Miracle-dz/UniFAR-FTUs huggingface dataset:
Cleft constructions in discourse.

This thesis presents an analysis of the structure and function of deft constructions in discourse. Drawing on a corpus of naturally-occurring spoken and written data, we present a multi-layered explanation of how it-clefts, wh-clefts, and reverse wh-clefts are different from non-clefts, and from one another. After a review of previous research on clefts in discourse, we explore the aspects of syntax, semantics, and pragmatics relevant to the structure and function of all three types of deft. The discussion falls into three main parts: " An analysis of the three deft types, within the framework of Generalized Phrase Structure Grammar (cf. Gazdar et aL [19851), in which particular attention is paid to the variety of constituents that can appear in particular positions in each type. The output of the grammar rules is compared to the examples that occur in the corpus of data. "A treatment of deft presupposition in terms of an analogy (suggested by van der Sandt [1988)) between presupposition and the treatment of pronominal anaphora in Kamp's [19811 Discourse Representation Theory. " An examination of the range of accentual patterns, presuppositional relations, and information structures typically appearing in clefts of all three kinds. We show that marked distinctions exist between the three cleft types in terms of all these factors, and suggest ways in which this helps to differentiate the range of discourse contexts in which clefts in general, and each cleft type in particular, are appropriate. At the end of the thesis we point to an analogy between the formal model for clefts presented and a psychological model of sentence processing. We also suggest how the conclusions regarding both the structure and function of clefts as a class of construction and the distinction between the three types of cleft could be synthesised in a decision procedure for syntactic choice. Finally, we suggest some related areas for further research.
Inbreeding in Gredos Mountain Range (Spain): Contribution of Multiple Consanguinity and Intervalley Variation

AbstractThe present paper examines consanguineous marriages occurring between 1874 and 1975 in three valleys (Tormes, Alberche, and Tiétar) in the Sierra de Gredos mountain range, Avila province, Spain. Information was obtained from parish registers of 42 localities, corresponding to a total of 41,696 weddings. Consanguineous marriages were defined as those up to the third degree of consanguinity (second cousins). From 1874 to 1975 the percentage of related mates was 4.45% and the inbreeding coefficient was 0.0011868 (for 1874 to 1917 corresponding figures up to the fourth degree were 16.44% and 0.0019085, respectively). In order to ascertain the characteristics and evolution of mating patterns in Gredos, the contribution of each degree of kinship was analyzed as a whole and then for each valley separately. Regarding total consanguineous marriages in Gredos, there is a low frequency of uncle-niece matings (0.21%) and a first-second cousin mating ratio (C22/C33) of 0.23 (up to the third degree of consanguinity). Before 1918 multiple matings (i.e., those involving more than a single relationship) accounted for 19.16% of consanguineous marriages (up to the fourth degree). The observed frequencies of multiple consanguineous marriages was, on average, about twice that expected at random, and the proportion of such marriages to total inbreeding was 34.65%. The temporal change of the Gredos inbreeding pattern was characterized by a recent decrease; the highest inbreeding levels correspond to the period from 1915 to 1944. Finally, intervalley differences (maximum inbreeding coefficient in the Tormes, minimum in the Tiétar) are interpreted considering the geography, population size, and population mobility for each valley
Stage-Specific Expression of Genes Associated with Rat Spermatogenesis: Characterization by Laser-Capture Microdissection and Real-Time Polymerase Chain Reaction1

Abstract Spermatogenesis in the rat consists of 14 unique morphologic cellular associations between Sertoli cells and developing germ cells within the seminiferous epithelium. The complexity of the cellular associations leads to difficulty in the isolation of individual cells at a defined stage of development for the study of their unique patterns of gene or protein expression. Thus, laser-capture microdissection is an ideal technique to permit such analysis. This study used laser-capture microdissection and real-time reverse transcription-polymerase chain reaction (RT-PCR) to quantitate the stage-specific expression of a series of genes of functional significance in hormonal regulation and cell-cell interactions in spermatogenesis, including cathepsin-L, CREM-τ, transition protein-1, androgen receptor, β1-integrin, N-cadherin, and hypoxanthine phosphoribosyltransferase (HPRT). Frozen sections (10 μm) were obtained from normal adult rat testes. Laser-capture microdissection (LCM) was used to capture all cells in cross-sections of seminiferous tubules that were grouped into stages I–V, VII–VIII, and IX–XIII. Transition protein-1 expression was lowest during stages I–V and increased 5.9-fold during stages VII–VIII and IX–XIII (P < 0.01). Cathepsin-L expression was highest during stages I–V and VII–VIII, falling 4.9-fold during stages IX–XIII (P < 0.05). Similarly, CREM-τ expression was highest during stages I–V and VII–VIII, falling 1.6-fold during stages IX–XIII (P < 0.05). A novel CREM-τ isoform lacking the phosphorylation domain was also characterized but was not stage-specific. β1-Integrin, N-cadherin, and androgen receptor expression did not change between the spermatogenic stages examined. HPRT housekeeper expression was lowest during stages I–V but increased 1.5-fold during stages VII–VIII and IX–XIII (P < 0.05). This study is the first to apply LCM and real-time RT-PCR analysis to quantitate stage-specific changes in the expression of multiple genes in the seminiferous epithelium.
Practice patterns of phosphate binder use and their associations with mortality in chronic kidney disease.

BACKGROUND Higher serum phosphorus is associated with an increased mortality among those with chronic kidney disease (CKD). We examined the practice patterns of phosphate binder use to lower serum phosphorus levels and their associations with mortality in the non-dialysisdependent CKD population. METHODS We examined the factors associated with the use of calcium and non-calcium phosphate binders in those with stage 3 and 4 CKD (eGFR 15 - 59 mL/min/1.73 m2) using logistic regression models. The associations between phosphate binder use and mortality were studied using propensity based analysis. RESULTS Out of 57,928 patients with eGFR 15 - 59 mL/min/1.73 m2, 13,325 (23%) patients had serum phosphorus levels measured. 945 patients were prescribed phosphate binders, with 238 (25%) of them prescribed non-calcium-based phosphate binders and the rest calcium-based phosphate binders. Higher BMI, higher serum phosphorus, and higher serum calcium were associated with higher odds of being prescribed a non-calcium-based binder. Phosphate binder use was not significantly associated with mortality in either the entire cohort or the matched cohort in the analysis limited to those who were treated for at least 6 months. In the matched cohort, those who were treated for 1 year with a phosphate binder had a non-significant lower mortality rate (hazard ratio (HR): 0.85, 95% CI 0.66, 1.10). CONCLUSIONS Phosphate binder use for 6 months and 1 year was not associated with reduced mortality in those with stage 3 and stage 4 CKD.
Metrological Characterization of Cold Plates for Power Converters

The reliability of a power converter can be improved using a well-dimensioned cold plate. For this purpose, it is necessary to realize a state-of-the-art cold plate by means of thermal-fluid dynamic numerical analysis and an ad hoc experimental test bench. Features and metrological characterization of a test bench for cold plate characterization are discussed in this paper. An infrared camera is used to measure the outer surfaces, and thermocouples are employed to measure the temperatures of some inner points, but not all the points of a structure under test are accessible to probes and sensing. An accurate 3-D numerical model has been set to widen the cold plate characterization investigating the values of the variables of interest, such as the temperature and the water velocity field, in all the points of the geometry. A case study is described, showing that using modeling with potentially high accuracy in designing new systems can be useful not only to choose, by comparison, the best solution, saving time and prototyping costs, but also to foresee the system performance.
Visibility enhancement for underwater visual SLAM based on underwater light scattering model

This paper presents a real-time visibility enhancement algorithm for effective underwater visual simultaneous localization and mapping (SLAM). Unlike an aerial environment, an underwater environment contains larger particles and is dominated by a different image degradation model. Our method starts with a thorough understanding of underwater particle physics (e.g., forward, back, multiple scattering, blur and noise). Targeting underwater image enhancement in a real-world application, we include an artificial light model in the derivation. The proposed method is effective for both color and gray images with substantial improvement in the process time compared to conventional methods. The proposed method is validated by using simulated synthetic images (color) and real-world underwater images (color and grayscale). Using two underwater image sets acquired from the same area but with different water turbidity, we evaluate the proposed visibility enhancement and camera registration improvement in SLAM.
In search for symmetries in the metabolism of cancer

Even though aerobic glycolysis, or the Warburg effect, is arguably the most common trait of metabolic reprogramming in cancer, it is unobserved in certain tumor types. Systems biology advocates a global view on metabolism to dissect which traits are consistently reprogrammed in cancer, and hence likely to constitute an obligate step for the evolution of cancer cells. We refer to such traits as symmetric. Here, we review early systems biology studies that attempted to reveal symmetric traits in the metabolic reprogramming of cancer, discuss the symmetry of reprogramming of nucleotide metabolism, and outline the current limitations that, if unlocked, could elucidate whether symmetries in cancer metabolism may be claimed. WIREs Syst Biol Med 2016, 8:23–35. doi: 10.1002/wsbm.1321
The University of California, San Francisco Family Alcoholism Study. I. Design, methods, and demographics.

BACKGROUND The University of California, San Francisco (UCSF) Family Alcoholism Study is a project designed to identify genetic loci that influence susceptibility to alcohol dependence and related phenotypes. Evidence supports a substantial genetic contribution to alcoholism susceptibility. However, the genetic epidemiology of alcoholism is complex, and its clinical manifestation is heterogeneous, making phenotype definition and demonstration of linkage difficult. Despite these challenges, some progress has been made toward identifying genes. METHODS The UCSF Family Alcoholism Study used a small family design, focusing primarily on sibling pairs and parent-child trios for linkage and association studies. Alcoholism-related phenotypes were assessed through interview and self-report questionnaires, with a focus on unidimensional and subphenotypical traits. Data-driven approaches to determining the most promising phenotypes for genetic analysis are being used. Both genome-wide scan and candidate gene approaches were used. RESULTS The study enrolled 2154 individuals from 970 families from December 1995 through January 2003. Test-retest and interrater reliability for clinical data are very good, and power estimates suggest that this study will have adequate power by linkage analysis to detect loci with moderate effects. Design, methods, and sample demographics of the UCSF Family Study are presented, along with intrafamilial correlations for primary diagnostic phenotypes. CONCLUSIONS Plans for genetic analysis, novel approaches to phenotype refinement, and the implications of ascertainment bias for heritability estimates are discussed.
Connexin 26 correlates with Bcl-xL and Bax proteins expression in colorectal cancer.

AIM To evaluate of Cx26 in correlation with Bcl-xL and Bax proteins in colorectal cancer. METHODS Immunohistochemical staining using specific antibodies was performed to evaluate the protein expression of Cx26, Bax and Bcl-xL in 152 colorectal cancer samples and the correlations among studied proteins as well as the relationships between the expression of Cx26, Bax, Bcl-xL and clinicopathological features were analyzed. RESULTS Both normal epithelial cells and carcinoma cells expressed Cx26, Bax and Bcl-xL, but Cx26 in cancer cells showed aberrant, mainly cytoplasmic staining. Expression of Cx26, Bax and Bcl-xL was observed in 55.9%, 55.5% and 72.4% of evaluated colorectal cancers respectively. We found the positive correlation between Cx26 and Bax expression (r = 0.561, P<0.0001), Cx26 and Bcl-xL (r = 0.409, P<0.0001) as well as between Bax and Bcl-xL (r = 0.486, P<0.0001). Association of Cx26, Bax and Bcl-xL expression with histological G2 grade of tumors was noted (P<0.005, P<0.001 and P<0.002 respectively). CONCLUSION Cytoplasmic presence of Cx26 and its association with apoptotic markers could indicate a distinct role from physiological functions of Cx26 in cancer cells and it could suggest that connexins might be a target point for modulations of apoptosis with therapeutic implications.
Triglyceride Concentration and Ischemic Heart Disease

Background—The role of triglycerides as a risk factor of ischemic heart disease (IHD) remains controversial. For the present study, we examined the relation between fasting triglycerides and risk of IHD in the Copenhagen Male Study. Methods and Results—Baseline measurements of fasting lipids and other IHD risk factors were obtained for 2906 white men (age range, 53 to 74 years) who were initially free of overt cardiovascular disease. During an 8-year follow-up period, 229 men had a first IHD event. Crude cumulative incidence rates of IHD were 4.6% for the lowest, 7.7% for the middle, and 11.5% for the highest third of triglyceride levels (P for trend <.001). Compared with the lowest third level and adjusted for age, body mass index, alcohol, smoking, physical activity, hypertension, non–insulin-dependent diabetes mellitus, social class, and LDL and HDL cholesterol, relative risks of IHD (95% confidence interval) were 1.5 (1.0 to 2.3; P=.05) and 2.2 (1.4 to 3.4; P<.001) for the middle and highest third of .
Analysis of secondary chromosomal alterations in 165 cases of follicular lymphoma with t(14;18)

Follicular lymphoma is characterized by the t(14;18) in up to 85% of cases. Almost all cases display evidence of secondary chromosomal alterations at initial diagnosis. The influence of recurrent secondary changes on disease progression has not been fully determined. The purpose of this study was to define the full spectrum of recurrent karyotypic events present at diagnosis in a large cohort of cases and to evaluate the sequence of cytogenetic evolution in relation to morphologic progression. A total of 165 cases of follicular lymphoma with t(14;18) were ascertained for which complete clinical information, histopathology, immunophenotype, and karyotype were available. One hundred sixty cases showed secondary alterations with an average of 7.9 additional changes per case. Recurrent alterations seen at the 10% or greater level included +X, +1q21–q44, +7, +12q, +18q, del(1)(p36), del(6q), del(10)(q22–q24), the development of polyploidy and sidelines, and the presence of extra marker chromosomes and chromosomal additions. Changes that correlated with morphologic progression included del(1)(p36), del(6q), del(10)(q22–q24), +7, the total number of abnormalities, the number of markers and additions, and the presence of polyploidy. The most frequent second event arising after the t(14;18) was duplication of the der(18)t(14;18). This study demonstrates that the number and type of secondary chromosomal alterations in follicular lymphoma is highly variable between cases, but that a relatively small number of changes are seen repeatedly in different combinations. A consistent pattern of cytogenetic evolution could not be identified. Potentially significant gene duplications or amplifications may be disguised within marker chromosomes and additions. Additional cytogenetic investigation is required to decipher the karyotypic complexity associated with the progression of follicular lymphoma. © 2001 Wiley‐Liss, Inc.
Assessing Anti-White Attitudes and Predicting Perceived Racism: The Johnson-Lecci Scale

Five studies are herein reported to describe the development and preliminary validation of the Johnson-Lecci Scale (JLS), a multicomponent self-report measure of anti-White attitudes held among Blacks. Items were generated from the everyday experiences of Black respondents using an act-frequency approach, and the scale configuration was derived using factor analysis. The factor structure was shown to be robust because it was cross-validated in an independent sample. The resulting JLS factors (subscales) were ingroup-directed stigmatization and discriminatory expectations, outgroup-directed negative beliefs, negative views toward ingroup-outgroup relations, and negative verbal expression toward the outgroup. These subscales were shown to predict the interpretations of ambiguously racist scenarios (i.e., perceived racism) and converged with peer evaluations of the target’s anti-White attitudes. The subscales also demonstrate both convergent and discriminant validity with other self-report assessments of bias relating to age, gender, education, socioeconomic status, and race.
Quantitative RT-PCR Analysis of the MOZ-CBP Fusion Transcript in Therapy-related Acute Myeloid Leukemia With t(8;16)(p11;p13)

We developed a real time reverse transcriptase polymerase chain reaction (RT-PCR) assay system for detecting the MOZ-CBP fusion transcript and used it to monitor minimal residual disease (MRD) status in a patient with therapy related acute myeloid leukemia (t-AML) harboring t(8;16)(p11;p13). Expression of the MOZ-CBP fusion transcript was determined by RT-PCR analysis of the patient’s bone marrow at the time of diagnosis. Thereafter, real time RT-PCR was used to evaluate MRD levels throughout the entire course of treatment. The sensitivity of quantitative RT-PCR for the MOZ-CBP fusion transcript was 10−5. Below this level, MRD was classified as negative. Real time RT-PCR of the bone marrow after induction therapy showed the reduction of MOZ-CBP transcript to approximately 10−3 level when compared to the diagnostic sample. MRD was classified as negative (<10−5 compared with that in the bone marrow at diagnosis) after 5 courses of chemotherapy, a level that was maintained post-allo-hematopoietic stem cell transplantation. Real time RT-PCR of the MOZ-CBP transcript is a useful tool for assessing MRD status for a patient with therapy related acute myeloid leukemia who was initially predicted to have a poor prognosis.
The eae gene of enteropathogenic Escherichia coli encodes a 94-kilodalton membrane protein, the expression of which is influenced by the EAF plasmid

The production of a characteristic intestinal histopathology called attaching and effacing (A/E) lesions by enteropathogenic Escherichia coli (EPEC) is a major characteristic of EPEC pathogenesis. We previously identified a chromosomal gene (eae) of EPEC necessary for the production of A/E lesions on human tissue culture cells. Using antiserum raised to an Eae-PhoA fusion protein, we found that the eae gene encodes a 94-kDa membrane protein. This antiserum recognized a 94-kDa membrane protein in parent strain E2348/69 and a protein of similar size in E. coli HB101 carrying eae on a plasmid but did not recognize any proteins in E. coli HB101 carrying a plasmid with an internal deletion in the eae gene. Antigenically related proteins of ca. 94 kDa were detected in a collection of EPEC strains representing seven EPEC serogroups and in two EHEC strains of serotype O26:H11. Volunteer sera drawn 28 days after but not before ingestion of strain E2348/69 recognized the 94-kDa Eae protein as well as a 128-kDa Eae-PhoA fusion protein, suggesting that the Eae protein is likely to be a previously reported 94-kDa protein shown to be immunogenic in volunteers. The amount of detectable Eae protein was increased in the presence of a high-molecular-weight plasmid which is associated with the ability to produce localized adherence to tissue culture cells. These data suggest that the virulence plasmid of EPEC strain E2348/69 may have a regulatory role in the production of A/E activity.
Genotyping of Varicella-Zoster Virus and the Discrimination of Oka Vaccine Strains by TaqMan Real-Time PCR

ABSTRACT Single nucleotide polymorphisms (SNPs) in five genes have been used to identify four major subtypes of wild-type varicella-zoster virus (VZV) A, B, C, and J. Additional SNPs, located in the IE62 major transactivating gene can be used to differentiate the Oka vaccine strain (vOka) from wild-type VZV. Primer-probe sets for the detection of the five polymorphic loci were designed by Applied Biosystems for the ABI 7900HT platform. Probes for each allele were labeled with VIC or 6-carboxyfluorescein fluorogenic markers. Each primer-probe set was validated to establish assay sensitivity and specificity using VZV DNA of predetermined copy number and genotype. Further evaluation was carried out using DNA samples from the vesicle fluid or skin swab of the rash of adult patients with herpes zoster or rashes due to vOka. Assay sensitivity ranged from 10 and 108 copies/ml of VZV DNA (equivalent to 2 to 20 copies per reaction). Statistical analyses showed that for each genotype, a set of two probes clearly differentiated the nucleotide present (allele) at that locus (P < 0.0001). It was possible to determine the genotype of wild-type VZV using one of four SNP assays and also to differentiate wild type from vOka using a single SNP assay. The assay can be used for diagnostic and epidemiological studies of VZV, including the differentiation of vOka from wild-type strains, investigation of breakthrough infections, and varicella outbreaks following immunization.