gebhart/patrepeval huggingface dataset:
Multi-atlas-based tissue identification in the lower leg using pQCT (2020)

Accurate and reproducible tissue identification techniques are essential for understanding structural and functional changes that either occur naturally with aging, or because of chronic disease, or in response to intervention therapies. These image analysis techniques are frequently utilized for characterization of changes in bone architecture to assess fracture risk, and for the assessment of loss of muscle mass and strength defined as sarcopenia. Peripheral quantitative computed tomography (pQCT) is widely employed for tissue identification and analysis. Advantages of pQCT scanners are compactness, portability, and low radiation dose. However, these characteristics imply limitations in spatial resolution and SNR. Therefore, there is still a need for segmentation methods that address image quality limitations and artifacts such as patient motion. In this paper, we introduce multi-atlas segmentation (MAS) techniques to identify soft and hard tissues in pQCT scans of the proximal tibia (~ 66% of tibial length) and to address the above factors that limit delineation accuracy. To calculate the deformation fields, we employed multi-grid free-form deformation (FFD) models with B-splines and a symmetric extension of the log-domain diffeomorphic demons (SDD). We then applied majority voting and Simultaneous Truth And Performance Level Estimation (STAPLE) for label fusion. We compared the results of our MAS methodology for each deformable registration model and each label fusion method, using Dice similarity coefficient scores (DSC). The results show that our technique utilizing SDD with STAPLE produces very good accuracy (DSC mean of 0.868) over all tissues, even for scans with considerable quality degradations caused by motion artifacts.
Supplemental Scleral Buckle for the Management of Rhegmatogenous Retinal Detachment by Pars Plana Vitrectomy: A Meta-Analysis of Randomized Controlled Trials (2021)

Low-certainty evidence from RCTs did not demonstrate a benefit in placement of a supplemental SB during vitrectomy for management of RRD in the current analysis. Additional high-quality trials are needed to provide more precise estimates of the effect.
Bipedal Robotic Running with DURUS-2D (2017)

Bipedal robotic running remains a challenging benchmark in the field of control and robotics because of its highly dynamic nature and necessarily underactuated hybrid dynamics. Previous results have achieved bipedal running experimentally with a combination of theoretical results and heuristic application thereof. In particular, formal analysis of the hybrid system stability is given based on a theoretical model, but due to the gap between theoretical concepts and experimental reality, extensive tuning is necessary to achieve experimental success. In this paper, we present a formal approach to bridge this gap, starting from theoretical gait generation to a provably stable control implementation, resulting in bipedal robotic running. We first use a large-scale optimization to generate an energy-efficient running gait, subject to hybrid zero dynamics conditions and feasibility constraints which incorporate practical limitations of the robot model based on physical conditions. The stability of the gait is formally guaranteed in the hybrid system model with an input to state stability (ISS) based control law. This implementation improves the stability under practical control limitations of the system. Finally, the methodology is experimentally realized on the planar spring-legged bipedal robot, DURUS-2D, resulting in sustainable running at 1.75m/s. The paper, therefore, presents a formal method that takes the first step toward bridging the gap between theory and experiment.
CAD issues for CMOS VLSI design in SOI (2002)

This paper reviews recent progress in making circuit-level CAD tools for the design of digital integrated circuits SOI-aware, specifically transistor-level static timing and static noise analysis tools. This involves abstracting the SOI device physics of the floating body, allowing estimates of the body voltage variation under various switching activity assumptions. These body voltage estimates are then applied as "initial conditions" in the constituent simulations of the static analyses. Results are presented for a prototype static timing analysis tool and a commercial static noise analysis tool.
A mouse model of seizures in anti–N‐methyl‐d‐aspartate receptor encephalitis (2019)

Our findings indicate that autoantibodies can induce seizures in anti-NMDAR encephalitis and offer a model for testing novel therapies for refractory autoimmune seizures.
Molecular Characterization of an Outer Membrane Protein of Actinobacillus actinomycetemcomitans Belonging to the OmpA Family (1998)

The major outer membrane protein (OMP) of Actinobacillus actinomycetemcomitans is an OmpA homolog that demonstrates electrophoretic heat modifiability. The gene encoding this protein was isolated from a genomic library of A. actinomycetemcomitans NCTC 9710 by immunoscreening with serum from a patient with localized juvenile periodontitis. Expression of the cloned gene in Escherichia coli and subsequent Western blot analysis revealed a protein with an approximate molecular mass of 34 kDa. The amino acid sequence predicted from the cloned gene demonstrated that the mature protein had a molecular mass of 34,911 Da and significant identity to members of the OmpA family of proteins. We have named the major OMP of A. actinomycetemcomitans Omp34, and its corresponding gene has been named omp34.
<title>Scalability of rf gas discharges for high-power CO<formula><inf><roman>2</roman></inf></formula> lasers</title> (1994)

For the development of compact high-power CO<SUB>2</SUB> lasers high input power densities in discharge tubes with sufficiently large cross sections are required. To achieve a uniform distribution of power deposition into the laser gas flowing in tubes with typically circular cross sections an appropriate electrode shaping is necessary. For this reason, experimental and theoretical investigations have been performed in a wide range of input power, starting from values typical for todays CO<SUB>2</SUB> lasers up to very high levels. Different electrode shapes have been used for optimized stability and homogeneity of the discharge in order to minimize the distortion of the intra-cavity wavefront. The occurrence of filaments limits the range of a stable discharge operation. The homogeneity of the discharge has been assessed by means of spatially resolved small signal gain measurements. Further, the homogeneity of the discharge as a prerequisite for minimal phase distortion has been investigated using an interferometer. A discharge with 17 kW input power at 13.56 MHz in a single tube element is presented showing a flat profile of the small signal gain and a phase distortion of 0.21 micrometers .
Neuregulin1 downregulates postsynaptic GABAa receptors at the hippocampal inhibitory synapse (2004)

The growth factor neuregulin 1 (NRG1) has been proposed to contribute to the formation and maturation of neuromuscular and interneuronal synapses by upregulating the expression of specific neurotransmitter receptor subunits. In the present report, we show that, in the hippocampus, NRG1 is expressed in a pattern suggesting that it regulates synapse development in the CA1 region. However, in contrast to what has been shown in other synapses, NRG1 reduces the expression of gamma-aminobutyric acid (GABA)A receptors alpha subunits in hippocampal slices, and the mean amplitude of GABAergic miniature inhibitory postsynaptic currents (IPSCs) in hippocampal CA1 pyramidal neurons, without affecting IPSC kinetics or frequency. These effects of NRG1 occur without concomitant changes in glutamate receptors and other synaptic proteins. We propose that the role of NRG1 in the formation and maturation in the hippocampal inhibitory synapse is downregulation, rather than upregulation, of receptor subunit expression. These results suggest that NRG1 may contribute to the reduction in GABAergic synaptic activity in hippocampal CA1 pyramidal neurons that normally occurs during early postnatal development, and that alterations in NRG1 signaling in the hippocampus may contribute to schizophrenia and epilepsy.
Latest Developments in Design and Application of Schade Stackers and Reclaimers (1996)

This paper has been developed with reference to two important papers - the first in 1981 and the second in 1983. In both cases the papers were prepared in context of the coal industry, which will be a large component of the focus in this paper. However, it is important to recognise the significant development in 'Schade' Stacking & Reclaiming Equipment which have taken place particularly since these papers were presented. Much of this developmental work has taken place in industries other than coal.
Design and Analysis of High-Accuracy Telecentric Surface Reconstruction System Based on Line Laser (2021)

Non-contact measurement technology based on triangulation with cameras is extensively applied to the development of computer vision. However, the accuracy of the technology is generally not satisfactory enough. The application of telecentric lenses can significantly improve the accuracy, but the view of telecentric lenses is limited due to their structure. To address these challenges, a telecentric surface reconstruction system is designed for surface detection, which consists of a single camera with a telecentric lens, line laser generator and one-dimensional displacement platform. The designed system can reconstruct the surface with high accuracy. The measured region is expanded with the used of the displacement platform. To achieve high-accuracy surface reconstruction, we propose a method based on a checkerboard to calibrate the designed system, including line laser plane and motor direction of the displacement platform. Based on the calibrated system, the object under the line laser is measured, and the results of lines are assembled to make the final surface reconstruction. The results show that the designed system can reconstruct a region of 20×40 mm2, up to the accuracy of micron order.
Human Papilloma Virus prevalence and type-specific relative contribution in invasive cervical cancer specimens from Italy (2010)

HPV16 and HPV18 accounted for almost 70% of all the HPV positive ICC cases. The study provides baseline information for further evaluation on the impact of recently introduced HPV vaccines in Italy.
Characteristics and Survival Patterns of Solid Organ Transplant Patients Developing De Novo Colon and Rectal Cancer (2004)

Transplant patients develop colorectal cancer at a younger age and exhibit worse five-year survival rates than the general population. These data suggest that chronic immunosuppression results in a more aggressive tumor biology. Frequent posttransplantation colorectal cancer screening program may be warranted.
Sliding Mode Control with RLSN Predictor-Based Perturbation Estimation (2006)

This paper presents the sliding mode control with the perturbation estimator for a nonlinear control system in the presence of perturbations including external disturbances, unpredictable parameter variations, and unstructured dynamics. The proposed perturbation estimator is based on the Recursive Linear Smoothed Newton predictive algorithm so that it is effective to attenuate an undesired noise in high frequency band and to predict the present perturbation signal from the previous ones. Compared to conventional sliding mode control (SMC) and sliding mode control with perturbation estimation (SMCPE) introduced by Elmali and Olgac, the control algorithm proposed in this study can offer better tracking control performances and more feasible estimation characteristics. The effectiveness and superiority of the proposed control strategy are demonstrated by a series of simulations on the position tracking control of a simple two-link robot manipulator subject to velocity feedback signals including white noises.
Enhanced Recovery of Crude Oil From Shale Formations by Gas Injection in Zipper-fractured Horizontal Wells (2015)

The zipper-frac technique is implemented in two adjacent horizontal wells to maximize the exposure of shale rocks. The hydraulic fractures are propagated in a manner in which they are connected with natural fracture network to improve the fracture complexity. In this study, the authors exploit the advantage of stimulated fracture complexity to access more of the hydrocarbons trapped in very low permeability of shale matrix. The recovery process efficiencies by cyclic CO2 injection and CO2 flooding in zipper-fractured horizontal wells are compared. The role of diffusion recovery mechanism in recovering oil from fractured shales will be discussed.
Opioid Treatment for Neonatal Opioid Withdrawal Syndrome: Current Challenges and Future Approaches (2020)

Chronic intrauterine exposure to psychoactive drugs often results in neonatal opioid withdrawal syndrome (NOWS). When nonpharmacologic measures are insufficient in controlling NOWS, morphine, methadone, and buprenorphine are first-line medications commonly used to treat infants with NOWS because of in utero exposure to opioids. Research suggests that buprenorphine may be the leading drug therapy used to treat NOWS when compared with morphine and methadone. Currently, there are no consensus or standardized treatment guidelines for medications prescribed for NOWS. Opioids used to treat NOWS exhibit large interpatient variability in pharmacokinetics (PK) and pharmacodynamic (PD) response in neonates. Organ systems undergo rapid maturation after birth that may alter drug disposition and exposure for any given dose during development. Data regarding the PK and PD of opioids in neonates are sparse. Pharmacometric methods such as physiologically based pharmacokinetic and population pharmacokinetic modeling can be used to explore factors predictive of some of the variability associated with the PK/PD of opioids in newborns. This review discusses the utility of pharmacometric techniques for enhancing precision dosing in infants requiring opioid treatment for NOWS. Applying these approaches may contribute to optimizing the outcome by reducing cumulative drug exposure, mitigating adverse drug effects, and reducing the burden of NOWS in neonates.
Specific NK Cell Activation to Treat Relapsed/Refractory (r/r) Hodgkin Lymphoma (HL) Patients – Final, Updated Data on Clinical Outcome, Pharmacokinetics and Pharmacodynamics of a Phase 1 Study Investigating AFM13, a Bispecific Anti-CD30/CD16A Tandab (2014)

Abstract Introduction: AFM13 is a bispecific, tetravalent TandAb antibody that targets CD16A and CD30. Preclinical data demonstrated that AFM13 specifically harnessed NK cells to exert potent cytotoxic effects on tumor cells expressing CD30. Furthermore, AFM13 showed a favorable toxicity profile in cynomolgus monkeys. HL is characterized by the presence of CD30+ Reed-Sternberg cells and by a high medical need in the r/r setting, especially since the response to brentuximab vedotin in this patient group is mostly short. Here, we present the final results of a phase 1 clinical study in r/r HL including a focus on the pre-treatment with brentuximab vedotin. Methods: Heavily pretreated patients (pts.) with r/r HL received stepwise escalated doses of intravenous AFM13 (0.01 to 7.0 mg/kg) weekly or 4.5 mg/kg twice weekly over 4 weeks. Primary objectives were safety and tolerability, secondary objectives included pharmacokinetics (PK), pharmacodynamics (PD), and clinical efficacy measured using Cheson criteria. Results: 28 pts. were recruited, 24 pts. received AFM13 weekly and 4 pts. received AFM13 twice weekly. AFM13 was well tolerated with mainly mild to moderate adverse events. The maximum tolerated dose was not reached. AFM13 demonstrated activity, which was consistently more pronounced for all assessed parameters at doses ≥1.5 mg/kg (n=13). 3 of 13 pts. (23%) exhibited partial responses and disease control was reached in 10 of 13 pats. (77%). Importantly, AFM13 was also active in pts. refractory to brentuximab vedotin as most recent treatment. PK data revealed an AFM13 half-life of up to 19 hours. In peripheral blood, the portion of activated NK cells (CD69+), relative to total number of NK cells, increased up to 3-fold 24 hours after infusion compared to baseline. Kinetics of NK cell activation corresponded to kinetics of AFM13 serum levels. Soluble CD30 declined to zero at the end of treatment in almost all pts. Conclusion: Phase 1 data indicate that AFM13 is active and well tolerated in heavily pretreated r/r HL pts. including brentuximab vedotin failures. To further enhance efficacy of AFM13 both, the dose regimen (based on PK/PD profile) and the duration of treatment, will be optimized in a phase 2 study. This study is currently in preparation by the German Hodgkin Study Group. Disclosures Topp: Affimed Therapeutics AG: Consultancy. von Tresckow:Takeda: Honoraria, Other; Novartis: Honoraria, Research Funding. Marschner:Affimed Therapeutics AG: Employment. Engert:Millenium Takeda: Consultancy; Affimed Therapeutics AG: Consultancy.
Synthesis, cationic polymerization and curing reaction with epoxy resin of 3,9-di(p-methoxybenzyl)-1,5,7,11-tetra-oxaspiro(5,5)undecane (2000)

A new spiro ortho carbonate, 3,9-di(p-methoxybenzyl)-1,5,7,11-tetra-oxaspiro(5,5)undecane was prepared by the reaction of 2-methoxybenzyl-1,3-propanediol with di(n-butyl)tin oxide, following with carbon disulfide. Its cationic polymerization was carried out in dichloromethane using BF3-OEt2 as catalyst. The [1H], [13C]NMR and IR data as well as elementary analysis of the polymers obtained indicated that it underwent double ring-opening polymerization. The polymerization mechanism is discussed. The curing reaction of bisphenol A type epoxy resin in the presence of the monomer and a curing agent was investigated. DSC measurements were used to follow the curing process. In the case of boron trifluoride-o-phenylenediamine (BF3-OPDA) as curing agent, two peaks were found on the DSC curves, one of which was attributed to the polymerization of the epoxy group, and the other to the copolymerization of the monomer with the isolated epoxy groups or homopolymerization. However, when BF3-H2NEt was used as curing agent, only one peak was present. IR measurement of the modified epoxy resin with various weight ratios of epoxy resin/monomer was performed in the presence of BF3-H2NEt as curing agent. The results demonstrate that the conversion of epoxy group increases as the content of monomer increases. The curing process and the structure of the epoxy resin network are discussed. © 2000 Society of Chemical Industry
Batch Optimization for DNA Synthesis (2020)

Large pools of synthetic DNA molecules have been recently used to reliably store significant volumes of digital data. While DNA as a storage medium has enormous potential because of its high storage density, its practical use is currently severely limited because of the high cost and low throughput of available DNA synthesis technologies. We study the role of batch optimization in reducing the cost of large scale DNA synthesis, which translates to the following algorithmic task. Given a large pool $\mathcal{S}$ of random quaternary strings of fixed length, partition $\mathcal{S}$ into batches in a way that minimizes the sum of the lengths of the shortest common supersequences across batches. We introduce two ideas for batch optimization that both improve (in different ways) upon a naive baseline: (1) using both $(ACGT)^{*}$ and its reverse $(TGCA)^{*}$ as reference strands, and batching appropriately, and (2) batching via the quantiles of an appropriate ordering of the strands. We also prove asymptotically matching lower bounds on the cost of DNA synthesis, showing that one cannot improve upon these two ideas. Our results uncover a surprising separation between two cases that naturally arise in the context of DNA data storage: the asymptotic cost savings of batch optimization are significantly greater in the case where strings in $\mathcal{S}$ do not contain repeats of the same character (homopolymers), as compared to the case where strings in $\mathcal{S}$ are unconstrained.
5-Azadibenzo[a,g]corannulene (2017)

The first azacorannulene with a nitrogen on the rim, has been synthesized in seven steps from 4-bromoisoquinoline.
Using Agile Management to Share Course Projects Among Multiple Classes (2006)

Project based courses have become popular as a way of engaging students and providing practical experiences. Sharing a single project between two course provides advantages of permitting more focus on the subject of each class, larger projects (more help and expertise is available) and greater opportunities for coordinated team work, and to appreciate how disciplines interact. A disadvantage is scheduling and managing class activities and risk to assure that useful project work is done at a pace benefiting both classes. This paper describes an experience in which an agile approach was used to successfully coordinate project activities among a software development course and a user interaction design course
Exploiting Spatial Degrees of Freedom for High Data Rate Ultrasound\n Communication with Implantable Devices (2017)

We propose and demonstrate an ultrasonic communication link using spatial\ndegrees of freedom to increase data rates for deeply implantable medical\ndevices. Low attenuation and millimeter wavelengths make ultrasound an ideal\ncommunication medium for miniaturized low-power implants. While small spectral\nbandwidth has drastically limited achievable data rates in conventional\nultrasonic implants, large spatial bandwidth can be exploited by using multiple\ntransducers in a multiple-input/multiple-output system to provide spatial\nmultiplexing gain without additional power, larger bandwidth, or complicated\npackaging. We experimentally verify the communication link in mineral oil with\na transmitter and receiver 5 cm apart, each housing two custom-designed\nmm-sized piezoelectric transducers operating at the same frequency. Two streams\nof data modulated with quadrature phase-shift keying at 125 kbps are\nsimultaneously transmitted and received on both channels, effectively doubling\nthe data rate to 250 kbps with a measured bit error rate below 1e-4. We also\nevaluate the performance and robustness of the channel separation network by\ntesting the communication link after introducing position offsets. These\nresults demonstrate the potential of spatial multiplexing to enable more\ncomplex implant applications requiring higher data rates.\n
Effect of Sucrose Concentration, Charcoal, and Indole-3-Butyric Acid on Germination of Abies Numidica Somatic Embryos (2001)

The dependency of radicle elongation in Abies numidica somatic embryos on germination media has been studied. No significant differences were detected between the Murashige and Skoog (MS) and Schenk and Hildebrandt (SH) medium. The addition of 10 g dm-3 activated charcoal or 0.05 mg dm-3 indole-3-butyric acid (IBA) into both media had positive influence on embryo germination. Difference between activated charcoal and IBA effects were significant. The high rooting percentage (85 %) was recorded on half SH medium with 10 g dm-3 sucrose and activated charcoal. After IBA addition rooting percentage was increased to 95 %. During 7 months 73 % of plantlets survived transfer to soil and in 54 % of plantlets shoot growth was observed.
TIME-DEPENDENT PREFERENTIAL IN VIVO D2 OCCUPANCY BY AMISULPRIDE IN THE MEDIAL STRIATUM – CONTINUOUS MEASUREMENT USING A BETA MICROPROBE SYSTEM (2009)

peer reviewed