gebhart/patrepeval huggingface dataset:
Calorie Restriction: Effect on Growth of Human Tumors Heterotransplanted in Nude Mice<xref ref-type="fn" rid="FN2">2</xref><xref ref-type="fn" rid="FN3">3</xref> (1982)

The presence of 4 human malignant tumors (1 breast, 1 lung, and 2 colon carcinomas) growing subcutaneously as heterotransplants in nude mice did not significantly affect the body weights of adult animals until the tumors reached very large dimensions (tumor wt greater than 15% of the body wt). However, a colon carcinoma (HT 29) induced a cessation of the natural rate of body weight increase when it grew in young adults (animals weighing approximately equal to 25 g which will gain 6 g or approximately equal to 25% body wt in 1 mo). Calorie restriction at all the levels tested (8, 6, 4, and 2 g/day/mouse) with standard pelletized mouse food produced both weight loss in the animals (with and without tumor) and a lowering of the growth rate of all the 4 tumors tested growing at a subcutaneous site and/or under the kidney capsule. Each tumor responded differently to the calorie restriction. The 4 tumors tested grew equally in both male and female nude mice. Young animals weighing 20 g inoculated with a fifth tumor (MeWo melanoma) exhibited tumor growth inhibition proportional to restriction of calorie intake. Their survival, however, did not improve.
Functional Genomic Screening Independently Identifies CUL3 as a Mediator of Vemurafenib Resistance via Src-Rac1 Signaling Axis (2020)

Patients with malignant melanoma have a 5-year survival rate of only 15-20% once the tumor has metastasized to distant tissues. While MAP kinase pathway inhibitors (MAPKi) are initially effective for the majority of patients with melanoma harboring BRAF<sup>V600E</sup> mutation, over 90% of patients relapse within 2 years. Thus, there is a critical need for understanding MAPKi resistance mechanisms. In this manuscript, we performed a forward genetic screen using a whole genome shRNA library to identify negative regulators of vemurafenib resistance. We identified loss of NF1 and CUL3 as drivers of vemurafenib resistance. NF1 is a known driver of vemurafenib resistance in melanoma through its action as a negative regulator of RAS. However, the mechanism by which CUL3, a key protein in E3 ubiquitin ligase complexes, is involved in vemurafenib resistance was unknown. We found that loss of CUL3 was associated with an increase in RAC1 activity and MEK<sup>S298</sup> phosphorylation. However, the addition of the Src family inhibitor saracatinib prevented resistance to vemurafenib in CUL3<sup>KD</sup> cells and reversed RAC1 activation. This finding suggests that inhibition of the Src family suppresses MAPKi resistance in CUL3<sup>KD</sup> cells by inactivation of RAC1. Our results also indicated that the loss of CUL3 does not promote the activation of RAC1 through stabilization, suggesting that CUL3 is involved in the stability of upstream regulators of RAC1. Collectively, our study identifies the loss of CUL3 as a driver of MAPKi resistance through activation of RAC1 and demonstrates that inhibition of the Src family can suppress the MAPKi resistance phenotype in CUL3<sup>KD</sup> cells by inactivating RAC1 protein.
Computation of Surface Orientation and Structure of Objects Using Grid Coding (1987)

In this correspondence, algorithms are introduced to infer surface orientation and structure of visible object surfaces using grid coding. We adopt the active lighting technique to spatially ``encode'' the scene for analysis. The observed objects, which can have surfaces of arbitrary shape, are assumed to rest on a plane (base plane) in a scene which is ``encoded'' with light cast through a grid plane. Two orthogonal grid patterns are used, where each pattern is obtained with a set of equally spaced stripes marked on a glass pane. The scene is observed through a camera and the object surface orientation is determined using the projected patterns on the object surface. If the surfaces under consideration obey certain smoothness constraints, a dense orientation map can be obtained through proper interpolation. The surface structure can then be recovered given this dense orientation map. Both planar and curved surfaces can be handled in a uniform manner. The algorithms we propose yield reasonably accurate results and are relatively tolerant to noise, especially when compared to shape-from-shading techniques. In contrast to other grid coding techniques reported which match the grid junctions for depth reconstruction under the stereopsis principle, our techniques use the direction of the projected stripes to infer local surface orientation and do not require any correspondence relationship between either the grid lines or the grid junctions to be specified. The algorithm has the ability to register images and can therefore be embedded in a system which integrates knowledge from multiple views.
PRIMROSE: a computer program for generating and estimating the phylogenetic range of 16S rRNA oligonucleotide probes and primers in conjunction with the RDP-II database (2002)

We describe PRIMROSE, a computer program for identifying 16S rRNA probes and PCR primers for use as phylogenetic and ecological tools in the identification and enumeration of bacteria. PRIMROSE is designed to use data from the Ribosomal Database Project (RDP) to find potentially useful oligonucleotides with up to two degenerate positions. The taxonomic range of these, and other existing oligonucleotides, can then be explored, allowing for the rapid identification of suitable oligonucleotides. PRIMROSE includes features to allow user-defined sequence databases to be used. An in silico trial of the program using the RDP database identified oligonucleotides that described their target taxa with a degree of accuracy far greater than that of equivalent currently used oligonucleotides. We identify oligonucleotides for subdivisions of the Proteobacteria and for the Cytophaga-Flexibacter-Bacteroides (CFB) division. These oligonucleotides describe up to 94.7% of their target taxon with fewer than 50 non-target hits, and the authors recommend that they be investigated further. A comparison with PROBE DESIGN within the ARB software package shows that PRIMROSE is capable of identifying oligonucleotides with a higher specificity. PRIMROSE has an intuitive graphical user interface and runs on the Microsoft Windows 95/NT/2000 operating systems. It is open source and is freely available from the authors.
5,10,15-Triphenylcorrole: a product from a modified Rothemund reaction (1999)

One-pot synthesis of 5,10,15-triphenylcorrole has been achieved by reaction of benzaldehyde with an excess of pyrrole; the triphenylphosphinocobalt complex of 5,10,15-triphenylcorrole has been structurally characterized using X-ray crystallography.
The Clinical Usefulness of Serum Prostate Specific Antigen After Hormonal Therapy of Metastatic Prostate Cancer (1992)

We longitudinally followed serum prostate specific antigen (PSA) levels in 48 patients who were treated with either orchiectomy, monthly luteinizing hormone-releasing hormone injection or continuous diethylstilbestrol for stage D2 prostate adenocarcinoma and achieved an objective response. Of the patients 34 had clinical evidence of disease progression (median remission duration 19 months). Median length of followup for the 14 patients who remained in remission was 42 months. Pretreatment performance status, pretreatment extent of metastases as measured by a bone scan and post-treatment nadir PSA level were univariately correlated with remission duration. After adjustment for the 2 former pretreatment variables, a highly significant independent effect of the nadir PSA level on remission duration persisted. Patients whose post-treatment nadir PSA level decreased below 4 ng./ml. had a significantly longer remission duration than those whose nadir PSA remained elevated (median 42 versus 10 months, p less than 0.0001). No cases were observed to progress (as defined by our criteria independent of PSA level) while the serial post-treatment PSA levels continued to decrease or remained at a plateau after reaching the nadir. The time at which the PSA began to increase once the nadir was reached predated objective evidence of progression in all patients except 2 in whom the 2 events occurred simultaneously (mean lead time 7.3 +/- 5.0 months). We conclude that following serial PSA levels in patients treated with androgen ablation for metastatic prostate cancer can aid in distinguishing favorable from nonfavorable responders early in the course of therapy and greatly assist in monitoring for progression.
Use of Bowel for Vaginal Reconstruction (1994)

There is a wide range of congenital vaginal abnormalities that can be reconstructed using bowel. From 1964 to 1993 we used bowel for vaginal reconstruction in 65 patients and all but 5 were treated since 1981. Patient age ranged from 9 months to 26 years. In 29 patients the bowel was used to extend a short vagina to the perineum, and in 36 the entire vagina was absent and required a substitute vagina. Indications for surgery included cloacal malformations in 34 cases, congenital absence of vagina in 12, cloacal exstrophy in 9 genetic male subjects, postoperative exenteration in 7, intersex in 2 and bladder exstrophy in 1. Rectum was used in 12 cases, sigmoid colon in 27 and small bowel in 26. Ten patients who are now adults have reported satisfactory coitus.
Electrochemical Investigation of Traps in a Nanostructured TiO2 Film (2001)

Electron traps at the nanostructured TiO2 (anatase)/aqueous electrolyte interface have been studied by means of electrochemical methods. The transient current decays at different potentials positive of the flat band potential clearly illustrate the trap-filling process. The more negative the potential, the shorter the trap-filling period. It is found that most traps locate positive of −0.9 V vs Ag/AgCl at pH 13, or positive of −0.3 V vs Ag/AgCl at pH 4.7. It is proposed that the trap distribution as a function of potential is directly proportional to dQ/dU, i.e., to the current density in a linear sweep voltammetry experiment. The trap densities in aqueous electrolytes are estimated to be 4 × 1011 cm-2 (microscopic area) at pH 4.7 and 5 × 1013 cm-2 (microscopic area) at pH 13. The pH dependency of the trap density indicates that traps investigated are surface-related.
The Netherlands protocol for standardisation and quantification of FDG whole body PET studies in multi-centre trials (2008)

The protocol was successfully implemented in the Netherlands and has been approved by the Netherlands Society of Nuclear Medicine.
Textual resource acquisition and engineering (2012)

A key requirement for high-performing question-answering (QA) systems is access to high-quality reference corpora from which answers to questions can be hypothesized and evaluated. However, the topic of source acquisition and engineering has received very little attention so far. This is because most existing systems were developed under organized evaluation efforts that included reference corpora as part of the task specification. The task of answering Jeopardy!™ questions, on the other hand, does not come with such a well-circumscribed set of relevant resources. Therefore, it became part of the IBM Watson™ effort to develop a set of well-defined procedures to acquire high-quality resources that can effectively support a high-performing QA system. To this end, we developed three procedures, i.e., source acquisition, source transformation, and source expansion. Source acquisition is an iterative development process of acquiring new collections to cover salient topics deemed to be gaps in existing resources based on principled error analysis. Source transformation refers to the process in which information is extracted from existing sources, either as a whole or in part, and is represented in a form that the system can most easily use. Finally, source expansion attempts to increase the coverage in the content of each known topic by adding new information as well as lexical and syntactic variations of existing information extracted from external large collections. In this paper, we discuss the methodology that we developed for IBM Watson for performing acquisition, transformation, and expansion of textual resources. We demonstrate the effectiveness of each technique through its impact on candidate recall and on end-to-end QA performance.
Amorphous Silicon Arrays For X-ray And Gamma-ray Medical Imaging (2005)

A novel form of x-ray and gamma-ray medical imaging device based upon the rapidly developing technology of hydrogenated amorphous silicon is under development by our collaboration. This imager features an array of amorphous silicon photodiode sensors and thin-film transistors arranged in a regular 2-dimensional pattern. The construction and operation of such arrays is described and their advantages for real-time megavoltage and diagnostic fluoroscopic imaging are discussed. Such arrays are under development by our collaboration.
Mineralocorticoid regulation of transcription of transfected mouse mammary tumor virus DNA in cultured kidney cells. (1988)

Renal cells contain two corticosteroid-binding entities defined on the basis of hormone-binding selectivity as type I (mineralocorticoid) and type II (glucocorticoid). The mineralocorticoid, aldosterone can bind to both type I and type II receptors. This poses problems in defining the characteristics of a true mineralocorticoid regulated expression of specific genes. We have used chimaeric constructs bearing the mouse mammary tumor virus (MMTV) promoter to study aldosterone action in the feline renal cell line CRFK. We have shown that in these cells aldosterone induces MMTV transcription through its own receptor (type I). This induction of MMTV transcription by aldosterone is a primary response to the hormone. We have shown that the DNA sequences that mediate the aldosterone response overlap the hormone response element (HRE) required for the glucocorticoid, progestin, and androgen induction of transcription at the MMTV long terminal repeat region. Thus the aldosterone regulation of MMTV long terminal repeat transcription is identical to the mode of action of the other steroid hormones at this promoter.
A proposed feeding strategy for the overproduction of recombinant proteins in Escherichia coli (2008)

Different feeding strategies for the production of human interferon-gamma using an isopropyl beta-D-thiogalactoside-inducible expression system in recombinant Escherichia coli BL21(DE3) (plasmid pET3a-ifngamma) were studied. Four fed-batch modes were designed to compare the effect of mu (specific growth rate) on recombinant-protein production, substrate consumption, by-product formation and plasmid stability during pre- and post-chemical induction in high-cell-density cultures of E. coli. It was found that Y(p/s), the product/substrate yield of interferon-gamma was significantly affected by mu throughout the process, but product/biomass yield (Y(p/x)) was influenced by mu at the pre-induction stage. By applying an efficient feeding strategy, in which the mu was maintained at the maximum attainable level, recombinant protein was accumulated up to a level of 60% of the total cell protein and its productivity was increased significantly. In this case, the overall productivities of biomass and recombinant protein were 6.36 g l(-1) h(-1) and 2.1 g l(-1) h(-1) respectively, in comparison with 1.91 g l(-1) h(-1) and 0.16 g l(-1) h(-1) during exponential feeding, in which the specific growth rate was kept constant throughout the entire process.
Ligation of MHC class I and class II molecules can lead to heterologous desensitization of signal transduction pathways that regulate homotypic adhesion in human lymphocytes. (1994)

Engagement of lymphocyte MHC class I and class II Ags activates an array of intracellular signal transduction pathways that up-regulates the activity of cell-surface adhesion receptors, resulting in homotypic cell-cell aggregation. In this study, engagement of MHC class I and class II molecules with specific mAbs was shown to also inhibit lymphocyte homotypic adhesion. Two mAbs reactive with class II Ag, homotypic adhesion blocking mAb (HAB)-2, and HAB-3, and one mAb reactive with class I Ag, HAB-4, were generated that inhibited homotypic adhesion of activated lymphocytes and B and T cell lines at concentrations as low as 0.1 microgram/ml. Binding of these mAbs resulted in heterologous desensitization of other surface signal transduction molecules as homotypic adhesion induced through class I, class II, CD19, CD20, CD39, CD40, Leu-13, and PMA was also inhibited. The spontaneous adhesion exhibited by some cell lines was also abrogated by binding of these mAbs. Abs that either induced, blocked, or had no effect on adhesion bound to distinct epitopes on class I, whereas the anti-class II mAbs recognized either distinct or overlapping epitopes. Thus, engagement of distinct epitopes on MHC molecules can result in homologous or heterologous desensitization of cell-surface signaling molecules. The induction or inhibition of homotypic adhesion through class I molecules did not require the presence of the cytoplasmic domain, as deletion of this portion of the class I molecule had no effect. In contrast, the transmembrane region was essential for signal transduction as the mAbs binding to a chimeric molecule in which the transmembrane and cytoplasmic domains of class I were exchanged with those of the HB15 molecule did not induce or inhibit homotypic adhesion. Although this report is the first demonstration that homotypic adhesion can be influenced in a negative manner through MHC molecules, these findings demonstrate a considerable level of cross-talk between MHC molecules and other cell-surface receptor systems and their signal transduction pathways, and suggests that MHC class I and class II molecules may serve important roles in the regulation of adhesive events during lymphocyte activation.
Vessel wall detection and blood noise reduction in intravascular ultrasound imaging (1996)

Scattering from blood limits the contrast between the vessel wall and the lumen in intravascular ultrasound imaging. This makes it difficult to localize the vessel wall, especially on still images. This paper presents a method for automatic detection of vessel walls and reduction of blood noise based on correlation of the RF-signal between adjacent frames. The ultrasound RF-signal is quadrature demodulated, digitized, stored in memory, and transferred to a computer for processing and analysis. The absolute value of the cross-correlation coefficient between two adjacent frames is used to differentiate between stationary and fluctuating signals. Models and numerical calculations presented in this work indicate that the cross-correlation coefficient obtained from a radially dilating vessel wall will be larger than 0.8 under standard 20 MHz imaging conditions. The corresponding value from blood is less than 0.2 for blood velocities exceeding 0.5 cm s/sup -1/. The blood-noise filter is based on detecting this difference in correlation and displays vessel wall regions with no modifications, while regions detected as blood are rejected. A simplified vessel-wall detector that is suitable for real-time implementation is proposed. The performance of this detector and the blood noise filter are demonstrated by in vitro experiments.
Surface plasmon polaritons on nanostructured surfaces and thin films (2005)

Surface plasmon polariton behaviour on periodically nanostructured metal surfaces and thin films is discussed. Such metallic nanostructures act as polaritonic crystals for surface polaritons, in analogy to photonic crystals for light waves. In this paper surface polariton Bloch mode spectrum on the structured surfaces and films is overviewed and manifestations of various surface plasmon modes in the optical properties of metallic nanostrnctures are considered. Surface plasmon polaritons me emerging as a new optical information carrier that enables signal manipulation and processing on the subwavelength scale and development of integrated photonic circuits.
Quantifying Layered Reservoir Properties With a Novel Permeability Test (1993)

ABSTRACT This paper presents a new test procedure designed to measure individual layer reservoir properties (permeability, skin factor, and reservoir pressure) in a single wellbore and in a reasonable amount of time for low permeability gas wells. The method involves (1) isolating a small interval with packers, either in an open- or cased-hole, (2) injecting nitrogen into the interval at a rate such that the bottomhole pressure builds up to a pre-determined value (below fracturing pressure), and (3) shutting in the well, preferably downhole, and monitoring the pressure falloff. The pressure falloff data is then analyzed to determine reservoir properties. Essentially, this method can be described as a nitrogen slug test and can be applied to any formation where single-phase gas is produced. We have found that average reservoir properties determined with conventional analyses of a single pressure buildup test conducted over a large interval can lead to optimistic predictions of the future performance of a well producing from a layered reservoir system. Therefore, being able to quantify individual layer properties can lead to better reservoir characterization, modified completions, and improved performance projections. Existing techniques, such as multiple pressure buildup tests, are inadequate for measuring reservoir permeability in several intervals in a single wellbore because, often in low productivity gas wells, either a pre-stimulation rate is not attained or the time required to reach the correct semilog straight line for a conventional well test analysis is too long. Knowledge of layered reservoir properties impacts completion decisions (where to perforate), fracture design considerations, and post-fracture analyses.
Review article: metoclopramide and tardive dyskinesia (2009)

Community prevalence and pharmacogenetic mechanisms involved in metoclopramide-induced tardive dyskinesia require further study to define the benefit-risk ratio more clearly.
A 13.56-MHz RFID System Based on Organic Transponders (2007)

RFID tags based on organic transistors are described, discussing in detail the IC blocks used to build the logic and the radio. Tags energized and read out at 13.56 MHz, de facto standard frequency for item-level identification, have been tested and enabled for the first time multiple-object identification, using different 6-bit codes. A complete 64-bit transponder, the most complex organic RFID tag reported to date, operates at 125 kHz and employs 1938 transistors
Effects of Inert Fat on Energy Balance, Plasma Concentrations of Hormones, and Reproduction in Dairy Cows (1993)

The objective was to determine the effects of dietary inert fat on estimated energy balance, hormones in plasma, and reproduction during early lactation. From wk 0 to 12 postpartum, 14 pluriparous Holstein cows were fed individually a TMR, and blood samples were taken twice weekly for quantification of IGF-I, progesterone, and cholesterol. During wk 5 to 12, one-half of the cows remained on the TMR, and the other half were fed the TMR containing inert fat at 1.8% of dietary DM. Estrous behavior was monitored twice daily, and body condition scores were recorded every 4 wk. Cows fed inert fat between wk 5 and 12 postpartum had similar concentrations of IGF-I in plasma but greater luteal phase progesterone secretions than cows fed the control diet. Total cholesterol in plasma also was greater in cows fed inert fat than in cows fed the control diet. Intervals to first, second, and third ovulation or estrus did not differ among cows fed control or inert fat diets. Body condition scores, daily DMI, and milk production were not affected by dietary inert fat. Inert fat fed to cows between wk 5 and 12 postpartum did not affect ovulatory activity but may enhance luteal activity.