the positive functions of PODs in plant growth and developmental activities, and response to stress stimuli. Further, based on the publically available RNA-sequence data, the expression patterns of PODs in tissue-specific response during several developmental stages revealed diverged expression patterns. Subsequently, 30 genes were selected for RT-PCR validation in response to (NaCl, drought, and ABA), which showed their critical role in grapevine.

Conclusions

In conclusion, we predict that these results will lead to novel insights regarding genetic improvement of grapevine.
Xylitol and erythritol inhibit real-time biofilm formation of Streptococcus mutans
Authors: Loimaranta Vuokko , Mazurel Danuta , Deng Dongmei , Söderling Eva
Published: June 2020

Background

Regular consumption of xylitol decreases the number of cariogenic streptococci in dental plaque. In vitro biofilm models to study the mechanism of xylitol action have been set-up, but the obtained results are contradictory. Biofilm growth is a dynamic process with time-specific characteristics that may remain undetected in conventional end-point biofilm tests. In this study we used an impedance spectroscopy instrument, xCELLigence Real Time Cell Analyzer (RTCA), that allows label-free, non-invasive real-time monitoring of biofilm formation, to explore effects of xylitol on biofilm formation by Streptococcus mutans. Based on the obtained information of biofilm dynamics, we assessed the number of viable bacteria, the polysaccharide content, and the expression levels of selected genes involved in glucan-mediated biofilm formation in different biofilm stages. Xylitol inhibition was compared with that of erythritol; another polyol suggested to have a positive impact on oral health.

Results

Our results showed that real-time monitoring provided new information of polyol-induced changes in S. mutans biofilm formation dynamics. The inhibitory effect of polyols was more pronounced in the early stages of biofilm formation but affected also the measured total amount of formed biofilm. Effects seen in the real-time biofilm assay were only partially explained by changes in CFU values and polysaccharide amounts in the biofilms. Both xylitol and erythritol inhibited real-time biofilm formation by all the nine tested S. mutans strains. Sensitivity of the strains to inhibition varied: some were more sensitive to xylitol and some to erythritol. Xylitol also modified the expression levels of gbpB, gtfB, gtfC and gtfD genes that are important in polysaccharide-mediated adherence of S. mutans.

Conclusion

The erythritol- and xylitol- induced inhibition of biofilm formation was only partly explained by decrease in the number of viable S. mutans cells or the amount of polysaccharides in the biofilm matrix, suggesting that in addition to reduced proliferation also the matrix composition and thereby the surface attachment quality of biofilm matrix may be altered by the polyols.
Genome-wide identification and integrated analysis of lncRNAs in rice backcross introgression lines (BC2F12)
Authors: Li Mengdi , Cao Aqin , Wang Ruihua , Li Zeyu , Li Shaoqing , Wang Jianbo
Published: June 2020

Background

Distant hybridization is an important way to create interspecific genetic variation and breed new varieties in rice. A lot of backcross introgression lines (BILs) had been constructed for the scientific issues in rice. However, studies on the critical regulatory factor lncRNA in cultivated rice, wild rice and their BIL progenies were poorly reported.

Results

Here, high-throughput RNA sequencing technology was used to explore the functional characteristics and differences of lncRNAs in O. sativa, O. longistaminata and their three BC2F12 progenies. A total of 1254 lncRNAs were screened out, and the number of differentially expressed lncRNAs between progenies and O. sativa were significantly less than that between progenies and O. longistaminata. Some lncRNAs regulated more than one mRNA, and 89.5% of lncRNAs regulated the expression of target genes through cis-acting. A total of 78 lncRNAs and 271 mRNAs were targeted by 280 miRNAs, and 22 lncRNAs were predicted to be the precursor of 20 microRNAs. Some miRNAs were found to target their own potential precursor lncRNAs. Over 50% of lncRNAs showed parental expression level dominance (ELD) in all three progenies, and most lncRNAs showed ELD-O. sativa rather than ELD-O. longistaminata. Further analysis showed that lncRNAs might regulate the expression of plant hormone-related genes and the adaptability of O. sativa, O. longistaminata and their progenies.

Conclusions

Taken together, the above results provided valuable clues for elucidating the functional features and expression differences of lncRNAs between O. sativa, O. longistaminata and their BIL progenies, and expanded our understanding about the biological functions of lncRNAs in rice.
Evolution of left ventricular function among subjects with ST-elevation myocardial infarction after percutaneous coronary intervention
Authors: Pahlm Ulrika , Ostenfeld Ellen , Seemann Felicia , Engblom Henrik , Erlinge David , Heiberg Einar , Arheden Håkan , Carlsson Marcus
Published: June 2020

Background

Atrioventricular plane displacement (AVPD) reflects longitudinal left ventricular (LV) systolic function, and wall thickening (WT) regional radial LV function. The temporal evolution of these measures after STEMI with CMR has not been evaluated. We aimed to investigate how AVPD and WT are affected globally and regionally from the sub-acute to the chronic phase after ST-elevation myocardial infarction (STEMI).

Methods

Healthy volunteers without cardiovascular disease and medication (controls, n = 20) and patients from the CHILL-MI study (NCT01379261) prospectively underwent magnetic resonance imaging (MRI) 2–6 days and 6 months after STEMI (n = 77). CHILL-MI randomized STEMI-patients to cooling therapy initiated before reperfusion or standard of care. AVPD was measured at six points in three long axis cine images and wall thickening in short axis cine images. Infarction was quantified using late gadolinium enhancement (LGE) and used to define infarct and remote segments.

Results

There were no difference in AVPD either at acute or chronic phase (p = 0.90 and p = 0.40) or WT (p = 0.85 and p = 0.99) between patients randomized to cooling therapy and standard of care. Therefore, the results are presented for the pooled cohort. Global AVPD was decreased in both the sub-acute (12 ± 2 mm, p < 0.001) and the chronic phase (13 ± 2 mm, p < 0.001) compared to controls (15 ± 2 mm) with a partial recovery of AVPD (p < 0.001) in the chronic phase. Patients with left anterior descending (LAD) and right coronary artery (RCA) infarcts had decreased AVPD in the chronic phase in both infarcted and remote segments. Mean WT was decreased in patients with LAD infarction both in the sub-acute and the chronic phase in both infarcted and remote segments. The decrease in WT in patients with RCA and left circumflex (LCx) infarcts was more affected in the infarcted segments, especially in the chronic phase.

Conclusion

AVPD was a global rather than regional marker of cardiac function in this STEMI study and this may explain the prognostic importance of local measurements of mitral annular plane systolic excursion (MAPSE). The decrease in WT in remote myocardium even in the chronic phase needs to be taken into consideration when combining functional measurements with infarct quantification for diagnosis of post-ischemic stunning and hibernation.
Promoting routine syphilis screening among men who have sex with men in China: study protocol for a randomised controlled trial of syphilis self-testing and lottery incentive
Authors: Cheng Weibin , Wang Cheng , Tang Weiming , Ong Jason J. , Fu Hongyun , Marks Michael , Smith M. Kumi , Li Changchang , Nie Juan , Zhao Peizhen , Zheng Heping , Yang Bin , Tucker Joseph D.
Published: June 2020

Background

Men who have sex with men (MSM) bear a high burden of syphilis infection. Expanding syphilis testing to improve timely diagnosis and treatment is critical to improve syphilis control. However, syphilis testing rates remain low among MSM, particularly in low- and middle-income countries. We describe the protocol for a randomised controlled trial (RCT) to assess whether provision of syphilis self-testing services can increase the uptake of syphilis testing among MSM in China.

Methods

Four hundred forty-four high-risk MSM will be recruited online and randomized in a 1:1:1 ratio to (1) standard syphilis self-testing arm; (2) a self-testing arm program enhanced with crowdsourcing and a lottery-based incentive, and (3) a standard of care (control). Self-testing services include a free syphilis self-test kit through the mail at monthly intervals. Participants in the lottery incentive arm will additionally receive health promotion materials generated from an open crowdsourcing contest and be given a lottery draw with a 10% chance to win 100 RMB (approximately 15 US Dollars) upon confirmed completion of syphilis testing. Syphilis self-test kits have step-by-step instructions and an instructional video. This is a non-blinded, open-label, parallel RCT. Participants in each arm will be followed-up at three and 6 months through WeChat (a social media app like Facebook messenger). Confirmation of syphilis self-test use will be determined by requiring participants to submit a photo of the used test kit to study staff via secure data messaging. Both self-testing and facility-based testing will be ascertained by sending a secure photographic image of the completed kit through an existing digital platform. The primary outcome is the proportion of participants who tested for syphilis in the past 3 months.

Discussion

Findings from this study will provide much needed insight on the impact of syphilis self-testing on promoting routine syphilis screening among MSM. The findings will also contribute to our understanding of the safety, effectiveness and acceptability of syphilis self-testing. These findings will have important implications for self-testing policy, both in China and internationally.

Trial registration

ChiCTR1900022409 (10 April, 2019).
An adult co-presented with varicella and herpes zoster caused by varicella zoster virus genotype J, China: a case report
Authors: Xie Guangcheng , Wei Qiongling , Guo Wenping , Li Dan , Sun Pingping , Wang Jiangli , Liu Houguang
Published: June 2020

Background

Varicella zoster virus (VZV) causes varicella primarily in childhood, and some rare adults also report varicella. Herpes zoster mainly occurs in adults by endogenous reactivation of latent VZV. Until now, varicella and herpes zoster have seldom been reported simultaneously in one patient. Here, we report a rare case co-presenting with varicella and herpes zoster in a Chinese adult.

Case presentation

A 44-year-old Chinese man suffered papules and vesicles with pain on the left ear. Five days after onset, he was admitted to the Department of Dermatology of The Third Hospital of Xiamen. Physical examination revealed that small vesicles surrounded by erythema had developed on his trunk, back and neck, and unilateral papules and vesicles in ribbons had also developed on the left ear. This patient was excluded from human immunodeficiency virus and Treponema pallidum infections by ELISA antibody tests. Laboratory tests revealed that the ratio of eosinophils (0.1%) and eosinophil count (0.0 × 109/L) were significantly downregulated. Treatment with valacyclovir, ebastine, mecobalamine, pregabalin and calamine lotion for 5 days was effective therapy for varicella and herpes zoster. Polymerase chain reaction for vesicular fluids from varicella and herpes zoster was positive for VZV, and further phylogenetic analysis and single nucleotide polymorphism variations confirmed that the VZV genotype was type J (clade 2).

Conclusions

This rare case highlights awareness of varicella and herpes zoster caused by VZV infection in adults. Our report provides novel insight into the rare clinical presentation of VZV genotype J.
Role of TSP-1 as prognostic marker in various cancers: a systematic review and meta-analysis
Authors: Sun Shengjie , Dong Huiyu , Yan Tao , Li Junchen , Liu Bianjiang , Shao Pengfei , Li Jie , Liang Chao
Published: June 2020

Background

Published studies present conflicting data regarding the impact of Thrombospondin-1 (TSP-1) expression on prognosis of various cancers. We performed this meta-analysis to illustrate the preliminary predictive value of TSP-1.

Methods

Twenty-four studies with a total of 2379 patients were included. A comprehensive literature search was performed by using PubMed, Cochrane Library, Web of Science, Embase, and hand searches were also conducted of relevant bibliographies. Pooled hazard ratios (HRs) with 95% confidence intervals (CIs) for patient survival and disease recurrence were initially identified to explore relationships between TSP-1 expression and patient prognosis.

Results

A total of 24 eligible studies were included in this meta-analysis. Our results showed that high level of TSP-1 was correlated significantly with poor overall survival (OS) (HR = 1.40, 95% CI: 1.17 ~ 1.68; P<0.001). However, high TSP-1 expression predicted no significant impact on progression-free survival (PFS)/ metastasis-free survival (MFS) (HR = 1.35, 95%CI: 0.87–2.10; P = 0.176) and disease-free survival (DFS)/ recurrence-free survival (RFS) (HR = 1.40, 95%CI: 0.77–2.53; P = 0.271). In addition, we performed subgroup analyses which showed that high TSP-1 expression predicted poor prognosis in breast cancer and gynecological cancer. Additionally, the relatively small number of studies on PFS/MFS and DFS/RFS is a limitation. The data extracted through Kaplan-Meier curves may not be accurate. Moreover, only English articles were included in this article, which may lead to deviations in the results.

Conclusions

Our findings indicated high TSP-1 expression may act as a promising biomarker of poor prognosis in cancers, especially in breast cancer and gynecological cancer.