gebhart/patrepeval huggingface dataset:
Nanocrystal Core High-Density Lipoproteins: A Multimodality Contrast Agent Platform (2008)

High density lipoprotein (HDL) is an important natural nanoparticle that may be modified for biomedical imaging purposes. Here we developed a novel technique to create unique multimodality HDL mimicking nanoparticles by incorporation of gold, iron oxide, or quantum dot nanocrystals for computed tomography, magnetic resonance, and fluorescence imaging, respectively. By including additional labels in the corona of the particles, they were made multifunctional. The characteristics of these nanoparticles, as well as their in vitro and in vivo behavior, revealed that they closely mimic native HDL.
FICUS: a very large scale reliable distributed file system (1992)

The dissertation presents the issues addressed in the design of Ficus, a large scale wide area distributed file system currently operational on a modest scale at UCLA. Key aspects of providing such a service include toleration of partial operation in virtually all areas; support for large scale, optimistic data replication; and a flexible, extensible modular design.
Ficus incorporates a stackable modular architecture and full support for optimistic replication. Replication is provided by a pair of layers operating in concert above a traditional filing service. A abstraction and on-the-fly volume grafting mechanism are used to manage the large scale file name space.
The replication service uses a family of novel algorithms to manage the propagation of changes to the filing environment. These algorithms are fully distributed, tolerate partial operation (including nontransitive communications), and display linear storage overhead and worst case quadratic message complexity.
High oleic sunflower: Physical and chemical characteristics (1986)

Abstract Treatment of normal varieties of sunflowerseed with chemical mutagens and development of their progenies have resulted in hydrids bearing oil with oleic acid contents in excess of 80% and linoleic acid contents less than 10%. Fatty acids compositions are unaffected by climatic conditions. Analyses of the seed, oil and meal produced from the first commercial U.S. production show values not to differ significantly from normal high linoleic sunflower, except where anticipated on the basis of fatty acid composition.
DEVELOPMENT OF TOLERANCE TO THE PROLONGATION OF HEXOBARBITONE SLEEPING TIME CAUSED BY CANNABIDIOL (1979)

1 The effects of acute and subacute cannabidiol (CBD) administration on hexobarbitone sleeping time and on some constituents of the hepatic microsomal drug-metabolizing system were assessed in the mouse.2 Acutely administered CBD prolonged sleeping time; but with subacute treatment, tolerance to the effect rapidly developed.3 Brain hexobarbitone concentration upon awakening was unchanged by either acute or subacute CBD treatment, which suggests that neither the prolongation of sleeping time nor the tolerance is the result of a change in sensitivity of the central nervous system to the barbiturate.4 Acute CBD treatment increased the half-time of hexobarbitone in the brain, which returned toward normal with the development of tolerance.5 Acutely, CBD caused a 30% decrease in hepatic cytochrome P-450 level; with tolerance, the cytochrome concentration returned to normal.6 The evidence suggests that the CBD-induced prolongation of barbiturate sleeping time and the tolerance to this effect are the result of changes in the rate of drug metabolism, which are related to changes in the amount of cytochrome P-450.7 The effects of CBD on the hepatic microsomal drug-metabolizing enzyme system are different from those attributed to SKF 525-A and piperonyl butoxide because the cannabinoid does not decrease cytochrome P-450 quantitatively by complex formation, it does not produce a recovery overshoot in the cytochrome concentration and, finally, it does not cause an induction of the hexobarbitone-metabolizing enzymes.
The Optimal Control of Partially Observable Markov Processes over a Finite Horizon (1973)

This paper formulates the optimal control problem for a class of mathematical models in which the system to be controlled is characterized by a finite-state discrete-time Markov process. The states of this internal process are not directly observable by the controller; rather, he has available a set of observable outputs that are only probabilistically related to the internal state of the system. The formulation is illustrated by a simple machine-maintenance example, and other specific application areas are also discussed. The paper demonstrates that, if there are only a finite number of control intervals remaining, then the optimal payoff function is a piecewise-linear, convex function of the current state probabilities of the internal Markov process. In addition, an algorithm for utilizing this property to calculate the optimal control policy and payoff function for any finite horizon is outlined. These results are illustrated by a numerical example for the machine-maintenance problem.
INTRODUCTION TO ELECTRONIC ANALOGUE COMPUTING (1960)

The design, operation, applications, limitations, and programming of an electronic analog computer are described. (C.J.G.)
Improving the Performance of a Quadrupole Time-of-Flight Instrument for Macromolecular Mass Spectrometry (2006)

We modified and optimized a first generation quadrupole time-of-flight (Q-TOF) 1 to perform tandem mass spectrometry on macromolecular protein complexes. The modified instrument allows isolation and subsequent dissociation of high-mass protein complexes through collisions with argon molecules. The modifications of the Q-TOF 1 include the introduction of (1) a flow-restricting sleeve around the first hexapole ion bridge, (2) a low-frequency ion-selecting quadrupole, (3) a high-pressure hexapole collision cell, (4) high-transmission grids in the multicomponent ion lenses, and (5) a low repetition rate pusher. Using these modifications, we demonstrate the experimental isolation of ions up to 12 800 mass-to-charge units and detection of product ions up to 38 150 Da, enabling the investigation of the gas-phase stability, protein complex topology, and quaternary structure of protein complexes. Some of the data reveal a so-far unprecedented new mechanism in gas-phase dissociation of protein oligomers whereby a tetramer complex dissociates into two dimers. These data add to the current debate whether gas-phase structures of protein complexes do retain some of the structural features of the corresponding species in solution. The presented low-cost modifications on a Q-TOF 1 instrument are of interest to everyone working in the fields of macromolecular mass spectrometry and more generic structural biology.
Copper toxicity towards Saccharomyces cerevisiae: dependence on plasma membrane fatty acid composition (1996)

One major mechanism of copper toxicity towards microorganisms is disruption of plasma membrane integrity. In this study, the influence of plasma membrane fatty acid composition on the susceptibility of Saccharomyces cerevisiae to Cu2+ toxicity was investigated. Microbial fatty acid composition is highly variable, depending on both intrinsic and environmental factors. Manipulation was achieved in this study by growth in fatty acid-supplemented medium. Whereas cells grown under standard conditions contained only saturated and monounsaturated fatty acids, considerable incorporation of the diunsaturated fatty acid linoleate (18:2) (to more than 65% of the total fatty acids) was observed in both whole-cell homogenates and plasma membrane-enriched fractions from cells grown in linoleate-supplemented medium. Linoleate enrichment had no discernible effect on the growth of S. cerevisiae. However, linoleate-enriched cells were markedly more susceptible to copper-induced plasma membrane permeabilization. Thus, after addition of Cu(NO3)2, rates of cellular K+ release (loss of membrane integrity) were at least twofold higher from linoleate-supplemented cells than from unsupplemented cells; this difference increased with reductions in the Cu2+ concentration supplied. Levels of cellular Cu accumulation were also higher in linoleate-supplemented cells. These results were correlated with a very marked dependence of whole-cell Cu2+ toxicity on cellular fatty acid unsaturation. For example, within 10 min of exposure to 5 microM Cu2+, only 3% of linoleate-enriched cells remained viable (capable of colony formation). In contrast, 100% viability was maintained in cells previously grown in the absence of a fatty acid supplement. Cells displaying intermediate levels of linoleate incorporation showed intermediate Cu2+ sensitivity, while cells enriched with the triunsaturated fatty acid linolenate (18:3) were most sensitive to Cu2+. These results demonstrate for the first time that changes in cellular and plasma membrane fatty acid compositions can dramatically alter microbial sensitivity to copper.
Potato lectin: a modular protein sharing sequence similarities with the extensin family, the hevein lectin family, and snake venom disintegrins (platelet aggregation inhibitors) (1994)

Potato (Solanum tuberosum) lectin, is a chimeric chitin-binding protein comprised of a lectin domain fused to a hydroxyproline-rich glycoprotein domain. Here peptide sequence information from both domains is presented. A partial sequence of a major tryptic peptide T2: Leu-Pro-Ser-Hyp-Hyp-Hyp-Hyp-Hyp-Hyp-(His)-Hyp-Ser-Hyp-Hyp- Hyp-Hyp-Ser-Hyp-Hyp-Ser-Hyp-Hyp-Hyp-Hyp-Ser-Hyp-Hyp- was similar to the 'P3' type extensin major repetitive sequence: Ser-Hyp-Hyp-Hyp-Hyp-Ser-Hyp-Ser-Hyp-Hyp-Hyp-Hyp- suggesting common evolutionary origins for the extensins and the hydroxyproline-rich glycoprotein (HRGP) domain of potato lectin. Furthermore, alignment of three chymotryptic peptides from potato lectin, C1: Cys-Gly-Thr-Thr-Ser-Asp-Tyr, C2: Cys-Ser-Pro-Gly-Tyr, and C8: Thr-Gly-Glu-Cys-Cys-Ser-Ile with similar sequences from the hevein lectin family indicates that they have homologous chitin-binding domains, and hence have common evolutionary origins. Finally, all plant chitin-binding domains examined bore a remarkable sequence similarity, particularly in the spacing of Cys residues, to the disintegrins (platelet aggregation inhibitors) which occur in crotalid and viperid snake venoms. As such, sequence similarities not only identify potato lectin as a member of both the hevein and extensin families of plant proteins, but also suggest that an archetypal polypeptide module gave rise to both the plant chitin-binding domain and the reptile disintegrins.
A double blind placebo controlled trial of low dose clotrimazole in rheumatoid arthritis. (1990)

Seventy-three patients with rheumatoid arthritis were randomized in a double blind study to receive either clotrimazole (20 mg/kg/day) 2 days a week for 12 weeks or matching placebo. Patients receiving clotrimazole had significant improvements (p less than 0.05) from baseline in measurements of grip strength, joint count, and patient assessment of pain, but did not show significant improvement over patients treated with placebo. More adverse experiences, predominantly gastrointestinal complaints, occurred in patients taking clotrimazole resulting in 9 patients discontinuing therapy.
Analysis of Cell-free Fetal DNA in Plasma and Serum of Pregnant Women (2005)

Sixty blood samples from pregnant women during gestational weeks 9-28 were investigated. Cell-free fetal DNA was extracted from maternal plasma or serum to be detected by nested PCR for determination of fetal gender. The SRY gene as a marker for fetal Y chromosome was detected in 34/36 women carrying a male fetus. In 3/24 women carrying female fetuses, the SRY sequence was also detected. Overall, fetal sex was correctly predicted in 91.7% of the cases. Therefore, the new, non-invasive method of prenatal diagnosis of fetal gender for women at risk of producing children with X-linked disorders is reliable, secure, and can substantially reduce invasive prenatal tests.
Disease Resistance and Immune Response Genes in Cattle: Strategies for Their Detection and Evidence of Their Existence (1989)

The possibility of breeding or genetically engineering cattle for resistance to disease has tremendous potential for increasing the efficiency of milk and meat production. In cattle and other species, major genes that control humoral and cellular immune responses to a variety of antigens have been mapped to a chromosomal region known as the major histocompatibility complex. However, resistance or susceptibility to viral, bacterial, and parasitic diseases in noninbred species is often a complex phenotype, with age, stress, and physiologic status all being important factors in the outcome of infection. This paper reviews the function of major histocompatibility complex gene products and the relationship between polymorphism of these genes and infectious diseases. A discussion of strategies for detecting immune response genes and disease associations is presented, with particular reference to the problems and advantages of working with cattle. The present knowledge of the bovine major histocompatibility complex and its relationship to immune responsiveness and disease resistance are also reviewed, with special consideration given to enzootic bovine leukosis because of the significant relationship between alleles of the bovine lymphocyte antigen system and resistance or susceptibility to subclinical progression of bovine leukemia virus infection. Finally, potential applications of this research to genetic improvement and animal health are considered.
Neural Transplantation: A Call for Patience Rather Than Patients (1988)

Research into embryonic cell grafting in human subjects suffering\nfrom Parkinson's disease should not repeat the mistakes made by adrenal\nautograft investigators, who operated on far more humans than on nonhuman\nprimates because of a single unconfirmed report of dramatic improvement in two\nMexican patients. Citing extensive data from experimental transplants\nconducted as early as 1944, the authors argue that, until a sufficient number\nof animal studies have been performed to answer many crucial questions about\nhuman fetal tissue transplants, researchers should refrain from experimenting\non human patients. (KIE abstract)
Aptamer-Based Colorimetric Probe for Cocaine (2002)

Complex of an anti-cocaine aptamer and the dye diethylthiotricarbocyanine behaves as a colorimetric sensor with attenuation in absorbance at 760 nm for cocaine in the concentration range of 2-600 muM. Mechanistic studies indicate an intermolecular displacement of the dye as the mechanism of action of the sensor. As the dye is insoluble in buffer, cocaine binding can be followed with the unaided eye as displaced dye precipitates and supernatant decolorizes.
Structural Innovations in Major Building Projects (1998)

The designs of three major building projects developed by Connell Wagner are described. Many interesting structural innovations were incorporated with effective cost savings and more functional layout. The three projects described are the Crown Entertainment Complex at Melbourne, Australia, The Hong Kong Airport Terminal Building at Chek Lap Kok, Hong Kong, and Melbourne Sports and Aquatic Centre at Melbourne, Australia.
Angiotensin-Converting Enzyme Inhibitors (1998)

ACE inhibitors have achieved widespread usage in the treatment of cardiovascular and renal disease. ACE inhibitors alter the balance between the vasoconstrictive, salt-retentive, and hypertrophic properties of angiotensin II (Ang II) and the vasodilatory and natriuretic properties of bradykinin and alter the metabolism of a number of other vasoactive substances. ACE inhibitors differ in the chemical structure of their active moieties, in potency, in bioavailability, in plasma half-life, in route of elimination, in their distribution and affinity for tissue-bound ACE, and in whether they are administered as prodrugs. Thus, the side effects of ACE inhibitors can be divided into those that are class specific and those that relate to specific agents. ACE inhibitors decrease systemic vascular resistance without increasing heart rate and promote natriuresis. They have proved effective in the treatment of hypertension, they decrease mortality in congestive heart failure and left ventricular dysfunction after myocardial infarction, and they delay the progression of diabetic nephropathy. Ongoing studies will elucidate the effect of ACE inhibitors on cardiovascular mortality in essential hypertension, the role of ACE inhibitors in patients without ventricular dysfunction after myocardial infarction, and the role of ACE inhibitors compared with newly available angiotensin AT1 receptor antagonists.
Photobleaching of Organic Laser Dyes in Solid Matrices (1972)

A technique is described for measuring the rate of photobleaching of anisotropic dye molecules in solid polymer matrices. Three dyes of different classes in two matrices (PMMA and epoxy resin) show bleaching rates that differ by a factor of 20. The bleaching rate is linearly proportional to the intensity of incident radiation, indicating a one-photon process; bleaching is probably due to a chemical reaction of the dye in its first excited singlet or lowest triplet state.
Automatic online adaptive radiation therapy techniques for targets with significant shape change: a feasibility study (2006)

This work looks at the feasibility of an online adaptive radiation therapy concept that would detect the daily position and shape of the patient, and would then correct the daily treatment to account for any changes compared with planning position. In particular, it looks at the possibility of developing algorithms to correct for large complicated shape change. For co-planar beams, the dose in an axial plane is approximately associated with the positions of a single multi-leaf collimator (MLC) pair. We start with a primary plan, and automatically generate several secondary plans with gantry angles offset by regular increments. MLC sequences for each plan are calculated keeping monitor units (MUs) and number of segments constant for a given beam (fluences are different). Bulk registration (3D) of planning and daily CT images gives global shifts. Slice-by-slice (2D) registration gives local shifts and rotations about the longitudinal axis for each axial slice. The daily MLC sequence is then created for each axial slice/MLC leaf pair combination, by taking the MLC positions from the pre-calculated plan with the nearest rotation, and shifting using a beam's-eye-view calculation to account for local linear shifts. A planning study was carried out using two head and neck region MR images of a healthy volunteer which were contoured to simulate a base-of-tongue treatment: one with the head straight (used to simulate the planning image) and the other with the head tilted to the left (the daily image). Head and neck treatment was chosen to evaluate this technique because of its challenging nature, with varying internal and external contours, and multiple degrees of freedom. Shape change was significant: on a slice-by-slice basis, local rotations in the daily image varied from 2 to 31 degrees, and local shifts ranged from -0.2 to 0.5 cm and -0.4 to 0.0 cm in right-left and posterior-anterior directions, respectively. The adapted treatment gave reasonable target coverage (100%, 90% and 80% of the base-of-tongue, left nodes and right nodes, respectively, receiving the daily prescription dose), and kept the daily cord dose below the limit used in the original plan (65%, equivalent to 46 Gy over 35 fractions). Most of the loss of coverage was due to one shoulder being raised more superior relative to the other shoulder compared with the plan. This type of skew-like motion is not accounted for by the proposed ART technique. In conclusion, this technique has potential to correct for fairly extreme daily changes in patient setup, but some control of the daily position would still be necessary. Importantly, it was possible to combine treatments from different plans (MLC sequences) to correct for position and shape change.
A Protein Class Database Organized with ProSite Protein Groups and PIR Superfamilies (1996)

A protein class (ProClass) database is developed as a "value-added" "second-generation" database organized according to family relationships. The database collects non-redundant protein sequence entries from SwissProt and PIR databases, and classifies them in families defined collectively by the ProSite protein groups and PIR superfamilies. The major objectives of the database are to maximize family information retrieval, to provide speedy family identification, and to help organizing existing protein sequence databases. The database has two sub-databases: PCFam (ProClass Family) to define protein families and provide links to ProSite patterns and PIR superfamilies, and PCSeq (ProClass Sequence) to describe sequence entries and provide links to PCFam, SwissProt, PIR, and ProSite databases. The current ProClass release has a total of 85,165 sequence entries, about half of which are classified in 3072 ProClass families; it also contains 10,431 newly established SwissProt-PIR links. The database can help reveal domain structures of related families, define new ProSite and PIR families, and provide family assignments for unclassified sequence entries. New ProSite and PIR family members are readily identified via database cross-reference, including 9437 SwissProt entries and 8522 PIR entries. False negative family members missed by both ProSite and PIR are detected using a neural network family identification system. The newly identified superfamily memberships are being incorporated into the current PIR database releases in a collaborative effort with the PIR. The ProClass database is accessible through anonymous FTP and on-line search on the World Wide Web.
Cross-Stitch Networks for Multi-task Learning (2016)

Multi-task learning in Convolutional Networks has displayed remarkable success in the field of recognition. This success can be largely attributed to learning shared representations from multiple supervisory tasks. However, existing multi-task approaches rely on enumerating multiple network architectures specific to the tasks at hand, that do not generalize. In this paper, we propose a principled approach to learn shared representations in ConvNets using multitask learning. Specifically, we propose a new sharing unit: "cross-stitch" unit. These units combine the activations from multiple networks and can be trained end-to-end. A network with cross-stitch units can learn an optimal combination of shared and task-specific representations. Our proposed method generalizes across multiple tasks and shows dramatically improved performance over baseline methods for categories with few training examples.
RNA interference of valosin-containing protein (VCP/p97) reveals multiple cellular roles linked to ubiquitin/proteasome-dependent proteolysis (2003)

We have used RNA interference (RNAi) to examine the functional relationship between valosin-containing protein (VCP/p97/Cdc48p/TER94) ATPase and the ubiquitin-proteasome system (UPS) in Drosophila S2 and human HeLa cells. In both cell types, RNAi of VCP (and, to a lesser extent, of certain VCP-interacting proteins) caused significant accumulation of high-molecular-weight conjugates of ubiquitin, an indication of inhibited UPS function. However, decreased VCP levels did not directly inhibit proteasome activity. In HeLa cells, polyubiquitinated proteins accumulated as dispersed aggregates rather than as single aggresomes, even in the presence of proteasome inhibitors, which normally promote aggresome formation. RNAi of VCP caused extensive vacuolization of the cytoplasm, and proteasome inhibitors exaggerated this feature. RNAi of VCP had little effect on S2 cell proliferation but blocked cell-cycle progression and induced mitotic abnormalities and apoptosis in HeLa cells. These results indicate that VCP plays an important general role in mediating the function of the UPS, probably by interacting with potential proteasome substrates before they are degraded by the proteasome.