gebhart/patrepeval huggingface dataset:
Fibrinogen Is a Ligand for the Staphylococcus aureus Microbial Surface Components Recognizing Adhesive Matrix Molecules (MSCRAMM) Bone Sialoprotein-binding Protein (Bbp) (2011)

Microbial surface components recognizing adhesive matrix molecules (MSCRAMMs) are bacterial surface proteins mediating adherence of the microbes to components of the extracellular matrix of the host. On Staphylococci, the MSCRAMMs often have multiple ligands. Consequently, we hypothesized that the Staphylococcus aureus MSCRAMM bone sialoprotein-binding protein (Bbp) might recognize host molecules other than the identified bone protein. A ligand screen revealed that Bbp binds human fibrinogen (Fg) but not Fg from other mammals. We have characterized the interaction between Bbp and Fg. The binding site for Bbp was mapped to residues 561-575 in the Fg Aα chain using recombinant Fg chains and truncation mutants in Far Western blots and solid-phase binding assays. Surface plasmon resonance was used to determine the affinity of Bbp for Fg. The interaction of Bbp with Fg peptides corresponding to the mapped residues was further characterized using isothermal titration calorimetry. In addition, Bbp expressed on the surface of bacteria mediated adherence to immobilized Fg Aα. Also, Bbp interferes with thrombin-induced Fg coagulation. Together these data demonstrate that human Fg is a ligand for Bbp and that Bbp can manipulate the biology of the Fg ligand in the host.
A strong correlation exists between platelet consumption and platelet hyperactivation in COVID-19 patients. Pilot study of the patient cohort from CCH RAS Hospital (Troitsk). (2021)

It is known that in COVID-19, hypercoagulation and sometimes thrombocytopenia are related to disease severity. There is also controversial data on platelet participation in COVID-19 pathology. We aimed to determine the degree of platelet hyperactivation in COVID-19 patients. Whole blood flow cytometry with Annexin-V and lactadherin staining ("PS+ platelets") was utilized. Additionally, a stochastic mathematical model of platelet production and consumption was developed. Here we demonstrated that the percentage of PS+ platelets in COVID-19 patients was twofold that of healthy donors. There was a significant correlation between the amount of PS+ platelets and the percentage of lung damage in patients. No connection was found between platelet senescence and hospital therapy or patients' chronic diseases, except for chronic lung disease. Although no thrombocytopenia was observed in patients, the observed increase in platelet size (FSC-A parameter in flow cytometry) could indicate that platelet age is decreased in patients. The developed computational model of platelet turnover confirms the possibility of intense platelet consumption without noticeable changes in platelet count. We conclude that the observed platelet hyperactivation in COVID-19 could be caused by platelet activation in circulation, leading to platelet consumption without significant thrombocytopenia.
Vibration analysis of axisymmetric multi-layer liquid-filled cylindrical containers using RD-finite element method (2008)

International Journal of Offshore and Polar Engineering
All-Digital On-Chip Monitor for PMOS and NMOS Process Variability Utilizing Buffer Ring with Pulse Counter (2011)

This paper proposes an all-digital process variability monitor which utilizes a simple buffer ring with a pulse counter. The proposed circuit monitors the process variability according to a count number of a single pulse which propagates on the buffer ring and a fixed logic level after the pulse vanishes. The proposed circuit has been fabricated in 65nm CMOS process and the measurement results demonstrate that we can monitor the PMOS and NMOS variabilities independently using the proposed monitoring circuit. The proposed monitoring technique is suitable not only for the on-chip process variability monitoring but also for the in-field monitoring of aging effects such as negative/positive bias instability (NBTI/PBTI).
Toward an Artificial Acetylcholinesterase (2000)

The methanolysis of choline p-nitrophenylcarbonate in chloroform containing 1% methanol is catalyzed with turnover by ditopic receptors 1 and 2, consisting of a calix[6]arene connected to a bicyclic guanidinium by means of a short spacer. The calix[6]arene subunit strongly binds to the trimethylammonium head group through cation-pi interactions, whereas the guanidinium moiety is deputed to stabilize through hydrogen bonding reinforced by electrostatic attraction the anionic tetrahedral intermediate resulting from methoxide addition to the ester carbonyl. The observed cholinesterase activity had been anticipated on the basis of the ability of the ditopic receptors 1 and 2 to bind strongly to the choline phosphate DOPC, which is a transition state analogue for the BAc2-type cleavage of choline esters.
COMSOC's chief information officer-technology serving the society (2008)

Previous President's Pages have touched on the wide range of activities conducted by the Communications Society. Many of these activities have evolved over many years, with beginnings even before personal computers and the Internet had become ubiquitous. With the advent of new information technologies, ComSoc realized it had an opportunity to significantly enhance existing services and introduce new services to its members. Achieving this would be no small task, and to provide proper focus on this challenge, the Board of Governors created the volunteer position of Chief Information Officer. This month's column is on the key role the Chief Information Officer (CIO) and the Information Technology (IT) department at ComSoc headquarters play in leveraging Information and Communications Technology (ICT) to keep up with the demands of our members for ever more valuable products and services- or "how to apply Web 2.0 to ComSoc 2.0." ComSoc's
Dynasthetics Disclosure (2011)

To the Editor A recent article about activated charcoal1 omitted the disclosure that we are cofounders of Dynasthetics LLC, the device manufacturer. We regret the omission. Dwayne Westenskow, PhD Joseph Orr, PhD Department of Anesthesiology University of Utah Salt Lake City, UT [email protected]
Stem Cell Factor Consistently Improves Thymopoiesis after Experimental Transplantation of Murine or Human Hematopoietic Stem Cells in Immunodeficient Mice (2011)

Deficient thymopoiesis is a pivotal determinant of impaired immune competence following hematopoietic stem cell transplantation (HSCT). Stem cell factor (SCF) is essentially involved in early thymopoiesis. We evaluated whether SCF administration would improve recovery of thymopoiesis following HSCT in immunodeficient mice receiving: 1) bone marrow (BM) transplantation of congenic mice; or 2) human fetal liver HSCT in the human immune system mouse model. Following murine BM transplantation, SCF significantly enhanced thymopoiesis and peripheral T cell recovery in lymph nodes and spleen. SCF did not affect BM lymphoid progenitor recovery and/or expansion. Median thymic cellularity increased from 0.9 in PBS- to 266 × 10(4)/thymus in SCF-treated mice (p = 0.05). Following human HSCT in human immune system mice, higher thymic cellularity was observed in SCF-treated mice. Double-negative and early double-positive thymocyte subsets increased, but especially late double-positive, CD4 single-positive, and CD8 single-positive thymocyte subsets were significantly enhanced (p < 0.05). These results show that exogenous supply of SCF may significantly improve murine and human posttransplant thymopoiesis, for which the effect is probably exerted by directly promoting T cell development intrathymically rather than by enhanced entry of prethymically expanded lymphoid progenitors.
Tin Oxide Nanoparticles and SnO<sub>2</sub>/SiO<sub>2</sub> Hybrid Materials by Twin Polymerization Using Tin(IV) Alkoxides (2013)

Twin polymerization was used to prepare composite materials composed of SnO<sub>2</sub> nanoparticles entrapped in a polymer matrix. Novel, well-defined tin-containing molecular precursors, so-called twin monomers, were synthesized by transesterification starting from Sn(OR)<sub>4</sub> (R=tBu, tAm) to give Sn(OCH<sub>2</sub> C<sub>4</sub> H<sub>3</sub> O)<sub>4</sub> (1), [Sn(OCH<sub>2</sub> C<sub>4</sub> H<sub>3</sub> S)<sub>4</sub> ⋅HOCH<sub>2</sub> C<sub>4</sub> H<sub>3</sub> S]<sub>2</sub> (2), [Sn(OCH<sub>2</sub> -2-OCH<sub>3</sub> C<sub>6</sub> H<sub>4</sub> )<sub>4</sub> ⋅HOCH<sub>2</sub> -2-OCH<sub>3</sub> C<sub>6</sub> H<sub>4</sub> ]<sub>2</sub> (3), [Sn(OCH<sub>2</sub> -2,4-(OCH<sub>3</sub> )<sub>2</sub> C<sub>6</sub> H<sub>3</sub> )<sub>4</sub> ⋅HOCH<sub>2</sub> -2,4-(OCH<sub>3</sub> )<sub>2</sub> C<sub>6</sub> H<sub>3</sub> ]<sub>2</sub> (4), 2,2'-spirobi[4H-1,3,2-benzodioxastannine] (5), 2,2'-spirobi[6-methylbenzo(4H-1,3,2)-dioxastannine] (6), and 2,2'-spirobi[6-methoxybenzo(4H-1,3,2)dioxastannine] (7). <sup>13</sup> C and <sup>119</sup> Sn NMR spectroscopy in the solid state and in solution as well as IR spectroscopy and elemental analysis were used to characterize the tin alkoxides. The molecular structures of compounds 2 and 3 were determined by single-crystal X-ray diffraction analysis. The moisture sensitivity of the tin(IV) alkoxides was demonstrated by the formation of the tin oxocluster [Sn<sub>3</sub> (μ<sub>3</sub> -O)(μ<sub>2</sub> -OH)(μ<sub>2</sub> -OCH<sub>2</sub> C<sub>4</sub> H<sub>3</sub> S)<sub>3</sub> (OCH<sub>2</sub> C<sub>4</sub> H<sub>3</sub> S)<sub>6</sub> (HOCH<sub>2</sub> C<sub>4</sub> H<sub>3</sub> S)]<sub>2</sub> (2 a), a hydrolysis product of compound 2. Polymerization reactions in the melt (for 1 and 5) and in solution (for 2-4) resulted in cross-linked nanocomposites of the type polymer/SnO<sub>2</sub> . Subsequent oxidation of the composites gave SnO<sub>2</sub> with BET surface areas up to 178 m<sup>2</sup> g<sup>-1</sup> . Simultaneous twin polymerization of compounds 5-7 with the silicon derivative 2,2'-spirobi[4H-1,3,2-benzodioxasiline] resulted in the formation of polymer/SnO<sub>2</sub> /SiO<sub>2</sub> hybrid materials. Oxidation gave porous materials with SnO<sub>2</sub> nanoparticles embedded in a silica network with BET surface areas up to 378 m<sup>2</sup> g<sup>-1</sup> . The silica acts as a crystal growth inhibitor, which prevents sintering of the SnO<sub>2</sub> nanoparticles 20-32 nm in size.
Supplementary Figure 1 from Adjuvant Sirolimus Does Not Improve Outcome in Pet Dogs Receiving Standard-of-Care Therapy for Appendicular Osteosarcoma: A Prospective, Randomized Trial of 324 Dogs (2023)

&lt;p&gt;Supplementary Fig. 1 depicts the chronology of clinical trial visits and associated procedures for dogs enrolled in this clinical trial.&lt;/p&gt;
The Fabry-Perot Etalon As An Rf Frequency Channelizer (1984)

This paper reports a demonstration of channelizing rf signals with optical techniques. RF signals are upconverted to optical frequencies and demultiplexed with an etalon. The etalon is used as a filter transmitting modulated light at discrete incidence angles. The band 100-1000 MHz is channelized into 70 MHz wide channels.
Effect of microvesicles from Moringa oleifera containing miRNA on proliferation and apoptosis in tumor cell lines (2020)

Human microvesicles are key mediators of cell-cell communication. Exosomes function as microRNA transporters, playing a crucial role in physiological and pathological processes. Plant microvesicles (MVs) display similar features to mammalian exosomes, and these MVs might enhance plant microRNA delivery in mammals. Considering that plant microRNAs have been newly identified as bioactive constituents in medicinal plants, and that their potential role as regulators in mammals has been underlined, in this study, we characterized MVs purified from <i>Moringa oleifera</i> seeds aqueous extract (MOES MVs) and used flow cytometry methods to quantify the ability to deliver their content to host cells. The microRNAs present in MOES MVs were characterized, and through a bioinformatic analysis, specific human apoptosis-related target genes of plant miRNAs were identified. In tumor cell lines, MOES MVs treatment reduced viability, increased apoptosis levels associated with a decrease in B-cell lymphoma 2 protein expression and reduced mitochondrial membrane potential. Interestingly, the effects observed with MOES MVs treatment were comparable to those observed with MOES treatment and transfection with the pool of small RNAs isolated from MOES, used as a control. These results highlight the role of microRNAs transported by MOES MVs as natural bioactive plant compounds that counteract tumorigenesis.
Mechanism of Stimulation of Human DNA Ligase I by the Rad9-Rad1-Hus1 Checkpoint Complex (2006)

Accumulating evidence suggests that the Rad9-Rad1-Hus1 (9-1-1) checkpoint complex, known to be a sensor of DNA damage, is also a component of DNA repair systems. Recent results show that 9-1-1 interacts with several base excision repair proteins. It binds the DNA glycosylase MutY homolog, and stimulates DNA polymerase beta, flap endonuclease 1, and DNA ligase I. 9-1-1 resembles proliferating cell nuclear antigen (PCNA), which stimulates some of these same repair enzymes, and is loaded onto DNA in a similar manner. The complex of 9-1-1 with DNA ligase I can be immunoprecipitated from human cells. Moreover, UV irradiation stimulates 9-1-1.ligase I complex formation, suggesting a role for 9-1-1 in DNA repair. Examining the nature of 9-1-1 interaction with DNA ligase I, we show that there is a similar degree of stimulation on ligation substrates with different structures, and that there is specificity for DNA ligase I. 9-1-1 improves the binding of DNA ligase I to nicked double strand DNA. Furthermore, although high concentrations of casein kinase II strongly inhibits DNA ligase I activity, it does not affect the ability of 9-1-1 to stimulate. This suggests that 9-1-1 is also an activator of DNA ligase I during DNA damage. Unlike PCNA, 9-1-1 stimulates DNA ligase I activity to the same extent on both linear and circular substrates, indicating that encirclement is not a requirement for stimulation. These data are consistent with a direct role for 9-1-1 in DNA repair, but possibly employing a different mechanism than PCNA.
Self- and Partner-Reported Subjective Memory Complaints: Association with Objective Cognitive Impairment and Risk of Decline (2022)

Partner-reported SMCs, using the PRMQ, have a stronger relationship with the neuroanatomic and cognitive changes associated with AD than patient-reported SMCs. Further work is needed to evaluate whether SMCs could be used to screen for future decline.
Identification and Characterization of a Putative Active Site for Peptide Methionine Sulfoxide Reductase (MsrA) and Its Substrate Stereospecificity (2000)

Peptide methionine sulfoxide reductases (MsrA) from many different organisms share a consensus amino acid sequence (GCFWG) that could play an important role in their active site. Site-directed single substitution of each of these amino acids except glycines in the yeast MsrA resulted in total loss of enzyme activity. Nevertheless, all the recombinant MsrA mutants and native proteins had a very similar circular dichroism spectrum. The demonstration that either treatment with iodoacetamide or replacement of the motif cysteine with serine leads to inactivation of the enzyme underscores the singular importance of cysteine residues in the activity of MsrA. The recombinant yeast MsrA was used for general characterization of the enzyme. Its K(m) value was similar to the bovine MsrA and appreciably lower than the K(m) of the bacterial enzyme. Also, it was shown that the enzymatic activity increased dramatically with increasing ionic strength. The recombinant yeast MsrA activity and the reduction activity of free methionine sulfoxide(s) were stereoselective toward the L-methionine S-sulfoxide and S-methyl p-tolyl sulfoxide. It was established that a methionine auxotroph yeast strain could grow on either form of L-methionine sulfoxide.
Efficient Synthesis and In Vivo Incorporation of Acridon-2-ylalanine, a Fluorescent Amino Acid for Lifetime and Förster Resonance Energy Transfer/Luminescence Resonance Energy Transfer Studies (2013)

The amino acid acridon-2-ylalanine (Acd) can be a valuable probe of protein conformational change because it is a long lifetime, visible wavelength fluorophore that is small enough to be incorporated during ribosomal biosynthesis. Incorporation of Acd into proteins expressed in Escherichia coli requires efficient chemical synthesis to produce large quantities of the amino acid and the generation of a mutant aminoacyl tRNA synthetase that can selectively charge the amino acid onto a tRNA. Here, we report the synthesis of Acd in 87% yield over five steps from Tyr and the identification of an Acd synthetase by screening candidate enzymes previously evolved from Methanococcus janaschii Tyr synthetase for unnatural amino acid incorporation. Furthermore, we characterize the photophysical properties of Acd, including quenching interactions with select natural amino acids and Förster resonance energy transfer (FRET) interactions with common fluorophores such as methoxycoumarin (Mcm). Finally, we demonstrate the value of incorporation of Acd into proteins, using changes in Acd fluorescence lifetimes, Mcm/Acd FRET, or energy transfer to Eu(3+) to monitor protein folding and binding interactions.
P1‐106: A HEAD‐TO‐HEAD COMPARISON OF LEAD CLINICAL ANTI‐Aβ ANTIBODIES (2018)

Approaches using monoclonal antibodies (mAbs) to target the amyloid β-protein (Aβ) constitute the largest and most advanced therapeutic effort to treat Alzheimer's disease (AD). Despite generally good outcomes in preclinical mouse models, anti-Aβ immunotherapy has yielded limited success in humans. While many reasons could explain poor translation of pre-clinical leads into viable therapies, the most pressing issue remains the lack of knowledge about whether trial antibodies engage the toxic forms of Aβ in human brain. Here, we report the development of an unbiased, medium-to-high throughput in vitro assay that combines the use of Aβ-rich human (AD) brain extracts and human iPSC-derived neurons to assess the relative ability of 5 clinical lead mAbs to engage with toxic Aβ. Aqueous extracts of temporal cortices from mild AD patients were prepared as described (Wang et al. 2017 J Neurosci) and a portion immunodepleted of Aβ using the novel pan anti-Aβ antiserum, S97. Human iPSCs were infected with appropriate vectors to drive neurogenin 2 differentiation and grown in 96-well plates at 5000 cells per well (Hong et al. 2018 Acta Neuropath). On day 21 post-induction, AD brain extracts (+/- immunodepletion) were added to neurons +/- test mAbs. Neurons were imaged every 2 hours for 4 days using an IncuCyte live-cell imaging system, and neurite number and density quantified. Five clinical mAbs, an in-house aggregate-specific mAb, 1C22, and a non-Aβ antibody (Avastin) were compared blind to mAb identity. Soluble AD brain extracts caused a time-, dose, and Aβ-dependent decrease in neurite length and branch points (but not cell bodies), whereas extracts immunodepleted of Aβ had no effect. When tested at a single concentration (1.5 mg/ml), comparator mAbs provided varying degrees of protection with 1C22 ∼SAR228810 >aducanumab ∼bapinezumab >gantenerumab >BAN2401. Control mAb (Avastin) afforded no protection. Dose curves of the best 3 mAbs confirmed this order of relative efficacy. While no single assay can predict the absolute utility of an anti-Aβ antibody when administered to humans, the novel quantitative paradigm described here, if widely adopted, would enable important objective preclinical comparisons of new anti-Aβ antibodies and current lead antibodies in human trials.
ChemInform Abstract: Palladium‐Catalyzed Aminosulfonylation of Aryl Halides. (2011)

Abstract The palladium‐catalyzed three‐component coupling of aryl iodides, sulfur dioxide, and hydrazines is described.
Functional Outcome and Gait Analysis After Triple or Double Arthrodesis (1999)

Thirteen patients who had undergone unilateral triple or double arthrodesis were studied an average of 5.2 years after surgery. Patients with a neuromuscular disorder; inflammatory arthritis; or any other focus of lower extremity arthritis, deformity, or joint dysfunction were excluded from the study. Clinical and radiological assessment of the patients was performed in addition to three-dimensional kinematic and kinetic gait analysis. Objective clinical outcome based on the American Orthopaedic Ankle and Foot Society score was rated as good or excellent for 10 patients, fair for 2, and poor for 1. Two patients developed radiological evidence of arthrosis affecting other tarsal joints that was not apparent on preoperative radiographs. Two other patients had some progression of radiological arthrosis that was identified before the index surgery. The presence of radiological ankle or tarsal arthritis did not correlate with the level of the patient's pain or functional disability. Gait analysis demonstrated a 13% increase in range of flexion of the ipsilateral knee during the third rocker period of stance. At the ankle, range of motion during the same period of stance was reduced by 33%. This was mostly the result of a 6 degrees (53%) loss of plantarflexion at toe-off. Analysis of the ankle kinetic data identified a mean 13% reduction in the peak external ankle dorsiflexion moment and a 45% reduction in mean maximum power generation at the ankle in comparison to the normal side. Unilateral triple or double arthrodesis was shown to predictably result in decreased pain and increased function in otherwise normal individuals.
[6]Saddlequat: a [6]helquat captured on its racemization pathway (2011)

A dicationic [6]helicene congener captured on the racemization pathway in its saddle-shaped geometry is introduced. Synthesis, structure, resolution, and dynamic properties of this chiral [6]saddlequat in-between and its highly stereocontrolled transformation into enantiopure [6]helquat are discussed and demonstrated. The dynamic aspects established by experiment and supported by detailed DFT-D calculations are presented visually in the form of a movie (electronic table-of-contents and electronic supplementary information). The title [6]saddlequat was found to be an isolable chiral species on the entirely chiral enantiomerization pathway of a [6]helquat that is discussed as an example of Mislow's “rubber glove” molecule.
Concomitant Herpes simplex and Epstein–Barr virus lymphadenitis with simultaneous lymph node metastases of an occult squamous cell carcinoma in a patient with chronic lymphocytic leukemia (2008)

Chronic lymphocytic leukemia (CLL) is the most frequent hematological neoplasm in human adults and is characterised by progressive defects in both humoral- [1] and cell-mediated immunity [2] leadin...
A Systematic Methodology for Developing Discrete Event Simulation Models of Software Development Processes (2014)

So far there have been several efforts for developing software process simulators. However, the approaches for developing the simulators seem to have been ad-hoc and no systematic methodology exists. Since modeling and simulation in support of software development should become more popular (and there are signs that it does), there is a need for migrating modeling from craft to engineering. This article proposes such a systematic method, focused on the development of discrete simulation-based decision models, but extensible to other modeling approaches as well.
Author Correction: High permeability sub-nanometre sieve composite MoS2 membranes (2020)

An amendment to this paper has been published and can be accessed via a link at the top of the paper.