gebhart/patrepeval huggingface dataset:
Functional multispectral optoacoustic tomography imaging of hepatic steatosis development in mice (2021)

The increasing worldwide prevalence of obesity, fatty liver diseases and the emerging understanding of the important roles lipids play in various other diseases is generating significant interest in lipid research. Lipid visualization in particular can play a critical role in understanding functional relations in lipid metabolism. We investigated the potential of multispectral optoacoustic tomography (MSOT) as a novel modality to non-invasively visualize lipids in laboratory mice around the 930nm spectral range. Using an obesity-induced non-alcoholic fatty liver disease (NAFLD) mouse model, we examined whether MSOT could detect and differentiate different grades of hepatic steatosis and monitor the accumulation of lipids in the liver quantitatively over time, without the use of contrast agents, i.e. in label-free mode. Moreover, we demonstrate the efficacy of using the real-time clearance kinetics of indocyanine green (ICG) in the liver, monitored by MSOT, as a biomarker to evaluate the organ's function and assess the severity of NAFLD. This study establishes MSOT as an efficient imaging tool for lipid visualization in preclinical studies, particularly for the assessment of NAFLD.
Optical coherence angiography to assess the dose-effect relationship of prenatal alcohol exposure on fetal brain vasculature (2023)

Prenatal alcohol exposure (PAE) is a leading cause of developmental disabilities worldwide and thus, is one of the best-known causes of preventable birth defects. Its effects can persist throughout life as physical and cognitive growth and development deficits. Previous studies have demonstrated that the acute effects of prenatal alcohol exposure on fetal brain vasculature diminish brain growth and decrease cerebrovascular blood flow. In this study, we use correlation mapping optical coherence angiography to assess the dose-effect relationship of prenatal alcohol exposure on fetal brain vasculature in utero in a mouse model (C57BL/6J). We evaluated multiple alcohol dosages (1.5 g/kg, 3.0 g/kg, and 4.5 g/kg) at gestational day (GD) 14.5 followed immediately by imaging at GD 14.5. We also studied multiple dosing effects by administering ethanol via intragastric gavage at GD 12.5, 13.5, and 14.5 for each dose (1.5 g/kg, 3.0 g/kg, and 4.5 g/kg) followed by imaging at GD 14.5. Results show vasoconstriction of the main imaged blood vessel after dosing for three consecutive days. When the embryo was exposed to the lowest dose, 1.5 g/kg of ethanol, there was a greater decrease in the main blood vessel diameter, compared to the highest dose, 4.5 g/kg of ethanol. For the acute dosing studies, where a single ethanol dose was administered at GD 14.5, the results show a higher percentage change in vessel diameter over time for 4.5 g/kg, which was the highest dose, but with a higher initial percentage change at a lower dose. The multiple dose and single dose exposure to ethanol results demonstrated significant changes in fetal brain vasculature. Multiple dosing of prenatal alcohol exposure shows a significant effect in the vasculature for each dosage, demonstrating the dose-effect relationship of multiple ethanol exposure on embryo brain vasculature compared to a single dose exposure.
NodeTrix: a Hybrid Visualization of Social Networks (2007)

The need to visualize large social networks is growing as hardware capabilities make analyzing large networks feasible and many new data sets become available. Unfortunately, the visualizations in existing systems do not satisfactorily resolve the basic dilemma of being readable both for the global structure of the network and also for detailed analysis of local communities. To address this problem, we present NodeTrix, a hybrid representation for networks that combines the advantages of two traditional representations: node-link diagrams are used to show the global structure of a network, while arbitrary portions of the network can be shown as adjacency matrices to better support the analysis of communities. A key contribution is a set of interaction techniques. These allow analysts to create a NodeTrix visualization by dragging selections to and from node-link and matrix forms, and to flexibly manipulate the NodeTrix representation to explore the dataset and create meaningful summary visualizations of their findings. Finally, we present a case study applying NodeTrix to the analysis of the InfoVis 2004 coauthorship dataset to illustrate the capabilities of NodeTrix as both an exploration tool and an effective means of communicating results.
Congenital Plaque‐Type Glomuvenous Malformations Associated with Fetal Pleural Effusion and Ascites (2010)

Glomuvenous malformations are hereditary vascular anomalies, usually without extracutaneous involvement. We report two cases of extensive thoracic plaque-type glomuvenous malformation in newborns who had previously been diagnosed in utero with pleural effusion and ascites, suggesting a pathogenic link between the two conditions.
In vivo dosimeters for HDR brachytherapy: A comparison of a diamond detector, MOSFET, TLD, and scintillation detector (2007)

The large dose gradients in brachytherapy necessitate a detector with a small active volume for accurate dosimetry. The dosimetric performance of a novel scintillation detector (BrachyFOD) is evaluated and compared to three commercially available detectors, a diamond detector, a MOSFET, and LiF TLDs. An 192Ir HDR brachytherapy source is used to measure the depth dependence, angular dependence, and temperature dependence of the detectors. Of the commercially available detectors, the diamond detector was found to be the most accurate, but has a large physical size. The TLDs cannot provide real time readings and have depth dependent sensitivity. The MOSFET used in this study was accurate to within 5% for distances of 20 to 50 mm from the 192Ir source in water but gave errors of 30%-40% for distances greater than 50 mm from the source. The BrachyFOD was found to be accurate to within 3% for distances of 10 to 100 mm from an HDR 192Ir brachytherapy source in water. It has an angular dependence of less than 2% and the background signal created by Cerenkov radiation and fluorescence of the plastic optical fiber is insignificant compared to the signal generated in the scintillator. Of the four detectors compared in this study the BrachyFOD has the most favorable combination of characteristics for dosimetry in HDR brachytherapy.
Quantum dot electrons as controllable scattering centers in the vicinity of a two-dimensional electron gas (2006)

Self-assembled InAs quantum dots can be controllably charged with a defined number of electrons per dot. We report on conductivity measurements of Al x Ga1−x As/GaAs heterostructures, where such quantum dots are embedded in the direct vicinity of a two-dimensional electron gas (2DEG). We demonstrate the controlled enhancement of the scattering rate in the 2DEG induced by charging the quantum dots with additional electrons. The resulting transport lifetimes are in good agreement with theoretical values for Coulomb scattering in two dimensions.
Effects of KiSS-1 Peptide, the Natural Ligand of GPR54, on Follicle-Stimulating Hormone Secretion in the Rat (2005)

KiSS-1 was originally identified as a metastasis suppressor gene encoding an array of structurally related peptides, namely kisspeptins, which acting through the G protein-coupled receptor GPR54 are able to inhibit tumor progression. Unexpectedly, a reproductive facet of this newly discovered system has recently arisen, and characterization of the role of the KiSS-1/GPR54 system in the neuroendocrine control of gonadotropin secretion has been initiated. However, such studies have been so far mostly restricted to LH, and very little is known about the actual contribution of this system in the regulation of FSH release. To address this issue, the effects of KiSS-1 peptide on FSH secretion were monitored in vivo and in vitro under different experimental conditions. Intracerebroventricular administration of KiSS-1 peptide significantly stimulated FSH secretion in prepubertal and adult rats. Yet, dose-response analyses in vivo demonstrated an ED(50) value for the FSH-releasing effects of KiSS-1 of 400 pmol, i.e. approximately 100-fold higher than that of LH. In addition, systemic (ip and iv) injection of KiSS-1 significantly stimulated FSH secretion in vivo. However, KiSS-1 failed to elicit basal FSH release directly at the pituitary level, although it moderately enhanced GnRH-stimulated FSH secretion in vitro. Finally, mechanistic studies revealed that the ability of KiSS-1 to elicit FSH secretion was abolished by the blockade of endogenous GnRH actions, but it was persistently observed in different models of leptin insufficiency and after blockade of endogenous excitatory amino acid and nitric oxide pathways, i.e. relevant signals in the neuroendocrine control of gonadotropin secretion. In summary, our results extend previous recent observations on the role of KiSS-1 in the control of LH secretion and provide solid evidence for a stimulatory effect of KiSS-1 on FSH release, acting at central level. Overall, it is proposed that the KiSS-1/GPR54 system is a novel, pivotal downstream element in the neuroendocrine network governing gonadotropin secretion.
A novel control concept for reliable operation of a three-phase three-switch buck-type unity power factor rectifier with integrated boost output stage under heavily unbalanced mains condition (2004)

In this paper the reliable operation of a three-phase three-switch buck-type PWM unity power factor rectifier with integrated boost output stage under heavily unbalanced mains, i.e. mains voltage unbalance, loss of one phase, short circuit of two phases or earth fault of one phase is investigated theoretically and experimentally. The analytical calculation of the relative on-times of the active switching states and of the DC link current reference value is treated in detail for active and deactivated boost output stage. Based on the theoretical considerations a control scheme which allows to control the system for any mains condition without change-over of the control structure is described. Furthermore, digital simulations as well as experimental results are shown which confirm the proposed control concept for different mains failure conditions and for the transition from balanced mains to a failure condition and vice versa. The experimental results are derived from a 5 kW prototype, input voltage range 208-480 V/sub rms/ line-to-line, output voltage 400 V/sub DC/ of the rectifier system, where the control is realized by a 32-bit digital signal processor.
Interaction of drugs of abuse and maintenance treatments with human P-glycoprotein (ABCB1) and breast cancer resistance protein (ABCG2) (2009)

Drug interaction with P-glycoprotein (P-gp) and breast cancer resistance protein (BCRP) may influence its tissue disposition including blood-brain barrier transport and result in potent drug-drug interactions. The limited data obtained using in-vitro models indicate that methadone, buprenorphine, and cannabinoids may interact with human P-gp; but almost nothing is known about drugs of abuse and BCRP. We used in vitro P-gp and BCRP inhibition flow cytometric assays with hMDR1- and hBCRP-transfected HEK293 cells to test 14 compounds or metabolites frequently involved in addiction, including buprenorphine, norbuprenorphine, methadone, ibogaine, cocaine, cocaethylene, amphetamine, N-methyl-3,4-methylenedioxyamphetamine, 3,4-methylenedioxyamphetamine, nicotine, ketamine, Delta9-tetrahydrocannabinol (THC), naloxone, and morphine. Drugs that in vitro inhibited P-gp or BCRP were tested in hMDR1- and hBCRP-MDCKII bidirectional transport studies. Human P-gp was significantly inhibited in a concentration-dependent manner by norbuprenorphine>buprenorphine>methadone>ibogaine and THC. Similarly, BCRP was inhibited by buprenorphine>norbuprenorphine>ibogaine and THC. None of the other tested compounds inhibited either transporter, even at high concentration (100 microm). Norbuprenorphine (transport efflux ratio approoximately 11) and methadone (transport efflux ratio approoximately 1.9) transport was P-gp-mediated; however, with no significant stereo-selectivity regarding methadone enantiomers. BCRP did not transport any of the tested compounds. However, the clinical significance of the interaction of norbuprenorphine with P-gp remains to be evaluated.
Synthesis of Partially meso-Free 2,3-Di(arylethynyl)porphyrins (2017)

Partially meso-free 2,3-di(arylethynyl)porphyrins were synthesized by the Sonogashira coupling reactions of 2,3-diiodoporphyrin, which is a useful precursor for β-substituted porphyrins. The porphyrins exhibited broadened and red-shifted absorption, suggesting effective π-conjugation between the porphyrin core and the aryl groups through the acetylene π-spacer.
Interleukin 2-dependent and interleukin 2-independent pathways of regulation of thymocyte function by interleukin 6. (1988)

Recombinant human interleukin 6 (IL-6), also termed B-cell-stimulatory factor 2 (BSF-2) or interferon-beta 2, was found to stimulate the proliferation of mouse thymocytes costimulated with phytohemagglutinin (PHA). In addition, IL-6 synergistically enhanced the stimulation of thymocyte proliferation by recombinant human interleukin 1 (IL-1) or interleukin 2 (IL-2). Mature thymocytes lacking peanut agglutinin receptor are the main target of IL-6 action. Incubation of thymocytes with IL-6 in the presence of PHA resulted in an increased expression of the IL-2 receptor (IL-2R) as demonstrated by flow cytometry. Monoclonal antibody specific for the p55 chain of the murine IL-2R significantly reduced IL-6-stimulated thymocyte proliferation in the presence of the optimal concentration of PHA. However, the same monoclonal antibody failed to reduce IL-6-driven thymocyte proliferation in the presence of a suboptimal PHA concentration, suggesting that IL-6 stimulates thymocyte proliferation by way of IL-2-dependent and IL-2-independent pathways. These results indicate that, in addition to its earlier demonstrated ability to promote B-cell differentiation and growth, IL-6 also acts as a growth regulator in cells of the T-lymphocyte lineage. IL-6 is emerging as an important regulatory cytokine with multiple actions on immune functions.
Predicting respiratory failure in amyotrophic lateral sclerosis: still a long way to go (2019)

<b>Prediction modelling is critical for improving ALS respiratory care. Assessing external validity of a model should account for discrimination, calibration, and cohort characteristics. Further work on outcomes is necessary before practice implementation.</b>http://bit.ly/2XbfeUq
High temperature phase transformation of tantalum nitride films deposited by plasma enhanced atomic layer deposition for gate electrode applications (2007)

Tantalum nitride thin films were deposited at 400°C by plasma enhanced atomic layer deposition using an amido-based metal organic tantalum precursor. An Ar∕N2∕H2 mixture was flowed upstream of a remote plasma system to produce the reactive species used for the nitridation process. The as-deposited film was amorphous and contained 15at.% oxygen in the bulk of the film. High resolution photoelectron spectroscopy studies of the Ta 4f feature were consistent with the presence of the semiconducting Ta3N5 phase in the as-deposited films. Electron diffraction studies were carried out by annealing the Ta3N5 film in situ in a transmission electron microscope. The high resistivity Ta3N5 phase crystallized into the cubic TaN phase at 850°C. This transformation appeared to coincide with outdiffusion of excess nitrogen from the Ta3N5 film during the anneal. The resistivity of the crystallized film was estimated to be 600μΩcm from four point probe measurements.
Dynamic interplay between antagonistic pathways controlling the σ 32 level in Escherichia coli (2000)

The heat-shock response in Escherichia coli depends primarily on the transient increase in the cellular level of heat-shock sigma factor final sigma(32) encoded by the rpoH gene, which results from both enhanced synthesis and transient stabilization of normally unstable final sigma(32). Heat-induced synthesis of final sigma(32) was previously shown to occur at the translation level by melting the mRNA secondary structure formed within the 5' coding sequence of rpoH including the translation initiation region. The subsequent decrease in the final sigma(32) level during the adaptation phase has been thought to involve both shutoff of synthesis (translation) and destabilization of final sigma(32)-mediated by the DnaK-DnaJ chaperones, although direct evidence for translational repression was lacking. We now show that the heat-induced synthesis of final sigma(32) does not shut off at the translation level by using a reporter system involving translational coupling. Furthermore, the apparent shutoff was not observed when the synthesis rate was determined by a very short pulse labeling (15 s). Examination of final sigma(32) stability at 10 min after shift from 30 to 42 degrees C revealed more extreme instability (t(1/2)=20 s) than had previously been thought. Thus, the dynamic change in final sigma(32) stability during the heat-shock response largely accounts for the apparent shutoff of final sigma(32) synthesis observed with a longer pulse. These results suggest a mechanism for maintaining the intricate balance between the antagonistic pathways: the rpoH translation as determined primarily by ambient temperature and the turnover of final sigma(32) as modulated by the chaperone (and presumably protease)-mediated autogenous control.
Sources of variability in uncertain medical decisions in the ICU: a process tracing study (2004)

<b>Background:</b> Consistency of medical decision making (equity) is an important component of quality of care. When patients with chronic obstructive pulmonary disease (COPD) present with an exacerbation needing respiratory support they may die if it is not provided. However, if the disease has reached its terminal stage, ventilation will prolong the process of dying. The ventilation outcome is uncertain and there is evidence of variability when this decision is made, the sources of which are not well understood. <b>Objectives:</b> To identify sources of variability and propose ways of tackling them in order to promote equity in this type of medical decision. <b>Methods:</b> Six case histories were selected from hospital records of COPD patients. Fourteen senior doctors from seven hospitals in the West Midlands participated. A process tracing approach was used which consisted of (1) withholding case information until specifically requested by the doctors, (2) estimating survival during the decision making process, and (3) concurrent questioning regarding information interpretation and its impact on survival estimates and decisions. <b>Results:</b> The observed decision variability was attributed to doctors attaching importance to different information, gathering different information, and interpreting information differently. There were significant differences between doctors in the amount of information requested. <b>Conclusions:</b> Differences in information gathering and interpretation by clinicians can result in different decisions being made about the same patient. This variation may exist for other uncertain medical decisions and may be tackled by providing clinicians with prognostic models in the form of usable decision aids.
Mutual information based feature selection for symbolic interval data (2014)

Feature selection is an important issue for data analysis. But almost all feature selection algorithms in machine learning have the weakness to process symbolic interval data because it is structured. In this paper we propose a feature selection method for interval data based on mutual information. The concept of heuristic mutual information is defined as a measure of relevance among features. Experiments on eight data sets show that the proposed method outperforms the previous ones both in accuracy and other criteria.
Imaging of Occlusive Thrombi in Acute Ischemic Stroke (2014)

Thrombi, or clots, often occlude proximal segments of the cerebral arterial circulation in acute ischemic stroke. Thromboembolic occlusion or thrombi superimposed on atherosclerotic plaque are the principal focus of acute stroke therapies such as thrombolysis or thrombectomy. We review the imaging characteristics of thrombi on multimodal computed tomography and magnetic resonance imaging, angiography, and ultrasonography, summarizing recent studies that facilitate therapeutic decision-making from these noninvasive studies. Information about the location, size, and imaging characteristics can be ascertained using these techniques. Imaging findings in relation to occlusive thrombus have been correlated with clot pathology, response to therapeutic interventions, and clinical outcome. Diagnostic evaluation of occlusive thrombi on noninvasive studies now constitutes an integral component of acute stroke management.
Structural and Optical Characteristics of InAs/InAlGaAs Quantum Dots Grown on InP/InGaAs/InP Distributed Feedback Grating Structure (2006)

We fabricated the distributed feedback (DFB) InP/InGaAs/InP grating structures on InP (100) substrates by metal-organic chemical vapor deposition, and their structural properties were investigated by atomic force microscopy and scanning electron microscopy. Self-assembled InAs/InAlGaAs quantum dots (QDs) were grown on the InP/InGaAs/InP grating structures by molecular beam epitaxy, and their optical properties were compared with InAs/InAlGaAs QDs without grating structure. The duty of the grating structures was about 30%. The PL peak position of InAs/InAlGaAs QDs grown on the grating structure was 1605 nm, which was red-shifted by 18 nm from that of the InAs/InAlGaAs QDs without grating structure. This indicates that the formation of InAs/InAlGaAs QDs was affected by the existence of the DFB grating structures.
CD30/TNF receptor-associated factor interaction: NF-kappa B activation and binding specificity. (1996)

CD30 is a member of the tumor necrosis factor (TNF) receptor superfamily. CD30 is expressed on normal activated lymphocytes, on several virally transformed T- or B-cell lines and on neoplastic cells of Hodgkin's lymphoma. The interaction of CD30 with its ligand induces pleiotropic effects on cells resulting in proliferation, differentiation, or death. The CD30 cytoplasmic tail interacts with TNF receptor-associated factors (TRAFs), which have been shown to transduce signals mediated by TNF-R2 and CD40. We demonstrate here that TRAF2 also plays an important role in CD30-induced NF-kappa B activation. We also show that TRAF2-mediated activation of NF-kappa B plays a role in the activation of HIV transcription induced by CD30 cross-linking. Detailed site-directed mutagenesis of the CD30 cytoplasmic tail reveals that there are two independent binding sites for TRAF, each interacting with a different domain of TRAF. Furthermore, we localized the TRAF-C binding site in CD30 to a 5-7 amino acid stretch.
OBJECT CODING OF HARMONIC SOUNDS USING SPARSE AND STRUCTURE D REPRESENTATIONS (2007)

Object coding allows audio compression at extremely low bit-rates, provided that the objects are correctly modelled and identified. In this study, a codec has been implemented on the basis of a sparse decomposition of the signal with a dictionary of Instrument-Specific Harmonic atoms. The decomposition algorithm extracts “molecules ” i.e. linear combinations of such atoms, considered as note-like objects. Thus, they can be coded efficiently using notespecific strategies. For signals containing only harmonic sounds, the obtained bitrates are very low, typically around 2 kbs, and informal listening tests against a standard sinusoidal coder show promising performances. 1.
Prider testing data and code, Biorxiv (2021)

The FASTA file sets and the R script used for the testing of the processing time of R package Prider.