gebhart/patrepeval huggingface dataset:
Synthesis and Photophysics of Phenylene Based Triplet Donor–Acceptor Dyads: ortho vs. para Positional Effect on Intramolecular Triplet Energy Transfer (2022)

Two phenylene based geometrical/isomeric triplet ortho- and para–dyads (o–3 and p–3, respectively) were synthesized and fully characterized using advanced photophysical tools and computations. In dyad o–3, the through-space donor-acceptor interactions led to simultaneous triplet energy transfer and charge transfer with identical kinetics. On the other hand, in the dyad p–3, it was found that the phenylene spacer favors a fast triplet energy delocalization over the charge transfer process. Furthermore, analysis of the results from the present investigation indicates that the deactivation of the photo-excited species (o–3)* occurs through both the intrinsic channel viz. S0←S1 and charge recombination. In the case of dyad p–3, the results indicate that the primary deactivation pathway is self-quenching or triplet-triplet annihilation involving the acceptor unit(s).
Activation of PPARγ Attenuates the Expression of Physical and Affective Nicotine Withdrawal Symptoms through Mechanisms Involving Amygdala and Hippocampus Neurotransmission (2019)

An isoform of peroxisome proliferator-activated receptors (PPARs), PPARγ, is the receptor for the thiazolidinedione class of anti-diabetic medications including pioglitazone. Neuroanatomical data indicate PPARγ localization in brain areas involved in drug addiction. Preclinical and clinical data have shown that pioglitazone reduces alcohol and opioid self-administration, relapse to drug seeking, and plays a role in emotional responses. Here, we investigated the behavioral effect of PPARγ manipulation on nicotine withdrawal in male Wistar rats and in male mice with neuron-specific PPARγ deletion (PPARγ<sup>(-/-)</sup>) and their littermate wild-type (PPARγ<sup>(+/+)</sup>) controls. Real-time quantitative RT-PCR and RNAscope <i>in situ</i> hybridization assays were used for assessing the levels of expression and cell-type localization of PPARγ during nicotine withdrawal. Brain site-specific microinjections of the PPARγ agonist pioglitazone were performed to explore the role of this system on nicotine withdrawal at a neurocircuitry level. Results showed that activation of PPARγ by pioglitazone abolished the expression of somatic and affective nicotine withdrawal signs in rats and in (PPARγ<sup>(+/+)</sup>) mice. This effect was blocked by the PPARγ antagonist GW9662. During early withdrawal and protracted abstinence, the expression of PPARγ increased in GABAergic and glutamatergic cells of the amygdala and hippocampus, respectively. Hippocampal microinjections of pioglitazone reduced the expression of the physical signs of withdrawal, whereas excessive anxiety associated with protracted abstinence was prevented by pioglitazone microinjection into the amygdala. Our results demonstrate the implication of the neuronal PPARγ in nicotine withdrawal and indicates that activation of PPARγ may offer an interesting strategy for smoking cessation.<b>SIGNIFICANCE STATEMENT</b> Smoking cessation leads the occurrence of physical and affective withdrawal symptoms representing a major burden to quit tobacco use. Here, we show that activation of PPARγ prevents the expression of both somatic and affective signs of nicotine withdrawal. At molecular levels results show that PPARγ expression increases in GABAergic cells in the hippocampus and in GABA- and glutamate-positive cells in the basolateral amygdala. Hippocampal microinjections of pioglitazone reduce the insurgence of the physical withdrawal signs, whereas anxiety linked to protracted abstinence is attenuated by pioglitazone injected into the amygdala. Our results demonstrate the implication of neuronal PPARγ in nicotine withdrawal and suggest that PPARγ agonism may represent a promising treatment to aid smoking cessation.
Direct Comparison between Five Different Microchannels, Part 1: Channel Manufacture and Measurement (2005)

Abstract This paper is the first in a two-part study of the pressure-flow characteristics for a range of microchannels. Here, the manufacture of the channels and the resulting quality in terms of the channels' closeness to target dimensions, channel-to-channel variation for each sample, and the difference in area between the assumed perfect rectangular/trapezoidal shape of the channels and their actual cross-section are addressed. Wet etching with KOH produced trapezoidal channels 577 μum wide and 413 μum high. DRIE produced rectangular channels 304 μum wide and 332 μum high. Mechanical sawing produced near rectangular channels in both silicon and plastic. The silicon channels were 52 μum wide and 423 μum deep, and the plastic channels were 203 μum wide × 344 or 382 μum deep. Channel dimensions were measured using a scanning electron microscope. This paper demonstrates the feasibility of producing relatively large microchannels in two materials by three methods.
TeTrIS: Template Transformer Networks for Image Segmentation With Shape Priors (2019)

In this paper, we introduce and compare different approaches for incorporating shape prior information into neural network-based image segmentation. Specifically, we introduce the concept of template transformer networks, where a shape template is deformed to match the underlying structure of interest through an end-to-end trained spatial transformer network. This has the advantage of explicitly enforcing shape priors, and this is free of discretization artifacts by providing a soft partial volume segmentation. We also introduce a simple yet effective way of incorporating priors in the state-of-the-art pixel-wise binary classification methods such as fully convolutional networks and U-net. Here, the template shape is given as an additional input channel, incorporating this information significantly reduces false positives. We report results on synthetic data and sub-voxel segmentation of coronary lumen structures in cardiac computed tomography showing the benefit of incorporating priors in neural network-based image segmentation.
Generalized anxiety disorder and irritable bowel syndrome: authors' reply (2009)

Sirs, Ford’s comments are well taken. The relatively small number of IBS individuals who also had generalized anxiety disorder (GAD) could be due to the telephone-based methodology used.1 We showed in a previous study that the diagnosis of GAD using this method was more stringent than that of clinician-administered face-to-face semi-structured interviews among a subsample of respondents who participated in a similar phone survey.2 Another reason was our using the 6-month duration criterion of GAD in accordance with the DSM-IV.3 In a recent cross-national study that re-examined the duration criterion of GAD, we found that generalized anxiety lasting 3–5 months did not differ significantly from that lasting 6–11 months in terms of impairment and comorbidity.4 It is worth noting that the clinical version of the ICD-10 requires ‘usually a few months’ for the diagnosis of GAD. Thus, we could have captured a relatively chronic and smaller subgroup of GAD in the study. In the weighed sample, this subgroup of a small number of GAD represented a substantial percentage in the general population. Had a shorter duration criterion been adopted, the prevalence of GAD in both IBS and non-IBS subjects would have been higher. It is certainly not essential for clinicians to wait for 6 months before a patient with IBS and shorter periods of impairing anxiety be treated. We support the suggestion that future treatment trials on IBS should measure anxiety and depression. The use of separate dimensional measures of anxiety and depression beyond categorical diagnoses of mental disorders and domains of functional impairment will shed light on the specificity of action of SSRIs. Given the substantial prevalence, impairment and health care utilization of individuals with functional somatic syndromes (of which functional GI disorder is one common form) in both community and primary care settings,5, 6 the need for these trials is obvious. Declaration of personal and funding interests: None.
Automated Non-invasive Detection of Pumping States in an Implantable Rotary Blood Pump (2006)

With respect to rotary blood pumps used as left ventricular assist devices (LVADs), it is clinically important to control pump flow to avoid complications associated with over-or under-pumping of the native heart. By employing only the non-invasive observer of instantaneous pump impeller speed to assess flow dynamics, a number of physiologically significant pumping states may be detected. Based on a number of acute animal experiments, five such states were identified: regurgitant pump flow (PR), ventricular ejection (VE), non-opening of the aortic valve (ANO), and partial collapse (intermittent and continuous) of the ventricle wall (PVC-I and PVC-C). Two broader states, normal (corresponding to VE, ANO) and suction (corresponding to PVC-I, PVC-C) were readily discernable in clinical data from human patients implanted with LVADs. Based on data from both the animal experiments (N=6) and the human patients (N=10), a strategy for the automated non-invasive detection of significant pumping states has been developed and validated. Employing a classification and regression tree (CART), this system detects pumping states with a high degree of accuracy: state VE -87.5/100.0% (sensitivity/specificity); state ANO - 98.1/92.5%; state PVC-I - 90.0/90.2%; state PVC-C - 61.2/98.0%. With a simplified binary scheme differentiating suction and normal states, both states were detected without error in data from the animal experiments, and with a sensitivity/specificity, for detecting suction, of 99.2/98.3% in the human patient data.
Phenotypic features and genetic characterization of male breast cancer families: identification of two recurrent BRCA2 mutations in north-east of Italy (2006)

The 9106C>T and the IVS16-2A>G mutations constitute recurrent BRCA2 mutations in MBC cases from the North-East of Italy and may be associated with a founder effect. Knowledge of these two recurrent BRCA2 mutations predisposing to MBC may facilitate the analyses aimed at the identification of mutation carriers in our geographic area.
Analysis of surface roughness and oxidation of FeNi-based metal amorphous nanocomposite alloys (2022)

We report on a systematic investigation of newly developed (Fe70Ni30)80Nb4B14Si2 metal amorphous nanocomposites (MANCs) and the factors affecting their surface roughness, including oxide formation and phase evolution during the nanocrystallization process. Analysis of surface roughness using atomic force microscopy (AFM) revealed an average roughness of 9.33 nm after heat treatment compared with as-cast amorphous ribbons, which exhibited a roughness of 4.21 nm. A surface oxide layer thickness has been determined using X-ray photoelectron spectroscopy (XPS). For samples annealed at 400 °C for 1 h, 450 °C for 1 h, and 550 °C for 3 h in air, the average surface oxide layer thickness was determined to be 10.9, 11.7, and 54.4 nm, respectively. It was observed that oxygen is enriched at the outermost surface and decreases rapidly as the XPS sputtering depth increases. Fe-oxide appeared as a predominant metal oxide at the top surface, followed by the presence of Nb oxide. A boron content increase was observed at the interface between the top surface oxide layer and the bulk of the sample. A protective surface oxide layer on FeNi-MANCs, such as observed in this work, can provide sufficient electrical insulation to reduce interlaminate eddy current losses and lower overall losses in magnetic components.
Evaluation of an alkali-treated and hydroxyapatite-coated orthopedic implant loaded with tobramycin (2019)

An approximately 1-µm thick hydroxyapatite coating was biomimetically deposited on an alkali-treated, commercially available orthopedic screw surface (type II anodized titanium). Tobramycin loaded into the coating via a simple soaking method was shown to provide a sustained release above the minimal inhibitory concentration 0.2 µg/µl for up to two days. Agar diffusion tests showed that the tobramycin-loaded coating was able to produce a zone of inhibition against Staphylococcus aureus for up to five days. Biocompatibility testing using outgrowth endothelial cells and primary osteoblasts suggested that good cell compatibility of the coating can be expected in vivo. A rabbit distal femur condyle model was used for in vivo evaluation of the antibacterial efficacy of the tobramycin-loaded coating, and this pilot study showed that the release of tobramycin was sufficient to locally eliminate very large amounts of bacteria in vivo (inoculation dose 10 4 –10 5 CFU S. aureus/test site).
Role of Aortic Geometry on Stroke Propensity based on Simulations of Patient-Specific Models (2017)

Stroke is a life threatening event that is expected to more than double over the next 40 years. Atrial fibrillation (AF) has been reported as a strong independent risk factor for stroke. We have previously shown that a hemodynamic perturbation by AF or reduced cardiac output and cycle length may have a significant impact on clot trajectory and thus embolic stroke propensity through the left common carotid artery using an idealized aortic arch model. Here, we show the dependence of flow patterns and hence stroke propensity on geometry of patient-specific aortas. We performed computational fluid dynamics (CFD) simulations to determine the variations of AF-induced stroke propensity over various image-based patient-dependent aorta models. The results demonstrated that curvature pattern of aorta can play a determinant role in AF-induced stroke propensity alteration. Specifically, it was shown that the hemodynamic perturbation by AF considered led to substantial increase in stroke propensity (i.e., 2.5~3.8 fold elevation) for lower curvature angle <90° while the changes in stroke propensity by AF are negligible for higher curvature angle >90°. The present simulations suggest that aortic arch curvature is an important risk factor for embolic stroke which should be tested in future clinical trials.
Theeffectsofweaningage,dietcomposition,andcategorisationof creepfeedintakebypigletsondiarrhoeaand performanceafterweaning ! (2007)

AbstractTh is stud y investigated the effects of w eaning age, diet, and classification of piglets as OeatersO or Ono n eatersO of cree p fee d inlactation, on prod uc tion an d diarrhoea after w eaning. F our antim icrobial-free diets we re offered in lactation an d for 14 days afterwe aning: (i) w heatÐ so y based diet wi th anim al and vegetable (Omi xe dO) protein so urces (C O M M ), (ii) heat-processed rice (H P R ) w ithbarley hu lls and po tato starch an d m ixed protein sources (R B H P S ),(iii) H P R wi th su ga r-be et pu lp and m ixed protein sources (R SB P) ,and (iv) H P R wi th mi xe d protein so urces (R ). P iglets we re individually ex am ined for diarrhoea da ily for 14 days after w eaning, andantibiotic trea tm en ts we re individually recorded. F aecal sw abs we re take n on day 10 after w eaning and scored for ! -hae mo lyticEs cherichia coli. T here we re significan t m ain effec ts of we aning age and diet (bo th P b 0.001) on daily gain betwe en we an ing and14 days after w eaning.P igs w eane d later grew 50 g/day m ore than pigs w eaned earlier,and pigs fed the CO M M dietgrew slow er thanpigs fed the rice -based diets.Th e num ber of antibiotic treatm ents w as influenced by diet(P b 0.001),w ith m osttreatm ents (2.1) given topigs fed the diet RB HP S . Fa ec al score w as influenced by a w eaning age and diet interaction (P b 0.01). Th ere w as no co rrelation(P N 0.05) betw een the num be r of antibiotics treatm ents an d the E. co liscore.© 2007 Elsevier B.V . All rights reserved.
Helix propagation and N‐cap propensities of the amino acids measured in alanine‐based peptides in 40 volume percent trifluoroethanol (1996)

The helix propagation and N-cap propensities of the amino acids have been measured in alanine-based peptides in 40 volume percent trifluoroethanol (40% TFE) to determine if this helix-stabilizing solvent uniformly affects all amino acids. The propensities in 40% TFE are compared with revised values of the helix parameters of alanine-based peptides in water. Revision of the propensities in water is the result of redefining the capping statistical weights and evaluating the helix nucleation constant with N-capping explicitly included in the helix-coil model. The propagation propensities of all amino acids increase in 40% TFE relative to water, but the increases are highly variable. In water, all beta-branched and beta-substituted amino acids are helix breakers. In 40% TFE, the propagation propensities of the nonpolar amino acids increase greatly, leaving charged and neutral polar, beta-substituted amino acids as helix breakers. Glycine and proline are strong helix breakers in both solvents. Free energy differences for helix propagation (delta delta G) between alanine and other nonpolar amino acids are twice as large in water as predicted from side-chain conformational entropies, but delta delta G values in 40% TFE are close to those predicted from side-chain entropies. This dependence of delta delta G on the solvent points to a specific role of water in determining the relative helix propensities of the nonpolar amino acids. The N-cap propensities converge toward a common value in 40% TFE, suggesting that differential solvation by water contributes to the diversity of N-cap values shown by the amino acids.
Hybrid ultrasound‐MRguidedHIFUtreatment method with 3Dmotion compensation (2017)

Hybrid US-MR-guided HIFU ablation with 3D motion compensation was demonstrated ex vivo together with a stable referenceless PRFS thermometry baseline in healthy volunteer liver acquisitions. Magn Reson Med 79:2511-2523, 2018. © 2017 International Society for Magnetic Resonance in Medicine.
Aspirin’s Active Metabolite Salicylic Acid Targets High Mobility Group Box 1 to Modulate Inflammatory Responses (2015)

Salicylic acid (SA) and its derivatives have been used for millennia to reduce pain, fever and inflammation. In addition, prophylactic use of acetylsalicylic acid, commonly known as aspirin, reduces the risk of heart attack, stroke and certain cancers. Because aspirin is rapidly de-acetylated by esterases in human plasma, much of aspirin's bioactivity can be attributed to its primary metabolite, SA. Here we demonstrate that human high mobility group box 1 (HMGB1) is a novel SA-binding protein. SA-binding sites on HMGB1 were identified in the HMG-box domains by nuclear magnetic resonance (NMR) spectroscopic studies and confirmed by mutational analysis. Extracellular HMGB1 is a damage-associated molecular pattern molecule (DAMP), with multiple redox states. SA suppresses both the chemoattractant activity of fully reduced HMGB1 and the increased expression of proinflammatory cytokine genes and cyclooxygenase 2 (COX-2) induced by disulfide HMGB1. Natural and synthetic SA derivatives with greater potency for inhibition of HMGB1 were identified, providing proof-of-concept that new molecules with high efficacy against sterile inflammation are attainable. An HMGB1 protein mutated in one of the SA-binding sites identified by NMR chemical shift perturbation studies retained chemoattractant activity, but lost binding of and inhibition by SA and its derivatives, thereby firmly establishing that SA binding to HMGB1 directly suppresses its proinflammatory activities. Identification of HMGB1 as a pharmacological target of SA/aspirin provides new insights into the mechanisms of action of one of the world's longest and most used natural and synthetic drugs. It may also provide an explanation for the protective effects of low-dose aspirin usage.
External refractive index insensitive air-cladlong period fibre grating (1999)

The first demonstration of long period gratings (LPGs) written in a novel air-clad fibre is reported. In contrast to conventional LPGs, this type of LPG is insensitive to the external refractive index.
Age-Related and Depot-Specific Changes in White Adipose Tissue of Growth Hormone Receptor-Null Mice (2013)

Growth hormone receptor-null (GHR(-/-)) mice are dwarf, insulin sensitive, and long-lived in spite of increased adiposity. However, their adiposity is not uniform, with select white adipose tissue (WAT) depots enlarged. To study WAT depot-specific effects on insulin sensitivity and life span, we analyzed individual WAT depots of 12- and 24-month-old GHR(-) (/-) and wild-type (WT) mice, as well as their plasma levels of selected hormones. Adipocyte sizes and plasma insulin, leptin, and adiponectin levels decreased with age in both GHR(-) (/-) and WT mice. Two-dimensional gel electrophoresis proteomes of WAT depots were similar among groups, but several proteins involved in endocytosis and/or cytoskeletal organization (Ehd2, S100A10, actin), anticoagulation (S100A10, annexin A5), and age-related conditions (alpha2-macroglobulin, apolipoprotein A-I, transthyretin) showed significant differences between genotypes. Because Ehd2 may regulate endocytosis of Glut4, we measured Glut4 levels in the WAT depots of GHR(-) (/-) and WT mice. Inguinal WAT of 12-month-old GHR(-) (/-) mice displayed lower levels of Glut4 than WT. Overall, the protein changes detected in this study offer new insights into possible mechanisms contributing to enhanced insulin sensitivity and extended life span in GHR(-) (/-) mice.
Abstract 5901: The role of POU3F2 in the aggressive behavior of neuroendocrine prostate cancer (2018)

Abstract Neuroendocrine and Small Cell Prostate Cancer (NEPC) is a lethal disease emerging from Castrate Resistant Prostate Cancer (CRPC) after treatment with next-generation anti-androgen therapies such as abiraterone and enzalutamide. The mechanisms by which treatment resistant prostate epithelial cancer cells trans-differentiate to poorly differentiated small cell cancer are not well understood. We and others found that Nervous System-Specific Octamer-Binding Transcription Factor (POU3F2) expression is induced in NEPC. POU3F2 is a reprogramming transcription factor that controls cellular differentiation and can induce stem-like cells from differentiated glioblastoma. POU3F2 also plays a critical role in melanoma progression and in small cell carcinoma of the lung. NEPC shares similarities with small cell carcinoma from other organs. We hypothesized that POU3F2 may be a key transcription factor that is required for transdifferentiation and the survival of NEPC cells. We further hypothesize that the underlying mechanism of therapy resistance in NEPC is that NEPC consists of stem-like cells that were reprogrammed from differentiated prostate cancer cells under the selective pressure of androgen receptor (AR) pathway-targeted therapy. We elucidated the functional role of POU3F2 in the aggressive cancer behavior of NEPC —including stem-cell properties, tumorigenesis, invasion, and chemo-resistance. We also characterized the mechanisms that regulate POU3F2 expression in therapy-resistant NEPC. The study provides a rational for targeted therapy for treatment of NEPC. It could also be used to design a strategy to halt the emergence of NEPC from CRPC. Citation Format: Naoko Kobayashi, Dai Hong, Chun Wang, Joyce Yamashiro, Johnny Guan, Robert E. Reiter. The role of POU3F2 in the aggressive behavior of neuroendocrine prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5901.