Miracle-dz/UniFAR-FTUs huggingface dataset:
Extracting schema from semistructured data

Semistructured data is characterized by the lack of any fixed and rigid schema, although typically the data has some implicit structure. While the lack of fixed schema makes extracting semistructured data fairly easy and an attractive goal, presenting and querying such data is greatly impaired. Thus, a critical problem is the discovery of the structure implicit in semistructured data and, subsequently, the recasting of the raw data in terms of this structure. In this paper, we consider a very general form of semistructured data based on labeled, directed graphs. We show that such data can be typed using the greatest fixpoint semantics of monadic datalog programs. We present an algorithm for approximate typing of semistructured data. We establish that the general problem of finding an optimal such typing is NP-hard, but present some heuristics and techniques based on clustering that allow efficient and near-optimal treatment of the problem. We also present some preliminary experimental results.
Gamete Release and Spawning Behavior in Broadcast Spawning Marine Invertebrates

The release of eggs and sperm into the environment for external fertilization is common (Giese & Kanatani 1987) and thought to be the ancestral mating strategy (Wray 1995). Most phyla have at least some species that release sperm into the environment (free spawning or spermcasting) and a majority have representatives that also release eggs (broadcast spawning) for external fertilization (Levitan 1998a). A common feature of broadcast spawning taxa is a lack of sexually dimorphic adult characters (Strathmann 1990; Levitan 1998a). The rare instances of adult morphological differences among sexes occur in pair-spawning species and include body size differences or specialized appendages for clasping females (Levitan 1998a). The general absence of sexual dimorphism has been used as evidence that broadcast spawning invertebrates are not under sexual selection (Darwin 1871). In contrast to this view on the nature of sexual selection based on sexual dimorphism, recent studies documenting the rapid evolution of gamete recognition proteins in external fertilizing species have invoked sexual selection and sexual confl ict as the driving force of positive selection (Palumbi 1999; Swanson & Vacquier 2002; Haygood 2004). Only recently have data been collected on the patterns of reproductive variance and the intensity of sexual selection in male and female broadcast spawners (Levitan 2004, 2005a, b; Levitan & Ferrell 2006; Levitan 2008). The results suggest that sexual selection can be intense in these species and that the nature of sexual selection is dependent on the distribution and abundance of individuals. Given the nature of external fertilization, where the competition among individuals for mates is played out among gametes in the water column, it is not surprising that the primary sexual characteristics targeted by selection are associated with the spawning behaviors that mediate gamete competition and the traits of the gametes themselves. The infl uence of sperm availability and sexual selection on gamete traits has already received some attention (Levitan 1998b, 2006). Below we briefl y summarize the relationship between gamete traits and fertilization and direct readers to the relevant literature. The remainder of the chapter is focused on the less studied question of how sexual selection might infl uence the evolution of the duration, release rate, and timing of gamete release. Because these features determine the size, shape, and duration of an individual’s gamete distribution, it defi nes the extent to which one individual can interact with mates and mate competitors.
Functional data analysis of knee joint kinematics in the vertical jump

Abstract Understanding of the motor development process is usually based on descriptive studies using either cross‐sectional or longitudinal designs. These data typically consist of sets of measurements on groups of individuals gathered during the performance of a single task. A natural approach is to represent the set of measurements for an individual as a single entity, a function. In practice, however, this approach is seldom applied. Typically, the analysis proceeds by reducing what are intrinsically functional responses to a single summary measurement and then using this to draw conclusions. As a result, many potentially informative data are ignored. Functional data analysis (FDA) is an emerging field in statistics that focuses on treating an entire sequence of measurements for an experimental unit as a single function. Therefore, functional data analysis appears to be inherently suitable for analysing kinematic data. In this paper, the key concepts and procedures of functional data analysis are introduced and illustrated using data obtained from a cross‐sectional study on the development of the vertical jump.
Stimulation of the Labellar Sugar Receptor of the Fleshfly by Mono- and Disaccharides

Responses of the labellar sugar receptor of the fleshfly, Boettcherisca peregrina, were studied over a wide range of concentrations of several sugars (sucrose, maltose, glucose, fructose, and mannose) in single solutions and in mixtures. The results suggest (a) that the receptor sites are not completely differentiated for glucose and for fructose combination, (b) that the receptor site is composed of two subunits. Such suggestions are based on the classical model, where the response is proportional to the number of the sites, two subunits of each site being simultaneously occupied with one molecule of disaccharides or two molecules of monosaccharides. It is shown, however, that an allosteric model gives a somewhat better interpretation of the experimental results.
Focal Adhesion Kinase as a RhoA-activable Signaling Scaffold Mediating Akt Activation and Cardiomyocyte Protection*

RhoA a small G-protein that has an established role in cell growth and in regulation of the actin cytoskeleton. Far less is known about whether RhoA can modulate cell fate. We previously reported that sustained RhoA activation induces cardiomyocyte apoptosis (Del Re, D. P., Miyamoto, S., and Brown, J. H. (2007) J. Biol. Chem. 282, 8069–8078). Here we demonstrate that less chronic RhoA activation affords a survival advantage, protecting cardiomyocytes from apoptotic insult induced by either hydrogen peroxide treatment or glucose deprivation. Under conditions where RhoA is protective, we observe Rho kinase-dependent cytoskeletal rearrangement and activation of focal adhesion kinase (FAK). Activation of endogenous cardiomyocyte FAK leads to its increased association with the p85 regulatory subunit of phosphatidylinositol-3-kinase (PI3K) and to concomitant activation of Akt. Treatment of isolated perfused hearts with sphingosine 1-phosphate recapitulates this response. The pathway by which RhoA mediates cardiomyocyte Akt activation is demonstrated to require Rho kinase, FAK and PI3K, but not Src, based on studies with pharmacological inhibitors (Y-27632, LY294002, PF271 and PP2) and inhibitory protein expression (FAK-related nonkinase). Inhibition of RhoA-mediated Akt activation at any of these steps, including inhibition of FAK, prevents RhoA from protecting cardiomyocytes against apoptotic insult. We further demonstrate that stretch of cardiomyocytes, which activates endogenous RhoA, induces the aforementioned signaling pathway, providing a physiologic context in which RhoA-mediated FAK phosphorylation can activate PI3K and Akt. We suggest that RhoA-mediated effects on the cardiomyocyte cytoskeleton provide a novel mechanism for protection from apoptosis.
Health related quality of life in patients treated with radical cystectomy and urinary diversion for urothelial carcinoma of the bladder: development and validation of a new disease specific questionnaire.

PURPOSE The impact of treatment on the health related quality of life (HRQOL) of patients is being recognized with increasing importance, particularly in those with urological malignancies. However, a validated disease and treatment specific instrument to assess HRQOL following radical cystectomy (RC) and urinary diversion (UD) is currently lacking. We report the results of a new questionnaire designed specifically to measure HRQOL in these patients. MATERIALS AND METHODS A 45-item questionnaire consisting of the Functional Assessment of Cancer Therapy (FACT)-General and 17 additional items designed to measure disease and treatment specific health outcomes were combined to form the Vanderbilt Cystectomy Index (FACT-VCI). FACT-VCI and the generic RAND 36-Item Health Survey (SF-36) were administered to 50 patients from our institution RC data base who were more than 1 year from the time of surgery. Each patient was asked to complete the survey at 1 and 4 weeks. The results of the SF-36 and FACT-VCI were correlated along with the first and second administration of the FACT-VCI. RESULTS Overall FACT-VCI was found to have adequate internal consistency (Cronbach's alpha >0.70). Furthermore, intraclass correlation for the first and second administration of the VCI was 0.79. In addition, there was good correlation between the validated SF-36 and FACT-VCI (r = 0.81). The result was initial validation of a questionnaire for the assessment of HRQOL in patients following RC and UD. CONCLUSIONS Instruments designed to measure accurately HRQOL following RC and UD are in early development. We have now constructed and validated a disease and treatment specific questionnaire that can objectively assess HRQOL following RC and UD. A prospective longitudinal study of FACT-VCI is currently ongoing.
Risk factors for fever in critically ill patients with acute new-onset stroke

Abstract Objective: The purpose of this project was to identify risk factors for fever among critically ill patients with acute new-onset stroke, treated in a neurological intensive care unit (NICU). The frequency and risk factors for fever in the stroke patients during the first 7 days after admission were retrospectively studied. Methods: Fever was defined as a patient's axillary temperature >37.5° C in two separate measurements or >37.8° C in one single measurement. Multivariable logistic regressions were applied to analyse the risk factors for any fever, explained infectious fever and unexplained fever. One hundred and thirty-seven patients were included in the final analysis. Results: Febrile episodes occurred in 65% (89/137) of the patients; 48.9% of the fever were explained by infection (predominantly pneumonia or bronchitis), and 15.3% were unexplained despite a complete diagnostic evaluation. Significant risk factors for any fever included age 65 years or older, impaired consciousness, extremity paralysis (muscle force ≤ grade 3), center venous catheterization and tracheal intubation. In addition to those risk factors, the length of the stay at NICU before the fever was also a significant risk factor for explained infectious fever. Brain midline shift and initial serum leucocyte count more than 12.0 × 109/l were significant risk factors for unexplained fever. Conclusion: These results suggest that critically ill and new-onset stroke patients treated in NICU often have fever. The risk factors for different types of fever vary considerably.
Two Coordinately Regulated Homologs of FLOWERING LOCUS T Are Involved in the Control of Photoperiodic Flowering in Soybean1[W][OA]

FLOWERING LOCUS T (FT) is a key flowering integrator in Arabidopsis (Arabidopsis thaliana), with homologs that encode florigens in many plant species regardless of the type of photoperiodic response. We identified 10 FT homologs, which were arranged as five pairs of linked genes in different homoeologous chromosomal regions, in soybean (Glycine max), a paleopolyploid species. Two of the FT homologs, GmFT2a and GmFT5a, were highly up-regulated under short-day (SD) conditions (inductive for flowering in soybean) and had diurnal expression patterns with the highest expression 4 h after dawn. Under long-day (LD) conditions, expression of GmFT2a and GmFT5a was down-regulated and did not follow a diurnal pattern. Flowering took much longer to initiate under LD than under SD, and only the GmFT5a transcript accumulated late in development under LD. Ectopic expression analysis in Arabidopsis confirmed that both GmFT2a and GmFT5a had the same function as Arabidopsis FT, but the effect of GmFT5a was more prominent. A double-mutant soybean line for two PHYTOCHROME A (PHYA) genes expressed high levels of GmFT2a and GmFT5a under LD, and it flowered slightly earlier under LD than the wild type grown under SD. The expression levels of GmFT2a and GmFT5a were regulated by the PHYA-mediated photoperiodic regulation system, and the GmFT5a expression was also regulated by a photoperiod-independent system in LD. Taken together, our results suggest that GmFT2a and GmFT5a coordinately control flowering and enable the adaptation of soybean to a wide range of photoperiodic environments.
Support Vector Machines and Kernels for Computational Biology

The increasing wealth of biological data coming from a large variety of platforms and the continued development of new high-throughput methods for probing biological systems require increasingly more sophisticated computational approaches. Putting all these data in simple-to-use databases is a first step; but realizing the full potential of the data requires algorithms that automatically extract regularities from the data, which can then lead to biological insight. Many of the problems in computational biology are in the form of prediction: starting from prediction of a gene's structure, prediction of its function, interactions, and role in disease. Support vector machines (SVMs) and related kernel methods are extremely good at solving such problems [1]–[3]. SVMs are widely used in computational biology due to their high accuracy, their ability to deal with high-dimensional and large datasets, and their flexibility in modeling diverse sources of data [2], [4]–[6]. The simplest form of a prediction problem is binary classification: trying to discriminate between objects that belong to one of two categories—positive (+1) or negative (−1). SVMs use two key concepts to solve this problem: large margin separation and kernel functions. The idea of large margin separation can be motivated by classification of points in two dimensions (see Figure 1). A simple way to classify the points is to draw a straight line and call points lying on one side positive and on the other side negative. If the two sets are well separated, one would intuitively draw the separating line such that it is as far as possible away from the points in both sets (see Figures 2 and ​and3). 3). This intuitive choice captures the idea of large margin separation, which is mathematically formulated in the section Classification with Large Margin. Open in a separate window Figure 1 A linear classifier separating two classes of points (squares and circles) in two dimensions. The decision boundary divides the space into two sets depending on the sign of f(x) = 〈w,x〉+b. The grayscale level represents the value of the discriminant function f(x): dark for low values and a light shade for high values.
Can the Ames test provide an insight into nano-object mutagenicity? Investigating the interaction between nano-objects and bacteria

Abstract The aim of this study was to assess the interaction of a series of well characterised nano-objects with the Gram negative bacterium Salmonella typhimurium, and how such an interaction may relate to the potential mutagenicity of nano-objects. Transmission electron microscopy showed that nano-objects (Au-PMA-ATTO NPs, CeO2 NPs, SWCNTs and MWCNTs), as well as CAFs entered S. typhimurium. Only DEPs did not penetrate/enter the bacteria, however, were the only particle stimulus to induce any significant mutagenicity through the Ames test. Comparison with a sophisticated 3D in vitro cell model showed CAFs, DEPs, SWCNTs and MWCNTs to cause a significant increase in mammalian cell proliferation, whilst both the Au-PMA-ATTO NPs and CeO2 NPs had not significant adverse effects. In conclusion, these results indicate that various of different nano-objects are able to penetrate the double-lipid bilayer of Gram negative bacteria, although the Ames test may not be a good indicator for nano-object mutagenicity.
Rank Selection in Nonnegative Matrix Factorization using Minimum Description Length

Abstract Nonnegative matrix factorization (NMF) is primarily a linear dimensionality reduction technique that factorizes a nonnegative data matrix into two smaller nonnegative matrices: one that represents the basis of the new subspace and the second that holds the coefficients of all the data points in that new space. In principle, the nonnegativity constraint forces the representation to be sparse and parts based. Instead of extracting holistic features from the data, real parts are extracted that should be significantly easier to interpret and analyze. The size of the new subspace selects how many features will be extracted from the data. An effective choice should minimize the noise while extracting the key features. We propose a mechanism for selecting the subspace size by using a minimum description length technique. We demonstrate that our technique provides plausible estimates for real data as well as accurately predicting the known size of synthetic data. We provide an implementation of our code in a Matlab format.
Testicular development involves the spatiotemporal control of PDGFs and PDGF receptors gene expression and action

Platelet-derived growth factors (PDGFs) are growth-regulatory molecules that stimulate chemotaxis, proliferation and metabolism primarily of cells of mesenchymal origin. In this study, we found high levels of PDGFs and PDGFs receptors (PDGFRs) mRNAs, and specific immunostaining for the corresponding proteins in the rat testis. PDGFs and PDGFRs expression was shown to be developmentally regulated and tissue specific. Expression of PDGFs and PDGFRs genes was observed in whole testis RNA 2 d before birth, increased through postnatal day 5 and fell to low levels in adult. The predominant cell population expressing transcripts of the PDGFs and PDGFRs genes during prenatal and early postnatal periods were Sertoli cells and peritubular myoid cells (PMC) or their precursors, respectively, while in adult animals PDGFs and PDGFRs were confined in Leydig cells. We also found that early postnatal Sertoli cells produce PDGF-like substances and that this production is inhibited dose dependently by follicle-stimulating hormone (FSH). The expression of PDGFRs by PMC and of PDGFs by Sertoli cells corresponds in temporal sequence to the developmental period of PMC proliferation and migration from the interstitium to the peritubulum. Moreover, we observed that all the PDGF isoforms and the medium conditioned by early postnatal Sertoli cells show a strong chemotactic activity for PMC which is inhibited by anti-PDGF antibodies. These data indicate that, through the spatiotemporal pattern of PDGF ligands and receptors expression, PDGF may play a role in testicular development and homeostasis.
MRT letter: A novel tegumental gland in female imagoes of the neotropical termite Cornitermes cumulans (Isoptera, termitidae, syntermitinae)

In general, the exocrine glands of social insects are structures involved in the chemical communication associated with social life. Here, we report the discovery of an unknown tegumental gland that is present in the female imagoes of Cornitermes cumulans and occurs next to the well‐developed tergal glands that have previously been described. The tegumental glands release their secretion in the intersegmental membrane and are composed of bicellular units, a secretory cell and a canal cell, that are closely located to the epidermal cells in the inferior part of the eighth and ninth tergites. The ultrastructure of the glandular cells showed abundant smooth endoplasmic reticulum, suggesting that the secretion may be pheromonal, although its function is still unknown. These exocrine structures are facing the tergal glands, and we hypothesized that they act synergistically with the tergal glands to generate short‐range attraction during tandem behavior. Microsc. Res. Tech., 2010. © 2010 Wiley‐Liss, Inc.
Solid-liquid transition in ultra-fine lead particles

Abstract We have studied the melting and the solidification of lead ultra-fine particles. We report on electron microscopy technique which enables the identification of the transition temperatures of each particle. The experimental results presented show a dependence of the melting and solidification temperatures on the particle size. The melting temperature results are compared with a new phenomenological model.
Delivery of noncarrier naked DNA vaccine into the skin by supersonic flow induces a polarized T helper type 1 immune response to cancer

DNA vaccine is a new and powerful approach to generate immunological responses against infectious disease and cancer. The T helper type (Th)1 immune response is usually required for generating effective anti‐tumor responses. A microparticulate bombardment system can induce an immune response using very low amounts of DNA. Using nozzle aerodynamics, a low pressure gene gun has been developed to decrease the noise associated with high pressure gene guns. Particles are propelled by supersonic flow through this novel nozzle. To test whether this gun could inoculate a DNA vaccine that stimulates an anti‐tumor Th1 immune response, we examined the effect of direct delivery of naked DNA (i.e. without any carrier) on the anti‐tumor immune response of mice.
Interventricular mechanical dyssynchrony: quantification with velocity-encoded MR imaging.

PURPOSE To evaluate the performance of velocity-encoded (VENC) magnetic resonance (MR) imaging, as compared with pulsed-wave echocardiography (PW-ECHO), in the quantification of interventricular mechanical dyssynchrony (IVMD) as a predictor of response to cardiac resynchronization therapy (CRT). MATERIALS AND METHODS The study was approved by the local ethics committee, and all patients provided written informed consent. The study involved the examination of 45 patients (nine women, 36 men; median age, 60 years; interquartile age range, 47-69 years) with New York Heart Association class 2.0-3.0 heart failure and a reduced left ventricular ejection fraction (median, 25%; interquartile range, 21%-32%), with (n = 25) or without (n = 20) left bundle branch block. Aortic and pulmonary flow curves were constructed by using VENC MR imaging and PW-ECHO. IVMD was defined as the difference between the onset of aortic flow and the onset of pulmonary flow. Intraclass correlation coefficient, Spearman correlation coefficient, Bland-Altman, and Cohen kappa analyses were used to assess agreement between observers and methods. RESULTS Inter- and intraobserver agreement regarding VENC MR imaging IVMD measurements was very good (intraclass r = 0.96, P < .001; mean bias, -3 msec +/- 11 [standard deviation] and 0 msec +/- 10, respectively). A strong correlation (Spearman r = 0.92, P < .001) and strong agreement (mean difference, -6 msec +/- 16) were found between VENC MR imaging and PW-ECHO in the quantification of IVMD. Agreement between VENC MR imaging and PW-ECHO in the identification of potential responders to CRT was excellent (Cohen kappa = 0.94). CONCLUSION VENC MR measurements of IVMD are equivalent to PW-ECHO measurements and can be used to identify potential responders to CRT.