gebhart/patrepeval huggingface dataset:
Familial factors affecting prostatic cancer risk and plasma sex‐steroid levels (1985)

Whether familial factors affect the frequency of prostatic cancer and the plasma content of sex-steroids was investigated. Brothers (n = 257) of probands (n = 150) diagnosed with prostatic cancer before age 62 years had a fourfold higher risk for developing the disease than men in the general population in the State of Utah and their brothers-in-law (n = 202). Familial factors markedly affected the plasma content of sex steroids (testosterone, dihydrotestosterone, the ratio of testosterone to DHT, sex-hormone binding globulin, and the free fraction of testosterone) in nonendocrinologically treated probands and their brothers and sons and in normal men in the general populations. Index cases and their brothers and sons had a significantly lower mean plasma testosterone content than controls of comparable age. Preliminary data suggest that the metabolic clearance rate of testosterone and the conversion ratio of testosterone to estradiol are relatively high in probands. The observations indicate that familial factors are potent risk factors for the development of prostatic cancer. They also suggest that plasma androgen values in families with prostatic cancer cluster in the lower range of normal and that plasma sex-steroid content is more similar in each brothers with or without prostatic cancer than among nonbrothers.
User simulation of space utilisation:system for office building usage simulation (2009)

previously mentioned PhD's in the Design Systems group.We spent much time on building this network, but even more time outside of work on social activities, like sailing, bowling or simply going for a drink after work (e.g. the Sky Bar).I hugely enjoyed the time we spent together and it contributed to enjoying being a PhD.I hope we can continue our friendship, even after we have spread all over the world.My appreciation also goes to all those who participated in my experiments.For the RFID experiment (and the task-sorter survey) I wish to thank all colleagues belonging to the
Disorder in a Target for the Smad2 Mad Homology 2 Domain and Its Implications for Binding and Specificity (2004)

The Smad2 Mad homology 2 (MH2) domain binds to a diverse group of proteins which do not share a common sequence motif. We have used NMR to investigate the structure of one of these interacting proteins, the Smad binding domain (SBD) of Smad anchor for receptor activation (SARA). Our results indicate that the unbound SBD is highly disordered and forms no stable secondary or tertiary structures. Additionally we have used fluorescence binding studies to study the interaction between the MH2 domain and SBD and find that no region of the SBD dominates the interaction between the MH2 and the SBD. Our results are consistent with a series of hydrophobic patches on the MH2 that are able to recognize disordered regions of proteins. These findings elucidate a mechanism by which a single domain (MH2) can specifically recognize a diverse set of proteins which are unrelated by sequence, lead to a clearer picture of how MH2 domains function in the transforming growth factor-beta-signaling pathway and suggest possible mechanisms for controlling interactions with MH2 domains.
Insulin-Like Growth Factor-1 Reduces Postischemic White Matter Injury in Fetal Sheep (2001)

Insulin-like growth factor-1 (IGF-1) is known to be important for oligodendrocyte survival and myelination. In the current study, the authors examined the hypothesis that exogenous IGF-1 could reduce postischemic white matter injury. Bilateral brain injury was induced in near-term fetal sheep by 30 minutes of reversible carotid artery occlusion. Ninety minutes after ischemia, either vehicle (n = 8) or a single dose of 3 microg IGF-1 (n = 9) was infused intracerebroventricularly over 1 hour. White matter changes were assessed after 4 days recovery in the parasagittal intragyral white matter and underlying corona radiata. Proteolipid protein (PLP) mRNA staining was used to identify bioactive oligodendrocytes. Glial fibrillary acidic protein (GFAP) and isolectin B-4 immunoreactivity were used to label astrocytes and microglia, respectively. Myelin basic protein (MBP) density and the area of the intragyral white matter tracts were determined by image analysis. Insulin-like growth factor-1 treatment was associated with significantly reduced loss of oligodendrocytes in the intragyral white matter (P < 0.05), with improved MBP density (P < 0.05), reduced tissue swelling, and increased numbers of GFAP and isolectin B-4 positive cells compared with vehicle treatment. After ischemia there was a close association of PLP mRNA labeled cells with reactive astrocytes and macrophages/microglia. In conclusion, IGF-1 can prevent delayed, postischemic oligodendrocyte cell loss and associated demyelination.
Physical aware frequency selection for dynamic thermal management in multi-core systems (2006)

In order to maintain performance per Watt in microprocessors, there is a shift towards the chip level multiprocessing paradigm. Microprocessor manufacturers are experimenting with tens of cores, forecasting the arrival of hundreds of cores per single processor die in the near future. With such large-scale integration and increasing power densities, thermal management continues to be a significant design effort to maintain performance and reliability in modern process technologies. In this paper, we present two mechanisms to perform frequency scaling as part of Dynamic Frequency and Voltage Scaling (DVFS) to assist Dynamic Thermal Management (DTM). Our frequency selection algorithms incorporate the physical interaction of the cores on a large-scale system onto the emergency intervention mechanisms for temperature reduction of the hotspot, while aiming to minimize the performance impact of frequency scaling on the core that is in thermal emergency. Our results show that our algorithm consistently succeeds in maximizing the operating frequency of the most critical core while successfully relieving the thermal emergency of the core. A comparison of our two alternative techniques reveals that our physical aware criticality-based algorithm results in 11.7% faster clock frequencies compared to our aggressive scaling algorithm. We also show that our technique is extremely fast and is suited for real time thermal management
Divergent Transcription from Active Promoters (2008)

Transcription initiation by RNA polymerase II (RNAPII) is thought to occur unidirectionally from most genes. Here, we present evidence of widespread divergent transcription at protein-encoding gene promoters. Transcription start site-associated RNAs (TSSa-RNAs) nonrandomly flank active promoters, with peaks of antisense and sense short RNAs at 250 nucleotides upstream and 50 nucleotides downstream of TSSs, respectively. Northern analysis shows that TSSa-RNAs are subsets of an RNA population 20 to 90 nucleotides in length. Promoter-associated RNAPII and H3K4-trimethylated histones, transcription initiation hallmarks, colocalize at sense and antisense TSSa-RNA positions; however, H3K79-dimethylated histones, characteristic of elongating RNAPII, are only present downstream of TSSs. These results suggest that divergent transcription over short distances is common for active promoters and may help promoter regions maintain a state poised for subsequent regulation.
SPECIFIC UNRESPONSIVENESS IN RATS WITH PROLONGED CARDIAC ALLOGRAFT SURVIVAL AFTER TREATMENT WITH CYCLOSPORINE (1993)

DA rats treated with a short course of cyclosporine develop specific unresponsiveness to RT1-incompatible PVG donor heart allografts. CD4+ cells, not CD8+ cells, transfer unresponsiveness to irradiated rats. However, host-derived CD8+ cells are important in reestablishing unresponsiveness. In this study, unfractionated lymphoid cells and W3/25+ (CD4+) cells from CsA-treated rats with long-surviving PVG allografts demonstrated normal alloreactivity to PVG alloantigen in the mixed lymphocyte culture and failed to suppress the proliferative response of naive W3/25+ cells to donor-specific alloantigen. MRC OX8+ (CD8+) cells did not proliferate. Sera from CsA-treated rats had no effect on the MLC reactivity of cells from CsA-treated rats, suggesting that blocking or antiidiotypic antibodies did not diminish alloreactivity. IL-2 production by W3/25+ cells from CsA-treated rats was similar to that by W3/25+ cells from naive rats. Specific cytotoxic T cells to PVG were generated in MLC, and the frequency of precursor cytotoxic lymphocytes in CsA-treated rats was similar to that in naive DA rats. In an in vitro assay testing response to idiotype, neither W3/25+ or MRC OX8+ cells from unresponsive rats proliferated. As CD4+ cells from CsA-treated rats lose their capacity to adoptively transfer specific unresponsiveness unless maintained in a cytokine-rich supernatant, all in vitro assays were performed with and without added cytokines, but no change in reactivity consistent with suppression was observed in any assay. CD4+ suppressor cells had no effect on conventional in vitro assays of alloreactivity, preventing the detection of the unresponsiveness in vitro.
Electrochemical polymerization of furfural on a platinum electrode in aqueous solutions of potassium biphthalate (2005)

Three different electrochemical methods confirm the growth processes of polyfurfural on platinum electrodes in aqueous solutions. The electrochemical oxidative polymerization of furfural occurs only with 0.10 mol L-1 potassium biphthalate as the supporting electrolyte. Electrochemical and spectroscopic methods are employed to characterize the polymeric film produced. Based on spectroscopic data, a polymeric structure involving furfural and biphthalate anions is discussed.
Damage on HfO2/SiO2 high-reflecting coatings under single and multiple Nd:YAG laser pulse irradiation (2005)

The single- and multi-shot damage behaviors of HfO2/SiO2 high-reflecting (HR) coatings under Nd:YAG laser exposure were investigated. Fundamental aspects of multi-shot laser damage, such as the instability due to pulse-to-pulse accumulation of absorption defect and structural defect effect, and the mechanism of laser induced defect generation, are considered. It was found in multi-shot damage, the main factors influencing laser-induced damage threshold (LIDT) are accumulation of irreversible changes of structural defects and thermal stress that induced by thermal density fluctuations.
Mesenteric Vein Thrombosis (1996)

Mesenteric vein thrombosis, an uncommon but important clinical entity, can cause ischemia or infarction of the small intestine. Mesenteric vein thrombosis was first described nearly a century ago, but diagnosis remains difficult because it can affect young individuals without any known predisposing disorder and because patients often present with nonspecific abdominal symptoms. We report 4 cases of small intestinal ischemia secondary to superior mesenteric vein thrombosis. Three were due to hypercoagulable states (protein-S deficiency, factor-VII abnormalities) and one was idiopathic. In recent years, the development of modern imaging techniques (particularly ultrasonography, duplex scanning, and computed tomography) have enabled early recognition of this disease. Anticoagulation is therapeutic acutely unless there are signs of peritonitis which necessitate surgical resection of the infarcted bowel.
Ehrlichia chaffeensis expresses an immunoreactive protein homologous to the Escherichia coli GroEL protein (1993)

A clone expressing a 58-kDa protein reactive with human convalescent-phase serum was isolated from a recombinant library of Ehrlichia chaffeensis, the etiologic agent of human ehrlichiosis. Sequencing identified two open reading frames, one encoding a 10.3-kDa polypeptide consisting of 94 amino acids and another encoding a 58-kDa polypeptide consisting of 550 amino acids. The sequences of the 10.3- and 58-kDa polypeptides were homologous to those of the Escherichia coli GroES and GroEL heat shock proteins, respectively.
Structuring Polymers for Delivery of DNA-Based Therapeutics: Updated Insights (2012)

Gene therapy offers greater opportunities for treating numerous incurable diseases from genetic disorders, infections, and cancer. However, development of appropriate delivery systems could be one of the most important factors to overcome numerous biological barriers for delivery of various therapeutic molecules. A number of nonviral polymer-mediated vectors have been developed for DNA delivery and offer the potential to surmount the associated problems of their viral counterpart. To address the concerns associated with safety issues, a wide range of polymeric vectors are available and have been utilized successfully to deliver their therapeutics in vivo. Today's research is mainly focused on the various natural or synthetic polymer-based delivery carriers that protect the DNA molecule from degradation, which offer specific targeting to the desired cells after systemic administration, have transfection efficiencies equivalent to virus-mediated gene delivery, and have long-term gene expression through sustained-release mechanisms. This review explores an updated overview of different nonviral polymeric delivery system for delivery of DNA-based therapeutics. These polymeric carriers have been evaluated in vitro and in vivo and are being utilized in various stages of clinical evaluation. Continued research and understanding of the principles of polymer-based gene delivery systems will enable us to develop new and efficient delivery systems for the delivery of DNA-based therapeutics to achieve the goal of efficacious and specific gene therapy for a vast array of clinical disorders as the therapeutic solutions of tomorrow.
Epithelial-stromal interactions and tumor progression: meeting summary and future directions. (2001)

The Epithelial-Stromal Interactions Workshop was organized with the purpose of accelerating progress in understanding the interrelationship between tumor cells and their microenvironment and applying this knowledge to the control of tumor progression. The format of the meeting was the presentation of brief reports that focused on concepts rather than specifics, with extensive discussion periods to identify the issues and barriers hindering progress in this area. This report summarizes the findings of this meeting, highlighting the intimate relationship between tumor cells and their environment and addressing the opportunities that manipulation of host-tumor interactions has for therapeutic intervention. Several specific recommendations are made to advance knowledge and progress in this field.
Rapid and Efficient Synthesis of 1,2,4-Oxadiazoles Utilizing Polymer-Supported Reagents under Microwave Heating (2005)

1,2,4-Oxadiazoles can be rapidly and efficiently synthesized from a variety of readily available carboxylic acids and amidoximes using either method A or method B. The use of commercially available polymer-supported reagents combined with microwave heating resulted in high yields and purities of the product 1,2,4-oxadiazoles in an expeditious manner. [structure: see text]
The Hedgehog and the hair follicle: a growing relationship (1999)

The various forms of hair loss (alopecia) constitute an extremely common complaint among both men and women. Although sometimes dismissed as merely cosmetic, these conditions can be psychologically and socially devastating. The desire to regrow hair is at the root of a multi-billion dollar industry worldwide; however, there are few truly effective treatments. Given the recent progress in elucidating some of the signals regulating hair follicle growth and development, there is hope that more useful therapies may soon be available. The timely report by Sato et al. (1) presents interesting new data bearing on this issue.
Modification of a Model for Cerebral Ischemia in the Cat: A New Method to Occlude the Middle Cerebral Artery (1989)

A modified method of occluding the middle cerebral artery (MCA) by inserting a tiny copper wire into the lumen of the vessel to make a model for cerebral ischemia in the cat is described. Of 22 cats, 4 were controls and the remaining 18 were divided into two groups. Bipolar electrocoagulation was used in 9 cats and copper wire insertion was used in the other 9 to occlude the MCA through a transorbital approach. Two cats died after surgery and were excluded from this study. Of the 16 cats in two experimental groups, 13 of 14 showed hemiplegia and the other 2 were killed under anesthesia. Typical ischemic changes can be seen in the territory of the occluded MCA. Increased water content and decreased amplitude of somatosensory evoked potentials can be found in the ischemic hemisphere. Histochemical fluorescence study demonstrated that the sympathetic nerve fibers normally existing on the MCA can be completely destroyed by electrocoagulation but may remain intact with the copper wire method. This new method may have less influence on the vascular regulative function of the autonomic nervous system and be more similar to the pathological changes of cerebral infarction in man. We think our method can be useful for further research in cerebral ischemic disease and the regulative effects of the nervous system on brain vessels. (Neurosurgery 25:49-53, 1989)
Using Phase Diagrams to Predict the Performance of Cosolvent Floods for NAPL Remediation (1998)

Abstract Cosolvent flooding using water miscible solvents such as alcohols has been proposed as an in situ NAPL remediation technique. This process is conceptually similar to enhanced oil recovery (EOR) using alcohols and some surfactant formulations. As a result of interest in the EOR aspects of these systems, analytical and graphical methods based on fractional flow theory were developed in the petroleum engineering literature for modeling theses floods. The existing fractional flow solutions have not been used previously in environmental applications of cosolvent flooding, but they are applicable and provide many useful insights into the process. These applications are discussed, with an emphasis on emplaining the mechanisms which tend to mobilize trapped NAPL during a cosolvent flood. The theory provides a simple way to predict the general behavior of a cosolvent flood using the phase diagram. It is concluded that the one‐dimensional performance of a cosolvent flood can be predicted largely by inspection of the ternary phase diagram. In particular, the nature of the cosolvent flood depends primarily on the position of the cosolvent injection concentration relative to a critical the line extension which passes through the plait point, tangent to the binodal curve.
Induction of caspase 8 by interferon gamma renders some neuroblastoma (NB) cells sensitive to tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) but reveals that a lack of membrane TR1/TR2 also contributes to TRAIL resistance in NB. (2003)

The resistance of neuroblastoma (NB) cells to tumor necrosis factor-related apoptosis-inducing ligand (TRAIL)-induced apoptosis has been attributed to a lack of caspase 8 expression. Here we demonstrate a clinically applicable molecular targeting strategy that not only increases caspase 8 expression ex vivo in NB cell lines but also in the tumor tissues of NB patients receiving IFN-gamma treatment. We identify the functional caspase 8 promoter, which is different from the methylated region reported previously, and show promoter activity is up-regulated by IFN-gamma through a IFN-gamma activation site-containing region. IFN-gamma also induces TRAIL expression in NB cell lines. However, the IFN-gamma restoration of caspase 8 in some NB cells revealed persistent TRAIL resistance in most NB cell lines examined. This additional lesion in the TRAIL path is because of a loss of cell membrane TRAIL receptors (TR1/TR2) not only in cell lines but in most of the NB tumor tissues evaluated. Restoration of TR2 expression by transfection enhances IFN-gamma-induced TRAIL sensitivity. Furthermore, we have found that we can improve TRAIL sensitivity in NB by reconstituting caspase 8 with IFN-gamma and TR2 with chemotherapeutic agents.
Diltiazem reduces retinal neovascularization in a mouse model of oxygen induced retinopathy (1999)

Diltiazem reduces oxygen induced retinopathy in the mouse as measured by a scoring system based on a retinal whole mount method of retinal neovascularization and by quantification of extra retinal neovascular nuclei.
An integrated encyclopedia of DNA elements in the human genome (2012)

The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research. Â© 2012 Macmillan Publishers Limited. All rights reserved.
Purification and characterization of short-chain, medium-chain, and long-chain acyl-CoA dehydrogenases from rat liver mitochondria. Isolation of the holo- and apoenzymes and conversion of the apoenzyme to the holoenzyme. (1985)

Short-chain, medium-chain, and long-chain acyl-CoA dehydrogenases were purified to homogeneity from rat liver mitochondria by sequential chromatography on DEAE-Sephadex A-50, hydroxyapatite, Matrex Gel Blue A, agarose-hexane-CoA, and Bio-Gel A-0.5m. Molecular, immunological, and catalytic properties of the pure acyl-CoA dehydrogenases were investigated. The native molecular weights of these three enzymes were 160,000, 180,000, and 180,000, respectively. The subunit molecular weights of the three enzymes were estimated to be 41,000, 45,000, and 45,000, respectively, indicating that these enzymes are each composed of four subunits of equal size. The FAD content was calculated to be 1 mol/mol of subunit. While FAD binding by short-chain acyl-CoA dehydrogenase was very tight, that by medium-chain acyl-CoA and long-chain acyl-CoA dehydrogenases was less tight. The medium- and long-chain acyl-CoA dehydrogenases were also purified to homogeneity as FAD-free apoenzymes. The apoenzymes were converted to the fully active holoenzymes by incubation with FAD. The three acyl-CoA dehydrogenases were immunologically distinct from each other, i.e. the antibodies raised against the individual enzymes were monospecific and did not cross-react with any other acyl-CoA dehydrogenases. Our preparations of the three enzymes exhibited substrate specificities (as defined in Vappmax and Kappmax) significantly more specific than those of the previous preparations isolated from other sources. The substrate specificities were assessed also by measuring the activities in mitochondrial sonicates after selectively precipitating each enzyme with their individual monospecific antibodies. Butyryl-CoA was almost exclusively dehydrogenated by short-chain acyl-CoA dehydrogenase while C6-C10 acyl-CoAs were mainly dehydrogenated by medium-chain acyl-CoA dehydrogenase. C14-C22 acyl-CoAs were exclusively dehydrogenated by long-chain acyl-CoA dehydrogenase. C24 acyl-CoAs were not dehydrogenated by this enzyme. Lauroyl-CoA appeared to be jointly dehydrogenated by the latter two enzymes. Branched-chain acyl-CoAs were not dehydrogenated by short-chain acyl-CoA dehydrogenase. In the presence of electron-transfer flavoprotein or phenazine methosulfate, 2-enoyl-CoAs were identified as products from the corresponding enzyme/acyl-CoA reactions.