Miracle-dz/UniFAR-FTUs huggingface dataset:
Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond

Advanced resources for genome-assisted research in barley (Hordeum vulgare) including a whole-genome shotgun assembly and an integrated physical map have recently become available. These have made possible studies that aim to assess genetic diversity or to isolate single genes by whole-genome resequencing and in silico variant detection. However such an approach remains expensive given the 5 Gb size of the barley genome. Targeted sequencing of the mRNA-coding exome reduces barley genomic complexity more than 50-fold, thus dramatically reducing this heavy sequencing and analysis load. We have developed and employed an in-solution hybridization-based sequence capture platform to selectively enrich for a 61.6 megabase coding sequence target that includes predicted genes from the genome assembly of the cultivar Morex as well as publicly available full-length cDNAs and de novo assembled RNA-Seq consensus sequence contigs. The platform provides a highly specific capture with substantial and reproducible enrichment of targeted exons, both for cultivated barley and related species. We show that this exome capture platform provides a clear path towards a broader and deeper understanding of the natural variation residing in the mRNA-coding part of the barley genome and will thus constitute a valuable resource for applications such as mapping-by-sequencing and genetic diversity analyzes.
Viral meningitis in child care center staff and parents: an outbreak of echovirus 30 infections.

OBJECTIVE A report of five cases of viral meningitis among adults with children enrolled in a child care center prompted an investigation of risk factors for viral transmission from children to adult household members. METHODS To determine recent echovirus 30 (E30) infections, the authors conducted a serologic survey. To determine risk factors for infection among adult household members, they conducted a retrospective cohort study using written questionnaires. RESULTS Recent E30 infections were found in 84% of children tested, 57% of adult household members tested, and 47% of staff members tested. Infected adults were more likely than infected children to have clinical meningitis. Among adult household members, changing diapers was a risk factor for recent infection. Women who changed > or = 90 diapers per month had a higher infection rate than women who changed fewer diapers; in contrast, men who changed > or = 90 diapers per month had a lower infection rate than men who changed fewer diapers. Handwashing was protective: there was a negative correlation between handwashing after diaper changes and E30 infection among adults with infected children in diapers. CONCLUSIONS Because child care centers can be a source of enteroviral infections among adult household members, adults with viral meningitis should be questioned about their children's day care or preschool attendance. The importance of handwashing should be stressed to adults with children in day care.
X‐linked mental retardation: vanishing boundaries between non‐specific (MRX) and syndromic (MRXS) forms

This review covers the history and nosology of X‐linked mental retardation (XLMR) in which the following, largely clinically based, subclassification was used: fragile X syndrome (FRAXA), syndromic forms (MRXS) and non‐specific forms (MRX). After the discovery of the FMR2 gene at the FRAXE site, 10 MRX genes have been identified in the last 6 years. A short description is given of the strategies used to identify the genes that cause mental retardation (MR). Furthermore, their potential functions and the association with MR will be discussed. It is emphasized that mutations in several of these MR genes can result in non‐specific, as well as in syndromic forms of XLMR. Present findings stress the importance of accurate clinical evaluation. Most considerably, genotype–phenotype correlation studies of affected individuals in XLMR families with MRX gene mutations are necessary to define the criteria of MRX vs MRXS subclassification.
The Role of Internet User Characteristics and Motives in Explaining Three Dimensions of Internet Addiction

In a little more than a decade, the Internet has revolutionized mediated communication and communication flow. With the pace of change and the emergence of new uses of the Internet (e.g., YouTube, MySpace) over this time, researchers have continued to struggle with explaining various positive and negative effects of Internet use that have garnered attention. Some have suggested that Internet use can enhance living conditions by providing access to diverse information (Bauer, Gai, Kim, Muth, & Wildman, 2002), widen users’ social circles (e.g., Hampton & Wellman, 2003; Katz & Aspden, 1997; Rheingold, 1993), and enhance psychological well-being (Chen, Boase, & Wellman, 2002; Kang, 2007). Others have considered some potential negative effects of the Internet, arguing that it can be an isolating medium leading to loneliness, less social interaction with family members and friends (e.g., Kraut, Patterson, Landmark, Kielser, Mukophadhyaya, & Scherlis, 1998; Sanders, Field, Diego, & Kaplan, 2000; Stoll, 1995; Turkle, 1996), and clinical depression (Young & Rogers, 1998). One negative effect that has received considerable attention over the last several years is the extent to which people may become addicted to the Internet. The ongoing evolution of Internet use and growth in the amount of time people spend using the Internet has fueled this concern. Researchers have used different terms to describe very similar types of behavior. These include problematic Internet use (Caplan, 2002; Davis, Besser, & Flett, 2002), pathological Internet use (Morahan-Martin, & Schumacher, 2000), Internet dependency (Anderson, 1998; Scherer, 1997), and Internet addiction (Beard & Wolf, 2001; Griffiths, 1996; Young, 1996a). In the current study we use the term Internet addiction for consistency. However, it must be noted that conceptual confusion surrounding this emotion-laden term has made it difficult to ascertain the precise psychopathology arguably associated with it (Shaffer, 2004). For example, whereas terms such as dependency and addiction have a longstanding history of being used interchangeably in the context of drug and alcohol abuse (Eisenman, Dantzker, & Ellis, 2004), in media studies such terms have very different historical meanings. For instance, dependence or reliance on a particular medium or
A versatile mm-wave micromachined anti-reflective layer

Micromachined millimeter-wave anti-reflective layers (mm-AR) offer a highly customizable and effective method to maximize power transmission through dielectric media. The power transmitted through an air-dielectric interface is maximized by adding an anti-reflective layer whose thickness is a quarter-wavelength and whose dielectric constant is the geometric mean of air and the dielectric, in analogous fashion to a quarter-wave transformer in transmission line theory. The mm-AR is an artificial dielectric material with controlled thickness and dielectric constant. A DRIE process forms a sub-wavelength lattice in a substrate that controls the material's effective dielectric response. The resulting anti-reflective layers were used to improve transmission through a silicon-air interface from an average of 40% across the W-band to 95%. While silicon was used in this work, the demonstrated impedance matching technique can be used for a wide variety of dielectric materials.
Recent trend of FinFET devices and its challenges: A review

Recent technological demand of FinFETs have been explored and reviewed in this work. The downscaling of the conventional MOSFET urge to the researchers to innovate new electronic switches with improved performance in low power parameters and reduced short channel effects (SCE). Control of gate over the channel charge could be increased by using FinFET based multi-gate technology. In this review paper, we have studied about the parasitic capacitances and low power FinFET applications. The challenges of the FinFET technologies have also addressed to explore the research discontinuity.
Thermal-Aware Clock Tree Design to Increase Timing Reliability of Embedded SoCs

Chip heating and nonuniform distribution of hot and cool zones on the die negatively affect reliability and robustness to failures of nanometer integrated circuits. In fact, signal propagation on interconnects slows down as temperature rises; for long wires crossing regions at different temperatures, such as the clock network, thermally induced delay and skew get altered and may result in timing faults. Failures of this kind are difficult to face due to their transient nature. This paper focuses on clock tree design for the class of embedded systems-on-chip with spatially nonuniform but temporally stationary thermal profiles. We contribute two algorithms for the thermal-aware clock network design that take into account on-chip temperature variations of this nature. The experimental results that we have collected on a number of examples and for different thermal profiles show that, in the presence of on-chip spatial temperature gradients, clock trees designed using a standard methodology incur very significant skew violations, thus originating circuit failures. Instead, clock networks designed using the algorithms presented in this paper always satisfy the initial skew bound.
Extracranial redistribution causing rapid spontaneous resolution of acute subdural hematoma.

A 3-year-old child presented in a drowsy state following a fall from a height of twelve feet. Initial head Computed Tomographic (CT) scan showed left frontotemporal acute subdural hematoma (ASDH) along with left coronal diastatic fracture with associated scalp hematoma. While awaiting surgery, an unexpected improvement in the child’s sensorium was noted within six hours of trauma. A repeat head CT scan showed significant resolution in ASDH with simultaneous increase in size of the overlying scalp hematoma. Rapid spontaneous ‘resolution’ of ASDH within a few hours is seen on the CT scan of brain in rare cases. This happens due to pressure-induced intracranial redistribution of hematoma due to brain swelling, elegantly demonstrated by Polman et al by doing an MRI on their patient, and which was subsequently reported by other authors. However, extracranial redistribution of ASDH through a skull fracture has not been demonstrated in any case till date. This is the
Modeling of flow around a wind rotor HAWT Application to the dynamic stall

The study of a horizontal axis wind turbine (HAWT) subject to operating conditions in the presence of wind is very complex, because the machine is subject to an instantaneous change in velocity and wind direction can lead inevitably turbine blades undergoing dynamic stall. The present work is a two-dimensional numerical simulation of the instantaneous variation of the wind direction relative to the turbine blade, compared to experimental data available in the literature. The effect of varying the angle of incidence of an S809 profile is studied using a URANS approach to predict the stall. The turbulence modeling is performed using the k-ε model and the k-ω SST. FLUENT software is used for the numerical solution of equations URANS. The results show the importance of taking into account the behavior of the unsteady flow analysis in order to obtain an accurate estimate of the aerodynamic loads acting on the turbine.
Microleakage of glass ionomer restoration in cavities prepared by Er,Cr:YSGG laser irradiation in primary teeth.

PURPOSE The purpose of this study was to evaluate microleakage of cavity preparation in primary teeth made with an Er, Cr:YSGG laser (L) or high-speed drill (HD) and conventional (CGIC) and resin-modified glass ionomer cement (RMGIC). METHODS One hundred primary teeth were divided into 10 groups (N=10): (a) groups 1 and 2 represented cavities prepared by a no. 1012 diamond bur with HD; (b) groups 3 through 10 represented cavities prepared with an Er, Cr:YSGG laser (with a repetition rate of 20 Hz power settings varying for enamel=2.5 W and 3 W and dentine=1.0 W and 1.5 W). After cavity preparation, samples were restored with CGIC (Ketac Molar Easy Mix) and RMGIC (Vitremer), impermeabilized, thermal cycled, stained, washed, and sectioned. The degree of dye penetration was scored by 3 standardized examiners using a light stereoscope at X30 magnification. RESULTS The Kruskal-Wallis test detected no statistical differences between the cavity preparation methods (P<.049). Neither of the GICs tested were able to avoid microleakage, and the RMGIC showed the lowest statistical degree of microleakage compared with CGIC for both types of cavity preparation. CONCLUSIONS The Er,Cr:YSGG laser provided an equivalent method of cavity preparation compared to the high-speed drill. The resin-modified glass ionomer cement showed the lowest degree of microleakage. This restorative material should be considered when choosing the cavity preparation method.
The New Generation of Automatic Landmark Detection Systems: Challenges and Guidelines

Abstract Landmarks are salient objects in an environment. They play an important role in navigation by serving as orientation aids and marking decision points. Recently, there have been several efforts to design methods to automatically designate certain buildings with salient features as landmarks. All of these methodologies consist of similar steps: (a) establishing a neighborhood, usually around an intersection, (b) performing statistical or data mining analysis to find the building with outlier characteristics, and (c) establishing this salient building as the local landmark. Although these advances are significant, we believe that there are still several key issues that need to be fully addressed in order to realize the new generation of Automatic Landmark Detection Systems (ALDSs). Currently, the main shortcomings in the domain of ALDSs is the lack of a thorough and systematic study of attributes of objects that are analyzed to select landmarks, and deficient experimental verification of the benefits of ALDSs to the end users. Unless, these shortcomings are thoroughly addressed, the viability, applicability, and usefulness of ALDSs are uncertain. On the other hand, automatic landmark detection has the potential to be a dynamic, fascinating, and interdisciplinary research topic with wide applicability. Therefore, the goal of this paper is to discuss the current shortcomings in the domain of landmark detection, propose some preliminary solutions, and provide general guidelines for implementation of the new generation of ALDSs. Specifically, we discuss and promote the importance of: (a) widening the types of attributes analyzed in the landmark detection process, (b) weighting each attribute relative to its significance, (c) extending the types of objects considered as landmark candidates beyond just buildings, (d) identifying landmarks outside the vicinity of intersections, (e) identifying false landmarks along routes, and (f) using virtual environments for experiments with ALDSs. Throughout the paper, we discuss several demonstrative examples and experiments to clarify and support the ideas and concepts that are being promoted.
Experimental studies of shift-work. 3. Stabilized 12-hour shift system.

Abstract Thirty-one subjects were employed in an experiment to determine whether the relationship between efficiency at mental tasks and the circadian rhythm of body temperature observed in an earlier study was affected by an increase in the length of the duty-spell from 4 to 8 hours. Subjects wore assigned either to a control ‘ day ’ shift (O800–1600), a ‘ night ’ shift (2200–0600) or a ( morning ) shift (0400–1200), and were tested for a period of 12 consecutive days on the same shift. The control shift-workers showed no consistent effects of fatigue due to the increased length of the duty-spell. Adaptation of temperature rhythm to work on the night shift was only partial, but was relatively closely reflected in the recorded performance trends. Very little adaptation to work on the morning shift was observed, and performance was thought to have been affected by partial sleep deprivation. It was concluded that body-temperature was as effective a predictor of overall mental efficiency in most industrial-t.
Sentence repetition and digit span: Potential markers of bilingual children with suspected SLI?

Abstract Purpose. Digit span and sentence repetition are identified as potential markers for specific language impairment (SLI). We investigated if language learning of bilingual children with suspected language impairment (biSLI) was also influenced and led by memory constraints. Method. In a retrospective study, 19 children with SLI and 25 controls (ages 4;9–5;9), as well as 15 biSLI children and 14 controls (ages 5;1–8;9) were compared with regard to their performance on a digit span and sentence repetition task. Results. Both groups with language impairment (SLI/biSLI) showed reduced performance on both tasks. Sentence repetition predicted language comprehension, and the digit span task predicted grammar abilities of the SLI, biSLI, and their controls. Conclusion. Sentence repetition and short-term memory provide information on language comprehension and grammar abilities in language-impaired mono- and bilingual children and confirm their function as SLI markers.
Pancreatic and duodenal homeobox gene 1 induces hepatic dedifferentiation by suppressing the expression of CCAAT/enhancer‐binding protein β

It is believed that adult tissues in mammals lack the plasticity needed to assume new developmental fates because of the absence of efficient pathways of dedifferentiation. However, the well‐documented ability of the transcription factor pancreatic and duodenal homeobox gene 1 (PDX‐1) to activate pancreatic lineage development and insulin production following ectopic expression in liver suggests a surprising degree of residual plasticity in adult liver cells. This study seeks a mechanistic explanation for the capacity of PDX‐1 to endow liver cells with pancreatic characteristics and function. We demonstrate that PDX‐1, previously shown to play an essential role in normal pancreatic organogenesis and pancreatic β‐cell function and to possess the potential to activate multiple pancreatic markers in liver, can also direct hepatic dedifferentiation. PDX‐1 represses the adult hepatic repertoire of gene expression and activates the expression of the immature hepatic marker α‐fetoprotein. We present evidence indicating that PDX‐1 triggers hepatic dedifferentiation by repressing the key hepatic transcription factor CCAAT/enhancer‐binding protein β. Hepatic dedifferentiation is necessary though not sufficient for the activation of the mature pancreatic repertoire in liver. Conclusion: Our study suggests a dual role for PDX‐1 in liver: inducing hepatic dedifferentiation and activating the pancreatic lineage. The identification of dedifferentiation signals may promote the capacity to endow mature tissues in mammals with the plasticity needed for acquiring novel developmental fates and functions to be implemented in the field of regenerative medicine. (HEPATOLOGY 2007.)
Do Improvements After Inpatient Dialectial Behavioral Therapy Persist in the Long Term?: A Naturalistic Follow-Up in Patients With Borderline Personality Disorder

Three months of inpatient dialectical behavior therapy proved to be highly effective in patients with borderline personality disorder. This study investigates whether the effects of DBT persist after the patients returned to their usual lives. Thirty-one patients with a diagnosis of borderline personality disorder (DSM-IV) were prospectively followed-up for an observation period of 21 months after discharge from the DBT program, under naturalistic conditions. Improvements as observed after discharge persisted over the full follow-up period. This is reflected in a steady rate of remitted patients and in a broad range of psychopathology showing statistically and clinically significant effect-sizes ranging from 0.70 to 1.71. Analyses of courses over time revealed a high intraindividual concordance, indicating that short term treatment response predicted remission after 2 years follow-up. The effects of inpatient dialectical behavior therapy seem to persist after patients returned to their usual lives.
Terahertz Light-Field Imaging

Light-field imaging is a highly versatile computational method that has been traditionally limited to the visible frequency range of the electromagnetic spectrum. This paper presents an implementation of the light-field technique in terahertz (THz) radiation for the first time. A silicon hyper-hemispherical lens-integrated 32 × 32 pixel CMOS camera was used as the THz light-field sampler and it was scanned across an image plane to record the complete static light-field from a point THz source. Two experiments have been performed to demonstrate the feasibility of light-fields at THz frequencies. In the first experiment, the light-field from a 16-pixel lens-coupled power source module operating at 0.53 THz was recorded and its radiation pattern was computationally rendered. In the other, light-field based transmission mode imaging was demonstrated for a ×48 multiplier based 25-dBi 0.65-THz source without the use of an external optical train.
Genome‐wide analysis of DNA copy number alterations and gene expression in gastric cancer

Genomic copy number aberrations (CNAs) are believed to play a major role in the development and progression of human cancers. Although many CNAs have been reported in gastric cancer, their genome‐wide transcriptional consequences are poorly understood. In this study, to reveal the impact of CNAs on genome‐wide expression in gastric cancer, we analysed 30 cases of gastric cancers for their CNAs by array comparative genomic hybridization (array CGH) and 24 of these 30 cases for their expression profiles by oligonucleotide‐expression microarray. We found that with the application of laser microdissection, most CNAs were detected at higher frequency than in previous studies. Notably, gain at 20q13 was detected in almost all cases (97%), suggesting that this may play an important role in the pathogenesis of gastric cancer. By comparing the array CGH data with expression profiles of the same samples, we showed that both genomic amplification and deletion strongly influence the expression of genes in altered genomic regions. Furthermore, we identified 125 candidate genes, consisting of 114 up‐regulated genes located in recurrent regions (>10%) of amplification and 11 down‐regulated genes located in recurrent regions of deletion. Up‐regulation of several candidate genes, such as CDC6, SEC61G, ANP32E, BYSL and FDFT1, was confirmed by immunohistochemistry. Interestingly, some candidate genes were localized at genomic loci adjacent to well‐known genes such as EGFR, ERBB2 and SMAD4, and concordantly deregulated by genomic alterations. Based on these results, we propose that our list of candidate genes may contain novel genes involved in the pathogenesis of advanced gastric cancer. Copyright © 2008 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.