bluuebunny/crossref_metadata_2025 huggingface dataset:
Landfast Ice and Coastal Wave Exposure in Northern Alaska
Authors: Hošeková Lucia , Eidam Emily , Panteleev Gleb , Rainville Luc , Rogers W. Erick , Thomson Jim
Published: November 2021

Observations of ocean surface waves at three sites along the northern coast of Alaska show a strong correlation with seasonal sea ice patterns. In the winter, ice cover is complete, and waves are absent. In the spring and early summer, sea ice retreats regionally, but landfast ice persists near the coast. The landfast ice completely attenuates waves formed farther offshore in the open water, causing up to a two‐month delay in the onset of waves near shore. In autumn, landfast ice begins to reform, though the wave attenuation is only partial due to lower ice thickness compared to spring. The annual cycle in the observations is reproduced by the ERA5 reanalysis product, but the product does not resolve landfast ice. The resulting ERA5 bias in coastal wave exposure can be corrected by applying a higher‐resolution ice mask, and this has a significant effect on the long‐term trends inferred from ERA5.
Capillary Heterogeneity Linked to Methane Lateral Migration in Shallow Unconfined Aquifers
Authors: Ershadnia Reza , Wallace Corey D. , Hosseini Seyyed Abolfazl , Dai Zhenxue , Soltanian Mohamad Reza
Published: November 2021

We investigate mechanisms that enhance lateral methane (CH4) plume migration in shallow aquifers that exhibit complex and multiscale sedimentary architecture. We show how heterogeneity in capillary pressure characteristics related to the sedimentary architecture causes gaseous CH4 to spread over larger areas by retarding, deviating, or blocking upward buoyancy‐driven CH4 migration. Simplifying or ignoring capillary pressure heterogeneity thus leads to overestimation of leaked CH4 to the atmosphere, and underestimation of mobile gaseous CH4 in aquifer. We show, both qualitatively and quantitatively, that meter‐scale sedimentary stratification contributes more to CH4 plume migration than the millimeter‐ and centimeter‐scale strata comprising them. Results indicate that the extent of gaseous CH4 leakage, and its associated impacts on groundwater quality and global warming, cannot be accurately assessed unless the sedimentary architecture and resulting heterogeneity in capillary pressure are represented.
A Simulation Study on the New Transport Pathways of Global Tropopause Dust Layer
Authors: Zhu Qingzhe , Liu Yuzhi , Shao Tianbin , Luo Run , Tan Ziyuan
Published: November 2021

Previous study of the tropopause aerosol layer is focused on the region surrounding the Tibetan Plateau. However, other transport pathways of the tropopause aerosol layer remain unclear. In this study, by simulating the dusts from different dust sources individually, we detected the Ethiopian Plateau and the Rocky Mountains are two new transport pathways of the global tropopause dust layer (GTDL). In addition, the contributions of different dust sources to the GTDL were quantified, the mass concentration percentage of dusts originating from Indian Peninsula in the GTDL at 100 hPa is 31.5%, which is the largest, followed by those of dusts from Middle East and Northwestern East Asia, dusts from North Africa contribute 17.3% to the GTDL at 100 hPa, which is the smallest. Our results demonstrate the existence of multiple transport pathways of the tropopause aerosol layer and clearly provide the contributions of each dust source to the GTDL.
Groundwater Affects the Geomorphic and Hydrologic Properties of Coevolved Landscapes
Authors: Litwin David G. , Tucker Gregory E. , Barnhart Katherine R. , Harman Ciaran J.
Published: November 2021

The hydrologic dynamics and geomorphic evolution of watersheds are intimately coupled—runoff generation and water storage are controlled by topography and properties of the surface and subsurface, while also affecting the evolution of those properties over geologic time. However, the large disparity between their timescales has made it difficult to examine interdependent controls on emergent hydrogeomorphic properties, such as hillslope length, drainage density, and extent of surface saturation. In this study, we develop a new model coupling hydrology and landscape evolution to explore how runoff generation affects long‐term catchment evolution, and analyze numerical results using a nondimensional scaling framework. We focus on hydrologic processes dominating in humid climates where storm runoff primarily arises from shallow subsurface flow and from precipitation on saturated areas. The model solves hydraulic groundwater equations to predict the water‐table elevation given prescribed, constant groundwater recharge. Water in excess of the subsurface capacity for transport becomes overland flow, which generates shear stress on the surface and may detach and transport sediment. This affects the landscape form that in turn affects runoff generation. We show that (a) four dimensionless parameters describe the possible steady state landscapes that coevolve under steady recharge; (b) hillslope length increases with increasing transmissivity relative to the recharge rate; (c) three topographic metrics—steepness index, Laplacian curvature, and topographic index—together provide a basis for interpreting landscapes that have coevolved with runoff generated via shallow subsurface flow. Finally we discuss the possibilities and limitations for quantitative comparisons between the model results and real landscapes.
Assessing the Role of Photochemistry in Driving the Composition of Dissolved Organic Matter in Glacier Runoff
Authors: Holt Amy D. , Kellerman Anne M. , Li Wenbo , Stubbins Aron , Wagner Sasha , McKenna Amy , Fellman Jason , Hood Eran , Spencer Robert G. M.
Published: November 2021

Dissolved organic matter (DOM) in glacier runoff is aliphatic‐rich, yet studies have proposed that DOM originates mainly from allochthonous, aromatic, and often aged material. Allochthonous organic matter (OM) is exposed to ultraviolet radiation both in atmospheric transport and post‐deposition on the glacier surface. Thus, we evaluate photochemistry as a mechanism to account for the compositional disconnect between allochthonous OM sources and glacier runoff DOM composition. Six endmember OM sources (including soils and diesel particulate matter) were leached and photo‐irradiated for 28 days in a solar simulator, until >90% of initial chromophoric DOM was removed. Ultrahigh‐resolution mass spectrometry was used to compare the molecular composition of endmember leachates pre‐ and post‐irradiation to DOM in supraglacial and bulk runoff from the Greenland Ice Sheet and Juneau Icefield (Alaska), respectively. Photo‐irradiation drove molecular level convergence between the initially aromatic‐rich leachates and aromatic‐poor glacial samples, selectively removing aromatic compounds (−80 ± 19% relative abundance) and producing aliphatics (+75 ± 35% relative abundance). Molecular level glacier runoff DOM composition was statistically indistinguishable to post‐irradiation leachates. Bray‐Curtis analysis showed substantial similarity in the molecular formulae present between glacier samples and post‐irradiation leachates. Post‐irradiation leachates contained 84 ± 7.4% of the molecular formulae, including 72 ± 17% of the aliphatic formulae, detected in glacier samples. Our findings suggest that photodegradation, either in transit to or on glacier surfaces, could provide a mechanistic pathway to account for the disconnect between proposed aromatic, aged sources of OM and the aliphatic‐rich fingerprint of glacial DOM.
The development of microfabricated solenoids with magnetic cores for micromagnetic neural stimulation
Authors: Khalifa Adam , Zaeimbashi Mohsen , Zhou Tony X. , Abrishami Seyed Mahdi , Sun Neville , Park Seunghyun , Šumarac Tamara , Qu Jason , Zohar Inbar , Yacoby Amir , Cash Sydney , Sun Nian X.
Published: November 2021

Electrical stimulation via invasive microelectrodes is commonly used to treat a wide range of neurological and psychiatric conditions. Despite its remarkable success, the stimulation performance is not sustainable since the electrodes become encapsulated by gliosis due to foreign body reactions. Magnetic stimulation overcomes these limitations by eliminating the need for a metal-electrode contact. Here, we demonstrate a novel microfabricated solenoid inductor (80 µm × 40 µm) with a magnetic core that can activate neuronal tissue. The characterization and proof-of-concept of the device raise the possibility that micromagnetic stimulation solenoids that are small enough to be implanted within the brain may prove to be an effective alternative to existing electrode-based stimulation devices for chronic neural interfacing applications.
Mutant p53 elicits context-dependent pro-tumorigenic phenotypes
Authors: McCann Jennifer J. , Vasilevskaya Irina A. , McNair Christopher , Gallagher Peter , Neupane Neermala Poudel , de Leeuw Renée , Shafi Ayesha A. , Dylgjeri Emanuela , Mandigo Amy C. , Schiewer Matthew J. , Knudsen Karen E.
Published: November 2021

The tumor suppressor geneTP53is the most frequently mutated gene in numerous cancer types, including prostate cancer (PCa). Specifically, missense mutations inTP53are selectively enriched in PCa, and cluster to particular “hot spots” in the p53 DNA binding domain with mutation at the R273 residue occurring most frequently. While this residue is similarly mutated to R273C-p53 or R273H-p53 in all cancer types examined, in PCa selective enrichment of R273C-p53 is observed. Importantly, examination of clinical datasets indicated thatTP53heterozygosity can either be maintained or loss of heterozygosity (LOH) occurs. Thus, to mimic tumor-associated mutant p53, R273C-p53 and R273H-p53 isogenic PCa models were developed in the presence or absence of wild-type p53. In the absence of wild-type p53, both R273C-p53 and R273H-p53 exhibited similar loss of DNA binding, transcriptional profiles, and loss of canonical tumor suppressor functions associated with wild-type p53. In the presence of wild-type p53 expression, both R273C-p53 and R273H-p53 supported canonical p53 target gene expression yet elicited distinct cistromic and transcriptional profiles when compared to each other. Moreover, heterozygous modeling of R273C-p53 or R273H-p53 expression resulted in distinct phenotypic outcomes in vitro and in vivo. Thus, mutant p53 acts in a context-dependent manner to elicit pro-tumorigenic transcriptional profiles, providing critical insight into mutant p53-mediated prostate cancer progression.
(R,S)-ketamine and (2R,6R)-hydroxynorketamine differentially affect memory as a function of dosing frequency
Authors: Riggs Lace M. , An Xiaoxian , Pereira Edna F. R. , Gould Todd D.
Published: November 2021

A single subanesthetic infusion of ketamine can rapidly alleviate symptoms of treatment-resistant major depression. Since repeated administration is required to sustain symptom remission, it is important to characterize the potential untoward effects of prolonged ketamine exposure. While studies suggest that ketamine can alter cognitive function, it is unclear to what extent these effects are modulated by the frequency or chronicity of treatment. To test this, male and female adolescent (postnatal day [PD] 35) and adult (PD 60) BALB/c mice were treated for four consecutive weeks, either daily or thrice-weekly, with (R,S)-ketamine (30 mg/kg, intraperitoneal) or its biologically active metabolite, (2R,6R)-hydroxynorketamine (HNK; 30 mg/kg, intraperitoneal). Following drug cessation, memory performance was assessed in three operationally distinct tasks: (1) novel object recognition to assess explicit memory, (2) Y-maze to assess working memory, and (3) passive avoidance to assess implicit memory. While drug exposure did not influence working memory performance, thrice-weekly ketamine and daily (2R,6R)-HNK led to explicit memory impairment in novel object recognition independent of sex or age of exposure. Daily (2R,6R)-HNK impaired implicit memory in the passive-avoidance task whereas thrice-weekly (2R,6R)-HNK tended to improve it. These differential effects on explicit and implicit memory possibly reflect the unique mechanisms by which ketamine and (2R,6R)-HNK alter the functional integrity of neural circuits that subserve these distinct cognitive domains, a topic of clinical and mechanistic relevance to their antidepressant actions. Our findings also provide additional support for the importance of dosing frequency in establishing the cognitive effects of repeated ketamine exposure.
The m6A “reader” YTHDF1 promotes osteogenesis of bone marrow mesenchymal stem cells through translational control of ZNF839
Authors: Liu Tao , Zheng Xinfeng , Wang Chenglong , Wang Chuandong , Jiang Shengdan , Li Bo , Chen Pengbo , Xu Wenning , Zheng Huoliang , Yang Runze , Huang Xingxu , Zhang Xiaoling , Jiang Leisheng
Published: November 2021

N6-methyladenosine (m6A) is required for differentiation of human bone marrow mesenchymal stem cells (hBMSCs). However, its intrinsic mechanisms are largely unknown. To identify the possible role of m6A binding protein YTHDF1 in hBMSCs osteogenesis in vivo, we constructed Ythdf1 KO mice and showed that depletion of Ythdf1 would result in decreased bone mass in vivo. Both deletion of Ythdf1 in mouse BMSCs and shRNA-mediated knockdown of YTHDF1 in hBMSCs prevented osteogenic differentiation of cells in vitro. Using methylated RNA immunoprecipitation (Me-RIP) sequencing and RIP-sequencing, we found that ZNF839 (a zinc finger protein) served as a target of YTHDF1. We also verified its mouse homolog, Zfp839, was translationally regulated by Ythdf1 in an m6A-dependent manner. Zfp839 potentiated BMSC osteogenesis by interacting with and further enhancing the transcription activity of Runx2. These findings should improve our understanding of the mechanism of BMSC osteogenesis regulation and provide new ideas for the prevention and treatment of osteoporosis.
Impact of high energy oral nutritional supplements consumed in the late afternoon on appetite, energy intake and cardio-metabolic risk factors in females with lower BMI
Authors: Fatima Sadia , Gerasimidis Konstantinos , Wright Charlotte , Malkova Dalia
Published: November 2021

Background/Objective

Morning consumption of a single dose of high-energy oral nutritional supplement (ONS) in females with a lower BMI displaces some of the food eaten at breakfast but increases overall daily energy intake. This study investigated the effectiveness of ONS intake in the late afternoon and for longer duration.

Subjects/Methods

Twenty-one healthy females (mean ± SD, age 25 ± 5 years; BMI 18.7 ± 1.2 kg/m2) participated in a randomised, crossover study with two experimental trials. In the afternoon of days 1–5, participants consumed either ONS (2.510 MJ) or low-energy PLACEBO drink (0.377 MJ) and recorded food eaten at home. On day six, energy intake was measured during buffet meals, and energy expenditure, appetite measurements and blood samples were collected throughout the day.

Result

Over the 5-day period, in the ONS trial energy intake from evening meals was lower (ONS, 2.7 ± 0.25 MJ; Placebo, 3.6 ± 0.25 MJ, P = 0.01) but averaged total daily energy intake was higher (ONS, 9.2 ± 0.3 MJ; PLACEBO, 8.2 ± 0.4 MJ, P = 0.03). On day six, energy intake, appetite scores, plasma GLP-1 and PYY, and energy expenditure were not significantly different between the two trials but fasting insulin concentration and HOMAIR, were higher (P < 0.05) and insulin sensitivity score based on fasting insulin and TAG lower (P < 0.05) in ONS trial.

Conclusion

Late afternoon consumption of ONS for five consecutive days by females with a lower BMI has only a partial and short-lived energy intake suppression and thus increases daily energy intake but reduces insulin sensitivity.
Burdens of post-acute sequelae of COVID-19 by severity of acute infection, demographics and health status
Authors: Xie Yan , Bowe Benjamin , Al-Aly Ziyad
Published: November 2021

The Post-Acute Sequelae of SARS-CoV-2 infection (PASC) have been characterized; however, the burden of PASC remains unknown. Here we used the healthcare databases of the US Department of Veterans Affairs to build a cohort of 181,384 people with COVID-19 and 4,397,509 non-infected controls and estimated that burden of PASC—defined as the presence of at least one sequela in excess of non-infected controls—was 73.43 (72.10, 74.72) per 1000 persons at 6 months. Burdens of individual sequelae varied by demographic groups (age, race, and sex) but were consistently higher in people with poorer baseline health and in those with more severe acute infection. In sum, the burden of PASC is substantial; PASC is non-monolithic with sequelae that are differentially expressed in various population groups. Collectively, our results may be useful in informing health systems capacity planning and care strategies of people with PASC.
Nuclear and cytoplasmic huntingtin inclusions exhibit distinct biochemical composition, interactome and ultrastructural properties
Authors: Riguet Nathan , Mahul-Mellier Anne-Laure , Maharjan Niran , Burtscher Johannes , Croisier Marie , Knott Graham , Hastings Janna , Patin Alice , Reiterer Veronika , Farhan Hesso , Nasarov Sergey , Lashuel Hilal A.
Published: November 2021

Despite the strong evidence linking the aggregation of the Huntingtin protein (Htt) to the pathogenesis of Huntington’s disease (HD), the mechanisms underlying Htt aggregation and neurodegeneration remain poorly understood. Herein, we investigated the ultrastructural properties and protein composition of Htt cytoplasmic and nuclear inclusions in mammalian cells and primary neurons overexpressing mutant exon1 of the Htt protein. Our findings provide unique insight into the ultrastructural properties of cytoplasmic and nuclear Htt inclusions and their mechanisms of formation. We show that Htt inclusion formation and maturation are complex processes that, although initially driven by polyQ-dependent Htt aggregation, also involve the polyQ and PRD domain-dependent sequestration of lipids and cytoplasmic and cytoskeletal proteins related to HD dysregulated pathways; the recruitment and accumulation of remodeled or dysfunctional membranous organelles, and the impairment of the protein quality control and degradation machinery. We also show that nuclear and cytoplasmic Htt inclusions exhibit distinct biochemical compositions and ultrastructural properties, suggesting different mechanisms of aggregation and toxicity.
Long-lived Paleoproterozoic eclogitic lower crust
Authors: Buntin Sebastian , Artemieva Irina M. , Malehmir Alireza , Thybo Hans , Malinowski Michal , Högdahl Karin , Janik Tomasz , Buske Stefan
Published: November 2021

The nature of the lower crust and the crust-mantle transition is fundamental to Earth sciences. Transformation of lower crustal rocks into eclogite facies is usually expected to result in lower crustal delamination. Here we provide compelling evidence for long-lasting presence of lower crustal eclogite below the seismic Moho. Our new wide-angle seismic data from the Paleoproterozoic Fennoscandian Shield identify a 6–8 km thick body with extremely high velocity (Vp ~ 8.5–8.6 km/s) and high density (>3.4 g/cm3) immediately beneath equally thinned high-velocity (Vp ~ 7.3–7.4 km/s) lowermost crust, which extends over >350 km distance. We relate this observed structure to partial (50–70%) transformation of part of the mafic lowermost crustal layer into eclogite facies during Paleoproterozoic orogeny without later delamination. Our findings challenge conventional models for the role of lower crustal eclogitization and delamination in lithosphere evolution and for the long-term stability of cratonic crust.
Van der Waals ferromagnetic Josephson junctions
Authors: Ai Linfeng , Zhang Enze , Yang Jinshan , Xie Xiaoyi , Yang Yunkun , Jia Zehao , Zhang Yuda , Liu Shanshan , Li Zihan , Leng Pengliang , Cao Xiangyu , Sun Xingdan , Zhang Tongyao , Kou Xufeng , Han Zheng , Xiu Faxian , Dong Shaoming
Published: November 2021

Superconductor-ferromagnet interfaces in two-dimensional heterostructures present a unique opportunity to study the interplay between superconductivity and ferromagnetism. The realization of such nanoscale heterostructures in van der Waals (vdW) crystals remains largely unexplored due to the challenge of making atomically-sharp interfaces from their layered structures. Here, we build a vdW ferromagnetic Josephson junction (JJ) by inserting a few-layer ferromagnetic insulator Cr2Ge2Te6 into two layers of superconductor NbSe2. The critical current and corresponding junction resistance exhibit a hysteretic and oscillatory behavior against in-plane magnetic fields, manifesting itself as a strong Josephson coupling state. Also, we observe a central minimum of critical current in some JJ devices as well as a nontrivial phase shift in SQUID structures, evidencing the coexistence of 0 and π phase in the junction region. Our study paves the way to exploring sensitive probes of weak magnetism and multifunctional building-blocks for phase-related superconducting circuits using vdW heterostructures.
The effects of ideological value framing and symbolic racism on pro-environmental behavior
Authors: Makovi Kinga , Kasak-Gliboff Hannah
Published: November 2021

Environmental degradation continues to be one of the greatest threats to human well-being, posing a disproportionate burden on communities of color. Environmental action, however, fails to reflect this urgency, leaving social-behavioral research at the frontier of environmental conservation, as well as environmental justice. Broad societal consensus for environmental action is particularly sparse among conservatives. The lack of even small personal sacrifices in favor of the environment could be attributed to the relatively low salience of environmental threats to white Americans and the partisan nature of environmentalism in America. We evaluate if (1) environmental action is causally related to the ideological value framing of an environmental issue; and (2) if the perceived race of impacted communities influences environmental action as a function of racial resentment. With this large-scale, original survey experiment examining the case of air-pollution, we find weak support for the first, but we do not find evidence for the second. We advance our understanding of environmental justice advocacy and environmental inaction in the United States.

Protocol registration

The stage 1 protocol for this Registered Report was accepted in principle on 10 June 2021. The protocol, as accepted by the journal, can be found at https://doi.org/10.6084/m9.figshare.14769558.
Calculation of the Gibbs–Donnan factors for multi-ion solutions with non-permeating charge on both sides of a permselective membrane
Authors: Waniewski Jacek , Pietribiasi Mauro , Pstras Leszek
Published: November 2021

Separation of two ionic solutions with a permselective membrane that is impermeable to some of the ions leads to an uneven distribution of permeating ions on the two sides of the membrane described by the Gibbs–Donnan (G–D) equilibrium with the G–D factors relating ion concentrations in the two solutions. Here, we present a method of calculating the G–D factors for ideal electroneutral multi-ion solutions with different total charge of non-permeating species on each side of a permselective membrane separating two compartments. We discuss some special cases of G–D equilibrium for which an analytical solution may be found, and we prove the transitivity of G–D factors for multi-ion solutions in several compartments interconnected by permselective membranes. We show a few examples of calculation of the G–D factors for both simple and complex solutions, including the case of human blood plasma and interstitial fluid separated by capillary walls. The article is accompanied by an online tool that enables the calculation of the G–D factors and the equilibrium concentrations for multi-ion solutions with various composition in terms of permeating ions and non-permeating charge, according to the presented method.
The influence of rainfall and tillage on wheat yield parameters and weed population in monoculture versus rotation systems
Authors: Gandía María Luisa , Del Monte Juan Pablo , Tenorio José Luis , Santín-Montanyá María Inés
Published: November 2021

Extreme climate events (ECEs) of drought are becoming common in Mediterranean areas and farmers need adapt agricultural practices to achieve sustainability. This field study took place in to gain insight into the effects of seasonal rainfall, tillage and crop systems on wheat yield and weed parameters. Conventional (CT), minimum (MT) and no-tillage (NT) systems in wheat monoculture and rotation cropping systems were tested during 3 years of study (2014–2015, 2015–2016 and 2016–2017). Growing Season Rainfall (GSR) was the most influential factor on yield parameters and weed population. In 2016–2017, categorized as an extreme climate event by drought, the GSR accounted for 43.4% of the historical average. This year, the wheat yield (373 kg ha−1) and harvest index (0.18) were the lowest. In 2015–2016, scarcer autumn rainfall (44 mm) affected the weed germination period, reducing the density (17 plants m−2) and diversity of weed species (3 species m−2) while yield was favoured by high winter and spring rainfall (247 mm). Our study revealed that tillage effects was not significant on wheat yield, but NT systems consistently showed higher weed density and diversity than CT and MT despite the irregular GSR during this study. The rotation system presented higher values of wheat grain yield (781 kg/ha) and dry straw biomass (1803 kg/ha) but also weed biomass (48.54 g m−2) compared to monoculture (27.50 g m−2). NT and rotation combined increased the weed community although did not reduce the wheat yield compare to conventional systems even with an ECE of drought.
Clinical characteristics and outcomes for patients with non‑metastatic castration-resistant prostate cancer
Authors: Arnold Peter , Penaloza-Ramos Maria Cristina , Adedokun Lola , Rees Sarah , Lockhat Mohamed , Spary Lisa , Watkins Alan , Gnanapragasam Vincent , Crabb Simon J.
Published: November 2021

This study used linked, routinely-collected datasets to explore incidence, clinical characteristics and outcomes of prostate cancer (PC) patients who experience a rise in prostate-specific antigen (PSA) levels despite androgen deprivation therapy (ADT), without evidence of metastases in their patient record, termed non-metastatic castration-resistant PC (nmCRPC). Routinely collected administrative data in Wales were used to identify patients diagnosed with PC and nmCRPC from 2000–2015. Logrank tests and Cox proportional hazard models were used to compare time-to-events across subgroups defined by PSA doubling time and age. Of 38,021 patients identified with PC, 1,465 met nmCRPC criteria. PC incidence increased over the study period, while nmCRPC categorizations reduced. Median time from PC diagnosis to nmCRPC categorization was 3.07 years (95% confidence interval [CI] 2.91–3.26) and from nmCRPC categorization to metastases/death was 2.86 years (95% CI 2.67–3.09). Shorter PSA doubling time (≤ 10 months, versus > 10 months) was associated with reduced time to metastases or death (2.11 years [95% CI 1.92–2.30] versus 5.22 years [95% CI 4.87–5.51]). Age was not significantly associated with time to metastases/death. Our findings highlight key clinical characteristics and outcomes for patients with nmCRPC prior to the introduction of recently approved treatments.
Automatic vertebrae localization and segmentation in CT with a two-stage Dense-U-Net
Authors: Cheng Pengfei , Yang Yusheng , Yu Huiqiang , He Yongyi
Published: November 2021

Automatic vertebrae localization and segmentation in computed tomography (CT) are fundamental for spinal image analysis and spine surgery with computer-assisted surgery systems. But they remain challenging due to high variation in spinal anatomy among patients. In this paper, we proposed a deep-learning approach for automatic CT vertebrae localization and segmentation with a two-stage Dense-U-Net. The first stage used a 2D-Dense-U-Net to localize vertebrae by detecting the vertebrae centroids with dense labels and 2D slices. The second stage segmented the specific vertebra within a region-of-interest identified based on the centroid using 3D-Dense-U-Net. Finally, each segmented vertebra was merged into a complete spine and resampled to original resolution. We evaluated our method on the dataset from the CSI 2014 Workshop with 6 metrics: location error (1.69 ± 0.78 mm), detection rate (100%) for vertebrae localization; the dice coefficient (0.953 ± 0.014), intersection over union (0.911 ± 0.025), Hausdorff distance (4.013 ± 2.128 mm), pixel accuracy (0.998 ± 0.001) for vertebrae segmentation. The experimental results demonstrated the efficiency of the proposed method. Furthermore, evaluation on the dataset from the xVertSeg challenge with location error (4.12 ± 2.31), detection rate (100%), dice coefficient (0.877 ± 0.035) shows the generalizability of our method. In summary, our solution localized the vertebrae successfully by detecting the centroids of vertebrae and implemented instance segmentation of vertebrae in the whole spine.
Machining feature recognition based on deep neural networks to support tight integration with 3D CAD systems
Authors: Yeo Changmo , Kim Byung Chul , Cheon Sanguk , Lee Jinwon , Mun Duhwan
Published: November 2021

Recently, studies applying deep learning technology to recognize the machining feature of three-dimensional (3D) computer-aided design (CAD) models are increasing. Since the direct utilization of boundary representation (B-rep) models as input data for neural networks in terms of data structure is difficult, B-rep models are generally converted into a voxel, mesh, or point cloud model and used as inputs for neural networks for the application of 3D models to deep learning. However, the model’s resolution decreases during the format conversion of 3D models, causing the loss of some features or difficulties in identifying areas of the converted model corresponding to a specific face of the B-rep model. To solve these problems, this study proposes a method enabling tight integration of a 3D CAD system with a deep neural network using feature descriptors as inputs to neural networks for recognizing machining features. Feature descriptor denotes an explicit representation of the main property items of a face. We constructed 2236 data to train and evaluate the deep neural network. Of these, 1430 were used for training the deep neural network, and 358 were used for validation. And 448 were used to evaluate the performance of the trained deep neural network. In addition, we conducted an experiment to recognize a total of 17 types (16 types of machining features and a non-feature) from the B-rep model, and the types for all 75 test cases were successfully recognized.
Isolation, phenotypic characterization and comparative genomic analysis of 2019SD1, a polyvalent enterobacteria phage
Authors: Kumar Prince , Meghvansi Mukesh K. , Kamboj D. V.
Published: November 2021

Shigellahas the remarkable capability to acquire antibiotic resistance rapidly thereby posing a significant public health challenge for the effective treatment of dysentery (Shigellosis). The phage therapy has been proven as an effective alternative strategy for controllingShigellainfections. In this study, we illustrate the isolation and detailed characterization of a polyvalent phage 2019SD1, which demonstrates lytic activity againstShigella dysenteriae,Escherichia coli, Vibrio cholerae, Enterococcus saccharolyticusandEnterococcus faecium.The newly isolated phage 2019SD1 shows adsorption time < 6 min, a latent period of 20 min and burst size of 151 PFU per bacterial cell. 2019SD1 exhibits considerable stability in a wide pH range and survives an hour at 50 °C. Under transmission electron microscope, 2019SD1 shows an icosahedral capsid (60 nm dia) and a 140 nm long tail. Further, detailed bioinformatic analyses of whole genome sequence data obtained through Oxford Nanopore platform revealed that 2019SD1 belongs to genusHanrivervirusof subfamilyTempevirinaeunder the familyDrexlerviridae. The concatenated protein phylogeny of 2019SD1 with the members ofDrexlerviridaetaking four genes (DNA Primase, ATP Dependent DNA Helicase, Large Terminase Protein, and Portal Protein) using the maximum parsimony method also suggested that 2019SD1 formed a distinct clade with the closest match of the taxa belonging to the genusHanrivervirus.The genome analysis data indicate the occurrence of putative tail fiber proteins and DNA methylation mechanism. In addition, 2019SD1 has a well-established anti-host defence system as suggested through identification of putative anti-CRISPR and anti-restriction endonuclease systems thereby also indicating its biocontrol potential.
Acoustic differentiation and classification of wild belugas and narwhals using echolocation clicks
Authors: Zahn Marie J. , Rankin Shannon , McCullough Jennifer L. K. , Koblitz Jens C. , Archer Frederick , Rasmussen Marianne H. , Laidre Kristin L.
Published: November 2021

Belugas (Delphinapterus leucas) and narwhals (Monodon monoceros) are highly social Arctic toothed whales with large vocal repertoires and similar acoustic profiles. Passive Acoustic Monitoring (PAM) that uses multiple hydrophones over large spatiotemporal scales has been a primary method to study their populations, particularly in response to rapid climate change and increasing underwater noise. This study marks the first acoustic comparison between wild belugas and narwhals from the same location and reveals that they can be acoustically differentiated and classified solely by echolocation clicks. Acoustic recordings were made in the pack ice of Baffin Bay, West Greenland, during 2013. Multivariate analyses and Random Forests classification models were applied to eighty-one single-species acoustic events comprised of numerous echolocation clicks. Results demonstrate a significant difference between species’ acoustic parameters where beluga echolocation was distinguished by higher frequency content, evidenced by higher peak frequencies, center frequencies, and frequency minimums and maximums. Spectral peaks, troughs, and center frequencies for beluga clicks were generally > 60 kHz and narwhal clicks < 60 kHz with overlap between 40–60 kHz. Classification model predictive performance was strong with an overall correct classification rate of 97.5% for the best model. The most important predictors for species assignment were defined by peaks and notches in frequency spectra. Our results provide strong support for the use of echolocation in PAM efforts to differentiate belugas and narwhals acoustically.
Adaptive neurons compute confidence in a decision network
Authors: Li Luozheng , Wang DaHui
Published: November 2021

Humans and many animals have the ability to assess the confidence of their decisions. However, little is known about the underlying neural substrate and mechanism. In this study we propose a computational model consisting of a group of ’confidence neurons’ with adaptation, which are able to assess the confidence of decisions by detecting the slope of ramping activities of decision neurons. The simulated activities of ’confidence neurons’ in our simple model capture the typical features of confidence observed in humans and animals experiments. Our results indicate that confidence could be online formed along with the decision formation, and the adaptation properties could be used to monitor the formation of confidence during the decision making.
Prenatal exposure to persistent organic pollutants and metals and problematic child behavior at 3–5 years of age: a Greenlandic cohort study
Authors: Kornvig Simon , Wielsøe Maria , Long Manhai , Bonefeld-Jørgensen Eva Cecilie
Published: November 2021

High levels of persistent organic pollutants (POPs) and heavy metals are found in Arctic populations. POP and heavy metals are linked to impaired cognitive development. This study examined associations between prenatal POP and metals exposure and problematic child behavior using the Strength and Difficulties Questionnaire (SDQ). POPs and metals were measured in 102 pregnant Greenlandic women. During follow-up at 3–5 years, parents answered an assisted questionnaire including children’s SDQ scores. Associations were analyzed using linear and logistic regression analyses and adjusted for maternal plasma cotinine, educational level and age at delivery. In the adjusted analyses, the medium tertile of hexachlorobenzene (β = 3.06,p = 0.010), β-hexachlorocyclohexane (β = 3.58,p = 0.004) and trans-nonachlor (β = 2.06,p = 0.082) were positively associated with SDQ scores. The continuous cis-nonachlor (OR = 1.09,p = 0.079), dichloro-diphenyl-dichloroethylene (OR = 1.01,p = 0.077), trans-nonachlor (OR = 1.01,p = 0.091), and sum Organochlorine-Pesticides (OR = 1.00,p = 0.094) were positively associated with abnormal SDQ score and the continuous mirex (OR = 1.28,p = 0.096), oxychlordane (OR = 1.04,p = 0.066), and trans-nonachlor (OR = 1.02,p = 0.071) with abnormal hyperactivity score. We found no consistent evidence of associations between polychlorinated biphenyls, perfluoroalkylated substances and heavy metals and problematic behavior. Prenatal organochlorine pesticide exposure associated significantly with problematic behavior in 3–5 year old children.
Prevalence of Toxoplasma gondii infection among small mammals in Tatarstan, Russian Federation
Authors: Shamaev Nikolai D. , Shuralev Eduard A. , Nikitin Oleg V. , Mukminov Malik N. , Davidyuk Yuriy N. , Belyaev Alexander N. , Isaeva Guzel Sh. , Ziatdinov Vasil B. , Khammadov Nail I. , Safina Regina F. , Salmanova Gaysha R. , Akhmedova Guzel M. , Khaertynov Kamil S. , Saito Taizo , Kitoh Katsuya , Takashima Yasuhiro
Published: November 2021

Toxoplasma gondii is a zoonotic parasite with a wide host range that includes humans, domestic animals and wild animals. Small mammals serve as intermediate hosts for T. gondii and may contribute to the persistence of this parasite in the environment. Mass mortality in wild animals and deaths in rare endemic species make the study of this parasite of growing importance. In this study, T. gondii infection prevalence was evaluated in brain tissues from 474 small mammals captured at 26 trapping points in urban and rural areas of Tatarstan, Russian Federation. Nested PCR was used to detect the T. gondii B1 gene in the samples. Overall, 40/474 samples (8.44%) showed B1 gene positivity. T. gondii infection among the wild small mammals trapped in the rural area was significantly higher as a whole than that of the urban area as a whole. Multivariate logistical regression analysis also showed that the trapping area (rural or urban) significantly contributed to T. gondii positivity. Vegetation in the trapping points, small mammal species, sex, age or distance from the trapping points to the nearest human settlements did not significantly affect T. gondii positivity in the sampled small mammals.
Unraveling the stepwise maturation of the yeast telomerase including a Cse1 and Mtr10 mediated quality control checkpoint
Authors: Hirsch Anna Greta , Becker Daniel , Lamping Jan-Philipp , Krebber Heike
Published: November 2021

Telomerases elongate the ends of chromosomes required for cell immortality through their reverse transcriptase activity. By using the model organism Saccharomyces cerevisiae we defined the order in which the holoenzyme matures. First, a longer precursor of the telomerase RNA, TLC1 is transcribed and exported into the cytoplasm, where it associates with the protecting Sm-ring, the Est and the Pop proteins. This partly matured telomerase is re-imported into the nucleus via Mtr10 and a novel TLC1-import factor, the karyopherin Cse1. Remarkably, while mutations in all known transport factors result in short telomere ends, mutation in CSE1 leads to the amplification of Y′ elements in the terminal chromosome regions and thus elongated telomere ends. Cse1 does not only support TLC1 import, but also the Sm-ring stabilization on the RNA enableling Mtr10 contact and nuclear import. Thus, Sm-ring formation and import factor contact resembles a quality control step in the maturation process of the telomerase. The re-imported immature TLC1 is finally trimmed into the 1158 nucleotides long mature form via the nuclear exosome. TMG-capping of TLC1 finalizes maturation, leading to mature telomerase.
The analysis of reference genes expression stability in susceptible and resistant Apera spica-venti populations under herbicide treatment
Authors: Wrzesińska Barbara , Kościelniak Karolina , Frąckowiak Patryk , Praczyk Tadeusz , Obrępalska-Stęplowska Aleksandra
Published: November 2021

Weed resistance to herbicides constitutes a serious problem to world crop production. One of the weeds that are significantly threatening the crops’ yield and quality isApera spica-venti. The target-site resistance (TSR) mechanism ofA. spica-ventihas been widely studied, though, little is known about its non-target-site resistance (NTSR) mechanisms at the molecular level. Molecular examination of NTSR is, to a great extent, based on the expression profiles of selected genes, e.g. those participating in detoxification. However, to obtain reliable results of gene expression analysis, the use of a normalizer is required. The aim of this study was to select the best reference genes inA. spica-ventiplants of both populations, susceptible and resistant to ALS inhibitor, under treatment with herbicide. Eleven housekeeping genes were chosen for their expression stability assessment. The efficiency correction of raw quantification cycles (Cq) was included in the gene expression stability analyses, which resulted in indicating the TATA-box binding protein (TBP), glyceraldehyde-3-phosphate dehydrogenase, cytosolic (GAPC), and peptidyl-prolylcis–transisomerase CYP28 (CYP28) genes as the most stably expressed reference genes. The obtained results are of vital importance for future studies on the expression of genes associated with the non-target-site resistance mechanisms in theA. spica-ventipopulations susceptible and resistant to herbicides.
Fatigue after acquired brain injury impacts health-related quality of life: an exploratory cohort study
Authors: Åkerlund Elisabeth , Sunnerhagen Katharina S. , Persson Hanna C.
Published: November 2021

This study aimed to identify the consequences of fatigue, fatigability, cognitive and executive functioning, and emotional state on health-related quality of life (HRQoL) in a clinical group of outpatients after acquired brain injury (ABI). This cross-sectional retrospective study included assessing outpatients at a rehabilitation clinic with WAIS-III working memory and coding subtests, and self-rating scales (Fatigue Impact Scale, Dysexecutive Questionnaire, Hospital Anxiety and Depression Scale, and the dimension of health-related quality of life from EQ-5D-3L). The predictive variables were investigated using a binary logistic regression with HRQoL as the dependent variable. Descriptive statistics and correlations were analyzed. Participants reported a lower than average HRQoL (95%), fatigue (90%), and executive dysfunction (75%). Fatigue had a significant impact and explained 20–33% of the variance in HRQoL with a moderate significance on depression (p = 0.579) and executive dysfunction (p = 0.555). Cognitive and executive function and emotional state showed no association with HRQoL. A lower HRQoL, as well as fatigue and cognitive and executive dysfunctions, are common after ABI, with fatigue is a partial explanation of a lower HRQoL.
Path to net zero is critical to climate outcome
Authors: Sun Tianyi , Ocko Ilissa B. , Sturcken Elizabeth , Hamburg Steven P.
Published: November 2021

Net zero greenhouse gas targets have become a central element for climate action. However, most company and government pledges focus on the year that net zero is reached, with limited awareness of how critical the emissions pathway is in determining the climate outcome in both the near- and long-term. Here we show that different pathways of carbon dioxide and methane—the most prominent long-lived and short-lived greenhouse gases, respectively—can lead to nearly 0.4 °C of warming difference in midcentury and potential overshoot of the 2 °C target, even if they technically reach global net zero greenhouse gas emissions in 2050. While all paths achieve the Paris Agreement temperature goals in the long-term, there is still a 0.2 °C difference by end-of-century. We find that early action to reduce both emissions of carbon dioxide and methane simultaneously leads to the best climate outcomes over all timescales. We therefore recommend that companies and countries supplement net zero targets with a two-basket set of interim milestones to ensure that early action is taken for both carbon dioxide and methane. A one-basket approach, such as the standard format for Nationally Determined Contributions, is not sufficient because it can lead to a delay in methane mitigation.
Factors associated with unplanned readmissions and costs following resection of brain metastases in the United States
Authors: Tonse Raees , Townsend Alexandra , Rubens Muni , Siomin Vitaly , McDermott Michael W. , Tom Martin C. , Hall Matthew D. , Odia Yazmin , Ahluwalia Manmeet S. , Mehta Minesh P. , Kotecha Rupesh
Published: November 2021

The purpose of this study was to critically analyze the risk of unplanned readmission following resection of brain metastasis and to identify key risk factors to allow for early intervention strategies in high-risk patients. We analyzed data from the Nationwide Readmissions Database (NRD) from 2010–2014, and included patients who underwent craniotomy for brain metastasis, identified using ICD-9-CM diagnosis (198.3) and procedure (01.59) codes. The primary outcome of the study was unplanned 30-day all-cause readmission rate. Secondary outcomes included reasons and costs of readmissions. Hierarchical logistic regression model was used to identify the factors associated with 30-day readmission following craniotomy for brain metastasis. During the study period, 44,846 index hospitalizations occurred for patients who underwent resection of brain metastasis. In this cohort, 17.8% (n = 7,965) had unplanned readmissions within the first 30 days after discharge from the index hospitalization. The readmission rate did not change significantly during the five-year study period (p-trend = 0.286). The median per-patient cost for 30-day unplanned readmission was $11,109 and this amounted to a total of $26.4 million per year, which extrapolates to a national expenditure of $269.6 million. Increasing age, male sex, insurance status, Elixhauser comorbidity index, length of stay, teaching status of the hospital, neurological complications and infectious complications were associated with 30-day readmission following discharge after an index admission for craniotomy for brain metastasis. Unplanned readmission rates after resection of brain metastasis remain high and involve substantial healthcare expenditures. Developing tools and interventions to prevent avoidable readmissions could focus on the high-risk patients as a future strategy to decrease substantial healthcare expense.