Question Popularity Analysis and Prediction in Community Question Answering Services

With the blooming of online social media applications, Community Question Answering (CQA) services have become one of the most important online resources for information and knowledge seekers. A large number of high quality question and answer pairs have been accumulated, which allow users to not only share their knowledge with others, but also interact with each other. Accordingly, volumes of efforts have been taken to explore the questions and answers retrieval in CQA services so as to help users to finding the similar questions or the right answers. However, to our knowledge, less attention has been paid so far to question popularity in CQA. Question popularity can reflect the attention and interest of users. Hence, predicting question popularity can better capture the users’ interest so as to improve the users’ experience. Meanwhile, it can also promote the development of the community. In this paper, we investigate the problem of predicting question popularity in CQA. We first explore the factors that have impact on question popularity by employing statistical analysis. We then propose a supervised machine learning approach to model these factors for question popularity prediction. The experimental results show that our proposed approach can effectively distinguish the popular questions from unpopular ones in the Yahoo! Answers question and answer repository.     

Error-tolerant pooling designs with inhibitors.

Pooling designs are used in clone library screening to efficiently distinguish positive clones from negative clones. Mathematically, a pooling design is just a nonadaptive group testing scheme which has been extensively studied in the literature. In some applications, there is a third category of clones called "inhibitors" whose effect is to neutralize positives. Specifically, the presence of an inhibitor in a pool dictates a negative outcome even though positives are present. Sequential group testing schemes, which can be modified to three-stage schemes, have been proposed for the inhibitor model, but it is unknown whether a pooling design (a one-stage scheme) exists. Another open question raised in the literature is whether the inhibitor model can treat unreliable pool outcomes. In this paper, we answer both open problems by giving a pooling design, as well as a two-stage scheme, for the inhibitor model with unreliable outcomes. The number of pools required by our schemes are quite comparable to the three-stage scheme.     

Economics, Biology, and Naturalism: Three Problems Concerning the Question of Individuality

The paper examines the ramifications of naturalism with regard to the question of individuality in economics and biology. Economic theory has to deal with whether households, firms, and states are individuals or are mere entities such as clubs, networks, and coalitions. Biological theory has to deal with the same question with regard to cells, organisms, family packs, and colonies. To wit, the question of individuality in both disciplines involves three separate problems: the metaphysical, phenomenist, and ontological. The metaphysical problem is concerned with purposeful action: Is the firm or organism exclusively the product of efficient causality (optimization) or is it motivated by final causality (purposefulness)? The phenomenist problem is interested in the substantiality of essences: Is the firm's or organism's scheme of institutions/traits deep or is it extraneous to identity? The ontological problem is related to the issue of reductionism: Is the behavior of lower-level organization governed by a pre-constituted entities or is it context-sensitive? The paper finds that theoretical differences run along the naturalist/anti-naturalist divide rather than along disciplinary specialization. Also, the paper finds that it is not inconsistent for the same theorist to be naturalist with regard to one problem and anti-naturalist with respect to the other two problems.     

Embryogenesis: a Question of Pattern

Embryogenesis in plants appears superficially to be a relativelysimple process in terms of morphological development and itis the case that most organogenesis takes place in the post-embryonicphase of the life cycle. This apparent simplicity allows usto exploit embryogenesis as a model experimental system to studythe relationship between gene expression and morphogenesis,which is arguably the most important question in developmentalbiology. However, we are only just beginning to describe changesin gene expression during embryogenesis and to identify regulatorynetworks. Recent work, exploiting transgenic techniques andthe generation and characterization of mutants, points the wayahead in dissecting this developmental process at the molecularlevel. Key words: Plant embryogenesis, pattern formation, developmental mutants, gene expression     

Question 3: The Problem of Macromolecular Sequences: The Forgotten Stumbling Block

The Author agrees in principle with the question/statement, but states also that an important qualification is needed within this question. In fact, it is not possible by the bottom up approach to find the conditions for the synthesis of our actual proteins—lysozyme, chymotrypsin or the like—however it is possible to show experimentally that co-oligopeptides chains of that length can be produced by prebiotic reactions. Considering such a synthesis, it is important to recall that proteins—and nucleic acids—are not simply polymers, but are co-polymers, and the kinetics and thermodynamics attending the synthesis of copolymers poses stringent constraints for the biogenesis and growth of specific sequences. Such constraints are examined and discussed. Presented at: International School of Complexity–4th Course: Basic Questions on the Origins of Life; “Ettore Majorana” Foundation and Centre for Scientific Culture, Erice, Italy, 1–6 October 2006.     

Anchoring Revisited: The Role of the Comparative Question

When people estimate a numeric value after judging whether it is larger or smaller than a high or low anchor value (comparative question), estimates are biased in the direction of the anchor. One explanation for this anchoring effect is that people selectively access knowledge consistent with the anchor value as part of a positive test strategy. Two studies (total N = 184) supported the alternative explanation that people access knowledge consistent with their own answer to the comparative question. Specifically, anchoring effects emerged when the answer to the comparative question was unexpected (lower than the low anchor or higher than the high anchor). For expected answers (lower than the high anchor or higher than the low anchor), however, anchoring effects were attenuated or reversed. The anchor value itself was almost never reported as an absolute estimate.     

The Question of the Total Gene Number in DROSOPHILA MELANOGASTER

A statistical analysis has been carried out on the distribution and allelism of nearly 500 sex-linked, X-ray-induced, cytologically normal and rearranged lethal mutations in Drosophila melanogaster that were obtained by G. Lefevre. The mutations were induced in four different regions of the X chromosome: (1) 1A1-3E8, (2) 6D1-8A5, (3) 9E1-11A7 and (4) 19A1-20F4, which together comprise more than one-third of the entire chromosome.--The analysis shows that the number of alleles found at different loci does not fit a Poisson distribution, even when the proper procedures are taken to accommodate the truncated nature of the data. However, the allele distribution fits a truncated negative binomial distribution quite well, with cytologically normal mutations fitting better than rearrangement mutations. This indicates that genes are not equimutable, as required for the data to fit a Poisson distribution.--Using the negative binomial parameters to estimate the number of genes that did not produce a detectable lethal mutation in our experiment (n0) gave a larger number than that derived from the use of the Poisson parameter. Unfortunately, we cannot estimate the total numbers of nonvital loci, loci with undetectable phenotypes and loci having extremely low mutabilities. In any event, our estimate of the total vital gene number was far short of the total number of bands in the analyzed regions; yet, in several short intervals, we have found more vital genes than bands; in other intervals, fewer. We conclude that the one-band, one-gene hypothesis, in its literal sense, is not true; furthermore, it is difficult to support, even approximately.--The question of the total gene number in Drosophila will, not doubt, eventually be solved by molecular analyses, not by statistical analysis of mutation data or saturation studies.     

Neutron Crystal Structure of RAS GTPase Puts in Question the Protonation State of the GTP γ-Phosphate

RAS GTPase is a prototype for nucleotide-binding proteins that function by cycling between GTP and GDP, with hydrogen atoms playing an important role in the GTP hydrolysis mechanism. It is one of the most well studied proteins in the superfamily of small GTPases, which has representatives in a wide range of cellular functions. These proteins share a GTP-binding pocket with highly conserved motifs that promote hydrolysis to GDP. The neutron crystal structure of RAS presented here strongly supports a protonated γ-phosphate at physiological pH. This counters the notion that the phosphate groups of GTP are fully deprotonated at the start of the hydrolysis reaction, which has colored the interpretation of experimental and computational data in studies of the hydrolysis mechanism. The neutron crystal structure presented here puts in question our understanding of the pre-catalytic state associated with the hydrolysis reaction central to the function of RAS and other GTPases.     

The Origin of Two Sexes Through Optimization of Recombination Entropy Against Time and Energy

Sexual reproduction in nature requires two sexes, which raises the question why the reproductive scheme did not evolve to have three or more sexes. Here we construct a constrained optimization model based on the communication theory to analyze trade-offs among reproductive schemes with arbitrary number of sexes. More sexes on one hand lead to higher reproductive diversity, but on the other hand incur greater cost in time and energy for reproductive success. Our model shows that the two-sexes reproduction scheme maximizes the recombination entropy-to-cost ratio, and hence is the optimal solution to the problem.     

An Open Question on the Origin of Life: The First Forms of Metabolism

The general framework of the origin of life on Earth is outlined, emphasizing that the so‐called prebiotic ‘RNA world’ is as yet on shaky scientific ground, and that one should any way ask the question of the structure of the first protocellular compartments capable of the initial forms of metabolism. This question is the basis of the research project on the minimal cells, containing the minimal and sufficient complexity capable of leading to life. Such research is briefly summarized, highlighting experiments with liposome‐based semisynthetic cells which are capable of ribosomal protein synthesis with a very minimal number of enzymes. The most recent finding in this area of research is the unexpected observation that the formation and closure of liposomes in situ acts as an attractor for the solute molecules in solution, bringing about a very high local concentration in some of the liposomes. It is argued that this spontaneous overcrowding, which permits reactions which are not possible in the original dilute solution, might be the origin of cellular metabolism for the origin of life on Earth.     

Does nitrogen uptake affect nitrogen uptake efficiency,or vice versa?

The aim of the paper is to enter into a discussion concerning the title question. In our opinion it is N uptake efficiency that affects N uptake, but not vice versa, mainly because the former is a genotypic characteristic, and as such is not influenced by N uptake. To support the conclusions we also show a similarity between the model used for the problem in question and a yield component model.     

Towards organizing health knowledge on community-based health services

Online community-based health services accumulate a huge amount of unstructured health question answering (QA) records at a continuously increasing pace. The ability to organize these health QA records has been found to be effective for data access. The existing approaches for organizing information are often not applicable to health domain due to its domain nature as characterized by complex relation among entities, large vocabulary gap, and heterogeneity of users. To tackle these challenges, we propose a top-down organization scheme, which can automatically assign the unstructured health-related records into a hierarchy with prior domain knowledge. Besides automatic hierarchy prototype generation, it also enables each data instance to be associated with multiple leaf nodes and profiles each node with terminologies. Based on this scheme, we design a hierarchy-based health information retrieval system. Experiments on a real-world dataset demonstrate the effectiveness of our scheme in organizing health QA into a topic hierarchy and retrieving health QA records from the topic hierarchy.     

Quantum Attack-Resistent Certificateless Multi-Receiver Signcryption Scheme

The existing certificateless signcryption schemes were designed mainly based on the traditional public key cryptography, in which the security relies on the hard problems, such as factor decomposition and discrete logarithm. However, these problems will be easily solved by the quantum computing. So the existing certificateless signcryption schemes are vulnerable to the quantum attack. Multivariate public key cryptography (MPKC), which can resist the quantum attack, is one of the alternative solutions to guarantee the security of communications in the post-quantum age. Motivated by these concerns, we proposed a new construction of the certificateless multi-receiver signcryption scheme (CLMSC) based on MPKC. The new scheme inherits the security of MPKC, which can withstand the quantum attack. Multivariate quadratic polynomial operations, which have lower computation complexity than bilinear pairing operations, are employed in signcrypting a message for a certain number of receivers in our scheme. Security analysis shows that our scheme is a secure MPKC-based scheme. We proved its security under the hardness of the Multivariate Quadratic (MQ) problem and its unforgeability under the Isomorphism of Polynomials (IP) assumption in the random oracle model. The analysis results show that our scheme also has the security properties of non-repudiation, perfect forward secrecy, perfect backward secrecy and public verifiability. Compared with the existing schemes in terms of computation complexity and ciphertext length, our scheme is more efficient, which makes it suitable for terminals with low computation capacity like smart cards.     

Role of substrate inhibition kinetics in enzymatic chemical oscillations.

Two chemical kinetic models are investigated using standard nonlinear dynamics techniques to determine the conditions under which substrate inhibition kinetics can lead to oscillations. The first model is a classical substrate inhibition scheme based on Michaelis-Menten kinetics and involves a single substrate. Only when this reaction takes place in a flow reactor (i.e., both substrate and product are taken to follow reversible flow terms) are oscillations observed; however, the range of parameter values over which such oscillations occur is so narrow it is experimentally unobservable. A second model based on a general mechanism applied to the kinetics of many pH-dependent enzymes is also studied. This second model includes both substrate inhibition kinetics as well as autocatalysis through the activation of the enzyme by hydrogen ion. We find that it is the autocatalysis that is always responsible for oscillatory behavior in this scheme. The substrate inhibition terms affect the steady-state behavior but do not lead to oscillations unless product inhibition or multiple substrates are present; this is a general conclusion we can draw from our studies of both the classical substrate inhibition scheme and the pH-dependent enzyme mechanism. Finally, an analysis of the nullclines for these two models allows us to prove that the nullcline slopes must have a negative value for oscillatory behavior to exist; this proof can explain our results. From our analysis, we conclude with a brief discussion of other enzymes that might be expected to produce oscillatory behavior based on a pH-dependent substrate inhibition mechanism.     

Transport of the substance through thin membranes with narrow pores after the preceding stage of surface diffusion

A model of the substance transport through thin membranes is discussed. Existence of a step of the surface diffusion of permeable particles is assumed preceding its entrance into membrane channel. An expression is given for the stationary flow, which has earlier been obtained for other transport models. It is shown that the permeant affinity to the membrane surface is the main condition for the validity of the scheme in question.     

Chemical aspects of synthetic biology

Synthetic biology as a broad and novel field has also a chemical branch: whereas synthetic biology generally has to do with bioengineering of new forms of life (generally bacteria) which do not exist in nature, 'chemical synthetic biology' is concerned with the synthesis of chemical structures such as proteins, nucleic acids, vesicular forms, and other which do not exist in nature. Three examples of this 'chemical synthetic biology' approach are given in this article. The first example deals with the synthesis of proteins that do not exist in nature, and dubbed as 'the never born proteins' (NBPs). This research is related to the question why and how the protein structures existing in our world have been selected out, with the underlying question whether they have something very particular from the structural or thermodynamic point of view (for example, the folding). The NBPs are produced in the laboratory by the modern molecular biology technique, the phage display, so as to produce a very large library of proteins having no homology with known proteins. The second example of chemical synthetic biology has also to do with the laboratory synthesis of proteins, but, this time, adopting a prebiotic synthetic procedure, the fragment condensation of short peptides, where short means that they have a length that can be obtained by prebiotic methods; for example, from the condensation of N-carboxy anhydrides. The scheme is illustrated and discussed, being based on the fragment condensation catalyzed by peptides endowed with proteolitic activity. Selection during chain growth is determined by solubility under the contingent environmental conditions, i.e., the peptides which result insoluble are eliminated from further growth. The scheme is tested preliminarily with a synthetic chemical fragment-condensation method and brings to the synthesis of a 44-residues-long protein, which has no homology with known proteins, and which has a stable tertiary folding. Finally, the third example, dubbed as 'the minimal cell project'. Here, the aim is to synthesize a cell model having the minimal and sufficient number of components to be defined as living. For this purpose, liposomes are used as shell membranes, and attempts are made to introduce in the interior a minimal genome. Several groups all around the world are active in this field, and significant results have been obtained, which are reviewed in this article. For example, protein expression has been obtained inside liposomes, generally with the green fluorescent protein, GFP. Our last attempts are with a minimal genome consisting of 37 enzymes, a set which is able to express proteins using the ribosomal machinery. These minimal cells are not yet capable of self-reproduction, and this and other shortcomings within the project are critically reviewed.     

The fitting of dynamic models to observed data

The question of how to fit a general cubic model of a multicomponent, interactive growth system to observed data is addressed. A multidimensional-polynomial type of regression analysis is used, with a least-squares criterion. By testing the scheme on a problem with known solution, the way in which the accuracy of the results varies with the number of datum points used is investigated in an heuristic manner.     

Distinguishing driver and passenger mutations in an evolutionary history categorized by interference

In many biological scenarios, from the development of drug resistance in pathogens to the progression of healthy cells toward cancer, quantifying the selection acting on observed mutations is a central question. One difficulty in answering this question is the complexity of the background upon which mutations can arise, with multiple potential interactions between genetic loci. We here present a method for discerning selection from a population history that accounts for interference between mutations. Given sequences sampled from multiple time points in the history of a population, we infer selection at each locus by maximizing a likelihood function derived from a multilocus evolution model. We apply the method to the question of distinguishing between loci where new mutations are under positive selection (drivers) and loci that emit neutral mutations (passengers) in a Wright-Fisher model of evolution. Relative to an otherwise equivalent method in which the genetic background of mutations was ignored, our method inferred selection coefficients more accurately for both driver mutations evolving under clonal interference and passenger mutations reaching fixation in the population through genetic drift or hitchhiking. In a population history recorded by 750 sets of sequences of 100 individuals taken at intervals of 100 generations, a set of 50 loci were divided into drivers and passengers with a mean accuracy of >0.95 across a range of numbers of driver loci. The potential application of our model, either in full or in part, to a range of biological systems, is discussed.     

Structure-function studies on the active site of the coelenterazine-dependent luciferase from Renilla

Renilla luciferase (RLUC) is a versatile tool for gene expression assays and in vivo biosensor applications, but its catalytic mechanism remains to be elucidated. RLUC is evolutionarily related to the alpha/beta hydrolase family. Its closest known homologs are bacterial dehalogenases, raising the question of how a protein with a hydrolase fold can function as a decarboxylating oxygenase. Molecular docking simulations with the coelenterazine substrate against an RLUC homology model as well as a recently determined RLUC crystal structure were used to build hypotheses to identify functionally important residues, which were subsequently tested by site-directed mutagenesis, heterologous expression, and bioluminescence emission spectroscopy. The data highlighted two triads of residues that are critical for catalysis. The putative catalytic triad residues D120, E144, and H285 bear only limited resemblance to those found in the active site of aequorin, a coelenterazine-utilizing photoprotein, suggesting that the reaction scheme employed by RLUC differs substantially from the one established for aequorin. The role of H285 in catalysis was further supported by inhibition using diethylpyrocarbonate. Multiple substitutions of N53, W121, and P220--three other residues implicated in product binding in the homologous dehalogenase Sphingomonas LinB--also supported their involvement in catalysis. Together with luminescence spectra, our data lead us to propose that the conserved catalytic triad of RLUC is directly involved in the decarboxylation reaction of coelenterazine to produce bioluminescence, while the other active-site residues are used for binding of the substrate.