Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Novel Proteins in Neospora caninum Using an Organelle Purification and Monoclonal Antibody Approach

Neospora caninum is an important veterinary pathogen that causes abortion in cattle and neuromuscular disease in dogs. Neospora has also generated substantial interest because it is an extremely close relative of the human pathogen Toxoplasma gondii, yet does not appear to infect humans. While for Toxoplasma there are a wide array of molecular tools and reagents available for experimental investigation, relatively few reagents exist for Neospora. To investigate the unique biological features of this parasite and exploit the recent sequencing of its genome, we have used an organelle isolation and monoclonal antibody approach to identify novel organellar proteins and develop a wide array of probes for subcellular localization. We raised a panel of forty-six monoclonal antibodies that detect proteins from the rhoptries, micronemes, dense granules, inner membrane complex, apicoplast, mitochondrion and parasite surface. A subset of the proteins was identified by immunoprecipitation and mass spectrometry and reveal that we have identified and localized many of the key proteins involved in invasion and host interaction in Neospora. In addition, we identified novel secretory proteins not previously studied in any apicomplexan parasite. Thus, this organellar monoclonal antibody approach not only greatly enhances the tools available for Neospora cell biology, but also identifies novel components of the unique biological characteristics of this important veterinary pathogen.
DomainFlow: practical flow management method using multiple flow tables in commodity switches

A scalable network with high bisection bandwidth and high availability requires efficient use of the multiple paths between pairs of end hosts. OpenFlow is an innovative technology and enables fine-grained, flow level control of Ethernet switching. However, the flow table structure defined by OpenFlow is not hardware friendly and the scalability is limited by the switch device. OpenFlow is also not sufficient for fast multipath failover. To overcome these limitations, we propose DomainFlow in which the network is split into sections and exact matches are used where possible to enable practical flow management using OpenFlow for commodity switches. We applied a prototype of DomainFlow to multipath flow management in the Virtual eXtensible LAN (VXLAN) overlay network environment. The total number of flow entries was reduced to 1/128 using currently available commodity switches, which was not possible before.
A Secure Environment for Untrusted Helper Applications ( Confining the Wily Hacker )

Many popular programs, such as Netscape, use untrusted helper applications to process data from the network. Unfortunately, the unauthenticated network data they interpret could well have been created by an adversary, and the helper applications are usually too complex to be bug-free. This raises signi cant security concerns. Therefore, it is desirable to create a secure environment to contain untrusted helper applications. We propose to reduce the risk of a security breach by restricting the program's access to the operating system. In particular, we intercept and lter dangerous system calls via the Solaris process tracing facility. This enabled us to build a simple, clean, user-mode implementation of a secure environment for untrusted helper applications. Our implementation has negligible performance impact, and can protect pre-existing applications.
Nonlinear Active Noise Control With NARX Models

The extension of active noise control (ANC) techniques to deal with nonlinear effects such as distortion and saturation requires the introduction of suitable nonlinear model classes and adaptive algorithms. Large sized models are typically used, resulting in an increased computational load, delayed convergence (and sometimes even algorithm instability), and other unwanted dynamical effects due to overparametrization. This paper discusses the usage of polynomial nonlinear autoregressive models with exogenous variables (NARX) models and model selection techniques to reduce the model size and increase its robustness, for more efficient and reliable ANC. An offline procedure is devised to identify the controller model structure, and the controller parameters are successively updated with an adaptive algorithm based on the error gradient and on the residual noise. Simulation experiments show the effectiveness of the proposed approach. A brief analysis of the involved computational complexity is also provided.
Take the Bullies to Task: Using Process Drama to Make a Stand

To “empower students to think and act more effectively” concerning violence and bullying within schools, Allison L. Baer and Jacqueline N. Glasgow suggest close examination and discussion of literature that foregrounds violence and bystander participation. Baer and Glasgow recommend several useful novels for addressing the various roles of bystanders. Additionally, they use process drama as a safe activity to help students creatively and realistically explore problems and solutions when confronted by violence.
Survey of fault tolerance techniques for shared memory multicore/multiprocessor systems

With the advent of modern nano-scale technology, it has become possible to implement multiple processing cores on a single die. The shrinking transistor sizes however have made reliability a concern for such systems as smaller transistors are more prone to permanent as well as transient faults. To reduce the probability of failures of such systems, online fault tolerance techniques can be applied. These techniques need to be efficient as they execute concurrently with applications running on such systems. This paper discusses the challenges involved in online fault tolerance and existing work which tackles these challenges. We classify fault tolerance into four different steps which are proactive fault management, error detection, fault diagnosis and recovery and discuss related work for each step, with focus on techniques for shared memory multicore/multiprocessor systems. We also highlight the additional difficulties in tolerating faults for parallel execution on shared memory multicore/multiprocessor systems.
Multi-resolution localization method based on time reversal and simulated annealing algorithm

In this paper, we propose a novel acoustic indoor localization system that is based on time reversal. The system estimates the target position with different precision. First, it uses a low frequency signal in order to localize the source in the whole area within coarse precision. Then, it switches to high frequency signal to estimate the target location in a reduced area within a fine precision. The system performance have been evaluated by simulations and by experiments conducted in a practical training room in the National School of Engineers of Le Mans. Results have shown that the system has subcentimeter accuracy.
A UNIVERSAL CENTRAL ENGINE HYPOTHESIS FOR SHORT AND LONG GAMMA-RAY BURSTS

It is noted that X-ray tails of short, hard γ-ray bursts (SHBs) are similar to X-ray flashes. We suggest a universal central engine hypothesis, as a way of accounting for this curiosity, in which SHBs differ from long γ-ray bursts in prompt emission because of the differences in the host star and attendant differences in the environment they present to the compact central engine (as opposed to differences in the central engine itself). Observational constraints and implications are discussed.
Cellular and Subcellular Specification of Na,K-ATPase α and β Isoforms in the Postnatal Development of Mouse Retina

The Na,K-ATPase is a dominant factor in retinal energy metabolism, and unique combinations of isoforms of its α and β subunits are expressed in different cell types and determine its functional properties. We used isoform-specific antibodies and fluorescence confocal microscopy to determine the expression of Na,K-ATPase α and β subunits in the mouse and rat retina. In the adult retina, α1 was found in Müller and horizontal cells, α2 in some Müller glia, and α3 in photoreceptors and all retinal neurons. β1 was largely restricted to horizontal, amacrine, and ganglion cells; β2 was largely restricted to photoreceptors, bipolar cells, and Müller glia; and β3 was largely restricted to photoreceptors. Photoreceptor inner segments have the highest concentration of Na,K-ATPase in adult retinas. Isoform distribution exhibited marked changes during postnatal development. α3 and β2 were in undifferentiated photoreceptor somas at birth but only later were targeted to inner segments and synaptic terminals. β3, in contrast, was expressed late in photoreceptor differentiation and was immediately targeted to inner segments. A high level of β1 expression in horizontal cells preceded migration, whereas increases in β2 expression in bipolar cells occurred very late, coinciding with synaptogenesis in the inner plexiform layer. Most of the spatial specification of Na,K-ATPase isoform expression was completed before eye opening and the onset of electroretinographic responses on postnatal day 13 (P13), but quantitative increase continued until P22 in parallel with synaptogenesis.
Irradiation attenuates neurogenesis and exacerbates ischemia‐induced deficits

Increased neurogenesis after cerebral ischemia suggests that functional recovery after stroke may be attributed, in part, to neural regeneration. In this study, we investigated the role of neurogenesis in the behavioral performance of gerbils after cerebral global ischemia. We used ionizing radiation to decrease neural regeneration, and 2 weeks later cerebral global ischemia was induced by bilateral common carotid artery occlusion. One month after the occlusion, the animals were behaviorally tested. Irradiation alone reduced neurogenesis but did not change vascular or dendritic morphology at the time of behavioral testing. Neither did irradiation, ischemia, or combined treatment impair rotor‐rod performance or alter open‐field activity. Gerbils subjected to both irradiation and ischemia demonstrated impaired performance in the water‐maze task, compared with those that received only ischemia, radiation, or no treatment. These impairments after cerebral global ischemia under conditions of reduced neurogenesis support a role for the production of new cells in mediating functional recovery.
Embedding Rule-Based Security Monitors into Java Programs

In this paper we study securing mobile code execution by embedding a rule-based security monitor into the mobile code before execution on a platform. A security monitor guards how the mobile code uses resources of the execution platform. We consider that this run-time monitoring approach is more practical than providing a proof of security properties along with the mobile code. Writing execution context related rule-based security policies enables us to be flexible with respect to the restrictions we wish to impose on the mobile code. In our opinion, establishing an authority for certifying the safety of mobile code is too inflexible, since depending on the situation the user might temporarily want to tighten the restrictions. We describe our language for expressing rule-based security policies and show how those policies can be translated into aspects, which together form a run-time security monitor. In practice, we translate our policy expression to AspectJ with our MPLc compiler and only consider embedding a run-time monitor into Java applications.
Genome-wide association study of susceptibility loci for cervical cancer.

BACKGROUND Cervical carcinoma has a heritable genetic component, but the genetic basis of cervical cancer is still not well understood. METHODS We performed a genome-wide association study of 731 422 single nucleotide polymorphisms (SNPs) in 1075 cervical cancer case subjects and 4014 control subjects and replicated it in 1140 case subjects and 1058 control subjects. The association between top SNPs and cervical cancer was estimated by odds ratios (ORs) and 95% confidence intervals (CIs) with unconditional logistic regression. All statistical tests were two-sided. RESULTS Three independent loci in the major histocompatibility complex (MHC) region at 6p21.3 were associated with cervical cancer: the first is adjacent to the MHC class I polypeptide-related sequence A gene (MICA) (rs2516448; OR = 1.42, 95% CI = 1.31 to 1.54; P = 1.6×10(-18)); the second is between HLA-DRB1 and HLA-DQA1 (rs9272143; OR = 0.67, 95% CI = 0.62 to 0.72; P = 9.3×10(-24)); and the third is at HLA-DPB2 (rs3117027; OR=1.25, 95% CI = 1.15 to 1.35; P = 4.9×10(-8)). We also confirmed previously reported associations of B*0702 and DRB1*1501-DQB1*0602 with susceptibility to and DRB1*1301-DQA1*0103-DQB1*0603 with protection against cervical cancer. The three new loci are statistically independent of these specific human leukocyte antigen alleles/haplotypes. MICA encodes a membrane-bound protein that acts as a ligand for NKG2D to activate antitumor effects. The risk allele of rs2516448 is in perfect linkage disequilibrium with a frameshift mutation (A5.1) of MICA, which results in a truncated protein. Functional analysis shows that women carrying this mutation have lower levels of membrane-bound MICA. CONCLUSIONS Three novel loci in the MHC may affect susceptibility to cervical cancer in situ, including the MICA-A5.1 allele that may cause impaired immune activation and increased risk of tumor development.
Spinal-Like Regulator Facilitates Control of a Two-Degree-of-Freedom Wrist

The performance of motor tasks requires the coordinated control and continuous adjustment of myriad individual muscles. The basic commands for the successful performance of a sensorimotor task originate in “higher” centers such as the motor cortex, but the actual muscle activation and resulting torques and motion are considerably shaped by the integrative function of the spinal interneurons. The relative contributions of brain and spinal cord are less clear for reaching movements than for automatic tasks such as locomotion. We have modeled a two-axis, four-muscle wrist joint with realistic musculoskeletal mechanics and proprioceptors and a network of regulatory circuitry based on the classical types of spinal interneurons (propriospinal, monosynaptic Ia-excitatory, reciprocal Ia-inhibitory, Renshaw inhibitory, and Ib-inhibitory pathways) and their supraspinal control (via biasing activity, presynaptic inhibition, and fusimotor gain). The modeled system has a very large number of control inputs, not unlike the real spinal cord that the brain must learn to control to produce desired behaviors. It was surprisingly easy to program this model to emulate actual performance in four very different but well described behaviors: (1) stabilizing responses to force perturbations; (2) rapid movement to position target; (3) isometric force to a target level; and (4) adaptation to viscous curl force fields. Our general hypothesis is that, despite its complexity, such regulatory circuitry substantially simplifies the tasks of learning and producing complex movements.
Representing Topics Using Images

Topics generated automatically, e.g. using LDA, are now widely used in Computational Linguistics. Topics are normally represented as a set of keywords, often the n terms in a topic with the highest marginal probabilities. We introduce an alternative approach in which topics are represented using images. Candidate images for each topic are retrieved from the web by querying a search engine using the top n terms. The most suitable image is selected from this set using a graph-based algorithm which makes use of textual information from the metadata associated with each image and features extracted from the images themselves. We show that the proposed approach significantly outperforms several baselines and can provide images that are useful to represent a topic.
Infection-induced lung injury is worsened after renal buffering of hypercapnic acidosis

Objective:Prolonged hypercapnia is commonly encountered during the treatment of acute respiratory distress syndrome and acute respiratory failure attributable to other causes with protective ventilation strategies. In these circumstances, compensatory renal buffering returns pH to normal establishing a condition of buffered hypercapnia. It is also common intensive care practice to correct the pH more rapidly using bicarbonate infusions. Although it is well-established that hypercapnic acidosis has potent anti-inflammatory and protective effects, the effect of buffered hypercapnia on acute lung injury and acute respiratory distress syndrome is unknown. We therefore wished to determine the effects of buffered hypercapnia on acute lung injury induced by endotoxin or Escherichia coli infection in vivo. Design:Prospective, randomized animal study. Setting:University research laboratory. Subjects:Adult male Sprague-Dawley rats. Interventions:We established buffered hypercapnia by exposing rats to a hypercapnic environment for 3 days before the induction of lung injury. Buffered hypercapnia rats (initial pH >7.35, FiCO2 = 0.05) and normocapnic controls (initial pH >7.35, FiCO2 = 0.00) were then anesthetized, mechanically ventilated, and lung injury induced by intra-tracheal inoculation of endotoxin (series I) or Escherichia coli (series II). Measurements and Main Results:Buffered hypercapnia significantly increased both endotoxin and Escherichia coli-induced lung injury when compared to normocapnic controls, as assessed by arterial oxygenation, lung compliance, pro-inflammatory pulmonary cytokine concentrations, and measurements of structural lung damage. In additional in vitro experiments buffered hypercapnia did not alter neutrophil phagocytosis ability but did impaired epithelial wound healing. Conclusions:Our results demonstrate that infection-induced injury in vivo is worsened after renal buffering of hypercapnic acidosis independently of any changes in tidal volume. These findings have important implications for our understanding of the pathogenesis of infection-induced lung injury during the use protective ventilation strategies that permits buffered hypercapnia and during infective exacerbations of chronic lung diseases associated with sustained hypercapnia.
Worldwide Patterns of Ancestry, Divergence, and Admixture in Domesticated Cattle

The domestication and development of cattle has considerably impacted human societies, but the histories of cattle breeds and populations have been poorly understood especially for African, Asian, and American breeds. Using genotypes from 43,043 autosomal single nucleotide polymorphism markers scored in 1,543 animals, we evaluate the population structure of 134 domesticated bovid breeds. Regardless of the analytical method or sample subset, the three major groups of Asian indicine, Eurasian taurine, and African taurine were consistently observed. Patterns of geographic dispersal resulting from co-migration with humans and exportation are recognizable in phylogenetic networks. All analytical methods reveal patterns of hybridization which occurred after divergence. Using 19 breeds, we map the cline of indicine introgression into Africa. We infer that African taurine possess a large portion of wild African auroch ancestry, causing their divergence from Eurasian taurine. We detect exportation patterns in Asia and identify a cline of Eurasian taurine/indicine hybridization in Asia. We also identify the influence of species other than Bos taurus taurus and B. t. indicus in the formation of Asian breeds. We detect the pronounced influence of Shorthorn cattle in the formation of European breeds. Iberian and Italian cattle possess introgression from African taurine. American Criollo cattle originate from Iberia, and not directly from Africa with African ancestry inherited via Iberian ancestors. Indicine introgression into American cattle occurred in the Americas, and not Europe. We argue that cattle migration, movement and trading followed by admixture have been important forces in shaping modern bovine genomic variation.
Spatiotemporal dynamics of neocortical excitation and inhibition during human sleep

Intracranial recording is an important diagnostic method routinely used in a number of neurological monitoring scenarios. In recent years, advancements in such recordings have been extended to include unit activity of an ensemble of neurons. However, a detailed functional characterization of excitatory and inhibitory cells has not been attempted in human neocortex, particularly during the sleep state. Here, we report that such feature discrimination is possible from high-density recordings in the neocortex by using 2D multielectrode arrays. Successful separation of regular-spiking neurons (or bursting cells) from fast-spiking cells resulted in well-defined clusters that each showed unique intrinsic firing properties. The high density of the array, which allowed recording from a large number of cells (up to 90), helped us to identify apparent monosynaptic connections, confirming the excitatory and inhibitory nature of regular-spiking and fast-spiking cells, thus categorized as putative pyramidal cells and interneurons, respectively. Finally, we investigated the dynamics of correlations within each class. A marked exponential decay with distance was observed in the case of excitatory but not for inhibitory cells. Although the amplitude of that decline depended on the timescale at which the correlations were computed, the spatial constant did not. Furthermore, this spatial constant is compatible with the typical size of human columnar organization. These findings provide a detailed characterization of neuronal activity, functional connectivity at the microcircuit level, and the interplay of excitation and inhibition in the human neocortex.
Markov chain Monte Carlo estimation of quantiles

We consider quantile estimation using Markov chain Monte Carlo and establish conditions under which the sampling distribution of the Monte Carlo error is approximately Normal. Further, we investigate techniques to estimate the associated asymptotic variance, which enables construction of an asymptotically valid interval estimator. Finally, we explore the finite sample properties of these methods through examples and provide some recommendations to practitioners.
Chemical inhibition of autophagy: Examining its potential to increase the specific productivity of recombinant CHO cell lines

Chinese hamster ovary (CHO) cells activate and undergo apoptosis and autophagy for various environmental stresses. Unlike apoptosis, studies on increasing the production of therapeutic proteins in CHO cells by targeting the autophagy pathway are limited. In order to identify the effects of chemical autophagy inhibitors on the specific productivity (qp), nine chemical inhibitors that had been reported to target three different phases of autophagy (metformin, dorsomorphin, resveratrol, and SP600125 against initiation and nucleation; 3‐MA, wortmannin, and LY294002 against elongation, and chloroquine and bafilomycin A1 against autophagosome fusion) were used to treat three recombinant CHO (rCHO) cell lines: the Fc‐fusion protein‐producing DG44 (DG44‐Fc) and DUKX‐B11 (DUKX‐Fc) and antibody‐producing DG44 (DG44‐Ab) cell lines. Among the nine chemical inhibitors tested, 3‐MA, dorsomorphin, and SP600125 significantly increased the qp of DG44‐Fc and DUKX‐Fc. In contrast, for DG44‐Ab, only 3‐MA significantly increased the qp. The autophagy‐inhibiting activity of the nine chemical inhibitors on the rCHO cell lines was evaluated through Western blot analysis and flow cytometry. Unexpectedly, some chemical inhibitors did not exhibit any apparent inhibition activity on autophagy. The chemical inhibitors that enhanced the qp, 3‐MA, dorsomorphin, and SP600125, exhibited instead an increased autophagic flux. Taken all together, the chemical inhibition of autophagy was not effective in increasing the qp in rCHO cell lines and the positive effect of 3‐MA, dorsomorphin, and SP600125 on the qp was not due to the inhibition of autophagy. Biotechnol. Bioeng. 2016;113: 1953–1961. © 2016 Wiley Periodicals, Inc.