gebhart/patrepeval huggingface dataset:
Electrospray/ion trap tandem mass spectrometry of small multiply-charged oligonucleotides with a modified base (1994)

The authors have recently described the tandem mass spectrometry of multiply-charged anions derived from various small oligonucleotides using electrospray combined with a quadrupole ion trap. They have found that, at least for small oligonucleotides (up to about 12 bases), extensive sequence information can be obtained via multiple stages of mass spectrometry. These results suggest that the identification and location of modified bases in an oligomer might be achieved using this approach.
Distance Dependence of Photoinduced Electron Transfer in Metalloporphyrin Dimers (1999)

To study the dynamics and mechanism of intramolecular photoinduced electron transfer (PET) reactions, a series of (ZnII−FeIII) meso-tetraarylmetalloporphyrin dimers were synthesized and the kinetics of their PET reactivity was measured. Molecular building blocks were prepared by selective nucleophilic aromatic substitution of a para fluorine on tetraarylporphyrins containing a single pentafluorophenyl group. This synthetic approach allows a wide variety of systematic modifications such as type and length of spacer, metal center, and redox-potential difference between donor and acceptor. The edge-to-edge distance between the two porphyrins varies from 14.4 to 27.3 Å. Into a symmetric dimer, with two identical porphyrins covalently linked by a rigid partly saturated bridge, one zinc(II) and one iron(III) can be inserted. From measurements of fluorescence lifetimes the rate constants for PET from the electronically excited state of the zinc porphyrin to the bis(imidazole)iron porphyrin cation were evaluated. The electron-transfer rate decreases by a factor of only 165 when the distance increases by 13 Å. This small decrease is indicative of a surprisingly weak attenuation of the electronic coupling with distance.
Focus on Physics of the Cytoskeleton (2007)

Living cells are organized by soft polymeric scaffolds which, from the perspective of condensed matter physics, are extraordinarily complex fluids. Cells are active, highly dynamic and far from equilibrium states. This dynamics is reflected in processes such as cell motility, mechanosensitivity, and cell division. The complexity of biological cells involves activation patterns of many genes and a vast set of molecular interactions of their products. By identifying cellular subunits which can act as independent functional modules, the complexity of biological cells becomes amenable to systematic study, both experimental and theoretical. Furthermore, the study of cellular systems can lead to new ideas to create artificial devices and machines on scales from nanometres to micrometres. An important example for such a module is the filament network known as the cytoskeleton together with sets of specific associated molecules.
Adenosine Triphosphatases Associated with Bovine Brain Microtubules. II. Properties of ATPases I and II (1983)

The catalytic properties of two ATPases which had been purified from bovine brain microtubules (Tominaga, S. & Kaziro, Y. (1983) J. Biochem. 93, 1085-1092) were studied. ATPase I, which had a molecular weight of 33,000, required the presence of 1.0 microM tubulin, 0.2 mM Mg2+, and 10 mM Ca2+ for maximal activity. The activation of ATPase I by tubulin was specific to the native form of tubulin, which could not be replaced by F-actin or tubulin denatured either by heat or more mildly by dialysis in the absence of glycerol. ATPase I was not specific to ATP, and GTP, and to a lesser extent, UTP and CTP were also hydrolyzed. Km for ATP of ATPase I was about 0.04 mM. ATPase I was inhibited by 5 mM Mg2+, 0.04 M K+, 10(-3) M vanadate, 10 mM N-ethylmaleimide, or 20% (v/v) glycerol. ATPase II, which was associated with membrane vesicles, required the presence of 0.2-2.0 mM Mg2+ and 20 mM KCl for activity. Tubulin stimulated the reaction of ATPase II only partially, and the addition of Ca2+ was rather inhibitory. ATPase II was specific to ATP with a Km value of 0.14 mM. It was inhibited by 1.6 mM N-ethylmaleimide and 20% (v/v) glycerol, but was not very sensitive to vanadate. Instead, ATPase II was inhibited by trifluoperazine, chlorpromazine, and nicardipin at 10(-3) M.
Educating Healthcare Professionals in Pharmacovigilance: Global Trends and Korea’s Status (2020)

This narrative review introduces global trends in pharmacovigilance (PV) education for healthcare professionals and the status of PV education in Korea. Proactive participation of healthcare professionals, including physicians, pharmacists, and nurses in reporting suspected adverse events is the main driving force for effective operation of the spontaneous adverse event reporting system database, which in turn facilitates early safety signal detection of otherwise unknown suspected adverse events. The World Health Organization recognizes PV education curriculum as a key aspect in promoting awareness of PV and adverse event reporting among healthcare professionals, and multiple studies have demonstrated that PV educational interventions for healthcare professionals have increased overall adverse event reporting. Considering the global trends in PV education, the curriculum in Korean universities still has room for improvement in promoting PV obligation among future healthcare professionals. Further research is needed to develop PV education curriculum. We suggest a three-step project for innovating PV education in Korea to meet the global PV educational standards: a survey to gauge current PV competencies among healthcare professionals, reform of current PV academic curriculum, and evaluation and fine-tuning of the reformed curriculum.
Raman spectroscopic study of complex formation between dimethyl sulfoxide and chloroform (1990)

Abstract The sulfur‐oxygen stretching region of dimethyl sulfoxide (DMSO) in chloroform solutions has been studied by means of Raman spectroscopy. The number of linearly independent spectral components in the SO stretching band envelope was determined to be four by factor analysis. The overall band envelope was fitted with five Lorentz‐Gaussian functions using a non‐linear least‐squares procedure. The results were found to be consistent with the formation of 1:1 and 1:2 DMSOCHCl 3 complexes, which give rise to bands centered at 1054 and 1032 cm −1 , respectively. Equilibrium constants could not be calculated because of coincidences between bands of pure DMSO and bands due to the two DMSOCHCl 3 complexes. The spectrum of a 0.0065 mole fraction DMSO solution in chloroform indicates a nearly complete conversion of DMSO species to the 1:1 chloroform complexes at this concentration. A very weak Raman band at 1018 cm −1 and an IR band of medium intensity at 1017 cm −1 in the spectra of pure DMSO were detected by the use of band‐fitting techniques. The assignments of these bands and the other bands in the methyl rocking region are discussed.
Multi-Layer Model for Network Fault Detection Based on Artificial Immune (2011)

In order to reduce the fault detection rate and improve the self-adaptive capability in network fault detection, an artificial immune mechanism which is inspired by multi-layer defense of a biological immune system is proposed to perform network fault detection. The immune model is composed of three parts: the inherent detection layer, fuzzy judgment layer and adaptive detection layer. Dendritic cells can influence the reaction of coordinating T-cells, which can be activate or tolerate so that induce adaptive immune responses and affirm the type of adaptive response. Inherent detection layer and fuzzy judgment layer interact with each other to reduce the error detection rate, while the adaptive detection layer is capable of learning unknown fault patterns.
Oral Bovine Milk Lactoferrin Administration Suppressed Myopia Development through Matrix Metalloproteinase 2 in a Mouse Model (2020)

Recent studies have reported an association between myopia development and local ocular inflammation. Lactoferrin (LF) is an iron-binding protein present in saliva, tears, and mother's milk. Furthermore, sequestering iron by LF can cause its antibacterial property. Moreover, LF has an anti-inflammatory effect. We aimed to determine the suppressive effect of LF against the development and progress of myopia using a murine lens-induced myopia (LIM) model. We divided male C57BL/6J mice (3 weeks old) into two groups. While the experimental group was orally administered LF (1600 mg/kg/day, from 3-weeks-old to 7-weeks-old), a similar volume of Ringer's solution was administered to the control group. We subjected the 4-week-old mice to -30 diopter lenses and no lenses on the right and left eyes, respectively. We measured the refraction and the axial length at baseline and 3 weeks after using a refractometer and a spectral domain optical coherence tomography (SD-OCT) system in both eyes. Furthermore, we determined the matrix metalloproteinase-2 (MMP-2) activity, and the amount of interleukin-6 (IL-6), MMP-2, and collagen 1A1 in the choroid or sclera. The eyes with a minus lens showed a refractive error shift and an axial length elongation in the control group, thus indicating the successful induction of myopia. However, there were no significant differences in the aforementioned parameters in the LF group. While LIM increased IL-6 expression and MMP-2 activity, it decreased collagen 1A1 content. However, orally administered LF reversed these effects. Thus, oral administration of LF suppressed lens-induced myopia development by modifying the extracellular matrix remodeling through the IL-6-MMP-2 axis in mice.
P17.59 * TRANSPLANTED MGMTP140K GENE-MODIFIED CD34+ CELLS IN PATIENTS WITH NEWLY DIAGNOSED GLIOBLASTOMA CHEMO-PROTECT BONE MARROW AND LEAD TO PROLONGED SURVIVAL (2014)

BACKGROUND: Glioblastoma is the most aggressive adult primary malignant brain tumor. It is associated with poor prognosis (median survival of 12-15 months) despite treatment. Combination chemotherapy with carmustine (BCNU) or temozolomide (TMZ) with the MGMT inhibitor O6-benzylguanine (O6BG) has been used but it has been associated with dose limiting hematopoietic toxicity. OBJECTIVE: To assess safety and efficacy of a retroviral vector encoding the O6BG-resistant MGMTP140K gene for transduction and autologous transplantation of hematopoietic stem cells (HSCs) in MGMT unmethylated, newly diagnosed GBM patients in an attempt to chemoprotect bone marrow during combination O6BG/TMZ therapy. METHODS: Seven patients have been enrolled in the first cohort of the study. Following tumor resection, patients underwent standard radiation therapy without TMZ followed by G-CSF mobilization, aphaeresis and conditioning with 600 mg/m2 BCNU prior to infusion of gene-modified cells. Post transplant, patients were treated with 28-day cycles of single dose TMZ (472mg/m2) with 48-hour intravenous O6BG (120mg/m2 bolus, followed by 30mg/m2/24h). RESULTS: The BCNU dose was nonmyeloablative. Gene marking in pre-infusion colony forming units (CFUs) was robust in most patients. Similarly, following engraftment, gene marking in white blood cells and sorted granulocytes assessed by real-time PCR was high. Patients have received up to nine cycles of O6BG/TMZ with evidence for selection of gene-modified cells and tolerable hematologic toxicity. This is significantly more cycles compared to recurrent patients receiving O6BG/TMZ in the absence of gene modified, chemoprotected cells (Quinn et al., 2005) (p < 0.05). No extra-hematopoietic toxicity has been observed thus far and all seven patients exhibited improved survival over historical controls. The longest surviving patient is 56+ months from the diagnosis without evidence of disease progression. CONCLUSIONS: These data demonstrate feasibility of achieving significant engraftment of MGMTP140K- modified cells with a well-tolerated dose of BCNU. Combination of TMZ and O6BG is well tolerated in this setting and patients with newly diagnosed GBM exhibiting unmethylated MGMT promoter achieve prolonged survivals.
A Comparison of Energy Densities of Prevalent Energy Sources in Units of Joules Per Cubic Meter (2008)

Typically, the energy densities of solids or liquids such as coal and oil are measured in dimensions of energy per unit volume or energy per unit mass, whereas solar, wind, and hydroelectric sources are rated in dimensions of power per unit area. This article provides a unifying framework for comparing several prevalent energy sources on an energy-per-unit volume basis for the purpose of unifying conventional metrics. The energy density of oil is 35 to 45 gigajoules (10,000 kWh) per cubic meter∗ ∗One gigajoule equals one billion joules, and there are 3,600,000 joules in a kWh. A cubic meter is about half the volume of a kitchen refrigerator. . When measured using the methods presented, solar energy has a density of 1.5 microjoules per cubic meter, over twenty quadrillion times less than oil. Human energy density is approximately 1000 J/m3, while other inexhaustibles such as wind and tidal have energy densities of 0.5 to 50 J/m3. This article provides an educational engineering mathematics framework for calculating energy densities of prevalent energy sources. The goal is to provide a new perspective on how to compare energy sources on a more fundamental basis. Finally, the article provides a method of estimating the dollars-per-joule for natural resources versus human resources and concludes with commentary on how political decisions may be affected by energy densities and energy costs.
p53 gene mutations and protein overexpression are associated with aggressive variants of mantle cell lymphomas (1996)

Mantle cell lymphoma (MCL) is molecularly characterized by bcl-1 rearrangement and cyclin D1/PRAD-1 gene overexpression. Some aggressive variants have been recognized with a blastic or large cell morphology, higher proliferative activity, and shorter survival. p53 gene mutations in lymphoid neoplasms have been detected mainly in high grade lymphomas and have been associated with tumor progression in follicular and small lymphocytic lymphomas. To determine the role of p53 alterations in MCL, we examined 35 typical and 8 aggressive variants (5 blastic and 3 large cell) of MCLs by a combination of immunohistochemistry, single-strand conformational polymorphism analysis of genomic DNA and/or cDNA obtained by reverse transcriptase-polymerase chain reaction, denaturing gradient gel electrophoresis, and sequencing. Of the 8 aggressive MCLs, 3 (38%) contained missense point mutations in axon 8 codon 278 (Pro --> Leu), exon 8 codon 273 Arg --> His), and exon 5 codon 151 (Pro --> Ser), respectively. A diffuse p53 protein overexpression was observed in more than 50% of the tumor cells in these 3 cases. A fourth blastic MCL also showed strong p53 immunoreactivity. However, no mutations were detected in exons 5-9 in this case. p53 expression was also detected in 10% of the cells in an additional large cell type of MCL and in less than 1% of the cells in 6 typical cases. No mutations were detected in any of these cases or in the remaining cases with no expression of the protein. Four nucleotide changes were observed by single-strand conformational polymorphism analysis in 4 typical MCLs with no overexpression of the protein. Direct sequencing showed that these nucleotide changes were located at exon 6 (1 case), intron 7 (2 cases), and intron 8 (1 case). The changes in exon 6 and intron 7 were known polymorphisms. The nucleotide change in intron 8 was outside splicing sites of the neighboring exons. The overall survival of the 3 patients with p53 mutations (median, 18.3 months) was significantly shorter than that of patients with the nonmutated MCLs (median, 49 months; P < .01). These findings indicate that p53 gene mutations are an infrequent phenomenon in MCLs and are associated with a subset of aggressive variants.
Effect of toothbrushing duration and dentifrice quantity on enamel remineralisation: An in situ randomized clinical trial (2016)

Abstract Objectives The influence of toothbrushing duration and dentifrice quantity on fluoride efficacy against dental caries is poorly understood. This study investigated effects of these two oral hygiene factors on enamel remineralisation (measured as surface microhardness recovery [SMHR]), enamel fluoride uptake (EFU), and net acid resistance (NAR) post-remineralisation in a randomized clinical study using an in situ caries model. Methods Subjects (n = 63) wore their partial dentures holding partially demineralised human enamel specimens and brushed twice-daily for two weeks, following each of five regimens: brushing for 120 or 45 s with 1.5 g of 1150 ppm F (as NaF) dentifrice; for 120 or 45 s with 0.5 g of this dentifrice; and for 120 s with 1.5 g of 250 ppm F (NaF) dentifrice. Results Comparing brushing for 120 s against brushing for 45 s, SMHR and EFU increased by 20.0% and 26.9% respectively when 1.5 g dentifrice was used; and by 22.8% and 19.9% respectively when 0.5 g dentifrice was used. Comparing brushing with 1.5 g against brushing with 0.5 g dentifrice, SMHR and EFU increased by 35.3% and 51.3% respectively when brushing for 120 s, and by 38.4% and 43.0% respectively when brushing for 45 s. Increasing brushing duration and dentifrice quantity also increased the NAR value. The effects of these two oral hygiene factors on SMHR, EFU, and NAR were statistically significant (p  Conclusion Brushing duration and dentifrice quantity have the potential to influence the anti-caries effectiveness of fluoride dentifrices. Study NCT01563172 on ClinicalTrials.gov . Clinical significance The effect of two key oral hygiene regimen factors – toothbrushing duration and dentifrice quantity – on fluoride’s anticaries effectiveness is unclear. This 2-week home-use in situ remineralisation clinical study showed both these factors can influence fluoride bioactivity, and so can potentially affect fluoride’s ability to protect against caries.
Titanium-Catalyzed Enantioselective S-Oxidation of 1,5-Benzothiazepines (2017)

Key words titanium catalysis - diethyl tartrate - oxidation - benzothiazepines
IgG4-RELATED KIDNEY DISEASE: A LONG-TERM FOLLOW UP CASE OF PSEUDOTUMOR OF THE RENAL PELVIS (2014)

A 69-year-old man had undergone left ureteronephrectomy because of a left renal pelvic tumor, however the pathological diagnosis was inflammatory pseudotumor. About 1 year later, computed tomography showed a mass at the right kidney near the hilar. Ureterorenoscopy and urine cytology were performed, and their results showed no evidence of malignancy. He had been followed closely without therapy. The mass increased in size during follow-up, and we reviewed the surgical specimen of the left ureteronephrectomy. Immunohistochemical studies revealed diffuse infiltration by IgG4 positive plasma cell. His serum IgG4 was high. We diagnosed him as IgG4-related kidney disease. In response to treatment with corticosteroid, the size of the tumor and serum IgG4 levels decreased. Most reported cases of IgG4-related disease involving kidney have a history of prior pancreatic involvement. We report a rare long term follow-up case of IgG4-related kidney disease without pancreatic involvement.
Relevant model complexity for non-charring polymer pyrolysis (2013)

The choice of the heat, mass and chemical mechanisms included in a pyrolysis model is often subjective, and detailed justifications of the inclusion or exclusion of the different mechanisms are infrequent. The implicit assumption that models with a higher number of mechanisms reproduce more accurately the reality has led to the recent growth of complexity in pyrolysis modelling seen in the literature. However, as we show in this work, the comparison of several conceptual models predicting the same experimental results does not support this assumption, but reveals the presence of unnecessary complexity and multiple sources of uncertainty. Using a novel approach corresponding to a mechanism sensitivity, the influence of the heat, mass and chemical mechanisms on the transient predictions of surface temperature and mass loss rate (non-flaming conditions) for PolyMethylMethAcrylate (PMMA) samples is investigated. While a small change in the chemical degradation mechanism has a large effect on the predictions of the mass loss rate, the surface temperature is not affected. The heat transfer mechanisms appear to have however a significant effect on both quantities of interest. This study demonstrates that the use of complex chemical mechanisms (e.g. multi-step reaction scheme or oxidative reaction) is not justified if the mechanisms of the heat transfer are kept simple. It is therefore recommended to use consistent levels of crudeness dictated by the heat transfer.
Exploiting a single intramolecular conformational switching Ni-TPP molecule to probe charge transfer dynamics at the nanoscale on bare Si(100)-2 × 1 (2017)

Acquiring quantitative information on charge transfer (CT) dynamics at the nanoscale remains an important scientific challenge. In particular, CT processes in single molecules at surfaces need to be investigated to be properly controlled in various devices. To address this issue, the dynamics of switching molecules can be exploited. Here, nickel-tetraphenylporphyrin adsorbed on the Si(100) surface is used to study the CT process ruling the reversible activation of two chiral molecular conformations. Via the electrons of a scanning tunneling microscope (STM), a statistical study of molecular switching reveals two specific locations of the molecule for which their efficiency is optimized. The CT mechanism is shown to propagate from two lateral aryl groups towards the porphyrin macrocycle inducing an intramolecular movement of two symmetric pyrroles. The measured switching efficiencies can thus be related to a Markus-Jordner model to estimate relevant parameters that describe the dynamics of the CT process. Numerical simulations provide a precise description of the molecular conformations and unveil the molecular energy levels that are involved in the CT process. This quantitative method opens a completely original approach to study CT at the nanoscale.
Poke Weed Mitogen Requires Toll-Like Receptor Ligands for Proliferative Activity in Human and Murine B Lymphocytes (2012)

Poke weed mitogen (PWM), a lectin purified from Phytolacca americana is frequently used as a B cell-specific stimulus to trigger proliferation and immunoglobulin secretion. In the present study we investigated the mechanisms underlying the B cell stimulatory capacity of PWM. Strikingly, we observed that highly purified PWM preparations failed to induce B cell proliferation. By contrast, commercially available PWM preparations with B cell activity contained Toll-like receptor (TLR) ligands such as TLR2-active lipoproteins, lipopolysaccharide and DNA of bacterial origin. We show that these microbial substances contribute to the stimulatory activity of PWM. Additional experimental data highlight the capacity of PWM to enable B cell activation by immunostimulatory DNA. Based on these findings we propose that the lectin sensitizes B cells for TLR stimulation as described for B cell receptor ligation and that B cell mitogenicity of PWM preparations results from synergistic activity of the poke weed lectin and microbial TLR ligands present in the PWM preparations.