Miracle-dz/UniFAR-FTUs huggingface dataset:
Multipoint linkage disequilibrium mapping approach: Incorporating evidence of linkage and linkage disequilibrium from unlinked region

Gene mapping for complex diseases is still a challenge in genetic studies. For family‐based studies, the single‐locus methods for detecting linkage and linkage disequilibrium (LD) one at a time may not capture the assumed interaction between multiple causal genes efficiently. We propose a multipoint LD approach for assessing the evidence of linkage and LD in a targeted chromosomal region by incorporating evidence from an unlinked region using the case‐parent trio design. The paternal and maternal preferential transmission statistics defined in Liang et al. ([2001] Am. J. Hum. Genet. 68:937–950) are the primary statistics for this approach. Our generalized estimating equation (GEE) method builds on a model using the expected preferential transmission statistic from the targeted region conditional on this same statistic from the unlinked region. The major assumption is that there is no more than one trait locus in both the targeted region and unlinked region. The map position of an unobserved trait locus and its confidence interval can be calculated. Finally, we apply this approach to the African‐American families drawn from the Collaborative Study on the Genetics of Asthma (CSGA). Previous analysis using this GEE approach developed by Liang et al. ([2001] Am. J. Hum. Genet. 68:937–950) suggested strong evidence of linkage and LD on chromosome 11, but only marginal evidence on chromosome 8. While conditioning on marker D11S937 on chromosome 11, a separate trait locus on chromosome 8 was estimated at $\hat\tau2 = 11.67{\rm cM}$, with a 95% confidence interval of (8.75, 14.59), and the test statistic shows significant evidence of linkage and LD (P‐value=0.0198) in this region of chromosome 8. Genet Epidemiol 25:1–13, 2003. © 2003 Wiley‐Liss, Inc.
9 Energy Metabolism Regulating Mammalian Oocyte Maturation

Oocyte maturation is a final step of gamete development that follows a prolonged period of cell growth within a growing follicle. Unlike oocyte growth that takes several weeks or months, maturation process is a short (hours or days), dynamic process. The period of oocyte maturation varies among species, ranging from 10-13 hours in the mouse (Edwards & Gates, 1959) to 16-24 hours in the cow (Dominko & First, 1997) and 48 -72 hours in the dog (Reynaud et al., 2005, Songsasen & Wildt, 2007). For an oocyte to fully capable of fertilizing and developing into an embryo, the gamete needs to undergo nuclear and cytoplasmic maturation. Nuclear maturation encompasses events associated with the separation of homologous chromosomes during meiosis I and the segregation of sister chromatids during meiosis 2 (Albertini & Limback, 2009). Events occur during this process include nuclear envelope breakdown, rearrangement of the cortical cytoskeleton and meiotic spindle assembly. Cytoplasmic maturation includes events of post-transcriptional and posttranslational processes, including mRNA synthesis, rearrangement of cytoplasmic organelles and glutathione production that are essential for successful fertilization and subsequent embryonic development (Albertini & Limback, 2009, Watson, 2007). For an oocyte to appropriately progress to these dynamic process of nuclear and cytoplasmic maturation, it requires enormous energy from various substrates, including glucose, amino acids and lipids (Sutton et al., 2003). In addition, tight regulation of reactive oxygen species (ROS) and calcium homeostasis are important during this process. This chapter will review current knowledge on mammalian oocyte development, the roles of mitochondria on cell functions and energy metabolism and its impact on gamete maturation.
The Caregivers for Alzheimer's disease Problems Scale (CAPS): development of a new scale within the LASER-AD study.

BACKGROUND we developed the Caregivers for Alzheimer's disease Problems Scale (CAPS) comprising common risk factors for anxiety and depression for family carers of people with dementia. OBJECTIVE to calculate the sensitivity and specificity of the CAPS in order to measure its usefulness in identifying dementia caregivers at risk of anxiety and depression and therefore whether it identifies clinically relevant areas for intervention or highlights the need for support if the problem could not be changed. METHOD 153 family caregivers were interviewed as part of a larger epidemiologically representative study of people with Alzheimer's disease and their caregivers. Caregiver anxiety and depression were measured using the Hospital Anxiety and Depression Scale (HADS). RESULTS the CAPS had high sensitivity and specificity in detecting caregivers with screen positive anxiety and depression. Five areas were indicated: neuropsychiatric symptoms and depression in the care-recipient, co-residence and relationships with the care-recipient, and physical health of the caregiver. CONCLUSIONS awareness of these problems can help clinicians identify those carers most likely to be anxious or depressed and indicate appropriate intervention and support. We recommend that this instrument be used as part of routine assessments of people with dementia and their families.
Hypofractionated Radiotherapy as Definitive Treatment of Stage I Non-Small Cell Lung Cancer in Older Patients

Purpose/Objective(s): We report our experience using hypofractionated radiotherapy in older patients. Materials/Methods: This analysis includes patients aged 60 years and older at our institution with inoperable Stage I (T1/T2 N0 M0) non–small-cell lung cancer that completed a curative course of radiotherapy alone using a hypofractionated schedule. Between 1991 and 2006, 75 such patients were identified with median age of 74 years (range, 60–86). Patient characteristics were as follows: male, 65/75 (86.7%); stage IA (T1N0), 47/75 (62.7%); stage IB (T2N0), 28/75 (37.3%). Patients received a median total dose of 6500 cGy using median daily dose fractions of 250 cGy. The following outcomes were analyzed: local failure free survival (time to local failure or death from any cause), time to distal failure as first event, and overall survival. Toxicities were evaluated using Common Terminology Criteria for Adverse Events v 3.0. Results: The median follow-up was 19.6 months (range: 4.0–128.8 months). Median local failure free survival was 19.6 months (95% confidence interval [CI]: 14.4–28.8 months); and median overall survival was 21.2 months (95% CI: 14.9–29.3 months). Analysis of competing risks showed that at 5 years, the probability of local failure as the first detected event was 22.1% (95% CI: 12.8%–32.9%); the probability of distal failure as the first detected event was 14.5% (95% CI: 7.3%–24.0%); and the probability of death without recording a failure was 48.6% (95% CI: 36.1%–60.1%). Radiation-related toxicity of grade 3 or greater was seen in 3 patients and there were no treatment-related deaths. Conclusions: Hypofractionated radiotherapy is an effective, safe treatment for older patients with stage I non–small-cell lung cancer.
Taxol, a microtubule stabilizer, improves cardiac functional recovery during postischemic reperfusion in rat in vitro.

AIMS Microtubule disruption contributes to cellular and organic dysfunction, and is implicated in ischemia/reperfusion (I/R) injury. The purpose of this study was to explore the effects of taxol, a microtubule stabilizer, on cardiac functional recovery during reperfusion. METHODS Left ventricular developed pressure, left ventricular end-diastolic pressure, maximal time derivatives of pressure and the severity of ventricular arrhythmias were analyzed in isolated rat heart. Microtubule structure was immunohistochemically measured. Apoptosis and necrosis was identified with TUNEL or TTC staining, respectively. Mitochondrial permeability transition pore (mPTP) mRNA expression was examined by real-time polymerase chain reactions. mPTP opening, reactive oxygen species (ROS), and oxidative enzyme activities were measured with fluorometric or spectrophotometric techniques. Intracellular calcium concentration ([Ca(2+) ](i) ) and Ca(2+) transients were examined by Fura-2-AM and Fluo-3-AM, respectively. Cytosolic cytochrome c, sarcoplasmic reticulum Ca(2+) -ATPase (SERCA2), ryanodine receptors (RyR), phospholamban (PLB), and PLB phosphorylation were analyzed by Western blot. Effective refractory period (ERP) and afterpotential-mediated activity were detected using microelectrode. RESULTS Taxol improved the functional recovery of post-I/R. Taxol preserved the intact microtubule structure in reperfusion. mPTP mRNA expression was unchanged while the mPTP opening was reduced by taxol, and this effect was accompanied by the decreased ROS level caused by oxidative enzymes activities' changes. Taxol reduced apoptosis and the level of cytosolic cytochrome c in reperfusion. Taxol also promoted rapid recovery of [Ca(2+) ](i) , prevented reduction of the amplitude of Ca(2+) transients and shortened the decay time of Ca(2+) transients. The protein expression of SERCA2, RyR, and PLB remained unchanged in reperfusion. Taxol prevented the increase of Phospho-Thr17-PLB and Phospho-Ser16-PLB in reperfusion. In addition, taxol facilitated rapid recovery of ERP and counter-acted afterpotential-mediated activity. CONCLUSION Taxol may effectively improve cardiac functional recovery during reperfusion via inhibiting mPTP opening, ameliorating abnormal calcium homeostasis, and reducing the substrates associated with arrhythmias.
PHYSICS TEACHERS’ BELIEFS ABOUT THE ATTAINMENT OF SKILL OBJECTIVES AND THE EXTENT OF THESE BELIEFS’ REFLECTION ON TEACHERS’ INSTRUCTIONAL PRACTICES

Turkish Ministry of National Education has made important changes in both primary and secondary school curricula in the last decade. The Turkish High School Physics Curriculum (THSPC) after these changes was put into practice first in 2008-2009 education year. Apart from being the first written curriculum with written objectives, this curriculum also contained—differently from other previous physics curricula—skill objectives. This included objectives related to problem solving skills (PSS) and information and communication skills (ICS) and physics-technology-society-environment objectives (PTSEO). No matter how well-prepared a curriculum for a subject is, whether it is implemented effectively depends on the teachers. One of the factors affecting proper implementation of curricula is teachers’ beliefs about the curricula as a whole and its constituent elements. Since the curriculum is relatively new, teachers’ beliefs and how these beliefs are reflected in their instructional practices are not yet known. Therefore, the purpose of this study was to investigate physics teachers’ beliefs about the attainment of PSS, PTSEO and ICS and the extent these beliefs were reflected in teachers’ instructional practices. Data were collected by administering an open-ended questionnaire to four in-service physics teachers and observing their instructional practices in the ‘nature of physics’ and ‘energy’ units. The results of this study showed that although physics teachers believed that majority of the skill objectives of the THSPC should be attained, they did not teach physics by taking these skill objectives into consideration. The physics teachers inclined more to help students attain PTSEO when compared with PSS and ICS. Keywords: Teachers’ Beliefs, Turkish High School Physics Curriculum, Skill Objectives
BİR SOSYAL POLİTİKA ARACI OLARAK DOĞRUDAN YABANCI YATIRIMLARIN İSTİHDAMA ETKİSİ

Turkiye'de issizlik yillardir onde gelen sosyo-ekonomik sorunlardan biridir ve artan yabanei yatirimlarin sorunun hafifleulmesinc yardimci olacagi genel kabul goren bir beklentidir. Bu konuda son yillarda ciddi bir hassasiyet olusmus, 2003 yilinda Yabanci Sermaye Kanunu'nunda yapilan revizyonla yabanci yatirimcilara onemli kolaylik ve avantajlar saglanarak yabanci sermaye girisinin artirilmasi hedeflenmistir. Dogrudan yabanci yatirimlar (DYY) onceleri daha ziyade gelismis ulkelerde yogunlasirken son birkac onyildan beri gelismekte olan ulkeler de kuresel DYY pastasindan gitgide daha fazla pay almaya baslamislardir. Farkli ulkeler icin yapilan analizlerde D Y Y ile istihdam arasinda genellikle anlamli ve olumlu bir uzun donem iliskisine ulasilmakla birlikte iki degisken arasinda herhangi bir nedensellige rastlanmayan ornekler de vardir. Bu sonucun ulkelerin kendilerine has yapisal karakteristiklerden kaynaklandigi dusunulebilir. Bu calismada da, Turkiye'de DYY girisleri ile istihdam arasindaki iliski zaman serileri yontemleri kullanilarak arastirilmistir. Elde edilen bulgular Turkiye'de D Y Y ile istihdam arasinda anlamli bir etkilesim bulunmadigini gostermektedir
Gravity and Faster than Light Particles

In this paper, I discuss whether superluminal particles exist in the general relativistic theory of gravity. It seems that the answer to this question is negative. In truth, the result may only represent a difficulty to special but not general relativity, the later allowing both Lorentzian and Euclidian metrics. An Euclidian metric does not restrict speed. Although only the Lorentzian metric is stable, an Euclidian metric can be created under special gravitational circumstances and persist in a limited region of space-time causing possible superluminality.
The anti‐tumor agent, 5,6‐dimethylxanthenone‐4‐acetic acid (DMXAA), induces IFN‐β‐mediated antiviral activity in vitro and in vivo

The 2009 outbreak of pandemic H1N1 influenza, increased drug resistance, and the significant delay in obtaining adequate numbers of vaccine doses have heightened awareness of the need to develop new antiviral drugs that can be used prophylactically or therapeutically. Previously, we showed that the experimental anti‐tumor drug DMXAA potently induced IFN‐β but relatively low TNF‐α expression in vitro. This study confirms these findings in vivo and demonstrates further that DMXAA induces potent antiviral activity in vitro and in vivo. In vitro, DMXAA protected RAW 264.7 macrophage‐like cells from VSV‐induced cytotoxicity and moreover, inhibited replication of influenza, including the Tamiflu®‐resistant H1N1 influenza A/Br strain, in MDCK cells. In vivo, DMXAA protected WT C57BL/6J but not IFN‐β−/− mice from lethality induced by the mouse‐adapted H1N1 PR8 influenza strain when administered before or after infection. Protection was accompanied by mitigation of weight loss, increased IFN‐β mRNA and protein levels in the lung, and significant inhibition of viral replication in vivo early after DMXAA treatment. Collectively, this study provides data to support the use of DMXAA as a novel antiviral agent.
Ultrafast All-Optical Wavelength Routing of Data Packets Utilizing an SOA-Based Wavelength Converter and a Monolithically Integrated Optical Flip–Flop

We demonstrate all-optical wavelength routing of 80 Gb/s data packets without using electronic control. The system consists of an optical wavelength converter and a monolithically integrated optical flip-flop memory. The integrated optical flip-flop is based on two coupled lasers, exhibiting single-mode operation, having a 35 dB contrast ratio between the states, and switching its state in about 2 ns. The wavelength converter is optically controlled by the optical flip-flop. We show that the optical set and reset pulses can force the optical flip-flop to switch its continuous-wave output light between two specific wavelength positions. The output light feeds the wavelength converter, which, in turn, converts the data packet into the flip-flop's output wavelength, causing the data packet to be routed into a specific port.
Identifying a speaker's regional origin:the role of temporal information

Previous studies have revealed that, depending on the language, listeners can identify speakers’ dialects quite well. The role of segments and prosody in this task is largely unknown, however. In a between-subjects design, we tested a total of 30 listeners in two conditions: in the unmorphed condition, listeners heard original sentences from two Swiss German dialects; in the duration morphed condition, listeners heard the same material, but with syllable durations exchanged between the two dialects. In a two-alternative forced choice design, subjects judged the regional origin of the stimuli heard. Results revealed near perfect identification performance for both conditions, thus underlining the overriding dominance of segmental cues in dialect identification tasks. The findings reported are pertinent to forensic phonetics, enhancing the diagnostic power of naive and expert listeners’ claims about suspect speakers’ voices.
About photo-damage of human hair

This paper reviews the current knowledge about human hair photodamage and the photodegradation mechanisms proposed in the literature. It is shown that there are still a number of questions without answer regarding this issue. For example, a better understanding of the hair structural changes caused by different radiationwavelengths is still lacking.We also find controversies about the effects of sun exposure on different hair types.Explanations to these questions are frequently sustained on the amount and type of melanin of each hair, but factors such as the absence of knowledge of melanin structure and of established methodologies to use in human hair studies make it difficult to reach a general agreement on these issues.
Head Start Graduate Student Research Grantees Local Stakeholder Perspectives on School Readiness : Implications for the National Reporting System

Using assessments to provide program-level accountability and to guide improvement is growing. The most notable and unprecedented example is the Head Start National Reporting System (NRS). Extensive controversy has broken out within the Head Start community and the early childhood field regarding what the NRS assesses (National Head Start Association, 2004; Meisels & Atkins-Burnett, 2004; Government Accounting Office, 2005; Raver & Zigler, 2004). Most notably, the NRS does not assess children’s social and emotional development. Linn (2001, 2004) argues that one of the issues that the development and use of assessment systems ought to explicitly address is what should be assessed. Such choices result in assumptions about ‘what matters. ’
Microvascular morphological type recognition using trainable feature extractor

This paper focuses on the problem of feature extraction and the classification task of microvascular morphological type to aid esophageal cancer detection. A specialized convolutional neural network (CNN) is designed to extract hierarchical features and Support Vector Machines (SVMs) are introduced to enhance the generalization ability of classifiers. Experiments are conducted on the NBI-ME dataset, achieving a recognition rate of 88.19% on patch level. The results show that the CNN-SVM model beats models of traditional features with SVM as well as the original CNN with softmax. The synthesis results indicate this system is able to assist clinical diagnose to a certain extent.
Evaluating the Effect of Daily PM10 Variation on Mortality

Many epidemiological studies have shown the association between daily mortality and daily average of PM10 level. Daily average of PM10 has been used for regression type time-series analysis. This article suggests that daily mean mortality is not only a function of daily mean but also a function of daily standard deviation of PM10. We used generalized additive Poisson regression model with overdispersion parameter to investigate this hypothesis using the data from Seoul, Korea, from 1997 to 2001. One interquartile range (IQR = 42.11 μg/m3) increase of daily mean level of PM10 was found to be associated with 2.1% increase of additional daily mortality (RR = 1.021, 95% CI = 1.009–1.035) after controlling for other confounders. Similarly, we also found that one IQR (11.93 μg/m3) increase in daily standard deviation of PM10 is associated with 2.5% increase of additional risk of death (RR = 1.025, 95% CI = 1.000–1.028) when other covariates remained the same. These findings may provide new insight into the possible explanation of health effect of PM10 and support the hypothesis that PM10 deviation is also an important risk factor after controlling for daily mean PM10 level.
On the precision of noise‐correlation interferometry.

Coda Wave Interferometry analyzes changes in diffuse waveforms when source and receiver are fixed. Changes are often due to changing acoustic wave speed, perhaps a change of temperature. Alternatively, changes can be studied in noise correlations. The advantage is in not having to wait for, or generate, a precisely identical source. But interpretation is problematic; changes in the correlation of noise fields due to an uncontrolled set of sources could be due to the sources, or to the environment. Recent studies of ambient seismic noise correlations have shown apparent stretches (potentially corresponding to wave speed slowing by parts in 10 000) over periods of weeks. Changes seen at La Reunion correlate with subsequent volcanic eruptions. Changes seen at Parkfield, California occur quickly after earthquakes and then relax back over many months. Potential for seismic monitoring motivates a study of the relative effects of source and medium changes on apparent stretching or compression. Here it is shown t.
Intraclass Correlations for Planning Group Randomized Experiments in Rural Education

This material is based upon work supported by the National Science Foundation under Grant No. 0129365. Correspondence concerning this article should be addressed to Larry V. Hedges, Northwestern University, WCAS Statistics Education & Social Policy Institute for Policy Research, Annenberg Hall EV2610, Evanston, IL 60208. (l-hedges@northwestern.edu) Citation: Hedges, L. & Hedberg, E.C. (2007, August 14). Intraclass correlations for planning group randomized experiments in rural education. Journal of Research in Rural Education, 22(10). Retrieved [date] from http://jrre.psu. edu/articles/22-10.pdf Intraclass Correlations for Planning Group Randomized Experiments in Rural Education
The spindle pole body component Spc98p interacts with the gamma‐tubulin‐like Tub4p of Saccharomyces cerevisiae at the sites of microtubule attachment.

Tub4p is a novel tubulin found in Saccharomyces cerevisiae. It most resembles gamma‐tubulin and, like it, is localized to the yeast microtubule organizing centre, the spindle pole body (SPB). In this paper we report the identification of SPC98 as a dosage‐dependent suppressor of the conditional lethal tub4–1 allele. SPC98 encodes an SPB component of 98 kDa which is identical to the previously described 90 kDa SPB protein. Strong overexpression of SPC98 is toxic, causing cells to arrest with a large bud, defective microtubule structures, undivided nucleus and replicated DNA. The toxicity of SPC98 overexpression was relieved by co‐overexpression of TUB4. Further evidence for an interaction between Tub4p and Spc98p came from the synthetic toxicity of tub4–1 and spc98–1 alleles, the dosage‐dependent suppression of spc98–4 by TUB4, the binding of Tub4p to Spc98p in the two‐hybrid system and the co‐immunoprecipitation of Tub4p and Spc98p. In addition, Spc98–1p is defective in its interaction with Tub4p in the two‐hybrid system. We suggest a model in which Tub4p and Spc98p form a complex involved in microtubule organization by the SPB.