Miracle-dz/UniFAR-FTUs huggingface dataset:
iGentifier: indexing and large-scale profiling of unknown transcriptomes

Development and refinement of methods to analyse differential gene expression has been essential in the progress of molecular biology. A novel approach called iGentifier is presented for profiling known and unknown transcriptomes, thus bypassing a major limitation in microarray analysis. The iGentifier technology combines elements of fragment display (e.g. Differential Display or RMDD) and tag sequencing (e.g. SAGE, MPSS) and allows for analysis of samples in high throughput using current capillary electrophoresis equipment. Application to epidermal tissue of wild-type and mlo5 barley (Hordeum vulgare) plants, infected with powdery mildew [Blumeria graminis (DC.) E.O. Speer f.sp. hordei], led to the identification of several 100 genes induced or repressed upon infection with many well known for their response to fungal pathogens or other stressors. Ten of these genes are suggested to be classified as marker genes for durable resistance mediated by the mlo5 resistance gene.
Comparative Genomics of the Listeria monocytogenes ST204 Subgroup

The ST204 subgroup of Listeria monocytogenes is among the most frequently isolated in Australia from a range of environmental niches. In this study we provide a comparative genomics analysis of food and food environment isolates from geographically diverse sources. Analysis of the ST204 genomes showed a highly conserved core genome with the majority of variation seen in mobile genetic elements such as plasmids, transposons and phage insertions. Most strains (13/15) harbored plasmids, which although varying in size contained highly conserved sequences. Interestingly 4 isolates contained a conserved plasmid of 91,396 bp. The strains examined were isolated over a period of 12 years and from different geographic locations suggesting plasmids are an important component of the genetic repertoire of this subgroup and may provide a range of stress tolerance mechanisms. In addition to this 4 phage insertion sites and 2 transposons were identified among isolates, including a novel transposon. These genetic elements were highly conserved across isolates that harbored them, and also contained a range of genetic markers linked to stress tolerance and virulence. The maintenance of conserved mobile genetic elements in the ST204 population suggests these elements may contribute to the diverse range of niches colonized by ST204 isolates. Environmental stress selection may contribute to maintaining these genetic features, which in turn may be co-selecting for virulence markers relevant to clinical infection with ST204 isolates.
Polymorphisms of C242T and A640G in CYBA Gene and the Risk of Coronary Artery Disease: A Meta-Analysis

Background Coronary artery disease (CAD) is a leading cause of mortality in many countries. Considerable studies have been carried out to investigate the relationship between the C242T and A640G polymorphisms of CYBA gene and CAD, but the results were still inconsistent. Hence we conducted a meta-analysis to clarify the association. Methods and Results A total of 21 eligible literatures were included in the meta-analysis. We observed a significant decreased risk of CAD for C242T polymorphism in Asian population under an allelic model (OR 0.75; 95% CI 0.67–0.84) and a dominant model (OR 0.69; 95% CI 0.61–0.79), however, in overall population and other population no significant association was revealed. We also found A640G polymorphism may contribute to reducing CAD risk under an allelic model (OR 0.84; 95% CI 0.75–0.93), dominant model (OR0.77; 95% CI 0.64–0.92) and recessive model (OR0.82; 95% CI 0.69–0.97). No publication bias was found. Conclusion Our meta-analysis confirmed a protective effect of C242Tpolymorphism on CAD in Asian population and indicated that A640G polymorphism was significantly associated with decreased risk of CAD.
The Career Path of an Indonesian EFL Teacher: A Professional Capital Perspective

Three components of teachers’ professional capital are human capital, social capital, and decisional capital according to Hargreaves and Fullan (2012). These three aspects of professional capital are meant to be part and parcel of developing the teaching profession. In this article, the author focusses on professional capital as a framework by putting the emphasis on the decisional aspect. In this study, the decisional capital is not only found at the micro level of education: the classroom and school level. Beyond that, a teacher also needs to make professional decisions that will affect her/his professional growth and trajectory. To illustrate this professional path through the lens of decisional capital, the author outlines the narrative of decision-making of an Indonesian English as a Foreign Language (EFL) teacher. The findings of the study shed light on the Indonesian teacher’s journey to becoming an English teacher and how the journey has been marked by her decisions regarding her career and her engagement with the professional communities in Indonesia.
Bounded version of bosonic creation and annihilation operators and their related quasicoherent states

Coherent states are usually defined as eigenstates of an unbounded operator, the so called annihilation operator. We propose here possible constructions of quasicoherent states, which turn out to be quasieigenstate of a bounded operator related to an annihilationlike operator. We use this bounded operator to construct a sort of modified harmonic oscillator and we analyze the dynamics of this oscillator from an algebraic point of view.
“We are Humans First”: Expanding Learning Outcomes in an Undergraduate Research Methods Course Through an Experiential Learning Project on Homelessness

This paper outlines my approach to and lessons learned from an experiential learning project on homelessness in an undergraduate research methods course for criminal justice majors. Students receive training in research ethics as well as interpretivist research epistemology and methods, and then conduct structured interviews with un-housed individuals. Drawing on a thematic analysis of students’ research reflection papers, I discuss three ways in which this approach can enhance and expand learning outcomes beyond what is conventionally achieved in a methods course: (1) developing competency in conducting human subjects research; (2) challenging pre-existing views on social issues; and (3) increasing empathy and enhancing communication skills, which may be particularly important for aspiring law enforcement officers.
Set‐membership parity space approach for fault detection in linear uncertain dynamic systems

In this paper, a set‐membership parity space approach for linear uncertain dynamic systems is proposed. First, a set of parity relations derived from the parity space approach is obtained by means of a transformation derived from the system characteristic polynomial. As a result of this transformation, parity relations can be expressed in regressor form. On the one hand, this facilitates the parameter estimation of those relations using a zonotopic set‐membership algorithm. On the other hand, fault detection is then based on checking, at every sample time, the non‐existence of a parameter value in the parameter uncertainty set such that the model is consistent with all the system measurements. The proposed approach is applied to two examples: a first illustrative case study based on a two‐tank system and a more realistic case study based on the wind turbine fault detection and isolation benchmark in order to evaluate its effectiveness. Copyright © 2014 John Wiley & Sons, Ltd.
Who Migrates? Tracking Gendered Access to Migration Within Households “In Flux” Across Time

ABSTRACT In Indonesia, traditional gender ideals tend to depict men as legitimate migrants while women who move are deemed “out of place. ” This male migrant-as-breadwinner household arrangement has been complicated in the past 30 years by gendered migration systems and practices in Asia that favor women. Drawing upon a household survey (N = 1,203) and in-depth interviews (N = 55), we use “time tracks” (Robertson, 2014) to interrogate gendered dynamics within the household “in flux” (Huijsmans, 2014). Foregrounding active negotiations within migrant households, we illustrate the continuously changing gender relations as they interact with, and respond to, the gendered migration systems and practices over time.
Religion and the Environment: Twenty-First Century American Evangelicalism and the Anthropocene

This paper provides an overview of the emergence of religion and the environment as an area of academic research and an assessment of the potential role religion can play in addressing anthropogenic climate change. Focusing on the United States of America the study traces the dynamics of anthropogenic climate change denial and offers an overview of the complex and far-reaching evangelical endeavours that seek to limit solutions and approaches to address global change issues. While much research has explored the positive role religion can play in addressing climate change, little research explores the lengths to which American evangelicals have sought to stymie climate change activism within their ranks and the potential political impact of their endeavours. As such the paper fits neatly with the theme of “Humanities for the Environment” special edition and has the capacity to contribute new insights on the impact of religion and the environment.
A Comparative Case Study

— The information revolution particularly e-resources has changed the shape of libraries and role of librarians. The present study has been undertaken to compare the level of awareness and utilization of electronic journals (e-journals) among faculty members and research scholars (RS) of Banasthali University (BU), Rajasthan, India. Further, the data is collected through a structured questionnaire distributed among faculty members. The awareness among the faculty members have been compared by the previous study of research scholars of Banasthali University. Also it highlights the problems encountered by the users and suggests the ways to implement user awareness programs in the library.
Validation of Router Models in OPNET

1 Research Assistant of the Fund of Scientific Research – Flanders (FWO-Vlaanderen) 2 ESAT-Telemic participates in the OPNET University Program for research [7, 8, 9] and educational projects [10, 11, 12]. Abstract OPNET contains a vast amount of node models that represent specific types of networking gear available in the marketplace. These models closely resemble their real-life counterparts in supported functionality, but in order for OPNET to generate representative simulation results they also have to accurately simulate the performance of the real devices.
Ultraviolet C Irradiation Induces Different Expression of Cyclooxygenase 2 in NIH 3T3 Cells and A431 Cells: The Roles of COX-2 Are Different in Various Cell Lines

Ultraviolet C (UVC) is a DNA damage inducer, and 20 J/m2 of UVC irradiation caused cell growth inhibition and induced cell death after exposure for 24–36 h. The growth of NIH 3T3 cells was significantly suppressed at 24 h after UVC irradiation whereas the proliferation of A431 cells was inhibited until 36 h after UVC irradiation. UVC irradiation increased COX-2 expression and such up-regulation reached a maximum during 3–6 h in NIH 3T3 cells. In contrast, UVC-induced COX-2 reached a maximum after 24–36 h in A431 cells. Measuring prostaglandin E2 (PGE2) level showed a biphasic profile that PGE2 release was rapidly elevated in 1–12 h after UVC irradiation and increased again at 24 h in both cell lines. Treatment with the selective COX-2 inhibitor, SC-791, during maximum expression of COX-2 induction, attenuated the UVC induced-growth inhibition in NIH 3T3 cells. In contrast, SC-791 treatment after UVC irradiation enhanced death of A431 cells. These data showed that the patterns of UVC-induced PGE2 secretion from NIH 3T3 cells and A431 cells were similar despite the differential profile in UVC-induced COX-2 up-regulation. Besides, COX-2 might play different roles in cellular response to UVC irradiation in various cell lines.
Can the Archaeology of Manual Specialization Tell Us Anything About Language Evolution? A Survey of the State of Play

In this review and position paper we explore the neural substrates for manual specialization and their possible connection with language and speech. We focus on two contrasting hypotheses of the origins of language and manual specialization: the language-first scenario and the tool-use-first scenario. Each one makes specific predictions about hand-use in non-human primates, as well as about the necessity of an association between speech adaptations and population-level right-handedness in the archaeological and fossil records. The concept of handedness is reformulated for archaeologists in terms of manual role specialization, using Guiard's model asymmetric bimanual coordination. This focuses our attention on skilled bimanual tasks in which both upper limbs play complementary roles. We review work eliciting non-human primate hand preferences in co-ordinated bimanual tasks, and relevant archaeological data for estimating the presence or absence of a population-level bias to the right hand as the manipulator in extinct hominin species and in the early prehistory of our own species.
What Is Left of the Active Externalism Debate

Since the publication of Clark and Chalmers' Extended Mind paper, the central claims of that paper, viz. the thesis that cognitive processes and cognitive or mental states extend beyond the brain and body, have been vigorously debated within philosophy of mind and philosophy of cognitive science. Both defenders and detractors of these claims have since marshalled an impressive battery of arguments for and against “active externalism. ” However, despite the amount of philosophical energy expended, this debate remains far from settled. We argue that this debate can be understood as answering two metaphysical questions. Yet prominent voices within the debate have assumed that there is a tight relationship between these two questions such that one question can be answered via the other. We defend an alternative ‘wide’ view, whereby mentality is understood as constituted by wide social and cultural factors. Our wide view entails that the two metaphysical questions are separate and should be kept distinct. This suggests that active externalism as understood by prominent voices within that debate requires dissolution, rather than solution. However, if the debate were instead understood as only focusing on the second of the two questions, then there could be a possible future for this debate.
The Multiplicative Anomaly for Determinants Revisited; Locality

Observing that the logarithm of a product of two elliptic operators differs from the sum of the logarithms by a finite sum of operator brackets, we infer that regularised traces of this difference are local as finite sums of noncommutative residues. From an explicit local formula for such regularised traces, we derive an explicit local formula for the multiplicative anomaly of ζ-determinants which sheds light on its locality and yields back previously known results.
Interactions between the Native and Second-language Phonetic Systems

Many studies in the past decade have shown that "earlier is better" as far as learning a second language (L2) is concerned. That is, individuals who began learning their L2 in late adolescence or early adulthood ("late bilinguals") usually resemble native speakers of the L2 less than individuals who began learning their L2 in childhood ("early bilinguals") do. Early bilinguals have been shown to resemble L2 native speakers to a greater extent than late bilinguals in terms of sensitivity to the grammatical properties of the L2 (Flege, Yeni-Komshian & Liu 1999; DeKeyser 2000) as well as in terms of the online processing of L2 sentences (Liu et al. 1992; McDonald 2000; Guillelmon & Grosjean 2001). Other studies have shown similar differences in the production and perception of L2 speech. For example, early bilinguals generally have milder foreign accents in the L2 than late bilinguals do (Flege et al. 1995a; Flege, Yeni-Komshian & Liu 1999). Also, early bilinguals have been found to produce and perceive L2 vowels more like L2 native speakers than late bilinguals do (Munro et al. 1996; Flege 1992; Flege, MacKay & Meador 1999; Piske et al. in press; Flege et al. submitted), to produce and perceive L2 consonants more accurately than late bilinguals do (Flege 1991; Flege et al. 1995b; MacKay, Meador & Flege 2001; MacKay, Flege, Piske & Schirru 2001), and to recognize L2 words presented in noise more effectively (Meador et al. 2000).
Co-adaptation of ball reception to the serve constrains outcomes in elite competitive volleyball

How impactful is volleyball’s “serve-reception game”? Its efficacy has been found to discriminate between winning and losing a match. But how does reception become (in)effective? Based on the theoretical rationale of ecological dynamics, we hypothesized that skilled receivers in volleyball would not display ready-made responses, but rather would co-adapt action modes during serve-reception to deal with the specific, emergent constraints of serve to achieve task goals. In order to examine this issue, we investigated whether the co-adaptation of serve and reception action modes was a significant predictor of set outcome in elite volleyball performance (win or loss), analyzing the first and last sets of the 2014 World League Finals matches (897 game-sequences). The power-jump and jump-float were the serving modes observed and the overhand, underhand-lateral, and underhand-frontal passes were the reception modes categorized. We found that the co-adaptation of serve and reception action modes predicted set outcome in the final set of a match. Receiving the jump-float serve with an overhand pass or underhand-lateral pass increased the odds of winning the final set by 200%. Results suggested that, at an expert level, mastering the overhand pass and the underhand-lateral pass gives teams a competitive edge. Receivers showing flexibility in action mode selection improved a team’s odds of successfully winning the final set of a match.
Anti-inflammatory, antioxidant and antitumor activities of ingredients of Curcuma phaeocaulis Val

Curcuma phaeocaulis Val. is used in Chinese Pharmacopoeia as health food and folk medicine for removing blood stasis, alleviating pain and tumor therapy. This research was aimed to explore and compare three main bioactivities including anti-oxidant, antitumor and anti-inflammatory activities between the ethanol extract of C. Phaeocaulis and its fractions using different in vitro models. Firstly, 70 % ethanol was used to extract C. Phaeocaulis, and then the crude extract was re-extracted, resulting in petroleum ether (EZ-PE), ethyl acetate (EZ-EA), and water fractions (EZ-W), respectively, and then a series of index was detected. Results showed that all the extracts had medium DPPH radical scavenging activity when the concentration was 200 μg/ml and their DPPH radical scavenging activity was in a concentration-dependent manner. The extracts except ethanol extract of C. Phaeocaulis had almost no cytotoxicity to the survival of RAW264.7 cell when the concentration reached 80 μg/ml, and all of them had medium inhibitory effect on nitrite release. Extracts of C. Phaeocaulis had medium intensity antitumor activity, EZ-PE and EZ-EA fractions significantly inhibited the proliferation of four tumor cells (SMMC-7721 cell lines, HepG-2 cell lines, A549 cell lines and Hela cell lines). C. Phaeocaulis had antioxidant and anti-inflammatory activities, which did not carry out centralized phenomenon when re-extracted. EZ-PE and EZ-EA were active antitumor sites of C. Phaeocaulis.
Assessment of low vitamin D among Saudi Arabians

Objectives: To compare the performance of 3 commonly used 25-hydroxyvitamin D (25-OHD) assays among a sample of the Saudi population. Methods: This cross-sectional study was carried out between January 2011 and December 2012 at King Fahd Hospital of the University, Al-Khobar, Saudi Arabia. After informed consent, blood samples for measurement of 25-OHD level was extracted from 200 adults. The vitamin D level of each individual were determined using chemiluminescence immunoassay (CLIA), radio-immuno assay (RIA), and liquid chromatography-tandem mass spectrometry (LC-MS/MS) assay. Assays were also compared through commonly used cut-points for classification of vitamin D deficiency. Bias between assays was evaluated using Bland-Altman plots. Results: The average age of patients was 45.7±16.1 years. A significant difference between the assays was found. The mean 25-OHD levels were highest for the LC-MS/MS (21.65 ng/mL, 95% CI 19.74-23.56), intermediate for RIA (16.607 ng/mL, 95% CI 14.87-18.32), and lowest for CLIA method (13.864 ng/mL, 95% CI 12.109-15.618). Using 30 ng/mL as a cutoff value, only 6% was found to have normal levels of 25-OHD using CLIA, 9% using RIA, and 22% using LC-MS/MS. Conclusion: Levels of 25-OHD and the prevalence of vitamin D deficiency are dependent on the assay used. The reported high prevalence of hypovitaminosis D among the Saudi population can be partially explained by the use of assays that underestimate vitamin D levels.
Conceptual Requirements for the Automatic Reconstruction of Building Information Models from Uninterpreted 3D Models

A multitude of new applications is quickly emerging in the field of Building Information Models (BIM). BIM models describe buildings with respect to their spatial and especially semantic and thematic characteristics. Since BIM models are manually created during the planning and construction phase, they are only available for newly planned or recently constructed buildings. In order to apply the new applications to already existing buildings, methods for the acquisition of BIM models for built-up sites are required. Primary data source are 3D geometry models obtained from surveying, CAD, or computer graphics. Automation of this process is highly desirable, but faces a range of specific problems setting the bar very high for a reconstruction process. This paper discusses these problems and identifies consequential requirements on reconstruction methods. Above, a two-step strategy for BIM model reconstruction is proposed which incorporates CityGML as an intermediate layer between 3D graphics models and IFC/BIM models.
Ramsey Meets Hosios: The Optimal Capital Tax and Labor Market Efficiency

Heterogeneity between unemployed and employed individuals matters for optimal fiscal policy. This paper considers the consequences of welfare heterogeneity between these two groups for the determination of optimal capital and labor income taxes in a model with matching frictions in the labor market. In line with a recent finding in the literature, we find that the optimal capital tax is typically non-zero because it is used to indirectly mitigate an externality along the extensive labor margin that arises from search and matching frictions. However, the consideration of heterogeneity makes our result differ in an important way: even for a well-known parameter configuration (the Hosios condition) that typically eliminates this externality, we show that the optimal capital income tax is still non-zero. We also show that labor adjustment along the intensive margin has an important effect on efficiency at the extensive margin, and hence on the optimal capital tax, independent of welfare heterogeneity. Taken together, our results show that these two empirically-relevant features of the labor market can have a quantitatively-important effect on the optimal capital tax.