gebhart/patrepeval huggingface dataset:
Formamide Adsorption at the Amorphous Silica Surface: A Combined Experimental and Computational Approach (2018)

Mineral surfaces have been demonstrated to play a central role in prebiotic reactions, which are understood to be at the basis of the origin of life. Among the various molecules proposed as precursors for these reactions, one of the most interesting is formamide. Formamide has been shown to be a pluripotent molecule, generating a wide distribution of relevant prebiotic products. In particular, the outcomes of its reactivity are strongly related to the presence of mineral phases acting as catalysts toward specific reaction pathways. While the mineral⁻products relationship has been deeply studied for a large pool of materials, the fundamental description of formamide reactivity over mineral surfaces at a microscopic level is missing in the literature. In particular, a key step of formamide chemistry at surfaces is adsorption on available interaction sites. This report aims to investigate the adsorption of formamide over a well-defined amorphous silica, chosen as a model mineral surface. An experimental IR investigation of formamide adsorption was carried out and its outcomes were interpreted on the basis of first principles simulation of the process, adopting a realistic model of amorphous silica.
ToIC and DsbA are needed for the secretion of ST<sub>B</sub>, a heat‐stable enterotoxin of <i>Escherichia coli</i> (1995)

STB secretion-deficient mutants were isolated using the synthetic transposon Tn beta laM. Cultures were plated using a double-membrane system of cellulose acetate and nitrocellulose placed on Luria agar plates containing carbenicillin. The STB bound to the underlying nitrocellulose membrane was detected with anti-STB antibodies. The altered genes of two STB secretion-deficient mutants were identified by conjugation and complementation as tolC and dsbA. In cultures of well-characterized dsbA and tolC mutants, STB was absent from the culture supernatant. The role of TolC and DsbA in the secretion of peptides is discussed.
Cracks and Atoms (1999)

Atomic features are essential for understanding some materials properties. The example of brittle fracture is reviewed here, concentrating on molecular dynamics simulations of silicon. The Figure shows a visualization of an unstable crack at 8.97 % strain along (111). The choice of the potential, the implementation of non-zero temperature, and comparison of the results with experiment are particularly emphasized.
Using a Generic Associated Channel Label as a Virtual Circuit Connectivity Verification Channel Indicator (2015)

The Virtual Circuit Connectivity Verification (VCCV) protocol
specified in RFC 5085 provides a control channel (CC) that is
associated with a pseudowire (PW). This document specifies an
additional VCCV control channel type to be used with pseudowires that
do not use the PW Control Word and that are carried over an MPLS
network. This new VCCV CC type uses the Generic Associated Channel
Label defined in RFC 5586 to distinguish VCCV packets from packets
carrying user data. This new VCCV CC type introduces compatibility
with the method of MPLS Label Switched Path Operations,
Administration, and Maintenance (OAM) identification, particularly in
MPLS Transport Profile (MPLS-TP) networks (RFC 5921).
First report of crown gall of apricot ( <i>Prunus armeniaca</i> ) caused by <i>Agrobacterium tumefaciens</i> in Turkey (2003)

In the winter of 2002, nearly 30% of 2-year-old apricot trees (Prunus armeniaca cv. Ninfa) in two commercial orchards in Adana and Mersin, in the eastern Mediterranean region of Turkey, were observed with crown gall symptoms. Tumours and galls were often found at or just below the soil surface on the roots or crown region of the apricot plants as described by Ogawa et al. (1995). A nonfluorescent, Gram-negative bacterium was isolated from diseased tissues onto King's medium B. Fifteen representative strains were characterized as aerobic, nonsporing, nonpigmented, rod-shaped, oxidase-negative and catalase-positive. Fatty acid analysis identified the strains as Agrobacterium tumefaciens with similarity indices ranging from 94·6 to 98·2% (Bouzar et al., 1993). Pathogenicity of the strains was tested on carrot slices in Petri dishes and 5-week-old tomato plants (cv. H-2274) by needle inoculation of bacterial suspensions containing 108 cfu mL−1 in 8·5 g L−1 saline. A reference strain of A. tumefaciens, GSPB 7 and saline were used as positive and negative controls, respectively. Inoculated and control plants were maintained in a controlled climate room, for 20 days at 25°C and 70% RH to observe symptom development. Gall symptoms on carrot slices developed within 7–8 days and on tomato plants within 15–20 days. No symptoms developed on negative control plants. The bacterium was re-isolated from inoculated tomato plants and identified as A. tumefaciens. The occurrence of crown gall disease on rose (Rosa spp.) cultivars in Turkey has been reported previously (Aysan & Sahin, 2003). However, this is the first report of the crown gall on apricot trees grown in Turkey. To the best of our knowledge, the apricot cuttings in both orchards were imported from outside of Turkey. Therefore, it is possible that the pathogen may have been introduced into Turkey with the cuttings.
Expression of monoacylglycerol lipase as a marker of tumour invasion and progression in malignant melanoma (2017)

The expression of MAGL in tumour cells reflects the aggressiveness of melanoma cells and may serve as a marker of tumour progression.
The Malaria Parasite Progressively Dismantles the Host Erythrocyte Cytoskeleton for Efficient Egress (2011)

Plasmodium falciparum is an obligate intracellular pathogen responsible for worldwide morbidity and mortality. This parasite establishes a parasitophorous vacuole within infected red blood cells wherein it differentiates into multiple daughter cells that must rupture their host cells to continue another infectious cycle. Using atomic force microscopy, we establish that progressive macrostructural changes occur to the host cell cytoskeleton during the last 15 h of the erythrocytic life cycle. We used a comparative proteomics approach to determine changes in the membrane proteome of infected red blood cells during the final steps of parasite development that lead to egress. Mass spectrometry-based analysis comparing the red blood cell membrane proteome in uninfected red blood cells to that of infected red blood cells and postrupture vesicles highlighted two temporally distinct events; (Hay, S. I., et al. (2009). A world malaria map: Plasmodium falciparum endemicity in 2007. PLoS Med. 6, e1000048) the striking loss of cytoskeletal adaptor proteins that are part of the junctional complex, including α/β-adducin and tropomyosin, correlating temporally with the emergence of large holes in the cytoskeleton seen by AFM as early ~35 h postinvasion, and (Maier, A. G., et al. (2008) Exported proteins required for virulence and rigidity of Plasmodium falciparum-infected human erythrocytes. Cell 134, 48-61) large-scale proteolysis of the cytoskeleton during rupture ~48 h postinvasion, mediated by host calpain-1. We thus propose a sequential mechanism whereby parasites first remove a selected set of cytoskeletal adaptor proteins to weaken the host membrane and then use host calpain-1 to dismantle the remaining cytoskeleton, leading to red blood cell membrane collapse and parasite release.
The SARS-CoV-2 transcriptome and the dynamics of the S gene furin cleavage site in primary human airway epithelia (2021)

Abstract The novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) caused the devastating ongoing coronavirus disease-2019 (COVID-19) pandemic which poses a great threat to global public health. The spike (S) polypeptide of SARS-CoV-2 consists of the S1 and S2 subunits and is processed by cellular proteases at the S1/S2 boundary. The inclusion of the 4 amino acids (PRRA) at the S1/S2 boundary forms a furin cleavage site (FCS), 682 RRAR↓S 686 , distinguishing SARS-CoV-2 from its closest relative, the SARS-CoV. Various deletions surrounding the FCS have been identified in patients. When SARS-CoV-2 propagated in Vero cells, the virus acquired various deletions surrounding the FCS. In the present study, we studied the viral transcriptome in SARS-CoV-2 infected primary human airway epithelia (HAE) cultured at an air-liquid interface (ALI) with an emphasis on the viral genome stability at the S1/S2 boundary using RNA-seq. While we found overall the viral transcriptome is similar to that generated from infected Vero cells, we identified a high percentage of mutated viral genome and transcripts in HAE-ALI. Two highly frequent deletions were found at the S1/S2 boundary of the S gene: one is a deletion of 12 amino acids, 678 TNSP RRAR↓S VAS 689 , which contains the FCS, another is a deletion of 5 amino acids, 675 QTQTN 679 , which is two amino acids upstream of the FCS. Further studies on the dynamics of the FCS deletions in apically released virions revealed that the selective pressure for the FCS maintains the S gene stability in HAE-ALI but with exceptions, in which the FCS deletions are remained at a high rate. Thus, our study presents evidence for the role of unique properties of human airway epithelia in the dynamics of the FCS region during infection of human airways, which is donor-dependent.
The effect of age on oxygen desaturation during histamine inhalation challenge in normal infants (1993)

Arterial oxygen saturation (SaO2) is usually measured during inhalation challenges in infants as desaturation has been demonstrated with provoked bronchoconstriction. We wished to examine whether measurement of SaO2 would provide a simple noninvasive indicator of respiratory function (RF) changes occurring during inhalation challenge in infants. Histamine inhalation challenges were performed longitudinally in 22 normal healthy infants at 4 and 26 weeks of age. RF was measured by calculating maximum forced expiratory flow at functional residual capacity (VmaxFRC) using the rapid thoracic compression technique. Airway responsiveness was assessed using histamine; the provoking concentration (PC) was that which caused a fall in VmaxFRC of at least 40% from baseline. The provocative concentration for an exact fall of 40% in VmaxFRC (PC40) from baseline was derived by linear interpolation. SaO2 was continuously monitored by pulse oximetry. One month old infants had higher SaO2 levels throughout the inhalation challenge in comparison to their SaO2 levels at 6 months of age. Significant falls in SaO2 were observed at the PC at both ages. However, at the age of 26 weeks the infants had greater median falls in SaO2 [PC, 4.5% (95%CI: 3.0, 7.0)] compared to the response at age 4 weeks [3.0% (95%CI: 1.0, 4.0) (P < 0.01)]. Median falls in VmaxFRC at the PC were not different between the ages. These results indicate an age-dependent discordance between airway and SaO2 response in healthy infants during histamine-induced bronchoconstriction.
Towards a Representative Rock Model from a Micro-CT Image (2014)

Digital rock physics combines modern imaging with advanced numerical simulations to analyze the physical properties of rocks. However, it remains difficult to resolve microstructures on submicrometer scale and image a representative volume at the same time, which is essential to understand the elastic properties of rocks. This leads to a mismatch between laboratory measurements and digital rock physics estimates. In this paper we suggest the usage of digital rock physics templates as recipe to obtain accurate numerical predictions. In those templates optimized pressure-dependent elastic properties are given for each phase of a rock identified on a micro-CT image. For one Berea sandstone sample we describe such a template by using a laboratory-based calibration technique.
Chirospecific synthesis of (1S,3R)-1-amino-3-(hydroxymethyl)cyclopentane, a precursor for carbocyclic nucleoside synthesis. Intramolecular aziridine cyclizations (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChirospecific synthesis of (1S,3R)-1-amino-3-(hydroxymethyl)cyclopentane, a precursor for carbocyclic nucleoside synthesis. Intramolecular aziridine cyclizationsStephen C. Bergmeier, Won Koo Lee, and Henry RapoportCite this: J. Org. Chem. 1993, 58, 18, 5019–5022Publication Date (Print):August 1, 1993Publication History Published online1 May 2002Published inissue 1 August 1993https://pubs.acs.org/doi/10.1021/jo00070a050https://doi.org/10.1021/jo00070a050research-articleACS PublicationsRequest reuse permissionsArticle Views483Altmetric-Citations29LEARN 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
Comparison of selenophene and thienothiophene incorporation into pentacyclic lactam-based conjugated polymers for organic solar cells (2015)

In this work, we compare the effect of incorporating selenophene <italic>versus</italic> thienothiophene spacers into pentacyclic lactam-based conjugated polymers for organic solar cells.
Data from Tebentafusp, A TCR/Anti-CD3 Bispecific Fusion Protein Targeting gp100, Potently Activated Antitumor Immune Responses in Patients with Metastatic Melanoma (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;Tebentafusp is a first-in-class bispecific fusion protein designed to target gp100 (a melanoma-associated antigen) through a high affinity T-cell receptor (TCR) binding domain and an anti-CD3 T-cell engaging domain, which redirects T cells to kill gp100-expressing tumor cells. Here, we report a multicenter phase I/II trial of tebentafusp in metastatic melanoma (NCT01211262) focusing on the mechanism of action of tebentafusp.&lt;/p&gt;Patients and Methods:&lt;p&gt;Eighty-four patients with advanced melanoma received tebentafusp. Treatment efficacy, treatment-related adverse events, and biomarker assessments were performed for blood-derived and tumor biopsy samples obtained at baseline and on-treatment.&lt;/p&gt;Results:&lt;p&gt;Tebentafusp was generally well-tolerated and active in both patients with metastatic uveal melanoma and patients with metastatic cutaneous melanoma. A 1-year overall survival rate of 65% was achieved for both patient cohorts. On-treatment cytokine measurements were consistent with the induction of IFNγ pathway–related markers in the periphery and tumor. Notably, tebentafusp induced an increase in serum CXCL10 (a T-cell attractant) and a reduction in circulating CXCR3&lt;sup&gt;+&lt;/sup&gt; CD8&lt;sup&gt;+&lt;/sup&gt; T cells together with an increase in cytotoxic T cells in the tumor microenvironment. Furthermore, increased serum CXCL10 or the appearance of rash (likely due to cytotoxic T cells targeting gp100-expressing skin melanocytes) showed a positive association with patient survival.&lt;/p&gt;Conclusions:&lt;p&gt;These data suggest that redirecting T cells using a gp100-targeting TCR/anti-CD3 bispecific fusion protein may provide benefit to patients with metastatic melanoma. Furthermore, the activity observed in these two molecularly disparate melanoma classes hints at the broad therapeutic potential of tebentafusp.&lt;/p&gt;&lt;/div&gt;
Verbenacine and Salvinine: Two New Diterpenes from Salvia verbenaca (2004)

Two new diterpenes namely verbenacine (1) and salvinine (2) have been isolated from the aerial parts of Salvia verbenaca. Their structures have been elucidated on the basis of chemical and spectral data as 3alpha-hydroxy-19-carboxykaur-15-ene and 19-hydroxy-12,14-dioxo labda-15,17-diene.
Representações e Processos de Raciocínio na Comparação e Ordenação de Números Racionais numa Abordagem Exploratória (2014)

O presente estudo tem por base uma unidade de ensino de cunho exploratório, em que alunos do 5.º ano de escolaridade (de 10-11 anos) trabalham com várias representações dos números racionais, em diferentes significados e tipos de grandeza. Procuramos saber em que medida esta unidade leva os alunos a desenvolver a sua capacidade de comparação e ordenação de números racionais, levando-os a usar diferentes representações e processos de raciocínio informais e formais. A metodologia de investigação é qualitativa e interpretativa, com observação participante das aulas e o estudo de caso de uma aluna. Os resultados mostram que esta aluna desenvolveu a sua compreensão da ordenação e comparação de números racionais, mostrando-se mais proficiente nas representações decimal e em fração. O estudo sugere que o trabalho com diferentes representações, numa abordagem exploratória, permite que os alunos aprendam a comparar e ordenar números racionais combinando adequadamente processos de raciocínio formais e informais.
Rapid Quantification of SARS-Cov-2 Spike Protein Enhanced with a Machine Learning Technique Integrated in a Smart and Portable Immunosensor (2022)

An IoT-WiFi smart and portable electrochemical immunosensor for the quantification of SARS-CoV-2 spike protein was developed with integrated machine learning features. The immunoenzymatic sensor is based on the immobilization of monoclonal antibodies directed at the SARS-CoV-2 S1 subunit on Screen-Printed Electrodes functionalized with gold nanoparticles. The analytical protocol involves a single-step sample incubation. Immunosensor performance was validated in a viral transfer medium which is commonly used for the desorption of nasopharyngeal swabs. Remarkable specificity of the response was demonstrated by testing H1N1 Hemagglutinin from swine-origin influenza A virus and Spike Protein S1 from Middle East respiratory syndrome coronavirus. Machine learning was successfully used for data processing and analysis. Different support vector machine classifiers were evaluated, proving that algorithms affect the classifier accuracy. The test accuracy of the best classification model in terms of true positive/true negative sample classification was 97.3%. In addition, the ML algorithm can be easily integrated into cloud-based portable Wi-Fi devices. Finally, the immunosensor was successfully tested using a third generation replicating incompetent lentiviral vector pseudotyped with SARS-CoV-2 spike glycoprotein, thus proving the applicability of the immunosensor to whole virus detection.
Probing the active site of mammalian pyruvate dehydrogenase (1996)

The pyruvate dehydrogenase (E1) is the first catalytic component of the multienzyme pyruvate dehydrogenase complex (PDC). El catalyzes the two partial reactions: the thiamin pyrophosphate (TPP)-dependent decarboxylation of pyruvic acid to 2-hydroxyethylidene-TPP (HETPP) [Eq. 1] and reductive acetylation of lipoic acid residues covalently linked to the second catalytic component — dihydrolipoamide acetyltransferase (E2) [Eq. 2] (Reed, 1974): [1] $$C{H_3}COC{O_2} - + E{1_ - }TPP \to C{H_3}C\left( {OH} \right) = TPP - E1 + C{O_2}$$ 2 $$C{H_3}C\left( {OH} \right) = TPP - E1 + E2 - lipoates\left( {{S_2}} \right) \to ETPP + E2 - lipoate\left( {SH} \right)SCOC{H_3}$$ Mammalian E1 is a heterotetramer (α[2]β2) containing two 41 kDa α subunits and two kDa β subunits. The role of individual subunits is not clear. It was proposed that E1α can catalyze the first partial reaction and E1β the second (Roche and Reed, 1972). E1α is thought to be involved in TPP binding as it contains TPP motif found by sequence comparison of several TPP requiring enzymes (Hawkins et al., 1989). Recent evidence indicates that both subunits are involved in TPP binding (Robinson and Chun, 1993; Ali et al., 1995; Korotchkina et al., 1995).
Supramolecular cuboctahedra with aggregation-induced emission enhancement and external binding ability (2022)

Beyond the AIE (aggregation-induced emission) phenomenon in small molecules, supramolecules with AIE properties have evolved in the AIE family and accelerated the growth of supramolecular application diversity. Inspired by its mechanism, particularly the RIV (restriction of intramolecular vibrations) process, a feasible strategy of constructing an AIE-supramolecular cage based on the oxidation of sulfur atoms and coordination of metals is presented. In contrast to previous strategies that used molecular stacking to limit molecular vibrations, we achieved the desired goal using the synergistic effects of coordination-driven self-assembly and oxidation. Upon assembling with zinc ions, S1 was endowed with a distinct AIE property compared with its ligand L1, while S2 exhibited a remarkable fluorescence enhancement compared to L2. Also, the single cage-sized nanowire structure of supramolecules was obtained <i>via</i> directional electrostatic interactions with multiple anions and rigid-shaped cationic cages. Moreover, the adducts of zinc porphyrin and supramolecules were investigated and characterized by 2D DOSY, ESI-MS, TWIM-MS, UV-vis, and fluorescence spectroscopy. The protocol described here enriches the ongoing research on tunable fluorescence materials and paves the way towards constructing stimuli-responsive luminescent supramolecular cages.
Modeling of CNR characteristics under bandwidth limitation on transmission systems employing optical super wide‐band FM technique (2003)

Abstract With regards to an optical transmission system employing the optical super wide‐band FM technique, which realizes multichannel video distribution on existing optical access networks, this paper examines the bandwidth limitation on the wide‐band FM signal as a factor of CNR degradation theoretically and experimentally. The required bandwidth for an FM signal has been estimated by the Komai‐Carson law, but there have been few studies of the quantitative relationship between that bandwidth and the amount of CNR degradation. To analyze such CNR degradation, we proposed a model for bandwidth limitation on the wide‐band FM signal with the “equivalent noise pulse.” The CNR theory on our proposed model can explain the actual CNR characteristics with bandwidth limitation. The results show that the bandwidth required is more than four times the standard deviation of the FM spectrum in order to maintain the CNR degradation of less than 1 dB. © 2003 Wiley Periodicals, Inc. Electron Comm Jpn Pt 1, 87(1): 81–89, 2004; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/ecja.1184