Miracle-dz/UniFAR-FTUs huggingface dataset:
HUMAN GENETIC VARIATION: THE MECHANISMS AND RESULTS OF MICROEVOLUTION ABSTRACT

This paper presents an overview of the patterns of human genetic variation and the processes that generate them. There are three principal goals. The first is to introduce the new concepts, terms, and methods that have emerged to meet the needs of direct observations on DNA. The second is to look at the extent and pattern of variation in human DNA sequences, and how a record of our evolution is embedded within the patterns of variation. The final objective is to evaluate whether or not race concepts are consistent with new findings. A brief introduction to the coalescent model is given. The coalescent model is an integrative framework for understanding patterns of variation in terms of the processes that generate them. Two data sets with DNA observations on humans from different regions of the world are discussed. Both data sets indicate that human populations differ in the amount of variation that they harbor. At most genetic loci, African populations harbor some relatively common alleles that are absent in non-African populations; however, most of the alleles that are common in non-African populations are also common in African populations. Thus, the pattern of genetic variation is one of nested subsets, such that the variation in non-African populations is a subset of the variation found in African populations. The recent out of Africa model, which postulates an ancient founder event that occurred with the human occupation of new continents, is the best current explanation for this pattern of variation. It is concluded that the typical definitions of human races do not fit the patterns of variation in DNA sequences very well, but it is difficult to get a firm handle on race because race concepts are often used in vague and imprecise ways. In conclusion, the architecture of human genetic variation is explained by the evolutionary history of our species and is best understood in that context.
Optimizing a Superscalar System using Multi-objective Design Space Exploration

One way to cope with a huge design space formed by several parameters is using methods for Automatic Design Space Exploration (ADSE). Recently we developed a Framework for Automatic Design Space Explorations focused on micro-architectural optimizations. In this article we evaluate the influence of three different evolutionary algorithms on the performance of design space explorations. More precisely, we selected two genetic algorithms, NSGA-II and SPEA2, as well as the bio-inspired SMPSO algorithm, running a particle swarm optimization. With these algorithms we run FADSE to optimize both the parameters of the Grid ALU Processor (GAP) microarchitecture and of the GAPtimize post-link code optimizer. An analysis of the simulation results showed a very good performance of the SMPSO algorithm during the design space exploration process on the GAP simulator. SPEA2 provided slightly better results than NSGA-II when they were used on the design space exploration of both GAP and GAPtimize.
Practitioners’ experiences of working collaboratively with interpreters to provide CBT and guided self-help (GSH) in IAPT; a thematic analysis

Abstract Within IAPT (Improving Access to Psychological Therapies), cognitive behavioural therapy (CBT) is offered to all clients regardless of gender, religion, culture and language. Hence, the demand for working with interpreters to facilitate communication during therapy in IAPT has increased. This study explored the experience of therapists working with interpreters to facilitate communication in psychological therapies with clients with mild to moderate anxiety and depression including those with co-morbid physical health problems. Thirteen participants, including six CBT therapists and seven Psychological Wellbeing Practitioners (PWPs) working in an NHS IAPT service, were interviewed. A qualitative approach, using semi-structured interviews and thematic analysis (Braun and Clarke, 2006), was implemented. The following four major themes were identified from the participants’ accounts: negotiating a three-way communication, difficulties in expressing empathy, a lack of shared understanding and working creatively with interpreters. During this collaborative working new understandings of engaging emerged leading participants to view this work as possible.
Case Study of Ecstatic Meditation: fMRI and EEG Evidence of Self-Stimulating a Reward System

We report the first neural recording during ecstatic meditations called jhanas and test whether a brain reward system plays a role in the joy reported. Jhanas are Altered States of Consciousness (ASC) that imply major brain changes based on subjective reports: (1) external awareness dims, (2) internal verbalizations fade, (3) the sense of personal boundaries is altered, (4) attention is highly focused on the object of meditation, and (5) joy increases to high levels. The fMRI and EEG results from an experienced meditator show changes in brain activity in 11 regions shown to be associated with the subjective reports, and these changes occur promptly after jhana is entered. In particular, the extreme joy is associated not only with activation of cortical processes but also with activation of the nucleus accumbens (NAc) in the dopamine/opioid reward system. We test three mechanisms by which the subject might stimulate his own reward system by external means and reject all three. Taken together, these results demonstrate an apparently novel method of self-stimulating a brain reward system using only internal mental processes in a highly trained subject.
Evidence on charter school practices related to student enrollment and retention

ABSTRACT Opponents of charter schools argue these schools “cream-skim” the best students from traditional public schools and push out hard-to-educate students. This paper reviews 22 studies of enrollment issues related to student achievement, special education status, English proficiency, and student discipline in US charter schools. Of the 22 studies, nine use student level data to rigorously test for evidence of strategic enrollment. While the charter sector as a whole tends to serve fewer special education students and English language learners, there is much within-sector variation. Over all, there is very little evidence of systematic “cream-skimming” or “push-out” in US charter schools.
Error correction based on verification techniques

In this paper we address the problem of correcting a combinational circuit that is an incorrect implementation of a given specification. Most existing error-correction approaches can only handle circuits with certain types of errors. Here, we propose a general approach that can correct a circuit with multiple errors without assuming any error model. We identify internal equivalent pairs to narrow down the possible error locations using local BDD's with dynamic support. We also employ a technique called back-substitution to correct the circuit incrementally. This approach can also be used to verify circuit equivalence. The experimental results of correcting fully SIS-optimized benchmark circuits with a number of injected errors are presented.
Motor Cortical Representation of Hand Translation and Rotation during Reaching

Previous studies have shown that hand translation is well represented by neuronal activity in the proximal arm area of primary motor cortex (M1). However, little is known about cortical representation of hand rotation in M1. In this study, single-unit activity was recorded from monkeys while they performed a “center-out with rotation” task. When reaching for a target, subjects had to match four separate kinematic parameters: three-dimensional location and one-dimensional orientation of the target. Among the 512 neurons modulated by hand movement, 446 were tuned to hand translation, 326 were tuned to hand rotation, and 260 neurons were tuned to both hand translation and hand rotation. Approximately half of the neurons that encoded both translation and rotation did so in a nonlinear manner. This nonlinear interaction can be modeled as a gain-field type of encoding whereby hand rotational velocity modulated the hand translational cosine tuning curves in a multiplicative manner. Furthermore, this study demonstrated that both hand translation and hand rotation can be decoded simultaneously from a population of motor cortical neurons.
Foreign Bodies Ingestion in Children: Experience of 61 Cases in a Pediatric Gastroenterology Unit from Romania

The ingestion of foreign bodies is a worldwide pediatric pathology. We assessed the clinical, endoscopic, and therapeutic aspects of this condition in a pediatric gastroenterology unit. We reviewed 61 patients (median age of 3.25 ± 4.7 years). The most frequently ingested objects were coins (26.23%), unidentified metal objects (13.11%), bones (8.19%), batteries, and buttons (6.55%). The clinical features we encountered included abdominal pain (55.73%), vomiting (34.42%), and asymptomatic children (29.5%). Routine X-ray examination enabled finding the foreign body in 42 of the cases. An esophagogastroduodenoscopy was performed within 24–72 hours. 25 cases resulted in a negative endoscopy (40.98%), 19 objects (31.14%) were removed using a polypectomy snare, and extraction failure occurred in 17 patients (27.86%). 28 foreign bodies were passed without incidents; in 14 cases, the swallowed objects were never found. In one case, a battery was stuck in the esophageal folds and led to tracheal-esophageal fistula and bronchopneumonia and later to esophageal stenosis. We report a large proportion of foreign bodies that could not be identified or removed due to lack of early endoscopy and poor technical settings. Batteries and sharp objects lead to severe complications and preschool-age children are at high risk for such events.
Homology class of a Lagrangian Klein bottle

It is shown that an embedded Lagrangian Klein bottle realises a non-zero mod 2 homology class in a compact symplectic four-manifold such that 0$ SRC=http://ej.iop. org/images/1064-5632/73/4/A03/tex_im_2462_img2. gif/>.
Langmuir probe analysis for high density plasmas

High-density, radio-frequency plasmas used in semiconductor processing have progressed to densities n⩾5×1011 cm−3, where the methods used to interpret Langmuir probe characteristics in low-density (109–11 cm−3) plasma reactors are no longer valid. Though theory and computations for arbitrarily dense collisionless plasmas exist, they are difficult to apply in real time. A new parametrization and iteration scheme is given which permits rapid analysis of Langmuir probe data using these theories. However, at high n, measured ion saturation curves are shown which do not agree in shape with the “correct” theory, yielding anomalously high values of n. The discrepancy with independent measures of n, which can exceed a factor of 2, is believed to be caused by charge-exchange collisions well outside the sheath. Probe designs for avoiding this discrepancy are suggested.
VIROME: a standard operating procedure for analysis of viral metagenome sequences

One consistent finding among studies using shotgun metagenomics to analyze whole viral communities is that most viral sequences show no significant homology to known sequences. Thus, bioinformatic analyses based on sequence collections such as GenBank nr, which are largely comprised of sequences from known organisms, tend to ignore a majority of sequences within most shotgun viral metagenome libraries. Here we describe a bioinformatic pipeline, the Viral Informatics Resource for Metagenome Exploration (VIROME), that emphasizes the classification of viral metagenome sequences (predicted open-reading frames) based on homology search results against both known and environmental sequences. Functional and taxonomic information is derived from five annotated sequence databases which are linked to the UniRef 100 database. Environmental classifications are obtained from hits against a custom database, MetaGenomes On-Line, which contains 49 million predicted environmental peptides. Each predicted viral metagenomic ORF run through the VIROME pipeline is placed into one of seven ORF classes, thus, every sequence receives a meaningful annotation. Additionally, the pipeline includes quality control measures to remove contaminating and poor quality sequence and assesses the potential amount of cellular DNA contamination in a viral metagenome library by screening for rRNA genes. Access to the VIROME pipeline and analysis results are provided through a web-application interface that is dynamically linked to a relational back-end database. The VIROME web-application interface is designed to allow users flexibility in retrieving sequences (reads, ORFs, predicted peptides) and search results for focused secondary analyses.
An air bearing table for satellite attitude control simulation

Attitude control of a spacecraft is critical for its operations, but at the same time poses a significant challenge to control engineers due to the non-linear behaviour of attitude dynamics. Hence, a physical ground testing platform for space-craft attitude dynamics and control is essential for verification of a control algorithm prior to its airborne application. In this paper, we present an air bearing based simulation platform which, unlike previous air bearing table designs, is small in size so that it can simulate the behaviour of smaller (nano) satellites such as CubeSat. Currently, the air bearing table is capable of unrestricted motion about the yaw axis and we demonstrate this by the implementation of a closed-loop yaw angle controller. However, gravitational torque prevents us from achieving a simulation about the pitch and roll axes, which should otherwise provide us with up to ±60 degrees of motion. Subsequently, an automatic counterweight system is currently being constructed to overcome this problem, and its governing algorithms are presented herein.
Imaging topography and viscoelastic properties by constant depth atomic force microscopy

Identification of mechanical properties of cells is known to be an effective tool for medical diagnosis, and holds potential for future developments in treatment of various diseases. In this paper a novel method for identification of viscoelastic properties of a soft sample using atomic force microscopy in dynamic mode is presented. The estimation scheme is based on parameter identification of a lumped spring-damper system model. The estimator guarantees exponentially fast parameter convergence. The indentation depth of the tip into the sample must be constant for viscoelastic properties to be consistent during a scan. A depth controller is designed to keep the indentation constant by utilizing the online estimates of the sample spring constant and topography. Simulations show the effectiveness of the presented method.
Estructura Factorial y Confiabilidad del Cuestionario de Motivación y Estrategias de Aprendizaje, MSLQ, en E studiantes Universitarios Chilenos de Primer Año

espanolEl presente estudio analiza la estructura factorial y confiabilidad del cuestionario de Motivacion y estrategias de aprendizaje (MSLQ) en una muestra de 409 estudiantes universitarios con edad promedio de 19.08 anos, quienes respondieron dicho cuestionario previo consentimiento informado. La estructura factorial se analizo a traves de un analisis factorial exploratorio. Los resultados revelan la formacion de nueve factores, tres corresponderian a la escala de motivacion y seis a la escala de estrategias de aprendizaje. El MSLQ muestra ser un instrumento confiable de medicion de la motivacion y las estrategias de aprendizaje, aplicable en contexto de investigacion, sin embargo es necesario realizar nuevas investigaciones que permitan indagar respecto de las discrepancias con el modelo factorial propuesto por sus autores. EnglishThis study analyzes the factorial structure and reliability of the motivation and learning strategies questionnaire (MSLQ) in a sample of 409 university students between with an average age of 19.08. An Exploratory Factor Analysis was carried out using the Principal Axis Extracting method (AEP). The results identified 9 factors, three fitting the scale of motivation and six fitting the scale of learning strategies. The MSLQ proves to be a reliable instrument for measuring motivation and learning strategies applicable in the research context, however further research is needed to investigate the discrepancies with the factor model proposed by their authors.
Coordinated Regulation and Complex Formation of YELLOW VARIEGATED1 and YELLOW VARIEGATED2, Chloroplastic FtsH Metalloproteases Involved in the Repair Cycle of Photosystem II in Arabidopsis Thylakoid Membranes Article, publication date, and citation information can be found at www.plantcell.org/cgi/d

Arabidopsis YELLOW VARIEGATED1 (VAR1) and VAR2 are separate loci that encode similar chloroplast FtsH proteases. To date, FtsH is the best-characterized protease in thylakoid membranes involved in the turnover of photosynthetic protein complexes. It comprises a protein family that is encoded by 12 different nuclear genes in Arabidopsis. We show here that nine FtsH proteins are located in the chloroplasts. Mutations in either VAR1 or VAR2 cause typical leaf variegation and sensitivity to photoinhibition. By contrast, none of these phenotypes was observed in T-DNA insertion mutants in other ftsH genes (ftsh1, ftsh6, and ftsh8) closely related to VAR1 and VAR2. This finding suggests that VAR1 and VAR2 play a predominant role in the photosystem II repair cycle in thylakoid membranes. By generating VAR1- and VAR2-specific antibodies, we found that loss of either VAR1 or VAR2 results in the decreased accumulation of the other. Thus, the genetic nonredundancy between VAR1 and VAR2 could be attributed to their coordinated regulation at the protein level. These observations led us to examine whether VAR1 and VAR2 form a complex. Sucrose density gradient and gel filtration analyses revealed a complex of ∼400 to 450 kD, probably representing a hexamer. Furthermore, VAR1 and VAR2 were shown to coprecipitate by immunoprecipitation using VAR1- and VAR2-specific antibodies. The majority of VAR1 appears to exist as heterocomplexes with VAR2, whereas VAR2 may be present as homocomplexes as well. Based on these results, we conclude that VAR1 and VAR2 are the major components of an FtsH complex involved in the repair of photodamaged proteins in thylakoid membranes.
Time and the Price Impact of a Trade

We use Hasbrouck's (1991) vector autoregressive model for prices and trades to empirically test and assess the role played by the waiting time between consecutive transactions in the process of price formation. We find that as the time duration between transactions decreases, the price impact of trades, the speed of price adjustment to trade-related information, and the positive autocorrelation of signed trades all increase. This suggests that times when markets are most active are times when there is an increased presence of informed traders; we interpret such markets as having reduced liquidity. Copyright The American Finance Association 2000.
A study of the evolution of mindfulness practice in an early childhood classroom

The following paper studies the use of mindfulness practice in a preschool classroom. Combining participant observation, personal journaling, and interviews with children, this study explores the relationship between the introduction of mindfulness practice, changes in classroom culture, and growth in emotional vocabulary. Implementing both kindness practices, and ongoing reflection on what it means to be kind this study questions the many factors that contribute to children’s perceptions of and ability to understand and identify acts of kindness. This study posits the introduction of mindfulness practice as one method to create space for children to make sense of what kindness looks like and how it is expressed, and to increase their own capacity to treat themselves and others with kindness.
Prediction of Multidimensional Emotional Ratings in Music from Audio Using Multivariate Regression Models

Content-based prediction of musical emotions and moods has a large number of exciting applications in Music Information Retrieval. However, what should be predicted, and precisely how, remain a challenge in the field. We provide an empirical comparison of two common paradigms of emotion representation in music, opposing a multidimensional space to a set of basic emotions. New groundtruth data consisting of film soundtracks was used to assess the compatibility of these models. The findings suggest that the two are highly compatible and a quantitative mapping between the two is provided. Next we propose a model predicting perceived emotions based on a set of features extracted from the audio. The feature selection and transformation is given special emphasis and three separate data reduction techniques are compared (stepwise regression, principal component analysis, and partial least squares regression). Best linear models consisting of 25 predictors from the data reduction process were able to account for between 58 and 85% of the variance. In general, partial least squares models performed the best and the data transformation has a significant role in building linear models.
Dynamic Support Service Selection for Business Transactions in Electronic Service Markets

Buisiness transactions in an electronic service market are expected to appear spontaneously, anonymously, and with varying requirements of infrastructural support. This support generally covers security requirements such as authentication, privacy, and public key certification as well as payment protokolls or the demand for notary services. The latter two aspects are concidered in particular in this paper. Due to the varity of ever-changing setting of such services, a flexible integration into electronic commerce infrastructures is required. This paper proposes the embedding of support services into business transactions at runtime on the basic of a CORBA DII distribution plattform. The architecturall approach is described.
Clinicopathologic characteristics and prognostic factors for HER2-positive patients with metastatic breast cancer in southern China

Introduction The aim of the study was to analyze clinicopathologic characteristics and survival and to identify prognostic factors for Chinese patients with HER2-positive metastatic breast cancer. Material and methods A total of 243 patients with HER2-positive metastatic breast cancer, treated during the period 2002 to 2009, were followed up from initial disease diagnosis to death or date of last follow-up (December 2011). Cumulative survival curves were created using Kaplan-Meier analysis with the log-rank test. Prognostic factors were analyzed by univariate and multivariate Cox proportional hazards regression analysis. Results During follow-up, 205 patients died, with a median OS of 27 months (95% CI: 23.5, 30.5 months), and the 1-, 3-, and 5-year survival rates were 84.4%, 38.6%, and 18.1%, respectively. The median OS of HR+ patients was significantly higher than that of HR– patients (p < 0.001). Surgery (hazard ratio = 0.60, p = 0.002), endocrine therapy (hazard ratio = 0.53, p < 0.01), and anti-HER2 therapy (hazard ratio = 0.63, p = 0.003) were favorable independent prognostic factors for patients with HER2-positive metastatic breast cancer. Conclusions These results indicated that surgical intervention, endocrine therapy, and anti-HER2 therapy were good for these HER2 positive patients with metastatic breast cancer, but ECOG performance status < 1 and metastasis to brain were unfavorable independent prognostic factors. HR status was not an independent prognostic factor.