Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolutionary changes in promoter and enhancer activity during human corticogenesis

Of mice, men, and macaque brains The human brain represents a unique evolutionary trajectory. To better understand how the human brain came to be, Reilly et al. sought to identify changes in gene expression between mice, macaques, and humans. They compared epigenetic marks in the embryonic cortex, which revealed changes in gene regulation in biological pathways associated with cortical development. Science, this issue p. 1155 Epigenetic marks associated with evolution of the human cortex gained activity relative to those in mice and monkeys. Human higher cognition is attributed to the evolutionary expansion and elaboration of the human cerebral cortex. However, the genetic mechanisms contributing to these developmental changes are poorly understood. We used comparative epigenetic profiling of human, rhesus macaque, and mouse corticogenesis to identify promoters and enhancers that have gained activity in humans. These gains are significantly enriched in modules of coexpressed genes in the cortex that function in neuronal proliferation, migration, and cortical-map organization. Gain-enriched modules also showed correlated gene expression patterns and similar transcription factor binding site enrichments in promoters and enhancers, suggesting that they are connected by common regulatory mechanisms. Our results reveal coordinated patterns of potential regulatory changes associated with conserved developmental processes during corticogenesis, providing insight into human cortical evolution.
The Arecibo 430 MHz Intermediate Galactic Latitude Survey: Discovery of Nine Radio Pulsars

We have used the Arecibo Radio Telescope to search for millisecond pulsars in two intermediate Galactic latitude regions (7° < |b| < 20°) accessible to this telescope. For these latitudes the useful millisecond pulsar search volume achieved by Arecibo's 430 MHz beam is predicted to be maximal. Searching a total of 130 deg2, we have discovered nine new pulsars and detected four previously known objects. We compare the results of this survey with those of other 430 MHz surveys carried out at Arecibo and an intermediate-latitude survey made at Parkes that included part of our search area; the latter independently found two of the nine pulsars we have discovered. At least six of our discoveries are isolated pulsars with ages between 5 and 300 Myr; one of these, PSR J1819+1305, exhibits very marked and periodic nulling. We have also found a recycled pulsar, PSR J2016+1948. With a rotational period of 65 ms, this is a member of a binary system with a 635 day orbital period. We discuss some of the properties of this system in detail and indicate its potential to provide a test of the strong equivalence principle. This pulsar and PSR J0407+16, a similar system now being timed at Arecibo, are by far the best systems known for such a test.
AGA technical review on irritable bowel syndrome.

Abstract The irritable bowel syndrome (IBS) is part of the larger group of functional gastrointestinal (GI) disorders that, despite differences in location and symptom patterns, share common features with regard to their motor and sensory physiology, central nervous system (CNS) relationships, and the approach to patient care.1 IBS is a functional bowel disorder characterized by symptoms of abdominal pain or discomfort that is associated with disturbed defecation.2 This disorder is highly prevalent and can be associated with significant emotional distress, impaired health-related quality of life (HRQL), disability, and high health care costs. Psychosocial factors, although not part of IBS per se, have an important role in modulating the illness experience and its clinical outcome.3 GASTROENTEROLOGY 2002;123:2108-2131
Mining Graph Patterns Efficiently via Randomized Summaries

Graphs are prevalent in many domains such as Bioinformatics, social networks, Web and cyber-security. Graph pattern mining has become an important tool in the management and analysis of complexly structured data, where example applications include indexing, clustering and classification. Existing graph mining algorithms have achieved great success by exploiting various properties in the pattern space. Unfortunately, due to the fundamental role subgraph isomorphism plays in these methods, they may all enter into a pitfall when the cost to enumerate a huge set of isomorphic embeddings blows up, especially in large graphs. The solution we propose for this problem resorts to reduction on the data space. For each graph, we build a summary of it and mine this shrunk graph instead. Compared to other data reduction techniques that either reduce the number of transactions or compress between transactions, this new framework, called Summarize-Mine, suggests a third path by compressing within transactions. Summarize-Mine is effective in cutting down the size of graphs, thus decreasing the embedding enumeration cost. However, compression might lose patterns at the same time. We address this issue by generating randomized summaries and repeating the process for multiple rounds, where the main idea is that true patterns are unlikely to miss from all rounds. We provide strict probabilistic guarantees on pattern loss likelihood. Experiments on real malware trace data show that Summarize-Mine is very efficient, which can find interesting malware fingerprints that were not revealed previously.
Adenosine A2B receptors.

Adenosine is an endogenous nucleoside that modulates many physiological processes. Its actions are mediated by interaction with specific cell membrane receptors. Four subtypes of adenosine receptors have been cloned: A1, A2A, A2B, and A3. Significant advancement has been made in the understanding of
Alert-QSAR. Implications for Electrophilic Theory of Chemical Carcinogenesis

Given the modeling and predictive abilities of quantitative structure activity relationships (QSARs) for genotoxic carcinogens or mutagens that directly affect DNA, the present research investigates structural alert (SA) intermediate-predicted correlations ASA of electrophilic molecular structures with observed carcinogenic potencies in rats (observed activity, A = Log[1/TD50], i.e., ASA=f(X1SA,X2SA,…)). The present method includes calculation of the recently developed residual correlation of the structural alert models, i.e., ARASA=f(A−ASA,X1SA,X2SA,…). We propose a specific electrophilic ligand-receptor mechanism that combines electronegativity with chemical hardness-associated frontier principles, equality of ligand-reagent electronegativities and ligand maximum chemical hardness for highly diverse toxic molecules against specific receptors in rats. The observed carcinogenic activity is influenced by the induced SA-mutagenic intermediate effect, alongside Hansch indices such as hydrophobicity (LogP), polarizability (POL) and total energy (Etot), which account for molecular membrane diffusion, ionic deformation, and stericity, respectively. A possible QSAR mechanistic interpretation of mutagenicity as the first step in genotoxic carcinogenesis development is discussed using the structural alert chemoinformation and in full accordance with the Organization for Economic Co-operation and Development QSAR guidance principles.
[Effect of electroacupuncture on the levels of amino acid neurotransmitters in the spinal cord in rats with chronic constrictive injury].

OBJECTIVE To observe the changes of amino acid neurotransmitter contents in the lumbar spinal cord after electroacupuncture (EA) in rats with neuropathic pain so as to study its spinal mechanism underlying pain relief. METHODS Forty SD rats were randomly divided into control, sham surgery, model and EA groups (n=10). Chronic constrictive injury (CCI) (neuropathic pain) model was duplicated by ligature of the right sciatic nerve with a piece of catgut. EA (1-3 mA, 2 Hz) was applied to "Huantiao" (GB 30) and "Weizhong" (BL 40) on the injured side for 30 minutes, once a day for 7 days. The mechanical and thermal pain thresholds were measured before and after CCI, and after EA intervention. Concentrations of glutamate (Glu), aspartate (Asp), glutamine (Gln), gamma-aminobutyric acid (GABA), Glycine (Gly) and taurine (Tau) in the lumbar spinal cord (L4-6) were detected by O-phthaladehyde derivatization + high performance liquid chromatography (HPLC). RESULTS Compared with the control group, both the mechanical and thermal pain thresholds of the model group were decreased significantly on day 10 and day 16 after CCI (P < 0.01). Compared with the model group, the mechanical and thermal pain thresholds in the EA group on day 16 after CCI were upregulated strikingly (P < 0.01). In comparison with the control group, Glu, Asp, Gin and GABA levels in the lumbar spinal cord were significantly higher in the model group (P < 0.05, P < 0.01), while Gly and Tau levels in the lumbar spinal cord were markedly lower in the model group (P < 0.05). In comparison with the model group, spinal Glu, Asp, and Gin contents were downregulated significantly in the EA group (P < 0.01), while Gly, GABA and Tau levels were upregulated obviously (P < 0.01, P < 0.05). No significant differences were found between the control and sham surgery groups in the mechanical and thermal pain thresholds, and in the spinal Glu, Asp, GIn, GABA, Gly and Tau levels (P > 0.05). CONCLUSION EA of GB 30 and BL 40 may alleviate neuropathic pain in CCI rats, which is closely with its effects in reducing the release of excitatory amino acids and promoting the release of inhibitory amino acid neurotransmitters.
Sex-Steroid Regulation of Relaxin Receptor Isoforms (RXFP1 & RXFP2) Expression in the Patellar Tendon and Lateral Collateral Ligament of Female WKY Rats

The incidence of non-contact knee injury was found higher in female than in male and is related to the phases of the menstrual cycle. This raised the possibility that female sex-steroids are involved in the mechanism underlying this injury via affecting the expression of the receptors for relaxin, a peptide hormone known to modulate ligament laxity. Therefore, this study aims to investigate the effect of sex-steroids on relaxin receptor isoforms (RXFP1 & RXFP2) expression in the ligaments and tendons of the knee. Methods: Ovariectomized adult female WKY rats were treated with different doses of estrogen (0.2, 2, 20 μg/kg), progesterone (4mg) and testosterone (125 & 250μg/kg) for three consecutive days. At the end of the treatment, the animals were sacrificed and the patellar tendon and lateral collateral ligament were harvested for mRNA and protein expression analyses by Real Time PCR and Western blotting respectively. Results: RXFP1, the main isoform expressed in these knee structures and RXFP2 showed a dose-dependent increase in expression with estrogen. Progesterone treatment resulted in an increase while testosterone caused a dose-dependent decrease in the mRNA and protein expression of both relaxin receptor isoforms. Discussion: Progesterone and high dose estrogen up-regulate while testosterone down-regulates RXFP1 and RXFP2 expression in the patellar tendon and lateral collateral ligament of rat's knee. Conclusion: Relaxin receptor isoforms up-regulation by progesterone and high dose estrogen could provide the basis for the reported increase in knee laxity while down-regulation of these receptor isoforms by testosterone could explain low incidence of non-contact knee injury in male.
Effects of Pb and Zn Stresses on Protective Enzyme Activities of Pb Accumulator Plant Pseudostellaria maximowicziana(Franch.et Savat.) Pax

To understand the physiological and biochemical response of the lead-accumulator plant pseudostellaria maximowicziana (Franch.et Savat.) Pax to lead and zinc stresses, the pot experiment was used to study the protective enzymes (SOD, CAT and POD) activity and MDA content of pseudostellaria maximowicziana under lead and zinc stresses. The results showed as follows: with the increase of lead concentration, SOD activity of plants had a decreasing trend before increase, and with the increase of zinc concentration, SOD activity had an increasing trend. CAT activities of plants had a trend of increase and POD activities had a decreasing trend before with increase of lead and zinc concentrations increasing. However, with lead and zinc concentrations increasing, MDA contents of plants had a wavy trend. ANOVA showed that the differences of the three kinds of protective enzyme activities among the concentration of lead, lead-zinc interaction and MDA content were extremely significant. While those of SOD and CAT activities by zinc concentrations were extremely significant, and POD activity and MDA content were significant.
High BRAF mutation frequency does not characterize all melanocytic tumor types

Cutaneous melanoma (CM) is the most lethal form of skin cancer. Along with some benign melanocytic tumors, the majority shows BRAF or NRAS mutation, but it is not known whether these are essential to all forms of melanocytic neoplasia. We screened 79 melanocytic tumors of different types for BRAF and NRAS mutations and looked at MAPK pathway activity using immunohistochemistry in a subset. Significant differences in BRAF exon 15 mutation frequency were found: 14/16 (87.5%) in common acquired naevi (CANs), 9/12 (75%) in CMs, 0/26 in Spitz naevi and 3/25 (12%) in blue naevi (p < 0.01). We looked at whether Spitz and blue naevi showed a compensatory increase in BRAF exon 11 and/or NRAS exons 1 and 2 mutations to account for the low BRAF exon 15 mutation frequency. NRAS mutations were found in only 1/16 (6.3%) Spitz naevi and 0/15 blue naevi. In addition, NRAS mutations were found in 2/11 (18.2%) CANs and 3/12 (25%) CMs. None of the tumors showed BRAF exon 11 mutations. Despite their low combined BRAF and NRAS mutation frequency, Spitz naevi showed strong MAPK pathway activation as measured by cytoplasmic expression of dually phosphorylated ERK1/2, while blue naevi had weak pathway activation. We conclude that BRAF and NRAS mutations are not necessary for melanocytic tumor development and that some types of tumor must arise by alternative mechanisms. © 2004 Wiley‐Liss, Inc.
From mouse to man: the 5-HT3 receptor modulates physical dependence on opioid narcotics

Objectives Addiction to opioid narcotics represents a major public health challenge. Animal models of one component of addiction, physical dependence, show this trait to be highly heritable. The analysis of opioid dependence using contemporary in-silico techniques offers an approach to discover novel treatments for dependence and addiction. Methods In these experiments, opioid withdrawal behavior in 18 inbred strains of mice was assessed. Mice were treated for 4 days with escalating doses of morphine before the administration of naloxone allowing the quantification of opioid dependence. After haplotypic analysis, experiments were designed to evaluate the top gene candidate as a modulator of physical dependence. Behavioral studies as well as measurements of gene expression on the mRNA and protein levels were completed. Finally, a human model of opioid dependence was used to quantify the effects of the 5-HT3 antagonist ondansetron on signs and symptoms of withdrawal. Results The Htr3a gene corresponding to the 5-HT3 receptor emerged as the leading candidate. Pharmacological studies using the selective 5-HT3 antagonist ondansetron supported the link in mice. Morphine strongly regulated the expression of the Htr3a gene in various central nervous system regions including the amygdala, dorsal raphe, and periaqueductal gray nuclei, which have been linked to opioid dependence in previous studies. Using an acute morphine administration model, the role of 5-HT3 in controlling the objective signs of withdrawal in humans was confirmed. Conclusion These studies show the power of in-silico genetic mapping, and reveal a novel target for treating an important component of opioid addiction.
Statistical Inference for Familial Disease Clusters

Summary. In many epidemiologic studies, the first indication of an environmental or genetic contribution to the disease is the way in which the diseased cases cluster within the same family units. The concept of clustering is contrasted with incidence. We assume that all individuals are exchangeable except for their disease status. This assumption is used to provide an exact test of the initial hypothesis of no familial link with the disease, conditional on the number of diseased cases and the distribution of the sizes of the various family units. New parametric generalizations of binomial sampling models are described to provide measures of the effect size of the disease clustering. We consider models and an example that takes covariates into account. Ascertainment bias is described and the appropriate sampling distribution is demonstrated. Four numerical examples with real data illustrate these methods.
Trainee teachers' views on what helps them to use information and communication technology effectively in their subject teaching

This study explored the views of initial teacher trainees on various components of their training in the use of new technology to teach their subject. The research focused on trainees' reflections on their experiences of trying to ‘get better’ at information and communication technology (ICT) in the course of their training. Data collection involved baseline and follow-up questionnaire surveys of trainees' attitudes to the use of ICT in subject teaching and the factors that they felt had hindered or promoted their development in the use of ICT, and focus group interviews with small groups of trainees. In spite of the importance attached to this facet of initial training, and significant investment in terms of time and training materials and resources, there is evidence to suggest that much of this investment is not found to be helpful by trainees. In particular, there appears to be a danger that they have simply been overwhelmed with information about the use of ICT to such an extent that they do not feel that they can realistically be expected to engage with many of the materials that have been produced. In addition to ascertaining trainees' views on strategies and interventions that they did not find helpful, the data identify some key factors and moments that trainees felt had a major impact on their progress in the use of ICT. The outcomes of the enquiry reveal clear preferences among trainees for modes of working with ICT, and in terms of the experiences that they felt had impacted on their ability to use ICT in their subject teaching. The concluding section of the paper considers the ways in which trainees' induction into the use of new technology might be made more effective.
A Global Linear Method for Camera Pose Registration

We present a linear method for global camera pose registration from pair wise relative poses encoded in essential matrices. Our method minimizes an approximate geometric error to enforce the triangular relationship in camera triplets. This formulation does not suffer from the typical `unbalanced scale' problem in linear methods relying on pair wise translation direction constraints, i.e. an algebraic error, nor the system degeneracy from collinear motion. In the case of three cameras, our method provides a good linear approximation of the trifocal tensor. It can be directly scaled up to register multiple cameras. The results obtained are accurate for point triangulation and can serve as a good initialization for final bundle adjustment. We evaluate the algorithm performance with different types of data and demonstrate its effectiveness. Our system produces good accuracy, robustness, and outperforms some well-known systems on efficiency.
Prosodic patterns of information structure in spoken discourse - a preliminary study of Mandarin spontaneous lecture vs. read speech

The aim of the study is to explore the prosodic patterns spontaneous lecture speech vs. read speech to show where and how these monologues differ and why by analyzing perceived emphasis and its acoustic features within and between speech paragraphs. Systematic but distinct patterns are found for both speech types in emphasis distribution across speech, overall and local tempo modulations. Read speech is characterized by discourse coherence while spontaneous information structure in addition. Intricate tempo modulations characterizing information structure are discussed.
Performance evaluation of an advanced local search evolutionary algorithm

One natural question when testing performance of global optimization algorithm is: how performances compare to a restart local search algorithm. One purpose of this paper is to provide results for such comparisons. To this end, the performances of a restart (advanced) local-search strategy, the CMA-ES with small initial step-size, are investigated on the 25 functions of the CEC 2005 real-parameter optimization test suit. The second aim is to clarify the theoretical background of the performance criterion proposed to quantitatively compare the search algorithms. The theoretical analysis allows us to generalize the criterion proposed and to define a new criterion that can be applied more appropriate in a different context.
Comparison of eluted monomer from different indirect and direct resin composites

Abstract Indirect resin composites used in indirect restorations have been used as alternative methods to avoid the negative effects of a direct application. The composition and structure of these are similar to a direct composite. Several authors have discussed the elution monomer from resin composites because it is a crucial factor in optimizing the physical properties and biocompatibility of resin composites. The aim of this study was to compare the elution of monomers from different resin composites using high-performance liquid chromatography (HPLC). Indirect composites including Signum, Gradia, and Solidex, and direct composite Filtek Ultimate were used. The samples (2 x 5 mm) were prepared and polymerized for 20 seconds with a light-emitting diode unit. A secondary curing was then applied to the indirect resin composites. After fabrication, each sample was immediately immersed in a 75 wt% ethanol/water solution and analyzed by HPLC. The obtained data were analyzed with one-way ANOVA and Tukey HSD (p < 0.05). Residual monomers were eluted from indirect and direct resin composites and the amount of eluted monomers increased over time. The highest mean concentrations of residual Bis-GMA, UDMA, TEGDMA, and HEMA were detected with the Filtek Ultimate (2,342 µM), Solidex (7,908 µM), Signum (2.8 µM), and Filtek Ultimate (9.7 µM), respectively. The highest amount of eluted monomer concentrations detected was viewed as critical for toxic reactions in human cells.
Exploring self-compassion and eudaimonic well-being in young women athletes.

Using a mixed methods research design, we explored self-compassion and eudaimonic well-being in young women athletes. In a quantitative study (n = 83), we found that self-compassion and eudaimonic well-being were positively related (r = .76, p < .01). A model of multiple mediation was proposed, with self-compassion, passivity, responsibility, initiative, and self-determination accounting for 83% of the variance in eudaimonic well-being. In a qualitative study (n = 11), we explored when and how self-compassion might be useful in striving to reach one's potential in sport. Self-compassion was described as advantageous in difficult sport-specific situations by increasing positivity, perseverance, and responsibility, as well as decreasing rumination. Apprehensions about fully embracing a self-compassionate mindset in sport warrant additional research to explore the seemingly paradoxical role of self-compassion in eudaimonic well-being.