bluuebunny/crossref_metadata_2025 huggingface dataset:
Spatial interpretation of high‐resolution environmental proxy data of the Middle Pleistocene Palaeolithic faunal kill site Schöningen 13 II‐4, Germany
Authors: Urban Brigitte , Krahn Kim J. , Kasper Thomas , García‐Moreno Alejandro , Hutson Jarod M. , Villaluenga Aritza , Turner Elaine , Gaudzinski‐Windheuser Sabine , Farghaly Dalia , Tucci Mario , Schwalb Antje
Published: June 2023

To spatially characterize the palaeolakeshore environment at the archaeological kill site Schöningen 13 II‐4 of the Middle Pleistocene Reinsdorf sequence, in‐depth palynological, geochemical, aquatic microfossil and archaeological analyses were undertaken on sediment sections with an average thickness of about 15 cm, concordantly overlain by faunal remains, dominated by horse, from the unique ‘Spear Horizon’ layers of the 1995 excavation campaign. The data reveal a distinctive lake level drop, documented by the change from a carbonate‐rich lake marl to a carbonate‐free organic mud with increased carbon content and decreasing C/N, Si/Al, Si/K and Fe/Al ratios, indicating a higher pedogenic supply of organic matter and drier conditions at the site. Compared with older, similar transitional phases of lake level changes occurring within the Reinsdorf sequence, it is important that these youngest sediments are undisturbed, indicating continuous development. Ostracod and diatom analyses indicate a lowering water level with higher salinities and rich aquatic vegetation. Mesorheophilic ostracod species along with tychoplanktic diatom taxa point to flowing waters and turbulence at the lakeshore, presumably related to spring‐fed streams originating from nearby highlands. Palynological results reveal a very diverse zonal vegetation pattern around the palaeolakeshore considering an area of investigation of approximately 50 × 75 m and a tessellated type of regional vegetation during the formation of the archaeological horizons. On topographically lower elevated areas, birch groves and taxa favouring wet, marshy conditions such as Cyperaceae, indicative of terrestrialization, were predominating, while other stands of this transitional phase reveal a very dry, grass‐dominated steppe woodland favouring a rich wildlife with a striking number of megaherbivores. Our results suggest that the lithological differences of the ‘Spear Horizon’ layers containing the archaeological finds were due to their respective topographical situation and that the layers were deposited almost simultaneously during the beginning of the lake level drop. Human activities seem to have concentrated in sparsely vegetated areas along the palaeolakeshore, rather than in areas of adjacent denser birch swamp forest stands.
Purification and structural analysis of a novel polysaccharide from Rehmannia Radix Praeparata
Authors: Liu Chongying , Zhang Tingting , Zhao Peng , Liu Simei , Li Xinyue , Yuan Yufang
Published: June 2023

In this paper, the purification, structure, and antioxidant activity of Rehmannia Radix Praeparata polysaccharide (RRPP) were studied. The RRPP was separated using DEAE‐52 cellulose and Sephadex G‐100. The RRPP consisted of xylose, glucose, rhamnose, galactose, and mannose in ratios of 10.64:5.58:3.52:1.39:1.0. No protein was detected in the RRPP fraction, and the molecular weight of RRPP was about 1.75 × 106 Da. The basic skeleton information was obtained using periodic acid oxidation—Smith degradation, and RRPP contained 1→, 1 → 2, 1 → 3, 1 → 4, 1 → 2,6, 1 → 4,6 or 1 → 6, 1 → 2,3, 1 → 2,3,4, and other glycosidic bonds. Fourier transform infrared spectroscopy also showed that RRPP has both α‐ and β‐glycosidic bonds. The in vitro antioxidant activity test showed that RRPP could potentialize scavenging effect on ABTS+· and its scavenging rate was 91.3%.
The designation, synthesis, and affinity determination of affinity peptide for anthrax protective antigen
Authors: Liang Ting , Chen Jingfei , Rui Yan , Hexi Li
Published: June 2023

Detection of anthrax protective antigen is an effective way to diagnose anthracnose, and it plays an important part in the treatment of anthracnose. Affinity peptides, as a miniature biological recognition element, can quickly and effectively detect anthrax protective antigens. Based on computer‐aided design technology (CAD), we have herein developed an affinity peptide design strategy for the detection of anthrax protective antigens. Firstly, six high‐value mutation sites were determined based on the molecular docking between the template peptide and the receptor, and then the multi‐site mutation of amino acids was carried out in order to establish a virtual peptide library. The library was selected by using molecular dynamics simulation and the best designed affinity peptide (code: P24) was found. The theoretical affinity with P24 peptide has increased by 19.8% compared with template peptide. Finally, the affinity with P24 peptide was measured by SPR technology to reach the nanomole level, which verified the effectiveness of the design strategy. The newly designed affinity peptide is expected to be used in the diagnosis of anthracnose.
“A morning cortisol is the most effective clinical predictor of short synacthen test outcome”: A tertiary care centre experience
Authors: Mathara Diddhenipothage Shani A. D. , Beck Katharina J. , Loo Helen , Amiyangoda Gayana K. , Pofi Riccardo , Tomlinson Jeremy W. , Pal Aparna
Published: June 2023

Objective

Increasing referrals to Endocrinology with nonspecific symptoms of suspected adrenal insufficiency (AI) has increased use of the short‐synacthen test (SST). Prevailing resource and safety concerns emphasise importance of patient selection criterion to optimise SST use. This study aimed to (1) document the adverse event profile of the SST (2) identify any pretest predictors of SST outcome.

Design, Patients and Measurements

Retrospective data analysis of all patients referred for SST in Oxford from 2017 to 2021. Pretest clinical variables (age, sex, BMI, blood pressure and electrolytes), symptoms (fatigue, dizziness, weight loss) and pretest morning cortisol were included in the statistical model with the aim of identifying any variables that could predict SST outcome in Group 1 primary AI, Group 2 central AI and Group 3 glucocorticoid induced AI. Symptoms and signs during and post SST were also noted with the aim of describing adverse effects to synacthen across a large cohort.

Results

A total 1480 SSTs (Males:38%, age 52 [39−66] years) were performed: 505 (34.1%) in Group 1, 838 (57%) in Group 2, and 137 (9.3%) in Group 3. Adverse‐effects were recorded in 1.8% of tests, including one episode of anaphylaxis. Pretest morning‐cortisol was the only predictor for an “SST pass” (whole cohort: B = 0.015, p < 0.001, Group 1: B = 0.018, p < .001; Group 2: B = 0.010, p < 0.012; Group 3: B = 0.018, p = <.001). A threshold of ≥343 nmol/l (receiver‐operating characteristic [ROC] area under the curve [AUC] = 0.725, 95% confidence interval [CI] 0.675−0.775, p < 0.001) for the whole cohort, ≥300 nmol/L (ROC AUC = 0.763, 95% CI 0.675 to 0.850, p < 0.001) for Group 1, ≥340 nmol/L (ROC AUC = 0.688, 95% CI 0.615 to 0.761, p < 0.001) for Group2, and ≥376 nmol/L [baseline cortisol] (ROC AUC = 0.783, 95% CI 0.708 to 0.859, p < 0.001) for Group 3, predicted an ‘SST pass’ with 100% specificity.

Conclusions

Adverse effects to synacthen are rare. Pretest morning cortisol is a reliable predictor for SST outcome and is a helpful tool to rationalise use of the SST. Predictive morning‐cortisol thresholds vary according to the aetiology of AI.
Parent–child relationship and parents' psychological well‐being among Malaysian families amid pandemic: The role of stress and gender
Authors: Tan Soon Aun , Pung Pit Wan , Wu Shin Ling , Yap Chin Choo , Jayaraja Anusha Raj , Chow Brenda Gynn
Published: June 2023

The COVID‐19 pandemic has taken most part of the world by surprise. The orders of nationwide movement control and social distancing by the Malaysian authority to curb the spread of the airborne virus have sent working‐class families into a novel work‐from‐home condition. This study aimed to examine the association between positive experiences in parent–child relationships, parental stress and working parents' psychological well‐being in Malaysia during the pandemic by considering the mediating role of parental stress and the moderating role of parental gender role. A total of 214 working‐from‐home parents (Mage = 46.39; SDage = 9.06; 51.9% working mothers; 76.6% Chinese) participated in a cross‐sectional quantitative online survey. A significant positive relationship was found between parent–child relationships and parents' psychological well‐being. Parental stress was negatively correlated with parent–child relationships and parents' psychological well‐being. Meanwhile, parental stress significantly mediates the link between parent–child relationships and parents' psychological well‐being. Besides, parental gender role was found to be a significant moderator where fathers experience better psychological well‐being when they have more positive parent–child relationships. The findings further support the importance of positive interaction between parents and children and parental stress, which could affect parents' psychological well‐being. This study may fill a knowledge gap by providing an overview of working parents' psychological well‐being in their experience of working from home during the pandemic.
Upregulation of lysine‐specific demethylase 6B aggravates inflammatory pain through H3K27me3 demethylation‐dependent production of TNF‐α in the dorsal root ganglia and spinal dorsal horn in rats
Authors: Qiao Yiming , Li Liren , Bai Liying , Gao Yan , Yang Yin , Wang Li , Wang Xueli , Liang Zongyi , Xu Ji‐Tian
Published: June 2023

Aims

Lysine‐specific demethylase 6B (KDM6B) serves as a key mediator of gene transcription. It regulates expression of proinflammatory cytokines and chemokines in variety of diseases. Herein, the role and the underlying mechanisms of KDM6B in inflammatory pain were studied.

Methods

The inflammatory pain was conducted by intraplantar injection of complete Freund's adjuvant (CFA) in rats. Immunofluorescence, Western blotting, qRT‐PCR, and chromatin immunoprecipitation (ChIP)‐PCR were performed to investigate the underlying mechanisms.

Results

CFA injection led to upregulation of KDM6B and decrease in the level of H3K27me3 in the dorsal root ganglia (DRG) and spinal dorsal horn. The mechanical allodynia and thermal hyperalgesia following CFA were alleviated by the treatment of intrathecal injection of GSK‐J4, and by microinjection of AAV‐EGFP‐KDM6B shRNA in the sciatic nerve or in lumbar 5 dorsal horn. The increased production of tumor necrosis factor‐α (TNF‐α) following CFA in the DRGs and dorsal horn was inhibited by these treatments. ChIP‐PCR showed that CFA‐induced increased binding of nuclear factor κB with TNF‐α promoter was repressed by the treatment of microinjection of AAV‐EGFP‐KDM6B shRNA.

Conclusions

These results suggest that upregulated KDM6B via facilitating TNF‐α expression in the DRG and spinal dorsal horn aggravates inflammatory pain.
Emotional and behavioral problems change the development of cerebellar gray matter volume, thickness, and surface area from childhood to adolescence: A longitudinal cohort study
Authors: Wang Yanpei , Ma Leilei , Chen Rui , Liu Ningyu , Zhang Haibo , Li Yuanyuan , Wang Jiali , Hu Mingming , Zhao Gai , Men Weiwei , Tan Shuping , Gao Jia‐Hong , Qin Shaozheng , He Yong , Dong Qi , Tao Sha
Published: June 2023

Aims

Increasing evidence indicates that major neurodevelopmental disorders have potential links to abnormal cerebellar development. However, the developmental trajectories of cerebellar subregions from childhood to adolescence are lacking, and it is not clear how emotional and behavioral problems affect them. We aim to map the developmental trajectories of gray matter volume (GMV), cortical thickness (CT), and surface area (SA) in cerebellar subregions from childhood to adolescence and examine how emotional and behavioral problems change the cerebellar development trajectory in a longitudinal cohort study.

Method

This population‐based longitudinal cohort study used data on a representative sample of 695 children. Emotional and behavioral problems were assessed at baseline and at three annual follow‐ups with the Strengths and Difficulties Questionnaire (SDQ).

Results

Using an innovative automated image segmentation technique, we quantified the GMV, CT, and SA of the whole cerebellum and 24 subdivisions (lobules I‐VI, VIIB, VIIIA&B, and IX‐X plus crus I‐II) with 1319 MRI scans from a large longitudinal sample of 695 subjects aged 6–15 years and mapped their developmental trajectories. We also examined sex differences and found that boys showed more linear growth, while girls showed more nonlinear growth. Boys and girls showed nonlinear growth in the cerebellar subregions; however, girls reached the peak earlier than boys. Further analysis found that emotional and behavioral problems modulated cerebellar development. Specifically, emotional symptoms impede the expansion of the SA of the cerebellar cortex, and no gender differences; conduct problems lead to inadequate cerebellar GMV development only in girls, but not boys; hyperactivity/inattention delays the development of cerebellar GMV and SA, with left cerebellar GMV, right VIIIA GMV and SA in boys and left V GMV and SA in girls; peer problems disrupt CT growth and SA expansion, resulting in delayed GMV development, with bilateral IV, right X CT in boys and right Crus I GMV, left V SA in girls; and prosocial behavior problems impede the expansion of the SA and lead to excessive CT growth, with bilateral IV, V, right VI CT, left cerebellum SA in boys and right Crus I GMV in girls.

Conclusions

This study maps the developmental trajectories of GMV, CT, and SA in cerebellar subregions from childhood to adolescence. In addition, we provide the first evidence for how emotional and behavioral problems affect the dynamic development of GMV, CT, and SA in the cerebellum, which provides an important basis and guidance for the prevention and intervention of cognitive and emotional behavioral problems in the future.
A neuromarker for deficit syndrome in schizophrenia from a combination of structural and functional magnetic resonance imaging
Authors: Gao Ju , Jiang Rongtao , Tang Xiaowei , Chen Jiu , Yu Miao , Zhou Chao , Wang Xiang , Zhang Hongying , Huang Chengbing , Yang Yong , Zhang Xiaobin , Cui Zaixu , Zhang Xiangrong
Published: June 2023

Aim

Deficit schizophrenia (DS), defined by primary and enduring negative symptoms, has been proposed as a promising homogeneous subtype of schizophrenia. It has been demonstrated that unimodal neuroimaging characteristics of DS were different from non‐deficit schizophrenia (NDS), however, whether multimodal‐based neuroimaging features could identify deficit syndrome remains to be determined.

Methods

Functional and structural multimodal magnetic resonance imaging of DS, NDS and healthy controls were scanned. Voxel‐based features of gray matter volume, fractional amplitude of low‐frequency fluctuations, and regional homogeneity were extracted. The support vector machine classification models were constructed using these features separately and jointly. The most discriminative features were defined as the first 10% of features with the greatest weights. Moreover, relevance vector regression was applied to explore the predictive values of these top‐weighted features in predicting negative symptoms.

Results

The multimodal classifier achieved a higher accuracy (75.48%) compared with the single modal model in distinguishing DS from NDS. The most predictive brain regions were mainly located in the default mode and visual networks, exhibiting differences between functional and structural features. Further, the identified discriminative features significantly predicted scores of diminished expressivity factor in DS but not NDS.

Conclusions

The present study demonstrated that local properties of brain regions extracted from multimodal imaging data could distinguish DS from NDS with a machine learning‐based approach and confirmed the relationship between distinctive features and the negative symptoms subdomain. These findings may improve the identification of potential neuroimaging signatures and improve the clinical assessment of the deficit syndrome.
A dual‐channel ensembled deep convolutional neural network for facial expression recognition in the wild
Authors: Saurav Sumeet , Saini Ravi , Singh Sanjay
Published: June 2023

Facial expression recognition (FER) in the wild is an active and challenging field of research. A system for automatic FER finds use in a wide range of applications related to advanced human–computer interaction (HCI), human–robot interaction (HRI), human behavioral analysis, gaming and entertainment, etc. Since their inception, convolutional neural networks (CNNs) have attained state‐of‐the‐art accuracy in the facial analysis task. However, recognizing facial expressions in the wild with high confidence running on a low‐cost embedded device remains challenging. To this end, this study presents an efficient dual‐channel ensembled deep CNN (DCE‐DCNN) for FER in the wild. Initially, two DCNNs, namely the and , are trained separately on the grayscale and Scharr‐convolved vertical gradient facial images, respectively. The proposed network later integrates the two pre‐trained DCNNs to obtain the dual‐channel integrated DCNN (DCI‐DCNN). Finally, all three neural networks, namely the , , and DCI‐DCNN, are jointly fine‐tuned to get a single dual‐channel‐multi‐output model. The multi‐output model produces three prediction scores for the given input facial image. The prediction scores are thus fused using the max‐voting ensemble scheme to obtain the DCE‐DCNN with the final classification label. On the FER2013, RAF‐DB, NCAER‐S, AffectNet, and CKPlus benchmark FER datasets, the proposed DCE‐DCNN consistently outperforms the two individual DCNNs and numerous state‐of‐the‐art CNNs. Moreover, the network achieves competitive recognition accuracy on all four FER in the wild datasets with reduced memory storage size and parameters. The proposed DCE‐DCNN model with high throughput on resource‐limited embedded devices is suitable for applications that seek real‐time classification of facial expressions in the wild with high confidence.
Advancing protected area effectiveness assessments by disentangling social‐ecological interactions: A case study from the Luangwa Valley, Zambia
Authors: Frietsch Marina , Zafra‐Calvo Noelia , Ghoddousi Arash , Loos Jacqueline
Published: June 2023

Protected and conserved areas (PCAs) target at biodiversity conservation and human well‐being, but often reflect low levels of effectiveness. Understanding PCAs social‐ecological systems in which people and nature interact in so‐called social‐ecological interactions is key to understanding the roots of (in)effectiveness, and to leverage change toward resilient and sustainable systems. Despite this potential, social‐ecological interactions in PCAs are commonly neglected in effectiveness evaluations. To address this gap, we elaborated a thorough understanding of the social‐ecological interactions in PCAs through the following steps: In a first step, we extracted from scientific literature which social‐ecological interactions influence the effectiveness of PCAs in general and derived influencing factors which shape those interactions. Based on these insights, we developed an analytical framework, which, in a second step, we applied to a case study in North Luangwa, Zambia. We elucidated three dimensions of social‐ecological interactions occurring in the study area: care (e.g., conservation programs), conflict (e.g., disease transmission), and use (e.g., hunting). We visualized relationships between these interactions and associated key variables in a causal loop diagram. Finally, we drew on the case study in Zambia's Luangwa Valley to propose system‐specific metrics for key variables central to the social‐ecological structure of the study area to make effectiveness measurable. Our approach allows for linking site‐specific social‐ecological interactions to PCA effectiveness. More generally, our findings call for the consideration of the relationships between people and nature when assessing conservation effectiveness.
Field validation as a tool for mitigating uncertainty in species distribution modeling for conservation planning
Authors: Johnson Sara , Molano‐Flores Brenda , Zaya David
Published: June 2023

Despite the success of species distribution models (SDMs) in rare species conservation planning, inherent uncertainty in predictions can facilitate misuse or misapplication. Field validation is important as model predictions can vary greatly due to low species prevalence or spatial bias; traits frequently encountered in rare species data. This study outlines an effective SDM approach to map the potential distribution of a Florida endemic plant species, Macbridea alba, which is transferable to other rare species that: (1) utilize presence data to create species distribution maps, (2) conduct field validation to gather independent data, (3) and use independent data for model evaluation and improvement. Independent data was used to assess each model's ability to predict the occurrence of M. alba and identify habitat for conservation and reintroduction efforts. Our study documents that for low prevalence species, models can produce significant variation in optimized threshold and evaluation metrics, which impact outcomes when converting continuous predictions to binary predictions, a common practice in model application. Our species distribution models were useful in finding new populations of M. alba. Field validation is vital to improving model performance, threshold selection, and evaluating model design and should be carefully considered when suggesting model use and application.
Responsible Behavior of Irresponsible Companies: Air Pollution and Charitable Donations of Polluting Companies
Authors: Li Weibing , Chen Siyuan , Zhang Kaixia
Published: June 2023

The relationship between air pollution and charitable donations of companies has received little attention from academia. To make up for this defect, we use a regression discontinuity design based on the spatial discontinuity in air pollution created by China's winter heating policy in the north of Qinling Mountains–Huai River line to examine whether severe air pollution may cause polluting companies to make charitable donations. Our results consistently show that air pollution has a positive impact on the donations of polluting companies, regardless of whether the absolute donations, the relative donations, or the willingness to donate are used to measure donations. A series of robustness tests confirm that this relationship is causal. Furthermore, we find that under severe air pollution, the motivations of polluting companies to implement donation behaviors are to decrease the probability of environmental penalties, reduce environmental pollution costs, and decrease the extent to which air pollution affects company reputations.
Impact of computer‐aided characterization for diagnosis of colorectal lesions, including sessile serrated lesions: Multireader, multicase study
Authors: Kato Shun , Kudo Shin‐ei , Minegishi Yosuke , Miyata Yuki , Maeda Yasuharu , Kuroki Takanori , Takashina Yuki , Mochizuki Kenichi , Tamura Eri , Abe Masahiro , Sato Yuta , Sakurai Tatsuya , Kouyama Yuta , Tanaka Kenta , Ogawa Yushi , Nakamura Hiroki , Ichimasa Katsuro , Ogata Noriyuki , Hisayuki Tomokazu , Hayashi Takemasa , Wakamura Kunihiko , Miyachi Hideyuki , Baba Toshiyuki , Ishida Fumio , Nemoto Tetsuo , Misawa Masashi ,   Collaborators
Published: June 2023

Objectives

Computer‐aided characterization (CADx) may be used to implement optical biopsy strategies into colonoscopy practice; however, its impact on endoscopic diagnosis remains unknown. We aimed to evaluate the additional diagnostic value of CADx when used by endoscopists for assessing colorectal polyps.

Methods

This was a single‐center, multicase, multireader, image‐reading study using randomly extracted images of pathologically confirmed polyps resected between July 2021 and January 2022. Approved CADx that could predict two‐tier classification (neoplastic or nonneoplastic) by analyzing narrow‐band images of the polyps was used to obtain a CADx diagnosis. Participating endoscopists determined if the polyps were neoplastic or not and noted their confidence level using a computer‐based, image‐reading test. The test was conducted twice with a 4‐week interval: the first test was conducted without CADx prediction and the second test with CADx prediction. Diagnostic performances for neoplasms were calculated using the pathological diagnosis as reference and performances with and without CADx prediction were compared.

Results

Five hundred polyps were randomly extracted from 385 patients and diagnosed by 14 endoscopists (including seven experts). The sensitivity for neoplasia was significantly improved by referring to CADx (89.4% vs. 95.6%). CADx also had incremental effects on the negative predictive value (69.3% vs. 84.3%), overall accuracy (87.2% vs. 91.8%), and high‐confidence diagnosis rate (77.4% vs. 85.8%). However, there was no significant difference in specificity (80.1% vs. 78.9%).

Conclusions

Computer‐aided characterization has added diagnostic value for differentiating colorectal neoplasms and may improve the high‐confidence diagnosis rate.
Molecular detection of reproductive symbionts and parthenogenesis experiments in Tuta absoluta from Argentina: facing potential for sustainable and specific pest control strategies
Authors: Cagnotti C. , Conte C. , Kramar J. , Lanzavecchia S. , López S.
Published: June 2023

Tomato leafminer, Tuta absoluta (Meyrick) (Lepidoptera: Gelechiidae), is a key pest of tomato crops. Specific and environmentally friendly control strategies against this pest, such as the sterile insect technique (SIT), are under development and sexual reproduction has emerged as a key focal point to ensure its success. In the present study, we analyzed four representative T. absoluta populations from Argentina, focusing on the molecular detection of endosymbionts potentially associated with reproductive abnormalities and on determining whether parthenogenesis can occur under laboratory conditions. Larvae of T. absoluta were collected in commercial tomato plantations from La Plata and Mar del Plata (both in Buenos Aires province), Bella Vista (Corrientes province), and Yuto (Jujuy province). Tuta absoluta adults were evaluated by standard PCR for the presence of reproductive endosymbionts (Wolbachia sp., Spiroplasma sp., Arsenophonus sp., Cardinium sp., and Rickettsia sp.). For parthenogenesis assays, 20–23 virgin females from each T. absoluta geographic population were life‐long isolated in Petri dishes with a tomato leaf. Fecundity, fertility, and female longevity were estimated and compared with results from mated females from each population. Our results showed the presence of a unique endosymbiont (Wolbachia sp. supergroup B, sequence type 41). Fecundity of the unmated females was significantly lower than fecundity of mated females in all T. absoluta populations. In addition, unmated females only laid infertile eggs. In conclusion, the absence of parthenogenesis in T. absoluta from representative geographic populations supports the implementation of SIT and mating disruption as effective control strategies against this pest in Argentina.
Assessing the impact of interfering organic matter on soil metaproteomic workflow
Authors: Waibel Matthias , McDonnell Kevin , Tuohy Maria , Shirran Sally , Synowsky Sylvia , Thornton Barry , Paterson Eric , Brennan Fiona , Abram Florence
Published: June 2023

Soil organic matter (SOM) is biologically, chemically, and physically complex. As a major store of nutrients within the soil, it plays an important role in nutrient provision to plants. An enhanced understanding of SOM utilisation processes could underpin better fertiliser management for plant growth, with reduced environmental losses. Metaproteomics can allow the characterisation of protein profiles and could help gain insights into SOM microbial decomposition mechanisms. Here, we applied three different extraction methods to two soil types to recover SOM with different characteristics. Specifically, water‐extractable organic matter, mineral‐associated organic matter and protein‐bound organic matter were targeted with the aim to investigate the metaproteome enriched in those extractions. As a proof‐of‐concept, replicated extracts from one soil were further analysed for peptide identification using liquid chromatography followed by tandem mass spectrometry. We employed a framework for mining mass spectra for both peptide assignment and fragmentation pattern characterisation. Different extracts were found to exhibit contrasting total protein and humic substance content for the two soils investigated. Overall, water extracts displayed the lowest humic substance content (in both soils) and the highest number of peptide identifications (in the soil investigated) with the most frequent peptide hits associated with diverse substrate/ligand binding proteins of Proteobacteria and derived taxa. Our framework also highlighted a strong peptidic signal in unassigned and unmatched spectra, information that is currently not captured by the pipelines employed in this study. Taken together, this work points to specific areas for optimisation in chromatography and mass spectrometry to adequately characterise SOM‐associated metaproteomes.
Pupal RNA interference methods for analyzing adult development in stag beetles
Authors: Hagiwara Jin , Nozawa Leon , Ohtsu Itsuki , Shinohara Tadashi , Gotoh Hiroki
Published: June 2023

Holometabolous insects dramatically change their morphology via molt, both from larva to pupa and from pupa to adult. In nonmodel insects, RNA interference (RNAi) is a strong tool for analyzing gene function during postembryonic development. In many cases, larval RNAi is effective for analyzing genes involved in morphogenesis via metamorphosis. However, RNAi of genes involved in development sometimes results in lethality before animals metamorphose to pupae and/or adults, making it impossible to analyze their function during the pupal period. In this study, we establish a pupal RNAi system in the stag beetle Dorcus rectus. We selected the genes white and scarlet for RNAi knockdown to investigate appropriate injection timing and position. Both genes are known to be involved in eye pigmentation. By using these candidate genes, we demonstrate the potential of pupal RNAi in this experimental system. This method will be useful for analyzing pupal‐specific morphogenesis including fine‐shaping of the enlarged male mandible in this species.
Celebrating Nicaea
Authors: Durber Susan
Published: June 2023

Why should Christians from churches of the Reformation be marking the 1700th anniversary of Nicaea? Some Christians from such churches regard Nicaea as emblematic of Christianity's “fall” from the radical and subversive faith of Jesus’ teaching, miracles, and welcome to become an abstract and theological discourse dependent not on the Bible but on Greek philosophy. Some ask why they should pay any attention to a long ago gathering of male bishops or let that gathering, rather than simply the Bible and their own personal faith experience, shape their understanding of Christianity. In this paper, the author, herself from a church often inclined to such Protestant critiques of Nicaea, suggests a more open approach and a positive understanding of Nicaea for today's church.
St Cyril of Alexandria and the Council of Nicaea
Authors: Serapion Metropolitan , Refela Macarius
Published: June 2023

In commemorating the Council of Nicaea, we are not looking solely at the document that it produced, nor simply the words contained in a manuscript, but the lived tradition that produced it and continues to refine our understanding. This article will therefore explore how in the century that followed the Council of Nicaea, St Cyril of Alexandria, in seeking to combat Nestorianism, in which Christ is asserted to have had distinct human and divine persons, and Mary denied the status of Theotokos (mother of God), argued not on the basis of the literal wording of the Creed of Nicaea, but on the lived tradition that produced it and continues to refine our understanding of it.
“Light from Light”
Authors: Munkholt Christensen Maria
Published: June 2023

This article examines the phrase “light from light” in the 4th‐century Nicene and Nicene‐Constantinopolitan creeds. The article begins by presenting the earliest use of light as a metaphor for Christ and his agency, as well as examples of similar language outside “orthodox” Christianity. It goes on to examine the meaning and use of “light from light” in the orthodox creeds and the debates that accompanied them before discussing the more popular use of “light from light” in Late antiquity/Byzantine piety. The article concludes by considering the contemporary potential in the formulation “light from light.”
Identifying and addressing methodological incongruence in phylogenomics: A review
Authors: Fleming James F. , Valero‐Gracia Alberto , Struck Torsten H.
Published: June 2023

The availability of phylogenetic data has greatly expanded in recent years. As a result, a new era in phylogenetic analysis is dawning—one in which the methods we use to analyse and assess our data are the bottleneck to producing valuable phylogenetic hypotheses, rather than the need to acquire more data. This makes the ability to accurately appraise and evaluate new methods of phylogenetic analysis and phylogenetic artefact identification more important than ever. Incongruence in phylogenetic reconstructions based on different datasets may be due to two major sources: biological and methodological. Biological sources comprise processes like horizontal gene transfer, hybridization and incomplete lineage sorting, while methodological ones contain falsely assigned data or violations of the assumptions of the underlying model. While the former provides interesting insights into the evolutionary history of the investigated groups, the latter should be avoided or minimized as best as possible. However, errors introduced by methodology must first be excluded or minimized to be able to conclude that biological sources are the cause. Fortunately, a variety of useful tools exist to help detect such misassignments and model violations and to apply ameliorating measurements. Still, the number of methods and their theoretical underpinning can be overwhelming and opaque. Here, we present a practical and comprehensive review of recent developments in techniques to detect artefacts arising from model violations and poorly assigned data. The advantages and disadvantages of the different methods to detect such misleading signals in phylogenetic reconstructions are also discussed. As there is no one‐size‐fits‐all solution, this review can serve as a guide in choosing the most appropriate detection methods depending on both the actual dataset and the computational power available to the researcher. Ultimately, this informed selection will have a positive impact on the broader field, allowing us to better understand the evolutionary history of the group of interest.
Model‐based offline reinforcement learning for sustainable fishery management
Authors: Ju Jun , Kurniawati Hanna , Kroese Dirk , Ye Nan
Published: June 2023

Fisheries, as indispensable natural resources for human, need to be managed with both short‐term economical benefits and long‐term sustainability in consideration. This has remained a challenge, because the population and catch dynamics of the fisheries are complex and noisy, while the data available is often scarce and only provides partial information on the dynamics. To address these challenges, we formulate the population and catch dynamics as a Partially Observable Markov Decision Process (POMDP), and propose a model‐based offline reinforcement learning approach to learn an optimal management policy. Our approach allows learning fishery management policies from possibly incomplete fishery data generated by a stochastic fishery system. This involves first learning a POMDP fishery model using a novel least squares approach, and then computing the optimal policy for the learned POMDP. The learned fishery dynamics model is useful for explaining the resulting policy's performance. We perform systematic and comprehensive simulation study to quantify the effects of stochasticity in fishery dynamics, proliferation rates, missing values in fishery data, dynamics model misspecification, and variability of effort (e.g., the number of boat days). When the effort is sufficiently variable and the noise is moderate, our method can produce a competitive policy that achieves 85% of the optimal value, even for the hardest case of noisy incomplete data and a misspecified model. Interestingly, the learned policies seem to be robust in the presence of model learning errors. However, non‐identifiability kicks in if there is insufficient variability in the effort level and the fishery system is stochastic. This often results in poor policies, highlighting the need for sufficiently informative data. We also provide a theoretical analysis on model misspecification and discuss the tendency of a Schaefer model to overfit compared with a Beverton–Holt model.
Social harvest control rules for sustainable fisheries
Authors: Barclay Kate M. , Bush Simon R. , Poos Jan Jaap , Richter Andries , van Zwieten Paul A. M. , Hamon Katell G. , Carballo‐Cárdenas Eira , Pauwelussen Annet P. , Groeneveld Rolf A. , Toonen Hilde M. , Schadeberg Amanda , Kraan Marloes , Bailey Megan , van Leeuwen Judith
Published: June 2023

Fisheries are supposed to be for the benefit of society, producing food, providing livelihoods and enabling cultural continuity. Biological productivity goals for fish stocks operationalised through Harvest Control Rules (HCRs) are central to contemporary fisheries management. While fisheries policies often state socio‐economic objectives, such as enhancing the livelihoods of coastal communities, those are rarely, if ever, incorporated into operationalised management procedures. The lack of articulation of social objectives and lack of monitoring of social outcomes around HCRs amounts to poor public policy. In this article, we explore the potential for social HCRs (sHCRs) with reference points and agreed predefined actions to make the social dimensions of fisheries explicit. sHCRs cannot cover all social dimensions, so should be considered as one tool within a broader framework of fisheries governance. Moreover, successful sHCRs would require sound deliberative and participatory processes to generate legitimate social objectives, and monitoring and evaluation of fisheries management performance against those objectives. We introduce two potential types of sHCRs, one based on allocation of catch within biological limit reference points, and one for when fishing exceeds biological limit reference points. The application of sHCRs, we argue, can foster accountability and help avoid non‐transparent negotiations on size and distribution of the catch. Our proposal is a call to action for policy makers and fisheries managers to properly integrate social criteria into fisheries governance, and for both biophysical fisheries scientists and social scientists to do better in practical collaboration for methods and knowledge development to support this integration.
Why do some fish grow faster than others?
Authors: Goodrich Harriet R. , Clark Timothy D.
Published: June 2023

All animals must acquire food to grow, but there is a vast diversity in how different species and even different individuals approach and achieve this task. Individuals within a species appear to fall along a bold‐shy continuum, whereby some fish acquire food aggressively and with seemingly high risk, while others appear more submissive and opportunistic. Greater food consumption generally results in faster growth, but only if the energy acquired through food is more than enough to compensate for heightened metabolism associated with a more active lifestyle. Fast‐growing phenotypes also tend to have elevated baseline metabolism – at least when food is plentiful – which may be linked with gut morphology and digestive efficiency. The net energy gained from a meal (as calculated from the specific dynamic action (SDA) coefficient) is optimised with larger meal sizes, but the digestion of large meals can erode the aerobic metabolic scope available for other critical activities such as predator avoidance, perhaps at an interindividual level. Thus, complex interactions between an individual's genes and environment are likely to regulate the growth phenotype. This review compiles available knowledge to shed light on the question: Why do some fish grow faster than others? We discuss the elaborate interrelationships between behaviour, physiology and the gut microbiome with a goal to better understand what drives interindividual differences in growth performance.
The North American Monsoon buffers forests against the ongoing megadrought in the Southwestern United States
Authors: Strange Brandon M. , Monson Russell K. , Szejner Paul , Ehleringer Jim , Hu Jia
Published: June 2023

The US Southwest has been entrenched in a two‐decade‐long megadrought (MD), the most severe since 800 CE, which threatens the long‐term vitality and persistence of regional montane forests. Here, we report that in the face of record low winter precipitation and increasing atmospheric aridity, seasonal activity of the North American Monsoon (NAM) climate system brings sufficient precipitation during the height of the summer to alleviate extreme tree water stress. We studied seasonally resolved, tree‐ring stable carbon isotope ratios across a 57‐year time series (1960–2017) in 17 Ponderosa pine forests distributed across the NAM geographic domain. Our study focused on the isotope dynamics of latewood (LW), which is produced in association with NAM rains. During the MD, populations growing within the core region of the NAM operated at lower intrinsic and higher evaporative water‐use efficiencies (WUEi and WUEE, respectively), compared to populations growing in the periphery of the NAM domain, indicating less physiological water stress in those populations with access to NAM moisture. The disparities in water‐use efficiencies in periphery populations are due to a higher atmospheric vapor pressure deficit (VPD) and reduced access to summer soil moisture. The buffering advantage of the NAM, however, is weakening. We observed that since the MD, the relationship between WUEi and WUEE in forests within the core NAM domain is shifting toward a drought response similar to forests on the periphery of the NAM. After correcting for past increases in the atmospheric CO2 concentration, we were able to isolate the LW time‐series responses to climate alone. This showed that the shift in the relation between WUEi and WUEE was driven by the extreme increases in MD‐associated VPD, with little advantageous influence on stomatal conductance from increases in atmospheric CO2 concentration.
Microbial communities in terrestrial surface soils are not widely limited by carbon
Authors: Cui Yongxing , Peng Shushi , Delgado‐Baquerizo Manuel , Rillig Matthias C. , Terrer César , Zhu Biao , Jing Xin , Chen Ji , Li Jinquan , Feng Jiao , He Yue , Fang Linchuan , Moorhead Daryl L. , Sinsabaugh Robert L. , Peñuelas Josep
Published: June 2023

Microbial communities in soils are generally considered to be limited by carbon (C), which could be a crucial control for basic soil functions and responses of microbial heterotrophic metabolism to climate change. However, global soil microbial C limitation (MCL) has rarely been estimated and is poorly understood. Here, we predicted MCL, defined as limited availability of substrate C relative to nitrogen and/or phosphorus to meet microbial metabolic requirements, based on the thresholds of extracellular enzyme activity across 847 sites (2476 observations) representing global natural ecosystems. Results showed that only about 22% of global sites in terrestrial surface soils show relative C limitation in microbial community. This finding challenges the conventional hypothesis of ubiquitous C limitation for soil microbial metabolism. The limited geographic extent of C limitation in our study was mainly attributed to plant litter, rather than soil organic matter that has been processed by microbes, serving as the dominant C source for microbial acquisition. We also identified a significant latitudinal pattern of predicted MCL with larger C limitation at mid‐ to high latitudes, whereas this limitation was generally absent in the tropics. Moreover, MCL significantly constrained the rates of soil heterotrophic respiration, suggesting a potentially larger relative increase in respiration at mid‐ to high latitudes than low latitudes, if climate change increases primary productivity that alleviates MCL at higher latitudes. Our study provides the first global estimates of MCL, advancing our understanding of terrestrial C cycling and microbial metabolic feedback under global climate change.
Quantifying carbon storage and sequestration by native and non‐native forests under contrasting climate types
Authors: Lázaro‐Lobo Adrián , Ruiz‐Benito Paloma , Cruz‐Alonso Verónica , Castro‐Díez Pilar
Published: June 2023

Non‐native trees may have significant impacts on the carbon sink capacity of forested lands. However, large‐scale patterns of the relative capacity of native and non‐native forests to uptake and store carbon remain poorly described in the literature, and this information is urgently needed to support management decisions. In this study, we analyzed 17,065 plots from the Spanish Forest Inventory (covering c. 30 years) to quantify carbon storage and sequestration of natural forests and plantations of native and non‐native trees under contrasting climate types, while controlling for the effects of environmental factors (forest structure, climate, soil, topography, and management). We found that forest origin (non‐native vs. native) highly influenced carbon storage and sequestration, but such effect was dependent on climate. Carbon storage was greater in non‐native than in native forests in both wet and dry climates. Non‐native forests also had greater carbon sequestration than native ones in the wet climate, due to higher carbon gains by tree growth. However, in the dry climate, native forests had greater carbon gains by tree ingrowth and lower carbon loss by tree mortality than non‐native ones. Furthermore, forest type (classified by the dominant species) and natural forests versus tree plantations were important determinants of carbon storage and sequestration. Native and non‐nativePinusspp. forests had low carbon storage, whereas non‐nativeEucalyptusspp. forests and nativeQuercusspp.,Fagus sylvatica, and Eurosiberian mixed forests (especially not planted ones) had high carbon storage. Carbon sequestration was greatest inEucalyptus globulus,Quercus ilex, andPinus pinasterforests. Overall, our findings suggest that the relative capacity of native and non‐native forests to uptake and store carbon depends on climate, and that the superiority of non‐native forests over native ones in terms of carbon sequestration declines as the abiotic filters become stronger (i.e., lower water availability and higher climate seasonality).