gebhart/patrepeval huggingface dataset:
A Facile Fabrication Strategy for Patterning Protein Chain Conformation in Silk Materials (2009)

Patterning of the secondary structure of silk films is achieved on the micrometer scale using a soft lithographic technique, as illustrated in the figure. The alternating areas of silk I and silk II structure have different mechanical, surface, and solubility properties but nominally the same chemical composition. This technique will enable the development of other tailored protein materials with selectively transformed localized secondary structure.
Phosphoproteomics identifies microglial Siglec-F inflammatory response during neurodegeneration (2020)

Summary Alzheimer’s disease (AD) is characterized by the appearance of amyloid-β plaques, neurofibrillary tangles, and inflammation in brain regions involved in memory. Using mass spectrometry, we have quantified the phosphoproteome of the CK-p25, 5XFAD, and Tau P301S mouse models of neurodegeneration. We identified a shared response involving Siglec-F which was upregulated on a subset of reactive microglia. The human paralog Siglec-8 was also upregulated on microglia in AD. Siglec-F and Siglec-8 were upregulated following microglial activation with interferon gamma (IFNγ) in BV-2 cell line and human stem-cell derived microglia models. Siglec-F overexpression activates an endocytic and pyroptotic inflammatory response in BV-2 cells, dependent on its sialic acid substrates and immunoreceptor tyrosine-based inhibition motif (ITIM) phosphorylation sites. Related human Siglecs induced a similar response in BV-2 cells. Collectively, our results point to an important role for mouse Siglec-F and human Siglec-8 in regulating microglial activation during neurodegeneration. Highlights Phosphoproteomics analysis of CK-p25, 5XFAD, and Tau P301S mouse models finds dysregulated signaling networks associated with Alzheimer’s disease pathologies. A phosphorylation site on Siglec-F is found to be upregulated across all three models of disease. Expression of Siglec-F and its human paralog Siglec-8 is increased in reactive microglia. Overexpression of Siglec-F and Siglec-8 in vitro drives an endocytic and pyroptotic inflammatory response. In Brief Phosphoproteome signaling changes associated with Alzheimer’s disease (AD) are poorly characterized. Here, Morshed et al. apply phosphoproteomics to mouse models of AD to uncover a novel microglial receptor, Siglec-F, that is upregulated on a subset of inflammatory microglia across models of neurodegeneration. The human paralog, Siglec-8 is also found to be upregulated in late-onset AD microglia. Overexpression of Siglec-F and related human Siglecs activates pro-inflammatory signaling responses in BV-2 cells.
Serologic Evidence for Reactivation of Cryptococcosis in Solid-Organ Transplant Recipients (2007)

Cryptococcosis is a significant infection with a high mortality in solid-organ transplant recipients. Nonetheless, the pathogenesis of this disease is poorly understood. It has been hypothesized that cryptococcosis may result from either primary infection or reactivation of a latent infection. Sera were obtained from transplant recipients prior to transplantation and at the time they developed cryptococcosis. Control sera were obtained before and after transplant from patients who did not develop cryptococcosis. Sera were tested for antibodies against Cryptococcus neoformans by using an immunoblot assay. Antibody responses were also compared with those observed in sera from rats with experimental pulmonary cryptococcosis. In all, 52% of the transplant recipients who developed cryptococcosis exhibited serologic evidence of cryptococcal infection before transplantation. These patients developed cryptococcosis significantly earlier after transplant than patients without preexisting reactivity did (5.6 +/- 3.4 months compared to 40.6 +/- 63.8 months, respectively [P = 0.0011]). The results from our study suggest that a substantial proportion of transplant-associated cryptococcosis cases result from the reactivation of a latent infection. These findings also highlight the potential utility of serologic studies in identifying patients at risk for the development of cryptococcosis after transplantation.
The origin of greater than 200:1 enantioselectivity in a catalytic Diels-Alder reaction as revealed by physical and chemical studies (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe origin of greater than 200:1 enantioselectivity in a catalytic Diels-Alder reaction as revealed by physical and chemical studiesE. J. Corey, Teck Peng Loh, Thomas D. Roper, Mihai D. Azimioara, and Mark C. NoeCite this: J. Am. Chem. Soc. 1992, 114, 21, 8290–8292Publication Date (Print):October 1, 1992Publication History Published online1 May 2002Published inissue 1 October 1992https://pubs.acs.org/doi/10.1021/ja00047a050https://doi.org/10.1021/ja00047a050research-articleACS PublicationsRequest reuse permissionsArticle Views1683Altmetric-Citations147LEARN 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
Nus transcription elongation factors and RNase III modulate small ribosome subunit biogenesis in Escherichia coli (2012)

Escherichia coli NusA and NusB proteins bind specific sites, such as those in the leader and spacer sequences that flank the 16S region of the ribosomal RNA transcript, forming a complex with RNA polymerase that suppresses Rho-dependent transcription termination. Although antitermination has long been the accepted role for Nus factors in rRNA synthesis, we propose that another major role for the Nus-modified transcription complex in rrn operons is as an RNA chaperone insuring co-ordination of 16S rRNA folding and RNase III processing that results in production of proper 30S ribosome subunits. This contrarian proposal is based on our studies of nusA and nusB cold-sensitive mutations that have altered translation and at low temperature accumulate 30S subunit precursors. Both phenotypes are suppressed by deletion of RNase III. We argue that these results are consistent with the idea that the nus mutations cause altered rRNA folding that leads to abnormal 30S subunits and slow translation. According to this idea, functional Nus proteins stabilize an RNA loop between their binding sites in the 5' RNA leader and on the transcribing RNA polymerase, providing a topological constraint on the RNA that aids normal rRNA folding and processing.
Styrketräning som behandling vid långvariga ländryggsbesvär (2017)

Fysisk traning ar viktigt for en god halsa och fungerar aven som behandlingsform vid manga sjukdomar, sa aven landryggsbesvar. Styrketraning har visat sig vara en mer effektiv traningsform an till ...
Incorporating trust in NFV: Addressing the challenges (2017)

Network Functions Virtualization (NFV) helps in reducing the dependency on hardware equipments by virtualizing the telecommunication network functions. While the current works have considered different frameworks for NFV and various challenges associated with it, only a few have considered trust as an aspect of NFV. In this paper, we discuss the challenges of incorporating trust in NFV. We discuss the importance of considering trust in NFV, followed by evaluating the requirements for establishing the trust. We also detail the terminologies associated with time and the components of NFV. The main contribution of this paper is the challenges we have encountered in incorporating trust in NFV environment and our approaches to address them.
Multiple Gamma-Ray Detection Capability of a CeBr3 Detector for Gamma Spectroscopy (2017)

The newly developed cerium tribromide (CeBr 3 ) detector has reduced intrinsic gamma-ray activity with gamma energy restricted to 1400–2200 keV energy range. This narrower region of background gamma rays allows the CeBr 3 detector to detect more than one gamma ray to analyze the gamma-ray spectrum. Use of multiple gamma-ray intensities in elemental analysis instead of a single one improves the accuracy of the estimated results. Multigamma-ray detection capability of a cylindrical 75 mm × 75 mm (diameter × height) CeBr 3 detector has been tested by analyzing the chlorine concentration in water samples using eight chlorine prompt gamma rays over 517 to 8578 keV energies utilizing a D-D portable neutron generator-based PGNAA setup and measuring the corresponding minimum detection limit (MDC) of chlorine. The measured MDC of chlorine for gamma rays with 517–8578 keV energies varies from 0.07 ± 0.02 wt% to 0.80 ± 0.24. The best value of MDC was measured to be 0.07 ± 0.02 wt% for 788 keV gamma rays. The experimental results are in good agreement with Monte Carlo calculations. The study has shown excellent detection capabilities of the CeBr 3 detector for eight prompt gamma rays over 517–8578 keV energy range without significant background interference.
Total Ginsenosides of Radix Ginseng Modulates Tricarboxylic Acid Cycle Protein Expression to Enhance Cardiac Energy Metabolism in Ischemic Rat Heart Tissues (2012)

To elucidate the underlying mechanism of cardio-protective activity of the total ginsenosides (TGS) of Radix Ginseng, proteomic analysis using two-dimensional gel electrophoresis (2-DE) and MALDI-TOF-TOF-MS techniques was employed for identifying the underlying targets of TGS on improvement of the energy metabolism of isolated rat heart tissues perfused in Langendorff system under ischemia-reperfusion injury conditions. The image analysis results revealed 11 differentially expressed proteins in the TGS-treated heart tissues; these proteins, including LDHB and ODP-2, were found to be closely related to the function of tricarboxylic acid (TCA) cycle that plays pivotal roles in cardiac energy metabolism. It is thus concluded that improvement of cardiac energy metabolism via activating proteins in TCA cycle could be the major action pathway and targets of TGS activity against rat heart tissue injury.
Assessing cellulose micro/nanofibre morphology using a high throughput fibre analysis device to predict nanopaper performance (2022)

Abstract Characterising cellulose nanofibre (CNF) morphology has been identified as a grand challenge for the nanocellulose research field. Direct techniques for CNF morphology characterisation exhibit various difficulties related to the material network structure and equipment cost, while indirect techniques that investigate fibre-light interaction, fibre-solvent interaction, fibre-fibre interaction, or specific fibre surface area involve relatively facile methods but may be more unreliable. Nanopaper mechanical testing is a prevalent metric for assessing fibre-fibre interaction, but is an off-line, time-consuming, and destructive methodology. In this study, an optical fibre morphology analyser (MorFi, Techpap) was employed as an on-line, high throughput, fast turnaround tool to assess micro/nanofibre pulp morphology and predict the properties of nanopaper material. Correlation analysis identified fibre content and fibre kink properties as most correlated with nanopaper strength and toughness, while fibre width and coarseness were most inversely correlated with nanopaper performance. Principal component analysis (PCA) was employed to visualise interdependent morphological and mechanical data. Subsequently, two data driven statistical models—multiple linear regression (MLR) and machine learning based support vector regression (SVR)—were established to predict nanopaper properties from fibre morphology data, with SVR generating a more accurate prediction across all nanopaper properties (NRMSE = 0.13–0.33) compared to the MLR model (NRMSE = 0.33–0.51). This study highlights that statistical methods are useful to disentangle and visualise interdependent morphological data from an on-line fibre analysis device, while regression models are also capable of predicting paper mechanical properties from CNF samples even though these devices do not operate at nanoscale resolution. Graphical abstract
Temperature and back-gate bias influence on the operation of lateral SOI PIN photodiodes (2014)

This paper presents a study of back-gate bias and temperature influence on the operation of lateral SOI PIN photodiodes. Experimental results showed that the operation mode of the photodiodes is affected by back-gate bias, modifying the photogenerated current, which has a strong influence on the illuminated to dark ratio, as well as, on the quantum efficiency. At lower temperatures, the results showed that the quantum efficiency can be improved by biasing the device in inversion mode, while at higher temperatures, the accumulation mode showed a higher illuminated to dark ratio.
Influence of 1 nm-thick structural "strained-layer" near SiO/sub 2//Si interface on sub-4 nm-thick gate oxide reliability (2002)

The relationship between the structural property and the electrical characteristics of thin SiO/sub 2/ below 4 nm is investigated. The structural "strained-layer" near SiO/sub 2//Si interface is confirmed to affect strongly the TDDB (time dependent dielectric breakdown) lifetime of the thin gate oxides. The increase of the built-in compressive strain analyzed by the XPS (X-ray photoelectron spectroscopy) based technique is experimentally found to decrease the TDDB lifetime.
The role of homeostatic regulation between tumor suppressor DAB2IP and oncogenic Skp2 in prostate cancer growth (2014)

Altered DAB2IP gene expression often detected in prostate cancer (PCa) is due to epigenetic silencing. In this study, we unveil a new mechanism leading to the loss of DAB2IP protein; an oncogenic S-phase kinase-associated protein-2 (Skp2) as E3 ubiquitin ligase plays a key regulator in DAB2IP degradation. In order to unveil the role of Skp2 in the turnover of DAB2IP protein, both prostate cell lines and prostate cancer specimens with a variety of molecular and cell biologic techniques were employed. We demonstrated that DAB2IP is regulated by Skp2-mediated proteasome degradation in the prostate cell lines. Further analyses identified the N-terminal DAB2IP containing the ubiquitination site. Immunohistochemical study exhibited an inverse correlation between DAB2IP and Skp2 protein expression in the prostate cancer tissue microarray. In contrast, DAB2IP can suppressSkp2 protein expression is mediated through Akt signaling. The reciprocal regulation between DAB2IP and Skp2 can impact on the growth of PCa cells. This reciprocal regulation between DAB2IP and Skp2 protein represents a unique homeostatic balance between tumor suppressor and oncoprotein in normal prostate epithelia, which is apparently altered in cancer cells. The outcome of this study has identified new potential targets for developing new therapeutic strategy for PCa.
Concise Synthesis of 1,4-Dideoxy-1,4-imino-l-arabinitol (LAB) from d-Xylose by Intramolecular Stereospecific Substitution of a Hydroxy Group (2023)

Abstract We report a concise and green total synthesis of 1,4-dideoxy-1,4-imino-l-arabinitol hydrochloride from naturally occurring d-xylose. The key step involves a stereospecific substitution of a hydroxy group, without prior derivatization, in which the only byproduct is water. This opens up a novel benign route to iminosugar derivatives with diverse biological activities.
Fast Wavelength Switching Digital Coherent OFDM Transceiver (2013)

Digital dynamic frequency offset removal and DC pilot tone assisted phase noise compensation enables the use of commercially available DS-DBR lasers as both the transmitter and LO in a coherent wavelength switched OFDM transceiver. A 1.5dB penalty relative to low linewidth static lasers is demonstrated under fast wavelength switched operation.
A General Thermal Index for Maize (1999)

Thermal indices predict and describe development rate more accurately than time in days and are commonly used to rate maize ( Zea mays L.) for maturity. Separate temperature response functions for the vegetative and grain‐filling periods predict more accurately time to maturity than a single function for the two periods combined. However, use of two functions requires a priori knowledge of the silking date, which becomes the transition date from the vegetative function to the grain‐filling function. The objective of this study was to evaluate the sensitivity of estimates of silking and maturity dates to the transition date between vegetative and grain‐filling functions and to develop a protocol to combine the two temperature response functions in a general thermal index (GTI) for maize. Frequency distributions of mean daily air temperatures for five 20‐d periods spanning mid‐June to late September at 19 locations in the northern USA and southern Ontario from 1992 to 1995 indicated few days (≤12%) with mean daily air temperatures less than 15°C before late August. This was significant, as the two response functions diverged significantly at temperatures below 15°C. Standard errors in estimating maturity date using different transition dates remained small (&lt;7.5 d) unless the transition date was delayed beyond the first week of September. Based on this analysis, a standard transition date of 1 August was proposed for the GTI. Testing on an independent data set indicated that the GTI and a transition date of 1 August provided more accurate estimates of the planting to maturity period than growing degree days (GDD) or crop heat units (CHU), with a standard error of 8.2 d (compared with 14.5 d using GDD and 12.5 d using CHU).
Guest Editors' Introduction: Hot Chips 21 (2010)

Hot Chips has emerged as the leading forum to present new processor architectures and other developments in chip design, with an emphasis on deep technical discussion of the detailed workings of upcoming commercial products. A few selected presentations from leading academic researchers complement the industry focus. To encourage busy industry engineers to submit to the conference, the submission guidelines require only a short abstract and the conference proceedings contain only the presentation slides. From more than 75 submissions, the program committee selected 27 presentations for the main conference. This special issue contains seven full-length articles representing the important themes discussed at the 21st annual Hot Chips conference.
20. MELANOMA CELL INTRINSIC GABAA RECEPTOR ENHANCEMENT POTENTIATES RADIATION AND IMMUNE CHECKPOINT INHIBITOR RESPONSE BY PROMOTING DIRECT AND T CELL-MEDIATED ANTI-TUMOR ACTIVITY (2020)

Abstract Most metastatic melanoma patients exhibit poor and variable response to radiotherapy and targeted therapies, including immune checkpoint inhibitors. There is a need for therapeutics that can potentiate existing treatments to positively impact clinical outcomes of metastatic melanoma patients. We reanalyzed melanoma TCGA transcriptomes and identified, as linked to previously defined molecular subgroups, enhanced expression of genes coding for subunits of the Type A GABA receptor (GABAAR), a chloride ion channel and major inhibitory neurotransmitter receptor. Using whole-cell patch clamp electrophysiology, we find that melanoma cells possess GABAARs that control membrane permeability to anions. Select benzodiazepines, by enhancing GABAAR mediated anion transport, depolarize melanoma cell mitochondrial membrane potential and impair cell viability in vitro. Using a syngeneic melanoma mouse model, we find that a benzodiazepine promotes reduction in tumor volume when administered alone and potentiated radiation or immune checkpoint inhibitor α-PD-L1. When a benzodiazepine is combined with concurrent α-PD-L1 and a sub-lethal radiation dose, there is near complete loss of tumor, beyond what is observed for benzodiazepine with radiation or α-PD-L1. Mechanistically, benzodiazepine with radiation or α-PD-L1 results in ipsilateral and an abscopal tumor volume reduction commensurate with enhanced infiltration into the tumor milieu of polyfunctional CD8 T-cells. There is also an increased expression of genes with roles in the cytokine-cytokine receptor and p53 signaling pathways. This study provides evidence for melanoma cell GABAARs as a therapeutic vulnerability with benzodiazepines promoting both direct and immune-mediated anti-tumor activity.
Combined FET PET/MRI radiomics differentiates radiation injury from recurrent brain metastasis (2019)

The aim of this study was to investigate the potential of combined textural feature analysis of contrast-enhanced MRI (CE-MRI) and static O-(2-[F-18]fluoroethyl)-L-tyrosine (FET) PET for the differentiation between local recurrent brain metastasis and radiation injury since CE-MRI often remains inconclusive.
Silk nanofibril self‐assembly versus electrospinning (2018)

Natural silk fibers represent one of the most advanced blueprints for (bio)polymer scientists, displaying highly optimized mechanical properties due to their hierarchical structures. Biotechnological production of silk proteins and implementation of advanced processing methods enabled harnessing the potential of these biopolymer not just based on the mechanical properties. In addition to fibers, diverse morphologies can be produced, such as nonwoven meshes, films, hydrogels, foams, capsules and particles. Among them, nanoscale fibrils and fibers are particularly interesting concerning medical and technical applications due to their biocompatibility, environmental and mechanical robustness as well as high surface-to-volume ratio. Therefore, we introduce here self-assembly of silk proteins into hierarchically organized structures such as supramolecular nanofibrils and fabricated materials based thereon. As an alternative to self-assembly, we also present electrospinning a technique to produce nanofibers and nanofibrous mats. Accordingly, we introduce a broad range of silk-based dopes, used in self-assembly and electrospinning: natural silk proteins originating from natural spinning glands, natural silk protein solutions reconstituted from fibers, engineered recombinant silk proteins designed from natural blueprints, genetic fusions of recombinant silk proteins with other structural or functional peptides and moieties, as well as hybrids of recombinant silk proteins chemically conjugated with nonproteinaceous biotic or abiotic molecules. We highlight the advantages but also point out drawbacks of each particular production route. The scope includes studies of the natural self-assembly mechanism during natural silk spinning, production of silk fibrils as new nanostructured non-native scaffolds allowing dynamic morphological switches, as well as studying potential applications. This article is categorized under: Biology-Inspired Nanomaterials > Peptide-Based Structures Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Biology-Inspired Nanomaterials > Protein and Virus-Based Structures.