gebhart/patrepeval huggingface dataset:
An efficient grid layout algorithm for biological networks utilizing various biological attributes (2007)

Layouts of the new grid layout algorithm are compared with that of the previous algorithm and human layout in an endothelial cell model, three times as large as the apoptosis model. The total cost of the result from the new grid layout algorithm is similar to that of the human layout. In addition, its convergence time is drastically reduced (40% reduction).
Optimal structure sampling for etch model calibration (2017)

Successful patterning requires good control of the photolithography and etch processes. While compact litho models, mainly based on rigorous physics, can predict very well the contours printed in photoresist, pure empirical etch models are less accurate and more unstable. Compact etch models are based on geometrical kernels to compute the litho-etch biases that measure the distance between litho and etch contours. The definition of the kernels as well as the choice of calibration patterns is critical to get a robust etch model. This work proposes to define a set of independent and anisotropic etch kernels designed to capture the finest details of the resist contours and represent precisely any etch bias. By evaluating the etch kernels on various structures it is possible to map their etch signatures in a multi-dimensional space and analyze them to find an optimal sampling of structures to train an etch model. The method was specifically applied to a contact layer containing many different geometries and was used to successfully select appropriate calibration structures. The proposed kernels evaluated on these structures were combined to train an etch model significantly better than the standard one.
Automatic Acquisition of Semantics from Text for Semantic Work Environments (2011)

This chapter presents an overview of techniques for semi-automatic extraction of semantics from text, to be integrated in a Semantic Work Environment. A focus is placed on the disambiguation of polysemous words, the automatic identification of entities of interest, and the annotation of relationships between them. The application of these topics falls into the intersection of three dynamic fields: the Semantic Web, Wiki and other work environments, and Information Extraction from text.
A phase I study of the raf kinase/VEGF-R inhibitor sorafenib in combination with bortezomib in patients with advanced malignancy (2008)

2569 Background: This phase I study was undertaken to define the toxicity and the maximum tolerated dose of the combination of sorafenib (BAY43–9006; a Raf kinase /VEGFR2 inhibitor) with bortezomib (a proteasome inhibitor) in patients (pts) with advanced solid tumors. The study also has an expanded cohort at MTD that will enroll pts with myeloma/ CLL to evaluate the pharmacodynamic/ pharmacokinetic parameters of therapy. Methods: Pts over 18 yrs with cytologic or histologic proof of unresectable solid tumors were enrolled to determine the MTD of the combination. Pts were treated with daily sorafenib and bortezomib on days 1, 4, 8 and 11 of a 3-week cycle. Toxicities were graded by the NCI CTC v.3. Pts are followed for a maximum of 3 mos after they go off treatment. The dose-escalation schema is in the table below. Results: Twelve pts (7 females, median age 63) have been enrolled on this study (6 each at dose level and 2). Tumor types included renal (3), lung (3), pancreas (2), breast (1), adrenal gland (1), melanoma (1) and spindle cell tumor (1). All pts are off treatment. Eight of these pts went off treatment due to disease progression (5 pts were treated at dose level 1 and 3 pts were treated at dose level 2). All 12 pts were evaluable for dose-limiting toxicity (DLT) analysis. DLT was seen in two pts at dose level 2 (one pt had grade 3 pain-abdominal and grade 4 lipase; and one pt had grade 3 vomiting). As a result, dose level 1 was declared as MTD. No grade 4 hematologic toxicities or grade 5 toxicities were seen. One grade 4 fatigue and lipase were reported in cycle 1. A median of 2 cycles of therapy (range 1–5) were administered. One pt had a partial response (renal), 4 had stable disease, 5 had progression and two pts were too early to evaluate for response. Conclusions: The combination of sorafenib and bortezomib appear to have antitumor activity and based on this study we recommend a dose of sorafenib at 200 mg twice daily continuously with bortezomib 1 mg/m2 on days 1, 4, 8, 11 of a 21 day cycle for further studies. Dose Escalation Schema Dose Level sorafenib (mg BID) bortezomib (mg/m2) 1 (Starting dose) 200 1.0 2 200 1.3 3 400 1.3 No significant financial relationships to disclose.
Normalized Cross-Correlation of Subsequent Strides for Evaluation of Walking Stability (2010)

Evaluation of walking stability is essential for the elderly population to prevent possible falls due to degradation of their walking stability caused by aging. Previous studies mainly focused on center of pressure (COP) and center of body mass (COM) and their relationship during walking. However COM can not be directly measured and existing COP parameters are mainly investigated within one stride and their effectiveness is not conclusive. In this study, new parameters are proposed based on normalized cross-correlation of subsequent strides (NCSS), derived from comparison of subsequent strides of foot plantar pressure. The mean and standard deviation of NCSS are calculated for three walking conditions that are progressively less stable (1 - normal walking, 2 - walking with eyes closed, and 3 - walking with eyes closed after being spun around) for six healthy subjects. Results show that the NCSS can effectively distinguish normal walking (1) and the less stable walking with eyes closed after being spun around (3). The mean of NCSS decreases from stable to less stable walking conditions, whereas the corresponding standard deviation of NCSS increases. For each subject the value of NCSS of walking with eyes closed (2) is between those of the other two walking conditions (1 and 3), although the value varies somewhat, depending on the controllability and adaptability of the subject.
ChemInform Abstract: Transition Metal Methylene Complexes. Part 58. Covalent AgRh<sub>2</sub>‐ and Ionic AgRh<sub>4</sub> Cluster Compounds via Addition of Silver(I) Halides to a Rhodium ‐ Rhodium Double Bond. (1986)

Abstract Silber(I)‐Salze reagieren mit dem Organorhodium‐Komplex (I) unter elektrophiler Addition an die Rh ‐ Rh‐Doppelbindung unter Bildung der kovalenten AgRhz‐Derivate (II) oder der salzartigen AgRm‐Clusterverbindungen (III).
Transdisciplinary Biomedical Instrumentation Laboratory (2020)

Abstract Transdisciplinary Biomedical Instrumentation LaboratoryThe paper describes a transdisciplinary biomedical instrumentation laboratory that will serve as aresearch, educational, and training facility for Biomedical Engineering, Biomedical EngineeringTechnology, and Nursing students of Drexel University. Each group of students will have theopportunity to participate in high impact laboratory experiences designed to promote clinicalefficiency and efficacy while improving medical device design and maintenance and thusreducing medical errors. This will involve creating teams of biomedical engineering, biomedicalengineering technology, and nursing students who participate in a series of laboratoryexperiences and clinical simulations designed to foster a deeper appreciation of the issues andopportunities faced by individuals in these different occupations. In a pilot-scale biomedicalinstrumentation laboratory, biomedical applications and techniques will be studied throughexperiments that closely simulate health care-relevant processes or scenarios. Student teams ofbiomedical engineers, technologists, and nursing students will work together to understandingfundamental issues involving medical device performance and maintenance. These teams willalso participate in clinical simulations so that biomedical engineering and technology studentswill come to understand the environment in which their devices must perform, the individualusers’ needs and expectations, and the workload as it relates to maintenance. The developedlaboratory procedures will expose students to typical applications of medical equipment invarious medical settings and will include characterization of this equipment based on specificregulations of health care industry, including safety and effectiveness issues.
Artificial Graphene with Tunable Interactions (2013)

We create an artificial graphene system with tunable interactions and study the crossover from metallic to Mott insulating regimes, both in isolated and coupled two-dimensional honeycomb layers. The artificial graphene consists of a two-component spin mixture of an ultracold atomic Fermi gas loaded into a hexagonal optical lattice. For strong repulsive interactions, we observe a suppression of double occupancy and measure a gapped excitation spectrum. We present a quantitative comparison between our measurements and theory, making use of a novel numerical method to obtain Wannier functions for complex lattice structures. Extending our studies to time-resolved measurements, we investigate the equilibration of the double occupancy as a function of lattice loading time.
Supplementary Data from Histone Deacetylase 8 in Neuroblastoma Tumorigenesis (2023)

Supplementary Data from Histone Deacetylase 8 in Neuroblastoma Tumorigenesis
A Study of Smoothing Algorithms for Item Categorization on e-Commerce Sites (2010)

One central issue in a long-tail online marketplace such as eBay is to automatically put user self-input items into a catalog in real time. This task is extremely challenging when the inventory scales up, the items become ephemeral, and the user input remains noisy. Indeed, catalog learning has emerged as a key technical property for other major online ecommerce applications including search and recommendation. We formulate the item cataloging task as a Bayesian classification problem, which shall scale well in very large data set and have good online prediction performance. The inherent data sparseness issue, especially for those tail categories, is key to the overall model performance. We address the data sparseness issue by adapting statistically sound smoothing methods well studied in language modeling tasks. However, there are data characteristics specific to the ecommerce domain, including short yet focused item description, very large and hierarchical catalog taxonomy, and highly skewed distribution over types of items. We investigate these domain-specific regularities empirically, and report practically significant results with real-world true-scale data.
Bridging homogeneous and heterogeneous catalysis with CAN·SiO<sub>2</sub>as a solid catalyst for four-component reactions for the synthesis of tetrasubstituted pyrroles (2014)

The attractive features of this methodology are newer and greener methods, simple procedures, reusability and high efficiency of the catalyst and easy workability.
1,6-Dimethyl-4-oxo-1,6,7,8,9,9a-hexahydro-4H-pyrido(1,2-a)- pyrimidine-3-carboxamide (Ch-127) protects against the intestinal damage in rats caused by two weeks' daily administration of indomethacin. (1987)

1,6-Dimethyl-4-oxo-1,6,7,8,9,9a-hexahydro-4H-pyrido 1,2-a pyrimidine-3-carboxamide (Ch-127) significantly inhibited the intestinal ulceration induced by a single dose of indomethacin (15 mg/kg p.o.). Moreover, indomethacin produced 75% lethality in the dose of 3.5 mg/kg p.o. administered daily for 2 weeks. The concurrent daily administration of Ch-127 (50 mg/kg p.o. +25 mg/kg s.c.) with indomethacin prevented the gastrointestinal mucosa from histologically detectable changes, and none of the animals died. The 80% lethality following the daily administration of naproxen (60 mg/kg p.o.) for two weeks was also significantly decreased by combining it with Ch-127 (50 mg/kg p.o.).
Inhibition of MAPK Kinase Signaling Pathways Suppressed Renal Cell Carcinoma Growth and Angiogenesis <i>In vivo</i> (2008)

The mitogen-activated protein kinase (MAPK) signaling pathways play essential roles in cell proliferation and differentiation. Recent studies also show the activation of MAPK signaling pathways in tumorigenesis, metastasis, and angiogenesis of multiple human malignancies, including renal cell carcinoma (RCC). To assess the role of this pathway in regulating the proliferation and survival of RCC cells, we first examined the expression of MAPK kinase (MKK) and MAPK in clear cell RCC and confirmed the overexpression of MKK1 and extracellular signal-regulated kinase 2 (ERK2) in these tumors. We then tested the effects of pharmacologic inhibition of MKK on human RCC cell lines, both in vitro and in vivo, using anthrax lethal toxin (LeTx), which cleaves and inactivates several MKKs. Western blotting showed that the phosphorylation levels of ERK, c-Jun-NH(2) kinase, and p38 MAPK decreased after 72 h of LeTx treatment. Exposure to LeTx for 72 h reduced cell proliferation by 20% without significant effects on cell cycle distribution and apoptosis. Anchorage-independent growth of RCC cells was dramatically inhibited by LeTx. In vivo studies showed that tumor growth of RCC xenografts could be suppressed by LeTx. Extensive necrosis and decreased tumor neovascularization were observed after LeTx treatment. LeTx also showed direct inhibition of proliferation of endothelial cells in vitro. Our results suggest that suppression of one or more MAPK signaling pathways may inhibit RCC growth through the disruption of tumor vasculature.
Prostatic Acid Phosphatase Is Not a Prostate Specific Target (2007)

Prostatic acid phosphatase (PAP) is currently evaluated as a target for vaccine immunotherapy of prostate cancer. This is based on the previous knowledge about secretory PAP and its high prostatic expression. We describe a novel PAP spliced variant mRNA encoding a type I transmembrane (TM) protein with the extracellular NH(2)-terminal phosphatase activity and the COOH-terminal lysosomal targeting signal (YxxPhi). TM-PAP is widely expressed in nonprostatic tissues like brain, kidney, liver, lung, muscle, placenta, salivary gland, spleen, thyroid, and thymus. TM-PAP is also expressed in fibroblast, Schwann, and LNCaP cells, but not in PC-3 cells. In well-differentiated human prostate cancer tissue specimens, the expression of secretory PAP, but not TM-PAP, is significantly decreased. TM-PAP is localized in the plasma membrane-endosomal-lysosomal pathway and is colocalized with the lipid raft marker flotillin-1. No cytosolic PAP is detected. We conclude that the wide expression of TM-PAP in, for instance, neuronal and muscle tissues must be taken into account in the design of PAP-based immunotherapy approaches.
A Review of Texture Classification Methods and Databases (2017)

In this survey, we present a review of methods and resources for texture recognition, presenting the most common techniques that have been used in the recent decades, along with current tendencies. That said, this paper covers since the most traditional approaches, for instance texture descriptors such as gray-level co-occurence matrices (GLCM) and Local Binary Patterns (LBP), to more recent approaches such as Convolutional Neural Networks (CNN) and multi-scale patch-based recognition based on encoding approaches such as Fisher Vectors. In addition, we point out relevant references for benchmark datasets, which can help the reader develop and evaluate new methods.
Coculture System to Assess Biocompatibility of Candidate Orthopaedic Materials (1999)

When examining the biocompatibility of materials for orthopaedic use, it is important to examine the in vitro response of osteoblasts and macrophages to the material. The purpose of the current study was to develop an in vitro system that more accurately models the dynamic macrophage and osteoblast interactive response to biomaterials. A filter coculture system was designed that enables two cell types to be separated, while permitting cellular mediators to diffuse through its porous membrane. Using the filter coculture system, macrophage and osteoblast interaction in response to polymethylmethacrylate particle exposure was examined. As a marker of bone resorption potential, the level of prostaglandin E2 released from the macrophage and osteoblast coculture was compared with traditionally used in vitro culture systems. Cells interacting in the filter coculture system were found to produce prostaglandin E2 levels significantly greater than those of traditional conditioned media transfer systems. This filter coculture system offers an in vitro model that accounts for the continual cell to cell mediator interaction of two cell types simultaneously exposed to an implant material. This system may be useful in examining the biocompatibility of candidate materials at the bone interface, and thus elucidating the mechanisms of material induced bone resorption.
Performance of Ultra-Thin Film Solid Oxide Fuel Cells in Methane and Natural Gas Fuels: The Role of Electrode Microstructure (2013)

This proceedings manuscript describes representative results of thin film micro-solid oxide fuel cells (micro-SOFCs) utilizing nano-porous ruthenium (Ru) and Ru – gadolinia doped ceria (CGO) nano-composite anodes, investigated for operation with various fuels. 8 mol% yttria-stabilized zirconia (8YSZ) and compositionally graded CGO-8YSZ thin films were fabricated on silicon substrates as self-supported electrolytes. Performance of devices integrating such electrodes and electrolytes are presented with methane and natural gas as fuels. Oscillations in fuel cell current were observed when nano-porous Ru and Ru-CGO anode micro-SOFCs were operated at constant voltage with methane. Degradation mechanisms of pure metallic electrodes are then compared to composite electrodes at the intermediate temperature range of 300 - 500 °C. New synthesis methods to realize percolating ultra-thin composite electrodes is highlighted as a promising research direction.
Foaming Performance of Linear Polypropylene Ionomers (2022)

Linear polypropylene (PP) exhibits poor foamability because of its inherently low melt strength. Incorporation of long-chain branches is a common approach to increase melt strength; however, it is a costly process. To bridge this gap, we set out to study the effect of ionic content on the foaming behavior of linear PP ionomers using a PP homopolymer as a control and a commercial high melt strength long-chain branched PP as a benchmark. Small-angle X-ray scattering confirms the presence of ion clusters in the ionomers, which act as physical cross-linking points as was recently shown, providing enhancement to the dynamic moduli, complex viscosity, and strain hardening behavior, even at ion contents below 0.1 mol %. We found that, upon foaming, the PP ionomer with a higher ionic content exhibited higher foam uniformity, higher cell density (∼108 cells/cm3), and smaller cell size (as small as 37 μm) compared to those of its linear counterpart. Furthermore, the linear ionomer resin and the commercial branched PP showed similar foam morphologies and mechanical responses under cyclic indentations over the temperature range 155–175 °C. These findings reveal a new, and potentially cost-effective, route to produce high performance foams using linear PPs that are compliant to industrial standards.
P1‐421: Topographic extent of cerebral hypometabolism predicts time of conversion from aMCI to Alzheimer's disease: Data from the Alzheimer's Disease Neuroimaging Initiative (2010)

Clinical trials to prevent Alzheimer's disease (AD) would be more efficient with a biomarker that could determine whether and when dementia is likely to develop in subjects with memory loss but no functional impairment. Hypometabolism measured with fluorodeoxyglucose positron emission tomography (FDG-PET) begins before deficits are apparent and becomes more extensive as cognitive deficits evolve from amnestic mild cognitive impairment (aMCI) to AD. Consequently, quantitative FDG-PET measures may help identify patients with prodromal AD who are likely to become demented over the brief course of a clinical trial. Examine the relationship between the topographic extent of glucose hypometabolism and timing of conversion to AD in subjects with aMCI. We evaluated all 161 baseline FDG-PET scans in subjects with clinically diagnosed aMCI followed for at least 1 year as part of the Alzheimer's Disease Neuroimaging Initiative (ADNI). Each scan was analyzed with Neurostat, providing 3D-stereotactic surface projection (3D-SSP) maps of glucose metabolism relative to pons and corresponding Z-score maps compared to 27 cognitively normal subjects (14 men, 13 women, mean age 69.6 ± 7.7). The number of pixels with metabolism 3 or more standard deviations below normal subjects was compared to the clinical judgment, independent of imaging results, of progression to AD at 6 and 12 months. 14.3% of aMCI subjects (14 men, 9 women, mean age 75.3 ± 6.5) converted from MCI to AD over 12 months. Gender and age did not differ from those who continued to have aMCI (92 men, 46 women, mean age 75.4 ± 6.5). FDG-PET scans in converters had significantly more hypometabolic pixels (511 ± 627 vs. 168 ± 283, p < 0.02). The extent of hypometabolism was greater in the 5 who converted after 6 months (1128 ± 1000 pixels) than the 18 that converted after 12 months (340 ± 363 pixels). The topographic extent of glucose hypometabolism on FDG-PET predicts the likelihood of conversion to AD in aMCI subjects. More extensive hypometabolism indicates conversion will occur sooner. Outcomes would be more predictable and clinical trials of prodromal AD more efficient using FDG-PET for subject selection.
P1‐007: POOR SLEEP IS ASSOCIATED WITH CSF‐MARKERS OF ALZHEIMER'S DISEASE IN 70‐YEAR‐OLDS WITHOUT DEMENTIA (2018)

It may be possible to detect changes in cerebrospinal fluid (CSF) markers decades before onset of Alzheimer's disease (AD). In order to find possible targets for treatment and prevention there is a need to know more about the clinical correlates of this preclinical phase. The aim of this study was to study the associations between subjective sleep disturbance and CSF-markers of Alzheimer's Disease in a population-based sample of 70-year-olds without dementia. A representative sample of 70-year-olds (N=1203, response rate=72%) were examined between 2014-2016 with comprehensive neuropsychiatric examinations. A subsample of 322 individuals (26%) consented to a lumbar puncture. Seven individuals were excluded due to dementia, leaving 315 for the analysis. Sleep disturbance was assessed with a subjective experience of decreased or increased sleep during the past month and a question on sleep medication. CSF-markers included Aβ42/Aβ40, total-tau (t-tau), phospho-tau (p-tau), neurofilament light (NFL), and neurogranin. CSF-markers were analyzed in ratio to Aβ42. We fitted linear multiple regression models to the data for each combination of subjective sleep disturbance and CSF-markers while controlling for several factors separately within a Bayesian framework. The parameter estimates were derived through a numerical approximation using a Markov Chain Monte Carlo (MCMC) Gibbs sampling in JAGS. Individuals with sleep disturbance and those taking sleep medication had lower ratio of Aβ42/Aβ40 than those without but there were no direct association between sleep measures and t-tau/Aβ42, p-tau/Aβ42, NFL/Aβ42 or neurogranin/Aβ42. However, we found interaction effects between both poor sleep and those taking sleep medication and APOEε4-carriers on both p-tau/Aβ42 and neurogranin/Aβ42 levels. Our findings suggest that poor sleep is associated with several CSF-markers of preclinical Alzheimer's disease and that the effect is stronger in APOEε4-carriers.