bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development and validation of an interpretable neural network for prediction of postoperative in-hospital mortality
Authors: Lee Christine K. , Samad Muntaha , Hofer Ira , Cannesson Maxime , Baldi Pierre 
Published: January 2021

AbstractWhile deep neural networks (DNNs) and other machine learning models often have higher accuracy than simpler models like logistic regression (LR), they are often considered to be “black box” models and this lack of interpretability and transparency is considered a challenge for clinical adoption. In healthcare, intelligible models not only help clinicians to understand the problem and create more targeted action plans, but also help to gain the clinicians’ trust. One method of overcoming the limited interpretability of more complex models is to use Generalized Additive Models (GAMs). Standard GAMs simply model the target response as a sum of univariate models. Inspired by GAMs, the same idea can be applied to neural networks through an architecture referred to as Generalized Additive Models with Neural Networks (GAM-NNs). In this manuscript, we present the development and validation of a model applying the concept of GAM-NNs to allow for interpretability by visualizing the learned feature patterns related to risk of in-hospital mortality for patients undergoing surgery under general anesthesia. The data consists of 59,985 patients with a feature set of 46 features extracted at the end of surgery to which we added previously not included features: total anesthesia case time (1 feature); the time in minutes spent with mean arterial pressure (MAP) below 40, 45, 50, 55, 60, and 65 mmHg during surgery (6 features); and Healthcare Cost and Utilization Project (HCUP) Code Descriptions of the Primary current procedure terminology (CPT) codes (33 features) for a total of 86 features. All data were randomly split into 80% for training (n = 47,988) and 20% for testing (n = 11,997) prior to model development. Model performance was compared to a standard LR model using the same features as the GAM-NN. The data consisted of 59,985 surgical records, and the occurrence of in-hospital mortality was 0.81% in the training set and 0.72% in the testing set. The GAM-NN model with HCUP features had the highest area under the curve (AUC) 0.921 (0.895–0.95). Overall, both GAM-NN models had higher AUCs than LR models, however, had lower average precisions. The LR model without HCUP features had the highest average precision 0.217 (0.136–0.31). To assess the interpretability of the GAM-NNs, we then visualized the learned contributions of the GAM-NNs and compared against the learned contributions of the LRs for the models with HCUP features. Overall, we were able to demonstrate that our proposed generalized additive neural network (GAM-NN) architecture is able to (1) leverage a neural network’s ability to learn nonlinear patterns in the data, which is more clinically intuitive, (2) be interpreted easily, making it more clinically useful, and (3) maintain model performance as compared to previously published DNNs.
Clinical outcomes of digital sensor alerting systems in remote monitoring: a systematic review and meta-analysis
Authors: Iqbal Fahad M. , Lam Kyle , Joshi Meera , Khan Sadia , Ashrafian Hutan , Darzi Ara 
Published: January 2021

AbstractAdvances in digital technologies have allowed remote monitoring and digital alerting systems to gain popularity. Despite this, limited evidence exists to substantiate claims that digital alerting can improve clinical outcomes. The aim of this study was to appraise the evidence on the clinical outcomes of digital alerting systems in remote monitoring through a systematic review and meta-analysis. A systematic literature search, with no language restrictions, was performed to identify studies evaluating healthcare outcomes of digital sensor alerting systems used in remote monitoring across all (medical and surgical) cohorts. The primary outcome was hospitalisation; secondary outcomes included hospital length of stay (LOS), mortality, emergency department and outpatient visits. Standard, pooled hazard ratio and proportion of means meta-analyses were performed. A total of 33 studies met the eligibility criteria; of which, 23 allowed for a meta-analysis. A 9.6% mean decrease in hospitalisation favouring digital alerting systems from a pooled random effects analysis was noted. However, pooled weighted mean differences and hazard ratios did not reproduce this finding. Digital alerting reduced hospital LOS by a mean difference of 1.043 days. A 3% mean decrease in all-cause mortality from digital alerting systems was noted. There was no benefit of digital alerting with respect to emergency department or outpatient visits. Digital alerts can considerably reduce hospitalisation and length of stay for certain cohorts in remote monitoring. Further research is required to confirm these findings and trial different alerting protocols to understand optimal alerting to guide future widespread implementation.
Backslide or forward progress? Virtual care at U.S. healthcare systems beyond the COVID-19 pandemic
Authors: Dorn Spencer D. 
Published: January 2021

AbstractThe COVID-19 pandemic forced most U.S. healthcare systems to quickly pivot to virtual care. However, since peaking in late April, care has largely shifted back to in-person. Health systems are now challenged to further develop and integrate useful, usable, and sustainable virtual care tools into their broader care model in ways that benefit their organizations and the communities they serve.
Peptide signaling without feedback in signal production operates as a true quorum sensing communication system in Bacillus subtilis
Authors: Dogsa Iztok , Spacapan Mihael , Dragoš Anna , Danevčič Tjaša , Pandur Žiga , Mandic-Mulec Ines 
Published: January 2021

AbstractBacterial quorum sensing (QS) is based on signal molecules (SM), which increase in concentration with cell density. At critical SM concentration, a variety of adaptive genes sharply change their expression from basic level to maximum level. In general, this sharp transition, a hallmark of true QS, requires an SM dependent positive feedback loop, where SM enhances its own production. Some communication systems, like the peptide SM-based ComQXPA communication system of Bacillus subtilis, do not have this feedback loop and we do not understand how and if the sharp transition in gene expression is achieved. Based on experiments and mathematical modeling, we observed that the SM peptide ComX encodes the information about cell density, specific cell growth rate, and even oxygen concentration, which ensure power-law increase in SM production. This enables together with the cooperative response to SM (ComX) a sharp transition in gene expression level and this without the SM dependent feedback loop. Due to its ultra-sensitive nature, the ComQXPA can operate at SM concentrations that are 100–1000 times lower than typically found in other QS systems, thereby substantially reducing the total metabolic cost of otherwise expensive ComX peptide.
Combinatorial targeting of multiple myeloma by complementing T cell engaging antibody fragments
Authors: Geis Maria , Nowotny Boris , Bohn Marc-Dominic , Kouhestani Dina , Einsele Hermann , Bumm Thomas , Stuhler Gernot 
Published: January 2021

AbstractBispecific T cell engaging antibodies (BiTEs) address tumor associated antigens that are over-expressed on cancer but that can also be found on healthy tissues, causing substantial on-target/off-tumor toxicities. To overcome this hurdle, we recently introduced hemibodies, a pair of complementary antibody fragments that redirect T cells against cancer-defining antigen combinations. Here we show that hemibodies addressing CD38 and SLAMF7 recruit T cells for the exquisite elimination of dual antigen positive multiple myeloma cells while leaving single antigen positive bystanders unharmed. Moreover, CD38 and SLAMF7 targeting BiTEs, but not hemibodies induce massive cytokine release and T cell fratricide reactions, a major drawback of T cell recruiting strategies. Together, we provide evidence in vitro and in vivo that hemibodies can be developed for the effective and highly specific immunotherapy of multiple myeloma.
Ontogenetic origins of cranial convergence between the extinct marsupial thylacine and placental gray wolf
Authors: Newton Axel H. , Weisbecker Vera , Pask Andrew J. , Hipsley Christy A. 
Published: January 2021

AbstractPhenotypic convergence, describing the independent evolution of similar characteristics, offers unique insights into how natural selection influences developmental and molecular processes to generate shared adaptations. The extinct marsupial thylacine and placental gray wolf represent one of the most extraordinary cases of convergent evolution in mammals, sharing striking cranial similarities despite 160 million years of independent evolution. We digitally reconstructed their cranial ontogeny from birth to adulthood to examine how and when convergence arises through patterns of allometry, mosaicism, modularity, and integration. We find the thylacine and wolf crania develop along nearly parallel growth trajectories, despite lineage-specific constraints and heterochrony in timing of ossification. These constraints were found to enforce distinct cranial modularity and integration patterns during development, which were unable to explain their adult convergence. Instead, we identify a developmental origin for their convergent cranial morphologies through patterns of mosaic evolution, occurring within bone groups sharing conserved embryonic tissue origins. Interestingly, these patterns are accompanied by homoplasy in gene regulatory networks associated with neural crest cells, critical for skull patterning. Together, our findings establish empirical links between adaptive phenotypic and genotypic convergence and provides a digital resource for further investigations into the developmental basis of mammalian evolution.
Chimpanzee histology and functional brain imaging show that the paracingulate sulcus is not human-specific
Authors: Amiez Céline , Sallet Jérôme , Novek Jennifer , Hadj-Bouziane Fadila , Giacometti Camille , Andersson Jesper , Hopkins William D. , Petrides Michael 
Published: January 2021

AbstractThe paracingulate sulcus -PCGS- has been considered for a long time to be specific to the human brain. Its presence/absence has been discussed in relation to interindividual variability of personality traits and cognitive abilities. Recently, a putative PCGS has been observed in chimpanzee brains. To demonstrate that this newly discovered sulcus is the homologue of the PCGS in the human brain, we analyzed cytoarchitectonic and resting-state functional magnetic resonance imaging data in chimpanzee brains which did or did not display a PCGS. The results show that the organization of the mid-cingulate cortex of the chimpanzee brain is comparable to that of the human brain, both cytoarchitectonically and in terms of functional connectivity with the lateral frontal cortex. These results demonstrate that the PCGS is not human-specific but is a shared feature of the primate brain since at least the last common ancestor to humans and great apes ~6 mya.
Pseudosparse neural coding in the visual system of primates
Authors: Lehky Sidney R. , Tanaka Keiji , Sereno Anne B. 
Published: January 2021

AbstractWhen measuring sparseness in neural populations as an indicator of efficient coding, an implicit assumption is that each stimulus activates a different random set of neurons. In other words, population responses to different stimuli are, on average, uncorrelated. Here we examine neurophysiological data from four lobes of macaque monkey cortex, including V1, V2, MT, anterior inferotemporal cortex, lateral intraparietal cortex, the frontal eye fields, and perirhinal cortex, to determine how correlated population responses are. We call the mean correlation the pseudosparseness index, because high pseudosparseness can mimic statistical properties of sparseness without being authentically sparse. In every data set we find high levels of pseudosparseness ranging from 0.59–0.98, substantially greater than the value of 0.00 for authentic sparseness. This was true for synthetic and natural stimuli, as well as for single-electrode and multielectrode data. A model indicates that a key variable producing high pseudosparseness is the standard deviation of spontaneous activity across the population. Consistently high values of pseudosparseness in the data demand reconsideration of the sparse coding literature as well as consideration of the degree to which authentic sparseness provides a useful framework for understanding neural coding in the cortex.
Charge transport and thermoelectric conversion in solution-processed semicrystalline polymer films under electrochemical doping
Authors: Ito Hiroshi , Mada Hiroaki , Watanabe Katsuya , Tanaka Hisaaki , Takenobu Taishi 
Published: January 2021

AbstractCharge transport and thermoelectric conversion mechanisms in doped semicrystalline polymer films are key issues in the field of wearable electronics, whereas the complex film structure consisting of crystalline domains and non-crystalline boundaries prevents sufficient understanding of them. In this study, we fully clarify the roles of the domains and the boundaries in a typical semicrystalline polymer on macroscopic charge transport under continuous electrochemical doping. In the crystalline domains, a multi-step transformation of the transport properties from effectively metallic behavior to weak localization (WL) to variable-range hopping (VRH) is found with decreasing temperature and doping level. On the other hand, at the domain boundaries, the effectively metallic conduction changes directly to VRH. Based on these results, the extremely complicated phase diagram, including the coexistence of the WL and VRH processes, is well explained. The proposed transport mechanism further explains the thermoelectric properties of the film.
The influence of NLTE effects in Fe I lines on an inverted atmosphere
Authors: Smitha H. N. , Holzreuter R. , van Noort M. , Solanki S. K. 
Published: January 2021

Context. This paper forms the second part of our study of how neglecting non-local thermodynamic equilibrium (NLTE) conditions in the formation of Fe I 6301.5 Å and the 6302.5 Å lines affects the atmosphere that is obtained by inverting the Stokes profiles of these lines in LTE. The main cause of NLTE effects in these lines is the line opacity deficit that is due to the excess ionisation of Fe I atoms by ultraviolet (UV) photons in the Sun.
Aims. In the first paper, these photospheric lines were assumed to have formed in 1D NLTE and the effects of horizontal radiation transfer (RT) were neglected. In the present paper, the iron lines are computed by solving the RT in 3D. We investigate the effect of horizontal RT on the inverted atmosphere and how it can enhance or reduce the errors that are due to neglecting 1D NLTE effects.
Methods. The Stokes profiles of the iron lines were computed in LTE, 1D NLTE, and 3D NLTE. They were all inverted using an LTE inversion code. The atmosphere from the inversion of LTE profiles was taken as the reference model. The atmospheres from the inversion of 1D NLTE profiles (testmodel-1D) and 3D NLTE profiles (testmodel-3D) were compared with it. Differences between reference and testmodels were analysed and correspondingly attributed to NLTE and 3D effects.
Results. The effects of horizontal RT are evident in regions surrounded by strong horizontal temperature gradients. That is, along the granule boundaries, regions surrounding magnetic elements, and its boundaries with intergranular lanes. In some regions, the 3D effects enhance the 1D NLTE effects, and in some, they weaken these effects. In the small region analysed in this paper, the errors due to neglecting the 3D effects are lower than 5% in temperature. In most of the pixels, the errors are lower than 20% in both velocity and magnetic field strength. These errors also persist when the Stokes profiles are spatially and spectrally degraded to the resolution of the Swedish Solar Telescope (SST) or Daniel K. Inouye Solar Telescope (DKIST).
Conclusions. Neglecting horizontal RT introduces errors not only in the derived temperature, but also in other atmospheric parameters. The error sizes depend on the strength of the local horizontal temperature gradients. Compared to the 1D NLTE effect, the 3D effects are more localised in specific regions in the atmosphere and are weaker overall.
A survey of the linear polarization of directly imaged exoplanets and brown dwarf companions with SPHERE-IRDIS
Authors: van Holstein R.G. , Stolker T. , Jensen-Clem R. , Ginski C. , Milli J. , de Boer J. , Girard J.H. , Wahhaj Z. , Bohn A.J. , Millar-Blanchaer M.A. , Benisty M. , Bonnefoy M. , Chauvin G. , Dominik C. , Hinkley S. , Keller C.U. , Keppler M. , Langlois M. , Marino S. , Ménard F. , Perrot C. , Schmidt T.O.B. , Vigan A. , Zurlo A. , Snik F. 
Published: January 2021

Context. Young giant planets and brown dwarf companions emit near-infrared radiation that can be linearly polarized up to several percent. This polarization can reveal the presence of an (unresolved) circumsubstellar accretion disk, rotation-induced oblateness of the atmosphere, or an inhomogeneous distribution of atmospheric dust clouds.
Aims. We aim to measure the near-infrared linear polarization of 20 known directly imaged exoplanets and brown dwarf companions.
Methods. We observed the companions with the high-contrast imaging polarimeter SPHERE-IRDIS at the Very Large Telescope. We reduced the data using the IRDAP pipeline to correct for the instrumental polarization and crosstalk of the optical system with an absolute polarimetric accuracy <0.1% in the degree of polarization. We employed aperture photometry, angular differential imaging, and point-spread-function fitting to retrieve the polarization of the companions.
Results. We report the first detection of polarization originating from substellar companions, with a polarization of several tenths of a percent for DH Tau B and GSC 6214-210 B in H-band. By comparing the measured polarization with that of nearby stars, we find that the polarization is unlikely to be caused by interstellar dust. Because the companions have previously measured hydrogen emission lines and red colors, the polarization most likely originates from circumsubstellar disks. Through radiative transfer modeling, we constrain the position angles of the disks and find that the disks must have high inclinations. For the 18 other companions, we do not detect significant polarization and place subpercent upper limits on their degree of polarization. We also present images of the circumstellar disks of DH Tau, GQ Lup, PDS 70, β Pic, and HD 106906. We detect a highly asymmetric disk around GQ Lup and find evidence for multiple scattering in the disk of PDS 70. Both disks show spiral-like features that are potentially induced by GQ Lup B and PDS 70 b, respectively.
Conclusions. The presence of the disks around DH Tau B and GSC 6214-210 B as well as the misalignment of the disk of DH Tau B with the disk around its primary star suggest in situ formation of the companions. The non-detections of polarization for the other companions may indicate the absence of circumsubstellar disks, a slow rotation rate of young companions, the upper atmospheres containing primarily submicron-sized dust grains, and/or limited cloud inhomogeneity.
Massive heartbeat stars from TESS
Authors: Kołaczek-Szymański P. A. , Pigulski A. , Michalska G. , Moździerski D. , Różański T. 
Published: January 2021

Context. Heartbeat stars are eccentric binaries that exhibit a characteristic shape of brightness changes close to the periastron passage, primarily caused by a variable tidal distortion of the components. Variable tidal potential can drive tidally excited oscillations (TEOs), which are usually gravity modes. Studies of heartbeat stars and TEOs open up new possibilities for probing the interiors of massive stars. There are only a few massive (masses of components ≳2 M⊙) systems of this type that are known thus far.
Aims. Using TESS data from the first 16 sectors, we searched for new massive heartbeat stars and TEOs using a sample of over 300 eccentric spectroscopic binaries.
Methods. We analysed 2 min and 30 min cadence TESS data. Then we fitted Kumar’s analytical model to the light curves of stars showing heartbeats and performed a times-series analysis of the residuals searching for TEOs and periodic intrinsic variability.
Results. We found 20 massive heartbeat systems, of which 7 exhibit TEOs. The TEOs occur at harmonics of orbital frequencies in the range between 3 and 36, with the median value equal to 9, which is lower than those in known Kepler systems with TEOs. The most massive system in this sample is the quadruple star HD 5980, a member of the Small Magellanic Cloud. With a total mass of ∼150 M⊙ it is the most massive system showing a heartbeat. Six stars in the sample of the new heartbeat stars are eclipsing. A comparison of the parameters derived from fitting Kumar’s model and from light-curve modelling shows that Kumar’s model does not provide reliable parameters. In other words, the orbital parameters can be reliably derived from fitting heartbeat light curves only if the model includes all proximity effects. Finally, intrinsic pulsations of β Cep, SPB, δ Sct, and γ Dor-type were found in nine heartbeat systems. This opens an interesting possibility for studies of pulsation-binarity interaction and the co-existence of forced and self-excited oscillations.