gebhart/patrepeval huggingface dataset:
Emergence and antibody evasion of BQ, BA.2.75 and SARS-CoV-2 recombinant sub-lineages in the face of maturing antibody breadth at the population level (2023)

This work was primarily supported by Australian Medical Foundation research grants MRF2005760 (SGT, GM & WDR), Medical Research Future Fund Antiviral Development Call grant (WDR), the New South Wales Health COVID-19 Research Grants Round 2 (SGT & FB) and the NSW Vaccine Infection and Immunology Collaborative (VIIM) (ALC). Variant modeling was supported by funding from SciLifeLab's Pandemic Laboratory Preparedness program to B.M. (VC-2022-0028) and by the European Union's Horizon 2020 research and innovation programme under grant agreement no. 101003653 (CoroNAb) to B.M.
Amazonia!: An Online Resource to Google and Visualize Public Human whole Genome Expression Data (2010)

Available transcriptome data accumulate in public repositories, individual web pages or as various supplemental data, but these published data cannot be routinely accessed. We have developed the web based tool Amazonia! to overcome this hurdle and provide the possibility to query and to visualize the expression of a given gene in representative and selected human transcriptome datasets. This expression atlas provides expression bar plots for single genes, across samples selected from a wide range of normal tissues and malignancies, including pluripotent stem cells. When produced by the same platform type, datasets were renormalized and combined in order to generate series of several hundreds samples. Samples types are colored and ordered, and grouped in thematic pages for ease of navigation. We also integrated gene lists provided by original publications describing these microarray data, allowing the scientific community to challenge the expression of genes in datasets other than those for which they were initially published. To illustrate the powerfulness of this simple tool, we show how Amazonia! reveals the specific expression of the tight junction protein Claudin 6 in human embryonic stem cells and human induced stem cells (iPS), or the tissue specific expression of some chemokines and their receptors such as CCL16 in liver and CX3CR1 in central nervous system samples. Thus, Amazonia! advantageously complements large public repositories by providing a simple way to query a compilation of selected human transcriptome data. The tool is freely available at http://www.amazonia.transcriptome.eu/
Generating Synthetic Complex-Structured XML Data. (2001)

Synthetically generated data has always been important for evaluating and understanding new ideas in database research. In this paper, we describe a data generator for generating synthetic complex-structured XML data that allows for a high level of control over the characteristics of the generated data. This data generator is certainly not the ultimate solution to the problem of generating synthetic XML data, but we have found it very useful in our research on XML data management, and we believe that it can also be useful to other researchers. Furthermore, we hope that this paper starts a discussion in the XML community about characterizing and generating XML data, and that it may serve as a first step towards developing a commonly accepted XML data generator for our community. 1
Suppressor Factor Secreted by T-Lymphocytes From Tumor-Bearing Mice 2 (1976)

Spleen cells from C57BL mice bearing the syngeneic carcinoma 3LL enhanced tumor growth. Tumor growth was also enhanced by a soluble factor found in the media of cultured spleen cells from tumor-bearing animals. This factor suppressed a protective immune response of the host and was found to be a product of T-lymphocytes. Removal of B-lymphocytes and macrophages did not prevent its appearance in the culture media, whereas removal of T-lymphocytes inhibited its appearance. Similar suppressor factors were obtained from C3H mice bearing the 3LL tumor and from mice with other tumors. The suppressing factor produced after the growth of 3LL tumor also enhanced the growth of other tumors. It could act on strains incompatible with the donor of the factor-producing cells. Hence tumor growth was possibly facilitated by soluble products of T-lymphocytes that were found in spleens of tumor-bearing mice and that nonspecifically suppressed immune defense mechanisms.
Glucocorticoid regulation of ATP release from spinal astrocytes underlies diurnal exacerbation of neuropathic mechanical allodynia (2016)

Diurnal variations in pain hypersensitivity are common in chronic pain disorders, but the underlying mechanisms are enigmatic. Here, we report that mechanical pain hypersensitivity in sciatic nerve-injured mice shows pronounced diurnal alterations, which critically depend on diurnal variations in glucocorticoids from the adrenal glands. Diurnal enhancement of pain hypersensitivity is mediated by glucocorticoid-induced enhancement of the extracellular release of ATP in the spinal cord, which stimulates purinergic receptors on microglia in the dorsal horn. We identify serum- and glucocorticoid-inducible kinase-1 (SGK-1) as the key molecule responsible for the glucocorticoid-enhanced release of ATP from astrocytes. SGK-1 protein levels in spinal astrocytes are increased in response to glucocorticoid stimuli and enhanced ATP release by opening the pannexin-1 hemichannels. Our findings reveal an unappreciated circadian machinery affecting pain hypersensitivity caused by peripheral nerve injury, thus opening up novel approaches to the management of chronic pain.
System model for characterizing and reducing the mutual coupling in multiple‐input multiple‐output antennas (2011)

Abstract A new approach for modeling the mutual coupling in multiple‐input multiple‐output antennas is introduced.The effects of the mutual coupling are described by a linear time invariant model. The introduced technique offers several advantages: first, an analytical model is achieved, and, from this description, a method for reducing the mutual coupling is proposed. © 2011 Wiley Periodicals, Inc. Microwave Opt Technol Lett 53:597–601, 2011; View this article at wileyonlinelibrary.com. DOI 10.1002/mop.25787
Numerical Flow Analysis Around Structures in Low Speed Fluids and its Application to Environmental Sciences (2019)

Importance and application of numerical flow analysis to environmental science and technology are outlined. Fluid phenomena in the ocean, rivers, atmosphere and the ground are investigated by means of numerical methods and in turn proposals for the control, restoration and counterplans against the so-called environmental disrupters which destroy natural environment as well as ecological systems in nature. All such environmental disrupters diffuse in and are transported by environmental fluids. Those disrupters sometimes react on some other chemicals to generate more poisonous materials. Environmental fluid dynamics is effective for the evaluation, prediction and restoration of the environmental damage. In this paper a mathematical model of environmental fluid is presented and results of numerical simulations based on the model are exhibited.
Development of Oxide Coatings for Matching Oxide Fiber-Oxide Matrix Composites (2008)

A composite of matching oxide matrix and oxide fibers, such as Al2O3/Al2O3, is an attractive system for high temperature applications answering the problems of thermal mismatch, creep and corrosion. The fracture toughness of such composites is governed by the strength and toughness of the fiber-matrix interfaces. A coating on a single crystal Al2O3 fiber with a layered structure, allowing the control of this interfacial strength is proposed and the method of achieving it is developed. The method of measuring the adhesive strength between the coating and the substrate is presented and its application to the particular coatings is discussed. The tensile strength of the interface between the coating and the fiber substrate for the pairs of Al2O3/TiO2 and Al2O3/ZrO2 is determined.
The Sodium Glucose Cotransporter 2 Inhibitor Ipragliflozin Promotes Preferential Loss of Fat Mass in Non-obese Diabetic Goto–Kakizaki Rats (2017)

Sodium glucose cotransporter 2 (SGLT2) inhibitors improve hyperglycemia in patients with type 2 diabetes mellitus (T2DM) by increasing urinary glucose excretion. In addition to their antihyperglycemic effect, SGLT2 inhibitors also reduce body weight and fat mass in obese and overweight patients with T2DM. However, whether or not SGLT2 inhibitors similarly affect body composition of non-obese patients with T2DM remains unclear. In this study, we investigated the effect of the SGLT2 inhibitor ipragliflozin on body composition in a Goto–Kakizaki (GK) rat model of non-obese T2DM. GK rats were treated with ipragliflozin once daily for 9 weeks, starting at 23 weeks of age. Body composition was then analyzed using dual-energy X-ray absorptiometry. Treatment with ipragliflozin increased urinary glucose excretion, reduced hemoglobin A1c (HbA1c) levels and suppressed body weight gain as the dose increased. Body composition analysis revealed that body fat mass was lower in the ipragliflozin-treated groups than in the control group, while lean body mass and bone mineral contents were comparable between groups. Thus, an SGLT2 inhibitor ipragliflozin was found to promote preferential loss of fat mass in a rat model of non-obese T2DM. Ipragliflozin might also promote preferential loss of fat in non-obese patients with T2DM.
Subcellular Localization and Topology of the p7 Polypeptide of Hepatitis C Virus (2002)

Although biological and biochemical data have been accumulated on most hepatitis C virus proteins, the structure and function of the 63-amino-acid p7 polypeptide of this virus have never been investigated. In this work, sequence analyses predicted that p7 contains two transmembrane passages connected by a short hydrophilic segment. The C-terminal transmembrane domain of p7 was predicted to function as a signal sequence, which was confirmed experimentally by analyzing the translocation of a reporter glycoprotein fused at its C terminus. The p7 polypeptide was tagged either with the ectodomain of CD4 or with a Myc epitope to study its membrane integration, its subcellular localization, and its topology. Alkaline extraction studies confirmed that p7 is an integral membrane polypeptide. The CD4-p7 chimera was detected by immunofluorescence on the surface of nonpermeabilized cells, indicating that it is exported to the plasma membrane. However, pulse-chase analyses showed that only approximately 20% of endoglycosidase H-resistant CD4-p7 was detected after long chase times, suggesting that a large proportion of p7 stays in an early compartment of the secretory pathway. Finally, by inserting a Myc epitope in several positions of p7 and analyzing the accessibility of this epitope on the plasma membrane of HepG2 cells, we showed that p7 has a double membrane-spanning topology, with both its N and C termini oriented toward the extracellular environment. Altogether, these data indicate that p7 is a polytopic membrane protein that could have a functional role in several compartments of the secretory pathway.
Interferometric optical fiber sensors (1993)

More systematic investigation of the aerosol field in the planet- ary boundary layer (PBL) over a part of Sofia city reveals the air pol- lution distribution, i.e. the structure of the stable stratification of PBL. Lidar data are compared with profiles of the atmospheric thermody- namic parameters, determined by conventional means.
Selective Hydraulic Fracturing of Multiple Perforated Intervals with a Coiled Tubing Conduit: A Case History of the Unique Process, Economic Impact and Related Production Improvements (1999)

This paper is a followup to SPE 46031, and will expand on economical shallow gas fracturing techniques utilizing a coiled tubing conduit. Hereinafter in this paper, the name CoilFRAC™ will used in place of the phrase ‘Coiled Tubing Conveyed.The wells in the area of study are located in southeastern Alberta. The reservoir pay intervals in these shallow gas wells consist of high clay content, low permeability sandstones with interbedded shales. The wells in the study have multiple zones of interest and further discussions will be based on these multiple zones.Due to the economics involved using conventional fracturing methods, the wells in this study have been treated with a unique multiple fracture program which allows access to typically bypassed pay.Treating multiple zones in a given well within one day has given the producer a new realized ROI by reducing well production downtime and economically increasing production. This technique has been continually improved and modified through unconventional designs since 1996 to what is today a very effective routine method of stimulating and increasing production today.The case study will define and present production and production logging data, relative to the associated costs, to demonstrate the impact this service has had on the operators' selection of workover candidates and new well optimization.Coiled Tubing technology has provided an efficient and economic alternative to bridge plug and service rig type of zonal isolation techniques when stimulating more than one zone of interest.
Preparation of deuterated organic compounds from activated organic halides by reduction with zinc-deuterium oxide (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPreparation of deuterated organic compounds from activated organic halides by reduction with zinc-deuterium oxideLarry S. Trzupek, Erwin R. Stedronsky, and George M. WhitesidesCite this: J. Org. Chem. 1972, 37, 21, 3300–3303Publication Date (Print):October 1, 1972Publication History Published online1 May 2002Published inissue 1 October 1972https://pubs.acs.org/doi/10.1021/jo00986a023https://doi.org/10.1021/jo00986a023research-articleACS PublicationsRequest reuse permissionsArticle Views651Altmetric-Citations11LEARN 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
In Vitro Biosynthesis of UDP-N,N‘-Diacetylbacillosamine by Enzymes of the Campylobacter jejuni General Protein Glycosylation System (2006)

In Campylobacter jejuni 2,4-diacetamido-2,4,6-trideoxy-alpha-d-glucopyranose, termed N,N'-diacetylbacillosamine (Bac2,4diNAc), is the first carbohydrate in the glycoprotein N-linked heptasaccharide. With uridine diphosphate-N-acetylglucosamine (UDP-GlcNAc) as a starting point, two enzymes of the general protein glycosylation (Pgl) pathway in C. jejuni (PglF and PglE) have recently been shown to modify this sugar nucleotide to form UDP-2-acetamido-4-amino-2,4,6-trideoxy-alpha-d-glycopyranose (UDP-4-amino-sugar) [Schoenhofen, I. C., et al. (2006) J. Biol. Chem. 281, 723-732]. PglD has been proposed to catalyze the final step in N,N'-diacetylbacillosamine synthesis by N-acetylation of the UDP-4-amino-sugar at the C4 position. We have cloned, overexpressed, and purified PglD from the pgl locus of C. jejuni NCTC 11168 and identified it as the acetyltransferase that modifies the UDP-4-amino-sugar to form UDP-N,N'-diacetylbacillosamine, utilizing acetyl-coenzyme A as the acetyl group donor. The UDP-N,N'-diacetylbacillosamine product was purified from the reaction by reverse phase C18 HPLC and the structure determined by NMR analysis. Additionally, the full-length PglF was overexpressed and purified in the presence of detergent as a GST fusion protein, allowing for derivation of kinetic parameters. We found that the UDP-4-amino-sugar was readily synthesized from UDP-GlcNAc in a coupled reaction using PglF and PglE. We also demonstrate the in vitro biosynthesis of the complete heptasaccharide lipid-linked donor by coupling the action of eight enzymes (PglF, PglE, PglD, PglC, PglA, PglJ, PglH, and PglI) in the Pgl pathway in a single reaction vessel.
ChemInform Abstract: The Effect of Substituents of α‐Alkyl Sidechains on Furan—Diazoester Interactions. (1999)

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.
Formation of a cathode crater in a low-voltage cold-cathode vacuum arc (1998)

The cathode crater in a low-voltage cold-cathode vacuum arc is planar. The area of the crater and the density of the current flowing through it depend on the thermal and electrical properties of the cathode metal.
α-1-Adrenergic Receptor Agonist Activity of Clinical α-Adrenergic Receptor Agonists Interferes with α-2-Mediated Analgesia (2009)

Alpha-1A receptor agonist activity can counterbalance alpha-2 receptor agonist-induced analgesia. Greater alpha-2 selectivity may enhance the therapeutic window of alpha-2 agonists in the treatment of pain.
Resonant scanning design and control for fast spatial sampling (2021)

Two-dimensional, resonant scanners have been utilized in a large variety of imaging modules due to their compact form, low power consumption, large angular range, and high speed. However, resonant scanners have problems with non-optimal and inflexible scanning patterns and inherent phase uncertainty, which limit practical applications. Here we propose methods for optimized design and control of the scanning trajectory of two-dimensional resonant scanners under various physical constraints, including high frame-rate and limited actuation amplitude. First, we propose an analytical design rule for uniform spatial sampling. We demonstrate theoretically and experimentally that by expanding the design space, the proposed designs outperform previous designs in terms of scanning range and fill factor. Second, we show that we can create flexible scanning patterns that allow focusing on user-defined Regions-of-Interest (RoI) by modulation of the scanning parameters. The scanning parameters are found by an optimization algorithm. In simulations, we demonstrate the benefits of these designs with standard metrics and higher-level computer vision tasks (LiDAR odometry and 3D object detection). Finally, we experimentally implement and verify both unmodulated and modulated scanning modes using a two-dimensional, resonant MEMS scanner. Central to the implementations is high bandwidth monitoring of the phase of the angular scans in both dimensions. This task is carried out with a position-sensitive photodetector combined with high-bandwidth electronics, enabling fast spatial sampling at [Formula: see text] Hz frame-rate.
Nutrition lipidique, inflammation et tissu osseux (2011)

Fats are prevalent in western diets; they have known deleterious effects on muscle insulin resistance and may contribute to bone loss most notably in the elderly population. Because current treatments for osteoporosis may lead to important side effects, several studies aimed at investigating the relevance of nutritional approaches and most notably the role of lipid diets on bone health status. Literature has widely linked lipid intake and inflammation status, a key protagonist involved in bone resorption. Regarding inflammation, lipids exhibit a duality, with both pro- and anti-inflammatory effects depending on their structures and metabolism. In this light, a growing body of evidence has revealed that ω-6 increase bone loss while ω-3 are believed to protect bone health. Nevertheless, this debate remains controversial and the mechanisms of action are poorly understood.
Transient gain dynamics of cascaded erbium doped fiber amplifiers with re-configured channel loading (2006)

Wavelength-division-multiplexed channel power transients are examined in cascaded EDFAs with variable pre-transient channel loading through the chain. We identify different orders of transient events and characterize their uncontrolled time response and steady-state power excursions.
New views of old proteins: clarifying the enigmatic proteome (2021)

All human diseases involve proteins, yet our current tools to characterize and quantify them are limited. To better elucidate proteins across space, time, and molecular composition, we provide provocative projections for technologies to meet the challenges that protein biology presents. With a broad perspective, we discuss grand opportunities to transition the science of proteomics into a more propulsive enterprise. Extrapolating recent trends, we offer potential futures for a next generation of disruptive approaches to define, quantify and visualize the multiple dimensions of the proteome, thereby transforming our understanding and interactions with human disease in the coming decade.
Antitumor activity of paclitaxel (taxol) analogues on MDR-positive human cancer cells. (1998)

A series of newly developed paclitaxel analogues have been tested for their growth inhibitory activity on two human breast cancer cell lines, one of which expresses the MDR (multidrug resistance) phenotype. Paclitaxel (taxol) was used as a reference compound. Three new classes of taxanes were analyzed: the cephalomannine compounds, the pyrazoline derivatives and the seco-derivatives. Our results demonstrated an increased antiproliferative activity of pyrazoline derivatives on drug-resistant cancer cells with respect to paclitaxel. These compounds were able to block MDR-bearing MCF-7 ADRr cells in the G2/M phase of cell cycle and, consequently, induce programmed cell death. In keeping with the antiproliferative effects, cells treated with paclitaxel derivatives showed a more pronounced cell cycle arrest than the parent compound paclitaxel. Also, apoptotic cell death, calculated as a percent of DNA fragmentation, occurred to a greater extent in cells exposed to pyrazoline derivatives. The development of new paclitaxel analogues with greater antitumour activity on MDR-positive cells may be useful in selecting new taxanes effective on resistant tumors.
Enhanced proton conductivity in amino acid based self-assembled non-porous hydrogen-bonded organic frameworks (2022)

β-Alaninium oxalate hemihydrate, glycinium oxalate, and L-leucinium oxalate salt-cocrystals as non-porous self-assembled hydrogen-bonded organic frameworks afforded proton conductivity of 2.43 × 10<sup>-2</sup> S cm<sup>-1</sup> (60 °C, 95% RH), 3.03 × 10<sup>-2</sup> S cm<sup>-1</sup> (60 °C, 95% RH), and 1.19 × 10<sup>-2</sup> S cm<sup>-1</sup> (80 °C, 95% RH), respectively. These materials possess an extensive 3-dimensional network of hydrogen bonds in their crystal structures, making them efficient proton conducting membranes. The reduction in conductivity values over 10<sup>-1</sup> S cm<sup>-1</sup> order upon exposure of the samples to a D<sub>2</sub>O atmosphere in extreme conditions ratified the role of humidity for the conduction of protons. This work explores the relationship between structural features and proton conductivity for the design of proton conducting membranes that are easy to synthesize, eco-friendly, and cheap with potential for futuristic applications.