gebhart/patrepeval huggingface dataset:
Mouse strain differences in metabolic fluxes and function of ex vivo working hearts (2013)

In mice, genetic background is known to influence various parameters, including cardiac function. Its impact on cardiac energy substrate metabolism-a factor known to be closely related to function and contributes to disease development-is, however, unclear. This was examined in this study. In commonly used control mouse substrains SJL/JCrNTac, 129S6/SvEvTac, C57Bl/6J, and C57Bl/6NCrl, we assessed the functional and metabolic phenotypes of 3-mo-old working mouse hearts perfused ex vivo with physiological concentrations of (13)C-labeled carbohydrates (CHO) and a fatty acid (FA). Marked variations in various functional and metabolic flux parameters were observed among all mouse substrains, although the pattern observed differed for these parameters. For example, among all strains, C57Bl/6NCrl hearts had a greater cardiac output (+1.7-fold vs. SJL/JCrNTac and C57Bl/6J; P < 0.05), whereas at the metabolic level, 129S6/SvEvTac hearts stood out by displaying (vs. all 3 strains) a striking shift from exogenous FA (~-3.5-fold) to CHO oxidation as well as increased glycolysis (+1.7-fold) and FA incorporation into triglycerides (+2-fold). Correlation analyses revealed, however, specific linkages between 1) glycolysis, FA oxidation, and pyruvate metabolism and 2) cardiac work, oxygen consumption with heart rate, respectively. This implies that any genetically determined factors affecting a given metabolic flux parameter may impact on the associated functional parameters. Our results emphasize the importance of selecting the appropriate control strain for cardiac metabolic studies using transgenic mice, a factor that has often been neglected. Understanding the molecular mechanisms underlying the diversity of strain-specific cardiac metabolic and functional profiles, particularly the 129S6/SvEvTac, may ultimately disclose new specific metabolic targets for interventions in heart disease.
DEVELOPMENT, VALIDATION, AND APPLICATION OF A NONINVASIVE SPINAL MOTION MEASUREMENT SYSTEM (2010)

Spontaneous vertebral fractures are a large and growing health care problem. Biomechanical factors, specifically, abnormal posture or gait‐related spinal motion may interact with age‐weakened bone to induce altered spinal biomechanics that in turn increase the likelihood of vertebral body fracture. This research takes steps towards the goal of reducing the number of vertebral fractures in two phases: 1) Validation of a noninvasive spinal motion measurement system in cadaver torsos and 2) Application of the measurement system in human subjects. The cadaver study compared vertebral motion at 4 levels (T7,T12,L3,L5) as measured by adhesive skin markers versus motion measured by bone pins implanted into the vertebrae. Cadaver torsos were tested in lateral‐bending, flexion and axialrotation. Mean differences in vertebral body angular motion between skin markers and bone pin markers were <0.5° around the anterior‐posterior and medial‐lateral axes and <0.9° around the superior‐inferior axis. This measurement method was able to accurately quantify vertebral body motion in cadaver torsos thus allowing for application to human subject testing. X‐rays and 3D motion capture were employed to quantify spinal posture and motion parameters during gait in 12 older and 12 younger normal, females. Vertebral motion around 3 axes was measured at 4 levels (T7,T10,T12,L2) using noninvasive retroreflective markers during treadmill gait at 3 speeds (0.5,0.7,0.9m/s). The average angular motion of all gait cycles at each speed was determined for each level. The triplanar ranges of motion and variability of motion were compared as a function of age. Older subjects had 31.7% larger frontal Cobb angles and up to 30.9% and 33.5% smaller ranges of spinal motion in the frontal and sagittal planes. Variability of motion in the sagittal plane was up to 42.9% less in older subjects. Decreased ranges of motion and variability of spinal motion observed in older subjects may imply that vertebral loading in these subjects may not be as uniformly distributed across the vertebrae as in younger subjects. Greater stresses may result from the abnormal motion, thus increasing fracture risk. Confirmation of this hypothesis requires a longitudinal study, but if verified, may lead to the development of inexpensive countermeasures to prevent fractures.
Investigation of carrier recombination process in top-down fabricated GaAs nano-disc array structure by photoluminescence measurements (2016)

This New top-down fabrication process using bio-template and neutral beam etching process have succeeded to grow GaAs quantum nano disc (ND) for optical communication devices. The size, the alignment and the density of ND were well controlled. Low temperature photoluminescence measurement confirmed that the quantum energy levels were formed in the present structure and made clear the usefulness of the top-down process toward a defect-free ND fabrication. Strong luminescence was observed even in an as-etched samples.
Human Amylin Stimulates Inflammatory Cytokine Secretion from Human Glioma Cells (2000)

Chronic neurodegeneration in the brains of Alzheimer's disease (AD) patients may be mediated, at least in part, by the ability of amyloid beta (Abeta) to exacerbate inflammatory pathways in a conformation-dependent manner. In this regard, we previously reported that the Abeta-peptide-mediated potentiation of inflammatory cytokine secretion from interleukin-1beta (IL-1beta)-stimulated human astrocytoma cells was conformation dependent. Other amyloidogenic peptides, such as human amylin, which display similar conformation-dependent neurotoxic effects, may also elicit inflammatory cytokine secretion from glial cells. To test this hypothesis, we compared human and rat amylin for the effects on cytokine production in U-373 MG human astrocytoma cells. Human amylin alone stimulated U-373 MG cells to secrete IL-6 and IL-8 in a concentration-dependent manner with maximum effects seen at 10-25 microM peptide. In addition, human amylin markedly potentiated IL-1beta-stimulated cytokine production with a similar concentration dependence. In contrast, nonamyloidogenic rat amylin modestly stimulated cytokine secretion, either alone or combined with IL-1beta. Aging human amylin resulted in diminished cytokine secretion, probably due to the formation of large, less active aggregates. In agreement with our previous studies using Abeta, extracellular Ca(2+) was necessary for human amylin stimulation of cytokine secretion. Our data suggest that amyloidogenic peptides promote cytokine secretion through similar beta-sheeted secondary-structure- and extracellular-Ca(2+)-dependent mechanisms.
[Catheter treatment of congenital heart defects. Arterial septal defects and open ductus arteriosus]. (1997)

The results of new methods for catheter treatment of congenital heart defects are presented. Between 1989 and 1996 closure of a patent ductus arteriosus was performed in 66 instances on 63 patients, eight of which were with coils. Three patients were treated twice, one with an additional umbrella, two with coils. The overall complete closure rate for umbrellas was 75%, after two ducts, which were initially totally occluded, recanalized. In six more patients the procedure was either aborted or indication was not present. All six ducts treated with coils as the first procedure were completely closed. One of two patients who had residual leak after previous umbrella treatment achieved complete closure after subsequent coil implantation. Closure of atrial septal defects in the oval fossa was performed using the Amplatzer septal occluder in seven children. Complete closure was achieved in all of them. There have been no complications, in particular there have been no cases of embolization in any of the groups. The results seem to indicate that coil occlusion of a persistently patent duct may be at least as good as the umbrella in terms of complete closure. So far both methods have been safe, but experience with coils is limited. The closure of atrial septal defects shows encouraging results. We will continue to offer this treatment as an alternative to open heart surgery in carefully selected patients.
Isolation and Characterization of the Protein Components of the Liver Microsomal O2-insensitive NADH-Benzamidoxime Reductase (1997)

Drugs containing strong basic nitrogen functional groups can be N-oxygenated to genotoxic products. While the reduction of such products is of considerable toxicological significance, most in vitro studies have focused on oxygen-sensitive reductase systems. However, an oxygen-insensitive microsomal hydroxylamine reductase consisting of NADH, cytochrome b5, its reductase, and a third unidentified protein component has been known for some time (Kadlubar, F. F., and Ziegler, D. M. (1974) Arch. Biochem. Biophys. 162, 83-92). This report describes the isolation and identification of all of the components required for the reconstitution of an oxygen-insensitive liver microsomal system capable of catalyzing the efficient reduction of primary N-hydroxylated structures such as amidines, guanidines, amidinohydrazones, and similar functional groups. In addition to cytochrome b5 and its reductase, the reconstituted system requires phosphatidylcholine and a P450 isoenzyme that has been purified to homogeneity from pig liver. The participation of cytochrome b5 and NADH cytochrome b5 reductase in cytochrome P450-dependent biotransformations has previously only been described for oxidative processes. The data presented suggest that this system may be an important catalyst in the reduction of genotoxic N-hydroxylated nitrogen components in liver. Their facile reduction by cellular NADH may be the reason why N-hydroxylated products can be missed by studies in vivo. Furthermore, the enzyme system is involved in the reduction of amidoximes and similar functional groups, which can be used as prodrug functionalities for amidines and related groups.
Optimizing the design of trefoil phase plates for wavefront coding (2017)

Wavefront Coding (WFC) is a technique which makes use of generalized aspheric optics and digital signal processing to greatly increase the depth of focus and/or reduce the cost of imaging systems. Usually, cubic phase elements are employed to obtain images that are insensitive to defocus and some aberrations. In this work we will show how to optimize the design of a trefoil phase plate in order to optimize its performance for large amounts of defocus.
Characteristics of Laminar Lifted Flames in a Partially Premixed Jet (1997)

Abstract The liftoff and blowout characteristics of laminar flames in a partially premixed jet are studied for propane and n-butane fuels mixed with air. As the flow rate increases, flame lifts off from a nozzle attached flame and liftoff height increases highly nonlinearly with flow rate, and then blowout occurs. The jet velocities at liftoff and at blowout decrease linearly with the increase in air dilution and are independent of nozzle diameter. The liftoff height at blowout is proportional to the square of nozzle diameter and to the square of fuel mass fraction. Correlations for the liftoff heights and blowout conditions are derived by using a cold jet theory for velocity and species concentrations, based on the tribrachial nature of lifted flames. That is, at the flame anchoring point, the flame has the characteristics of a stoichiometric flame and its propagation speed balances axial flow velocity. The experimental findings of liftoff and blowout are successfully predicted.
Deep learning-based medical image segmentation with limited labels (2020)

Deep learning (DL)-based auto-segmentation has the potential for accurate organ delineation in radiotherapy applications but requires large amounts of clean labeled data to train a robust model. However, annotating medical images is extremely time-consuming and requires clinical expertise, especially for segmentation that demands voxel-wise labels. On the other hand, medical images without annotations are abundant and highly accessible. To alleviate the influence of the limited number of clean labels, we propose a weakly supervised DL training approach using deformable image registration (DIR)-based annotations, leveraging the abundance of unlabeled data. We generate pseudo-contours by utilizing DIR to propagate atlas contours onto abundant unlabeled images and train a robust DL-based segmentation model. With 10 labeled TCIA dataset and 50 unlabeled CT scans from our institution, our model achieved Dice similarity coefficient of 87.9%, 73.4%, 73.4%, 63.2% and 61.0% on mandible, left & right parotid glands and left & right submandibular glands of TCIA test set and competitive performance on our institutional clinical dataset and a third party (PDDCA) dataset. Experimental results demonstrated the proposed method outperformed traditional multi-atlas DIR methods and fully supervised limited data training and is promising for DL-based medical image segmentation application with limited annotated data.
<i>De novo</i> design of ACE2 protein decoys to neutralize SARS-CoV-2 (2020)

There is an urgent need for the ability to rapidly develop effective countermeasures for emerging biological threats, such as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes the ongoing coronavirus disease 2019 (COVID-19) pandemic. We have developed a generalized computational design strategy to rapidly engineer <i>de novo</i> proteins that precisely recapitulate the protein surface targeted by biological agents, like viruses, to gain entry into cells. The designed proteins act as decoys that block cellular entry and aim to be resilient to viral mutational escape. Using our novel platform, in less than ten weeks, we engineered, validated, and optimized <i>de novo</i> protein decoys of human angiotensin-converting enzyme 2 (hACE2), the membrane-associated protein that SARS-CoV-2 exploits to infect cells. Our optimized designs are hyperstable de novo proteins (∼18-37 kDa), have high affinity for the SARS-CoV-2 receptor binding domain (RBD) and can potently inhibit the virus infection and replication in vitro. Future refinements to our strategy can enable the rapid development of other therapeutic <i>de novo</i> protein decoys, not limited to neutralizing viruses, but to combat any agent that explicitly interacts with cell surface proteins to cause disease.
Increased neurophysin I and II cerebrospinal fluid concentrations from bipolar versus unipolar depressed patients. (1983)

peer reviewed
A new noninvasive approach in breast cancer therapy using magnetic resonance imaging-guided focused ultrasound surgery. (2001)

An ideal vision of modern medicine includes tumor surgery with the human body remaining completely intact. A noninvasive therapy could avoid infections and scar formation; it would require less anesthesia, reduce recovery time, and possibly also reduce costs. This study investigated whether human breast cancer can be effectively treated with a novel combination of image guidance and energy delivery, noninvasive magnetic resonance imaging (MRI)-guided focused ultrasound (FUS). We have developed a FUS therapy unit guided by MRI for the treatment of human breast tumors in a clinical 1.5 T MR scanner. With interactive target segmentation on MRI, defined volumes could be noninvasively treated in a single session with on-line MR temperature control. The ultrasound waves were focused through the intact skin and resulted in the localized thermal tissue ablation at a maximum temperature of 70 degrees C. The therapy principle was first demonstrated in sheep breast in vivo and was then applied in a patient with core biopsy-proven invasive breast cancer 5 days before breast-conserving surgery. MRI proved suitable to delineate the breast cancer, served as stereotactic treatment planning platform, and delineated the FUS-related tissue changes such as interruption of tumor blood flow. Furthermore, MRI localized the hot spot in the tumor and measured temperature elevation during the treatment. This allowed us to monitor the efficacy and safety of FUS therapy. Immunohistochemistry of the resected specimen demonstrated that FUS homogeneously induced lethal and sublethal tumor damage with consecutive up-regulation of p53 and loss of proliferative activity. This effect was realized without anesthesia and damage to the surrounding healthy tissue or systemic effects. Overall, our results show that noninvasive MRI-guided therapy of breast cancer is feasible and effective. Thus, MRI-guided FUS may represent a new strategy for the neoadjuvant, adjuvant, or palliative treatment in selected breast cancer patients and in patients with other soft-tissue tumors.
Photosensitive Polyimide having low loss tangent for RF application (2018)

Abstract Progress of 5G telecommunication and mm radar for autopilot, high frequency operation is required. Insulator materials having low loss at high frequency is desired for the applications. We designed the low dielectric constant, and low dielectric loss materials examined molecular structure of the polyimide and found that permittivity 2.6 at 20GHz, dielectric loss 0.002. Furthermore, in consideration of mechanical properties such as the toughness and adhesion to copper from a point of practical use. Dielectric properties largely turned worse when giving photosensitivity. To overcome the poor dielectric properties, we designed the photosensitive system. After all, we successfully obtained 3.5 of dielectric constant and 0.004 of dielectric loss, and 100% of elongation at break. In addition, we offered a B stage sheet as well as varnish. These materials are applicable to re-distribution layer of FO-WLP, Interposer and other RF applications for microelectronics.
Nitrogen oxides and ozone exchange above a coniferous forest in the Netherlands (2011)

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The Effect of Direct Current Stimulation versus T‐Wave Shock on Defibrillation Threshold Testing (2015)

There is no significant difference in induced TCL or complications between the DC stim and T-shock. The induced TCL is significantly shorter than clinical TCL regardless of induction method.
Laser Spectroscopy Applied to the Environmental and Medical Fields (2008)

An overview of applied laser-based diagnostics as pursued at the Atomic Physics Division, Lund University, is given. The fields of application range from environmental monitoring including cultural heritage assessment to biomedical applications. General aspects of laser-based methods are non-intrusiveness, high spectral and spatial resolution, and data production in real-time. Different applications are frequently generically very similar irrespective of the particular context, which however, decides the spatial and temporal scales as well as the size of the optics employed. Thus, volcanic plume mapping by lidar and optical mammography are two manifestations of the same principle, as is fluorescence imaging of a human bronchus by an endoscope and the scanning of a cathedral using a fluorescence lidar system. Recent applications include remote laser-induced break-down spectroscopy (LIBS) and gas monitoring in scattering media (GASMAS).Sune Svanberg is Head of the Atomic Physics Division, Lund University, and director of the Lund Laser Centre, Sweden. He got his PhD in optical resonance spectroscopy in 1972 from Goteborg University, Sweden, where he stayed on till 1980, when he moved to Lund University. He spent research periods at the Technical University Berlin, Columbia University, Stanford University and MIT. His research field is basic and applied laser spectroscopy, presently with the emphasis on environmental and medical applications. He has well over 500 scientific papers, several patents and helped in the formation of several spin-off companies. He is a member of several academies including the Royal Academy of Sciences, Stockholm, where he for 10 years served on the Nobel Committee for Physics. He has many prizes and award including the Quantum Electronics Award of the EPS, the Azko-Nobel Science Award, the Willis E. Lamb Medal and the Celsius Medal. He is honorary doctor or professor at several universities including Jilin University, Harbin Institute of Technology and Zhejiang University. He is also Einstein Professor with the Chinese Academy of Sciences. He served on the Board of Directors of the Optical Society of America, and is presently on the Board of the Swedish Research Council. Article not available.
Defining Improvement in Nonalcoholic Steatohepatitis for Treatment Trial Endpoints: Recommendations From the Liver Forum (2019)

Identifying effective therapies for nonalcoholic steatohepatitis (NASH) with fibrosis is a pressing challenge, with 1%-2% of the population in developed nations at risk of developing NASH cirrhosis and its complications. The design of NASH clinical therapeutic trials is hampered by the long period of minimally symptomatic disease that typically precedes the development of decompensated cirrhosis and the accompanying uncertainties regarding the best precirrhotic trial endpoints that reliably reflect a subsequent reduction in liver-related morbidity and mortality. The Liver Forum is a multistakeholder organization comprised of academic, industry, and regulatory experts working from a regulatory science perspective to identify barriers, prioritize research, and identify solutions to accelerate therapeutic development for NASH. Past work of The Liver Forum has focused on recommendations for disease definitions and baseline parameters to be implemented in clinical trials that are designed to assess disease status and prevent progression to cirrhosis, liver transplantation, hepatocellular carcinoma, and death. The purpose of this summary is to review currently available clinical data to identify parameters that change in parallel with liver histology and are likely to reflect clinically meaningful reductions in the risk of developing cirrhosis and its complications. We review available data on exploratory histological, blood-based, and imaging pharmacodynamic biomarkers that may reflect meaningful treatment responses and provide recommendations regarding measurements to be considered in phase 2 and 3 trials as well as during postmarketing monitoring trials.
Studies on analogs of DAMASCENOLIDETM: Part 3. Synthesis and odor evaluation of dimethylated, cyclopropanated, and other analogs of DAMASCENOLIDETM (2020)

DAMASCENOLIDETM [1, 4-(4-methylpent-3-en-1-yl)furan-2(5H)-one], which has a citrus-like odor, is an important aroma component of roses. We have previously reported on the synthesis and odor evaluation of 24 analogs of 1 as part of our new aroma compound developing project. To accumulate more information on structure-odor relationships, 10 more promising analogs such as dimethylated and cyclopropanated analogs were synthesized and subjected to odor evaluation. As a result, it was found that dimethylation of the furanone ring affected the odor. It was also found that cyclopropanation of 1 affected the odor, whereas cyclopropanation of the double bond isomer of 1 did not significantly affect the odor. The effects on the odor caused by ring size expansion and replacement of the side chain were also investigated.