nils-herrmann/clean_scirepeval huggingface dataset:
An individual of flying squirrel (Pteromys volans) belonging to the Far Eastern philogenetic lineage was found in the suburbs of Moscow
Venue: Russian Journal of Biological Invasions

The southern border of the flying squirrel (Pteromys volans) natural range goes through the northern and eastern parts of the Moscow oblast. However, near Zvenigorod (western part of the Moscow oblast) there is a population formed by animals brought to the Zvenigorod Biological Station of the Moscow State University from other areas, including the Far Eastern part of the species range. Since 2010, flying squirrels have been registered in the Troitsk district, southwest from the urban part of the city of Moscow. Genetic analysis of a dead animal found in this district showed a high similarity of the sequence of mtDNA fragment with sequences typical for the Russian Far East but not for the European part of the species range. It is suggested that descendants of the Far Eastern flying squirrels unintentionally introduced near Zvenigorod are actively expanding their range throughout the Moscow oblast.
The role of enzymes in the adaptation of soybean of different philogenetic origin to growing conditions

For the first time, the relation between the variety of enzyme forms and different growing conditions of soybeans is studied. Data on the obtained electrophoretic spectra of catalase, peroxidase, acid phosphatase, esterase and amylase of wild and cultivated soybean seeds were analyzed in detail and systematized. It was found that wild soybean has a high adaptive capacity and is characterized by high specific activity and a small number of studied enzyme forms. Low specific activity of soybean enzymes is compensated by a larger number of their forms, which increases the resistance of soybean in different growing conditions. Adaptive changes in specific activity and the number of enzyme forms under the influence of growing conditions cause changes in biometric and biochemical parameters of soybean of different phylogenetic origin. It is shown that the specific activity and multiple forms of catalases, peroxidases, acid phosphatases, esterases and amylases of soybean seeds can be used as markers of its adaptation to different growing conditions.
Beyond poverty: Engaging with input in generative SLA

A generative approach to language acquisition is no different from any other in assuming that target language input is crucial for language acquisition. This discussion note addresses the place of input in generative second language acquisition (SLA) research and the perception in the wider field of SLA research that generative SLA 'ignores' the input. This impression may have arisen because generative SLA researchers have tended not to systematically study quantitative distribution of input properties, nor qualitative properties of the input available to learners. We argue that precisely these sorts of studies would be at least beneficial, if not indispensable, to the development of a comprehensive (generative) theory of SLA. Furthermore, a welcome side effect of more systematic engagement with input would be potential for greater accessibility for generative SLA in the wider field of second language (L2) studies.
Variational Inference: A Review for Statisticians
Venue: ArXiv

One of the core problems of modern statistics is to approximate difficult to compute probability densities. This problem is especially important in Bayesian statistics, which frames all inference about unknown quantities as a calculation involving the posterior density. In this article, we review variational inference (VI) a method from machine learning that approximates probability densities through optimization. VI has been used in many applications and tends to be faster than classical methods, such as Markov chain Monte Carlo sampling. The idea behind VI is to first posit a family of densities and then to find a member of that family which is close to the target density. Closeness is measured by Kullback Leibler divergence. We review the ideas behind mean field variational inference, discuss the special case of VI applied to exponential family models, present a full example with a Bayesian mixture of Gaussians, and derive a variant that uses stochastic optimization to scale up to massive data. We discuss modern research in VI and highlight important open problems. VI is powerful, but it is not yet well understood. Our hope in writing this article is to catalyze statistical research on this class of algorithms.
The cellular composition of the human immune system is shaped by age and cohabitation
Venue: Nature Immunology

Detailed population level description of the human immune system has recently become achievable. We used a 'systems level' approach to establish a resource of cellular immune profiles of 670 healthy individuals. We report a high level of interindividual variation, with low longitudinal variation, at the level of cellular subset composition of the immune system. Despite the profound effects of antigen exposure on individual antigen specific clones, the cellular subset structure proved highly elastic, with transient vaccination induced changes followed by a return to the individual's unique baseline. Notably, the largest influence on immunological variation identified was cohabitation, with 50% less immunological variation between individuals who share an environment (as parents) than between people in the wider population. These results identify local environmental conditions as a key factor in shaping the human immune system.
Impact of iron deficiency anemia on the function of the immune system in children
Venue: Medicine

AbstractThe importance of iron deficiency as a public health problem is based ultimately on the seriousness of its consequences on health. The most extensively investigated consequences of iron deficiency involve work performance and immune function. The significance of the effects on work performance is generally accepted. In contrast, data on the influence of iron deficiency on immune function are often perceived as being confusing and contradictory.We aimed to evaluate the effect of iron deficiency anemia on humoral, cellular, nonspecific immunity, and also the effect on the cytokines that are the key factors of many immunologic steps.Forty children with iron deficiency anemia and 20 age and sex matched healthy children were included. All children were subjected to full medical history, thorough clinical examination, complete blood count, iron indices (serum iron, serum total iron binding capacity, serum ferritin, and transferrin saturation) immunoglobulin assay (IgA, IgG, and IgM) interleukin (IL) 6 serum level, study of T lymphocyte subsets, and evaluation of phagocytic function of macrophages and oxidative burst activity of neutrophils.Patients had significantly lower IgG levels, IL 6, phagocytic activity, and oxidative burst of neutrophils than controls, although there was no significant difference between patients and controls with regard to other immunoglobulins and CD4/CD8 ratio. There was significantly positive correlation between serum iron and IL 6 serum level.We concluded that humoral, nonspecific immunity (phagocytic activity and oxidative burst) and the IL 6 are influenced in patients with iron deficiency anemia. Study of these abnormalities after correction of iron deficiency is strongly needed.
Barriers to Implementation of Information and Communication (ICT) in Public Sudanese Secondary Schools: Teacher's Prospective

This study examines the current situation of ICT implementation at five public secondary schools in Sudan. The study adopted the quantitative method where a sample of five secondary schools was selected. A total of 40 secondary school teachers responded to the designed questionnaire. By using Statistic Package of Social Science (SPSS) the data was analyzed. The findings indicate that the ICT implementation at the five secondary schools was poorly achieved, and school teachers still have not acquired the necessary skills of ICT that enable them to implement ICT in classrooms. Further, the lack financial support, insufficient existence of computer labs, low internet connectivity, inadequate technical support and lack of time were main barriers that prevent the implementation of ICT in schools.
Soft Robotics Commercialization: Jamming Grippers from Research to Product.
Venue: Soft robotics

Recent work in the growing field of soft robotics has demonstrated a number of very promising technologies. However, to make a significant impact in real world applications, these new technologies must first transition out of the laboratory through successful commercialization. Commercialization is perhaps the most critical future milestone facing the field of soft robotics today, and this process will reveal whether the apparent impact we now perceive has been appropriately estimated. Since 2012, Empire Robotics has been one of the first companies to attempt to reach this milestone through our efforts to commercialize jamming based robotic gripper technology in a product called VERSABALL(r) However, in spring 2016 we are closing our doors, having not been able to develop a sustainable business around this technology. This article presents some of the key takeaways from the technical side of the commercialization process and lessons learned that may be valuable to others. We hope that sharing this information will provide a frame of reference for technology commercialization that can help others motivate research directions and maximize research impact.
Understanding the connection between self esteem and aggression: The mediating role of emotion dysregulation.
Venue: Aggressive behavior

The purpose of the present study was to extend previous knowledge concerning the link between self esteem and aggression by examining the mediating role of emotion dysregulation among offenders and community participants. A sample of 153 incarcerated violent offenders and a community sample of 197 individuals completed self report measures of self esteem level, emotion dysregulation, and trait aggression. Offenders reported lower levels of self esteem than community participants, as well as greater levels of emotional nonacceptance and hostility. Bootstrapping analyses were performed to test whether emotion dysregulation mediated the association between self esteem level and aggression. In the offender sample, mediation models were significant for three of the four aspects of trait aggression that were considered. Emotion dysregulation fully mediated the links that low self esteem had with physical aggression, anger, and hostility. The same pattern (with the addition of full mediation for verbal aggression) was confirmed in the community sample. Our findings suggest that emotion dysregulation may play an important role in the connection between low self esteem and aggression. Alternative models of the associations among these variables were tested and discussed. As a whole, the present results are consistent with those of other studies and suggest that it may be beneficial to include emotion regulation modules as part of prevention and treatment programs for violent offenders.
Dynamics of Sulfentrazone Applied to Sugarcane Crop Residues
Venue: Weed Science

The sulfentrazone is regularly applied to sugarcane crop harvest residue for PRE control of weedy species, especially in the dry season during the year, but little is known about how rainfall timing or crop residue mass affect the release of sulfentrazone into the soil and its subsequent effectiveness. Two experiments were conducted to examine the effects of sugarcane residue mass (5, 10, 15, and 20 t ha 1) and rainfall timing (1, 30, and 60 d after herbicide application) on sulfentrazone retention. Rainfall volumes were simulated at 2.5, 5, 10, 20, 35, 50, and 100 mm. A 20 mm rainfall volume was simulated at 7 and 14 d after the first simulated event. The water passing through the straw was collected after each rainfall simulation. The concentration of sulfentrazone was measured by liquid chromatography and mass spectrometry. The initial 20 mm of rain released the maximum mass of sulfentrazone from the sugarcane residue. The mass of sugarcane residue affected the amount of sulfentrazone recovered. The amount of sulfentrazone released from the residue was significantly reduced by the persistence on the residue surface for long periods before the occurrence of rain. During periods of low rainfall, recommendations for sulfentrazone rate must take into account losses that occur when applied over the harvest residues to design a weed management plan that does not compromise efficacy and duration of the residual effects.  Sulfentrazone; sugarcane; Saccharum interspecific hybrids
HIV Integration Site Analysis of Cellular Models of HIV Latency with a Probe Enriched Next Generation Sequencing Assay
Venue: Journal of Virology

Antiretroviral therapy (ART) is successful in the suppression of HIV but cannot target and eradicate the latent proviral reservoir. The location of retroviral integration into the human genome is thought to play a role in the clonal expansion of infected cells and HIV persistence. We developed a high throughput targeted sequence capture assay that uses a pool of HIV specific probes to enrich Illumina libraries prior to deep sequencing. Using an expanded clonal population of ACH 2 cells, we demonstrate that this sequence capture assay has an extremely low false positive rate. This assay assessed four cellular models commonly used to study HIV latency and latency reversing agents: ACH 2 cells, J Lat cells, the Bcl 2 transduced primary CD4+ model, and the cultured TCM (central memory) CD4+ model. HIV integration site characteristics and genes were compared between these cellular models and to previously reported patient data sets. Across these cellular models, there were significant differences in integration site characteristics, including orientation relative to that of the host gene, the proportion of clonally expanded sites, and the proportion located within genic regions and exons. Despite a greater diversity of minority integration sites than expected in ACH 2 cells, their integration site characteristics consistently differed from those of the other models and from the patient samples. Gene ontology analysis of highly represented genes from the patient samples found little overlap with HIV containing genes from the cell lines. These findings show that integration site differences exist among the commonly used cellular models of HIV latency and in comparison to integration sites found in patient samples.  Despite the success of ART, currently there is no successful therapy to eradicate integrated proviruses. Cellular models of HIV latency are used to test the efficacy of latency reversing agents, but it is unclear how well these models reflect HIV integration into the human genome in vivo. We have developed a novel probe based sequence enrichment assay to sequence and analyze integrated HIV. We compared HIV integration site characteristics between four cellular models and to previously described patient data sets. Significant differences were detected in the distribution of HIV integration sites between cellular models of HIV latency and compared to data sets from patient samples. The results from this study have implications for how well these cellular models of HIV infection truly reflect HIV integration in vivo and their applicability in drug discovery for novel latency reversing agents.
HIV integration sites in latently infected cell lines: evidence of ongoing replication
Venue: Retrovirology

BackgroundAssessing the location and frequency of HIV integration sites in latently infected cells can potentially inform our understanding of how HIV persists during combination antiretroviral therapy. We developed a novel high throughput sequencing method to evaluate HIV integration sites in latently infected cell lines to determine whether there was virus replication or clonal expansion in these cell lines observed as multiple integration events at the same position.ResultsWe modified a previously reported method using random DNA shearing and PCR to allow for high throughput robotic processing to identify the site and frequency of HIV integration in latently infected cell lines. Latently infected cell lines infected with intact virus demonstrated multiple distinct HIV integration sites (28 different sites in U1, 110 in ACH 2 and 117 in J1.1 per 150,000 cells) In contrast, cell lines infected with replication incompetent viruses (J Lat cells) demonstrated single integration sites. Following in vitro passaging of the ACH 2 cell line, we observed a significant increase in the frequency of unique HIV integration sites and there were multiple mutations and large deletions in the proviral DNA. When the ACH 2 cell line was cultured with the integrase inhibitor raltegravir, there was a significant decrease in the number of unique HIV integration sites and a transient increase in the frequency of 2 LTR circles consistent with virus replication in these cells.ConclusionCell lines latently infected with intact HIV demonstrated multiple unique HIV integration sites indicating that these cell lines are not clonal and in the ACH 2 cell line there was evidence of low level virus replication. These findings have implications for the use of latently infected cell lines as models of HIV latency and for the use of these cells as standards.
HIV integration and the establishment of latency in CCL19 treated resting CD4+ T cells require activation of NF kB
Venue: Retrovirology

Eradication of HIV cannot be achieved with combination antiretroviral therapy (cART) because of the persistence of long lived latently infected resting memory CD4+ T cells. We previously reported that HIV latency could be established in resting CD4+ T cells in the presence of the chemokine CCL19. To define how CCL19 facilitated the establishment of latent HIV infection, the role of chemokine receptor signalling was explored.ResultsIn resting CD4+ T cells, CCL19 induced phosphorylation of RAC alpha serine/threonine protein kinase (Akt) nuclear factor kappa B (NF kB) extracellular signal regulated kinase (ERK) and p38. Inhibition of the phosphoinositol 3 kinase (PI3K) and Ras/Raf/Mitogen activated protein kinase/ERK kinase (MEK)/ERK signalling pathways inhibited HIV integration, without significant reduction in HIV nuclear entry (measured by Alu LTR and 2 LTR circle qPCR respectively) Inhibiting activation of MEK1/ERK1/2, c Jun N terminal kinase (JNK) activating protein 1 (AP 1) and NF kB, but not p38, also inhibited HIV integration. We also show that HIV integrases interact with Pin1 in CCL19 treated CD4+ T cells and inhibition of JNK markedly reduced this interaction, suggesting that CCL19 treatment provided sufficient signals to protect HIV integrase from degradation via the proteasome pathway. Infection of CCL19 treated resting CD4+ T cells with mutant strains of HIV, lacking NF kB binding sites in the HIV long terminal repeat (LTR) compared to infection with wild type virus, led to a significant reduction in integration by up to 40 fold (range 1 115.4, p 0.03) This was in contrast to only a modest reduction of 5 fold (range 1.7 11, p 0.05) in fully activated CD4+ T cells infected with the same mutants. Finally, we demonstrated significant differences in integration sites following HIV infection of unactivated, CCL19 treated, and fully activated CD4+ T cells.ConclusionsHIV integration in CCL19 treated resting CD4+ T cells depends on NF kB signalling and increases the stability of HIV integrase, which allow subsequent integration and establishment of latency. These findings have implications for strategies needed to prevent the establishment, and potentially reverse, latent infection.
The role of HIV integration in viral persistence: no more whistling past the proviral graveyard.
Venue: The Journal of clinical investigation

A substantial research effort has been directed to identifying strategies to eradicate or control HIV infection without a requirement for combination antiretroviral therapy (cART) A number of obstacles prevent HIV eradication, including low level viral persistence during cART, long term persistence of HIV infected cells, and latent infection of resting CD4+ T cells. Mechanisms of persistence remain uncertain, but integration of the provirus into the host genome represents a central event in replication and pathogenesis of all retroviruses, including HIV. Analysis of HIV proviruses in CD4+ lymphocytes from individuals after prolonged cART revealed that a substantial proportion of the infected cells that persist have undergone clonal expansion and frequently have proviruses integrated in genes associated with regulation of cell growth. These data suggest that integration may influence persistence and clonal expansion of HIV infected cells after cART is introduced, and these processes may represent key mechanisms for HIV persistence. Determining the diversity of host genes with integrants in HIV infected cells that persist for prolonged periods may yield useful information regarding pathways by which infected cells persist for prolonged periods. Moreover, many integrants are defective, and new studies are required to characterize the role of clonal expansion in the persistence of replication competent HIV.
Process guidelines for establishing Intercoder Reliability in qualitative studies

Qualitative interviews are increasingly being utilized within the context of intervention trials. While there is emerging assistance for conducting and reporting qualitative analysis, there are limited practical resources available for researchers engaging in a group coding process and interested in ensuring adequate Intercoder Reliability (ICR) the amount of agreement between two or more coders for the codes applied to qualitative text. Assessing the reliability of the coding helps establish the credibility of qualitative findings. We discuss our experience calculating ICR in the context of a behavioural HIV prevention trial for young women in South Africa which involves multiple rounds of longitudinal qualitative data collection. We document the steps that we took to improve ICR in this study, the challenges to improving ICR, and the value of the process to qualitative data analysis. As a result, we provide guidelines for other researchers to consider as they embark on large qualitative projects.
Identification of hydroxylcinnamoyl tartaric acid esters in Bidens pilosa by UPLC tandem mass spectrometry

Bidens pilosa is a medicinal plant used for the treatment of several physiological illnesses. In South Africa, as the case may be for other African countries, this plant is equally consumed as a vegetable. In the current study, pressurized hot water extraction (PHWE) technology was employed for the extraction of polyphenolic compounds from leaves of B. pilosa under two different temperature conditions (100 and 150 degC) Accordingly, extraction of these compounds was made possible at 150 degC and analysis of these extracts using UPLC qTOF MS/MS revealed the presence of several hydoxylcinnamoyl tartaric acids. Here, different isomers of coutaric caftaric fertaric chicoric acid and caftaric acid glycosides were detected. The contribution of mass spectrometry fragmentation towards the characterization of these molecules is also presented. To the best of our knowledge, this is the first report of these molecules in B. pilosa.