gebhart/patrepeval huggingface dataset:
Organ Preservation: Current Concepts and New Strategies for the Next Decade (2011)

SUMMARY: Organ transplantation has developed over the past 50 years to reach the sophisticated and integrated clinical service of today through several advances in science. One of the most important of these has been the ability to apply organ preservation protocols to deliver donor organs of high quality, via a network of organ exchange to match the most suitable recipient patient to the best available organ, capable of rapid resumption of life-sustaining function in the recipient patient. This has only been possible by amassing a good understanding of the potential effects of hypoxic injury on donated organs, and how to prevent these by applying organ preservation. This review sets out the history of organ preservation, how applications of hypothermia have become central to the process, and what the current status is for the range of solid organs commonly transplanted. The science of organ preservation is constantly being updated with new knowledge and ideas, and the review also discusses what innovations are coming close to clinical reality to meet the growing demands for high quality organs in transplantation over the next few years.
Reagents and methods for the solid-phase synthesis of protein-EDTA for use in affinity cleaving (1990)

Synthetic procedures for the introduction of the metal chelator ethylenediaminetetraacetic acid (EDTA) at unique amino acid positions of proteins by solid-phase methods are described. Two protected derivatives of EDTA compatible with Merrifield solid-phase protein synthesis employing N-tert-butyloxycarbonyl- (Boc-) protected amino acids were developed. The first reagent is a dipeptide with three of four carboxyl groups of EDTA protected as benzyl esters and the fourth coupled to a γ-aminobutanoic acid linker, referred to as tribenzyl-EDTA-CABA (BEG). A second reagent is the tricyclohexyl ester of EDTA, TCE. BEG and TCE allow the modification of the NH_2 terminus and/or lysine side chains of resin-bound peptides and proteins. Upon deprotection and cleavage from the resin, a protein is produced with EDTA at a defined amino acid position. The availability of protein-EDTA conjugates extends the affinity cleaving method to the study of protein-DNA complexes in solution.
Pharmaceutical review - a lost opportunity? -editorial- (2006)

Pharmaceutical review essentially brings together the principles of the Quality Use of Medicines, the Guiding Principles for Medicines Management in the Community and The Society of Hospital Pharmacists of Australia's Standards of Practice for Clinical Pharmacy. Importantly it needs to function not only at the individual patient level but also at the hospital and health systems level. It thus needs to be a multidisciplinary approach with the need to break down the silos between the different health professionals involved in patient care. Pharmacists are ideally placed for this task. (non-author abstract)
Outcomes of treatment of neovascular glaucoma with intravitreal bevacizumab (2008)

Intravitreal bevacizumab is now a frequently used adjunct for the treatment of NVG. Eyes must be monitored closely after initial injection of intravitreal bevacizumab, regardless of initial angle status, as many may still require surgery to lower IOP or repeat injections of intravitreal bevacizumab.
Epitopes for natural antibodies of human immunodeficiency virus (HIV)-negative (normal) and HIV-positive sera are coincident with two key functional sequences of HIV Tat protein. (1993)

We have previously shown that IgM antibodies that react with human immunodeficiency virus (HIV) Tat, a regulatory protein essential for viral replication, are present in sera of all normal, HIV-negative individuals and deficient in sera of HIV-positive individuals at progressively greater frequency as diagnosis of AIDS nears. That IgM was designated as a set of natural antibodies, a repertoire of the normal humoral immune system believed to provide early defense against infectious invaders. In the prior study, by means of a series of synthetic peptides representing the amino acid sequence of HIV-1 Tat, one epitope for the IgM natural antibodies was defined within the cysteine-rich domain, shown in cell transfection studies to participate in Tat function. In this study we have defined another epitope, within the basic domain, with which the natural antibodies react. The specific sequence and amino acid residues required for that epitope are coincident with those required for the role of Tat in viral replication. The IgM antibodies reactive with the two epitopes of Tat make up two distinct sets, which, together, account for the total Tat reactivity of both HIV-negative and HIV-positive sera. The striking coincidence of the two epitopes with the two functional sequences of Tat suggests a potential role of those natural antibodies in control of HIV pathogenesis. By inference from the extensive evidence for the presence of extracellular Tat in cultures of HIV-infected cells, Tat may be expected to be present in the circulating plasma of infected people. We propose, therefore, that the Tat-reactive natural antibodies, documented in these studies to be present in the circulating plasma in the pre-AIDS stages of HIV infection, may inhibit cell entry of plasma-borne Tat and thereby curtail HIV propagation. Thus, those natural antibodies may be a host factor for delay in HIV pathogenetic progression.
One Point of View: Risk Was His Friend: Edison's Legacy to Innovation Leaders (1995)

"One Point of View: Risk Was His Friend: Edison's Legacy to Innovation Leaders." Research-Technology Management, 38(4), pp. 8–9
The Use of Fibrin Beads for Tissue Engineering and Subsequential Transplantation (2001)

New biological technologies such as tissue engineering procedures require the transplantation of functionally active cells within supportive carrier matrices. This paper describes a sequential culture procedure for different types of cells. The technique includes the initial preparation of a mixed alginate-fibrin vehicle that guaranteed an initial cell proliferation and differentiation to establish a stable matrix structure, and the subsequent removal of the alginate component prior to transplantation to circumvent the problem of missing bioresorbability. The resulting biodegradable carrier is mechanically stable and promotes further tissue maturation. Chondrocytes, periosteal-derived cells, as well as nucleus pulposus cells were entrapped in fibrin-alginate beads and in fibrin beads. The results indicate a promising technical approach to create stable transplants for reconstructive surgery of cartilage and bone.
SOX9 Elevation in the Prostate Promotes Proliferation and Cooperates with PTEN Loss to Drive Tumor Formation (2010)

Dysregulation of tissue development pathways can contribute to cancer initiation and progression. In murine embryonic prostate epithelia, the transcription factor SOX9 is required for proper prostate development. In this study, we examined a role for SOX9 in prostate cancer in mouse and human. In Pten and Nkx3.1 mutant mice, cells with increased levels of SOX9 appeared within prostate epithelia at early stages of neoplasia, and higher expression correlated with progression at all stages of disease. In transgenic mice, SOX9 overexpression in prostate epithelia increased cell proliferation without inducing hyperplasia. In transgenic mice that were also heterozygous for mutant Pten, SOX9 overexpression quickened the induction of high-grade prostate intraepithelial neoplasia. In contrast, Sox9 attenuation led to a decrease proliferating prostate epithelia cells in normal and homozygous Pten mutant mice with prostate neoplasia. Analysis of a cohort of 880 human prostate cancer samples showed that SOX9 expression was associated with increasing Gleason grades and higher Ki67 staining. Our findings identify SOX9 as part of a developmental pathway that is reactivated in prostate neoplasia where it promotes tumor cell proliferation.
Reaction of nitric oxide with heme proteins and model compounds of hemoglobin (1987)

Rates for the reaction of nitric oxide with several ferric heme proteins and model compounds have been measured. The NO combination rates are markedly affected by the presence or absence of distal histidine. Elephant myoglobin in which the E7 distal histidine has been replaced by glutamine reacts with NO 500-1000 times faster than do the native hemoglobins or myoglobins. By contrast, there is no difference in the CO combination rate constants of sperm whale and elephant myoglobins. Studies on ferric model compounds for the R and T states of hemoglobin indicate that their NO combination rate constants are similar to those observed for the combination of CO with the corresponding ferro derivatives. The last observation suggests that the presence of an axial water molecule at the ligand binding site of ferric hemoglobin A prevents it from exhibiting significant cooperativity in its reactions with NO.
Bacterial CpG-DNA and lipopolysaccharides activate Toll-like receptors at distinct cellular compartments (2002)

Recognition by innate immune cells of the pathogen associated molecular patterns (PAMP) lipopolysaccharide (LPS) from Gram-negative bacteria and bacterial CpG-DNA depends on Toll-like receptor4 (TLR4) and TLR9, respectively. To define differences in the response to these distinct PAMP we compared a key intracellular event, namely recruitment of myeloid differentiation marker 88 (MyD88) to the respective PAMP-initiated TLR signaling. Using MyD88-GFP fusion protein expressing macrophages we demonstrate that LPS and CpG-DNA trigger signaling from two different cellular locations: theformer at the cell membrane and the latter at the lysosomal compartment. While LPS does not require endocytosis to functionally associate with the membrane expressed TLR4/MD2 complex, internalization and endosomal maturation is conditional for CpG-DNA to activate TLR9. In support of these data TLR9 is not localized at the cell surface, but intracellularily. These data stress the need to characterize individual TLR at the very beginning of signal initiation in order to understand their diverse biological functions.
NADPH oxidase 4 regulates homocysteine metabolism and protects against acetaminophen-induced liver damage in mice (2015)

Glutathione is the major intracellular redox buffer in the liver and is critical for hepatic detoxification of xenobiotics and other environmental toxins. Hepatic glutathione is also a major systemic store for other organs and thus impacts on pathologies such as Alzheimer's disease, Sickle Cell Anaemia and chronic diseases associated with aging. Glutathione levels are determined in part by the availability of cysteine, generated from homocysteine through the transsulfuration pathway. The partitioning of homocysteine between remethylation and transsulfuration pathways is known to be subject to redox-dependent regulation, but the underlying mechanisms are not known. An association between plasma Hcy and a single nucleotide polymorphism within the NADPH oxidase 4 locus led us to investigate the involvement of this reactive oxygen species- generating enzyme in homocysteine metabolism. Here we demonstrate that NADPH oxidase 4 ablation in mice results in increased flux of homocysteine through the betaine-dependent remethylation pathway to methionine, catalysed by betaine-homocysteine-methyltransferase within the liver. As a consequence NADPH oxidase 4-null mice display significantly lowered plasma homocysteine and the flux of homocysteine through the transsulfuration pathway is reduced, resulting in lower hepatic cysteine and glutathione levels. Mice deficient in NADPH oxidase 4 had markedly increased susceptibility to acetaminophen-induced hepatic injury which could be corrected by administration of N-acetyl cysteine. We thus conclude that under physiological conditions, NADPH oxidase 4-derived reactive oxygen species is a regulator of the partitioning of the metabolic flux of homocysteine, which impacts upon hepatic cysteine and glutathione levels and thereby upon defence against environmental toxins.
Cooperative robot localization with vision-based mapping (2003)

Two stereo vision-based mobile robots navigate and autonomously explore their environment safely while building occupancy grid maps of the environment. A novel landmark recognition system allows one robot to automatically find suitable landmarks in the environment. The second robot uses these landmarks to localize itself relative to the first robot's reference frame, even when the current state of the map is incomplete. The robots have a common local reference frame so that they can collaborate on tasks, without having a prior map of the environment. Stereo vision processing and map updates are done at 5 Hz and the robots move at 200 cm/s. Using occupancy grids the robots can robustly explore unstructured and dynamic environments. The map is used for path planning and landmark detection. Landmark detection uses the map's corner features and least-squares optimization to find the transformation between the robots' coordinate frames. The results provide very accurate relative localization without requiring highly accurate sensors. Accuracy of better than 2 cm was achieved in experiments.
Self-Assembly of Amphiphilic Polymeric Dendrimers Synthesized with Selective Degradable Linkages (2007)

Enhancing the structural complexity and functionality of building blocks allows the design and synthesis of complex macromolecular architectures. In this work, we use a combination of atom transfer radical polymerization to produce polymers with well-defined chain length and telechelic end group functionality and “click” reactions to quantitatively couple these polymer chains together to form functional second- and third-generation dendrimers. Importantly, this methodology provides starting polymers in combination with linkers and end group protecting chemistries to design dendrimers with degradable linkages between the desired generations and incorporates functionality at the polymer chain ends of each generation. We have synthesized second- and third-generation homo- and amphiphilic diblock copolymer dendrimers and specifically designed third-generation dendrimers in pure form such that the peripheral generational layer could be selectively cleaved off from the second-generation. The degradation of the peripheral polymer layer is a useful feature in biomedical delivery devices for slow and controlled release of its payload. These dendrimers also have either “free” or protected hydroxyl groups on the peripheral ends, which are useful for further chemical modification or chemical coupling to important biomolecules. The amphiphilic dendrimers self-assemble in water to form well-defined micelles of near identical size (18.2 nm, PDI = 1.04), each consisting of approximately 19 individual dendrimers. The dense core of the spherical micelles found from sizing measurements supports the postulate that these amphiphilic dendrimers have no mutual interpenetration and thus pack uniformly to form the micelles.
High‐Temperature Healing of Lithographically Introduced Cracks in Sapphire (1990)

A new method for producing controlled‐geometry, controlled‐crystallography, cracklike defects using photolithography has been developed. The method has been applied to sapphire, and used to study crack healing behavior at 1800°C. Effects of crack face and crack perimeter crystallography, crack face microstructure, and impurities on healing behavior have been identified.
Iterative minimization techniques forab initiototal-energy calculations: molecular dynamics and conjugate gradients (1992)

This article describes recent technical developments that have made the total-energy pseudopotential the most powerful ab initio quantum-mechanical modeling method presently available. In addition to presenting technical details of the pseudopotential method, the article aims to heighten awareness of the capabilities of the method in order to stimulate its application to as wide a range of problems in as many scientific disciplines as possible.
Tracking Mobile Users in Wireless Networks via Semi-Supervised Colocalization (2011)

Recent years have witnessed the growing popularity of sensor and sensor-network technologies, supporting important practical applications. One of the fundamental issues is how to accurately locate a user with few labeled data in a wireless sensor network, where a major difficulty arises from the need to label large quantities of user location data, which in turn requires knowledge about the locations of signal transmitters or access points. To solve this problem, we have developed a novel machine learning-based approach that combines collaborative filtering with graph-based semi-supervised learning to learn both mobile users' locations and the locations of access points. Our framework exploits both labeled and unlabeled data from mobile devices and access points. In our two-phase solution, we first build a manifold-based model from a batch of labeled and unlabeled data in an offline training phase and then use a weighted k-nearest-neighbor method to localize a mobile client in an online localization phase. We extend the two-phase colocalization to an online and incremental model that can deal with labeled and unlabeled data that come sequentially and adapt to environmental changes. Finally, we embed an action model to the framework such that additional kinds of sensor signals can be utilized to further boost the performance of mobile tracking. Compared to other state-of-the-art systems, our framework has been shown to be more accurate while requiring less calibration effort in our experiments performed on three different testbeds.
Hypertension among adults in a deprived urban area of Peru – Undiagnosed and uncontrolled? (2008)

Levels of awareness and control in this population were low. Lack of control is likely to be due to both a failure to diagnose hypertension, especially among men, and initiate or comply with treatment, especially among women. These results suggest a considerable burden of undiagnosed hypertension, and poor levels of control in those treated, in a deprived urban area of Lima, Peru.
Local Gene Delivery Within the Media of Rabbit Iliac Arteries by Using the Infiltrator Intramural Delivery Device (1999)

Percutaneous transluminal angioplasty continues to be limited by restenosis. Prevention of restenosis is now focusing on local delivery of therapeutic agents, such as proliferation-inhibiting genes, directly to the site of arterial injury. We evaluated use of the Infiltrator catheter (IVT, San Diego, CA. U.S.A.) for gene delivery within the arterial media. The goals of our study were to evaluate the histologic effects of the injection and the suitability of the Infiltrator catheter for local delivery of viral therapy. We injected the femoral arteries of 21 New Zealand White rabbits. Six animals were used for an evaluation of the intramural distribution of dextran/rhodamine injected via the Infiltrator catheter. In seven animals, injection site histology and in vitro vasoreactivity were studied after an injection of saline. In the remaining eight animals, a replication-deficient adenovirus encoding for the firefly luciferase gene (Ad RSVLuc) was injected, and luciferase activity was quantified 3 and 8 days later. After injection via the Infiltrator catheter, the fluorescent tracer was distributed throughout the entire circumference and width of the arteries. Histologic examination showed minimal damage with partial endothelial abrasion and disruption of the internal elastic lamina confined to the penetration sites. In vitro endothelium-dependent vasodilation was present at a reduced level after injection via the Infiltrator (maximal endothelium-dependent acetylcholine-induced relaxation, 51.5 +/- 7.4% vs. 23.8 +/- 14.6%; p < 0.05). Significant luciferase expression was found in all the arteries, with a significant increase from day 3 to day 8 (5,392.5 +/- 2,300 vs. 2,012 +/- 471 cpm/mg; p < 0.05). These data obtained in a rabbit iliac artery model show that the Infiltrator catheter is an efficient and safe local intramural delivery device that provides significant transgene expression in the arterial wall without causing significant structural damage.
Review Oncologic, Endocrine & Metabolic: Inhibitors of protein farnesylation: A new approach to cancer chemotherapy (1995)

The Ras protein functions at a critical point in the signalling pathway between extracellular growth regulatory messengers and the nuclear factors that are responsible for the initiation of cellular replication. The action of mutant, oncogenic Ras proteins is implicated in a significant fraction of human tumours. All Ras proteins appear to require post-translational lipidation for their function. The key lipidation event is the attachment of a farnesyl unit to a cysteine near the carboxyl terminus of the protein. Recently, the possibility of interfering with Ras-mediated cell transformation through inhibition of protein farnesylation has attracted significant attention. This review surveys the types of compounds that are reported to inhibit the enzyme protein farnesyltransferase and the biological effects of these compounds in vitro and in vivo.
Preload — An Adaptive Prefetching Daemon (2006)

In this thesis we develop preload, a daemon that prefetches binaries and shared libraries from the hard disk to main memory on desktop computer systems, to achieve faster application start-up times. Preload is adaptive: it monitors applications that the user runs, and by analyzing this data, predicts what applications she might run in the near future, and fetches those binaries and their dependencies into memory. We build a Markov-based probabilistic model capturing the correlation between every two applications on the system. The model is then used to infer the probability that each application may be started in the near future. These probabilities are used to choose files to prefetch into the main memory. Special care is taken to not degrade system performance and only prefetch when enough resources are available. Preload is implemented as a user-space application running on Linux 2.6 systems.
An HIV Vaccine — Evolving Concepts (2007)

The unique features of the human immunodeficiency virus (HIV) envelope protein have thwarted efforts to identify a protective vaccine. However, a vaccine that does not prevent infection but reduces HIV levels and preserves memory CD4+ T cells could benefit both the recipient and the community at risk. Several vaccines that induce T-cell responses are now in early clinical trials. This review summarizes the science and strategies in the search for an effective vaccine to control HIV infection.
Cytokine Profiles in Crevicular Fluid During Orthodontic Tooth Movement of Short and Long Durations (2007)

Once the microenvironment of periodontal tissue is activated by an orthodontic force, several key PICs are produced to trigger a cascade of cellular events. The periodontal system stabilizes at a new physiological homeostasis as indicated by the downregulation of the early-phase PICs.