gebhart/patrepeval huggingface dataset:
Oblivious multi-party machine learning on trusted processors (2016)

Privacy-preserving multi-party machine learning allows multiple organizations to perform collaborative data analytics while guaranteeing the privacy of their individual datasets. Using trusted SGX-processors for this task yields high performance, but requires a careful selection, adaptation, and implementation of machine-learning algorithms to provably prevent the exploitation of any side channels induced by data-dependent access patterns.

We propose data-oblivious machine learning algorithms for support vector machines, matrix factorization, neural networks, decision trees, and k-means clustering. We show that our efficient implementation based on Intel Skylake processors scales up to large, realistic datasets, with overheads several orders of magnitude lower than with previous approaches based on advanced cryptographic multi-party computation schemes.
Snapshot hyperspectral imaging in ophthalmology (2007)

Retinal imaging spectroscopy can provide functional maps using chromophore spectra. For example, oxygen saturation maps show ischemic areas from diabetes and venous occlusions. Obtaining retinal spatial-spectral data has been difficult due to saccades and long data acquisition times (>5 s). We present a snapshot imaging spectrometer with far-reaching applicability that acquires a complete spatial-spectral image cube in approximately 3 ms from 450 to 700 nm with 50 bands, eliminating motion artifacts and pixel misregistration. Current retinal spectral imaging approaches are incapable of true snapshot operation over a wide spectral range with a large number of spectral bands. Coupled to a fundus camera, the instrument returns true color retinal images for comparison to standard fundus images and for image validation while the patient is still dilated. Oxygen saturation maps were obtained with a three-wavelength algorithm: for healthy subjects arteries were approximately 95% and veins 30 to 35% less. The instrument is now undergoing clinical trials.
Human α- l -iduronidase uses its own N -glycan as a substrate-binding and catalytic module (2013)

N-glycosylation is a major posttranslational modification that endows proteins with various functions. It is established that N-glycans are essential for the correct folding and stability of some enzymes; however, the actual effects of N-glycans on their activities are poorly understood. Here, we show that human α-l-iduronidase (hIDUA), of which a dysfunction causes accumulation of dermatan/heparan sulfate leading to mucopolysaccharidosis type I, uses its own N-glycan as a substrate binding and catalytic module. Structural analysis revealed that the mannose residue of the N-glycan attached to N372 constituted a part of the substrate-binding pocket and interacted directly with a substrate. A deglycosylation study showed that enzyme activity was highly correlated with the N-glycan attached to N372. The kinetics of native and deglycosylated hIDUA suggested that the N-glycan is also involved in catalytic processes. Our study demonstrates a previously unrecognized function of N-glycans.
Proliferation of glioma cells in serum-free defined medium. (1981)

The requirement for a serum supplement to basal culture medium to support the growth and viability of cells in vitro has been a major hindrance to reducing and thereby controlling experimental variables. The complexity and undefined nature of serum as well as the variability of serum lots make it difficult to reproduce data and to interpret results of experiments. This paper presents preliminary results obtained with C6 glioma cell cultures in which serum was replaced by growth factors and a hormone. A brief review of the use of serum-free defined medium for the culture of tumor cells and the potential uses of defined media that are cell-type specific are also presented.
A High Glycolytic Flux Supports the Proliferative Potential of Murine Embryonic Stem Cells (2007)

Embryonic stem (ES) cells are immortal and present the ability to self-renew while retaining their ability to differentiate. In contrast, most primary cells possess a limited proliferative potential, and when this is exhausted, undergo an irreversible growth arrest termed senescence. In primary cells, senescence can be also triggered by a variety of stress to which ES cells are highly refractory. Here the authors report that the proliferative capacity of murine ES cells closely correlates with high activity of different glycolytic enzymes, elevated glycolytic flux, and low mitochondrial oxygen consumption. The direct relation between glycolytic flux and the ability of ES cells to proliferate is further remarked in experiments where glycolysis or ES cell self-renewal was specifically inhibited. It was previously reported that the upregulation of glycolysis in primary cells results in life span extension. The authors hypothesize that the naturally high glycolytic flux observed in murine ES cells can be responsible for their unlimited proliferative potential.
Synthesis and characterization of hybrid nanostructures (2011)

There has been significant interest in the development of multicomponent nanocrystals formed by the assembly of two or more different materials with control over size, shape, composition, and spatial orientation. In particular, the selective growth of metals on the tips of semiconductor nanorods and wires can act to couple the electrical and optical properties of semiconductors with the unique properties of various metals. Here, we outline our progress on the solution-phase synthesis of metal-semiconductor heterojunctions formed by the growth of Au, Pt, or other binary catalytic metal systems on metal (Cd, Pb, Cu)-chalcogenide nanostructures. We show the ability to grow the metal on various shapes (spherical, rods, hexagonal prisms, and wires). Furthermore, manipulating the composition of the metal nanoparticles is also shown, where PtNi and PtCo alloys are our main focus. The magnetic and electrical properties of the developed hybrid nanostructures are shown.
Discovery of blood transcriptomic markers for depression in animal models and pilot validation in subjects with early-onset major depression (2012)

Early-onset major depressive disorder (MDD) is a serious and prevalent psychiatric illness in adolescents and young adults. Current treatments are not optimally effective. Biological markers of early-onset MDD could increase diagnostic specificity, but no such biomarker exists. Our innovative approach to biomarker discovery for early-onset MDD combined results from genome-wide transcriptomic profiles in the blood of two animal models of depression, representing the genetic and the environmental, stress-related, etiology of MDD. We carried out unbiased analyses of this combined set of 26 candidate blood transcriptomic markers in a sample of 15-19-year-old subjects with MDD (N=14) and subjects with no disorder (ND, N=14). A panel of 11 blood markers differentiated participants with early-onset MDD from the ND group. Additionally, a separate but partially overlapping panel of 18 transcripts distinguished subjects with MDD with or without comorbid anxiety. Four transcripts, discovered from the chronic stress animal model, correlated with maltreatment scores in youths. These pilot data suggest that our approach can lead to clinically valid diagnostic panels of blood transcripts for early-onset MDD, which could reduce diagnostic heterogeneity in this population and has the potential to advance individualized treatment strategies.
Characterization of biofilm matrix, degradation by DNase treatment and evidence of capsule downregulation in Streptococcus pneumoniae clinical isolates (2008)

All pneumococcal strains developed biofilms that exhibited extracellular dsDNA in the biofilm matrix, however strains with a high BFI correlated with greater carbohydrate-associated structural complexity and antibiotic resistance. Furthermore, all strains of S. pneumoniae showed downregulation of the cpsA gene during biofilm growth compared to planktonic culture, regardless of BFI ranking, suggesting downregulation of capsule expression occurs generally during adherent growth.
Monoclonal antibodies reactive with mucin glycoproteins found in sera from breast cancer patients. (1988)

Monoclonal antibodies to mucin glycoproteins have previously been shown to detect elevated antigen levels in sera from breast cancer patients. To determine whether different mucin epitopes represent better targets for serum assays, we have produced and characterized 14 new monoclonal antibodies directed against the mucin glycoproteins detected by antibody W1. Many of the new antibodies differed from each other in their ability to bind to mucins from various sources. Cross-competition analyses of antibody binding indicated that while epitopes for some antibodies were distinct, most epitopes showed complex structural or steric relationships with those for other antibodies. Antibody M26 bound glycolipids from meconium and kidney, indicating that it recognized a carbohydrate epitope. Antibodies M15, M22, M23, and M27 bound to structurally or sterically related epitopes on deglycosylated milk-derived mucin, suggesting that they recognized core protein epitopes. Enzyme immunoassays were developed with the new antibodies and evaluated for their ability to discriminate between sera from breast cancer patients and from controls with benign breast disease. The best single test in terms of sensitivity and specificity used a combination of two antibodies, antibody M29 for antigen capture and antibody M38 for antigen detection. A second test using antibody M26 for antigen capture and antibody M38 for antigen detection detected elevated antigen levels in sera from some patients which were in the control range of the M29/M38 test. By combining results from these tests, significantly more cancer patients were detected than with the W1 and CA 15.3 tests.
Assessing the efficacy of medical treatments for alcohol use disorders (2004)

Alcohol use disorders (AUDs) are common health problems that have a significant impact on society as a whole. There is a need for more effective treatments. In the last two decades, evidence for the efficacy of pharmacological approaches to treatment has increased. Although it has long been clear that medications are needed for the treatment of the alcohol withdrawal syndrome, the important role of medications in the longer-term treatment of AUDs has only recently been appreciated. In particular, naltrexone, acamprosate and topiramate appear to be efficacious treatments, especially when combined with psychosocial interventions that emphasise compliance with medication and encourage treatment retention. The goal of this review is to bring together the existing literature supporting the usefulness of pharmacological treatments for the alcohol withdrawal syndrome, for longer-term treatment of AUDs, and for comorbid AUDs and other psychiatric disorders. In addition, opportunities for future research will be identified.
Use of tumor genomic profiling to reveal mechanisms of resistance to the BTK inhibitor ibrutinib in chronic lymphocytic leukemia (CLL). (2013)

7014 Background: Ibrutinib interacts covalently with cysteine 481 of Bruton tyrosine kinase (BTK), resulting in targeted inhibition of B cell receptor signaling. Early trials of ibrutinib mono- or combination therapy enrolled 246 CLL patients receiving a median of 14 months of ibrutinib. 20 patients (8%) experienced progressive disease (PD), including 8 patients with Richter's transformation. Here we examine changes to the CLL genome in 3 patients that acquired resistance to ibrutinib. Methods: Ibrutinib resistance was defined as patients achieving partial response (PR) or better lasting ≥ 6 months, then developing PD without Richter’s transformation. RNAseq and whole exome sequencing (WES) followed by comparative genome analysis was performed at baseline and after PD and confirmed by Sanger sequencing. RNAseq and WES data were aligned using TopHat and BWA software. Single nucleotide variations (SNVs) were identified using SAMtools mpileup. Results: Compared to patients who relapsed from conventional chemotherapy, minimal genomic changes were acquired in ibrutinib resistant patients, reflecting relative genomic stability. SNVs were discovered in 3 patients specific to the relapse sample (Table). 2 out of 3 patients had distinct SNVs that each encode a cysteine-to-serine substitution at position 481of BTK (C481S). Homologous cysteine residues in BMX, ITK, TEC and BLK were wild-type (WT). Ibrutinib inhibited recombinant C481S 25 fold less potently than WT, and could not covalently bind C481S expressed in cells. The third patient had WT BTK, but acquired a potential gain-of-function mutation encoding a R665W substitution in PLCg2, a substrate of BTK, consistent with constitutive PLCg2 activation. Conclusions: Although rare, the acquisition of C481S BTK and R665W PLCg2 mutations in the setting of resistance confirms BTK as an important pharmacologic target of ibrutinib, and suggests mechanisms of ibrutinib resistance. [Table: see text]
Chemical composition of nonsmoking tobacco products (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChemical composition of nonsmoking tobacco productsWilliam J. Chamberlain, William S. Schlotzhauer, and Orestes T. ChortykCite this: J. Agric. Food Chem. 1988, 36, 1, 48–50Publication Date (Print):January 1, 1988Publication History Published online1 May 2002Published inissue 1 January 1988https://pubs.acs.org/doi/10.1021/jf00079a012https://doi.org/10.1021/jf00079a012research-articleACS PublicationsRequest reuse permissionsArticle Views293Altmetric-Citations16LEARN 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
A Novel and Highly Divergent Homolog of Human Eosinophil Granule Major Basic Protein (1999)

Eosinophils are important effector cells in defense against helminth infection and in allergic diseases. To identify novel eosinophil proteins, large scale sequencing of a cDNA library prepared from interleukin-5-stimulated umbilical cord precursor cells was performed, and the major genes expressed by maturing eosinophils were determined. This resulted in the identification of a cDNA with 64% identity to human prepro-major basic protein (hprepro-MBP). This cDNA was designated hprepro-MBP homolog (hprepro-MBPH). Interestingly, the calculated pI values for hMBPH and hMBP differed by >100-fold, with pI values of 8.7 and 11.4, respectively. Given this pronounced basicity difference, the homolog transcript's abundance (1.1%), and MBP's critical role in eosinophil biological activity, we further characterized the homolog. Reverse transcription-polymerase chain reaction detected transcription of hprepro-MBPH in bone marrow only, and this result was confirmed by analysis of a large cDNA data base (electronic Northern). hMBPH was isolated from human eosinophil granule lysates, and its identity was verified by amino acid sequencing and by mass spectrometry. Analyses of the biological activities showed that hMBPH had effects similar to hMBP in cell killing and neutrophil (superoxide anion production and interleukin-8 release) and basophil (histamine and leukotriene C4 release) stimulation assays, but usually with reduced potency. Overall, this novel homolog's unique physical properties indicated that the high net positive charge of hMBP is important but not essential for biological activity.
Establishment of Cell Lines with High and Low Metastatic Potential from A549 Human Lung Adenocarcinoma (2002)

This article reports the establishment of variant cell lines with high and low metastatic potential by the dilution plating technique. Two clones with high metastatic potential, 2S Lu‐4 and 11S Lu‐1 and two clones with low metastatic potential, 8S and 16S were established from A549 human lung adenocarcinoma. The high‐metastatic cell lines produced enhanced lung metastases, but the low‐ metastatic cell lines did not produce lung metastasis after injection into the tail vein of 5‐week‐old BALB/c nude mice. The primary tumors produced by the two high‐metastatic cells grew fast and showed enhanced angiogenesis. The high‐metastatic cells were small and flat‐shaped, while the low‐ metastatic cells were large and flat‐shaped. When the four variant cell lines and original A549 cells were embedded in collagen gels, the colonies of 2S Lu‐4, 11S Lu‐1 and A549 grew actively, whereas almost of all the colonies of 8S and 16S did not survive after 35 days in culture. These four cloned cell lines originated from heterogeneous populations of the parental A549 cells should be an excellent tool for studying the process of metastasis of lung cancer.
Operating Characteristics of Prostate-Specific Antigen in Men With an Initial PSA Level of 3.0 ng/mL or Lower (2005)

There is no cutpoint of PSA with simultaneous high sensitivity and high specificity for monitoring healthy men for prostate cancer, but rather a continuum of prostate cancer risk at all values of PSA.
Cell-Permeable Bicyclic Peptidyl Inhibitors against NEMO-IκB Kinase Interaction Directly from a Combinatorial Library (2018)

Macrocyclic peptides are capable of binding to flat protein surfaces such as the interfaces of protein-protein interactions with antibody-like affinity and specificity, but generally lack cell permeability in order to access intracellular targets. In this work, we designed and synthesized a large combinatorial library of cell-permeable bicyclic peptides, in which the first ring consisted of randomized peptide sequences for potential binding to a target of interest, while the second ring featured a family of different cell-penetrating motifs, for both cell penetration and target binding. The library was screened against the IκB kinase α/β (IKKα/β)-binding domain of NF-κB essential modulator (NEMO), resulting in the discovery of several cell-permeable bicyclic peptides, which inhibited the NEMO-IKKβ interaction with low μM IC<sub>50</sub> values. Further optimization of one of the hits led to a relatively potent and cell-permeable NEMO inhibitor (IC<sub>50</sub> = 1.0 μM), which selectively inhibited canonical NF-κB signaling in mammalian cells and the proliferation of cisplatin-resistant ovarian cancer cells. The inhibitor provides a useful tool for investigating the biological functions of NEMO/NF-κB and a potential lead for further development of a novel class of anti-inflammatory and anticancer drugs.
Kinetics of Hydrolytic Aging of Polyester Urethane Elastomers (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTKinetics of Hydrolytic Aging of Polyester Urethane ElastomersDaniel W. Brown, Robert E. Lowry, and Leslie E. SmithCite this: Macromolecules 1980, 13, 2, 248–252Publication Date (Print):March 1, 1980Publication History Published online1 May 2002Published inissue 1 March 1980https://pubs.acs.org/doi/10.1021/ma60074a009https://doi.org/10.1021/ma60074a009research-articleACS PublicationsRequest reuse permissionsArticle Views817Altmetric-Citations76LEARN 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
Anatomy of a color histogram (2003)

It is shown that the color histogram has an even closer relationship to scene properties than has been previously described. Color histograms have identifiable features that relate in a precise mathematical way to scene properties. Object color and illumination color are the most obvious properties that are related to color distribution, and their extraction has already been described. It is shown here that the histogram of color variation may be further exploited to relate its shape to surface roughness and imaging geometry. An understanding of these features allows an improved estimate of illumination color and object color to be made.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Syntheses of heteroaromatic carboxylic acids closely related to fusaric acid. (1983)

In order to investigate the generality of a chain-elongation reaction observed in the metabolism of fusaric acid (5-butyl-2-pyridinecarboxylic acid) and its derivatives, various heteroaromatic (diazine, 1, 3-azole, and 1, 2-azole) carboxylic acids with a normal alkyl side-chain were synthesized.
Computer Vision based Weed Identification under Field Conditions using Controlled Lighting (2001)

The methods of digital image analysis were used to develop an identification system for weeds in crops. Two vegetable crops (cabbage and carrots) and a number of naturally occurring weed species were used to develop the classification algorithms. Considering the rougher environment, special attention was given to the open field experiments. The images were obtained with a device that provided controlled lighting conditions. The analysis was carried out off line. Eight different morphological features and three colour features were calculated for each single object to build a joint feature space. On the basis of sample data sets of each class, statistics were carried out to determine the features, which are suitable for discrimination. A membership function based on a fuzzy logic approach was formed and used for the classification. The experiments showed that colour features can help to increase the classification accuracy. Moreover, colour was used successfully for the segmentation procedure of plants and soil. Depending on growth stage, weed density and method of calculation between 51 and 95% of the plants were classified correctly. Problems still exists by separating and allocating single plants in plant stands where the plants have grown together. Compared to other studies the plant identification system presented is an improvement, especially considering that the experiments were carried out under field conditions.