bluuebunny/crossref_metadata_2025 huggingface dataset:
Changes in the functional diversity of birds due to habitat loss in the Brazil Atlantic Forest
Authors: Mariano-Neto Eduardo , Santos Rafael A. S.
Published: February 2023

Landscape changes due to habitat loss and fragmentation can result in complex changes in biodiversity and functional diversity. On the other hand, the functional diversity changes also reflect the modifications in the ecosystem functions, patterns of resources use by the species, and species interactions. In the present work, we evaluated how habitat loss at a landscape scale influences the functional diversity of different bird communities (total community, frugivorous, and insectivorous birds) in landscapes of 5–60% of forest cover in the Bahia Atlantic Forest. In a sample design that aimed to minimize the effects of some landscape-scale possible bias, we randomly selected twelve 6 km × 6 km landscapes, and we surveyed eight plots randomly located in forested areas within each landscape. We focused on the species classified as forest-dependent. We calculated the total richness and each species’ relative abundance in each landscape. To evaluate functional diversity, 19 functional traits were chosen for the total community, 11 for the frugivore birds, and 12 for the insectivore birds. The choice of traits represents how species use their resources and the use of these in other studies of functional diversity. As biodiversity changes to habitat loss could be non-linear, we evaluated the response pattern of bird functional diversity to habitat loss using three different metrics (FRic, FEve, and FDiv) for all communities (total community, frugivorous and insectivorous birds). Model selection was used to evaluate the response models (null, linear, and logistical). Our results indicated that as forest amount decreases, we found a sharp decrease in FRic, significantly below 30% forest cover. That suggests a reduction in resource use by species in those landscapes. FEve also showed a sharp decline in landscapes below 15% of habitat, indicating a possible reduction in the structural complexity. Fdiv also decreases dramatically in landscapes below 15% of forest amount, which suggests a decrease in functional dissimilarity between species, probably due to environmental filtration, which can lead to taxonomic homogenization. Therefore, we assessed the importance of forests for providing the resources for the permanence of species and their functions, and as a population source. Our study provides quantitative indicators of the relationship between functional diversity and habitat loss, which can be crucial in implementing more robust conservation actions to preserve the Atlantic Forest and its ecosystem services.
Wanted: A systematic review of the most trafficked songbirds in a Neotropical hotspot
Authors: Ferrari Giuliana C. P. , Rheingantz Marcelo Lopes , Rajão Henrique , Lorini Maria Lucia
Published: February 2023

The illegal wildlife trade is one of the main factors of biodiversity loss worldwide. Brazil, the largest country in South America, is a hub of wildlife trafficking, but availability of information on the issue is constrained to specific regions and to Portuguese speakers. Knowledge gaps hinder the establishment of targeted countermeasures in the fight against the illegal wildlife trade. Thousands of animals are seized from IWT and sent to wildlife centers each year. Here, we reviewed the literature on seized songbirds for the Brazilian Atlantic Forest (BAF), a global hotspot of biodiversity. Using a systematic review approach, we compiled a database with all available papers containing seizure records for the Brazilian Atlantic Forest. We focused on the 10 most seized species in each study to construct a comprehensive view of the main victims of the illegal trade. We reported 23 studies in 20 locations throughout the BAF. In 19 years, 139,000 passerines were recorded, distributed in 47 species – and two genera – across 10 families. Thraupidae was the most important family, with 27 species in the list and comprising 70% of individuals recorded. We highlighted the preference for granivorous birds and birds deemed good singers. There were few threatened species in the top list, but many of the ones included have population trends of decline, indicating a conservation issue that can direly affect even currently common species if the high demand continues. We appointed knowledge gaps within the Brazilian scenario of wildlife trafficking and provided practical recommendations on the issue considering the global scenario of IWT.
Compensatory responses of leaf physiology reduce effects of spring frost defoliation on temperate forest tree carbon uptake
Authors: Reinmann Andrew B. , Bowers Justin T. , Kaur Prableen , Kohler Clare
Published: February 2023

Spring frosts can defoliate trees, reduce canopy carbon assimilation, and alter interspecific competition dynamics. These events may become more common with climate change, but our understanding of the associated ecological impacts is limited by the stochastic nature of their occurrences. In 2020, a late spring frost defoliated oak (Quercus spp.), but not co-occurring maples (Acer spp.) across temperate broadleaf forests of the Hudson Highlands in southern New York State, U.S.A. Defoliation impacted 60% of this region’s forests and delayed full leaf expansion of oaks by ∼17 days. We used this event as an opportunity to advance understanding of how leaf-level physiology, radial growth, and interspecific competition dynamics of mature trees respond to frost-induced defoliation. We quantified leaf-level photosynthetic capacity, stomatal conductance, and water-use efficiency (WUE), as well as basal area increment of defoliated red oak (Q. rubra) trees and non-defoliated red maple (A. rubrum) trees in 2020 (“defoliation year”) and 2021 (“reference year”). Oak defoliation provided red maple trees with a competitive edge in terms of photosynthetic capacity early in the growing season. However, the second cohort of red oak leaves that developed following defoliation had photosynthetic capacities that were 3–4 times higher than red maple trees by the second half of the growing season, likely facilitated by higher rates of stomatal conductance. The growing season mean photosynthetic capacities for the defoliation year were significantly higher for red oaks than red maples. Red oak basal area increment tended to be higher than red maple during both the defoliation and reference years. For both species basal area increment was significantly higher during the reference year than defoliation year, but the reasons remain unclear. Taken together, these findings demonstrate that temporal patterns of photosynthesis in temperate broadleaf forests are altered by defoliation events, but enhanced photosynthetic capacities of second cohort leaves can reduce the negative effects of delayed leaf expansion and mitigate competitive advantages conferred to undefoliated co-occurring tree species. We suggest that understanding a tree species’ ability to compensate for frost-induced defoliation is essential to accurately predict effects of extreme climate events on tree competition dynamics and ecosystem processes.
Population structure and diversity of the needle pathogen Dothistroma pini suggests human-mediated movement in Europe
Authors: van der Nest Ariska , Wingfield Michael J. , Sadiković Dušan , Mullett Martin S. , Marçais Benoit , Queloz Valentin , Adamčíková Katarina , Davydenko Kateryna , Barnes Irene
Published: February 2023

Dothistroma needle blight (DNB) is an important disease of Pinus species that can be caused by one of two distinct but closely related pathogens; Dothistroma septosporum and Dothistroma pini. Dothistroma septosporum has a wide geographic distribution and is relatively well-known. In contrast, D. pini is known only from the United States and Europe, and there is a distinct lack of knowledge regarding its population structure and genetic diversity. The recent development of 16 microsatellite markers for D. pini provided an opportunity to investigate the diversity, structure, and mode of reproduction for populations collected over a period of 12 years, on eight different hosts in Europe. In total, 345 isolates from Belgium, the Czech Republic, France, Hungary, Romania, Western Russia, Serbia, Slovakia, Slovenia, Spain, Switzerland, and Ukraine were screened using microsatellite and species-specific mating type markers. A total of 109 unique multilocus haplotypes were identified and structure analyses suggested that the populations are influenced by location rather than host species. Populations from France and Spain displayed the highest levels of genetic diversity followed by the population in Ukraine. Both mating types were detected in most countries, with the exception of Hungary, Russia and Slovenia. Evidence for sexual recombination was supported only in the population from Spain. The observed population structure and several shared haplotypes between non-bordering countries provides good evidence that the movement of D. pini in Europe has been strongly influenced by human activity in Europe.
Case report: Electrocardiographic changes in pembrolizumab-induced fatal myocarditis
Authors: Nishiyama Kazuhiro , Morikawa Kei , Shinozaki Yusuke , Ueno Junko , Tanaka Satoshi , Tsuruoka Hajime , Azagami Shinya , Ishida Atsuko , Yanagisawa Nobuyuki , Akashi Yoshihiro J. , Mineshita Masamichi
Published: February 2023

Immune checkpoint inhibitor (ICI)-induced myocarditis is rare but fatal. Because of the rapid course of ICI-induced myocarditis, understanding of clinical course is only possible through information from case reports. We report a case of pembrolizumab-induced myocarditis in which we were able to document the course of electrocardiographic changes from onset to death. A 58-year-old woman with stage IV lung adenocarcinoma, who had completed her first cycle of pembrolizumab, carboplatin, and pemetrexed, was admitted with pericardial effusion. She underwent pericardiocentesis after admission. A second cycle of chemotherapy was administered 3 weeks after the first cycle. Twenty-two days after admission, she developed a mild sore throat and tested positive for SARS-CoV-2 antigen. She was diagnosed with mild coronavirus disease 2019 (COVID-19), isolated, and treated with sotrovimab. Thirty-two days after admission, an electrocardiogram showed monomorphic ventricular tachycardia (VT). Suspecting myocarditis caused by pembrolizumab, the patient was started on daily methylprednisolone after coronary angiography and endocardial biopsy. Eight days after the start of methylprednisolone administration, she was considered to have passed the acute stage. However, four days later, R-on-T phenomenon triggered polymorphic VT and she died. The impact of viral infections such as COVID-19 on patients be treated with immune checkpoint inhibitors is still unknown and we need to be careful with systemic management after viral infections.
Translatome analyses by bio-orthogonal non-canonical amino acid labeling reveal that MR1-activated MAIT cells induce an M1 phenotype and antiviral programming in antigen-presenting monocytes
Authors: Jakob Josefine , Kröger Andrea , Klawonn Frank , Bruder Dunja , Jänsch Lothar
Published: February 2023

MAIT cells are multifunctional innate-like effector cells recognizing bacterial-derived vitamin B metabolites presented by the non-polymorphic MHC class I related protein 1 (MR1). However, our understanding of MR1-mediated responses of MAIT cells upon their interaction with other immune cells is still incomplete. Here, we performed the first translatome study of primary human MAIT cells interacting with THP-1 monocytes in a bicellular system. We analyzed the interaction between MAIT and THP-1 cells in the presence of the activating 5-OP-RU or the inhibitory Ac-6-FP MR1-ligand. Using bio-orthogonal non-canonical amino acid tagging (BONCAT) we were able to enrich selectively those proteins that were newly translated during MR1-dependent cellular interaction. Subsequently, newly translated proteins were measured cell-type-specifically by ultrasensitive proteomics to decipher the coinciding immune responses in both cell types. This strategy identified over 2,000 MAIT and 3,000 THP-1 active protein translations following MR1 ligand stimulations. Translation in both cell types was found to be increased by 5-OP-RU, which correlated with their conjugation frequency and CD3 polarization at MAIT cell immunological synapses in the presence of 5-OP-RU. In contrast, Ac-6-FP only regulated a few protein translations, including GSK3B, indicating an anergic phenotype. In addition to known effector responses, 5-OP-RU-induced protein translations uncovered type I and type II Interferon-driven protein expression profiles in both MAIT and THP-1 cells. Interestingly, the translatome of THP-1 cells suggested that activated MAIT cells can impact M1/M2 polarization in these cells. Indeed, gene and surface expression of CXCL10, IL-1β, CD80, and CD206 confirmed an M1-like phenotype of macrophages being induced in the presence of 5-OP-RU-activated MAIT cells. Furthermore, we validated that the Interferon-driven translatome was accompanied by the induction of an antiviral phenotype in THP-1 cells, which were found able to suppress viral replication following conjugation with MR1-activated MAIT cells. In conclusion, BONCAT translatomics extended our knowledge of MAIT cell immune responses at the protein level and discovered that MR1-activated MAIT cells are sufficient to induce M1 polarization and an anti-viral program of macrophages.
Dynamics of cell cycle proteins involved in Toxoplasma gondii-induced bovine NET formation
Authors: Velásquez Zahady D. , Peixoto Raquel , Gärtner Ulrich , Hermosilla Carlos , Taubert Anja , Conejeros Iván
Published: February 2023

Neutrophil extracellular traps (NET) formation is one important host innate defense mechanism elicited by polymorphonuclear neutrophils (PMN). NETs are composed by chromatin and proteins with microbicidal and signaling activity. So far, there is one report on Toxoplasma gondii-triggered NETs in cattle, however, exact mechanisms, including signalling pathways and dynamics governing this reaction remain largely unknown. Recently, involvement of cell cycle proteins was demonstrated for phorbol myristate acetate (PMA)-triggered human PMN-derived NETs. Here, we studied the involvement of cell cycle proteins in T. gondii-induced NETs in exposed bovine PMN. Through confocal and transmission electron microscopy we discovered that Ki-67 and lamin B1 signals are upregulated and relocated during T. gondii-induced NETosis. Nuclear membrane disruption was also observed as a hallmark of NET formation in bovine PMN confronted with viable T. gondii tachyzoites, mimicking some steps of mitosis. However, we did not observe centrosome duplication as previously described for human PMN-derived NET formation stimulated with PMA.
Benchmarking of automatic quality control checks for ocean temperature profiles and recommendations for optimal sets
Authors: Good Simon , Mills Bill , Boyer Tim , Bringas Francis , Castelão Guilherme , Cowley Rebecca , Goni Gustavo , Gouretski Viktor , Domingues Catia M.
Published: February 2023

Millions of in situ ocean temperature profiles have been collected historically using various instrument types with varying sensor accuracy and then assembled into global databases. These are essential to our current understanding of the changing state of the oceans, sea level, Earth’s climate, marine ecosystems and fisheries, and for constraining model projections of future change that underpin mitigation and adaptation solutions. Profiles distributed shortly after collection are also widely used in operational applications such as real-time monitoring and forecasting of the ocean state and weather prediction. Before use in scientific or societal service applications, quality control (QC) procedures need to be applied to flag and ultimately remove erroneous data. Automatic QC (AQC) checks are vital to the timeliness of operational applications and for reducing the volume of dubious data which later require QC processing by a human for delayed mode applications. Despite the large suite of evolving AQC checks developed by institutions worldwide, the most effective set of AQC checks was not known. We have developed a framework to assess the performance of AQC checks, under the auspices of the International Quality Controlled Ocean Database (IQuOD) project. The IQuOD-AQC framework is an open-source collaborative software infrastructure built in Python (available from https://github.com/IQuOD). Sixty AQC checks have been implemented in this framework. Their performance was benchmarked against three reference datasets which contained a spectrum of instrument types and error modes flagged in their profiles. One of these (a subset of the Quality-controlled Ocean Temperature Archive (QuOTA) dataset that had been manually inspected for quality issues by its creators) was also used to identify optimal sets of AQC checks. Results suggest that the AQC checks are effective for most historical data, but less so in the case of data from Mechanical Bathythermographs (MBTs), and much less effective for Argo data. The optimal AQC sets will be applied to generate quality flags for the next release of the IQuOD dataset. This will further elevate the quality and historical value of millions of temperature profile data which have already been improved by IQuOD intelligent metadata and observational uncertainty information (https://doi.org/10.7289/v51r6nsf).
Sediment gravity flow frequency offshore central California diminished significantly following the Last Glacial Maximum
Authors: Dobbs Stephen C. , Paull Charles K. , Lundsten Eve M. , Gwiazda Roberto , Caress David W. , McGann Mary , Coholich Marianne M. , Walton Maureen A. L. , Nieminski Nora M. , McHargue Tim , Graham Stephan A.
Published: February 2023

A high-resolution multibeam survey from a portion of the San Simeon Channel (offshore Morro Bay, California) captured a zone of recurring troughs and ridges adjacent to prominent submarine meander bends. Through an integrated study using surveying data, sediment core analysis, radiocarbon dating, and stable isotope measurements, we hypothesize that turbidity current event frequency was higher during the late Pleistocene than at present conditions. We speculate that the rise in sea-level following the Last Glacial Maximum sequestered sedimentation largely to the shelf during the Holocene. This work suggests that the occurrence of sediment gravity flows in this region, particularly away from any submarine channels, is appreciably lower than at times of continental shelf subaerial exposure.
N2O production by mussels: Quantifying rates and pathways in current and future climate settings
Authors: Voet Helena , Soetaert Karline , Moens Tom , Bodé Samuel , Boeckx Pascal , Van Colen Carl , Vanaverbeke Jan
Published: February 2023

Blue mussels (Mytilus edulis) are an abundant and economically important species across the North Sea. Partly because of their potent filter feeding and associated shell biofilm, they are able to influence and alter the surrounding marine ecosystem. As a result of proliferating offshore wind farms (OWFs), whose turbine foundations are rapidly colonised by suspension feeding artificial hard substrate communities dominated by M. edulis, as well as planned co-location strategies of these OWFs with mussel mariculture, their numbers will only increase towards the future. On top of these local stressors, global climate change is exerting additional pressure on the marine environment. This study focusses on the link between M. edulis, its microbial shell biofilm and the local nitrogen cycling by quantifying the magnitude and underlying pathways of mussel-associated nitrous oxide (N2O) production. A set of closed-core incubations established nitrifier denitrification as the main chemical pathway of M. edulis related N2O production, although ammonium, nitrite and nitrate all acted as possible precursors. Additional future-climate experiments revealed that blue mussel’s total N2O production, as well as its metabolic activity and the relative contribution of its shell biofilm, were affected by warming (+ 3°C), acidification (- 0.3 pH units), or the combination of both. Because the effects of temperature and acidity were often of an antagonistic nature, the results suggest a relatively small net effect on local N2O production in future-climate marine environments. However, N2O production rates were several orders of magnitude lower than other measured N species (NH4+, NO2− and NO3-), making substantial mussel-associated N2 production likely. This would greatly affect the local eutrophication levels or even bioavailable nitrogen concentrations.
Clinical implications of interstitial pneumonia with autoimmune features diagnostic criteria in idiopathic pulmonary fibrosis: A case control study
Authors: Tomassetti Sara , Ravaglia Claudia , Puglisi Silvia , Wells Athol U. , Ryu Jay H. , Bosi Marcello , Dubini Alessandra , Piciucchi Sara , Girelli Francesco , Parronchi Paola , Lavorini Federico , Rosi Elisabetta , Luzzi Valentina , Cerinic Marco Matucci , Poletti Venerino
Published: February 2023

Background

A subgroup of IPF patients can meet IPAF criteria (features suggesting an underlying autoimmune process without fulfilling established criteria for a CTD). This study was aimed to evaluate whether IPAF/IPF patients compared to IPF patients differ in clinical profile, prognosis and disease course.

Methods

This is a retrospective, single center, case–control study. We evaluated 360 consecutive IPF patients (Forlì Hospital, between 1/1/2002 and 28/12/2016) and compared characteristics and outcome of IPAF/IPF to IPF.

Results

Twenty-two (6%) patients met IPAF criteria. IPAF/IPF patients compared to IPF were more frequently females (N = 9/22, 40.9% vs. N = 68/338, 20.1%, p = 0.02), suffered more frequently from gastroesophageal reflux (54.5% vs. 28.4%, p = 0.01), and showed a higher prevalence of arthralgias (86.4% vs. 4.8%, p < 0.0001), myalgias (14.3% vs. 0.3%, p = 0.001) and fever (18.2% vs. 1.9%, p = 0.002). The serologic domain was detected in all cases (the most frequent were ANA in 17 and RF in nine cases) and morphologic domain (histology features) was positive in 6 out of 10 lung biopsies (lymphoid aggregates). Only patients with IPAF/IPF evolved to CTD at follow-up (10/22, 45.5%; six rheumatoid arthritis, one Sjögren’s and three scleroderma). The presence of IPAF was a positive prognostic determinant (HR 0.22, 95% CI 0.08–0.61, p = 0.003), whereas the isolated presence of circulating autoantibody did not impact prognosis (HR 1.00, 95% CI 0.67–1.49, p = 0.99).

Conclusion

The presence of IPAF criteria in IPF has a major clinical impact correlating with the risk of evolution to full blown-CTD during follow-up and identifying a subgroup of patients with a better prognosis.
Video-capillaroscopy, a promising tool for the clinical evaluation of patients with chronic venous insufficiency
Authors: Carpentier Patrick H. , Trolliet Corine , Cornu-Thénard André , Chamberod Rémy , Laurès Jérôme , Noilhetas Janick , Chauvin Eric
Published: February 2023

Background

The cutaneous microangiopathy plays a key role in the development of the skin clinical lesions of venous insufficiency. Capillaroscopy allows a non-invasive observation of the superficial skin capillaries of the lower leg, which have previously been shown to be altered in patients with advanced venous disease. As it is now available in a friendly, easy to handle way through modern video devices, we report our findings in a short series of patients with C3–C5 chronic venous disorders using this technique.

Methods

A total of 21 patients with venous insufficiency (C3–C5 on at least one leg) underwent a capillaroscopic examination of both legs and pictures recorded from the sites of the most severe venous skin lesions. This was performed with a CapXview handheld video-capillaroscope (×100 magnification), allowing easy manual measurement of maximum capillary bulk diameter and capillary density.

Results

Dramatic changes in capillary density, size, and shape were easily observed at the site of the venous skin lesions. A significant negative linear relationship was found between capillary density and the “C” classes (r = −0.45; P < 0.001). A significant negative correlation was also found between capillary density and bulk diameter (r = −0.52; P < 0.001). The area under the ROC curve for the mathematical prediction of venous skin changes by capillary density was 0.842, which shows the strength of the link between the microvascular and the clinical status.

Conclusion

Video-capillaroscopy allows a direct observation of the cutaneous venous microangiopathy and provides the possibility to measure capillary density which allows its quantification. This simple to use technique shows the potential for a more precise follow-up and treatment evaluation of the cutaneous consequences of venous disease, which remains to be further investigated.
Roles of conserved active site residues in the IscS cysteine desulfurase reaction
Authors: Pang Yilin , Wang Jing , Gao Xueping , Jiang Mengyao , Zhu Lifei , Liang Feng , Liang Mengxiang , Wu Xiaolin , Xu Xianxian , Ren Xiaojun , Xie Ting , Wang Wu , Sun Qianqian , Xiong Xiaojun , Lyu Jianxin , Li Jianghui , Tan Guoqiang
Published: February 2023

Escherichia coli cysteine desulfurase (CD), IscS, modifies basal metabolism by transferring sulphur (S) from L-cysteine to numerous cellular pathways, whereas NFS1, a human CD, is active only in the formation of the [Acp]2:[ISD11]2:[NFS1]2 complex. Despite the accumulation of red-coloured IscS in E. coli cells as a result of the deficiency of accessible iron, as revealed in our previous studies, the mechanism of the potential enzymatic reaction remains unclear. In this study, the N-terminus of IscS was fused with the C-terminus of NFS1, which was reported to be almost fully active as IscS and exhibits a pyridoxal 5′-phosphate (PLP) absorption peak at 395 nm. Moreover, SUMO-EH-IscS exhibited significant growth recovery and NADH-dehydrogenase I activity in the iscS mutant cells. Furthermore, through in vitro and in vivo experiments combined with high-performance liquid chromatography and ultra-performance liquid chromatography–tandem mass spectrometry, it was shown that the new absorption peaks of the IscS H104Q, IscS Q183E, IscS K206A, and IscS K206A&C328S variants at 340 and 350 nm may correspond to the enzyme reaction intermediates, Cys-ketimine and Cys-aldimine, respectively. However, after mutation of the conserved active-site residues, additional absorption peaks at 420 and 430 nm were associated with PLP migration in the active-site pocket. Additionally, the corresponding absorption peaks of Cys-quinonoid, Ala-ketimine, and Ala-aldimine intermediates in IscS were 510, 325, and 345 nm, respectively, as determined by site-directed mutagenesis and substrate/product-binding analyses during the CD reaction process. Notably, red IscS formed in vitro by incubating IscS variants (Q183E and K206A) with excess L-alanine and sulphide under aerobic conditions produced an absorption peak similar to the wild-type IscS, at 510 nm. Interestingly, site-directed mutation of IscS with hydrogen bonds to PLP at Asp180 and Gln183 resulted in a loss of enzymatic activity followed by an absorption peak consistent with NFS1 (420 nm). Furthermore, mutations at Asp180 or Lys206 inhibited the reaction of IscS in vitro with L-cysteine (substrate) and L-alanine (product). These results suggest that the conserved active site residues (His104, Asp180, and Gln183) and their hydrogen bond with PLP in the N-terminus of IscS play a key role in determining whether the L-cysteine substrate can enter the active-site pocket and regulate the enzymatic reaction process. Therefore, our findings provide a framework for evaluating the roles of conserved active-site residues, motifs, and domains in CDs.
Evaluation of environmental factors and microbial community structure in an important drinking-water reservoir across seasons
Authors: Feng Jie , Zhou Letian , Zhao Xiaochao , Chen Jianyi , Li Zhi , Liu Yongfeng , Ou Lei , Xie Zixin , Wang Miao , Yin Xue , Zhang Xin , Li Yan , Luo Mingjie , Zeng Lidong , Yan Qin , Xie Linshen , Sun Lei
Published: February 2023

The composition of microbial communities varies in water and sediments, and changes in environmental factors have major effects on microbiomes. Here, we characterized variations in microbial communities and physicochemical factors at two sites in a large subtropical drinking water reservoir in southern China. The microbiomes of all sites, including the diversity and abundance of microbial species, were determined via metagenomics, and the relationships between microbiomes and physicochemical factors were determined via redundancy analysis. The dominant species in sediment and water samples differed; Dinobryon sp. LO226KS and Dinobryon divergens were dominant in sediment samples, whereas Candidatus Fonsibacter ubiquis and Microcystis elabens were dominant in water. The diversity was also significantly different in microbial alpha diversity between water and sediment habitats (p < 0.01). The trophic level index (TLI) was the major factor affecting the microbial community in water samples; Mycolicibacterium litorale and Mycolicibacterium phlei were significantly positively related to TLI. Furthermore, we also studied the distribution of algal toxin-encoding genes and antibiotic-resistant genes (ARGs) in the reservoir. It found that water samples contained more phycotoxin genes, with the cylindrospermopsin gene cluster most abundant. We found three genera highly related to cylindrospermopsin and explored a new cyanobacteria Aphanocapsa montana that may produce cylindrospermopsin based on the correlation through network analysis. The multidrug resistance gene was the most abundant ARG, while the relationship between ARGs and bacteria in sediment samples was more complicated than in water. The results of this study enhance our understanding of the effects of environmental factors on microbiomes. In conclusion, research on the properties, including profiles of algal toxin-encoding genes and ARGs, and microbial communities can aid water quality monitoring and conservation.
Comparative analysis of four nuclei in the human brainstem: Individual differences, left-right asymmetry, species differences
Authors: Baizer Joan S. , Witelson Sandra F.
Published: February 2023

Introduction

It is commonly thought that while the organization of the cerebral cortex changes dramatically over evolution, the organization of the brainstem is conserved across species. It is further assumed that, as in other species, brainstem organization is similar from one human to the next. We will review our data on four human brainstem nuclei that suggest that both ideas may need modification.

Methods

We have studied the neuroanatomical and neurochemical organization of the nucleus paramedianus dorsalis (PMD), the principal nucleus of the inferior olive (IOpr), the arcuate nucleus of the medulla (Arc) and the dorsal cochlear nucleus (DC). We compared these human brainstem nuclei to nuclei in other mammals including chimpanzees, monkeys, cats and rodents. We studied human cases from the Witelson Normal Brain collection using Nissl and immunostained sections, and examined archival Nissl and immunostained sections from other species.

Results

We found significant individual variability in the size and shape of brainstem structures among humans. There is left-right asymmetry in the size and appearance of nuclei, dramatically so in the IOpr and Arc. In humans there are nuclei, e.g., the PMD and the Arc, not seen in several other species. In addition, there are brainstem structures that are conserved across species but show major expansion in humans, e.g., the IOpr. Finally, there are nuclei, e.g. the DC, that show major differences in structure among species.

Discussion

Overall, the results suggest several principles of human brainstem organization that distinguish humans from other species. Studying the functional correlates of, and the genetic contributions to, these brainstem characteristics are important future research directions.
A multi-faceted role of dual-state dopamine signaling in working memory, attentional control, and intelligence
Authors: Matzel Louis D. , Sauce Bruno
Published: February 2023

Genetic evidence strongly suggests that individual differences in intelligence will not be reducible to a single dominant cause. However, some of those variations/changes may be traced to tractable, cohesive mechanisms. One such mechanism may be the balance of dopamine D1 (D1R) and D2 (D2R) receptors, which regulate intrinsic currents and synaptic transmission in frontal cortical regions. Here, we review evidence from human, animal, and computational studies that suggest that this balance (in density, activity state, and/or availability) is critical to the implementation of executive functions such as attention and working memory, both of which are principal contributors to variations in intelligence. D1 receptors dominate neural responding during stable periods of short-term memory maintenance (requiring attentional focus), while D2 receptors play a more specific role during periods of instability such as changing environmental or memory states (requiring attentional disengagement). Here we bridge these observations with known properties of human intelligence. Starting from theories of intelligence that place executive functions (e.g., working memory and attentional control) at its center, we propose that dual-state dopamine signaling might be a causal contributor to at least some of the variation in intelligence across individuals and its change by experiences/training. Although it is unlikely that such a mechanism can account for more than a modest portion of the total variance in intelligence, our proposal is consistent with an array of available evidence and has a high degree of explanatory value. We suggest future directions and specific empirical tests that can further elucidate these relationships.
Prognostic role of dynamic neutrophil-to-lymphocyte ratio in acute ischemic stroke after reperfusion therapy: A meta-analysis
Authors: Wu Bing , Liu Fang , Sun Guiyan , Wang Shuang
Published: February 2023

Background

The prognostic role of the neutrophil-to-lymphocyte ratio (NLR), an inflammatory marker, in acute ischemic stroke (AIS) after reperfusion therapy remains controversial. Therefore, this meta-analysis sought to assess the correlation between the dynamic NLR and the clinical outcomes of patients with AIS after reperfusion therapy.

Methods

PubMed, Web of Science, and Embase databases were searched to identify relevant literature from their inception to 27 October 2022. The clinical outcomes of interest included poor functional outcome (PFO) at 3 months, symptomatic intracerebral hemorrhage (sICH), and 3-month mortality. The NLR on admission (pre-treatment) and post-treatment was collected. The PFO was defined as a modified Rankin scale (mRS) of >2.

Results

A total of 17,232 patients in 52 studies were included in the meta-analysis. The admission NLR was higher in the 3-month PFO (standardized mean difference [SMD] = 0.46, 95% confidence interval [CI] = 0.35–0.57), sICH (SMD = 0.57, 95% CI = 0.30–0.85), and mortality at 3 months (SMD = 0.60, 95% CI = 0.34–0.87). An elevated admission NLR was associated with an increased risk of 3-month PFO (odds ratio [OR] = 1.13, 95% CI = 1.09–1.17), sICH (OR = 1.11, 95% CI = 1.06–1.16), and mortality at 3 months (OR = 1.13, 95% CI = 1.07–1.20). The post-treatment NLR was significantly higher in the 3-month PFO (SMD = 0.80, 95% CI = 0.62–0.99), sICH (SMD = 1.54, 95% CI = 0.97–2.10), and mortality at 3 months (SMD = 1.00, 95% CI = 0.31–1.69). An elevated post-treatment NLR was significantly associated with an increased risk of 3-month PFO (OR = 1.25, 95% CI = 1.16–1.35), sICH (OR = 1.14, 95% CI = 1.01–1.29), and mortality at 3 months (OR = 1.28, 95% CI = 1.09–1.50).

Conclusion

The admission and post-treatment NLR can be used as cost-effective and easily available biomarkers to predict the 3-month PFO, sICH, and mortality at 3 months in patients with AIS treated with reperfusion therapy. The post-treatment NLR provides better predictive power than the admission NLR.

Systematic review registration

https://www.crd.york.ac.uk/PROSPERO/, identifier: CRD42022366394.
Converging theories on dreaming: Between Freud, predictive processing, and psychedelic research
Authors: Koslowski Michael , de Haas Max-Pelgrom , Fischmann Tamara
Published: February 2023

Dreams are still an enigma of human cognition, studied extensively in psychoanalysis and neuroscience. According to the Freudian dream theory and Solms' modifications of the unconscious derived from it, the fundamental task of meeting our emotional needs is guided by the principle of homeostasis. Our innate value system generates conscious feelings of pleasure and unpleasure, resulting in the behavior of approaching or withdrawing from the world of objects. Based on these experiences, a hierarchical generative model of predictions (priors) about the world is constantly created and modified, with the aim to optimize the meeting of our needs by reducing prediction error, as described in the predictive processing model of cognition. Growing evidence from neuroimaging supports this theory. The same hierarchical functioning of the brain is in place during sleep and dreaming, with some important modifications like a lack of sensual and motor perception and action. Another characteristic of dreaming is the predominance of primary process thinking, an associative, non-rational cognitive style, which can be found in similar altered states of consciousness like the effect of psychedelics. Mental events that do not successfully fulfill an emotional need will cause a prediction error, leading to conscious attention and adaptation of the priors that incorrectly predicted the event. However, this is not the case for repressed priors (RPs), which are defined by the inability to become reconsolidated or removed, despite ongoing error signal production. We hypothesize that Solms' RPs correspond with the conflictual complexes, as described by Moser in his dream formation theory. Thus, in dreams and dream-like states, these unconscious RPs might become accessible in symbolic and non-declarative forms that the subject is able to feel and make sense of. Finally, we present the similarities between dreaming and the psychedelic state. Insights from psychedelic research could be used to inform dream research and related therapeutic interventions, and vice versa. We propose further empirical research questions and methods and finally present our ongoing trial “Biological Functions of Dreaming” to test the hypothesis that dreaming predicts intact sleep architecture and memory consolidation, via a lesion model with stroke patients who lost the ability to dream.
A study on the clusterability of latent representations in image pipelines
Authors: Wheeldon Adrian , Serb Alexander
Published: February 2023

Latent representations are a necessary component of cognitive artificial intelligence (AI) systems. Here, we investigate the performance of various sequential clustering algorithms on latent representations generated by autoencoder and convolutional neural network (CNN) models. We also introduce a new algorithm, called Collage, which brings views and concepts into sequential clustering to bridge the gap with cognitive AI. The algorithm is designed to reduce memory requirements, numbers of operations (which translate into hardware clock cycles) and thus improve energy, speed and area performance of an accelerator for running said algorithm. Results show that plain autoencoders produce latent representations which have large inter-cluster overlaps. CNNs are shown to solve this problem, however introduce their own problems in the context of generalized cognitive pipelines.
Comparison of Yizhiqingxin formula extraction methods and their pharmacodynamic differences
Authors: Wei Wei , Pei Hui , Ma Li-Na , Zheng Rui , Huang Qiao-Yi , Chang Su-rui , Cao Yu , Li Hao
Published: February 2023

Objectives

This study compared different extraction methods of Yizhiqingxin formula (YQF) and its neuroprotective effects based on pharmacodynamic indices such as learning and memory ability, brain tissue histopathology and morphology, and inflammatory factor expression in a mouse model of Alzheimer’s disease (AD).

Methods

The pharmaceutical components of YQF were extracted using three extraction processes, and the components were analyzed by high performance liquid chromatography. Donepezil hydrochloride was used as a positive control drug. Fifty 7–8-month-old 3 × Tg AD mice were randomly divided into three YQF groups (YQF-1, YQF-2, and YQF-3), a donepezil group, and a model group. Ten age-matched C57/BL6 mice were used as normal controls. YQF and Donepezil were administered by gavage at a clinically equivalent dose of 2.6 and 1.3 mg⋅kg–1⋅d–1, respectively, with a gavage volume of 0.1 ml/10 g. Control and model groups received equal volumes of distilled water by gavage. After 2 months, the efficacy was evaluated using behavioral experiments, histopathology, immunohistochemistry, and serum assays.

Results

The main components in YQF are ginsenoside Re, ginsenoside Rg1, ginsenoside Rb1, epiberberine, coptisine chloride, palmatine, berberine, and ferulic acid. YQF-3 (alcohol extraction) has the highest content of active compounds, followed by YQF-2 (water extraction and alcohol precipitation method). Compared to the model group, the three YQF groups showed alleviated histopathological changes and improved spatial learning and memory, with the effect in YQF-2 being the most significant. YQF showed protection of hippocampal neurons, most significantly in the YQF-1 group. YQF significantly reduced Aβ pathology and tau hyperphosphorylation, decreased expressions of serum pro-inflammatory factors interleukin-2 and interleukin-6 as well as serum chemokines MCP-1 and MIG.

Conclusion

YQF prepared by three different processes showed differences in pharmacodynamics in an AD mouse model. YQF-2 was significantly better than the other extraction processes in improving memory.
Alteration of brain network centrality in CTN patients after a single triggering pain
Authors: Ge Xiuhong , Wang Luoyu , Wang Mengze , Pan Lei , Ye Haiqi , Zhu Xiaofen , Fan Sandra , Feng Qi , Du Quan , Wenhua Yu , Ding Zhongxiang
Published: February 2023

Objective

The central nervous system may also be involved in the pathogenesis of classical trigeminal neuralgia (CTN). The present study aimed to explore the characteristics of static degree centrality (sDC) and dynamic degree centrality (dDC) at multiple time points after a single triggering pain in CTN patients.

Materials and methods

A total of 43 CTN patients underwent resting-state function magnetic resonance imaging (rs-fMRI) before triggering pain (baseline), within 5 s after triggering pain (triggering-5 s), and 30 min after triggering pain (triggering-30 min). Voxel-based degree centrality (DC) was used to assess the alteration of functional connection at different time points.

Results

The sDC values of the right caudate nucleus, fusiform gyrus, middle temporal gyrus, middle frontal gyrus, and orbital part were decreased in triggering-5 s and increased in triggering-30 min. The sDC value of the bilateral superior frontal gyrus were increased in triggering-5 s and decreased in triggering-30 min. The dDC value of the right lingual gyrus was gradually increased in triggering-5 s and triggering-30 min.

Conclusion

Both the sDC and dDC values were changed after triggering pain, and the brain regions were different between the two parameters, which supplemented each other. The brain regions which the sDC and dDC values were changing reflect the global brain function of CTN patients, and provides a basis for further exploration of the central mechanism of CTN.
Brain activation of the PFC during dual-task walking in stroke patients: A systematic review and meta-analysis of functional near-infrared spectroscopy studies
Authors: Wang Qinglei , Dai Wenjun , Xu Sheng , Zhu Shizhe , Sui Youxin , Kan Chaojie , Shen Ying , Zhu Yi , Guo Chuan , Wang Tong
Published: February 2023

Background

Dual-task walking is a good paradigm to measure the walking ability of stroke patients in daily life. It allows for a better observation of brain activation under dual-task walking to assess the impact of the different tasks on the patient when combining with functional near-infrared spectroscopy (fNIRS). This review aims to summarize the cortical change of the prefrontal cortex (PFC) detected in single-task and dual-task walking in stroke patients.

Methods

Six databases (Medline, Embase, PubMed, Web of Science, CINAHL, and Cochrane Library) were systematically searched for relevant studies, from inception to August 2022. Studies that measured the brain activation of single-task and dual-task walking in stroke patients were included. The main outcome of the study was PFC activity measured using fNIRS. In addition, a subgroup analysis was also performed for study characteristics based on HbO to analyze the different effects of disease duration and the type of dual task.

Results

Ten articles were included in the final review, and nine articles were included in the quantitative meta-analysis. The primary analysis showed more significant PFC activation in stroke patients performing dual-task walking than single-task walking (SMD = 0.340, P = 0.02, I2 = 7.853%, 95% CI = 0.054–0.626). The secondary analysis showed a significant difference in PFC activation when performing dual-task walking and single-task walking in chronic patients (SMD = 0.369, P = 0.038, I2 = 13.692%, 95% CI = 0.020–0.717), but not in subacute patients (SMD = 0.203, P = 0.419, I2 = 0%, 95% CI = −0.289–0.696). In addition, performing walking combining serial subtraction (SMD = 0.516, P < 0.001, I2 = 0%, 95% CI = 0.239–0.794), obstacle crossing (SMD = 0.564, P = 0.002, I2 = 0%, 95% CI = 0.205–0.903), or a verbal task (SMD = 0.654, P = 0.009, I2 = 0%, 95% CI = 0.164–1.137) had more PFC activation than single-task walking, while performing the n-back task did not show significant differentiation (SMD = 0.203, P = 0.419, I2 = 0%, 95% CI = −0.289–0.696).

Conclusions

Different dual-task paradigms produce different levels of dual-task interference in stroke patients with different disease durations, and it is important to choose the matching dual-task type in relation to the walking ability and cognitive ability of the patient, in order to better improve the assessment and training effects.

Systematic review registration

https://www.crd.york.ac.uk/prospero/, identifier: CRD42022356699.