bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbial carrying capacity and carbon biomass of plastic marine debris
Authors: Zhao Shiye , Zettler Erik R , Amaral-Zettler Linda A , Mincer Tracy J 
Published: September 2020

Abstract
Trillions of plastic debris fragments are floating at sea, presenting a substantial surface area for microbial colonization. Numerous cultivation-independent surveys have characterized plastic-associated microbial biofilms, however, quantitative studies addressing microbial carbon biomass are lacking. Our confocal laser scanning microscopy data show that early biofilm development on polyethylene, polypropylene, polystyrene, and glass substrates displayed variable cell size, abundance, and carbon biomass, whereas these parameters stabilized in mature biofilms. Unexpectedly, plastic substrates presented lower volume proportions of photosynthetic cells after 8 weeks, compared to glass. Early biofilms displayed the highest proportions of diatoms, which could influence the vertical transport of plastic debris. In total, conservative estimates suggest 2.1 × 1021 to 3.4 × 1021 cells, corresponding to about 1% of the microbial cells in the ocean surface microlayer (1.5 × 103 to 1.1 × 104 tons of carbon biomass), inhabit plastic debris globally. As an unnatural addition to sea surface waters, the large quantity of cells and biomass carried by plastic debris has the potential to impact biodiversity, autochthonous ecological functions, and biogeochemical cycles within the ocean.
SH003 activates autophagic cell death by activating ATF4 and inhibiting G9a under hypoxia in gastric cancer cells
Authors: Kim Tae Woo , Cheon Chunhoo , Ko Seong-Gyu 
Published: September 2020

AbstractIn gastric cancer (GC), hypoxia is one of the greatest obstacles to cancer therapy. In this present study, we report that SH003, an herbal formulation, induces ER stress via PERK-ATF4-CHOP signaling in GC. SH003-mediated ER stress inhibits G9a, a histone methyltransferase, by reducing STAT3 phosphorylation and activates autophagy, indicating to the dissociation of Beclin-1 and autophagy initiation from Bcl-2/Beclin-1 complex. However, the inhibition of PERK and CHOP inhibited SH003-induced cell death and autophagy activation. Moreover, targeting autophagy using specific siRNAs of LC3B or p62 or the autophagy inhibitor 3-MA also inhibited SH003-induced cell death in GC. Interestingly, SH003 induces BNIP3-mediated autophagic cell death under hypoxia than normoxia in GC. These findings reveal that SH003-induced ER stress regulates BNIP3-induced autophagic cell death via inhibition of STAT3-G9a axis under hypoxia in GC. Therefore, SH003 may an important tumor therapeutic strategy under hypoxia-mediated chemo-resistance.
Dietary diversity is associated with longitudinal changes in hippocampal volume among Japanese community dwellers
Authors: Otsuka Rei , Nishita Yukiko , Nakamura Akinori , Kato Takashi , Iwata Kaori , Tange Chikako , Tomida Makiko , Kinoshita Kaori , Nakagawa Takeshi , Ando Fujiko , Shimokata Hiroshi , Arai Hidenori 
Published: September 2020

Abstract
Background/Objectives
Dietary habits are known to affect health, including the rate of brain ageing and susceptibility to diseases. This study examines the longitudinal relationship between dietary diversity and hippocampal volume, which is a key structure of memory processing and is known to be impaired in dementia.

Subjects/Methods
Subjects were aged 40–89 years (n = 1683, men: 50.6%) and participated in a 2-year follow-up study of the National Institute for Longevity Sciences-Longitudinal Study of Aging. Dietary intake was calculated from 3-day dietary records, and dietary diversity was determined using the Quantitative Index for Dietary Diversity at baseline. Longitudinal changes in hippocampal and total grey matter volumes were estimated by T1-weighted brain magnetic resonance imaging and FreeSurfer software. Estimated mean brain volume change in relation to dietary diversity score quintiles was assessed by the general linear model, adjusted for age, sex, education, smoking status, alcohol intake, physical activity, and comorbidities.

Results
The mean (± standard deviation) % decreases in hippocampal and total grey matter volume during the 2-year follow-up were 1.00% (±2.27%) and 0.78% (±1.83%), respectively. Multivariate-adjusted decreases in total grey matter volume were associated with dietary diversity score (p = 0.065, p for trend = 0.017), and the % decrease in hippocampal volume was more strongly associated with the dietary diversity score: the estimated mean (± standard error) values were 1.31% (±0.12%), 1.07% (±0.12%), 0.98% (±0.12%), 0.81% (±0.12%), and 0.85% (±0.12%), according to dietary diversity quintiles in ascending order (p = 0.030, p for trend = 0.003).

Conclusions
Among community dwellers, increased dietary diversity may be a new nutritional strategy to prevent hippocampal atrophy.
Sex-biased patterns shaped the genetic history of Roma
Authors: García-Fernández C. , Font-Porterias N. , Kučinskas V. , Sukarova-Stefanovska E. , Pamjav H. , Makukh H. , Dobon B. , Bertranpetit J. , Netea M. G. , Calafell F. , Comas D. 
Published: September 2020

AbstractThe Roma population is a European ethnic minority characterized by recent and multiple dispersals and founder effects. After their origin in South Asia around 1,500 years ago, they migrated West. In Europe, they diverged into ethnolinguistically distinct migrant groups that spread across the continent. Previous genetic studies based on genome-wide data and uniparental markers detected Roma founder events and West-Eurasian gene flow. However, to the best of our knowledge, it has not been assessed whether these demographic processes have equally affected both sexes in the population. The present study uses the largest and most comprehensive dataset of complete mitochondrial and Y chromosome Roma sequences to unravel the sex-biased patterns that have shaped their genetic history. The results show that the Roma maternal genetic pool carries a higher lineage diversity from South Asia, as opposed to a single paternal South Asian lineage. Nonetheless, the European gene flow events mainly occurred through the maternal lineages; however, a signal of this gene flow is also traceable in the paternal lineages. We also detect a higher female migration rate among European Roma groups. Altogether, these results suggest that sociocultural factors influenced the emergence of sex-biased genetic patterns at global and local scales in the Roma population through time.
Identification of 12 immune-related lncRNAs and molecular subtypes for the clear cell renal cell carcinoma based on RNA sequencing data
Authors: Zhong Weimin , Chen Bin , Zhong Hongbin , Huang Chaoqun , Lin Jianqiong , Zhu Maoshu , Chen Miaoxuan , Lin Ying , Lin Yao , Huang Jiyi 
Published: September 2020

AbstractClear cell renal cell carcinoma (ccRCC) is the most common type of renal cell carcinoma (RCC). Despite the existing extensive research, the molecular and pathogenic mechanisms of ccRCC are elusive. We aimed to identify the immune-related lncRNA signature and molecular subtypes associated with ccRCC. By integrating 4 microarray datasets from Gene Expression Omnibus database, we identified 49 immune-related genes. The corresponding immune-related lncRNAs were further identified in the TCGA dataset. 12-lncRNAs prognostic and independent signature was identified through survival analysis and survival difference between risk groups was further identified based on the risk score. Besides, we identified 3 molecular subtypes and survival analysis result showed that cluster 2 has a better survival outcome. Further, ssGSEA enrichment analysis for the immune-associated gene sets revealed that cluster 1 corresponded to a high immune infiltration level. While cluster 2 and cluster 3 corresponded to low and medium immune infiltration level, respectively. In addition, we validated the 12-lncRNA prognostic signature and molecular subtypes in an external validation dataset from the ICGC database. In summary, we identified a 12-lncRNA prognostic signature which may provide new insights into the molecular mechanisms of ccRCC and the molecular subtypes provided a theoretical basis for personalized treatment by clinicians.
Novel miRNA signature for predicting the stage of hepatocellular carcinoma
Authors: Yerukala Sathipati Srinivasulu , Ho Shinn-Ying 
Published: September 2020

AbstractHepatocellular carcinoma (HCC) is one of the leading causes of cancer deaths worldwide. Recently, microRNAs (miRNAs) are reported to be altered and act as potential biomarkers in various cancers. However, miRNA biomarkers for predicting the stage of HCC are limitedly discovered. Hence, we sought to identify a novel miRNA signature associated with cancer stage in HCC. We proposed a support vector machine (SVM)-based cancer stage prediction method, SVM-HCC, which uses an inheritable bi-objective combinatorial genetic algorithm for selecting a minimal set of miRNA biomarkers while maximizing the accuracy of predicting the early and advanced stages of HCC. SVM-HCC identified a 23-miRNA signature that is associated with cancer stages in patients with HCC and achieved a 10-fold cross-validation accuracy, sensitivity, specificity, Matthews correlation coefficient, and area under the receiver operating characteristic curve (AUC) of 92.59%, 0.98, 0.74, 0.80, and 0.86, respectively; and test accuracy and test AUC of 74.28% and 0.73, respectively. We prioritized the miRNAs in the signature based on their contributions to predictive performance, and validated the prognostic power of the prioritized miRNAs using Kaplan–Meier survival curves. The results showed that seven miRNAs were significantly associated with prognosis in HCC patients. Correlation analysis of the miRNA signature and its co-expressed miRNAs revealed that hsa-let-7i and its 13 co-expressed miRNAs are significantly involved in the hepatitis B pathway. In clinical practice, a prediction model using the identified 23-miRNA signature could be valuable for early-stage detection, and could also help to develop miRNA-based therapeutic strategies for HCC.
Centers of endemism of freshwater protists deviate from pattern of taxon richness on a continental scale
Authors: Olefeld Jana L. , Bock Christina , Jensen Manfred , Vogt Janina C. , Sieber Guido , Albach Dirk , Boenigk Jens 
Published: September 2020

AbstractHere, we analyzed patterns of taxon richness and endemism of freshwater protists in Europe. Even though the significance of physicochemical parameters but also of geographic constraints for protist distribution is documented, it remains unclear where regional areas of high protist diversity are located and whether areas of high taxon richness harbor a high proportion of endemics. Further, patterns may be universal for protists or deviate between taxonomic groups. Based on amplicon sequencing campaigns targeting the SSU and ITS region of the rDNA we address these patterns at two different levels of phylogenetic resolution. Our analyses demonstrate that protists have restricted geographical distribution areas. For many taxonomic groups the regions of high taxon richness deviate from those having a high proportion of putative endemics. In particular, the diversity of high mountain lakes as azonal habitats deviated from surrounding lowlands, i.e. many taxa were found exclusively in high mountain lakes and several putatively endemic taxa occurred in mountain regions like the Alps, the Pyrenees or the Massif Central. Beyond that, taxonomic groups showed a pronounced accumulation of putative endemics in distinct regions, e.g. Dinophyceae along the Baltic Sea coastline, and Chrysophyceae in Scandinavia. Many other groups did not have pronounced areas of increased endemism but geographically restricted taxa were found across Europe.
Spectral dynamics on saturable absorber in mode-locking with time stretch spectroscopy
Authors: Suzuki Masayuki , Boyraz Ozdal , Asghari Hossein , Jalali Bahram 
Published: September 2020

AbstractA mode-locked laser that can produce a broadband spectrum and ultrashort pulse has been applied for many applications in an extensive range of scientific fields. To obtain stable mode-locking during a long time alignment-free, a semiconductor saturable absorber is one of the most suitable devices. Dynamics from noise to a stable mode-locking state in the spectral-domain are known as complex and a non-repetitive phenomenon with the time scale from nanoseconds to milliseconds. Thus, a conventional spectrometer, which is composed of a grating and line sensor, cannot capture the spectral behavior from noise to stable mode-locking. As a powerful spectral measurement technique, a time-stretch dispersive Fourier transformation (TS-DFT) has been recently used to enable a successive single-shot spectral measurement over a couple of milliseconds time span. Here, we experimentally demonstrate real-time spectral evolution of femtosecond pulse build-up in a homemade passive mode-locked Yb fiber laser with a semiconductor saturable absorber mirror using TS-DFT. Capturing 700 consecutive spectra (~ 17 µs time window) in real-time using the time-stretch technique, we are able to resolve the transient dynamics that lead to stable mode-locking. Before setting stable mode-locking, an oscillating or shifting fringe pattern in the consecutive spectra was detected. This signature proves the existence of multiple pulses (including a soliton molecule) which is temporally separated with a different relative phase. The dynamics on multiple pulses is originated from a fast relaxation time of the saturable absorption effect. This study provides novel insights into understanding the pulse behavior during the birth of an ultrafast mode-locked laser pulse and the stable single-pulse operation which is highly stabilized.
Eye-background contrast as a quantitative marker for pupal age in a forensically important carrion beetle Necrodes littoralis L. (Silphidae)
Authors: Novák M. , Frątczak-Łagiewska K. , Mądra-Bielewicz A. , Matuszewski S. 
Published: September 2020

AbstractInsect pupae sampled at a death scene may be used to estimate the post-mortem interval. The pupal age is however difficult to estimate, as there are no good quantitative markers for the age of a pupa. We present a novel method for pupal age estimation based on the quantification of contrast in intensity between the eyes of a pupa and the middle grey photography card as a standard background. The intensity is measured on a standardized scale from 0 (perfect black) to 255 (perfect white) using computer graphical software and pictures of the eye and the background taken with a stereomicroscope. Eye-background contrast is calculated by subtracting the average intensity of the eye from the average intensity of the background. The method was developed and validated using pupae of Necrodes littoralis (Linnaeus, 1758) (Coleoptera: Silphidae), one of the most abundant beetle species on human cadavers in Central Europe. To develop the model, pupae were reared in 17, 20 and 23 °C, with a total of 120 specimens. The method was validated by three raters, using in total 182 pupae reared in 15, 17, 20, 23 and 25 °C. We found a gradual increase in eye-background contrast with pupal age. Changes followed generalized logistic function, with almost perfect fit of the model. Using our method pupal age was estimated with the average error of 8.1 accumulated degree-days (ADD). The largest error was 27.8 ADD and 95% of age estimates had errors smaller than 20 ADD. While using the method, different raters attained similar accuracy. In conclusion, we have demonstrated that eye-background contrast is a good quantitative marker for the age of N. littoralis pupae. Contrast measurements gave accurate estimates for pupal age. Our method is thus proven to be a candidate for a reliable approach to age insect pupae in forensic entomology.
Increased levels of histidine-rich glycoprotein are associated with the development of post-thrombotic syndrome
Authors: Siudut Jakub , Natorska Joanna , Son Maksim , Plens Krzysztof , Undas Anetta 
Published: September 2020

AbstractDenser fibrin networks which are relatively resistant to lysis can predispose to post-thrombotic syndrome (PTS). Histidine-rich glycoprotein (HRG), a blood protein displaying antifibrinolytic properties, is present in fibrin clots. We investigated whether HRG may affect the risk of PTS in relation to alterations to fibrin characteristics. In venous thromboembolism (VTE) patients, we evaluated plasma HRG levels, plasma clot permeability, maximum absorbance, clot lysis time and maximum rate of increase in D-dimer levels released from clots after 3 months of the index event. We excluded patients with cancer and severe comorbidities. After 2 years of follow-up, 48 patients who developed PTS had 18.6% higher HRG at baseline. Baseline HRG positively correlated with clot lysis time, maximum absorbance, and thrombin-activatable fibrinolysis inhibitor (TAFI) activity but was inversely correlated with plasma clot permeability and maximum rate of increase in D-dimer levels released from clots. On multivariate regression model adjusted for age, fibrinogen and glucose, independent predictors of PTS were recurrent VTE, baseline HRG level, and TAFI activity. VTE recurred in 45 patients, including 30 patients with PTS, and this event showed no association with elevated HRG. Our findings suggest that increased HRG levels might contribute to the development of PTS, in part through prothrombotic fibrin clot properties.
Robustness and rich clubs in collaborative learning groups: a learning analytics study using network science
Authors: Saqr Mohammed , Nouri Jalal , Vartiainen Henriikka , Tedre Matti 
Published: September 2020

AbstractProductive and effective collaborative learning is rarely a spontaneous phenomenon but rather the result of meeting a set of conditions, orchestrating and scaffolding productive interactions. Several studies have demonstrated that conflicts can have detrimental effects on student collaboration. Through the application of network science, and social network analysis in particular, this learning analytics study investigates the concept of group robustness; that is, the capacity of collaborative groups to remain functional despite the withdrawal or absence of group members, and its relation to group performance in the frame of collaborative learning. Data on all student and teacher interactions were collected from two phases of a course in medical education that employed an online learning environment. Visual and mathematical analysis were conducted, simulating the removal of actors and its effect on the group’s robustness and network structure. In addition, the extracted network parameters were used as features in machine learning algorithms to predict student performance. The study contributes findings that demonstrate the use of network science to shed light on essential elements of collaborative learning and demonstrates how the concept and measures of group robustness can increase understanding of the conditions of productive collaborative learning. It also contributes to understanding how certain interaction patterns can help to promote the sustainability or robustness of groups, while other interaction patterns can make the group more vulnerable to withdrawal and dysfunction. The finding also indicate that teachers can be a driving factor behind the formation of rich clubs of well-connected few and less connected many in some cases and can contribute to a more collaborative and sustainable process where every student is included.
Hybrid Harris hawks optimization with cuckoo search for drug design and discovery in chemoinformatics
Authors: Houssein Essam H. , Hosney Mosa E. , Elhoseny Mohamed , Oliva Diego , Mohamed Waleed M. , Hassaballah M. 
Published: September 2020

AbstractOne of the major drawbacks of cheminformatics is a large amount of information present in the datasets. In the majority of cases, this information contains redundant instances that affect the analysis of similarity measurements with respect to drug design and discovery. Therefore, using classical methods such as the protein bank database and quantum mechanical calculations are insufficient owing to the dimensionality of search spaces. In this paper, we introduce a hybrid metaheuristic algorithm called CHHO–CS, which combines Harris hawks optimizer (HHO) with two operators: cuckoo search (CS) and chaotic maps. The role of CS is to control the main position vectors of the HHO algorithm to maintain the balance between exploitation and exploration phases, while the chaotic maps are used to update the control energy parameters to avoid falling into local optimum and premature convergence. Feature selection (FS) is a tool that permits to reduce the dimensionality of the dataset by removing redundant and non desired information, then FS is very helpful in cheminformatics. FS methods employ a classifier that permits to identify the best subset of features. The support vector machines (SVMs) are then used by the proposed CHHO–CS as an objective function for the classification process in FS. The CHHO–CS-SVM is tested in the selection of appropriate chemical descriptors and compound activities. Various datasets are used to validate the efficiency of the proposed CHHO–CS-SVM approach including ten from the UCI machine learning repository. Additionally, two chemical datasets (i.e., quantitative structure-activity relation biodegradation and monoamine oxidase) were utilized for selecting the most significant chemical descriptors and chemical compounds activities. The extensive experimental and statistical analyses exhibit that the suggested CHHO–CS method accomplished much-preferred trade-off solutions over the competitor algorithms including the HHO, CS, particle swarm optimization, moth-flame optimization, grey wolf optimizer, Salp swarm algorithm, and sine–cosine algorithm surfaced in the literature. The experimental results proved that the complexity associated with cheminformatics can be handled using chaotic maps and hybridizing the meta-heuristic methods.
Sylvian fissure development is linked to differential genetic expression in the pre-folded brain
Authors: Mallela Arka N. , Deng Hansen , Brisbin Alyssa K. , Bush Alan , Goldschmidt Ezequiel 
Published: September 2020

AbstractThe mechanisms by which the human cerebral cortex folds into its final form remain poorly understood. With most of the current models and evidence addressing secondary folds, we sought to focus on the global geometry of the mature brain by studying its most distinctive feature, the Sylvian fissure. A digital human fetal brain atlas was developed using previously obtained MRI imaging of 81 healthy fetuses between gestational ages 21 and 38 weeks. To account for the development of the Sylvian fissure, we compared the growth of the frontotemporal opercula over the insular cortex and compared the transcriptome of the developing cortices for both regions. Spatiotemporal mapping of the lateral hemispheric surface showed the highest rate of organized growth in regions bordering the Sylvian fissure of the frontal, parietal and temporal lobes. Volumetric changes were first observed in the posterior aspect of the fissure moving anteriorly to the frontal lobe and laterally in the direction of the temporal pole. The insular region, delineated by the limiting insular gyri, expanded to a much lesser degree. The gene expression profile, before folding begins in the maturing brain, was significantly different in the developing opercular cortex compared to the insula. The Sylvian fissure forms by the relative overgrowth of the frontal and temporal lobes over the insula, corresponding to domains of highly expressed transcription factors involved in neuroepithelial cell differentiation.