Miracle-dz/UniFAR-FTUs huggingface dataset:
LIWBC: a bigram algorithm to enhance results in polarity classification

The text mining literature shows a growing body of work concerned with the automatic identification of sentiment in text. Sentiment polarity classification is one of the most important text mining tasks. The typical approach to polarity classification uses lexicons to count word usage from linguistic or emotional aspects. One of the most widely used lexicons is the Linguistic Inquiry and Word Count (LIWC). LIWC assigns words to categories (e.g., positive emotion) based on a lexicon of words associated with psycholinguist categories. It has been widely used in polarity classification task with good results. However, it only accounts for word count, discarding the text structure and ignoring important semantic relationships between words. In this work, we present LIWBC, an algorithm to count bigrams using the lexicon provided by LIWC. The goal is to incorporate text structure information to improve the polarity classification task with LIWC lexicon. We conducted experiments to evaluate LIWBC with two real datasets: the first one consists of blogger posts; the second one is the movie reviews dataset, which contains full-text movie reviews from IMDB. Both datasets were processed with LIWC and LIWBC. After that, we ran four classification algorithms in the data processed by LIWC and LIWBC. The SVM algorithm executed with LIWBC data yielded the best result in both datasets. The F1 score of SVM in blogger posts and movie reviews dataset had an improvement of 2.2% and 2.5%, respectively.
Facial Asymmetry-Based Anthropometric Differences between Gender and Ethnicity

Bilateral facial asymmetry is frequently exhibited by humans but its combined evaluation across demographic traits including gender and ethnicity is still an open research problem. In this study we measure and evaluate facial asymmetry across gender and different ethnic groups and investigate the differences in asymmetric facial dimensions among the subjects from two public face datasets, the MORPH and FERET. To this end, we detect 28 facial asymmetric dimensions from each face image using an anthropometric technique. An exploratory analysis is then performed via a multiple linear regression model to determine the impact of gender and ethnicity on facial asymmetry. Post-hoc Tukey test has been used to validate the results of the proposed method. The results show that out of 28 asymmetric dimensions, females differ in 25 dimensions from males. African, Asian, Hispanic and other ethnic groups have asymmetric dimensions that differ significantly from those of Europeans. These findings could be important to certain applications like the design of facial fits, as well as guidelines for facial cosmetic surgeons. Lastly, we train a neural network classifier that employs asymmetric dimensions for gender and race classification. The experimental results show that our trained classifier outperforms the support vector machine (SVM) and k-nearest neighbors (kNN) classifiers.
Lineage‐specific duplication and adaptive evolution of bitter taste receptor genes in bats

By generating raw genetic material and diverse biological functions, gene duplication represents a major evolutionary mechanism that is of fundamental importance in ecological adaptation. The lineage‐specific duplication events of bitter taste receptor genes (Tas2rs) have been identified in a number of vertebrates, but functional evolution of new Tas2r copies after duplication remains largely unknown. Here, we present the largest data set of bat Tas2rs to date, identified from existing genome sequences of 15 bat species and newly sequenced from 17 bat species, and demonstrate lineage‐specific duplications of Tas2r16, Tas2r18 and Tas2r41 that only occurred in Myotis bats. Myotis bats are highly speciose and represent the only mammalian genus that is naturally distributed on every continent except Antarctica. The occupation of such diverse habitats might have driven the Tas2r gene expansion. New copies of Tas2rs in Myotis bats have shown molecular adaptation and functional divergence. For example, three copies of Tas2r16 in Myotis davidii showed differential sensitivities to arbutin and salicin that may occur in their insect prey, as suggested by cell‐based functional assays. We hypothesize that functional differences among Tas2r copies in Myotis bats would increase their survival rate through preventing the ingestion of an elevated number of bitter‐tasting dietary toxins from their insect prey, which may have facilitated their adaptation to diverse habitats. Our study demonstrates functional changes of new Tas2r copies after lineage‐specific duplications in Myotis bats and highlights the potential role of taste perception in exploiting new environments.
Functional organization of face processing in the human superior temporal sulcus: a 7T high-resolution fMRI study

Abstract The superior temporal sulcus (STS) is a major component of the human face perception network, implicated in processing dynamic changeable aspects of faces. However, it remains unknown whether STS holds functionally segregated subdivisions for different categories of facial movements. We used high-resolution functional magnetic resonance imaging (fMRI) at 7T in 16 volunteers to compare STS activation with faces displaying angry or happy expressions, eye-gaze shifts and lip-speech movements. Combining univariate and multivariate analyses, we show a systematic topological organization within STS, with gaze-related activity predominating in the most posterior and superior sector, speech-related activity in the anterior sector and emotional expressions represented in the intermediate middle STS. Right STS appeared to hold a finer functional segregation between all four types of facial movements, and best discriminative abilities within the face-selective posterior STS (pSTS). Conversely, left STS showed greater overlap between conditions, with a lack of distinction between mouth movements associated to speech or happy expression and better discriminative abilities (for gaze and speech vs emotion conditions) outside pSTS. Differential sensitivity to upper (eye) or lower (mouth) facial features may contribute to, but does not appear to fully account for, these response patterns.
An Image Signal Accumulation Multi-Collection-Gate Image Sensor Operating at 25 Mfps with 32 × 32 Pixels and 1220 In-Pixel Frame Memory

The paper presents an ultra-high-speed image sensor for motion pictures of reproducible events emitting very weak light. The sensor is backside-illuminated. Each pixel is equipped with the multiple collection gates (MCG) at the center of the front side. Each collection gate is connected to an in-pixel large memory unit, which can accumulate image signals captured by repetitive imaging. The combination of the backside illumination, image signal accumulation, and slow readout from the in-pixel signal storage after an image capturing operation offers a very high sensitivity. Pipeline signal transfer from the MCG to the in-pixel memory units enables the sensor to achieve a large frame count and a very high frame rate at the same time. A test sensor was fabricated with a pixel count of 32 × 32 pixels. Each pixel is equipped with four collection gates, each connected to a memory unit with 305 elements; thus, with a total frame count of 1220 (305 × 4) frames. The test camera achieved 25 Mfps, while the sensor was designed to operate at 50 Mfps.
Efficient Bioinformatics Computations through GPU Accelerated Web Services

Web services have become a common means of addressing distributed task execution. There are several such services available at present that cater to the requirements in the domain of bioinformatics. However, it is challenging to find efforts made to utilize Graphics Processing Unit (GPU) accelerated binaries to optimize web services for bioinformatics analyses. Most of the bioinformatics related algorithms are compute-intensive due to their exponential time complexities. Corresponding execution times are further increased as the sequence databases grow rapidly. However, harnessing parallel computational power gives us a pathway to execute these algorithms and allows us to obtain results from web services more efficiently. The work presented in this paper demonstrates the utilization of web services to provide GPU accelerated bioinformatics computations for analytical purposes. A unified service platform is developed in the form of a collection of web services. It utilizes both GPU and CPU processing in order to perform compute-intensive tasks related to biological data analysis. Furthermore, the evaluation results show gains in speed over three folds with improving performance as the length of queries increases.
Reflexively-Fused Cylinders

The present paper introduces a method for designing 3D objects that are initially incomplete, but become complete when they are augmented by their mirror reflections. Physically, the mirror image is plane-symmetric with respect to the original object, but the perceived shape is not necessarily symmetric because of optical illusion. In the proposed method, a 2D shape that is not necessarily symmetric is divided into two halves, one of which is used to construct a solid object. When we place the solid object on a plane mirror, the other half is generated by the mirror, and thus, a whole shape is realized. In the present study, the design algorithm and examples are shown, and the condition for constructability is also presented.
Is Arthrodesis a Reliable Salvage Option following Two-Stage Revision for Suspected Infection in Proximal Tibial Replacements? A Multi-Institutional Study

Abstract The aim of this multicentric retrospective study was to verify whether knee arthrodesis (KA) is a viable reconstructive option after two-stage revision for infection of proximal tibia (PT) endoprosthetic reconstruction (EPR). Sixty patients who underwent a two-stage revision were included. Definitive EPR or a KA with a modular system was performed following consideration of soft tissue and extensor mechanism conditions. Patients were evaluated with Musculoskeletal Tumor Society Score and Oxford Knee Score. Implant survival was assessed on the basis of recurrence of infection. Five patients did not receive any reconstruction after the first stage. In 14 cases, a KA was performed, and in 41, an EPR was implanted. At 5 years follow-up, reinfection rate in the KA group was lower (10 vs. 17.5% in KA and EPR groups, respectively). In reinfected patients, the KA group had a reduced rate of amputation when compared with those with EPR (50 vs. 88%). Functional evaluation did not show any significant differences between the two groups. A successful KA using a modular implant can eradicate infection and allow preservation of the limb with good function and good pain relief in after two-stage revision for an infected PT EPR.
Tumor Growth Inhibition Modelling Based on Receptor Occupancy and Biomarker Activity of a New Bcl-2 Inhibitor in Mice

The Bcl-2 inhibitor S 55746 ((S)-N-(4-hydroxyphenyl)-3-(6-(3-(morpholinomethyl)-1,2,3,4-tetrahydroisoquinoline-2-carbonyl)benzo[d][1,3]dioxol-5-yl)-N-phenyl-5,6,7,8-tetrahydroindolizine-1-carboxamide) is able to restore apoptosis functions impaired by tumorigenesis in mice. Data from pharmacokinetic (PK), biomarker, and tumor growth studies in a xenograft mouse model were considered for population modeling. The aim of the modeling exercise was to link the kinetics of the drug to the biomarker and tumor-size time profiles to better understand its dose-effect relationship. The PK, caspase kinetics, and tumor dynamics were successfully characterized by the proposed pharmacokinetic-pharmacodynamic model. The nonlinear plasma PK was best described by a two-compartment disposition model with both saturable absorption and elimination. Caspase was activated above the effective drug-concentration threshold (CTHRE), at which near-maximal activity was reached. Increasing the dose did not increase the activation but better sustained it. Tumor growth followed a biphasic pattern, with caspase having an all-or-none inhibiting effect, consistent with the bistability property of the caspase pathway. For tumor eradication, the CTHRE in plasma was 2876 ng ml−1, and the relative caspase activity threshold (CaspTHRE) was 46.5. There was a strong relationship between the time spent above these thresholds and tumor growth inhibition. Tumor growth was inhibited by 50% when CaspTHRE was exceeded 13.8% of the time and when CTHRE was exceeded 8.1% of the time per dosing. This semimechanistic approach, based on experimental mice data and in vitro parameters, provides an interesting tool to quantify or simulate antitumor effects and, eventually, to plan phase 1 studies.
Comparative evaluation of autocontouring in clinical practice: A practical method using the Turing test

PURPOSE Automated techniques for estimating the contours of organs and structures in medical images have become more widespread and a variety of measures are available for assessing their quality. Quantitative measures of geometric agreement, for example, overlap with a gold-standard delineation, are popular but may not predict the level of clinical acceptance for the contouring method. Therefore, surrogate measures that relate more directly to the clinical judgment of contours, and to the way they are used in routine workflows, need to be developed. The purpose of this study is to propose a method (inspired by the Turing Test) for providing contour quality measures that directly draw upon practitioners' assessments of manual and automatic contours. This approach assumes that an inability to distinguish automatically produced contours from those of clinical experts would indicate that the contours are of sufficient quality for clinical use. In turn, it is anticipated that such contours would receive less manual editing prior to being accepted for clinical use. In this study, an initial assessment of this approach is performed with radiation oncologists and therapists. METHODS Eight clinical observers were presented with thoracic organ-at-risk contours through a web interface and were asked to determine if they were automatically generated or manually delineated. The accuracy of the visual determination was assessed, and the proportion of contours for which the source was misclassified recorded. Contours of six different organs in a clinical workflow were for 20 patient cases. The time required to edit autocontours to a clinically acceptable standard was also measured, as a gold standard of clinical utility. Established quantitative measures of autocontouring performance, such as Dice similarity coefficient with respect to the original clinical contour and the misclassification rate accessed with the proposed framework, were evaluated as surrogates of the editing time measured. RESULTS The misclassification rates for each organ were: esophagus 30.0%, heart 22.9%, left lung 51.2%, right lung 58.5%, mediastinum envelope 43.9%, and spinal cord 46.8%. The time savings resulting from editing the autocontours compared to the standard clinical workflow were 12%, 25%, 43%, 77%, 46%, and 50%, respectively, for these organs. The median Dice similarity coefficients between the clinical contours and the autocontours were 0.46, 0.90, 0.98, 0.98, 0.94, and 0.86, respectively, for these organs. CONCLUSIONS A better correspondence with time saving was observed for the misclassification rate than the quantitative contour measures explored. From this, we conclude that the inability to accurately judge the source of a contour indicates a reduced need for editing and therefore a greater time saving overall. Hence, task-based assessments of contouring performance may be considered as an additional way of evaluating the clinical utility of autosegmentation methods.
A novel reliability analysis approach for component‐based software based on the complex network theory

Traditional software reliability evaluation approaches lack the analysis of intercomponent interactions of component‐based software systems, necessitating software reliability evaluation based on the reliabilities of the overall architecture and each component. In this paper, we propose a reliability evaluation model and an importance assessment technique for component‐based software based on the complex network theory. The components of a software system are identified and divided into 2 categories, input/output components and ordinary components. Then, the impact factors of ordinary components and input/output components are calculated based on the complex network theory and execution probabilities, respectively. Finally, the impact factors are used to evaluate the reliability of the software system and assess the importance of each component. Experimental results show that the proposed approach is able to estimate the reliability of component‐based software and provide relative priorities of the components that can be used to guide the system reliability optimization.
The Rosario dataset: Multisensor data for localization and mapping in agricultural environments

In this paper we present the Rosario dataset, a collection of sensor data for autonomous mobile robotics in agricultural scenes. The dataset is motivated by the lack of realistic sensor readings gathered by a mobile robot in such environments. It consists of six sequences recorded in soybean fields showing real and challenging cases: highly repetitive scenes, reflection, and burned images caused by direct sunlight and rough terrain among others. The dataset was conceived in order to provide a benchmark and contribute to the agricultural simultaneous localization and mapping (SLAM)/odometry and sensor fusion research. It contains synchronized readings of several sensors: wheel odometry, inertial measurement unit (IMU), stereo camera, and a Global Positioning System real-time kinematics (GPS-RTK) system. The dataset is publicly available from http://www.cifasis-conicet.gov. ar/robot/.
Maintaining Canonical Form After Edge Deletion

Waddle is a research intermediate-form optimizer that strictly maintains a canonical form similar to the loop-simplify form used in LLVM. The properties of this canonical form simplify movement of instructions to the edges of loops and often localize the effect on variables to the loop in which they are defined. The guarantee of canonical form preservation allows program transformations to rely on the presence of certain program properties without a necessary sanity-check or recalculation pre-step and does not impose an order of transformations in which reconstruction passes must be inserted. In this paper, we present a form-preserving edge deletion operation, in which a provably unreachable branch between two basic blocks is removed from the control flow graph. Additionally, we showa distinct application of the block ejection operation, a core procedure used for loop body reconstruction, as utilized in a function inlining transformation.
Energy Expenditure as a Function of Activity Level After Spinal Cord Injury: The Need for Tetraplegia-Specific Energy Balance Guidelines

The World Health Organization recognizes obesity as a global and increasing problem for the general population. Because of their reduced physical functioning, people with spinal cord injury (SCI) face additional challenges for maintaining an appropriate whole body energy balance, and the majority with SCI are overweight or obese. SCI also reduces exercise capacity, particularly in those with higher-level injury (tetraplegia). Tetraplegia-specific caloric energy expenditure (EE) data is scarce. Therefore, we measured resting and exercise-based energy expenditure in participants with tetraplegia and explored the accuracy of general population-based energy use predictors. Body composition and resting energy expenditure (REE) were measured in 25 adults with tetraplegia (C4/5 to C8) and in a sex-age-height matched group. Oxygen uptake, carbon dioxide production, heart rate, perceived exertion, and exercise intensity were also measured in 125 steady state exercise trials. Those with motor-complete tetraplegia, but not controls, had measured REE lower than predicted (mean = 22% less, p < 0.0001). REE was also lower than controls when expressed per kilogram of lean mass. Nine had REE below 1200 kcal/day. We developed a graphic compendium of steady state EE during arm ergometry, wheeling, and hand-cycling. This compendium is in a format that can be used by persons with tetraplegia for exercise prescription (calories, at known absolute intensities). EE was low (55–450 kcal/h) at the intensities participants with tetraplegia were capable of maintaining. If people with tetraplegia followed SCI-specific activity guidelines (220 min/week) at the median intensities we measured, they would expend 563–1031 kcal/week. Participants with tetraplegia would therefore require significant time (4 to over 20 h) to meet a weekly 2000 kcal exercise target. We estimated total daily EE for a range of activity levels in tetraplegia and compared them to predicted values for the general population. Our analysis indicated that the EE values for sedentary through moderate levels of activity in tetraplegia fall well below predicted sedentary levels of activity for the general population. These findings help explain sub-optimal responses to exercise interventions after tetraplegia, and support the need to develop tetraplegia-specific energy-balance guidelines that reflects their unique EE situation.
Population structure, genetic diversity and selection signatures within seven indigenous Pakistani goat populations

Goat farming in Pakistan depends on indigenous breeds that have adapted to specific agro-ecological conditions. Pakistan has a rich resource of goat breeds, and the genetic diversity of these goat breeds is largely unknown. In this study, genetic diversity and population structure were characterized from seven indigenous goat breeds using the goat 50K SNP chip. The genetic diversity analysis showed that Bugi toori goats have the highest inbreeding level, consistent with the highest linkage disequilibrium, lowest diversity and long run of heterozygosity segments. This indicates that this breed should be prioritized in future conservation activities. The population structure analysis revealed four fairly distinct clusters (including Bugi toori, Bari, Black Tapri and some Kamori) and three other breeds that are seemingly the results of admixture between these or related groups (some Kamori, Pateri, Tapri and White Tapri). The selection signatures were evaluated in each breed. A total of 2508 putative selection signals were reported. The 26 significant windows were identified in more than four breeds, and selection signatures spanned several genes that directly or indirectly influence traits included coat colour variation (KIT), reproduction (BMPR1B, GNRHR, INSL6, JAK2 and EGR4), body size (SOCS2), ear size (MSRB3) and milk composition (ABCG2, SPP1, CSN1S2, CSN2, CSN3 and PROLACTIN).