Miracle-dz/UniFAR-FTUs huggingface dataset:
Protein-protein interface: database, analysis and prediction

Protein-protein interaction plays a pivotal role in biological metabolism. It directs many cellular processes like signal transduction, DNA replication and RNA splicing, etc. Identification of protein-protein interaction sites is important to identification of protein functions, improvement of protein-protein docking and rational drug design. Experimental methods to identify protein-protein interaction sites are always time-consuming and costly, which calls for computational methods to be applied in this area. The research work focuses on three parts: (1) We have built a Protein-Protein Interface Database (PPIDB) which extracted 71, 486 protein-protein interfaces from experimentally determined protein complex structures in the current version of Protein Data Bank. It facilitates construction of well-characterized datasets of protein-protein interface residues for computational analyses. The database is accessible through the Web Interface http://ppidb.cs. iastate.edu and a set of Web services. (2) We have made a comprehensive analysis of protein-protein dimeric interfaces, which consists of thirteen physic-chemical properties. The results disclose that interface residues have side chains pointing inward; interfaces are rougher, tend to be flat, moderately convex or concave and protrude more relative to non-interface surface residues; interface residues tend to be surrounded by hydrophobic neighbors. (3) We have developed NB PPIPS, a Naive Bayes method to predict protein-protein interaction sites on protein surfaces. Trained over a non-redundant data set consisting of 2, 383 proteins and fed with sequence, evolutionary and structural properties, NB PPIPS achieves 60.7% recall and 34.6% precision in 10 fold cross-validation, which greatly improves over the baseline classifier that only utilizes protein sequence information. Attempts are made to apply the NB PPIPS in a two stage prediction of protein-protein interfaces when only protein sequence is known. Modeled protein structures are generated via homologue modeling and fed as inputs into NB PPIPS. The results show that good predictions are obtained only for well modeled structures. NB PPIPS is implemented as an online server to facilitate its usage. It is accessible at http://watson.cs. iastate.edu/nb_ppips.
Pollution and Human Capital Migration: Evidence from Corporate Executives

We study the impact of pollution on the migration of high human capital employees. We link data on the opening of toxic-emitting plants with the career paths of executives at S&P 1500 firms. We discover that toxic-emitting plant openings increase executive departures from neighboring firms with adverse effects on stock prices. The results: are larger when polluting plants and firms are geographically closer, hold only for executives physically-based at treated firms, hold only for the opening of polluting plants, do not reflect other local factors or prior stock price performance, and are larger among executives with more general human capital.
Cooking quality and in vitro digestibility of legumes cooked in different media.

Legumes namely blackgram (Phaseolus mungo Roxb.), field bean (Dolichos lablab). lentil (Lens esculenta) and moth bean (Phaseolus aconitifolius Jacq.) were analyzed for proteins, fat, total ash, neutral detergent fibre, calcium, phosphorus and iron. The expansion volumes of legumes after soaking and cooking were recorded. The effect of cooking media (salt, soda, tartaric acid, citric acid at 1% level and water) on in vitro protein and starch digestibilities were analyzed. Results indicated that nutrient contents of legumes were in the following ranges : protein 21-25%, fat 0.8-1.5%, total ash 1.8-3.1%, neutral detergent fibre 11.2-20.0%, phosphorus 220-330 mg%, calcium 93-296 mg% and iron 3.3-5.8 mg%. Legumes recorded an average increase in expansion volume of 269% on soaking and 316% on cooking. The protein digestibility of control samples ranged from 91-97%, which were brought down on addition of soda (70-87%), salt (79-93%), tartaric acid (48-72%) and citric acid (75-81%). The starch digestibility values were 65-67% for blackgram and lentil, 35% for field bean and 44% for moth bean. Alkaline and salt media reduced starch digestibility to 64 and 55% in blackgram, 33% in field bean and 54 and 55% in lentils, respectively. With tartaric acid and citric acid, it increased significantly.
Faktor-Faktor yang Berhubungan dengan Usia Menarche Siswi SMP Adabiah

Abstrak Menarche (menars) adalah haid pertama dari uterus yang merupakan awal dari fungsi menstruasi dan tanda telah terjadinya pubertas pada remaja putri. Pada dekade terakhir menunjukkan kecenderungan pergeseran usia menars ke arah umur yang lebih muda. Tujuan penelitian ini adalah menentukan faktor-faktor yang berhubungan dengan usia menars. Jenis penelitian ini adalah analitik observasional dalam bentuk rancangan cross sectional study. Populasi dalam penelitian ini adalah seluruh siswi SMP Adabiah kelas VII dan VIII tahun ajaran 2012/2013. Jumlah sampel sebanyak 72 siswi yang diambil secara Simple Random Sampling. Data dikumpulkan dengan angket dan pengukuran tinggi dan berat badan responden. Pengolahan data dilakukan secara komputerisasi dan analisis dengan uji chi-square pada α = 0,05. Hasil penelitian didapatkan bahwa usia menars rata-rata siswi SMP Adabiah adalah 12,29 ± 0,49 tahun. Uji statistik menunjukkan terdapat hubungan yang bermakna antara tingkat pendapatan per kapita dan status gizi dengan usia menars sedangkan tingkan pendidikan orang tua dan paparan media massa tidak terdapat hubungan yang bermakna dengan usia menars. Kata kunci: usia menars, pendapatan per kapita, status gizi Abstract Menarche is the first menstruation or bleeding of the uterus that is the beginning of the menstrual function and mark the occurrence of puberty in young girls. In the past decade shows a shift in the age of menarche trend toward younger age. The objective of this study was to determine the associated factors to age of menarche. This type of research is observational analytic with cross sectional study design. The population in this study were all junior high school students of class VII and VIII academic year 2012/2013. The total sample of 72 student were taken by simple random sampling. Data were collected by questionnaire and measurement of height and weight. Data was analyzed by chi-square test at α = 0,005. The result showed that the average age of menarche Adabiah junior high school student was 12.29 ± 0.49 years. There is a significant correlation between the level of per capita income and nutritional status with age of menarche, while the level of parental education and exposure to mass media have no significant correlation with age of menarche. Keywords: menarche age, per capita income, nutritional status
A Glia-Mediated Feedback Mechanism for the Termination of Drosophila Visual Response: A Dissertation

High temporal resolution of vision relies on the rapid kinetics of the photoresponse in the light-sensing photoreceptor neurons. It is well known that the rapid recovery of photoreceptor membrane potential at the end of light stimulation depends on timely deactivation of the visual transduction cascade within photoreceptors. Whether any extrinsic factor contributes to the termination speed of the photoresponse is unknown. In this thesis, using Drosophila as a model system, I show that a feedback circuit mediated by both neurons and glia in the visual neuropile lamina is required for rapid repolarization of the photoreceptor at the end of the light response. In the first part of my thesis work, I provide evidence that lamina epithelial glia, the major glia in the visual neuropile, is involved in a retrograde regulation that is critical for rapid repolarization of the photoreceptor at the end of light stimulation. I identified the gene affected in a slrp (slow receptor potential) mutant that is defective in photoreceptor response termination, and found it needs to be expressed in both neurons and epithelial glia to rescue the mutant phenotype. The gene product SLRP, an ADAM (a disintegrin and metalloprotease) protein, is localized in a special structure of epithelial glia, gnarl, and is required for gnarl formation. This glial function of SLRP is independent of the metalloprotease activity. In the second part of my thesis work, I demonstrate that glutamatergic transmission
Optimisation of Raman spectroscopy for the analysis of Basidiomycota: spores, latex and mycelium

For several decades, Raman spectroscopy has been used in different research fields. As a result of progression in the instrumentation during the last years, Raman spectroscopy became available for the analysis of complex biomaterials. In this work, the opportunities of the technique for the analysis of Basidiomycota are explored. The chemical composition of spores of Lactarius species is studied. These spores are mostly comprised of lipids and saccharides: they contain large amounts of triolein and smaller amounts of amylopectin (amyloid ornamention) and chitin. Furthermore, the Raman spectra are compared with those of spores of the genera Collybia, Laccaria, Mycena and Russula. By using a chemometric identification protocol (interference elimination, autoscaling, PCA and LDA) the genus was correctly assigned to a spore print in 90% of the cases, whereas the species could not be deduced from the Raman spectra. It is shown that Raman spectroscopy is a good additional method for the analysis of Lactarius latex. 2D correlation analysis of the latex spectra gives an overview of the major compositional changes and may discriminate between the different reaction steps. The reaction sequence of Lactarius lacunarum latex is studied. Different types of reaction sequences are observed in different species, which might be of taxonomic importance. The last section of this work discusses an explorative study of mycelium cultures of common wood rots. The Raman spectra are discussed and compared with the Raman spectra of infected and unifected Fagus and Pinus wood. In this way, it was shown that hyphae of a wood rot fungus can be detected in infected wood, although the spectral differences in cellulose and lignin bands can be much larger relative to the bands of the fungus. White rots can be detected through the presence of several Raman bands (e.g. at 916 and between 1000 and 1008 cm-1), whereas carotenoid vibration bands between 1510 and 1540 cm-1 are typical for brown rots.
Percentagem de gordura de cavalos criados em região tropical

Determinacao da percentagem de gordura corporal (PG) pode contribuir para avaliar praticas de manejo nutricional e de treinamento. O objetivo do trabalho foi determinar a PG em equinos em condicoes tropicais. Froram analisados 121 cavalos, agrupados em: reproducao (subgrupos: jovens, eguas vazias, egua gestacao I e II, egua lactacao I e II e garanhao) e atletas (subgrupos: vaquejada e marcha). A PG foi avaliada a partir da camada de gordura pela ultrassonografia. Os resultados foram submetidos a ANOVA e o metodo de Tukey para animais de reproducao e o teste T para atletas. Demonstrou-se variacao na PG no grupo reproducao, sendo que os jovens (~10,4%) apresentaram menor PG que o garanhao (~16,6%), egua vazia (~14,0%) e egua gestante I (~14,8%) e II (~15,5%) (p
Population structure of the vernal pool fairy shrimp (Branchinecta lynchi) at two spatial scales

Author(s): McClintock, Kelly Marie | Advisor(s): Aguilar, Andres | Abstract: Patterns of dispersal and gene-flow in freshwater invertebrates have often been difficult to interpret. Despite the assumed high potential for dispersal, populations of freshwater invertebrates display high genetic differentiation over small distances. There have been several explanations posed for this gene flow dispersal paradox, including strong priority effects or low realized dispersal. This study explores the spatial genetic structure of the freshwater invertebrate Branchinecta lynchi, a threatened vernal pool inhabitant, at two scales with a goal to determine the scale at which gene flow is important in shaping these patterns. Vernal pools were sampled at two different localities the San Luis National Wildlife Refuge Complex and a preserve adjacent to the University of California, Merced. Individuals were genotyped using both the mitochondrial cytochrome oxidase I subunit (COI) and nuclear amplified fragment length polymorphisms (AFLPs). Pairwise Fst values showed that genetic structure for this species was high, however, the only geographic pattern that emerged was isolation by distance at the local scale for the COI marker. Discrepancies between mitochondrial and AFLP markers may be explained several ways, including genotyping error, sex-biased dispersal and/or the longer time to equilibrium of the nuclear genome. These results suggest that gene flow is important at the local scale, at least for mitochondrial DNA, while historical colonization patterns are likely maintained at the regional scale by priority effects. I infer that maintaining connectivity among vernal pool complexes through local dispersal vectors should be a management priority.
Cytogenetic Studies on the Origin of Camellia vernalis

The chromosome numbers of the natural seedlings of Camellia×vernalis, cv. ‘Gaisen’ (tetraploid, n=15) and cv. ‘Bokyo’ (pentaploid) were determined and the origin of red pigmentation in C. sasanqua is discussed. The seedlings of C. ×vernalis cv. ‘Gaisen’ were triploid, tetraploid and pentaploid. When C. sasanqua was abundant around the parent tree, pentaploid seedlings were more numerous than triploid ones. The pentaploid seedlings were considered to be backcrosses with C. sasanqua (hexaploid), and the triploid to he backcrosses with C. japonica (diploid). The chromosome numbers of the seedlings of C. ×vernalis cv. ‘Bokyo’, a pentaploid, ranged from 2n=79 to 86, suggesting that only backcrosses to C. sasanqua are occurring. If C. ×vernalis hybrids typically only backcross with the C. sasanqua parent, and some fertility is maintained in the interspecific backcrosses with C. sasanqua, then this backcrossing system becomes a mechanism for the flow of C. japonica genes into the species C. sasanqua. Thus, the red flowers of C. sasanqua are thought to have originated from repetitive backcrossing (introgression) with C. ×vernalis.
A Study on the Influence of Software and Hardware Features on Program Energy

Software energy consumption has emerged as a growing concern in recent years. Managing the energy consumed by a software is, however, a difficult challenge due to the large number of factors affecting it -- namely, features of the processor, memory, cache, and other hardware components, characteristics of the program and the workload running, OS routines, compiler optimisations, among others. In this paper we study the relevance of numerous architectural and program features (static and dynamic) to the energy consumed by software. The motivation behind the study is to gain an understanding of the features affecting software energy and to provide recommendations on features to optimise for energy efficiency. In our study we used 58 subject desktop programs, each with their own workload, and from different application domains. We collected over 100 hardware and software metrics, statically and dynamically, using existing tools for program analysis, instrumentation and run time monitoring. We then performed statistical feature selection to extract the features relevant to energy consumption. We discuss potential optimisations for the selected features. We also examine whether the energy-relevant features are different from those known to affect software performance. The features commonly selected in our experiments were execution time, cache accesses, memory instructions, context switches, CPU migrations, and program length (Halstead metric). All of these features are known to affect software performance, in terms of running time, power consumed and latency.
Screening and evaluation of white rot fungi to decolourise synthetic dyes, with particular reference to Antrodiella albocinnamomea

The ability of 60 white-rot fungal strains (38 species) to decolourise six structurally different synthetic dyes, namely Congo red, Orange G, Alizarin red, Crystal violet, Neutral red and Methylene blue, which, respectively, belong to the azo, anthraquinone-based, triphenylmethane and heterocyclic dye groups, were investigated by agar plate tests. Effects of different culture conditions on the decolourisation of Alizarin red by the Chinese-specific species of white-rot fungus, Antrodiella albocinnamomea, were investigated using liquid cultures. The results show that most of the isolates had the capacity to decolourise all synthetic dyes. Antrodiella albocinnamomea was first reported as having a strong decolourizing capacity and is closely related to Cerrena unicolor in the phylogenetic tree. In liquid culture, the optimum pH was 5.5 and, compared to other carbon and nitrogen sources tested, glucose and malt extracts resulted in the best decolourisation performances. The high activity of laccase produce by A. albocinnamomea was mainly responsible for its high decolourisation efficiency.
Response of late-sown gram (Cicer arietinum) to irrigation and phosphorus

Response of late-sown gram or chickpea (Cicer arielinum L.) to 4 levels of irrigation (no post-sowing irrigation, Post-sowing irrigation at irrigation depth: cumulative pan-evaporation ratios 0.2, 0.4 and 0.6) and phosphorus (0, 8.8, 17.6 and 26.4 kg P/ha) was investigated at Hisarin the winter seasons of 1986-87 . and 1987-88. The unirrigated plants had lower leaf-water potential, evapo-transpiration, stomatal conductance, light absorption, leaf -area index, yield components and grain yield compared with irrigated plants, but had higher canopy temperature. Among yield components, water stress primarily affected the number of pods/m row length and had litile effect on grains/pod. P application improved the leaf-water potential, stomatal conductance,light absorption,leaf-area index, seed yield and water-use efficiency and decreased the canopy temperature. The combination of irrigation water: cumulative pan-evaporation ratio 0.4 with 26.4 kg/ha gave significantly higher grain yield than other treatments.
Mathematical modelling of mitotic exit control in budding yeast cell cycle

The operating principles of complex regulatory networks are more easily understood with mathematical modelling than by intuitive reasoning. In this thesis, I study the dynamics of the mitotic exit control system in budding yeast. I present a comprehensive mathematical model, which provides a system’s-level understanding of the mitotic exit process. This model captures the dynamics of classic experimental situations reported in the literature, and overcomes a number of limitations present in previous models. Analysis of the model led to a number of breakthroughs in the understanding of mitotic exit control. Firstly, numerical analysis of the model quantified the dependence of mitotic exit on the proteolytic and non-proteolytic functions of separase. It was shown that the requirement for the non-proteolytic function of separase depends on cyclin-dependent kinase activity. Secondly, APC/Cdc20 is a critical node that controls the phosphatase (Cdc14) branch and both cyclin (Clb2 and Clb5) branches of the cell cycle regulatory network. Thirdly, the model proved to be a useful tool for the systematic analysis of the recently discovered phenomenon of Cdc14 endocycles. Most proteins belonging to the cell cycle control network are regulated at the level of synthesis, degradation and activity. Presumably, these multiple layers of regulation facilitate robust cell cycle behaviour in the face of genetic and environmental perturbations. To falsify this hypothesis, I subjected the model to global parameter perturbations and tested viability against pre-defined criteria. According to these analyses, the regulated transcription and degradation of proteins make different contributions to cell cycle control. Regulated degradation confers cell cycle oscillations with robustness against perturbations, while regulated transcription plays a major role in controlling the period of these oscillations. Both regulated transcription and degradation are part of important feedback loops, that combined promote robust behaviour in the face of parametric variations.
Do Financial Ratios Affect Stock Returns in the Athens Stock Exchange

This study examines whether selected financial ratios can be used to explain stock price movement in the Athens stock exchange (ASE) for the period between 2005 and 2014. Information about potential driving factors of stock returns can be useful to capital market analysts and investors when trying to predict stock price movements and also to the managers of the underlying companies when they are planning their strategies. The financial ratios selected are the return on equity, the net profit margin, the assets turnover ratio, the assets to equity ratio, the current ratio and the dividend payout ratio. The empirical results of our study showed that during the examined period a statistically significant relation was not in generally observed between stock returns and the examined ratios. This was also the case when the periods from 2005 to 2009 and from 2010 to 2014 were examined separately. Only the return on equity was found to be significant for the overall period, as well as for the period from 2010 to 2014. Opposite to what we expected, the ROE coefficient was found to be negatively related to stock returns.
LIVING ON THE EDGE: A COMPARATIVE PHYLOGEOGRAPHIC STUDY OF REFUGIAL AND INSULAR FRAGMENTATION

Pleistocene glacial-interglacial cycles resulted in population isolation that led to interand intraspecific genetic divergence in many North American species. The magnitude of isolation also influenced species response to these climatic changes and set the stage for contemporary gene flow. We can refine our understanding of species response to historical climate change by identifying regions of ice-free persistence and refugia during glacial maxima, and geographic locations and genetic dynamics of postglacial secondary contact. This dissertation examines the role of glacial cover, geographic barriers, habitat fragmentation as a result of changes in sea level, and insularity on the contemporary genetic structure of three widespread, co-distributed, and ecologically distinct small mammals across western North America, with emphasis on the Pacific Northwest. Previous work on long-tailed voles (Microtus longicaudus), northwestern deer mice (Peromyscus keeni), and dusky shrews (Sorex monticolus) was used to formulate hypotheses of geographic distribution of genetic variation, timing of divergence, and regions of glacial persistence. This dissertation uses multilocus genetic data and historical climatic conditions to address these hypotheses. I identify regions of glacial persistence, the effects of historical sea levels on island connectivity, and regions
Gorgonian community structure and reef zonation patterns on Yucatan coral reefs

The community structure and zonation of gorgonian fauna were studied to determine whether it represented the traditional zonation pattern of the reef as influenced by scleractinian fauna and topographic relief.Seeking to avoid the effect of local variability, a large reef area was quantitavely sampled on the east coast of the Yucatan Peninsula