Miracle-dz/UniFAR-FTUs huggingface dataset:
Direct and Indirect Control of the Initiation of Meiotic Recombination by DNA Damage Checkpoint Mechanisms in Budding Yeast

Meiotic recombination plays an essential role in the proper segregation of chromosomes at meiosis I in many sexually reproducing organisms. Meiotic recombination is initiated by the scheduled formation of genome-wide DNA double-strand breaks (DSBs). The timing of DSB formation is strictly controlled because unscheduled DSB formation is detrimental to genome integrity. Here, we investigated the role of DNA damage checkpoint mechanisms in the control of meiotic DSB formation using budding yeast. By using recombination defective mutants in which meiotic DSBs are not repaired, the effect of DNA damage checkpoint mutations on DSB formation was evaluated. The Tel1 (ATM) pathway mainly responds to unresected DSB ends, thus the sae2 mutant background in which DSB ends remain intact was employed. On the other hand, the Mec1 (ATR) pathway is primarily used when DSB ends are resected, thus the rad51 dmc1 double mutant background was employed in which highly resected DSBs accumulate. In order to separate the effect caused by unscheduled cell cycle progression, which is often associated with DNA damage checkpoint defects, we also employed the ndt80 mutation which permanently arrests the meiotic cell cycle at prophase I. In the absence of Tel1, DSB formation was reduced in larger chromosomes (IV, VII, II and XI) whereas no significant reduction was found in smaller chromosomes (III and VI). On the other hand, the absence of Rad17 (a critical component of the ATR pathway) lead to an increase in DSB formation (chromosomes VII and II were tested). We propose that, within prophase I, the Tel1 pathway facilitates DSB formation, especially in bigger chromosomes, while the Mec1 pathway negatively regulates DSB formation. We also identified prophase I exit, which is under the control of the DNA damage checkpoint machinery, to be a critical event associated with down-regulating meiotic DSB formation.
Interpreting multiple environmental tracer data with a groundwater model in a perialpine catchment

Environmental tracers are isotopic and chemical compounds which have been increasingly used in hydrological sciences to investigate the water cycle. Early studies in the seventies demonstrated the potential of environmental tracers also in groundwater investigations in providing information about groundwater age, travel times, streamline information, ratio of fluxes and recharge rates. Compared to artificial tracer tests over short time scales, transient environmental tracers released into the atmosphere since the early fifties provide a tool to investigate the groundwater flow and transport over time scales of up to 50 years. A case study for the environmental tracers Tritium (H), Helium-3 (decay product of H) and Krypton-85 in a small catchment in Northern Switzerland, near Baltenswil, is presented. It contains a sandy-gravel aquifer with groundwater residence times of two to fifteen years. Its small size (9 square kilometers) and its hydrogeology being well known, thanks to former groundwater investigations and local artificial tracer test campaigns, make this aquifer an excellent test site for environmental tracer modeling. During the years 2003 to 2006 a new sampling campaign, undertaken by EAWAG Dübendorf and IPB Bern for the present study, provided a new set of Tritium, Helium-3 and Krypton-85 data. In particular, Krypton-85 data show at some locations significant variations on a seasonal timescale without an apparent trend. Integrating the information coming from different tracers into a groundwater modeling effort is the main intention of this thesis. Following a method from Gomez-Hernandez (1991), the transmissivity field is stochastically modeled. The groundwater flow model is identified by means of Stochastic Inverse Modeling in a transient regime. Available transient hydraulic head data together with local measurement of transmissivities (T) are used for calibration of the T-field, performed with the code INVERTO (Hendricks-Franssen, 2001). The evaluation of the aquifer recharge by precipitation and discharge via drains (natural springs) is performed through comparison of the calculated and measured time-varying hydraulic heads after the inversion procedure. Despite a complete lack of knowledge about the aquifer’s natural discharge rates, a fair reproduction of the observed water table variations for the last ten years is obtained. Stochastic inverse modeling allows a reliable estimate of the water budget of the aquifer system and selecting the ensemble of possible T-fields governing the real but unknown transient flow field. A number of equally-likely T-realizations honoring both T and time-varying head measurements are generated. The calibrated T-fields share common pattern features. Considering an ensemble of T-realizations,
Three-Dimensional Information in Face Representations Revealed by Identity Aftereffects

Representations of individual faces evolve with experience to support progressively more robust recognition. Knowledge of three-dimensional face structure is required to predict an image of a face as illumination and viewpoint change. Robust recognition across such transformations can be achieved with representations based on multiple two-dimensional views, three-dimensional structure, or both. We used face-identity adaptation in a familiarization paradigm to address a long-standing controversy concerning the role of two-dimensional versus three-dimensional information in face representations. We reasoned that if three-dimensional information is coded in the representations of familiar faces, then learning a new face using images generated by one three-dimensional transformation should enhance the robustness of the representation to another type of three-dimensional transformation. Familiarization with multiple views of faces enhanced the transfer of face-identity adaptation effects across changes in illumination by compensating for a generalization cost at a novel test viewpoint. This finding demonstrates a role for three-dimensional information in representations of familiar faces.
Occupational health risks of barbers and coiffeurs in Izmir

The objective of this study was to examine self-reported occupational health risks and health complaints of barbers and hairdressers. A total of 1284 individuals from 300 workplaces in Izmir participated in this study. The workers completed the questionnaires during their training in occupational health. Self-reported symptoms were allergy: 35% and musculoskeletal symptoms: 32%. The frequency of allergy complaints was found to be significantly higher in older individuals and in women. Allergic complaints were more frequent in i) those having history of allergy, ii) in the group where the use of protective clothing and gloves was lower, iii) in smokers and in those who found ventilation in the workplace to be inadequate. Only 41.2% reported that they used gloves and 15.2% reported the use of protective clothing within the last month. It appears that poor occupational factors in barbers' salons and exposure to hairdressing chemicals bring about health problems of the hairdressers.
A palaeolimnological record of diatom-community dynamics and late-Holocene climatic changes from Prescott Island, Nunavut, central Canadian Arctic

Palaeolimnological analyses from Lake PW03, a small, dilute lake on crystalline bedrock on Prescott Island, Nunavut, Canada (73°07′ N, 96°41′ W, 243 m a.s.l.), provide a sensitive record of the impacts of Holocene climatic change on diatom communities. A high-resolution sequence from 3500 cal. BP to present indicates that a significant change in diatom assemblages takes place at 2300 cal. BP, when alkaliphilous fragilarioids and planktonic taxa are replaced by benthic, epiphytic and acidophilous diatoms. These changes coincide with the onset of neoglacial cooling and likely reflect more persistent ice-cover and associated acidification of lake water. Maximum diatom species richness occurs during this period of transition. Dense bryophyte communities in the littoral zone provide habitats to sustain diatom production even under the cooler conditions following 2300 cal. BP. The concentration of diatom valves declines at 500 cal. BP, coincident with cooling at the time of the `Little Ice Age', and minor changes in species composition take place at that time. The sediments deposited over the past 150 years show modest increases in fragilarioids and planktonic diatoms, in response to a longer ice-free season under a warmer climate. Diatom valve production increases significantly in these recent sediments but increases in diversity are relatively small. Diatom diversity, production and the species composition of diatom communities do not change simultaneously in response to climatic changes.
Midlife Women Online: Evaluation of an Internet-Based Program to Prevent Unintended Pregnancy & STIs

Background: Midlife women are an underserved population in the areas of unintended pregnancy and STI prevention yet remain at risk for both health conditions. Methods: A randomized controlled trial of an Internet-based multimedia program to reduce risk of unintended pregnancy and STIs among midlife women was conducted with 164 women ages 40–55 years of age. Results: Women in the treatment condition compared to the control condition reported significant gains in attitudes, self-efficacy, and behavioral intentions at posttest. Conclusion: Interventions specifically targeted to midlife women can impact constructs known to reduce risk. Implications for future research and intervention development are presented.
Electrofragmentation modeling of conductive coatings on polymer substrates

Received 8 June 2009; accepted 26 October 2009; published online 3 December 2009Damage occurring under tensile loading and the resulting increase in electrical resistance oftin-doped indium oxide and amorphous graphite coatings on various polymer substrates areinvestigated, using an electrofragmentation method
Low redshift AGN in the Hamburg/ESO survey - I. The local AGN luminosity function

We present a determination of the local (z ≈ 0) luminosity function of optically selected type 1 (broad-line) active galactic nuclei. Our primary resource is the Hamburg/ESO survey (HES), which provides a well-defined sample of more than 300 optically bright AGN with redshifts z MBJ > −26), the two measures are tightly correlated. The resulting AGN luminosity function (AGNLF) is consistent with a single power law, also when considering the effects of number density evolution within the narrow redshift range. We compared our AGNLF with the Hα luminosity function of lower luminosity Seyfert 1 galaxies by Hao et al. (2005a, AJ, 129, 1795) and found a smooth transition between both, with excellent agreement in the overlapping region. From the combination of HES and SDSS samples we constructed a single local AGNLF spanning more than 4 orders of magnitude in luminosity. It shows only mild curvature which can be well described as a double power law with slope indices of −2.0 for the faint end and −2.8 for the bright end. We predicted the local AGNLF in the soft X-ray domain and compared this to recent literature data. The quality of the match depends strongly on the adopted translation of optical to X-ray luminosities and is best for an approximately constant optical/X-ray ratio. We also compared the local AGNLF with results obtained at higher redshifts and find strong evidence for luminosity-dependent evolution, in the sense that AGN with luminosities around MB �− 19 are as common in the local universe as they were at z = 1.5. This supports the “AGN downsizing” picture first found from X-ray selected AGN samples.
Cosmological Evolution of Supergiant Star-forming Clouds

In an exploration of the birthplaces of globular clusters, we present a careful examination of the formation of self-gravitating gas clouds within assembling dark matter haloes in a hierarchical cosmological model. Our high-resolution smoothed particle hydrodynamical simulations are designed to determine whether or not hypothesized supergiant molecular clouds (SGMCs) form and, if they do, to determine their physical properties and mass spectra. It was suggested in earlier work that clouds with a median mass of several 108 M☉ are expected to assemble during the formation of a galaxy and that globular clusters form within these SGMCs. Our simulations show that clouds with the predicted properties are indeed produced as smaller clouds collide and agglomerate within the merging dark matter haloes of our cosmological model. We find that the mass spectrum of these clouds obeys the same power-law form, dN/dM ∝ M-1.7±0.1, observed for globular clusters, molecular clouds, and their internal clumps in galaxies, and predicted for the supergiant clouds in which globular clusters may form. We follow the evolution and physical properties of gas clouds within small dark matter haloes up to z = 1, after which prolific star formation is expected to occur. Finally, we discuss how our results may lead to more physically motivated "rules" for star formation in cosmological simulations of galaxy formation.
Causal Inference without Balance Checking: Coarsened Exact Matching

We discuss a method for improving causal inferences called “Coarsened Exact Matching” (CEM), and the new “Monotonic Imbalance Bounding” (MIB) class of matching methods from which CEM is derived. We summarize what is known about CEM and MIB, derive and illustrate several new desirable statistical properties of CEM, and then propose a variety of useful extensions. We show that CEM possesses a wide range of statistical properties not available in most other matching methods but is at the same time exceptionally easy to comprehend and use. We focus on the connection between theoretical properties and practical applications. We also make available easy-to-use open source software for R, Stata, and SPSS that implement all our suggestions.
Determination of serum hepatitis B virus DNA in chronic HBsAg carriers: clinical significance and correlation with serological markers.

BACKGROUND/AIMS Hepatitis B virus infection is among the most devastating health problems in the world, including Turkey. In this cross-sectional study, we aimed to investigate the correlations between hepatitis B virus genomic load and various measures of the progression of chronic hepatitis B virus infection. METHODS A total of 354 chronic HBsAg carriers [126 inactive HBsAg carriers, 50 asymptomatic replicative carriers (immune tolerant patients), 90 chronic hepatitis B patients and 88 patients with liver cirrhosis] were enrolled into the study. Eligible patients included males and females, 14-62 years of age, with detectable serum HBsAg, HBeAg or anti-HBe in serum at the time of screening and for at least six months before study entry. Serum hepatitis B virus DNA was detected by liquid hybridization, and results under the level of 1 pg/ml were additionally confirmed by polymerase chain reaction. RESULTS Of 354 patients, 118 (33%) were HBeAg-positive and 236 (67%) HBeAg-negative. Of HBeAg-negative patients, 126 (53%) had normal alanine aminotransferase, 31 (13%) had elevated alanine aminotransferase (chronic hepatitis B) and 79 (33%) had evidence of cirrhosis; corresponding figures in the HBeAg-positive patients were 50 (42%), 59 (50%) and 9 (8%). There is a significant correlation between transaminase values and histological liver damage, whereas no correlation was found between viral replication and liver damage. CONCLUSIONS Hepatitis B virus DNA is an important and specific marker for ongoing hepatitis B virus related liver disease, but alanine aninotransferase was shown to be the best marker for liver inflammation and not hepatitis B virus viral load. Although these findings are not new, they are of some utility since they prevent unnecessary and cost-intensive viral load determinations in chronic HBsAg carriers.
Inferring Narrative Causality between Event Pairs in Films

To understand narrative, humans draw inferences about the underlying relations between narrative events. Cognitive theories of narrative understanding define these inferences as four different types of causality, that include pairs of events A, B where A physically causes B (X drop, X break), to pairs of events where A causes emotional state B (Y saw X, Y felt fear). Previous work on learning narrative relations from text has either focused on “strict” physical causality, or has been vague about what relation is being learned. This paper learns pairs of causal events from a corpus of film scene descriptions which are action rich and tend to be told in chronological order. We show that event pairs induced using our methods are of high quality and are judged to have a stronger causal relation than event pairs from Rel-Grams.
Essays in Information and Asset Pricing

Esta tesis estudia las caracteristicas de la formacion y del equilibrio de los precios de los activos financieros cuando los agentes que participan en los mercados estan informados de forma asimetrica. En el primer capitulo analizo un modelo con agentes presumidos y racionales y adquisicion costosa de la informacion. Demuestro que los precios del equilibrio son equivalentes a un mercado en el cual todos los agentes sean racionales. En el segundo capitulo estudio la venta de informacion por un monopolista a mercados no competitivos. La asignacion optima de la informacion resulta tener dos formas posibles: (i) venta de una informacion muy imprecisa a tantos agentes como sea posible; (ii) venta de senales tan exactos como sea posible a un grupo muy restringido. Los mercado market-order son mas eficientes que los limit-order y el modelo estrategico es mas eficientes que el competitivo. En el tercer capitulo investigo la relacion positiva entre la informacion asimetrica y la premia de riego bajo la asuncion que los especuladores informados sean estrategicos y que negocian contra un mercado contrario al riesgo.
Multiple evidence strands suggest that there may be as few as 19 000 human protein-coding genes

Determining the full complement of protein-coding genes is a key goal of genome annotation. The most powerful approach for confirming protein-coding potential is the detection of cellular protein expression through peptide mass spectrometry (MS) experiments. Here, we mapped peptides detected in seven large-scale proteomics studies to almost 60% of the protein-coding genes in the GENCODE annotation of the human genome. We found a strong relationship between detection in proteomics experiments and both gene family age and cross-species conservation. Most of the genes for which we detected peptides were highly conserved. We found peptides for >96% of genes that evolved before bilateria. At the opposite end of the scale, we identified almost no peptides for genes that have appeared since primates, for genes that did not have any protein-like features or for genes with poor cross-species conservation. These results motivated us to describe a set of 2001 potential non-coding genes based on features such as weak conservation, a lack of protein features, or ambiguous annotations from major databases, all of which correlated with low peptide detection across the seven experiments. We identified peptides for just 3% of these genes. We show that many of these genes behave more like non-coding genes than protein-coding genes and suggest that most are unlikely to code for proteins under normal circumstances. We believe that their inclusion in the human protein-coding gene catalogue should be revised as part of the ongoing human genome annotation effort.
Estimating handover rate in heterogeneous mobility and cell types

This paper provides a general analytic method to estimate the handover rate in mobile packet systems with heterogeneous cell types and multimedia services. The handover rate is derived as a closed-form function of the Laplace transform of the session time distribution. The proposed model can be easily extended to analyze the mobility feature of the heterogeneous mobile systems with hierarchical cell structure.
Linearization of differential CMOS low noise amplifier using cross-coupled post distortion canceller

A post-linearization technique for the differential CMOS LNA is presented. The proposed method uses an additional cross-coupled FET pair which generates the 3rd-order inter-modulation (IM3) current to cancel out the IM3 current of the differential amplifier while minimizing the degradation of noise figure and avoiding the gain reduction. This technique is applied to enhance the linearity of the differential CMOS LNA using 0.18-mum technology. The LNA achieved +10.2-dBm IIP3 with 13.7-dB gain and 1.68-dB NF at 2 GHz consuming 11.8-mA from a 1.8-V supply.
Accounting for a Quantitative Trait Locus for Plasma Triglyceride Levels: Utilization of Variants in Multiple Genes

Background For decades, research efforts have tried to uncover the underlying genetic basis of human susceptibility to a variety of diseases. Linkage studies have resulted in highly replicated findings and helped identify quantitative trait loci (QTL) for many complex traits; however identification of specific alleles accounting for linkage remains elusive. The purpose of this study was to determine whether with a sufficient number of variants a linkage signal can be fully explained. Method We used comprehensive fine-mapping using a dense set of single nucleotide polymorphisms (SNPs) across the entire quantitative trait locus (QTL) on human chromosome 7q36 linked to plasma triglyceride levels. Analyses included measured genotype and combined linkage association analyses. Results Screening this linkage region, we found an over representation of nominally significant associations in five genes (MLL3, DPP6, PAXIP1, HTR5A, INSIG1). However, no single genetic variant was sufficient to account for the linkage. On the other hand, multiple variants capturing the variation in these five genes did account for the linkage at this locus. Permutation analyses suggested that this reduction in LOD score was unlikely to have occurred by chance (p = 0.008). Discussion With recent findings, it has become clear that most complex traits are influenced by a large number of genetic variants each contributing only a small percentage to the overall phenotype. We found that with a sufficient number of variants, the linkage can be fully explained. The results from this analysis suggest that perhaps the failure to identify causal variants for linkage peaks may be due to multiple variants under the linkage peak with small individual effect, rather than a single variant of large effect.
Syndromic surveillance on the Victorian chief complaint data set using a hybrid statistical and machine learning technique

Emergency Department Chief Complaints have been used to detect the size and the spread of disease outbreaks in the past. Chief complaints are readily available in digital formats and provide a good data source for syndromic surveillance. This paper reports our findings on the identification of the distribution of a few syndromes over time using the Victorian Syndromic Surveillance (SynSurv) data set. We utilized a machine learning-based Näıve Bayes classifier to predict the syndromic group of unseen chief complaints. Then, we analyzed the patterns of the distributions of three syndromes in the SynSurv data, specifically the Flu-like Illness, Acute Respiratory, and Diarrhoea syndromes, over sliding windows of time using the EARS C1, C2, and C3 aberrancy detection algorithms. The results of our analyses demonstrate that applying aberrancy algorithms over the variance data between two consecutive weeks reduces the large number of possible disease outbreaks detected using raw frequencies of the syndromic groups in the same time period, resulting in a more feasible approach for practical syndromic surveillance.