bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plant phylogeny drives arboreal caterpillar assemblages across the Holarctic
Authors: Seifert Carlo L. , Volf Martin , Jorge Leonardo R. , Abe Tomokazu , Carscallen Grace , Drozd Pavel , Kumar Rajesh , Lamarre Greg P.A. , Libra Martin , Losada Maria E. , Miller Scott E. , Murakami Masashi , Nichols Geoffrey , Pyszko Petr , Šigut Martin , Wagner David L. , Novotný Vojtěch 
Published: November 2020

Abstract

Assemblages of insect herbivores are structured by plant traits such as nutrient content, secondary metabolites, physical traits, and phenology. Many of these traits are phylogenetically conserved, implying a decrease in trait similarity with increasing phylogenetic distance of the host plant taxa. Thus, a metric of phylogenetic distances and relationships can be considered a proxy for phylogenetically conserved plant traits and used to predict variation in herbivorous insect assemblages among co‐occurring plant species.

Using a Holarctic dataset of exposed‐feeding and shelter‐building caterpillars, we aimed at showing how phylogenetic relationships among host plants explain compositional changes and characteristics of herbivore assemblages.

Our plant–caterpillar network data derived from plot‐based samplings at three different continents included >28,000 individual caterpillar–plant interactions. We tested whether increasing phylogenetic distance of the host plants leads to a decrease in caterpillar assemblage overlap. We further investigated to what degree phylogenetic isolation of a host tree species within the local community explains abundance, density, richness, and mean specialization of its associated caterpillar assemblage.

The overlap of caterpillar assemblages decreased with increasing phylogenetic distance among the host tree species. Phylogenetic isolation of a host plant within the local plant community was correlated with lower richness and mean specialization of the associated caterpillar assemblages. Phylogenetic isolation had no effect on caterpillar abundance or density. The effects of plant phylogeny were consistent across exposed‐feeding and shelter‐building caterpillars.

Our study reveals that distance metrics obtained from host plant phylogeny are useful predictors to explain compositional turnover among hosts and host‐specific variations in richness and mean specialization of associated insect herbivore assemblages in temperate broadleaf forests. As phylogenetic information of plant communities is becoming increasingly available, further large‐scale studies are needed to investigate to what degree plant phylogeny structures herbivore assemblages in other biomes and ecosystems.
Detecting fish assemblages with environmental DNA: Does protocol matter? Testing eDNA metabarcoding method robustness
Authors: Coutant Opale , Cantera Isabel , Cilleros Kévin , Dejean Tony , Valentini Alice , Murienne Jérôme , Brosse Sébastien 
Published: November 2020

AbstractEnvironmental DNA (eDNA) metabarcoding has recently gain much attention to assess aquatic environment biodiversity. A great variety of protocols have been developed to collect, extract, and analyze eDNA, some of which are continuously evolving and optimized with technological improvements. Such technological shifts might deprecate the biological data produced with earlier protocols, leading to a loss of biological knowledge. Here, we investigated the robustness of an aquatic eDNA metabarcoding method through the comparison of two biodiversity datasets generated by two optimized protocols with different collection and extraction steps. To this end, we compared fish community richness and composition of 12 streams and 3 rivers from French Guiana, sampled with two distinct protocols commonly used in aquatic eDNA studies. Although sample collection with each protocol was not achieved the same year, our results show that species richness and species composition were only slightly affected by the protocol choice, both protocols producing similar fish assemblages at each sample site. Both protocols had a higher replicability in streams than in rivers, strengthening the importance to adapt sampling effort to waterbody type as rivers host a larger number of species than small streams. Despite the need for a standardized approach in eDNA metabarcoding studies, testing the robustness of datasets to protocol variations remains crucial to valorize old data, time series, or data collected in difficult to access locations.
Settling of a charged hydrophobic rigid colloid in aqueous media under generalized gravitational field
Authors: Kundu Dipankar , Bhattacharyya Somnath , Gopmandal Partha P. , Ohshima Hiroyuki 
Published: November 2020

AbstractThe hindrance created by the induced electric filed on the sedimentation of a charged colloid in an aqueous media is studied through numerical modeling. The colloid is considered to be hydrophobic, sedimenting under gravity or a centrifugal force (generalized gravity). The deformation of the charge cloud around the colloid induces an electric field, which generates electrical dipole force on the colloid. The sedimentation velocity is governed by the balance of an electric force, hydrodynamic drag, and gravitational force. Governing equations based on the first principle of electrokinetics is solved numerically through a control volume approach. The dependence of the sedimentation velocity on the electrical properties and slip length of the colloid is investigated. The sedimentation velocity of the charged colloid is slower than the corresponding uncharged particle and this deviation magnifies as the charge density as well as particle slip length is increased. An enhanced g‐factor creates a size dependency of the charged colloids. The induced sedimentation field is obtained to analyze the electrokinetics. Surface hydrophobicity enhances the sedimentation velocity, which in turn manifests the induced sedimentation field. However, the sedimentation velocity of a charged hydrophobic colloid is lower than the corresponding uncharged hydrophobic particle and this deviation manifests as slip length is increased.
Impact of diagnostic delay on seizure outcome in newly diagnosed focal epilepsy
Authors: Parviainen Laura , Kälviäinen Reetta , Jutila Leena 
Published: November 2020

AbstractObjectiveIn the current study, we aimed to assess the diagnostic delay and the impact of diagnostic delay on seizure outcome in a cohort of newly diagnosed patients with focal epilepsy.MethodsThe study material was compiled from eight clinical antiseizure medication monotherapy trials conducted at Kuopio Epilepsy Center during 1995‐2016. We analyzed the time from first seizure to diagnosis, the number of seizures before diagnosis, and the response to treatment at five years.ResultsOf the 176 patients (age range 15‐75 years) in the cohort, 135 (77%) had had more than two seizures before treatment. The majority of these (79 patients, 45%) had had three to ten seizures. Median number of all seizures before diagnosis was 5 (range 2‐2000). Focal aware seizures and focal impaired awareness seizures were more frequent than focal to bilateral tonic‐clonic seizures; median number 45 (range 2‐2000), 11 (range 2‐220), and 3 (range 2‐30), respectively (P < .001). Median delay was 12 months (range 0‐362). Diagnostic delay alone did not correlate with the treatment response at five years. However, an increasing number of seizures before diagnosis indicated a worse seizure outcome (P < .001).SignificanceThis study shows that patients with focal epilepsy experience significant delays in diagnosis even in developed countries, especially with seizure types other than tonic‐clonic seizures. In these cases, a long delay in diagnosis alone might not affect the long‐term outcome. However, when accompanied with recurrent seizures misinterpreted by the patient or healthcare providers, the effect of such delay on prognosis can be considerable.
A review on dill essential oil and its chief compounds as natural biocide
Authors: Kaur Vishaldeep , Kaur Ramandeep , Bhardwaj Urvashi 
Published: November 2020

AbstractAnethum graveolensL. (dill), a member of Umbelliferae family, is an important essential oil‐bearing herb native to the Mediterranean and West Asia. It is well documented for its medicinal and traditional uses. The chemical composition of dill seed essential oil showed the presence of numerous volatile compounds with carvone, limonene, α‐phellandrene, β‐phellandrene and p‐cymene being the major ones in almost all its aerial parts. Thus, the main focus of this updated review is to highlight the biological importance of dill essential oil and its major constituents (carvone and limonene) reported till date. Although the number of reviews has been published on its chemical composition and medicinal uses, its role in the field of agriculture to develop commercial formulations is still needed to be explored. In brief, the information presented in this review will be useful in creating interest in the use of dill essential oil and its major constituents for the development of commercial plant‐based pesticides.
Fluorescence interference of polyphenols in assays screening for dipeptidyl peptidase IV inhibitory activity
Authors: Dirimanov Stoyan , Högger Petra 
Published: November 2020

AbstractPolyphenols are plant‐derived natural compounds, which are attributed to various beneficial effects on human health. Therefore, they are extensively investigated in different experimental setups. These compounds exhibit favorable antidiabetic effects in various clinical trials. However, their mode of action is not completely elucidated. A potential molecular target of certain polyphenols could be the dipeptidyl peptidase IV (DPP IV). This enzyme is abundant in human serum and represents a serine exopeptidase that cleaves and thus rapidly deactivates incretin hormones which are responsible for adequate postprandial insulin secretion from the pancreas. Multiple inhibitors of DPP IV have already been approved as antidiabetic drugs. In the course of screening assays exploring in vitro DPP IV inhibitory activities of polyphenols, some implausible observations prompted a detailed analysis of the interaction of polyphenols with fluorescence signals. The results revealed that quercetin quenched the fluorescence intensity, while 6‐methoxyflavone and urolithin B enhanced fluorescence signals depending on particular experimental conditions such as solvent composition. Thus, individual polyphenols might conflict with the experimental setup of fluorescence‐based DPP IV inhibitor screening assays. To avoid false positive or false negative results, polyphenols under investigations should be carefully controlled for potential assay interferences.
Immune checkpoint expression in HNSCC patients before and after definitive chemoradiotherapy
Authors: Doescher Johannes , Minkenberg Peter , Laban Simon , Kostezka Ulrike , von Witzleben Adrian , Hoffmann Thomas Karl , Schuler Patrick Johannes , Weissinger Stephanie Ellen 
Published: November 2020

AbstractBackgroundPrimary platinum‐based chemoradiotherapy (CRT) remains the treatment of choice for nonresectable squamous cell carcinoma of the head and neck (HNSCC). Immune‐checkpoint modulators are used as palliative therapy and studied in combination with definitive CRT. However, the immunological changes by CRT need yet to be understood.MethodsA cohort consisting of 67 paired tissue biopsies (N = 134) of HNSCC patients before and after CRT was created. The expression of PD‐1, PD‐L1, and CD27 of tumor and immune cells by immunohistochemistry was evaluated.ResultsPD‐L1 expression on immune cells of non‐responders was significantly lower before CRT (P = .008). CD27 was expressed only on immune cells and not on cancer cells. A significant lower CD27‐expression score was observed following CRT (P = .019).ConclusionsConventional CRT changes the expression of CD27 in the tumor microenvironment. Whether this is due to a loss of expression or a reduction of CD27+ cells must be evaluated in further analyses.
HBV RNA Profiles in Patients With Chronic Hepatitis B Under Different Disease Phases and Antiviral Therapy
Authors: Mak Lung‐Yi , Cloherty Gavin , Wong Danny Ka‐Ho , Gersch Jeffrey , Seto Wai‐Kay , Fung James , Yuen Man‐Fung 
Published: November 2020

Background and Aims
Large‐scale comprehensive studies on HBV RNA in chronic hepatitis B are lacking. We aimed to study the HBV RNA profile and its correlation with other viral markers in patients with chronic hepatitis B who are treatment‐naïve and patients receiving nucleos(t)ide analogues (NA).

Approach and Results
Biomarkers, including HBV RNA and hepatitis B core‐related antigen (HBcrAg), were measured in 388 patients. Of these, 246 were treatment‐naïve and were categorized into HBeAg‐positive chronic infection (n = 41), HBeAg‐positive chronic hepatitis (n = 81), HBeAg‐negative chronic infection (n = 39), HBeAg‐negative chronic hepatitis (n = 66), and HBsAg seroclearance (n = 19). These biomarkers were also measured in 142 patients who were NA‐treated receiving tenofovir or entecavir at baseline, week 48, and week 96. The pattern of serum HBV RNA levels mirrored HBV DNA (1‐2 logs higher than HBV RNA) and HBcrAg in patients who were treatment‐naïve. HBV RNA correlated best with HBcrAg (r = 0.84) and to a lesser extent with HBV DNA (r = 0.737) (both P < 0.001). In patients with HBsAg seroclearance, 15.8% and 15.8% had detectable serum HBV RNA and HBcrAg, respectively. NA treatment reduced serum HBV RNA by 1.46 logs and 1.77 logs at weeks 48 and 96, respectively. At week 96 of NA therapy, only 19.1% patients who were tenofovir‐treated and 25.7% patients who were entecavir‐treated had unquantifiable HBV RNA (P > 0.05). In patients who were treated and had undetectable HBV DNA, 77.5% and 30% had quantifiable HBV RNA and HBcrAg, respectively.

Conclusions
HBV RNA showed distinct and corresponding profiles in patients with HBV in different disease phases. HBV RNA and HBcrAg could be used to monitor residual transcriptional activities in patients with HBsAg seroclearance. NA led to reduction of serum HBV RNA. Monitoring of viral activities can still be achieved in patients with undetectable HBV DNA by serum HBV RNA.
Endothelial p300 Promotes Portal Hypertension and Hepatic Fibrosis Through C‐C Motif Chemokine Ligand 2–Mediated Angiocrine Signaling
Authors: Gao Jinhang , Wei Bo , Liu Mengfei , Hirsova Petra , Sehrawat Tejasav S. , Cao Sheng , Hu Xiao , Xue Fei , Yaqoob Usman , Kang Ningling , Cui Huarui , Pomerantz William C.K. , Kostallari Enis , Shah Vijay H. 
Published: November 2020

Background and Aims
During liver fibrosis, liver sinusoidal endothelial cells (LSECs) release angiocrine signals to recruit inflammatory cells into the liver. p300, a master regulator of gene transcription, is associated with pathological inflammatory response. Therefore, we examined how endothelial p300 regulates angiocrine signaling and inflammation related to portal hypertension and fibrogenesis.

Approach and Results
CCl4 or partial inferior vena cava ligation (pIVCL) was used to induce liver injury. Mice with LSEC‐specific p300 deletion (p300
LSECΔ/Δ) or C‐C motif chemokine ligand 2 (Ccl2) deficiency, nuclear factor kappa B (NFκB)–p50 knockout mice, and bromodomain containing 4 (BRD4) inhibitors in wild‐type mice were used to investigate mechanisms of inflammation regulation. Leukocytes were analyzed by mass cytometry by time‐of‐flight. Epigenetic histone marks were modified by CRISPR endonuclease‐deficient CRISPR‐associated 9‐fused with the Krüppel associated box domain (CRISPR‐dCas9‐KRAB)–mediated epigenome editing. Portal pressure and liver fibrosis were reduced in p300
LSECΔ/Δ mice compared to p300
fl/fl mice following liver injury. Accumulation of macrophages was also reduced in p300
LSECΔ/Δ mouse livers. Ccl2 was the most up‐regulated chemokine in injured LSECs, but its increase was abrogated in p300
LSECΔ/Δ mice. While the macrophage accumulation was increased in NFκB‐p50 knockout mice with enhanced NFκB activity, it was reduced in mice with LSEC‐specific Ccl2 deficiency and mice treated with specific BRD4 inhibitors. In vitro, epigenome editing of CCL2 enhancer and promoter regions by CRISPR‐dCas9‐KRAB technology repressed TNFα‐induced CCL2 transcription through H3K9 trimethylation. In contrast, TNFα activated CCL2 transcription by promoting p300 interaction with NFκB and BRD4, leading to histone H3 lysine 27 acetylation at CCL2 enhancer and promoter regions.

Conclusions
In summary, endothelial p300 interaction with NFκB and BRD4 increases CCL2 expression, leading to macrophage accumulation, portal hypertension, and liver fibrosis. Inhibition of p300 and its binding partners might serve as therapy in the treatment of liver diseases.
Atg16l1 in dendritic cells is required for antibacterial defense and autophagy in murine colitis
Authors: Zhang Hong , Wang Dong , Shihb David Q. , Zhang Xiao‐Lan 
Published: November 2020

AbstractAutophagy‐related 16‐like 1 (Atg16l1) contributes to the susceptibility to ulcerative colitis (UC). The functional consequences of Atg16l1 in UC pathogenesis are poorly understood. We aimed to confirm how Atg16l1 deficiency in dendritic cells (DCs) affects murine colitis development. Atg16l1f/f mice and mice with Atg16l1 deficiency in CD11c+DCs (Atg16l1ΔDC) were generated for colitis models induction. Disease activity index, weight loss, colon score/length, and histopathological analysis were assessed for colitis severity. Mononuclear cells from mesenteric lymph node (MLN) were extracted for CD44/CD69 measurement by flow cytometry. Bacterial cultures of MLN and stool homogenates were used to evaluate the bacterial translocation. Bone marrow‐derived dendritic cells (BMDCs) were isolated and cultured for immunofluorescence of autophagy‐related proteins. Atg16l1 knockout in CD11c+DCs exacerbated intestinal inflammation of dextran sulfate sodium (DSS)‐induced colitis in vivo. Atg16l1 deficiency in CD11c+DCs had no effect on the expression of CD44 and CD69. Bacterial translocation showed that bacteria amount in MLN and stool of DSS‐induced colitis with Atg16l1 deficiency significantly higher than that of control. Immunofluorescence revealed that Atg16l1 deficiency obviously inhibited co‐expression of LC3 and Lamp1 with S. typhimurium, enhanced co‐expression of rab5 and rab7 with S. typhimurium, while did not affect Beclin1. We confirmed that Atg16l1 deficiency in DCs exacerbated the intestinal inflammation of DSS‐induced colitis. Atg16l1 deficiency in DCs promotes the bacterial translocation of DSS‐induced colitis in vivo and regulates autophagy and phagocytosis in BMDCs. Findings provided a novel perspective to study UC pathogenesis.
Low expression of hsa_circ_0001811 in gastric cancer and its role in clinical diagnosis
Authors: Zhang Haiyan , Li Zhe , Ruan Yao , Sun Weiliang , Yu Rui 
Published: November 2020

AbstractBackgroundAs far as gastric cancer is concerned, there is a lack of specific early diagnostic biomarkers in clinical diagnosis. Circular RNAs (circRNAs) have been found to be stable in gastric cancer tissues and plasma, so they have the potential to become new type of diagnostic biomarkers for gastric cancer.Materials and MethodsThe hsa_circ_0001811 expressions in gastric cancer tissues and paired non‐cancer tissues, preoperative and postoperative plasma of patients with gastric cancer, and plasma of healthy volunteers were detected using quantitative reverse transcription‐polymerase chain reaction. The receiver operating characteristic (ROC) curves were drawn; and the combined ROC curves were used to analyze their diagnostic values. The correlation between the plasma or tissue hsa_circ_0001811 levels and the clinicopathological factors of gastric cancer was further analyzed.ResultsHsa_circ_0001811 was found to be lowly expressed in gastric cancer tissues and plasma from patients with gastric cancer. The area under the ROC curve (AUC) in the gastric cancer tissues and the plasma of patients with gastric cancer was 0.658 and 0.747, respectively. The AUC increased to 0.824 after combination of both. The expression level of hsa_circ_0001811 in gastric cancer tissue correlated with carcinoembryonic antigen (CEA) (P = .0347), tissue differentiation (P = .0138), and lymph node metastasis (P = .0234), while plasma hsa_circ_0001811 level was related to carbohydrate antigen (CA19‐9) (P = .0278), lymph node metastasis (P = .0469), distant metastasis (P = .0384), and age (P = .0085).ConclusionsThe above results indicate that hsa_circ_0001811 may become a new biomarker for clinical diagnosis of gastric cancer.
Effects of different smoking methods on sensory properties, free amino acids and volatile compounds in bacon
Authors: Guo Jie , Wang Qiong , Chen Conggui , Yu Hai , Xu Baocai 
Published: November 2020

AbstractBACKGROUNDThe aim of this study was to investigate the effects of different smoking methods on sensory properties, free amino acids (FAAs) and volatile compounds (VCs) of bacon. Descriptive analysis was performed using a highly trained panel (n = 9) to evaluate four bacons in sextuplicate. VCs of bacons were analyzed using solid‐phase microextraction (SPME) coupled with gas chromatography–mass spectrometry (GC–MS).RESULTSBacons were significantly different in sensory properties (P < 0.05). Wood smoked bacon (WSB) had a higher smoky and fatty aroma, liquid smoked bacon (LSB) had a higher red color intensity and yellow color intensity, and paper smoked bacon (PSB) had an outstanding texture. Different smoking methods resulted in an increase in total FAAs content, of which paper smoking was significantly higher than the others (P < 0.05). Also, a total of 59 volatile flavor compounds were identified for bacons, aldehydes were the most abundant groups of compounds. Principal component analysis (PCA) can effectively separate the bacons that underwent different smoking methods.CONCLUSIONThe aldehydes and hydrocarbons with high content in PSB improved the overall taste intensity. The color in the sensory attributes was more obvious after LSB processing. The phenols and aromatic hydrocarbons in WSB contributed significantly to the pleasant properties (smoky, fatty). © 2020 Society of Chemical Industry
Survival impact based on hepatic artery lymph node status in pancreatic adenocarcinoma: A study of patients receiving modern chemotherapy
Authors: Perlmutter Breanna C. , Hossain Mir Shanaz , Naples Robert , Tu Chao , Vilchez Valery , McMichael John , Tullio Katherine , Simon Robert , Walsh R. Matthew , Augustin Toms 
Published: November 2020

AbstractBackgroundChemotherapy for pancreatic adenocarcinoma (PDAC) has significantly improved in recent years. While the involvement of the hepatic artery lymph node (HALN; station 8a lymph node) likely represents advanced disease, a comparison to patients with metastases on modern chemotherapy is lacking.MethodsPatients who underwent pancreatoduodenectomy with HALN sent for pathologic review at a single institution from 2003 to 2018 were reviewed. Patients who presented with liver‐only metastases at the time of PDAC diagnosis (Stage IV) and received chemotherapy were identified. Multivariate Cox proportional hazards regression modeling was utilized and overall survival (OS) was estimated using Kaplan–Meier analysis.ResultsOf the 112 patients with a HALN sent for analysis, 17 (15%) were positive and 13 (76%) received chemotherapy. Ninety‐four stage IV patients were identified and were significantly more likely to have received a multiagent rather than single‐agent chemotherapy regimen compared to HALN positive patients (79.8% vs. 38.5%, p < .001). Median OS was significantly longer in all patients who underwent surgical resection, regardless of HALN status, compared to stage IV patients.ConclusionsPatients undergoing pancreatoduodenectomy with HALN positivity have significantly improved OS compared to patients with stage IV disease. HALN involvement does not significantly alter survival among resected patients and does not warrant preoperative endoscopic ultrasound‐guided biopsy.