Miracle-dz/UniFAR-FTUs huggingface dataset:
Qualitative and Quantitative Analysis of the Binding of GII.4 Norovirus Variants onto Human Blood Group Antigens

ABSTRACT Noroviruses (NoVs) are one of the leading causes of gastroenteritis in children and adults. For the last 2 decades, genogroup II genotype 4 (GII.4) NoVs have been circulating worldwide. GII.4 NoVs can be divided into variants, and since 2002 they have circulated in the population before being replaced every 2 or 3 years, which raises questions about the role of their histo-blood group antigen (HBGA) ligands in their evolution. To shed light on these questions, we performed an analysis of the interaction between representative GII.4 variants and HBGAs, and we determined the role of selected amino acids in the binding profiles. By mutagenesis, we showed that there was a strict structural requirement for the amino acids, directly implicated in interactions with HBGAs. However, the ablation of the threonine residue at position 395 (ΔT395), an epidemiological feature of the post-2002 variants, was not deleterious to the binding of the virus-like particle (VLP) to the H antigen, while binding to A and B antigens was severely hampered. Nevertheless, the ΔT395 VLPs gained the capacity to bind to the Lewis x and sialyl-Lewis x antigens in comparison with the wild-type VLP, demonstrating that amino acid residues outside the HBGA binding site can modify the binding properties of NoVs. We also analyzed the attachment of baculovirus-expressed VLPs from six variants (Bristol, US95/96, Hunter, Yerseke, Den Haag, and Osaka) that were isolated from 1987 to 2007 to phenotyped saliva samples and synthetic HBGAs. We showed that the six variants could all attach to saliva of secretors irrespective of the ABO phenotype and to oligosaccharides characteristic of the secretor phenotype. Interestingly, Den Haag and Osaka variants additionally bound to carbohydrates present in the saliva of Lewis-positive nonsecretors. The carbohydrate binding profile and the genetic and mutagenesis analysis suggested that GII.4 binding to Lewis x and sialyl-Lewis x antigens might be a by-product of the genetic variation of the amino acids located in the vicinity of the binding site. Analysis of the binding properties for the six variants by surface plasmon resonance showed that only post-2002 variants (i.e., Hunter, Yerseke, Den Haag, and Osaka) presented strong binding to A and B antigens, suggesting that the GII.4 evolution could be related to an increased affinity for HBGAs for the post-2002 variants. The combination of increased affinity for ABH antigens and of a newly acquired ability to recognize glycans from Lewis-positive nonsecretors could have contributed to the epidemiological importance of strains such as the Den Haag GII.4 subtype.
A Joint EOQ Model for supplier and retailer with deteriorating items

The paper studies the joint inventory model between supplier and retailer relying on mutual cooperation. Unlike other studies, the deteriorated rate and partial back-ordering are consistent with assumptions for dealing with more general cases. Since it is difficult to solve this problem directly, we derived the sufficient and necessary conditions in the planning horizon, and proposed a procedure to find the optimal solution. Numerical examples and sensitivity analyses are also provided to illustrate the solution procedure. The results reveal that the extensions of the model provide a wider and reasonable situation in practice, and that they also reduce the total cost.
Train the Machine with What It Can Learn—Corpus Selection for SMT

Statistical machine translation relies heavily on available parallel corpora, but SMT may not have the ability or intelligence to make full use of the training set. Instead of collecting more and more parallel training corpora, this paper aims to improve SMT performance by exploiting the full potential of existing parallel corpora. We first identify literally translated sentence pairs via lexical and grammatical compatibility, and then use these data to train SMT models. One experiment indicates that larger training corpora do not always lead to higher decoding performance when the added data are not literal translations. And another experiment shows that properly enlarging the contribution of literal translation can improve SMT performance significantly.
Elgot Algebras: (Extended Abstract)

Iterative algebras, i. e. , algebras A in which flat recursive equations e have unique solutions e^@? , are generalized to Elgot algebras, where a choice [email protected]? e^@? of solutions of all such equations e is specified. This specification satisfies two simple and well motivated axioms: functoriality (stating that solutions are ''uniform'') and compositionality (stating how to perform simultaneous recursion). These two axioms stem canonically from Elgot's iterative theories: We prove that the category of Elgot algebras is the Eilenberg-Moore category of the free iterative monad.
University T-cell number and subtype influence the disease course of primary chronic lymphocytic leukaemia xenografts in alymphoid mice

Chronic lymphocytic leukaemia (CLL) cells require microenvironmental support for their proliferation. This can be recapitulated in highly immunocompromised hosts in the presence of T cells and other supporting cells. Current primary CLL xenograft models suffer from limited duration of tumour cell engraftment coupled with gradual T-cell outgrowth. Thus, a greater understanding of the interaction between CLL and T cells could improve their utility. In this study, using two distinct mouse xenograft models, we investigated whether xenografts recapitulate CLL biology, including natural environmental interactions with B-cellreceptorsand T cells,and whethermanipulation of autologous T cells can expand the duration of CLL engraftment. We observed that primary CLL xenografts recapitulated both the tumour phenotype and T-cell repertoire observed in patients and that engraftment was significantly shorter for progressive tumours. A reduction in the number of patient T cells that were injected into the mice to 2-5% of the initial number or specific depletion of CD8 + cells extended the limited xenograft duration of progressive cases to that characteristic of indolent disease. We conclude that manipulation of T cells can enhance current CLL xenograft models and thus expand their utility for investigation of tumour biology and pre-clinical drug assessment. cells, T cells and other microenvironmental factors, and of the impact of this interaction on disease progression, subclonal diversity and treatment response, would direct the identification of novel treatments. Also, patient-relevant in vivo models of sufficient duration that are able to recapitulate the subclonal complexity of CLL are an essential component of preclinical drug assessment and can inform tailored treatment regimens. Results This work provides an in-depth analysis of T cells in primary CLL xenografts and describes a simple adaptation of current models that enables long-term analysis of CLL progression. The authors show, for the first time, that T-cell numbers affect the course of CLL xenografts in alymphoid mice. Specifically, minimisation of T cells, particularly of the CD8 + subset, in aggressive samples extended graft duration to that of indolent (non-aggressive) xenografts. The xenograft models retained several biological properties of primary leukaemias, including disease course, T-cell repertoire and microenvironmental interactions (B-cell receptor signalling and T-cell engagement). All these observations were evident in both of the xenograft models assessed, i.e. CLL xenografts generated by injection of either allogeneic umbilical-cord blood-derived cells or allogeneic monocytes.
J‐refocused coherence transfer spectroscopic imaging at 7 T in human brain

Short echo spectroscopy is commonly used to minimize signal modulation due to J‐evolution of the cerebral amino acids. However, short echo acquisitions suffer from high sensitivity to macromolecules which make accurate baseline determination difficult. In this report, we describe implementation at 7 T of a double echo J‐refocused coherence transfer sequence at echo time (TE) of 34 msec to minimize J‐modulation of amino acids while also decreasing interfering macromolecule signals. Simulation of the pulse sequence at 7 T shows excellent resolution of glutamate, glutamine, and N‐acetyl aspartate. B1 sufficiency at 7 T for the double echo acquisition is achieved using a transceiver array with radiofrequency (RF) shimming. Using an alternate RF distribution to minimize receiver phase cancellation in the transceiver, accurate phase determination for the coherence transfer is achieved with rapid single scan calibration. This method is demonstrated in spectroscopic imaging mode with n = 5 healthy volunteers resulting in metabolite values consistent with literature and in a patient with epilepsy. Magn Reson Med, 2010. © 2010 Wiley‐Liss, Inc.
Sleep duration, nightshift work, and the timing of meals and urinary levels of 8-isoprostane and 6-sulfatoxymelatonin in Japanese women

ABSTRACT It has been hypothesized that disruption of circadian rhythms affects human health. Shift work and sleep deprivation are thought to disrupt the normal light–dark cycle, although the disruption due to shiftwork may be dependent on sleep deprivation. Both conditions have been suggested to be associated with an increased risk of cardiometabolic disorders. Non-photic environmental factors, such as the timing of eating, are also thought to regulate circadian rhythm and thus, may have effects on health, but the evidence from human studies is scarce. Oxidative stress is a risk factor of cardiometabolic disorders. Some laboratory studies suggest an involvement of circadian clock genes in the regulation of the redox system. The present study aimed to examine the association of sleeping habits, nightshift work, and the timing of meals with urinary levels of 8-isoprostane, a marker of oxidative stress, and 6-sulfatoxymelatonin, the principal metabolite of melatonin. Study subjects were 542 women who had previously attended a breast cancer mass screening in a community in Japan. Information on bedtimes and wake-up times, history of nightshift work, and the timing of meals was obtained by a self-administered questionnaire. The 8-isoprostane and 6-sulfatoxymelatonin were measured using the first morning void of urine and expressed per mg of creatinine. The geometric mean of 8-isoprostane levels was 12.1% higher in women with ≤6 hours of sleep than that in those with >8 hours of sleep on weekdays, and longer sleep duration on weekdays was significantly associated with lower urinary levels of 8-isoprostane after controlling for covariates (p for trend = 0.04). Women who were currently working the nightshift had a 33.3% higher geometric mean of 8-isoprostane levels than those who were not working nightshift (p = 0.03). Urinary 6-sulfatoxymelatonin levels were unrelated to sleep habits or nightshift work. Women who ate breakfast at irregular times had a 19.8% higher geometric mean of 8-isoprostane levels than those who ate breakfast at a regular time or who did not eat (p = 0.02). Women who ate nighttime snacks at irregular times had a 16.2% higher geometric mean of 8-isoprostane levels than those who did not eat nighttime snacks or who ate nighttime snacks at a regular time (p = 0.003). Among women who ate dinner at a regular time, earlier times for dinner were associated with higher 8-isoprostane and 6-sulfatoxymelatonin levels (p values for trends were 0.01 and 0.02, respectively). However, the times of dinner and nighttime snack are overlapping, and the time of last meal of the day was not associated with 8-isoprostane and 6-sulfatoxymelatonin levels. The time of breakfast or lunch was not associated with these biomarkers among women who ate the meal at regular times. Disturbing the rhythmicity of daily life may be associated with oxidative stress.
Addressing biological circuit simulation accuracy: Reachability for parameter identification and initial conditions

Accurate simulation of biological networks is difficult not only due to the computational cost associated with large-scale systems simulation, but also due to the inherent limitations of mathematical models. We address two components to improve biological circuit simulation accuracy: 1) feasible initial conditions, and 2) identification of critical yet unknown model parameters. For those parameters that may not be available from experimental data, we incorporate reachability analysis to enhance our optimization/simulation framework and estimate those parameters that are capable of creating behaviors consistent with known experimental data. We apply these techniques to a biological circuit model of tryptophan biosynthesis in E. coli, and quantify the improvement in simulation accuracy when reachability analysis is used.
Community Based Maternal and Child Health Nutrition Project, Uttar Pradesh: An Innovative Strategy Focusing on “At Risk” Families

Research Question: Use of community based volunteers, frequently reaching and counseling a selected group of prioritized families, can make a substantial difference in improving maternal and child care practices and in reducing child undernutrition. Setting: Program Rural Uttar Pradesh, India. Study Design: A comparison of baseline and endline surveys following 4 years of community based project intervention Participants: “At risk” undernutrition families comprising mothers of under twos, newlyweds, and severely undernourished children below 6 years. Intervention: Mapping and counseling of “at risk” families. Measuring impact on maternal-child care practices, underweight status. Results: Trained community mobilizers identified and counseled selected “at risk” families. Following 4 years of implementation in 907 villages of 8 blocks of four districts, significant improvement was noted in practices of early initiation of breastfeeding, feeding colostrum, timely introduction of complementary feeding, and washing the hands after defecation. Percentage of mothers exclusively breastfeeding at 6 months was only 2.1% with 78% receiving prelacteal feeds. A small increase in normal and mild malnutrition and a significant reduction of 43% in severe malnutrition was noted. Conclusion: Frequently counseling by accredited social health activists by focusing on selected defined “at risk” families of under twos and those with severe malnourished children could result in increasing acceptability of correct child health, feeding, and care practices and in contributing to improving nutritional status scenario.
Vitamin D Status in Patients with Recurrent Kidney Stones

Data regarding the prevalence of 25-hydroxyvitamin D (25(OH)D) insufficiency in patients with nephrolithiasis, and the effects of vitamin D supplementation on parathyroid hormone (PTH) are few and conflicting. In this article, we examined the prevalence of vitamin D insufficiency and deficiency in 236 recurrent kidney stone formers and the correlation of vitamin D levels with other parameters of stone formation. The prevalent stone composition was calcium oxalate (80.4%) and uric acid (16.45%). One third of stone formers had vitamin D insufficiency and a quarter of them high PTH levels (PTH >7.5 pmol/l) with normal serum (total and ionized) calcium values. Predictor of high PTH was low 25(OH)D level (r = 0.989, r2 = 0.977, p < 0.001). Stone formers with hypercalciuria had higher 25(OH)D values (72.26 ± 4.21 vs. 59.29 ± 1.76, p = 0.0013) compared to stone formers with urine calcium within normal ranges. Further studies are needed in order to better define the consequences of vitamin D insufficiency and to evaluate the impact of the therapeutic interventions in this cohort.
Lipid-lowering medication use and aggression scores in women: a report from the NHLBI-sponsored WISE study.

AIM The aim of this study was to examine the association between the use of lipid-lowering medication and aggressive responding, hostility, cynicism, and depression scores in women undergoing coronary angiography. METHODS The cohort included 498 women from the National Heart, Lung and Blood Institute (NHLBI)-sponsored Women's Ischemia Syndrome Evaluation (WISE) study. WISE is a four-center study of women with chest pain who underwent quantitative coronary angiography for suspected myocardial ischemia. The psychosocial indices included the Cook Medley Hostility questionnaire, measuring aggression, hostility, and cynicism, and the Beck Depression Inventory (BDI). RESULTS Compared to those not on lipid-lowering medication, women receiving lipid-lowering pharmacotherapy were older (62 vs. 55 years, p < 0.001) and had more hypertension, dyslipidemia, diabetes, and coronary artery disease (CAD, defined as > or =50% stenoses in at least one epicardial artery) (all p < 0.003). Women on lipid-lowering medication had higher aggressive responding scores than those not on medication, 3.0 +/- 1.8 vs. 2.7 +/- 1.7, respectively (age-adjusted p < 0.003). This association persisted after adjustment for coronary risk factors, education, and extent of angiographic disease (CAD) (p < 0.005), and after exclusion of women using psychotropic medications (p < 0.001). Hostility, cynicism, and depression scores did not differ by medication use.
Adoption of travel information in user-generated content on social media: the moderating effect of social presence

Travel patterns have gradually changed from group travel to individual travel. An increasing number of people acquire travel information through various types of media. One of the alternative information sources is social media, which enables users to exchange information among members. However, one of the characteristics of social media is information sharing, not information search, which involves both giving (i.e. posting) and taking (i.e. selective reading, forwarding, replying, linking, and liking) information. Compared to the ‘giving’ side of information-sharing research, less effort has been spent on the ‘taking’ side of information research. Therefore, we investigate travel information adoption in social media as well as how individuals communicate with each other. We use the elaboration likelihood model, which measures the impact of central (e.g. argument quality) and peripheral (e.g. credibility) cues on traveller information-sharing behaviour corresponding with social presence on social media. The results of an empirical analysis of 527 respondents, who were experienced in travel information adoption via social media, were examined. Our findings revealed that argument quality had a positive effect on perceived usefulness and source credibility positively affected perceived usefulness and social relationships. Perceived usefulness had a significant positive effect on social relationships. Both perceived usefulness and social relationships affected travel information adoption. Lastly, the levels of argument quality and source credibility perceived by social media members were found to differ according to the level of social presence.
Longitudinal Assessment of Self- and Informant-Subjective Cognitive Complaints in a Sample of Healthy Late-Middle Aged Adults Enriched with a Family History of Alzheimer’s Disease

Abstract Objectives: The purpose of this study was to investigate the longitudinal trajectory of self- and informant-subjective cognitive complaints (SCC), and to determine if SCC predict longitudinal changes in objective measures (OM) of cognitive function. Methods: The study included healthy and cognitively normal late middle-aged adults enriched with a family history of AD who were evaluated at up to three visits over a 4-year period. At each visit (Visit 1–3), self- and informant-SCC and OM were evaluated. Linear mixed models were used to determine if the longitudinal rate of change of self- and informant-SCC were associated with demographic variables, depressive symptoms, family history (FH), and apolipoprotein epsilon 4 (APOE4) status. The same modeling approach was used to examine the effect of Visit 1 SCC on longitudinal cognitive change after controlling for the same variables. Results: At Visit 1, more self-SCC were associated with fewer years of education and more depressive symptoms. SCC were also associated with poorer performance on cognitive measures, such that more self-SCC at Visit 1 were associated with poorer performance on memory and executive functioning measures at Visit 1, while more informant-SCC were associated with faster rate of longitudinal decline on a measure of episodic learning and memory. FH and APOE4 status were not associated with SCC. Discussion: Self- and informant-SCC showed an association with OM, albeit over different time frames in our late middle-aged sample. Additional longitudinal follow-up will likely assist in further clarifying these relationships as our sample ages and more pronounced cognitive changes eventually emerge. (JINS, 2017, 23, 617–626)
On the Pseudospectra of Matrix Polynomials

The pseudospectra of a matrix polynomial $P(\lambda)$ are sets of complex numbers that are eigenvalues of matrix polynomials which are near to $P(\lambda)$; i.e., their coefficients are within some fixed magnitude of the coefficients of $P(\lambda)$. Pseudospectra provide important insights into the sensitivity of eigenvalues under perturbations and have several applications. First, qualitative properties concerning boundedness and connected components of pseudospectra are obtained. Then an accurate continuation algorithm for the numerical determination of the boundary of pseudospectra of matrix polynomials is devised and illustrated. This algorithm is based on a prediction-correction scheme.
Using Recipient’s Middle Hepatic Vein for Drainage of the Right Paramedian Sector in Right Liver Graft

Background. Congestion in the right paramedian sector of a right liver graft without a middle hepatic vein (MHV) may lead to graft dysfunction. To solve this problem, we have developed a technique for reconstructing the MHV tributaries of the right liver grafts by using the preserved recipient’s native MHV trunk. Methods. Between 2005 and 2007, among 34 right liver graft liver transplant patients with significant MHV tributaries (>5 mm in diameter), 21 patients underwent right liver graft living-donor liver transplantation: draining MHV tributaries with recipient’s native MHV trunk. We evaluated the patency of the reconstructed MHV tributaries, graft regeneration, and graft survival. Results. The 3-month patency rates of the reconstructed V8 and V5 were 92% and 76%, respectively. The 1-year survival rate and the regeneration index of the right paramedian sector 6 months after transplantation were higher in patients with reconstructed MHV tributaries than that for patients without reconstructed MHV tributaries. Conclusion. The use of the recipient’s MHV trunk for the reconstruction of the MHV tributaries of the right liver grafts is considered to be a valuable and a feasible strategy in right liver graft living-donor liver transplantation.
SAR Polarimetry to Observe Oil Spills

A study on sea oil spill observation by means of polarimetric synthetic aperture radar (SAR) data is accomplished. It is based on the use of a polarimetric constant false alarm rate filter to detect dark patches over SAR images. Then, the target decomposition theorem is exploited to distinguish oil spills and look-alikes. Experiments are conducted on polarimetric SAR data acquired during the SIR-C/X-SAR mission on October 1994. The data were processed and calibrated at the Jet Propulsion Laboratory, National Aeronautics and Space Administration. Results show that the new polarimetric approach is able to assist classification