gebhart/patrepeval huggingface dataset:
Geometry and Topology for Mesh Generation (2001)

The book combines topics in mathematics (geometry and topology), computer science (algorithms), and engineering (mesh generation). The motivation for these topics is the difficulty, both conceptually and in the technical execution, of combining elements of combinatorial and of numerical algorithms. Mesh generation is a topic where a meaningful combination of these different approaches to problem solving is inevitable. The book develops methods from both areas that are amenable to combination, and explains breakthrough solutions to meshing that fit into this category. This book emphasizes topics that are elementary, attractive, useful, interesting, and lend themselves to teaching, making it an ideal graduate text for courses on mesh generation.
The Significance of Responses of the Genome to Challenge (1984)

From asymmetrical to balanced genomic diversification during rediploidization: Subgenomic evolution in allotetraploid fish,
Fragment-Based Discovery of Potent and Selective DDR1/2 Inhibitors (2015)

The DDR1 and DDR2 receptor tyrosine kinases are activated by extracellular collagen and have been implicated in a number of human diseases including cancer. We performed a fragment-based screen against DDR1 and identified fragments that bound either at the hinge or in the back pocket associated with the DFG-out conformation of the kinase. Modeling based on crystal structures of potent kinase inhibitors facilitated the "back-to-front" design of potent DDR1/2 inhibitors that incorporated one of the DFG-out fragments. Further optimization led to low nanomolar, orally bioavailable inhibitors that were selective for DDR1 and DDR2. The inhibitors were shown to potently inhibit DDR2 activity in cells but in contrast to unselective inhibitors such as dasatinib, they did not inhibit proliferation of mutant DDR2 lung SCC cell lines.
The complex nature of constitutional de novo apparently balanced translocations in patients presenting with abnormal phenotypes (2005)

This high level of unexpected rearrangement complexity, if generally confirmed in the study of further patients, will have an impact on current diagnostic investigations of this type and provides an argument for the more widespread adoption of microarray analysis or other high resolution genome-wide screens for chromosome imbalance and rearrangement.
ROLE OF BACTERIAL ENDOTOXIN IN CHRONIC HEART FAILURE (2007)

Proinflammatory cytokines are now thought to play a key role in the pathophysiology of chronic heart failure, driving both symptomatic presentation and disease progression. We propose that this proinflammatory state, in turn, may be sustained through a chronic release of enterically derived bacterial endotoxin. Human trials have indicated that bacterial decontamination of the gut with concomitant decrease in lipopolysaccharide (LPS) has a positive outcome on heart disease patients. Antiendotoxin antibodies may thus represent therapeutic agents in this setting. Previously, antiendotoxin antibodies were targeted to the inner hydrophobic lipid A moiety of endotoxin in an attempt to neutralize its toxicity. These antibodies failed because they lacked specificity and bound to LPS weakly. In contrast, our studies on antiendotoxin antibodies have revealed that antibodies targeted to the hydrophilic oligosaccharides of the endotoxin have the potential to bind specifically with high affinity. Development of immunotherapeutics that can reduce systemic LPS or other agents, such as bactericidal/permeability-increasing protein that can neutralize LPS and limit inflammation safely, will enable the role of LPS in chronic heart failure to be elucidated and may pave the way to develop a new generation of effective therapeutic agents that may be directed to the treatment of chronic heart failure.
Specific action of T4 endonuclease V on damaged DNA in xeroderma pigmentosum cells in vivo. (1977)

The specific action of T4 endonuclease V on damaged DNA in xeroderma pigmentosum cells was examined using an in vivo assay system with hemagglutinating virus of Japan (Sendai virus) inactivated by UV light. A clear dose response was observed between the level of UV-induce unscheduled DNA synthesis of xeroderma pigmentosum cells and the amount of T4 endonuclease V activity added. The T4 enzyme was unstable in human cells, and its half-life was 3 hr. Fractions derived from an extract of Escherichia coli infected with T4V1, a mutant defective in the endonuclease V gene, showed no ability to restore the UV-induced unscheduled DNA synthesis of xeroderma pigmentosum cells. However, fractions derived from an extract of T4D-infected E. coli with endonuclease V activity were effective. The T4 enzyme was effective in xeroderma pigmentosum cells on DNA damaged by UV light but not in cells damaged by 4-nitroquinoline 1-oxide. The results of these experiments show that the T4 enzyme has a specific action on human cell DNA in vivo. Treatment with the T4 enzyme increased the survival of group A xeroderma pigmentosum cells after UV irradiation.
A dual‐frequency equilateral‐triangular microstrip antenna with a pair of narrow slots (1999)

A new design of a slot-loaded equilateral-triangular microstrip antenna for dual-frequency operation is presented. Results show that, by loading a pair of narrow slots centered in the triangular patch and oriented parallel to the patch's center line, a single-feed dual-frequency operation can be achieved. The two operating frequencies are associated with the perturbed TM10- and TM20-modes of the triangular microstrip antenna, and the two frequencies are of the same polarization planes and similar broadside radiation characteristics. Also, by controlling the length of the slots and the spacing between the two slots, the frequency ratio of the two frequencies is tunable within a range of about 1.35–1.5. ©1999 John Wiley & Sons, Inc. Microwave Opt Technol Lett 23: 82–84, 1999.
Studies to Prevent Degradation of Recombinant Fc-Fusion Protein Expressed in Mammalian Cell Line and Protein Characterization (2016)

Clipping of recombinant proteins is a major issue in animal cell cultures. A recombinant Fc-fusion protein, VEGFR1(D1-D3)-Fc expressed in CHOK1SV GS-KO cells was observed to be undergoing clippings in lab scale cultures. Partial cleaving of expressed protein initiated early on in cell culture and was observed to increase over time in culture and also on storage. In this study, a few parameters were explored in a bid to inhibit clipping in the fusion protein The effects of culture temperature, duration of culture, the addition of an anti-clumping agent, ferric citrate and use of protease inhibitor cocktail on inhibition of proteolysis of the Fc fusion were studied. Lowering of culture temperature from 37 to 30 °C alone appears to be the best solution for reducing protein degradation from the quality, cost and regulatory points of view. The obtained Fc protein was characterized and found to be in its stable folded state, exhibiting a high affinity for its ligand and also biological and functional activities.
Broadband, high-resolution spatial heterodyne spectrometer (2008)

Design and performance parameters for a broadband, high-resolution spatial heterodyne spectrometer (SHS) are reported. The Mark 1 SHS achieves more than a factor of 5 in continuous wavenumber coverage with a design resolving power in the hundreds of thousands.
An ultrathin (∼100μm thick) flexible light plate fabricated using self-alignment and lift-off techniques (2007)

An ultrathin (∼100μm thick) flexible light plate was designed and fabricated on a parylene template using a combination of self-alignment and lift-off techniques. The solid-state InGaN light-emitting diodes (LEDs) (λp=465nm) was used as the light source to overcome the problem of conventional organic light-emitting devices which require perfect encapsulation against the permeation of water and oxygen. After the sidewalls of LEDs were passivated by the photodefinable polymer, the LED chip array can be further sandwiched by the indium-tin oxide (ITO) and Al electrodes to form a thin-film package with all the processing temperatures below 250°C. The ITO-coated transparent parylene template can be peeled off from the glass carrier after forming the ultrathin LED light plate. The flexible light plates present no damage even after they were flexed 1000 times around a 3-cm-diameter cylinder. The present self-alignment or mask-less process is a very promising approach to flexible backlight applications.
Development of Flexible Self Adhesive Patch for Professional Heat Stress Monitoring Service (2005)

Too much exposure in a very hot environment can cause heat stress which leads to the fatal heat stroke. To prevent heat stress related diseases, flexible self adhesive patch for professional heat stress monitoring service has been developed. By using flexible printed circuit board (PCB) and silicone based packaging, high level of robustness and ease of usage has been accomplished. This patch can be repeatedly attached to the chest of the user with comfort. And it can stand the sweat and be washed with water to reuse. For this patch is small in size (9 cm triangle shape) and light in weight (55g), it can be used in the most demanding situation. To analyze the heat stress of user, it records 1 lead electrocardiogram, body temperature, humidity and 2-axis acceleration. It's Bluetoothtrade communication module can connect various terminal device according to the configuration. With the body weight input by user and 3 week work log it can estimate user work load, acclimatization, total amount of work done, wet bulb globe temperature (WBGT) index, which is the screening criteria for heat stress exposure.
Sensitivity to gefitinib (Iressa, ZD1839) in non-small cell lung cancer cell lines correlates with dependence on the epidermal growth factor (EGF) receptor/extracellular signal-regulated kinase 1/2 and EGF receptor/Akt pathway for proliferation (2004)

Gefitinib (Iressa, ZD1839), a quinazoline tyrosine kinase inhibitor that targets the epidermal growth factor receptor (EGFR), is approved for patients with advanced non-small cell lung cancer (NSCLC) in several countries including Japan. However, the mechanism of drug sensitivity to gefitinib is not fully understood. In this study, we examined the molecular basis of sensitivity to gefitinib using nine human lung cancer cell lines derived from NSCLC. PC9 was the most sensitive to gefitinib of the nine NSCLC cell lines when assayed either by colony formation or MTS assays. The various cell lines expressed different levels of EGFR, HER2, HER3, and HER4, but there was no correlation between levels of EGFR and/or HER2 expression and drug sensitivity. Phosphorylation of EGFR, protein kinase B/AKT (Akt), and extracellular signal-regulated kinase (ERK) 1/2 was inhibited by much lower concentration of gefitinib in PC9 cells than in the other eight cell lines under exponential growing conditions. About 80% of cell surface EGFR in PC-9 was internalized within 10 min, whereas only about 30-50% of the cell surface EGFR was internalized in more drug-resistant cell lines in 15-60 min. The present study is the first to demonstrate that sensitivity to growth inhibition by gefitinib in NSCLC cell lines under basal growth condition is associated with dependence on Akt and ERK1/2 activation in response to EGFR signaling for survival and proliferation and also that drug sensitivity may be related to the extent of EGF-induced down-regulation of cell surface EGFR.
WDM-enabled, 40 Gb/s hybrid integrated all-optical regenerator (2005)

We demonstrate a WDM-enabled optical regenerator incorporating wavelength selective filters for signal combining and filtering. The consequent 3 dB loss reduction allows ultra-low power switching and error-free BER performance at 40 Gb/s for all PRBS pattern lengths. (2 pages)
Isolation and characterization of a novel human papillomavirus type 6 DNA from an invasive vulvar carcinoma (1986)

Human papillomavirus type 6 (HPV-6) DNA was detected in a rapidly growing vulvar verrucous carcinoma and two recurrent tumor samples. The viral DNA (HPV-6vc) was molecularly cloned and found to have a high degree of DNA sequence homology to HPV-6b DNA. Comparison of restriction endonuclease cleavage patterns between HPV-6b and HPV-6vc genomes and DNA sequencing analysis demonstrated an additional 106 bases in the HPV-6vc genome. These additional nucleotides were located in the noncoding region of the viral genome which contains the putative viral DNA replication and early gene transcriptional control elements. Seventy-four of the additional 106 nucleotides were found as one insert in the purine-thymidine-rich region 3' to the end of the L1 open reading frame. This 74-base-pair addition had homology with viral sequences immediately upstream to it and to poly(dG-dT) sequences found in the human genome including the conserved repeated sequences in human DNA (EC1) and in the human cardiac muscle actin gene. Two smaller inserts, 19 and 15 nucleotides, were found upstream from the transcriptional control elements and demonstrate homology with regions of human alpha and gamma interferon genes.
Additive effects of obesity, hypertension, and type 2 diabetes on insulin resistance. (1994)

Resistance to insulin-mediated glucose disposal has been previously shown to be increased in association with obesity, high blood pressure, and non-insulin-dependent diabetes mellitus. We initiated the present study to quantify the separate effects of hypertension and non-insulin-dependent diabetes mellitus on insulin resistance in both nonobese and obese subjects. To accomplish this, 88 subjects were divided into the following five experimental groups: normal blood pressure, nonobese (n = 17); normal blood pressure, obese (n = 18); high blood pressure, nonobese (n = 18); high blood pressure, obese (n = 19); and high blood pressure, obese, non-insulin-dependent diabetes mellitus (n = 16). Plasma glucose and insulin concentrations were measured before and after a 75-g oral glucose load. Resistance to insulin-mediated glucose disposal was estimated by determining the steady-state plasma insulin and glucose concentrations during the last 30 minutes of a continuous infusion of somatostatin (5 micrograms/min), exogenous insulin (25 mU/m2 per minute), and glucose (240 mg/m2 per minute). Since the steady-state plasma insulin concentrations are similar in all subjects, the higher the steady-state plasma glucose, the more insulin resistant the individual. Nonobese subjects with normal blood pressure had the lowest plasma glucose and insulin responses and steady-state plasma glucose concentrations, and their values were significantly different from the other four groups. Obese or nonobese subjects with high blood pressure had significantly higher plasma glucose responses and steady-state plasma glucose concentrations than did their respective weight-matched control subjects.(ABSTRACT TRUNCATED AT 250 WORDS)
Progress of Islet Transplantation over the Last 15 Years (2015)

Diabetes mellitus prevalence is increasing worldwide. Type 1 diabetes (T1DM), which is caused mainly by autoimmune destruction of beta cells, accounts for approximately 5–10 % of all diabetes. Intensive glycemic control has been shown to reduce complications of T1DM. However, this has been difficult to achieve and is usually associated with frequent hypoglycemia. Islet transplantation (IT) has emerged as an acceptable method for the treatment of patients with T1DM who suffer for frequent severe hypoglycemia and/or glycemic lability. Although initial success was limited, improvement in IT has been observed over the last 15 years. The 5-year insulin independence rate approaches 30–50 % in some experienced centers. Even without achieving insulin independence, IT has significant benefits including prevention of hypoglycemia, stabilization of glycemic control, reduction in some complications of diabetes, and improvement in quality of life. Here, we provide a brief review on IT including its history, selection of IT candidates, description, and complications of the procedure and outcomes.
Using Gold Nanorods to Probe Cell-Induced Collagen Deformation (2006)

In biological tissue, complex mechanisms of cellular response are closely linked to the mechanical environment that cells experience. The key to understanding these mechanisms may lie in measurement of local mechanical fields near living cells and between cells. We have developed a novel optical measurement technique which combines the light elastically scattered from gold nanorods with digital image analysis to track local deformations that occur in vitro between cells, in real time, under darkfield optical microscopy. We find that measurable tension and compression exist in the intercellular matrix at the length scale of micrometers, as the cells assess, adapt, and rearrange their environment.
Tuberculosis immunology in children: diagnostic and therapeutic challenges and opportunities. (2004)

Tuberculosis (TB) is one of the most important causes of infectious morbidity and mortality worldwide. Young children are more likely to develop severe disease from the causative agent Mycobacterium tuberculosis. These clinical observations likely reflect fundamental differences in the immune systems of young children and adults. Essential to effective TB immunity are functioning macrophages, dendritic cells, strong Th1-type T-cell immunity and a relative absence of Th2-type T-cell immunity. Critical differences between adults and children relevant to TB immunity include deficiencies in macrophage and dendritic cell function, deficiencies in the development of Th1-type T-cells in response to pathogens, and the propensity for infants and young children to develop Th2-type CD4+ T-cells in response to immunogens. In this article, knowledge about the requisite components of protective immunity, differences between the immune systems of children and adults relevant to pediatric tuberculosis, M. tuberculosis-specific T-cell immunity in children, and potential application to immunodiagnostics and vaccine development will be reviewed.
Inhibition of hepatic metastasis from a human pancreatic adenocarcinoma (RWP-2) in the nude mouse by prostacyclin, forskolin, and ketoconazole (1990)

Metastasis is a multistep phenomenon in which platelets appear to play an important role. This study examined several compounds for their effects on experimental hepatic metastasis and on human pancreatic tumor cell-platelet interactions. Prostacyclin (PGI2) and forskolin (stimulators of platelet adenylate cyclase) and ketoconazole (inhibitor of lipoxygenese and thromboxane synthetase) were used in order to investigate their effects on hepatic metastases from a human pancreatic tumor cell (RWP-2) in the nude mouse. The tumor cells were injected intrasplenically and the animals were divided into control, prostacyclin (PGI2 200 micrograms), forskolin (150 micrograms), and ketoconazole (180 micrograms) groups. All three drugs were administered intraperitoneally 30 minutes before and 24 hours after the tumor cell injections. Statistically significant differences were observed between control and treated groups in tumor surface area (P less than 0.001), percentage of liver surface area occupied by tumor (P less than 0.001), and number of tumor colonies (P less than 0.004 for prostacyclin, P less than 0.005 for forskolin, and P less than 0.001 for ketoconazole). These agents also strongly inhibited RWP-2-induced platelet aggregation in human platelet-rich plasma.
Noradrenergic-specific transcription of the dopamine beta-hydroxylase gene requires synergy of multiple cis-acting elements including at least two Phox2a-binding sites. (1998)

Dopamine beta-hydroxylase (DBH) catalyzes the conversion of dopamine to noradrenaline and is selectively expressed in noradrenergic and adrenergic neurons and neuroendocrine cells. Recent data from this laboratory showed that a paired-like homeodomain (HD) protein, Phox2a, interacts with the HD-binding site residing within a composite promoter of the human DBH gene, designated domain IV, in a cell-specific manner and directly controls noradrenergic-specific DBH promoter activity. In this report, we demonstrate that three additional protein-binding sites (i.e., domains I, II, and III) between domain IV and the TATA box are critical for intact DBH promoter activity in noradrenergic cells and that they activate DBH transcription in a highly concerted manner. Transient transfection assays of mutant DBH reporter constructs indicated that domain I was active in every cell line tested, whereas domain III was preferentially active in DBH-positive cells. Remarkably, mutation of domain II was associated with inactivation of DBH promoter activity exclusively in DBH-positive cell lines, defining it as another noradrenergic-specific promoter element. The cell-specific profile of the promoter function of these sequence motifs was further supported by in vitro DNA-binding studies and Southwestern analysis. Furthermore, competition and antibody supershift assays show that transcription factors Sp1 and AP2 are the cognate nuclear factors interacting with domains I and III, respectively. Parallel evidence indicates that domain II is another Phox2a-binding site, demonstrating at least two binding sites for this factor in the upstream DBH promoter. Strikingly, four tandem copies of domain II increased the promoter activity of a minimal DBH promoter by 100- to 200-fold in DBH-positive cell lines without compromising cell specificity. Cotransfection of Phox2a-expression vector dramatically increased the activity of the multiple domain II promoter only in DBH-negative cell lines, confirming that domain II is responsive to Phox2a. Collectively, this study emphasizes a critical role of Phox2a as well as its functional synergism with other transcription factors (e.g., CREB, AP2, and Sp1) in transcriptional activation of the DBH gene.
Molecular Manipulation of Microstructures: Biomaterials, Ceramics, and Semiconductors (1997)

Organic molecules can alter inorganic microstructures, offering a very powerful tool for the design of novel materials. In biological systems, this tool is often used to create microstructures in which the organic manipulators are a minority component. Three groups of materials-biomaterials, ceramics, and semiconductors-have been selected to illustrate this concept as used by nature and by synthetic laboratories exploring its potential in materials technology. In some of nature's biomaterials, macromolecules such as proteins, glycoproteins, and polysaccharides are used to control nucleation and growth of mineral phases and thus manipulate microstructure and physical properties. This concept has been used synthetically to generate apatite-based materials that can function as artificial bone in humans. Synthetic polymers and surfactants can also drastically change the morphology of ceramic particles, impart new functional properties, and provide new processing methods for the formation of useful objects. Interesting opportunities also exist in creating semiconducting materials in which molecular manipulators connect quantum dots or template cavities, which change their electronic properties and functionality.