gebhart/patrepeval huggingface dataset:
Comparative study of generalized Born models: Protein dynamics (2005)

In this work, we compare the results of molecular dynamics simulations involving the application of three generalized Born (GB) models to 10 different proteins. The three GB models, the Still, HCT, and modified analytical generalized Born models, were implemented in the computationally efficient gromacs package. The performance of each model was assessed from the backbone rms deviation from the native structure, the number of native hydrogen bonds retained in the simulation, and the experimental and calculated radius of gyration. Analysis of variance (ANOVA) was used to analyze the results of the simulations. The rms deviation measure was found to be unable to distinguish the quality of the results obtained with the three different GB models, whereas the number of native hydrogen bonds and radius of gyration yielded a statistically meaningful discrimination among models. Our results suggest that, of the three, modified analytical generalized Born yields the best agreement between calculated and experimentally derived structures. More generally, our study highlights the need both to evaluate the effects of different variables on the results of simulations and to verify that the results of molecular dynamics simulations are statistically meaningful.
Effects of HO-/MeO-PBDEs on Androgen Receptor: In Vitro Investigation and Helix 12-Involved MD Simulation (2013)

Hydroxylated and methoxylated polybrominated diphenyl ethers (HO-/MeO-PBDEs) have received increasing attention for their potential endocrine disrupting activities and widely environmental distribution. However, little information is available for the anti-androgenic activities, and the molecular mechanism of interactions with androgen receptor (AR) is not fully understood. In the present study, cell line assay and computational simulation were integrated to systematically explore the molecular mechanism of interactions between chemicals and AR. The metabolites with similar molecular structures exhibited different anti-androgenic activity while none of them showed androgenic activity. According to the multisystem molecular dynamics simulation, minute differences in the structure of ligands induced dramatic different conformational transition of AR-ligand binding domain (LBD). The Helix12 (H12) component of active ligands occupied AR-LBD could become stable, but this component continued to fluctuate in inactive ligands occupied AR-LBD. Settling time and reposition of H12 obtained in dynamics process are important factors governing anti-androgenic activities. The related settling times were characteristic of anti-androgenic potencies of the tested chemicals. Overall, in our study, the stable reposition of H12 is characterized as a computational mark for identifying AR antagonists from PBDE metabolites, or even other various environmental pollutants.
Patient management by telephone by child health associates and pediatric house officers (1974)

Log in or Register Subscribe to journalSubscribe Get new issue alertsGet alerts Enter your Email address: Wolters Kluwer Health may email you for journal alerts and information, but is committed to maintaining your privacy and will not share your personal information without your express consent. For more information, please refer to our Privacy Policy. Subscribe to eTOC Secondary Logo Journal Logo All Articles Images Videos Podcasts Blogs Advanced Search Toggle navigation Subscribe Register Login Articles & Issues Current IssuePrevious IssuesPublished Ahead-of-Print Collections Editorials of Laura Weiss Roberts, MD, MAAM Last PageCOVID-19 and Medical EducationAddressing Race and Racism in Medical EducationeBooksView All For Authors Submit a ManuscriptInformation for AuthorsLanguage Editing ServicesAuthor Permissions Journal Info About the JournalAbout the AAMCJournal MastheadSubmit a ManuscriptAdvertising InformationSubscription ServicesReprints and Back IssuesClassified AdsRights and PermissionsFor ReviewersFor MediaFor Trainees All Articles Images Videos Podcasts Blogs Advanced Search
Prevention of Venous Thromboembolism in Cancer Using Low-Molecular-Weight Heparins (1997)

Patients with cancer are at increased risk for venous and arterial thromboembolism and the principal interventions in such patients--surgical operation, chemotherapy or venous catheterization--heighten this risk. Thromboprophylaxis is indicated in cancer patients undergoing surgical operation and there is also evidence that thrombopropylaxis appears beneficial during chemotherapy, particularly for breast cancer, and possibly for ovarian and pancreatic carcinoma. Low-molecular-weight heparins (LMWHs) have shown promise as a thromboprophylactic agent in oncology patients, and offer significant benefits over standard heparin because of their improved safety profile and ease of use. There is emerging evidence that LMWHs may also favourably influence survival, possibly as a result of direct anti-tumour effects.
Sexual Dysfunction in Male Psychiatric Outpatients: Validity of the Massachusetts General Hospital Sexual Functioning Questionnaire (2001)

Sexual dysfunction is highly prevalent in psychiatric outpatients. The MGH is a valid clinical measure to determine sexual dysfunction.
Cobalt: Its chemistry, metallurgy and uses (Young, Roland S., ed.) (1961)

ADVERTISEMENT RETURN TO ISSUEPREVBook and Media Revie...Book and Media ReviewNEXTCobalt: Its chemistry, metallurgy and uses (Young, Roland S., ed.)John C. Bailar Jr.Cite this: J. Chem. Educ. 1961, 38, 7, A498Publication Date (Print):July 1, 1961Publication History Received3 August 2009Published online1 July 1961Published inissue 1 July 1961https://doi.org/10.1021/ed038pA498RIGHTS & PERMISSIONSArticle Views301Altmetric-Citations1LEARN 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 InReddit PDF (1 MB) Get e-Alerts Get e-Alerts
DNA–Metal Base Pairs (2007)

Recent developments show encouraging results for the use of DNA as a construction material for nanometer-sized objects. Today, however, DNA-based molecular nanoarchitectures are constructed with mainly unmodified or at best end-modified oligonucleotides, thus shifting the development of functionalized DNA structures into the limelight. One of most recent developments in this direction is the substitution of the canonical Watson-Crick base pairs by metal complexes. In this way "metal-base pairs" are created, which could potentially impart magnetic or conductive properties to DNA-based nanostructures. This review summarizes research which started almost 45 years ago with the investigation of how metal ions interact with unmodified DNA and which recently culminated in the development of artificial ligand-like nucleobases so far able to coordinate up to ten metal ions inside a single DNA duplex in a programmable fashion.
Signaling by lymphocyte function-associated antigen 1 (LFA-1) in B cells: enhanced antigen presentation after stimulation through LFA-1. (1992)

To examine the role of lymphocyte function-associated antigen 1 (LFA-1) expression on murine B cells as it pertains to their function in T cell activation, we carried out antigen-presentation assays in tissue culture wells coated with a purified, secreted form of the murine intercellular adhesion molecule 1 (ICAM-1). We observed a significant decrease in the concentration of antigen required to activate a T cell hybridoma and primary T cells in wells coated with ICAM-1. This effect was dependent on the amount of ICAM-1 used to coat the wells and was also observed in wells coated with anti-LFA-1-monoclonal antibodies and was blocked by soluble anti-LFA-1 antibodies. The effect on antigen dose was most pronounced in assays carried out with an ICAM-1-deficient mutant B lymphoma cell line, small resting primary B cells, and unfractionated primary B cells at low concentrations. No decrease in the antigen dose was observed if the B cells were chemically fixed or treated with ricin, or when antigen was presented by a HeLa cell line transfected with murine class II major histocompatibility complex (MHC) genes, indicating that the immobilized ICAM-1 was mediating its effect through B cell LFA-1, and that B cell protein synthesis was required. The enhancing effect was also observed if the B cells were prepulsed with antigen, indicating that improved uptake or processing of antigen, or increased class II MHC expression were unlikely mechanisms.
The 4-(<i>N</i>-Dichloroacetyl-<i>N</i>-methylamino)benzyloxymethyl Group for 2‘-Hydroxyl Protection of Ribonucleosides in the Solid-Phase Synthesis of Oligoribonucleotides (2008)

Emerging RNA-based technologies for controlling gene expression have triggered a high demand for synthetic oligoribonucleotides and have motivated the development of ribonucleoside phosphoramidites that would exhibit coupling kinetics and coupling efficiencies comparable to those of deoxyribonucleoside phosphoramidites. To fulfill these needs, the novel 4-(N-dichloroacetyl-N-methylamino)benzyloxymethyl group for 2'-hydroxyl protection of ribonucleoside phosphoramidites 9a-d has been implemented (Schemes 1 and 2). The solid-phase synthesis of AUCCGUAGCUAACGUCAUGG was then carried out employing 9a-d as 0.2 M solutions in dry MeCN and 5-benzylthio-1H-tetrazole as an activator. The coupling efficiency of 9a-d averaged 99% within a coupling time of 180 s. Following removal of all base-sensitive protecting groups, cleavage of the remaining 2'-[4-(N-methylamino)benzyl] acetals from the RNA oligonucleotide was effected in buffered 0.1 M AcOH (pH 3.8) within 30 min at 90 degrees C. RP-HPLC and PAGE analyses of the fully deprotected AUCCGUAGCUAACGUCAUGG were comparable to those of a commercial RNA oligonucleotide sharing an identical sequence. Enzymatic digestion of the RNA oligomer catalyzed by bovine spleen phosphodiesterase and bacterial alkaline phosphatase revealed no significant amounts of RNA fragments containing (2'-->5')-internucleotidic phosphodiester linkages or noteworthy nucleobase modifications.
Cellular distribution of phosphorothioate oligodeoxynucleotides in normal rodent tissues. (1997)

The distribution of intravenously injected phosphorothioate oligodeoxynucleotides (P = S ODN) was studied in vivo in rodent tissues using three histologic methods: immunohistochemistry with a monoclonal antibody that recognizes P = S ODN ISIS 2105; direct fluorescence microscopy of P = S ODN ISIS 2105 conjugated to rhodamine; and autoradiography of 14C-labeled P = S ODN ISIS 2302. All three methods gave the same pattern of oligonucleotide distribution, and the intensity of the histologic signal agreed with previously published pharmacokinetic data on the relative concentration of P = S ODN in different organs. Proximal tubule cells in the kidney and Kupffer and endothelial cells in the liver were among the most heavily labeled with P = S ODN at all doses and time-points. Connective tissues proper, such as the lamina propria and submucosa of the intestine and the dermis and subcutaneous layer of the skin, were also labeled, whereas the P = S ODN signal was weak or negative in epithelial and muscle cells in the skin and intestine. At 2 hours postinjection, P = S ODN were clearly detectable in the extracellular matrix in loose and dense connective tissues, although by 24 hours, the label was predominantly intracellular. Large, nucleated cells in red marrow, and the connective tissues around bone and skeletal muscle cells and lining the knee joint, were positive for oligonucleotide, whereas P = S ODN were not detected in erythrocytes, cartilage, compact bone, and skeletal muscle. In spleen, white pulp was negative for P = S ODN, whereas cells surrounding the sinusoids and nucleated cells in the red pulp were strongly positive for P = S ODN. Our results provide specific information on the tissue and cellular localization of P = S ODN within organs in vivo. The data presented will be used as a reference for studies of P = S ODN distribution in diseased tissues and the distribution of modified oligonucleotides. Furthermore, because our results indicate which cell types are likely to be affected by antisense oligonucleotides, they can be used to guide future in vivo applications of the technology.
Orchids : A review of uses in traditional medicine, its phytochemistry and pharmacology (2010)

Many of the epiphytic orchids are used as traditional medicine. Chemical components and pharmacology have been studied in recent 15 years. Medicinal orchids, in general, are not subjected to detailed pharmacological studies. A wide range of chemical compounds are presented including alkaloids, bibenzyl derivatives, flavonoids, phenanthrenes and terpenoids which have been isolated recently from this species. Extracts and metabolites of these plants, particularly those from flowers and leaves, possess useful pharmacological activities. Particular attention has been given to diuretic, anti-rheumatic, anti-inflammatory, anti-carcinogenic, hypoglycemic activities, antimicrobial, anticonvulsive, relaxation, neuroprotective, and antivirus, activities. A comprehensive account of chemical constituents and biological activities is presented and a critical appraisal of the ethnopharmacological issues is included in view of the many recent findings of importance of these orchids. A large number of orchids have been empirically used for treatment of different diseases, thus, several studies have been undertaken to provide scientific proof to justify the medicinal use of various plants in treatment of diseases. The aim of this review is to up-date and to present a comprehensive analysis of traditional and folklore uses, pharmacological reports and phyto-constituents isolated from the orchids family.

	 

	Key words: Orchids, medicinal plant, traditional uses, chemical constituents, biological activities.
Minimum Exponential Cost Allocation of Sure-Fit Tolerances (1975)

The least cost allocation of sure-fit machine tolerances for Speckhart’s exponential cost model is solved in closed form, without numerical iteration, as a geometric program with zero degrees of difficulty. The results show the importance of an exponential cost sensitivity parameter defined as the “characteristic tolerance”. The theoretical minimum cost can be determined without specifying the corresponding tolerances. Specific minimum cost tolerances can be computed later in closed form if potential cost savings are significant.
Antineutrophil antibody: a test for autoimmune primary sclerosing cholangitis in childhood? (1993)

The detection of an antineutrophil antibody which is highly sensitive and specific for adult primary sclerosing cholangitis using indirect immunoalkaline phosphatase has been previously described. In this study, the diagnostic potential of this method in childhood primary sclerosing cholangitis is described. A range of 72 blinded children's sera (36 boys), aged six months to 21 years (10 primary sclerosing cholangitis, eight autoimmune chronic active hepatitis, 10 alpha-1 antitrypsin deficiency, 12 extrahepatic bile duct atresia, 11 ulcerative colitis and 21 normal subjects) was assayed. Eight of the 10 primary sclerosing cholangitis patients were correctly identified. Three patients with chronic active hepatitis also showed the characteristic primary sclerosing cholangitis pattern of staining. No ulcerative colitis patients or any other patients showed this pattern of staining. All normal subjects were negative. As in adult primary sclerosing cholangitis, there is a specific antineutrophil antibody in childhood primary sclerosing cholangitis and this provides further evidence towards an autoimmune aetiology of this condition. The test may have diagnostic potential.
Minimum-dissipation transport enhancement by flow destabilization: Reynolds’ analogy revisited (1988)

A classical transport enhancement problem is concerned with increasing the heat transfer in a system while minimizing penalties associated with shear stress, pressure drop, and viscous dissipation. It is shown by Reynolds' analogy that viscous dissipation in a wide class of flows scales linearly with the Nusselt number and quadratically with the Reynolds number. It thus follows that transport enhancement optimization is equivalent to a problem in hydrodynamic stability theory; a more unstable flow will achieve the same Nusselt number at a lower Reynolds number, and therefore at a fraction of the dissipative cost. This transport-stability theory is illustrated in a numerical study of supercritical (unsteady) two-dimensional flow in an eddy-promoter channel comprising a plane channel with an infinite periodic array of cylindrical obstructions. It is shown that the addition of small cylinders to a plane channel results in stability modes that are little changed in form or frequency from plane-channel Tollmien-Schlichting waves. However, eddy-promoter flows are dramatically less stable than their plane-channel counterparts owing to cylinder-induced shear-layer instability (with critical Reynolds numbers on the order of hundreds rather than thousands), and thus these flows yield heat transfer rates commensurate with those of a plane-channel turbulent flow but at much lower Reynolds number. Small-cylinder supercritical eddy-promoter flows are shown to roughly preserve the convective-diffusive Reynolds analogy, and it thus follows from the transport-stability theory that eddy-promoter flows achieve the same heat transfer rates as plane-channel turbulent flows while incurring significantly less dissipation.
Increased expression of centrosomal α, γ‐tubulin in atypical ductal hyperplasia and carcinoma of the breast (2009)

Centrosomal abnormalities have been found in various cancer types. We sought to determine whether centrosomal dysfunctions occur in the atypical ductal hyperplasia (ADH)-carcinoma sequence of breast cancer. As alpha and gamma-tubulins are the structural components of centrosomes, we performed real time quantitative polymerase chain reaction (qPCR), in situ hybridization (ISH) and immunnohistochemistry (IHC) to determine the DNA copy levels, messenger RNA (mRNA) expression, and protein expression of alpha and gamma-tubulins respectively. Gamma-tubulin staining was used for the localization and quantification of centrosomes. We found that alpha-tubulin or gamma-tubulin mRNA was increasingly expressed from normal breast tissue (NBT) to ADH, ductal carcinoma in situ (DCIS), and infiltrative ductal carcinoma (IDC), respectively, with the highest expressions being found in DCIS. The expression profiles of alpha, gamma-tubulin proteins were concordant with that of mRNA, except that the highest expression was found in IDC. Similarly, DNA copies of alpha, gamma-tubulins showed a rising tendency, with the highest level for gamma-tubulin attained in IDC and that for alpha-tubulin was found in DCIS. However, there was no significant difference of alpha, gamma-tubulin DNA copy levels, mRNA expression, and protein expression between DCIS and IDC. Our results demonstrate that centrosomal aberrations may play key roles in the early stage of breast tumorogenesis. The malignant transformation sequence is probably attributable to the amplification of centrosomal DNA leading to mRNA and protein over-expression of these centrosomal proteins. Furthermore, determination of alpha, gamma-tubulins using combined qPCR with ISH may be useful in assisting the diagnosis of premalignant lesions of the breast.
Development of a photofragmentation laser-induced-fluorescence laser sensor for detection of 2,4,6-trinitrotoluene in soil and groundwater (1999)

Laser photofragmentation (PF) and subsequent nitric oxide (NO) laser-induced fluorescence (LIF) have been developed to measure the concentration of energetic materials (EM's), such as 2, 4, 6-trinitrotoluene (TNT), in soil and other media. Gas-phase EM's photodissociate, releasing NO(2), when exposed to laser radiation near 226 nm. Laser-excited NO(2) predissociates to form NO that gives an intense fluorescence when excited near 226 nm. The EM concentration is inferred from the intensity of the NO fluorescence. A PF-LIF laser-based sensor is being developed to be used with the U.S. Army Corps of Engineers' Waterways Experiment Station's cone penetrometer to measure in situ the concentration of subsurface TNT. Several factors that affect the PF-LIF signal waveforms, such as sample temperature, laser power, and heating time, were investigated. Also, effects on the PF-LIF signal of adding water and fertilizer to the TNT mixtures were studied. Decay times were determined by least-squares fitting of the exponential PF-LIF signal waveforms. The use of PF-LIF waveforms promises to enable diagnostics of the sample's characteristics that would otherwise not be possible in situ.
The Second Imperalist War (1940)

Journal Article The Second Imperialist War Get access * The Second Imperialist War. By Earl Browder. 1940. (New York : International Publishers. 8vo. viii + 309 pp. $2.75.) C. Waley Cohen C. Waley Cohen Search for other works by this author on: Oxford Academic Google Scholar International Affairs Review Supplement, Volume 19, Issue 3-4, December 1940, Pages 194–195, https://doi.org/10.2307/3025729 Published: 01 December 1940
Reduction of Synaptojanin 1 Ameliorates Synaptic and Behavioral Impairments in a Mouse Model of Alzheimer's Disease (2012)

Decades of research have correlated increased levels of amyloid-β peptide (Aβ) with neuropathological progression in Alzheimer's disease (AD) patients and transgenic models. Aβ precipitates synaptic and neuronal anomalies by perturbing intracellular signaling, which, in turn, may underlie cognitive impairment. Aβ also alters lipid metabolism, notably causing a deficiency of phosphatidylinositol 4,5-bisphosphate [PI(4,5)P(2)], a phospholipid that regulates critical neuronal functions. Haploinsufficiency of the gene encoding synaptojanin 1 (Synj1), a major PI(4,5)P(2) phosphatase in the brain, provided protection against PI(4,5)P(2) breakdown and electrophysiological deficits attributable to Aβ. Based on these data, we tested whether reduction of Synj1 could rescue cognitive deficits and Aβ-induced morphological alterations of synapses. We found that hemizygous deletion of Synj1 in the context of a mouse model expressing the Swedish mutant of amyloid precursor protein rescues deficits in learning and memory without affecting amyloid load. Synj1 heterozygosity also rescued PI(4,5)P(2) deficiency in a synaptosome-enriched fraction from the brain of Tg2576 mice. Genetic disruption of Synj1 attenuated Aβ oligomer-induced changes in dendritic spines of cultured hippocampal neurons, sparing mature spine classes, which corroborates the protective role for Synj1 reduction against Aβ insult at the synapse. These results indicate that Synj1 reduction ameliorates AD-associated behavioral and synaptic deficits, providing evidence that Synj1 and, more generally, phosphoinositide metabolism may be promising therapeutic targets. Our work expands on recent studies identifying lipid metabolism and lipid-modifying enzymes as targets of AD-associated synaptic and behavioral impairment.