gebhart/patrepeval huggingface dataset:
First principles multielectron mixed quantum/classical simulations in the condensed phase. II. The charge-transfer-to-solvent states of sodium anions in liquid tetrahydrofuran (2010)

Gas-phase atomic anions lack bound electronic excited states, yet in solution many of these anions exhibit intense absorption bands due to the presence of excited states, referred to as charge-transfer-to-solvent (CTTS) states that are bound only by the presence of the solvent. CTTS spectra thus serve as delicate probes of solute-solvent interactions, but the fact that they are created by the interactions of a solute with many solvent molecules makes them a challenge to describe theoretically. In this paper, we use mixed quantum/classical molecular dynamics with the two-electron Fourier-grid (2EFG) electronic structure method presented in the previous paper [W. J. Glover, R. E. Larsen, and B. J. Schwartz, J. Chem. Phys. 132, 144101 (2010)] to simulate the CTTS states of a sodium anion in liquid tetrahydrofuran, Na(-)/THF. Since our 2EFG method is based on configuration interaction with single and double excitations in a grid basis, it allows for an exact treatment of the two valence electrons of the sodium anion. To simulate Na(-)/THF, we first develop a new electron-THF pseudopotential, and we verify the accuracy of this potential by reproducing the experimental absorption spectrum of an excess electron in liquid THF with near quantitative accuracy. We also are able to reproduce the CTTS spectrum of Na(-)/THF and find that the CTTS states of Na(-) exhibit a Rydberg-like progression due to the pre-existing long-range solvent polarization around the anion. We also find that the CTTS states are highly mixed with the disjoint electronic states supported by naturally occurring solvent cavities that exist in liquid THF. This mixing explains why the solvated electrons that are ejected following CTTS excitation appear with their equilibrium absorption spectrum. The mixing of the CTTS and solvent-cavity states also explains why the recombination of the electron and its geminate Na(0) partner occurs on slower time scales when photoexciting in the blue compared to in the red of the CTTS band: blue excitation accesses CTTS states whose charge densities lies further from the position of the anion, whereas red excitation accesses CTTS states that lie primarily within the anion's first solvation shell. Finally, we see that the radial character of the CTTS states near the Na(+) core matches that of Na(0), explaining why the spectrum of this species appears instantly after photoexciting Na(-).
Hypoxia inducible factors regulate infectious SARS-CoV-2, epithelial damage and respiratory symptoms in a hamster COVID-19 model (2022)

ABSTRACT Understanding the host pathways that define susceptibility to SARS-CoV-2 infection and disease are essential for the design of new therapies. Oxygen levels in the microenvironment define the transcriptional landscape, however the influence of hypoxia on virus replication and disease in animal models is not well understood. In this study, we identify a role for the hypoxic inducible factor (HIF) signalling axis to inhibit SARS-CoV-2 infection, epithelial damage and respiratory symptoms in Syrian hamsters. Pharmacological activation of HIF with the prolyl-hydroxylase inhibitor FG-4592 significantly reduced the levels of infectious virus in the upper and lower respiratory tract. Nasal and lung epithelia showed a reduction in SARS-CoV-2 RNA and nucleocapsid expression in treated animals. Transcriptomic and pathological analysis showed reduced epithelial damage and increased expression of ciliated cells. Our study provides new insights on the intrinsic antiviral properties of the HIF signalling pathway in SARS-CoV-2 replication that may be applicable to other respiratory pathogens and identifies new therapeutic opportunities.
Atomic Oxygen Resistant Polysiloxane Coatings for Low Earth Orbit Space Structures (2015)

Polysiloxane resin copolymer was synthesized through acid catalyzed hydrolysis of methyl triethoxysilane (MTEOS) and diethoxytetramethyldisiloxane (DEOTMDS). The effect of reaction time on the properties of the polymer was studied and this copolymer was characterized by GPC, 29 Si NMR, IR, TGA, viscosity, refractive index, specific gravity and solid content. 29 Si NMR and IR showed characteristic signals of Si-O-Si linkage which confirmed the formation of the polymer. GPC and solid content analysis showed an increasing trend in molecular weight with reaction time. Thermo gravimetric analysis showed that the polymer was thermally stable upto ≈ 260°C and all the polymers gave a ceramic residue in the range of 77-80% at 900°C. Siloxane prepared inhouse and methyl phenyl silsequioxane (control) were used as coating materials and atomic oxygen (AO) resistance was evaluated on Al-Kapton, carbon polyimide composite and glass polyimide composite. The mass loss and surface morphology of the coated samples were measured at different time intervals. It is observed that mass loss of polysiloxane coated samples was very less, compared to coated control samples. The morphology of all the samples were studied using FESEM. Erosion kinetics and surface morphology investigation indicate that the polysiloxane coating possesses excellent AO resistance, and displays better cracking resistance on AO exposure.
Interaction between Warfarin and Trazodone (2000)

The use of trazodone on an as-needed basis for sleep is strongly discouraged in patients who are receiving warfarin, due to the difficulty of achieving a therapeutic PT and INR. Until more is known, patients and clinicians should be educated about this potential interaction and monitor for changes in the anticoagulant effects when trazodone is initiated or stopped.
The automation of controlled vocabulary subject indexing of medical journal articles (2000)

This article discusses the possibility of the automation of sophisticated subject indexing of medical journal articles. Approaches to subject descriptor assignment in information retrieval research are usually either based upon the manual descriptors in the database or generation of search parameters from the text of the article. The principles of the Medline indexing system are described, followed by a summary of a pilot project, based upon the Amed database. The results suggest that a more extended study, based upon Medline, should encompass various components: Extraction of ‘concept strings’ from titles and abstracts of records, based upon linguistic features characteristic of medical literature. Use of the Unified Medical Language System (UMLS) for identification of controlled vocabulary descriptors. Coordination of descriptors, utilising features of the Medline indexing system. The emphasis should be on system manipulation of data, based upon input, available resources and specifically designed rules.
Abstract 12079: Genetic Susceptibility to Atrial Fibrillation is Associated With Left Atrial Electrical Remodeling and Adverse Post-ablation Outcome (2019)

Background: Genome-wide association studies have identified a highly significant locus for AF on chromosome 4q25. However, the disease-associated phenotype remains unknown. Methods: We prospectivel...
Velocity field of a lifting rotor blade in hover (1988)

The authors gratefully acknowledge the support of this work
by the U.S. Army Research Office as part of the Center for
Rotary Wing Aircraft Technology, Contract DAAG29-82-K-
0094, monitored by Dr. Robert E. Singleton.
Use of Coronary Calcification Scores to Predict Coronary Heart Disease (2004)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA HomeNew OnlineCurrent IssueFor Authors Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA journal
Pseudidiomarina maritima Wu et al. 2009 is a later heterotypic synonym of Pseudidiomarina tainanensis Jean et al. 2009 and emended description of the species (2019)

A comparative analysis of the two type strains of <i>Pseudidiomarina maritima</i> 908087<sup>T</sup> and <i>Pseudidiomarina tainanensis</i> PIN1<sup>T</sup> was performed to examine their taxonomic relationship. The 16S rRNA gene sequence of <i>P. maritima</i> 908087<sup>T</sup> shared a high similarity (99.8 %) with that of <i>P. tainanensis</i> PIN1<sup>T</sup>. The phylogenetic trees based on 16S rRNA gene sequences indicated that the two strains formed a tight cluster within the genus <i>Pseudidiomarina</i>. Whole genomic comparison between the two strains revealed a digital DNA-DNA hybridization estimate of 75.8 % and an average nucleotide identity value of 97.3 %, strongly indicating that they represented a single species. In addition, the strains did not display any striking differences in their metabolic, physiological or chemotaxonomic features. Therefore, we propose that <i>Pseudidiomarina maritima</i> is a later heterotypic synonym of <i>Pseudidiomarina tainanensis</i>.
Mycoplanecins, novel antimycobacterial antibiotics from Actinoplanes awajinensis subsp. mycoplanecinus subsp. nov.. II. Isolation, physico-chemical characterization and biological activities of mycoplanecin A. (1983)

New antibiotics, mycoplanecins, were found in the culture broth of an actinomycete identified as Actinoplanes awajinensis subsp. mycoplanecinus subsp. nov. Mycoplanecin complex was extracted with organic solvents both from the culture filtrate and mycelium and purified by column chromatography on silica gel and Florisil. Mycoplanecin A, a major component, was separated by high performance liquid chromatography on Prep PAK-500/C18 column. The physico-chemical characterization revealed that mycoplanecin A was a new cyclic peptide antibiotic. Mycoplanecins exhibited strong activities primarily against mycobacteria and related microorganisms.
Oligonucleotide−RGD Peptide Conjugates for Surface Modification of Titanium Implants and Improvement of Osteoblast Adhesion (2009)

A new concept for modular biosurface engineering of titanium implants based on the self-assembly of complementary oligonucleotides was biochemically investigated and optimized. This study describes the synthesis and characterization (RP-HPLC and Sakaguchi assay) of oligodeoxyribonucleotide (ODN) conjugates of the hexapeptide GRGDSP containing the RGD sequence as the recognition motif for cellular adhesion receptors (integrins). The peptide was chosen exemplarily as a model molecule, because it is a simple but potent bioactive molecule and relatively well investigated. The conjugation products must fulfill two main requirements: (I) the ability to hybridize and (II) the preservation of biological activity of the RGD peptide for the enhancement of osteoblast adhesion. In the following text, the term "hybridization" is generally used for Watson-Crick base pairing. The ability of the conjugates to hybridize to surface-immobilized complementary ODN was verified by competitive hybridization with radiolabeled ((32)P) complementary strands and by hybridization experiments using a quartz crystal microbalance (QCM). Surface hybridization was further characterized using different adsorption isotherms (e.g., Freundlich and Frumkin types), since the type of isotherm and the derived thermodynamic parameters may reveal characteristic differences between ODN and conjugates thereof. Biological activity of the conjugates was examined in vitro with osteoblasts. The cells were either cultured directly on the ODN-GRGDSP modified titanium implants or used for competition adhesion studies with dissolved ODN-GRGDSP conjugates. All results support the successful establishment of the new surface modification system. Hybridization of RGD peptide-modified nucleic acids to ODN-modified titanium implant materials is thus a promising method for osteoblast attachment in a modular and self-organizing system on implant surfaces.
Diagnosis and Successful Management of an Unusual Presentation of Chronic Foot Pain Using Positron Emission Tomography/Magnetic Resonance Imaging and a Simple Surgical Procedure (2019)

A 61-year-old man presented with chronic dorsal foot pain of 9 years that worsened with ambulation. Conventional diagnostic imaging and medical workup were unrevealing, and ankle arthrodesis had been recommended by an orthopedic surgeon for pain relief. Instead, the patient participated in a clinical imaging trial designed for identifying pain generators using whole-body fluorodeoxyglucose (18F-FDG) positron emission tomography/magnetic resonance imaging (PET/MRI). The scan revealed not only high 18F-FDG uptake at the site of pain, but also a hematoma and an inflamed, fibrotic, ruptured plantaris muscle. The fibrotic plantaris likely altered biomechanics with walking, explaining why symptoms worsened with activity. A simple tenotomy of the plantaris tendon was performed to decouple ankle movement from the plantaris injury, resulting in pain relief. This case illustrates the potential of whole-body 18F-FDG PET/MRI to better localize pain generators.
Routine tumor next-generation sequencing (NGS) to identify rare germline lung cancer risk mutations in EGFR and ERBB2. (2017)

1513 Background: New insights into lung cancer genomics has required a new look at genetic determinants of inherited lung cancer risk. There are now four germline mutations in lung cancer oncogenes (EGFR T790M, V843I, R776H; and ERBB2 G660D) which have been reported in kindreds with a high prevalence of lung cancer in nonsmokers. We hypothesized that routine tumor NGS could be used to find rare kindreds with inherited lung cancer risk. Methods: An institute-wide database of tumor NGS results was queried for cases positive for one of the reported germline risk alleles in EGFR or ERBB2. At our center, tumor NGS is performed using a hybrid-capture platform spanning exons and key introns of ~400 cancer related genes, and is available for patients (pts) with consent to a research protocol. For living pts with a mutation detected at an allelic fraction (AF) &gt; 25%, and excluding acquired T790M, genetic counseling and CLIA germline testing was provided. For pts with EGFR T790M, testing was performed on the INHERIT EGFR study (NCT01754025; ALCMI). Results: 51 cases were identified from a total of 13,488 cancers with NGS results: 45 with EGFR T790M (all lung cancer), 4 with EGFR R776H (NSCLC, endometrial cancer, and 2 glioma), 2 with ERBB2 G660D (NSCLC and glioblastoma). 34 pts with T790M detected after EGFR inhibitor were excluded, leaving 17 pts of interest. Germline testing was performed on 9 living pts with &gt; 25% AF on NGS, and was positive in 8; 6 of these had germline EGFR T790M. Additionally, germline EGFR R776H was found in a never-smoker with metastatic endometrial cancer; she had a prior a history of NSCLC, and family history was notable for multiple members with lung, breast, and colon cancer. Germline ERBB2 G660D was found in a young never-smoker with metastatic NSCLC and a family history significant for lung cancer in multiple first-degree relatives. Conclusions: Rare germline lung cancer risk mutations in EGFR and ERBB2 can be identified on routine tumor NGS, and may indicate a risk of inherited lung cancer. Our study includes the second known report of a germline EGFR R776H or ERBB2 G660D mutations. Commercial germline NGS assays could be expanded to cover these rare but potentially high-penetrance variants.
Involvement of Neuropeptides in the Allergic Nasal Obstruction in Guinea Pigs (2001)

The purposes of the present study were i) to determine whether neuropeptides induce the nasal obstruction in guinea pigs, and ii) to examine the possible involvement of neuropeptides in allergic nasal obstruction. The decrease in nasal cavity volume was determined by acoustic rhinometry as an index of nasal obstruction. In non-sensitized guinea pigs, substance P (SP), neurokinin A (NKA) and calcitonin gene-related peptide (CGRP) caused the nasal obstruction 10 to 30 min after their intranasal application. LY303870 (1 mg/kg), a tachykinin NK1-receptor antagonist; SR48968 (1 mg/kg), a tackykinin NK2-receptor antagonist; and CGRP(8-37) (50 nmol/kg), a CGRP1-receptor antagonist, administered intravenously before the intranasal application of the neuropeptides, inhibited the responses induced by SP, NKA and CGRP, respectively. In the guinea pigs sensitized with dinitrophenyl-coupled Ascaris suum allergenic extract, the intranasal antigen challenge caused nasal obstruction. The response was biphasic and consisted of the early phase response (EPR) and the late phase response (LPR), which developed 30 min and 6 h, respectively, after the antigen challenge. Intravenous administration of LY303870 (1 mg/kg) before the antigen challenge inhibited the EPR, while those of SR48968 (1 mg/kg) and CGRP(8-37) (50 nmol/kg) inhibited the LPR. The present results suggest that neuropeptides are involved in the allergic nasal obstruction.
Synthesis and characterization of novel symmetrical two-photon chromophores derived from bis(triphenylaminotetrathienoacenyl) and fused-thiophene units (2015)

Four new donor–π–donor (D–π<sub>1</sub>–π<sub>2</sub>–π<sub>1</sub>–D) fused-thiophene-based chromophores, end-functionalized with electron-donating triphenylamine (TPA) groups, were developed and characterized for a two-photon absorption study.
Reg family proteins contribute to inflammation and pancreatic stellate cells activation in chronic pancreatitis (2023)

Chronic pancreatitis (CP) is a disease characterized by the inflammation and destruction of pancreatic tissue, leading to the replacement of functional tissue with fibrotic tissue. The regenerating gene (Reg) family proteins have recently been implicated in the repair and regeneration of inflamed pancreatic tissue, though the exact mechanisms of their involvement in the pathogenesis of CP are not yet fully understood. To investigate the role of Reg family proteins in CP, we generated global knockout mice (Reg<sup>-/-</sup>) for Reg1-3 (Reg1,2,3a,3b,3d,3g) genes using the CRISPR/Cas9 system. We then investigated the effect of Reg family protein deficiency in a genetic model of CP (X-SPINK1) mice by knocking out Reg1-3 genes. We examined pancreatic morphology, inflammatory cytokines expression, and activation of pancreatic stellate cells (PSCs) at different ages. Reg<sup>-/-</sup> mice showed no abnormalities in general growth and pancreas development. Deficiency of Reg1-3 in CP mice led to a reduction in pancreatic parenchymal loss, decreased deposition of collagen, and reduced expression of proinflammatory cytokines. Additionally, Reg proteins were found to stimulate PSCs activation. Overall, our study suggests that Reg1-3 deficiency can lead to the remission of CP and Reg family proteins could be a potential therapeutic target for the treatment of CP.
Combined trisomy 9 and Ullrich-Turner syndrome in a girl with a 46,X,der(9)t(X;9)(q12;q32) karyotype (1998)

Total trisomy 9 is a rare disorder with most patients dying before age 4 months. Herein, we report a 9-year-old girl with mental retardation, short stature, a peculiar face and other minor defects, who was diagnosed as having an unbalanced de novo X-autosome translocation with a 46,X,der(9)t(X;9) (q12;q32) karyotype resulting in almost a full trisomy 9(pter→q32) and a partial monosomy X(q12→pter). The clinical findings of our patient, almost exclusively resemble those of trisomy 9p and the Ullrich-Turner syndromes and has few manifestations of 9q trisomy. BrdU replication studies by Giemsa staining showed an earlier replication of 9p in the translocated chromosome, but a marked late-replication pattern for almost the complete 9q arm involved in the translocation. FISH studies confirmed the presence of three 9 centromeres, excluded the presence of the X centromere signal in the rearranged chromosome, and showed that both Xq telomeric sequences were present. BrdU replication studies by FISH showed an usual pattern of striking late-replication around the XIC of the derivative chromosome, but early replication of the chromosome 9p segment and distal Xq. Am. J. Med. Genet. 80:199–203, 1998. © 1998 Wiley-Liss, Inc.
Parallel unsymmetric-pattern multifrontal sparse LU with column preordering (2008)

We present a new parallel sparse LU factorization algorithm and code. The algorithm uses a column-preordering partial-pivoting unsymmetric-pattern multifrontal approach. Our baseline sequential algorithm is based on UMFPACK 4, but is somewhat simpler and is often somewhat faster than UMFPACK version 4.0. Our parallel algorithm is designed for shared-memory machines with a small or moderate number of processors (we tested it on up to 32 processors). We experimentally compare our algorithm with SuperLU_MT, an existing shared-memory sparse LU factorization with partial pivoting. SuperLU_MT scales better than our new algorithm, but our algorithm is more reliable and is usually faster. More specifically, on matrices that are costly to factor, our algorithm is usually faster on up to 4 processors, and is usually faster on 8 and 16. We were not able to run SuperLU_MT on 32. The main contribution of this article is showing that the column-preordering partial-pivoting unsymmetric-pattern multifrontal approach, developed as a sequential algorithm by Davis in several recent versions of UMFPACK, can be effectively parallelized.
Different ratios in 20 S proteasomes and regulatory subunit complexes in two isoforms of the 26 S proteasome purified from rabbit skeletal muscle (1993)

A ubiquitin/ATP-dependent proteinase complex (26 S proteasome) was highly purified from rabbit skeletal muscle. The purified 26 S proteasome easily dissociated into a 20 S proteasome and a regulatory subunit complex on non-denaturing PAGE. By using cleavable and non-cleavable cross-linkers, it was revealed that the 26 S proteasome exists in two isoforms: one (D complex) consists of the 20 S proteasome and the regulatory subunit complex in the ratio of one to two, while the other (C complex) exists in an equal molar ratio. Molecular masses of the former and the latter isoforms were estimated to be 1,700 kDa and 1,400 kDa, respectively, by gel filtration, and 2,400 kDa and 1,400 kDa, respectively, by Ferguson plot analysis. Furthermore, both isoforms efficiently hydrolyzed Suc-Leu-Leu-Val-Tyr-MCA and ubiquitin-conjugated [125I]lysozyme. These results suggest that the D and C complexes are active proteinase complexes, most probably corresponding to the dumbbell-like and mushroom-like (or space capsule-like) molecules, respectively.