gebhart/patrepeval huggingface dataset:
Comparison of the Bacterial Clearing Effects of Different Biologic Dressings on Granulating Wounds Following Thermal Injury (1980)

In 16 patients with thermal injury, no difference in bacterial clearing was noted when wounds were dressed with cadaver homograft skin, porcine skin, either mesh or sheet, and with amnion. Because of cost and ease we prefer fresh porcine skin for second- and third-degree burns.
Biochemistry of carbohydrate‐protein interaction 1 (1992)

Recognition of glycoconjugates is an important event in biological systems, and is frequently in the form of carbohydrate-protein interactions. To thoroughly understand these interactions, well-defined carbohydrate ligands must be available. Naturally derived glycoconjugates can be highly purified, and their structures (including conformational structures) can be elucidated to provide such ligands. This requires highly effective methods of separation, such as various forms of high-performance liquid chromatography. Alternatively, structurally well-defined glycoconjugates can be synthesized for this purpose. These include conjugates of carbohydrate derivatives to proteins, lipids, and nonbiological carriers and polymers. The efficacy of these conjugates is amply demonstrated in the studies of carbohydrate-binding proteins from animals. Hepatic carbohydrate receptors, requiring calcium for binding, recognize only the terminal sugar residues. Although different sugar specificities are manifested by different species, there is some commonality in the requirement of the substituents of the sugar rings. Clustering of the target sugars in proper geometric arrangement greatly enhances the binding by these proteins. Some other animal carbohydrate-binding proteins, however, may require penultimate sugars for optimal binding.
A theoretically grounded application of dropout in recurrent neural networks (2016)

Recurrent neural networks (RNNs) stand at the forefront of many recent developments in deep learning. Yet a major difficulty with these models is their tendency to overfit, with dropout shown to fail when applied to recurrent layers. Recent results at the intersection of Bayesian modelling and deep learning offer a Bayesian interpretation of common deep learning techniques such as dropout. This grounding of dropout in approximate Bayesian inference suggests an extension of the theoretical results, offering insights into the use of dropout with RNN models. We apply this new variational inference based dropout technique in LSTM and GRU models, assessing it on language modelling and sentiment analysis tasks. The new approach outperforms existing techniques, and to the best of our knowledge improves on the single model state-of-the-art in language modelling with the Penn Treebank (73.4 test perplexity). This extends our arsenal of variational tools in deep learning.
Replication Defect of Moloney Murine Leukemia Virus with a Mutant Reverse Transcriptase That Can Incorporate Ribonucleotides and Deoxyribonucleotides (1998)

Reverse transcriptase (RT) plays a critical role in retrovirus replication, directing the synthesis of a double- stranded DNA copy of the viral RNA genome. We have previously described a mutant RT of the Moloney murine leukemia virus in which F155 was replaced by valine, and we demonstrated that this substitution allowed the enzyme to incorporate ribonucleotides to form RNA while still retaining its normal ability to incorporate deoxyribonucleotides to form DNA. When introduced into the viral genome, this mutation rendered the virus incapable of replication. Characterization of the mutant virus revealed that the enzyme was still active and able to synthesize minus-strand strong stop DNA and some longer products but failed to make full-length minus-strand DNA. We propose that the failure of the enzyme to complete DNA synthesis in vivo resulted from its ability to incorporate ribonucleotides into the products, which served as inhibitors for DNA synthesis. We also tested seven other amino acid residues for their abilities to substitute for F155 in virus replication; of these, only tyrosine could support virus replication. In an attempt to select for second-site suppressor mutations, the F155V mutant was subjected to random mutagenesis and was used as a parent for the isolation of revertant viruses. Two independent revertants were found to have changed the valine residue at position 155 back to the wild- type phenylalanine. These results suggest that an aromatic ring at this position is important for virus replication.
A Computer-Controlled Super-8 Projector (1977)

Research conducted within Project C-BE (Computer-Based Science and Engineering Education) and other research has identified the need for random access computer-controlled motion-picture output at interactive computer terminals. The Kodak Supermatic 60 Super 8 magnetic sound motion picture projector was chosen for modification because it featured through-the-gate rewinding, auto-threading from cassettes, high reliability, and electrical controls. Mechanical modifications, included within the standard housing, involved adding four units (a fast-forward clutch with an actuator solenoid, a feed reel brake, a separate rewind clutch solenoid, and photodiodes in the film path to provide sprocket-hole motion signals). The projector is controlled by an electronic interface and control unit which receives its commands from the time-shared computer. The interface unit scans ASCII characters received from the computer and responds to control commands by performing the necessary operations without operator intervention. Search speed, forward and reverse, is about 450 frames/s and search accuracy is within four frames or better. Although the system is being used to teach observation skills in the area of child development, numerous other possible applications are envisioned. To the authors' knowledge, this is the only low-cost device to provide random access sound motion-picture output at a computer terminal.
Targeted insertion results in a Rhombomere 2‐specific Hoxa2 knockdown and ectopic activation of Hoxa1 expression (2002)

Recent studies indicated that retention of selectable marker cassettes in targeted Hox loci may cause unexpected phenotypes in mutant mice, due to neighborhood effects. However, the molecular mechanisms have been poorly investigated. Here, we analysed the effects of the targeted insertion of a PGK-neo cassette in the 3' untranslated region of Hoxa2. Even at this 3' position, the insertion resulted in homozygous mutants that unexpectedly did not survive beyond 3 weeks of age. Molecular analysis of the targeted allele revealed a selective "knockdown" of Hoxa2 expression in rhombomere 2 and associated patterning abnormalities. Moreover, Hoxa1 was ectopically expressed in the hindbrain and branchial arches of mutant embryos. Of interest, we demonstrated that the ectopic expression was due to the generation of neo-Hoxa1 fusion transcripts, resulting from aberrant alternative splicing. These defects could be rescued after removal of the PGK-neo cassette by Flp-mediated recombination. These results underscore the complexity of transcriptional regulation at Hox loci and provide insights into the in vivo regulation of Hoxa2 segmental expression. They also provide a molecular basis for the interpretation of unexpected Hox knockout phenotypes in which the targeted selectable marker is retained in the locus.
Meta-Information for Knowledge Navigation and Retrieval: What's In There (1995)

Knowledge navigation in the business world is oftell a difficult and expensive process. Commercial databases are notoriously incomplete and inaccurate, access charges can run into hundreds of dollars per hour, and the client always wants the answer yesterday. In coping with such problems, professionals who search for information on a daily basis rely on metainformation that goes beyond standard descriptions of the of data sources. For example, in working with information specialists at Price Waterhouse LLP (PW), a large professional services provider, one point we were advised, you’re looking for quick information about foreign companies that’s not too out-of-date, use database so-and-so because the vendor is offering free connect time this month. Such a heuristic does involve the source’s semantic content, of course, but also refers to resources (money) available for the retrieval, and quality (timeliness) of the retrieved data. If the tools we build are to make knowledge navigation in the business world any easier, they will have to exploit, or at least represent, this type of meta-information in choosing information search and retrieval strategies. A number of researchers have noted the importance of meta-information. KQML [Finin et al., 1994] provides an interprocess communication language for information agents, but makes few commitments about the semantics of the meta-information to be communicated. MCC’s Carnot project [Collet el al., 1991] introduced some of the necessary computational infrastructure with concept matching and resource models. The SIMS project [Arens el al., 1993] exploits some semantic and run-time recta-information to produce efficient query plans. Yet there has been little reported in the literature on exactly what meta-information is important for describing real-world task contexts. We present our preliminary findings on this subject in this paper. Our goal is to create a content theory on which to base languages and support tools for the delivery of knowledge services, in contrast to focusing more narrowly on answering queries in isolation. We define a knowledge service as the provision of in some form and at some level of quality, subject to constraints on the resources needed to perform the service. This paper begins with some conceptual preliminaries, and then discuss these four elements in more detail. As illustrative examples of the use of meta-information, the paper describes two knowledge services: monitoring management changes, and search for potential conflicts of interest in prospective litigation support clients.
A Model for the Spectral Albedo of Snow. I: Pure Snow (1980)

Abstract We present a method for calculating the spectral albedo of snow which can be used at any wavelength in the solar spectrum and which accounts for diffusely or directly incident radiation at any zenith angle. For deep snow, the model contains only one adjustable parameter, an effective grain size, which is close to observed grain sizes. A second parameter, the liquid-equivalent depth, is required only for relatively thin snow. In order for the model to make realistic predictions, it must account for the extreme anisotropy of scattering by snow particles. This is done by using the “delta-Eddington” approximation for multiple scattering, together with Mie theory for single scattering. The spectral albedo from 0.3 to 5 μm wavelength is examined as a function of the effective grain size, the solar zenith angle, the snowpack thickness, and the ratio of diffuse to direct solar incidence. The decrease in albedo due to snow aging can be mimicked by reasonable increases in grain size (50–100 μm for new snow...
GITR-GITRL System, A Novel Player in Shock and Inflammation (2007)

Glucocorticoid-induced TNFR-Related (GITR) protein is a member of the tumor necrosis factor receptor superfamily that modulates acquired and natural immune response. It is expressed in several cells and tissues, including T cells, natural killer cells, and, at lower levels, in cells of innate immunity. GITR is activated by its ligand, GITRL, mainly expressed on antigen presenting and endothelial cells. Recent evidence suggests that the GITR/GITRL system participates in the development of inflammatory responses, including shock, either due to early response of neutrophils and macrophages, or together with autoimmune/allergic pathogenesis. The pro-inflammatory role of the GITR/GITRL system is due to: 1) modulation of the extravasation process, 2) activation of innate immunity cells, 3) activation of effector T cells also favored by partial inhibition of suppressor T cells and modulation of dendritic function. This review summarizes the in vivo role of the GITR/GITRL system in inflammation and shock, explaining the mechanisms responsible for their effects, considering the interplay among the different cells of the immune system and transduction pathways activated by GITR and GITRL triggering. The hidden aspects about GITR/GITRL function, crucial for treatment planning of inflammatory diseases and shock by modulation of this system is stressed.
‘Giant’ CdSe/CdS Core/Shell Nanocrystal Quantum Dots As Efficient Electroluminescent Materials: Strong Influence of Shell Thickness on Light-Emitting Diode Performance (2011)

We use a simple device architecture based on a poly(3,4-ethylendioxythiophene):poly(styrenesulfonate) (PEDOT:PSS)-coated indium tin oxide anode and a LiF/Al cathode to assess the effects of shell thickness on the properties of light-emitting diodes (LEDs) comprising CdSe/CdS core/shell nanocrystal quantum dots (NQDs) as the emitting layer. Specifically, we are interested in determining whether LEDs based on thick-shell nanocrystals, so-called "giant" NQDs, afford enhanced performance compared to their counterparts incorporating thin-shell systems. We observe significant improvements in device performance as a function of increasing shell thickness. While the turn-on voltage remains approximately constant for all shell thicknesses (from 4 to 16 CdS monolayers), external quantum efficiency and maximum luminance are found to be about one order of magnitude higher for thicker shell nanocrystals (≥13 CdS monolayers) compared to thinner shell structures (<9 CdS monolayers). The thickest-shell nanocrystals (16 monolayers of CdS) afforded an external quantum efficiency and luminance of 0.17% and 2000 Cd/m(2), respectively, with a remarkably low turn-on voltage of ~3.0 V.
Serum‐free culture of normal human melanocytes: Growth kinetics and growth factor requirements (1989)

Normal human epidermal melanocytes were selectively propagated from mixed (keratinocyte-melanocyte) cultures and primary epidermal cell suspensions in serum-free medium, MCDB 153 containing insulin, bovine pituitary extract (BPE), phorbol-12-myristate-13-acetate (PMA), ethanolamine, phosphoethanolamine, and hydrocortisone. Neonatal foreskin melanocytes (NFMs) replicated more readily than adult melanocytes in culture. Early passage NFMs grown in serum-free medium exhibited a population generation time of 24-48 hours. NFMs assumed a less dendritic appearance and were less pigmented than adult melanocytes. PMA or other protein kinase C-activating phorbol esters significantly enhanced mitogenesis of NFMs; however, cAMP-elevating agents were not required for efficient replication of NFMs. Basic fibroblast growth factor (bFGF) was a potent mitogen for NFMs and replaced the requirement for BPE in the culture medium. NFMs expressed a single class of specific, high-affinity receptors for bFGF, exhibiting a Kd = 3 x 10(-11) M and approximately 76,500 receptors/cell. Neither EGF nor TGF-alpha were mitogenic for NFMs, and TGF-beta reversibly inhibited NFM growth. Rapidly growing, early passage NFMs were shown to have cell cycle times of 19.5, 7.5, and 9 hours for G1, S, and G2/M phases of the cell cycle, respectively. Culture of NFMs to confluence or depletion of growth factors from the culture medium caused reversible, G1 phase-specific, cell cycle growth arrest. Senescence of NFMs was associated with irreversible growth arrest in the G1 phase after 40-45 population doublings in culture. Our data demonstrate that basal medium MCDB 153 can be supplemented with defined factors to cultivate selectively two major constituent cell types of the epidermis, the melanocyte and the keratinocyte.
Hierarchical, learning-based automatic liver segmentation (2008)

In this paper we present a hierarchical, learning-based approach for automatic and accurate liver segmentation from 3D CT volumes. We target CT volumes that come from largely diverse sources (e.g., diseased in six different organs) and are generated by different scanning protocols (e.g., contrast and non-contrast, various resolution and position). Three key ingredients are combined to solve the segmentation problem. First, a hierarchical framework is used to efficiently and effectively monitor the accuracy propagation in a coarse-to-fine fashion. Second, two new learning techniques, marginal space learning and steerable features, are applied for robust boundary inference. This enables handling of highly heterogeneous texture pattern. Third, a novel shape space initialization is proposed to improve traditional methods that are limited to similarity transformation. The proposed approach is tested on a challenging dataset containing 174 volumes. Our approach not only produces excellent segmentation accuracy, but also runs about fifty times faster than state-of-the-art solutions [7, 9].
Vaxfectin: a versatile adjuvant for plasmid DNA- and protein-based vaccines (2010)

Vaxfectin has effectively boosted the immune response against a range of pDNA-expressed pathogenic antigens in preclinical models extending from rodents to non-human primates. In the clinic, Vaxfectin-adjuvanted pDNA-based H5N1 influenza vaccines have been shown to be well tolerated and to result in durable immune responses within the predicted protective range reported for protein-based vaccines.
Effects of glucose and fructose solutions on food intake and gastric emptying in nonobese women (1994)

The differential effects of fructose and glucose on food intake were studied by giving two concentrations (1 and 10%) of glucose and fructose solutions (500 ml) to one group of women 30 min, and to another 135 min, before a meal of macaroni and beef. The 1% solutions of each sugar were sweetened to match 10% fructose by selective additions of aspartame. Gastric emptying of the 10% solutions and water was measured for 90 min. Under the 30-min delay, subjects ate a mean of 75.8 g more (P < 0.05) after the 1% solutions than after water, and 52.2 g (P > 0.05) less after the 10% solutions than after water, but there were no differences in intake between types of sugar under either delay nor between concentrations at the 135-min delay. However, 10% fructose and 1% glucose sweetened to match it reduced intake significantly compared with water. Glucose (10%) emptied significantly slower (t1/2 = 93.61 min) than water (t1/2 = 29.77 min), while fructose (10%) was intermediate (t1/2 = 65.45 min). Therefore, gastric emptying differences did not account for these results. We conclude that sweetener-enhanced dilute sugar solutions may increase subsequent intake at 30 min, but dilute glucose solutions may have potential for substantial energy savings if consumed 135 min before a meal.
Addition of p-Azido-l-phenylalanine to the Genetic Code of Escherichia coli (2002)

We report the selection of a new orthogonal aminoacyl tRNA synthetase/tRNA pair for the in vivo incorporation of a photocrosslinker, p-azido-l-phenylalanine, into proteins in response to the amber codon, TAG. The amino acid is incorporated in good yield with high fidelity and can be used to crosslink interacting proteins.
The molecular mechanisms that control thrombopoiesis (2005)

Our understanding of thrombopoiesis--the formation of blood platelets--has improved greatly in the last decade, with the cloning and characterization of thrombopoietin, the primary regulator of this process. Thrombopoietin affects nearly all aspects of platelet production, from self-renewal and expansion of HSCs, through stimulation of the proliferation of megakaryocyte progenitor cells, to support of the maturation of these cells into platelet-producing cells. The molecular and cellular mechanisms through which thrombopoietin affects platelet production provide new insights into the interplay between intrinsic and extrinsic influences on hematopoiesis and highlight new opportunities to translate basic biology into clinical advances.
Neurosteroid Analogues. 6. The Synthesis and GABAA Receptor Pharmacology of Enantiomers of Dehydroepiandrosterone Sulfate, Pregnenolone Sulfate, and (3α,5β)-3-Hydroxypregnan-20-one Sulfate (1998)

The unnatural enantiomers of dehydroepiandrosterone sulfate (1), pregnenolone sulfate (2), and (3alpha,5beta)-3-hydroxypregnan-20-one sulfate (3), compounds 4-6, respectively, were prepared by total steroid synthesis. The enantioselectivity of the compounds as negative modulators of the GABAA receptors present in cultured rat hippocampal neurons was examined using electrophysiological methods. Enantioselectivity was found for the inhibitory actions of the dehydroepiandrosterone enantiomers. The IC50s for compounds 1 and 4 were 11 +/- 1 and 80 +/- 14 microM, respectively. Little, if any, enantioselectivity was found for the other two pairs of steroid sulfate inhibitors. The IC50s for compounds 2 and 5 were 82 +/- 12 and 76 +/- 27 microM, respectively. The IC50s for compounds 3 and 6 were 39 +/- 7 and 46 +/- 2 microM, respectively. The results suggest that the sites of action for the androstane and pregnane series of steroid sulfate blockers of GABA-mediated current are different. The observed enantioselectivity for the actions of dehydroepiandrosterone sulfate indicates that its inhibitory actions are mediated via a chiral recognition site and provides new evidence in support of the earlier hypothesis that there is a binding site for this compound on GABAA receptors. Conversely, the failure to observe enantioselectivity for the actions of pregnenolone sulfate and steroid sulfate 3 indicates that a chiral recognition site for these steroids does not exist on GABAA receptors and suggests that the effects of these compounds on this receptor's function may arise indirectly as a consequence of steroid-induced membrane perturbation.
Prospective Early Response Imaging Biomarker for Neoadjuvant Breast Cancer Chemotherapy (2007)

Diffusion MRI was shown to detect early changes in the tumor microenvironment, which correlated with standard measures of tumor response as well as overall outcome. Moreover, these findings show the feasibility of using diffusion MRI for assessing treatment response of a breast tumor model in a neoadjuvant setting.
Dynamic Network Energy Management via Proximal Message Passing (2014)

Dynamic Network Energy Management via Proximal Message Passing presents a fully decentralized method for dynamic network energy management based on message passing between devices. It considers a network of devices, such as generators, fixed loads, deferrable loads, and storage devices, each with its own dynamic constraints and objective, connected by AC and DC lines. The problem is to minimize the total network objective subject to the device and line constraints, over a given time horizon. This is a large optimization problem, with variables for consumption or generation for each device, power flow for each line, and voltage phase angles at AC buses, in each time period. This text develops a decentralized method for solving this problem called proximal message passing. The method is iterative: At each step, each device exchanges simple messages with its neighbors in the network and then solves its own optimization problem, minimizing its own objective function, augmented by a term determined by the messages it has received. It is shown that this message passing method converges to a solution when the device objective and constraints are convex. The method is completely decentralized, and needs no global coordination other than synchronizing iterations; the problems to be solved by each device can typically be solved extremely efficiently and in parallel. The method is fast enough that even a serial implementation can solve substantial problems in reasonable time frames. Results for several numerical experiments are reported, demonstrating the method's speed and scaling, including the solution of a problem instance with over ten million variables in under fifty minutes for a serial implementation; with decentralized computing, the solve time would be less than one second.