gebhart/patrepeval huggingface dataset:
Mass Spectrometry Identifiable Cross-Linking Strategy for Studying Protein−Protein Interactions (2004)

A new mass spectrometry identifiable cross-linking strategy has been developed to study protein-protein interactions. The new cross-linker was designed to have two low-energy MS/MS-cleavable bonds in the spacer chain to provide three primary benefits: First, a reporter tag can be released from cross-link due to cleavage of the two labile bonds in the spacer chain. Second, a relatively simple MS/MS spectrum can be generated owing to favorable cleavage of labile bonds. And finally, the cross-linked peptide chains are dissociated from each other, and each then can be fragmented separately to get sequence information. Therefore, this novel type of cross-linker was named protein interaction reporter (PIR). To this end, two RINK groups were utilized to make our first-generation cross-linker using solid-phase peptide synthesis chemistry. The RINK group contains a bond more labile than peptide bonds during low-energy activation. The new cross-linker was applied to cross-link ribonuclease S (RNase S), a noncovalent complex of S-peptide and S-protein. The results demonstrated that the new cross-linker effectively reacted with RNase S to generate various types of cross-linked products. More importantly, the cross-linked peptides successfully released reporter ions during selective MS/MS conditions, and the dissociated peptide chains remained intact during MS(2), thus enabling MS(3) to be performed subsequently. In addition, dead-end, intra-, and inter-cross-linked peptides can be distinguished by analyzing MS/MS spectra.
Identification of screwworm species by polymerase chain reaction‐restriction fragment length polymorphism (1996)

Restriction fragment length polymorphisms in polymerase chain reaction amplified fragments (PCR-RFLP) of mitochondrial DNA were used to differentiate species of New World screwworms (Diptera: Calliphoridae). Twenty-seven restriction enzymes were screened on five regions of mtDNA. Eleven restriction fragment length patterns differentiated New World screwworm, Cochliomyia hominivorax (Coquerel), from secondary screwworm, Cochliomyia macellaria (F.). Five restriction fragment length patterns were polymorphic in C.hominivorax while all fragment patterns were fixed in C.macellaria. Diagnostic restriction fragment length patterns were used for species diagnosis, whereas intraspecific variable patterns were used to characterize field samples and laboratory strains. The PCR-RFLP technique is flexible with regard to developmental stage of the sample and method of preservation. We were able to characterize specimens of all life stages from egg to adult including larvae preserved in alcohol and pinned adults. PCR-RFLP is rapid and inexpensive, enabling specimens to be characterized within 24 h for less than $2.50.
Elimination of the concentration dependence in mass isotopomer abundance mass spectrometry of methyl palmitate using metastable atom bombardment (2001)

An important problem in mass isotopomer abundance mass spectrometry (MIAMS) is the dependence of measured mass isotopomer abundances on sample concentration. We have evaluated the role of ionization energy on mass isotopomer abundance ratios of methyl palmitate as a function of sample concentration. Ionization energy was varied using electron impact ionization (EI) and metastable atom bombardment (MAB). The latter generates a beam of metastable species capable of ionizing analyte molecules by Penning ionization. We observed that ionization of methyl palmitate by EI (70 eV) showed the greatest molecular ion fragmentation and also showed the greatest dependence of relative isotopomer abundance ratios on sample concentration. Ionization using the 3P2 and 3P0 states of metastable krypton (9.92 and 10.56 eV, respectively) resulted in almost no molecular ion fragmentation, and the isotopomer abundances quantified were essentially independent of sample concentration. Ionization using the 3P2 and 3P0 states of metastable argon (11.55 and 11.72 eV, respectively) showed molecular ion fragmentation intermediate between that of EI and MAB(Kr) and showed an isotopomer concentration dependence which was less severe than that observed with EI but more severe than that observed with MAB(Kr). The observed decrease in the dependence of isotopomer abundance on sample concentration with a decrease in molecular ion fragmentation is consistent with the hypothesis that proton transfer from a fragment cation to a neutral molecule is the gas phase reaction mechanism responsible for the concentration dependence. Alternative explanations, e.g., hydrogen abstraction from a neutral molecule to a molecular cation, is not supported by these results. Moreover, the MAB ionization technique shows potential for eliminating one source of error in MIAMS measurements of methyl palmitate, in particular, and of fatty acids methyl esters, in general.
Fluorocarbon-Based Heterophase Polymeric Materials. 1. Block Copolymer Surfactants for Carbon Dioxide Applications (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFluorocarbon-Based Heterophase Polymeric Materials. 1. Block Copolymer Surfactants for Carbon Dioxide ApplicationsZhibin Guan and J. M. DeSimoneCite this: Macromolecules 1994, 27, 20, 5527–5532Publication Date (Print):September 1, 1994Publication History Published online1 May 2002Published inissue 1 September 1994https://pubs.acs.org/doi/10.1021/ma00098a002https://doi.org/10.1021/ma00098a002research-articleACS PublicationsRequest reuse permissionsArticle Views442Altmetric-Citations96LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Improving Robustness Without Sacrificing Accuracy with Patch Gaussian Augmentation (2019)

Deploying machine learning systems in the real world requires both high accuracy on clean data and robustness to naturally occurring corruptions. While architectural advances have led to improved accuracy, building robust models remains challenging. Prior work has argued that there is an inherent trade-off between robustness and accuracy, which is exemplified by standard data augment techniques such as Cutout, which improves clean accuracy but not robustness, and additive Gaussian noise, which improves robustness but hurts accuracy. To overcome this trade-off, we introduce Patch Gaussian, a simple augmentation scheme that adds noise to randomly selected patches in an input image. Models trained with Patch Gaussian achieve state of the art on the CIFAR-10 and ImageNetCommon Corruptions benchmarks while also improving accuracy on clean data. We find that this augmentation leads to reduced sensitivity to high frequency noise(similar to Gaussian) while retaining the ability to take advantage of relevant high frequency information in the image (similar to Cutout). Finally, we show that Patch Gaussian can be used in conjunction with other regularization methods and data augmentation policies such as AutoAugment, and improves performance on the COCO object detection benchmark.
CAT constructions with multiple unique restriction sites for the functional analysis of eukaryotic promoters and regulatory elements (1987)

The coding region of the bacterial chloramphenicol acetyltransferase (CAT) gene is widely used as an indicator gene in gene transfer experiments dealing with regulation of transcription in eukaryotes. Chimaeric CAT fusion genes are especially useful because no endogenous CAT activity is present in eukaryotic cells and because CAT enzyme activity can be monitored by a rapid and sensitive assay (1). In order to simplify the construction of hybrid CAT genes, we have constructed the plasmids pBLCAT2 and pBLCAT3. The coding region of the CAT gene as well as the small t intron and polyadenylation signals from SV40 were inserted into the polylinker region of the high copy number plasmid pUC18 (2). Unique BgHI and Xhol restriction sites were introduced upstream of the CAT coding region by insertion of synthetic linkers. A BamHI site at the 3' end of the transcription unit was converted into a dam methylation sensitive Clal site by partial digestion with BamHI, filling -in and re -ligation. In the promoterless construction pBLCAT3 eight unique restriction sites are suitable for insertion of different eukaryotic promoters at the 5' end of the CAT gene. Four additional unique restriction sites make the insertion of regulatory signals 3' of the CAT gene possible and enable the excision of the intact fusion gene from the prokaryotic vector. The presence of die Herpes simplex virus tk promoter in pBLCAT2 permits die analysis of the effects of putative regulatory elements on a heterologous eukaryotic promoter. A BamHI/Bglll fragment from the HSV tk linker scanning mutant LS -115/ -105 (3) spanning the promoter from -105 to +51 was inserted into the corresponding restriction sites of pBLCAT3 thereby generating pBLCAT2. The modified polylinker regions at the 5' and the 3' ends have been sequenced and compiled sequences for both plasmids are available on request.
Activation of Klebsiella pneumoniae and Rhizobium meliloti nitrogenase promoters by gln (ntr) regulatory proteins. (1983)

We have studied the expression, in different Escherichia coli gln (ntr) mutants, of fusions (constructed in vitro) of the nifHDK (nitrogenase) promoters from Klebsiella pneumoniae and Rhizobium meliloti to E. coli lacZ. Derepression of the K. pneumoniae nifH::lacZ fusion requires the glnF (ntrA) gene product in addition to the K. pneumoniae nifA gene product, indicating that regulation of the K. pneumoniae nif genes is more closely integrated with the overall nitrogen control system than previously demonstrated. Derepression of the R. meliloti nifH::lacZ fusion in E. coli by the K. pneumoniae nifA gene product (which we had previously shown) exhibits the same requirement for glnF. Derepression of the R. meliloti nifH::lacZ fusion, but not the K. pneumoniae nifH::lacZ fusion, can be mediated by the glnG (ntrC) gene product, suggesting that the gln regulatory genes might directly regulate the symbiotic nitrogen fixation genes in Rhizobium.
Persistence and Expression of Human Papillomavirus DNA in Genital Cancer (2007)

There is mounting evidence that certain types of human papillomaviruses (HPV types 16 and 18) are associated with human genital cancer. Other virus types, such as HPV-6 or HPV-11, are more regularly found in benign genital warts. Since all viruses can be present in putative precancerous lesions of the uterine cervix (dysplasia, cervical intraepithelial neoplasia) it has been postulated that individual HPV types have different 'oncogenic potential'. The molecular basis for this difference is not known. The question of the natural reservoir for the oncogenic viruses is discussed. Expression of parts of the early region of the HPV genome in cell lines established from genital cancer supports the hypothesis that papillomaviruses are involved in inducing and/or maintaining the transformed phenotype of cancer cells.
High performance 0.1 μm partially depleted SOI CMOSFET (2002)

The partially depleted SOI MOSFET (PD-SOI) has been found to be an attractive device due to advantages such as full dielectric isolation and reduced junction capacitance compared to the bulk Si device (Assaderaghi et al, 1997; Maeda et al, 2000). However, the floating body effect occurs on PD-SOI devices, resulting in threshold voltage reduction and noise overshoot (Tseng et al, 1997). Body contact structures have been proposed to improve the floating body effect (Huang et al, 1998). This paper describes high performance 0.1 /spl mu/m generation SOI MOSFET technology with body contact structure (BC-SOI) which was used to investigate the device characteristics as well as thermal effects in comparison with the floating body SOI MOSFET (FB-SOI), which is without body contact. The dynamic-threshold voltage SOI MOSFET (DTMOS) was also investigated.
Delirium at Home (2008)

Delirium is a challenging, under-appreciated problem in the home care setting. When it is not detected early and managed effectively, delirium adversely affects outcomes and quality of life. Home healthcare nurses play a key role in the assessment, early identification, and management of delirium and in the support and education of patients and their family caregivers. This article reviews delirium and describes strategies for detecting and managing delirium in the home care setting.
Characteristics of plasma enhanced chemical vapor deposited tungsten nitride thin films (1993)

Low resistive tungsten nitride (W100−xNx) thin films have been deposited at 350–400 °C by plasma enhanced chemical vapor deposition. X-ray photoemission spectroscopy, Rutherford backscattering spectrometry, and x-ray diffraction show that the nitrogen composition in W100−xNx films can be easily controlled between 15 and 72 at. % corresponding to an increase of the NH3/WF6 partial pressure ratio and fcc structure W2N can be obtained. The resistivities of W100−xNx films are varied from 70 to 440 μΩ cm according to nitrogen composition.
Proliferation, migration, and ERK activation in human retinal endothelial cells through A(2B) adenosine receptor stimulation. (2001)

The selective A(2B) AdoR antagonists, enprofylline and IPDX, inhibited NECA-stimulated proliferation, ERK activation, cell migration, and capillary tube formation. A(2B) AdoR inhibition may offer a way to inhibit retinal angiogenesis and provide a novel therapeutic approach to treatment of diseases associated with aberrant neovascularization, such as diabetic retinopathy and retinopathy of prematurity.
Single-strand conformation polymorphism analysis by capillary zone electrophoresis in neutral pH buffer (2000)

Sensitivity of single-strand conformation polymorphism (SSCP) analysis of polymerase chain reaction (PCR) products was reported to be lower in capillary zone electrophoresis (CZE) compared to conventional slab gel electrophoresis. We examined the effects of buffer ion type, pH, and temperature in an attempt to improve the mutation detectability in the SSCP-CZE mode. It was noted that, by utilizing short-chain polyacrylamide as sieving media while simultaneously lowering the temperature, there was no improvement of conformer detectability. On the contrary, there was a large increment in conformers' resolution by running samples in a lower-pH buffer system. The effects of different buffering ions and pH values were investigated. By using a new buffer system, consisting of 35 mM 2-(N-morpholino)propanesulfonic acid (MES), 30 mM tris(hydroxymethyl)aminomethane (Tris), 1 mM ethylene diaminetetraacetic acid (EDTA), pH 6.8, and keeping constant all the other conditions, such as temperature, sieving, applied voltage, capillary length, and inner diameter (ID), there was a remarkable improvement in resolution and the sensitivity became comparable to that of slab gel systems.
Streptavidin facilitates internalization and pulmonary targeting of an anti-endothelial cell antibody (platelet-endothelial cell adhesion molecule 1): A strategy for vascular immunotargeting of drugs (1999)

Conjugation of drugs with antibodies to surface endothelial antigens is a potential strategy for drug delivery to endothelium. We studied antibodies to platelet-endothelial adhesion molecule 1 (PECAM-1, a stably expressed endothelial antigen) as carriers for vascular immunotargeting. Although 125I-labeled anti-PECAM bound to endothelial cells in culture, the antibody was poorly internalized by the cells and accumulated poorly after intravenous administration in mice and rats. However, conjugation of biotinylated anti-PECAM (b-anti-PECAM) with streptavidin (SA) markedly stimulated uptake and internalization of anti-PECAM by endothelial cells and by cells expressing PECAM. In addition, conjugation with streptavidin markedly stimulated uptake of 125I-labeled b-anti-PECAM in perfused rat lungs and in the lungs of intact animals after either intravenous or intraarterial injection. The antioxidant enzyme catalase conjugated with b-anti-PECAM/SA bound to endothelial cells in culture, entered the cells, escaped intracellular degradation, and protected the cells against H2O2-induced injury. Anti-PECAM/SA/125I-catalase accumulated in the lungs after intravenous injection or in the perfused rat lungs and protected these lungs against H2O2-induced injury. Thus, modification of a poor carrier antibody with biotin and SA provides an approach for facilitation of antibody-mediated drug targeting. Anti-PECAM/SA is a promising candidate for vascular immunotargeting of bioactive drugs.
Graph Partitioning with Natural Cuts (2011)

We present a novel approach to graph partitioning based on the notion of cuts. Our algorithm, called PUNCH, has two phases. The first phase performs a series of minimum-cut computations to identify and contract dense regions of the graph. This reduces the graph size, but preserves its general structure. The second phase uses a combination of greedy and local search heuristics to assemble the final partition. The algorithm performs especially well on road networks, which have an abundance of natural cuts (such as bridges, mountain passes, and ferries). In a few minutes, it obtains the best known partitions for continental-sized networks, significantly improving on previous results.
Structural Basis for Inhibiting Porcine Epidemic Diarrhea Virus Replication with the 3C-Like Protease Inhibitor GC376 (2020)

Porcine epidemic diarrhea virus (PEDV), being highly virulent and contagious in piglets, has caused significant damage to the pork industries of many countries worldwide. There are no commercial drugs targeting coronaviruses (CoVs), and few studies on anti-PEDV inhibitors. The coronavirus 3C-like protease (3CL<sup>pro</sup>) has a conserved structure and catalytic mechanism and plays a key role during viral polyprotein processing, thus serving as an appealing antiviral drug target. Here, we report the anti-PEDV effect of the broad-spectrum inhibitor GC376 (targeting 3Cpro or 3CL<sup>pro</sup> of viruses in the picornavirus-like supercluster). GC376 was highly effective against the PEDV 3CL<sup>pro</sup> and exerted similar inhibitory effects on two PEDV strains. Furthermore, the structure of the PEDV 3CL<sup>pro</sup> in complex with GC376 was determined at 1.65 Å. We elucidated structural details and analyzed the differences between GC376 binding with the PEDV 3CL<sup>pro</sup> and GC376 binding with the transmissible gastroenteritis virus (TGEV) 3CL<sup>pro</sup>. Finally, we explored the substrate specificity of PEDV 3CL<sup>pro</sup> at the P2 site and analyzed the effects of Leu group modification in GC376 on inhibiting PEDV infection. This study helps us to understand better the PEDV 3CL<sup>pro</sup> substrate specificity, providing information on the optimization of GC376 for development as an antiviral therapeutic against coronaviruses.
Design and application of stimulus-responsive peptide systems (2007)

The ability of peptides and proteins to change conformations in response to external stimuli such as temperature, pH and the presence of specific small molecules is ubiquitous in nature. Exploiting this phenomenon, numerous natural and designed peptides have been used to engineer stimulus-responsive systems with potential applications in important research areas such as biomaterials, nanodevices, biosensors, bioseparations, tissue engineering and drug delivery. This review describes prominent examples of both natural and designed synthetic stimulus-responsive peptide systems. While the future looks bright for stimulus-responsive systems based on natural and rationally engineered peptides, it is expected that the range of stimulants used to manipulate such systems will be significantly broadened through the use of combinatorial protein engineering approaches such as directed evolution. These new proteins and peptides will continue to be employed in exciting and high-impact research areas including bionanotechnology and synthetic biology.
Characterization of a rat oral squamous cell carcinoma cell line UHG-RaC '93 induced by 4-nitroquinoline-1-oxide in vivo (1995)

This study describes several characteristics of a cell line, UHG-RaC '93 derived from rat oral squamous cell carcinoma induced by the carcinogen 4-nitroquinoline-1-oxide (4NQO). The cell line was established from explant cultures without support of fibroblast feeder cells and continued for > 30 passages. UHG-RaC '93 had a high mitotic rate with a population doubling time of 25 h and a high rate of squame production. The first passage had a low colony-forming efficiency in agarose gel, whereas later passages did not grow at all in semi-solid medium. Phenotype selection was furthermore apparent from a gradual increase of the trypsin-detachment time. Cytogenetic analysis showed that UHG-RaC '93 was hypotetraploid with an average of 74 chromosomes. Abnormalities compared to the normal karyotype were assessed and consisted mainly of breakpoints at (1)(q5?3), (3)(p1), (3)(q11q23), (11)(p?11), (13)(p13) and a derivative (12)t(12;13)(q10;q10). The karyotype remained stable for at least 26 passages. The expression of typical epithelioid markers like cytokeratins and desmoglein corresponded with normal rat oral keratinocytes. However expression of alpha 6 beta 4-integrin was altered. Squame production, immunophenotype and anchorage dependency indicated that UHG-RaC '93 had the same features of a well-differentiated carcinoma with a low degree of agressiveness as the original tumour. The stable karyotype of this cell line provides a basis for further analysis of the effect of 4NQO on the genotype, phenotype and behaviour of rat oral keratinocytes.
Online Detection and Classification of Moving Objects Using Progressively Improving Detectors (2005)

Boosting based detection methods have successfully been used for robust detection of faces and pedestrians. However, a very large amount of labeled examples are required for training such a classifier. Moreover, once trained, the boosted classifier cannot adjust to the particular scenario in which it is employed. In this paper, we propose a co-training based approach to continuously label incoming data and use it for online update of the boosted classifier that was initially trained from a small labeled example set. The main contribution of our approach is that it is an online procedure in which separate views (features) of the data are used for co-training, while the combined view (all features) is used to make classification decisions in a single boosted framework. The features used for classification are derived from principal component analysis of the appearance templates of the training examples. In order to speed up the classification, background modeling is used to prune away stationary regions in an image. Our experiments indicate that starting from a classifier trained on a small training set, significant performance gains can be made through online updation from the unlabeled data.