Miracle-dz/UniFAR-FTUs huggingface dataset:
Dynamic Interplay between Histone H3 Modifications and Protein Interpreters: Emerging Evidence for a “Histone Language”

Histone proteins organize DNA into dynamic chromatin structures and regulate processes such as transcription, repair, and replication. Control of chromatin function and structure is mediated in part by reversible post‐translational modifications (PTMs) on histones. The most N‐terminal region of histone H3 contains a high density of modifiable residues. Here we focus on the dynamic interplay between histone modification states on the H3 N terminus and the binding modules that recognize these states. Specifically, we discuss the effect of auxiliary modifications to H3K4unmod/me3 binding modules (specifically H3R2 methylation, H3T3 phosphorylation, and H3T6 phosphorylation). Emerging evidence suggests that histone PTMs behave less like a strict “code”, but more like a “language”, which better illustrates the importance of context. Using androgen‐receptor‐mediated gene activation as an example, we propose a model of how the combinatorial natures of PTMs on the H3 N terminus and the complexes that recognize these epigenetic modifications control gene expression.
Estimated Nutritive Value of Low-Price Model Lunch Sets Provided to Garment Workers in Cambodia

Background: The establishment of staff canteens is expected to improve the nutritional situation of Cambodian garment workers. The objective of this study is to assess the nutritive value of low-price model lunch sets provided at a garment factory in Phnom Penh, Cambodia. Methods: Exemplary lunch sets were served to female workers through a temporary canteen at a garment factory in Phnom Penh. Dish samples were collected repeatedly to examine mean serving sizes of individual ingredients. Food composition tables and NutriSurvey software were used to assess mean amounts and contributions to recommended dietary allowances (RDAs) or adequate intake of energy, macronutrients, dietary fiber, vitamin C (VitC), iron, vitamin A (VitA), folate and vitamin B12 (VitB12). Results: On average, lunch sets provided roughly one third of RDA or adequate intake of energy, carbohydrates, fat and dietary fiber. Contribution to RDA of protein was high (46% RDA). The sets contained a high mean share of VitC (159% RDA), VitA (66% RDA), and folate (44% RDA), but were low in VitB12 (29% RDA) and iron (20% RDA). Conclusions: Overall, lunches satisfied recommendations of caloric content and macronutrient composition. Sets on average contained a beneficial amount of VitC, VitA and folate. Adjustments are needed for a higher iron content. Alternative iron-rich foods are expected to be better suited, compared to increasing portions of costly meat/fish components. Lunch provision at Cambodian garment factories holds the potential to improve food security of workers, approximately at costs of <1 USD/person/day at large scale. Data on quantitative total dietary intake as well as physical activity among workers are needed to further optimize the concept of staff canteens.
Increased mitochondrial ROS generation mediates the loss of the anti‐contractile effects of perivascular adipose tissue in high‐fat diet obese mice

Obesity is associated with structural and functional changes in perivascular adipose tissue (PVAT), favouring release of reactive oxygen species (ROS), vasoconstrictor and proinflammatory factors. The cytokine TNF‐α induces vascular dysfunction and is produced by PVAT. We tested the hypothesis that obesity‐associated PVAT dysfunction was mediated by augmented mitochondrial ROS (mROS) generation due to increased TNF‐α production in this tissue.
Cognitive challenges to minimising low value care

Clinical decisions often rely on pattern recognition, simple rules of thumb, tacit knowledge and habit. In many instances, such intuitive decisions are fast and accurate, but they can be subject to cognitive biases leading to delivery of care of low value at odds with scientific evidence of best practice. If programmes, such as EVOLVE (Evaluating Evidence, Enhancing Efficiencies) and Choosing Wisely are to have maximal impact in minimising low value care, such biases, and the factors that hide and accentuate them, need to be exposed and addressed in a collegiate and non‐judgemental manner.
Histamine H2 receptor signaling × environment interactions determine susceptibility to experimental allergic encephalomyelitis

Histamine and its receptors are important in both multiple sclerosis and experimental allergic encephalomyelitis (EAE). C57BL/6J (B6) mice deficient for the histamine H2 receptor (H2RKO) are less susceptible to EAE and exhibit blunted Th1 responses. However, whether decreased antigen‐specific T‐cell effector responses in H2RKO mice were due to a lack of H2R signaling in CD4+ T cells or antigen‐presenting cells has remained unclear. We generated transgenic mice expressing H2R specifically in T cells on the H2RKO background, and, using wild‐type B6 and H2RKO mice as controls, induced EAE either in the presence or absence of the ancillary adjuvant pertussis toxin (PTX), which models the effects of infectious inflammatory stimuli on autoimmune disease. We monitored the mice for clinical signs of EAE and neuropathology, as well as effector T‐cell responses using flow cytometry. EAE severity and neuropathology in H2RKO mice expressing H2R exclusively in T cells become equal to those in wild‐type B6 mice only when PTX is used to elicit disease. EAE complementation was associated with frequencies of CD4+IFN‐γ+ and CD4+IL‐17+ cells that are equal to or greater than those in wild‐type B6, respectively. Thus, the regulation of enceph‐alitogenic T‐cell responses and EAE susceptibility by H2R signaling in CD4+ T cells is dependent on gene × environment interactions. —Saligrama, N. , Case, L. K. , Krementsov, D. N. , Teuscher, C. Histamine H2 receptor signaling × environment interactions determine susceptibility to experimental allergic encephalomyelitis. FASEB J. 28, 1898–1909 (2014). www.fasebj. org
Melatonin delays photoreceptor degeneration in a mouse model of autosomal recessive retinitis pigmentosa

Retinitis pigmentosa (RP) comprises a group of incurable inherited retinal degenerations. Targeting common processes, instead of mutation‐specific treatment, has proven to be an innovative strategy to combat debilitating retinal degeneration. Growing evidence indicates that melatonin possesses a potent activity against neurodegenerative disorders by mitigating cell damage associated with apoptosis and inflammation. Given the pleiotropic role of melatonin in central nervous system, the aim of the present study was to investigate whether melatonin would afford protection against retinal degeneration in autosomal recessive RP (arRP). Rd10, a well‐characterized murine model of human arRP, received daily intraperitoneal injection of melatonin (15 mg/kg) between postnatal day (P) 13 and P30. Retinas treated with melatonin or vehicle were harvested for analysis at P30 and P45, respectively. The findings showed that melatonin could dampen the photoreceptors death and delay consequent retinal degeneration. We also observed that melatonin weakened the expression of glial fibrillary acidic protein (GFAP) in Müller cells. Additionally, melatonin could alleviate retinal inflammatory response visualized by IBA1 staining, which was further corroborated by downregulation of inflammation‐related genes, such as tumor necrosis factor alpha (Tnf‐α), chemokine (C‐C motif) ligand 2 (Ccl2), and chemokine (C‐X‐C motif) ligand 10 (Cxcl10). These data revealed that melatonin could ameliorate retinal degeneration through potentially attenuating apoptosis, reactive gliosis, and microglial activation in rd10 mice. Moreover, these results suggest melatonin as a promising agent improving photoreceptors survival in human RP.
Association of angiotensin-converting enzyme gene I/D polymorphism with chronic obstructive pulmonary disease: a meta-analysis

Objectives: We conducted a meta-analysis of published studies on the angiotensin-converting enzyme (ACE) gene insertion/deletion (I/D) polymorphism associated with the risk of chronic obstructive pulmonary disease, as well as with pulmonary function and circulating angiotensin-converting enzyme changes. Methods: A literature search, quality assessment and data extraction were completed independently and in duplicate. Results: A total of 16 articles were meta-analysed, including 12 articles (2113 patients and 8786 controls) for chronic obstructive pulmonary disease risk and eight articles (11,664 subjects) for pulmonary and circulating phenotypes. In overall and subgroup analyses, no significance was noted between the I/D polymorphism and chronic obstructive pulmonary disease risk under all genetic models (P>0.05), without heterogeneity or publication bias. Carriers of II, ID and II plus ID genotypes had significantly lower levels of circulating angiotensin-converting enzyme than those with the DD genotype (weighted mean difference −13.35, −8.13 and −10.74 U/L, respectively, P<0.001). For forced expiratory volume in one second (FEV1)/forced vital capacity, carriers of the DD genotype had marginally lower levels than those with the DD genotype (weighted mean difference –1.66, P=0.034). Furthermore in the case of FEV1 of 50% or greater of predicted FEV1, FEV1 was marginally lower in ID genotype carriers than DD genotype carriers (weighted mean difference −3.50, P=0.056). Conclusions: Our meta-analytical findings demonstrated that the ACE gene I/D polymorphism was not associated with the risk of chronic obstructive pulmonary disease.
The Behavior of Turkish Lira forward and Spot Foreign Exchange Rates

The purpose of this study is twofold; firstly, the behavior of Turkish lira (TRL) forward rates against US Dollar (USD) and Euro will be evaluated; whether the interest rate parity holds and the market participants quote the forward foreign exchange rates according to the interest rate differentials. It is also analyzed whether the forward foreign exchange rate coincides with the spot exchange rate at the relevant maturity. Secondly, the unbiased forward rate hypothesis (UFH) is tested by the use of regression method. The finding is that for TRL against USD and Euro, the forward rate is a biased predictor of the future spot rate. Going the same way with the previous researchers, the source of the bias is examined. The explanations set by early researchers for the finding of bias in the forward markets for different currencies have been generally based on two different sets of explanations. The first category of explanation maintains the assumption of rational expectations and interprets the systematic component of the forward marketâ€™s prediction errors as a risk premium. The second category attributes the systematic component of the forward rateâ€™s prediction errors to expectation errors on the part of market participants that are themselves systematic.
Travel-related Zika virus cases in Canada: October 2015-June 2017.

Background Zika virus (ZIKV) is an emerging mosquito-borne disease that can cause severe birth defects if contracted congenitally. Since late 2015, there has been a large increase in the number of travel-related cases of Zika virus infection in Canada. Objective The objective of this study was to describe the epidemiology of travel-related Zika cases in Canada from October 2015 to June 2017 and review them in the context of the international outbreak in the Americas. Methods Zika virus infections were confirmed by polymerase chain reaction (PCR) detection of viral RNA and/or the serological identification of ZIKV-specific antibodies in serum. Cases of ZIKV infection were identified by provincial and territorial health authorities, and reported on a regular basis to the Public Health Agency of Canada (PHAC). Case information requested included date of illness onset, age category, sex, pregnancy status, and location(s) and dates of travel. Estimates for the monthly number of Canadians travelling outside of Canada to other countries in the Americas were obtained from Statistics Canada and the International Air Transport Association (IATA). Data to produce the epidemic curves of autochthonous cases for each region of the Americas were extracted from country-specific epidemic curves on the Pan American Health Organization website. Results As of June 7, 2017, 513 laboratory confirmed cases and two Zika-related birth/fetal anomalies were reported across all 10 provinces. Illness in Canadian travellers generally coincided with outbreak intensity in the country of exposure rather than travel volume. There has been no evidence of autochthonous (local) transmission in Canada. Currently, cases are on the decline both in Canada and internationally. Conclusion The surge in Canadian ZIKV infections in 2016 was directly related to the incursion and spread of ZIKV into the Americas. Although cases are now on the decline worldwide, it remains to be seen whether a resurgence of cases in previously affected or new areas will occur. Both outbreak intensity and seasonality of ZIKV transmission should be monitored over time in order to inform the timing of public health education campaigns, as some may turn out to be more effective in the off-peak travel season when the risk of disease transmission may be higher. Ongoing education and awareness among travellers, particularly for pregnant women and those planning pregnancies, is still indicated.
Metachronous Testicular Cancer After Orchiectomy: A Rare Case

Testicular cancer represents approximately 1% of all cancers diagnosed in males. The prevalence of bilateral testicular germ cell tumor cases varies from 1% to 5%. Intratubular germ cell neoplasia (ITGCN) is a precursor for almost all testicular germ cell tumors (TGCT) and is one of the highest risks of developing contralateral testicular cancer. The radical orchiectomy is still preferred for the treatment of testicular cancer. However, in some cases like solitary testis, bilateral cancer or if the tumor size is under 30% percent of the testicular extent, organ-sparing surgery can be an option. There are just a few published reports of metachronous contralateral testicular cancer, developed after orchiectomy with the histopathology of the intratubular germ cell neoplasia.
Limited time to make a change : an investigation into charitable behaviour around a deadline.

I conduct a laboratory experiment to analyse the effect of deadlines and deadline length on charitable giving. Individuals may postpone or procrastinate making a donation, and then forget about doing so due to inattention. This behavioural problem is called inertia. In other contexts, deadlines are a useful tool to prevent inertia. I examine their use in the context of charitable giving using a dictator game where the recipient is a local charity. Participants are either constrained by a one week deadline, a two week deadline, or no deadline. I find no statistically significant evidence of an inertia effect in charitable giving. Furthermore, I find no evidence that the use of a deadline increases the number of donations, or the average donation of participants. The length of the deadline does not change this result. Examining positive donations, there is a significantly higher average donation with the use of a two week deadline compared to no deadline, but this result does not carry through to other comparisons. Overall, I find that deadlines do not appear to help, nor hinder, charitable campaigns.
Information-theoretically secure quantum homomorphic encryption and its limitations

In this brief survey, we expand on the arguments of [1] detailing the inefficiency of informationtheoretically secure (ITS) quantum fully homomorphic encryption (QFHE). We summarize these results in the context of other work [2, 3], and existing workarounds that limit the number of implementable homomorphisms or weaken security. Finally, we discuss some subtleties of the imposed restrictions, and potential avenues for expanding them.
Tunable Wettability by Clicking Counterions Into Polyelectrolyte Brushes

Polymer brushes have recently emerged as an extremely versatile way to modify surface properties in a robust and controlled way. The introduction of responsive polymers and block copolymers in polymer‐brush systems has also opened up new routes to ‘smart' surfaces with switchable surface properties. Here, the use of polyelectrolyte brushes as a supramolecular platform for the immobilization of a wide range of species, leading to a tunable wettability of substrates, is presented.
Effects of Crop Level on Chemical Composition and Headspace Volatiles of Lodi Zinfandel Grapes and Wines

A method is given for quantitative analysis of wine headspace. The reproducibility of the method, for 24 identified peaks, is ±10-15% if internal standards are chosen correctly. Unidentified peaks of lesser intensity generally have larger coefficients of variation. Variations in headspace analysis between field replications were too large for the data to be pooled. All calculations were done on individual field replicates. Stepwise discriminant analysis was used to show that the wines could be correctly sorted on the basis of analysis of either must, wine, or headspace. Selective must, wine, and headspace data were correlated linearly with crop levels.
Geobacter lovleyi sp. nov. Strain SZ, a Novel Metal-Reducing and Tetrachloroethene-Dechlorinating Bacterium

ABSTRACT A bacterial isolate, designated strain SZ, was obtained from noncontaminated creek sediment microcosms based on its ability to derive energy from acetate oxidation coupled to tetrachloroethene (PCE)-to-cis-1,2-dichloroethene (cis-DCE) dechlorination (i.e., chlororespiration). Hydrogen and pyruvate served as alternate electron donors for strain SZ, and the range of electron acceptors included (reduced products are given in brackets) PCE and trichloroethene [cis-DCE], nitrate [ammonium], fumarate [succinate], Fe(III) [Fe(II)], malate [succinate], Mn(IV) [Mn(II)], U(VI) [U(IV)], and elemental sulfur [sulfide]. PCE and soluble Fe(III) (as ferric citrate) were reduced at rates of 56.5 and 164 nmol min−1 mg of protein−1, respectively, with acetate as the electron donor. Alternate electron acceptors, such as U(VI) and nitrate, did not inhibit PCE dechlorination and were consumed concomitantly. With PCE, Fe(III) (as ferric citrate), and nitrate as electron acceptors, H2 was consumed to threshold concentrations of 0.08 ± 0.03 nM, 0.16 ± 0.07 nM, and 0.5 ± 0.06 nM, respectively, and acetate was consumed to 3.0 ± 2.1 nM, 1.2 ± 0.5 nM, and 3.6 ± 0.25 nM, respectively. Apparently, electron acceptor-specific acetate consumption threshold concentrations exist, suggesting that similar to the hydrogen threshold model, the measurement of acetate threshold concentrations offers an additional diagnostic tool to delineate terminal electron-accepting processes in anaerobic subsurface environments. Genetic and phenotypic analyses classify strain SZ as the type strain of the new species, Geobacter lovleyi sp. nov., with Geobacter (formerly Trichlorobacter) thiogenes as the closest relative. Furthermore, the analysis of 16S rRNA gene sequences recovered from PCE-dechlorinating consortia and chloroethene-contaminated subsurface environments suggests that Geobacter lovleyi belongs to a distinct, dechlorinating clade within the metal-reducing Geobacter group. Substrate versatility, consumption of electron donors to low threshold concentrations, and simultaneous reduction of electron acceptors suggest that strain SZ-type organisms have desirable characteristics for bioremediation applications.
Sample size determinations for group-based randomized clinical trials with different levels of data hierarchy between experimental and control arms

We derived sample size formulae for detecting main effects in group-based randomized clinical trials with different levels of data hierarchy between experimental and control arms. Such designs are necessary when experimental interventions need to be administered to groups of subjects whereas control conditions need to be administered to individual subjects. This type of trial, often referred to as a partially nested or partially clustered design, has been implemented for management of chronic diseases such as diabetes and is beginning to emerge more commonly in wider clinical settings. Depending on the research setting, the level of hierarchy of data structure for the experimental arm can be three or two, whereas that for the control arm is two or one. Such different levels of data hierarchy assume correlation structures of outcomes that are different between arms, regardless of whether research settings require two or three level data structure for the experimental arm. Therefore, the different correlations should be taken into account for statistical modeling and for sample size determinations. To this end, we considered mixed-effects linear models with different correlation structures between experimental and control arms to theoretically derive and empirically validate the sample size formulae with simulation studies.
Test-retest reliability of knee extensor rate of velocity and power development in older adults using the isotonic mode on a Biodex System 3 dynamometer

Isotonic testing and measures of rapid power production are emerging as functionally relevant test methods for detection of muscle aging. Our objective was to assess reliability of rapid velocity and power measures in older adults using the isotonic mode of an isokinetic dynamometer. Sixty-three participants (aged 65 to 82 years) underwent a test-retest protocol with one week time interval. Isotonic knee extension tests were performed at four different loads: 0%, 25%, 50% and 75% of maximal isometric strength. Peak velocity (pV) and power (pP) were determined as the highest values of the velocity and power curve. Rate of velocity (RVD) and power development (RPD) were calculated as the linear slopes of the velocity- and power-time curve. Relative and absolute measures of test-retest reliability were analyzed using intraclass correlation coefficients (ICC), standard error of measurement (SEM) and Bland-Altman analyses. Overall, reliability was high for pV, pP, RVD and RPD at 0%, 25% and 50% load (ICC: .85 - .98, SEM: 3% - 10%). A trend for increased reliability at lower loads seemed apparent. The tests at 75% load led to range of motion failure and should be avoided. In addition, results demonstrated that caution is advised when interpreting early phase results (first 50ms). To conclude, our results support the use of the isotonic mode of an isokinetic dynamometer for testing rapid power and velocity characteristics in older adults, which is of high clinical relevance given that these muscle characteristics are emerging as the primary outcomes for preventive and rehabilitative interventions in aging research.
uasi-static fault-tolerant scheduling schemes for energy-efficient hard eal-time systems

This paper investigates fault tolerance and dynamic voltage scaling (DVS) in hard real-time systems. The authors present quasi-static task scheduling algorithms that consist of offline components and online components. The offline components are designed the way they enable the online components to achieve energy savings by using the dynamic slack due to variations in task execution times and uncertainties in vailable online 28 January 2012