gebhart/patrepeval huggingface dataset:
Glycolytic fast‐twitch muscle fiber restoration counters adverse age‐related changes in body composition and metabolism (2013)

Aging is associated with the development of insulin resistance, increased adiposity, and accumulation of ectopic lipid deposits in tissues and organs. Starting in mid-life there is a progressive decline in lean muscle mass associated with the preferential loss of glycolytic, fast-twitch myofibers. However, it is not known to what extent muscle loss and metabolic dysfunction are causally related or whether they are independent epiphenomena of the aging process. Here, we utilized a skeletal-muscle-specific, conditional transgenic mouse expressing a constitutively active form of Akt1 to examine the consequences of glycolytic, fast-twitch muscle growth in young vs. middle-aged animals fed standard low-fat chow diets. Activation of the Akt1 transgene led to selective skeletal muscle hypertrophy, reversing the loss of lean muscle mass observed upon aging. The Akt1-mediated increase in muscle mass led to reductions in fat mass and hepatic steatosis in older animals, and corrected age-associated impairments in glucose metabolism. These results indicate that the loss of lean muscle mass is a significant contributor to the development of age-related metabolic dysfunction and that interventions that preserve or restore fast/glycolytic muscle may delay the onset of metabolic disease.
New algorithms for placement and routing of custom analog cells in ACACIA (2002)

KOAN and ANAGRAM II, novel analog placement and routing tools in the CMU ACACIA system are presented. Together, these tools support a more general model of analog layout than conventional analog macrocell systems. KOAN dynamically merges devices, supports complex symmetry constraints, and automatically generates well and bulk contacts. ANAGRAM II routes arbitrary-width wires, and supports over-the-device and symmetric differential wiring. Both tools have more support for interactive use than their predecessor, the original ANAGRAM system. Preliminary results are encouraging.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
SPIX: A new software package to reveal chemical reactions at trace amounts in very complex mixtures from high‐resolution mass spectra dataset (2020)

SPIX has shown its ability to reveal relevant modifications between two series of large datasets, allowing, for instance, the study of the consequences of a given event on a complex substrate. Most of all - and it is to our knowledge the only software currently available allowing this - it can reveal and monitor any kind of reaction in all types of mixture.
Sodium‐glucose cotransporter 2 inhibitors for treatment of diabetes mellitus after kidney transplantation (2022)

SGLT2i may be a safe and effective treatment for diabetes in kidney transplant recipients. Cost is a barrier to SGLT2i therapy, and UTIs were the most frequently encountered adverse events in this cohort. More studies are needed to understand the safety profile and determine the effect of SGLT2i on diabetes-related comorbidities among kidney transplant recipients.
Anatomy of Penile Venous Drainage in Potent and Impotent Men During Cavernosography (1989)

Recent data suggest that approximately 80 per cent of the men with vasculogenic impotence have evidence of failure to store blood (venous leakage) within the corpora cavernosa. To identify the venous channels into which corporeal blood drains in impotent men, we performed cavernosograms after intracorporeal injection of papaverine in 44 consecutive men presenting with erectile dysfunction and these were compared to studies in 10 potent men. The cavernosograms were examined for evidence of venous drainage from the penis and the site of leakage was identified. It was determined that among the impotent population with vasculogenic impotence 37 of 40 evaluable men (92.5 per cent) demonstrated contrast medium in the venous system draining the penis: the deep dorsal vein was visualized in 55 per cent, proximal cavernosal and crural veins in 55 per cent, deep dorsal and proximal veins in 22.5 per cent and corpus spongiosum in 25 per cent. Only 2 of the 10 potent men demonstrated contrast medium in the venous channels draining the penis. From these observations we conclude that in men suspected of having venogenic impotence identification of the drainage vessels by cavernosography appears to be important in planning any surgical approach to occlude these veins. However, the finding of a venous leak by cavernosography must not be considered a sine qua non diagnosis of venogenic impotence, since a certain percentage of potent men will demonstrate this radiographic finding.
p120 catenin induces opposing effects on tumor cell growth depending on E-cadherin expression (2008)

p120 catenin regulates the activity of the Rho family guanosine triphosphatases (including RhoA and Rac1) in an adhesion-dependent manner. Through this action, p120 promotes a sessile cellular phenotype when associated with epithelial cadherin (E-cadherin) or a motile phenotype when associated with mesenchymal cadherins. In this study, we show that p120 also exerts significant and diametrically opposing effects on tumor cell growth depending on E-cadherin expression. Endogenous p120 acts to stabilize E-cadherin complexes and to actively promote the tumor-suppressive function of E-cadherin, potently inhibiting Ras activation. Upon E-cadherin loss during tumor progression, the negative regulation of Ras is relieved; under these conditions, endogenous p120 promotes transformed cell growth both in vitro and in vivo by activating a Rac1-mitogen-activated protein kinase signaling pathway normally activated by the adhesion of cells to the extracellular matrix. These data indicate that both E-cadherin and p120 are important regulators of tumor cell growth and imply roles for both proteins in chemoresistance and targeted therapeutics.
A variable gain low-noise amplifier with noise and nonlinearity cancellation for DVB applications (2009)

A variable gain low-noise amplifier (LNA) RFIC with noise and nonlinearity cancellation is developed in 0.18-¿m CMOS technology. This variable gain LNA is designed for the need of low power consumption and high performance in DVB applications. The variable gain LNA achieves the maximum gain of 9.2-14.4 dB from 50 MHz to 860 MHz, which also provides the dynamic range more than 30 dB. The input and output return losses less than -5.6 dB and -10 dB, respectively. The supply voltage is 1.8 V and power consumption is 19.8 mW. With the success of cancellation, the variable gain LNA with maximum gain has the measured noise figure of 2.5-3.5 dB and the measured OIP <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> of 10-17 dBm from 50 MHz to 860 MHz. The chip area of the implemented variable gain LNA RFIC is 0.78×0.85 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .
Impacts of P inputs on availability of Fe, Mn, Zn and Se in soils (2023)

PHOSPHATE IONS are hard-Lewis-bases, , which might not preferably bind with Fe, Mn and Zn (borderline Lewis acids); though P-applications diminish considerably availability of micronutrients and other elements such as selenium. Interactions between P and these elements are still in need for more detailed investigations. Therefore, the current study was executed as a trial to through more light on such mutual relations. A pot experiment was, therefore, conducted following a complete randomized-design to attain this aim. Briefly, the soils under study (a clayey non-calcareous soil and a sandy calcareous one) were enriched with 5 mg Fe, 1 mg Mn, 1.5 mg Zn and 10 mg Se kg-1 .Thereafter, they received elevated P -doses (15, 30, 60 and120 mg P kg-1) and incubated for 72 h while keeping soil moisture gravimetrically at field capacity throughout this study. Key results revealed that AB-DTPA-extractable-P increased significantly with increasing the rate of applied-P and such increases were noticeable with ageing. In contrast, AB-DTPA-Fe content was not affected significantly by P-applications. Regarding AB-DTPA-extractable-Mn and Zn, their contents increased progressively in the non-calcareous soil upon application of P at 60 mg P kg-1 soil (P60) or the higher for an incubation period extended up to 48h while remained statistically unchangeable in the non-calcareous soil. In both soils, the dose of applied-P did not significantly affect AB-DTPA-Se, yet this available fraction was affected by soil ageing showing fluctuations cycles of increases and decreases. More experiments are needed using additional time sequences within the first 48h of P-application
Abstract 5569: Paracrine Effects of Cardiomyocyte STAT3 Determine the Vasculogenic Differentiation Potential of Cardiac Progenitor Cells: Potential Role of Endogenous Erythropoietin (2008)

Mice with a cardiomyocyte-restricted knock out of STAT3 (αMHC-Cretg/+; STAT3flox/flox, STAT3-KO) show a continuous decrease of cardiac vascularization and develop heart failure beyond the age of 9 months. We investigated the role of cardiomyocyte STAT3-driven paracrine effects on Sca-1+ cardiac progenitor cells (CPC) in the mouse heart. CPC were immunomag-netically isolated from KO and wildtype (STAT3flox/flox, WT) hearts (age: 3 months). PCR and Western blot confirmed deletion of STAT3 in cardiomyocytes of KO mice, while CPC from KO showed normal expression of STAT3. The total number of CPC per heart was similar between WT and KO mice. FACS analysis revealed a reduced number of endothelial progenitor cells (defined by co-expression of Sca-1, CD31 and CD38, −25%, P&lt;0.05) in CPC from KO compared to CPC from WT. In vitro culture for 4 weeks on fibronectin-coated plates of CPC from KO revealed reduced proliferation (−33%, p&lt;0.01), impaired endothelial cell (EC) tubeformation (monitored with Tie2, eNOS and CD31 immunohistochemistry (IHC), p&lt;0.01) and enhanced adipocyte differentiation (oil red staining and RT-PCR, p&lt;0.05) compared with CPC from WT. Microarray of freshly isolated CPC reflected this differences in EC and adipocyte differentiation on the mRNA level (i.e. EC marker Prostaglandin E Rezeptor-3: 2.3-fold lower; adipocyte marker Lipocalin-2 2.7-fold higher in CPC from KO hearts). Microarray results from whole left ventricular tissue showed a decrease in gene expression of Erythropoietin (Epo) in KO hearts (-9,25-fold). ELISA, IHC and methylcellulose assay confirm expression of active EPO by cardiomyocytes. CPC express high levels of EPO receptor (IHC, RT-PCR). Epo enhanced tube formation and sprouting of EC and attenuated adipocyte differentiation of CPCs from KO. In vivo treatment with Epo rescued impaired proliferation, promoted EC differentiation and attenuated adipocyte differentiation of CPC from KO hearts. Conclusion: STAT3-dependent paracrine factors from cardiomyocytes regulate proliferation, differentiation and vasculogenic properties of CPCs. Cardiomyocyte derived EPO is an important paracrine mediator that promotes differentiation into EC and attenuates differentiation into adipocytes from CPCs in the adult heart.
Antibiotic Susceptibility of Bacteria Infecting Total Joint Arthroplasty Sites (2006)

Empiric antibiotic treatment for suspected periprosthetic infection should be guided by the class of the infection and the findings of Gram staining. We believe that, until the final culture results are available, acute hematogenous infections should initially be treated by a combination of cefazolin and gentamicin therapy. All chronic and acute postoperative infections with Gram-positive bacteria and all cases in which a Gram stain fails to identify bacteria should be managed with vancomycin. Infections with Gram-negative bacteria should be managed with a third or fourth-generation cephalosporin. Infections with mixed Gram-positive and Gram-negative bacteria should be managed with a combination of vancomycin and a third or fourth-generation cephalosporin. Furthermore, we believe that if culture results and other confirmatory tests are not positive by the fourth postoperative day, termination of empiric antibiotic therapy should be considered.
Infectious Agents (2021)

Fungi are a diverse group of eukaryotes that includes yeasts, molds, mushrooms, rusts, smuts, and the recently reclassified microsporidia. Filamentous saprophytic fungi, represented by hyaline hyphomycetes, dematiaceous hyphomycetes and zygomycetes, are by far the most commonly encountered agents producing bovine mycotic abortion. The most likely routes for exposure to fungi causing mycotic placentitis and abortion are the respiratory and gastrointestinal tracts. Diagnosis of mycotic abortion can be aided by gross, microscopic, histopathologic, or cultural methods of examination. Specimens for mycotic abortion can be used for gross examination, direct microscopic and histopathologic examination, fungal culture, and molecular detection. A common medium for the culture and isolation of fungi is Sabouraud's dextrose agar with and without the addition of antibiotics. The microscopic morphology and characteristics of the fungi can aid in identification and confirmation of the cultural isolate.
“ Campylobacter jejuni motility integrates specialized cell shape, flagellar filament, and motor, to coordinate action of its opposed flagella in viscous media” (2019)

Abstract Campylobacter jejuni rotates a flagellum at each pole to swim through the viscous mucosa of its hosts’ gastrointestinal tracts. Despite their importance for host colonization, however, how C. jejuni coordinates rotation of these two opposing flagella is unclear. As well as their polar placement, C. jejuni’s flagella deviate from the Enterobacteriaceael norm in other ways: their flagellar motors produce much higher torque and their flagellar filament is made of two different zones of two different flagellins. To understand how C. jejuni’s opposed motors coordinate, and what contribution these factors play in C. jejuni motility, we developed strains with flagella that could be fluorescently labeled, and observed them by high-speed video microscopy. We found that C. jejuni coordinates its dual flagella by wrapping the leading filament around the cell body during swimming in high-viscosity media and that its differentiated flagellar filament has evolved to facilitate this wrapped-mode swimming. Unexpectedly, C. jejuni ’s helical body is important for facile unwrapping of the flagellar filament from the cell body during switching of swimming trajectory. Our findings demonstrate how multiple facets of C. jejuni’s flagella and cell plan have co-evolved for optimal motility in high-viscosity environments.
Potential histamine H2-receptor antagonists. Synthesis, conformational studies and activity of novel 3-oxo-1,2,5-thiadiazole 1,1-dioxide derivatives. (1990)

New histamine H2-receptor antagonists bearing a novel "urea equivalent", the 3-oxo-1,2,5-thiadiazole 1,1-dioxide ring, have been synthesized in a transamination reaction. Open chain derivatives have also been obtained. Theoretical conformational analysis of the compounds has been carried out using a molecular modelling program. Semiempirical CNDO/2 calculations have also been performed. The antisecretory and cytoprotective activities of the compounds have been evaluated.
Three-dimensional deconvolution of complex fields (2011)

We present a technique for 3-D image processing of complex fields acquired by digital holographic microscopy. It consists in inverting the coherent imaging by filtering the complex spectrum with a pseudo three-dimensional coherent transfer function.
Self‐Affinity in Braided Rivers (1996)

Three braided rivers of different scales and different hydrologic/geomorphologic characteristics (the Aichilik and Hulahula in Alaska and the Brahmaputra in Bangladesh) are analyzed for spatial scaling using a logarithmic correlation integral method developed earlier by the authors. It is shown that the rivers exhibit anisotropic scaling (self‐affinity) with fractal exponents v x = 0.72–0.74 and v y = 0.51‐0.52, the x axis being oriented along the river and the y axis in the perpendicular direction. The fact that despite large differences in scales (0.5–15 km in braid plain width), slopes (7 × 10 −3 to 8 × 10 −5 ), and types of bed material (gravel to sand), the analyzed braided rivers show similar spatial scaling deserves special attention. It might indicate the presence of universal features in the underlying mechanisms responsible for the formation of the spatial structure of braided rivers. Also, comparison of fractal characteristics of braided rivers with those of single‐channel rivers and river networks suggests that braided rivers form a class of fractal objects lying between the classes of single‐channel rivers and river networks.
Predicting undetected glaucoma according to age and IOP: a prediction model developed from a primarily European‐derived population (2018)

We created a model estimating the combined effect of IOP and age on the likelihood of undetected glaucoma. The model may facilitate case-finding in European-derived populations. Despite the important impact of IOP on the risk of glaucoma, a large proportion of subjects with undetected glaucoma had IOP ≤ 21 mmHg.
Comprehensive AAV capsid fitness landscape reveals a viral gene and enables machine-guided design (2019)

Adeno-associated virus (AAV) capsids can deliver transformative gene therapies, but our understanding of AAV biology remains incomplete. We generated the complete first-order AAV2 capsid fitness landscape, characterizing all single-codon substitutions, insertions, and deletions across multiple functions relevant for in vivo delivery. We discovered a frameshifted gene in the VP1 region that expresses a membrane-associated accessory protein that limits AAV production through competitive exclusion. Mutant biodistribution revealed the importance of both surface-exposed and buried residues, with a few phenotypic profiles characterizing most variants. Finally, we algorithmically designed and experimentally verified a diverse in vivo targeted capsid library with viability far exceeding random mutagenesis approaches. These results demonstrate the power of systematic mutagenesis for deciphering complex genomes and the potential of empirical machine-guided protein engineering.
Perceptual Learning During Action Video Game Playing (2009)

Action video games have been shown to enhance behavioral performance on a wide variety of perceptual tasks, from those that require effective allocation of attentional resources across the visual scene, to those that demand the successful identification of fleetingly presented stimuli. Importantly, these effects have not only been shown in expert action video game players, but a causative link has been established between action video game play and enhanced processing through training studies. Although an account based solely on attention fails to capture the variety of enhancements observed after action game playing, a number of models of perceptual learning are consistent with the observed results, with behavioral modeling favoring the hypothesis that avid video game players are better able to form templates for, or extract the relevant statistics of, the task at hand. This may suggest that the neural site of learning is in areas where information is integrated and actions are selected; yet changes in low-level sensory areas cannot be ruled out.
Nitrogen-Containing Aromatic Radical Anions Perform Multiple Proton and Electron Transfers Near-Simultaneously with Multiply Protonated Cations (2021)

Gas phase ion/ion reactions between singly charged radical reagent anions and multiply charged cation precursors primarily result in either proton or electron transfer. These ion/ion reactions have been extensively studied for bioanalysis, and many reagent anions have been tested and reported. Here, nitrogen-containing aromatic radical anions were tested for the ability to conduct proton or electron transfer by their reaction with the ubiquitin [M + 13H]<sup>+13</sup> precursor. The singly charged anion of 2,2'-biquinoline was found to undergo charge inversion to singly protonated cations via near-simultaneous proton and electron transfers while reactants were bound in a single ion/ion reaction complex. Although the focus of this paper was 2,2'-biquinoline, all three nitrogen-containing aromatic compounds tested produced similar results.
River: an intermediate language for stream processing (2015)

This paper presents both a calculus for stream processing, named Brooklet, and its realization as an intermediate language, named River. Because River is based on Brooklet, it has a formal semantics that enables reasoning about the correctness of source translations and optimizations. River builds on Brooklet by addressing the real-world details that the calculus elides. We evaluated our system by implementing front-ends for three streaming languages, and three important optimizations, and a back-end for the System S distributed streaming runtime. Overall, we significantly lower the barrier to entry for new stream-processing languages and thus grow the ecosystem of this crucial style of programming. Copyright © 2015 John Wiley & Sons, Ltd.
Figure S1 from The MD Anderson Prostate Cancer Patient-derived Xenograft Series (MDA PCa PDX) Captures the Molecular Landscape of Prostate Cancer and Facilitates Marker-driven Therapy Development (2023)

&lt;p&gt;PDXs derived from mixed adeno- and neuroendocrine human prostate carcinoma recapitulating only one morphologic component&lt;/p&gt;
Design of a 12kW vertical axis wind turbine equipped with a direct driven PM synchronous generator (2006)

Design of a 12kW vertical axis wind turbine equipped with a direct driven PM synchronous generator
Bright trion emission from semiconductor nanoplatelets (2020)

The trion, a quasiparticle comprising one exciton and an additional charge carrier, offers unique opportunities for generating spin-photon interfaces that can be used in developing quantum networks. Trions are also actively sought after for integrated optoelectronic devices including photovoltaics, photodetectors, and spintronics. However, formation of trions in strongly confined low-dimensional materials is often deemed detrimental. This is because trion emission in such materials is typically prohibited due to the predominant nonradiative Auger recombination processes. Semiconductor nanoplatelets with their strong confinement in the thickness direction and extended lateral geometries exhibit large exciton coherence sizes and reduced carrier-carrier interactions that may enable unprecedented trion properties. Here, we perform optical spectroscopic studies of individual CdSe nanoplatelets at cryogenic temperatures and observe bright trion emission with intensities comparable to that of neutral exciton emission. We perform carrier dynamics studies of the nanoplatelets and find that due to their extended lateral geometry, the fast radiative decay rate of the nanoplatelets at cryogenic temperatures is comparable to the inhibited Auger recombination rate, leading to the bright trion emission. Our tight-binding theory further reveals distinct size-tunable trion emission in the nanoplatelets that is advantageous for efficient trion emission. These properties make semiconductor nanoplatelets potential candidates as photon sources for optoelectronic and quantum logic devices.