Miracle-dz/UniFAR-FTUs huggingface dataset:
Pairs in Yeast.

Genes encoded close to one another on the chromosome are often coexpressed, by a mechanism and regulatory logic that remain poorly understood. We surveyed the yeast genome for tandem gene pairs oriented tail-to-head at which expression antisense to the upstream gene was conserved across species. The intergenic region at most such tandem pairs is a bidirectional promoter, shared by the downstream gene mRNA and the upstream antisense transcript. Genomic analyses of these intergenic loci revealed distinctive patterns of transcription factor regulation. Mutation of a given transcription factor veriﬁed its role as a regulator in trans of tandem gene pair loci, including the proximally initiating upstream antisense transcript and downstream mRNA and the distally initiating upstream mRNA. To investigate cis -regulatory activity at such a locus, we focused on the stress-induced NAD(P)H dehydratase YKL151C and its downstream neighbor, the metabolic enzyme GPM1 . Previous work has implicated the region between these genes in regulation of GPM1 expression; our mutation experiments established its function in rich medium as a repressor in cis of the distallyinitiating YKL151C senseRNA,andanactivatoroftheproximallyinitiating YKL151C antisenseRNA.Wild-typeexpressionofall three transcripts required the transcription factor Gcr2. Thus, at this locus, the intergenic region serves as a focal point of regulatory input, driving antisense expression and mediating the coordinated regulation of YKL151C and GPM1 . Together, our ﬁndings impli-cate transcription factors in the joint control of neighboring genes specialized to opposing conditions and the antisense transcripts expressed between them.
Approaches for Utility-Based QOE/QOS Architecture for Streaming Server in a Heterogeneous Wireless Device Based on SVM

: The convergence of developing real-time interactive program services, the cumulative coverage of wireless networks and the ever-growing admiration of mobile devices, are important in an era of user-centric multimedia wireless services. In this state, heterogeneous infrastructures will co-exist and make certain that the end-user is continuously best associated. The arduous networking loads of wireless multimedia classifications, farther than quality-oriented regulator approaches, are essential to guarantee the best user knowledge terminated time. This paper benevolences some of the current developments in multimedia networking directing principally in areas that have been receiving consideration recently and are predictable to continue to make supplementary interests in the coming years. These areas consist of Quality of Experience (QoE) and a number of related calibration issues, Content Distribution Networks (CDNs), multimedia infrastructures. Simulation consequences illustration the impact and benefit of the proposed result in multi access and multi-operator wireless circumstances by using independent and individual QoE metrics.
Statistical Issues in Combining Multiple Genomic Studies: Quality Assessment, Dimension Reduction and Integration of Transcriptomic and Phenomic Data

Genomic meta-analysis has been applied to many biological problems to gain more power from increased sample sizes and to validate the result from an individual study. As for the study selection criteria, however, most literatures depend on qualitative or ad-hoc numerical methods, and there has not been an effort to develop a rigorous quantitative evaluation framework. In this thesis, we proposed several quantitative measures to assess the quality of a study for a meta-analysis. We have applied the proposed integrative criteria to multiple microarray studies to screen out inappropriate studies and also confirmed the necessity of proper exclusion criteria using real meta-analyses. By simulation studies, we showed the effectiveness and robustness of the proposed criteria. Secondly, we have investigated simultaneous dimension reduction frameworks for down-stream genomic meta-analysis. Currently, most microarray meta-analyses focus on detecting biomarkers; however, it is also valuable to seek a possibility of meta-analysis in unsupervised or supervised machine learning, particularly dimension reduction when multiple studies are combined. We proposed several simultaneous dimension reduction methods using principal component analysis (PCA). Using five examples of real microarray data, we showed the information gain obtained by adopting our proposed procedures in terms of better visualization and prediction accuracy. In the third component, we pursued a novel approach to elucidate undefined disease phenotypes between interstitial lung disease (ILD) or chronic obstructive pulmonary disease (COPD). By applying unsupervised learning technique to both clinical phenotypes and gene expression data obtained from well characterized large number of cohort, we successfully showed the existence of intermediate phenotypic group who have both disease characteristics and divergent phenotypes in clinical and molecular features. Public health importance of our findings is that we showed current clinical definitions and classification do not account for the large number of patients having intermediate phenotypes or less common features that are often excluded from clinical trials and epidemiology reports.
Neighbour urban wastewater treatment plants display distinct profiles of bacterial community and resistance genes

29 Urban wastewater treatment plants (UWTPs) are among the major recipients of antibiotic- 30 resistant bacteria (ARB), antibiotic resistance genes (ARGs) and antibiotic residues in urban 31 environments. Although during treatment bacteria of human and animal origin are removed, 32 some are able to survive, persisting in the final effluent. The occurrence of these bacteria, 33 especially those harbouring ARGs, may have a direct impact on the quality of the treated 34 wastewater that is returned to the environment. In this study, we aimed to assess if the final 35 effluent bacterial communities of three UWTPs (PT1, PT2, and PT3) located next to each other, 36 were distinct and if such differences were related with the antibiotic resistance profiles. 37 It was observed that the bacterial community (16S rRNA gene Illumina sequencing) and load 38 of selected ARGs of final effluent differed among the three UWTP, irrespective of sampling 39 time. Members of the families Aeromonadaceae , Campylobacteraceae , Veillonellaceae, 40 Weeksellaceae , and Porphyromonadaceae were observed to be positively correlated with some 41 ARGs ( bla CTX–M , bla OXA-A , bla SHV ) and intI1 (p<0.05), while Intrasporangiaceae were observed to 42 be negatively correlated. While Aeromonadaceae are recognized relevant ARGs harbours, the 43 other bacterial families may represent bacteria that co-exist with the ARGs hosts, which may 44 belong to minor bacterial groups, omitted in the analyses. These findings suggest the 45 importance of bacterial dynamics during treatment to the ARB&ARGs removal, a rationale that 46 may contribute to design new strategies to apply in the UWTPs to prevent the spread of 47 antibiotic resistance.
A Mathematical Model and MATLAB Code for Muscle–Fluid–Structure Simulations Integrative and Comparative Biology

symposium and Faculty to Quantitative Biology Through Active Learning’’ Synopsis This article provides models and code for numerically simulating muscle–fluid–structure interactions (FSIs). This work was presented as part of the symposium on Leading Students and Faculty to Quantitative Biology through Active Learning at the society-wide meeting of the Society for Integrative and Comparative Biology in 2015. Muscle mechanics and simple mathematical models to describe the forces generated by muscular contractions are introduced in most biomechanics and physiology courses. Often, however, the models are derived for simplifying cases such as isometric or isotonic contractions. In this article, we present a simple model of the force generated through active contraction of muscles. The muscles’ forces are then used to drive the motion of flexible structures immersed in a viscous fluid. An example of an elastic band immersed in a fluid is first presented to illustrate a fully-coupled FSI in the absence of any external driving forces. In the second example, we present a valveless tube with model muscles that drive the contraction of the tube. We provide a brief overview of the numerical method used to generate these results. We also include as Supplementary Material a MATLAB code to generate these results. The code was written for flexibility so as to be easily modified to many other biological applications for educational purposes.
Carbon Dioxide and Ozone in High School Classrooms APPROVED BY SUPERVISING COMMITTEE:

This paper reports findings about ventilation taken from a larger study of 30 high school classrooms in central Texas. Classrooms in portable buildings and permanent structures were sampled twice for four consecutive school days in the 2015-2016 school year. Carbon dioxide (CO2) concentrations were measured in the supply airstream and the general room space. Average and peak CO2 concentrations were used to estimate the risk of cold and flu transmission in schools during months of elevated sickness. It was found that average CO2 concentrations during the occupied period in 81% of classrooms sampled in Fall 2015 and 72% of classrooms sampled in Spring 2016 exceeded the ASHRAE 62.1 recommendation for fresh air. When peak CO2 concentrations during the same time periods were considered, 92% and 95% of classrooms in Fall 2015 and Spring 2016 exceeded this recommendation, respectively. Nighttime air exchange rates and occupied fresh air exchange rates were calculated for portable and permanent classrooms, and findings indicate that portable classrooms are dominated by occupant behavior, leaky building envelopes, and weather patterns.
The student resilience survey

Background: Policies, designed to promote resilience, and research, to understand the determinants and correlates of resilience, require reliable and valid measures to ensure data quality. The student resilience survey (SRS) covers a range of external supports and internal characteristics which can potentially be viewed as protective factors and can be crucial in exploring the mechanisms between protective factors and risk factors, and to design intervention and prevention strategies. This study examines the validity of the SRS. Methods: 7663 children (aged 11–15 years) from 12 local areas across England completed the SRS, and questionnaires regarding mental and physical health. Psychometric properties of 10 subscales of the SRS (family connection, school connection, community connection, participation in home and school life, participation in community life, peer support, self-esteem, empathy, problem solving, and goals and aspirations) were investigated by confirmatory factor analysis (CFA), differential item functioning (DIF), differential test functioning (DTF), Cronbach’s α and McDonald’s ω . The associations between the SRS scales, mental and physical health outcomes were examined. Results: The results supported the construct validity of the 10 factors of the scale and provided evidence for acceptable reliability of all the subscales. Our DIF analysis indicated differences between boys and girls, between primary and secondary school children, between children with or without special educational needs (SEN) and between children with or without English as an additional language (EAL) in terms of how they answered the peer support subscale of the SRS. Analyses did not indicate any DIF based on free school meals (FSM) eligibility. All subscales, except the peer support subscale, showed small DTF whereas the peer support subscale showed moderate DTF. Correlations showed that all the student resilience subscales were negatively associated with mental health difficulties, global subjective distress and impact on health. Random effects linear regression models showed that family connection, self-esteem, problem solving and peer support were negatively associated with all the mental health outcomes. Conclusions: The findings suggest that the SRS is a valid measure assessing these relevant protective factors, thereby serving as a valuable tool in resilience and mental health research.
A Specific Inhibitor of Phosphatidylinositol 3=Kinase,

Phosphatidylinositol (PtdIns) 3-kinase is an enzyme implicated in growth factor signal transduction by asso-ciating with receptor and nonreceptor tyrosine kinases, including the platelet-derived growth factor receptor. Inhibitors of PtdIns 3-kinase could potentially give a better understanding of the function and regulatory mechanisms of the enzyme. Quercetin, a naturally occurring bioflavinoid, was previously shown to inhibit PtdIns 3-kinase with an ICm of 1.3 pg/ml (3.8 p ~ ) ; inhibition appeared to be directed at the ATP-binding site of the kinase. Analogs of quercetin were investigated as PtdIns 3-kinase inhibitors, with the most potent ones exhibiting IC,, values in the range of 1.7-8.4 pg/ml. In contrast, genistein, a potent tyrosine kinase inhibitor of the isoflavone class, did not inhibit PtdIns 3-kinase sig- nificantly (ICso > 30 pg/ml). Since quercetin has also been shown to inhibit other PtdIns and protein kinases, other chromones were evaluated as inhibitors of PtdIns 3-kinase without affecting PtdIns 4-kinase or selected protein kinases. One such compound, 2-(4-morpholinyl)-8-phenyl-4H-l-benzopyran-4-one (also known as 2-(4-morpholinyl)-8-phenylchromone, mg/ml phosphati- dylinositol, and 20 PM [y-"P]ATP (0.08 mCi/ml) for 10 as described under "Experimental Procedures. " PtdIns 4-kinase was assayed in the presence of 0.05% Nonidet P-40. Reaction was analyzed by autoradiography following thin layer chromatography, and products were quanti- tated using liquid scintillation counting. for providing cultured rabbit aortic smooth muscle cells. extend our gratitude to for performing the assays against MAP kinase and S6 kinase, for in vitro testing of LY294002 against protein kinase C, investigating the
An Efficient Technique for Calculating Exact Nearest-Neighbor Classification Accuracy

We present a technique for calculating exact nearest-neighbor classification accuracy. This is equivalent to averaging the results of an exponential number of trials (all test/train splits), yet it can be performed very efficiently. The technique is applied to each of four common classification experiment types. Complexity analysis and empirical results demonstrate the superiority of this algorithm over the customary approach of estimating accuracy by averaging several randomized test/train splits. This algorithm offers significant practical benefits to researchers in terms of vastly reduced computation time.
Subcellular Trafficking, Pentameric Assembly, and Subunit Stoichiometry of Neuronal Nicotinic Acetylcholine Receptors Containing Fluorescently Labeled (cid:1) 6 and (cid:2) 3 Subunits □ S

Neuronal nicotinic acetylcholine (ACh) receptors are ligand- gated, cation-selective ion channels. Nicotinic receptors containing (cid:1) 4, (cid:1) 6, (cid:2) 2, and (cid:2) 3 subunits are expressed in midbrain dopaminergic neurons, and they are implicated in the response to smoked nicotine. Here, we have studied the cell biological and biophysical properties of receptors containing (cid:1) 6 and (cid:2) 3 subunits by using fluorescent proteins fused within the M3-M4 intracellular loop. Receptors containing fluorescently tagged (cid:2) 3 subunits were fully functional compared with receptors with untagged (cid:2) 3 subunits. We find that (cid:2) 3- and (cid:1) 6-containing receptors are highly expressed in neurons and that they colo- calize with coexpressed, fluorescent (cid:1) 4 and (cid:2) 2 subunits in neuronal soma and dendrites. Fo¨rster resonance energy trans- fer (FRET) reveals efficient, specific assembly of (cid:2) 3 and (cid:1) 6 into nicotinic receptor pentamers of various subunit compositions. Using FRET, we demonstrate directly that only a single (cid:2) 3 subunit is incorporated into nicotinic acetylcholine receptors (nAChRs) containing this subunit, whereas multiple subunit stoichiometries exist for (cid:1) 4- and (cid:1) 6-containing receptors. Fi-nally, we demonstrate that nicotinic ACh receptors are localized in distinct microdomains at or near the plasma membrane using total internal reflection fluorescence (TIRF) We suggest that contain pools of assembled, which may provide them with the to responses endogenous ligands as ACh, or to exogenous agents as nicotine. Furthermore, this is the first to directly measure nAChR subunit stoichiometry using FRET and plasma membrane localization of (cid:1) 6- and (cid:2) 3-containing receptors using TIRF.
EFFECT OF 2,4-D ON CALLUS INDUCTION IN LEAF EXPLANTS OF PEACH PALM D ON CALLUS INDUCTION IN LEAF EXPLANTS OF PEACH PALM (BACTRIS GASIPAES H.B.K.)

The objective of this research was to determine the effect of dichlorophenoxyacetic acid (2,4 in peach somatic embryos. The explants were inoculated in 8.0 g.L in a growth room at 24±2°C under light conditions (50 µmol.m also under dark conditions, in factorial arrangement: 2 (light and dark conditions) x 8 (2,4 concentrations), totaling 16 treatments. On the 14 necrosis of the explants were observed and, on the 35 percentage of explant area covered by callus cells (EACC) were evaluated. Oxidation was more intense in the cultivations under light conditions, and reduced as the 2,4 However, the highest of 10 mg.L kept in the dark. This concentration also resulted in the highest EAC the explant area covered by callus cells. ABSTRACT The objective of this research was to determine the effect of dichlorophenoxyacetic acid (2,4 peach friable calluses in leaf explants of Bactris gasipaes H.B.K., aiming for further induction of somatic embryos. The explants were inoculated in MS medium supplemented with 30.0 g.L 8.0 g.L -1 agar and 2,4-D (0.0, 0.31, 0.62, 1.25, 2.5, 5.0, 10.0, and 20.0 mg.L in a growth room at 24±2°C under light conditions (50 µmol.m under dark conditions, in factorial arrangement: 2 (light and dark conditions) x 8 (2,4 concentrations), totaling 16 treatments. On the 14 th day of cultivation, occurrences of oxidation and necrosis of the explants were observed and, on the 35 th day, the formation of friable calluses, and the percentage of explant area covered by callus cells (EACC) were evaluated. Oxidation was more intense in the cultivations under light conditions, and reduced as the 2,4 However, the highest concentration, 20.0 mg.L -1 , caused necrosis of the explants. The concentration of 10 mg.L -1 was the most efficient for friable callus induction reaching all the explants in the cultures kept in the dark. This concentration also resulted in the highest EAC the explant area covered by callus cells. percentage of explant area covered by callus cells (EACC) were evaluated. Oxidation was more intense in the cultivations under light conditions, and reduced as the 2,4-D concentrationsincreased. , caused necrosis of the explants. The concentration was the most efficient for friable callus induction reaching all the explants in the cultures kept in the dark. This concentration also resulted in the highest EACC, with an average of 56.5% of is an open access article distributed under the Creative Commons use, distribution, and reproduction in any medium, provided the original work is properly cited.
Vibration-based health monitoring of lighting poles

The health and integrity of lighting poles must be ensured as they are often installed at public places and as they must withstand severe conditions. Corrosive deterioration of lighting poles is dangerous and difficult to forecast due to their varying operating conditions of the poles. The Roch’s study on structural stability of pole systems “Infrastrukturprojekt Straßenbeleuchtung 2000” (Infrastructure Project: Street Lighting 2000), which is representative on a Germany-wide scale, found that 3.3% of all poles pose a hazard [2]. To prevent pole collapse, the poles are regularly replaced, e.g. every 15 years. Such solution is expensive, workforce demanding and unreliable. Some poles are damaged sooner due to more sever conditions, but some poles may withstand much longer. The corrosive damage of the pole occurs usually at the pole base, often under the surface. The corrosion on the top of the pole is less frequent. In any case, the damage is not apparent and localizable (Fig. 1).
Study of an inhomogeneous spin-orbit coupling in topological semiconducting wires

The present End-of-Degree Thesis is framed within the context of Majorana fermions in Condensed Matter, and it focusses on the Rashba nanowire, a realistic system which allows the emergence of Majorana zero modes . After having introduced the present state of affairs in the field, the original proposal is reviewed, and subsequently, a nanowire with inhomogeneous spin-orbit coupling is analysed. Utilizing numerical techniques, it is shown that under precise conditions a defect in the spin-orbit coupling can originate zero-energy fermionic bound states akin to the original Majorana zero modes. Finally, a finite-size effect induced by the presence of the defect is investigated. End-Of-Degree Thesis to be understood as the combination of two self-contained pieces. The elaboration of the main work ( Study of an inhomogeneous spin-orbit coupling in topological semiconducting wires ) was preceded by an introductory bibliographical survey on the topic. The report which details this initial work ( Introduction to Topological Bound States ) has been incorporated as an appendix of the main body owing to bureaucratic matters; nevertheless, both texts can be considered independently, having their own introduction and bibliography, and existing some partial overlapping of content.
Efﬁcacy and safety of teicoplanin plus rifampicin in the treatment of bacteraemic infections caused by Staphylococcus aureus

An open study was carried out on 16 patients with hospital-acquired, bacteraemic Staphylococcus aureus infections to evaluate the safety and efﬁcacy of teicoplanin plus rifampicin. Patients received teicoplanin 400 mg bd for the ﬁrst 24 h followed by 400 mg od thereafter, and rifampicin 600 mg bd. Both agents were given intravenously. Serum samples were collected to determine trough and peak antibiotic concentrations. The MIC of teicoplanin and rifampicin and the MBC of teicoplanin were determined for all S. aureus isolates. Time–kill curves were performed for the drugs individually and in combination. Clinical efﬁcacy was assessed by the APACHE II scoring system. Bacteriological success was evaluated by elimination, persistence or recurrence of S. aureus . Safety was carefully monitored by regular biochemical and haematological testing and recording of adverse events. Fifteen patients were evaluable, of whom 13 (86.7%) were clinically cured with elimination of S. aureus . One patient died, but death was not attributed to the study drugs. Treatment failed in another patient who relapsed with a high fever. S. aureus was recovered from blood cultures from this patient, and resistance to rifampicin had developed. Time–kill curves all showed adequate killing of S. aureus at the drug concentrations measured in vivo . Neither synergy nor antagonism between teicoplanin and rifampicin was demonstrated. The combination of teicoplanin and rifampicin is an effective and well-tolerated treatment for bacteraemic S. aureus infections, but in deep-seated foci of infection resistance to rifampicin may develop.