Miracle-dz/UniFAR-FTUs huggingface dataset:
Histone H2A phosphorylation in DNA double‐strand break repair

DNA repair must take place within the context of chromatin, and it is therefore not surprising that many aspects of both chromatin components and proteins that modify chromatin have been implicated in this process. One of the best‐characterized chromatin modification events in DNA‐damage responses is the phosphorylation of the SQ motif found in histone H2A or the H2AX histone variant in higher eukaryotes. This modification is an early response to the induction of DNA damage, and occurs in a wide range of eukaryotic organisms, suggesting an important conserved function. One function that histone modifications can have is to provide a unique binding site for interacting factors. Here, we review the proteins and protein complexes that have been identified as H2AS129ph (budding yeast) or H2AXS139ph (human) binding partners and discuss the implications of these interactions.
Homogeneity test of rate ratios in stratified matched‐pair studies

This paper investigates homogeneity test of rate ratios in stratified matched‐pair studies on the basis of asymptotic and bootstrap‐resampling methods. Based on the efficient score approach, we develop a simple and computationally tractable score test statistic. Several other homogeneity test statistics are also proposed on the basis of the weighted least‐squares estimate and logarithmic transformation. Sample size formulae are derived to guarantee a pre‐specified power for the proposed tests at the pre‐given significance level. Empirical results confirm that (i) the modified score statistic based on the bootstrap‐resampling method performs better in the sense that its empirical type I error rate is much closer to the pre‐specified nominal level than those of other tests and its power is greater than those of other tests, and is hence recommended, whilst the statistics based on the weighted least‐squares estimate and logarithmic transformation are slightly conservative under some of the considered settings; (ii) the derived sample size formulae are rather accurate in the sense that their empirical powers obtained from the estimated sample sizes are very close to the pre‐specified nominal powers. A real example is used to illustrate the proposed methodologies.
Caloric restriction in leptin deficiency does not correct myocardial steatosis: failure to normalize PPARα/PGC1α and thermogenic glycerolipid/fatty acid cycling

J. Eduardo Rame,* Lili A. Barouch,* Michael N. Sack, Edward G. Lynn, Mones Abu-Asab, Maria Tsokos, Steven J. Kern, Jennifer J. Barb, Peter J. Munson, Marc K. Halushka, Karen L. Miller, Karen Fox-Talbot, Jianhua Zhang, Joshua M. Hare, Michael A. Solomon, and Robert L. Danner Cardiovascular Medicine Division, University of Pennsylvania, Philadelphia, Pennsylvania; Division of Cardiology, Johns Hopkins University, Baltimore; Translational Medicine Branch, National Heart, Lung and Blood Institute, Laboratory of Pathology, National Cancer Institute, Functional Genomics and Proteomics Facility, Critical Care Medicine Department, Clinical Center, Mathematical and Statistical Computing Laboratory, Center for Information Technology, National Institutes of Health, Bethesda; Department of Pathology, Johns Hopkins University, Baltimore, Maryland; Interdisciplinary Stem Cell Institute, Cardiovascular Division, Department of Medicine, University of Miami School of Medicine, Miami, Florida
Hollow cathode discharge: application of a deposition treatment in the iron sintering

The influence of a previous deposition treatment on the final amount of alloying elements (Cr and Ni) deposited and diffused into the surface of iron parts sintered in hollow cathode discharge (HCD) was studied. Cylindrical pure iron pressed samples, being a central cathode, were placed concentrically in the interior of an AISI 310 steel machine-made outer cathode, resulting in a 6 mm inter-cathode radial spacing. The study was divided in two steps: a) deposition treatment with the outer cathode acting as target and the iron sample acting as substrate (1123K -850 oC- and 60 minutes deposition temperature and time, respectively); and b) deposition treatment plus HCD sintering (1423K -1150 oC- and 60 minutes sintering temperature and time, respectively). The electrical discharge was generated using a pulsed voltage power source. The results indicate the presence of 6.5 at. % Cr and 6.9 at. % Ni on the samples surface. The concentration profiles were mathematically treated to quantify the actual amounts of Cr and Ni deposited on and diffused into the samples, and the integration of the fitted equations yielded the calculated areas of 133 (µm × at.% Cr) and 105 (µm × at.% Ni), respectively.
Preparation and Therapeutic Efficacy of Polysorbate-80-Coated Amphotericin B/PLA-b-PEG Nanoparticles

Amphotericin B (AmB)/poly(lactic acid)-b-poly(ethylene glycol) (PLA-b-PEG) nanoparticles coated with polysorbate 80 (Tween-80) were prepared by nanoprecipitation for transport across the blood–brain barrier (BBB). The effects of Tween-80 on the size and distribution, entrapment efficiency and release behavior of AmB/PLA-b-PEG nanoparticles were investigated. Furthermore, the brain targeting and curative effect of coated nanoparticles were also investigated. The entrapment efficiency was significantly enhanced when nanoparticles were coated with Tween-80. The prepared nanoparticles were spherical with homogeneous distribution. Drug concentration in mice brain was greatly enhanced, which indicated that the coated nanoparticles could get across the BBB. Meanwhile, the AmB/PLA-b-PEG nanoparticles are able to reduce the toxicity of AmB to liver, kidney and blood system with improved therapeutic effect.
Effects of theophylline and enprofylline on diaphragmatic contractility.

Experimental data suggest that theophylline (T) enhances diaphragmatic contractility by increasing the influx of calcium at the cell membrane level through an inhibition of adenosine receptors (Aubier et al., J. Appl. Physiol. 54: 460-4, 1983). Enprofylline (E) is a xanthine drug that has poor ability to antagonize physiological actions of adenosine. The aim of this study was to compare the effects on diaphragmatic contractility of T and E in order to determine whether antagonism of adenosine receptors was the underlying mechanism of the inotropic effect of T on diaphragmatic contractility. Ten normal subjects were studied in the sitting position. The contractile properties of the diaphragm were assessed by measuring the transdiaphragmatic pressure (Pdi) generated at functional residual capacity during bilateral electrical stimulation of the phrenic nerves. The subjects were randomized, and after control measurements were performed, they received T or E. This was a double-blind crossover study, the measurements being repeated with the second drug after one week. Both drugs were administered intravenously with a loading dose of 6 and 2 mg/kg administered in 30 min for T and E and a maintenance dose of 0.9 and 0.075 mg.kg-1 X h-1 for T and E, respectively. Measurements were performed before and 60 min after T or E administration. Plasmatic levels of both drugs were also analyzed. In all the subjects, therapeutic levels of T or E were reached (14.8 +/- 0.6 and 3.9 +/- 0.42 mg/l for T and E, respectively, at 30 min). (ABSTRACT TRUNCATED AT 250 WORDS)
Fast voltage gating of Ca2+ release in frog skeletal muscle revealed by supercharging pulses

1 In single frog skeletal muscle fibres, we utilized supercharging voltage clamp command pulses to boost the rate of depolarization in the transverse tubular system (T‐system) such that 95 % of steady‐state potential is achieved in < 2 ms (as indicated by fluorescent potentiometric dye signals detected from a global illumination region). Signals detected near the edge of muscle fibres indicate that peripheral regions of the T‐system are not significantly overcompensated under these conditions. 2 We explored the impact of accelerating T‐system depolarization on voltage‐dependent events of excitation‐contraction (E‐C) coupling by measuring charge movement currents (CMCs) and Ca2+ fluorescence transients in response to both supercharging and conventional step pulses. 3 When compared with CMCs elicited by step pulses, supercharging CMCs are larger, and their kinetics more closely resemble those of gating current records reported for ionic channels. Furthermore, they decay bi‐exponentially (τfast range, 1.3‐1.8 ms; τslow range, 7.3‐11.9 ms), whereas step CMCs fall with a single exponential time course (τ range, 12.5‐26.7 ms). 4 Similarly, supercharging produces a distinct acceleration in Ca2+ release transients, which show little evidence of the voltage‐dependent onset latencies previously encountered using step pulses. 5 The use of this novel methodology in skeletal muscle unveils a previously undetected component of charge movement, the rapid, voltage‐dependent recruitment of which may provide the basis for understanding the fast gating of physiological E‐C coupling.
Rapid detection of TiO2 (E171) in table sugar using Raman spectroscopy

ABSTRACT The potential toxic effects of titanium dioxide (TiO2) to humans remain debatable despite its broad application as a food additive. Thus, confirmation of the existence of TiO2 particles in food matrices and subsequently quantifying them are becoming increasingly critical. This study developed a facile, rapid (< 30 min) and highly reliable method to detect and quantify TiO2 particles (E171) from food products (e.g., table sugar) by Raman spectroscopy. To detect TiO2 particles from sugar solution, sequential centrifugation and washing procedures were effectively applied to separate and recover 97% of TiO2 particles from the sugar solution. The peak intensity of TiO2 sensitively responded to the concentration of TiO2 with a limit of detection (LOD) of 0.073 mg kg–1. In the case of sugar granules, a mapping technique was applied to directly estimate the level of TiO2, which can be potentially used for rapid online monitoring. The plot of averaged intensity to TiO2 concentration in the sugar granules exhibited a good linear relationship in the wide range of 5–2000 mg kg–1, with an LOD of 8.46 mg kg–1. Additionally, we applied Raman spectroscopy to prove the presence of TiO2 in sugar-coated doughnuts. This study begins to fill in the analytical gaps that exist regarding the rapid detection and quantification of TiO2 in food, which facilitate the risk assessment of TiO2 through food exposure. GRAPHICAL ABSTRACT
A free-form lensing grid solution for A1689 with new multiple images

JMD acknowledges support of the consolider project CAD2010-00064 and AYA2012-39475-C02-01 funded by the Ministerio de Economia y Competitividad. KU acknowledges partial support from the National Science Council of Taiwan (grant NSC100-2112-M-001-008-MY3). MS acknowledges financial support from the agreement ASI/INAF/023/12/0. NB and TB acknowledge support of the grants AYA2010- 22111-C03-01 funded by the Ministerio de Economia y Competitividad and PEX/10-CFQM-6444 of the Junta de Andalucia.
Effect of powdered spice treatments on mycelial growth, sporulation and production of aflatoxins by toxigenic fungi

O efeito de dez plantas condimentares em po foi avaliado nas concentracoes de 1, 2, 3 e 4%, para observar o desenvolvimento micelial e esporulacao de Aspergillus niger e Eurotium repens. Os condimentos foram adicionados aos meios de cultura BDA e CYA 20S. O cravo inibiu completamente o desenvolvimento micelial dos fungos testados. Os outros condimentos: canela, alho, tomilho, menta, erva-doce, oregano e cebola foram, em ordem decrescente, antifungicos promissores. Louro e manjericao nao apresentaram um efeito fungistatico pronunciado. O potencial antitoxigenico dos condimentos foi testado contra uma cepa de Aspergillus flavus, produtora de aflatoxina. Os condimentos foram testados nas mesmas concentracoes previamente mencionadas e foram adicionados ao meio de cultura YES, apropriado para a producao daqueles metabolitos. O cravo inibiu completamente o desenvolvimento micelial do Aspergillus flavus. A canela e erva-doce inibiram totalmente a producao de aflatoxina B1 e B2. Louro e manjericao inibiram a sintese de aflatoxina a partir da concentracao de 2%. Os outros condimentos nao apresentaram um efeito antiaflatoxigenico pronunciado.
Morphometry of the human cochlear wall and implications for cochlear surgery*

Objective—To study the lateral wall of the cochlea in human temporal bones (TBs), in order to evaluate the feasibility of performing micro-dissection of the spiral ligament and an endosteal electrode implantation. Material and Methods—We reviewed the database of the TB bank of The House Ear Institute in search of bones that did not distort the otic capsule or spiral ligament, and selected 36 horizontally sectioned TBs. All bones had been removed using the en bloc technique, fixed in formalin, decalcified in EDTA, embedded in celloidin and cut into 20-μm serial sections. We evaluated sections stained with hematoxylin–eosin under a microscope, and made several measurements of the lateral wall of the cochlea using optical appliances. A total of 20 measurements were made at 3 levels: midmodiolar sections; sections at the round window niche; and sections containing the anterior border of the stapes footplate. Results—The selected sections provide useful data when applied during surgery. All the numerical data were analyzed statistically and, although individual variability occurred, most of the measurements seemed to be quite homogeneous. Conclusions—A greater understanding of the microscopic anatomy and dimensions of the human TB will help to understand the surgical relationships at the lateral wall of the cochlea. Our study provides some numerical references for the dimensions of the cochlea that may help in cochlear surgery. These dimensions would be of particular interest in cochlear implantation, especially in the design of endosteal electrodes.
Temperature and carbonate ion effects on Mg/Ca and Sr/Ca ratios in benthic foraminifera: Aragonitic species Hoeglundina elegans

Received 16 March 2005; revised 20 June 2005; accepted 3 November 2005; published 21 February 2006. [1] Core top samples from Atlantic (Little Bahama Banks (LBB)) and Pacific (Hawaii and Indonesia) depth transects have been analyzed in order to assess the influence of bottom water temperature (BWT) and aragonite saturation levels on Mg/Ca and Sr/Ca ratios in the aragonitic benthic foraminifer Hoeglundina elegans. Both the Mg/Ca and Sr/Ca ratios in H. elegans tests show a general decrease with increasing water depth. Although at each site the decreasing trends are consistent with the in situ temperature profile, Mg/Ca and Sr/Ca ratios in LBB are substantially higher than in Indonesia and Hawaii at comparable water depths with a greater difference observed with increasing water depth. Because we find no significant difference between results obtained on ‘‘live’’ and ‘‘dead’’ specimens, we propose that these differences are due to primary effects on the metal uptake during test formation. Evaluation of the water column properties at each site suggests that in situ CO3 ion concentrations play an important role in determining the H. elegans Mg/Ca and Sr/Ca ratios. The CO3 ion effect is limited, however, only to aragonite saturation levels ([DCO3]aragonite) below 15 mmol kg � 1 . Above this level, temperature exerts a dominant effect. Accordingly, we propose that Mg/Ca and Sr/Ca in H. elegans tests can be used to reconstruct thermocline temperatures only in waters oversaturated with respect to the mineral aragonite using the following relationships: Mg/Ca = (0.034 ± 0.002)BWT + (0.96 ± 0.03) and Sr/Ca = (0.060 ± 0.002)BWT + (1.53 ± 0.03) (for [DCO3]aragonite >1 5mmol kg � 1 ). The standard error associated with these equations is about ±1.1� C. Reconstruction of deeper water temperatures is complicated because in undersaturated waters, changes in Mg/Ca and Sr/Ca ratios reflect a combination of changes in [CO3] and BWT. Overall, we find that Sr/Ca, rather than Mg/Ca, in H. elegans may be a more accurate proxy for reconstructing paleotemperatures.
Does it matter who owns Moody’s?

This paper examines the potential influence of Moody’s ownership structure on its rating policies. During the ten years following Moody’s IPO in 2000, Moody’s had two stable large shareholders, Berkshire Hathaway and Davis Selected Advisors, who collectively own about 23.5% of Moody’s. We document that Moody’s ratings on corporate bonds issued by important investee firms of these two large shareholders were more favorable relative to S&P’s ratings on the same bonds. We also find favorable treatment by Moody’s towards its owners in their ratings on commercial mortgage backed securities (CMBS). The results cannot be explained by issuer characteristics or by greater informativeness of Moody's ratings. Lastly, indirect ownership by an institution through a large shareholding in McGraw-Hill, S&P’s parent, does not affect S&P’s ratings. The evidence suggests that direct and stable large shareholders affect the ratings process. These findings are consistent with regulatory concerns about the public ownership of credit rating agencies. JEL classification: G32; L32
Teachers’ Participation in Research Programs Improves Their Students’ Achievement in Science

Teaching Teacher High-school science teachers rarely have an opportunity to participate in scientific research. A program from Columbia University studies what happens when these teachers do get laboratory experience. After a summer program spanning 2 years, including professional development programs, as well as laboratory research, Silverstein et al. (p. 440) show that the teachers' students benefit. Students of teachers who participated in this summer research experience showed greater pass rates on the tough New York State Regents exams than did students of teachers who did not participate in the program. Students of U.S. high school teachers given science research experiences show improved success rates on science exams. Research experience programs engage teachers in the hands-on practice of science. Program advocates assert that program participation enhances teachers’ skills in communicating science to students. We measured the impact of New York City public high-school science teachers’ participation in Columbia University’s Summer Research Program on their students’ academic performance in science. In the year before program entry, students of participating and nonparticipating teachers passed a New York State Regents science examination at the same rate. In years three and four after program entry, participating teachers’ students passed Regents science exams at a rate that was 10.1% higher (P = 0.049) than that of nonparticipating teachers’ students. Other program benefits include decreased teacher attrition from classroom teaching and school cost savings of U.S. $1.14 per $1 invested in the program.
Possessive with in Germanic: have and the Role of P

A central question regarding the syntax–semantics interface is the extent to which semantic primitives correspond one-to-one with syntactic primitives. Den Dikken (1995) proposed that all possession structures can be derived from an underlying locative structure, extending the work of Freeze (1992). This paper argues that such a unified approach is untenable, as there are possession expressions in Icelandic that cannot be derived from locative structures. The Icelandic vera með construction, translated as ‘is with’, provides important insight into the nature of have verbs. It is argued, along the lines of Kayne 1993 and Harley 2002, that have is derived from nonlocative prepositions like English with as in the man with blue eyes. A microcomparative investigation within Germanic supports an analysis whereby the variation in incorporation is correlated with variations in p heads. This analysis allows for a more natural account of the differences between have and be languages beyond Germanic.
Acute intermittent hypoxia increases both phrenic and sympathetic nerve activities in the rat

The respiratory system expresses multiple forms of plasticity, defined as alterations in the breathing pattern that persist or develop after a stimulus. Stimulation of breathing with intermittent hypoxia (IH) elicits long‐term facilitation (LTF), a type of plasticity in which respiratory motor activity progressively increases in anaesthetized animals, even after the stimuli have ceased and blood gases have normalized. It is unknown whether the sympathetic nervous system similarly expresses IH‐induced plasticity, but we predicted that IH would evoke LTF in sympathetic nerve activity (SNA) because respiratory and sympathetic control systems are coupled. To test this idea, we recorded splanchnic (sSNA) and phrenic nerve activities (PNA) in equithesin‐anaesthetized rats. Animals were exposed to 10 45 s episodes of 8% O2–92% N2, separated by 5 min intervals of 100% O2, and recordings were continued for 60 min following the last hypoxic exposure. Cycle‐triggered averages of integrated PNA and sSNA from periods preceding, and 5 and 60 min following the hypoxic stimuli were compared. Intermittent hypoxia significantly increased both sSNA and PNA. Treatment with methysergide (3 mg kg−1, i.v.) 20 min before the intermittent hypoxic exposures prevented the increases in integrated PNA and sSNA 60 min after IH, indicating a role of serotonergic pathways in this form of plasticity. No increases in PNA and sSNA occurred at comparable times (60 and 120 min) in rats not exposed to hypoxia. The increased sSNA was not simply tonic, but was correlated with respiratory bursts, and occurred predominantly during the first half of expiration. These findings support the hypothesis that sympathorespiratory coupling may underlie the sustained increase in SNA associated with the IH that occurs during sleep apnoea.
Diagnosing Culture 1 Diagnosing Organizational Cultures : A Conceptual and Empirical Review of Culture Effectiveness Surveys Short title : Diagnosing Organizational Cultures

Methodological reviews within the organizational culture domain have repeatedly called for additional research evaluating the reliability and validity of survey measures of organizational culture. In this review, we first trace the development of survey research within the organizational culture tradition, focusing specifically on the category of instruments that assess aspects of culture related to organizational effectiveness. Although surveys of this kind are the most direct diagnostic assessments of organizational culture, our review suggests that research support is generally inadequate to establish the reliability and validity of the majority of instruments in this category. Next, our review identifies several considerations that are unique to the development and validation of culture effectiveness surveys, and thus warrant special attention. We identify three key challenges for future culture researchers to address: testing nested models, aggregating data to the organizational level, and establishing criterion-related validity. Finally, using archival data collected with the Denison Organizational Culture Survey, we present an empirical illustration of the three challenges identified above and conclude by considering limitations and opportunities for future research.