Miracle-dz/UniFAR-FTUs huggingface dataset:
A scheme to deal accurately and efficiently with complex angular masks in galaxy surveys

This paper presents a scheme to deal accurately and efficiently with complex angular masks, such as occur typically in galaxy surveys. An angular mask is taken to be an arbitrary union of arbitrarily weighted angular regions bounded by arbitrary numbers of edges. The restrictions on the mask are (i) that each edge must be part of some circle on the sphere (but not necessarily a great circle), and (ii) that the weight within each subregion of the mask must be constant. The scheme works by resolving a mask into disjoint polygons, convex angular regions bounded by arbitrary numbers of edges. The polygons may be regarded as the ‘pixels’ of a mask, with the feature that the pixels are allowed to take a rather general shape, rather than following some predefined regular pattern. Among other things, the scheme includes facilities to compute the spherical harmonics of the angular mask, and Data–Random and Random–Random angular integrals. A software package mangle that implements this scheme, along with complete software documentation, is available at http://casa.colorado. edu/~ajsh/mangle/.
Occupation and Upper Aerodigestive Tract Cancers: A Follow-Up Study in Sweden

Objectives: We sought to examine the associations between occupation and upper aerodigestive tract cancers at various anatomic sites. Methods: The Swedish Family-Cancer Database was used to calculate standardized incidence ratios for different occupational groups, adjusted for age, period, and socioeconomic status. Results: Male dentists showed an increased risk for tongue cancer; hairdressers had an increased risk for tongue and larynx cancers among men and pharynx cancer among women; launderers and dry cleaners showed an increased risk for pharynx cancer among men and lip cancer among women; outdoor occupations such as fishermen, seamen, transport, and construction workers showed increased risks for lip cancer. Conclusions: Although smoking and alcohol drinking can explain some of these results, increased risks found for dentists, hairdressers, and launderers and dry cleaners may partly be explained by their work-related exposures; increased risks of lip cancer in outdoor occupations can be explained by sunlight exposure.
Response, remission and drop-out rates following high-frequency repetitive transcranial magnetic stimulation (rTMS) for treating major depression: a systematic review and meta-analysis of randomized, double-blind and sham-controlled trials

Background Meta-analyses have shown that high-frequency (HF) repetitive transcranial magnetic stimulation (rTMS) has antidepressant properties when compared with sham rTMS. However, its overall response and remission rates in major depression (MD) remain unclear. Thus, we have systematically and quantitatively assessed the efficacy of HF-rTMS for MD based on randomized, double-blind and sham-controlled trials (RCTs). Method We searched the literature from 1995 through to July 2012 using MEDLINE, EMBASE, PsycINFO, Cochrane Central Register of Controlled Trials, SCOPUS, and ProQuest Dissertations & Theses. We used a random-effects model, odds ratios (ORs) and the number needed to treat (NNT). Results Data from 29 RCTs were included, totaling 1371 subjects with MD. Following approximately 13 sessions, 29.3% and 18.6% of subjects receiving HF-rTMS were classified as responders and remitters, respectively (compared with 10.4% and 5% of those receiving sham rTMS). The pooled OR was 3.3 (p < 0.0001) for both response and remission rates (with associated NNTs of 6 and 8, respectively). Furthermore, we found HF-rTMS to be equally effective as an augmentation strategy or as a monotherapy for MD, and when used in samples with primary unipolar MD or in mixed samples with unipolar and bipolar MD. Also, alternative stimulation parameters were not associated with differential efficacy estimates. Moreover, baseline depression severity and drop-out rates at study end were comparable between the HF-rTMS and sham rTMS groups. Finally, heterogeneity between the included RCTs was not statistically significant. Conclusions HF-rTMS seems to be associated with clinically relevant antidepressant effects and with a benign tolerability profile.
Association of Vitamin D Levels With Multiple Sclerosis Activity and Progression in Patients Receiving Interferon Beta-1b.

IMPORTANCE Low serum 25-hydroxyvitamin D (25[OH]D) levels are associated with an increased risk of multiple sclerosis (MS) as well as with increased disease activity and rate of progression in clinically isolated syndromes and early MS. OBJECTIVE To assess the association between 25(OH)D and disease course and prognosis in patients with relapsing-remitting MS treated with interferon beta-1b. DESIGN, SETTING, AND PARTICIPANTS We conducted a prospective cohort study assessing 25(OH)D levels and subsequent MS disease course and progression characterized by magnetic resonance imaging (MRI) and clinical end points. The study took place between November 2003 and June 2005; data analysis was performed between June 2013 and December 2014. The study was conducted among participants in the Betaferon Efficacy Yielding Outcomes of a New Dose (BEYOND) study, a large, phase 3, prospective, multicenter, blinded, randomized clinical trial. Patients were monitored for at least 2 years. Clinic visits were scheduled every 3 months, and MRI was performed at baseline and annually thereafter. Eligible patients included 1482 participants randomized to receive 250 μg or 500 μg of interferon-1b with at least 2 measurements of 25(OH)D obtained 6 months apart. EXPOSURES Serum 25(OH)D measurements were performed at baseline, 6 months, and 12 months. MAIN OUTCOMES AND MEASURES Main outcomes included cumulative number of new active lesions (T2 lesions and gadolinium acetate-enhancing lesions), change in normalized brain volume, relapse rate, and progression determined by the Expanded Disability Status Scale (EDSS). Statistical analyses were adjusted for age, sex, randomized treatment, region, disease duration, and baseline EDSS score. RESULTS Overall, average 25(OH)D levels in 1482 patients were significantly inversely correlated with the cumulative number of new active lesions between baseline and the last MRI, with a 50.0-nmol/L increase in serum 25(OH)D levels associated with a 31% lower rate of new lesions (relative rate [RR], 0.69; 95% CI, 0.55-0.86; P = .001). The lowest rate of new lesions was observed among patients with 25(OH)D levels greater than 100.0 nmol/L (RR, 0.53; 95% CI, 0.37-0.78; P = .002). No significant associations were found between 25(OH)D levels and change in brain volume, relapse rates, or EDSS scores. Results were consistent following adjustment for HLA-DRB1*15 or vitamin D-binding protein status. CONCLUSIONS AND RELEVANCE Among patients with MS treated with interferon beta-1b, higher 25(OH)D levels were associated with lower rates of MS activity observed on MRI. Results for brain atrophy and clinical progression were more equivocal.
Atypical parkinsonism caused by Pro105Leu mutation of prion protein

Objective: To delineate molecular and clinical characteristics of 3 families with PRNP P105L mutation, a variant of Gerstmann-Sträussler-Scheinker syndrome whose main motor symptoms were parkinsonism and/or involuntary movements. Methods: The causative mutation was first determined in the affected patients of family 1 using whole-exome sequencing, and then mutational analysis was extended to families 2 and 3. The clinical features of the patients of these 3 families were summarized. Haplotype analysis was performed using high-density single nucleotide polymorphism array. Results: The whole-exome sequencing revealed that the heterozygous mutation c.314C>T (p.P105L) in PRNP was the only known pathogenic mutation shared by the 3 patients of the family with autosomal dominant parkinsonism. We further identified the same mutation in patients of the other 2 families with autosomal dominant parkinsonism and/or involuntary movements. The clinical features of our patients with PRNP P105L mutation included various motor symptoms such as parkinsonism and involuntary movements in addition to progressive dementia. The clinical features in part overlapped with those of other forms of inherited prion diseases, such as fatal familial insomnia and Huntington disease-like type 1. The patients with PRNP P105L mutation shared a haplotype spanning 7.1 Mb around PRNP, raising the possibility that the mutations in the patients originated from a common founder. Conclusion: Most of the patients presented with parkinsonism in addition to progressive dementia. Although spastic paraparesis has been emphasized as the main clinical feature, the clinical spectrum of patients with PRNP P105L is broader than expected.
Structured Principal Component Analysis

Many tasks involving high-dimensional data, such as face recognition, suffer from the curse of dimensionality: the number of training samples required to accurately learn a classifier increases exponentially with the dimensionality of the data. Structured Principal Component Analysis (SPCA) reduces the dimensionality of the data while preserving its discriminative power. The algorithm finds clusters of similar features, where the similarity between features is measured using the class-conditional Chi-squared distance between the distributions of the features. As features in a cluster are similar and thus redundant, an entire cluster can be represented by a small number of principal components extracted from each cluster. We test the algorithm on two face recognition databases, the Ekman and Friesen Pictures of Facial Affect Database and the Yale Face Database, with encouraging results.
Linguistic Issues in Language Technology Lilt Bootstrapping a Persian Dependency Treebank Bootstrapping a Persian Dependency Treebank Bootstrapping a Persian Dependency Treebank

This paper presents an ongoing project whose goal is to create a freely available dependency treebank for Persian. The data is taken from the Bijankhan corpus, which is already annotated for parts of speech, and a syntactic dependency annotation based on the Stanford Typed Dependencies is added through a bootstrapping procedure involving the open-source dependency parser MaltParser. We report preliminary parsing experiments with promising results after training the parser on a manually annotated seed data set of 215 sentences.
Multidrug Efflux Systems in Helicobacter cinaedi

Helicobacter cinaedi causes infections, such as bacteremia, diarrhea and cellulitis in mainly immunocompromised patients. This pathogen is often problematic to analyze, and insufficient information is available, because it grows slowly and poorly in subculture under a microaerobic atmosphere. The first-choice therapy to eradicate H. cinaedi is antimicrobial chemotherapy; however, its use is linked to the development of resistance. Although we need to understand the antimicrobial resistance mechanisms of H. cinaedi, unfortunately, sufficient genetic tools for H. cinaedi have not yet been developed. In July 2012, the complete sequence of H. cinaedi strain PAGU 611, isolated from a case of human bacteremia, was announced. This strain possesses multidrug efflux systems, intrinsic antimicrobial resistance mechanisms and typical mutations in gyrA and the 23S rRNA gene, which are involved in acquired resistance to fluoroquinolones and macrolides, respectively. Here, we compare the organization and properties of the efflux systems of H. cinaedi with the multidrug efflux systems identified in other bacteria.
A new adaptive filtering algorithm based on discrete wavelet transforms

The wavelet transform domain LMS algorithm are integrated with variable step-size LMS algorithm, from which a new adaptive filtering algorithm is presented based on discrete wavelet transforms (NDWT-LMS). The algorithm can reduce the self-correlation of input signals effectively and can overcome the conflict between high convergence rate and low steady-state error in LMS algorithm which leading by fixed step-size, The computer simulation results indicate that the new algorithm has higher convergence rate and lower steady-state error to compared with LMS algorithm, it can be applied effectively in the adaptive systems.
Aversive Motivational Traits and Web-based Training Outcomes

Web-based training is frequently used by modern organizations as a convenient and low-cost way to administer training programs to employees. This study investigates the relationship of motivational traits, particularly those concerning fear of failure and anxiety, to skill attainment in a Web-based training program. Participants completed a Web-based training program consisting of difficult tasks in Excel while data tracking software recorded their activities. Results show that aversive motivational traits are related to evaluation apprehension, which is in turn related to skill attainment.
Transcriptional profiling on all open reading frames of Saccharomyces cerevisiae

Open reading frames (6116) of the budding yeast Saccharomyces cerevisiae were PCR‐amplified from genomic DNA using 12,232 primers specific to the ends of the coding sequences; the success rate of amplification was 97%. PCR‐products were made accessible to hybridization by being arrayed at very high density on solid support media using various robotic devices. Probes made from total RNA preparations were hybridized for the analysis of the transcriptional activity of yeast under various growth conditions and of different strains. Experimental factors that proved critical to the performance, such as different RNA isolation procedures and the assessment of hybridization results, for example, were investigated in detail. Various software tools were developed that permit convenient handling and sound analysis of the large data quantities obtained from transcriptional profiling studies. Comprehensive arrays are being distributed within the European Yeast Functional Analysis Network (EUROFAN) and beyond. © 1998 John Wiley & Sons, Ltd.
Keratin 19 demonstration of canal of hering loss in primary biliary cirrhosis: “Minimal Change PBC”?

Liver biopsy is important for diagnosing primary biliary cirrhosis (PBC). Prior investigations suggest that immunostaining for biliary keratin 19 (K19) may show the earliest changes suspicious for PBC, namely, loss of the canals of Hering (CoH). We aimed to study the clinical outcomes of patients whose biopsy specimens appeared histologically near normal or with minimal inflammatory changes, but in which K19 staining revealed widespread periportal CoH loss, a finding we termed “minimal change PBC. ” Ten patients were identified prospectively as having nearly normal or mildly inflamed biopsy specimens without diagnostic or suggestive histologic features of PBC, but with near complete CoH loss; six had available follow‐up clinical data, one had follow‐up biopsy. Controls for clinical and/or K19 analysis included six normal livers and biopsy specimens from 10 patients with confirmed early PBC, 10 with early stage chronic hepatitis C (CHC), and nine with resolving, self‐limited hepatitis (RSLH). Staining for K19 in normal controls, livers with “minimal change” PBC, CHC, and RSLH showed 9.2 ± 6.0, 0.44 ± 0.37 (P < 0.0001), 5.7 ± 4.6 (n.s.), 4.1 ± 2.1 (P < 0.02) CoH per portal tract, respectively. Patients with available clinical follow up, compared to patients with diagnostic early‐stage PBC biopsies, showed identical treatment responses to ursodeoxycholic acid, similar rates and types of nonhepatic autoimmune diseases, and/or subsequent development of autoimmune hepatitis overlap syndrome. Conclusion: We suggest that CoH loss demonstrated by K19 immunostaining is an early feature in PBC. Clinical findings in the years following biopsy, including response to ursodeoxycholic acid, show identical changes to patients with biopsy confirmed PBC. We suggest that this “minimal change” feature may support a clinical diagnosis of PBC even in the absence of characteristic, granulomatous, duct destructive lesions. (HEPATOLOGY 2013)
Molecular cloning and characterization of rat sperm surface antigen 2B1, a glycoprotein implicated in sperm‐zona binding

The rat sperm surface antigen, 2B1, that has been proposed to play a key role in sperm adhesion to the zona pellucida, has been cloned and its entire cDNA sequenced. Northern blot analysis indicates that 2B1 is encoded by a 2.2‐kb RNA transcript that is abundantly expressed in the testis. The deduced protein sequence contains 512 amino‐acid residues with a strong candidate signal sequence and C‐terminal transmembrane domain. Data base searches reveal a high degree of sequence similarity to guinea pig, rabbit, monkey, and human PH20 sperm surface antigens, and a lower degree of similarity to honey bee and whiteface hornet venom hyaluronidases. Rat 2B1 antigen also possesses hyaluronidase activity, suggesting that it is a bifunctional protein with putative roles in the dispersion of cumulus oophorus cells as well as zona adhesion. However, while it would appear that 2B1 is the rat homologue of the guinea pig PH20 antigen, they differ in a number of important biochemical respects (including their mode of attachment to the sperm membrane and distribution between soluble and membrane‐bound fractions), as well as in their localization on the sperm membrane. Expression of regions of the 2B1 protein in recombinant bacterial cells has allowed a preliminary mapping of the 2B1 epitope, and has provided more definitive information on the endoproteolytic processing of 2B1 during epidicymal transit. © 1996 Wiley‐Liss, Inc.
Histone H 1 Subtypes and phosphorylation in cell life and death

10 POPULÄRVETENSKAPLIG SAMMANFATTNING. 12 PAPERS IN THE PRESENT THESIS . 15 ABBREVIATIONS . 16 INTRODUCTION. 17 THE ORGANISATION OF DNA INTO CHROMATIN . 17 DNA and the chromosomes . 17 The nucleosome . 18 Chromosome structure . 20 REGULATION OF THE CHROMATIN STRUCTURE-REGULATION OF GENES. 21 THE STRUCTURAL ROLE AND PHYSIOLOGICAL FUNCTION OF HISTONE H1 . 22 Chromatin structure. 22 Gene regulation . 22 Inhibition of replication. 23 Apoptosis. 23 THE STRUCTURE OF HISTONE H1. 25 HISTONE H1 GENES, REGULATION AND EXPRESSION . 29 HISTONE H1 SUBTYPES. 30 THE SIGNIFICANCE OF MULTIPLE H1 SUBTYPES . 34 Sequence conservation . 34 Gene regulation . 34 Knock-out experiments . 34 Affinity for DNA and chromatin. 35 Distribution in chromatin . 35 POSTTRANSLATIONAL MODIFICATIONS OF H1 HISTONES . 36 PHOSPHORYLATION OF HISTONE H1 . 38 Significance of H1 phosphorylation. 38 Histone H1 phosphorylating and dephosphorylating enzymes. 38 H1 phosphorylation in gene regulation . 40 Histone H1 phosphorylation and chromatin condensation . 40 H1 phosphorylation in the cell cycle. 41 Histone H1 phosphorylation in apoptosis . 43 Histone H1 phosphorylation pattern in malignant transformation. 44 AIMS OF THE THESIS. 45 MATERIAL AND METHODS. 47 HISTONE H1 EXTRACTION . 48 SEPARATION OF H1 HISTONES AND THEIR PHOSPHORYLATED VARIANTS. 50 Reversed Phase-High Performance Liquid Chromatography (RP-HPLC) of H1 histones . 50 Hydrophilic Interaction Liquid Chromatography (HILIC) . 51 High Performance Capillary Electrophoresis (HPCE). 51 GENETIC ANALYSIS . 52 DNA-samples. 52 PCR amplification of H1 genes or gene fragments. 53 DNA sequencing . 54 Detection of sequence variations . 54 Restriction Fragment Length Polymorphism (RFLP) analysis . 54 Denaturing HPLC (Wave) . 55 FLOW CYTOMETRY . 57 Cell cycle distribution . 58 Cell tracing . 60 Apoptosis detection. 60 Cell Sorting using FACS Aria Special order system . 63 CELL CULTURE . 64 Jurkat . 64 T cell activation. 64 Ag1523. 65 IMMUNOCYTOCHEMISTRY . 65 RESULTS AND DISCUSSION . 67 THE EXISTENCE OF H1 MICROSEQUENCE VARIANTS . 67 HISTONE H1 AND H1 PHOSPHORYLATION IN APOPTOSIS. 68 HISTONE H1 SUBTYPE DISTRIBUTION DURING CELL DIVISION. 70 HISTONE H1 PHOSPHORYLATION IN THE CELL CYCLE. 72 CONCLUSIONS. 75 FUTURE ASPECTS . 77 ACKNOWLEDGEMENTS. 79 REFERENCES . 84 PAPERS . 99
Diagnosis and Fault Equivalence in Combinational Circuits

Two procedures are presented: one for diagnosis of single-gate failures and the other for deriving equivalence classes of single faults. Both procedures require use of a diagnostic table which lists gate sensitivities and primary output values for all input patterns in a set of tests which contains at most U tests, where U is an upper bound derived in the text. A gate is defined to be an n-input single-output combinational circuit (n ≥ 1) and a failure is any detectable transformation of the correct gate function. The information contained in a diagnostic table can be used to locate a faulty gate and describe its failed function. Equivalence classes are derived from a diagnostic table by first specifying the primary output values in accordance with a theorem given in the text and then deriving the corresponding gate functions. Examples are given to illustrate both the procedures.
Flip‐Flopping: Ideological Adjustment Costs in the United States Senate

Models of electoral competition in which candidates can change position at no cost predict the convergence of platforms in a two-candidate election. Such convergence is at odds with empirical observation. In this paper, I undertake a study of candidate positioning in the United States Senate and determine the extent to which electoral costs associated with changing position explain the ideological positions taken by Senators. Using over 50 years of roll call voting data, I use a simulated method of moments approach to estimate a dynamic model of candidate positioning for U.S. Senators. The ﬁndings support a model in which Senators face convex costs to changing position, with the best ﬁtting model being one with linear costs of adjustment. The model thus predicts severe punishments for “ﬂip-ﬂopping” Senators (those who make large changes in position). As a result of the signiﬁcant costs associated with adjusting position, the empirical validity of the Median Voter Theorem (which depends upon candidates being able to change position at no cost) is called into question.
Linking plant ecology and long-term hydrology to improve wetland restoration success

Although millions of dollars are spent restoring wetlands, failures are common, in part because the planted vegetation cannot survive in the restored hydrology. Wetland restoration would be more successful if the hydrologic requirements of wetland plant communities were known so that the most appropriate plants could be selected for the range of projected hydrology at the site. Here we describe how hydrologic models can be used to characterize the long-term hydrology of wetland plant communities, and we show how these results can be used to define wetland design criteria. In our study, we quantified differences in long-term (40-year) hydrologic characteristics of the pond pine woodland (PPW), nonriverine swamp forest (NRSF), high pocosin (HP), and bay forest (BF) plant communities native to the North Carolina Coastal Plain. We found that the median water level was 8 cm below the land surface in PPW and 9, 2, and 8 cm above the land surface for NRSF, HP, and BF, respectively. When the land surface was inundated, the median duration of inundation was 91 d year-1 for PPW and 317, 243, and 307 d year-1 for NRSF, HP, and BF, respectively. Our models suggested that the PPW received an average of 15% of its water input from groundwater inflow, whereas the other communities we modeled did not appear to receive groundwater inflow. Using these results and soil organic layer thickness, we developed and propose design criteria linking soil, vegetation, and hydrology parameters that should contribute to improved restoration success.