gebhart/patrepeval huggingface dataset:
Atkins’ Physical Chemistry (2022)

<italic>Physical Chemistry</italic> provides a comprehensive overview of this topic. It starts off with looking into the properties of gases. It then covers the First, Second, and Third Laws. Next it looks into physical transformations of pure substances, simple mixtures, and chemical equilibrium. The text also considers quantum theory, atomic structure and spectra, molecular structure, molecular symmetry, and molecular spectroscopy. There follows a chapter about magnetic resonance. The text then looks at statistical thermodynamics. The last quarter of the book considers molecular interactions, solids, molecules in motion, chemical kinetic, and reaction dynamics. The last chapter covers processes at solid surfaces.
Crystal structure of the Streptococcus pneumoniae mevalonate kinase in complex with diphosphomevalonate (2007)

Streptococcus pneumoniae, a ubiquitous gram-positive pathogen with an alarming, steadily evolving resistance to frontline antimicrobials, poses a severe global health threat both in the community and in the clinic. The recent discovery that diphosphomevalonate (DPM), an essential intermediate in the isoprenoid biosynthetic pathway, potently and allosterically inhibits S. pneumoniae mevalonate kinase (SpMK) without affecting the human isozyme established a new target and lead compound for antimicrobial design. Here we present the crystal structure of the first S. pneumoniae mevalonate kinase, at a resolution of 2.5 A and in complex with DPM.Mg(2+) in the active-site cleft. Structural comparison of SpMK with other members of the GHMP kinase family reveals that DPM functions as a partial bisubstrate analog (mevalonate linked to the pyrophosphoryl moiety of ATP) in that it elicits a ternary-complexlike form of the enzyme, except for localized disordering in a region that would otherwise interact with the missing portion of the nucleotide. Features of the SpMK-binding pockets are discussed in the context of established mechanistic findings and inherited human diseases linked to MK deficiency.
Electrical field interactions in different cochlear implant systems (2003)

The goal of this study was to evaluate electrical field interactions produced by the stimulation of different types of intracochlear electrodes in 12 adult subjects (three Ineraid, four Clarion S-Series, three S-Series with the electrode positioning system-EPS and two Clarion HiFocus-I with the EPS). Psychophysical measurements were conducted with biphasic stimuli (813 pulse per second, 153.8 micros/phase). "Perturbation" signals (300 ms) were applied to one electrode chosen at the middle of the array and their effects on detection thresholds of "probe" signals (30 ms) were measured on the neighbor basal electrode. Perturbation levels were set below the detection threshold of the perturbation electrode (-2 dB re threshold). Measurements were first conducted for simultaneous stimulation of the probe and of the perturbation electrodes, for monopolar for all subjects and for bipolar stimulus configurations for both Clarion HiFocus-I subjects. The tested Clarion electrodes did not present lower monopolar interactions than the Ineraid electrodes. Nevertheless, considering the shorter distance between electrodes for the Clarion than for the Ineraid, the tested Clarion electrodes might be more selective than the Ineraid. We did not find any significant monopolar electrical field-interaction differences between subjects who received the S-Series array with and without the EPS. We did not find lower interactions for both subjects who received the HiFocus-I array than for subjects who received the S-Series. Electrical field interactions were lower for bipolar than for monopolar configurations for both HiFocus-I subjects. A second set of measurements was conducted for nonsimultaneous stimulation similar to the one used in continuous interleaved sampling sound strategy. These measurements showed that interactions evaluated for simultaneous biphasic stimuli were larger than for nonsimultaneous stimulation.
Terahertz sensing of corneal hydration (2010)

An indicator of ocular health is the hydrodyanmics of the cornea. Many corneal disorders deteriorate sight as they upset the normal hydrodynamics of the cornea. The mechanisms include the loss of endothelial pump function of corneal dystophies, swelling and immune response of corneal graft rejection, and inflammation and edema, which accompany trauma, burn, and irritation events. Due to high sensitivity to changes of water content in materials, a reflective terahertz (300 GHz and 3 THz) imaging system could be an ideal tool to measure the hydration level of the cornea. This paper presents the application of THz technology to visualize the hydration content across ex vivo porcine corneas. The corneas, with a thickness variation from 470 - 940 µm, were successfully imaged using a reflective pulsed THz imaging system, with a maximum SNR of 50 dB. To our knowledge, no prior studies have reported on the use of THz in measuring hydration in corneal tissues or other ocular tissues. These preliminary findings indicate that THz can be used to accurately sense hydration levels in the cornea using a pulsed, reflective THz imaging system.
Do an Altered Gut Microbiota and an Associated Leaky Gut Affect COVID-19 Severity? (2021)

Coronavirus disease 2019 (COVID-19), which has been declared a pandemic, has exhibited a wide range of severity worldwide. Although this global variation is largely affected by socio-medical situations in each country, there is also high individual-level variation attributable to elderliness and certain underlying medical conditions, including high blood pressure, diabetes, and obesity. As both elderliness and the aforementioned chronic conditions are often associated with an altered gut microbiota, resulting in disrupted gut barrier integrity, and gut symptoms have consistently been associated with more severe illness in COVID-19 patients, it is possible that dysfunction of the gut as a whole influences COVID-19 severity. This article summarizes the accumulating evidence that supports the hypothesis that an altered gut microbiota and its associated leaky gut may contribute to the onset of gastrointestinal symptoms and occasionally to additional multiorgan complications that may lead to severe illness by allowing leakage of the causative coronavirus into the circulatory system.
The structural biology of enzymes involved in natural product glycosylation (2012)

The glycosylation of microbial natural products often dramatically influences the biological and/or pharmacological activities of the parental metabolite. Over the past decade, crystal structures of several enzymes involved in the biosynthesis and attachment of novel sugars found appended to natural products have emerged. In many cases, these studies have paved the way to a better understanding of the corresponding enzyme mechanism of action and have served as a starting point for engineering variant enzymes to facilitate to production of differentially-glycosylated natural products. This review specifically summarizes the structural studies of bacterial enzymes involved in biosynthesis of novel sugar nucleotides.
Noninvasive prenatal aneuploidy testing of chromosomes 13, 18, 21, X, and Y, using targeted sequencing of polymorphic loci (2012)

This informatics-based method noninvasively detected fetuses with trisomy 13, 18, and 21, 45,X, and 47,XXY with high sample-specific calculated accuracies for each individual chromosome and across all five chromosomes.
Study of Ti-Ni-Nb Shape Memory Alloys with a Wide Hysteresis (2000)

It has been shown that TiNiNb shape memory alloys exhibit a wide transformation hysteresis compared to TiNi binary alloys (about 145°C versus 30°C). This wide hysteresis has important engineering utility. The present paper was undertaken to review of the microstructure. mechanical behavior, deformation-induced martensitic transformation and the effect of deformation on the stability of martensite and its reverse transformation in TiNiNb alloys. Simultaneously, the strain recovery characteristic and interface structure of martensite were explained, and the mechanism for increasing martensite stability by deformation was discussed. In addition, the microstructure and interface structure inside the stress-induced martensite (SIM) variants were evaluated. It is found that the morphology and substructure of SIM depend on deformation condition. The tensile deformation at parent phase condition has great influence on the substructure and interface structure of SIM variants. The most distinctive substructural feature of the stress-induced martensite is the presence of the various secondary twins. Based on the analysis of the stability and shape memory effect of various kinds of martensite, the concept of stability of deformed stress-induced martensite was proposed and explained by the mechanism for the formation of several secondary deformation twins.
Educación para el desarrollo o educación orientada a la transformación social (2016)

El presente artículo tiene como objetivo principal realizar un análisis referente al tipo de desarrollo que se pretende lograr en la sociedad a partir de la implementación de un enfoque pedagógico en las instituciones de educación en Colombia; de igual forma, pretende exhortar a los autores de la academia a la reflexión acerca de su papel en los procesos de enseñanza aprendizaje y la importancia que tiene adoptar una actitud humanística en su práctica docente que vaya más allá de la transmisión de conocimiento a los estudiantes; sino que se logre, convencerlos mediante el ejemplo, que la felicidad y el desarrollo profesional y personal, no puede depender del consumismo y de los malos hábitos, los cuales pueden tener consecuencias globales. Es decir, enseñarles a los estudiantes a ser responsables de sus decisiones, pensando siempre en el efecto que éstas pueden tener en la sociedad.
xCell: digitally portraying the tissue cellular heterogeneity landscape (2017)

Tissues are complex milieus consisting of numerous cell types. Several recent methods have attempted to enumerate cell subsets from transcriptomes. However, the available methods have used limited sources for training and give only a partial portrayal of the full cellular landscape. Here we present xCell, a novel gene signature-based method, and use it to infer 64 immune and stromal cell types. We harmonized 1822 pure human cell type transcriptomes from various sources and employed a curve fitting approach for linear comparison of cell types and introduced a novel spillover compensation technique for separating them. Using extensive in silico analyses and comparison to cytometry immunophenotyping, we show that xCell outperforms other methods. xCell is available at http://xCell.ucsf.edu/ .
Sexual dimorphism in reduced-size liver ischemia and reperfusion injury in mice: Role of endothelial cell nitric oxide synthase (2003)

We have recently reported that female mice are protected to a much greater extent from the injurious effects of reduced-size liver ischemia and reperfusion (RSL+I/R) than are males by an estrogen-dependent mechanism. The objective of this study was to examine the possibility that the protective effect observed in female mice depends on the up-regulation and/or activation of endothelial cell NO synthase (eNOS). Anesthetized female and male wild-type or eNOS-deficient C57BL/6 mice were subjected to 70% liver ischemia for 45 min followed by resection of the remaining 30% nonischemic lobes and reperfusion of ischemic tissue. Survival was monitored daily, whereas liver injury was quantified by using serum alanine aminotransferase determinations and histopathology. Hepatic eNOS mRNA, protein, and enzymatic activity were determined in male and female mice subjected to RSL+I/R. We found that liver injury was reduced and survival increased in female mice compared with males. This protective effect correlated with significant increases in hepatic eNOS message levels and enzyme activity but not protein expression compared with males subjected to the surgery. Furthermore, N(omega)-nitro-L-arginine methyl ester-treated or eNOS-deficient female mice responded to RSL+I/R with dramatic increases in liver injury and 100% mortality within 2 days of surgery. Finally, we found that pravastatin pretreatment significantly attenuated hepatocellular injury and increased survival of male mice, which was associated with enhanced expression of eNOS message. We conclude that the protective effect afforded female mice is due to the activation of hepatic eNOS activity and enhanced NO production.
Chemiluminescence from cis-diethoxy-1,2-dioxetane. Unexpected effect of oxygen (1971)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChemiluminescence from cis-diethoxy-1,2-dioxetane. Unexpected effect of oxygenTherese Wilson and A. Paul SchaapCite this: J. Am. Chem. Soc. 1971, 93, 17, 4126–4136Publication Date (Print):August 1, 1971Publication History Published online1 May 2002Published inissue 1 August 1971https://pubs.acs.org/doi/10.1021/ja00746a005https://doi.org/10.1021/ja00746a005research-articleACS PublicationsRequest reuse permissionsArticle Views329Altmetric-Citations159LEARN 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
Characterization of a Bifunctional Enzyme Fusion of Trehalose-6-Phosphate Synthetase and Trehalose-6-Phosphate Phosphatase of Escherichia coli (2000)

To test the effect of the physical proximity of two enzymes catalyzing sequential reactions, a bifunctional fusion enzyme, TPSP, was constructed by fusing the Escherichia coli genes for trehalose-6-phosphate (T6P) synthetase (TPS) and trehalose-6-phosphate phosphatase (TPP). TPSP catalyzes the sequential reaction in which T6P is formed and then dephosphorylated, leading to the synthesis of trehalose. The fused chimeric gene was overexpressed in E. coli and purified to near homogeneity; its molecular weight was 88,300, as expected. The K(m) values of the TPSP fusion enzyme for the sequential overall reaction from UDP-glucose and glucose 6-phosphate to trehalose were smaller than those of an equimolar mixture of TPS and TPP (TPS/TPP). However, the k(cat) values of TPSP were similar to those of TPS/TPP, resulting in a 3.5- to 4.0-fold increase in the catalytic efficiency (k(cat)/K(m)). The K(m) and k(cat) values of TPSP and TPP for the phosphatase reaction from T6P to trehalose were quite similar. This suggests that the increased catalytic efficiency results from the proximity of TPS and TPP in the TPSP fusion enzyme. The thermal stability of the TPSP fusion enzyme was quite similar to that of the TPS/TPP mixture, suggesting that the structure of each enzyme moiety in TPSP is unperturbed by intramolecular constraint. These results clearly demonstrate that the bifunctional fusion enzyme TPSP catalyzing sequential reactions has kinetic advantages over a mixture of both enzymes (TPS and TPP). These results are also supported by the in vivo accumulation of up to 0.48 mg of trehalose per g of cells after isopropyl-beta-D-thiogalactopyranoside treatment of cells harboring the construct encoding TPSP.
The complete amino acid sequence of human serum transferrin. (1982)

The complete amino acid sequence of human serum transferrin has been determined by aligning the structures of the 10 CNBr fragments. The order of these fragments in the polypeptide chain is deduced from the structures of peptides overlapping methionine residues and other evidence. Human transferrin contains 678 amino acid residues and--including the two asparagine-linked glycans--has an overall molecular weight of 79,550. The polypeptide chain contains two homologous domains consisting of residues 1-336 and 337-678, in which 40% of the residues are identical when aligned by inserting gaps at appropriate positions. Disulfide bond arrangements indicate that there are seven residues between the last half-cystine in the first domain and the first half-cystine in the second domain and therefore, a maximum of seven residues in the region of polypeptide between the two domains. Transferrin--which contains two Fe-binding sites--has clearly evolved by the contiguous duplication of the structural gene for an ancestral protein that had a single Fe-binding site and contained approximately 340 amino acid residues. The two domains show some interesting differences including the presence of both N-linked glycan moieties in the COOH-terminal domain at positions 413 and 610 and the presence of more disulfide bonds in the COOH-terminal domain (11 compared to 8). The locations of residues that may function in Fe-binding are discussed.
Three-body recombination rate of atomic nitrogen in low-pressure plasma flows (1996)

A nonlinear collisional-radiative model for atomic nitrogen has been developed in order to determine effective recombination and associated ionization coefficients for either optically thin or optically thick plasmas where ${10}^{18}$ ${\mathrm{m}}^{\mathrm{\ensuremath{-}}3}$\ensuremath{\leqslant}${\mathit{n}}_{\mathit{e}}$\ensuremath{\leqslant}${10}^{21}$ ${\mathrm{m}}^{\mathrm{\ensuremath{-}}3}$ and 2000 K\ensuremath{\leqslant}${\mathit{T}}_{\mathit{e}}$\ensuremath{\leqslant}12 000 K. A time-dependent approach confirms the importance of the quasi-steady-state condition to derive meaningful rate coefficients. In order to implement these coefficients in plasma flow codes, simple analytical expressions are proposed. Significant discrepancies with existing literature values are pointed out and discussed. In recombining conditions, the relaxation time necessary to reach the quasi-steady-state is calculated, and depends on the electron number density and on the electron temperature. This time limits the validity of the recombination coefficient, especially in optically thick cases. Finally, for practical applications, the number of levels in Saha-Boltzmann equilibrium at the quasi-steady-state is also examined. \textcopyright{} 1996 The American Physical Society.
MaxiK channel partners: physiological impact (2005)

The basic functional unit of the large‐conductance, voltage‐ and Ca 2 + ‐activated K + (MaxiK, BK, BK Ca ) channel is a tetramer of the pore‐forming α‐subunit (MaxiKα) encoded by a single gene, Slo , holding multiple alternative exons. Depending on the tissue, MaxiKα can associate with modulatory β‐subunits (β1–β4) increasing its functional diversity. As MaxiK senses and regulates membrane voltage and intracellular Ca 2 + , it links cell excitability with cell signalling and metabolism. Thus, MaxiK is a key regulator of vital body functions, like blood flow, uresis, immunity and neurotransmission. Epilepsy with paroxysmal dyskinesia syndrome has been recognized as a MaxiKα‐related disorder caused by a gain‐of‐function C‐terminus mutation. This channel region is also emerging as a key recognition module containing sequences for MaxiKα interaction with its surrounding signalling partners, and its targeting to cell‐specific microdomains. The growing list of interacting proteins highlights the possibility that associations with the C‐terminus of MaxiKα are dynamic and depending on each cellular environment. We speculate that the molecular multiplicity of the C‐terminus (and intracellular loops) dictated by alternative exons may modulate or create additional interacting sites in a tissue‐specific manner. A challenge is the dissection of MaxiK macromolecular signalling complexes in different tissues and their temporal association/dissociation according to the stimulus.
Modeling active RNA structures using the intersection of conformational space: Application to the lead-activated ribozyme (1998)

The Pb2+ cleavage of a specific phosphodiester bond in yeast tRNA(Phe) is the classical model of metal-assisted RNA catalysis. In vitro selection experiments have identified a tRNA(Phe) variant, the leadzyme, that is very active in cleavage by Pb2+. We present here a three-dimensional modeling protocol that was used to propose a structure for this ribozyme, and is based on the computation of the intersection of conformational space of sequence variants and the use of chemical modification data. Sequence and secondary structure data were used in a first round of computer modeling that allowed identification of conformations compatible with all known leadzyme variants. Common conformations were then tested experimentally by evaluating the activity of analogues containing modified nucleotides in the catalytic core. These experiments led to a new structural hypothesis that was tested in a second round of computer modeling. The resulting proposal for the active conformation of the leadzyme is consistent with all known structural data. The final model suggests an in-line SN2 attack mechanism and predicts two Pb2+ binding sites. The protocol presented here is generally applicable in modeling RNAs whenever the catalytic or binding activity of structural analogues is known.
High intratumoral expression of fibroblast activation protein (FAP) in colon cancer is associated with poorer patient prognosis (2013)

An active stroma is important for cancer cell invasion and metastasis. We investigated the expression of fibroblast activation protein (FAP) in relation to patient prognosis in colorectal cancer. Colorectal cancer specimens from 449 patients were immunohistochemically stained with a FAP antibody and evaluated in the tumor center and tumor front using a semiquantitative four-level scale. FAP was expressed by fibroblasts in 85-90 % of the tumors examined. High versus no/low expression in the tumor center was associated with poor prognosis (multivariate hazard ratio, HR = 1.72; 95 % CI 1.07-2.77, p = 0.025). FAP expression in the tumor front, though more frequent than in the tumor center, was not associated with prognosis. FAP expression in the tumor center was more common in specimens with positive microsatellite instability (MSI) screening status and in patients with high CpG island methylator phenotype (CIMP) status. However, inclusion of MSI screening status and CIMP status in the multivariate analysis strengthened the risk estimates for high FAP expression in the tumor center (HR = 1.89; 95 % CI 1.13-3.14; p = 0.014), emphasizing the role of FAP as an independent prognostic factor. Stromal FAP expression is common in colorectal cancer, and we conclude that high FAP expression in the tumor center, but not the tumor front, is an independent negative prognostic factor.
Intraoperative Brief Electrical Stimulation of the Spinal Accessory Nerve (BEST SPIN) for prevention of shoulder dysfunction after oncologic neck dissection: A double-blinded, randomized controlled trial (2018)

Clinicaltrials.gov ( NCT02268344 , October 17, 2014).