gebhart/patrepeval huggingface dataset:
Competitive Cytokeratin 19 RT-PCR for Quantification of Breast Cancer Cells in Blood Cell Suspensions (2000)

Detection of residual tumor cells in BM and PBPC products has been correlated with worse outcome of breast cancer patients. Still, there is a considerable demand for studies investigating the influence of the actual tumor cell number on prognosis, as quantification routinely has been cumbersome and time consuming and, thus, was evaded. We developed and evaluated a competitive RT-PCR-ELISA assay for cytokeratin 19 (CK19) with standard curve quantification that allows quantification of multiple samples within a working day; mRNA isolation, RT-PCR reaction, and automated ELISA detection were carried out using commercial kits. Results were expressed as OD420nm ratios of CK19 and an internal competitor. Values were then converted into tumor cell numbers using a standard curve of MCF-7 tumor cells. The assay had high specificity because of primers and capture probes with great heterogeneity to both published pseudogenes, which was confirmed by BLAST sequence alignment. We achieved a sensitivity of detecting 1 tumor cell per 10(6) mononuclear cells (MNC). Between-batch precision (n = 8) for quantification was consistent and reasonable, with a coefficient of variation around 25%. Therefore, this assay should be suitable and sufficient for routine quantification of tumor cell numbers in BM or PBPC samples.
Characterization and Estimation of Proanthocyanidins and Other Phenolics in Coffee Pulp (Coffea arabica) by Thiolysis−High-Performance Liquid Chromatography (2004)

Fresh and 3-day-old coffee pulp of the Arabica variety were analyzed for polyphenol composition followed by characterization by two different methods. The first method consisted in subjecting coffee pulp powder to direct thiolysis. For the second method, coffee pulp was subjected to successive solvent extractions, followed by thiolysis. Quantification of phenolic compounds was then achieved by high-performance liquid chromatography (HPLC) analysis of thiolysis products. Four major classes of polyphenols were identified: flavan-3-ols (monomers and procyanidins), hydroxycinnamic acids, flavonols, and anthocyanidins. Differences in concentration of procyanidins were observed between fresh and 3-day-old coffee pulp. Constitutive units were mainly epicatechin, representing more than 90% of the proanthocyanidin units, with average degrees of polymerization in the range of 3.8-9.1. Monomer to hexamer units of flavan-3-ols from fresh coffee pulp were separated by normal-phase HPLC. Molecular size of oligomeric proanthocyanidins was obtained by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Results obtained confirm the presence of oligomers of the flavan-3-ol (-)-epicatechin.
Investigation of the effects of bio-fouling on the performance of a tethered float breakwater (1976)

This report reviews the results of an experiment testing tethered floats in breakwater for fouling. Ten percent of the floats were treated with an anti-fouling paint against the remaining floats that went untreated. The results provided the opportunity to test a theoretical model for the performance alterations caused by bio-fouling.
Rational vector design and multi-pathway modulation of HEK 293E cells yield recombinant antibody titers exceeding 1 g/l by transient transfection under serum-free conditions (2008)

Transient transfection allows for fast production of recombinant proteins. However, the current bottlenecks in transient transfection are low titers and low specific productivity compared to stable cell lines. Here, we report an improved transient transfection protocol that yields titers exceeding 1 g/l in HEK293E cells. This was achieved by combining a new highly efficient polyethyleneimine (PEI)-based transfection protocol, optimized gene expression vectors, use of cell cycle regulators p18 and p21, acidic Fibroblast Growth Factor, exposure of cells to valproic acid and consequently the maintenance of cells at high cell densities (4 million cells/ml). This protocol was reproducibly scaled-up to a working volume of 2 l, thus delivering >1 g of purified protein just 2 weeks after transfection. This is the fastest approach to gram quantities of protein ever reported from cultivated mammalian cells and could initiate, upon further scale-up, a paradigm shift in industrial production of such proteins for any application in biotechnology.
Automatic Three-Dimensional Cephalometric Landmarking via Deep Learning (2022)

Abstract The increasing use of three-dimensional (3D) imaging by orthodontists and maxillofacial surgeons to assess complex dentofacial deformities and plan orthognathic surgeries implies a critical need for 3D cephalometric analysis. Although promising methods were suggested to localize 3D landmarks automatically, concerns about robustness and generalizability restrain their clinical use. Consequently, highly trained operators remain needed to perform manual landmarking. In this retrospective diagnostic study, we aimed to train and evaluate a deep learning (DL) pipeline based on SpatialConfiguration-Net for automatic localization of 3D cephalometric landmarks on computed tomography (CT) scans. A retrospective sample of consecutive presurgical CT scans was randomly distributed between a training/validation set ( n = 160) and a test set ( n = 38). The reference data consisted in 33 landmarks, manually localized once by 1 operator ( n = 178) or twice by 3 operators ( n = 20, test set only). After inference on the test set, one CT scan showed “very low” confidence level predictions; we excluded it from the overall analysis but still assessed and discussed the corresponding results. The model performance was evaluated by comparing the predictions with the reference data; the outcome set included localization accuracy, cephalometric measurements and comparison to manual landmarking reproducibility. On the hold-out test set, the mean localization error was 1.0 ± 1.3mm, while success detection rates for 2.0, 2.5 and 3.0mm were 90.4%, 93.6% and 95.4%, respectively. Mean errors were −0.3 ± 1.3° and −0.1 ± 0.7mm for angular and linear measurements, respectively. When compared to manual reproducibility, the measurements were within the Bland-Altman 95% limits of agreement for 91.9% and 71.8% of skeletal and dentoalveolar variables, respectively. To conclude, while our DL method still requires improvement, it provided highly accurate 3D landmark localization on a challenging test set, with a reliability for skeletal evaluation on par with what clinicians obtain.
Electrochemical Etching of Gold within Nanoshaved Self-Assembled Monolayers (2013)

Wet etching of metal substrates with patterned self-assembled monolayers (SAMs) is an inexpensive and convenient method to produce metal nanostructures. For this method to be relevant to the fabrication of high precision plasmonic structures, the kinetics of nanoscale etching process, particularly in the lateral direction, must be elucidated and controlled. We herein describe an in situ atomic force microscopy (AFM) study to characterize the etching process within patterned SAMs with nanometer resolution and in real time. The in situ study was enabled by several unique elements, including single crystalline substrates to minimize the variability of facet-dependent etch rate, high-resolution nanoshaved SAM patterns, electrochemical-potential-controlled etching, and AFM kymographs to improve temporal resolution. Our approach has successfully quantified the extent of both lateral etching and vertical etching at different potentials. Our study reveals the presence of an induction period prior to the onset of significant lateral etching, which would be difficult to observe with the limited time resolution and sample-to-sample variation of ex situ studies. By increasing the vertical etch rate during this induction period with higher potentials, gold was etched up to 40 nm in the vertical direction with minimal lateral etching. High-resolution etching was also demonstrated on single crystal gold microplates, which are high quality gold thin films suitable for plasmonics studies.
Myxococcal predation on cyanobacterial populations: Nutrient effects1 (1988)

Myxococcus fulvus BGO2, a cyanobacteriolytic bacterium, reduced densities of the cyanobacteria Nostoc muscorum and Phormidium luridum in six inorganic media and in filtered water from Lake Erie when inoculated to give initial myxococcal densities of 5 × 10 6 cells ml −1 . When initial myxococcal densities were lower, the reduction in Nostoc density was delayed in a nutrient‐rich medium and did not occur in a nutrient‐poor medium. These laboratory results suggest that the absence of myxobacteria in cyanobacterial blooms and the absence of cyanobacterial population control by related lytic bacteria, found in natural blooms, may be due, in part, to insufficient inorganic nutrient fertility to support growth of lytic bacterial populations to densities necessary to cause significant cell lysis in host populations.
Real-Time 3D Model Reconstruction and Mapping for Fashion (2020)

Recent developments in the apparel market created new tasks for computer vision application. One such challenge is designing a system for trying on clothes virtually in real-time. Proposed solutions require setting up a special stationary system for body capture and mostly generate animated avatar instead of overlaying the garments in real-time. We propose a framework that utilizes state-of-the-art monocular-based 3D skeleton reconstruction and parametric body generation techniques allowing to operate under constrained resources, such as smartphones. In addition, we also consider the problem of dealing with visual artifacts as a result of 3D projection on a real-time image and design a solution to reduce them based on iterative closest point method.
Cultural and psychological factors in cyber-security (2016)

Increasing cyber-security presents an ongoing challenge to security professionals. Research continuously suggests that online users are a weak link in information security. This research explores the relationship between cyber-security and cultural, personality and demographic variables.
Chalcogen Extrusion from Heteroallenes and Carbon Monoxide by a Three-Coordinate Rh(I) Disilylamide (2015)

We report the reactions of several heteroallenes (carbon disulfide, carbonyl sulfide, and phenyl isocyanate) and carbon monoxide with a three-coordinate, bis(phosphine)-supported Rh(I) disilylamide (1). Carbon disulfide reacts with 1 to afford a silyltrithiocarbonate complex similar to an intermediate previously invoked in the deoxygenation of CO2 by 1, and prolonged heating affords a structurally unusual μ-κ(2)(S,S'):κ(2)(S,S')-trithiocarbonate dimer. Carbonyl sulfide reacts with 1 to afford a structurally unique Rh(SCNCS) metallacycle derived from two insertions of OCS and N-to-O silyl-group migrations. Phenyl isocyanate reacts with 1 to afford a dimeric bis(phenylcyanamido)-bridged complex resulting from multiple silyl-group migrations and nitrogen-for-oxygen metathesis, akin to reactivity previously observed with carbon dioxide. The ability of 1 to activate carbon-chalcogen multiple bonds via silyl-group migration is further supported by its reactivity with carbon monoxide, where a nitrogen-for-oxygen metathesis is also observed with expulsion of hexamethyldisiloxane. For all reported reactions, intermediates are observable under appropriate conditions, allowing the formulation of mechanisms where insertion of the unsaturated substrate is followed by one or more silyl-group migrations to afford the observed products. This rich variety of reactivity confirms the ability of metal silylamides to activate exceptionally strong carbon-element multiple bonds and suggests that silylamides may be useful intermediates in nitrogen-atom and nitrene-group-transfer schemes.
Gas permeability in the polystyrene films uniaxially drawn under CO2 plasticizing (1997)

Gas permeability coefficients, Ps, of CO2, O2, and N2 have been measured in four kinds of polystyrene (PS) films: an unconditioned film with no orientation (1), a high pressure CO2-conditioned film with no orientation (2), an uniaxially hot-drawn film with some orientation (3), and a film uniaxially drawn under CO2 plasticizing with some orientation (4). Wide angle X-ray diffraction (WAXD) scans for each sample have also been made. High-pressure CO2-conditioning effect was confirmed from the result that P values for any permeation gas in sample 2 were larger than those in sample 1. Values of P for any gas in sample 3 were almost close to those in sample 1 and decreased slightly with Hermans orientation function, f Gas permeability coefficients in sample 4 are larger than those in sample 3 over the whole range of f studied in this work and increased with f. These results were discussed from a viewpoint of inter-segmental distances for PS films.
Security games: solution concepts and algorithms (2013)

Algorithms for finding game-theoretic solutions are now used in several real-world security applications. Many of these applications are based on different but related game-theoretical models collectively known as security games. Much of the research in this area has focused on the two-player setting in which the first player (leader, defender) commits to a strategy, after which the second player (follower, attacker) observes that strategy and responds to it. This is commonly known as the Stackelberg, or leader-follower, model. If none of the players can observe the actions of the others then such a setting is called a simultaneous-move game. A common solution concept in simultaneous-move games is the Nash equilibrium (NE). In the present dissertation, we contribute to this line of research in two ways. 
First, we consider new ways of modeling commitment. We propose the new model in which the leader can commit to a correlated strategy. We show that this model is equivalent to the Stackelberg model in two-player games and is different from the existing models in games with three or more players. We propose an algorithm for computing a solution to this model in polynomial time. We also consider a leader-follower setting in which the players are uncertain about whether the follower can observe. We describe an iterative algorithm for solving such games. 
Second, we analyze the computational complexity of computing Stackelberg and NE strategies in security games. We describe algorithms to solve some variants of the security game model in polynomial time and prove NP-hardness of solving other variants of the model. We also extend the family of security games by allowing the attacker have multiple resources. We provide an algorithm for computing an NE of such games in polynomial time, and we show that computing a Stackelberg strategy is NP-hard.
Construction of a dense genetic map of the Malus fusca fire blight resistant accession MAL0045 using tunable genotyping-by-sequencing SNPs and microsatellites (2020)

Although, the Pacific crabapple, Malus fusca, is a hardy and disease resistant species, studies relating to the genetics of its unique traits are very limited partly due to the lack of a genetic map of this interesting wild apple. An accession of M. fusca (MAL0045) of Julius Kühn-Institut collection in Germany is highly resistant to fire blight disease, incited by different strains of the causative pathogen-Erwinia amylovora. This is the most destructive bacterial disease of Malus of which most of the domesticated apples (Malus domestica) are susceptible. Using a scarcely dense genetic map derived from a population of 134 individuals of MAL0045 × 'Idared', the locus (Mfu10) controlling fire blight resistance mapped on linkage group 10 (LG10) and explained up to 66% of the phenotypic variance with different strains. Although the development of robust and tightly linked molecular markers on LG10 through chromosome walking approach led to the identification of a major candidate gene, any minor effect locus remained elusive possibly due to the lack of marker density of the entire genetic map. Therefore, we have developed a dense genetic map of M. fusca using tunable genotyping-by-sequencing (tGBS) approach. Of thousands of de novo SNPs identified, 2677 were informative in M. fusca and 90.5% of these successfully mapped. In addition, integration of SNP data and microsatellite (SSR) data resulted in a final map comprising 17 LGs with 613 loci spanning 1081.35 centi Morgan (cM). This map will serve as a template for mapping using different strains of the pathogen.
Allergens with Protease Activity from House Dust Mites (2017)

Globally, house dust mites (HDM) are one of the main sources of allergens causing Type I allergy, which has a high risk of progressing into a severe disabling disease manifestation such as allergic asthma. The strong protease activities of a number of these allergens are thought to be involved in several steps of the pathophysiology of this allergic disease. It has been a common notion that protease activity may be one of the properties that confers allergenicity to proteins. In this review we summarize and discuss the roles of the different HDM proteases in the development of Type I allergy.
Noncoding RNA and Cardiomyocyte Proliferation (2017)

It is acknowledged that postnatal mammalian cardiomyocytes (CMs) turn over with a very limited efficacy in both physiological and pathological conditions. Recent studies showed that those newly formed CMs are derived from preexisting CMs. Thus, stimulating CM proliferation becomes a promising strategy for inducing cardiac regeneration. Noncoding RNAs were found differently expressed in CMs with different proliferation potential. Moreover, manipulation of noncoding RNAs, in particular microRNAs, was proved to promote or suppress CM proliferation, indicating that noncoding RNAs are involved in the underlying mechanism of CM proliferation. This review mainly summarizes the roles of noncoding RNAs, as a class of influential factors, in the regulation of CM proliferation.
Differential privacy as a protocol constraint (2012)

Differential privacy, introduced in 2006, has become a standard definition of privacy for statistical computations. Most of the research on differential privacy has explored questions arising in the client-server setting, where privacy guarantees are one-sided and cover data held by just one of the protocol participants. We observe that differential privacy complements the classic definition of secure multi-party computations by allowing one to quantify information leaked through the output of the computation. This view leads to a number of interesting questions, where differential privacy is treated as a constraint on the protocol. We survey the state-of-the-art of differential privacy in a multi-party setting and formulate several open problems.
<title>Firewall systems: the next generation</title> (1996)

To be competitive in today's globally connected marketplace, a company must ensure that their internal network security methodologies and supporting policies are current and reflect an overall understanding of today's technology and its resultant threats. Further, an integrated approach to information security should ensure that new ways of sharing information and doing business are accommodated; such as electronic commerce, high speed public broadband network services, and the federally sponsored National Information Infrastructure. There are many challenges, and success is determined by the establishment of a solid and firm baseline security architecture that accommodate today's external connectivity requirements, provides transitional solutions that integrate with evolving and dynamic technologies, and ultimately acknowledges both the strategic and tactical goals of an evolving network security architecture and firewall system. This paper explores the evolution of external network connectivity requirements, the associated challenges and the subsequent development and evolution of firewall security systems. It makes the assumption that a firewall is a set of integrated and interoperable components, coming together to form a `SYSTEM' and must be designed, implement and managed as such. A progressive firewall model will be utilized to illustrates the evolution of firewall systems from earlier models utilizing separate physical networks, to today's multi-component firewall systems enabling secure heterogeneous and multi-protocol interfaces.
ChemInform Abstract: Diels—Alder Cycloadditions of Stabilized 2,3‐Pyridynes. (2001)

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.
BMI1 collaborates with BCR-ABL in leukemic transformation of human CD34+ cells (2010)

The major limitation for the development of curative cancer therapies has been an incomplete understanding of the molecular mechanisms driving cancer progression. Human models to study the development and progression of chronic myeloid leukemia (CML) have not been established. Here, we show that BMI1 collaborates with BCR-ABL in inducing a fatal leukemia in nonobese diabetic/severe combined immunodeficiency mice transplanted with transduced human CD34(+) cells within 4-5 months. The leukemias were transplantable into secondary recipients with a shortened latency of 8-12 weeks. Clonal analysis revealed that similar clones initiated leukemia in primary and secondary mice. In vivo, transformation was biased toward a lymphoid blast crisis, and in vitro, myeloid as well as lymphoid long-term, self-renewing cultures could be established. Retroviral introduction of BMI1 in primary chronic-phase CD34(+) cells from CML patients elevated their proliferative capacity and self-renewal properties. Thus, our data identify BMI1 as a potential therapeutic target in CML.
General discussion (1983)

L. Monnerie, W. W. Graessley, G. B. Mckenna, M. Adam, B. Ewen, M. Muthukumar, K. F. Freed, R. A. Pethrick, M. Delsanti, J. F. Douglas, A. Baumgärtner, K. Kremer, K. Binder, R. F. T. Stepto, F. Boué, J. S. Higgins, F. Ganazzoli, J. L. Viovy, J. M. Deutsch, A. Perico, M. Doi, A. M. Jameison, M. P. Dare-Edward, H. Killesreiter, A. R. Rennie, R. R. Rahalkar, S. B. Ross-Murphy, W. Burchard, E. R. Morris, R. K. Richardson, P. Thirion, J. Klein, P. Richmond, J. L. Schrag, D. S. Pearson and J. Roovers, Faraday Symp. Chem. Soc., 1983, 18, 199 DOI: 10.1039/FS9831800199
Impact of Mild Head Injury on Neuropsychological Performance in Healthy Older Adults: Longitudinal Assessment in the AIBL Cohort (2016)

Traumatic brain injury (TBI) is suggested to be a significant risk factor for dementia. However, little research has been conducted into long-term neuropsychological outcomes after head trauma. Participants from the Australian Imaging, Biomarkers and Lifestyle Study of Ageing (AIBL) who had recovered after sustaining a mild TBI involving loss of consciousness more than 5 years previously were compared with matched controls across a 3-year period. Bayesian nested-domain modeling was used to estimate the effect of TBI on neuropsychological performance. There was no evidence for a chronic effect of mild TBI on any neuropsychological domain compared to controls. Within the TBI group, there was some evidence suggesting that the age that the head trauma occurred and the duration of unconsciousness were modulators of episodic memory. However, these findings were not robust. Taken together, these findings indicate that adults who have sustained a TBI resulting in loss of consciousness, but who recover to a healthy level of cognitive functioning, do not experience frank deficits in cognitive ability.