Miracle-dz/UniFAR-FTUs huggingface dataset:
Male-female differences in aortic valve and combined aortic valve/coronary surgery: a national cohort study in the Netherlands

Objective The outcome of female patients after adult cardiac surgery has been reported to be less favourable compared with the outcome of male patients. This study compares men with women with respect to patient and procedural characteristics and early mortality in a contemporary national cohort of patients who underwent aortic valve (AV) and combined aortic valve/coronary (CABG/AV) surgery. Methods All patients who underwent AV (n=8717, 56% male) or a combined CABG/AV surgery (n=5867, 67% male) in the Netherlands between January 2007 and December 2011 were included. Results In both groups, women were generally older than men (p<0.001) and presented with higher logistic EuroSCORES. In isolated AV surgery, men and women had comparable in-hospital mortality (OR 1.20, 95% CI 0.90 to 1.61; p=0.220). In concomitant CABG/AV surgery, in-hospital mortality was higher in women compared with men (OR 2.00, 95% CI 1.44 to 2.79; p<0.001). The area under the curve for logistic EuroSCORE 1 was systematically higher for men versus women in isolated AV surgery 0.82 (95% CI 0.78 to 0.86) vs 0.75 (95% CI 0.69 to 0.80) and in concomitant CABG/AV surgery 0.78 (95% CI 0.73 to 0.82) vs 0.69 (95% CI 0.63 to 0.74). Finally, (the weight of) risk factors associated with in-hospital mortality differed between men and women. Conclusions There are substantial male-female differences in patient presentation and procedural aspects in isolated AV and concomitant CABG/AV surgery in the Netherlands. Further studies are necessary to explore the mechanisms underlying the observed differences. In addition, the observation that standard risk scores perform worse in women warrants exploration of male-female specific risk models for patients undergoing cardiac surgery.Brief title:
3D Reconstruction in an Illumination Dome

The illumination dome provides a stable environment for photography of cultural heritage objects with multi-directional lighting. Photogrammetry for 3D reconstruction, on the other hand, is usually based on an image set taken under ambient lighting by a hand-held camera moved to many positions around the object. This study investigated whether the photogrammetric image sets could be captured entirely within the dome and compared their accuracy with laser scan data.
Stepwise oral immunotherapy for 10 days in an egg-white allergy mouse model did not ameliorate the severity of allergy but induced the production of allergen-specific IgA

ABSTRACT We examined whether the stepwise oral immunotherapy (OIT) for 10 days ameliorates the severity of allergy and the biomarkers in an allergy mouse model. The OIT could not protect anaphylaxis symptoms after allergen challenges but promote the production of antibodies, especially allergen-specific IgA. It was suggested that this OIT influenced the function of immuno response against the allergen. Abbreviations: EW: egg white; IFC: intraperitoneal food challenge; IFN-γ: interferon-γ; IL: interleukin; OVA: ovalbumin; OM: ovomucoid; OFC: oral food challenge; OIT: oral immunotherapy.
Jagged1/Notch2 controls kidney fibrosis via Tfam-mediated metabolic reprogramming

While Notch signaling has been proposed to play a key role in fibrosis, the direct molecular pathways targeted by Notch signaling and the precise ligand and receptor pair that are responsible for kidney disease remain poorly defined. In this study, we found that JAG1 and NOTCH2 showed the strongest correlation with the degree of interstitial fibrosis in a genome wide expression analysis of a large cohort of human kidney samples. RNA sequencing analysis of kidneys of mice with folic acid nephropathy, unilateral ureteral obstruction, or APOL1-associated kidney disease indicated that Jag1 and Notch2 levels were higher in all analyzed kidney fibrosis models. Mice with tubule-specific deletion of Jag1 or Notch2 (Kspcre/Jag1flox/flox, and Kspcre/Notch2flox/flox) had no kidney-specific alterations at baseline, but showed protection from folic acid induced kidney fibrosis. Tubule-specific genetic deletion of Notch1 and global knock-out of Notch3 had no effect on fibrosis. In vitro chromatin immunoprecipitation experiments and genome-wide expression studies identified the mitochondrial transcription factor A (Tfam) as a direct Notch target. Re-expression of Tfam in tubule cells prevented Notch-induced metabolic and profibrotic reprogramming. Kidney tubule specific deletion of Tfam resulted in perinatal lethality. In summary, Jag1/Notch2 plays a key role in kidney fibrosis development by regulating Tfam expression and metabolic reprogramming.
The Role of Amygdala in Patients With Euthymic Bipolar Disorder During Resting State

The current study aims to explore the functional changes of the amygdala in patients with euthymic Bipolar Disorder (BD) using resting state fMRI (rs-fMRI). Twenty-one euthymic patients with bipolar disorder and 28 healthy controls participated in this study. Two of the euthymic patients with BD and three of the healthy controls were excluded due to excessive head motion. We found that patients with euthymia (38.79 ± 12.03) show higher fALFF (fractional Amplitude of low-frequency fluctuation) value of the amygdala (t = 2.076, P = 0.044), and lower functional connectivity between the amygdala and supplementary motor area (p < 0.01, GRF corrected) than healthy controls (33.40 ± 8.21). However, euthymic patients did not show a differential activity in ReHo (Regional Homogeneity) and gray matter of the amygdala region as compared to healthy controls. Thus, despite the absence of clinical symptoms in euthymic patients with BD, the amygdala functional activity and its connectivity to other brain regions remain altered. Further investigation of negative emotions and social functioning in euthymic patients with BD are needed and can help pave the way for a better understanding of BD psychopathology.
Interflow: interprocedural flow-sensitive type inference and method duplication

Scala heavily relies on a number of object-oriented abstractions to support its feature-rich collections library. There are known techniques that optimize those abstractions away in just-in-time (JIT) compilers, but applying them in the ahead-of-time (AOT) setting is problematic. Profile-guided optimization (PGO) lets AOT compilers apply some of the same optimizations that JIT compilers employ, but it comes at a high complexity cost. In this paper, we introduce Interflow, an alternative approach towards ahead-of-time optimization of Scala programs which relies on interprocedural flow-sensitive type inference and method duplication. Our evaluation shows that an Interflow-based optimizing compiler built on top of the Scala Native toolchain outperforms existing PGO-based optimizing compilers for Scala. Moreover, we demonstrate that Interflow and PGO can be combined to achieve further improvements. On our benchmarks, with both Interflow and PGO enabled, the Scala Native toolchain approaches the performance of the HotSpot JVM.
Combined functions of two RRMs in Dead‐end1 mimic helicase activity to promote nanos1 translation in the germline

Dead‐end1 (Dnd1) expression is restricted to the vertebrate germline where it is believed to activate translation of messenger RNAs (mRNAs) required to protect and promote that unique lineage. Nanos1 is one such germline mRNA whose translation is blocked by a secondary mRNA structure within the open reading frame (ORF). Dnd1 contains a canonical RNA recognition motif (RRM1) in its N‐terminus but also contains a less conserved RRM2. Here we provide a mechanistic picture of the nanos1 mRNA–Dnd1 interaction in the Xenopus germline. We show that RRM1, but not RRM2, is required for binding nanos1. Similar to the zebrafish homolog, Xenopus Dnd1 possesses ATPase activity. Surprisingly, this activity appears to be within the RRM2, different from the C‐terminal region where it is found in zebrafish. More importantly, we show that RRM2 is required for nanos1 translation and germline survival. Further, Dnd1 functions as a homodimer and binds nanos1 mRNA just downstream of the secondary structure required for nanos1 repression. We propose a model in which the RRM1 is required to bind nanos1 mRNA while the RRM2 is required to promote translation through the action of ATPase. Dnd1 appears to use RRMs to mimic the function of helicases.
Targeting intramolecular proteinase NS2B/3 cleavages for trans-dominant inhibition of dengue virus

Significance Inhibitors of dengue virus, a mosquito-borne pathogen, are urgently needed. Virally encoded NS2B/3, a two-subunit serine proteinase, is responsible for many cleavages within the viral polyprotein. We demonstrate that two cleavage sites flanking NS3 and one that is internal are self-processing. This strict intramolecular cleavage dictates that, if uncleaved precursors can inhibit viral growth, this phenotype will be trans-dominant. Indeed, a mutation that abrogates one of the self-processing sites caused trans-dominant inhibition of wild-type virus. This site is also the most susceptible to a dengue proteinase inhibitor, providing a compelling rationale for its efficacy. We suggest that explicit targeting of specific intramolecular cleavage sites will be an effective antiviral strategy that can suppress multiple variants in an intracellular quasispecies. Many positive-strand RNA viruses translate their genomes as single polyproteins that are processed by host and viral proteinases to generate all viral protein products. Among these is dengue virus, which encodes the serine proteinase NS2B/3 responsible for seven different cleavages in the polyprotein. NS2B/3 has been the subject of many directed screens to find chemical inhibitors, of which the compound ARDP0006 is among the most effective at inhibiting viral growth. We show that at least three cleavages in the dengue polyprotein are exclusively intramolecular. By definition, such a cis-acting defect cannot be rescued in trans. This creates the possibility that a drug-susceptible or inhibited proteinase can be genetically dominant, inhibiting the outgrowth of drug-resistant virus via precursor accumulation. Indeed, an NS3-G459L variant that is incapable of cleavage at the internal NS3 junction dominantly inhibited negative-strand RNA synthesis of wild-type virus present in the same cell. This internal NS3 cleavage site is the junction most inhibited by ARDP0006, making it likely that the accumulation of toxic precursors, not inhibition of proteolytic activity per se, explains the antiviral efficacy of this compound in restraining viral growth. We argue that intramolecularly cleaving proteinases are promising drug targets for viruses that encode polyproteins. The most effective inhibitors will specifically target cleavage sites required for processing precursors that exert trans-dominant inhibition.
Gamification in Software Testing: A Characterization Study

Context: Testing is a fundamental activity in the software development cycle. Revealing software faults is its main objective. Despite that, testing is considered unpleasant, dull and tedious. As a result, there is a lack of expertise among professionals while many projects fail. Gamification is a promising way to address testing issues; it is a new trend being used mostly to increase motivation, engagement and performance with the use of game elements in non-game contexts. Objective: To describe results of a study that aimed to characterize how gamification has been explored to support software testing. Method: The studies that compose our baseline for analysis and discussion were obtained through a systematic mapping carried out following a research protocol. To retrieve relevant literature, we applied automatic search and backward snowballing. At the end, we selected 15 studies that we analyzed and classified according to six perspectives: application context, used gamifcation elements, gamification goals, testing techniques, testing levels, and testing process phases. Results: The most used gamification elements are points, leader boards, and levels, and unit testing and functional testing are the level and technique most addressed in the studies, respectively. Conclusion: Gamification is a rising research topic, especially in the software testing field. The increasing interest for gamification has the potential do lead to positive outcomes. The map presented in this paper can be a useful resource for the identification of gaps and for triggering new research initiatives.
Estimating the Physical Distance between Two Locations with Wi-Fi Received Signal Strength Information Using Obstacle-aware Approach

This study presents a new method for estimating the physical distance between two locations using Wi-Fi signals from APs observed by Wi-Fi signal receivers such as smartphones. We assume that a Wi-Fi signal strength vector is observed at location A and another Wi-Fi signal strength vector is observed at location B. With these two Wi-Fi signal strength vectors, we attempt to estimate the physical distance between locations A and B. In this study, we estimate the physical distance based on supervised machine learning and do not use labeled training data collected in an environment of interest. Note that, because signal propagation is greatly affected by obstacles such as walls, precisely estimating the distance between locations A and B is difficult when there is a wall between locations A and B. Our method first estimates whether or not there is a wall between locations A and B focusing on differences in signal propagation properties between 2.4 GHz and 5 GHz signals, and then estimates the physical distance using a neural network depending on the presence of walls. Because our approach is based on Wi-Fi signal strengths and does not require a site survey in an environment of interest, we believe that various context-aware applications can be easily implemented based on the distance estimation technique such as low-cost indoor navigation, the analysis and discovery of communities and groups, and Wi-Fi geo-fencing. Our experiment revealed that the proposed method achieved an MAE of about 3-4 meters and the performance is almost identical to an environment-dependent method, which is trained on labeled data collected in the same environment.
Studying believability assessment in racing games

Believability is a hard concept to define in video games. It depends on how and what one considers to be "believable", which is often very subjective. In previous years, several researchers have tried to find ways of assessing such concepts in games through Turing Tests on agents, which were programmed to behave like a human instead of focusing only on winning. Examples are the Mario AI Competition and the 2K BotPrize. Given the small pool of explored parameters and a focus on programming the bots rather than the assessment, in this paper we present work examining different methods of evaluating believability in video games. We explore believability through recorded gameplay and allow judges to analyze it. However, we use different parameters - such as ranking rather than binary answers - for asking how human-like the presented behaviours are. The objective of this study is to analyze the different ways believability can be assessed, for humans and non-player characters (NPCs) by comparing how results between them and scores are affected in both when changing the parameters. In order to provide a more general analysis, the study is carried out using two different racing games rather than one. Results show that these parameters have indeed changed the overall results of the study and how important it is to be able to generalize these concepts in game AI, given how clear it is that believability is dependent on genre, game and even the design of the questionnaire.
Tpr regulates the total number of nuclear pore complexes per cell nucleus

In this study, McCloskey et al. investigated the underlying mechanisms that control how many nuclear transport channels are assembled into a given nuclear envelope. Their results show that depletion of the NPC basket protein Tpr, but not Nup153, dramatically increases the total NPC number in various cell types and provide insight into a critical role of the nucleoporin Tpr in coordinating signal transduction pathways during cell proliferation and the dynamic organization of the nucleus.
Effects of Formulation and Process Variables on Gastroretentive Floating Tablets with A High-Dose Soluble Drug and Experimental Design Approach

To develop sustained release gastro-retentive effervescent floating tablets (EFT), a quality-based experimental design approach was utilized during the composing of a hydrophilic matrix loaded with a high amount of a highly water-soluble model drug, metformin HCl. Effects of the amount of polyethylene oxide WSR 303 (PEO), sodium bicarbonate, and tablet compression force were used as independent variables. Various times required to release the drug, tablet tensile strength, floating lag time, tablet ejection force, and tablet porosity, were selected as the responses. Polymer screening showed that PEO had the highest gel strength among the various tested polymers. Sodium bicarbonate had the most significant effect on the release rate and floating lag time by retarding the rate from the hydrophilic matrices, whilst tablet compression force and PEO exerted the greatest influence on tablet properties (p < 0.0001). The design space was built in accordance with the drug release profiles, tensile strength, and floating lag time, following failure probability analysis using Monte Carlo simulations. The kinetic modeling revealed that the release mechanism was best described by the Korsmeyer-Peppas model. Overall, the current study provided a perspective on the systematic approach of gastro-retentive EFT, loaded with highly water-soluble drugs by applying quality by design concepts.
TeamSense

Continuous monitoring with unobtrusive wearable social sensors is becoming a popular method to assess individual affect states and team effectiveness in human research. A large number of applications have demonstrated the effectiveness of applying wearable sensing in corporate settings; for example, in short periodic social events or in a university campus. However, little is known of how we can automatically detect individual affect and group cohesion for long duration missions. Predicting negative affect states and low cohesiveness is vital for team missions. Knowing team members' negative states allows timely interventions to enhance their effectiveness. This work investigates whether sensing social interactions and individual behaviors with wearable sensors can provide insights into assessing individual affect states and group cohesion. We analyzed wearable sensor data from a team of six crew members who were deployed on a four-month simulation of a space exploration mission at a remote location. Our work proposes to recognize team members' affect states and group cohesion as a binary classification problem using novel behavior features that represent dyadic interaction and individual activities. Our method aggregates features from individual members into group levels to predict team cohesion. Our results show that the behavior features extracted from the wearable social sensors provide useful information in assessing personal affect and team cohesion. Group task cohesion can be predicted with a high performance of over 0.8 AUC. Our work demonstrates that we can extract social interactions from sensor data to predict group cohesion in longitudinal missions. We found that quantifying behavior patterns including dyadic interactions and face-to-face communications are important in assessing team process.
Adaptive fuzzy clustering-based texture analysis for classifying liver cancer in abdominal CT images

Segmentation of diseased liver in abdominal CT images is a challenging task due to variations in shapes, tissue similarity between adjoining organs. We propose an automatic detection technique that integrates the fuzzy clustering with adaptive thresholding for segmenting the liver and finding the tumour region in abdominal CT images. Various features like texture features, morphological features and statistical features have been extracted from the output images and used as input to the neural network classifier to classify the malignant and benign tumour of the liver. The method was evaluated in a series of 45 images collected from medical image computing and computer assisted intervention (MICCAI) database and the efficiency is tested in terms of sensitivity, specificity, and accuracy. We obtained the accuracy of 97.82%, 95.74% in BPN and LVQ and higher accuracy of 98.82% is achieved with PNN in detecting tumours which are comparable to published results.
High‐throughput identification of factors promoting neuronal differentiation of human neural progenitor cells in microscale 3D cell culture

Identification of conditions for guided and specific differentiation of human stem cell and progenitor cells is important for continued development and engineering of in vitro cell culture systems for use in regenerative medicine, drug discovery, and human toxicology. Three‐dimensional (3D) and organotypic cell culture models have been used increasingly for in vitro cell culture because they may better model endogenous tissue environments. However, detailed studies of stem cell differentiation within 3D cultures remain limited, particularly with respect to high‐throughput screening. Herein, we demonstrate the use of a microarray chip‐based platform to screen, in high‐throughput, individual and paired effects of 12 soluble factors on the neuronal differentiation of a human neural progenitor cell line (ReNcell VM) encapsulated in microscale 3D Matrigel cultures. Dose–response analysis of selected combinations from the initial combinatorial screen revealed that the combined treatment of all‐trans retinoic acid (RA) with the glycogen synthase kinase 3 inhibitor CHIR‐99021 (CHIR) enhances neurogenesis while simultaneously decreases astrocyte differentiation, whereas the combined treatment of brain‐derived neurotrophic factor and the small azide neuropathiazol enhances the differentiation into neurons and astrocytes. Subtype specification analysis of RA‐ and CHIR‐differentiated cultures revealed that enhanced neurogenesis was not biased toward a specific neuronal subtype. Together, these results demonstrate a high‐throughput screening platform for rapid evaluation of differentiation conditions in a 3D environment, which will aid the development and application of 3D stem cell culture models.