Miracle-dz/UniFAR-FTUs huggingface dataset:
Large‐scale species delimitation method for hyperdiverse groups

Accelerating the description of biodiversity is a major challenge as extinction rates increase. Integrative taxonomy combining molecular, morphological, ecological and geographical data is seen as the best route to reliably identify species. Classic molluscan taxonomic methodology proposes primary species hypotheses (PSHs) based on shell morphology. However, in hyperdiverse groups, such as the molluscan family Turridae, where most of the species remain unknown and for which homoplasy and plasticity of morphological characters is common, shell‐based PSHs can be arduous. A four‐pronged approach was employed to generate robust species hypotheses of a 1000 specimen South‐West Pacific Turridae data set in which: (i) analysis of COI DNA Barcode gene is coupled with (ii) species delimitation tools GMYC (General Mixed Yule Coalescence Method) and ABGD (Automatic Barcode Gap Discovery) to propose PSHs that are then (iii) visualized using Klee diagrams and (iv) evaluated with additional evidence, such as nuclear gene rRNA 28S, morphological characters, geographical and bathymetrical distribution to determine conclusive secondary species hypotheses (SSHs). The integrative taxonomy approach applied identified 87 Turridae species, more than doubling the amount previously known in the Gemmula genus. In contrast to a predominantly shell‐based morphological approach, which over the last 30 years proposed only 13 new species names for the Turridae genus Gemmula, the integrative approach described here identified 27 novel species hypotheses not linked to available species names in the literature. The formalized strategy applied here outlines an effective and reproducible protocol for large‐scale species delimitation of hyperdiverse groups.
Lack of association between the –759C/T polymorphism of the 5-HT2C receptor gene and clozapine-induced weight gain among German schizophrenic individuals

Weight gain is a major side effect of treatment with clozapine and other antipsychotics. Recent studies suggest an important role of the serotonin type 2C receptor gene (5-HT2CR) in antipsychotic-induced weight gain. However, investigations pertaining to a possible association between a –759C/T polymorphism (C allele) of the 5-HT2CR and weight gain induced by clozapine and/or other antipsychotics have yielded inconsistent results. We investigated the –759C/T polymorphism of the 5-HT2CR in relation to clozapine-induced change in body mass index (BMI) (kg/m2) in 97 German patients with schizophrenia and found no association between the –759C allele and weight gain after 12 weeks of clozapine treatment. In addition, confounding effects of initial BMI, age, sex and duration of illness on change in BMI could not be detected by multiple linear regression analysis. Our data do not support an involvement of the –759C/T polymorphism of the 5-HT2CR in clozapine-induced weight gain in German patients with schizophrenia. Further pharmacogenetic studies pertaining to antipsychotic-induced weight gain are warranted.
Volunteer farmer-trainer motivations in East Africa: practical implications for enhancing farmer-to-farmer extension

Farmer-to-farmer extension (FFE) has received considerable interest in developing countries due to a decline in government extension services. There are, however, questions as to how FFE can be improved to enhance effectiveness and sustainability of the approach. One area that may hold the key is to understand volunteer farmer-trainer (VFT) motivations. Informal and formal interviews were held with VFTs in a smallholder dairy development project in Kenya, Uganda and Rwanda. Data were collected on the reasons why VFTs became trainers and why they continue to train. Findings of the study showed that VFTs were motivated by a combination of intrinsic and extrinsic factors. These factors are not static; they change over time. Gaining knowledge and skills as well as altruism were found to be the most important motivating factors for becoming trainers in the three countries. However, a few years after becoming trainers, income earned from selling inputs and specialized services associated with training was an important motivating factor to VFTs in Kenya. In Uganda gaining knowledge and skills remained the most important whereas in Rwanda, a new motivation, increased demand for training, was the most important reason for continuing to train. These findings point to the fact that the general reasons that motivate VFTs irrespective of context are similar; however, the importance attached to motivations is context specific. These motivations can provide insights into which incentives can be enhanced to improve effectiveness and sustainability of FFE.
Rev and the fate of pre-mRNA in the nucleus: implications for the regulation of RNA processing in eukaryotes

Although a great deal is known about the regulation of gene expression in terms of transcription, relatively little is known about the modulation of pre-mRNA processing. In this study, we exploited a genetically regulated system, human immunodeficiency virus type 1 (HIV-1) and its trans-activator Rev, to examine events that occur between the synthesis of pre-mRNA in the nucleus and the translation of mRNA in the cytoplasm. Unlike the majority of eukaryotic pre-mRNAs whose introns are efficiently recognized and spliced prior to nucleocytoplasmic transport, HIV-1 mRNAs containing functional introns must be exported to the cytoplasm for the expression of many viral proteins. Using human T cells containing stably integrated proviruses, we demonstrate that such incompletely spliced viral mRNAs are exported to the cytoplasm only in the presence of the Rev trans-activator. In the absence of Rev, these intron-containing RNAs are sequestered in the T-cell nucleus and either spliced or, more commonly, degraded. Because Rev does not inhibit the expression of fully spliced viral mRNA species in T cells, we propose that Rev, rather than inhibiting viral pre-mRNA splicing, is acting here both to prevent the nuclear degradation of HIV-1 pre-mRNAs and to induce their translocation to the cytoplasm. Taken together, these findings indicate that the cellular factors responsible for the nuclear retention of unspliced pre-mRNAs, although most probably splicing factors, do not invariably commit these RNAs to productive splicing and can, instead, program such transcripts for degradation.
Poxvirus Infection-Associated Downregulation of C-Type Lectin-Related-b Prevents NK Cell Inhibition by NK Receptor Protein-1B

Innate immune recognition of virus-infected cells includes NK cell detection of changes to endogenous cell-surface proteins through inhibitory receptors. One such receptor system is the NK cell receptor protein-1B (NKR-P1B) and its ligand C-type lectin-related-b (Clr-b). NKR-P1B and Clr-b are encoded within the NK cell gene complex, a locus that has been linked to strain-dependent differences in susceptibility to infection by poxviruses. In this study, we report the impact of vaccinia virus (VV) and ectromelia virus infection on expression of Clr-b and Clr-b–mediated protection from NK cells. We observed a loss of Clr-b cell-surface protein upon VV and ectromelia virus infection of murine cell lines and bone marrow-derived macrophages. The reduction of Clr-b is more rapid than MHC class I, the prototypic ligand of NK cell inhibitory receptors. Reduction of Clr-b requires active viral infection but not expression of late viral genes, and loss of mRNA appears to lag behind loss of Clr-b surface protein. Clr-b–mediated protection from NK cells is lost following VV infection. Together, these results provide the second example of Clr-b modulation during viral infection and suggest reductions of Clr-b may be involved in sensitizing poxvirus-infected cells to NK cells.
Non-referenced genome assembly from epigenomic short-read data

Current computational methods used to analyze changes in DNA methylation and chromatin modification rely on sequenced genomes. Here we describe a pipeline for the detection of these changes from short-read sequence data that does not require a reference genome. Open source software packages were used for sequence assembly, alignment, and measurement of differential enrichment. The method was evaluated by comparing results with reference-based results showing a strong correlation between chromatin modification and gene expression. We then used our de novo sequence assembly to build the DNA methylation profile for the non-referenced Psammomys obesus genome. The pipeline described uses open source software for fast annotation and visualization of unreferenced genomic regions from short-read data.
Effects of language processing in Turkish authorship attribution

In this study we present a text categorization approach for stylometric analysis of Turkish documents. To this end we extend traditional features and take advantage of linguistic processing. We experiment with a combination of bag of stems and additional features such as function words, part of speech tags and morpho-syntactic tags in datasets having varying number of authors. Based on the characteristics of Turkish (agglutinative language) we expected morpho-syntactic tags to perform better. However, neither part of speech tags nor morpho syntactic tags has showed a significant gain in our settings. Our findings suggest that the main performance is dominated with bag of stem features and the best performance is achieved with combination of bag of stems and function words.
SPECTRE: supporting consumption policies in window-based parallel complex event processing

Distributed Complex Event Processing (DCEP) is a paradigm to infer the occurrence of complex situations in the surrounding world from basic events like sensor readings. In doing so, DCEP operators detect event patterns on their incoming event streams. To yield high operator throughput, data parallelization frameworks divide the incoming event streams of an operator into overlapping windows that are processed in parallel by a number of operator instances. In doing so, the basic assumption is that the different windows can be processed independently from each other. However, consumption policies enforce that events can only be part of one pattern instance; then, they are consumed, i.e., removed from further pattern detection. That implies that the constituent events of a pattern instance detected in one window are excluded from all other windows as well, which breaks the data parallelism between different windows. In this paper, we tackle this problem by means of speculation: Based on the likelihood of an event's consumption in a window, subsequent windows may speculatively suppress that event. We propose the SPECTRE framework for speculative processing of multiple dependent windows in parallel. Our evaluations show an up to linear scalability of SPECTRE with the number of CPU cores.
Resource exploitation in multi-carrier multi-cellular networks

The purpose of this paper is to examine the algorithmic quality of a semi-Random subcarrier allocation strategy and a Block Anti-Jamming Subcarrier Scavenging (BAJSS) strategy in terms of mean capacity, mean Bit Error Rate (BER), complexity as well as Jain's fairness index (power, capacity). These strategies are implemented in a LTE OFDMA multicellular network platform, which executes a fixed, sufficient for convergence, Monte Carlo (MC) runs. Both strategies are based on anti-jamming criteria so as to further mitigate Intra-Channel Interference (ICI). According to the results, semiRandom outperforms BAJSS and the traditional random strategy in terms of mean capacity, mean BER and power dissipation at the cost however of increased computational complexity.
Sleep quality and sleep hygiene behaviors of adolescents during chemotherapy.

STUDY OBJECTIVES Describe the self-reported sleep quality and sleep hygiene behaviors of adolescents before diagnosis and during chemotherapy (CTX), compare their sleep quality and sleep hygiene behaviors with published normative data for healthy adolescents and adolescents with chronic pain, and explore factors that predict sleep quality. METHODS Subjects were 51 adolescents (10 to 19 years) receiving CTX for cancer. A questionnaire was used to assess sleep patterns prior to the adolescent's cancer diagnosis, and a 7-day sleep diary was used to assess subjective sleep-wake activity during CTX. Sleep quality was assessed using the Adolescent Sleep Wake Scale, and sleep-facilitating and sleep-inhibiting behaviors using the Adolescent Sleep Hygiene Scale. RESULTS Adolescents receiving CTX reported significantly worse sleep quality and sleep hygiene behaviors than healthy adolescents, and better sleep quality but similar sleep hygiene behaviors to adolescents with chronic pain. Significant interactions were found between bedtimes and wake-times on weekdays and weekends before diagnosis and during CTX. Sleep hygiene and demographic variables accounted for 24% of the variance in sleep quality. The cognitive and emotional subscales of the sleep hygiene scale and demographic variables accounted for 36% of the variance in sleep quality. CONCLUSIONS Both the weekday and weekend sleep-wake patterns of adolescents receiving CTX resembled their weekend sleep patterns prior to diagnosis.
Tweeted Anger Predicts County-Level Results of the 2016 United States Presidential Election

In the aftermath of the 2016 United States presidential election, experts and journalists speculated that angry voters had supported the unexpected winner Donald Trump. The present study used a sample of 148 million tweets posted by U.S. citizens from across 1,347 counties, classified with regard to emotional content, to predict the election results at county level. As expected, Donald Trump received more support in counties where people tweeted more anger and negative emotions, even when various county characteristics and conservative vote choice in the preceding presidential election were controlled. These findings might be an outcome of emotional resonance—voters being attracted by political appeals that match their emotions—because Trump used more anger and negative emotion words in his campaign than the other presidential candidates in 2012 and 2016. The findings suggest that negative emotions played a critical role in the 2016 presidential election.
Nuclear antigen detected in hepatoma cell lines containing integrated hepatitis B virus DNA

We identified, by anticomplement immunofluorescence, a nuclear antigen (hepatitis B virus-associated nuclear antigen [HBNA]) in two human hepatoma cell lines containing integrated hepatitis B virus DNA but not in three hepatoma cell lines lacking it. The antigen resembled neoantigens associated with the oncogenesis of certain papovaviruses, adenoviruses, and herpesviruses. Antibody to the antigen (anti-HBNA) was found in 7.3% of hepatitis B surface antigen-positive sera from patients with hepatocellular carcinoma but not in surface antigen-negative sera. The staining of HBNA was characterized by two patterns, reticular nuclear fluorescence and nucleolar fluorescence. The expression of HBNA did not parallel the production of extracellular hepatitis B surface antigen. Treatment of cells with proteinase K, RNase, DNase, or cycloheximide significantly diminished the staining of HBNA.
Why Does It Not Make Sense to Create a Monetary Union in MERCOSUR? A Keynesian Alternative Proposal

Abstract: The article has two objectives. On one hand, it intends to show how inconsistent the proposal of creating a currency union among the countries of MERCOSUR is, as the final step of an integration process in this region. On the other hand, it argues that only a (Post) Keynesian alternative proposal of (1) managing fiscal and monetary policies, and (2) requiring appropriate institutional arrangements can reconcile the full employment with external equilibrium to the MERCOSUR countries in a global world.
Analyzing housing affordability of U.S. renters during the Great Recession, 2007 to 2009

ABSTRACT During the somewhat recent Great Recession, there was a popular notion that housing affordability for all renters had deteriorated. In this study, we investigate this notion by utilizing two national merged American Housing Survey (AHS) data sets from 2007 to 2009. We analyze housing affordability for renters, comparing and contrasting four subgroups in terms of their monthly average household incomes and housing costs, among other variables. We conduct descriptive statistics and multinomial logit analyses in order to predict the probability of a renter being in a given subgroup. We find that 62.90% of renters had increased household incomes but decreased housing cost burdens or decreased household incomes and decreased housing cost burdens, dispelling the notion that housing affordability has deteriorated. We also find that changes in average household income and staying or becoming employed or married translates into high odds of being in subgroups with increased household incomes.
Functional and molecular characterization of the endothelin system in retinal arterioles.

PURPOSE Activation of the endothelin (ET) system has been implicated in the pathogenesis of retinal ischemic disease. Although ET-1, the predominant endogenous isoform of ET, has been shown to cause constriction of retinal vessels, the expression and functional significance of its synthesis and the involved specific ET receptors in retinal arterioles remain unknown. The authors examined the roles of ET(A) and ET(B) receptors and of endothelin-converting enzyme (ECE)-1 in ET-1-induced vasomotor responses of single retinal arterioles. METHODS To exclude systemic confounding effects, porcine retinal arterioles were isolated for vasoreactivity and molecular studies. RESULTS Isolated and pressurized retinal arterioles developed basal tone and constricted in a manner dependent on concentration to ET-1. ET-1 precursor big ET-1 elicited time-dependent vasoconstriction over 20 minutes, which was blocked by the ECE-1 inhibitor phosphoramidon. ET(A) receptor antagonist BQ123 inhibited most (approximately 90%) of vasoconstrictions to ET-1 and big ET-1. ET(B) receptor agonist sarafotoxin also elicited concentration-dependent constriction of retinal arterioles but with significantly less potency than ET-1. ET(B) receptor antagonist BQ788 abolished vasoconstriction to sarafotoxin but only slightly reduced responses to ET-1 and big ET-1. Protein and mRNA expressions of ET(A), ET(B), and ECE-1 were detected in retinal arterioles. Immunohistochemistry revealed ET(A) and ET(B) receptors predominantly in smooth muscle and ECE-1 predominantly in endothelium and smooth muscle. CONCLUSIONS ET-1 elicits constriction of retinal arterioles predominantly through the activation of smooth muscle ET(A) receptors. Endogenous production of ET-1 from vascular ECE-1 is sufficient to evoke ET(A) receptor-dependent constriction in retinal arterioles.
Kiblat and the Mediatic Jew

Practically speaking, there are no Jews in Indonesia. Nor do Indonesians usually claim that there are. But it is now said that there is strong Jewish influence corrupting Islam, sometimes disguised as orthodox Islamic truth and producing political unrest. There has long been anti-Semitism in Indonesia, but the amount of anti-Semitic material increased greatly during the regime of President Suharto. The Protocols of the Elders of Zion have been republished several times, as well as much else in the way of anti-Semitic literature.2 Nor is it unusual to hear Jews referred to as the cause of Indonesia's present economic crisis.
Searching for Affirmation: Relationships Between Ethnic Identity and Language

Despite proposed links between social context and language acquisition (Bialystok, 2007; Hoff, 2008), few studies have explored the role of ethnicity on second language (L2) learning motivation. The present study addresses this issue by investigating the role that the strength of one's ethnic identity plays in the pursuit of an L2. Participants were German language learners who completed a battery of surveys to assess their language histories, the strength of their ethnic identities, and their German language proficiency before participating in a semi-structured interview. Results suggest that students who feel less strongly connected to their ethnic identity are likely to study longer than their more affirmed peers. It was concluded that although integrative and instrumental orientations play a strong role in L2 motivation, effects of ethnic identity are also important.
FACTOR PROPORTIONS AND THE STRUCTURE OF INTER- REGIONAL TRADE: THE CASE OF JAPAN*

results.1 However, there exists little evidence in economic literature to support an alternative hypothesis of the pattern of trade based on the Heckscher-Ohlin (H-O) theory. The hypothesis, stated in a simple version amenable to empirical investigation, is that a country's exports require in their production a relatively intensive use of the country's relatively abundant factor of production.2 As is well known, Leontief [12; 13] found that the U.S. exports of 1947 and 1951 were generally more labor-intensive (relative to capital) than the corresponding competitive imports, contrary to what may be expected on the basis of the H-O theory. Subsequent investigations by other writers into the trade patterns of additional countries resulted in mixed (mostly negative)
Variability in Secondary Structure of 18S Ribosomal RNA as Topological Marker for Identification of Paramecium species

Besides cytological and molecular applications, Paramecium is being used in water quality assessment and for determination of saprobic levels. An unambiguous identification of these unicellular eukaryotes is not only essential, but its ecological diversity must also be explored in the local environment. 18SrRNA genes of all the strains of Paramecium species isolated from waste water were amplified, cloned and sequenced. Phylogenetic comparison of the nucleotide sequences of these strains with 23 closely related Paramecium species from GenBank Database enabled identification of Paramecium multimicronucleatum and Paramecium jenningsi. Some isolates did not show significant close association with other Paramecium species, and because of their unique position in the phylogenetic tree, they were considered new to the field. In the present report, these isolates are being designated as Paramecium caudatum pakistanicus. In this article, secondary structure of 18SrRNA has also been analyzed as an additional and perhaps more reliable topological marker for species discrimination and for determining possible phylogenetic relationship between the ciliate species. On the basis of comparison of secondary structure of 18SrRNA of various isolated Paramacium strains, and among Paramecium caudatum pakistanicus, Tetrahymena thermophila, Drosophila melanogaster, and Homo sapiens, it can be deduced that variable regions are more helpful in differentiating the species at interspecific level rather than at intraspecific level. It was concluded that V3 was the least variable region in all the organisms, V2 and V7 were the longest expansion segments of D. melanogaster and there was continuous mutational bias towards G.C base pairing in H. sapiens. J. Cell. Biochem. 115: 2077–2088, 2014. © 2014 Wiley Periodicals, Inc.