Miracle-dz/UniFAR-FTUs huggingface dataset:
Network Coding Fundamentals

Network coding is an elegant and novel technique introduced at the turn of the millennium to improve network throughput and performance. It is expected to be a critical technology for networks of the future. This tutorial addresses the first most natural questions one would ask about this new technique: how network coding works and what are its benefits, how network codes are designed and how much it costs to deploy networks implementing such codes, and finally, whether there are methods to deal with cycles and delay that are present in all real networks. A companion issue deals primarily with applications of network coding.
Stable Isotope Analysis Of Two Mephitidae Species Reflects Population Trends And Landscape Structure

The eastern spotted skunk (Spilogale putorius) is a small omnivorous Carnivora similar in much of its natural history to the commonly found striped skunk (Mephitis mephitis). Spilogale putorius has experienced drastic population declines over a large portion of its geographic range. Many hypotheses for the decline of S. putorius have been proposed. δ13C and δ15N isotope analysis provides a unique opportunity to examine diet over an expanded time span. Thus was used on hair sampled from natural history collections, teaching collections, and road kills to examine dietary change for both S. putorius and M. mephitis from 1852 to 2012. Because stable isotope values of hair reflect the diet at the time the hair was grown, knowledge of molting patters is necessary when using hair in stable isotope studies. I determined molting patterns in S. putorius were similar to M. mephitis. When compared to M. mephitis molting patterns in S. putorius were delayed by approximately a month. Long-term farm and crop trends have not been examined in Kansas. I examined trends in average farm size, percent of land in farms, number of farms, number of irrigated farms, hectares of woodland, and hectares of17 different crops across Kansas from 1880 to 2007. Trends were observed in most crop types and provided support for a slow transition from small diversely planted farms to large scale monoculture in Kansas. I analyzed Kansas fur harvest trends for M. mephitis and S. putorius and detected corresponding declines in Kansas for both species. These declines were correlated with a reduction of maize in the landscape and agricultural intensification. Studies indicate the presence of melanin in colored feathers affects the δ13C and δ15N values of feather samples. I examined the effect of melanin on δ13C and δ15N values of hair from 8 mammal species but detected no effect. The effects of preservation techniques on δ13C and δ15N values of mammalian samples are also not well understood. I examined the effect of tanning as a preparation technique on δ13C and δ15N values of M. mephitis. Tanned hides were depleted in both stable isotopes compared to non-tanned hides. Diet of S. putorius and M. mephitis was related to landscape structure. Maize composed the highest proportion of the diet for both S. putorius and M. mephitis and has experienced change in the diet of S. putorius over time. In addition, increased δ15N variability was observed over time in these species, potentially suggesting decline of or exclusion from historical diet sources. This research provided useful insights into the effects of landscape structure on a declining mesocarnivore, and provided additional support for dietary change as a contributing factor to the decline of S. putorius. When combined, these data potentially provide evidence for a decline in S. putorius based in part on a reduction in the amount of maize in the landscape and agricultural intensification.
Physicochemical Controls on Spatiotemporal Distribution and Benthic Mat Severity of Didymosphenia geminata in Pine Creek, an Unregulated Watershed in Northern Pennsylvania

Didymosphenia geminata (Didymo) is a benthic freshwater diatom that has been globally expanding its range and extracellular stalk production in freshwater ecosystems. Didymo has been observed in reaches downstream of hypolimnetic reservoir releases in the northeastern US since 2007. This study focused on a newly observed (2013) Didymo occurrence in Pine Creek, a highly forested and unregulated watershed in north-central Pennsylvania. Study objectives included comparing contemporary distribution with historical data to provide insight on historical occurrence, quantifying physicochemical controls on Didymo distribution and benthic mat severity, and examining historical changes in water chemistry that might affect habitat suitability. At present, Didymo cellular distribution is limited to upper reaches of Pine Creek where median soluble reactive phosphorus (SRP) is 2.7 µg/L; median SRP was 4.8 µg/L at sites where Didymo was absent. At the epicenter of distribution in Pine Creek where SRP was consistently <2 µg/L, increased streamflow flashiness and water temperature were associated with decreased benthic mat severity. My results suggest SRP thresholds for Didymo proliferation may vary depending on whether streams are regulated by reservoirs with hypolimnetic releases. Mann–Kendall trends tests of a ∼20-y water chemistry dataset show that orthophosphate and sulfate concentrations decreased while pH increased within Pine Creek, which may have implications for Didymo habitat suitability. Further research is warranted to determine whether improving water quality following the industrial era may facilitate Didymo colonization.
Exploiting PLSA model and conditional random field for refining image annotation

This paper presents a new method for refining image annotation by integrating probabilistic latent semantic analysis(PLSA) with conditional random field(CRF). First a PLSA model with asymmetric modalities is constructed to predict a candidate set of annotations with confidence scores,and then model semantic relationship among the candidate annotations by leveraging conditional random field.In CRF,the confidence scores generated by the PLSA model and the Flickr distance between pairwise candidate annotations are considered as local evidences and contextual potentials respectively.The novelty of our method mainly lies in two aspects:exploiting PLSA to predict a candidate set of annotations with confidence scores as well as CRF to further explore the semantic context among candidate annotations for precise image annotation.To demonstrate the effectiveness of the method proposed in this paper,an experiment is conducted on the standard Corel dataset and its results are compared favorably with several state-of-the-art approaches.
Genome of octoploid plant maca (Lepidium meyenii) illuminates genomic basis for high altitude adaptation in the central Andes

Maca (Lepidium meyenii Walp, 2n = 8× = 64) of Brassicaceae family is an Andean economic plant cultivated on the 4000-4500 meters central sierra in Peru. Considering the rapid uplift of central Andes occurred 5 to 10 million years ago (Mya), an evolutionary question arises on how plants like maca acquire high altitude adaptation within short geological period. Here, we report the high-quality genome assembly of maca, in which two close-spaced maca-specific whole genome duplications (WGDs, ∼ 6.7 Mya) were identified. Comparative genomics between maca and close-related Brassicaceae species revealed expansions of maca genes and gene families involved in abiotic stress response, hormone signaling pathway and secondary metabolite biosynthesis via WGDs. Retention and subsequent evolution of many duplicated genes may account for the morphological and physiological changes (i.e. small leaf shape and loss of vernalization) in maca for high altitude environment. Additionally, some duplicated maca genes under positive selection were identified with functions in morphological adaptation (i.e. MYB59) and development (i.e. GDPD5 and HDA9). Collectively, the octoploid maca genome sheds light on the important roles of WGDs in plant high altitude adaptation in the Andes.
Integrated Identification of Disease Specific Pathways Using Multi-omics data

Motivation Identification of biological pathways plays a central role in understanding both human health and diseases. Although much work has previously been done to explore the biological pathways by using single omics data, little effort has been reported using multi-omics data integration, mainly due to methodological and technological limitations. Compared to single omics data, multi-omics data will help identifying disease specific functional pathways with both higher sensitivity and specificity, thus gaining more comprehensive insights into the molecular architecture of disease processes. Results In this paper, we propose two computational approaches that integrate multi-omics data and identify disease-specific biological pathways with high sensitivity and specificity. Applying our methods to an experimental multi-omics data dataset on muscular dystrophy subtypes, we identified disease-specific pathways of high biological plausibility. The developed methodology will likely have a broad impact on improving the molecular characterization of many common diseases. Contact yuewang@vt.edu Supplementary information Supplementary information attached.
Efficient Multi-GPU Algorithm for All-Pairs Shortest Paths

The shortest-path problem is a fundamental computer science problem with applications in diverse areas such as transportation, robotics, network routing, and VLSI design. The problem is to find paths of minimum weight between pairs of nodes in edge-weighted graphs, where the weight of a path p is defined as the sum of the weights of all edges of p. The distance between two nodes v and w is defined as the minimum cost of a path between v and w. The objective of the all-pairs shortest path (APSP) problem is to compute the distances between all pairs of nodes of a graph. In this paper, we present a new approach to solving the APSP problem for planar graphs that exploits the massive on-chip parallelism available in today's Graphics Processing Units (GPU). To harness this computing power for solving path problems in planar graphs, we exploit the community structure of input graphs and reformulate the problem in terms of matrix computations. Our algorithm, based on the Floyd-Warshall algorithm, has near quadratic complexity with respect to the number of nodes, while its matrix-based structure is regular enough to allow for efficient parallel implementation on the GPUs. By applying a divide-and-conquer approach, we are able to make use of multi-node GPU clusters, resulting in more than an order of magnitude speedup over fastest known Dijkstra-based GPU implementation and a two-fold speedup over a parallel Dijkstra-based CPU implementation.
Visualizing metabolic pathways: comparative genomics and expression analysis

As a large number of genomes are sequenced, interest turns to the functions and dynamics of the identified genes and how these influence the physiology of the organisms. Many genes code for enzymes that catalyze metabolic reactions producing energy and various molecules that constitute the core activities of the cell. Most of these reactions occur in a step-wise manner involving several enzymes and intermediates, and these can be portrayed graphically in the form of metabolic pathway maps. The ability to collect information en masse about expression profiles provides an opportunity to study the regulation of individual enzymes as well as of the pathways in which they exert their function. This article describes two integrated databases of metabolic pathways and genomes, available via the internet. We discuss how the analysis of metabolic pathways can provide support for the determination of gene functions, for comparisons of cellular networks and for the design of novel antimicrobial drugs.
Impact of Different Shading Levels on Growth, Yield and Quality of Potato (Solanum tuberosum L.)

In agroforestry systems (AFS), trees shade the understory crop to a certain extent. Potato is considered a shade-tolerant crop and was thus tested under the given total solar irradiance and climatic conditions of Southwestern Germany for its potential suitability in an AFS. To gain a better understanding of the effects of shade on growth, yield and quality; a three-year field experiment with different artificial shading levels (12%, 26% and 50%) was established. Significant changes in growth occurred at 50% shading. While plant emergence was not affected by shade, flowering was slightly delayed by about three days. Days until senescence also showed a delay under 50% shade. The number of tubers per plant and tuber mass per plant were reduced by about 53% and 69% under 50% shade. Depending on the year, tuber dry matter yield showed a decrease of 19–44% at 50% shade, while starch content showed no significant differences under shade compared to unshaded treatment. The number of stems per plant, plant height and foliage mass per plant as well as tuber fraction, black spot bruise and macronutrient content were unaffected. Overall, potato seems to tolerate shading and can therefore be integrated in an AFS, and can cope with a reduced total irradiance up to 26%.
DETERMINATION OF GENETIC VARIATION OF EGYPTIAN COWPEA (VIGNA UNGUICULATA (L.) WALP.) USING RAPD-PCR PATTERNS

Cowpea (Vigna unguiculata (L.) Walp. ) is the most important grain legume crop grown in tropical and subtropical regions. Seeds of cowpea have a high nutritional value containing high amount of protein (23–29%). Seeds of 19 landraces of cowpea (Vigna unguiculata) were obtained from gene bank of Cairo University (11 landraces) and from Agricultural Research Station Kafr El-Sheikh (Sakha) (8 varieties). The seeds planted till maturity. Random amplified polymorphic DNA (RAPD) was assayed to determine the genetic variation of 19 varieties of cowpea cultivated in different regions of Egypt. A total of five random primers were used in the study. Amplification of genomic DNA of Egyptian cowpea landraces with these RAPD primers yielded 54 fragments that could be scored, of which 45 were polymorphic. Number of amplified fragments with random primers ranged from 4 (OP 856) to 14 (OP 880). Percentage polymorphism ranged from 75% (OP 856) to a maximum of 100% (OP 889, OP 868, Op 808 and OP 880), with an average of 95%. A dendrogram produced by the Unweighted Pair Group Method with Arithmetic Mean (UPGMA) based on Jaccard‟s similarity coefficient revealed that the cowpea varieties divided into two groups which showed variability that may be exploited for crop improvement. The overall range of genetic similarities ranged from 0.48 to 0.93 in 19 landraces of cowpea which indicates there was high variability among the varieties. Based on genetic distance in RAPD analysis the landraces no. 9 and 12 appeared as most divergent and could be used in breeding programme of cowpea. It could be concluded that RAPD markers are important tools for genetic analysis for cowpea(Vigna unguiculata (L.) Walp. ).
Round Table: The Use of Metrics in Evaluating Research

The use of metrics for evaluating research is a hotly debated issue. The IMU/ICIAM/IMS report on Citation Statistics [1] highlighted the dangers of uncritical use of impact factors, which play an increasing role in funding, promotions and library purchases. Are impact factors and other such indices good measures of journal quality, and should they be used to evaluate research and individuals? What can be done about unethical practices like impact factor manipulation? Is there a role for metrics in evaluating research? Are there better alternatives? These were the topics of discussion at the ICM 2010 Round Table on Thursday, 26 August, between 6 and 8 p.m. It was chaired by John Ball, and organized by IMU’s Committee on Electronic Information and Communication (CEIC). This record of the Round Table consists of edited and shortened versions of the presentations by the panellists, together with excerpts from some of the contributions by participants in the discussion. A complete video is available at the IMU website http://www.mathunion. org/publications/ historic-material.
GENOME-WIDE ASSOCIATION STUDY FOR SOME MORPHOLOGICAL TRAITS IN IRANIAN BUFFALO

A genome-wide association study (GWAS) was carried out on Iranian water buffaloes with the objective of detecting genomic regions associated with some morphological traits. For this propos, a set of 376 water buffalo with phenotypic data from Azeri (N=246), Khuzestani (N=109) and Mazandarani (N=20) breeds were genotyped with Axiom® Buffalo Genotyping Array which contains 89,988 single nucleotide polymorphism (SNP) markers. Detecting genomic regions that associated with type traits was done using GenABEL package in R. In total, 8, 9, 9, 5, 7, 5, 12, 8 and 7genomic regions were detected that maybe associated with body length (BL), heart girth (HG - represented the circumference of the chest just behind the forelimbs), chest depth (CD), height-at-withers (HAW), and hip width (HIW), pin width (PW), hip to pin length (HP) and head size (HS) and horn length (HL) morphological traits, respectively. Annotation of these regions using the UMD3.1 Bostaurus Genome Assembly was performed to find putative candidate genes within the selected regions. Among the candidate genes identified in these regions GRB10, EGR1, ACAT2, SLC25A25, NRP1, FOXC2 and ABR genes are related to biological cell growth pathways and BMP2K, EGR1, CCIN, FRMPD1, ARPC5L, DNM1, FOXC2, ABR and MPP1 are related skeletal bone development biological pathways such as bone mineralization. Further investigation of these regions with additional data is necessary to confirm the associations and fine-map the QTL regions. Keywords: Genome wide association study, single nucleotide polymorphisms, Azeri, Khuzestaniand Mazandrani buffalo breeds.
A re-inducible gap gene cascade patterns the anterior-posterior axis of insects in a threshold-free fashion

Gap genes mediate the division of the anterior-posterior axis of insects into different fates through regulating downstream hox genes. Decades of tinkering the segmentation gene network of the long-germ fruit fly Drosophila melanogaster led to the conclusion that gap genes are regulated (at least initially) through a threshold-based French Flag model, guided by both anteriorly- and posteriorly-localized morphogen gradients. In this paper, we show that the expression patterns of gap genes in the intermediate-germ beetle Tribolium castaneum are mediated by a threshold-free ‘Speed Regulation’ mechanism, in which the speed of a genetic cascade of gap genes is regulated by a posterior gradient of the transcription factor Caudal. We show this by re-inducing the leading gap gene (namely, hunchback) resulting in the re-induction of the gap gene cascade at arbitrary points in time. This demonstrates that the gap gene network is self-regulatory and is primarily under the control of a posterior speed regulator in Tribolium and possibly all insects.
Archaeal ribosomal proteins possess nuclear localization signal-type motifs: implications for the origin of the cell nucleus

Eukaryotic cells are divided into the nucleus and the cytosol, and, to enter the nucleus, proteins typically possess short signal sequences, known as nuclear localization signals (NLSs). Although NLSs have long been considered as features unique to eukaryotic proteins, we show here that similar or identical protein segments are present in ribosomal proteins from the Archaea. Specifically, the ribosomal proteins uL3, uL15, uL18, and uS12 possess NLS-type motifs that are conserved across all major branches of the Archaea, including the most ancient groups Microarchaeota and Diapherotrites, pointing to the ancient origin of NLS-type motifs in the Archaea. Furthermore, by using fluorescence microscopy, we show that the archaeal NLS-type motifs can functionally substitute eukaryotic NLSs and direct the transport of ribosomal proteins into the nuclei of human cells. Collectively, these findings illustrate that the origin of NLSs preceded the origin of the cell nucleus, suggesting that the initial function of NLSs was not related to intracellular trafficking. Overall, our study reveals rare evolutionary intermediates among archaeal cells that can help elucidate the sequence of events that led to the origin of the eukaryotic cell.
Evidencia serológica de infección por herpesvirus caprino tipo 1 en cabras en México

En México no se han realizado estudios serológicos sobre herpesvirus caprino tipo 1 con el propósito de saber el estado de la infección por CpHV-1. Se llevó a cabo un análisis serológico para determinar la presencia de anticuerpos contra el virus usando un ELISA de bloqueo comercial para detección de anticuerpos contra la glicoproteína B (gB) y glicoproteína E (gE) del herpesvirus bovino tipo 1, de acuerdo con la prueba diagnóstica que se utiliza de forma rutinaria. De un total de 838 animales analizados, 123 (14.68 %) resultaron positivos a la prueba de ELISA. En los estados de Puebla, Morelos, Nuevo León, Ciudad de México, Guanajuato y Querétaro se encontró evidencia serológica de la presencia del CpHV-1 en cabras. Este reporte es el primer estudio que señala la presencia de anticuerpos contra herpesvirus caprino en cabras en México.
Maturation, Fertilization and Implantation of Cattle Ova Cultured in Different Media

Several experiments have been conducted to study factors affecting the maturation and fertilization of the cattle ova in the laboratory. Ovaries were collected from 77 cow reproductive systems in Al- Shuala Massacre- Baghdad. Oocytes have been obtained from these samples by OCRC method and finishing. Oocytes were classified into several grades from both methods, and then oocytes class A and B only were chosen for maturation, where oocytes were incubated in multiple media including; TCM-199, MEM, SOF, SOF+BCS, SOF+BSA in incubator 5% CO2, 90% humidity at 38.5oC temperature for 24 hours. Semen has been obtained by extracting of the epididymal tail, and then collected by using a sterile 5 ml syringe containing MEM media. Sperms were incubated with mature oocytes at a concentration of 1 × 10 6/ml of the cultivated media in the incubator for 30 hours for the fertilization and to obtain on zygotes. Zygotes were then isolated in the growing media. The developing embryos were monitored every 24 hours and up to 9 days until the reach blastocyst stage. Results indicate the possibility of obtaining embryos in vitro fertilization in an average 6.31% (111/1604), and the best media was by via using SOF + BCS media. The study also determined appropriate technologies to enhance in vitro fertilization. ORCS method showed a positive effect on increasing the rate of embryos production in vitro.
Attitudes toward Mathematics and Predictors of College Mathematics Grades: Gender Differences in a 4-Year Business College.

Abstract Differences between genders in previous math experience, perceived ability, and attitudes toward math have all been suggested as explanations for male superiority on standardized tests of mathematics. This study explored gender differences in attitudes in the context of a 4-year business college, a setting in which math backgrounds and perceived ability are virtually identical for males and females. Significant gender differences were found in several areas, and attitude variables were found to be useful in predicting grades. Results support the hypothesis that females prefer rote versus autonomous learning and that they choose familiar over novel situations. They are also less confident than males about their ability to do word problems.