gebhart/patrepeval huggingface dataset:
Parameters of helix–coil transition theory for alanine‐based peptides of varying chain lengths in water (1991)

Thermal unfolding curves have been measured for a series of short alanine-based peptides that contain repeating sequences and varying chain lengths. Standard helix-coil theory successfully fits the observed transition curves, even for these short peptides. The results provide values for sigma, the helix nucleation constant, delta H0, the enthalpy change on helix formation, and for s (0 degree C), the average helix propagation parameter at 0 degree C. The enthalpy change agrees with the value determined calorimetrically. The success of helix-coil theory in describing the unfolding transitions of short peptides in water indicates that helical propensities, or s values, can be determined from substitution experiments in short alanine-based peptides.
Polyaniline and polypyrrole: Where are we headed? (1997)

The tremendous advances made during the past decade in the chemistry, electrochemistry, physics, theory and processing of polyaniline and polypyrrole and their derivatives provide a broad solid foundation for future studies and technological applications. Selected examples of recent progress will be illustrated by: (i) the synthesis of polyaniline oligomers and chiral polyaniline films, (ii) use of polyaniline in light-emitting devices, (iii) effect of substrate surface on properties of polyaniline and polypyrrole films deposited upon them, (iv) use of polypyrrole films in flexible, liquid crystal light valves, (v) preparation of patterned polyaniline and polypyrrole films by microcontact printing and (vi) application of soluble polypyrrole in sensors for volatile organic compounds.
Robust Patterns in Food Web Structure (2002)

We analyze the properties of seven community food webs from a variety of environments, including freshwater, marine-freshwater interfaces, and terrestrial environments. We uncover quantitative unifying patterns that describe the properties of the diverse trophic webs considered and suggest that statistical physics concepts such as scaling and universality may be useful in the description of ecosystems. Specifically, we find that several quantities characterizing these diverse food webs obey functional forms that are universal across the different environments considered. The empirical results are in remarkable agreement with the analytical solution of a recently proposed model for food webs.
Stereochemistry of 19-hydroxy-19a-methyl-steroids (1966)

E. Caspi and J. Wicha, Chem. Commun. (London), 1966, 209 DOI: 10.1039/C19660000209
Universal and rapid salt-extraction of high quality genomic DNA for PCR- based techniques (1997)

A very simple, fast, universally applicable and reproducible method to extract high quality megabase genomic DNA from different organisms is described. We applied the same method to extract high quality complex genomic DNA from different tissues (wheat, barley, potato, beans, pear and almond leaves as well as fungi, insects and shrimps' fresh tissue) without any modification. The method does not require expensive and environmentally hazardous reagents and equipment. It can be performed even in low technology laboratories. The amount of tissue required by this method is approximately 50-100 mg. The quantity and the quality of the DNA extracted by this method is high enough to perform hundreds of PCR-based reactions and also to be used in other DNA manipulation techniques such as restriction digestion, Southern blot and cloning.
The PapC usher forms an oligomeric channel: Implications for pilus biogenesis across the outer membrane (1998)

Bacterial virulence factors are typically surface-associated or secreted molecules that in Gram-negative bacteria must cross the outer membrane (OM). Protein translocation across the bacterial OM is not well understood. To elucidate this process we studied P pilus biogenesis in Escherichia coli. We present high-resolution electron micrographs of the OM usher PapC and show that it forms an oligomeric complex containing a channel approximately 2 nm in diameter. This is large enough to accommodate pilus subunits or the linear tip fibrillum of the pilus but not large enough to accommodate the final 6.8-nm-wide helical pilus rod. We show that P pilus rods can be unraveled into linear fibers by incubation in 50% glycerol. Thus, they are likely to pass through the usher in this unwound form. Packaging of these fibers into their final helical structure would only occur outside the cell, a process that may drive outward growth of the pilus organelles. The usher complex appears to be similar to complexes formed by members of the PulD/pIV family of OM proteins, and thus these two protein families, previously thought to be unrelated, may share structural and functional homologies.
Visualizing and modeling scattered multivariate data (1991)

Visualizing two types of scattered data-volumetric data sampled in a three-dimensional volume and surface-on-surface data sampled on a three-dimensional surface-is addressed. Since measurements are often sampled at discrete scattered locations, mathematical models that are defined over the entire domain and that interpolate or approximate the given scattered data are used. The modeling function can be evaluated over a grid, so that a conventional, off-the-shelf visualization tool that applies to data on a uniform grid can be used. Volumes, gradient, centroids, and other quantities can be computed from the model. Even though the two kinds of data and their problems look similar in their mathematical descriptions, they are solved by different methods, and the various solutions are visualized with methods that are quite different.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Introduction (2013)

Abstract The Introduction posits the book's guiding question: How did popular songs influence the industrial organization and narrative form of Hollywood cinema during the conversion to sound, from 1927 through 1931? A case is presented for studying the use of songs in non-musical films, a loose category of genre consisting of films that tended to showcase, motivate, and integrate songs in ways that could not always be explained by appealing to the conventions of Broadway musical genres. Over the course of the transition to sound, the status of the popular song performance in non-musical films shifted from modular attraction to integrated narrative device. A study of this shift and its industrial context illuminates a rich period of heterogeneity of film form and style. The Introduction closes with brief summaries of the book's five chapters.
Liver-directed neonatal gene therapy prevents cardiac, bone, ear, and eye disease in mucopolysaccharidosis I mice (2004)

Mucopolysaccharidosis I (MPS I) due to deficient alpha-L-iduronidase (IDUA) activity results in accumulation of glycosaminoglycans in many cells. Gene therapy could program liver to secrete enzyme with mannose 6-phosphate (M6P), and enzyme in blood could be taken up by other cells via the M6P receptor. Newborn MPS I mice were injected with 10(9) (high dose) or 10(8) (low dose) transducing units/kg of a retroviral vector (RV) expressing canine IDUA. Most animals achieved stable expression of IDUA in serum at 1240 +/- 147 and 110 +/- 31 units/ml, respectively. At 8 months, untreated MPS I mice had aortic insufficiency, increased bone mineral density (BMD), and reduced responses to sound and light. In contrast, MPS I mice that received high-dose RV had normal echocardiograms, BMD, auditory-evoked brain-stem responses, and electroretinograms. This is the first report of complete correction of these clinical manifestations in any model of mucopolysaccharidosis. Biochemical and pathologic evaluation confirmed that storage was reduced in these organs. Mice that received low-dose RV and achieved 30 units/ml of serum IDUA activity had no or only partial improvement. We conclude that high-dose neonatal gene therapy with an RV reduces some major clinical manifestations of MPS I in mice, but low dose is less effective.
Non-penetrating Rigid Body Simulation (1993)

This paper surveys recent work on dynamic simulation of rigid bodies with non-interpenetration constraints. The problems of collision detection and contact force determination are discussed, along with both frictionless and frictional collision and contact. For the collision-detection problem, methods which deal with objects&amp;apos; motion as a single continuous function of time are compared and contrasted to discretization methods. For the problem of determining interaction forces between contacting objects, both penalty and constraint-based methods are considered. This is an electronic reprint. Permission is granted to copy part or all of this paper for noncommercial use provided that the title and this copyright notice appear. This electronic reprint is c fl1994 by CMU. The original printed paper is c fl1994 by the Eurographics Association. Author address (May 1994): David Baraff, School of Computer Science, Carnegie Mellon University, Pittburgh, PA 15213, USA. Email: baraff@cs.cmu.edu Eurographics &amp;apos;93 State of the Art Reports Non-penetrating Rigid Body Simulation 1.0 Introduction The disparity between what we can model and visualize on a computer versus what we can physically simulate has become quite large. We have become fairly adept at creating high-quality images of complex models, but our ability to perform realistic physical simulation on these models lags far behind our ability to visualize them. In computer graphics and robotics applications, a major concern is modeling systems of objects&amp;apos; motions over time. For the most part, we wish to simulate objects&amp;apos; motions as realistically as is practical for a particular application. In particular, since most physical objects are impenetrable, it is important that our simulations correctly handle the issues of collision a...
Induction of osteoclast formation by parathyroid hormone depends on an action on stromal cells (1998)

It is believed that parathyroid hormone (PTH) increases the resorptive activity of pre-existing osteoclasts through a primary interaction with cells of the osteoblastic lineage. Much less is known, however, of the mechanisms by which PTH induces osteoclast formation. It is known that osteoclast formation occurs through a contact-dependent interaction between stromal cells and haemopoietic precursors, but it is not known whether PTH acts on stromal cells or precursors to induce osteoclast formation. To address this issue, we compared the ability of haemopoietic cultures to generate osteoclasts, identified as calcitonin receptor positive (CTRP) cells, and to resorb bone in response to PTH and 1,25(OH)2 vitamin D3 (1,25(OH)2D3). We found that when murine haemopoietic tissues were incubated at densities sufficiently high to support haemopoiesis, both PTH and 1,25(OH)2D3 induced bone resorption in bone marrow cells, but in cultures of haemopoietic spleen only 1,25(OH)2D3 induced CTRP cells, and neither hormone induced bone resorption. To determine whether these differences were attributable to differences in stromal cells or haemopoietic precursors, lower densities of haemopoietic spleen cells were incubated on osteoblastic (UMR 106), splenic or bone marrow stromal cells. We found that the behaviour of the cocultures reflected the characteristics and origin of the stromal cells. Thus, the ability of both osteoblastic and splenic stromal cells to induce CTRP cells with 1,25(OH)2D3, while only osteoblastic cells induced osteoclasts with PTH, from the same precursors, suggests that the ability of PTH to induce osteoclastic differentiation cannot be attributed to a hormonal action on osteoclast precursors, but depends on a response in stromal cells.
Pulmonary Endothelial Cell Barrier Enhancement by Sphingosine 1-Phosphate (2004)

We recently reported the critical importance of Rac GTPase-dependent cortical actin rearrangement in the augmentation of pulmonary endothelial cell (EC) barrier function by sphingosine 1-phosphate (S1P). We now describe functional roles for the actin-binding proteins cortactin and EC myosin light chain kinase (MLCK) in mediating this response. Antisense down-regulation of cortactin protein expression significantly inhibits S1P-induced barrier enhancement in cultured human pulmonary artery EC as measured by transendothelial electrical resistance (TER). Immunofluorescence studies reveal rapid, Rac-dependent translocation of cortactin to the expanded cortical actin band following S1P challenge, where colocalization with EC MLCK occurs within 5 min. Adenoviral overexpression of a Rac dominant negative mutant attenuates TER elevation by S1P. S1P also induces a rapid increase in cortactin tyrosine phosphorylation (within 30 s) critical to subsequent barrier enhancement, since EC transfected with a tyrosine-deficient mutant cortactin exhibit a blunted TER response. Direct binding of EC MLCK to the cortactin Src homology 3 domain appears essential to S1P barrier regulation, since cortactin blocking peptide inhibits both S1P-induced MLC phosphorylation and peak S1P-induced TER values. These data support novel roles for the cytoskeletal proteins cortactin and EC MLCK in mediating lung vascular barrier augmentation evoked by S1P.
Altered Airway Responsiveness in CD38-Deficient Mice (2004)

Cyclic ADP-ribose (cADPR) mobilizes calcium from intracellular stores and contributes to agonist-induced intracellular calcium elevation in airway smooth muscle (ASM). In this study we determined the functional role of CD38/cADPR signaling in the regulation of airway tone using CD38 deficient (cd38(-/-)) mice. The responsiveness to different doses of methacholine, as determined by changes in lung resistance and dynamic compliance, was significantly (P < or = 0.05) lower in cd38(-/-) mice compared with wild-type controls. To determine the mechanism responsible for the reduced responsiveness, we measured the intracellular calcium responses to contractile agonists in ASM cells. In ASM cells isolated from cd38(-/-) mice, the intracellular calcium responses to acetylcholine and endothelin-1 were significantly lower than in controls. Pretreatment of ASM cells with a cADPR antagonist resulted in attenuated intracellular calcium responses to endothelin-1 in cells isolated from wild-type mice, but not in those isolated from the cd38(-/-) mice. Very low cADPR levels and no detectable ADP-ribosyl cyclase activity were observed in lung tissue from cd38(-/-) mice, suggesting that CD38 is a critical source for cADPR synthesis. The results of the present study demonstrate that CD38/cADPR contributes to airway smooth muscle tone and responsiveness through its effects on agonist-induced elevation of intracellular calcium in ASM cells.
The establishment of a predictive mutational model of the forkhead domain through the analyses of FOXC2 missense mutations identified in patients with hereditary lymphedema with distichiasis (2005)

The FOX family of transcription factor genes is an evolutionary conserved, yet functionally diverse class of transcription factors that are important for regulation of energy homeostasis, development and oncogenesis. The proteins encoded by FOX genes are characterized by a conserved DNA-binding domain known as the forkhead domain (FHD). To date, disease-causing mutations have been identified in eight human FOX genes. Many of these mutations result in single amino acid substitutions in the FHD. We analyzed the molecular consequences of two disease-causing missense mutations (R121H and S125L) occurring in the FHD of the FOXC2 gene that were identified in patients with hereditary lymphedema with distichiasis (LD) to test the predictive capacity of a FHD structure/function model. On the basis of the FOXC2 solution structure, both FOXC2 missense mutations are located on the DNA-recognition helix of the FHD. A mutation model based on the parologous FOXC1 protein predicts that these FOXC2 missense mutations will impair the DNA-binding and transcriptional activation ability of the FOXC2 protein. When these mutations were analyzed biochemically, we found that both mutations did indeed reduce the DNA binding and transcriptional capacity. In addition, the R121H mutation affected nuclear localization of FOXC2. Together, these data indicate that these FOXC2 missense mutations are functional nulls and that FOXC2 haploinsufficiency underlies hereditary LD and validates the predictive ability of the FOXC1-based FHD mutational model.
Incidence and Management of CoreValve Dislocation During Transcatheter Aortic Valve Implantation (2010)

CoreValve dislocation during transcatheter aortic valve implantation occurred in 10% of the cases and significantly increases perioperative risk for severe complications or death. It requires individual specific management and can be managed either interventionally or, rarely, results in open surgery.
Web 2.0 and Podcasting: Implications for Health Care (2006)

Almost 12 years ago, I wrote an article for the Health Policy Newsletter called “Health Care and the Iway.” 1,2 In 1995, the World Wide Web was not yet a household concept, early adopters used Lynx or Mosaic, not Internet Explorer or Firefox, and used telephone dial-up not broadband (cable or DSL) to access the Internet from home. We’ve since survived the “dot com” crash, geared up for HIPAA, and can’t live without our email, cell phones, Blackberries or instant messaging. The Web (1.0) has become a marketing must for health care providers, an important resource for health care consumers, and a commercial success.
HSI color model based lane-marking detection (2006)

Lane-marking detection is one of the major concerned topics in the field of driving safety and intelligent vehicle. In this paper, a new method using HSI color model for lane-marking detection, HSILMD, is proposed. In HSILMD, full color images are converted into HSI color representation, within the region of interest (ROI) aiming to detect road surface on host vehicle, the difference of intensity distribution of a row of pixels within ROI is recorded and clustered with fuzzy c-means algorithm. Thresholds of intensity and saturation are selected accordingly. With simple thresholds and operations, lane markings on various road scene images are detected. Results are compared with the same scheme using RGB color model and a different scheme. Robustness of this reduced computation consumption system is observed
Inflammasome-IL-1-Th17 response in allergic lung inflammation (2011)

Allergic asthma has increased dramatically in prevalence and severity over the last three decades. Both clinical and experimental data support an important role of Th2 cell response in the allergic response. Recent investigations revealed that airway exposure to allergen in sensitized individuals causes the release of ATP and uric acid, activating the NLRP3 inflammasome complex and cleaving pro-IL-1β to mature IL-1β through caspase-1. The production of pro-IL-1β requires a toll-like receptor (TLR) 4 signal which is provided by the allergen. IL-1β creates a pro-inflammatory milieu with the production of IL-6 and chemokines which mobilize neutrophils and enhance Th17 cell differentiation in the lung. Here, we review our results showing that NLRP3 inflammasome activation is required to develop allergic airway inflammation in mice and that IL-17 and IL-22 production by Th17 cells plays a critical role in established asthma. Therefore, inflammasome activation leading to IL-1β production contributes to the control of allergic asthma by enhancing Th17 cell differentiation.
Effects of granulocyte colony-stimulating factor and granulocyte-macrophage colony-stimulating factor on lung cancer: Roles of cyclooxygenase-2 (2007)

We examined the effects of granulocyte colony-stimulating factor (G-CSF) and granulocyte-macrophage colony-stimulating factor (GM-CSF) on the lung cancer cell lines PC-9, LA-1 and A549. In addition, we examined if the effects of the cytokines on the cell lines are mediated by activation of cyclooxygenase (COX)-2. The three cell lines did not constitutively produce either G-CSF or GM-CSF. G-CSF did not influence cell growth in the three cell lines, while GM-CSF increased cell growth in the A549 and LA-1 lines. G-CSF and GM-CSF dose-dependently decreased cell death in the three cell lines. RT-PCR demonstrated GM-CSF receptor expression in the three lung cancer cell lines, whereas the G-CSF receptor exists only in the PC-9 line. We suggest that G-CSF might rescue the tumor cells from cytotoxicity due to serum deprivation through cellular pathways independent of the G-CSF receptor. G-CSF and GM-CSF increased cyclooxygenase-2 (COX-2) expression in PC-9 and LA-1 cells whereas they decreased COX-2 expression in A549 cells. The COX-2 inhibitor NS-398 increased cell death in PC-9 and LA-1 cells, whereas it decreased cell death in A549 cells. PC-9 and LA-1 clones transfected with sense G-CSF- or GM-CSF showed an increase in COX-2 expression, while COX-2 expression was decreased in transfected A549 clones. COX-2 expression was increased in anti-sense G-CSF- and GM-CSF-transfected A549 clones. Thus, although COX-2 activation seems to induce different biological behavior depending on the cell type, we propose that G-CSF and GM-CSF might accelerate tumor progression by directly regulating COX-2 expression, independently of an autocrine mechanism.
Islet Transplantation in Seven Patients with Type 1 Diabetes Mellitus Using a Glucocorticoid-Free Immunosuppressive Regimen (2000)

Our observations in patients with type 1 diabetes indicate that islet transplantation can result in insulin independence with excellent metabolic control when glucocorticoid-free immunosuppression is combined with the infusion of an adequate islet mass.