Miracle-dz/UniFAR-FTUs huggingface dataset:
Online Multi-Instance Multi-Label learning for protein function prediction

Protein function prediction is a challenging and essential research problem in the field of computational biology. Conventionally, a protein consists of a number of structural domains and performs multiple function. By representing proteins, domains and functions by bags as well as instances and classes respectively, we are able to model the protein function prediction task as the Multi-Instance Multi-Label (MIML) learning problem. Existing MIML algorithms mainly focus on batch setting where training examples are available before learning. Such offline paradigm works well in simulation, but it may be not feasible for real-world online applications where data comes one by one or chunk by chunk. In this paper, we investigate the protein function prediction problem under a new learning framework, called Online Multi-Instance Multi-Label (OMIML) learning, where MIML protein examples arrive sequentially in an online setting, and develop two OMIML algorithms (OMIML-I and OMIML-B) to make predictions for the incoming data. In the proposed OMIML algorithms, variable-length features are constructed to represent the MIML protein examples based on an incremental vocabulary mechanism. In particular, the incremental vocabularies that OMIML-I and OMIML-B are based on consist of instances and bags, respectively. Then we seek an online prediction for each new arrived protein example by incorporating the constructed features into an online multi-label learning algorithm which is constructed by introducing an artificial label into an online multi-label ranking model. We evaluate the algorithms on the protein dataset consisting of seven real-world organisms. Experimental results have demonstrated the effectiveness of the proposed OMIML algorithms for protein function prediction.
Radio continuum surveys: lessons learned

While making and using radio continuum surveys, radio astronomers have had many learning experiences, as in “Oh, no! Not another learning experience! ” They include problems with confusion from multiple sources in each beam area, insensitivity to low-brightness sources, correcting source counts for partially resolved or missing sources, and ignoring systematic errors, particularly the consequences of limited dynamic range. The principal lessons that I have learned from these experiences are: (1) The universe is not a vacuum. The design of surveys (and survey telescopes) should take into account known source properties, not just purely instrumental parameters such as “survey speed. ” (2) The radiometer equation and Gaussian statistics are insensitive to the most insidious problems that plague radio continuum surveys. More sophisticated mathematical analyses are needed to optimize telescope and survey design. (3) Never forget the difference between flux density (Jy) and peak flux density (Jy beam−1 or K), which is a surface brightness. Ideally a survey is complete to some flux density (a source property), but all survey images are sensitivity limited by surface brightness (Jy beam−1), which depends on the instrumental beam solid angle. (4) Resolution corrections to counts of faint sources are so large and poorly understood that they limit the usefulness of sub-mJy surveys. These lessons are applied to design a possible Jansky Very Large Array (VLA) “wedding cake” survey that could provide a strong extinction-free constraint on the cosmological evolution of the star formation rate over the redshift range 0≤ z . 3 in which most stars were formed.
ASSESSMENT AND PREDICTION OF PROTEIN STRUCTURES

Author(s): Eramian, David Edward | Advisor(s): Sali, Andrej | Abstract: An ambitious goal of modern biology is to understand the structure(s), interaction(s) and function(s) of each protein within cells and organisms. Understanding the nature of the interactions a protein makes is important because no protein exists in isolation, but rather functions through interactions with other macromolecules. Knowledge about the function of proteins is essential to understanding biological processes. Structure is the unifying component: both interactions and functions are intrinsically related to structure, as the structure of a protein helps define its function and affects the nature, type, and number of interactions it has with other macromolecules. Great attention has been paid to the development of methods for both the theoretical prediction and experimental determination of protein structure. Though experimentally-derived structures are more accurate, they are relatively scarce: of the millions of known protein sequences, well fewer than 1% of their corresponding structures have been solved experimentally. In the absence of an experimentally determined structure, computational models are often valuable for generating testable hypotheses and giving insight into existing experimental data. Such computational structure models are available for over two orders of magnitude more protein sequences than are experimentally determined structures, yet suffer from two limitations that experimentally determined structures do not: they frequently contain significant errors, and their accuracy cannot be readily assessed. The research described herein sought to increase the accuracy and applicability of computational protein models by addressing these two limitations. This broad goal was approached in four principal ways: (1) identifying the most native-like models from among sets of similar models; (2) predicting the absolute accuracy of protein structure models; (3) improving the accuracy of target/template alignments to increase the accuracy of comparative models built from distantly related template structures; and (4) developing a unified protein structure prediction protocol that makes the best use of all available information about the structure of a given protein, regardless of whether it is directly based on experiment, on the broader knowledge base, on statistical potentials, or intuition.
Why Being Single? : A Research For The Delayed Marriage Among People (Aged 25-35) In Shanghai, China

Get married is the rite of passage that coincides with exit from the parental household, solemnizing the establishment of a new household and commitment to a sexual partner (Allan, G. et al, 2003:135), which is a ubiquitous phenomenon across human society. Almost all adult men and women seek to marry or form a permanent stable relationship with another person for the sake of bear children and raise a family in a secure, loving, and fulfilling environment. However, in Shanghai of China, more and more people have exceeded the normal matrimonial age but remaining unmarried, those who are intituled as "Young but Old people (DA LING QINGNIAN)". It is previously deemed by Chinese people as "A Man Should Get Married On Coming Of Age, A Girl Should Be Married Upon Reaching Womanhood (NAN DA DANG HUN, NV DA DANG JIA)", but nowadays, the conventional conception of marriage seems to be toppled down especially in big cities of China, like Shanghai. "Young but Old people" has turned into an age group in which not being married in statistically normal. It is, therefore, attracted people's attention that whether being single is lived as a positive social category for both woman and men. People may pose questions such as: How it comes the delayed marriage? What single young people seek and expect of relationships? Is there any gender difference of staying alone? Are they enjoying the experiences of being single? What are the young people's plans and expectations about the future of their personal life? To give the reader some idea of what to expect in the following pages, the main concern of this thesis paper is related to the possible causations of being single and the attitude and plans of young people who are somewhat in the shadow of marriage
A Comparative View Of Applying Linear And Non-Linear Visualisation Approaches To Protein Dataset

This novel method enlivened via cartographic maps in the geology area and this technique has been utilized to reintroduce in the visualization space lost data in which the non-linear mapping brings about. The diagnostic measurement of such a bending has been communicated as Magnification Factors, and after that computed then envisioned together as the Cartogram maps We improved interpretability Linear model apply through drtoolbox where cyan circles represent HLA-A, red plus sign represents HLA-B and blue square represents HLA-C. Basic purpose behind this study was that previously for large amount of data set, clustering and classifications techniques were used, but through drtoolbox, it is used in MATLAB. The researcher has visualized data for better understanding. This data was aligned in class I HLA-A, HLA-B and HLA-C. Data was available in the form of groups, when it was aligned horizontally then there were 372 rows and 12458 columns. After sorting of data 180 columns remained, Then this data was checked column wise check. The dashes present in the data was replaced by the alphabet displayed at the top of each column. The data coding was done on 12458 rows and data was converted into nominal form. Consensus sequence of data was checked later, the purpose of this sequence is to check the occurrence of each alphabet in a column. The alphabet that was maximum was converted to binary code 1 and remaining were converted to 0. When the data was converted in to binary then models were applied on the data. If the data is in linear form then linear model is better and if the data is in non linear form then non linear model is better, it depends on the results of the data. But in case of this study non linear models showed worst visualization. PCA which is a linear model has showed much better visualization.
Physiological effects of dominance hierarchies: laboratory artefacts or natural phenomena?

Studies of fish behaviour have demonstrated the existence of social interactions that result in dominance hierarchies. In environments in which resources, such as food, shelter and mates, are limited, social competition results in some fish becoming dominant and occupying the most profitable positions. This behaviour has been observed in natural environments and also in many laboratory-based experiments. When two fish have been confined in a small tank, one of them usually has exhibited behaviour that suggests it is dominant over the other submissive animal. Physiological consequences of social interaction can be seen in both dominants and subordinates but are more extreme in the subordinate. However, this scenario is without doubt an artificial situation. Fewer experiments have been conducted using laboratory experiments that are more socially and physically complex than those experienced by dyads in tanks. In simple fluvial tanks, through which water is recirculated, the physiological responses of fish to social competition have generally been qualitatively similar to those recorded among dyads. However, when environmental disturbances, complex resource distributions, increase in water flushing, presence of predators and competing species of fish have been included in experimen-tal designs, there have been fewer, diminished or no physiological dierences between dominant and subordinate fish. There have been very few studies of physiology in relation to dominance in natural habitats, and those that have been conducted suggest that under some circumstances hierarchies may cause less intense physiological responses than have been suggested based on results of laboratory studies in simple environments. Possible reasons for these variations are discussed. The need is identified for a well structured experimental approach to the investi-gation of the causes and consequences of hierarchies if the ecology of wild fish is to be modelled eectively based on physiological processes. It is also suggested that the further development and application of techniques for monitoring physiologies of fish in the wild is important.
Female mice exposed to low-doses of dioxin during pregnancy and lactation have increased susceptibility to diet-induced obesity and diabetes

Objective Exposure to persistent organic pollutants is consistently associated with increased diabetes risk in humans. We investigated the short- and long-term impact of chronic low-dose dioxin (aka 2,3,7,8-tetrachlorodibenzo-p-dioxin, TCDD) exposure during pregnancy and lactation on glucose homeostasis and beta cell function in female mice, including their response to a metabolic stressor later in life. Methods Female mice were injected with either corn oil (CO; vehicle control) or 20 ng/kg/d TCDD 2x/week throughout mating, pregnancy, and lactation, and then tracked for 6-10 weeks after chemical exposure stopped. A subset of CO- and TCDD-exposed dams were then transferred to a 45% high fat diet (HFD) or remained on standard chow diet for an additional 11 weeks to assess long-term effects of TCDD on adaptability to a metabolic stressor. Results Dioxin-exposed dams were hypoglycemic at birth but otherwise had normal glucose homeostasis during and post-dioxin exposure. However, dioxin-exposed dams on chow diet were modestly heavier than controls starting 5 weeks after the last dioxin injection, and their weight gain accelerated after transitioning to a HFD. Dioxin-exposed dams also had accelerated onset of hyperglycemia, dysregulated insulin secretion, reduced islet size, increased MAFA- beta cells, and increased proinsulin accumulation following HFD feeding compared to control dams. Conclusions Our mouse model suggests that chronic low-dose dioxin exposure may be a contributing factor to obesity and diabetes pathogenesis in females.
Welfare to Work in Australia: Disability Income Support, Housing Affordability and Employment Incentives

Abstract Internationally, considerable policy attention is being paid to increasing the employment participation of disabled working-age people. Like other OECD countries, Australia has experienced growth in the number of Disability Support Pension (DSP) recipients due to changes in industry structure and increases in precarious employment. This history is well-rehearsed in policy debates. However, little research attention has been given to the housing circumstances of DSP recipients. This is important, particularly when we note the increasing incidence of working-age DSP recipients in the private rental market and public housing. For public renters the incidence has more than tripled to 27 per cent over the period 1982–2002. This paper addresses two questions: ‘What are the housing circumstances of DSP recipients? ’ and ‘What are the likely consequences of programme changes aimed at increasing employment participation of DSP recipients? ’ Using Australia as an example, this article considers interactions between the new disability payment system being implemented through Welfare to Work, housing costs and employment income.
Using ICT to transform education

s Please provide an abstract of approximately 100 words. The abstract should be included with the rest of your article in the submission file, but it should also be copied into the appropriate text box during the on-line submission process. Biography Please supply a short (100 word) biography for each author. This should include the name, rank, institution, institutional address, and email address. Do not place the biography in your submission file but copy it into the appropriate text box during the on-line submission process. Style Submitted manuscripts must be written in the Harvard editorial style: o References should relate only to material cited within the manuscript and be listed in alphabetical order, including the author's name, complete title of the cited work, title of the source, volume, issue, year of publication, and pages cited. See the following examples: Marshall, S. (1991), "A genre-based approach to the teaching of report-writing". English for Specific Purposes, vol. 10, no.1, pp. 3-13. Taylor, W. & Marshall, S. (2002), "Collaboration: the Key to Establishing Community Networks in Regional Australia", Informing Science, vol. 5, pp. 155-162. Marshall, S. , Taylor, W. , & Yu, X. (eds.) (2003), Closing the Digital Divide: Transforming Regional Economies and Communities with Information Technology, Greenwood Publishing, Westport CT. viii IJEDICT Volume 3, Issue 1 (2007) o Citations in the text should include the author's name and year of publication where you use the source in the text, as in the following examples: In this way, information technology can be seen to effect and influence changes in organisational structure (Orlikowski & Robey 1991). Edwards (1995, p.250) views the globalising of distance education as "invested with the uniform cultural messages of modernity". Globalisation, especially in relation to open and distance education, will reduce the tolerance of difference and so "how can local issues and contexts be addressed? " (Evans 1995, p.314). o Further information about the Harvard editorial style can be found at: http://lisweb.curtin. edu.au/referencing/harvard.html http://www.library. uwa.edu.au/guides/citingsources/harvard.html
Managing Internationalization through Innovation: A Viewpoint from a Developing Country

The aim of this paper is to study the aspects that influence export activity of companies in developing countries, with a particular focus on their innovative behavior. Most studies have analyzed this issue in advanced countries and only recently, several studies have started to analyze this aspect in developing countries. Our main conclusion -in the case of Mexicos that innovative behavior is directly associated with exporting behavior. All econometric studies that we analyzed define this relation as linear; however, our results show that this conclusion needs reviewing. We show -with empirical data for the case of Mexico- that this linear model could be erroneous. Using a logistic regression model to examine the effect of innovative behavior on export probability, our data reflect a non-linear relationship in the form of an inverted "U". The least innovative companies have a lower export probability, and are followed by the most innovative firms; however, companies with a "medium" level of innovative behavior are the most competitive in the world market. Taken from the company standpoint, we hope to shed light on why innovative behavior should be an important factor when building an internationalization strategy
Use of the nicotine skin patch by smokers in 20 communities in the United States, 1992-1993.

OBJECTIVE: To measure the characteristics of smokers associated with the use of the nicotine skin patch in the general population and to evaluate whether use of the patch is associated with successful smoking cessation. DESIGN: Data from two surveys conducted in 20 communities in the United States as part of the National Cancer Institute's Community Intervention Trial for Smoking Cessation (COMMIT) study. Nicotine patch prevalence was estimated using data from a 1993 cross-sectional survey of 13691 current and former smokers. The effectiveness of the nicotine skin patch as a smoking cessation aid was evaluated adjusting for other covariants using data from a cohort tracking study of 9809 smokers who were followed between 1988 and 1993. As the nicotine patch was not available to consumers until January 1992, analyses were restricted to respondents who reported themselves to be current smokers in 1993 or former smokers who reported quitting after January 1992. OUTCOME MEASURES: Current and former smokers who reported having made a serious effort to stop smoking in the past five years were asked to indicate whether they had used the nicotine skin patch to help them stop smoking. Those answering "Yes", were classified as nicotine patch users. Smoking cessation was based on self-report. A "quitter" was defined as someone who had been a smoker as of January 1992 who reported in 1993 not smoking any cigarettes for the preceding six months or longer. RESULTS: The prevalence of nicotine patch use by smokers averaged across the 20 study communities was 12.8%, making the patch one of the most popular cessation methods used by smokers. Compared with non-users, patch users were more likely to be female, white, have higher annual household incomes, be more motivated to stop smoking, and to smoke more heavily. Among low-income smokers (annual household income below US$10000), nicotine patch use was significantly higher among those who lived in a state where the public insurance programme (Medicaid or Medi-Cal) included the patch as a benefit (12.1% vs 7.7%). Among those who made an attempt to quit smoking, the likelihood of successful quitting was more than twice as high among patch users compared with non-users. Among patch users, the highest quit rates were observed among those who used the patch for between one and three months. CONCLUSIONS: The nicotine skin patch is a popular and effective means of smoking cessation. Use of the nicotine patch, especially by low-income smokers, could be increased by reducing the out-of-pocket expenditure required for smokers to get the product.
Alterations of the Wnt /-catenin Signaling Pathway in Cancer of the Ampulla of Vater Corresponding

Background : Carcinoma of the ampulla of Vater is rare and its pathogenesis is unclear. The role of epigenetic changes in the APC or CDH1, in the Wnt pathway, has not been reported in ampullary carcinomas. Methods : We performed immunohistochemistry on 73 sporadic ampullary carcinomas to identify Wnt-related molecules (APC, -catenin, E-cadherin, c-erbB2, cyclin D1) and examined mutations in the CTNNB1, loss of heterozygosity of 5q21, and the methylation status of the CpG island of APC and CDH1. Results : Thirteen tumors (17.8%) showed abnormal nuclear localization of -catenin; this was more prominent in the intestinal type than in the pancreaticobiliary type (p=0.01). The loss of APC correlated with the loss of -catenin or c-erb B2 (p<0.01). The prognosis was worse in the group with APC loss than when APC was maintained (p<0.05). There was no mutation identified in CTNNB1. Six (24%) out of 25 informative cases had 5q21 allelic loss. CpG island methylation in APC and CDH1 was detected in 33 (45.2%) and 29 (31.5%) cases, respectively. Conclusions : The absence of mutations in CTNNB1 and the epigenetic alteration of APC and CDH1, might be characteristic changes in the Wnt/ -catenin signaling pathway during the carcinogenesis of ampullary carcinomas.
Congenital dyserythropoietic anemia type II: ultrastructural and radioautographic studies of blood and bone marrow.

A 12-yr-old white girl with congenital dyserythropoietic anemia (CDA) type II was studied. Excessive cytoplasmic membranes (appearing like "double membranes") were found in the majority of the normoblasts. There was marked decrease in the uptake of tritiated thymidine in the binucleated normoblasts as demonstrated by radioautography. The results suggest that the cells with more severe structural cytoplasmic abnormalities and/or decreased DNA synthesis are destroyed within the bone marrow, and the circulating red cells are derived from a less abnormal population of precursors.
Regulation of enzyme function.

INTRODUCTION • . ' " . • • . • . • . • • . • . • . 47 Experimental test in vivo of suggested regulatory effects and interactions. 48 Molecular basis for regulatory phenomena . '" . 49 Unidirectional inhibition or stimulation. 51 METABOLIC REGULATION-GENERAL CONSIDERATIONS. • • . 51 Adenylate control. 52 REGULATION OF GLYCOLYSIS AND THE CITRATE CYCLE. 56 Pyruvate kinase. 56 Lactic dehydrogenase. 57 Pyruvate dehydrogenase. 57 Citrate synthetase. 57 Isocitrate dehydrogenase. 58 3-C to 4-C conversions. 58 Glyoxylate cycle. 59 Glutamate dehydrogenase. 59 BroSYNTHETIC FEEDBACK INHIBITION. 59 Aspartokinase. 59