Miracle-dz/UniFAR-FTUs huggingface dataset:
Tools for Predicting the Functional Impact of Nonsynonymous Genetic Variation

As personal genome sequencing becomes a reality, understanding the effects of genetic variants on phenotype—particularly the impact of germline variants on disease risk and the impact of somatic variants on cancer development and treatment—continues to increase in importance. Because of their clear potential for affecting phenotype, nonsynonymous genetic variants (variants that cause a change in the amino acid sequence of a protein encoded by a gene) have long been the target of efforts to predict the effects of genetic variation. Whole-genome sequencing is identifying large numbers of nonsynonymous variants in each genome, intensifying the need for computational methods that accurately predict which of these are likely to impact disease phenotypes. This review focuses on nonsynonymous variant prediction with two aims in mind: (1) to review the prioritization methods that have been developed to date and the principles on which they are based and (2) to discuss the challenges to further improving these methods.
Concepts for Hybrid FRP Bridge Deck Systems

This paper presents selected structural concepts for modular bridge deck systems taking into account the limitations imposed by fabrication processes for polymer matrix composites. An idealized structural model is developed for the analysis of such composite structures when subjected to traffic loads. This model uses averaged engineering constants for the laminate, while the designs assume special ply stacking sequences to achieve optimum structural performance. A consequence of such stacking sequences is to reduce the anisotropy of the laminate. A finite element analysis is performed to evaluate the mechanical performance of the proposed deck systems. As is characteristic of fiber-reinforced plastics, the design of the deck systems is governed by the deflection limit state rather than the strength limit state which is typical for conventional structural materials. A hybrid FRP/concrete system is found to be promising particularly from the viewpoint of cost. The objective of the concrete in the hybrid concept is to resist the compressive force. However, in order to keep the use of FRP at a minimum it is necessary to subject parts of the concrete to tensile forces. The use of fiber-reinforced concrete as opposed to plain reinforced concrete is recommended under these conditions.
Situation Assessment and Information Fusion: an experimental framework for performance evaluation

Abstract : This report results from a contract tasking Universita di Roma as follows: The Grantee will perform high-level Information Fusion research based on multi-agent information monitoring and fusion. The goal is to develop situation assessment techniques and strategies which focus on evolving, dynamic scenarios such as natural disasters (e.g. earthquakes or other catastrophic events). Complete details of expected results and technical contributions are found the research proposal.
Electrolytic etching of fine stainless-steel pipes patterned by laser-scan lithography

Recently, it is required to develop a method for fabricating cylindrical micro-components in the field of measurement and medical engineering. Here, electrolytic etching of fine stainless-steel pipes patterned by laser-scan lithography was researched. The pipe diameter was 100 μm. At first, a pipe coated with 3-7 μm thick positive resist (tok, PMER P LA-900) was exposed to a violet laser beam with a wavelength of 408 nm (Neoark,TC20-4030-45). The laser beam was reshaped in a circle by placing a pinhole, and irradiated on the pipe by reducing the size in 1/20 using a reduction projection optics. Linearly arrayed 22 slit patterns with a width of 25 μm and a length of 175 μm were delineated in every 90-degree circumferential direction. That is, 88 slits in total were delineated at an exposure speed of 110 μm/s. In the axial direction, patterns were delineated at intervals of 90 μm. Following the pattern delineation, the pipe masked by the resist patterns was electrolytically etched. The pipe was used as an anode and an aluminum cylinder was set as a cathode around the pipe. As the electrolyte, aqueous solution of NaCl and NH4Cl was used. After etching the pipe, the resist was removed by ultrasonic cleaning in acetone. Although feasibility for fabricating multi-slit pipes was demonstrated, sizes of the etched slits were enlarged being caused by the undercut, and the shapes were partially deformed, and all the pipes were snapped at the chuck side.
Selecting News and Elders in Unstructured Peer-to-Peer Network under Churn

The concept of Churn is the continuous process of node arrival and departure in distributed peer-to-peer network. There exists two eprotocol Selecting News and Eldersxtreme cases. The first one is that enormous nodes joining the system concurrently, which results in a flash crowd scenario for special nodes in the system. The other is that enormous nodes crashed or the connections between nodes are failed in a moment, which comes out a shrink search later. In this paper, we present a novel protocol Selecting News and Elders (SNE) with positive communication policy among peers and conservative neighbor maintenance scheme under churn, to keep desirable properties such as a low network diameter and clustering. The protocol is resilient against different churn and fit for P2P information dissemination and file sharing systems especially.
Evaluating and mitigating a Collusive version of the Interest Flooding Attack in NDN

Named-Data Networking (NDN) is a promising architecture for the future Internet. However, it is hampered by interest flooding, an NDN-tailored DDoS attack which has been shown to cause dropping majority of legitimate packets. While several defence mechanisms have been suggested against it, they cannot protect NDN against the Collusive Interest Flooding Attack (CIFA), a previously disregarded version of interest flooding. In CIFA, malicious clients issue interest packets that can be satisfied only by a malicious server. The server, in turn, responds with data packets just before expiration of the corresponding PIT entries. We study the effect of CIFA. Extensively simulating CIFA, we show that it affects the network and legitimate users almost as badly as an extensively researched version of interest flooding. Subsequently, we develop a generic defence mechanism against interest flooding attacks. The mechanism is based on CoMon, our framework for coordination in NDN. Thanks to CoMon, the attacks are detected and mitigated at an early stage by only a few routers. Via realistic simulations, we show that our defence decreases the amount of dropped legitimate packets remarkably, incurring a very low signalling overhead.
Dynamics of CD4 and CD8 T-Cell Subsets and Inflammatory Biomarkers during Early and Chronic HIV Infection in Mozambican Adults

During primary HIV infection (PHI), there is a striking cascade response of inflammatory cytokines and many cells of the immune system show altered frequencies and signs of extensive activation. These changes have been shown to have a relevant role in predicting disease progression; however, the challenges of identifying PHI have resulted in a lack of critical information about the dynamics of early pathogenic events. We studied soluble inflammatory biomarkers and changes in T-cell subsets in individuals at PHI (n = 40), chronic HIV infection (CHI, n = 56), and HIV-uninfected (n = 58) recruited at the Manhiça District Hospital in Mozambique. Plasma levels of 49 biomarkers were determined by Luminex and ELISA. T-cell immunophenotyping was performed by multicolor flow cytometry. Plasma HIV viremia, CD4, and CD8 T cell counts underwent rapid stabilization after PHI. However, several immunological parameters, including Th1-Th17 CD4 T cells and activation or exhaustion of CD8 T cells continued decreasing until more than 9 months postinfection. Importantly, no sign of immunosenescence was observed over the first year of HIV infection. Levels of IP-10, MCP-1, BAFF, sCD14, tumor necrosis factor receptor-2, and TRAIL were significantly overexpressed at the first month of infection and underwent a prompt decrease in the subsequent months while, MIG and CD27 levels began to increase 1 month after infection and remained overexpressed for almost 1 year postinfection. Early levels of soluble biomarkers were significantly associated with subsequently exhausted CD4 T-cells or with CD8 T-cell activation. Despite rapid immune control of virus replication, the stabilization of the T-cell subsets occurs months after viremia and CD4 count plateau, suggesting persistent immune dysfunction and highlighting the potential benefit of early treatment initiation that could limit immunological damage.
An Evaluation of Procedural Instructional Text

This paper presents an evaluation of the instructional text generated by Isolde, an authoring tool for technical writers that automates the production of procedural on-line help. The evaluation compares the effectiveness of the instructional text produced by Isolde with that of professionally authored instructions, such as MS Word Help. The results suggest that the documentation produced by Isolde is of comparable quality to similar texts found in commercial manuals.
True and false memories in the DRM paradigm on a forced choice test

Participants studied lists of semantic associates that converged on a non-presented critical word (e.g., sleep; Deese, 1959; Roediger & McDermott, 1995) and took a two-alternative forced choice test. At test, each critical non-presented word was paired with a studied word from the same list. The test was administered either immediately or 7 days after the study phase. Accuracy in distinguishing between the non-presented critical word and the studied list word was above chance at immediate testing. After a 7-day retention interval, however, accuracy did not differ from chance performance: participants were as likely to choose the non-presented critical word as the studied list word.
Peripersonal Space: An Index of Multisensory Body–Environment Interactions in Real, Virtual, and Mixed Realities

Human-environment interactions normally occur in the physical milieu, and thus by medium of the body and within the space immediately adjacent to and surrounding the body; the peri-personal space (PPS). However, human interactions increasingly occur with or within virtual environments, and hence novel approaches and metrics must be developed to index human-environment interactions in virtual reality (VR). Here we present a multisensory task that measures the spatial extent of human PPS in real, virtual, and augmented realities. We validated it in a mixed reality ecosystem in which real environment and virtual objects are blended together in order to administer and control visual, auditory, and tactile stimuli in ecologically valid conditions. Within this mixed-reality environment, participants are asked to respond as fast as possible to tactile stimuli on their body, while task-irrelevant visual or audio-visual stimuli approach their body. Results demonstrate that, in analogy with observations derived from monkey electrophysiology and in real environmental surroundings, tactile detection is enhanced when visual or auditory stimuli are close to the body, and not when far from it. We then calculate the location where this multisensory facilitation occurs as a proxy of the boundary of PPS. We observe that mapping of PPS via audio-visual, as opposed to visual alone, looming stimuli results in sigmoidal fits – allowing for the bifurcation between near and far space – with greater goodness of fit. In sum, our approach is able to capture the boundaries of PPS on a spatial continuum, at the individual-subject level, and within a fully controlled and previously laboratory-validated setup, while maintaining the richness and ecological validity of real-life events. The task can therefore be applied to study the properties of peri-personal space in humans and to index the features governing human-environment interactions in virtual or mixed reality. We propose PPS as an ecologically valid and neurophysiologically established metric in the study of the impact of VR and related technologies on society and individuals.
A state management protocol for IntServ, DiffServ and label switching

Providing quality of service (QoS) in an efficient and scalable manner in the Internet is a topic of active research. The technologies that have drawn the most attention are integrated services (IntServ), differential services (DiffServ) and label switching (MPLS). While these technologies are orthogonal in many respects and can coexist, they are all similar with respect to the fact that some or all the routers in such networks need to be programmed with state information associating data flows with QoS classes or priorities or labels. This paper describes a protocol called SSP (state setup protocol) which is designed to disseminate and manage this state information. In addition to a simple design which makes fast implementations feasible, SSP provides many features like state aggregation and third party signaling which makes SSP a suitable tool for network configuration, management and provisioning as well. A detailed discussion of SSP is presented along with numerous examples and performance measurements.
Combining SVM and Rule-Based classifiers for optimal classification in breast cancer diagnosis

Mammography is accepted as the most effective method to detect breast cancer. Breast microcalcifications are considered very important findings, which may be associated to the existence or not of breast cancer. It has been proven that in some cases the evaluation of their characteristics contributes to the early diagnosis of breast cancer. A computer aided diagnosis (CAD) system has been already developed in the lab based on detailed analysis and evaluation of related features of microcalcifications and a subsequent decision tree classification scheme. This system has very good sensitivity while suffering from low specificity. In this paper, we present a binary classifier which combines the aforementioned rule-based classifier with certain classification schemes based on the support vector machines (SVM) methodology. We evaluated the performance of the proposed binary classifier and we compared it with the existing CAD system using a database of 195 (153 benign and 42 malignant) clinical mammograms provided from collaborating diagnostic centers focused on breast examination. All 195 cases have undergone biopsy in regions where there were clustered microcalcifications, thus there is histological verification of their status. In our experiments, the binary classifier reinforces the computer-aided diagnosis system. While a sensitivity as high as 94.12% and a specificity equal to 31.51% was achieved by the decision tree classification scheme, the binary classifier provided a sensitivity equal to 82.35%, but a higher specificity equal to 65.75%, classifying correctly more benign cases. In other words, the binary classifier is able to reinforce the diagnosis of the CAD system by highly improving the specificity of the system with a little cost in terms of sensitivity.
The Economic Costs of Progressive Supranuclear Palsy and Multiple System Atrophy in France, Germany and the United Kingdom

Progressive supranuclear palsy (PSP) and multiple system atrophy (MSA) are progressive disabling neurological conditions usually fatal within 10 years of onset. Little is known about the economic costs of these conditions. This paper reports service use and costs from France, Germany and the UK and identifies patient characteristics that are associated with cost. 767 patients were recruited, and 760 included in the study, from 44 centres as part of the NNIPPS trial. Service use during the previous six months was measured at entry to the study and costs calculated. Mean six-month costs were calculated for 742 patients. Data on patient sociodemographic and clinical characteristics were recorded and used in regression models to identify predictors of service costs and unpaid care costs (i.e., care from family and friends). The mean six-month service costs of PSP were €24,491 in France, €30,643 in Germany and €25,655 in the UK. The costs for MSA were €28,924, €25,645 and €19,103 respectively. Unpaid care accounted for 68–76%. Formal and unpaid costs were significantly higher the more severe the illness, as indicated by the Parkinson's Plus Symptom scale. There was a significant inverse relationship between service and unpaid care costs.
Cytidine metabolism in photoreceptor cells of the rat

During brief (30-min) incubations, isolated rat retinas accumulated [3H]cytidine, converted it to cytidine triphosphate (CTP), and incorporated it into RNA and cytidine diphosphate-diacylglyceride (CDG), a phospholipid precursor of phosphatidylinositol (Pl). Labeled CTP, RNA, and CDG contents were found to be two- to three-fold higher in photoreceptor cells than in cells of the inner retina. Autoradiograms showed that, within photoreceptor cells, silver grains representing RNA were concentrated over the nuclei in dark and light, while silver grains representing CDG were concentrated over the inner segments only after incubation in dark. The formation of labeled CTP and the synthesis of RNA were enhanced in light, while labeled CDG levels became reduced in light concurrent with an increase in the incorporation of labeled inositol into Pl. The 3H-labeled CDG content, however, was increased two- to fourfold in light in the presence of actinomycin D, and autoradiograms show a heavy concentration of silver grains over the inner segments of photoreceptor cells. These findings establish a role for cytidine nucleotides in photoreceptor cell metabolism and in light-dependent increases in RNA and Pl synthesis. Furthermore, the observations indicate that a competition may exist in light for cytidine or CTP and suggest that availability of cytidine for CDG synthesis may have a regulatory role in Pl metabolism within the photoreceptor cells.
Fabrication of biomimetic gecko setae by direct photolithography and micromolding processes

In nature, geckos have developed complex adhesion structures capable of smart adhesion, the ability to cling to different smooth and rough surfaces, even ceilings, and detach at will. The hierarchical structure of gecko foot hair, consisting of microscale setae, branches and nanoscale spatula, contributes to the strong adhesion on different surfaces. In this paper, we present two approaches to fabricating high-aspect-ratio polymer fiber arrays mimicking gecko setae. SU-8 photoresist has been applied, and SU-8 fiber arrays with aspect ratio of 10 were obtained. Polydimethyl-siloxane (PDMS) microfiber arrays were fabricated through a micromolding process and the master template for this process was fabricated by using inductively coupled plasma (ICP) technology. The contact angle of water droplets on PDMS microfiber arrays shows increased hydrophobic property of PDMS microfiber arrays than non-patterned PDMS surface, from 102° to 137°.
Gathering text entry metrics on android devices

We developed an application to gather text entry speed and accuracy metrics on Android devices. This paper details the features of the application and describes a pilot study to demonstrate its utility. We evaluated and compared three mobile text entry methods: QWERTY typing, handwriting recognition, and shape writing recognition. Handwriting was the slowest and least accurate technique. QWERTY was faster than shape writing, but we found no significant difference in accuracy between the two techniques.
Kaiso Represses the Cell Cycle Gene cyclin D1 via Sequence-Specific and Methyl-CpG-Dependent Mechanisms

Kaiso is the first member of the POZ family of zinc finger transcription factors reported to bind DNA with dual-specificity in both a sequence- and methyl-CpG-specific manner. Here, we report that Kaiso associates with and regulates the cyclin D1 promoter via the consensus Kaiso binding site (KBS), and also via methylated CpG-dinucleotides. The methyl-CpG sites appear critical for Kaiso binding to the cyclin D1 promoter, while a core KBS in close proximity to the methyl-CpGs appears to stabilize Kaiso DNA binding. Kaiso’s binding to both sites was demonstrated in vitro using electrophoretic mobility shift assays (EMSA) and in vivo using Chromatin immunoprecipitation (ChIP). To elucidate the functional relevance of Kaiso’s binding to the cyclin D1 promoter, we assessed Kaiso overexpression effects on a minimal cyclin D1 promoter-reporter that contains both KBS and CpG sites. Kaiso repressed this minimal cyclin D1 promoter-reporter in a dose-dependent manner and transcriptional repression occurred in a KBS-specific and methyl-CpG-dependent manner. Collectively our data validates cyclin D1 as a Kaiso target gene and demonstrates a mechanism for Kaiso binding and regulation of the cyclin D1 promoter. Our data also provides a mechanistic basis for how Kaiso may regulate other target genes whose promoters possess both KBS and methyl-CpG sites.
Efficient Multi-Channel Acoustic Echo Cancellation Using Constrained Sparse Filter Updates in the Subband Domain

In this paper we present constrained sparse tap-selection schemes for updating Multi-Channel Acoustic Echo Cancellation (MAEC) filters in the subband domain. At first, M-Max tap-selection on the complete multi-channel reference spectra is performed and the effect of the subsequent sparse filter update on the speed of convergence of the MAECfilters is investigated. We consider a measure to quantify signal sparsity, and use it to investigate the spectral and inter-channel sparsity present in real-world surround sound signals. A heuristic tap-selection scheme is proposed which exploits the signal sparsity properties, and performs tap-selection with much lower computational effort as compared to the M-Max and the full-update tapselection schemes, while giving similar echo cancellation performance.