gebhart/patrepeval huggingface dataset:
Emergence of order in visual system development. (1996)

Neural connections in the adult central nervous system are highly precise. In the visual system, retinal ganglion cells send their axons to target neurons in the lateral geniculate nucleus (LGN) in such a way that axons originating from the two eyes terminate in adjacent but nonoverlapping eye-specific layers. During development, however, inputs from the two eyes are intermixed, and the adult pattern emerges gradually as axons from the two eyes sort out to form the layers. Experiments indicate that the sorting-out process, even though it occurs in utero in higher mammals and always before vision, requires retinal ganglion cell signaling; blocking retinal ganglion cell action potentials with tetrodotoxin prevents the formation of the layers. These action potentials are endogenously generated by the ganglion cells, which fire spontaneously and synchronously with each other, generating "waves" of activity that travel across the retina. Calcium imaging of the retina shows that the ganglion cells undergo correlated calcium bursting to generate the waves and that amacrine cells also participate in the correlated activity patterns. Physiological recordings from LGN neurons in vitro indicate that the quasiperiodic activity generated by the retinal ganglion cells is transmitted across the synapse between ganglion cells to drive target LGN neurons. These observations suggest that (i) a neural circuit within the immature retina is responsible for generating specific spatiotemporal patterns of neural activity; (ii) spontaneous activity generated in the retina is propagated across central synapses; and (iii) even before the photoreceptors are present, nerve cell function is essential for correct wiring of the visual system during early development. Since spontaneously generated activity is known to be present elsewhere in the developing CNS, this process of activity-dependent wiring could be used throughout the nervous system to help refine early sets of neural connections into their highly precise adult patterns.
The Schedule-Dependent Effects of the Novel Antifolate Pralatrexate and Gemcitabine Are Superior to Methotrexate and Cytarabine in Models of Human Non-Hodgkin's Lymphoma (2006)

These data show that the combination of pralatrexate followed by gemcitabine was superior to methotrexate/ara-C in vitro and in vivo, and was far more potent in inducing apoptosis in a large B-cell lymphoma. These data provide strong rationale for further study of this combination in lymphomas where methotrexate and ara-C are used.
CHD7 Expression Predicts Survival Outcomes in Patients with Resected Pancreatic Cancer (2014)

Pancreatic ductal adenocarcinoma (PDAC) is a devastating disease with poor outcomes with current therapies. Gemcitabine is the primary adjuvant drug used clinically, but its effectiveness is limited. In this study, our objective was to use a rationale-driven approach to identify novel biomarkers for outcome in patients with early-stage resected PDAC treated with adjuvant gemcitabine. Using a synthetic lethal screen in human PDAC cells, we identified 93 genes, including 55 genes linked to DNA damage responses (DDR), that demonstrated gemcitabine sensitization when silenced, including CHD7, which functions in chromatin remodeling. CHD7 depletion sensitized PDAC cells to gemcitabine and delayed their growth in tumor xenografts. Moreover, CHD7 silencing impaired ATR-dependent phosphorylation of CHK1 and increased DNA damage induced by gemcitabine. CHD7 was dysregulated, ranking above the 90th percentile in differential expression in a panel of PDAC clinical specimens, highlighting its potential as a biomarker. Immunohistochemical analysis of specimens from 59 patients with resected PDAC receiving adjuvant gemcitabine revealed that low CHD7 expression was associated with increased recurrence-free survival (RFS) and overall survival (OS), in univariate and multivariate analyses. Notably, CHD7 expression was not associated with RFS or OS for patients not receiving gemcitabine. Thus, low CHD7 expression was correlated selectively with gemcitabine sensitivity in this patient population. These results supported our rationale-driven strategy to exploit dysregulated DDR pathways in PDAC to identify genetic determinants of gemcitabine sensitivity, identifying CHD7 as a novel biomarker candidate to evaluate further for individualizing PDAC treatment.
Plaque Characteristics of Asymptomatic Carotid Stenosis and Risk of Stroke (2012)

In addition to medical history and sonographic findings, a lipid-rich necrotic core within the plaque turned out as a predictor of cerebrovascular events. Therefore, MR imaging of carotid plaques deserves further attention and might be helpful to improve risk stratification of asymptomatic carotid disease. The identified predictors could be combined in a risk model and tested in larger prospective studies.
Cytotoxic chemotherapy for advanced hormone-resistant prostate cancer (1993)

Although multidrug resistance may explain the marginal efficacy of cytotoxic drugs, methods to overcome such resistance and, more importantly, new classes of agents must be developed. In addition, reliable disease markers must be found for osseous and visceral metastases to avoid the prevailing confusion in evaluating more precisely the destruction of prostate cancer cells.
Immunological method for mapping genes on Drosophila polytene chromosomes. (1982)

A method is described for localizing DNA sequences hybridized in situ to Drosophila polytene chromosomes. This procedure utilizes a biotin-labeled analog of TTP that can be incorporated enzymatically into DNA probes by nick-translation. After hybridization in situ, the biotin molecules in the probe serve as antigens which bind affinity-purified rabbit antibiotin antibodies. The site of hybridization is then detected either fluorimetrically, by using fluorescein-labeled goat anti-rabbit IgG, or cytochemically, by using an anti-rabbit IgG antibody conjugated to horseradish peroxidase. When combined with Giemsa staining, the immunoperoxidase detection method provides a permanent record that is suitable for detailed cytogenetic analysis. This immunological approach offers four advantages over conventional autoradiographic procedures for detecting in situ hybrids: (i) the time required to determine the site of hybridization is decreased markedly, (ii) biotin-labeled probes are chemically stable and give reproducible results for many months; (iii) biotin-labeled probes appear to produce less background noise than do radiolabeled probes; and (iv) the resolving power is equal to and often greater than that achieved autoradiographically.
WCET(m) Estimation in Multi-core Systems Using Single Core Equivalence (2015)

Multi-core platforms represent the answer of the industry to the increasing demand for computational capabilities. From a real-time perspective, however, the inherent sharing of resources, such as memory subsystem and I/O channels, creates inter-core timing interference among critical tasks and applications deployed on different cores. As a result, modular per-core certification cannot be performed, meaning that: (1) current industrial engineering processes cannot be reused, (2) software developed and certified for single-core chips cannot be deployed on multi-core platforms as is. In this work, we propose the Single Core Equivalence (SCE) technology: a framework of OS-level techniques designed for commercial (COTS) architectures that exports a set of equivalent single-core virtual machines from a multi-core platform. This allows per-core schedulability results to be calculated in isolation and to hold when multiple cores of the system run in parallel. Thus, SCE allows each core of a multi-core chip to be considered as a conventional single-core chip, ultimately enabling industry to reuse existing software, schedulability analysis methodologies and engineering processes.
Specific Inhibition of DNMT1 by Antisense Oligonucleotides Induces Re-expression of Estrogen Receptor a (ER) in ER-negative Human Breast Cancer Cell Lines (2003)

Recent studies have shown that changes in epigenetic regulation, such as DNA methylation and histone acetylation, are associated with silencing of the estrogen receptor a (ER) gene in ER-negative human breast cancer cells. Treatment of these cells with the general DNMT inhibitor, 5-aza-2'deoxycytidine, led to reactivation of functional ER protein. This study addresses the hypothesis that specific inhibition of the maintenance DNA methyltransferase, DNMT1, by antisense oligonucleotides (DNMT1 ASO) is sufficient to re-express the ER gene in ER-negative human breast cancer cell lines. MDA-MB-231 and Hs578t cells were transfected with 100 nM and 150 nM DNMT1 ASO respectively for three consecutive days and evidence of DNMT1 downregulation and functional ER re-expression was sought. Significant growth reduction was observed within 48 hr and persisted after 96 hr. DNMT1 expression was blocked after exposure to DNMT1 ASO as detected by RT-PCR, Western blot and enzymatic assay whereas a mutant DNMT1 ASO had little effect. This was associated with enhanced ER mRNA and protein expression and restoration of estrogen responsiveness in MDA-MB-231 cells as demonstrated by the ability of the induced ER protein to elicit ERE-regulated reporter activity from a luciferase reporter construct. Methylation specific PCR showed that the ER CpG island was minimally demethylated, suggesting that other epigenetic events, introduced by specific DNMT1 inhibition, might also be involved in ER re-expression. Our results suggest that specific inhibition of DNMT1 expression alone is sufficient to re-express ERa in human breast cancer cell lines.
Campylobacter Polysaccharide Capsules: Virulence and Vaccines (2012)

Campylobacter jejuni remains a major cause of bacterial diarrhea worldwide and is associated with numerous sequelae, including Guillain Barré Syndrome, inflammatory bowel disease, reactive arthritis, and irritable bowel syndrome. C. jejuni is unusual for an intestinal pathogen in its ability to coat its surface with a polysaccharide capsule (CPS). These capsular polysaccharides vary in sugar composition and linkage, especially those involving heptoses of unusual configuration and O-methyl phosphoramidate linkages. This structural diversity is consistent with CPS being the major serodeterminant of the Penner scheme, of which there are 47 C. jejuni serotypes. Both CPS expression and expression of modifications are subject to phase variation by slip strand mismatch repair. Although capsules are virulence factors for other pathogens, the role of CPS in C. jejuni disease has not been well defined beyond descriptive studies demonstrating a role in serum resistance and for diarrhea in a ferret model of disease. However, perhaps the most compelling evidence for a role in pathogenesis are data that CPS conjugate vaccines protect against diarrheal disease in non-human primates. A CPS conjugate vaccine approach against this pathogen is intriguing, but several questions need to be addressed, including the valency of CPS types required for an effective vaccine. There have been numerous studies of prevalence of CPS serotypes in the developed world, but few studies from developing countries where the disease incidence is higher. The complexity and cost of Penner serotyping has limited its usefulness, and a recently developed multiplex PCR method for determination of capsule type offers the potential of a more rapid and affordable method. Comparative studies have shown a strong correlation of the two methods and studies are beginning to ascertain CPS-type distribution worldwide, as well as examination of correlation of severity of illness with specific CPS types.
A.C. Light Emitting Devices Based on Conjugated Polymers. (1996)

Abstract : Most polymer electrolumininescent devices to date are represented as tunnel diodes and operate under DC driving field. Here we report the fabrication of symmetrically configured AC light emitting (SCALE) devices based on conjugated polymers. The new devices consist of an emissive polymer layer sandwiched between two redox polymer layers. This configuration enables the SCALE devices to work under both forward and reverse DC bias as well as in AC modes. The nearly ohmic electrode/redox polymer contacts improve the charge injection efficiency significantly and make the SCALE device operation insensitive to electrode workfunctions. Symmetric operation supports the key role of redox polymer/emissive polymer interface states.
MULTIVARIABLE PROGNOSTIC MODELS: ISSUES IN DEVELOPING MODELS, EVALUATING ASSUMPTIONS AND ADEQUACY, AND MEASURING AND REDUCING ERRORS (1996)

Multivariable regression models are powerful tools that are used frequently in studies of clinical outcomes. These models can use a mixture of categorical and continuous variables and can handle partially observed (censored) responses. However, uncritical application of modelling techniques can result in models that poorly fit the dataset at hand, or, even more likely, inaccurately predict outcomes on new subjects. One must know how to measure qualities of a model's fit in order to avoid poorly fitted or overfitted models. Measurement of predictive accuracy can be difficult for survival time data in the presence of censoring. We discuss an easily interpretable index of predictive discrimination as well as methods for assessing calibration of predicted survival probabilities. Both types of predictive accuracy should be unbiasedly validated using bootstrapping or cross-validation, before using predictions in a new data series. We discuss some of the hazards of poorly fitted and overfitted regression models and present one modelling strategy that avoids many of the problems discussed. The methods described are applicable to all regression models, but are particularly needed for binary, ordinal, and time-to-event outcomes. Methods are illustrated with a survival analysis in prostate cancer using Cox regression.
Visual metrology with uncalibrated radial distorted images (2008)

Visual metrology methods with radial distorted images usually require a radial distortion model and a pre-calibration. In this paper, we propose a novel 3D metrology algorithm with at least three uncalibrated radial distorted images, and also derive a 2D metrology algorithm with at least two uncalibrated radial distorted images. The algorithm does not require a radial distortion model or calibrating camera intrinsic parameters except for radial distortion center, which can be usually known as a prior or computed easily, and correspondences of control points with known coordinates. The algorithm is of high accuracy, and robust to noise due to no requirement for specific radial distortion models. Experimental results show the feasibility and accuracy of the algorithm.
Estrogen and Prolactin Regulation of Rat Dorsal and Lateral Prostate in Organ Culture* (1991)

Besides androgens, estrogen (E) and PRL are thought to have important roles in the regulation of the growth and function of the prostate. We have established organ cultures of rat dorsolateral prostate for the analysis of the multiple hormone actions. Explants of dorsal prostate (DP) and lateral prostate (LP) were cultured in a serum-free basal medium containing insulin and corticosterone with or without the hormones studied. The viability and overall integrity of the tissues were maintained for at least 14 days. The morphology of the explants showed castration-like changes in the basal medium, but the addition of testosterone (T) prevented them. Androgen receptors in the prostate cultured with T were demonstrated by immunohistochemistry. When the explants were grown with E the epithelium became stratified, and the cells were flat. The epithelium was also layered when the explants were grown with PRL, but the epithelial cells were hypersecretory and large. The glandular morphology of the cultured prostate was, however, best preserved if T was added along with E or PRL. The wet weights and DNA contents of the explants declined during the culture, but they were better maintained if T, E, or PRL were added to the medium. The rate of DNA labeling with [3H]thymidine was activated in the cultured explants, but it was higher in those grown with T, E, or PRL than in those grown in the basal medium. The tissue specific functions were evaluated by measuring the expression of the genes RWB and M-40.3 encoding androgen-regulated secretory proteins. The steady state levels of RWB and M-40.3 mRNA were low in the explants grown in the basal medium but in the presence of T they were high. E and PRL also increased the expression of RWB and M-40.3 messenger RNA, although the responses in DP and LP were somewhat different. The antihormones cyproterone and toremifene opposed the increase of M-40.3 messenger RNA by T and E, respectively. The results show that the cultured DP and LP of the rat maintain the androgen responsiveness and tissue-specific functions in vitro. In addition, E and PRL have androgen-independent, direct effects in them. Rat dorsolateral prostate in culture thus provides a useful model for the studies on the mechanisms of hormone regulation of the prostate.
Protein Engineering of Protein Kinase A Catalytic Subunits Results in the Acquisition of Novel Inhibitor Sensitivity (2002)

Analysis of the role of specific protein kinases in signal transduction networks has relied heavily on ATP analog inhibitors. Currently used agents, however, often do not distinguish between kinase family members. Genetic approaches can also be used to inactivate a specific kinase, but these techniques do not afford the rapid kinetics possible with pharmacological inhibitors. To circumvent this problem, modification of the structure of a particular protein kinase can be performed to engineer a drug-target interaction of choice. We have used this method to create protein kinase A (PKA) catalytic subunits with modifications that confer sensitivity to novel ATP analog inhibitors. Mutation of methionine 120 to alanine or glycine in either the Calpha or Cbeta subunits of PKA induces sensitivity to a series of C-3 derivatized pyrazolo[3,4-d]pyrimidine-based inhibitors. Modification of threonine 183 enhances this inhibitor sensitivity. The IC(50) values in cell culture of the most broadly effective agent, 1-NM, ranged from 25 to 200 nm depending upon the combination of modified amino acids and were significantly higher than the potencies observed with H-89. Despite their high sequence conservation, Cbeta enzymes with inhibitor-sensitive amino acids at position 120 showed a substantial loss of overall catalytic activity when used to induce reporter gene transcription in transfected cells. Conversion of position 46 (lysine to isoleucine) rescued the ability of position 120 mutated Cbeta enzymes to induce gene transcription. Application of this combined genetic and pharmacological approach should allow analysis of the specific roles of PKA isoforms in cell culture and in vivo.
Selective and Potent Morpholinone Inhibitors of the MDM2–p53 Protein–Protein Interaction (2014)

We previously reported the discovery of AMG 232, a highly potent and selective piperidinone inhibitor of the MDM2-p53 interaction. Our continued search for potent and diverse analogues led to the discovery of novel morpholinone MDM2 inhibitors. This change to a morpholinone core has a significant impact on both potency and metabolic stability compared to the piperidinone series. Within this morpholinone series, AM-8735 emerged as an inhibitor with remarkable biochemical potency (HTRF IC50 = 0.4 nM) and cellular potency (SJSA-1 EdU IC50 = 25 nM), as well as pharmacokinetic properties. Compound 4 also shows excellent antitumor activity in the SJSA-1 osteosarcoma xenograft model with an ED50 of 41 mg/kg. Lead optimization toward the discovery of this inhibitor as well as key differences between the morpholinone and the piperidinone series will be described herein.
Anatomy and Immunology of the Ocular Surface (2007)

The ocular surface, in a strict sense, consists of the cornea and its major support tissue, the conjunctiva. In a wider anatomical, embryological, and also functional sense, the ocular mucosal adnexa (i.e. the lacrimal gland and the lacrimal drainage system) also belong to the ocular surface. This definition includes the source and the eventual drainage of the tears that are of utmost importance to ocular surface integrity. The ocular surface is directly exposed to the external environment, and therefore is endangered by a multitude of antigens and pathogenic microorganisms. As a mucosa, it is protected by the mucosal immune system that uses innate and adaptive effector mechanisms present in the tissue and tear film. Immune protection has two partly opposing tasks: the destruction of invading pathogens is counterbalanced by the limitation of inflammatory events that could be deleterious to the subtle structure of the eye. The immune system of the ocular surface forms an eye-associated lymphoid tissue (EALT) that is recognized as a new component of the mucosal immune system. The latter consists of the mucosa-associated lymphoid tissues in different organs of the body. Mucosa- and hence eye-associated lymphoid tissues have certain characteristics that discriminate them from the central immune system. The mechanisms applied are immunological ignorance, tolerance, or an immunosuppressive local microenvironment, all of which prefer non-reactivity and anti-inflammatory immunological responses. The interaction of these mechanisms results in immune privilege of the ocular surface. During eye closure, the ocular surface appears to have different requirements that make an innate pro-inflammatory environment more attractive for immune defense. The structural and functional components that contribute to this special immune regulation will be the focus of this chapter.
Xampling: Signal Acquisition and Processing in Union of Subspaces (2011)

We introduce Xampling, a unified framework for signal acquisition and processing of signals in a union of subspaces. The main functions of this framework are two: Analog compression that narrows down the input bandwidth prior to sampling with commercial devices followed by a nonlinear algorithm that detects the input subspace prior to conventional signal processing. A representative union model of spectrally sparse signals serves as a test-case to study these Xampling functions. We adopt three metrics for the choice of analog compression: robustness to model mismatch, required hardware accuracy, and software complexities. We conduct a comprehensive comparison between two sub-Nyquist acquisition strategies for spectrally sparse signals, the random demodulator and the modulated wideband converter (MWC), in terms of these metrics and draw operative conclusions regarding the choice of analog compression. We then address lowrate signal processing and develop an algorithm for that purpose that enables convenient signal processing at sub-Nyquist rates from samples obtained by the MWC. We conclude by showing that a variety of other sampling approaches for different union classes fit nicely into our framework.