Miracle-dz/UniFAR-FTUs huggingface dataset:
Recognition of Histo-Blood Group Antigen-Like Carbohydrates in Lettuce by Human GII.4 Norovirus

ABSTRACT Human norovirus (HuNoV) genogroup II genotype 4 (GII.4) strains account for about 80% of the gastroenteritis outbreaks in the United States. Contaminated food is a major transmission vehicle for this virus. In humans, pigs, and oysters, histo-blood group antigens (HBGAs) act as attachment factors for HuNoVs. In lettuce, although the virus-like particles (VLPs) of a GII.4 HuNoV were found to bind to cell wall carbohydrates, the exact binding site has not been investigated. Here, we show the presence of HBGA-like carbohydrates in the cell wall of lettuce. The digestion of lettuce leaves with cell wall-degrading enzymes exposed more binding sites and significantly increased the level of binding of GII.4 HuNoV VLPs. Competition assays showed that both the HBGA monoclonal antibody, recognizing the H type, and plant lectins, recognizing α-l-fucose in the H type, effectively inhibited VLP binding to lettuce tissues. Lettuce cell wall components were isolated and their NoV VLP binding characteristics were tested by enzyme-linked immunosorbent assays. The binding was inhibited by pretreatment of the lettuce cell wall materials with α-1,2-fucosidase. Collectively, our results indicate that H-type HBGA-like carbohydrates exist in lettuce tissues and that GII.4 HuNoV VLPs can bind the exposed fucose moiety, possibly in the hemicellulose component of the cell wall. IMPORTANCE Salad crops and fruits are increasingly recognized as vehicles for human norovirus (HuNoV) transmission. A recent study showed that HuNoVs specifically bind to the carbohydrates of the lettuce cell wall. Histo-blood group antigens (HBGAs) are carbohydrates and are known as the attachment factors for HuNoV infection in humans. In this study, we show the presence of HBGA-like carbohydrates in lettuce, to which HuNoVs specifically bind. These results suggest that specifically bound HuNoVs cannot be removed by simple washing, which may allow viral transmission to consumers. Our findings provide new information needed for developing potential inhibitors to block binding and prevent contamination.
Peopling of the northern Tibetan Plateau

Abstract Early archaeological investigations on the Tibetan Plateau concluded that this harsh, high-elevation environment was successfully colonized around 30,000 years ago. Genetic studies have tended to support this view on the assumption that the uniquely evolved physiological capacities seen among modern Tibetan populations required long-term exposure to high-elevation selective pressures. Archaeological evidence amassed over the last decade suggests, however, that colonization leading to full-time occupation occurred much later. Seasonal foraging forays into high-elevation settings at c. 30 and 15 cal. ka appear to have been limited ‘adaptive radiations’ coincident, respectively, with the appearance of early and late Upper Palaeolithic adaptations in low-elevation source areas around the plateau. More permanent occupation of the plateau probably did not begin before c. 8200 cal. bp and may have been driven by ‘competitive exclusion’ of late Upper Palaeolithic foragers from low-elevation environments by emerging settled agricultural groups. The appearance of specialized epi-Palaeolithic blade and bladelet technologies on the high plateau, after 8200 cal. ka, may indicate ‘directional selection’ impacting on these new full-time residents. An ‘adaptive radiation’ of agriculturalists into the mid-elevations of the plateau, this time leading to year-round occupation, is again seen after 6000 cal. bp.
Construction and reification in nation building: The case of Yugoslavia fully explained?

The study of nations and ethnicities has been subject to recent trends, particularly, those denying substance to ethnicity and nation, but focusing on the way ethnicity and nation are socially constructed and ‘reified’ (constructivism–reificationism). In this article, this idea is tested on the Yugoslav case, where cases of reification are said to have been ‘arbitrary’. Such a position suggests that members of the Yugoslav federation went on their own ways because of ‘reification’ in the form of the republics and provinces. Although it is found that the republics and one province did enhance the process of national constitution, and although ‘ethnic entrepreneurs’ were active in the 1980s—a fact that is in line with a constructivist–reificationist theoretical position—there is one distinctive case that directly challenges such a position: Vojvodina did not opt for independence but, because of its Serb majority, it swiftly became integrated into Serbia. Moreover, the current article presents additional information to suggest that, although constructionist–reificationist approaches are relevant, they do not suffice to explain ‘nation’.
Impact of Tenofovir on Renal Function in HIV-Infected, Antiretroviral-Naive Patients

Objective:To better characterize the long-term effects of tenofovir on renal function in a large managed care organization. Methods:We performed a retrospective cohort analysis in Kaiser Permanente for years 2002 to 2005 comparing renal function among antiretroviral naïve patients initiating a tenofovir-containing regimen (964 patients) or tenofovir-sparing regimens (683 patients). We evaluated glomerular filtration rate (GFR, [Modification of Diet in Renal Disease equation]), serum creatinine, and the development of renal proximal tubular dysfunction. We report multivariable hazard ratios (HR, Cox modeling) and linear outcomes (repeated measures) with predictors retained if P < 0.10 (backward selection). Potential predictor variables included in multivariate models were age, sex, Black race, baseline laboratories (including CD4 count), history of diabetes mellitus, hypertension, malignancy, hepatitis, and concurrent medications. Results:Overall, tenofovir-exposed patients had a larger relative decline in GFR through 104 weeks (−7.6 mL/min/1.73 m2 relative to tenofovir-sparing, P < 0.001); the degree of the difference varied by baseline GFR, with the greatest effect seen in those patients with GFR greater than 80 mL/min/1.73 m2. Tenofovir-exposed patients had greater development of proximal tubular dysfunction over time (at 52 wk: HRadjusted = 1.95 [P = 0.01] and at 104 wk: HRadjusted = 5.23 [P = 0.0004]) and had greater risk of medication discontinuation (HRadjusted = 1.21, P = 0.02), especially as renal function worsened. Viral control and CD4 count changes were similar between the two groups. Conclusions:Tenofovir is associated with greater effect on decline in renal function and a higher risk of proximal tubular dysfunction in antiretroviral naïve patients initiating antiretroviral therapy.
Fast Link Adaptation for MIMO OFDM

We investigate link-quality metrics (LQMs) based on raw bit-error-rate, effective signal-to-interference-plus-noise ratio, and mutual information (MI) for the purpose of fast link adaptation (LA) in communication systems employing orthogonal frequency-division multiplexing and multiple-input-multiple-output (MIMO) antenna technology. From these LQMs, the packet error rate (PER) can be estimated and exploited to select the modulation and coding scheme (MCS) among a class of candidate MCSs that achieves the maximum throughput for the current channel state under a specified target PER objective. We propose a novel MI-based LQM and compare the PER-estimation accuracy obtained with this LQM with that resulting from using other LQMs by means of comprehensive Monte Carlo simulations. Search methods for the MCS in the class that is most suitable for a given channel state are presented. An algorithm for obtaining a practical upper bound on the throughput of any LA scheme is proposed. The investigated LQMs are applied to the IEEE 802.11n standard with a 2 × 2 MIMO configuration and practical channel estimation. The proposed MI-based LQM yields the highest PER estimation accuracy, and its throughput shows only 1.7 dB signal-to-noise-ratio (SNR) loss with respect to the upper bound but up to 9.5 dB SNR gain, compared to the MCS maximizing the throughput for the current noise variance.
Molecular Epidemiology of Panton-Valentine Leukocidin-Positive Staphylococcus aureus in Spain: Emergence of the USA300 Clone in an Autochthonous Population

ABSTRACT We characterized all of the Panton-Valentine leukocidin (PVL)-positive Staphylococcus aureus isolates collected between 2005 and 2008 in the Bilbao, Spain, area. For the first time, the USA300 clone is reported as predominant among PVL-positive clones in a European autochthonous population, requiring active monitoring of the incidence of USA300 in Spain and throughout Europe.
Treating hyperglycemia improves skeletal muscle protein metabolism in cancer patients after major surgery

Objective:Cancer and surgical stress interact to aggravate insulin resistance, protein catabolism, and glutamine depletion in skeletal muscle. We compared the effects of insulin-mediated euglycemia and moderate hyperglycemia on kinetics of protein and selected amino acids in skeletal muscle of female cancer patients after major surgery. Design:In each patient, a 24-hr period of insulin-mediated tight euglycemia (mean blood glucose, 5.8 ± 0.4 mmol/L) preceded or followed a 24-hr control period of moderate hyperglycemia (mean blood glucose, 9.6 ± 0.6 mmol/L) on the first and second day after surgery, in randomized order, according to a crossover experimental design. Setting:Intensive care unit, cancer hospital. Patients:Cancer patients after abdominal radical surgery combined with intraoperative radiation therapy. Interventions:Intensive (57 ± 11 units/24 hrs) and conventional (25 ± 5 units/24 hrs) insulin treatment during total parenteral nutrition. Measurements and Main Results:Muscle metabolism was assessed at the end of each 24-hr period of euglycemia and of hyperglycemia by leg arteriovenous catheterization with stable isotopic tracers. We found that euglycemia as compared with hyperglycemia was associated with higher (p < .05) fractional glucose uptake (16% ± 4% vs. 9% ± 3%); higher (p < .05) muscle protein synthesis and neutral net protein balance (−3 ± 3 vs. −11 ± 3 nmol phenylalanine·100 mL−1·min−1, respectively); lower (−52% ± 12%, p < .01) muscle nonprotein leucine disposal (an index of leucine oxidation) and higher (p < .05) plasma leucine concentrations; and higher (3.6 ± 1.7 times, p < .01) net de novo muscle glutamine synthesis and plasma glutamine concentrations (p < .05). Euglycemia was associated with higher (23% ± 7%, p < .05) plasma concentrations of arginine but did not affect either arginine release from muscle or plasma concentration and muscle flux of asymmetrical dimethylarginine. Rate of muscle proteolysis correlated (p < .05) with muscle release of asymmetrical dimethylarginine. Conclusions:Treating hyperglycemia improves skeletal muscle protein and amino acid metabolism in cancer patients after major surgery.
Collaborative Filtering with Generalized Laplacian Constraint via Overlapping Decomposition

Real-world data are seldom unstructured, yet traditional Matrix Factorization (MF) models, as one of the most powerful collaborative filtering approaches, generally rely on this assumption to recover the low-rank structures for recommendation. However, few of them are able to explicitly consider structured constraint with the underlying low-rank assumption to model complex user interests. To solve this problem, we propose a unified MF framework with generalized Laplacian constraint for collaborative filtering. We investigate the connection between the recently proposed Laplacian constraint and the classical normalized cut problem, and make it possible to extend the original non-overlapping prior, to capture the overlapping case via learning the decomposed multi-facet graphs. Experiments on realworld datasets demonstrate the effectiveness of the proposed method.
Competition and Diversification Effects in Supply Chains with Supplier Default Risk

We study the effects of disruption risk in a supply chain where one retailer deals with competing risky suppliers who may default during their production lead times. The suppliers, who compete for business with the retailer by setting wholesale prices, are leaders in a Stackelberg game with the retailer. The retailer, facing uncertain future demand, chooses order quantities while weighing the benefits of procuring from the cheapest supplier against the advantages of order diversification. For the model with two suppliers, we show that low supplier default correlations dampen competition among the suppliers, increasing the equilibrium wholesale prices. Therefore the retailer prefers suppliers with highly correlated default events, despite the loss of diversification benefits. In contrast, the suppliers and the channel prefer defaults that are negatively correlated. However, as the number of suppliers increases, our model predicts that the retailer may be able to take advantage of both competition and diversification.
Lactation and Progression to Type 2 Diabetes Mellitus After Gestational Diabetes Mellitus: A Prospective Cohort Study.

BACKGROUND Lactation improves glucose metabolism, but its role in preventing type 2 diabetes mellitus (DM) after gestational diabetes mellitus (GDM) remains uncertain. OBJECTIVE To evaluate lactation and the 2-year incidence of DM after GDM pregnancy. DESIGN Prospective, observational cohort of women with recent GDM. (ClinicalTrials.gov: NCT01967030). SETTING Integrated health care system. PARTICIPANTS 1035 women diagnosed with GDM who delivered singletons at 35 weeks' gestation or later and enrolled in the Study of Women, Infant Feeding and Type 2 Diabetes After GDM Pregnancy from 2008 to 2011. MEASUREMENTS Three in-person research examinations from 6 to 9 weeks after delivery (baseline) and annual follow-up for 2 years that included 2-hour, 75-g oral glucose tolerance testing; anthropometry; and interviews. Multivariable Weibull regression models evaluated independent associations of lactation measures with incident DM adjusted for potential confounders. RESULTS Of 1010 women without diabetes at baseline, 959 (95%) were evaluated up to 2 years later; 113 (11.8%) developed incident DM. There were graded inverse associations for lactation intensity at baseline with incident DM and adjusted hazard ratios of 0.64, 0.54, and 0.46 for mostly formula or mixed/inconsistent, mostly lactation, and exclusive lactation versus exclusive formula feeding, respectively (P trend = 0.016). Time-dependent lactation duration showed graded inverse associations with incident DM and adjusted hazard ratios of 0.55, 0.50, and 0.43 for greater than 2 to 5 months, greater than 5 to 10 months, and greater than 10 months, respectively, versus 0 to 2 months (P trend = 0.007). Weight change slightly attenuated hazard ratios. LIMITATION Randomized design is not feasible or desirable for clinical studies of lactation. CONCLUSION Higher lactation intensity and longer duration were independently associated with lower 2-year incidences of DM after GDM pregnancy. Lactation may prevent DM after GDM delivery. PRIMARY FUNDING SOURCE National Institute of Child Health and Human Development.
Hodgkin lymphoma patients in first remission: routine positron emission tomography/computerized tomography imaging is not superior to clinical follow‐up for patients with no residual mass

There is no consensus regarding optimal follow‐up mode for Hodgkin lymphoma (HL) patients that achieve complete remission following chemotherapy or combined chemo‐ and radiation therapy. Several studies demonstrated high sensitivity of positron emission tomography/computerized tomography (PET/CT) in detecting disease progression; however, these techniques are currently not recommended for routine follow‐up. This retrospective study conducted in two Israeli (N = 291) and one New Zealand academic centres (N = 77), compared a group of HL patients, followed‐up with routine imaging every 6 months during the first 2 years after achieving remission, once in the third year, with additional dedicated studies performed due to symptoms or physical findings (Group I) to a group of patients without residual masses who underwent clinically‐based surveillance with dedicated imaging upon relapse suspicion (Group II). Five‐year overall survival (OS) was 94% and median time to relapse was 8·6 months for both modes. Relapse rates in Groups I and II were 13% and 9%, respectively. During the first 3 years of follow‐up, 47·5 and 4·7 studies were performed per detected relapse in Groups I and II, respectively. The current study demonstrated no benefit in either progression‐free survival (PFS) or OS in HL patients followed by routine imaging versus clinical follow‐up. The cost was 10 times higher for routine imaging.
Sensing Urban Patterns with Antenna Mappings: The Case of Santiago, Chile

Mobile data has allowed us to sense urban dynamics at scales and granularities not known before, helping urban planners to cope with urban growth. A frequently used kind of dataset are Call Detail Records (CDR), used by telecommunication operators for billing purposes. Being an already extracted and processed dataset, it is inexpensive and reliable. A common assumption with respect to geography when working with CDR data is that the position of a device is the same as the Base Transceiver Station (BTS) it is connected to. Because the city is divided into a square grid, or by coverage zones approximated by Voronoi tessellations, CDR network events are assigned to corresponding areas according to BTS position. This geolocation may suffer from non negligible error in almost all cases. In this paper we propose “Antenna Virtual Placement” (AVP), a method to geolocate mobile devices according to their connections to BTS, based on decoupling antennas from its corresponding BTS according to its physical configuration (height, downtilt, and azimuth). We use AVP applied to CDR data as input for two different tasks: first, from an individual perspective, what places are meaningful for them? And second, from a global perspective, how to cluster city areas to understand land use using floating population flows? For both tasks we propose methods that complement or improve prior work in the literature. Our proposed methods are simple, yet not trivial, and work with daily CDR data from the biggest telecommunication operator in Chile. We evaluate them in Santiago, the capital of Chile, with data from working days from June 2015. We find that: (1) AVP improves city coverage of CDR data by geolocating devices to more city areas than using standard methods; (2) we find important places (home and work) for a 10% of the sample using just daily information, and recreate the population distribution as well as commuting trips; (3) the daily rhythms of floating population allow to cluster areas of the city, and explain them from a land use perspective by finding signature points of interest from crowdsourced geographical information. These results have implications for the design of applications based on CDR data like recommendation of places and routes, retail store placement, and estimation of transport effects from pollution alerts.
Smoking is associated with steatosis and severe fibrosis in chronic hepatitis C but not B

Objective. The results of retrospective studies suggest an association between smoking, insulin resistance, steatosis and fibrosis in patients with chronic hepatitis C (CHC); no data are available for chronic hepatitis B (CHB). The purpose of this study was to evaluate the relationship, if any, of such factors on liver fibrosis in a cohort of patients with CHB and CHC. Material and methods. The study prospectively included 271 consecutive patients with CHB (n=95) or CHC (n=176) who had undergone liver biopsies. Each patient completed a questionnaire on smoking habits; anthropometric measurements and laboratory examinations were carried out and histological lesions were recorded. Results. In CHC patients, severe fibrosis was independently associated with a higher body mass index (BMI) (OR: 1.180, 95% CI: 1.028–1.354; p=0.019), heavy smoking (OR: 3.923, 95% CI: 1.356–11.348; p=0.012), higher alanine aminotransferase (ALAT) levels (OR: 1.010, 95% CI: 1.003–1.017; p=0.005) and alkaline phosphatase (ALP) levels (OR: 1.016, 95% CI: 1.001–1.030; p=0.03) and presence of necroinflammation (OR: 11.165, 95% CI: 1.286–96.970; p=0.029). Moreover, steatosis was independently associated with high gamma-glutamyl transpeptidase (GGT) values, heavy smoking and presence of necroinflammation. In CHB patients, no association between smoking habits and fibrosis or steatosis was noted. Conclusions. Heavy smoking is associated with severe fibrosis in CHC but not CHB. Heavy smoking is also significantly associated with steatosis in CHC and this could be the link between smoking and fibrosis progression.
Effects of five natural gonadotropin-releasing hormones on cell suspensions of marine bivalve gonad: stimulation of gonial DNA synthesis.

Gonadotropin-releasing hormones (GnRH) constitute a family of neuropeptides which are important regulators of reproduction in vertebrates. The effect of mammalian GnRH (mGnRH), salmon GnRH, chicken GnRH-I, chicken GnRH-II, and lamprey GnRH-I on [3H]thymidine incorporation into DNA of dissociated gonadal cells of marine bivalves has been studied. The incorporation of [3H]thymidine is linear between 1.5 and 8 h of incubation. All five GnRHs significantly increased DNA synthesis in gonial cells of Crassostrea gigas. The maximal activation was about of 135-140% above control. The activation is dose dependent, over the range 10(-11) to 10(-6) M, but is modulated by the physiological condition of the cells and the stage of sexual maturity of the gonad. mGnRH has also a mitogenic effect in dissociated mantle cells of Mytilus edulis. The effect of mGnRH is blocked by a GnRH antagonist ([D-pGlu1,D-Phe2, D-Trp3,6]GnRH, 5 x 10(-6)M) in C. gigas as well as in M. edulis, suggesting that the GnRH action in the gonad is mediated by specific receptors for GnRH or GnRH-like peptides. The existence of GnRH-immunoreactive neurons and fibers in the cerebral and pedal ganglia of M. edulis was demonstrated by immunocytochemistry. They are located principally in the anterior internal area of the cerebral ganglia, close to the cerebral commissure and in the posterior part of the pedal ganglia. The presence of GnRH-responsive cells and GnRH-like immunoreactive material suggests that peptides of the GnRH-like family are present and functional in bivalve molluscs.
The time course of auditory perceptual learning: neurophysiological changes during speech‐sound training

HERE we report that training-associated changes in neural activity can precede behavioral learning. This finding suggests that speech-sound learning occurs at a pre-attentive level which can be measured neurophysiologically (in the absence of a behavioral response) to assess the efficacy of training. Children with biologically based perceptual learning deficits as well as people who wear cochlear implants or hearing aids undergo various forms of auditory training. The effectiveness of auditory training can be difficult to assess using behavioral methods because these populations are communicatively impaired and may have attention and/or cognitive deficits. Based on our findings, if neurophysiological changes are seen during auditory training, then the training method is effectively altering the neural representation of the speech/sounds and changes in behavior are likely to follow.