bluuebunny/crossref_metadata_2025_split huggingface dataset:
An End‐To‐End Earthquake Detection Method for Joint Phase Picking and Association Using Deep Learning
Authors: Zhu Weiqiang , Tai Kai Sheng , Mousavi S. Mostafa , Bailis Peter , Beroza Gregory C. 
Published: March 2022

AbstractEarthquake monitoring by seismic networks typically involves a workflow consisting of phase detection/picking, association, and location tasks. In recent years, the accuracy of these individual stages has been improved through the use of machine learning techniques. In this study, we introduce a new end‐to‐end approach that improves overall earthquake detection accuracy by jointly optimizing each stage of the detection pipeline. We propose a neural network architecture for the task of multi‐station processing of seismic waveforms recorded over a seismic network. This end‐to‐end architecture consists of three sub‐networks: a backbone network that extracts features from raw waveforms, a phase picking sub‐network that picks P‐ and S‐wave arrivals based on these features, and an event detection sub‐network that aggregates the features from multiple stations to associate and detect earthquakes across a seismic network. We use these sub‐networks together with a shift‐and‐stack module based on back‐projection that introduces kinematic constraints on arrival times, allowing the neural network model to generalize to different velocity models and to variable station geometry in seismic networks. We evaluate our proposed method on the STanford EArthquake Dataset (STEAD) and on the 2019 Ridgecrest, CA earthquake sequence. The results demonstrate that our end‐to‐end approach can effectively pick P‐ and S‐wave arrivals and achieve earthquake detection accuracy rivaling that of other state‐of‐the‐art approaches. Because our approach preserves information across tasks in the detection pipeline, it has the potential to outperform approaches that do not.
Spatial Variability of Radon Production Rates in an Alluvial Aquifer Affects Travel Time Estimates of Groundwater Originating From a Losing Stream
Authors: Schaper Jonas L. , Zarfl Christiane , Meinikmann Karin , Banks Eddie W. , Baron Sandra , Cirpka Olaf A. , Lewandowski Joerg 
Published: March 2022

AbstractAssessing water travel times in hyporheic and adjacent alluvial sediments is important to quantify exchange rates, biogeochemical turnover, and pollution dynamics across groundwater‐surface water interfaces and in floodplain aquifers. Heat and 222Rn are useful natural tracers for this purpose. While heat transport is commonly simulated via the convection‐conduction equation, the transport of 222Rn is often simulated assuming purely advective transport and a homogenous distribution of 222Rn production rates across the model domain. In the present study, we explicitly model the production, transport, and radioactive decay of 222Rn after surface water infiltration into an alluvial aquifer with the numerical models MODFLOW‐NWT and MT3D‐USGS. Using field observations, numerical modeling, and laboratory experiments, we show that 222Rn production rates vary substantially in the alluvial aquifer of a lowland river. Distributions of mean river‐to‐groundwater travel time in the alluvial aquifer, estimated via a Bayesian approach, shifted considerably depending on whether 222Rn and time series of groundwater heads and temperature were jointly inverted and whether 222Rn production rates were allowed to vary spatially. With distance to the river, differences between the median river‐to‐groundwater travel time and apparent 222Rn ages increased by factors ranging from 1.4 at 4 m to 11.9 at 59 m, a finding that highlights the need to simulate 222Rn transport explicitly. The joint inversion of 222Rn, groundwater heads, and temperature reduced uncertainty associated with mean travel times, suggesting that the uncertainty introduced by spatially varying 222Rn production rates can at least partly be compensated by using a combination of natural tracers.
Advanced Testing of Low, Medium, and High ECS CMIP6 GCM Simulations Versus ERA5‐T2m
Authors: Scafetta Nicola 
Published: March 2022

AbstractThe equilibrium climate sensitivity (ECS) of the CMIP6 global circulation models (GCMs) varies from 1.83°C to 5.67°C. Herein, 38 GCMs are grouped into three ECS classes (low, 1.80–3.00°C; medium, 3.01–4.50°C; high, 4.51–6.00°C) and compared against the ERA5‐T2m records from 1980–1990 to 2011–2021. We found that all models with ECS > 3.0°C overestimate the observed global surface warming and that spatial t‐statistics rejects the data‐model agreement over 60% (using low‐ECS GCMs) to 81% (using high‐ECS GCMs) of the Earth's surface. Thus, the high and medium‐ECS GCMs are unfit for prediction purposes. The low‐ECS GCMs are not fully satisfactory yet, but they are also found unalarming because by 2050 they predict a moderate warming (ΔTpreindustrial→2050 ≲ 2°C).
The Cooling Over Northeast Asia in June Over the Most Recent Decade: A Possible Response to Declining Bering Sea Sea Ice in March
Authors: Ma Shuangmei , Zhu Congwen 
Published: March 2022

AbstractIn sharp contrast to rapid global warming, the surface air temperature (SAT) in Northeast Asia (NEA) has exhibited strong cooling in June since 2010. Our results show that this cooling is a possible response to declining Bering Sea sea ice concentrations (BSICs) in March. A physical process analysis shows that decreasing BSICs provoke a south‐eastward‐propagating Rossby wave train and induce a strong anomalous anticyclone over the midlatitude Northwest Atlantic, resulting in tripolar anomalous sea surface temperature (SST) pattern with warm anomalies in the midlatitude Northwest Atlantic. These persistent tripolar SST anomalies generate a new Rossby wave across Eurasia in June, which enhances the cyclonic atmosphere circulation anomaly over NEA and leads to the cold SAT anomalies observed in this area. Correspondingly, in response to the sharp decline in BSIC in March, the NEA has exhibited an unprecedented cooling trend in June over the most recent decade.
Sub‐Structures of the Separatrix Region During Magnetic Reconnection
Authors: Jiang K. , Huang S. Y. , Yuan Z. G. , Deng X. H. , Wei Y. Y. , Xiong Q. Y. , Xu S. B. , Zhang J. , Zhang Z. H. , Lin R. T. , Yu L. 
Published: March 2022

AbstractUtilizing data from the Magnetospheric Multiscale mission, the sub‐structures of the separatrix region during reconnection are investigated. A small current system in the separatrix region is embedded in the large Hall current system, which appears as a quadrupole current. This small current system has an opposite direction to the Hall current and cancels part of the Hall magnetic field. The formation of the quadrupole current is possibly related to the patchy parallel electric field. The electric field in the separatrix region can be divided into three sub‐layers according to the electron frozen‐in condition. En enhances in two outside sub‐layers, where the strong En is supported by the Hall term and electron pressure gradient term, and the nearly zero En, separating the enhanced electric fields, is caused by a small flow and electron density gradient. Our observations imply complex dynamics in the separatrix region during magnetic reconnection.
Supershear Rupture During the 2021 MW 7.4 Maduo, China, Earthquake
Authors: Zhang Xu , Feng Wanpeng , Du Hailin , Samsonov Sergey , Yi Lei 
Published: March 2022

AbstractCombined with the multi‐array back‐projection and finite‐fault joint inversion methods, we investigate the detailed spatiotemporal rupture complexity of the 2021 MW 7.4 Maduo earthquake using seismic and geodetic data. Our results reveal that this earthquake ruptured bilaterally 170 km long fault segments with a duration of 38 s. The obtained back‐projection results, specific aftershock signature of the supershear earthquake, and observations of far‐field Love Mach waves consistently validate that this earthquake is a supershear event. Furthermore, by analyzing global large strike‐slip earthquakes, we find that the moment‐scaled radiated energies of previously well confirmed supershear earthquakes with relatively simple fault geometries are similar to that of the 2021 MW 7.4 Maduo earthquake, which are significantly smaller than those of subshear strike‐slip events. This new finding provides additional supporting evidence to validate the supershear rupture during the 2021 MW 7.4 Maduo earthquake.
Scalable and automated CRISPR-based strain engineering using droplet microfluidics
Authors: Iwai Kosuke , Wehrs Maren , Garber Megan , Sustarich Jess , Washburn Lauren , Costello Zachary , Kim Peter W. , Ando David , Gaillard William R. , Hillson Nathan J. , Adams Paul D. , Mukhopadhyay Aindrila , Garcia Martin Hector , Singh Anup K. 
Published: March 2022

AbstractWe present a droplet-based microfluidic system that enables CRISPR-based gene editing and high-throughput screening on a chip. The microfluidic device contains a 10 × 10 element array, and each element contains sets of electrodes for two electric field-actuated operations: electrowetting for merging droplets to mix reagents and electroporation for transformation. This device can perform up to 100 genetic modification reactions in parallel, providing a scalable platform for generating the large number of engineered strains required for the combinatorial optimization of genetic pathways and predictable bioengineering. We demonstrate the system’s capabilities through the CRISPR-based engineering of two test cases: (1) disruption of the function of the enzyme galactokinase (galK) in E. coli and (2) targeted engineering of the glutamine synthetase gene (glnA) and the blue-pigment synthetase gene (bpsA) to improve indigoidine production in E. coli.
Effects of the age of vaccination on the humoral responses to a human papillomavirus vaccine
Authors: Nicoli Francesco , Mantelli Barbara , Gallerani Eleonora , Telatin Valentina , Squarzon Laura , Masiero Serena , Gavioli Riccardo , Palù Giorgio , Barzon Luisa , Caputo Antonella 
Published: March 2022

AbstractAdult vaccination programs are receiving increasing attention however, little is known regarding the impact of age on the maintenance of the immune response. We investigated this issue in the context of a human papillomavirus (HPV) vaccination program collecting real-world data on the durability of humoral immunity in 315 female subjects stratified according to vaccination age (adolescents and adults) and sampled at early or late time points after the last vaccine dose. HPV-specific IgGs, but not memory B cells, were induced and maintained at higher levels in subjects vaccinated during adolescence. Nonetheless, antibody functions waned over time to a similar degree in adolescents and adults. To shed light on this phenomena, we analyzed quantitative and qualitative properties of lymphocytes. Similar biochemical features were observed between B-cell subsets from individuals belonging to the two age groups. Long term humoral responses toward vaccines administered at an earlier age were comparably maintained between adolescents and adults. The percentages of naïve B and CD4+T cells were significantly higher in adolescents, and the latter directly correlated with IgG titers against 3 out of 4 HPV types. Our results indicate that age-specific HPV vaccine responsiveness is mostly due to quantitative differences of immune cell precursors rather than qualitative defects in B cells. In addition, our results indicate that adults also have a good humoral immunogenic profile, suggesting that their inclusion in catch-up programmes is desirable.
Advances in purification of SARS-CoV-2 spike ectodomain protein using high-throughput screening and non-affinity methods
Authors: Cibelli Nicole , Arias Gabriel , Figur McKenzie , Khayat Shireen S. , Leach Kristin , Loukinov Ivan , Shadrick William , Chuenchor Watchalee , Tsybovsky Yaroslav ,   Vaccine Production Program Analytical Development, Patel Aakash , Mai Misa , Wang Xin , Vickery Karen , Khin Tina , Skubutyte Renata , Vejzagic Farah , Bastani Niutish , Vinitsky Alison , Lei Q. Paula , Gulla Krishana , Gowetski Daniel B. 
Published: March 2022

AbstractThe spike (S) glycoprotein of the pandemic virus, SARS-CoV-2, is a critically important target of vaccine design and therapeutic development. A high-yield, scalable, cGMP-compliant downstream process for the stabilized, soluble, native-like S protein ectodomain is necessary to meet the extensive material requirements for ongoing research and development. As of June 2021, S proteins have exclusively been purified using difficult-to-scale, low-yield methodologies such as affinity and size-exclusion chromatography. Herein we present the first known non-affinity purification method for two S constructs, S_dF_2P and HexaPro, expressed in the mammalian cell line, CHO-DG44. A high-throughput resin screen on the Tecan Freedom EVO200 automated bioprocess workstation led to identification of ion exchange resins as viable purification steps. The chromatographic unit operations along with industry-standard methodologies for viral clearances, low pH treatment and 20 nm filtration, were assessed for feasibility. The developed process was applied to purify HexaPro from a CHO-DG44 stable pool harvest and yielded the highest yet reported amount of pure S protein. Our results demonstrate that commercially available chromatography resins are suitable for cGMP manufacturing of SARS-CoV-2 Spike protein constructs. We anticipate our results will provide a blueprint for worldwide biopharmaceutical production laboratories, as well as a starting point for process intensification.
Analysis of gut microbiome profiles in common marmosets (Callithrix jacchus) in health and intestinal disease
Authors: Sheh Alexander , Artim Stephen C. , Burns Monika A. , Molina-Mora Jose Arturo , Lee Mary Anne , Dzink-Fox JoAnn , Muthupalani Sureshkumar , Fox James G. 
Published: March 2022

AbstractChronic gastrointestinal (GI) diseases are the most common diseases in captive common marmosets. To understand the role of the microbiome in GI diseases, we characterized the gut microbiome of 91 healthy marmosets (303 samples) and 59 marmosets diagnosed with inflammatory bowel disease (IBD) (200 samples). Healthy marmosets exhibited “humanized,”Bacteroidetes-dominant microbiomes. After up to 2 years of standardized diet, housing and husbandry, marmoset microbiomes could be classified into four distinct marmoset sources based onPrevotellaandBacteroideslevels. Using a random forest (RF) model, marmosets were classified by source with an accuracy of 93% with 100% sensitivity and 95% specificity using abundance data from 4Prevotellaceaeamplicon sequence variants (ASVs), as well as single ASVs fromCoprobacter, Parabacteroides, Paraprevotella, Phascolarctobacterium, OribacteriumandFusobacterium.A single dysbiotic IBD state was not found across all marmoset sources, but IBD was associated with lower alpha diversity and a lowerBacteroides:Prevotella copriratio within each source. IBD was highest in aPrevotella-dominant cohort, and consistent withPrevotella-linked diseases, pro-inflammatory genes in the jejunum were upregulated. RF analysis of serum biomarkers identified serum calcium, hemoglobin and red blood cell (RBC) counts as potential biomarkers for marmoset IBD. This study characterizes the microbiome of healthy captive common marmosets and demonstrates that source-specific microbiomes can be retained despite standardized diets and husbandry practices. Marmosets with IBD had decreased alpha diversity and a shift in the ratio ofBacteroides:Prevotella copricompared to healthy marmosets.
Cardiovascular imaging following perioperative myocardial infarction/injury
Authors: Arslani Ketina , Gualandro Danielle M. , Puelacher Christian , Lurati Buse Giovanna , Lampart Andreas , Bolliger Daniel , Schulthess David , Glarner Noemi , Hidvegi Reka , Kindler Christoph , Blum Steffen , Cardozo Francisco A. M. , Caramelli Bruno , Gürke Lorenz , Wolff Thomas , Mujagic Edin , Schaeren Stefan , Rikli Daniel , Campos Carlos A. , Fahrni Gregor , Kaufmann Beat A. , Haaf Philip , Zellweger Michael J. , Kaiser Christoph , Osswald Stefan , Steiner Luzius A. , Mueller Christian ,   BASEL-PMI Investigators, Gueckel Johanna , Liffert Marcel , Kanhouche Gabriel , Sazgary Lorraine , Yu Pai C. , Prepoudis Alexandra , Shrestha Samyut , Lopez-Ayala Pedro , Freese Michael , Mitrovic Sandra , Rentsch Katharina , Hammerer-Lerchner Angelika 
Published: March 2022

AbstractPatients developing perioperative myocardial infarction/injury (PMI) have a high mortality. PMI work-up and therapy remain poorly defined. This prospective multicenter study included high-risk patients undergoing major non-cardiac surgery within a systematic PMI screening and clinical response program. The frequency of cardiovascular imaging during PMI work-up and its yield for possible type 1 myocardial infarction (T1MI) was assessed. Automated PMI detection triggered evaluation by the treating physician/cardiologist, who determined selection/timing of cardiovascular imaging. T1M1 was considered with the presence of a new wall motion abnormality within 30 days in transthoracic echocardiography (TTE), a new scar or ischemia within 90 days in myocardial perfusion imaging (MPI), and Ambrose-Type II or complex lesions within 7 days of PMI in coronary angiography (CA). In patients with PMI, 21% (268/1269) underwent at least one cardiac imaging modality. TTE was used in 13% (163/1269), MPI in 3% (37/1269), and CA in 5% (68/1269). Cardiology consultation was associated with higher use of cardiovascular imaging (27% versus 13%). Signs indicative of T1MI were found in 8% of TTE, 46% of MPI, and 63% of CA. Most patients with PMI did not undergo any cardiovascular imaging within their PMI work-up. If performed, MPI and CA showed high yield for signs indicative of T1MI.Trial registration:https://clinicaltrials.gov/ct2/show/NCT02573532.
Radiomics analysis based on CT’s greater omental caking for predicting pathological grading of pseudomyxoma peritonei
Authors: Zhou Nan , Dou Ruixue , Zhai Xichao , Fang Jingyang , Wang Jiajun , Ma Ruiqing , Xu Jingxu , Cui Bin , Liang Lei 
Published: March 2022

AbstractThe objective of this study was to predict the preoperative pathological grading and survival period of Pseudomyxoma peritonei (PMP) by establishing models, including a radiomics model with greater omental caking as the imaging observation index, a clinical model including clinical indexes, and a combined model of these two. A total of 88 PMP patients were selected. Clinical data of patients, including age, sex, preoperative serum tumor markers [CEA, CA125, and CA199], survival time, and preoperative computed tomography (CT) images were analyzed. Three models (clinical model, radiomics model and combined model) were used to predict PMP pathological grading. The models’ diagnostic efficiency was compared and analyzed by building the receiver operating characteristic (ROC) curve. Simultaneously, the impact of PMP’s different pathological grades was evaluated. The results showed that the radiomics model based on the CT’s greater omental caking, an area under the ROC curve ([AUC] = 0.878), and the combined model (AUC = 0.899) had diagnostic power for determining PMP pathological grading. The imaging radiomics model based on CT greater omental caking can be used to predict PMP pathological grading, which is important in the treatment selection method and prognosis assessment.
Association between urine and serum estradiol levels in in vitro fertilization cycles
Authors: Chotboon Chokchai , Salang Lingling , Buppasiri Pranom , Amnatbuddee Siriruthai , Eamudomkarn Nuntasiri 
Published: March 2022

AbstractTo study the correlation between urine and serum estradiol (E2) controlled ovarian hyperstimulation (COH). This is a cross-sectional analytical study that was conducted in a tertiary care hospital. Seventy-seven urine and blood samplings were collected from infertile women who were treated with COH. An electrochemiluminescent immunoassay was performed to evaluate E2 levels between urine and serum samples on the 6th day and the day of ovarian trigger. In addition, the correlations were evaluated between urine E2 level and number of follicles, retrieved, metaphase II oocytes, and fertilization rate. A sub-analysis was performed for age, responding status and BMI. Seventy-seven infertile women were recruited. The medians of serum and urine E2 level levels on the day 6th of ovarian stimulation were 833.20 pg/ml (IQR; 516.90–1371.00) and 3.67 (IQR; 2.84–4.81), respectively. On the day of ovarian trigger, the median of serum E2 level was 2113.00 pg/ml (IQR; 1382.00–3885.00) and urine E2 level (E2/creatinine) was 6.84 (IQR; 5.34–8.70). The correlation between serum and urine E2 level on day 6th was 0.53 and the day of ovarian trigger was 0.59, p < 0.001. Moreover, the correlations of urine E2 level on the day of ovarian trigger to number of follicles, number of oocytes retrieved, metaphase II oocytes and fertilization rate were 0.57, 0.58, 0.61, and 0.64 (p < 0.001). The urine E2 level was moderately correlated to serum E2, number of follicles growth, oocytes retrieved and fertilization rate.
Cell segmentation for immunofluorescence multiplexed images using two-stage domain adaptation and weakly labeled data for pre-training
Authors: Han Wenchao , Cheung Alison M. , Yaffe Martin J. , Martel Anne L. 
Published: March 2022

AbstractCellular profiling with multiplexed immunofluorescence (MxIF) images can contribute to a more accurate patient stratification for immunotherapy. Accurate cell segmentation of the MxIF images is an essential step. We propose a deep learning pipeline to train a Mask R-CNN model (deep network) for cell segmentation using nuclear (DAPI) and membrane (Na+K+ATPase) stained images. We used two-stage domain adaptation by first using a weakly labeled dataset followed by fine-tuning with a manually annotated dataset. We validated our method against manual annotations on three different datasets. Our method yields comparable results to the multi-observer agreement on an ovarian cancer dataset and improves on state-of-the-art performance on a publicly available dataset of mouse pancreatic tissues. Our proposed method, using a weakly labeled dataset for pre-training, showed superior performance in all of our experiments. When using smaller training sample sizes for fine-tuning, the proposed method provided comparable performance to that obtained using much larger training sample sizes. Our results demonstrate that using two-stage domain adaptation with a weakly labeled dataset can effectively boost system performance, especially when using a small training sample size. We deployed the model as a plug-in to CellProfiler, a widely used software platform for cellular image analysis.