bluuebunny/crossref_metadata_2025_split huggingface dataset:
In Vivo Water Dynamics in Shewanella oneidensis Bacteria at High Pressure
Authors: Foglia Fabrizia , Hazael Rachael , Meersman Filip , Wilding Martin C. , Sakai Victoria García , Rogers Sarah , Bove Livia E. , Koza Michael Marek , Moulin Martine , Haertlein Michael , Forsyth V. Trevor , McMillan Paul F. 
Published: June 2019

AbstractFollowing observations of survival of microbes and other life forms in deep subsurface environments it is necessary to understand their biological functioning under high pressure conditions. Key aspects of biochemical reactions and transport processes within cells are determined by the intracellular water dynamics. We studied water diffusion and rotational relaxation in liveShewanella oneidensisbacteria at pressures up to 500 MPa using quasi-elastic neutron scattering (QENS). The intracellular diffusion exhibits a significantly greater slowdown (by −10–30%) and an increase in rotational relaxation times (+10–40%) compared with water dynamics in the aqueous solutions used to resuspend the bacterial samples. Those results indicate both a pressure-induced viscosity increase and slowdown in ionic/macromolecular transport properties within the cells affecting the rates of metabolic and other biological processes. Our new data support emerging models for intracellular organisation with nanoscale water channels threading between macromolecular regions within a dynamically organized structure rather than a homogenous gel-like cytoplasm.
A fractional diffusion random laser
Authors: Chen Yuyao , Fiorentino Alfredo , Dal Negro Luca 
Published: June 2019

AbstractThe goal of this letter is to introduce the concept of a non-resonant fractional random laser. This is achieved by extending the classical Letokhov model of photon diffusion through disordered gain media to fractional differential operators in space and time. Fractional transport equations effectively describe anomalous photon sub-diffusion phenomena in non-uniform random scattering media with memory and long-range spatial correlation effects. In particular, by analytically solving fractional transport equations in the one-dimensional slab geometry we obtain simple closed-form expressions for the critical amplification volumes required to initiate the laser action in both fractional-order (FO) and distributed-order (DO) space-time fractional reaction-diffusion equations. Our findings demonstrate the benefits of anomalous sub-diffusive photon transport in active media with correlated disorder and stimulate the engineering of novel non-resonant random lasers with significantly reduced footprint and amplification volumes beyond the limitations of uniform disorder and Markovian diffusion processes.
Meniscus-Derived Matrix Scaffolds Promote the Integrative Repair of Meniscal Defects
Authors: Ruprecht Jacob C. , Waanders Taylor D. , Rowland Christopher R. , Nishimuta James F. , Glass Katherine A. , Stencel Jennifer , DeFrate Louis E. , Guilak Farshid , Weinberg J. Brice , McNulty Amy L. 
Published: June 2019

AbstractMeniscal tears have a poor healing capacity, and damage to the meniscus is associated with significant pain, disability, and progressive degenerative changes in the knee joint that lead to osteoarthritis. Therefore, strategies to promote meniscus repair and improve meniscus function are needed. The objective of this study was to generate porcine meniscus-derived matrix (MDM) scaffolds and test their effectiveness in promoting meniscus repair via migration of endogenous meniscus cells from the surrounding meniscus or exogenously seeded human bone marrow-derived mesenchymal stem cells (MSCs). Both endogenous meniscal cells and MSCs infiltrated the MDM scaffolds. In the absence of exogenous cells, the 8% MDM scaffolds promoted the integrative repair of an in vitro meniscal defect. Dehydrothermal crosslinking and concentration of the MDM influenced the biochemical content and shear strength of repair, demonstrating that the MDM can be tailored to promote tissue repair. These findings indicate that native meniscus cells can enhance meniscus healing if a scaffold is provided that promotes cellular infiltration and tissue growth. The high affinity of cells for the MDM and the ability to remodel the scaffold reveals the potential of MDM to integrate with native meniscal tissue to promote long-term repair without necessarily requiring exogenous cells.
Severe pulmonary disease in an adult primary ciliary dyskinesia population in Brazil
Authors: Olm Mary Anne Kowal , Marson Fernando Augusto Lima , Athanazio Rodrigo Abensur , Nakagawa Naomi Kondo , Macchione Mariangela , Loges Niki Tomas , Omran Heymut , Rached Samia Zahi , Bertuzzo Carmen Sílvia , Stelmach Rafael , Saldiva Paulo Hilário Nascimento , Ribeiro José Dirceu , Jones Marcus Herbert , Mauad Thais 
Published: June 2019

AbstractPrimary Ciliary Dyskinesia (PCD) is underdiagnosed in Brazil. We enrolled patients from an adult service of Bronchiectasis over a two-year period in a cross-sectional study. The inclusion criteria were laterality disorders (LD), cough with recurrent infections and the exclusion of other causes of bronchiectasis. Patients underwent at least two of the following tests: nasal nitric oxide, ciliary movement and analysis of ciliary immunofluorescence, and genetic tests (31 PCD genes + CFTR gene). The clinical characterization included the PICADAR and bronchiectasis scores, pulmonary function, chronic Pseudomonas aeruginosa (cPA) colonization, exhaled breath condensate (EBC) and mucus rheology (MR). Forty-nine of the 500 patients were diagnosed with definite (42/49), probable (5/49), and clinical (2/49) PCD. Twenty-four patients (24/47) presented bi-allelic pathogenic variants in a total of 31 screened PCD genes. A PICADAR score > 5 was found in 37/49 patients, consanguinity in 27/49, LD in 28/49, and eight PCD sibling groups. FACED diagnosed 23/49 patients with moderate or severe bronchiectasis; FEV1 ≤ 50% in 25/49 patients, eight patients had undergone lung transplantation, four had been lobectomized and cPA+ was determined in 20/49. The EBC and MR were altered in all patients. This adult PCD population was characterized by consanguinity, severe lung impairment, genetic variability, altered EBC and MR.
B-mode ultrasound for the assessment of hepatic fibrosis: a quantitative multiparametric analysis for a radiomics approach
Authors: D’Souza Julia C. , Sultan Laith R. , Hunt Stephen J. , Schultz Susan M. , Brice Angela K. , Wood Andrew K. W. , Sehgal Chandra M. 
Published: June 2019

AbstractHepatic fibrosis and cirrhosis are a growing global health problem with increasing mortality rates. Early diagnosis and staging of hepatic fibrosis represent a major challenge. Currently liver biopsy is the gold standard for fibrosis assessment; however, biopsy requires an invasive procedure and is prone to sampling error and reader variability. In the current study we investigate using quantitative analysis of computer-extracted features of B-mode ultrasound as a non-invasive tool to characterize hepatic fibrosis. Twenty-two rats were administered diethylnitrosamine (DEN) orally for 12 weeks to induce hepatic fibrosis. Four control rats did not receive DEN. B-mode ultrasound scans sampling throughout the liver were acquired at baseline, 10, and 13 weeks. Computer extracted quantitative parameters representing brightness (echointensity, hepatorenal index) and variance (heterogeneity, anisotropy) of the liver were studied. DEN rats showed an increase in echointensity from 37.1 ± SD 7.8 to 53.5 ± 5.7 (10 w) to 57.5 ± 6.1 (13 w), while the control group remained unchanged at an average of 34.5 ± 4.5. The three other features studied increased similarly over time in the DEN group. Histologic analysis showed METAVIR fibrosis grades of F2-F4 in DEN rats and F0-F1 in controls. Increasing imaging parameters correlated with increasing METAVIR grades, and anisotropy showed the strongest correlation (ρ = 0.58). Sonographic parameters combined using multiparametric logistic regression were able to differentiate between clinically significant and insignificant fibrosis. Quantitative B-mode ultrasound imaging can be implemented in clinical settings as an accurate non-invasive tool for fibrosis assessment.
Functional characterization of retinal ganglion cells using tailored nonlinear modeling
Authors: Shi Qing , Gupta Pranjal , Boukhvalova Alexandra K. , Singer Joshua H. , Butts Daniel A. 
Published: June 2019

AbstractThe mammalian retina encodes the visual world in action potentials generated by 20–50 functionally and anatomically-distinct types of retinal ganglion cell (RGC). Individual RGC types receive synaptic input from distinct presynaptic circuits; therefore, their responsiveness to specific features in the visual scene arises from the information encoded in synaptic input and shaped by postsynaptic signal integration and spike generation. Unfortunately, there is a dearth of tools for characterizing the computations reflected in RGC spike output. Therefore, we developed a statistical model, the separable Nonlinear Input Model, to characterize the excitatory and suppressive components of RGC receptive fields. We recorded RGC responses to a correlated noise (“cloud”) stimulus in an in vitro preparation of mouse retina and found that our model accurately predicted RGC responses at high spatiotemporal resolution. It identified multiple receptive fields reflecting the main excitatory and suppressive components of the response of each neuron. Significantly, our model accurately identified ON-OFF cells and distinguished their distinct ON and OFF receptive fields, and it demonstrated a diversity of suppressive receptive fields in the RGC population. In total, our method offers a rich description of RGC computation and sets a foundation for relating it to retinal circuitry.
Differences in the constituent fiber types contribute to the intermuscular variation in the timing of the developmental synapse elimination
Authors: Lee Young il 
Published: June 2019

AbstractThe emergence of a mature nervous system requires a significant refinement of the synaptic connections initially formed during development. Redundant synaptic connections are removed in a process known as synapse elimination. Synapse elimination has been extensively studied at the rodent neuromuscular junction (NMJ). Although several axons initially converge onto each postsynaptic muscle fiber, all redundant inputs are removed during early postnatal development until a single motor neuron innervates each NMJ. Neuronal activity as well as synaptic glia influence the course of synapse elimination. It is, however, unclear whether target muscle fibers are more than naïve substrates in this process. I examined the influence of target myofiber contractile properties on synapse elimination. The timing of redundant input removal in muscles examined correlates strongly with their proportion of slow myofibers: muscles with more slow fibers undergo elimination more slowly. Moreover, this intermuscular difference in the timing of synapse elimination appears to result from local differences in the rate of elimination on fast versus slow myofibers. These results, therefore, imply that differences in the constituent fiber types help account for the variation in the timing of the developmental synapse elimination between muscles and show that the muscle plays a role in the process.
Locally advanced rectal cancer transcriptomic-based secretome analysis reveals novel biomarkers useful to identify patients according to neoadjuvant chemoradiotherapy response
Authors: Canto Luisa Matos do , Cury Sarah Santiloni , Barros-Filho Mateus Camargo , Kupper Bruna Elisa Catin , Begnami Maria Dirlei Ferreira de Souza , Scapulatempo-Neto Cristovam , Carvalho Robson Francisco , Marchi Fabio Albuquerque , Olsen Dorte Aalund , Madsen Jonna Skov , Havelund Birgitte Mayland , Aguiar Samuel , Rogatto Silvia Regina 
Published: June 2019

AbstractMost patients with locally advanced rectal cancer (LARC) present incomplete pathological response (pIR) to neoadjuvant chemoradiotherapy (nCRT). Despite the efforts to predict treatment response using tumor-molecular features, as differentially expressed genes, no molecule has proved to be a strong biomarker. The tumor secretome analysis is a promising strategy for biomarkers identification, which can be assessed using transcriptomic data. We performed transcriptomic-based secretome analysis to select potentially secreted proteins using an in silico approach. The tumor expression profile of 28 LARC biopsies collected before nCRT was compared with normal rectal tissues (NT). The expression profile showed no significant differences between complete (pCR) and incomplete responders to nCRT. Genes with increased expression (pCR = 106 and pIR = 357) were used for secretome analysis based on public databases (Vesiclepedia, Human Cancer Secretome, and Plasma Proteome). Seventeen potentially secreted candidates (pCR = 1, pIR = 13 and 3 in both groups) were further investigated in two independent datasets (TCGA and GSE68204) confirming their over-expression in LARC and association with nCRT response (GSE68204). The expression of circulating amphiregulin and cMET proteins was confirmed in serum from 14 LARC patients. Future studies in liquid biopsies could confirm the utility of these proteins for personalized treatment in LARC patients.
Redox balance, metabolic fingerprint and physiological characterization in contrasting North East Indian rice for Aluminum stress tolerance
Authors: Awasthi Jay Prakash , Saha Bedabrata , Panigrahi Jogeswar , Yanase Emiko , Koyama Hiroyuki , Panda Sanjib Kumar 
Published: June 2019

AbstractAluminum (Al) toxicity is a serious problem for rice crop productivity in acidic soils worldwide. The present work was conducted to look out for the alteration in ROS homeostasis; metabolic fingerprint; and morphology in two contrasting Indica rice cultivars of North East India (NE India) to Al toxicity. Al stress led to excess accumulation of ROS (H2O2 and O2−), and this in turn induced ROS mediated cellular damage, as indicated by lipid peroxidation both qualitatively as well as quantitatively. This excessive ROS production also led to significant reduction in chlorophyll content and stomatal conductance. This was followed by the loss of photosynthetic efficiency as detected by chlorophyll fluorescence. This excessive damage due to ROS prompted us to check the anti-oxidative machinery. Antioxidants, especially enzymes (SOD, APX, POX, GR, CAT, DHAR, MDHAR) are very important players in maintenance of ROS homeostasis. In tolerant variety Disang, higher activity of these enzymes and vice versa in sensitive variety, was observed in response to Al treatment. The non-enzymatic antioxidants (proline, ascorbate and glutathione) also showed similar trend. Though the tolerant variety showed strong anti-oxidative machinery, it was unable to completely nullify the stress experienced by the seedlings. Organic acids are also important players in detoxification of Al stress through efflux in the rhizosphere. In tolerant genotype, citrate exudate was found to be more when compared to sensitive genotypes on exposure to high dose of Al. This is supported by higher abundance of FRDL4, a citrate transporter. Not only FRDL4, other stakeholders for Al stress response like ART1 and ALS1 depicted prominent transcript abundance in the tolerant variety. In conclusion, through this study detailed physiological and metabolic characterisation of two contrasting Indica rice varieties Disang and Joymati, native to NE India for Al tolerance was performed for the very first time.
Rosmarinic acid suppresses Alzheimer’s disease development by reducing amyloid β aggregation by increasing monoamine secretion
Authors: Hase Tomoki , Shishido Syun , Yamamoto So , Yamashita Rei , Nukima Haruka , Taira Shu , Toyoda Tsudoi , Abe Keiko , Hamaguchi Tsuyoshi , Ono Kenjiro , Noguchi-Shinohara Moeko , Yamada Masahito , Kobayashi Shoko 
Published: June 2019

AbstractA new mechanism is revealed by which a polyphenol, rosmarinic acid (RA), suppresses amyloid β (Aβ) accumulation in mice. Here we examined the brains of mice (Alzheimer’s disease model) using DNA microarray analysis and revealed that the dopamine (DA)-signaling pathway was enhanced in the group fed RA versus controls. In the cerebral cortex, the levels of monoamines, such as norepinephrine, 3,4-dihydroxyphenylacetic acid, DA, and levodopa, increased after RA feeding. The expression of DA-degrading enzymes, such as monoamine oxidase B (Maob), was significantly downregulated in the substantia nigra and ventral tegmental area, both DA synthesis regions. Followingin vitrostudies showing that monoamines inhibited Aβ aggregation, thisin vivostudy, in which RA intake increased concentration of monoamine by reducingMaobgene expression, builds on that knowledge by demonstrating that monoamines suppress Aβ aggregation. In conclusion, RA-initiated monoamine increase in the brain may beneficially act against AD.
Quantification of fixed adherent cells using a strong enhancer of the fluorescence of DNA dyes
Authors: Ligasová Anna , Koberna Karel 
Published: June 2019

AbstractCell quantification is widely used in basic or applied research. The current sensitive methods of cell quantification are exclusively based on the analysis of non-fixed cells and do not allow the simultaneous detection of various cellular components. A fast, sensitive and cheap method of the quantification of fixed adherent cells is described here. It is based on the incubation of DAPI- or Hoechst 33342-stained cells in a solution containing SDS. The presence of SDS results in the quick de-staining of DNA and simultaneously, in an up-to-1,000-fold increase of the fluorescence intensity of the used dyes. This increase can be attributed to the micelle formation of SDS. The method is sufficiently sensitive to reveal around 50–70 human diploid cells. It is compatible with immunocytochemical detections, the detection of DNA replication and cell cycle analysis by image cytometry. The procedure was successfully tested for the analysis of cytotoxicity. The method is suitable for the quantification of cells exhibiting low metabolic activity including senescent cells. The developed procedure provides high linearity and the signal is high for at least 20 days at room temperature. Only around 90 to 120 minutes is required for the procedure’s completion.
Coordination between vapor pressure deficit and CO2 on the regulation of photosynthesis and productivity in greenhouse tomato production
Authors: Jiao Xiao-Cong , Song Xiao-Ming , Zhang Da-Long , Du Qing-Jie , Li Jian-Ming 
Published: June 2019

AbstractThe high vapor pressure deficit (VPD) in some arid and semi-arid climates creates undesirable conditions for the growth of tomato plants (Solanum lycopersicumL., cv. Jinpeng). The global CO2concentration ([CO2]) has also risen in recent years to levels above 400 μmol·mol−1. However, the coordinated effect of VPD and [CO2] on tomato plant growth remains unclear, especially at VPDs of 5–6 kPa or even higher that are extremely detrimental to plant growth. Here, we explore the interaction of VPD and [CO2] on plant water status, stomatal characteristics, and gas exchange parameters in summer greenhouses in a semi-arid area. Plants were grown in four adjacent glass greenhouses with different environmental conditions: (i) high VPD + low [CO2] representing natural/control conditions; (ii) high VPD + high [CO2] representing enriched CO2; (iii) low VPD + low [CO2] representing reduced VPD; and (iv) low VPD + high [CO2] representing reduced VPD and enriched CO2. Reducing the VPD alleviated the water stress of the plant and increased the gas exchange area of the leaf, which was beneficial to the entry of CO2into the leaf. At this time, the increase of [CO2] was more beneficial to promote the photosynthetic rate and then improve the water use efficiency and yield.
The SRP signal sequence of KdpD
Authors: Pross Eva , Kuhn Andreas 
Published: June 2019

AbstractKdpD is a four-spanning membrane protein that has two large cytoplasmic domains at the amino- and at the carboxyterminus, respectively. During its biogenesis KdpD binds to the signal recognition particle (SRP) of Escherichia coli that consists of a 48-kDa protein Ffh and a 4.5S RNA. The protein is targeted to the inner membrane surface and is released after contacting the SRP receptor protein FtsY. The information within the KdpD protein that confers SRP interaction was found in the amino-terminal cytoplasmic domain of KdpD, particularly at residues 22–48. Within this sequence a Walker A motif is present at residues 30–38. To determine the actual sequence specificity to SRP, a collection of mutants was constructed. When the KdpD peptides (residues 22–48) were fused to sfGFP the targeting to the membrane was observed by fluorescence microscopy. Further, nascent chains of KdpD bound to ribosomes were purified and their binding to SRP was analysed by microscale thermophoresis. We found that the amino acid residues R22, K24 and K26 are important for SRP interaction, whereas the residues G30, G34 and G36, essential for a functional Walker A motif, can be replaced with alanines without affecting the affinity to SRP-FtsY and membrane targeting.
Ancient introgression drives adaptation to cooler and drier mountain habitats in a cypress species complex
Authors: Ma Yazhen , Wang Ji , Hu Quanjun , Li Jialiang , Sun Yongshuai , Zhang Lei , Abbott Richard J. , Liu Jianquan , Mao Kangshan 
Published: June 2019

AbstractIntrogression may act as an important source of new genetic variation to facilitate the adaptation of organisms to new environments, yet how introgression might enable tree species to adapt to higher latitudes and elevations remains unclear. Applying whole-transcriptome sequencing and population genetic analyses, we present an example of ancient introgression from a cypress species (Cupressus gigantea) that occurs at higher latitude and elevation on the Qinghai-Tibet Plateau into a related species (C. duclouxiana), which has likely aided the latter species to extend its range by colonizing cooler and drier mountain habitats during postglacial periods. We show that 16 introgressed candidate adaptive loci could have played pivotal roles in response to diverse stresses experienced in a high-elevation environment. Our findings provide new insights into the evolutionary history of Qinghai-Tibet Plateau plants and the importance of introgression in the adaptation of species to climate change.
Functional annotation and Bayesian fine-mapping reveals candidate genes for important agronomic traits in Holstein bulls
Authors: Jiang Jicai , Cole John B. , Freebern Ellen , Da Yang , VanRaden Paul M. , Ma Li 
Published: June 2019

AbstractA hundred years of data collection in dairy cattle can facilitate powerful studies of complex traits. Cattle GWAS have identified many associated genomic regions. With increasing numbers of cattle sequenced, fine-mapping of causal variants is becoming possible. Here we imputed selected sequence variants to 27,214 Holstein bulls that have highly reliable phenotypes for 35 production, reproduction, and body conformation traits. We performed single-marker scans for the 35 traits and multi-trait tests of the three trait groups, revealing 282 candidate QTL for fine-mapping. We developed a Bayesian Fine-MAPping approach (BFMAP) to integrate fine-mapping with functional enrichment analysis. Our fine-mapping identified 69 promising candidate genes, including ABCC9, VPS13B, MGST1, SCD, MKL1, CSN1S1 for production, CHEK2, GC, KALRN for reproduction, and TMTC2, ARRDC3, ZNF613, CCND2, FGF6 for conformation traits. Collectively, these results demonstrated the utility of BFMAP, identified candidate genes, and enhanced our understanding of the genetic basis of cattle complex traits.