Miracle-dz/UniFAR-FTUs huggingface dataset:
A Pathogenic Role for CD4+ T Cells during Chikungunya Virus Infection in Mice

Chikungunya virus (CHIKV) is an alphavirus that causes chronic and incapacitating arthralgia in humans. Injury to the joint is believed to occur because of viral and host immune-mediated effects. However, the exact involvement of the different immune mediators in CHIKV-induced pathogenesis is unknown. In this study, we assessed the roles of T cells in primary CHIKV infection, virus replication and dissemination, and virus persistence, as well as in the mediation of disease severity in adult RAG2−/−, CD4−/−, CD8−/−, and wild-type CHIKV C57BL/6J mice and in wild-type mice depleted of CD4+ or CD8+ T cells after Ab treatment. CHIKV-specific T cells in the spleen and footpad were investigated using IFN-γ ELISPOT. Interestingly, our results indicated that CHIKV-specific CD4+, but not CD8+, T cells are essential for the development of joint swelling without any effect on virus replication and dissemination. Infection in IFN-γ−/− mice demonstrated that pathogenic CD4+ T cells do not mediate inflammation via an IFN-γ–mediated pathway. Taken together, these observations strongly indicate that mechanisms of joint pathology induced by CHIKV in mice resemble those in humans and differ from infections caused by other arthritogenic viruses, such as Ross River virus.
Semiautomatische Metadaten-Extraktion und Qualitätsmanagement in Workflow-Systemen zur Digitalisierung historischer Dokumente

Performing Named Entity Recognition on ancient documents is a time-consuming, complex and error-prone manual task. It is a prerequisite though to being able to identify related documents and correlate between named entities in distinct sources, helping to precisely recreate historic events. In order to reduce the manual effort, automated classification approaches could be leveraged. Classifying terms in ancient documents in an automated manner poses a difficult task due to the sources’ challenging syntax and poor conservation states. This thesis introduces and evaluates approaches that can cope with complex syntactial environments by using statistical information derived from a term’s context and combining it with domain-specific heuristic knowledge to perform a classification. Furthermore this thesis demonstrates how metadata generated by these approaches can be used as error heuristics to greatly improve the performance of workflow systems for digitizations of early documents.
Chest radiograph or computed tomography in the intensive care unit?

Chest radiography has recently lost its exalted position in the management of critically ill or injured patients. In the acute management of blunt chest trauma, it is shown to have a very low sensitivity for pneumothorax, pulmonary contusion, and atelectasis (1, 2). "Routine" postoperative radiographic studies of the chest in the postanesthesia care unit as well as "routine" daily radiographs in the intensive care unit (ICU) are increasingly considered neither necessary nor cost-effective (3, 4). How good, then, are the ICU portable chest radiographs that are done for a specific indication (evaluation of suspected pneumonia, pneumothorax, or effusions, etc.)? Several series, dating back to the late 1980s, suggest that these are not very reliable (5, 6). Consequently, other tools, such as computerized tomography (CT), have become attractive alternatives for the ICU patient. In the current issue of Critical Care Medicine, Dr. Voggenreiter and colleagues (7), from the University of Essen in Germany, present further evidence that CT examination has a superior sensitivity to chest radiographs for diagnosing intrathoracic lesions and also for evaluating response to therapy (e.g., prone positioning for acute respiratory distress syndrome) in multiple trauma patients in the ICU. Their experience suggests that CT scanning of the chest can be performed easily, improves diagnostic accuracy, precisely defines anatomical abnormalities, and frequently alters treatment decisions. Examples of correctable lesions include pneumothoraces, pulmonary abscesses, and pleural effusions. In this series, chest CT findings in 84% of the 101 scans have changed therapeutic plans and facilitated the decision to perform 11 thoracotomies. Of note, the diagnoses on CT were not evident in 57% of the radiographs. These data are similar to another recent series that analyzed 108 consecutive thoracic CT examinations and the associated bedside chest radiographs in 85 ICU patients (8). Of the 232 chest radiographic findings, 199 (86%) were confirmed by CT. Furthermore, the agreement improved to 93% when the diagnosis of mild congestive heart failure was excluded. Thirty-two (30%) of the 108 CT examinations had at least one new clinically important finding not evident on radiograph. The new findings included abscesses or postoperative fluid collections, unsuspected pneumonia or pleural effusions, and malignancies. The CT findings resulted in management changes in 24 (22%) of the 108 examinations. These observations have been supported by other reviews (9).
Fingertips detection and tracking based on active shape models and an ellipse

Detecting and tracking fingertips are significant techniques for recognizing hand gestures. Many patterns and skin color information are used to extract and trace features [1, 2]. However, to find correct shapes is difficult and there is limitation to express the diversity of models. In this paper, we describe a method of detecting and tracking fingertips based on Active Shape Models (ASMs) and an ellipse equation. ASM is an effective tool to obtain features of a specific object in images by using a trained model. The ellipse equation helps a template follow the object without skin color information. We show how well fingertips are extracted and traced through some experiments.
Developing of New Facets of Indirect Modeling in the Geosciences

In this paper, we describe some applications of Self Organizing feature map Neuro-Fuzzy Inference System (SONFIS) and Self Organizing feature map Rough Set (SORST) in analysis of permeability at a dam site and lost circulation in the drilling of three wells in Iran. Elicitation of the best rules on the information tables, exploration of the dominant structures on the behaviour of systems while they fall in to the balance of the second granulation level (rules) and highlighting of most effective attributes (parameters) on the selected systems, are some of the benefits of the proposed methods. In the other process, using complex networks (graphs) theory - as another method in not 1:1 modelling branch- mechanical behaviour of a rock joint has been investigated. Keywords: Information Granules; SONFIS; SORST; Complex Networks; Permeability; Lost Circulation; Mechanical Behavior of a Rock Joint
Inhibition of HCV Replication in HCV Replicon by shRNAs

We show that the vector-derived long dsRNA specifically inhibits the replication of HCV RNA in HCV replicon. We designed a long dsRNA targeted to the full-length HCV IRES/core elements (1-to 377-nt). Our results revealed that the replication of HCV RNA was reduced to near background levels in a sequence-specific manner by the long dsRNAs in the HCV replicon. We also designed four shRNAs against several regions (120- to 139-nt, 260- to 279-nt, 330- to 349-nt, and 340- to 359-nt) of the HCV IRES/Core elements. The two HCV IRES/core-specific shRNAs, 330- to 349-nt and 340- to 359-nt, containing the AUG initiation codon sequence showed stronger HCV inhibitory effects than the other two shRNAs, 120- to 139-nt and 260- to 279-nt.
Cold tolerance of Drosophila species is tightly linked to the epithelial K+ transport capacity of the Malpighian tubules and rectal pads

ABSTRACT Insect chill tolerance is strongly associated with the ability to maintain ion and water homeostasis during cold exposure. Maintenance of K+ balance is particularly important due to its role in setting the cell membrane potential that is involved in many aspects of cellular function and viability. In most insects, K+ balance is maintained through secretion at the Malpighian tubules, which balances reabsorption from the hindgut and passive leak arising from the gut lumen. Here, we used the scanning ion-selective electrode technique (SIET) at benign (23°C) and low (6°C) temperatures to examine K+ flux across the Malpighian tubules and the rectal pads in the hindgut in five Drosophila species that differ in cold tolerance. We found that chill-tolerant species were better at maintaining K+ secretion and suppressing reabsorption during cold exposure. In contrast, chill-susceptible species exhibited large reductions in secretion with no change, or a paradoxical increase, in K+ reabsorption. Using an assay to measure paracellular leak, we found that chill-susceptible species experience a large increase in leak during cold exposure, which could explain the apparent increase in K+ reabsorption found in these species. Our data therefore strongly support the hypothesis that cold-tolerant Drosophila species are better at maintaining K+ homeostasis through an increased ability to maintain K+ secretion rates and through reduced movement of K+ towards the hemolymph. These adaptations are manifested both at the Malpighian tubule and at the rectal pads in the hindgut, and ensure that cold-tolerant species experience less perturbation of K+ homeostasis during cold stress. Summary: The scanning ion-selective electrode technique reveals that cold tolerance in Drosophila is linked to the ability to maintain ion balance through adaptive changes in epithelial K+ transport.
Inorganic Phosphate Removal during Different Dialytic Procedures

In order to clarify the influence of membrane surface, membrane composition, dialysate buffer and convective transfer on the dialytic removal of inorganic phosphate (Pi), 11 uremic patients were studied. Each patient underwent 7 different dialysis techniques: conventional hemodialysis with acetate buffer and different surface or composition of the membrane, bicarbonate dialysis and a “soft” hemodiafiltration, also termed biofiltration, with post-dilution infusion of 4 liters. The treatment time was fixed at 4 hours. Our study showed that the dialyzer surface area and the ultrafiltration rate were the major factors in dialytic inorganic phosphorus (Pi) removal. The dialysate buffer does not modify dialytic Pi removal but may influence the rebound phenomenon.
Transformerless Series Dip/Sag Compensation with Ultracapacitors using a new Multilevel Boost DC-to-AC Topology

Multilevel power converters that provide more than two levels of voltage to achieve smoother and less distorted ac-to-dc, dc-to-ac, and dc-to-dc power conversion, have attracted many contributors. This paper presents a new multilevel topology that can be used in series dip/sag compensators using ultracapacitors. This boost dc-to-ac multilevel topology has self voltage balancing of cells and may be derived from the generalized multilevel inverter topology presented by Peng. The new dc-to-ac topology is a unique solution that makes the use of ultracapacitors with relative low voltage ratings cost efficient for dip compensation on low voltage and high voltage lines. As there exists no neutral connection in the series dip compensator, little isolation restraints exist when using this inverter on high voltage lines. A functional 20 kVA single phase dip compensator based on the new multilevel topology is presented to verify the theory
FPGA based implementation and testing of OVSF code

The orthogonal variable spreading factor (OVSF) code is widely used for preserving the orthogonality between physical channels. They provide multiple data rates for supporting different bandwidth requirements in a communication system. As the Penetration of FPGA devices is increased because of its reusability and less time to market, still impracticality exists for attaching test equipment probes to such devices under test. The Xilinx ChipScope™ Pro tool provides the integration of logic analyser and other test and measurement hardware components as a software core with the targeted design. This paper presents the hardware realization of parameterised OVSF code with classical counter based approach and its testing on FPGA using Xilinx ChipScope Pro software tools. The OVSF generation is first modelled in MATLAB Simulink and then implemented in VHDL for delay synthesis, timing analysis and validating for software testing as per required standard for WCDMA i.e. TCHIP is 260ns or FCHIP 3.84 MHz. The target FPGA device is Virtex-5 (XC5VLX50T-lff1136).
Binding affinities of the SH2 domains of ZAP‐70, p56/ck and Shc to the chain ITAMs of the T‐cell receptor determined by surface plasmon resonance

The chains of the T cell receptor complex play a critical role in the initiation of proximal signaling events upon T cell activation. Three pairs of potential tyrosine phosphorylation sites are located within the cytoplasmic domains of the chains. Subsequent to engagement of the T cell receptor, one or more of these tyrosine residues is phosphorylated. The phosphotyrosine residues, along with flanking amino acids, form an activation motif (and are shared by signaling subunits in the TCR, B cell receptor, and FcγRI) termed tyrosine‐based activation motifs (ITAMs). ITAMs serve as binding sites for SH2 domain‐containing proteins. Recent evidence suggests that the chains provide docking space for several key signal transduction molecules such as ZAP‐70, p56 lck, and Shc. To determine if ZAP‐70, p56 lck, and Shc bind to particular chain ITAM sequences, quantitative free‐solution measurements of binding affinities (Kd) were obtained by use of surface plasmon resonance technology. The results indicate that binding affinities of distinct SH2 domains to individual and paired phosphorylation sites greatly differ, and may dictate the sequence of signal transduction events.
Avian Contraceptive Tools: One Size Does Not Fit All

Author(s): Yoder, Christi A. ; Miller, Lowell A. | Abstract: Avian contraception is a nonlethal management tool that can be utilized in conjunction with other management techniques to help manage bird populations causing damage. Because management situations vary with respect to the type of damage, species involved, location, and nontarget hazards, it is necessary to develop multiple contraceptive tools to allow management flexibility. DiazaCon™ and nicarbazin have already been developed at the National Wildlife Research Center as avian contraceptives. Although both of these are promising contraceptive agents, more are needed for a wider variety of situations. Current research is focusing on other cholesterol inhibitors, inhibitors of the P450 side chain cleavage enzyme, and aromatase inhibitors. Because cholesterol is needed for steroid reproductive hormone production, inhibition of cholesterol impairs reproduction by preventing the formation of the necessary hormones. The P450 side chain cleavage enzyme is needed to convert cholesterol to pregnenolone, the precursor to progesterone and testosterone. Progesterone is needed for egg formation, ovulation, and oviposition, and testosterone is needed for sperm production. Aromatase is needed to convert testosterone to estradiol, which is needed in females to stimulate the production of egg yolk precursors in the liver. Inhibition of either of these enzymes should result in impaired reproduction. In the future, natural plant products with contraceptive activity, such as neem seed, will also be investigated. Because development of avian contraceptives is time intensive, an efficient screening process needs to be in place. Population models can assist in choosing specific agents to test for a given species and management situation. Although contraception is unlikely to be useful as a stand-alone tool, it can be included in integrated management plans.
A Single Event Latch-up protection method for SRAM FPGA

The state-of-the-art SRAM FPGAs show great potentials for aerospace applications because of their high performance, low power consumption and flexible configuration features. However, as typical CMOS devices, SRAM FPGAs are prone to Single Event Latchup(SEL) which may cause permanent damage to the device in the space radiation environment. This paper proposes a restorable anti-SEL method for SRAM FPGAs. The method can immediately disconnect the power supply when SEL occurs and restore power supply after the fault is solved. The experiments results show that the method can accurately detect the occurrence of SEL, and effectively release the SEL. Thus, it can help to improve the stability and reliability of SRAM FPGAs space application.
Application to Resource Allocation Problems in a Flow-Shop Manufacturing System

This paper proposes an agent-based architecture for a Web-based DSS. The basic research consideration is that Internet facilitates access to data, information, and knowledge sources available online. The proposed DSS mainly includes five components: Analyzer Agent (AA), Proposal Agent (PrA), Resource agent (RA), Production Agent (PA), and Coordinator Agent (CA). In particular, the agents are used to collect information and generate alternatives that would allow the user to focus on significant solutions. They communicate through the JADE platform, and exploit the potential advantages of Web 2.0 tools and Web services in carrying out their different tasks. We also present in this work the coordination protocol that supports the distributed and decentralized task achievement. The functions of each component are discussed and a corresponding prototype system is developed. Finally, some simple scenarios are given for the purpose of illustrating the feasibility of our approach.
Bone morphogenetic protein signaling pathway plays multiple roles during gastrointestinal tract development

The bone morphogenetic protein (BMP) signaling pathway plays an essential role during gastrointestinal (GI) tract development in vertebrates. In the present study, we use an antibody that recognizes the phosphorylated and activated form of Smad1, 5, and 8 to examine (by immunohistochemistry) the endogenous patterns of BMP signaling pathway activation in the developing GI tract. We show that the endogenous BMP signaling pathway is activated in the mesoderm, the endoderm, and the enteric nervous system (ENS) of the developing chick GI tract and is more widespread than BMP ligand expression patterns. Using an avian‐specific retroviral misexpression technique to activate or inhibit BMP signaling pathway activity in the mesoderm of the gut, we show that BMP activity is required for the pattern, the development, and the differentiation of all three tissue types of the gut: mesoderm (that forms the visceral smooth muscle), endoderm (that forms the epithelium), and ectoderm (that forms the ENS). These results demonstrate that BMP signaling is activated in all the tissue layers of the GI tract during the development and plays a role during interactions and reciprocal communications of these tissue layers. Developmental Dynamics 234:312–322, 2005. © 2005 Wiley‐Liss, Inc.
Muscle thickness measurement from ultrasonic wave using continuous wavelet analysis

A novel method of muscular thickness measurement based on reflection echo from the boundary surface of different layer of target area using ultrasonic wave is presented. By exploring the traveling direction of ultrasonic wave at the interface of fat-muscle or muscle-fat, the difference of the generated reflection echo can be measured. In the proposed method, ultrasonic waves were irradiated to a biological phantom using ultrasound single probe with center frequency of 5.0 MHz to acquire the reflection echo. The boundary surface was identified by applying continuous wavelet transform (CWT) where Mexican hat served as mother wavelet. In an experimental environment, the proposed method was applied to a 3-layer phantom consist of fat-muscle-fat and muscle thickness was measured. The mean absolute error of muscle thickness was measured as 0.03237 mm.
Implementing ML Algorithms with

An increase in cloud-based computing leads to an increased worry in the security of user data. Typically, data is sent to a third-party server which performs analytics or machine learning on the data. However, in most of these scenarios, the data involved is sensitive and should remain private. Homomorphic encryption, a form of encryption that allows functions to be performed on encrypted ciphertext, allows privacy-preserving data analysis of existing large private, sensitive data sets. We implement and analyze the performance of linear regression and K-means clustering using the homomorphic encryption library SEAL and provide an extension of the SEAL library to matrix operations.
Novel indication for cancer therapy: Chk1 inhibition sensitizes tumor cells to antimitotics

Paclitaxel (Taxol) is the most‐prescribed anti‐mitotic agent for a variety of advanced metastatic cancers. It induces mitotic arrest leading to apoptosis through microtubule stabilization. Chk1 is the major cell‐cycle checkpoint kinase mediating S‐ and G2‐arrests in response to various DNA‐damages. Chk1 inhibitor is anticipated and has been demonstrated to potentiate the cytotoxicity of DNA‐damaging agents through abrogation of cell‐cycle checkpoints. Paclitaxel does not, however, induce Chk1 activation, and Chk1 has not been shown to function in mitotic checkpoint. Thus, Chk1 inhibitor is not expected to enhance the toxicity of paclitaxel. Here we show that downregulation of Chk1 sensitizes tumor cells to the toxicity of paclitaxel in cell proliferation assay. Fluorescence microscopy showed that Chk1 knockdown augments mitotic catastrophe and apoptosis in paclitaxel‐treated cancer cells. Further, we elucidated the mechanism of this sensitization. Chk1 inhibition facilitates paclitaxel‐induced M‐phase entry by activation of Cdc2 kinase and accumulation of cyclin B1, the required cofactor for Cdc2 kinase activity. Moreover, Chk1 downregulation inhibits M phase exit through induction of the anaphase inhibitor, securin/PDS1. Collectively, Chk1 elimination sustains a more effective mitotic arrest as demonstrated by the more efficient accumulation of M‐phase marker phospho‐histone H3. We show that Chk1 elimination attenuates the paclitaxel‐induced activation of the anti‐apoptotic p42/p44 (ERK1/2) MAP kinase pathway, additionally contributing to the sensitization. Our results suggest that in addition to its well‐established role as an enforcer of S and G2‐checkpoints in response to genotoxic stress, Chk1 also plays a protective role in mitotic checkpoint to lessen mitotic catastrophe and thereby limits cell‐death. Therefore Chk1 downregulation can not only potentiate DNA‐damaging agents, but also enhance the toxicity of anti‐microtubule agents, which significantly broadens its therapeutic applications. © 2005 Wiley‐Liss, Inc.