gebhart/patrepeval huggingface dataset:
Resilin-mimetics as a smart biomaterial platform for biomedical applications (2021)

Intrinsically disordered proteins have dramatically changed the structure-function paradigm of proteins in the 21<sup>st</sup> century. Resilin is a native elastic insect protein, which features intrinsically disordered structure, unusual multi-stimuli responsiveness and outstanding resilience. Advances in computational techniques, polypeptide synthesis methods and modular protein engineering routines have led to the development of novel resilin-like polypeptides (RLPs) including modular RLPs, expanding their applications in tissue engineering, drug delivery, bioimaging, biosensors, catalysis and bioelectronics. However, how the responsive behaviour of RLPs is encoded in the amino acid sequence level remains elusive. This review summarises the milestones of RLPs, and discusses the development of modular RLP-based biomaterials, their current applications, challenges and future perspectives. A perspective of future research is that sequence and responsiveness profiling of RLPs can provide a new platform for the design and development of new modular RLP-based biomaterials with programmable structure, properties and functions.
Germline BRCA1 Mutations and a Basal Epithelial Phenotype in Breast Cancer (2003)

A basal epithelial phenotype is found in not more than 15% of all invasive breast cancers. Microarray studies have shown that this phenotype is associated with breast cancers that express neither estrogen receptor (ER) nor erbB-2 (HER2/neu) (i.e., ER/erbB-2-negative tumors). The ER/erbB-2- negative phenotype is also found in breast cancers occurring in BRCA1 mutation carriers (i.e., BRCA1-related breast cancers). We tested the hypothesis that BRCA1-related breast cancers are more likely than non-BRCA1/ 2-related breast cancer to express a basal epithelial phenotype. Among 292 breast cancer specimens previously analyzed for ER, erbB-2, p53, and germline mutations in BRCA1 and BRCA2, we identified 76 that did not overexpress ER or erbB-2. Of the 72 specimens with sufficient material for testing, 40 expressed stratified epithelial cytokeratin 5 and/or 6 (5/6). In univariate analysis, the expression of cytokeratin 5/6 was statistically significantly associated with BRCA1-related breast cancers (odds ratio = 9.0, 95% confidence interval = 1.9 to 43; P =.002, two-sided Fisher's exact test). Thus, germline BRCA1 mutations appear to be associated with a distinctive breast cancer phenotype.
Tentative molecular mechanism for germination stimulation of Striga and Orobanche seeds by strigol and its synthetic analogs (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTentative molecular mechanism for germination stimulation of Striga and Orobanche seeds by strigol and its synthetic analogsEddy M. Mangnus and Binne. ZwanenburgCite this: J. Agric. Food Chem. 1992, 40, 6, 1066–1070Publication Date (Print):June 1, 1992Publication History Published online1 May 2002Published inissue 1 June 1992https://doi.org/10.1021/jf00018a032Request reuse permissionsArticle Views728Altmetric-Citations112LEARN 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 InReddit PDF (661 KB) Get e-Alertsclose Get e-Alerts
A perspective on paper-based microfluidics: Current status and future trends (2012)

"Paper-based microfluidics" or "lab on paper," as a burgeoning research field with its beginning in 2007, provides a novel system for fluid handling and fluid analysis for a variety of applications including health diagnostics, environmental monitoring as well as food quality testing. The reasons why paper becomes an attractive substrate for making microfluidic systems include: (1) it is a ubiquitous and extremely cheap cellulosic material; (2) it is compatible with many chemical/biochemical/medical applications; and (3) it transports liquids using capillary forces without the assistance of external forces. By building microfluidic channels on paper, liquid flow is confined within the channels, and therefore, liquid flow can be guided in a controlled manner. A variety of 2D and even 3D microfluidic channels have been created on paper, which are able to transport liquids in the predesigned pathways on paper. At the current stage of its development, paper-based microfluidic system is claimed to be low-cost, easy-to-use, disposable, and equipment-free, and therefore, is a rising technology particularly relevant to improving the healthcare and disease screening in the developing world, especially for those areas with no- or low-infrastructure and limited trained medical and health professionals. The research in paper-based microfluidics is experiencing a period of explosion; most published works have focused on: (1) inventing low-cost and simple fabrication techniques for paper-based microfluidic devices; and (2) exploring new applications of paper-based microfluidics by incorporating efficient detection methods. This paper aims to review both the fabrication techniques and applications of paper-based microfluidics reported to date. This paper also attempts to convey to the readers, from the authors' point of view the current limitations of paper-based microfluidics which require further research, and a few perspective directions this new analytical system may take in its development.
Binding of Virus-Like Particles of Norwalk Virus to Romaine Lettuce Veins (2010)

Noroviruses (NoV) annually cause millions of cases of gastrointestinal disease in the United States. NoV are associated with raw shellfish outbreaks, particularly oysters, which are thought to bioaccumulate NoV particles during the filter-feeding process. NoV outbreaks, however, have also been known to occur from other common-source food-borne vehicles, such as lettuce, frozen raspberries, and salad. In this study, we evaluated romaine lettuce as a potential vehicle for NoV transmission by testing the binding and distribution of NoV to the surface of romaine. Recombinant Norwalk virus-like particles (rNVLP) applied to the surface of romaine lettuce localized as large clusters primarily on the leaf veins. An extract of romaine lettuce leaves in phosphate-buffered saline (PBS) (romaine extract [RE]) bound rNVLP in a dose-dependent manner. RE did not bind rNVLP by histo-blood group antigens (HBGA), nor was RE competitive with rNVLP binding to porcine gastric mucin. These results suggested that non-HBGA molecules in RE bind rNVLP by a binding site(s) that is different from the defined binding pocket on the virion. Extracts of cilantro, iceberg lettuce, spinach, and celery also bound rNVLP. Samples of each of the vegetables spiked with rNVLP and tested with anti-NVLP antibody revealed by confocal microscopy the presence of rNVLP not only on the veins of cilantro but also throughout the surface of iceberg lettuce.
Accurate indoor localization with zero start-up cost (2014)

Recent years have seen the advent of new RF-localization systems that demonstrate tens of centimeters of accuracy. However, such systems require either deployment of new infrastructure, or extensive fingerprinting of the environment through training or crowdsourcing, impeding their wide-scale adoption.
The Optical Resonances in Carbon Nanotubes Arise from Excitons (2005)

Optical transitions in carbon nanotubes are of central importance for nanotube characterization. They also provide insight into the nature of excited states in these one-dimensional systems. Recent work suggests that light absorption produces strongly correlated electron-hole states in the form of excitons. However, it has been difficult to rule out a simpler model in which resonances arise from the van Hove singularities associated with the one-dimensional band [corrected] structure of the nanotubes. Here, two-photon excitation spectroscopy bolsters the exciton picture. We found binding energies of approximately 400 millielectron volts for semiconducting single-walled nanotubes with 0.8-nanometer diameters. The results demonstrate the dominant role of many-body interactions in the excited-state properties of one-dimensional systems.
Evaluation of Low Intensity Laser Effects on the Thyroid Gland of Male Mice (2005)

It was concluded that low-level laser therapy (LLLT) of the thyroid gland may affect the level of thyroidal hormones.
A Three-Terminal Carbon Nanorelay (2004)

Three-terminal nanorelay structures were fabricated with multiwall carbon nanotubes (MWNTs). The nanotube relays were deflected by applying a gate voltage until contact (mechanical and/or electrical) was made with a drain electrode, thus closing the circuit. It was possible to achieve multiple switching cycles, showing that carbon nanotubes are suitable and practical systems for developing nanoelectromechanical devices of this kind.
Prediction of ‘High-Risk’ Cervical Papillomavirus Infection by Biopsy Morphology (1989)

Certain human papillomavirus (HPV) types (such as type 16) have been linked to high-grade precancers and invasive carcinomas of the cervix. However, the accuracy with which morphologic characteristics will predict the presence and type of HPV infection is controversial. Three pathologists independently classified 102 consecutive cervical biopsies with the use of specific criteria and correlated their findings with the presence of HPV 11, 16, and 18 RNA sequences by in situ hybridization. Based on the presence and distribution of nuclear atypia, abnormal mitotic figures, and koilocytosis, biopsies were classified into borderline condyloma, condyloma, borderline cervical intraepithelial neoplasia (CIN) with koilocytotic atypia (CINK), and CIN. Two or more observers agreed on the diagnosis in 96% of cases. HPV 16-related sequences alone were detected in 0% of borderline condylomata, 17% of flat condylomata, 43% of borderline CINK, 67% of CINK, and 77% of CIN lesions. Other HPVs, including those producing signals with more than one probe, were present in 0, 50, 14, 9, and 0% of these lesions, respectively. The authors data suggest that consistent identification of HPV-related cervical disease requires the presence of specific cytologic changes. In the authors' series, when HPV-related disease is present, CIN is the most common lesion and most (71%) contain HPV 16-related nucleic acids. Thus, a high proportion (88%) of histologic abnormalities associated with HPV-16 could be distinguished as CIN by morphologic characteristics alone, and this distinction could be made by most observers.
Recent Advances in Dendritic Cell Vaccines for Cancer Treatment (2001)

Dendritic cells (DC) are special subsets of antigen presenting cells characterized by their unique abilities to efficiently take up, process, and present various forms of antigens to immunologically naive T cells. Recent advances in the understanding of molecular mechanisms regulating the functions of DC have allowed the investigators to "design" innovative DC-based vaccine formats for the treatment of cancer patients. In this article, we will review the most advanced DC vaccine strategies, focusing on three major areas: a) new ex vivo protocols for DC loading with tumor-associated antigens (TAA), b) genetic approaches to load skin-resident Langerhans cells (LC) with TAA, and c) chemokine-mediated LC entrapment and in situ loading of LC with TAA at the entrapment sites. We believe that these new classes of DC vaccine strategies will soon become applicable to the treatment of patients with malignant tumors.
Structure from Motion with Known Camera Positions (2006)

The wide availability of GPS sensors is changing the landscape in the applications of structure from motion techniques for localization. In this paper, we study the problem of estimating camera orientations from multiple views, given the positions of the viewpoints in a world coordinate system and a set of point correspondences across the views. Given three or more views, the above problem has a finite number of solutions for three or more point correspondences. Given six or more views, the problem has a finite number of solutions for just two or more points. In the three-view case, we show the necessary and sufficient conditions for the three essential matrices to be consistent with a set of known baselines. We also introduce a method to recover the absolute orientations of three views in world coordinates from their essential matrices. To refine these estimates we perform a least-squares minimization on the group cross product SO(3) × SO(3) × SO(3). We report experiments on synthetic data and on data from the ICCV2005 Computer Vision Contest.
Identification of Non-Heme Diiron Proteins That Catalyze Triple Bond and Epoxy Group Formation (1998)

Acetylenic bonds are present in more than 600 naturally occurring compounds. Plant enzymes that catalyze the formation of the Delta12 acetylenic bond in 9-octadecen-12-ynoic acid and the Delta12 epoxy group in 12,13-epoxy-9-octadecenoic acid were characterized, and two genes, similar in sequence, were cloned. When these complementary DNAs were expressed in Arabidopsis thaliana, the content of acetylenic or epoxidated fatty acids in the seeds increased from 0 to 25 or 15 percent, respectively. Both enzymes have characteristics similar to the membrane proteins containing non-heme iron that have histidine-rich motifs.
Chemical deposition methods to the rescue (2018)

Imagine trying to paint the sharp edge rather than the flat face of every blade of grass in a little garden patch—without leaving a dab of paint anywhere else. That’s roughly the gargantuan challenge facing microelectronics manufacturers today. For decades, manufacturers have steadily shrunk electronic circuits, thereby creating mobile phones and other devices that are ever faster and more powerful. But the time-honored technique they’ve been using to accomplish these feats—top-down lithography—depends on masks and photoresists for patterning and numerous deposition and etching steps to transform bulk silicon wafers into ever-smaller electronic structures. And that method is now running up against the limits of what it can do. Transistors in today’s microelectronics already sport structures such as electrodes with 10-nm dimensions, and 7-nm circuit components are now making their way into high-volume manufacturing, according to Dennis M. Hausmann, a senior staff scientist at Lam Research, which makes semiconductor processing equipment.
Improved chiral derivatizing agents for the chromatographic resolution of racemic primary amines (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTImproved chiral derivatizing agents for the chromatographic resolution of racemic primary aminesWilliam H. Pirkle and Kirk A. SimmonsCite this: J. Org. Chem. 1983, 48, 15, 2520–2527Publication Date (Print):July 1, 1983Publication History Published online1 May 2002Published inissue 1 July 1983https://pubs.acs.org/doi/10.1021/jo00163a019https://doi.org/10.1021/jo00163a019research-articleACS PublicationsRequest reuse permissionsArticle Views2586Altmetric-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
Kinase-Deficient Pak1 Mutants Inhibit Ras Transformation of Rat-1 Fibroblasts (1997)

Among the mechanisms by which the Ras oncogene induces cellular transformation, Ras activates the mitogen-activated protein kinase (MAPK or ERK) cascade and a related cascade leading to activation of Jun kinase (JNK or SAPK). JNK is additionally regulated by the Ras-related G proteins Rac and Cdc42. Ras also regulates the actin cytoskeleton through an incompletely elucidated Rac-dependent mechanism. A candidate for the physiological effector for both JNK and actin regulation by Rac and Cdc42 is the serine/threonine kinase Pak (p65pak). We show here that expression of a catalytically inactive mutant Pak, Pak1(R299), inhibits Ras transformation of Rat-1 fibroblasts but not of NIH 3T3 cells. Typically, 90 to 95% fewer transformed colonies were observed in cotransfection assays with Rat-1 cells. Pak1(R299) did not inhibit transformation by the Raf oncogene, indicating that inhibition was specific for Ras. Furthermore, Rat-1 cell lines expressing Pak1(R299) were highly resistant to Ras transformation, while cells expressing wild-type Pak1 were efficiently transformed by Ras. Pak1(L83,L86,R299), a mutant that fails to bind either Rac or Cdc42, also inhibited Ras transformation. Rac and Ras activation of JNK was inhibited by Pak1(R299) but not by Pak1(L83,L86,R299). Ras activation of ERK was inhibited by both Pak1(R299) and Pak1(L83,L86,R299), while neither mutant inhibited Raf activation of ERK. These results suggest that Pak1 interacts with components essential for Ras transformation and that inhibition can be uncoupled from JNK but not ERK signaling.
Potentiation of Temozolomide Cytotoxicity by Inhibition of DNA Polymerase β Is Accentuated by BRCA2 Mutation (2009)

Base excision repair (BER) plays a critical role in the repair of bases damaged by oxidative metabolism or alkylating agents, such as those commonly used in cancer therapy. Incomplete BER generates intermediates that require activation of homology-dependent DNA repair to resolve. We investigated the effects of lithocholic acid (LCA), an inhibitor of the key BER enzyme DNA polymerase beta (pol beta), in cells deficient in expression of the homology-dependent repair factor BRCA2. In vitro studies show that LCA suppresses the DNA polymerase and 5'-deoxyribose phosphate lyase activities of DNA pol beta by preventing the formation of a stable pol beta-DNA complex, reducing BER effectiveness. Cytotoxicity assays based on colony formation revealed that LCA exhibits synergism with the alkylating agent temozolomide, which engages BER through DNA methylation, and that the degree of synergism is increased in cells lacking functional BRCA2. BRCA2-deficient cells also showed heightened susceptibility to both LCA and temozolomide individually. The potentiation of temozolomide cytotoxicity by LCA owes to the conversion of single-stranded DNA breaks generated through incomplete BER of methylated nucleotides into double-stranded breaks during DNA replication, as indicated by gammaH2AX immunofluorescence. Death seems to be induced in cotreated cells through an accumulation of persistent double-stranded DNA breaks. Mutations of the BRCA2 gene have been extensively characterized and are present in various cancers, implying that inhibition of BER may offer a means to augment tumor selectivity in the use of conventional cancer therapies.
Coamplification and coexpression of human tissue-type plasminogen activator and murine dihydrofolate reductase sequences in Chinese hamster ovary cells. (1985)

Expression of human tissue-type plasminogen activator (t-PA) at high levels has been achieved in Chinese hamster ovary (CHO) cells by cotransfection and subsequent coamplification of the transfected sequences. Expression vectors containing the t-PA cDNA gene and dihydrofolate reductase (DHFR) cDNA gene were cotransfected into CHO DHFR-deficient cells. Transformants expressing DHFR were selected by growth in media lacking nucleosides and contained low numbers of t-PA genes and DHFR genes. Stepwise selection of the DHFR+ transformants in increasing concentrations of methotrexate generated cells which had amplified both DHFR genes and t-PA genes over 100-fold. These cell lines expressed elevated levels of enzymatically active t-PA. To optimize both t-PA sequence amplification and t-PA expression, various modifications of the original procedure were used. These included alterations to the DHFR expression vector, optimization of the molar ratio of t-PA to DHFR sequences in the cotransfection, and modification of the methotrexate resistance selection procedure. The structure of the amplified DNA, its chromosomal location, and its stability during growth in the absence of methotrexate are reported.
Neuroprotection in glaucoma. (2003)

Currently, glaucoma is recognised as an optic neuropathy. Selective death of retinal ganglion cells (RGC) is the hallmark of glaucoma, which is also associated with structural changes in the optic nerve head. The process of RGC death is thought to be biphasic: a primary injury responsible for initiation of damage that is followed by a slower secondary degeneration related to noxious environment surrounding the degenerating cells. For example, retinal ishaemia may establish a cascade of changes that ultimately result in cell death: hypoxia leads to excitotoxic levels of glutamate, which cause a rise in intra-cellular calcium, which in turn, leads to neuronal death due to apoptosis or necrosis. Neuroprotection is a process that attempts to preserve the cells that were spared during the initial insult, but are still vulnerable to damage. Although not yet available, a neuroprotective agent would be of great use in arresting the progression of glaucoma. There is evidence that neuroprotection can be achieved both pharmacologically and immunologically. Pharmacological intervention aims at neutralising some of the effects of the nerve-derived toxic factors, thereby increasing the ability of the spared neurons to cope with stressful conditions. On the other hand, immunological interventions boost the body's own repair mechanisms for counteracting the toxic effects of various chemicals generated during the cascade. This review, based on a literature search using MEDLINE, focuses on diverse cellular events associated with glaucomatous neurodegeneration, and discusses some pharmacological agents believed to have a neuroprotective role in glaucoma.
Exact synthesis of multiqubit Clifford+Tcircuits (2013)

We prove that a unitary matrix has an exact representation over the Clifford+$T$ gate set with local ancillas if and only if its entries are in the ring $\mathbb{Z}[\frac{1}{\sqrt{2}},i]$. Moreover, we show that one ancilla always suffices. These facts were conjectured by Kliuchnikov, Maslov, and Mosca. We obtain an algorithm for synthesizing a exact Clifford+$T$ circuit from any such $n$-qubit operator. We also characterize the Clifford+$T$ operators that can be represented without ancillas.