Miracle-dz/UniFAR-FTUs huggingface dataset:
Intravenous Mouse Infection Model for Studying the Pathology of Enterococcus faecalis Infections

ABSTRACT An intravenous mouse infection model was used to compare the virulence of Enterococcus faecalis strains, to study bacterial localization and organ histopathology, and to examine the effects of Nramp1 and gamma interferon (IFN-γ) on the course of infection. Infection of BALB/c mice with 5 × 108 CFU of E. faecalis JH2-2, MGH-2, 418, DS16C2, or OG1X revealed the following virulence ranking (from highest to lowest): MGH-2, 418, DS16C2, JH2-2, and OG1X. Discernible differences in the number of MGH-2 and JH2-2 bacteria were observed at 7 days (168 h) in the blood (P = 0.037), at 72 h in the liver (P = 0.002), and at 8 h in the spleen (P = 0.036). At these time points, the number of MGH-2 bacteria was higher in the blood and liver while the number of JH2-2 bacteria was higher in the spleen. At 72 h, livers from MGH-2-infected mice had higher numbers of coalescing aggregates of leukocytes and a greater degree of caseous necrosis than those from JH2-2-infected mice. These results indicate a correlation between the virulence of the E. faecalis strain, the number of bacteria in the liver, and the degree of histopathology of the liver at 72 h postinfection. IFN-γ was important in E. faecalis infection, since IFN-γ gene knockout mice had reduced mortality and massive coagulative necrosis was observed in wild-type mice. The contribution of Nramp1 was unclear, since Nramp1−/− mice and the respective control mice were innately resistant to E. faecalis. The mortality of mice in this model is probably due to induction of cytokine release and massive coagulative necrosis.
An Efficient and Reliable Statistical Method for Estimating Functional Connectivity in Large Scale Brain Networks Using Partial Correlation

Currently, network-oriented analysis of fMRI data has become an important tool for understanding brain organization and brain networks. Among the range of network modeling methods, partial correlation has shown great promises in accurately detecting true brain network connections. However, the application of partial correlation in investigating brain connectivity, especially in large-scale brain networks, has been limited so far due to the technical challenges in its estimation. In this paper, we propose an efficient and reliable statistical method for estimating partial correlation in large-scale brain network modeling. Our method derives partial correlation based on the precision matrix estimated via Constrained L1-minimization Approach (CLIME), which is a recently developed statistical method that is more efficient and demonstrates better performance than the existing methods. To help select an appropriate tuning parameter for sparsity control in the network estimation, we propose a new Dens-based selection method that provides a more informative and flexible tool to allow the users to select the tuning parameter based on the desired sparsity level. Another appealing feature of the Dens-based method is that it is much faster than the existing methods, which provides an important advantage in neuroimaging applications. Simulation studies show that the Dens-based method demonstrates comparable or better performance with respect to the existing methods in network estimation. We applied the proposed partial correlation method to investigate resting state functional connectivity using rs-fMRI data from the Philadelphia Neurodevelopmental Cohort (PNC) study. Our results show that partial correlation analysis removed considerable between-module marginal connections identified by full correlation analysis, suggesting these connections were likely caused by global effects or common connection to other nodes. Based on partial correlation, we find that the most significant direct connections are between homologous brain locations in the left and right hemisphere. When comparing partial correlation derived under different sparse tuning parameters, an important finding is that the sparse regularization has more shrinkage effects on negative functional connections than on positive connections, which supports previous findings that many of the negative brain connections are due to non-neurophysiological effects. An R package “DensParcorr” can be downloaded from CRAN for implementing the proposed statistical methods.
A non-projective greedy dependency parser with bidirectional LSTMs

The LyS-FASTPARSE team present BIST-COVINGTON, a neural implementation of the Covington (2001) algorithm for non-projective dependency parsing. The bidirectional LSTM approach by Kiperwasser and Goldberg (2016) is used to train a greedy parser with a dynamic oracle to mitigate error propagation. The model participated in the CoNLL 2017 UD Shared Task. In spite of not using any ensemble methods and using the baseline segmentation and PoS tagging, the parser obtained good results on both macro-average LAS and UAS in the big treebanks category (55 languages), ranking 7th out of 33 teams. In the all treebanks category (LAS and UAS) we ranked 16th and 12th. The gap between the all and big categories is mainly due to the poor performance on four parallel PUD treebanks, suggesting that some ‘suffixed’ treebanks (e.g. Spanish-AnCora) perform poorly on cross-treebank settings, which does not occur with the corresponding ‘unsuffixed’ treebank (e.g. Spanish). By changing that, we obtain the 11th best LAS among all runs (official and unofficial). The code is made available at https://github.com/CoNLL-UD-2017/LyS-FASTPARSE
Uncertainty in bipolar preference problems

Preferences and uncertainty are common in many real-life problems. In this article, we focus on bipolar preferences and uncertainty modelled via uncontrollable variables, and we assume that uncontrollable variables are specified by possibility distributions over their domains. To tackle such problems, we concentrate on uncertain bipolar problems with totally ordered preferences, and we eliminate the uncertain part of the problem, while making sure that some desirable properties hold about the robustness of the problem and its relationship with the preference of the optimal solutions. We also consider several semantics to order the solutions according to different attitudes with respect to the notions of preference and robustness.
Location Estimation in a Smart Home: System Implementation and Evaluation Using Experimental Data

In the context of a constantly increasing aging population with cognitive deficiencies, insuring the autonomy of the elders at home becomes a priority. The DOMUS laboratory is addressing this issue by conceiving a smart home which can both assist people and preserve their quality of life. Obviously, the ability to monitor properly the occupant's activities and thus provide the pertinent assistance depends highly on location information inside the smart home. This paper proposes a solution to localize the occupant thanks to Bayesian filtering and a set of anonymous sensors disseminated throughout the house. The localization system is designed for a single person inside the house. It could however be used in conjunction with other localization systems in case more people are present. Our solution is functional in real conditions. We conceived an experiment to estimate precisely its accuracy and evaluate its robustness. The experiment consists of a scenario of daily routine meant to maximize the occupant's motion in meaningful activities. It was performed by 14 subjects, one subject at a time. The results are satisfactory: the system's accuracy exceeds 85% and is independent of the occupant's profile. The system works in real time and behaves well in presence of noise.
Spell-out, Chains, and Long Distance Wh-movement in Seereer

Author(s): Baier, Nicholas | Abstract: In this paper, I examine novel data from long distance wh-dependencies in Seereer, an Atlantic language of Senegal. Seereer long distance wh-questions are characterized by (a) the presence of an obligatory pronoun at the edge of each embedded clause and (b) the presence of special morphology on each verb along the path of the extraction. Thus, Seereer provides striking evidence that long distance wh-movement proceeds successive cyclically through the edge of each clause. I argue that this verbal morphology spells out a valued wh-probe on C, which triggers the movement of a wh-phrase to its Spec. I show that the pronouns present at the edge of each embedded clause have the properties of copies and not of resumptive pronouns, and argue that they are in fact spelled out intermediate copies of the moved wh-phrase. I propose that such multiple copy spell out is possible precisely because they enter into a feature valuation relationship with C. Speciﬁcally, I propose that valuation of an wh-probe deﬁnes a copy as the head of an A’-chain. Thus, the application of successive cyclic movement does not result in one long chain, but instead in a series of smaller chains. This view of the structure of long A’-chains, when combined with the independently motivated principle of spelling out the heads of chains, results in the pattern of multiple copy spell out that occurs in Seereer.
Assessing the Performance of Question-and-Answer Communities Using Survival Analysis

Question-&-Answer (QA) websites have emerged as efficient platforms for knowledge sharing and problem solving. In particular, the Stack Exchange platform includes some of the most popular QA communities to date, such as Stack Overflow. Initial metrics used to assess the performance of these communities include summative statistics like the percentage of resolved questions or the average time to receive and validate correct answers. However, more advanced methods for longitudinal data analysis can provide further insights on the QA process, by enabling identification of key predictive factors and systematic comparison of performance across different QA communities. In this paper, we apply survival analysis to a selection of communities from the Stack Exchange platform. We illustrate the advantages of using the proposed methodology to characterize and evaluate the performance of QA communities, and then point to some implications for the design and management of QA platforms.
The TFPI-2 Derived Peptide EDC34 Improves Outcome of Gram-Negative Sepsis

Sepsis is characterized by a dysregulated host-pathogen response, leading to high cytokine levels, excessive coagulation and failure to eradicate invasive bacteria. Novel therapeutic strategies that address crucial pathogenetic steps during infection are urgently needed. Here, we describe novel bioactive roles and therapeutic anti-infective potential of the peptide EDC34, derived from the C-terminus of tissue factor pathway inhibitor-2 (TFPI-2). This peptide exerted direct bactericidal effects and boosted activation of the classical complement pathway including formation of antimicrobial C3a, but inhibited bacteria-induced activation of the contact system. Correspondingly, in mouse models of severe Escherichia coli and Pseudomonas aeruginosa infection, treatment with EDC34 reduced bacterial levels and lung damage. In combination with the antibiotic ceftazidime, the peptide significantly prolonged survival and reduced mortality in mice. The peptide's boosting effect on bacterial clearance paired with its inhibiting effect on excessive coagulation makes it a promising therapeutic candidate for invasive Gram-negative infections.
Finding the transition state without initial guess: The growing string method for Newton trajectory to isomerization and enantiomerization reaction of alanine dipeptide and poly(15)alanine

We report a new, high‐dimensional application of a method for finding a transition state (TS) between a reactant and a product on the potential energy surface: the search of a growing string along a reaction path defined by any Newton trajectory in combination with the Berny method (Quapp, J Chem Phys (2005), 122, 174106; we have provided this algorithm on a web page). Two given minima are connected by a one‐dimensional, but usually curvilinear reaction coordinate. It leads to the TS region. The application of the method to alanine dipeptide finds the TS of the isomerisation C7 ax → C5, some TSs of the enantiomerisation of C7 ax from L‐form to quasi‐D‐form, and it finds the TS region of a transition of a partly unfolded, bent structure which turns back into a mainly α‐helix in the Ac(Ala)15NHMe polyalanine (all at the quantum mechanical level B3LYP/6‐31G: the growing string calculation is interfaced with the Gaussian03 package). The formation or dissolvation of some α‐ or 310‐hydrogen bonds of the helix are discussed along the TS pathway, as well as the case of an enantiomer at the central residue of the helix. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
On the Mechanical Behaviour of Intervertebral Discs

The response to compression, shear, bending, and axial rotation of an intervertebral disc is studied by using a theoretical disc model. The annulus fibrosus is modelled by ten fibre layers with alternating fibre inclination. The nucleus pulposus as well as the substance filling the space between the fibre layers is assumed to consist of an incompressible fluid. The end-plates are assumed to bulge at action of the pressure in the fluid phase. Geometry of fibre layers and end-plates are chosen to agree as closely as possible with what is representative for lumbar discs. The results show considerable increase of the different stiffnesses at increasing levels of the axial load. They also show quite large fibre strains, well over 10% at motions within normal physiological limits.
Counting with Combined Splitting and Capture–Recapture Methods

We apply the splitting method to three well-known counting problems, namely 3-SAT, random graphs with prescribed degrees, and binary contingency tables. We present an enhanced version of the splitting method based on the capture-recapture technique, and show by experiments the superiority of this technique for SAT problems in terms of variance of the associated estimators, and speed of the algorithms.
Widespread Defects in the Primary Olfactory Pathway Caused by Loss of Mash1 Function

MASH1, a basic helix-loop-helix transcription factor, is widely expressed by neuronal progenitors in the CNS and PNS, suggesting that it plays a role in the development of many neural regions. However, in mice lacking a functional Mash1 gene, major alterations have been reported in only a few neuronal populations; among these is a generalized loss of olfactory receptor neurons of the olfactory epithelium. Here, we use a transgenic reporter mouse line, in which the cell bodies and growing axons of subsets of central and peripheral neurons are marked by expression of a tau-lacZ reporter gene (the Tattler-4 allele), to look both more broadly and deeply at defects in the nervous system of Mash1−/−mice. In addition to the expected lack of olfactory receptor neurons in the main olfactory epithelium, developingMash1−/−;Tattler-4+/− mice exhibited reductions in neuronal cell number in the vomeronasal organ and in the olfactory bulb; the morphology of the rostral migratory stream, which gives rise to olfactory bulb interneurons, was also abnormal. Further examination of cell proliferation, cell death, and cell type-specific markers inMash1−/− animals uncovered parallels between the main olfactory epithelium and the vomeronasal organ in the regulation of sensory neuron development. Interestingly, this analysis also revealed that, in the olfactory epithelium of Mash1−/− animals, there is an overproduction of proliferating cells that co-express markers of both neuronal progenitors and supporting cells. This finding suggests that olfactory receptor neurons and olfactory epithelium supporting cells may share a common progenitor, and that expression ofMash1 may be an important factor in determining whether these progenitors ultimately generate neurons or glia.
CANINE MIXED LEUKOCYTE REACTIVITY AND TRANSPLANTATION ANTIGENS

SUMMARY A mixed leukocyte culture method was adapted for study of canine cells. The uptake of tritiated thymidine by reacting cells was measured following stimulation by cells inactivated by radiation. The results of histoeompatibility typing with this method bore a significant correlation (P < 0.01) to results obtained from typing with four cytotoxic antisera known to identify important transplantation antigens in this species.
Heritability of personality disorder traits: a twin study

Genetic and non‐genetic influences on the hierarchy of traits that delineate personality disorder as measured by the Dimensional Assessment of Personality Problems (DAPP‐DQ) scale were examined using data from a sample of 483 volunteer twin pairs (236 monozygotic pairs and 247 dizygotic pairs). The DAPP‐DQ assesses four higher‐order factors, 18 basic dimensions and 69 facet traits of personality disorder. The correlation coefficients for monozygotic and dizygotic twin pairs ranged from 0.26 to 0.56 and from 0.03 to 0.41, respectively. Broad heritability estimates ranged from 0 to 58% (median value, 45%). Additive genetic effects and unique environmental effects emerged as the primary influences on these scales, with unique environmental influences accounting for the largest proportion of the variance for most traits at all levels of the hierarchy.
Primary Group Contact and Elderly Morale: An Exchange/Power Analysis

Using a sample of 757 middle-aged and older residents of the Atlanta metropolitan region, the relationship between primary group contact and morale was investigated. Controlling on sex and dependency, it was found that interaction with children had a negative impact on the morale of dependent, older males. This finding was explained in terms of the power-dependence relationships that exist within the family. It was argued that visits with children and grand­ children are perceived by the dependent older male as a drama in which the ascending genera­ tions legitimate their claims to leadership through a gradual process of situation redefinition. One manifest result of having to cede control to his middle-aged offspring is lower morale. Contrary to what sometimes passes as conventional wisdom, old people do not, for the most part, live a life in isolation from their families. Although it is true that multigenerational households in the United States are not very common, crossgenerational kin contact is far from rare. A n umber of studies, in fact, indicate that interaction among family members (particularly the contact of close kin like parents and children) is a routinized characteristic of everyday life in old age (Adams, 1968; Britton et al., 1961; Rosenberg, 1970; Sussman, 1965; Winch and Greer, 1968). In a large-scale study of old people in three industrialized societies, Shanas et at. (1968) reported that 84 per cent of the American respondents had seen at least one of their children the previous week. It remains unclear, however, whether the frequency of family contact has any impact upon the quality of life of its older members. Some research has shown, *The data on which this research is based were collected in late spring and early summer, 1977. This research was supported by a grant from the Administration on Aging (No.90-A1010-2). The views expressed are those of the authors.
Review of Privacy Preserving Public Auditing Techniques

computing provides services where users can store their data remotely on cloud and can access their data from anywhere, anytime by means of internet. Cloud computing enables users to use the data stored on cloud as if the data is local without worrying about its accuracy and reliability. But a major challenge in cloud computing is to ensure the integrity of user"s outsourced data on cloud server. Public auditing service makes use of an independent third party to check data storage correctness on cloud on behalf of data owner itself. This paper analyzes various techniques employed in order to perform secure cloud auditing to verify the integrity of outsourced data on cloud. Also it discusses limitations associated with these protocols and lastly proposes a scheme to ensure privacy and security in public auditing for cloud storage Keywordscomputing; Data Integrity; ElGamal algorithm; SHA- 256; Third party auditor.
Interleukin-10 rs2227307 and CXCR2 rs1126579 polymorphisms modulate the predisposition to septic shock

Despite major improvements in its treatment and diagnosis, sepsis is still a leading cause of death and admittance to the intensive care unit (ICU). Failure to identify patients at high risk of developing septic shock contributes to an increase in the sepsis burden and rapid molecular tests are currently the most promising avenue to aid in patient risk determination and therapeutic anticipation. The primary goal of this study was to evaluate the genetic susceptibility that affects sepsis outcome in 72 sepsis patients admitted to the ICU. Seven polymorphisms were genotyped in key inflammatory response genes in sepsis, including tumour necrosis factor-α, interlelukin (IL)-1β, IL-10, IL-8, Toll-like receptor 4, CXCR1 and CXCR2. The primary finding showed that patients who were homozygous for the major A allele in IL-10 rs1800896 had almost five times higher chance to develop septic shock compared to heterozygotes. Similarly, selected clinical features and CXCR2 rs1126579 single nucleotide polymorphisms modulated septic shock susceptibility without affecting survival. These data support the hypothesis that molecular testing has clinical usefulness to improve sepsis prognostic models. Therefore, enrichment of the ICU portfolio by including these biomarkers will aid in the early identification of sepsis patients who may develop septic shock.
Planning system for indoor wireless network

A novel wireless LAN prediction tool using the genetic algorithm and neural network has been proposed. We establish a site survey tool system to predict the received signal strength index (RSSI) in an indoor environment. The system includes six items. (1) The fading function: it corrects the functional characteristics of the RSSI for different types of wireless LAN cards in free space. (2) The setting of the attributes of obstacles in the indoor environment: the idea of a "single attribute of local area" is proposed. If there are the same obstacles in one area, we set the area as one attribute. (3) The genetic algorithm: where we use reproduction, crossover and mutation to obtain the propagation loss through the different obstacles (Li). (4) The neural network: we use neural network concept to correct the prediction error arising from the multipath effect in the indoor environment. (5) The auxiliary judgment for the sampling points: the method is helpful to users in establishing the best sampling points. (6) The calibration of prediction results: we use calibration to correct the prediction error arisen from Li.