Miracle-dz/UniFAR-FTUs huggingface dataset:
Predicting subcellular localization of proteins based on their N-terminal amino acid sequence.

A neural network-based tool, TargetP, for large-scale subcellular location prediction of newly identified proteins has been developed. Using N-terminal sequence information only, it discriminates between proteins destined for the mitochondrion, the chloroplast, the secretory pathway, and "other" localizations with a success rate of 85% (plant) or 90% (non-plant) on redundancy-reduced test sets. From a TargetP analysis of the recently sequenced Arabidopsis thaliana chromosomes 2 and 4 and the Ensembl Homo sapiens protein set, we estimate that 10% of all plant proteins are mitochondrial and 14% chloroplastic, and that the abundance of secretory proteins, in both Arabidopsis and Homo, is around 10%. TargetP also predicts cleavage sites with levels of correctly predicted sites ranging from approximately 40% to 50% (chloroplastic and mitochondrial presequences) to above 70% (secretory signal peptides). TargetP is available as a web-server at http://www.cbs. dtu.dk/services/TargetP/.
Assessment of health risk from organochlorine pesticides residues in high-fat spreadable foods produced in Poland

Currently, butter and margarine are food products attracting wide customer interest. Every day, consumers around the world buy these products for human consumption. Butter is obtained from milk fat, while margarine is derived from vegetable oils. The content of organochlorine pesticide (OCP) residues was examined in both types of these high fatty products. A gas chromatograph with MSD (HP 5973) detector was used for the determination of pesticides such as α-HCH, β-HCH, γ-HCH, DDT, DDD, DDE, aldrin, dieldrin, endrin, heptachlor and heptachlor epoxide. The examined products had diverse concentrations of the analyzed compounds. Visible was the division based on the origin of the product, which might be composed of animal or vegetable fats. The research has revealed the presence of OCP residues in all examined spreads. Quantities of organochlorine compounds did not pose an immediate danger to the consumers’ health. Human and environmental health risk assessment was carried out by the estimation of lifetime average daily dose (LADD) and non-carcinogenic health hazard quotient (HQ). Total estimated LADD ranged between 1.3 × 10−5 and 3.1 × 10−5 mg kg−1 d−1 for butter, and 1.9 × 10−6 and 4.6 × 10−6 mg kg−1 d−1 for margarine and mix spread. The HQ ranged between 1.1 × 10−4 and 3.7 × 10−4 for butter, and 1.4 × 10−5 and 9.0 × 10−6 for margarine and mix spread for adults. These estimated HQs were within the safe acceptable limits, indicating a negligible risk to the residents of the study area.
Differential Roles of Insulin Receptor Substrates in Brown Adipocyte Differentiation

ABSTRACT Insulin promotes adipocyte differentiation via a complex signaling network involving multiple insulin receptor substrates (IRSs). In cultured brown preadipocytes, expression of IRS-1 and IRS-2 mRNAs and proteins was at relatively high levels before and after differentiation into mature fat cells, while IRS-3 transcript was not detectable in preadipocytes but increased during the course of differentiation, and IRS-4 mRNA was barely detected in both states. To determine more precisely the roles of various IRS proteins in adipogenesis, we established and characterized brown preadipocyte cell lines from wild-type and IRS knockout (KO) animals. While wild-type, IRS-2 KO, and IRS-4 KO cells fully differentiated into mature adipocytes, IRS-3 KO cells showed a moderate defect in differentiation and IRS-1 KO cells exhibited a severe defect in the process. Cells lacking both IRS-1 and IRS-3 completely failed to differentiate. Expression of the adipogenic markers peroxisome proliferator-activated receptor gamma (PPARγ), CCAAT/enhancer-binding protein alpha, fatty acid synthase, glucose transporter 4, and the transcription factor signal transducer and activator of transcription 5, as well as the brown-fat-specific markers PPARγ coactivator 1 alpha and uncoupling protein 1, mirrored the differentiation pattern. Reconstitution of the IRS-1 KO cells with IRS-1 and IRS-4, but not IRS-2 or IRS-3, compensated for the lack of differentiation in IRS-1 KO cells. A chimeric molecule containing the N terminus of IRS-1 and the C terminus of IRS-2, but not one with the N terminus of IRS-2 and the C terminus of IRS-1, also rescued differentiation. Expression of Wnt 10a, a molecule known to inhibit adipogenesis, was dramatically increased in the IRS-1 KO cells, and this could be reduced by overexpression of IRS-1 or IRS-4, which was correlated with restoration of differentiation. These data indicate that both IRS-1 and -3 play important roles in the differentiation of brown adipocytes and that the N terminus of IRS-1 is more important for this function of the molecule. Although IRS-4 is not essential for the process, overexpression of IRS-4 can compensate for the deficiency in differentiation in IRS-1 KO cells.
Driver internal state estimative model for distracted state detection

For this study, using Bayesian Network (BN) to graphically express the interrelationship between safety confirmation behaviors for driving scene and driver's internal state, we analyze correlations between characteristic body information (i.e., eye-gaze / face orientation) and operation information (i.e., steering wheel, accelerator, and brake), when switching from "concentrating state" to "distracted state".
LONG‐TERM COST OF REPRODUCTION WITH AND WITHOUT ACCELERATED SENESCENCE IN CALLOSOBRUCHUS MACULATUS: ANALYSIS OF AGE‐SPECIFIC MORTALITY

Age‐specific mortality is measured to characterize the costs of reproduction in the beetle Callosobruchus maculatus, providing explicit details of the timing, duration, magnitude, and acceleration of mortality. We experimentally manipulated reproductive effort in four cohorts of 200 individually housed females by controlling exposure to males and to an artificial oviposition substrate. We demonstrate that (1) early reproduction produces long‐term increases in age‐specific mortality; (2) egg‐laying effort affects the onset of age‐specific mortality but not its shape or rate of change; and (3) mating with subsequent reproduction increases the rate of change in age‐specific mortality relative to virgins. Accelerated senescence is defined demographically as an increase in the rate of change of age‐specific mortality. Our results challenge the hypothesis that reproductive effort accelerates senescence but provides evidence that mating itself may have this effect.
Bathymetric mapping by means of remote sensing : methods , accuracy and limitations

Bathymetry has been traditionally charted via shipboard echo sounding. Alhough able to generate accurate depth measurements at points or along transects, this method is constrained by its high operating cost, ineffi ciency, and inapplicability to shallow waters. By comparison, remote sensing methods offer more fl exible, effi cient and cost-effective means of mapping bathymetry over broad areas. Remote sensing of bathymetry falls into two broad categories: non-imaging and imaging methods. The non-imaging method (as typifi ed by LiDAR) is able to produce accurate bathymetric information over clear waters at a depth up to 70 m. However, this method is limited by the coarse bathymetric sampling interval and high cost. The imaging method can be implemented either analytically or empirically, or by a combination of both. Analytical or semianalytical implementation is based on the manner of light transmission in water. It requires inputs of a number of parameters related to the properties of the atmosphere, water column, and bottom material. Thus, it is rather complex and diffi cult to use. By comparison, empirical implementation is much simpler and requires the input of fewer parameters. Both implementations can produce fi ne-detailed bathymetric maps over extensive turbid coastal and inland lake waters quickly, even though concurrent depth samples are essential. The detectable depth is usually limited to 20 m. The accuracy of the retrieved bathymetry varies with water depth, with the accuracy substantially lower at a depth beyond 12 m. Other infl uential factors include water turbidity and bottom materials, as well as image properties.
Function and Hormonal Regulation of GATA3 in Human First Trimester Placentation1

ABSTRACT Pregnancies resulting from fresh in vitro fertilization (IVF) cycles exposed to supraphysiologic estrogen levels have been associated with higher rates of low birth weight and small for gestational age babies. We identified GATA3, a transcription factor selectively expressed in the trophectoderm during the blastocyst stage of embryo development, in an upstream analysis of genes that were differentially methylated in chorionic villus samples between IVF and non-IVF infertility treatment pregnancies. In this study, we investigate the hypothesis that GATA3 is hormonally regulated and plays an important functional role in trophoblast migration, invasion, and placentation. We found that GATA3 expression was hormonally regulated by estradiol in HTR8/SVneo first trimester trophoblast cells; however, no change in expression was seen with progesterone treatment. Furthermore, GATA3 knockdown resulted in decreased HTR8/SVneo cell migration and invasion compared with controls. RNA sequencing of GATA3 knockdown cells demonstrated 96 differentially regulated genes compared with controls. Genes known to play an important role in cell-cell and cell-extracellular matrix interactions, cell invasion, and placentation were identified, including CTGF, CYR61, ADAMTS12, and TIMP3. Our results demonstrate estradiol down-regulates GATA3, and decreased GATA3 expression leads to impaired trophoblast cell migration and invasion, likely through regulation of downstream genes important in placentation. These results are consistent with clinical data suggesting that supraphysiologic estrogen levels seen in IVF pregnancies may play an important role in attenuated trophoblast migration, invasion, and impaired placentation. GATA3 appears to be an important regulator of placentation and may play a role in impaired outcomes associated with fresh IVF cycles.
Studies in Knockout Mice Reveal that Anti‐Chlamydial Protection Requires TH1 Cells Producing IFN‐γ: Is this True for Humans?

Chlamydia trachomatis is one of the major causes of infertility and preventable blindness in the world. The organism is of particular interest from an immunological point of view because it is one of the few obligate intracellular bacterial pathogens. There is some evidence that repeated infections in humans stimulate protective immunity. However, until recently, it was unclear which components of the adaptive immune system give rise to protection. Studies in gene knockout mice reported here and elsewhere now give a coherent and cogent picture of the importance of the Th1 response, in particular IFN‐γ, for the localization and eradication of C. trachomatis genital tract infection. The key questions still to be addressed are the identity of the IFN‐γ responsive cells and whether the mouse is truly representative of host protection against chlamydiae in humans.
Non-contact structural health monitoring of a cable-stayed bridge: case study

Abstract In this article, the condition assessment of a cable-stayed bridge using remote sensing is presented. The displacement influence line (DIL) of the bridge under the live load tests is measured for a discrete number of target points. Three different remote sensing techniques including, laser scanning, terrestrial robotic total station and digital levelling are adopted for this purpose. It is demonstrated that DIL obtained by non-contact system is capable of identifying an emulated damage in an actual operating system. The contribution of the work is fourfold. First, a damage index based on the displacement profile of the bridge under the weigh-in-motion is extracted from the non-contact sensing system. Second, our study compares three different remote sensing techniques, namely, digital levelling, robotic total station and laser scanning and uses the measurements to validate the finite element model. Third, the effectiveness of the proposed method for structural damage identification is validated in a real-world large-scale operating structure. Finally, it is validated that strain-based influence line is highly likely to misidentify damage especially when the location of damage is not in the close proximity of the sensor; however, DIL is a better damage indicator even if damage occurs far from the measurement point.
Robotic yo-yo: modelling and control strategies

In the paper we address a problem of controlling an oscilmotion with a robot. As the object we have selected a yo-yo. First we have measured and analysed the motion of different yo-yos. We have developed a simplified model of a yo-yo which has one degree-of-freedom, and the behaviour at the end of the string is modelled as an impact. Next, we discuss the control strategy. Our results show, that for playing a yo-yo it is important to start the upward motion before the yo-yo reaches the bottom position and the acceleration has to be reversed after the bottom impact. We present two control strategies: one based on predefined hand motion pattern and and the other generating the hand motion on-line. Both allow playing the yo-yo at a selected top height. The theoretical results have been proven by experiments on a real robot system.
Graph clustering using heat kernel embedding and spectral geometry

In this paper we study the manifold embedding of graphs resulting from the Young-Householder decomposition of the heat kernel. We aim to explore how the sectional curvature associated with the embedding can be used as feature for the purposes of gauging the similarity of graphs, and hence clustering them. The curvature is computed from the difference between the geodesic (edge weight) and the Euclidean embedding distance between pairs of nodes. To gauge the similarity of pairs of graphs, we require a means of comparing sets of such features without explicit correspondences between the nodes of the graphs being considered. To this end, the Hausdorff distance, and a robust modified variant of the Hausdorff distance are used. We experiment on sets of graphs representing the proximity image features in different views of different objects. By applying multidimensional scaling to the Hausdorff distances between the different object views, it is demonstrated that our sectional curvature representation is capable of clustering the different views of the same object together.
Models of Robustness in Scheduling and Temporal Planning Based on Optimisation with Dynamic Controllability Constraints

Robustness is vital in some scheduling and temporal planning problems, such as evacuation planning (Even, Pillac, and Hentenryck 2014). However, it is hard to measure robustness directly, so some metrics measuring relative features have been introduced (e.g., Cesta, Oddi, and Smith 1998; Aloulou and Portmann 2003; Wilson et al. 2014), as well as algorithms for finding high-robustness schedules (e.g., Aloulou and Portmann 2003; Policella et al. 2009; Banerjee and Haslum 2011). The goal of my PhD thesis is to explore and compare existing measures that measure robustness or other features related to robustness, try to provide new robustness models and try to get more robust schedules or plans.
Cell Line Generation of integration free induced pluripotent stem cells from fi brodysplasia ossi fi cans progressiva ( FOP ) patients from urine samples

Article history: Received 26 November 2015 Accepted 27 November 2015 Available online 1 December 2015 Fibrodysplasia ossificans progressiva (FOP) is an extremely rare, autosomal dominant transmitted genetic disease. Patients experience progressive bone formation replacing tendons, ligaments, muscle and soft tissue. Cause of FOP are gain-of-functionmutations in the BoneMorphogenetic Protein (BMP) receptorActivin A receptor type 1 (ACVR1) (Kaplan et al., 2008). The most common mutation is R206H, which leads to the substitution of codon 206 from arginine to histidine (Shore et al., 2006). Here, we describe the derivation and characterization of two hiPSC lines from two FOP patients, both carrying the mutation R206H. Cells were isolated from urine and reprogrammed using integration free Sendai virus vectors under defined conditions. © 2015 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
Serologic Evidence Incriminating a Recently Isolated Virus (ATCC VR-2332) as the Cause of Swine Infertility and Respiratory Syndrome (SIRS)

and swine infertility and respiratory syndrome (SIRS). tality ranged from 37% to 83% and was accompanied by late term (>day 100) abortion in all but 1 herd. The absence of anorexia in 2 herds and absence of dyspnea in 1 herd may reflect a failure of detection rather than absence of these clinical signs (Table 2). Each case herd was matched with a herd located within 10 miles, of similar size and type of production, and having no history of undiagnosed reproductive failure or respiratory disease in the last 3 years. Sera were collected from approximately 30 representative sows at each of these 16 herds.
Murine Model of Pulmonary Anthrax: Kinetics of Dissemination, Histopathology, and Mouse Strain Susceptibility

ABSTRACT Bioweapons are most often designed for delivery to the lung, although this route is not the usual portal of entry for many of the pathogens in the natural environment. Vaccines and therapeutics that are efficacious for natural routes of infection may not be effective against the pulmonary route. Pulmonary models are needed to investigate the importance of specific bacterial genes in virulence, to identify components of the host immune system that are important in providing innate and acquired protection, and for testing diagnostic and therapeutic strategies. This report describes the characteristics of host and Bacillus anthracis interactions in a murine pulmonary-infection model. The infective dose varied depending on the route and method of inoculation. The germination process in the lung began within 1 h of inoculation into the lung, although growth within the lung was limited. B. anthracis was found in the lung-associated lymph nodes ∼5 h after infection. Minimal pneumonitis was associated with the lung infection, but significant systemic pathology was noted after dissemination. Infected mice typically succumbed to infection ∼3 to 4 days after inoculation. The 50% lethal doses differed among inbred strains of mice, but within a given mouse strain, neither the age nor the sex of the mice influenced susceptibility to B. anthracis.
Noncausal affine processes with applications to derivative pricing

Linear factor models, where the factors are affine processes, play a key role in Finance, since they allow for quasi‐closed form expressions of the term structure of risks. We introduce the class of noncausal affine linear factor models by considering factors that are affine in reverse time. These models are especially relevant for pricing sequences of speculative bubbles. We show that they feature nonaffine dynamics in calendar time, while still providing (quasi) closed form term structures and derivative pricing formulas. The framework is illustrated with term structure of interest rates and European call option pricing examples.
Unstructured data extraction of Chinese expert web page

Aiming at the problem of requiring a lot of human intervention in the process of unstructured data extraction from expert page based on traditional extraction methods, this paper proposes a method which detects data template automatically based on similarities and differences between HTML tags and strings, uses the lattice theory to find the location of the data grid region storing unstructured expert data, thus accesses to unstructured expert data. Firstly, with the help of the classifier on Chinese Expert Entity Homepages, a lot of expert pages are acquired by expert web crawler. Secondly, divide the expert pages into two types, list type and document type, then extract respectively the unstructured data from the two different types. Lastly, the extraction experiments are conducted on different types of web pages by improving open source code of Roadrunner. Experimental results show that, in the case of unsupervised, this method performs effectively on extraction of unstructured web data from Chinese expert pages.
Importance of Complement Source in Measuring Meningococcal Bactericidal Titers

ABSTRACT Complement-mediated bactericidal antibodies in serum confer protection against meningococcal disease. The minimum protective titer is estimated to be between 1:4 and 1:8 when measured by the Goldschneider assay performed with human complement, the assay used in the 1960s to establish the correlation between bactericidal antibodies and protection. A more recently described bactericidal assay standardized by an international consortium uses rabbit complement, which is known to augment bactericidal titers. To define a protective titer measured by the standardized assay, we compared bactericidal titers against serogroup C strains measured by this assay to titers measured by the assay described by Goldschneider et al. A titer of ≥1:128 measured by the standardized assay was needed to predict with ≥80% certainty a positive titer of ≥1:4 as measured by the Goldschneider assay. However, the majority of samples with titers of 1:4 measured by the Goldschneider assay had titers of <1:128 when measured by the standardized assay. Therefore, by the results of the standardized assay such persons would be falsely categorized as being susceptible to disease. In conclusion, high bactericidal titers measured with the standardized assay performed with rabbit complement are predictive of protection, but no threshold titer is both sensitive and specific for predicting a positive titer measured by the Goldschneider assay using human complement. Up to 10% of the U.S. adult population lacks intrinsic bactericidal activity against serogroup C strains in serum and can serve as complement donors. Therefore, use of the Goldschneider assay or an equivalent assay performed with human complement is preferred over assays that use rabbit complement.