gebhart/patrepeval huggingface dataset:
Accuracy of fecal occult blood screening for colorectal neoplasia. A prospective study using Hemoccult and HemoQuant tests. (1993)

Based on our observations in the screening setting, fecal blood appears to be a poor marker for colorectal neoplasia. Most cancers and the vast majority of polyps will be missed. Hemoccult and HemoQuant are similarly insensitive.
Inhibition of cyclooxygenase 2 blocks human cytomegalovirus replication (2002)

Cyclooxygenase 2 (COX-2) mRNA, protein, and activity are transiently induced after infection of human fibroblasts with human cytomegalovirus. Prostaglandin E(2), the product of COX-2 activity, is transiently increased by a factor of >50 in cultures of virus-infected fibroblasts. Both specific (BMS-279652, 279654, and 279655) and nonspecific (indomethacin) COX-2 inhibitors can abrogate the virus-mediated induction of prostaglandin E(2) accumulation. Levels of COX-2 inhibitors that completely block the induction of COX-2 activity, but do not compromise cell viability, reduce the yield of human cytomegalovirus in human fibroblasts by a factor of >100. Importantly, the yield of infectious virus can be substantially restored by the addition of prostaglandin E(2) together with the inhibitory drug. This finding argues that elevated levels of prostaglandin E(2) are required for efficient replication of human cytomegalovirus in fibroblasts. COX-2 inhibitors block the accumulation of immediate-early 2 mRNA and protein, but have little effect on the levels of immediate-early 1 mRNA and protein. Viral DNA replication and the accumulation of some, but not all, early and late mRNAs are substantially blocked by COX-2 inhibitors. Elevated levels of prostaglandin E(2) apparently facilitate the production of immediate-early 2 protein. The failure to produce normal levels of this critical viral regulatory protein in the presence of COX-2 inhibitors might block normal progression beyond the immediate-early phase of human cytomegalovirus infection.
Somatic mutations of the lysyl oxidase gene on chromosome 5q23.1 in colorectal tumors (2001)

Lysyl oxidase (LOX), a copper-dependent amine oxidase, has been implicated in tumor suppression and cell growth regulation. The chromosomal locus of LOX, 5q23, is affected by loss of heterozygosity (LOH) in colon cancer, suggesting that the LOX gene could be affected by LOH and consequently, loss or reduction of LOX function contribute to the tumorigenic process. Identification of microsatellite markers within the LOX locus has allowed us to map the LOX gene within the 5q23.1 region. Analysis of this locus and flanking loci in matched tumor and blood DNA samples from a panel of colorectal cancer patients, demonstrated that 38% (16/42) of informative samples were affected by LOH or allelic imbalance. Furthermore, 75% (6/8) of these tumor samples were shown to have significantly reduced LOX mRNA levels. Similar reduction in LOX levels were detected in a panel of matched normal colon and colon tumor samples. Tumor samples demonstrating LOH by RFLP, were subject to mutational analysis, including RT-PCR, exonic deletion detection by PCR, cDNA and genomic DNA sequencing, and were found to have a spectrum of alterations and mutations affecting the LOX gene. These results confirm that loss or reduction of LOX function during tumor development is a direct consequence of somatic mutations and is associated with colon tumor pathogenesis.
Eleven-CIS Vitamin A in the Treatment of Retinitis Pigmentosa (1968)

Previous studies demonstrated that the 11-cis isomer of vitamin A prevented retinal rod degeneration in rats. Uncontrolled human studies suggested that 11-cis vitamin A given intramuscularly benefited patients with retinitis pigmentosa. A long-term rigidly controlled study was performed to determine whether or not 11-cis vitamin A may be of value in the treatment of retinitis pigmentosa. Final results were negative.
A calcium-sensitive fluorescent analog of calmodulin based on a novel calmodulin-binding fluorophore (1990)

Structure-activity studies of tetramethinemerocyanine fluorophores enabled the synthesis of novel dyes which showed spectral changes during reversible, calcium-dependent association with calmodulin. These spectral changes were greatly enhanced in dyes with a quaternary nitrogen and specifically placed hydrophobic chains. One such dye was covalently attached to calmodulin, producing a calmodulin analog with calcium-sensitive fluorescence. The analog, MeroCaM, showed a calcium-induced 3.4-fold increase in excitation ratio (608/532 nm excitation, 623 nm emission), which was fully reversed by lowering free calcium levels. MeroCaM's excitation ratio showed a half-maximal change at 300-400 nM calcium, below calcium concentrations reported to produce half-maximal saturation of calcium-calmodulin binding. However, the calcium dependence of MeroCaM's phosphodiesterase activation paralleled that of calmodulin. MeroCaM's fluorescence changes therefore appear to reflect primarily calcium binding to high affinity sites. MeroCaM's maximal phosphodiesterase activation was 30-40% that of calmodulin. In myosin light chain kinase activation, MeroCaM and calmodulin displayed indistinguishable maximal activation levels and concentration dependence of activation. Changes in MeroCaM's calcium affinity induced by magnesium, phosphodiesterase, and melittin were similar to those reported for calmodulin. Experiments with melittin revealed that target protein interaction could alter the fluorescence changes produced by calcium binding. MeroCaM showed promising brightness and photostability when imaged in individual living fibroblasts. The long excitation and emission wavelengths of MeroCaM, and the strong dependence of its excitation ratio on calcium concentrations, suit it well for use as a probe of calmodulin-dependent calcium signaling in living cells, as well as for experiments in vitro.
Alpha-2 Adrenergic Receptor Agonists are Neuroprotective in Experimental Models of Glaucoma (2001)

Having demonstrated that: a. the specific receptor target of brimonidine is located in the retina, which is important for optic neuroprotection, b. the agent shows neuroprotective ability in animal models, c. pharmacological concentrations of the drug can be reached in the retina, clinical trial has been initiated to determine whether brimonidine is neuroprotective in patients with nonarteritic ischaemic optic neuropathy.
The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches (2008)

A novel family of riboswitches, called SAM-IV, is the fourth distinct set of mRNA elements to be reported that regulate gene expression via direct sensing of S-adenosylmethionine (SAM or AdoMet). SAM-IV riboswitches share conserved nucleotide positions with the previously described SAM-I riboswitches, despite rearranged structures and nucleotide positions with family-specific nucleotide identities. Sequence analysis and molecular recognition experiments suggest that SAM-I and SAM-IV riboswitches share similar ligand binding sites, but have different scaffolds. Our findings support the view that RNA has considerable structural versatility and reveal that riboswitches exploit this potential to expand the scope of RNA in genetic regulation.
Specificity of antigen processing for MHC class I restricted presentation is conserved between mouse and man (1992)

Alloreactive mouse cytotoxic T lymphocytes (CTL) specific for particular peptides presented by H-2Kb molecules on mouse cells were found to recognize human cells transfected with Kb. The CTL-recognized peptides (probably derived from conserved proteins) were extracted from Kb-expressing human or mouse cells, respectively, and compared biochemically by high resolution high performance liquid chromatography. The results strongly suggest identity of peptides processed by cells from both species and thus indicate that the specificity of the processing machinery used in the major histocompatibility complex (MHC) class I-restricted pathway, probably including enzymes, transport mechanisms, and chaperons, is highly conserved across species. The results are consistent with the notion that MHC molecules themselves have an instructive role in processing.
An efficient kernel for multilingual generation in speech-to-speech dialogue translation (1998)

We present core aspects of a fully implemented generation component in a multilingual speech-to-speech dialogue translation system. Its design was particularly influenced by the necessity of real-time processing and usability for multiple languages and domains. We developed a general kernel system comprising a microplanning and a syntactic realizer module. The microplanner performs lexical and syntactic choice, based on constraint-satisfaction techniques. The syntactic realizer processes HPSG grammars reflecting the latest developments of the underlying linguistic theory, utilizing their pre-processing into the TAG formalism. The declarative nature of the knowledge bases, i.e., the microplanning constraints and the HPSG grammars allowed an easy adaption to new domains and languages. The successful integration of our component into the translation system Verbmobil proved the fulfillment of the specific real-time constraints.
Headache pathogenesis : monoamines, neuropeptides, purines, and nitric oxide (1997)

General aspects of messenger molecules, localization, methods for measurement, receptors and second messengers messenger molecules in cranial blood vessels role of messenger molecules in pain processing involvement of amines and amino acids in primary headache involvement of neuropeptides in primary headaches involvement of nitric oxide-cyclic GMP pathway products in primary headache.
Cis-elements of protein transport to the plant vacuoles (1999)

plast is required for the turgor pressure.Vacuoles store proteins, polysaccharides, organic acids, and pigments.Vacuolar proteins are synthesized and translocated Detoxified compounds are deposited in vacuoles, but also into the endoplasmic reticulum and transported to the precursors of toxic compounds needed for defence ( Wink, vacuoles through the secretory pathway.Three differ-1993).The vacuoles belong to the secretory pathway, since ent types of vacuolar sorting signals have been identithey are derived from the endoplasmic reticulum (ER), fied, carried by N-or C-terminal propeptides or internal where both its soluble and tonoplast proteins are synthesequences.These signals are needed to target prosized.The soluble proteins of the secretory pathway require teins to the different types of vacuoles that can coexist a signal sequence for synthesis by membrane-bound riboin a single plant cell.A conserved motif (NPIXL or somes on the ER.After the protein entered the ER, its NPIR) was identified within N-terminal propeptides, but signal sequence is removed and the protein is released into can also function in a C-terminal propeptide and tarthe ER lumen.Membrane proteins are similarly inserted gets proteins in a receptor-mediated manner to a lytic into the ER membrane.These proteins are exported from vacuole.Binding to a family of putative sorting recepthe ER and targeted to their final destinations by vesicular tors for sequence-specific vacuolar sorting signals has transport.The final location depends on targeting informabeen used as an assay to identify further peptides with tion within the polypeptides (Ho fte et al., 1991).This review other binding motifs.No motif was found in C-terminal will focus on the structural determinants that are required sorting sequences, which need an accessible terfor the sorting of vacuolar protein precursors and for their minus, suggesting that they are recognized from the transport to the final compartment.The identification of end by a still unknown receptor.The phosphatidylinosthree different types of sorting signals will be linked to the itol kinase inhibitor wortmannin differentially affects recent visualization of different vacuolar compartments sorting mediated by these two sorting sequences, sugwithin a single plant cell and to the differential effect of the gesting different sorting mechanisms.Less is known lipid kinase inhibitor, wortmannin, on the sorting of two about sorting mediated by internal protein sequences, different vacuolar proteins.There will be a short discussion which do not contain the conserved motif identified in N-terminal propeptides and may function by aggrega-of tonoplast protein sorting, for which there is only scant tion, leading to transport by coat-less dense vesicles information.to protein storage vacuoles.Even less is known about the sorting of tonoplast proteins, for which several Targeting of soluble proteins to a vacuole requires sorting systems will also be needed. specific peptide informationKey words: Protein trafficking
Involvement of mitochondrial aldehyde dehydrogenase ALD5 in maintenance of the mitochondrial electron transport chain inSaccharomyces cerevisiae (1999)

The physiological role of mitochondrial aldehyde dehydrogenase (ALD5) was investigated by analysis of the ald5 mutant (AKD321) in Saccharomyces cerevisiae. K(+)-activated ALDH activity of the ald5 mutant was about 80% of the wild-type in the mitochondrial fraction, while the respiratory activity of the ald5 mutant was greatly reduced. Cytochrome content was also reduced in the ald5 mutant. Enzymatic analysis revealed that the alcohol dehydrogenase activity of the ald5 mutant was higher than that of the wild-type, while glycerol 3-phosphate dehydrogenase activity was the same in the two strains. Ethanol as a carbon source or addition of 1 M NaCl with glucose as the carbon source in the growth medium increased beta-galactosidase activity from an ALD5-lacZ fusion. Overexpression of another mitochondrial ALDH gene (ALD7) had no effect on increasing respiratory function of the ald5 mutant, but showed improved growth on ethanol. These observations show that mitochondrial ALD5 plays a role in regulation or biosynthesis of electron transport chain components.
3-D Scene Reconstruction from Multiple Photometric Images (2007)

This thesis deals with the problem of three dimensional scene reconstruction from multiple camera images. This is a well established problem in computer vision and has been significantly researched. In recent years some excellent results have been achieved, however existing algorithms often fall short of many biological systems in terms of robustness and generality. The aim of this research was to develop improved algorithms for reconstructing 3D scenes, with a focus on accurate system modelling and correctly dealing with occlusions. With scene reconstruction the objective is to infer scene parameters describing the 3D structure of the scene from the data given by camera images. This is an illposed inverse problem, where an exact solution cannot be guaranteed. The use of a statistical approach to deal with the scene reconstruction problem is introduced and the differences between maximum a priori (MAP) and minimum mean square estimate (MMSE) considered. It is discussed how traditional stereo matching can be performed using a volumetric scene model. An improved model describing the relationship between the camera data and a discrete model of the scene is presented. This highlights some of the common causes of modelling errors, enabling them to be dealt with objectively. The problems posed by occlusions are considered. Using a greedy algorithm the scene is progressively reconstructed to account for visibility interactions between regions and the idea of a complete scene estimate is established. Some simple and improved techniques for reliably assigning opaque voxels are developed, making use of prior information. Problems with variations in the imaging convolution kernel between images motivate the development of a pixel dissimilarity measure. Belief propagation is then applied to better utilise prior information and obtain an improved global optimum. A new volumetric factor graph model is presented which represents the joint probability distribution of the scene and imaging system. By utilising the structure of the local compatibility functions, an efficient procedure for updating the messages is detailed. To help convergence, a novel approach of accentuating beliefs is shown. Results demonstrate the validity of this approach, however the reconstruction error is similar or slightly higher than from the Greedy algorithm. To simplify the volumetric model, a new approach to belief propagation is demonstrated by applying it to a dynamic model. This approach is developed as an alternative to the full volumetric model because it is less memory and computationally intensive. Using a factor graph, a volumetric known visibility model is presented which ensures the scene is complete with respect to all the camera images. Dynamic updating is also applied to a simpler single depth-map model. Results show this approach is unsuitable for the volumetric known visibility model, however, improved results are obtained with the simple depth-map model.
Oxidation Catalysis of Nb(salan) Complexes: Asymmetric Epoxidation of Allylic Alcohols Using Aqueous Hydrogen Peroxide as an Oxidant (2010)

Several optically active Nb(salan) complexes were synthesized, and their oxidation catalysis was examined. A dimeric mu-oxo Nb(salan) complex that was prepared from Nb(OiPr)(5) and a salan ligand was found to catalyze the asymmetric epoxidation of allylic alcohols using a urea-hydrogen peroxide adduct as an oxidant with good enantioselectivity. However, subsequent studies of the time course of this epoxidation and of the relationship between the ee of the ligand and the ee of the product indicated that the mu-oxo dimer dissociates into a monomeric species prior to epoxidation. Moreover, monomeric Nb(salan) complexes prepared in situ from Nb(OiPr)(5) and salan ligands followed by water treatment were found to catalyze the epoxidation of allylic alcohols better using aqueous hydrogen peroxide in CHCl(3)/brine or toluene/brine solution with high enantioselectivity ranging from 83 to 95% ee, except for the reaction of cinnamyl alcohol that showed a moderate ee of 74%. This is the first example of the highly enantioselective epoxidation of allylic alcohols using aqueous hydrogen peroxide as an oxidant.
RH10 provides superior transgene expression in mice when compared with natural AAV serotypes for neonatal gene therapy (2010)

The impact of tissue and organ growth on the stability of AAV expression will be important if neonatal gene transfer is to be considered as a modality for human gene therapy. Although all vectors did demonstrate expression, rh10 holds the greater promise of the vectors tested to maintain copy number in both mitotic and post-mitotic tissues.
Isolation and characterization of antibody fragments selective for specific protein morphologies from nanogram antigen samples (2013)

We developed atomic force microscope (AFM)-based protocols that enable isolation and characterization of antibody-based reagents that selectively bind target protein variants using low nanogram amounts or less of unpurified starting material. We isolated single-chain antibody fragments (scFvs) that specifically recognize an oligomeric beta-amyloid (Aβ) species correlated with Alzheimer's disease (AD) using only a few nanograms of an enriched but not purified sample obtained from human AD brain tissue. We used several subtractive panning steps to remove all phage binding nondesired antigens and then used a single positive panning step using minimal antigen. We also used AFM to characterize the specificity of the isolated clones, again using minimal material, selecting the C6 scFv based on expression levels. We show that C6 selectively binds cell and brain-derived oligomeric Aβ. The protocols described are readily adapted to isolating antibody-based reagents against other antigenic targets with limited availability.
Weight Loss Precedes Dementia in Community‐Dwelling Older Adults (1996)

Weight loss precedes mild to moderate dementia; early weight loss is, therefore, unlikely to be a consequence of AD patients being unable or unwilling to eat.
Quilt Packaging: A New Paradigm for Interchip Communication (2006)

"Quilt packaging," (QP) a new paradigm for interchip communication, is presented. QP uses conducting modules that protrude from the sides of integrated circuits to affect an enhanced-speed, reduced-power method of interfacing multiple die together within a package or on a multichip module. The concept of QP is introduced along with a discussion of advantages over traditional system-on-chip and system-in-package technologies. Details of a process flow and preliminary results are presented. Simulations show expected signal propagation between adjacent die of greater than 150 GHz.
RPGR ORF15 isoform co-localizes with RPGRIP1 at centrioles and basal bodies and interacts with nucleophosmin (2005)

The ORF15 isoform of RPGR (RPGR(ORF15)) and RPGR interacting protein 1 (RPGRIP1) are mutated in a variety of retinal dystrophies but their functions are poorly understood. Here, we show that in cultured mammalian cells both RPGR(ORF15) and RPGRIP1 localize to centrioles. These localizations are resistant to the microtubule destabilizing drug nocodazole and persist throughout the cell cycle. RPGR and RPGRIP1 also co-localize at basal bodies in cells with primary cilia. The C-terminal (C2) domain of RPGR(ORF15) (ORF15(C2)) is highly conserved across 13 mammalian species, suggesting that it is a functionally important domain. Using matrix-assisted laser desorption ionization time-of-flight mass spectrometry, we show that this domain interacts with a 40 kDa shuttling protein nucleophosmin (NPM). The RPGR(ORF15)-NPM interaction was confirmed by (i) yeast two-hybrid analyses; (ii) binding of both recombinant and native HeLa cell NPM to RPGR(ORF15) fusion proteins in vitro; (iii) co-immunoprecipitation of native NPM, RPGR(ORF15) and RPGRIP1 from bovine retinal extracts and of native HeLa cell NPM and transfected RPGR(ORF15) from cultured cells and (iv) co-localization of NPM and RPGR(ORF15) at metaphase centrosomes in cultured cells. NPM is a multifunctional protein chaperone that shuttles between the nucleoli and the cytoplasm and has been associated with licensing of centrosomal division. RPGR and RPGRIP1 join a growing number of centrosomal proteins involved in human disease.
Vitamin Levels in Chronic Renal Failure and Need for Supplementation (1985)

Deficiencies of water-soluble vitamins may occur in uremic patients mainly because of restricted consumption and of loss during chronic hemo- and peritoneal dialysis. Although the daily requirement for most vitamins is not well defined in chronic renal failure supplementation of the vitamins thiamine, riboflavin, pyridoxine, pantothenic acid, niacin and ascorbic acid, the form of one multivitamin preparation without vitamin A as well as folic acid in dialysis patients after each dialysis is recommended. There is no need for vitamin B12, vitamin A and vitamin E.