Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of the Early Steps of Hepatitis C Virus Infection by Using Luciferase Reporter Viruses

ABSTRACT The lack of an efficient system to produce hepatitis C virus (HCV) particles has impeded the analysis of the HCV life cycle. Recently, we along with others demonstrated that transfection of Huh7 hepatoma cells with a novel HCV isolate (JFH1) yields infectious viruses. To facilitate studies of HCV replication, we generated JFH1-based bicistronic luciferase reporter virus genomes. We found that RNA replication of the reporter construct was only slightly attenuated and that virus titers produced were only three- to fivefold lower compared to the parental virus, making these reporter viruses an ideal tool for quantitative analyses of HCV infections. To expand the scope of the system, we created two chimeric JFH1 luciferase reporter viruses with structural proteins from the Con1 (genotype 1b) and J6CF (genotype 2a) strains. Using these and the authentic JFH1 reporter viruses, we analyzed the early steps of the HCV life cycle. Our data show that the mode of virus entry is conserved between these isolates and involves CD81 as a key receptor for pH-dependent virus entry. Competition studies and time course experiments suggest that interactions of HCV with cell surface-resident glycosaminoglycans aid in efficient infection of Huh7 cells and that CD81 acts during a postattachment step. The reporter viruses described here should be instrumental for investigating the viral life cycle and for the development of HCV inhibitors.
Harmonic power flow determination using the fast fourier transform

Multichannel data acquisition systems and commercially available digital signal processing software packages make the determination of harmonic power flow possible provided the limitations of the analysis techniques are understood. The authors describe how data from a typical acquisition system can be processed using the fast Fourier transform and discuss possible errors (e.g. those due to leakage) and how to avoid them using techniques such as skewing correction and windowing. Guidelines on the practical application of the transform in analyzing measured data are presented. The analysis method has been used successfully to analyze data obtained at a traction (railway supply) substation which had a sixth-harmonic resonance caused by the interaction of a harmonic filter and the only supply system. >
Chip-level design and optimization for digital microfluidic biochips

Recently, digital microfluidic biochips (DMFBs) have revolutionized many biochemical laboratory procedures and received much attention due to their advantages such as high throughput, automatic control, and low cost. To meet the challenges of increasing design complexity, computer-aided-design (CAD) tools have been involved to build DMFBs efficiently, where a two-stage design flow of fluidic-level synthesis followed by chip-level design are generally applied. Regarding fluidic-level synthesis, many related studies and CAD tools have been well-developed to synthesize the fluidic behaviors efficiently and effectively. However, research findings being highly-concerned with the chip-level design are still critically lacking. In this paper, we shall focus on chiplevel design and discuss related background and two major optimization problems posed by electrode addressing and control pin routing. We show how CAD tools are involved to automate and optimize the two design problems. With this assistance, users can concentrate on the development and abstraction of nanoscale bioassays while leaving chip optimization and implementation details to CAD tools.
Adenoid cystic carcinoma of head and neck: A single institutional analysis of 66 patients treated with multi-modality approach

Abstract Background: Adenoid cystic carcinoma (ACC) accounts for 1% of all head and neck (HN) cancers. Materials and Methods: Demographic, clinical, treatment, and survival details of 66 patients were collected (1995-2011) and analyzed. Disease-free survival (DFS) was estimated by Kaplan-Meier method. Results: Primary disease sites were sinonasal (n = 27), salivary gland (n = 30), and others (n = 9). Median follow-up was 23 months (range: 12-211 months). Estimated DFS at 2- and 5-year were 75% and 67.2%, respectively. On univariate analysis, intra-cranial extension (ICE) (hazard ratio [HR]: 3.59, P = 0.0071), lymph node involvement (HR: 4.05, P = 0.0065), treatment modality (others vs. surgery plus adjuvant radiotherapy, HR: 2.39, P = 0.0286) and T stage (T3/4 vs. T1/2, HR: 3.27, P = 0.007) had significant impact on DFS. Lymph node involvement (P = 0.038) and ICE (P = 0.038) continued to have significant impact on DFS on multivariate analysis. Conclusion: Surgery followed by adjuvant radiotherapy remains the treatment of choice for HN ACC. Lymph node involvement and ICE confer poor prognosis.
Diversity of proteobacterial endosymbionts in hemlock woolly adelgid (Adelges tsugae) (Hemiptera: Adelgidae) from its native and introduced range.

Knowledge of intraspecific variation in symbioses may aid in understanding the ecology of widespread insects in different parts of their range. We investigated bacterial symbionts of Adelges tsugae, a pest of hemlocks in eastern North America introduced from Asia. Amplification, cloning, and sequencing of bacterial 16S rDNA, in situ hybridizations, and electron microscopy revealed that A. tsugae harbours up to five bacterial phylotypes, according to population. Three Gammaproteobacteria species are maternally transmitted. The first, designated 'Ca. Pseudomonas adelgestsugas' resides in the haemocoel, and was detected in all populations except Taiwan. The second phylotype, 'Ca. Serratia symbiotica', resides in bacteriocytes of populations on Tsuga sieboldii in Japan and in E. North America. The third phylotype, designated 'Ca. Annandia adelgestsuga', clustered within a lineage of several insect endosymbionts that included Buchnera aphidicola. It was detected in bacteriocytes in all populations, and in salivary glands of first instars. Two Betaproteobacteria phylotypes were detected in some Japanese T. sieboldii and eastern North America populations, and were observed only in salivary glands with no evidence of maternal transmission. Our results support the ideas that symbiont gain and loss has been volatile in adelgids, and that symbionts may help to trace the source of invasive species.
Multiplex LightCycler PCR Assay for Detection and Differentiation of Bordetella pertussis and Bordetella parapertussis in Nasopharyngeal Specimens

ABSTRACT A rapid real-time multiplex PCR assay for detecting and differentiating Bordetella pertussis and Bordetella parapertussis in nasopharyngeal swabs was developed. This assay (LC-PCR-IS) targets the insertion sequences IS481 and IS1001 of B. pertussis and B. parapertussis, respectively, and is performed using the LightCycler (Roche Molecular Biochemicals, Indianapolis, Ind.). The analytical sensitivity is less than one organism per reaction. Results for Bordetella culture and/or direct fluorescent antibody testing and a second LightCycler PCR assay (target, pertussis toxin gene) were compared to results of the LC-PCR-IS assay for 111 nasopharyngeal swabs submitted for pertussis testing. Of the specimens, 12 were positive (9 B. pertussis and 3 B. parapertussis) and 68 specimens were negative by all methods. Three other specimens were positive for B. pertussis by at least two of the methods (including the LC-PCR-IS assay), and another 28 specimens were positive for B. pertussis by the LC-PCR-IS assay only. No specimens were negative by the LC-PCR-IS assay and positive by the other methods. A conventional PCR method (target, IS481) was also compared to the LC-PCR-IS assay for a different group of nasopharyngeal swab specimens (n = 96): 44 specimens were positive and 41 specimens were negative for B. pertussis with both PCR methods. Nine specimens were positive for B. pertussis by the LC-PCR-IS assay and negative by the conventional PCR assay, and two specimens were positive for B. pertussis by the conventional PCR assay and negative by the LC-PCR-IS assay. Positivity of the two assays was not significantly different (P = 0.0654). The insertion sequence IS481 is also present in Bordetella holmesii; specimens containing B. holmesii may yield false-positive results. The LC-PCR-IS assay takes approximately 45 min to complete post-nucleic acid extraction, compared to 24 h for the conventional PCR assay previously used in our laboratory. The LC-PCR-IS assay is easier to perform than the conventional PCR assay, and the closed system decreases the chance of contamination. All of these characteristics represent a significant improvement in the detection of B. pertussis and B. parapertussis in nasopharyngeal specimens.
Noncompliance with tuberculosis treatment by patients at a tuberculosis and AIDS reference hospital in midwestern Brazil.

INTRODUCTION In developing countries, there is little information about the risk factors that predict noncompliance with tuberculosis (TB) treatment in hospitals. OBJECTIVE This study analyzes possible factors associated with noncompliance with TB treatment among patients treated at HAA. DESIGN A retrospective cohort study was made including all patients who initiated TB treatment at HAA, from January to December 1998. A standard form was used to review medical records and to collect data on each patient. This data was evaluated in comparison with data from the state TB control program. RESULTS Of the 341 patients included in the study, 186 (61.2%) were considered cured and 67 (22%) were non-compliant. The factors associated with noncompliance were: previous anti-TB treatment (RR = 1.95, 95% CI 1.29 to 2.93), prescription of drugs other than the standard first-line regimen proposed by the Brazilian Health Ministry (Rifampin + Isoniazide + Pyrazinamide) (RR = 0.54, 95% CI 0.35 to 0.83), the need for hospitalization (RR = 2.19, 95% CI 1.46 to 3.29) and non-inclusion in the hospital s TB Control Program for treatment follow up (RR = 0.54, 95% CI 0.35 to 0.82). SETTING Anuar Auad Hospital (HAA) Goiânia, Goiás, Brazil. CONCLUSION Our results indicate the importance of establishing Tuberculosis Control Programs in hospitals, while paying special attention to patients with risk factors for noncompliance with TB treatment.
Training Induces Scapular Dyskinesis in Pain-Free Competitive Swimmers: A Reliability and Observational Study

Objective:Scapular dyskinesis is a major etiological factor in overhead athletes' shoulder problems. Our hypotheses were to evaluate if (1) visual observation of scapular dyskinesis during scaption has substantial interobserver reliability, and (2) scapular dyskinesis may be induced by swim training in pain-free swimmers. Design:A reliability and observational study. Setting:Bachelor project at a college institution and at a private sports orthopedic hospital. Participants:Seventy-eight competitive swimmers with no history of shoulder pain were included in the study. Fourteen swimmers were evaluated regarding reliability. Inclusion criteria were competitive swimmers with high training volume who previously had no shoulder pain. Interventions:Observations of scapular dyskinesis (yes/no) during simple scaption. The interobserver reliability of scaption and wall push-up was evaluated in 14 swimmers using kappa analysis. Main Outcome Measures:Prevalence of scapular dyskinesis at 4 time intervals during a swim training session. Results:The scaption test resulted in a weighted kappa value of 0.75. Scapular dyskinesis was seen in 29 shoulders (37%) after the first time interval, in another 24 (cumulated prevalence 68%) after one-half of the training session, and in an additional 4 swimmers (cumulated prevalence 73%) after three-quarters of the training session. During the last quarter of the training session, another 7 swimmers had dyskinesis, resulting in a cumulated prevalence of 82%. Conclusions:The prevalence of abnormal scapular kinesis during a normal training session is high in previously pain-free swimmers. The prevalence increases with more training and occurs early during the training session.
Changes in Creatine Kinase and Cortisol in National Collegiate Athletic Association Division I American Football Players During a Season

Abstract Kraemer, WJ, Looney, DP, Martin, GJ, Ratamess, NA, Vingren, JL, French, DN, Hatfield, DL, Fragala, MS, Spiering, BA, Howard, RL, Cortis, C, Szivak, TK, Comstock, BA, Dunn-Lewis, C, Hooper, DR, Flanagan, SD, Volek, JS, Anderson, JM, Maresh, CM, and Fleck, SJ. Changes in creatine kinase and cortisol in national collegiate athletic association division I American football players during a season. J Strength Cond Res 27(2): 434–441, 2013—The purpose of this study was to track creatine kinase (CK) and serum cortisol over an American college football season starting with the preseason practice. A secondary purpose was to observe changes in basic clinical chemistries. Twenty-two National Collegiate Athletic Association Division I football players (age: 20.4 ± 1.1 years, height: 188.27 ± 8.3 cm, weight: 115.8 ± 29.7 kg) volunteered to participate in this study. Each of the players had participated in the summer strength and conditioning supervised program. Resting blood samples were obtained just before the start of preseason practice (T-1), 2 weeks later (T-2), and the day after game 2 (T-3), game 4 (T-4), game 6 (T-5), and game 9 (T-6) of a 12-game season. Creatine kinase, a panel of clinical chemistries, cortisol, and testosterone were assayed at each time point. No significant changes in CK concentrations were observed over the season with peak values of each range ⩽1,070.0 IU·L−1, but the largest range was observed at T-6 after game 9 (119–2,834 IU·L−1. The analysis of covariance analysis demonstrated that the number of plays in the ninth game (T-6) explained the magnitude of the changes in CK. No changes in serum cortisol concentrations were observed yet, again large variations existed with peak values of each range ⩽465.0 nmol·L−1. Clinical chemistries showed various significant changes from T-1, but none were considered clinically relevant changes for any player over the time course of the study. In conclusion, the strength and conditioning program before preseason camp or the structure of summer camp practices and the in-season strength and conditioning appeared to mute muscle damage and the stress response of cortisol. Such data demonstrate that changes in muscle damage and adrenal cortical stress over the season are minimal, yet large individual variations can be observed. Management of these variables appears to be related to optimal strength and conditioning and sports medicine programs. Thus, the greater concerns for student-athlete safety in the sport of American football are related to preventing sudden death, traumatic injury, and managing concussion syndromes.
The Light-Response BTB1 and BTB2 Proteins Assemble Nuclear Ubiquitin Ligases That Modify Phytochrome B and D Signaling in Arabidopsis1[W][OA]

Members of the Bric-a-Brac/Tramtrack/Broad Complex (BTB) family direct the selective ubiquitylation of proteins following their assembly into Cullin3-based ubiquitin ligases. Here, we describe a subfamily of nucleus-localized BTB proteins encoded by the LIGHT-RESPONSE BTB1 (LRB1) and LRB2 loci in Arabidopsis (Arabidopsis thaliana) that strongly influences photomorphogenesis. Whereas single lrb1 and lrb2 mutants are relatively normal phenotypically, double mutants are markedly hypersensitive to red light, but not to far-red or blue light, and are compromised in multiple photomorphogenic processes, including seed germination, cotyledon opening and expansion, chlorophyll accumulation, shade avoidance, and flowering time. This red light hypersensitivity can be overcome by eliminating phytochrome B (phyB) and phyD, indicating that LRB1/2 act downstream of these two photoreceptor isoforms. Levels of phyB/D proteins but not their messenger RNAs are abnormally high in light-grown lrb1 lrb2 plants, implying that their light-dependent turnover is substantially dampened. Whereas other red light-hypersensitive mutants accumulate phyA protein similar to or higher than the wild type in light, the lrb1 lrb2 mutants accumulate less, suggesting that LRB1/2 also positively regulate phyA levels in a phyB/D-dependent manner. Together, these data show that the BTB ubiquitin ligases assembled with LRB1/2 function redundantly as negative regulators of photomorphogenesis, possibly by influencing the turnover of phyB/D.
Rule Extraction from Blog Using Inductive Logic Programming

Information recommender system attempts to present information that is likely to be useful for the user. Showing recommendation reason is an important role of the system. However, current recommender systems give only simple or quantitative reasons for the recommendation. In this paper, we aim at giving precise and non-quantitative reasons which are also easy to understand. We make use of formulas in first-order predicate logic for explaining the reason. In order to build such formulas, we use Inductive Logic Programming. We succeeded to extract several useful formulas from blogs.
Frequency of Long-Term Nonprogressors in HIV-1 Seroconverters From Rakai Uganda

Objective:Studies on long-term nonprogressors (LTNP) have been conducted in the USA and Europe. This study examined the frequency of LTNPs and HIV controllers among 637 HIV-1 seroconverters in rural Uganda. Design and Methods:LTNPs were defined as being infected for more than 7 years with a CD4+ T-cell count above 600 cells per microliter, and HIV controllers as having undetectable viral loads on 3 separate occasions without antiretroviral treatment. HIV-1 viral load and subtype distribution between LTNP and non-LTNP populations were determined. Results:Of the HIV seroconverters, 9.1% (58/637) were LTNPs and 1.4% (9/637) were HIV controllers. LTNPs had a significantly lower viral load at set point than non-LTNP participants (P < 0.001). The Kaplan-Meier joint probability of surviving to 7 years with a CD4 count >600 was 19.2%. Individuals who survived 7 years had a significantly higher frequency of HIV-1 subtype A (P < 0.05), but seroconverters infected with HIV-1A did not have a significantly higher probability of becoming an LTNP. Conclusions:The frequency of LTNPs appears to be relatively high in Uganda and it may be important to take this into account when designing studies of viral pathogenesis and performing HIV vaccine trials in sub-Saharan Africa.
Postimplantation Audition and Educational Attainment in Children with Prelingually Acquired Profound Deafness

Language and educational attainment were evaluated over a 4-year period in 8 profoundly deaf, orally trained child users of the Nucleus multichannel implant with the spectral peak (SPEAK) processor. The average age at implantation was 5.8 years. In terms of audition and language, these children resembled severely deaf children, with unaided hearing losses in the region of 70 to 75 dB, who use hearing aids. In tests of educational attainment and literacy, average performance lagged behind grade placement by an amount that increased with increasing language demand of the task. The benefits of implantation are considerable; nevertheless, auditory limitations, combined with language deficits already present at the time of implantation, present a continuing educational challenge. Earlier implantation, when the auditory system is more plastic and language delays are automatically minimized, may well produce better outcomes, but this advantage remains to be demonstrated.
Changing the conversation about prostate cancer among African Americans: results of formative research

Objectives. To understand obstacles to and opportunities for improving prostate cancer communication to and within African American communities. Design. Researchers conducted interviews with 19 community leaders and five focus groups with healthy men and survivors. The team also conducted process evaluations of two outreach projects in which survivors spoke to African American men about prostate cancer and screening. Results. Three levels of obstacles to prostate cancer screening and treatment were identified. Individual-level obstacles included limited knowledge about the condition, about prevention and treatment, and fear of cancer. Socio-cultural barriers included distrust of the medical system, lack of a provider for routine and preventive care, reluctance to talk about cancer, and aversion to aspects of screening. Institutional deficits included the scarcity of educational efforts targeting prostate cancer. Outreach project evaluations suggested that survivors can be effective in building prostate cancer knowledge, promoting positive attitudes toward screening, and fostering conversations about prostate cancer. Educational efforts included little information about screening risks and decision-making however. Conclusions. The findings suggest that most potent interventions may combine survivor-led education with mass media and institution-based outreach. Such comprehensive programs could shift social norms that inhibit conversation and foster fear, leading in turn to more informed decisions and better treatment outcomes.
Parent expectations for antibiotics, physician-parent communication, and satisfaction.

OBJECTIVES To explore how parents communicate their preferences for antibiotics to their child's physician and to examine whether physicians can communicate why antibiotics are not being prescribed in a way that maintains satisfaction with the visit. DESIGN Previsit survey of parents, audiotaping of the study encounters, and a postvisit survey of parents and physicians. SETTING Two private pediatric practices. PARTICIPANTS Ten physicians (response rate = 77%) and a consecutive sample of 295 eligible parents (response rate = 86%) who attended acute care visits for their children between October 1996 and March 1997. MAIN OUTCOME MEASURES Physician-perceived pressure to prescribe antibiotics and parental visit-specific satisfaction. RESULTS Fifty percent of parents expressed a previsit expectation for antibiotics. Among these parents, only 1% made a direct verbal request for them. Even when no direct requests for antibiotics were made, physicians still perceived an expectation for antibiotics 34% of the time. Among parents who did not receive expected antibiotics, those offered a contingency plan from the physician (i.e., the possibility of receiving antibiotics in the future if their child did not get better) had a higher mean satisfaction score than parents not receiving a contingency plan (76 vs. 58.9; P<.05). CONCLUSION Physicians should consider providing a contingency plan to parents who expect antibiotics for their children when there is no clinical indication. Further study is needed to determine how parents indirectly communicate their desire for antibiotics and what additional communication techniques physicians can use to resist the overprescribing of antibiotics.