gebhart/patrepeval huggingface dataset:
Effects of ACTH-Induced Long-Term Hypercortisolism on the Transcriptome of Canine Visceral Adipose Tissue (2022)

Cushing’s syndrome, or hypercortisolism (HC), a common endocrinopathy in adult dogs, is caused by chronic hypercortisolemia. Among different metabolic disorders, this syndrome is associated with enhanced subcutaneous lipolysis and visceral adiposity. However, effects of HC in adipose tissue, especially regarding visceral adipose tissue (VAT), are still poorly understood. Herein, the transcriptomic effects of chronic HC on VAT of dogs were evaluated. For this, subcutaneously implanted ACTH-releasing pumps were used, followed by deep RNA sequencing of the canine VAT. Prolonged HC seems to affect a plethora of regulatory mechanisms in VAT of treated dogs, with 1190 differentially expressed genes (DEGs, p and FDR < 0.01) being found. The 691 downregulated DEGs were mostly associated with functional terms like cell adhesion and migration, intracellular signaling, immune response, extracellular matrix and angiogenesis. Treatment also appeared to modulate local glucocorticoid and insulin signaling and hormonal sensitivity, and several factors, e.g., TIMP4, FGF1, CCR2, CXCR4 and HSD11B1/2, were identified as possible important players in the glucocorticoid-related expansion of VAT. Modulation of their function during chronic HC might present interesting targets for further clinical studies. Similarities in the effects of chronic HC on VAT of dogs and humans are highlighted.
Paradox of the drinking-straw model of the butterfly proboscis (2014)

Fluid-feeding Lepidoptera use an elongated proboscis, conventionally modeled as a drinking straw, to feed from pools and films of liquid. Using the monarch butterfly, Danaus plexippus (Linnaeus), we show that the inherent structural features of the lepidopteran proboscis contradict the basic assumptions of the drinking-straw model. By experimentally characterizing permeability and flow in the proboscis, we show that tapering of the food canal in the drinking region increases resistance, significantly hindering the flow of fluid. The calculated pressure differential required for a suction pump to support flow along the entire proboscis is greater than 1 atm (~101 kPa) when the butterfly feeds from a pool of liquid. We suggest that behavioral strategies employed by butterflies and moths can resolve this paradoxical pressure anomaly. Butterflies can alter the taper, the interlegular spacing and the terminal opening of the food canal, thereby controlling fluid entry and flow, by splaying the galeal tips apart, sliding the galeae along one another, pulsing hemolymph into each galeal lumen, and pressing the proboscis against a substrate. Thus, although physical construction of the proboscis limits its mechanical capabilities, its functionality can be modified and enhanced by behavioral strategies.
Rapid and Homogeneous Dispersion of Pt Catalyst Particles on Multi-Walled Carbon Nanotubes by Temperature-Controlled Microwave Polyol Method (2008)

Fuel cells, particularly direct methanol fuel cells (DMFCs), have great potential as mobile power sources. It has been extensively reported that the DMFC performance strongly depends on the electrode catalyst, and many research groups have focused on the preparation of high efficiency cathode catalysts using all types of metal nanoparticle and support. However, most of these methods are either time-consuming with multiple-steps or there is low loading of the nanocatalyst dispersed on the supports. In this study, platinum nanoparticles of uniform diameter (approximately 4.3 nm) were efficiently dispersed on multi-walled carbon nanotubes (MWCNTs) by the temperature-controlled, microwave-assisted polyol method with the addition of sodium dodecyl sulfate (SDS) and [poly(vinyl pyrrolidone)] (PVP). The addition of SDS and PVP in chloroplatinic acid/ethylene glycol (EG) solution can cause the efficient and homogeneous dispersion of the catalyst particles on MWCNTs, enhance the adsorption of platinum particles, and reduce the residue of platinum particles. Moreover, temperature was determined to be the most important factor affecting the reduction of Pt in the process, and large amounts of Pt particles were characterized when the temperature ranged from 140 to 160 °C. The results indicate that the optimum temperature ranges from 140 to 160 °C, and that the loading amount of Pt/CNTs can reach more than 50 wt % in only 90 s of processing time. The significant improvements in dispersion and loading are due to the ability of SDS, to wrap the PVP-stabilized Pt nanoparticles around the surface of the carbon nanotubes. The characterization analyses were conducted by scanning electron microscopy (SEM), transmission electron microscopy (TEM), X-ray diffractometry (XRD), X-ray photoelectron spectroscopy (XPS), and thermal gravimetric analysis (TGA).
Effect of Fermented Soybean Meal by Bacillus subtilis in Pacific White Shrimp Litopenaeus vannamei Diets on Growth Performance, Innate Immunity and Disease Resistance (2017)

A feeding trial was conducted to evaluate the effect of dietary supplementation with fermented soybean meal by Bacillus subtilis (BFSBM) on growth performance, feed utilization, innate immunity, water quality, and disease resistance of Litopenaeus vannamei. A basal fish meal-based diet was regarded as a control and two other diets were prepared by replacing 30% fish meal with either soybean meal (SBM) or BFSBM. Triplicate groups of shrimp (<TEX>$0.80{\pm}0.010g$</TEX>) were fed one of the experimental diets for 6 weeks. No differences were found in final body weight, feed conversion ratio, or survival among all dietary treatments after the feeding trial. Shrimp fed the BFSBM diet had significantly higher phagocytic and phenoloxidase activities than those of shrimp fed the SBM diet. Total ammonia concentrations in culture water during a zero water exchange test tended to decrease in tanks where BFSBM diet was provided. Disease resistance of shrimp to Vibrio harveyi tended to increase in the BFSBM group during 14 days of challenge compared to that in the control (CON) and SBM groups. These results show that dietary supplementation with BFSBM can enhance the innate immunity of Pacific white shrimp and replace at least 30% of dietary fish meal.
Annealing effects on flexible multi-layered parylene-based sensors (2014)

To mitigate long term, soaking-induced delamination failure of multi-layered Parylene C devices, a post-process annealing step can be employed to increase adhesion between the Parylene layers. However, it has been shown that annealing of Parylene thin films can alter the bulk properties of the polymer, and thus impact final device performance. To elucidate these effects, the mechanical and electrochemical properties, and sensing performance of untreated and annealed Parylene C-platinum electrochemical impedance-based force sensors were compared. Annealing reduced the height (~3%) and increased the stiffness of the Parylene C sensing channel structure (~1.6x), affecting the sensor's mechanical response. Furthermore, the electrode surface was smoothed as built-in residual stresses were removed during annealing, altering the sensor's electrochemical properties. Together, these phenomena resulted in a 24% reduction in sensor sensitivity. These results indicate that heat-based effects cannot be ignored for Parylene-metal device systems, including neural microelectrode implants, and that mechanical and electrochemical properties and performance must be determined after heat treatment, such as annealing and sterilization.
PF373 IMPACT OF ATM ALTERATIONS ON CHRONIC LYMPHOCYTIC LEUKEMIA IN GENERAL PRACTICE IN THE AREA OF NEXT GENERATION SEQUENCING (2019)

Background: Chronic Lymphocytic Leukemia (CLL) is characterized by a very heterogeneous clinical course. Del11q22–23 affecting ATM gene is the most common cytogenetic abnormality associated with poor prognosis. Clinical significance of ATM mutations, isolated or associated with del11q22–23, remains unclear specifically since the widespread use of new therapeutic agents. Aims: Evaluate frequency, associations and clinical significance of ATM alterations in a daily clinical practice cohort. Methods: We retrospectively analyzed a cohort of 268 CLL patients tested by NGS (Next Generation Sequencing) including ATM mutations in daily clinical practice. Results: We identified 50 different ATM mutations among 42 patients (15.7%) by NGS, including a majority of missense mutations and 35 del11q using FISH. Bi‐allelic ATM alterations ( ATM mutation and del11q) were found in only 13 patients (37.5% of the del11q patients and 31% of the ATM mutated patients). All but 11 patients with ATM alterations received anti‐CD20 combined chemotherapy directly after NGS realization. ATM alterations had no significant impact on overall survival (OS) but significantly affected time to first treatment (TTFT) in univariate analysis (median of 2.4 years versus 6.1 years (p = 0.004)) ( Figure 1A ) as well as in multivariate analysis (HR 1.6 IC 95% 1–2.6 ‐ p = 0.023). ATM alterations also affected significantly the time to next treatment (TTNT) with a median time of 2.0 years versus non‐reached in the absence of ATM alteration (p = 0.003) ( Figure 1B ).Outcome in the bi‐allelic ATM alterations subgroup was particularly pejorative with a median TTNT of 5.5 months (IC 95% 4.8–6.2 months). In multivariate analysis, only ATM mutation had a significant impact on TTNT (HR 3.98 IC 95% 1.45–10.9 ‐ p = 0.008) even when BCR‐inhibitors were used. Summary/Conclusion: ATM alterations are frequent in CLL either at diagnosis or at relapse. They confer worse disease evolutionary profile and earlier relapses, especially in case of bi‐allelic inactivation or multiple‐hit profile. These findings emphasize the importance of integrating ATM gene in a targeted NGS panel to better characterize CLL patients while waiting availability ofnew therapeutic agents targeting ATM deficiency. image
Chemokines Fail to Up-Regulate β1 Integrin-Dependent Adhesion in Human Th2 T Lymphocytes (2000)

Th1 and Th2 cells are functionally distinct subsets of CD4+ T lymphocytes whose tissue-specific homing to sites of inflammation is regulated in part by the differential expression of P- and E-selectin ligands and selected chemokine receptors. Here we investigated the expression and function of beta 1 integrins in Th1 and Th2 cells polarized in vitro. Th1 lymphocytes adhere transiently to the extracellular matrix ligands laminin 1 and fibronectin in response to chemokines such as RANTES and stromal cell-derived factor-1, and this process is paralleled by the activation of the Rac1 GTPase and by a rapid burst of actin polymerization. Selective inhibitors of phosphoinositide-3 kinase prevent efficiently all of the above processes, whereas the protein kinase C inhibitor bisindolylmaleimide prevents chemokine-induced adhesion without affecting Rac1 activation and actin polymerization. Notably, chemokine-induced adhesion to beta 1 integrin ligands is markedly reduced in Th2 cells. Such a defect cannot be explained by a reduced sensitivity to chemokine stimulation in this T cell subset, nor by a defective activation of the signaling cascade involving phosphoinositide-3 kinase, Rac1, and actin turnover, as all these processes are activated at comparable levels by chemokines in the two subsets. We propose that reduced beta 1 integrin-mediated adhesion in Th2 cells may restrain their ability to invade and/or reside in sites of chronic inflammation, which are characterized by thickening of basement membranes and extensive fibrosis, requiring efficient interaction with organized extracellular matrices.
IC‐P‐146: MCI Trial Enrichment Using MRI Hippocampus Texture (2016)

Magnetic resonance imaging (MRI) hippocampal volume has been qualified by the European Medicines Agency (EMA) as an enrichment biomarker for mild cognitive impairment (MCI) trials [[1]]. We tested the potential of adding MRI hippocampal texture [[2]] for further enrichment of MCI trials. The MCI subjects from the “complete annual year 2 visit” 1.5T standardized Alzheimer’s Disease Neuroimaging Initiative (ADNI) dataset [[3]] that had an associated cerebrospinal fluid (CSF) measurement available from the Center for Neurodegenerative Disease Research, University of Pennsylvania School of Medicine, Philadelphia [[4]] were identified (127 subjects, age 74.5±7.4, 30.7% female, mini-mental state examination [MMSE] 26.9±1.8, Alzheimer’s Disease Assessment Scale-cognitive subscale [ADAS-Cog] 18.6±6.2).Two T1-weighted MRI biomarkers were computed: hippocampal volume divided by intra-cranial volume (cross-sectional FreeSurfer v.5.1.0, default parameters), and hippocampal texture (in house software). In addition, we used log(total tau / Aβ 1 to 42 peptide) as CSF biomarker. Biomarkers were combined using linear regression with change in cognitive score over two years as dependent variable. Costs were computed based on sample size estimates and using the same price for MRI and CSF assessment. Effect size and corresponding cost were monitored as a function of number of subjects selected for both MMSE and ADAS-cog (see Figure). Texture generally demonstrated larger effect size while at the same time maintaining a lower cost across the range of selected subjects compared to volume. Combining MRI and CSF was generally beneficial.
state-Space Modeling oif a Series Compensated Long Distance Transmission System Through Graph-Theoretic Approach (1978)

The paper demonstrates a powerful application of graph-theoretic approach in developing a linearized state-model for a typical hydro- power system effectively and systematically. The linearized d-q state models of basic components of power system such as generator, transformer, transmission line are formulated (conceptually, in isolation) in a synchronousiy rotating frame which permits ease of inter- connection without involving any intermediary of axis transformations. The formulation of model in general, is applicable to multi- machine system and is easily amenable to digital simulation. It is hoped that the system state-model formulation through graph-the- oretic approach would strongly appeal to power system engineers engaged in large-scale comprehensive dynamical system studies.
Antihypertensive Drugs in the Stroke-Prone Spontaneously Hypertensive Rat (1997)

The stroke-prone spontaneously hypertensive rat (SHR-SP) is an experimental model that has been widely used to investigate the potential preventive effects vs stroke and mortality of numerous antihypertensive agents. Among the latter, angiotensin I-converting enzyme inhibitors, angiotensin II AT1-receptor blockers and calcium antagonists have proven to be very effective. The mechanisms involved in their beneficial effects include limitation of the age-related alterations of large cerebral arteries' functional parameters, prevention of fibrinoid necrosis formation in cerebral arterioles and, to a lesser extent, limitation of the blood pressure rise.
Introducing Savie: A Biodegradable Surfactant Enabling Chemo- and Bio-catalysis & Related Reactions in Recyclable Water (2022)

Savie is a biodegradable surfactant derived from vitamin E and polysarcosine (PSar) developed for organic synthesis in water. This includes homogeneous catalysis (including examples employing only ppm levels of catalyst), heterogeneous catalysis, and biocatalytic transformations, including a 3-step, 1-pot chemoenzymatic sequence. Savie frequently enables significantly higher yields than conventional surfactants, while obviating the need for environmentally egregious organic solvents.
Developmental, organ-specific, and light-dependent expression of the tomato ribulose-1,5-bisphosphate carboxylase small subunit gene family. (1987)

The tomato gene family for the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase [3-phospho-D-glycerate carboxy-lyase (dimerizing); EC 4.1.1.39] has five genes, designated Rbcs-1, -2, -3A, -3B, and -3C. We have measured the steady-state mRNA levels for each of the five genes in various tomato organs using gene-specific oligonucleotides. All five genes are highly expressed in leaves, and transcripts of two genes, Rbcs-3B and Rbcs-3C, account for approximately equal to 60% of the total leaf transcripts. The relative transcript levels in the stem, in nature fruits, and etiolated seedlings (plants germinated and grown in the dark) correspond to 3.2%, 6.5%, and 4.6%, respectively, of the ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit mRNA level in leaves, and no transcripts have been detected in roots and ripe tomato fruits. Only Rbcs-1 and Rbcs-2 are expressed during the photosynthetically active phase of fruit development. Transcripts from these genes and from the Rbcs-3A locus are also present in etiolated seedlings. Rbcs-3B and Rbcs-3C transcripts, which are the most abundant mRNAs of the ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit gene family in the leaf, are undetectable in dark-grown seedlings and immature fruit. The selective expression of Rbcs-1 and Rbcs-2 in the dark and in the pericarp of green fruit and the induction and rapid mRNA accumulation for Rbcs-3B and Rbcs-3C after illumination may reflect different regulatory mechanism(s) that control the expression of individual members in the tomato ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit gene family.
Asynchronous, all-optical signal processing based on the self-frequency shift of a gigahertz Raman soliton (2005)

Ultrafast asynchronous all-optical signal processing is experimentally demonstrated. It is based on the intensity-dependent, self-frequency shift of a gigahertz Raman soliton. We demonstrate error-free, asynchronous, all-optical, bit-by-bit, self-signal recognition and demultiplexing from contended optical packets without use of an optical buffer, control pulse, or bit-phase synchronization. Fourfold, contended, 9.95-Gbit/s optical packets are transmitted through a conventional repeater span of 80 km and simultaneously demultiplexed to multiwavelength 9.95-Gbit/s optical packets with 0.5-dB processing sensitivity. Furthermore, we successfully accomplish demultiplexing from overlapping signals in contended optical packets with better than 3-dB recognition sensitivity. We confirm the capability of realizing a 3x cascade operation from bit-error-rate measurements.
Silica-carbon nanotubes composite coatings as saturable absorbers (2012)

Currently, fabrication of CNT and polymer composites for saturable absorbers is very popular. But due to nature of organic polymer matrix, these composites are unstable on higher temperatures or in high energy light exposition. Therefore a sol-gel process for the fabrication for inorganic (i.e. silica) or semi-organic (organic-modified silica) matrix can be a promising way to produce photo-chemically and thermally stable CNT composites. In this work was investigated SWCNT's solubility in ethanol using different surfactants - Triton, polyvinylpyrrolidone (PVP), and Poly(4-vinylpyridine) (P4VP). Most stable colloidal solution was obtained using a P4VP as surfactant - solutions were stable up to 6 weeks. Therefore this surfactant was used for the fabrication of SWCNT/Silica composite coatings. SWCNT's was directly dispensed in a colloidal silica sol and coatings made by spin-coating technique. Samples were investigated under optical, atomic force microscopy methods, and optical non-linearity was measured. Thermal stability was investigated using Raman spectroscopy.
Large‐Scale‐Compatible Stabilization of a 2D Semiconductor Platform toward Discrete Components (2021)

Abstract Atomically thin 2D materials have drawn considerable attention in the past years with potential ranging from transistors to optoelectronics. As such, they are now foreseen as strong candidates for epitaxy‐free technologies and the tetrad of size‐weight‐power‐and‐cost (SWAP‐C) reduction. Targeting radiofrequency (RF) applications, the 2D semiconducting transition metal dichalcogenides (TMDC) family can offer the opportunity of wide tunability of their electronic properties, providing a large variety of band gaps. However, evaluation and integration of those materials into discrete components requires a stabilization of their properties. This work focuses on the evaluation of a large‐scale compatible fabrication/passivation process on large area (&gt;1000 µm 2 ) monolayers of the prototypical 2D semiconductor MoS 2 . The process is developed including pre‐ and post‐patterning protection/passivation layers. It is shown to reduce the initial natural p‐doping of the sample, leading to lower transistor threshold voltages, a 10 6 I ON / I OFF ratio, and an effective averaged field‐effect mobility under ambient conditions of 20 cm 2 V −1 s −1 (up to 35 cm 2 V −1 s −1 for some devices), which represents an increase by a 40‐fold factor compared to a conventional process carried on the large scale platform. This work represents an important step toward the integration of 2D TMDCs in discrete RF circuits and components.
Modeling and simulation of cyberattacks for resilient cyber-physical systems (2017)

Securing cyber-physical systems (CPS) is an active area of research. For example, manufacturing and military CPS have been traditionally designed without an emphasis on cybersecurity. This paper presents a model-based secure-by-design approach for modeling and simulating the cybersecurity aspects of CPS. We demonstrate our systematic approach by modeling several classes of cyberattacks that may affect the normal operations of CPS, and evaluate the impact of these attacks on the system through the use of simulation. We follow a functional modeling approach that may reduce the engineering effort and increase the quality of the developed system, while also increasing the resilience of the system when exposed to cyberattacks.
Synthesis of mesoporous silica spheres under quiescent aqueous acidic conditions (1998)

A gyroid-to-sphere shape transition has been unveiled in the growth of mesoporous silica morphologies that are synthesized under quiescent acidic aqueous conditions. It can be induced by a decrease of the acidity for a surfactant-based gyroid preparation. As the acidity is gradually lowered from the gyroid domain, the growth process changes from one involving a smooth continuous deposition of silicate–surfactant micellar solute species onto specific regions of an evolving silicate liquid crystal seed, to one in which deposition instead occurs on non-specific regions of the seed. This creates multigranular gyroid morphologies which at lower acidity emerge as sphere shapes. The gyroid-to-sphere metamorphosis appears to correlate with an acidity and/or temperature dependent switch in the mode of formation, from the gyroid involving fast and local polymerization of a growing silicate liquid crystal seed, to the sphere based upon a slower and global polymerization of a silicate liquid crystal droplet. Surface tension will cause such a droplet to adopt a spherical shape, ultimately to be rigidified in the form of a mesoporous silica sphere. Comparative gyroid and sphere information is presented on synthesis-size-shape-channel plan relations, degree of orientational order of the channels, extent of polymerization of the silica, thermal stability and nitrogen adsorption properties. The ability to synthesize 1–10 µm diameter mesoporous silica spheres with a narrow sphere size and pore size distribution portends a myriad of applications in large molecule catalysis, chromatographic separations and nanocomposites.