Miracle-dz/UniFAR-FTUs huggingface dataset:
K-Boost: A Scalable Algorithm for High-Quality Clustering of Microarray Gene Expression Data

Microarray technology for profiling gene expression levels is a popular tool in modern biological research. Applications range from tissue classification to the detection of metabolic networks, from drug discovery to time-critical personalized medicine. Given the increase in size and complexity of the data sets produced, their analysis is becoming problematic in terms of time/quality trade-offs. Clustering genes with similar expression profiles is a key initial step for subsequent manipulations and the increasing volumes of data to be analyzed requires methods that are at the same time efficient (completing an analysis in minutes rather than hours) and effective (identifying significant clusters with high biological correlations). In this paper, we propose K-Boost, a clustering algorithm based on a combination of the furthest-point-first (FPF) heuristic for solving the metric k-center problem, a stability-based method for determining the number of clusters, and a k-means-like cluster refinement. K-Boost runs in O (|N| x k) time, where N is the input matrix and k is the number of proposed clusters. Experiments show that this low complexity is usually coupled with a very good quality of the computed clusterings, which we measure using both internal and external criteria. Supporting data can be found as online Supplementary Material at www.liebertonline. com.
Chip-to-Chip Switched Beam 60 GHz Circular Patch Planar Antenna Array and Pattern Considerations

A 60 GHz switched beam chip-to-chip antenna array is introduced. The array consists of four center fed circular patch elements with side vias in a $2{\times} 2$ grid arrangement forming a planar array. The array is designed to fit on a typical multicore chip for reconfigurable interchip wireless communication. The array main beam is switched by changing the interelement phase shifts in the azimuth plane. The switching of the main beam is analyzed and verified through full-wave simulation. The design presented is an improvement over a previous design of a two-element antenna array. The Friis transmission equation with polarization components taken into account is used to model the interchip wireless link. To verify the model, a transmission coefficient measurement is made between a pair of the two-element arrays separated by a 10 mm distance. Both simulated and measured radiation patterns of the two-element array are presented for use in the Friis equation to calculate the transmission coefficients. Full-wave simulation of the array pair is also performed. The calculated results obtained from the Friis model agree well with both the measured and full-wave simulation results. The Friis model is used to calculate both signal and interference levels.
A Critical Determinant of Neurological Disease Associated with Highly Pathogenic Tick-Borne Flavivirus in Mice

ABSTRACT Tick-borne encephalitis virus (TBEV) and Omsk hemorrhagic fever virus (OHFV) are highly pathogenic tick-borne flaviviruses; TBEV causes neurological disease in humans, while OHFV causes a disease typically identified with hemorrhagic fever. Although TBEV and OHFV are closely related genetically, the viral determinants responsible for these distinct disease phenotypes have not been identified. In this study, chimeric viruses incorporating components of TBEV and OHFV were generated using infectious clone technology, and their pathological characteristics were analyzed in a mouse model to identify virus-specific determinants of disease. We found that only four amino acids near the C terminus of the NS5 protein were primarily responsible for the development of neurological disease. Mutation of these four amino acids had no effect on viral replication or histopathological features, including inflammatory responses, in mice. These findings suggest a critical role for NS5 in stimulating neuronal dysfunction and degeneration following TBEV infection and provide new insights into the molecular mechanisms underlying the pathogenesis of tick-borne flaviviruses. IMPORTANCE Tick-borne encephalitis virus (TBEV) and Omsk hemorrhagic fever virus (OHFV) belong to the tick-borne encephalitis serocomplex, genus Flavivirus, family Flaviviridae. Although TBEV causes neurological disease in humans while OHFV causes a disease typically identified with hemorrhagic fever. In this study, we investigated the viral determinants responsible for the different disease phenotypes using reverse genetics technology. We identified a cluster of only four amino acids in nonstructural protein 5 primarily involved in the development of neurological disease in a mouse model. Moreover, the effect of these four amino acids was independent of viral replication property and did not affect the formation of virus-induced lesions in the brain directly. These data suggest that these amino acids may be involved in the induction of neuronal dysfunction and degeneration in virus-infected neurons, ultimately leading to the neurological disease phenotype. These findings provide new insight into the molecular mechanisms of tick-borne flavivirus pathogenesis.
Managing Web-Based Information

The heterogeneity and the lack of structure of World Wide Web make automated discovery, organization, and management of Web-based information a non-trivial task. Traditional search and indexing tools provide some comfort to users, but they generally provide neither structured information nor categorize, filter, or interpret documents in an automated way. In recent years, these factors have prompted the need for developing data mining techniques applied to the web, giving rise to the term “Web Mining”. This paper introduces the problem of web data extraction and gives a brief analysis of the various techniques to address it. Then, News Miner, a tool for Web Content Mining applied to the news retrieval is presented.
Stress Induced Expression of c-fos mRNA in the Brain by Experimental Occlusal Interference in Rats-Relationship with Stress-

目的: 実験的咬合干渉が, ストレスとして脳内で認知されるかを明らかにすることを目的とした. 方法: 実験には, 生後11週齢の雄性Wistarラットを用い, 金網拘束ケージ内に, 30分間拘束した拘束群 (6匹), 同ケージに水を入れ腹部が浸かる水位で30分間拘束した水拘束群 (6匹), 右側上顎大臼歯部に高さ1. 0mmの干渉を付与した干渉群 (6匹), および対照群 (6匹) とした. 拘束, 水拘束群はストレス付与開始後60分に, 干渉群は干渉付与24時間後に採血し, 生化学的観察として全群同時間帯における血中コルチコステロン濃度を分析し, 分子組織学的観察としてIn situ hybridization法にて, 脳内c-fos mRNA陽性細胞を扁桃体, 梨状葉皮質, 海馬, 帯状回皮質, 視床下部室傍核, 青斑核, 大縫線核, 中心灰白質で観察した. 結果: 実験的咬合干渉は, 拘束ストレス2群と比較して脳内c-fos mRNA陽性細胞の発現の程度は異なるが, すべての観察部位において発現を認めた. また, 干渉群の扁桃体, 梨状葉皮質では左右半球差を認めた. 血中コルチコステロン濃度は, 水拘束, 拘束, 干渉, 対照群の順で高値を示した. 結論: ラッフへの実験的咬合干渉の付与は, 明らかにストレスとして脳内および生体で認知, 応答され, また, 身体および精神的要因をもったストレス応答であった.
RRDVCR: Real-time reliable data delivery based on virtual coordinating routing for Wireless Sensor Networks

Real-time industrial application requires routing protocol that guarantees data delivery with reliable, efficient and low end-to-end delay. Existing Routing(THVR) [13] is based velocity of Two-Hop Velocity and protocol relates two-hop velocity to delay to select the next forwarding node, that has overhead of exchanging control packets, and depleting the available energy in nodes. We propose a Real-Time Reliable Data delivery based on Virtual Coordinates Routing (RRDVCR) algorithm, based on the number of hops to the destination rather than geographic distance. Selection of forwarding node is based on packet progress offered by two-hops, link quality and available energy at the forwarding nodes. All these metric are co-related by dynamic co-relation factor. The proposed protocol uses selective acknowledgment scheme that results in lower overhead and energy consumption. Simulation results shows that there is about 22% and 9.5% decrease in energy consumption compared to SPEED [8] and THVR [13] respectively, 16% and 38% increase in packet delivery compared to THVR [13] and SPEED [8] respectively, and overhead is reduced by 50%.
A Review of Multi-Stack PEM Fuel Cell Systems: Advantages, Challenges and On-Going Applications in the Industrial Market

The purpose of this paper is to provide a conceptual framework of the Multi-stack Proton exchange membrane Fuel cell technology (PEMFC) system state of the art. Recent developments in the fuel cell (FC) researches have increased the need of raising the system reliability, its life time and its efficiency. The electrical configuration of a multi-stack FC system, the power sharing and the hybridization rate are the main topics in this paper. There was a significant positive correlation between increasing the Multi-Stack Fuel Cell's (MSFC) system application in the industry especially in the transportation sector, and the decreasing of the current environmental pollution crisis. Keywords- Multi-stack Fuel Cell system; PEMFC; Energy management; Redundancy; Electrical Architecture.
Second-line therapy in diffuse large B-cell lymphoma (DLBCL): treatment patterns and outcomes in older patients receiving outpatient chemotherapy

Abstract Using SEER-Medicare linked data we identified elderly patients diagnosed with diffuse large B-cell lymphoma (DLBCL) between January 2000 and December 2007 who received second-line outpatient chemotherapy for relapsed or refractory disease. Second-line regimens were classified into three mutually exclusive groups: aggressive, conventional, and palliative. Of the 632 (426 relapsed, 206 refractory) patients in the cohort, 27.8% received aggressive second-line therapy, 39.1% received conventional therapy, and 33.1% received palliative therapy. There were no differences in survival by type of therapy received, either for relapsed or refractory patients, although the patient risk profile differed significantly. However, duration of remission, male gender, and anemia at diagnosis were important predictors in relapsed patients, and male gender, B-symptoms, comorbidity burden, and poverty status were important predictors in refractory patients. Survival in elderly patients receiving second-line therapy remains poor, and the 24-month cost of all care exceeds $97,000. Patients would benefit from improved treatment options.
Ranking of Wikipedia articles in search engines revisited: Fair ranking for reasonable quality?

This paper aims to review the fiercely discussed question of whether the ranking of Wikipedia articles in search engines is justified by the quality of the articles. After an overview of current research on information quality in Wikipedia, a summary of the extended discussion on the quality of encyclopedic entries in general is given. On this basis, a heuristic method for evaluating Wikipedia entries is developed and applied to Wikipedia articles that scored highly in a search engine retrieval effectiveness test and compared with the relevance judgment of jurors. In all search engines tested, Wikipedia results are unanimously judged better by the jurors than other results on the corresponding results position. Relevance judgments often roughly correspond with the results from the heuristic evaluation. Cases in which high relevance judgments are not in accordance with the comparatively low score from the heuristic evaluation are interpreted as an indicator of a high degree of trust in Wikipedia. One of the systemic shortcomings of Wikipedia lies in its necessarily incoherent user model. A further tuning of the suggested criteria catalog, for instance, the different weighing of the supplied criteria, could serve as a starting point for a user model differentiated evaluation of Wikipedia articles. Approved methods of quality evaluation of reference works are applied to Wikipedia articles and integrated with the question of search engine evaluation. © 2011 Wiley Periodicals, Inc.
Hydrolysis Activity of Virgin Coconut Oil Using Lipase from Different Sources

Two types of lipase, Candida rugosa lipase (CRL) and porcine pancreas lipase (PPL), were used to hydrolyze virgin coconut oil (VCO). The hydrolysis process was carried out under four parameters, VCO to buffer ratio, lipase concentration, pH, and temperature, which have a significant effect on hydrolysis of lipase. CRL obtained the best hydrolysis condition at 1 : 5 of VCO to buffer ratio, 1.5% of CRL concentration, pH 7, and temperature of 40°C. Meanwhile, PPL gave different results at 1 : 4 of VCO to buffer ratio, 2% of lipase concentration, pH 7.5, and 40°C. The highest hydrolysis degree of CRL and PPL was obtained after 16 hours and 26 hours, reaching 79.64% and 27.94%, respectively. Besides, the hydrolysis process was controlled at different time course (every half an hour) at the first 4 hours of reaction to compare the initial hydrolysis degree of these two lipase types. FFAs from hydrolyzed products were isolated and determined the percentage of each fatty acid which contributes to the FFAs mixture. As a result, medium chain fatty acids (MCFAs) made up the main contribution in composition of FFAs and lauric acid (C12) was the largest segment (47.23% for CRL and 44.23% for PPL).
Inhibition of Vpx-Mediated SAMHD1 and Vpr-Mediated Host Helicase Transcription Factor Degradation by Selective Disruption of Viral CRL4 (DCAF1) E3 Ubiquitin Ligase Assembly

ABSTRACT The lentiviral accessory proteins Vpx and Vpr are known to utilize CRL4 (DCAF1) E3 ligase to induce the degradation of the host restriction factor SAMHD1 or host helicase transcription factor (HLTF), respectively. Selective disruption of viral CRL4 (DCAF1) E3 ligase could be a promising antiviral strategy. Recently, we have determined that posttranslational modification (neddylation) of Cullin-4 is required for the activation of Vpx-CRL4 (DCAF1) E3 ligase. However, the mechanism of Vpx/Vpr-CRL4 (DCAF1) E3 ligase assembly is still poorly understood. Here, we report that zinc coordination is an important regulator of Vpx-CRL4 E3 ligase assembly. Residues in a conserved zinc-binding motif of Vpx were essential for the recruitment of the CRL4 (DCAF1) E3 complex and Vpx-induced SAMHD1 degradation. Importantly, altering the intracellular zinc concentration by treatment with the zinc chelator N,N,N′-tetrakis-(2′-pyridylmethyl)ethylenediamine (TPEN) potently blocked Vpx-mediated SAMHD1 degradation and inhibited wild-type SIVmac (simian immunodeficiency virus of macaques) infection of myeloid cells, even in the presence of Vpx. TPEN selectively inhibited Vpx and DCAF1 binding but not the Vpx-SAMHD1 interaction or Vpx virion packaging. Moreover, we have shown that zinc coordination is also important for the assembly of the HIV-1 Vpr-CRL4 E3 ligase. In particular, Vpr zinc-binding motif mutation or TPEN treatment efficiently inhibited Vpr-CRL4 (DCAF1) E3 ligase assembly and Vpr-mediated HLTF degradation or Vpr-induced G2 cell cycle arrest. Collectively, our study sheds light on a conserved strategy by the viral proteins Vpx and Vpr to recruit host CRL4 (DCAF1) E3 ligase, which represents a target for novel anti-human immunodeficiency virus (HIV) drug development. IMPORTANCE The Vpr and its paralog Vpx are accessory proteins encoded by different human immunodeficiency virus (HIV)/simian immunodeficiency virus (SIV) lentiviruses. To facilitate viral replication, Vpx has evolved to induce SAMHD1 degradation and Vpr to mediate HLTF degradation. Both Vpx and Vpr perform their functions by recruiting CRL4 (DCAF1) E3 ligase. In this study, we demonstrate that the assembly of the Vpx- or Vpr-CRL4 E3 ligase requires a highly conserved zinc-binding motif. This motif is specifically required for the DCAF1 interaction but not for the interaction of Vpx or Vpr with its substrate. Selective disruption of Vpx- or Vpr-CRL4 E3 ligase function was achieved by zinc sequestration using N,N,N′-tetrakis-(2′-pyridylmethyl)ethylenediamine (TPEN). At the same time, zinc sequestration had no effect on zinc-dependent cellular protein functions. Therefore, information obtained from this study may be important for novel anti-HIV drug development.
NV-Dedup: High-Performance Inline Deduplication for Non-Volatile Memory

The byte-addressable non-volatile memory (NVM) is a promising medium for data storage. NVM-oriented file systems have been designed to explore NVM's performance potential. Meanwhile, applications may write considerable duplicate data. For NVM, a removal of duplicate data can promote space efficiency, improve write endurance, and potentially improve the performance by avoidance of repeatedly writing the same data. However, we have observed severe performance degradations when implementing a state-of-the-art inline deduplication algorithm in an NVM-oriented file system. A quantitative analysis reveals that, with NVM, 1) the conventional way to manage deduplication metadata for block devices, particularly in light of consistency, is inefficient, and, 2) the performance with deduplication becomes more subject to fingerprint calculations. We hence propose a deduplication algorithm called <italic>NV-Dedup </italic>. NV-Dedup manages deduplication metadata in a fine-grained, CPU and NVM-favored way, and preserves the metadata consistency with a lightweight transactional scheme. It also does workload-adaptive fingerprinting based on an analytical model and a transition scheme among fingerprinting methods to reduce calculation penalties. We have built a prototype of NV-Dedup in the Persistent Memory File System (PMFS). Experiments show that, NV-Dedup not only substantially saves NVM space, but also boosts the performance of PMFS by up to 2.1<inline-formula> <tex-math notation="LaTeX">$\times$</tex-math><alternatives><inline-graphic xlink:href="wang-ieq1-2774270.gif"/> </alternatives></inline-formula>.
Lignocellulose biodegradation and applications in biotechnology

Lignocellulosic biomass such as agricultural and forestry residues and herbaceous energy crops can serve as low cost feedstocks for production of fuel ethanol and other value-added commodity chemicals. However, development of efficient pretreatment and cost-effective enzymatic conversion of any lignocellulosic biomass to fermentable sugars is a key issue. In this overview chapter, various pretreatment options (dilute acid, steam explosion, alkaline peroxide) and enzymes (mainly cellulases and hemicellulases) involved in lignocellulose degradation are presented Mixed sugars generated by lignocellulose biodegradation are fermented to fuel ethanol, xylitol, 2-3-butanediol and other value-added products. Recent advances in the developments on lignocellulose biodegradation and applications in biotechnology are reviewed.
Energy Consumption and Economic Growth Revisited: Structural Breaks and Cross-Section Dependence

This paper examines the causal relationship between real GDP and energy consumption for 23 OECD countries from 1971 to 2009. Using recently developed panel econometric techniques the present paper takes into account structural breaks and cross-section dependence when analysing the energy consumption-growth nexus. The empirical results of this study indicate that there exists a long-run equilibrium relationship between real GDP and energy consumption, and the impact of real GDP on energy consumption is larger than vice versa. Furthermore, the empirical evidence of a dynamic panel error-correction model reveals a bidirectional causal relationship between economic growth and energy consumption in both the short and long run.
A Practical Partial Parser for Biomedical Literature Summarization

We present a partial parser called TeLePaPa (TextLens Partial Parser) to identify subjects and predicate verbs (SPVs) in a sentence of abstracts of MEDLINE citations. The performance of TeLePaPa is the precision of 96.7% and 97.1% for the SPV detection, respectively, and the recall of 91.3% and 94.9%, respectively. We found that there was a similarity in the distribution of the pairs of SPV over different research topics in the domain. In addition, we found that the power law holds for the relationship of the number of citations uncovered by SPV pairs and its rank. That is, only a half of the pairs covered about 90% of all the citations. This fact enables us to efficiently scan the huge amount of biomedical literature.
The effect of platelet-rich fibrin membrane on the repair of perforated tympanic membrane: an experimental study

Abstract Conclusion: Platelet-rich fibrin (PRF) membrane could be used successfully in the repair of tympanic membrane perforation and wound healing. Objectives: To evaluate the effect of platelet-rich fibrin membrane in the repair of perforated tympanic membrane. Methods: After otoscopic examination, a 3-mm perforation was made in the posterior quadrant of both tympanic membranes of 50 adult male Sprague-Dawley rats. Venous blood was withdrawn from the rats, then centrifuged. PRF was obtained in membrane form. The membrane was placed on the right tympanic membrane perforation. The perforations on the left side were left to spontaneously heal and, thus, formed the control group. Daily examinations were made of 20 rats and the time to healing of the tympanic membrane was recorded. The remaining 30 rats were separated into five groups of six, and histopathological examination was made. Evaluation was made in respect of the presence of oedema in the lamina propria, neovascularization, fibroblastic reaction, and inflammatory cells. Results: The healing time of the tympanic membrane perforation was determined as mean 10.3 ± 2.18 days in the study group applied with PRF and 17 ± 2.40 days in the control group. Higher values in respect of fibrosis and neovascularization were obtained in the study group.
Impact of a Safety Huddle‐Based Intervention on Monitor Alarm Rates in Low‐Acuity Pediatric Intensive Care Unit Patients

BACKGROUND: Physiologic monitors generate high rates of alarms in the pediatric intensive care unit (PICU), yet few are actionable. OBJECTIVE: To determine the association between a huddle‐based intervention focused on reducing unnecessary alarms and the change in individual patients' alarm rates in the 24 hours after huddles. DESIGN: Quasi‐experimental study with concurrent and historical controls. SETTING: A 55‐bed PICU. PARTICIPANTS: Three hundred low‐acuity patients with more than 40 alarms during the 4 hours preceding a safety huddle in the PICU between April 1, 2015, and October 31, 2015. INTERVENTION: Structured safety huddle review and discussion of alarm causes and possible monitor parameter adjustments to reduce unnecessary alarms. MAIN MEASUREMENTS: Rate of priority alarms per 24 hours occurring for intervention patients as compared with concurrent and historical controls. Balancing measures included unexpected changes in patient acuity and code blue events. RESULTS: Clinicians adjusted alarm parameters in the 5 hours following the huddles in 42% of intervention patients compared with 24% of control patients (P = .002). The estimate of the effect of the intervention adjusted for age and sex compared with concurrent controls was a reduction of 116 priority alarms (95% confidence interval, 37–194) per 24 hours (P = .004). There were no unexpected changes in patient acuity or code blue events related to the intervention. CONCLUSION: Integrating a data‐driven monitor alarm discussion into safety huddles was a safe and effective approach to reducing alarms in low‐acuity, highalarm PICU patients.
Influence of Volume Fraction, Voltage and Temperature on the Volume Resistivity and Break Down Voltage of Carbon Black Filled SBR Composites

A series of carbon black (CB) filled styrene butadiene rubber (SBR) composites have been prepared with different dosage of CB content, viz. 10, 20, 30, 50, 70, and 90 phr. The prepared composites have been characterized for electrical properties such as volume resistivity and breakdown voltage. The effect of volume fraction of conducting filler, temperature, and voltage on these properties were established. The normalized capacitance and breakdown voltage have been calculated theoretically using mathematical models and the results are correlated with the experimental results.