gebhart/patrepeval huggingface dataset:
Engineers are from PDMS-land, Biologists are from Polystyrenia (2012)

As the integration of microfluidics into cell biology research proceeds at an ever-increasing pace, a critical question for those working at the interface of both disciplines is which device material to use for a given application. While PDMS and soft lithography methods offer the engineer rapid prototyping capabilities, PDMS as a material has characteristics that have known adverse effects on cell-based experiments. In contrast, while polystyrene (PS), the most commonly used thermoplastic for laboratory cultureware, has provided decades of grounded and validated research conclusions in cell behavior and function, PS as a material has posed significant challenges in microfabrication. These competing issues have forced microfluidics engineers and biologists to make compromises in how they approach specific research questions, and furthermore, have attenuated the impact of microfluidics on biological research. In this review, we provide a comparison of the attributes of PDMS and PS, and discuss reasons for their popularity in their respective fields. We provide a critical evaluation of the strengths and limitations of PDMS and PS in relation to the advancement and future impact on microfluidic cell-based studies and applications. We believe that engineers have a responsibility to overcome any challenges associated with microfabrication, whether with PS or other materials, and that engineers should provide options and solutions that assist biologists in their experimental design. Our goal is not to advocate for any specific material, but provide guidelines for researchers who desire to choose the most suitable material for their application, and suggest important research directions for engineers working at the interface between microfabrication technology and biological application.
A cofactor‐dependent phosphoglycerate mutase homolog from Bacillus stearothermophilus is actually a broad specificity phosphatase (2001)

The distribution of phosphoglycerate mutase (PGM) activity in bacteria is complex, with some organisms possessing both a cofactor-dependent and a cofactor-independent PGM and others having only one of these enzymes. Although Bacillus species contain only a cofactor-independent PGM, genes homologous to those encoding cofactor-dependent PGMs have been detected in this group of bacteria, but in at least one case the encoded protein lacks significant PGM activity. Here we apply sequence analysis, molecular modeling, and enzymatic assays to the cofactor-dependent PGM homologs from B. stearothermophilus and B. subtilis, and show that these enzymes are phosphatases with broad substrate specificity. Homologs from other gram-positive bacteria are also likely to possess phosphatase activity. These studies clearly show that the exploration of genomic sequences through three-dimensional modeling is capable of producing useful predictions regarding function. However, significant methodological improvements will be needed before such analysis can be carried out automatically.
Ad-MDA-7; INGN 241: a review of preclinical and clinical experience (2008)

The melanoma differentiation-associated gene-7 (MDA-7) was isolated while screening for upregulated genes in terminally differentiated melanoma cell lines. Preclinical studies attempted to test the theory that oncogenesis arises from a cellular differentiation process culminating in dysregulation of the cell cycle and ultimately malignancy. The MDA-7 gene (gene symbol IL-24) has been classified as part of the IL-10 family of cytokines demonstrating significant anticancer potential. Preclinical studies have shown that MDA-7/IL-24 is effective in inducing cancer cell death by several pathways in various tumor models. A Phase I clinical trial studying intratumoral injections of solid tumors showed evidence of clinical activity with limited toxicity. This small trial suggested therapeutic potential. Results are reviewed. Future opportunities involve combination with different gene delivery systems with systemic potential.
Trichostatin A is a histone deacetylase inhibitor with potent antitumor activity against breast cancer in vivo. (2001)

The present studies confirm the potent dose-dependent antitumor activity of TSA against breast cancer in vitro and in vivo, strongly supporting HDAC as a molecular target for anticancer therapy in breast cancer.
A customized design of DRAM controller for on-chip 3D DRAM stacking (2010)

To address the “memory wall” challenge, on-chip memory stacking has been proposed as a promising solution. The stacking memory adopts three-dimensional (3D) IC technology, which leverages through-silicon-vias (TSVs) to connect layers, to dramatically reduce the access latency and improve the bandwidth without the constraint of I/O pins. To demonstrate the feasibility of 3D memory stacking, this paper introduces a customized 3D Double-Data-Rate (DDR) SDRAM controller design, which communicates with DRAM layers by TSVs. In addition, we propose a parallel access policy to further improve the performance. The 3D DDR controller is integrated in a 3D stacking System-on-Chip (SoC) architecture, where a high-bandwidth 3D DRAM chip is stacked on the top. The 3D SoC is divided into two logic layers with each having an area of 2.5 × 5.0mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , with a 3-layer 2Gb DRAM stacking. The whole chip has been fabricated in Chartered 130nm low-power process and Tezzaron's 3D bonding technology. The simulation result shows that the on-chip DRAM controller can run as fast as 133MHz and provide 4.25GB/s data bandwidth in a single channel and 8.5GB/s with parallel access policy.
Effect of Solvent on the Excited-state Photophysical Properties of Curcumin¶ (2000)

Photophysical properties of curcumin, 1,7-bis-(4-hydroxy-3-methoxy phenyl)-1,6-heptadiene-2,5-dione, a pigment found in the rhizomes of Curcuma longa (turmeric) have been studied in different kinds of organic solvent and also in Triton X-100 aqueous micellar media using time-resolved fluorescence and transient absorption techniques having pico and nanosecond time resolution, in addition to steady-state absorption and fluorescence spectroscopic techniques. Steady-state absorption and fluorescence characteristics of curcumin have been found to be sensitive to the solvent characteristics. Large change (delta mu = 6.1 Debye) in dipole moments due to photoexcitation to the excited singlet state (S1) indicates strong intramolecular charge transfer character of the latter. Curcumin is a weakly fluorescent molecule and the fluorescence decay properties in most of the solvents could be fitted well to a double-exponential decay function. The shorter component having lifetime in the range 50-350 ps and percent contribution of amplitude more than 90% in different solvents may be assigned to the enol form, whereas the longer component, having lifetime in the range 500-1180 ps with less than 10% contribution may be assigned to the di-keto form of curcumin. Our nuclear magnetic resonance study in CDCl3 and dimethyl sulfoxide-D6 also supports the fact that the enol form is present in the solution by more than about 95% in these solvents. Excited singlet (S1) and triplet (T1) absorption spectrum and decay kinetics have been characterized by pico and nanosecond laser flash photolysis. Quantum yield of the triplet is low (phi T < or = 0.12). Both the fluorescence and triplet quantum yields being low (phi f + phi T < 0.18), the photophysics of curcumin is dominated by the energy relaxation mechanism via the internal conversion process.
In Situ X-ray Absorption Spectroscopic Study on LiNi0.5Mn0.5O2 Cathode Material during Electrochemical Cycling (2003)

We have investigated the local electronic and atomic structure of the LiMn0.5Ni0.5O2 electrode during the first charge and discharge process using in situ X-ray absorption spectroscopy (XAS) of the Mn and Ni K-edges. The Ni K-edge structure in the XANES spectrum shifts to higher energy during charge and shifts back reversibly during discharge in the higher voltage region of ∼4 V, whereas the Mn K-edge structure does not appear to exhibit a rigid edge shift. Further Li-ion intercalation during extended discharge in the 1-V plateau leads to the reduction of Mn4+ ions suggesting that the charge compensation in this region is achieved via the reduction of Mn4+ ions to Mn2+. Mn K-edge EXAFS results indicate that a small amount of Li is found in the Ni2+/Mn4+ layers. These Li ions in the transition metal layers are primarily present in the second coordination shell of Mn and not around Ni. Ni K-edge EXAFS fitting results suggest that the oxidation process upon Li deintercalation takes place in two steps: Ni2+ to Ni3+ first, and then Ni3+ to Ni4+.
Configuration prefetching techniques for partial reconfigurable coprocessor with relocation and defragmentation (2002)

One of the major overheads for reconfigurable computing is the time it takes to reconfigure the devices in the system. This overhead limits the speedup possible in this paradigm. In this paper we explore configuration prefetching techniques for reducing this overhead. By overlapping the configuration loadings with the computation on the host processor the reconfiguration overhead can be reduced. Our prefetching techniques target to the reconfigurable systems containing a Partial Reconfigurable FPGA with Relocation + Defragmentation (R+D model) since the R+D FPGA showed high hardware utilization. We have investigated various techniques including static configuration prefetching, dynamic configuration pre-fetching, and hybrid prefetching. We have developed prefetching algorithms that significantly reduce the reconfiguration overhead.
Acquired Immune Deficiency Syndrome Occurring Within 5 Years of Infection with Human Immunodeficiency Virus Type-1 (1992)

The objective of this study is to describe participants in the Multicenter AIDS Cohort Study (MACS) with incident infection due to the human immunodeficiency virus type-1 (HIV-1) in whom AIDS developed by March 1990 and within 5 years of seroconversion (group A). Secondly, behavioral, clinical, and immunologic characteristics of these men are compared to those of matched seroconverters remaining AIDS free (group B). Between entry into the MACS (April 1984-March 1985) and July 1989, 345 seronegative homosexual/bisexual men had HIV-1 antibody; of these men, AIDS developed in 32 by March 1990. The Kaplan-Meier estimates of the proportion of men with incident HIV-1 infection with AIDS were 6 months, 0%; 12 months, 1%; 24 months, 3%; and 48 months, 10%. These 32 men engaged in receptive anal intercourse with more partners before (p less than 0.005) and after seroconversion (p less than 0.005) and reported more sexually transmitted disease preseroconversion (p = 0.05) than did group B. These findings suggest that sexually transmitted co-factors, preseroconversion and/or postseroconversion, play a role in the progression of HIV-1 infection. Alternatively, greater sexual activity could increase the hazard of exposure to a more virulent HIV-1 strain.
Amplified integrated star couplers with zero loss (1991)

It is shown that it is possible to compensate for the approximately 17 dB splitting and excess loss of a 19*19 integrated star coupler with erbium-doped fibers (EDFs) connected to the output channels. The amplifier fibers are pumped to near-quantum-limited noise performance using only one laser source at 0.98 mu m, which is connected to one of the input ports and is distributed to the EDFs through the star itself. The integrated star coupler's near-wavelength-independent performance is able to transmit both the pump light at 0.98 mu m and the signal at 1.55 mu m with a loss differential on the order of only 1 dB.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Recent developments in islanding detection for distributed power generation (2004)

The aim of this paper is to review recent developments in anti-islanding techniques for distributed resources interconnected with electric power systems. The techniques may be classified as remote and local. Remote techniques are associated with island detection on the utility side while local techniques are associated with island detection on the distributed power generation side. Local techniques may further be classified as passive and active.
Small molecule-mediated inhibition of myofibroblast transdifferentiation for the treatment of fibrosis (2017)

Fibrosis, a disease in which excessive amounts of connective tissue accumulate in response to physical damage and/or inflammatory insult, affects nearly every tissue in the body and can progress to a state of organ malfunction and death. A hallmark of fibrotic disease is the excessive accumulation of extracellular matrix-secreting activated myofibroblasts (MFBs) in place of functional parenchymal cells. As such, the identification of agents that selectively inhibit the transdifferentiation process leading to the formation of MFBs represents an attractive approach for the treatment of diverse fibrosis-related diseases. Herein we report the development of a high throughput image-based screen using primary hepatic stellate cells that identified the antifungal drug itraconazole (ITA) as an inhibitor of MFB cell fate in resident fibroblasts derived from multiple murine and human tissues (i.e., lung, liver, heart, and skin). Chemical optimization of ITA led to a molecule (CBR-096-4) devoid of antifungal and human cytochrome P450 inhibitory activity with excellent pharmacokinetics, safety, and efficacy in rodent models of lung, liver, and skin fibrosis. These findings may serve to provide a strategy for the safe and effective treatment of a broad range of fibrosis-related diseases.
pUV I: a new vaccinia virus insertion and expression vector (1987)

Journal Article pUV I: a new vaccinia virus insertion and expression vector Get access Falko G. Falkner, Falko G. Falkner Laboratory of Viral Diseases, National Institute of Allergy and Infections DiseasesBethesda, MD 20892, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Sekhar Chakrabarti, Sekhar Chakrabarti Laboratory of Viral Diseases, National Institute of Allergy and Infections DiseasesBethesda, MD 20892, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Bernard Moss Bernard Moss Laboratory of Viral Diseases, National Institute of Allergy and Infections DiseasesBethesda, MD 20892, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 15, Issue 17, 11 September 1987, Page 7192, https://doi.org/10.1093/nar/15.17.7192 Published: 11 September 1987 Article history Received: 30 July 1987 Published: 11 September 1987
Leptin expression and action: New experimental paradigms (1997)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Thy-1 expression is linked to functional properties of primitive hematopoietic progenitor cells from human umbilical cord blood (1994)

We have previously shown that the most primitive human hematopoietic cells are included within a cell subpopulation expressing high levels of CD34 and low or undetectable levels of CD45RA and CD71. In this study, cord blood cells with this phenotype were sorted and further separated based on their expression on the Thy-1 antigen. The proliferation and differentiation of the purified cell fractions in response to a mixture of hematopoietic cytokines was analyzed in serum- and stroma-free liquid cultures. Thy-1+ cells (25% of CD34+ CD45RAlo CD71lo cells) were particularly enriched for high proliferative potential colony-forming cells (HPP-CFC; up to 45% of the clonogenic cells), whereas Thy-1- cells were enriched for multipotential colony-forming cells (CFU-MIX; up to 46% of the clonogenic cells). When both subpopulations were cultured in serum-free liquid cultures supplemented with a cytokine mixture that included steel factor, interleukin-6 (IL-6), granulocyte-macrophage colony-stimulating factor (GM-CSF)/IL-3 fusion protein, M-CSF, G-CSF, and erythropoietin, Thy-1+ cells showed a much higher numerical expansion of CD34+ cells (30,000-fold) and colony-forming cells (4,700-fold) than was observed in cultures initiated with Thy-1- cells (900-fold increase in CD34+ cell numbers and 241-fold increase in CFC numbers). Cells coexpressing CD34 and Thy-1 were only transiently expanded (up to 29-fold) and were not detected after day 22 of culture. When CD34+ CD45RAlo CD71lo Thy-1+ cells were cultured, either in semi-solid or liquid cultures, in the presence of anti-Thy-1 antibody, a significant reduction in progenitor cell numbers (particularly HPP-CFC) was observed. In contrast, CD34+ CD45RAlo CD71lo Thy-1- cells were not affected by anti-Thy-1. The results of this study indicate that Thy-1 is expressed on primitive cord blood progenitors with the highest in vitro proliferative potential, and further suggest that Thy-1 is involved in hematopoietic cell development, possibly by mediating a negative signal that results in inhibition of primitive cell proliferation.
Identification of RF Harmonic Distortion on Si Substrates and its Reduction Using a Trap-Rich Layer (2008)

Harmonic distortion (HD) is measured arising from coplanar waveguide structures on various substrates at 900 MHz, and significant distortion for silicon substrates is demonstrated for the first time. For an input power of +35 dBm, 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">nd</sup> harmonic power of -47 dBm and 3 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">rd</sup> of -57 dBm are measured for a thru calibration structure on oxidized high-resistivity silicon (HRS) substrates, and 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">nd</sup> harmonic of -23 and 3 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">rd</sup> of -20 dBm for a longer line on a thinner oxide. These levels are high compared to a full cellular transmit switch product specification of -45 and -40 dBm for 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">nd</sup> and 3 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">rd</sup> harmonics, respectively, at similar power levels. The contribution of the silicon substrate to high harmonic levels is investigated experimentally, and an efficient technological solution based on the introduction of a trap-rich layer is demonstrated.
Microlens systems for fluorescence detection in chemical microsystems (2001)

Micro-optical systems based on refractive microlenses are investigated. These systems are integrated on a chemical chip. They focus an excitation beam into the detection volume (microliter or even submicroliter scale) and collect the emitted light from fluorescent molecules. The fluorescence must be carefully separated by spatial and spectral filtering from the excitation. This paper presents the ray tracing simulation, fabrication, and measurement of three illumination systems. The measurements show that an adroit placement and combination of microfabricated lenses and stops can increase the separation between the excitation light and the fluorescence light. Moreover we present the successful detection of a 20 nM Cy5 (Amersham Life Science Ltd.) solution in a 100-m-wide and 50-m-deep microchannel (excitation volume 250 pL) using one of these illumination systems. The microchemical chip with the micro-optical system has a thickness of less than 2 mm.
The nuclear receptor CAR (NR1I3) regulates serum triglyceride levels under conditions of metabolic stress (2008)

The nuclear receptor constitutive androstane receptor (CAR) (NR1I3) regulates hepatic genes involved in xenobiotic detoxification as well as genes involved in energy homeostasis. We provide data that extend the role of CAR to regulation of serum triglyceride levels under conditions of metabolic/nutritional stress. The typically high serum triglyceride levels of ob/ob mice were completely normalized when crossed onto a Car(-/-) (mice deficient for the Car gene) genetic background. Moreover, increases in serum triglycerides observed after a high-fat diet (HFD) regime were not observed in Car(-/-) animals. Conversely, pharmacological induction of CAR activity using the selective mouse CAR agonist TCPOBOP during HFD feeding resulted in a CAR-dependent increase in serum triglyceride levels. A major regulator of hepatic fatty oxidation is the nuclear receptor PPARalpha (NR1C1). The expression of peroxisome proliferator-activated receptor alpha (PPARalpha) target genes was inversely related to the activity of CAR. Consistent with these observations, Car(-/-) animals exhibited increased hepatic fatty acid oxidation. Treatment of mice with 1,4-bis[2-(3,5-dichloropyridyloxy)]benzene (TCPOBOP) significantly decreased expression of PPARalpha mRNA as well as Cyp4a14, CPT1alpha, and cytosolic Acyl-CoA thioesterase (CTE) in the liver. These data have implications in disease therapy such as for diabetes and nonalcoholic steatohepatitis (NASH).
Deep biomarkers of human aging: Application of deep neural networks to biomarker development (2016)

One of the major impediments in human aging research is the absence of a comprehensive and actionable set of biomarkers that may be targeted and measured to track the effectiveness of therapeutic interventions. In this study, we designed a modular ensemble of 21 deep neural networks (DNNs) of varying depth, structure and optimization to predict human chronological age using a basic blood test. To train the DNNs, we used over 60,000 samples from common blood biochemistry and cell count tests from routine health exams performed by a single laboratory and linked to chronological age and sex. The best performing DNN in the ensemble demonstrated 81.5 % epsilon-accuracy r = 0.90 with R(2) = 0.80 and MAE = 6.07 years in predicting chronological age within a 10 year frame, while the entire ensemble achieved 83.5% epsilon-accuracy r = 0.91 with R(2) = 0.82 and MAE = 5.55 years. The ensemble also identified the 5 most important markers for predicting human chronological age: albumin, glucose, alkaline phosphatase, urea and erythrocytes. To allow for public testing and evaluate real-life performance of the predictor, we developed an online system available at http://www.aging.ai. The ensemble approach may facilitate integration of multi-modal data linked to chronological age and sex that may lead to simple, minimally invasive, and affordable methods of tracking integrated biomarkers of aging in humans and performing cross-species feature importance analysis.