gebhart/patrepeval huggingface dataset:
Abstract 332: Extracellular matrix stiffness regulates metabolic state in metastatic, but not quiescent, breast carcinoma cells (2015)

Abstract Increased breast density is associated with a 4-6 fold increased risk of developing breast cancer, and is associated with an increase in deposition of extracellular matrix (ECM) proteins, most abundantly collagen I. Collagen, like other ECM proteins, plays a structural role fundamental to tissue organization. High levels of collagen deposition correspond with a stiffer ECM, which is emerging as an important regulator of cell proliferation and tumor progression. Our previously reported microarray implicated changes in mammary epithelial cell metabolism in response to increased matrix stiffness, consistent with the expanding role of the ECM in tumor cell signaling. Here we report that increased matrix stiffness regulates the expression of pyruvate dehydrogenase kinase 1, a key regulator between lactic acid production and pyruvate entry into the mitochondria, in highly metastatic 4T1 breast carcinoma cells. Interestingly, we do not observe this same metabolic regulation in quiescent (dormant) 4T07 tumor cells of the same lineage. These alterations in protein expression correlated to changes in cellular NADH metabolism observed by several independent approaches, including metabolic flux analysis and quantitative imaging fluorescence lifetime microscopy. Thus, we find that alterations in collagen stiffness cause metabolic shifts between oxidative phosphorylation and aerobic glycolysis in highly metastatic cells, but not in quiescent cells. These findings identify stiffness of the ECM as an important regulator of metabolic state, and further identify quiescence as a dominant trait that is not overcome by ECM stiffness. Citation Format: Brett A. Morris, Brian Burkel, Suzanne Ponik, Kevin Eliceiri, Julio Aguirre-Ghiso, John Condeelis, James Castracane, Patricia J. Keely. Extracellular matrix stiffness regulates metabolic state in metastatic, but not quiescent, breast carcinoma cells. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 332. doi:10.1158/1538-7445.AM2015-332
A design of subthreshold SRAM cell based on RSCE and RNCE (2015)

Traditional size-adjustment method of SRAM could not effectively work in the subthreshold region due to the severe penalty of cell area and supportive circuit. This paper introduces the reverse short channel effect and the reverse narrow channel effect to the size-adjustment method of the SRAM, which not only effectively solves the problem of the area penalty but also improves the static noise margin of the SRAM with fast read and write speed. Based on the SMIC 130nm process, subthreshold 10T SRAM cell is designed, and measurements indicate that the employment of the effects can promote the static noise margin by 30.5% compared to tradition ways. The SRAM can stably work at the voltage of 320mV.
Be ready to answer travelers’ questions about novel viruses (2013)

Families planning international travel this summer may not only seek guidance regarding immunizations and malaria prophylaxis, they also may have concerns regarding human infections with novel viruses. Pediatric health care professionals should be prepared to answer questions about emerging
Proposal to Subclassify Stage IV Gastric Cancer Into IVA, IVB, and IVM (2009)

Each subgroup of stage IV gastric cancer had different clinical outcomes, including histological behavior, recurrence pattern, survival, and prognostic factors. Therefore, subclassification of stage IV gastric cancer into IVA (T1-3N3M0), IVB (T4N1-3M0), and IVM (T[any]N[any]M1) might be useful for a more accurate prediction of prognosis and selection of appropriate therapeutic options.
Implementatie emissiemanagementsysteem grondgebonden teelten (2014)

Bij telers bleek een sterke behoefte voor een eenvoudiger en goedkopere versie van de eerder ontwikkelde lysimeter met automatische drainmeter. Daarom is er een zogenaamde “light” versie van de lysimeter ontwikkeld, met een handmatige meting van de drain. Verder is er een inventarisatie gedaan naar alternatieven voor de eerder gebruikte vochtsensoren. Helaas zijn er (nog) geen sensoren die aan álle randvoorwaarden voldoen voor grondgebonden kasteelten. Met de ontwikkelde tools: lysimeter, drainmeter, sensoren en modellen, kan de watergift en bemesting geoptimaliseerd worden en bijdragen tot emissievermindering bij grondteelten. Bedrijven die de tools actief gebruiken bleken in staat de uitspoeling sterk te kunnen beperken. De interpretatie van vochtsensoren blijft een lastig fenomeen, vanwege de grote verschillen tussen grondsoorten en aspecten van de bedrijfsvoering. Dit vraagt de nodige ervaring die in de loop van meerdere teelten en jaren moet worden opgedaan. De resultaten van de waterbalansen op de bedrijven laten zien dat het goed mogelijk is de berekeningen via het verdampingsmodel en de gegevens van de lysimeter met elkaar in overeenstemming te brengen via een calibratiefactor.
Development and Clinical Validation of an In Situ Biopsy-Based Multimarker Assay for Risk Stratification in Prostate Cancer (2015)

The 8-biomarker assay provided individualized, independent prognostic information relative to current risk stratification systems, and may improve the precision of clinical decision making following prostate biopsy.
Quantitating morphological changes in biological samples during scanning electron microscopy sample preparation with correlative super-resolution microscopy (2017)

Sample preparation is critical to biological electron microscopy (EM), and there have been continuous efforts on optimizing the procedures to best preserve structures of interest in the sample. However, a quantitative characterization of the morphological changes associated with each step in EM sample preparation is currently lacking. Using correlative EM and superresolution microscopy (SRM), we have examined the effects of different drying methods as well as osmium tetroxide (OsO4) post-fixation on cell morphology during scanning electron microscopy (SEM) sample preparation. Here, SRM images of the sample acquired under hydrated conditions were used as a baseline for evaluating morphological changes as the sample went through SEM sample processing. We found that both chemical drying and critical point drying lead to a mild cellular boundary retraction of ~60 nm. Post-fixation by OsO4 causes at least 40 nm additional boundary retraction. We also found that coating coverslips with adhesion molecules such as fibronectin prior to cell plating helps reduce cell distortion from OsO4 post-fixation. These quantitative measurements offer useful information for identifying causes of cell distortions in SEM sample preparation and improving current procedures.
Blind Clustering of Popular Music Recordings Based on Singer Voice Characteristics (2004)

September 01 2004 Blind Clustering of Popular Music Recordings Based on Singer Voice Characteristics Wei-Ho Tsai, Wei-Ho Tsai Institute of Information Science, Academia Sinica, Nankang, 115, Taipei, Taiwan, Republic of China, sovideo.iis.sinica.edu.tw/SLG, wesley@iis.sinica.edu.tw Search for other works by this author on: This Site Google Scholar Dwight Rodgers, Dwight Rodgers Institute of Information Science, Academia Sinica, Nankang, 115, Taipei, Taiwan, Republic of China, sovideo.iis.sinica.edu.tw/SLG, dwight00@alumni.princeton.edu Search for other works by this author on: This Site Google Scholar Hsin-Min Wang Hsin-Min Wang Institute of Information Science, Academia Sinica, Nankang, 115, Taipei, Taiwan, Republic of China, sovideo.iis.sinica.edu.tw/SLG, whm@iis.sinica.edu.tw Search for other works by this author on: This Site Google Scholar Author and Article Information Wei-Ho Tsai Institute of Information Science, Academia Sinica, Nankang, 115, Taipei, Taiwan, Republic of China, sovideo.iis.sinica.edu.tw/SLG, wesley@iis.sinica.edu.tw Dwight Rodgers Institute of Information Science, Academia Sinica, Nankang, 115, Taipei, Taiwan, Republic of China, sovideo.iis.sinica.edu.tw/SLG, dwight00@alumni.princeton.edu Hsin-Min Wang Institute of Information Science, Academia Sinica, Nankang, 115, Taipei, Taiwan, Republic of China, sovideo.iis.sinica.edu.tw/SLG, whm@iis.sinica.edu.tw Online Issn: 1531-5169 Print Issn: 0148-9267 © 2004 Massachusetts Institute of Technology2004 Computer Music Journal (2004) 28 (3): 68–78. https://doi.org/10.1162/0148926041790630 Cite Icon Cite Permissions Share Icon Share Facebook Twitter LinkedIn MailTo Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Search Site Citation Wei-Ho Tsai, Dwight Rodgers, Hsin-Min Wang; Blind Clustering of Popular Music Recordings Based on Singer Voice Characteristics. Computer Music Journal 2004; 28 (3): 68–78. doi: https://doi.org/10.1162/0148926041790630 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsComputer Music Journal Search Advanced Search This content is only available as a PDF. © 2004 Massachusetts Institute of Technology2004 Article PDF first page preview Close Modal You do not currently have access to this content.
8-Bit Approximations for Parallelism in Deep Learning (2015)

The creation of practical deep learning data-products often requires parallelization across processors and computers to make deep learning feasible on large data sets, but bottlenecks in communication bandwidth make it difficult to attain good speedups through parallelism. Here we develop and test 8-bit approximation algorithms which make better use of the available bandwidth by compressing 32-bit gradients and nonlinear activations to 8-bit approximations. We show that these approximations do not decrease predictive performance on MNIST, CIFAR10, and ImageNet for both model and data parallelism and provide a data transfer speedup of 2x relative to 32-bit parallelism. We build a predictive model for speedups based on our experimental data, verify its validity on known speedup data, and show that we can obtain a speedup of 50x and more on a system of 96 GPUs compared to a speedup of 23x for 32-bit. We compare our data types with other methods and show that 8-bit approximations achieve state-of-the-art speedups for model parallelism. Thus 8-bit approximation is an efficient method to parallelize convolutional networks on very large systems of GPUs.
NHLBI support of systems biology (2013)

The National Heart, Lung, and Blood Institute (NHLBI) has recognized the importance of the systems biology approach for understanding normal physiology and perturbations associated with heart, lung, blood, and sleep diseases and disorders. In 2006, NHLBI announced the Exploratory Program in Systems Biology program, followed in 2010 by the NHLBI Systems Biology Collaborations program. The goal of these programs is to support collaborative teams of investigators in using experimental and computational strategies to integrate the component parts of biological networks and pathways into computational models that are based firmly on and validated using experimental data. These validated models are then applied to gain insights into the mechanisms of altered system function in disease, to generate novel hypotheses regarding these mechanisms that can be tested experimentally, and to then use the results of experiments to refine the models. This perspective reviews the history of dedicated systems biology programs at NHLBI and reviews some promising directions for future research in this area.
Alternative Injection Schemes for the NSLS-II Storage Ring (2009)

KEK has been investigating the use of pulsed multipoles for injection the Photon Factory and for KEKB. A pulsed quadrupole magnet was installed in the PF. It worked successfully with the exception that it caused beam envelope oscillations when pulsed. They have subsequently designed a pulsed sextupole for injection. The goal would be to have a null field for the stored beam with no gradient and still have an off axis field for the injected beam. In this document we look at the possibility of using a pulsed sextupole in the NSLS-II Storage Ring for injection.
Hyponatremia Predicts Right Heart Failure and Poor Survival in Pulmonary Arterial Hypertension (2008)

Hyponatremia is strongly associated with right heart failure and poor survival in PAH.
Preconditioning Concepts in Polymer Flooding in High-Salinity Reservoirs: Laboratory Investigations and Case Histories (1990)

Summary In polymer-flood field projects with partially hydrolized polyacrylamide (PH PAA) solutions, Deutsche Texaco A.G. (DTA) has applied two methods of preconditioning: a preflush with fresh water and the use of a relatively small slug of a less-salt-sensitive polymer. Results of laboratory work that led to an improved preconditioning concept with polymer are described. Case histories of two projects with two different preconditioning processes are presented and discussed in detail.
Oxygen-oxidation of coal tar pitch in NaOH solutions. (1990)

コールタールピヅチ(C:92.8%)を水酸化ナトリウム(NaOH)溶液中において酸素酸化した。NaOH濃度,反応温度,反応時聞ダ酸素分圧,かきまぜ速度の影響を検討し.水可溶芳香族酸生成の最適条件を明らかにした。最適条件はNaOH濃度1～5mol/kg-H20,反応温度538K程度,反応時間2～3時間,酸素分圧5MPaであり,水可溶芳香族酸収率は仕込ピッチに対し,約50wt%であった。水可溶芳香族酸中には,フタル酸,1,2, 3-ベンゼントリカルボン酸,1,2,3,5-ベンゼンテトラカルボン酸,1,2,4-ベンゼントリカルボン酸をはじめとするベンゼンカルボン酸が多く.18～51wt%に達した.ピッチの酸化過程は定性的には,高炭化度炭の酸化過程と類似するが,最適条件下でも30%程度の未反応ピッチが残留した。ピヅチ反応率を高めるためには,ピッチの前処理などの工夫が必要であると考えられる。
An ocular perfusion system. (1980)

An enclosed system is described utilizing an osmotically driven pump to continuously deliver a solution to a variety of intraocular locations. The behavior of this system is illustrated by using it to measure the fluorescein turnover rate in the anterior chamber.
Parametric Study and Optimization of a Piezoelectric Energy Harvester from Flow Induced Vibration (2018)

Self-powered systems have become the need of the hour and several devices and techniques were proposed in favour of this crisis. Among the various sources, vibrations, being the most practical scenario, is chosen in the present study to investigate for the possibility of harvesting energy. Various methods were devised to trap the energy generated by vibrating bodies, which would otherwise be wasted. One such concept is termed as flow-induced vibration which involves the flow of a fluid across a bluff body that oscillates due to a phenomenon known as vortex shedding. These oscillations can be converted into electrical energy by the use of piezoelectric patches. A two degree of freedom system containing a cylinder as the primary mass and a cantilever beam as the secondary mass attached with a piezoelectric circuit, was considered to model the problem. Three wake oscillator models were studied in order to determine the one which can generate results with high accuracy. It was found that Facchinetti model produced better results than the other two and hence a parametric study was performed to determine the favourable range of the controllable variables of the system. A fitness function was formulated and optimization of the selected parameters was done using genetic algorithm. The parametric optimization led to a considerable improvement in the harvested voltage from the system owing to the high displacement of secondary mass.
Biocatalysis on Porous Materials (2018)

Edited by Vincent Blay, Luis F. Bobadilla, Alejandro Cabrera-García.
The N-terminal half of the core protein of hepatitis C virus is sufficient for nucleocapsid formation (2004)

The core (C) protein of hepatitis C virus (HCV) appears to be a multifunctional protein that is involved in many viral and cellular processes. Although its effects on host cells have been extensively discussed in the literature, little is known about its main function, the assembly and packaging of the viral genome. We have studied the in vitro assembly of several deleted versions of recombinant HCV C protein expressed in E. coli. We demonstrated that the 75 N-terminal residues of the C protein were sufficient to assemble and generate nucleocapsid-like particles (NLPs) in vitro. However, homogeneous particles of regular size and shape were observed only when NLPs were produced from at least the first 79 N-terminal amino acids of the C protein. This small protein unit fused to the endoplasmic reticulum-anchoring domain also generated NLPs in yeast cells. These data suggest that the N-terminal half of the C protein is important for formation of NLPs. Similarities between the HCV C protein and C proteins of other members of the Flaviviridae are discussed.
Akt pathway activation converts anaplastic astrocytoma to glioblastoma multiforme in a human astrocyte model of glioma. (2001)

Human malignant gliomas are thought to develop as the result of stepwise accumulations of multiple genetic alterations. Recently, we showed that E6/E7-mediated inactivation of p53/pRb, ras pathway activation (initiated by expression of mutant H-Ras), and expression of human telomerase reverse transcriptase (hTERT) in combination converted normal human astrocytes into cells that formed intracranial tumors resembling human anaplastic astrocytoma (AA). In this study, we created human astrocytes that, in addition to expressing E6/E7, hTERT, and Ras, also expressed a constitutive activated form of Akt intended to mimic the Akt activation noted in grade IV glioblastoma multiforme (GBM). Although these cells grew no differently than astrocytes expressing E6, E7, and H-Ras in vitro or in the first 28 days following s.c. implantation, they ultimately formed tumors four to six times larger than those formed by the E6/E7/hTERT/Ras cells. Unlike the poorly vascularized, necrosis-free AA formed by E6/E7/hTERT/Ras cells, the tumors formed by s.c. or intracranial injection of Akt-expressing cells had large areas of necrosis surrounded by neovascularization and were consistent in appearance with grade IV human GBM. These results show that activation of the Akt pathway is sufficient to allow conversion of human AA to human GBM.
DrillCutTM vs. VersaCutTM prostate tissue morcellation devices after holmium laser enucleation: A prospective, randomized controlled trial (2018)

Despite the small sample size, the DrillCut™ was associated with lower morcellation rate when compared with the VersaCut<sup>TM</sup>. However, this difference may not be clinically significant. Although both morcellators were comparable in their safety, the DrillCut<sup>TM</sup> was associated with higher cost of disposables when compared with the VersaCut<sup>TM</sup>.
Current Therapies for ANCA-Associated Vasculitis (2014)

The ANCA-associated vasculitides, granulomatosis with polyangiitis (GPA, formerly Wegener's), microscopic polyangiitis (MPA), and eosinophilic granulomatosis with polyangiitis (EGPA, formerly Churg-Strauss), are a group of multisystem autoimmune diseases characterized by necrotizing small- to medium-vessel vasculitis and the presence of anti-neutrophil cytoplasmic antibodies. Current therapeutic strategies consist of glucocorticoids in conjunction with either conventional or biologic agents for both induction of remission and remission maintenance. Treatment goals include reducing toxicity of induction therapy, preventing disease relapse, and limiting overall accrual of both disease-related damage and treatment-related morbidity. Future research directions include investigation of the optimal duration and frequency of maintenance therapy as well as development of targeted therapeutic agents, which is enhanced by emerging insights into disease pathogenesis.
Anethole inhibits growth of recently emerged multidrug resistant toxigenic <i>Vibrio cholerae</i> O1 El Tor variant strains <i>in vitro</i> (2015)

To search natural compounds having inhibitory effect on bacterial growth is important, particularly in view of growing multidrug resistant (MDR) strains of bacterial pathogens. Like other bacterial pathogens, MDR Vibrio cholerae, the causative agent of diarrheal disease cholera, is becoming a great concern. As an approach of searching new antimicrobial agents, here, we show that anethole, a well-studied natural component of sweet fennel and star anise seeds, could potentially inhibit the growth of MDR O1 El Tor biotype, the ongoing 7th cholera pandemic variant strains of toxigenic V. cholerae. The minimum inhibitory concentration (MIC) of anethole against diverse O1 El Tor biotype strains is evaluated as 200 µg/ml. Moreover, the effect of anethole is bactericidal and exerts rapid-killing action on V. cholerae cells. This study is the first report which demonstrates that anethole, purified from natural compound, is a potent inhibitor of growth of toxigenic V. cholerae. Our data suggest that anethole could be a potential antimicrobial drug candidate, particularly against MDR V. cholerae mediated infections.
Ratio method for 11C-PBR28 detects increase in translocator protein binding in Alzheimer’s disease (2015)

250 Objectives Patients with Alzheimer’s disease (AD) have increased expression of the 18 kDa translocator protein (TSPO), a marker of microglial activation. Measuring TSPO with second generation PET radioligands requires arterial catheterization and determination of TSPO genotype, as a polymorphism causes differential affinity binding. We sought to determine if a ratio method for 11C-PBR28 detected differences between AD patients and controls without requiring arterial catheterization or TSPO genotyping. Methods Twenty-one AD patients, 15 mild cognitive impairment patients, and 25 older controls underwent 11C-PBR28 imaging. PET images were analyzed by either 1) two-tissue compartment model with metabolite corrected arterial input function to calculate total distribution volume corrected for free fraction of radioligand in plasma (VT/fP), or 2) a standardized uptake ratio (SUVR) method using images 60-90 min post-injection with cerebellum as pseudo-reference region. Results Absolute binding (VT/fP) did not differ in cerebellum among groups. Both VT/fP and SUVR were greater in AD patients than controls in temporo-parietal regions. However, SUVR resulted in lower P values, with more regions reaching statistical significance. Variability (measured as %coefficient of variance) was ~60% lower for SUVR. TSPO genotype correction improved sensitivity to detect group differences for both VT/fP and SUVR. Both VT/fP and SUVR correlated with Clinical Dementia Rating scale score in middle and inferior temporal cortex. Conclusions SUVR method for 11C-PBR28 detects differences between AD patients and controls with even greater sensitivity than VT/fP due to lower variability. SUVR also reduces scan time and removes need for arterial catheterization, which is expected to improve patient tolerability. This ratio method does not completely remove effect of TSPO affinity status and genotyping is still recommended.
An expert system to assist neonatal intensive care (1997)

An expert system for neonatal intensive care (ESNIC) for the management of mechanically ventilated neonates on intermittent positive pressure ventilation (IPPV) has been developed. The system uses the rule based expert system shell XiPlus (Inference Inc.) and runs on an IBM-compatible PC. The rules have been derived from the knowledge of two consultant paediatricians. The inputs to the system are the current ventilator settings, blood gas tensions and pH. The output of the system is a set of suggested new ventilator settings. The aim of the system is to provide ventilator settings which will maintain the arterial blood gas tensions within an acceptable range, reducing pressures whenever feasible and increasing pressures only as a last resort. In addition, ESNIC provides data archiving, graphical displays of all parameters, ventilation and discharge summaries. With the 63 patients in the study ESNIC was consulted for 76% of all ventilator adjustments and the advice given was accepted on 83% of these occasions.