bluuebunny/crossref_metadata_2025_split huggingface dataset:
Widespread transfer of mobile antibiotic resistance genes within individual gut microbiomes revealed through bacterial Hi-C
Authors: Kent Alyssa G. , Vill Albert C. , Shi Qiaojuan , Satlin Michael J. , Brito Ilana Lauren 
Published: September 2020

AbstractThe gut microbiome harbors a ‘silent reservoir’ of antibiotic resistance (AR) genes that is thought to contribute to the emergence of multidrug-resistant pathogens through horizontal gene transfer (HGT). To counteract the spread of AR, it is paramount to know which organisms harbor mobile AR genes and which organisms engage in HGT. Despite methods that characterize the overall abundance of AR genes in the gut, technological limitations of short-read sequencing have precluded linking bacterial taxa to specific mobile genetic elements (MGEs) encoding AR genes. Here, we apply Hi-C, a high-throughput, culture-independent method, to surveil the bacterial carriage of MGEs. We compare two healthy individuals with seven neutropenic patients undergoing hematopoietic stem cell transplantation, who receive multiple courses of antibiotics, and are acutely vulnerable to the threat of multidrug-resistant infections. We find distinct networks of HGT across individuals, though AR and mobile genes are associated with more diverse taxa within the neutropenic patients than the healthy subjects. Our data further suggest that HGT occurs frequently over a several-week period in both cohorts. Whereas most efforts to understand the spread of AR genes have focused on pathogenic species, our findings shed light on the role of the human gut microbiome in this process.
Generation, localization and functions of macrophages during the development of testis
Authors: Lokka Emmi , Lintukorpi Laura , Cisneros-Montalvo Sheyla , Mäkelä Juho-Antti , Tyystjärvi Sofia , Ojasalo Venla , Gerke Heidi , Toppari Jorma , Rantakari Pia , Salmi Marko 
Published: September 2020

AbstractIn the testis, interstitial macrophages are thought to be derived from the yolk sac during fetal development, and later replaced by bone marrow-derived macrophages. By contrast, the peritubular macrophages have been reported to emerge first in the postnatal testis and solely represent descendants of bone marrow-derived monocytes. Here, we define new monocyte and macrophage types in the fetal and postnatal testis using high-dimensional single-cell analyses. Our results show that interstitial macrophages have a dominant contribution from fetal liver-derived precursors, while peritubular macrophages are generated already at birth from embryonic precursors. We find that bone marrow-derived monocytes do not substantially contribute to the replenishment of the testicular macrophage pool even after systemic macrophage depletion. The presence of macrophages prenatally, but not postnatally, is necessary for normal spermatogenesis. Our multifaceted data thus challenge the current paradigms in testicular macrophage biology by delineating their differentiation, homeostasis and functions.
Identifying priority habitat for conservation and management of Australian humpback dolphins within a marine protected area
Authors: Hunt Tim N. , Allen Simon J. , Bejder Lars , Parra Guido J. 
Published: September 2020

AbstractIncreasing human activity along the coast has amplified the extinction risk of inshore delphinids. Informed selection and prioritisation of areas for the conservation of inshore delphinids requires a comprehensive understanding of their distribution and habitat use. In this study, we applied an ensemble species distribution modelling approach, combining results of six modelling algorithms to identify areas of high probability of occurrence of the globally Vulnerable Australian humpback dolphin in northern Ningaloo Marine Park (NMP), north-western Australia. Model outputs were based on sighting data collected during systematic, boat-based surveys between 2013 and 2015, and in relation to various ecogeographic variables. Water depth and distance to coast were identified as the most important variables influencing dolphin presence, with dolphins showing a preference for shallow waters (5–15 m) less than 2 km from the coast. Areas of high probability (> 0.6) of dolphin occurrence were primarily (90%) in multiple use areas where extractive human activities are permitted, and were poorly represented in sanctuary (no-take) zones. This spatial mismatch emphasises the need to reassess for future spatial planning and marine park management plan reviews for NMP. Shallow, coastal waters identified here should be considered priority areas for the conservation of this Vulnerable species.
Reproducible production and image-based quality evaluation of retinal pigment epithelium sheets from human induced pluripotent stem cells
Authors: Ye Ke , Takemoto Yuto , Ito Arisa , Onda Masanari , Morimoto Nao , Mandai Michiko , Takahashi Masayo , Kato Ryuji , Osakada Fumitaka 
Published: September 2020

AbstractTransplantation of retinal pigment epithelial (RPE) sheets derived from human induced pluripotent cells (hiPSC) is a promising cell therapy for RPE degeneration, such as in age-related macular degeneration. Current RPE replacement therapies, however, face major challenges. They require a tedious manual process of selecting differentiated RPE from hiPSC-derived cells, and despite wide variation in quality of RPE sheets, there exists no efficient process for distinguishing functional RPE sheets from those unsuitable for transplantation. To overcome these issues, we developed methods for the generation of RPE sheets from hiPSC, and image-based evaluation. We found that stepwise treatment with six signaling pathway inhibitors along with nicotinamide increased RPE differentiation efficiency (RPE6iN), enabling the RPE sheet generation at high purity without manual selection. Machine learning models were developed based on cellular morphological features of F-actin-labeled RPE images for predicting transepithelial electrical resistance values, an indicator of RPE sheet function. Our model was effective at identifying low-quality RPE sheets for elimination, even when using label-free images. The RPE6iN-based RPE sheet generation combined with the non-destructive image-based prediction offers a comprehensive new solution for the large-scale production of pure RPE sheets with lot-to-lot variations and should facilitate the further development of RPE replacement therapies.
Spatial tracking of individual fluid dispersed particles via Raman spectroscopy
Authors: Hogan Benjamin Thomas , O’Dowd Jennifer , Faneca Ruedas Joaquin , Baranov Alexander , Baldycheva Anna 
Published: September 2020

AbstractWe demonstrate a method for the spatial tracking of individual particles, dispersed in a fluid host, via Raman spectroscopy. The effect of moving a particle upon the intensity of different bands within its Raman spectrum is first established computationally through a scattering matrix method. By comparing an experimental spectrum to the computational analysis, we show that the position of the particle can be obtained. We apply this method to the specific cases of molybdenum disulfide and graphene oxide particles, dispersed in a nematic liquid crystal, and contained within a microfluidic channel. By considering the ratio and difference between the intensities of the two Raman bands of molybdenum disulfide and graphene oxide, we demonstrate that an accurate position can be obtained in two dimensions.
Robotic environmental DNA bio-surveillance of freshwater health
Authors: Sepulveda Adam J. , Birch James M. , Barnhart Elliott P. , Merkes Christopher M. , Yamahara Kevan M. , Marin Roman , Kinsey Stacy M. , Wright Peter R. , Schmidt Christian 
Published: September 2020

AbstractAutonomous water sampling technologies may help to overcome the human resource challenges of monitoring biological threats to rivers over long time periods and across large geographic areas. The Monterey Bay Aquarium Research Institute has pioneered a robotic Environmental Sample Processor (ESP) that overcomes some of the constraints associated with traditional sampling since it can automate water sample filtration and preservation of the captured material. The ESP was originally developed for marine environment applications. Here we evaluated whether the ESP can provide reliable, timely information on environmental (e)DNA detections of human and fish pathogens and introduced fishes at U.S. Geological Survey streamgage sites in freshwater rivers. We compared eDNA collected via ESP at high frequency (e.g., every 3 h) with manual eDNA collections collected at lower frequency (e.g., weekly). We found that water samples filtered and preserved by ESPs successfully detected the DNA of human pathogens, fish pathogens and introduced fishes. Both ESP and manually collected samples provided similar information about target DNA presence. We suggest that the greatest current benefit of the ESP is the cost savings of high frequency, bio-surveillance at remote or hard to access sites. The full potential of robotic technologies like the ESP will be realized when they can more easily execute in situ analyses of water samples and rapidly transmit results to decision-makers.
Ischemia/reperfusion injured intestinal epithelial cells cause cortical neuron death by releasing exosomal microRNAs associated with apoptosis, necroptosis, and pyroptosis
Authors: Hsu Chien-Chin , Huang Chien-Cheng , Chien Lan-Hsiang , Lin Mao-Tsun , Chang Ching-Ping , Lin Hung-Jung , Chio Chung-Ching 
Published: September 2020

AbstractTo date, there is no good evidence that intestine epithelial cells (IEC) affected by ischemia/reperfusion (I/R) injury are able to cause cortical neuron injury directly. Additionally, it remains unclear whether the neuronal damage caused by I/R injured IEC can be affected by therapeutic hypothermia (TH, 32 °C). To address these questions, we performed an oxygen–glucose deprivation (OGD) affected IEC-6-primary cortical neuron coculture system under normothermia (37 °C) or TH (32 °C) conditions. It was found that OGD caused hyperpermeability in IEC-6 cell monolayers. OGD-preconditioned IEC-6 cells caused cortical neuronal death (e.g., decreased cell viability), synaptotoxicity, and neuronal apoptosis (evidenced by increased caspase-3 expression and the number of TUNEL-positive cells), necroptosis (evidenced by increased receptor-interacting serine/threonine-protein kinase-1 [RIPK1], RIPK3 and mixed lineage kinase domain-like pseudokinase [MLKL] expression), and pyroptosis (evidenced by an increase in caspase-1, gasdermin D [GSDMD], IL-1β, IL-18, the apoptosis-associated speck-like protein containing a caspase recruitment domain [ASC], and nucleotide oligomerization domain [NOD]-like receptor [NLRP]-1 expression). TH did not affect the intestinal epithelial hyperpermeability but did attenuate OGD-induced neuronal death and synaptotoxicity. We also performed quantitative real-time PCR to quantify the genes encoding 84 exosomal microRNAs in the medium of the control-IEC-6, the control-neuron, the OGD-IEC-6 at 37 °C, the OGD-IEC-6 at 32 °C, the neuron cocultured with OGD-IEC-6 at 37 °C, and the neurons cocultured with OGD-IEC-6 at 32 °C. We found that the control IEC-6 cell s or cortical neurons are able to secrete a basal level of exosomal miRNAs in their medium. OGD significantly up-regulated the basal level of each parameter for IEC-6 cells. As compared to those of the OGD-IEC-6 cells or the control neurons, the OGD-IEC-6 cocultured neurons had significantly higher levels of 19 exosomal miRNAs related to apoptosis, necroptosis, and/or pyroptosis events. Our results identify that I/R injured intestinal epithelium cells can induce cortical neuron death via releasing paracrine mediators such as exosomal miRNAs associated with apoptosis, necroptosis, and/or pyroptosis, which can be counteracted by TH.
Evidence for repeated failure of the giant Yigong landslide on the edge of the Tibetan Plateau
Authors: Guo Changbao , Montgomery David R. , Zhang Yongshuang , Zhong Ning , Fan Chun , Wu Ruian , Yang Zhihua , Ding Yingying , Jin Jijun , Yan Yiqiu 
Published: September 2020

AbstractField surveys and radiocarbon dating of detrital materials provide evidence that repeated landslides dammed the Yigong Tsangpo River ca. 3500 bc, 1300 bc, 1000 bc, 600 bc, and twice more recently. Together with historical slides in 1900 and 2000, these six older slides make for a total of eight known channel-damming landslide events at the same location over the past six millennia, indicating sub-millennia recurrence intervals over this time period. Together with the likely incomplete nature of the sedimentary record of past channel-damming episodes uncovered to date, our findings indicate late Holocene multi-century-scale recurrence intervals for large landslides at this location. Hence, the riverbed at and immediately upstream of this location may have been inundated by sediment, and therefore not incising, for much of the post-glacial period. Together with the location of this landslide complex at the head of the major knickzone defining the fluvial edge of the Tibetan Plateau, our findings support the hypothesis that repeated glacial and landslide damming in this region inhibited headward propagation of river incision into the Tibetan Plateau.
Heritability of haemodynamics in the ascending aorta
Authors: McGurk Kathryn A. , Owen Benjamin , Watson William D. , Nethononda Richard M. , Cordell Heather J. , Farrall Martin , Rider Oliver J. , Watkins Hugh , Revell Alistair , Keavney Bernard D. 
Published: September 2020

AbstractBlood flow in the vasculature can be characterised by dimensionless numbers commonly used to define the level of instabilities in the flow, for example the Reynolds number, Re. Haemodynamics play a key role in cardiovascular disease (CVD) progression. Genetic studies have identified mechanosensitive genes with causal roles in CVD. Given that CVD is highly heritable and abnormal blood flow may increase risk, we investigated the heritability of fluid metrics in the ascending aorta calculated using patient-specific data from cardiac magnetic resonance (CMR) imaging. 341 participants from 108 British Caucasian families were phenotyped by CMR and genotyped for 557,124 SNPs. Flow metrics were derived from the CMR images to provide some local information about blood flow in the ascending aorta, based on maximum values at systole at a single location, denoted max, and a ‘peak mean’ value averaged over the area of the cross section, denoted pm. Heritability was estimated using pedigree-based (QTDT) and SNP-based (GCTA-GREML) methods. Estimates of Reynolds number based on spatially averaged local flow during systole showed substantial heritability ($${\hbox {h}}^{2}_{Ped} = 41\% \,[\hbox {P}=0.001]$$

h

Ped

2

=
41
%

[
P
=
0.001
]

, $${\hbox {h}}^{2}_{SNP} = 39\%\, [\hbox {P}=0.002]$$

h

SNP

2

=
39
%

[
P
=
0.002
]

), while the estimated heritability for Reynolds number calculated using the absolute local maximum velocity was not statistically significant (12–13%; $$\hbox {P}>0.05$$

P
>
0.05

). Heritability estimates of the geometric quantities alone; e.g. aortic diameter ($${\hbox {h}}^{2}_{Ped} = 29\%\, [\hbox {P}=0.009]$$

h

Ped

2

=
29
%

[
P
=
0.009
]

, $${\hbox {h}}^{2}_{SNP} = 30\%\, [\hbox {P}=0.010]$$

h

SNP

2

=
30
%

[
P
=
0.010
]

), were also substantially heritable, as described previously. These findings indicate the potential for the discovery of genetic factors influencing haemodynamic traits in large-scale genotyped and phenotyped cohorts where local spatial averaging is used, rather than instantaneous values. Future Mendelian randomisation studies of aortic haemodynamic estimates, which are swift to derive in a clinical setting, will allow for the investigation of causality of abnormal blood flow in CVD.
Axillary shoot proliferation and plant regeneration in Euryodendron excelsum H. T. Chang, a critically endangered species endemic to China
Authors: Chen Shuangyan , Xiong Yuping , Wu Teng , Wu Kunlin , da Silva Jaime A. Teixeira , Xiong Youhua , Zeng Songjun , Ma Guohua 
Published: September 2020

AbstractEuryodendron excelsum H. T. Chang is a single-type, rare and endangered woody plant unique to China. In this study, young stems were used as explants and cultured on Woody Plant Medium (WPM) supplemented with 5.0 μM 6-benzyladenine (BA), were subcultured for more than 15 times over a total of more than 3 years and finally an efficient axillary shoot proliferation and plantlet regeneration system was established in which one shoot could proliferate an average of 5.1 axillary shoots every 2 months on the medium supplemented with 5.0 μM BA and 0.5 μM α-naphthaleneacetic acid (NAA). Shoots rooted at a moderate frequencies (50.1%) on agarized WPM supplemented with 0.5 μM NAA but 100% of shoots rooted in agar-free vermiculite-based WPM after culture for 2 months. Plantlets, when transplanted to peat soil: vermiculite (1:1), showed the highest 95.1% survival within 1 month.
Accumulation of synovial fluid CD19+CD24hiCD27+ B cells was associated with bone destruction in rheumatoid arthritis
Authors: Guo Xiaofeng , Xu Tingting , Zheng Jing , Cui Xiangjun , Li Ming , Wang Kai , Su Min , Zhang Huifang , Zheng Ke , Sun Chongling , Song Shulin , Liu Hongjiang 
Published: September 2020

AbstractRegulatory CD19+CD24hiCD27+ B cells were proved to be numerically decreased and functionally impaired in the peripheral blood (PB) from rheumatoid arthritis (RA), with the potential of converting into osteoclast-priming cells. However, the distribution and function of CD19+CD24hiCD27+ B cells in RA synovial fluid (SF) were unclear. In this study, we investigated whether RA SF CD19+CD24hiCD27+ B cells were increased and associated with bone destruction. We found that the proportion of RA SF CD19+CD24hiCD27+ B cells was increased significantly, and was positively correlated with swollen joint counts, tender joint counts and disease activity. CXCL12, CXCL13, CCL19 contributed to the recruitment of CD19+CD24hiCD27+ B cells in RA SF. Notably, CD19+CD24hiCD27+ B cells in the SF from RA expressed significantly more RANKL compared to OA and that in the PB from RA. Critically, RA CD19+CD24hiCD27+ B cells promoted osteoclast (OC) differentiation in vitro, and the number of OCs was higher in cultures with RA SF CD19+CD24hiCD27+ B cells than in those derived from RA PB. Collectively, these findings revealed the accumulation of CD19+CD24hiCD27+ B cells in SF and their likely contribution to joint destruction in RA. Modulating the status of CD19+CD24hiCD27+ B cells might provide novel therapeutic strategies for RA.
Method of surface energy investigation by lateral AFM: application to control growth mechanism of nanostructured NiFe films
Authors: Zubar T. I. , Fedosyuk V. M. , Trukhanov S. V. , Tishkevich D. I. , Michels D. , Lyakhov D. , Trukhanov A. V. 
Published: September 2020

AbstractA new method for the specific surface energy investigation based on a combination of the force spectroscopy and the method of nanofriction study using atomic force microscopy was proposed. It was shown that air humidity does not affect the results of investigation by the proposed method as opposed to the previously used methods. Therefore, the method has high accuracy and repeatability in air without use of climate chambers and liquid cells. The proposed method has a high local resolution and is suitable for investigation of the specific surface energy of individual nanograins or fixed nanoparticles. The achievements described in the paper demonstrate one of the method capabilities, which is to control the growth mechanism of thin magnetic films. The conditions for the transition of the growth mechanism of thin Ni80Fe20 films from island to layer-by-layer obtained via electrolyte deposition have been determined using the proposed method and the purpose made probes with Ni coating.
Mammographic image classification with deep fusion learning
Authors: Yu Xiangchun , Pang Wei , Xu Qing , Liang Miaomiao 
Published: September 2020

AbstractTo better address the recognition of abnormalities among mammographic images, in this study we apply the deep fusion learning approach based on Pre-trained models to discover the discriminative patterns between Normal and Tumor categories. We designed a deep fusion learning framework for mammographic image classification. This framework works in two main steps. After obtaining the regions of interest (ROIs) from original dataset, the first step is to train our proposed deep fusion models on those ROI patches which are randomly collected from all ROIs. We proposed the deep fusion model (Model1) to directly fuse the deep features to classify the Normal and Tumor ROI patches. To explore the association among channels of the same block, we propose another deep fusion model (Model2) to integrate the cross-channel deep features using 1 × 1 convolution. The second step is to obtain the final prediction by performing the majority voting on all patches' prediction of one ROI. The experimental results show that Model1 achieves the whole accuracy of 0.8906, recall rate of 0.913, and precision rate of 0.8077 for Tumor class. Accordingly, Model2 achieves the whole accuracy of 0.875, recall rate of 0.9565, and precision rate 0.7,586 for Tumor class. Finally, we open source our Python code at https://github.com/yxchspring/MIAS in order to share our tool with the research community.
Concealed information revealed by involuntary eye movements on the fringe of awareness in a mock terror experiment
Authors: Rosenzweig Gal , Bonneh Yoram S. 
Published: September 2020

AbstractInvoluntary eye movements during fixation are typically inhibited following stimulus onset (Oculomotor Inhibition, OMI), depending on the stimulus saliency and attention, with an earlier and longer OMI for barely visible familiar faces. However, it is still unclear whether OMI regarding familiarities and perceptual saliencies differ enough to allow a reliable OMI-based concealed information test (CIT). In a “mock terror” experiment with 25 volunteers, 13 made a concealed choice of a “terror-target” (one of eight), associated with 3 probes (face, name, and residence), which they learned watching text and videos, whereas 12 “innocents” pre-learned nothing. All participants then watched ~ 25 min of repeated brief presentations of barely visible (masked) stimuli that included the 8 potential probes, as well as a universally familiar face as a reference, while their eye movements were monitored. We found prolonged and deviant OMI regarding the probes. Incorporated with the individual pattern of responses to the reference, our analysis correctly identified 100% of the terror targets, and was 95% correct in discriminating “terrorists” from “innocents”. Our results provide a “proof of concept” for a novel approach to CIT, based on involuntary oculomotor responses to barely visible stimuli, individually tailored, and with high accuracy and theoretical resistance to countermeasures.