gebhart/patrepeval huggingface dataset:
Mechanical Environment Modulates Biological Properties of Oligodendrocyte Progenitor Cells (2012)

Myelination and its regenerative counterpart remyelination represent one of the most complex cell-cell interactions in the central nervous system (CNS). The biochemical regulation of axon myelination via the proliferation, migration, and differentiation of oligodendrocyte progenitor cells (OPCs) has been characterized extensively. However, most biochemical analysis has been conducted in vitro on OPCs adhered to substrata of stiffness that is orders of magnitude greater than that of the in vivo CNS environment. Little is known of how variation in mechanical properties over the physiological range affects OPC biology. Here, we show that OPCs are mechanosensitive. Cell survival, proliferation, migration, and differentiation capacity in vitro depend on the mechanical stiffness of polymer hydrogel substrata. Most of these properties are optimal at the intermediate values of CNS tissue stiffness. Moreover, many of these properties measured for cells on gels of optimal stiffness differed significantly from those measured on glass or polystyrene. The dependence of OPC differentiation on the mechanical properties of the extracellular environment provides motivation to revisit results obtained on nonphysiological, rigid surfaces. We also find that OPCs stiffen upon differentiation, but that they do not change their compliance in response to substratum stiffness, which is similar to embryonic stem cells, but different from adult stem cells. These results form the basis for further investigations into the mechanobiology of cell function in the CNS and may specifically shed new light on the failure of remyelination in chronic demyelinating diseases such as multiple sclerosis.
Biology of Colorectal Cancer (2010)

Significant advances have been made in understanding the biology of colorectal cancer. In this chapter, we review the key signaling pathways that play key roles in maintaining the growth and proliferation of colorectal cancer. The pathways that will be discussed include Wnt/beta-catenin, TGF-beta/SMAD, Notch, Hedgehog, epidermal growth factor receptor, Ras, and PI3K/Akt. In addition, we review the growing role of colon cancer stem cells in mediating cellular drug resistance and cancer recurrence. This enhanced understanding of cancer biology provides important insights for developing novel therapies that target specific growth factor receptors and/or certain critical signal transduction pathways. These targeted therapies can then be used alone or in combination with standard cytotoxic chemotherapy regimens.
Electrochemical Detection of Parts-Per-Billion Lead via an Electrode-Bound DNAzyme Assembly (2006)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTElectrochemical Detection of Parts-Per-Billion Lead via an Electrode-Bound DNAzyme AssemblyYi Xiao, Aaron A. Rowe, and Kevin W. PlaxcoView Author Information Department of Physics, Materials Department, and Institute for Polymers and Organic Solids, Department of Chemistry and Biochemistry, and Program in BioMolecular Science and Engineering, University of California, Santa Barbara, California 93106. Cite this: J. Am. Chem. Soc. 2007, 129, 2, 262–263Publication Date (Web):December 20, 2006Publication History Received11 October 2006Published online20 December 2006Published inissue 1 January 2007https://doi.org/10.1021/ja067278xCopyright © 2007 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views4886Altmetric-Citations423LEARN 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 InReddit Read OnlinePDF (62 KB) Get e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Electrodes,Genetics,Ions,Sensors,Soils Get e-Alerts
A Kinetics Study of the Bond Strength of Direct Bonded Wafers (1994)

In order to determine whether low temperature wafer bonding is thermodynamically prohibited or simply a slow kinetic reaction, a systematic evaluation of the interface bond kinetics of silicon direct wafer bonding was performed over the temperature range of 200–1000°C for annealing times ranging from 15 min to 45 days. The tensile, shear, and torsion tests were developed to monitor the strength kinetics of silicon and silicon dioxide bonded wafers. The strength evolution is found to obey an Arrhenius relationship over the temperature range of 200–1000°C. Tensile strength of Si‐Si bonded substrates varies from a minimum of 0.08 MPa at contact to a maximum of 4.25 MPa after high temperature thermal annealing. The failure of low temperature annealed samples to develop strong bonding in short periods of time has been correlated to microvoid formation at the interface as determined by TEM examination. Geometrical studies indicate that the microvoid formation is the result of trapped gases and can be reduced by appropriate choices of bonded geometries.
Phase II study evaluating lapatinib in combination with nab-paclitaxel in HER2-overexpressing metastatic breast cancer patients who have received no more than one prior chemotherapeutic regimen (2012)

Lapatinib, an oral, reversible inhibitor of epidermal growth factor receptor and human epidermal growth factor receptor 2 (HER2) tyrosine kinase, has proven antitumor activity in HER2-positive metastatic breast cancer (MBC). Nanoparticle albumin-bound paclitaxel (nab-paclitaxel) is indicated for the treatment of breast cancer after failure of combination chemotherapy for metastatic disease or relapse within 6 months of adjuvant chemotherapy. This was an open-label, single-arm, multicenter, Phase II study to evaluate the efficacy and safety of nab-paclitaxel plus lapatinib in women with HER2 over-expressing MBC who had received no more than one prior chemotherapeutic regimen. The primary efficacy endpoint was the overall response rate (ORR). This was defined as the percentage of patients having either a complete response (CR) or partial response (PR). Secondary efficacy endpoints included progression-free survival (PFS), overall survival, duration of response (DoR), time to response (TTR), and time to progression (TTP). Investigator-assessed ORR was 53 % (n = 32, 95 % confidence interval (CI): 40.7-66.0) with the majority of patient responses demonstrating a PR (47 %). Four (7 %) patient responses demonstrated a CR, and ten (17 %) a stable disease. The median Kaplan-Meier estimate of investigator-assessed PFS, DoR, TTR, and TTP was 39.7 weeks (95 % CI 34.1-63.9), 48.7 weeks (95 % CI 31.7-57.1), 7.8 weeks (95 % CI 7.4-8.1), and 41 weeks (95 % CI 39.1-64.6), respectively. Lapatinib 1,000 mg with nab-paclitaxel 100 mg/m(2) IV is feasible with manageable and predictable toxicity and an ORR of 53 % comparing favorably with other HER2-based combinations in this setting.
Growth of semipolar {11$ \bar 2 $2} GaN using SiNx intermediate layer by hydride vapor phase epitaxy (2014)

Abstract Semipolar {11‐22} plane GaN layer was grown using a SiN x intermediate layer by hydride vapor phase epitaxy (HVPE). By optimizing the deposition time of the SiN x intermediate layer, the dislocation density decreased compared to that of a conventional {11‐22} GaN layer. The reduction in the dislocation density was due to three dimensional regrowth of the {11‐22} GaN layer at the interface. However, basal plane stacking faults (BSFs) were increased by use of the SiN x intermediate layer, and with increasing the SiN x deposition time. (© 2014 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Scaling and Benchmarking Self-Supervised Visual Representation Learning (2019)

Self-supervised learning aims to learn representations from the data itself without explicit manual supervision. Existing efforts ignore a crucial aspect of self-supervised learning - the ability to scale to large amount of data because self-supervision requires no manual labels. In this work, we revisit this principle and scale two popular self-supervised approaches to 100 million images. We show that by scaling on various axes (including data size and problem 'hardness'), one can largely match or even exceed the performance of supervised pre-training on a variety of tasks such as object detection, surface normal estimation (3D) and visual navigation using reinforcement learning. Scaling these methods also provides many interesting insights into the limitations of current self-supervised techniques and evaluations. We conclude that current self-supervised methods are not 'hard' enough to take full advantage of large scale data and do not seem to learn effective high level semantic representations. We also introduce an extensive benchmark across 9 different datasets and tasks. We believe that such a benchmark along with comparable evaluation settings is necessary to make meaningful progress. Code is at: https://github.com/facebookresearch/fair_self_supervision_benchmark.
Polyvalent human immunodeficiency virus synthetic immunogen comprised of envelope gp120 T helper cell sites and B cell neutralization epitopes. (1989)

In previous studies, we have used antisera raised to envelope (env)-gene-encoded synthetic peptides to identify a region of (HIV) glycoprotein (gp) 120 env protein designated SP10 that contains a type-specific neutralizing determinant. To develop a polyvalent, synthetic peptide inoculum that can evoke both neutralizing antibodies and T cell proliferative responses to more than one HIV isolate, synthetic peptides containing type-specific neutralizing determinants of gp120 from HIV isolates HTLV-IIIB (IIIB), HTLV-IIIMN (MN) and HTLV-IIIRF (RF) were coupled to a 16 amino acid T cell epitope (T1) of HIV-IIIB gp120 and used to immunize goats. Goat antisera to each T1-SP10 peptide derived from the SP10 region of gp120 of IIIB, MN, and RF neutralized HIV isolates IIIB, MN and RF in a type-specific manner. Moreover, peripheral blood T cells from immunized goats also proliferated in a type-specific manner to peptides derived from gp120 of IIIB, MN, and RF. When combined in a trivalent inoculum, T1-SP10 peptides from HIV-1 isolates IIIB, MN, and RF evoked a high titered neutralizing antibody response to isolates IIIB, MN, and RF in goats and as well induced immune T cells to undergo blast transformation in the presence of peptides derived from gp120 of all three HIV isolates. The T1 portion of the T1-SP10 construct was shown to induce a B cell antibody response against determinants within the T1 peptide in addition to inducing T cell proliferative responses in immune goat T cells. Moreover, the SP10 portion of the T1-SP10 constructs not only induced B cell antibody production but also induced type-specific T cell proliferative responses localized to the C-terminal variable sequences of the SP10 peptides. Finally, the T1-SP10 peptide construct induced memory T cell proliferative responses to native gp120 env protein. Thus, combinations of homologous SP10 region synthetic peptides containing type-specific neutralizing determinants and T cell epitopes of HIV gp120 may be useful in man to elicit high titered neutralizing B cell responses and, as well, T cell responses to more than one HIV isolate.
Growth of Three-Shell Onionlike Bimetallic Nanoparticles (2003)

We show by molecular dynamics simulations on three systems (B/A=Pd/Ag, Cu/Ag, and Ni/Ag) that three-shell metallic nanoparticles made by a core of a metal A, an intermediate shell of metal B and an external shell of metal A (A-B-A nanoparticles) can be grown by deposition of B atoms onto an A core. The growth of the intermediate B shell is triggered by the fact that the most favorable positions for isolated B impurities inside A clusters are located just one layer below the cluster surface.
New Potential Monomers for Solid Phase Synthesis of Hydrazinopeptoids: theN α-Substituted-N β-Protected Hydrazinoglycines and Hydrazinoglycinals (2000)

Various N α-substituted-N β-protected hydrazinoglycinates 3, easily prepared from N α-substituted-N β-protected hydrazine and esters of bromoacetate, are described as precursors of new potential monomers for solid phase synthesis. An easily attainable deprotection route of 3 affords the N α-substituted-N β-protected hydrazinoglycines, or the N α-substituted-hydrazino glycinates. Reduction and oxidation of 3 lead to N α-substituted-N β-protected hydrazino glycinals 8.
Independent Photoreceptive Circadian Clocks Throughout Drosophila (1997)

Transgenic Drosophila that expressed either luciferase or green fluorescent protein driven from the promoter of the clock gene period were used to monitor the circadian clock in explanted head, thorax, and abdominal tissues. The tissues (including sensory bristles in the leg and wing) showed rhythmic bioluminescence, and the rhythms could be reset by light. The photoreceptive properties of the explanted tissues indicate that unidentified photoreceptors are likely to contribute to photic signal transduction to the clock. These results show that autonomous circadian oscillators are present throughout the body, and they suggest that individual cells in Drosophila are capable of supporting their own independent clocks.
Positive selection and sequence rearrangements generate extensive polymorphism in the gamete recognition protein bindin (1996)

Bindin is a gamete recognition protein of sea urchins that mediates species-specific attachment of sperm to an egg-surface receptor during fertilization. Sequences of bindin from closely related urchins show fixed species-specific differences. Within species, highly polymorphic bindin alleles result from point substitution, insertion/deletion, and recombination. Since speciation, positive selection favoring allelic variants has generated diversity in bindin polypeptides. Intraspecific bindin variation can be tolerated by the egg receptor, which suggests functional parallels between this system and other flexible recognition systems, including immune recognition. These results show that polymorphism in mate recognition loci required for rapid evolution of sexual isolation can arise within natural populations.
Particulate-Cell Interactions and Pulmonary Cytokine Expression (1997)

Jacob N. Finkelstein, Carl Johnston, Ted Barrett, , Particulate-Cell Interactions and Pulmonary Cytokine Expression, Environmental Health Perspectives, Vol. 105, Supplement 5: Particle Toxicity (Sep., 1997), pp. 1179-1182
p53 Down-regulates Human Matrix Metalloproteinase-1 (Collagenase-1) Gene Expression (1999)

Recent studies show that the p53 tumor suppressor protein is overexpressed in rheumatoid arthritis (RA) synovium and that somatic mutations previously identified in human tumors are present in RA synovium (Firestein, G. S., Echeverri, F., Yeo, M., Zvaifler, N. J., and Green, D. R. (1997) Proc. Natl. Acad. Sci. U. S. A. 94, 10895-10900; Firestein, G. S., Nguyen, K., Aupperle, K. R., Yeo, M., Boyle, D. L., and Zvaifler, N. J. (1996) Am. J. Pathol. 149, 2143-2151; Reme, T., Travaglio, A., Gueydon, E., Adla, L., Jorgensen, C., and Sany, J. (1998) Clin. Exp. Immunol. 111, 353-3581). We hypothesize that the abnormality of p53 seen in RA synovium may contribute to joint degeneration through the regulation of human matrix metalloproteinase-1 (hMMP-1, collagenase-1) gene expression. Transcription assays were performed with luciferase reporters driven by the promoter of the hMMP-1 gene or by a minimal promoter containing tandem repeats of the consensus binding sequence for activator protein-1, cotransfected with p53-expressing plasmids. The results revealed that (i) wild-type (wt) p53 down-regulated the promoter activity of hMMP-1 in a dose-dependent fashion; (ii) four of six p53 mutants (commonly found in human cancers) lost this repression activity; and (iii) this p53 repression activity was mediated at least in part by the activator protein-1 sites found in the hMMP-1 promoter. These findings were further confirmed by Northern analysis. The down-regulation of hMMP-1 gene expression by endogenous wt-p53 was shown by treatment of U2-OS cells, a wt-p53-containing osteogenic sarcoma line, and Saos-2 cells, a p53-negative osteogenic sarcoma line, with etoposide, a potent inducer of p53 expression. p53, activated by etoposide, appears to block hMMP-1 promoter activity induced by etoposide in U2-OS cells. In summary, we have shown for the first time that the hMMP-1 gene is a p53 target gene, subject to p53 repression. Because MMP-1 is principally responsible for the irreversible destruction of collagen in articular tissue in RA, abnormality of p53 may contribute to joint degeneration through the regulation of MMP-1 expression.
Therapy planning and monitoring of tissue ablation by high intensity focused ultrasound (HIFU) using imaging and simulation (2008)

High intensity focused ultrasound (HIFU) 'cooks' or ablates the target tissue at the focus of the ultrasound beam by thermal and cavitation effects. The HIFU is emerging as a non-invasive method for tumor ablation. The HIFU application for tissue ablation requires tools for dosimetry therapy planning, and real-time feedback of the intended and actual target tissues. Pretreatment planning is an important step for a successful HIFU therapy outcome. Typically, the therapy planning approach involves the use of pretreatment imaging data, defining the target and surrounding tissues by manual or semiautomatic segmentation, development of a 3-D anatomy model of the region of interest from segmentation or registration with a reference dataset, simulation of the HIFU beam and thermal dosimetry around the target tissue, display and 3-D visualization of imaging and simulation data, and review of the treatment plan options. Recent developments in therapy planning using imaging are targeted for specific applications such as prostate cancer using 3-D ultrasound images and uterine fibroids using MRI. However, significant developments have been accomplished in image guidance and feedback during the delivery of HIFU treatments. This talk reviews recent work towards therapy planning and presents approaches for developing strategies for HIFU therapy. It describes general and target-specific techniques and software tools for HIFU treatment planning using pretherapy imaging, and monitoring and controlling the HIFU delivery and tissue lesion using 1D, 2D and 3D ultrasound imaging. This aids development of optimized, high-precision HIFU applications for a controlled ablation of the target tumor. It also potentially reduces the overall treatment duration and exposure to non-target tissues.
AUGUSTUS: ab initio prediction of alternative transcripts (2006)

AUGUSTUS is a software tool for gene prediction in eukaryotes based on a Generalized Hidden Markov Model, a probabilistic model of a sequence and its gene structure. Like most existing gene finders, the first version of AUGUSTUS returned one transcript per predicted gene and ignored the phenomenon of alternative splicing. Herein, we present a WWW server for an extended version of AUGUSTUS that is able to predict multiple splice variants. To our knowledge, this is the first ab initio gene finder that can predict multiple transcripts. In addition, we offer a motif searching facility, where user-defined regular expressions can be searched against putative proteins encoded by the predicted genes. The AUGUSTUS web interface and the downloadable open-source stand-alone program are freely available from http://augustus.gobics.de.
Markerless Motion Capture using multiple Color-Depth Sensors (2011)

With the advent of the Microsoft Kinect, renewed focus has been put on monocular depth-based motion capturing. However, this approach is limited in that an actor has to move facing the camera. Due to the active light nature of the sensor, no more than one device has been used for motion capturing so far. In effect, any pose estimation must fail for poses occluded to the depth camera. Our work investigates on reducing or mitigating the detrimental effects of multiple active light emitters, thereby allowing motion capture from all angles. We systematically evaluate the concurrent use of one to four Kinects, including calibration, error measures and analysis, and present a time-multiplexing approach.
Targeted gene suppression by inducing de novo DNA methylation in the gene promoter (2014)

Epigenetic studies can provide useful data for the selection of suppressors in constructing therapeutic vectors for targeted gene silencing.
Fast occluded object tracking by a robust appearance filter (2004)

We propose a new method for object tracking in image sequences using template matching. To update the template, appearance features are smoothed temporally by robust Kalman filters, one to each pixel. The resistance of the resulting template to partial occlusions enables the accurate detection and handling of more severe occlusions. Abrupt changes of lighting conditions can also be handled, especially when photometric invariant color features are used. The method has only a few parameters and is computationally fast enough to track objects in real time.
The performance impact of flexibility in the Stanford FLASH multiprocessor (1994)

A flexible communication mechanism is a desirable feature in multiprocessors because it allows support for multiple communication protocols, expands performance monitoring capabilities, and leads to a simpler design and debug process. In the Stanford FLASH multiprocessor, flexibility is obtained by requiring all transactions in a node to pass through a programmable node controller, called MAGIC. In this paper, we evaluate the performance costs of flexibility by comparing the performance of FLASH to that of an idealized hardwired machine on representative parallel applications and a multiprogramming workload. To measure the performance of FLASH, we use a detailed simulator of the FLASH and MAGIC designs, together with the code sequences that implement the cache-coherence protocol. We find that for a range of optimized parallel applications the performance differences between the idealized machine and FLASH are small. For these programs, either the miss rates are small or the latency of the programmable protocol can be hidden behind the memory access time. For applications that incur a large number of remote misses or exhibit substantial hot-spotting, performance is poor for both machines, though the increased remote access latencies or the occupancy of MAGIC lead to lower performance for the flexible design. In most cases, however, FLASH is only 2%–12% slower than the idealized machine.