gebhart/patrepeval huggingface dataset:
FLOCCULATION, REINFORCEMENT, AND GLASS TRANSITION EFFECTS IN SILICA-FILLED STYRENE-BUTADIENE RUBBER (2011)

Abstract The introduction of silanes to improve processability and properties of silica-reinforced rubber compounds is critical to the successful commercial use of silica as a filler in tires and other applications. The use of silanes to promote polymer–filler interactions is expected to limit the development of a percolated filler network and may also affect the mobility of polymer chains near the particles. Styrene-butadiene rubber (SBR) was reinforced with silica particles at a filler volume fraction of 0.19, and various levels of filler–filler shielding agent ( n -octyltriethoxysilane) and polymer–filler coupling agent (3-mercaptopropyltrimethoxysilane) were incorporated. Both types of silane inhibited the filler flocculation process during annealing the uncured rubber materials, thus reducing the magnitude of the Payne effect. In contrast to the significant reinforcement effects noted in the strain-dependent shear modulus, the bulk modulus from hydrostatic compression was largely unaltered by the silanes. Addition of polymer–filler linkages using the coupling agent yielded bound rubber values up to 71%; however, this bound rubber exhibited glass transition behavior which was similar to the bulk SBR response, as determined by calorimetry and viscoelastic testing. Modifying the polymer–filler interface had a strong effect on the nature of the filler network, but it had very little influence on the segmental dynamics of polymer chains proximate to filler particles.
Synthesis of photoacid crosslinkable hydrogels for the fabrication of soft, biomimetic microlens arrays (2005)

Soft, biomimetic microlens arrays were fabricated by interference lithography from the copolymers of poly(2-hydroxyethyl methacrylate), whose hydroxyl groups were crosslinked by photoacids and external crosslinkers.
Effective redundant constraints for online scheduling (1997)

The use of heuristics as a means to improve constraint solver performance has been researched widely. However, most work has been on problem-independent heuristics (e.g., variable and value ordering), and has focused on offline problems (e.g., one-shot constraint satisfaction). In this paper, we present an online scheduling problem for which we are developing a real-time scheduling algorithm. While we can and do use generic heuristics in the scheduler, here we focus on the use of domain-specific redundant constraints to effectively approximate optimal offline solutions. We present a taxonomy of redundant domain constraints, and examine their impact on the effectiveness of the scheduler. We also describe several techniques for generating redundant constraints, which can be applied to a large class of job shop scheduling problems.
Ontogeny of growth hormone (GH)-secreting cells during chicken embryonic development: initial somatotrophs are responsive to GH-releasing hormone. (1995)

In the present study, a reverse hemolytic plaque assay (RHPA) for chicken GH was established and used to study the ontogeny of somatotroph differentiation and functional responsiveness to GH-releasing hormone (GHRH) during chicken embryonic development. Anterior pituitaries from embryos on days 10, 12, 14, and 16 of incubation were isolated and dissociated into single cells with trypsin. The resulting cells were then subjected to the GH plaque assay under basal and GHRH-stimulated conditions. No GH-releasing cells were detected on day 10 or 12 of embryonic development. In contrast, a few somatotrophs (< 2% of all cells) were consistently found on day 14, and a statistically significant population existed on day 16, when 6.3 +/- 1.4% of all anterior pituitary cells secreted GH. Thus, GH-secreting cells differentiated by embryonic day 16. Treatment of pituitary cells from day 16 embryos with GHRH was found to increase the proportion of GH plaque-forming cells during a shortened assay interval from 1.8 +/- 0.3% under basal conditions to 6.7 +/- 1.2% in the presence of GHRH. This nearly 4-fold increase in the proportion of plaque-forming cells indicates that at least 70% of the initial somatotrophs present on day 16 were responsive to the stimulatory effects of GHRH. To test whether the absence of GH cells on day 12 of embryonic development was due to the presence of cells that produced but did not release GH, pituitary cells from day 12 and day 16 embryos were subjected to immunocytochemistry for GH and to the GH RHPA in parallel. No significant differences were found in the percentage of cells that either contained or released GH on the two embryonic ages tested. On day 12, 1.1 +/- 0.8% of all cells contained GH, as determined by immunocytochemistry, whereas 0.5 +/- 0.5% released GH as determined by RHPA. By day 16, the proportions of cells that contained and released GH had increased to 9.5 +/- 0.6 and 11.2 +/- 2.5%, respectively. Taken together, these results indicate that GH-secreting cells differentiate by day 16 of chicken embryonic development and that these initial somatotrophs are responsive to GHRH. Given that growth and metabolism are regulated in part by GH in chick embryos, these findings suggest that these processes may be under hypothalamic control during late embryonic development in the chicken.
Microbial Contamination of Clinical Islet Transplant Preparations Is Associated with Very Low Risk of Infection (2013)

Microbiological contamination of the final islet preparation appears to have little or no effect on patients or on islet survival when appropriate antibiotics are given. However, preparation sterility should be guaranteed at all cost in order maximize patient safety and avoid potential complications in immunosuppressed patients.
Solving the Batch Stochastic Bin Packing Problem in Cloud (2022)

This paper investigates a critical resource allocation problem in the first party cloud: scheduling containers to machines. There are tens of services, and each service runs a set of homogeneous containers with dynamic resource usage; containers of a service are scheduled daily in a batch fashion. This problem can be naturally formulated as Stochastic Bin Packing Problem (SBPP). However, traditional SBPP research often focuses on cases of empty machines, whose objective, i.e., to minimize the number of used machines, is not well-defined for the more common reality with nonempty machines. This paper aims to close this gap. First, we define a new objective metric, Used Capacity at Confidence (UCaC), which measures the maximum used resources at a probability and is proved to be consistent for both empty and nonempty machines and reformulate the SBPP under chance constraints. Second, by modeling the container resource usage distribution in a generative approach, we reveal that UCaC can be approximated with Gaussian, which is verified by trace data of real-world applications. Third, we propose an exact solver by solving the equivalent cutting stock variant as well as two heuristics-based solvers -- UCaC best fit, bi-level heuristics. We experimentally evaluate these solvers on both synthetic datasets and real application traces, demonstrating our methodology's advantage over traditional SBPP optimal solver minimizing the number of used machines, with a low rate of resource violations.
Supplemental Table S5 from An Endothelial Gene Signature Score Predicts Poor Outcome in Patients with Endocrine-Treated, Low Genomic Grade Breast Tumors (2023)

&lt;p&gt;Change in MV score (14 days - baseline) vs. RECIST response&lt;/p&gt;
Cervical Laminectomy Width and Spinal Cord Drift Are Risk Factors for Postoperative C5 Palsy (2012)

A wider laminectomy at C5 was associated with an increased risk of postoperative C5 palsy. Increased preoperative spinal canal diameter is also associated with increased risk of C5 palsy. In addition, patients who experienced C5 nerve palsy had a significantly greater posterior spinal cord drift. Strategies to reduce postoperative laminectomy trough width and spinal cord drift may reduce the risk of postoperative C5 palsy.
New Tools for Molecular Imaging of Redox Metabolism:  Development of a Fluorogenic Probe for 3α-Hydroxysteroid Dehydrogenases (2004)

A new fluorogenic substrate was developed for 3alpha-hydroxysteroid dehydrogenases (3alpha-HSD), including the human enzymes implicated in important physiological functions (androgen deactivation, neurosteroid activation). While ketone 5 is nonfluorescent, the corresponding alcohol exhibits high fluorescence with emission maximum at 510 nm, thus constituting a redox optical switch. This study began with a chemical concept of a ketone-alcohol optical switch which guided the synthesis of a focused array of compounds. Subsequently, seven compounds were selected (1-7) on the basis of their optical and chemical (stability) properties and were submitted to a screen against a panel of dehydrogenase enzymes. Probe 5 was found to be highly selective for bacterial, rat, and human 3alpha-HSD enzymes. The kinetic parameters were obtained for human 3alpha-HSD enzyme (type 2 isozyme, AKR 1C3; Km = 2.5 muM, kcat = 8.2 min-1). Remarkably, comparison to 5alpha-dihydrotestosterone (5alpha-DHT, Km = 26 muM, kcat = 0.25 min-1, Figure 4), a likely physiological substrate in prostate, revealed that synthetic probe 5 is in fact a far better substrate for this enzyme. Structure 5 represents an exciting lead for the development of a redox imaging probe.
Training a universal instance segmentation network for live cell images of various cell types and imaging modalities (2022)

We share our recent findings in an attempt to train a universal segmentation network for various cell types and imaging modalities. Our method was built on the generalized U-Net architecture, which allows the evaluation of each component individually. We modified the traditional binary training targets to include three classes for direct instance segmentation. Detailed experiments were performed regarding training schemes, training settings, network backbones, and individual modules on the segmentation performance. Our proposed training scheme draws minibatches in turn from each dataset, and the gradients are accumulated before an optimization step. We found that the key to training a universal network is all-time supervision on all datasets, and it is necessary to sample each dataset in an unbiased way. Our experiments also suggest that there might exist common features to define cell boundaries across cell types and imaging modalities, which could allow application of trained models to totally unseen datasets. A few training tricks can further boost the segmentation performance, including uneven class weights in the cross-entropy loss function, well-designed learning rate scheduler, larger image crops for contextual information, and additional loss terms for unbalanced classes. We also found that segmentation performance can benefit from group normalization layer and Atrous Spatial Pyramid Pooling module, thanks to their more reliable statistics estimation and improved semantic understanding, respectively. We participated in the 6th Cell Tracking Challenge (CTC) held at IEEE International Symposium on Biomedical Imaging (ISBI) 2021 using one of the developed variants. Our method was evaluated as the best runner up during the initial submission for the primary track, and also secured the 3rd place in an additional round of competition in preparation for the summary publication.
A sesquiterpene lactone antrocin from Antrodia camphorata negatively modulates JAK2/STAT3 signaling via microRNA let-7c and induces apoptosis in lung cancer cells (2013)

Lung cancer is the leading cause of cancer deaths worldwide and current therapies fail to treat this disease in majority of cases. Antrodia camphorata is a medicinal mushroom being widely used as food dietary supplement for cancer prevention. The sesquiterpene lactone antrocin is the most potent among >100 secondary metabolites isolated from A. camphorata. However, the molecular mechanisms of antrocin-mediated anticancer effects remain unclear. In this study, we found that antrocin inhibited cell proliferation in two non-small-cell lung cancer cells, namely H441 (wild-type epidermal growth factor receptor, IC50 = 0.75 μM) and H1975 (gefitnib-resistant mutant T790M, IC50 = 0.83 μM). Antrocin dose dependently suppressed colony formation and induced apoptosis as evidenced by activated caspase-3 and increased Bax/Bcl2 ratio. Gene profiling studies indicated that antrocin downregulated Janus kinase/signal transducer and activator of transcription (JAK/STAT) signaling pathway. We further demonstrated that antrocin suppressed both constitutively activated and interleukin 6-induced STAT3 phosphorylation and its subsequent nuclear translocation. Such inhibition is found to be achieved through the suppression of JAK2 and interaction between STAT3 and extracellular signal-regulated kinase. Additionally, antrocin increased microRNA let-7c expression and suppressed STAT signaling. The combination of antrocin and JAK2/STAT3 gene silencing significantly increased apoptosis in H441 cells. Such dual interruption of JAK2 and STAT3 pathways also induced downregulation of antiapoptotic protein mcl-1 and increased caspase-3 expression. In vivo intraperitoneal administration of antrocin significantly suppressed the growth of lung cancer tumor xenografts. Our results indicate that antrocin may be a potential therapeutic agent for human lung cancer cells through constitutive inhibition of JAK2/STAT3 pathway.
Efficient Simulation and Optimization of Nanoloop Antennas (2018)

In this paper, a leap-frog continuous-discontinuous Galerkin time domain (CDGTD) method is proposed to efficiently simulate plasmonic architectures by incorporating the Drude model. The technique is used to perform fast parametric sweeps to study the wideband properties of nanoantennas. Moreover, the covariance matrix adaptation evolutionary strategy (CMA-ES) is employed to optimize an array of nanoloop antennas. A high endfire gain is achieved, which is superior to previously reported results.
Encoding Self-Motion and External Motion during Pursuit Eye Movement, A Study at 9.4T (2015)

Here we propose to use ultra-high-field (9.4T) human fMRI in order to answer two questions: firstly, is there a differential involvement of cortical layers in the processing of retinal motion and of objective motion in high-level visual areas? Second: is there a columnar organisation segregating retinal and objective motion processing? A differential laminar response profile to the two motion types would provide important cues with regards to the hierarchy of processing involved in different areas, with modulation of upper, middle, or lower layers speaking for feedback, bottom-up or output sources of the different signals, respectively. A columnar segregation would indicate specialized and segregated circuits within a given area.
Endoscopic harvesting of the radial artery for neurovascular bypass (2008)

Endoscopic harvesting of the radial artery is feasible, faster, and produces a more aesthetically pleasing result than standard open harvesting. The learning curve associated with the endoscope can be overcome by practice on cadavers and by collaboration with a cardiac surgical team.
Improved digital signature scheme based on discrete exponentiation (1990)

A method of generating and verifying a digital signature is examined. The scheme is tested using a microprocessor and demonstrates fast signature generation.
Composite aerogels for sensing applications (1999)

Composite aerogels are nanoscale mesoporous materials that retain both the meso- and nanoscopic properties of each component. Colloidal metal-silica aerogels (in which the colloidal metal is Au or Pt) exhibit both the transparency and porosity of silica aerogel and the optical behavior of the metal colloid. The silica aerogel essentially acts as a transparent matrix for the isolated metal colloids, which remain accessible to external reagents. Sensing elements adsorbed to the surface of the metal in colloidal Au-silica aerogels are also addressable. For dyes with absorption spectra complementary to that of the metal plasmon resonance, spectral changes due to alteration of the dye environment may be optically monitored. By dispersing the metal colloids in an about-to-gel silica sol, the properties of the metal colloid (i.e. size, which determines the position and FWHM of the plasmon resonance) can be tailored prior to immobilization. The ability to modify the colloidal metal surface either prior to or following gelation in the silica matrix coupled with gentle processing conditions permit modification of the metal surface with, for example, temperature-sensitive biomolecules. Composite colloidal metal-silica aerogels therefore provide a novel method for the nanoscale engineering of optical sensors with rapid response times due to the high mesoporosity of the silica matrix.
Data from The Mechanism of DAB2IP in Chemoresistance of Prostate Cancer Cells (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; The docetaxel-based chemotherapy is the standard of care for castration-resistant prostate cancer (CRPC), inevitably, patients develop resistance and decease. Until now, the mechanism and predictive marker for chemoresistance are poorly understood.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Immortalized normal prostate and cancer cell lines stably manipulated with different DAB2IP expression levels were used and treated with chemotherapeutic drugs commonly used in prostate cancer therapy. Cell proliferation was measured using MTT assay; Western blot, quantitative PCR, and luciferase reporter assays were used to analyze Clusterin gene regulation by DAB2IP. Immunohistochemical analysis was conducted for evaluating DAB2IP, Clusterin and Egr-1 expression in human prostate cancer tissue.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; DAB2IP Knockdown (KD) cells exhibited resistance to several chemotherapeutic drugs, whereas increased DAB2IP in C4-2 cells restored the drug sensitivity. Parallel, DAB2IP KD cells exhibited higher expression of Clusterin, an antiapoptotic factor, whereas elevated DAB2IP in C4-2 cells decreased Clusterin expression. Functionally, knocking down Clusterin by short-hairpin RNA or antisense oligonucleotide OGX-011 decreased drug resistance, whereas overexpressing Clusterin in C4-2 D2 enhanced drug resistance. Mechanistically, DAB2IP blocked the cross-talk between Wnt/β-catenin and IGF-I signaling, leading to the suppression of Egr-1 that is responsible for Clusterin expression. A similar result was observed in the prostate of DAB2IP knockout animals. In addition, we observed a significantly inverse correlation between DAB2IP and Egr-1 or Clusterin expression from clinical tissue microarray.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; This study unveils a new regulation of the Egr-1/Clusterin signaling network by DAB2IP. Loss of DAB2IP expression in CRPC cells signifies their chemoresistance. Clusterin is a key target for developing more effective CRPC therapy. &lt;i&gt;Clin Cancer Res; 19(17); 4740–9. ©2013 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Subsea All-Electric (2017)

Abstract The trend in subsea development is heading towards simplification, industrialization, digitalization and commercial optimization in an environment of longer step-out and deep / ultra-deep water applications. With that the limitation of existing electro hydraulic systems as exposed. Statoil has launched an All-Electric Subsea (AES) initiative to prove the feasibility of new flexible, cost efficient subsea production system (SPS) to meet future demands. While most of the main technology elements are available and proven in use, full market and operator acceptance seems to be a challenge. However, in the current and future situation and with the experience gained from the Åsgard subsea compression system, all electric is considered as a feasible future option for SPS. The strategy for the AES initiate is to identify all electric concepts with SPS vendors in order to establish cost effective solutions and strive for standardization of products and interfaces. The AES initiative aims to have system approach and examine the impact on all elements of a subsea development, i.e. covering topside, umbilical, SPS and downhole etc. This will ensure the benefit of an all-electric implementation is presented. The intention is to present the advantages seen with an all-electric for all aspects, i.e. with respect to cost, project execution, operational flexibility, standardization. This paper will present the current status of the AES initiative covering: –the fundamental features of the AES technology and concepts–the potential of this technology for operation in production control systems–status of the all-electric initiative with respect to technology maturity–the activities required to close the identified technical gaps–the implementation of all electric SPS solutions
Reduced levels of miR‐34a in neuroblastoma are not caused by mutations in the TP53 binding site (2009)

Neuroblastoma (NB) is the most common extracranial solid tumor in children below the age of 5 years. miR-34a, located in chromosome band 1p36, has been recently implicated as a tumor suppressor gene in NB. In addition, it has been shown that miR-34a is activated by TP53 by binding to a TP53 binding site upstream to the mature miR-34a. We studied NB tumors from 57 patients for miR-34a expression levels, 1p status, mutations in the TP53 coding region and mutations of the TP53 binding site. Reduced expression levels of miR-34a were identified in tumors harboring 1p36.3 Loss (P = 0.028). No mutations were identified in the coding region of TP53, or in the TP53 binding site. Thus, mutations in the binding site are not an additional mechanism for the inactivation of miR-34a in NB. Other regulatory mechanisms controlling miR-34a expression and its relationship to TP53 should be further explored.
O-Linked Glycosylation of the Mucin Domain of the Herpes Simplex Virus Type 1-specific Glycoprotein gC-1 Is Temporally Regulated in a Seed-and-spread Manner (2014)

The herpes simplex virus type 1 (HSV-1) glycoprotein gC-1, participating in viral receptor interactions and immunity interference, harbors a mucin-like domain with multiple clustered O-linked glycans. Using HSV-1-infected diploid human fibroblasts, an authentic target for HSV-1 infection, and a protein immunoaffinity procedure, we enriched fully glycosylated gC-1 and a series of its biosynthetic intermediates. This fraction was subjected to trypsin digestion and a LC-MS/MS glycoproteomics approach. In parallel, we characterized the expression patterns of the 20 isoforms of human GalNAc transferases responsible for initiation of O-linked glycosylation. The gC-1 O-glycosylation was regulated in an orderly manner initiated by synchronous addition of one GalNAc unit each to Thr-87 and Thr-91 and one GalNAc unit to either Thr-99 or Thr-101, forming a core glycopeptide for subsequent additions of in all 11 GalNAc residues to selected Ser and Thr residues of the Thr-76-Lys-107 stretch of the mucin domain. The expression patterns of GalNAc transferases in the infected cells suggested that initial additions of GalNAc were carried out by initiating GalNAc transferases, in particular GalNAc-T2, whereas subsequent GalNAc additions were carried out by followup transferases, in particular GalNAc-T10. Essentially all of the susceptible Ser or Thr residues had to acquire their GalNAc units before any elongation to longer O-linked glycans of the gC-1-associated GalNAc units was permitted. Because the GalNAc occupancy pattern is of relevance for receptor binding of gC-1, the data provide a model to delineate biosynthetic steps of O-linked glycosylation of the gC-1 mucin domain in HSV-1-infected target cells.
Author Correction: A pandemic-enabled comparison of discovery platforms demonstrates a naive antibody library can match the best immune-sourced antibodies (2022)

replaces this sentence with 'Presently, 103 vaccines against 32 different organisms (including strains) are approved for use in the US'.