Miracle-dz/UniFAR-FTUs huggingface dataset:
The Potential Rate of Increase of Corcyra Cephalonica (Staint.) On Sorghum

Abstract—A laboratory study of the biology of Corcyra cephalonica (Staint.) was made at 30°C and 70% r.h. on sorghum. The number of eggs laid per female, oviposition period, development time and survival from egg to adult were determined. The data were used to estimate the finite rate of increase and the intrinsic rate of natural increase of the moth. For the finite rate of increase (λ) the estimated value was 18 per lunar month, corresponding to an intrinsic rate of natural increase (r) of 2.9. The results are compared with published data and it is concluded that the pest potential of C. cephalonica has been, hitherto, underestimated. Résumé—Une étude sur la vie et le développement de Corcyra cephalonica (Staint.) à été effectuée en laboratoire a 30°C et à 70% r.h. sur le sorgho. Au cours de cette étude ont été calculés: le nombre d’oeufs pondus par femelle, la période de la ponte, la durée du développement et elle du. Passage de l’oeuf à l’adulte. Les données ont été utilisées pour déterminer le taux de croissance et le taux de multiplication natveelle de l’insecte. En ce qui concerne le taux de croissance (λ) il est de 18 par mois lunaise, le taux de multiplication (r), lui, est de 2.9. La comparaison des résultats de cette étude avec les données déjà publiées a démontre que le pouvoir dévasteur de cette insecte à été jusqu’à present sousestime.
Intercalative DNA binding governs fluorescence enhancement of SYBR Gold

SYBR Gold is a commonly used and particularly bright fluorescent DNA stain, however, its binding mode to DNA remains controversial. Here, we quantitate SYBR Gold binding to DNA using two complementary approaches. We use mechanical micromanipulation with magnetic tweezers (MT) to determine the effects of SYBR Gold binding on DNA length, twist, and mechanical properties. The MT assay reveals systematic lengthening and unwinding of DNA upon SYBR Gold binding, consistent with an intercalative binding mode where every SYBR Gold molecule unwinds DNA by 19.1° ± 0.7°. We complement the MT data with a spectroscopic characterization of SYBR Gold fluorescence upon addition to DNA. The data are well described by a global binding model for dye concentrations ≤1 μM, with binding parameters that quantitatively agree with the MT results. The fluorescence signal increases linearly with the number of intercalated SYBR Gold molecules. At dye concentrations >1 μM, fluorescence quenching and inner filter effects become relevant and it is required to correct the SYBR Gold fluorescence signals for quantitative assessment of DNA concentrations. In summary, we provide a mechanistic understanding of DNA-SYBR Gold interactions and present practical guidelines for optimal DNA detection and quantitative DNA sensing applications using SYBR Gold.
Quantitative analysis questions the role of MeCP2 as a global regulator of alternative splicing

MeCP2 is an abundant protein in mature nerve cells, where it binds to DNA sequences containing methylated cytosine. Mutations in the MECP2 gene cause the severe neurological disorder Rett syndrome (RTT), provoking intensive study of the underlying molecular mechanisms. Multiple functions have been proposed, one of which involves a regulatory role in splicing. Here we leverage the recent availability of high-quality transcriptomic data sets to probe quantitatively the potential influence of MeCP2 on alternative splicing. Using a variety of machine learning approaches that can capture both linear and non-linear associations, we show that widely different levels of MeCP2 have a minimal effect on alternative splicing in three different systems. Alternative splicing was also apparently indifferent to developmental changes in DNA methylation levels. Our results suggest that regulation of splicing is not a major function of MeCP2. They also highlight the importance of multi-variate quantitative analyses in the formulation of biological hypotheses.
STUDIES ON THE EVOLUTION OF THE OPHRYOSCOLECIDAE (CILIATA: OLIGOTRICHA): II. ON THE ORIGIN OF THE HIGHER OPHRYOSCOLECIDAE

A comparison of the structure of Diplodinium s. str. and Entodinium of the "caudatum–laterale" group leads to the conclusion that Diplodinium originated from Entodinium as the result of torsional displacement of the nuclear apparatus, the left lateral groove, and the contractile vacuole from the dorsal side to the ventral. The ventral side of Entodinium was thus transformed into the "dorsal" side of Diplodinium The probable influence of this new conception of the comparative morphology of the Ophryoscolecidae is discussed.
Truss-based Community Search over Large Directed Graphs

Community search enables personalized community discovery and has wide applications in large real-world graphs. While community search has been extensively studied for undirected graphs, the problem for directed graphs has received attention only recently. However, existing studies suffer from several drawbacks, e.g., the vertices with varied in-degrees and out-degrees cannot be included in a community at the same time. To address the limitations, in this paper, we systematically study the problem of community search over large directed graphs. We start by presenting a novel community model, called D-truss, based on two distinct types of directed triangles, i.e., flow triangle and cycle triangle. The D-truss model brings nice structural and computational properties and has many advantages in comparison with the existing models. With this new model, we then formulate the D-truss community search problem, which is proved to be NP-hard. In view of its hardness, we propose two efficient 2-approximation algorithms, named Global and Local, that run in polynomial time yet with quality guarantee. To further improve the efficiency of the algorithms, we devise an indexing method based on D-truss decomposition. Consequently, the D-truss community search can be solved upon the D-truss index without time-consuming accesses to the original graph. Experimental studies on real-world graphs with ground-truth communities validate the quality of the solutions we obtain and the efficiency of the proposed algorithms.
Visual information routes in the posterior dorsal and ventral face network studied with intracranial neurophysiology, and white matter tract endpoints

Occipito-temporal regions within the face network process perceptual and socio-emotional information, but the dynamics and interactions between different nodes within this network remain unknown. Here, we analyzed intracerebral EEG from 11 epileptic patients viewing a stimulus sequence beginning with a neutral face with direct gaze. The gaze could avert or remain direct, while the emotion changed to fearful or happy. N200 field potential peak latencies indicated that face processing begins in inferior occipital cortex and proceeds anteroventrally to fusiform and inferior temporal cortices, in parallel. The superior temporal sulcus responded preferentially to gaze changes with augmented field potential amplitudes for averted versus direct gaze, and large effect sizes relative to other regions of the network. An overlap analysis of posterior white matter tractography endpoints (from 1066 healthy brains) relative to active intracerebral electrodes from the 11 patients showed likely involvement of both dorsal and ventral posterior white matter pathways. The inferior occipital and temporal sulci likely broadcast their information - the former dorsally to intraparietal sulcus, and the latter between fusiform and superior temporal cortex. Overall, our data call for inclusion of inferior temporal cortex in face processing models, and anchor the superior temporal cortex in dynamic gaze processing.
Marriage in the Melting Pot: An Evolutionary Approach to European Ancestry, Homogamy, and Fertility in the United States

Objective To understand marriage patterns, homogamy and fertility of women of European ancestry in the United States from an evolutionary perspective we aim to investigate if a prevalence for ancestral homogamy exists, the factors influencing a female preference for an ancestral homogamous vs. an heterogamous marriage, if an ancestral homogamous vs. heterogamous marriages influences fertility and if there is an inherted component of the tendency to marry homogamously vs. heterogamously. Furthermore we aim to determine the heritability of homogamous vs. heterogamous marriage behaviour. Methods We used the census data of 369,121 US women married only once and aged between 46 and 60 years, provided by IPUMS USA (https://usa.ipums.org/usa/). We used linear mixed models to determine associations of the probability of a homogamous vs. heterogamous marriage and the individual fertility of a women. We aimed to estimate the heritability (in our case genetic & parental environment) of marriage behaviour using a linear mixed model. Results We found, that ancestral heterogamous marriages are more frequent (56.5%), compared to homogamous marriages (43.5%). Most of the variance in inter- ancestry marriage and fertility is explained by ancestry per se, followed by the ratio of individuals of a certain ancestral background in a county: the more individuals of a certain ancestry live in a county the lower is the tendency to marry someone of a different ancestral background. Furthermore we found that about 11.8% of the marriage behaviour is heritable. Being in a homogamous marriage as well as the income of the spouse are both significantly positively associated with the number of children a women has and the probability that a women has at least one child. Discussion The most important explaining factor (in terms of variance explained) for being in an ancestral homogamous vs. heterogamous marriage, for number of children, as well as childlessness is the ancestry of the women. Albeit we are not able to distinguish the genetic and social heritability on basis of our data, with a total value of 11.8% variance explained, only a small heritability for in-group vs, out-group marriage behaviour is indicated.
SLFN11 captures cancer-immunity interactions associated with platinum sensitivity in ovarian cancer

Large independent analyses on cancer cell lines followed by functional studies have identified Schlafen 11 (SLFN11), a putative DNA/RNA helicase, as the strongest predictor of sensitivity to DNA-damaging agents. However, its role as a prognostic biomarker is undefined, partially due to the lack of validated methods to score SLFN11 in human tissues. Here, we implemented a pipeline to quantify SLFN11 in human cancer samples. By analyzing a cohort of high-grade serous ovarian carcinoma specimens prior platinum-based chemotherapy treatment, we demonstrate that SLFN11 is expressed by infiltrating innate and adaptive immune cells. We show, for the first time, that SLFN11 density in both the neoplastic and microenvironmental components was independently associated with favorable outcome. Transcriptomic analyses suggested the presence of a hitherto modulation of the cancer-immunity cycle orchestrated by SLFN11. We propose SLFN11 as a dual biomarker capturing simultaneously interconnected immunological and cancercell-intrinsic functional dispositions associated with sensitivity to DNA damaging agents.
In silico Proteome analysis of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (2019-nCoV), is a positive-sense, single-stranded RNA coronavirus. The virus is the causative agent of coronavirus disease 2019 (COVID-19) and is contagious through human-to-human transmission. The present study reports sequence analysis, complete coordinate tertiary structure prediction and in silico sequence-based and structure-based functional characterization of full SARS-CoV-2 proteome based on the NCBI reference sequence NC_045512 (29903 bp ss-RNA) which is identical to GenBank entry MN908947 and MT415321. The proteome includes 12 major proteins namely orf1ab polyprotein (includes 15 proteins), surface glycoprotein, ORF3a protein, envelope protein, membrane glycoprotein, ORF6 protein, ORF7a protein, orf7b, ORF8, Nucleocapsid phosphoprotein and ORF10 protein. Each protein of orf1ab polyprotein group has been studied separately. A total of 25 polypeptides have been analyzed out of which 15 proteins are not yet having experimental structures and only 10 are having experimental structures with known PDB IDs. Out of 15 newly predicted structures six (6) were predicted using comparative modeling and nine (09) proteins having no significant similarity with so far available PDB structures were modeled using ab-initio modeling. Structure verification using recent tools QMEANDisCo 4.0. 0 and ProQ3 for global and local (per-residue) quality estimates indicate that the all-atom model of tertiary structure of high quality and may be useful for structure-based drug designing targets. The study has identified nine major targets (spike protein, envelop protein, membrane protein, nucleocapsid protein, 2’-O-ribose methyltransferase, endoRNAse, 3’-to-5’ exonuclease, RNA-dependent RNA polymerase and helicase) for which drug design targets could be considered. There are other 16 nonstructural proteins (NSPs), which may also be percieved from the drug design angle. The protein structures have been deposited to ModelArchive. Tunnel analysis revealed the presence of large number of tunnels in NSP3, ORF 6 protein and membrane glycoprotein indicating a large number of transport pathways for small ligands influencing their reactivity.
Bioelectrochemical fuel‐cells operated by the cyanobacterium, Anabaena variabilis

Substantial electric output was delivered from the bioelectrochemical fuel-cells operated under anaerobic conditions by Anabaena variabilis strain M-2 and 2-hydroxy-1,4-naphthoquinone. There was a linear relationship between the coulombic output of the fuel-cells operated in the dark and the glycogen content of the organisms. The coulombic output was increased substantially in the light; the increase was observed even in the absence of CO2. Oxygen was evolved by Anabaena cells under the operating conditions of the fuel-cells. The results demonstrated that the source of electricity obtained from the fuel-cells is endogenous glycogen in the dark and both glycogen and electrons produced by photosynthetic oxidation of water in the light.
Supracategorical fear information revealed by aversively conditioning multiple categories

Fear-generalization is a critical function for survival, in which an organism extracts information from a specific instantiation of a threat (e.g., the western diamondback rattlesnake in my front yard on Sunday) and learns to fear—and accordingly respond to—pertinent higher-order information (e.g., snakes live in my yard). Previous work investigating fear-conditioning in humans has used functional magnetic resonance imaging (fMRI) to demonstrate that activity-patterns of stimuli from an aversively-conditioned category (CS+) are more similar to each other than those of a neutral category (CS-). Here we designed a three-phase (i.e., baseline, conditioned, extinction) experiment using fMRI and multiple aversively-conditioned categories to ask whether we would find only similarity increases within the CS+ categories or also an increase in similarity between the CS+ categories. Using representational similarity analysis, we correlated a set of models to activity-patterns underlying several regions of interest and found that, following fear-conditioning, between-category and within-category similarity increased for the CS+ categories in the superior frontal gyrus (SFG) and the right temporal pole (rTP). Activity patterns in the object-selective lateral occipital cortex tended to prefer the semantic model, regardless of the experimental phase. These results advance prior pattern-based neuroimaging work by exploring the effect of aversively-conditioning multiple categories and indicate an extended role for the SFG and rTP in potentially linking discrete information or abstractly representing supracategorical information during fear-learning for the purpose of proper generalization.
Peptide recognition and dephosphorylation by the vaccinia VH1 phosphatase

The VH1 protein encoded by the highly conserved H1 locus of orthopoxviruses is a dual-specificity phosphatase (DUSPs) that hydrolyzes phosphate groups from phosphorylated tyrosine, serine, and threonine residues of viral and host cell proteins. Because the DUSP activities are required for virus replication, VH1 is a prime target for the development of therapeutic inhibitors. However, the presentation of a shallow catalytic site has thwarted all drug development efforts. As an alternative to direct targeting of catalytic pockets, we describe surface contacts between VH1 and substrates that are essential for full activity and provide a new pathway for developing inhibitors of protein-protein interactions. Critical amino acid residues were manipulated by site-directed mutagenesis of VH1, and perturbation of peptide substrate interactions based on these mutations were assessed by high-throughput assays that employed surface plasmon resonance and phosphatase activities. Two positively-charged residues (Lys-20 and Lys-22) and the hydrophobic side chain of Met-60 appear to orient the polarity of the pTyr peptide on the VH1 surface, while additional amino acid residues that flank the catalytic site contribute to substrate recognition and productive dephosphorylation. We propose that the enzyme-substrate contact residues described here may serve as molecular targets for the development of inhibitors that specifically block VH1 catalytic activity and thus poxvirus replication.
Computer code comprehension shares neural resources with formal logical inference in the fronto-parietal network

Despite the importance of programming to modern society, the cognitive and neural bases of code comprehension are largely unknown. Programming languages might ‘recycle’ neurocognitive mechanisms originally used for natural languages. Alternatively, comprehension of code could depend on fronto-parietal networks shared with other culturally derived symbol systems, such as formal logic and math. Expert programmers (average 11 years of programming experience) performed code comprehension and memory control tasks while undergoing fMRI. The same participants also performed language, math, formal logic, and executive control localizer tasks. A left-lateralized fronto-parietal network was recruited for code comprehension. Patterns of activity within this network distinguish between “for” loops and “if” conditional code functions. Code comprehension overlapped extensively with neural basis of formal logic and to a lesser degree math. Overlap with simpler executive processes and language was low, but laterality of language and code covaried across individuals. Cultural symbol systems, including code, depend on a distinctive fronto-parietal cortical network.
Effective Travel Time Estimation: When Historical Trajectories over Road Networks Matter

In this paper, we study the problem of origin-destination (OD) travel time estimation where the OD input consists of an OD pair and a departure time. We propose a novel neural network based prediction model that fully exploits an important fact neglected by the literature -- for a past OD trip its travel time is usually affiliated with the trajectory it travels along, whereas it does not exist during prediction. At the training phase, our goal is to design novel representations for the OD input and its affiliated trajectory, such that they are close to each other in the latent space. First, we match the OD pairs and their affiliated (historical) trajectories to road networks, and utilize road segment embeddings to represent their spatial properties. Later, we match the timestamps associated with trajectories to time slots and utilize time slot embeddings to represent the temporal properties. Next, we build a temporal graph to capture the weekly and daily periodicity of time slot embeddings. Last, we design an effective encoding to represent the spatial and temporal properties of trajectories. To bind each OD input to its affiliated trajectory, we also encode the OD input into a hidden representation, and make the hidden representation close to the spatio-temporal representation of the trajectory. At the prediction phase, we only use the OD input, get the hidden representation of the OD input, and use it to generate the travel time. Extensive experiments on real datasets show that our method achieves high effectiveness and outperforms existing methods.
Storage of Osmotically Active Compounds in the Taproot of Daucus carota L.

The osmotic potential of cell sap from the storage root, lateral roots and shoots of carrot (Daucus carota L., cv. Amsterdamse Bak) was calculated from the concentration of osmotically active compounds in these tissues. The osmotic potential of the taproot did not change with age prior to and during the storage of osmotically active sugars, as sucrose and reducing sugars. The increased contribution of soluble sugars in the osmotic potential was accompanied by a proportionally decreased contribution of potassium and organic acids. Before storage of soluble sugars in the taproot occurred, potassium and organic acids contributed 80% to the total osmotic value, in contrast with lateral root tissue, where potassium and nitrate were the main osmotic solutes. The concentration of osmotically active solutes was lower in lateral root tissue than in storage root tissue. Shoot tissue resembled taproot tissue before storage, in having potassium and organic acids as the main osmotic solutes. The concentration of osmotically active solutes was highest in shoot tissue and it increased towards the end of the experimental period. The calculated osmotic potentials were in good agreement with the experimental values, as determined from the molecular depression of the freezing point of cell sap. Storage of reducing sugars and sucrose is discussed in relation to acid and neutral invertase activities.
A new root disease of goldenseal (Hydrastis canadensis) caused by Cylindrocladium colhounii

A new disease of the medicinal herb goldenseal (Hydrastis canadensis) is described. Dried rhizomes and roots of goldenseal, a plant species indigenous to eastern North America, have traditionally been harvested from natural stands and used for medicinal purposes. Recently, growing demand for rhizomes has led to the cultivation of H. canadensis under plastic shade cloth. Commercial plantings of this crop in Ontario, Canada, were observed to be severely affected by a previously unreported root disease. A fungus isolated from diseased roots was shown to be pathogenic to H. canadensis. Morphological and genetic-sequence data established that the causal agent was Cylindrocladium colhounii. This is the first report of a Cylindrocladium sp. affecting H. canadensis.