gebhart/patrepeval huggingface dataset:
SARS-CoV-2 transmission in classroom settings: Effects of mitigation, age, and Delta variant (2021)

Traditional, in-person classroom settings have been limited during the COVID-19 pandemic due to their potential to transmit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) among students, teachers, and other educational workers. Using computational fluid dynamics simulations, mitigation strategies that span approaches using face coverings, various ventilation schemes, air purifiers/cleaners, and desk shields are systematically evaluated in thermally controlled classrooms. Individually, face coverings and source control were the most effective, which was followed by well-designed ventilation systems. The use of desk shields was also studied and appeared to be ineffective. The best mitigation approach is shown to be through multiple measures-using face coverings and ventilation systems combined with air purifiers. The studies were extended to elementary schools and consider Delta variants of SARS-CoV-2. In elementary settings, the reduced pulmonary and viral emission rates of small children are observed to drive reduced transmission rates, to values even lower than those observed with several mitigation methods for classrooms with adults. The Delta variant, with adults, was evaluated by considering an increase in quanta and indicated higher transmission probabilities. These increases are levels that are controllable by increasing the mitigation methods. Results indicate several plans of action for schools to return to in-person schooling in the context of age and new variants.
ChemInform Abstract: Zwittermicin A, an Antifungal and Plant Protection Agent from Bacillus cereus. (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Bounded Memory Adversarial Bandits with Composite Anonymous Delayed Feedback (2022)

We study the adversarial bandit problem with composite anonymous delayed feedback. In this setting, losses of an action are split into d components, spreading over consecutive rounds after the action is chosen. And in each round, the algorithm observes the aggregation of losses that come from the latest d rounds. Previous works focus on oblivious adversarial setting, while we investigate the harder nonoblivious setting. We show nonoblivious setting incurs Omega(T) pseudo regret even when the loss sequence is bounded memory. However, we propose a wrapper algorithm which enjoys o(T) policy regret on many adversarial bandit problems with the assumption that the loss sequence is bounded memory. Especially, for K armed bandit and bandit convex optimization, our policy regret bound is in the order of T to the two third. We also prove a matching lower bound for K armed bandit. Our lower bound works even when the loss sequence is oblivious but the delay is nonoblivious. It answers the open problem proposed in [Wang, Wang, Huang 2021], showing that nonoblivious delay is enough to incur the regret in the order of T to the two third.
Noursamycins, Chlorinated Cyclohexapeptides Identified from Molecular Networking of <i>Streptomyces noursei</i> NTR-SR4 (2019)

The noursamycins A-F are chlorinated cyclic hexapeptides, which were identified and isolated from the strain Streptomyces noursei NTR-SR4 overexpressing a LuxR-like transcriptional activator. The molecules were structurally characterized by mass spectrometric analyses and 1D and 2D NMR spectroscopic techniques. The enzymatic machinery involved in the biosynthesis of these peptides is represented by a modular nonribosomal peptide synthetase (NRPS), and the corresponding gene cluster was identified in the S. noursei genome. The latter suggested the biosynthetic pathway for the noursamycins. Spectral networking analysis uncovered noursamycin derivatives that were later found to result from a relaxed substrate specificity of the A<sub>3</sub> and A<sub>4</sub> adenylation domains of the NRPS. The stereochemistry of the amino acid constituents of the noursamycins was resolved by chemical derivatization, subsequent enantiomer analytics by GC-EIMS, and in silico data analyses. Noursamycins A and B exhibited antibacterial activity against Gram-positive and Gram-negative bacteria, while no apparent cytotoxicity was observed.
Response: Prognosis of stage I/II nonnasal extranodal NK/T cell lymphoma (2009)

between nasal and extranasal origins. Patients who initially presented with localized disease (clinical stage I or II) included 84 (68%) of those with ENKL of nasal origin, but only 10 (37%) of those with ENKL of extranasal origin. This difference is also documented in the literature, [3][4][5] as well as in the result from the PTCL project. 1 Notably, the prognostic difference disappeared after stratification by clinical stage (Figure We absolutely agree with the notion of Au et al that clinical behaviors of nasal and extranasal ENKLs are significantly different, but we should aware that the prognostic difference is derived from the different extent of each disease.
Nanoradioliposomes molecularly modulated to study the lung deep lymphatic drainage (2009)

the proposed method enables visualization of deep lymphatic lung network and lymph nodes. Besides, this technique involving the modulation of nanoradioliposomes targeting specific organs or tissues may be an important tool for diagnostic or even for therapeutic purposes.
On-chip measurements of protein unfolding from direct observations of micron-scale diffusion (2018)

Investigations of protein folding, unfolding and stability are critical for the understanding of the molecular basis of biological structure and function. We describe here a microfluidic approach to probe the unfolding of unlabelled protein molecules in microliter volumes. We achieve this objective through the use of a microfluidic platform, which allows the changes in molecular diffusivity upon folding and unfolding to be detected directly. We illustrate this approach by monitoring the unfolding of bovine serum albumin in solution as a function of pH. These results show the viability of probing protein stability on chip in small volumes.
Development of neutron spectrum unfolding method for advanced nuclear emulsion (2014)

In order to realize neutron spectroscopy in high-intensity gamma ray fields such as those present in spent nuclear fuel storage facilities using an advanced nuclear emulsion based on a non-sensitized OPERA film with AgBr grain sizes of 60 nm, a new neutron spectrum unfolding method has been developed. The response functions were evaluated in the neutron energy range between 0.1 and 4.5 MeV by Monte Carlo calculations. To realize a highly reliable unfolding method that does not require an initial guess spectrum, an algorithm was formulized based on the maximum entropy principle and the maximum likelihood method, and the new unfolding code MEALU was developed. The code performance was checked by analyses of mock-up data. As an example, the neutron spectrum from fresh fuel of the experimental fast reactor Joyo was calculated and track lengths were simulated using the calculated response function and the estimated spectrum. Comparison between the original neutron spectrum and the unfolded one confirmed the effectiveness of the proposed method.
Bioelectrical Impedance Analysis—An Easy Tool for Quantifying Body Composition in Infancy? (2020)

There has been increasing interest in understanding body composition in early life and factors that may influence its evolution. While several technologies exist to measure body composition in infancy, the equipment is typically large, and thus not readily portable, is expensive, and requires a qualified operator. Bioelectrical impedance analysis shows promise as an inexpensive, portable, and easy to use tool. Despite the technique being widely used to assess body composition for over 35 years, it has been seldom used in infancy. This may be related to the evolving nature of the fat-free mass compartment during this period. Nonetheless, a number of factors have been identified that may influence bioelectrical impedance measurements, which, when controlled for, may result in more accurate measurements. Despite this, questions remain in infants regarding the optimal size and placement of electrodes, the standardization of normal hydration, and the influence of body position on the distribution of water throughout the body. The technology requires further evaluation before being considered as a suitable tool to assess body composition in infancy.
Panel: Getting Global With It: Youth Global Participation in the Digital Age (2013)

With an internationally interdependent economy, unprecedented migration, and information continuously circulating the planet, children are growing up in a globalized world. In this 21st century world, children need to learn about international issues, develop intercultural understanding, and participate in the global society. Modern digital technologies provide new avenues for helping children gain these critical skills. At the click of a button, children in different countries can have a virtual playdate, collaborate on a project, or share media about their cultures. This panel brings together experts from technology companies, international NGOs, and nonprofits to discuss innovative initiatives that use technology to help children ages 7 – 11 learn about international issues, connect across cultures, and participate in the global society.
Evaluation of high-frequency vibrations using electronic speckle pattern interferometry (2003)

The available techniques for the study of high frequency vibration using electronic speckle pattern interferometry (ESPI) are briefly surveyed. We concentrate on two methods in particular. The first is a straightforward approach in which a CCD camera is used having a frame rate of at least twice the highest vibration frequency so that the sampling criterion is satisfied. The images are processed and analysed off-line. Digital phase shifting can be also implemented for detailed fringe analysis. The second approach is time-averaged ESPI in which the Bessel fringe function can be analysed in real time by modulating the optical path difference in the interferometer. This can be done either by using a vibrating component or, as in the present work, by direct modulation of the laser wavelength at the frequency of the vibrating mode.
Development of spirulina for the manufacture and oral delivery of protein therapeutics (2022)

The use of the edible photosynthetic cyanobacterium Arthrospira platensis (spirulina) as a biomanufacturing platform has been limited by a lack of genetic tools. Here we report genetic engineering methods for stable, high-level expression of bioactive proteins in spirulina, including large-scale, indoor cultivation and downstream processing methods. Following targeted integration of exogenous genes into the spirulina chromosome (chr), encoded protein biopharmaceuticals can represent as much as 15% of total biomass, require no purification before oral delivery and are stable without refrigeration and protected during gastric transit when encapsulated within dry spirulina. Oral delivery of a spirulina-expressed antibody targeting campylobacter-a major cause of infant mortality in the developing world-prevents disease in mice, and a phase 1 clinical trial demonstrated safety for human administration. Spirulina provides an advantageous system for the manufacture of orally delivered therapeutic proteins by combining the safety of a food-based production host with the accessible genetic manipulation and high productivity of microbial platforms.
Methylomic and phenotypic analysis of the ModH5 phasevarion of Helicobacter pylori (2017)

The Helicobacter pylori phase variable gene modH, typified by gene HP1522 in strain 26695, encodes a N<sup>6</sup>-adenosine type III DNA methyltransferase. Our previous studies identified multiple strain-specific modH variants (modH1 - modH19) and showed that phase variation of modH5 in H. pylori P12 influenced expression of motility-associated genes and outer membrane protein gene hopG. However, the ModH5 DNA recognition motif and the mechanism by which ModH5 controls gene expression were unknown. Here, using comparative single molecule real-time sequencing, we identify the DNA site methylated by ModH5 as 5'-G<sup>m6</sup>ACC-3'. This motif is vastly underrepresented in H. pylori genomes, but overrepresented in a number of virulence genes, including motility-associated genes, and outer membrane protein genes. Motility and the number of flagella of H. pylori P12 wild-type were significantly higher than that of isogenic modH5 OFF or ΔmodH5 mutants, indicating that phase variable switching of modH5 expression plays a role in regulating H. pylori motility phenotypes. Using the flagellin A (flaA) gene as a model, we show that ModH5 modulates flaA promoter activity in a GACC methylation-dependent manner. These findings provide novel insights into the role of ModH5 in gene regulation and how it mediates epigenetic regulation of H. pylori motility.
Understanding the structure details when drying hydrate crystals of pharmaceuticals – interpretations from diffuse scattering and inter-modulation satellites of a partially dehydrated crystal (2014)

Simplified models for the crystal lattice of the sesquihydrate form of the hemi-sulfate salt of (5S,6S,9R)-5-amino-6-(2,3-difluorophenyl)-6,7,8,9-tetrahydro-5H-cyclohepta[b]pyridin-9-yl 4-(2-oxo-2,3-dihydro-1H-imidazol[4,5b]pyridin-1-yl)-1-piperidine carboxylate (BMS-927711, C28H29F2N6O3(+)) are used to calculate diffuse diffraction features in order to develop a mechanistic understanding of the dehydration process with respect to disruption of the lattice, since a Bragg model cannot be established. The model demonstrates that what we observe when the water leaves the crystal is partial transformation from the parent form to a child form (a new form, less hydrated and structurally related to the parent). Yet this `dried' structure is not a pure phase. It consists of semi-random layers of both child, parent and an interfacial layer which has a modulated structure that represents a transitory phase. Understanding the fact that a single `dried' crystal can have the disordered layer structure described as well as understanding mechanistic relationships between the phases involved can have implications in understanding the effect of common large scale bulk drying procedures. During the development of BMS-927711, difficulties did arise during characterization of the dried bulk when using only routine solid-state analysis. The material is now better understood from this diffraction study. The diffraction experiments also reveal intermodulation satellites, which upon interpretation yield even more structural information about the crystal transformation. The model suggests the mechanism of transformation is laminar in which layers of the crystal are driven to approach a stable B-centered supercell phase of lower water content.
Zoledronic acid inhibits the earliest stages of vasculogenesis: blockage of the transdifferentiation of monocytes into endothelial cells induced by pleiotrophin and mCSF (2007)

4651 We have discovered a novel mechanism leading to blood vessel formation that involves the transdifferentiation of monocytes into endothelial cells by tumor cell production of pleiotrophin (PTN), a protein highly produced by myeloma (Chen et al, Blood 2005; Yeh et al, Br J Haematol 2006) and breast cancer (Zhang et al, JBC 1997) cells. The nitrogen-containing bisphosphonate zoledronic acid has been shown to inhibit bone loss and recent studies also demonstrate profound anti-angiogenic effects of this drug. The inhibitory effects of zoledronic acid on blood vessel formations remain unknown. We purified human monocytes (CD14+) and cultured these cells on collagen I-coated dishes. mCSF was added to the cells after 1 hour of culture. PTN was added twice to the culture, once after 24 hoursand again after 5 days with or without zoledronic acid or bortezomib. FLK-1 expression (VEGFR-2) showed that the cells incubated on collagen I without drugs formed tube-like structures in the presence of PTN and mCSF. However, the tube-like structures disappeared after adding zoledronic acid at either 1.5 or 0.15 uM. In order to examine whether zoledronic acid also reduces the expression of endothelial genes and proteins when monocytes are induced to transdifferentiate in the presence of these cytokines, we used RT-PCR and Western blot analysis on the endothelial cell markers Flk-1 Tie-2 and von Willebrand factor (vWF). The results of both RT-PCR and Western blot analysis showed that the expression of endothelial markers was blocked at zoledronic acid concentrations of 15uM, 1.5uM and 0.15uM. We further examined the effects of zoledronic acid on early stage angiogenesis in vivo using the chorioallantoic membrane (CAM) assay. Fertilized chick eggs were incubated horizontally at 38°C in a humidified incubator, windowed by day 3 of incubation and processed by day 8. The tested micro-sponge with zoledronic acid (1.5uM) or control reagents was implanted on the CAM. The eggs were sealed with adhesive tape and returned to the incubation for 48 hours. The assay scored positive when two independent observers reported a significant reduction of vessels in the treated area. The results of the CAM assay showed that compared to saline, zoledronic acid significantly reduced new macroscopic and microscopic vessel formation. These experiments define a previously unrecognized novel mechanism by which zoledronic acid may inhibit new blood vessel formation in cancer patients_preventing the transdifferentiation of monocytes into endothelial cells induced by PTN. They also suggest a specific new mechanism through which zoledronic acid has anti-angiogenic effects which provides further support for the potential anti-cancer effects of this agent.
Visions and reality: the idea of competence-oriented assessment for German medical students is not yet realised in licensing examinations (2017)

<b>Objective:</b> Competence orientation, often based on the CanMEDS model, has become an important goal for modern curricula in medical education. The National Competence Based Catalogue of Learning Objectives for Undergraduate Medical Education (NKLM) has been adopted in Germany. However, it is currently unknown whether the vision of competence orientation has also reached the licensing examination procedures. <b>Methods:</b> Therefore, a prospective, descriptive, single-centre, exemplary study design was applied to evaluate 4051 questions/tasks (from 28 examiners at 7 two-day licensing oral-practical exams) for undergraduate medical students at the University of Ulm. The oral and practical questions/tasks as well as the real bedside assessment were assigned to specific competence roles (NKLM section I), categories (NKLM section II) and taxonomy levels of learning domains. <b>Results:</b> Numerous questions/tasks were set per candidate (day 1/2: 70±24/86±19 questions) in the licensing oral-practical exam. Competence roles beyond the "medical expert" were scarcely considered. Furthermore, practical and communication skills at the bedside were hardly addressed (less than 3/15 min). Strikingly, there was a significant predominance of questions with a low-level taxonomy. <b>Conclusions:</b> The data indicate a misalignment of competence-oriented frameworks and the "real world" licensing practical-oral medical exam, which needs improvement in both evaluation and education processes.
Comparison of serum creatinine and serum cystatin C as biomarkers to detect sepsis-induced acute kidney injury and to predict mortality in CD-1 mice (2014)

Acute kidney injury (AKI) dramatically increases sepsis mortality, but AKI diagnosis is delayed when based on serum creatinine (SCr) changes, due in part, to decreased creatinine production. During experimental sepsis, we compared serum cystatin C (sCysC), SCr, and blood urea nitrogen (BUN) to inulin glomerular filtration rate (iGFR) before or 3-18 h after cecal ligation and puncture (CLP)-induced sepsis in CD-1 mice. sCysC had a faster increase and reached peak levels more rapidly than SCr in both sepsis and bilateral nephrectomy (BiNx) models. sCysC was a better surrogate of iGFR than SCr during sepsis. Combining sCysC with SCr values into a composite biomarker improved correlation with iGFR better than any biomarker alone or any other combination. We determined the renal contribution to sCysC handling with BiNx. sCysC and SCr were lower post-BiNx/CLP than post-BiNx alone, despite increased inflammatory and nonrenal organ damage biomarkers. Sepsis decreased CysC production in nephrectomized mice without changing body weight or CysC space. Sepsis decreased sCysC production and increased nonrenal clearance, similar to effects of sepsis on SCr. sCysC, SCr, and BUN were measured 6 h postsepsis to link AKI with mortality. Mice with above-median sCysC, BUN, or SCr values 6 h postsepsis died earlier than mice with below-median values, corresponding to a substantial AKI association with sepsis mortality in this model. sCysC performs similarly to SCr in classifying mice at risk for early mortality. We conclude that sCysC detects AKI early and better reflects iGFR in CLP-induced sepsis. This study shows that renal biomarkers need to be evaluated in specific contexts.
Hydrolysis Deposition of Thin Films of Antimony‐Doped Tin Oxide (2001)

Thin films of antimony‐doped tin oxide have been obtained by a new technique, the so‐called hydrolysis deposition method, in which hydrolyzed solids are precipitated from metal fluoride solutions. Mixed solutions of SnF 3 and SbF 3 produce antimony‐ and fluorine‐doped tin oxide films. The amount of antimony can be controlled in a wide range by adjusting the initial fluoride concentrations of the solution. The film containing 2.9 mol% antimony heated at 500°C has an electrical resistivity of 1.0 × 10 − 3 Ω·cm, which is lower than previously obtained by wet‐chemical techniques.
Gα<sub>olf</sub>Levels Are Regulated by Receptor Usage and Control Dopamine and Adenosine Action in the Striatum (2001)

In the striatum, dopamine D(1) and adenosine A(2A) receptors stimulate the production of cAMP, which is involved in neuromodulation and long-lasting changes in gene expression and synaptic function. Positive coupling of receptors to adenylyl cyclase can be mediated through the ubiquitous GTP-binding protein Galpha(S) subunit or through the olfactory isoform, Galpha(olf), which predominates in the striatum. In this study, using double in situ hybridization, we show that virtually all striatal efferent neurons, identified by the expression of preproenkephalin A, substance P, or D(1) receptor mRNA, contained high amounts of Galpha(olf) mRNA and undetectable levels of Galpha(s) mRNA. In contrast, the large cholinergic interneurons contained both Galpha(olf) and Galpha(s) transcripts. To assess the functional relationship between dopamine or adenosine receptors and G-proteins, we examined G-protein levels in the striatum of D(1) and A(2A) receptor knock-out mice. A selective increase in Galpha(olf) protein was observed in these animals, without change in mRNA levels. Conversely, Galpha(olf) levels were decreased in animals lacking a functional dopamine transporter. These results indicate that Galpha(olf) protein levels are regulated through D(1) and A(2A) receptor usage. To determine the functional consequences of changes in Galpha(olf) levels, we used heterozygous Galpha(olf) knock-out mice, which possess half of the normal Galpha(olf) levels. In these animals, the locomotor effects of amphetamine and caffeine, two psychostimulant drugs that affect dopamine and adenosine signaling, respectively, were markedly reduced. Together, these results identify Galpha(olf) as a critical and regulated component of both dopamine and adenosine signaling.