Miracle-dz/UniFAR-FTUs huggingface dataset:
MicroRNAs mir‐184 and let‐7 alter Drosophila metabolism and longevity

MicroRNAs (miRNAs) are small RNA molecules that regulate gene expression associated with many complex biological processes. By comparing miRNA expression between long‐lived cohorts of Drosophila melanogaster that were fed a low‐nutrient diet with normal‐lived control animals fed a high‐nutrient diet, we identified miR‐184, let‐7, miR‐125, and miR‐100 as candidate miRNAs involved in modulating aging. We found that ubiquitous, adult‐specific overexpression of these individual miRNAs led to significant changes in fat metabolism and/or lifespan. Most impressively, adult‐specific overexpression of let‐7 in female nervous tissue increased median fly lifespan by ~22%. We provide evidence that this lifespan extension is not due to alterations in nutrient intake or to decreased insulin signaling.
Heterologous expression, characterization and possible functions of the chitin deacetylases, Cda1 and Cda2, from mushroom Coprinopsis cinerea

Two chitin deacetylases, Cda1 and Cda2, from Coprinopsis cinerea were expressed and characterized. Cda1 preferably deacetylates the nonreducing end residue of (GlcNAc)2, the internal or nonreducing end residue of (GlcNAc)3 and the nonreducing residue of (GlcNAc)6 after deacetylating the internal residues. In contrast, Cda2 preferably deacetylates the reducing end residue of (GlcNAc)2, the internal or reducing end residue of (GlcNAc)3 and the reducing residue of (GlcNAc)6 after deacetylating the internal residues. Furthermore, Cda1 prefers chitohexaose with higher degrees of acetylation for deacetylation, while Cda2 shows a weaker preference for chitohexaose with varying degrees of acetylation. The predicted Cda1 structure shows more hydrophobic aromatic amino acids on the surface near subsite +1 in the active site than on the surface near subsite -1, whereas the predicted Cda2 structure has more hydrophobic aromatic amino acids on the surface near subsite -1 than on the surface near subsite +1, which may be the molecular basis of the distinctive catalytic features between Cda1 and Cda2. Notably, Cda1 has a high transcription level in the nonelongating basal stipe region, whereas Cda2 has a high transcription level in the elongating apical stipe region, and the transcription level of the former is approximately five times that of the latter. Correspondingly, the molar ratio of GlcN/GlcNAc increased from 0.15 in the cell wall of the apical stipe region to 0.22 in the cell wall of the basal stipe region. Different modes of action of Cda1 and Cda2 may be related to their functions in the different stipe regions.
Multichannel Opportunistic Carrier Sensing for Stable Channel Access Control in Cognitive Radio Systems

In this paper we propose to use the well known game theoretic Gale-Shapley stable marriage theorem from game theory as a basis for spectrum allocation in cognitive radio networks. We analyze the performance of the proposed solution and provide tight lower and upper bounds on both the stable allocation and the optimal allocation performance. Then we present a novel opportunistic multichannel medium access control technique that achieves stable allocation within a single CSMA contention window. We discuss practical implementation issues and put forward two other varieties of the algorithm which have lower implementation complexity. Finally, we provide simulated examples.
Physics-based electron device modelling and computer-aided MMIC design

On overview on the state of the art and future trends in physics-based electron device modelling for the computer-aided design of monolithic microwave ICs is provided. After a review of the main physics-based approaches to microwave modeling, special emphasis is placed on innovative developments relevant to circuit-oriented device performance assessment, such as efficient physics-based noise and parametric sensitivity analysis. The use of state-of-the-art physics-based analytical or numerical models for circuit analysis is discussed, with particular attention to the role of intermediate behavioral models in linking multidimensional device simulators with circuit analysis tools. Finally, the model requirements for yield-driven MMIC design are discussed, with the aim of pointing out the advantages of physics-based statistical device modeling; the possible use of computationally efficient approaches based on device sensitivity analysis for yield optimization is also considered. >
Are Diet and Physical Activity Patterns Related to Cigarette Smoking in Adolescents? Findings From Project EAT

Introduction An inadequate diet and physical inactivity may compound the many deleterious effects of smoking on health. Some research indicates that smoking behavior is related to other health behaviors, but little research has examined how smoking may be related to dietary intake of key nutrients, consumption of fast food, sedentary lifestyle, or weight status. The purpose of this study was to describe smoking frequency among adolescents and its relationship to physical activity and dietary patterns. Methods The research study employed a cross-sectional, population-based design. Adolescents self-reported cigarette smoking, physical activity, and eating behaviors on the Project EAT (Eating Among Teens) survey and reported dietary intake on a food frequency questionnaire completed in school classrooms. The sample included 4746 middle school and high school students from Minneapolis-St. Paul public schools. Mixed-model regression, which was controlled for sex, race and ethnicity, socioeconomic status, grade level (middle school or high school), and school, was used to examine the association of smoking with diet and physical activity patterns. Results Overall, reported smoking frequency was inversely related to participating in team sports, eating regular meals, and consuming healthful foods and nutrients. Smoking frequency was directly related to frequency of fast-food and soft drink consumption. Conclusion Adolescents who smoke cigarettes may be less likely to engage in health-promoting lifestyle behaviors. Interventions are needed to prevent smoking and the unhealthy dietary practices and physical activity behaviors that may be associated with it.
Wavelets, Detection, Estimation, and Sparsity

Abstract Questions concerning the detection and estimation of signals in noise using the discrete wavelet transform are considered. A theorem is presented that shows the discrete wavelet transform of white noise is spread out over all the transform plane. It is established that a signal which is represented by a small number of wavelet coefficients can be accurately estimated. Moreover, it is also shown that the number of wavelet coefficients needed to represent a signal has a dramatic effect on the ability to estimate the signal. Specifically, two estimation techniques are presented and analyzed. Probability of detection and probability of false alarm results are given for a wide variety of signals. An example is presented to demonstrate the results.
Clinical Outcomes of Treatment for Intracranial Aneurysm in Elderly Patients

Objective The aim of this study is to evaluate the clinical course of intracranial aneurysm in patients aged 65 years and older and the immediate outcome after its aggressive management. Materials and Methods We performed a retrospective analysis using the medical records of 159 elderly patients managed at our institute from September 2008 to December 2013. Obtained clinical information included age, sex, Hunt and Hess grade (HHG), aneurysm location, Fisher grade (FG) and the treatment modality. Concomitant clinical data aside from cerebrovascular condition (hypertension, diabetes, previous medication) were evaluated to determine risk factors that might affect the functional outcomes. Results A total of 108 patients (67.9%) presented with subarachnoid hemorrhage (SAH), and 51 (32.1%) with unruptured intracranial aneurysms (UIAs). Coiling was performed in 101 patients and 58 patients underwent clipping. In the SAH population, 62 patients (57.4%) showed favorable outcomes, with a mortality rate of 11.3% (n = 18). In the UIAs population, 50 (98%) patients achieved 'excellent' and one (2%) achieved 'good' outcome. Factors including high-grade HHG (p < 0.001), advanced age (p = 0.014), and the presence of intraventricular hematoma (IVH) (p = 0.017) were significant predictors of poor outcome. Conclusion SAH patients with high grade HHG and IVH are associated with poor outcome with statistical significance, all the more prominent the older the patient is. Therefore, the indication for aggressive therapy should be considered more carefully in these patients. However, as the outcomes for elderly patients with UIAs were excellent regardless of the treatment modality, aggressive treatment could always be considered in UIAs cases.
Association Between Infrapatellar Fat Pad Volume and Knee Structural Changes in Patients with Knee Osteoarthritis

Objective. The function of the infrapatellar fat pad (IPFP) in knee osteoarthritis (OA) remains uncertain. This study aimed to examine cross-sectional associations between IPFP volume and knee structures in patients with knee OA. Methods. The study included 174 patients with clinical knee OA (mean age, 55.5 yrs). Fat-suppressed 3-D T1-weighted spoiled gradient recall magnetic resonance imaging (MRI) was used to measure the IPFP and cartilage volume. T2-weighted fast spin echo MRI was used to assess cartilage defects and bone marrow lesions (BML). Radiographic knee osteophytes and joint space narrowing (JSN) were assessed using the Osteoarthritis Research Society International atlas. Results. After adjustment for potential confounders, greater IPFP volume was associated with greater tibial and patellar cartilage volume (all p < 0.05), and fewer cartilage defects at all sites (OR 0.88–0.91, all p < 0.05). IPFP volume was associated with presence of BML at lateral tibial and medial femoral sites (OR 0.88–0.91, all p < 0.05) and osteophytes at lateral tibiofemoral compartment (OR 0.88, p < 0.05). IPFP volume was not significantly associated with JSN. Conclusion. Greater IPFP volume was associated with greater knee cartilage volume and fewer structural abnormalities, suggesting a protective role of IPFP size in knee OA.
Venous Thromboembolism, Myocardial Infarction, and Stroke Among Transdermal Contraceptive System Users

OBJECTIVE: To estimate the incidence of venous thromboembolism, acute myocardial infarction, and ischemic stroke among transdermal contraceptive system users compared with users of norgestimate-containing oral contraceptives with 35 mcg ethinyl estradiol. METHODS: We began with insurance claims data from UnitedHealthcare. We identified women exposed to the transdermal contraceptive system or norgestimate-containing oral contraceptives from April 2002 through December 2004. Outcomes were confirmed from medical records. We calculated incidence rates and age-adjusted incidence rate ratios. In a nested case-control analysis, we investigated and controlled for confounding. RESULTS: There were 49,048 woman-years of transdermal contraceptive system exposure and 202,344 woman-years of norgestimate-containing oral contraceptives exposure. There was a more than two-fold increase in the venous thromboembolism rate (incidence rate ratio 2.2, 95% confidence interval [CI] 1.3–3.8) among transdermal contraceptive system users (20 cases, 40.8 per 100,000 woman-years) compared with norgestimate-containing oral contraceptives users (37 cases, 18.3 per 100,000 woman-years). Acute myocardial infarction occurred in three transdermal contraceptive system users compared with seven among norgestimate-containing oral contraceptives users (incidence rate ratio 1.8, 95% CI 0.5–6.8). No strokes occurred among transdermal contraceptive system users, whereas 10 occurred among norgestimate-containing oral contraceptives users. In the nested case-control analysis, after exclusions for high-risk factors, the odds ratio for venous thromboembolism was 2.4 (95% CI 1.1–5.5). CONCLUSION: There was a more than two-fold increase in the risk of venous thromboembolism associated with use of the transdermal contraceptive system. Acute myocardial infarction and stroke occurred too rarely to ascertain precise risk estimates. LEVEL OF EVIDENCE: II
International Union of Pharmacology. XXXVI. Current Status of the Nomenclature for Receptors for Corticotropin-Releasing Factor and Their Ligands

Receptors for corticotropin-releasing factor (CRF) are members of a family of G protein-coupled receptors (“Family B”) that respond to a variety of structurally dissimilar releasing factors, neuropeptides, and hormones (including secretin, growth hormone-releasing factor, calcitonin, parathyroid hormone, pituitary adenylate cyclase-activating polypeptide, and vasoactive intestinal polypeptide) and signal through the cyclic AMP and/or calcium pathways. To date, three genes encoding additional CRF-like peptides (urocortins) have been identified in mammals. The urocortins and CRF bind with differential ligand selectivity at the two mammalian CRF receptors. This report was prepared by the International Union of Pharmacology Subcommittee on CRF Receptors, to summarize the current state of CRF receptor biology and to propose changes in the classification and nomenclature of CRF ligands and receptors.
MICROCRACKING OF PLAIN CONCRETE UNDER UNIAXIAL COMPRESSIVE LOADING

FAILURE OF CONCRETE UNDER UNIAXIAL COMPRESSIVE LOADING HAS BEEN STUDIED WITH REFERENCE TO THE DEVELOPMENT OF INTERNAL CRACKING AND THE PROGRESSIVE FORMATION OF MICROCRACKS. CONCRETE CUBES WERE LOADED BY AXIAL COMPRESSION TO VARIOUS PERCENTAGES OF THEIR ULTIMATE STRENGTH. THIN SLICES WERE TAKEN FROM THE STRAINED SPECIMENS, AND THE GROWTH OF INTERNAL CRACKS IN THEM STUDIED UNDER A MICROSCOPE. THE TOTAL LENGTH AND THE MAXIMUM WIDTH OF BOND, MORTAR AND AGGREGATE CRACKS WERE MEASURED AT VARIOUS STRAINS, AND THE RESULTS ARE DISCUSSED IN THE PAPER. /A/RRL/
Theorems on the variable-length intrinsic randomness

We address variable-length intrinsic randomness problems (in the sense of Vembu and Verdu (1995)) for countably infinite source alphabet /spl chi/ under the (unnormalized) divergence distance, the normalized conditional divergence distance, and the variational distance. It turns out that under all three kinds of approximation measures the variable-length intrinsic randomness still takes the same value, called the inf-entropy rate of the source.
Behavioral consequences following AAV mediated hippocampal EAAC1 knockdown

The neuronal glutamate transporter EAAC1 (EAAT3) is present in hippocampal neurons to prevent excessive glutamate accumulation. Glutamate receptor-dependent synaptic plasticity is important for learning and memory. The present study investigates behavior associated with blocking the glutamate transporter EAAC1. To manipulate EAAC1 function, rats were intrahippocampally injected with a adeno-associated viral (AAV) vector encoding an EAAC1 antisense mRNA sequence or an AAV empty cassette. Twenty-eight days following surgery, rats were tested in a delayed matching-toplace (DMTP) watermaze task to examine spatial memory, which is hippocampaldependent. Rats treated with EAAC1 antisense exhibited shorter latencies to locate the target platform relative to controls (p < 0.05). These data indicate that microinfusion of AAV encoding EAAC1 antisense significantly altered performance on task involving glutamate transmission and the hippocampus.
Examination of the clock gene Cryptochrome 1 in bipolar disorder: mutational analysis and absence of evidence for linkage or association

Bipolar disorder is associated with malfunctions of the circadian system, which regulates individual circadian rhythms and which enables the adaptation to a daily 24-h cycle and seasonal change. One of the human circadian clock genes, cryptochrome 1 (Cry1) (located on 12q23-q24.1) was analyzed because of its close correspondence to a linkage hotspot for bipolar disorder. We found no evidence for linkage of 52 bipolar families to two Cry1 flanking microsatellites under several parametric and non-parametric models. In order to employ association for a more sensitive test, 25 affected subjects selected from families with positive LOD scores were screened for mutations by sequencing 9.5% of the Cry1 gene. A total of 16 single nucleotide polymorphisms (SNPs) and a 3 base pair insertion were identified. However, no mutations with probable functional impact were found. These novel SNPs and data on allele frequency and linkage disequilibrium structure will be useful for future association analyses. Nine SNPs have been analyzed in a set of 159 parent proband triads. Linkage disequilibrium analyses using single SNPs and haplotypes showed no association to bipolar disease. Additional, more powerful, studies involving Cry1 and other circadian clock genes need to be tested before an association of circadian abnormalities with bipolar disorder can be excluded.
REPRODUCTIVE ISOLATION BETWEEN ANOPHELES SINENSIS AND ANOPHELES PULLUS IN KOREA

ABSTRACT Anopheles sinensis and An. pullus, the 2 predominant anopheline mosquito species in Korea, are major malaria vectors. Their morphological similarity makes them difficult to distinguish, and their taxonomic relationship remains unclear. Kanda and Oguma produced fertile F1 An. sinensis × An. pullus hybrids, suggesting a conspecific relationship. However, our recent internal transcribed spacer 2 DNA sequence comparison of these taxa revealed 32.9% divergence, suggesting that An. sinensis and An. pullus may be distinct species. In the present study, we reassessed the relationship of An. sinensis and An. pullus in hybridization experiments. Laboratory-raised isofemale lines of An. sinensis form B and An. pullus form A and B were reciprocally crossed. The 3 isofemale lines were established from fully engorged females caught from the wild and morphologically identified as An. sinensis or An. pullus. The isofemale lines represented 3 distinct metaphase karyotypes: An. sinensis form B (X, Y2) and An. pullus form A (X1, Y1) and form B (X2, Y2). The F1 hybrid larvae showed low viability and completely asynaptic salivary gland polytene chromosomes. The subset of F1 hybrids that developed to adults showed sex-ratio distortion; ovarian follicles developed abnormally in females, and males suffered atrophy of accessory glands and testes. These results strongly suggest that the Korean morphological species An. sinensis and An. pullus are biological species, separated by complete postzygotic reproductive isolation.
Scholarly use of social media and altmetrics: A review of the literature

Social media has become integrated into the fabric of the scholarly communication system in fundamental ways, principally through scholarly use of social media platforms and the promotion of new indicators on the basis of interactions with these platforms. Research and scholarship in this area has accelerated since the coining and subsequent advocacy for altmetrics—that is, research indicators based on social media activity. This review provides an extensive account of the state‐of‐the art in both scholarly use of social media and altmetrics. The review consists of 2 main parts: the first examines the use of social media in academia, reviewing the various functions these platforms have in the scholarly communication process and the factors that affect this use. The second part reviews empirical studies of altmetrics, discussing the various interpretations of altmetrics, data collection and methodological limitations, and differences according to platform. The review ends with a critical discussion of the implications of this transformation in the scholarly communication system.
One-step versus two-step culture of mouse preimplantation embryos: is there a difference?

BACKGROUND A comparison has been made of the development of mouse zygotes in either one-step or two-step culture systems. METHODS Embryo culture, blastocyst cell counts and embryo transfer were done. RESULTS No significant differences were observed in the proportions of blastocysts, rates of hatching, numbers of cells in the inner cell mass (ICM) and trophectoderm (TE) that developed in protocols: one-step culture in potassium-enriched simplex optimized medium supplemented with glucose and amino acids (KSOMg(AA)), two-step culture in KSOMg(AA)/KSOMg(AA), and two-step culture in G1.2/G2.2. No gross abnormalities were observed in the fetuses that developed from zygotes in the one-step protocol using KSOMg(AA) and a two-step protocol using G1.2/G2.2. The body weights of these two groups of fetuses were not significantly different and no developmental abnormalities were observed. No significant differences were observed in the proportions of blastocysts, rates of hatching, numbers of cells in the ICM and TE that developed in protocols: one-step culture in KSOMg(AA), two-step culture in KSOMg(AA)/KSOMg(AA), and two-step culture in DM2/DM1. EDTA is not toxic to the initial cleavage stages of development at a concentration of 0.01 mmol/l in KSOMg(AA). CONCLUSIONS Two-step culture protocols are sufficient for the support of preimplantation mouse development in vitro but they are not necessary.
Refining homology models by combining replica‐exchange molecular dynamics and statistical potentials

A protocol is presented for the global refinement of homology models of proteins. It combines the advantages of temperature‐based replica‐exchange molecular dynamics (REMD) for conformational sampling and the use of statistical potentials for model selection. The protocol was tested using 21 models. Of these 14 were models of 10 small proteins for which high‐resolution crystal structures were available, the remainder were targets of the recent CASPR exercise. It was found that REMD in combination with currently available force fields could sample near‐native conformational states starting from high‐quality homology models. Conformations in which the backbone RMSD of secondary structure elements (SSE‐RMSD) was lower than the starting value by 0.5–1.0 Å were found for 15 out of the 21 cases (average 0.82 Å). Furthermore, when a simple scoring function consisting of two statistical potentials was used to rank the structures, one or more structures with SSE‐RMSD of at least 0.2 Å lower than the starting value was found among the five best ranked structures in 11 out of the 21 cases. The average improvement in SSE‐RMSD for the best models was 0.42 Å. However, none of the scoring functions tested identified the structures with the lowest SSE‐RMSD as the best models although all identified the native conformation as the one with lowest energy. This suggests that while the proposed protocol proved effective for the refinement of high‐quality models of small proteins scoring functions remain one of the major limiting factors in structure refinement. This and other aspects by which the methodology could be further improved are discussed. Proteins 2008. © 2008 Wiley‐Liss, Inc.
The effect of test conditions on the sensitivity and resolution of SRET signal response

Purpose – The aim of this paper is to study and analyse the advantages and limitations of the scanning reference electrode technique (SRET) to detect and assess localised electrochemical activity based on an evaluation of the influence of the principal test parameters on the sensitivity and resolution of the technique.Design/methodology/approach – Measurements of Ohmic potential gradients induced by ionic flux close to a point current source (PCS) were carried out using a scanning reference electrode technique (SRET) instrument, which comprised a vertical rotating working electrode and a scanning probe formed by a pair of platinum electrodes of approximately 200 μm of diameter. Ionic flux was induced by anodic polarisation applied to a gold micro‐disc electrode, which acted as the PCS. Measurements were conducted in electrolytes of ten different conductivities, using different scanning probe tips to sample surface distance and different working electrode rotation rates. The range of conductivities used in.