gebhart/patrepeval huggingface dataset:
Survival of acute myeloid leukemia cells requires PI3 kinase activation (2003)

The mechanisms that regulate the growth and survival of acute myeloid leukemia (AML) cells are largely unknown. We hypothesized that constitutive activation of phosphatidyl-inositide 3 kinase (PI3 kinase) could regulate survival in primary cells from patients with AML. Here we demonstrate that Akt, a critical substrate of PI3 kinase, is activated in AML blasts. In a short-term culture system, most AML patient samples showed a dose-dependent decrease in survival after incubation with the PI3 kinase inhibitor LY294002. This decrease in survival was partially due to the induction of apoptosis. Furthermore, we have shown that p70 S6 kinase and 4EBP-1, downstream mediators of Akt signaling, also are phosphorylated in AML blasts. Phosphorylation of these proteins is inhibited by the mTOR inhibitor RAD001. Incubation of AML blasts with RAD001 induces only a small decrease in survival of the cells; however, when combined with Ara-C, RAD001 enhances the toxicity of Ara-C. These results demonstrate that constitutive activation of the PI3 kinase pathway is necessary for the survival of AML blasts and that targeting of this pathway with pharmacologic inhibitors may be of clinical benefit in treatment of AML.
The Relationship between Pulse Transit Time and Systolic Blood Pressure on Individual Subjects after Exercises (2006)

Continuous monitoring of blood pressure (BP) is always important to critically ill patients and to the patients who undergo major vascular and intracavitary surgeries. Pulse transit time (PTT) is one of the potential parameters which can be utilized for non-invasive and continuous monitoring of BP. PTT <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">p</sub> and PTT <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">f</sub> are the time intervals measured from the R-wave of electrocardiographic signal to the peak and the foot of photoplethysmographic signal respectively. In this study, the relationship between systolic blood pressure (SBP) and PTTs on 12 healthy subjects, aged 25plusmn2 years, was investigated after exercises. Results showed that SBP was correlated with PTT <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">p</sub> and PTT <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">f</sub> wherein the means of individual correlation were r=-0.77 and r=-0.92 respectively. The means of the standard deviation of the difference between the measured SBP and the SBP predicted from regression lines in scatter plots of SBP~PTT <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">p </sub> and SBP~PTT <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">f</sub> were 6.6 mmHg and 4.3 mmHg respectively. In summary, the results supported that PTT <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">f</sub> was a potential parameter which could be implemented in a personalized wearable device for continuous SBP monitoring at home
A new approach to template purification for sequencing applications using paramagnetic particles. (1992)

A new method using traditional hybridization methodology, coupled with the new magnetic particle technology, has been developed for DNA purification, specifically for sequencing applications. The method is similar to the reverse hybridization blot system; however, a specific oligonucleotide probe was attached to the paramagnetic particle instead of a sheet membrane. The target DNA containing the complementary sequence of the probe hybridizes to the probe that is attached to the bead and is then magnetically removed from solution, washed and collected. This system eliminates the need of organic extractions and precipitation/concentration steps. The entire hybridization-purification system can be done in a 1.5-ml microcentrifuge tube making the method ideal for automation. M13 phage clones were purified with this method, both by manual means and by using the CATALYST 800 Molecular Biology LabStation fitted with a prototype magnetic station, and then sequenced. DNA sequencing results obtained with this system were reproducible and gave excellent length of read with low background.
Loops in Globular Proteins: A Novel Category of Secondary Structure (1986)

The protein loop, a novel category of nonregular secondary structure, is a segment of contiguous polypeptide chain that traces a "loop-shaped" path in three-dimensional space; the main chain of an idealized loop resembles a Greek omega (omega). A systematic study was made of 67 proteins of known structure revealing 270 omega loops. Although such loops are typically regarded as "random coil," they are, in fact, highly compact substructures and may also be independent folding units. Loops are almost invariably situated at the protein surface where they are poised to assume important roles in molecular function and biological recognition. They are often observed to be modules of evolutionary exchange and are also natural candidates for bioengineering studies.
The Path Forward for Biofuels and Biomaterials (2006)

Biomass represents an abundant carbon-neutral renewable resource for the production of bioenergy and biomaterials, and its enhanced use would address several societal needs. Advances in genetics, biotechnology, process chemistry, and engineering are leading to a new manufacturing concept for converting renewable biomass to valuable fuels and products, generally referred to as the biorefinery. The integration of agroenergy crops and biorefinery manufacturing technologies offers the potential for the development of sustainable biopower and biomaterials that will lead to a new manufacturing paradigm.
Herpes simplex virus infection: part I--Biology, clinical presentation and latency. (2005)

Oro-facial manifestations of herpes simplex virus (HSV) infections are very common, and include primary herpetic gingivo-stomatitis, recurrent herpes labialis and recurrent intra-oral herpes. Recent research in molecular biology has advanced our knowledge of the HSV pathogenesis and behavior. Understanding the exact mechanism of HSV latency and reactivation enables improvement of drug therapy and prevention strategies of HSV infections. The aim of this review is to update the recent development in the biological and clinical research related to HSV infection, focusing on oral and perioral lesions.
Diabetic Retinopathy: Surrogate Outcomes for Drug Development for Diabetic Retinopathy (2000)

Diabetic retinopathy remains the most frequent cause of new cases of blindness among adults aged 20-74 years. A number of large clinical trials have validated treatment methods now considered standard. However, the disease continues to progress in approximately 50% of the eyes treated by photocoagulation. Other forms of therapy targeted at the earliest stages of retinal disease are needed. The difficulties in defining and accepting surrogate outcomes appropriate to evaluate the earlier stages of retinopathy are discussed. Special attention is given to trial design and the most likely possibilities for surrogate outcomes: mean difference on the Early Treatment Diabetic Retinopathy Study retinopathy scale of at least 2 steps per eye, reduction in macular thickening and reduction in fluorescein leakage.
Cationic Metallocene Polymerization Catalysts. Synthesis and Properities of the First Base‐Free Zirconocene Hydride (1992)

High electrophilicity and polymerization activity as well as ion‐pairing effects not based on the bridging hydrogen atoms are the most notable characteristics of the cation in 2 , a model compound for Ziegler‐Natta catalysts. This hydrido complex is accessible by hydrogenolysis of 1 or by hydride abstraction from 3 . equation image
Delineating and Quantifying Ground Water Discharge Zones Using Streambed Temperatures (2004)

Streambed temperature mapping, hydraulic testing using minipiezometers, and geochemical analyses of interstitial water of the streambed were used to delineate the pattern of ground water discharge in a sandy streambed and to develop a flux-based conceptual model for ground water/surface water interactions. A new and simple empirical method was used to relate fluxes obtained from minipiezometer data to streambed temperatures. The relationship allowed flux to be calculated at locations where only streambed temperature measurements were made. Slug testing and potentiomanometer measurements at 34 piezometers indicated ground water discharge ranged from 0.03 to 446 L/m2/day (and possibly as high as 7060 L/m2/day) along a 60 m long by 11 to 14 m wide reach of river. Complex but similar plan-view patterns of flux were calculated for both summer and winter using hundreds of streambed temperatures measured on a 1 by 2 m grid. The reach was dominated by ground water discharge and 5% to 7% of the area accounted for approximately 20% to 24% of the total discharge. < 12% of the total area consisted of recharge zones or no-discharge zones. A conceptual model for ground water/surface water interactions consisting of five different behaviors was developed based on the magnitude and direction of flux across the surface of the streambed. The behaviors include short-circuit discharge (e.g., high-flow springs), high discharge (e.g., preferential flowpaths), low to moderate discharge, no discharge (e.g., horizontal hyporheic or ground water flow), and recharge. Geological variations at depth played a key role in determining which type of flow behavior occurred in the streambed.
Increased dependence on blood glucose after acclimatization to 4,300 m (1991)

To evaluate the hypothesis that altitude exposure and acclimatization result in increased dependency on blood glucose as a fuel, seven healthy males (23 +/- 2 yr, 72.2 +/- 1.6 kg, mean +/- SE) on a controlled diet were studied in the postabsorptive condition at sea level (SL), on acute altitude exposure to 4,300 m (AA), and after 3 wk of chronic altitude exposure to 4,300 m (CA). Subjects received a primed continuous infusion of [6,6-2D]glucose and rested for a minimum of 90 min, followed immediately by 45 min of exercise at 101 +/- 3 W, which elicited 51.1 +/- 1% of the SL maximal O2 consumption (VO2 max; 65 +/- 2% of altitude VO2 max). At SL, resting arterial glucose concentration was 82.4 +/- 3.2 mg/dl and rose significantly to 91.2 +/- 3.2 mg/dl during exercise. Resting glucose appearance rate (Ra) was 1.79 +/- 0.02 mg.kg-1.min-1; this increased significantly during exercise at SL to 3.71 +/- 0.08 mg.kg-1.min-1. On AA, resting arterial glucose concentration (85.8 +/- 4.1 mg/dl) was not different from sea level, but Ra (2.11 +/- 0.14 mg.kg-1.min-1) rose significantly. During exercise on AA, glucose concentration rose to levels seen at SL (91.4 +/- 3.0 mg/dl), but Ra increased more than at SL (to 4.85 +/- 0.15 mg.kg-1.min-1; P less than 0.05). Resting arterial glucose was significantly depressed with CA (70.8 +/- 3.8 mg/dl), but resting Ra increased to 3.59 +/- 0.08 mg.kg-1.min-1, significantly exceeding SL and AA values.(ABSTRACT TRUNCATED AT 250 WORDS)
Immune sera and monoclonal antibodies define two configurations for the sialyl Tn tumor antigen. (1995)

Sialyl Tn (sTn) is a mucin-associated carbohydrate antigen expressed in most types of human adenocarcinoma. Defining the configuration of tumor cell surface sTn recognized by antibodies is important for understanding the basis for the cancer cell specificity of sTn-reactive mAbs, for the development of more effective mAbs, and for designing cancer vaccines against sTn. In this study, we compared the immunogenicity of synthetic single sTn disaccharide epitopes and clusters [sTn(C)] of 3 sTn epitopes covalently linked via serine to keyhole limpet hemocyanin [KLH; sTn-KLH and sTn(C)-KLH, respectively]. The cell surface sTn configurations were analyzed with the use of sera from mice immunized with these neoglycoproteins and a panel of sTn-reactive mAb. Sera from mice immunized with sTn-KLH reacted in direct and inhibition assays with sTn-human serum albumin (HSA) but only weakly with sTn(C)-HSA, whereas sera from mice immunized with sTn(C)-KLH reacted with sTn(C)-HSA but not with sTn-HSA. Both anti-sTn and anti-sTn(C) sera reacted with ovine submaxillary mucin (a natural source of sTn) and with sTn-positive human tumor cell line LS-C but not with sTn-negative LS-B cells. With regard to the sTn-reactive mAbs, B72.3 reacted exclusively with clustered sTn, whereas mAb B195.3R11 reacted preferentially with unclustered sTn. Results with mAbs TKH2, B239.1, and CC49 were less clear, although all reacted more strongly with clustered sTn than with unclustered sTn. These results suggest that sTn is recognized at the tumor cell surface in at least two quite distinct configurations, as clustered and nonclustered arrays.
Quantifying changes in the rates of forest clearing in Indonesia from 1990 to 2005 using remotely sensed data sets (2009)

Timely and accurate data on forest change within Indonesia is required to provide government, private and civil society interests with the information needed to improve forest management. The forest clearing rate in Indonesia is among the highest reported by the United Nations Food and Agriculture Organization (FAO), behind only Brazil in terms of forest area lost. While the rate of forest loss reported by FAO was constant from 1990 through 2005 (1.87 Mha yr−1), the political, economic, social and environmental drivers of forest clearing changed at the close of the last century. We employed a consistent methodology and data source to quantify forest clearing from 1990 to 2000 and from 2000 to 2005. Results show a dramatic reduction in clearing from a 1990s average of 1.78 Mha yr−1 to an average of 0.71 Mha yr−1 from 2000 to 2005. However, annual forest cover loss indicator maps reveal a near-monotonic increase in clearing from a low in 2000 to a high in 2005. Results illustrate a dramatic downturn in forest clearing at the turn of the century followed by a steady resurgence thereafter to levels estimated to exceed 1 Mha yr−1 by 2005. The lowlands of Sumatra and Kalimantan were the site of more than 70% of total forest clearing within Indonesia for both epochs; over 40% of the lowland forests of these island groups were cleared from 1990 to 2005. The method employed enables the derivation of internally consistent, national-scale changes in the rates of forest clearing, results that can inform carbon accounting programs such as the Reducing Emissions from Deforestation and Forest Degradation in Developing Countries (REDD) initiative.
The human cGMP-PDE beta-subunit promoter region directs expression of the gene to mouse photoreceptors. (2000)

Photoreceptor-specific reporter gene expression is driven in vivo by a 350-bp segment of the beta-PDE 5' flanking sequence. This study demonstrates the utility of the human beta-PDE promoter for directing the expression of foreign genes to photoreceptors and suggests that the -297 to +53 beta-PDE 5' flanking region fragment may have important implications for therapeutic gene delivery to the visual cells.
Engineering a device for electron-beam probing (1989)

The principles of electron-beam probing for diagnostic work are described. Guidelines are presented to help users of electron-beam probe stations optimize their IC design and manufacturing procedures for electron-beam probing. The guidelines cover: observability, maintaining line of sight, direct versus indirect measuring, using test points, accuracy, improving signal-to-noise ratio, reducing crosstalk, maintaining a consistent environment, usability, reducing acquisition time, packaging, and linking with CAD/CAE databases.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Prophylaxis of Hemodialysis Graft Thrombosis with Fish Oil (2002)

Diets enriched with fish oil may favorably affect the vascular perturbations underlying synthetic graft thrombosis. Therefore, these studies were designed to test the hypothesis that diets enriched with fish oil would decrease the incidence of thrombosis in newly constructed polytetrafluorethylene grafts. A double-blind, randomized trial was conducted. Twenty-four patients were randomized to receive 4000 mg of fish oil or 4000 mg of control oil. Both preparations were enriched with antioxidants and deodorized with peppermint. Patients began therapy within 2 wk after graft placement and were monitored for 12 mo or until thrombosis developed. With a permuted-block randomization schedule, 12 patients received fish oil and 12 patients received control oil. The primary patency rates at 365 d were 14.9% for the control group and 75.6% for the fish oil-treated group. Survival analysis revealed a significant difference between fish oil-treated and untreated patients (P < 0.03, Mantel-Cox test), with a power of 90%. Moreover, analysis of covariables, including age of > or =50 yr, gender, race, body weight, diabetes mellitus, bleeding times, and lipid profiles, indicated that this effect occurred principally as a result of fish oil administration. Importantly, fish oil treatment also decreased venous outflow resistance and systemic BP, compared with control values. Fish oils possess unique biologic properties that favorably affect the incidence of polytetrafluorethylene graft thrombosis, and they thus represent a potential treatment strategy for the prevention of access thrombosis.
IMpact-RSV Study Group Report (1999)

To the Editor. 

The authors of the IMpact-RSV Study Group are to be commended for successfully carrying out the large multicenter trial of palivizumab.1 I wish to offer the following comments regarding the study:

The authors have not stated that education regarding prevention of respiratory syncytial virus (RSV) was done similarly in the treatment and placebo groups. Simple measures like hand-washing and limiting contact with older siblings and adults can reduce RSV transmission. Despite blinding of the nature of the intervention, it is possible that these measures were unevenly distributed in the two groups and led to reduced hospitalization, thereby confounding the effects of palivizumab.

The authors have not stated the sample size computation. Also, it is not clear if the analysis of results was performed on an “intention-to-treat” basis.

The primary outcome of the study was a reduction in hospitalization for RSV infection from 10.6% to 4.8%. With this absolute risk reduction of 5.8% the number needed-to-treat works out to be 17 with 95% confidence limits of 11 to 36. This would mean that anywhere from 11 to 36 infants would have to be treated with monthly injections of palivizumab for 5 months to prevent one hospitalization from RSV. The average duration of hospitalization in the placebo group was 2.4 days per infant. The cost of one injection of palivizumab is approximately $1200, which means that anywhere from $66 000 to $216 000 would have to be spent to prevent one such hospitalization. This is not including the costs of the special clinics that are being set up to administer palivizumab, costs for the parents to travel to these clinics or to the pediatrician's office, the costs of missing work to keep this appointment, the expense of the parents paying for the drug themselves, and other possible expenses. In the …
Criteria for Identifying and Evaluating the Presence of Chiasmus (1995)

Abstract This article defines fifteen criteria one can use to measure the strength or weakness of a proposed chiastic pattern in a given text. The need for rigor in such studies depends primarily on how the results of the proposed structural analyses will be used. Ultimately, analysts may not know with certainty whether an author created inverted parallel structures intentionally or not; but by examining a text from various angles, one may assess the likelihood that an author consciously employed chiasmus to achieve specific literary purposes.
Validity of the Hamilton Rating Scale for Depression (1977)

Summary In 26 depressed patients, a high correlation (0·89) was found between the Hamilton score and a psychiatrist's global rating and between the change (0 · 68) in these ratings during treatment. The Hamilton scale was able to differentiate at the 0·01 level four degrees of severity based on the global rating. Limiting the range of severity measured was found to lower significantly the correlation between the ratings. A prospective examination of a six-item sub-scale of the Hamilton scale developed by Beck and associates failed to confirm its claimed improvement in sensitivity or validity.
Potential Role of a Novel Psychrotolerant Member of the FamilyGeobacteraceae,Geopsychrobacter electrodiphilusgen. nov., sp. nov., in Electricity Production by a Marine Sediment Fuel Cell (2004)

Previous studies have shown that members of the family Geobacteraceae that attach to the anodes of sediment fuel cells are directly involved in harvesting electricity by oxidizing organic compounds to carbon dioxide and transferring the electrons to the anode. In order to learn more about this process, microorganisms from the anode surface of a marine sediment fuel cell were enriched and isolated with Fe(III) oxide. Two unique marine isolates were recovered, strains A1(T) and A2. They are gram-negative, nonmotile rods, with abundant c-type cytochromes. Phylogenetic analysis of the 16S rRNA, recA, gyrB, fusA, rpoB, and nifD genes indicated that strains A1(T) and A2 represent a unique phylogenetic cluster within the Geobacteraceae. Both strains were able to grow with an electrode serving as the sole electron acceptor and transferred ca. 90% of the electrons available in their organic electron donors to the electrodes. These organisms are the first psychrotolerant members of the Geobacteraceae reported thus far and can grow at temperatures between 4 and 30 degrees C, with an optimum temperature of 22 degrees C. Strains A1(T) and A2 can utilize a wide range of traditional electron acceptors, including all forms of soluble and insoluble Fe(III) tested, anthraquinone 2,6-disulfonate, and S(0). In addition to acetate, both strains can utilize a number of other organic acids, amino acids, long-chain fatty acids, and aromatic compounds to support growth with Fe(III) nitrilotriacetic acid as an electron acceptor. The metabolism of these organisms differs in that only strain A1(T) can use acetoin, ethanol, and hydrogen as electron donors, whereas only strain A2 can use lactate, propionate, and butyrate. The name Geopsychrobacter electrodiphilus gen. nov., sp. nov., is proposed for strains A1(T) and A2, with strain A1(T) (ATCC BAA-880(T); DSM 16401(T); JCM 12469) as the type strain. Strains A1(T) and A2 (ATCC BAA-770; JCM 12470) represent the first organisms recovered from anodes that can effectively couple the oxidation of organic compounds to an electrode. Thus, they may serve as important model organisms for further elucidation of the mechanisms of microbe-electrode electron transfer in sediment fuel cells.