Miracle-dz/UniFAR-FTUs huggingface dataset:
Chemical-induced disease relation extraction with various linguistic features

Understanding the relations between chemicals and diseases is crucial in various biomedical tasks such as new drug discoveries and new therapy developments. While manually mining these relations from the biomedical literature is costly and time-consuming, such a procedure is often difficult to keep up-to-date. To address these issues, the BioCreative-V community proposed a challenging task of automatic extraction of chemical-induced disease (CID) relations in order to benefit biocuration. This article describes our work on the CID relation extraction task on the BioCreative-V tasks. We built a machine learning based system that utilized simple yet effective linguistic features to extract relations with maximum entropy models. In addition to leveraging various features, the hypernym relations between entity concepts derived from the Medical Subject Headings (MeSH)-controlled vocabulary were also employed during both training and testing stages to obtain more accurate classification models and better extraction performance, respectively. We demoted relation extraction between entities in documents to relation extraction between entity mentions. In our system, pairs of chemical and disease mentions at both intra- and inter-sentence levels were first constructed as relation instances for training and testing, then two classification models at both levels were trained from the training examples and applied to the testing examples. Finally, we merged the classification results from mention level to document level to acquire final relations between chemicals and diseases. Our system achieved promising F-scores of 60.4% on the development dataset and 58.3% on the test dataset using gold-standard entity annotations, respectively. Database URL: https://github.com/JHnlp/BC5CIDTask
Learning transfer rules for machine translation with limited data

The transfer-based approach to machine translation (MT) captures structural transfers between the source language and the target language, with the goal of producing grammatical translations. The major drawback of the approach is the development bottleneck, requiring many human-years of rule development. On the other hand, data-driven approaches such as example-based and statistical MT achieve fast system development by deriving mostly non-structural translation information from bilingual corpora. This thesis aims at striking a balance between both approaches by inferring transfer rules automatically from bilingual text, aiming specifically at scenarios where bilingual data is in sparse supply. The rules are learned using a variety of information, such as parses that are available for one of the languages, and morphological information that is available for both languages. They are learned in three stages, first producing an initial hypothesis, then capturing the syntactic structure, and finally adding appropriate unification constraints. The learned rules are used in a run-time translation system, a statistical transfer system which is a combination of a transfer engine and a statistical decoder. We demonstrate the effectiveness of the learned rules on Hebrew→English and a Hindi→English translation tasks. The main contribution of this thesis is a new framework for inferring structural information with feature constraints from bilingual text, as well as an investigation of the taxonomy of learnable rules and their effectiveness. The framework is designed to be applicable for any language pair, and the inferred rules can be used in conjunction with a statistical decoder. In addition to presenting methods to integrate syntactic and statistical information, the thesis makes a case for inferring information from very small training corpora, and provides methods to do so.
Loss formulas and their application to optimization for cellular networks

We develop a performance model of a cell in a wireless communication network where the effect of handoff arrival and the use of guard channels is included. Past recursive formulas for the loss probabilities of new calls and handoff calls are developed. Monotonicity properties of the loss probabilities are proven. Algorithms to determine the optimal number of guard channels and the optimal number of channels are given. Finally, a fixed-point iteration scheme is developed in order to determine the handoff arrival rate into a cell. The uniqueness of the fixed point is shown.
Non‐self‐similar source property for microforeshocks of the 2014 Mw 6.2 Northern Nagano, central Japan, earthquake

Foreshocks are considered as part of the preparation process for large earthquakes and, as such, can provide important constraints on earthquake generation. We examine the characteristics of the 4 day long foreshock sequence of the 2014 Northern Nagano earthquake (Mw 6.2) using seismograms recorded by a dense seismic observation network including data from a deep borehole closest to the foreshock region. The improved earthquake catalog shows a slow‐speed migration of the sequence toward the main shock hypocenter, implying possible slow‐slip transients which should have caused stress loading at the main shock hypocenter. An analysis of source spectra reveals that foreshocks for Mw < 1.5 display a weaker dependence of corner frequency on magnitude than expected for self‐similar scaling, suggesting that these microforeshocks can be regarded as small low‐frequency earthquakes. So far, we might have missed the expected weak low‐frequency preseismic signals, because they emerge only below a certain magnitude and are generally embedded in background noise.
VISUAL CONCENTRATION BASED ON BAG OF WORDS IMAGE INDICATION FOR OBJECT DETECTION

In order to facilitate the property of the object detection, we have proposed a Bag of Words image indication method aroused by visual concentration which could apply computational visual version concentration technology to the indication of images. As we all know, a computational visual concentration model was built on the authentic eye chasing data. By using this concentration model, we can discern the most salient regions from the images. Next, we indicate the image by emphasizing the graphic words within these regions. Then accordingly, we can obtain a Bag of Words image indication with more discriminative power. Meanwhile, this method can also reduce the disorder trespassed by the backdrop on the images. In addition to ascertaining the objects from the images, with the guidance of the ocular concentration model, we are also able to find their locations. This experimental tests and verifies the effectiveness of the aforementioned method that proposed. The results show that the proposed method facilitates the capability of the object detection algorithm.
Creating principal 3D curves with digital tape drawing

Previous systems have explored the challenges of designing an interface for automotive styling which combine the metaphor of 2D drawing using physical tape with the simultaneous creation and management of a corresponding virtual 3D model. These systems have been limited to only 2D planar curves while typically the principal characteristic curves of an automotive design are three dimensional and non-planar. We present a system which addresses this limitation. Our system allows a designer to construct these non-planar 3D curves by drawing a series of 2D curves using the 2D tape drawing technique and interaction style. These results are generally applicable to the interface design of 3D modeling applications and also to the design of arm's length interaction on large scale display systems
Cluster analysis of consensus water sites in thrombin and trypsin shows conservation between serine proteases and contributions to ligand specificity

Cluster analysis is presented as a technique for analyzing the conservation and chemistry of water sites from independent protein structures, and applied to thrombin, trypsin, and bovine pancreatic trypsin inhibitor (BPTI) to locate shared water sites, as well as those contributing to specificity. When several protein structures are superimposed, complete linkage cluster analysis provides an objective technique for resolving the continuum of overlaps between water sites into a set of maximally dense microclusters of overlapping water molecules, and also avoids reliance on any one structure as a reference. Water sites were clustered for ten superimposed thrombin structures, three trypsin structures, and four BPTI structures. For thrombin, 19% of the 708 microclusters, representing unique water sites, contained water molecules from at least half of the structures, and 4% contained waters from all 10. For trypsin, 77% of the 106 microclusters contained water sites from at least half of the structures, and 57% contained waters from all three. Water site conservation correlated with several environmental features: highly conserved microclusters generally had more protein atom neighbors, were in a more hydrophilic environment, made more hydrogen bonds to the protein, and were less mobile. There were significant overlaps between thrombin and trypsin conserved water sites, which did not localize to their similar active sites, but were concentrated in buried regions including the solvent channel surrounding the Na+ site in thrombin, which is associated with ligand selectivity. Cluster analysis also identified water sites conserved in thrombin but not trypsin, and vice versa, providing a list of water sites that may contribute to ligand discrimination. Thus, in addition to facilitating the analysis of water sites from multiple structures, cluster analysis provides a useful tool for distinguishing between conserved features within a protein family and those conferring specificity.
Wolbachia-Mediated Male Killing Is Associated with Defective Chromatin Remodeling

Male killing, induced by different bacterial taxa of maternally inherited microorganisms, resulting in highly distorted female-biased sex-ratios, is a common phenomenon among arthropods. Some strains of the endosymbiont bacteria Wolbachia have been shown to induce this phenotype in particular insect hosts. High altitude populations of Drosophila bifasciata infected with Wolbachia show selective male killing during embryonic development. However, since this was first reported, circa 60 years ago, the interaction between Wolbachia and its host has remained unclear. Herein we show that D. bifasciata male embryos display defective chromatin remodeling, improper chromatid segregation and chromosome bridging, as well as abnormal mitotic spindles and gradual loss of their centrosomes. These defects occur at different times in the early development of male embryos leading to death during early nuclear division cycles or large defective areas of the cellular blastoderm, culminating in abnormal embryos that die before eclosion. We propose that Wolbachia affects the development of male embryos by specifically targeting male chromatin remodeling and thus disturbing mitotic spindle assembly and chromosome behavior. These are the first observations that demonstrate fundamental aspects of the cytological mechanism of male killing and represent a solid base for further molecular studies of this phenomenon.
Maximum-Gain Working Set Selection for SVMs

Support vector machines are trained by solving constrained quadratic optimization problems. This is usually done with an iterative decomposition algorithm operating on a small working set of variables in every iteration. The training time strongly depends on the selection of these variables. We propose the maximum-gain working set selection algorithm for large scale quadratic programming. It is based on the idea to greedily maximize the progress in each single iteration. The algorithm takes second order information from cached kernel matrix entries into account. We prove the convergence to an optimal solution of a variant termed hybrid maximum-gain working set selection. This method is empirically compared to the prominent most violating pair selection and the latest algorithm using second order information. For large training sets our new selection scheme is significantly faster.
MECHANICALLY- AND BIOCHEMICALLY-INDUCED DIFFERENTIATIONOF BONE MARROW MESENCHYMAL STEM CELLS TO SMOOTH MUSCLECELLS IN A THREE-DIMENSIONAL FIBRIN MATRIX

Bone marrow mesenchymal stem cells (BMMSCs) may serve as an alternative source toterminally differentiated cells for tissue engineering applications. Our group has demonstratedthat BMMSCs subjected to a mechanical environment may differentiate toward a smooth musclecell (SMC) phenotype. Growth factors in conjunction with mechanical stimulation have beenshown in prior work to have a significant effect in regulating SMC phenotype in 2D.Simultaneous stimulation with mechanical strain and TGF-â has been shown to increase a-actinexpression in SMCs when compared to mechanical strain alone. Taken together, this previouswork suggests that mechanical and chemical factors may work together to promotedifferentiation of BMMSCs toward an SMC phenotype. Consequently, the hypothesis of thecurrent work is that uniaxial cyclic strain and biochemical stimulation with TGF-â willdifferentiate BMMSCs towards an SMC-like lineage in a synergistic manner in 3D.To evaluate this hypothesis, rat BMMSCs suspended in a fibrin gel were subjected tocyclic mechanical strains and frequencies physiologically consistent with the arterial system, incombination with chemical stimulation with TGF-â. Changes in morphology, proliferation,collagen production, and qualitative protein expression were assessed to determine if there wereany synergistic effects between mechanical and chemical stimulation.Results revealed that BMMSCs subjected to both mechanical and biochemicalstimulation led to an increase in production of contractile machinery intrinsic to terminally-differentiated SMCs, an increase in expression of SMC marker proteins, and an increase incollagen production when compared to control groups. These results support our hypothesis andsuggest that combined mechanical and biochemical stimulation may be important in stem cellbasedregenerative medicine applications involving SMCs.Future work will evaluate SMC gene expression and functionality to better define the roleof mechanical and biochemical stimuli in differentiating BMMSCs toward a terminallydifferentiated SMC phenotype.
PMaC Binary Instrumentation Library for PowerPC/AIX

The decommissioning of Alpha AXP-based systems carrying the ATOM toolkit has left the need for an efficient, flexible binary instrumentation tool-building framework for another platform. PMaCinst is a binary instrumentation toolkit that operates on XCOFF binaries on AIX for PowerPC processors. PMaCinst has a C++ API that provides the means to inject code and data into a binary file In this paper, we first present the mechanisms for performing these modifications along with the key parts of the API. We then present three example rewriting tools that have been built using PMaCinst, which help to highlight some of the correctness and efficiency issues that can be encountered by tool writers. Finally, we show that programs instrumented with PMaCinst slow down at rates that are comparable to equivalently instrumented programs created with ATOM.
Real-time joint estimation of camera orientation and vanishing points

A widely-used approach for estimating camera orientation is to use points at infinity, i.e., vanishing points (VPs). By enforcing the orthogonal constraint between the VPs, called the Manhattan world constraint, a drift-free camera orientation estimation can be achieved. However, in practical applications this approach suffers from many spurious parallel line segments or does not perform in non-Manhattan world scenes. To overcome these limitations, we propose a novel method that jointly estimates the VPs and camera orientation based on sequential Bayesian filtering. The proposed method does not require the Manhattan world assumption, and can perform a highly accurate estimation of camera orientation in real time. In addition, in order to enhance the robustness of the joint estimation, we propose a feature management technique that removes false positives of line clusters and classifies newly detected lines. We demonstrate the superiority of the proposed method through an extensive evaluation using synthetic and real datasets and comparison with other state-of-the-art methods.
A new assessment of the self-limiting hot-carrier degradation in LDD NMOSFET's by charge pumping measurement

By progressively lowering the gate-base level in the charge pumping (CP) measurement, the channel accumulation layer is caused to advance into the LDD gate-drain overlap and spacer-oxide regions, extending the interface that can be probed. This constitutes the basis of a new technique that separates the hot-carrier-induced interface states in the respective regions. Linear drain current degradation, measured at low and high gate bias, provides clear evidence that interface state generation initiates in the spacer region and progresses rapidly into the overlap/channel regions with stress time in a two-stage mechanism, involving first a series resistance increase and saturation, followed by a carrier mobility reduction.
People counting base on head and shoulder information

This paper presents an application for counting the people who pass through the supervised area. Instead of traditional camera, this study used Kinect 2 to get the depth information of image. The processes of our approach includes preprocessing, candidate detection, tracking, identification and people counting. In the preprocessing stage, the foreground object was sliced by depth information to make detection result more robust and to reduce the computation time. In the candidate detection stage, Hough Circle Transform was applied on color image to find candidates and depth image. Calculating pixels by a circle can decide whether candidate is people or not. Finally, the results of secondary stage provide the candidate's center coordinates that was used by nearest point tracking method to track path in 30 fps.
Crystal Structure of a Novel FAD-, FMN-, and ATP-containing l-Proline Dehydrogenase Complex from Pyrococcus horikoshii*

Two novel types of dye-linked l-proline dehydrogenase complex (PDH1 and PDH2) were found in a hyperthermophilic archaeon, Pyrococcus horikoshii OT3. Here we report the first crystal structure of PDH1, which is a heterooctameric complex (αβ)4 containing three different cofactors: FAD, FMN, and ATP. The structure was determined by x-ray crystallography to a resolution of 2.86 Å. The structure of the β subunit, which is an l-proline dehydrogenase catalytic component containing FAD as a cofactor, was similar to that of monomeric sarcosine oxidase. On the other hand, the α subunit possessed a unique structure composed of a classical dinucleotide fold domain with ATP, a central domain, an N-terminal domain, and a Cys-clustered domain. Serving as a third cofactor, FMN was located at the interface between the α and β subunits in a novel configuration. The observed structure suggests that FAD and FMN are incorporated into an electron transfer system, with electrons passing from the former to the latter. The function of ATP is unknown, but it may play a regulatory role. Although the structure of the α subunit differs from that of the β subunit, except for the presence of an analogous dinucleotide domain with a different cofactor, the structural characteristics of PDH1 suggest that each represents a divergent enzyme that arose from a common ancestral flavoenzyme and that they eventually formed a complex to gain a new function. The structural characteristics described here reveal the PDH1 complex to be a unique diflavin dehydrogenase containing a novel electron transfer system.
Unsupervised Gesture Segmentation by Motion Detection of a Real-Time Data Stream

Continuous and real-time gesture spotting is a key factor in the development of novel human–machine interaction modalities. Gesture recognition can be greatly improved with previous reliable segmentation. This paper introduces a new unsupervised threshold-based hand/arm gesture segmentation method to accurately divide continuous data streams into dynamic and static segments from unsegmented and unbounded input data. This segmentation may reduce the number of wrongly classified gestures in real-world conditions. The proposed approach identifies sudden inversions of movement direction, which are a cause of oversegmentation (excessive segmentation). This is achieved by the analysis of velocities and accelerations numerically derived from positional data. A genetic algorithm is used to compute feasible thresholds from calibration data. Experimental tests with three different subjects demonstrated an average oversegmentation error of 2.70% in a benchmark for motion segmentation with a feasible sliding window size.
Control of Cell Wall Assembly by a Histone-Like Protein in Mycobacteria

ABSTRACT Bacteria coordinate assembly of the cell wall as well as synthesis of cellular components depending on the growth state. The mycobacterial cell wall is dominated by mycolic acids covalently linked to sugars, such as trehalose and arabinose, and is critical for pathogenesis of mycobacteria. Transfer of mycolic acids to sugars is necessary for cell wall biogenesis and is mediated by mycolyltransferases, which have been previously identified as three antigen 85 (Ag85) complex proteins. However, the regulation mechanism which links cell wall biogenesis and the growth state has not been elucidated. Here we found that a histone-like protein has a dual concentration-dependent regulatory effect on mycolyltransferase functions of the Ag85 complex through direct binding to both the Ag85 complex and the substrate, trehalose-6-monomycolate, in the cell wall. A histone-like protein-deficient Mycobacterium smegmatis strain has an unusual crenellated cell wall structure and exhibits impaired cessation of glycolipid biosynthesis in the growth-retarded phase. Furthermore, we found that artificial alteration of the amount of the extracellular histone-like protein and the Ag85 complex changes the growth rate of mycobacteria, perhaps due to impaired down-regulation of glycolipid biosynthesis. Our results demonstrate novel regulation of cell wall assembly which has an impact on bacterial growth.
Biogeochemical cycling of carbon dioxide in estuaries and the continental shelf of the southeastern United States

The partial pressure of carbon dioxide (pCO2), concentration of total dissolved inorganic carbon (DIC) and total alkalinity (TA) were measured at both high tide and low tide in the surface water of three Georgia (United States of America) estuaries from September 2002 to May 2004. Of the three estuaries, Sapelo and Doboy Sounds are marine-dominated estuaries, while Altamaha Sound is a river-dominated estuary. During all sampling months, the three estuaries were supersaturated in CO2 with respect to the atmosphere (39.5-342.5 Pa, or 390 3380 μatm) due to CO2 inputs from the estuarine zone (mainly intertidal marshes) and the river. The calculated annual air-water CO2 flux in Altamaha Sound (69.3 mmol m -2 d -1 ) was 2.4 times that of Sapelo and Doboy Sounds (28.7-29.4 mmol m -2 d -1 ). Findings show that the higher CO2 degassing in the river-dominated estuary was largely fueled by CO2 loading from the river. Due to the substantial differences between riverand marine-dominated estuaries, the current estimates of air-water CO2 fluxes in global estuaries (which are based almost entirely on riverdominated estuaries) could be overestimated.