bluuebunny/crossref_metadata_2025_split huggingface dataset:
Heat-induced changes in molecular biosignatures and the influence of Mars-relevant minerals
Authors: Haezeleer Bettina , Fox Stefan , Strasdeit Henry 
Published: February 2023

AbstractThe search for signs of life is a major objective in the exploration of Mars. Of particular interest are chemical biosignatures such as biomolecules. However, molecular biosignatures are susceptible to extreme environmental conditions such as heat, ionising radiation and strong oxidants. Therefore, a knowledge of the stability of possible biosignature molecules under present and past conditions on Mars is important, as well as the nature of possible alteration products. In the light of the long volcanically active history of Mars, we have studied the thermal behaviour of selected biological compounds, namely, haemin (an iron porphyrin closely related to the haem prosthetic group), cytochrome c (a small protein) and lecithin (a mixture of phospholipids). Samples were exposed to temperatures up to 900°C under an inert atmosphere of nitrogen, either in neat form or in mineral matrices. The matrix materials used were sodium chloride, gypsum (CaSO4 ⋅ 2H2O), Ca-montmorillonite (STx-1b), the Martian regolith simulant JSC Mars-1A and some mixtures thereof. Key results are: (1) The onset of significant decomposition for haemin, cytochrome c and lecithin occurs around 240°C. At slightly higher temperatures the disappearance of all characteristic infrared spectral bands indicates complete decomposition and loss of the primary biosignatures. (2) Haemin stoichiometrically releases CO2 and HCl during the initial thermal decomposition phase, at the end of which the iron porphyrin core is still intact. High-temperature products of haemin include graphite, α-iron and cementite (Fe3C). (3) Neat lecithin forms long-chain polyphosphates at 500°C, whereas lecithin‒NaCl mixtures form diphosphate (pyrophosphate). As these anions are absent and rare, respectively, in minerals, they may potentially serve as secondary biosignatures. (4) Heating a mixture of NaCl and JSC Mars-1A at 800°C in the presence of lecithin produces the aluminosilicate mineral sodalite (Na8[AlSiO4]6Cl2), which however appears to be of limited use as a secondary biosignature.
Visualization and quality control tools for large-scale multiplex tissue analysis in TissUUmaps3
Authors: Behanova Andrea , Avenel Christophe , Andersson Axel , Chelebian Eduard , Klemm Anna , Wik Lina , Östman Arne , Wählby Carolina 
Published: February 2023

Abstract
Large-scale multiplex tissue analysis aims to understand processes such as development and tumor formation by studying the occurrence and interaction of cells in local environments in, for example, tissue samples from patient cohorts. A typical procedure in the analysis is to delineate individual cells, classify them into cell types, and analyze their spatial relationships. All steps come with a number of challenges, and to address them and identify the bottlenecks of the analysis, it is necessary to include quality control tools in the analysis workflow. This makes it possible to optimize the steps and adjust settings in order to get better and more precise results. Additionally, the development of automated approaches for tissue analysis requires visual verification to reduce skepticism with regard to the accuracy of the results. Quality control tools could be used to build users’ trust in automated approaches. In this paper, we present three plugins for visualization and quality control in large-scale multiplex tissue analysis of microscopy images. The first plugin focuses on the quality of cell staining, the second one was made for interactive evaluation and comparison of different cell classification results, and the third one serves for reviewing interactions of different cell types.
Summer Marine Fog Distribution in the Chukchi–Beaufort Seas
Authors: Yi Li , Li King‐Fai , Chen Xianyao , Tung Ka‐Kit 
Published: February 2023

AbstractWe study the spatial and temporal variability of summer marine fog in the Chukchi–Beaufort region (175°E−150°W, 70°–86°N) using the in‐situ visibility measurements aboard the Chinese research fleet Xuelong (I and II) and a fog product we derive using the Vertical Feature Mask product of the spaceborne Cloud‐Aerosol Lidar and Infrared Pathfinder Satellite Observation (CALIPSO) observations. The Xuelong in‐situ observations show that the fog frequency in the Chukchi–Beaufort region has a maximum of ∼18% in the early morning and is less than 10% in the rest of the day. The latitudinal distribution of the Xuelong‐based in‐situ fog frequency further shows high fog occurrences at 74°N and 79°N, which are related to the local high fog occurrences near 72°–74°N and 76°–80°N in the central Chukchi–Beaufort region, as revealed by the longitude‐latitude pattern of the CALIPSO‐based spaceborne fog frequency distribution. The CALIPSO‐based fog frequency is also shown to be lower along the continental coastlines than in the Chukchi–Beaufort region. This longitude‐latitude distribution may be explained by a reduced fog formation due to the Pacific warm current flowing into the Arctic region through the Bering Strait in the summer as well as an enhanced fog formation in the Chukchi–Beaufort region when the southward flow of the Beaufort Gyre interacts with the Pacific warm current.
The Impact of the Eastern Pacific Fresh and Warm Pools on the Bimodal Seasonality of Barrier Layers
Authors: Chi Jianwei , Du Yan , Qi Jifeng , Wang Minyang , Chen Ruyan 
Published: February 2023

AbstractObservations of Argo profiles and TAO/TRITON array confirm the significant seasonality of the barrier layer (BL) and temperature inversion (TI) in the northeastern tropical Pacific (NETP). Statistical result of the occurrence based on the Argo profiles reveals a bimodal variability of the BL, with two peaks in July and October. This bimodal seasonality of BL is attributed to the out‐of‐phase variations of the eastern Pacific fresh and warm pools. The fresh and warm pools both expand westward from May to July, when the Inter‐Tropical Convergence Zone (ITCZ) becomes intense and broad. Heavy rainfall is the dominant contributor to the extension of the fresh and warm pools, leading to a high frequency of thick BL (40%). This frequent thick BL provides a precondition for its another development after August. The fresh pool is stable from August to November, while the warm pool contracts sharply. The cold tongue becomes active due to a prevailing trade wind and horizontal advection transports surface cold water to the northeastern warm pool. This cold advection deepens the isothermal layer and contributes to a frequent TI (30%) and thick BL (46%). The results suggest that the ITCZ rainfall and northward cold advection from equator dominate the upper layer stratification of NETP in summer and autumn, respectively.
Variability of Atmospheric CO2 Over the Arctic Ocean: Insights From the O‐Buoy Chemical Observing Network
Authors: Graham K. A. , Holmes C. D. , Friedrich G. , Rauschenberg C. D. , Williams C. R. , Bottenheim J. W. , Chavez F. P. , Halfacre J. W. , Perovich D. K. , Shepson P. B. , Simpson W. R. , Matrai P. A. 
Published: February 2023

AbstractAs the Arctic climate rapidly warms, there is a critical need for understanding variability and change in the Arctic carbon cycle, but sparse spatial coverage of observations has hindered progress. This work analyzes measurements of atmospheric CO2 in the Arctic from long‐term on‐ice measurements (the O‐Buoy Network), as well as coastal observatories from 2009 to 2016. The on‐ice measurements showed smaller seasonal amplitudes than coastal observatories, in contrast to the general observation of poleward increases of seasonal cycle amplitude. Average on‐ice measurements were also lower than their coastal counterparts during winter and spring, contradicting the expectation that CO2 increases poleward in boreal winter. We compared the observations to CO2 simulated in an updated version of GEOS‐Chem 3‐D chemical transport model, which includes new tracers of airmass history and CO2 sources and sinks. The model reproduced the observed features of the seasonal cycle and showed that terrestrial biosphere fluxes and synoptic transport explain most CO2 variability (both synoptic and interannual) over the Arctic Ocean surface. The polar airmass partially isolates the Arctic Ocean surface air from terrestrial CO2 exchange, which explains the reduced seasonal cycle amplitude and winter maxima. All Arctic coastal sites had similar CO2 interannual variability, particularly in summer, which was largely reproduced by the model. The interannual variability observed over sea ice, however, was distinct from the coastal sites and not reproduced by the model. Air‐sea CO2 exchange in and around sea ice, which was once thought to be negligible, may be an important driver of interannual variability over the Arctic Ocean.
High‐Resolution, Basin‐Scale Simulations Reveal the Impact of Intermediate Zonal Jets on the Atlantic Oxygen Minimum Zones
Authors: Calil Paulo H. R. 
Published: February 2023

AbstractEastward zonal jets at intermediate depths of 300–800 m connect the oxygen‐rich western boundary of the Atlantic basin with the oxygen minimum zones (OMZs) on the eastern boundary. They are not well represented in climate models because the low horizontal resolution of these models yields excessive viscosity. We use two physical‐biogeochemical model configurations of the Tropical Atlantic to show that the increase in resolution results in more robust intermediate zonal jets and a better representation of the OMZs. The OMZ structure is distorted at low‐resolution as surface, westward jets advect low‐oxygen waters from the eastern boundary much further west than in the climatology. The emergence of robust eastward jets in the high‐resolution run alleviate this problem and reproduce the Atlantic OMZs more accurately. The asymmetry between westward and eastward jets occurs because the former are associated with homogenous potential vorticity regions originating in the eastern boundary while the latter are associated with potential vorticity gradients. Intermediate, eastward jets constrain the westward expansion of the OMZs by supplying oxygen to their western edge. Within the OMZs, higher resolution allows a better representation of the boundary current system and eddying processes at depth which redistribute of low oxygen values from the productive eastern boundary. Basin‐scale, high‐resolution simulations reproduce more accurately the transfer of energy across scales that results in robust zonal jets as well as their impact on the ocean biogeochemistry. Accurate model predictions provide a pathway to disentangle natural and anthropogenic causes of ocean deoxygenation.
Two Alternatives to the Two‐Source Energy Balance Evapotranspiration Model
Authors: Wei Guoxiao , Zhao Zijing , Tian Wei , Qiu Zhongqi , Yang Zewei , Wang Fubing 
Published: February 2023

AbstractEnvironmental models are sensitive to inaccuracies in their approximation algorithms, which can bias model simulations and even lead to incorrect concepts. We present two alternatives to the two‐source evapotranspiration (ET) model, which utilize a more accurate approximation of the Clausius‐Clapeyron relation. Model performance was evaluated through a comparison with observed half‐hourly eddy covariance fluxes. Modeled representations of sensible heat dynamics and the limiting behaviors were also evaluated to identify the causes of model inaccuracies. Our analysis shows that the new exponential approximation used here significantly reduces errors that stem from solutions to the energy balance equations. The proposed parallel and series models are both more accurate than the Shuttleworth‐Wallace (SW) model under the conditions evaluated here, but we cannot conclude that the new models are consistently more accurate over a broader range of conditions. The new models can correctly reproduce several theoretical limiting behaviors, whereas the SW model generates conceptually incorrect results for several important limiting cases in which some key conductances approach both zero and infinity. Importantly, these models seriously underestimate the observed latent heat fluxes at night; the major causes of the nighttime model inadequacies are thought to be uncertainties of the estimated conductances and forcing data errors. The central concepts and processes related to new models are described via plots of temperature versus specific humidity to explore the theory behind an ET model. Through these efforts, we anticipate making more reliable ET predictions that will lead to a complete understanding of vegetation–atmosphere interactions.
Tailoring chiral optical properties by femtosecond laser direct writing in silica
Authors: Lu Jiafeng , Tian Jing , Poumellec Bertrand , Garcia-Caurel Enrique , Ossikovski Razvigor , Zeng Xianglong , Lancry Matthieu 
Published: February 2023

AbstractAn object that possesses chirality, that is, having its mirror image not overlayed on itself by rotation and translation, can provide a different optical response to a left- or right-handed circular polarized light. Chiral nanostructures may exhibit polarization-selective optical properties that can be controlled for micro-to-nano optical element engineering. An attractive way to induce such complex nanostructures in three-dimension in glass is femtosecond laser direct writing. However, the mechanism of femtosecond laser induced chirality remains to be unveiled due to complex physical and chemical processes occurring during the ultrashort light-matter interaction. Here, a phenomenological model is proposed and is built on two-layers phase shifters to account for this laser-induced optical chirality in an initially achiral material (silica glass). This model is based on the observation that femtosecond laser induced nanogratings own two principal contributions to its aggregate birefringent response: a form and a stress-related one. By refining this formalism, a multilayer approach is developed to imprint on demand optical rotation. Values up to +/-60° at 550 nm within an optimal 80 μm thickness in silica glass are possible, corresponding to the highest value in a glass to date. These results provide new insights of circular-optical control in micro-nano optical manufacturing and open new opportunities for photonics applications.
Chemogenetic rectification of the inhibitory tone onto hippocampal neurons reverts autistic-like traits and normalizes local expression of estrogen receptors in the Ambra1+/- mouse model of female autism
Authors: Pignataro Annabella , Krashia Paraskevi , De Introna Margherita , Nobili Annalisa , Sabetta Annamaria , Stabile Francesca , La Barbera Livia , D’Addario Sebastian Luca , Ventura Rossella , Cecconi Francesco , D’Amelio Marcello , Ammassari-Teule Martine 
Published: February 2023

AbstractFemale, but not male, mice with haploinsufficiency for the proautophagic Ambra1 gene show an autistic-like phenotype associated with hippocampal circuits dysfunctions which include loss of parvalbuminergic interneurons (PV-IN), decrease in the inhibition/excitation ratio, and abundance of immature dendritic spines on CA1 pyramidal neurons. Given the paucity of data relating to female autism, we exploit the Ambra1+/− female model to investigate whether rectifying the inhibitory input onto hippocampal principal neurons (PN) rescues their ASD-like phenotype at both the systems and circuits level. Moreover, being the autistic phenotype exclusively observed in the female mice, we control the effect of the mutation and treatment on hippocampal expression of estrogen receptors (ER). Here we show that excitatory DREADDs injected in PV_Cre Ambra1+/− females augment the inhibitory input onto CA1 principal neurons (PN), rescue their social and attentional impairments, and normalize dendritic spine abnormalities and ER expression in the hippocampus. By providing the first evidence that hippocampal excitability jointly controls autistic-like traits and ER in a model of female autism, our findings identify an autophagy deficiency-related mechanism of hippocampal neural and hormonal dysregulation which opens novel perspectives for treatments specifically designed for autistic females.
Skeletal phenotypes in secreted frizzled-related protein 4 gene knockout mice mimic skeletal architectural abnormalities in subjects with Pyle’s disease from SFRP4 mutations
Authors: Brommage Robert , Liu Jeff , Powell David R. 
Published: February 2023

AbstractMutations in SFRP4 cause Pyle’s bone disease with wide metaphyses and increased skeletal fragility. The WNT signaling pathway plays important roles in determining skeletal architecture and SFRP4 is a secreted Frizzled decoy receptor that inhibits WNT signaling. Seven cohorts of male and female Sfrp4 gene knockout mice, examined through 2 years of age, had a normal lifespan but showed cortical and trabecular bone phenotypes. Mimicking human Erlenmeyer flask deformities, bone cross-sectional areas were elevated 2-fold in the distal femur and proximal tibia but only 30% in femur and tibia shafts. Reduced cortical bone thickness was observed in the vertebral body, midshaft femur and distal tibia. Elevated trabecular bone mass and numbers were observed in the vertebral body, distal femur metaphysis and proximal tibia metaphysis. Midshaft femurs retained extensive trabecular bone through 2 years of age. Vertebral bodies had increased compressive strength, but femur shafts had reduced bending strength. Trabecular, but not cortical, bone parameters in heterozygous Sfrp4 mice were modestly affected. Ovariectomy resulted in similar declines in both cortical and trabecular bone mass in wild-type and Sfrp4 KO mice. SFRP4 is critical for metaphyseal bone modeling involved in determining bone width. Sfrp4 KO mice show similar skeletal architecture and bone fragility deficits observed in patients with Pyle’s disease with SFRP4 mutations.
Serine hydroxymethyltransferase 2 knockdown induces apoptosis in ccRCC by causing lysosomal membrane permeabilization via metabolic reprogramming
Authors: Liu Zhangnan , Fan Mengzhen , Hou Junqing , Pan Sijing , Xu Yanxin , Zhang Hailong , Liu Chen , Hao Xiangjun , Li Xia , Wang Huijuan 
Published: February 2023

AbstractSerine hydroxymethyltransferase 2 (SHMT2) plays an important role in converting serine to glycine and supplying carbon to one-carbon metabolism to sustain cancer cell proliferation. However, the expression, function, and underlying mechanisms of SHMT2 in clear cell renal cell carcinoma (ccRCC) remain largely unknown. In this study, we demonstrated that SHMT2 was upregulated in ccRCC tissues compared with controls and associated with patient survival. SHMT2 knockdown inhibited proliferation, migration, and invasion in ccRCC cells. Overexpression of SHMT2 promoted tumor progression. Mechanistically, SHMT2 depletion disrupted one-carbon metabolism, increased reactive oxygen species (ROS) levels, and decreased ATP levels via metabolic reprogramming, which destroyed cell homeostasis. The SHMT2 knockdown-induced stress activated autophagy. A mass of autophagosomes fused with lysosomes, resulting in lysosomal membrane permeabilization (LMP) and leakage of lysosomal contents into the cytoplasm, which eventually led to apoptosis. Our work reveals that SHMT2 functions as an oncogenic gene to promote ccRCC progression. SHMT2 depletion induces apoptosis by causing LMP through excessive activation of the autophagy-lysosome pathway via metabolic reprogramming.
TIM-4 orchestrates mitochondrial homeostasis to promote lung cancer progression via ANXA2/PI3K/AKT/OPA1 axis
Authors: Wang Yuzhen , Wang Yingchun , Liu Wen , Ding Lu , Zhang Xiaodi , Wang Bo , Tong Zheng , Yue Xuetian , Li Chunyang , Xu Liyun , Wu Zhuanchang , Liang Xiaohong , Ma Chunhong , Gao Lifen 
Published: February 2023

AbstractMitochondrial function and homeostasis are critical to the proliferation of lung cancer cells. T-cell immunoglobulin and mucin domain-containing molecule 4 (TIM-4) promotes the development and progression of lung cancer. However, the role of TIM-4 in mitochondria homeostasis in tumor cells remains completely unknown. In this study, we found that TIM-4 promoted growth and proliferation of lung cancer cells by the oxidative phosphorylation (OXPHOS) pathway. Consistently, inhibition of OXPHOS reversed TIM-4-induced proliferation of lung cancer cells. Notably, TIM-4 promoted mitochondrial fusion via enhancing L-OPA1 protein expression. Mechanistically, TIM-4 regulated protein of L-OPA1 through the PI3K/AKT pathway, and TIM-4 interacted with ANXA2 to promote the activation of PI3K/AKT signaling. Collectively, TIM-4 promotes oxidative phosphorylation of lung cancer cells to accelerate tumor progress via ANXA2/PI3K/AKT/OPA1 axis, which sheds significant new lights on the potential role of TIM-4 in regulating tumor cell metabolism.
KidneyNetwork: using kidney-derived gene expression data to predict and prioritize novel genes involved in kidney disease
Authors: Boulogne Floranne , Claus Laura R. , Wiersma Henry , Oelen Roy , Schukking Floor , de Klein Niek , Li Shuang , Westra Harm-Jan , van der Zwaag Bert , van Reekum Franka ,   Genomics England Research Consortium, Sierks Dana , Schönauer Ria , Li Zhigui , Bijlsma Emilia K. , Bos Willem Jan W. , Halbritter Jan , Knoers Nine V. A. M. , Besse Whitney , Deelen Patrick , Franke Lude , van Eerde Albertien M. 
Published: February 2023

Abstract
Genetic testing in patients with suspected hereditary kidney disease may not reveal the genetic cause for the disorder as potentially pathogenic variants can reside in genes that are not yet known to be involved in kidney disease. We have developed KidneyNetwork, that utilizes tissue-specific expression to inform candidate gene prioritization specifically for kidney diseases. KidneyNetwork is a novel method constructed by integrating a kidney RNA-sequencing co-expression network of 878 samples with a multi-tissue network of 31,499 samples. It uses expression patterns and established gene-phenotype associations to predict which genes could be related to what (disease) phenotypes in an unbiased manner. We applied KidneyNetwork to rare variants in exome sequencing data from 13 kidney disease patients without a genetic diagnosis to prioritize candidate genes. KidneyNetwork can accurately predict kidney-specific gene functions and (kidney disease) phenotypes for disease-associated genes. The intersection of prioritized genes with genes carrying rare variants in a patient with kidney and liver cysts identified ALG6 as plausible candidate gene. We strengthen this plausibility by identifying ALG6 variants in several cystic kidney and liver disease cases without alternative genetic explanation. We present KidneyNetwork, a publicly available kidney-specific co-expression network with optimized gene-phenotype predictions for kidney disease phenotypes. We designed an easy-to-use online interface that allows clinicians and researchers to use gene expression and co-regulation data and gene-phenotype connections to accelerate advances in hereditary kidney disease diagnosis and research.

Translational statement
Genetic testing in patients with suspected hereditary kidney disease may not reveal the genetic cause for the patient’s disorder. Potentially pathogenic variants can reside in genes not yet known to be involved in kidney disease, making it difficult to interpret the relevance of these variants. This reveals a clear need for methods to predict the phenotypic consequences of genetic variation in an unbiased manner. Here we describe KidneyNetwork, a tool that utilizes tissue-specific expression to predict kidney-specific gene functions. Applying KidneyNetwork to a group of undiagnosed cases identified ALG6 as a candidate gene in cystic kidney and liver disease. In summary, KidneyNetwork can aid the interpretation of genetic variants and can therefore be of value in translational nephrogenetics and help improve the diagnostic yield in kidney disease patients.