gebhart/patrepeval huggingface dataset:
Transgenic Rabbits Expressing Human Apolipoprotein A-I in the Liver (1996)

Human apolipoprotein A-I (apo A-I) transgenic rabbits were created by use of an 11-kb genomic human apo A-I construct containing a liver-specific promoter. Five independent transgenic lines were obtained in which human apo A-I gene had integrated and was expressed. Plasma levels of human apo A-I ranged from 8 to 100 mg/dL for the founder and up to 175 mg/dL for the progeny. Rabbit apo A-I levels were substantially decreased in the transgenic rabbits. HDL cholesterol (HDL-C) levels were higher in two of the five transgenic rabbit lines than in controls (line 20 versus nontransgenic littermate, HDL-C = 80 +/- 7 versus 37 +/- 6 mg/dL; line 8 versus nontransgenic littermate, HDL-C = 54 +/- 16 versus 35 +/- 6 mg/dL). This resulted in less atherogenic lipoprotein profiles, with very low (VLDL + LDL-C)/HDL-C ratios. HDL size and protein and lipid compositions were similar between transgenic and littermate nontransgenic rabbits. However, a large amount of pre-beta apo A-I-containing lipoproteins was observed in the plasma of the highest human apo A-I expressor. Cell cholesterol efflux was evaluated with the incubation of whole serum from transgenic and control rabbits. Cell cholesterol efflux was highly correlated with HDL cholesterol, with apo A-I, and with the presence of pre-beta apo A-I-containing lipoproteins. These rabbits will be an extremely useful model for the evaluation of the effect of increased hepatic apo A-I expression on atherosclerosis.
Serum sex hormones and breast cancer risk factors in postmenopausal women. (2003)

Postmenopausal women with elevated serum estrogens and androgens are at an increased risk of breast cancer. We evaluated associations of serum estrogen and androgen levels with age, anthropometry, and reproductive history to assess whether these characteristics could potentially modify breast cancer risk through hormonal mechanisms. A cross-sectional study was conducted among 133 postmenopausal women who donated blood to the serum bank (Columbia, MO) and served as controls in a previous prospective nested case control study of serum hormones and breast cancer risk. Standard regression methods were used to calculate adjusted means and test for trends in relationships of serum hormone concentrations with breast cancer risk factors. All analyses were performed on the log(e) scale, and all models included assay batch, date, and time of blood collection. Serum levels of estradiol, non-sex hormone binding globulin bound estradiol, estrone, estrone sulfate, and testosterone increased significantly with increasing body mass index (BMI), whereas sex hormone binding globulin levels decreased. After adjusting for BMI, nulliparous women tended to have higher testosterone levels compared with parous women (P = 0.05), but there was no evidence of a trend of decreasing testosterone with increasing parity. Dehydroepiandrosterone, its sulfate, and androstenediol decreased significantly with increasing age. Although BMI and parity could potentially modify breast cancer risk through hormonal mechanisms, age-related increases in breast cancer incidence do not appear to be mediated through changes in serum levels of the hormones evaluated.
Immunization With Melan-A Peptide-Pulsed Peripheral Blood Mononuclear Cells Plus Recombinant Human Interleukin-12 Induces Clinical Activity and T-Cell Responses in Advanced Melanoma (2003)

This immunization approach may be more straightforward than dendritic cell strategies and seems to have clinical activity that can be correlated to a biologic end point.
Nucleotide sequence of the human parathyroid hormone gene. (1983)

From a lambda phage gene library we have isolated phage containing the gene encoding human preproparathyroid hormone. The phage were isolated by using both the plaque-hybridization technique and the in vivo recombination-selection technique. The human preproparathyroid hormone gene contains two intervening sequences that separate the gene into a 5' noncoding domain, a "prepro" sequence domain, and a domain containing the parathyroid hormone sequence and the 3' noncoding region. The gene is approximately 4,200 base pairs long. Restriction endonuclease analysis of human leukocyte DNA shows that the haploid human genome contains one copy of the preproparathyroid hormone gene. A 14-base-pair sequence of alternating purines and pyrimidines that has the potential of adopting the Z-DNA conformation lies 134 base pairs upstream from the presumed site of initiation of transcription.
From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later (2009)

Comparative genomics is the cornerstone of identification of gene functions. The immense number of living organisms precludes experimental identification of functions except in a handful of model organisms. The bacterial domain is split into large branches, among which the Firmicutes occupy a considerable space. Bacillus subtilis has been the model of Firmicutes for decades and its genome has been a reference for more than 10 years. Sequencing the genome involved more than 30 laboratories, with different expertises, in a attempt to make the most of the experimental information that could be associated with the sequence. This had the expected drawback that the sequencing expertise was quite varied among the groups involved, especially at a time when sequencing genomes was extremely hard work. The recent development of very efficient, fast and accurate sequencing techniques, in parallel with the development of high-level annotation platforms, motivated the present resequencing work. The updated sequence has been reannotated in agreement with the UniProt protein knowledge base, keeping in perspective the split between the paleome (genes necessary for sustaining and perpetuating life) and the cenome (genes required for occupation of a niche, suggesting here that B. subtilis is an epiphyte). This should permit investigators to make reliable inferences to prepare validation experiments in a variety of domains of bacterial growth and development as well as build up accurate phylogenies.
Design and characterization of a ligand-binding metallopeptide (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDesign and characterization of a ligand-binding metallopeptideDenise L. Merkle, Michael H. Schmidt, and Jeremy M. BergCite this: J. Am. Chem. Soc. 1991, 113, 14, 5450–5451Publication Date (Print):July 1, 1991Publication History Published online1 May 2002Published inissue 1 July 1991https://pubs.acs.org/doi/10.1021/ja00014a045https://doi.org/10.1021/ja00014a045research-articleACS PublicationsRequest reuse permissionsArticle Views265Altmetric-Citations49LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Multiparameter metabolic analysis reveals a close link between attenuated mitochondrial bioenergetic function and enhanced glycolysis dependency in human tumor cells (2006)

Increased conversion of glucose to lactic acid associated with decreased mitochondrial respiration is a unique feature of tumors first described by Otto Warburg in the 1920s. Recent evidence suggests that the Warburg effect is caused by oncogenes and is an underlying mechanism of malignant transformation. Using a novel approach to measure cellular metabolic rates in vitro, the bioenergetic basis of this increased glycolysis and reduced mitochondrial respiration was investigated in two human cancer cell lines, H460 and A549. The bioenergetic phenotype was analyzed by measuring cellular respiration, glycolysis rate, and ATP turnover of the cells in response to various pharmacological modulators. H460 and A549 cells displayed a dependency on glycolysis and an ability to significantly upregulate this pathway when their respiration was inhibited. The converse, however, was not true. The cell lines were attenuated in oxidative phosphorylation (OXPHOS) capacity and were unable to sufficiently upregulate mitochondrial OXPHOS when glycolysis was disabled. This observed mitochondrial impairment was intimately linked to the increased dependency on glycolysis. Furthermore, it was demonstrated that H460 cells were more glycolytic, having a greater impairment of mitochondrial respiration, compared with A549 cells. Finally, the upregulation of glycolysis in response to mitochondrial ATP synthesis inhibition was dependent on AMP-activated protein kinase activity. In summary, our results demonstrate a bioenergetic phenotype of these two cancer cell lines characterized by increased rate of glycolysis and a linked attenuation in their OXPHOS capacity. These metabolic alterations provide a mechanistic explanation for the growth advantage and apoptotic resistance of tumor cells.
Computation of linear elastic properties from microtomographic images: Methodology and agreement between theory and experiment (2002)

Abstract Elastic property-porosity relationships are derived directly from microtomographic images. This is illustrated for a suite of four samples of Fontainebleau sandstone with porosities ranging from 7.5% to 22%. A finite-element method is used to derive the elastic properties of digitized images. By estimating and minimizing several sources of numerical error, very accurate predictions of properties are derived in excellent agreement with experimental measurements over a wide range of the porosity. We consider the elastic properties of the digitized images under dry, water-saturated, and oil-saturated conditions. The observed change in the elastic properties due to fluid substitution is in excellent agreement with the exact Gassmann's equations. This shows both the accuracy and the feasibility of combining microtomographic images with elastic calculations to accurately predict petrophysical properties of individual rock morphologies. We compare the numerical predictions to various empirical, effective medium and rigorous approximations used to relate the elastic properties of rocks to porosity under different saturation conditions.
Towards unified and native enrichment in event processing systems (2013)

Events are encapsulated pieces of information that flow from one event agent to another. In order to process an event, additional information that is external to the event is often needed. This is achieved using a process called event enrichment. Current approaches to event enrichment are external to event processing engines and are handled by specialized agents. Within large-scale environments with high heterogeneity among events, the enrichment process may become difficult to maintain. This paper examines event enrichment in terms of information completeness and presents a unified model for event enrichment that takes place natively within the event processing engine. The paper describes the requirements of event enrichment and highlights its challenges such as finding enrichment sources, retrieval of information items, finding complementary information and its fusion with events. It then details an instantiation of the model using Semantic Web and Linked Data technologies. Enrichment is realised by dynamically guiding a spreading activation algorithm in a Linked Data graph. Multiple spreading activation strategies have been evaluated on a set of Wikipedia events and experimentation shows the viability of the approach.
Predictors of arrhythmia recurrence in patients with lone atrial fibrillation (2007)

AimsThe need for antiarrhythmic drugs (AAD) after a first episode of atrial fibrillation (AF) is determined by the probability of recurrence. The aim of this study was to asses the probability of relapse and the predictors of recurrence in patients with idiopathic AF.
IRS and TOR nutrient-signaling pathways act via juvenile hormone to influence honey bee caste fate (2011)

Regardless of genetic makeup, a female honey bee becomes a queen or worker depending on the food she receives as a larva. For decades, it has been known that nutrition and juvenile hormone (JH) signaling determine the caste fate of the individual bee. However, it is still largely unclear how these factors are connected. To address this question, we suppressed nutrient sensing by RNA interference (RNAi)-mediated gene knockdown of IRS (insulin receptor substrate) and TOR (target of rapamycin) in larvae reared on queen diet. The treatments affected several layers of organismal organization that could play a role in the response to differential nutrition between castes. These include transcript profiles, proteomic patterns, lipid levels, DNA methylation response and morphological features. Most importantly, gene knockdown abolished a JH peak that signals queen development and resulted in a worker phenotype. Application of JH rescued the queen phenotype in either knockdown, which demonstrates that the larval response to JH remains intact and can drive normal developmental plasticity even when IRS or TOR transcript levels are reduced. We discuss our results in the context of other recent findings on honey bee caste and development and propose that IRS is an alternative substrate for the Egfr (epidermal growth factor receptor) in honey bees. Overall, our study describes how the interplay of nutritional and hormonal signals affects many levels of organismal organization to build different phenotypes from identical genotypes.
A MEMS Low-Noise Sound Pressure Gradient Microphone With Capacitive Sensing (2014)

A silicon microelectromechanical systems microphone is described that detects sound pressure gradients. The diaphragm consists of a stiffened plate that rotates around a central axis in response to sound pressure gradients. The motion of the diaphragm is converted into an electronic signal through the use of interdigitated comb fins that enable capacitive sensing. Measured results show that the microphone achieves a substantially lower low-frequency sound pressure-referred noise floor than can be achieved using existing dual miniature microphone systems. Measured directivity patterns are shown to be very close to what is expected for sound pressure gradient receivers over a broad range of frequencies.
A Work-Optimal Deterministic Algorithm for the Certified Write-All Problem with a Nontrivial Number of Asynchronous Processors (2005)

Martel [C. Martel, A. Park, and R. Subramonian, SIAM J. Comput., 21 (1992), pp. 1070--1099] posed a question for developing a work-optimal deterministic asynchronous algorithm for the fundamental load-balancing and synchronization problem called Certified Write-All (CWA). In this problem, introduced in a slightly different form by Kanellakis and Shvartsman in a PODC'89 paper [P. C. Kanellakis and A. A. Shvartsman, Distributed Computing, 5 (1992), pp. 201--247], p processors must update n memory cells and only then signal the completion of the updates. It is known that solutions to this problem can be used to simulate synchronous parallel programs on asynchronous systems with worst-case guarantees for the overhead of a simulation. Such simulations are interesting because they may increase productivity in parallel computing since synchronous parallel programs are easier to reason about than are asynchronous ones. This paper presents the first solution to the question of Martel, Park, and Subramonian. Specifically, we show a deterministic asynchronous algorithm for the CWA problem. Our algorithm has the work complexity of O(n+p4 log n). This work complexity is asymptotically optimal for a nontrivial number of processors $p \leq \left(n/\log n\right)^{1/4}$. In contrast, all known deterministic algorithms require superlinear in n work when p = n1/r for any fixed $r \geq 1$. Our algorithm generalizes the collision principle introduced by Buss et al. [J. Buss, P. C. Kanellakis, P. L. Ragde, and A. A. Shvartsman, J. Algorithms, 20 (1996), pp. 45--86] in 1996, which has not been previously generalized despite various attempts. Each processor maintains a collection of intervals of {1,2,...,n}. Any processor iteratively selects an interval and works from its tip toward the other tip until it finishes the work or collides with another processor. Collisions are detected effectively using a special Read-Modify-Write operation. In any case, the processor transforms its collection appropriately. Our analysis shows that the transformations preserve some structural properties of collections of intervals. This guarantees that work is assigned to processors in an efficient manner.
A method for modeling laterally asymmetric proton beamlets resulting from collimation (2015)

The analytical model is capable of accurately representing individual asymmetric beamlets resulting from use of the DCS. This method enables integration of the DCS into a treatment planning system to perform dose computation in patient datasets. The method could be generalized for use with any SS collimation system in which blades, leaves, or trimmers are used to laterally sharpen beamlets.
A Novel Live Pichinde Virus-Based Vaccine Vector Induces Enhanced Humoral and Cellular Immunity after a Booster Dose (2015)

We have developed a novel Pichinde virus (PICV)-based live viral vector, rP18tri, that packages three RNA segments and encodes as many as two foreign genes. Using the influenza virus HA and NP genes as model antigens, we show that this rP18tri vector can induce strong humoral and cellular immunity via different immunization routes and can lead to protection in mice. Interestingly, a booster dose further enhances the immune responses, a feature that distinguishes this from other known live viral vectors. In summary, our study demonstrates a unique feature of this live rP18tri vector to be used as a novel vaccine platform for a prime-and-boost vaccination strategy.
Dual role for DOCK7 in tangential migration of interneuron precursors in the postnatal forebrain (2017)

Throughout life, stem cells in the ventricular-subventricular zone generate neuroblasts that migrate via the rostral migratory stream (RMS) to the olfactory bulb, where they differentiate into local interneurons. Although progress has been made toward identifying extracellular factors that guide the migration of these cells, little is known about the intracellular mechanisms that govern the dynamic reshaping of the neuroblasts' morphology required for their migration along the RMS. In this study, we identify DOCK7, a member of the DOCK180-family, as a molecule essential for tangential neuroblast migration in the postnatal mouse forebrain. DOCK7 regulates the migration of these cells by controlling both leading process (LP) extension and somal translocation via distinct pathways. It controls LP stability/growth via a Rac-dependent pathway, likely by modulating microtubule networks while also regulating F-actin remodeling at the cell rear to promote somal translocation via a previously unrecognized myosin phosphatase-RhoA-interacting protein-dependent pathway. The coordinated action of both pathways is required to ensure efficient neuroblast migration along the RMS.
Turf Battles in Coronary Revascularization (2005)

When percutaneous transluminal coronary angioplasty (PTCA) entered mainstream use in the early 1980s, it represented a suboptimal substitute for coronary-artery bypass grafting (CABG). Over time, however, the outcomes of PTCA improved, and the technique became a viable alternative to CABG, even in the treatment of patients with advanced coronary disease. Nevertheless, the extent of the diffusion of PTCA as compared with CABG varied widely among hospitals. Several years after the introduction of PTCA, traditional CABG surgery was faced with a new competitor — minimally invasive cardiac surgery. Although the less invasive technique had clear advantages for some types of patients, . . .
The Use of Compact Cyclotrons for Producing Fast Neutrons for Therapy in a Rotatable Isocentric Gantry (1979)

This paper discusses the design and performance of a fast neutron therapy system which transports a cyclotron beam onto a beryllium target mounted in a rotatable isocentric gantry structure. Fast neutrons produced by either the proton or deuteron on beryllium reaction are directed towards the isocenter with appropriate shielding, collimation and dosimetry to control and monitor the radiation delivered onto a defined patient area. The beam optics and shielding considerations of such a radiotherapy apparatus are discussed. This paper also presents the dosimetric properties of neutron beams from different proton energies on beryllium and lithium targets.
Episodic Luteinizing Hormone (LH) Secretion and the Response of LH and Follicle-Stimulating Hormone to LH-Releasing Hormone in Aged Men: Evidence for Coexistent Primary Testicular Insufficiency and an Impairment in Gonadotropin Secretion* (1982)

The influence of aging on episodic LH secretion and the release of LH and FSH after LRH administration was studied in 14 healthy men, aged 65-80 yr. Mean morning serum testosterone levels were reduced by 16% (P less than 0.05) and serum LH and FSH concentrations were increased by nearly 2- and 3-fold, respectively (P less than 0.01), compared to levels in young men. LH secretory episodes were evident and did not differ significantly in either amplitude or frequency from those of young men in spite of the higher mean LH concentrations. The increments in serum LH and FSH levels after LRH and the areas under the response curves were similar in aged and young men. However, the time of the peak LH response was significantly delayed with aging (P less than 0.001), suggesting an alteration in the control of the releasable LH pool. Further, LH levels were slower to fall after the peak in elderly men (P less than 0.01), suggesting prolonged secretion of hormone after LRH stimulation. These changes did not relate to the basal hypersecretion of LH in elderly men, as the responses in young men with primary gonadal failure did not differ from those in healthy young men (P = NS). The possibility that increased LH molecular size leads to its reduced clearance was not supported by the similar Sephadex G-100 elution profiles for LH in both basal and post-LRH sera from young and old men. Our data indicate that Leydig cell function is impaired in healthy elderly men as a result of primary testicular insufficiency. These studies further reveal the presence of an additional hypothalamic-pituitary disorder of gonadotropin secretion associated with the aging process.