nils-herrmann/clean_scirepeval huggingface dataset:
A contaminant free assessment of Endogenous Retroviral RNA in human plasma
Venue: Scientific reports

Endogenous retroviruses (ERVs) comprise 6 8% of the human genome. HERVs are silenced in most normal tissues, up regulated in stem cells and in placenta but also in cancer and HIV 1 infection. Crucially, there are conflicting reports on detecting HERV RNA in non cellular clinical samples such as plasma that suggest the study of HERV RNA can be daunting. Indeed, we find that the use of real time PCR in a quality assured clinical laboratory setting can be sensitive to low level proviral contamination. We developed a mathematical model for low level contamination that allowed us to design a laboratory protocol and standard operating procedures for robust measurement of HERV RNA. We focus on one family, HERV K HML 2 (HK2) that has been most recently active even though they invaded our ancestral genomes almost 30 millions ago. We extensively validated our experimental design on a model cell culture system showing high sensitivity and specificity, totally eliminating the proviral contamination. We then tested 236 plasma samples from patients infected with HIV 1, HCV or HBV and found them to be negative. The study of HERV RNA for human translational studies should be performed with extensively validated protocols and standard operating procedures to control the widespread low level human DNA contamination.
Identifying Stable Reference Genes for qRT PCR Normalisation in Gene Expression Studies of Narrow Leafed Lupin (Lupinus angustifolius L.
Venue: PloS one

Transcription PCR (qRT PCR) is currently one of the most popular, high throughput and sensitive technologies available for quantifying gene expression. Its accurate application depends heavily upon normalisation of gene of interest data with reference genes that are uniformly expressed under experimental conditions. The aim of this study was to provide the first validation of reference genes for Lupinus angustifolius (narrow leafed lupin, a significant grain legume crop) using a selection of seven genes previously trialed as reference genes for the model legume, Medicago truncatula. In a preliminary evaluation, the seven candidate reference genes were assessed on the basis of primer specificity for their respective targeted region, PCR amplification efficiency, and ability to discriminate between cDNA and gDNA. Following this assessment, expression of the three most promising candidates [Ubiquitin C (UBC) Helicase (HEL) and Polypyrimidine tract binding protein (PTB) was evaluated using the NormFinder and RefFinder statistical algorithms in two narrow leafed lupin lines, both with and without vernalisation treatment, and across seven organ types (cotyledons, stem, leaves, shoot apical meristem, flowers, pods and roots) encompassing three developmental stages. UBC was consistently identified as the most stable candidate and has sufficiently uniform expression that it may be used as a sole reference gene under the experimental conditions tested here. However, as organ type and developmental stage were associated with greater variability in relative expression, it is recommended using UBC and HEL as a pair to achieve optimal normalisation. These results highlight the importance of rigorously assessing candidate reference genes for each species across a diverse range of organs and developmental stages. With emerging technologies, such as RNAseq, and the completion of valuable transcriptome data sets, it is possible that other potentially more suitable reference genes will be identified for this species in future.
Behavioral and neural inhibitory control moderates the effects of reward sensitivity on adolescent substance use
Venue: Neuropsychologia

The developmental period of adolescence is characterized by increasing incidence of health risk behaviors, including experimenting with drugs and alcohol. We examined how inhibitory control interacts with reward and punishment sensitivity to predict substance use severity and age of onset among early adolescents. The sample was comprised of 157 early adolescents (13 14 years of age, 52% male) Composite scores for behavioral activation system (BAS) behavioral inhibition system (BIS) and substance use severity and onset were computed using adolescents' questionnaire data, and inhibitory control was assessed based on adolescents' behavioral performance and brain imaging during the Multiple Source Interference Task (MSIT) Structural equation modeling analyses indicated that for both behavioral performance and neural activity indicators of inhibitory control, high levels of BAS predicted earlier onset of substance use among adolescents with low inhibitory control but not among adolescents with high inhibitory control. BIS was not related to substance use severity and onset among adolescents. The results support the theoretically hypothesized moderating role of inhibitory control and its associated frontal cortex functioning, and offer new insights into the identification of adolescents with neurobehavioral vulnerabilities to developing maladaptive substance use behaviors.
Neural Correlates of Reward Processing in Depressed and Healthy Preschool Age Children.
Venue: Journal of the American Academy of Child and Adolescent Psychiatry

Adults and adolescents with major depressive disorder (MDD) show a blunted neural response to rewards. Depression has been validated in children as young as age 3; however, it remains unclear whether blunted response to reward is also a core feature of preschool onset depression. If so, this would provide further validation for the continuity of the neural correlates of depression across the life span and would identify a potential target for treatment in young children.  Fifty three 4 to 7 year old children with depression and 25 psychiatrically healthy 4 to 7 year old children completed a simple guessing task in which points could be won or lost on each trial while event related potentials (ERPs) were recorded. Psychiatric diagnosis was established using a preschool version of the Kiddie Schedule for Affective Disorders and Depression.  Young children with depression showed a reduced differentiation between response to gains and losses, and this finding was driven by a blunted response to reward (i.e. the reward positivity [RewP] These findings held even when controlling for co occurring attention deficit/hyperactivity disorder, oppositional defiant disorder, and generalized anxiety disorder. The RewP did not vary as a function of depression severity within the group with depression.  Similar to adults and adolescents with depression, preschoolers with depression display reductions in responsivity to rewards as indexed by the RewP. These findings provide further evidence for continuity in the neural mechanisms associated with depression across the lifespan, and point to altered reward sensitivity as an early emerging potential target for intervention in preschool onset depression.
Leading changes: Why transformation explanations fail

Professor John Kotter (1995) claimed in Leading change: Why transformation efforts fail to have identified eight leadership errors which resulted in transformation failures. He followed this up in 1996 with his best selling book Leading Change, prescribing an eight step model for leading transformations encouraging change leaders to create a sense of urgency, build powerful guiding coalitions and develop visions. Kotter openly acknowledged that he neither drew examples nor major ideas from any published source, except his own writing. In the 2012 edition of his book, which included a new preface, Kotter claimed that his book was now more relevant than when it was first published. As leaders knowingly or unknowingly still use Kotter's steps and academics still cite this book, this paper critically assesses Kotter's claim about the relevance of Leading Change. Three conclusions are drawn; Leading Change remains an enduring landmark leadership study, but Leading Change is stuck in the past and paradoxically today discourages change.
High power, high efficiency diode pumped Raman fiber laser

We demonstrate a high power high efficiency Raman fiber laser pumped directly by a laser diode module at 976 nm. 80 Watts of CW power were obtained at a wavelength of 1020 nm with an optical to optical efficiency of 53% When working quasi CW, at a duty cycle of 30% 85 W of peak power was produced with an efficiency of 60% A commercial graded index (GRIN) core fiber acts as the Raman fiber in a power oscillator configuration, which includes spectral selection to prevent generation of the 2nd Stokes. In addition, significant brightness enhancement of the pump beam is attained due to the Raman gain distribution profile in the GRIN fiber. To the best of our knowledge, this is the highest power Raman fiber laser directly pumped by laser diodes, which also exhibits a record efficiency for such a laser. In addition, it is the highest power Raman fiber laser (regardless of pumping source) demonstrated based on a GRIN fiber.
DEVELOPMENT OF ENTREPRENEURSHIP IN RURAL AREAS OF NORTH EASTERN POLAND

Rural areas are characterised by a considerable diversification of their natural, demographic, historical, spatial and socio economic conditions. These conditions caused disproportions in the density of entities of national economy in the rural areas of North eastern Poland. The main aim of article is the presentation of both the growth of non agricultural activity in the rural areas of the Warminsko Mazurskie and Podlaskie Voivodships in 2014 and the dynamics of changes in relation to 2004. Upon the analyses it was concluded that the density level of entities of national economy and the dynamics of change in entities of national economy featured by large disproportions across rural communes. The biggest changes characterised mainly the rural communes lying near the largest towns in the region: Olsztyn, Elblag and Bialystok. The highest dynamics of increase among the rural communes of North eastern Poland were mainly recorded in the Warminsko Mazurskie voivodship; whereas the most noteworthy decrease in the number of entities of national economy was in the rural communes situated along the Eastern border of the Podlaskie voivodship, which is the reflection of their poor economic activity. For a more profound analysis of the spatial distribution of the growth of entrepreneurship, the study results were juxtaposed to the existing demographic potential of the rural areas in North eastern Poland. The results of the study revealed the following tendency: the higher the demographic potential of rural communes was, the more favourable indicators of growth of entrepreneurship appeared. It proves that demographic potential of workforce has a considerable impact on the development of the rural areas of North eastern Poland.
Provoking identities: entrepreneurship and emerging identity positions in rural development

This article discusses entrepreneurship in a depleted community in transition. The purpose is to develop knowledge about how discourses are used in the positioning of identity in regional development. The concept positioning illustrates how identities are provoked, challenged, negotiated and moved into identity positions that break away from the idea of imitating successful and wealthy regions; instead, locality, place and history emerge as important resources from where local actors obtain agency and recognize new opportunities. Ethnographic data of a single case were collected over a six year period between 2005 and 2010. The longitudinal nature of the study made it possible to incorporate how local stakeholders took on new identity positions, while handling their inspiration as well as their frustration. Results show how rural change was conditioned by discourses and how entrepreneurship challenged and reframed dominating structures through interaction between entrepreneurship and community. Four discourses, expressed as dichotomies available to people in this depleted community, illustrate the interactive process of positioning: change vs. traditions, rational vs. irrational, spectacular vs. mundane and individual vs. collective. The results support research emphasizing perspectives that acknowledge interaction between entrepreneurship and context as well as discursive aspects of regional development.
The Contribution of Women Entrepreneurship in Family Socio Economic Development in Rural Areas, Rwanda

The study on women entrepreneurs and family social economic development aimed at assessing whether there was a positive correlation between women in entrepreneurship and their family socioeconomic development. This research targeted women members of a handcraft making cooperative in Muhanga District and Women's Opportunity Center in Eastern province (Rwanda) with a connection to Gahaya Links Company. The study used stratified and simple random sampling techniques. The data entry and management was undertaken using the Statistical Package for Social Sciences (SPSS, 16 version) where both descriptive and correlational statistics were used in the study. The study revealed that women entrepreneurs affect social economic development at the rate of 78.3% This research concluded that there was a positive and strong relationship between women entrepreneurship and family socio economic development. The research recommends that women entrepreneurs must minimize all loss caused by lack of training and low level of education that leads to lack of managerial skills in order to achieve high level of performance in their routine activities of business.
Biodegradation of diesel fuel hydrocarbons by mangrove fungi from Red Sea Coast of Saudi Arabia
Venue: Saudi journal of biological sciences

Mangrove sediments were collected from major mangrove stands on the Red Sea Coast of Saudi Arabia. Forty five isolates belonging to 12 genera were purified and five isolates as well as their consortium were found to be able to grow in association with petroleum oil as sole carbon source under in vitro conditions. The isolated strains were identified based on internal transcribed spacer (ITS) rDNA sequence analysis. The fungal strains with the greatest potentiality to degrade diesel oil, without developing antagonistic activity, were identified as Alternaria alternata, Aspergillus terreus, Cladosporium sphaerospermum, Eupenicillium hirayamae and Paecilomyces variotii. As compared to the controls, these fungi accumulated significantly higher biomass, produced extracellular enzymes and liberated larger volumes of CO2. These observations with GC MS data confirm that these isolates displayed rapid diesel oil bioremoval and when used together as a consortium, there was no antagonistic activity.
Spectrum and Frequency of the GJB2 Gene Pathogenic Variants in a Large Cohort of Patients with Hearing Impairment Living in a Subarctic Region of Russia (the Sakha Republic)
Venue: PloS one

Pathogenic variants in the GJB2 gene, encoding connexin 26, are known to be a major cause of hearing impairment (HI) More than 300 allelic variants have been identified in the GJB2 gene. Spectrum and allelic frequencies of the GJB2 gene vary significantly among different ethnic groups worldwide. Until now, the spectrum and frequency of the pathogenic variants in exon 1, exon 2 and the flanking intronic regions of the GJB2 gene have not been described thoroughly in the Sakha Republic (Yakutia) which is located in a subarctic region in Russia. The complete sequencing of the non coding and coding regions of the GJB2 gene was performed in 393 patients with HI (Yakuts 296, Russians 51, mixed and other ethnicities 46) and in 187 normal hearing individuals of Yakut (n 107) and Russian (n 80) populations. In the total sample (n 580) we revealed 12 allelic variants of the GJB2 gene, 8 of which were recessive pathogenic variants. Ten genotypes with biallelic recessive pathogenic variants in the GJB2 gene (in a homozygous or a compound heterozygous state) were found in 192 out of 393 patients (48.85% We found that the most frequent GJB2 pathogenic variant in the Yakut patients was c. 23+1G>A (51.82% and that the second most frequent was c.109G>A (2.37% followed by c.35delG (1.64% Pathogenic variants s.35delG (22.34% c. 23+1G>A (5.31% and c.313_326del14 (2.12% were found to be the most frequent among the Russian patients. The carrier frequencies of the c. 23+1G>A and s.109G>A pathogenic variants in the Yakut control group were 10.20% and 2.80% respectively. The carrier frequencies of s.35delG and c.101T>C were identical (2.5% in the Russian control group. We found that the contribution of the GJB2 gene pathogenic variants in HI in the population of the Sakha Republic (48.85% was the highest among all of the previously studied regions of Asia. We suggest that extensive accumulation of the c. 23+1G>A pathogenic variant in the indigenous Yakut population (92.20% of all mutant chromosomes in patients) and an extremely high (10.20% carrier frequency in the control group may indicate a possible selective advantage for the c. 23+1G>A carriers living in subarctic climate.
Update of the spectrum of GJB2 gene mutations in 152 Moroccan families with autosomal recessive nonsyndromic hearing loss.
Venue: European journal of medical genetics

Deafness is one of the most common genetic diseases in humans and is subject to important genetic heterogeneity. The most common cause of non syndromic hearing loss (NSHL) is mutations in the GJB2 gene. This study aims to update and evaluate the spectrum of GJB2 allele variants in 152 Moroccan multiplex families with non syndromic hearing loss. Seven different mutations were detected: c.35delG, p.V37I, p.E47X, p.G200R, p.Del120E, p.R75Q, the last three mutations were described for the first time in Moroccan deaf patients, in addition to a novel nonsense mutation, the c.385G>T which is not referenced in any database. Sixty six families (43.42% have mutations in the coding region of GJB2, while the homozygous c.35delG mutation still to date the most represented 51/152 (33.55% The analysis of the geographical distribution of mutations located in GJB2 gene showed more allelic heterogeneity in the north and center compared to the south of Morocco. Our results showed that the GJB2 gene is a major contributor to non syndromic hearing loss in Morocco. Thus, this report of the GJB2 mutations spectrum all over Morocco has an important implication for establishing a suitable molecular diagnosis.
Can We Predict the Presence and Severity of Intra Abdominal Adhesions before Cesarean Delivery
Venue: Gynecologic and Obstetric Investigation

The study aimed to investigate whether we can predict the presence and severity of intra abdominal adhesions before cesarean delivery using patient history, symptoms, and abdominal skin scar characteristics.  In this prospective study, 143 pregnant women with history of previous abdominal surgery were included and they delivered by cesarean. Preoperative abdominal scar characteristics and symptoms as well as intraoperative abdominal adhesions were evaluated using the Manchester Scar Scale, a symptomatology questionnaire and the More Comprehensive Adhesion Scoring Method, respectively.  Patients with adhesions (n 98) and without adhesions (n 45) had similar baseline characteristics. In the adhesion group, abdominal scar scoring parameters were significantly increased. However, there was no significant correlation among total scar score, adhesion score, and symptom score.  Despite the availability of many proposed methods, accurate prediction of the severity of surgery related adhesions is beyond our current abilities. Therefore, as healthcare providers, obstetricians should avoid unnecessary use of the cesarean approach. This approach is more effective, beneficial, realizable, and reasonable than the prediction of surgery related adhesions.
Comparison of the effects of Mitomycin C and sodium hyaluronate/carboxymethylcellulose [NH/CMC] (Seprafilm) on abdominal adhesions
Venue: SpringerPlus

IntroductionIntra abdominal adhesions (IA) may occur after abdominal surgery and also may lead to complications such as infertility, intestinal obstruction and chronic pain. The aim of this study was to compare the effects of Mitomycin C (MM C) and sodium hyaluronate/carboxymethylcellulose [NH/CMC] on abdominal adhesions in a cecal abrasion model and to investigate the toxicity of MM C on complete blood count (CBC) and bone marrow analyses.MethodsThe study comprised forty rats in four groups (Control, Sham, Cecal abrasion MM C, and Cecal abrasion NH/CMC) On postoperative day 21, all rats except for the control (CBC femur resection) group, were sacrificed. Macroscopical and histopathological evaluations of abdominal adhesions were performed. In order to elucidate the side effects of MM C; CBC analyses and femur resections were performed to examine bone marrow cellularity.ResultsCBC analyses and bone marrow cellularity assessment revealed no statistically significant differences between MM C, NH/CMC and control groups. No significant differences in inflammation scores were observed between the groups. The MM C group had significantly lower fibrosis scores compared to the NH/CMC and sham groups. Although the adhesion scores were lower in the MM C group, the differences were not statistically significant.ConclusionDespite its potential for systemic toxicity, MM C may show some anti fibrosis and anti adhesive effects. MM C is a promising agent for the prevention of IAs, and as such, further trials are warranted to study efficacy.
Fatigue Damage Spectrum calculation in a Mission Synthesis procedure for Sine on Random excitations

In many real life environments, certain mechanical and electronic components may be subjected to Sine on Random vibrations, i.e. excitations composed of random vibrations superimposed on deterministic (sinusoidal) contributions, in particular sine tones due to some rotating parts of the system (e.g. helicopters, engine mounted components, These components must be designed to withstand the fatigue damage induced by the "composed" vibration environment, and qualification tests are advisable for the most critical ones. In the case of an accelerated qualification test, a proper test tailoring which starts from the real environment (measured vibration signals) and which preserves not only the accumulated fatigue damage but also the "nature" of the excitation (i.e. sinusoidal components plus random process) is important to obtain reliable results. In this paper, the classic time domain approach is taken as a reference for the comparison of different methods for the Fatigue Damage Spectrum (FDS) calculation in case of Sine on Random vibration environments. Then, a methodology to compute a Sine on Random specification based on a mission FDS is proposed.