Miracle-dz/UniFAR-FTUs huggingface dataset:
HCV Genotype-1 Subtypes and Resistance-Associated Substitutions in Drug-Naive and in Direct-Acting Antiviral Treatment Failure Patients

Background Direct-acting antiviral (DAA) treatment regimens and response rates of patients with HCV genotype-1 (GT1) are currently considered subtype-dependent. Identification of clinically relevant resistance-associated substitutions (RASs) in the NS3 and NS5A proteins at baseline and in DAA failures, may also impact clinical decisions. Methods In a multicentre cohort study (n=308), NS3 or NS5B sequencing (n=248) was used to discriminate between GT1 subtypes. The correlation between baseline NS3 and NS5A RASs on the 12-week sustained virological response (SVR12) rates of 160 of the patients treated with second-generation DAAs was also assessed. Post-treatment resistance analysis was performed on samples from 58 patients exhibiting DAA virological failure. Results GT1a, GT1b and GT1d subtypes were identified in 23.0%, 75.4% and 1.2% of tested samples. GT1b was most prevalent (97.7%, 128/131) among patients born in the former Soviet Union. The Q80K NS3 RAS was identified in 17.5% (10/57) of the GT1a carriers, most of whom were Israeli-born. NS3 and NS5A baseline RASs showed a negligible correlation with SVR12 rates. Treatment-emergent RASs were observed among 8.9% (4/45) and 76.9% (10/13) of first- and second-generation DAA failures, respectively, with D168V/E (NS3), Y93H and L31M (NS5A) being the most prevalent mutations. Conclusions NS3 sequencing analysis can successfully discriminate between GT1 subtypes and identify NS3 amino acid substitutions. While pre-treatment NS3 and NS5A RASs marginally affect second-generation DAA SVR12 rates, post-treatment resistance analysis should be considered prior to re-therapy.
Lessons Learned from EPA's Climate Leaders Program: An Evaluation to Fortify Voluntary Environmental Initiatives

A voluntary environmental program (VEP) called Climate Leaders was recently cancelled by the U.S. Environmental Protection Agency (EPA). To find out why and gather lessons learned, the program was examined using a three-pronged approach: 1) a meta-analysis of program evaluation theory literature, 2) a review of guides and external reports on Climate Leaders, and 3) interviews with former program participants and implementers. Findings reveal that environmental protection is best achieved by combining regulation with voluntary methods as they complement and buttress each other. Recommendations were compiled to help future VEPs minimize wasted resources and improve environmental conditions. These recommendations were vetted by industry, and ultimately contribute to a comprehensive “guiding framework” for the design, implementation, and evaluation of VEPs. Existing VEP models and evaluative tools still lack the perspective of several key disciplines, so additional program evaluations are necessary to capture all of the primary characteristics correlated with program success and complete the guiding framework. Disciplines Earth Sciences | Physical Sciences and Mathematics Comments Presented to the Faculties of the University of Pennsylvania in Partial Fulfillment of the Requirements for the Degree of Master of Environmental Studies 2011. This thesis or dissertation is available at ScholarlyCommons: http://repository.upenn. edu/mes_capstones/41 LESSONS LEARNED FROM EPA’S CLIMATE LEADERS PROGRAM: AN EVALUATION TO FORTIFY VOLUNTARY ENVIRONMENTAL INITIATIVES
Current status and challenges of cytokine pharmacology

The major concern of pharmacology about cytokines has originated from plentiful data showing association between gross changes in their production and pathophysiological processes. Despite the enigmatic role of cytokines in diseases, a number of them have become a subject of cytokine and anti‐cytokine immunotherapies. Production of cytokines can be influenced by many endogenous and exogenous stimuli including drugs. Cells of the immune system, such as macrophages and lymphocytes, are richly endowed with receptors for the mediators of physiological functions, such as biogenic amines, adenosine, prostanoids, steroids, etc. Drugs, agonists or antagonists of these receptors can directly or indirectly up‐ and down‐regulate secretion of cytokines and expression of cytokine receptors. Vice versa, cytokines interfere with drug pharmacokinetics and pharmacodynamics through the interactions with cytochrome P450 and multiple drug resistance proteins. The aim of the review is to encourage more intensive studies in these fields of cytokine pharmacology. It also outlines major areas of searching promising candidates for immunotherapeutic interventions.
Methods for Identifying Versioned and Plagiarized Documents

The widespread use of on-line publishing of text promotes storage of multiple versions of documents and mirroring of documents in multiple locations, and greatly simplifies the task of plagiarizing the work of others. We evaluate two families of methods for searching a collection to find documents that are coderivative, that is, are versions or plagiarisms of each other. The first, the ranking family, uses information retrieval techniques; extending this family, we propose the identity measure, which is specifically designed for identification of co-derivative documents. The second, the fingerprinting family, uses hashing to generate a compact document description, which can then be compared to the fingerprints of the documents in the collection. We introduce a new method for evaluating the effectiveness of these techniques, and demonstrate it in practice. Using experiments on two collections, we demonstrate that the identity measure and the best fingerprinting technique are both able to accurately identify coderivative documents. However, for fingerprinting parameters must be carefully chosen, and even so the identity measure is clearly superior.
A conceptual model for analysing informal learning in online social networks for health professionals

Online social networking (OSN) provides a new way for health professionals to communicate, collaborate and share ideas with each other for informal learning on a massive scale. It has important implications for ongoing efforts to support Continuing Professional Development (CPD) in the health professions. However, the challenge of analysing the data generated in OSNs makes it difficult to understand whether and how they are useful for CPD. This paper presents a conceptual model for using mixed methods to study data from OSNs to examine the efficacy of OSN in supporting informal learning of health professionals. It is expected that using this model with the dataset generated in OSNs for informal learning will produce new and important insights into how well this innovation in CPD is serving professionals and the healthcare system.
RANTES, TNF-α, Oxidative Stress, and Hematological Abnormalities in Hepatitis C Virus Infection

Background Chronic infection with hepatitis C virus (HCV) is associated with failures of T-cell–mediated immune clearance and with abnormal B-cell growth and activation. Hepatitis C virus infection is characterized by a systemic oxidative stress that is most likely caused by a combination of chronic inflammation, iron overload, liver damage, and proteins encoded by HCV. After a viral infection, multiple proinflammatory mediators contribute to recruitment of immune cells to the liver and to the generation of an antiviral immune response. Recent publications mark chemokines and their receptors as key players in leukocyte recirculation through the inflamed liver. Materials and Methods The present study involved 75 male subjects, divided into 2 groups: group 1 (n = 30), control group; group 2 (n = 45), patients with chronic HCV. For all subjects, the following investigations were performed: estimation of the levels of bilirubin, albumin, prothrombin concentration, glycosylated hemoglobin, creatinine, α-fetoprotein, HCV RNA, and activities of alanine and aspartate transaminases as well as alkaline phosphatase. In addition, regulated on activation normal T cell expressed and secreted (RANTES), tumor necrosis factor alpha, malondialdehyde (MDA) and nitric oxide (NO) were assessed. Plasma HCV-RNA concentration (viral load) was determined by real-time polymerase chain reaction (PCR) StepOne system using Applied Biosystem. Complete blood picture was assayed using Abbott Cell-Dyn 3700 hematology analyzer. Results There were significant increases of the levels of RANTES, tumor necrosis factor alpha, MDA, and NO in HCV-infected patients compared with the control group (P <0.05); and in these patients, these levels showed significant positive correlation with the HCV RNA viral load. Also, mild leukopenia, thrombocytopenia, neutropenia, and lymphocytosis, with consequent significant increase in the lymphocytes/neutrophils ratio, were detected in these patients. Conclusion The data support the concept of chemokines (RANTES) as mediators of liver cell injury in HCV infection. In addition, MDA and NO levels might be used as monitoring markers for oxidative stress in hepatitis C infection.
Predicting IUCN Extinction Risk Categories for the World's Data Deficient Groupers (Teleostei: Epinephelidae)

Groupers are highly susceptible to human‐induced impacts, making them one of the most threatened fish families globally. Extinction risk assessments are important in endangered threatened species management, however the most comprehensive—the International Union for Conservation of Nature (IUCN) Red List—cannot classify approximately one‐third of grouper species due to data deficiency. We used an ordinal analytical approach to model relationships between species‐level traits and extinction risk categories. We found that larger species and those with shallower maximum depths and smaller geographic ranges had higher extinction risk. Using our best fitting model, we classified data deficient grouper species into IUCN's extinction risk categories based on traits. Most of these species were predicted to be of least concern. However, 12% were predicted to be endangered or vulnerable, suggesting that they may be of conservation interest. Importantly, we provide a quantitative method for overcoming data gaps that can be applied to conservation of other species.
Activations of Human Auditory Cortex During Visual and Auditory Selective Attention Tasks with Varying Difficulty

The present study was designed to directly test the hypothesis that suppression of activations to task-irrelevant sounds contributes to the attention-related modulations of auditory cortex (AC) activations observed in previous fMRI studies. Subjects selectively attended to auditory (broadband noise bursts with pitch) or visual (Gabor gratings) asynchronous fast-rate stimulus streams concurrently presented to left-ear, right-ear, above-fixation, or below-fixation. Auditory and visual task difficulty was parametrically manipulated in three levels. Behavioral data obtained during fMRI indicated that subjects achieved acceptable performance levels in all tasks and that the task-difficulty manipulation was effective. Consistent with previous studies, AC activations strongly depended on the direction of attention. AC activations to sounds were higher during auditory than during visual tasks and AC activations were higher in the hemisphere contralateral to the attended ear. However, the effects of task difficulty on AC activations were weak or non-existent. In particular, increasing task difficulty was not associated with a systematic decrease of AC activations in areas that were modulated by attention. These results suggest that suppression of AC activations to task-irrelevant sounds is likely to be small or negligible as compared with the strong activation enhancements observed in fMRI during active auditory tasks.
Modelling Inside GIS: Part 1. Model Structures, Exploratory Spatial Data Analysis and Aggregation

Abstract This is the first of two papers elaborating a framework for embedding urban models within GIS. This framework is based upon using the display capabilities of GIS as the user interface to the conventional modelling process, beginning with data selection and analysis, moving to model specification and calibration, and thence to prediction. In this paper, we outline how various stages in this process based on purpose-built software outside the system, are accessed and operated through the GIS. We first deal with display based on thematic maps, surfaces, graphs and linked windows, standard to any data from whatever source, be it observations, model estimates or predictions. We then describe how various datasets are selected, how the spatial system can be partitioned or aggregated, and how rudimentary exploratory spatial data analysis enables scatterplots to be associated with thematic maps. We illustrate all these functions and operations using the proprietary GIS ARC-INFO applied to population data .
Dietary Phospholipids and Intestinal Cholesterol Absorption

Experiments carried out with cultured cells and in experimental animals have consistently shown that phospholipids (PLs) can inhibit intestinal cholesterol absorption. Limited evidence from clinical studies suggests that dietary PL supplementation has a similar effect in man. A number of biological mechanisms have been proposed in order to explain how PL in the gut lumen is able to affect cholesterol uptake by the gut mucosa. Further research is however required to establish whether the ability of PLs to inhibit cholesterol absorption is of therapeutic benefit.
Medication Reconciliation at Hospital Discharge: Evaluating Discrepancies

Background: Hospital discharge is an interlace of care when patients are at a high risk of medication discrepancies as they transition from hospital to home. These discrepancies are important, as they may contribute to drug-related problems, medication errors, and adverse drug events. Objective: To Identify, characterize, and assess the clinical impact of unintentional medication discrepancies at hospital discharge. Methods: All consecutive general internal medicine patients admitted for at least 72 hours to a tertiary care teaching hospital were prospectively assessed. Patients were excluded if they were discharged with verbal prescriptions; died during hospitalization; or transferred from or to a nursing home, another institution, or another unit within the same hospital. The primary endpoint was to determine the number of patients with at least one unintended medication discrepancy on hospital discharge. Medication discrepancies were assessed through comparison of a best possible medication discharge list with the actual discharge prescriptions. Secondary objectives were to characterize and assess the potential clinical impact of the unintentional discrepancies. Results: From March 14,2006, to June 2,2006,430 patients were screened for eligibility; 150 patients were included in the study. Overall, 106 (70.7%) patients had at least one actual or potential unintentional discrepancy. Sixty-two patients (41.3%) had at least one actual unintentional medication discrepancy al hospital discharge and 83 patients (55.3%) had at least one potential unintentional discrepancy. The most common unintentional discrepancies were an incomplete prescription requiring clarification, which could result in a patient delay in obtaining medications (49.5%), and the omission of medications (22.9%). Of the 105 unintentional discrepancies, 31 (29.5%) had the potential to cause possible or probable patient discomfort and/or clinical deterioration. Conclusions: Medication discrepancies occur commonly on hospital discharge. Understanding the type and frequency of discrepancies can help clinicians better understand ways to prevent them. Structured medication reconciliation may help to prevent discharge medication discrepancies.
Does Sympathy Motivate Prosocial Behaviour in Great Apes?

Prosocial behaviours such as helping, comforting, or sharing are central to human social life. Because they emerge early in ontogeny, it has been proposed that humans are prosocial by nature and that from early on empathy and sympathy motivate such behaviours. The emerging question is whether humans share these abilities to feel with and for someone with our closest relatives, the great apes. Although several studies demonstrated that great apes help others, little is known about their underlying motivations. This study addresses this issue and investigates whether four species of great apes (Pongo pygmaeus, Gorilla gorilla, Pan troglodytes, Pan paniscus) help a conspecific more after observing the conspecific being harmed (a human experimenter steals the conspecific’s food) compared to a condition where no harming occurred. Results showed that in regard to the occurrence of prosocial behaviours, only orangutans, but not the African great apes, help others when help is needed, contrasting prior findings on chimpanzees. However, with the exception of one population of orangutans that helped significantly more after a conspecific was harmed than when no harm occurred, prosocial behaviour in great apes was not motivated by concern for others.
A Study of the Granulomatous Responses Induced by Different Strains of Schistosoma mansoni

The increased pathogenesis of the Schistosoma mansoni BH strain compared with the SJ strain has been attributed to the number of granulomas formed in experimental infections, which increase the mortality in definitive hosts. The aim of the present study was to investigate the development of granulomas around the eggs of the S. mansoni BH and SJ strains and to determine whether this host reaction was strain specific. Four experimental groups were analyzed. Two groups contained mice inoculated in the caudal vein with eggs from the S. mansoni BH or SJ strains and the other two contained mice that were infected with cercariae of the BH strain prior to being inoculated with eggs. The number of granulomas per tissue area in the lungs and liver, as well as the size of the granulomas, was analyzed to characterize the response to schistosome infection. The largest granulomatous responses were observed around eggs of the BH strain. Granulomas covered a larger area in the lungs of mice that were previously infected with cercariae and subsequently inoculated with eggs of the BH strain. These results indicated that specific granulomatous responses occurred following an infection with the BH and SJ strains of S. mansoni.
QoS-Aware Adaptive Internet Gateway Selection in Ad Hoc Wireless Internet Access Networks

In ad hoc networks with Internet connectivity, an Internet gateway (IG) is used to connect ad hoc mobile nodes to the Internet. Multiple Internet gateways may be deployed in order to provide more scalable and robust ubiquitous coverage. In this case, we need to solve the Internet gateway selection problem in order for successful integration of the Internet with mobile ad hoc networks. An ad hoc mobile node first discovers available Internet gateways, and then the node selects a serving gateway among those candidates for optimal performance. In this paper, we propose an adaptive Internet gateway selection scheme using redirecting selection method which is based on QoS attributes such as hop-count and residual capacity. Our objective is to design a selection method for providing enhanced performance. Simulation results show that our adaptive Internet gateway selection scheme achieves better performance as well as better load balancing than existing selection schemes.
Intra‐blood‐brain barrier synthesis of IgG

We evaluated four formulas for estimating the intra-blood-brain barrier (IBBB) synthesis of IgG in a computer model of two types of BBB damage and in 1,629 consecutively received pairs of CSF and serum. These four formulas were the IgG synthesis rate (SR), IgG(loc) (ie, local), IgG index, and IgG extended index. Results from the 1,629 specimens and the computer model of type 2 BBB damage (partial or total loss of selective filtration) accurately predicted problems encountered with the IgG SR in clinical practice. In both the model and with the results from the 1,629 specimens, the combination of the IgG(loc) and IgG index formulas minimized the possibility of false-positive and false-negative results and yielded the most reliable results for IBBB synthesis of IgG in the presence or absence of increased permeability of the BBB. Additional studies with detailed clinical correlations will allow an accurate assessment of how effectively this combination of formulas can help to rule in or out the diagnosis of a particular disease or inflammatory condition of the CNS.
Content-aware image resizing by quadratic programming

We present a new method for content-aware image resizing based on a framework of global optimization. We show that the basic resizing problem can be formulated as a convex quadratic program. Furthermore, we demonstrate how the basic framework may be extended to prevent foldovers of the underlying mesh; encourage the magnification of salient regions; and preserve straight line structures. We show results demonstrating the effectiveness of the proposed method by comparing with four leading competitor methods.
fWLR supported process development based on V- and J-ramp stress tests

In this work ramp stress procedures were utilized to support both process development as well as continued improvement in the reliability of tunnel oxides used in EEPROM devices of automotive applications. In order to enhance the reliability assessment opportunities trapped oxide charge (Δqot) breakdown distributions were constructed by combining the measured charge-to-breakdown (qbd) distributions with representative difference IV-curves [1] recorded during breakdown measurements. While the qbd-data regularly used for interface quality assessment strongly depends on the type of ramp test, e.g. linearly RVS(T) (ramped voltage stress(test)), ERCS (exponentially ramped current stress), linear RCS (ramped current stress) and also its ramp speed, the tapped charge at breakdown is less dependent on measurement type and also very sensitive to interface properties.
Symptomatic primary Cytomegalovirus infection in a HIV-positive pregnant woman

We describe a case of symptomatic primary Cytomegalovirus infection in a HIV-positive pregnant woman on antiretroviral treatment with a CD4 count >200 × 106/l requiring intravenous ganciclovir. No adverse consequences from ganciclovir or evidence of congenital Cytomegalovirus infection were found.
MicroRNA regulation of the CUC genes is required for boundary size control in Arabidopsis meristems

We have analysed the role of a microRNA, miR164, in boundary formation during organ initiation from Arabidopsis meristems. The establishment and maintenance of the boundary domain are controlled by three partially redundant genes, CUP-SHAPED COTYLEDON1 (CUC1), CUC2 and CUC3. We show that miR164 overexpression phenocopies the cuc1 cuc2 double mutant by inducing post-transcriptional downregulation of CUC1 and CUC2 but not CUC3 mRNA levels. Disruption of CUC2 regulation by miR164, either by making CUC2 resistant to the miRNA or by reducing miRNA levels leads to similar enlarged boundary domains. We relate this enlargement to the division patterns of the boundary cells. We propose that miR164 constrains the expansion of the boundary domain, by degrading CUC1 and CUC2 mRNAs.