Miracle-dz/UniFAR-FTUs huggingface dataset:
Revisiting the Ancylostoma caninum secretome provides new information on hookworm-host interactions

Hookworm infection is a major tropical parasitic disease affecting almost 500 million people worldwide. These soil-transmitted helminths can survive for many years in the intestine of the host, where they feed on blood, causing iron deficiency anaemia and other complications. To avoid the host’s immune response the parasite releases excretory/secretory products (ESPs), a complex mixture of glycans, lipids and proteins that represent the major host-parasite interface. Using a combination of separation techniques such as SDS-PAGE and OFFGEL electrophoresis, in combination with state-of-the-art mass spectrometry we have reanalysed the dog hookworm, Ancylostoma caninum, ESPs (AcES). We identified 315 proteins present in the AcES, compared with just 105 identified in previous studies. The most highly represented family of proteins is the SCP/TAPs (90 of the 315 proteins), and the most abundant constituents of AcES are homologues of the tissue inhibitors of metalloproteases (TIMP) family. We identified putative vaccine candidates and proteins that could have immunomodulatory effects for treating inflammatory diseases. This study provides novel information about the proteins involved in host-hookworm interactions, and constitutes a comprehensive dataset for the development of vaccines and the discovery of new immunoregulatory biologics.
Extreme copy number variation at a tRNA ligase affecting phenology and fitness in yellow monkeyflowers

Copy number variation (CNV) is a major part of the genetic diversity segregating within populations, but remains poorly understood relative to single nucleotide variation. Here, we report on a tRNA ligase gene (Migut.N02091; RLG1a) exhibiting unprecedented, and fitness-relevant, CNV within an annual population of the yellow monkeyflower Mimulus guttatus. RLG1a variation was associated with multiple traits in pooled population sequencing (PoolSeq) scans of phenotypic and phenological cohorts. Resequencing of inbred lines revealed intermediate frequency three-copy variants of RLG1a (trip+; 5/35 = 14%), and trip+ lines exhibited elevated RLG1a expression under multiple conditions. trip+ carriers, in addition to being over-represented in late-flowering and large-flowered PoolSeq populations, flowered later under stressful conditions in a greenhouse experiment (P < 0.05). In wild population samples, we discovered an additional rare RLG1a variant (high+) that carries 250-300 copies of RLG1a totaling ∼5.7Mb (20-40% of a chromosome). In the progeny of a high+ carrier, Mendelian segregation of diagnostic alleles and qPCR-based copy counts indicate that high+ is a single tandem array unlinked from the single copy RLG1a locus. In the wild, high+ carriers had highest fitness in two particularly dry and/or hot years (2015 and 2017; both p < 0.01), while single copy individuals were twice as fecund as either CNV type in a lush year (2016: p < 0.005). Our results demonstrate fluctuating selection on CNVs affecting phenological traits in a wild population, suggest that plant tRNA ligases mediate stress-responsive life-history traits, and introduce a novel system for investigating the molecular mechanisms of gene amplification.
Evaluating Methods of Correcting for Multiple Comparisons Implemented in SPM12 in Social Neuroscience fMRI Studies: An Example from Moral Psychology

In fMRI research, the goal of correcting for multiple comparisons is to identify areas of activity that reflect true effects, and thus would be expected to replicate in future studies. Finding an appropriate balance between trying to minimize false positives (Type I error) while not being too stringent and omitting true effects (Type II error) can be challenging. Furthermore, the advantages and disadvantages of these types of errors may differ for different areas of study. In many areas of social neuroscience that involve complex processes and considerable individual differences, such as the study of moral judgment, effects are typically smaller and statistical power weaker, leading to the suggestion that less stringent corrections that allow for more sensitivity may be beneficial, but also result in more false positives. Using moral judgment fMRI data, we evaluated four commonly used methods for multiple comparison correction implemented in SPM12 by examining which method produced the most precise overlap with results from a meta-analysis of relevant studies and with results from nonparametric permutation analyses. We found that voxel-wise thresholding with family-wise error correction based on Random Field Theory provides a more precise overlap (i.e., without omitting too few regions or encompassing too many additional regions) than either clusterwise thresholding, Bonferroni correction, or false discovery rate correction methods.
Investigation of a calibration concept for optimum performance of adaptive antenna systems

A calibration concept for an adaptive antenna system has been developed. It consists of two steps: (1) an off-line calibration of passive components after manufacture; and (2) an on-line calibration of active components during operation. Off-line calibration measurements have been performed and analyzed using an array antenna for the 1.71-1.785 GHz frequency range, which is equipped with calibration ports for precise phase and amplitude calibration of the element coefficients. The influence of calibration-inaccuracies, mutual coupling effects, and nonideal beam-patterns are critically discussed.
Short title: Response to iron deficiency during germination Title: Vacuolar iron stores gated by NRAMP3 and NRAMP4 are the primary source of iron in germinating seeds

During seed germination, iron (Fe) stored in vacuoles is exported by the redundant NRAMP3 and NRAMP4 transporter proteins. A double nramp3 nramp4 mutant is unable to mobilize Fe stores and does not develop in the absence of external Fe. We used RNA sequencing to compare gene expression in nramp3 nramp4 and wild type during germination and early seedling development. Even though sufficient Fe was supplied, the Fe-responsive transcription factors bHLH38, 39, 100 and 101 and their downstream targets FRO2 and IRT1 mediating Fe uptake were strongly upregulated in the nramp3 nramp4 mutant. Activation of the Fe deficiency response was confirmed by increased ferric chelate reductase activity in the mutant. At early stages, genes important for chloroplast redox control (FSD1, SAPX), Fe homeostasis (FER1, SUFB) and chlorophyll metabolism (HEMA1, NYC1) were downregulated, indicating limited Fe availability in plastids. In contrast, expression of FRO3, encoding a ferric reductase involved in Fe import into the mitochondria, was maintained and Fe-dependent enzymes in the mitochondria were unaffected in nramp3 nramp4. Together these data show that a failure to mobilize Fe stores during germination triggered Fe deficiency responses and strongly affected plastids but not mitochondria. Author contributions: E.L. B, V.S. G.T. , A.E. M. , R.T. G. performed the experiments; E.L. B. , V.S. G.T. , S.M. analysed the RNA-seq data set; S.T. and J.B. conceived the project; E.L. B, S.T. and J.B. wrote the article with contributions of the other authors. CC-BY-ND 4.0 International license available under a not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which was this version posted April 24, 2018. ; https://doi.org/10.1101/306894 doi: bioRxiv preprint
NemaLife: A structured microfluidic culture device optimized for aging studies in crawling C. elegans

Caenorhabditis elegans is a powerful animal model in aging research. Standard longevity assays on agar plates involve the tedious task of picking and transferring animals to prevent younger progeny from contaminating age-synchronized adult populations. Large-scale studies employ progeny-blocking drugs or sterile mutants to avoid progeny contamination, but such manipulations change adult physiology and alter the influence of reproduction on normal aging. Moreover, for some agar growth-based technology platforms, such as automated lifespan machines, reagents such as food or drugs cannot be readily added/removed after initiation of the study. Current microfluidic approaches are well-suited to address these limitations, but in their liquid-based environments animals swim rather than crawl, introducing swim-induced stress in the lifespan analysis. Here we report a simple microfluidic device that we call NemaLife that features: 1) an optimized micropillar arena in which animals can crawl, 2) sieve channels that separate progeny and prevent the loss of adults from the arena during culture maintenance, and 3) ports which allow rapid accessibility to feed the adult-only population and introduce reagents as needed. Culture maintenance and liquid manipulation are performed with simple hand-held syringes to facilitate integration of our technology into general laboratory protocols. Additionally, device geometry and feeding protocols were designed to emulate the body gait, locomotion, and lifespan of animals reared on agar. We validated our approach with longevity analyses of classical aging mutants (daf-2, age-1, eat-2, and daf-16) and animals subjected to RNAi knockdown of age-related genes (age-1 and daf-16). We also showed that healthspan measures such as pharyngeal pumping and tap-induced stimulated reversals can be scored across the lifespan. Overall, the capacity to generate reliable lifespan and physiological data from the NemaLife chip underscores the potential of this device to accelerate healthspan and lifespan investigations in C. elegans.
Dynamic state feedback control of constrained robot manipulators

The problem of simultaneous motion and force control of a constrained robot manipulator is studied. It is recognized that the degrees of freedom of the manipulator are reduced in the presence of constraints. A dynamic model suitable for motion and force control is derived. Both motion and force control loops are exactly linearized and decoupled by using a dynamic nonlinear state feedback and a nonlinear state transformation. Separate inputs are designated for control of the end effector motion and the constraint force. The system stability, in particular the force control stability, is theoretically analyzed. The application of the proposed control method to redundant manipulators is discussed. <<ETX>>
Reinforcement learning method for DEDS supervision

In this paper, based on a new way of specifying the system close-loop behavior, we propose a reinforcement learning method for discrete event dynamic system (DEDS) supervision. By means of the concept of subconnection neural networks we develop a new reinforcement learning structure which is adaptive to DEDS supervision, present the close relationship between reinforcement learning and the neural network, and build a foundation for the further development of our reinforcement learning based on neural network theory. Using two examples about the optimization and control of telecommunication networks, we have illustrated the application prospect of our method. Computer simulations have confirmed its effectiveness.
Effect of growth stage on fodder yield and quality of dual purpose sorghum

Mwangi PG, Gachuiri CK, Mbugua PN. 2017. Effect of growth stage on fodder yield and quality of dual purpose sorghum. Trop Drylands 1: 100-104. Improved Dual Purpose Sorghum (IDPS) (Sorghum bicolor-Var Ikinyaruka) were yielded at six physiological growth stages to evaluate the impact of growth stage on crop and feed quality. Six treatments based on sorghum growth’s physiological stage were randomly administered to the plot in a block and replicated three times. The treatments were IDPS yielded at bloom stage (PS1), soft dough stage (PS2), hard dough stage (PS3), physiological maturity stage (stalks with grains), (PS4), physiological maturity stage (stalks without grains) (PS5), and 1 month post grain reap (PS6). The parameters monitored were Dry Matter (DM) crop, Crude Protein (CP), Neutral Detergent fiber (NDF), Acid Detergent Fiber (ADF), Acid Detergent Lignin (ADL), In vitro Dry Matter Digestibility (IVDMD) and shoot count. The highest DM crop (18.0 ton/ha) was achieved at PS4 secernated with 8.69, 12.75, 16.27 17.04 and 13.04 ton/ha for PS1, PS2, PS3, PS5 and PS6, respectively. CP reduced with maturity from 8.6 at PS1 to 7.98, 7.96, 7.61, and 6.77 to 6.72 at PS2, PS3, PS4, PS5 and PS6 respectively. NDF and ADF at PS1, PS2, PS3, PS4, PS5 and PS6 were 54.4, 60.8, 65.71, 65.93, 66.73 70.3 and 27.93, 35.96, 41.98, 41.97, 42.04, 46.05 respectively. ADL was 3.44, 5.03, 7.38, 7.39, 7.42, and 8.3 for PS1, PS2, PS3, PS4, PS5 and PS6 respectively. Highest fodder IVDMD of 60.72 was at PS1 secernated with 60.12, 54.73, 53.82, 53.56 and 45.75 achieved at PS2, PS3, PS4, PS5 and PS6 respectively. The PS3 growth stage yielded in fodder material with highest nutritive value while highest fodder yields were achieved at PS4. Reaping at PS5 supplied both fodder and grains for livestock and human consumption respectively. It was proven that crop and quality of IDPS were affected by age at reaping time.
Version Control with Git: Powerful Tools and Techniques for Collaborative Software Development

Version Control with Git takes you step-by-step through ways to track, merge, and manage software projects, using this highly flexible, open source version control system. Git permits virtually an infinite variety of methods for development and collaboration. Created by Linus Torvalds to manage development of the Linux kernel, it's become the principal tool for distributed version control. But Git's flexibility also means that some users don't understand how to use it to their best advantage. Version Control with Git offers tutorials on the most effective ways to use it, as well as friendly yet rigorous advice to help you navigate Git's many functions. With this book, you will: Learn how to use Git in several real-world development environments Gain insight into Git's common-use cases, initial tasks, and basic functions Understand how to use Git for both centralized and distributed version control Use Git to manage patches, diffs, merges, and conflicts Acquire advanced techniques such as rebasing, hooks, and ways to handle submodules (subprojects) Learn how to use Git with Subversion Git has earned the respect of developers around the world. Find out how you can benefit from this amazing tool with Version Control with Git.
Toward Endemic Deployment of Educational Simulation Games: A Review of Progress and Future Recommendations

This article presents a conceptual analysis of simulation game adoption and use across university faculty. The metaphor of epidemiology is used to characterize the diffusion of simulation games for teaching and learning. A simple stock-flow diagram is presented to illustrate this dynamic. Future scenarios for simulation game adoption are presented, based on alternative diffusion behaviors. University strategies for increasing simulation game use are explored. It is concluded that while creating endemic use of simulation games by faculty is unlikely, we can employ measures that will significantly expand the stock of faculty acting as simulation game instructors.
Interneuronal mechanisms of hippocampal theta oscillation in full-scale model of the CA1 circuit

The hippocampal theta rhythm plays important roles in information processing; however, the mechanisms of its generation are not well understood. We developed a data-driven, supercomputer-based, full-scale (1:1) model of the CA1 area and studied its interneurons during theta oscillations. Theta rhythm with phase-locked gamma oscillations and phase-preferential discharges of distinct in terneuronal types spontaneously emerged from the isolated CA1 circuit without rhythmic inputs. Perturbation experiments identified parvalbumin-expressing interneurons and neurogliaform cells, as well as interneuronal diversity itself, as important factors in theta generation. These simulations reveal new insights into the spatiotemporal organization of the CA1 circuit during theta oscillations.
Intraspecific variations in macronutrient, amino acid, and fatty acid composition of mass-cultured Teleaulax amphioxeia (Cryptophyceae) strains

To compare the nutritional quality of TPG (Teleaulax / Plagioselmis / Geminigera) clade species of cryptomonads with that of RHO (Rhodomonas / Rhinomonas / Storeatula) clade species 6 Teleaulax amphioxeia (TA) and 1 Rhinomonas sp. strains were mass-cultured in newly designed 500-L photobioreactors to the end of exponential growth phase. Intraspecific variations (IVs) in terms of one standard deviation among the 6 TA strains in the compositions of the three macronutrients were 41.5 (protein), 89.8 (lipid), and 15.6% (carbohydrate) of the mean. When harvested from stationary growth phase mean compositions of essential amino acids (EAAs, 47.3%) and non-EAAs (52.7%) of the 2 TA strains, CR-MAL07 and CR-MAL08-2, were similar to those of a Chroomonas strain. The IVs between the 2 TA strains in the composition of EAAs (10.3 and 2.4) and non-EAAs (8.5 and 2.1% of the mean) were rather smaller than those of saturated fatty acids (30.3 and 26.1) and unsaturated fatty acids (UFAs, 12.0 and 12.5% of the mean) in f/2-Si and urea-based compound fertilizer (UCF) culture media, respectively. Mean compositions of eicosapentaenoic acid (EPA, 17.9%) and docosahexaenoic acid (DHA, 12.7%) of total fatty acids of the 2 TA strains were higher than those that of a Chroomonas strain. EPA and DHA compositions exhibited similar level of IVs between the 2 TA strains in f/2-Si (14.6 and 11.0) and UCF media (12.6 and 13.5% of the mean). Thus, the nutritional quality in terms of amino acids, UFAs, EPA, and DHA in a TPG clade species, T. amphioxeia was comparable to those of RHO clade species with notable IVs. Practically, biotechnological targets for TPG clade cryptomonad strains might be subspecies or clone level.
Caenorhabditis elegans heterochromatin factor SET-32 plays an essential role in transgenerational establishment of nuclear RNAi-mediated epigenetic silencing

Epigenetic inheritance contributes fundamentally to transgenerational physiology and fitness. Mechanistic understanding of RNA-mediated chromatin modification and transgenerational epigenetic inheritance, which in C. elegans can be triggered by exogenous double-stranded RNA (exo-dsRNA) or facilitated by endogenous small interfering RNAs (endo-siRNAs), has mainly been limited to the post-initiation phases of silencing. Indeed, the dynamic process by which nuclear RNAi engages a transcriptionally active target, before the repressive state is stably established, remains largely a mystery. Here we found that the onset of exo-dsRNA-induced nuclear RNAi is a transgenerational process, and that establishment requires SET-32, one of the three putative histone methyltransferases (HMTs) that are required for H3K9me3 deposition at the nuclear RNAi targets. We also performed multigenerational whole-genome analyses to examine the establishment of silencing at endogenous targets of germline nuclear RNAi. The nuclear Argonaute protein HRDE-1 is essential for the maintenance of nuclear RNAi. Repairing a loss-of-function mutation in hrde-1 by CRISPR restored the silencing of endogenous targets in animals carrying wild type set-32. However, for numerous endogenous targets, repairing the hrde-1 mutation in a set-32;hrde-1 double mutant failed to restore their silencing states in up to 20 generations after the hrde-1 repair, using a similar genome editing approach. We found that despite a prominent role in the establishment of silencing, however, set-32 is completely dispensable for the maintenance of silencing once HRDE-1-dependent gene repression is established. Our study indicates that: 1) establishment and maintenance of siRNA-guided transcriptional repression are two distinct processes with different genetic requirements; and 2) the rate-limiting step of the establishment phase is a transgenerational, chromatin-based process. In addition, our study reveals a novel paradigm in which a heterochromatin factor primarily functions to promote the establishment of transgenerational silencing, expanding mechanistic understanding of the well-recognized role of heterochromatin in epigenetic maintenance.
Genome-wide analyses of empathy and systemizing: correlations with psychiatric conditions, psychological traits, and education

Background: Empathy and systemizing are dimensions of individual differences in cognition, and reveal areas of difficulty or strength in different psychiatric conditions. However, it is unclear how they contribute to genetic risk or resilience in various psychiatric conditions. Methods: Here we report the largest genome-wide association study (GWAS) to date of empathy and systemizing using the Empathy Quotient (EQ) (n = 46,861) and the Systemizing Quotient-Revised (SQ-R) (n = 51,564) in participants from 23andMe, Inc. Results: Both traits had a modest but significant narrow-sense heritability (EQ: 0.11; se = 0.014; P= 1.7x10-14 and SQ-R: 0.12; se = 0.012; P=1.2x10-20). As predicted, based on earlier work, we confirmed a female-advantage on the EQ and a male-advantage on the SQ-R in our large sample. However, we did not identify significant differences in heritability between sexes. We found significant genetic correlation between the variants conferring higher EQ scores and higher risk for schizophrenia (P_FDRadjusted = 1.84x10-4) and anorexia nervosa (P_FDRadjusted = 4.05x10-3), extraversion, NEO-conscientiousness, and subjective wellbeing. The genetic variants conferring higher scores for the SQ-R were correlated with higher risk for schizophrenia (P_FDRadjusted = 8.64x10-3), with NEO-Openness to experience, and measures of educational attainment. Conclusions: This study provides the first genetic confirmation of the roles of empathy and systemizing in psychiatric conditions, psychological traits and education.
The Particular Mapping of the Web Graph

The paper presents an approach to particular mapping of a web sub-graph. This sub-graph contain the nearest surroundings of an actual web page. Our work deals with acquiring relevant hyperlinks of a base web site, generation of adjacency matrix, distance matrix and matrix of converted distances of hyperlinks, detection of compactness of web representation and visualization of its graphical representation. The paper introduces LWP algorithm - our design of technique for the hyperlink filtration. Our access attempts to help user in the orientation within the web graph.