Miracle-dz/UniFAR-FTUs huggingface dataset:
Developing a Measure of General Academic Ability

This article is concerned with developing a measure of general academic ability (GAA) for high school graduates who apply to colleges, as well as with the identification of optimal weights of the GAA indicators in a linear combination that yields a composite score with maximal reliability and maximal predictive validity, employing the framework of the popular latent variable modeling methodology. The approach to achieving this goal is illustrated with data for 6,640 students with major in Science and 3,388 students with major in Art from colleges in Saudi Arabia. The indicators (observed measures) of the targeted GAA construct were selected from assessments that include the students’ high school grade and their scores on two standardized tests developed by the National Center for Assessment in Higher Education in Saudi Arabia, General Aptitude Test (GAT) and Standardized Achievement Admission Test (SAAT). A unidimensional measure of GAA was developed initially, with different sets of indicators for colleges with major in Science and for colleges with major in Art. Appropriate indicators for colleges with major in Science were the high school grade, total score on GAT, and four SAAT subscales on Biology, Chemistry, Physics, and Math. With respect to colleges with major in Art, appropriate GAA indicators were the students’ high school grade and their scores on GAT-Verbal, GAT-Quantitative, and SAAT. Although the case study is Saudi Arabia, the methods and procedures discussed in this article have broader utility and can be used in different contexts of educational and psychological assessment.
Preferential Targeting of Lateral Entorhinal Inputs onto Newly Integrated Granule Cells

Mature dentate granule cells in the hippocampus receive input from the entorhinal cortex via the perforant path in precisely arranged lamina, with medial entorhinal axons innervating the middle molecular layer and lateral entorhinal cortex axons innervating the outer molecular layer. Although vastly outnumbered by mature granule cells, adult-generated newborn granule cells play a unique role in hippocampal function, which has largely been attributed to their enhanced excitability and plasticity (Schmidt-Hieber et al., 2004; Ge et al., 2007). Inputs from the medial and lateral entorhinal cortex carry different informational content. Thus, the distribution of inputs onto newly integrated granule cells will affect their function in the circuit. Using retroviral labeling in combination with selective optogenetic activation of medial or lateral entorhinal inputs, we examined the functional innervation and synaptic maturation of newly generated dentate granule cells in the mouse hippocampus. Our results indicate that lateral entorhinal inputs provide the majority of functional innervation of newly integrated granule cells at 21 d postmitosis. Despite preferential functional targeting, the dendritic spine density of immature granule cells was similar in the outer and middle molecular layers, which we speculate could reflect an unequal distribution of shaft synapses. However, chronic blockade of neurotransmitter release of medial entorhinal axons with tetanus toxin disrupted normal synapse development of both medial and lateral entorhinal inputs. Our results support a role for preferential lateral perforant path input onto newly generated neurons in mediating pattern separation, but also indicate that medial perforant path input is necessary for normal synaptic development. SIGNIFICANCE STATEMENT The formation of episodic memories involves the integration of contextual and spatial information. Newly integrated neurons in the dentate gyrus of the hippocampus play a critical role in this process, despite constituting only a minor fraction of the total number of granule cells. Here we demonstrate that these neurons preferentially receive information thought to convey the context of an experience. Each newly integrated granule cell plays this unique role for ∼1 month before reaching maturity.
CBTracer: Continuously Building Datasets for Binary Vulnerability and Exploit Research

Vulnerability discovery and exploiting are critical to software security. Emerging intelligent vulnerability discovery solutions usually require a large number of training data. Studying exploits also requires a set of existing exploit samples. As a result, building a dataset for vulnerability and exploit research is necessary. In this paper, we present CBTracer, able to catch real-time I/O traffic of target applications and monitor their runtime executions, to build an evolving dataset for kinds of security analysis, including vulnerability discovery and exploit generation. CBTracer is a lightweight framework designed to be deployed easily in various CTF competitions by different organizers to build a bigger dataset. We used CBTracer to collect data from CGC challenges and deployed it in several real-world CTF challenges, showing that it could efficiently collects security-related data.
MolGAN: An implicit generative model for small molecular graphs

eep generative models for graph-structured data offer a new angle on the problem of chemical synthesis: by optimizing differentiable models that directly generate molecular graphs, it is pos-sible to side-step expensive search procedures in the discrete and vast space of chemical structures. We introduce MolGAN, an implicit, likelihood-free generative model for small molecular graphs that circumvents the need for expensive graph matching procedures or node ordering heuris-tics of previous likelihood-based methods. Our method adapts generative adversarial networks (GANs) to operate directly on graph-structured data. We combine our approach with a reinforce-ment learning objective to encourage the genera-tion of molecules with specific desired chemical properties. In experiments on the QM9 chemi-cal database, we demonstrate that our model is capable of generating close to 100% valid com-pounds. MolGAN compares favorably both to recent proposals that use string-based (SMILES) representations of molecules and to a likelihood-based method that directly generates graphs, al-beit being susceptible to mode collapse.
The use of iPTD engineered antifreeze proteins for cryopreservation of cells

ii Preface . iii Table of contents. iv List of figures.vii List of abbreviations.x Acknowledgements.xi Dedication.xii Chapter 1: Introduction and background.1 1.1: Antifreeze protein origins and properties.1 1.2: Applications of antifreeze proteins in literature and biotechnology.2 1.3: Cryobiology of biological samples.2 1.4: Plasma Membrane.5 1.5: iProgen intracellular delivery technology.6 1.6: Red blood cell cryopreservation.7 Chapter 2: Protein production and delivery kinetics.9 2.1: Protein production and purification.9 v 2.1.1: Materials and Methods.9 2.1.2: Results.11 2.2: Flow cytometry analysis of iPTD delivery kinetics.15 2.2.1: Materials and Methods.15 2.2.2: Results.16 2.3: Multiphoton Microscopy.18 2.3.1: Materials and Methods.18 2.3.2: Results.18 Chapter 3: AFP-iPTD Functional Analysis.21 3.1: Membrane integrity assessed by LDH assay.21 3.1.1: Materials and Methods.21 3.1.2: Results.23 3.2: Development of Calcein dye release assay.29 3.2.1: Materials and Methods.30 3.2.2: Results.31 Chapter 4: Antifreeze protein’s effect on cell recovery.37 4.1: Trypan blue exclusion assay.37 vi 4.1.1: Materials and Methods.37 4.1.2: Results.38 4.2: MTS Assay.43 4.2.1: Materials and Methods.43 4.2.2: Results.44 Chapter 5: AFP in Red Blood Cell Cryopreservation.50 5.1: Red blood cell hemolysis and ATP retention.50 5.1.1: Materials and Methods.50 5.1.2: Results.53 Chapter 6: Discussion and Conclusion.60 Chapter 7: Future Directions.68 Bibliography.69
High Rate of Drug‐Free Remission After Induction Therapy With Golimumab in Early Peripheral Spondyloarthritis

New treatment algorithms using tumor necrosis factor (TNF) blockers in early stages of spondyloarthritis (SpA) induce high rates of clinical remission or low disease activity. It could be anticipated that such early intervention strategies in peripheral SpA may induce drug‐free remission. We undertook this study to evaluate drug‐free clinical remission after induction therapy with golimumab in patients with very early active peripheral SpA, and to identify patient characteristics that predict sustained drug‐free remission.
Zewen at SemEval-2018 Task 1: An Ensemble Model for Affect Prediction in Tweets

This paper presents a method for Affect in Tweets, which is the task to automatically determine the intensity of emotions and intensity of sentiment of tweets. The term affect refers to emotion-related categories such as anger, fear, etc. Intensity of emo-tions need to be quantified into a real valued score in [0, 1]. We propose an en-semble system including four different deep learning methods which are CNN, Bidirectional LSTM (BLSTM), LSTM-CNN and a CNN-based Attention model (CA). Our system gets an average Pearson correlation score of 0.682 in the subtask EI-reg and an average Pearson correlation score of 0.784 in subtask V-reg, which ranks 17th among 48 systems in EI-reg and 19th among 38 systems in V-reg.
Vertebral fracture assessment, trabecular bone score and handgrip in a group of postmenopausal women with vertebral fractures – preliminary study

Objectives The aim of our study was to determine a possible correlation between vertebral fractures (indicated by VFA – vertebral fracture assessment), TBS (trabecular bone score) and muscle strength (measured by means of handgrip strength test results) in a group of postmenopausal women. Material and methods The study was conducted between 2014 and 2015 in a group of patients of Krakow Medical Centre (KMC). Women who participated in the study were referred to KMC by an attending physician for suspected vertebral fracture. Apart from VFA, patients were additionally tested for bone density (including TBS), muscle strength (by means of a handgrip strength test) and height loss. Altogether 35 patients with an average age of 69.7 years (49–95, SD = 10.49) were included in the study. Results In the group of 35 women, VFA analysis demonstrated vertebral fractures in 17 patients (40%). Vertebral height loss suggesting a fracture was revealed in 77 vertebrae. The mean result of the TBS was 1.195 (0.982–1.409, SD = 0.09), which suggests high risk of fracture. The majority of the subjects (65.7%) displayed major bone microarchitecture degradation (TBS < 1.23) and also the highest number of fractures (n = 62, 80.5% of all). There was no correlation between the spine bone mineral density (BMD) score and the TBS result, which confirms studies showing that subjects with the same bone density may have completely different TBS. Bone density (spine BMD) was similar (osteopenic) in groups with or without vertebral fracture (in VFA). We noted a significant correlation (r = 0.45, p < 0.05) between the number of fractured vertebrae and the handgrip score. Conclusions VFA should be a part of a standard diagnostic procedure for patients with osteoporotic fractures. When it comes to identifying patients at risk of fracturing vertebrae, muscle strength (handgrip) may have potential use in clinical practice. The predictive value of the TBS in reference to vertebral fractures should be evaluated in bigger randomized studies.
Journal of Neuroscience Methods

Background: A touchscreen interface permits rich user interactions for research in many ﬁ elds, but is rarely found within a Magnetic Resonance Imaging (MRI) environment due to di ﬃ culties adapting conventional technologies to the strong electromagnetic ﬁ elds. Conventional MR-compatible video display technology uses either large-screen displays that are placed outside of the bore of the MRI itself, or projectors located beyond the participant's reach, making touch interfaces impossible. New method: Here, we describe the MR-compatibility of the ‘ MRItab ’ in terms of MR safety and image quality. The MRItab adapts inexpensive o ﬀ -the-shelf components with special signal-driver circuitry and shielding to bring the touchscreen interface into the MR environment, without adversely a ﬀ ecting MRI image quality, thereby making touch interfaces possible. Results: Our testing demonstrated that the functioning of the MRItab was not a ﬀ ected by the functioning of the MRI scanner and that the MRItab did not adversely a ﬀ ect the image data acquired. Participants were able to interact naturally with the MRItab during MRI scanning. Comparison with other method (s): The MRItab is the ﬁ rst MR-compatible touchscreen device with video-display screen capabilities designed for use in the MRI environment. This interactive digital device is the ﬁ rst to allow participants to see their hands directly as they interact with a touch-sensitive display screen, resulting in high ecological validity. Conclusions: The MRItab provides a methodological advantage for research in many ﬁ elds, given the realistic human-computer interaction it supports.
The mechanism of two-phase motility in the spirochete Leptospira: Swimming and crawling

Rotation of a helical cell body and mobility of cell-surface adhesins result in surface motility of the spirochete Leptospira. Many species of bacteria are motile, but their migration mechanisms are considerably diverse. Whatever mechanism is used, being motile allows bacteria to search for more optimal environments for growth, and motility is a crucial virulence factor for pathogenic species. The spirochete Leptospira, having two flagella in the periplasmic space, swims in liquid but has also been previously shown to crawl over solid surfaces. The present motility assays show that the spirochete movements both in liquid and on surfaces involve a rotation of the helical cell body. Direct observations of cell-surface movement with amino-specific fluorescent dye and antibody-coated microbeads suggest that the spirochete attaches to the surface via mobile, adhesive outer membrane components, and the cell body rotation propels the cell relative to the anchoring points. Our results provide models of how the spirochete switches its motility mode from swimming to crawling.
Process Algebraic Architectural Description Languages: Generalizing Component-Oriented Mismatch Detection in the Presence of Nonsynchronous Communications

In the original paper, we showed how to enhance the expressiveness of a typical process algebraic architectural description language by including the capability of representing nonsynchronous communications. In particular, we extended the language by means of additional qualifiers enabling the designer to distinguish among synchronous, semi-synchronous, and asynchronous ports. Moreover, we showed how to modify techniques for detecting coordination mismatches such as the compatibility check for star topologies and the interoperability check for cycle topologies, in such a way that those two checks are applicable also in the presence of nonsynchronous communications. In this addendum, we generalize those results by showing that it is possible to verify in a component-oriented way an arbitrary property of a certain class (not only deadlock) over an entire architectural type having an arbitrary topology (not only stars and cycles) by considering also behavioral variations, exogenous variations, endogenous variations, and multiplicity variations, so to deal with the possible presence of nonsynchronous communications. The proofs are at the basis of some results mentioned in the book "A Process Algebraic Approach to Software Architecture Design" by Alessandro Aldini, Marco Bernardo, and Flavio Corradini, published by Springer in 2010.
Sports skill frequency analysis with motion image data

This paper addresses skill frequency analysis with motion image data of volleyball attack. We try to justify a assumption that expert skills have relatively low frequency motions rather than novice skills as the similarity of human postural control. For this purpose we have experiments and analyze sports skills as for frequency of motion using time series motion images of volleyball attacks. In our research, volleyball play is analyzed with motion image data recorded by hi-speed cam-coder, where we do not use physical information such as body skeleton model. Time series data are obtained from the motion image data with four marking points, and analyzed in terms of motion frequency. As the experiment results, we in some content classify expert, middle, and novice skill image using frequency data.
Low-dose minocycline mediated neuroprotection on retinal ischemia-reperfusion injury of mice

Purpose The aim of this study was to investigate the effect of minocycline (MC) on the survival of retinal ganglion cells (RGCs) in an ischemic-reperfusion (I/R) injury model of retinal degeneration. Methods Retinal I/R injury was induced in the left eye of mice for 60 min by maintaining intraocular pressure at 90 mmHg. Low- or high-dose MC (20 or 100 mg/kg, respectively) was administered by intravenous injection at 5 min after the retinal ischemic insult and then administered once daily until the mice were euthanized. RGCs and microglial cells were counted using immunofluorescence staining. Functional changes in the RGCs were evaluated using electroretinography. The visual function was assessed using an optokinetic test. Results The data demonstrated that the effect of MC was dose dependent. Low-dose MC showed protective effects, with reduced RGC loss and microglial activation, while the high-dose MC showed damage effects, with more RGC loss and microglial activation when compared with the vehicle group. The electroretinography and optokinetic test results were consistent with the morphologic observations. Conclusions These data suggested that appropriate concentrations of MC can protect the retina against retinal ischemic-reperfusion injury, while excessive MC has detrimental effects.
Messaging Circumstances and Economic Pressures as Influences on Linkage to Medical Male Circumcision following Community-Based HIV Testing for Men in Rural Southwest Uganda: A Qualitative Study

Voluntary medical male circumcision (MMC) reduces risk of HIV infection, but uptake remains suboptimal among certain age groups and locations in sub-Saharan Africa. We analysed qualitative data as part of the Linkages Study, a randomized controlled trial to evaluate community-based HIV testing and follow-up as interventions promoting linkage to HIV treatment and prevention in Uganda and South Africa. Fifty-two HIV-negative uncircumcised men participated in the qualitative study. They participated in semistructured individual interviews exploring (a) home HTC experience; (b) responses to test results; (c) efforts to access circumcision services; (d) outcomes of efforts; (e) experiences of follow-up support; and (f) local HIV education and support. Interviews were audio-recorded, translated, transcribed, and summarized into “linkage summaries. ” Summaries were analysed inductively to identify the following three thematic experiences shaping men's circumcision choices: (1) intense relief upon receipt of an unanticipated seronegative diagnosis, (2) the role of peer support in overcoming fear, and (3) anticipation of missed economic productivity. Increased attention to the timing of demand creation activities, to who delivers information about the HIV prevention benefits of MMC, and to the importance of missed income during recovery as a barrier to uptake promises to strengthen and sharpen future MMC demand creation strategies.
Duplicate Detection in Programming Question Answering Communities

Community-based Question Answering (CQA) websites are attracting increasing numbers of users and contributors in recent years. However, duplicate questions frequently occur in CQA websites and are currently manually identified by the moderators. Automatic duplicate detection, on one hand, alleviates this laborious effort for moderators before taking close actions, and, on the other hand, helps question issuers quickly find answers. A number of studies have looked into related problems, but very limited works target Duplicate Detection in Programming CQA (PCQA), a branch of CQA that is dedicated to programmers. Existing works framed the task as a supervised learning problem on the question pairs and relied on only textual features. Moreover, the issue of selecting candidate duplicates from large volumes of historical questions is often un-addressed. To tackle these issues, we model duplicate detection as a two-stage “ranking-classification” problem over question pairs. In the first stage, we rank the historical questions according to their similarities to the newly issued question and select the top ranked ones as candidates to reduce the search space. In the second stage, we develop novel features that capture both textual similarity and latent semantics on question pairs, leveraging techniques in deep learning and information retrieval literature. Experiments on real-world questions about multiple programming languages demonstrate that our method works very well; in some cases, up to 25% improvement compared to the state-of-the-art benchmarks.
Microfluidic Spun Alginate Hydrogel Microfibers and Their Application in Tissue Engineering

Tissue engineering is focusing on processing tissue micro-structures for a variety of applications in cell biology and the “bottom-up” construction of artificial tissue. Over the last decade, microfluidic devices have provided novel tools for producing alginate hydrogel microfibers with various morphologies, structures, and compositions for cell cultivation. Moreover, microfluidic spun alginate microfibers are long, thin, and flexible, and these features facilitate higher-order assemblies for fabricating macroscopic cellular structures. In this paper, we present an overview of the microfluidic spinning principle of alginate hydrogel microfibers and their application as micro-scaffolds or scaffolding elements for 3D assembly in tissue engineering.
The Role of Fluoxetine in Activating Wnt/β-Catenin Signaling and Repressing β-Amyloid Production in an Alzheimer Mouse Model

Fluoxetine (FLX) is one of the selective serotonin reuptake inhibitors (SSRIs) antidepressants, which could be used to relieve depression and anxiety among AD patients. This study was designed to search for new mechanisms by which fluoxetine could activate Wnt/β-catenin signaling pathway and reduce amyloidosis in AD brain. Fluoxetine was administered via intragastric injection to APP/tau/PS1 mouse model of Alzheimer’s disease (3×Tg-AD) mice for 4 months. In the hippocampus of AD mouse model, there could be observed neuronal apoptosis, as well as an increase in Aβ (amyloid-β) production. Moreover, there is a strong association between down-regulation of Wnt/β-catenin signaling and the alteration of AD pathology. The activity of protein phosphatases of type 2A (PP2A) could be significantly enhanced by the treatment of fluoxetine. The activation of PP2A, caused by fluoxetine, could then play a positive role in raising the level of active β-catenin, and deliver a negative impact in GSK3β activity in the hippocampal tissue. Both the changes mentioned above would lead to the activation of Wnt/β-catenin signaling. Meanwhile, fluoxetine treatment would reduce APP cleavage and Aβ generation. It could also prevent apoptosis in 3×Tg-AD primary neuronal cell, and have protective effects on neuron synapse. These findings imply that Wnt/β-catenin signaling could be a potential target outcome for AD prevention, and fluoxetine has the potential to be a promising drug in both AD prevention and treatment.