gebhart/patrepeval huggingface dataset:
Tracing the Migration History of Metal Catalysts in Metal-Assisted Chemically Etched Silicon (2013)

Three-dimensional (3D) visualization of complex embedded nanopore networks in silicon requires expensive machinery and tedious sample preparation procedures such as electron tomography, also known as 3D transmission electron microscopy. In this article, we report a new, fast, powerful, and low-cost three-dimensional imaging technique with sub-5 nm resolution. This new imaging method is applied to metal-assisted chemically etched monocrystalline Si to demonstrate its capabilities. The AFEI (atomic layer deposition-fill-etch-imaging) technique consists of three simple process steps that are available in most material research settings. First the porous substrate is conformally coated with an atomic layer deposition (ALD) metal oxide layer. ALD is able to penetrate deep into complex, high aspect ratio pores, as it is a sequential gas-phase deposition process. Next, the cross-section of the ALD-filled porous Si substrate is etched with high-density fluorine-based plasma processing, which yields very high selectivity toward Si (e.g., >400:1 for Si:ZnO). This step removes the bulk Si and exposes the metal oxide structures grown inside the pores. In the last step, the sample cross-section is examined using a standard scanning electron microscope at various angles, which allows precise imaging of hidden features and reconstruction of a 3D model of the embedded pore network.
Hand-held arthroscopic optical coherence tomography for in vivo high-resolution imaging of articular cartilage (2003)

We describe a novel hand-held polarization optical coherence tomographic (OCT) probe that can be inserted into mammalian joints to permit real-time cross-sectional imaging of articular cartilage. The transverse and axial resolutions of the arthroscopic OCT device are roughly 17 and 10 microm, respectively. Two-dimensional cross-sectional images of cartilage tissue with 500 x 1000 pixels covering an area 6 mm in length and 2.8 mm in depth can be acquired at nearly five frames/s and with over 100 dB of dynamic range. Design of an OCT as a hand-held device capable of providing such an optical biopsy of articular cartilage allows eventual in vivo detection of microstructural changes in articular cartilage that are not apparent using conventional arthroscopic cameras. The OCT probe can be easily incorporated in a conventional arthroscope for cartilage site guidance. The optical arrangement in the OCT scope minimizes specular back-reflection of the probe end face and absorption of body fluid in the path and ensures in-focus OCT imaging when it is in contact with the cartilage specimen to be examined. Successful application of in vivo arthroscopy to porcine articular cartilage demonstrates sufficient resolution and practicality for use in human joints.
A study of the double mutation of dnaJ and cbpA, whose gene products function as molecular chaperones in Escherichia coli (1995)

The CbpA protein is an analog of the DnaJ molecular chaperone of Escherichia coli. To gain insight into the function of CbpA, we examined the nature of a cbpA null mutation with special reference to those of dnaK and dnaJ null mutations. In particular, the cbpA dnaJ double-null mutant was found to exhibit severe defects in cell growth, namely, a very narrow temperature range for growth, a defect in cell division, and susceptibility to killing by carbon starvation. These phenotypes are very similar to those reported for dnaK null mutants but not to those of dnaJ null mutants. Our results are best interpreted by assuming that CbpA is capable of compensating for DnaJ for cell growth and thus that the function(s) of CbpA is closely related to that of DnaJ.
Protein Purification (2006)

Protein purification is the process of separating a given protein from all the other proteins, nucleic acids, polysaccharides, lipids, metabolites, and other small molecules in a cell extract. This purification is done ideally with reasonable speed, yield, final purity, and economy, while retaining the biological activity and chemical and structural integrity. A purification scheme involves a series of fractionation steps that exploit the many differences in the properties of the protein of interest and the other components in the mixture. Design of such fractionation steps must take into account the molecular forces that determine molecular interactions between proteins and various materials used in purification. Care must be taken to prevent inactivation, degradation or absorptive losses during the purification. In recent years, most researchers purify recombinant proteins whose genes have been cloned into an expression vector and expressed in a suitable expression host organism, often the bacterium Escherichia coli . The use of purification tags to aid in affinity purification is common. Sometimes, the overproduced protein is found as an insoluble inclusion body that must be isolated, solubilized by denaturants, and then refolded.
On the pharmacokinetics of tobacco-specific N-nitrosamines in Fischer rats (1985)

Methods were developed to determine the biological half-lives and rates of distribution and elimination of N'-nitrosonornicotine (NNN), N'-nitrosoanatabine (NAT), 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) and 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol (NNAL) in the F344 rat. The formation and persistence of an in vivo equilibrium between NNK and NNAL were also studied. The method consists of extraction and elution of the nitrosamines through a Clin-Elut column with ethyl acetate, followed by concentration and analysis by a gas chromatography-thermal energy analyzer. The biological half-lives for NNN and NAT were 184 and 540 min, those for NNK and NNAL ranged from 25 to 37 and 184 to 298 min, respectively. A relatively short biological half-life for the TSNA suggests a correlation with carcinogenic potency.
THE CORNEA-SCIENTIFIC FOUNDATIONS AND CLINICAL PRACTICE (1983)

REVIEWER'S ADDRESS: William M. Lyle School of Optometry University of Waterloo Waterloo, Ontario Canada N2L 3G1
Ação Isolada ou Combinada de Ácidos Orgânicos e Promotor de Crescimento em Rações de Frangos de Corte (2000)

O experimento teve como objetivo verificar a ação da apramicina (10 ppm) e dos ácidos fórmico + propiônico (0,0; 0,1 e 0,2%) no desempenho de frangos de corte sexados. A mistura dos ácidos orgânicos foi de 1:1. O delineamento foi inteiramente casualizado, em esquema fatorial 2 x 3 x 2 (apramicina x ácidos orgânicos x sexos), com 4 repetições de 45 aves por parcela, totalizando 2.160 pintos Cobb de 1 dia. As aves receberam ração à vontade. Na fase inicial, a adição da apramicina (10 ppm) e 0,1% dos ácidos orgânicos, isoladamente, melhorou o ganho de peso das aves. A adição conjunta dos produtos não promoveu ganho acumulado. Na presença da apramicina, a adição dos ácidos orgânicos piorou a conversão alimentar. Nas fases final e total, os dados de desempenho não apresentaram diferenças significativas. O rendimento de carcaça foi prejudicado com a adição conjunta da apramicina e 0,1% dos ácidos orgânicos.
Evaluation of polymerase chain reaction for diagnosis of pneumococcal pneumonia (1993)

To test the ability of the polymerase chain reaction (PCR) to detect Streptococcus pneumoniae in blood, we generated two sets of nested primers. The first defined 559-bp and 649-bp regions of the pneumolysin gene, and the second defined 445-bp and 553-bp regions of the autolysin gene. These nucleotide segments were detected in DNAs from isolates of all 20 pneumococcal serotypes tested, but they were not detected when used to test DNAs from 41 isolates of nonpneumococcal bacteria and fungi. The sensitivity was evaluated by using purified pneumococcal DNA. We were able to detect 10 fg of S. pneumoniae DNA, or 4.3 genome equivalents. Blood samples were obtained from 16 patients with culture-proven pneumococcal bacteremia and were subjected to PCR analysis. Of eight buffy coat fractions tested, six showed reactivity in the PCR with the pneumolysin primers, and five of the eight produced the expected products when tested with the autolysin primers (sensitivities, 75 and 63%, respectively). Of the eight whole-blood specimens tested, only three produced the expected products with either set of primers. Additionally, we tested 14 samples from patients with bacteremia that were culture positive for nonpneumococcal bacterial species, and 13 were negative (specificity, 93%). This combination of sensitivity and specificity may make detection of S. pneumoniae in blood by PCR in comparison with that by blood culture a very promising alternative for a means of definitive diagnosis.
Fame and future of faecal transplantations – developing next‐generation therapies with synthetic microbiomes (2013)

While practised for over thousand years, there is presently a renaissance in the interest of using of faecal transplantations to modify the intestinal microbiota of patients. This clinical practice consists of delivering large amounts of bowel microbes in various forms into the intestinal tract of the recipient that usually has been cleared previously. The major reason for the popularity of faecal transplantations is their effectiveness in treating a variety of diseases. Hence, there is a need to develop this procedure to the next level. While there are various developments to select, standardize and store the donor microbiota, it is more challenging to understand the intestinal microbial communities and develop ways to deliver these via robust biotechnological processes. The various approaches that have been followed to do so are discussed in this contribution that is also addressing the concept of the minimal microbiome as well as the production of the synthetic communities that can be instrumental in new therapeutic avenues to modify the intestinal microbiota.
Electrophoretic transfer of proteins from polyacrylamide gels to nitrocellulose sheets: procedure and some applications. (1979)

A method has been devised for the electrophoretic transfer of proteins from polyacrylamide gels to nitrocellulose sheets. The method results in quantitative transfer of ribosomal proteins from gels containing urea. For sodium dodecyl sulfate gels, the original band pattern was obtained with no loss of resolution, but the transfer was not quantitative. The method allows detection of proteins by autoradiography and is simpler than conventional procedures. The immobilized proteins were detectable by immunological procedures. All additional binding capacity on the nitrocellulose was blocked with excess protein; then a specific antibody was bound and, finally, a second antibody directed against the first antibody. The second antibody was either radioactively labeled or conjugated to fluorescein or to peroxidase. The specific protein was then detected by either autoradiography, under UV light, or by the peroxidase reaction product, respectively. In the latter case, as little as 100 pg of protein was clearly detectable. It is anticipated that the procedure will be applicable to analysis of a wide variety of proteins with specific reactions or ligands.
MLCapsule: Guarded Offline Deployment of Machine Learning as a Service (2021)

Machine Learning as a Service (MLaaS) is a popular and convenient way to access a trained machine learning (ML) model trough an API. However, if the user’s input is sensitive, sending it to the server is not an option. Equally, the service provider does not want to share the model by sending it to the client for protecting its intellectual property and pay-per-query business model. As a solution, we propose MLCapsule, a guarded offline deployment of MLaaS. MLCapsule executes the machine learning model locally on the user’s client and therefore the data never leaves the client. Meanwhile, we show that MLCapsule is able to offer the service provider the same level of control and security of its model as the commonly used server-side execution. Beyond protecting against direct model access, we demonstrate that MLCapsule allows for implementing defenses against advanced attacks on machine learning models such as model stealing, reverse engineering and membership inference.
Crystal and molecular structure of a 2:1 complex of 1-methylthymine-mercury(II) (1974)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCrystal and molecular structure of a 2:1 complex of 1-methylthymine-mercury(II)Linda D. Kosturko, Cynthia Folzer, and Robert F. StewartCite this: Biochemistry 1974, 13, 19, 3949–3952Publication Date (Print):September 1, 1974Publication History Published online1 May 2002Published inissue 1 September 1974https://pubs.acs.org/doi/10.1021/bi00716a020https://doi.org/10.1021/bi00716a020research-articleACS PublicationsRequest reuse permissionsArticle Views476Altmetric-Citations118LEARN 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
Rex-dependent nucleolar accumulation of HTLV-I mRNAs. (1991)

The regulator of virion protein expression (Rex) of the human T-cell leukemia virus type I (HTLV-I) modulates the pattern and level of spliced and unspliced retroviral mRNA species in the cytoplasm. The elucidation of the molecular basis for this regulation is likely to throw light on new regulatory mechanisms of the host cell. We have investigated the possibility that Rex acts to direct unspliced viral RNA to the nucleolus. To test this possibility, we used in situ hybridization to detect HTLV-I envelope protein (env) transcripts formed in the nucleolus in the presence and absence of the Rex protein. The HTLV-I env sequences are normally removed by splicing from the HTLV-I RNA in the absence of Rex. The experiments presented here show that the accumulation of HTLV-I env sequences in the nucleolus is significantly increased in the presence of Rex. The results raise the possibility that Rex directs unspliced viral mRNA to the nucleolus whence it is exported to the cytoplasm for translation. The association between the nucleolus and retroviral mRNA was lost in purified nucleoli after cellular fractionation.
Analysis of the Bacteriolytic Enzymes of the Autolytic Lactococcus lactis subsp. cremoris Strain AM2 by Renaturing Polyacrylamide Gel Electrophoresis: Identification of a Prophage-Encoded Enzyme (1998)

Lactococcus lactis subsp. cremoris AM2 was previously shown to lyse early and extensively during cheese ripening (M.-P. Chapot-Chartier, C. Deniel, M. Rousseau, L. Vassal, and J.-C. Gripon, Int. Dairy J. 4:251-269, 1994). We analyzed the bacteriolytic activities of autolytic strain AM2 by using renaturing sodium dodecyl sulfate-polyacrylamide gel electrophoresis performed with two different substrates in the gel, Micrococcus lysodeikticus and L. lactis autoclaved cells. Several lytic activities were detected in L. lactis AM2; a major lytic activity, designated A2 (46 kDa), was found only with the L. lactis cell substrate. This activity appears to be different from major peptidoglycan hydrolase AcmA characterized previously (G. Buist, J. Kok, K. J. Leenhouts, M. Dabrowska, G. Venema, and A. J. Haandrickman, J. Bacteriol. 177:1554-1563, 1995), which has a similar molecular mass. The two enzymes differ in substrate specificity as well as in sensitivity to pH and different chemical compounds. L. lactis AM2 is lysogenic and mitomycin C inducible. Enzyme A2 was shown to be inducible by mitomycin C and to be prophage encoded. It was identified as an enzyme similar to the lysin encoded by lactococcal small isometric temperate bacteriophages. A prophage-cured derivative of L. lactis AM2 was obtained, and this isolate exhibited different autolytic properties than AM2. After prolonged incubation in the stationary phase after growth on M17 medium, the extent of lysis of an AM2 culture was 60%, whereas over the same period there was almost no lysis in a prophage-cured derivative strain culture. These results suggest that the prophage lytic system is involved in the strain AM2 lysis observed in liquid medium and that it could also be involved in the lysis observed during cheese ripening.
ChemInform Abstract: Synthesis of Arylzinc Thiolates Containing Perfluoroalkyl Chains. Model Catalyst Precursors for the Enantioselective Zinc‐Mediated 1,2‐Addition of Dialkylzincs to Aldehydes in Fluorous Biphase Systems. (1999)

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.
On the difficulty of training Recurrent Neural Networks (2012)

There are two widely known issues with prop-erly training Recurrent Neural Networks, the vanishing and the exploding gradient prob-lems detailed in Bengio et al. (1994). In this paper we attempt to improve the under-standing of the underlying issues by explor-ing these problems from an analytical, a geo-metric and a dynamical systems perspective. Our analysis is used to justify a simple yet ef-fective solution. We propose a gradient norm clipping strategy to deal with exploding gra-dients and a soft constraint for the vanishing gradients problem. We validate empirically our hypothesis and proposed solutions in the experimental section. 1.
Role of Mitogen-Activated Protein Kinase Pathways in Multifactorial Adverse Cardiac Remodeling Associated with Metabolic Syndrome (2013)

Metabolic syndrome has been widely associated with an increased risk for acute cardiovascular events. Emerging evidence supports metabolic syndrome as a condition favoring an adverse cardiac remodeling, which might evolve towards heart dysfunction and failure. This pathological remodeling has been described to result from the cardiac adaptive response to clinical mechanical conditions (such as hypertension, dyslipidemia, and hyperglycemia), soluble inflammatory molecules (such as cytokines and chemokines), as well as hormones (such as insulin), characterizing the pathophysiology of metabolic syndrome. Moreover, these cardiac processes (resulting in cardiac hypertrophy and fibrosis) are also associated with the modulation of intracellular signalling pathways within cardiomyocytes. Amongst the different intracellular kinases, mitogen-activated protein kinases (MAPKs) were shown to be involved in heart damage in metabolic syndrome. However, their role remains controversial. In this paper, we will discuss and update evidence on MAPK-mediated mechanisms underlying cardiac adverse remodeling associated with metabolic syndrome.
CD27 Expression Promotes Long-Term Survival of Functional Effector–Memory CD8+Cytotoxic T Lymphocytes in HIV-infected Patients (2004)

Human immunodeficiency virus (HIV)-specific CD8(+) T cells persist in high frequencies in HIV-infected patients despite impaired CD4(+) T helper response to the virus, but, unlike other differentiated effector cytotoxic T lymphocytes, most continue to express the tumor necrosis factor receptor family member CD27. Because the ligand for CD27 (CD70) is also overexpressed in HIV-infected hosts, we examined the nature of expression and potential functional consequences of CD27 expression on HIV-specific CD8(+) T cells. Analysis of CD27(+) and CD27(-) T cells derived from the same HIV-specific clone revealed that retention of CD27 did not interfere with acquisition of effector functions, and that after T cell receptor stimulation, CD27(+) cells that concurrently were triggered via CD27 exhibited more resistance to apoptosis, interleukin 2 production, and proliferation than CD27(-) T cells. After transfer back into an HIV-infected patient, autologous HIV-specific CD27(-) T cells rapidly disappeared, but CD27(+) T cells derived from the same clone persisted at high frequency. Our findings suggest that the CD27-CD70 interaction in HIV infection may provide CD27(+) CD8(+) T cells with a survival advantage and compensate for limiting or absent CD4(+) T help to maintain the CD8 response.
The Involvement of Multiple Tumor Necrosis Factor Receptor (TNFR)-associated Factors in the Signaling Mechanisms of Receptor Activator of NF-κB, a Member of the TNFR Superfamily (1998)

Receptor activator of NF-kappaB (RANK) is a recently identified member of the tumor necrosis factor receptor superfamily and is expressed on activated T cells and dendritic cells. Its cognate ligand (RANKL) plays significant roles in the activation of dendritic cell function and osteoclast differentiation. We demonstrate here the interaction of RANK with tumor necrosis factor receptor-associated factors (TRAFs) 1, 2, 3, 5, and 6 both in vitro and in cells. Mapping of the structural requirements for TRAF/RANK interaction revealed multiple TRAF binding sites clustered in two distinct domains in the RANK cytoplasmic tail. These TRAF binding domains were shown to be functionally important for the RANK-dependent induction of NF-kappaB and c-Jun NH2-terminal kinase activities. Site-directed mutagenesis demonstrated that these TRAF binding sites exhibited selective binding for different TRAF proteins. In particular, TRAF6 interacted with membrane-proximal determinants distinct from those binding TRAFs 1, 2, 3, and 5. When this membrane-proximal TRAF6 interaction domain was deleted, RANK-mediated NF-kappaB signaling was completely inhibited while c-Jun NH2-terminal kinase activation was partially inhibited. An NH2-terminal truncation mutant of TRAF6 inhibited RANKL-mediated NF-kappaB activation, but failed to affect constitutive signaling induced by receptor overexpression, revealing a selective role for TRAF6 in ligand-induced activation events.