bluuebunny/crossref_metadata_2025 huggingface dataset:
An Entropy Framework for Evaluating Reflectance Observations for Climate Studies
Authors: Shea Yolanda L. , Lukashin Constantine , Liu Xu , Feldman Daniel R. , Pilewskie Peter
Published: April 2022

This study evaluated the comparative entropy represented in shortwave (300–1,750 nm) passive remote sensing measurements from conceptual instruments with varying systematic measurement uncertainties and spectral resolutions. The focus was on spectral and broadband reflectance averaged over large spatial scales typically relevant for climate change studies. Information theory was applied to quantify how the normalized Shannon entropy changed for different conceptual instruments and over different spatial scales. Reflectance measurements from the Scanning Imaging Absorption Spectrometer for Atmospheric Cartography (SCIAMACHY) were used to represent the observed reflectance, and simulated reflectance from climate Observing System Simulations Experiments (OSSEs) were used to represent decadal‐ and centennial‐length data sets free from instrument artifacts. Similar to previous studies, the simulated OSSE spectra were shown to be a sufficient proxy for the observed reflectance. As hypothesized, the normalized entropy decreased with increasing measurement uncertainty and increasing spectral bandwidth. Additionally, the entropy decreased for increasingly large spatial scales, particularly for measurement uncertainties larger than 2%. When applied to OSSE reflectance simulated from a forced CMIP3 climate model simulation, the change in entropy with measurement uncertainty and spectral resolution provided insight into measurement attributes needed to monitor a changing climate system and highlighted the importance of sufficiently high accuracy and spectral resolution for detecting and attributing climate trends. These preliminary studies illustrate the value of this information theory‐based framework in instrument design by calculating the entropy, used to represent information in measurements from different conceptual instruments.
Metabolism and Soil Water Viscosity Control Diel Patterns of Nitrate and DOC in a Low Order Temperate Stream
Authors: Oviedo‐Vargas Diana , Peipoch Marc , Dow Charles
Published: April 2022

We investigated diel dissolved organic carbon (DOC) and nitrate (NO3−) dynamics in White Clay Creek, a third‐order stream in Pennsylvania, USA. High‐frequency DOC and NO3− concentrations were modeled from absorbance spectra collected with a deployable spectrophotometer. Periodicities of 24 hr in solute concentrations and streamflow were frequent throughout the year. To test potential drivers of diel oscillations, we focused on five periods with at least 5 days of clear diel changes that were not drastically influenced by high‐flow events. Maxima and minima of the diel variation in solute concentrations, and significant correlations between their daily amplitude and gross primary production (GPP) indicate that stream metabolism was the major driver diel oscillations in April (r = 0.86 and −0.87 for GPP vs. DOC and NO3−, respectively) and May (r = 0.86 and −0.90 for GPP vs. DOC and NO3−, respectively). In summer, drivers of daily oscillations of DOC and NO3− were unclear but likely influenced by stream metabolism. In winter, we observed no correlation between GPP and amplitude of daily concentration change, instead streamflow was the dominant driver via the viscosity effect (r = −0.92 and 0.89 for streamflow vs. DOC and NO3− respectively). As the hydraulic conductivity of the riparian soil increased throughout the daytime, the contribution of DOC‐rich and NO3−‐poor soil water to the stream relative to groundwater also increased. Results from this work highlight that watershed processes influence stream solutes on widely variable time scales, ranging from hours to centuries; and that underlying controls depend highly on seasonality.
Newly Digitized Data From Scandinavian Magnetometer Array Network Shows Large Regional Differences in Magnetic Environment
Authors: Kärhä O. , Tanskanen E. I.
Published: April 2022

The International Magnetospheric Study (IMS) took place from 1977 to 1979. An objective was to study the magnetosphere at different heights on the Earth and in space simultaneously. The Scandinavian Magnetometer Array (SMA), where a dense magnetometer array was placed in the northern part of Scandinavia, was part of the IMS. This array extended 1,570 km in north‐south and 1,290 km in east‐west directions. The SMA‐magnetometers contained a camera with 35 mm film and three wire‐suspended magnets. These instruments recorded the movement of the magnets optically on the film. The usability of the SMA data has been limited by time‐consuming digitization by hand. Thus, most of the recordings has been left nondigitized and unstudied. We have developed a method, named DigiMAG, to digitize the SMA recordings by using a custom‐built device. This article presents the high‐latitude dynamics of the strongest magnetic storm in 1977 between October 26 and 30. We analyze newly digitized data from Rostadalen (ROS), Evenes (EVE), Ritsemjokk (RIJ), and Kiruna (KIR) stations for the three storm‐time substorms on October 26–29, 1977. The results show that in the vicinity of the 65° latitude, the storm‐time differences of horizontal magnetic components can exceed 500 nT. During the recovery phase of a substorm, 2.8 nT km−1 difference arises over a distance of 167 km between the H‐component time derivatives of ROS and RIJ stations in 3 minutes.
SARS-CoV-2 Omicron variant: recent progress and future perspectives
Authors: Fan Yao , Li Xiang , Zhang Lei , Wan Shu , Zhang Long , Zhou Fangfang
Published: April 2022

Since the outbreak of the coronavirus disease 2019 (COVID-19) pandemic, there have been a few variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), one of which is the Omicron variant (B.1.1.529). The Omicron variant is the most mutated SARS-CoV-2 variant, and its high transmissibility and immune evasion ability have raised global concerns. Owing to its enhanced transmissibility, Omicron has rapidly replaced Delta as the dominant variant in several regions. However, recent studies have shown that the Omicron variant exhibits reduced pathogenicity due to altered cell tropism. In addition, Omicron exhibits significant resistance to the neutralizing activity of vaccines, convalescent serum, and most antibody therapies. In the present review, recent advances in the molecular and clinical characteristics of the infectivity, pathogenicity, and immune evasion of Omicron variant was summarized, and potential therapeutic applications in response to Omicron infection were discussed. Furthermore, we highlighted potential response to future waves and strategies to end the pandemic.
Different responses to risperidone treatment in Schizophrenia: a multicenter genome-wide association and whole exome sequencing joint study
Authors: Zhao Mingzhe , Ma Jingsong , Li Mo , Zhu Wenli , Zhou Wei , Shen Lu , Wu Hao , Zhang Na , Wu Shaochang , Fu Chunpeng , Li Xianxi , Yang Ke , Tang Tiancheng , Shen Ruoxi , He Lin , Huai Cong , Qin Shengying
Published: April 2022

Risperidone is routinely used in the clinical management of schizophrenia, but the treatment response is highly variable among different patients. The genetic underpinnings of the treatment response are not well understood. We performed a pharmacogenomic study of the treatment response to risperidone in patients with schizophrenia by using a SNP microarray -based genome-wide association study (GWAS) and whole exome sequencing (WES)-based GWAS. DNA samples were collected from 189 patients for the GWAS and from 222 patients for the WES after quality control in multiple centers of China. Antipsychotic response phenotypes of patients who received eight weeks of risperidone treatment were quantified with percentage change on the Positive and Negative Syndrome Scale (PANSS). The GWAS revealed a significant association between several SNPs and treatment response, such as three GRM7 SNPs (rs141134664, rs57521140, and rs73809055). Gene-based analysis in WES revealed 13 genes that were associated with antipsychotic response, such as GPR12 and MAP2K3. We did not identify shared loci or genes between GWAS and WES, but association signals tended to cluster into the GPCR gene family and GPCR signaling pathway, which may play an important role in the treatment response etiology. This study may provide a research paradigm for pharmacogenomic research, and these data provide a promising illustration of our potential to identify genetic variants underlying antipsychotic responses and may ultimately facilitate precision medicine in schizophrenia.
Intrahepatic cholangiocarcinoma hidden within cancer of unknown primary
Authors: Conway Alicia-Marie , Morris Georgina C. , Smith Sarah , Vekeria Monique , Manoharan Prakash , Mitchell Claire , Backen Alison , Oliveira Pedro , Hubner Richard A. , Lamarca Angela , McNamara Mairéad G. , Valle Juan W. , Cook Natalie
Published: April 2022

Background

Many patients referred with a provisional diagnosis of cancer of unknown primary (pCUP) present with presumed metastatic disease to the liver. Due to the lack of definitive histological markers, intrahepatic cholangiocarcinoma (iCCA) may be overlooked. This study assessed the frequency of iCCA within a pCUP cohort.

Methods

A single UK cancer-center study of sequential patients referred with pCUP from January 2017 to April 2020. Baseline diagnostic imaging was reviewed independently by a radiologist and oncologist; those with radiological features of iCCA (dominant liver lesion, capsular retraction) were identified.

Results

Of 228 patients referred with pCUP, 72 (32%) had malignancy involving the liver. 24/72 patients had radiological features consistent with iCCA; they were predominantly female (75%) with an average age of 63 years and 63% had an ECOG PS ≤ 2. The median overall survival (OS) of the iCCA group and the remaining liver-involved CUP group were similar (OS 4.1 vs 4.4 months, p-value = 0.805). Patients, where a primary diagnosis was subsequently determined, had better OS (10.2 months, p-values: iCCA = 0.0279: cCUP = 0.0230).

Conclusions

In this study, 34% of patients with liver-involved pCUP, fulfilled the radiological criteria for an iCCA diagnosis. Consideration of an iCCA diagnosis in patients with CUP could improve timely diagnosis, molecular characterisation and treatment.
The car tank lid bacteriome: a reservoir of bacteria with potential in bioremediation of fuel
Authors: Vidal-Verdú Àngela , Gómez-Martínez Daniela , Latorre-Pérez Adriel , Peretó Juli , Porcar Manuel
Published: April 2022

Bioprospecting of microorganisms suitable for bioremediation of fuel or oil spills is often carried out in contaminated environments such as gas stations or polluted coastal areas. Using next-generation sequencing (NGS) we analyzed the microbiota thriving below the lids of the fuel deposits of diesel and gasoline cars. The microbiome colonizing the tank lids differed from the diversity found in other hydrocarbon-polluted environments, with Proteobacteria being the dominant phylum and without clear differences between gasoline or diesel-fueled vehicles. We observed differential growth when samples were inoculated in cultures with gasoline or diesel as the main carbon source, as well as an increase in the relative abundance of the genus Pseudomonas in diesel. A collection of culturable strains was established, mostly Pseudomonas, Stenotrophomonas, Staphylococcus, and Bacillus genera. Strains belonging to Bacillus, Pseudomonas, Achromobacter, and Isoptericola genera showed a clear diesel degradation pattern when analyzed by GC-MS, suggesting their potential use for bioremediation and a possible new species of Isoptericola was further characterized as hydrocarbon degrader.
Spatial interplay of lymphocytes and fibroblasts in estrogen receptor-positive HER2-negative breast cancer
Authors: Nederlof I. , Hajizadeh S. , Sobhani F. , Raza S. E. A. , AbdulJabbar K. , Harkes R. , van de Vijver M. J. , Salgado R. , Desmedt C. , Kok M. , Yuan Y. , Horlings H. M.
Published: April 2022

In estrogen-receptor-positive, HER2-negative (ER+HER2−) breast cancer, higher levels of tumor infiltrating lymphocytes (TILs) are often associated with a poor prognosis and this phenomenon is still poorly understood. Fibroblasts represent one of the most frequent cells in breast cancer and harbor immunomodulatory capabilities. Here, we evaluate the molecular and clinical impact of the spatial patterns of TILs and fibroblast in ER+HER2− breast cancer. We used a deep neural network to locate and identify tumor, TILs, and fibroblasts on hematoxylin and eosin-stained slides from 179 ER+HER2− breast tumors (ICGC cohort) together with a new density estimation analysis to measure the spatial patterns. We clustered tumors based on their spatial patterns and gene set enrichment analysis was performed to study their molecular characteristics. We independently assessed the spatial patterns in a second cohort of ER+HER2− breast cancer (N = 630, METABRIC) and studied their prognostic value. The spatial integration of fibroblasts, TILs, and tumor cells leads to a new reproducible spatial classification of ER+HER2− breast cancer and is linked to inflammation, fibroblast meddling, or immunosuppression. ER+HER2− patients with high TIL did not have a significant improved overall survival (HR = 0.76, P = 0.212), except when they had received chemotherapy (HR = 0.447). A poorer survival was observed for patients with high fibroblasts that did not show a high level of TILs (HR = 1.661, P = 0.0303). Especially spatial mixing of fibroblasts and TILs was associated with a good prognosis (HR = 0.464, P = 0.013). Our findings demonstrate a reproducible pipeline for the spatial profiling of TILs and fibroblasts in ER+HER2− breast cancer and suggest that this spatial interplay holds a decisive role in their cancer-immune interactions.
Is conservative management of ductal carcinoma in situ risky?
Authors: Zheng Lan , Gökmen-Polar Yesim , Badve Sunil S.
Published: April 2022

Nonsurgical management of ductal carcinoma in situ is controversial and little is known about the long-term consequences of this approach. In this study, we aimed to determine the risk of (a) upstaging to invasive carcinoma at excision and (b) ipsilateral breast cancer events in patients who might have been eligible for nonsurgical management of DCIS trials. Data from women aged 20 years or older with a biopsy diagnosis of DCIS between January 1, 2010 to December 31, 2014 were collated. The women underwent biopsy and surgical resection (lumpectomy or mastectomy) and were treated with radiation or endocrine therapy as per treating physicians’ choice. The development of ipsilateral breast cancer events (IBEs) was analyzed in patients with at least 5 years of follow-up after standard of care therapy for DCIS. Subset-analysis was undertaken to identify the incidence of IBEs in patients eligible for nonsurgical management trials. The study population consisted of 378 patients with matched cases of biopsy and surgical excision. The overall upstaging rate to IBC was 14.3 and 12.9% for COMET, 8.8% for LORIS, and 10.7% for LORD trial “eligible” patients. At 5 years of follow-up, ~11.5% of overall and trial eligible patients developed IBEs of which approximately half were invasive IBEs. In conclusion, women with DCIS who would have been eligible for nonsurgical management trials have a significantly high risk of developing ipsilateral breast events within 5 years of diagnosis. Better selection criteria are needed to identify DCIS patients who are at very low risk for the development of IBC.
Discovering plasticity models without stress data
Authors: Flaschel Moritz , Kumar Siddhant , De Lorenzis Laura
Published: April 2022

We propose an approach for data-driven automated discovery of material laws, which we call EUCLID (Efficient Unsupervised Constitutive Law Identification and Discovery), and we apply it here to the discovery of plasticity models, including arbitrarily shaped yield surfaces and isotropic and/or kinematic hardening laws. The approach isunsupervised, i.e., it requires no stress data but only full-field displacement and global force data; it deliversinterpretablemodels, i.e., models that are embodied by parsimonious mathematical expressions discovered through sparse regression of a potentially large catalog of candidate functions; it isone-shot, i.e., discovery only needs one experiment. The material model library is constructed by expanding the yield function with a Fourier series, whereas isotropic and kinematic hardening is introduced by assuming a yield function dependency on internal history variables that evolve with the plastic deformation. For selecting the most relevant Fourier modes and identifying the hardening behavior, EUCLID employs physics knowledge, i.e., the optimization problem that governs the discovery enforces the equilibrium constraints in the bulk and at the loaded boundary of the domain. Sparsity promoting regularization is deployed to generate a set of solutions out of which a solution with low cost and high parsimony is automatically selected. Through virtual experiments, we demonstrate the ability of EUCLID to accurately discover several plastic yield surfaces and hardening mechanisms of different complexity.
Delocalization of dark and bright excitons in flat-band materials and the optical properties of V2O5
Authors: Gorelov Vitaly , Reining Lucia , Feneberg Martin , Goldhahn Rüdiger , Schleife André , Lambrecht Walter R. L. , Gatti Matteo
Published: April 2022

The simplest picture of excitons in materials with atomic-like localization of electrons is that of Frenkel excitons, where electrons and holes stay close together, which is associated with a large binding energy. Here, using the example of the layered oxide V2O5, we show how localized charge-transfer excitations combine to form excitons that also have a huge binding energy but, at the same time, a large electron-hole distance, and we explain this seemingly contradictory finding. The anisotropy of the exciton delocalization is determined by the local anisotropy of the structure, whereas the exciton extends orthogonally to the chains formed by the crystal structure. Moreover, we show that the bright exciton goes together with a dark exciton of even larger binding energy and more pronounced anisotropy. These findings are obtained by combining first principles many-body perturbation theory calculations, ellipsometry experiments, and tight binding modelling, leading to very good agreement and a consistent picture. Our explanation is general and can be extended to other materials.
Modeling and simulation of microstructure in metallic systems based on multi-physics approaches
Authors: Mianroodi Jaber Rezaei , Shanthraj Pratheek , Liu Chuanlai , Vakili Samad , Roongta Sharan , Siboni Nima Hamidi , Perchikov Nathan , Bai Yang , Svendsen Bob , Roters Franz , Raabe Dierk , Diehl Martin
Published: April 2022

The complex interplay between chemistry, microstructure, and behavior of many engineering materials has been investigated predominantly by experimental methods. Parallel to the increase in computer power, advances in computational modeling methods have resulted in a level of sophistication which is comparable to that of experiments. At the continuum level, one class of such models is based on continuum thermodynamics, phase-field methods, and crystal plasticity, facilitating the account of multiple physical mechanisms (multi-physics) and their interaction during microstructure evolution. This paper reviews the status of simulation approaches and software packages in this field and gives an outlook towards promising research directions.
A deep learned nanowire segmentation model using synthetic data augmentation
Authors: Lin Binbin , Emami Nima , Santos David A. , Luo Yuting , Banerjee Sarbajit , Xu Bai-Xiang
Published: April 2022

Automated particle segmentation and feature analysis of experimental image data are indispensable for data-driven material science. Deep learning-based image segmentation algorithms are promising techniques to achieve this goal but are challenging to use due to the acquisition of a large number of training images. In the present work, synthetic images are applied, resembling the experimental images in terms of geometrical and visual features, to train the state-of-art Mask region-based convolutional neural networks to segment vanadium pentoxide nanowires, a cathode material within optical density-based images acquired using spectromicroscopy. The results demonstrate the instance segmentation power in real optical intensity-based spectromicroscopy images of complex nanowires in overlapped networks and provide reliable statistical information. The model can further be used to segment nanowires in scanning electron microscopy images, which are fundamentally different from the training dataset known to the model. The proposed methodology can be extended to any optical intensity-based images of variable particle morphology, material class, and beyond.
Nucleosome footprinting in plasma cell-free DNA for the pre-surgical diagnosis of ovarian cancer
Authors: Vanderstichele Adriaan , Busschaert Pieter , Landolfo Chiara , Olbrecht Siel , Coosemans An , Froyman Wouter , Loverix Liselore , Concin Nicole , Braicu Elena Ioana , Wimberger Pauline , Van Nieuwenhuysen Els , Han Sileny N. , Van Gorp Toon , Venken Tom , Heremans Ruben , Neven Patrick , Bourne Tom , Van Calster Ben , Timmerman Dirk , Lambrechts Diether , Vergote Ignace
Published: April 2022

Fragmentation patterns of plasma cell-free DNA (cfDNA) are known to reflect nucleosome positions of cell types contributing to cfDNA. Based on cfDNA fragmentation patterns, the deviation in nucleosome footprints was quantified between diagnosed ovarian cancer patients and healthy individuals. Multinomial modeling was subsequently applied to capture these deviations in a per sample nucleosome footprint score. Validation was performed in 271 cfDNAs pre-surgically collected from women with an adnexal mass. We confirmed that nucleosome scores were elevated in invasive carcinoma patients, but not in patients with benign or borderline disease. Combining nucleosome scores with chromosomal instability scores assessed in the same cfDNA improved prediction of malignancy. Nucleosome scores were, however, more reliable to predict non-high-grade serous ovarian tumors, which are characterized by low chromosomal instability. These data highlight that compared to chromosomal instability, nucleosome footprinting provides a complementary and more generic read-out for pre-surgical diagnosis of invasive disease in women with adnexal masses.
The effect of bubble nucleation on the performance of a wickless heat pipe in microgravity
Authors: Yu Jiaheng , Pawar Anisha , Plawsky Joel L. , Chao David F.
Published: April 2022

Bubble nucleation was investigated in a 20-mm-long, wickless heat pipe on the International Space Station. Over 20 h of running experiments using pentane as the working fluid, more than 100 nucleation events were observed. Bubble nucleation at the heater end temporarily boosted peak pressures and vapor temperatures in the device. At the moment of nucleation, the heater wall temperature significantly decreased due to increased evaporation and the original vapor bubble collapsed due to increased pressure. A thermal model was developed and using the measured temperatures and pressures, heat transfer coefficients near the heater end of the system were extracted. Peak heat transfer coefficients during the nucleation event were over a factor of three higher than at steady-state. The heat transfer coefficient data were all collapsed in the form of a single, linear correlation relating the Nusselt number to the Ohnesorge number.
An ultralight, flexible, and biocompatible all-fiber motion sensor for artificial intelligence wearable electronics
Authors: Lin Sen , Hu Shuang , Song Wei , Gu Miaoqing , Liu Junchen , Song Jianan , Liu Zhenglian , Li Ziwei , Huang Kun , Wu Yufeng , Lei Ming , Wu Hui
Published: April 2022

New-generation human body motion sensors for wearable electronics and intelligent medicine are required to comply with stringent requirements in terms of ultralight weight, flexibility, stability, biocompatibility, and extreme precision. However, conventional sensors are hard to fulfill all these criteria due to their rigid structure, high-density sensing materials used as the constituents, as well as hermetical and compact assembly strategy. Here, we report an ultralight sensing material based on radial anisotropic porous silver fiber (RAPSF), which has been manufactured by phase separation and temperature-controlled grain growth strategy on a modified blow-spinning system. The resistance of RAPSF could be dynamically adjusted depending on the deflected shape. Furthermore, an all-fiber motion sensor (AFMS) with an ultra-low density of 68.70 mg cm−3and an overall weigh of 7.95 mg was fabricated via layer-by-layer assembly. The sensor exhibited outstanding flexibility, breathability, biocompatibility, and remarkable body motion recognition ability. Moreover, the AFMS was shown to have great potential as an artificial intelligence throat sensor for throat state identification at the accuracy above 85%, allowing one to spot the early onset of the viral throat illness.
Coherence of a charge stabilised tin-vacancy spin in diamond
Authors: Görlitz Johannes , Herrmann Dennis , Fuchs Philipp , Iwasaki Takayuki , Taniguchi Takashi , Rogalla Detlef , Hardeman David , Colard Pierre-Olivier , Markham Matthew , Hatano Mutsuko , Becher Christoph
Published: April 2022

Quantum information processing (QIP) with solid state spin qubits strongly depends on the efficient initialisation of the qubit’s desired charge state. While the negatively charged tin-vacancy (SnV−) centre in diamond has emerged as an excellent platform for realising QIP protocols due to long spin coherence times at liquid helium temperature and lifetime limited optical transitions, its usefulness is severely limited by termination of the fluorescence under resonant excitation. Here, we unveil the underlying charge cycle, potentially applicable to all group IV-vacancy (G4V) centres, and exploit it to demonstrate highly efficient and rapid initialisation of the desired negative charge state of single SnV centres while preserving long term stable optical resonances. In addition to investigating the optical coherence, we all-optically probe the coherence of the ground state spins by means of coherent population trapping and find a spin dephasing time of 5(1) μs. Furthermore, we demonstrate proof-of-principle single shot spin state readout without the necessity of a magnetic field aligned to the symmetry axis of the defect.
Quantum process tomography on holographic metasurfaces
Authors: Wu Qing-Yuan , Meng Zhe , Yang Jia-Zhi , Zhang An-Ning
Published: April 2022

Holographic metasurfaces and their applications have garnered significant attention owing to their role in polarization control. In this study, we demonstrate that the quantum properties of holographic metasurfaces can be obtained by quantum state tomography (QST) and quantum process tomography (QPT). We perform QST to obtain the experimental output states by extracting information from holograms encoded on the holographic metasurface, and develop a QPT-based method to estimate the quantum process of the metasurface. The theoretical output states derived from the estimated quantum process are in good agreement with the experimental output states, proving the effectiveness of our method. Our work not only provides theoretical and experimental analysis for understanding the quantum properties of holographic metasurfaces, but also paves the way for the application of holographic metasurfaces in quantum field.
Empirical evidence for recent global shifts in vegetation resilience
Authors: Smith Taylor , Traxl Dominik , Boers Niklas
Published: April 2022

The character and health of ecosystems worldwide is tightly coupled to changes in Earth’s climate. Theory suggests that ecosystem resilience—the ability of ecosystems to resist and recover from external shocks such as droughts and fires—can be inferred from their natural variability. Here, we quantify vegetation resilience globally with complementary metrics based on two independent long-term satellite records. We first empirically confirm that the recovery rates from large perturbations can be closely approximated from internal vegetation variability across vegetation types and climate zones. On the basis of this empirical relationship, we quantify vegetation resilience continuously and globally from 1992 to 2017. Long-term vegetation resilience trends are spatially heterogeneous, with overall increasing resilience in the tropics and decreasing resilience at higher latitudes. Shorter-term trends, however, reveal a marked shift towards a global decline in vegetation resilience since the early 2000s, particularly in the equatorial rainforest belt.
A European-wide dataset to uncover adaptive traits of Listeria monocytogenes to diverse ecological niches
Authors: Félix Benjamin , Sevellec Yann , Palma Federica , Douarre Pierre Emmanuel , Felten Arnaud , Radomski Nicolas , Mallet Ludovic , Blanchard Yannick , Leroux Aurélie , Soumet Christophe , Bridier Arnaud , Piveteau Pascal , Ascensio Eliette , Hébraud Michel , Karpíšková Renáta , Gelbíčová Tereza , Torresi Marina , Pomilio Francesco , Cammà Cesare , Di Pasquale Adriano , Skjerdal Taran , Pietzka Ariane , Ruppitsch Werner , Canelhas Monica Ricão , Papić Bojan , Hurtado Ana , Wullings Bart , Bulawova Hana , Castro Hanna , Lindström Miia , Korkeala Hannu , Šteingolde Žanete , Kramarenko Toomas , Cabanova Lenka , Szymczak Barbara , Gareis Manfred , Oswaldi Verena , Marti Elisabet , Seyfarth Anne-Mette , Leblanc Jean-Charles , Guillier Laurent , Roussel Sophie
Published: April 2022

Listeria monocytogenes (Lm) is a ubiquitous bacterium that causes listeriosis, a serious foodborne illness. In the nature-to-human transmission route, Lm can prosper in various ecological niches. Soil and decaying organic matter are its primary reservoirs. Certain clonal complexes (CCs) are over-represented in food production and represent a challenge to food safety. To gain new understanding of Lm adaptation mechanisms in food, the genetic background of strains found in animals and environment should be investigated in comparison to that of food strains. Twenty-one partners, including food, environment, veterinary and public health laboratories, constructed a dataset of 1484 genomes originating from Lm strains collected in 19 European countries. This dataset encompasses a large number of CCs occurring worldwide, covers many diverse habitats and is balanced between ecological compartments and geographic regions. The dataset presented here will contribute to improve our understanding of Lm ecology and should aid in the surveillance of Lm. This dataset provides a basis for the discovery of the genetic traits underlying Lm adaptation to different ecological niches.
Dental pulp stem cells as a therapy for congenital entero-neuropathy
Authors: Yoshimaru Koichiro , Yamaza Takayoshi , Kajioka Shunichi , Sonoda Soichiro , Yanagi Yusuke , Matsuura Toshiharu , Yoshizumi Junko , Oda Yoshinao , Iwata Naoko , Takai Chiho , Nakayama Shinsuke , Taguchi Tomoaki
Published: April 2022

Hirschsprung’s disease is a congenital entero-neuropathy that causes chronic constipation and intestinal obstruction. New treatments for entero-neuropathy are needed because current surgical strategies have limitations5. Entero-neuropathy results from enteric nervous system dysfunction due to incomplete colonization of the distal intestine by neural crest-derived cells. Impaired cooperation between the enteric nervous system and intestinal pacemaker cells may also contribute to entero-neuropathy. Stem cell therapy to repair these multiple defects represents a novel treatment approach. Dental pulp stem cells derived from deciduous teeth (dDPSCs) are multipotent cranial neural crest-derived cells, but it remains unknown whether dDPSCs have potential as a new therapy for entero-neuropathy. Here we show that intravenous transplantation of dDPSCs into the Japanese Fancy-1 mouse, an established model of hypoganglionosis and entero-neuropathy, improves large intestinal structure and function and prolongs survival. Intravenously injected dDPSCs migrate to affected regions of the intestine through interactions between stromal cell-derived factor-1α and C-X-C chemokine receptor type-4. Transplanted dDPSCs differentiate into both pacemaker cells and enteric neurons in the proximal colon to improve electrical and peristaltic activity, in addition to their paracrine effects. Our findings indicate that transplanted dDPSCs can differentiate into different cell types to correct entero-neuropathy-associated defects.
Non-melancholic depressive symptoms are associated with above average fat mass index in the Helsinki birth cohort study
Authors: Eriksson Mia D. , Eriksson Johan G. , Korhonen Päivi , Salonen Minna K. , Mikkola Tuija M. , Kajantie Eero , Wasenius Niko S. , von Bonsdorff Mikaela , Kautiainen Hannu , Laine Merja K.
Published: April 2022

There is an existing link between two of the most common diseases, obesity and depression. These are both of great public health concern, but little is known about the relationships between the subtypes of these conditions. We hypothesized that non-melancholic depressive symptoms have a stronger relationship with both body composition (lean mass and fat mass) and dysfunctional glucose metabolism than melancholic depression. For this cross-sectional study 1510 participants from the Helsinki Birth Cohort Study had their body composition evaluated as lean mass and fat mass (Lean Mass Index [LMI, kg/m2] + Fat Mass Index [FMI kg/m2] = Body Mass Index). Participants were evaluated for depressive symptoms utilizing the Beck depression inventory, and had laboratory assessments including an oral glucose tolerance test. Higher than average FMI was associated with a higher percentage (mean [%], 95% CI) of participants scoring in the depressive range of the Beck depression inventory (20.2, 17.2–23.2) compared to those with low FMI (16.3, 13.8–18.9; p = 0.048) when adjusted for age, sex, education, and fasting plasma glucose concentration. Higher FMI was associated with a higher likelihood of having depressive symptoms (OR per 1-SD FMI = 1.37, 95% CI 1.13–1.65), whereas higher LMI was associated with a lower likelihood of having depressive symptoms (OR per 1-SD LMI = 0.76, 95% CI 0.64–0.91). Participants with an above average FMI more frequently (mean [%], 95% CI) had non-melancholic depressive symptoms (14.7, 11.8–17.7) as compared to those with low FMI (9.7, 7.6–11.9; p = 0.008) regardless of LMI levels. There was no difference between the body composition groups in the likelihood of having melancholic depressive symptoms. The non-melancholic group had higher (mean [kg/m2], SD) FMI (9.6, 4.1) than either of the other groups (BDI < 10: 7.7, 3.1; melancholic: 7.9, 3.6; p < 0.001), and a higher (mean [mmol/l], SD) 2-h glucose concentration (7.21, 1.65) than the non-depressed group (6.71, 1.70; p = 0.005). As hypothesized, non-melancholic depressive symptoms are most closely related to high fat mass index and dysfunctional glucose metabolism.
Ultra-low binder content 3D printed calcium phosphate graphene scaffolds as resorbable, osteoinductive matrices that support bone formation in vivo
Authors: Daneshmandi Leila , Holt Brian D. , Arnold Anne M. , Laurencin Cato T. , Sydlik Stefanie A.
Published: April 2022

Bone regenerative engineering could replace autografts; however, no synthetic material fulfills all design criteria. Nanocarbons incorporated into three-dimensional printed (3DP) matrices can improve properties, but incorporation is constrained to low wt%. Further, unmodified nanocarbons have limited osteogenic potential. Functionalization to calcium phosphate graphene (CaPG) imparts osteoinductivity and osteoconductivity, but loading into matrices remained limited. This work presents ultra-high content (90%), 3DP-CaPG matrices. 3DP-CaPG matrices are highly porous (95%), moderately stiff (3 MPa), and mechanically robust. In vitro, they are cytocompatible and induce osteogenic differentiation of human mesenchymal stem cells (hMSCs), indicated by alkaline phosphatase, mineralization, and COL1α1 expression. In vivo, bone regeneration was studied using a transgenic fluorescent-reporter mouse non-union calvarial defect model. 3DP-CaPG stimulates cellular ingrowth, retains donor cells, and induces osteogenic differentiation. Histology shows TRAP staining around struts, suggesting potential osteoclast activity. Apparent resorption of 3DP-CaPG was observed and presented no toxicity. 3DP-CaPG represents an advancement towards a synthetic bone regeneration matrix.
Dopamine influences attentional rate modulation in Macaque posterior parietal cortex
Authors: van Kempen Jochem , Brandt Christian , Distler Claudia , Bellgrove Mark A. , Thiele Alexander
Published: April 2022

Cognitive neuroscience has made great strides in understanding the neural substrates of attention, but our understanding of its neuropharmacology remains incomplete. Although dopamine has historically been studied in relation to frontal functioning, emerging evidence suggests important dopaminergic influences in parietal cortex. We recorded single- and multi-unit activity whilst iontophoretically administering dopaminergic agonists and antagonists while rhesus macaques performed a spatial attention task. Out of 88 units, 50 revealed activity modulation by drug administration. Dopamine inhibited firing rates according to an inverted-U shaped dose–response curve and increased gain variability. D1 receptor antagonists diminished firing rates according to a monotonic function and interacted with attention modulating gain variability. Finally, both drugs decreased the pupil light reflex. These data show that dopamine shapes neuronal responses and modulates aspects of attentional processing in parietal cortex.
Body size variability across habitats in the Brachionus plicatilis cryptic species complex
Authors: Walczyńska Aleksandra , Serra Manuel
Published: April 2022

The body size response to temperature is one of the most recognizable but still poorly understood ecological phenomena. Other covarying environmental factors are frequently invoked as either affecting the strength of that response or even driving this pattern. We tested the body size response in five species representing the Brachionus plicatilis cryptic species complex, inhabiting 10 brackish ponds with different environmental characteristics. Principal Component Analysis selected salinity and oxygen concentration as the most important factors, while temperature and pH were less influential in explaining variation of limnological parameters. Path analysis showed a positive interclonal effect of pH on body size. At the interspecific level, the size response was species- and factor-dependent. Under the lack of a natural thermo-oxygenic relationship, the negative response of size to temperature, expected according to ‘size-to-temperature response’ rules, disappeared, but a positive response of size to oxygen, expected according to predictions selecting oxygen as a factor actually driving these rules, remained. Our results confirm the crucial role of oxygen in determining the size-to-temperature patterns observed in the field.
Effects of rice straw biochar on microbial community structure and metabolic function during anaerobic digestion
Authors: Wang Su , Shi Fengmei , Li Pengfei , Yang Fengshan , Pei Zhanjiang , Yu Qiuyue , Zuo Xin , Liu Jie
Published: April 2022

Anaerobic digestion technology mitigates agricultural organic waste pollution, thereby alleviating the energy crisis. Biochar materials increase the utilisation rate of biomass resources and promote the enrichment and growth of microorganisms. Biochar is an effective exogenous additive that stabilises the anaerobic digestion, improves anaerobic digestion efficiency and gas production. Herein, biochar materials were prepared from rice straw utilising the sequencing batch anaerobic digestion process. The biochar microstructure was characterised by scanning electron microscopy (SEM) and Brunauer–Emmett–Teller (BET) analysis, and microbial succession and metabolic pathways were analysed using 16S rRNA sequencing to reveal the molecular mechanisms. Rice straw biochar addition increased gas production during anaerobic fermentation. SEM revealed that numerous cocci and microbacteria became agglomerated and attached to the surface and pores of biochar, which was revealed by BET analysis to be a good habitat for microorganisms. After anaerobic digestion, the specific surface area and total pore volume of biochar decreased. 16S rRNA gene sequencing showed that biochar affected the abundance of certain bacteria and archaea. Biochar had no obvious effect on the function of bacterial flora but inhibited carbohydrate metabolism by bacteria and glycan biosynthesis and metabolism by archaea in the anaerobic fermentation system while promoting lipid metabolism by archaea. Biochar addition inhibited acetic acid production in the anaerobic fermentation system and promoted methane production based on hydrogen and carbon dioxide levels.
Interaction of human CRX and NRL in live HEK293T cells measured using fluorescence resonance energy transfer (FRET)
Authors: Zhuo Xinming , Knox Barry E.
Published: April 2022

CRX and NRL are retina-specific transcription factors that control rod photoreceptor differentiation and synergistically activate rod phototransduction gene expression. Previous experiments showed they interact in vitro and in yeast two-hybrid assays. Here, we examined CRX-NRL interaction in live HEK293T cells using two fluorescence resonance energy transfer (FRET) approaches: confocal microscopy and flow cytometry (FC-FRET). FC-FRET can provide measurements from many cells having wide donor–acceptor expression ranges. FRET efficiencies were calibrated with a series of donor (EGFP)-acceptor (mCherry) fusion proteins separated with linkers between 6–45 amino acids. CRX and NRL were fused at either terminus with EGFP or mCherry to create fluorescent proteins, and all combinations were tested in transiently transfected cells. FRET signals between CRX or NRL homo-pairs were highest with both fluorophores fused to the DNA binding domains (DBD), lower with both fused to the activation domains (AD), and not significant when fused on opposite termini. NRL had stronger FRET signals than CRX. A significant FRET signal between CRX and NRL hetero-pairs was detected when donor was fused to the CRX DNA binding domain and the acceptor fused to the NRL activation domain. FRET signals increased with CRX or NRL expression levels at a rate much higher than expected for collisional FRET alone. Together, our results show the formation of CRX-NRL complexes in live HEK293T cells that are close enough for FRET.
Circulating microRNA profiling is altered in the acute respiratory distress syndrome related to SARS-CoV-2 infection
Authors: Garcia-Giralt Natalia , Du Juan , Marin-Corral Judith , Bódalo-Torruella Marta , Blasco-Hernando Fabiola , Muñoz-Bermúdez Rosana , Clarós Miquel , Nonell Lara , Perera-Bel Julia , Fernandez-González Marta , Nogues Xavier , Sorli-Redó Luisa , Güerri-Fernández Robert
Published: April 2022

One of the hallmarks of SARS-CoV-2 infection is an induced immune dysregulation, in some cases resulting in cytokine storm syndrome and acute respiratory distress syndrome (ARDS). Several physiological parameters are altered as a result of infection and cytokine storm. Among them, microRNAs (miRNAs) might reflect this poor condition since they play a significant role in immune cellular performance including inflammatory responses. Circulating miRNAs in patients who underwent ARDS and needed mechanical ventilation (MV+; n = 15) were analyzed by next generation sequencing in comparison with patients who had COVID-19 poor symptoms but without intensive care unit requirement (MV−; n = 13). A comprehensive in silico analysis by integration with public gene expression dataset and pathway enrichment was performed. Whole miRNA sequencing identified 170 differentially expressed miRNAs between patient groups. After the validation step by qPCR in an independent sample set (MV+  = 10 vs. MV− = 10), the miR-369-3p was found significantly decreased in MV+ patients (Fold change − 2.7). After integrating with gene expression results from COVID-19 patients, the most significant GO enriched pathways were acute inflammatory response, regulation of transmembrane receptor protein Ser/Thr, fat cell differentiation, and regulation of biomineralization and ossification. In conclusion, miR-369-3p was altered in patients with mechanical ventilation requirement in comparison with COVID-19 patients without this requirement. This miRNA is involved in inflammatory response which it can be considered as a prognosis factor for ARDS in COVID-19 patients.
Airway epithelial interferon response to SARS-CoV-2 is inferior to rhinovirus and heterologous rhinovirus infection suppresses SARS-CoV-2 replication
Authors: Vanderwall Elizabeth R. , Barrow Kaitlyn A. , Rich Lucille M. , Read David F. , Trapnell Cole , Okoloko Oghenemega , Ziegler Steven F. , Hallstrand Teal S. , White Maria P. , Debley Jason S.
Published: April 2022

Common alphacoronaviruses and human rhinoviruses (HRV) induce type I and III interferon (IFN) responses important to limiting viral replication in the airway epithelium. In contrast, highly pathogenic betacoronaviruses including SARS-CoV-2 may evade or antagonize RNA-induced IFN I/III responses. In airway epithelial cells (AECs) from children and older adults we compared IFN I/III responses to SARS-CoV-2 and HRV-16, and assessed whether pre-infection with HRV-16, or pretreatment with recombinant IFN-β or IFN-λ, modified SARS-CoV-2 replication. Bronchial AECs from children (ages 6–18 years) and older adults (ages 60–75 years) were differentiated ex vivo to generate organotypic cultures. In a biosafety level 3 (BSL-3) facility, cultures were infected with SARS-CoV-2 or HRV-16, and RNA and protein was harvested from cell lysates 96 h. following infection and supernatant was collected 48 and 96 h. following infection. In additional experiments cultures were pre-infected with HRV-16, or pre-treated with recombinant IFN-β1 or IFN-λ2 before SARS-CoV-2 infection. In a subset of experiments a range of infectious concentrations of HRV-16, SARS-CoV-2 WA-01, SARS-CoV-2 Delta variant, and SARS-CoV-2 Omicron variant were studied. Despite significant between-donor heterogeneity SARS-CoV-2 replicated 100 times more efficiently than HRV-16. IFNB1, INFL2, and CXCL10 gene expression and protein production following HRV-16 infection was significantly greater than following SARS-CoV-2. IFN gene expression and protein production were inversely correlated with SARS-CoV-2 replication. Treatment of cultures with recombinant IFNβ1 or IFNλ2, or pre-infection of cultures with HRV-16, markedly reduced SARS-CoV-2 replication. In addition to marked between-donor heterogeneity in IFN responses and viral replication, SARS-CoV-2 (WA-01, Delta, and Omicron variants) elicits a less robust IFN response in primary AEC cultures than does rhinovirus, and heterologous rhinovirus infection, or treatment with recombinant IFN-β1 or IFN-λ2, reduces SARS-CoV-2 replication, although to a lesser degree for the Delta and Omicron variants.