Miracle-dz/UniFAR-FTUs huggingface dataset:
RECEIPT: REfine CoarsE-grained IndePendent Tasks for Parallel Tip decomposition of Bipartite Graphs

Tip decomposition is a crucial kernel for mining dense subgraphs in bipartite networks, with applications in spam detection, analysis of affiliation networks etc. It creates a hierarchy of vertex-induced subgraphs with varying densities determined by the participation of vertices in butterflies (2,2-bicliques). To build the hierarchy, existing algorithms iteratively follow a delete-update(peeling) process: deleting vertices with the minimum number of butterflies and correspondingly updating the butterfly count of their 2-hop neighbors. The need to explore 2-hop neighborhood renders tip-decomposition computationally very expensive. Furthermore, the inherent sequentiality in peeling only minimum butterfly vertices makes derived parallel algorithms prone to heavy synchronization. In this paper, we propose a novel parallel tip-decomposition algorithm -- REfine CoarsE-grained Independent Tasks (RECEIPT) that relaxes the peeling order restrictions by partitioning the vertices into multiple independent subsets that can be concurrently peeled. This enables RECEIPT to simultaneously achieve a high degree of parallelism and dramatic reduction in synchronizations. Further, RECEIPT employs a hybrid peeling strategy along with other optimizations that drastically reduce the amount of wedge exploration and execution time. We perform detailed experimental evaluation of RECEIPT on a shared-memory multicore server. It can process some of the largest publicly available bipartite datasets orders of magnitude faster than the state-of-the-art algorithms -- achieving up to 1100x and 64x reduction in the number of thread synchronizations and traversed wedges, respectively. Using 36 threads, RECEIPT can provide up to 17.1x self-relative speedup. Our implementation of RECEIPT is available at this https URL.
Efecto del tratamiento térmico sobre la presencia de virus en bulbos de ajo (Allium sativum L.)

Se evaluó la presencia de virus en bulbos de 24 variedades de ajo antes y después de ser termo tratadas usando la técnica serológica DAS-ELISA para los virus TEV, SLV, GarCLV, OYDV y LYSV. Los bulbos de ajo fueron expuestos a temperatura de 33 ± 1°C durante un período de seis semanas. Después del tratamiento térmico, 23 variedades tenían al menos un virus, sin embargo, ninguno de los cinco virus fue detectado en los bulbillos de la variedad Español, también, la variedad ChJO 13 fue positiva solamente a TEV. TEV fue el virus más persistente a través del tratamiento térmico. Independientemente del virus o variedad, el porcentaje de bulbillos positivos virus fue de 53,5 y 45,1% antes y después del tratamiento térmico respectivamente. La mayoría de los bulbillos mostró infecciones múltiples en diversas combinaciones. Solamente TEV y SLV aparecieron en infecciones simples o con un solo agente viral; después del tratamiento térmico solo el TEV conservó esta característica. La concentración viral de TEV no mostró cambios significativos antes y después del tratamiento térmico.
Preparation of strawberry jam and estimation of its nutritive value during storage

The processing of jam from strawberry was studied during storage and found successful from the sensory evaluation the mean score showed that T 2 (pulp to sugar ratio 1:1.25) was most preferred considering all the characters as colour, flavour, sweetness and overall acceptability followed by T 1 . After 2, 4 and 6 month of storage the moisture content had slightly increased. The initial TSS and total sugar content of strawberry jam was maximum in T 3 (67.25 % and 41.50 %, respectively) while these were minimum in T 1 (66.12 % and 40.07 %, respectively). This study revealed at the end of storage 0.29 to 1.00 % TSS and 5.14 to 5.89 % total sugar were reduced. At initial stage titratable acidity and pH level was found higher in T 1 (0.65 % and 2.81, respectively) and at the end of 6 months of storage titratable acidity and pH of this treatment were 0.69 % and 2.78, respectively. Ascorbic acid content of strawberry jam was found very low (14.75-17.49 mg 100 g -1 ). This study revealed ascorbic acid content of strawberry jam decreased during storage. After 6 month of storage the maximum reduction of ascorbic acid was noted in T 3 (14.44 %), while minimum in T 2 (11.06 %). Just after cooking β -carotene content of strawberry jam was found higher at T 1 (1.81 μg 100 g -1 ), and at the end of storage period it was 1.69 μg 100 g -1 . During 6 months of storage, maximum reduction of β -carotene was recorded in T 1 (6.6 %), while minimum in (3.5 %) from T 3 . Considering sensory evolution, nutrients content and storage study jam prepared form 1:1.25 pulp to sugar ratio i.e.T 2 formulation was found better.
Inheritance and molecular mapping of leaf rust resistance gene in hexaploid wheat Synthetic 45

To contain the infection of newly evolved leaf rust virulence(s), diverse source of germplasm need to be explored for identification of novel genes. In order to exploit wild resources, CIMMYT has developed a series of synthetic hexaploid wheat (SHW) by combining the accessions of D genome donor Triticum tauschii and T. durum. In the present study, Synthetic 45, was evaluated for effectiveness of its resistance against diverse leaf rust pathotypes. Mode of inheritance of resistance to understand the nature of genetics and molecular mapping to locate its chromosomal position were studied. Characterization of leaf rust resistance in Synthetic 45 by multi-pathotype tests showed a high degree of seedling resistance to 20 diverse pathotypes of leaf rust pathogen and adult plant resistance against two most prevalent pathotypes, 77-5 and 104-2. Inheritance studies showed that resistance in Synthetic 45 was governed by a single recessive gene. Molecular mapping and linkage with microsatellite markers, Xwmc432 and Xcfd15 have indicated that the resistance gene is located on short arm of 1D chromosome with 6.1 cM distal to Xwmc432 and 10.6 cM to Xcfd15 with 4.6 cM distance among the two markers. The gene identified in Synthetic 45 has been tentatively designated as LrSyn45.
Insulin Signaling-independent Activation of DAF-16 Shapes the Transcriptome during Normal Aging

The roles and regulatory mechanisms of transriptome changes during aging are unclear. It has been proposed that the transcriptome suffers decay during aging owing to age-associated down-regulation of transcription factors. In this study, we characterized the role of a transcription factor DAF-16, which is a highly conserved lifespan regulator, in the normal aging process of Caenorhabditis elegans. We found that DAF-16 translocates into the nucleus in aged wild-type worms and activates the expression of hundreds of genes in response to age-associated cellular stress. Most of the age-dependent DAF-16 targets are different from the canonical DAF-16 targets downstream of insulin signaling, indicating that activation of DAF-16 during aging is not due to reduced insulin signaling from DAF-2. Further analysis showed that it is due to the loss of proteostasis during aging, at least in part. We also found that without daf-16, dramatic gene expression changes occur as early as on adult day 2, indicating that DAF-16 acts to stabilize the transcriptome during normal aging. Our results thus reveal that normal aging is not simply a process in which the gene expression program descends into chaos due to loss of regulatory activities; rather, there is active transcriptional regulation that fights aging.
Oxford Nanopore sequencing in a research-based undergraduate course

Background Nanopore sequencing is a third generation genomic sequencing method that offers real time sequencing of DNA samples. Nanopore sequencing is an excellent tool for teaching because it involves cutting-edge sequencing methods and also helps students to develop a research mindset, where students can learn to identify and resolve problems that arise during an experiment. Results We, as a group of undergraduate biology students, were able to use nanopore sequencing to analyze a sample of pupfish DNA. We were able to accomplish this without computer science backgrounds and only some basic DNA extraction training. Although there were issues, such as inconsistent results across runs, we found it useful as a research learning experience and an application of the skills we learned. Conclusions As students, it was exciting to be able to experience this technology first hand and apply what we learned in the classroom. Nanopore sequencing holds potential for DNA sequencing of large fragments in real time. It allows students to be acquainted with novel technologies and the theories behind them. However, as with all new techniques, it does not have the same established support, and when students run into difficulties while using nanopore sequencing, it is often difficult to identify what went wrong.
Quantity and quality of particulate organic matter controls bacterial production in the Columbia River estuary

Estuaries function as “bioreactors” for fluvial materials in which microbial, biogeochemical, and ecological processes transform organic matter and nutrients prior to export to coastal oceans. The impact of estuarine bioreactors is linked to the bioavailability and residence time of fluvial material, and to rates of microbial activity. In the Columbia River estuary, water residence time is short (approximately 2 d), but particle residence time is extended by estuarine turbidity maxima (ETM). To investigate relationships between organic matter and microbial activity, samples were collected in spring and fall 2012 and summer 2013, and ETM particles were fractionated by settling velocity using an Owen‐style settling column. Data were also analyzed from 16 other sampling campaigns conducted in 1990–2009. The composition of suspended particulate matter shifted seasonally following the spring freshet and river phytoplankton bloom with decreasing organic content, increasing C/N ratio, and an increasing contribution of autochthonous particulate organic matter (POM) produced in four shallow lateral bays (based on del‐PO13C and pigment ratios). Heterotrophic bacterial production responded to seasonal changes in POM and correlated most strongly with estimates of labile particulate nitrogen during any particular season, and with the riverine flux of chlorophyll a (Chl a) across all seasons. Regression models suggest that labile particulate nitrogen and bacterial production can be predicted from sensor‐based measurements including turbidity, salinity, and temperature in the estuary and Chl a in the river. These results demonstrate that heterotrophic activity in the Columbia River estuary is controlled by POM lability, and by the degree to which ETM retain and concentrate POM.
Binding of the GTPase Sar1 to a Lipid Membrane Monolayer: Insertion and Orientation Studied by Infrared Reflection–Absorption Spectroscopy

Membrane-interacting proteins are polyphilic polymers that engage in dynamic protein–protein and protein–lipid interactions while undergoing changes in conformation, orientation and binding interfaces. Predicting the sites of interactions between such polypeptides and phospholipid membranes is still a challenge. One example is the small eukaryotic GTPase Sar1, which functions in phospholipid bilayer remodeling and vesicle formation as part of the multimeric coat protein complex (COPII). The membrane interaction of Sar1 is strongly dependent on its N-terminal 23 amino acids. By monolayer adsorption experiments and infrared reflection-absorption spectroscopy (IRRAS), we elucidate the role of lipids in inducing the amphipathicity of this N-terminal stretch, which inserts into the monolayer as an amphipathic helix (AH). The AH inserting angle is determined and is consistent with the philicities and spatial distribution of the amino acid monomers. Using an advanced method of IRRAS data evaluation, the orientation of Sar1 with respect to the lipid layer prior to the recruitment of further COPII proteins is determined. The result indicates that only a slight reorientation of the membrane-bound Sar1 is needed to allow coat assembly. The time-course of the IRRAS analysis corroborates a role of slow GTP hydrolysis in Sar1 desorption from the membrane.
Role of the Sh3 and Cysteine-Rich Domain 3 (STAC3) Gene in Proliferation and Differentiation of Bovine Satellite Cells

The STAC3 gene is a functionally undefined gene predicted to encode a protein containing two SH3 domains and one cysteine-rich domain. In this study, we determined the potential role of the STAC3 gene in proliferation and differentiation of bovine satellite cells. We isolated satellite cells from skeletal muscle of adult cattle and transfected them with STAC3 small interfering RNA (siRNA) or scrambled siRNA. Cell proliferation assays revealed that STAC3 knockdown had no effect on the proliferation rate of bovine satellite cells. We assessed the differentiation status of bovine satellite cells by quantifying the expression levels of myogenin and myosin heavy chain genes, and by quantifying fusion index. STAC3 knockdown stimulated mRNA and protein expression of myogenin, and myosin heavy chain 3 and 7, and increased fusion index of bovine satellite cells. These data together suggest that STAC3 inhibits differentiation of bovine satellite cells into myotubes. To determine the underlying mechanism, we identified and validated AP1μ1 as a STAC3-interacting protein by yeast two-hybrid screening and coimmunoprecipitation. In C2C12 cells, STAC3 knockdown decreased the expression level of AP1μ1 protein. In bovine satellite cells, STAC3 knockdown increased the membrane localization of glucose transporter 4 (GLUT4) and glucose uptake. These data together suggest the following mechanism by which STAC3 inhibits differentiation of bovine satellite cells: STAC3 increases AP1μ1 stability in cells; a high level of AP1μ1 keeps
Design of a Novel Serum-free Monolayer Differentiation System for Murine Embryonic Stem Cell-derived Chondrocytes for Potential High-content Imaging Applications

Cartilage defects have limited capacity for repair and are often replaced by fibrocartilage with inferior mechanical properties. To overcome the limitations of artificial joint replacement, high throughput screens (HTS) could be developed to identify molecules that stimulate differentiation and/or proliferation of articular cartilage for drug therapy or tissue engineering. Currently embryonic stem cells (ESCs) can differentiate into articular cartilage by forming aggregates (embryoid body (EB), pellet, micromass), which are difficult to image. I present a novel, singlestep method of generating murine ESC (mESC)-derived chondrocytes in monolayer cultures in chemically defined conditions. Mesoderm induction was achieved in cultures supplemented with BMP4, Activin A or Wnt3a. Prolonged culture with sustained Activin A, TGFβ3 or BMP4 supplementation led to robust chondrogenic induction. A short pulse of Activin A or BMP4 also induced chondrogenesis efficiently while Wnt3a acted as a later inducer. Long-term supplementation with Activin A or with Activin A followed by TGFβ3 may specifically promote iii articular cartilage formation. Thus, I devised a serum-free (SF) culture system to generate ESCderived chondrocytes without the establishment of 3D cultures or the aid of cell sorting. Cultures were governed by the same signaling pathways as 3D ESC differentiation systems and limb bud mesenchyme or articular cartilage explant cultures. I am also in the process of creating a Col2a1 promoter-controlled, Cre-inducible reporter cell line to be used in my SF culture system using the Multisite Gateway® cloning technology. ESCs undergoing chondrogenic differentiation can be identified and quantified in HTS via the expression of fluorescent proteins. In addition, this transgenic line can be used to isolate ESC-derived chondrocytes as well as their progeny via cell sorting or antibiotic selection for in-depth characterization. The modular design of my construct system allows transgenic lines to be generated using various promoters of chondrogenic marker genes to perform parallel HTS analyses.
A set of Arabidopsis genes involved in the accommodation of the downy mildew pathogen Hyaloperonospora arabidopsidis

The intracellular accommodation structures formed by plant cells to host arbuscular mycorrhiza fungi and biotrophic hyphal pathogens are cytologically similar but it remains unclear whether these interactions build on an overlapping genetic framework. In legumes, the malectin-like domain leucine-rich repeat receptor kinase SYMRK, the cation channel POLLUX and members of the nuclear pore NUP107-160 subcomplex are essential for symbiotic signal transduction and arbuscular mycorrhiza development. Here we identified members of these three groups in Arabidopsis thaliana and explored their impact on the interaction with the oomycete downy mildew pathogen Hyaloperonospora arabidopsidis (Hpa). We report that mutations in the corresponding genes reduced the reproductive success of Hpa as determined by sporangiophore and spore counts. We discovered that a developmental transition of haustorial shape occurred significantly earlier and at higher frequency in the mutants. Analysis of the multiplication of extracellular bacterial pathogens, Hpa-induced cell death or callose accumulation, as well as Hpa- or flg22-induced defence marker gene expression, did not reveal any traces of constitutive or exacerbated defence responses. These findings point towards an overlap between the plant genetic toolboxes involved in the interaction with biotrophic intracellular hyphal symbionts and pathogens in terms of the gene families involved. Author Summary Our work reveals genetic commonalities between biotrophic intracellular interactions with symbiotic and pathogenic hyphal microbes. The majority of land plants engages in arbuscular mycorrhiza (AM) symbiosis with phosphate-acquiring arbuscular mycorrhizal fungi to avoid phosphate starvation. Nutrient exchange in this interaction occurs via arbuscules, tree-shaped fungal structures, hosted within plant root cells. A series of plant genes including the Symbiosis Receptor-like kinase (SYMRK), members of the NUP107-160 subcomplex and nuclear envelope localised cation channels are required for a signalling process leading to the development of AM. The model plant Arabidopsis thaliana lost the ability to form AM. Although the ortholog of SYMRK was deleted during evolution, members of the malectin-like domain leucine-rich repeat receptor kinases (MLD-LRR-RKs) gene family, components of the NUP107-160 subcomplex, and an ortholog of the nuclear envelope-localized cation channel POLLUX, are still present in the Arabidopsis genome, and Arabidopsis leaf cells retained the ability to accommodate haustoria, presumed feeding structures of the obligate biotrophic downy mildew pathogen Hyaloperonospora arabidopsidis. We discovered that both of these plant-microbe interactions utilize a corresponding set of genes including the ortholog of POLLUX, members of the NUP107-160 subcomplex and members of the MLD-LRR-RK gene family, thus revealing similarities in the plant program for the intracellular accommodation of biotrophic organisms in symbiosis and disease.
The importance of phenotypic plasticity for plant success under environmental change

100 Introduction . 101 Materials and methods . 102 Results . 107 Discussion . 108 Conslusions . 113 Acknowledgements . 113 Supplementary materials . 114 General discussion . 126 Plant invasion under changes in mean environmental conditions . 126 Plant invasion under nutrient fluctuation . 129 Adaptive phenotypic plasticity. 131 Conclusion . 132 Author contributions . 133 Cited references . 134 Acknowledgements . 147
Location-specific consequences of beach seine and gillnet capture on upriver-migrating sockeye salmon migration behavior and fate

Fish released after capture, or fish interacting with gear but escaping, sometimes experience fishing-related incidental mortality (FRIM). For adult Pacific salmon migrations, knowing the magnitude of FRIM is important to estimate escapement accurately and to understand the total impact of a specific fishery. To determine how multiple gear types are associated with FRIM at different levels of maturity, we captured sockeye salmon (Oncorhynchus nerka) by both gill net and beach seine at three locations along their migration route (10%, 26%, and 72% of a 500 km freshwater migration) and determined their migratory success using biotelemetry. FRIM was higher for fish captured by gill net except at the location closest to spawning grounds. In addition, salmon captured by gill net at the lower river locations temporarily delayed migration, potentially indicating a requirement for lengthier recovery time compared with beach-seined fish. These results provide the first empirical and parallel comparison of these two common in-river fishing methods for salmon, revealing clear differences in FRIM between the two fishing methods in lower river fisheries and the importance of maturity.
TahcoRoll: An Efficient Approach for Signature Profiling in Genomic Data through Variable-Length k-mers

k-mer profiling has been one of the trending approaches to analyze read data generated by high-throughput sequencing technologies. The tasks of k-mer profiling include, but are not limited to, counting the frequencies and determining the occurrences of short sequences in a dataset. The notion of k-mer has been extensively used to build de Bruijn graphs in genome or transcriptome assembly, which requires examining all possible k-mers presented in the dataset. Recently, an alternative way of profiling has been proposed, which constructs a set of representative k-mers as genomic markers and profiles their occurrences in the sequencing data. This technique has been applied in both transcript quantification through RNA-Seq and taxonomic classification of metagenomic reads. Most of these applications use a set of fixed-size k-mers since the majority of existing k-mer counters are inadequate to process genomic sequences with variable-length k-mers. However, choosing the appropriate k is challenging, as it varies for different applications. As a pioneer work to profile a set of variable-length k-mers, we propose TahcoRoll in order to enhance the Aho-Corasick algorithm. More specifically, we use one bit to represent each nucleotide, and integrate the rolling hash technique to construct an efficient in-memory data structure for this task. Using both synthetic and real datasets, results show that TahcoRoll outperforms existing approaches in either or both time and memory efficiency without using any disk space. In addition, compared to the most efficient state-of-the-art k-mer counters, such as KMC and MSBWT, TahcoRoll is the only approach that can process long read data from both PacBio and Oxford Nanopore on a commodity desktop computer. The source code of TahcoRoll is implemented in C++14, and available at https://github.com/chelseaju/TahcoRoll.git.