julilili42/papers huggingface dataset:
A flexible Bayesian framework for unbiased estimation of timescales
2020-08-12

Abstract Timescales characterize the pace of change for many dynamic processes in nature. Timescales are usually estimated by fitting the exponential decay of data autocorrelation in the time or frequency domain. We show that this standard procedure often fails to recover the correct timescales due to a statistical bias arising from the finite sample size. We develop an alternative approach to estimating timescales by fitting the sample autocorrelation or power spectrum with a generative model based on a mixture of Ornstein-Uhlenbeck processes using adaptive Approximate Bayesian Computations. Our method accounts for finite sample size and noise in data and returns a posterior distribution of timescales that quantifies the estimation uncertainty and can be used for model selection. We demonstrate the accuracy of our method on synthetic data and illustrate its application to recordings from the primate cortex. We provide a customizable Python package implementing our framework with different generative models suitable for diverse applications.
Multiwavelength modelling of the circumstellar environment of the massive protostar AFGL 2591 VLA 3
2020-08-12

ABSTRACT We have studied the dust density, temperature, and velocity distributions of the archetypal massive young stellar object (MYSO) AFGL 2591. Given its high luminosity ( _{\\odot} ) and distance (d = 3.3 kpc), AFGL 2591 has one of the highest ratio, giving better resolved dust emission than any other MYSO. As such, this paper provides a template on how to use resolved multiwavelength data and radiative transfer to obtain a well-constrained 2D axisymmetric analytic rotating infall model. We show for the first time that the resolved dust continuum emission from Herschel 70- μm observations is extended along the outflow direction, whose origin is explained in part from warm dust in the outflow cavity walls. However, the model can only explain the kinematic features from CH3CN observations with unrealistically low stellar masses (&amp;lt;15 M⊙), indicating that additional physical processes may be playing a role in slowing down the envelope rotation. As part of our three-step continuum and line fitting, we have identified model parameters that can be further constrained by specific observations. High-resolution mm visibilities were fitted to obtain the disc mass (6 M⊙) and radius (2200 au). A combination of SED and near-infrared observations were used to estimate the luminosity and envelope mass together with the outflow cavity inclination and opening angles.
Perceptions of genetic testing in patients with hereditary chronic pancreatitis and their families: a qualitative triangulation
2020-08-12

Abstract Hereditary chronic pancreatitis (HCP) is a genetically determined condition characterized by intermittent acute episodes of pancreatitis and long-term impairment of the exocrine and endocrine pancreatic functions. Genetic test results can have substantial psychological and social consequences for the individuals tested and their families. Nevertheless, little is known so far about the subjective experience of individuals genetically tested for HCP. This qualitative study examines the viewpoints of HCP patients and their relatives in order to identify the psychosocial and ethical implications related to genetic testing within families. Semi-structured qualitative individual interviews and a focus group with HCP patients and their family members were conducted. Data were audio-recorded, transcribed verbatim and analysed using qualitative content analysis. A total of 28 individuals were enrolled in the study: 24 individuals (17 patients, 7 relatives) were interviewed in semi-structured one-on-one interviews and 4 individuals (2 patients, 2 life partners) participated in the focus group. Emerging topics covered (1) genetic testing in childhood, (2) genetic testing within the family and (3) family planning. The study reveals that genetic testing for HCP has a wide influence in familial contexts and is accompanied by normative issues, such as autonomy, reproductive decisions and sharing of information within the family. The results raise the awareness of the complexity of family contexts: familial relationships and dynamics can have great influence on the individual decisions related to genetic testing. Increased understanding of these relational contexts can help health professionals, for example, in counselling, to discuss genetic testing better with patients and families.
Association between tissue hypoxia, perfusion restrictions, and microvascular architecture alterations with lesion-induced impairment of neurovascular coupling
2020-08-12

Functional magnetic resonance imaging (fMRI) has been mainly utilized for the preoperative localization of eloquent cortical areas. However, lesion-induced impairment of neurovascular coupling (NVC) in the lesion border zone may lead to false-negative fMRI results. The purpose of this study was to determine physiological factors impacting the NVC. Twenty patients suffering from brain lesions were preoperatively examined using multimodal neuroimaging including fMRI, magnetoencephalography (MEG) during language or sensorimotor tasks (depending on lesion location), and a novel physiologic MRI approach for the combined quantification of oxygen metabolism, perfusion state, and microvascular architecture. Congruence of brain activity patterns between fMRI and MEG were found in 13 patients. In contrast, we observed missing fMRI activity in perilesional cortex that demonstrated MEG activity in seven patients, which was interpreted as lesion-induced impairment of NVC. In these brain regions with impaired NVC, physiologic MRI revealed significant brain tissue hypoxia, as well as significantly decreased macro- and microvascular perfusion and microvascular architecture. We demonstrated that perilesional hypoxia with reduced vascular perfusion and architecture is associated with lesion-induced impairment of NVC. Our physiologic MRI approach is a clinically applicable method for preoperative risk assessment for the presence of false-negative fMRI results and may prevent severe postoperative functional deficits.
Dissociating harmonic and non-harmonic phase-amplitude coupling in the human brain
2020-08-12

Abstract Phase-amplitude coupling (PAC) has been hypothesized to coordinate cross-frequency interactions of neuronal activity in the brain. However, little is known about the distribution of PAC across the human brain and the frequencies involved. Furthermore, it remains unclear to what extend PAC may reflect spurious cross-frequency coupling induced by physiological artifacts or rhythmic non-sinusoidal signals with higher harmonics. Here, we combined MEG, source-reconstruction and different measures of cross-frequency coupling to systematically characterize PAC across the resting human brain. We show that cross-frequency measures of phase-amplitude, phase-phase, and amplitude-amplitude coupling are all sensitive to signals with higher harmonics. In conjunction, these measures allow to distinguish harmonic and non-harmonic PAC. Based on these insights, we found no evidence for non-harmonic PAC in resting-state MEG. Instead, we found cortically and spectrally wide-spread PAC driven by harmonic signals. Furthermore, we show how physiological artifacts and spectral leakage cause spurious PAC across wide frequency ranges. Our result clarify how different measures of cross-frequency interactions can be combined to characterize PAC and cast doubt on the presence of prominent non-harmonic phase-amplitude coupling in human resting-state MEG.
Predictors of Mortality in Patients With Biopsy‐Proven Viral Myocarditis: 10‐Year Outcome Data
2020-08-13

Background There is scarce data about the long‐term mortality as well as the prognostic value of cardiovascular magnetic resonance and late gadolinium enhancement (LGE) in patients with biopsy‐proven viral myocarditis. We sought to investigate: (1) mortality and (2) prognostic value of LGEcardiovascular magnetic resonance (location, pattern, extent, and distribution) in a &gt;10‐year follow‐up in patients with biopsy‐proven myocarditis. Methods and Results Two‐hundred three consecutive patients with biopsy‐proven viral myocarditis and cardiovascular magnetic resonance were enrolled; 183 patients were eligible for standardized follow‐up. The median follow‐up was 10.1 years. End points were all‐cause death, cardiac death, and sudden cardiac death (SCD). We found substantial long‐term mortality in patients with biopsy‐proven myocarditis (39.3% all cause, 27.3% cardiac, and 10.9% SCD); 101 patients (55.2%) demonstrated LGE. The presence of LGE was associated with a more than a doubled risk of death (hazard ratio [HR], 2.40; 95% CI], 1.30–4.43), escalating to a HR of 3.00 (95% CI, 1.41–6.42) for cardiac death, and a HR of 14.79 (95% CI, 1.95–112.00) for SCD; all P ≤0.009. Specifically, midwall, (antero‐) septal LGE, and extent of LGE were highly associated with death, all P &lt;0.001. Septal LGE was the best independent predictor for SCD (HR, 4.59; 95% CI, 1.38–15.24; P =0.01). Conclusions In patients with biopsy‐proven viral myocarditis, the presence of midwall LGE in the (antero‐) septal segments is associated with a higher rate of mortality (including SCD) compared with absent LGE or other LGE patterns, underlining the prognostic benefit of a distinct LGE analysis in these patients.
Constraining Central Himalayan (Nepal) Fault Geometry Through Integrated Thermochronology and Thermokinematic Modeling
2020-08-13

Abstract Constraining the subsurface structural geometry of the central Himalaya continues to prove difficult, even after the 2015 Gorkha earthquake and the resulting insights into the trajectory of the Main Himalayan thrust (MHT). To this end, we apply a thermokinematic model to evaluate four possible balanced cross section geometries based on three estimates of the MHT in central Nepal. We compare the effect of different décollement and duplex geometries on predicted cooling ages and compare these to new and published ages. We find that the best‐fit geometry able to reproduce the cooling ages at the surface is a hinterland‐dipping duplex, which has been translated over a mid‐crustal ramp located ~110 km north of the Main Frontal thrust. We find that the temporal evolution of the duplex and MHT mid‐crustal ramp both play an integral role in producing the observed cooling ages, implying that the common assumption that the active décollement and ramp geometry solely control the distribution of cooling ages is incorrect. Furthermore, results indicate that the Ramgarh‐Munsiari thrust was emplaced between 17 and ~10 Ma, followed by the Trishuli thrust. Duplex growth occurs between 6.5 and 0.75 Ma, with its constituent thrust sheets moving at variable rates between 10 and 42 mm/yr. Young out‐of‐sequence thrusting (5 km of displacement) in the hinterland produces a slightly improved fit to the cooling ages. Finally, the resulting thermal field modeled from our best‐fit geometry suggests a possible basis for the nucleation and rupture characteristics of the Gorkha earthquake.
Can a Novel Deep Neural Network Improve the Computer-Aided Detection of Solid Pulmonary Nodules and the Rate of False-Positive Findings in Comparison to an Established Machine Learning Computer-Aided Detection?
2020-08-13

Objective The aim of this study was to compare the performance of 2 approved computer-aided detection (CAD) systems for detection of pulmonary solid nodules (PSNs) in an oncologic cohort. The first CAD system is based on a conventional machine learning approach (VD10F), and the other is based on a deep 3D convolutional neural network (CNN) CAD software (VD20A). Methods and Materials Nine hundred sixty-seven patients with a total of 2451 PSNs were retrospectively evaluated using the 2 different CAD systems. All patients had thin-slice chest computed tomography (0.6 mm) using 100 kV and 100 mAs and a high-resolution kernel (I50f). The CAD images generated by VD10F were transferred to the PACS for evaluation. The images generated by VD20A were evaluated using a Web browser–based viewer. Finally, a senior radiologist who was blinded for the CAD results examined the thin-slice images of every patient (ground truth). Results A total of 2451 PSNs were detected by the senior radiologist. CAD-VD10F detected 1401 true-positive, 143 false-negative, 565 false-positive (FP), and 342 true-negative PSNs, resulting in sensitivity of 90.7%, specificity of 37.7%, positive predictive value of 0.71, and negative predictive value of 0.70. CAD-VD20A detected 1381 true-positive, 163 false-negative, 337 FP, and 570 true-negative PSNs, resulting in sensitivity of 89.4%, specificity of 62.8%, positive predictive value of 0.80, and negative predictive value 0.77, respectively. The rate of FP per scan was 0.6 for CAD-VD10F and 0.3 for CAD-VD20A. Conclusions The new deep learning–based CAD software (VD20A) shows similar sensitivity with the conventional CAD software (VD10F), but a significantly higher specificity.
Incidence of Quantum Confinement on Dark Triplet Excitons in Carbon Nanotubes
2020-08-13

The photophysics of single-wall carbon nanotubes (SWCNTs) is intensively studied due to their potential application in light harvesting and optoelectronics. Excited states of SWCNTs form strongly bound electron-hole pairs, excitons, of which only singlet excitons participate in application relevant optical transitions. Long-living spin-triplet states hinder applications, but they emerge as candidates for quantum information storage. Therefore, knowledge of the triplet exciton energy structure, in particular in a SWCNT chirality dependent manner, is greatly desired. We report the observation of light emission from triplet state recombination, i.e., phosphorescence, for several SWCNT chiralities using a purpose-built spectrometer. This yields the singlet-triplet gap as a function of the SWCNT diameter, and it follows predictions based on quantum confinement effects. Saturation under high microwave power (up to 10 W) irradiation allows the spin-relaxation time for triplet states to be determined. Our study sensitively discriminates whether the lowest optically active state is populated from an excited state on the same nanotube or through Förster exciton energy transfer from a neighboring nanotube.
Distinct Relationship Between Cognitive Flexibility and White Matter Integrity in Individuals at Risk of Parkinson’s Disease
2020-08-13

Based on our results, PD-RP do no exhibit white matter changes or impaired cognitive flexibility. However, specific executive functions in PD-RP are more related to white matter alterations than in healthy older adults.
Electrospun Bioactive Wound Dressing Containing Colloidal Dispersions of Birch Bark Dry Extract
2020-08-14

Novel birch bark dry extract (TE)-loaded polyvinyl alcohol (PVA) fiber mats intended for wound therapy were developed through an electrospinning process. Colloidal dispersions containing TE as the active substance were prepared by the high-pressure homogenization (HPH) technique using hydrogenated phospholipids as stabilizer. Subsequently, the colloidal dispersions were blended with aqueous PVA solutions in the ratio of 60:40 (wt.%) and electrospun to form the nanofiber mats. Fiber morphology examined using scanning electron microscopy (SEM) indicated that fibers were uniform and achieved diameters in the size range of 300–1586 nm. Confocal Raman spectral imaging gave good evidence that triterpenes were encapsulated within the electrospun mats. In vitro drug release and ex vivo permeation studies indicated that the electrospun nanofibers showed a sustained release of betulin, the main component of birch bark dry extract, making the examined dressings highly applicable for several wound care applications. Ex vivo wound healing studies proved that electrospun fiber mats containing TE accelerated wound healing significantly more than TE oleogel, which was comparable to an authorized product that consists of TE and sunflower oil and has proved to enhance wound healing. Therefore, our results conclude that the developed TE-PVA-based dressings show promising potential for wound therapy, an area where effective remedy is needed.
Annexin A7 Regulates Endometrial Receptivity
2020-08-14

A limited window of receptivity is a prerequisite of reproductive success. Indispensable receptivity genes include cyclooxygenase 2 (COX2), an enzyme accomplishing formation of prostaglandin E<sub>2</sub> (PGE<sub>2</sub>). A powerful regulator of PGE<sub>2</sub> formation is Annexin A7 (<i>ANXA7</i>). The present study thus explored whether ANXA7 impacts on implantation and fertility. Here we show that <i>ANXA7</i> is expressed in endometrial tissue and increases upon decidual transformation of human endometrial stromal cells (HESCs) in a time-dependent manner. Silencing ANXA7 significantly decreased the expression of <i>PRL</i> and <i>IGFBP1</i>, canonical decidual marker genes, but enhances COX2 and PGE<sub>2</sub> levels. Genetic knockout of <i>AnxA7</i> in mice significantly increases the number of implantation sites and litter sizes. Further, analysis of human endometrial biopsies showed that <i>ANXA7</i> transcript and protein levels are decreased during the midluteal window of implantation in women suffering from recurrent pregnancy loss (RPL) when compared to subfertile patients. Taken together, the data indicate that ANXA7 has a conserved role in regulating endometrial receptivity and implantation.
Lateralized Cerebral Processing of Abstract Linguistic Structure in Clear and Degraded Speech
2020-08-14

Abstract Human cortical activity measured with magnetoencephalography (MEG) has been shown to track the temporal regularity of linguistic information in connected speech. In the current study, we investigate the underlying neural sources of these responses and test the hypothesis that they can be directly modulated by changes in speech intelligibility. MEG responses were measured to natural and spectrally degraded (noise-vocoded) speech in 19 normal hearing participants. Results showed that cortical coherence to “abstract” linguistic units with no accompanying acoustic cues (phrases and sentences) were lateralized to the left hemisphere and changed parametrically with intelligibility of speech. In contrast, responses coherent to words/syllables accompanied by acoustic onsets were bilateral and insensitive to intelligibility changes. This dissociation suggests that cerebral responses to linguistic information are directly affected by intelligibility but also powerfully shaped by physical cues in speech. This explains why previous studies have reported widely inconsistent effects of speech intelligibility on cortical entrainment and, within a single experiment, provided clear support for conclusions about language lateralization derived from a large number of separately conducted neuroimaging studies. Since noise-vocoded speech resembles the signals provided by a cochlear implant device, the current methodology has potential clinical utility for assessment of cochlear implant performance.
Propofol Affects Cortico-Hippocampal Interactions via β3 Subunit-Containing GABAA Receptors
2020-08-14

Background: General anesthetics depress neuronal activity. The depression and uncoupling of cortico-hippocampal activity may contribute to anesthetic-induced amnesia. However, the molecular targets involved in this process are not fully characterized. GABAA receptors, especially the type with β3 subunits, represent a main molecular target of propofol. We therefore hypothesized that GABAA receptors with β3 subunits mediate the propofol-induced disturbance of cortico-hippocampal interactions. Methods: We used local field potential (LFP) recordings from chronically implanted cortical and hippocampal electrodes in wild-type and β3(N265M) knock-in mice. In the β3(N265M) mice, the action of propofol via β3subunit containing GABAA receptors is strongly attenuated. The analytical approach contained spectral power, phase locking, and mutual information analyses in the 2–16 Hz range to investigate propofol-induced effects on cortico-hippocampal interactions. Results: Propofol caused a significant increase in spectral power between 14 and 16 Hz in the cortex and hippocampus of wild-type mice. This increase was absent in the β3(N265M) mutant. Propofol strongly decreased phase locking of 6–12 Hz oscillations in wild-type mice. This decrease was attenuated in the β3(N265M) mutant. Finally, propofol reduced the mutual information between 6–16 Hz in wild-type mice, but only between 6 and 8 Hz in the β3(N265M) mutant. Conclusions: GABAA receptors containing β3 subunits contribute to frequency-specific perturbation of cortico-hippocampal interactions. This likely explains some of the amnestic actions of propofol.
A Study of Expert/Novice Perception in Arthroscopic Shoulder Surgery
2020-08-14

Arthroscopic shoulder surgery is an advanced orthopedic surgical procedure, which is particularly challenging due to the complex anatomy of the shoulder, and tight spaces for navigation, which also limits the view from the arthroscope. In carrying out arthroscopy, the ability to quickly and effectively navigate through the joint to reach a desired location is essential. Novices often experience confusion in trying to triangulate the information from arthroscopy output with the background knowledge of anatomy while orienting and navigating the instruments. In this paper, we report on the results of the first cadaveric eye-tracking study of arthroscopic surgery in which we investigate differences in perception between experts and novices. Novices' perception is analyzed with cognitive load analysis throughout the procedure and specifically, during the portions of the procedure in which subjects are observed to be confused. In investigating such portions, the gaze data analysis is supplemented with head rotations and acceleration information from gyroscope and accelerometer sensors from the eye tracker. We also use the gathered eye tracking metrics to construct a model to classify subjects into expert/novice. We find statistically significant relations between head movement as well as pupil diameter and periods of confusion. We identify a subset of the metrics that we use to build a simple classifier that is able to distinguish between novices and experts with accuracy of 84%.