gebhart/patrepeval huggingface dataset:
An Improved United Atom Force Field for Simulation of Mixed Lipid Bilayers (2009)

We introduce a new force field (43A1-S3) for simulation of membranes by the Gromacs simulation package. Construction of the force fields is by standard methods of electronic structure computations for bond parameters and charge distribution and specific volumes and heats of vaporization for small-molecule components of the larger lipid molecules for van der Waals parameters. Some parameters from the earlier 43A1 force field are found to be correct in the context of these calculations, while others are modified. The validity of the force fields is demonstrated by correct replication of X-ray form factors and NMR order parameters over a wide range of membrane compositions in semi-isotropic NTP 1 atm simulations. 43-A1-S3 compares favorably with other force fields used in conjunction with the Gromacs simulation package with respect to the breadth of phenomena that it accurately reproduces.
Electroencephalographic and Behavioral Studies of Monomethyl Hydrazine Toxicity in the Cat (2010)

The toxicity of monomethyl hydrazine (MMH) administered intraperitoneally in the cat was studied by reference to behavioral and neurophysiological indices. The acute lethal toxicity value (LD 50 ) for MMH was established at 15 mg=kg, and the convulsive toxicity value (CD 50 ) at 7 m=kg. Doses of 18, 9, and 5 mg=kg were then studied systematically in an effort to classify lethal, convulsive, and subconvulsive symptoms. For these doses, a preconvulsive syndrome was described involving recurrent and sustained symptoms, including vomiting, panting, rapid respiration, viscous salivation, hyperactivity, and subcortical seizure activity. The onset latency of these symptoms was directly related to dose. Several lines of evidence suggested at least a partial independence between biochemical and neurophysiological events responsible, on one hand, for convulsions and, on the other, for this preconvulsive syndrome. Convulsions were specifically delayed or prevented in animals trained to suppress movement through the use of a special EEG conditioning technique.
Dynamic Adiabatic Calorimeter: An Improved Calorimetric Apparatus (1964)

An apparatus and technique for the simple but rapid determination of specific and latent heat data are described. The apparatus records automatically the energy-temperature plot for the sample on a conventional emf vs time strip-chart recorder; most of the components required are commercially available. The calorimetric assembly embodies the major advantages of adiabatic, heat-flow, differential-thermal-analysis, and thermal-analysis calorimeters. An accuracy of ±2% can be readily attained; with some care, errors can be reduced greatly in many cases.
Shortage of mitogen-activated protein kinase is responsible for resistance to AP-1 transactivation and transformation in mouse JB6 cells (1998)

The JB6 mouse epidermal cell system, which includes tumor promotion-sensitive (P+) and tumor promotion-resistant (P-) cells, is a well-established and extensively used cell culture model for studying the mechanism of late-stage tumor promotion. Tumor promoters, such as 12-O-tetradecanoylphorbol 13-acetate (TPA) or epidermal growth factor (EGF), induce high levels of activator protein 1 (AP-1) activity and large, tumorigenic, anchorage-independent colonies in soft agar at a high frequency in JB6 P+ cells, but not in JB6 P- cells. We report here a molecular explanation for the defect in the AP-1 activation and promotion-resistant phenotype of P- cells. We demonstrate that the lack of AP-1 activation and cell transformation responses to TPA and EGF in P- cells appears attributable to the low level of mitogen-activated protein kinase (MAPK) (extracellular signal-regulated protein kinase, Erk) in these cells. TPA and EGF induce transactivation of AP-1 activity in P+ cells but not in P- cells. Nonphosphorylated forms and TPA- or EGF-induced phosphorylated forms of Erks (Erk1 and Erk2) in P- cells were much lower than those in P+ cells. Stable transfection of wild-type MAPK (Erk2) into P- cells restored its response to TPA and EGF for both AP-1 activation and cell transformation. These results suggest that the shortage of MAPK (Erk1 and Erk2) appears to be an important contributor to the tumor promotion-resistant phenotype in JB6 cells.
Lamarck and the nucleosome: evolution and environment across 200 years (2013)

Amongst prominent biological scientists of the past 300 years, Lamarck is one of the most widely misunderstood. His distinguished and influential contributions to the taxonomy of plants and invertebrates have been all but lost amidst the furore surrounding attempts to prove or discredit a mechanism he proposed to explain how major phenotypic differences might evolve, namely the inheritance of acquired characteristics. In the present article, Lamarck's ideas on evolution and the processes by which it might occur are described using his own words, and placed in the context of his career and the revolutionary times in which he lived. A thought experiment brings Lamarck into the twenty-first century to solicit his views on the paradigms and preoccupations that underpin present-day molecular biology. His evolutionary ideas are translated into modern terminology to assess their continuing validity. Stripped to their essential elements, Lamarck's ideas are coincident with recent suggestions that environmentally driven, epigenetic processes play a role in evolutionary change. They can be incorporated into a new synthesis in which a trinity of genetic, epigenetic and environmental factors, linked to Darwinian natural selection, provides a new conceptual framework within which evolutionary processes can be explored.
Mononuclear Organomolybdenum(VI) Dioxo Complexes:  Synthesis, Reactivity, and Catalytic Applications (2006)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMononuclear Organomolybdenum(VI) Dioxo Complexes: Synthesis, Reactivity, and Catalytic ApplicationsFritz E. Kühn, Ana M. Santos, and Marta AbrantesView Author Information Instituto Tecnológico e Nuclear (ITN), Estrada Nacional No. 10, 2686-953 Sacavem, Portugal Cite this: Chem. Rev. 2006, 106, 6, 2455–2475Publication Date (Web):April 22, 2006Publication History Received5 December 2005Published online22 April 2006Published inissue 1 June 2006https://pubs.acs.org/doi/10.1021/cr040703phttps://doi.org/10.1021/cr040703presearch-articleACS PublicationsCopyright © 2006 American Chemical SocietyRequest reuse permissionsArticle Views2018Altmetric-Citations203LEARN 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 SUBJECTS:Alkyls,Catalysts,Ligands,Organic reactions,Oxides Get e-Alerts
Biosynthesis of the streptovaricins: 3-Amino-5-hydroxybenzoic acid as a precursor to the meta-C7N unit. (1991)

[Carboxy-14C]-3-amino-5-hydroxybenzoic acid (AHBA) has been shown to be incorporated by Streptomyces spectabilis to the extent of greater than 0.1% (35: 1 dilution) in the ansamycin antibiotic streptovaricin C, the major component of the streptovaricin complex. When [carboxy-13C]AHBA was similarly administered, C-21 (quinone methide carbonyl at 188.3 ppm) of streptovaricin C was specifically labeled (at twenty one times natural abundance). In preparation for the 13C incorporation study the 13C NMR spectrum of streptovaricin C was investigated, making extensive use of short- and long-range HETCOR. These assignments revise some of those proposed earlier for streptovaricin C.
Abstract 098: Foxp3+ T Regulatory Lymphocytes Counteract Angiotensin Ii-induced Vascular Injury (2014)

Objective: T effector lymphocytes contribute to vascular injury in angiotensin (Ang) II-induced hypertension, but the role of T regulatory lymphocytes (Tregs) is unclear. Ang II-induced hypertension is blunted in T and B lymphocyte-deficient (Rag1-/-) mice, and restored with reconstitution of T cells. We hypothesized that adoptive transfer of FOXP3-deficient Scurfy (Sf) vs. wild-type (WT) T cells will exacerbate Ang II-induced vascular damage in Rag1-/- mice. Methods: Eleven-week old male Rag1-/- mice were injected IV with vehicle, 10 million WT or Sf T cells, 1 million CD4+CD25+ Tregs alone or with Sf T cells, and 2 weeks later were infused or not with Ang II (490 ng/kg/min, SC) for 14 days (n=3-8). Telemetric BP, vascular function and structure, and reactive oxygen species (ROS) production and fibronectin expression in mesenteric arteries (MA) were determined. Results: Ang II induced a 40 mmHg systolic BP rise in all the groups, but diastolic BP rise was ~10 mmHg greater in WT and Sf T cell-injected mice than in controls (P<0.01). Treg injection alone or with Sf T cells prevented or delayed by 7 days the BP rise, respectively (P<0.05). Ang II did not induce endothelial dysfunction in vehicle or Treg only-injected mice. Adoptive transfer of WT T cells restored Ang II induced-endothelial dysfunction (60±5% vs. 83±4%, P<0.05), which was exaggerated in Sf T cell-injected mice (56±6% vs. 97±7%, P<0.01), but reduced by Treg co-injection (74±4%, P<0.05). Ang II increased ROS production in MA wall (239±32% vs. 119±20%) and perivascular fat (369±39% vs. 84±8%) in Sf T cell-injected mice (P<0.01), but not when co-injected with Tregs. Ang II induced increased vascular stiffness (P<0.01) and media/lumen (M/L, P<0.05) in vehicle (strain at 140 mmHg: 0.60±0.02 vs. 0.80±0.02; M/L: 4.1±0.2 vs. 2.9±0.2%) and Sf T cell-injected mice (strain at 140 mmHg: 0.63±0.01 vs. 0.89±0.04; M/L: 4.7±0.3 vs. 2.9±0.1%). Ang II increased MA fibronectin expression (P<0.01) in vehicle (113±12 vs. 51±14 RFU/μm2) and Sf T cell-injected mice (85±7 vs. 36±9 RFU/μm2). Conclusion: These results demonstrate that Foxp3+ Tregs have a protective role against Ang II-induced vascular dysfunction, remodeling and oxidative stress.
Role of 5-hydroxytryptamine in platelet thrombus formation and mechanisms of inhibition of thrombus formation by 5-hydroxytryptamine2A antagonists in rabbits. (1997)

The role of 5-hydroxytryptamine (5-HT) in platelet thrombus formation and in the mechanisms of inhibition of thrombus formation by 5-HT2A antagonists was investigated using a turbidimetric method. Collagen-induced platelet aggregation occurred simultaneously with a release of 5-HT from the platelets. The supernatant of collagen-aggregated platelets induced a further aggregation volume-dependently. This supernatant-induced aggregation was inhibited by either 5-HT2A antagonists or adenosine-diphosphate (ADP) scavenging. 5-Hydroxytryptamine and a small amount of the supernatant shifted the dose-response curves of collagen to the left. The aggregation velocity and the onset of aggregation by collagen were significantly increased by the supernatant, but not by 5-HT. The 5-HT2A antagonists, ketanserin and MCI-9042, returned the dose-response curves of the maximum aggregation and of the aggregation velocity of collagen, which were already amplified by the supernatant, to the original values. The onset of aggregation was delayed by the antagonists, but was not completely returned to the original points. There were distinct differences between the effects of endogenous 5-HT, derived from platelets which were stimulated by collagen, and those of exogenous 5-HT on both extensive platelet activation and amplification of the collagen-induced aggregation. These findings suggest that endogenous 5-HT activates platelets in synergism with ADP. The 5-HT2A antagonists used, block the synergism via 5-HT2A receptors and lead to inhibition of a positive feedback loop of thrombus formation.
Integrin Gene Targeting (2003)

Gene ablation, also known as knockout, is a powerful method to analyze gene function in vivo. Many integrin genes have been disrupted already, confirming but also contradicting previous results (). In addition, new functions have been revealed, significantly increasing our understanding of the biological roles of integrins. Knockout of the remaining integrins will similarly elucidate their function during development. In addition, knockins of subtle mutations (,) and conditional knockouts (,), resulting in tissue-specific or temporally restricted gene ablation, will allow us to assess structure-function relationships of integrins in vivo and to investigate the function of integrins in a specific cell type at a specific time point in development.
EXPERIENCE WITH PROTOCOL BIOPSIES AFTER SOLITARY PANCREAS TRANSPLANTATION1 (1995)

The early detection of allograft rejection remains elusive after solitary pancreas transplantation (PTX). We have previously described a modified technique of cystoscopic transduodenal PTX biopsy using the Biopty gun under ultrasound guidance. During the last 2 years, we performed 24 solitary PTXs with prospective protocol biopsy monitoring as well as biopsies performed whenever clinically indicated. The study group included 17 pancreas transplants alone, 6 sequential pancreas after kidney transplants, and 1 sequential pancreas after liver transplant. Five patients received pancreas retransplants. A total of 92 cystoscopically directed core PTX biopsies were performed, including 50 protocol biopsies (mean 2.1 per patient). Protocol biopsies were performed at 1 month (19), 2 months (3), 3 months (20), 6 months (7), and 12 months (1) after PTX. Adequate PTX tissue for histopathologic examination was obtained in 49 cases (98%). Biopsy findings included no rejection (34), mild rejection (13), pancreatitis (1), and cytomegalovirus infection (1). Overall, 15 of the 49 evaluable biopsies (31%) had significant histopathologic findings. All but 1 of the cases of mild rejection were treated with bolus steroids. Eight of these patients subsequently developed recurrent biopsy-proven rejection within 2 months; 5 grafts were subsequently lost to rejection between 3 and 13 months after PTX. Three biopsy complications occurred: 1 hematoma, 1 pancreatitis, and 1 ileus. Patient survival is 96% and PTX graft survival (complete insulin independence) is 75% after a mean follow-up of 15 months. In the remaining 42 clinically indicated biopsies, 3 were insufficient, 8 showed no rejection, and 31 (79%) had rejection. In half of these cases, the rejection was graded as moderate to severe. In conclusion, prospective monitoring with protocol PTX biopsies may result in the earlier detection of allograft rejection and have a direct effect on improving results after solitary PTX.
PatientService: electronic patient record redaction and delivery in pervasive environments (2004)

E-healthcare today is moving away from the tethered domain and becoming diffused into an environment rich with portable digital devices. In this evolving environment, the need to deliver information such as electronic patient records at the point-of-care is a prime factor in managing the healthcare system efficiently. This however presents serious security challenges in pervasive environments such as wirelessly-connected hospitals; where protecting the confidentiality of the information, while at the same time allowing authorized user to access it conveniently is the core issue in the paradigm. We describe the security challenges in pervasive computing environments, and explain why traditional security mechanisms fail to meet the demands of these environments. We use an architecture that incorporates policy based security and distributed trust management to provide a highly flexible approach for accessing electronic patient records that are electronically reacted depending on the users digital credentials. We then present a prototype of the system using a variety of portable devices with wireless technology and include the policy used to test the system.
Predicting bug inducing source code change patterns (2016)

A change in source code without the prior analysis of its impact may generate one or more defects. Fixing of such defects consumes maintenance time which ultimately increases the cost of software maintenance. Therefore, in the recent years, several research works have been done to develop techniques for the automatic impact analysis of changes in source code. In this paper, we propose to use Frequent Pattern Mining (FPM) technique of machine learning for the automatic impact analysis of those changes in source code which may induce bugs. Therefore, to find patterns associated with some specific types of software changes, we applied FPM's algorithms' Apriori and Predictive Apriori on the stored data of software changes of the following three Open-Source Software (OSS) projects: Mozilla, GNOME, and Eclipse. We grouped the data of software changes into two major categories: changes to meet bug fixing requirements and changes to meet requirements other than bug fixing. In the case of bug fixing requirements, we predict source files which are frequently changed together to fix any one of the following four types of bugs related to: memory (MEMORY), variables locking (LOCK), system (SYSTEM) and graphical user interface (UI). Our experimental results predict several interesting software change patterns which may induce bugs. The obtained bug inducing patterns have high confidence and accuracy value i.e., more than 90%.
The contribution of common CYP2A6 alleles to variation in nicotine metabolism among European–Americans (2011)

Among European-Americans, seven polymorphisms in the CYP2A6 gene explain the majority of variability in the metabolism of nicotine to cotinine after oral administration. Parameters determined from this in-vivo experiment can be used to predict nicotine metabolism based on CYP2A6 genotype.
Accumulation of electric-field-stabilized geminate polaron pairs in an organic semiconductor to attain high excitation density under low intensity pumping (2006)

The recombination dynamics of geminate polaron pair (PP) states are investigated by monitoring electric-field-induced delayed fluorescence in thin films consisting of the green laser dye, Coumarin-6 (C6) doped at 1wt% into 4,4′-bis(N-carbazolyl)biphenyl. We find that the PP decay follows τ−m (with m∼0.1), where τ is the time that the PPs are held in the field. This sublinear decay suggests the possibility for accumulation of PPs over time that can then be reconverted into excitons upon field removal. We demonstrate the generation of short (∼50ns full width at half maximum) bursts of C6 fluorescence with peak intensities &gt;20 times the steady-state fluorescence intensity (corresponding to a C6 singlet exciton density NS&gt;4×1015cm3) when pumped continuously by a low intensity (&lt;1W∕cm2) laser in the presence of a pulsed electric field.
Identification of time-varying biological systems from ensemble data (joint dynamics application) (1992)

The theory underlying a new method for the identification of time-varying systems is described. The method uses singular value decomposition to obtain least-squares estimates of time-varying impulse response functions from an ensemble of input-output realizations. No a priori assumptions regarding the system structure or form of the time-variation are required and there are few restrictions on the input signal. Simulation studies, using a model of time-varying joint dynamics, show that the method can track rapid changes in system dynamics accurately and is robust in the presence of output noise. An application of the method is demonstrated by using it to track dynamic ankle stiffness during a rapid, voluntary, isometric contraction. During the transient phase of the contraction, low-frequency ankle stiffness gain decreased in a manner which could not be described with the second-order model of joint dynamics often used under stationary conditions.
Second Generation Antimigraine S-Ht1BID Agonists: Structure Activity Relationship and Preclinical Pharmacological Distinctions (1997)

The discovery and development of the 5-HT1810 agonist sumatriptan for alleviating migraine pain has been an important advance in the field of modern headache treatment and research. This important therapeutic advance is not without it's shortcomings. When administered orally, it is poorly absorbed with clinically relevant headache relief occurring at least two hours after drug administration. Due to its agonist action at peripherovascular 5-HT1D-Iike receptors, it is contraindicated in patients with coronary artery disease. Furthermore, headache recurs within a 24 hour period in 40% of patients treated. Given the large unmet medical need, market size and sumatriptan's shortcomings, a number of second-generation agents have been developed which are structurally and pharmacologically similar to sumatriptan, but have improved oral pharmacokinetic profiles. These include zolmitriptan, naratriptan, rizatriptan, avitriptan, alniditan, eletriptan and BMS-181885, all of which have been shown to be clinically effective. In this review, the SAR of the second-generation triptans at the 5-HT 18 and 5-HT10 receptors as well as distinct pharmacological actions in novel animal models are discussed.
Tread Wear and Wet Skid Resistance of Butadiene-Styrene Elastomers and Blends (1971)

Abstract 1. Car, wheel position, driver, inflation pressure, and shoulder drop have a statistically significant effect upon wear loss and need to bo taken into consideration before material factors affecting wear can be studied. 2. Variations in macrostructure of the polymers are not found to have a significant effect on wear as compared to microstructure variations. 3. At least two material factors control wear loss of tire treads. 4. When polymers are tested near their glass transition temperature (within 80° C), wear loss is dominated by viscoelastic properties. Viscoelastic properties can be related to wear loss through T g or the combined effect of the cis, trans , vinyl, and styrene content. 5. At higher test temperatures (over 100° C above T g ) wear loss is dominated by a material factor that has a positive correlation with temperature. This is particularly noticeable when treads are worn under mild conditions. However, there is evidence that this wear factor is present at the testing nearer to T g but is masked by the dominant viscoelastic effect. 6. The combined effect upon wear of the different material factors leads to an optimum wear resistance for any polymer in the butadiene—styrene system in the range of 75°–105° C above the T g for that polymer. 7. For polymers tested at the same ambient temperature, ( T ), the effect of viscoelastic properties decreases non-linearly as T−T g increases. 8. In the range of test severity studied, severity has little effect upon the inter-relationship of material factors. 9. In the range of test temperature where T g dominates wear loss, skid distance on wet asphalt pavement is inversely related to wear rating.