bluuebunny/crossref_metadata_2025 huggingface dataset:
P53-regulated miR-320a targets PDL1 and is downregulated in malignant mesothelioma
Authors: Costa Caterina , Indovina Paola , Mattioli Eliseo , Forte Iris Maria , Iannuzzi Carmelina Antonella , Luzzi Luca , Bellan Cristiana , De Summa Simona , Bucci Enrico , Di Marzo Domenico , De Feo Marisa , Mutti Luciano , Pentimalli Francesca , Giordano Antonio
Published: September 2020

Malignant pleural mesothelioma (MPM) is an aggressive cancer, related to asbestos exposure, which has a dismal prognosis. MPM diagnosis is late and often challenging, suggesting the need to identify more reliable molecular biomarkers. Here, we set out to identify differentially expressed miRNAs in epithelioid, biphasic, and sarcomatoid MPMs versus normal mesothelium and explored specific miRNA contribution to mesothelial tumorigenesis. We screened an LNA™-based miRNA-microrray with 14 formalin-fixed paraffin-embedded (FFPE) MPMs and 6 normal controls. Through real-time qRT-PCR we extended the analysis of a miRNA subset and further investigated miR-320a role through state-of-the-art techniques. We identified 16 upregulated and 32 downregulated miRNAs in MPMs versus normal tissue, including the previously identified potential biomarkers miR-21, miR-126, miR-143, miR-145. We showed in an extended series that miR-145, miR-10b, and miR-320a levels can discriminate tumor versus controls with high specificity and sensitivity. We focused on miR-320a because other family members were found downregulated in MPMs. However, stable miR-320a ectopic expression induced higher proliferation and migration ability, whereas miR-320a silencing reduced these processes, not supporting a classic tumor-suppressor role in MPM cell lines. Among putative targets, we found that miR-320a binds the 3′-UTR of the immune inhibitory receptor ligand PDL1 and, consistently, miR-320a modulation affects PDL1 levels in MPM cells. Finally, we showed that p53 over-expression induces the upregulation of miR-320a, along with miR-200a and miR-34a, both known to target PDL1, and reduces PDL1 levels in MPM cells. Our data suggest that PDL1 expression might be due to a defective p53-regulated miRNA response, which could contribute to MPM immune evasion or tumorigenesis through tumor-intrinsic roles.
The roles of long noncoding RNAs in breast cancer metastasis
Authors: Liu Lingxia , Zhang Yu , Lu Jun
Published: September 2020

Breast cancer is the most significant threat to female health. Breast cancer metastasis is the major cause of mortality in breast cancer patients. To fully unravel the molecular mechanisms that underlie the breast cancer cell metastasis is critical for developing strategies to improve survival and prognosis in breast cancer patients. Recent studies have revealed that the long noncoding RNAs (lncRNAs) are involved in breast cancer metastasis through a variety of molecule mechanisms, though the precise functional details of these lncRNAs are yet to be clarified. In the present review, we focus on the functions of lncRNAs in breast cancer invasion and metastasis, with particular emphasis on the functional properties, the regulatory factors, the therapeutic promise, as well as the future challenges in studying these lncRNA.
Quantitative genetic architecture of adaptive phenology traits in the deciduous tree, Populus trichocarpa (Torr. and Gray)
Authors: Richards Thomas J. , Karacic Almir , Apuli Rami-Petteri , Weih Martin , Ingvarsson Pär K. , Rönnberg-Wästljung Ann Christin
Published: September 2020

In a warming climate, the ability to accurately predict and track shifting environmental conditions will be fundamental for plant survival. Environmental cues define the transitions between growth and dormancy as plants synchronise development with favourable environmental conditions, however these cues are predicted to change under future climate projections which may have profound impacts on tree survival and growth. Here, we use a quantitative genetic approach to estimate the genetic basis of spring and autumn phenology in Populus trichocarpa to determine this species capacity for climate adaptation. We measured bud burst, leaf coloration, and leaf senescence traits across two years (2017–2018) and combine these observations with measures of lifetime growth to determine how genetic correlations between phenology and growth may facilitate or constrain adaptation. Timing of transitions differed between years, although we found strong cross year genetic correlations in all traits, suggesting that genotypes respond in consistent ways to seasonal cues. Spring and autumn phenology were correlated with lifetime growth, where genotypes that burst leaves early and shed them late had the highest lifetime growth. We also identified substantial heritable variation in the timing of all phenological transitions (h2 = 0.5–0.8) and in lifetime growth (h2 = 0.8). The combination of additive variation and favourable genetic correlations in phenology traits suggests that populations of cultivated varieties of P. Trichocarpa may have the capability to adapt their phenology to climatic changes without negative impacts on growth.
IL-20 antagonist suppresses PD-L1 expression and prolongs survival in pancreatic cancer models
Authors: Lu Shao-Wei , Pan Hong-Chin , Hsu Yu-Hsiang , Chang Kung-Chao , Wu Li-Wha , Chen Wei-Yu , Chang Ming-Shi
Published: September 2020

Pancreatic ductal adenocarcinoma (PDAC) and cancer-associated cachexia (CAC) are multifactorial and characterized by dysregulated inflammatory networks. Whether the proinflammatory cytokine IL-20 is involved in the complex networks of PDAC and CAC remains unclear. Here, we report that elevated IL-20 levels in tumor tissue correlate with poor overall survival in 72 patients with PDAC. In vivo, we establish a transgenic mouse model (KPC) and an orthotopic PDAC model and examine the therapeutic efficacy of an anti-IL-20 monoclonal antibody (7E). Targeting IL-20 not only prolongs survival and attenuates PD-L1 expression in both murine models but also inhibits tumor growth and mitigates M2-like polarization in the orthotopic PDAC model. Combination treatment with 7E and an anti-PD-1 antibody shows better efficacy in inhibiting tumor growth than either treatment alone in the orthotopic PDAC model. Finally, 7E mitigates cachexic symptoms in CAC models. Together, we conclude IL-20 is a critical mediator in PDAC progression.
Dual blockade of CD47 and HER2 eliminates radioresistant breast cancer cells
Authors: Candas-Green Demet , Xie Bowen , Huang Jie , Fan Ming , Wang Aijun , Menaa Cheikh , Zhang Yanhong , Zhang Lu , Jing Di , Azghadi Soheila , Zhou Weibing , Liu Lin , Jiang Nian , Li Tao , Gao Tianyi , Sweeney Colleen , Shen Rulong , Lin Tzu-yin , Pan Chong-xian , Ozpiskin Omer M. , Woloschak Gayle , Grdina David J. , Vaughan Andrew T. , Wang Ji Ming , Xia Shuli , Monjazeb Arta M. , Murphy William J. , Sun Lun-Quan , Chen Hong-Wu , Lam Kit S. , Weichselbaum Ralph R. , Li Jian Jian
Published: September 2020

Although the efficacy of cancer radiotherapy (RT) can be enhanced by targeted immunotherapy, the immunosuppressive factors induced by radiation on tumor cells remain to be identified. Here, we report that CD47-mediated anti-phagocytosis is concurrently upregulated with HER2 in radioresistant breast cancer (BC) cells and RT-treated mouse syngeneic BC. Co-expression of both receptors is more frequently detected in recurrent BC patients with poor prognosis. CD47 is upregulated preferentially in HER2-expressing cells, and blocking CD47 or HER2 reduces both receptors with diminished clonogenicity and augmented phagocytosis. CRISPR-mediated CD47 and HER2 dual knockouts not only inhibit clonogenicity but also enhance macrophage-mediated attack. Dual antibody of both receptors synergizes with RT in control of syngeneic mouse breast tumor. These results provide the evidence that aggressive behavior of radioresistant BC is caused by CD47-mediated anti-phagocytosis conjugated with HER2-prompted proliferation. Dual blockade of CD47 and HER2 is suggested to eliminate resistant cancer cells in BC radiotherapy.
Unique S-scheme heterojunctions in self-assembled TiO2/CsPbBr3 hybrids for CO2 photoreduction
Authors: Xu Feiyan , Meng Kai , Cheng Bei , Wang Shengyao , Xu Jingsan , Yu Jiaguo
Published: September 2020

Exploring photocatalysts to promote CO2 photoreduction into solar fuels is of great significance. We develop TiO2/perovskite (CsPbBr3) S-scheme heterojunctions synthesized by a facile electrostatic-driven self-assembling approach. Density functional theory calculation combined with experimental studies proves the electron transfer from CsPbBr3 quantum dots (QDs) to TiO2, resulting in the construction of internal electric field (IEF) directing from CsPbBr3 to TiO2 upon hybridization. The IEF drives the photoexcited electrons in TiO2 to CsPbBr3 upon light irradiation as revealed by in-situ X-ray photoelectron spectroscopy analysis, suggesting the formation of an S-scheme heterojunction in the TiO2/CsPbBr3 nanohybrids which greatly promotes the separation of electron-hole pairs to foster efficient CO2 photoreduction. The hybrid nanofibers unveil a higher CO2-reduction rate (9.02 μmol g–1 h–1) comparing with pristine TiO2 nanofibers (4.68 μmol g–1 h–1). Isotope (13CO2) tracer results confirm that the reduction products originate from CO2 source.
Prior knowledge promotes hippocampal separation but cortical assimilation in the left inferior frontal gyrus
Authors: Bein Oded , Reggev Niv , Maril Anat
Published: September 2020

An adaptive memory system rarely learns information tabula rasa, but rather builds on prior knowledge to facilitate learning. How prior knowledge influences the neural representation of novel associations remains unknown. Here, participants associated pairs of faces in two conditions: a famous, highly familiar face with a novel face or two novel faces while undergoing fMRI. We examine multivoxel activity patterns corresponding to individual faces before and after learning. The activity patterns representing members of famous-novel pairs becomes separated in the hippocampus, that is, more distinct from one another through learning, in striking contrast to paired novel faces that become similar. In the left inferior frontal gyrus, however, prior knowledge leads to integration, and in a specific direction: the representation of the novel face becomes similar to that of the famous face after learning, suggesting assimilation of new into old memories. We propose that hippocampal separation might resolve interference between existing and newly learned information, allowing cortical assimilation. Thus, associative learning with versus without prior knowledge relies on radically different computations.
Senescence and entrenchment in evolution of amino acid sites
Authors: Stolyarova A. V. , Nabieva E. , Ptushenko V. V. , Favorov A. V. , Popova A. V. , Neverov A. D. , Bazykin G. A.
Published: September 2020

Amino acid propensities at a site change in the course of protein evolution. This may happen for two reasons. Changes may be triggered by substitutions at epistatically interacting sites elsewhere in the genome. Alternatively, they may arise due to environmental changes that are external to the genome. Here, we design a framework for distinguishing between these alternatives. Using analytical modelling and simulations, we show that they cause opposite dynamics of the fitness of the allele currently occupying the site: it tends to increase with the time since its origin due to epistasis (“entrenchment”), but to decrease due to random environmental fluctuations (“senescence”). By analysing the genomes of vertebrates and insects, we show that the amino acids originating at negatively selected sites experience strong entrenchment. By contrast, the amino acids originating at positively selected sites experience senescence. We propose that senescence of the current allele is a cause of adaptive evolution.
An investigation of causal relationships between prediabetes and vascular complications
Authors: Mutie Pascal M. , Pomares-Millan Hugo , Atabaki-Pasdar Naeimeh , Jordan Nina , Adams Rachel , Daly Nicole L. , Tajes Juan Fernandes , Giordano Giuseppe N. , Franks Paul W.
Published: September 2020

Prediabetes is a state of glycaemic dysregulation below the diagnostic threshold of type 2 diabetes (T2D). Globally, ~352 million people have prediabetes, of which 35–50% develop full-blown diabetes within five years. T2D and its complications are costly to treat, causing considerable morbidity and early mortality. Whether prediabetes is causally related to diabetes complications is unclear. Here we report a causal inference analysis investigating the effects of prediabetes in coronary artery disease, stroke and chronic kidney disease, complemented by a systematic review of relevant observational studies. Although the observational studies suggest that prediabetes is broadly associated with diabetes complications, the causal inference analysis revealed that prediabetes is only causally related with coronary artery disease, with no evidence of causal effects on other diabetes complications. In conclusion, prediabetes likely causes coronary artery disease and its prevention is likely to be most effective if initiated prior to the onset of diabetes.
Ignoring correlated activity causes a failure of retinal population codes
Authors: Ruda Kiersten , Zylberberg Joel , Field Greg D.
Published: September 2020

From 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

The 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

Metabolic 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

It 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

Humic 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

There 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

Efforts 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

Structurally-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

Global 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

Recent 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

The 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

In 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

A 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.
Tracheal colonization factor A (TcfA) is a biomarker for rapid and specific detection of Bordetella pertussis
Authors: Burnham-Marusich Amanda R. , Olsen Ryan K. , Scarbrough Jacqueline , Kvam Alexander , Yang Wei , Zimmerman Lindsey , Dunn James J. , Merkel Tod , Kozel Thomas R.
Published: September 2020

Pertussis is a highly contagious disease for which prompt, point-of-care diagnosis remains an unmet clinical need. Results from conventional test modalities (nucleic acid detection, serology, and culture) take hours to days. To overcome this challenge, we identified a new biomarker (tracheal colonization factor A, TcfA) for detection of Bordetella pertussis infection by lateral flow immunoassay (LFIA). We developed a library of 28 epitope-mapped monoclonal antibodies against TcfA and incorporated three antibodies into a LFIA. The LFIA did not cross-react with common bacterial or fungal organisms, but did react with nine distinct B. pertussis strains. The minimal linear epitope sequences targeted by the LFIA were conserved in 98% of 954 B. pertussis isolates collected across 12 countries from 1949–2017. The LFIA’s limit of detection was 3.0 × 105 CFU/mL with B. pertussis cells in buffer, 6.2 × 105 CFU/mL with nasopharyngeal washes from a non-human primate model, and 2.3 ng/mL with recombinant TcfA. The LFIA reacted with patient nasopharyngeal swab specimens containing as few as 1.8 × 106B. pertussis genomes/mL and showed no false-positives. Rapid (< 20 min) LFIA detection of TcfA as a biomarker for B. pertussis infection is feasible and may facilitate early detection of pertussis.
Associations of procalcitonin, C-reaction protein and neutrophil-to-lymphocyte ratio with mortality in hospitalized COVID-19 patients in China
Authors: Xu Jian-bo , Xu Chao , Zhang Ru-bing , Wu Meng , Pan Chang-kun , Li Xiu-jie , Wang Qian , Zeng Fang-fang , Zhu Sui
Published: September 2020

Coronavirus disease 2019 (COVID-19) is an important and urgent threat to global health. Inflammation factors are important for COVID-19 mortality, and we aim to explore whether the baseline levels of procalcitonin (PCT), C-reaction protein (CRP) and neutrophil-to-lymphocyte ratio (NLR) are associated with an increased risk of mortality in patients with COVID-19. A retrospective study was conducted and a total of 76 patients with confirmed COVID-19 were included between January 17, 2020 to March 2, 2020, of these cases, 17 patients were dead. After adjusting covariates, PCT (≥ 0.10 ng/mL) and CRP (≥ 52.14 mg/L) exhibited independent increasing risks of mortality were used hazard ratio (HR) of 52.68 (95% confidence interval [CI]: 1.77–1571.66) and 5.47 (95% CI: 1.04–28.72), respectively. However, NRL (≥ 3.59) was not found to be an independent risk factor for death in our study. Furthermore, the elevated PCT levels were still associated with increasing risk of mortality in the old age group (age ≥ 60 y), and in the critically severe and severe patients after adjustment for complications. Thu Baseline levels of PCT and CRP have been addressed as independent predictors of mortality in patients with COVID-19.
Contrasting volcano spacing along SW Japan arc caused by difference in age of subducting lithosphere
Authors: Tatsumi Yoshiyuki , Suenaga Nobuaki , Yoshioka Shoichi , Kaneko Katsuya , Matsumoto Takumi
Published: September 2020

The SW Japan arc built by subduction of the Philippine Sea (PHS) plate exhibits uneven distribution of volcanoes: thirteen Quaternary composite volcanoes form in the western half of this arc, Kyushu Island, while only two in the eastern half, Chugoku district. Reconstruction of the PHS plate back to 14 Ma, together with examinations based on thermal structure models constrained by high-density heat flow data and a petrological model for dehydration reactions suggest that fluids are discharged actively at depths of 90–100 km in the hydrous layer at the top of the old (> 50 Ma), hence, cold lithosphere sinking beneath Kyushu Island. In contrast, the young (15–25 Ma) oceanic crust downgoing beneath Chugoku district releases fluids largely at shallower depths, i.e. beneath the non-volcanic forearc, to cause characteristic tectonic tremors and low-frequency earthquakes (LFEs) and be the source of specific brine springs. Much larger amounts of fluids supplied to the magma source region in the western SW Japan arc could build more densely-distributed volcanoes.
Global chemical modifications comparison of human plasma proteome from two different age groups
Authors: Liu Yongtao , Pan Xuanzhen , Zhao Mindi , Gao Youhe
Published: September 2020

In this study, two groups of human plasma proteome at different age groups (old and young) were used to perform a comparison of global chemical modifications, as determined by tandem mass spectrometry (MS/MS) combined with non-limiting modification identification algorithms. The sulfhydryl in the cysteine A total of 4 molecular modifications were found to have significant differences passing random grouping tests: the succinylation and phosphorylation modification of cysteine (Cys, C) and the modification of lysine (Lys, K) with threonine (Thr, T) were significantly higher in the old group than in the young group, while the carbamylation of lysine was lower in the young group. We speculate that there is an increase in certain modified proteins in the blood of the old people which, in turn, changes the function of those proteins. This change may be one of the reasons why old people are more likely than young people to be at risk for age-related diseases, such as metabolic diseases, cerebral and cardiovascular diseases, and cancer.
Histopathological imaging features- versus molecular measurements-based cancer prognosis modeling
Authors: Zhang Sanguo , Fan Yu , Zhong Tingyan , Ma Shuangge
Published: September 2020

For lung and many other cancers, prognosis is essentially important, and extensive modeling has been carried out. Cancer is a genetic disease. In the past 2 decades, diverse molecular data (such as gene expressions and DNA mutations) have been analyzed in prognosis modeling. More recently, histopathological imaging data, which is a “byproduct” of biopsy, has been suggested as informative for prognosis. In this article, with the TCGA LUAD and LUSC data, we examine and directly compare modeling lung cancer overall survival using gene expressions versus histopathological imaging features. High-dimensional penalization methods are adopted for estimation and variable selection. Our findings include that gene expressions have slightly better prognostic performance, and that most of the gene expressions are weakly correlated imaging features. This study may provide additional insight into utilizing the two types of important data in cancer prognosis modeling and into lung cancer overall survival.
Altered neuronal habituation to hearing others’ pain in adults with autistic traits
Authors: Meng Jing , Li Zuoshan , Shen Lin
Published: September 2020

This study tested the hypothesis that autistic traits influence the neuronal habituation that underlies the processing of others’ pain. Based on their autism-spectrum quotient (AQ), two groups of participants were classified according to their autistic traits: High-AQ and Low-AQ groups. Their event-related potentials in response to trains of three identical audio recordings, exhibiting either painful or neutral feelings of others, were compared during three experimental tasks. (1) In a Pain Judgment Task, participants were instructed to focus on pain-related cues in the presented audio recordings. (2) In a Gender Judgment Task, participants were instructed to focus on non-pain-related cues in the presented audio recordings. (3) In a Passive Listening Task, participants were instructed to passively listen. In the High-AQ group, an altered empathic pattern of habituation, indexed by frontal-central P2 responses of the second repeated painful audio recordings, was found during the Passive Listening Task. Nevertheless, both High-AQ and Low-AQ groups exhibited similar patterns of habituation to hearing others’ voices, both neutral and painful, in the Pain Judgment and Gender Judgment Tasks. These results suggest altered empathic neuronal habituation in the passive processing of others’ vocal pain by individuals with autistic traits.
Author Correction: Label-Free Imaging of Tissue Architecture during Axolotl Peripheral Nerve Regeneration in Comparison to Functional Recovery
Authors: Uckermann Ortrud , Hirsch Joana , Galli Roberta , Bendig Jonas , Later Robert , Koch Edmund , Schackert Gabriele , Steiner Gerald , Tanaka Elly , Kirsch Matthias
Published: September 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Comparative study of serum sample preparation methods in aggregation-based plasmonic sensing
Authors: Liang Zeren , Gao Kai , Lu Mengdi , Peng Wei , Zhu Shenggeng , Huang Yixiu , Hong Long , Masson Jean-Francois
Published: September 2020

The use of nanoparticle-based colorimetric methods has received considerable attention for clinical analysis in biofluids. Sample preparation methods are surveyed here to minimize the impact of the sample matrix on the performance of a nanoparticle aggregation assay.
Colorimetric detection of Hg2+ with an azulene-containing chemodosimeter via dithioacetal hydrolysis
Authors: López-Alled Carlos M. , Murfin Lloyd C. , Kociok-Köhn Gabriele , James Tony D. , Wenk Jannis , Lewis Simon E.
Published: September 2020

A simple azulene-dithiane gives a selective colorimetric response to mercury(ii) in both mixed and purely aqueous solvent, which is clearly visible to the human eye.
A critical view at the ISO 13528 and IUPAC's harmonized protocol approach for proficiency testing for homogeneity assessment for quantitative variables
Authors: Coucke Wim , Soumali Mohamed Rida
Published: September 2020

Current PT sample homogeneity test has high risk of accepting heterogeneous.
Economically feasible strategy for confirmation of pharmaceuticals in hospital effluent using screening analysis
Authors: Cardoso Renata M. , Dallegrave Alexsandro , Becker Raquel W. , Araújo Débora S. , Sirtori Carla
Published: September 2020

The contamination of aquatic systems by pharmaceuticals has received considerable attention in recent decades, because these substances are increasingly detected in the environment.
Electroswitching of the single-molecule magnet behaviour in an octahedral spin crossover cobalt(ii) complex with a redox-active pyridinediimine ligand
Authors: Rabelo Renato , Toma Luminita , Moliner Nicolás , Julve Miguel , Lloret Francesc , Pasán Jorge , Ruiz-Pérez Catalina , Ruiz-García Rafael , Cano Joan
Published: September 2020

A unique example of electroswitchable spin crossover molecular nanomagnet which proceeds through one-electron oxidation of the slow-relaxing paramagnetic low-spin CoIIion (SCo= 1/2, ON) to the diamagnetic low-spin CoIIIion (SCo= 0, OFF).
Precursor-directed biosynthesis of catechol compounds in Acinetobacter bouvetii DSM 14964
Authors: Reitz Zachary L. , Butler Alison
Published: September 2020

Genome mining for VibH homologs reveals several Acinetobacter species with a gene cluster putatively encoding biosynthesis of catechol siderophores with an amine core. Enzyme flexibility allows for in vivo synthesis of non-native catechol compounds.
Late-stage peptide and protein modifications through phospha-Michael addition reaction
Authors: He Pei-Yang , Chen Huai , Hu Hong-Guo , Hu Jin-Jian , Lim Yeh-Jun , Li Yan-Mei
Published: September 2020

A chemoselective peptide and protein modification strategy of dehydroalanine (Dha) specifically reacting with phosphines for attachment of different functional groups.
In situ formation of surface and bulk oxides in small palladium nanoparticles
Authors: Bugaev Aram L. , Zabilskiy Maxim , Skorynina Alina A. , Usoltsev Oleg A. , Soldatov Alexander V. , van Bokhoven Jeroen A.
Published: September 2020

Evolution of surface and bulk palladium oxides in supported palladium nanoparticles was followed in situ using X-ray absorption spectroscopy.