Miracle-dz/UniFAR-FTUs huggingface dataset:
Low-Rate Emergence of Thymidine Analogue Mutations and Multi-Drug Resistance Mutations in the HIV-1 Reverse Transcriptase Gene in Therapy-Naive Patients Receiving Stavudine plus Lamivudine Combination Therapy

Objectives Mutations usually associated with zidovudine exposure have been observed in zidovudine-naive patients treated by stavudine in combination. These mutations were named thymidine analogue mutations (TAMs). This fact, combined with phenotypical and biochemical findings provided additional evidence for cross-resistance between zidovudine and stavudine. A recent genotypic study in naive patients receiving stavudine/didanosine combination showed emergence of TAMs and a multidrug-resistance mutation (MDR), Q151M, in 36 and 10% of cases, respectively. Stavudine plus lamivudine is one of the most used binucleoside associations in the antiretroviral combinations. The objective of this study was to assess the genotypic changes in the HIV-1 reverse transcriptase (RT) gene in antiretroviral-naive patients treated by stavudine plus lamivudine. Methods We analysed the RT gene of 44 HIV-1 patients, naive of antiretroviral therapy, who were treated for 24 or 48 weeks with stavudine/lamivudine. Results: At the end of the follow-up, all patients acquired the lamivudine-associated mutation M184V. Only two subjects (4.5%) developed a TAM (T215Y; M41L), one subject developed a V75T/A mutation and one subject developed the particular MDR pattern F116Y, Q151M. Conclusions Our study clearly demonstrated that naive subjects treated with stavudine/lamivudine for 24–48 weeks selected a low rate of TAMs and MDR Q151M. One hypothesis explaining these results could be the development of the M184V mutation.
Patterns of differentiation and proliferation in intraductal carcinoma of the prostate: Significance for cancer progression

Cribriform prostatic intraepithelial neoplasia (C‐PIN) identifies a unique histological pattern: dysplastic cells line ductal/acinar walls but also span across gland lumens. C‐PIN is distinct from other forms of dysplasia; it is seldom seen except within invasive cancer, it is more frequent in larger/higher‐grade cancers; and it appears to contribute independently to aggressive behavior. Hence, C‐PIN may represent a separate, more aggressive entity: intraductal carcinoma of the prostate (IDC‐P). Here, support for that distinction stems from a histologic/biologic subclassification of IDC‐P, whose elements are linked to features of invasive cancer.
The effects of brand attachment on behavioral loyalty in the luxury restaurant sector

Purpose The purpose of this study is to examine the relationship between satisfaction, congruence, nostalgic connections and trust with reference to brand attachment and behavioral loyalty. Behavioral loyalty was examined through the customer’s intention to continue the relationship, as well as proselytism and resistance upwards of the price in the luxury restaurant sector. Design/methodology/approach A questionnaire was developed and distributed via email and different Facebook groups which specialized in the luxury restaurant sector in Tunisia. A total of 310 questionnaires were completed and structural equation modeling with AMOS was used to test the hypothesis. Findings The findings suggest that brand attachment clearly explains the behavioral loyalty of consumers because it contributes toward maintaining the relationship with the brand in terms of repetitive buying behavior. Only satisfaction and nostalgic connection was found to influence brand attachment and satisfaction has a bearing on proselytism. Brand attachment in turn influences the intention to continue the relationship and the resistance to upward pricing, but not toward proselytism. Practicalimplications The managerial implications can guide managers toward enhancing the behavior loyalty of customers through better relational marketing practices. Originality/value The research is original in terms of conceptualizing and empirically testing the relation between brand attachment and behavior loyalty within the luxury restaurant sector with a specific focus on Tunisia. This study is one of the first to examine the relationship between brand attachment and behavioral loyalty in the restaurant sector.
Transistor design for 5nm and beyond: Slowing down electrons to speed up transistors

Analysis of the key band structure properties for MOSFET channel material are investigated in a wide range for nanowires with design rules scaling from 5 nm down to 2 nm. Three-dimensional Non-Equilibrium Green's Functions (NEGF) method is employed to calculate the on-state currents for different channel band structures. Results of the analysis show that the optimal effective mass increases with transistor scaling from 0.1 at 5 nm design rules up to 0.4 at 2 nm design rules. There is a gentle performance degradation for effective masses that are heavier than optimal, and there is a steep performance penalty for the lighter electrons due to the direct source-to-drain tunneling through the source junction barrier. Different Si crystal orientations can be chosen to get close to theoretically possible optimal performance, or stress can be used to slow down the electrons. Silicon scales well down to at least 2 nm technology node, and properties of typical 2D materials like MoS2 are close to optimal. However, high-mobility materials like Ge or III-V are far outside of the optimal property range and do not scale well. One other key aspect of transistor scaling potential is its inherent random variability. Analysis of transistor performance sensitivity to geometry fluctuations shows that nanowires with 5 nm design rules are less sensitive than FinFETs to the channel length variation, but sharply more sensitive than FinFETs to fin width variation. Specific FinFET and nanowire sensitivity to geometry fluctuations can be used to determine the spec for future equipment that is necessary for high yield nanowire manufacturing.
Diffusion-controlled and replacement microtextures in alkali feldspars from two pegmatites: Perth, Ontario and Keystone, South Dakota

Abstract Macro- and micro-perthitic microclines from pegmatites from Perth, Ontario (Wards catalogue 46 E 0510) and Keystone, South Dakota (Wards 46 E 5125) have been studied using light and electron microscopy. A sample of the type perthite from Perth, Ontario (Hunterian Museum, Glasgow, M2361) was compared using light microscopy. It differs in bulk composition and microtexture from the Wards sample. The Perth sample from Wards is a mesoperthite, with sub-periodic ~mm-thick albite veins near (100), with irregular surfaces. The microcline has regular tartan twins and formed from orthoclase by a continuous process. The Keystone sample is a microperthite, with non-periodic albite veins mainly in {110}. Irregular tartan twins, volumes of irregular microcline and subgrains suggest that the microcline formed by dissolution- reprecipitation. Microcline in both samples contains semicoherent cryptoperthitic albite films that formed after the development of tartan twins. The bulk compositions of these intergrowths imply exsolution below ~400°C. Diffusion parameters imply sustained heating for between 0.11 My at 400°C, 1.5 GPa and 8.4 My at 300°C, 1 GPa. Unrealistic times are required at 200°C. Subsequently, the crystals reacted with a fluid leading to replacive growth of the vein perthites. Unusually, Albite twin composition planes in replacive subgrains have sub-periodic dislocations, formed by coalescence of advancing growth twins. Processes that might lead to periodic, replacive intergrowths are discussed. The Perth and Keystone feldspars have been used for experimental work on dissolution during weathering and on anomalous thermoluminescence fading. Their microtextures make them unsuitable for obtaining properties that can be extrapolated to feldspars in general.
Planar high gain antenna for 5.8-GHz WiMAX operation

In this paper, the high gain patch antenna design using meta-material technology, composed of 4 layer of metallic rings and 3 layer of Rogers 5880 substrate, is successfully constructed and measured. With the thin meta-material antenna radome (only 0.06lambda0 including the air gap between the antenna radome and the patch antenna), the improved antenna gain can be up to 2.3 dB in the WiMAX 5.8- GHz band compared with ordinary FR4 substrate patch antenna. The impedance bandwidth of the proposed antenna is about 350 MHz (5.56-5.91-GHz, defined by 2:1 VSWR). The far-field radiation characteristics of both E-plane and H-plane of the proposed antenna are also measured and will be discuss in this paper.
Flooding risks and housing markets: a spatial hedonic analysis for La Plata City

Abstract On 2 April 2013 a major flood struck the City of La Plata, Argentina, killing 89 people and displacing thousands of others. That event, the worst flood the city has suffered in the past 100 years, prompted plans for a new hydraulic infrastructure. Although such an investment is necessary, little is known about its benefits. This paper intends to shed some light on this issue by estimating the willingness to pay to avoid the risk of experiencing a flooding event. For this purpose, we have taken thousands of real estate prices in the La Plata Metropolitan Area and combined them with a high-resolution flood risks map to estimate spatial hedonic price models. The results show significant price discounting for properties in flood-prone areas.
Validating Algorithmic Optimization of Patient Allocation at Medical Schools: Which Patient is the Best Fit for Undergraduate Training?

Limited access to patients is an increasing problem in medical education. In order to reduce patient shortage, we previously proposed a strategy for assigning patients to courses of future curricula based on routinely available patient and educational data. However, this algorithm did not consider challenges of an existing curriculum, thus greatly limiting its applicability in actual practise. This paper introduces a corresponding refinement of the algorithm together with its implementation of three algorithm variants approaches for resolving medical school courses that are affected by patient shortage. An evaluation of the new approach yielded that approximately two thirds of all respective course sessions could be resolved by applying several variants of the algorithm, each of which proved to have different strengths.
Microbiota and diabetes: an evolving relationship

The gut microbiota affects numerous biological functions throughout the body and its characterisation has become a major research area in biomedicine. Recent studies have suggested that gut bacteria play a fundamental role in diseases such as obesity, diabetes and cardiovascular disease. Data are accumulating in animal models and humans suggesting that obesity and type 2 diabetes (T2D) are associated with a profound dysbiosis. First human metagenome-wide association studies demonstrated highly significant correlations of specific intestinal bacteria, certain bacterial genes and respective metabolic pathways with T2D. Importantly, especially butyrate-producing bacteria such as Roseburia intestinalis and Faecalibacterium prausnitzii concentrations were lower in T2D subjects. This supports the increasing evidence, that butyrate and other short-chain fatty acids are able to exert profound immunometabolic effects. Endotoxaemia, most likely gut-derived has also been observed in patients with metabolic syndrome and T2D and might play a key role in metabolic inflammation. A further hint towards an association between microbiota and T2D has been derived from studies in pregnancy showing that major gut microbial shifts occurring during pregnancy affect host metabolism. Interestingly, certain antidiabetic drugs such as metformin also interfere with the intestinal microbiota. Specific members of the microbiota such as Akkermansia muciniphila might be decreased in diabetes and when administered to murines exerted antidiabetic effects. Therefore, as a ‘gut signature’ becomes more evident in T2D, a better understanding of the role of the microbiota in diabetes might provide new aspects regarding its pathophysiological relevance and pave the way for new therapeutic principles.
Well‐differentiated thyroid carcinoma: The role of post‐operative radioactive iodine administration

Post‐operative management of differentiated thyroid cancer (DTC) often involves administration of radioactive iodine (RAI) for remnant ablation or adjuvant therapy. However, given the favorable prognosis associated with DTC, the risk versus benefit ratio of RAI remains unclear. RAI is associated with substantial, albeit rare side effects, including a possible increased risk of secondary malignancy and altered fertility, which must be balanced against the magnitude of benefit for decreasing recurrence and improving survival. J. Surg. Oncol. 2013;107:665–672. © 2012 Wiley Periodicals, Inc.
Pathway‐Based Analysis of Microarray and RNAseq Data Using Pathway Processor 2.0

The constant improvement of high‐throughput technologies has led to a great increase in generated data per single experiment. Pathway analysis is a widespread method to understand experimental results at the system level. Pathway Processor 2.0 is an upgrade over the original Pathway Processor program developed in 2002, extended to support more species, analysis methods, and RNAseq data in addition to microarrays through a simple Web‐based interface. The tool can perform two different types of analysis: the first covers the traditional Fisher's Test used by Pathway Processor and topology‐aware analyses, which take into account the propagation of changes over the whole structure of a pathway, and the second is a new pathway‐based method to investigate differences between phenotypes of interest. Common problems and troubleshooting are also discussed. Curr. Protoc. Bioinform. 41:7.6. 1‐7.6. 12. © 2013 by John Wiley & Sons, Inc.
Toolbox for retrovectorologists

Retroviral vectors have actively contributed to the advent of gene therapy as a realistic approach in human therapeutics. At the beginning, the use of retroviral vectors was thought to be as simple as the collection of a viral supernatant that was applied to the desired cell. Rapidly, target resistance to transduction appeared in various conditions, ex vivo as well as in vivo. At that time, retrovectorologists entered an active “back to the bench” era. This phase was thought to have reached its conclusion with the generation of theoretically safe lentiviral vectors and when, in 2000, a first clinical trial using retroviral vectors proved to be successful. Unfortunately, recent developments have shown that we still need to improve our knowledge of several steps in the retroviral life cycle before we can accurately adapt vectors to target specific cells.
AlGaN/GaN metal–oxide–semiconductor heterostructure field-effect transistors on SiC substrates

We report on AlGaN/GaN metal–oxide–semiconductor heterostructure field-effect transistors (MOS-HFETs) grown over insulating 4H–SiC substrates. We demonstrate that the dc and microwave performance of the MOS-HFETs is superior to that of conventional AlGaN/GaN HFETs, which points to the high quality of SiO2/AlGaN heterointerface. The MOS-HFETs could operate at positive gate biases as high as +10 V that doubles the channel current as compared to conventional AlGaN/GaN HFETs of a similar design. The gate leakage current was more than six orders of magnitude smaller than that for the conventional AlGaN/GaN HFETs. The MOS-HFETs exhibited stable operation at elevated temperatures up to 300 °C with excellent pinch-off characteristics. These results clearly establish the potential of using AlGaN/GaN MOS-HFET approach for high power microwave and switching devices.
Pre-leveled 16-QAM OFDM modulation of an 850-nm VCSEL for 56-Gbit/s transmission

An 850-nm VCSEL carried 16-QAM OFDM transmission at 56 Gbit/s is demonstrated by using the pre-leveling technology, which reveals an optimized signal-to-noise ratio, error vector magnitude and bit-error-rate of 16.4 dB, 15.1% and 1.2×10−3, respectively.
Do human rights violations increase the risk of civil war?

Despite the fact that there are strong assumptions surrounding the effects of human rights violations on the risk of civil war, very few researchers have tested the relationship in an empirical and systematic manner. By drawing on both human rights- and civil war research, this article presents an integrated human rights peace and conflict theory. The effects of rights violations are tested by applying quantitative research methods. The main finding is that violations of economic and social rights and physical integrity rights increase the risk of civil war, while violations of other civil and political rights play only a minor role.
Comparison of Statistical Methods to Classify Environmental Genomic Fragments

“Binning” (or taxonomic classification) of DNA sequence reads is an initial step to analyzing an environmental biological sample. Currently, a homology-based tool, BLAST, is one of the most commonly used tools to label DNA reads, but it is argued that BLAST will quickly lose its classification ability as the genome databases grow. In this paper, we compare the accuracies of a naïve Bayes classifier (NBC) and statistical language model to BLAST for binning reads and demonstrate that NBC obtains good performance for the low cost of computational complexity. On the other hand, the back-off n-gram language model can improve accuracy when only partial training data is available (such as in-progress sequencing projects). NBC demonstrates comparable performance to BLAST and can also be optimized on partial training datasets by adjusting the word feature size. A fivefold cross validation is conducted to compare each method's accuracy for determining novel genomes at different taxonomic levels, with NBC outperforming BLAST for species-level classification but BLAST outperforming NBC for genus-level and phyla-level classification. In conclusion, the NBC is a competitive taxonomic classifier, and language models can improve performance when only partial training data is available.
Ovarian response to injections of charcoal-extracted porcine follicular fluid and porcine follicle-stimulating hormone in gilts fed a progesterone agonist (altrenogest).

This experiment was conducted to compare the negative effects of charcoal-extracted porcine follicular fluid (pFF) and the positive effects of purified porcine follicle-stimulating hormone (pFSH) on growth of follicles and on plasma hormone concentrations. Twenty gilts were fed altrenogest for 18 days (20 mg.day-1.gilt-1) to suppress spontaneous growth of large follicles (greater than 6 mm in diameter). Gilts, assigned at random to receive pFF and pFSH administered in a 2 x 2 factorial arrangement, were injected 9 times at 8-h intervals starting 48 h before the last feeding of altrenogest and ending 8 h before slaughter (24 h after the last feeding of altrenogest). Blood was collected periodically through vena cava catheters. Treatment groups and mean number of medium follicles (3 to 6 mm in diameter)/gilt at necropsy were 1) 20 ml of charcoal-extracted porcine serum i.v. + 4 ml saline i.m. , 30.8; 2) 20 ml of pFF i.v. + saline i.m. , 0.2; 3) serum i.v. + 8 micrograms of pFSH (USDA-pFSH-B1)/kg BW in saline i.m. , 59.0; and 4) pFF i.v. + pFSH in saline i.m. , 36.2. Injections of pFF decreased (p less than 0.01) and injections of pFSH increased the number of medium follicles, and the interaction of pFF and pFSH was not significant. Plasma FSH decreased (p less than 0.01) during pFF treatment of saline-injected gilts at a rate of 0.29 ng.ml-1.h-1. During pFSH treatment, plasma FSH increased (p less than 0.05) at statistically identical rates of 0.33 and 0.32 ng.ml-1.h-1 in serum- and pFF-injected gilts. (ABSTRACT TRUNCATED AT 250 WORDS)
Refining and validating a two-stage and web-based cancer risk assessment tool for village doctors in China.

The big gap between efficacy of population level prevention and expectations due to heterogeneity and complexity of cancer etiologic factors calls for selective yet personalized interventions based on effective risk assessment. This paper documents our research protocol aimed at refining and validating a two-stage and web- based cancer risk assessment tool, from a tentative one in use by an ongoing project, capable of identifying individuals at elevated risk for one or more types of the 80% leading cancers in rural China with adequate sensitivity and specificity and featuring low cost, easy application and cultural and technical sensitivity for farmers and village doctors. The protocol adopted a modified population-based case control design using 72, 000 non-patients as controls, 2, 200 cancer patients as cases, and another 600 patients as cases for external validation. Factors taken into account comprised 8 domains including diet and nutrition, risk behaviors, family history, precancerous diseases, related medical procedures, exposure to environment hazards, mood and feelings, physical activities and anthropologic and biologic factors. Modeling stresses explored various methodologies like empirical analysis, logistic regression, neuro-network analysis, decision theory and both internal and external validation using concordance statistics, predictive values, etc.
Distributed Estimation with Channel Estimation Error over Orthogonal Fading Channels

We study distributed estimation of a source corrupted by an additive Gaussian noise and observed by sensors which are connected to a fusion center with unknown orthogonal (parallel) flat Rayleigh fading channels. The fading communication channels are estimated with training. Subsequently, source estimation given the channel estimates and transmitted sensor observations is performed. We consider a setting where the estimated channels are fed-back to the sensors for optimal power allocation which leads to a threshold behavior of sensors with bad channels being unused (inactive). We also show that at least half of the total power should be used for training. Simulation results corroborate our analytical findings.
German and British Consumer Willingness to Pay for Beef Labeled with Food Safety Attributes

The European Union has implemented some of the most stringent food safety policies for beef globally, ranging from banning growth hormones to mandating country of origin labeling. Using choice experiments and random parameter logit models, we examine German and British consumer willingness to pay (WTP) for American, Canadian, Argentinian, French, German and British beef, quality assurance seals, hormone-free beef production and a gourmet label. We also determine how consumer WTP for these food safety and quality attributes is affected by the extent to which consumers consider food safety issues (FSI). Results indicate that British consumers had the lowest WTP for beef from Argentina and German consumers had the lowest WTP for beef from Great Britain. The hormone-free label was the relatively most preferred label by consumers in both countries, and by those who considered FSI to affect their meat consumption patterns.