bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metastatic breast cancer cells induce altered microglial morphology and electrical excitability in vivo
Authors: Simon Anna , Yang Ming , Marrison Joanne L. , James Andrew D. , Hunt Mark J. , O’Toole Peter J. , Kaye Paul M. , Whittington Miles A. , Chawla Sangeeta , Brackenbury William J. 
Published: March 2020

Abstract
Background
An emerging problem in the treatment of breast cancer is the increasing incidence of metastases to the brain. Metastatic brain tumours are incurable and can cause epileptic seizures and cognitive impairment, so better understanding of this niche, and the cellular mechanisms, is urgently required. Microglia are the resident brain macrophage population, becoming “activated” by neuronal injury, eliciting an inflammatory response. Microglia promote proliferation, angiogenesis and invasion in brain tumours and metastases. However, the mechanisms underlying microglial involvement appear complex and better models are required to improve understanding of function.

Methods
Here, we sought to address this need by developing a model to study metastatic breast cancer cell-microglial interactions using intravital imaging combined with ex vivo electrophysiology. We implanted an optical window on the parietal bone to facilitate observation of cellular behaviour in situ in the outer cortex of heterozygous Cx3cr1GFP/+ mice.

Results
We detected GFP-expressing microglia in Cx3cr1GFP/+ mice up to 350 μm below the window without significant loss of resolution. When DsRed-expressing metastatic MDA-MB-231 breast cancer cells were implanted in Matrigel under the optical window, significant accumulation of activated microglia around invading tumour cells could be observed. This inflammatory response resulted in significant cortical disorganisation and aberrant spontaneously-occurring local field potential spike events around the metastatic site.

Conclusions
These data suggest that peritumoral microglial activation and accumulation may play a critical role in local tissue changes underpinning aberrant cortical activity, which offers a possible mechanism for the disrupted cognitive performance and seizures seen in patients with metastatic breast cancer.
Astrocyte-derived exosomes enriched with miR-873a-5p inhibit neuroinflammation via microglia phenotype modulation after traumatic brain injury
Authors: Long Xiaobing , Yao Xiaolong , Jiang Qian , Yang Yiping , He Xuejun , Tian Weidong , Zhao Kai , Zhang Huaqiu 
Published: March 2020

Abstract
Background
The interaction between astrocytes and microglia plays a vital role in the damage and repair of brain lesions due to traumatic brain injury (TBI). Recent studies have shown that exosomes act as potent mediators involved in intercellular communication.

Methods
In the current study, the expression of inflammatory factors and miR-873a-5p in the lesion area and oedema area was evaluated in 15 patients with traumatic brain injury. Exosomes secreted by astrocytes were detected by immunofluorescence, Western blot and electron microscopy. A mouse model of TBI and an in vitro model of LPS-induced primary microglia were established to study the protective mechanism of exosomes from miR-873a-5p overexpressing in TBI-induced nerve injury.

Results
We discovered that exosomes derived from activated astrocytes promote microglial M2 phenotype transformation following TBI. More than 100 miRNAs were detected in these astrocyte-derived exosomes. miR-873a-5p is a major component that was highly expressed in human traumatic brain tissue. Moreover, miR-873a-5p significantly inhibited LPS-induced microglial M1 phenotype transformation and the subsequent inflammation through decreased phosphorylation of ERK and NF-κB p65. This effect also greatly improved the modified neurological severity score (mNSS) and attenuated brain injury in a strictly controlled cortical impact mouse model.

Conclusions
Taken together, our research indicates that miRNAs in the exosomes derived from activated astrocytes play a key role in the astrocyte-microglia interaction. miR-873a-5p, as one of the main components of these astrocyte-derived exosomes, attenuated microglia-mediated neuroinflammation and improved neurological deficits following TBI by inhibiting the NF-κB signalling pathway. These findings suggest a potential role for miR-873a-5p in treating traumatic brain injury.
MiR-29c-3p, a target miRNA of LINC01296, accelerates tumor malignancy: therapeutic potential of a LINC01296/miR-29c-3p axis in ovarian cancer
Authors: Xu Hui , Mao Hong-Luan , Zhao Xin-Rui , Li Yue , Liu Pei-Shu 
Published: March 2020

AbstractAs one of the main gynecological cancers, ovarian cancer (OC) has an unfavourable outcomes owing to its high recurrence and metastasis rate. Our previous studies have revealed that LINC01296 functions as an oncogene in OC, but the underlying mechanism has not been explored. The aim of this paper was to further investigate that how LINC01296 plays a role in OC. Through online software prediction, miR-29c-3p has been discriminated as the target miRNA of LINC01296 for further research, and subsequent luciferase assay confirmed bioinformatics prediction. Then the data obtained from the two databases (GSE119055 and GSE83693) were analyzed by GEO2R for differential gene analysis. The results indicated that the miR-29c-3p was lowly expressed in OC tissues than that in normal ovarian tissues, and its expression in recurrent OC tissues was lower than that in primary OC tissues. Simultaneously, Kaplan-Meier survival analysis illustrated that the lower expression of miR-29c-3p was interrelated to unfavourable outcomes of OC. Further, the qRT-PCR data revealed that the miR-29c-3p expression in OC cell lines (SKOV-3 and OVCAR-3) was markedly declined than that in normal control cells (IOSE80). Subsequently, the functional experiments, such as CCK8, colony formation and Transwell assays, prompted that inhibition of miR-29c-3p can obviously increase the proliferation, invasion and migration of OVCAR3 and SKOV3 cells compared with control group, while downregulation of LINC01296 showed an opposite result. It is worth noting that downregulation of LINC01296 can reverse the effect of miR-29c-3p suppression on OC cells. Finally, we detected the changes of EMT-related proteins by western blot experiment, and reached a similar conclusion that knockdown of LINC01296 reversed the EMT caused by miR-29c-3p inhibition. In sum up, the cancer-promoting function of LINC01296 was achieved by regulating the expression of miR-29c-3p, and LINC01296/miR-29c-3p axis mediates the mechanical regulation of EMT in OC cells, hoping to provide the novel biomarkers and possibilities for OC therapy.
Risk factors for candidemia: a prospective matched case-control study
Authors:   the FUNGINOS, Poissy Julien ,   Allfun French Study Groups, Damonti Lauro , Bignon Anne , Khanna Nina , Von Kietzell Matthias , Boggian Katia , Neofytos Dionysios , Vuotto Fanny , Coiteux Valérie , Artru Florent , Zimmerli Stephan , Pagani Jean-Luc , Calandra Thierry , Sendid Boualem , Poulain Daniel , van Delden Christian , Lamoth Frédéric , Marchetti Oscar , Bochud Pierre-Yves 
Published: March 2020

Abstract
Background
Candidemia is an opportunistic infection associated with high morbidity and mortality in patients hospitalized both inside and outside intensive care units (ICUs). Identification of patients at risk is crucial to ensure prompt antifungal therapy. We sought to assess risk factors for candidemia and death, both outside and inside ICUs.

Methods
This prospective multicenter matched case-control study involved six teaching hospitals in Switzerland and France. Cases were defined by positive blood cultures for Candida sp. Controls were matched to cases using the following criteria: age, hospitalization ward, hospitalization duration, and, when applicable, type of surgery. One to three controls were enrolled by case. Risk factors were analyzed by univariate and multivariate conditional regression models, as a basis for a new scoring system to predict candidemia.

Results
One hundred ninety-two candidemic patients and 411 matched controls were included. Forty-four percent of included patients were hospitalized in ICUs, and 56% were hospitalized outside ICUs. Independent risk factors for candidemia in the ICU population included total parenteral nutrition, acute kidney injury, heart disease, prior septic shock, and exposure to aminoglycoside antibiotics. Independent risk factors for candidemia in the non-ICU population included central venous catheter, total parenteral nutrition, and exposure to glycopeptides and nitroimidazoles. The accuracy of the scores based on these risk factors is better in the ICU than in the non-ICU population. Independent risk factors for death in candidemic patients included septic shock, acute kidney injury, and the number of antibiotics to which patients were exposed before candidemia.

Discussion
While this study shows a role for known and novel risk factors for candidemia, it specifically highlights important differences in their distribution according to the hospital setting (ICU versus non-ICU).

Conclusion
This study provides novel risk scores for candidemia accounting for the hospital setting and recent progress in patients’ management strategies and fungal epidemiology.
Dynamics of plasma biomarkers in Down syndrome: the relative levels of Aβ42 decrease with age, whereas NT1 tau and NfL increase
Authors: Mengel David , Liu Wen , Glynn Robert J. , Selkoe Dennis J. , Strydom Andre , Lai Florence , Rosas H. Diana , Torres Amy , Patsiogiannis Vasiliki , Skotko Brian , Walsh Dominic M. 
Published: March 2020

AbstractBackgroundDown syndrome (DS) is the most common genetic cause of Alzheimer’s disease (AD), but diagnosis of AD in DS is challenging due to the intellectual disability which accompanies DS. When disease-modifying agents for AD are approved, reliable biomarkers will be required to identify when and how long people with DS should undergo treatment. Three cardinal neuropathological features characterize AD, and AD in DS—Aβ amyloid plaques, tau neurofibrillary tangles, and neuronal loss. Here, we quantified plasma biomarkers of all 3 neuropathological features in a large cohort of people with DS aged from 3 months to 68 years. Our primary aims were (1) to assess changes in the selected plasma biomarkers in DS across age, and (2) to compare biomarkers measured in DS plasma versus age- and sex-matched controls.MethodsUsing ultra-sensitive single molecule array (Simoa) assays, we measured 3 analytes (Aβ42, NfL, and tau) in plasmas of 100 individuals with DS and 100 age- and sex-matched controls. Tau was measured using an assay (NT1) which detects forms of tau containing at least residues 6–198. The stability of the 3 analytes was established using plasma from ten healthy volunteers collected at 6 intervals over a 5-day period.ResultsHigh Aβ42 and NT1 tau and low NfL were observed in infants. Across all ages, Aβ42 levels were higher in DS than controls. Levels of Aβ42 decreased with age in both DS and controls, but this decrease was greater in DS than controls and became prominent in the third decade of life. NT1 tau fell in adolescents and young adults, but increased in older individuals with DS. NfL levels were low in infants, children, adolescents, and young adults, but thereafter increased in DS compared to controls.ConclusionsHigh levels of Aβ42 and tau in both young controls and DS suggest these proteins are produced by normal physiological processes, whereas the changes seen in later life are consistent with emergence of pathological alterations. These plasma biomarker results are in good agreement with prior neuropathology studies and indicate that the third and fourth decades (i.e., 20 to 40 years of age) of life are pivotal periods during which AD processes manifest in DS. Application of the assays used here to longitudinal studies of individuals with DS aged 20 to 50 years of age should further validate the use of these biomarkers, and in time may allow identification and monitoring of people with DS best suited for treatment with AD therapies.
Microbial community diversity of traditional dough starter (Jiaozi) from two provinces in northwest China
Authors: Liu Ting , Kang Jiamu , Liu Liu , Hu Xinzhong , Wang Xiaolong , Li Xiaoping , Ma Zhen , Ren Tian 
Published: March 2020

Abstract
Purpose
Microbial community composition is crucial for the flavor and quality of fermented foods. However, the microbiota of Chinese traditional dough starter (Jiaozi) from different origins has scarcely been studied. The aim of this study was to determine the composition of bacterial and fungal communities in six Jiaozi collected from two provinces in northwest China.

Methods
Our study determined the composition of bacterial and fungal communities in six Jiaozi through Illumina MiSeq sequencing of the 16S rRNA gene and the ITS regions.

Result
A total of 234 operational taxonomic units (OTUs) for bacteria and 490 OTUs for fungi were identified. Furthermore, Lactobacillus, Weissella, Acetobacter, Sphingomonas, and Serratia were identified as the predominant bacterial genera in Jiaozi samples, while Saccharomyces, Candida, Alternaria, unclassified Filobasidiales, and Mycosphaerella were the most abundant fungal genera. The results revealed that the six samples could be grouped into two groups based on their province of origin. In the results of PCA and HCA analysis, the first three principal components which were chosen could explain 99.93% and 90.99% of the total bacterial and fungal communities, respectively.

Conclusion
The results indicated high levels of bacteria and fungi in traditional Jiaozi and highlighted the possible influence of geographic areas on microbial diversity.
Facial fractures: classification and highlights for a useful report
Authors: Gómez Roselló Eva , Quiles Granado Ana M. , Artajona Garcia Miquel , Juanpere Martí Sergi , Laguillo Sala Gemma , Beltrán Mármol Briggitte , Pedraza Gutiérrez Salvador 
Published: March 2020

AbstractIn patients with facial trauma, multidetector computed tomography is the first-choice imaging test because it can detect and characterize even small fractures and their associated complications quickly and accurately. It has helped clinical management and surgical planning, so radiologists must communicate their findings to surgeons effectively. In Le Fort fractures, there is a breach between the pterygoid plates and the posterior maxilla. These fractures are classified in three basic patterns that can be combined and associated with various complications. Conceptualized when low-speed trauma was predominant, the Le Fort classification system has become less relevant giving more importance on maxillary occlusion-bearing segments. The classification of naso-orbito-ethmoid depends on the extent of injury to the attachment of the medial canthal tendon, with possible complications like nasofrontal duct disruption. Displaced fractures of the zygomaticomaxillary complex often widen the angle of the lateral orbital wall, resulting in increased orbital volume and sometimes in enophthalmos. Severe comminution or angulation can lead to wide surgical exposure. In orbital fractures, entrapment of the inferior rectus muscles can lead to diplopia, so it is important to assess its positioning and morphology. Orbital fractures can also result in injuries to the globe or infraorbital nerve. Frontal sinus fractures that extend through the posterior sinus wall can create a communication with the anterior cranial fossa resulting in leakage of cerebrospinal fluid, intracranial bleeding. It is essential to categorize fracture patterns and highlight features that may affect fracture management in radiology reports of facial trauma.
Attractivity for Hilfer fractional stochastic evolution equations
Authors: Yang Min , Alsaedi Ahmed , Ahmad Bashir , Zhou Yong 
Published: March 2020

AbstractThis article is devoted to the study of the attractivity of solutions to a class of stochastic evolution equations involving Hilfer fractional derivative. By employing the semigroup theory, fractional calculus and the fixed point technique, we establish new alternative criteria to ensure the existence of globally attractive solutions for the Cauchy problem when the associated semigroup is compact.
Stability and bifurcation in a single species logistic model with additive Allee effect and feedback control
Authors: Lv Yangyang , Chen Lijuan , Chen Fengde 
Published: March 2020

AbstractIn this paper, we propose a single species logistic model with feedback control and additive Allee effect in the growth of species. The basic aim of the paper is to discuss how the additive Allee effect and feedback control influence the above model’s dynamical behaviors. Firstly, the existence and stability of equilibria are discussed under three different cases, i.e., weak Allee effect, strong Allee effect, and the critical case. Secondly, we prove the occurrence of saddle-node bifurcation and transcritical bifurcation with the help of Sotomayor’s theorem. The above dynamical behaviors are richer and more complex than those in the traditional logistic model with feedback control. We find that both Allee effect and feedback control can increase the species’ extinction property. We also reveal some new bifurcation phenomena which do not exist in the single-species model with feedback control (Fan and Wang in Nonlinear Anal., Real World Appl. 11(4):2686–2697, 2010 and Lin in Adv. Differ. Equ. 2018:190, 2018).
Topographic analysis of macular choriocapillaris flow deficits in diabetic retinopathy using swept–source optical coherence tomography angiography
Authors: Gendelman Isaac , Alibhai A. Yasin , Moult Eric M. , Levine Emily S. , Braun Phillip X. , Mehta Nihaal , Zhao Yi , Ishibazawa Akihiro , Sorour Osama A. , Baumal Caroline R. , Witkin Andre J. , Reichel Elias , Fujimoto James G. , Duker Jay S. , Waheed Nadia K. 
Published: March 2020

Abstract
Background
The purpose of this study was to investigate the association between diabetic retinopathy (DR) severity and macular choriocapillaris (CC) flow deficit percentage (FD %) in different macular regions using swept-source optical coherence tomography angiography (SS-OCTA).

Methods
Diabetic patients with SS-OCTA images were graded by severity and retrospectively assessed. CC FD % was calculated in four different regions of the OCTA image: inner, middle, outer, and full-field region. The generalized estimating equations (GEE) approach for clustered eye data was used to determine effect size and significance of age and disease severity on FD % for each region.

Results
160 eyes from 90 total diabetic patients met inclusion criteria. Out of 90 patients, 33 had no DR, 17 had mild nonproliferative DR (NPDR), 8 had moderate NPDR, 10 had severe NPDR and 22 had proliferative DR. Age and DR severity had a significant positive association with FD % for each region studied with a greater effect in the two centermost regions. The increase in flow deficit percentage per year of age by region was: inner 0.12 (p < 0.001), middle 0.09 (p < 0.001), outer 0.05 (p < 0.001, full-field 0.06 (p < 0.001). The increase in flow deficit percentage per increase in diabetic retinopathy severity stage by region was: inner 0.65 (p < 0.0087), middle 0.56 (p < 0.0012), outer 0.33 (p < 0.045), full-field 0.36 (p < 0.018).

Conclusions
Topographic analysis of the CC FD % in diabetic eyes suggests that CC flow impairment corresponds to DR severity, with all studied regions of the CC significantly affected. There was greater regional impairment due to age and disease severity in the inner and middle regions.
Preliminary study of central nervous system tumors’ prevalence and incidence in Isfahan Province Iran
Authors: Tolou-Ghamari Zahra 
Published: March 2020

Abstract
Background
Metastatic or primary cancers of the central nervous system are a dissimilar cluster of neoplasms with different consequences and management plans. The aim of this study was to obtain prevalence and incidence of brain and other nervous system tumors.

Results
In all, 423 females and 620 males were identified. For the total population the period prevalence (PP) was calculated as 20.9 per 100,000 persons. This value corresponded to a PP of 24.5 for males and 17.2 for females. The mean (SD, range) age of the patients was 52.0 (20.7, 1–99) years. In the 7% of the population studied, age was under 20 years old of life, and in the 71%, it occurred around the age of 20 to 70 years old. In both genders, incidence rate (IR) increased from 4.2 to 5.7 per 100,000 persons. The changes of IR in males versus females were 8.2 versus 3.0 from 2011 to 6.4 versus 5.0 to 2015 per 100,000 persons.

Conclusions
Among the total population studied, there were 586 reported deaths. The PP in the male population was 1.4-times higher than females. There was a 35.7% increase in the IR over the study period.
Ultrasonic characterization of anisotropic rocks: Impact of transducers’ size and geometry on data interpretation
Authors: Kovalyshen Yevhen , Sarout Joel , Dautriat Jeremie , Maney Bruce , Lebedev Maxim 
Published: March 2020

Typical ultrasonic laboratory measurements of rock physical properties are conducted with ultrasonic transducers that are relatively large compared to the rock sample. We have determined the impact of the transducer size on the resulting velocity estimations. To improve data interpretation, we explore two complementary avenues: (1) explicitly account for the finite size of the transducers as part of the data interpretation/correction workflow, rather than assuming point sources, and (2) reducing the effective size of the transducers at the hardware design level. Both approaches as well as their combination have been tested successfully on multiple data sets including artificial homogeneous and isotropic samples as well as natural anisotropic rocks such as shales.
CIViCpy: A Python Software Development and Analysis Toolkit for the CIViC Knowledgebase
Authors: Wagner Alex H. , Kiwala Susanna , Coffman Adam C. , McMichael Joshua F. , Cotto Kelsy C. , Mooney Thomas B. , Barnell Erica K. , Krysiak Kilannin , Danos Arpad M. , Walker Jason , Griffith Obi L. , Griffith Malachi 
Published: March 2020

PURPOSE Precision oncology depends on the matching of tumor variants to relevant knowledge describing the clinical significance of those variants. We recently developed the Clinical Interpretations for Variants in Cancer (CIViC; civicdb.org ) crowd-sourced, expert-moderated, and open-access knowledgebase. CIViC provides a structured framework for evaluating genomic variants of various types (eg, fusions, single-nucleotide variants) for their therapeutic, prognostic, predisposing, diagnostic, or functional utility. CIViC has a documented application programming interface for accessing CIViC records: assertions, evidence, variants, and genes. Third-party tools that analyze or access the contents of this knowledgebase programmatically must leverage this application programming interface, often reimplementing redundant functionality in the pursuit of common analysis tasks that are beyond the scope of the CIViC Web application. METHODS To address this limitation, we developed CIViCpy ( civicpy.org ), a software development kit for extracting and analyzing the contents of the CIViC knowledgebase. CIViCpy enables users to query CIViC content as dynamic objects in Python. We assess the viability of CIViCpy as a tool for advancing individualized patient care by using it to systematically match CIViC evidence to observed variants in patient cancer samples. RESULTS We used CIViCpy to evaluate variants from 59,437 sequenced tumors of the American Association for Cancer Research Project GENIE data set. We demonstrate that CIViCpy enables annotation of > 1,200 variants per second, resulting in precise variant matches to CIViC level A (professional guideline) or B (clinical trial) evidence for 38.6% of tumors. CONCLUSION The clinical interpretation of genomic variants in cancers requires high-throughput tools for interoperability and analysis of variant interpretation knowledge. These needs are met by CIViCpy, a software development kit for downstream applications and rapid analysis. CIViCpy is fully documented, open-source, and available free online.