Miracle-dz/UniFAR-FTUs huggingface dataset:
Ordered Histone Modifications Are Associated with Transcriptional Poising and Activation of the phaseolin Promoter

The phaseolin (phas) promoter drives copious production of transcripts encoding the protein phaseolin during seed embryogenesis but is silent in vegetative tissues, in which a nucleosome is positioned over its three-phased TATA boxes. Transition from the inactive state in transgenic Arabidopsis thaliana leaves was accomplished by ectopic expression of the transcription factor Phaseolus vulgaris ABI3-like factor (ALF) and application of abscisic acid (ABA). Placement of hemagglutinin-tagged ALF expression under the control of an estradiol-inducible promoter permitted chromatin immunoprecipitation analysis of chronological changes in histone modifications, notably increased acetylation of H3-K9 and H4-K12, as phas chromatin was remodeled (potentiated). A different array of changes, including acetylation of H3-K14 and methylation of H3-K4, was found to be associated with ABA-mediated activation. Thus, temporal separation of phas potentiation from activation revealed that histone H3 and H4 Lys residues are not globally hyperacetylated during phas expression. Whereas decreases in histone H3 and H4 levels were detected during ALF-mediated remodeling, slight increases occurred after ABA-mediated activation, suggesting the restoration of histone–phas interactions or the replacement of histones in the phas chromatin. The observed histone modifications provide insight into factors involved in the euchromatinization and activation of a plant gene and expand the evidence for histone code conservation among eukaryotes.
Acute IGF-1, Cortisol and Creatine Kinase Responses to Very Short Rest Intervals Between Sets During Resistance Exercise to Failure in Men

Insulin-like growth factor-1 (IGF-1) peptides exist as single chain polypeptides consisting of about 70 amino acid residues which stimulate muscle hypertrophy via PI-3K-Akt-mTOR signaling. The purpose of the present study was to investigate the effect of a resistance exercise (RE) protocol (4 sets of squat and bench press with 85 % of 1RM) at different rest intervals between sets on serum IGF-1, cortisol (CO), creatine kinase (CK) and blood lactate concentrations. Hence, ten recreationally resistance-trained men (Mean ± SD, age=20.37 ± 2.44 years, body mass= 65.6 ± 26.70 kg) volunteered as subjects that in 4 separate sessions with 48 h from each other performed a RE protocol with 60, 90 and 120 second rest period between sets. Blood samples were collected before (Pre), immediately after (Post) and 30 min after the exercise protocols (30Post). Changes in serum IGF-1 levels were not significant between protocols. However, serum IGF-1concentration was significantly increased by 3.6 and 23 percent during RT with 60 second rest between sets at Pre and 30Post. Serum CO concentrations were significantly higher in 60 and 90 second rest protocol than 120 second protocol. Changes in serum CK and blood lactate concentrations were not significant between protocols but post exercise levels significantly increased in each protocol. The data indicate that although rest period between sets in RE to failure resulted in a significant change in CO levels, it had no effect on plasma IGF-1, CK and lactate levels. However, post exercise serum IGF-1 concentrations significantly increased only at RE to failure with 60s rest between sets.
Prevalence of linked angina and gastroesophageal reflux disease in general practice.

AIM To evaluate the association between gastroesophageal reflux diseases (GERD) and coronary heart diseases. METHODS One thousand nine hundred and seventy consecutive patients who attended our hospital were enrolled. All of the patients who first attend our hospital were asked to respond to the F-scale questionnaire regardless of their chief complaints. All patients had a careful history taken, and resting echocardiography (ECG) was performed by physicians if the diagnostic necessity arose. Patients with ECG signs of coronary artery ischemia were defined as ST-segment depression based on the Minnesota code. RESULTS Among 712 patients (36%) with GERD, ECG was performed in 171 (24%), and ischemic changes were detected in eight (5%). Four (50%) of these patients with abnormal findings upon ECG had no chest symptoms such as chest pain, chest oppression, or palpitations. These patients (0.6%; 4/712) were thought to have non-GERD heartburn, which may be related to ischemic heart disease. Of 281 patients who underwent ECG and did not have GERD symptoms, 20 (7%) had abnormal findings upon ECG. In patients with GERD symptoms and ECG signs of coronary artery ischemia, the prevalence of linked angina was considered to be 0.4% (8/1970 patients). CONCLUSION The present study suggested that ischemic heart disease might be found although a patient was referred to the hospital with a complaint of GERD symptoms. Physicians have to be concerned about missing clinically important coronary artery disease while evaluating patients for GERD symptoms.
How members of the public account for the England Riots of summer 2011

The purpose of this study is to gain knowledge of how the general public viewed the England riots of 2011 in order to gain a fuller understanding of the riots and their impact on society. The study involved the thematic analysis of four semi-structured focus groups that were conducted with a total of eighteen participants from differing backgrounds. The analysis identified five themes: how participants draw on traditional theories of the crowd; the Police were deemed to be ‘damned if they do and damned if they don’t’; opportunism was used to account for looting; the media were viewed as aiding the spread of the riots but also as informative and as aiding the cleanup after the riots ended; and the riots were presented as being understandable, but in no way acceptable. This demonstrates how public understanding of the riots differs from the psychological literature. Practical recommendations are suggested including the need to give a platform to crowd psychologists.
A clathrin coat assembly role for the muniscin protein central linker revealed by TALEN-mediated gene editing

Clathrin-mediated endocytosis is an evolutionarily ancient membrane transport system regulating cellular receptivity and responsiveness. Plasmalemma clathrin-coated structures range from unitary domed assemblies to expansive planar constructions with internal or flanking invaginated buds. Precisely how these morphologically-distinct coats are formed, and whether all are functionally equivalent for selective cargo internalization is still disputed. We have disrupted the genes encoding a set of early arriving clathrin-coat constituents, FCHO1 and FCHO2, in HeLa cells. Endocytic coats do not disappear in this genetic background; rather clustered planar lattices predominate and endocytosis slows, but does not cease. The central linker of FCHO proteins acts as an allosteric regulator of the prime endocytic adaptor, AP-2. By loading AP-2 onto the plasma membrane, FCHO proteins provide a parallel pathway for AP-2 activation and clathrin-coat fabrication. Further, the steady-state morphology of clathrin-coated structures appears to be a manifestation of the availability of the muniscin linker during lattice polymerization. DOI: http://dx.doi. org/10.7554/eLife.04137. 001
Diagnosis of surgical sinusitis using nasal endoscopy and computerized tomography

The ability to identify surgical sinus disease using diagnostic nasal endoscopy and coronal CT scanning of the paranasal sinuses is studied prospectively. Fifty consecutive patients with symptoms of chronic sinusitis lacking surgical indications by traditional work‐up comprise the patient population. Sixty percent had endoscopic or CT indications for surgery. There was a 90% correlation between endoscopy and CT examination with the combined work‐up being more accurate than either modality alone. Functional endoscopic sinus surgery was performed in 18 cases. There were no major complications. Approximately 89% of the postoperative group report significant improvement, with 55.6% reporting total relief of symptoms.
Subchondral bone marrow edema in patients with degeneration of the articular cartilage of the knee joint.

PURPOSE To retrospectively determine at magnetic resonance (MR) imaging the prevalence of subchondral bone marrow edema beneath arthroscopically proved articular cartilage defects. MATERIALS AND METHODS The study was performed in compliance with HIPAA regulations, and a waiver of informed consent was obtained from the institutional review board before the study was performed. The study consisted of 132 patients (70 men, 62 women; average age, 53 years) with articular cartilage defects of the knee joint who underwent MR imaging of the knee and subsequent arthroscopic knee surgery. At the time of arthroscopy, each articular cartilage lesion was graded by using the Noyes classification system. MR examinations were retrospectively reviewed to determine the size, depth, and location of subchondral bone marrow edema without knowledge of the arthroscopic findings. Pairwise Fisher exact tests and two-sample t tests were used to correlate MR imaging findings of subchondral bone marrow edema with the arthroscopic grade of articular cartilage degeneration. RESULTS Subchondral bone marrow edema was seen beneath 105 (19%) of 554 articular cartilage defects identified at arthroscopy. It was not observed beneath any of the six grade 1 cartilage defects but was observed beneath eight (4.9%) of 163 grade 2A defects, 40 (14.4%) of 278 grade 2B defects, 54 (55.1%) of 98 grade 3A defects, and three (33.3%) of nine grade 3B defects. Subchondral bone marrow edema was also seen beneath four (1.4%) of 238 articular surfaces that appeared normal at arthroscopy. The mean depth and cross-sectional area of subchondral bone marrow edema increased with increasing grade of the articular cartilage lesion. CONCLUSION Higher grades of articular cartilage defects are associated with higher prevalence and greater depth and cross-sectional area of subchondral bone marrow edema.
Two Types of Monetarism

THE 1970s witnessed the rise of two --fashionable macroeconomic schools of thought-monetarism and the so-called "new classical" macroeconomics, the latter usually closely identified with one of its fundamental components, the rational expectations hypothesis. Both schools trace their ancestory to older economic doctrines, but it is just in the last decade that they have moved into the mainstream of post-war macroeconomics. The increasing importance of monetarist and new classical thinking naturally resulted in attempts to define each doctrine and to classify disparate thinkers as adherents or opponents. Monetarism has been surveyed, inter alia, in Thomas Mayer (1978), Jerome Stein (1976), Douglas Purvis (1980), David Laidler (1981, 1982), and James Meade (1981). Despite these attempts no universally accepted definition of monetarism and, hence, no universally accepted classification of who is and who is not a monetarist has emerged. The reason is, of course, that any economist is described most fully by a vector of characteristics. Any definition emphasizes some of the elements of this vector, while playing down related ones. Another definition may take the related ones to be more important. The borders of such categories are bound to be poorly defined. Although the definitions may be arbitrary, the attempts to formulate them are not sterile. Individual monetarists may bear only a family resemblance to one another; nevertheless, the effort of classifying them yields clarification as a by-product. The new classical economics has not been surveyed in quite the same spirit as monetarism. The emphasis has been on its relationship to other distinct doctrines, rather than on who is or is not a new classical (Brian Kantor, 1979; Stein, 1982). Indeed, the question of whether or not the new classicals are monetarists has loomed large in these discussions. James Tobin (1980, 1981) calls the new classicals "monetarists mark II. " He bases the title on the similarity of the two schools' policy prescriptions. Frank Hahn (1980) agrees that they are monetarists, but bases the judgment on the similarity of their theoretical presuppositions. Laidler (1981, 1982), on the other hand, finds that they are not
The effect of section of the carotid sinus and aortic nerves on the cardiac output of the rabbit.

The findings on the effects of acute carotid occlusion, or section of the carotid and aortic nerves, on the cardiac output have been conflicting in anaesthetized and unanaesthetized animals (Heymans & Neil, 1958). In the only study on the effects on cardiac output of chronic section of the carotid sinus and aortic nerves Bing, Thomas & Waples (1945) observed an increase in output in the conscious dog. The present report examines the effects on cardiac output, determined by the thermodilution method (Fegler, 1954), of chronic section of these nerves in the unanaesthetized rabbit, and also considers the acute effects of carotid sinus and aortic nerve section under anaesthesia. The rabbit has the anatomical advantage of aortic depressor nerves distinct from the main vagal trunks, so that combined bilateral section of carotid sinus and aortic nerves results in section of the great majority of arterial chemoreceptor and baroreceptor fibres (Heymans & Neil, 1958). This advantage has been utilized in previous studies of neurogenic hypertension (Koch & Mies, 1929; Kremer, Wright & Scarff, 1933) but the effects on cardiac output have not so far been examined.
Forecasting net ecosystem CO2 exchange in a subalpine forest using model data assimilation combined with simulated climate and weather generation

Forecasting the carbon uptake potential of terrestrial ecosystems in the face of future climate change has proven challenging. Process models, which have been increasingly used to study ecosystem‐atmosphere carbon and water exchanges when conditioned with tower‐based eddy covariance data, have the potential to inform us about biogeochemical processes in future climate regimes, but only if we can reconcile the spatial and temporal scales used for observed fluxes and projected climate. Here, we used weather generator and ecosystem process models conditioned on observed weather dynamics and carbon/water fluxes, and embedded them within climate projections from a suite of six Earth Systems Models. Using this combination of models, we studied carbon cycle processes in a subalpine forest within the context of future (2080–2099) climate regimes. The assimilation of daily averaged, observed net ecosystem CO2 exchange (NEE) and evapotranspiration (ET) into the ecosystem process model resulted in retrieval of projected NEE with a level of accuracy that was similar to that following the assimilation of half‐daily averaged observations; the assimilation of 30 min averaged fluxes or monthly averaged fluxes caused degradation in the model's capacity to accurately simulate seasonal patterns in observed NEE. Using daily averaged flux data with daily averaged weather data projected for the period 2080–2099, we predicted greater forest net CO2 uptake in response to a lengthening of the growing season. These results contradict our previous observations of reduced CO2 uptake in response to longer growing seasons in the current (1999–2008) climate regime. The difference between these analyses is due to a projected increase in the frequency of rain versus snow during warmer winters of the future. Our results demonstrate the sensitivity of modeled processes to local variation in meteorology, which is often left unresolved in traditional approaches to earth systems modeling, and the importance of maintaining similarity in the timescales used in ecosystem process models driven by downscaled climate projections.
Household Animal and Human Medicine Use and Animal Husbandry Practices in Rural Bangladesh: Risk Factors for Emerging Zoonotic Disease and Antibiotic Resistance

Animal antimicrobial use and husbandry practices increase risk of emerging zoonotic disease and antibiotic resistance. We surveyed 700 households to elicit information on human and animal medicine use and husbandry practices. Households that owned livestock (n = 265/459, 57.7%) reported using animal treatments 630 times during the previous 6 months; 57.6% obtained medicines, including antibiotics, from drug sellers. Government animal healthcare providers were rarely visited (9.7%), and respondents more often sought animal health care from pharmacies and village doctors (70.6% and 11.9%, respectively), citing the latter two as less costly and more successful based on past performance. Animal husbandry practices that could promote the transmission of microbes from animals to humans included the following: the proximity of chickens to humans (50.1% of households reported that the chickens slept in the bedroom); the shared use of natural bodies of water for human and animal bathing (78.3%); the use of livestock waste as fertilizer (60.9%); and gender roles that dictate that females are the primary caretakers of poultry and children (62.8%). In the absence of an effective animal healthcare system, villagers must depend on informal healthcare providers for treatment of their animals. Suboptimal use of antimicrobials coupled with unhygienic animal husbandry practices is an important risk factor for emerging zoonotic disease and resistant pathogens.
Examining the Pathogenesis of Breast Cancer Using a Novel Agent-Based Model of Mammary Ductal Epithelium Dynamics

The study of the pathogenesis of breast cancer is challenged by the long time-course of the disease process and the multi-factorial nature of generating oncogenic insults. The characterization of the longitudinal pathogenesis of malignant transformation from baseline normal breast duct epithelial dynamics may provide vital insight into the cascading systems failure that leads to breast cancer. To this end, extensive information on the baseline behavior of normal mammary epithelium and breast cancer oncogenesis was integrated into a computational model termed the Ductal Epithelium Agent-Based Model (DEABM). The DEABM is composed of computational agents that behave according to rules established from published cellular and molecular mechanisms concerning breast duct epithelial dynamics and oncogenesis. The DEABM implements DNA damage and repair, cell division, genetic inheritance and simulates the local tissue environment with hormone excretion and receptor signaling. Unrepaired DNA damage impacts the integrity of the genome within individual cells, including a set of eight representative oncogenes and tumor suppressors previously implicated in breast cancer, with subsequent consequences on successive generations of cells. The DEABM reproduced cellular population dynamics seen during the menstrual cycle and pregnancy, and demonstrated the oncogenic effect of known genetic factors associated with breast cancer, namely TP53 and Myc, in simulations spanning ∼40 years of simulated time. Simulations comparing normal to BRCA1-mutant breast tissue demonstrated rates of invasive cancer development similar to published epidemiologic data with respect to both cumulative incidence over time and estrogen-receptor status. Investigation of the modeling of ERα-positive (ER+) tumorigenesis led to a novel hypothesis implicating the transcription factor and tumor suppressor RUNX3. These data suggest that the DEABM can serve as a potentially valuable framework to augment the traditional investigatory workflow for future hypothesis generation and testing of the mechanisms of breast cancer oncogenesis.
Associative Texture Is Lost In Translation

We present a suggestive finding regarding the loss of associative texture in the process of machine translation, using comparisons between (a) original and backtranslated texts, (b) reference and system translations, and (c) better and worse MT systems. We represent the amount of association in a text using word association profile ‐ a distribution of pointwise mutual information between all pairs of content word types in a text. We use the average of the distribution, which we term lexical tightness, as a single measure of the amount of association in a text. We show that the lexical tightness of humancomposed texts is higher than that of the machine translated materials; human references are tighter than machine translations, and better MT systems produce lexically tighter translations. While the phenomenon of the loss of associative texture has been theoretically predicted by translation scholars, we present a measure capable of quantifying the extent of this phenomenon.
Streptococcus and rheumatic fever

Purpose of reviewTo give an overview of the current hypotheses of the pathogenesis of rheumatic fever and group A streptococcal autoimmune sequelae of the heart valve and brain. Recent findingsHuman monoclonal antibodies (mAbs) derived from rheumatic heart disease have provided evidence for crossreactive autoantibodies that target the dominant group A streptococcal epitope of the group A carbohydrate, N-acetyl-beta-D-glucosamine (GlcNAc), and heart valve endothelium, laminin and laminar basement membrane. T cells in peripheral blood and in rheumatic heart valves revealed the presence of T cells crossreactive with streptococcal M protein and cardiac myosin. For initiation of disease, evidence suggests a two-hit hypothesis for antibody attack on the valve endothelium with subsequent extravasation of T cells through activated endothelium into the valve to form granulomatous lesions and Aschoff bodies. Autoantibodies against the group A streptococcal carbohydrate epitope GlcNAc and cardiac myosin and its peptides appear during progression of rheumatic heart disease. However, autoantibodies against collagen that are not crossreactive may form because of the release of collagen from damaged valve or to responses to collagen bound in vitro by certain serotypes of streptococci. In Sydenham chorea, human mAbs derived from disease target the group A carbohydrate epitope GlcNAc and gangliosides and dopamine receptors found on the surface of neuronal cells in the brain. Human mAbs and autoantibodies in Sydenham chorea were found to signal neuronal cells and activate calcium calmodulin-dependent protein kinase II (CaMKII) in neuronal cells and recognize the intracellular protein biomarker tubulin. SummaryTo summarize, pathogenic mechanisms of crossreactive autoantibodies which target the valve in rheumatic heart disease and the neuronal cell in Sydenham chorea share a common streptococcal epitope GlcNAc and target intracellular biomarkers of disease including cardiac myosin in the myocardium and tubulin, a protein abundant in the brain. However, intracellular antigens are not believed to be the basis for disease. The theme of molecular mimicry in streptococcal autoimmune sequelae is the recognition of targeted intracellular biomarker antigens such as cardiac myosin and brain tubulin, while targeting extracellular membrane antigens such as laminin on the valve surface endothelium or lysoganglioside and dopamine receptors in the brain. Antibody binding to these cell surface antigens may lead to valve damage in rheumatic heart disease or neuropsychiatric behaviors and involuntary movements in Sydenham chorea.
House prices , monetary policy and regional heterogeneity ∗

The effectiveness of monetary policy in affecting house prices depend both on the nature of the shock; expansionary versus contractionary, and on local housing market characteristics. In particular, our results suggest that monetary policy is more effective when it is expansionary and in markets with low housing supply elasticities. While expansionary and contractionary shocks have similar impacts on house prices in markets with an elastic housing supply, the effect of expansionary shocks are markedly larger than the impact of contractionary shocks in supply inelastic areas. These conclusions are drawn based on an empirical examination of the effects of exogenous monetary policy shocks on house prices using local projection methods on a panel of the 100 largest metro areas in the US over the period 1980Q1–2008Q4.