gebhart/patrepeval huggingface dataset:
Conditional Transgene and Gene Targeting Methodologies in Zebrafish (2006)

The zebrafish has become a powerful tool for dissecting vertebrate gene function during embryogenesis. Numerous molecular systems have been developed to examine gene function in zebrafish, including transgenics for creating lineage-tracer lines of zebrafish that express a fluorescent protein as a marker for specific populations of cells, and antisense strategies, primarily morpholinos, for knocking down gene function. The focus of this review is to summarize the pros and cons of the currently available systems for functional genomics in zebrafish, and to discuss the need for future methodologies.
Structural heterogeneity of the μ-opioid receptor’s conformational ensemble in the apo state (2017)

G-protein coupled receptors (GPCRs) are the largest and most pharmaceutically relevant family of membrane proteins. Here, fully unbiased, enhanced sampling simulations of a constitutively active mutant (CAM) of a class A GPCR, the μ-opioid receptor (μOR), demonstrates repeated transitions between the inactive (IS) and active-like (AS-L) states. The interconversion features typical activation/inactivation patterns involving established conformational rearrangements of conserved residues. By contrast, wild-type μOR remains in IS during the same course of simulation, consistent with the low basal activity of the protein. The simulations point to an important role of residue W293<sup>6.48</sup> at the "toggle switch" in the mutation-induced constitutive activation. Such role has been already observed for other CAMs of class A GPCRs. We also find a significantly populated intermediate state, rather similar to IS. Based on the remarkable accord between simulations and experiments, we suggest here that this state, which has escaped so far experimental characterization, might constitute an early step in the activation process of the apo μOR CAM.
Metabolic Abnormalities Associated With Renal Calculi in Patients with Horseshoe Kidneys (2004)

All patients with renal calculi in horseshoe kidneys were noted to have metabolic abnormalities predisposing to stone formation. In this initial series of 11 patients, hypovolemia, hypercalcuria and hypocitraturia were most common metabolic defects. These findings suggest that metabolic derangements play a role in stone formation in patients with a horseshoe kidney. Patients with calculi in anatomically abnormal kidneys should be considered for a metabolic evaluation to identify their stone-forming risk factors in order to initiate preventative selective medical therapy and reduce the risk of recurrent calculus formation.
Zevalin: the first radioimmunotherapy approved for the treatment of lymphoma (2002)

Conjugated antibodies have been in clinical trials for over 30 years. Immunotoxins, chemotherapy conjugates and radioimmunotherapies have been evaluated. Zevalin, the first conjugated antibody for the treatment of non-hodgkin's lymphoma (NHL) (and the first radioimmunotherapeutic for cancer) was approved by the US FDA on 19 February 2002 (approval is pending in the EEC). Zevalin (90Yttrium ibritumomab tiuxetan) has been in clinical trials since 1992. Several studies have been conducted including a randomized Phase III trial where it showed superiority to rituximab in overall response rate and in complete response rate. The current indications are: low-grade or follicular lymphoma refractory to rituximab, and relapsed or refractory, low-grade, follicular or transformed lymphoma. Additional studies have been initiated to further define the role of this new therapy in the treatment of patients with B-cell non-hodgkin's lymphoma.
Diagnostic Evaluation of Multiplexed Reverse Transcription-PCR Microsphere Array Assay for Detection of Foot-and-Mouth and Look-Alike Disease Viruses (2008)

A high-throughput multiplexed assay was developed for the differential laboratory detection of foot-and-mouth disease virus (FMDV) from viruses that cause clinically similar diseases of livestock. This assay simultaneously screens for five RNA and two DNA viruses by using multiplexed reverse transcription-PCR (mRT-PCR) amplification coupled with a microsphere hybridization array and flow-cytometric detection. Two of the 17 primer-probe sets included in this multiplex assay were adopted from previously characterized real-time RT-PCR (rRT-PCR) assays for FMDV. The diagnostic accuracy of the mRT-PCR assay was evaluated using 287 field samples, including 247 samples (213 true-positive samples and 35 true-negative samples) from suspected cases of foot-and-mouth disease collected from 65 countries between 1965 and 2006 and 39 true-negative samples collected from healthy animals. The mRT-PCR assay results were compared to those of two singleplex rRT-PCR assays, using virus isolation with antigen enzyme-linked immunosorbent assays as the reference method. The diagnostic sensitivity of the mRT-PCR assay for FMDV was 93.9% (95% confidence interval [CI], 89.8 to 96.4%), and the sensitivity was 98.1% (95% CI, 95.3 to 99.3%) for the two singleplex rRT-PCR assays used in combination. In addition, the assay could reliably differentiate between FMDV and other vesicular viruses, such as swine vesicular disease virus and vesicular exanthema of swine virus. Interestingly, the mRT-PCR detected parapoxvirus (n = 2) and bovine viral diarrhea virus (n = 2) in clinical samples, demonstrating the screening potential of this mRT-PCR assay to identify viruses in FMDV-negative material not previously recognized by using focused single-target rRT-PCR assays.
Tissue Distribution and Retinoid-Mediated Downregulation of an FGF-Binding Protein FGF-BP) in the Rat (2000)

We showed previously that a secreted fibroblast growth factor-binding protein (FGF-BP) can mobilize and bioactivate locally-stored FGFs from the extracellular matrix. This FGF-BP is upregulated in various cancers and plays a rate limiting role as an angiogenic switch molecule during tumor growth. In this paper, we describe the cloning and sequence analysis of the rat homologue of FGF-BP and show its expression pattern and retinoid-mediated downregulation in normal adult rat tissues. The rat FGF-BP amino acid sequence is 91% and 70% homologous to mouse and human, respectively, and contains 10 cysteine residues whose position is conserved across species. In Northern blots, FGF-BP mRNA was detected in the gut, eye, thymus, skin, lung and tongue. Immunohistochemistry confirmed this tissue distribution with cerebellar Purkinje cells, the cerebral chorioid plexus and the eye showing the most distinctive staining patterns. Oral treatment of animals with all-trans-retinoic acid for one and two days induced a significant decrease of FGF-BP protein in tissues from stomach, eye and lung suggesting that regulation of FGF-BP can be one effector mechanism through which retinoids affect normal and pathological processes.
High-pressure synthesis and physical properties of perovskite and post-perovskite Ca1−xSrxIrO3 (2011)

The post-perovskite (pPv) is the high-pressure phase of some highly distorted perovskites. The pPv phase of MgSi${O}_{3}$ stabilized under 125 GPa and 2000 K cannot be quenched to ambient pressure. In contrast, the pPv CaIr${O}_{3}$ can be synthesized under a modest pressure or even at ambient pressure. However, the pPv CaIr${O}_{3}$ has not been fully characterized. We report here systematic structural studies, measurements of transport and magnetic properties including critical phenomena, specific heat, and thermal conductivity in a series of samples Ca${}_{1\ensuremath{-}x}$Sr${}_{x}$Ir${O}_{3}$ synthesized under high pressure. The Ca${}_{1\ensuremath{-}x}$Sr${}_{x}$Ir${O}_{3}$ samples exhibit an evolution from the pPv phase to the perovskite phase. We have also prepared the perovskite (Pv phase) CaIr${O}_{3}$ with the wet chemical method. Rietveld refinements of the pPv and Pv phase CaIr${O}_{3}$ have been made based on high-resolution synchrotron diffraction. In comparison with effects of the chemical substitution on the crystal structure and physical properties, we have studied the structure and magnetic properties of the pPv CaIr${O}_{3}$ under hydrostatic pressure. Results have been discussed in the context of orbital ordering biased on the intrinsic structural distortion and the strong spin-orbit coupling that is much enhanced in these 5$d$ oxides with the pPv structure.
Sinewave generation using bit-streams (2008)

A new method for the generation of high quality sinusoidal signals is presented. Multi-bit binary signals are represented using uniformly weighted single bit-streams which can then be processed by digital logic. Building blocks useful for the construction of the sinusoidal generator are also presented. The bit-stream representation has the advantage of having the characteristics of a classical PWM signal and hence can be used to drive high power switching devices with minimal conditioning. The technique is simple and can be easily implemented using digital logic on a field programmable gate array (FPGA). The operation of a single phase inverter using the proposed technique is demonstrated using an Altera StratixTM FPGA and a custom built power stage. The complete digital design uses less than 200 logic elements (LE). The performance of this technique is quantified using simulations and practical measurements. Practical implementations lead to total harmonic distortion (THD) measures ranging between 0.75% to 4.92%.
Carbohydrate metabolism by murine ovarian follicles and oocytes grown in vitro (2007)

Metabolic markers are potentially valuable for assessment of follicle development in vitro. Carbohydrate metabolism of murine preantral follicles grown to maturity over 13 days in vitro has been measured, and metabolism of resulting oocyte-cumulus complexes (OCCs) and denuded oocytes has been compared with in vivo ovulated control counterparts. Spent follicle culture media were analysed for glucose, lactate and pyruvate concentrations. During follicle in vitro growth, glycolysis accounted for a rise from approximately 24 to 60% of all glucose consumed. Ovulation induction caused a significant increase in glucose uptake and lactate production by in vitro-grown follicles to 71.7+/-1.2 and 96.6+/-4.8 nmoles/day respectively. OCCs grown in vitro had significantly higher rates of glucose consumption and lactate and pyruvate production (110.1+/- 3.5, 191.8+/- 8.9 and 31.7+/- 1.7 pmoles/h respectively) than in vivo ovulated controls (67.4+/- 8.1, 113.9+/- 17.1 and 20.2+/- 4.0 pmoles/h respectively), but a reduced capacity for pyruvate consumption (1.13+/- 0.06 vs 1.49+/- 0.06 pmoles/h by in vivo ovulated oocytes). Metabolism of OCCs was affected by the quality of the original follicle. In vitro-grown oocytes had a reduced cytoplasmic volume when compared with controls (168.3+/- 2.0 vs 199.0+/- 3.2 proportionately respectively) but a similar rate of metabolism per unit volume. Meiotic status influenced metabolism of both OCCs and denuded oocytes. In conclusion, glucose consumption and lactate production by cultured follicles increased in tandem with developmental progression and were stimulated prior to ovulation. Additionally, the metabolic profiles of in vitro produced OCCs and the oocytes within them are affected by long-term exposure to the culture environment.
Catalytic Enantioselective Addition of Diorganozinc Reagents to Vinyl Sulfones (2008)

An efficient method for the catalytic asymmetric conjugate addition of diorganozinc reagents to vinyl sulfones is reported. Using a Binap•Cu complex, enantioselectivities up to 98% ee and high yields can be attained for a variety of substrates. Several dialkylzinc reagents are also compatible with this procedure.
Performance Implications of Periodic Checkpointing on Large-Scale Cluster Systems (2005)

Large-scale systems like BlueGene/L are susceptible to a number of software and hardware failures that can affect system performance. Periodic application checkpointing is a common technique for mitigating the amount of work lost due to job failures, but its effectiveness under realistic circumstances has not been studied. In this paper, we analyze the system-level performance of periodic application checkpointing using parameters similar to those projected for BlueGene/L systems. Our results reflect simulations on a toroidal interconnect architecture, using a real job log from a machine similar to BlueGene/L, and with a real failure distribution from a large-scale cluster. Our simulation studies investigate the impact of parameters such as checkpoint overhead and checkpoint interval on a number of performance metrics, including bounded slowdown, system utilization, and total work lost. The results suggest that periodic checkpointing may not be an effective way to improve the average bounded slowdown or average system utilization metrics, though it reduces the amount of work lost due to failures. We show that overzealous checkpointing with high overhead can amplify the effects of failures. The study also suggests that new metrics and checkpointing techniques may be required to effectively handle job failures on large-scale machines like BlueGene/L.
The autophagy-blocker chloroquine promotes tumor vessel normalization by increasing Notch-signaling (2012)

status: Published
A New Breed of Wet-Developable BARC Materials (2009)

A new family of materials has been developed to serve as a wet-developable bottom antireflective coating (D-BARC) for patterning levels that have a strong need to avoid dry-etch processes for BARC-open steps. Such include some implant levels, where dry-etch introduces surface damage that consequently affects the final electrical performance of a device. Other levels that might benefit from all-wet patterning are those using special substrates such as high-k metal-gate (HKMG) levels. Our design of D-BARC materials combines the unique properties of traditional BARC as well as those of a photoresist to deliver a D-BARC solution that is photoimageable in nature. It was found that isotropically developable (i.e., non-imageable) D-BARCs do not provide viable solutions that satisfy the resolution requirements of the current 32 nm technology node and provide the extendibility to future nodes. The optical properties of the D-BARC material are critical for reflectivity control but high optical density can negatively impact the imaging performance of the material. Therefore a balance is needed where the D-BARC is co-optimized with the photoresist as a system, achieves good reflectivity control, residue-free imaging and process gains.
Role of caveolae in shear stress-mediated endothelium-dependent dilation in coronary arteries (2013)

Integrity of caveolae is critical for endothelium-dependent SSD in MCA. Cav-1(-/-) endothelium is deficient in shear stress-mediated generation of vasodilators including NO, prostaglandins, and epoxyeicosatrienoic acids. Caveolae plays a critical role in endothelial signal transduction from shear stress to vasodilator production and release.
Comment on Weber et al. Mayenite-Based Electride C12A7e−: A Reactivity and Stability Study. Catalysts 2021, 11, 334 (2021)

In 2012, we reported that C12A7 electride (C12A7: e−) significantly promotes the catalytic activity of Ru nanoparticles for ammonia synthesis through the electron donation from the C12A7: e− with a low work function (2.4 eV) to Ru [...]
Optimal Combinations of Broadly Neutralizing Antibodies for Prevention and Treatment of HIV-1 Clade C Infection (2016)

The identification of a new generation of potent broadly neutralizing HIV-1 antibodies (bnAbs) has generated substantial interest in their potential use for the prevention and/or treatment of HIV-1 infection. While combinations of bnAbs targeting distinct epitopes on the viral envelope (Env) will likely be required to overcome the extraordinary diversity of HIV-1, a key outstanding question is which bnAbs, and how many, will be needed to achieve optimal clinical benefit. We assessed the neutralizing activity of 15 bnAbs targeting four distinct epitopes of Env, including the CD4-binding site (CD4bs), the V1/V2-glycan region, the V3-glycan region, and the gp41 membrane proximal external region (MPER), against a panel of 200 acute/early clade C HIV-1 Env pseudoviruses. A mathematical model was developed that predicted neutralization by a subset of experimentally evaluated bnAb combinations with high accuracy. Using this model, we performed a comprehensive and systematic comparison of the predicted neutralizing activity of over 1,600 possible double, triple, and quadruple bnAb combinations. The most promising bnAb combinations were identified based not only on breadth and potency of neutralization, but also other relevant measures, such as the extent of complete neutralization and instantaneous inhibitory potential (IIP). By this set of criteria, triple and quadruple combinations of bnAbs were identified that were significantly more effective than the best double combinations, and further improved the probability of having multiple bnAbs simultaneously active against a given virus, a requirement that may be critical for countering escape in vivo. These results provide a rationale for advancing bnAb combinations with the best in vitro predictors of success into clinical trials for both the prevention and treatment of HIV-1 infection.
APPLICATION OF TIME‐RESOLVED DIFFUSE REFLECTANCE TECHNIQUES IN STUDIES OF REACTION INTERMEDIATES IN SUSPENSIONS OF BACILLUS SUBTILIS (1992)

Short lived reaction intermediates such as triplet states and free radicals can be detected in vivo using laser photolysis techniques with time-resolved diffuse reflectance detection. This novel approach is illustrated for bacterial suspensions of Bacillus subtilis.
Comparison of aerial conidia and blastospores from two entomopathogenic fungi against Diaphorina citri (Hemiptera: Liviidae) under laboratory and greenhouse conditions (2018)

This study compared the insecticidal activity of liquid culture-produced blastospores and solid substrate-produced aerial conidia of Beauveria bassiana GHA and Isaria fumosorosea ARSEF3581 strains against Diaphorina citri adults. Insects exposed to 107 propagules/ml in a spray residue contact leaf bioassay died within 6 days at 25°C, with no significant differences between fungal treatments. At higher concentrations (108 propagules/ml), I. fumosorosea conidia killed psyllids faster compared to its blastospore formulation, i.e. 4 versus 5 days, respectively. In greenhouse tests, the same treatments applied to infested citrus plants (2 × 106 spores/ml) all significantly reduced the number of nymphs compared with the untreated controls over 3 weeks; however, only I. fumosorosea blastospores significantly reduced the number of F1 adult psyllids when compared with controls. Similar results were observed in the follow-up greenhouse test, where I. fumosorosea blastospores were the most effective treatment overall, reducing D. citri populations by about 60% after 21 days; by contrast, imidacloprid killed almost 100% of psyllids within a week in both tests. Fewer psyllids exhibited mycosis in the greenhouse (i.e. ≈20 versus ≥ 87% in the laboratory). This is the first report comparing both conidial and blastospore formulations of B. bassiana and I. fumosorosea for the control of a psyllid pest. Field testing is required to determine how successful different spore formulations might be under various environmental conditions.
Novel CCTT-core split-winding integrated magnetic for High-Power DC-DC converters (2011)

A novel CCTT-core split-winding integrated magnetic (IM) structure is presented in this paper. The IM device is optimized for use in high-power dc-dc converters. The IM structure uses a split-winding configuration which allows for the reduction of external leakage inductance, which is a problem for many IM designs. Magnetic poles are incorporated to help shape and contain the leakage flux within the core window. Low cost and low power loss ferrite is used which results in a very efficient design. An IM design algorithm is developed and implemented in Mathematica for design and optimization. FEA and experimental results from a 80 kW prototype validates the new IM concept and the CCTT magnetic was shown to be 99.7% efficient at full load.
Information, Finance and General Equilibrium (2001)

Information, Finance and General Equilibrium brings together the seminal papers on which Charles R. Plott has founded our understanding of experimental economics and political science.
Tri-Gate Normally-Off GaN Power MISFET (2012)

We present a new normally-off GaN transistor-the tri-gate normally-off GaN metal-insulator-semiconductor field- effect transistor (MISFET). Due to the excellent channel control of a new 3-D gate structure, a breakdown voltage of 565 V has been achieved at a drain leakage current of 0.6 μA/mm and V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">gs</sub> = 0. The new device has an on/off current ratio of more than eight orders of magnitude and a subthreshold slope of 86 ± 9 mV/decade. The threshold voltage of the new device is 0.80 ± 0.06 V with a maximum drain current of 530 mA/mm. These results confirm the great potential of the tri-gate normally-off GaN-on-Si MISFETs for the next generation of power electronics.