Miracle-dz/UniFAR-FTUs huggingface dataset:
MULTIDIMENSIONAL ADAPTIVE EVOLUTION OF A FEED‐FORWARD NETWORK AND THE ILLUSION OF COMPENSATION

When multiple substitutions affect a trait in opposing ways, they are often assumed to be compensatory, not only with respect to the trait, but also with respect to fitness. This type of compensatory evolution has been suggested to underlie the evolution of protein structures and interactions, RNA secondary structures, and gene regulatory modules and networks. The possibility for compensatory evolution results from epistasis. Yet if epistasis is widespread, then it is also possible that the opposing substitutions are individually adaptive. I term this possibility an adaptive reversal. Although possible for arbitrary phenotype‐fitness mappings, it has not yet been investigated whether such epistasis is prevalent in a biologically realistic setting. I investigate a particular regulatory circuit, the type I coherent feed‐forward loop, which is ubiquitous in natural systems and is accurately described by a simple mathematical model. I show that such reversals are common during adaptive evolution, can result solely from the topology of the fitness landscape, and can occur even when adaptation follows a modest environmental change and the network was well adapted to the original environment. The possibility of adaptive reversals warrants a systems perspective when interpreting substitution patterns in gene regulatory networks.
In Silico Protein-Ligand Docking Studies on Thiazolidinediones as Potential Anticancer Agents

Molecular docking study was performed on a series of 24 Thiazolidinediones MM1-MM24 as potential epiderma1 growth factor receptor (EGFRR) inhibitors. The docking technique was applied to dock a set of representative compounds within the active site region of 1M17 using Molegro Virtual Docker v 5.0. For these compounds, the binding free energy (kcal/mol) was determined. The docking simulation clearly predicted the binding mode that is nearly similar to the crystallographic binding mode with 1.34A RMSD. Based on the validations and hydrogen bond interactions made by R substituents were considered for evaluation. The results avail to understand the type of interactions that occur between thiazolidinediones with 1M17 binding site region and explain the importance of R substitution on thiazolidinedione basic nucleus.
Identification of genes regulated in the mouse extended amygdala by excessive ethanol drinking associated with dependence

Alcoholism is characterized by a progressive loss of control over ethanol intake. The purpose of this study was to identify transcriptional changes selectively associated with excessive ethanol drinking in dependent mice, as opposed to non‐dependent mice maintaining a stable voluntary consumption or mice solely undergoing forced intoxication. We measured expression levels of 106 candidate genes in the extended amygdala, a key brain structure for the development of drug addiction. Cluster analysis identified 17 and 15 genes selectively induced or repressed, respectively, under conditions of excessive drinking. These genes belong to signaling pathways involved in neurotransmission and transcriptional regulation.
Heart rate, ischaemic heart disease, and sudden cardiac death in middle-aged British men.

OBJECTIVE--To examine the relation between resting heart rate and new major ischaemic heart disease events in middle aged men with and without pre-existing ischaemic heart disease. DESIGN--Prospective study of a cohort of men with eight years follow up for cardiovascular morbidity and mortality for all men. SETTING--General practices in 24 British towns (the British Regional Heart study). SUBJECTS--7735 men aged 40-59 years drawn at random from the age-sex registers of one general practice in each town. MAIN OUTCOME MEASURES--Major ischaemic heart disease events such as sudden cardiac death, other deaths attributed to ischaemic heart disease, and non-fatal myocardial infarction. RESULTS--During the follow up period of eight years, 488 men had a major ischaemic heart disease event (217 fatal and 271 non-fatal). Of these, 117 were classified as sudden cardiac death (death within one hour of the start of symptoms). The relation between heart rate and risk of all major ischaemic heart disease events, ischaemic heart disease deaths, and sudden cardiac death was examined separately in men with and without pre-existing ischaemic heart disease. In men with no evidence of ischaemic heart disease, there was a strong positive association between resting heart rate and age adjusted rates of all major ischaemic heart disease events (fatal and non-fatal), ischaemic heart disease deaths, and sudden cardiac death. This association remained significant even after adjustment for age, systolic blood pressure, blood cholesterol, smoking, social class, heavy drinking, and physical activity, with particularly high risk in those with heart rate > or = 90 beats/min. The increased risk seen in those with increased heart rate was largely due to a significantly increased risk of sudden cardiac death, which was five times higher than in those with heart rate < 60 beats/min. The effect of heart rate on sudden cardiac death was present irrespective of blood pressure or smoking state. In men with pre-existing ischaemic heart disease a positive association was seen between raised heart rate and risk of all major ischaemic heart disease events, ischaemic heart disease death, and sudden cardiac death, but the effect was less noticeable than in men without pre-existing ischaemic heart disease. CONCLUSION--In this study of middle aged British men increased heart rate > or = 90 beats/min) is a risk factor for fatal ischaemic heart disease events but particularly for sudden cardiac death. The effect is not dependent on the presence of other established coronary risk factors and is most clearly seen in men free of pre-existing ischaemic heart disease at initial examination.
Depressed Mood Is Related to High-Frequency Heart Rate Variability During Stressors

Objective The purpose of this study was to examine the relationships between depressed mood and parasympathetic control of the heart in healthy men and women at rest and during two stressors. Methods Fifty-three healthy college students completed a laboratory stress protocol that included a baseline resting period, a challenging speech task, and a forehead cold pressor task. Depressed mood was assessed using the Beck Depression Inventory (BDI). Parasympathetic cardiac control was measured as the high-frequency (0.12–0.40 Hz) component (HF) of heart rate variability using power spectrum analysis. Blood pressure, respiration rate, and respiration amplitude were measured simultaneously. Results Participants were categorized as having a high or low depressed mood on the basis of median splits of their BDI scores. Those in the high depressed mood group had significantly greater reductions in HF during the speech task and significantly smaller increases in HF during the forehead cold pressor task than those in the low depressed mood group. Women had significantly greater reductions in HF during the speech task and smaller increases in HF during the forehead cold pressor task than men. However, gender and depressed mood did not interact to predict changes in HF. Conclusions Depressed mood is related to the magnitude of decrease in parasympathetic cardiac control during stressors in healthy men and women. These findings extend those of previous studies, in which a similar phenomenon was observed among patients with cardiac disease. Because the participants in this study were healthy, the relationship between depressed mood and parasympathetic cardiac control does not seem to be secondary to cardiovascular disease.
Animal Models of Acute Moderate Hypoxia Are Associated with a Down-Regulation of CYP1A1, 1A2, 2B4, 2C5, and 2C16 and Up-Regulation of CYP3A6 and P-glycoprotein in Liver

In humans, indirect evidence suggests that hypoxia reduces the rate of biotransformation of drugs cleared by cytochrome P450 (P450) subfamilies CYP1A, 2B, and 2C. The aim of this study was to assess whether acute moderate hypoxia modulates the expression of CYP2B4, 2C5, and 2C16 in vivo, and to determine whether the changes in hepatic P450 are conveyed by serum mediators. Moreover, because hypoxia increases the expression of P-glycoprotein in vitro, we examined whether in vivo acute moderate hypoxia modulates the expression of several membrane transporters in the liver. Rabbits and rats were exposed to a fractional concentration of oxygen of 8% for 48 h to generate a stable arterial partial pressure of O2 of 34 ± 1 mm Hg. Compared with rabbits breathing room air, hypoxia in rabbits reduced the amount of CYP1A1, 1A2, 2B4, 2C5, and 2C16 proteins and increased the expression of CYP3A6. Sera of rabbits with hypoxia were fractionated by size exclusion chromatography, the fractions were tested for their ability to modify the expression of P450 isoforms, and serum mediators were identified through neutralization experiments. The serum mediators responsible for the down-regulation of P450 isoforms were interferon-γ, interleukin-1β (IL-1β), and IL-2. In vivo, in rats, hypoxia increased the mRNA and protein expression of P-glycoprotein but did not affect the mRNA of breast cancer resistance protein and organic anion-transporting polypeptide 2. It is concluded that in vivo, hypoxia down-regulates rabbit hepatic CYP1A1, 1A2, 2B4, 2C5, and 2C16 and up-regulates CYP3A6. CYP3A11 and P-glycoprotein were up-regulated in the livers of hypoxic rats.
Molecular Investigation of Oxidized Graphene: Anatomy of the Double-Layer Structure and Ion Dynamics

We investigated the influence of surface oxidization of planar graphene electrodes on charge storage and ion dynamics of supercapacitors. Our approach compared two distinct ionic liquid (IL) electrolytes: tetraethylammonium tetrafluoroborate solvated in acetonitrile (TEA-BF4/ACN) and 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide solvated in acetonitrile (EMIm-TFSI/ACN). Both experimental electrochemical tests and molecular dynamics (MD) simulations showed positive, electrolyte-specific influences of hydroxyl-free electrode interfaces on capacitance. In the EMIm-TFSI/ACN system, the hydroxylated surface, because of its strong interaction with anions, impeded surface charge storage. On the other hand, in the case of TEA-BF4/ACN, the distribution and orientation of ACN across the system exerted vital influence on the capacitance, especially on the positive hydroxyl-free electrode. Furthermore, MD simulations of ion mobility with respect to the electrode surface in the lateral and perpendicula.
The Interplay between Internal and External Conflict: Managing Conflict between and within Teams for Trust in China

Trusting relationships are increasingly considered vital for making teams productive but within organizations team members confront many obstacles and pressures that can interfere. This study proposes, in contrast to traditional theorizing about Chinese values, that the cooperative management of conflict can help Chinese team members deal with incompatibilities so that they become convinced that their teammates are trustworthy. Results also support the theorizing that the how teams manage conflict with each other affects within team conflict management. Specifically, the structural equation analysis supported the reasoning that cooperative conflict between teams helps teams manage their internal conflicts cooperatively that in turns builds trust. Results were interpreted as providing support for the universalistic aspirations of the theory of cooperation and competition and that managing conflict cooperatively is a foundation for strong trusting relationships in China as well as in the West.
Stability and periodic solution on a robot trajectory generation model

Robot motion planning is an important topic, which is widely studied. In this paper, a neural network model, which is inspired biologically to construct the robot trajectory, is discussed. Both global exponential stability and periodic solutions of the neural network, which are also two of the most important characters of a dynamic system, are analyzed via the method of constructing suitable Lyapunov functions. Simple sufficient conditions are given for exponential stability and the existence of periodic solutions. The conditions in the results are presented in terms of the parameters of the connection matrix, which are easy to be checked and are helpful in practice.
A New Panel Dataset of Potential Determinants of Economic Growth

This paper makes two contributions to the literature of economic growth. First, I construct an extensive panel dataset of potential determinants of economic growth (90 variables to be exact). The significance of considering an extensive set of potential determinants of economic growth is to reduce the chance of omission relevant variables. Second, I address the missing observations problem by using multiple imputation.
Inhibiting lentiviral replication by HEXIM1, a cellular negative regulator of the CDK9/cyclin T complex

Objective:Tat-dependent transcriptional elongation is crucial for the replication of HIV-1 and depends on positive transcription elongation factor b complex (P-TEFb), composed of cyclin dependent kinase 9 (CDK9) and cyclin T. Hexamethylene bisacetamide-induced protein 1 (HEXIM1) inhibits P-TEFb in cooperation with 7SK RNA, but direct evidence that this inhibition limits the replication of HIV-1 has been lacking. In the present study we examined whether the expression of FLAG-tagged HEXIM1 (HEXIM1-f) affected lentiviral replication in human T cell lines. Methods:HEXIM1-f was introduced to five human T cell lines, relevant host for HIV-1, by murine leukemia virus vector and cells expressing HEXIM1-f were collected by fluorescence activated cell sorter. The lentiviral replication kinetics in HEXIM1-f-expressing cells was compared with that in green fluorescent protein (GFP)-expressing cells. Results:HIV-1 and simian immunodeficiency virus replicated less efficiently in HEXIM1-f-expressing cells than in GFP-expressing cells of the five T cell lines tested. The viral revertants were not immediately selected in culture. In contrast, the replication of vaccinia virus, adenovirus, and herpes simplex virus type 1 was not limited. The quantitative PCR analyses revealed that the early phase of viral life cycle was not blocked by HEXIM1. On the other hand, Tat-dependent transcription in HEXIM1-f-expressing cells was substantially repressed as compared with that in GFP-expressing cells. Conclusion:These data indicate that HEXIM1 is a host factor that negatively regulates lentiviral replication specifically. Elucidating the regulatory mechanism of HEXIM1 might lead to ways to control lentiviral replication.
Impaired sensory functioning in elders: the relation with its potential determinants and nutritional intake.

This study assessed the relation of an impaired taste and smell perception with (a) potential determinants and (b) nutritional intake and status in elderly people. Determinants examined were age, gender, functional category (institutionalized vs independently living), dental state, illnesses, smoking behavior, drug usage, and saliva excretion and composition. Nutritional intake and status were measured by an "appetite and hunger" questionnaire, a food frequency questionnaire, and body mass index (BMI). In order to have access to a large heterogeneous group, two different categories of elderly people were studied. We enrolled independently living elders (n=89) assumed to have a relatively good taste and smell perception, and institutionalized elders (n=67) with a potential poorer taste and smell perception. Scores at the smell identification (range: 0-10) and taste perception (range: 0-4) test were, respectively, 5.7 (independently living) versus 3.5 (institutionalized); p < . 0001 and 3.3 versus 3.0; p < . 05. Correlation between smell test scores and outcomes of the "appetite and hunger" questionnaire ranged from r: . 19 to . 50; p values < . 05. There was, however, no clear correlation of any sensory outcome with energy and food intake, nor with BMI. Regression analyses revealed that age and the functional category were the most important determinants of the scores on the taste perception and smell identification tests. It is concluded that a poor performance on sensory tests is related to a poor appetite but not necessarily to low energy intake or low BMI. Age-related factors and smoking are important determinants of impaired sensory functioning.
Unbiaedness and Cointegration Testing: The Case of AFET

This paper studies the efficiency in the Agricultural Futures Exchange of Thailand or AFET by means of the unbiased expectation hypothesis of futures. With non-stationarity problem in financial time series leading to unreliable results, this paper applies Cointegration methodology to solve the problem and employs the unbiased expectation hypothesis as the model for the empirical test. Though futures and spot prices are cointegrated, the rejection of the parameters restriction test is found. The final result shows that the futures of Ribbed Smoked Sheet no.3 (RSS3) is the only unbiased predictor, while White Rice 5% (BWR5) and Tapioca Chip (TC) are not.
Consumer Demand for Dairy Alternative Beverages in the United States and its Implications to U.S. Dairy Industry

Production and consumption of dairy alternative beverages in the United States has been on the rise as per capita consumption of fluid milk continues to fall. Almond milk and soymilk are the fastest growing categories in the U.S. dairy alternative marketplace. Using household-level purchase data from 2011 Nielsen Homescan panel and tobit econometric procedure, the conditional and unconditional own-price, cross-price and income elasticities for soymilk and almond milk will be estimated. Income, age, employment status, education level, race, ethnicity, region and presence of children are significant drivers affecting the demand for dairy alternative beverages, such as almond milk and soy milk. This paper investigates the growth of the dairy alternative beverage market in the United States and its implications for dairy farmer welfare.
Recovery from Crises and Lending

During the recovery from the recent crisis, the general role of lending in economic growth, and particularly in the recovery from financial crises, has become an important issue. In this paper, we review the major differences between creditless recovery episodes and recoveries accompanied by growth of credit. Based on the literature, we find that creditless recoveries are relatively frequent phenomena: a quarter or one-fifth of all real economy recoveries take place without the growth of credit. The rate of economic growth is permanently lower during creditless recoveries than in episodes accompanied by credit expansion. Thus, lending activity of the financial intermediary system is usually necessary for fast recovery. When analysing the recovery from the current crisis, we find that a number of factors exist that predispose to creditless recovery. The current growth, the rate of which is lower than before the crisis, is taking place – both in the Member States of the European Union and in Hungary – with a decrease or stagnation of the credit stock. In the medium and long term, it is essential for the sustained growth of the real economy that loans granted by the financial intermediary system once again start to increase.
A gene expression profile for non-smoking and non-drinking patients with head and neck cancer.

OBJECTIVE A small subset of patients with head and neck squamous cell carcinoma are non-smoking and non-drinking and have distinct clinical characteristics. We aimed to identify a possible different genetic profile for these patients when compared with their smoking and drinking counterparts. MATERIALS AND METHODS The gene expression data previously detected from primary tumors located in the oral cavity and oropharynx, using DNA microarray was analyzed for their differential expression between non-smoking and non-drinking patients (n = 15) and smoking and drinking patients (n = 89). Student's T-test (P < 0.05) and 10-fold cross-validation procedure (100 times repeated) were performed to determine differentially expressed genes. RESULTS Non-smoking and non-drinking patients were older, mostly female and had oral cavity-localized tumors, whereas smoking and drinking patients were younger male patients with 81% oral cavity and 19% oropharynx tumors. A set of 49 differentially expressed genes were detected. Among others, seven genes related to interferon-γ were upregulated and two genes linked to NFKB pathway were downregulated. CONCLUSIONS Differentially expressed genes in non-smoking and non-drinking patients possibly indicate the presence of a different cellular response to carcinogenic events in these patients. Further studies are warranted to validate this gene set and explore possible therapeutic implications to improve prognosis for these patients.
Neurofibromin Is Required for Barrel Formation in the Mouse Somatosensory Cortex

The rodent barrel cortex is a useful system to study the role of genes and neuronal activity in the patterning of the nervous system. Several genes encoding either intracellular signaling molecules or neurotransmitter receptors are required for barrel formation. Neurofibromin is a tumor suppressor protein that has Ras GTPase activity, thus attenuating the MAPK (mitogen-activated protein kinase) and and PI-3 kinase (phosphatidylinositol 3-kinase) pathways, and is mutated in humans with the condition neurofibromatosis type 1 (NF1). Neurofibromin is widely expressed in the developing and adult nervous system, and a common feature of NF1 is deficits in intellectual development. In addition, NF1 is an uncommonly high disorder among individuals with autism. Thus, NF1 may have important roles in normal CNS development and function. To explore roles for neurofibromin in the development of the CNS, we took advantage of a mouse conditional allele. We show that mice that lack neurofibromin in the majority of cortical neurons and astrocytes fail to form cortical barrels in the somatosensory cortex, whereas segregation of thalamic axons within the somatosensory cortex appears unaffected.
Romanian intra-industry trade: a panel data approach

This research examines the determinants of intra-industry trade (IIT) in the automobile components sector in Romania. Following previous studies, our manuscript applies a gravity model equation with panel data. The dependent variable used is IIT in automobile components. The analysis of the determinants of IIT is undertaken using a panel approach. The panel data models were estimated with Pooled OLS, fixed effects (FE) and random effects (RE) estimators. The results are presented with country characteristics as explanatory variables, and the models have four statistically significant variables. This research adds significant contribution to the intra-industry trade topic. Little academic attention has been devoted to the Romanian experience. The trade in the automobile components sector between Romania and some European countries (Austria, Belgium, Bulgaria, Croatia, Czech Republic, France, Germany, Hungary, Italy, Netherlands, Poland and Turkey) was examined, between 1995 and 2008. Using a panel data approach, the results show a positive correlation between endowments and IIT. The results indicate that the Romanian IIT is explained by differentiated quality, i.e. vertical specialization. Our study also consider economic dimension, this proxy confirms the positive effect of IIT, and so the market size is important to differentiated product. The economic model also confirms the hypothesis that volume of trade increases if the transportation costs decreases.