bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ignoring correlated activity causes a failure of retinal population codes
Authors: Ruda Kiersten , Zylberberg Joel , Field Greg D. 
Published: September 2020

AbstractFrom starlight to sunlight, adaptation alters retinal output, changing both the signal and noise among populations of retinal ganglion cells (RGCs). Here we determine how these light level-dependent changes impact decoding of retinal output, testing the importance of accounting for RGC noise correlations to optimally read out retinal activity. We find that at moonlight conditions, correlated noise is greater and assuming independent noise severely diminishes decoding performance. In fact, assuming independence among a local population of RGCs produces worse decoding than using a single RGC, demonstrating a failure of population codes when correlated noise is substantial and ignored. We generalize these results with a simple model to determine what conditions dictate this failure of population processing. This work elucidates the circumstances in which accounting for noise correlations is necessary to take advantage of population-level codes and shows that sensory adaptation can strongly impact decoding requirements on downstream brain areas.
Geometric analysis of shape transition for two-layer carbon–silicon nanotubes
Authors: Luo Xiangyan , Xie Quan , Tian Zean , Guo Xiaotian , Zhang Jinmin , Gao Tinghong , Liang Yongchao 
Published: September 2020

AbstractThe two-layer nanotubes consisted of carbon atoms on the outside layer and silicon atoms on the inside layer (CNT@SiNT) show a series of diversity in the shape transitions, for instance transforming from a circle through an oval to a rectangle. In this paper, we investigate this geometric change from three perspectives. In the first aspect, we stationary time, followed by quantize in the three-dimensional Z-axis of nanotubes. In the second aspect, we stationary Z-axis, followed by quantize in the time. Finally, we tracked distance of nanotubes flattest section and roundest section. At the stationary time, the overall image of different Z-axis distance distributions is similar to a plan view of multiple ice creams, regardless of whether CNT or SiNT are on the same Z-axis, their slice plans are circle or rectangle of the projection of the Z-axis section on the XOY plane. In the stationary Z-axis, the nanotubes periodically change from a circle to an oval, and then from an oval to a rectangle at different times. Most remarkably, the distance value of deformation which we track the flattest and roundest is a constant value, and in the same distance period, there is only one roundest circle and one longest rectangle at different section and different time. The geometric analysis provided theoretical reference for the preparation of various devices and semiconductor nano-heterojunctions.
An integrated RF-receive/B0-shim array coil boosts performance of whole-brain MR spectroscopic imaging at 7 T
Authors: Esmaeili Morteza , Stockmann Jason , Strasser Bernhard , Arango Nicolas , Thapa Bijaya , Wang Zhe , van der Kouwe Andre , Dietrich Jorg , Cahill Daniel P. , Batchelor Tracy T. , White Jacob , Adalsteinsson Elfar , Wald Lawrence , Andronesi Ovidiu C. 
Published: September 2020

AbstractMetabolic imaging of the human brain by in-vivo magnetic resonance spectroscopic imaging (MRSI) can non-invasively probe neurochemistry in healthy and disease conditions. MRSI at ultra-high field (≥ 7 T) provides increased sensitivity for fast high-resolution metabolic imaging, but comes with technical challenges due to non-uniform B0 field. Here, we show that an integrated RF-receive/B0-shim (AC/DC) array coil can be used to mitigate 7 T B0 inhomogeneity, which improves spectral quality and metabolite quantification over a whole-brain slab. Our results from simulations, phantoms, healthy and brain tumor human subjects indicate improvements of global B0 homogeneity by 55%, narrower spectral linewidth by 29%, higher signal-to-noise ratio by 31%, more precise metabolite quantification by 22%, and an increase by 21% of the brain volume that can be reliably analyzed. AC/DC shimming provide the highest correlation (R2 = 0.98, P = 0.001) with ground-truth values for metabolite concentration. Clinical translation of AC/DC and MRSI is demonstrated in a patient with mutant-IDH1 glioma where it enables imaging of D-2-hydroxyglutarate oncometabolite with a 2.8-fold increase in contrast-to-noise ratio at higher resolution and more brain coverage compared to previous 7 T studies. Hence, AC/DC technology may help ultra-high field MRSI become more feasible to take advantage of higher signal/contrast-to-noise in clinical applications.
Understanding and predicting ciprofloxacin minimum inhibitory concentration in Escherichia coli with machine learning
Authors: Pataki Bálint Ármin , Matamoros Sébastien , van der Putten Boas C. L. , Remondini Daniel , Giampieri Enrico , Aytan-Aktug Derya , Hendriksen Rene S. , Lund Ole , Csabai István , Schultsz Constance ,   SPS COMPARE ML-AMR group, Matamoros S. , Janes V. , Hendriksen R. S. , Lund O. , Clausen P. , Aarestrup F. M. , Koopmans M. , Pataki B. , Visontai D. , Stéger J. , Szalai-Gindl J M. , Csabai I. , Pakseresht N. , Rossello M. , Silvester N. , Amid C. , Cochrane G. , Schultsz C. , Pradel F. , Westeel E. , Fuchs S. , Kumar S. Malhotra , Xavier B. Britto , Ngoc M. Nguyen , Remondini D. , Giampieri E. , Pasquali F. , Petrovska L. , Ajayi D. , Nielsen E. M. , Trung N. V. , Hoa N. T. , Ishii Y. , Aoki K. , McDermott P. 
Published: September 2020

AbstractIt is important that antibiotics prescriptions are based on antimicrobial susceptibility data to ensure effective treatment outcomes. The increasing availability of next-generation sequencing, bacterial whole genome sequencing (WGS) can facilitate a more reliable and faster alternative to traditional phenotyping for the detection and surveillance of AMR. This work proposes a machine learning approach that can predict the minimum inhibitory concentration (MIC) for a given antibiotic, here ciprofloxacin, on the basis of both genome-wide mutation profiles and profiles of acquired antimicrobial resistance genes. We analysed 704 Escherichia coli genomes combined with their respective MIC measurements for ciprofloxacin originating from different countries. The four most important predictors found by the model, mutations in gyrA residues Ser83 and Asp87, a mutation in parC residue Ser80 and presence of the qnrS1 gene, have been experimentally validated before. Using only these four predictors in a linear regression model, 65% and 93% of the test samples’ MIC were correctly predicted within a two- and a four-fold dilution range, respectively. The presented work does not treat machine learning as a black box model concept, but also identifies the genomic features that determine susceptibility. The recent progress in WGS technology in combination with machine learning analysis approaches indicates that in the near future WGS of bacteria might become cheaper and faster than a MIC measurement.
Humic acid enhances heat stress tolerance via transcriptional activation of Heat-Shock Proteins in Arabidopsis
Authors: Cha Joon-Yung , Kang Sang-Ho , Ali Imdad , Lee Sang Cheol , Ji Myung Geun , Jeong Song Yi , Shin Gyeong-Im , Kim Min Gab , Jeon Jong-Rok , Kim Woe-Yeon 
Published: September 2020

AbstractHumic acid (HA) is composed of a complex supramolecular association and is produced by humification of organic matters in soil environments. HA not only improves soil fertility, but also stimulates plant growth. Although numerous bioactivities of HA have been reported, the molecular evidences have not yet been elucidated. Here, we performed transcriptomic analysis to identify the HA-prompted molecular mechanisms in Arabidopsis. Gene ontology enrichment analysis revealed that HA up-regulates diverse genes involved in the response to stress, especially to heat. Heat stress causes dramatic induction in unique gene families such asHeat-Shock Protein(HSP) coding genes includingHSP101,HSP81.1,HSP26.5,HSP23.6, andHSP17.6A. HSPs mainly function as molecular chaperones to protect against thermal denaturation of substrates and facilitate refolding of denatured substrates. Interestingly, wild-type plants grown in HA were heat-tolerant compared to those grown in the absence of HA, whereas ArabidopsisHSP101null mutant (hot1) was insensitive to HA. We also validated that HA accelerates the transcriptional expression of HSPs. Overall, these results suggest thatHSP101is a molecular target of HA promoting heat-stress tolerance in Arabidopsis. Our transcriptome information contributes to understanding the acquired genetic and agronomic traits by HA conferring tolerance to environmental stresses in plants.
Tumor metabolic volume by 18F-FDG-PET as a prognostic predictor of first-line pembrolizumab for NSCLC patients with PD-L1 ≥ 50%
Authors: Yamaguchi Ou , Kaira Kyoichi , Hashimoto Kosuke , Mouri Atsuto , Shiono Ayako , Miura Yu , Murayama Yoshitake , Kobayashi Kunihiko , Kagamu Hiroshi , Kuji Ichiei 
Published: September 2020

AbstractThere is a lack of markers for predicting favorable outcomes after pembrolizumab therapy in patients with non-small cell lung cancer (NSCLC) with programmed death ligand-1 (PD-L1) expression ≥ 50%. This retrospective study examined the prognostic significance of 2-deoxy-2-[18F] fluoro-d-glucose (18F-FDG) uptake as a predictive marker of first-line pembrolizumab. Forty-eight patients with previously untreated NSCLC and PD-L1 expression levels ≥ 50% who underwent 18F-FDG-positron emission tomography (PET) just before administration of pembrolizumab monotherapy were eligible and underwent assessment of metabolic tumor volume (MTV), total lesion glycolysis (TLG), and maximum of standardized uptake value (SUVmax) on 18F-FDG uptake. The objective response rate, median progression-free survival, and median overall survival were 51.1%, 7.1 months, and 18.6 months, respectively. In univariate survival analyses, high MTV was barely a significant prognostic predictor and was confirmed as an independent factor linked to worse outcomes in multivariate analysis, predominantly in patients with a histological diagnosis of adenocarcinoma. A high MTV was significantly associated with distant metastases (especially bone metastasis), C-reactive protein (CRP) level, and PD-L1 expression ≥ 75%. Metabolic tumor activity assessed as MTV from 18F-FDG uptake predicted the prognosis after first-line pembrolizumab treatment in patients with NSCLC and PD-L1 expression ≥ 50%, especially for adenocarcinoma.
Long-term modulation of cardiac activity induced by inhibitory control over emotional memories
Authors: Legrand Nicolas , Etard Olivier , Vandevelde Anaïs , Pierre Melissa , Viader Fausto , Clochon Patrice , Doidy Franck , Peschanski Denis , Eustache Francis , Gagnepain Pierre 
Published: September 2020

AbstractEfforts to exclude past experiences from conscious awareness can lead to forgetting. Memory suppression is central to affective disorders, but we still do not really know whether emotions, including their physiological causes, are also impacted by this process in normal functioning individuals. In two studies, we measured the after-effects of suppressing negative memories on cardiac response in healthy participants. Results of Study 1 revealed that efficient control of memories was associated with long-term inhibition of the cardiac deceleration that is normally induced by disgusting stimuli. Attempts to suppress sad memories, by contrast, aggravated the cardiac response, an effect that was closely related to the inability to forget this specific material. In Study 2, electroencephalography revealed a reduction in power in the theta (3–8 Hz), alpha (8–12 Hz) and low-beta (13–20 Hz) bands during the suppression of unwanted memories, compared with their voluntary recall. Interestingly, however, the reduction of power in the theta frequency band during memory control was related to a subsequent inhibition of the cardiac response. These results provide a neurophysiological basis for the influence of memory control mechanisms on the cardiac system, opening up new avenues and questions for treating intrusive memories using motivated forgetting.
Cultural isolation of spore-forming bacteria in human feces using bile acids
Authors: Tanaka Masaru , Onizuka Sakura , Mishima Riko , Nakayama Jiro 
Published: September 2020

AbstractStructurally-diversified bile acids (BAs) are involved in shaping of intestinal microbiota as well as absorption of dietary lipids. Taurocholic acid, a conjugated form of BA, has been reported to be a factor triggering germination of a wide range of spore-forming bacteria in intestine. To test a hypothesis that other BAs also promote germination of intestinal bacteria, we attempted culture of bacteria from ethanol-treated feces by using a series of BAs. It was found that conjugated-BAs, notably three glycine-conjugated BAs, glycodeoxycholic acid and glycochenodeoxycholic acid, significantly increased the number and the species variety of colonies formed on the agar plate. These colonized bacteria mostly belonged to class Clostridia, mainly consisting of families Lachnospiraceae, Clostridiaceae, and Peptostreptococcaceae. There were several types of bacteria associated with different sensitivity to each BA. Eventually, we isolated 72 bacterial species of which 61 are known and 11 novel. These results demonstrate that the culturable range of bacteria in intestine can be widened using the germination-inducing activity of BAs. This approach would advance the research on spore-forming Clostridia that contains important but difficult-to-cultured bacteria associate with host health and diseases.
Population genetic analysis in old Montenegrin vineyards reveals ancient ways currently active to generate diversity in Vitis vinifera
Authors: Maraš Vesna , Tello Javier , Gazivoda Anita , Mugoša Milena , Perišić Mirko , Raičević Jovana , Štajner Nataša , Ocete Rafael , Božović Vladan , Popović Tatjana , García-Escudero Enrique , Grbić Miodrag , Martínez-Zapater José Miguel , Ibáñez Javier 
Published: September 2020

AbstractGlobal viticulture has evolved following market trends, causing loss of cultivar diversity and traditional practices. In Montenegro, modern viticulture co-exists with a traditional viticulture that still maintains ancient practices and exploits local cultivars. As a result, this region provides a unique opportunity to explore processes increasing genetic diversity. To evaluate the diversity of Montenegrin grapevines and the processes involved in their diversification, we collected and analyzed 419 samples in situ across the country (cultivated plants from old orchards and vines growing in the wild), and 57 local varieties preserved in a grapevine collection. We obtained 144 different genetic profiles, more than 100 corresponding to cultivated grapevines, representing a surprising diversity for one of the smallest European countries. Part of this high diversity reflects historical records indicating multiple and intense introduction events from diverse viticultural regions at different times. Another important gene pool includes many autochthonous varieties, some on the edge of extinction, linked in a complex parentage network where two varieties (Razaklija and Kratošija) played a leading role on the generation of indigenous varieties. Finally, analyses of genetic structure unveiled several putative proto-varieties, likely representing the first steps involved in the generation of new cultivars or even secondary domestication events.
Prolonged bedrest reduces plasma high-density lipoprotein levels linked to markedly suppressed cholesterol efflux capacity
Authors: Trakaki Athina , Scharnagl Hubert , Trieb Markus , Holzer Michael , Hinghofer-Szalkay Helmut , Goswami Nandu , Marsche Gunther 
Published: September 2020

AbstractRecent observations strongly connect high-density lipoproteins (HDL) function and levels with coronary heart disease outcomes and risk for infections and sepsis. To date, our knowledge of factors determining this connection is still very limited. The immobility associated with prolonged bedrest is detrimental to health, affecting several systems, including the cardiovascular, pulmonary, gastrointestinal, musculoskeletal and urinary. Effects of prolonged bedrest on the composition and functional properties of HDL remain elusive. We evaluated metrics of HDL composition and function in healthy male volunteers participating in a randomized, crossover head-down bedrest study. We observed that HDL cholesterol efflux capacity was profoundly decreased during bedrest, mediated by a bedrest associated reduction in plasma levels of HDL-cholesterol and major apolipoproteins (apo) apoA-I and apoA-II. Paraoxonase activity, plasma anti-oxidative capacity and the activities of lecithin-cholesterol acyltransferase and cholesteryl ester transfer protein were not affected. No change was observed in the content of HDL-associated serum amyloid A, a sensitive marker of inflammation. Resistive vibration exercise countermeasure during bedrest did not correct impaired cholesterol efflux capacity and only tended to increase arylesterase activity of HDL-associated paraoxonase. In conclusion, prolonged bedrest reduces plasma HDL levels linked to markedly suppressed HDL cholesterol efflux capacity. Resistive vibration exercise during bedrest did not correct HDL levels and impaired cholesterol efflux capacity.
Seeds attached to refrigerated shipping containers represent a substantial risk of nonnative plant species introduction and establishment
Authors: Lucardi Rima D. , Bellis Emily S. , Cunard Chelsea E. , Gravesande Jarron K. , Hughes Steven C. , Whitehurst Lauren E. , Worthy Samantha J. , Burgess Kevin S. , Marsico Travis D. 
Published: September 2020

AbstractThe initial processes for successful biological invasions are transport, introduction, and establishment. These can be directly influenced or completely avoided through activities that reduce the number and frequency of entering nonnative propagules. Economic and environmental benefits through preventative monitoring programs at early stages of invasion far outweigh the long-term costs associated with mitigating ecological and economic impacts once nonnative species establish and spread. In this study, we identified 30 taxa of hitchhiking plant propagules on the air-intake grilles of refrigerated shipping containers arriving into a United States seaport from a port on the Pacific coast of South America. The four monocotyledonous taxa with the highest number of seeds collected were analyzed; we estimated propagule pressure, germination, and survivorship of these taxa, and we used the estimates to determine likelihood of establishment. At the levels of propagule pressure estimated here, non-zero germination and survival rates resulted in high establishment probabilities even when escape rates from shipping containers were modelled to be exceedingly low. Our results suggest high invasion risk for nonnative taxa including Saccharum spontaneum L., a listed Federal Noxious Weed. Currently, not all shipping containers arriving at USA ports are thoroughly inspected due to limited personnel and funding for biological invasion prevention. Our results indicate that there is a significant risk from only a few propagules escaping into the environment from this source, and we propose possible solutions for reducing this risk.
Effects of water stress on spectral reflectance of bermudagrass
Authors: Caturegli Lisa , Matteoli Stefania , Gaetani Monica , Grossi Nicola , Magni Simone , Minelli Alberto , Corsini Giovanni , Remorini Damiano , Volterrani Marco 
Published: September 2020

AbstractIn the south-central Italy, during summer rainfall does not supply a sufficient amount of water. Therefore, irrigation management during dry periods is important for maintaining turf quality. The hybrid bermudagrass (Cynodon dactylon (L.) Pers. × Cynodon transvaalensis Burtt–Davy) is known to represent the dominant warm-season turfgrass in warm to temperate climatic regions and its drought tolerance make bermudagrass a competitive turfgrass. A greenhouse experiment was conducted using uniform cores of hybrid bermudagrass, which were secured in a polyvinyl chloride cylinders and watered by constant sub-irrigation. The objectives of the present research were to measure the spectral reflectance with a new generation handheld spectroradiometer on hybrid bermudagrass and to explore various vegetation indices to be used as future detecting tool to study water stress in bermudagrass. Moreover, the potential uses of multivariate processing techniques for discriminating different water stress conditions in turfgrass has been investigated. Besides spectral indices, multivariate methods, although performed on a data set limited in terms of sample size, have shown a great potential for water stress monitoring in turfgrass and surely deserve further investigations. There are different indices that use distinct water absorption features independent of chlorophyll concentration, such as water index (WI = R900/R970) that has been reported to be a robust index of canopy water content and is used as an active indicator of changes in Leaf Relative Water Content (LRWC). Also, the ratio of WI with NDVI (WI/NDVI = (R900/R970)/((R800 − R680)/(R800 + R680)]) was found to be an effective indicator of water stress. Another vegetation index to detect water features is normalized difference water index (NDWI), designed to maximize reflectance of water by using green wavelengths. In our trial in bermudagrass the relationships studied, suggest that WI (900/970) and WI/NDVI, among the indices studied, are the more effective indicators of water stress. In fact, lower values of WI indicate higher water stress, while higher values of WI/NDVI indicate higher water stress levels.
Sympathetic nerves control bacterial clearance
Authors: Lankadeva Yugeesh R. , May Clive N. , McKinley Michael J. , Neeland Melanie R. , Ma Shuai , Hocking Dianna M. , Robins-Browne Roy , Bedoui Sammy , Farmer David G. S. , Bailey Simon R. , Martelli Davide , McAllen Robin M. 
Published: September 2020

AbstractA neural reflex mediated by the splanchnic sympathetic nerves regulates systemic inflammation in negative feedback fashion, but its consequences for host responses to live infection are unknown. To test this, conscious instrumented sheep were infected intravenously with live E. coli bacteria and followed for 48 h. A month previously, animals had undergone either bilateral splanchnic nerve section or a sham operation. As established for rodents, sheep with cut splanchnic nerves mounted a stronger systemic inflammatory response: higher blood levels of tumor necrosis factor alpha and interleukin-6 but lower levels of the anti-inflammatory cytokine interleukin-10, compared with sham-operated animals. Sequential blood cultures revealed that most sham-operated sheep maintained high circulating levels of live E. coli throughout the 48-h study period, while all sheep without splanchnic nerves rapidly cleared their bacteraemia and recovered clinically. The sympathetic inflammatory reflex evidently has a profound influence on the clearance of systemic bacterial infection.