Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection of an object inside a phantom tissue using a spatial filter

We report the detection of an object inside a phantom tissue using a spatial filter and a 5-mW He-Ne Laser. The phantom tissue is composed of 8% scattering polystyrene spheres and is diluted to different concentrations in water. The solution is placed inside of a cuvette of length 5 cm and width 5 cm. The spatial filter, composed of a 4-cm plano-convex lens and a 10-micrometers pinhole, is able to extract ballistic and quasi-ballistic photons from the transmitted light. A photomultiplier tube is used for detection, and a lock-in amplifier is used to reduce the amount of noise in the signal. We are able to detect the object in a phantom tissue of 20 mean free paths [mfp] with a contrast of 99.0%. The contrast in a tissue with 30 mfp is 22.7%.
Obesity, starch digestion and amylase: association between copy number variants at human salivary (AMY1) and pancreatic (AMY2) amylase genes

The human salivary amylase genes display extensive copy number variation (CNV), and recent work has implicated this variation in adaptation to starch-rich diets, and in association with body mass index. In this work, we use paralogue ratio tests, microsatellite analysis, read depth and fibre-FISH to demonstrate that human amylase CNV is not a smooth continuum, but is instead partitioned into distinct haplotype classes. There is a fundamental structural distinction between haplotypes containing odd or even numbers of AMY1 gene units, in turn coupled to CNV in pancreatic amylase genes AMY2A and AMY2B. Most haplotypes have one copy each of AMY2A and AMY2B and contain an odd number of copies of AMY1; consequently, most individuals have an even total number of AMY1. In contrast, haplotypes carrying an even number of AMY1 genes have rearrangements leading to CNVs of AMY2A/AMY2B. Read-depth and experimental data show that different populations harbour different proportions of these basic haplotype classes. In Europeans, the copy numbers of AMY1 and AMY2A are correlated, so that phenotypic associations caused by variation in pancreatic amylase copy number could be detected indirectly as weak association with AMY1 copy number. We show that the quantitative polymerase chain reaction (qPCR) assay previously applied to the high-throughput measurement of AMY1 copy number is less accurate than the measures we use and that qPCR data in other studies have been further compromised by systematic miscalibration. Our results uncover new patterns in human amylase variation and imply a potential role for AMY2 CNV in functional associations.
Simulated Annealing Neural Network for Software Failure Prediction

Various models for software reliability prediction were proposed by many researchers. In this work we present a hybrid approach based on the Neural Networks and Simulated Annealing. An adaptive simulated Annealing algorithm is used to optimize the mean square of the error produced by training the Neural Network, predicting software cumulative failure. To evaluate the predictive capability of the proposed approach various projects were used. A comparison between this approach and others is presented. Numerical results show that both the goodness-of-fit and the next-step-predictability of our proposed approach have greater accuracy in predicting software cumulative failure compared with other approaches.
Audio-visual speech translation with automatic lip syncqronization and face tracking based on 3-D head model

Speech-to-speech translation has been studied to realize natural human communication beyond language barriers. Toward further multi-modal natural communication, visual information such as face and lip movements will be necessary. In this paper, we introduce a multi-modal English-to-Japanese and Japanese-to-English translation system that also translates the speaker's speech motion while synchronizing it to the translated speech. To retain the speaker's facial expression, we substitute only the speech organ's image with the synthesized one, which is made by a three-dimensional wire-frame model that is adaptable to any speaker. Our approach enables image synthesis and translation with an extremely small database. We conduct subjective evaluation by connected digit discrimination using data with and without audiovisual lip-synchronicity. The results confirm the sufficient quality of the proposed audio-visual translation system.
Discovery and Enhancement of Learning Model Analysis through Semantic Process Mining

Semantic concepts can be layered on top of existing learner information asset to provide a more conceptual analysis of real time processes capable of providing real world answers that are closer to human understanding. Challenges from current research shows that even though learning data are captured and modelled with acceptable performance to accurately reflect process executions, they are still limited for many process mining analysis because they lack the abstraction level required from real world perspectives. The work in this paper describes a Semantic Process Mining approach directed towards enriching streams of event data logs from a learning process using semantic descriptions that references concepts in an Ontology specifically designed for representing learning processes. The proposed approach involves the extraction of process history data from learning execution environments unfolding how we extract the input data necessary to be mapped unto the learning process logs, which is then followed by submitting the resulting eXtensible Event Streams XES and Mining eXtensible Markup Language MXML format to the process analytics environment for mining and further analysis. The consequence is a learning process model which we semantically annotate with concepts they represent in real time using semantic descriptions, and then linking them to an ontology to allow for analysis of the extracted event logs streams based on concepts rather than the event tags of the process. The aim is to provide real time knowledge about the learning process which are more intuitive and closer to human understanding. By referring to ontologies and piloting series of validation experiments, the approach provides us with the capability to infer new and discover relationships the process instances share amongst themselves and to address the problem of determining the presence of different learning patterns within the learning knowledge base. To this end, we demonstrate how data from learning process can be extracted, semantically prepared, and transformed into mining executable formats to enable prediction of individual learning patterns and outcomes through further semantic analysis of the discovered models. Therefore, our approach is grounded on Process Mining and Semantic Modelling Techniques.
The Effect of Product Ratings on Viral Marketing CS 224 W Project Final Report

In network-based marketing, social influence is considered in order to optimize marketing strategies. Social influence in e-commerce has been studied for more than one and a half decades, to a large extent in the context of product endorsements and chains of recommendations. In this work, we study friends’ influence in social networks exerted through reviews that include rankings, which means that a review can be anything from a recommendation to disapproval. We use the data from the recent Round 8 Yelp Dataset Challenge and determine the degree to which friends influence the decision to choose and review businesses, broken down by the ranking of the business. We discuss the effectiveness of different figures of merit for this analysis, including the exposure, contagion count, and spreading concentration. We find that encouraging influence by friends is more likely to occur for highly rated businesses than for poorly rated ones. This conclusion is corroborated by results on artificial networks fashioned after the Yelp dataset.
Microdialysis Glucose Sensor System Compared With Needle Type Glucose Sensor In Vivo During OGTT And Physical Exercise

The 'subcutaneous glucose monitoring system' (SCGM) is based on microdialysis and allows continuous glucose monitoring in abdominal adipose tissue of diabetic patients up to 5 days. In the current in vivo study we compared the SCGM system with a commercially available needle type glucose sensor during an oral glucose tolerance test (OGTT) and during physical exercise. The SCGM had a good in vivo performance that was comparable to the needle type sensor. The inherent safe measuring technology of microdialysis and sensor stability of the SCGM makes it a likely candidate for online glucose measurement in diabetic patients. However, the overall system configuration is too bulky to wear comfortably and the measured values have a time lag of 35 min. The SCGM system will be the base for the future development of a miniaturized integrated microdialysis sensor system using lab-on-a-chip technology.
Comparison of dynamic CT and stable xenon CT in ischemic cerebrovascular disease.

PURPOSE To investigate a new hemodynamic parameter that can be obtained by dynamic CT and that reflects cerebral blood flow (CBF), in patients with ischemic cerebrovascular disease. METHODS CBF and hemodynamic parameters including the area under the time-dependent contrast-medium dilution curve (A) and mean transit time (MTT) were measured in 23 patients with ischemic cerebrovascular disease. They included 17 patients in the chronic stage (more than 1 month after onset) and six with acute occlusion of the internal carotid or middle cerebral artery (within 24 hours of onset). CBF measurement was conducted by inhalation of stable xenon during CT scan and the hemodynamic study was performed using dynamic CT. RESULTS CBF in the territory of the middle cerebral artery had an inverse correlation with MTT. (A) divided by (MTT) defined as (f) had a significantly positive correlation with CBF (MTT = 18.66 - 0.495.CBF + 0.005.CBF2, r = .730, P < .001). CONCLUSION This parameter (f) is thought to represent a relative CBF and it can be used in evaluation of the hemodynamic status in ischemic cerebrovascular disease.
deepTools: a flexible platform for exploring deep-sequencing data

We present a Galaxy based web server for processing and visualizing deeply sequenced data. The web server's core functionality consists of a suite of newly developed tools, called deepTools, that enable users with little bioinformatic background to explore the results of their sequencing experiments in a standardized setting. Users can upload pre-processed files with continuous data in standard formats and generate heatmaps and summary plots in a straight-forward, yet highly customizable manner. In addition, we offer several tools for the analysis of files containing aligned reads and enable efficient and reproducible generation of normalized coverage files. As a modular and open-source platform, deepTools can easily be expanded and customized to future demands and developments. The deepTools webserver is freely available at http://deeptools.ie-freiburg.mpg. de and is accompanied by extensive documentation and tutorials aimed at conveying the principles of deep-sequencing data analysis. The web server can be used without registration. deepTools can be installed locally either stand-alone or as part of Galaxy.
Object release under varying task constraints in children with hemiplegic cerebral palsy

Considerable attention has been given in recent years to fingertip force coordination during grasping and lifting small objects in children with cerebral palsy (CP). However, little is known about the children's ability to replace and release an object from grasp. The present study examined the coordination of fingertip forces during replacement and release of an object from grasp under varying task constraints in the involved hand of 15 children (10 males, five females, age range 7 to 14 years) with hemiplegic CP and in the non‐dominant hand of 15 age‐matched, typically‐developing children (seven males, eight females). Participants released an object, instrumented with force transducers and held with a precision grip, onto a stable surface and onto an unstable surface (requiring higher accuracy) at self‐paced and fast‐as‐possible speeds. Temporal and force measures were recorded and the dependent measures were tested using analyses of variance. Results showed that force coordination was impaired in children with hemiplegia, resulting in prolonged and uncoordinated replacement and release of the object (p<0.05). Differences between controls and children with hemiplegia were greater when speed and accuracy constraints were imposed (i.e. task performance was affected by these constraints to a greater extent in the children with CP, p<0.05). Impairments in temporal coordination of object release were also observed in the non‐involved hand under all conditions (p<0.05). These results provide additional information about impaired hand function in children with hemiplegic CP. Clinical implications of these findings are discussed.
Modeling Interventions Using Belief Causal Networks

Causality plays an important role in our comprehension of the world. It amounts to determine what truly causes what and what it matters. Interventions allow the identification of elements in a sequence of events that are related in a causal way. In this paper, we introduce belief causation and we proposea method for handling interventions in graphical model under an uncertain environment where the uncertainty is represented by belief masses, so-called belief causal networks. More specifically, we propose a generalization of the “DO” operator and explain the needed changes on the structure of the graph to model a belief causal network on which interventions are proceeded.
ERK5 Is a Novel Type of Mitogen-Activated Protein Kinase Containing a Transcriptional Activation Domain

ABSTRACT Previous studies have shown that upregulation of the orphan steroid receptor Nur77 is required for the apoptosis of immature T cells in response to antigen receptor signals. Transcriptional upregulation of Nur77 in response to antigen receptor signaling involves two binding sites for the MEF2 family of transcription factors located in the Nur77 promoter. Calcium signals greatly increase the activity of MEF2D in T cells via a posttranslational mechanism. The mitogen-activated protein (MAP) kinase ERK5 was isolated in a yeast two-hybrid screen using the MADS-MEF2 domain of MEF2D as bait. ERK5 resembles the other MAP kinase family members in its N-terminal half, but it also contains a 400-amino-acid C-terminal domain of previously uncharacterized function. We report here that the C-terminal region of ERK5 contains a MEF2-interacting domain and, surprisingly, also a potent transcriptional activation domain. These domains are both required for coactivation of MEF2D by ERK5. The MEF2-ERK5 interaction was found to be activation dependent in vivo and inhibitable in vitro by the calcium-sensitive MEF2 repressor Cabin 1. The transcriptional activation domain of ERK5 is required for maximal MEF2 activity in response to calcium flux in T cells, and it can activate the endogenous Nur77 gene when constitutively recruited to the Nur77 promoter via MEF2 sites. These studies provide insights into a mechanism whereby MEF2 activity can respond to calcium signaling and suggest a novel, unexpected mechanism of MAP kinase function.
Study of circulating immune complexes in thyroid diseases: comparison of Raji cell radioimmunoassay and specific thyroglobulin-antithyroglobulin radioassay.

Circulating soluble immune complexes (ICs) were studied by Raji cell RIA in a series of patients with and without thyroid disorders. Clearly elevated IC levels (>41.2 egeq/ml; i.e. >3 SD above the mean value of the normal controls) were found in 3 of 18 patients with Hashimoto's thyroiditis, in 4 of 39 with differentiated thyroid carcinoma, and in none of 21 patients with Graves' disease as well as in none of 21 normal healthy controls. Thyroglobulin (Tg) was not found in the ICs bound to Raji cells when sought by a sensitive radiolabeled antibody technique. Furthermore, experiments carried out with radiolabeled Tg-anti- Tg ICs (Tg-ICs) obtained by mixing Tg with homologous (Hashimoto's sera) antibody revealed that homologous Tg-ICs did not bind to Raji cells, while the ICs prepared from heterologous (rabbit) antibody did bind. Tg-ICs were also assayed in the same sera and in additional samples from 29 normal controls and 12 patients with Graves' disease by a recently developed specific immunoradiometric .
Vulnerabilities as Blind Spots in Developer's Heuristic-Based Decision-Making Processes

The security community spares no effort in emphasizing security awareness and the importance of building secure software. However, the number of new vulnerabilities found in today's systems is still increasing. Furthermore, old and well-studied vulnerability types such as buffer overflows and SQL injections, are still repeatedly reported in vulnerability databases. Historically, the common response has been to blame the developers for their lack of security education. This paper discusses a new hypothesis to explain this problem by introducing a new security paradigm where software vulnerabilities are viewed as developers' blind spots in their decision making. We argue that such a flawed mental process is heuristic-based, where humans solve problems without considering all the information available, just like taking shortcuts. This paper's thesis is that security thinking tends to be left out by developers during their programming, as vulnerabilities usually exist in corner cases with unusual information flows. Leveraging this paradigm, this paper introduces a novel methodology for capturing and understanding security-related blind spots in Application Programming Interfaces (APIs). Finally, it discusses how this methodology can be applied to the design and implementation of the next generation of automated diagnosis tools.
Recursively querying monitoring data in NFV environments

In Network Function Virtualization (NFV), a network service is created by combining interconnected virtual network functions (VNF), which may include nested VNFs or end points. Querying the performance of a high-level, abstract network service is challenging due to the recursivity of the NFV architecture and the elasticity and dynamicity provided by the NFV infrastructure, typically realized by Cloud virtualization technologies. In this paper, we propose to use Datalog, a declarative logic programming language, to build a query engine which can provide recursive query capabilities on performance metrics of network services. We present the language and describe some example use cases for both compute and network metrics. We describe the design of a query engine utilizing the language, based on which we implemented a proof of concept system. The resulting experimental system has shown the effectiveness of the query language to recursively retrieve monitoring results of NFV environments.
Using a Probabilistic Class-Based Lexicon for Lexical Ambiguity Resolution

This paper presents the use of probabilistic class-based lexica for disambiguation in target-word selection. Our method employs minimal but precise contextual information for disambiguation. That is, only information provided by the target-verb, enriched by the condensed information of a probabilistic class-based lexicon, is used. Induction of classes and fine-tuning to verbal arguments is done in an unsupervised manner by EM-based clustering techniques. The method shows promising results in an evaluation on real-world translations.
Local binary patterns as features for speaker recognition

The i-vector framework witnessed great success in the past years in speaker recognition (SR). The feature extraction process is central in SR systems and many features have been developed over the years to improve the recognition performance. In this paper, we present a new feature representation which bor-rows a concept initially developed in computer vision to characterize textures called Local Binary Patterns (LBP). We explore the use of LBP as features for speaker recognition and show that using them as descriptors for cepstral coefﬁcients dynamics (replacing ∆ and ∆∆ in the regular MFCC representation) results in more efﬁcient features and yield up to 15% of relative improvement compared to the baseline system performance in both clean and noisy conditions.
Sedation in mechanically ventilated children: we are advancing.

A ventilacao mecânica (VM) e um elemento essencial de suporte da insuficiencia respiratoria, das lesoes do sistema nervoso central e nos cuidados pos-operatorios de adultos, criancas e recem-nascidos. Este suporte, juntamente com a monitoracao invasiva que frequentemente se faz necessaria, pode ocasionar ansiedade, agitacao e dor. (1) As criancas admitidas na unidade de terapia intensiva sofrem o medo e a ansiedade de se verem separadas de seus pais e se encontrarem em um ambiente estressante, onde sao constantemente submetidas a exames e procedimentos dolorosos. (2) Em particular, as criancas menores apresentam significativas alteracoes fisiologicas em resposta a pequenos estimulos alem de nao serem capazes de verbalizar adequadamente a intensidade e localizacao da dor, tornando muito dificil a diferenciacao entre a sedacao e analgesia. (3) No entanto, existe um consenso de que o uso de sedacao e analgesia e essencial para o conforto e a seguranca dos pacientes em VM. De fato, a utilizacao de sedacao e analgesia comprovadamente diminui o desconforto associado a VM, diminuindo o consumo de oxigenio, modulando a intensidade da resposta ao estresse, reduzindo os riscos de lesoes relacionadas a agitacao e ao deslocamento de dispositivos invasivos, promovendo, assim, a seguranca do paciente e, por fim, facilitando os cuidados de beira de leito. (4-7) A tecnologia de suporte ventilatorio, evoluiu consideravelmente e o suporte ventilatorio mecânico e frequentemente fornecido como um complemento, e nao como um substituto total do esforco respiratorio espontâneo. Apesar de todos os avancos nas tecnicas de VM, a procrastinacao da retirada gradual da ventilacao pulmonar mecânica pode gerar desconforto desnecessario no paciente intubado e aumento do risco de complicacoes relacionadas a intubacao traqueal e a VM. Considerando-se que somente a retirada gradual da ventilacao e responsavel por ate 40% do tempo total em que o paciente recebe este suporte(8) e dada a grande quantidade de modos de ventilacao e estrategias ventilatorias para diferentes tipos de doencas, foi natural partir-se para o desenvolvimento de protocolos de retirada da ventilacao, etapa comum a todos os pacientes em suporte ventilatorio. Ainda assim, metodos para desmame do suporte respiratorio em criancas nunca foram rigorosamente estudados(9) e quando estudados, os metodos de desmame sao extrapolados de estudos em pacientes adultos e recem-nascidos prematuros, o que pode ser inapropriado. A compreensao que a sedacao e analgesia profundas ou prolongadas tem o potencial de aumentar a morbidade e mortalidade levou a concepcao de um novo modelo que destaca a otimizacao do conforto dos pacientes os mantendo interativos, orientados e capazes de seguir instrucoes. (10) Este novo modelo se baseia em Marcelo Cunio Machado Fonseca1, Werther Brunow de Carvalho2