gebhart/patrepeval huggingface dataset:
Functional Nanomaterials for Phototherapies of Cancer (2014)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTFunctional Nanomaterials for Phototherapies of CancerLiang Cheng, Chao Wang, Liangzhu Feng, Kai Yang, and Zhuang Liu*View Author Information Institute of Functional Nano & Soft Materials (FUNSOM) & Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou 215123, China*E-mail: [email protected]Cite this: Chem. Rev. 2014, 114, 21, 10869–10939Publication Date (Web):September 26, 2014Publication History Received25 September 2013Published online26 September 2014Published inissue 12 November 2014https://pubs.acs.org/doi/10.1021/cr400532zhttps://doi.org/10.1021/cr400532zreview-articleACS PublicationsCopyright © 2014 American Chemical SocietyRequest reuse permissionsArticle Views41560Altmetric-Citations2058LEARN 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 SUBJECTS:Cancer,Cells,Nanoparticles,Rodent models,Tumors Get e-Alerts
<title>VIDA: an environment for multidimensional image display and analysis</title> (1992)

Since the first dynamic volumetric studies were done in the early 1980s on the dynamic spatial reconstructor (DSR), there has been a surge of interest in volumetric and dynamic imaging using a number of tomographic techniques. Knowledge gained in handling DSR image data has readily transferred to the current use of a number of other volumetric and dynamic imaging modalities including cine and spiral CT, MR, and PET. This in turn has lead to our development of a new image display and quantitation package which we have named VIDATM (volumetric image display and analysis). VIDA is written in C, runs under the UNIXTM operating system, and uses the XView toolkit to conform to the Open LookTM graphical user interface specification. A shared memory structure has been designed which allows for the manipulation of multiple volumes simultaneously. VIDA utilizes a windowing environment and allows execution of multiple processes simultaneously. Available programs include: oblique sectioning, volume rendering, region of interest analysis, interactive image segmentation/editing, algebraic image manipulation, conventional cardiac mechanics analysis, homogeneous strain analysis, tissue blood flow evaluation, etc. VIDA is a built modularly, allowing new programs to be developed and integrated easily. An emphasis has been placed upon image quantitation for the purpose of physiological evaluation.
Dual suppression of inner and outer mitochondrial membrane functions augments apoptotic responses to oncogenic MAPK inhibition (2018)

Mitogen-activated protein kinase (MAPK) pathway inhibitors show promise in treating melanoma, but are unsuccessful in achieving long-term remission. Concordant with clinical data, BRAF<sup>V600E</sup> melanoma cells eliminate glycolysis upon inhibition of BRAF<sup>V600E</sup> or MEK with the targeted therapies Vemurafenib or Trametinib, respectively. Consequently, exposure to these therapies reprograms cellular metabolism to increase mitochondrial respiration and restrain cell death commitment. As the inner mitochondrial membrane (IMM) is sub-organellar site of oxidative phosphorylation (OXPHOS), and the outer mitochondrial membrane (OMM) is the major site of anti-apoptotic BCL-2 protein function, we hypothesized that suppressing these critical mitochondrial membrane functions would be a rational approach to maximize the pro-apoptotic effect of MAPK inhibition. Here, we demonstrate that disruption of OXPHOS with the mitochondria-specific protonophore BAM15 promotes the mitochondrial pathway of apoptosis only when oncogenic MAPK signaling is inhibited. Based on RNA-sequencing analyses of nevi and primary melanoma samples, increased pro-apoptotic BCL-2 family expression positively correlates with high-risk disease suggesting a highly active anti-apoptotic BCL-2 protein repertoire likely contributes to worse outcome. Indeed, combined inhibition of the anti-apoptotic BCL-2 repertoire with BH3-mimetics, OXPHOS, and oncogenic MAPK signaling induces fulminant apoptosis and eliminates clonogenic survival. Altogether, these data suggest that dual suppression of IMM and OMM functions may unleash the normally inadequate pro-apoptotic effects of oncogenic MAPK inhibition to eradicate cancer cells, thus preventing the development of resistant disease, and ultimately, supporting long-term remission.
Query-Oriented Multi-Document Summarization via Unsupervised Deep Learning (2021)

Extractive style query-oriented multi-document summarization generates the summary by extracting a proper set of sentences from multiple documents based on the pre-given query. This paper proposes a novel multi-document summarization framework via deep learning model. This uniform framework consists of three parts: concepts extraction, summary generation, and reconstruction validation, which work together to achieve the largest coverage of the documents content. A new query-oriented extraction technique is proposed to concentrate distributed information to hidden units layer by layer. Then, the whole deep architecture is fine-tuned by minimizing the information loss of reconstruction validation. According to the concentrated information, dynamic programming is used to seek most informative set of sentences as the summary. Experiments on three benchmark datasets demonstrate the effectiveness of the proposed framework and algorithms.
Fully Convolutional Neural Networks for Page Segmentation of Historical Document Images (2018)

We propose a high-performance fully convolutional neural network (FCN) for historical document segmentation that is designed to process a single page in one step. The advantage of this model beside its speed is its ability to directly learn from raw pixels instead of using preprocessing steps e. g. feature computation or superpixel generation. We show that this network yields better results than existing methods on different public data sets. For evaluation of this model we introduce a novel metric that is independent of ambiguous ground truth called Foreground Pixel Accuracy (FgPA). This pixel based measure only counts foreground pixels in the binarized page, any background pixel is omitted. The major advantage of this metric is, that it enables researchers to compare different segmentation methods on their ability to successfully segment text or pictures and not on their ability to learn and possibly overfit the peculiarities of an ambiguous hand-made ground truth segmentation.
CaO- and/or MgO-Swelling Cements: A Key for Providing a Better Annular Sealing? (1993)

Abstract The use of expanding cements for improving the sealing efficacy of annulus cementing has been considered for a long time as a possible solution to existing problems. In this paper, the processes of volumetric shrinkage of cements due to hydration as well as the effective mechanisms of CaO and MgO swelling cements are explained. Preliminary results of the current investigations at ITE for testing cement systems of this kind for application in the borehole are presented. The expansion of the cement matrix has been determined with the use of atmospheric and HPHT expansion cells specially developed for this purpose. Further parameters under investigation include the permeability of the system comprising the cement and steel pipe as well as the strength properties. Formation of voluminous Ca(OH)2 and Mg(OH)2 crystals on the surfaces of the cement particles resulted in matrix expansion by more than 10 percent, even under a hydrostatic pressure of 120 MPa and at borehole temperatures up to 175°C. The swelling cements under investigation exhibited especially high shear bond strength. The test results hitherto obtained already indicate that the sealing action of annulus cementing can be improved with CaO swelling cements when employed preferentially in storage wells with BHST up to 70°C, and with MgO swelling cements in deep gas wells with BHST up to 175 °C.
Acute postnatal ablation of <i>Hif-2</i> α results in anemia (2007)

Adaptive transcriptional responses to oxygen deprivation (hypoxia) are mediated by the hypoxia-inducible factors (HIFs), heterodimeric transcription factors composed of two basic helix-loop-helix-PAS family proteins. The transcriptional activity of HIF is determined by the hypoxic stabilization of the HIF-alpha proteins. HIF-1alpha and HIF-2alpha exhibit high sequence homology but have different mRNA expression patterns; HIF-1alpha is expressed ubiquitously whereas HIF-2alpha expression is more restricted to certain tissues, e.g., the endothelium, lung, brain, and neural crest derivatives. Germ-line deletion of either HIF subunit is embryonic lethal with unique features suggesting important roles for both HIF-alpha isoforms. Global deletion of Hif-2alpha results in distinct phenotypes depending on the mouse strain used for the mutation, clearly demonstrating an important role for HIF-2alpha in mouse development. The function of HIF-2alpha in adult life, however, remains incompletely understood. In this study, we describe the generation of a conditional murine Hif-2alpha allele and the effect of its acute postnatal ablation. Under very stringent conditions, we ablate Hif-2alpha after birth and compare the effect of acute global deletion of Hif-2alpha and Hif-1alpha. Our results demonstrate that HIF-2alpha plays a critical role in adult erythropoiesis, with acute deletion leading to anemia. Furthermore, although HIF-1alpha was first purified and cloned based on its affinity for the human erythropoietin (EPO) 3' enhancer hypoxia response element (HRE) and regulates Epo expression during mouse embryogenesis, HIF-2alpha is the critical alpha isoform regulating Epo under physiologic and stress conditions in adults.
Trans-Encoder: Unsupervised sentence-pair modelling through self- and mutual-distillations (2021)

In NLP, a large volume of tasks involve pairwise comparison between two sequences (e.g. sentence similarity and paraphrase identification). Predominantly, two formulations are used for sentence-pair tasks: bi-encoders and cross-encoders. Bi-encoders produce fixed-dimensional sentence representations and are computationally efficient, however, they usually underperform cross-encoders. Cross-encoders can leverage their attention heads to exploit inter-sentence interactions for better performance but they require task fine-tuning and are computationally more expensive. In this paper, we present a completely unsupervised sentence representation model termed as Trans-Encoder that combines the two learning paradigms into an iterative joint framework to simultaneously learn enhanced bi- and cross-encoders. Specifically, on top of a pre-trained Language Model (PLM), we start with converting it to an unsupervised bi-encoder, and then alternate between the bi- and cross-encoder task formulations. In each alternation, one task formulation will produce pseudo-labels which are used as learning signals for the other task formulation. We then propose an extension to conduct such self-distillation approach on multiple PLMs in parallel and use the average of their pseudo-labels for mutual-distillation. Trans-Encoder creates, to the best of our knowledge, the first completely unsupervised cross-encoder and also a state-of-the-art unsupervised bi-encoder for sentence similarity. Both the bi-encoder and cross-encoder formulations of Trans-Encoder outperform recently proposed state-of-the-art unsupervised sentence encoders such as Mirror-BERT and SimCSE by up to 5% on the sentence similarity benchmarks.
Mitogenic signal transduction in normal and transformed 32D hematopoietic cells (1991)

We studied mitogenic signal transduction in normal and oncogene-transformed 32D cells, a murine hematopoietic cell line that is normally dependent on interleukin-3 (IL3) for proliferation and survival. The formation of second messengers was measured in normal cells stimulated with IL3, and in cells transfected with foreign growth factor receptor genes and stimulated with appropriate growth factors. We also measured the steady-state level of second messengers in 32D cells transformed by erbB, abl, and src oncogenes which abrogate growth factor requirement. We found that IL3 stimulated the formation of diacylglycerol independently of inositol lipid turnover, but concomitantly with increased turnover of phosphatidylcholine. Epidermal growth factor (EGF), and platelet-derived growth factor (PDGF) stimulated the 'classical' turnover of inositol lipids with formation of diacylglycerol and calcium-mobilizing inositol phosphates. Colony stimulating factor-1 triggered inositol lipid turnover, although to a much lower extent than EGF and PDGF. Transformed cells showed elevated levels of diacylglycerol together with increased turnover of phosphoinositides and phosphatidylcholine. Taken together these results indicate that different growth factors and oncoproteins associate with multiple signalling pathways in 32D cells.
Computer Analysis and Field Measurements of Stresses in Long Drill Strings Suspended from a Floating Vessel (1984)

Sea 55 Safe Operation Of Drill String 56 Resonant Heave Period Of Drill String With Heave Compensator....
Low-Power Testing for Low-Power Devices (2010)

Low-power devices are indispensable for modern electronic applications, and numerous hardware/software techniques have been developed for drastically reducing functional power dissipation. However, the testing of such low-power devices has increasingly become a serious problem, especially in at-speed scan testing where a transition is launched at the output of a flip-flop and the corresponding circuit response is captured by a flip-flop with a functional clock pulse. The reason is that most or all of the functional constraints with respect to circuit operations and clocking are ignored in at-speed scan testing, which may make test power several times higher than functional power.
Darstellung sowie IR‐ und<sup>51</sup>V‐NMR‐spektroskopische Untersuchungen an Arsin‐, Stibin‐ und Bismutin‐Derivaten von [Et<sub>4</sub>N][V(CO)<sub>6</sub>] und [η<sup>5</sup>‐CpV(CO)<sub>4</sub>] (1978)

Abstract Durch photoinduzierte Substitution von CO in Tetraethylammonium‐hexacarbonylvanadat(−I) bzw. Tetracarbonyl(η 5 ‐cyclopentadienyl)vanadium( + I) wurden die Komplexe[Et 4 N][V(CO) 5 EZ 3 ] bzw. [η 5 ‐CpV(CO) 3 EZ 3 ] (EZ 3 = AsPh 3 , AsMe 2 Ph, AsEt 3 , As(OEt) 3 , SbPh 3 , SbEt 3 , Sb(OEt) 3 , BiEt 3 ) und der Komplex cis ‐[η 5 ‐CpV(CO) 2 (BiEt 3 ) 2 ] dargestellt und bezüglich ihrer spektroskopischen Eigenschaften mit den analogen Phosphin‐Komplexen verglichen. IR‐spektroskopische Untersuchungen (Schwingungskraftkonstanten k 1 ) ergeben eine vom Donoratom E weitgehend unabhängige Reihung der Liganden nach zunehmender π‐Akzeptorstärke gemäß EEt 3 < EMe 2 Ph ⪅ EPh 3 < E(OEt) 3 . 51 V‐NMR‐chemische Verschiebungen andererseits gestatten die Klassifizierung der Liganden hinsichtlich ihrer integralen Ligandenstärke gemäß EPh 3 < EMe 2 Ph ≈︁ EEt 3 < E(OEt) 3 (für E = P, As) und BiEt 3 < AsZ 3 < PZ 3 < SbZ 3 . Die Ergebnisse werden auf der Grundlage der Ligandenfeldaufspaltung Δ E , kovalenter Bindungsanteile in der Metall‐Ligand‐Bindung, nephelauxetischer Effekte durch das Donoratom E sowie induktiver Einflüsse seitens der Substituenten Z diskutiert.
ChemInform Abstract: Glycosides and Disaccharides (1986)

Abstract Review: (178 refs.
Automatic generation of primary sequence patterns from sets of related protein sequences. (1990)

We have developed a computer algorithm that can extract the pattern of conserved primary sequence elements common to all members of a homologous protein family. The method involves clustering the pairwise similarity scores among a set of related sequences to generate a binary dendrogram (tree). The tree is then reduced in a stepwise manner by progressively replacing the node connecting the two most similar termini by one common pattern until only a single common "root" pattern remains. A pattern is generated at a node by (i) performing a local optimal alignment on the sequence/pattern pair connected by the node with the use of an extended dynamic programming algorithm and then (ii) constructing a single common pattern from this alignment with a nested hierarchy of amino acid classes to identify the minimal inclusive amino acid class covering each paired set of elements in the alignment. Gaps within an alignment are created and/or extended using a "pay once" gap penalty rule, and gapped positions are converted into gap characters that function as 0 or 1 amino acid of any type during subsequent alignment. This method has been used to generate a library of covering patterns for homologous families in the National Biomedical Research Foundation/Protein Identification Resource protein sequence data base. We show that a covering pattern can be more diagnostic for sequence family membership than any of the individual sequences used to construct the pattern.
A New Kullback–Leibler VAD for Speech Recognition in Noise (2004)

This letter shows an innovative voice activity detector (VAD) based on the Kullback-Leibler (KL) divergence measure. The algorithm is evaluated in the context of the recently approved ETSI standard for distributed speech recognition (DSR). The VAD uses long-term information of the noisy speech signal in order to define a more robust decision rule yielding high accuracy. The mel-scaled filter bank log-energies (FBE) are modeled by means of Gaussian distributions, and a symmetric KL divergence is used for the estimation of the distance between speech and noise distributions. The decision rule is formulated in terms of the average subband KL divergence that is compared to a noise-adaptable threshold. An exhaustive analysis using the AURORA databases is conducted in order to assess the performance of the proposed method and to compare it to existing standard VAD methods.
Energy efficient programming of nanoelectronic synaptic devices for large-scale implementation of associative and temporal sequence learning (2011)

A nanoscale, two-terminal device emulating plasticity and energy efficiency of biological synapses is a critical element for realizing brain-inspired computational systems and real-time brain simulators. In this work, we explore the use of phase change materials (PCM), widely used for memory applications, to build electronic synapses which implement synaptic plasticity with picojoule level energy consumption. Gradual switching characteristics and different spike schemes are discussed from implementation of synaptic plasticity and energy consumption perspectives. Our simulations demonstrate that a recurrent network of PCM synapses in a crossbar array can achieve brain-like associative and temporal sequence learning. Asymmetric plasticity is shown to transform temporal information into spatial information for sequence learning. Symmetric plasticity enables the storage and recall of certain patterns associatively by acting as a coincidence detector for neuronal activity.
Targeted gene knock-in by homology-directed genome editing using Cas9 ribonucleoprotein and AAV donor delivery (2017)

Realizing the full potential of genome editing requires the development of efficient and broadly applicable methods for delivering programmable nucleases and donor templates for homology-directed repair (HDR). The RNA-guided Cas9 endonuclease can be introduced into cells as a purified protein in complex with a single guide RNA (sgRNA). Such ribonucleoproteins (RNPs) can facilitate the high-fidelity introduction of single-base substitutions via HDR following co-delivery with a single-stranded DNA oligonucleotide. However, combining RNPs with transgene-containing donor templates for targeted gene addition has proven challenging, which in turn has limited the capabilities of the RNP-mediated genome editing toolbox. Here, we demonstrate that combining RNP delivery with naturally recombinogenic adeno-associated virus (AAV) donor vectors enables site-specific gene insertion by homology-directed genome editing. Compared to conventional plasmid-based expression vectors and donor templates, we show that combining RNP and AAV donor delivery increases the efficiency of gene addition by up to 12-fold, enabling the creation of lineage reporters that can be used to track the conversion of striatal neurons from human fibroblasts in real time. These results thus illustrate the potential for unifying nuclease protein delivery with AAV donor vectors for homology-directed genome editing.
Peptide N‐Amination Supports β‐Sheet Conformations (2017)

The conformational heterogeneity of backbone N-substituted peptides limits their ability to adopt stable secondary structures. Herein, we describe a practical synthesis of backbone aminated peptides that readily adopt β-sheet folds. Data derived from model N-amino peptides suggest that extended conformations are stabilized through cooperative steric, electrostatic, and hydrogen-bonding interactions.
Understanding and Improving Regression Test Selection in Continuous Integration (2019)

Developers rely on regression testing in their continuous integration (CI) environment to find changes that introduce regression faults. While regression testing is widely practiced, it can be costly. Regression test selection (RTS) reduces the cost of regression testing by not running the tests that are unaffected by the changes. Industry has adopted module-level RTS for their CI environment, while researchers have proposed class-level RTS. In this paper, we compare module-and class-level RTS techniques in a cloud-based CI environment, Travis. We also develop and evaluate a hybrid RTS technique that combines aspects of the module-and class-level RTS techniques. We evaluate all the techniques on real Travis builds. We find that the RTS techniques do save testing time compared to running all tests (RetestAll), but the percentage of time for a full build using RTS (76.0%) is not as low as found in previous work, due to the extra overhead in a cloud-based CI environment. Moreover, we inspect test failures from RetestAll builds, and although we find that RTS techniques can miss to select failed tests, these test failures are almost all flaky test failures. As such, RTS techniques provide additional value in helping developers avoid wasting time debugging failures not related to the recent code changes. Overall, our results show that RTS can be beneficial for the developers in the CI environment, and RTS not only saves time but also avoids misleading developers by flaky test failures.
Synthesis of Antitumor Carbazole‐Amonafide Structural Hybrids (2015)

Abstract A facile synthesis of new antitumor [4,5‐ bc ]carbazole‐amonafide derivatives is described. These compounds represent a new class of structural hybrids that contain the medicinally important carbazole and amonafide cores. The synthesis involves a Suzuki–Miyaura coupling of bromoamonafide with arylboronic acid reagents followed by the introduction of an azide group and subsequent regiospecific thermal nitrene insertion to yield carbazole‐amonafide hybrids in good yields. Preliminary antiproliferative assays against cancer and benign cell lines identified compounds with selective antitumor activity that exhibited submicromolar IC 50 values.