gebhart/patrepeval huggingface dataset:
Micromethod (Spot-Plate) Determination of In Vitro Antibiotic Susceptibility (1965)

The spot-plate method for determining in vitro antibiotic susceptibility is a modified version of the standard tube dilution technique, with the same principle of twofold dilution. Results of the spot-plate method are compared with those of the standard tube dilution technique. It is proposed that the spot-plate method is an equally accurate, but more rapid and economical, technique for determining in vitro antibiotic susceptibility.
Heterodimeric DNA Binding by the Vitamin D Receptor and Retinoid X Receptors Is Enhanced by 1,25-Dihydroxyvitamin D3 and Inhibited by 9-cis-Retinoic Acid (1998)

Gel mobility shift analysis was utilized to investigate the molecular function of 1alpha,25-dihydroxyvitamin D3 (1,25-(OH)2D3) and 9-cis-retinoic acid (9-cis-RA) ligands in the binding of the vitamin D receptor (VDR) and retinoid X receptor (RXR) to mouse osteopontin and rat osteocalcin vitamin D-response elements (VDREs). At physiological ionic strength and reduced concentrations of expressed proteins, efficient binding to either VDRE occurs as a VDR. RXR heterodimer, not as a VDR homodimer. 1,25-(OH)2D3 dramatically enhances heterodimer-VDRE interaction, whereas somewhat higher concentrations of 9-cis-RA inhibit this association, perhaps related to the role of this retinoid in facilitating RXR homodimer formation. Interestingly, if VDR is occupied by 1,25-(OH)2D3 prior to complexing with RXR, the resulting heterodimer is relatively resistant to dissociation and diversion to other pathways by 9-cis-RA. Therefore, a proposed molecular action of 1,25-(OH)2D3 is to generate an allosteric switch in VDR to a form that not only binds to the VDRE with high affinity and specificity as a heterodimer with RXR, but also interacts with the RXR partner to conformationally restrict the action of its cognate ligand.
High-Throughput Cellular Profiling of Targeted Protein Degradation Compounds Using HiBiT CRISPR Cell Lines (2020)

Targeted protein degradation compounds, including molecular glues or proteolysis targeting chimeras, are an exciting new therapeutic modality in small molecule drug discovery. This class of compounds induces protein degradation by bringing into proximity the target protein and the E3 ligase machinery proteins required to ubiquitinate and ultimately degrade the target protein through the ubiquitin-proteasomal pathway (UPP). Profiling of target protein degradation in a high-throughput fashion, however, remains highly challenging given the complexity of cellular pathways required to achieve degradation. Here we present a protocol and screening strategy based on the use of CRISPR/Cas9 endogenous tagging of target proteins with the 11 amino acid HiBiT tag which complements with high affinity to the LgBiT protein, to produce a luminescent protein. These CRISPR targeted cell lines with endogenous tags can be used to measure compound induced degradation in either real-time, kinetic live cell or endpoint lytic modes by monitoring luminescent signal using a luminescent plate-based reader. Here we outline the recommended screening protocols for the different formats, and also describe the calculation of key degradation parameters of rate, Dmax, DC50, Dmax50, as well as multiplexing with cell viability assays. These approaches enable rapid discovery and triaging of early stage compounds while maintaining endogenous expression and regulation of target proteins in relevant cellular backgrounds, allowing for efficient optimization of lead therapeutic compounds.
Alignment of carbon nanotubes and reinforcing effects in nylon-6 polymer composite fibers (2008)

Alignment of pristine carbon nanotubes (P-CNTs) and fluorinated carbon nanotubes (F-CNTs) in nylon-6 polymer composite fibers (PCFs) has been achieved using a single-screw extrusion method. CNTs have been used as filler reinforcements to enhance the mechanical and thermal properties of nylon-6 composite fibers. The composites were fabricated by dry mixing nylon-6 polymer powder with the CNTs as the first step, then followed by the melt extrusion process of fiber materials in a single-screw extruder. The extruded fibers were stretched to their maxima and stabilized using a godet set-up. Finally, fibers were wound on a Wayne filament winder machine and tested for their tensile and thermal properties. The tests have shown a remarkable change in mechanical and thermal properties of nylon-6 polymer fibers with the addition of 0.5 wt% F-CNTs and 1.0 wt% of P-CNTs. To draw a comparison between the improvements achieved, the same process has been repeated with neat nylon-6 polymer. As a result, tensile strength has been increased by 230% for PCFs made with 0.5% F-CNTs and 1% P-CNTs as additives. These fibers have been further characterized by DSC, Raman spectroscopy and SEM which confirm the alignment of CNTs and interfacial bonding to nylon-6 polymer matrix.
Fluctuation-dissipation in thermoelectric sensors (2023)

Abstract Thermoelectric materials exhibit correlated transport of charge and heat. The Johnson-Nyquist noise formula 4 k B T R for the spectral density of voltage fluctuations accounts for fluctuations associated solely with Ohmic dissipation. Applying the fluctuation-dissipation theorem, we generalize the Johnson-Nyquist formula for thermoelectrics, finding an enhanced voltage fluctuation spectral density 4 k B T R (1 + Z D T ) at frequencies below a thermal cut-off frequency f T , where Z D T is the dimensionless thermoelectric device figure of merit. The origin of the enhancement in voltage noise is thermoelectric coupling of temperature fluctuations. We use a wideband , integrated thermoelectric micro-device to experimentally confirm our findings. Measuring the Z D T enhanced voltage noise, we experimentally resolve temperature fluctuations with a root mean square amplitude of at a mean temperature of 295 K. We find that thermoelectric devices can be used for thermometry with sufficient resolution to measure the fundamental temperature fluctuations described by the fluctuation-dissipation theorem.
Bandwidth allocation policies for unicast and multicast flows (1999)

Using multicast delivery to multiple receivers reduces the aggregate bandwidth required from the network compared to using unicast delivery to each receiver. To encourage the use of multicast delivery, a higher amount of bandwidth should be allocated to a multicast row as compared to a unicast row that share the same bottleneck, but without starving the unicast flow. We investigate three bandwidth allocation policies for multicast flows and evaluate their impact on the bandwidth received by the individual receivers. The policy that allocates the available bandwidth as a logarithmic function of the number of receivers downstream of the bottleneck achieves the best trade-off between maximizing the receiver satisfaction and keeping fairness high.
Facile Approach to Enhance Oxygen Reduction Activity by Modification of Platinum Nanoparticles by Melamine-Formaldehyde Polymer (2019)

For the development of better cathode catalysts for use in polymer electrolyte fuel cells, Pt/C catalyst is modified with poly(melamine-co-formaldehyde) methylated (PMF) by simple coating treatment directly on an electrode. Although this modification almost halves the electrochemical surface area due to PMF covering the Pt surface, the mass activity of the oxygen reduction reaction (ORR) is increased ca. 2-fold. This indicates that the ORR activity of uncovered active sites of Pt is increased by ca. 4-fold by this modification. A similar improvement of ORR is also observed after a Pt/C catalyst electrode is dipped into aqueous solutions of some aminated 1,3,5-triazine derivatives including melamine. These aminated 1,3,5-triazine derivatives such as PMF and melamine positively shift the redox peaks of the adsorption/desorption of OHad which can act as an inhibitor of ORR on Pt. This could result in higher ORR activity.
Expression of Vascular Endothelial Growth Factor and the Effects on Bone Remodeling during Experimental Tooth Movement (2003)

Vascular endothelial growth factor (VEGF) has an ability to induce functional osteoclasts as well as neovascularization. We recently reported that the number of osteoclasts was enhanced by the injection of recombinant human VEGF (rhVEGF) with the application of mechanical force for experimental tooth movement. In this study, the expression of VEGF was detected in osteoblasts on the tension side of the alveolar bone. Moreover, the rate of tooth movement was significantly increased in the rhVEGF injection groups compared with the controls. These results suggested that VEGF, highly expressed by mechanical stimuli, enhances the number of osteoclasts as a paracrine factor, and that the amount of tooth movement is accelerated by both endogenous VEGF and injected rhVEGF.
Abstract 19865: Rem-GTPase Regulates Cardiac Myocyte L-type Calcium Current (2010)

The L-type calcium channels (LTCC) are critical for maintaining Ca2+-homeostasis. In turn, Ca2+-homeostasis is critical for cardiac myocyte growth. In heterologous expression studies, the RGK-class...
Foxp3+ regulatory T cells, immune stimulation and host defence against infection (2011)

The immune system is intricately regulated allowing potent effectors to expand and become rapidly mobilized after infection, while simultaneously silencing potentially detrimental responses that averts immune-mediated damage to host tissues. This relies in large part on the delicate interplay between immune suppressive regulatory CD4(+) T (Treg) cells and immune effectors that without active suppression by Treg cells cause systemic and organ-specific autoimmunity. Although these beneficial roles have been classically described as counterbalanced by impaired host defence against infection, newfound protective roles for Treg cells against specific viral pathogens (e.g. herpes simplex virus 2, lymphocytic choriomeningitis virus, West Nile virus) have been uncovered using transgenic mice that allow in vivo Treg-cell ablation based on Foxp3 expression. In turn, Foxp3(+) Treg cells also provide protection against some parasitic (Plasmodium sp., Toxoplasma gondii) and fungal (Candida albicans) pathogens. By contrast, for bacterial and mycobacterial infections (e.g. Listeria monocytogenes, Salmonella enterica, Mycobacterium tuberculosis), experimental manipulation of Foxp3(+) cells continues to indicate detrimental roles for Treg cells in host defence. This variance is probably related to functional plasticity in Treg cell suppression that shifts discordantly following infection with different types of pathogens. Furthermore, the efficiency whereby Treg cells silence immune activation coupled with the plasticity in Foxp3(+) cell activity suggest that overriding Treg-mediated suppression represents a prerequisite 'signal zero' that together with other stimulation signals [T-cell receptor (signal 1), co-stimulation (signal 2), inflammatory cytokines (signal 3)] are essential for T-cell activation in vivo. Herein, the importance of Foxp3(+) Treg cells in host defence against infection, and the significance of infection-induced shifts in Treg-cell suppression are summarized.
Quantum efficiency of exciton-to-charge generation in organic photovoltaic devices (2001)

We present an analysis of the internal monochromatic quantum efficiency of photovoltaic devices based on polymer and polymer/fullerene thin films. A quantum efficiency of exciton-to-charge generation is defined as the external monochromatic quantum efficiency normalized to the absorption in the active materials of the device. An upper limit of the efficiency can be determined, and results show that much of the light is absorbed in photoactive layers of the device, whereas only a fraction of the generated excitons is converted to charge carriers and can be collected as photocurrent.
Unusual Dinuclear Hydridorhodium(III) Complexes Containing Bulky Phosphanyl(stibanyl)methanes as Chelating Ligands (1997)

Abstract The mononuclear starting materials [Rh(η 4 ‐C 8 H 12 )(k 2 ‐ P ,Sb‐ i Pr 2 PCH 2 SbR 2 )]PF 6 ( la, b ) react with CF 3 CO 2 H in the presence of H 2 to give the dinuclear hydridorhodium(II1) complexes [{RhH(k 2 ‐ P ,Sb‐ i Pr 2 PCH 2 SbR 2 )]PF 6 ( 2a, b ) in almost quantitative yield. The X‐ray crystal structural analysis of 2b (R = t Bu) reveals a distorted octahedral geometry around the two metal centers with the two phosphanyl(stibanyl)methanes in a chelating and the two trifluoracetate ligands in a bridging coordination mode.
Glucosylceramide Synthase Blockade Down-Regulates P-Glycoprotein and Resensitizes Multidrug-Resistant Breast Cancer Cells to Anticancer Drugs (2005)

Overexpression of glucosylceramide synthase (GCS), a pivotal enzyme in glycolipid biosynthesis, contributes to cancer cell resistance to chemotherapy. We previously showed that transfection of doxorubicin-resistant MCF-7-AdrR cells with GCS antisense restored cell sensitivity to doxorubicin and greatly enhanced sensitivity to vinblastine and paclitaxel. In that study, doxorubicin promoted generation of ceramide in MCF-7-AdrR/GCS antisense cells; the present study implicates factors in addition to ceramide that augment sensitivity to chemotherapy. Although GCS antisense cells showed enhanced ceramide formation compared with MCF-7-AdrR when challenged with paclitaxel, GCS antisense cells also showed a 10-fold increase in levels of intracellular drug (paclitaxel and vinblastine). In addition, transfected cells had dramatically decreased expression (80%) of P-glycoprotein and a 4-fold decrease in the level of cellular gangliosides. Chemical inhibition of GCS produced the same effects as antisense transfection: exposure of MCF-7-AdrR cells to the GCS inhibitor 1-phenyl-2-palmitoylamino-3-morpholino-1-propanol (PPMP, 5.0 micromol/L, 4 days) decreased ganglioside levels, restored sensitivity to vinblastine, enhanced vinblastine uptake 3-fold, and diminished expression of MDR1 by 58%, compared with untreated controls. A similar effect was shown in vinblastin-resistant KB-V0.01 cells; after 7 days with PPMP (10 micromol/L), MDR1 expression fell by 84% and P-glycoprotein protein levels decreased by 50%. MCF-7-AdrR cells treated with small interfering RNAs to specifically block GCS also showed a dramatic decrease in MDR1 expression. This work shows that limiting GCS activity down-regulates the expression of MDR1, a phenomenon that may drive the chemosensitization associated with blocking ceramide metabolism. The data suggest that lipids play a role in the expression of multidrug resistance.
Measurement of inflammation and oxidative stress following drastic changes in air pollution during the Beijing Olympics: a panel study approach (2010)

Ambient air pollution has been linked to cardiovascular and respiratory morbidity and mortality in epidemiology studies. Frequently, oxidative and nitrosative stress are hypothesized to mediate these pollution effects, however precise mechanisms remain unclear. This paper describes the methodology for a major panel study to examine air pollution effects on these and other mechanistic pathways. The study took place during the drastic air pollution changes accompanying the 2008 Olympics in Beijing, China. After a general description of air pollution health effects, we provide a discussion of panel studies and describe the unique features of this study that make it likely to provide compelling results. This study should lead to a clearer and more precise definition of the role of oxidative and nitrosative stress, as well as other mechanisms, in determining acute morbidity and mortality from air pollution exposure.
In-flight performance of III-V multi-junction solar cells from the Forward Technology Solar Cell Experiment (2008)

The Materials on the International Space Station Experiments (MISSE) present a unique opportunity in space science by offering a low-cost platform to expose materials directly to the space environment on the International Space Station (ISS). MISSE experiments consist of a “suitcase” like package known as the “Passive Experiment Carrier” (PEC) that can be carried by astronauts and mounted externally to the ISS. The 5 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sup> MISSE payload (MISSE-5) contained both passive and active experiments. The Forward Technology Solar Cell Experiment (FTSCE) on MISSE-5 measured current-voltage (I–V) characteristics on 36 solar cells of various types. Over 1500 I–V curves were recorded on each cell during a 13-month period. This paper analyses the results for all the III–V multi-junction cells flown, including state-of-the-art space qualified cells and next generation metamorphic cells.
Development of immune checkpoint therapy for cancer (2019)

Since the early 20th century, immunologists have investigated mechanisms that protect vertebrates from damaging immune responses against self-antigens by mature lymphocytes, i.e., peripheral tolerance. These mechanisms have been increasingly delineated at the molecular level, ultimately culminating in new therapeutics that have revolutionized clinical oncology. Here, we describe basic science and clinical discoveries that converge mainly on two molecules, CTLA-4 and PD-1, that were recognized with the 2018 Nobel Prize in Physiology or Medicine awarded to James Allison and Tasuku Honjo. We discuss their investigations and those of many others in the field that contravene tolerance through checkpoint inhibition to boost immune killing of malignant cells. We also discuss the mechanisms underlying each therapy, the efficacy achieved, and the complications of therapy. Finally, we hint at research questions for the future that could widen the success of cancer immunotherapy.
New insights on the anatomy and function of the retina in sickle cell disease (2017)

Introduction The recent rise of OCT showed that asymptomatic atrophy of the median temporal raphe of the retina ( ATR ) was a frequent occurrence in sickle cell disease ( SCD ). However, the prevalence, mechanisms and significance of ATR is not known, especially in the paediatric field. Methods SCD ‐children prospectively underwent a fundus examination and an OCT of the macula and the temporal retina. Atrophy of the MTR was quantified on thickness maps. Data from brain imaging were collected in SS ‐type SCD children. Results Eighty‐one children were studied; 64.2% exhibited ATR , while 29.2% had peripheral SCD retinopathy. ATR was often limited to areas located temporally from the usual macular map OCT programs, so that it could be missed with these programs. Patients with peripheral retinopathy were more likely to also exhibit ATR (p = 0.02). While peripheral retinopathy was significantly associated with the children age (p = 0.02), ATR was not. Conclusion ATR seems to occur very early in children with SCD and to display most distinct features from the well‐known peripheral SCD retinopathy.
Thermodynamics and reaction mechanism of urea decomposition (2019)

The selective catalytic reduction technique for automotive applications depends on ammonia production from a urea-water solution via thermolysis and hydrolysis. In this process, undesired liquid and solid by-products are formed in the exhaust pipe. The formation and decomposition of these by-products have been studied by thermogravimetric analysis and differential scanning calorimetry. A new reaction scheme is proposed that emphasizes the role of thermodynamic equilibrium of the reactants in liquid and solid phases. Thermodynamic data for triuret have been refined. The observed phenomenon of liquefaction and re-solidification of biuret in the temperature range of 193-230 °C is explained by formation of a eutectic mixture with urea.
Effect of cell‐free hemoglobin transfusion and 20‐HETE synthesis inhibition on pial arteriolar diameter during middle cerebral artery occlusion (2007)

Transfusion of cell‐free hemoglobin polymers (Hb) during middle cerebral artery occlusion (MCAO) can decrease infarct volume. Without MCAO, Hb transfusion produces pial arteriolar constriction that is blocked by the 20‐HETE synthesis inhibitor HET0016. We tested whether superfusion of 1 uM HET0016 in a cranial window would augment pial arteriolar dilation after Hb exchange transfusion during MCAO. In anesthetized rats MCAO initially produced 36±10% dilation which subsided to 19±6% dilation at 30 min of MCAO in the MCA border region. Subsequent exchange transfusion with 5% albumin solution resulted in no further change in diameter (22±16% of preischemia at 2h MCAO). In a group with initial dilation of 37±17%, HET0016 superfusion did not attenuate the loss of dilation at 30 min (25±12%) or the level of dilation after albumin transfusion (26±23%). Exchange transfusion of Hb resulted in a greater loss of dilation (4±19% of preischemia at 2h MCAO). Prior superfusion of HET0016 failed to block this loss of dilation (1±13%). Therefore, blunted vasodilation after Hb transfusion may limit efficacy of this O 2 carrier during MCAO. Blunted vasodilation is not dependent on 20‐HETE synthesis. (Supported by NS38684)
Human-Chromatin-Related Protein Interactions Identify a Demethylase Complex Required for Chromosome Segregation (2014)

Chromatin regulation is driven by multicomponent protein complexes, which form functional modules. Deciphering the components of these modules and their interactions is central to understanding the molecular pathways these proteins are regulating, their functions, and their relation to both normal development and disease. We describe the use of affinity purifications of tagged human proteins coupled with mass spectrometry to generate a protein-protein interaction map encompassing known and predicted chromatin-related proteins. On the basis of 1,394 successful purifications of 293 proteins, we report a high-confidence (85% precision) network involving 11,464 protein-protein interactions among 1,738 different human proteins, grouped into 164 often overlapping protein complexes with a particular focus on the family of JmjC-containing lysine demethylases, their partners, and their roles in chromatin remodeling. We show that RCCD1 is a partner of histone H3K36 demethylase KDM8 and demonstrate that both are important for cell-cycle-regulated transcriptional repression in centromeric regions and accurate mitotic division.
Biphase-Interface Enhanced Sodium Storage and Accelerated Charge Transfer: Flower-Like Anatase/Bronze TiO2/C as an Advanced Anode Material for Na-Ion Batteries (2017)

Flower-like assembly of ultrathin nanosheets composed of anatase and bronze TiO<sub>2</sub> embedded in carbon is successfully synthesized by a simple solvothermal reaction, followed with a high-temperature annealing. As an anode material in sodium-ion batteries, this composite exhibits outstanding electrochemical performances. It delivers a reversible capacity of 120 mA h g<sup>-1</sup> over 6000 cycles at 10 C. Even at 100 C, there is still a capacity of 104 mA h g<sup>-1</sup>. Besides carbon matrix and hierarchical structure, abundant interfaces between anatase and bronze greatly enhance the performance by offering additional sites for reversible Na<sup>+</sup> storage and improving the charge-transfer kinetics. The interface enhancements are confirmed by discharge/charge profiles, rate performances, electrochemical impedance spectra, and first-principle calculations. These results offer a new pathway to upgrade the performances of anode materials in sodium-ion batteries.