Miracle-dz/UniFAR-FTUs huggingface dataset:
TAGster: efficient selection of LD tag SNPs in single or multiple populations

UNLABELLED Genetic association studies increasingly rely on the use of linkage disequilibrium (LD) tag SNPs to reduce genotyping costs. We developed a software package TAGster to select, evaluate and visualize LD tag SNPs both for single and multiple populations. We implement several strategies to improve the efficiency of current LD tag SNP selection algorithms: (1) we modify the tag SNP selection procedure of Carlson et al. to improve selection efficiency and further generalize it to multiple populations. (2) We propose a redundant SNP elimination step to speed up the exhaustive tag SNP search algorithm proposed by Qin et al. (3) We present an additional multiple population tag SNP selection algorithm based on the framework of Howie et al., but using our modified exhaustive search procedure. We evaluate these methods using resequenced candidate gene data from the Environmental Genome Project and show improvements in both computational and tagging efficiency. AVAILABILITY The software Package TAGster is freely available at http://www.niehs. nih.gov/research/resources/software/tagster/
A novel role for the integrin-binding III-10 module in fibronectin matrix assembly

Fibronectin matrix assembly is a cell-dependent process which is upregulated in tissues at various times during development and wound repair to support the functions of cell adhesion, migration, and differentiation. Previous studies have demonstrated that the alpha 5 beta 1 integrin and fibronectin's amino terminus and III-1 module are important in fibronectin polymerization. We have recently shown that fibronectin's III-1 module contains a conformationally sensitive binding site for fibronectin's amino terminus (Hocking, D.C., J. Sottile, and P.J. McKeown-Longo. 1994. J. Biol. Chem. 269: 19183- 19191). The present study was undertaken to define the relationship between the alpha 5 beta 1 integrin and fibronectin polymerization. Solid phase binding assays using recombinant III-10 and III-1 modules of human plasma fibronectin indicated that the III-10 module contains a conformation-dependent binding site for the III-1 module of fibronectin. Unfolded III-10 could support the formation of a ternary complex containing both III-1 and the amino-terminal 70-kD fragment, suggesting that the III-1 module can support the simultaneous binding of III-10 and 70 kD. Both unfolded III-10 and unfolded III-1 could support fibronectin binding, but only III-10 could promote the formation of disulfide-bonded multimers of fibronectin in the absence of cells. III-10-dependent multimer formation was inhibited by both the anti-III-1 monoclonal antibody, 9D2, and amino-terminal fragments of fibronectin. A fragment of III-10, termed III-10/A, was able to block matrix assembly in fibroblast monolayers. Similar results were obtained using the III-10A/RGE fragment, in which the RGD site had been mutated to RGE, indicating that III-I0/A was blocking matrix assembly by a mechanism distinct from disruption of integrin binding. Texas red- conjugated recombinant III-1,2 localized to beta 1-containing sites of focal adhesions on cells plated on fibronectin or the III-9,10 modules of fibronectin. Monoclonal antibodies against the III-1 or the III-9,10 modules of fibronectin blocked binding of III-1,2 to cells without disrupting focal adhesions. These data suggest that a role of the alpha 5 beta 1 integrin in matrix assembly is to regulate a series of sequential self-interactions which result in the polymerization of fibronectin.
Volume of spheres in doubling metric measured spaces and in groups of polynomial growth

(Volume de spheres dans les espaces metriques mesures doublants et dans les groupes a croissance polynomiale) Soit G un groupe localement compact, compactement engendre et U une partie compacte generatrice. On prouve que si G est a croissance polynomiale, alors la suite des puissances de U forme une suite de Folner et on montre que le rapport μ(U n+1 -U n ) μ(U n ) tend polynomialement vers 0. La demonstration n'utilise que deux ingredients: le fait qu'un groupe a croissance polynomiale est doublant, et une propriete de faible geodesicite: la propriete (M). Par consequent ce resultat s'etend a une large classe d'espaces metriques mesures doublants, comme les graphes et les varietes riemanniennes. Comme application, nous obtenons un theoreme ergodique presque sur et dans L P (1 < p < oo) pour les moyennes sur les boules d'un groupe a croissance polynomiale.
Patent foramen ovale is an important predictor of adverse outcome in patients with major pulmonary embolism.

BACKGROUND Right-to-left shunt through a patent foramen ovale is frequently diagnosed by contrast echocardiography and can be particularly prominent in the presence of elevated pressures in the right side of the heart. Its prognostic significance in patients with pulmonary thromboembolism, however, is unknown. METHODS AND RESULTS The present prospective study included 139 consecutive patients with major pulmonary embolism diagnosed on the basis of clinical, echocardiographic, and cardiac catheterization criteria. All patients underwent contrast echocardiography at presentation. The end points of the study were overall mortality and complicated clinical course during the hospital stay defined as death, cerebral or peripheral arterial thromboembolism, major bleeding, or need for endotracheal intubation or cardiopulmonary resuscitation. Patent foramen ovale was diagnosed in 48 patients (35%). These patients had a death rate of 33% as opposed to 14% in patients with a negative echo-contrast examination (P=.015). Logistic regression analysis demonstrated that the only independent predictors of mortality in the study population were a patent foramen ovale (odds ratio [OR], 11.4; P<.001) and arterial hypotension at presentation (OR, 26.3; P<.001). Patients with a patent foramen ovale also had a significantly higher incidence of ischemic stroke (13% versus 2.2%; P=.02) and peripheral arterial embolism (15 versus 0%; P<.001). Overall, the risk of a complicated in-hospital course was 5.2 times higher in this patient group (P<.001). CONCLUSIONS In patients with major pulmonary embolism, echocardiographic detection of a patent foramen ovale signifies a particularly high risk of death and arterial thromboembolic complications.
Estimating Economic Benefits of Water Clarity to Downstream Lakes from Constructed Wetlands

ii Dedication . iv Aknowledgements. v Vita . vii List of Tables . ixix List of Figures . x Chapter 1: Introduction . 1 Chapter 2: Methods and Materials . 5 2.1 Study Site . 5 2.2 Data Sources . 6 2.3 Statistical Analysis . 7 2.3.1 Economic Benefits of Water Quality Improvements to Lakes in Ohio . 7 2.3.1.1 Derivation of Log-Log and Log-Linear Willingness to Pay (WTP) Values. 8 2.3.2 Fixed Variable Lake Effects . 9 2.3.3 Cost of Constructed Wetlands . 12 viii Chapter 3: Results . 16 3.1 Log-Linear vs. Log-Log WTP and Net Economic Gains . 17 3.2 Effects of Watershed Variables on Wetland Costs . 18 3.3 Effects of Willingnes to Pay on Net Economic Gains (NEGs) . 18 Chapter 4: Discussion . 24 4.1 Log-Linear vs. Log-Log WTP . 24 4.2 Watershed Variables Influencing NEGs . 28 4.3 Other Benefits Associated with Wetlands . 29 4.4 Recommendations . 30 Chapter 5: Conclusion. 32 References . 34 Appendix A: Table Summary of Lake Attributes . 40 Appendix B: Table Summary of Cost and Benefits for all Lakes . 44 Appendix C: Random Effects Lake Model . 53
Simultaneous Predistortion and Nonlinear Detection for Nonlinearly Distorted OFDM Signals

Orthogonal Frequency Division Multiplexing (OFDM) is vulnerable with respect to nonlinear distortions caused, for example, by a nonlinear high power amplifier. In the presence of nonlinear high power amplification, OFDM suffers from crosstalk between all subcarriers. Furthermore, the power density spectrum is significantly widened. In this paper, we simultaneously use a memoryless predistorter at the transmitter side and a nonlinear detector at the receiver side. The predistorter reduces the out-of-band power, whereas the nonlinear detector improves the bit error rate. Since maximum-likelihood detection is prohibitive, a novel reducedstate symbol detector derived from the maximum-likelihood detector is proposed. For a QPSK/OFDM system in the presence of a memoryless solid-state power amplifier it is shown that the predistorter is not only useful for spectral shaping, but also in order to reduce the computational complexity of the nonlinear detector and to provide more robustness concerning an incomplete knowledge of the characteristics of the nonlinearity at the receiver. The overall raw bit error performance is shown to be close to that of a linear QPSK/OFDM system.
Sustainability Debt: A Portfolio-Based Approach for Evaluating Sustainability Requirements in Architectures

Architectural Sustainability refers to the ability of an architecture to achieve its goals while sustaining its value on dimensions related to environmental, social, economic, individual and/or technical during its operation and evolution. While the process of architectural design implies a fit between the requirements, system conditions and constraints; incomplete information and uncertainty may increase the cost of the architecture, introduce risks, alter its value and influence the extent to which it can evolve and sustain. We propose an economics-driven architectural evaluation method which extends the Cost Benefits Analysis Method (CBAM) and integrates principles of modern portfolio theory to control the risks when linking sustainability concern to architectural design decisions. The method aims at identifying portfolio(s) of architecture design decisions which are more promising for adding/delivering value while reducing risk on the sustainability dimensions. The method quantifies the sustainability debt of these decisions. The ultimate goal is to develop an objective decision-support framework for reasoning about sustainability requirements in relation architecture decisions in the presence of uncertainty. We evaluate the approach with an Emergency Deployment System (EDS). The results show that the method can make the value, cost and risks of architectural design decisions and sustainability requirements explicit.
Purification and Characterization of a Vasoactive Intestinal Polypeptide-degrading Endoprotease from Porcine Antral Mucosal Membranes (*)

A neutral endoprotease was isolated from porcine antral mucosa and purified to homogeneity as examined by SDS-polyacrylamide gel electrophoresis (PAGE). Throughout the purification, t-butyloxycarbonyl-Arg-Val-Arg-Arg-4-methylcoumaryl-7-amide (MCA) was used as a substrate, which was found to be hydrolyzed specifically by the enzyme at the Arg-Arg bond. Unexpectedly, however, the enzyme was also found to hydrolyze vasoacive intestinal polypeptide (VIP) fairly specifically and more efficiently when various neuropeptides and related peptides were examined as substrates. It could degrade VIP by cleaving three peptide bonds not containing an arginine residue(s) with K = 7.7 × 10M and k/K = 7.4 × 106M s (at pH 7.6 in the presence of 0.1% Lubrol PX), whereas only secretin, substance P, and a few others were hydrolyzed at much slower rates among the various peptides examined. Both activities toward the MCA substrate and VIP behaved in parallel throughout the purification procedures and showed essentially the same pH optimum and susceptibility toward various inhibitors and detergents. Therefore, both activities are thought to be due to the same enzyme. This endoprotease required 0.001% or a higher concentration of a detergent such as Lubrol PX or Triton X-100 for its maximal activity. Its optimum pH was about 7.5 and the molecular weight was estimated to be approximately 37,000 by SDS-PAGE. This enzyme was strongly inhibited by serine protease inhibitors such as diisopropylfluorophosphate and phenylmethanesulfonyl fluoride. It was also inhibited by p-chloromercuribenzoic acid, but not by some other cysteine protease inhibitors. Therefore, the enzyme appears to be most likely a kind of serine protease although its possibility as a cysteine protease cannot be completely excluded. Analysis of its cleavage specificity toward various oligopeptides indicated the possibility that the protease might recognize a specific amino acid sequence(s) and/or conformation in the vicinity of the cleavage site of the target peptide. Various characteristics of the endoprotease suggest that it is a novel membrane-bound neuropeptide-degrading endoprotease fairly specific for VIP.
Rodent Thyroid, Liver, and Fetal Testis Toxicity of the Monoester Metabolite of Bis-(2-ethylhexyl) Tetrabromophthalate (TBPH), a Novel Brominated Flame Retardant Present in Indoor Dust

Background: Bis-(2-ethylhexyl) tetrabromophthalate (TBPH) is widely used as a replacement for polybrominated diphenyl ethers (PBDEs) in commercial flame retardant mixtures such as Firemaster 550. It is also used in a commercial mixture called DP 45. Mono-(2-ethyhexyl) tetrabromophthalate (TBMEHP) is a potentially toxic metabolite. Objectives: We used in vitro and rodent in vivo models to evaluate human exposure and the potential metabolism and toxicity of TBPH. Methods: Dust collected from homes, offices, and cars was measured for TBPH by gas chromatography followed by mass spectrometry. Pregnant rats were gavaged with TBMEHP (200 or 500 mg/kg) or corn oil on gestational days 18 and 19, and dams and fetuses were evaluated histologically for toxicity. We also assessed TBMEHP for deiodinase inhibition using rat liver microsomes and for peroxisome proliferator-activated receptor (PPAR) α and γ activation using murine FAO cells and NIH 3T3 L1 cells. Results: TBPH concentrations in dust from office buildings (median, 410 ng/g) were higher than in main living areas in homes (median, 150 ng/g). TBPH was metabolized by purified porcine esterases to TBMEHP. Two days of TBMEHP exposure in the rat produced maternal hypothyroidism with markedly decreased serum T3 (3,3´,5-triiodo-l-thyronine), maternal hepatotoxicity, and increased multinucleated germ cells (MNGs) in fetal testes without antiandrogenic effects. In vitro, TBMEHP inhibited deiodinase activity, induced adipocyte differentiation in NIH 3T3 L1 cells, and activated PPARα- and PPARγ-mediated gene transcription in NIH 3T3 L1 cells and FAO cells, respectively. Conclusions: TBPH a) is present in dust from indoor environments (implying human exposure) and b) can be metabolized by porcine esterases to TBMEHP, which c) elicited maternal thyrotoxic and hepatotoxic effects and d) induced MNGs in the fetal testes in a rat model. In mouse NIH 3T3 L1 preadipocyte cells, TBMEHP inhibited rat hepatic microsome deiodinase activity and was an agonist for PPARs in murine FAO and NIH 3T3 L1 cells.
Relationship between General and Specific Coordination in 8- to 17-Year-Old Male Basketball Players

The purpose of the present study was to investigate the relationships between general coordination, sport-specific coordination, and sport-specific fitness of 8- to 17-year-old male basketball players. 312 males with training experience ranging from one year in the 8-year-old cohort up to 10 years for the 17-yearolds performed basketball-specific fitness (20 m sprint, Illinois, countermovement jump), general coordination (20 m run with three obstacles), semi-basketball-specific coordination (20 m sprint dribbling two balls, countermovement jump with arm swing) and basketball-specific coordination (Illinois ball dribbling) tests. There were moderate to large correlations between the results of both general and basketball-specific coordination with the results of most basketball-specific coordination tests in all age groups. Correlations between general and basketball-specific coordination were large in four age groups (11–14 yr., r = .52 to r = .76), moderate in five groups (8–10, 15 & 16 yr., r = .37 to r = .46), while not significant in the 17-year-olds. These results suggest that the importance of general coordination for sport-specific skills improvements during a sports-specific skill acquisition phase, remains high at the skill refinement phase, and decreases when sport-specific skills have been mastered to near-perfection.
InSAR Simulations for SWOT and Dual Frequency Processing for Topographic Measurements

INSAR SIMULATIONS FOR SWOT AND DUAL FREQUENCY PROCESSING FOR TOPOGRAPHIC MEASUREMENTS FEBRUARY 2019 GERARD MASALIAS HUGUET B.S., POLYTECHNIC UNIVERSITY OF CATALONIA M.S., UNIVERSITY OF MASSACHUSETTS AMHERST Directed by: Professor Paul R. Siqueira In Earth remote sensing precise characterization of the backscatter coefficient is important to extract valuable information about the observed target. A system that eliminates platform motion during near-nadir airborne observations is presented in this thesis, showing an improvement on the accuracy of measurements for a Kaband scatterometer previously developed at Microwave Remote Sensing Laboratory (MIRSL). These very same results are used to simulate the reflectivity of such targets as seen from a spaceborne radar and estimate height errors based on mission-specific geometry. Finally, data collected from a dual-frequency airborne interferometer comprised by the Ka-band system and an S-band radar is processed and analyzed to estimate forest heights.
Axial Length of Myopia: A Review of Current Research

Myopia, or nearsightedness, is a worldwide common type of refractive error. It is a non-life-threatening disorder with huge social and economic consequences due to its increasing prevalence. Axial length (AL) is the primary determinant of non-syndromic myopia. It is a parameter representing the combination of anterior chamber depth, lens thickness and vitreous chamber depth of the eye. AL can also be treated as an endophenotype of myopia and may provide extra advantages in the investigation of its genetic basis. The study of AL will not only identify the determinants of eye elongation, but also provide aetiological evidence for myopia. The purpose of this review is to outline the current state of AL research. Epidemiological evidence, genetic determinants, the relationship with other eye components and relative animal models of AL are summarised.
Organization of an actin filament-membrane complex. Filament polarity and membrane attachment in the microvilli of intestinal epithelial cells

The association of actin filaments with membranes is now recognized as an important parameter in the motility of nonmuscle cells. We have investigated the organization of one of the most extensive and highly ordered actin filament-membrane complexes in nature, the brush border of intestinal epithelial cells. Through the analysis of isolated, demembranated brush borders decorated with the myosin subfragment, S1, we have determined that all the microvillar actin filaments have the same polarity. The S1 arrowhead complexes point away from the site of attachment of actin filaments at the apical tip of the microvillar membrane. In addition to the end-on attachment of actin filaments at the tip of the microvillus, these filaments are also connected to the plasma membrane all along their lengths by periodic (33 nm) cross bridges. These bridges were best observed in isolated brush borders incubated in high concentrations of Mg++. Their visibility is attributed to the induction of actin paracrystals in the filament bundles of the microvilli. Finally, we present evidence for the presence of myosinlike filaments in the terminal web region of the brush border. A model for the functional organization of actin and myosin in the brush border is presented.
Leber’s Congenital Amaurosis as the Retinal Degenerative Phenotype in Thiamine Responsive Megaloblastic Anemia: A Case Report

Abstract Background: Thiamine responsive megaloblastic anemia syndrome (TRMA), an autosomal recessive disorder is caused by mutations in the SLC19A2 gene which encodes for thiamine transporter 1 (THTR1) protein. TRMA presents with a triad of clinical features that includes diabetes mellitus, megaloblastic anemia and sensorineural hearing loss. Apart from the triad, reported ophthalmic features include cone rod dystrophy, optic atropy and retinitis pigmentosa. Materials and Methods: A female child presented with Leber’s congenital amaurosis at 10 months of age, later diagnosed with hearing impairment at 1 year, diabetes mellitus and megaloblastic anemia at 3 and a half years of age and hence as a case of thiamine responsive megaloblastic anemia. Six exons of the candidate gene SLC19A2 were screened by PCR and direct sequencing. SIFT and PolyPhen analysis was done to predict the probable effect of the mutation. Results: Sequence analysis of the SLC19A2 coding region revealed a novel missense mutation in exon 2; c.314 G > A (p.G105E). Segregation analysis revealed parents heterozygous for the mutation and unaffected sib homozygous for wild type. SIFT and PolyPhen analyses predicted the mutation to be “damaging” (score-0.02) and “probably damaging” (score-0.994), respectively. Conclusions: SLC19A2, the high-affinity thiamine transporter, is the only gene known to be associated with TRMA. Here we describe for the first time Leber’s congenital amaurosis as the retinal phenotype and also report a novel point mutation in the SLC19A2 gene that co-segregated with the disease in a TRMA patient.
Tree-local MCTAG with Shared Nodes: Word Order Variation in German and Korean

Tree Adjoining Grammars (TAG) are known not to be powerful enough to deal with scrambling in free word order languages. The TAGvariants proposed so far in order to account for scrambling are not entirely satisfying. Therefore, an alternative extension of TAG is introduced based on the notion of node sharing. Considering data from German and Korean, it is shown that this TAG-extension can adequately analyse scrambling data, also in combination with extraposition and topicalization.
Evaluation of a language identification system for mono- and multilingual text documents

Language identification is an important task for web information retrieval. This paper presents the implementation of a tool for language identification in mono- and multi-lingual documents. The tool implements four algorithms for language identification. Furthermore, we present a n-gram approach for the identification of languages in multi-lingual documents. An evaluation for monolingual texts of varied length is presented. Results for eight languages including Ukrainian and Russian are presented. It could be shown that n-gram-based approaches outperform word-based algorithms for short texts. For longer texts, the performance is comparable. The evaluation for multi-lingual documents is based on real world web documents. Our tool is able to recognize the languages present in a document with reasonable accuracy.
Autotuning and Self-Adaptability in Concurrency Libraries

Autotuning is an established technique for optimizing the performance of parallel applications. However, programmers must prepare applications for autotuning, which is tedious and error prone coding work. We demonstrate how applications become ready for autotuning with few or no modifications by extending Threading Building Blocks (TBB), a library for parallel programming, with autotuning. The extended TBB library optimizes all application-independent tuning parameters fully automatically. We compare manual effort, autotuning overhead and performance gains on 17 examples. While some examples benefit only slightly, others speed up by 28% over standard TBB.