gebhart/patrepeval huggingface dataset:
Enabling Real-Time Adaptivity in MOOCs with a Personalized Next-Step Recommendation Framework (2017)

In this paper, we demonstrate a first-of-its-kind adaptive intervention in a MOOC utilizing real-time clickstream data and a novel machine learned model of behavior. We detail how we augmented the edX platform with the capabilities necessary to support this type of intervention which required both tracking learners' behaviors in real-time and dynamically adapting content based on each learner's individual clickstream history. Our chosen pilot intervention was in the category of adaptive pathways and courseware and took the form of a navigational suggestion appearing at the bottom of every non-forum content page in the course. We designed our pilot intervention to help students more efficiently navigate their way through a MOOC by predicting the next page they were likely to spend significant time on and allowing them to jump directly to that page. While interventions which attempt to optimize for learner achievement are candidates for this adaptive framework, behavior prediction has the benefit of not requiring causal assumptions to be made in its suggestions. We present a novel extension of a behavioral model that takes into account students' time spent on pages and forecasts the same. Several approaches to representing time using Recurrent Neural Networks are evaluated and compared to baselines without time, including a basic n-gram model. Finally, we discuss design considerations and handling of edge cases for real-time deployment, including considerations for training a machine learned model on a previous offering of a course for use in a subsequent offering where courseware may have changed. This work opens the door to broad experimentation with adaptivity and serves as a first example of delivering a data-driven personalized learning experience in a MOOC.
Functions of the cytoplasmic domain of the βPS integrin subunit during <i>Drosophila</i> development (1994)

Integrins constitute a family of membrane-spanning, heterodimeric proteins that mediate adhesive interactions between cells and surrounding extracellular matrices (or other cells) and participate in signal transduction. We are interested in assessing integrin functions in the context of developing Drosophila melanogaster. This report, using mutants of the beta PS subunit encoded by the myospheroid (mys) locus, analyzes the relationships between integrin protein structure and developmental functions in an intact organism. As a first step in this analysis, we demonstrated the ability of a fragment of wild-type mys genomic DNA, introduced into the germ line in a P-element vector P[mys+], to rescue phenotypes attributed to lack of (or defects in) the endogenous beta PS during several discrete morphogenetic events. We then produced in vitro a series of modifications of the wild-type P[mys+] transposon, which encode beta PS derivatives with mutations within the small and highly conserved cytoplasmic domain. In vivo analysis of these mutant transposons led to the following conclusions. (1) The cytoplasmic tail of beta PS is essential for all developmental functions of the protein that were assayed. (2) An intron at a conserved position in the DNA sequence encoding the cytoplasmic tail is thought to participate in important alternative splicing events in vertebrate beta integrin subunit genes, but is not required for the developmental functions of the mys gene assayed here. (3) Phosphorylation on two conserved tyrosines found in the C terminus of the beta PS cytoplasmic tail is not necessary for the tested developmental functions. (4) Four highly conserved amino acid residues found in the N-terminal portion of the cytoplasmic tail are important but not critical for the developmental functions of beta PS; furthermore, the efficiencies with which these mutant proteins function during different morphogenetic processes vary greatly, strongly suggesting that the cytoplasmic interactions involving PS integrins are developmentally modulated.
Development and Evaluation of a Multiplexed Immunoassay for Simultaneous Detection of Serum IgG Antibodies to Six Human Coronaviruses (2019)

Known human coronaviruses (hCoV) usually cause mild to moderate upper-respiratory tract illnesses, except SARS-CoV and MERS-CoV, which, in addition to mild illness can also be associated with severe respiratory diseases and high mortality rates. Well-characterized multiplexed serologic assays are needed to aid in rapid detection and surveillance of hCoVs. The present study describes development and evaluation of a multiplexed magnetic microsphere immunoassay (MMIA) to simultaneously detect immunoglobulin G (IgG) antibodies specific for recombinant nucleocapsid proteins (recN) from hCoVs 229E, NL63, OC43, HKU1, SARS-CoV, and MERS-CoV. We used paired human sera to screen for IgG with reactivity against six hCoVs to determine assay sensitivity, specificity and reproducibility. We found no signal interference between monoplex and multiplex assay formats (R<sup>2</sup> range = 0.87-0.97). Screening of paired human sera using MMIA, resulted in 92 of 106 (sensitivity: 86%) as positive and 68 of 80 (specificity: 84%) as negative. This study serves as a proof of concept that it is feasible to develop and use a multiplexed microsphere immunoassay as a next generation screening tool for use in large scale seroprevalence studies of hCoVs.
Predicting <i>in vitro</i> drug sensitivity using Random Forests (2010)

Abstract Motivation: Panels of cell lines such as the NCI-60 have long been used to test drug candidates for their ability to inhibit proliferation. Predictive models of in vitro drug sensitivity have previously been constructed using gene expression signatures generated from gene expression microarrays. These statistical models allow the prediction of drug response for cell lines not in the original NCI-60. We improve on existing techniques by developing a novel multistep algorithm that builds regression models of drug response using Random Forest, an ensemble approach based on classification and regression trees (CART). Results: This method proved successful in predicting drug response for both a panel of 19 Breast Cancer and 7 Glioma cell lines, outperformed other methods based on differential gene expression, and has general utility for any application that seeks to relate gene expression data to a continuous output variable. Implementation: Software was written in the R language and will be available together with associated gene expression and drug response data as the package ivDrug at http://r-forge.r-project.org. Contact: riddickgp@mail.nih.gov Supplementary Information: Supplementary data are available at Bioinformatics online.
An effective method for improving IC package die failure during assembly punch processing (2005)

Singulation by a punch process is a major manufacturing step in the package assembly process. The punch process induces dynamic stress waves in the package which transfer stress to the die. This could be a potential factor to crack or pop the die during punching. The objective of this paper is to investigate an effective method to minimize stress transfer. This method uses a pre-groove technique in the lead frame design to reduce the punch stress during singulation. A 3D transient dynamic large deformation finite element method is used to determine what stresses are going to be induced during singulation of the package, to check if the package can withstand punch induced stress waves and to determine potential design weaknesses both with and without the pre-groove. Different locations of the pre-groove, different shape parameters of the groove and different punch contact shapes are simulated and studied to get the optimized results. Tests of the punching process including a group of samples with and without pre-groove have been developed. The results show that dynamic stresses transferred to die without groove are much greater than with the groove, there is an optimized shape and location of the groove that may reduce stress to a maximum degree. While changing the design of punch contact head, such as narrowing the width of contact punch head area, it also reduced the die stresses in punching singulation, but not as significantly as with pre-groove cases. Both modeling and testing have confirmed that pre-groove is an effective method to remove the die crack/pop failure.
Identification of IS1356, a new insertion sequence, and its association with IS402 in epidemic strains of Burkholderia cepacia infecting cystic fibrosis patients (1996)

Burkholderia cepacia is now recognized as an important opportunistic pathogen in cystic fibrosis (CF) and other compromised patients. Epidemicity among CF patients has been attributed to at least one particularly infectious strain (strain ET12), and both genetic evidence and anecdotal evidence suggest that this strain, currently endemic in Ontario, and those causing an epidemic in the United Kingdom, are indeed the same. Our study was conducted to determine whether there was any association between the presence of various insertion sequence (IS) elements, the cable pilin subunit gene (cblA), electrophoretic type (ET), and ribotype (RT) in a collection of 97 clinical and 2 environmental isolates of B. cepacia. No apparent linkage was found for IS elements IS401, IS402, IS406, IS407, and IS408 with ET or RT. The cblA target, said to be a marker for high infectivity, was detected in 100% (38 of 38) of strains of B. cepacia ET12 and in a single strain of ET13 that differed in a single enzyme allele. A new IS, IS1356, identified during the investigation, was present in 71.7% of all isolates, and 50.7% of these isolates harbored IS1356 as a hybrid IS element inserted into IS402. IS1356 is 1,353 bp in length, and when it is inserted into IS402 it results in a 10-bp duplication at the site of insertion. IS1356 contains one major open reading frame of 1,260 bp coding for a putative transposase which has significant homology to ISRm3 in Rhizobium meliloti (59%) and to an undesignated IS element in Corynebacterium diphtheriae (49%). The IS402-IS1356 element was found exclusively in the epidemic strains from Ontario and the United Kingdom, being detected in 94.7% (36 of 38 isolates) of B. cepacia ET12 isolates. Of the two ET12 isolates found to be devoid of the IS402-IS1356 element, both contained IS1356 unassociated with IS402, one was temporally unrelated to the epidemic, and the other was from a CF patient in a geographic area remote from Ontario and the United Kingdom. It is evident that the IS402-IS1356 hybrid element, the cblA pilin subunit gene, and the allelic suite represented by multilocus enzyme electrophoretic type ET12 may provide useful markers for the epidemic, highly transmissible transatlantic strain isolated in Ontario and the United Kingdom.
Putative role of hepatitis B virus X protein in hepatocarcinogenesis: Effects on apoptosis, DNA repair, mitogen‐activated protein kinase and JAK/STAT pathways (2000)

Chronic infection with hepatitis B virus (HBV) is a major risk factor for the development of hepatocellular carcinoma (HCC). The pathogenesis of HBV-induced malignant transformation is, however, incompletely understood. HBx, the protein encoded by the X open reading frame, is a transcriptional activator that has been implicated in hepatocarcinogenesis. HBx inhibits the function of the tumour suppressor protein p53 in what is thought to be an early event in hepatocyte transformation before the later accumulation of inactivating p53 point mutations. HBx inhibits apoptosis but also exerts pro-apoptotic effects. The effects of HBx on apoptosis may be important not only for the development of HCC but also for the establishment of HBV infection. Further implication of HBx in hepatocyte transformation has been the demonstration that it inhibits the repair of damaged hepatocyte DNA. This effect may be mediated by interaction with p53 or through binding to the damaged DNA binding protein (DDB), which plays an accessory role in nucleotide excision repair. In addition, HBx activates cell signalling cascades involving mitogen-activated protein kinase (MAPK) and Janus family tyrosine kinases (JAK)/signal transducer and activators of transcription (STAT) pathways. The implications of these modulating effects of HBx are not fully understood, but they are likely to have wide-ranging effects on hepatocyte proliferation, apoptosis and the regulation of cell growth checkpoints. The cellular functions ascribed to HBx are unusually diverse, and defining the biologically important role of HBx during HBV replication will go some way to understanding the sequelae of chronic HBV infection.
Self-timed precharge latch (2002)

The use of a self-timed precharge latch (STPL) is proposed for the design of self-timed systems based on the four-cycle and two-cycle handshaking protocols. The techniques allow different data to be stored and computed in consecutive pipeline stages simultaneously without using a conventional data register. The techniques allow the propagation of data across the pipeline stage in a fast domino manner, parallel with the handshaking signals. The variable-length FIFOs designed using these techniques result in a significant reduction in silicon area and fall-through delay compared with those designed based on other techniques.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Prediction of Cerebral Vasospasm in Patients Presenting with Aneurysmal Subarachnoid Hemorrhage: A Review (2005)

To date, a large blood burden is the only consistently demonstrated risk factor for the prediction of cerebral vasospasm after SAH. Because vasospasm is such a multifactorial problem, attempts to predict its occurrence will probably require several different approaches and methodologies, as is done at present. Future improvements in the prevention of cerebral vasospasm from aneurysmal SAH will most likely require advances in our understanding of its pathophysiology and our ability to predict its onset.
Expression of acetylcholine receptor genes in human thymic epithelial cells: implications for myasthenia gravis (1996)

The intrathymic presence of the muscle acetylcholine receptor (AChR) is controversial, and the nature of the cell(s) expressing it is unclear. We thus analyzed the molecular expression of muscle AChR in human thymi. mRNA studies indicated that the two isoforms (P3A+ and P3A-) of the alpha-subunit were present in thymic extracts and in cultured thymic epithelial cells (TEC), while expression in thymocytes was low and not consistently detectable. The amount of mRNA coding for the alpha-subunit, evaluated by means of quantitative PCR, was about 20 times less in TEC than in muscle, and was similar in TEC from normal subjects and from patients with myasthenia gravis (MG). The beta- and epsilon-subunits present in adult AChR were also expressed in TEC (but not in thymocytes), while the embryonic subunit (gamma) was absent. In TEC cultures, the AChR alpha- and epsilon-subunit mRNA levels were down-regulated by forskolin, as also observed in the TE671 rhabdomyosarcoma cell line, suggesting similar regulation of AChR subunits in thymus and muscle. Protein expression was evidenced on TEC (but not on thymocytes), by Western blotting as well as by immunofluorescence, thus demonstrating AChR expression on human thymic epithelial cells. There was no difference in the expression of AChR between TEC from MG patients and controls, meaning that the expression of AChR subunits alone is not sufficient to explain the onset of MG.
Gene Transfer (1989)

The current status of gene transfer experiments indicates that it is possible to provide (1) safe and efficient retroviral packaging lines for gene transfer; and (2) vectors containing the human beta-globin genes and selectable marker genes which can be transmitted into erythroid cells and are appropriately expressed. In animal autologous bone marrow transplantation experiments, stable and high-level expression of retroviral vectors containing human beta-globin genes has not yet been achieved. New retroviral vectors are being tested that contain different components of the retrovirus as well as the newly described enhancer elements 5' to the epsilon gene and surrounding the beta-globin gene. The long-term goal of human gene therapy for sickle cell disease then consists of constructing optimally safe and efficient retroviral packaging lines as well as retroviral vectors containing the human beta-globin gene and selectable markers such as the neoR gene. One would then remove bone marrow cells from patients with sickle cell disease, transfer the retroviral vectors into the bone marrow cells, and subject the cells to G418 selection in vitro. Next, one would ablate the host bone marrow and autotransplant the manipulated bone marrow bearing the retroviral vector. Finally, one would analyze the reconstituted bone marrow for human beta-globin gene expression. These experiments must await the demonstration of safe and efficient gene transfer in animals, and particularly experiments must be done in monkeys prior to the use of these approaches in humans. Alternative approaches to gene therapy include direct correction of the defect in the beta-globin gene by site-specific recombination of the defective gene with incoming normal gene sequences. This technology is not yet achievable, although preliminary experiments have been performed in which gene correction at a low frequency has been obtained. The obvious advantage of this approach is that the native human beta gene would be reconstituted. Site-specific recombination and addition of normal beta genes to the human genome represent exciting and feasible approaches to human gene therapy using the extraordinary resources of modern molecular and cellular biology. Success in treating disorders of human hemoglobin only awaits additional technical advances for increasing the efficiency of gene transfer and the level of gene expression.
A Galvanotaxis Assay for Analysis of Neural Precursor Cell Migration Kinetics in an Externally Applied Direct Current Electric Field (2012)

The discovery of neural stem and progenitor cells (collectively termed neural precursor cells) (NPCs) in the adult mammalian brain has led to a body of research aimed at utilizing the multipotent and proliferative properties of these cells for the development of neuroregenerative strategies. A critical step for the success of such strategies is the mobilization of NPCs toward a lesion site following exogenous transplantation or to enhance the response of the endogenous precursors that are found in the periventricular region of the CNS. Accordingly, it is essential to understand the mechanisms that promote, guide, and enhance NPC migration. Our work focuses on the utilization of direct current electric fields (dcEFs) to promote and direct NPC migration - a phenomenon known as galvanotaxis. Endogenous physiological electric fields function as critical cues for cell migration during normal development and wound repair. Pharmacological disruption of the trans-neural tube potential in axolotl embryos causes severe developmental malformations(1). In the context of wound healing, the rate of repair of wounded cornea is directly correlated with the magnitude of the epithelial wound potential that arises after injury, as shown by pharmacological enhancement or disruption of this dcEF(2-3). We have demonstrated that adult subependymal NPCs undergo rapid and directed cathodal migration in vitro when exposed to an externally applied dcEF. In this protocol we describe our lab's techniques for creating a simple and effective galvanotaxis assay for high-resolution, long-term observation of directed cell body translocation (migration) on a single-cell level. This assay would be suitable for investigating the mechanisms that regulate dcEF transduction into cellular motility through the use of transgenic or knockout mice, short interfering RNA, or specific receptor agonists/antagonists.
Scoliosis treatment using a combination of manipulative and rehabilitative therapy: a retrospective case series (2004)

The combined use of spinal manipulation and postural therapy appeared to significantly reduce the severity of the Cobb angle in all 19 subjects. These results warrant further testing of this protocol.
Field-Programmable Crossbar Array (FPCA) for Reconfigurable Computing (2017)

For decades, advances in electronics were directly driven by the scaling of CMOS transistors according to Moore's law. However, both the CMOS scaling and the classical computer architecture are approaching fundamental and practical limits, and new computing architectures based on emerging devices, such as resistive random-access memory (RRAM) devices, are expected to sustain the exponential growth of computing capability. Here, we propose a novel memory-centric, reconfigurable, general purpose computing platform that is capable of handling the explosive amount of data in a fast and energy-efficient manner. The proposed computing architecture is based on a uniform, physical, resistive, memory-centric fabric that can be optimally reconfigured and utilized to perform different computing and data storage tasks in a massively parallel approach. The system can be tailored to achieve maximal energy efficiency based on the data flow by dynamically allocating the basic computing fabric for storage, arithmetic, and analog computing including neuromorphic computing tasks.
HLA A2601-restricted CTLs recognize a peptide antigen expressed on squamous cell carcinoma. (1995)

The CD4-CD8+ CTL (KE-4 CTL) cell line against autologous tumor cells was established in a patient with esophageal cancer. This KE-4 CTL recognized a peptide antigen on esophageal and lung squamous cell carcinomas in an HLA A2601-restricted manner, as evaluated by cytotoxicity against a panel of tumor cells, transfection experiments with HLA A2601 cDNA, and reconstitution with eluted peptides. None of the normal cells tested was lysed by this CTL. These results suggest the existence of HLA A2601-restricted CTL precursors recognizing a peptide antigen on SCC in a patient with esophageal cancer.
Differentiating and growth inhibitory effects of diallyl disulfide on cancer cells (1997)

Diallyl disulfide caused growth inhibition and differentiation of DS19 mouse erythroleukemic cells as judged by hemoglobin synthesis and induction of acetylcholinesterase activity. There was a 50% inhibition of cell division at about 0.25 mM diallyl disulfide which was much more effective than diallyl sulfide. K562 human erythroleukemia cells and mouse melanoma cells were more resistant to the action of diallyl disulfide. Thymidine incorporation into DNA in 7800NJ and 7288CTC rat hepatoma cells and in T47D and MCF7 human breast cancer cells was inhibited by 1-2 mM diallyl disulfide. Administration of diallyl disulfide to rats bearing Morris hepatomas caused marked inhibitory effects on precursor incorporation into DNA and protein in both hepatomas and in livers after a dose of 400 mg/kg body weight, but only small differences were seen at a less toxic dose of 200 mg/kg.
Glass as Encapsulation for Low-Cost Photovoltaic Solar Arrays (1981)

In photovoltaic systems, the encapsulant material that protects the solar cells should be highly transparent and very durable. Glass satisfies these two criteria and is considered a primary candidate for low-cost, photovoltaic encapsulation systems. In this paper, various aspects of glass encapsulation are treated that are important for the designer of photovoltaic systems. Candidate glasses and available information defining the state of the art of glass encapsulation materials and processes for automated, high volume production of terrestrial photovoltaic devices and related applications are presented. The desired characteristics of glass encapsulation are (a) low degradation rates, (b) high transmittance, (c) high reliability, (d) low-cost and (e) high annual production capacity. The glass design areas treated herein include the types of glass, sources, prices, physical properties and glass modifications, such as antireflection coatings.