Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural analysis of the RSC chromatin-remodeling complex

Electron microscopy of the RSC chromatin-remodeling complex reveals a ring of protein densities around a central cavity. The size and shape of the cavity correspond closely to those of a nucleosome. Results of nuclease protection analysis are consistent with nucleosome binding in the cavity. Such binding could explain the ability of RSC to expose nucleosomal DNA in the presence of ATP without loss of associated histones.
Low‐rate dynamic contact angles on polystyrene and the determination of solid surface tensions

Low-rate dynamic contact angles of 13 liquids on a polystyrene polymer are measured by an automated axisymmetric drop shape analysis - profile (ADSA-P). It is found that 7 liquids yielded non-constant contact angles, and/or dissolved the polymer on contact. From the experimental contact angles of the other 6 liquids, it is found that the liquid-vapor surface tension times cosine of the contact angle changes smoothly with the liquid-vapor surface tension, i.e. γ lυ cosθ depends only on γ lυ for a given solid surface (or solid surface tension). This contact angle pattern is in harmony with those from other inert and non-inert (polar and non-polar) surfaces (7-13, 24-26). The solid-vapor surface tension calculated from the equation-of-state approach for solid-liquid interfacial tensions (33) is found to be 29.8 mJ/m 2 . with a 95% confidence limit of ±0.5 mJ/m 2 from the experimental contact angles of 6 liquids.
Misdiagnosing delirium as depression in medically ill elderly patients.

BACKGROUND Delirium, a common and often overlooked syndrome in acutely ill elderly patients, may present with signs and symptoms of depression. OBJECTIVE To determine (1) how often health care providers mistake delirium for a depressive disorder in older hospitalized patients referred to a psychiatric consultation service for depressive symptoms and (2) which signs and symptoms of depression and delirium characterize these patients. SUBJECTS Patients older than 60 years, admitted to a Veterans Affairs teaching hospital, and consecutively referred to a psychiatric consultation service for evaluation and treatment of a depressive disorder. METHODS The diagnosis of delirium was based on two independent assessments: (1) a clinical interview by a member of the psychiatric consultation service and (2) a structured bedside evaluation performed by one of the investigators, who was not a member of the psychiatric consultation service. The investigator administered the Confusion Assessment Method Instrument, Mini-Mental State Examination, digit span forward, and months of year backward. The investigator also administered the Diagnostic Interview Schedule items for depression to elicit depressive symptoms. RESULTS Twenty-eight (41.8%) of the 67 subjects referred for evaluation or treatment of a depressive disorder were found to be delirious. Compared with nondelirious subjects, the delirious subjects were older and more impaired in activities of daily living. The delirious subjects often endorsed depressive symptoms, such as low mood (60%), worthlessness (68%), and frequent thoughts of death (52%). The referring health care provider had considered delirium in the differential diagnosis of the mood disturbance in only three subjects. CONCLUSION Health care providers should consider the diagnosis of delirium in hospitalized elderly patients who appear to be depressed.
Effects of Calcium Ion, Calpains, and Calcium Channel Blockers on Retinitis Pigmentosa

Recent advances in molecular genetic studies have revealed many of the causative genes of retinitis pigmentosa (RP). These achievements have provided clues to the mechanisms of photoreceptor degeneration in RP. Apoptosis is known to be a final common pathway in RP and, therefore, a possible therapeutic target for photoreceptor rescue. However, apoptosis is not a single molecular cascade, but consists of many different reactions such as caspase-dependent and caspase-independent pathways commonly leading to DNA fractionation and cell death. The intracellular concentration of calcium ions is also known to increase in apoptosis. These findings suggest that calpains, one of the calcium-dependent proteinases, play some roles in the process of photoreceptor apoptosis and that calcium channel antagonists may potentially inhibit photoreceptor apoptosis. Herein, the effects of calpains and calcium channel antagonists on photoreceptor degeneration are reviewed.
What are the breast support choices of Australian women during physical activity?

Objectives: This study aimed to quantify the breast support wearing and purchasing habits of young women and to assess factors that affect their sports bra usage during physical activity. Design: Study results were obtained from a self-administered mail survey, which was posted to participants after gaining their verbal consent via random telephone recruitment. Participants: 413 women aged 20 to 35 years were recruited from New South Wales, Australia. Results: From the returned (65%) surveys only 41% of respondents currently wore an encapsulating sports bra during physical activity, primarily due to a lack of awareness of the importance of good breast support during physical activity. Bra size was a predictor of sports bra usage, whereby participants with large breasts were more than twice as likely to wear a sports bra as their smaller-breasted counterparts. Conclusions: It was concluded that, although encapsulating sports bras have been shown to effectively reduce breast motion and associated exercise-induced breast discomfort, these bras were not the breast support option most commonly chosen by young women during physical activity. It is recommended that all women, irrespective of breast size, be educated on the importance of wearing a well-fitted and supportive bra during physical activity to decrease excessive strain on breast tissue structures and related breast discomfort.
Efficacy and Safety of Tadalafil Monotherapy for Lower Urinary Tract Symptoms Secondary to Benign Prostatic Hyperplasia: A Meta-Analysis

Objective: To evaluate the efficacy and safety of tadalafil monotherapy for lower urinary tract symptoms secondary to benign prostatic hyperplasia (LUTS/BPH). Methods: A comprehensive search was done to identify randomized controlled trials comparing the efficacy and safety of tadalafil for LUTS/BPH with placebos. Meta-analytical techniques were applied to evaluate the differences in the study results. Results: Eight studies were identified and analyzed. Compared with placebo, tadalafil was associated with significant improvements in the International Prostate Symptom Score (IPSS) (mean difference = -2.19, p < 0.00001) and the International Index of Erectile Function (IIEF) score (mean difference = +4.66, p < 0.00001), despite the concomitant presence of erectile dysfunction. Significant differences were also observed in the IPSS irritative and obstructive subscores, IPSS quality of life index and BPH impact index. After pooling four doses (2.5, 5, 10 and 20 mg), tadalafil failed to produce a significant outcome in maximal urinary flow rate (Qmax) (mean difference = +0.26 ml/s, p = 0.14), but 5 mg of tadalafil significantly improved Qmax (mean difference = +0.63 ml/s, p = 0.04). No significant difference was detected in the incidence of serious adverse events (risk ratio = 1.00, p = 1.00) after tadalafil treatment. Conclusions: Tadalafil showed good efficacy and safety for improving LUTS and erectile dysfunction in men with BPH, and 5 mg of tadalafil significantly improved Qmax.
Asymptotic Model Selection for Naive Bayesian Networks

We develop a closed form asymptotic formula to compute the marginal likelihood of data given a naive Bayesian network model with two hidden states and binary features. This formula deviates from the standard BIC score. Our work provides a concrete example that the BIC score is generally not valid for statistical models that belong to a stratified exponential family. This stands in contrast to linear and curved exponential families, where the BIC score has been proven to provide a correct approximation for the marginal likelihood.
Influence of Turning and Environmental Contamination on the Dynamics of Populations of Lactic Acid and Acetic Acid Bacteria Involved in Spontaneous Cocoa Bean Heap Fermentation in Ghana

ABSTRACT The influence of turning and environmental contamination on six spontaneous cocoa bean heap fermentations performed in Ghana was studied through a multiphasic approach, encompassing both microbiological (culture-dependent and culture-independent techniques) and metabolite target analyses. A sensory analysis of chocolate made from the fermented, dried beans was performed as well. Only four clusters were found among the isolates of acetic acid bacteria (AAB) identified: Acetobacter pasteurianus, Acetobacter ghanensis, Acetobacter senegalensis, and a potential new Acetobacter lovaniensis-like species. Two main clusters were identified among the lactic acid bacteria (LAB) isolated, namely, Lactobacillus plantarum and Lactobacillus fermentum. No differences in biodiversity of LAB and AAB were seen for fermentations carried out at the farm and factory sites, indicating the cocoa pod surfaces and not the general environment as the main inoculum for spontaneous cocoa bean heap fermentation. Turning of the heaps enhanced aeration and increased the relative population size of AAB and the production of acetic acid. This in turn gave a more sour taste to chocolate made from these beans. Bitterness was reduced through losses of polyphenols and alkaloids upon fermentation and cocoa bean processing.
Spectroscopic Discovery of the Supernova 2003dh Associated with GRB 030329

We present early observations of the afterglow of GRB 030329 and the spectroscopic discovery of its associated supernova SN 2003dh. We obtained spectra of the afterglow of GRB 030329 each night from March 30.12 (0.6 days after the burst) to April 8.13 (UT) (9.6 days after the burst). The spectra cover a wavelength range of 350-850 nm. The early spectra consist of a power-law continuum (Fν ∝ ν-0.9) with narrow emission lines originating from H II regions in the host galaxy, indicating a low redshift of z = 0.1687. However, our spectra taken after 2003 April 5 show broad peaks in flux characteristic of a supernova. Correcting for the afterglow emission, we find that the spectrum of the supernova is remarkably similar to the Type Ic "hypernova" SN 1998bw. While the presence of supernovae has been inferred from the light curves and colors of gamma-ray burst afterglows in the past, this is the first direct, spectroscopic confirmation that a subset of classical gamma-ray bursts originate from supernovae.
Statistical analysis of area and volume effects on breakdown voltage in liquid nitrogen using Weibull distribution

We measured breakdown voltage in liquid nitrogen (LN/sub 2/) with sphere to plane electrode and coaxial cylindrical electrode configurations, and discussed them with stressed electrode area (SEA) and/or stressed liquid volume (SLV). We also carried out statistical analysis of the results using Weibull distribution to examine the area and volume effects on breakdown voltage in LN/sub 2/. The dc and ac breakdown strength in LN/sub 2/ decreased to 1/4/spl sim/1/5 with increasing the SSEA (statistical stressed electrode area) and SSLV (statistical stressed liquid volume). These results permitted us to confirm that the area and volume effects definitely determined the dc and ac breakdown strength in LN/sub 2/. Next, Weibull shape parameter m for sphere to plane and coaxial cylindrical electrodes were estimated to be about 6/spl sim/8 and 11/spl sim/13, respectively. The results of the Weibull statistics were compared with the conventional concept of the SEA or SLV. Consequently, SSEA or SSLV was found to be nearly equal to 80/spl sim/85% of SEA or SLV. This result indicates that at least 80/spl sim/85% of the maximum electric field strength should be considered for the insulation design in LN/sub 2/ when the area and volume effects are involved. <<ETX>>
Comparative proteome analysis of Helicobacter pylori

Helicobacter pylori, the causative agent of gastritis, ulcer and stomach carcinoma, infects approximately half of the worlds population. After sequencing the complete genome of two strains, 26695 and J99, we have approached the demanding task of investigating the functional part of the genetic information containing macromolecules, the proteome. The proteins of three strains of H. pylori, 26695 and J99, and a prominent strain used in animal models SS1, were separated by a high‐resolution two‐dimensional electrophoresis technique with a resolution power of 5000 protein spots. Up to 1800 protein species were separated from H. pylori which had been cultivated for 5 days on agar plates. Using matrix‐assisted laser desorption/ionization mass spectrometry (MALDI‐MS) peptide mass fingerprinting we have identified 152 proteins, including nine known virulence factors and 28 antigens. The three strains investigated had only a few protein spots in common. We observe that proteins with an amino acid exchange resulting in a net change of only one charge are shifted in the two‐dimensional electrophoresis (2‐DE) pattern. The expression of 27 predicted conserved hypothetical open reading frames (ORFs) and six unknown ORFs were confirmed. The growth conditions of the bacteria were shown to have an effect on the presence of certain proteins. A preliminary immunoblotting study using human sera revealed that this approach is ideal for identifying proteins of diagnostic or therapeutic value. H. pylori 2‐DE patterns with their identified protein species were added to the dynamic 2D‐PAGE database (http://www.mpiib‐berlin.mpg.de/2D‐PAGE/). This basic knowledge of the proteome in the public domain will be an effective instrument for the identification of new virulence or pathogenic factors, and antigens of potentially diagnostic or curative value against H. pylori.
The Influence of Hyperbaric Oxygen Treatment on the Healing of Experimental Defects Filled with Different Bone Graft Substitutes

To assess potential effects of hyperbaric oxygen (HBOT) on artificial bone grafts, β - Tricalcium phosphate (β-TCP) and calcium phosphate coated bovine bone (CPCBB) substitutes were applied to standard bone defects in rat tibiae. The control defects were left empty. Half of the animals received 60 minutes of 2.4 atmosphere absolute (ATA) of HBOT. Rats were sacrificed at one, two and four weeks. Bone healing was assessed histologically and histomorphometrically using light microscopy. The periosteum over the bone defects was examined ultrastructurally. Cardiac blood was collected to determine the serum osteocalcin levels. The HBOT increased new bone formation in the unfilled controls and β-TCP groups and significantly decreased cartilage matrix and fibrous tissue formations in all groups. Active osteoblasts and highly organized collagen fibrils were prominent in the periosteum of β-TCP and control groups. Serum osteocalcin levels also increased with HBOT. The healing of defects filled with CPCBB was similar to the controls and it did not respond to HBOT. These findings suggested that the HBOT had beneficial effects on the healing of unfilled bone defects and those filled with β-TCP bone substitute but not with CPCBB, indicating a material-specific influence pattern of HBOT.
Identification of Nrf 2-regulated Genes Induced by the Chemopreventive Agent Sulforaphane by Oligonucleotide Microarray 1

Electrophiles formed during metabolic activation of chemical carcinogens and reactive oxygen species generated from endogenous and exogenous sources play a significant role in carcinogenesis. Cancer chemoprevention by induction of phase 2 proteins to counteract the insults of these reactive intermediates has gained considerable attention. Nuclear factor E2 p45-related factor 2 (Nrf2), a bZIP transcription factor, plays a central role in the regulation (basal and or inducible expression) of phase 2 genes by binding to the “antioxidant response element” in their promoters. Identification of novel Nrf2-regulated genes is likely to provide insight into cellular defense systems against the toxicities of electrophiles and oxidants and may define effective targets for achieving cancer chemoprevention. Sulforaphane is a promising chemopreventive agent that exerts its effect by strong induction of phase 2 enzymes via activation of Nrf2. In the present study, a transcriptional profile of small intestine of wild-type (nrf2 / ) and knock out (nrf2 / ) mice treated with vehicle or sulforaphane (9 mol/day for 1 week, p.o.) was generated using the Murine Genome U74Av2 oligonucleotide array (representing 6000 well-characterized genes and nearly 6000 expressed sequence tags). Comparative analysis of gene expression changes between different treatment groups of wild-type and nrf2-deficient mice facilitated identification of numerous genes regulated by Nrf2 including previously reported Nrf2-regulated genes such as NAD(P)H:quinone reductase (NQO1), glutathione S-transferase (GST), -glutamylcysteine synthetase (GCS), UDP-glucuronosyltransferases (UGT), epoxide hydrolase, as well as a number of new genes. Also identified were genes encoding for cellular NADPH regenerating enzymes (glucose 6-phosphate dehydrogenase, 6-phosphogluconate dehydrogenase, and malic enzyme), various xenobiotic metabolizing enzymes, antioxidants (glutathione peroxidase, glutathione reductase, ferritin, and haptaglobin), and biosynthetic enzymes of the glutathione and glucuronidation conjugation pathways. The data were validated by Northern blot analysis and enzyme assays of selected genes. This investigation expands the horizon of Nrf2-regulated genes, highlights the cross-talk between various metabolic pathways, and divulges the pivotal role played by Nrf2 in regulating cellular defenses against carcinogens and other toxins.
Supporting operator problem solving through ecological interface design

This paper describes two experiments evaluating ecological interface design (EID), a novel theoretical framework for the design of interfaces for complex human-machine systems. According to EID, to properly support operator problem solving activities, an interface should display both the physical and functional properties of the work domain in the form of a multilevel representation based on the abstraction hierarchy. To evaluate this claim, two interfaces for a thermal-hydraulic process simulation were developed, one based on a traditional format containing only physical information (P) and another based on EID which also contained information about higher-order functional variables (P+F). The findings of Experiment 1 are consistent with the claim that an interface based on an abstraction hierarchy representation can provide more support for problem solving than an interface based on physical variables alone, thereby providing some initial support for the EID framework. There was also some evidence to indicate that theoretical expertise is required to enjoy the full benefits of the P+F interface. The findings of Experiment 2 indicate that subjects who exhibited effective diagnosis performance using the P+F interface tended to start their search at a high level of abstraction and gradually work their way down to more detailed levels, as predicted. Furthermore, previous experience with the DURESS system was found to be the most reliable background variable that predicted performance. >
Health-related quality of life in adults with irritable bowel syndrome in a Mexican specialist hospital. A cross-sectional study.

BACKGROUND Evidence shows the negative impact of irritable bowel syndrome on the quality of life of patients who suffer from the condition as compared to the general population. OBJECTIVE The objective of this study was to determine the health-related quality of life in adults with irritable bowel syndrome who are receiving treatment at a specialist hospital. MATERIAL AND METHODS The study had a cross-sectional prospective design. The study included consecutive patients diagnosed with irritable bowel syndrome under the Rome III criteria and attending outpatient appointments. The SF-36 questionnaire was applied in its standard Spanish version and the results were compared with population reference scores in Mexico. Statistical analysis was performed with the Student's t test, analysis of variance and the Chi-squared test, considering a significance of 0.05%. RESULTS One hundred and fifty-four patients were included in the study, 137 (89%) women and 17 (11%) men, with an average age of 52.8 (SD 12.6). The constipation, diarrhea and mixed subtypes comprised 85 (55.2%), 27 (17.5%) and 42 (27.3%) patients, respectively. The quality of life of patients with irritable bowel syndrome vs the population reference scores in Mexico were 50 vs 79 for the physical health sub-scale and 59.1 vs 76.7 for the mental health sub-scale, respectively (p = 0.000). No significant difference was found in quality of life among the irritable bowel syndrome subtypes (p > 0.05). CONCLUSIONS Health-related quality of life is lower in patients with irritable bowel syndrome in a population in the North East of Mexico compared to the data taken from a population reference study undertaken in the same country, enabling an inference in the female population and a cautious one from the results found in the small male sample studied. There was no significant difference found in the quality of life according to the clinical subtype of irritable bowel syndrome.
Distinct Neural Correlates for Volitional Generation and Inhibition of Saccades

The antisaccade task has proven highly useful in basic and clinical neuroscience, and the neural structures involved are well documented. However, the cognitive and neural mechanisms that mediate task performance are not yet understood. An event-related fMRI study was designed to dissociate the neural correlates of two putative key functions, volitional saccade generation and inhibition of reflexive saccades, and to investigate their interaction. Nineteen healthy volunteers performed a task that required (a) to initiate saccades volitionally, either with or without a simultaneous demand to inhibit a reflexive saccade; and (b) to inhibit a reflexive saccade, either with or without a simultaneous demand to initiate a saccade volitionally. Analysis of blood oxygen level-dependent signal changes confirmed a major role of the frontal eye fields and the supplementary eye fields in volitional saccade generation. Inhibition-related activation of a specific fronto-parietal network was highly consistent with previous evidence involved in inhibitory processes. Unexpectedly, there was little evidence of specific brain activation during combined generation and inhibition demands, suggesting that the neural processing of generation and inhibition in antisaccades is independent to a large extent.
Achieving large spectral efficiency with TDD and not-so-many base-station antennas

Time-Division duplexing (TDD) allows to estimate the downlink channels for an arbitrarily large number of base station antennas by using a finite number of orthogonal pilot signals in the uplink, by exploiting channel reciprocity. Based on this observation, a recently proposed “Massive MIMO” scheme was shown to achieve unprecedented system spectral efficiency using a very simple beamforming scheme and a very large number of base station antennas per active user per cell. In this work, we consider a more sophisticated system design that partition the users' population in geographically determined “bins” and for each bin selects the best scheme in a family of network- MIMO schemes defined by the type of linear beamforming, cooperation among base stations, frequency reuse, pilot reuse and user loading factors. The spectral efficiency obtained by the proposed architecture is similar to that achieved by “Massive MIMO”, with a 10-fold reduction in the number of antennas at the base stations (roughly, from 500 to 50 antennas).