Miracle-dz/UniFAR-FTUs huggingface dataset:
A Comprehensive Review of Sensors and Instrumentation Methods in Devices for Musical Expression

Digital Musical Instruments (DMIs) are musical instruments typically composed of a control surface where user interaction is measured by sensors whose values are mapped to sound synthesis algorithms. These instruments have gained interest among skilled musicians and performers in the last decades leading to artistic practices including musical performance, interactive installations and dance. The creation of DMIs typically involves several areas, among them: arts, design and engineering. The balance between these areas is an essential task in DMI design so that the resulting instruments are aesthetically appealing, robust, and allow responsive, accurate and repeatable sensing. In this paper, we review the use of sensors in the DMI community as manifested in the proceedings of the International Conference on New Interfaces for Musical Expression (NIME 2009–2013). Focusing on the sensor technologies and signal conditioning techniques used by the NIME community. Although it has been claimed that specifications for artistic tools are harder than those for military applications, this study raises a paradox showing that in most of the cases, DMIs are based on a few basic sensors types and unsophisticated engineering solutions, not taking advantage of more advanced sensing, instrumentation and signal processing techniques that could dramatically improve their response. We aim to raise awareness of limitations of any engineering solution and to assert the benefits of advanced electronics instrumentation design in DMIs. For this, we propose the use of specialized sensors such as strain gages, advanced conditioning circuits and signal processing tools such as sensor fusion. We believe that careful electronic instrumentation design may lead to more responsive instruments.
Genetic variation in the brain derived neurotrophic factor gene in Alzheimer's disease

Genes known to contribute to the genetic predisposition to Alzheimer's disease (AD) are active in pathways of neurodegeneration but explain only a minority of the genetic contribution to AD. A protein of importance in cerebral neurodegeneration is the brain‐derived neurotrophic factor (BDNF). Variations in two single‐nucleotide polymorphisms (SNPs) within the BDNF gene have previously been associated with AD, and one of these SNPs has also been associated with memory loss and affective disorders. We performed a case control study of three BDNF SNPs in 250 neuropathologically confirmed cases of AD and 194 unrelated controls. We did not find a significant association between the three BDNF SNPs studied and AD when evaluated individually or with haplotype analysis. Nor did BDNF genotype appear to affect the APOE ε4 association with AD. The three SNPs studied were closely linked (D′ = 0.99 across the region). We discuss possible reasons for our failure to confirm the previously reported associations. © 2004 Wiley‐Liss, Inc.
Endocytosis and degradation of interstitial retinol-binding protein: differential capabilities of cells that border the interphotoreceptor matrix

Between the pigment epithelium and the outer limiting membrane of the retina is an extracellular compartment filled with the interphotoreceptor matrix (IPM). A prominent component of the IPM is a glycoprotein known as interstitial retinol-binding protein (IRBP). Using in vitro techniques, we compared the ability of the cells that border this compartment to internalize colloidal gold (CG) coated with either IRBP or ovalbumin, a glycoprotein not found in the IPM. Neither IRBP-CG nor ovalbumin-CG was internalized by the Muller's cells. Both rod and cone photoreceptors take up IRBP-CG, which is observed in small vesicles and multivesicular bodies. Neither photoreceptor type takes up ovalbumin-CG. Acid phosphatase cytochemistry indicates that acid phosphatase reaction product in the multivesicular bodies co-localizes with IRBP-CG, which suggests that this molecule is degraded by rod and cone photoreceptors and is not recycled. The pigment epithelium internalizes IRBP-CG and ovalbumin-CG, both of which remain in small cytoplasmic vesicles near the apical plasma membrane. There is no indication that vesicles that contain either IRBP-CG or ovalbumin-CG fuse with the lysosomal system in the pigment epithelial cells during the incubation.
Association of Prostate Cancer Risk Variants with Gene Expression in Normal and Tumor Tissue

Background: Numerous germline genetic variants are associated with prostate cancer risk, but their biologic role is not well understood. One possibility is that these variants influence gene expression in prostate tissue. We therefore examined the association of prostate cancer risk variants with the expression of genes nearby and genome-wide. Methods: We generated mRNA expression data for 20,254 genes with the Affymetrix GeneChip Human Gene 1.0 ST microarray from normal prostate (N = 160) and prostate tumor (N = 264) tissue from participants of the Physicians' Health Study and Health Professionals Follow-up Study. With linear models, we tested the association of 39 risk variants with nearby genes and all genes, and the association of each variant with canonical pathways using a global test. Results: In addition to confirming previously reported associations, we detected several new significant (P < 0.05) associations of variants with the expression of nearby genes including C2orf43, ITGA6, MLPH, CHMP2B, BMPR1B, and MTL5. Genome-wide, five genes (MSMB, NUDT11, RBPMS2, NEFM, and KLHL33) were significantly associated after accounting for multiple comparisons for each SNP (P < 2.5 × 10−6). Many more genes had an FDR <10%, including SRD5A1 and PSCA, and we observed significant associations with pathways in tumor tissue. Conclusions: The risk variants were associated with several genes, including promising prostate cancer candidates and lipid metabolism pathways, suggesting mechanisms for their impact on disease. These genes should be further explored in biologic and epidemiologic studies. Impact: Determining the biologic role of these variants can lead to improved understanding of prostate cancer etiology and identify new targets for chemoprevention. Cancer Epidemiol Biomarkers Prev; 24(1); 255–60. ©2014 AACR.
Detecting Content Spam on the Web through Text Diversity Analysis

Web spam is considered to be one of the greatest threats to modern search engines. Spammers use a wide range of content generation techniques known as content spam to fill search results with low quality pages. We argue that content spam must be tackled using a wide range of content quality features. In this paper we propose a set of content diversity features based on frequency rank distributions for terms and topics. We combine them with a wide range of other content features to produce a content spam classifier that outperforms existing results.
LigandScout: 3-D Pharmacophores Derived from Protein-Bound Ligands and Their Use as Virtual Screening Filters

From the historically grown archive of protein-ligand complexes in the Protein Data Bank small organic ligands are extracted and interpreted in terms of their chemical characteristics and features. Subsequently, pharmacophores representing ligand-receptor interaction are derived from each of these small molecules and its surrounding amino acids. Based on a defined set of only six types of chemical features and volume constraints, three-dimensional pharmacophore models are constructed, which are sufficiently selective to identify the described binding mode and are thus a useful tool for in-silico screening of large compound databases. The algorithms for ligand extraction and interpretation as well as the pharmacophore creation technique from the automatically interpreted data are presented and applied to a rhinovirus capsid complex as application example.
Recovering Software Specifications with Inductive Logic Programming

We consider using machine learning techniques to help understand a large software system. In particular, we describe how learning techniques can be used to reconstruct abstract Datalog specifications of a certain type of database software from examples of its operation. In a case study involving a large (more than one million lines of C) real-world software system, we demonstrate that off-the-shelf inductive logic programming methods can be successfully used for specification recovery; specifically, Grendel2 can extract specifications for about one-third of the modules in a test suite with high rates of precision and recall. We then describe two extensions to Grendel2 which improve performance on this task: one which allows it to output a set of candidate hypotheses, and another which allows it to output specifications containing determinations. In combination, these extensions enable specifications to be extracted for nearly two-thirds of the benchmark modules with perfect recall, and precision of better than 60%.
Sentiment Composition Using a Parabolic Model

In this paper, we propose a computational model that accounts for the effects of negation and modality on opinion expressions. Based on linguistic experiments informed by native speakers, we distil these effects according to the type of modality and negation. The model relies on a parabolic representation where an opinion expression is represented as a point on a parabola. Negation is modelled as functions over this parabola whereas modality through a family of parabolas of different slopes; each slope corresponds to a different certainty degree. The model is evaluated using two experiments, one involving direct strength judgements on a 7-point scale and the other relying on a sentiment annotated corpus. The empirical evaluation of our model shows that it matches the way humans handle negation and modality in opinionated sentences
Caracterização geomorfológica do município de Luís Eduardo Magalhães, oeste baiano, escala 1:100.000.

Este trabalho apresenta a caracterizacao geomorfologica do municipio de Luis Eduardo Magalhaes, BA, na escala 1:100.000. A metodologia utilizada para o mapeamento geomorfologico foi baseada no uso de imagens de altimetria Shuttlle Radas Topografhy Mission (SRTM), de tecnicas de geoprocessamento e de trabalhos de campo. A geomorfologia foi caracterizada em tres niveis taxonomicos: 1. nivel: dominio morfoestrutural, composto pela cobertura sedimentar Sao Franciscana (100%); 2. nivel: regioes geomorfologicas compostas pelas chapadas do Sao Francisco (28,7%) e 3. nivel: unidades geomorfologicas, formado pelas unidades chapadas intermediarias (42%), topos (26%), frente de recuo erosivo (22%), planicie intraplanaltica (7%) e veredas (3%). O mapeamento geomorfologico possibilitou o conhecimento ampliado do relevo da regiao e dos outros fatores da paisagem associados a ele, facilitando a identificacao das potencialidades e fragilidades ambientais do municipio.
Enhancing design robustness with reliability-aware resynthesis and logic simulation

While circuit density and power efficiency increase with each major advance in IC technology, reliability with respect to soft errors tends to decrease. Current solutions to this problem such as TMR require high area and power overhead. In this work, soft-error reliability is improved with minimal area overhead by careful, localized circuit restructuring. The key idea is to increase logic masking of errors by taking advantage of conditions already present in the circuit, such as observability don't-cares. We describe two circuit modification techniques to improve reliability: don't-care-based resynthesis and local rewriting. A key feature of these techniques is fast, on-the-fly estimation of soft error rate (SER) using our reliability evaluator AnSER. This tool is compared against prior SER evaluators and found to run orders of magnitude faster. We show empirically that our reliability-driven synthesis methods can reduce SER by 29-40% with only 5-13% area overhead.
Leveraging Social Connections to Improve Personalized Ranking for Collaborative Filtering

Recommending products to users means estimating their preferences for certain items over others. This can be cast either as a problem of estimating the rating that each user will give to each item, or as a problem of estimating users' relative preferences in the form of a ranking. Although collaborative-filtering approaches can be used to identify users who rate and rank products similarly, another source of data that informs us about users' preferences is their set of social connections. Both rating- and ranking-based paradigms are important in real-world recommendation settings, though rankings are especially important in settings where explicit feedback in the form of a numerical rating may not be available. Although many existing works have studied how social connections can be used to build better models for rating prediction, few have used social connections as a means to derive more accurate ranking-based models. Using social connections to better estimate users' rankings of products is the task we consider in this paper. We develop a model, SBPR (Social Bayesian Personalized Ranking), based on the simple observation that users tend to assign higher ranks to items that their friends prefer. We perform experiments on four real-world recommendation data sets, and show that SBPR outperforms alternatives in ranking prediction both in warm- and cold-start settings.
Identification of Novel Point Mutations in ERK2 That Selectively Disrupt Binding to MEK1*

Extracellular signal-regulated kinases 1 and 2 (ERK1 and ERK2) are essential components of pathways through which signals received at membrane receptors are converted into specific changes in protein function and gene expression. As with other members of the mitogen-activated protein (MAP) kinase family, ERK1 and ERK2 are activated by phosphorylations catalyzed by dual-specificity protein kinases known as MAP/ERK kinases (MEKs). MEKs exhibit stringent specificity for individual MAP kinases. Indeed, MEK1 and MEK2 are the only known activators of ERK1 and ERK2. ERK2·MEK1/2 complexes can be detected in vitro and in vivo. The biochemical nature of such complexes and their role in MAP kinase signaling are under investigation. This report describes the use of a yeast two-hybrid screen to identify point mutations in ERK2 that impair its interaction with MEK1/2, yet do not alter its interactions with other proteins. ERK2 residues identified in this screen are on the surface of the C-terminal domain of the kinase, either within or immediately preceding α-helix G, or within the MAP kinase insert. Some mutations identified in this manner impaired the two-hybrid interaction of ERK2 with both MEK1 and MEK2, whereas others had a predominant effect on the interaction with either MEK1 or MEK2. Mutant ERK2 proteins displayed reduced activation in HEK293 cells following epidermal growth factor treatment, consistent with their impaired interaction with MEK1/2. However, ERK2 proteins containing MEK-specific mutations retained kinase activity, and were similar to wild type ERK2 in their activation following overexpression of constitutively active MEK1. Unlike wild type ERK2, proteins containing MEK-specific point mutations were constitutively localized in the nucleus, even in the presence of overexpressed MEK1. These data suggest an essential role for the MAP kinase insert and residues within or just preceding α-helix G in the interaction of ERK2 with MEK1/2.
Inconsistency Detection in Semantic Annotation

Inconsistencies are part of any manually annotated corpus. Automatically finding these inconsistencies and correcting them (even manually) can increase the quality of the data. Past research has focused mainly on detecting inconsistency in syntactic annotation. This work explores new approaches to detecting inconsistency in semantic annotation. Two ranking methods are presented in this paper: a discrepancy ranking and an entropy ranking. Those methods are then tested and evaluated on multiple corpora annotated with multiword expressions and supersense labels. The results show considerable improvements in detecting inconsistency candidates over a random baseline. Possible applications of methods for inconsistency detection are improving the annotation procedure as well as the guidelines and correcting errors in completed annotations.
Regulation of the stringent response is the essential function of the conserved bacterial G protein CgtA in Vibrio cholerae

The gene encoding the conserved bacterial G protein CgtA (Obg) is essential for viability in every organism in which it has been studied. CgtA has been reported to be involved in several diverse bacterial functions, including ribosome assembly, DNA repair, sporulation, and morphological development. However, none of these functions have been identified as essential. Here we show that depletion of CgtA in Vibrio cholerae causes global changes in gene expression that are consistent with induction of a classical low nutrient stress response or “stringent” response. We show that depletion of CgtA leads to increased ppGpp levels that correlate with induction of the global stress response and cessation of growth. The enzyme RelA is responsible for synthesis of the alarmone ppGpp during the stringent response. We show that CgtA is no longer essential in a relA deletion mutant and thus conclude that the essentiality of CgtA is directly linked to its ability to affect ppGpp levels. The enzyme SpoT degrades ppGpp, and here we show that SpoT is essential in a RelA+ CgtA+ background but not in a relA deletion mutant. We also confirmed that CgtA interacts with SpoT in a two-hybrid assay. We suggest that the essential function of CgtA is as a repressor of the stringent response that acts by regulating SpoT activity to maintain low ppGpp levels when bacteria are growing in a nutrient-rich environment.
Ubi-Finger : Gesture Input Device for Mobile Use

We propose a novel interface in mobile environment called “Ubi-Finger” that realizes sensuous operations for PDA and information appliances by gestures of fingers. Since gestures are usual methods of non-verbal communications and enables sensuous operations for users, many researches on them carried out especially in the field of Virtual Reality. However most of those existing gesture-input systems are either very expensive or large, and have not been used in mobile environment. In contrast, Ubi-Finger is a gesture-input device, which is simple, compact, and optimized for mobile use. We develop prototype systems, and evaluate how effective our approach works.
A nano-graphite cold cathode for an energy-efficient cathodoluminescent light source

Summary The development of new types of light sources is necessary in order to meet the growing demands of consumers and to ensure an efficient use of energy. The cathodoluminescence process is still under-exploited for light generation because of the lack of cathodes suitable for the energy-efficient production of electron beams and appropriate phosphor materials. In this paper we propose a nano-graphite film material as a highly efficient cold cathode, which is able to produce high intensity electron beams without energy consumption. The nano-graphite film material was produced by using chemical vapor deposition techniques. Prototypes of cathodoluminescent lamp devices with a construction optimized for the usage of nano-graphite cold cathodes were developed, manufactured and tested. The results indicate prospective advantages of this type of lamp and the possibility to provide advanced power efficiency as well as enhanced spectral and other characteristics.
Motion adaptation for humanoid robots in constrained environments

This paper presents a new method to synthesize full body motion for controlling humanoid robots in highly constrained environments. Given a reference motion of the robot and the corresponding environment configuration, the spatial relationships between the robot body parts and the environment objects are extracted as a representation called the Interaction Mesh. Such a representation is then used in adapting the reference motion to an altered environment. By preserving the spatial relationships while satisfying physical constraints, collision-free and well balanced motions can be generated automatically and efficiently. Experimental results show that the proposed method can adapt different full body motions in significantly modified environments. Our method can be applied in precise robotic controls under complicated environments, such as rescue robots in accident scenes and searching robots in highly constrained spaces.
In Vivo Imaging of HIF-Active Tumors by an Oxygen-Dependent Degradation Protein Probe with an Interchangeable Labeling System

Hypoxia-inducible factor (HIF) functions as a master transcriptional regulator for adaptation to hypoxia by inducing adaptive changes in gene expression for regulation of proliferation, angiogenesis, apoptosis and energy metabolism. Cancers with high expression of the alpha subunit of HIF (HIFα) are often malignant and treatment-resistant. Therefore, the development of a molecular probe that can detect HIF activity has great potential value for monitoring tumor hypoxia. HIF prolyl hydroxylases (HPHDs) act as oxygen sensors that regulate the fate of HIFα protein through its oxygen-dependent degradation (ODD) domain. We constructed a recombinant protein PTD-ODD-HaloTag (POH) that is under the same ODD regulation as HIFα and contains protein transduction domain (PTD) and an interchangeable labeling system. Administration of near-infrared fluorescently labeled POH (POH-N) to mouse models of cancers allowed successful monitoring of HIF-active regions. Immunohistochemical analysis for intratumoral localization of POH probe revealed its specificity to HIF-active cells. Furthermore, lack of the PTD domain or a point mutation in the ODD domain abrogated the specificity of POH-N to HIF-active cells. Overall results indicate that POH is a practical probe specific to HIF-active cell in cancers and suggest its large potential for imaging and targeting of HIF-related diseases.
Can Naive Viewers Put Themselves in the Patients’ Shoes?: Reliability and Validity of the Analogue Patient Methodology

Background:Analogue patients (APs) are untrained viewers given the task of viewing and rating their impressions of a medical interaction while taking on the patient role. This methodology is often used to assess patient perceptions when using real patient (RP) populations is unethical or impractical. Objectives:This study examines the reliability and validity of the AP methodology and its optimal implementation. Research Design:Forty-six videotaped interactions of RP-physician interactions, where RP satisfaction scores existed, were viewed by 216 APs, who rated satisfaction. Interrater reliability for AP satisfaction scores was evaluated. AP and RP satisfaction scores were compared with each other and correlated with the physician’s observer-coded patient-centeredness. Measures:RP satisfaction was measured with a 15-item scale after the whole interaction. Physicians’ patient-centered behavior was coded with the Four Habits Coding Scheme. AP satisfaction was measured after viewing the entire interaction with a single satisfaction question, a 4-item satisfaction scale including that single item, and the original 15-item satisfaction scale used by the RPs. Results:AP satisfaction ratings were reliable (=0.70 for 4 APs). AP satisfaction was a significant predictor of RP satisfaction (r=0.29, P=0.05), especially when the analysis was limited to the RPs who reported being less than perfectly satisfied (r=0.65, P=0.002). AP satisfaction was a better predictor than RP satisfaction of providers’ patient-centered behaviors in the interaction. Conclusions:The AP methodology is a valid and reliable approach to gathering patient perception data about provider-patient interactions. Results suggest practical advice for researchers using the AP methodology.