bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integration of voltammetric analysis, protein electrophoresis and pH measurement for diagnosis of pleural effusions: a non-conventional diagnostic approach
Authors: Pipita Maria Elena , Santonico Marco , Pennazza Giorgio , Zompanti Alessandro , Fazzina Sara , Cavalieri Danilo , Bruno Francesca , Angeletti Silvia , Pedone Claudio , Incalzi Raffaele Antonelli 
Published: September 2020

AbstractPleural effusion is very common, but an etiologic diagnosis is often difficult. We used three unconventional diagnostic techniques (voltammetric analysis, protein electrophoresis and pH measurement) performed on pleural effusion to do a preliminary distinction between a neoplastic and a non-neoplastic origin. Pleural fluid samples were collected through thoracentesis, thoracoscopy, or post-surgery pleural drainage of 116 patients admitted to acute care wards. Samples were analyzed with the three unconventional techniques: voltammetric analysis using the BIONOTE system, capillary electrophoresis and pH measurement using a potentiometric method. The BIONOTE system is an innovative system that performs a cyclic voltammetric analysis of a biological liquid sample. The final output of the electrochemical analysis is an electrical pattern that represents a fingerprint of the analyzed sample and each sample has a different fingerprint. Data from the three unconventional diagnostic techniques were analyzed using partial least squares discriminant analysis to discriminate neoplastic from non-neoplastic effusions; we also evaluated sensitivity, specificity and percentage of correct classification. The mean age was 68 years (SD: 12); 78 (67.24%) participants were men. Results obtained from all the unconventional techniques employed showed that neoplastic and non-neoplastic pleural effusions were correctly classified in 80.2% of cases, with a sensitivity of 77% and specificity of 83%. The combined use of voltammetric analysis, protein electrophoresis and pH measurement of pleural fluid can easily and quickly distinguish a neoplastic from a non-neoplastic pleural effusion with reliable accuracy and represents an innovative diagnostic approach. In fact, this protocol can be executed in just few minutes directly in the patient's bed and it holds great promise to improve the prognosis and therapeutic chances.
Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum
Authors: Ben Chehida Yacine , Thumloup Julie , Schumacher Cassie , Harkins Timothy , Aguilar Alex , Borrell Asunción , Ferreira Marisa , Rojas-Bracho Lorenzo , Robertson Kelly M. , Taylor Barbara L. , Víkingsson Gísli A. , Weyna Arthur , Romiguier Jonathan , Morin Phillip A. , Fontaine Michael C. 
Published: September 2020

AbstractHistorical variation in food resources is expected to be a major driver of cetacean evolution, especially for the smallest species like porpoises. Despite major conservation issues among porpoise species (e.g., vaquita and finless), their evolutionary history remains understudied. Here, we reconstructed their evolutionary history across the speciation continuum. Phylogenetic analyses of 63 mitochondrial genomes suggest that porpoises radiated during the deep environmental changes of the Pliocene. However, all intra-specific subdivisions were shaped during the Quaternary glaciations. We observed analogous evolutionary patterns in both hemispheres associated with convergent evolution to coastal versus oceanic environments. This suggests that similar mechanisms are driving species diversification in northern (harbor and Dall’s) and southern species (spectacled and Burmeister’s). In contrast to previous studies, spectacled and Burmeister’s porpoises shared a more recent common ancestor than with the vaquita that diverged from southern species during the Pliocene. The low genetic diversity observed in the vaquita carried signatures of a very low population size since the last 5,000 years. Cryptic lineages within Dall’s, spectacled and Pacific harbor porpoises suggest a richer evolutionary history than previously suspected. These results provide a new perspective on the mechanisms driving diversification in porpoises and an evolutionary framework for their conservation.
Small-scale volcanic aerosols variability, processes and direct radiative impact at Mount Etna during the EPL-RADIO campaigns
Authors: Sellitto Pasquale , Salerno Giuseppe , La Spina Alessandro , Caltabiano Tommaso , Scollo Simona , Boselli Antonella , Leto Giuseppe , Zanmar Sanchez Ricardo , Crumeyrolle Suzanne , Hanoune Benjamin , Briole Pierre 
Published: September 2020

AbstractThe aerosol properties of Mount Etna’s passive degassing plume and its short-term processes and radiative impact were studied in detail during the EPL-RADIO campaigns (summer 2016–2017), using a synergistic combination of observations and radiative transfer modelling. Summit observations show extremely high particulate matter concentrations. Using portable photometers, the first mapping of small-scale (within $$\sim 20\,\hbox {km}$$

∼
20

km

from the degassing craters) spatial variability of the average size and coarse-to-fine burden proportion of volcanic aerosols is obtained. A substantial variability of the plume properties is found at these spatial scales, revealing that processes (e.g. new particle formation and/or coarse aerosols sedimentation) are at play, which are not represented with current regional scale modelling and satellite observations. Statistically significant progressively smaller particles and decreasing coarse-to-fine particles burden proportion are found along plume dispersion. Vertical structures of typical passive degassing plumes are also obtained using observations from a fixed LiDAR station constrained with quasi-simultaneous photometric observations. These observations are used as input to radiative transfer calculations, to obtain the shortwave top of the atmosphere (TOA) and surface radiative effect of the plume. For a plume with an ultraviolet aerosol optical depth of 0.12–0.14, daily average radiative forcings of $$-\;4.5$$

-

4.5

and $$-\;7.0\,\hbox {W/m}^2$$

-

7.0

W/m
2

, at TOA and surface, are found at a fixed location $$\sim 7\,\hbox {km}$$

∼
7

km

downwind the degassing craters. This is the first available estimation in the literature of the local radiative impact of a passive degassing volcanic plume.
LAMP3 induces apoptosis and autoantigen release in Sjögren’s syndrome patients
Authors: Tanaka Tsutomu , Warner Blake M. , Odani Toshio , Ji Youngmi , Mo Ying-Qian , Nakamura Hiroyuki , Jang Shyh-Ing , Yin Hongen , Michael Drew G. , Hirata Noriyuki , Suizu Futoshi , Ishigaki Satoko , Oliveira Fabiola Reis , Motta Ana Carolina F. , Ribeiro-Silva Alfredo , Rocha Eduardo M. , Atsumi Tatsuya , Noguchi Masayuki , Chiorini John A. 
Published: September 2020

AbstractPrimary Sjögren’s syndrome (pSS) is a complex autoimmune disease characterized by dysfunction of secretory epithelia with only palliative therapy. Patients present with a constellation of symptoms, and the diversity of symptomatic presentation has made it difficult to understand the underlying disease mechanisms. In this study, aggregation of unbiased transcriptome profiling data sets of minor salivary gland biopsies from controls and Sjögren’s syndrome patients identified increased expression of lysosome-associated membrane protein 3 (LAMP3/CD208/DC-LAMP) in a subset of Sjögren’s syndrome cases. Stratification of patients based on their clinical characteristics suggested an association between increased LAMP3 expression and the presence of serum autoantibodies including anti-Ro/SSA, anti-La/SSB, anti-nuclear antibodies. In vitro studies demonstrated that LAMP3 expression induces epithelial cell dysfunction leading to apoptosis. Interestingly, LAMP3 expression resulted in the accumulation and release of intracellular TRIM21 (one component of SSA), La (SSB), and α-fodrin protein, common autoantigens in Sjögren’s syndrome, via extracellular vesicles in an apoptosis-independent mechanism. This study defines a clear role for LAMP3 in the initiation of apoptosis and an independent pathway for the extracellular release of known autoantigens leading to the formation of autoantibodies associated with this disease.ClinicalTrials.gov Identifier: NCT00001196, NCT00001390, NCT02327884.
IMPROvER: the Integral Membrane Protein Stability Selector
Authors: Harborne Steven P. D. , Strauss Jannik , Boakes Jessica C. , Wright Danielle L. , Henderson James G. , Boivineau Jacques , Jaakola Veli-Pekka , Goldman Adrian 
Published: September 2020

AbstractIdentifying stabilising variants of membrane protein targets is often required for structure determination. Our new computational pipeline, the Integral Membrane Protein Stability Selector (IMPROvER) provides a rational approach to variant selection by employing three independent approaches: deep-sequence, model-based and data-driven. In silico tests using known stability data, and in vitro tests using three membrane protein targets with 7, 11 and 16 transmembrane helices provided measures of success. In vitro, individual approaches alone all identified stabilising variants at a rate better than expected by random selection. Low numbers of overlapping predictions between approaches meant a greater success rate was achieved (fourfold better than random) when approaches were combined and selections restricted to the highest ranked sites. The mix of information IMPROvER uses can be extracted for any helical membrane protein. We have developed the first general-purpose tool for selecting stabilising variants of $$\upalpha$$
α
-helical membrane proteins, increasing efficiency and reducing workload. IMPROvER can be accessed at http://improver.ddns.net/IMPROvER/.
Major QTL with pleiotropic effects controlling time of leaf budburst and flowering-related traits in walnut (Juglans regia L.)
Authors: Bükücü Şakir Burak , Sütyemez Mehmet , Kefayati Sina , Paizila Aibibula , Jighly Abdulqader , Kafkas Salih 
Published: September 2020

AbstractBreeding studies in walnut (Juglans regiaL.) are usually time consuming due to the long juvenile period and therefore, this study aimed to determine markers associated with time of leaf budburst and flowering-related traits by performing a genome-wide association study (GWAS). We investigated genotypic variation and its association with time of leaf budburst and flowering-related traits in 188 walnut accessions. Phenotypic data was obtained from 13 different traits during 3 consecutive years. We used DArT-seq for genotyping with a total of 33,519 (14,761 SNP and 18,758 DArT) markers for genome-wide associations to identify marker underlying these traits. Significant correlations were determined among the 13 different traits. Linkage disequilibrium decayed very quickly in walnut in comparison with other plants. Sixteen quantitative trait loci (QTL) with major effects (R2between 0.08 and 0.23) were found to be associated with a minimum of two phenotypic traits each. Of these QTL, QTL05 had the maximum number of associated traits (seven). Our study is GWAS for time of leaf budburst and flowering-related traits inJuglans regiaL. and has a strong potential to efficiently implement the identified QTL in walnut breeding programs.
The effect of Mass Drug Administration for trachoma on antibodies to Chlamydia trachomatis pgp3 in children
Authors: West Sheila K. , Munoz Beatriz , Mkocha Harran , Gaydos Charlotte A. , Quinn Thomas C. 
Published: September 2020

AbstractA serologic test for antibodies to chlamydia may be a useful tool for trachoma surveillance. However, little is known about the longitudinal stability of antibody status, especially following Mass Drug Administration (MDA), which is critical to understanding serostatus in trachoma-endemic areas. A longitudinal cohort of 1908 children ages 1–9 years in Tanzania from 50 communities were followed at baseline and for 6 months after MDA. They were evaluated for clinical trachoma, conjunctival swabs were tested for chlamydial infection using GeneXpert platform, and blood spots were collected on filter paper and dried to test for antibodies to Chlamydia trachomatis pgp3 using the Luminex platform. 6.3% of children in the study had infection, and coverage with MDA was 97%. 670 (35%) were sero-positive for pgp3 antibodies at baseline, and 4.0% of these seroreverted to negative following MDA. Of those seronegative at baseline, 3.6% seroconverted. The individual change in log median fluorescence intensity(MFI-BG) values was -0.15 overall (p < .001). Seroconversion rates were lower following MDA and seroreversion rates were slightly higher compared to rates in this same cohort in the absence of MDA. MDA has a small effect on reduction of MFI-BG.
Hemoglobin stimulates vigorous growth of Streptococcus pneumoniae and shapes the pathogen's global transcriptome
Authors: Akhter Fahmina , Womack Edroyal , Vidal Jorge E. , Le Breton Yoann , McIver Kevin S. , Pawar Shrikant , Eichenbaum Zehava 
Published: September 2020

AbstractStreptococcus pneumoniae (Spn) must acquire iron from the host to establish infection. We examined the impact of hemoglobin, the largest iron reservoir in the body, on pneumococcal physiology. Supplementation with hemoglobin allowed Spn to resume growth in an iron-deplete medium. Pneumococcal growth with hemoglobin was unusually robust, exhibiting a prolonged logarithmic growth, higher biomass, and extended viability in both iron-deplete and standard medium. We observed the hemoglobin-dependent response in multiple serotypes, but not with other host proteins, free iron, or heme. Remarkably, hemoglobin induced a sizable transcriptome remodeling, effecting virulence and metabolism in particular genes facilitating host glycoconjugates use. Accordingly, Spn was more adapted to grow on the human α − 1 acid glycoprotein as a sugar source with hemoglobin. A mutant in the hemoglobin/heme-binding protein Spbhp-37 was impaired for growth on heme and hemoglobin iron. The mutant exhibited reduced growth and iron content when grown in THYB and hemoglobin. In summary, the data show that hemoglobin is highly beneficial for Spn cultivation in vitro and suggest that hemoglobin might drive the pathogen adaptation in vivo. The hemoglobin receptor, Spbhp-37, plays a role in mediating the positive influence of hemoglobin. These novel findings provide intriguing insights into pneumococcal interactions with its obligate human host.
Effect of elicitors on holm oak somatic embryo development and efficacy inducing tolerance to Phytophthora cinnamomi
Authors: Morcillo M. , Sales E. , Ponce L. , Guillén A. , Segura J. , Arrillaga I. 
Published: September 2020

AbstractHolm oak trees (Quercus ilex L.) mortality is increasing worryingly in the Mediterranean area in the last years. To a large degree this mortality is caused by the oomycete Phytophthora spp., which is responsible for forest decline and dieback in evergreen oak forest areas of the southwestern Iberian Peninsula. This study is based on the possibility of applying chemical elicitors or filtered oomycete extracts to holm oak somatic embryos (SE) in order to induce epigenetic memory, priming, that may increase tolerance to the pathogen in future infections. To this end, we first examined the effect of priming treatments on SE development and its oxidative stress state, to avoid elicitors that may cause damage to embryogenic tissues. Both, the sterile oomycete extracts and the chemical elicitor methyl jasmonate (MeJA) did not produce any detrimental effect on SE growth and development, unlike the elicitors benzothiadiazole (BTH) and p-aminobenzoic acid (PABA) that reduced the relative weight gain and resulted in necrotic and deformed SE when were applied at high concentrations (25 µM BTH or 50 µM PABA) in accordance with their high malondialdehyde content. No significant differences among elicitation treatments were found in dual culture bioassays, although those SEs elicited with 50 µM MeJA increased H2O2 production after challenged against active oomycete indicating the activation of stress response. Since this elicitation treatment did not produce any adverse effect in the embryogenic process we suggest that could be used in further priming experiments to produce holm oak plants adapted to biotic stress.
Honey isomaltose contributes to the induction of granulocyte-colony stimulating factor (G-CSF) secretion in the intestinal epithelial cells following honey heating
Authors: Xu Xin , Asai Koshi , Kato Daiki , Ishiuchi Kan’ichiro , Ding Kewen , Tabuchi Yoshiaki , Ota Misato , Makino Toshiaki 
Published: September 2020

AbstractWe have previously discovered that heated honey but not unheated honey could induce the secretion of granulocyte-colony stimulating factor (G-CSF) in the MCE301 intestinal epithelial cells. The objective of this study was to identify compounds in honey that could contribute to this activity. We bought several kinds of commercial honey samples derived from different flowers, as well as corn syrup samples, in the markets of China and Japan, and heated them at 180 °C for 30 min. MCE301 cells were treated with the medium containing the samples, and G-CSF levels in the medium were measured by ELISA. By comparing their activities and sugar contents, we discovered that isomaltose was primarily implicated. The optimum heating conditions for isomaltose were at 180 °C for 60 min or at 200 °C for 15–30 min, and these time- and temperature-dependencies were similar to those of honey in our previous study. When heated isomaltose was partitioned by dialysis, the active ingredients were transferred into a high-molecular-weight fraction. By size-exclusion HPLC analysis, the average molecular weight of heated isomaltose was 790 kDa. When heated isomaltose was hydrolyzed by acids, glucose was subsequently produced. Maltose, sucrose, turanose, and trehalose did not exhibited any activity when heated at 180 °C for 60 min, indicating that the glucose groups with α(1 → 6)-binding in the isomaltose molecule play important roles in its activity when oxidatively polymerized by heat. The stimulating activity of heated isomaltose was inhibited by toll-like receptor 4 (TLR4) inhibitor, suggesting that heated isomaltose activates TLR4 to induce G-CSF. Since G-CSF is clinically used for cancer patients to accelerate their recovery from neutropenia following chemotherapy or accompanied with aplastic anemia, these findings indicate that honey which contains high level of isomaltose could improve immunosuppressive conditions when honey is heated, and that heated isomaltose might be of potential therapeutic use in patients with compromised immunity caused by chemotherapeutic agents.
Formalin-fixed paraffin-embedded renal biopsy tissues: an underexploited biospecimen resource for gene expression profiling in IgA nephropathy
Authors: Cox Sharon Natasha , Chiurlia Samantha , Divella Chiara , Rossini Michele , Serino Grazia , Bonomini Mario , Sirolli Vittorio , Aiello Francesca B. , Zaza Gianluigi , Squarzoni Isabella , Gangemi Concetta , Stangou Maria , Papagianni Aikaterini , Haas Mark , Schena Francesco Paolo 
Published: September 2020

AbstractPrimary IgA nephropathy (IgAN) diagnosis is based on IgA-dominant glomerular deposits and histological scoring is done on formalin-fixed paraffin embedded tissue (FFPE) sections using the Oxford classification. Our aim was to use this underexploited resource to extract RNA and identify genes that characterize active (endocapillary–extracapillary proliferations) and chronic (tubulo-interstitial) renal lesions in total renal cortex. RNA was extracted from archival FFPE renal biopsies of 52 IgAN patients, 22 non-IgAN and normal renal tissue of 7 kidney living donors (KLD) as controls. Genome-wide gene expression profiles were obtained and biomarker identification was carried out comparing gene expression signatures a subset of IgAN patients with active (N = 8), and chronic (N = 12) renal lesions versus non-IgAN and KLD. Bioinformatic analysis identified transcripts for active (DEFA4,TNFAIP6,FAR2) and chronic (LTB,CXCL6, ITGAX) renal lesions that were validated by RT-PCR and IHC. Finally, two of them (TNFAIP6 for active and CXCL6 for chronic) were confirmed in the urine of an independent cohort of IgAN patients compared with non-IgAN patients and controls. We have integrated transcriptomics with histomorphological scores, identified specific gene expression changes using the invaluable repository of archival renal biopsies and discovered two urinary biomarkers that may be used for specific clinical decision making.
Host phylogeny and life history stage shape the gut microbiome in dwarf (Kogia sima) and pygmy (Kogia breviceps) sperm whales
Authors: Denison Elizabeth R. , Rhodes Ryan G. , McLellan William A. , Pabst D. Ann , Erwin Patrick M. 
Published: September 2020

AbstractGut microbiomes perform crucial roles in host health and development, but few studies have explored cetacean microbiomes especially deep divers. We characterized the gut microbiomes of stranded dwarf (Kogia sima) and pygmy (K. breviceps) sperm whales to examine the effects of phylogeny and life stage on microbiome composition and diversity. 16S rRNA gene sequence analysis revealed diverse gut communities (averaging 674 OTUs) dominated by a few symbiont taxa (25 OTUs accounted for 64% of total relative abundance). Both phylogeny and life stage shaped community composition and diversity, with species-specific microbiome differences present early in life. Further analysis showed evidence of microbiome convergence with host maturity, albeit through different processes: symbiont ‘accumulation’ in K. sima and ‘winnowing’ in K. breviceps, indicating different methods of community assembly during host development. Furthermore, culture-based analyses yielded 116 pure cultures matching 25 OTUs, including one isolate positive for chitin utilization. Our findings indicate that kogiid gut microbiomes are highly diverse and species-specific, undergo significant shifts with host development, and can be cultivated on specialized media under anaerobic conditions. These results enhance our understanding of the kogiid gut microbiome and may provide useful information for symbiont assessment in host health.
Comparative proteomic profiling reveals mechanisms for early spinal cord vulnerability in CLN1 disease
Authors: Nelvagal Hemanth R. , Hurtado Maica Llavero , Eaton Samantha L. , Kline Rachel A. , Lamont Douglas J. , Sands Mark S. , Wishart Thomas M. , Cooper Jonathan D. 
Published: September 2020

AbstractCLN1 disease is a fatal inherited neurodegenerative lysosomal storage disease of early childhood, caused by mutations in the CLN1 gene, which encodes the enzyme Palmitoyl protein thioesterase-1 (PPT-1). We recently found significant spinal pathology in Ppt1-deficient (Ppt1−/−) mice and human CLN1 disease that contributes to clinical outcome and precedes the onset of brain pathology. Here, we quantified this spinal pathology at 3 and 7 months of age revealing significant and progressive glial activation and vulnerability of spinal interneurons. Tandem mass tagged proteomic analysis of the spinal cord of Ppt1−/−and control mice at these timepoints revealed a significant neuroimmune response and changes in mitochondrial function, cell-signalling pathways and developmental processes. Comparing proteomic changes in the spinal cord and cortex at 3 months revealed many similarly affected processes, except the inflammatory response. These proteomic and pathological data from this largely unexplored region of the CNS may help explain the limited success of previous brain-directed therapies. These data also fundamentally change our understanding of the progressive, site-specific nature of CLN1 disease pathogenesis, and highlight the importance of the neuroimmune response. This should greatly impact our approach to the timing and targeting of future therapeutic trials for this and similar disorders.