Miracle-dz/UniFAR-FTUs huggingface dataset:
Approaching complete peroxisome characterization by gas‐phase fractionation

We examined the utility of gas‐phase fractionation (GPF) in the m/z dimension to increase proteome coverage and reproducibility of peptide ion selection by direct microliquid chromatography/electrospray ionization‐tandem mass spectrometry (νLC/ESI‐MS/MS) analysis of the peptides produced by proteolytic digestion of unfractionated proteins from a yeast whole‐cell lysate and in a peroxisomal membrane protein fraction derived from isolated yeast peroxisomes. We also investigated GPF in the relative ion intensity dimension and propose denoting the two types of GPF as GPFm/z and GPFRI. Comparison of results of direct νLC/ESI‐MS/MS analysis of the unfractionated mixture of peptides from proteolysis of a yeast whole cell lysate by DD ion selection from 400–1800 m/z in triplicate and GPFm/z from 400–800, 800–1200 and 1200–1800 produced the following results: (i) 1.3× more proteins were identified by GPFm/z for an equal amount of effort (i.e., 3 νLC/ESI‐MS/MS) and (ii) proteins identified by GPFm/z had a lower average codon bias value. Use of GPFRI identified more proteins per m/z unit scanned than GPFm/z or triplicate analysis over a wide m/z range. After tryptic digestion of all the proteins from a discontinuous Nycodenz gradient fraction known to be enriched with yeast peroxisomal membrane proteins we detected 93% (38/41) of known peroxisomal proteins using GPFm/z, but only 73% using a standard wide m/z range survey scan.
Chronic ethanol treatment and withdrawal alter ACPD-evoked calcium signals in developing Purkinje neurons.

BACKGROUND Alcohol exposure during human fetal development can result in fetal alcohol syndrome, a condition characterized by central nervous system dysfunction. Detailed studies in animal models of fetal alcohol syndrome show that the cerebellar region is particularly sensitive to alcohol exposure during early development; however, the cellular mechanisms underlying the alcohol sensitivity of the immature cerebellum are poorly understood. METHODS Primary neuronal cultures of cerebellar cells were prepared from embryonic day 20 rat pups. Cultures were exposed to ethanol (33 mM; 150 mg/100 ml) during the main period of morphological development of the Purkinje neurons, from 6 to 17 days in vitro. After the ethanol treatment, the response of Purkinje neurons to the selective metabotropic glutamate receptor (mGluR) agonist (1S,3R)-1-aminocyclopentane-1,3-dicarboxylic acid (ACPD; 300 microM) was examined in parallel fura-2 Ca2+ imaging and current-clamp experiments. In an additional set of experiments, ethanol-treated cultures were allowed to withdraw from ethanol overnight before recordings were performed. RESULTS In Ca2+ imaging studies, the mean peak amplitude of ACPD-evoked Ca2+ signals was depressed in the dendritic region of chronic ethanol-treated Purkinje neurons compared with control neurons (p < 0.05, unpaired t test), whereas there was no apparent difference in the somatic region. In contrast, peak ACPD-evoked Ca2+ signals were enhanced in both the somatic and dendritic regions of withdrawn Purkinje neurons compared with control neurons. Parallel current-clamp studies showed no consistent effect of chronic ethanol treatment or ethanol withdrawal on the membrane response to ACPD. CONCLUSIONS These results show that prolonged ethanol exposure and early withdrawal lead to alterations in mGluR-evoked Ca2+ signaling in cerebellar Purkinje neurons. Metabotropic GluRs in the Purkinje neuron play important roles in cerebellar development and function, suggesting that alterations of mGluR signaling pathways by ethanol may play a key role in the actions of ethanol on the developing cerebellum.
Neurotrophic Activity of Neudesin, a Novel Extracellular Heme-binding Protein, Is Dependent on the Binding of Heme to Its Cytochrome b5-like Heme/Steroid-binding Domain*

Neudesin is a secreted protein with neurotrophic activity in neurons and undifferentiated neural cells. We report here that neudesin is an extracellular heme-binding protein and that its neurotrophic activity is dependent on the binding of heme to its cytochrome b5-like heme/steroid-binding domain. At first, we found that at least a portion of the purified recombinant neudesin appeared to bind hemin because the purified neudesin solution was tinged with green and had a sharp absorbance peak at 402 nm. The addition of exogenous hemin extensively increased the amount of hemin-bound neudesin. In contrast, neudesinΔHBD, a mutant lacking the heme-binding domain, could not bind hemin. The neurotrophic activity of the recombinant neudesin that bound exogenous hemin (neudesin-hemin) was significantly greater than that of the recombinant neudesin in either primary cultured neurons or Neuro2a cells, suggesting that the activity of neudesin depends on hemin. The neurotrophic activity of neudesin was enhanced by the binding of Fe(III)-protoporphyrin IX, but neither Fe(II)-protoporphyrin IX nor protoporphyrin IX alone. The inhibition of endogenous neudesin by RNA interference significantly decreased cell survival in Neuro2a cells. This indicates that endogenous neudesin possibly contains hemin. The experiment with anti-neudesin antibody suggested that the endogenous neudesin detected in the culture medium of Neuro2a cells was associated with hemin because it was not retained on a heme-affinity column at all. Neudesin is the first extracellular heme-binding protein that shows signal transducing activity by itself. The present findings may shed new light on the function of extracellular heme-binding proteins.
Medicinal plants with anti-inflammatory activity

Inflammation is part of the body's immune response. There can be four primary indicators of inflammation: pain, redness, heat or warmness and swelling. Plants have the ability to synthesize a wide verity of phytochemical compounds as secondary metabolites which shows anti-inflammatory activity. In the present review an attempt has been made to investigate the anti-inflammatory activity of some medicinal plants.
Asexuality: What It Is and Why It Matters

In this review article, human asexuality, a relatively understudied phenomenon, is discussed. Specifically, definitions and conceptualizations of asexuality (e.g., is it a unique category of sexual orientation? ), biological and historical contexts, identity issues, discrimination against asexual people relative to other minorities, origins, and variations, including gender differences, are reviewed. Whether asexuality should be construed as a disorder is also discussed. The study of asexuality allows for a better understanding of an underrecognized sexual minority but also affords a unique opportunity to examine and better understand human sexuality.
Thermoregulation during exercise in severely burned children

Introduction: Severe burns result in skeletal muscle catabolism and weakness, which is worsened by prolonged physical inactivity. Exercise would be an ideal tool in the rehabilitation of burned children. However, it has been postulated that burned children may have an excessive rise in body temperature during exercise compared to non-burned children, partly due to the reduced area available for heat dissipation, thereby questioning the safety of exercise in burned children. Methods: Children (n = 15) with >40% total body surface area (TBSA) burns and non-burned children (n = 13) successfully completed this study. All subjects completed 20 minutes of treadmill exercise at ∼75% of their peak aerobic power. Tympanic temperature (Ttym), burned and unburned skin temperature were recorded pre-exercise, every 2 minutes during exercise and during recovery. Results: Within burned children, significant differences between the temperature of unburned skin and burned skin, during later stages of sub-maximal exercise (minutes 12–20) were present. However, there were no significant differences between burned and non-burned children in Ttym or unburned skin temperature indicating that severely burned children do not demonstrate an impaired thermoregulatory response to 20 minutes of sub-maximal exercise at room temperatures. Conclusion: It is concluded that exercise at moderate intensities conducted at room temperature is safe in burned children with <75% TBSA burns.
Muscle hypertrophy following 5-week resistance training using a non-gravity-dependent exercise system.

AIM The efficacy of a mechanical, gravity-independent resistance exercise (RE) system to induce strength gains and muscle hypertrophy was validated. Designed for space crew in orbit, this technique offers resistance during coupled concentric and eccentric actions by utilizing the inertia of a rotating flywheel(s), set in motion by the trainee. METHODS Ten middle-aged (30-53 years) men and women performed four sets of seven maximal, unilateral (left limb) knee extensions two or three times weekly for 5 weeks. Knee extensor force and electromyographic (EMG) activity of the three superficial quadriceps muscles were measured before and after this intervention. In addition, with the use of magnetic resonance imaging (MRI), volume of individual knee extensor and ankle plantar flexor muscles was assessed. RESULTS Over the 12 training sessions, the average concentric (CON) and eccentric (ECC) force generated during exercise increased by 11% (P < 0.05). Likewise, maximal isometric strength (maximal voluntary contraction, MVC) at 90 and 120 degrees knee angle increased by (P < 0.05) 11 and 12% respectively, after training. Neither individual quadriceps muscle showed a change (P > 0.05) in maximal integrated EMG (iEMG) activity. Quadriceps muscle volume increased by 6.1% (P < 0.05). Although the magnitude of response varied, all individual quadriceps muscles showed increased (P < 0.05) volume after training. As expected, ankle plantar flexor volume of the trained limb was unchanged (P > 0.05). Likewise, MVC, CON and ECC force, iEMG and knee extensor and plantar flexor muscle volume were unaltered (P > 0.05) in the right, non-trained limb. CONCLUSION The results of this study show that the present RE regimen produces marked muscle hypertrophy and important increases in maximal voluntary strength and appears equally effective as RE paradigms using gravity-dependent weights, in this regard.
Comparison of symptom response following advice for a diet low in fermentable carbohydrates (FODMAPs) versus standard dietary advice in patients with irritable bowel syndrome.

BACKGROUND Emerging evidence indicates that the consumption of fermentable oligosaccharides, disaccharides, monosaccharides and polyols (FODMAPs) may result in symptoms in some patients with irritable bowel syndrome (IBS). The present study aimed to determine whether a low FODMAP diet is effective for symptom control in patients with IBS and to compare its effects with those of standard dietary advice based on the UK National Institute for Health and Clinical Excellence (NICE) guidelines. METHODS Consecutive patients with IBS who attended a follow-up dietetic outpatient visit for dietary management of their symptoms were included. Questionnaires were completed for patients who received standard (n = 39) or low FODMAP dietary advice (n = 43). Data were recorded on symptom change and comparisons were made between groups. RESULTS In total, more patients in the low FODMAP group reported satisfaction with their symptom response (76%) compared to the standard group (54%, P = 0.038). Composite symptom score data showed better overall symptom response in the low FODMAP group (86%) compared to the standard group (49%, P < 0.001). Significantly more patients in the low FODMAP group compared to the standard group reported improvements in bloating (low FODMAP 82% versus standard 49%, P = 0.002), abdominal pain (low FODMAP 85% versus standard 61%, P = 0.023) and flatulence (low FODMAP 87% versus standard 50%, P = 0.001). CONCLUSIONS A low FODMAP diet appears to be more effective than standard dietary advice for symptom control in IBS.
Objective Assessment of Covert Antisocial Behavior: Predictive Validity and Ethical Considerations

Although less observable than the overt actions of fighting and assault, covert antisocial behaviors such as stealing and property destruction comprise an important subclass of externalizing behavior patterns, displaying considerable predictive power toward delinquency in adolescence. I discuss a laboratory paradigm for objective observation of such behaviors in children that has shown impressive concurrent and predictive validity among samples of boys with and without attention deficit hyperactivity disorder. Addressed herein are crucial questions regarding the ethics of tempting children to steal objects and small amounts of money and to deface property as well as the types of informed consent and debriefing procedures utilized in research with this paradigm. Weighing ethical considerations alongside the ability to predict delinquent behavior presents provocative issues for those interested in understanding the development of antisocial behavior.
Spirituality, Happiness, and Psychological Well-being in 13- to 15-year olds: A Cross-country Longitudinal RCT Study

Based on a study of 5339 adolescents from 60 schools across 15 countries, this paper reports on the effect of spirituality on their happiness and psychological well-being. A customized spiritual program was administered and post-treatment outcome variable scores of the experimental group were higher. Adolescents from relatively affluent nations, boys, Christians, and those who self-practiced scored higher post-test. This makes a case for nominating spirituality as an important developmental variable for 13- to 15-year olds.
Antidepressants and Incident Hypertension in Primary Care Patients

Objective: Many ADMs can alter blood pressure (BP), but the research on the effect of antidepressant medication (ADMs) on incident hypertension is mixed. We investigated whether the use of ADMs was associated with the subsequent development of hypertension. Methods: A retrospective cohort study was conducted using electronic medical record data from 6224 patients with primary care visits from 2008 to 2015. Prescription orders were used to identify ADM use, and hypertension was defined by medical record diagnosis. Using package insert warnings, a 3-level ADM exposure variable was created: ADMs that increase BP (ADM BP+), ADMs that do not increase BP, and no ADM. Unadjusted and adjusted Cox proportional hazard models were computed to estimate the association between the ADM exposure and incident hypertension. Results: Unadjusted results revealed that ADM BP+ use compared with the no ADM group was significantly associated with incident hypertension (hazard ratio, 1.30; 95% confidence interval, 1.08–1.57). After adjusting for covariates, ADM BP+ use was no longer significantly associated with incident hypertension (hazard ratio, 1.20; 95% confidence interval, 0.97–1.49). Conclusions: Commonly used ADMs were not associated with incident hypertension after controlling for other factors associated with ADM use and hypertension. Research on potential dose and duration effects is warranted.
Depression, marijuana use and early‐onset marijuana use conferred unique effects on neural connectivity and cognition

Marijuana (MJ) use is common. Research shows risks for psychiatric illnesses, including major depressive disorder (MDD) and cognitive deficits with MJ use, particularly early‐onset use. We investigated cognitive function, functional connectivity, and genetic risk with MDD alone and combined with MJ use, and differences between early‐vs. late‐onset/non‐MJ use in youth.
Effect Analysis of Coding Convention Violations on Readability of Post-Delivered Code

Adherence to coding conventions during the code production stage of software development is essential. Benefits include enabling programmers to quickly understand the context of shared code, communicate with one another in a consistent manner, and easily maintain the source code at low costs. In reality, however, programmers tend to doubt or ignore the degree to which the quality of their code is affected by adherence to these guidelines. This paper addresses research questions such as “Do violations of coding conventions affect the readability of the produced code? ”, “What kinds of coding violations reduce code readability? ”, and “How much do variable factors such as developer experience, project size, team size, and project maturity influence coding violations? ” To respond to these research questions, we explored 210 open-source Java projects with 117 coding conventions from the Sun standard checklist. We believe our findings and the analysis approach used in the paper will encourage programmers and QA managers to develop their own customized and effective coding style guidelines. key words: coding conventions, coding style standard, code readability, software quality, empirical study.
Coeliac disease: more than villous atrophy.

A continuing flow of new scientific developments concerning coeliac disease in the last decade asks for the formulation of a new concept of pathophysiology and clinical approach of the coeliac condition. Immunogenetic studies have shown a correlation of the disease to the HLA region on the short arm of chromosome 6. Immunological research has led to the concept of a T-cell driven immunologic response of the small intestine, with the identification of highly sensitive and specific antibodies, and in addition the understanding of the histopathology of coeliac disease has changed dramatically, initiated by the proposition of a spectrum of gluten sensitive enteropathy by Marsh in 1992. Clinical studies report a significant change in patient characteristics and epidemiology. The incidence of the disease has shifted to a majority of adult coeliacs and the disease may present with less severe symptoms of malabsorption while screening studies suggest an overall prevalence of up to 1 in 200-300. In the present paper (an update on histopathology) we specifically describe the work of our group in Arnhem, concerning the identification and validation of the spectrum of intestinal histopathology in gluten sensitive enteropathy, i.e. lymphocytic enteritis (Marsh I lesion), lymphocytic enteritis with crypthyperplasia (Marsh II lesion), and villous atrophy, subdivided in partial villous atrophy (Marsh IIIA), subtotal villous atrophy (Marsh IIIB) and total villous atrophy (Marsh IIIC). Special attention is given to a subgroup of "refractory coeliacs", including the identification of (pre-) malignant aberrant T-cells in the intestinal mucosa of these patients. The new data on immunogenetics, epidemiology, histo-pathology and patient characteristics point to a significant change of views on coeliac disease.
Social Capital and Public Financial Performance: Lessons from Florida

ABSTRACT This article investigates the role of social capital in public financial performance in the United States—a topic that has not been adequately examined in the public administration literature. Research in this area will provide insight into how the public sector can be managed more effectively, efficiently, and innovatively. Moreover, this research is timely, given the context of financial and economic recession that has left local governments in the United States with persistent and long-term fiscal challenges. Using county-level panel data from the state of Florida over a seven-year period, the article finds strong support for the hypothesis that community social capital is positively and significantly associated with public financial performance. Findings reinforce the need for deeper understanding of social capital, as well as other community-level factors that are external to public sector agencies, in investigations of the different dimensions of public sector performance. The article includes policy recommendations on how to recognize and build community social capital due to its instrumental value in public management.
Contribution to the Integrated Control of Biped Locomotion Mechanisms

This work is concerned with the integrated dynamic control of humanoid locomotion mechanisms based on the spatial dynamic model of the humanoid mechanism, a servo system model, and an environment model. The control scheme was synthesized using the centralized model of the system and the hierarchical principle, with tactical and executive control levels. The proposed structure of the dynamic controller involves four feedback loops: position-velocity feedback at the robotic mechanism joints, dynamic reaction feedback at Zero-Moment Point, impact force feedback at the instant when the foot strikes the ground, and the load feedback of the mechanism joints. Simulation experiments are carried out for a number of characteristic examples. The numerical results obtained, along with theoretical study, serve as the basis for a critical evaluation of the performance of the devised controller.
Bisphenol A alters the development of the rhesus monkey mammary gland

The xenoestrogen bisphenol A (BPA) used in the manufacturing of various plastics and resins for food packaging and consumer products has been shown to produce numerous endocrine and developmental effects in rodents. Exposure to low doses of BPA during fetal mammary gland development resulted in significant alterations in the gland’s morphology that varied from subtle ones observed during the exposure period to precancerous and cancerous lesions manifested in adulthood. This study assessed the effects of BPA on fetal mammary gland development in nonhuman primates. Pregnant rhesus monkeys were fed 400 μg of BPA per kg of body weight daily from gestational day 100 to term, which resulted in 0.68 ± 0.312 ng of unconjugated BPA per mL of maternal serum, a level comparable to that found in humans. At birth, the mammary glands of female offspring were removed for morphological analysis. Morphological parameters similar to those shown to be affected in rodents exposed prenatally to BPA were measured in whole-mounted glands; estrogen receptor (ER) α and β expression were assessed in paraffin sections. Student's t tests for equality of means were used to assess differences between exposed and unexposed groups. The density of mammary buds was significantly increased in BPA-exposed monkeys, and the overall development of their mammary gland was more advanced compared with unexposed monkeys. No significant differences were observed in ER expression. Altogether, gestational exposure to the estrogen-mimic BPA altered the developing mammary glands of female nonhuman primates in a comparable manner to that observed in rodents.
Sum-rate based opportunistic relay selection with channel estimation error for a dual-hop multiple half/full-duplex bi-directional wireless relaying networks

This paper investigates the channel estimation error effects on the opportunistic relay selection strategy. The opportunistic relay selection strategy is based on selecting the maximum sum-rate of half/full-duplex relay terminal among N. The investigation considers a dual-hop multiple half/full-duplex bi-directional wireless relaying networks in the system model. According to Monte-Carlo simulation results, sum-rate based relay selection strategy achieves cooperative diversity in high signal-to-noise regimes both for half/full-duplex cases. However, for the full-duplex based case, if the loop interference variances are relatively high, the achievable cooperative diversity turns out to be 0 from N while also causes system coding gain losses. The CEE causes system coding gain losses in low signal-to-noise ratio regimes. However, in high signal-to-noise ratio regimes, the CEE effects turn out to be at negligible levels.