gebhart/patrepeval huggingface dataset:
Protein Cysteine Modifications: (1) Medicinal Chemistry for Proteomics (2009)

Protein cysteines (cysteinyl residues) play critical roles in biological processes. In the course of protein evolution under oxidizing atmosphere of the Earth, organisms have utilized highly reactive cysteines in many proteins essential for maintenance of life, i.e. enzymes, transcriptional factors, cytoskeletons, and receptors. In some enzymes, sophistical cysteine modification characterizes each catalytic mechanism. In vivo modification of protein cysteines with natural chemical compounds modulates protein functions as a molecular switch. Oxidation/reduction, thiol-disulfide exchange, nitrosylation, sulfuration, thiolation, acylation and prenylation are involved. Some protein cysteines coordinate metals or metal cofactors such as a heme or an iron sulfur cluster to form metalloproteins, serving as sensor proteins, metalloenzymes or transcriptional factors. Information on the in vitro chemical modifications and their reaction specificities of protein cysteines are essential for the investigation of the mechanisms and functions of in vivo protein cysteine modifications. In this review, we also mention historically important knowledge other than recent results on protein cysteine modification and modulation of protein function to fertilize medical proteomics.
Denaturation via Surfactants Changes Composition of Protein Corona (2018)

The use of nanocarriers as drug delivery vehicles brings them into contact with blood plasma proteins. Polymeric nanocarriers require some sort of surfactant to ensure colloidal stability. Formation of the protein corona is therefore determined not only by the intrinsic properties of the nanocarrier itself but also by the accompanying surfactant. Although it is well-known that surfactants have an impact on protein structure, only few studies were conducted on the specific effect of surfactants on the composition of protein corona of nanocarriers. Therefore, we analyzed the composition of the protein corona on "stealth" nanoparticles with additional surfactant (cetyltrimethylammonium chloride, CTMA-Cl) after plasma incubation. Additional CTMA-Cl led to an enrichment of apolipoprotein-A1 and vitronectin in the corona, while less clusterin could be found. Further, the structural stability of apolipoprotein-A1 and clusterin was monitored for a wide range of CTMA-Cl concentrations. Clusterin turned out to be more sensitive to CTMA-Cl, with denaturation occurring at lower concentrations.
Complementary Roles of Farnesoid X Receptor, Pregnane X Receptor, and Constitutive Androstane Receptor in Protection against Bile Acid Toxicity (2003)

The nuclear receptors, farnesoid X receptor (FXR) and pregnane X receptor (PXR), are important in maintaining bile acid homeostasis. Deletion of both FXR and PXR in vivo by cross-breeding B6;129-Fxrtm1Gonz (FXR-null) and B6;129-Pxrtm1Glaxo-Wellcome (PXR-null) mice revealed a more severe disruption of bile acid, cholesterol, and lipid homeostasis in B6;129-Fxrtm1Gonz Pxrtm1Glaxo-Wellcome (FXR-PXR double null or FPXR-null) mice fed a 1% cholic acid (CA) diet. Hepatic expression of the constitutive androstane receptor (CAR) and its target genes was induced in FXR- and FPXR-null mice fed the CA diet. To test whether up-regulation of CAR represents a means of protection against bile acid toxicity to compensate for the loss of FXR and PXR, animals were pretreated with CAR activators, phenobarbital or 1,4-bis[2-(3,5-dichlorpyridyloxy)]benzene (TCPOBOP), followed by the CA diet. A role for CAR in protection against bile acid toxicity was confirmed by a marked reduction of serum bile acid and bilirubin concentrations, with an elevation of the expression of the hepatic genes involved in bile acid and/or bilirubin metabolism and excretion (CYP2B, CYP3A, MRP2, MRP3, UGT1A, and glutathione S-transferase alpha), following pretreatment with phenobarbital or TCPOBOP. In summary, the current study demonstrates a critical and combined role of FXR and PXR in maintaining not only bile acid but also cholesterol and lipid homeostasis in vivo. Furthermore, FXR, PXR, and CAR protect against hepatic bile acid toxicity in a complementary manner, suggesting that they serve as redundant but distinct layers of defense to prevent overt hepatic damage by bile acids during cholestasis.
ChemInform Abstract: Synthesis of Some Derivatives Based on the 4‐Benzyl‐1H‐pyrazole‐3,5‐diamine core. (2011)

Abstract A facile three‐step synthesis of the title pyrazole derivatives (IV) (15 examples) from commercially available aldehydes (I) involving a Knoevenagel condensation and cycloaddition step is developed.
A Cost-effective Control Flow Checking using Loop Detection and Prediction (2005)

Recently, concurrent error detection for the processor becomes important. But it imposes too much overhead to adopt concurrent error detection capability on the system. In this paper, a new approach to resolve the problems of concurrent error detection is proposed. A loop detection scheme is introduced to reduce the repetitive loop iteration and memory access. To reduce the memory overheat an offset to calculate the target address of branching node is proposed. Performance evaluation shows that the new architecture has lower memory overhead and frequency of memory access than previous works. In addition, the new architecture provides the same error coverage and requires nearly constant memory size regardless of the size of the application program. Consequently, the proposed architecture can be used as an cost effective method to detect control flow errors in the commercial on the shelf products.
DISC (Degenerate-Disc Infection Study with Contaminant Control) Discussion on Methods, Interim Analysis, and the Pitfalls of not Sending Contaminant Control (2015)

Introduction Studies that implicate disc infection in the majority of patients with axial back/neck pain or leg/arm pain is potentially scandalous and irresponsible. The majority of these studies are underpowered and lack a contaminant arm, the current study is aimed to fulfil these basic criteria. Material and Methods A prospective case–control multicentric study (HREC 13/218) including cases discectomy for degenerative disc pathology and controls are patients undergoing discectomy for nondegenerate pathology. True disc positivity was inferred if the culture of disc was positive and the paraspinal tissue sample was negative. A total of 400 patients have been enrolled. In degenerative disc cases, 8.7% were true positive (disc +ve/paraspinal −ve) with paraspinal-positive samples in 38.4% on its own. In control cases there was 40% positive for disc culture together with paraspinal tissue. The organisms in disc or paraspinal culture were very similar with 85% having same organisms. On generalized linear model analysis of disc-culture positivity using binomial sets there were no statistical significant findings when comparing disc positivity to demography, type of surgery, modic changes or level of surgery. Conclusions (1) The true rate of disc culture positivity in the degenerative disc population is significantly lower than previous literature reports. (2) At the interim analysis stage, the DISC study heavily favors performing disc cultures strictly with a contaminant control.
Supplementary Figure S1 from Array-Based Comparative Genomic Hybridization Analysis Identified Cyclin D1 as a Target Oncogene at 11q13.3 in Nasopharyngeal Carcinoma (2023)

Supplementary Figure S1 from Array-Based Comparative Genomic Hybridization Analysis Identified Cyclin D1 as a Target Oncogene at 11q13.3 in Nasopharyngeal Carcinoma
An all electronic passive millimetre wave imaging system (2005)

The need to develop passive millimetre wave imaging systems which have better spatial resolution and sensitivity, to offer powerful discrimination capabilities, is great. On the other hand, many deployment scenarios dictate the system footprint to be smaller than that of existing imagers. This dilemma may be resolved by replacing the bulky quasi-optics of existing imaging systems with two dimensional antenna arrays and electronic processors. This paper discusses initial design work for a demonstrator of an all electronic passive millimetre wave imager. This approach to the all electronic imaging system, endeavours to create ultimately an 'imager skin', which has essentially a two dimensional architecture, the minimum requirement for the collection of millimetre wave radiation for imaging. The physics of the imaging process and possible routes to electronic imaging are discussed. Possible arrays are investigated and a point spread function of the demonstrator imager is modelled. The results of using this imager system for a security scanning application are presented and conclusions about relevant technologies are given.
The Ly‐1. 1 and Ly‐1. 2 epitopes of murine CD5 map to the membrane distal scavenger receptor cysteine‐rich domain (1997)

CD5 is a member of a superfamily of proteins which contain one or more extracellular domains homologous to the type I macrophage Scavenger Receptor cysteine-rich (SRCR) domain. The extracellular region of CD5 is composed of three SRCR domains (D1, D2, D3). Murine CD5 (mCD5) is polymorphic (Ly-1.1 and Ly-1.2 alleles), however, the only murine CD5 gene characterized to date encodes the Ly-1.2 allele (mCD5.2). Likewise, the domain specificity of many of the available anti-mCD5 mAb recognizing either Ly-1.1 or Ly-1.2 or both has not been examined. Herein we describe the isolation and characterization of cDNA encoding the Ly1.1 allele (mCD5.1) and map the location and molecular nature of the mCD5 allelic variation. We also determined which SRCR domain of mCD5 is recognized by a panel of anti-mCD5 mAb. The mCD5.1 protein differs from mCD5.2 in only three amino acids, all of which map to the most amino terminal SRCR domain (D1) of mCD5. An additional seven silent substitutions were observed in the nucleotide sequence encoding mCD5 D1, D2 and transmembrane domains. Immunoglobulin (Ig) fusion proteins consisting of various combinations of mCD5.1 or mCD5.2 SRCR domains were produced and used to determine that allele specific mAb bound to D1, confirming sequence data. MAb against monomorphic determinants on mCD5 bound to each mCD5D11g.
Data for: Neu3CA-RT: A Framework for Real-Time fMRI Analysis (2018)

Neu3-CA-RT sample Matlab script containing a full explanation of how to run the script and where to find sample data
Chemical and Biophysical Modulation of Cas9 for Tunable Genome Engineering (2016)

The application of the CRISPR-Cas9 system for genome engineering has revolutionized the ability to interrogate genomes of mammalian cells. Programming the Cas9 endonuclease to induce DNA breaks at specified sites is achieved by simply modifying the sequence of its cognate guide RNA. Although Cas9-mediated genome editing has been shown to be highly specific, cleavage events at off-target sites have also been reported. Minimizing, and eventually abolishing, unwanted off-target cleavage remains a major goal of the CRISPR-Cas9 technology before its implementation for therapeutic use. Recent efforts have turned to chemical biology and biophysical approaches to engineer inducible genome editing systems for controlling Cas9 activity at the transcriptional and protein levels. Here, we review recent advancements to modulate Cas9-mediated genome editing by engineering split-Cas9 constructs, inteins, small molecules, protein-based dimerizing domains, and light-inducible systems.
Monitoring the Evolution of Asynchrony between Mean Arterial Pressure and Mean Cerebral Blood Flow via Cross-Entropy Methods (2022)

Cerebrovascular control is carried out by multiple nonlinear mechanisms imposing a certain degree of coupling between mean arterial pressure (MAP) and mean cerebral blood flow (MCBF). We explored the ability of two nonlinear tools in the information domain, namely cross-approximate entropy (CApEn) and cross-sample entropy (CSampEn), to assess the degree of asynchrony between the spontaneous fluctuations of MAP and MCBF. CApEn and CSampEn were computed as a function of the translation time. The analysis was carried out in 23 subjects undergoing recordings at rest in supine position (REST) and during active standing (STAND), before and after surgical aortic valve replacement (SAVR). We found that at REST the degree of asynchrony raised, and the rate of increase in asynchrony with the translation time decreased after SAVR. These results are likely the consequence of the limited variability of MAP observed after surgery at REST, more than the consequence of a modified cerebrovascular control, given that the observed differences disappeared during STAND. CApEn and CSampEn can be utilized fruitfully in the context of the evaluation of cerebrovascular control via the noninvasive acquisition of the spontaneous MAP and MCBF variability.
Purification and characterization of a soluble catalytic fragment of the human transmembrane leukocyte antigen related (LAR) protein tyrosine phosphatase from an E. coli expression system (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPurification and characterization of a soluble catalytic fragment of the human transmembrane leukocyte antigen related (LAR) protein tyrosine phosphatase from an E. coli expression systemHyeongjin Cho, Shawn E. Ramer, Michiyasu Itoh, David G. Winkler, Eric Kitas, Willi Bannwarth, Paul Burn, Haruo Saito, and Christopher T. WalshCite this: Biochemistry 1991, 30, 25, 6210–6216Publication Date (Print):June 25, 1991Publication History Published online1 May 2002Published inissue 25 June 1991https://pubs.acs.org/doi/10.1021/bi00239a019https://doi.org/10.1021/bi00239a019research-articleACS PublicationsRequest reuse permissionsArticle Views199Altmetric-Citations51LEARN 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
Interactions Between Tumor Biology and Targeted Nanoplatforms for Imaging Applications (2020)

Although considerable efforts have been conducted to diagnose, improve, and treat cancer in the past few decades, existing therapeutic options are insufficient, as mortality and morbidity rates remain high. Perhaps the best hope for substantial improvement lies in early detection. Recent advances in nanotechnology are expected to increase the current understanding of tumor biology, and will allow nanomaterials to be used for targeting and imaging both in vitro and in vivo experimental models. Owing to their intrinsic physicochemical characteristics, nanostructures (NSs) are valuable tools that have received much attention in nanoimaging. Consequently, rationally designed NSs have been successfully employed in cancer imaging for targeting cancer-specific or cancer-associated molecules and pathways. This review categorizes imaging and targeting approaches according to cancer type, and also highlights some new safe approaches involving membrane-coated nanoparticles, tumor cell-derived extracellular vesicles, circulating tumor cells, cell-free DNAs, and cancer stem cells in the hope of developing more precise targeting and multifunctional nanotechnology-based imaging probes in the future.
Photonic applications in wireless terminal networks (2002)

Wireless communications are rapidly becoming the means of data and information transfer for a broad range of applications. As wireless communication applications continue to expand, the information transfer rates are evolving toward the Gigabit per second data rate and, for some applications, there is even a need for terabit per second data rate transfer in the wireless network. In addition, wireless terminals often require instantaneous switching and communications between network members. For most applications directional antennas are needed to support the high data throughput requirements, and phased array antennas are the only high gain, directional antennas that can be rapidly switched to provide instantaneous communications among network members scattered geographically. Wireless terminal equipment is currently designed to operate in the 1 to 60 GHz frequency range and, traditionally, these equipment are designed with RF hardware. More recently, optics technology has been demonstrated to play an important role in RF systems as the True-Time-Delay in the phased array antenna, and, for some systems operating at high data rates, optical interconnects at the baseband level require E-O and O-E conversions. This paper discusses the considerations in using optics technology in the design of the wireless terminal network including optical signal processing, optical backplanes, optical networking, optical interconnects, and optical components. This paper also describes the architecture of an RF wireless communications network using a range of optical technologies.
Factor (F)VIII/VIIa enhances global haemostatic function in the co‐presence of bypassing agents and FVIII among patients with haemophilia A with inhibitor (2018)

Bypassing therapy is essential for the haemostatic management of patients with haemophilia A with inhibitor (PWHA-inh), but the therapeutic effects are inconsistent. We previously reported that activated prothrombin complex concentrates (aPCC) activated factor (F)VIIIin vitro, and was mediated mainly by the activated FVII (FVIIa) contained in aPCC. We have extended those studies to assess global coagulation in whole blood from 18 PWHA-inh in the co-presence of aPCC and FVIII using Ca<sup>2+</sup> -triggered rotational thromboelastometry. The clot times (CTs) in the presence of both aPCC (0·05 iu/ml) and recombinant (r)FVIII (1 iu/ml) ex vivo were shortened compared to the aPCC alone (P < 0·01). These enhancing effects of rFVIII were observed, irrespective of recognizing inhibitor epitopes; however, the clot formation time and 'α'-angle were not significantly different. In samples from 7 PWHA-inh post-infusion of aPCC (70-80 iu/kg), only the CTs were shortened in the presence of rFVIIIex vivo compared to its absence (P < 0·05), indicating that the enhanced activity centred on the initiation phase of coagulation. Furthermore, experiments in the co-presence of rFVIIa and rFVIII demonstrated that FVIII accelerated only the CTs. We concluded that FVIII/FVIIa-related coagulation mechanism enhanced global haemostatic function by the co-presence of bypassing agents and FVIII in PWHA-inh.
Residual Expansion Algorithm: Fast and Effective Optimization for Nonconvex Least Squares Problems (2017)

We propose the residual expansion (RE) algorithm: a global (or near-global) optimization method for nonconvex least squares problems. Unlike most existing nonconvex optimization techniques, the RE algorithm is not based on either stochastic or multi-point searches; therefore, it can achieve fast global optimization. Moreover, the RE algorithm is easy to implement and successful in high-dimensional optimization. The RE algorithm exhibits excellent empirical performance in terms of k-means clustering, point-set registration, optimized product quantization, and blind image deblurring.
Extremely Gradual Spin-Crossover Phenomenon in a Cyano-Bridged Fe−Mo Bimetallic Assembly (2009)

We report a unique type of spin-crossover phenomenon in a three-dimensional (3-D) Fe−Mo network with a cubic structure, Fe2[Mo(CN)8]·(3-pyCH2OH)8·3H2O (3-py = 3-pyridyl). This compound exhibits an extremely gradual FeII spin-crossover over a wide temperature range, which is more gradual than the crossover according to the Boltzmann distribution. The electronic states at 320 and 50 K are represented as (FeIIhs)2[MoIV(CN)8]·(3-pyCH2OH)8·3H2O and (FeIIhs)0.48(FeIIls)1.52[MoIV(CN)8]·(3-pyCH2OH)8·3H2O, respectively, where hs and ls denote high spin (S = 2) and low spin (S = 0), respectively. The model calculation based on Slichter−Drickamer’s model suggests this extremely gradual spin-crossover can be explained by the contribution of 3-D alternating alignment of hs and ls sites, i.e., −hs−ls−hs−ls−. This system is a strongly correlated system of spin-crossover sites because the spin-crossover FeII sites are directly linked by −NC−Mo−CN− with a high symmetry (FeII sites have one type of symmetry). The elastic interaction due to the volume change in a spin-crossover site isotropically propagates in the whole crystal. Since the CN bridges cannot be disconnected during spin-crossover, a 3-D alternating order of hs and ls sites is considered to be preferable.
Can Blood Gene Expression Predict Which Patients with Multiple Sclerosis Will Respond to Interferon? (2005)

Gene expression patterns from peripheral blood cells may be useful as biomarkers for monitoring MS progression and response to therapy, argue Kaminski and Achiron
Operation of Lateral SOI PIN Photodiodes with Back-Gate Bias and Intrinsic Length Variation (2013)

This paper presents an analysis of the operation of lateral thin-film SOI PIN photodiodes for the detection of short wavelengths. Experimental measurements were done varying the back-gate bias in order to point out the behavior of the device. The temperature influence was also analyzed in 300K to 500K range. In addition, by using two-dimensional numerical simulations, the intrinsic length (L I ) was changed, with the purpose of predicting the performance of this photodetector in more advanced technologies.
Optically Controlled Reconfigurable NRI-TL Phase Shifter for 5G Antenna Applications (2021)

An optically-controlled reconfigurable NRI-TL metamaterial phase shifter operating at 3.6 GHz is proposed. A host transmission line with a fixed length loaded with series capacitors and shunt inductors is used to achieve reconfigurability, while the optical control is introduced by integrating highly resistive silicon switches within the shunt branches of the NRI-TL design. The two states of the phase shifter result in a phase shift of ±60° leading to a differential phase shift of 120° with an insertion loss of 1.3 dB and 1.8 dB respectively. The operational bandwidth of the phase shifter is between 3.45-3.75 GHz. The versatile optical control and the high-frequency response make the proposed NRI-TL phase shifter well suited for 5G antenna array applications.