gebhart/patrepeval huggingface dataset:
E1A gene therapy inhibits angiogenesis in a Ewing's sarcoma animal model. (2003)

We assessed vascular endothelial growth factor (VEGF) expression in four different human Ewing's sarcoma cell lines (TC71, SK-ES, RD, and A4573) and in tumors in nude mice induced following s.c. injection of TC71 cells. Three of the four cell lines (TC71, SK-ES, and A4573) expressed significantly higher levels of VEGF than did normal human osteoblasts. Transfection of the adenovirus type 5 early region 1A (E1A) gene into TC71 cells down-regulated VEGF expression in vitro. In the mice bearing TC71 cell tumors, intratumoral injections of an adenoviral vector containing the E1A gene (Ad-E1A) decreased VEGF expression, inhibited tumor growth, and increased the survival rates in comparison with the mice given injections of PBS or an adenoviral vector containing beta-galactosidase (Ad-beta-gal). E1A gene therapy also significantly reduced blood vessel density and induced cell apoptosis in the tumors. These results demonstrate that E1A gene therapy inhibits angiogenesis, most likely by suppression of VEGF expression. Thus, E1A gene therapy may be a new therapeutic approach for Ewing's sarcoma.
Anti-Parkinson's disease drugs and pharmacogenetic considerations (2013)

The goal of pharmacogenomic testing for anti-Parkinson's disease drugs should be conservative and aimed at selecting determined drugs for determined patients. However, much additional research is still needed to obtain reliable pre-prescription tests.
Living With Chronic Venous Leg Ulcers: A Descriptive Study of Knowledge and Functional Health Status (2000)

A descriptive design was used to identify the functional health status and knowledge level of individuals living at home with chronic venous leg ulcers (N = 21). Limitations in physical function and vitality were moderate to severe, impacting on study participants' productive activities and activities of daily living. Severe to moderate pain was experienced by 19% of the participants. In addition, knowledge deficits were apparent regarding the cause and treatment of leg ulcers. Findings of this study suggest the importance of assessing these factors in addition to the wound when caring for individuals in the community with chronic venous leg ulcers.
Mining SNPs From EST Databases (1999)

There is considerable interest in the discovery and characterization of single nucleotide polymorphisms (SNPs) to enable the analysis of the potential relationships between human genotype and phenotype. Here we present a strategy that permits the rapid discovery of SNPs from publicly available expressed sequence tag (EST) databases. From a set of ESTs derived from 19 different cDNA libraries, we assembled 300,000 distinct sequences and identified 850 mismatches from contiguous EST data sets (candidate SNP sites), without de novo sequencing. Through a polymerase-mediated, single-base, primer extension technique, Genetic Bit Analysis (GBA), we confirmed the presence of a subset of these candidate SNP sites and have estimated the allele frequencies in three human populations with different ethnic origins. Altogether, our approach provides a basis for rapid and efficient regional and genome-wide SNP discovery using data assembled from sequences from different libraries of cDNAs.
Cognitive deficits in psychiatric disorders: Current status (2006)

Cognition denotes a relatively high level of processing of specific information including thinking, memory, perception, motivation, skilled movements and language. Cognitive psychology has become an important discipline in the research of a number of psychiatric disorders, ranging from severe psychotic illness such as schizophrenia to relatively benign, yet significantly disabling, non-psychotic illnesses such as somatoform disorder. Research in the area of neurocognition has started unlocking various secrets of psychiatric disorders, such as revealing the biological underpinnings, explaining the underlying psychopathology and issues related to course, outcome and treatment strategies. Such research has also attempted to uproot a number of previously held concepts, such as Kraepelin's dichotomy. Although the range of cognitive problems can be diverse, there are several cognitive domains, including executive function, attention and information processing, and working memory, which appear more frequently at risk. A broad range of impairment across and within the psychiatric disorders are highlighted in this oration. The oration summarizes the studies investigating cognitive processing in different psychiatric disorders. I will also discuss the findings of my own research on neurocognitive deficits in mood disorders, schizophrenia, obsessive-compulsive disorder, somatoform disorder, including studies on 'high-risk' individuals. Tracing the evaluation of neurocognitive science may provide new insights into the pathophysiology and treatment of psychiatric disorders.
A multi‐dimensional integration (MDI) strategy for MR <i>T</i><sub>2</sub>* mapping (2021)

MRI signals are intrinsically multi-dimensional, and signal behavior may be orthogonal among different dimensions. Such dimensional orthogonality can be utilized to eliminate unwanted effects and facilitate mathematical simplicity during image processing for improved outcomes. In this work, we will demonstrate and analyze the principles and performance of a newly developed multi-dimensional integration (MDI) strategy in MR T<sub>2</sub> * mapping. By constructing a complex signal function to extract the inter-echo signal changes, MDI solves an optimization problem by processing all signal dimensions (eg echoes, flip angles and coil channels) in one integrative step. MDI was compared with routine curve fitting methods on noise behavior, quantification accuracy and computational efficiency. All methods were tested and compared on simulation, phantom and knee data. Monte Carlo simulations were performed on simulation and all MRI data to investigate noise propagation from k space to T<sub>2</sub> * maps. For phantom tests, T<sub>2</sub> * values in regions of interest were extracted on a voxel-wise basis and analyzed using a paired t-test between scanning parameters and mapping methods, with p < 0.05 being significantly different. MDI facilitated a straightforward processing procedure, yielding homogeneous, high-signal-to-noise-ratio (SNR) and artifact-free T<sub>2</sub> * maps without explicit coil combination or additional measures. Compared with routine fitting methods, MDI offered significantly (p < 0.05) improved SNR and quantitative accuracy/robustness, with two to three orders higher computational efficiency. MDI also represented low-SNR signals with low T<sub>2</sub> * values, avoiding misinterpretation with long-T<sub>2</sub> * species.
The Hook (1999)

The seagull was very hungry. He was soaring above the fishing village with his legs hanging down, his wings perfectly still, his head turned to one side and his sharp little eyes blinking. Above him and a little to the right, a large white flock of seagulls was cackling and diving about furiously. He alone was sailing on his own, very near the ground and perfectly silent. He saw something that he didn't want the other seagulls to see until he should get an opportunity of securing it for himself.KeywordsFemale BirdFishing VillageMale BirdSharp KnifeWhite ScaleThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
Prominin–1 (CD133): from progenitor cells to human diseases (2006)

AbstractProminin-1 (CD133) is a pentaspan membrane glycoprotein that binds to plasma membrane cholesterol and concentrates selectively in plasma membrane protrusions. In recent years, this molecule has received considerable interest due to its expression in various progenitors, including those derived from the neural and hematopoietic system, as well as in cancer originating from these systems. Prominin-1 is also the target of mutations leading to retinal degeneration. In the future, prominin-1-positive progenitor cells might become clinically significant, particularly with regard to tissue engineering, and prominin-1 itself might reveal some fundamental cell biological aspects concerning the self-renewal capacity of somatic stem cells.
Syntrophy Goes Electric: Direct Interspecies Electron Transfer (2017)

Direct interspecies electron transfer (DIET) has biogeochemical significance, and practical applications that rely on DIET or DIET-based aspects of microbial physiology are growing. Mechanisms for DIET have primarily been studied in defined cocultures in which Geobacter species are one of the DIET partners. Electrically conductive pili (e-pili) can be an important electrical conduit for DIET. However, there may be instances in which electrical contacts are made between electron transport proteins associated with the outer membranes of the partners. Alternatively, DIET partners can plug into conductive carbon materials, such as granular activated carbon, carbon cloth, and biochar, for long-range electron exchange without the need for e-pili. Magnetite promotes DIET, possibly by acting as a substitute for outer-surface c-type cytochromes. DIET is the primary mode of interspecies electron exchange in some anaerobic digesters converting wastes to methane. Promoting DIET with conductive materials shows promise for stabilizing and accelerating methane production in digesters, permitting higher organic loading rates. Various lines of evidence suggest that DIET is important in terrestrial wetlands, which are an important source of atmospheric methane. DIET may also have a role in anaerobic methane oxidation coupled to sulfate reduction, an important control on methane releases. The finding that DIET can serve as the source of electrons for anaerobic photosynthesis further broadens its potential environmental significance. Microorganisms capable of DIET are good catalysts for several bioelectrochemical technologies and e-pili are a promising renewable source of electronic materials. The study of DIET is in its early stages, and additional investigation is required to better understand the diversity of microorganisms that are capable of DIET, the importance of DIET to carbon and electron flow in anaerobic environments, and the biochemistry and physiology of DIET.
Ras (CXXX) and Rab (CC/CXC) prenylation signal sequences are unique and functionally distinct (2021)

Rab proteins typically lack the consensus carboxyl-terminal CXXX motif that signals isoprenoid modification of Ras and other isoprenylated proteins and, instead, terminate in either CC or CXC sequences (C = cysteine, X = any amino acid). To compare the functional relationship between the Ras CXXX and the Rab CC/CXC motifs, we have generated chimeric Ras proteins terminating in Rab carboxyl-terminal CC or CXC sequences. These mutant Ras proteins were not isoprenylated in vitro or in vivo, demonstrating that the CC and CXC sequences alone are not sufficient to replace a CXXX sequence to signal Ras isoprenoid modification. Surprisingly, chimeric Ras/Rab proteins terminating in significant lengths of carboxyl-terminal sequences from Rab1b (7-139 residues), Rab2 (5-151 residues), or Rab3a (12 residues) were also not isoprenylated. These results demonstrate that the sequence requirements for isoprenoid modification of Rab proteins are more complex than the simple tetrapeptide CXXX sequence for isoprenoid modification of Ras proteins and suggest that the Rab geranylgeranyl transferase(s) requires recognition of protein conformation to signal the addition of geranylgeranyl groups. Finally, competition studies demonstrate that a common geranylgeranyl transferase activity is responsible for the modification of Rab proteins terminating in CC or CXC motifs.
A qualitative analysis of software build system changes and build ownership styles (2014)

<u>Context:</u> Recent empirical studies have shown quantitatively how software build systems, which are responsible for converting software artifacts into an installable deliverable for the end user, induce considerable overhead on software developers, taking away their focus from actual development.
A Linear Kronig‐Kramers Transform Test for Immittance Data Validation (1995)

A method is described with which immittance data can be tested for Kronig‐Kramers compliance. In contrast with other procedures, this method is linear in nature and is based on a predetermined set of relaxation times. The model contains as many parameters (or less) as there are data sets. Three modes of operation are described, the first two are based on a linear fit of the model function to the imaginary part or to the real part of the data set. With the fit parameters the corresponding real or imaginary dispersion can be calculated and compared with the actual measurement. In the third mode a complex model function is fitted to the complete data set. As the model function does comply with (a relaxed set of) the Kronig‐Kramers (K‐K) rules, it will not be able to reproduce the data set satisfactory in the case of nonK‐K behavior, as can be observed from the residuals plot. Due to its linear nature, no starting values are needed for the data validation. The main limitation of this procedure is the size of the matrix and the accuracy of the matrix inversion.
Transition from a meiotic to a somatic-like DNA damage response during the pachytene stage in mouse meiosis (2019)

Homologous recombination (HR) is the principal mechanism of DNA repair acting during meiosis and is fundamental for the segregation of chromosomes and the increase of genetic diversity. Nevertheless, non-homologous end joining (NHEJ) mechanisms can also act during meiosis, mainly in response to exogenously-induced DNA damage in late stages of first meiotic prophase. In order to better understand the relationship between these two repair pathways, we studied the response to DNA damage during male mouse meiosis after gamma radiation. We clearly discerned two types of responses immediately after treatment. From leptotene to early pachytene, exogenous damage triggered the massive presence of γH2AX throughout the nucleus, which was associated with DNA repair mediated by HR components (DMC1 and RAD51). This early pathway finished with the sequential removal of DMC1 and RAD51 and was no longer inducible at mid pachytene. However, from mid-pachytene to diplotene, γH2AX appeared as large discrete foci. This late repair pattern was mediated initially by NHEJ, involving Ku70 and XRCC4, which were constitutively present, and 53BP1, which appeared at sites of damage soon after irradiation. Nevertheless, 24 hours after irradiation, a HR pathway involving RAD51 but not DMC1 mostly replaced NHEJ. Additionally, we observed the occurrence of synaptonemal complex bridges between bivalents, most likely representing chromosome translocation events that may involve DMC1, RAD51 or 53BP1. Our results reinforce the idea that the early "meiotic" repair pathway that acts by default at the beginning of meiosis is replaced from mid-pachytene onwards by a "somatic-like" repair pattern. This shift might be important to resolve DNA damage (either endogenous or exogenous) that could not be repaired by the early meiotic mechanisms, for instance those in the sex chromosomes, which lack a homologous chromosome to repair with. This transition represents another layer of functional changes that occur in meiotic cells during mid pachytene, in addition to epigenetic reprograming, reactivation of transcription, changes in the gene expression profile and acquisition of competence to proceed to metaphase.
MOSFET CURRENT SOURCE GATE DRIVERS AND TOPOLOGIES FOR HIGH EFFICIENCY AND HIGH FREQUENCY VOLTAGE REGULATOR MODULES (2009)

Thesis (Ph.D, Electrical & Computer Engineering) -- Queen's University, 2009-04-23 08:59:12.699
A distinguishing gene signature shared by tumor-infiltrating Tie2-expressing monocytes, blood “resident” monocytes, and embryonic macrophages suggests common functions and developmental relationships (2009)

We previously showed that Tie2-expressing monocytes (TEMs) have nonredundant proangiogenic activity in tumors. Here, we compared the gene expression profile of tumor-infiltrating TEMs with that of tumor-associated macrophages (TAMs), spleen-derived Gr1(+)Cd11b(+) neutrophils/myeloid-derived suppressor cells, circulating "inflammatory" and "resident" monocytes, and tumor-derived endothelial cells (ECs) by quantitative polymerase chain reaction-based gene arrays. TEMs sharply differed from ECs and Gr1(+)Cd11b(+) cells but were highly related to TAMs. Nevertheless, several genes were differentially expressed between TEMs and TAMs, highlighting a TEM signature consistent with enhanced proangiogenic/tissue-remodeling activity and lower proinflammatory activity. We validated these findings in models of oncogenesis and transgenic mice expressing a microRNA-regulated Tie2-GFP reporter. Remarkably, resident monocytes and TEMs on one hand, and inflammatory monocytes and TAMs on the other hand, expressed coordinated gene expression profiles, suggesting that the 2 blood monocyte subsets are committed to distinct extravascular fates in the tumor microenvironment. We further showed that a prominent proportion of embryonic/fetal macrophages, which participate in tissue morphogenesis, expressed distinguishing TEM genes. It is tempting to speculate that Tie2(+) embryonic/fetal macrophages, resident blood monocytes, and tumor-infiltrating TEMs represent distinct developmental stages of a TEM lineage committed to execute physiologic proangiogenic and tissue-remodeling programs, which can be co-opted by tumors.
Redefining Genomic Privacy: Trust and Empowerment (2014)

Fulfilling the promise of the genetic revolution requires the analysis of large datasets containing information from thousands to millions of participants. However, sharing human genomic data requires protecting subjects from potential harm. Current models rely on de-identification techniques in which privacy versus data utility becomes a zero-sum game. Instead, we propose the use of trust-enabling techniques to create a solution in which researchers and participants both win. To do so we introduce three principles that facilitate trust in genetic research and outline one possible framework built upon those principles. Our hope is that such trust-centric frameworks provide a sustainable solution that reconciles genetic privacy with data sharing and facilitates genetic research.
A new non-invasive voltage measurement method for wireless analysis of electrical parameters and power quality (2013)

The analysis of voltage and current waveforms is important for estimating the quality of the electric power system. In this paper we propose a non-invasive approach for measuring the voltage waveform of conductive elements such as wires or cables. This non-intrusive sensor does not require any electrical contact to the mains electricity, which makes the measurement much safer and easy. The voltage is measured by exploiting coupling-capacitance elements. With this approach, the harmonic content and the amplitude of the voltage signal is evaluated and transmitted. We also present a wireless sensor network designed to implement the proposed non-invasive voltage measurement method. Each node features a low-power, 32-bit microcontroller and a wireless transceiver to send data via the IEEE 802.15.4 standard. Finally, we compare the proposed non-intrusive method with measurements using the direct access to the wire and we demonstrate that we achieve high accuracy with a maximum error lower than 1%.
Multi-stage Multi-recursive-input Fully Convolutional Networks for Neuronal Boundary Detection (2017)

In the field of connectomics, neuroscientists seek to identify cortical connectivity comprehensively. Neuronal boundary detection from the Electron Microscopy (EM) images is often done to assist the automatic reconstruction of neuronal circuit. But the segmentation of EM images is a challenging problem, as it requires the detector to be able to detect both filament-like thin and blob-like thick membrane, while suppressing the ambiguous intracellular structure. In this paper, we propose multi-stage multi-recursiveinput fully convolutional networks to address this problem. The multiple recursive inputs for one stage, i.e., the multiple side outputs with different receptive field sizes learned from the lower stage, provide multi-scale contextual boundary information for the consecutive learning. This design is biologically-plausible, as it likes a human visual system to compare different possible segmentation solutions to address the ambiguous boundary issue. Our multi-stage networks are trained end-to-end. It achieves promising results on two public available EM segmentation datasets, the mouse piriform cortex dataset and the ISBI 2012 EM dataset.
Automating Decision Making to Help Establish Norm-Based Regulations (2017)

Norms have been extensively proposed as coordination mechanisms for both agent and human societies. Nevertheless, choosing the norms to regulate a society is by no means straightforward. The reasons are twofold. First, the norms to choose from may not be independent (i.e, they can be related to each other). Second, different preference criteria may be applied when choosing the norms to enact. On the one hand, this paper considers norm representation power and cost as alternative preference criteria. On the other hand, it identifies three different norm relationships --namely, generalisation, exclusivity, and substitutability. We show that the decisionmaking problem faced by policy makers can be encoded as a linear program, and hence solved with the aid of state-of-the-art solvers.
Towards Security and Privacy for Multi-user Augmented Reality: Foundations with End Users (2018)

Immersive augmented reality (AR) technologies are becoming a reality. Prior works have identified security and privacy risks raised by these technologies, primarily considering individual users or AR devices. However, we make two key observations: (1) users will not always use AR in isolation, but also in ecosystems of other users, and (2) since immersive AR devices have only recently become available, the risks of AR have been largely hypothetical to date. To provide a foundation for understanding and addressing the security and privacy challenges of emerging AR technologies, grounded in the experiences of real users, we conduct a qualitative lab study with an immersive AR headset, the Microsoft HoloLens. We conduct our study in pairs - 22 participants across 11 pairs - wherein participants engage in paired and individual (but physically co-located) HoloLens activities. Through semi-structured interviews, we explore participants' security, privacy, and other concerns, raising key findings. For example, we find that despite the HoloLens's limitations, participants were easily immersed, treating virtual objects as real (e.g., stepping around them for fear of tripping). We also uncover numerous security, privacy, and safety concerns unique to AR (e.g., deceptive virtual objects misleading users about the real world), and a need for access control among users to manage shared physical spaces and virtual content embedded in those spaces. Our findings give us the opportunity to identify broader lessons and key challenges to inform the design of emerging single-and multi-user AR technologies.
Genomic integration of bovine leukemia provirus: comparison of persistent lymphocytosis with lymph node tumor form of enzootic. (1980)

Integration of bovine leukemia proviral DNA in the genome of infected cells was investigated in cattle affected by either the persistent lymphocytosis or the lymph node tumor form of enzootic bovine leukosis. In persistent lymphocytosis, proviral DNA was found to be integrated at a large number of genomic sites in one-fourth to one-third of circulating leukocytes. In the lymph node tumor form, in contrast, proviral DNA was found to be integrated at one or very few sites in the genomes of a larger fraction of both circulating leukocytes and lymph node tumor cells.