Miracle-dz/UniFAR-FTUs huggingface dataset:
Tracing Evolutionary Footprints to Identify Novel Gene Functional Linkages

Systematic determination of gene function is an essential step in fully understanding the precise contribution of each gene for the proper execution of molecular functions in the cell. Gene functional linkage is defined as to describe the relationship of a group of genes with similar functions. With thousands of genomes sequenced, there arises a great opportunity to utilize gene evolutionary information to identify gene functional linkages. To this end, we established a computational method (called TRACE) to trace gene footprints through a gene functional network constructed from 341 prokaryotic genomes. TRACE performance was validated and successfully tested to predict enzyme functions as well as components of pathway. A so far undescribed chromosome partitioning-like protein ro03654 of an oleaginous bacteria Rhodococcus sp. RHA1 (RHA1) was predicted and verified experimentally with its deletion mutant showing growth inhibition compared to RHA1 wild type. In addition, four proteins were predicted to act as prokaryotic SNARE-like proteins, and two of them were shown to be localized at the plasma membrane. Thus, we believe that TRACE is an effective new method to infer prokaryotic gene functional linkages by tracing evolutionary events.
CD133 Is a Marker of Bioenergetic Stress in Human Glioma

Mitochondria dysfunction and hypoxic microenvironment are hallmarks of cancer cell biology. Recently, many studies have focused on isolation of brain cancer stem cells using CD133 expression. In this study, we investigated whether CD133 expression is regulated by bioenergetic stresses affecting mitochondrial functions in human glioma cells. First, we determined that hypoxia induced a reversible up-regulation of CD133 expression. Second, mitochondrial dysfunction through pharmacological inhibition of the Electron Transport Chain (ETC) produced an up-regulation of CD133 expression that was inversely correlated with changes in mitochondrial membrane potential. Third, generation of stable glioma cells depleted of mitochondrial DNA showed significant and stable increases in CD133 expression. These glioma cells, termed rho 0 or ρ0, are characterized by an exaggerated, uncoupled glycolytic phenotype and by constitutive and stable up-regulation of CD133 through many cell passages. Moreover, these ρ0 cells display the ability to form “tumor spheroids” in serumless medium and are positive for CD133 and the neural progenitor cell marker, nestin. Under differentiating conditions, ρ0 cells expressed multi-lineage properties. Reversibility of CD133 expression was demonstrated by transfering parental mitochondria to ρ0 cells resulting in stable trans-mitochondrial “cybrid” clones. This study provides a novel mechanistic insight about the regulation of CD133 by environmental conditions (hypoxia) and mitochondrial dysfunction (genetic and chemical). Considering these new findings, the concept that CD133 is a marker of brain tumor stem cells may need to be revised.
Case Study of Feed-in Tariff Personal Carbon Allowance

Since the Great East Japan Earthquake, Japanese energy and climate problems have reached a critical junction that requires an innovative energy and environmental policy. The idea of a Personal Carbon Allowance (PCA) system, which has been under discussion in the United Kingdom, is one of the innovative policies with the potential to solve related issues in Japan. The authors are proposing a Feed-in Tariff PCA (FIT-PCA) as a suitable policy for Japan to encourage citizens to manage CO2 emissions in their daily personal lives and to improve their attitudes towards global environmental issues. In the psychological model we developed to study behavioural changes arising from the use of a PCA system, one assumption was that the experience of living with a FIT-PCA would stimulate loss aversion, goal setting, eudaimonia and pro-environmental life style changes. We conducted a simulation for six months with the cooperation of 30 households to investigate the validity of the model, monitor changes in energy reduction behaviours and encourage more responsible attitudes towards global environmental issues.
Total calories, body weight, and tumor incidence in mice.

The relation between total caloric intake, body weight, and tumorigenesis, as well as the independence of these effects from those of dietary fat, were evaluated using data from 82 published experiments involving several tumor sites in mice. Comparing experimental (calorie restricted) to control (ad libitum) groups showed that the former consumed 29% fewer calories (experimental groups consumed fewer calories than control groups in all but a few isocaloric experiments), 50% less total fat, 11% less protein, and weighed 25% less than control animals. Adult body weight was highly correlated to caloric intake in both males (r = 0.85) and females (r = 0.74), although this correlation decreased with increasing caloric intake. Cumulative tumor incidence was, on average, 42% lower in the restricted groups. Multivariate regression analyses revealed that, regardless of the level of dietary fat, tumor incidence increased with increasing caloric intake and body weight over a wide range of intakes, including moderate caloric restriction (i.e., 7-20%). These data indicate that total caloric intake is an important determinant of tumorigenesis in mice, and that body weight may be a more sensitive indicator for this effect than is caloric intake alone.
On Signal Detection in the Presence of Weakly Correlated Noise over Fading Channels

In cognitive radio networks, in order to avoid interference form secondary users to the primary license holders of the spectrum, reliable spectrum sensing is necessary. In scenarios where the noise samples are correlated, the spectrum sensing methods optimized considering impairment by independent noise samples will not provide optimum performances. To address this issue, a locally optimum detection method for random signals under a weakly correlated noise model over fading channels is proposed. The probabilities of false alarm and detection of the proposed detector in the low signal to noise ratio regime are analyzed. The average probabilities are calculated over different channel gains. Numerical and simulation results demonstrate the superiority of the proposed method over the known energy detection method with comparable complexities. Furthermore, we consider the scenario where the estimated correlation is different from the real correlation and investigate the effect of this correlation mismatch on the probabilities of false alarm and detection of the proposed method.
The Future Euro-Polity and its Impact upon Private Interest Governance within Member-States

Le futur systeme politique europeen et son impact sur les gouvernements prives au niveau national. Les gouvernements d'interets par association privee (GIAPs) sont menaces au niveau national et faiblement encourages au niveau supra-national par l'Acte Unique et le Traite de Maastricht. On commence seulement a entrevoir l'impact du marche unique et du principe de reconnaissance mutuelle sur les GIAPs les plus enracines. Le resultat eventuel dependra de la competition entre deux principes de la prise de decision dans la Communaute : celui de la regionalisation et celui de la sectorisation, aussi bien que de l'emergence de systemes plus directs de regulation politique.
USER-PREFERENCE PARTICLE SWARM ALGORITHM FOR AIRFOIL DESIGN ARCHITECTURE

Airfoil optimization frameworks rely on extensive computational resources to provide the most feasible design for the required flight condition. Extending the framework to encompass multiple design criteria adds further complexity due to the conflicting nature of the design objectives. In this paper, we propose the integration of designerdriven preferences into a multi-objective particle swarm heuristic to efficiently navigate the design space. This results in a highly accurate and proficient rate of convergence, since only preferred regions of the Pareto landscape are explored. The algorithm is introduced and applied to a typical transonic airfoil design scenario where the objective value is provided by a Reynolds-averaged Navier-Stokes solver. Experimental case-studies are presented, which highlight the computational efficiency of the user-preference algorithm.
UP-TO-DATE CORONARY ARTERY BYPASS GRAFT SURGERY

The experimental and clinical efforts of Demikov and Kolesov between 1952 and 1964 related to coronary anastomosis between the internal thoracic artery and left anterior descending artery on a beating heart. Sones and Shirey (Cleveland, 1962) were pioneers of selective coronary angiography. The first coronary artery bypass grafting using a saphenous vein graft was performed by Garrett, Dennis, and DeBakey in Houston in 1964. Since that time, coronary surgery has become one of the most frequently performed surgical procedures in the world. Coronarography can be considered the golden standard of diagnostics. Current supplements to coronarography are: functional assesment of the fractional flow reserve; intravascular ultrasound; and optical coherence tomography, for the estimation of atherosclerotic plaque. When combined, these techniques provide high-quality diagnoses. Diagnostic coronarography is followed by percutaneous coronary procedures, the results of which are comparable to those of coronary surgery. Prerequisites of coronary artery bypass grafting (CABG) are grafts and vascular conduits. Alternative flow into ischaemic myocardial territory takes place across these vascular conduits. Usage of the left internal mammary artery is a proven superior standard in operative surgery, due to its better survival rates and prevention of massive myocardial reinfarction. Saphenous vein grafts are most frequently used in the myocardial territory that is not supplied by the left anterior descending artery. In 2018, we will have the final results of the ART trial, which is testing the usage of arterial grafts in coronary surgery. Preliminary results show superiority of the right internal mammary artery as a graft when compared with other arterial grafts (except the left internal mammary artery). Nowadays, myocardial revascularisation with cardiopulmonary bypass is perfomed in 7580% of cases. Off-pump coronary artery bypass (beating heart) surgery is performed in 20% of cases. Besides these procedures, there are less invasive procedures such as minimal invasive direct coronary bypass (MIDCAB), totally endoscopic coronary bypass (TECAB) and
Bladder cancer stem cells: clonal origin and therapeutic perspectives

In this article, we review the origin and therapeutic perspectives of bladder cancer stem cells (BCSCs), which are integral to the initiation, high recurrence and chemoresistance of bladder cancer. BCSCs are heterogenous and originate from multiple cell types, including urothelial stem cells and differentiated cell types, including basal, intermediate stratum and umbrella cells. Cell surface markers, including CD44, CD67LR, EMA, ALDH1A1 and BCMab1, are used to identify and isolate BCSCs. The Hedgehog, Notch, Wnt and JAK-STAT signaling pathways play key roles in maintaining the stemness, self-renewal and proliferative potential of BCSCs. High expression of ABC transporters, acetaldehyde dehydrogenase, antioxidants and apoptosis resistance proteins in BCSCs play a critical role in chemoresistance. Consequently, a greater understanding of the biology of BCSCs will be important for identifying effective therapeutic targets to improve clinical outcomes for bladder cancer patients.
Organizational Values and Their Relation to Organizational Performance Outcomes

The communication of organizational values and their relation to employee outcomes is evaluated between two departments within a Health Care Organization. Organizational values that are congruent with employees' values have been shown to increase employee satisfaction, commitment, and performance outcomes. This article discusses how values are defined and different ways that values can be communicated to acquire improved organizational outcomes. Past research on values within organizations is reviewed. Questions from the Organizational Culture Survey and the Communication Satisfaction Questionnaire are combined to measure employee satisfaction, morale, and perceived involvement in decision making. The organization provided data on employee absenteeism, turnover, and performance ratings. An analysis of the results indicates employees in departments that have clearly defined and communicated organizational values perceive they are more involved in the organization and more participatory in decision making. Implications of the results for organizations are detailed.
Synthesis of Enantiomerically Pure Bis(hydroxymethyl)-Branched Cyclohexenyl and Cyclohexyl Purines as Potential Inhibitors of HIV.

The synthesis of the enantiomerically pure bis(hydroxymethyl)-branched cyclohexenyl and cyclohexyl purines is described. Racemic trans-4,5-bis(methoxycarbonyl)cyclohexene [(+/-)-6] was reduced with lithium aluminum hydride to give the racemic diol (+/-)-7. Resolution of (+/-)-7 via a transesterification process using lipase from Pseudomonas sp. (SAM-II) gave both diols in enantiomerically pure form. The enantiomerically pure diol (S,S)-7was benzoylated and epoxidized to give the epoxide 9. Treatment of the epoxide 9 with trimethylsilyl trifluoromethanesulfonate and 1,5-diazabicyclo[5.4. 0]undec-5-ene followed by dilute hydrochloric acid gave (1R,4S,5R)-4,5-bis[(benzoyloxy)methyl]-1-hydroxycyclohex-2-ene (10). Acetylation of 10 gave (1R,4S,5R)-1-acetoxy-4,5-bis[(benzoyloxy)methyl]cyclohex-2-ene (11). (1R,4S,5R)-1-Acetoxy-4,5-bis[(benzoyloxy)methyl]cyclohex-2-ene (11) was converted to the adenine derivative 12 and guanine derivative 13 via palladium(0)-catalyzed coupling with adenine and 2-amino-6-chloropurine, respectively. Hydrogenation of 12 and 13 gave the correspondning saturated adenine derivative 14 and guanine derivative 15. (1R,4S,5R)-4,5-Bis[(benzoyloxy)methyl]-1-hydroxycyclohex-2-ene (10) was converted to the adenine derivative 16 and guanine derivative 17 via coupling with 6-chloropurine and 2-amino-6-chloropurine, respectively, using a modified Mitsunobu procedure. Hydrogenation of 16 and 17 gave the corresponding saturated adenine derivative 18 and guanine derivative 19. Compounds 12-19 were evaluated for activity against human immunodeficiency virus (HIV), but were found to be inactive. Further biological testings are underway.
Emergence of Aminoglycoside Resistance Due to armA methylase in Multi-drug Resistant Acinetobacter Baumannii Isolates in a University Hospital in Nepal.

BACKGROUND The emergence of multidrug-resistant Acinetobacter baumannii associated with hospital-acquired infections has been increasingly reported worldwide. 16S rRNA methylase producing Gram-negative bacteria are highly resistant to all clinically important aminoglycosides. We analyzed A. baumannii clinical isolates resistant to aminoglycosides from hospitalized patients. The objective of this study was to investigate the emergence of armA in A.baumannii species associated with nosocomial infection in a university hospital in Nepal. METHODS This was a cross-sectional study conducted at the department of Clinical Microbiology, Tribhuvan University Teaching Hospital (TUTH), from December 2013 to December 2014. A total of 246 Acinetobacter species were isolated from different patients were screened for MDR A. baumannii. Identification at the species level was confirmed by 16S rRNA sequencing. Drug susceptibility testing was performed by Kirby- Bauer disc diffusion method and minimum inhibitory concentrations (MICs) were determined using the guidelines of the Clinical and Laboratory Standards Institute (CLSI). Screening for 16S rRNA methylase-production was done for the isolates resistant to gentamicin and amikacin. Detection of 16S rRNA methylase gene was done by PCR. RESULTS All 122 multidrug-resistant A. baumanniiisolates were resistant to majority of the antibiotics used except polymyxin and tigecycline. Ninty-six MDR A. baumannii isolates had MICs of > 512 mg/L to amikacin and arbekacin indicating their high resistance to aminoglycosides.Of the 96 pan-aminoglycoside resistant isolates, 75 isolates had 16SrRNAmethylasewith all isolates harboring armA gene. CONCLUSIONS This is the first report describing multidrug-resistant A. baumannii strains harboring armA from hospitalized patients in Nepal. A methylase gene (armA), conferring high level of resistance to aminoglycosides, was detected in majority of our isolates.
Rule Extraction From Support Vector Machines Using Ensemble Learning Approach: An Application for Diagnosis of Diabetes

Diabetes mellitus is a chronic disease and a worldwide public health challenge. It has been shown that 50-80% proportion of T2DM is undiagnosed. In this paper, support vector machines are utilized to screen diabetes, and an ensemble learning module is added, which turns the “black box” of SVM decisions into comprehensible and transparent rules, and it is also useful for solving imbalance problem. Results on China Health and Nutrition Survey data show that the proposed ensemble learning method generates rule sets with weighted average precision 94.2% and weighted average recall 93.9% for all classes. Furthermore, the hybrid system can provide a tool for diagnosis of diabetes, and it supports a second opinion for lay users.
Rate-distortion analysis for MPEG-4 binary shape coding

In this paper, we propose a statistical learning based approach to analyze the rate-distortion characteristics of MPEG-4 binary shape coding. We employ the polynomial kernel function and /spl epsi/-insensitive loss function for our support vector regression. Our experimental results show that the proposed approach can achieve good performance, e.g., modelling the rate-distortion curves accurately.
11-Deoxycortisol is a corticosteroid hormone in the lamprey

Corticosteroid hormones are critical for controlling metabolism, hydromineral balance, and the stress response in vertebrates. Although corticosteroid hormones have been well characterized in most vertebrate groups, the identity of the earliest vertebrate corticosteroid hormone has remained elusive. Here we provide evidence that 11-deoxycortisol is the corticosteroid hormone in the lamprey, a member of the agnathans that evolved more than 500 million years ago. We used RIA, HPLC, and mass spectrometry analysis to determine that 11-deoxycortisol is the active corticosteroid present in lamprey plasma. We also characterized an 11-deoxycortisol receptor extracted from sea lamprey gill cytosol. The receptor was highly specific for 11-deoxycortisol and exhibited corticosteroid binding characteristics, including DNA binding. Furthermore, we observed that 11-deoxycortisol was regulated by the hypothalamus–pituitary axis and responded to acute stress. 11-Deoxycortisol implants reduced sex steroid concentrations and up-regulated gill Na+, K+-ATPase, an enzyme critical for ion balance. We show here that 11-deoxycortisol functioned as both a glucocorticoid and a mineralocorticoid in the lamprey. Our findings indicate that a complex and highly specific corticosteroid signaling pathway evolved at least 500 million years ago with the arrival of the earliest vertebrate.
Detecting depression: A comparison between spontaneous and read speech

Major depressive disorders are mental disorders of high prevalence, leading to a high impact on individuals, their families, society and the economy. In order to assist clinicians to better diagnose depression, we investigate an objective diagnostic aid using affective sensing technology with a focus on acoustic features. In this paper, we hypothesise that (1) classifying the general characteristics of clinical depression using spontaneous speech will give better results than using read speech, (2) that there are some acoustic features that are robust and would give good classification results in both spontaneous and read, and (3) that a `thin-slicing' approach using smaller parts of the speech data will perform similarly if not better than using the whole speech data. By examining and comparing recognition results for acoustic features on a real-world clinical dataset of 30 depressed and 30 control subjects using SVM for classification and a leave-one-out cross-validation scheme, we found that spontaneous speech has more variability, which increases the recognition rate of depression. We also found that jitter, shimmer, energy and loudness feature groups are robust in characterising both read and spontaneous depressive speech. Remarkably, thin-slicing the read speech, using either the beginning of each sentence or the first few sentences performs better than using all reading task data.
Flexible and streamline composite material optical fibre connector-less interface

A flexible, streamline and lightweight optical fibre connector-less interface composed of composite materials has been developed. Light is coupled in and out of the interface via a fibre launch system. A fibre Bragg grating (FBG) is embedded into the composite structure in order to investigate the optical performance of the interface. It is shown that an optical connection is maintained between the interface and multimode fibre in the cyclic test.
Sphere and Dot Product Representations of Graphs

A graph G is a k-sphere graph if there are k-dimensional real vectors v1,…,vn such that ij∈E(G) if and only if the distance between vi and vj is at most 1. A graph G is a k-dot product graph if there are k-dimensional real vectors v1,…,vn such that ij∈E(G) if and only if the dot product of vi and vj is at least 1.By relating these two geometric graph constructions to oriented k-hyperplane arrangements, we prove that the problems of deciding, given a graph G, whether G is a k-sphere or a k-dot product graph are NP-hard for all k>1. In the former case, this proves a conjecture of Breu and Kirkpatrick (Comput. Geom. 9:3–24, 1998). In the latter, this answers a question of Fiduccia et al. (Discrete Math. 181:113–138, 1998). Furthermore, motivated by the question of whether these two recognition problems are in NP, as well as by the implicit graph conjecture, we demonstrate that, for all k>1, there exist k-sphere graphs and k-dot product graphs such that each representation in k-dimensional real vectors needs at least an exponential number of bits to be stored in the memory of a computer. On the other hand, we show that exponentially many bits are always enough. This resolves a question of Spinrad (Efficient Graph Representations, 2003).
Phase Noise Performances of a Cross-Coupled CMOS VCO with Resistor Tail Biasing

The voltage controlled oscillator (VCO) is a fundamental block in RF IC architectures. Today's wireless communication applications do require a high level of performances from such a circuit, and specifically its phase noise figure and its power consumption. In fact, modern standards often demand for phase noise level better than -95 dBc/Hz at 100 KHz in the vast majority of cases, with supply voltages approaching the 1 V range. This paper presents the design challenges of a cross-coupled 1.8 GHz CMOS voltage controlled oscillator with a tuning range of 7%, and a phase noise figure of -113 dBc/Hz at an offset frequency of 100 KHz. It employs a resistor for biasing, avoiding in this way the common tail current source based on active circuitry (e.g. current mirrors in CMOS designs). This choice prevents the 1/f device noise upconversion, leading to an improved spectral purity. Since phase noise also varies with the reciprocal of the tail current, a trade-off can be established between noise performances and power consumption by simply changing the biasing resistor. The same circuit topology may thus be useful for building VCOs whose applications range from high performance wireless standards where an extremely low phase noise is mandatory, to low-cost portable systems where the reduced power drain is of major concern