Miracle-dz/UniFAR-FTUs huggingface dataset:
PCA based sequential feature space learning for gene selection

The expression of genes could be used for tumor subtype classification, clinical diagnosis and prognosis outcome prediction, but the underlying mechanism remains unknown. It is possible for data-based machine learning method to be employed for phenotype classification problem. But high dimensionality and small sample size make many machine learning methods fail. In this research, a PCA based sequential feature space learning method is proposed for gene selection. A two level feature selection process is conducted. In the first level PCA decomposition is conducted to obtain the orthogonal axis, and then features are projected and evaluated on the orthogonal axis. In second level, the features that have large projections are selected to form the feature space. Then the projections of all features onto the feature space are evaluated. Only features that have large projections both on orthogonal axis and feature subspace are selected as the feature subset. Then a neural network (NN) is employed to learn the classification model. The PCA based feature space learning is processed in a sequential manner until the classification performance is under pre-specified threshold and stable. The proposed methods have been applied to two gene microarray databases and showing good results.
PepCyber:P∼PEP: a database of human protein–protein interactions mediated by phosphoprotein-binding domains

Phosphoprotein-binding domains (PPBDs) mediate many important cellular and molecular processes. Ten PPBDs have been known to exist in the human proteome, namely, 14-3-3, BRCT, C2, FHA, MH2, PBD, PTB, SH2, WD-40 and WW. PepCyber:P∼PEP is a newly constructed database specialized in documenting human PPBD-containing proteins and PPBD-mediated interactions. Our motivation is to provide the research community with a rich information source emphasizing the reported, experimentally validated data for specific PPBD–PPEP interactions. This information is not only useful for designing, comparing and validating the relevant experiments, but it also serves as a knowledge-base for computationally constructing systems signaling pathways and networks. PepCyber:P∼PEP is accessible through the URL, http://www.pepcyber. org/PPEP/. The current release of the database contains 7044 PPBD-mediated interactions involving 337 PPBD-containing proteins and 1123 substrate proteins.
The diffusion sensitivity of fast steady‐state free precession imaging

Steady‐state free precession (SSFP) imaging with an added field gradient pulse is strongly sensitive to self‐diffusion and other motions of water. In an earlier theoretical analysis of diffusion attenuation due to a single gradient pulse Wu and Buxton (J. Magn. Reson. 90, 243, 1990) concluded that the diffusion sensitivity would be increased with smaller flip angles. In this paper a partial partition analysis of the different echo pathways contributing to the signal is used to illustrate the contribution of stimulated echo pathways with long diffusion times as the source of the enhanced diffusion sensitivity with low flip angles. Experimental imaging studies in phantoms and the brain of a human subject demonstrate substantially greater signal attenuation with small flip angles (<30°). The theoretical equation of Wu and Buxton provides a reasonable fit to the experimental data, accounting for the flip angle and TR dependence, but the estimated diffusion coefficients are larger than expected from previous studies. The large attenuation observed in the human studies, particularly in cerebrospinal fluid, is most likely due to other tissue motions. Both the theoretical calculations and the experimental data show that for the same gradient strength the diffusion sensitivity of SSFP is much greater than the diffusion sensitivity of conventional spin‐echo methods.
Self-Energy Recycling for RF Powered Multi-Antenna Relay Channels

We investigate self-energy recycling (S-ER)-based RF powered multi-antenna relay channels (RCs) for the coverage extension in sensor networks or small cells. In the S-ER-based RF powered RC, the power used at the relay station for data transmission depends only on the energy from the access point and the recycled energy from its own transmission. We propose an optimal beamforming scheme with associated protocols and study their behaviors for both cases of downlink only and joint up–down link. Strategies for the power allocation between data transmission and RF powering are provided and a comparison with the conventional RF powered RC is made. For the proposed power allocation strategies, the performance of the conventional RC is achieved by the proposed RF powered RC only when infinite RF power is available. A high value of S-ER helps the proposed systems to reach the performance of conventional relay systems. In the joint up–down link protocol, we show that the up–down rate region can simply be constructed with easy power allocation strategy.
Hepatitis C Virus Activates Bcl-2 and MMP-2 Expression through Multiple Cellular Signaling Pathways

ABSTRACT Hepatitis C virus (HCV) infection is associated with numerous liver diseases and causes serious global health problems, but the mechanisms underlying the pathogenesis of HCV infections remain largely unknown. In this study, we demonstrate that signal transducer and activator of transcription 3 (STAT3), matrix metalloproteinase-2 (MMP-2), and B-cell lymphoma 2 (Bcl-2) are significantly stimulated in HCV-infected patients. We further show that HCV activates STAT3, MMP-2, Bcl-2, extracellular regulated protein kinase (ERK), and c-Jun N-terminal kinase (JNK) in infected Huh7.5. 1 cells. Functional screening of HCV proteins revealed that nonstructural protein 4B (NS4B) is responsible for the activation of MMP-2 and Bcl-2 by stimulating STAT3 through repression of the suppressor of cytokine signaling 3 (SOCS3). Our results also demonstrate that multiple signaling cascades, including several members of the protein kinase C (PKC) family, JNK, ERK, and STAT3, play critical roles in the activation of MMP-2 and Bcl-2 mediated by NS4B. Further studies revealed that the C-terminal domain (CTD) of NS4B is sufficient for the activation of STAT3, JNK, ERK, MMP-2, and Bcl-2. We also show that amino acids 227 to 250 of NS4B are essential for regulation of STAT3, JNK, ERK, MMP-2, and Bcl-2, and among them, three residues (237L, 239S, and 245L) are crucial for this regulation. Thus, we reveal a novel mechanism underlying HCV pathogenesis in which multiple intracellular signaling cascades are cooperatively involved in the activation of two important cellular factors, MMP-2 and Bcl-2, in response to HCV infection.
Overview and evaluation of fuel ethanol from cellulosic biomass

▪ Abstract Ethanol is a high performance fuel in internal combustion engines. It is a liquid, which is advantageous in terms of storage, delivery, and infrastructural compatability. Ethanol burns relatively cleanly, especially as the amount of gasoline with which it is blended decreases. Evaporative and toxicity-weighted air toxics emissions are consistently lower for ethanol than for gasoline. It is likely that vehicles can be configured so that exhaust emissions of priority pollutants are very low for ethanol-burning engines, although the same can probably be said for most other fuels under consideration. Recent work suggests that ethanol may be more compatible with fuel cell—powered vehicles than has generally been assumed. Research and development—driven advances have clear potential to lower the price of cellulosic ethanol to a level competitive with bulk fuels. Process areas with particular potential for large cost reductions include biological processing (with consolidated bioprocessing particularl.
Sorafenib versus Hepatic Arterial Infusion Chemotherapy as Initial Treatment for Hepatocellular Carcinoma with Advanced Portal Vein Tumor Thrombosis

Objective: To investigate the validity of hepatic arterial infusion chemotherapy with low-dose 5-fluorouracil and cisplatin (LFP) versus sorafenib as first-line treatment for hepatocellular carcinoma (HCC) with portal vein tumor thrombosis (Vp3, Vp4). Patients and Methods: We retrospectively reviewed the cases of Child-Pugh A advanced HCC with Vp3 or Vp4 treated with LFP or sorafenib between October 2002 and December 2013. Results: There were 32 patients in the LFP group and 14 patients in the sorafenib group. The objective response rate/disease control rate was 31.3/56.3% in the LFP group and 0/28.6% in the sorafenib group. The median survival time (MST) (309 vs. 120 days; p = 0.009) and the median time to treatment failure (109 vs. 37 days; p = 0.022) were significantly longer in the LFP group than in the sorafenib group. In the LFP group, a relatively favorable outcome (MST, 622 days) was obtained among the response cases. Among the nonresponse cases in the LFP group, at the time of cessation of LFP, 70.4% of cases were Child-Pugh A and 88.9% of cases maintained a score of ≤7 points; of the cases in whom Child-Pugh A was maintained, the survival period from the time of LFP discontinuation was significantly longer in the cases in whom sorafenib was introduced as a secondary treatment after LFP than in the cases treated with best supportive care (220 vs. 89 days; p = 0.002). The main adverse event with LFP was grade 3 or higher cytopenia, which was manageable, and adverse event-induced discontinuation was significantly lower as compared with sorafenib (p = 0.002). Conclusion: For the treatment of HCC with Vp3/Vp4, it is desirable to initially use LFP and then immediately change to sorafenib if no response is obtained.
BBX19 Interacts with CONSTANS to Repress FLOWERING LOCUS T Transcription, Defining a Flowering Time Checkpoint in Arabidopsis[C][W]

BBX19, a transcription factor with two B-Box motifs, is a clock output component that functions as a flowering time checkpoint by physically interacting with CO and depleting the CO pool required for FT activation. The integrity of the Box1 motif is necessary for the functionality of BBX19. The timely transition of vegetative to reproductive development is coordinated through quantitative regulation of floral pathway genes in response to physiological and environmental cues. Here, we show that the circadian-controlled expression of the Arabidopsis thaliana floral transition regulators FLOWERING LOCUS T (FT) and CONSTANS (CO) is antiphasic to that of BBX19, a transcription factor with two B-Box motifs. Diminished expression of BBX19 by RNA interference accelerates flowering, and constitutive expression of BBX19 delays flowering under inductive photoperiods. This delay is not accompanied by the alteration of CO expression levels but rather by a reduction of transcript levels of FT and the FT-regulated genes SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1, LEAFY, and FRUITFUL. Similar to CO, BBX19 is expressed in vasculature. BBX19 and CO colocalize in the nucleus and interact physically in vivo. In transient assays, coinfiltration of 10-fold more CO overcomes the BBX19-mediated repression of FT activation. Substitution of the conserved Cys-25 to Ser in the BBX19 Box1 motif abolishes the BBX19–CO interaction and eliminates the negative regulation of flowering time, while the analogous C76S substitution in the Box2 motif is ineffective. Together, these results implicate BBX19 as a circadian clock output that depletes the active CO pool to accurately monitor daylength and precisely time FT expression.
On the Observed Near Cancellation between Longwave and Shortwave Cloud Forcing in Tropical Regions

Abstract Observations based on Earth Radiation Budget Experiment (ERBE) satellite data indicate that there is a near cancellation between tropical longwave and shortwave cloud forcing in regions of deep convective activity. Cloud forcing depends on both cloud macrophysical properties (e.g., cloud amount, cloud height, etc.) and on microphysical properties (e.g., cloud particle size, particle shape, etc.). Hence, the near cancellation in the tropics could be due to either the macrophysical or the microphysical properties of these clouds, or a combination of these effects. By using satellite data from the ERBE and International Satellite Cloud Climatology Project (ISCCP) and recent in situ observations of tropical anvils, it is argued that the observed near cancellation in the tropics is mainly a result of the tropical tropopause height. This conclusion depends on two observational results from comparison of ERBE and ISCCP data: 1) Both the longwave and shortwave cloud forcing are predominately due to high .
Short-time Viterbi for online HMM decoding: Evaluation on a real-time phone recognition task

In this paper we present the implementation of an online HMM decoding process. The algorithm derives an online version of the Viterbi algorithm on successive variable length windows, iteratively storing portions of the optimal state path. We explicit the relation between the hidden layer's topology and the applicability and performance prediction of the algorithm. We evaluate the validity and performance of the algorithm on a phone recognition task on a database of continuous speech from a native French speaker. We specifically study the latency-accuracy performance of the algorithm.
Information Extraction in Medical Domain Using Ontology and Knowledge Graphs

Medical documents contain lots of information which can be useful to build many health related applications. Since medical documents present unstructured information in nonstandard natural language so it is difficult to extract this information and present in a structured manner. We propose a model named "Feature Based Relation Extraction with Relational Learning using Medical Ontology" which maps the clinical entities to concepts in the medical ontology such as UMLS, extracts relations between clinical entities, inference out of the UMLS relations and converts the unstructured medical text into structured information. Our model uses linguistic features and existing relational learning approaches to learn the relations with the help of the UMLS knowledge graph.
Internal reflection pattern of Korea Strait shelf mud (Nakdong River subaqueous delta) off southeast Korea and implications for Holocene relative base‐level change

The Korea Strait shelf mud (KSSM) (Nakdong River subaqueous delta) is the most conspicuous Holocene sedimentary feature in the inner shelf off southeast Korea. Analysis of multi‐channel sparker profiles and 14C ages of sediment cores reveals that the KSSM consists of three seismic units at the depocenter (>60 m thick): (i) the thin transgressive bottom (>ca 8000 cal bp); (ii) thick (>40 m) obliquely progradational middle (ca 8000–ca 2600 cal bp); and (iii) thin transgressive top (ca 2600 cal bp–present) units. The relative base level, predicted from the internal reflection pattern of the KSSM, remained significantly deeper (up to >70 m) than global sealevel during much of the Holocene. The apparent gradual drop (∼20 m) of the relative base level during the deposition of the middle unit, followed by a rise, further suggests that base level does not conform to sealevel and is more sensitive than the relative sealevel is to the local oceanographic regime and processes.
Very Fast Region-Connected Segmentation for Spatial Data: Case Study

In this paper, we design fast algorithms for segmenting/classifying 2D images or 2D spatial data. The data is stored in quadtree and Rtree formats, and it may be extracted from spatial databases. The topological and graph-theoretic properties will be used to speed up the segmentation process. The key feature of this paper is to perform a segmentation process without restore data frames. In other words, this segmentation will be done in a virtual or abstracted manner. Based on local connectedness and value-homogeneity, we implemented lambda-connected segmentation and the mean-based region growing segmentation to solve our problem. We will also discuss threshold segmentation. In this paper, we first design the segmentation algorithms for quadtree indexed images, then discuss the algorithms for R-trees indexed data. We will implement Rtree segmentation algorithms in the near future. Our algorithms will make the segmentation process much faster by not decoding the quadtree indexing code before the segmentation. The new algorithm for stream data will modify the boundaries of the segments in previous frames to predict the segments in upcoming frames. This could lead to the widespread use of segmentation technology for computer vision and geo-data processing, medical image processing, object tracking, geometrical simulation, and database application and data-mining as well as multi-dimensional data sets.
Vulnerability and Capacity: Explaining Local Commitment to Climate-Change Policy

We examine the reasons why a US locality would voluntarily commit to the Cities for Climate Protection (CCP) campaign. Using geographic information systems analytic techniques, we map and measure a locality's vulnerability to climate-change impacts at the county level of spatial precision. We analyze multiple measures of climate-change vulnerability, including expected temperature change, extreme weather events, and coastal proximity, as well as economic variables, demographic variables, and civic-participation variables that constitute a locality's socioeconomic capacity to commit to costly climate-change policy initiatives. Bivariate and logistic regression results indicate that CCP-committed localities are quantitatively different to noncommitted localities on both climate-change risk and socioeconomic-capacity dimensions. On vulnerability measures, the odds of CCP-campaign participation increase significantly with the number of people killed and injured by extreme weather events, projected temperature change, and coastal proximity. On socioeconomic-capacity measures, the odds of CCP-campaign involvement increase with the percentage of citizens that vote Democrat and recycle, as well as the number of nonprofit organizations with an environment focus. The odds decrease in a county area as the percentage of the labor force employed in carbon-intensive industries increases.
Diagrammatic Ontology Engineering

Ontology engineering involves defining axioms to capture required constraints when modelling a domain of interest. Ontologies arise in many areas, with potentially a diverse range of end users involved in their creation. This leads to the requirement for accessible approaches to ontology engineering, as some stakeholders need not be fluent or trained in symbolic notations such as OWL. This paper summarises concept diagrams and property diagrams which are designed to be an accessible alternative to OWL. The paper reports on two empirical studies, the first of which focuses on how to choose effective concept diagrams for expressing simple OWL axioms. The second study compares these effective diagrams to both OWL and DL, demonstrating that they can bring about significant improvements in task performance for novice users. These results support the incorporation of concept diagrams into ontology engineering tools, such as Prot´eg´e or WebProtege. This is an exciting prospect, allowing more stakeholders to fully engage with the ontology engineering process, leading to more efficiently produced and robust ontologies in the future.
Can a Nonspecific Bias Toward Top-Heavy Patterns Explain Newborns' Face Preference?

This study examined newborns' face preference using images of natural and scrambled faces in which the location of the inner features was distorted. The results demonstrate that newborns' face preference is not confined to schematic configurations, but can be obtained also with veridical faces. Moreover, this phenomenon is not produced by a specific bias toward the face geometry, but derives from a domain-general bias toward configurations with more elements in the upper than in the lower half (i.e., top-heavy patterns). These results suggest that it may be unnecessary to assume the existence of a prewired tendency to orient toward the face geometry, and support the idea that faces do not possess a special status in newborns' visual world.
The Dansgaard‐Oeschger cycles discovered in the up stream source region of the North Pacific Intermediate Water formation

Millennial‐scale oceanographic oscillations were identified in the southern Okhotsk Sea based on high‐resolution measurements of total organic carbon (TOC), C/N ratios, and biogenic opal, employing Core MD01‐2412 (53 m) with the bottom age of 115 ka. The oscillations are linked with the Dansgaard‐Oeschger (D‐O) climatic cycles. Inadequate data existed in the source regions of the North Pacific Intermediate Water (NPIW) formation thus far. We report the first decisive documentation of the D‐O cycles in the up stream source region of the NPIW, illustrating that the D‐O cycles observed in the down stream regions (e.g., Santa Barbara Basin) due to expansion of the NPIW were in part governed by the climatic variations occurred in the Okhotsk Sea. Increases in TOC and C/N ratios reflect abrupt sea level rises associated with 14 interstadial events over the past 115 kyrs, attributing to the downward transport of eroded continental shelf sediments.
A Geometric Interpretation of the Open String Tachyon

Unstable, non-BPS D-branes in weakly coupled ten dimensional string theory have many mysterious properties. Among other things, it is not clear what sets their tension, what is their relation to the better understood BPS D-branes, and why the open string tachyon on them is described by an effective Lagrangian which suggests that the tachyon corresponds to an extra spatial dimension transverse to the branes. We point out that the dynamics of D-branes in the presence of Neveu-Schwarz fivebranes on a transverse R^3 times S^1 provides a useful toy model for studying these issues. From the point of view of a 5+1 dimensional observer living on the fivebranes, BPS D-branes in ten dimensions give rise to two kinds of D-branes, which are BPS or non-BPS depending on whether they do or do not wrap the S^1. Their tensions are related, since from a higher dimensional perspective, they are the same objects. D-branes localized on the S^1 have a tachyon corresponding to their position on the circle. This field is described by the same Lagrangian as that of a tachyon on a non-BPS D-brane in ten dimensions. Its geometrical interpretation is useful for clarifying the properties of non-BPS branes in six dimensions. If the lessons from the six dimensional system can be applied in ten dimensions, the existence of non-BPS D-branes seems to suggest the presence of at least one extra dimension in critical type II string theory.
Player tracking using prediction after intersection based particle filter for volleyball match video

Player tracking plays a key role in volleyball tactics analysis. Therefore, many tracking algorithms have been proposed to track and locate the players' positions. However, in a volleyball match, intersection of players wearing the same uniform occurs frequently. Conventional tracking algorithms can hardly handle such complicated situation with high accuracy. This paper proposes a prediction after intersection based Particle Filter to track players distinctively in intersection events of volleyball. As for likelihood models in the proposed particle filter, a labeling likelihood to distinguish each tracking object and a distance likelihood to prevent particles from concentrating in only one tracking object are employed. As for prediction models, two re-detection models, Crash Pattern Model (CPM) and Others Pattern Model (OPM), are used to detect each tracking object after intersection. Experimental results reveal that the proposed algorithm attains high tracking accuracy for various kinds of intersection scenes. The tracking accuracy of player using whole scenes of a volleyball match is around 80% while conventional method is only 30%.