bluuebunny/crossref_metadata_2025_split huggingface dataset:
OVS‐Net: An effective feature extraction network for optical coherence tomography angiography vessel segmentation
Authors: Zhu Chengzhang , Wang Han , Xiao Yalong , Dai Yulan , Liu Zixi , Zou Beiji 
Published: July 2022

AbstractOptical coherence tomography angiography (OCTA), as a noninvasive imaging modality, has been widely used in clinical ophthalmology. However, the segmentation of retinal vessels in OCTA is under‐studied due to OCTA is a relatively new technology. In this article, an effective feature extraction network, OVS‐Net, is proposed for OCTA vessel segmentation. The OVS‐Net is divided into coarse stage and refine stage which structures are basically the same. In each stage, we utilize OctaveResBlock as the basic block to better extract the hierarchical multifrequency features of OCTA and capture the multiscale semantic features of the vessels. In order to improve the feature characterization, feature enhanced attention block is introduced into the network, which is proved to be more conducive for microvessel segmentation in our experiments. Multiscale feature blocks are introduced into the network to promote the deep integration of semantic features at different scales. Experiments on OCTA‐SS and OCTA‐500 datasets show that our proposed OVS‐Net achieves more competitive segmentation results than the existing methods, especially for microvessel segmentation.
Low‐grade serous carcinoma detected from intraoperative peritoneal washings: Cytological findings and detection of KRAS mutation
Authors: Yamamoto Eriko , Warigaya Kenji , Kinoshita Yuichi , Yamamoto Ayana , Murata Shin‐ichi 
Published: July 2022

AbstractBackgroundLow‐grade serous carcinoma (LGSC) of the ovary, which is extremely rare tumor, has better prognosis than high‐grade serous carcinoma (HGSC). Genetic backgrounds of those are different, so that LGSC usually shows KRAS or BRAF mutation, whereas HGSC does not show such mutations. Since treatment strategies of those are different, differential pathological diagnosis between LGSC and HGSC is very important.CaseWe report a case of LGSC that was diagnosed by both cytological findings and genetic analysis using small amount cells from cytological specimen. The 30‐year‐old Japanese woman with bilateral ovarian tumors underwent salpingo‐oopherectomy. The peritoneal washing cytologic specimen and touched cytologic specimen from the tumor included non‐complex clusters with psammoma bodies composed of tumor cells with mild to moderate atypia and without bizarre nuclei. The ovarian tumor was histologically diagnosed as LGSC. The genetic analysis that was done using exfoliated cells from peritoneal washings specimen by idensy™, detected KRAS mutation at codon 12/13.ConclusionThe genetic investigation using cytological specimen as well as characteristic cytological findings were useful to make differential diagnosis between LGSC and HGSC.
Sowing date affects soybean biological nitrogen fixation
Authors: Barat‐Carnino Mercedes , Santachiara Gabriel A. , Borras Lucas , Rotundo Jose L. 
Published: July 2022

AbstractIn many temperate soybean [Glycine max (L.) Merr.] production systems sowing date expands for several months. Early sowing dates commonly show maximum yields, but their consequences for crop N uptake and biological nitrogen fixation (BNF) are unknown. Our objective was to evaluate the role of sowing date, a major management variable defining soybean yield, on BNF. We hypothesized BNF is maximum at intermediate sowings because BNF is limited by low soil temperatures at early sowing dates and by high soil nitrate concentrations at later sowings. Four genotypes (maturity groups [MGs] IV and V) were tested over a 16‐wk sowing date period, and a N fertilizer treatment at sowing was added in all sowing date by genotype combinations (0 and 100 kg N ha–1). The N fertilization treatment helped to test sowing date effects independently of soil N availability. Seed yield and total N uptake were affected by sowing date and genotype, but not by the N treatment. Both seed yield and total N uptake followed similar quadratic responses, but MG V genotypes maximized yield and N uptake at the earliest sowing while MG IV cultivars maximized both traits at intermediate sowings. However, delaying sowing date always decreased the proportion of total aboveground N that came from BNF (average decline 0.22% d–1). Nitrogen fertilization reduced BNF by 15% across sowing dates and genotypes, with no yield effect. The linear decline in BNF with delayed sowing dates, instead of an optimum response, supports the concept that soil nitrates are the main driver of soybean BNF in this production system.
Inflammasome activation: from molecular mechanisms to autoinflammation
Authors: Lara‐Reyna Samuel , Caseley Emily A , Topping Joanne , Rodrigues François , Jimenez Macias Jorge , Lawler Sean E , McDermott Michael F 
Published: July 2022

AbstractInflammasomes are assembled by innate immune sensors that cells employ to detect a range of danger signals and respond with pro‐inflammatory signalling. Inflammasomes activate inflammatory caspases, which trigger a cascade of molecular events with the potential to compromise cellular integrity and release the IL‐1β and IL‐18 pro‐inflammatory cytokines. Several molecular mechanisms, working in concert, ensure that inflammasome activation is tightly regulated; these include NLRP3 post‐translational modifications, ubiquitination and phosphorylation, as well as single‐domain proteins that competitively bind to key inflammasome components, such as the CARD‐only proteins (COPs) and PYD‐only proteins (POPs). These diverse regulatory systems ensure that a suitable level of inflammation is initiated to counteract any cellular insult, while simultaneously preserving tissue architecture. When inflammasomes are aberrantly activated can drive excessive production of pro‐inflammatory cytokines and cell death, leading to tissue damage. In several autoinflammatory conditions, inflammasomes are aberrantly activated with subsequent development of clinical features that reflect the degree of underlying tissue and organ damage. Several of the resulting disease complications may be successfully controlled by anti‐inflammatory drugs and/or specific cytokine inhibitors, in addition to more recently developed small‐molecule inhibitors. In this review, we will explore the molecular processes underlying the activation of several inflammasomes and highlight their role during health and disease. We also describe the detrimental effects of these inflammasome complexes, in some pathological conditions, and review current therapeutic approaches as well as future prospective treatments.
Monocyte biomarkers define sargramostim treatment outcomes for Parkinson's disease
Authors: Abdelmoaty Mai M. , Machhi Jatin , Yeapuri Pravin , Shahjin Farah , Kumar Vikas , Olson Katherine E. , Mosley R. Lee , Gendelman Howard E. 
Published: July 2022

AbstractBackgroundDysregulation of innate and adaptive immunity heralds both the development and progression of Parkinson's disease (PD). Deficits in innate immunity in PD are defined by impairments in monocyte activation, function, and pro‐inflammatory secretory factors. Each influences disease pathobiology.Methods and ResultsTo define monocyte biomarkers associated with immune transformative therapy for PD, changes in gene and protein expression were evaluated before and during treatment with recombinant human granulocyte‐macrophage colony‐stimulating factor (GM‐CSF, sargramostim, Leukine®). Monocytes were recovered after leukapheresis and isolation by centrifugal elutriation, before and 2 and 6 months after initiation of treatment. Transcriptome and proteome biomarkers were scored against clinical motor functions. Pathway enrichments from single cell‐RNA sequencing and proteomic analyses from sargramostim‐treated PD patients demonstrate a neuroprotective signature, including, but not limited to, antioxidant, anti‐inflammatory, and autophagy genes and proteins (LRRK2, HMOX1, TLR2, TLR8, RELA, ATG7, and GABARAPL2).ConclusionsThis monocyte profile provides an “early” and unique biomarker strategy to track clinical immune‐based interventions, but requiring validation in larger case studies.
Patient‐derived renal cell carcinoma organoids for personalized cancer therapy
Authors: Li Zhichao , Xu Haibo , Yu Lei , Wang Jia , Meng Qian , Mei Hongbing , Cai Zhiming , Chen Wei , Huang Weiren 
Published: July 2022

AbstractBackgroundKidney cancer is one of the most common solid tumors. The advancement of human kidney cancer research and treatment has been hindered by a lack of research models that faithfully recapitulate the diversity of the disease.MethodsWe established an effective three‐dimensional culture system for generating kidney cancer organoids from clinical renal cell carcinoma samples. Renal cell carcinoma (RCC) organoids were characterized by H&E staining, immunofluorescence, whole‐exome sequencing, RNA sequencing and single‐cell RNA sequencing. The use of RCC organoids in personalized cancer therapy was assessed by testing their responses to treatment drugs and chimeric antigen receptor T cells.ResultsUsing this organoid culture system, 33 kidney cancer organoid lines from common kidney cancer subtypes, including clear cell renal cell carcinoma (ccRCC), papillary renal cell carcinoma (pRCC), and chromophobe renal cell carcinoma (chRCC), were generated. RCC organoids preserved the histological architectures, mutational landscapes, and transcriptional profile of the parental tumor tissues. Single‐cell RNA‐sequencing revealed inter‐ and intra‐tumoral heterogeneity in RCC organoids. RCC organoids allowed for in vitro drug screening and provided a tool for assessing the efficacy of chimeric antigen receptor T cells.ConclusionsPatient‐derived RCC organoids are valuable pre‐clinical models for academic research and personalized medicine.
Privacy Risks in Microbiome Research: Public Perspectives before and during a Global Pandemic
Authors: Shin Andrea , Xu Huiping 
Published: July 2022

ABSTRACTWe assessed public perspectives of microbiome research privacy risks before and after a nationwide emergency was declared in the United States regarding the Covid‐19 pandemic. From January to July of 2020, we conducted an online survey of perceived privacy risks of microbiome research among U.S. adults. Among 3,106 participants (the preemergency group), most expressed that the microbiome posed privacy risks similar to those associated with DNA (60.3%) or medical records (50.6%) and that they would prefer detailed explanations (70.2%) of risk in consent materials. Only 8.9% reported moderate to high familiarity with microbiome privacy risks. In adjusted analyses, individuals who participated in the study after the Covid‐19 emergency was declared (the Covid‐19 emergency group) were less likely to express that microbiome privacy risks were similar to those of DNA or medical records and more likely to report familiarity with the privacy risks of microbiomes. There was a trend toward increased concern after the Covid‐19 emergency was declared (p = 0.053). Overall, the study revealed that many U.S. adults believe that microbiome privacy risks are similar to those associated with DNA or medical records, and they prefer detailed explanations in consent documents. Individuals who participated after the Covid‐19 emergency was declared reported greater knowledge of microbiome privacy risks but had more concern.
Urban biotic homogenization: Approaches and knowledge gaps
Authors: Lokatis Sophie , Jeschke Jonathan M. 
Published: July 2022

AbstractUrbanization is restructuring ecosystems at an unprecedented pace, with complex and profound consequences for life on Earth. One of the hypothesized trajectories of urban ecosystems and species communities is biotic homogenization, possibly leading to very similar species assemblages in cities across the globe. Urbanization can, however, also have the opposite effect: biotic diversification, with cities, at least at the local scale, becoming biologically more diverse, mainly as a consequence of high species introduction rates and habitat diversification. Applying the hierarchy‐of‐hypotheses approach, we systematically map and structure the comprehensive body of literature on the urban biotic homogenization (UBH) hypothesis, comprising 225 individual studies (i.e., tests of the hypothesis) retrieved from 145 publications. The UBH hypothesis is studied at multiple levels with a multitude of approaches and underlying assumptions. We show that UBH is generally used with two very different connotations: about half of the studies investigated a potential increase in community similarity across cities, whereas the other half investigated biotic homogenization within cities, the latter being supported more frequently. We also found strong research biases: (1) a taxonomic bias towards birds and plants, (2) a bias towards small and medium distances (<5000 km) in comparisons across cities, (3) a dominance of studies substituting space for time versus true temporal studies, (4) a strong focus on terrestrial versus aquatic systems, (5) more extraurban (including periurban) areas than natural or rural ecosystems for comparison to urban systems, (6) a bias towards taxonomic versus functional, phylogenetic, and temporal homogenization, and (7) more studies undertaken in Europe and North America than in other continents. The overall level of empirical support for the UBH hypothesis was mixed, with 55% of the studies reporting supporting evidence. Results significantly differed when a natural/nature reserve, an extraurban, or rural/agricultural area served as reference to infer biotic homogenization, with homogenization being detected least frequently when urban systems were compared to agricultural, i.e., other anthropogenically influenced, study sites. We provide an evidence map and a bibliographic network and identify key references on UBH with the goal to enhance accessibility and orientation for future research on this topic.
Defining, estimating, and understanding the fundamental niches of complex animals in heterogeneous environments
Authors: Matthiopoulos Jason 
Published: July 2022

AbstractDuring the past century, the fundamental niche, the complete set of environments that allow an individual, population, or species to persist, has shaped ecological thinking. It is a crucial concept connecting population dynamics, spatial ecology, and evolutionary theory, and a prerequisite for predictive ecological models at a time of rapid environmental change. Yet, its properties have eluded quantification, particularly for mobile, cognitively complex organisms. These difficulties are mainly a result of the separation between niche theory and field data, and the dichotomy between environmental and geographical spaces. Here, I combine recent mathematical and statistical results linking habitats to population growth, to achieve a quantitative and intuitive understanding of the fundamental niches of animals. I trace the development of niche ideas from the early steps of ecology to their use in modern statistical and conservation practice. I examine how animal mobility and behavior may blur the division between geographical and environmental space. I discuss how the central models of population and spatial ecology lead to a concise mathematical equation for the fundamental niche of animals and demonstrate how fitness parameters can be understood and directly estimated by fitting this model simultaneously to data on population growth and spatial distributions. I first illustrate these concepts theoretically for territorial species. I then fit the fundamental niche model to a data set of house sparrow colonies to quantify how a species of selective animals can increase their fitness in heterogeneous environments. This work confirms ideas that had been anticipated in the historical niche literature. Specifically, within traditionally defined environmental spaces, habitat heterogeneity and behavioral plasticity make the fundamental niche more complex and malleable than was historically envisaged. However, once examined in higher‐dimensional environmental spaces, accounting for spatial heterogeneity, the niche is more predictable than recently suspected. This re‐evaluation quantifies how organisms might buffer themselves from change by bending the boundaries of viable environmental space and offers a framework for designing optimal habitat interventions to protect biodiversity or obstruct invasive species. It therefore promotes the fundamental niche as a key concept for understanding animal responses to changing environments and a central tool for environmental management.
A Person‐Centred Prehabilitation Program based on Cognitive Behavioural Physical Therapy for patients scheduled for Lumbar Fusion surgery: A mediation analysis to assess fear of movement (kinesiophobia), self‐efficacy and catastrophizing as mediators of health outcomes
Authors: Mansell Gemma , den Hollander Marlies , Lotzke Hanna , Smeets Rob J. E. M. , Lundberg Mari 
Published: July 2022

AbstractObjectiveTo investigate whether early changes in fear of movement (kinesiophobia), self‐efficacy and catastrophizing were mediators of the relationship between allocation to the pre‐habilitation intervention and later changes in health outcomes.MethodsThe original pre‐habilitation trial (PREPARE, ISRCTN17115599) recruited 118 participants awaiting lumbar fusion surgery, half of whom received a prehabilitation intervention designed based on the modified fear‐avoidance model and half of whom received usual care. Mediation analysis was performed to test each mediator separately. Analysis was performed on each outcome of interest separately (Oswestry disability index, patient‐specific function, EQ general health and moderate/vigorous physical activity). Mediation analysis was carried out using PROCESS. Beta coefficients and bootstrapped 95% CIs were used to interpret the results.ResultsNone of the potential mediators was found to mediate the relationship between allocation to the intervention and 3‐month scores on any of the health outcomes tested.ConclusionsScreening patients for higher levels of catastrophizing and fear avoidance and lower levels of self‐efficacy could help ensure only the patients who are most likely to benefit from the intervention are included.SignificancePrehabilitation interventions for spinal fusion surgery have been found to improve health outcomes for patients. Theory‐based interventions that target key mechanisms are more effective at improving outcomes than non‐theory‐based interventions. While no mediating effects were found for this particular intervention, the analysis suggests that the underlying theoretical model and treatment targets are appropriate and could drive improvement if more strongly targeted.
Body composition does not influence conditioned pain modulation and exercise‐induced hyperalgesia in healthy males and females
Authors: Peterson Jessica A. , Lohman Cameron , Larson Rebecca D. , Bemben Michael G. , Black Christopher D. 
Published: July 2022

AbstractBackgroundObese individuals report a higher susceptibility to chronic pain. Females are more likely to have chronic pain and excess adipose tissue. Chronic pain is associated with dysfunctional pain‐modulatory mechanisms. Body composition differences may be associated with pain modulation differences in males and females. The purpose of this study was to investigate body composition (lean vs fat mass) differences and pain‐modulatory functioning in healthy males and females.MethodsPressure pain thresholds (PPT) of 96 participants (47 M; 49F) were assessed in both arms and legs before and after a double‐footed ice bath (2°C) for 1 min and an isometric knee extension, time to failure task. The difference between post‐ and pre‐measures was defined as conditioned pain‐modulatory (CPM) response (ice bath) and exercise‐induced hypoalgesia (EIH) response. Whole‐body and site‐specific fat and lean tissue were assessed via the DXA scan.ResultsSex differences were found in whole‐body lean mass (61.5 ± 6.7 kg vs 41.2 ± 5.4 kg; p < 0.001) but not fat mass amount (17.2 ± 10.5 kg vs 21.0 ± 9.7 kg; p = 0.068). No effect of sex was found between limb CPM (p = 0.237) and limb EIH (p = 0.512). When controlling for lean mass, there was no significant effect of sex on CPM (p = 0.732) or EIH (p = 0.474) response. Similar findings were found for fat mass.ConclusionThe lack of difference suggests that males and females have similar modulatory functioning. It appears that in healthy adults free from chronic pain, neither fat mass nor lean mass has an influence on endogenous pain‐modulatory function.SignificanceMen and women exhibited similar CPM and EIH despite marked differences in body composition. Our findings suggest whole‐body and limb‐specific lean tissue mass and fat mass do not influence CPM and EIH in adults without chronic pain.
Deciphering the pharmacological mechanisms of Chaenomeles Fructus against rheumatoid arthritis by integrating network pharmacology and experimental validation
Authors: Sun Mengjia , Zhao Haijun , Liu Yuecheng , Ma Yanni , Tian Zhenhua , Wang Huanjun , Wei Sheng , Guo Qingmei , Gu Zhengwei , Jiang Haiqiang 
Published: July 2022

AbstractChaenomeles Fructus is a plant that can be used for both food and medicine. Modern studies have shown that Chaenomeles Fructus has anti‐inflammatory and immunosuppressive effects on arthritis. However, the mechanism of action of Chaenomeles Fructus on rheumatoid arthritis (RA) and its main active ingredients are still unclear. This study was aimed at devising an integrated strategy for investigating the bioactivity constituents and possible pharmacological mechanisms of Chaenomeles Fructus against RA. The components of Chaenomeles Fructus were analyzed using UPLC‐Q‐Exactive orbitrap MS techniques and applied to screen the active components of Chaenomeles Fructus according to their oral bioavailability and drug‐likeness index. Then, we speculated on the potential molecular mechanisms of Chaenomeles Fructus against RA through a network pharmacology analysis. Finally, the potential molecular mechanisms of Chaenomeles Fructus against RA were validated in a complete Freund's adjuvant (CFA)‐induced RA rat model. We identified 48 components in Chaenomeles Fructus and screened seven bioactive ingredients. The results of the network pharmacology prediction and the experimental verification results were analyzed by Venn analysis, and the experimental results concluded that Chaenomeles Fructus mainly interferes with the inflammation of RA by inhibiting arachidonic acid metabolism and the MAPK signaling pathway. This study identified the ingredients of Chaenomeles Fructus by UPLC‐Q‐Exactive orbitrap MS and explained the possible mechanisms of Chaenomeles Fructus against RA by integrating network pharmacology and experimental validation.
Performance of the Neck Imaging Reporting and Data System as applied by general neuroradiologists to predict recurrence of head and neck cancers
Authors: Lee Jonathan , Kaht Dagan , Ali Syed , Johnson Scott , Bullen Jennifer , Karakasis Christopher , Lamarre Eric , Geiger Jessica , Koyfman Shlomo , Stock Sarah 
Published: July 2022

AbstractBackgroundThe Neck Imaging Reporting and Data System (NI‐RADS) is used to assess imaging after head and neck cancer treatment. We evaluated NI‐RADS with general neuroradiologists rather than with head and neck subspecialists.MethodsComputed tomography and magnetic resonance imaging examinations with/without positron emission tomography from May 2018 to September 2020 were retrospectively identified. NI‐RADS scores at the primary site and lymph nodes were provided by 21 neuroradiologists. Recurrence status was based on clinical and imaging findings. Area under the curve (AUC) was used to assess accuracy.ResultsWe assessed 608 scans from 464 patients. For NI‐RADS categories 1, 2, and 3, primary site recurrence rates were 5%, 29%, and 65% with AUC of 0.765, while lymph node recurrence rates were 3%, 10%, and 80% with AUC of 0.820.ConclusionsNI‐RADS as used by general neuroradiologists is effective in separating head and neck cancers into discrete categories for predicting recurrent disease.