Miracle-dz/UniFAR-FTUs huggingface dataset:
21.10 n&v 915 MH

an article entitled “Finishing the euchromatic sequence of the human genome”. It has been authored by members of the International Human Genome Sequencing Consortium (IHGSC), and appears on page 931. The article marks the latest, but by no means the last, milestone in this historic project. But readers can be forgiven for being a bit confused by the announcement. Wasn’t the human genome ‘finished’ several years ago? The answer is ‘yes’ — and ‘no’. Early in 2001, the duelling IHGSC (public) and Celera Corporation (private) groups published papers in Nature and Science 3 describing the completion of so-called ‘draft’ sequences. These sequences have revolutionized molecular biology by largely eliminating the need to clone and sequence genes involved in human health and disease. Instead of going to the bench, biologists now go to the web to look up gene sequences in public online databases. But despite their immediate usefulness, the draft sequences were far from perfect. Both drafts were missing some 10% of the so-called ‘euchromatin’ — the gene-rich portion of the genome — and some 30% of the genome as a whole (which includes the genepoor regions of ‘heterochromatin’). The drafts contained hundreds of thousands of gaps, and had misassembled regions where portions of the genome were flipped or misplaced.As a result, any large-scale analyses of the genome, such as studies of the mechanisms of gene evolution or the long-range structure of the genome,had to contend with numerous uncertainties and artefacts. For example, studies of ‘pseudogenes’, the dying remnants of genes that have accumulated mutations that render them non-functional, had to contend with the possibility that any apparent pseudogene was instead the result of a sequencing error. Since the publication of the drafts, the IHGSC sequencing centres have quietly undertaken a laborious ‘finishing’process, in which each gap in the draft was individually examined and subjected to a battery of steps involving cloning and resequencing stretches of DNA. The sequence announced today has just 341 gaps remaining, and consists of contiguous runs of sequence averaging 38 million base pairs. The authors estimate that the finished sequence covers 99% of the euchromatic portion of the genome and that the overall error rate is less than 1 error per 100,000 base pairs.This substantially exceeds the original goals for the project. The finishing procedure roughly doubled the total time and cost of the project. Does it contribute anything new to our understanding of the genome? It does indeed, and to prove the point the authors of the current paper describe several large-scale analyses of the genome that would have been difficult to perform on the draft sequence.One analysis studied the processes of gene birth and death. The authors find 1,183 human genes that show evidence of having been recently ‘born’ by a process of gene duplication and divergence. They also find 37 genes that seem to have recently ‘died’ by acquiring a news and views
Robust Wi-Fi indoor localization with KPCA feature extraction of dual band signals

Indoor localization system based Wi-Fi received signal strength (RSS) has gained popularity in recent years, as wireless local area networks and Wi-Fi enabled mobile devices are pervasive penetration. Unfortunately, the Wi-Fi RSS measurements are susceptible by device heterogeneity, multipath and signal noise, etc. To remedy these problems, we propose a robust Wi-Fi fingerprint-based indoor localization system. The proposed algorithm extract a robust positioning feature from Wi-Fi signals in both 2.4 GHz band and 5 GHz band by kernel principal component analysis (KPCA). Furthermore, we utilize Wi-Fi signal selection algorithm and coarse localization scheme for increasing localization accuracy and reducing the computational burden. Finally, the weighted k nearest neighbor method (WKNN) is used to obtain the estimated location. The proposed system implemented in a realistic indoor Wi-Fi environment, and results indicate that it is efficient in improving the positioning performance.
Differential regulation of arginases and inducible nitric oxide synthase in murine macrophage cells.

Activated macrophages avidly consume arginine via the action of inducible nitric oxide synthase (iNOS) and/or arginase. In contrast to our knowledge regarding macrophage iNOS expression, the stimuli and mechanisms that regulate expression of the cytosolic type I (arginase I) or mitochondrial type II (arginase II) isoforms of arginase in macrophages are poorly defined. We show that one or both arginase isoforms may be induced in the RAW 264.7 murine macrophage cell line and that arginase expression is regulated independently of iNOS expression. For example, 8-bromo-cAMP strongly induced both arginase I and II mRNAs but not iNOS. Whereas interferon-γ induced iNOS but not arginase, 8-bromo-cAMP and interferon-γ mutually antagonized induction of iNOS and arginase I mRNAs. Dexamethasone, which did not induce either arginase or iNOS, almost completely abolished induction of arginase I mRNA by 8-bromo-cAMP but enhanced induction of arginase II mRNA. Lipopolysaccharide (LPS) induced arginase II mRNA, but 8-bromo-cAMP plus LPS resulted in synergistic induction of both arginase I and II mRNAs. In all cases, increases in arginase mRNAs were sufficient to account for the increases in arginase activity. These complex patterns of expression suggest that the arginase isoforms may play distinct, although partially overlapping, functional roles in macrophage arginine metabolism.
Coupled dipole approximation across the Γ-point in a finite-sized nanoparticle array

We study the response of a finite-sized nanoparticle array to an incident field in the vicinity of the Γ-point of the lattice. Using the coupled dipole approximation, we find that the dipole distributions can be strongly inhomogeneous and that strong modulations appear as the energy is above the Γ-point. We highlight how this is reflected in real-space extinction efficiencies as well as in radiation patterns from the finite-sized array. This article is part of the themed issue ‘New horizons for nanophotonics’.
Magnetohydrodynamic effects in liquid metal batteries

Liquid metal batteries (LMBs) consist of two liquid metal electrodes and a molten salt ionic conductor sandwiched between them. The density ratios allow for a stable stratification of the three layers. LMBs were already considered as part of energy conversion systems in the 1960s and have recently received renewed interest for economical large-scale energy storage. In this paper, we concentrate on the magnetohydrodynamic aspects of this cell type with special focus on electro-vortex flows and possible effects of the Tayler instability.
Using Machine Learning Techniques to Analyze and Support Mediation of Student E-Discussions

Students are starting to use networked visual argumentation tools to discuss, debate, and argue with one another about topics presented by a teacher. However, this development gives rise to an emergent issue for teachers: how do they support students during these e-discussions? The ARGUNAUT system aims to provide the teacher (or moderator) with tools that will facilitate effective moderation of several simultaneous e-discussions. Awareness Indicators, provided as part of a moderator's user interface, help monitor the progress of discussions on several dimensions (e.g., critical reasoning). In this paper we discuss preliminary steps taken in using machine learning techniques to support the Awareness Indicators. Focusing on individual contributions (single objects containing textual content, contributed in the visual workspace by students) and sequences of two linked contributions (two objects, the connection between them, and the students' textual contributions), we have run a series of machine learning experiments in an attempt to train classifiers to recognize important student actions, such as using critical reasoning and raising and answering questions. The initial results presented in this paper are encouraging, but we are only at the beginning of our analysis.
Simulation of the Forming of a Superelastic Anchoring Stent and its Deployment in the Coronary Vein

Mitral valve regurgitation (MR) occurs when a flaw in the mitral valve causes backflow of blood into the left atrium. It is possible to reduce the amount of MR by reshaping the mitral annulus which, in turn, changes the configuration of the valve leaflets. A new percutaneously- delivered device which induces this reshaping is currently under development at Edwards Lifesciences. The device, which is placed in the coronary sinus (CS), is essentially a spring with anchoring stents at each end. This study examines the mechanical behavior of one of the anchoring stents, from its forming from a small diameter tube to its deployment into the coronary sinus. The anchoring stent is modeled using the ABAQUS Superelastic constitutive model, and the CS is modeled using a hyperelastic constitutive model.
Neural network estimators: application to ship position estimation

Ship motion prediction is an important practical problem in design of many ocean systems i.e. fire controls, air craft landing and take off. As such the problem has received considerable attention in the past and various attempts for designing estimators via the statistical methodology were made. In this paper the design of the ship position estimator via neural networks is considered. The ship position estimation is viewed as an adaptive estimation problem for partially unknown systems. New powerful neural estimators based on dynamic recurrent neural networks are applied to the solution of the ship position problem. The new proposed neural estimators, and the state of the art statistical filters, are comparatively evaluated via extensive simulations. The results show that the neural algorithms have excellent performance, achieving significant computational savings due to their massively parallel structure. <<ETX>>
Substratum stiffness tunes proliferation downstream of Wnt3a in part by regulating integrin-linked kinase and frizzled-1

ABSTRACT The Wnt/β-catenin pathway controls a variety of cellular behaviors, aberrant activation of which are associated with tumor progression in several types of cancer. The same cellular behaviors are also affected by the mechanical properties of the extracellular matrix (ECM) substratum, which induces signaling through integrins and integrin-linked kinase (ILK). Here, we examined the role of substratum stiffness in the regulation of cell proliferation downstream of Wnt3a. We found that treatment with Wnt3a increased proliferation of cells cultured on stiff substrata, with compliances characteristic of breast tumors, but not of cells on soft substrata, with compliances comparable to that of normal mammary tissue. Depleting ILK rendered cells unresponsive to Wnt3a on both substrata. Ectopic expression of ILK permitted Wnt3a to induce proliferation of cells on both microenvironments, although proliferation on soft substrata remained lower than that on stiff substrata. We further showed that ILK regulates expression of the Wnt receptor frizzled-1 (Fzd1), suggesting the presence of a positive feedback loop between Wnt3a, ILK and Fzd1. These findings suggest that tissue mechanics regulates the cellular response to Wnt under physiological and pathological microenvironmental conditions. This article has an associated First Person interview with the first author of the paper. Highlighted Article: Stiff extracellular matrix signals through integrin-linked kinase to enhance the expression of frizzled-1, thus promoting signaling and proliferation downstream of Wnt3a in mammary epithelial cells.
Cardiovascular safety of low-dose fenfluramine in Dravet syndrome: a review of its benefit-risk profile in a new patient population

Abstract Objective: Dravet syndrome (DS) is a rare, treatment-resistant epilepsy syndrome for which current treatment regimens are often ineffective. Fenfluramine is currently in development for treatment of DS, based on reports in the 1980s and 1990s of its anti-epileptic activity in pediatric patients with intractable epilepsy. However, fenfluramine was withdrawn from global markets in 1997 following reports of its association with pulmonary hypertension and heart valve disease in adult patients treated for obesity. This review was conducted to assess cardiac safety of fenfluramine when used at lower doses for treatment of DS. Methods: Pubmed was searched for clinical studies of fenfluramine in obese adults who reported incidence of heart valve disease. These data were reviewed against published results from Belgian patients with DS who have been treated with low-dose fenfluramine for up to 28 years. Results: Nine controlled studies of fenfluramine and related compounds (dexfenfluramine and/or phentermine) which assessed incidence and severity of cardiac valve disease in 3,268 treated patients and 2,017 control subjects have been reported. Mild or greater aortic valve regurgitation was found in 9.6% of treated patients compared with 3.9% of control subjects, and moderate or greater mitral valve regurgitation was found in 3.1% of treated patients and 2.5% of control subjects. Nineteen DS patients have been treated for up to 28 years with 10–20 mg/day fenfluramine, with no clinical signs or symptoms of cardiac valve disease or pulmonary hypertension. Slight and clinically unimportant changes in valve structure have been seen on echocardiography in five patients at some time during the observation period. Conclusions: A different benefit-risk relationship appears to be emerging when fenfluramine is used at low doses for extended periods in young patients with DS. Continued cardiac assessments during ongoing Phase 3 clinical trials will provide additional safety information for this potential new and effective treatment.
The Value of In Vitro Tests to DiminishDrug Challenges

Drug hypersensitivity reactions have multiple implications for patient safety and health system costs, thus it is important to perform an accurate diagnosis. The diagnostic procedure includes a detailed clinical history, often unreliable; followed by skin tests, sometimes with low sensitivity or unavailable; and drug provocation testing, which is not risk-free for the patient, especially in severe reactions. In vitro tests could help to identify correctly the responsible agent, thus improving the diagnosis of these reactions, helping the physician to find safe alternatives, and reducing the need to perform drug provocation testing. However, it is necessary to confirm the sensitivity, specificity, negative and positive predictive values for these in vitro tests to enable their implementation in clinical practice. In this review, we have analyzed these parameters from different studies that have used in vitro test for evaluating drug hypersensitivity reactions and estimated the added value of these tests to the in vivo diagnosis.
Perceptions of Masculinity and Fatherhood Among Men Experiencing Homelessness

This study explored the perceptions of fatherhood held by 11 men living in a homeless shelter. Using consensual qualitative research methodology (CQR; Hill, 2012), we investigated perceptions of masculinity and fatherhood among fathers experiencing homelessness. Participants described (a) their perceptions of masculinity and fatherhood and changes resulting from homelessness, (b) physical and psychological challenges of being a father experiencing homelessness, and (c) expectations of homeless fathers. The fathers generally expressed feelings of low self-esteem related to their perceived difficulty fulfilling the role of providers for their family; however, they also adapted their view of fatherhood to include roles suited to their situation, such as that of guide, teacher, and role model. Suggestions are made for clinicians in helping fathers navigate and develop these roles, and limitations and directions for future research are discussed.
Research and Characterization of QCM Immunobiosensor for Escherichia Coli O157:H7 Detection

A quartz crystal microbalance(QCM) piezoelectric immunobiosensor was developed for rapid detection of Escherichia coli O157:H7.The affinity-purified antibodies to O157:H7 were immobilized onto a monolayer of 16-mercaptohexadecanoic acid(MHDA),which was self-assembled on the Au electrode surface of QCM with N-hydroxysuccinimide(NHS) ester as a reactive intermediate.The binding of target bacteria with the immobilized antibodies would decrease the sensor resonant frequency,and the frequency shift was correlated to the bacterial concentration.The stepwise fabrication and detection of immunosensor were manifested by scanning electron microscopy(SEM) and cyclic voltammetry(CV) techniques.The results show that the 2.0×102~2.0×108 CFU/mL cells can be detected by the sensor within 1.5 h,and the regenerative possibility for the immunosensor was explored.
SANTA domain: a novel conserved protein module in Eukaryota with potential involvement in chromatin regulation

Since packaging of DNA in the chromatin structure restricts the accessibility for regulatory factors, chromatin remodeling is required to facilitate nuclear processes such as gene transcription, replication, and genome recombination. Many conserved non-enzymatic protein domains have been identified that contribute to the activities of multiprotein remodeling complexes. Here we identified a novel conserved protein domain in Eukaryota whose putative function may be in regulating chromatin remodeling. Since this domain is associated with a known SANT domain in several vertebrate proteins, we named it the SANTA (SANT Associated) domain. Sequence analysis showed that the SANTA domain is approximately a 90 amino acid module and likely composed of four central beta-sheets and three flanking alpha-helices. Many hydrophobic residues exhibited high conservation along the domain, implying a possible function in protein-protein interactions. The SANTA domain was identified in mammals, chicken, frog, fish, sea squirt, sea urchin, worms and plants. Furthermore, a phylogenetic tree of SANTA domains showed that one plant-specific duplication event happened in the Viridiplantae lineage.
Ascorbic acid disposition kinetics in the plasma and tissues of calves.

Kinetic plasma disposition parameters and tissue distribution of ascorbic acid (AA) and dihydroascorbic acid (DHA) were determined in newborn calves. After a radiolabeled AA intravenous administration, the plasma clearance (Cl) was low (40.8 ± 9.5 ml ⋅ kg-1 ⋅ h-1), the steady-state volume of distribution (Vss) was very high (8.9 ± 2.2 l/kg), and the AA mean residence time (MRT) was long (230 ± 85 h). After administration of a 3-g dose of AA, the Cl was high (450 ± 146 ml ⋅ kg-1 ⋅ h-1), the Vss was low (0.658 ± 0.236 l/kg), and the MRT was short (1.49 ± 0.41 h), indicating a strong nonlinearity of AA disposition in calves and the impossibility of preventing scurvy with the use of a loading AA dose. Nonlinearity was explained by the saturation of both kidney reabsorption and tissue uptake. The estimated AA body pool size was 23.1 ± 6.8 mg/kg. On the basis of a compartmental analysis and actual tissue concentration measurements, it is suggested that the lung (19% of the pool) constitutes a low-capacity but rapidly mobilized pool able to cover an acute need for AA, whereas muscle and liver (40 and 33% of the pool, respectively) are high-capacity AA pools, but slowly mobilized and involved in covering the calf's long-term AA requirements. The average daily AA entry rate over the first 7 days of life was 3.43 ± 1.16 mg/kg, and it is suggested that the calf is able to synthesize AA at an early stage.
Disturbance Frequency and Community Stability in Native Tallgrass Prairie

Ecological communities are spatially and temporally variable in response to a variety of biotic and abiotic forces. It is not always clear, however, if spatial and temporal variability leads to instability in communities. Instability may result from strong biotic interactions or from stochastic processes acting on small populations. I used 10–15 yr of annual data from the Konza Prairie Long‐Term Ecological Research site to examine whether plant, breeding bird, grasshopper, and small mammal communities in tallgrass prairie exhibit stability or directional change in response to different experimentally induced fire frequencies. Based on ordination and ANOVA, plant and grasshopper communities on annually burned sites differed significantly from plant and grasshopper communities on less frequently burned sites. Breeding birds and small mammals differed among sites as well, but these differences were not clearly related to disturbance frequency. A modified time series analysis indicated that plant communities were undergoing directional change (unstable) on all watersheds, regardless of fire frequency. Contrary to expectations, directional change was greatest on the annually burned sites and lowest on the infrequently burned sites. Unlike the plant communities, breeding bird, grasshopper, and small mammal communities were temporally stable, despite high‐compositional variability from 1 yr to the next. Stability among the consumer communities within these dynamic plant communities occurs because three‐dimensional vegetation structure does not change over time, despite changes in plant species composition. Evidence suggests that instability in the plant community results from strong biotic interactions among temporally persistent core species and stochastic dynamics among infrequent satellite species. Overall, community stability cannot be assessed if the pattern of temporal dynamics is unknown. Long‐term empirical studies of different taxa under different disturbance regimes are needed to determine over what time frames and spatial scales communities may be stable. Such studies are essential for the development of generalities regarding the relationship between disturbance frequency and community stability in terrestrial and aquatic systems.
Processing-adhesion relations for die attach adhesives and underfill resins

Adhesion is a major consideration in the quality and reliability of new packaging technologies. In PQFPs, adhesive failure is often seen between the die attach adhesive and copper bond pad. In the case of flip chip technology, delamination is often seen between the underfill resin and organic passivation layer. Some of these failures may be attributed to process, i.e. improper cure schedules. Previous work on adhesion-processing relationships for die attach adhesives in PQFPs led to the development of bondability diagrams for isothermal cure conditions, which identified various phenomena that influenced the adhesive bond strength. Similar adhesion-processing relationships can be developed for underfill resins used in flip-chip packaging. However, underfill resins are seldom processed under isothermal conditions and one must also consider the flow process, which was not a concern for die attach adhesives. Underfill material adhesion properties and flow characteristics are the dominant factors that determine the number of cycles to failure of flip-chip packages. Clearly, understanding the cure behavior of polymeric adhesives should provide a valuable insight on delamination and interfacial failure. The purpose of this work is to study the nonisothermal cure behaviour of die attach adhesives and underfill resins in attempt to understand the relationships between processing conditions and bond strength.