Miracle-dz/UniFAR-FTUs huggingface dataset:
An Amino Acid in the Stalk Domain of N1 Neuraminidase Is Critical for Enzymatic Activity

ABSTRACT Neuraminidase (NA) is a sialidase expressed on the surface of influenza A viruses that releases progeny viruses from the surface of infected cells and prevents viruses becoming trapped in mucus. It is a homotetramer, with each monomer consisting of a transmembrane region, a stalk, and a globular head with sialidase activity. We recently characterized two swine viruses of the pandemic H1N1 lineage, A/swine/Virginia/1814-1/2012 (pH1N1low-1) and A/swine/Virginia/1814-2/2012 (pH1N1low-2), with almost undetectable NA enzymatic activity compared to that of the highly homologous A/swine/Pennsylvania/2436/2012 (pH1N1-1) and A/swine/Minnesota/2499/2012 (pH1N1-2) viruses. pH1N1-1 transmitted to aerosol contact ferrets, but pH1N1low-1 did not. The aim of this study was to identify the molecular determinants associated with low NA activity as potential markers of aerosol transmission. We identified the shared unique substitutions M19V, A232V, D248N, and I436V (N1 numbering) in pH1N1low-1 and pH1N1low-2. pH1N1low-1 also had the unique Y66D substitution in the stalk domain, where 66Y was highly conserved in N1 NAs. Restoration of 66Y was critical for the NA activity of pH1N1low-1 NA, although 19M or 248D in conjunction with 66Y was required to recover the level of activity to that of pH1N1 viruses. Studies of NA stability and molecular modeling revealed that 66Y likely stabilized the NA homotetramer. Therefore, 66Y in the stalk domain of N1 NA was critical for the stability of the NA tetramer and, subsequently, for NA enzymatic activity. IMPORTANCE Neuraminidase (NA) is a sialidase that is one of the major surface glycoproteins of influenza A viruses and the target for the influenza drugs oseltamivir and zanamivir. NA is important as it releases progeny viruses from the surface of infected cells and prevents viruses becoming trapped in mucus. Mutations in the globular head domain that decrease enzymatic activity but confer resistance to NA inhibitors have been characterized; however, the importance of specific mutations in the stalk domain is unknown. We identified 66Y (N1 numbering), a highly conserved amino acid that was critical for the stability of the NA tetramer and, subsequently, for NA enzymatic activity.
diffloop: a computational framework for identifying and analyzing differential DNA loops from sequencing data

The three-dimensional architecture of DNA within the nucleus is a key determinant of interactions between genes, regulatory elements, and transcriptional machinery. As a result, differences in loop structure are associated with differences in gene expression and cell state. Here, we introduce diffloop, an R/Bioconductor package for identifying differential DNA looping between samples. The package additionally provides a suite of functions for the quality control, statistical testing, annotation and visualization of DNA loops. We demonstrate this functionality by detecting differences in DNA loops between ENCODE ChIA-PET datasets and relate looping to differences in epigenetic state and gene expression.
Connecting the Edges: A Universal, Mobile-Centric, and Opportunistic Communications Architecture

The Internet has crossed new frontiers with access to it getting faster and cheaper. Considering that the architectural foundations of today's Internet were laid more than three decades ago, the Internet has done remarkably well until today coping with the growing demand. However, the future Internet architecture is expected to support not only the ever growing number of users and devices, but also a diverse set of new applications and services. Departing from the traditional host-centric access paradigm, where access to a desired content is mapped to its location, an information-centric model enables the association of access to a desired content with the content itself, irrespective of the location where it is being held. UMOBILE tailors the information-centric communication model to meet the requirements of opportunistic communications, integrating those connectivity approaches into a single architecture. By pushing services near the edge of the network, such an architecture can pervasively operate in any networking environment and allows for the development of innovative applications, providing access to data independent of the level of end-to-end connectivity availability.
Context of Use: The Final Frontier in the Practice of User-Centered Design?

Abstract User-centered design (UCD) practitioners in industrial context are often faced with multilevel factors that hinder their effort to involve users in the context of use, and so meet one of the core UCD principles. Seen the heterogeneous and dynamic context of mobile system use, applying this principle becomes more challenging. Based on in-depth interviews with various mobile practitioners in Finland and the Netherlands, we explore the core factors that affect UCD practitioners in meeting this challenge. Our findings confirm the impact of the professional–client relationship as a key factor that inhibits the involvement of users. Novelty aspects, e.g. practitioners’ unfamiliarity with the users and the perceived innovativeness of the designed system, largely explain the involvement of users in situ. Interestingly, these conditions are not idiosyncratic to mobile computing. We discuss the contextual factors’ implications on UCD and emphasize alternative strategies that support practitioners in their effort to involve users.
The characterization of dislocation loops in neutron irradiated zirconium

Abstract Dislocation loops formed in zirconium after neutron irradiation and subsequent annealing between 450° and 500°C are not pure edge loops. A general method for analysing such loops by transmission electron microscopy is discussed briefly and a technique for determining the loop plane normal to within ± 5° is described. The Burgers vectors of the loops in annealed irradiated zirconium are found to be of the type a/3 〈1120〉 while the loop plane normal is tilted by up to 35° towards the adjacent {2021} pole. Two thirds of the loops present after annealing at 490°C are vacancy loops, while the remainder are interstitial. Zirconium irradiated at 300°C and not annealed also shows only loops with a/3 〈1120〉 Burgers vectors. The significance of these results in interpreting previously reported irradiation growth data is briefly discussed.
Revealing prediction uncertainty in artificial neural network based reconstruction of missing data in stochastic process records utilizing extreme learning machines

An artificial neural network (ANN) based approach is developed for reconstructing gappy stochastic process records. ANNs can be utilized to capture stochastic patterns in process records in an “average sense”, however individual predictions of missing data can be unreliable. This is both due to the inherent uncertainty introduced by the stochastic process itself, and to uncertainties relating to ANN parameters. Here, instead of relying on single network predictions, an ensemble of networks are trained on the data, the outputs of which are used to estimate statistical distributions for random variables which replace deterministic predictions. In order for this approach to be computationally viable, single-layer feed-forward networks, initialized with random weights are trained via fast, non-iterative least-squares fitting, popularly known as Extreme Learning Machine (ELM) networks. Examples are provided with real data to demonstrate both network prediction effectiveness and uncertainties revealed by varying network parameters.
Changes in Distress Measured by the Distress Thermometer as Reported by Patients in Home Palliative Care in Germany

Aim: To identify changes in distress as reported by patients in a home palliative care program over a 2-week period. Methods: Prospective study in West Germany with consecutive patients cared for at home by a palliative care specialty team. Exclusion criteria were patients under 18 years of age, mentally or physically not able to complete the assessment questionnaires, or unable to comprehend German language. Distress was measured using the distress thermometer (DT); sociodemographic and medical data were collected from the patients’ records. Results: One hundred three participated in the study (response rate of 69%) and 39 participants completed DT at 2-week follow-up (T1; response rate = 38%; mean age = 67; female = 54.4%; married = 67%; living home with relatives = 60.2%; oncological condition = 91.3%; Karnofsky performance status [KPS] 0-40 = 18.9%, KPS 50-70 = 70.3%, KPS >80 = 10.8%). The mean DT score at the first visit (T0) was 5.9 (2.3), with 82.1% of the participants scoring DT ≥5. At the 2-week follow-up (T1), mean DT score was 5.0 (2.0), with 64.1% scoring DT ≥5, showing a statistically significant difference between T0 and T1. Comparing the single scores at T0 and T1 of each participant, the difference in DT scores was −0.9 (2.27). Conclusion: The DT is a useful tool for screening severity and changes in psychological distress as well as sources of distress. The DT detected change in self-reported distress within a short treatment period, indicating success or failure of the palliative care treatment approaches.
Bike Share Demand Prediction using RandomForests

Bike Sharing System is an emerging mode of transport in the world and most of the developing countries are on the path of following the western model of Bike Sharing Systems.In India some entrepreneurs have tried to setup a bike share system and have failed in the past as they have failed to use data analytics properly. There is a possibility that bike stations can be full or empty when a traveler comes to the station. Thus to predict the use of such system can be helpful for the users to plan their travels and also for the entrepreneurs to setup the system properly. This paper presents different ways to predict the number of bikes that can be rented in such a system, for case study purpose we have used a public data set. The predictions are made for every hour of a day. Keywords—bike sharing system, randomforests,prediction
Data embedding in scalable coded video

In this paper, a self-cancelling method is proposed to embed data into multiple layers of a spatial scalable coded video. Correlation of prediction mode from multiple layers are analyzed and exploited to offset the distortion introduced at the base layer(BL) when embedding data at the enhancement layer (EL). Specifically, in the base layer, the prediction modes are divided into two groups, where one group encodes '0' while another encodes '1'. Data embedding in the enhancement layer is designed to compensate the errors introduced in the base layer. Experiment results show that the scalable coded video can effectively carry additional payload in multiple layers while maintaining the video quality and bit rate. In the best case scenario, when 104,141 bits are embedded into the BasketballDrive (BL: 1280 × 720 and EL: 1920 × 1080) video sequence, the bit rate is slightly increased while insignificant degradation in perceptual quality is observed.
Tumour lysis syndrome and acute kidney injury in high‐risk haematology patients in the rasburicase era. A prospective multicentre study from the Groupe de Recherche en Réanimation Respiratoire et Onco‐Hématologique

In tumour lysis syndrome (TLS), metabolic alterations caused by the destruction of malignant cells manifest as laboratory abnormalities with (clinical TLS) or without (laboratory TLS) organ dysfunction. This prospective multicentre cohort study included 153 consecutive patients with malignancies at high risk for TLS (median age 54 years (interquartile range, 38–66). Underlying malignancies were acute leukaemia (58%), aggressive non‐Hodgkin lymphoma (29.5%), and Burkitt leukaemia/lymphoma (12.5%). Laboratory TLS developed in 17 (11.1%) patients and clinical TLS with acute kidney injury (AKI) in 30 (19.6%) patients. After adjustment for confounders, admission phosphates level (odds ratio [OR] per mmol/l, 5.3; 95% confidence interval [95% CI], 1.5–18.3), lactic dehydrogenase (OR per x normal, 1.1; 95%CI, 1.005–1.25), and disseminated intravascular coagulation (OR, 4.1; 95%CI, 1.4–12.3) were associated with clinical TLS; and TLS was associated with day‐90 mortality (OR, 2.45; 95%CI, 1.09–5.50; P = 0.03). In this study, TLS occurred in 30.7% of high‐risk patients. One third of all patients experienced AKI, for which TLS was an independent risk factor. TLS was associated with increased mortality, indicating a need for interventional studies aimed at decreasing early TLS‐related deaths in this setting.
Broadband Electromagnetic Dipole Resonance by the Coupling Effect of Multiple Dielectric Nanocylinders

Broadband resonant scattering in a visible region that can be obtained by coupled multiple silicon nanocylinders. For a single high refractive index silicon nanocylinder, the electric dipole and magnetic dipole resonances can be observed. By constructing a silicon nanocylinder dimer, the interaction between the particles plays an important role in broadband scattering. Interestingly, due to magnetic-magnetic dipole interaction, a splitting phenomenon of magnetic resonance mode is revealed. A new magnetic resonant mode emerges at a longer wavelength in dimer and trimer by changing the diameter of one nanocylinder in dimer or trimer, and the gap size between nanocylinders. The scattering bandwidth can further increase with the effect of substrate, which is attributed to the extension of resonant mode into substrate. The broadband optical response can be revealed by the calculated scattering resonant spectra and the spatial electromagnetic field distributions. Furthermore, the transmission of periodic nanocylinder structure, including single nanocylinder and dimer, is demonstrated. By decreasing the gap between nanocylinders in dimer for periodic array structure, a new electric resonant mode occurs. These results can provide a guideline to realize broadband resonant optical elements.
Ten Years of External Quality Control for Cellular Therapy Products in France

The French Health Products Agency (Afssaps) was created in 1998 within a national context of strengthened health monitoring and control. The Afssaps evaluates the safety, the efficacy and the quality of health products. The law 96-452 of May, 28th 1996 and the law 98-535 of July 1st 1998, published in the “Public Health Regulation” have established rules for the use of cell therapy products. The Laboratories and Controls Department (DLC) is in charge of external quality control of cell therapy products since 1999. In this French regular context and because haematopoietic cells are the main cellular products used in routine in Europe (Gratwohl et al., 2006) as they are in the US (Read & Sullivan, 2004), control was first developed for these. Haematopoietic stem cells are populations of primitive multipotent cells capable of self-renewal as well as differentiation and maturation into all haematopoietic lineages. They are found in small numbers in the bone marrow, in the mononuclear cell fraction of circulating blood (peripheral blood stem cells or PBSC) and in umbilical cord blood (umbilical or placental stem cells). For the twenty-five last years, important progresses have been obtained in the treatment of onco-hematology diseases, especially with the advent of therapeutic intensification following by a graft of haematopoietic stem cells (Copelan, 2006). The infused haematopoietic progenitor cell populations can originate from the recipient (autologous) or from another individual (allogeneic) but until now, most of the grafts are made in an autologous context. Also, 85% of the PBSC samples received for the control at Afssaps had an autologous status. Considering peripheral blood stem cells, the major criteria retained for clinical decision is the positive cell number for the CD34 antigen (Bender et al., 1993; Allan et al., 2002; Weaver et al., 1995). However, as there is no target value for CD34+ cells according to the nature of the product, there was a strong need for efficient methods to guarantee the CD34 value and thus make reliable the clinical decision. Numeration by flow cytometry method is currently
Evaluating the Long-Term Durability of Externally Bonded FRP via Field Assessments

AbstractFiber-reinforced polymer composites (FRP) are an attractive repair option for reinforced concrete structures, but whereas laboratory durability tests have indicated that FRP generally performs well in many environments, their long-term performance in field environments is not well understood. This case study describes an effort to collect in situ data about the FRP used to repair a concrete arch bridge 8 years after the FRP was originally placed. On-site assessment efforts included inspection for voids between the concrete and FRP using acoustic sounding and thermographic imaging and pull-off tests to check the bond strength. Large debonded regions of FRP were also cut from the structure and tested in tension in the laboratory. Results generally pointed to some level deterioration. Many new voids were found, existing voids had grown, pull-off testing showed weaker bond strengths, and the tensile strengths were quite low compared to design values. However, a lack of initial data make it difficult t.
Is there any association between retroperitoneal lymphadenectomy and survival benefit in ovarian clear cell carcinoma patients?

BACKGROUND To estimate the survival impact of systemic retroperitoneal lymphadenectomy in patients diagnosed with International Federation of Gynecology and Obstetrics pTI-IIb clear cell carcinoma of the ovary (CCC). PATIENTS AND METHODS Demographic and clinicopathologic data were obtained from the Tokai Ovarian Tumor Study Group between 1986 and 2006. Survival curves were calculated using the Kaplan-Meier method. Differences in survival rates were analyzed using the log-rank test. RESULTS A total of 205 patients had clinical pTI-IIb CCC (median age: 52 years, range: 30-75). One hundred and four (50.7%) patients underwent systemic retroperitoneal lymphadenectomy. Lymphadenectomy was not associated with improved disease-free and overall survival in all patients (P = 0.353 and P = 0.645, respectively). Moreover, lymphadenectomy did not improve the overall survival in those with pTIc CCC (P = 0.433). Similarly, on univariate analysis, age, volume of ascites, preoperative CA 125 values, and regimen of chemotherapy were not significant factors. In addition, there was no significant difference in the ratio of positive lymph node metastases regardless of the completion of lymphadenectomy (P = 0.955). CONCLUSION Our data suggest that patients with pTI-IIb CCC who underwent lymphadenectomy did not show a significant improvement in survival. There was no significant difference in the overall and disease-free survival rates in pTI-IIb CCC patients regardless of the completion of surgical staging lymphadenectomy.
Production of morphologically derived words in the semantic variant of primary progressive aphasia: preserved decomposition and composition but impaired validation

Abstract Although there is growing interest in inflectional morphology in semantic variant primary progressive aphasia (svPPA), derivational morphology has rarely been studied in this population. This study reports the performance of N.G. , a 72-year-old-woman with svPPA in a verb production task designed to entail morphological processing (composition, decomposition) and self-appraisal of her productions. N.G. demonstrated an over-reliance on morphological processing and failures in her appraisal of root/affix combinations that resulted in the production of morphological paraphasias and neologisms. Her performance in lexical decision of verbs and pseudo-verbs points to the involvement of semantic impairment in these difficulties.
Evaluation of animal models for intestinal first-pass metabolism of drug candidates to be metabolized by CYP3A enzymes via in vivo and in vitro oxidation of midazolam and triazolam

Abstract 1. To search an appropriate evaluation methodology for the intestinal first-pass metabolism of new drug candidates, grapefruit juice (GFJ)- and vehicle (tap water)-pretreated mice or rats were orally administered midazolam (MDZ) or triazolam (TRZ), and blood levels of the parent compounds and their metabolites were measured by liquid chromatography/MS/MS. A significant effect of GFJ to elevate the blood levels was observed only for TRZ in mice. 2. In vitro experiments using mouse, rat and human intestinal and hepatic microsomal fractions demonstrated that GFJ suppressed the intestinal microsomal oxidation of MDZ and especially TRZ. Substrate inhibition by MDZ caused reduction in 1′-hydroxylation but not 4-hydroxylation in both intestinal and hepatic microsomal fractions. The kinetic profiles of MDZ oxidation and the substrate inhibition in mouse intestinal and hepatic microsomal fractions were very similar to those in human microsomes but were different from those in rat microsomes. Furthermore, MDZ caused mechanism-based inactivation of cytochrome P450 3A-dependent TRZ 1′-hydroxylation in mouse, rat and human intestinal microsomes with similar potencies. 3. These results are useful information in the analysis of data obtained in mouse and rat for the evaluation of first-pass effects of drug candidates to be metabolized by CYP3A enzymes.
Union Status, Educational Attainment, and Body Mass Index Among Emerging Adults

This study uses fixed-effects regression modeling and three waves of data from the National Longitudinal Study of Adolescent to Adult Health (Add Health) to examine whether union status and educational attainment interact to influence change in body mass index (BMI) during emerging adulthood. The results support the hypothesis that the effect of union status on change in BMI is smaller for those with more educational attainment. In particular, emerging adults with no college education experience significant increases in BMI associated with both marriage and cohabitation. The increases in BMI associated with marriage and cohabitation are significantly smaller for those with some college education—but are still somewhat present. Among emerging adults with college degrees, however, involvement in cohabitation/marriage is not associated with increases in BMI at all. Potential explanations for this pattern of results and suggestions for future research are discussed.
Dihedral Angle Mesh Error: a fast perception correlated distortion measure for fixed connectivity triangle meshes

In computer graphics, triangle meshes are ubiquitous as a representation of surface models. Processing of this kind of data, such as compression or watermarking, often involves an unwanted distortion of the surface geometry. Advanced processing algorithms are continuously being proposed, aiming at improving performance (compression ratio, watermark robustness and capacity), while minimizing the introduced distortion.
Unhappiness, health and cognitive ability in old age

Background To test whether scores on depression inventories on entry to a longitudinal study predict mental ability over the next 4–16 years. Method Associations between scores on the Beck Depression Inventory and on tests of intelligence, vocabulary and memory were analysed in 5070 volunteers aged 49–93 years after differences in prescribed drug consumption, death and drop-out, sex, socio-economic advantage and recruitment cohort effects had also been considered. Results On all cognitive tasks Beck scores on entry, even in the range 0–7 indicating differences in above average contentment, affected overall levels of cognitive performance but not rates of age-related cognitive decline suggesting effects of differences in life satisfaction rather than in depression. Conclusions A new finding is that, in old age, increments in life satisfaction are associated with better cognitive performance. Implications for interpreting associations between depression inventory scores and cognitive performance in elderly samples are discussed.