bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantifying Seasonal‐to‐Interannual‐Scale Storm Impacts on Morphology Along a Cuspate Coast With a Hybrid Empirical Orthogonal Function Approach
Authors: Conlin Matthew P. , Adams Peter N. , Jaeger John M. , MacKenzie Richard 
Published: October 2020

AbstractThe direct impacts of storms on beaches have been well studied; less well understood are the controls of storms on their seasonal‐interannual evolution. We apply a novel empirical orthogonal function (EOF) analysis to a 5‐year data set of monthly subaerial beach topography at Kennedy Space Center, Florida, to extract dominant spatiotemporal topographic patterns. Our hybrid surface EOF (SEOF) approach applies 1‐D EOF techniques to a data set varying in two dimensions, thereby extracting topographic patterns in the longshore and cross‐shore simultaneously while preserving the analytical simplicity of 1‐D approaches. These topographic patterns are then linked to observations of storm impacts. Our approach comprehensively illustrates that storms influenced local topographic evolution over event‐to‐interannual‐timescales. The first mode of topographic variability captures an interannual‐scale change in behavior triggered by the impact of Hurricane Sandy (2012), whereby a cape feature began and sustained rapid aggradation following the event. This pattern is likely linked to storm‐response processes and pre‐existing morphodynamic feedbacks, illustrating that storm response can dictate poststorm recovery processes. This pattern overwhelmed a spatially uniform, seasonal topographic signal, which we attribute to seasonal variability in water level and storminess forcings. The third mode shows links to local framework geology and suggests that some storms can create and/or destroy subaerial berms at this site, where spatial variability of berm existence in discrete longshore compartments can remain stable until a future event. Our results illustrate mechanisms by which storms can create persistent topographic imprints that remain visible for months‐years following events, potentially influencing response to future storms.
Dynamics of Marsh‐Derived Sediments in Lagoon‐Type Estuaries
Authors: Donatelli Carmine , Kalra Tarandeep Singh , Fagherazzi Sergio , Zhang Xiaohe , Leonardi Nicoletta 
Published: October 2020

AbstractSalt marshes are valuable ecosystems that must trap sediments and accrete in order to counteract the deleterious effect of sea level rise. Previous studies have shown that the capacity of marshes to build up vertically depends on both autogenous and exogenous processes including ecogeomorphic feedbacks and sediment supply from in‐land and coastal ocean. There have been numerous efforts to quantify the role played by the sediments coming from marsh edge erosion on the resistance of salt marshes to sea level rise. However, the majority of existing studies investigating the interplay between lateral and vertical dynamics use simplified modeling approaches, and they do not consider that marsh retreat can affect the regional‐scale hydrodynamics and sediment retention in back‐barrier basins. In this study, we evaluated the fate of the sediments originating from marsh lateral loss by using high‐resolution numerical model simulations of Jamaica Bay, a small lagoonal estuary located in New York City. Our findings show that up to 42% of the sediment released during marsh edge erosion deposits on the shallow areas of the basin and over the vegetated marsh platforms, contributing positively to the sediment budget of the remaining salt marshes. Furthermore, we demonstrate that with the present‐day sediment supply from the ocean, the system cannot keep pace with sea level rise even accounting for the sediment liberated in the bay through marsh degradation. Our study highlights the relevance of multiple sediment sources for the maintenance of the marsh complex.
Human cerebral organoids establish subcortical projections in the mouse brain after transplantation
Authors: Dong Xin , Xu Shi-Bo , Chen Xin , Tao Mengdan , Tang Xiao-Yan , Fang Kai-Heng , Xu Min , Pan Yufeng , Chen Yuejun , He Shuijin , Liu Yan 
Published: October 2020

AbstractNumerous studies have used human pluripotent stem cell-derived cerebral organoids to elucidate the mystery of human brain development and model neurological diseases in vitro, but the potential for grafted organoid-based therapy in vivo remains unknown. Here, we optimized a culturing protocol capable of efficiently generating small human cerebral organoids. After transplantation into the mouse medial prefrontal cortex, the grafted human cerebral organoids survived and extended projections over 4.5 mm in length to basal brain regions within 1 month. The transplanted cerebral organoids generated human glutamatergic neurons that acquired electrophysiological maturity in the mouse brain. Importantly, the grafted human cerebral organoids functionally integrated into pre-existing neural circuits by forming bidirectional synaptic connections with the mouse host neurons. Furthermore, compared to control mice, the mice transplanted with cerebral organoids showed an increase in freezing time in response to auditory conditioned stimuli, suggesting the potentiation of the startle fear response. Our study showed that subcortical projections can be established by microtransplantation and may provide crucial insights into the therapeutic potential of human cerebral organoids for neurological diseases.
Integrated phosphoproteomic and metabolomic profiling reveals perturbed pathways in the hippocampus of gut microbiota dysbiosis mice
Authors: Wang Haiyang , Liu Lanxiang , Rao Xuechen , Zeng Benhua , Yu Ying , Zhou Chanjuan , Zeng Li , Zheng Peng , Pu Juncai , Xu Shaohua , Cheng Ke , Zhang Hanping , Ji Ping , Wei Hong , Xie Peng 
Published: October 2020

AbstractThe dysbiosis of gut microbiota is an important environmental factor that can induce mental disorders, such as depression, through the microbiota–gut–brain axis. However, the underlying pathogenic mechanisms are complex and not completely understood. Here we utilized mass spectrometry to identify the global phosphorylation dynamics in hippocampus tissue in germ-free mice and specific pathogen-free mice (GF vs SPF), fecal microbiota transplantation (FMT) model (“depression microbiota” and the “healthy microbiota” recipient mice). As a result, 327 phosphosites of 237 proteins in GF vs SPF, and 478 phosphosites of 334 proteins in “depression microbiota” vs “healthy microbiota” recipient mice were identified as significant. These phosphorylation dysregulations were consistently associated with glutamatergic neurotransmitter system disturbances. The FMT mice exhibited disturbances in lipid metabolism and amino acid metabolism in both the periphery and brain through integrating phosphoproteomic and metabolomic analysis. Moreover, CAMKII-CREB signaling pathway, in response to these disturbances, was the primary common perturbed cellular process. In addition, we demonstrated that the spliceosome, never directly implicated in mental disorders previously, was a substantially neuronal function disrupted by gut microbiota dysbiosis, and the NCBP1 phosphorylation was identified as a novel pathogenic target. These results present a new perspective to study the pathologic mechanisms of gut microbiota dysbiosis related depression and highlight potential gut-mediated therapies for depression.
Synergistic tumor inhibition of colon cancer cells by nitazoxanide and obeticholic acid, a farnesoid X receptor ligand
Authors: Yu Junhui , Yang Kui , Zheng Jianbao , Zhao Wei , Sun Xuejun 
Published: October 2020

AbstractThe tumor-suppressive role of Farnesoid X receptor (FXR) in colorectal tumorigenesis supports restoring FXR expression as a novel therapeutic strategy. However, the complicated signaling network and tumor heterogeneity hinder the effectiveness of FXR agonists in the clinical setting. These difficulties highlight the importance of identifying drug combinations with potency and specificity to enhance the antitumor effects of FXR agonists. In this study, we found that the β-catenin level affected the antitumor effects of the FXR agonist OCA on colon cancer cells. Mechanistic studies identified a novel FXR/β-catenin complex in colon cancer cells. Furthermore, the depletion of β-catenin expedited FXR nuclear localization and enhanced its occupancy of the SHP promoter and thereby sensitized colon cancer cells to OCA. Furthermore, we utilized a drug combination study and identified that the antiparasitic drug nitazoxanide (NTZ) abrogated β-catenin expression and acted synergistically with OCA in colon cancer cells. The combination of OCA plus NTZ exerts synergistic tumor inhibition in CRC both in vitro and in vivo by cooperatively upregulating SHP expression. In conclusion, our study offers useful evidence for the clinical use of FXR agonists combined with β-catenin inhibitors in combating CRC.
NLRP3-dependent microglial training impaired the clearance of amyloid-beta and aggravated the cognitive decline in Alzheimer’s disease
Authors: He Xiao-fei , Xu Jing-hui , Li Ge , Li Ming-yue , Li Li-li , Pei Zhong , Zhang Li-ying , Hu Xi-quan 
Published: October 2020

AbstractAlzheimer’s disease (AD), the most common form of dementia, is marked by progressive cognitive decline, deposition of misfolded amyloid-β (Aβ) peptide and formation of neurofibrillary tangles. Recently, microglial training has emerged as an important contributor to neurological diseases, which augments the subsequent inflammation. However, how it affects the pathology of AD remains unknown. Here, using a mouse model of sporadic Alzheimer’s disease (SAD) induced by streptozotocin injection, we demonstrated that microglial training exacerbated Aβ accumulation, neuronal loss, and cognitive impairment. In addition, we injected MCC950 to inhibit NLRP3 activation and used an inducible Cre recombinase to delete the NLRP3 gene in microglia. Inhibition or depletion of microglial NLRP3 could protect against the pathologies of SAD and abolish the effects of microglial training. Our results identified microglial training as an important modifier of neuropathology in SAD and demonstrated that activation of NLRP3 inflammasome contributed to the pathologies and microglial training in SAD. Therefore, NLRP3 could be a potential therapeutic target for SAD treatment.
Impact of varied combinatorial mixture of non-fishmeal ingredients on growth, metabolism, immunity and gut microbiota of Lates calcarifer (Bloch, 1790) fry
Authors: Gupta Sanjay K. , Fotedar Ravi , Foysal Md. Javed , Priyam Manisha , Siddik Muhammad A. B. , Chaklader Md. Reaz , Dao Thi Thanh Thuy , Howieson Janet 
Published: October 2020

AbstractThe search for suitable fish meal replacements in aqua-diets is a salient agenda in the constant effort of making aquaculture practices more sustainable. In this study, we tested four customised diets composed by systematic inclusion of pre-selected fish meal substitutes, lupin kernel meal, BSF meal, TH and PBM on growth, metabolism, cytokine profile, gut morphology and microbiota of juvenile Lates calcarifer. Five isoproteic and isoenergetic diets were prepared viz. FM100 as a control (without fish meal substitute), while FM75, FM50, FM25 and FM0 indicates replacement of fish meal (FM) at 25%, 50%, 75%, and 100%, respectively by a mixture of four different pre-selected non-fish meal (NFM) ingredients. Fish fed FM100, FM75, FM50, FM25 exhibited consistent growth and haematological response, while the fish fed no fishmeal (FM0) showed significant decline in final body weight (FBW) and specific growth rate (SGR). The poor growth performance was correlated with a decrease in villous width, microvilli height and goblet cells density. A significant shift in abundance profile of Psychrobacter in the gut microbial profile of fish fed FM50 was noticed compared to fish fed FM100. The results of qRT-PCR showed up-regulated expression of innate immune responsive genes in the FM50 group. The adverse impacts on growth performance and gut health of fish fed FM0 suggest that the complete substitution of fishmeal is not advisable and the inclusion range of these alternatives should be decided for a species only after examining their effect on maximal physiological performance.
Survival prediction of patients with sepsis from age, sex, and septic episode number alone
Authors: Chicco Davide , Jurman Giuseppe 
Published: October 2020

AbstractSepsis is a life-threatening condition caused by an exaggerated reaction of the body to an infection, that leads to organ failure or even death. Since sepsis can kill a patient even in just one hour, survival prediction is an urgent priority among the medical community: even if laboratory tests and hospital analyses can provide insightful information about the patient, in fact, they might not come in time to allow medical doctors to recognize an immediate death risk and treat it properly. In this context, machine learning can be useful to predict survival of patients within minutes, especially when applied to few medical features easily retrievable. In this study, we show that it is possible to achieve this goal by applying computational intelligence algorithms to three features of patients with sepsis, recorded at hospital admission: sex, age, and septic episode number. We applied several data mining methods to a cohort of 110,204 admissions of patients, and obtained high prediction scores both on this complete dataset (top precision-recall area under the curve PR AUC = 0.966) and on its subset related to the recent Sepsis-3 definition (top PR AUC = 0.860). Additionally, we tested our models on an external validation cohort of 137 patients, and achieved good results in this case too (top PR AUC = 0.863), confirming the generalizability of our approach. Our results can have a huge impact on clinical settings, allowing physicians to forecast the survival of patients by sex, age, and septic episode number alone.
Low frequency oscillations assessed by diffuse speckle contrast analysis for foot angiosome concept
Authors: Yeo Chaebeom , Jung Hanbeen , Lee Kijoon , Song Cheol 
Published: October 2020

AbstractAn angiosome refers to a 3D tissue volume that is vascularized by a single artery and is a relatively new concept that is useful in vascular surgery; however, the direct relationship between arterial blood flow and micro-perfusion is still controversial. Here, we propose a diffuse speckle contrast analysis (DSCA), which is an emerging tissue perfusion monitoring modality, to investigate the correlations among low frequency oscillations (LFOs) measured from different areas on the feet of healthy subjects. We obtained reproducible results from the correlation analyses of LFOs, and their physiological implications were discussed. In order to confirm the changes in the frequency oscillations, we analyzed and compared the power spectral density changes due to heart rate variability in the electrocardiographic signal during reactive hyperemia and head-up tilt protocols.
Exploration into biomarker potential of region-specific brain gene co-expression networks
Authors: Hang Yuqing , Aburidi Mohammed , Husain Benafsh , Hickman Allison R. , Poehlman William L. , Feltus F. Alex 
Published: October 2020

AbstractThe human brain is a complex organ that consists of several regions each with a unique gene expression pattern. Our intent in this study was to construct a gene co-expression network (GCN) for the normal brain using RNA expression profiles from the Genotype-Tissue Expression (GTEx) project. The brain GCN contains gene correlation relationships that are broadly present in the brain or specific to thirteen brain regions, which we later combined into six overarching brain mini-GCNs based on the brain’s structure. Using the expression profiles of brain region-specific GCN edges, we determined how well the brain region samples could be discriminated from each other, visually with t-SNE plots or quantitatively with the Gene Oracle deep learning classifier. Next, we tested these gene sets on their relevance to human tumors of brain and non-brain origin. Interestingly, we found that genes in the six brain mini-GCNs showed markedly higher mutation rates in tumors relative to matched sets of random genes. Further, we found that cortex genes subdivided Head and Neck Squamous Cell Carcinoma (HNSC) tumors and Pheochromocytoma and Paraganglioma (PCPG) tumors into distinct groups. The brain GCN and mini-GCNs are useful resources for the classification of brain regions and identification of biomarker genes for brain related phenotypes.
Circulating antibodies against age-modified proteins in patients with coronary atherosclerosis
Authors: Korça Edina , Piskovatska Veronika , Börgermann Jochen , Navarrete Santos Alexander , Simm Andreas 
Published: October 2020

AbstractAdvanced glycation endproducts (AGEs) are formed in a series of non-enzymatic reactions between reducing sugars and the amino groups of proteins and accumulate during aging, diabetes mellitus, chronic kidney disease and other chronic diseases. Accumulation of AGE-modifications alters protein structure and function, transforming these molecules into potential targets of the immune system, presumably triggering the production of autoantibodies against AGEs. In this study, we detected autoantibodies against AGE-modified proteins with ELISA in plasma samples of 91 patients with documented coronary artery disease (CAD), who underwent coronary artery bypass grafting (CABG) surgery. Patients with high levels of autoantibodies had a higher body mass index (BMI 28.6 vs 27.1 kg/m2; p = 0.046), were more likely to suffer from chronic obstructive pulmonary disease (COPD 30% vs 9.8%; p = 0.018), and more likely to need dialysis after the surgery (10% vs 0%; p = 0.037). Our findings show a weak link between the levels of autoantibodies against AGEs and diabetes mellitus (DM 44% vs 24.4%; p = 0.05). In a small subpopulation of patients, antibodies against native bovine serum albumin (BSA) were detected. A growing body of research explores the potential role of antibodies against AGE-modified proteins in pathogenesis of different chronic diseases; our data confirms the presence of AGE-autoantibodies in patients with CAD and that in parallel to the AGEs themselves, they may have a potential role in concomitant clinical conditions in patients undergoing CABG surgery. Further research is necessary to verify the molecular role of these antibodies in different pathological conditions.
Healthcare resources attributable to methicillin-resistant Staphylococcus aureus orthopedic surgical site infections
Authors: Fukuda Haruhisa , Sato Daisuke , Iwamoto Tetsuya , Yamada Koji , Matsushita Kazuhiko 
Published: October 2020

AbstractThe number of orthopedic surgeries is increasing as populations steadily age, but surgical site infection (SSI) rates remain relatively consistent. This study aimed to quantify the healthcare resources attributable to methicillin-resistant Staphylococcus aureus (MRSA) SSIs in orthopedic surgical patients. The analysis was conducted using a national claims database comprising data from almost all Japanese residents. We examined patients who underwent any of the following surgeries between April 2012 and March 2018: amputation (AMP), spinal fusion (FUSN), open reduction of fracture (FX), hip prosthesis (HPRO), knee prosthesis (KPRO), and laminectomy (LAM). Propensity score matching was performed to identify non-SSI control patients, and generalized estimating equations were used to estimate the differences in outcomes between the case and control groups. The numbers of MRSA SSI cases (infection rates) ranged from 64 (0.03%) to 1,152 (2.33%). MRSA SSI-attributable increases in healthcare expenditure ranged from $11,630 ($21,151 vs. $9,521) for LAM to $35,693 ($50,122 vs. $14,429) for FX, and increases in hospital stay ranged from 40.6 days (59.2 vs. 18.6) for LAM to 89.5 days (122.0 vs. 32.5) for FX. In conclusion, MRSA SSIs contribute to substantial increases in healthcare resource utilization, emphasizing the need to implement effective infection prevention measures for orthopedic surgeries.
Family history of diabetes is associated with diabetic foot complications in type 2 diabetes
Authors: Xiong Xiao-fen , Wei Ling , Xiao Ying , Han Ya-Chun , Yang Jinfei , Zhao Hao , Yang Ming , Sun Lin 
Published: October 2020

AbstractTo investigate the relationship between diabetic foot complications (DFCs) and clinical characteristics, especially the number and types of first-degree family members with diabetes. A total of 8909 type 2 diabetes patients were enrolled. The clinical characteristics of these patients, including DFCs and family history of diabetes (FHD), were collected from medical records. Multiple regression was used to investigate the association between FHD and DFCs after adjusting for confounding factors. The patients with one and more than one first-degree family member with diabetes accounted for 18.7% and 12.8%, respectively. The proportions of the participants with a father with diabetes, a mother with diabetes, both parents with diabetes, siblings with diabetes, father and siblings with diabetes, mother and siblings with diabetes, and both parents and siblings with diabetes were 3.5%, 6.2%, 1.1%, 14.4%, 1.5%, 4%, and 0.7%, respectively. The multiple regression analysis showed that the number of family members with diabetes was positively associated with DFCs. However, among the different types of FHD, only the patients with a mother with diabetes showed a statistical association with DFCs. In addition to FHD, other factors, including gender, body mass index, platelet count, hemoglobin levels, albumin levels, high-density cholesterol levels, diabetic peripheral neuropathy, and the use of lipid-lowering agents, oral hypoglycemic agents, and insulin, were also associated with DFCs. DFCs were associated with different numbers of family members with diabetes and types of FHD. This association reveals the importance of genetic and environmental factors in DFCs and highlights the importance of adding FHD to public health strategies targeting detecting and preventing the disease.
EEG microstates of dreams
Authors: Bréchet Lucie , Brunet Denis , Perogamvros Lampros , Tononi Giulio , Michel Christoph M. 
Published: October 2020

AbstractWhy do people sometimes report that they remember dreams, while at other times they recall no experience? Despite the interest in dreams that may happen during the night, it has remained unclear which brain states determine whether these conscious experiences will occur and what prevents us from waking up during these episodes. Here we address this issue by comparing the EEG activity preceding awakenings with recalled vs. no recall of dreams using the EEG microstate approach. This approach characterizes transiently stable brain states of sub-second duration that involve neural networks with nearly synchronous dynamics. We found that two microstates (3 and 4) dominated during NREM sleep compared to resting wake. Further, within NREM sleep, microstate 3 was more expressed during periods followed by dream recall, whereas microstate 4 was less expressed. Source localization showed that microstate 3 encompassed the medial frontal lobe, whereas microstate 4 involved the occipital cortex, as well as thalamic and brainstem structures. Since NREM sleep is characterized by low-frequency synchronization, indicative of neuronal bistability, we interpret the increased presence of the “frontal” microstate 3 as a sign of deeper local deactivation, and the reduced presence of the “occipital” microstate 4 as a sign of local activation. The latter may account for the occurrence of dreaming with rich perceptual content, while the former may account for why the dreaming brain may undergo executive disconnection and remain asleep. This study demonstrates that NREM sleep consists of alternating brain states whose temporal dynamics determine whether conscious experience arises.