Miracle-dz/UniFAR-FTUs huggingface dataset:
Repertoire of Bovine miRNA and miRNA-Like Small Regulatory RNAs Expressed upon Viral Infection

MicroRNA (miRNA) and other types of small regulatory RNAs play a crucial role in the regulation of gene expression in eukaryotes. Several distinct classes of small regulatory RNAs have been discovered in recent years. To extend the repertoire of small RNAs characterized in mammals and to examine relationship between host miRNA expression and viral infection we used Illumina's ultrahigh throughput sequencing approach. We sequenced three small RNA libraries prepared from cell line derived from the adult bovine kidney under normal conditions and upon infection of the cell line with Bovine herpesvirus 1. We used a bioinformatics approach to distinguish authentic mature miRNA sequences from other classes of small RNAs and short RNA fragments represented in the sequencing data. Using this approach we detected 219 out of 356 known bovine miRNAs and 115 respective miRNA* sequences. In addition we identified five new bovine orthologs of known mammalian miRNAs and discovered 268 new cow miRNAs many of which are not identifiable in other mammalian genomes and thus might be specific to the ruminant lineage. In addition we found seven new bovine mirtron candidates. We also discovered 10 small nucleolar RNA (snoRNA) loci that give rise to small RNA with possible miRNA-like function. Results presented in this study extend our knowledge of the biology and evolution of small regulatory RNAs in mammals and illuminate mechanisms of small RNA biogenesis and function. New miRNA sequences and the original sequencing data have been submitted to miRNA repository (miRBase) and NCBI GEO archive respectively. We envisage that these resources will facilitate functional annotation of the bovine genome and promote further functional and comparative genomics studies of small regulatory RNA in mammals.
Text classification based on limited bibliographic metadata

In this paper, we introduce a method for categorizing digital items according to their topic, only relying on the document's metadata, such as author name and title information. The proposed approach is based on a set of lexical resources constructed for our purposes (e.g., journal titles, conference names) and on a traditional machine-learning classifier that assigns one category to each document based on identified core features. The system is evaluated on a real-world data set and the influence of different feature combinations and settings is studied. Although the available information is limited, the results show that the approach is capable to efficiently classify data items representing documents.
Irinotecan (CPT-11) Chemotherapy Alters Intestinal Microbiota in Tumour Bearing Rats

Intestinal microbiota mediate toxicity of irinotecan (CPT-11) cancer therapies and cause systemic infection after CPT-11-induced loss of barrier function. The intestinal microbiota and their functions are thus potential targets for treatment to mitigate CPT-11 toxicity. However, microbiota changes during CPT-11 therapy remain poorly described. This study analysed changes in intestinal microbiota induced by CPT-11 chemotherapy. Qualitative and quantitative taxonomic analyses, and functional analyses were combined to characterize intestinal microbiota during CPT-11-based chemotherapy, and in presence or absence of oral glutamine, a treatment known to reduce CPT-11 toxicity. In the first set of experiments tumour-bearing rats received a dose-intensive CPT-11 regimen (125 mg kg−1×3 days), with or without oral glutamine bolus (0.75 g kg−1). In a subsequent more clinically-oriented chemotherapy regimen, rats received two cycles of CPT-11 (50 mg kg−1) followed by 5-flurouracil (50 mg kg−1). The analysis of fecal samples over time demonstrated that tumours changed the composition of intestinal microbiota, increasing the abundance of clostrridial clusters I, XI, and Enterobacteriaceae. CPT-11 chemotherapy increased cecal Clostridium cluster XI and Enterobacteriaceae, particularly after the dose-intensive therapy. Glutamine treatment prevented the reduced abundance of major bacterial groups after CPT-11 administration; i.e. total bacteria, Clostridium cluster VI, and the Bacteroides-group. Virulence factor/toxin genes of pathogenic Escherichia coli and Clostridium difficile were not detected in the cecal microbiota. In conclusion, both colon cancer implantation and CPT-11-based chemotherapies disrupted the intestinal microbiota. Oral glutamine partially mitigated CPT-11 toxicity and induced temporary changes of the intestinal microbiota.
Education in Emergencies: A Review of Theory and Research

In this article, we conduct an integrative and rigorous review of theory and research on education in emergencies programs and interventions as international agencies implement them in areas of armed conflict. We ask several questions. How did this subfield emerge and what are the key conceptual frameworks that shape it today? How do education in emergencies programs affect access, learning, and protection in conflict-affected contexts? To answer these questions, we identify the conceptual frameworks and theoretical advances that have occurred since the inception of the field in the mid-1990s. We review the theories that frame the relationship between education and conflict as well as empirical research that tests assumptions that underpin this relationship. Finally, we assess what we know to date about “what works” in education in emergencies based on intervention research. We find that with regard to access, diminished or inequitable access to education drives conflict; conflict reduces boys’ and girls’ access to education differently; and decreased distance to primary school increases enrollment and attendance significantly for boys and even more so for girls. With regard to learning, education content likely contributes to or mitigates conflict, although the mechanisms through which it does so remain underspecified; and peace education programs show promise in changing attitudes and behaviors toward members of those perceived as the “other,” at least in the short term. Finally, providing children living in emergency and postemergency situations with structured, meaningful, and creative activities in a school setting or in informal learning spaces improves their emotional and behavioral well-being.
Morality and Competence in Shaping the Images of Political Leaders

Psychological models of forming impressions about other people assume that this process is strictly connected with social categorization. Therefore, it is clear that the results of many studies show that the evaluations of other people are based on two crucial and separable criteria: morality and competence. Obviously morality and competence are two fundamental and distinct dimensions of the perception of politicians. These dimensions substantially influence voters’ behavior toward politicians and are clearly visible both in the preelection polls as well as in the scientific analyses concerning forming the images of politicians. The evaluations of politicians on the morality and competence dimensions are central in forming the interpersonal attitudes in which the dominant elements are affect and respect toward the evaluated person. Consequently, affect and respect are crucial factors in establishing the support of candidates for political offices. The morality and competence dimensions trigger the causal structures in the voter's mind in which formed attitude creates affect and respect, which determine voting behavior.
A mixture of amino acids and other small molecules present in the serum suppresses the growth of murine and human tumors in vivo

Previously we have hypothesized that the small molecules which are selectively accumulated in cancer cells might participate in a non‐immunological antitumor surveillance mechanism. We demonstrated earlier that a mixture of experimentally selected substances (“active mixture”, AM: L‐arginine, L‐histidine, L‐methionine, L‐phenylalanine, L‐tyrosine, L‐tryptophan, L‐ascorbate, D‐biotin, pyridoxine, riboflavin, adenine, L(‐)malate) possesses a selective toxic effect in vitro on a variety of tumor cell lines, and we have shown that the AM selectively induces apoptosis of cancer cells in vitro. To explore the in vivo significance of our earlier findings we examined the antitumor effect of AM in Colon 26 murine colorectal adenocarcinoma, B16 murine melanoma, MXT murine mammary carcinoma, S180 murine sarcoma, P388 murine lymphoid leukemia, HL‐60 human promyeloid leukemia, PC‐3 human prostate carcinoma, and HT‐29 human colon carcinoma tumor models. Treatment of tumor bearing mice with AM inhibited the growth of the tumors investigated, with an inhibitory effect ranging from 40 to 69%. The AM had a comparable antitumor effect with 5‐fluorouracil and cisplatin in the Colon‐26 tumor model, and combined treatment with AM and 5‐fluorouracil or cisplatin resulted in an enhanced tumor growth inhibitory effect. The AM induced apoptosis through the mitochondrial pathway and induced G1 arrest in PC‐3 cells and increased the number of apoptotic cells in PC‐3 xenografts. These findings suggest that the AM might offer an interesting perspective in the treatment of cancer and in combination with other treatments may offer hope for a more effective cancer therapy.
Substrate Sequence Selection by Retroviral Integrase

ABSTRACT Integration of retrovirus DNA is a specific process catalyzed by the integrase protein acting to join the viral substrate DNA (att) sequences of about 10 bases at the ends of the long terminal repeat (LTR) to various sites in the host target cell DNA. Although the interaction is sequence specific, the att sequences of different retroviruses are largely unrelated to one another and usually differ between the two ends of the viral DNA. To define substrate sequence specificity, we designed an “in vitro evolution” scheme to select an optimal substrate sequence by competitive integration in vitro from a large pool of partially randomized substrates. Integrated substrates are enriched by PCR amplification and then regenerated and subjected to subsequent cycles of selection and enrichment. Using this approach, we obtained the optimal substrate sequence of 5′-ACGACAACA-3′ for avian sarcoma-leukosis virus (ASLV) and 5′-AACA(A/C)AGCA-3′ for human immunodeficiency virus type 1, which differed from those found at both ends of the viral DNA. Clonal analysis of the integration products showed that ASLV integrase can use a wide variety of substrate sequences in vitro, although the consensus sequence was identical to the selected sequence. By a competition assay, the selected nucleotide at position 4 improved the in vitro integration efficiency over that of the wild-type sequence. Viral mutants bearing the optimal sequence replicated at wild-type levels, with the exception of some mutations disrupting the U5 RNA secondary structure important for reverse transcription, which were significantly impaired. Thus, maximizing the efficiency of integration may not be of major importance for efficient retrovirus replication.
ANALISIS KEMAMPUAN BERPIKIR KOMPLEKS SISWA MELALUI PEMBELAJARAN BERBASIS MASALAH BERBANTUAN MIND MAPPING

Abstract Complex thinking skills is a dynamic process that requires variety of complex ideas in order to increase student understanding. The purpose of this study was to analyze the complex thinking skills of grade VII students in the city of Sukabumi through problem-based learning using mind mapping. Complex thinking skills researched in this study consisted of problem solving skills, decision making skills, critical thinking skills, and creative thinking skills. This study used a quasi experiment method with 38 students. The instruments were a test of complex thinking skills, mind mapping assignment, and the observation sheet. The results showed that 1) the complex thinking skills of the students have increased after the implementation of problem-based learning using mind mapping, with the normalized gain of 50.60% (medium); 2) the skills that have increased the most were problem solving skills and decision making skills. Abstrak Kemampuan berpikir kompleks merupakan sebuah proses dinamis yang menuntut beragam ide kompleks sehingga terjadi peningkatan pemahaman siswa. Tujuan penelitian ini adalah untuk menganalisis kemampuan berpikir kompleks siswa SMP kelas VII di salah satu SMP di Kota Sukabumi melalui pembelajaran berbasis masalah berbantuan mind mapping . Kemampuan berpikir kompleks yang diteliti meliputi kemampuan pemecahan masalah, kemampuan pengambilan keputusan, kemampuan berpikir kritis, dan kemampuan berpikir kreatif. Penelitian ini menggunakan metode penelitian kuasi eksperimen dengan 38 siswa. Instrumen yang digunakan adalah tes kemampuan berpikir kompleks, penilaian mind mapping , dan lembar observasi. Hasil penelitian menunjukkan bahwa 1) Kemampuan berpikir kompleks siswa mengalami peningkatan setelah diterapkan pembelajaran berbasis masalah berbantuan mind mapping , dengan gain yang dinormalisasi sebesar 50,60% (sedang); 2) kemampuan berpikir kompleks yang mengalami peningkatan paling baik adalah pada kemampuan pemecahan masalah dan kemampuan pengambilan keputusan. Permalink/ DOI: http://dx.doi. org/10.15408/es.v8i1. 1805
A Task Parallel Implementation of Fast Multipole Methods

This paper describes a task parallel implementation of ExaFMM, an open source implementation of fast multipole methods (FMM), using a lightweight task parallel library MassiveThreads. Although there have been many attempts on parallelizing FMM, experiences have almost exclusively been limited to formulation based on flat homogeneous parallel loops. FMM in fact contains operations that cannot be readily expressed in such conventional but restrictive models. We show that task parallelism, or parallel recursions in particular, allows us to parallelize all operations of FMM naturally and scalably. Moreover it allows us to parallelize a “mutual interaction” for force/potential evaluation, which is roughly twice as efficient as a more conventional, unidirectional force/potential evaluation. The net result is an open source FMM that is clearly among the fastest single node implementations, including those on GPUs; with a million particles on a 32 cores Sandy Bridge 2.20GHz node, it completes a single time step including tree construction and force/potential evaluation in 65 milliseconds. The study clearly showcases both programmability and performance benefits of flexible parallel constructs over more monolithic parallel loops.
Anodal Transcranial Direct Current Stimulation Shows Minimal, Measure-Specific Effects on Dynamic Postural Control in Young and Older Adults: A Double Blind, Sham-Controlled Study

We investigated whether stimulating the cerebellum and primary motor cortex (M1) using transcranial direct current stimulation (tDCS) could affect postural control in young and older adults. tDCS was employed using a double-blind, sham-controlled design, in which young (aged 18–35) and older adults (aged 65+) were assessed over three sessions, one for each stimulatory condition–M1, cerebellar and sham. The effect of tDCS on postural control was assessed using a sway-referencing paradigm, which induced platform rotations in proportion to the participant’s body sway, thus assessing sensory reweighting processes. Task difficulty was manipulated so that young adults experienced a support surface that was twice as compliant as that of older adults, in order to minimise baseline age differences in postural sway. Effects of tDCS on postural control were assessed during, immediately after and 30 minutes after tDCS. Additionally, the effect of tDCS on corticospinal excitability was measured by evaluating motor evoked potentials using transcranial magnetic stimulation immediately after and 30 minutes after tDCS. Minimal effects of tDCS on postural control were found in the eyes open condition only, and this was dependent on the measure assessed and age group. For young adults, stimulation had only offline effects, as cerebellar stimulation showed higher mean power frequency (MPF) of sway 30 minutes after stimulation. For older adults, both stimulation conditions delayed the increase in sway amplitude witnessed between blocks one and two until stimulation was no longer active. In conclusion, despite tDCS’ growing popularity, we would caution researchers to consider carefully the type of measures assessed and the groups targeted in tDCS studies of postural control.
Steroid Interaction with a Single Potentiating Site Is Sufficient to Modulate GABA-A Receptor Function

Neuroactive steroids are efficacious potentiators of GABA-A receptors. Recent work has identified a site in the α1 subunit of the GABA-A receptor, that is essential for potentiation by steroids. However, each receptor contains two copies of the α1 subunit. We generated concatemers of subunits so that the α1 subunits could be mutated separately and examined the consequences of mutations that remove potentiation by most neurosteroids (α1 Q241L, α1 Q241W). Concatemers were expressed in Xenopus laevis oocytes, and activation by GABA, potentiation by neurosteroids, and the agonist activity of piperidine-4-sulfonic acid (P4S) were determined. When the α1 Q241L mutation is present in α1 subunits the EC50 for activation by GABA is shifted to higher concentration and potentiation by neurosteroids is diminished. When the α1 Q241W mutation is expressed, the EC50 for GABA is shifted to lower concentration, the relative efficacy of P4S is increased, and potentiation by neurosteroids is diminished. Mutation of only one α1 subunit does not produce the full effect of mutating both sites. Overall, the data demonstrate that at a macroscopic level, the presence of a single wild-type steroid-binding site is sufficient to mediate responses to steroid, but both must be mutated to completely remove the effects of steroids. Differences between the two sites seem to be relatively subtle.
Geometric lower bounds for generalized ranks

We revisit a geometric lower bound for Waring rank of polynomials (symmetric rank of symmetric tensors) of Landsberg and Teitler and generalize it to a lower bound for rank with respect to arbitrary varieties, improving the bound given by the "non-Abelian" catalecticants recently introduced by Landsberg and Ottaviani. This is applied to give lower bounds for ranks of multihomogeneous polynomials (partially symmetric tensors); a special case is the simultaneous Waring decomposition problem for a linear system of polynomials. We generalize the classical Apolarity Lemma to multihomogeneous polynomials and give some more general statements. Finally we revisit the lower bound of Ranestad and Schreyer, and again generalize it to multihomogeneous polynomials and some more general settings.
Functional Specificity of Callosal Connections in Tree Shrew Striate Cortex

Although callosal connections have been shown to link extensive regions of primary visual cortex, the distribution of these connections with respect to the map of visual space and the map of orientation preference remains unclear. Here we combine optical imaging of intrinsic signals with injection of fluorescent microspheres to assess the functional specificity of callosal connections in the tree shrew. By imaging both hemispheres simultaneously while presenting a series of spatially restricted stimuli, we find that a substantial region of visual space is represented bilaterally. Each hemisphere includes a representation of the ipsilateral visual field that is highly compressed relative to that of the contralateral visual field and is most extensive in the lower visual field, where ∼30ο of central visual space are represented bilaterally. Callosal connections extend throughout the region of bilateral representation but terminate in a spatially restricted manner that links visuotopically corresponding sites in the two hemispheres. In contrast, callosal connections appear to terminate without regard for the map of orientation preference, showing little sign of the orientation-specific modular and axial specificity that is characteristic of long-range horizontal connections. By coordinating the activity in the two hemispheres in a way that preserves nearest neighbor relationships, callosal connections may best be viewed as elements of local circuits that operate within a single bilateral representation of visual space.
Strategy use, listening problems, and motivation of high- and low-proficiency Chinese listeners

ABSTRACT Building on previous listening strategy research, the author aimed to explore the differences between Chinese high-proficiency listeners (HLs) and low-proficiency listeners (LLs) on their strategy use, problems, and motivation in native language (L1) listening. It involved 1,290 Grade 7 and 1,515 Grade 9 students. Both quantitative and qualitative methods, including a listening comprehension test, questionnaires, and interviews, were adopted. The findings indicated that HLs possessed more types of strategies and used strategies more frequently and effectively than LLs. HLs not only reported fewer listening problems but also had a better awareness of listening problems and use of problem-solving strategies than LLs. Both HLs and LLs agreed with the importance of listening but showed little interest in doing listening tasks. The similarities and differences between the findings of this study and those of second-language listening research and implications for planning effective instruction to enhance native language listening proficiency are discussed.
Bone marrow-derived cells can acquire cardiac stem cells properties in damaged heart

Experimental data suggest that cell‐based therapies may be useful for cardiac regeneration following ischaemic heart disease. Bone marrow (BM) cells have been reported to contribute to tissue repair after myocardial infarction (MI) by a variety of humoural and cellular mechanisms. However, there is no direct evidence, so far, that BM cells can generate cardiac stem cells (CSCs). To investigate whether BM cells contribute to repopulate the Kit+ CSCs pool, we transplanted BM cells from transgenic mice, expressing green fluorescent protein under the control of Kit regulatory elements, into wild‐type irradiated recipients. Following haematological reconstitution and MI, CSCs were cultured from cardiac explants to generate ‘cardiospheres’, a microtissue normally originating in vitro from CSCs. These were all green fluorescent (i.e. BM derived) and contained cells capable of initiating differentiation into cells expressing the cardiac marker Nkx2.5. These findings indicate that, at least in conditions of local acute cardiac damage, BM cells can home into the heart and give rise to cells that share properties of resident Kit+ CSCs.