Miracle-dz/UniFAR-FTUs huggingface dataset:
The hydration of amides in helices; a comprehensive picture from molecular dynamics, IR, and NMR

We examined the hydration of amides of α3D, a simple, designed three‐helix bundle protein. Molecular dynamics calculations show that the amide carbonyls on the surface of the protein tilt away from the helical axis to interact with solvent water, resulting in a lengthening of the hydrogen bonds on this face of the helix. Water molecules are bonded to these carbonyl groups with partial occupancy (∼50%–70%), and their interaction geometries show a large variation in their hydrogen bond lengths and angles on the nsec time scale. This heterogeneity is reflected in the carbonyl stretching vibration (amide I′ band) of a group of surface Ala residues. The surface‐exposed amides are broad, and shift to lower frequency (reflecting strengthening of the hydrogen bonds) as the temperature is decreased. By contrast, the amide I′ bands of the buried 13C‐labeled Leu residues are significantly sharper and their frequencies are consistent with the formation of strong hydrogen bonds, independent of temperature. The rates of hydrogen‐deuterium exchange and the proton NMR chemical shifts of the helical amide groups also depend on environment. The partial occupancy of the hydration sites on the surface of helices suggests that the interaction is relatively weak, on the order of thermal energy at room temperature. One unexpected feature that emerged from the dynamics calculations was that a Thr side chain subtly disrupted the helical geometry 4–7 residues N‐terminal in sequence, which was reflected in the proton chemical shifts and the rates of amide proton exchange for several amides that engage in a mixed 310/α/π‐helical conformation.
Neurosteroids: The StAR Protein in the Brain

The nervous system is a well‐known target for steroid hormones, as these hormones regulate brain functions that include neuronal survival and differentiation, myelination, neurogenesis, plasticity and repair after injury. Furthermore, the brain is also a steroidogenic tissue because it possesses the enzymes required to metabolize the common precursor, cholesterol, into steroids, named ‘neurosteroids’. The rate‐limiting step in the synthesis of steroid hormones is the access of cholesterol, accumulated in the outer mitochondrial membrane, to the first steroidogenic enzyme, P450scc (cholesterol side‐chain cleavage enzyme), located in the inner mitochondrial membrane. In the ovary and the adrenal gland, which comprise classic steroidogenic tissues, this process requires the steroidogenic acute regulatory protein (StAR) to facilitate the shuttle of cholesterol through the intermembrane space. The mechanism used by the brain to regulate the first stage of steroidogenesis remains unknown. Recently, several groups have investigated the potential presence of StAR in the nervous tissue and have concluded that StAR is widely expressed throughout the brain, although restricted to specific cell populations. New results concerning localization, regulation and possible functions of StAR in the brain are discussed.
Noisy Softplus: an activation function that enables SNNs to be trained as ANNs

We extended the work of proposed activation function, Noisy Softplus, to fit into training of layered up spiking neural networks (SNNs). Thus, any ANN employing Noisy Softplus neurons, even of deep architecture, can be trained simply by the traditional algorithm, for example Back Propagation (BP), and the trained weights can be directly used in the spiking version of the same network without any conversion. Furthermore, the training method can be generalised to other activation units, for instance Rectified Linear Units (ReLU), to train deep SNNs off-line. This research is crucial to provide an effective approach for SNN training, and to increase the classification accuracy of SNNs with biological characteristics and to close the gap between the performance of SNNs and ANNs.
Aspirin resistance in patients with impaired renal functions.

BACKGROUND Cardiovascular diseases (CVD) are the leading cause of death in patients with chronic kidney diseases (CKD). Aspirin resistance (AR) worsens prognosis in CVD. AIM The aim of this study was to detect AR prevalence in this patient group. METHODS The 203 patients (mean age 61.84 ± 11.51 years, 128 [63.1%] male) with stable coronary artery disease included in the study were grouped into four study groups according to their estimated glomerular filtration rate (eGFR) values. Multiplate test was used to determine AR. Platelet aggregation results were presented as aggregation unit (AU) × min and values over 300 AU × min were accepted as AR. RESULTS 61 (30.04%) patients in the whole study population were found to have AR. Differences were detected between AR ratios and multiplate values of the patient groups (p = 0.006 and p = 0.002). AR ratio was highest in patient group 4 (eGFR < 30 mL/min/1.73 m²) and/or on chronic haemodialysis therapy, whereas there was little difference among the other three groups. In multivariate analysis, while AR status was independently related to female sex (OR = 2.31,CI 1.14-4.65, p = 0.019) and mean platelet volume (MPV) (OR = 1.68, CI 1.21-2.33, p = 0.002), multiplate test results were independently related to MPV (b = 0.265, p < 0.0001) and eGFR (b = -0.165, p = 0.025). CONCLUSIONS The AR ratio was found to be high in severe CKD patients, especially haemodialysis patients, but not in mild and moderate CKD patients. This increased AR ratio in severe CKD patients may affect the prognosis in patients who already have an increased risk for cardiovascular complications.
Influence of electric fields and pH on biofilm structure as related to the bioelectric effect

Mixed species biofilms of Klebsiella pneumoniae, Pseudomonas fluorescens, and Pseudomonas aeruginosa were grown in a flow cell fitted with two platinum wire electrodes. The biofilm growing on the wires reached a thickness of approximately 50 microm after 3 days. When a voltage was applied with oscillating polarity, the biofilm attached to the wire expanded and contracted. The biofilm expanded by approximately 4% when the wire was cathodic but was reduced to 74% of the original thickness when the wire was anodic. The phenomenon was reproduced by alternately flushing the flow cell with media adjusted to pH 3 and pH 10 with no electric current. At pH 10 the biofilm was unaltered, but it became compacted to 69% of the original thickness at pH 3. We explained these phenomena in terms of the molecular interactions between charged acidic groups in the biofilm slime and the bacterial cell walls. Contraction of the biofilm under acidic conditions may be caused by (i) the elimination of electrostatic repulsion from neutralization of negatively charged carboxylate groups through protonation and (ii) subsequent hydrogen bonding between the carboxylic acids and oxygen atoms in the sugars. Electrostatic interactions between negatively charged groups in the biofilm and the charged wire may also be expected to cause biofilm expansion when the wire was cathodic and contraction when the wire was anodic. The consequences of the explanation of the increased susceptibility of biofilm cells to antibiotics in an electric field, the "bioelectric effect," are discussed.
Association Between Women’s Empowerment and Maternal and Child Nutrition in Kalalé District of Northern Benin

Background: Evidence on effectiveness of women’s empowerment (WE) to reduce undernutrition is limited in sub-Sahara Africa, and few studies incorporate multidimensional measures of WE. Objective: To examine whether a WE status, in sum and across leadership, decision-making, mobility, economic security, male involvement in housework, and nonfamily group domains, is associated with women and their children nutritional status in Kalalé district of northern Benin. Methods: Data were obtained from the 2014 Solar Market Garden baseline study: 767 paired reproductive-age women aged 15 to 49 years and children 6 to 59 months old. Exploratory principal component (cross-validate with confirmatory) factor analysis was first conducted to identify the structure of empowerment. Then, using a new survey-based index, regression analysis was conducted to examine associations between WE measures and maternal dietary diversity score (DDS) and body mass index (BMI), as well as their child’s DDS, height-for-age z score (HAZ), weight-for-height z score (WHZ), and weight-for-age z score (WAZ). Results: Positive associations were observed between women’s composite empowerment, leadership, maternal DDS and BMI, and female child’s DDS. However, opposite signs were found between economic security and child’s DDS. Mobility was positively associated with female children’s WHZ and male children’s HAZ and WAZ, while decision-making was correlated with male child’s WHZ and female children’s WAZ. Conclusions: Women’s empowerment can be associated with undernutrition. Efforts to improve nutrition may benefit from empowerment initiatives that promote women’s self-confidence and decision-making in Benin. However, additional qualitative and longitudinal research may enhance understanding of WE in the present area.
Percutaneous ethanol injection for treatment of cervical lymph node metastases in patients with papillary thyroid carcinoma.

OBJECTIVE The objective of this study was to evaluate the technique, efficacy, and side effects of percutaneous ethanol injection in patients with limited cervical nodal metastases from papillary thyroid carcinoma. SUBJECTS AND METHODS Fourteen patients who had undergone thyroidectomy for papillary thyroid carcinoma presented with limited nodal metastases (one to five involved nodes) in the neck between May 1993 and April 2000. All patients had received previous iodine-131 ablative therapy with a mean total dose per patient of 7,548 MBq. Ten of the patients either were considered poor surgical candidates or preferred not to have surgery, and all were unresponsive to iodine-131 therapy. Each metastatic lymph node was treated with percutaneous ethanol injection, and patients received both clinical and sonographic follow-up. RESULTS Twenty-nine metastatic lymph nodes in our 14 patients were injected. Mean sonographic follow-up was 18 months (range, from 2 months to 6 years 5 months). All treated lymph nodes decreased in volume from a mean of 492 mm(3) before percutaneous ethanol injection to a mean volume of 76 mm(3) at 1 year and 20 mm(3) at 2 years after treatment. Six nodes were re-treated 2-12 months after initial percutaneous ethanol injection because of persistent flow on color Doppler sonography (n = 4), stable size (n = 1), or increased size (n = 1). Two patients developed four new metastatic nodes during the follow-up period that were amenable to percutaneous ethanol injection. Two patients developed innumerable metastatic nodes that precluded retreatment with percutaneous ethanol injection. No major complications occurred. All patients experienced long-term local control of metastatic lymph nodes treated by percutaneous ethanol injection. In 12 of 14 patients, percutaneous ethanol injection was successful in controlling all known metastatic adenopathy. CONCLUSION Sonographically guided percutaneous ethanol injection is a valuable treatment option for patients with limited cervical nodal metastases from papillary thyroid cancer who are not amenable to further surgical or radioiodine therapy.
Federalism and Corporate Law: The Race to Protect Managers from Takeovers

This paper analyzes certain important shortcomings of state competition in corporate law. In particular, we show that, with respect to takeovers, states have incentives to produce rules that excessively protect incumbent managers. The development of state takeover law, we argue, is consistent with our theory. States have adopted antitakeover statutes that have little policy basis, and, more importantly, they have provided managers with a wider and more open-ended latitude to engage in defensive tactics than endorsed even by the commentators most favorable to such tactics. Furthermore, states have elected, even though they could have done otherwise, to impose antitakeover protections on shareholders, who did not appear to favor them, in a way that left shareholders with little choice or say. Finally, we conclude by pointing out that proponents of state competition cannot reconcile their views with the evolution of state takeover law--and should, therefore, reconsider their unqualified support of state competition.
Trajectories of depressive symptoms, dopamine D2 and D4 receptors, family socioeconomic status and social support in adolescence and young adulthood

Objectives The purpose of this study is two-fold. First, we tested the association between dopamine D2 and D4 receptors and a trajectory of depressive symptoms in adolescence and young adulthood. Second, we reestimated the association between the dopamine receptors and depression after taking into account the effects of socioeconomic disparity and child–parent ties and social support. Methods The study uses the DNA sample of approximately 2500 individuals in the National Longitudinal Study of Adolescent Health (Add Health). Each individual was measured three times in 1994, 1996, and 2002. Results This study has yielded robust associations of the DRD2 and DRD4 variants with depressive symptoms among male adolescents and young adults. The DRD2*304/178 genotype is associated with a level of depressive symptoms 0.04–0.07 points (3–5% of the mean) higher than the DRD2*178/178 genotype. Relative to the other more common DRD4 variants, the DRD4*379/379 genotype raises the level of depression by about 0.25 points (about 17% of the mean). These findings hold after adjusting for the effects of socioeconomic status (family structure, parental education, family income, mother's employment status, and whether attending public school) and child–parent ties/social support (conflict with parent(s), closeness to parent(s), parental availability, and social support). Although the gene–sex interaction is clearly present, the tests of gene-lifecourse interaction did not yield any significant results. Conclusion Our findings emphasize the importance of joint influences of genetic propensities and social environment on depressive symptoms.
MicroRNA expression profiling in children with different asthma phenotypes

An improved understanding of the molecular mechanisms in asthma through exploring the role of microRNAs may offer promise to reveal new approaches for primary prevention and identification of new therapeutic targets in childhood asthma. The primary goal of this study is to identify the microRNAs that play a role in the pathogenesis of asthma in pediatric age group. The secondary goal is to analyze these microRNAs according to the asthma phenotype, atopic status, and severity of the disease exacerbation. To our knowledge, this is the first research project in the literature which studies the relationship between microRNA expression and the severity of childhood asthma. One hundred children between 6 and 18 years old with a diagnosis of asthma, and 100 age‐matched healthy children were enrolled in this study, and the analyses of microRNA expression profiles were performed in the Medical Genetics Laboratories of Ege University between November 2009 and June 2010. The expression of 10 microRNAs were shown to be higher in patients with more severe asthma, and the expression of these microRNAs were also found to be higher in patients who present with more severe acute asthma exacerbation symptoms (P < 0.001). Also, five microRNAs were found to be expressed more than twofold in allergic patients when compared to non‐allergic participants (P <0.001). Asthma is one of the best examples of complex genetic diseases, and further studies, which will investigate the relationship between these microRNA's and their target genes, are needed to learn more about the specific roles of microRNAs in respiratory diseases. Pediatr Pulmonol. 2016;51:582–587. © 2015 Wiley Periodicals, Inc.
Sensitivity and Specificity of Three Third‐Generation Anti‐Hepatitis C Virus ELISAs

Three commercially available 3rd‐generation anti‐HCV ELISAs (Abbott, Murex and Ortho) were evaluated in various serum panels: (A) blood donor samples (n = 403) with 1st‐ or 2nd‐generation anti‐HCV ELISA (various manufacturers) positive test results; (B) non‐A, non‐B hepatitis patients (n = 212); (C) multitransfused patients (n = 253); (D) serial dilutions of HCV confirmed (RIBA and PCR) positive blood donors (n = 24), and (E) first‐time blood donors (n = 1,055). All samples of panels A, B and C were tested in PCR and RIBA‐2. In panels A, B and C, 398 samples were HCV PCR positive: all were detected by Abbott and Ortho, and 397 (99.7%) by Murex. The sample missed by the Murex ELISA showed an isolated anti‐C33c reactivity in RIBA‐2. In panels A–C, 442 samples were RIBA‐2 positive and all were detected by the 3 tests. With Probit analysis on results of panel D, no significant difference in sensitivity was observed between the 3 evaluated ELISAs. Specificities of Abbott, Murex and Ortho in 1,055 blood donors were 99.7, 99.3 and 99.9%, respectively (NS, χ2). We conclude that the sensitivity and specificity of the 3 ELISAs are comparable although the C33c antigen in the Murex VK47 test should be improved.
Regulation of prolactin secretion by alpha-amino-3-hydroxy-5-methylisoxazole-4-propionic acid receptors in male rats.

The secretion of PRL is controlled by different hypothalamic signals. Depending on the experimental model, PRL secretion increases or decreases after activation of N-methyl-d -aspartic acid and kainate receptors. Recently we have described that activation of alpha-amino-3-hydroxy-5-methylisoxazole-4-propionic acid (AMPA) receptors inhibits PRL secretion in prepubertal male rats. The aim of present study was to examine (1) the physiological relevance of this finding, (2) the possible age-related changes observed after activation or blockade of AMPA receptors, (3) the specificity of the AMPA effect, (4) the hypothalamic and/or pituitary localization of AMPA action, and (5) the mechanism(s) of action of AMPA agonists. In a first set of experiments, neonatal males (5 and 10 days old) and prepubertal (23 days old) male rats were injected with AMPA (1, 2.5 or 5 mg/kg) or the antagonist of AMPA receptors 1,2,3, 4-tetrahydro-6-nitro-2,3-dioxo-! benzo (f) quinoxaline-7-sulfonamide (NBQX; 0.25 or 0.50 mg/kg). Serum PRL concentrations decreased significantly 15 and 30 min after i.p. administration of AMPA in prepubertal male rats, while the inhibitory effect of AMPA was not observed in 5- and 10-day-old males. The effect of AMPA was abolished by NBQX but not by MK-801 (a selective antagonist of NMDA receptors). NBQX alone (0.25 or 0.50 mg/kg) had no effect on PRL release. In vitro, AMPA slightly stimulated PRL secretion by hemipituitaries from prepubertal males, suggesting that the hypothalamus is likely the site of action for the reported inhibitory action of AMPA on PRL release. In this sense, the blockade of AMPA effects in animals pretreated with domperidone (a dopaminergic antagonist) or alpha-methyl-p-tyrosine (an inhibitor of dopamine synthesis) suggests that an increase in the release of hypothalamic dopamine is probably the mechanism i! nvolved in the effect of AMPA. In a second set of experiments, the effects of AMPA (2.5 mg/kg i.p.) and NBQX (0.5 mg/kg i.p. and 20 or 40 nmol i.c.v.) were tested in freely moving adult male rats sampled during periods of 2, 3 or 6 h. In contrast with data obtained in prepubertal rats, neither AMPA nor NBQX affected PRL secretion. In conclusion, these data indicate that activation of AMPA receptors inhibits PRL secretion in prepubertal male rats. This effect probably involves the release of dopamine from the hypothalamus and disappears in adulthood.
Differentiation between mucus secretion and endoluminal tumors in the airway: analysis and comparison of CT findings.

OBJECTIVE The objective of our study was to suggest CT features that help differentiate transient mucus secretion from airway tumors in the evaluation of soft-tissue nodular lesions confined within the airway lumen. MATERIALS AND METHODS Forty-two patients with airway tumors (mean age, 57.6 ± 14.9 [SD] years) and 48 patients with secretion (mean age, 67.8 ± 13.4 years) were included. Two observers analyzed the following features on contrast-enhanced CT in consensus readings: shape (round, ovoid, lobulating, or complex); margin (circumscribed or uncircumscribed); size (including change in size between mediastinal and lung window images); location (anterior, posterior, or unclear); angle between the lesion and contacting airway wall (acute, obtuse, or unclear); attenuation (quantitative and qualitative analyses); and presence of air, fat, or calcification within the lesion. The positive predictive value (PPV) of each CT finding was calculated for secretion and tumor, respectively. RESULTS Round (90.0%) or lobulating (92.9%) shape, uncircumscribed margin (100.0%), unclear location (87.5%), unclear angle (87.5%), a CT number of 21.7 HU or more (91.7%), and internal features such as fat (100.0%) or calcification (100.0%) showed high PPVs for tumors. Complex shape (100.0%), change in size of more than 15.9% (96.8%), a CT number of less than 21.7 HU (83.3%), and internal air density (100.0%) showed high PPVs for secretion. CONCLUSION On contrast-enhanced CT, the evaluation of shape, change in size between mediastinal and lung window images, the measurement of CT number, and internal features such as air, fat, or calcification might help differentiate secretion from tumors.
Microarray and proteomics expression profiling identifies several candidates, including the valosin‐containing protein (VCP), involved in regulating high cellular growth rate in production CHO cell lines

A high rate of cell growth (µ) leading to rapid accumulation of viable biomass is a desirable phenotype during scale up operations and the early stages of production cultures. In order to identify genes and proteins that contribute to higher growth rates in Chinese hamster ovary (CHO) cells, a combined approach using microarray and proteomic expression profiling analysis was carried out on two matched pairs of CHO production cell lines that displayed either fast or slow growth rates. Statistical analysis of the microarray and proteomic data separately resulted in the identification of 118 gene transcripts and 58 proteins that were differentially expressed between the fast‐ and slow‐growing cells. Overlap comparison of both datasets identified a priority list of 21 candidates associated with a high growth rate phenotype in CHO. Functional analysis (by siRNA) of five of these candidates identified the valosin‐containing protein (VCP) as having a substantial impact on CHO cell growth and viability. Knockdown of HSPB1 and ENO1 also had an effect on cell growth (negative and positive, respectively). Further functional validation in CHO using both gene knockdown (siRNA) and overexpression (cDNA) confirmed that altered VCP expression impacted CHO cell proliferation, indicating that VCP and other genes and proteins identified here may play an important role in the regulation of CHO cell growth during log phase culture and are potential candidates for CHO cell line engineering strategies. Biotechnol. Bioeng. 2010; 106: 42–56. © 2010 Wiley Periodicals, Inc.