Miracle-dz/UniFAR-FTUs huggingface dataset:
Diagnostic models of the pre-test probability of stable coronary artery disease: A systematic review

A comprehensive search of PubMed and Embase was performed in January 2015 to examine the available literature on validated diagnostic models of the pre-test probability of stable coronary artery disease and to describe the characteristics of the models. Studies that were designed to develop and validate diagnostic models of pre-test probability for stable coronary artery disease were included. Data regarding baseline patient characteristics, procedural characteristics, modeling methods, metrics of model performance, risk of bias, and clinical usefulness were extracted. Ten studies involving the development of 12 models and two studies focusing on external validation were identified. Seven models were validated internally, and seven models were validated externally. Discrimination varied between studies that were validated internally (C statistic 0.66-0.81) and externally (0.49-0.87). Only one study presented reclassification indices. The majority of better performing models included sex, age, symptoms, diabetes, smoking, and hyperlipidemia as variables. Only two diagnostic models evaluated the effects on clinical decision making processes or patient outcomes. Most diagnostic models of the pre-test probability of stable coronary artery disease have had modest success, and very few present data regarding the effects of these models on clinical decision making processes or patient outcomes.
RNA secondary structure prediction using stochastic context-free grammars and evolutionary history

MOTIVATION Many computerized methods for RNA secondary structure prediction have been developed. Few of these methods, however, employ an evolutionary model, thus relevant information is often left out from the structure determination. This paper introduces a method which incorporates evolutionary history into RNA secondary structure prediction. The method reported here is based on stochastic context-free grammars (SCFGs) to give a prior probability distribution of structures. RESULTS The phylogenetic tree relating the sequences can be found by maximum likelihood (ML) estimation from the model introduced here. The tree is shown to reveal information about the structure, due to mutation patterns. The inclusion of a prior distribution of RNA structures ensures good structure predictions even for a small number of related sequences. Prediction is carried out using maximum a posteriori estimation (MAP) estimation in a Bayesian approach. For small sequence sets, the method performs very well compared to current automated methods.
Recombinant Production of Horseradish Peroxidase Conjugates with Fab Antibodies in Pichia pastoris for Analytical Applications

Recombinant immunoconjugates of marker enzymes with antigens or antibodies present considerably more advantages than those obtained by conventional methods of chemical synthesis; i.e. they are homogeneous, have a strictly determined stoichiometry, and retain the functional activity of both a marker protein and an antigen/antibody. Based on the pPICZαB shuttle vector, we first managed to obtain a recombinant conjugate of key marker enzyme horseradish peroxidase (HRP) withFabfragments of antibodies against atrazine. The resulting genetic construction allows us to switch to any other antibody sequence, via the simple re-cloning of variable parts and an additional reporter enzyme. Conjugates were successfully produced in thePichia pastorismethylotrophic yeast expression system. The target activity of the conjugates (both enzymatic and antigen-binding) has been demonstrated by ELISA method.
Brief report: parent report about health care use: relationship to child's and parent's psychosocial problems.

OBJECTIVE To investigate the potential utility of asking parents about health care utilization as a means of identifying individuals at risk for psychosocial problems. METHOD Parents of 366 children ages 2 to 16 completed questionnaires about their own, their child's, and their family's psychosocial functioning and health care utilization. RESULTS Children and parents with high health care utilization were more likely to have psychosocial problems than those with low health care utilization. Sensitivity and specificity of health care utilization as a marker for psychosocial problems ranged from 43.8% to 68.8%. CONCLUSIONS Although high rates of child health care utilization are related to the presence of psychosocial problems, use of this measure alone could result in many false-positive and false-negative identifications. Rather, use of health care utilization data in conjunction with other screening measures may be useful for alerting physicians to the possibility of both child and parent psychosocial problems.
Site-specific inductive and inhibitory activities of MMP-2 and MMP-3 orchestrate mammary gland branching morphogenesis

During puberty, mouse mammary epithelial ducts invade the stromal mammary fat pad in a wave of branching morphogenesis to form a complex ductal tree. Using pharmacologic and genetic approaches, we find that mammary gland branching morphogenesis requires transient matrix metalloproteinase (MMP) activity for invasion and branch point selection. MMP-2, but not MMP-9, facilitates terminal end bud invasion by inhibiting epithelial cell apoptosis at the start of puberty. Unexpectedly, MMP-2 also represses precocious lateral branching during mid-puberty. In contrast, MMP-3 induces secondary and tertiary lateral branching of ducts during mid-puberty and early pregnancy. Nevertheless, the mammary gland is able to develop lactational competence in MMP mutant mice. Thus, specific MMPs refine the mammary branching pattern by distinct mechanisms during mammary gland branching morphogenesis.
The cell proliferation antigen Ki-67 organises heterochromatin

Antigen Ki-67 is a nuclear protein expressed in proliferating mammalian cells. It is widely used in cancer histopathology but its functions remain unclear. Here, we show that Ki-67 controls heterochromatin organisation. Altering Ki-67 expression levels did not significantly affect cell proliferation in vivo. Ki-67 mutant mice developed normally and cells lacking Ki-67 proliferated efficiently. Conversely, upregulation of Ki-67 expression in differentiated tissues did not prevent cell cycle arrest. Ki-67 interactors included proteins involved in nucleolar processes and chromatin regulators. Ki-67 depletion disrupted nucleologenesis but did not inhibit pre-rRNA processing. In contrast, it altered gene expression. Ki-67 silencing also had wide-ranging effects on chromatin organisation, disrupting heterochromatin compaction and long-range genomic interactions. Trimethylation of histone H3K9 and H4K20 was relocalised within the nucleus. Finally, overexpression of human or Xenopus Ki-67 induced ectopic heterochromatin formation. Altogether, our results suggest that Ki-67 expression in proliferating cells spatially organises heterochromatin, thereby controlling gene expression. DOI: http://dx.doi. org/10.7554/eLife.13722. 001
Along‐axis variation in crustal thickness at the ultraslow spreading Southwest Indian Ridge (50°E) from a wide‐angle seismic experiment

The Southwest Indian Ridge (SWIR) is characterized by an ultraslow spreading rate, thin crust, and extensive outcrops of serpentinized peridotite. Previous studies have used geochemical and geophysical data to suggest the presence of a thicker crust at the central and shallowest portions of the SWIR, from the Prince Edward (35°30′E) to the Gallieni (52°20′E) fracture zones. Here we present a new analysis of wide‐angle seismic data along the ridge 49°17′E–50°49′E. Our main conclusions are as follows: (1) we find an oceanic layer 2 of roughly constant thickness and steep velocity gradient, underlain by a layer 3 with variable thickness and low velocity gradient; (2) the crustal thickness varies from ∼5 km beneath nontransform discontinuities (NTDs) up to ∼10 km beneath a segment center; (3) the melt supply is focused in segment centers despite a small NTD between adjacent segments; (4) the presence of a normal upper mantle velocity indicates that no serpentinization occurs beneath this thick crust. Our observation of thick crust at an ultraslow spreading ridge adds further complexity to relationships between crustal thickness and spreading rate, and supports previous suggestions that the extent of mantle melting is not a simple function of spreading rate, and that mantle temperature or chemistry (or both) must vary significantly along axis.
Robotic Tasks Modeling and Analysis Based on Petri Nets ∗

This paper proposes a method of defining and analysing robotic tasks using Petri Nets. Both the robot behaviors and environment are modelled using Generalized Stochastic Petri Nets (GSPNs). Each action is modelled separately and composed with others to provide a complete task execution. The use of Petri Nets allows the qualitative and quantitative analysis of the task execution.
Assessment of Metals Concentration and Ecotoxicology of the Sediment Core of Rehri Creek, Karachi Coast, Pakistan

Trace metal concentrations were investigated in a recent sediment core collected from the Rehri Creek area of the Karachi coast, Sindh ‐ Pakistan. The core was sliced horizontally at 2.5‐cm intervals to determine grain size, sediment composition, pH, organic matter, and acid‐leach able trace metals: cadmium, chromium, copper, lead, and zinc. The trace metals were analyzed by ICP. To separate anthropogenic from geogenic input, several approaches were made, including comparison with sediment quality guidelines—ecotoxicological sense of heavy metal contamination and classification by quantitative indexes. Grain‐size analysis and sediment composition of core sample show a sandy nature with neutral pH. Elemental sequence (ES) of the trace metals is in the order of Zn (19.2–109.56 ppm) > Si (66.46–101.71 ppm) > Ba (12.05–26.86 ppm) > As (8.18–17.36 ppm) > Ni (4.2–14.69 ppm) > Cr (3.02–9.62 ppm) > Pb (2.79–6.83 ppm) > Cu (2.2–5.29 ppm) > Co (0.9–2.05 ppm). Thus it is likely that the area may face a serious threat of metal pollution with the present deposition rates unless stringent pollution control norms are adopted. The Sediment Geo‐accumulation Index shows that there is no Cr, Cu, Ni, Pb, Zn, or Fe pollution; however, the former index and the Pollution Load Index indicate arsenic pollution in the sediments.
A portable and extensible community object

Many community networks have emerged on the Internet. They provide various functionalities to serve the community users. However, most of the community networks lacks of the convenient tools in packaging the information users are interested in. Therefore, the information posted and exchanged in the community networks is not easy to be extracted and reused somewhere else. In another aspect, the functions and services provided by the community networks are not fully satisfactory to most users. The community networks in general do not provide the mechanism to extend or modify the functions or services provided for users. In this paper, we apply the information object model to construct a portable and extensible community object for organize a small and personalized virtual community. An actor object and a community object are applied to serve as a user and a community respectively. The actor object is an entity represents the user. A service which is provided or needed by the user can be installed to the entity as a method of the actor object. Similarly, the community object is an entity represents the community. A service provided by the community can be installed to the community object as a method. In our development, an actor object or a community object is basically an information object which is portable and extensible in functionality. We will describe the basic concept of the actor object and the community object and the design of the prototype system developed on the Web platform.
Convergence rates for persistence diagram estimation in topological data analysis

Computational topology has recently seen an important development toward data analysis, giving birth to Topological Data Analysis. Persistent homology appears as a fundamental tool in this field. We show that the use of persistent homology can be naturally considered in general statistical frameworks . We establish convergence rates of persistence diagrams associated to data randomly sampled from any compact metric space to a well defined limit diagram encoding the topological features of the support of the measure from which the data have been sampled. Our approach relies on a recent and deep stability result for persistence that allows to relate our problem to support estimation problems (with respect to the Gromov-Hausdorff distance). Some numerical experiments are performed in various contexts to illustrate our results.
No more bricolage!: methods and tools to characterize, replicate and compare pointing transfer functions

Transfer functions are the only pointing facilitation technique actually used in modern graphical interfaces involving the indirect control of an on-screen cursor. But despite their general use, very little is known about them. We present EchoMouse, a device we created to characterize the transfer functions of any system, and libpointing, a toolkit that we developed to replicate and compare the ones used by Windows, OS X and Xorg. We describe these functions and report on an experiment that compared the default one of the three systems. Our results show that these default functions improve performance up to 24% compared to a unitless constant CD gain. We also found significant differences between them, with the one from OS X improving performance for small target widths but reducing its performance up to 9% for larger ones compared to Windows and Xorg. These results notably suggest replacing the constant CD gain function commonly used by HCI researchers by the default function of the considered systems.
Interactive storytelling via video content recombination

In the paper we present a prototype of video-based storytelling that is able to generate multiple story variants from a baseline video. The video content for the system is generated by an adaptation of forefront video summarisation techniques that decompose the video into a number of Logical Story Units (LSU) representing sequences of contiguous and interconnected shots sharing a common semantic thread. Alternative storylines are generated using AI Planning techniques and these are used to direct the combination of elementary LSU for output. We report early results from experiments with the prototype in which the reordering of video shots on the basis of their high-level semantics produces trailers giving the illusion of different storylines.
Ice images processing interface for automatic features extraction

Canadian Coast Guard has the mandate to maintain the navigability of the St.-Lawrence seaway. It must prevent ice jam formation. Radar, sonar sensors and cameras are used to verify ice movement and keep a record of pertinent data. The cameras are placed along the seaway at strategic locations. Images are processed and saved for future reference. The Ice Images Processing Interface (IIPI) is an integral part of Ices Integrated System (IIS). This software processes images to extract the ice speed, concentration, roughness, and rate of flow. Ice concentration is computed from image segmentation using color models and a priori information. Speed is obtained from a region-matching algorithm. Both concentration and speed calculations are complex, since they require a calibration step involving on-site measurements. Color texture features provide ice roughness estimation. Rate of flow uses ice thickness, which is estimated from sonar sensors on the river floor. Our paper will present how we modeled and designed the IIPI, the issues involved and its future. For more reliable results, we suggest that meteorological data be provided, change in camera orientation be changed, sun reflections be anticipated, and more a priori information, such as radar images available at some sites, be included.
p16Ink4a inhibits histologic progression and angiogenic signaling in min colon tumors

The Ink4a/Arf tumor suppressor locus is widely inactivated in cancer but little is known about the tumor biology of its two products, p16Ink4a (p16) and Arf. Both the p16 and Arf promoters are methylated in a significant fraction of human colon carcinomas, implying a functional role. We have demonstrated previously that Ink4a/Arf-null colon tumors display increased growth and vascularity in C57Bl6 mice carrying the Min (multiple intestinal neoplasia) mutation. We present here an analysis in a mixed genetic background of Min colon tumors (N = 215) in mice with or without selective deficiencies in p16 or Arf, respectively. Absence of Arf did not significantly alter tumor formation. In contrast, tumors in mice lacking p16 were moderately larger and redder. Histological analysis demonstrated that these tumors contained significantly more pockets of necrosis (P = 0.02), a marker of carcinoma in situ; less apoptosis (P = 0.02); and higher red blood cell density (P = 0.02, 0.006 within vessels). Biochemical analyses demonstrated increased levels of vascular endothelial cell growth factor (VEGF, P < 0.01). Exogenous p16 expression in human colon tumor cells in vitro inhibited VEGF production. These results suggest that p16 constrains colon tumor progression, in part through inhibiting angiogenic signaling.
IMPROVING RTISI PHASE ESTIMATION WITH ENERGY ORDER AND PHASE UNWRAPPING

This paper presents two ways to improve the Real-Time Iterative Spectrogram Inversion (RTISI) algorithm. The standard RTISI phase estimator with look-ahead processes the buffered frames in reverse order. We show that better results are achieved by controlling this order according to frame energy. Another improvement is to initialize the last row of the phase estimator buffer by progressing the unwrapped phase difference of the previous frames. Furthermore, we extend these improvements to dual window length phase estimation and analyze the performance in SER with respect to different analysis window lengths.
A demonstration of a transportable radio interferometric surveying system with 3‐cm accuracy on a 307‐m base line

A precision geodetic measurement system (Aries for Astronomical Radio Interferometric Earth Surveying) based on the technique of very long base line interferometry has been designed and implemented through the use of a 9-m transportable antenna and the NASA 64-m antenna of the Deep Space Communications Complex at Goldstone, California. A series of experiments designed to demonstrate the inherent accuracy of a transportable interferometer was performed on a 307-m base line during the period from December 1973 to June 1974. This short base line was chosen in order to obtain a comparison with a conventional survey with a few-centimeter accuracy and to minimize Aries errors due to transmission media effects, source locations, and earth orientation parameters. The base line vector derived from a weighted average of the measurements, representing approximately 24 h of data, possessed a formal uncertainty of about 3 cm in all components. This average interferometry base line vector was in good agreement with the conventional survey vector within the statistical range allowed by the combined uncertainties (3–4 cm) of the two techniques.
Regulatory subunit (CNB1 gene product) of yeast Ca2+/calmodulin-dependent phosphoprotein phosphatases is required for adaptation to pheromone

By using an assay specific for detection of calcineurin, a Ca2+/calmodulin-dependent phosphoprotein phosphatase, this enzyme was purified approximately 5,000-fold from extracts of the yeast Saccharomyces cerevisiae. Cna1p and Cna2p, the products of two yeast genes encoding the catalytic (A) subunits of calcineurin, were major constituents of the purified fraction. A third prominent component of apparent molecular mass 16 kDa displayed several properties, including ability to bind 45Ca2+, that are characteristic of the regulatory (B) subunit of mammalian calcineurin and was recognized by an antiserum raised against bovine calcineurin. These antibodies were used to isolate the structural gene (CNB1) encoding this protein from a yeast expression library in the vector lambda gt11. The nucleotide sequence of CNB1 predicted a polypeptide similar in length and highly related in amino acid sequence (56% identity) to the mammalian calcineurin B subunit. Like its counterpart in higher cells, yeast Cnb1p was myristoylated at its N terminus. Mutants lacking Cnb1p, or all three calcineurin subunits (Cna1p, Cna2p, and Cnb1p), were viable. Extracts of cnb1 delta mutants contained no detectable calcineurin activity, even though Cna1p and Cna2p were present at normal levels, suggesting that the B subunit is required for full enzymatic activity in vitro. As was observed previously for MATa cna1 cna2 double mutants, MATa cnb1 mutants were defective in their ability to recover from alpha-factor-induced growth arrest. Thus, the B subunit also is required for the function of calcineurin in promoting adaptation of haploid yeast cells to pheromone in vivo.
Predictable Reliability and Packet Loss Domain Separation for IP Media Delivery

Internet protocol (IP) based media delivery enables applications such as Voice over IP or, most recently, stereoscopic HD-TV. Suchlike transport of typically time-constrained media between two end-points has a number of important characteristics, both on the transport and content side. We focus on live streams of audio-visual data that are assumed as time-constrained and loss-tolerant. We aim at optimizing IP transport over heterogeneous networks by hybrid and loss domain separated error correction with residual error. Hybrid error correction (HEC) approaches the channel capacity dynamically and achieves predictable reliability and predictable delay (PRPD) when residual loss is tolerable, while loss domain separation applies optimally chosen HEC parameters to individual network segments. In this paper, we apply an atomic HEC coding unit to individual segments of network links between source and sink, and show by analysis and example how redundancy is distributed optimally.
Fast, Flexible, and Declarative Construction of Abstract Syntax Trees with PEGs

We address a declarative construction of abstract syntax trees with Parsing Expression Grammars. AST operators (constructor, connector, and tagging) are newly defined to specify flexible AST constructions. A new challenge coming with PEGs is the consistency management of ASTs in backtracking and packrat parsing. We make the transaction AST machine in order to perform AST operations in the context of the speculative parsing of PEGs. All the consistency control is automated by the analysis of AST operators. The proposed approach is implemented in the Nez parser, written in Java. The performance study shows that the transactional AST machine requires 25\% approximately more time in CSV, XML, and C grammars.