Miracle-dz/UniFAR-FTUs huggingface dataset:
A graph-clustering approach to search important molecular markers and pathways of Parkinson’s disease

Parkinson disease is the second most common neurodegenerative disorder. Therefore, it is worthwhile to search for important molecular markers and pathways that hold great promise for further treatment of patients with Parkinson’s disease. DNA-microarray-based technologies allow simultaneous analysis of expression of thousands of genes. Here, we performed a comprehensive gene level assessment of Parkinson’s disease using 16 colorectal cancer samples and nine normal samples. The results show that SLC6A3, SLC18A2, and EN1, etc., are related to Parkinson’s disease. Besides, we further mined the underlying molecular mechanism within these different genes. The results indicate that tyrosine metabolism pathway and Parkinson's disease pathway were two significant pathways, with hope to provide insights into the development of novel therapeutic targets and pathways. Key words: Microarrays, graph-cluster, Parkinson’s disease, gene ontology (GO), pathway.
Which schools and pupils respond to educational achievement surveys?: a focus on the English Programme for International Student Assessment sample

Non‐response is a major problem facing research in the social sciences including in education surveys. Hence, research is needed to understand non‐response patterns better as well as non‐response as a social phenomenon. Findings may contribute to improvements in the future designs of such surveys. Using logistic and multilevel logistic modelling we examine correlates of non‐response at the school and pupil level in the important educational achievement survey the ‘Programme for International Student Assessment’ (PISA) for England. The analysis exploits unusually rich auxiliary information on all schools and pupils sampled for PISA, whether responding or not, from two large‐scale administrative sources on pupils’ socio‐economic background and results in national public examinations. This information correlates highly with the PISA target variable. Findings show that characteristics that are associated with non‐response differ between the school and pupil levels. Our results also indicate that schools matter in explaining pupil level response, which is often ignored in non‐response analysis. Our findings have important implications for future education surveys. For example, if replacement schools are used to improve response, our results suggest that it may be more important to match initial and replacement schools on the socio‐economic composition of their pupils than on any of the factors that are currently used.
Temperature effect on growth and larval duration of plaice Pleuronectes platessa in three regions of the Northeast Atlantic

Transport models for planktonic fish eggs and larvae often use temperature to drive growth because temperature data are readily available. This pragmatic approach can be criticised as too simplistic as it ignores additional factors, such as food availability and growth-rate-depen- dent mortality. We examined the extent to which temperature could explain the larval duration and growth variability in post-settlement plaice from the southern North Sea, Irish Sea and west of Ireland. Larval duration and individual growth were estimated from the otolith microstructure of juvenile plaice collected from nursery grounds in each region, and average sea surface temper- atures were reconstructed for each region from satellite data. Hatch dates, larval duration and set- tlement dates all differed among the regions, reflecting the timing of spawning and the physical characteristics of each region. Models incorporating presumed temperature history and region explained 73% of variability in individual larval growth (as estimated from otolith microincrement widths), again demonstrating important differences among the regions. The results suggest that sea temperature can be used to drive growth models of plaice larvae, although allowance must then be made for inter-regional differences. However, larval duration can be estimated using a pan-regional model based on the average temperature experienced during the larval phase.
Autonomy or conservative adjustment? The effect of public policies and educational attainment on third births in Austria, 1975-96

The standardized rate of third births declined by over 50 percent in Austria between the late 1970s and the mid-1990s. The third birth was also postponed gradually over the years until 1991-92, after which the tempo of childbearing suddenly increased in response to a change in the parental-leave policy. This new policy inadvertently favoured women who had their second or subsequent child shortly after their previous one. We cannot find any indication that the general decline in third births can be seen as a consequence of women's increasing independence from their husbands at the stage in life we study. Furthermore, it still seems to be more difficult to combine motherhood and labour-force participation in Austria than in Sweden, which is a leader in reducing this incompatibility. These developments reflect the tension between advancing gender equality and the dominance of traditional norms in Austria.
ASYMPTOTIC EXPANSIONS FOR CERTAIN $q$-SERIES, $q$-INTEGRALS, $q$-DIFFERENTIALS AND A FORMULA OF RAMANUJAN FOR SPECIFIC VALUES OF $\zeta(s)$ (Analytic Number Theory : Arithmetic Properties of Transcendental Functions and their Applications)

This is a summarized version of the author’s papers [22] [24] on asymptotic aspects of the $q$ -series of Lambert type, $q$ -hypergeometric function, $q$ -integrals and q-diﬀerentials. Major portions of the results in these papers are rearranged to state in Parts I and II respectively; the ﬁrst part is devoted to showing intrinsic linkage between asymptotics of certain $q$ -series and a formula of Ramanujan for speciﬁc values of the Riemann zeta-function $ \zeta(s)$ , while several complete asymptotic expansions for multiple $q$ -integrals and $q$ -diﬀerentials of Thomae-Jackson type are presented in the second part. -integral, multiple $q$ -diﬀerential, Mellin-transform, asymptotic expansion, Lerch zeta-function.
Engineering Crises: Favoritism and Strategic Fiscal Indiscipline

If people understand that some macroeconomic policies are unsustainable, why would they vote for them in the . first place? We develop a political economy theory of the endogenous emergence of fiscal crises, based on the idea that the adjustment mechanism to a crisis favors some social groups, that may be induced ex-ante to vote in favor of policies that are more likely to lead to a crisis. People are entitled to a certain level of a publicly provided good, which may be rationed in times of crises. After voting on that level, society votes on the extend to which it will be financed by debt. Under bad enough macro shocks, a crisis arises: taxes are set at their maximum but despite that some agents do not get their entitlement. Some social groups do better in this rationing process than others. We show that public debt . which makes crises more likely . is higher, as is the probability of a crisis, the greater the level of favoritism. If the favored group is important enough to be pivotal when society votes on the entitlement level, favoritism also leads to greater public expenditure. We show that the favored group may strategically favor a weaker state in order to make crises more frequent. Finally, the decisive voter when choosing expenditure may be different from the one when voting on debt. In such a case, constitutional limits on debt may raise the utility of all the poor, relative to the equilibrium outcome absent such limits.
Genetic variation and association analysis of some important traits related to grain in rice (Oryza sativa L.) germplasm

The identification of genomic loci involved in control of quantitative traits receives growing attent ion in plant molecular breeding. The present study was carried out to evaluate the genetic variability among 48 rice genotypes and determine the genomic regions associated with ten grain related important traits. A total number of 63 alleles were detected by 18 selected SSR markers from different chromosomes with an average of 3.5 alleles per marker. A model - based Bayesian approach subdivided 48 evaluated rice genotypes into three major subgroups with the consideration of the highest value of Δ K. The mean r 2 value for all loci pairs on the same chromosome was 0.053. A total of 38 significant marker - trait associations were identified (P< 0.05) that explaining more than 32% of the total variation. RM315, RM3428, RM289, RM16, RM574 and RM156 markers had highest R 2 and most association with assayed traits, respectively. The findings of this study revealed association of grain properties in rice with some SSR markers that could serve as target genomic regions for further research such as MAS, fine mapping and cand idate gene discovery in rice breeding programs.
Skeletal Morphology and Material Properties of a Fragmenting Gorgonian Coral

Among species in which fragmentation is an important mode of asexual reproduction, mechanisms that facilitate fragmentation should be advantageous. The Caribbean gorgonian Plex- aura kuna readily fragments on reefs of the San Blas Islands, Panama, to form aggregations of genet- ically identical colonies. To understand the mechanics of fragmentation and the role of structural properties, the force required to break branches was measured on live colonies in the field, and mor- phology, flexibility, and strength of the axial skeleton were measured in laboratory experiments. Young's modulus, used as a measure of stiffness, was higher in P. kuna than in many other gorgoni- ans and significantly varied among clones, ranging from 2.859 to 6.073 GN m -2 . This level of varia- tion indicates that drag should vary among clones due to differences in their flexibility. Of the mor- phological traits measured, coplanar constrictions influenced the force required to break a branch while anti-planar constrictions and branch anisotropy did not. The modulus of rupture, a measure of the strength of the branch, significantly varied among clones of P. kuna, ranging from 50.87 to 92.58 MN m -2 . Using hydrodynamic theory we predict that the 55% variation in skeletal strength is sufficient to produce variation in fragmentation rate among clones. The stiffness of the skeleton of some colonies may prevent bending and shedding of drag resulting in failure due to the weakness of the skeleton. Clonal variation in flexibility and strength provides a mechanism through which selection may act to favor fragmentation and clonal growth.
Analysis of HLM on PISA 2003 based on Networked Readiness Index of Countries and Mathematics Learning of Students

The purpose of this study is to investigate the PISA 2003 database by Hierarchical Linear model (HLM). The plan of PISA 2003 aimed at the evaluation of mathematics learing of 15-year-old students. The sample included 41 countries. There will be estimation errors if all the task-takers were put in the same level when it went to analyze all the casual relation between the variables of countries and students. Therefore, HLM of two levels is used to analyze the PISA 2003 database. The unit in level-1 is students. The variables belonging to the level-1 are mathematics cognition, mathematics view and mathematics thinking. As to the level-2, the unit is countries and the variable is Networked Readiness Index (NRI). There are four submodels in this study. Based on the four submodels, the relationship between mathematics learning of students and NRI of countries are clearly understood. Finally, some suggesstions and recommendations for future research are provided.
Ab initio calculation of the phase stability in Au-Pd and Ag-Pt alloys

The phase stability of superstructures based on the fcc lattice in the Au-Pd and Ag-Pt alloy systems are examined from the fully relativistic electronic density functional theory. The electron-ion interaction is described by the projector augmented-wave PAW method and the exchange-correlation effects are treated in the generalized gradient approximation GGA. The cluster expansion method is used to obtain effective cluster interactions on the fcc lattice and is used also to guide a systematic ground state search for both alloy systems. The ground state analysis reveals a multitude of ground states in Au-Pd, especially at the Au-rich side. Possibly long-period super-structures occur near the Au70Pd30 composition. The ground state analysis indicates a uniquely stable AgPt compound with the L11 structure CuPt prototype and it also suggests a marginally stable ordered compound for Ag3Pt. However, our ab initio study rules out the existence of the remarkably stable Ag3Pt phase with L12 structure, reported first more than half a century ago and since then included in many assessments. We also find no indication for a stable ordered state at the AgPt3 composition. The cluster variation method CVM with a large maximal cluster is used to compute the enthalpy of mixing of the disordered solid solutions and the solid portion of the Au-Pd and Ag-Pt phase diagrams. These results are critically compared with experimental data and phase diagram assessments. It is shown that cluster expansions cannot account for the high-temperature miscibility gap in the Ag-Pt system when the effective cluster interactions do not reach beyond the second nearest neighbor. Only when third nearest neighbors are included in the cluster expansion is it possible to obtain a phase diagram that agrees qualitatively with the assessed Ag-Pt phase diagram.
Dichotomous transformations for statistical inference about odds ratios

Dichotomous transformations for continuous outcomes are commonly used. In this paper, we investigate dichotomisation for statistical inference about odds ratios in a situation where two underlying distributions from which independent samples are drawn are skewed and unknown. Under some mild conditions it is shown that a suitable choice of the cutpoint of a dichotomous transformation must lie within the range bounded by the two medians of the two underlying distributions, within which there exists a unique optimal cutpoint in terms of the asymptotic efficiency of point estimation and hypothesis testing. The issue of selecting a cutpoint is also linked to the choice amongst some existing non-parametric tests.
Reactive Oxygen Species Modulation of the Mu-Opioid Receptor By 1 1

One aspect of this project set out to examine the effects of methamphetamine (METH) on the accumulation of cellular reactive oxygen species (ROS) and the expression of the mu-opioid receptor (MOR) in a dopaminergic cell line, SH-SY5Y, in order to delineate a possible role for ROS signaling in the coupling of dopaminergic and opioidergic pathways in neuronal cells. Prior evidence indicates neuronal cells treated with METH accumulate dopamine in the synaptic cleft which can lead to increased levels of ROS. Uncovering a role for ROS in increasing MOR expression in response to METH may provide a therapeutic target aimed at reducing the already established phenomenon of METH cross-sensitization to morphine, two drugs with high potential for abuse. A second aspect of this project investigated the mechanism by which lipopolysaccharide (LPS) exposure alters MOR expression in immune and neuronal cells. Previous research notes the exposure to LPS increases the production of ROS in murine macrophages. Also, activation of MOR effects functions associated with the immune response. Therefore, uncovering a role for ROS in increasing MOR expression in immune and neuronal cell types could provide additional insights in how to address problems associated with LPSinduced inflammatory response and the subsequent acceleration of sepsis seen with morphine treatment. The data presented here show that METH's effect on MOR expression is dependent upon sub-lethal levels of intracellular ROS increased by METH treatment, which suggests a possible coupling of METHand opiate-mediated intracellular signaling. In addition, work from the second portion of this project found that LPS stimulated the intracellular ROS accumulation and MOR expression in macrophage-like TPA-HL-60 cells. Conditioned medium from the LPS-stimulated TPA-HL-60 cells increased MOR expression in SH-SY5Y cells, a neuronal cell model, through actions mediated by TPA-HL-60 secreted TNF-a and GM-CSF. These data indicate that the endotoxin, LPS, modulates MOR expression in nervous and immune cells via ROS signaling, and demonstrates the crosstalk that exists within the neuroimmune axis.
The impact of financial market on industry growth: an evidence from Russia and Iran

The relationship between financial markets and industry growth has been approved by many previous studies. In this paper, as an innovative research, we try to find the impact of market capitalization in financial market as a proxy for financial market on the industry growth in Russia and Iran. In fact, these two countries are classified as developing economies in which the financial markets can play a powerful engine to improve the industries’ performances. Hence, it would be interesting to compare market capitalization-industry growth nexus in Russia and Iran as two developing countries. In order to fulfill this purpose, an econometric model called Vector Autoregressive Model (VAR) is applied for the annual data over the period of 1992-2014. The finding proves the positive relationship between market capitalization and industry growth in both countries, Iran and Russia. Based on the results, a 1% increase in market capitalization in Iran and Russia increases the industry growth by 0.07% and 0.02%, respectively. It has been concluded that market capitalization can play a significant role in order to grow the industry in Iran and Russia. However, these two countries need to improve the efficiency of their financial markets to improve the positive impact of these markets on their industrial growth. The novelty of this research can be highlighted in this way that the financial market in oil exporting countries, Russia and Iran as our case studies, may be a golden key to reach to a positive and stable economic growth. Thereby, oil exporting countries should try to implement good financial policies and improve the efficiency of financial market.
Shale Diagenesis in the Bergen High Area, North Sea

Illite diagenesis in Tertiary and Mesozoic shales in the Bergen High area, northern North Sea, was studied using mineralogic, isotopic, and computerized thermal modeling techniques. The Tertiary shales are dominated by smectite, with lesser amounts of illite, kaolinite, and chlorite. At present burial temperatures of >70°C smectite is absent, and the shales contain abundant lath-shaped illite which yields a mixed-layer illite/smectite (I/S) X-ray powder diffraction (XRD) pattern. Transmission electron microscopy (TEM) indicates that the illite laths increase in abundance and thickness with increasing depth; XRD patterns indicate a progressive increase in the illite component of the I/S. The deepest samples were found to contain long-range ordered (R=3) I/S, which showed platy particle morphology with the TEM. K-Ar ages of most of the <0.1-μm-size illite separates imply that illitization was a relatively brief event affecting a thick sequence of sediments during late Cretaceous to early Paleocene time (65–87 Ma); however, measured ages were affected by trace levels of detrital Ar contamination and do not represent the true age of diagenesis.Several methods of quantifying Ar contamination were used to correct measured ages to obtain a reasonable estimate of the true age of diagenesis. The corrected ages are imprecise due to uncertainties in quantifying the levels of sample contamination, but generally suggest a Paleogene (38–66 Ma) period of illitization. In contrast, simple kinetic models of smectite-illitization suggest much younger ages of diagenesis (0–40 Ma at the Veslefrikk field; 0–60 Ma at the Huldra field). The timing of the diagenesis and the morphologic aspects of the authigenic illite suggest that illite precipitated before late Tertiary compaction and resulted in a decrease in fluid permeability. Low trapping efficiency of early Tertiary sediments, vertical escape of warm fluid from the Brent sandstone, and high heat flow may have promoted illite diagenesis in the shales prior to deep late-Tertiary burial.
Improved representation of variance in measures of vowel merger

The difference between two vowels has most commonly been measured using F1, F2, or Euclidean distances (between averages or between minimal pairs). But relying on averaged data or minimal pair data only captures some of the variability; average obscure the amount of variability within a given vowel class, while calculating distance between minimal pairs is difficult with naturalistic data. Hay, Warren, and Drager (2006) introduced an alternative approach that accounts for the variability between those clusters, taking token-specific formant values, rather than averages, as input. The measure is the Pillai-Bartlett statistic, an output of a Multivariate Analysis of Variance (MANOVA), which represents the proportion of one variance that can be predicted by another variance. A higher Pillai indicates a lower degree of overlap between two vowel clusters in F1/F2 space. Since the value is derived from a MANOVA, Pillais can account for known internal factors influencing the production of merger, such as phonological environment. This paper applies the method to results from low back merger in California English (Hall-Lew 2009), and further suggests that the Pillai is useful for any vowel change, taking the fronting of the mid- and high back vowels as an example.
WHY DID SPANISH REGIONS NOT CONVERGE BEFORE THE CIVIL WAR? AGGLOMERATION ECONOMIES AND (REGIONAL) GROWTH REVISITED*

ABSTRACT In this paper we explore the relationship between the presence of agglomeration economies and regional economic growth in Spain during the period 1870-1930. The study allows us to revisit the existence of a trade-off between economic growth and territorial cohesion, and also to examine whether the existence of agglomeration economies could explain the upswing in regional income inequality during the early stages of development. In doing so, we present alternative indicators for agglomeration economies and estimate conditional growth regressions at province (NUTS3) level. In line with new economic geography models, agglomeration economies in a context of market integration widened regional inequality in the second half of the 19th century and hindered its reduction during the early decades of the 20th. RESUMEN En este artículo se analiza la existencia de una relación entre la presencia de economías de aglomeración y el crecimiento económico regional en España durante el periodo 1870-1930. El estudio permite revisitar la existencia de un trade-off entre crecimiento económico y cohesión territorial y, además, examinar si las economías de aglomeración fueron un elemento clave a la hora de explicar el incremento de la desigualdad económica regional en España a lo largo de las primeras fases del desarrollo. Para ello, se presentan diferentes indicadores de aglomeración a nivel provincial (NUTS3) que posteriormente se incluyen en la estimación de regresiones de crecimiento condicionadas. En la línea de los modelos de Nueva Geografía Económica (NEG), sugerimos que la presencia de economías de aglomeración en un contexto de integración de mercado favoreció la aparición de una causación acumulativa que amplió la desigualdad regional en la segunda mitad del siglo XIX y dificultó su reducción durante las primeras décadas del siglo XX.