Miracle-dz/UniFAR-FTUs huggingface dataset:
Whole-genome draft assembly of Populus tremula x P. alba clone INRA 717-1B4

Abstract Populus trichocarpa and P. deltoides are the only Populus species known to date to have a publicly available nuclear genome sequence that has been assembled to chromosomes and annotated (https://phytozome.jgi.doe.gov/). Here we focus on the clone INRA 717-1B4, a female P. tremula x P. alba (P. x canescens) interspecific hybrid that is universally used by scientists worldwide as a tree model in transgenic experiments. The already available INRA 717-1B4 nuclear genomic resource (v1.1 of sPta717 at http://aspendb.uga.edu/index.php/databases/spta-717-genome) presents only INRA 717-1B4 genomic regions with high similarity to the P. trichocarpa genomic reference sequences. We assembled draft genomic scaffolds by a combination of de novo assembly with reference-based assembly using 30x resequencing NGS data (Illumina MiSeq® and Ion Torrent Ion PGM™) of INRA 717-1B4. In total, 419,969 scaffolds of length larger than 500 bp were generated. The mean length of the scaffolds is 2,166 bp and the size of the largest scaffold 84,573 bp. The N50 contig length is 3,850 bp when considering contigs larger than 1,000 bp. Probably due to the high level of heterozygosity of this interspecific hybrid, the accumulated scaffold length is with 0.9 GB about twice the expected size of the haploid nuclear genome. DNA sequences of the genomic scaffolds of INRA 717-1B4 are publicly available for Blast analyses and download via the new INRA web portal at https://urgi.versailles. inra.fr/Species/Forest-trees/Populus/Clone-INRA-717-1B4/. This new genomic sequence resource will complement the already available INRA 717-1B4 resources and will facilitate the future optimization of genetic transformation experiments to discover gene function.
Effect of substituting guinea grass with sunflower hulls on production performance and digestion traits in fattening rabbits

The objective of this study was to evaluate the use of sunflower hulls (SH) to substitute guinea grass (GG), traditionally used as a fibre source in the diets of fattening rabbits, on production performance, coefficients of total tract apparent digestibility (CTTAD) of nutrients, gastrointestinal tract development and caecal fermentation. A total of 160 mixed sex Hyla commercial meat rabbits were allocated to 4 experimental groups (40 per treatment) differing in the SH level inclusion in the diet offered to rabbits from 40 to 90 d of age: 0, 30, 60 and 90 g/kg on as-fed basis: SH0, SH30, SH60 and SH90 groups, respectively. Growth performance was recorded from 47 to 90 d of age, CTTAD of nutrients from 86 to 90 d of age, and gastrointestinal tract development, caecal fermentation and carcass traits were determined at 90 d of age. Increasing substitutions of SH in the diet indicated effects on growth performance, as higher feed intake and lower feed efficiency were observed in SH90 compared with SH0 (P-linear<0.05). Moreover, the higher SH substitution diet (SH60 and SH90) increased the relative caecum weight (P-linear<0.05). A linear negative effect of SH inclusion was observed for the digestibility of neutral detergent fibre (CTTAD from 0.294 to 0.232) and acid detergent fibre (CTTAD from 0.182 to 0.136; P-linear<0.05). Dietary SH substitution level had a quadratic effect on the villus height of the duodenum, jejunum and ileum obtained (P-quadratic<0.05), and the highest were observed in the SH60 group. There was a quadratic effect on the pH of caecum content (P-quadratic<0.05), and the lowest was 6.08 in SH30 group. The total volatil fatty acids increased linearly with increasing SH in diets (from 71.11 to 76.98 mmol/L; P-linear<0.05), and when dietary SH increased, the proportion of acetate tended to increase (P-linear<0.05), and the proportions of propionic and butyric were decreased (P-linear<0.05, respectively). Substitution of GG with SH had no effect on carcass characteristics and meat quality. The current work shows that SH can replace up to 60 g/kg in diets for fattening rabbits, with no adverse impact on aspects of production performance or digestion traits.
Isolation and identification of enteroviruses from sewage and sewage-contaminated water samples from Ibadan, Nigeria, 2012-2013

In 2010, we described sewage contaminated water (SCW) bodies that consistently yielded enteroviruses (EVs) in enterovirus surveillance (ES) sites in Lagos, Nigeria. By 2012, we demonstrated the presence and circulation of Wild Poliovirus 3 (WPV3) in these ES sites. Here we describe ES sites that consistently yield EVs in Ibadan metropolis southwest Nigeria. Twenty-five ES samples were collected by grab method from nine sites between October, 2012 and March, 2013. Samples were concentrated and four (RD, HEp2C, MCF-7 and L20B) different cell lines used for virus isolation from the concentrates. Isolates were subjected to RNA extraction, cDNA synthesis, PanEnterovirus 5l-UTR and VP1 assays. Unidentifiable isolates were further subjected to species-specific RT-PCR assays. Amplicons were sequenced, isolates identified and subjected to phylogenetic analysis. Twenty-five isolates were recovered from 8 (32%) of the 25 ES samples collected. Twenty-three of the isolates were identified as EVs by the PanEntero5l-UTR assay. Thirteen (57%) of the 23 EVs were positive for the VP1 assay, and identified as Coxsackievirus B3 (CVB3) (1 isolate), CVB6 (1 isolate), E6 (2 isolates), E7 (5 isolates), E11 (1 isolate), E12 (1 isolate) and E13 (2 isolates). None and 2 (25%) of the remaining isolates were positive for the EV-B and EV-C assays, respectively. The 2 EV-C positive enteroviruses were isolated on MCF-7. This study describes three very productive ES sites, and documents the presence of CVB3, CVB6, E6, E7, E11, E12 and, E13 in Ibadan, Nigeria. It shows that including other cell lines in EV isolation protocols can broaden the diversity of EV types recoverable.
Association between the brain-derived neurotrophic factor Val66Met polymorphism and overweight/obesity in Mexican pediatric population

Background The functional brain-derived neurotrophic factor (BDNF) rs6265 (G196A; Val66Met) single nucleotide polymorphism has been associated with eating disorders, BMI and obesity in distinct populations, both adult and pediatric, with contradictory results involving either Val or Met as the risk variant. Aim of the study To determine the association between the BDNF Val66Met polymorphism and BMI in Mexican children and adolescents. Methods BDNF Val66Met genotyping by restriction fragment length polymorphism and nutritional status characterized by their BMI-for-age z-scores (BAZ) from pediatric volunteers recruited in Mexico City (n=498) were analyzed by Fisher’s exact test association analysis. Standardized residuals (R) were used to determine which genotype/allele had the major influence on the significant Fisher’s exact test statistic. Odds ratios were analyzed to measure the magnitude and direction of the association between genotype and normal weight (≥ −2 SD < +1 SD) and overweight (≥ +1 SD, including obesity, Ow+Ob) status with 95% confidence intervals to estimate the precision of the effect as well as 95% credible intervals to obtain the most probable estimate. Results Comparisons between GG (Val/Val), GA (Val/Met) and AA (Met/Met) genotypes or Met homozygotes vs. Val carriers (combination of GG and GA genotypes) showed significant differences (p=0.034 and p=0.037, respectively) between normal weight and the combined overweight and obese pediatric subjects. Our data showed that children/adolescents homozygous for the A allele have increased risk of overweight compared to the Val carriers (Bayes OR= 4.2, 95% CI**[1.09 - 33.1]). Conclusion This is the first study showing the significant association between the BDNF rs6265 AA (Met/Met) genotype and overweight/obesity in Mexican pediatric population. Mexico has one of the highest pediatric overweight and obesity prevalence BDNF has been associated with body weight regulation. The BDNF rs6265 SNP (G196A; Val66Met) has been associated with eating disorders, BMI and obesity, with contradictory results in both adults and children. We found significant associations between BDNF Val66Met AA (Met/) genotype and overweight/obesity in Mexican pediatric population Met homozygote children/adolescents increased the risk almost seven times of being classified in the overweight group (Ow+Ob) relative to Val carriers Abbreviations BDNF brain-derived neurotrophic factor WHO World Health Organization CNS central nervous system RFLP restriction fragment length polymorphism SNP single nucleotide polymorphism BAZ BMI-for-age z-score SD standard deviation Ow overweight Ob obesity OR odds ratio CI confidence interval CI** credible interval
Giant cell tumor of dorsal vertebrae-a rare case report with review of literature

A 32-year-old well-built male presented to the Orthopaedics clinic with major complaints of low backache with both lower limbs weakness and disturbed bladder/ bowel habits. An osteolytic lesion was seen at tenth thoracic vertebra with anterior compression on the spinal cord on radio-imaging. Giant cell tumor (GCT) of dorsal vertebral body is an uncommon entity and total en bloc excision is difficult. Complete intralesional tumor excision with reconstruction was performed. Histopathological examination was suggestive of GCT. Our patient is doing well after one year of followup, without any signs of recurrence of the tumor and is ambulant with support. We discuss in brief about incidence, presentation and various treatment modalities available for spinal GCT.
Clustering of Brown Planthopper Biotype Based on RAPD-PCR

Random amplified polymorphic DNA (RAPD) technique was used to differentiate two brown planthopper biotypes, that were multiplied in the greenhouse. Ten selected random decamer RAPD primers produced unique DNA band patterns for each individual brown planthopper. However, no single primer produced DNA band that could differentiate the two brown planthopper biotype populations. Nonetheless, analysis of the DNA band patterns was able to cluster the majority of the individual samples according to their respective biotypes. Molecular data analysis also indicated greater genetic variation within biotype population than among biotypes.
Analysis of multihop lightwave networks

The authors present an analytical solution to the performance analysis of multihop lightwaves networks for both store-and-forward and hot potato routing with packet compression, taking into account the effects of packet misrouting and time out. The inefficiencies due to both misrouting and time out are investigated. The two schemes are compared on the basis of total delay experienced by a packet in the network and the mean number of hops. Numerical results show that the inefficiencies arising from misrouting and reinjection can be offset if the compression ratio is sufficiently high. For example, in a 10240 user network, with a compression ratio of 10, the maximum number of new packets which can be placed onto the network per unit of time for the hot potato algorithm can be a factor of 4 larger than that for store and forward. Compression is therefore worthwhile. For smaller compression ratios, the inefficiencies due to misrouting and time out are severe. For the same 10240 user network with a fixed arrival rate ( lambda =0.05), it is observed that a small compression ratio (C=2) produces no advantage and that for very high compression ratios (C>or=15) an asymptotic limit on improvement sets in. <<ETX>>
Targeting stromal remodeling and cancer stem cell plasticity to overcome chemoresistance in triple negative breast cancer

The cellular and molecular basis of stromal cell recruitment, activation and crosstalk in carcinomas is poorly understood, limiting the development of targeted anti-stromal therapies. In mouse models of triple negative breast cancer (TNBC), Hh ligand produced by neoplastic cells reprogrammed cancer-associated fibroblast (CAF) gene expression, driving tumor growth and metastasis. Hh-activated CAFs upregulated expression of FGF5 and production of fibrillar collagen, leading to FGFR and FAK activation in adjacent neoplastic cells, which then acquired a stem-like, drug-resistant phenotype. Treatment with smoothened inhibitors (SMOi) reversed these phenotypes. Stromal treatment of TNBC patient-derived xenograft (PDX) models with SMOi downregulated the expression of cancer stem cell markers and sensitized tumors to docetaxel, leading to markedly improved survival and reduced metastatic burden. In the phase I clinical trial EDALINE, 3 of 12 patients with metastatic TNBC derived clinical benefit from combination therapy with the SMOi Sonidegib and docetaxel chemotherapy, with one patient experiencing a complete response. Markers of pathway activity correlated with response. These studies identify Hh signaling to CAFs as a novel mediator of cancer stem cell plasticity and an exciting new therapeutic target in TNBC. SIGNIFICANCE Compared to other breast cancer subtypes, TNBCs are associated with significantly worse patient outcomes. Standard of care systemic treatment for patients with non-BRCA1/2 positive TNBC is cytotoxic chemotherapy. However, the failure of 70% of treated TNBCs to attain complete pathological response reflects the relative chemoresistance of these tumors. New therapeutic strategies are needed to improve patient survival and quality of life. Here, we provide new insights into the dynamic interactions between heterotypic cells within a tumor. Specifically, we establish the mechanisms by which CAFs define cancer cell phenotype and demonstrate that the bidirectional CAF-cancer cell crosstalk can be successfully targeted in mice and humans using anti-stromal therapy.
SWEET11 and 15 as key players in seed filling in rice

Despite the relevance of seed filling mechanisms for crop yield, we still have only a rudimentary understanding of the pathways and transport processes for supplying the caryopsis with sugars. We hypothesized that the recently identified SWEET sucrose transporters may play important roles in nutrient import pathways in the rice caryopsis. We used a combination of mRNA quantification, histochemical analyses, translational promoter-reporter fusions and analysis of knock out mutants created by genomic editing to evaluate the contribution of SWEET transporters to seed filling. In rice caryopses, SWEET11 and 15 had the highest mRNA levels and proteins localized to four key sites: the nucellus proper at early stages, the nucellar projection close to the dorsal vein, the nucellar epidermis that surrounds the endosperm, and the aleurone. ossweet11;15 double knock-out lines accumulated starch in the pericarp while caryopses did not contain a functional endosperm. Jointly, SWEET11 and 15 show all hallmarks of being responsible for seed filling with sucrose efflux function at the nucellar projection and transfer across the nucellar epidermis/aleurone interface, delineating two major steps for apoplasmic seed filling, observations that are discussed in relation to observations made in rice and barely on the relative prevalence of these two potential import routes.
POWER CONTROL WITH ENERGY EFFICIENT AND RELIABLE ROUTING MAC PROTOCOL FOR WIRELESS SENSOR NETWORKS

In this paper a Distributed Power Control with Energy Efficient and Reliable Routing Protocol (DPC-EERRP) is developed in order to prolong the network life time with minimum energy consumption to enable continuous data forwarding without incurring energy waste of unrelated nodes by using E3-MAC Algorithm which enables all nodes on the path to stay active and/or increase their duty cycles and all other nearby nodes to sleep. To establish an effective transmission power control mechanism, the dynamics between LQI and RSSI values are studied. In order to minimize energy consumption Energy Efficient forwarding scheme is used in which the data forwarding probability is adaptively adjusted based on the measured loss conditions at the sink. To show the performance of our algorithm we compare the proposed routing protocol with Adaptive Energy Efficient Forwarding Routing (AEERRP). Simulation result shows the proposed scheme performs better than AEERRP
Analysis of active feature selection in optic nerve data using labeled fuzzy C-means clustering

Describes an iterative analysis technique that aids in the process of searching for an optimal set of features for classification, and its application to detection of early glaucoma from optic nerve data in an evolving data acquisition system. The selection and evaluation of features were done using fuzzy C-means clustering and support vector machines. The clustering method was updated using a semi-supervised process. The search space for feature selection was reduced using an active feature selection algorithm. Data samples from different stages of the evolving system are analyzed and evaluated.
Categorizing Web documents using competitive learning: an ingredient of a personal adaptive agent

This paper describes the application of competitive learning to categorize Web documents, which is one component of our adaptive Web agent. The agent learns the different categories of Web documents that the user is interested in, then finds and suggests new similar documents. We discuss the framework of the Web agent, the implementation of the document clustering and current results. This work therefore suggests a new application, rather than an improved learning algorithm.
A 1-GHz single-chip quadrature modulator

The design of an integrated quadrature modulator for a 800-MHz to 1-GHz frequency range is presented. It is shown that this modulator achieves a phase error of less than +or-3 degrees without any trimming or tuning. This performance was achieved by reducing the number of building blocks and keeping a symmetrical transistor structure even in the layout. To overcome the amplitude difference of the phase-shifted signals, a modulator principle is used rather than a multiplier principle. The circuit was implemented in a bipolar transistor array with an f/sub T/ of 9 GHz. >
Long Noncoding RNAs in Diabetes and Diabetic Complications.

SIGNIFICANCE Diabetes is associated with markedly accelerated rates of micro- and macrovascular complications that increase morbidity and mortality. Understanding the molecular mechanisms can promote much needed therapeutics. Recent Advances: Long noncoding RNAs (lncRNAs) are important regulators of gene regulation and cellular function and are emerging as important players in diabetes and its complications. There are number of examples in which lncRNAs are responsive to hyperglycemia and clearly involved in regulation of genes and pathways associated with the development of diabetic complications. CRITICAL ISSUES As there are likely thousands of lncRNAs that are expressed in any given tissue, understanding how they are regulated and function in the normal healthy state as well as pathological states is a challenge. FUTURE DIRECTIONS Further studies in how lncRNAs are involved in the development and progression of diabetic complications as well as development of methods to target dysregulated lncRNAs or evaluate them as biomarkers of early detection of organ dysfunction will be highly beneficial to treating diabetic patients.
Hybrid Apriori- An Improvement

In recent years, there has been a huge accumulation of data. The amount of data collected is said to be almost doubled every year. The paper explores the sense of Data Explosion . Seeking knowledge from massive data is one of the most desired attributes of Data Mining. Several techniques have evolved in order to retrieve the interesting patterns by data mining. One of them is Apriori Algorithm, which scans the database several times before pointing out the frequent patterns. But its drawback is that the time and cost of this algorithm is very high because of repetitive scanning of database. So, our approach focuses on removing this drawback. Our algorithm scans the database only once, and produces the frequent patterns in almost constant time. We have run our algorithm on databases having 100 to 10000 transactions, which showed that it took almost constant time.
A genetically encoded Ca2+ indicator based on circularly permutated sea anemone red fluorescent protein

Genetically-encoded calcium ion (Ca2+) indicators (GECIs) are indispensable tools for measuring Ca2+ dynamics and neuronal activities in vitro and in vivo. Red fluorescent protein (RFP)-based GECIs enable multicolor visualization with blue or cyan-excitable fluorophores and combined use with blue or cyan-excitable optogenetic actuators. Here we report the development, structure, and validation of a new red fluorescent Ca2+ indicator, K-GECO1, based on a circularly permutated RFP derived from the sea anemone Entacmaea quadricolor. We characterized the performance of K-GECO1 in cultured HeLa cells, dissociated neurons, stem cell derived cardiomyocytes, organotypic brain slices, zebrafish spinal cord in vivo, and mouse brain in vivo.
Force-dependent binding of vinculin to α-catenin regulates cell-cell contacts stability and collective cell behavior

The shaping of a multicellular body and repair of adult tissues require fine-tuning of cell adhesion, cell mechanics and intercellular transmission of mechanical load. Adherens junctions (AJs) are the major intercellular junctions by which cells sense and exert mechanical force on each other. However, how AJs adapt to mechanical stress and how this adaptation contributes to cell-cell cohesion and eventually to tissue-scale dynamics and mechanics remains largely unknown. Here, by analyzing the tension-dependent recruitment of vinculin, α-catenin and F-actin in function of stiffness, as well as the dynamics of GFP-tagged wt and mutated α-catenins, altered for their binding capability to vinculin, we demonstrate that the force-dependent binding of vinculin stabilizes α-catenin and is responsible for AJ adaptation to force. Challenging cadherin complexes mechanical coupling with magnetic tweezers, and cell-cell cohesion during collective cell movements, further highlight that tension-dependent adaptation of AJs regulates cell-cell contact dynamics and coordinated collective cell migration. Altogether, these data demonstrate that the force-dependent α-catenin/vinculin interaction, manipulated here by mutagenesis and mechanical control, is a core regulator of AJ mechanics and long-range cell-cell interactions. Summary statement Combining cell biology and biomechanical analysis, we show here that the coupling between cadherin complexes and actin trough tension-dependent α-catenin/vinculin association is regulating AJ stability and dynamics as well as tissue-scale mechanics.