Miracle-dz/UniFAR-FTUs huggingface dataset:
Application of Pyrosequencing Method for Investigating the Diversity of Synechococcus Subcluster 5.1 in Open Ocean

Synechococcus are distributed throughout the world’s oceans and are composed of diverse genetic lineages. However, as they are much less abundant than Prochlorococcus in oligotrophic open oceans, their in-depth genetic diversity cannot be investigated using commonly used primers targeting both Prochlorococcus and Synechococcus. Thus, in this study, we designed a primer specific to the 16S–23S rRNA internal transcribed spacer (ITS) of the Synechococcus subcluster 5.1. Using the primer, we could selectively amplify Synechococcus sequences in oligotrophic seawater samples. Further, we showed that a barcoded amplicon pyrosequencing method could be applicable to investigate Synechococcus diversity using sequences retrieved in GenBank and obtained from environmental samples. Allowing sequence analyses of a large number of samples, this high-throughput method would be useful to study global biodiversity and biogeographic patterns of Synechococcus in marine environments.
Effects of 17β-oestradiol and norethisterone acetate on sulfonation and sialylation of gonadotrophins in post-menopausal women

Abstract Background. The number of terminal sialic acid and sulfonated N-acetylgalactosamine (SO3-GalNAc) on gonadotrophins in serum varies during the menstrual cycle and changes at menopause, suggesting that gonadal steroids modify their oligosaccharide synthesis. Our objective was to determine the effects of 17β-oestradiol (E2) and a progestogen, norethisterone acetate (NETA), on the sulfonation and sialylation of gonadotrophins in post-menopausal women. Methods. Serum samples were obtained from eight post-menopausal women treated with 20 mg E2 implants every 6 months, from four women who in addition were treated daily with 5 mg NETA orally for a 2-week period, and from four women who got this NETA treatment during a 4-week period. Sera from 11 non-treated post-menopausal women served as a reference group. The gonadotrophin serum concentrations, the number of SO3-GalNAc and sialic acid residues per serum luteinizing hormone (LH) and follicle-stimulating hormone (FSH) molecule, and the distributions of molecules with 0-1-2-3-4 sulfonated residues were measured. Results. The E2-treated post-menopausal women had considerably less (P < 0.001) sialic acid and slightly more (P < 0.01) SO3-GalNAc per serum LH and FSH molecule than the non-treated. Two weeks of NETA treatment increased the sulfonation of LH (P < 0.01) and FSH (P < 0.05) concomitantly with decreased (P < 0.05) sialylation of LH. Conclusion. The primary effect of E2 treatment was a decrease in sialylation and, due to competition for the same substrate, a secondary and consequentially minor increase in sulfonation of LH and FSH. The primary effect of the NETA therapy was an increase in the sulfonation of LH and FSH concomitantly with secondary and consequentially decreases in sialylation of LH.
Sparse Algorithms Are Not Stable: A No-Free-Lunch Theorem

We consider two desired properties of learning algorithms: sparsity and algorithmic stability. Both properties are believed to lead to good generalization ability. We show that these two properties are fundamentally at odds with each other: A sparse algorithm cannot be stable and vice versa. Thus, one has to trade off sparsity and stability in designing a learning algorithm. In particular, our general result implies that ℓ1-regularized regression (Lasso) cannot be stable, while ℓ2-regularized regression is known to have strong stability properties and is therefore not sparse.
External Validation of the Derived Neutrophil to Lymphocyte Ratio as a Prognostic Marker on a Large Cohort of Pancreatic Cancer Patients

Background With growing evidence on the role of inflammation in cancer biology, the presence of a systemic inflammatory response has been postulated as having prognostic significance in a wide range of cancer types. The derived neutrophil to lymphocyte ratio (dNLR), which represents an easily determinable potential prognostic marker in daily practise and clinical trials, has never been externally validated in pancreatic cancer (PC) patients. Methods Data from 474 consecutive PC patients, treated between 2004 and 2012 at a single centre, were evaluated retrospectively. Cancer-specific survival (CSS) was assessed using the Kaplan-Meier method. To evaluate the prognostic relevance of dNLR, univariate and multivariate Cox regression models were applied. Results We calculated by ROC analysis a cut-off value of 2.3 for the dNLR to be ideal to discriminate between patients’ survival in the whole cohort. Kaplan-Meier curve reveals a dNLR≥2.3 as a factor for decreased CSS in PC patients (p<0.001, log-rank test). An independent significant association between high dNLR≥2.3 and poor clinical outcome in multivariate analysis (HR = 1.24, CI95% = 1.01–1.51, p = 0.041) was identified. Conclusion In the present study we confirmed elevated pre-treatment dNLR as an independent prognostic factor for clinical outcome in PC patients. Our data encourage independent replication in other series and settings of this easily available parameter as well as stratified analysis according to tumor resectability.
The Relational View: Future challenges for a non-confirmed expectation

Purpose – Despite its theoretical potential, the relational view proposed by Dyer and Singh (1998) has not been established as a dominant theoretical framework, since the concomitant use of its main constructs is rare. This paper intended to test the relational view considering the impact of its constructs on the economic value created in relationships between buyers and suppliers. Design/methodology/approach – A cross-sectional survey with 121 respondents was conducted in the Brazilian chemical sector. To analyze the measurement models and test the hypotheses, confirmatory factor analysis and multiple linear regression were used. Findings – The limited support for the hypotheses tested suggests that the operationalization of the relational view as an explanatory theory requires further study. Asset specificity seems to be the most solid construct, with a relevant effect on the relational value, and it is present in some moderating effects on environmental variables. The results also suggest that relational governance has some effect on the value captured by the supplier. Originality/value – In addition to the need to review the operationalization of the Relational View, the proposed value measurement model contributed to identifying differences between the value created for the buyer and the value created for the supplier. The measurement scales of value creation presented good quality of fit and also represent a contribution for further research.
Protostellar collapse induced by compression

We present numerical simulations of the evolution of low-mass, isothermal, molecular cores which are subjected to an increase in external pressure Pext.If Pext increases very slowly, the core approaches instability quite quasi-statically.However, for larger (but still quite modest) dPext/dt a compression wave is driven into the core, thereby triggering collapse from the outside in.If collapse of a core is induced by increasing Pext, this has a number of interesting consequences. (i) The density profile is approximately flat in the centre during the pre-stellar phase (i.e.before the compression wave converges on the centre creating the central protostar). (ii) During the pre-stellar phase there are (subsonic) inward velocities in the outer layers of the core, whilst the inner parts are still approximately at rest. (iii) There is an initial short phase of rapid accretion (notionally the Class 0 phase), followed by a longer phase of slower accretion (the Class I phase). All these features accord well with observation, but are at variance with the predictions of the standard theory of star formation based on the inside-out collapse of a singular isothermal sphere.We note that the setting up of a coherent inward velocity field appears to be a generic feature of compression waves; and we speculate that interactions and interference between such velocity fields may play a crucial role in initiating the fragmentation of cores and the genesis of multiple star systems.
The Economics of the Trade Union

This book analyses the crucial features of unionised labour markets. The models in the book refer to labour contracts between unions and management, but the method of analysis is also applicable to non-union labour markets where workers have some market power. In this book, Alison Booth, a researcher in the field, emphasises the connection between theoretical and empirical approaches to studying unionised labour markets. She also highlights the importance of taking into account institutional differences between countries and sectors when constructing models of the unionised labour market. While the focus of the book is on the US and British unionised labour markets, the models and analytical methods are applicable to other industrialised countries with appropriate modifications.
Association between type‐three metabotropic glutamate receptor gene (GRM3) variants and symptom presentation in treatment refractory schizophrenia

Positive associations between polymorphisms in the type‐three metabotropic glutamate receptor gene (GRM3) and the pathogenesis of schizophrenia as well as response to antipsychotic treatment have been reported. The objective of this study was to determine whether refractory psychiatric symptoms in antipsychotic non‐responders are related to polymorphisms in GRM3.
Social Identity and Attitudes toward HIV Pre-exposure Prophylaxis: A Structural Equation Model

Abstract This study focuses on the role of social identity and prejudice as causal variables in public attitudes toward pre-exposure prophylaxis (PrEP) in a UK sample. In all, 222 participants participated in an experimental vignette study with a 2 × 2 × 2 design with between-participants factors of ethnicity, sexual orientation and gender, and completed measures of attitudes toward gay men, Black Africans, and PrEP. Kruskal–Wallis tests showed significant effects of gender on attitudes toward gay men and Black Africans; of ethnicity on attitudes toward gay men and PrEP; and of religion on attitudes toward gay men. A univariate analysis of variance (ANOVA) revealed more positive attitudes toward PrEP when it was presented as benefitting men (vs. women). Structural equation modeling showed that the relationship between the independent variables of gender, ethnicity, and religion and the dependent variable of attitudes toward PrEP was mediated by attitudes toward gay men and Black Africans. Individuals must perceive the principal beneficiaries of PrEP (i.e., gay men and Black Africans) positively to endorse PrEP for these groups, and sexism may reduce public acceptability of PrEP for women. Future research should use representative samples and alternative experimental manipulations, and include strength of social identification as an independent variable.
Does Computer Use Increase Educational Achievements? Student-level Evidence from PISA

The aim of this paper is to assess whether the use of ICT has an impact on student performances as measured in the OECD Programme for International Student Assessment (PISA) 2006. After controlling for observable students’ characteristics and self-selection, we did find a positive and significant effect of the frequency of computer use on science scores. In most countries, however, this effect seems larger when computer is used at home rather than at school. This finding questions the effectiveness of educational policies aimed at promoting computer use at school as a tool for learning.
MAPS OF BOUNDED RATIONALITY: A PERSPECTIVE ON INTUITIVE JUDGMENT AND CHOICE

The work cited by the Nobel committee was done jointly with the late Amos Tversky (1937‐1996) during a long and unusually close collaboration. Together, we explored the psychology of intuitive beliefs and choices and examined their bounded rationality. This essay presents a current perspective on the three major topics of our joint work: heuristics of judgment, risky choice, and framing effects. In all three domains we studied intuitions ‐ thoughts and preferences that come to mind quickly and without much reflection. I review the older research and some recent developments in light of two ideas that have become central to social-cognitive psychology in the intervening decades: the notion that thoughts differ in a dimension of accessibility ‐ some come to mind much more easily than others ‐ and the distinction between intuitive and deliberate thought processes. Section 1 distinguishes two generic modes of cognitive function: an intuitive mode in which judgments and decisions are made automatically and rapidly, and a controlled mode, which is deliberate and slower. Section 2 describes the factors that determine the relative accessibility of different judgments and responses. Section 3 explains framing effects in terms of differential salience and accessibility. Section 4 relates prospect theory to the general * This essay revisits problems that Amos Tversky and I studied together many years ago, and continued to discuss in a conversation that spanned several decades. The article is based on the Nobel lecture, which my daughter Lenore Shoham helped put together. It builds on an analysis of judgment heuristics that was developed in collaboration with Shane Frederick (Kahneman and Frederick, 2002). Shane Frederick, David Krantz, and Daniel Reisberg went well beyond the call of friendly duty in helping with this effort. Craig Fox, Peter McGraw, Daniel Read, David Schkade and Richard Thaler offered many insightful comments and suggestions. Kurt Schoppe provided valuable assistance, and Geoffrey Goodwin and Amir Goren helped with scholarly factchecking. My research is supported by NSF 285-6086 and by the Woodrow Wilson School for Public and International Affairs at Princeton University. A different version of this article is to ap
Efficient Arabic text extraction and recognition using thinning and dataset comparison technique

The objective of this research paper is to propose a novel technique for Arabic text extraction and recognition which is a part of research work aimed at developing a system for moving Arabic video text extraction for efficient content based indexing and searching. Numerous techniques were proposed in the past for text extraction but very few of them focus on Arabic text. All the earlier proposed implementations are not successful in attaining 100 % accuracy in text extraction and recognition process. The proposed technique is new and is based on thinning the given sample image containing Arabic text and splitting the resulting image horizontally (X-axis direction) from right to left in equal intervals. Compare each part of the image for equal number of white pixels to those of samples in the dataset. Upon matching, with the help of index value the corresponding character is stored in an array. This process is repeated by varying the splitting interval until all the characters in the sample image are recognized. To our knowledge, our research is the primary to address the above problem and propose a solution with increased retrieval accuracy and reduced computation time for Arabic text extraction and recognition.
Exploiting Depth and Highway Connections in Convolutional Recurrent Deep Neural Networks for Speech Recognition

Deep neural network models have achieved considerable success in a wide range of fields. Several architectures have been proposed to alleviate the vanishing gradient problem, and hence enable training of very deep networks. In the speech recognition area, convolutional neural networks, recurrent neural networks, and fully connected deep neural networks have been shown to be complimentary in their modeling capabilities. Combining all three components, called CLDNN, yields the best performance to date. In this paper, we extend the CLDNN model by introducing a highway connection between LSTM layers, which enables direct information flow from cells of lower layers to cells of upper layers. With this design, we are able to better exploit the advantages of a deeper structure. Experiments on the GALE Chinese Broadcast Conversation/News Speech dataset indicate that our model outperforms all previous models and achieves a new benchmark, which is 22.41% character error rate on the dataset.
Methods to detect DNA damage by free radicals: relation to exercise

Epidemiological investigations repeatedly show decreased morbidity from regular exercise compared with sedentary life. A large number of investigations have demonstrated increased oxidation of important cellular macromolecules, whereas other investigators have found no effects or even signs of lowering of oxidation of macromolecules. In particular, extreme and long-duration strenuous exercise appears to lead to deleterious oxidation of cellular macromolecules. The oxidation of DNA is important because the oxidative modifications of DNA bases, particularly the 8-hydroxylation of guanine, are mutagenic and have been implicated in a variety of diseases such as ageing and cancer. The methodologies for further investigation of the relationship between DNA oxidation and exercise are available. The preferred methods rely on HPLC or GC-mass spectrometry; whereas the theoretically-attractive liquid chromatography- tandem mass spectrometry is being developed. Caution should be taken to avoid artifacts because of the six orders of magnitude of difference between oxidized and non-oxidized DNA bases in tissues. The methods can be used to estimate tissue levels, i.e. a local concentration of oxidized DNA, or to estimate the rate of body DNA oxidation by the urinary output of repair products, the latter being a method that is independent of repair. During exercise there appears to be a shifting of dietary-dependent antioxidant, e.g. vitamin C and vitamin E, from muscle to plasma, and an increased oxidation in plasma of these antioxidants. Supplementation trials with antioxidants have not been able to increase exercise performance; however, optimum nutrition with antioxidants and possibly supplementation, could be important in the prevention of diseases in the long term. The pattern from these observations appears to be quite consistent; immediately after exercise, regardless of how intense, there do not appear to be any signs of oxidative damage to DNA. Acute or prolonged moderate exercise does not produce signs of oxidative DNA damage and might even be associated with lowering of the levels of oxidation of tissue DNA; however, after long-duration and intense exercise an increase in oxidative DNA modifications is apparent. We suggest as a hypothesis that the relationship between exercise and health is U-shaped. This hypothesis needs to be tested in detail in order to establish the maximum beneficial exercise level with regard to oxidative DNA modification, and also the level that could be deleterious and might even increase the risk for cancer and other diseases.
Leptin-Induced Nuclear Translocation of STAT3 Immunoreactivity in Hypothalamic Nuclei Involved in Body Weight Regulation

Leptin is involved in the hypothalamic control of food intake and body weight. Fos immunohistochemistry has been used to functionally map leptin target neurons involved in these regulatory processes. However, only a subset of hypothalamic neurons expressing the long form of the leptin receptor (Ob-Rb) also coexpress the neuronal activation marker Fos after leptin stimulation. To functionally map all leptin target neurons, regardless of whether leptin-mediated neuronal activation or inhibition occurs, we immunohistochemically investigated the leptin-induced nuclear translocation of the signal transducer and activator of transcription molecule STAT3, which represents a crucial step in the regulation of leptin-dependent gene expression. As proven by colocalization studies with the nuclear 4′,6-diamidino-2-phenylindole dilactate stain, intracerebroventricular leptin treatment, but not intracerebroventricular application of pyrogen-free saline, induced a time-dependent nuclear translocation of STAT3 immunoreactivity in hypothalamic nuclei, with strong nuclear STAT3 signals detectable in the arcuate nucleus, the lateral hypothalamus, and the ventromedial and dorsomedial hypothalamic nuclei. This leptin-induced STAT3 translocation pattern proved to be distinct from that induced by interleukin-6, another cytokine using STAT3 in its signaling pathway. Combined immunohistochemical STAT3 and Fos detection after leptin treatment revealed a higher number of STAT3-positive than Fos-positive cell nuclei in the aforementioned hypothalamic structures and showed that Fos immunoreactivity colocalized only in a subset of all leptin-responsive STAT3 nuclei. These results suggest that the detection of nuclear STAT3 immunoreactivity represents a new neuroanatomical tool to functionally map central leptin actions. They further support the importance of ventrally located caudal hypothalamic structures representing the main leptin targets involved in body weight regulation.
Evidence for Novel Pharmacological Sensitivities of Transient Receptor Potential (TRP) Channels in Schistosoma mansoni

Schistosomiasis, caused by parasitic flatworms of the genus Schistosoma, is a neglected tropical disease affecting hundreds of millions globally. Praziquantel (PZQ), the only drug currently available for treatment and control, is largely ineffective against juvenile worms, and reports of PZQ resistance lend added urgency to the need for development of new therapeutics. Ion channels, which underlie electrical excitability in cells, are validated targets for many current anthelmintics. Transient receptor potential (TRP) channels are a large family of non-selective cation channels. TRP channels play key roles in sensory transduction and other critical functions, yet the properties of these channels have remained essentially unexplored in parasitic helminths. TRP channels fall into several (7–8) subfamilies, including TRPA and TRPV. Though schistosomes contain genes predicted to encode representatives of most of the TRP channel subfamilies, they do not appear to have genes for any TRPV channels. Nonetheless, we find that the TRPV1-selective activators capsaicin and resiniferatoxin (RTX) induce dramatic hyperactivity in adult worms; capsaicin also increases motility in schistosomula. SB 366719, a highly-selective TRPV1 antagonist, blocks the capsaicin-induced hyperactivity in adults. Mammalian TRPA1 is not activated by capsaicin, yet knockdown of the single predicted TRPA1-like gene (SmTRPA) in S. mansoni effectively abolishes capsaicin-induced responses in adult worms, suggesting that SmTRPA is required for capsaicin sensitivity in these parasites. Based on these results, we hypothesize that some schistosome TRP channels have novel pharmacological sensitivities that can be targeted to disrupt normal parasite neuromuscular function. These results also have implications for understanding the phylogeny of metazoan TRP channels and may help identify novel targets for new or repurposed therapeutics.
Event-based bipartite consensus on signed networks

In this paper, a bipartite consensus problem for a multi-agent system is formulated firstly. Then an event-based interaction rule is proposed for the multi-agent system with antagonistic interactions. The bipartite consensus stability is analyzed on the basis of spectral properties of the signed Laplacian matrix associated with multi-agent networks. Some simulation results are presented to illustrate the bipartite consensus with the proposed interaction rule.