gebhart/patrepeval huggingface dataset:
Glucose repression in Saccharomyces cerevisiae is directly associated with hexose phosphorylation by hexokinases PI and PII (1991)

Genetic and biochemical analyses showed that hexokinase PII is mainly responsible for glucose repression in Saccharomyces cerevisiae, indicating a regulatory domain mediating glucose repression. Hexokinase PI/PII hybrids were constructed to identify the supposed regulatory domain and the repression behavior was observed in the respective transformants. The hybrid constructs allowed the identification of a domain (amino acid residues 102-246) associated with the fructose/glucose phosphorylation ratio. This ratio is characteristic of each isoenzyme, therefore this domain probably corresponds to the catalytic domain of hexokinases PI and PII. Glucose repression was associated with the C-terminal part of hexokinase PII, but only these constructs had high catalytic activity whereas opposite constructs were less active. Reduction of hexokinase PII activity by promoter deletion was inversely followed by a decrease in the glucose repression of invertase and maltase. These results did not support the hypothesis that a specific regulatory domain of hexokinase PII exists which is independent of the hexokinase PII catalytic domain. Gene disruptions of hexokinases further decreased repression when hexokinase PI was removed in addition to hexokinase PII. This proved that hexokinase PI also has some function in glucose repression. Stable hexokinase PI overproducers were nearly as effective for glucose repression as hexokinase PII. This showed that hexokinase PI is also capable of mediating glucose repression. All these results demonstrated that catalytically active hexokinases are indispensable for glucose repression. To rule out any further glycolytic reactions necessary for glucose repression, phosphoglucoisomerase activity was gradually reduced. Cells with residual phosphoglucoisomerase activities of less than 10% showed reduced growth on glucose. Even 1% residual activity was sufficient for normal glucose repression, which proved that additional glycolytic reactions are not necessary for glucose repression. To verify the role of hexokinases in glucose repression, the third glucose-phosphorylating enzyme, glucokinase, was stably overexpressed in a hexokinase PI/PII double-null mutant. No strong effect on glucose repression was observed, even in strains with 2.6 U/mg glucose-phosphorylating activity, which is threefold increased compared to wild-type cells. This result indicated that glucose repression is only associated with the activity of hexokinases PI and PII and not with that of glucokinase.
DEP actuated nanoliter droplet dispensing using feedback control (2008)

Dielectrophoretic (DEP) droplet dispensing using dielectric-coated coplanar electrode structures provides an ideal platform for testing smart control systems for high-speed microfluidic devices. Open-loop control of DEP droplet dispensing is not sufficiently robust for precision droplet dispensing because unavoidable surface property variations of the substrates and other parameters such as liquid viscosity introduce uncertainty in the motion. Closed-loop systems employing distributed optical sensors and feedback provide flexibility, sensitivity, and reliability. In this new scheme, an array of distributed optical sensors detects fluid motion and, through a programmable control module, triggers application of AC voltage bursts of appropriate magnitude, duration, and frequency to control liquid motion and droplet formation. Reconfiguring the module connections and reprogramming the control module permits testing of a variety of control strategies.
Immunotherapy of advanced prostate cancer: a phase I/II trial using Mycobacterium vaccae (SRL172) (1998)

Two patients with advanced hormone-refractory prostate cancer had a PSA response to the vaccination with SRL172. The proportion of PBMC secreting IL2 is a potential marker of response to immunotherapy.
Effects of Initial Seeding Density and Fluid Perfusion Rate on Formation of Tissue-Engineered Bone (2008)

We describe a novel bioreactor system for tissue engineering of bone that enables cultivation of up to six tissue constructs simultaneously, with direct perfusion and imaging capability. The bioreactor was used to investigate the relative effects of initial seeding density and medium perfusion rate on the growth and osteogenic differentiation patterns of bone marrow-derived human mesenchymal stem cells (hMSCs) cultured on three-dimensional scaffolds. Fully decellularized bovine trabecular bone was used as a scaffold because it provided suitable "biomimetic" topography, biochemical composition, and mechanical properties for osteogenic differentiation of hMSCs. Trabecular bone plugs were completely denuded of cellular material using a serial treatment with hypotonic buffers and detergents, seeded with hMSCs, and cultured for 5 weeks. Increasing seeding density from 30 x 10(6) cells/mL to 60 x 10(6) cells/mL did not measurably influence the characteristics of tissue-engineered bone, in contrast to an increase in the perfusion rate from 100 microms(-1) to 400 microms(-1), which radically improved final cell numbers, cell distributions throughout the constructs, and the amounts of bone proteins and minerals. Taken together, these findings suggest that the rate of medium perfusion during cultivation has a significant effect on the characteristics of engineered bone.
<title>Large-scale neural network model for multiclass pattern recognition</title> (1993)

This paper presents a large-scale neural network training model--a gray-scale interpattern association neural network model for feature extraction and fast training. A neural network based composite filter (NNCF) concept is proposed for neural network training of Fourier plane filters. The NNCF generation methods can selectively enhance features in the Fourier domain. The nonlinear combination of multiple filters through neural network training enables multi-class pattern recognition.
Feature Denoising for Improving Adversarial Robustness (2018)

Adversarial attacks to image classification systems present challenges to convolutional networks and opportunities for understanding them. This study suggests that adversarial perturbations on images lead to noise in the features constructed by these networks. Motivated by this observation, we develop new network architectures that increase adversarial robustness by performing feature denoising. Specifically, our networks contain blocks that denoise the features using non-local means or other filters; the entire networks are trained end-to-end. When combined with adversarial training, our feature denoising networks substantially improve the state-of-the-art in adversarial robustness in both white-box and black-box attack settings. On ImageNet, under 10-iteration PGD white-box attacks where prior art has 27.9% accuracy, our method achieves 55.7%; even under extreme 2000-iteration PGD white-box attacks, our method secures 42.6% accuracy. Our method was ranked first in Competition on Adversarial Attacks and Defenses (CAAD) 2018 --- it achieved 50.6% classification accuracy on a secret, ImageNet-like test dataset against 48 unknown attackers, surpassing the runner-up approach by ~10%. Code is available at https://github.com/facebookresearch/ImageNet-Adversarial-Training.
Mineralocorticoid Action: Target Tissue Specificity Is Enzyme, Not Receptor, Mediated (1988)

Mineralocorticoid receptors, both when in tissue extracts and when recombinant-derived, have equal affinity for the physiological mineralocorticoid aldosterone and for the glucocorticoids cortisol and corticosterone, which circulate at much higher concentrations than aldosterone. Such receptors are found in physiological mineralocorticoid target tissues (kidney, parotid, and colon) and in nontarget tissues such as hippocampus and heart. In mineralocorticoid target tissues the receptors are selective for aldosterone in vivo because of the presence of the enzyme 11 beta-hydroxy-steroid dehydrogenase, which converts cortisol and corticosterone, but not aldosterone, to their 11-keto analogs. These analogs cannot bind to mineralocorticoid receptors.
Intrinsic mechanical properties of the extracellular matrix affect the behavior of pre-osteoblastic MC3T3-E1 cells (2006)

Mechanical cues present in the ECM have been hypothesized to provide instructive signals that dictate cell behavior. We probed this hypothesis in osteoblastic cells by culturing MC3T3-E1 cells on the surface of type I collagen-modified hydrogels with tunable mechanical properties and assessed their proliferation, migration, and differentiation. On gels functionalized with a low type I collagen density, MC3T3-E1 cells cultured on polystyrene proliferated twice as fast as those cultured on the softest substrate. Quantitative time-lapse video microscopic analysis revealed random motility speeds were significantly retarded on the softest substrate (0.25 +/- 0.01 microm/min), in contrast to maximum speeds on polystyrene substrates (0.42 +/- 0.04 microm/min). On gels functionalized with a high type I collagen density, migration speed exhibited a biphasic dependence on ECM compliance, with maximum speeds (0.34 +/- 0.02 microm/min) observed on gels of intermediate stiffness, whereas minimum speeds (0.24 +/- 0.03 microm/min) occurred on both the softest and most rigid (i.e., polystyrene) substrates. Immature focal contacts and a poorly organized actin cytoskeleton were observed in cells cultured on the softest substrates, whereas those on more rigid substrates assembled mature focal adhesions and robust actin stress fibers. In parallel, focal adhesion kinase (FAK) activity (assessed by detecting pY397-FAK) was influenced by compliance, with maximal activity occurring in cells cultured on polystyrene. Finally, mineral deposition by the MC3T3-E1 cells was also affected by ECM compliance, leading to the conclusion that altering ECM mechanical properties may influence a variety of MC3T3-E1 cell functions, and perhaps ultimately, their differentiated phenotype.
Pharmacogenomics — Drug Disposition, Drug Targets, and Side Effects (2003)

It is well recognized that different patients respond in different ways to the same medication. These differences are often greater among members of a population than they are within the same person at different times (or between monozygotic twins).1 The existence of large population differences with small intrapatient variability is consistent with inheritance as a determinant of drug response; it is estimated that genetics can account for 20 to 95 percent of variability in drug disposition and effects.2 Although many nongenetic factors influence the effects of medications, including age, organ function, concomitant therapy, drug interactions, and the nature of the . . .
Facile Synthesis of Cyclopropylalkadienes (1979)

1,3-Dipolar cyclodditions of diazo compounds (1) to 1,3,5-trienes (2) open up a facile route to cyclopropanes such as (4) with dienyl side chains.—Compounds of this kind have been isolated from algae.
The current state of preclinical prostate cancer animal models (2008)

Prostate cancer continues to be a major cause of morbidity and mortality in men around the world. The field of prostate cancer research continues to be hindered by the lack of relevant preclinical models to study tumorigenesis and to further development of effective prevention and therapeutic strategies. The Prostate Cancer Foundation held a Prostate Cancer Models Working Group (PCMWG) Summit on August 6th and 7th, 2007 to address these issues. The PCMWG reviewed the state of prostate cancer preclinical models and identified the current limitations of cell line, xenograft and genetically engineered mouse models that have hampered the transition of scientific findings from these models to human clinical trials. In addition the PCMWG identified administrative issues that inhibit the exchange of models and impede greater interactions between academic centers and these centers with industry. The PCMWG identified potential solutions for discovery bottlenecks that include: (1) insufficient number of models with insufficient molecular and biologic diversity to reflect human cancer, (2) a lack of understanding of the molecular events that define tumorigenesis, (3) a lack of tools for studying tumor-host interactions, (4) difficulty in accessing model systems across institutions, and (5) addressing why preclinical studies appear not to be predictive of human clinical trials. It should be possible to apply the knowledge gained molecular and epigenetic studies to develop new cell lines and models that mimic progressive and fatal prostate cancer and ultimately improve interventions.
Efficacy of prophylactic aerosol amphotericin B lipid complex in a rat model of pulmonary aspergillosis (1997)

Invasive pulmonary aspergillosis remains an important cause of morbidity and mortality among transplant recipients and patients receiving cancer chemotherapy. The lipid-associated formulation of amphotericin B (AmB), AmB lipid complex (ABLC), was evaluated for its prophylactic efficacy when it was administered as an aerosol in a rat model of pulmonary aspergillosis. Aerosol ABLC (aero-ABLC), in doses from 0.4 to 1.6 mg/kg of body weight given 2 days before infection, significantly delayed mortality compared to the mortality of rats given placebo (P < 0.001). At day 10 postinfection, 50% of rats in the 0.4-mg/kg group and 75% of rats in the 1.6-mg/kg group were alive, while all control animals had died. In a second trial aero-ABLC was more effective than an equivalent dose of aerosol AmB (aero-AmB) in prolonging survival, with 100% survival at day 14 postinfection in the ABLC group, compared to 62.5% survival in the AmB group. Mean concentrations of AmB in lungs were 3.7 times higher at day 1 (P < 0.002) and almost six times higher at day 7 (P < 0.001) after treatment with aero-ABLC than after treatment with a similar dose of aero-AmB. We conclude that aero-ABLC provided higher and more prolonged levels of the parent compound in the lungs than aero-AmB and was more effective in delaying mortality from aspergillosis in this model.
Molecular Forms of Human Rhodopsin Kinase (GRK1) (1998)

The G protein-coupled receptor kinases (GRKs) are critical enzymes in the desensitization of activated G protein-coupled receptors. Six members of the GRK family have been identified to date. Among these enzymes, GRK1 (rhodopsin kinase) is involved in phototransduction and is the most specialized of the family. GRK1 phosphorylates photoactivated rhodopsin, initiating steps in its deactivation. In this study, we found that human retina expressed all GRKs except GRK4. Based on results of molecular cloning and immunolocalization, it appears that both rod and cone photoreceptors express GRK1. This conclusion was supported by the cloning of only GRK1 from cone-dominated chicken retina. Human photoreceptors also transcribe a splice variant of GRK1, which differs in its C-terminal region next to the catalytic domain. This novel variant, GRK1b, is produced by retention of the last intron. mRNA encoding GRK1b is exported to the cytosol; however, the level of the protein is relatively low compared with GRK1 (now called GRK1a), and GRK1b appears to have very low catalytic activity. Thus, these studies suggest that rods and cones, express the same form of GRK1.
A comparative study of epidermal growth factor receptor (EGFR) and MDM2 gene amplification and protein immunoreactivity in human glioblastomas. (1998)

The gene of epidermal growth factor receptor (EGFR) is often altered in human astrocytomas and its amplification, rearrangement and overexpression occur almost exclusively in high grade tumours (glioblastomas). MDM2 gene is amplified in a small proportion of glioblastomas, and MDM2 immunoreactivity has also been found in this group. However, the relation between gene amplification and protein overexpression depends on several factors. Thus, the study on mutual relationship between these events needs to be clarified. In a series of 28 glioblastomas, we analysed MDM2 and EGFR gene amplification by differential PCR and protein overexpression was evaluated by immunohistochemistry. Thirteen cases (45%) presented immunopositivity for EGFR. A significant amplification of EGFR gene (the EGFR/SOD ratio above the control value +/- 3 SD) was observed in 9 tumours among which, one revealed no EGFR-immunopositivity. Three tumours displayed the ratio +/- 2-3 SD but these tumours also presented immunoreactivity for EGFR. Two other glioblastomas, with weak EGFR-expression, showed no gene amplification. The immunohistochemical staining for MDM2 revealed strong positivity only in one case, and this tumour also presented MDM2 gene amplification. On the contrary, another tumour which showed MDM2 gene amplification showed no MDM2 immunopositivity. In conclusion, our results demonstrate that there is no strict correlation between gene amplification at the DNA level and protein overexpression.
Novel cross-linked homogeneous polyacrylamide gels with improved separation properties: Investigation of the cross-linker functionality (2001)

Polyacrylamide (PAAm) gels were synthesized using cross-linkers with their potential functionality (twice the number of double bonds of a cross-linker) varying from six to sixteen. Improved electrophoretic separation and highly desirable porosity and sieving properties were observed for most of the PAAm gels containing novel cross-linkers. An increase in the potential functionality of cross-linkers used in PAAm gels was an important factor, influencing the pore size and pore size distribution of the network.
Dublin Bus Tracking Service Design and implementation of a device independent passenger information system (2000)

-scale capital intensive projects, which means only large organisations and governments can implement them. The most expensive component of the system is the automatic vehicle location (AVL) system. This thesis proposes a new type of AVL system based on third generation mobile positioning technology that significantly reduces the cost of implementing a passenger information system. A best-of-breed architecture for implementing passenger information systems is described. It uses a service chain architecture to aggregate content and services from multiple sources to provide a coherent interface to the end user. The interface can be delivered to multiple devices with different display characteristics. A prototype implementation of this architecture is implemented in Java. 6 CONTENTS 1 INTRODUCTION ....................................................................................................................... 10 1.1 THESIS
City Data Fusion: Sensor Data Fusion in the Internet of Things (2015)

Internet of Things (IoT) has gained substantial attention recently and play a significant role in smart city application deployments. A number of such smart city applications depend on sensor fusion capabilities in the cloud from diverse data sources. We introduce the concept of IoT and present in detail ten different parameters that govern our sensor data fusion evaluation framework. We then evaluate the current state-of-the art in sensor data fusion against our sensor data fusion framework. Our main goal is to examine and survey different sensor data fusion research efforts based on our evaluation framework. The major open research issues related to sensor data fusion are also presented.
Bilinear CNN Models for Fine-Grained Visual Recognition (2015)

We propose bilinear models, a recognition architecture that consists of two feature extractors whose outputs are multiplied using outer product at each location of the image and pooled to obtain an image descriptor. This architecture can model local pairwise feature interactions in a translationally invariant manner which is particularly useful for fine-grained categorization. It also generalizes various orderless texture descriptors such as the Fisher vector, VLAD and O2P. We present experiments with bilinear models where the feature extractors are based on convolutional neural networks. The bilinear form simplifies gradient computation and allows end-to-end training of both networks using image labels only. Using networks initialized from the ImageNet dataset followed by domain specific fine-tuning we obtain 84.1% accuracy of the CUB-200-2011 dataset requiring only category labels at training time. We present experiments and visualizations that analyze the effects of fine-tuning and the choice two networks on the speed and accuracy of the models. Results show that the architecture compares favorably to the existing state of the art on a number of fine-grained datasets while being substantially simpler and easier to train. Moreover, our most accurate model is fairly efficient running at 8 frames/sec on a NVIDIA Tesla K40 GPU. The source code for the complete system will be made available at http://vis-www.cs.umass.edu/bcnn.
NADPH oxidase-derived reactive oxygen species are essential for differentiation of a mouse macrophage cell line (RAW264.7) into osteoclasts (2009)

Reactive oxygen species (ROS) derived from NADPH oxidase (Nox) homologues have been suggested to regulate osteoclast differentiation. However, no bone abnormalities have been documented in Nox1 deficient, Nox2 deficient, or Nox3 mutant mice. During receptor activator of nuclear factor-kappaB ligand (RANKL)-stimulated differentiation of a mouse macrophage cell line (RAW264.7) into osteoclasts, mRNA levels of Nox enzymes (Nox1-4) and their adaptor proteins were monitored by real-time reverse transcriptase PCR. RAW264.7 cells constitutively expressed abundant Nox2 mRNA and small amounts of Nox1 and Nox3 transcripts. RANKL markedly attenuated Nox2 mRNA expression in association with reciprocal up-regulation of Nox1 and Nox3 transcripts. Introduction of small interference RNA targeting p67(phox) or p22(phox) into RAW264.7 cells effectively down-regulated ROS generation and significantly suppressed the RANKL-stimulated differentiation, which was assessed by appearance of tartrate resistant acid phosphatase (TRAP)-positive, multinucleated cells having an ability to form resorption pits on calcium phosphate thin film-coated disks, and by expression of osteoclast marker genes (TRAP, cathepsin K, Atp6i, ClC-7, and NFATc1). Our results suggest that RANKL may stimulate switching between Nox homologues during osteoclast differentiation, and Nox-derived ROS may be crucial for RANKL-induced osteoclast differentiation.
High Incidence of Metabolically Active Brown Adipose Tissue in Healthy Adult Humans (2009)

Our findings, being against the conventional view, indicate the high incidence of metabolically active BAT in adult humans and suggest a role in the control of body temperature and adiposity.
Effective targeting of tumor vasculature by the angiogenesis inhibitors vasostatin and interleukin-12 (2000)

Solid tumors are dependent on preexisting vasculature and neovascularization for their growth. Successful cancer therapies targeting the tumor vasculature would be expected to block the existing tumor blood supply and to prevent tumor neovascularization. We tested the antitumor activity of experimental therapy with 2 distinct antiangiogenic drugs. Vasostatin inhibits endothelial cell growth and neovascularization, and interleukin-12 (IL-12) targets the tumor vasculature acting through interferon-gamma (IFN-gamma) and the downstream chemokines interferon-inducible protein-10 (IP-10) and monokine induced by IFN-gamma. Individually, vasostatin and IL-12 produced distinct efficacy profiles in trials aimed at reducing tumor growth in athymic mice. In combination, these inhibitors halted the growth of human Burkitt lymphoma, colon carcinoma, and ovarian carcinoma. Thus, cancer therapy that combines distinct inhibitors of angiogenesis is a novel, effective strategy for the experimental treatment of cancer. (Blood. 2000;96:1900-1905)