gebhart/patrepeval huggingface dataset:
Nonspecific Cleavages Arising from Reconstitution of Trypsin under Mildly Acidic Conditions (2020)

Abstract Tryptic digestion of proteins followed by liquid chromatography with tandem mass spectrometry analysis is an extensively used approach in proteomics research and biopharmaceutical product characterization, owing to the high level of cleavage fidelity produced with this technique. However, nonspecific trypsin cleavages have been frequently reported and shown to be related to a number of digestion conditions and predigestion sample treatments. In this work, we reveal that, for a number of commercial trypsins, reconstitution and storage conditions can have a significant impact on the occurrence of trypsin nonspecific cleavages. We analyzed the tryptic digestion of a variety of biotherapeutics, using trypsins reconstituted under different conditions. The results indicate that, for many commercial trypsins, commonly recommended reconstitution/storage conditions (mildly acidic, e.g., 50 mM acetic acid, 1 mM HCl) can actually promote nonspecific trypsin activities, which are time dependent and can be as high as 20% in total relative abundance. In contrast, using water for reconstitution and storage can effectively limit nonspecific cleavages to 1%. Interestingly, the performances of different commercial trypsins were found to be quite distinct in their levels of nonspecific cleavages and responses to the two reconstitution conditions. Our findings demonstrate the importance of choosing the appropriate trypsin for tryptic digestion and the necessity of assessing the impact of trypsin reconstitution and storage on nonspecific cleavages. We advocate for manufacturers of commercial trypsins to reevaluate manufacturing processes and reconstitution/storage conditions to provide good cleavage specificity.
Evidence for intracellular down-regulation of the epidermal growth factor (EGF) receptor during adenovirus infection by an EGF-independent mechanism (1992)

We have reported previously that human group C adenoviruses down-regulate the epidermal growth factor (EGF) receptor (EGF-R) (C. R. Carlin, A. E. Tollefson, H. A. Brady, B. L. Hoffman, and W. S. M. Wold, Cell 57:135-144, 1989). Expression of a 13.7-kDa protein encoded by a gene in the E3 transcription unit is necessary and sufficient for this effect (Carlin et al., Cell, 1989; B. L. Hoffman, A. Ullrich, W. S. M. Wold, and C. R. Carlin, Mol. Cell. Biol. 10:5521-5524, 1990). We show here that EGF-R down-regulation is accelerated in cells which overexpress the receptor when these cells are infected with virus mutants that overproduce the 13.7-kDa protein compared with wild-type virus. This is in contrast to EGF stimulation, for which others have shown that high concentrations of ligand are associated with low rates of receptor internalization in EGF-R-overexpressing cells (D. Kuppuswamy and L. J. Pike, J. Biol. Chem. 264:3357-3363, 1989; H. S. Wiley, J. Cell Biol. 107:801-810, 1988). We also show that the E3 protein is not present in media conditioned by infected cells and that it does not induce secretion of an EGF-like autocrine factor. Moreover, while mature membrane-bound EGF-R is down-regulated, the precursor of the membrane-bound form is not. Adenovirus infection also does not affect receptor-related molecules expressed in the secretory pathway. Interestingly, adenovirus-induced down-regulation is not regulated by concentrations of EGF associated with a slow rate of internalization in A431 cells. This suggests that 13.7-kDa protein expression triggers receptor entry by a novel ligand-independent pathway or, alternatively, that it compensates for a cellular factor that may be rate limiting during EGF-mediated endocytosis.
A 2-stage, 50Ω RF-DC Charge-pump with Load Lines for high RF-DC Voltage Conversion (2019)

A novel 2-stage RF-DC charge-pump circuit (RFCP) with a 50 ohm input impedance and higher RF-DC voltage conversion without an external input-matching network or output DC-filter for ambient wireless energy-harvesting (WEH) in the 2.4 GHz band is presented. The novelty of this RFCP is the use of near quarter-wavelength transmission lines on the load-side of each half-wave rectifying stage in the RFCP to induce a standing wave maxima at each of the diode inputs at 2.4 GHz. Doing so minimizes diode losses and maximize RF-DC voltage conversion of the charge-pump while still achieving a near 50 ohm input impedance. Simulations and measurements show the proposed design generating a higher DC output of 2.12V and energy efficiency of 18% with just -6dBm of RF input; an RF sensitivity of -7.2dBm for 1.8V output; and a 50Ω input impedance (reflection coefficient = -11dB) in the 2.4 GHz band.
Inhibition of<i>Escherichia coli</i>-Induced Meningitis by Carboxyfullerence (1999)

The effect of a water-soluble malonic acid derivative of carboxyfullerence (C60) against Escherichia coli-induced meningitis was tested. C60 can protect the mice from E. coli-induced death in a dose-dependent manner. C60 administered intraperitoneally as late as 9 h after E. coli injection was still protective. The C60-treated mice had less tumor necrosis factor alpha and interleukin-1beta production by staining of brain tissue compared to the levels of production for nontreated mice. The E. coli-induced increases in blood-brain barrier permeability and inflammatory neutrophilic infiltration were also inhibited. These data suggest that C60 is a potentially therapeutic agent for bacterial meningitis.
An Ex Vivo Erythrocyte Model for Investigating Oxidative Metabolism (2003)

The technology of opening and resealing the erythrocytes can be used successfully to investigate several basic aspects of cellular metabolism, including oxidative metabolism. Human and animal erythrocytes can be loaded with different kinds of molecules (enzymes, metabolites, immunoglobulins, exogenous substances, etc.) to modify cellular metabolism, through procedures easy to perform, reproducible, and highly conservative (1,2). Use of these procedures, notably those based on hypotonic hemolysis, isotonic resealing, and reannealing leads to intact and fully viable erythrocytes.
ChemInform Abstract: Synthesis and Antiproliferative Evaluation of 7‐Aminosubstituted Pyrroloiminoquinone Derivatives. (2000)

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.
Antenna-in-package solution for millimeter-wave applications: Slotted-patch in a multilayer PCB (2012)

An antenna-in-package solution implemented in a multi-layer PCB technology is introduced. The antenna is a slotted patch which is fed by a CPW line through a capacitive coupling mechanism. The structure yields return losses better than 10 dB from 65 GHz to 85 GHz. Moreover, there is an acceptable agreement between simulated and measured patterns which shows the applicability of the proposed solution for millimeter wave applications.
N-[1-(Benzotriazol-1-yl)alkyl]amides, versatile amidoalkylation reagents. Part 4. A New Synthetic Route to 4H-1,3-Oxazines (1992)

A variety of 2,4,6-tri- and 2,4,5,6-tetrasubstituted 4H-1,3-oxazines (7a – i) were synthesized in excellent yields by the reaction of acetylens (5) in the presence of aluminum chloride with N-[1-(benzotriazol-1-yl)alkyl]amides 4, themselves readily prepared from benzotriazole (1) with amides (2) and aldehydes (3).
Inherited Colorectal Cancer Registries in the United States (2004)

The United States is underserved by registries for inherited colorectal cancer, having enrolled only a small proportion of the families theoretically available. Registries differ in fundamental aspects of function. More collaboration and more registries are needed.
Effect of Traffic Load Measurement Bias on Pavement Life Prediction (2008)

The new Mechanistic-Empirical Pavement Design Guide (MEPDG) requires comprehensive traffic inputs to predict pavement performance. Axle load spectra play a critical role in the impact of traffic on pavement performance. Weigh-in-motion (WIM) systems are becoming widely used as an efficient means of collecting traffic load data for mechanistic pavement design. The quality of the WIM-based data, however, remains a concern among pavement engineers. Previous research showed that WIM equipment calibration bias may lead to significant bias in the estimation of equivalent single-axle loads. This study investigated the effect of traffic load measurement bias due to WIM measurement errors on pavement life prediction on the basis of the mechanistic-empirical approach proposed by MEPDG. The results of this study not only support but also advance the existing research in this critical area. The findings of this study can be used to estimate pavement life prediction bias when inaccurate WIM data are used. They can also serve as guidelines for state highway agencies for the selection of WIM equipment and the establishment of criteria for equipment calibration.
Intra-cavity semiconductor laser tuning using a frequency compensating acousto-optic tunable filter pair (2019)

We have investigated the effect of the frequency shift associated with an acousto-optic (AO) interaction on the spectral quality of acousto-optically tuned external cavity semiconductor lasers. A ring-cavity was built and the wavelength controlled by a frequency compensating acousto-optic tunable filter pair, which allowed user control over the frequency shift of the interacting light. Laser spectra were recorded for a range of frequency shifts, and a 30 kHz driving frequency gave the optimal spectral response where the output spectral shape did not vary as a function of operating wavelength and resulted in &lt;0.1 nm linewidths.
Mechanism of on-current and off-current instabilities under electrical stress in polycrystalline silicon thin-film transistors (2005)

The on-current (I/sub on/) and off-current (I/sub off/) instabilities of polycrystalline silicon thin-film transistors (poly-Si TFTs) were investigated under various electrical stress conditions. The stress-induced device degradation was studied by measuring the dependences of I/sub on/ and I/sub off/, on the drain/gate voltages. Using this technique, dissimilar variations of I/sub on/ and I/sub off/ after stress were observed. The differences can be attributed to the variances in the amount of charges trapped in the gate oxide and the spatial distributions of the trap states generated in the poly-Si channel. These results suggested a comprehensive model for the I/sub on/ and I/sub off/ instabilities of poly-Si TFTs.
Selective virus inhibitors. (1990)

Our recent efforts have been directed at the development of selective inhibitors of different classes of viruses, including adeno, pox, and herpesviruses [herpes simplex virus type 1 (HSV-1) and type 2 (HSV-2), varicella-zoster (VZV), cytomegalovirus (CMV), Epstein-Barr virus (EBV)], (+/-)RNA viruses (reo- and rotavirus), (-)RNA viruses (influenza, parainfluenza, measles, respiratory syncytial, vesicular stomatitis and rabies virus) and retroviruses [i.e. human immunodeficiency virus (HIV), the causative agent of AIDS]. In this search, the following molecular targets were envisaged: for DNA viruses in general, the viral DNA polymerase; for herpes simplex virus and varicella-zoster virus, the viral DNA polymerase via a specific phosphorylation by the viral 2'-deoxythymidine (dThd) kinase; for (+/-)RNA and (-)RNA viruses, S-adenosylhomocysteine (SAH) hydrolase, a key enzyme in transmethylation reactions required for the maturation of viral mRNA; for retroviruses, reverse transcriptase as initiator of virus replication and/or cell transformation; and for several enveloped viruses (i.e. retro-, herpes- and rhabdoviruses), virus adsorption to the outer cell membrane. Several new compounds have been developed that appear to act at these targets: i.e. (E)-5-(2-bromovinyl)-2'-deoxyuridine [bromovinyldeoxyuridine (BVDU)] and derivatives thereof [i.e. carbocyclic BVDU (C-BVDU)] as well as derivatives of acyclovir (i.e. 8-substituted acyclovir derivatives) as inhibitors of herpesviruses; (S)-9-(3-hydroxy-2-phosphonylmethoxypropyl)adenine [(S)-HPMPA], 9-(2-phosphonylmethoxyethyl)adenine (PMEA) and other phosphonylmethoxyalkylpurines and -pyrimidines as inhibitors of DNA viruses and retroviruses; acyclic and carbocyclic analogues of adenosine [such as (S)-9-(2,3-dihydroxypropyl)adenine [S)-DHPA), carbocyclic 3-deazaadenosine (C-c3Ado), (RS)-3-adenin-9-yl-2-hydroxypropanoic acid (AHPA) alkyl esters, neplanocin A, 3-deazaneplanocin A and the 5'-nor derivatives of neplanocin A and 3-deazaneplanocin A] as inhibitors of (+/-)RNA and (-)RNA viruses; 2',3'-dideoxynucleoside analogues as inhibitors of retroviruses; and sulfated polysaccharides (i.e. heparin, dextran sulfate, pentosan polysulfate, mannan sulfate), sulfated polyvinylalcohol and co-polymers of sulfated polyvinylalcohol with acrylic acid as inhibitors of retro-, herpes- and rhabdoviruses.
<i>Miscanthus</i> grass-derived carbon dots to selectively detect Fe<sup>3+</sup> ions (2019)

Novel fluorescent carbon dots (CDs) were synthesized using an economically feasible and green one-step heating process. <i>Miscanthus</i>, a perennial grass and an inexpensive sustainable biomass, was utilized as the starting material to prepare CDs and doped CDs (nitrogen, phosphorous and nitrogen-phosphorous dual doped). The abundance of oxygen-containing functional groups in <i>Miscanthus</i>-derived CDs (MCD) and doped MCD was confirmed <i>via</i> Fourier-transform infrared (FTIR) and energy dispersive X-ray spectroscopy (EDS). The average size of MCD, N-doped MCD, P-doped MCD and dual-doped MCDs was found to be 7.87 ± 0.27, 4.6 ± 0.21, 6.7 ± 0.38 and 5.3 ± 0.32 nm, respectively. The synthesized MCD and doped MCD exhibited a quantum yield (QY) of 4.71, 11.65, 2.33 and 9.63% for the MCD, N-doped MCD, P-doped MCD and dual-doped MCD, respectively. MCD and doped MCD exhibited excellent excitation-dependent photoluminescence properties, with strong blue fluorescence upon irradiation with UV-light (365 nm). N-doped MCD exhibited superb selectivity towards Fe<sup>3+</sup> ions, with a detection limit of 20 nM and a detection range from 0.02 to 2000 μM. The normalized linear relationship between the intensity of fluorescence emission of the prepared N-doped MCD and the concentration of Fe<sup>3+</sup> ions was utilized to selectively and sensitively detect Fe<sup>3+</sup> ions.
Long-term safety and anti-tumour activity of olaparib monotherapy after combination with carboplatin and paclitaxel in patients with advanced breast, ovarian or fallopian tube cancer (2015)

Continued long-term daily olaparib was found to be safe and tolerable. Encouragingly, patients who showed a favourable response on earlier combination therapy maintained this response on olaparib monotherapy.
Salicylate‐induced translocation of prestin having mutation in the GTSRH sequence to the plasma membrane (2010)

Prestin is a key molecule for mammalian hearing. The present study investigated changes in characteristics of prestin by culturing prestin-transfected cells with salicylate, an antagonist of prestin. As a result, the plasma membrane localization of prestin bearing a mutation in the GTSRH sequence, which normally accumulates in the cytoplasm, was recovered. Moreover, the nonlinear capacitance of the majority of the mutants, which is a signature of prestin activity, was also recovered. Thus, the present study discovered a new effect of salicylate on prestin, namely, the promotion of the plasma membrane expression of prestin mutants in an active state.
Identifying patient-important outcomes for treatment of bipolar disorder: a systematic review protocol (2021)

Introduction Treatment of bipolar disorder is the focus of several clinical trials, however the understanding of the outcomes for establishing treatment effectiveness within these trials is limited. Further, there is limited literature which reports on the outcomes considered to be important to patients, indicating that patient perspectives are often not considered when selecting outcomes of effectiveness within trials. This protocol describes a systematic review which aims to describe the outcomes being used within trials to measure treatment effectiveness, commenting on the inclusion of patient-important outcomes within previous trials. Methods and analysis This protocol is reported using the Preferred Reporting Items for Systematic Reviews and Meta-analyses Protocols statement. OVID MEDLINE, OVID Embase, OVID APA PsycINFO, Web of Science, the Wiley Cochrane Library, ClinicalTrials.gov and the International Clinical Trials Registry Platform databases will be searched for eligible studies. Screening, full-text and data extraction stages will be completed in duplicate using the Covidence platform for systematic reviews. Eligible studies will include clinical trials of interventions in bipolar disorder, in order to identify outcomes used to assess treatment effectiveness, and qualitative studies, to determine which outcomes have been reported as important by patients. Risk of bias for included studies will be assessed using the Cochrane Risk of Bias Tool for randomised controlled trials, and the Newcastle-Ottawa Scale for observational research. Ethics and dissemination This review will involve dissemination to key stakeholders, including primary end users such as patients, clinicians and trialists. Knowledge translation tools will be generated to share the relevant conclusions of this review. Results will be communicated to the scientific community through peer-reviewed publications, conferences and workshops. No ethics approval will be sought as this study is based on literature. PROSPERO registration number CRD42021214435.
Fibre Bragg grating sensors for micrometeoroids and small orbital debris (2019)

This chapter summarised the classical and innovative methods of protecting spacecraft or satellite components against small space debris. It also presented the detection and sensing methods proposed to monitor the impact and its characteristic. The FBG sensors are very promising to monitor the micrometeorites and small space debris starting from their impact and fast effect with the possibility of comparing the effect at long term after the impact which common sensors cannot perform.Their signal can be easily correlated with that given by other sensors, to measure, for example, the shock propagation speed within the target.
Activity representation and management for crisis action planning (2002)

This work presents the development of a multi-user virtual environment in support of crisis management planning activities. Coupling ongoing work in activity representation with analysis of the domain, an extensible domain ontology was developed. Studying the domain, several challenges became apparent: (1) the need to support extensive dynamic and distributed collaboration, (2) the need for a flexible, open architecture, (3) the need for views of the information tailored to the activities of the planning team, and (4) the opportunity to leverage past and current related efforts in the domain. This project developed a Java-based collaboration architecture around a multi-user domain (MUD) to provide presence and access to collaborative services. The collaborative infrastructure layer provides persistence, user authentication, and access control. Built upon this substrate are collaborative services. The target use of MAST is to represent and track workflow in the crisis action planning done by the Operations Planning Team of the US Pacific Command. The design approach was to base MAST on a reusable class library which implements a rich ontology structure and represents key elements of the domain. Our ontology draws on the SPOT project and the Shared Planning and Activity Representation (SPAR) project. The resulting ontology, implemented in Java, is compliant with the SPAR Reference Object Model Specification. A strength of this work is the extensibility, flexibility and openness both of the representation and the system architecture.
Broad spectrum antibiotic activity of skin‐PYY (1996)

Neuropeptide Y (NPY) and polypeptide YY (PYY) are two ubiquitous neuropeptides, found in brain and intestines, respectively, where they exert important regulatory functions. In this study, a new member of the YY family recently isolated from amphibian skin, skin-PYY (SPYY), is reported to inhibit irreversibly the proliferation of a broad spectrum of pathogenic microorganisms. NPY and PYY are shown to be endowed with the same activity. Their potency is similar to that of other antibacterial peptides which have been shown to exert their function by disintegrating the bacterial membrane. These findings and the fact that the C-terminal alpha-helical domain SPYY14-36, which is highly conserved among family members, was responsible for killing microorganisms and for permeation of phospholipid vesicles, suggested that the antibiotic activity may emerge via a membrane permeation mechanism. These findings also raise the question whether NPY and PYY exert in vivo a similar function in mammals.
Gene expression analysis of B‐lymphoma cells resistant and sensitive to bortezomib* (2006)

The proteasome inhibitor bortezomib has shown impressive clinical activity alone and in combination with conventional and other novel agents for the treatment of multiple myeloma (MM). Although bortezomib is known to be a selective proteasome inhibitor, the downstream mechanisms of cytotoxicity and drug resistance are poorly understood. However, resistance to bortezomib as a single agent develops in the majority of patients, and activity in other malignancies has been less impressive. To elucidate mechanisms of bortezomib resistance, we compared differential gene expression profiles of bortezomib-resistant SUDHL-4 and bortezomib-sensitive SUDHL-6 diffuse large B-cell lymphoma lines in response to bortezomib. At concentrations that effectively inhibited proteasome activity, bortezomib induced apoptosis in SUDHL-6 cells, but not in SUDHL-4 cells. We showed that overexpression of activating transcription factor 3 (ATF3), ATF4, ATF5, c-Jun, JunD and caspase-3 is associated with sensitivity to bortezomib-induced apoptosis, whereas overexpression of heat shock protein (HSP)27, HSP70, HSP90 and T-cell factor 4 is associated with bortezomib resistance.
Electronic Structure from First-Principles of LiBH<sub>4</sub>·NH<sub>3</sub>, Sr(NH<sub>2</sub>BH<sub>3</sub>)<sub>2</sub>, and Li<sub>2</sub>Al(BH<sub>4</sub>)<sub>5</sub>·6NH<sub>3</sub>for Hydrogen Storage Applications (2011)

A series of compounds containing boron, nitrogen, and hydrogen atoms, namely, LiBH4·NH3, Sr(NH2BH3)2, and Li2Al(BH4)5·6NH3, were synthesized recently, and found to be promising for hydrogen storage. We have conducted the corresponding ab initio calculations using density functional theory and analyzed the corresponding electron density as well as derived properties. Also, molecular dynamics simulations were performed to study the diffusion of hydrogen in this series of compounds. We found that despite having widely different crystal structures and difference in their chemical composition, these compounds share common features at the level of their electronic structure. Moreover, diffusion of hydrogen appears to be more favorable in LiBH4·NH3 than in Sr(NH2BH3)2 and Li2Al(BH4)5·6NH3.
First record of an association between a phyllosoma larva and a Prayid siphonophore (2007)

A scyllarid lobster phyllosoma larva was observed attached to the siphosome of a prayid siphonophore while SCUBA diving in the Canary Islands. The phyllosoma was straddling the siphosome, which was still alive, with one pereiopodal endopodite per siphosomal cormidia and used its pereiopodal exopodites to pull the siphosome through the water. It did not detach, even after repeated disturbances, and it is proposed that the phyllosoma may be using the prayid siphosome as both food and for protection from predators.