bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of congruence between co-occurrence and functional networks: A new framework for revealing community assembly rules
Authors: Legras Gaëlle , Loiseau Nicolas , Gaertner Jean-Claude , Poggiale Jean-Christophe , Ienco Dino , Mazouni Nabila , Mérigot Bastien 
Published: December 2019

AbstractDescribing how communities change over space and time is crucial to better understand and predict the functioning of ecosystems. We propose a new methodological framework, based on network theory and modularity concept, to determine which type of mechanisms (i.e. deterministicversusstochastic processes) has the strongest influence on structuring communities. This framework is based on the computation and comparison of two networks: the co-occurrence (based on species abundances) and the functional networks (based on the species traits values). In this way we can assess whether the species belonging to a given functional group also belong to the same co-occurrence group. We adapted the Dg index of Gauzenset al. (2015) to analyze congruence between both networks. This offers the opportunity to identify which assembly rule(s) play(s) the major role in structuring the community. We illustrate our framework with two datasets corresponding to different faunal groups and ecosystems, and characterized by different scales (spatial and temporal scales). By considering both species abundance and multiple functional traits, our framework improves significantly the ability to discriminate the main assembly rules structuring the communities. This point is critical not only to understand community structuring but also its response to global changes and other disturbances.
Biochemical and structural insights into the cytochrome P450 reductase from Candida tropicalis
Authors: Ebrecht Ana C. , van der Bergh Naadia , Harrison Susan T. L. , Smit Martha S. , Sewell B. Trevor , Opperman Diederik J. 
Published: December 2019

AbstractCytochrome P450 reductases (CPRs) are diflavin oxidoreductases that supply electrons to type II cytochrome P450 monooxygenases (CYPs). In addition, it can also reduce other proteins and molecules, including cytochrome c, ferricyanide, and different drugs. Although various CPRs have been functionally and structurally characterized, the overall mechanism and its interaction with different redox acceptors remain elusive. One of the main problems regarding electron transfer between CPRs and CYPs is the so-called “uncoupling”, whereby NAD(P)H derived electrons are lost due to the reduced intermediates’ (FAD and FMN of CPR) interaction with molecular oxygen. Additionally, the decay of the iron-oxygen complex of the CYP can also contribute to loss of reducing equivalents during an unproductive reaction cycle. This phenomenon generates reactive oxygen species (ROS), leading to an inefficient reaction. Here, we present the study of the CPR from Candida tropicalis (CtCPR) lacking the hydrophobic N-terminal part (Δ2–22). The enzyme supports the reduction of cytochrome c and ferricyanide, with an estimated 30% uncoupling during the reactions with cytochrome c. The ROS produced was not influenced by different physicochemical conditions (ionic strength, pH, temperature). The X-ray structures of the enzyme were solved with and without its cofactor, NADPH. Both CtCPR structures exhibited the closed conformation. Comparison with the different solved structures revealed an intricate ionic network responsible for the regulation of the open/closed movement of CtCPR.
Genetic species identification of ecologically important planthoppers (Prokelisia spp.) of coastal Spartina saltmarshes using High Resolution Melting Analysis (HRMA)
Authors: Espinoza G. Janelle , Alvarado Bremer Jaime R. 
Published: December 2019

AbstractPhloem-feeding planthoppers of the genus Prokelisia rank among the most abundant and ecologically important browsers of coastal saltmarsh grasses of eastern North America and the Caribbean. Along the Spartina marshes of the northern Gulf of Mexico, the sympatric species P. marginata and P. dolus are the most abundant, but are difficult to distinguish from each other based solely on morphology. This study seeks to design a molecular assay based on High Resolution Melting Analysis (HRMA) as a fast, cost-effective alternative to differentiate these species. A 450 base pairs (bp) segment of cytochrome c oxidase subunit I (COI) was amplified and sequenced for representative samples of both species, and a short amplicon (SA) HRMA was designed based on the presence of fixed nucleotide differences between species found along a 60 bp segment of COI. The unambiguous identification of individual specimens of P. marginata or P. dolus was possible due to easily discernable differences in the melting temperatures of the two species along this mini barcode. This assay may prove useful for future genetic studies involving these species by preventing the overestimation of genetic diversity via inclusion of conspecifics, and in ecological studies by improving data on the effects of individual species of Prokelisia.
Interactions with humans shape coyote responses to hazing
Authors: Young Julie K. , Hammill Edd , Breck Stewart W. 
Published: December 2019

AbstractMedium and large carnivores coexist with people in urban areas globally, occasionally resulting in negative interactions that prompt questions about how to reduce human-wildlife conflict. Hazing, i.e., scaring wildlife, is frequently promoted as an important non-lethal means for urbanites to reduce conflict but there is limited scientific evidence for its efficacy. We used a population of captive coyotes (Canis latrans) to simulate urban human-coyote interactions and subsequent effects of hazing on coyote behavior. Past experiences with humans significantly affected the number of times a coyote approached a human to necessitate hazing. Coyotes that had been hand fed by adults had to be more frequently hazed than coyotes with other or no past experiences with adults. Past experience with children had no impact on the number of hazing events. The number of times a coyote approached an adult or child was reduced across days based on the accumulative number of times hazed, suggesting coyotes learn to avoid behaviors warranting hazing and that this could be used as a non-lethal management tool. However, prior experience and whether the interaction is with an adult or child can alter the outcomes of hazing and must be considered in determining the efficacy of hazing programs.
Multimodal Machine Learning-based Knee Osteoarthritis Progression Prediction from Plain Radiographs and Clinical Data
Authors: Tiulpin Aleksei , Klein Stefan , Bierma-Zeinstra Sita M. A. , Thevenot Jérôme , Rahtu Esa , Meurs Joyce van , Oei Edwin H. G. , Saarakkala Simo 
Published: December 2019

AbstractKnee osteoarthritis (OA) is the most common musculoskeletal disease without a cure, and current treatment options are limited to symptomatic relief. Prediction of OA progression is a very challenging and timely issue, and it could, if resolved, accelerate the disease modifying drug development and ultimately help to prevent millions of total joint replacement surgeries performed annually. Here, we present a multi-modal machine learning-based OA progression prediction model that utilises raw radiographic data, clinical examination results and previous medical history of the patient. We validated this approach on an independent test set of 3,918 knee images from 2,129 subjects. Our method yielded area under the ROC curve (AUC) of 0.79 (0.78–0.81) and Average Precision (AP) of 0.68 (0.66–0.70). In contrast, a reference approach, based on logistic regression, yielded AUC of 0.75 (0.74–0.77) and AP of 0.62 (0.60–0.64). The proposed method could significantly improve the subject selection process for OA drug-development trials and help the development of personalised therapeutic plans.
Collagen fibrils and proteoglycans of peripheral and central stroma of the keratoconus cornea - Ultrastructure and 3D transmission electron tomography
Authors: Alkanaan Aljoharah , Barsotti Robert , Kirat Omar , Khan Adnan , Almubrad Turki , Akhtar Saeed 
Published: December 2019

AbstractKeratoconus (KC) is a progressive corneal disorder in which vision gradually deteriorates as a result of continuous conical protrusion and the consequent altered corneal curvature. While the majority of the literature focus on assessing the center of this diseased cornea, there is growing evidence of peripheral involvement in the disease process. Thus, we investigated the organization of collagen fibrils (CFs) and proteoglycans (PGs) in the periphery and center of KC corneal stroma. Three-dimensional transmission electron tomography on four KC corneas showed the degeneration of microfibrils within the CFs and disturbance in the attachment of the PGs. Within the KC corneas, the mean CF diameter of the central-anterior stroma was significantly (p ˂ 0.001) larger than the peripheral-anterior stroma. The interfibrillar distance of CF was significantly (p ˂ 0.001) smaller in the central stroma than in the peripheral stroma. PGs area and the density in the central KC stroma were larger than those in the peripheral stroma. Results of the current study revealed that in the pre- Descemet’s membrane stroma of the periphery, the degenerated CFs and PGs constitute biomechanically weak lamellae which are prone to disorganization and this suggests that the peripheral stroma plays an important role in the pathogenicity of the KC cornea.
High-fat diet-induced metabolic syndrome and oxidative stress in obese rats are ameliorated by yogurt supplementation
Authors: Lasker Shoumen , Rahman Md Mizanur , Parvez Faisal , Zamila Mushfera , Miah Pintu , Nahar Kamrun , Kabir Fariha , Sharmin Surovi Binte , Subhan Nusrat , Ahsan Gias U. , Alam Md Ashraful 
Published: December 2019

AbstractThe main objective of this experiment was to determine the effects of yogurt supplementation on fat deposition, oxidative stress, inflammation and fibrosis in the liver of rats with high-fat (HF) diet-induced obesity. Male Wistar rats were used in this study and were separated into the following four different groups: the control, control + yogurt, high fat and high fat+ yogurt groups. The high fat groups received a HF diet for eight weeks. A 5% yogurt (w/w) supplement was also provided to rats fed the HF diet. Yogurt supplementation prevented glucose intolerance and normalized liver-specific enzyme activities in the HF diet-fed rats. Yogurt supplementation also significantly reduced the levels of oxidative stress markers in the plasma and liver of HF diet-fed rats. Moreover, inflammatory cell infiltration, collagen deposition and fibrosis in the liver of HF diet-fed rats were also prevented by yogurt supplementation. Furthermore, yogurt supplementation normalized the intestinal lining and brush border in HF diet-fed rats. This study suggests that yogurt supplementation potentially represents an alternative therapy for the prevention of metabolic syndrome in HF diet-fed rats.
Meal timing, meal frequency, and breakfast skipping in adult individuals with type 1 diabetes – associations with glycaemic control
Authors: Ahola Aila J. , Mutter Stefan , Forsblom Carol , Harjutsalo Valma , Groop Per-Henrik 
Published: December 2019

AbstractWe assessed meal timing, meal frequency, and breakfast consumption habits of adult individuals with type 1 diabetes (n = 1007) taking part in the Finnish Diabetic Nephropathy Study, and studied whether they are associated with glycaemic control. Data on dietary intake and blood glucose measurements were retrieved from food records. HbA1cwas measured at the study visit. In the whole sample, four peaks of energy intake emerged. Energy intake was the greatest in the evening, followed by midday. Altogether 7% of the participants reported no energy intake between 05:00 and 09:59 (breakfast skippers). While breakfast skippers reported lower number of meals, no difference was observed in the total energy intake between those eating and omitting breakfast. In a multivariable model, skipping breakfast was associated with higher mean blood glucose concentrations and lower odds of good glycaemic control. A median of 6 daily meals was reported. Adjusted for confounders, the number of meals was negatively associated with HbA1c, and the mean of the blood glucose measurements, but positively associated with the variability of these measurements. Our observations support the habit of a regular meal pattern, including consumption of breakfast and multiple smaller meals for good glycaemic control in adults with type 1 diabetes. However, an increase in the blood glucose variability may additionally be expected with an increase in the number of meals eaten.
Early postoperative weight gain is associated with increased risk of graft failure in living donor liver transplant recipients
Authors: Jeong Hye-Won , Jung Kyeo-Woon , Kim Seon-Ok , Kwon Hye-Mee , Moon Young-Jin , Jun In-Gu , Song Jun-Gol , Hwang Gyu-Sam 
Published: December 2019

AbstractFluid overload (FO) has been shown to adversely affect multiple organs and survival in critically ill patients. Liver transplantation (LT) carries the risk of massive transfusion, which frequently results in FO. We investigated the association of postoperative weight gain with graft failure, early allograft dysfunction (EAD), and overall mortality in LT. 1833 living donor LT (LDLT) recipients were retrospectively analysed. Patients were divided into 2 groups according to postoperative weight gain (<3% group [n = 1391] and ≥3% group [n = 442]) by using maximally selected log-rank statistics for graft failure. Multivariate Cox and logistic regression analyses were performed. The ≥3% group was associated with graft failure (adjusted HR [aHR], 1.763; 95% CI, 1.248–2.490; P = 0.001). When postoperative weight change was used as a continuous variable, the aHR for each 1% increase in postoperative weight was 1.045 (95% CI, 1.009–1.082; P = 0.015). In addition, the ≥3% group was associated with EAD (adjusted OR [aOR], 1.553; 95% CI, 1.024–2.356; P = 0.038) and overall mortality (aHR, 1.731; 95% CI, 1.182–2.535; P = 0.005). In conclusion, postoperative weight gain may be independently associated with increased risk of graft failure, EAD, and mortality in LDLT recipients.
Increasing Recombinant Strains Emerged in Norovirus Outbreaks in Jiangsu, China: 2015–2018
Authors: Fu Jianguang , Bao Changjun , Huo Xiang , Hu Jianli , Shi Chao , Lin Qin , Zhang Jun , Ai Jing , Xing Zheng 
Published: December 2019

AbstractFrom January 2015 to December 2018, 213 norovirus outbreaks with 3,951 patients were reported in Jiangsu, China. Based on viral RdRp and VP1 genes, eight genotypes, GII.2[P16] (144, 67.6%), GII.3[P12] (21, 9.9%), GII.6[P7] (5, 2.3%), GII.14[P7] (4, 1.9%), GII.4 Sydney[P31] (3, 1.4%), GII.1[P33] (1, 0.5%), GII.2[P2] (3, 1.4%), and GII.17[P17] (16, 7.5%) were identified throughout the study period. These genotypes were further regrouped as GII.R (Recombinant) and GII.Non-R (Non-recombinant) strains. In this report we showed that GII.R strains were responsible for at least 178 (83.6%) of 213 norovirus-positive outbreaks with a peak in 2017 and 2018. Most norovirus outbreaks occurred in primary schools and 94 of 109 (86.2%) outbreaks in primary schools were caused by GII.R, while GII.Non-R and GII.NT (not typed) strains accounted for 6 (5.5%) and 9 (8.3%) norovirus outbreaks, respectively. The SimPlot analysis showed recombination breakpoints near the ORF1/2 junction for all six recombinant strains. The recombination breakpoints were detected at positions varying from nucleotides 5009 to 5111, localized in the ORF1 region for four strains (GII.2[P16], GII.3[P12], GII.6[P7], and GII.14[P7]) and in the ORF2 region for the other (GII.4 Sydney[P31] and GII.1[P33]). We identified four clusters, Cluster I through IV, in the GII.P7 RdRp gene by phylogenetic analysis and the GII.14[P7] variants reported here belonged to Cluster IV in the RdRp tree. The HBGA binding site of all known GII.14 strains remained conserved with several point mutations found in the predicted conformational epitopes. In conclusion, gastroenteritis outbreaks caused by noroviruses increased rapidly in the last years and these viruses were classified into eight genotypes. Emerging recombinant noroviral strains have become a major concern and challenge to public health.
Predictive imaging for tumor response to drug-eluting microsphere transarterial chemoembolization in patients with BCLC-C advanced hepatocellular carcinoma
Authors: Chang Kai-Hsiang , Hwang Zhen-An , Chang Ping-Ying , Lin Hsuan-Hwai , Shih Yu-Lueng , Chang Wei-Chou , Huang Guo-Shu , Hsu Hsian-He 
Published: December 2019

AbstractDrug-eluting microsphere transarterial chemoembolization (DEM-TACE) has been introduced to ensure more sustained and tumor-selective drug delivery for permanent embolization of HCC. The aim of this study was to determine the imaging characteristics that related to favourable treatment response in BCLC-C HCC patients treated with DEM-TACE. In total, 64 patients with BCLC-C HCC that treated with DEM-TACE using doxorubicin-eluted microspheres were retrospectively included. The images were assessed at baseline and at 4–12 weeks follow-up after receiving DEM-TACE. Pre- and post-procedural imaging characteristics were analysed by two independent radiologists and treatment response was evaluated using the modified Response Evaluation Criteria in Solid Tumors criteria. Multivariate analysis showed that vascular lake phenomenon (OR = 5.94, p = 0.03*), and homogeneous tumor enhancement (HTE) on cone-beam computed tomography (CBCT) during angiography (OR = 11.66, p < 0.001*) are associated with better radiological response. In contrast, residual tumor blush (OR = 0.11, p < 0.001*) is associated with worse radiological response. In conclusion, the initial tumor burden <50% (p = 0.012*) and HTE on CBCT (p = 0.040*) are good predictors for locoregional tumor control in patients with advanced HCCs, which can potentially improve patients’ outcome.
Intermittent treatment interruption and its effect on multidrug resistant tuberculosis treatment outcome in Ethiopia
Authors: Tola Habteyes H. , Holakouie-Naieni Kourosh , Mansournia Mohammad A. , Yaseri Mehdi , Tesfaye Ephrem , Mahamed Zemedu , Sisay Million Molla 
Published: December 2019

AbstractTreatment interruption is one of the main risk factors of poor treatment outcome and occurrence of additional drug resistant tuberculosis. This study is a national retrospective cohort study with 10 years follow up period in MDR-TB patients in Ethiopia. We included 204 patients who had missed the treatment at least for one day over the course of the treatment (exposed group) and 203 patients who had never interrupted the treatment (unexposed group). We categorized treatment outcome into successful (cured or completed) and unsuccessful (lost to follow up, failed or died). We described treatment interruption by the length of time between interruptions, time to first interruption, total number of interruption episodes and percent of missed doses. We used Poisson regression model with robust standard error to determine the association between treatment interruption and outcome. 82% of the patients interrupted the treatment in the first six month of treatment period, and considerable proportion of patients demonstrated long intervals between two consecutive interruptions. Treatment interruption was significantly associated with unsuccessful treatment outcome (Adjusted Risk Ratio (ARR) = 1.9; 95% CI (1.4–2.6)). Early identification of patients at high risk of interruption is vital in improving successful treatment outcome.
Potential neuroprotective and anti-inflammatory effects provided by omega-3 (DHA) against Zika virus infection in human SH-SY5Y cells
Authors: Braz-De-Melo Heloísa Antoniella , Pasquarelli-do-Nascimento Gabriel , Corrêa Rafael , das Neves Almeida Raquel , de Oliveira Santos Igor , Prado Paulo Sousa , Picolo Victor , de Bem Andreza Fabro , Pizato Nathalia , Magalhães Kelly Grace 
Published: December 2019

AbstractZika virus (ZIKV) has a strong tropism for the nervous system and has been related to post-infection neurological syndromes. Once neuronal cells are infected, the virus is capable of modulating cell metabolism, leading to neurotoxicity and cellular death. The negative effect of ZIKV in neuron cells has been characterized. However, the description of molecules capable of reversing these cytotoxic effects is still under investigation. In this context, it has been largely demonstrated that docosahexaenoic acid (DHA), an omega-3 polyunsaturated fatty acid, is highly neuroprotective. Here, we hypothesized that DHA’s neuroprotective proprieties could have an influence on ZIKV-induced neurotoxicity in SH-SY5Y cells. Our data showed that pre-treatment of SH-SY5Y cells with DHA increased the cell viability and proliferation in ZIKV-infected cells. Moreover, DHA triggered an anti-inflammatory response in those infected cells. Besides, DHA was capable of restoring mitochondria function and number in ZIKV-infected SH-SY5Y cells. In addition, cells pre-treated with DHA prior to ZIKV infection presented a lower viral load at different times of infection. Taking together, these results demonstrated that DHA has a potential anti-inflammatory and neuroprotective effect against ZIKV infection in these neuron-like cells and could be a useful tool in the treatment against this virus.
P2X7 Receptor Stimulation Is Not Required for Oxalate Crystal-Induced Kidney Injury
Authors: Luz Hannah L. , Reichel Martin , Unwin Robert J. , Mutig Kerim , Najenson Ana C. , Tonner Louise M. , Eckardt Kai-Uwe , Tam Frederick W. K. , Knauf Felix 
Published: December 2019

AbstractOxalate crystal-induced renal inflammation is associated with progressive kidney failure due to activation of the NLRP3/CASP-1 inflammasome. It has been suggested previously that purinergic P2X7 receptor signaling is critical for crystal-induced inflammasome activation and renal injury. Therefore, we investigated the role of the P2X7 receptor in response to crystal-induced cytokine release, inflammation, and kidney failure using in vitro and in vivo models. Dendritic cells and macrophages derived from murine bone marrow and human peripheral blood mononucleated cells stimulated with calcium-oxalate crystals, monosodium urate crystals, or ATP lead to the robust release of interleukin-1beta (IL-1ß). Treatment with the P2X7 inhibitor A740003 or the depletion of ATP by apyrase selectively abrogated ATP-induced, but not oxalate and urate crystal-induced IL-1ß release. In line with this finding, dendritic cells derived from bone marrow (BMDCs) from P2X7−/− mice released reduced amounts of IL-1ß following stimulation with ATP, while oxalate and urate crystal-induced IL-1ß release was unaffected. In sharp contrast, BMDCs from Casp1−/− mice exhibited reduced IL-1ß release following either of the three stimulants. In addition, P2X7−/− mice demonstrated similar degrees of crystal deposition, tubular damage and inflammation when compared with WT mice. In line with these findings, increases in plasma creatinine were no different between WT and P2X7−/− mice. In contrast to previous reports, our results indicate that P2X7 receptor is not required for crystal-induced CKD and it is unlikely to be a suitable therapeutic target for crystal-induced progressive kidney disease.