gebhart/patrepeval huggingface dataset:
Effects of Electrodes on Dielectric and Piezoelectric Properties of Lead Magnesium Niobate–Lead Titanate Single-Crystal Transducer (2011)

The effects of four types of electrodes, sputtered gold (Au), titanium/Au (Ti/Au), chromium/Au (Cr/Au), and fired silver (Ag), on the dielectric and piezoelectric properties of a lead magnesium niobate–lead titanate (PMN–PT) single-crystal transducer near the morphotropic phase boundary composition were investigated to obtain better properties of the transducer for application in medical ultrasound probes. The Au electrode sample showed the highest piezoelectric constant d33 = 1710 pC/N and the Cr/Au electrode sample showed the highest coercive field Ec = 3.1 kV/cm. Those differences were derived from several factors, namely, the dielectric constant at phase change temperature, the crystallinity on the surface caused by electrode forming treatment, adhesion strength, and the thickness of the electrodes. Changing the electrode is an easier way to realize the desired piezoelectric properties than crystal composition control. Thus, this information can prove useful for the application of the PMN–PT transducer in medical ultrasound probes.
Endoscopic Ultrasound Facilitates Histological Diagnosis of Renal Cell Cancer (2008)

Over two-thirds of renal masses noted incidentally on abdominal CT scans performed for nonurological indications are most likely renal cell carcinoma (RCC). The prognosis in these instances is often quite favorable, as early diagnosis offers the best hope of a complete cure. We report the identification of a RCC incidentally at endoscopic ultrasound (EUS) while an earlier CT scan of abdomen was negative. The mass was biopsied resulting in a histological confirmation of RCC and successful surgical resection.
Genetic Engineering of <em>Dictyostelium discoideum</em> Cells Based on Selection and Growth on Bacteria (2019)

Dictyostelium discoideum is an intriguing model organism for the study of cell differentiation processes during development, cell signaling, and other important cellular biology questions. The technologies available to genetically manipulate Dictyostelium cells are well-developed. Transfections can be performed using different selectable markers and marker re-cycling, including homologous recombination and insertional mutagenesis. This is supported by a well-annotated genome. However, these approaches are optimized for axenic cell lines growing in liquid cultures and are difficult to apply to non-axenic wild-type cells, which feed only on bacteria. The mutations that are present in axenic strains disturb Ras signaling, causing excessive macropinocytosis required for feeding, and impair cell migration, which confounds the interpretation of signal transduction and chemotaxis experiments in those strains. Earlier attempts to genetically manipulate non-axenic cells have lacked efficiency and required complex experimental procedures. We have developed a simple transfection protocol that, for the first time, overcomes these limitations. Those series of large improvements to Dictyostelium molecular genetics allow wild-type cells to be manipulated as easily as standard laboratory strains. In addition to the advantages for studying uncorrupted signaling and motility processes, mutants that disrupt macropinocytosis-based growth can now be readily isolated. Furthermore, the entire transfection workflow is greatly accelerated, with recombinant cells that can be generated in days rather than weeks. Another advantage is that molecular genetics can further be performed with freshly isolated wild-type Dictyostelium samples from the environment. This can help to extend the scope of approaches used in these research areas.
Effect of ultrasonic irradiation on membrane fouling and membrane wetting in direct contact membrane distillation process (2016)

Membrane distillation (MD) is a novel separation process that have drawn attention as an affordable alternative to conventional desalination processes. However, membrane fouling and pore wetting are issues to be addressed prior to widespread application of MD. In this study, the influence of ultrasonic irradiation on fouling and wetting of MD membranes was investigated for better understanding of the MD process. Experiments were carried out using a direct contact membrane distillation apparatus Colloidal silica was used as a model foulants in a synthetic seawater (35,000 mg/L NaCl solution). A vibrator was directed attached to membrane module to generate ultrasonic waves from 25 kHz (the highest energy) to 75 kHz (the lowest energy). Flux and TDS for the distillate water were continuously monitored. Results suggested that ultrasonic irradiation is effective to retard flux decline due to fouling only in the early stage of the MD operation. Moreover, wetting occurred by a long-term application of ultrasonic rradiation at 75 kHz. These results suggest that the conditions for ultrasonic irradiation should be carefully optimized to maximize fouling control and minimize pore wetting.
Whole exome sequencing for the identification of CYP3A7 variants associated with tacrolimus concentrations in kidney transplant patients (2018)

The purpose of this study was to identify genotypes associated with dose-adjusted tacrolimus trough concentrations (C<sub>0</sub>/D) in kidney transplant recipients using whole-exome sequencing (WES). This study included 147 patients administered tacrolimus, including seventy-five patients in the discovery set and seventy-two patients in the replication set. The patient genomes in the discovery set were sequenced using WES. Also, known tacrolimus pharmacokinetics-related intron variants were genotyped. Tacrolimus C<sub>0</sub>/D was log-transformed. Sixteen variants were identified including novel CYP3A7 rs12360 and rs10211 by ANOVA. CYP3A7 rs2257401 was found to be the most significant variant among the periods by ANOVA. Seven variants including CYP3A7 rs2257401, rs12360, and rs10211 were analyzed by SNaPshot in the replication set and the effects on tacrolimus C<sub>0</sub>/D were verified. A linear mixed model (LMM) was further performed to account for the effects of the variants and clinical factors. The combined set LMM showed that only CYP3A7 rs2257401 was associated with tacrolimus C<sub>0</sub>/D after adjusting for patient age, albumin, and creatinine. The CYP3A7 rs2257401 genotype variant showed a significant difference on the tacrolimus C<sub>0</sub>/D in those expressing CYP3A5, showing its own effect. The results suggest that CYP3A7 rs2257401 may serve as a significant genetic marker for tacrolimus pharmacokinetics in kidney transplantation.
Survey of <I>Solenopsis</I> Fire Ants and Their Parasitoid Flies (Diptera: Phoridae: <I>Pseudacteon</I>) in Central Chile and Central Western Argentina (2007)

Abstract Twenty-two species of Pseudacteon flies (Diptera: Phoridae) are known to attack fire ants (Solenopsis spp.) in Argentina, Brazil, Bolivia, and Paraguay, but none are known in Chile. Surveys were conducted in central Chile and at similar latitudes in western Argentina to detect the presence of fire ants and parasitoid flies and to determine their relationship. Flies and fire ants were much more common and abundant in Argentina. In total, 100 colonies of four fire ant species were found at 63.6% of the sites surveyed. In contrast, only six colonies of one species, Solenopsis gayi (Spinola), were found at 4.7% of the sites surveyed in Chile. Our survey includes the first record of five parasitic fly species in central western Argentina and a new host, Solenopsis quinquecuspis Forel. The large form of Pseudacteon obtusus Borgmeier was found attacking S. gayi in Chile, which is the first record in that country, and the first record on this host species. The southern-most and western-most records were established for fire ant-decapitating flies. Mitochondrial DNA (mtDNA) indicates that S. gayi is genetically closer to the Argentine fire ants (saevissima-group) than the North American S. geminata-group. However, S. gayi venom alkaloid composition is similar to S. geminata-group, whereas cuticular hydrocarbon composition has characteristics of both groups. Analysis of mtDNA from the collected flies supports the monophyly of P. obtusus and suggests that the Chilean population is similar to populations in eastern Argentina. The presence of P. obtusus in Chile could be explained by immigrant parasitized fire ant species from Argentina or by an accidental introduction.
Ron receptor deficient alveolar myeloid cells exacerbate LPS-induced acute lung injury in the murine lung (2010)

Previous studies have shown that the Ron receptor tyrosine kinase is an important regulator of the acute lung inflammatory response induced by intranasal administration of bacterial LPS. Compared to wild-type mice, complete loss of the Ron receptor in all cell types in vivo was associated with increased lung damage as determined by histological analyses and several markers of lung injury including increases in pro-inflammatory cytokines such as TNF-α. Tumor-necrosis factor-α is a multifunctional cytokine secreted by macrophages, which plays a major role in inflammation and is a central mediator of several disease states including rheumatoid arthritis and sepsis. Based on increased TNF-α production observed in the Ron-deficient mice, we hypothesized that Ron receptor function in the inflammatory cell compartment is essential for the regulating lung injury in vivo. To test this hypothesis, we generated myeloid lineage-specific Ron-deficient mice. In this study, we report that loss of Ron signaling selectively in myeloid cells results in increased lung injury following intranasal administration of LPS as measured by increases in TNF-α production, ensuing neutrophil accumulation and increased lung histopathology. These findings corroborate the role of Ron receptor tyrosine kinase as a negative regulator of inflammation and further demonstrate the in vivo significance of Ron signaling selectively in myeloid cells as a major regulator of this response in vivo. These data authenticate Ron as a potential target in innate immunity and TNF-α-mediated pathologies.
<title>Designing adaptive neural network architectures and their learning parameters using genetic algorithms</title> (1993)

This report describes a GA (Genetic Algorithms) method that evolves multi-layered feedforward neural network architectures for specific mappings. The network is represented as a genotype that has six kinds of genes. They are a learning rate, a slant of sigmoid function, a coefficient of momentum term, an initializing weights range, the number of layers and the unit numbers of each layer. Genetic operators affect populations of these genotypes to produce adaptive networks with higher fitness values. We define three kinds of fitness functions that evaluate networks generated by the GA method. Their fitnesses are assessed for the generated network trained with BP (Back Propagation) algorithm by several network performances. In our experiments, we train the networks for the XOR mapping. They are designed systematically and easily using the GA method. These generated networks require fewer training cycles then networks used until now, and a rate of convergence is improved.
Hexahapto‐Metal Complexes of Single‐Walled Carbon Nanotubes (2012)

Abstract We report the preparation of organometallic side‐wall complexes of single‐walled carbon nanotubes (SWNTs) under conditions, which allow the study of both mono‐ and bis‐hexahapto SWNT coordination compounds [(η 6 ‐SWNT)Cr(CO) 3 , (η 6 ‐SWNT)Cr(η 6 ‐C 6 H 6 ), (η 6 ‐SWNT) 2 Cr]. The results are interpreted in terms of exohedral and endohedral binding of chromium to the SWNT sidewalls and ligand competition reactions suggest that endohedral binding provides a very stable and kinetically inert mode of organometallic bonding. We demonstrate that the electrical conductivity of SWNT thin films are significantly enhanced by side‐wall bonding to Group 6 transition metals (M = Cr, Mo, and W), which serve to reduce the inter‐carbon nanotube junction electrical resistance by the formation of SWNT interconnects [(η 6 ‐SWNT) 2 M].
Automated Dynamic Clamp for Simulation of IK1 in Human Induced Pluripotent Stem Cell–Derived Cardiomyocytes in Real Time Using Patchliner Dynamite8 (2019)

Current in vitro assays typically poorly predict cardiac liability as they focus on single ion channels overexpressed in cell lines. Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs), on the other hand, provide a unique opportunity for drug testing on human cardiomyocytes using high-throughput systems. However, these cells can differ from adult cardiomyocytes in their ion channel expression and, therefore, electrophysiologic properties. One of the main challenges of hiPSC-CMs is the physiologic expression of ion channels such as the inward rectifiers (e.g., Kir2.1-2.3), which conduct the cardiac inward rectifier potassium current (I<sub>K1</sub> ). I<sub>K1</sub> is one of the primary contributors in maintaining a stable resting membrane potential in cardiac cells, which is essential for excitability. This is only expressed in low levels, or sometimes not at all, in hiPSC-CMs as shown by patch clamp studies. Dynamic clamp is a method of electronically introducing ion currents (e.g., I<sub>K1</sub> ) into cells to compensate for the lack of endogenous expression, thus offering the potential to record more stable action potentials in hiPSC-CMs. In this article, we describe the method of using hiPSC-CMs on an automated patch clamp device (Patchliner) coupled with the automated dynamic clamp add-on (Dynamite<sup>8</sup> ). We describe protocols for optimized cell handling and harvesting for use on the Patchliner and the steps required for automated execution of experiments and data analysis in dynamic clamp mode. © 2019 by John Wiley & Sons, Inc. Basic Protocol: Recording action potential pharmacology from human induced pluripotent stem cell-derived cardiomyocytes in automated patch clamp combined with dynamic clamp to introduce simulated I<sub>K1</sub> and compensate seal resistance Support Protocol 1: Cardiomyocyte plating and culture Support Protocol 2: Cell harvesting and dissociation Alternate Protocol: Recording action potential pharmacology at physiologic temperatures.
Proteinase-Activated Receptor 2 Mediates Thermal Hyperalgesia and Is Upregulated in a Rat Model of Chronic Pancreatitis (2011)

The thermal hyperalgesia in CP is associated with an up-regulation of the PAR2 in DRGs. Proteinase-activated receptor 2 was involved in the pain generation in rats with CP.
A TCP-friendly Congestion Control Mechanism Combined with the Routers (2007)

From end-to-end strategy and router congestion control, an ECN-based and enhanced-fairness TCP-friendly congestion control mechanism (EETCC) is proposed in this paper. The sender can adjust the sending rate of UDP flows by TCP response function, and have good TCP-friendly and send data flows smoothly. The router is early notified to the sender using ECN, and can response to congestion fleetly. This mechanism adopted ERED algorithm to improve the situation where the bandwidth is influenced by packet size in the router. EETCC can enhance fairness of link bandwidth allotment, and guarantee quality of service of the special applications. The simulations validate that EETCC flows share the bandwidth of bottle-neck links with TCP flows.
Analysis of the Salivary Gland Transcriptome of Frankliniella occidentalis (2014)

Saliva is known to play a crucial role in insect feeding behavior and virus transmission. Currently, little is known about the salivary glands and saliva of thrips, despite the fact that Frankliniella occidentalis (Pergande) (the western flower thrips) is a serious pest due to its destructive feeding, wide host range, and transmission of tospoviruses. As a first step towards characterizing thrips salivary gland functions, we sequenced the transcriptome of the primary salivary glands of F. occidentalis using short read sequencing (Illumina) technology. A de novo-assembled transcriptome revealed 31,392 high quality contigs with an average size of 605 bp. A total of 12,166 contigs had significant BLASTx or tBLASTx hits (E≤1.0E-6) to known proteins, whereas a high percentage (61.24%) of contigs had no apparent protein or nucleotide hits. Comparison of the F. occidentalis salivary gland transcriptome (sialotranscriptome) against a published F. occidentalis full body transcriptome assembled from Roche-454 reads revealed several contigs with putative annotations associated with salivary gland functions. KEGG pathway analysis of the sialotranscriptome revealed that the majority (18 out of the top 20 predicted KEGG pathways) of the salivary gland contig sequences match proteins involved in metabolism. We identified several genes likely to be involved in detoxification and inhibition of plant defense responses including aldehyde dehydrogenase, metalloprotease, glucose oxidase, glucose dehydrogenase, and regucalcin. We also identified several genes that may play a role in the extra-oral digestion of plant structural tissues including β-glucosidase and pectin lyase; and the extra-oral digestion of sugars, including α-amylase, maltase, sucrase, and α-glucosidase. This is the first analysis of a sialotranscriptome for any Thysanopteran species and it provides a foundational tool to further our understanding of how thrips interact with their plant hosts and the viruses they transmit.
Investigation of heavy current discharges with high initial gas density (1996)

Piezoelectric pressure transducers, with noise immunity and time resolution of 0,5 μs were used to measure pulse pressures of 430 MPa along the axis of an electrical discharge channel. Initial concentration of He was 2,7⋅1021 cm−3, dI/dt=6⋅1011 A/s, and Imax=560 kA. Shock waves with amplitudes exceeding the pressure along the axis, were detected by a pressure transducer on the wall of the discharge chamber. Typical shock velocities were 2⋅4 km/s. Average pressure measurements along the discharge axis at different radii were used to estimate the current density distribution along the canal radius. The presence of the shock waves, promoting the additional hydrogen heating in the discharge chamber, has been registered during the discharge in hydrogen for Imax∼1 MA and an initial concentration of 1021 cm−3.
Molecular Characterization of the Transition to Malignancy in a Genetically Engineered Mouse-Based Model of Ductal Carcinoma In situ (2004)

A transplantable model of human ductal carcinoma in situ that progresses to invasive carcinoma was developed from a genetically engineered mouse (GEM). Additional lines were established using early mammary premalignant lesions from transgenic MMTV-PyV-mT mice. These lines were verified to be premalignant and transplanted repeatedly to establish stable and predictable properties. Here, we report the first in-depth molecular analysis of neoplastic progression occurring in one premalignant transplantable GEM-derived line. Oligonucleotide microarrays showed that many genes are differentially expressed between the quiescent and prelactating mammary gland and the premalignant GEM outgrowth. In contrast, a small but consistent group of genes was associated with the transformation from premalignancy to tumor. This suggests that the majority of gene expression changes occur during the premalignant transition from normal to premalignancy, whereas many fewer changes occur during the malignant transition from premalignancy to invasive carcinoma. The premalignant transition is associated with several cell cycle-related genes and the up-regulation of oncogenes is associated with various cancers (Ccnd11, Cdk4, Myb, and Ect2). The changes identified in the malignant transition included genes previously associated with human breast cancer progression. Misregulation of the insulin-like growth factor and transforming growth factor-beta signaling pathways and the stromal-epithelial interaction were implicated. Our results suggest that this transplantable GEM-based model recapitulates human ductal carcinoma in situ at both histologic and molecular levels. With consistent tumor latency and molecular profiles, this model provides an experimental platform that can be used to assess functional genomics and molecular pharmacology and to test promising chemoprevention strategies.
Noninvasive evaluation of intragraft immune responses in upper extremity transplantation (2021)

In vascularized composite allotransplantation (VCA), invasive tissue biopsies remain the gold standard in diagnosing rejection carrying significant morbidity. We aimed to show feasibility of tape-stripping for noninvasive immune monitoring in VCA. Tape-stripping was performed on allografts and native skin of upper extremity transplant recipients. Healthy nontransplanted individuals served as controls. The technique was also used in swine on naïve skin in nontransplanted animals, native skin of treated, transplanted swine, nonrejecting VCAs, and rejecting VCAs. Extracted protein was analyzed for differences in cytokine expression using Luminex technology. Significantly decreased levels of INFγ and IL-1Ra were seen between human allograft samples and native skin. In swine, rejecting grafts had increased IL-1Ra compared to naïve and native skin, decreased levels of GM-CSF compared to native skin, and decreased IL-10 compared to nonrejecting grafts. Unsupervised hierarchical clustering revealed rejecting grafts separated from the nonrejecting (P = 0.021). Variable importance in projection scores identified GM-CSF, IL-1Ra, and IL-2 as the most important profiles for group discrimination. Differences in cytokine expression are detectable in human VCA patient native skin and VCA graft skin using a noninvasive tape-stripping method. Swine studies suggest that differences in cytokines between rejecting and nonrejecting grafts are discernable.
Artemin Overexpression in Skin Enhances Expression of TRPV1 and TRPA1 in Cutaneous Sensory Neurons and Leads to Behavioral Sensitivity to Heat and Cold (2006)

Artemin, a neuronal survival factor in the glial cell line-derived neurotrophic factor family, binds the glycosylphosphatidylinositol-anchored protein GFRalpha3 and the receptor tyrosine kinase Ret. Expression of the GFRalpha3 receptor is primarily restricted to the peripheral nervous system and is found in a subpopulation of nociceptive sensory neurons of the dorsal root ganglia (DRGs) that coexpress the Ret and TrkA receptor tyrosine kinases and the thermosensitive channel TRPV1. To determine how artemin affects sensory neuron properties, transgenic mice that overexpress artemin in skin keratinocytes (ART-OE mice) were analyzed. Expression of artemin caused a 20.5% increase in DRG neuron number and increased the level of mRNA encoding GFRalpha3, TrkA, TRPV1, and the putative noxious cold-detecting channel TRPA1. Nearly all GFRalpha3-positive neurons expressed TRPV1 immunoreactivity, and most of these neurons were also positive for TRPA1. Interestingly, acid-sensing ion channel (ASIC) 1, 2a, 2b, and 3 mRNAs were decreased in the DRG, and this reduction was strongest in females. Analysis of sensory neuron physiological properties using an ex vivo preparation showed that cutaneous C-fiber nociceptors of ART-OE mice had reduced heat thresholds and increased firing rates in response to a heat ramp. No change in mechanical threshold was detected. Behavioral testing of ART-OE mice showed that they had increased sensitivity to both heat and noxious cold. These results indicate that the level of artemin in the skin modulates gene expression and response properties of afferents that project to the skin and that these changes lead to behavioral sensitivity to both hot and cold stimuli.