Miracle-dz/UniFAR-FTUs huggingface dataset:
Generation of regulatory dendritic cells and CD4+Foxp3+ T cells by probiotics administration suppresses immune disorders

The beneficial effects of probiotics have been described in many diseases, but the mechanism by which they modulate the immune system is poorly understood. In this study, we identified a mixture of probiotics that up-regulates CD4+Foxp3+ regulatory T cells (Tregs). Administration of the probiotics mixture induced both T-cell and B-cell hyporesponsiveness and down-regulated T helper (Th) 1, Th2, and Th17 cytokines without apoptosis induction. It also induced generation of CD4+Foxp3+ Tregs from the CD4+CD25− population and increased the suppressor activity of naturally occurring CD4+CD25+ Tregs. Conversion of T cells into Foxp3+ Tregs is directly mediated by regulatory dendritic cells (rDCs) that express high levels of IL-10, TGF-β, COX-2, and indoleamine 2,3-dioxygenase. Administration of probiotics had therapeutical effects in experimental inflammatory bowel disease, atopic dermatitis, and rheumatoid arthritis. The therapeutical effect of the probiotics is associated with enrichment of CD4+Foxp3+ Tregs in the inflamed regions. Collectively, the administration of probiotics that enhance the generation of rDCs and Tregs represents an applicable treatment of inflammatory immune disorders.
MicroRNA miR-34 Inhibits Human Pancreatic Cancer Tumor-Initiating Cells

Background MicroRNAs (miRNAs) have been implicated in cancer initiation and progression via their ability to affect expression of genes and proteins that regulate cell proliferation and/or cell death. Transcription of the three miRNA miR-34 family members was recently found to be directly regulated by p53. Among the target proteins regulated by miR-34 are Notch pathway proteins and Bcl-2, suggesting the possibility of a role for miR-34 in the maintenance and survival of cancer stem cells. Methodology/Principal Findings We examined the roles of miR-34 in p53-mutant human pancreatic cancer cell lines MiaPaCa2 and BxPC3, and the potential link to pancreatic cancer stem cells. Restoration of miR-34 expression in the pancreatic cancer cells by either transfection of miR-34 mimics or infection with lentiviral miR-34-MIF downregulated Bcl-2 and Notch1/2. miR-34 restoration significantly inhibited clonogenic cell growth and invasion, induced apoptosis and G1 and G2/M arrest in cell cycle, and sensitized the cells to chemotherapy and radiation. We identified that CD44+/CD133+ MiaPaCa2 cells are enriched with tumorsphere-forming and tumor-initiating cells or cancer stem/progenitor cells with high levels of Notch/Bcl-2 and loss of miR-34. More significantly, miR-34 restoration led to an 87% reduction of the tumor-initiating cell population, accompanied by significant inhibition of tumorsphere growth in vitro and tumor formation in vivo. Conclusions/Significance Our results demonstrate that miR-34 may restore, at least in part, the tumor suppressing function of the p53 in p53-deficient human pancreatic cancer cells. Our data support the view that miR-34 may be involved in pancreatic cancer stem cell self-renewal, potentially via the direct modulation of downstream targets Bcl-2 and Notch, implying that miR-34 may play an important role in pancreatic cancer stem cell self-renewal and/or cell fate determination. Restoration of miR-34 may hold significant promise as a novel molecular therapy for human pancreatic cancer with loss of p53–miR34, potentially via inhibiting pancreatic cancer stem cells.
Further experiments in biocomputational structural analysis of malware

Initial work on structural analysis of malware using the nature-inspired technique of projecting malware signatures into the amino acid/protein domain was promising in a number of ways, including the demonstration of potential links with real-world pathogen proteins. That initial work was necessarily speculative and limited by a number of experimental factors. The aim of the research reported here is to address some of these limitations and to repeat, with malware code and signatures that can be assured as genuine, the experiments previously reported but with enhancements and improvements. Intriguingly, the outcome is the same: for some reason that is not yet known, matching artificial malware code consensuses after multiple alignment against protein databases returns a high proportion of naturally occurring viral proteins.
MB-LITE: A robust, light-weight soft-core implementation of the MicroBlaze architecture

Due to the ever increasing number of microprocessors which can be integrated in very large systems on chip the need for robust, easily modifiable microprocessors has emerged. Within this paper a light-weight cycle compatible implementation of the MicroBlaze architecture called MB-LITE is presented in an attempt to fill the gap in quality between commercial and open source processors. Experimental results showed that MB-LITE obtains very high performance compared with other open source processors while using very few hardware resources. The microprocessor can be easily extended with existing IP thanks to an easily configurable data memory bus and a wishbone bus adapter. All components are modular to optimize design reuse and are developed using a two-process design methodology for improved performance, simulation and synthesis speeds. All components have been thoroughly tested and verified on a FPGA. Currently an architecture with four MB-LITE cores in a NoC architecture is in development which will be implemented in 90nm process technology.
Algunos datos sobre la profundidad que alcanza el arte de cerco en la pesqueria atunera tropical

The fishing gear is, together with the fishing vessel, one of the essential elements of the fishing activity. In the case of purse seine, the length and size of the net plays an important part in fishing efficiency. This paper tries to establish some relationships between the physical characteristics of the purse seine net and the effective depth which it reaches, by placing a depth meter on the net, close to the netting, which registered the depth of the net during each of the 32 trips carried out in the Atlantic and Indian Oceans. The data obtained, from two different vessels, show that the maximum depths reached by the net were 74% and 67% of the draft of the vessels, which were 220 and 272 m, respectively. The maximum speed of the descent of the net was attained, in most cases, in the first two minutes after the start of the operation.
Interventions to improve water quality for preventing diarrhoea.

BACKGROUND Diarrhoeal diseases are a leading cause of mortality and morbidity, especially among young children in developing countries. While many of the infectious agents associated with diarrhoeal disease are potentially waterborne, the evidence for reducing diarrhoea in settings where it is endemic by improving the microbiological quality of drinking water has been equivocal. OBJECTIVES To assess the effectiveness of interventions to improve water quality for preventing diarrhoea. SEARCH STRATEGY We searched the Cochrane Infectious Diseases Group Specialized Register (December 2005), CENTRAL (The Cochrane Library 2005, Issue 4), MEDLINE (December 2005), EMBASE (December 2005), and LILACS (December 2005). We also handsearched relevant conference proceedings, contacted researchers and organizations working in the field, and checked references from identified studies. SELECTION CRITERIA Randomized and quasi-randomized controlled trials comparing interventions aimed at improving the microbiological quality of drinking water with no intervention in children and adults living in settings where diarrhoeal disease is endemic. DATA COLLECTION AND ANALYSIS Two authors independently assessed trial quality and extracted data. We used meta-analyses to estimate pooled measures of effect, where appropriate, and investigated potential sources of heterogeneity using subgroup analyses. MAIN RESULTS Thirty trials (including 38 independent comparisons) covering over 53,000 participants met the inclusion criteria. Differences between the trials limited the comparability of results and pooling by meta-analysis. In general, the evidence suggests that interventions to improve the microbiological quality of drinking water are effective in preventing diarrhoea both for populations of all ages and children less than five years old. Subgroup analyses suggest that household interventions are more effective in preventing diarrhoea than interventions at the water source. Effectiveness was positively associated with compliance. Effectiveness was not conditioned on the presence of improved water supplies or sanitation in the study setting, and was not enhanced by combining the intervention to improve water quality with other common environmental interventions intended to prevent diarrhoea. AUTHORS' CONCLUSIONS Interventions to improve water quality are generally effective in preventing diarrhoea, and interventions to improve water quality at the household level are more effective than those at the source. Significant heterogeneity among the trials suggests that the actual level of effectiveness may depend on a variety of conditions that research to date cannot fully explain. Rigorous, blinded, multi-arm randomized controlled trials conducted over a longer duration in a variety if settings may help clarify the potential effectiveness.
Bilateral Simultaneous Rhegmatogenous Retinal Detachment following Laser in situ Keratomileusis

A 21-year-old woman developed simultaneous rhegmatogenous retinal detachment after laser in situ keratomileusis (LASIK) in both eyes. She underwent pars plana vitrectomy surgery combined with endolaser photocoagulation and silicone oil tamponade in the right eye. A week later, pneumatic retinopexy was done in the left eye. As the retinal tear did not seal, 360° scleral buckling surgery was performed and retina was attached. Bilateral simultaneous rhegmatogenous retinal detachment after LASIK for correction of myopia can be a serious complication. Patients should be informed about the possibility of this complication.
Variable phenotypic expressivity in a Swiss family with autosomal dominant retinitis pigmentosa due to a T494M mutation in the PRPF3 gene

Purpose To characterize the clinical, psychophysical, and electrophysiological phenotypes in a five-generation Swiss family with dominantly inherited retinitis pigmentosa caused by a T494M mutation in the Precursor mRNA-Processing factor 3 (PRPF3) gene, and to relate the phenotype to the underlying genetic mutation. Methods Eleven affected patients were ascertained for phenotypic and genotypic characterization. Ophthalmologic evaluations included color vision testing, Goldmann perimetry, and digital fundus photography. Some patients had autofluorescence imaging, Optical Coherence Tomography, and ISCEV-standard full-field electroretinography. All affected patients had genetic testing. Results The age of onset of night blindness and the severity of the progression of the disease varied between members of the family. Some patients reported early onset of night blindness at age three, with subsequent severe deterioration of visual acuity, which was 0.4 in the best eye after their fifties. The second group of patients had a later onset of night blindness, in the mid-twenties, with a milder disease progression and a visual acuity of 0.8 at age 70. Fundus autofluorescence imaging and electrophysiological and visual field abnormalities also showed some degree of varying phenotypes. The autofluorescence imaging showed a large high-density ring bilaterally. Myopia (range: −0.75 to −8) was found in 10/11 affected subjects. Fundus findings showed areas of atrophy along the arcades. A T494M change was found in exon 11 of the PRPF3 gene. The change segregates with the disease in the family. Conclusions A mutation in the PRPF3 gene is rare compared to other genes causing autosomal dominant retinitis pigmentosa (ADRP). Although a T494M change has been reported, the family in our study is the first with variable expressivity. Mutations in the PRPF3 gene can cause a variable ADRP phenotype, unlike in the previously described Danish, English, and Japanese families. Our report, based on one of the largest affected pedigree, provides a better understanding as to the phenotype/genotype description of ADRP caused by a PRPF3 mutation.
Helical Structure and Packing Orientation of the S2 Segment in the Shaker K+ Channel

Six transmembrane segments, S1–S6, cluster around the central pore-forming region in voltage-gated K+ channels. To investigate the structural characteristics of the S2 segment in the Shaker K+ channel, we replaced each residue in S2 singly with tryptophan (or with alanine for the native tryptophan). All but one of the 23 Trp mutants expressed voltage-dependent K+ currents in Xenopus oocytes. The effects of the mutations were classified as being of low or high impact on channel gating properties. The periodicity evident in the effects of these mutations supports an α-helical structure for the S2 segment. The high- and low-impact residues cluster onto opposite faces of a helical wheel projection of the S2 segment. The low-impact face is also tolerant of single mutations to asparagine. All results are consistent with the idea that the low-impact face projects toward membrane lipids and that changes in S2 packing occur upon channel opening. We conclude that the S2 segment is a transmembrane α helix and that the high-impact face packs against other transmembrane segments in the functional channel.
Morphological Plasticity and Phylogeny in a Monogenean Parasite Transferring between Wild and Reared Fish Populations

It is widely accepted that disease interactions between cultured and wild fish occur repeatedly, although reported cases have mainly relied just on the observation of similar symptoms in affected populations. Whether there is an explicit pathogen transfer between fish stocks, or each develops its own pathogen population, has been insufficiently studied and rarely supported by molecular tools. In this study, we used population dynamics and genetic structure of the monogenean Furnestinia echeneis in reared and neighbouring wild sea bream to indicate pathogen transfer, characterized by the phenotypic plasticity of the parasite attachment apparatus and the lack of phylogenetic differentiation. The observed pattern of genetic variation inferred by nuclear DNA Internal Transcribed Spacer 1 (ITS1) and mtDNA cytochrome C oxidase 1 (COI), between parasite populations is most likely caused by a recent shared demographic history like a reduced species area in the last glacial period. In spite of such recent expansion that populations underwent, F. echeneis shows differentiation in haptor morphometry as an adaptive trait in closely related populations at the aquaculture site. This suggests that differentiation in morphology may occur relatively rapidly in this species and that adaptive forces, not the speciation process, drives this monogenean parasitation. On the other hand, the observed phylogenetic inertia suggests a low to moderate gene flow (based on FST) between parasites in cultured and wild fish, evidencing for the first time the transfer of pathogens at the aquaculture site inferred by a molecular tool.
Demand Forecasting in Deregulated Electricity Markets

day ahead demand forecasting is essential for the efficient operation of electricity companies in the competitive electricity markets. Both the power producers and consumer needs single compact and robust demand forecasting tool for the efficient power system planning and execution. This research work proposes a day ahead short term demand forecasting for the competitive electricity markets using Artificial Neural Networks (ANNs). Historical demand data are collected for the month of January 2014 from PJM electricity markets. The work proposes the approach to reduce prediction error for electricity demands and aims to enhance the accuracy of next day electricity demand forecasting. Two types of demand forecasting models: classical forecasting and correlation forecasting models are proposed, explained and checked against each other. Proposed models are applied on real world case, PJM electricity markets for forecasting the demand on weekly working day, weekly off day and weekly middle day. The Mean Absolute Percentage Error (MAPE) for the two proposed models in the three respective cases is evaluated and analyzed. Results present that with all respects a day ahead demand forecasting through the correlation model are best and suitable for PJM electricity markets and produce less error with comparison of other classical models.
Onco-Regulon: an integrated database and software suite for site specific targeting of transcription factors of cancer genes

Transcription factors (TFs) bind at multiple sites in the genome and regulate expression of many genes. Regulating TF binding in a gene specific manner remains a formidable challenge in drug discovery because the same binding motif may be present at multiple locations in the genome. Here, we present Onco-Regulon (http://www.scfbio-iitd.res.in/software/onco/NavSite/index.htm), an integrated database of regulatory motifs of cancer genes clubbed with Unique Sequence-Predictor (USP) a software suite that identifies unique sequences for each of these regulatory DNA motifs at the specified position in the genome. USP works by extending a given DNA motif, in 5′→3′, 3′ →5′ or both directions by adding one nucleotide at each step, and calculates the frequency of each extended motif in the genome by Frequency Counter programme. This step is iterated till the frequency of the extended motif becomes unity in the genome. Thus, for each given motif, we get three possible unique sequences. Closest Sequence Finder program predicts off-target drug binding in the genome. Inclusion of DNA-Protein structural information further makes Onco-Regulon a highly informative repository for gene specific drug development. We believe that Onco-Regulon will help researchers to design drugs which will bind to an exclusive site in the genome with no off-target effects, theoretically. Database URL: http://www.scfbio-iitd.res.in/software/onco/NavSite/index.htm
An alternative strategy for high throughput generation and characterization of monoclonal antibodies against human plasma proteins using fractionated native proteins as immunogens

Construction of a monoclonal antibody (mAb) bank containing a vast variety of antibodies against human tissue proteins is important for proteomic research. A novel strategy of subtractive immunization using fractionated native proteins was developed for high throughput generation of mAb against human plasma proteins. By this novel approach, the bottleneck of antigen preparation can be overcome by combining repeated immunization of animals with subtracted fractions of plasma or tissue proteins and identification of target antigen by immunoprecipitation/mass spectrum strategies. Plasma freshly collected from healthy adults was pooled and three fractions were prepared by size exclusion chromatography. Mice were immunized with the fractionated plasma proteins, and 205 strains of hybridomas secreting mAb were obtained after two‐round subtractive immunizations and cell fusions. In the first round, 110 strains of hybridomas were established, in which 77 strains secreting mAb were identified against 10 human plasma high‐abundant proteins. In the second round, plasma fraction I was absorbed with mAb against IgM, IgG, ceruloplasmin and haptoglobin. The absorbed fraction I was used as immunogen for the second round immunization and cell fusion. Ninety‐five strains of hybridomas secreting mAb were obtained. Although the target antigens of mAb from 82 strains of hybridomas were identified as IgM, IgA, α2‐macroglobulin and fibrinogen, about 85% antibodies obtained from this round were identified as new antibodies when compared with mAb obtained in the first round immunization with plasma fraction I. The results suggest that subtractive immunization with fractionated plasma proteins followed by identification of antigens with immunoprecipitation/mass spectrum may be an effective approach for rapid preparation of mAb against high‐and medium‐abundant plasma or tissue proteins.
Addressing learning and complexity: Application of a farmer-expert joint learning approach to improve soil conservation: The cases of Angereb and Enkulal watersheds, Lake Tana sub-basin

In the highlands of Ethiopia, where intensive agriculture is practiced, land resources are being depleted at an alarming rate. Balancing soil and water conservation (SWC) measures with the use of effective technologies and farm management practices against the current level of land degradation is a growing challenge to smallholder farmers, who are striving to meet immediate economic objectives, on the one hand, and sustainable environment, on the other. Past SWC programs focused more on land degradation and they used a top-down approach. Top-down programs tended to focus more on the symptoms of erosion through subsidized terracing rather than on the root causes of land resource degradation. There was less emphasis on integrating local knowledge of land users and planning together with farmers.
Perspectives on Neuroscience and Behavior

adult hippocampal neurogenesis supports pattern separation, which can facilitate adaptation to complex environments. Now it has been shown that within a group of genetically identical mice, those that roamed through a larger area of a complex environment had greater hippocampal neurogenesis. Forty inbred female mice were placed in a complex environment at 5 weeks of age and their movement was monitored with a radiofrequency identification passive integrated transponder for 15 weeks and then hippocampal neurogenesis was assessed. Locomotion measured as total number of antenna contacts did not significantly relate to neurogenesis (r = 0.13), but neurogenesis did relate to distance traveled as measured by unique, nonrepetitive antenna contacts (r = 0.34). The variability of cumulative roaming entropy (cRE), a measure of the territorial range covered, increased over the 15 weeks, and during the last 24 days, it more strongly related to neurogenesis (r = 0.46) than locomotion or distance traveled. although there were reliable differences in cRE during the first 24 days, this did not relate significantly to neurogenesis (r = 0.24), indicating that it is the increase in individual differences in cRE that emerged during the observation period that best relate to neurogenesis (Freund and others 2013). as cRE is low if mice travel longer distances to just attend to a few stable spots and cRE is high if mice spend their travel evenly over the entire cage, it is the mastery of the additional cognitive challenge met by the high cRE mice that best relates to neurogenesis. Thus, not only do stable individual differences in exploratory activity emerge over time in genetically identical mice but also the mastery of the cognitive challenge in navigating a complex environment relates best to increased neurogenesis. It should now be possible to independently vary mastery of cognitive challenges and neurogenesis to better understand the temporal relationships and mechanisms involved. an improved understanding of this process can have important applications at the clinical level.