gebhart/patrepeval huggingface dataset:
A Novel Concept for Combinatorial Chemistry in Solution: Synthesis of Highly Substituted Pyrrolidines by Multicomponent Domino Reactions (2002)

Abstract The multicomponent domino Knoevenagel hetero‐ Diels  Alder hydrogenation process of N ‐[(benzyloxy)carbonyl(Cbz)‐protected amino aldehydes with N , N ‐dimethylbarbituric acid and the trimethylsilyl enol ethers 1 – 3 leads to the formation of the substituted pyrrolidines 12 – 15 . Under the same conditions, reaction of the trimethylsilyl enol ether 4 , obtained from acetophenone, gave the primary amines 18a , b probably due to a hydrogenolytic cleavage of the intermediately formed pyrrolidines. The zwitterionic products were obtained in high purity simply by precipitation with Et 2 O.
Influence of methionine biosynthesis on serine transhydroxymethylase regulation in Salmonella typhimurium LT2 (1977)

The enzyme serine transhydroxymethylase (EC 2.1.2.1; L-serine:tetrahydrofolate-5,10-hydroxymethyltransferase) is responsible both for the synthesis of glycine from serine and production of the 5,10-methylenetetrahydrofolate necessary as a methyl donor for methionine synthesis. Two mutants selected for alteration in serine transhydroxymethylase regulation also have phenotypes characteristic of metK (methionine regulatory) mutants, including ethionine, norleucine, and alpha-methylmethionine resistance and reduced levels of S-adenosylmethionine synthetase (EC 2.5.1.6; adenosine 5'-triphosphate:L-methionine S-adenosyltransferase) activity. Because this suggested the existence of a common regulatory component, the regulation of serine transhydroxymethylase was examined in other methionine regulatory mutants (metK and metJ mutants). Normally, serine transhydroxymethylase levels are repressed three- to sixfold in cells grown in the presence of serine, glycine, methionine, adenine, guanine, and thymine. This does not occur in metK and metJ mutants; thus, these mutations do affect the regulation of both serine transhydroxymethylase and the methionine biosynthetic enzymes. Lesions in the metK gene have been reported to reduce S-adenosylmethionine synthetase levels. To determine whether the metK gene actually encodes for S-adenosylmethionine synthetase, a mutant was characterized in which this enzyme has a 26-fold increased apparent Km for methionine. This mutation causes a phenotype associated with metK mutants and is cotransducible with the serA locus at the same frequency as metK lesions. Thus, the affect of metK mutations on the regulation of glycine and methionine synthesis in Salmonella typhimurium appears to be due to either an altered S-adenosylmethionine synthetase or altered S-adenosylmethionine pools.
Low-Latency and Secure Computation Offloading Assisted by Hybrid Relay-Reflecting Intelligent Surface (2021)

Recently, the hybrid relay-reflecting intelligent surface (HRRIS) has been introduced as a spectral- and energy-efficient architecture to assist wireless communication systems. In the HRRIS, a single or few active relay elements are deployed along with a large number of passive reflecting elements, allowing it to not only reflect but also amplify the incident signals. In this work, we investigate the potential of the HRRIS in aiding the computation offloading in a single-user mobile edge computing system. The objective is to minimize the offloading latency while ensuring the secrecy of user data against a malicious eavesdropper. We develop efficient solutions to this latency minimization problem based on alternating optimization. Through numerical results, we show that the deployment of the HRRIS can result in a considerable reduction in latency. Furthermore, the latency reduction gain offered by the HRRIS is much more significant than that of the conventional reconfigurable intelligent surface (RIS).
RNA-seq analysis does not substantiate a causative link between herpes virus infection and IPF (2015)

There are a number of publications showing an association between herpes virus infection and idiopathic pulmonary fibrosis (IPF). These reports use immunohistochemistry and/or PCR, which are susceptible to specificity artifacts. Thus, we investigated the possible association between IPF and viral RNA expression using next-generation sequencing, which has the potential to provide both a high degree of sensitivity as well as specificity. We quantified viral RNA expression for 740 viruses in 21 IPF patient lung biopsy samples and 17 age-matched controls. Our RNA-seq results were confirmed using Real-time RT-PCR for select viruses (EBV, herpes Saimiri and HERV-k). HERV-k expression was examined because of reports indicating that it is elevated in other fibrotic diseases, and because conceptually HERV-k could promote fibrogenesis by inducing cellular stress. Moreover, HERV-k expression is reported to be enhanced in response to herpes virus infection. Although we identified sporadic low-level evidence of viral infections in our lung tissue samples, we did not find statistical difference for expression of any virus, including HERV-k, between IPF and control lungs. To our knowledge, this is the first report that employs RNA-seq to assess whether or not viral infections are linked to IPF. Our results do not address the role of viral infection in the so-called acute exacerbation of IPF, however, they clearly do not support a causative connection between herpes virus infection and IPF.
Ab Initio Investigation of Strain Dependent Atomistic Interactions at Two Tropocollagen-Hydroxyapatite Interfaces (2013)

Tropocollagen (TC) and hydroxyapatite (HAP) interfaces are one of the main load bearing entities in bone family of materials. Atomistic interactions in such interfaces occur in a variety of chemical environments under a range of biomechanical loading conditions. It is challenging to investigate such interactions using traditional analytical or using classical molecular simulation approaches owing to their limitations in predicting bond strength change as a function of change in chemical environment. In the present work, 3D ab initio molecular dynamics simulations are used to understand such atomistic interactions by analyzing tensile strain dependent deformation mechanism and strength of two structurally distinct idealized TC-HAP interfaces in hydrated as well as unhydrated environments. Analyses suggest that the presence of water molecules leads to modification of H-bond density at the interfaces that also depends upon the level of strain. TC molecules become stiffer in the presence of water due to the presence of H-bonds. Bond forming-and-breaking cycle change as a function of H-bond density lies at the heart of TC-HAP interfacial shear deformation. Consequently, interfaces with TC molecule placed flat on the HAP crystal surface experience significantly higher shear stress during deformation in comparison to the interfaces with TC molecule placed with their axes perpendicular to the HAP surface.
Models of chronic disease management in primary care for patients with mild‐to‐moderate asthma or COPD: a narrative review (2008)

The role of primary health care in management of mild-to-moderate asthma and COPD requires further investigation using randomised controlled trials.
Current challenges and solutions of de novo assembly (2019)

Background Next‐generation sequencing (NGS) technologies have fostered an unprecedented proliferation of high‐throughput sequencing projects and a concomitant development of novel algorithms for the assembly of short reads. However, numerous technical or computational challenges in de novo assembly still remain, although many new ideas and solutions have been suggested to tackle the challenges in both experimental and computational settings. Results In this review, we first briefly introduce some of the major challenges faced by NGS sequence assembly. Then, we analyze the characteristics of various sequencing platforms and their impact on assembly results. After that, we classify de novo assemblers according to their frameworks (overlap graph‐based, de Bruijn graph‐based and string graph‐based), and introduce the characteristics of each assembly tool and their adaptation scene. Next, we introduce in detail the solutions to the main challenges of de novo assembly of next generation sequencing data, single‐cell sequencing data and single molecule sequencing data. At last, we discuss the application of SMS long reads in solving problems encountered in NGS assembly. Conclusions This review not only gives an overview of the latest methods and developments in assembly algorithms, but also provides guidelines to determine the optimal assembly algorithm for a given input sequencing data type.
CTX Prophages in Vibrio cholerae O1 Strains (2014)

The classical biotype strains of the Vibrio cholerae O1 serogroup harbor the biotype-specific cholera-toxin encoding phage (CTX) CTX(cla), and the El Tor biotype strains contain CTX-1. Although the classical biotype strains have become extinct, a remnant of classical CTX phage is transferred to the El Tor biotype strains. The prototype El Tor strains, which produce the biotype-specific cholera toxin, are now being replaced by atypical El Tor variant strains producing classical biotype cholera toxin. The genome sequences of the CTX phages in atypical El Tor strains indicate that the CTX phages in atypical El Tor strains are a mosaic of CTXcla and CTX-1. Before the emergence of atypical El Tor stains in the early 1990s, unusual pre-seventh pandemic strains were isolated in the US Gulf Coast between 1973 and 1986. These strains have characteristics of atypical El Tor strains since they are El Tor biotype strains containing CTX(cla), yet the genome sequence of this CTX phage indicates that it is different from CTXcla and is therefore classified separately as CTX(US Gulf).
Coronary computed tomography: choosing the right patient for the right clinical entity. (2005)

In the past 3 years, immense progress has been made in the development of a new non-invasive diagnostic technique for the evaluation of coronary artery disease – coronary CT angiography. The current IMAJ issue includes two original studies that evaluate this new and promising imaging modality in patients with suspected CAD [1,2]. The principles of computed tomography were first investigated in the mid-1950s, but it was not until 1972 that the first generation of CT scanners was introduced. Invented by British engineer Godfrey Hounsfield of EMI Laboratories, England, the first CT scanner required several hours to acquire the raw data for a single scan or “slice,” and days to reconstruct a single image from these raw data. Hounsfield was later awarded the Nobel Peace Prize for his contributions to medicine and science. The first clinical CT scanners were installed between 1974 and 1976. At that time, approximately 5 minutes were needed to acquire one tomographic image. Initial scanners were only suitable for head examinations because the opening in the gantry was small. Improvements in components of the scanners and techniques allowed scanning of any part of the body, and in 1976 whole-body scanners became available. By the early 1980s CT technology was used widely. The last 20 years have seen the development of several generations of CT scanners. The most important was the introduction of the technique in the early 1990s. With this technique (also known as volumetric scanning), the X-ray point source and the detector array are placed on opposite sides of the patient on a ring-like structure called the gantry. The patient on the table is moved continuously through the scan field in the z direction while the gantry performs multiple rotations around the patient. The X-ray thus traces a spiral around the body and produces a data volume. This large data volume is then sent to a computer that can reconstruct multiple overlapping axial slices, as much as needed, with no additional cost of ionizing radiation exposure to the patient. Overlapping axial images enable the reformation of various types of high quality three-dimensional images on a post-processing station. The
Influenza virus infection of human ciliated respiratory epithelial cells in culture (2013)

Introduction: Influenza is a major cause of paediatric respiratory disease initially infecting and replicating in the respiratory epithelium. Data is limited on the initial effects of influenza A virus on human ciliated respiratory epithelium. In this study we investigated the earliest stages of infection of ciliated epithelial cultures from healthy individuals. Methods Ciliated epithelial cells were cultured from nasal brush biopsies (n=7). Cells were infected with Influenza A/PR8 for up to 24h. Cilia were videoed using a high speed digital camera and the number of motile ciliated cells in each sample area was counted, half of which were used to determine the average CBF. Apical fluid was removed for evaluation of cytokine and chemokine response before and after infection. Cells were fixed and stained using anti-influenza HA antigen (Alexa594) and anti-β tubulin (FITC) antibodies. Confocal optical sectioning of stained slides was performed. Results Ciliary beat frequency was unaffected by influenza A infection over 24 hours, however, the number of motile ciliated cells (median (IQR)) was significantly decreased from 13 (6-14) to 5 (5-7) cells/4.2mm2 following infection. Influenza A infection caused a significant (P Conclusion Ciliary beat frequency was unaffected by influenza A infection over 24 hours, however, a significant reduction in cells with beating cilia was observed.
A novel approach of generating stereoscopic images using defocus (2016)

Direct 2D-to-3D conversion is an important task with various manual or automatic methods to satisfy the rapidly increasing requirements on stereoscopic contents. In order to construct stereoscopic images, defocus is adopted to estimate the depth from a single image and a novel layered structure is proposed in this paper. A simple searching and filtering-based method is proposed for finding the best layering result with a comparison of performances between our method and certain existing unsupervised learning methods to determine the optimum approach for automatic choice of the layered threshold, which can be used to generate a set of layered RGB images by combining with the depth map. Then the planar layered model is constructed and texture is mapped from image onto the planes. With the help of the proposed approach, a layered model can be created from a single defocused image to provide stereoscopic feelings. The proposed approach has also been expanded to construct layered stereoscopic panorama, which shows its great application potentials.
Freezing of Raindrops in Deep Convective Updrafts: A Microphysical and Polarimetric Model (2012)

Abstract Polarimetric radar observations of convective storms routinely reveal positive differential reflectivity ZDR extending above the 0°C level, indicative of the presence of supercooled liquid particles lofted by the storm’s updraft. The summit of such “ZDR columns” is marked by a zone of enhanced linear depolarization ratio LDR or decreased copolar cross-correlation coefficient ρhv and a sharp decrease in ZDR that together mark a particle freezing zone. To better understand the relation between changes in the storm updraft and the observed polarimetric variables, it is necessary to first understand the physics governing this freezing process and the impact of freezing on the polarimetric variables. A simplified, one-dimensional explicit bin microphysics model of stochastic drop nucleation by an immersed foreign particle and subsequent deterministic freezing is developed and coupled with an electromagnetic scattering model to explore the impact of the freezing process on the polarimetric radar variables. As expected, the height of the ZDR column is closely related to the updraft strength and initial drop size distribution. Additionally, the treatment of the stochastic nucleation process can also affect the depth of the freezing zone, underscoring the need to accurately depict this process in parameterizations. Representation of stochastic nucleation and deterministic freezing for each drop size bin yields better agreement between observations and the modeled vertical profiles of the surface reflectivity factor ZH and ZDR than bulk microphysics schemes. Further improvements in the representation of the LDR cap, the observed ZDR gradient in the freezing zone, and the magnitude of the ρhv minimum may require inclusion of accretion, which was not included in this model.
Influences of time of day on generalization (2020)

Abstract Extracting shared structure across our experiences allows us to generalize our knowledge to novel contexts. How do different brain states influence this ability to generalize? Using a novel category learning paradigm, we assess the effect of both sleep and time of day on generalization that depends on the flexible integration of recent information. Counter to our expectations, we found no evidence that this form of generalization is better after a night of sleep relative to a day awake. Instead, we observed an effect of time of day, with better generalization in the morning than the evening. This effect also manifested as increased false memory for generalized information. In a nap experiment, we found that generalization did not benefit from having slept recently, suggesting a role for circadian rhythms apart from sleep. We found, however, that this time of day effect appears to be sensitive to category structure and to task engagement more generally. We propose that a state of lowered inhibition in the morning may facilitate spreading activation between otherwise separate memories, promoting this form of generalization.
Chordomas with malignant spindle cell components. A DNA flow cytometric and immunohistochemical study with histogenetic implications. (1990)

The authors studied four chordomas with malignant spindle cell components (SCs) and 12 conventional chordomas (CCs) by DNA flow cytometry using paraffin-embedded tissue. In addition, immunohistochemical stains for a variety of epithelial and mesenchymal markers were performed. The four SCs contained areas histologically identical to conventional chordomas, as well as a high-grade malignant spindle cell component. All four (100%) SCs had an aneuploid-multiploid DNA content. Of interest, the conventional chordoma areas in these tumors had DNA contents different from those containing the high-grade malignant spindle cells. In contrast, only three (27%) of the 11 conventional chordomas with analyzable histograms had an aneuploid-multiploid DNA content. Immunohistochemical studies performed on the four SCs showed the high-grade malignant spindle cells to stain strongly for vimentin and weakly for cytokeratin, S-100 protein, and epithelial membrane antigen (EMA), whereas the areas of conventional chordoma in these same neoplasms stained moderately for vimentin and S-100 protein, and strongly for cytokeratin and EMA. In two cases, the staining for EMA and cytokeratin highlighted a gradual transition between the areas of conventional chordoma and the spindle cell areas. The immunohistochemical staining pattern of the 12 conventional chordomas was similar to that seen in the conventional chordoma components of the four chordomas with malignant spindle cell components. These results suggest that: 1) aneuploidy is more common in SCs than in CCs, and 2) some SCs are multipotential neoplasms in which the neoplastic cells are capable of differentiation along both epithelial and mesenchymal pathways.
New Methods for C-C Bond Construction: The Burke Synthesis of (-)-Peridinin (2013)

Hideki Yorimitsu and Koichiro Oshima of Kyoto University observed (J. Am. Chem. Soc. 2010, 132, 8878) that Rh-catalyzed addition of 2 to a terminal allene 1 generated an allylic organometallic, which coupled with electrophiles to give the branched product 3. Regan J. Thomson of Northwestern University devised (Nat. Chem. 2010, 2, 294) the reagent 5, which added to an aldehyde 4 to give the reduced allylically coupled product 6. Nuno Maulide of the Max-Planck-Institut, Mülheim, noted (Angew. Chem. Int. Ed. 2010, 49, 1583) the remarkable rearrangement of 7 to 8. Jon A. Tunge of the University of Kansas showed (Organic Lett. 2010, 12, 740) that nitronate allylation could be effected by the Pd-mediated decarboxylation of 9. Takashi Tomioka of the University of Mississippi developed (Organic Lett. 2010, 12, 2171) a convenient reagent for the conversion of an aldehyde 11 to the Z -unsaturated nitrile 12 . Xiaodong Shi of the University of West Virginia established (Organic Lett. 2010, 12, 2088) that Au-mediated rearrangement of 13 led to the Z -iodo enone 14. T. V. RajanBabu of Ohio State University developed (Organic Lett. 2010, 12, 2622) a Pd catalyst for the selective double functionalization of a terminal alkyne 15 to the stannane 16. The subsequent tandem Stille and Suzuki couplings proceeded efficiently. The controlled construction of tetrasubstituted alkenes is particularly challenging. Kohei Endo and Takanori Shibata of Waseda University put forward (J. Org. Chem. 2010, 75, 3469) what promises to be a general solution to this problem: the addition of the bis-boronate 17 to a ketone 18. Alkynes are usually prepared by direct alkylation. Gérard Cahiez of the Université de Paris 13 established (Angew. Chem. Int. Ed. 2010, 49, 1278) an alternative: the coupling of a Grignard reagent with a 1-bromoalkyne 20. Gregory B. Dudley of Florida State University developed (J. Org. Chem. 2010, 75, 3260) a complementary route to internal alkynes based on the fragmentation of 22. Enantiomerically pure allenes are ubiquitous components of physiologically active natural products. Weiping Tang of the University of Wisconsin optimized (J. Am. Chem. Soc. 2010, 132, 3664) the bromolactonization of a Z enyne 24 to give the allene 25.
<title>Thermomechanical analysis of a user filter assembly for undulator/wiggler operations at the Advanced Photon Source</title> (1996)

This paper reports a thermo-mechanical study of a beamline filter for undulator/wiggler operations.It is deployed in conjunction with the current commissioning window assembly on the APS insertion device (ID) front ends. The beamline filter at the APS will eventually be used in windowless operations also. Hence survival and reasonable life expectancy of the filters under intense ID heat flux are crucial to the beamline operations. To accommodate various user requirements, the filter is configured to be a multi- choice type and 'smart' to a low only those filter combinations that will be safe to operate with a given ring current and beamline insertion device gap. However, this paper addresses only the thermo-mechanical analysis of individual filter integrity and safety in all combinations possible. The current filter design is configured to have four filter frames in a cascade with each frame holding five filters. This allows a potential 625 total filter combinations. Thermal analysis for all of these combinations becomes a mammoth task considering the desired choices for filter materials, filter thicknesses, undulator gaps, and the beam currents. The paper addresses how this difficult task has been reduced to a reasonable effort and computational level. Results from thermo-mechanical analyses of the filter combinations are presented both in tabular and graphical format.
Total Soluble and Endogenous Secretory Receptor for Advanced Glycation End Products as Predictive Biomarkers of Coronary Heart Disease Risk in Patients With Type 2 Diabetes (2011)

Higher levels of sRAGE and esRAGE are associated with incident CHD but not stroke in type 2 diabetes.