Miracle-dz/UniFAR-FTUs huggingface dataset:
A mutation profile for top-k patient search exploiting Gene-Ontology and orthogonal non-negative matrix factorization

Motivation: As the quantity of genomic mutation data increases, the likelihood of finding patients with similar genomic profiles, for various disease inferences, increases. However, so does the difficulty in identifying them. Similarity search based on patient mutation profiles can solve various translational bioinformatics tasks, including prognostics and treatment efficacy predictions for better clinical decision making through large volume of data. However, this is a challenging problem due to heterogeneous and sparse characteristics of the mutation data as well as their high dimensionality. Results: To solve this problem we introduce a compact representation and search strategy based on Gene-Ontology and orthogonal non-negative matrix factorization. Statistical significance between the identified cancer subtypes and their clinical features are computed for validation; results show that our method can identify and characterize clinically meaningful tumor subtypes comparable or better in most datasets than the recently introduced Network-Based Stratification method while enabling real-time search. To the best of our knowledge, this is the first attempt to simultaneously characterize and represent somatic mutational data for efficient search purposes. Availability: The implementations are available at: https://sites.google. com/site/postechdm/research/implementation/orgos. Contact: sael@cs.stonybrook. edu or hwanjoyu@postech.ac. kr Supplementary information: Supplementary data are available at Bioinformatics online.
The impact of serious mental illness on health and healthcare.

BACKGROUND Patients with serious mental illness (SMI; e.g., psychotic disorders and major mood disorders) die earlier, have more medical illnesses, and receive worse medical care than those in the general population. OBJECTIVE The aims of this article are to review the data on medical morbidity and mortality in those with SMI, to highlight the factors that lead to such disparities, and to discuss potential solutions to the problem. METHOD The authors reviewed the literature on medical morbidity and mortality in those with SMI. RESULTS Adults with SMI in the United States die 25 years earlier than those in the general population; cardiovascular disease is responsible for the majority of this excess mortality, accounting for roughly 50%-60% of the deaths due to medical illness. Patient, provider, and system-level factors interact to contribute to poor health outcomes in people with SMI. CONCLUSION Patients with SMI are losing many years of life to preventable and treatable medical illnesses. Solutions to the problem will require attention to patient, provider, and system-level factors.
Overview of the TREC 2004 Terabyte Track

The Terabyte Track explores how adhoc retrieval and evaluation techniques can scale to terabyte-sized collections. For TREC 2004, our (cid:12)rst year, 50 new adhoc topics were created and evaluated over a a 426GB collection of 25 million documents taken from the . gov Web domain. A total of 70 runs were submitted by 17 groups. Along with the top documents, each group reported average query times, indexing times, index sizes, and hardware and software characteristics for their systems.
A Novel Method for Segmentation of Remote Sensing Images based on Hybrid GA-PSO

segmentation is defined as the process of dividing an image into disjoint homogenous regions and it could be regarded as the fundamental step in various image processing applications. In this paper, a novel multilevel thresholding segmentation method is proposed for grouping the pixels of remote sensing (RS) images into different homogenous regions. In this way, Hybrid Genetic Algorithm-Particle Swarm Optimization (HGAPSO) is used for finding the optimal set of threshold values. The new method is tested on two different study areas and results are compared with PSO-based image segmentation comprehensively. Results show HGAPSO based image segmentation performs better than PSO-based method in different points of view.
Exploiting fast carry-chains of FPGAs for designing compressor trees

Fast carry chains featuring dedicated adder circuitry is a distinctive feature of modern FPGAs. The carry chains bypass the general routing network and are embedded in the logic blocks of FPGAs for fast addition. Conventional intuition is that such carry chains can be used only for implementing carry-propagate addition; state-of-the-art FPGA synthesizers can only exploit the carry chains for these specific circuits. This paper demonstrates that the carry chains can be used to build compressor trees, i.e., multi-input addition circuits used for parallel accumulation and partial product reduction for parallel multipliers implemented in FPGA logic. The key to our technique is to program the lookup tables (LUTs) in the logic blocks to stop the propagation of carry bits along the carry chain at appropriate points. This approach improves the area of compressor trees significantly compared to previous methods that synthesized compressor trees solely on LUTs, without compromising the performance gain over trees built from ternary carry-propagate adders.
First Microlens Mass Measurement: PLANET Photometry of EROS BLG-2000-5

We analyze PLANET photometric observations of the caustic-crossing binary lens microlensing event, EROS BLG-2000-5, and find that modeling the observed light curve requires incorporation of the microlens parallax and the binary orbital motion. The projected Einstein radius (E = 3.61 ± 0.11 AU) is derived from the measurement of the microlens parallax, and we are also able to infer the angular Einstein radius (θE = 1.38 ± 0.12 mas) from the finite source effect on the light curve, combined with an estimate of the angular size of the source given by the source position in a color-magnitude diagram. The lens mass, M = 0.612 ± 0.057 M☉, is found by combining these two quantities. This is the first time that parallax effects are detected for a caustic-crossing event and also the first time that the lens mass degeneracy has been completely broken through photometric monitoring alone. The combination of E and θE also allows us to conclude that the lens lies in the near side of the disk, within 2.6 kpc of the Sun, while the radial velocity measurement indicates that the source is a Galactic bulge giant.
Commonsense computing (episode 3): concurrency and concert tickets

As the third in a series of projects investigating commonsense computing -- the relevant knowledge that students have before any formal study of computing -- we examine students' commonsense understanding of concurrency. Specifically, we replicated (with modifications) an experiment by Ben-David Kolikant. [2] Ben-David Kolikant's data were gathered from high-school seniors who had previously studied computing, at the beginning of an advanced class in concurrent and distributed programming. Modifying one of her questions to reflect our students' lack of background, we asked students at five different institutions, in the first week of CS1, to describe in English the problems that might arise when more than one person is selling seats to a concert. Almost all students (97%) identified the problem of interest -- that a race condition may occur between sellers. 73% of students identified at least one possible solution. We found that the categorizations developed by Ben-David Kolikant were also meaningful when applied to our data, that our beginning CS1 students are more likely to give centralized solutions (as opposed to decentralized ones) than Ben-David Kolikant's concurrency students, and that the granularity of solutions is finer among the more experienced students.
Overexpression of the Lens Epithelium-Derived Growth Factor/p75 Integrase Binding Domain Inhibits Human Immunodeficiency Virus Replication

ABSTRACT We initially identified lens epithelium-derived growth factor/p75 (LEDGF/p75) as a binding partner of human immunodeficiency virus type 1 (HIV-1) integrase. To investigate the role of LEDGF/p75 in HIV replication and its potential as a new antiviral target, we stably overexpressed two different fragments containing the integrase binding domain (IBD) of LEDGF/p75 fused to enhanced green fluorescent protein (eGFP). HIV-1 replication was severely inhibited by overexpression of the eGFP-IBD fusion proteins, while no inhibition was observed in cell lines overexpressing the interaction-deficient D366A mutant. Quantitative PCR pinpointed the block to the integration step, whereas nuclear import was not affected. Competition of the IBD fusion proteins with endogenous LEDGF/p75 for binding to integrase led to a potent defect in HIV-1 replication in both HeLaP4- and MT-4-derived cell lines. A previously described diketo acid-resistant HIV-1 strain remained fully susceptible to inhibition, suggesting that this strategy will also work in patients who harbor strains resistant to the current experimental integrase inhibitors. These data support LEDGF/p75 as an important cofactor for HIV replication and provide proof of concept for the LEDGF/p75-integrase interaction as a novel target for treating HIV-1 infection.
Multi-mode Precoding for Correlated MIMO Channels with Minimum BER Selection Criterion

We propose a robust multi-mode linear precoder based on minimum bit error rate (MBER) selection criterion for multi-input-multi-output (MIMO) systems when transmitter only acquires the fading correlations of antennas. The key point of the scheme is that the number of substreams and modulation mode change adaptively to minimize the mean of BER by using channel correlation matrix. In addition, we analyze two special cases with very high or low correlation coefficients. Simulation results state that the proposed scheme selects the most powerful spatial mode and improves the system performance significantly
A double-blind, placebo-controlled, multi-dose evaluation of the acute behavioural effects of guaraná in humans

The present study aimed to systematically assess acute, dose-related behavioural effects of an extract of guaraná plant for the first time in humans. This double-blind, counterbalanced, placebo-controlled study (n = 26) assessed the acute mood and cognitive effects throughout the day of four different doses (37.5mg, 75mg, 150mg and 300mg) of a standardised guaraná extract (PC-102). Assessment included the Cognitive Drug Research computerized test battery and Bond-Lader mood scales. Guaraná improved secondary memory performance and increased alert and content mood ratings. The two lower doses produced more positive cognitive effects than the higher doses. This research supports previous findings of cognitive improvements following 75mg guaraná and provides the first exploration of different dose effects of guaraná in humans. The findings suggest that the effects cannot be attributed to caffeine alone.
Decitabine inhibits T cell proliferation via a novel TET2-dependent mechanism and exerts potent protective effect in mouse auto- and allo-immunity models

Multiple sclerosis (MS) is an autoimmune disease characterized by the dysregulated immune response including innate and adaptive immune responses. Increasing evidence has proven the importance of epigenetic modification in the progression of MS. Recent studies revealed that low-dose decitabine (Dec, 5-Aza-2′-deoxycytidine), which incorporates into replicating DNA and inhibits DNA methylation, could prevent experimental autoimmune encephalomyelitis (EAE) development by increasing the number of regulatory T cells (Tregs). Here, we showed that higher-dose decitabine relative to previous studies could also distinctly protect mice from EAE and allogeneic cardiac transplantation. Mechanistic studies revealed decitabine suppressed innate responses in EAE mice through inhibiting the activation of microglia and monocyte-derived macrophages that contributed to reduce the severity of EAE. Furthermore, differentiation of naïve CD4+ T cells into Th1 and Th17 cells was significantly suppressed by decitabine in vivo and in vitro. Though in vitro studies showed decitabine could induce Treg differentiation, there was no obvious change in the percentage of Tregs in Dec-treated EAE mice. Most importantly, we found that T cell proliferation was potently inhibited in vivo and in vitro by higher-dose decitabine through increased gene expression of the DNA dioxygenase TET2 which facilitated the expression of several cell cycle inhibitors. Collectively, our study provides novel mechanistic insights of using the epigenetic modifying agents in the management of both allo- and auto-immune responses.
Nano-silver – a review of available data and knowledge gaps in human and environmental risk assessment

Nano-silver is used in an increasing number of products. Some of the applications have resulted in the concern of governments and the public, since little is known about the potential risks of nano-silver. In this review, an inventory is made to identify knowledge gaps that have to be filled before risks for both man and the environment can be assessed as reliable as for ‘non-nanosized’ chemicals. It is hypothesized that the toxic effects of nano-silver are due to a combination of the specific properties of silver nanoparticles and the generation of ions from them. The main topic for future research is validation of our ‘0-hypothesis’ that toxic effects of nano-silver are proportional to the activity of free silver ions released by the nanoparticles. Furthermore, it must be determined whether – or to what extent – nano-silver particles will enter the body. The outcomes of these tests will determine the requirements for further toxicity testing.
Project-Team Parole Analysis, Perception and speech recognition

Our activities are structured in two topics: (cid:15) Speech analysis. Our works are concerned with automatic extraction and perception of acoustic cues, acoustic-to-articulatory inversion and speech analysis. These themas give rise to a number of ongoing or future applications: vocal rehabilitation, improvement of hearing aids, language learning. (cid:15) Modeling speech for automatic recognition. Our works are concerned with stochastic models (HMM 1 , bayesian networks and missing data models), multiband approach, adaptation of a recognition system to a new speaker or to the communication channel, and with language models. These topics give also rise to a number of ongoing or future applications: automatic speech recognition, automatic translation, text-to-speech alignment, audio indexing. language learning or multiband that simultaneously require competence in automatic recognition and where (cid:22) is the weight of the repulsive force and n gives the neighboring tracks. For the second formant F2 n corresponds to F1 and F2 and for F3 n corresponds to F2 . For the ﬁrst formant F1 n corresponds to F2 and an artiﬁcial ﬁxed formant (at 0 Hz) to prevent F1 from becoming negative. This way, formants are deformed by taking into account the deformations of their neighboring formants with two advantages: a better coverage of the spectrogram energy, a simpler and more robust control strategy. Moreover, the initialization stage can be substantially simpliﬁed because the interdependency of formant tracks enables an more dynamic exploration of solutions than that possible with the labelling of elementary tracks based on a static strategy. This new strategy turns out to be more efﬁcient than that reported in previous papers.
In situ microtensile testing and X-ray microtomography-based finite element modelling of open-cell metal foam struts and sandwich panels

Microtensile testing was used to determine the mechanical properties of individual aluminium alloy foam struts. Finite element modelling of as-tested struts was carried out using X-ray microtomography scans of the undeformed struts to define the geometry. Strut deformation was described by continuum viscoplastic damage constitutive equations calibrated by microtensile test data of the aluminium alloy in its optimally aged condition. The as-tested strut finite element model was used to develop a procedure that compensates for the effect of grip slippage inherent in the microtensile testing of metal foam struts, which results in a considerable reduction in observed elastic stiffness compared to the typical value of 70 GPa for aluminium alloys. The calibrated constitutive equations were then implemented in finite element models of sandwich panels with the aluminium metal foam as its core material. The finite element models were used in simulations of cases of low energy impact to represent tool drop conditions in order to investigate the suitability of new wing skin designs using metal foam core sandwich panels. An optimal strut aspect ratio was identified through simulation that provides the greatest energy absorption per unit mass while ensuring core damage is accurately reflected by facesheet deformation, which is necessary for detection and repair.
Elaboration de revêtements à base de tantale et de nanotubes de carbone sur titane et Nitinol : vers de nouvelles plateformes pour biomatériaux osseux

Every year, several million people worldwide must appeal to orthopedic surgery to repair osseous defects due to diseases or traumatic events. Corresponding medical needs are in constant evolution, as well for implant durability (depending of patient’s age, morphology…) as for therapeutic efficiency (reduction of immune risks – allergies, carcinogenic effets…). Scientific research related to the design and optimization of platform (bio)materials for bone substitutes takes thus on crucial importance. In this context, the present work specifically focus on the reinforcement of surface properties of metallic platforms based on titanium and Nitinol (nickel-titanium alloy), whose biochemical and mechanical characteristics (biocompatibility, corrosion resistance, density, strength, shape memory effect and superelasticity for Nitinol) are particularly interesting for further uses in orthopedic medicine. Different approaches are considered to this end in order to consolidate the barrier effect at the material-host interface and to improve the bioactive capacities for inducing and guiding the osseous (re)growth after implantation: sol-gel and electrochemical deposition of thin tantalum oxide coatings, molecular self-assembly of multifunctional organophosphonic acids, and incorporation of chemically-modified carbon nanotubes. The main goal of this study aims at the in-depth investigation of the phenomena underlying the exploited surface treatments. It also intends to highlight their direct consequences in terms of films composition and morphology, as well as their protective and functional abilities. This will be undertaken through spectroscopic (XPS, EDX), microscopic (SEM, TEM, AFM) and electrochemical (CV, LSV, SECM) characterizations.
Syntactic Analysis of Message Sequence Chart Specifications

Message Sequence Charts (MSCs) are gaining popularity in software engineering methods for concurrent and real-time systems. They are increasingly supported in software engineering tools to capture, for instance, system requirements, test scenarios, and simulation traces. MSCs have been standardized by ITU-T in Recommendation Z.120 [15]. However, various aspects of environment behavior remain underspeci ed in MSCs, e.g., the presence of resources for inter-process communication and the coordination of concurrent processes at points of control branching. Such underspeci cations can result in ambiguities in an MSC speci cation and discrepancies between an MSC speci cation and its implementation. In this paper we characterize two consequences of harmful underspeci cations: process divergence and non-local branching choice. We also present two syntax-based analysis algorithms that detect both problems. The syntactic characterization of these problems requires an MSC speci cation to be deadlock-free. Therefore, we also discuss deadlock detection in MSC speci cations. 2
Molecular Characterization of TP53 Gene in Human Populations Exposed to Low-Dose Ionizing Radiation

Ionizing radiation, such as that emitted by uranium, may cause mutations and consequently lead to neoplasia in human cells. The TP53 gene acts to maintain genomic integrity and constitutes an important biomarker of susceptibility. The present study investigated the main alterations observed in exons 4, 5, 6, 7, and 8 of the TP53 gene and adjacent introns in Amazonian populations exposed to radioactivity. Samples were collected from 163 individuals. Occurrence of the following alterations was observed: (i) a missense exchange in exon 4 (Arg72Pro); (ii) 2 synonymous exchanges, 1 in exon 5 (His179His), and another in exon 6 (Arg213Arg); (iii) 4 intronic exchanges, 3 in intron 7 (C → T at position 13.436; C → T at position 13.491; T → G at position 13.511) and 1 in intron 8 (T → G at position 13.958). Alteration of codon 72 was found to be an important risk factor for cancer development (P = 0.024; OR = 6.48; CI: 1.29–32.64) when adjusted for age and smoking. Thus, TP53 gene may be an important biomarker for carcinogenesis susceptibility in human populations exposed to ionizing radiation.
Genome-wide association and genetic functional studies identify autism susceptibility candidate 2 gene (AUTS2) in the regulation of alcohol consumption

Alcohol consumption is a moderately heritable trait, but the genetic basis in humans is largely unknown, despite its clinical and societal importance. We report a genome-wide association study meta-analysis of ∼2.5 million directly genotyped or imputed SNPs with alcohol consumption (gram per day per kilogram body weight) among 12 population-based samples of European ancestry, comprising 26,316 individuals, with replication genotyping in an additional 21,185 individuals. SNP rs6943555 in autism susceptibility candidate 2 gene (AUTS2) was associated with alcohol consumption at genome-wide significance (P = 4 × 10−8 to P = 4 × 10−9). We found a genotype-specific expression of AUTS2 in 96 human prefrontal cortex samples (P = 0.026) and significant (P < 0.017) differences in expression of AUTS2 in whole-brain extracts of mice selected for differences in voluntary alcohol consumption. Down-regulation of an AUTS2 homolog caused reduced alcohol sensitivity in Drosophila (P < 0.001). Our finding of a regulator of alcohol consumption adds knowledge to our understanding of genetic mechanisms influencing alcohol drinking behavior.
A Liquid contact angles on biocompatible surfaces

Measurements of liquid contact angles on biocompatible surfaces have been performed at the Physics Department of Messina University. Biological solutions, polymers, ceramics and metals have been studied. Surface treatments by using different laser irradiations, depending on the laser intensity and wavelength, permit to change drastically the wet-ability of many materials and to enhance their biocompatibility and functionality. Results of our investigations put in evidence the best materials to increase or to reduce the wetability of the biological liquids. Results will be presented and discussed in detail with special regard to their applications in biological environment where the materials can be embedded.