Miracle-dz/UniFAR-FTUs huggingface dataset:
Different roles for CD4+ and CD8+ T lymphocytes and macrophage subsets in the control of a generalized virus infection

The importance of T-lymphocyte subsets in the control of poxvirus infections is controversial. To determine the relative contribution of lymphocyte subsets important for recovery from infection with ectromelia virus (EV), a natural murine poxvirus pathogen, C57BL/6 (B6) mice lacking functional CD8+ T cells because of disruption of the beta2-microglobulin gene or lacking functional CD4+ T cells because of disruption of the I-(A)beta gene, acutely depleted of CD8+ or CD4+ T cells with monoclonal antibody, or depleted of macrophage subsets by the macrophage suicide technique were used. Recovery from infection was strictly dependent on the effector functions of CD8+ T cells, in the absence of which 100% mortality resulted. This lymphocyte population had demonstrable antiviral activity early in the infection process even before class I major histocompatibility complex (MHC)-restricted CD8+ cytotoxic T-lymphocyte (CTL) activity was detectable. CD4+ T cells were found to be necessary for the generation of an optimal virus-specific, class I MHC-restricted CD8+ CTL response and contributed to virus clearance not involving cytolytic mechanisms. In both models of CD4+ T-cell deficiency, virus clearance was incomplete and persisted at low levels in most organs and at very high levels in the skin, but the animals did not die. The elimination of macrophage subpopulations impeded virus clearance, impaired the generation of class I MHC-restricted antiviral CTL response, and resulted in 100% mortality. These findings establish an absolute requirement for CD8+ and CD4+ T lymphocytes and macrophage subsets in the elimination of a natural murine poxvirus infection and support the idea that macrophages may be essential accessory cells for the generation of class I MHC-restricted antiviral CTL responses.
Bacteriological and Molecular Analysis of Rifampin-Resistant Mycobacterium tuberculosis Strains Isolated in Australia

ABSTRACT To develop a better understanding of the epidemiology and molecular biology of rifampin-resistant Mycobacterium tuberculosisstrains in Australia, 50 clinical isolates (33 rifampin-resistant and 17 rifampin-sensitive strains) cultured between 1990 and 1997 were analyzed by a number of bacteriological and molecular techniques. Examination of the drug resistance profiles of the 33 rifampin-resistant isolates revealed that 91% were resistant to rifampin in combination with resistance to isoniazid, 88% were resistant to rifampin on first isolation, and 81% showed cross-resistance with rifabutin. On the basis of the demographic data provided for the patients infected with the rifampin-resistant strains, 90% of the patients were born overseas. Of these patients, 64% developed clinical symptoms within 5 years of residence in Australia. On a molecular level, analysis of the rpoB gene revealed that 97% of the rifampin-resistant isolates had missense mutations within a conserved region of the gene, and eight types of missense mutations were detected. Of the 31 rifampin-resistant isolates that were typed by restriction fragment length polymorphism (RFLP) analysis, 28 distinct patterns were obtained by RFLP analysis with IS6110, and three clusters of genetically related isolates were identified. All isolates within the clusters were from patients who were born overseas and who had the same country of origin. The results from this study provide an overview of the current situation of rifampin resistance in Australia and can serve as a basis for continued monitoring of drug-resistant M. tuberculosis strains isolated within the country.
A comparison of the reproducibility of the parameters of the 13C-aminopyrine breath test for the assessment of hepatic function

This study determined the within-subject and between-subject variability of different ways of expressing the results of the 13C-aminopyrine breath test (13C-ABT) and the effect of shortening the test duration. The 13C-ABT was conducted on three separate occasions in 10 healthy volunteers and on a single occasion in 22 patients with established liver cirrhosis. The within-subject variability of cumulative percentage dose recovered (cPDR), using measured CO2 production rate (VCO2), in the reference group over three trials was 15% over 120 min. Higher within-subject variability in cPDR would have been evident if the test was terminated at either 30 or 60 min. Substitution of predicted VCO2 to calculate cPDR yielded comparable values at all time points. Significant differences between cirrhotics and reference group were evident after just 10 min using PDR/h, cPDR or enrichment (all P<0.05). The ABT demonstrates clinically acceptable reproducibility. Shortening of the duration may make the test more acceptable clinically, but it is associated with increasing imprecision.
An RFID-Enabled Wireless Sensor Network (WSN) Monitoring System for Biological and Pharmaceutical Products

Biological and pharmaceutical (B&P) products are essential and important for human being. In current era, the demand and requirement of these products are dramatically growing, product quality and integrity then become the most concerning part. As a key factor for ensuring the quality and integrity, the current product status monitoring system needs to be enhanced in a more sophisticated and comprehensive way. This research aims to design a Radio Frequency Identification (RFID) enabled Wireless Sensor Network (WSN) monitoring system for B&P products supply chain management. In this study, the basic design factors of a WSN are reviewed. It is found that battery capacity causes a bottle neck in the WSN. Therefore, system architecture is presented based on the proposed framework. The framework aims to develop a common approach to improve the energy efficiency of the WSN. It consists of three processes, the first one is to generate a WSN with full coverage, the second one is to determine the optimal position of the sink, and the last process is to add additional relay nodes for recharging or replacing the battery-exhausted nodes without affecting the network operation. Finally, a simulated case about B&P product storage in a hospital is conducted to show the overall procedures of the framework.
Ontogenetic Diet Shifts and Digestive Constraints in the Omnivorous Freshwater Turtle Trachemys scripta

Many reptiles undergo an ontogenetic diet shift from carnivory to herbivory. In this study, we used the yellow‐bellied slider turtle, Trachemys scripta, as a model to evaluate whether juvenile turtles are carnivorous because physiological constraints preclude herbivory. We conducted feeding trials in which we fed juvenile and adult turtles a duckweed plant, Lemna valdiviana, or a freshwater grass shrimp, Palaemontes paludosus, for 5 wk. During the trials, we measured mass‐specific intake, digestibility, and digestible intake for both size classes, as well as juvenile growth. At the end of the trials, we measured the nutrient composition of the juvenile turtles. Juveniles fed shrimp grew 3.2 times faster than those fed duckweed and had equivalent lipid stores. Digestive processing in juveniles was extremely efficient on the shrimp diet, with higher mass‐specific intakes than adults and very high digestibilities (97%). Juveniles digested duckweed as well as adults did; however, their intake of this diet was limited, possibly by the time required for fermentation. We concluded that although juveniles can process plant material, an animal diet allows for greater juvenile growth, which in turtles is linked to higher survivorship and increased future reproductive success.
Quantitative Analysis of Calcium Spikes in Noisy Fluorescent Background

Intracellular calcium signals are studied by laser-scanning confocal fluorescence microscopy. The required spatio-temporal resolution makes description of calcium signals difficult because of the low signal-to-noise ratio. We designed a new procedure of calcium spike analysis based on their fitting with a model. The accuracy and precision of calcium spike description were tested on synthetic datasets generated either with randomly varied spike parameters and Gaussian noise of constant amplitude, or with constant spike parameters and Gaussian noise of various amplitudes. Statistical analysis was used to evaluate the performance of spike fitting algorithms. The procedure was optimized for reliable estimation of calcium spike parameters and for dismissal of false events. A new algorithm was introduced that corrects the acquisition time of pixels in line-scan images that is in error due to sequential acquisition of individual pixels along the space coordinate. New software was developed in Matlab and provided for general use. It allows interactive dissection of temporal profiles of calcium spikes from x-t images, their fitting with predefined function(s) and acceptance of results on statistical grounds, thus allowing efficient analysis and reliable description of calcium signaling in cardiac myocytes down to the in situ function of ryanodine receptors.
Biochemical Characterization of the Human RAD51 Protein

Adenosine nucleotides affect the ability of RecA·single-stranded DNA (ssDNA) nucleoprotein filaments to cooperatively assume and maintain an extended structure that facilitates DNA pairing during recombination. Here we have determined that ADP and ATP/ATPγS affect the DNA binding and aggregation properties of the human RecA homolog human RAD51 protein (hRAD51). These studies have revealed significant differences between hRAD51 and RecA. In the presence of ATPγS, RecA forms a stable complex with ssDNA, while the hRAD51 ssDNA complex is destabilized. Conversely, in the presence of ADP and ATP, the RecA ssDNA complex is unstable, while the hRAD51 ssDNA complex is stabilized. We identified two hRAD51·ssDNA binding forms by gel shift analysis, which were distinct from a well defined RecA·ssDNA binding form. The available evidence suggests that a low molecular weight hRAD51·ssDNA binding form (hRAD51·ssDNAlow) correlates with active ADP and ATP processing. A high molecular weight hRAD51·ssDNA aggregate (hRAD51·ssDNAhigh) appears to correlate with a form that fails to process ADP and ATP. Our data are consistent with the notion that hRAD51 is unable to appropriately coordinate ssDNA binding with adenosine nucleotide processing. These observations suggest that other factors may assist hRAD51 in order to mirror RecA recombinational function.
Multi-dimensional sequential web mining by utilizing fuzzy interferencing

There are several applications of sequential web mining, which is used to find the frequent subsequences in a web log in the World Wide Web (the web). We implemented a tool to analyze the sequential behavior of web log access patterns in multiple-dimensions. Sequences of frequent access patterns may change temporally and spatially. Based on the specified criteria like year, month, day, hours and location, the end-user is able to tune the minimum support threshold parameter intuitively using the fuzzy inference mechanism. Domain experts are can access several criteria, including minimum support threshold and number of accesses according to the user intuition, which is later, transformed into fuzzy inference parameters. We propose two different types of rule bases by considering the (support-minimum support, minimum support) and (support, minimum support), i.e., interval and case-based. To test our proposal, we used the web log dataset of the Department of Computer at the University of Calgary to analyze sequential access patterns of students during February and March carried out in the campus by taking the midterm dates into account. The results reported in this paper are promising; they demonstrate the applicability and effectiveness of the proposed approach.
Endoscopic management and long-term follow-up of Dieulafoy's lesions in the upper GI tract.

BACKGROUND The aim of this study was to retrospectively evaluate the short-and long-term effectiveness of different methods of endoscopic treatment for bleeding Dieulafoy's lesions. METHODS Patients were allocated into 2 groups according to the hemostatic method applied: (1) injection group (epinephrine and/or ethanolamine oleate), and (2) thermal coagulation group (heat probe), either alone or combined with epinephrine injection. The combination of epinephrine and ethanolamine oleate was used in 5 patients, epinephrine alone in 3, ethanolamine oleate alone in one, heat probe and epinephrine in 8, and heat probe alone in 1 patient. RESULTS Dieulafoy's lesions were found in 18 (1%) of 1750 patients with acute nonvariceal upper GI bleeding. Comorbid conditions were present in 5 (28%) patients. Initial hemostasis was achieved endoscopically in 13 patients (72%) and permanent hemostasis in 17 patients (94%). Bleeding recurred in 5 patients (2 with concomitant disease) in the injection group; 3 were successfully retreated by heat probe coagulation and epinephrine injection, 1 with hemoclip application and 1 by surgery. There was no recurrent bleeding in thermal treatment group. Thermal treatment was significantly superior to injection (p = 0.0029). CONCLUSIONS Endoscopic thermal coagulation with or without epinephrine injection should be the initial treatment of choice for Dieulafoy's lesions. Mortality is lowest in patients with no significant comorbidity and an unremarkable medical history.
Compact non‐contact total emission detection for in vivo multiphoton excitation microscopy

We describe a compact, non‐contact design for a total emission detection (c‐TED) system for intra‐vital multiphoton imaging. To conform to a standard upright two‐photon microscope design, this system uses a parabolic mirror surrounding a standard microscope objective in concert with an optical path that does not interfere with normal microscope operation. The non‐contact design of this device allows for maximal light collection without disrupting the physiology of the specimen being examined. Tests were conducted on exposed tissues in live animals to examine the emission collection enhancement of the c‐TED device compared to heavily optimized objective‐based emission collection. The best light collection enhancement was seen from murine fat (5×–2× gains as a function of depth), whereas murine skeletal muscle and rat kidney showed gains of over two and just under twofold near the surface, respectively. Gains decreased with imaging depth (particularly in the kidney). Zebrafish imaging on a reflective substrate showed close to a twofold gain throughout the entire volume of an intact embryo (approximately 150 μm deep). Direct measurement of bleaching rates confirmed that the lower laser powers, enabled by greater light collection efficiency, yielded reduced photobleaching in vivo. The potential benefits of increased light collection in terms of speed of imaging and reduced photo‐damage, as well as the applicability of this device to other multiphoton imaging methods is discussed.
Cooperation between Ha‐ras and fos or transforming growth factor α overcomes a paradoxic tumor‐inhibitory effect of p53 loss in transgenic mouse epidermis

To investigate the role of loss of the p53 tumor suppressor gene in skin carcinogenesis, p53 knockout (p53−/−) mice were mated with transgenic mice coexpressing v‐Ha‐ras, v‐fos, or human transforming growth factor α (TGFα) exclusively in the epidermis by using human keratin 1 (HK1)–based vectors (HK1.ras/fos, HK1.ras/α, and HK1.fos/α). HK1.ras/fos and HK1.ras/α mice displayed epidermal hyperplasia and autonomous benign papillomas to an identical degree between p53+/+ and p53+/− genotypes. However, HK1.ras/fos mice with the p53−/− genotype were born with papillomatous skin and died soon after birth. HK1.ras/α‐p53−/− mice also exhibited an increased epidermal hyperplasia, and, similar to HK1.ras/α mice with p53+/+ and p53+/− genotypes, these mice rapidly developed spontaneous and 12‐O‐tetradecanoylphorbol‐13‐acetate (TPA)‐induced papillomas. These results are in contrast to our previous observation that, HK1.ras, HK1.fos, and HK1. TGFα transgenic mice with the p53−/− genotype display an unexpected delay in both spontaneous and TPA‐promoted papilloma formation compared with mice with p53+/+ and p53+/− genotypes. Taken collectively, our mating experiments between HK1 oncogenic transgenic mice and p53 knockout mice may identify a backup system that effectively compensates for p53 loss. Activation of multiple oncogenes not only partly overcomes such compensation but also synergizes with p53 loss. However, HK1.fos/α‐p53−/− mice failed to exhibit either an increased newborn epidermal hyperplasia or an accelerated spontaneous or TPA‐induced papillomas, suggesting that certain combinations of oncogenes, such as with activated Ha‐ras, are required for this process. Because neither spontaneous nor TPA‐elicited papillomas in p53−/− mice progressed to malignancy, additional genetic insults appear to be required for malignant progression. Mol. Carcinog. 29:67–75, 2000. © 2000 Wiley‐Liss, Inc.
Comparative effectiveness of fecal immunochemical test outreach, colonoscopy outreach, and usual care for boosting colorectal cancer screening among the underserved: a randomized clinical trial.

IMPORTANCE Colorectal cancer (CRC) screening saves lives, but participation rates are low among underserved populations. Knowledge on effective approaches for screening the underserved, including best test type to offer, is limited. OBJECTIVE To determine (1) if organized mailed outreach boosts CRC screening compared with usual care and (2) if FIT is superior to colonoscopy outreach for CRC screening participation in an underserved population. DESIGN, SETTING, AND PARTICIPANTS We identified uninsured patients, not up to date with CRC screening, age 54 to 64 years, served by the John Peter Smith Health Network, Fort Worth and Tarrant County, Texas, a safety net health system. INTERVENTIONS Patients were assigned randomly to 1 of 3 groups. One group was assigned to fecal immunochemical test (FIT) outreach, consisting of mailed invitation to use and return an enclosed no-cost FIT (n = 1593). A second was assigned to colonoscopy outreach, consisting of mailed invitation to schedule a no-cost colonoscopy (n = 479). The third group was assigned to usual care, consisting of opportunistic primary care visit–based screening (n = 3898). In addition, FIT and colonoscopy outreach groups received telephone follow-up to promote test completion. MAIN OUTCOME MEASURES Screening participation in any CRC test within 1 year after randomization. RESULTS Mean patient age was 59 years; 64% of patients were women. The sample was 41% white, 24% black, 29% Hispanic, and 7% other race/ethnicity. Screening participation was significantly higher for both FIT (40.7%) and colonoscopy outreach (24.6%) than for usual care (12.1%) (P < .001 for both comparisons with usual care). Screening was significantly higher for FIT than for colonoscopy outreach (P < .001). In stratified analyses, screening was higher for FIT and colonoscopy outreach than for usual care, and higher for FIT than for colonoscopy outreach among whites, blacks, and Hispanics (P < .005 for all comparisons). Rates of CRC identification and advanced adenoma detection were 0.4% and 0.8% for FIT outreach, 0.4% and 1.3% for colonoscopy outreach, and 0.2% and 0.4% for usual care, respectively (P < .05 for colonoscopy vs usual care advanced adenoma comparison; P > .05 for all other comparisons). Eleven of 60 patients with abnormal FIT results did not complete colonoscopy. CONCLUSIONS AND REVELANCE: Among underserved patients whose CRC screening was not up to date, mailed outreach invitations resulted in markedly higher CRC screening compared with usual care. Outreach was more effective with FIT than with colonoscopy invitation. TRIAL REGISTRATION clinicaltrials.gov Identifier: NCT01191411.
Behavioral Pure-Tone Threshold Shifts Caused by Tympanic Membrane Electrodes

Objective: To determine whether tympanic membrane (TM) electrodes induce behavioral pure-tone threshold shifts. Design: Pure-tone thresholds (250 to 8000 Hz) were measured twice in test (n = 18) and control (n = 10) groups. TM electrodes were placed between first and second threshold measurements in the test group, whereas the control group did not receive electrodes. Pure-tone threshold shifts were compared between groups. The effect of TM electrode contact location on threshold shifts was evaluated in the test group. Results: TM electrodes significantly increased average low-frequency thresholds, 7.5 dB at 250 Hz and 4.2 dB at 500 Hz, and shifts were as large as 25 dB in individual ears. Also, threshold shifts did not appear to vary at any frequency with TM electrode contact location. Conclusions: Low-frequency threshold shifts occur when using TM electrodes and insert earphones. These findings are relevant to interpreting electrocochleographic responses to low-frequency stimuli.
A Traceable Outsourcing CP-ABE Scheme with Attribute Revocation

Ciphertext-Policy Attribute-based Encryption (CP-ABE) is a useful cryptographic scheme and is being considered for cloud application as more and more users leverage cloud platforms to store and process their data. However, existing CP-ABE schemes still have a number of limitations that make it not effective to be used in a practical application. Firstly, the size of the ciphertext and the time for decryption grow with the complexity of the access formula. This efficiency issue becomes a problem when using a cloudplatform and mobile devices with limited processing capacity. Secondly, in reality, the attributes of users may be changed from time to time, or some users may eventually leave the system due to resignation. This practical concern requires a scheme with flexible and fine-grained revocation optionsupporting attribute-level changes. Lastly, traceability is also an important feature to track potential traitors who leak the partial decryption keys if ABE is used in a real scenario. None of the existing CP-ABE schemes are able to satisfy these three properties simultaneously. In this paper, we propose apractical CP-ABE that can achieve all three requirements. Our system adopts techniques on secure outsourcing of pairings to support efficient outsourcing computation and makes use of a subset cover algorithm to meet the requirements of revocation and traceability. Our scheme is proved to be a selectively replayable chosen-ciphertext attack (RCCA) secure in random oracle model. The result of our work could provide a feasible, reliable and practical CP-ABE scheme for the realistic application.
Biochemical and immunological studies on clathrin light chains and their binding sites on clathrin triskelions.

Clathrin light chains from bovine brain tissue (LC alpha and LC beta) are monomeric proteins with an average mol. wt. of approximately 33,000, as determined by sedimentation equilibrium. Solution studies on purified light chains indicate a large Stokes radius (Re = 3.3 nm) and little defined secondary structure. Both light chains bind specifically and with high affinity (KA approximately 5 x 10(7)/M) to overlapping sites on clathrin heavy chains. These binding sites are contained within a 125,000 dalton heavy chain fragment that forms truncated triskelions with legs, 15 nm shorter than those of intact triskelions. As judged by immuno‐electron microscopy, light chain‐specific IgG molecules bind mostly to the center of triskelions, but there are also sites that are scattered some 16 nm along the proximal part of triskelion legs. From heterologous binding experiments using human placenta light chains and heavy chain fragments from bovine brain clathrin, it is concluded that the domains of light and heavy chains that are involved in the interaction are conserved across tissue and species boundaries.