Miracle-dz/UniFAR-FTUs huggingface dataset:
ERCC4 (XPF) encodes a human nucleotide excision repair protein with eukaryotic recombination homologs

ERCC4 is an essential human gene in the nucleotide excision repair (NER) pathway, which is responsible for removing UV-C photoproducts and bulky adducts from DNA. Among the NER genes, ERCC4 and ERCC1 are also uniquely involved in removing DNA interstrand cross-linking damage. The ERCC1-ERCC4 heterodimer, like the homologous Rad10-Rad1 complex, was recently found to possess an endonucleolytic activity that incises on the 5' side of damage. The ERCC4 gene, assigned to chromosome 16p13.1-p13.2, was previously isolated by using a chromosome 16 cosmid library. It corrects the defect in Chinese hamster ovary (CHO) mutants of NER complementation group 4 and is implicated in complementation group F of the human disorder xeroderma pigmentosum. We describe the ERCC4 gene structure and functional cDNA sequence encoding a 916-amino-acid protein (104 kDa), which has substantial homology with the eukaryotic DNA repair and recombination proteins MEI-9 (Drosophila melanogaster), Rad16 (Schizosaccharomyces pombe), and Rad1 (Saccharomyces cerevisiae). ERCC4 cDNA efficiently corrected mutants in rodent NER complementation groups 4 and 11, showing the equivalence of these groups, and ERCC4 protein levels were reduced in mutants of both groups. In cells of an XP-F patient, the ERCC4 protein level was reduced to less than 5%, consistent with XPF being the ERCC4 gene. The considerable identity (40%) between ERCC4 and MEI-9 suggests a possible involvement of ERCC4 in meiosis. In baboon tissues, ERCC4 was expressed weakly and was not significantly higher in testis than in nonmeiotic tissues.
KUDA : GPU Accelerated Split Race Checker Position paper

We propose a novel approach for runtime verification on computers with a large number of computation cores, without any hardware extension to mainstream PC environment. The goal of the approach is making use of all hardware resources to decouple the computational overhead of traditional race checkers via parallelizing the runtime verification. We distinguish between two kinds of computational overhead: (i) overhead caused by monitoring, and (ii) overhead due to the verification algorithm(s). So far, runtime verification algorithms have been designed to run on the same threads as the code being monitored and both (i) and (ii) contribute to the slowdown of the program being monitored. The framework we propose allows us to carry out (ii) on separate, dedicated cores and threads. As a result, the program being monitored only experiences slowdown due to (i) and plus the communication of the events to be monitored. There exists related work showing that with some inexpensive hardware support (i) can be reduced to negligible levels. By parallelizing analyses our experiments show that they run as fast as the program being monitored, but on separate computational resources, one can potentially use this approach for monitoring, error detection, containment, and recovery from errors. As a demonstration of concept, we investigate runtime monitoring for concurrency bugs, in particular, data race detection. We use a few CPU threads and a large number of cores on a GPU to minimize the slowdown of the application on which race detection is being run.
Machine Learning of Syntactic Attachment from Morphosyntactic and Semantic Co-occurrence Statistics

The paper presents a novel approach to extracting dependency information in morphologically rich languages using co-occurrence statistics based not only on lexical forms (as in previously described collocation-based methods), but also on morphosyntactic and wordnet-derived semantic properties of words. Statistics generated from a corpus annotated only at the morphosyntactic level are used as features in a Machine Learning classifier which is able to detect which heads of groups found by a shallow parser are likely to be connected by an edge in the complete parse tree. The approach reaches the precision of 89% and the recall of 65%, with an extra 6% recall, if only words present in the wordnet are considered.
Teaching for Commitment: Liberal Education, Indoctrination, and Christian Nurture

Thiessen calls for reconstruction of the Enlightenment ideal of liberal education from which the charge of indoctrination typically arises. He argues that liberal education necessarily builds on nurture and therefore needs to be more sensitive to the traditions into which a child is initiated. The ideals of autonomy, rationality, and critical openness - all closely related to the ideal of liberal education - need to be modified if they are to be both realistic and philosophically defensible. Once this is done it can be seen that confessional religious education without indoctrination is possible. Teaching for Commitment is an interdisciplinary study covering the fields of religion, philosophy, epistemology, ethics, and education. The very practical nature of the problem being examined, and Thiessen's straightforward and non-technical presentation, will be of interest to parochial and public school boards, teachers, and parents, as well as religious institutions, educationalists, and philosophers of education.
Games and Culture: Using Online-gaming Data to Cluster Chinese Regional Cultures

To identify cluster of societies and cultures is not easy in subject to the availability of data. In this study, we propose a novel method to cluster Chinese regional cultures. Using geotagged online-gaming data of Chinese internet users playing online card and board games with regional features, 336 Chinese cities are grouped into 17 clusters. The distribution of clustering units shows great geographical proximity when the boundary of the clusters coincides well with the geographical boundary of provinces.
Complex Dynamics: Literature, Science, and Postdisciplinarity@@@Reconnection: Dualism to Holism in Literary Study@@@Shaping Written Knowledge: The Genre and Activity of the Experimental Article in Science

A wager: postdisciplinarity will be to the 1990s what deconstruction was to the 1980s. This bet will, no doubt, offer scant comfort to those who thought it was safe to go back into the classroom, that "history"new, old, or repackaged-had re-emerged to provide a basis from which to hold forth on Milton, Blake, Shelley, and other canonical figures. Postdisciplinarity has not yet caught on as a catchphrase nor sharply etched itself on the collective critical consciousness as a sequel to interdisciplinary study. But with postmodernism, post-Marxism, and other "posts" now seeming a bit shopworn, postdisciplinarity stands a fair chance of emerging in the next decade as a radical force that will extend questions debated by literary theorists in the 1980s to a wide range of disciplines-specifically, the natural sciences-in the 1990s. Because there is still an ongoing debate about precisely what theory achieved in the 1980s, it seems difficult to predict what postdisciplinary study will mean ten years from now or, more crucially, what the disciplines themselves-literature, history, psychology, philosophy, physics, biology, and so forth-will look like; what insti-
Prevalence of Metabolic Syndrome and Its Components among Japanese Workers by Clustered Business Category

The present study was a cross-sectional study conducted to reveal the prevalence of metabolic syndrome and its components and describe the features of such prevalence among Japanese workers by clustered business category using big data. The data of approximately 120,000 workers were obtained from a national representative insurance organization, and the study analyzed the health checkup and questionnaire results according to the field of business of each subject. Abnormalities found during the checkups such as excessive waist circumference, hypertension or glucose intolerance, and metabolic syndrome, were recorded. All subjects were classified by business field into 18 categories based on The North American Industry Classification System. Based on the criteria of the Japanese Committee for the Diagnostic Criteria of Metabolic Syndrome, the standardized prevalence ratio (SPR) of metabolic syndrome and its components by business category was calculated, and the 95% confidence interval of the SPR was computed. Hierarchical cluster analysis was then performed based on the SPR of metabolic syndrome components, and the 18 business categories were classified into three clusters for both males and females. The following business categories were at significantly high risk of metabolic syndrome: among males, Construction, Transportation, Professional Services, and Cooperative Association; and among females, Health Care and Cooperative Association. The results of the cluster analysis indicated one cluster for each gender with a higher prevalence of metabolic syndrome components; among males, a cluster consisting of Manufacturing, Transportation, Finance, and Cooperative Association, and among females, a cluster consisting of Mining, Transportation, Finance, Accommodation, and Cooperative Association. These findings reveal that, when providing health guidance and support regarding metabolic syndrome, consideration must be given to its components and the variety of its prevalence rates by business category and gender.
Prediction of disease-resistant gene in rice based on SVM-RFE

Gene expression data possess two main features: small samples and high dimensions. There are many difficulties on analyzing gene expression data using the traditional machine learning methods. In this paper we use an SVM-RFE based method to obtain the set of trait genes that are related to the disease-resistance property in rice and evaluate these genes according to some heuristics. And then we query the genes in the GEO database whose query results in turn provide us with the important rice disease resistance and disease susceptible gene IDs. Therefore, we can determine the rice genes that cause the rice to grow normally and illy. The method not only reduces the dimensionality and improves the classification accuracy substantially compared to other classification methods, but also carries significant biological implications.
The LIUM Arabic/English statistical machine translation system for IWSLT 2008.

This paper describes the system developed by the LIUM laboratory for the 2008 IWSLT evaluation. We only participated in the Arabic/English BTEC task. We developed a statistical phrase-based system using the Moses toolkit a nd SYSTRAN’s rule-based translation system to perform a morphological decomposition of the Arabic words. A continuous space language model was deployed to improve the modeling of the target language. Both approaches achieved significan t improvements in the BLEU score. The system achieves a score of 49.4 on the test set of the 2008 IWSLT evaluation.
Which region of the median palate is a suitable location of temporary orthodontic anchorage devices? A histomorphometric study on human cadavers aged 15-20 years.

INTRODUCTION Endosseus implants can provide a reliable anchorage during orthodontic treatment. The midpalatal structures around the sutura palatina mediana (SPM) are of special interest due to increasing placement of orthodontic implants in this area. Knowledge about the osseous conditions at this site is necessary to predict the expected degree of implant osseointegration. METHODS The upper jaws of 10 human cadavers, aged 15-20 years, were decalcified, and cross-sectional specimens were obtained from four anterior-to-posterior palatal regions for histomorphometric analysis. The analyses focused on the amount of bone and the width of the SPM to determine the anatomical requirements for reliable insertion of palatal implants. RESULTS Bone density [bone-volume (BV)/ tissue-volume (TV)] in all measured areas was 40-60%. The maximum density was measured at the level of the first premolars (54.9+/-5.9%) and the least values (44.2+/-9.6%) were measured at the level of the interconnecting line of the canines. The mean width of the SPM varies from 1.2 to 0.3 mm in different sections of the palate. In the median sagittal plane, the mean values of bone height to nasal cavity reached >5 mm as far as the level distal of the second premolars. Bone height 2 mm paramedian to the SPM decreased consistently from anterior (4.3+/-0.9 mm) to posterior (2.5+/-0.8 mm). CONCLUSIONS Our results indicate that the amount and quality of bone along the anterior palatal midline in 15-to-20-year olds is sufficient for orthodontic implantation. Even implantation posterior to the recommended first premolar level, at which orthodontic implants are most often placed, may be suitable. There are some limitations, however, due to small number of samples and variations of anatomical structures.
Social Recommendation Based on Multi-relational Analysis

Social recommendation methods, often taking only one kind of relationship in social network into consideration, still faces the data sparsity and cold-start user problems. This paper presents a novel recommendation method based on multi-relational analysis: first, combine different relation networks by applying optimal linear regression analysis, and then, based on the optimal network combination, put forward a recommendation algorithm combined with multi-relational social network. The experimental results on Epinions dataset indicate that, compared with existing algorithms, can effectively alleviate data sparsity as well as cold-start issues, and achieve better performance.
Polymorphism of intron‐1 in the voltage‐gated sodium channel gene of Anopheles gambiae s.s. populations from Cameroon with emphasis on insecticide knockdown resistance mutations

Sequence variation at the intron‐1 of the voltage‐gated sodium channel gene in Anopheles gambiae M‐ and S‐forms from Cameroon was assessed to explore the number of mutational events originating knockdown resistance (kdr) alleles. Mosquitoes were sampled between December 2005 and June 2006 from three geographical areas: (i) Magba in the western region; (ii) Loum, Tiko, Douala, Kribi, and Campo along the Atlantic coast; and (iii) Bertoua, in the eastern continental plateau. Both 1014S and 1014F kdr alleles were found in the S‐form with overall frequencies of 14% and 42% respectively. Only the 1014F allele was found in the M‐form at lower frequency (11%). Analysis of a 455 bp region of intron‐1 upstream the kdr locus revealed four independent mutation events originating kdr alleles, here named MS1 ‐1014F, S1‐1014S and S2‐1014S kdr‐intron‐1 haplotypes in S‐form and MS3‐1014F kdr‐intron‐1 haplotype in the M‐form. Furthermore, there was evidence for mutual introgression of kdr 1014F allele between the two molecular forms, MS1 and MS3 being widely shared by them. Although no M/S hybrid was observed in analysed samples, this wide distribution of haplotypes MS1 and MS3 suggests inter‐form hybridizing at significant level and emphasizes the rapid diffusion of the kdr alleles in Africa. The mosaic of genetic events found in Cameroon is representative of the situation in the West–Central African region and highlights the importance of evaluating the spatial and temporal evolution of kdr alleles for a better management of insecticide resistance.
FILTERING BOOSTED BY UNLABELED DATA

This paper describes three learning methods for document filtering that use unlabeled data. The proposed methods are based on a committee of the classifiers which are trained on a small set of labeled data and then augmented by a large number of unlabeled data. By taking advantage of unlabeled data, the effective number of labeled data needed is significantly reduced and the filtering accuracy is increased. The use of unlabeled data is important because obtaining labeled data is difficult and timeconsuming, while unlabeled data are abundant. For all proposed methods, the experimental results show that the accuracy is improved up to 9.2% with only two-thirds as many labeled data as the method which does not use unlabeled data.
Symmetric and Asymmetric Multi-modality Biclustering Analysis for Microarray Data Matrix

Machine learning techniques offer a viable approach to cluster discovery from microarray data, which involves identifying and classifying biologically relevant groups in genes and conditions. It has been recognized that genes (whether or not they belong to the same gene group) may be co-expressed via a variety of pathways. Therefore, they can be adequately described by a diversity of coherence models. In fact, it is known that a gene may participate in multiple pathways that may or may not be co-active under all conditions. It is therefore biologically meaningful to simultaneously divide genes into functional groups and conditions into co-active categories--leading to the so-called biclustering analysis. For this, we have proposed a comprehensive set of coherence models to cope with various plausible regulation processes. Furthermore, a multivariate biclustering analysis based on fusion of different coherence models appears to be promising because the expression level of genes from the same group may follow more than one coherence models. The simulation studies further confirm that the proposed framework enjoys the advantage of high prediction performance.
Expression of type 1 corticotropin‐releasing factor receptor in the guinea pig enteric nervous system

Reverse transcription‐polymerase chain reaction (RT‐PCR), immunohistochemistry, electrophysiological recording, and intraneuronal injection of the neuronal tracer biocytin were integrated in a study of the functional expression of corticotropin‐releasing factor (CRF) receptors in the guinea pig enteric nervous system. RT‐PCR revealed expression of CRF1 receptor mRNA, but not CRF2, in both myenteric and submucosal plexuses. Immunoreactivity for the CRF1 receptor was distributed widely in the myenteric plexus of the stomach and small and large intestine and in the submucosal plexus of the small and large intestine. CRF1 receptor immunoreactivity was coexpressed with calbindin, choline acetyltransferase, and substance P in the myenteric plexus. In the submucosal plexus, CRF1 receptor immunoreactivity was found in neurons that expressed calbindin, substance P, choline acetyltransferase, or neuropeptide Y. Application of CRF evoked slowly activating depolarizing responses associated with elevated excitability in both myenteric and submucosal neurons. Histological analysis of biocytin‐filled neurons revealed that both uniaxonal neurons with S‐type electrophysiological behavior and neurons with AH‐type electrophysiological behavior and Dogiel II morphology responded to CRF. The CRF‐evoked depolarizing responses were suppressed by the CRF1/CRF2 receptor antagonist astressin and the selective CRF1 receptor antagonist NBI27914 and were unaffected by the selective CRF2 receptor antagonist antisauvagine‐30. The findings support the hypothesis that the CRF1 receptor mediates the excitatory actions of CRF on neurons in the enteric nervous system. Actions on enteric neurons might underlie the neural mechanisms by which stress‐related release of CRF in the periphery alters intestinal propulsive motor function, mucosal secretion, and barrier functions. J. Comp. Neurol. 481:284–298, 2005. © 2004 Wiley‐Liss, Inc.
Block Acquisition of Weak GPS Signals in a Software Receiver

Block algorithms have been developed to acquire very weak Global Positioning System (GPS) coarse/acquisition (C/A) signals in a software receiver. These algorithms are being developed in order to enable the use of weak GPS signals in applications such as geostationary orbit determination. The algorithms average signals over multiple GPS data bits after a squaring operation that removes the bits’ signs. Methods have been developed to ensure that the pre-squaring summation intervals do not contain data bit transitions. The algorithms make judicious use of Fast Fourier Transform (FFT) and inverse FFT (IFFT) techniques in order to speed up operations. Signals have been successfully acquired from 4 seconds worth of bitgrabbed data with signal-to-noise ratios (SNRs) as low as 21 dB Hz.
Teacher Effectiveness on High- and Low-Stakes Tests.

A large literature finds substantial variation in teachers’ effects on student achievement. Moreover, this research finds that little of this variation in effectiveness can be explained by traditional measures of quality, such as years of teaching experience. There remains, however, a gap in our understanding of how the choice of outcome measure—and teachers’ own stake in the test outcome—affects inferences about teacher quality. For example, test-based accountability policies may incentivize teachers to focus efforts on short-term, test-specific skills which may not generalize to other tests. In this paper, we use data from a large urban school district to estimate teacher effects on highand low-stakes tests of the same content areas. We find that: (1) teacher effects are 15-31% larger on the high-stakes test, (2) teacher effects on the high-stakes test are only a modest predictor of effectiveness on the low-stakes test, (3) returns to experience differ across tests in ways consistent with teachers’ incentives to invest early in teaching skills and content specific to the high-stakes test, and (4) teacher effects on the high-stakes test decay at a faster rate than those on the low-stakes test. ∗We would like to thank the Houston Independent School District for providing necessary data, and the IES pre-doctoral training program for providing research support. Jennings received additional support for this project from IES-AERA and Spencer Foundation dissertation fellowships. Rachel Cole provided expert research assistance. We thank seminar participants at NYU, the University of Notre Dame, Stanford University, and the Institute for Research on Poverty Summer Workshop for useful feedback. Dan McCaffrey, Doug Harris, Susanna Loeb, Sean Reardon, and Matthew Wiswall provided especially helpful comments on an earlier draft. All remaining errors are our own. †Contact author. NYU Steinhardt School of Culture, Education, and Human Development, 665 Broadway Suite 805, New York, NY 10012. Phone: (212) 992-9468 E-mail: sean.corcoran@nyu.edu.
Automated formal analysis and verification: an overview

This paper provides an overview of various existing approaches to automated formal analysis and verification. The most space is devoted to the approach of model checking, including its basic principles as well as the different techniques that have been proposed for dealing with the state space explosion problem in model checking. This paper, however, includes a brief discussion of theorem proving and static analysis too. All of the discussed approaches are introduced mostly on an informal level, with an attempt to provide the reader with their basic ideas and references to works where more details can be found.
Understanding the Heterogeneity of Soil Moisture and Evapotranspiration Using Multiscale Observations From Satellites, Airborne Sensors, and a Ground-Based Observation Matrix

This letter summarizes a special stream of the IEEE Geoscience and Remote Sensing Letters devoted to understanding the heterogeneity in soil moisture, evapotranspiration, and other related ecohydrological variables based on multiscale observations from satellite-based and airborne remote sensors, a flux observation matrix, and an ecohydrological wireless sensor network in the Heihe Watershed Allied Telemetry Experimental Research project. Scaling and uncertainty are the key issues in the remote-sensing research community, especially regarding the heterogeneous land surface. However, a lack of understanding and an inadequate theoretical basis impede the development and innovation of forward radiative transfer models, as well as the quantitative retrieval and validation of remote-sensing products. We summarize the prior considerations regarding surface heterogeneity research and report the main outcomes and contributions of this special stream. The highlights of this stream are related to spatial sampling, upscaling, uncertainty analysis, the validation of remote-sensing products, and accounting for heterogeneity in remote-sensing models.