Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative myology of the unicornfishes, Naso (Acanthuridae, Percomorpha), with implications for phylogenetic analysis

Striated muscles of 15 species of unicornfishes (Naso, Acanthuridae) are described in detail. Of 93 muscles dissected, only five demonstrate intrageneric variation, providing only ten characters suitable for phylogenetic analysis. Thus, myology appears to be highly conservative at the species level and has been so for approximately 50–55 million years in this particular group of fishes. Furthermore, myology is static relative to osteology in Naso and at any taxonomic rank within fishes, implying osteology provides a larger but not necessarily more valuable data source for systematic studies. Although important for their epistomological value, these descriptions provide a basis for further studies ranging from functional, comparative, and systematic analyses, ultimately with the potential to address questions of historical ecology (i.e., speciation, adaptation, coevolution) within Naso. J. Morphol. 239:191–224, 1999. © 1999 Wiley‐Liss, Inc.
Spatial and Time Domain Feature of ERP Speller System Extracted via Convolutional Neural Network

Feature of event-related potential (ERP) has not been completely understood and illiteracy problem remains unsolved. To this end, P300 peak has been used as the feature of ERP in most brain–computer interface applications, but subjects who do not show such peak are common. Recent development of convolutional neural network provides a way to analyze spatial and temporal features of ERP. Here, we train the convolutional neural network with 2 convolutional layers whose feature maps represented spatial and temporal features of event-related potential. We have found that nonilliterate subjects' ERP show high correlation between occipital lobe and parietal lobe, whereas illiterate subjects only show correlation between neural activities from frontal lobe and central lobe. The nonilliterates showed peaks in P300, P500, and P700, whereas illiterates mostly showed peaks in around P700. P700 was strong in both subjects. We found that P700 peak may be the key feature of ERP as it appears in both illiterate and nonilliterate subjects.
Function of the Nonconserved N-Terminal Domain of Pseudorabies Virus pUL31 in Nuclear Egress

ABSTRACT Nuclear egress of herpesvirus capsids is mediated by the conserved nuclear egress complex (NEC), composed of the membrane-anchored pUL34 and its nucleoplasmic interaction partner, pUL31. The recently solved crystal structures of the NECs from different herpesviruses show a high structural similarity, with the pUL34 homologs building a platform recruiting pUL31 to the inner nuclear membrane. Both proteins possess a central globular fold, while the conserved N-terminal portion of pUL31 forms an extension reaching around the core of pUL34. However, the extreme N terminus of the pUL31 homologs, which is highly variable in length and amino acid composition, had to be removed for crystallization. Several pUL31 homologs contain a classical nuclear localization signal (NLS) within this part mediating efficient nuclear import. In addition, membrane-binding activity, blocking premature interaction with pUL34, nucleocapsid trafficking, and regulation of NEC assembly and disassembly via phosphorylation were assigned to the extreme pUL31 N terminus. To test the functional importance in the alphaherpesvirus pseudorabies virus (PrV) pUL31, N-terminal truncations and site-specific mutations were generated, and the resulting proteins were tested for intracellular localization, interaction with pUL34, and functional complementation of PrV-ΔUL31. Our data show that neither the bipartite NLS nor the predicted phosphorylation sites are essential for pUL31 function during nuclear egress. Moreover, nearly the complete variable N-terminal part was dispensable for function as long as a stretch of basic amino acids was retained. Phosphorylation of this domain controls efficient nucleocapsid release from the perinuclear space. IMPORTANCE Nuclear egress of herpesvirus capsids is a unique vesicle-mediated nucleocytoplasmic transport. Crystal structures of the heterodimeric NECs from different herpesviruses provided important details of this viral nuclear membrane deformation and scission machinery but excluded the highly variable N terminus of the pUL31 component. We present here a detailed mutagenesis study of this important portion of pUL31 and show that basic amino acid residues within this domain play an essential role for proper targeting, complex formation, and function during nuclear egress, while phosphorylation modulates efficient release from the perinuclear space. Thus, our data complement previous structure-function assignments of the nucleocapsid-interacting component of the NEC.
Dose dependent anti-obesity effect of three different Lactobacillus sakei strains using a diet induced obese murine model

Dose dependent anti-obesity effect of three different Lactobacillus sakei strains 1 using a diet induced obese murine model 2 3 Yosep Ji1, Young Mee Chung2, Soyoung Park1, Dahye Jeong2, Bongjoon Kim2, Wilhelm Heinrich 4 Holzapfel1 5 6 1Department of Advanced Green Energy and Environment, Handong Global University, Pohang, 7 Gyungbuk 37554, Republic of Korea 8 9 2CJ Blossom Park, 42, Gwanggyo-ro, Yeongtong-gu, Suwon, Gyeonggi, 16495, Republic of Korea 10 11 12 13 Corresponding Author: 14 Wilhelm Holzapfel 15 Email address: wilhelm@woodapple.net 16 17 18 19 20 21 22 23 24 25 26 27 28
Prediction of improved survival in patients with pancreatic cancer via IL-21 enhanced detection of mesothelin epitope-reactive T-cell responses

Most patients with pancreatic cancer present with extensive metastasis at diagnosis, with a 5-year survival rate of approximately 5%, despite chemotherapy and surgery. New treatment modalities are needed to improve survival. Mesothelin is a tumor-associated antigen (TAA) in patients with pancreatic cancer that could be used to gauge cellular immune responses directed against transformed cells since up to 100 percent of pancreatic ductal adenocarcinoma cells have been shown to strongly express mesothelin. A prospective, observational study was carried out in twenty-six, chemotherapy-naïve patients with resectable pancreatic ductal adenocarcinoma. Participants were between 48 and 81 years (median age: 64.5 years), 15 males and 11 females. All participants were clinically followed-up between 439 and 853 days post-surgery (n=14) or until death (n=12). Peripheral blood drawn on the day of surgery was stimulated with a mesothelin peptide pool (42 peptides, non-overlapping), individual mesothelin peptides, positive (anti-CD3 antibody, OKT3) and negative controls (medium) with or without adding IL-21. Kaplan-Meier estimators were used to gauge patients’ survival pattern in relation to mesothelin-specific IFN-γ responses. A survival benefit was linked with IFN-γ responses to peptides corresponding to mature mesothelin (p=0.018) and targeted recognition of the mesothelin601-615 epitope (MQEALSGTPCLLGPG) (p=0.006) in the presence of IL-21. Conversely, production of high levels of IFN-γ to OKT3 stimulation with IL-21 conditioning was associated with reduced survival of patients (p=0.016). Gauging anti-Mesothelin- directed immune responses will aid to identify patients i) in need of a more intensive clinical follow-up and ii) who may benefit from immunotherapeutic approaches targeting mesothelin.
Yokukansan, a Traditional Japanese Medicine, Enhances the Glutamate Transporter GLT-1 Function in Cultured Rat Cortical Astrocytes

Astrocytes carry two glutamate transporters—GLAST and GLT-1—the latter of which is responsible for >90% of glutamate uptake activity in the brain; however, under culture conditions, the GLT-1 expression in astrocytes is exceedingly low, as is the glutamate uptake activity mediated by GLT-1. This study aimed to elucidate the effects of yokukansan (YKS) in relation to the GLT-1-mediated regulation of extracellular glutamate concentrations. Thus, we treated cultured astrocytes with tumor necrosis factor-α (TNF-α) and dibutyryl-cAMP (dBcAMP) (hereinafter, referred to as “TA”) to increase GLT-1 expression and then functionally examined how YKS would affect glutamate uptake ability derived from GLT-1. Contrary to expectations, although the TA treatments did not affect the uptake activity, YKS significantly augmented it. Conversely, GLAST-derived glutamate uptake was significantly reduced by TA treatments but was unaffected by YKS. Subsequently, we analyzed the GLT-1 protein and mRNA levels and found that TA treatments had significantly increased them, which were then further augmented by YKS. These findings suggest that YKS enhances GLT-1-derived glutamate transport functions in TA-treated cultured astrocytes and that this process entails increased GLT-1 protein and mRNA levels. This type of mechanism may contribute to the YKS-mediated regulation of extracellular glutamate concentrations.
Inflammasomes: a novel therapeutic target in pulmonary hypertension?

Pulmonary hypertension (PH) is a rare, progressive pulmonary vasculopathy characterized by increased mean pulmonary arterial pressure, pulmonary vascular remodelling and right ventricular failure. Current treatments are not curative, and new therapeutic strategies are urgently required. Clinical and preclinical evidence has established that inflammation plays a key role in PH pathogenesis, and recently, inflammasomes have been suggested to be central to this process. Inflammasomes are important regulators of inflammation, releasing the pro‐inflammatory cytokines IL‐1β and IL‐18 in response to exogenous pathogen‐ and endogenous damage‐associated molecular patterns. These cytokines are elevated in PH patients, but whether this is a consequence of inflammasome activation remains to be determined. This review will briefly summarize current PH therapies and their pitfalls, introduce inflammasomes and the mechanisms by which they promote inflammation and, finally, highlight the preclinical and clinical evidence for the potential involvement of inflammasomes in PH pathobiology and how they may be targeted therapeutically.
Exploiting Textual and Citation Information to Identify and Summarize Influential Publications

Given a group of publications, we investigate the problem of identifying the papers with the most impact on others. We refer to these papers as influential in the sense that they introduce new concepts and language that will affect how future articles are written. In this paper we propose weighted PageRank algorithm that uses textual information from articles and information from citation graph to rank the impact of publications, then we automatically summarize these publications and extract important keywords. We show that using our algorithm outperforms default citation-based techniques in ranking influential papers (those which won best paper award) with no less than 2% in F1-score and NDCG. We also show that our algorithm outperforms previous graphbased keyword extraction techniques with no less than 1.5% in F1-score.
Unleash the Power for Tensor: A Hybrid Malware Detection System Using Ensemble Classifiers

The extensive growth of smartphones has spawned the propagation of malicious applications. Due to the increasing use of polymorphic malware, detection is becoming more difficult. To this end, ensemble learning has been proposed to improve accuracy in malware detection, without severely sacrificing time complexity. In this paper, we propose a hybrid detection system, TFBOOST, which incorporates the tensor filter algorithm into boosting ensemble generalization architecture, in order to improve detection efficacy. TFBOOST uses a static analysis to extract features and a level-by-level boosting structure with re-sampling process to diversify base learners. Experimental results show that TFBOOST generally outperforms state-of-the-art ensemble algorithms with higher detection precision and lower false positive rates. Finally, we visually interpret the high-level results of TFBOOST and conjecture that repackaged malware is the mainstay of potential malware.
The Effect of Short Pulse Width Settings on the Therapeutic Window in Subthalamic Nucleus Deep Brain Stimulation for Parkinson's disease.

BACKGROUND Subthalamic nucleus deep brain stimulation (STN-DBS) is an established treatment for selected Parkinson's disease (PD) patients, but therapy is often limited by side effects. Previous studies indicate an inverse relationship of the therapeutic window (TW) to pulse width (PW) settings down to 60μs, but there is limited data available on the effect of shorter PWs. OBJECTIVE To define the TW of STN-DBS in PD at PW of 30μs (PW30) relative to standard PW settings at 60μs (PW60), and to compare speed of gait and speech intelligibility on the two PW conditions. METHODS Monopolar review data of 15 consecutive PD patients who had screening of contacts performed at PW60 and PW30 was used to calculate the TW at each contact. We compared the TWs of the most efficacious contact per STN, and a secondary analysis was performed comparing all contacts. Speed of gait with a timed 10 metre walk test, speech intelligibility, and perceptual characteristics of speech were also compared at the efficacy thresholds for PW60 and PW30. RESULTS The TW was significantly greater at PW30 [3.8±1.6mA] than at PW60 [1.7±1.1mA]. In the secondary analysis, 110 TWs could be calculated and these remained significantly higher at PW30. The timed 10 metre walk at PW30 was faster than at PW60, and perceptual rating scores of speech were significantly improved at PW30. CONCLUSIONS STN-DBS in PD patients using a PW of 30μs significantly increases the TW compared to standard PW settings, and this effect is consistent across all contacts of an electrode. Speed of gait and perceptual speech scores are also improved at 30μs settings.
Knock-Down of CsNRT2.1, a Cucumber Nitrate Transporter, Reduces Nitrate Uptake, Root length, and Lateral Root Number at Low External Nitrate Concentration

Nitrogen (N) is a macronutrient that plays a crucial role in plant growth and development. Nitrate (NO3-) is the most abundant N source in aerobic soils. Plants have evolved two adaptive mechanisms such as up-regulation of the high-affinity transport system (HATS) and alteration of the root system architecture (RSA), allowing them to cope with the temporal and spatial variation of NO3-. However, little information is available regarding the nitrate transporter in cucumber, one of the most important fruit vegetables in the world. In this study we isolated a nitrate transporter named CsNRT2.1 from cucumber. Analysis of the expression profile of the CsNRT2.1 showed that CsNRT2.1 is a high affinity nitrate transporter which mainly located in mature roots. Subcellular localization analysis revealed that CsNRT2.1 is a plasma membrane transporter. In N-starved CsNRT2.1 knock-down plants, both of the constitutive HATS (cHATS) and inducible HATS (iHATS) were impaired under low external NO3- concentration. Furthermore, the CsNRT2.1 knock-down plants showed reduced root length and lateral root numbers. Together, our results demonstrated that CsNRT2.1 played a dual role in regulating the HATS and RSA to acquire NO3- effectively under N limitation.
CODE: Incorporating Correlation and Dependency for Task Scheduling in Data Center

The popularity of data-parallel applications and big data platforms has led to a variety of communication patterns in data center, which brings more complexity to task scheduling. Existing works try to minimize the overall completion time (i.e. makespan) of tasks but fail to take a full consideration of the relationship among tasks. Focusing on this, we propose a novel task scheduling scheme, CODE, which incorporates both the correlation and dependency among tasks for scheduling. We formulate the problem as a variant of Flexible Job Scheduling Problem (FJSP) to minimize the makespan. Firstly, we propose a novel network abstraction to describe the tasks as well as their relationship. Then the problem is formulated into an extensive FJSP and we solve it with a Tabu Search Algorithm. The evaluation has demonstrated the effectiveness of our method. Specifically, there is a reduction of over 16% in makespan with CODE compared with baseline scheduling scheme.
Comparative Analysis of Noise Removal Algorithms

This project shows Analysis of various Image Filtering Algorithms implemented over C language on bitmap image format. The Ultimate plan is to research the behavior of noisy image on application of various filtering algorithms to find the best output. Images will be processed or modified on an existing image in an exceedingly desired manner as they represent convertible data. The system shows the difference between the original image and the changed Image once the appliance of algorithms. In this study, it has been noticed that instances of image process occurring all the time in daily lives by using Image Processors. The objective of the image processing is to boost visually or statistically enhance an aspect of image that is bettering it’s quality that do not seem to be proper under the original image. The basic principle of the image processing operations over image data that builds a bigger perception, vision and clarity of the image but will not add any new info to the image. This objective is carried throughout the development and implementation of image processing system [1]. Image processing is nothing, but however manipulating an image knowledge to realize an clear and better the quality for higher pictures. However, image processing is nothing however a method of translation between of human visual senses and digital imaging gadgets [2]. The human visual senses does not perceive the globe within the same manner as digital image detectors, with present show technology devices imposing extra noise and information measure restrictions. Important variations between the human and digital sensors are some basic image knowledge manipulating steps for achieving higher transformation for clear pictures. Image processing System therefore ought to be achieved in a manner that with keeping with this scientific methodologies intact so others would possibly reproduce, and validate results. This includes recording and reporting and methodology actions, and applying similar methods to enhance photos.
UWB at SemEval-2018 Task 1: Emotion Intensity Detection in Tweets

This paper describes our system created for the SemEval-2018 Task 1: Affect in Tweets (AIT-2018). We participated in both the regression and the ordinal classification subtasks for emotion intensity detection in English, Arabic, and Spanish. For the regression subtask we use the AffectiveTweets system with added features using various word embeddings, lexicons, and LDA. For the ordinal classification we additionally use our Brainy system with features using parse tree, POS tags, and morphological features. The most beneficial features apart from word and character n-grams include word embeddings, POS count and morphological features.
Hybrid Learning Model with Barzilai-Borwein Optimization for Context-aware Recommendations

We propose an improved learning model for non-negative matrix factorization in the context-aware recommendation. We extend the collective non-negative matrix factorization through hybrid regularization method by combining multiplicative update rules with Barzilai-Borwein optimization. This provides new improved way of learning factorized matrices. We combine ratings, content features, and contextual information in three different 2-dimensional matrices. We study the performance of the proposed method on recommending top-N items. The method was empirically tested on 4 datasets, including movies, music, and mobile apps, showing an improvement in comparison with other state-of-the-art for top-N recommendations, and time convergence to the stationary point for larger datasets.
Planning protected areas network that are relevant today and under future climate change is possible: the case of Atlantic Forest endemic birds

Background A key strategy in biodiversity conservation is the establishment of protected areas. In the future, however, the redistribution of species in response to ongoing climate change is likely to affect species’ representativeness in those areas. Here we quantify the effectiveness of planning protected areas network to represent 151 birds endemic to the Brazilian Atlantic Forest hotspot, under current and future climate change conditions for 2050. Methods We combined environmental niche modeling and systematic conservation planning using both a county and a regional level planning strategy. We recognized the conflict between biodiversity conservation and economic development, including socio-economic targets (as opposed to biological only) and using planning units that are meaningful for policy-makers. Results We estimated an average contraction of 29,500 km2 in environmentally suitable areas for birds, representing 52% of currently suitable areas. Still, the most cost-effective solution represented almost all target species, requiring only ca. 10% of the Atlantic Forest counties to achieve that representativeness, independent of strategy. More than 50% of these counties were selected both in the current and future planned networks, representing >83% of the species. Discussion Our results indicate that: (i) planning protected areas network currently can be useful to represent species under climate change; (ii) the overlapped planning units in the best solution for both current and future conditions can be considered as “no regret” areas; (iii) priority counties are spread throughout the biome, providing specific guidance wherever the possibility of creating protected area arises; and (iv) decisions can occur at different administrative spheres (Federal, State or County) as we found quite similar numerical solutions using either county or regional level strategies.
Myosin-dependent actin stabilization as revealed by single-molecule imaging of actin turnover

How mechanical stress applied to the actin network modifies actin turnover has attracted considerable attention. Actomyosin exerts the major force on the actin network, which has been implicated in actin stability regulation. However, direct monitoring of immediate changes in F-actin stability on alteration of actomyosin contraction has not been achieved. Here we reexamine myosin regulation of actin stability by using single-molecule speckle analysis of actin. To avoid possible errors attributable to actin-binding probes, we employed DyLight-labeled actin that distributes identical to F-actin in lamellipodia. We performed time-resolved analysis of the effect of blebbistatin on actin turnover. Blebbistatin enhanced actin disassembly in lamellipodia of fish keratocytes and lamellar of Xenopus XTC cells at an early stage of the inhibition, indicating that actomyosin contraction stabilizes cellular F-actin. In addition, our data show a previously unrecognized relationship between the actin network-driving force and the actin turnover rates in lamellipodia. These findings point to the power of direct viewing of molecular behavior in elucidating force regulation of actin filament turnover.