gebhart/patrepeval huggingface dataset:
Epithelial-Mesenchymal Plasticity Induced by Discontinuous Exposure to TGFβ1 Promotes Tumour Growth (2022)

Transitions between epithelial and mesenchymal cellular states (EMT/MET) contribute to cancer progression. We hypothesize that EMT followed by MET promotes cell population heterogeneity, favouring tumour growth. We developed an EMT model by on and off exposure of epithelial EpH4 cells (E-cells) to TGFβ1 that mimics phenotypic EMT (M-cells) and MET. We aimed at understanding whether phenotypic MET is accompanied by molecular and functional reversion back to epithelia by using RNA sequencing, immunofluorescence (IF), proliferation, wound healing, focus formation and mamosphere formation assays as well as cell xenografts in nude mice. Phenotypic reverted epithelial cells (RE-cells) obtained after MET induction presented epithelial morphologies and proliferation rates resembling E cells. However, the RE transcriptomic profile and IF staining of epithelial and mesenchymal markers revealed a uniquely heterogeneous mixture of cell subpopulations with a high self-renewal ability. RE cell heterogeneity was stably maintained for long periods after TGFβ1 removal both in vitro and in large tumours derived from the nude mice. Overall, we show that phenotypic reverted epithelial cells (RE cells) do not return to the molecular and functional epithelial state and present mesenchymal features related to aggressiveness and cellular heterogeneity that favour tumour growth in vivo. This work strengthens epithelial cell reprogramming and cellular heterogeneity fostered by inflammatory cues as a tumour growth-promoting factor in vivo.
The Revised (2013) Banff Classification for Antibody-Mediated Rejection of Renal Allografts: Update, Difficulties, and Future Considerations (2015)

The Banff 2013 classification (Banff 2013) for antibody-mediated rejection (ABMR) in renal allografts represents the first major revision of the original Banff classification for ABMR that was published in 2003. The main impetus for this revision was the need to include C4d-negative ABMR, although this revised classification contains a number of additional features based on findings reported from 2007 to 2013. Since its publication, several studies have examined the validity of different aspects of Banff 2013 and compared it to earlier (2003, 2007) versions of the Banff ABMR classification. Recent evidence, albeit limited, indicates that Banff 2013 represents an improvement over the previous versions, enhancing our ability to accurately diagnose cases of acute/active and chronic active ABMR on renal allograft biopsy. Molecular studies appear to justify the threshold value of glomerulitis plus peritubular capillaritis score ≥2 required by Banff 2013 for the diagnosis of C4d-negative ABMR; however, other aspects of the classification, including its overall interobserver reproducibility, the clinical significance of the category of C4d staining without evidence of rejection, and whether surrogate markers might potentially substitute for the requirement for the presence of donor-specific antibodies, require additional investigation.
Low-complexity memory-assisted adaptive-threshold detection scheme for on-OFF-keying diffusion-based molecular communications (2017)

In this paper, a novel Memory-Assisted Adaptive-Threshold detection (MAAT) scheme for diffusion-based molecular communications (MC) systems is proposed. The proposed scheme applies to MC systems in which single-type of molecules is assumed to carry the information from the transmitting nano-machine, through a fluid medium, to the receiving nano-machine. The information is represented by the received concentration of the information molecules. We consider a single transmitter (Tx) and receiver (Rx) problem, where the communication takes place in a three-dimensional free-flow diffusion-based unbounded propagation environment. We present a novel adaptive-threshold detection algorithm suitable for binary On-OFF Keying (BOOK signaling), where the Rx adapts the 1/0 bit detection threshold based on past received bits. The adjustment of the 1/0 detection threshold based on past received bits helps to alleviate the inter-symbol interference resulting from residual (tail) diffusion molecules arriving at the receiver due to past bit transmissions and noise molecules. Performance evaluation shows a promising improvement in the un-coded BER performance of our proposed scheme compared with the traditional Fixed-Threshold Detection (FTD) approach. In addition, our proposed approach delivers BER levels comparable with considerably more complex approaches found in the literature.
Simplifying data integration: the design of the desert software development environment (1996)

This paper describes the design and motivations behind the Desert environment. The Desert environment has been created to demonstrate that the facilities typically associated with expensive data integration can be provided inexpensively in an open framework. It uses three integration mechanisms: control integration, simple data integration based on fragments, and a common editor. It offers a variety of capabilities including hyperlinks and the ability to create virtual files containing only the portions of the software that are relevant to the task on hand. It does this in an open environment that is compatible with existing tools and programs. The environment currently consists of a set of support facilities including a context database, a fragment database, scanners, and a ToolTalk interface, as well as a preliminary set of programming tools including a context manager and extensions to FrameMaker to support program editing and insets for non-textual software artifacts.
Some complete cycles on the 𝑛-cube (1963)

1. Let Q * be the n-dimensional hypercube (or n-cube) whose vertices are the 2n vectors of dimension n with components 0's and l's. Let Qn be the graph that consists of the edges and vertices of Q,,*. A complete cycle (or Hamilton circuit) on Qn is a cyclic path on the graph Qn that passes through each vertex once and onlly once. Let C be such a cycle and let P1, P2, * * *, P2n=Po be the consecutive vertices of C. Any two consecutive vertices Pi, Pi+, differ in exactly one component. Let Ai denote the index of that component. Then A is called the ith change number of C. The subscripts i in the Pi and the Ai are taken modulo 2 . Clearly C is determined by P1 and tlle sequence of 2n change numbers
The androgen receptor gene mutations database: 2012 update (2012)

The current version of the androgen receptor gene (AR) mutations database is described. A major change to the database is that the nomenclature and numbering scheme now conforms to all Human Genome Variation Society norms. The total number of reported mutations has risen from 605 to 1,029 since 2004. The database now contains a number of mutations that are associated with prostate cancer (CaP) treatment regimens, while the number of AR mutations found in CaP tissues has more than doubled from 76 to 159. In addition, in a number of androgen insensitivity syndrome (AIS) and CaP cases, multiple mutations have been found within the same tissue samples. For the first time, we report on a disconnect within the AIS phenotype-genotype relationship among our own patient database, in that over 40% of our patients with a classic complete AIS or partial AIS phenotypes did not appear to have a mutation in their AR gene. The implications of this phenomenon on future locus-specific mutation database (LSDB) development are discussed, together with the concept that mutations can be associated with both loss- and gain-of-function, and the effect of multiple AR mutations within individuals. The database is available on the internet (http://androgendb.mcgill.ca), and a web-based LSDB with the variants using the Leiden Open Variation Database platform is available at http://www.lovd.nl/AR.
Targeting Defects in the Cellular DNA Damage Response for the Treatment of Pancreatic Ductal Adenocarcinoma (2018)

Pancreatic cancer is one of the most common causes of cancer-related mortality in the Western world and pancreatic ductal adenocarcinoma (PDAC) is by far the most common pancreatic cancer entity. Locally advanced or metastatic PDAC remains a major clinical challenge, and the prognosis of affected patients is dismal despite substantial research efforts in this area. Recent large-scale genomic analyses of PDAC revealed that KRAS is the most frequently mutated driver gene in this entity. In addition, a relatively large proportion of PDAC patients displays germline variants in genes involved in DNA repair, particularly DNA double-strand repair. Similarly, a sizable fraction of sporadic PDAC cases harbor mutations in genome maintenance genes, such as BRCA1, BRCA2, and ATM. While direct targeting of oncogenic KRAS is currently not possible in the clinical setting, these defects in DNA repair may open new therapeutic avenues. Here, we discuss the potential use of compounds that interfere with DNA repair and genome maintenance mechanisms for the treatment of PDAC. We particularly focus on the genotype-tailored use of compounds, such as PARP inhibitors, as well as ATR- and DNA-protein kinase catalytic subunit (PKcs) inhibitors.
A Family Longevity Selection Score: Ranking Sibships by Their Longevity, Size, and Availability for Study (2009)

Family studies of exceptional longevity can potentially identify genetic and other factors contributing to long life and healthy aging. Although such studies seek families that are exceptionally long lived, they also need living members who can provide DNA and phenotype information. On the basis of these considerations, the authors developed a metric to rank families for selection into a family study of longevity. Their measure, the family longevity selection score (FLoSS), is the sum of 2 components: 1) an estimated family longevity score built from birth-, gender-, and nation-specific cohort survival probabilities and 2) a bonus for older living siblings. The authors examined properties of FLoSS-based family rankings by using data from 3 ongoing studies: the New England Centenarian Study, the Framingham Heart Study, and screenees for the Long Life Family Study. FLoSS-based selection yields families with exceptional longevity, satisfactory sibship sizes and numbers of living siblings, and high ages. Parameters in the FLoSS formula can be tailored for studies of specific populations or age ranges or with different conditions. The first component of the FLoSS also provides a conceptually sound survival measure to characterize exceptional longevity in individuals or families in various types of studies and correlates well with later-observed longevity.
Multidimensional Localization of Multiple Sound Sources Using Blind Adaptive MIMO System Identification (2006)

The TDOA-based acoustic source localization approach is a powerful and widely-used method which can be applied for one source in several dimensions or several sources in one dimension. However the localization turns out to be more challenging when multiple sound sources should be localized in multiple dimensions, due to a spatial ambiguity phenomenon which requires to perform an intermediate step after the TDOA estimation and before the calculation of the geometrical source positions. In order to obtain the required set of TDOA estimates for the multidimensional localization of multiple sound sources, we apply a recently presented TDOA estimation method based on blind adaptive multiple-input-multiple-output (MIMO) system identification. We demonstrate that this localization method also provides valuable side information which allows us to resolve the spatial ambiguity without any prior knowledge about the source positions. Furthermore we show that the blind adaptive MIMO system identification allows a high spatial resolution. Experimental results for the localization of two sources in a two-dimensional plane show the effectiveness of the proposed scheme
TBCRC-010: Phase I/II Study of Dasatinib in Combination with Zoledronic Acid for the Treatment of Breast Cancer Bone Metastasis (2016)

Combination therapy was well tolerated and produced responses in bone in patients with HR-positive tumors. Clin Cancer Res; 22(23); 5706-12. ©2016 AACR.
Activation of mitogen-activated protein kinase during meiotic maturation in porcine oocytes (1995)

To investigate the involvement of mitogen-activated protein kinase (MAP kinase) in meiotic maturation of porcine oocytes, we assayed MAP kinase activity using myelin basic protein (MBP) as a substrate. MAP kinase activity was low during the germinal vesicle stage, 0-20 h of culture. An abrupt increase was observed at metaphase I (30 h of culture), and activity remained significantly higher than that at 0 h until 50 h of culture, with a transient slight decrease at the time of first polar body extrusion (40 h). Detection of the kinase activity by an in-gel phosphorylation assay confirmed that the 42 and 44 kDa MAP kinases were significantly activated in 45 h cultured oocytes but not in 0 h oocytes, and just slightly in 20 h oocytes. In immunoblotting, however, the 42 and 44 kDa bands were detected in 0, 20 and 45 h cultured oocytes. Furthermore, the signal strength of the two bands did not change during the period of culture, but shifted up to 45 h, indicating that the activation of MAP kinase depended not on the synthesis but on the phosphorylation of this enzyme. These results suggest that the activation of MAP kinase is involved in the regulation of meiotic maturation of porcine oocytes, and especially in the regulation after germinal vesicle breakdown.
Multifilamentary Bi-2223 composite tapes made by a metallic precursor route (1993)

A process based on metallic precursors has been developed for manufacturing high filament count oxide superconductor-silver composite tapes with critical current densities of up to 7.5 kA/cm/sup 2/ at 77 K in zero field. A 30-cm prototype multistrand conductor made of these tapes has a critical current of 240 A at 77 K over a 9 cm gauge length, with an average critical current density of 6 kA/cm/sup 2/. The mechanical properties of tapes made from metallic precursors containing up to 10000 Bi-2223 superconducting oxide filaments were investigated. Critical tensile strains average 0.6%, and bend tests show negligible dropoff in current density up to a 0.70% surface strain. The critical current decrease beyond the 0.70% surface bend strain follows a simple model based on extensive filament damage beyond the critical tensile strain. Increased flow stresses of the composite tapes, compared to similarly processed silver, indicate considerable strengthening of the composite by the oxide filaments.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A fast two-dimensional median filtering algorithm (1979)

We present a fast algorithm for two-dimensional median filtering. It is based on storing and updating the gray level histogram of the picture elements in the window. The algorithm is much faster than conventional sorting methods. For a window size of m × n, the computer time required is 0(n).
Modeling and prediction for the acute toxicity of pesticide mixtures to the freshwater luminescent bacterium Vibrio qinghaiensis sp.-Q67 (2010)

在中国，由杀虫剂混合物的水污染由于潜在的毒性和 bioaccumulation 组成了一个严重环境问题。但是很少杀虫剂联合有行动的确切类似、不一样的机制。为这个目的，在有淡水的测试光细菌(Vibrio qinghaiensis sp.-Q67 ) ，包括三除草剂和七杀虫药剂，十杀虫剂作为测试物质被选择。集中反应分析为十种单个物质，并且为在 12 不同集中比率包含所有十种物质的混合物被执行(基于 UDCR 和 EECR 方法) 。观察混合毒性与由二个模型，集中增加(CA ) 和独立行动(IA ) 的预言相比。测试混合物的毒性显示出一个好协议，除了四 UDCR 混合物，那些由 CA 的概念预言了：UD10-2， UD10-4， UD10-8 和 UD10-10。在四 UDCR 混合物检验 imidacloprid 的影响(UD10-2， UD10-4， UD10-8， UD10-10 ) ，它从十杀虫剂的混合物并且留下被移开九化学药品基于 UDCR 方法在一样的相对比例被联合(UD9-2， UD9-4， UD9-8， UD9-10 ) 。从为有省略 imidacloprid 的九留下的杀虫剂的散布的点的 CA 没有重要离开。因此， imidacloprid 可以显著地由于它的性质影响另外的杀虫剂。
QUANTITATIVE STUDY OF THE NUCLEOPHILICITY OF THE THIOCARBONYL GROUP IN HETEROCYCLIC COMPOUNDS (1976)

Abstract When the kinetic constants of reactions between alkyl iodides and a number of hetero-cyclic thiocarbonyl derivatives are measured in solvent acetone, the reactivity extends over three orders of magnitude. The increasing nucleophiliticy is found in the series: Bulkiness of the alkyl group in the alkylating agent has little influence when compared to the pyridine case. A correlation is found between the nucleophilic polarization energy calculated with HMO approximation and the measured constants.
Hierarchical Hole-Filling For Depth-Based View Synthesis in FTV and 3D Video (2012)

Three-dimensional television (3DTV) is believed to be the future of television broadcasting that would replace current 2D HDTV technology. Future 3DTV would bring a more life-like and visually immersive home entertainment experience, in which users will have the freedom to navigate through the scene to choose a different viewpoint. A desired view can be synthesized at the receiver side using depth image-based rendering (DIBR). While this approach has many advantages, one of the key challenges in DIBR is how to fill the holes caused by disocclusion regions and wrong depth values. In this paper, we propose two new approaches for disocclusion removal in DIBR. Both approaches namely hierarchical hole-filling (HHF) and depth adaptive hierarchical hole-filling eliminate the need for any smoothing or filtering of the depth map. Both techniques use a pyramid-like approach to estimate the hole pixels from lower resolution estimates of the 3D wrapped image. The lower resolution estimates involve a pseudo zero canceling plus Gaussian filtering of the wrapped image. The depth adaptive HHF incorporates the depth information to produce a higher resolution rendering around previously occluded areas. Experimental results show that HHF and depth adaptive HHF yield virtual images and stereoscopic videos that are free of geometric distortions and a better rendering quality both subjectively and objectively than traditional hole-filling approaches.
Carbon Nanotubes, Multi‐Walled (2005)

Abstract Well‐aligned carbon multiwalled nanotubes (MWNTs) have been synthesized continuously by pyrolysis of xylene–ferrocene mixtures. To study the MWNT growth mechanism, two‐step processes and various chemical vapor deposition (CVD) parameters have been employed. Transmission electron microscopy observations support a tip‐root growth model of MWNTs by floating catalytic CVD. Hydrocarbon analyzer is used to measure the total carbon balance within the CVD reactor, while mass spectra analyses monitor the concentrations of hydrocarbon species, which helps to understand the catalyst deactivation and pyrolysis chemistry of xylene over catalyst Fe(C) nanoparticles. MWNTs can be treated to attach required functional groups on nanotube walls and/or caps for specific applications by various methods including acid oxidation, reduction, addition of radicals, and cycloadditions. Carbon nanotubes (CNTs) have shown promising applications in advanced CNT–polymer composites. To realize CNT potentials to enhance the properties of matrices, several important issues such as dispersion, orientation, interfacial effects, and processing parameters have been addressed. The dependence of the CNT–polymer composite properties on CNT diameter, length, and interfacial effects has been used to develop models to predict and optimize variables for maximum composite performance. CNT–polymer composites have been developed for enhanced mechanical, electrical, and thermal properties, which have wide applications for the next generation of truly multifunctional materials as well as lighter weights and increased manufacturability over current materials.
Changes in oxygenation of intracranial tumors with carbogen: A BOLD MRI and EPR oximetry study (2002)

EPR results indicate that glial sarcomas may be radiobiologically hypoxic. Both EPR and BOLD data indicate that carbogen breathing increases brain tumor oxygenation. These data support the use of BOLD imaging to monitor changes in oxygenation in brain tumors.
NMR evidence for dynamic secondary structure in helixes II and III of the 5S RNA of Escherichia coli (1986)

A new ribonuclease A (RNase A) resistant fragment of the 5S ribonucleic acid (RNA) from Escherichia coli has been isolated and characterized. This fragment comprises helix III and most of helix II of the parent molecule, a part of the 5S RNA molecule for which several energetically equivalent secondary structures have been proposed [De Wachter, R., Chen, M.-W., & Vandenberghe, A. (1984) Eur. J. Biochem. 143, 175-182]. The imino proton spectrum of this fragment has been studied by nuclear magnetic resonance methods at 500 MHz. The data obtained are readily rationalized in terms of one of the structures proposed for this region of 5S RNA. They also suggest that upon heating, this structure is replaced by a second, different one, consistent with the view that the helix II-helix III region of 5S RNA is able to switch between alternative structures. Among the products of the nucleolytic digestion of 5S RNA is a species whose sequence indicates that RNase A can ligate RNA as well as hydrolyze it.
Modeling and Synthesis of Realistic Visual Speech in 3D (2011)

The problem of realistic face animation is a difficult one. This is hampering a further breakthrough of some high-tech domains, such as special effects in the movies, the use of 3D face models in communications, the use of avatars and likenesses in virtual reality, and the production of games with more subtle scenarios. This work attempts to improve on the current state-of-the-art in face animation, especially for the creation of highly realistic lip and speech-related motions. To that end, 3D models of faces are used and — based on the latest technology — speech-related 3D face motion will be learned from examples. Thus, the chapter subscribes to the surging field of image-based modeling and widens its scope to include animation. The exploitation of detailed 3D motion sequences is quite unique, thereby narrowing the gap between modeling and animation. From measured 3D face deformations around the mouth area, typical motions are extracted for different “visemes”. Visemes are the basic motion patterns observed for speech and are comparable to the phonemes of auditory speech. The visemes are studied with sufficient detail to also cover natural variations and differences between individuals. Furthermore, the transition between visemes is analyzed in terms of co-articulation effects, i.e., the visual blending of visemes as required for fluent, natural speech. The work presented in this chapter also encompasses the animation of faces for which no visemes have been observed and extracted. The “transplantation” of visemes to novel faces for which no viseme data have been recorded and for which only a static 3D model is available allows for the animation of faces without an extensive learning procedure for each individual.Request access from your librarian to read this chapter's full text.
Diversity-Performance Relationship in a Handwriting Recognition System Based on Bit-Plane Decomposition (2004)

The success gained by applying bit-plane decomposition methods to handwriting recognition have been demonstrated in our previous work [S. Hoque et al., 2003, 2002]. In this paper we address the relationship between the diversity and the improvements obtained by applying multiple combinations of various layers. These layers are obtained by applying a method based on an n-tuple based classification system, namely, the random decomposition technique proposed in S. Hoque et al. (2003). We investigated 5 combination methods and 9 diversity measures using data extracted from the NIST database. Results presented in this paper support the use of the bit-plane decomposition approach as a diversification method. Strong correlation was found between both the accuracy and the improvements and the diversity measures in the majority of the combination methods investigated.