gebhart/patrepeval huggingface dataset:
Effects of Weight Loss on Mechanisms of Hyperglycemia in Obese Non-Insulin-Dependent Diabetes Mellitus (1986)

To quantitate the effects of weight loss on the mechanisms responsible for hyperglycemia in non-insulin-dependent diabetes mellitus (NIDDM), eight obese subjects with NIDDM were studied before and after weight reduction with posttreatment assessment after 3 wks of isocaloric (weight maintenance) refeeding. After weight loss of 16.8 ± 2.7 kg (mean ± SE), the fasting plasma glucose level decreased 55% from 277 ± 21 to 123 ± 8 mg/dl. The individual fasting glucose levels were highly correlated with the elevated basal rates of hepatic glucose output (HGO) (r = 0.91, P &amp;lt; .001), which fell from 138 ± 11 to 87 ± 5 mg · m2 · min1 after weight loss. The change in fasting plasma glucose also correlated significantly with the change in the basal rates of HGO (r = 0.74, P &amp;lt; .05). This was associated with reduced fasting serum levels of glucagon (from 229 ± 15 to 141 ± 12 pg/ml), reduced free fatty acids (from 791 ± 87 to 379 ± 35 μeq/L), and unchanged basal insulin levels (17 ± 4 to 15 ± 2 fill/ml). Peripheral glucose disposal, assessed by the euglycemic glucose-clamp technique, at insulin infusion rates of 120 and 1200 mU · m2 · min1 increased between 135 and 165%, from 128 ± 17 to 288 ± 24 mg · m2 · min1 during the 120-mU · m2 · min1 studies and from 159 ± 19 to 318 ± 24 mg · m2 · min1 during the 1200-mU · m2 · min1 clamp studies, despite comparable steady-state serum insulin levels at each infusion rate before and after weight loss. HGO during the 120-mU · m2 · min1 clamp studies increased from 85% to complete (100%) suppression after treatment. Adipocyte size was reduced 44% (851 ± 91 to 475 ± 48 pi), whereas surface area decreased by 32% (4.30 × 104 to 2.92 × 104 μm2cell). Insulin binding to isolated adipocytes was unchanged, whereas basal in vitro rates of 3-O-methylglucose transport increased from 0.21 ± 0.13 to 0.53 ± 0.24 pmol/(2 × 109 μm2) × (10 s−1) and maximal glucose transport rates increased from 0.64 ± 0.29 to 1.18 ± 0.48 pmol/(2 × 105 cells) × (10 s−1) and 0.42 ± 0.20 to 1.04 ± 0.30 pmol/(2 × 109 μm2) × (10 s−1). Finally, absolute serum insulin levels during oral glucose-tolerance tests and meal-tolerance tests were unchanged by weight reduction, whereas plasma glucose levels were markedly reduced. We conclude that in obese NIDDM, weight loss results in improved glucose homeostasis with 1) reducedbasal HGO predominently responsible for the lowering of fasting glucose levels; 2) improved postprandial glucose excursions with marked amelioration of peripheral insulin resistance due to improved postreceptor insulin action, which is at least partly due to enhanced glucose transport system activity; and 3) unchanged absolute insulin levels in the face of markedly reduced glycemia, indicative of enhanced p-cell sensitivity to insulinogenic stimuli.
Comparison of sustained off‐resonance irradiation collisionally activated dissociation and multipole storage‐assisted dissociation for top‐down protein analysis (2004)

Tandem mass spectrometric data acquired for small (8-18 kDa) intact proteins by sustained off-resonance irradiation collisionally activated dissociation (SORI-CAD) and multipole storage-assisted dissociation (MSAD) were compared, and the results indicate that the two activation methods do not always provide the same fragmentation patterns. In MSAD experiments, the charge state distribution made available by the ionization conditions may dictate the range of fragment ions that can be generated. In addition, conditions of high space charge within the hexapole impair transmission and/or trapping of high m/z species, which can result in loss of important precursor and product ions. Finally, the non-resonant nature of activation in MSAD can provide access to secondary dissociation processes that are not available by SORI. Because of these considerations, MSAD is less reliable than SORI for generating sequence tag data. However, it appears that MSAD samples 'preferred' cleavage processes (i.e. those occurring at D and P residues) just as well as SORI, which implies that MSAD data may be somewhat more compatible with search algorithms that utilize unprocessed fragment ion masses.
Resolution of housekeeping gene sequences used in MLSA for the genus Streptomyces and reclassification of Streptomyces anthocyanicus and Streptomyces tricolor as heterotypic synonyms of Streptomyces violaceoruber (2022)

Although 16S rRNA gene sequences are conventionally analysed in bacterial systematics, their resolution is not sufficient for species identification. Multilocus sequence analysis (MLSA) is a powerful method for species identification as well as the elucidation of phylogenetic relationships in the genus <i>Streptomyces</i>. Gene sequences of <i>atpD, gyrB, recA, rpoB</i> and <i>trpB</i> are generally used in MLSA for <i>Streptomyces</i> species. This study aims to evaluate the sequence analysis of one gene instead of all five genes to be employed for species identification. The resolution of <i>atpD</i> gene sequences was not necessarily able to distinguish closely related species. In contrast, <i>trpB</i> gene sequence similarities correlated to the MLSA-based evolutionary distances, especially among closely related strains. A pairwise similarity of 97.9 % in <i>trpB</i> gene sequences was proposed as the threshold for species delineation based on the feasibility examined using strain pairs that shared >99.93 % pairwise 16S rRNA gene sequence similarities. Resequencing the five housekeeping genes followed by MLSA suggested that <i>Streptomyces anthocyanicus</i> and <i>Streptomyces tricolor</i> are synonyms of <i>Streptomyces violaceoruber</i>.
Serum from Laron Mice Partially Protects against <i>Trypanosoma Cruzi</i> Infection (2022)

Chagas disease (CD) is one of the most devasting parasitic diseases in the Americas affecting 7 to 8 million people worldwide. In vitro and in vivo experiments have demonstrated that decreased growth hormone (GH) serum levels occur as CD progresses. Interestingly, inactivating mutations in the GH receptor in humans induce Laron syndrome (LS), a clinical entity characterized by increased GH and decreased insulin growth factor-1 (IGF-1) serum levels. The largest cohort of LS subjects lives in the southern provinces of Ecuador. Remarkably, CD prevalence in these individuals is diminished despite living in highly endemic areas. In the current ex vivo study, we employed serum from GHR -/- mice, also known as LS mice (a model of GH resistance with high GH and low IGF-1 levels), and serum from bovine GH (bGH) transgenic mice (high GH and IGF-1), to test the effect on T. cruzi infection. We infected mouse fibroblast L-cells treated with serum from each type of mouse with metacyclic trypomastigotes from Trypanosoma cruzi (etiological CD infectious agent). Treatment with GHR-/- serum (LS mice) significantly decreased infection by 28% compared to 48% seen in control wild-type mouse serum (WT). Treatment with bGH mouse serum significantly decreased infection by only 41% compared to 54% from WT controls. Our results suggest that high GH and low IGF-1 in blood circulation, as typically seen in LS individuals, confers partial protection against T. cruzi infection.
PRODUCTION OF A PRELIMINARY QUALITY CONTROL PIPELINE FOR SINGLE NUCLEI RNA-SEQ AND ITS APPLICATION IN THE ANALYSIS OF CELL TYPE DIVERSITY OF POST-MORTEM HUMAN BRAIN NEOCORTEX (2016)

Next generation sequencing of the RNA content of single cells or single nuclei (sc/nRNA-seq) has become a powerful approach to understand the cellular complexity and diversity of multicellular organisms and environmental ecosystems. However, the fact that the procedure begins with a relatively small amount of starting material, thereby pushing the limits of the laboratory procedures required, dictates that careful approaches for sample quality control (QC) are essential to reduce the impact of technical noise and sample bias in downstream analysis applications. Here we present a preliminary framework for sample level quality control that is based on the collection of a series of quantitative laboratory and data metrics that are used as features for the construction of QC classification models using random forest machine learning approaches. We've applied this initial framework to a dataset comprised of 2272 single nuclei RNA-seq results and determined that ~79% of samples were of high quality. Removal of the poor quality samples from downstream analysis was found to improve the cell type clustering results. In addition, this approach identified quantitative features related to the proportion of unique or duplicate reads and the proportion of reads remaining after quality trimming as useful features for pass/fail classification. The construction and use of classification models for the identification of poor quality samples provides for an objective and scalable approach to sc/nRNA-seq quality control.
Cross-Layer Management for Multiple Adaptive Streaming Clients in Wireless Home Networks (2018)

In this letter, we propose a solution for managing multiple adaptive streaming clients running on different devices in a wireless home network. Our solution consists of two main aspects: a manager that determines bandwidth allocated for each client and a client-based throughput control mechanism that regulates the video traffic throughput of each client. The experimental results using a real test-bed show that our solution is able to effectively improve the quality for concurrent streaming clients.
Simulation study of a piezoelectric micromachined ultrasonic transducer as terahertz differentiator (2020)

We propose a simple method to differentiate a THz pulse using a piezoelectric micromachined ultrasonic transducer (PMUT). We demonstrate with simulations that the modulated THz signal after PMUT is proportional to the first-order derivative of the THz pulse.
Vertically Aligned Single-Walled Carbon Nanotubes as Low-cost and High Electrocatalytic Counter Electrode for Dye-Sensitized Solar Cells (2011)

A novel dye-sensitized solar cell (DSSC) structure using vertically aligned single-walled carbon nanotubes (VASWCNTs) as the counter electrode has been developed. In this design, the VASWCNTs serve as a stable high surface area and highly active electrocatalytic counter-electrode that could be a promising alternative to the conventional Pt analogue. Utilizing a scalable dry transfer approach to form a VASWCNTs conductive electrode, the DSSCs with various lengths of VASWCNTs were studied. VASWCNTs-DSSC with 34 μm original length was found to be the optimal choice in the present study. The highest conversion efficiencies of VASWCNTs-DSSC achieved 5.5%, which rivals that of the reference Pt DSSC. From the electrochemical impedance spectroscopy analysis, it shows that the new DSSC offers lower interface resistance between the electrolyte and the counter electrode. This reproducible work emphasizes the promise of VASWCNTs as efficient and stable counter electrode materials in DSSC device design, especially taking into account the low-cost merit of this promising material.
A flexible 300 mm integrated Si MOS platform for electron- and hole-spin qubits exploration (2021)

We report on a flexible 300 mm process that optimally combines optical and electron beam lithography to fabricate silicon spin qubits. It enables on-the-fly layout design modifications while allowing devices with either n- or p-type ohmic implants, a pitch smaller than 100 nm, and uniform critical dimensions down to 30 nm with a standard deviation ~ 1.6 nm. Various n- and p-type qubits are characterized in a dilution refrigerator at temperatures ~ 10 mK. Electrical measurements demonstrate well-defined quantum dots, tunable tunnel couplings, and coherent spin control, which are essential requirements for the implementation of a large-scale quantum processor.
Supplemental Figure S3 from <i>KRAS</i> Genomic Status Predicts the Sensitivity of Ovarian Cancer Cells to Decitabine (2023)

&lt;p&gt;A, cell viability after treatment with decitabine (AUC, x-axis) was plotted against DNMT3a or DNMT3b mRNA expression (log2, y-axis). B, western blot analysis was performed after treatment with decitabine (0.5 ÃŽÂ¼M) or DMSO for nine days in eight ovarian cancer cell lines. C, quantification of western blot analysis of DNMT1 after treatment with selumetinib for six days in two KRAS-mutant ovarian cancer cell lines as depicted in the main text.&lt;/p&gt;
Reflective binary amplitude grating for soft x-ray shearing and Hartmann wavefront sensing (2020)

We demonstrate a reflective wavefront sensor grating suitable for the characterization of high-quality x-ray beamlines and optical systems with high power densities. Operating at glancing incidence angles, the optical element is deeply etched with a two-level pattern of shearing interferometry gratings and Hartmann wavefront sensor grids. Transverse features block unwanted light, enabling binary amplitude in reflection with high pattern contrast. We present surface characterization and soft x-ray reflectometry of a prototype grating array to demonstrate function prior to wavefront measurement applications. A simulation of device performance is shown.
Separating thermal coagulation and cavitation effects in HIFU attenuation measurements (2003)

HIFU can be used to destroy tumors. The conversion of acoustic energy into heat causes protein coagulation (Lesion) in tissue. Attenuation measurements have been proposed to monitor the progression of thermal therapy. The goal of this work is to study and separate the effects of cavitation and thermal coagulation in attenuation measurements. A HIFU transducer was used to treat Bovine liver. A receiving transducer mounted across from the transmitting HIFU transducer measured attenuation during the treatment. A pressure chamber provided static pressure greater than the pressure amplitude of the HIFU wave, which suppressed cavitation. rf data from a commercial ultrasound scanner was also obtained. A large increase in attenuation was observed with cavitation present, while a subtle increase in attenuation was observed with cavitation suppressed. Attenuation estimated from the RF data showed an increase in attenuation downstream of the location of the lesion with cavitation present, while a subtle increase in attenuation was observed at the location of the lesion with cavitation suppressed. It has been found that attenuation measurements are greatly affected by the presence of cavitation, and the actual effect of thermal coagulation on attenuation is quite small. [Work supported by NIH, NSF, NSBRI.]
Understanding the Antibody Repertoire in Neuropsychiatric Systemic Lupus Erythematosus and Neuromyelitis Optica Spectrum Disorder (2017)

Patients with demyelinating NPSLE should be tested for IgG antibodies to AQP-4, MOG, and DWEYS. IgG anti-AQP-4 can be considered diagnostic for NMOSD, whereas none of these antibodies appear to be diagnostic for demyelinating NPSLE. Moreover, IgG anti-dsDNA are present in patients with NMOSD but are not cross-reactive with IgG anti-DWEYS, indicating that the antigenic stimulus and mechanisms of tissue damage are potentially different between demyelinating NPSLE and NMOSD.
Activation of Neural Cell Fate Programs Toward Direct Conversion of Adult Human Fibroblasts into Tri-Potent Neural Progenitors Using OCT-4 (2014)

Several transcription factors and methods have been used to convert fibroblasts directly to neural fate and have provided insights into molecular mechanisms as to how each of these required factors orchestrate neural fate conversion. Here, we provide evidence and detailed characterization of the direct conversion process of primary adult human fibroblasts (hFib) to neural progenitor cells (NPC) using OCT4 alone. Factors previously associated with neural cell fate conversion were induced during hFib-NPC(OCT-4) generation, where OCT-4 alone was sufficient to induce neural fate conversion without the use of promiscuous small-molecule manipulation. Human Fib-NPC(OCT-4) proliferate, express neural stem/progenitor markers, and possess developmental potential that gives rise to all three major subtypes of neural cells: astrocytes, oligodendrocytes, and neurons with functional capacity. We propose a de-convoluted reprogramming approach for neural fate conversion in which OCT4 is sufficient for inducing neural conversion from hFib for disease modeling as well as the fundamental study of early neural fate induction.
Conjugate Adder Net (CAddNet) - a Space-Efficient Approximate CNN (2022)

The AdderNet was recently developed as a way to implement deep neural networks without needing multiplication operations to combine weights and inputs. Instead, absolute values of the difference between weights and inputs are used, greatly reducing the gate-level implementation complexity. Training of AdderNets is challenging, however, and the loss curves during training tend to fluctuate significantly. In this paper we propose the Conjugate Adder Network, or CAddNet, which uses the difference between the absolute values of conjugate pairs of inputs and the weights. We show that this can be implemented simply via a single minimum operation, resulting in a roughly 50% reduction in logic gate complexity as compared with AdderNets. The CAddNet method also stabilizes training as compared with AdderNets, yielding training curves similar to standard CNNs.
Bridging Between Photonic Scales (2005)

Abstract : We show confinement of light traveling in micron-size waveguides into nm-size regions. Most photonic dielectric cavities have been traditionally limited to sizes that are on the order of the wavelength of light. Here we show a decrease in mode volume by several orders of magnitude over previous dielectric microcavities based on wavelength independent dielectric discontinuities. The principle of reduction of effective mode volume, well below the dimensions of the wavelength of light can be applied to nearly every existing microcavity resonator to enhance not only light emission but also non-linear effects. Such a reduction can enable the demonstration of effective mode volumes of nm-size and increase of Purcell factor by orders of magnitude. This technique may enable new experiments in cavity Quantum Electrodynamics, ultra-sensitive single atom detection, and low threshold lasers
Derivation of instantaneous current references for three phase PV inverter connected to grid with active and reactive power flow control (2011)

In this paper, inverter reference current generation for a three phase grid connected PV inverter under generalized grid voltage conditions is proposed. The proposed method facilitates high bandwidth grid active and reactive power flow control along with minimum DC link ripples with grid current THD control facility by finding suitable current reference directly in the a-b-c frame. The proposed method is much faster than the conventional methods because of the absence of phase lock loop (PLL) and Park's transformation requirements. The proposed method is also independent of grid voltage fundamental frequency and capable of rejecting the grid voltage harmonics. These advantages make it more suitable for micro-grid applications. The proposed method is validated with rigorous experiments and test results presented depict the efficacy of the proposed system.
Hexahedral LED Arrays with Row and Column Control Lines Formed by Selective Liquid‐Phase Plasticization and Nondisruptive Tucking‐Based Origami (2020)

Abstract Origami/kirigami of flexible electronics is a promising way to produce 3D electronics because well‐developed silicon‐based technologies can be used for the planar circuitry layout. However, it is still a challenge to enable general row and column control lines to develop 3D addressable sensory and display systems. This study addresses this issue via selective plasticization of an acrylonitrile butadiene styrene (ABS) film with N , N ‐dimethylformamide (DMF) through polydimethylsiloxane (PDMS) microfluidic channels. The use of DMF provides plasticization in a controllable manner because of the fast absorption of the DMF in the liquid phase during the plasticization process, a prolonged retention time of DMF in the ABS film at room temperature during the transformation process, and fast desorption at 60– 80 °C for the deplasticization process. The use of microfluidic channels allows high‐resolution selective plasticization to enable extreme cases of local bending or even folding inward and outward, thereby enabling tucking‐based origami with no crack generation. The lamination of membrane‐type electronic devices to an ABS film followed by selective plasticization and transformation enables nondisruptive tucking‐based origami at the electronics level, such as for the demonstration of a hexahedral light‐emitting diode (LED) array with general row and column control lines.
Integration of GaN and Diamond Using Epitaxial Lateral Overgrowth (2020)

Growth of single-crystalline GaN on polycrystalline diamond is reported for the first time. The structure was achieved using a combined process including selective diamond growth on GaN/Si wafers using hot filament chemical vapor deposition (CVD) and epitaxial lateral overgrowth of GaN on the window region between then above the diamond stripes via metal organic CVD. Optimization of the growth was performed by varying the ammonia to trimethylgallium mole ratio (V/III), chamber pressure, and temperature in the range of 8000-1330, 40-200 Torr, and 975-1030 °C, respectively. A lower pressure, higher V/III ratio, higher temperature, and GaN window mask openings along [11̅00] resulted in enhanced lateral growth of GaN. Complete lateral coverage and coalescence of GaN were achieved over a [11̅00]-oriented 5 μm-wide GaN window between 5 μm diamond stripes when using V/III = 7880, <i>P</i> = 100 Torr, and <i>T</i> = 1030 °C. The crystalline quality of overgrown GaN was confirmed using cross-sectional scanning electron microscopy, high-resolution X-ray diffraction, micro-Raman spectroscopy, transmission electron microscopy, and selective-area electron diffraction.
Entangled quantum-key-distribution randomness (2008)

Random number generators are important components of information security systems. In particular, cryptography standards require that the numbers generated by quantum key distribution applications meet a rigorous set of standardized randomness tests. To date, implementations of entangled quantum key distribution (EQKD) have not included any randomness assessment. We report on the results of randomness tests and highlight how typical EQKD system operation affects the successes and failures in meeting the fundamental test criteria.
Localized 4 Integrin Phosphorylation Directs Shear Stress-Induced Endothelial Cell Alignment (2020)

Vascular endothelial cells respond to laminar shear stress by aligning in the direction of flow, a process which may contribute to athero-protection. Here we report that localized α4 integrin phosphorylation is a mechanism for establishing the directionality of shear stress-induced alignment in microvascular endothelial cells. Within 5 minutes of exposure to a physiological level of shear stress, endothelial α4 integrins became phosphorylated on Ser988. In wounded monolayers, phosphorylation was enhanced at the downstream edges of cells relative to the source of flow. The shear-induced α4 integrin phosphorylation was blocked by inhibitors of cAMP-dependent protein kinase A (PKA), an enzyme involved in the alignment of endothelial cells under prolonged shear. Moreover, shear-induced localized activation of the small GTPase Rac1, which specifies the directionality of endothelial alignment, was similarly blocked by PKA inhibitors. Furthermore, endothelial cells bearing a non-phosphorylatable α4(S988A) mutation failed to align in response to shear stress, thus establishing α4 as a relevant PKA substrate. We thereby show that shear-induced PKA-dependent α4 integrin phosphorylation at the downstream edge of endothelial cells promotes localized Rac1 activation, which in turn directs cytoskeletal alignment in response to shear stress.