gebhart/patrepeval huggingface dataset:
Improving livestock for agriculture – technological progress from random transgenesis to precision genome editing heralds a new era (2014)

Humans have a long history in shaping the genetic makeup of livestock to optimize production and meet growing human demands for food and other animal products. Until recently, this has only been possible through traditional breeding and selection, which is a painstakingly slow process of accumulating incremental gains over a long period. The development of transgenic livestock technology offers a more direct approach with the possibility for making genetic improvements with greater impact and within a single generation. However, initially the technology was hampered by technical difficulties and limitations, which have now largely been overcome by progressive improvements over the past 30 years. Particularly, the advent of genome editing in combination with homologous recombination has added a new level of efficiency and precision that holds much promise for the genetic improvement of livestock using the increasing knowledge of the phenotypic impact of genetic sequence variants. So far not a single line of transgenic livestock has gained approval for commercialization. The step change to genome-edited livestock with precise sequence changes may accelerate the path to market, provided applications of this new technology for agriculture can deliver, in addition to economic incentives for producers, also compelling benefits for animals, consumers, and the environment.
Establishment of the circumferential actin filament network is a prerequisite for localization of the cadherin-catenin complex in epithelial cells. (1999)

With the adhesion molecules, the actin cytoskeleton controls cell-cell and cell-substrate interactions and participates in transmembrane signaling. The relationships between actin and adhesion complexes at the sites of adhesion have been well documented. Here we investigate by a series of studies whether a relationship exists between actin organization and the localization and function of the components of the cadherin-catenin complex (CCC) that participates in the cell-cell adherens junction. Reversible actin depolymerization reversibly affects the peripheral distribution of CCCs. Mutations in adenovirus E1A and the small GTPase rac1, but not Ha-ras, disrupt the circumferential, cortical actin filament (CAF) network and the targeting of CCC components to the cell surface. Disruption of actin stress fibers or microtubules does not interfere with CCC localization and function. Constitutive loss of the apical cortical actin ring results in epithelial cells in which components of the CCCs are found only in intracellular vesicles and never at the surface. A kinetic analysis of the de novo appearance of the CAF network and the CCCs at the cell surface was also conducted. When F-actin was dissolved, surface CCC components were internalized. Reestablishment of CAFs required about 4 h, during which time E-cadherin and alpha-catenin were found first in a juxtanuclear location and then in intracellular vesicles or post-Golgi carriers, similar to what was observed in cells expressing mutant E1A or rac1. Thus, disruption of preexisting CCCs resulted in their internalization and recycling to the Golgi. It was only after the regeneration of the filamentous actin ring beneath the cell surface that peripheral localization of CCCs was observed. A similar result was observed with dominant negative rac1. These data suggest that the status of cortical actin is assessed and transduced and thereby regulates the transport and delivery of cadherin and catenins to the cell surface.
From Space to Sequence and Back Again: Iterative DNA Proximity Ligation and its Applications to DNA-Based Imaging (2018)

Abstract We extend the concept of DNA proximity ligation from a single readout per oligonucleotide pair to multiple reversible, iterative ligations re-using the same oligonucleotide molecules. Using iterative proximity ligation (IPL), we can in principle capture multiple ligation events between each oligonucleotide and its various neighbors and thus recover a far richer knowledge about their relative positions than single, irreversible ligation events. IPL would thus act to sample and record local molecular neighborhoods. By integrating a unique DNA barcode into each participating oligonucleotide, we can catalog the individual ligation events and thus capture the positional information contained therein in a high throughput manner using next-generation DNA sequencing. We propose that by interpreting IPL sequencing results in the context of graph theory and by applying spring layout algorithms, we can recover geometric patterns of objects labeled by DNA. Using simulations, we demonstrate that we can in principle recover letter patterns photolithographed onto slide surfaces using only IPL sequencing data, illustrating how our technique maps complex spatial configurations into DNA sequences and then – using only this sequence information – recovers them. We complement our theoretical work with an experimental proof-of-concept of iterative proximity ligation on an oligonucleotide population.
The effects of blending agents on alcohol-gasoline fuels (1993)

One of the most restrictive factors in the use of alcohol-gasoline blends as engine fuel is phase separation. This can cause problems in blending and storage, during distribution to retail outlets and when the fuel is in the vehicle. Problems such as starting difficulties, cycle-to-cycle variation and misfiring can lead to poor power output and even to internal engine damage. In this research the phase separation of ethanol- and methanol-gasoline blends is solved by the introduction of C 3 , C 4 , C 5 iso and normal and mono alcohols as blending agents. Their effects were investigated and compared
Stimulation of glucose catabolism in Escherichia coli by a potential futile cycle (1992)

Fifteen-fold overexpression of phosphoenolpyruvate synthase (Pps) (EC 2.7.9.2) in Escherichia coli stimulated oxygen consumption in glucose minimal medium. A further increase in Pps overexpression to 30-fold stimulated glucose consumption by approximately 2-fold and resulted in an increased excretion of pyruvate and acetate. Insertion of two codons at the PvuII site in the pps gene abolished the enzymatic activity and eliminated the above-described effects. Both the active and the inactive proteins were detected at the predicted molecular weight by polyacrylamide gel electrophoresis. Therefore, the observed physiological changes were due to the activity of Pps. The higher specific rates of consumption of oxygen and glucose indicate a potential futile cycle between phosphoenolpyruvate (PEP) and pyruvate. A model for the stimulation of glucose uptake is presented; it involves an increased PEP/pyruvate ratio caused by the overexpressed Pps activity, leading to a stimulation of the PEP:sugar phosphotransferase system.
Early endothelial and haematological response to cryoplasty compared with balloon angioplasty of the superficial femoral artery – a pilot study (2007)

The purpose of the present study was to assess the course of adhesion molecules (intercellular adhesion molecule (ICAM), vascular cell adhesion molecule (VCAM), e-selectin, p-selectin and monocyte chemoatlractant protein 1 (MCP-1)), growth factors (transforming growth factor beta (TGFbeta) and basic fibroblast growth factor (bFGF)) and the cytokine tumour necrosis factor alpha (TNFalpha) after both angioplasty and cryoplasty. Recently cryoplasty has been suggested as a new method to oppose neointimal hyperplasia resulting in restenosis formation. While in vitro models have shown that the application of cryothermal energy to the endothelium during angioplasty leads to apoptosis induction and reduced proliferation rates, no human in vivo proof for an inhibition of neointimal hyperplasia exists. For restenosis initiation adhesion molecules, growth factors and cytokines play an important role. One possibility to investigate the endothelial response to angioplasty is the measurement of the soluble forms of adhesion molecules, growth factors and cytokines that are released into the circulation after denuding the vessel wall. In the present study we assessed the distribution pattern of the soluble forms of e-selectin, p-selectin, ICAM, VCAM, MCP-1, TGFbeta, bFGF and TNFalpha after angiography, angioplasty and cryoplasty of the femoropopliteal artery in the early course of 4 weeks in 29 patients with peripheral arterial occlusive disease. During the 4 weeks after intervention levels of e-selectin, ICAM, VCAM and MCP-1 increased after both angioplasty and cryoplasty. The course of the screened biomarkers was similar between angioplasty and cryoplasty. P-selectin and TGFbeta both decreased after cryoplasty, but not significantly. The present results show that the release of adhesion molecules, growth factors and cytokines is similar between balloon angioplasty and cryoplasty.
Some studies on the composition and surface properties of oil bodies from the seed cotyledons of safflower (Carthamus tinctorius) and linseed (Linum ustatissimum) (1980)

1. The average oil-body diameter in intact cells of developing linseed (Linum usitatissimum) and safflower (Carthamus tinctorius) cotyledons was similar (about 1.4 micrometer), and there was little change in size after oil bodies were isolated and repeatedly washed. 2. The glycerolipid composition of washed oil bodies from both developing and mature cotyledons of the two species was similar; oil bodies from ten different batches of cotyledons contained 4.3 +/- 0.16 mumol of 3-sn-phosphatidylcholine and 25.2 +/- 1.7 mumol of diacylglycerol per 1000 mumol of triacylglycerol. During four successive washings of a once-washed oil-body preparation, the proportion of diacylglycerol to triacylglycerol remained constant and that of 3-sn-phosphatidylcholine to triacylglycerol decreased by only 20%. 3. The protein content of thrice-washed oil bodies from the two species was similar, about 2.4% of the weight of glycerolipids, and appeared to be independent of the stage of cotyledon maturity. Sodium dodecyl sulphate/polyacrylamide-gel electrophoresis indicated that the protein of purified oil bodies from the two species consisted mainly of only four polypeptides and that two of the polypeptides from each species had apparent mol.wts. of 17500 and 15500. Similar patterns of polypeptides were obtained after the hydrolysis of the 15500-mol.wt. polypeptides from linseed and safflower oil bodies by Staphylococcus aureus V8 proteinase, whereas the proteolysis of the 17500-mol.wt. polypeptides from the two species produced different patterns of polypeptides. 4. The 3-sn-phosphatidylcholine in oil-body preparations was hydrolysed about 85% by bee-venom phospholipase A2 without any apparent coalescence of the oil bodies. Incubation with lipase from Rhizopus arrhizus caused rapid coalescence of the oil bodies, and this lipase appeared to initially hydrolyse diacylglycerols in preference to triacylglycerol. 5. Oil bodies from both species were almost completely dispersed in suspensions of pH between 7.1 and 8.3, but formed large aggregates at pH values between 6.7 and 3.9; pH-induced aggregation caused no coalescence. Aggregates formed under acidic conditions were dispersed by re-adjusting the pH of suspensions to 8.3. 6. A freeze-etch electron-microscopic examination of isolated oil bodies indicated that these organelles were bounded by some form of membrane with a particle-free outer surface.
Terpenoid-based defenses in conifers: cDNA cloning, characterization, and functional expression of wound-inducible ( E )-α-bisabolene synthase from grand fir ( Abies grandis ) (1998)

(E)-alpha-Bisabolene synthase is one of two wound-inducible sesquiterpene synthases of grand fir (Abies grandis), and the olefin product of this cyclization reaction is considered to be the precursor in Abies species of todomatuic acid, juvabione, and related insect juvenile hormone mimics. A cDNA encoding (E)-alpha-bisabolene synthase was isolated from a wound-induced grand fir stem library by a PCR-based strategy and was functionally expressed in Escherichia coli and shown to produce (E)-alpha-bisabolene as the sole product from farnesyl diphosphate. The expressed synthase has a deduced size of 93.8 kDa and a pI of 5. 03, exhibits other properties typical of sesquiterpene synthases, and resembles in sequence other terpenoid synthases with the exception of a large amino-terminal insertion corresponding to Pro81-Val296. Biosynthetically prepared (E)-alpha-[3H]bisabolene was converted to todomatuic acid in induced grand fir cells, and the time course of appearance of bisabolene synthase mRNA was shown by Northern hybridization to lag behind that of mRNAs responsible for production of induced oleoresin monoterpenes. These results suggest that induced (E)-alpha-bisabolene biosynthesis constitutes part of a defense response targeted to insect herbivores, and possibly fungal pathogens, that is distinct from induced oleoresin monoterpene production.
User Type Classification of Tweets with Implications for Event Recognition (2014)

Twitter has become one of the foremost platforms for information sharing. Consequently, it is beneficial for the consumers of Twitter to know the origin of a tweet, as it affects how they view and interpret this information. In this paper, we classify tweets based on their origin, exploiting only the textual content of tweets. Specifically, using a rich, linguistic feature set and a supervised classifier framework, we classify tweets into two user types -organizations and individual persons. Our user type classifier achieves an 89% F 1 -score for identifying tweets that originate from organizations in English and an 87% F 1 -score for Spanish. We also demonstrate that classifying the user type of a tweet can improve downstream event recognition tasks. We analyze several schemes that exploit user type information to enhance Twitter event recognition and show that substantial improvements can be achieved by training separate models for different user types.
Do intravenous and subcutaneous angiotensin II increase blood pressure by different mechanisms? (2013)

Angiotensin (Ang) II plays a key role in blood pressure regulation. Mechanisms of the pressor effect of chronic intravenous AngII administration include vasoconstriction, stimulation of the sympathetic nervous system and aldosterone production, as well as direct effects on renal excretion of sodium and water. Chronic AngII administration by subcutaneous minipump at doses higher than required to increase blood pressure by the intravenous route has identified additional pressor mechanisms, including the immune system, cytokines and matrix metalloproteinases. However, pressor doses of subcutaneous AngII may exceed the angiotensinogen synthesis rate and produce inflammation, fibrosis and necrosis of skin overlying the minipump. Evidence that chronic subcutaneous and intravenous AngII increase blood pressure by different mechanisms includes the prevention of the pressor effects of subcutaneous, but not intravenous, AngII by angiotensin-converting enzyme inhibition. Furthermore, low doses of subcutaneous AngII reduce blood pressure of female, but not male, rodents and higher doses are less pressor in females than in males, whereas intravenous AngII is equally pressor in males and females. Pressor doses of chronic subcutaneous AngII produce greater weight loss, anorexia and reduced kidney weight and cause greater vascular, cardiac and renal pathology than equally pressor doses of chronic intravenous AngII. The different effects of chronic intravenous and subcutaneous AngII suggest that these two models of hypertension give different information and may differ in their relevance to blood pressure regulation in physiological and pathological states such as hypertension in humans.
Index (1999)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
Women Who Discovered the World (2011)

An uncertain stream of women travel writers do exist through history that have in some way helped discover the world. Many young Australian women have also ventured into the world of travel writing and been successful are highlighted.
p16/MTS1 inactivation in ovarian carcinomas: High frequency of reduced protein expression associated with hyper-methylation or mutation in endometrioid and mucinous tumors (1998)

Inactivation of the tumor-suppressor gene p16 (MTS1/ CDKN2/INK4a) has been described in various human malignancies. Although p16 deletion has been found in various ovarian tumor cell lines, p16 inactivation by homozygous deletion or mutation has been reported only sporadically in primary ovarian carcinomas. In a comprehensive study, we analyzed p16 protein expression by immuno-histochemistry (IHC) on paraffin sections of 94 primary ovarian carcinomas of different histological subtype. Loss of expression was detected in 19 primary tumors (20%), mainly mucinous and endometrioid carcinomas. To reveal the cause of suppressed expression, we performed (i) analysis of homozygous deletions by comparative PCR after micro-dissection, (ii) mutation analysis by single-strand conformation polymorphism analysis and subsequent direct sequencing and (iii) methylation-specific PCR to determine the methylation status of 5'-CpG islands. Loss of or weak p16 expression was caused by hyper-methylation (12/19 IHC-negative cases), somatic mutation (10 tumors) or homozygous deletion (1 case). Aberrant p 16 results by one of these methods were detected in 71-79% of endometrioid and mucinous, but in only 10% of serous-papillary, carcinomas. Our data suggest that p16 inactivation is a typical feature of certain subtypes of ovarian carcinoma.
Ruthenium catalysed N-alkylation of amines with alcohols (2007)

The conversion of primary amines into secondary amines has been achieved using alcohols as the alkylating agent, catalysed by [Ru(p-cymene)Cl2]2 and a bidentate phosphine ligand.
Inhibitory activity of cranberry juice on adherence of type 1 and type P fimbriated Escherichia coli to eucaryotic cells (1989)

Inhibition of bacterial adherence to bladder cells has been assumed to account for the beneficial action ascribed to cranberry juice and cranberry juice cocktail in the prevention of urinary tract infections (A. E. Sobota, J. Urol. 131:1013-1016, 1984). We have examined the effect of the cocktail and juice on the adherence of Escherichia coli expressing surface lectins of defined sugar specificity to yeasts, tissue culture cells, erythrocytes, and mouse peritoneal macrophages. Cranberry juice cocktail inhibited the adherence of urinary isolates expressing type 1 fimbriae (mannose specific) and P fimbriae [specific for alpha-D-Gal(1----4)-beta-D-Gal] but had no effect on a diarrheal isolate expressing a CFA/I adhesin. The cocktail also inhibited yeast agglutination by purified type 1 fimbriae. The inhibitory activity for type 1 fimbriated E. coli was dialyzable and could be ascribed to the fructose present in the cocktail; this sugar was about 1/10 as active as methyl alpha-D-mannoside in inhibiting the adherence of type 1 fimbriated bacteria. The inhibitory activity for the P fimbriated bacteria was nondialyzable and was detected only after preincubation of the bacteria with the cocktail. Cranberry juice, orange juice, and pineapple juice also inhibited adherence of type 1 fimbriated E. coli, most likely because of their fructose content. However, the two latter juices did not inhibit the P fimbriated bacteria. We conclude that cranberry juice contains at least two inhibitors of lectin-mediated adherence of uropathogens to eucaryotic cells. Further studies are required to establish whether these inhibitors play a role in vivo.
Artificial neural networks improve the accuracy of cancer survival prediction (1997)

Artificial neural networks are significantly more accurate than the TNM staging system when both use the TNM prognostic factors alone. New prognostic factors can be added to artificial neural networks to increase prognostic accuracy further. These results are robust across different data sets and cancer sites.
A Small, Nonpeptidyl Mimic of Granulocyte-Colony- Stimulating Factor (1998)

A nonpeptidyl small molecule SB 247464, capable of activating granulocyte–colony-stimulating factor (G-CSF) signal transduction pathways, was identified in a high-throughput assay in cultured cells. Like G-CSF, SB 247464 induced tyrosine phosphorylation of multiple signaling proteins and stimulated primary murine bone marrow cells to form granulocytic colonies in vitro. It also elevated peripheral blood neutrophil counts in mice. The extracellular domain of the murine G-CSF receptor was required for the activity of SB 247464, suggesting that the compound acts by oligomerizing receptor chains. The results indicate that a small molecule can activate a receptor that normally binds a relatively large protein ligand.
O1–04–05: Six‐month cerebral metabolic declines in Alzheimer's disease, amnestic mild cognitive impairment and elderly normal control groups: Preliminary findings from the Alzheimer's disease neuroimaging initiative (2007)

In a previous FDG PET study, we found that patients with Alzheimer's disease (AD) had one-year declines in the regional cerebral metabolic rate for glucose (CMRgl), and we used that information to estimate the number of patients needed to evaluate putative disease-slowing treatments in one-year clinical trials (Alexander et al, 2002). To characterize approximately six-month CMRgl declines in patients with AD, patients with amnestic mild cognitive impairment (MCI) and elderly normal controls (NC), and to estimate the number of AD and MCI patients needed to evaluate a putative disease-slowing treatment in a six-month clinical trial, using PET images from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database (www.loni.ucla.edu\ADNI). Baseline and approximately six-month follow-up ADNI PET images were compared in separate analyses of 16 AD patients, 27 MCI patients and 27 NC using SPM5. Using the atlas coordinate with the maximally significant CMRgl decline in the respective AD and MCI comparison, power analyses were performed to estimate the number of patients needed to evaluate a putative primary prevention therapy in a six-month multi-center clinical trial. There was a trend for approximately six-month MMSE declines in the AD patients (P=0.06) and MCI patients (P=0.06) but not in the NC (P=0.86). The AD patients had six-month CMRgl declines in left temporal, parietal and precuneus regions (maximal reduction 3.0%), the MCI patients had six-month CMRgl declines in bilateral temporal, right parietal and right frontal regions (maximal reduction 2.0%), and the NC had had six-month declines in the left temporal cortex (P<0.001, uncorrected for multiple comparisons). Using the maximal, left temporal CMRgl declines in each patient group, we estimate the need for at least 224 AD patients or 642 MCI patients per treatment arm to detect a putative disease-slowing treatment efficacy to reduce six-month CMRgl declines by 25% with 80% power (one-tailed P=0.005, uncorrected for multiple comparisons) in a multi-center clinical trial. This study provides preliminary information about six-month CMRgl declines in AD and MCI patients and a preliminary estimate of the number of patients needed to detect CMRgl effects in six-month clinical trials of putative disease-slowing treatments.