gebhart/patrepeval huggingface dataset:
Differential regulation of NGF receptors in primary sensory neurons by adjuvant-induced arthritis in the rat (2001)

In the adult brain, neurotrophins play a key role in adaptive processes linked to increased neuronal activity. A growing body of evidence suggests that chronic pain results from long-term plasticity of central pathways involved in nociception. We have investigated the involvement of nerve growth factor (NGF) in adaptive responses of primary sensory neurons during the course of a long-lasting inflammatory pain model. The amount and distribution of the NGF receptors p75(NTR) and TrkA were measured in the dorsal horn and dorsal root ganglia (DRG) of animals subjected to Freund's adjuvant-induced arthritis (AIA). We observed an increased immunoreactivity of both receptors in the central terminals of primary sensory neurons in the arthritic state. The increases were seen in the same population of afferent terminals in deep dorsal horn laminae. These changes paralleled the variations of clinical and behavioral parameters that characterize the course of the disease. They occurred in NGF-sensitive, but not GDNF-sensitive, nerve terminals. However, p75(NTR) and TrkA protein levels in the DRG (in the cell body of these neurons) showed different response patterns. An immediate rise of p75(NTR) was seen in parallel with the initial inflammation that developed after administration of Freund's adjuvant in hindpaws. In contrast, increases of the mature (gp140(trk)) form of TrkA occurred later and seemed to be linked to the development of the long-lasting inflammatory response. The changes in receptor expression were observed exclusively at lumbar levels, L3-L5, somatotopically appropriate for the inflammation. Together, these results implicate NGF in long-term mechanisms accompanying chronic inflammatory pain, via the up-regulation of its high affinity receptor, and offer additional evidence for differential processes underlying short- versus long-lasting inflammatory pain.
Ethiopia - Gilgel Gibe Hydroelectric (Energy II) Project : environmental impact assessment (1997)

This environmental impact assessment (EIA) identifies and assesses five negative environmental impacts likely to result from preparing, constructing, and operating the Gilgel Gibe Hydroelectric Project. These are identified on the basis of their intensity, area covered and/or size of human population affected as: 1) Dislocation of people -those who reside within the reservoir area and those who live outside of the area to be flooded and who rely on lands within and outside of the reservoir area- is mitigated by a comprehensive resettlement plan. 2) Intensification of diseases linked to water -malaria, onchocerciasis, and schistosomiasis- and of sexually transmitted diseases, is mitigated by building a buffer around and deepening the margins of the reservoir; and providing health education; preventing shanty town development near construction camps; providing separate dwellings within the camp for men and women; and distributing free condoms. 3) Loss of food production due to the permanent loss of agricultural lands may be alleviated by more intensive agriculture and improved livestock management, and bringing fallow land into production. 4) Loss of biodiversity, specifically, the loss of riverine forest and water flows, which fauna and flora rely on as their habitat, generally cannot be mitigated. However, forest can be established elsewhere to replace total biomass loss, and the reservoir will develop its own ecological system over time. Recommended is formal protection of the forested valley between the dam and the tailrace to ensure that this area's riverine forest is protected. 5) The loss of downstream aquatic habitat can be partially mitigated by providing a compensation flow, a consideration to be weighed against lost hydropower. Other potential and less disruptive impacts are envisioned as humidity rise, change in water quality in the reservoir and downstream, shoreline dumping, reservoir sedimentation and flushing, and eutrophication. Recommendations for alleviation include: water management through a release program, containing pollutants, stabilizing the shoreline with suitable vegetative species, reducing soil erosion with watershed management, and removing large plants before the reservoir is filled to prevent nutrient overload.
Tripodal Aminophenolate Ligand Complexes of Aluminum(III), Gallium(III), and Indium(III) in Water (1997)

Four water-soluble amine phenols have been prepared: tris(((2-hydroxy-5-sulfobenzyl)amino)ethyl)amine (H6TRNS), 1,1,1-tris(((2-hydroxy-5-sulfobenzyl)amino)methyl)ethane (H6TAMS), 1,2,3-tris((2-hydroxy-5-sulfobenzyl)amino)propane (H6TAPS), and cis,cis-1,3,5-tris((2-hydroxy-5-sulfobenzyl)amino)cyclohexane (H6TACS). Complex formation constants have been measured at 25 °C (μ = 0.16 M NaCl): log K [M(TRNS)]3- ([M(HTRNS)]2-) M = Ga 28.55 (36.90), In 29.3 (34.9); log K [M(TAMS)]3- ([M(HTAMS)]2-) M = Al 22.5 (29.3), Ga 31.83, In 28.49; log K [M(TAPS)]3- ([M(HTAPS)]2-) M = Al 22.8 (29.0), Ga 31.54 (35.15), In 27.56 (31.93). The order of stability is Ga(III) > In(III) > Al(III) for H6TAMS and H6TAPS, while for H6TRNS it is Ga(III) ≈ In(III) > Al(III). The solution structures of the complexes have been probed by multinuclear NMR (1H, 13C, 27Al, 71Ga, 115In) and UV spectroscopic studies, and these solution structures are compared with solid state structures for analogous complexes. The 1H NMR spectrum in D2O establishes TAPS to be preorganized for metal ion binding. H6TACS exists in the wrong conformation for metal ion binding, and this results in slow complexation kinetics and relatively weaker binding.
Size effects on reactivity of Pt nanoparticles in CO monolayer oxidation: The role of surface mobility (2003)

In the present paper we study the reactivity of model Pt nanoparticles supported on glassy carbon. The particle size effect is rationalized for CO monolayer oxidation exploring electrochemical methods (stripping voltammetry and chronoamperometry) and modelling. Significant size effects are observed in the particle size interval from ca. 1 to 4 nm, including the positive shift of the CO stripping peak with decreasing particle size and a pronounced asymmetry of the current transients at constant potential. The latter go through a maximum at low COads conversion and exhibit tailing, which is the longer the smaller the particle size. Neither mean field nor nucleation & growth models give a coherent explanation of these experimental findings. We, therefore, suggest a basic model employing the active site concept. With a number of reasonable simplifications a full analytical solution is obtained, which allows a straightforward comparison of the theory with the experimental data. A good correspondence between experiment and theory is demonstrated. The model suggests restricted COads mobility at Pt nanoparticles below ca. 2 nm size, with the diffusion coefficient strongly dependent on the particle size, and indicates a transition towards fast diffusion when the particle size exceeds ca. 3 nm. Estimates of relevant kinetic parameters, including diffusion coefficient, reaction constant etc. are obtained and compared to the literature data for extended Pt surfaces.
Saving islets from allograft rejection (2005)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Acquired erythropoietin responsiveness of interleukin-2-dependent T lymphocytes retrovirally transduced with genes encoding chimeric erythropoietin/interleukin-2 receptors (1995)

Adoptive immunotherapy with tumor-infiltrating lymphocytes (TILs) causes regression of some human tumors. However, the sustained proliferation and antitumor activity of TILs requires the coadministration of potentially toxic amounts of interleukin-2 (IL-2). In an effort to overcome the requirement by T cells for IL-2, we have introduced alternative growth factor receptors that use the relatively nontoxic cytokine erythropoietin (Epo) as a ligand. In our model system, the coexpression of chimeric receptors consisting of the extracellular portion of the Epo receptor (EpoR) and the intracellular portions of the IL-2 receptor subunits, beta and gamma, conferred Epo responsiveness on a T-cell line. By contrast, cells expressing the wild-type EpoR did not proliferate in response to Epo. This suggested that Epo binding caused the activation of an IL-2 signal pathway mediated by the chimeric receptors. This approach can be used to minimize toxicity and potentially improve cancer immunotherapy with TILs.
Plasma Vitamin D Metabolite Concentrations in Chronic Renal Failure: Effect of Oral Administration of 25-Hydroxyvitamin D3* (1984)

The circulating concentrations of 1,25-dihydroxyvitamin D and 24,25-dihydroxyvitamin D are abnormally low in patients with chronic renal failure (CRF). To determine the importance of substrate (25-hydroxyvitamin D) concentration in this phenomenon, five patients with end stage renal disease treated with hemodialysis were given 25-hydroxyvitamin D3 (25-OH-D3) orally for 4 weeks. The serum concentration of 25-OH-D3 increased from a mean (+/- SEM) of 26 +/- 5 ng/ml immediately before therapy to a maximum of 108 +/- 5 ng/ml 4 weeks after beginning administration of 25-OH-D3. The concentrations of 1,25-dihydroxyvitamin D3 (1,25(OH)2D3), 24,25-dihydroxyvitamin D3 (24,25(OH)2D3), and 25,26-dihydroxyvitamin D3 (25,26(OH)2D3) increased from 6.6 +/- 0.8 pg/ml, 0.29 +/- 0.10 ng/ml, and 0.36 +/- 0.06 ng/ml, respectively, immediately before 25-OH-D3 administration to 21.7 +/- 2.2 pg/ml, 0.48 +/- 0.09 ng/ml; and 0.78 +/- 0.12 ng/ml, respectively, after 4 weeks of administration of 25-OH-D3. These results suggest that substrate availability may be an important determinant of the circulating concentrations of these metabolites in patients with CRF. It seems possible that the therapeutic effects of 25-OH-D3 administration to the CRF patient may be mediated through the normal actions of 1,25-dihydroxyvitamin D3, 24,25-dihydroxyvitamin D3, and perhaps other metabolites rather than through analog effects of 25-OH-D3.
Family system outcome following acquired brain injury: clinical and research perspectives (2002)

Family members identified distressed family functioning across all domains compared to survivors and compared to population norms. The FAM-III provides clinical utility in assessing family system functioning and shows promise as a family system outcome measure.
Demystifying Heparan Sulfate–Protein Interactions (2014)

Numerous proteins, including cytokines and chemokines, enzymes and enzyme inhibitors, extracellular matrix proteins, and membrane receptors, bind heparin. Although they are traditionally classified as heparin-binding proteins, under normal physiological conditions these proteins actually interact with the heparan sulfate chains of one or more membrane or extracellular proteoglycans. Thus, they are more appropriately classified as heparan sulfate-binding proteins (HSBPs). This review provides an overview of the various modes of interaction between heparan sulfate and HSBPs, emphasizing biochemical and structural insights that improve our understanding of the many biological functions of heparan sulfate.
Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA (2009)

The method was implemented in Perl and relies on the opensource software Maq for read mapping and SNP calling. The Perl script is freely available from ftp://ftp.sanger.ac.uk/pub/pathogens/pools/.
Two novel classes of neuroactive fatty acid amides are substrates for mouse neuroblastoma ‘anandamide amidohydrolase’ (1995)

The endogenous cannabimimetic substance, anandamide (N-arachidonoyl-ethanolamine) and the recently isolated sleep-inducing factor, oleoyl-amide (cis-9,10-octadecenoamide), belong to two neuroactive fatty acid amide classes whose action in mammals has been shown to be controlled by enzymatic amide bond hydrolysis. Here we report the partial characterisation and purification of 'anandamide amidohydrolase' from membrane fractions of N18 neuroblastoma cells, and provide evidence for a further and previously unsuspected role of this enzyme. An enzymatic activity catalysing the hydrolysis of [14C]anandamide was found in both microsomal and 10,000 x g pellet fractions. The latter fractions, which displayed the highest Vmax for anandamide, were used for further characterisation of the enzyme, and were found to catalyse the hydrolysis also of [14C]oleoyl-amide, with an apparent Km of 9.0 +/- 2.2 microM. [14C]anandamide- and [14C]oleoyl-amide-hydrolysing activities: (i) exhibited identical pH- and temperature-dependency profiles; (ii) were inhibited by alkylating agents; (iii) were competitively inhibited by the phospholipase A2 inhibitor arachidonyl-trifluoromethyl-ketone with the same IC50 (3 microM); (iv) were competitively inhibited by both anandamide (or other polyunsaturated fatty acid-ethanolamides) and oleoyl-amide. Proteins solubilised from 10,000 x g pellets were directly analysed by isoelectric focusing, yielding purified fractions capable of catalysing the hydrolysis of both [14C]anandamide and [14C]oleoyl-amide. These data suggest that 'anandamide amidohydrolase' enzymes, such as that characterised in this study, may be used by neuronal cells also to hydrolyse the novel sleep-inducing factor oleoyl-amide.
Nonlinear mixed-effects modelling for single cell estimation: when, why, and how to use it (2015)

When considering uninformative single-cell data, NLME yields more accurate parameter and noise estimates, compared to more traditional approaches, such as STS and JLH.
Evaluation of an orally administered vaccine, using hydrogels containing bacterial exotoxins of Pasteurella haemolytica, in cattle (1994)

Poly(methacrylic acid) hydrogels were tested for oral delivery of a vaccine against Pasteurella haemolytica infection in cattle. Culture supernatants of P haemolytica, the most common bacterium associated with pneumonia in cattle, were used as the antigens in the vaccine. Hydrogels containing culture supernatants were administered orally to calves. Calves were then challenge-exposed with virulent P haemolytica. Calves were euthanatized 3 days after challenge exposure. The lungs of each calf were scored for severity and size of pneumonic lesions. Results indicated that vaccinated calves had smaller, less severe pneumonic lesions and lived longer than nonvaccinated calves. These results indicated that hydrogels can be used to deliver vaccines orally to calves to enhance resistance to pneumonia caused by P haemolytica.
Amplifying and Quantifying HIV-1 RNA in HIV Infected Individuals with Viral Loads Below the Limit of Detection by Standard Clinical Assays (2011)

Amplifying viral genes and quantifying HIV-1 RNA in HIV-1 infected individuals with viral loads below the limit of detection by standard assays (below 50-75 copies/ml) is necessary to gain insight to viral dynamics and virus host interactions in patients who naturally control the infection and those who are on combination antiretroviral therapy (cART). Here we describe how to amplify viral genomes by single genome sequencing (the SGS protocol) (13, 19) and how to accurately quantify HIV-1 RNA in patients with low viral loads (the single-copy assay (SCA) protocol) (12, 20). The single-copy assay is a real-time PCR assay with sensitivity depending on the volume of plasma being assayed. If a single virus genome is detected in 7 ml of plasma, then the RNA copy number is reported to be 0.3 copies/ml. The assay has an internal control testing for the efficiency of RNA extraction, and controls for possible amplification from DNA or contamination. Patient samples are measured in triplicate. The single-genome sequencing assay (SGS), now widely used and considered to be non-labor intensive (3, 7, 12, 14, 15),is a limiting dilution assay, in which endpoint diluted cDNA product is spread over a 96-well plate. According to a Poisson distribution, when less than 1/3 of the wells give product, there is an 80% chance of the PCR product being resultant of amplification from a single cDNA molecule. SGS has the advantage over cloning of not being subjected to resampling and not being biased by PCR-introduced recombination (19). However, the amplification success of SCA and SGS depend on primer design. Both assays were developed for HIV-1 subtype B, but can be adapted for other subtypes and other regions of the genome by changing primers, probes, and standards.
The human cost of not achieving full remission in depression. (2004)

Depression is among the most disabling and costly illnesses in the world. Despite good short-term efficacy outcomes in the treatment of depression, long-term outcomes remain disappointing. Depression continues to be missed or underdiagnosed and undertreated, and comorbidities are frequently not identified. Of particular concern is the low rate of depression treated to full remission. Treating only to response leaves patients with residual depressive symptoms and an increased risk of a recurrent or chronic course. Anything less than full remission should be considered a treatment failure. This article examines the substantial psychiatric, medical, functional, and economic costs associated with not achieving remission. Available pharmacoeconomic data and randomized, controlled clinical trials published in the last 5 years identified through Medline searches with terms including burden, cost, economics, serotonin reuptake inhibitors (also, specific agents), venlafaxine, nefazadone, mirtazapine, psychotherapy, remission, and depression were reviewed. One of the limiting factors to this review is that few trials have compared the effects of various antidepressant strategies on clinically relevant outcomes such as depression-free days and patient productivity, making the full benefit of remission more difficult to measure. Patients who fail to achieve a full remission have a more recurrent and chronic course, increased medical and psychiatric comorbidities, greater functional burden, and increased social and economic costs. Cost-effective treatment for depression includes antidepressant therapies with higher remission rates. Antidepressants with a dual mechanism of action and combination therapies are associated with higher remission rates, more depression-free days, reduced pain-symptom morbidity, reduced health service utilization, and improved productivity.
Correlation Based Search Algorithms for Motion Estimation (1999)

† Work supported in part by Institute for Information Industry. Abstract The measure of the ‘goodness’ of a motion estimation algorithm is governed by it’s speed, the quality of motion compensation it provides, and the size of the resulting bitstream. Hence, algorithms should be evaluated based on this ‘speed-quality-bitrate’ tradeoff. Previously introduced fast motion estimation algorithms focus mainly on the speed vs. quality of motion compensation. In this paper, we introduce several new algorithms and evaluate them based on all three parameters. All these new algorithms exploit spatial correlation of motion vectors. These algorithms include a MAD (Mean Absolute Distortion) based spiral search, an Adaptive Window Size algorithm and two Majority Voting schemes. The algorithms are evaluated on several test sequences in the H.263 framework and the results obtained are very encouraging.
Seeing Mt. Rainier: Lucky imaging for multi-image denoising, sharpening, and haze removal (2010)

Photographing distant objects is challenging for a number of reasons. Even on a clear day, atmospheric haze often represents the majority of light received by a camera. Unfortunately, dehazing alone cannot create a clean image. The combination of shot noise and quantization noise is exacerbated when the contrast is expanded after haze removal. Dust on the sensor that may be unnoticeable in the original images creates serious artifacts. Multiple images can be averaged to overcome the noise, but the combination of long lenses and small camera motion as well as time varying atmospheric refraction results in large global and local shifts of the images on the sensor. An iconic example of a distant object is Mount Rainier, when viewed from Seattle, which is 90 kilometers away. This paper demonstrates a methodology to pull out a clean image of Mount Rainier from a series of images. Rigid and non-rigid alignment steps brings individual pixels into alignment. A novel local weighted averaging method based on ideas from “lucky imaging” minimizes blur, resampling and alignment errors, as well as effects of sensor dust, to maintain the sharpness of the original pixel grid. Finally, dehazing and contrast expansion results in a sharp clean image.
Low phase noise and spurious level in multi-loop opto-electronic oscillators (2004)

We report on substantial improvements of the phase noise, and especially the spurious level of the opto-electronic oscillator (OEO) by using multiple optical loops. We demonstrated a spurious level reduction of more than 30 dB in a dual loop OEO compared with that of a single loop OEO. We found the OEO's closed loop transfer function to describe very well the spurious pattern and to provide an excellent tool for the design of a low spurious multi-loop OEO. The advantages of the multi-loop OEO configuration for a widely tunable OEO will be discussed as well.
Interworking scenarios between TINA and IN (2002)

The author discusses: evolution path aspects, conceptual differences between intelligent networks (INs) and Telecommunications Information Networking Architecture (TINA), migration and interworking, reference scenario, IN migration to TINA.
Genotoxicity, cytotoxicity and gene expression in patients undergoing elective surgery under isoflurane anaesthesia (2011)

There are numerous studies reporting on the effects of inhalation anaesthesia in cells of exposed individuals but not much is known about the ability of isoflurane (ISF) to induce oxidative DNA damage. However, surgery is often associated with a temporary perioperative immunological alteration, and some volatile anaesthetics seem to contribute to a transient lymphocytopenia after surgery. We conducted a study to evaluate a possible genotoxic effect, including oxidative DNA damage, and apoptosis in peripheral lymphocytes of 20 patients American Society of Anaesthesiologists physical status I undergoing minor elective surgery lasting at least 120 min, under anaesthesia with ISF. We also investigated the expression of several genes in blood cells. Blood samples were collected at three time points: before anaesthesia (T(1)), 2 h after the beginning of anaesthesia (T(2)) and on the first post-operative day (T(3)). General DNA damage and oxidised bases (Fpg and endo III-sites) in blood lymphocytes were evaluated using the comet assay. Lymphocytes were phenotyped and apoptosis was evaluated by flow cytometry. In addition, expressions of hOGG1 and XRCC1, genes involved in DNA repair, and BCL2, a gene related to apoptosis, were assessed by quantitative real-time polymerase chain reaction. Results showed no statistically significant difference in the level of DNA damage and oxidised bases among the three sampling times. Anaesthesia with ISF did not increase the percentage of cells in early or late apoptosis in cytotoxic or helper T lymphocytes. Lower hOGG1 and BCL2 expressions were detected at T(3) in comparison to the other two previous time points, and there was significantly lower expression of XRCC1 at T(3) in relation to T(2). In conclusion, the exposure to ISF did not result in genotoxicity and cytotoxicity in lymphocytes and in toxicogenomic effect in leukocytes, although DNA repair and apoptosis-related genes were down-regulated on the first post-operative day.
Studies of the chemiluminescence of luminol. (1969)

Massachusetts Institute of Technology. Dept. of Chemistry. Thesis. 1969. Ph.D.