Miracle-dz/UniFAR-FTUs huggingface dataset:
Proteomic analysis of Paracoccidioides brasiliensis complex isolates: Correlation of the levels of differentially expressed proteins with in vivo virulence

Background Paracoccidioidomycosis (PCM) is a systemic mycosis commonly found in Latin America that is caused by distinct species of Paracoccidioides genus: Paracoccidioides brasiliensis complex (S1, PS2, PS3 and PS4) and Paracoccidioides lutzii. Its pathobiology has been recently explored by different approaches to clarify the mechanisms of host-pathogen interactions underpinning PCM. The diversity of clinical forms of this disease has been attributed to both host- and fungus-related factors. Methodology/Principal findings For better understanding of the molecular underpinnings of host-fungus interactions, we evaluated in vivo virulence of nine Paracoccidioides brasiliensis complex isolates and correlated it to protein expression profiles obtained by two-dimensional gel electrophoresis. Based on the recovery of viable fungi from mouse organs, the isolates were classified as those having low, moderate, or high virulence. Highly virulent isolates overexpressed proteins related to adhesion process and stress response, probably indicating important roles of those fungal proteins in regulating the colonization capacity, survival, and ability to escape host immune system reaction. Moreover, highly virulent isolates exhibited enhanced expression of glycolytic pathway enzymes concomitantly with repressed expression of succinyl-CoA ligase beta chain, a protein related to the tricarboxylic acid cycle. Conclusions/Significance Our findings may point to the mechanisms used by highly virulent P. brasiliensis isolates to withstand host immune reactions and to adapt to transient iron availability as strategies to survive and overcome stress conditions inside the host.
Tick-borne encephalitis virus: molecular determinants of neuropathogenesis of an emerging pathogen

Abstract Tick-borne encephalitis virus (TBEV) is a zoonotic agent causing severe encephalitis. The transmission cycle involves the virus, the Ixodes tick vector, and a vertebrate reservoir, such as small mammals (rodents, or shrews). Humans are accidentally involved in this transmission cycle. Tick-borne encephalitis (TBE) has been a growing public health problem in Europe and Asia over the past 30 years. The mechanisms involved in the development of TBE are very complex and likely multifactorial, involving both host and viral factors. The purpose of this review is to provide an overview of the current literature on TBE neuropathogenesis in the human host and to demonstrate the emergence of common themes in the molecular pathogenesis of TBE in humans. We discuss and review data on experimental study models and on both viral (molecular genetics of TBEV) and host (immune response, and genetic background) factors involved in TBE neuropathogenesis in the context of human infection.
A low-cost architecture for real-time processing and analysis of binary images

An architecture is presented for low-cost and flexible realisation of image processing and analysis algorithms of binary images. The flexibility of the architecture is due to reconfigurable network of simple boolean functions. It is shown that this architecture can readily be implemented by low-cost off-the-shelf components. This is illustrated by some simulations of a hypothetical realisation. <<ETX>>
TP53BP1 regulates chromosome alignment and spindle bipolarity in mouse oocytes

Meiotic oocytes lack classic centrosomes; therefore, bipolar spindle assembly depends on the clustering of acentriolar microtubule‐organizing centers (MTOCs) into two poles. The bipolar spindle is an essential cellular component that ensures accurate chromosome segregation during anaphase. If the spindle does not form properly, it can result in aneuploidy or cell death. However, the molecular mechanism by which the bipolar spindle is established is not yet fully understood. Tumor suppressor p53‐binding protein 1 (TP53BP1) is known to mediate the DNA damage response. Several recent studies have indicated that TP53BP1 has noncanonical roles in processes, such as spindle formation; however, the role of TP53BP1 in oocyte meiosis is currently unclear. Our results show that TP53BP1 knockdown affects spindle bipolarity and chromatin alignment by altering MTOC stability during oocyte maturation. TP53BP1 was localized in the cytoplasm and displayed an irregular cloud pattern around the spindle/chromosome region. TP53BP1 was also required for the correct localization of MTOCs into the two spindle poles during pro‐meiosis I. TP53BP1 deletion altered the MTOC‐localized Aurora Kinase A. TP53BP1 knockdown caused the microtubules to detach from the kinetochores and increased the rate of aneuploidy. Taken together, our data show that TP53BP1 plays crucial roles in chromosome stability and spindle bipolarity during meiotic maturation.
Performance Enhancement of Mobile Ad-Hoc Network Using Delay Aware Routing Protocol

A Mobile Ad Hoc Network (MANET) is a network comprising of a set of mobile hosts proficient of communicating with each other without the help of base stations. In view of the fact that MANET is an independent system of functionality equivalent mobile nodes, which have to be able to communicate while moving without any kind of wired infrastructure to this end, mobile nodes must work together to provide the routing services. A large number of MANET routing protocols have been projected in the last era. These protocols can be categorized according to the routing approach that they follow to determine route to the destination. These protocols execute variously depending on type of traffic, number of nodes, rate of mobility, etc. Routing protocols categorized into 3 categories. These are Proactive protocols, Reactive protocols and Hybrid protocols. There are Metrics which are accountable to the Performance of MANET & to achieve the Quality of Services for a mobile Adhoc network these metrics play a major role. Delay is one of the major metrics of Quality of Services. Which describes the delay of data packets at the destination node. This Paper presents the concept and approach that how we can improve the performance of MANET by decreasing the delay using any particular delay aware routing protocol. This paper also presents the comparison of different routing protocol on the basis of Delay Metrics.
Toward learning time-varying functions with high input dimensionality

Adaptive control problems in which the control law changes over time are considered. Such problems arise in robotics applications in which unanticipated variations in sensors, effectors, and the work environment change the desired input/output behavior of the controller. The problems are characterized in terms of learning an input/output function, and algorithms are presented for quick learning of such time-varying functions. The techniques presented are particularly effective for problems with input spaces of high dimensionality. The authors discuss why many existing algorithms are unsuitable for this type of problem and propose additional techniques for reducing the dimensionality of input spaces. <<ETX>>
Dietary fibre and cardiovascular health: a review of current evidence and policy

Dietary fibre comprises many different, mainly plant-based, compounds that are not fully digested in the human gut. Insoluble fibres include cellulose, hemi-celluloses and lignin and soluble fibres include pectins, β-glucan and hydro-colloids. In the UK, the daily recommended amount has increased to 30 g but only 13 % of men and 4 % of women meet this recommendation. Currently the mean intake for adults is 21 g for men and 17 g for women. There is a wealth of epidemiological evidence based on systematic reviews of trials and cohorts to support the higher fibre recommendation. This includes evidence of reductions in the risk for CVD (both heart disease and stroke) and lower risk of type 2 diabetes, lower blood pressure, lower LDL-cholesterol, as well as some cancers. Beneficial effects of fibre operate via a diverse range of mechanisms throughout the digestive system including the mouth, stomach and small and large intestine; some of which are still not completely understood. The updated recommendation for fibre is a long way from a typical British diet and requires several daily portions of fruit and vegetables and wholegrain foods. Improving dietary fibre intakes will require a variety of actions and policies from stakeholders; however, there is currently more of a focus on reducing sugar than increasing fibre. In order to increase the number of adults meeting the fibre recommendation, social marketing and labelling of high-fibre foods are warranted as well as reformulation and wider availability of wholegrain versions of popular foods.
TCP performance over cdma2000 RLP

This paper provides performance results for TCP over cdma2000 radio link protocol (RLP). The simulations are performed for a single user running a long FTP application with "infinite" data backlog. With the assumption of a long FTP application, maximum TCP throughput is the relevant optimization metric. The goal is to analyze the impact of TCP window size, RTT, wireless channel bandwidth, FER model and RLP transmission delays on end-to-end transport. The IS-95 and its evolutions (i.e. IS-95B and cdma2000) use a NAK-based RLP. The number of rounds of NAKs and the number of retransmissions in each round is varied. We analyze the impact of varying different RLP parameters and retransmission schemes on TCP throughput. Our findings demonstrate that the (1,1,1,1,1) NAK scheme outperforms the (2,3) NAK scheme when the errors are correlated. This is also true for non-correlated error case and larger TCP window size. However, with non-correlated errors and comparatively smaller TCP window size, the (2,3) NAK scheme performs better. It was also observed that the TCP throughput is not severely penalized up to link error rates of 10% (approximately 15% loss in TCP throughput at 10% FER).
Maintaining Predictions over Time without a Model

A common approach to the control problem in partially observable environments is to perform a direct search in policy space, as defined over some set of features of history. In this paper we consider predictive features, whose values are conditional probabilities of future events, given history. Since predictive features provide direct information about the agent's future, they have a number of advantages for control. However, unlike more typical features defined directly over past observations, it is not clear how to maintain the values of predictive features over time. A model could be used, since a model can make any prediction about the future, but in many cases learning a model is infeasible. In this paper we demonstrate that in some cases it is possible to learn to maintain the values of a set of predictive features even when a learning a model is infeasible, and that natural predictive features can be useful for policy-search methods.
Retrieval of land surface albedo from satellite observations: a simulation study

Surface albedo retrieved from satellite observations at one atmospheric condition may not be suitable for application to other atmospheric conditions. In this paper the authors separate the apparent surface albedo from the inherent surface albedo, which is independent of atmospheric conditions, based on extensive radiative transfer simulations under a variety of atmospheric conditions. The conversion coefficients of the surface inherent narrowband albedos derived from the MODIS (Moderate-Resolution Imaging Spectroradiometer) and the MISR (Multiangle Imaging Spectroradiometer) instruments to the surface broadband inherent albedo are reported. A new approach of predicting broadband surface inherent albedos from MODIS or MISR TOA (top of atmosphere) narrowband albedos using a neural network is proposed.
SURVEY ON TRADITIONAL AND EVOLUTIONARY CLUSTERING APPROACHES

Clustering deals with grouping up of similar object s. Unlike classification, clustering tries to group a set of objects and find whether there is some relationship between the objects wher eas in classification a set of predefined classes w ill be known and it is enough to find which class a object belongs. Simply, classifi cation is a supervised learning technique and clust ering is an unsupervised learning technique. Clustering techniques apply when there i s no class to be predicted but rather when the inst ances are to be divided into natural groups. These clusters presumably reflect smechanism at work in the domain from which inst ances are drawn, a mechanism that causes some instances to bear a stro nger resemblance to each other than they do to the remaining instances. It naturally requires different techniques to the clas sification and association learning methods . Cluste ring has many applications in various fields. In Software engineering it helps in reverse engineering, software maintenance and for re-building systems. It aims at breaking a larger problem into small pieces of unde rstanding elements. There are many approaches avail able to carry out clustering. Since clustering has no particular methodology ther e are many methods available for carrying out clust ering. There are many traditional as well as evolutionary methods availab le for carrying out clustering. In this paper vario us types of the above mentioned methods are described and some of them are compared . Each method has its own advantage and they can be used according to the needs of the user.
Multidimensional Gains for Stochastic Approximation

This paper deals with iterative Jacobian-based recursion technique for the root-finding problem of the vector-valued function, whose evaluations are contaminated by noise. Instead of a scalar step size, we use an iterate-dependent matrix gain to effectively weigh the different elements associated with the noisy observations. The analytical development of the matrix gain is built on an iterative-dependent linear function interfered by additive zero-mean white noise, where the dimension of the function is <inline-formula> <tex-math notation="LaTeX">$ {M\ge 1}$ </tex-math></inline-formula> and the dimension of the unknown variable is <inline-formula> <tex-math notation="LaTeX">$ {N\ge 1}$ </tex-math></inline-formula>. Necessary and sufficient conditions for <inline-formula> <tex-math notation="LaTeX">$ {M\ge N}$ </tex-math></inline-formula> algorithms are presented pertaining to algorithm stability and convergence of the estimate error covariance matrix. Two algorithms are proposed: one for the case where <inline-formula> <tex-math notation="LaTeX">$ {M\ge N}$ </tex-math></inline-formula> and the second one for the antithesis. The two algorithms assume full knowledge of the Jacobian. The recursive algorithms are proposed for generating the optimal iterative-dependent matrix gain. The proposed algorithms here aim for per-iteration minimization of the mean square estimate error. We show that the proposed algorithm satisfies the presented conditions for stability and convergence of the covariance. In addition, the convergence rate of the estimation error covariance is shown to be inversely proportional to the number of iterations. For the antithesis <inline-formula> <tex-math notation="LaTeX">$ {M< N}$ </tex-math></inline-formula>, contraction of the error covariance is guaranteed. This underdetermined system of equations can be helpful in training neural networks. Numerical examples are presented to illustrate the performance capabilities of the proposed multidimensional gain while considering nonlinear functions.
Human Mutation

Correspondence Isabelle Richard, INTEGRARE Research Unit (UMR951), Genethon, INSERM, Univ. Paris‐ Saclay, 91002 Evry, France. Email: richard@genethon.fr Abstract Genetic variants in Fukutin‐related protein (FKRP), an essential enzyme of the glycosylation pathway of α‐dystroglycan, can lead to pathologies with different severities affecting the eye, brain, and muscle tissues. Here, we generate an in vitro cellular system to characterize the cellular localization as well as the functional potential of the most common FKRP patient missense mutations. We observe a differential retention in the endoplasmic reticulum (ER), the indication of misfolded proteins. We find data supporting that mutant protein able to overcome this ER‐ retention through overexpression present functional levels comparable to the wild‐ type. We also identify a specific region in FKRP protein localized between residues 300 and 321 in which genetic variants found in patients lead to correctly localized proteins but which are nevertheless functionally impaired or catalytically dead in our model, indicating that this particular region might be important for the enzymatic activity of FKRP within the Golgi. Our system thus allows the functional testing of patient‐specific mutant proteins and the identification of candidate mutants to be further explored with the aim of finding pharmacological treatments targeting the protein quality control system.
A new power combining and outphasing modulation system for high-efficiency power amplification

This paper describes a new power combining and outphasing system that provides both high efficiency and linear output control. Whereas conventional outphasing systems utilize two power amplifiers, the system introduced here combines power from four or more amplifiers. The proposed technique overcomes the loss and reactive loading problems of previous outphasing systems. It provides ideally lossless power combining, along with nearly resistive loading of the individual power amplifiers over a very wide output power range.
M-Crawler: Crawling Rich Internet Applications Using Menu Meta-Model

Web applications have come a long way both in terms of adoption to provide information and services and in terms of the technologies to develop them. With the emergence of richer and more advanced technologies such as Ajax, web applications have become more interactive, responsive and user friendly. These applications, often called Rich Internet Applications (RIAs) changed the traditional web applications in two primary ways: Dynamic manipulation of client side state and Asynchronous communication with the server. At the same time, such techniques also introduce new challenges. Among these challenges, an important one is the difficulty of automatically crawling these new applications. Crawling is not only important for indexing the contents but also critical to web application assessment such as testing for security vulnerabilities or accessibility. Traditional crawlers are no longer sufficient for these newer technologies and crawling in RIAs is either inexistent or far from perfect. There is a need for an efficient crawler for web applications developed using these new technologies. Further, as more and more enterprises use these new technologies to provide their services, the requirement for a better crawler becomes inevitable. This thesis studies the problems associated with crawling RIAs. Crawling RIAs is fundamentally more difficult than crawling traditional multi-page web applications. The thesis also presents an efficient RIA crawling strategy and compares it with existing methods. iii Acknowledgement First and foremost, I am indebted to my supervisors, Dr. Bochmann for their constant support, encouragement and guidance. They have always been very amiable and approachable advisors. Their brilliance, perseverance, and pursuit of excellence will continue to inspire me for years. This thesis would not be possible without their knowledge, encouragement, and guidance. I would also like to thank my colleague Emre Dinçtürk and the members of the Software Security Research Group at University of Ottawa, including Dr. Vio Onut (IBM) for all the insightful discussions and suggestions. I would also like to thank Seyed M. Mirtaheri for helping me with all the test applications for experimental studies. I would like to convey my regards to Bo Wan for all the help and advice. of Canada for all their help and support. I am also grateful to the AppScan® team at IBM.
Targeted genetic screening in mice through haploid embryonic stem cells identifies critical genes in bone development

Mutagenic screening is powerful for identifying key genes involved in developmental processes. However, such screens are successful only in lower organisms. Here, we develop a targeted genetic screening approach in mice through combining androgenetic haploid embryonic stem cells (AG-haESCs) and clustered regularly interspaced palindromic repeats/CRISPR-associated protein 9 (CRISPR-Cas9) technology. We produced a mutant semi-cloned (SC) mice pool by oocyte injection of AG-haESCs carrying constitutively expressed Cas9 and an single guide RNA (sgRNA) library targeting 72 preselected genes in one step and screened for bone-development–related genes through skeletal analysis at birth. This yielded 4 genes: Zic1 and Clec11a, which are required for bone development, and Rln1 and Irx5, which had not been previously considered. Whereas Rln1−/− mice exhibited small skeletal size only at birth, Irx5−/− mice showed skeletal abnormalities both in postnatal and adult phases due to decreased bone mass and increased bone marrow adipogenesis. Mechanistically, iroquois homeobox 5 (IRX5) promotes osteoblastogenesis and inhibits adipogenesis by suppressing peroxisome proliferator activated receptor γ (PPARγ) activation. Thus, AG-haESC-mediated functional mutagenic screening opens new avenues for genetic interrogation of developmental processes in mice.
Trends in Diverting Loop Ileostomy vs Total Abdominal Colectomy as Surgical Management for Clostridium Difficile Colitis.

Importance Diverting loop ileostomy and colonic lavage has generated much interest since it was first reported as a potential alternative to total abdominal colectomy for treating Clostridium difficile colitis in 2011. To our knowledge, few studies have validated the benefit reported in the initial description, and the association of this new approach with practice patterns has not been described. Objective To examine the national adoption pattern and outcomes of diverting loop ileostomy vs total abdominal colectomy as treatment for fulminant C difficile colitis. Design, Setting, and Participants This retrospective cohort study used data from hospitals participating in the National Inpatient Sample database across the United States from January 2011 to September 2015 and included 3021 adult patients who underwent surgery for C difficile colitis during the study period, comprising 2408 subtotal colectomies and 613 loop ileostomies. The data were analyzed between November 2018 and April 2019. Exposures Loop ileostomy as surgery of choice. Main Outcomes and Measures In-hospital mortality. Results Of 2408 participants, 1416 (58.8%) were women, 1781 (78.4%) were white, and 627 (21.6%) were individuals of color and the mean (SD) age was 68.2 (14.8) years. During the overall study period, 613 patients (20.28%) underwent diverting loop ileostomy without total abdominal colectomy. The annual proportion of patients undergoing only diversion increased from 11.16% in 2011 to 25.30% in 2015. Significantly more loop ileostomies were performed within the first day of hospitalization, in contrast to subtotal colectomies (23.31% vs 12.21%; P < .01). There was no significant difference in in-hospital mortality rates between the 2 groups (25.98% vs 31.18%; P = .28). Conclusions and Relevance This study demonstrates the adoption of diverting loop ileostomy to treat C difficile colitis across the United States. While fulminant C difficile colitis remains a condition with high mortality rates, no significant difference in this outcome was observed between loop ileostomy and total abdominal colectomy. Loop ileostomy may represent a viable surgical alternative to total abdominal colectomy, although the grounds for selection of treatment need to be clarified.