Miracle-dz/UniFAR-FTUs huggingface dataset:
A comparison of scoring functions for protein sequence profile alignment

MOTIVATION In recent years, several methods have been proposed for aligning two protein sequence profiles, with reported improvements in alignment accuracy and homolog discrimination versus sequence-sequence methods (e.g. BLAST) and profile-sequence methods (e.g. PSI-BLAST). Profile-profile alignment is also the iterated step in progressive multiple sequence alignment algorithms such as CLUSTALW. However, little is known about the relative performance of different profile-profile scoring functions. In this work, we evaluate the alignment accuracy of 23 different profile-profile scoring functions by comparing alignments of 488 pairs of sequences with identity < or =30% against structural alignments. We optimize parameters for all scoring functions on the same training set and use profiles of alignments from both PSI-BLAST and SAM-T99. Structural alignments are constructed from a consensus between the FSSP database and CE structural aligner. We compare the results with sequence-sequence and sequence-profile methods, including BLAST and PSI-BLAST. RESULTS We find that profile-profile alignment gives an average improvement over our test set of typically 2-3% over profile-sequence alignment and approximately 40% over sequence-sequence alignment. No statistically significant difference is seen in the relative performance of most of the scoring functions tested. Significantly better results are obtained with profiles constructed from SAM-T99 alignments than from PSI-BLAST alignments. AVAILABILITY Source code, reference alignments and more detailed results are freely available at http://phylogenomics.berkeley. edu/profilealignment/
Comparison of a Diffracting and a Non-Diffracting Circular Acoustic Array

Localization of acoustic sources has been an area of research starting primarily with underwater acoustics. Recently, localization of sources in air has become a topic of interest for automatic detection, surveillance and tracking for military applications. Other application include novel teleconference devices, specifically automatic focusing on the person currently speaking. Current technology relies on free-field localization arrays, and there is a plethora of literature on array beam-forming of these arrays. This paper introduces a new technology of diffracting arrays and novel signal processing methods for characterization of these arrays and localization of acoustic sources. The theory and experimental implementation of an acoustic diffracting array (ADA) is presented, including singular value decomposition and the effect of robustness. The results indicate that ADA results in increased localization accuracy, and more directional point spread functions due to increased magnitude and phase differences compared to a free-field array
Fatigue behaviour and life estimation of Mg/Al ultrasonic spot weld bonding welds

Mg/Al dissimilar joints with favourable static and dynamic mechanical properties were obtained utilising ultrasonic spot welding and ultrasonic spot weld bonding technology. The fatigue behaviour, fatigue failure mode, and typical fatigue fracture surface morphology of Mg/Al ultrasonic spot welding and ultrasonic spot weld bonding joints were compared and observed to get a better understanding of the fatigue failure mechanism. In general, the Mg/Al ultrasonic spot weld bonding joint exhibited better fatigue performance than the ultrasonic spot welding joint. The two kinds of joints presented different fatigue failure modes with decreasing applied load level. A fatigue life prediction model was established, and the fatigue life prediction results were in good agreement with the experimental fatigue results.
Update on Pyrin Functions and Mechanisms of Familial Mediterranean Fever

Mutations in the MEFV gene, which encodes the protein named pyrin (also called marenostrin or TRIM20), are associated with the autoinflammatory disease familial Mediterranean fever (FMF). Recent genetic and immunologic studies uncovered novel functions of pyrin and raised several new questions in relation to FMF pathogenesis. The disease is clinically heterogeneous reflecting the complexity and multiplicity of pyrin functions. The main functions uncovered so far include its involvement in innate immune response such as the inflammasome assemblage and, as a part of the inflammasome, sensing intracellular danger signals, activation of mediators of inflammation, and resolution of inflammation by the autophagy of regulators of innate immunity. Based on these functions, the FMF-associated versions of pyrin confer a heightened sensitivity to a variety of intracellular danger signals and postpone the resolution of innate immune responses. It remains to be demonstrated, however, what kind of selective advantage the heterozygous carriage conferred in the past to be positively selected and maintained in populations from the Mediterranean basin.
Responses of Two CAM Species to Different Irradiances during Growth and Susceptibility to Photoinhibition by High Light.

Two CAM species, Kalanchoë daigremontiana Hamet et Perrier and Hoya carnosa (L.) R. Br. , were grown under a range of five photon flux area densitites (PFD) and then characterized. Significant acclimation to shade was indicated by progressive decreases in leaf thickness, rates of respiratory O(2) uptake, light compensation point, maximum rates of photosynthetic O(2) evolution, nocturnal acid accumulation, and delta(13)C values, and increases in chlorophyll concentration and absolute levels of room temperature (25 degrees C) and 77K fluorescence. Quantum yields (as measured by O(2) exchange) and the ratio of variable 77K fluorescence over the maximum yield (F(v)/F(m)) were relatively constant across the treatments. The only significant deviation from the above characteristics was in H. carnosa grown under full glasshouse PFD, where it apparently experienced photoinhibition. Following a photoinhibitory treatment, K. daigremontiana exhibited increases in the light compensation point and progressively greater reductions in the quantum yield, maximum photosynthetic rate, F(v)/F(m), and the variable component of room temperature fluorescence with increasing shade during growth. Thus although Crassulacean acid metabolism plants can adjust to shaded conditions, they are susceptible to photoinhibition when exposed to higher PFD than that experienced during growth.
Population Differentiation in Common Walnut (Juglans regia L.) across Major Parts of Its Native Range—Insights from Molecular and Morphometric Data

Juglans regia is an economically highly important species for fruit and wood production in the warm temperate and subtropical zones of the Northern Hemisphere. Besides the natural influence of climatic and geomorphological barriers, its genetic structure has been strongly modified by humans and the population history is still unclear. For this reason, we investigated mainly natural walnut populations across the Eurasian continent on a molecular (44 populations, 581 trees) and morphometric level (23 populations, 1391 ripe nuts). Population genetic diversity and differentiation were examined by using 7 microsatellite loci. Morphometric characteristics of the nuts (mainly roundness index and nut density) were used to estimate trait variation and population differentiation. Highest allelic richness Rs12 = 7.05 was observed in a Pakistani and the lowest value Rs12 = 3.04 in a Kyrgyz population. The genetic differentiation among populations was high (FST = 0.217; RST = 0.530) indicating a strong phylogeographic pattern. While variation of the roundness index within single populations was high, this trait neither differentiated geographical regions nor was it associated to genetic clusters. Approximated QST based on this trait equalled FST, while approximated QST based on nut density considerably exceeded FST, indicating selection. Nut density was moderately correlated with altitude, latitude, and longitude, and differentiated populations according to their origin. Pakistani and Indian populations showed highest nut densities. These South Asian populations contain putatively ancestral nut forms, which probably have been lost in other populations as a consequence of human selection.
5Gen: A Framework for Prototyping Applications Using Multilinear Maps and Matrix Branching Programs

Secure multilinear maps (mmaps) have been shown to have remarkable applications in cryptography, such as multi-input functional encryption (MIFE) and program obfuscation. To date, there has been little evaluation of the performance of these applications. In this paper we initiate a systematic study of mmap-based constructions. We build a general framework, called 5Gen, to experiment with these applications. At the top layer we develop a compiler that takes in a high-level program and produces an optimized matrix branching program needed for the applications we consider. Next, we optimize and experiment with several MIFE and obfuscation constructions and evaluate their performance. The 5Gen framework is modular and can easily accommodate new mmap constructions as well as new MIFE and obfuscation constructions, as well as being an open-source tool that can be used by other research groups to experiment with a variety of mmap-based constructions.
Treatment of Root Surface Covering By Acellular Dermal Matrix

Gingival recession has been defined as the displacement of the marginal gingival to the apical of the enamel-cement boundary (1). In the United States, gingival recession was reported in 22.5% (about 23.8 million people) of individuals aged 30 years or older (2). However, it is thought that the prevalence, size and severity of gingival recession increase with age (3). Anatomical factors of gingiva, chronic trauma, periodontitis and sequencing of the teeth are the main conditions leading to the formation of gingival recessions (4-6). It can be seen in individuals with a good oral hygiene as well as in individuals with poor oral care (7-10). Gingival recession disrupts the aesthetics, increases the likelihood of the root surface caries and causes dentin sensitivity (2, 11-13).
Sodium nitrate alleviates functional muscle ischaemia in patients with Becker muscular dystrophy

Dystrophin deficiency disrupts sarcolemmal targeting of neuronal nitric oxide synathase, resulting in functional muscle ischaemia. Chronic treatment of dystrophic mice with an inorganic nitric oxide (NO) donor alleviates this ischaemia and improves many features of the dystrophic phenotype. The present study translates this preclinical work by showing that a single oral dose of sodium nitrate,which serves as a NO donor when reduced to circulating nitrite by the commensal bacteria in the oral cavity, alleviates functional muscle ischaemia and restores normal blood flow regulation in human patients with dystrophinopathy. The results of the present study further support the mechanistic hypothesis that circulating nitrite serves as an alternative NO donor when reduced by deoxyhaemoglobin and/or deoxymyoglobin in exercising muscle.
Effect of Calcium-Modulating Cyclophilin Ligand on Human Immunodeficiency Virus Type 1 Particle Release and Cell Surface Expression of Tetherin

ABSTRACT The human immunodeficiency virus type 1 (HIV-1) accessory protein Vpu enhances virus particle release by counteracting a host factor that retains virions at the surfaces of infected cells. It was recently demonstrated that cellular protein BST-2/CD317/Tetherin restricts HIV-1 release in a Vpu-dependent manner. Calcium-modulating cyclophilin ligand (CAML) was also proposed to be involved in this process. We investigated whether CAML is involved in cell surface expression of Tetherin. Here, we show that CAML overexpression in permissive Cos-7 cells or CAML depletion in restrictive HeLa cells has no effect on HIV-1 release or on Tetherin surface expression, indicating that CAML is not required for Tetherin-mediated restriction of HIV-1 release.
Influence of caffeine on 3,4‐methylenedioxymethamphetamine‐induced dopaminergic neuron degeneration and neuroinflammation is age‐dependent

Previous studies have demonstrated that caffeine administration to adult mice potentiates glial activation induced by 3,4‐methylenedioxymethamphetamine (MDMA). As neuroinflammatory response seems to correlate with neurodegeneration, and the young brain is particularly vulnerable to neurotoxicity, we evaluated dopamine neuron degeneration and glial activation in the caudate‐putamen (CPu) and substantia nigra pars compacta (SNc) of adolescent and adult mice. Mice were treated with MDMA (4 × 20 mg/kg), alone or with caffeine (10 mg/kg). Interleukin (IL)‐1β, tumor necrosis factor (TNF)‐α, neuronal nitric oxide synthase (nNOS) were evaluated in CPu, whereas tyrosine hydroxylase (TH), glial fibrillary acidic protein, and CD11b were evaluated in CPu and SNc by immunohistochemistry. MDMA decreased TH in SNc of both adolescent and adult mice, whereas TH‐positive fibers in CPu were only decreased in adults. In CPu of adolescent mice, caffeine potentiated MDMA‐induced glial fibrillary acidic protein without altering CD11b, whereas in SNc caffeine did not influence MDMA‐induced glial activation. nNOS, IL‐1β, and TNF‐α were increased by MDMA in CPu of adults, whereas in adolescents, levels were only elevated after combined MDMA plus caffeine. Caffeine alone modified only nNOS. Results suggest that the use of MDMA in association with caffeine during adolescence may exacerbate the neurotoxicity and neuroinflammation elicited by MDMA.
Recharge mechanism of near‐equatorial hydrogen on Mars: Atmospheric redistribution or sub‐surface aquifer

The geographical distribution of water‐equivalent‐hydrogen (WEH) near the equator of Mars was compared with the topography and distribution of atmospheric water vapor to constrain possible recharge mechanisms of near‐surface water (<1 m of the surface). Recharge through a subsurface conduit provided by an aquifer, although possible, seems less likely than recharge through the atmosphere. Although the spatial distribution of WEH does not correspond to the current distribution of water vapor in the atmosphere, several terrestrial analogs indicate that dynamics of atmospheric circulation during periods of higher obliquity prior to the present epoch can qualitatively account for the observed WEH distribution.
Critical role of CCL22/CCR4 axis in the maintenance of immune homeostasis during apoptotic cell clearance by splenic CD8α+ CD103+ dendritic cells

Macrophages and dendritic cells (DCs) in murine spleen are essential for the maintenance of immune homeostasis by elimination of blood‐borne foreign particles and organisms. It has been reported that splenic DCs, especially CD8α+ CD103+ DCs, are responsible for tolerance to apoptosis‐associated antigens. However, the molecular mechanism by which these DCs maintain immune homeostasis by blood‐borne apoptotic cell clearance remains elusive. Here, we found that the CCL22/CCR4 axis played a critical role in the maintenance of immune homeostasis during apoptotic cell clearance by splenic CD8α+ CD103+ DCs. The present results revealed that systemic administration of apoptotic cells rapidly induced a large number of CCL22 and CCR4+ regulatory T (Treg) cells in the spleen of C57BL/6J mice. Further study demonstrated that CD8α+ CD103+ DCs dominantly produce much higher CCL22 than CD8α+ CD103− DCs. Moreover, the transient deletion of CD8α+ CD103+ DCs caused a decrease in CCL22 levels together with CCR4+ Treg cell percentage. Subsequently, the levels of some pro‐inflammatory cytokines, such as interleukin‐17 and interferon‐γ in the spleen with the absence of CD8α+ CD103+ DCs increased in response to the administration of apoptotic cells. Hence, intravenous injection of apoptotic cells induced a subsequent increase in CCL22 expression and CCR4+ Treg cells, which contribute to the maintenance of immune homeostasis at least partially by splenic CD8α+ CD103+ DCs.
Consumer's expectations from mobile CRM services: a banking context

Purpose – The purpose of this paper is to develop an understanding of the primary concerns of a customer when they use mobile banking services and identify factors that can be used for making better mobile customer relationship management (mobile CRM) services in banking.Design/methodology/approach – The paper empirically explores the underlying factors by the application of exploratory factor analysis. The study sample consists of 272 respondents, with a usable response rate of 68 per cent.Findings – The empirical findings reveal that perceived utility value is regarded as the most important factor for mobile CRM services. The other factors which emerged were ease of use, context, compatibility, cost, risk, and personal innovativeness. In addition, negative attitude towards technology also emerged as a factor, which needs further investigation.Research limitations/implications – The study had a few limitations, such as selection of the sample from a limited number of places, which may induct some bias du.
An Electromechanical Approach to a Printed Circuit Board Design Course

This paper describes a printed circuit board (PCB) design course based on electromechanical workflow. The course relies on the premise that a PCB is an integral component of any electronic apparatus, along with its other electromechanical and mechanical components. To emphasize this to students, electrical and mechanical computer-aided design tools are used in synergy. The course content is described in detail, and the design workflow is illustrated, using a project to design a data acquisition instrument as an example.
Biodegradable Conduit Small Gap Tubulization for Peripheral Nerve Mutilation: A Substitute for Traditional Epineurial Neurorrhaphy

Nerve regeneration and re-innervation are usually difficult after peripheral nerve injury. Epineurium neurorrhaphy to recover the nerve continuity is the traditional choice of peripheral nerve mutilation without nerve defects, whereas the functional recovery remains quite unsatisfactory. Based on previous research in SD rats and Rhesus Monkeys, a multiple centers clinical trial about biodegradable conduit small gap tubulization for peripheral nerve mutilation to substitute traditional epineurial neurorrhaphy was carried out. Herein, the authors reviewed the literature that focused on peripheral nerve injury and possible clinical application, and confirmed the clinical possibilities of biodegradable conduit small gap tubulization to substitute traditional epineurial neurorrhaphy for peripheral nerve mutilation. The biodegradable conduit small gap tubulization to substitute traditional epineurial neurorrhaphy for peripheral nerve mutilation may be a revolutionary innovation in peripheral nerve injury and repair field.
Comparative analysis of three histologic grading methods for squamous cell carcinoma of the lip.

OBJECTIVES The aim of this study was to evaluate three histologic grading methods for squamous cell carcinoma (SCC) of the lip, the conventional three-grade model proposed by the World Health Organization, tumor budding and depth of invasion (BD) model, and histologic risk assessment (HRA) model, and to correlate them with prognosis. MATERIALS AND METHODS Fifty-three patients with lip SCC were evaluated. RESULTS The mean age was 65 years, 69.8% of the participants were men, and 66.0% of the patients had early-stage tumors. Using the BD and conventional three-grade methods, 52.8% and 64.2% of the cases were graded as low risk, respectively. The HRA model graded 54.7% of the cases as medium risk. In the BD model, the higher histologic grade was associated with worse prognosis (P = 0.045). Overall survival at 5 years was 87.8%. Tumor size (T3 + T4) and lymph node involvement (N+) were associated with reduced overall survival and recurrence-free survival (RFS) (P = 0.002 and 0.005; 0.007 and 0.01, respectively). Surgical treatment combined with radiotherapy was associated with lower RFS (P = 0.03). CONCLUSIONS High-grade lip SCC in advanced stages is associated with a poor prognosis. The BD model is a simple and effective tool for the prognostic evaluation of lip SCC.
Overload based explicit rate switch schemes with MCR guarantees

An explicit rate switch scheme monitors the load at each link and gives feedback to the sources. We define the overload factor as the ratio of the input rate to the available capacity. In this paper, we present three overload-based switch schemes which provide MCR (minimum cell rate) guarantees for the ATM (asynchronous transfer mode) ABR (available bit rate) service. The switch schemes proposed use the overload factor and other terms including current source rate and target utilization to calculate feedback rates. A dynamic queue control mechanism is used to achieve efficient usage of the link, control queues and, achieve constant queuing delay at steady state. The proposed algorithms are studied and compared using several configurations. The configurations were chosen to test the performance of the algorithms in the presence of link bottlenecks, source bottlenecks and transient sources. Finally, a comparison of the proposed algorithms based on the simulation results is given.
Feature Ranking , Selection and Discretization

Many indices for evaluation of features have been considered. Applied to single features they allow for filtering irrelevant attributes. Algorithms for selection of subsets of features also remove redundant features. Hashing techniques enable efficient application of feature relevance indices to selection of feature subsets. A number of such methods have been applied to artificial and real-world data. Strong influence of continuous feature discretization and very good performance of separability-based discretization has been noted.