gebhart/patrepeval huggingface dataset:
Atmospheric correlation-time measurements and effects on coherent Doppler lidar (1987)

The time for which the backscatter from an ensemble of atmospheric aerosol particles remains coherent was studied by using a pulsed TEA CO2 lidar with coherent detection. Experimental results are compared with predictions by using model pulse shapes appropriate for TEA CO2 laser transmitters. The correlation time of the backscatter return signal is important in studies of atmospheric turbulence and its effects on optical propagation and backscatter. Techniques for its measurement are discussed and evaluated.
Parenteral Nutrition Utilization in Bone Marrow Transplant Recipients (2014)

Bone marrow transplant (BMT) recipients often require parenteral nutrition (PN) to meet their nutrient needs. While general guidelines for the provision of PN support by nutrition support teams (NSTs) have been shown to decrease inappropriate PN use, recommendations for nutrition in BMT recipients are lacking.
Integrated acoustic sample preparation for rapid sepsis diagnostics (2014)

We present a novel, integrated microfluidic system based on acoustophoretic cell-handling that detects bacteria in whole blood in less than 2 hours, substantially faster than current standard methods for detection of sepsis-causing bacteria. Bacteria are acoustically separated from 1 ml blood, enriched by acoustic trapping and finally detected using a dry-reagent PCR-chip.
A transgenic rabbit model for human hypertrophic cardiomyopathy (1999)

Certain mutations in genes for sarcomeric proteins cause hypertrophic cardiomyopathy (HCM). We have developed a transgenic rabbit model for HCM caused by a common point mutation in the beta-myosin heavy chain (MyHC) gene, R400Q. Wild-type and mutant human beta-MyHC cDNAs were cloned 3' to a 7-kb murine beta-MyHC promoter. We injected purified transgenes into fertilized zygotes to generate two lines each of the wild-type and mutant transgenic rabbits. Expression of transgene mRNA and protein were confirmed by Northern blotting and 2-dimensional gel electrophoresis followed by immunoblotting, respectively. Animals carrying the mutant transgene showed substantial myocyte disarray and a 3-fold increase in interstitial collagen expression in their myocardia. Mean septal thicknesses were comparable between rabbits carrying the wild type transgene and their nontransgenic littermates (NLMs) but were significantly increased in the mutant transgenic animals. Posterior wall thickness and left ventricular mass were also increased, but dimensions and systolic function were normal. Premature death was more common in mutant than in wild-type transgenic rabbits or in NLMs. Thus, cardiac expression of beta-MyHC-Q(403) in transgenic rabbits induced hypertrophy, myocyte and myofibrillar disarray, interstitial fibrosis, and premature death, phenotypes observed in humans patients with HCM due to beta-MyHC-Q(403).
Multiplex PCR Protocol for the Diagnosis of Staphylococcal Infection (2001)

We report the development of a multiplex PCR protocol for the diagnosis of staphylococcal infection. The protocol was designed to (i) detect any staphylococcal species to the exclusion of other bacterial pathogens (based on primers corresponding to Staphylococcus-specific regions of the 16S rRNA genes), (ii) distinguish between S. aureus and the coagulase-negative staphylococci (CNS) (based on amplification of the S. aureus-specific clfA gene), and (iii) provide an indication of the likelihood that the staphylococci present in the specimen are resistant to oxacillin (based on amplification of the mecA gene). The expected fragments were amplified from each of 60 staphylococcal isolates (13 oxacillin-resistant S. aureus isolates, 23 oxacillin-sensitive S. aureus isolates, 17 oxacillin-resistant CNS, and 7 oxacillin-sensitive CNS). No amplification products were observed with template DNA from nonstaphylococcal species, and the efficiency of amplification of staphylococcal targets was not adversely affected by the presence of DNA from other bacterial species in the same sample. The utility of the protocol for the analysis of clinical samples was verified by analysis of aliquots taken directly from BacT/Alert blood culture bottles. Of 77 blood cultures tested, only 7 yielded results inconsistent with those of conventional methods of diagnosis and susceptibility testing. Of those, one was identified as a CNS species by PCR and S. aureus by conventional methods. We also identified two isolates that were mecA positive but were oxacillin sensitive according to conventional methods. The other four samples failed to yield any amplification product even with a control set of primers corresponding to a conserved region of the eubacterial rRNA genes.
Stem cell transplantation for inflammatory bowel disease: practical and ethical issues (2000)

2] However, this would raise practical and ethical issues not encountered in other conditions. Inflammatory bowel disease activity involves a delicate and unpredictable balance between tolerance and immune reactivity to luminal factors that makes the outcome of stem cell transplantation diYcult to predict. Ethically, stem cell transplantation is more acceptable in some cases of systemic sclerosis where life expectancy is reduced or in multiple sclerosis where, additionally, there are few alternative eVective treatments. Neither of these principles apply to inflammatory bowel disease.
Chronic caloric restriction reduces tissue damage and improves spatial memory in a rat model of traumatic brain injury (2010)

Although it has been known for some time that chronic caloric or dietary restriction reduces the risk of neurodegenerative disorders and injury following ischemia, the possible role of chronic restriction in improving outcomes after traumatic brain injury (TBI) has not been previously studied. Therefore, 2-month-old male Sprague-Dawley rats were divided into two dietary groups, an ad libitum fed group (AL) and a caloric-restriction group (CR) that was provided with 70% of the food intake of AL rats (n = 10/group). After 4 months, a weight-drop device (300 g) was used to produce a 2-mm bilateral medial frontal cortex contusion following craniotomy. Additional animals in each dietary group (n = 10) were used as sham-operated controls. The CR diet resulted in body weights that were reduced by 30% compared with AL controls. Not only did CR decrease the size of the cortical lesion after injury, there were marked improvements in spatial memory as measured by Morris water maze that included an increase in the number of animals successfully finding the platform as well as significantly reduced time to finding the hidden platform. Western analysis, used to examine the expression of proteins that play a role in neuronal survival, revealed significant increases in brain-derived neurotrophic factor (BDNF) in the cortical region around the site of injury and in the hippocampus in CR rats after injury. These findings suggest that molecular mechanisms involved in cell survival may play a role in reducing tissue damage and improving cognition after TBI and that these mechanisms can be regulated by dietary interventions.
The dual impact of coxsackie and adenovirus receptor expression on human prostate cancer gene therapy. (2000)

In a recent paper, we reported a significant difference in coxsackie and adenovirus receptor (CAR) from several human bladder cancer cell lines that correlated with their sensitivities to adenoviral infection (Y. Li, R-C. Pong, J. M. Bergelson, M. C. Hall, A. I. Sagalowsky, C-P. Tseng, Z. Wang, and J. T. Hsieh, Cancer Res., 59: 325-330, 1999). In human prostate cancer, CAR protein is down-regulated in the highly tumorigenic PC3 cell line, which suggests that, in addition to its function as a viral receptor, CAR may have a pathophysiological role in prostate cancer progression. In this paper, we document that CAR does not merely enhance the viral sensitivity of prostate cancer cells but also acts as a tumor inhibitor for androgen-independent prostate cancer cells. Our data indicate that CAR is a potential therapeutic agent for increasing the efficacy of prostate cancer therapy.
Preparation of alkenyl succinic anhydrides from vegetable oil FAME (2003)

Abstract Sunflower oil and oleic motif‐enriched sunflower oil methyl esters were used to prepare alkenyl succinic anhydrides. A classic batch reactor was selected to carry out the synthesis. The range in which the temperature, reaction time, and molar ratio between the number of moles of maleic anhydride and the equivalent number of double bonds present in the unsaturated vegetable oil methyl esters (the most influential factors in the process) varied was determined in a preliminary study. A secondorder Doehlert uniform network design was used to investigate the influence of the temperature and molar ratio for all the methyl esters on the yield of alkenyl succinic anhydride from methyl oleate, the conversion of methyl oleate, the formation of side reaction products, the Gardner color of the product, and viscosity. The optimal reaction conditions for obtaining the maximal yield (around 95%) of alkenyl succinic anhydride from methyl oleate were 235°C, a molar ratio of 1.5, and a reaction lasting 8 h. However, the products synthesized under these conditions showed high viscosity (215 cP), a very dark color (18+ Gardner color), and a high content of undesirable side products (4%), which hindered their direct industrial use. The increase in the product viscosity was probably due to the formation of side reaction products. A molar ratio of less than 1.5 led to a less viscous product, although with a lower alkenyl succinic anhydride content.
Linkage of Familial Amyotrophic Lateral Sclerosis With Frontotemporal Dementia to Chromosome 9q21-q22 (2000)

These data suggest that a defective gene located in the chromosome 9q21-q22 region may be linked to ALS with FTD. JAMA. 2000;284:1664-1669.
Biologic and immunologic erythropoietin in extracts from hypoxic whole rat kidneys and in their glomerular and tubular fractions. (1984)

The relationship between plasma erythropoietin levels and kidney erythropoietin content was studied in rats subjected to hypoxia for various periods. Plasma and kidney erythropoietin followed a parallel course with detectable levels observed as early as after 1 hour of hypoxia. However, the kidney erythropoietin content reached a maximum at 6 hours, and its plasma erythropoietin content reached its maximum at 24 hours. Despite continuous hypoxia, the erythropoietin in both kidney and plasma decreased after reaching their maximal values, and leveled off after 72 hours. This parallel decrease in plasma and kidney erythropoietin suggests that this decrease in plasma erythropoietin observed after prolonged hypoxia is secondary to a decrease in erythropoietin production rather than to an increase in peripheral consumption. To identify the cell(s) involved in erythropoietin production, kidney cells from anemic-hypoxic animals were separated into their glomerular and tubular components utilizing a successive sieving procedure. Measurement of erythropoietin by bioassay revealed four to five times as much erythropoietin in the tubular fraction as in the glomerular fraction. Radioimmunoassay of these fractions revealed erythropoietin content similar to that by bioassay, ruling out the possible presence of biologically nonactive material. Renin activity, on the other hand, was about equally distributed between both of these fractions. Although our studies do not rule out participation of glomerular or juxtaglomerular cells in erythropoietin production, they suggest that a tubular origin of the bulk of renal erythropoietin is more likely.
Mathematical models of the acute inflammatory response (2004)

Purpose of review Trauma and infection elicit an acute inflammatory response. In certain circumstances the degree of the acute inflammatory response may result in pathologic manifestations, namely, sepsis and multiple organ failure. Despite an extensive series of clinical trials designed to modulate inflammation in sepsis, only one compound, activated protein C, has emerged from more than 250 failed trials. There is a growing recognition that the complexity of the acute inflammatory response precludes the efficient development of therapies for sepsis and multiple organ failure until systems approaches are brought to bear on this problem. Recent findings Work carried out by the authors’ groups suggests that mathematical modeling can provide a means by which in vitro and in vivo data can be synthesized into system-level analytic models of the acute inflammatory response. The authors have focused on agent-based modeling and modeling with ordinary differential equations. Some of the advantages and disadvantages of these modeling approaches are presented, and methods for calibration and validation of these models are discussed. Finally, the usefulness of mathematical models to evaluate the prospective therapeutic strategies in clinical trials of sepsis and trauma is examined. Summary Simulations using various methods can shed insight into the pathophysiology of the acute inflammatory response and may lead to better design of clinical trials in sepsis and trauma.
Human homologues of Delta-1 and Delta-4 function as mitogenic regulators of primitive human hematopoietic cells (2001)

Delta-mediated Notch signaling controls cell fate decisions during invertebrate and murine development. However, in the human, functional roles for Delta have yet to be described. This study reports the characterization of Delta-1 and Delta-4 in the human. Human Delta-4 was found to be expressed in a wide range of adult and fetal tissues, including sites of hematopoiesis. Subsets of immature hematopoietic cells, along with stromal and endothelial cells that support hematopoiesis, were shown to express Notch and both Delta-1 and Delta-4. Soluble forms of human Delta-1 (hDelta-1) and hDelta-4 proteins were able to augment the proliferation of primitive human hematopoietic progenitors in vitro. Intravenous transplantation of treated cultures into immune-deficient mice revealed that hDelta-1 is capable of expanding pluripotent human hematopoietic repopulating cells detected in vivo. This study provides the first evidence for a role of Delta ligands as a mitogenic regulator of primitive hematopoietic cells in the human.
The DARPA WNaN network architecture (2011)

The warfighter network of the future needs to be low-cost, instantly deployable, self-organizing, robust, and scale with both size and density. DARPA's Wireless Network after Next (WNaN) meets these challenges using an architecture that combines several innovative features for the first time in a real functional system: dynamic spectrum access (DSA), adaptive multi-transceiver frequency assignment, multi-channel medium access, highly scalable routing and disruption-tolerant networking (DTN). The WNaN system has been successfully demonstrated in real-world military experiments for up to 100 nodes - the largest military MANET demonstration on record. We present the network architecture of the WNaN system, focusing mainly on the medium access and sub-network layers. We briefly describe how key protocols work in tandem, and how they are implemented on the objective platform. Finally, we discuss some future plans.
Neuronal and glial markers are differently associated with computed tomography findings and outcome in patients with severe traumatic brain injury: a case control study (2011)

Relationships between structural changes detected by neuroimaging and biomarkers indicate each biomarker may reflect a different injury pathway. These results suggest that protein biomarkers could provide better characterization of subjects at risk for specific types of cellular damage than that obtained with neuroimaging alone, as well as provide valuable information about injury severity and outcome after severe TBI.
Homogeneous Fluorescence-Based DNA Detection with Water-Soluble Conjugated Polymers (2004)

Methods for real-time, high-sensitivity polynucleotide detection are of vast scientific and economic importance. Homogeneous biosensor assays that take advantage of the collective response of water-soluble conjugated polymers and the self-assembly characteristic of aqueous polyelectrolytes have shown potential for improvements over small molecule methods. Cationic polythiophenes transduce oligonucleotide hybridization into a colorimetric output based on conformational changes of the polymer upon interaction with single-stranded DNAs or double-stranded DNAs. Cationic poly(fluorene-co-phenylene) materials serve as donors in fluorescence energy-transfer assays which display signal amplification. Signal transduction in aqueous media is controlled by specific electrostatic interactions.
A model-based approach for assessingin vivocombination therapy interactions (1999)

We present an approach for evaluating the efficacy of combination antitumor agent schedules that accounts for order and timing of drug administration. Our model-based approach compares in vivo tumor volume data over a time course and offers a quantitative definition for additivity of drug effects, relative to which synergism and antagonism are interpreted. We begin by fitting data from individual mice receiving at most one drug to a differential equation tumor growth/drug effect model and combine individual parameter estimates to obtain population statistics. Using two null hypotheses: (i) combination therapy is consistent with additivity or (ii) combination therapy is equivalent to treating with the more effective single agent alone, we compute predicted tumor growth trajectories and their distribution for combination treated animals. We illustrate this approach by comparing entire observed and expected tumor volume trajectories for a data set in which HER-2/neu-overexpressing MCF-7 human breast cancer xenografts are treated with a humanized, anti-HER-2 monoclonal antibody (rhuMAb HER-2), doxorubicin, or one of five proposed combination therapy schedules.
Procedure Guideline for Adult Solid-Meal Gastric-Emptying Study 3.0 (2009)

I. PURPOSE The purpose of this guideline is to assist nuclear medicine practitioners in recommending, performing, interpreting, and reporting the results of gastric-emptying and motility studies in adults. II. BACKGROUND INFORMATION AND DEFINITIONS Radionuclide studies of gastric emptying and motility are the most comprehensive and physiologic studies of gastric motor function available. The studies are noninvasive, use a physiologic meal (solids with or without liquids), and are quantitative. Serial testing can determine the effectiveness of therapy. The Society of Nuclear Medicine (SNM) and the American Neurogastroenterological and Motility Society have recently agreed on a standard meal and a standard imaging protocol for measurement of gastric emptying. The recommended meal is intended to simplify and standardize the methodology and reference values based on a large, multiinstitutional investigation of 123 healthy subjects. This standardization will alleviate the problem of comparing results between institutions that did not use the same meal or imaging protocol. The detailed recommendations for the recommended meal and the imaging protocol can be found in the paper by Abell et al. listed in the bibliography of this guideline.
Effects of mutant Ran/TC4 proteins on cell cycle progression. (1994)

Ran/TC4, a member of the RAS gene superfamily, encodes an abundant nuclear protein that binds and hydrolyzes GTP. Transient expression of a Ran/TC4 mutant protein deficient in GTP hydrolysis blocked DNA replication, suggesting a role for Ran/TC4 in the regulation of cell cycle progression. To test this possibility, we exploited an efficient transfection system, involving the introduction of cDNAs in the pMT2 vector into 293/Tag cells, to analyze phenotypes associated with mutant and wild-type Ran/TC4 expression. Expression of a Ran/TC4 mutant protein deficient in GTP hydrolysis inhibited proliferation of transfected cells by arresting them predominantly in the G2, but also in the G1, phase of the cell cycle. Deletion of an acidic carboxy-terminal hexapeptide from the Ran/TC4 mutant did not alter its nuclear localization but did block its inhibitory effect on cell cycle progression. These data suggest that normal progression of the cell cycle is coupled to the operation of a Ran/TC4 GTPase cycle. Mediators of this coupling are likely to include the nuclear regulator of chromosome condensation 1 protein and the mitosis-promoting factor complex.
A rational basis for mucosal vaccination against HIV infection (1999)

The lack of success in the development of an effective conventional vaccine against HIV has focused attention on mucosal immunity. This is a rational move, since HIV is transmitted mostly by the mucosal route. The mucosal strategy is based on the concept that: a) HIV/SIV has to cross the mucosal-regional lymph node-blood barriers, each of which can prevent viral transmission or decrease the viral load. b) Immunization has to target directly the mucosal tissues or indirectly the regional lymph nodes, in order to prevent or control viral replication. This strategy is consistent with antigen localization and effective entry into the lymph nodes, driving the immune response. c) A dual immune mechanism may be necessary for effective mucosal protection, mediated by specific CD4 and CD8 T-cell and antibody responses to the immunizing antigens, and innate antiviral factors and beta-chemokines which down-modulate CCR5 co-receptors. Targeted iliac lymph node immunization with SIVgp120 and p27 in alum prevents SIV infection or significantly decreases the viral load when challenged by the rectal route. Indeed, in addition to specific immunity, including significant sIgA antibody-forming cells in the iliac lymph nodes, CD8-suppressor factor and the three beta-chemokines (RANTES, macrophage inflammatory protein (MIP)-1 alpha and MIP-1 beta) are significantly associated with protection against rectal mucosal SIV infection.
A myelin basic protein-specific T lymphocyte line that mediates experimental autoimmune encephalomyelitis. (1985)

A T lymphocyte line, BP-1, expressing the T helper phenotype was selected from Lewis rats immunized with guinea pig myelin basic protein (GP-BP) in complete Freund's adjuvant (CFA). The BP-1 line responded specifically to GP-BP but not to PPD after the first round of selection, and responded to rat but not human or bovine BP. When injected i.p. into histocompatible Lewis or F1 (Lewis X P2) recipients, the BP-1 line induced both clinical signs of experimental autoimmune encephalomyelitis (EAE) and delayed type hypersensitivity (DTH) reactions in ears challenged intradermally with GP-BP but not PPD. The severity of clinical signs and the degree of ear swelling were dependent on the dose of BP-1 cells injected. Both activities were detectable with as few as 0.1 X 10(6) BP-1 line cells and required prior activation of the line cells with GP-BP presented by accessory cells. Lewis rats that had recovered from EAE induced by injection of GP-BP in CFA were more susceptible than naive rats to BP-1 line-mediated disease, requiring as few as 0.03 X 10(6) line cells. Clinical EAE and DTH could be serially transferred into F1 (Lewis X P2) recipients with BP-1 cells and back to nonirradiated Lewis parents with activated splenocytes, suggesting that BP-1 cells persist in recipient rats. These results demonstrate the potent biologic activities of an autoreactive BP-specific T lymphocyte line. This line possesses properties similar to BP lines described previously as well as to culture-conditioned splenic T effector cells; thus, the data presented here bridge the gap between these two approaches for studying T effector lymphocyte functions.