Miracle-dz/UniFAR-FTUs huggingface dataset:
Association between tuberculin skin test reactivity, the memory CD4 cell subset, and circulating FoxP3-expressing cells in HIV-infected persons.

BACKGROUND Lack of reactivity to the tuberculin skin test (TST) is widely observed in individuals with advanced human immunodeficiency virus type 1 (HIV-1) infection. METHODS Biopsy specimens from the TST reaction site and from skin not infiltrated with purified protein derivative were obtained from 15 HIV-1-infected and 23 uninfected persons who did not have active tuberculosis and who were from a community in which the incidence of tuberculosis was very high. Histologic sections (size, 8 mum) were immunohistochemically stained for CD4, CD8, CD28, CD45RA, CD45RO, CD62L, CD1a, human leukocyte antigen (HLA)-DR, granulysin, interferon-gamma, and FoxP3 and were analyzed by single-cell in situ digital imaging. Peripheral blood mononuclear cells were analyzed using a fluorescence-activated cell sorter. RESULTS Biopsy specimens obtained from TST-reactive skin of HIV-1-infected persons demonstrated fewer CD4(+) T cells at the TST site (P = .36) but more HLA-DR(+) T cells (P = .037) than did such biopsy specimens obtained from HIV-1-uninfected persons. Among HIV-1-infected persons, the total number of cells (P = .008) and numbers of CD45RO(+) memory T cells (P = .003) were significantly higher in TST-reactive persons than in TST-unreactive persons. For HIV-1-infected persons, TST induration was inversely correlated with the numbers of FoxP3(+) T cells in the blood (P = .026) but was unrelated to the number of circulating CD4(+) T cells. CONCLUSIONS For HIV-1 infected persons, the TST depends on memory T cells and is more strongly associated with the numbers of circulating FoxP3(+)CD4(+) T cells than with the total number of CD4(+) T cells.
Learning from “Learning from Notes”

I am a slow learner. I, like many of us, take a while to assimilate new ways of thinking. Thus I was a slow learner with Orlikowski's 1992 CSCW paper, " Learning from Notes: Organizational Issues in Groupware Implementation. " And, in the end she didn't take me wholly to her side (see later comments about her philosophy). But I was significantly impacted by this paper in that it changed what I focused on in research and how I approached the issues. In " Learning from Notes, " Orlikowski reports on an in-depth analysis of one consulting office's adoption of Lotus Notes. Orlikowski, as an ethnomethodologist, views this situation from the lens of structuration theory, which focuses not on the individual but the social order in which people are situated—the cultural norms, the reward structure, the distribution of power, etc. (Giddens 1986). Interestingly, neither the word " structuration theory " nor Giddens appear in the paper. With a keen ear she heard about a number of incidents where people expressed their frustration both with the rapid roll-out of the technology and their limited understanding of what Notes could do for their work. As a consequence, Notes was considered a failure, not in that it wasn't used, but that people were not using the power of Notes. Instead of taking Notes as a " breakthrough technology, " as the CIO had hoped, people merely used it to support the activities that had already been part of their work. Instead of sharing information, e.g.
Conversion of the enzyme guanylate kinase into a mitotic-spindle orienting protein by a single mutation that inhibits GMP-induced closing

New protein functions can require complex sequence changes, but the minimal path is not well understood. The guanylate kinase enzyme (GKenz), which catalyzes phosphotransfer from ATP to GMP, evolved into the GK domain (GKdom), a protein-binding domain found in membrane associate guanylate kinases that function in mitotic spindle orientation and cell adhesion. Using an induced polarity assay for GKdom function, we show that a single serine to proline mutation is sufficient to switch extant GKenz into a functional GKdom. The mutation blocks catalysis (GKenz function) but allows protein binding and spindle orientation (GKdom function). Furthermore, whereas the GKenz undergoes a large closing motion upon GMP binding, fluorescence quenching and NMR demonstrate that the S → P mutation inhibits GMP-induced GK movements. Disrupting GK closing with a mutation at a different position also leads to GKdom function, suggesting that blocking the GKenz closing motion is sufficient for functional conversion of GKenz to GKdom. Although subtle changes in protein function can require complex sequence paths, our work shows that entirely new functions can arise from single mutations that alter protein dynamics.
Genome Re-Sequencing of Semi-Wild Soybean Reveals a Complex Soja Population Structure and Deep Introgression

Semi-wild soybean is a unique type of soybean that retains both wild and domesticated characteristics, which provides an important intermediate type for understanding the evolution of the subgenus Soja population in the Glycine genus. In this study, a semi-wild soybean line (Maliaodou) and a wild line (Lanxi 1) collected from the lower Yangtze regions were deeply sequenced while nine other semi-wild lines were sequenced to a 3-fold genome coverage. Sequence analysis revealed that (1) no independent phylogenetic branch covering all 10 semi-wild lines was observed in the Soja phylogenetic tree; (2) besides two distinct subpopulations of wild and cultivated soybean in the Soja population structure, all semi-wild lines were mixed with some wild lines into a subpopulation rather than an independent one or an intermediate transition type of soybean domestication; (3) high heterozygous rates (0.19–0.49) were observed in several semi-wild lines; and (4) over 100 putative selective regions were identified by selective sweep analysis, including those related to the development of seed size. Our results suggested a hybridization origin for the semi-wild soybean, which makes a complex Soja population structure.
Synchronization of coupled nonidentical genetic oscillators

The study of the collective dynamics of synchronization among genetic oscillators is essential for the understanding of the rhythmic phenomena of living organisms at both molecular and cellular levels. Genetic oscillators are biochemical networks, which can generally be modelled as nonlinear dynamic systems. We show in this paper that many genetic oscillators can be transformed into Lur'e form by exploiting the special structure of biological systems. By using a control theory approach, we provide a theoretical method for analysing the synchronization of coupled nonidentical genetic oscillators. Sufficient conditions for the synchronization as well as the estimation of the bound of the synchronization error are also obtained. To demonstrate the effectiveness of our theoretical results, a population of genetic oscillators based on the Goodwin model are adopted as numerical examples.
Molecularly Imprinted Quartz Crystal Microbalance Sensor (QCM) for Bilirubin Detection

This study aims the preparation of a QCM sensor for the detection of bilirubin in human plasma. Bilirubin-imprinted poly-(2-hydroxyethyl methacrylate-N-methacryloyl-l-tryptophan methyl ester) (PHEMATrp) nanofilm (MIP) on the gold surface of a QCM chip was synthesized by the molecular imprinting technique. Meanwhile, the non-imprinted PHEMATrp (NIP) nanofilm was synthesized by the same experimental technique to examine the imprinting effect. Characterization of MIP and NIP nanofilms on the QCM chip surface was achieved by atomic force microscopy (AFM), ellipsometry, Fourier transform infrared spectrophotometry-attenuated total reflectance (FTIR-ATR) and contact angle measurements (CA). The observations indicated that the nanofilm was almost in a monolayer. Thereinafter, the imprinted and the non-imprinted QCM chips were connected to the QCM system to investigate kinetic and affinity properties. In order to examine the selectivity of the MIP-PHEMATrp nanofilm, competitive adsorption of bilirubin with cholesterol and estradiol was performed. Limit of detection (LOD) and limit of quantitation (LOQ) values were calculated as 0.45 μg/mL and 0.9 μg/mL, respectively.
Violent Aggression Exposure, Psychoemotional Distress, Aggressive Behavior, and Academic Performance Among Adolescents

Violent Aggression Exposure, Psychoemotional Distress, Aggressive Behavior, and Academic Performance Among Adolescents by Joyce Renee’ Evans MS, Coppin State College, 2000 BS, Coppin State College, 1985 Dissertation Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy
2013 7th International Conference on Pervasive Computing Technologies for Healthcare and Workshops a Research Platform Using Active Local Cooling Directed at Minimizing the Blood Flow in Human Fingers

Patients undergoing chemotherapy for the treatment of cancer often sufl'er from deterioration of extremities, such as neuropathy and onycholysis, a condition which leads to the partial detachment of the nail from the nail bed. To prevent these deterioration, cryotherapy is often used during the application of chemotherapy by means of e.g. frozen gel gloves or socks or ice baths. While effective, current cryotherapy is often unpleasant and unpractical for the patients involved such that the therapy is not accepted by a significant part of the patients involved. Furthermore, the classical cryotherapies leave little room for researching the underlying prevention mechanism through active control of the applied temperatures. A crucial step is to direct applied temperatures at minimizing the blood flow for it is widely assumed that the efficacy of the therapy lies in local vasoconstriction induced by the applied cooling, limiting the blood flow to the fingers. This paper proposes a platform which allows researchers to investigate the effect of controlled cooling on the blood flow in fingers and nail bed on blood circulation at extremities. Preliminary results indicate that local cooling indeed can invoke local vasoconstriction, resulting in a decreased blood flow measured using Laser-Doppler flowmetry.
Light alcohol drinking and cancer: a meta-analysis.

BACKGROUND There is convincing evidence that alcohol consumption increases the risk of cancer of the colorectum, breast, larynx, liver, esophagus, oral cavity and pharynx. Most of the data derive from studies that focused on the effect of moderate/high alcohol intakes, while little is known about light alcohol drinking (up to 1 drink/day). PATIENTS AND METHODS We evaluated the association between light drinking and cancer of the colorectum, breast, larynx, liver, esophagus, oral cavity and pharynx, through a meta-analytic approach. We searched epidemiological studies using PubMed, ISI Web of Science and EMBASE, published before December 2010. RESULTS We included 222 articles comprising ∼92 000 light drinkers and 60 000 non-drinkers with cancer. Light drinking was associated with the risk of oropharyngeal cancer [relative risk, RR = 1.17; 95% confidence interval (CI) 1.06-1.29], esophageal squamous cell carcinoma (SCC) (RR = 1.30; 95% CI 1.09-1.56) and female breast cancer (RR = 1.05; 95% CI 1.02-1.08). We estimated that ∼5000 deaths from oropharyngeal cancer, 24 000 from esophageal SCC and 5000 from breast cancer were attributable to light drinking in 2004 worldwide. No association was found for colorectum, liver and larynx tumors. CONCLUSIONS Light drinking increases the risk of cancer of oral cavity and pharynx, esophagus and female breast.
Decentralized Virtual Internet Deployment using DANSE

DANSE (Dynamic Network Synthesizer) is a system and architecture to deploy virtual networks in a decentralized way using network-specific, platformindependent and reusable deployment strategies. DANSE combines network virtualization with decentralized control to provide a simple and generic control architecture in which sophisticated network control algorithms can be expressed. Further, DANSE provides the basic building blocks necessary to create evolvable IP networks. The latter has applications in the network management domain including automated network (re)configuration without flag days and selforganization.
Degradation of Human α- and β-Defensins by Culture Supernatants of Porphyromonas gingivalis Strain 381

Porphyromonas gingivalis produces proteases capable of degrading cytokines, host heme proteins and some antimicrobial peptides. In this study, we show that P. gingivalis culture supernatants fully or partially degrade human neutrophil peptide α-defensins and human β-defensins after 30 min. This observation suggests that proteases from P. gingivalis degrade defensins and this activity could abrogate defensin-related innate immune functions.
Determination of Mercury in Ayurvedic Dietary Supplements That Are Not Rasa Shastra Using the Hydra-C Direct Mercury Analyzer

Mercury has been determined in Ayurvedic dietary supplements (Trifala, Trifala Guggulu, Turmeric, Mahasudarshan, Yograj, Shatawari, Hingwastika, Shatavari, and Shilajit) by inductively coupled plasma-mass spectrometry (ICP-MS) and direct mercury analysis using the Hydra-C direct mercury analyzer (Teledyne Leeman Labs Hudson, NH, USA). Similar results were obtained from the two methods, but the direct mercury analysis method was much faster and safer and required no microwave digestion (unlike ICP-MS). Levels of mercury ranged from 0.002 to 56 μg/g in samples of dietary supplements. Standard reference materials Ephedra 3240 and tomato leaves that were from the National Institute of Standard and Technology (NIST) and dogfish liver (DOLT3) that was from the Canadian Research Council were analyzed using Hydra-C method. Average mercury recoveries were 102% (RSD% 0.0018), 100% (RSD% 0.0009), and 101% (RSD% 0.0729), respectively. Hydra-C method Limit Of Quantitation was 0.5 ng.
Coffee Intake Is Associated with a Lower Liver Stiffness in Patients with Non-Alcoholic Fatty Liver Disease, Hepatitis C, and Hepatitis B

There is emerging evidence for the positive effects or benefits of coffee in patients with liver disease. We conducted a retrospective cross-sectional study on patients with non-alcoholic fatty liver disease (NAFLD), hepatitis C virus (HCV), and hepatitis B virus (HBV) infection to determine the effects of coffee intake on a non-invasive marker of liver fibrosis: liver stiffness assessed by transient elastography (TE). We assessed coffee and tea intake and measured TE in 1018 patients with NAFLD, HCV, and HBV (155 with NAFLD, 378 with HCV and 485 with HBV). Univariate and multivariate regression models were performed taking into account potential confounders. Liver stiffness was higher in males compared to females (p < 0.05). Patients with HBV had lower liver stiffness than those with HCV and NAFLD. After adjustment for age, gender, smoking, alcohol consumption, M or XL probe, and disease state (NAFLD, HCV, and HBV status), those who drank 2 or more cups of coffee per day had a lower liver stiffness (p = 0.044). Tea consumption had no effect (p = 0.9). Coffee consumption decreases liver stiffness, which may indicate less fibrosis and inflammation, independent of disease state. This study adds further evidence to the notion of coffee maybe beneficial in patients with liver disease.
Importance of medical herbs in animal feeding: A review

Herbs have been used by all cultures for centuries; each area of the world uses herbs local to that area. Western herbs tend to work slowly to restore health and balance to the body, while Chinese herbology contains some fast acting herbs. Oriental herbs can be divided into two categories, food and medical. Herbal medicines have always been a form of therapy for livestock among resource poor smallholder farmers. This article is a review of present literature data on the usage of medical herbs properties (including improve digestibility, antimicrobial, antiinflammatory, anti-oxidant and immunostimulant) in animal's nutrition.
Multiscale Air Quality Simulation Platform (MAQSIP): Initial applications and performance for tropospheric ozone and particulate matter

[1] The performance of the Multiscale Air Quality Simulation Platform (MAQSIP) in simulating the regional distributions of tropospheric ozone and particulate matter (PM) is evaluated through comparisons of model results from three-dimensional simulations against available surface and aircraft measurements. These applications indicate that the model captures the dynamic range of observations and the spatial trends represented in measurements. Some discrepancies also exist, however, and they are discussed in the context of model formulation, input data specification and assumptions, and variability and bias in measurements. The daily normalized bias (within ±20%) and normalized gross errors (<25%) for predicted surface level O3 over an entire summer season are within the suggested performance criteria for management evaluation studies and are comparable to, if not smaller than, those reported previously for other regional O3 models. Comparisons of modeled PM composition with speciated fine particle concentration measurements show that the model is able to capture the spatial variability in fine PM mass as well as in the inorganic component fractions. Both measurements and model results show that in the summertime in the eastern U.S., SO42− is a relatively large component of fine PM mass; in contrast, NO3− is a significant fraction in the western U.S. in the wintertime case studied. The ability of the model to simulate the observed visibility indices (extinction coefficient and deciview) are evaluated through comparisons of model estimates using both a detailed Mie theory-based calculation (based on predicted aerosol size and number distributions) and an empirical mass reconstruction algorithm. Both modeled and observed data show that among the various aerosol components, in the eastern U.S. SO42− contributes the largest fraction to the aerosol extinction (35–85%), while organic mass contributes up to 20–25%. In contrast, in the western U.S., SO42− and NO3− have comparable contributions (20–50%) to the observed aerosol extinction. Comparisons with limited observational aircraft data, however, show moderate to poor correlation with measurements in the free troposphere. While these discrepancies can be attributed in part to model initialization and lateral boundary conditions specification, there is a need for further evaluation of the representation of boundary layer-free troposphere exchange mechanisms as well as the chemical mechanisms currently used in the model for representing chemistry in the free troposphere.
Client Buffering Considerations for Video Streaming

An important issue in the performance of Video Streaming systems is the data transmission mechanism used by the server. Streaming servers can use a variety of techniques, which have an impact on a number of metrics associated with the performance and the quality of the video presentation. One of the related issues is the assignment of buffer space at the client in order to hold data that has arrived earlier than their playback time. In this article, we conduct a number of experiments with MPEG-4 compressed video, in order to obtain buffering occupancy values for various transmission mechanisms. In particular, we consider some of the mechanisms used by YouTube video servers, and contrast their performance with that of other mechanisms.
Obstacles Detection on a Road by Dense Stereovision with 1D Correlation Windows and Fuzzy Filtering

In this paper, we propose an original approach to obstacles detection based on stereovision with mono-dimensional correlation windows. The result of the algorithm is a dense disparity map associated with a confidence map. For each pixel, correlation indices are computed for several widths of windows and several positions of the window centre. Three criteria, extracted from each correlation curve, are combined by a fuzzy filter to define a confidence measure. Our 1D method is compared to a classical 2D method and shows better results in term of errors and density rate. In the context of obstacle detection, we show that a basic segmentation of our disparity map yields a better detection and marking of the obstacles. The method is validated on synthetic image sequences and our results are compared with those obtained using a classical 2D method
A Chinese fuzzy autocompletion approach

Autocompeltion is a feature for predicting a word or phrase that the user wants to type in without actually typing it completely. Fuzzy autocompletion technologies have been presented recently to deal with the typing error. However, they do not perform well in Chinese circumstance. In the paper, it extends autocompletion by (1) supporting Chinese character fuzzy match (2) considering phonetic similarity and shape similarity of Chinese characters(3) allowing infix match as well as prefix match. When typing a Chinese character string, minor mistakes are tolerated and expected autocompletion strings are presented to user. Our empirical evaltuation demonstrates that our autocompletion algorithm has high-real-time performance to meet the demand of user interaction. We have developed a autocompletion framework using this algorithm and has been used in a Traditional Chinese medicine (TCM) application.
Efficient Motion Deblurring for Information Recognition on Mobile Devices

In this paper, a new method for the identification and removal of image artefacts caused by linear motion blur is presented. By transforming the image into the frequency domain and computing its logarithmic power spectrum, the algorithm identifies the parameters describing the camera motion that caused the blur. The spectrum is analysed using an adjusted version of the Radon transform and a straightforward method for detecting local minima. Out of the computed parameters, a blur kernel is formed, which is used to deconvolute the image. As a result, the algorithm is able to make previously unrecognisable features clearly legible again. The method is designed to work in resource-constrained environments, such as on mobile devices, where it can serve as a preprocessing stage for information recognition software that uses the camera as an additional
Design of Complex Engineered Systems Using Multi-Agent Coordination

interactions lead to global behavior. The results of this paper demonstrate that a team of autonomous agents using a cooperative coevolutionary algorithm (CCEA) can effectively design a complex engineered system. This paper uses a system model of a Formula SAE racing vehicle to illustrate and simulate the methods and potential results. By designing complex systems with a multi-agent coordination approach, a design methodology can be developed to reduce design uncertainty and provide mechanisms through which the system level impact of decisions can be estimated without explicitly modeling such interactions. [DOI: 10.1115/1.4038158]
Globalisation and the Euro Area: Simulation Based Analysis Using the New Area Wide Model

In this paper, we utilise the multi-country version of the NAWM to analyse the impact of globalisation on euro area macroeconomic aggregates. We provide alternative model-based definitions of globalisation associated with an increase in potential output in emerging Asia and its impact on total factor productivity in the euro area, and a shift in international specialisation patterns leading to changes in relative demand and import substitutions. The results indicate that globalisation has a positive impact on output, consumption, investment and real labour income in the long-run. This impact is driven by the improvement in the terms of trade and associated positive wealth effects, as well as by spillovers of higher potential output in emerging Asia on euro area total factor productivity. Additionally, we provide evidence that structural reforms in goods and labour markets would amplify the benefits associated with globalisation. JEL Classification: E32, E62