gebhart/patrepeval huggingface dataset:
Conformational consequences of protein glycosylation: Preparation of O‐mannosyl serine and threonine building blocks, and their incorporation into glycopeptide sequences derived from α‐dystroglycan (2007)

With the goal to investigate the structural impact of O-mannosyl glycosylation on alpha-dystroglycan, a glycoprotein that has an important role in the extracellular organization of muscle, glycopeptides derived from its mucin-like sequence have been prepared by solid-phase peptide synthesis. Two approaches have been explored to obtain needed mannosylated serine and threonine building blocks. With the alpha-carboxyl group unprotected, and with tetraaceto-1-fluoro-alpha-D-mannose as the sugar donor, the desired alpha-O-mannosyl-Fmoc-Ser/Thr formed, along with mannosyl ester isomers and the species with mannose attached to both hydroxyl and carboxyl functions. Relevant mechanistic questions and stability issues were elucidated. Alternatively, building blocks were made with the alpha-carboxyl protected/activated as the pentafluorophenyl (Pfp) ester. Glycopeptides synthesized herein contained 5-9 residues, and featured one, two, and four consecutive Ser and/or Thr residues O-glycosylated with mannose. Circular dichroism (CD) spectra for Man-containing glycopeptides recorded in water show them to be not well ordered. For one of the alpha-dystroglycan-derived sequences, the comparative conformational consequences of glycosylation by either Man or GalNAc have been examined by CD and NMR, with both methods showing a more organized structure when GalNAc is present.
Agent-Free Super-Resolution High-Speed Photoacoustic Microscopy (2019)

Photoacoustic microscopy (PAM) based on the photoacoustic (PA) effect showed the ability of anatomical, functional, metabolic and pathological imaging of animals and humans in vivo. However, the developed PAM systems have not achieved a fast temporal resolution and a high spatial resolution due to physical constraints. To overcome this, microelectromechanical systems (MEMS) scanners have been used for fast scanning speed and super-resolution technologies have been applied for the high spatial resolution. However, the MEMS scanners have shown unstable scanning patterns, and the super-resolution methods have slowed down imaging and required an external contrast agent. Here, we report an agent-free super-resolution high-speed PAM based on a fast scanner (AF-SR-PAM) that overcomes both the spatial and temporal resolution limitations. The scanner was used to steer the optical beam and acoustic wave together, achieving a high signal-to-noise ratio and a B-mode image rate of 500 Hz. Furthermore, by applying our super-resolution method, unresolved micro-vessels in a conventional PAM system are separated in the PA images of AF-SR-PAM. This improvement enables the observation of microvasculature in animals in vivo.
S2099 Persistent Damage to the Gut Microbiome Following Messenger RNA SARS-CoV-2 Vaccine (2022)

Introduction: Messenger RNA vaccines for SARS-CoV-2 are widely distributed, yet their effect on the human gut microbiome, especially long-term up to one year, is unknown. The human gut microbiome is an essential determinant of human health. Genus Bifidobacteria decline is associated with inflammatory bowel disease, obesity, neurological disorders, C. diffícile infection and severe COVID-19.1,2,3 Case Description/Methods: We longitudinally recorded the relative abundance of genus Bifidobacteria in 4 subjects before receiving mRNA vaccine (Pfizer or Moderna), approximately one month after vaccine, and 6 to 9 months later. Additional SARS-CoV-2 vaccines were given during that period, totaling 2 to 3 doses. Samples were collected at the timepoints mentioned. There were no diet changes or new medication’s during the entire period and subjects were told to stay on the same regimen throughout the 6 months. Metagenomic next generation sequencing-based methods were applied to samples obtained from fecal collection. DNA was extracted, and the library prepped, enriched and sequenced on an Illumina Nextseq 550 system. Relative abundance of Bifidobacteria decreased after 1 month to in 3 of 4 subjects to: 38%, 258%, 49% and 90% of pre-vaccine levels. After 6-9 months, all Bifidobacteria relative abundance decreased to: 15%, 0%, 35%, and 60% of pre-vaccine levels. This study is IRB approved (Figure 1). Discussion: This is the first study to demonstrate a decrease in relative abundance of genus Bifidobacteria bacteria 6-9 months after SARS-CoV-2 vaccination. All subjects dropped below a 1% relative abundance. Although a small sample, these findings may suggest a potential mechanism for post-vaccination complications; however, no subjects in the study demonstrated significant complications. Gut dysbiosis post mRNA SARS-CoV-2 vaccines could potentially be a future indication for restoration of Bifidobacteria either orally or directly via fecal transplant.Figure 1.: Bifidobacteria relative abundance demonstrates a lasting decline after SARS-CoV-2 mRNA vaccination.
Abstract 10559: Causes of Early Mortality After Transvenous Lead Removal (2022)

Background: Recognition of the causes of early mortality after transvenous lead removal (TLR) is an essential step for the development of quality improvement programs. Objective: This study sought to determine the causes of early mortality after TLR and to further understand the circumstances surrounding death after TLR. Methods: We performed a retrospective analysis of all patients undergoing TLR from January 1, 2001, to January 1, 2021 at the Mayo Clinic (Rochester, Phoenix, and Jacksonville). Causes of death were identified through a detailed chart review of the electronic health record from within the Mayo Clinic system and outside records when available. The causes of death were further characterized based on whether it was related to the TLR procedure. Results: A total of 2,319 patients were included in the study. The overall 30-day all-cause mortality rate was 3%. Among all 30-day deaths, infection was the most common primary cause of death (42%). This was followed by decompensated heart failure (17%), procedure-related death (10%), sudden cardiac arrest (7%), and respiratory failure (6%). The 30-day mortality rate directly due to complications associated with the TLR procedure was 0.3% due to vascular tear and cardiac perforation. A third of deaths (33%) occurred after discharge from index hospitalization, among which 43% were readmitted before their death, 35% died at home or a nursing facility, and 22% were discharged on comfort care and died in hospice. The main reasons for readmission prior to death were sepsis and decompensated heart failure. Conclusions: The majority (90%) of 30-day mortality after TLR was not due to complications associated with TLR procedures. The primary causes were infection and decompensated heart failure. This highlights the importance of further research to reduce postoperative mortality from these factors, including deaths after hospital discharge.
Fitting of photoluminescence spectra for structural characterisation of high current density resonant tunnelling diodes for THz applications (2021)

High-resolution X-ray diffraction (HR-XRD), and low-temperature photoluminescence spectroscopy (LT-PL) are used to investigate the structural properties and inhomogeneities of high current density InGaAs/AlAs/InP resonant tunnelling diode (RTD) wafer structures. The non-destructive assessment of these structures is challenging, with structural variables: well and barriers thickness and the well indium molar fraction, in addition to electronic variables such as the band-offsets being functions of strain, growth sequence, etc.. Experimental PL data are compared with simulations allowing the deconvolution of the PL spectra, that includes Type I and Type II transitions broadened by interface fluctuations on length scales smaller and much larger than the exciton. This method provides details of the non-uniformity of the epitaxial material nondestructively.
New pathways to heteroepitaxial GaN by inorganic CVD synthesis and characterization of related Ga-C-N novel systems (1997)

The authors describe the development of a new deposition method for thin oriented films of GaN on basal plane sapphire using an exclusively inorganic single-source precursor free of carbon and hydrogen, Cl{sub 2}GaN{sub 3}. The films have been characterized by Rutherford backscattering spectroscopy (RBS) and cross sectional transmission electron microscopy (TEM) for composition morphology and structure. RBS analysis confirmed stoichiometric GaN and TEM observations of the highly conformal films revealed heteroepitaxial columnar growth of crystalline wurtzite material on sapphire. Auger and RBS oxygen and carbon resonance profiles indicated that the films were pure and highly homogeneous. They also report the reactions of Cl{sub 2}GaN{sub 3} with organometallic nitrides to yield a crystalline, novel gallium carbon nitride of composition GaC{sub 3}N{sub 3}. Quantitative X-ray powder diffraction has been used to refine the cubic structure of this material which consists of Ga atoms octahedrally surrounded by on the average three C and three N atoms. The structurally analogous LiGaC{sub 4}N{sub 4} phase has also been prepared and characterized.
Dual Time Delay Digital Tanlock Loop with improved performance (2011)

A dual Time Delay Digital Tanlock Loop (D-TDTL) topology is proposed in this work. The system consists of a stacked dual loop of which the top one acts as a Frequency Lock loop (FLL) for the bottom loop, while the latter is a phase lock loop (PLL) that enhances the overall phase of the system. The main advantage of the proposed system is the large reduction of phase noise or jitter which makes it well suited to operate in noisy environment. The performance of the D-TDTL system was demonstrated using frequency shift keying (FSK) input signal with AWGN noise.
Universal stability and cost optimization in controlled queueing networks (2012)

The control of large queueing networks is a notoriously difficult problem. Recently, an interesting new policy design framework for the control problem called h-MaxWeight has been proposed: h-MaxWeight is a natural generalization of the famous MaxWeight policy where instead of the quadratic any other surrogate value function can be applied. Stability of the policy is then achieved through a perturbation technique. However, stability crucially depends on parameter choice which has to be adapted in simulations. In this paper we use a different perturbation technique where the required properties are much easier to implement. Specifically, we derive the theoretical fundamentals which guarantee universal stability while still operating `close' to the underlying cost criterion. Simulation examples suggest that the new approach to policy synthesis can provide significantly higher gains irrespective of any further assumptions on the network model or parameter choice.
Reclassification of Streptomyces fulvissimus as a later heterotypic synonym of Streptomyces microflavus (2020)

We investigated the taxonomic relationships among <i>Streptomyces fulvissimus</i>, <i>Streptomyces fulvorobeus</i> and <i>Streptomyces microflavus</i>. These type strains shared the same 16S rRNA gene sequence. Digital DNA-DNA relatedness and average nucleotide identity analyses using whole genome sequences suggested that <i>S. fulvissimus</i> and <i>S. microflavus</i> belong to the same genomospecies, whereas <i>S. fulvorobeus</i> does not. In addition to previously reported phenotypic data, the presence of almost the same set of secondary metabolite-biosynthetic gene clusters for polyketides and nonribosomal peptides also supported the synonymy between <i>S. fulvissimus</i> and <i>S. microflavus</i>. Therefore, <i>S. fulvissimus</i> should be reclassified as a later heterotypic synonym of <i>S. microflavus</i>.
The impact of commonly used approximations on the computation of the Seebeck coefficient and mobility of polar semiconductors (2012)

Seebeck coefficient modeling and measurement has important applications in direct thermal to electrical energy conversion and solid-state physics. The computations of the Seebeck coefficient and mobility of polar semiconductors in the literature often employ certain approximations, notably the relaxation time approximation (RTA) and the truncation of the Boltzmann transport equation. We study the accuracy of these approximations as a function of the effective mass, temperature, and carrier concentration using a recently developed technique for rigorous solution of the Boltzmann transport equation. We find that the approximations give rise to considerable error in the computed Seebeck coefficients of heavily doped semiconductors with a low effective mass, and that the RTA is entirely inapplicable for the accurate computation of the mobility of several important materials.
Photoacoustic image-guided needle biopsy of sentinel lymph nodes (2011)

We have implemented a hand-held photoacoustic and ultrasound probe for image-guided needle biopsy using a modified clinical ultrasound array system. Pulsed laser light was delivered via bifurcated optical fiber bundles integrated with the hand-held ultrasound probe. We photoacoustically guided needle insertion into rat sentinel lymph nodes (SLNs) following accumulation of indocyanine green (ICG). Strong photoacoustic image contrast of the needle was achieved. After intradermal injection of ICG in the left forepaw, deeply positioned SLNs (beneath 2-cm thick chicken breast) were easily indentified in vivo and in real time. Further, we confirmed ICG uptake in axillary lymph nodes with in vivo and ex vivo fluorescence imaging. These results demonstrate the clinical potential of this hand-held photoacoustic system for facile identification and needle biopsy of SLNs for cancer staging and metastasis detection in humans.
Cardiac Dysfunction and Noncardiac Dysfunction as Precursors of Heart Failure With Reduced and Preserved Ejection Fraction in the Community (2011)

Antecedent cardiac dysfunction and noncardiac organ dysfunction are associated with increased incidence of HF, supporting the notion that HF is a progressive syndrome and underscoring the importance of noncardiac factors in its occurrence.
Large-scale enzyme-catalyzed synthesis of ATP from adenosine and acetyl phosphate. Regeneration of ATP from AMP (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTLarge-scale enzyme-catalyzed synthesis of ATP from adenosine and acetyl phosphate. Regeneration of ATP from AMPRichard L. Baughn, Orn Adalsteinsson, and George M. WhitesidesCite this: J. Am. Chem. Soc. 1978, 100, 1, 304–306Publication Date (Print):January 1, 1978Publication History Published online1 May 2002Published inissue 1 January 1978https://pubs.acs.org/doi/10.1021/ja00469a063https://doi.org/10.1021/ja00469a063research-articleACS PublicationsRequest reuse permissionsArticle Views518Altmetric-Citations62LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Nucleic acid based tools for pharmacology and nano-engineering (2011)

We have developed modular assays based on aptamer displacement or protein-dependent reporter ribozymes for the screening of small molecule inhibitors. Thereby, chemical space can be explored in a rapid, focused, and modular manner, by indirectly taking advantage of the highest molecular diversity currently amenable to screening, namely that of 10 16 different nucleic acid sequences. In this account, we discuss the application of these approaches to find new inhibitors for target proteins. Examples showing that these modulators can be used as tools for gaining novel biological insight are provided. We also discuss some recent data on interlocked DNA architectures such as entirely double-stranded DNA rotaxanes.
Socioeconomic status and overweight/obesity in an adult chinese population in Singapore (2007)

BACKGROUND: Studies from industrialized Western countries have reported an inverse association between socioeconomic status and overweight/obesity. In contrast, few studies from newly industrialized countries in Asia have examined this association. In this context, we examined the association between socioeconomic status and overweight/obesity by gender in Chinese adults in Singapore.METHODS: A population-based cross sectional study of 942 participants (57.3% women, 40-81 years) residing in the Tanjong Pagar district of Singapore was conducted. Education, income, and housing type were used as socioeconomic status indicators. Main outcome-of-interest was the presence of overweight/obesity (n=313), classified by body mass index as overweight (25- 29.9 kg/m(2)), or obese (&gt;= 30 kg/m(2))RESULTS: The prevalence of overweight/obesity was 33% in men and 34% in women. In men, SES indicators were not associated with overweight/obesity. In women, SES indicators were found to be inversely associated with overweight/obesity. Compared to women with secondary/higher education, the odds ratio (OR) (95% confidence interval [CI]) of overweight/obesity in women with primary/lower education was 2.5 (1.5-4.0). Compared to women earning &gt; Singapore dollar (SGD) 1,000 per month, the OR (95% CI) of overweight/obesity among women earning &lt;= SGD 1,000 was 2.5 (1.4-4.5). Compared to women living in large size public apartments or private houses, the OR (95% CI) of overweight/obesity in women living in small/medium size public apartments was 1.8 (1.2-2.7).CONCLUSIONS: Lower socioeconomic status, defined by education, income, and housing type was associated with overweight/obesity in Chinese Singaporean women.
Supplementary Table 1 from A Pilot Trial Using Lymphocytes Genetically Engineered with an NY-ESO-1–Reactive T-cell Receptor: Long-term Follow-up and Correlates with Response (2023)

&lt;p&gt;Supplementary Table 1. Melanoma patients: Prior treatments&lt;/p&gt;
Berechnung und Auslegung von Bauteilen (2011)

Das Pleuel überträgt die auf den translatorisch bewegten Kolben wirkenden Gaskräfte und die oszillierenden Massenkräfte des Triebwerks auf den rotierenden Hubzapfen der Kurbelwelle. Daraus resultieren folgende Anforderungen an dieses Bauteil:
Kont: Computing Tradeoffs in Normative Multiagent Systems (2017)

We propose Kont, a formal framework for comparing normative multiagent systems (nMASs) by computing tradeoffs among liveness (something good happens) and safety (nothing bad happens). Safety-focused nMASs restrict agents' actions to avoid undesired enactments. However, such restrictions hinder liveness, particularly in situations such as medical emergencies. We formalize tradeoffs using norms, and develop an approach for understanding to what extent an nMAS promotes liveness or safety. We propose patterns to guide the design of an nMAS with respect to liveness and safety, and prove their correctness. We further quantify liveness and safety using heuristic metrics for an emergency healthcare application. We show that the results of the application corroborate our theoretical development.
Selected Ion Recording (SIR) (2016)

This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and definitions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy’s Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some additional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, particularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrometry terminology that represents the current consensus of the mass spectrometry community.
Anti–LFA-1 Blocking Antibodies Prevent Mobilization of Hematopoietic Progenitor Cells Induced by Interleukin-8 (1998)

Previously, we have shown that interleukin (IL)-8 induces the rapid (15 to 30 minutes) mobilization of hematopoietic progenitor cells (HPC) in mice. Because integrins are essential for adhesion and transendothelial migration of HPC, we studied the involvement of the β2-integrin leukocyte function-associated antigen-1 (LFA-1) in IL-8–induced mobilization. After a single injection of blocking anti–LFA-1 antibodies, no mobilization of colony-forming cells was observed. In addition, when mice were pretreated with anti–LFA-1 or saline and subsequently injected with 30 μg of IL-8, mobilization of HPC was completely blocked. We showed that this was not due to anti–LFA-1 antibodies affecting colony formation, as addition of anti–LFA-1 antibodies to colony cultures in semisolid medium had no inhibitory activity. Also, anti-intercellular adhesion molecule (ICAM)-1 antibodies, directed to the main ligand of LFA-1 significantly inhibited the IL-8–induced mobilization. Furthermore, IL-1–induced mobilization was significantly inhibited by anti–LFA-1 antibodies. Because LFA-1 is reported to be expressed on more differentiated HPC, it was considered that the IL-8–induced mobilization of more primitive HPC would not be blocked by anti–LFA-1 antibodies. Transplantation of blood-derived mononuclear cells (MNC) from IL-8–mobilized animals pretreated with anti–LFA-1 antibodies protected only 25% of lethally irradiated recipient mice, whereas the radioprotection rate of control mice transplanted with MNC derived from IL-8-mobilized animals was 86% (P &lt; .01). Anti-LFA–1 antibodies did not interfere with stem cell homing, as transplantation of IL-8-mobilized blood MNC, incubated in vitro with these antibodies resulted in 100% radioprotection. We conclude that anti–LFA-1 antibodies completely prevent the rapid mobilization of colony-forming cells and of cells with radioprotective capacity induced by IL-8. These results indicate a major role for the β2-integrin LFA-1 in the IL-8–induced mobilization of hematopoietic stem cells.
Fullerene acting as an electron donor in a donor–acceptor dyad to attain the long-lived charge-separated state by complexation with scandium ion (2006)

A long-lived charge-separated (CS) state of fullerene-trinitrofluorenone linked dyad in which fullerene acts as an electron donor is formed by photoinduced electron transfer from C60 to TNF in the presence of Sc(OTf)3; the CS lifetime is determined as 23 ms in PhCN at 298 K.