Miracle-dz/UniFAR-FTUs huggingface dataset:
Deadeye: A Novel Preattentive Visualization Technique Based on Dichoptic Presentation

Preattentive visual features such as hue or flickering can effectively draw attention to an object of interest – for instance, an important feature in a scientific visualization. These features appear to pop out and can be recognized by our visual system, independently from the number of distractors. Most cues do not take advantage of the fact that most humans have two eyes. In cases where binocular vision is applied, it is almost exclusively used to convey depth by exposing stereo pairs. We present Deadeye, a novel preattentive visualization technique based on presenting different stimuli to each eye. The target object is rendered for one eye only and is instantly detected by our visual system. In contrast to existing cues, Deadeye does not modify any visual properties of the target and, thus, is particularly suited for visualization applications. Our evaluation confirms that Deadeye is indeed perceived preattentively. We also explore a conjunction search based on our technique and show that, in contrast to 3D depth, the task cannot be processed in parallel.
Measuring Social Capital in the Prison Setting

Social capital has been associated with improved health outcomes. Measures of social capital have been developed specifically for different population groups, cultures, and contexts; however, there is no readily available measure for use among inmates in the prison setting. This study sought to translate a community concept into the prison setting through the development and piloting of the Inmate Social Capital Questionnaire (ISCQ). Thirty male inmates (living with hepatitis C) participated in the pilot phase of the ISCQ (n = 23 sentenced and n = 7 held on remand). Dimensions of social capital were influenced by length of incarceration (time already served as well as time to release), connections with family, and duration at current prison.
Interactive Visualization of 3D Histopathology in Native Resolution

We present a visualization application that enables effective interactive visual analysis of large-scale 3D histopathology, that is, high-resolution 3D microscopy data of human tissue. Clinical work flows and research based on pathology have, until now, largely been dominated by 2D imaging. As we will show in the paper, studying volumetric histology data will open up novel and useful opportunities for both research and clinical practice. Our starting point is the current lack of appropriate visualization tools in histopathology, which has been a limiting factor in the uptake of digital pathology. Visualization of 3D histology data does pose difficult challenges in several aspects. The full-color datasets are dense and large in scale, on the order of $100,000\times 100,000\times 100$ voxels. This entails serious demands on both rendering performance and user experience design. Despite this, our developed application supports interactive study of 3D histology datasets at native resolution. Our application is based on tailoring and tuning of existing methods, system integration work, as well as a careful study of domain specific demands emanating from a close participatory design process with domain experts as team members. Results from a user evaluation employing the tool demonstrate a strong agreement among the 14 participating pathologists that 3D histopathology will be a valuable and enabling tool for their work.
Establishment and characterization of human theca stem cells and their differentiation into theca progenitor cells

In this study, we have characterized the human theca stem cells (hTSCs) and their differentiation into human theca progenitor cells (hTPCs). hTSCs were isolated from the theca layer of small antral follicles (3‐5 mm in size). Alkaline phosphatase activity, cell cycle status, and cell surface markers were evaluated in hTSCs. The differentiation potential of these cells was investigated via differentiation of hTSCs into adipocyte‐, osteocyte‐, and chondrocyte‐like cells. The cells also differentiated into hTPCs. The hTSCs were morphologically similar to human fibroblast cells (hFCs). Some of the cells were positive for alkaline phosphatase activity. The expression of OCT4 in hTSCs was significantly higher than that of human bone marrow mesenchymal stem cells (hBMSCs) and hFCs. To determine the type of OCT4 (isoform A or B), RT PCR was performed. The data showed that OCT‐4A was expressed in hBMSCs and hTSCs but immunofluorescence analyses using the OCT‐4A‐specific and OCT4 antibodies did not show OCT‐4A protein. In addition, cell cycle status showed that the number of hTSCs in the S phase was significantly higher than that of hFCs. CD29, CD44, CD73, CD90, and CD105 were present in hTSCs. Osteogenic, adipogenic, and chondrogenic differentiation was confirmed by cytochemical staining and lineage‐specific transcripts. Our results showed that specific Dulbecco modified Eagle medium F12 culture medium results in the presence of hTPC markers. hTPCs displayed lipid droplets, appropriate gene expression, and secreted dehydroepiandrosterone and estradiol. hTSCs have the ability to differentiate into mesenchymal lineages and hTPCs. This study may provide a novel in vitro model for further investigation of theca cell maturation and differentiation.
Precise Extraction of Malicious Behaviors

In recent years, the damage cost caused by malwares is huge. Thus, malware detection is a big challenge. The task of specifying malware takes a huge amount of time and engineering effort since it currently requires the manual study of the malicious code. Thus, in order to avoid the tedious manual analysis of malicious codes, this task has to be automatized. To this aim, we propose in this work to represent malicious behaviors using extended API call graphs, where nodes correspond to API function calls, edges specify the execution order between the API functions, and edge labels indicate the dependence relation between API functions parameters. We define new static analysis techniques that allow to extract such graphs from programs, and show how to automatically extract, from a set of malicious and benign programs, an extended API call graph that represents the malicious behaviors. Finally, We show how this graph can be used for malware detection. We implemented our techniques and obtained encouraging results: 95.66% of detection rate with 0% of false alarms.
Watset: Local-Global Graph Clustering with Applications in Sense and Frame Induction

We present a detailed theoretical and computational analysis of the Watset meta-algorithm for fuzzy graph clustering, which has been found to be widely applicable in a variety of domains. This algorithm creates an intermediate representation of the input graph that reflects the “ambiguity” of its nodes. Then, it uses hard clustering to discover clusters in this “disambiguated” intermediate graph. After outlining the approach and analyzing its computational complexity, we demonstrate that Watset shows competitive results in three applications: unsupervised synset induction from a synonymy graph, unsupervised semantic frame induction from dependency triples, and unsupervised semantic class induction from a distributional thesaurus. Our algorithm is generic and can be also applied to other networks of linguistic data.
Knowledge, attitudes and beliefs on contributing factors among low back pain patients attending outpatient physiotherapy treatment in Malawi

Background Low back pain (LBP) affects many people globally. Its aetiology is not clear. Patients lack knowledge of its contributing factors and have negative perception about their LBP. This study aimed to identify knowledge, attitudes and beliefs regarding the perceived contributing factors to LBP among patients attending physiotherapy outpatient departments in Malawi. This information can possibly facilitate planning of a LBP education programme in Malawi. Methods A quantitative cross-sectional survey was conducted, using a six-part self-administered questionnaire with questions on demographic information, participants’ attitudes and beliefs regarding their LBP, knowledge about the course and causes of LBP, beliefs regarding nine contributing factors to LBP (identified in a Delphi study) and the sources of the participants’ knowledge. Data were analysed descriptively using the Statistical Package for Social Sciences (version 19.0). A Chi-square test was used to determine any association between variables (alpha 0.05). All ethical procedures were strictly followed. Results Most participants (186, 91.2 %) did not manage to answer all six questions regarding knowledge correctly and were regarded as ‘partially knowledgeable’ about the course and causes of LBP. More than half (67%) portrayed negative attitudes and beliefs about LBP in general. The findings also showed a statistically significant relationship between knowledge, attitudes and beliefs (p = 0.04). Conclusion This study highlighted that many patients with LBP in Malawi are not adequately knowledgeable about LBP and hold negative attitudes and beliefs regarding their LBP. Therefore, LBP management programmes in Malawi should include education programmes aimed at empowering patients with knowledge regarding LBP, as well as changing their negative attitudes and beliefs about their pain. Patients’ understanding of the cause and nature of their pain may enhance the achievement of treatment goals.
Neuritis and vinblastine-induced axonal transport disruption lead to signs of altered dorsal horn excitability

Background Many patients with neuropathic pain present without signs of nerve injury on routine clinical examination. Some of these patients may have inflamed peripheral nerves (neuritis). In this study, we have examined whether neuritis causes changes within the dorsal horn that may contribute to a central pain mechanism. Comparisons have been made to a model of axonal transport disruption induced using vinblastine, since neuritis disrupts such processes. Results At the peak of cutaneous hypersensitivities, recordings from wide dynamic range neurons revealed increases in wind-up following neuritis but not vinblastine treatment. Ongoing activity from these neurons was unchanged. Vinblastine treatment caused a reduction in the responses of wide dynamic range neurons to noxious mechanical stimulation of the receptive field. The response of neurons to innocuous mechanical stimulation was also reduced in wide dynamic range neurons that were at a depth ≥550 µm following vinblastine treatment. An examination of the superficial dorsal horn revealed an increase in c-Fos–positive neurons in both groups following electrical stimulation of the sciatic nerve. The area of dorsal horn expressing substance P was also decreased following vinblastine treatment. Conclusion These findings indicate that a minor nerve insult, such as neuritis, can lead to changes within the dorsal horn that are consistent with a central neuropathic pain mechanism.
Moving Into Action: The Master Key to Patient Education

Background: Illness and hospitalization are situations that increase the need for assistance and education. Poor education is currently the most common source of patient complaints in the health sector in Iran. Purpose: The aim of this study was to explore the perspectives and recommendations of nurses to improve patient education. Methods: This research followed a qualitative exploratory design with a qualitative content analysis approach. The study participants, including eight head nurses and 16 staff nurses, were selected through purposive sampling. The data were collected through semistructured interviews, focus group sessions, and observations during 2016. Results: Coding and analysis of the data generated one main theme, two subthemes, and four categories. The subthemes were “strengthen total commitment” and “reconstructing the infrastructure,” and the categories were “developing motivational factors,” “facilitating change by every impetus,” “systematizing activities,” and “contextual promotion. ” Conclusions: Study findings provide a complete picture of patient education and challenge managers to develop new strategies to plan and implement appropriate changes.
The impact of model assumptions in scalar‐on‐image regression

Complex statistical models such as scalar‐on‐image regression often require strong assumptions to overcome the issue of nonidentifiability. While in theory, it is well understood that model assumptions can strongly influence the results, this seems to be underappreciated, or played down, in practice. This article gives a systematic overview of the main approaches for scalar‐on‐image regression with a special focus on their assumptions. We categorize the assumptions and develop measures to quantify the degree to which they are met. The impact of model assumptions and the practical usage of the proposed measures are illustrated in a simulation study and in an application to neuroimaging data. The results show that different assumptions indeed lead to quite different estimates with similar predictive ability, raising the question of their interpretability. We give recommendations for making modeling and interpretation decisions in practice based on the new measures and simulations using hypothetic coefficient images and the observed data.
Case Report: Managing the postoperative exposure of a non-resorbable membrane surgically

Alveolar ridge deformities can be caused by several factors. Managing alveolar deformities prior to implant placement is essential to increase bone width, height or both. Several techniques and materials are now available to perform ridge augmentation procedures. The postoperative exposure of the membrane is the most frequent postoperative complications of ridge augmentation procedures. The present case describes the horizontal ridge augmentation procedure and the outcome of surgical attempt to manage post-operative membrane exposure, and shows the unpredictability of managing postoperative membrane exposure surgically.
Approximation of Time-Consuming Simulation Based on Generative Adversarial Network

A simulation model often has parameters to be calibrated through evaluation against data obtained by experiments. The process could be prohibitively expensive if the execution of the model requires huge computational resources and/or the parameter search space is vast. For technology CAD (TCAD) topography simulation, used in semiconductor manufacturing, this is exactly the case. We present a method to replace the simulation with approximate computation based on Generative Adversarial Network. The method receives pairs of a simulation parameter set and a simulation result image as training examples and learns a model to mimic the simulation. Unlike most GANbased models, its learning is carried out in a supervised manner. We evaluate its performance by cross-validation and comparison with a human expert. Despite the small size of the available dataset, our method successfully generates an image close to the ground truth in 71% of the cases and qualitatively reproduces the educated guesses of the human expert on the behavior of the simulator.
Phosphoproteomic analysis of chimeric antigen receptor signaling reveals kinetic and quantitative differences that affect cell function

How potently CAR T cells with CD28 or 4-1BB costimulatory domains stimulate intracellular signaling correlates with treatment efficacy. Strength limits potency T cells engineered to express chimeric antigen receptors (CARs) may represent a curative treatment for B cell malignancies. To understand how to optimize these therapies, Salter et al. used phosphoproteomics to compare the activities of CARs encoding CD28 or 4-1BB costimulatory domains in primary human T cells. Although CARs with CD28 domains provoked more robust signaling than did CARs with 4-1BB domains (due to constitutive Lck association), both CARs activated overlapping T cell signaling pathways. However, CARs that initiated stronger signals also exhibited increased T cell dysfunction, which reduced their potency in a mouse model of lymphoma. These data indicate that the CAR costimulatory domain does not predict the signaling pathways activated in CAR T cells but instead suggest that reducing the strength of signaling may counterintuitively enhance CAR T cell therapeutic efficacy. Chimeric antigen receptors (CARs) link an antigen recognition domain to intracellular signaling domains to redirect T cell specificity and function. T cells expressing CARs with CD28/CD3ζ or 4-1BB/CD3ζ signaling domains are effective at treating refractory B cell malignancies but exhibit differences in effector function, clinical efficacy, and toxicity that are assumed to result from the activation of divergent signaling cascades. We analyzed stimulation-induced phosphorylation events in primary human CD8+ CD28/CD3ζ and 4-1BB/CD3ζ CAR T cells by mass spectrometry and found that both CAR constructs activated similar signaling intermediates. Stimulation of CD28/CD3ζ CARs activated faster and larger-magnitude changes in protein phosphorylation, which correlated with an effector T cell–like phenotype and function. In contrast, 4-1BB/CD3ζ CAR T cells preferentially expressed T cell memory–associated genes and exhibited sustained antitumor activity against established tumors in vivo. Mutagenesis of the CAR CD28 signaling domain demonstrated that the increased CD28/CD3ζ CAR signal intensity was partly related to constitutive association of Lck with this domain in CAR complexes. Our data show that CAR signaling pathways cannot be predicted solely by the domains used to construct the receptor and that signal strength is a key determinant of T cell fate. Thus, tailoring CAR design based on signal strength may lead to improved clinical efficacy and reduced toxicity.
Decision Making Support of UAV Path Planning for Efficient Sensing in Radiation Dose Mapping

This paper introduces a UAV path planning system to provide path plans for radiation dose mapping near residential area in meter-level resolution. The proposed method first identifies void areas, i.e., the GPS coordinates without sufficient measured points within a search radius, from the observation result of the previous UAV flight. The proposed method employs the flood-fill algorithm for path planning within each chunk of adjacent void areas, and the 2-opt algorithm performs path planning between the chunks of void areas. From the result obtained in our real-world case study of radiation dose mapping near an area affected by the Fukushima Daiichi Nuclear Power Plant disaster, the proposed method significantly reduces flight time compared to the results given from the algorithms of 2-opt only and flood-fill only, respectively. More importantly, one of our findings is that, even if multi-rotor UAV is used, the number of turns during the flight is the major factor of actual flight cost.
Large-Scale Certificate Management on Multi-Tenant Web Servers

In large-scale certificate management on multi-tenant web servers, preloading a large number of certificates for managing a large number of hosts under the single server process results in increasing the required memory usage due to the respective page table entry manipulation, which may be poor resource efficiency and reduced capacity. To solve this issue, we propose a method to dynamically load the certificates bound to the hostnames found during the SSL/TLS handshake sequences without preloading, provided the Server Name Indication (SNI) extension is available. We implement the function of choosing the respective certificates with the ngx_mruby module which extend Web server functions using mruby with small memory footprint while maintaining the execution speed. We also evaluated the proposed method on a Web hosting service of authors' place of an employer.
Increased DHA Production in Seed Oil Using a Selective Lysophosphatidic Acid Acyltransferase

Metabolic engineering of the omega-3 (ω3) long chain polyunsaturated fatty acid biosynthesis pathway has generated fish oil-like levels of pharmaceutically and nutritionally important docosahexaenoic acid (DHA) in plant seeds. However, the majority of DHA has been accumulated at the sn-1 and sn-3 positions of triacylglycerol (TAG) in these engineered seeds, leaving only a minor amount (∼10%) at sn-2 position and indicating a strong discrimination (or, a very poor specificity) for DHA by seed lysophosphatidic acid acyltransferases (LPAATs), which mediate the acylation of sn-2 position of glycerol backbone. In order to increase the level of DHA at sn-2 position of TAG and to increase overall DHA level in seeds, we attempted to discover DHA-preferring LPAATs. Several LPAATs for acylation of the sn-2 position of the TAG glycerol backbone were investigated for substrate preference for DHA. In transiently expressing these LPAATs in Nicotiana benthamiana, a Mortierella alpina LPAAT had the highest substrate specificity for accumulating DHA onto oleoyl-lysophosphatidic acid (oleoyl-LPA), while the plant LPAATs tested showed lower preference for DHA. In a competition assay with a pool of four ω3 acyl-Coenzyme A (CoA) substrates involved in the DHA biosynthesis pathway, LPAATs from both M. alpina and Emiliania huxleyi showed a high preference for DHA-CoA acylation onto oleoyl-LPA. When docosahexaenoyl-LPA was used as the acyl receiver, M. alpina LPAAT also showed a high preference for DHA-CoA. Stable overexpression of M. alpina LPAAT in an Arabidopsis line that expressed the DHA biosynthesis pathway significantly increased both the total DHA levels and the distribution of DHA onto the sn-2 position of seed TAG. LC-MS analysis of the seed TAG species also confirmed that overexpression of M. alpina LPAAT increased di-DHA and tri-DHA TAGs, suggesting that the M. alpina LPAAT could enrich DHA at the TAG sn-2 position, leading to a metabolic engineering of oil seed for channeling DHA into the sn-2 position of TAG and to a higher DHA level.
A2AR Antagonism with CPI-444 Induces Antitumor Responses and Augments Efficacy to Anti–PD-(L)1 and Anti–CTLA-4 in Preclinical Models

Adenosine signaling in tumors can lead to suppression of antitumor responses. A new adenosine receptor antagonist, CPI-444, neutralized this suppression, resulting in tumor regression and immune memory, and when combined with immune checkpoint blockade, further enhanced antitumor responses. Adenosine signaling through A2A receptors (A2AR) expressed on immune cells suppresses antitumor immunity. CPI-444 is a potent, selective, oral A2AR antagonist. Blockade of A2AR with CPI-444 restored T-cell signaling, IL2, and IFNγ production that were suppressed by adenosine analogues in vitro. CPI-444 treatment led to dose-dependent inhibition of tumor growth in multiple syngeneic mouse tumor models. Concentrations of extracellular adenosine in the tumor microenvironment, measured using microdialysis, were approximately 100–150 nmol/L and were higher than corresponding subcutaneous tissue. Combining CPI-444 with anti–PD-L1 or anti–CTLA-4 treatment eliminated tumors in up to 90% of treated mice, including restoration of immune responses in models that incompletely responded to anti–PD-L1 or anti–CTLA-4 monotherapy. Tumor growth was fully inhibited when mice with cleared tumors were later rechallenged, indicating that CPI-444 induced systemic antitumor immune memory. CD8+ T-cell depletion abrogated the efficacy of CPI-444 with and without anti–PD-L1 treatment, demonstrating a role for CD8+ T cells in mediating primary and secondary immune responses. The antitumor efficacy of CPI-444 with and without anti–PD-L1 was associated with increased T-cell activation, a compensatory increase in CD73 expression, and induction of a Th1 gene expression signature consistent with immune activation. These results suggest a broad role for adenosine-mediated immunosuppression in tumors and justify the further evaluation of CPI-444 as a therapeutic agent in patients with solid tumors. Cancer Immunol Res; 6(10); 1136–49. ©2018 AACR.