bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hamiltonian Monte Carlo Probabilistic Joint Inversion of 2D (2.75D) Gravity and Magnetic Data
Authors: Zunino Andrea , Ghirotto Alessandro , Armadillo Egidio , Fichtner Andreas 
Published: October 2022

AbstractTwo‐dimensional modeling of gravity and magnetic anomalies in terms of polygonal bodies is a popular approach to infer possible configurations of geological structures in the subsurface. Alternatively to the traditional trial‐and‐error manual fit of measured data, here we illustrate a probabilistic strategy to solve the inverse problem. First we derive a set of formulae for solving a 2.75‐dimensional forward model, where the polygonal bodies have a given finite lateral extent, and then we devise a Hamiltonian Monte Carlo algorithm to jointly invert gravity and magnetic data for the geometry and properties of the polygonal bodies. This probabilistic approach fully addresses the nonlinearity of the forward model and provides uncertainty estimation. The result of the inversion is a collection of models which represent the posterior distribution, analysis of which provides estimates of sought properties and may reveal different scenarios.
Steady Long‐Term Slip Rate on the Blue Cut Fault: Implications for Strain Transfer Between the San Andreas Fault and Eastern California Shear Zone
Authors: Guns K. A. , Bennett R. , Blisniuk K. , Walker A. , Hidy A. , Heimsath A. 
Published: October 2022

AbstractThe Eastern Transverse Ranges (ETR) province of California contains a system of E‐W‐trending left‐lateral faults accommodating clockwise block rotation between the San Andreas Fault (SAF) system in the Coachella Valley and the Eastern California Shear Zone (ECSZ) in the Mojave Desert. Building upon established geometric relationships, we estimate that this rotation across the ETR may transfer right‐lateral strain from the SAF to the ECSZ at a time‐averaged rate of ∼4.3–7.7 mm/yr. Through geomorphic mapping and the analysis of 3810Be surface exposure samples, we derive a long‐term slip rate of 1.26 ± 0.50 (2σ) mm/yr over the late Pleistocene, yet analysis of the displacement record indicates a rate decrease ∼71 kya. While a rate change on this fault could have implications for possible plate boundary reorganization in this area, we argue that this slip rate variability more likely reflects routine fluctuation about a steady lifetime slip rate.
Mapping Phyllosilicates on the Asteroid Bennu Using Thermal Emission Spectra and Machine Learning Model Applications
Authors: Breitenfeld L. B. , Rogers A. D. , Glotch T. D. , Kaplan H. H. , Hamilton V. E. , Christensen P. R. 
Published: October 2022

AbstractBennu, the target of the OSIRIS‐REx mission, is an asteroid with compositions analogous to low petrologic type CI, CM, CR, and/or ungrouped carbonaceous chondrites. Asteroids like Bennu provide information about the building blocks of the early Solar System. Analysis of the mid‐infrared remote sensing data informs mineral quantification. We apply a phyllosilicate specific model, developed by Breitenfeld et al. (2021, https://doi.org/10.1029/2021je007035) that distinguishes between Mg and Fe serpentines, to Baseball Diamond 1 (BBD1), equatorial station 3 (EQ3), and touch‐and‐go OSIRIS‐REx thermal emission spectrometer data. The average total phyllosilicate predictions are 73 (BBD1) and 72 vol% (EQ3). We observe higher Fe‐cronstedtite and lower Mg‐rich serpentine content in the equatorial region of Bennu than average. Mid‐infrared spectral variability may be explained by sorting effects through mass movement.
Hybrid Simulations of the Cusp and Dayside Magnetosheath Dynamics Under Quasi‐Radial Interplanetary Magnetic Fields
Authors: Ng J. , Chen L.‐J. , Omelchenko Y. , Zou Y. , Lavraud B. 
Published: October 2022

AbstractUnder quasi‐radial interplanetary magnetic fields (IMF), foreshock turbulence can have an impact on the magnetosheath and cusps depending on the location of the quasi‐parallel shock. We perform three‐dimensional simulations of Earth's dayside magnetosphere using the hybrid code HYPERS, and compare northward and southward quasi‐radial IMF configurations. We study the magnetic field configuration, fluctuations in the magnetosheath and the plasma in the regions around the northern cusp. Under northward IMF with Earthward Bx, there is a time‐varying plasma depletion layer immediately outside the northern cusp. In the southward IMF case, the impact of foreshock turbulence and high‐speed jets, together with magnetopause reconnection, can lead to strong density enhancements in the cusp.
Regulation of Bacterial Metabolic Activities and Community Composition by Temperature in a Fringing Coral Reef
Authors: Hu Xin , Li Xiangfu , He Maoqiu , Long Aimin , Xu Jie 
Published: October 2022

AbstractIn coral reefs, heterotrophic bacteria play an important role in driving carbon cycle and sustaining coral health. Bacterial production (BP), bacterial respiration (BR) and bacterial community composition (BCC) were determined in the Luhuitou fringing reef and the surrounding ocean in the northern South China Sea on a seasonal basis, in order to examine bacterial metabolic activity and effect of temperature on bacterial community in the fringing coral reef. Our results showed that higher BP (3.52–12.45 μg C L−1 d−1) and bacterial growth efficiency (0.16–0.28) and lower cellular BR (8.34–31.73 fg C cell−1 d−1) in the Luhuitou fringing reef than the surrounding ocean was more likely attributed to substrate availability. Enhanced dissolved organic nitrogen availability preferentially triggered the growth of bacteria with high nucleic acid content (HNA bacteria), which was most possibly responsible for high BP in the coral reef. Heterotrophic bacteria were more sensitive to temperature in the highly productive Luhuitou fringing reef than the surrounding ocean. Temperature shaped BCC by mediating enzymatic activity in the coral reef, likely triggering opportunistic infections. Warming might not only promote the growth of HNA bacteria and shift BCC in the coral reef, which was partly responsible for coral disease, but also reduce oxygen replenishment from the surface due to stratification and elevate the oxygen consumption owing to high BR, consequently threatening the survival of corals. Our findings helped to better understand how heterotrophic bacteria mediated the survival of corals in response to fluctuations of temperature.
Color-selective three-dimensional polarization structures
Authors: Intaravanne Yuttana , Wang Ruoxing , Ahmed Hammad , Ming Yang , Zheng Yaqin , Zhou Zhang-Kai , Li Zhancheng , Chen Shuqi , Zhang Shuang , Chen Xianzhong 
Published: October 2022

AbstractPolarization as an important degree of freedom for light plays a key role in optics. Structured beams with controlled polarization profiles have diverse applications, such as information encoding, display, medical and biological imaging, and manipulation of microparticles. However, conventional polarization optics can only realize two-dimensional polarization structures in a transverse plane. The emergent ultrathin optical devices consisting of planar nanostructures, so-called metasurfaces, have shown much promise for polarization manipulation. Here we propose and experimentally demonstrate color-selective three-dimensional (3D) polarization structures with a single metasurface. The geometric metasurfaces are designed based on color and phase multiplexing and polarization rotation, creating various 3D polarization knots. Remarkably, different 3D polarization knots in the same observation region can be achieved by controlling the incident wavelengths, providing unprecedented polarization control with color information in 3D space. Our research findings may be of interest to many practical applications such as vector beam generation, virtual reality, volumetric displays, security, and anti-counterfeiting.
Identification of phenocopies improves prediction of targeted therapy response over DNA mutations alone
Authors: Bakhtiar Hamza , Helzer Kyle T. , Park Yeonhee , Chen Yi , Rydzewski Nicholas R. , Bootsma Matthew L. , Shi Yue , Harari Paul M. , Sharifi Marina , Sjöström Martin , Lang Joshua M. , Yu Menggang , Zhao Shuang G. 
Published: October 2022

AbstractDNA mutations in specific genes can confer preferential benefit from drugs targeting those genes. However, other molecular perturbations can “phenocopy” pathogenic mutations, but would not be identified using standard clinical sequencing, leading to missed opportunities for other patients to benefit from targeted treatments. We hypothesized that RNA phenocopy signatures of key cancer driver gene mutations could improve our ability to predict response to targeted therapies, despite not being directly trained on drug response. To test this, we built gene expression signatures in tissue samples for specific mutations and found that phenocopy signatures broadly increased accuracy of drug response predictions in-vitro compared to DNA mutation alone, and identified additional cancer cell lines that respond well with a positive/negative predictive value on par or better than DNA mutations. We further validated our results across four clinical cohorts. Our results suggest that routine RNA sequencing of tumors to identify phenocopies in addition to standard targeted DNA sequencing would improve our ability to accurately select patients for targeted therapies in the clinic.
Life expectancy changes since COVID-19
Authors: Schöley Jonas , Aburto José Manuel , Kashnitsky Ilya , Kniffka Maxi S. , Zhang Luyin , Jaadla Hannaliis , Dowd Jennifer B. , Kashyap Ridhi 
Published: October 2022

AbstractThe COVID-19 pandemic triggered an unprecedented rise in mortality that translated into life expectancy losses around the world, with only a few exceptions. We estimate life expectancy changes in 29 countries since 2020 (including most of Europe, the United States and Chile), attribute them to mortality changes by age group and compare them with historic life expectancy shocks. Our results show divergence in mortality impacts of the pandemic in 2021. While countries in western Europe experienced bounce backs from life expectancy losses of 2020, eastern Europe and the United States witnessed sustained and substantial life expectancy deficits. Life expectancy deficits during fall/winter 2021 among people ages 60+ and <60 were negatively correlated with measures of vaccination uptake across countries (r60+ = −0.86; two-tailed P < 0.001; 95% confidence interval, −0.94 to −0.69; r<60 = −0.74; two-tailed P < 0.001; 95% confidence interval, −0.88 to −0.46). In contrast to 2020, the age profile of excess mortality in 2021 was younger, with those in under-80 age groups contributing more to life expectancy losses. However, even in 2021, registered COVID-19 deaths continued to account for most life expectancy losses.
An optimized method for purifying, detecting and quantifying Mycobacterium tuberculosis RNA from sputum for monitoring treatment response in TB patients
Authors: Zainabadi Kayvan , Lee Myung Hee , Walsh Kathleen Frances , Vilbrun Stalz Charles , Mathurin Laurent Daniel , Ocheretina Oksana , Pape Jean William , Fitzgerald Daniel W. 
Published: October 2022

AbstractDiagnostics that more accurately detect and quantify viable Mycobacterium tuberculosis (Mtb) in the sputum of patients undergoing therapy are needed. Current culture- and molecular-based tests have shown limited efficacy for monitoring treatment response in TB patients, either due to the presence of viable sub-populations of Mtb which fail to grow under standard culture conditions (termed differentially detectable/culturable Mtb, DD Mtb) or the prolonged half-life of Mtb DNA in sputum. Here, we report an optimized RNA-based method for detecting and quantifying viable Mtb from patient sputum during the course of therapy. We first empirically derived a novel RNA extraction protocol from sputum that improves recovery of Mtb RNA while almost completely eliminating contamination from Mtb DNA and host nucleic acids. Next, we identified five Mtb 16S rRNA primer sets with varying limits of detection that were capable of distinguishing between live versus dead H37Rv Mtb. This combined protocol was then tested on sputa from a longitudinal cohort of patients receiving therapy for drug sensitive (DS) or drug resistant (DR) TB with first-line or second-line regimens, respectively. Results were compared with that of culture, including CFU, BACTEC MGIT, and a limiting dilution assay capable of detecting DD Mtb. The five 16S rRNA primer sets positively identified nearly all (range 94–100%) culture positive sputa, and a portion (19–37%) of culture negative sputa. In comparison, ten highly expressed Mtb mRNAs showed positivity in 72–86% of culture positive sputa, and in 0–13% of culture negative sputa. Two of the five 16S rRNA primer sets were able to positively identify 100% of culture positive sputa, and when tested on culture negative sputa from the DS cohort at 2 months post-initiation of therapy, identified 40% of samples as positive; a percentage that is in line with expected treatment failure rates when first-line therapy is discontinued early. These two primer sets also detected 16S rRNA in 13–20% of sputa at 6 months post-initiation of therapy in the DR cohort. Cycle threshold values for 16S rRNA showed a strong correlation with Mtb numbers as determined by culture (R > 0.87), including as Mtb numbers declined during the course of treatment with first-line and second-line regimens. The optimized molecular assay outlined here may have utility for monitoring treatment response in TB patients.
Generalizable deep learning model for early Alzheimer’s disease detection from structural MRIs
Authors: Liu Sheng , Masurkar Arjun V. , Rusinek Henry , Chen Jingyun , Zhang Ben , Zhu Weicheng , Fernandez-Granda Carlos , Razavian Narges 
Published: October 2022

AbstractEarly diagnosis of Alzheimer’s disease plays a pivotal role in patient care and clinical trials. In this study, we have developed a new approach based on 3D deep convolutional neural networks to accurately differentiate mild Alzheimer’s disease dementia from mild cognitive impairment and cognitively normal individuals using structural MRIs. For comparison, we have built a reference model based on the volumes and thickness of previously reported brain regions that are known to be implicated in disease progression. We validate both models on an internal held-out cohort from The Alzheimer's Disease Neuroimaging Initiative (ADNI) and on an external independent cohort from The National Alzheimer's Coordinating Center (NACC). The deep-learning model is accurate, achieved an area-under-the-curve (AUC) of 85.12 when distinguishing between cognitive normal subjects and subjects with either MCI or mild Alzheimer’s dementia. In the more challenging task of detecting MCI, it achieves an AUC of 62.45. It is also significantly faster than the volume/thickness model in which the volumes and thickness need to be extracted beforehand. The model can also be used to forecast progression: subjects with mild cognitive impairment misclassified as having mild Alzheimer’s disease dementia by the model were faster to progress to dementia over time. An analysis of the features learned by the proposed model shows that it relies on a wide range of regions associated with Alzheimer's disease. These findings suggest that deep neural networks can automatically learn to identify imaging biomarkers that are predictive of Alzheimer's disease, and leverage them to achieve accurate early detection of the disease.
Ecological sensitivity and vulnerability of fishing fleet landings to climate change across regions
Authors: Albo-Puigserver Marta , Bueno-Pardo Juan , Pinto Miguel , Monteiro João N. , Ovelheiro Andreia , Teodósio Maria A. , Leitão Francisco 
Published: October 2022

AbstractThe degree of exposure of fishing communities to environmental changes can be partially determined by the vulnerability of the target species and the landings composition. Hence, identifying the species that ecologically most contribute to the vulnerability of the landings are key steps to evaluate the risk posed by climate change. We analyse the temporal variability in intrinsic sensitivity and the ecological vulnerability of the Portuguese fisheries landings, considering the species proportions derived both from the weights and revenues. To account for the diversification of species of each fleet, we explored the species dependence of the fishery in combination with the vulnerability of them. The analyses were carried out separately for three fleet typologies and three regions. Opposite to what has been observed at a global scale, the ecological sensitivity of the fisheries landings between 1989 and 2015 did not display a decline across areas or fishing fleets. Considering each fleet independently, for trawling, where average vulnerability was lower than in the other fleets, the sensitivity of the landings increased since the 2000s. On the other hand, the high vulnerability found in multi-gear fleets was compensated by diversification of the species caught, while purse-seine fleets targeted low vulnerability species but presented a high fishery dependence on few species. The results highlight the importance of combining information on ecological vulnerability and diversification of fishing resources at a regional scale while providing a measure of the ecological exposure to climate change.
Effect of Weiss ring on peripapillary retinal nerve fiber layer thickness measurements using SD-OCT
Authors: Kim Min-Su , Nam Ki-Yup , Hwang Young Hoon , Lee Min-Woo , Lee Woo-Hyuk , Lim Hyung-Bin , Kim Jung-Yeul 
Published: October 2022

AbstractSpectral-domain optical coherence tomography (SD-OCT) must accurately identify and measure the peripapillary retinal nerve fiber layer (pRNFL) thickness to improve the repeatability and reproducibility, and reduce measurement errors. Because Weiss ring can be located in front of the optic disc, we hypothesized that it may affect pRNFL thickness measurements obtained using SD-OCT. We retrospectively reviewed the medical records of patients with (group W) and without (group N) Weiss ring, observed on OCT fundus image and an RNFL map devised using SD-OCT. Optic disc cube scans (200 × 200) were obtained to measure pRNFL thicknesses (superior, temporal, inferior, nasal, and average) at two consecutive visits. Pearson's correlation coefficient (r), intraclass correlation coefficient (ICC), and coefficient of variation (CV) were calculated. The r and ICC values for the pRNFL thickness measurements at the two visits were lower for group W compared to group N, but statistical significance was reached only for inferior pRNFL thickness. In addition, CV values were greater for group W compared to group N, but the differences were significant only for inferior and average pRNFL thickness measurements (p < 0.001 and p = 0.004, respectively). Weiss ring located near the optic disc can affect pRNFL thickness measurements and repeatability thereof, especially the inferior quadrant and average values. Therefore, it is important to identify the presence of Weiss ring when analyzing pRNFL thickness values.
The effect of putrescine on space use and activity in sea lamprey (Petromyzon marinus)
Authors: Mensch Emily L. , Dissanayake Amila A. , Nair Muraleedharan G. , Wagner C. Michael 
Published: October 2022

AbstractFish use odor to avoid exposure to predation and disease. Harnessing these odors as repellents is proving useful for management initiatives that conserve native species or control invasive populations. Here, we evaluated the behavioral response of invasive sea lamprey to putrescine, a decay molecule that many prey organisms avoid. Putrescine is found in tissue extracts that contain sea lamprey alarm cue, and human saliva, two mixtures known to elicit flight and avoidance responses in migratory sea lamprey. We used two behavioral assays to evaluate metrics of repellency: behavioral preference (space use) and change in activity rates and found context-dependent results. In smaller assays with individual fish, we found that putrescine had no effect on sea lamprey activity but did induce avoidance. In larger assays with multiple animals, sea lamprey did not avoid putrescine. Our results also showed consistent changes in activity and avoidance behavior in sea lamprey exposed to alarm cue in the smaller assay, concluding that this design could prove useful as a high-throughput screening tool. We also investigated a novel odor identified in sea lamprey skin, petromyzonacil, and found no behavioral effects to this odor on its own or in synergy with putrescine. Our results show limited evidence that putrescine acts as robust repellent for sea lamprey and highlight the importance of environmental context when interpreting avoidance behavior in laboratory settings.
Characteristics of hospitalized patients with SARS-CoV-2 infection during successive waves of the COVID-19 pandemic in a reference hospital in Spain
Authors: Iftimie Simona , López-Azcona Ana F. , Lozano-Olmo Maria José , Hernández-Aguilera Anna , Sarrà-Moretó Salvador , Joven Jorge , Camps Jordi , Castro Antoni 
Published: October 2022

AbstractSince the beginning of the COVID-19 pandemic and until September 2021, Spain suffered five waves of infection, the latter being related to the expansion of the Delta variant and with a high incidence. A vaccination campaign began in December 2020 and by the end of the fifth wave 77.3% of people had been fully vaccinated. Examining the changing dynamics of COVID-19 pandemic and its impact on outcomes among those hospitalized is essential. Our objective was to ascertain any differences in the characteristics and outcomes of hospitalized patients during that period compared to previous waves. We prospectively enrolled 200 consecutively admitted hospital patients from each wave and collected their clinical and demographic data from the medical records, including symptoms, comorbidities, deaths and whether they needed to be admitted to the Intensive Care Unit to receive assisted ventilation. We found that patients in the fifth wave were considerably younger than before, and the mortality rate fell from 22.5 to 2.0%. Admissions to the Intensive Care Unit decreased from 10 to 2%. Patients in the fifth wave had fewer comorbidities, and the age of the patients who died was higher than those who survived. Our results show a marked improvement in patient outcomes in the fifth wave, suggesting success of the vaccination campaign despite the explosion in cases due to the Delta variant.
Stacking ensemble learning model to predict 6-month mortality in ischemic stroke patients
Authors: Hwangbo Lee , Kang Yoon Jung , Kwon Hoon , Lee Jae Il , Cho Han-Jin , Ko Jun-Kyeung , Sung Sang Min , Lee Tae Hong 
Published: October 2022

AbstractPatients with acute ischemic stroke can benefit from reperfusion therapy. Nevertheless, there are gray areas where initiation of reperfusion therapy is neither supported nor contraindicated by the current practice guidelines. In these situations, a prediction model for mortality can be beneficial in decision-making. This study aimed to develop a mortality prediction model for acute ischemic stroke patients not receiving reperfusion therapies using a stacking ensemble learning model. The model used an artificial neural network as an ensemble classifier. Seven base classifiers were K-nearest neighbors, support vector machine, extreme gradient boosting, random forest, naive Bayes, artificial neural network, and logistic regression algorithms. From the clinical data in the International Stroke Trial database, we selected a concise set of variables assessable at the presentation. The primary study outcome was all-cause mortality at 6 months. Our stacking ensemble model predicted 6-month mortality with acceptable performance in ischemic stroke patients not receiving reperfusion therapy. The area under the curve of receiver-operating characteristics, accuracy, sensitivity, and specificity of the stacking ensemble classifier on a put-aside validation set were 0.783 (95% confidence interval 0.758–0.808), 71.6% (69.3–74.2), 72.3% (69.2–76.4%), and 70.9% (68.9–74.3%), respectively.