bluuebunny/crossref_metadata_2025_split huggingface dataset:
SH3KBP1 scaffolds endoplasmic reticulum and controls skeletal myofibers architecture and integrity
Authors: Guiraud Alexandre , Christin Emilie , Couturier Nathalie , Kretz-Remy Carole , Janin Alexandre , Ghasemizadeh Alireza , Durieux Anne-Cécile , Arnould David , Romero Norma Beatriz , Bui Mai Thao , Buchman Vladimir L. , Julien Laura , Bitoun Marc , Gache Vincent 
Published: May 2020

AbstractThe building block of skeletal muscle is the multinucleated muscle fiber, formed by the fusion of hundreds of mononucleated precursor cells, myoblasts. In the normal course of muscle fiber development or regeneration, myonuclei are actively positioned throughout muscular development and adopt special localization in mature fibers: regular spacing along muscle fibers periphery, raising the notion of MyoNuclear Domains (MNDs). There is now growing support for a direct connection between myonuclear positioning and normal function of muscles, but how myonuclei affects muscle function remains poorly characterized.To identify new factors regulating forces applied on myonuclei in muscles fibers, we performed a siRNA screen and identified SH3KBP1 as a new factor controlling myonuclear positioning in early phases of myofibers formation. Depletion of SH3KBP1 induces a reset of MNDs establishment in mature fibers reflected by a dramatic reduction in pairwise distance between myonuclei. We show that SH3KBP1 scaffolds Endoplasmic Reticulum (ER) in myotubes that in turn controls myonuclei velocity and localization and thus myonuclear domains settings. Additionally, we show that in later phases of muscle maturation, SH3KBP1 contributes to the formation and maintenance of Sarcoplasmic Reticulum (SR) and Transverse-tubules (T-tubules). We also demonstrate that in muscle fibers, GTPase dynamin-2 (DNM2) binds to SH3 domains of SH3KBP1. Interestingly, we observed thatSh3kbp1mRNA is up regulated in a mouse model harboring the most frequent mutation for Autosomal Dominant CentroNuclear Myopathy (AD-CNM):Dnm2+/R465W. SH3KBP1 thus appears as a compensation mechanism in this CNM model since its depletion contributes to an increase of CNM-like phenotypes (reduction of muscle fibers Cross-section Areas (CSA) and increase in slow fibers content).Altogether our results identify SH3KBP1 as a new regulator of myonuclear domains establishment in the early phase of muscle fibers formation through ER scaffolding and later in myofibers integrity through T-tubules scaffolding/maintenance.SummaryMyonuclei are actively positioned throughout muscular development. Guiraud, Christin, Couturieret alshow that SH3KBP1 scaffolds the ER through Calnexin interaction and controls myonuclei motion during early steps of muscle fibers formation. Besides SH3KBP1 participates in cell fusion and T-tubules formation/maintenance in mature skeletal muscle fibers and contributes to slow-down CNM-like phenotypes.
A Comparative Analysis of Different Feature Extraction Techniques for Palm-print Images
Authors: Pratyasha Prateek , Swarnkar Bharati , Padhy Aditya Prasad 
Published: May 2020

AbstractIn this advanced decade, automatic identification of individuals is a significant achievement due to the high demand of security system. Hence, individual recognition using biometrics data is leading in the field of image processing. Although biometrics data analysis using thumb impression and finger-prints are very popular since many years, sometimes it leads to false acceptance and rejection if any physical change occurs in the finger ridges. There may be a high risk of hacking the biometrics data which is now a big challenge for cyber security employees. This paper captures the palm-print images of individuals as referred biometrics data for individual recognition. The research work is based on one of the prior issue that is feature extraction to extract the features of palm-print image such as principle lines, textures, ridges and pores etc. For this, some of the feature extraction techniques such as Derivatives of Gaussian filter (DoG), Discrete Cosine Transform (DCT), Fast Fourier Transform (FFT) and competitive coding. Two types of filters: Gaussian Filter and Gabor filter are combined with each of the feature extraction scheme for the matching of sampled image with testing image. In the result, the error rates of each of the feature extraction algorithms are compared to recognize the palm image of two different individuals.
Seasonal dynamics of methane cycling microbial communities in Amazonian floodplain sediments
Authors: Gontijo Júlia B. , Venturini Andressa M. , Yoshiura Caio A. , Borges Clovis D. , Moura José Mauro S. , Bohannan Brendan J. M. , Nüsslein Klaus , Rodrigues Jorge L. Mazza , Paula Fabiana S. , Tsai Siu M. 
Published: May 2020

AbstractThe Amazonian floodplain forests are dynamic ecosystems of great importance for the regional hydrological and biogeochemical cycles and provide a significant contribution to the global carbon balance. Unique geochemical factors may drive the microbial community composition and, consequently, affect CH4emissions across floodplain areas. Here we provide the first report of thein situseasonal dynamics of CH4cycling microbial communities in Amazonian floodplains. We asked how abiotic factors may affect both overall and CH4cycling microbial communities and further investigated their responses to seasonal changes. We collected sediment samples during wet and dry seasons from three different types of floodplain forests, along with upland forest soil samples, from the Eastern Amazon, Brazil. We used high-resolution sequencing of archaeal and bacterial 16S rRNA genes combined with real-time PCR to quantify Archaea and Bacteria, as well as key functional genes indicative of the methanogenic (methyl coenzyme-M reductase –mcrA) and methanotrophic (particulate methane monooxygenase –pmoA) metabolisms. Methanogens were found to be present in high abundance in floodplain sediments and they seem to resist to dramatic seasonal environmental changes. Methanotrophs known to use different pathways to oxidise CH4were detected, including anaerobic archaeal and bacterial taxa, indicating that a wide metabolic diversity may be harboured in this highly variable environment. The floodplain environmental variability, which is affected by the river origin, drives not only the sediment chemistry, but also the composition of the microbial communities. The results presented may contribute to the understanding of the current state of CH4cycling in this region.
Where does it go? The fate of thiocyanate in the aquarium water and blood plasma ofAmphiprion clarkiiafter exposure to cyanide
Authors: Bonanno J. Alexander , Breen Nancy E. , Tlusty Michael F. , Andrade Lawrence J. , Rhyne Andrew L. 
Published: May 2020

ABSTRACTThe illegal practice of cyanide fishing continues to damage coral reef ecosystems throughout the Indo-Pacific. To combat this destructive fishing method, a simple, reliable test to detect whether or not a fish has been captured using cyanide (CN) is needed. This study analyzed the toxicokinetics of acute, pulsed CN exposure as well as chronic exposure to thiocyanate (SCN), the major metabolite of CN, in the clownfish species,Amphiprion clarkii. Fish were pulse exposed to 50 ppm CN for 20 or 45 seconds or chronically exposed to 100 ppm SCN for 12 days. Blood plasma levels of SCN were measured following derivatization to SCN-bimane using an Acquity UPLC I-Class and Q-Exactive hybrid Quadrupole-Orbitrap HRAM mass spectrometer or directly by HPLC-UV. After exposure to CN, depending on the duration of exposure, SCN plasma levels reached a maximum concentration (300–470 ppb) 0.13–0.17 days after exposure, had a 0.1 to 1.2 day half-life, and often did not return to baseline levels. The half-life of plasma SCN after direct exposure to SCN was found to be 0.13 days, similar to the CN exposure, and that SCN in the holding water would often drop below detection. Finally, we observed that when a fish, never exposed to SCN, was placed in aquarium water spiked with SCN, there was a steady decrease in aqueous SCN concentration over 24 hours until it could no longer be detected. This pattern was repeated with a second sequential dose. These results demonstrate thatA. clarkiido not excrete SCN after CN exposure, but in fact can absorb low concentrations of SCN from water, refuting several publications. It appears thatA. clarkiiexhibit a classic two compartment model where SCN is rapidly eliminated from the blood plasma and is distributed throughout the tissue but not excreted in their urine. This study demonstrates that SCN may be used as a marker of CN exposure only if fish are tested shortly after exposure. There is species specific variability in response to CN, and studies of other taxa need to be performed before this test can be deployed in the field.
Dexmedetomidine attenuates the injury of H9C2 cardiomyocytes under Hypoxia/reoxygenation condition partly through the inhibition of endoplasmic reticulum stress
Authors: Zhu Zhipeng , Ling Xiaoyan , Zhou Hongmei , Zhang Caijun 
Published: May 2020

BackgroundMyocardial ischemia-reperfusion injury (MIRI) has been confirmed to induce endoplasmic reticulum stress(ERS) during downstream cascade reaction when myocardial cell function keep deteriorating to a certain degree. The fact of matter is the clinical inconsistence with experimental outcomes still exist due to the mechanism has not been entirely clarified. Dexmedetomidine (DEX), a new generation anti-inflammatory and organ protector, has been testified can attenuate the IRI of heart. This study aimed to find out if DEX had the capacity to protect the injured cardiomyocytes under in vitro hypoxia/reoxygenation circumstance and if the ERS was totally or partly intervened.MethodsH9C2 cells were subjected to cytotoxicity detection for 24h with DEX normally cultivated in several different concentrations. The proper hypoxia/reoxygenation (H/R) model parameter were concluded by the cell viability and injuries by cell counting kit-8(CCK8) and lactate dehydrogenase (LDH) release, when undergoing hypoxic condition for 3 h and reoxygenated for 3h, 6h,12h, and 24h, respectively. Also, the above index was assessed for H/R cardiomyocytes cultivated by various concentrations of DEX. The apoptosis, expression of) Glucose-regulated protein 78(GRP78), C/EBP homologous protein (CHOP), and caspase-12 were also examined in all groups.Results1, 5 and 10 μM DEX in normal culture could significantly promote the proliferation of H9C2 (> 80%); the activity of H9c2 cells decreased to 62.67% (P < 0.05) at 3h of reoxygenation and to 36% at 6h of reoxygenation followed by 3h anoxic treatment; The cell viability of H9c2 cells in H/R groups incubated with 1 μM DEX increased 61.3%, and the LDH concentration in the supernatant was effectively lowered (−13.7, P < 0.05); H/R dramatically decreased the proportion of flow cytometry apoptosis and increased the expression of GRP78, CHOP and caspase-12, while both DEX and 4-phenyl butyric acid (4-PBA) could significantly reverse those above indicators. Additionally, DEX could induce deeper alterations than 4-PBA on the basis of H/R.Conclusion1 μM DEX can dramatically attended the cell injuries, apoptosis, the expression of GRP78, CHOP and caspase-12 of H9C2 induced by 3h’ hypoxia and 3h’s reoxygenation. moreover, the functions of DEX went beyond the inhibition of ERS under this situation.
Neurocognitive processing efficiency for non-alarm rather than alarm signaling in human scream calls
Authors: Frühholz Sascha , Dietziker Joris , Staib Matthias , Trost Wiebke 
Published: May 2020

ABSTRACTAcross many species, scream calls signal the affective significance of events to other agents. Scream calls were often supposed to be of generic alarming and fearful nature to signal potential threats including their instantaneous, involuntary, and accurate recognition by perceivers. However, scream calls are more diverse in their affective signaling nature than being limited to fearfully alarm a threat, and thus the broader sociobiological relevance of various scream types is unclear. Here we used four different psychoacoustic, perceptual decision-making, and neuroimaging experiments in humans to demonstrate, first, the existence of at least six generic and psycho-acoustically distinctive types of scream calls of both an alarming and a non-alarming nature, rather than being limited to only screams caused by fear or aggression. Second, based on perceptual and processing sensitivity measures for decision-making during scream recognition, we found that alarming screams (with some exceptions) were overall discriminated the worst, were responded to the slowest and were associated with the lower perceptual sensitivity for their recognition compared with non-alarm screams. Third, the neural processing of alarm compared with non-alarm screams during an implicit processing task elicited only minimal neural signal and connectivity in perceivers, contrary to the frequent assumption of a threat processing bias of the primate neural system. These findings show that scream calls are more diverse in their signaling and communicative nature in humans and that especially non-alarming screams, and positive screams in particular, seem to have higher efficiency in the cognitive, neural, and communicative processing in humans.
Developingin vivoassays for investigation of p75NTRand NRH1 transmembrane domain cleavage events using zebrafish embryos
Authors: Jayne Tanya , Newman Morgan , Lardelli Michael 
Published: May 2020

Abstractγ-secretase is an important protease complex responsible for the cleavage of over 100 substrates within their transmembrane domains. γ-secretase acts in Alzheimer’s disease by cleavage of AMYLOID BETA (A4) PRECURSOR PROTEIN to produce aggregation-prone Amyloid beta peptide. Other γ-secretase substrates such as p75NTRare also relevant to Alzheimer’s disease. How γ-secretase cleavage site specificity is determined is still unclear. A previous study usingXenopus laevisto investigate the proteolytic processing of p75NTRand its homolog NRH1 found that transmembrane cleavage of NRH1 was not sensitive to the γ-secretase inhibitor DAPT, suggesting that it is not processed by γ-secretase. To investigate this further, we identified zebrafish orthologues of the genes p75NTRand NRH1 and developedin vivoassays to assess cleavage of the resultant p75NTRand Nrh1 proteins. Our observations from these assays in zebrafish are consistent with theXenopus laevisstudy. Inhibition of γ-secretase by DAPT treatment results in accumulation of uncleaved p75NTRsubstrate, while cleavage of Nrh1 is not affected. This supports that p75NTRis cleaved by γ-secretase while Nrh1 is cleaved by a separate γ-secretase-like activity. We extended our approach by generating a chimeric Nrh1 protein in which the Nrh1 transmembrane domain was replaced by that of p75NTR, in an attempt to determine whether it is the p75NTRTMD that confers susceptibility for γ-secretase cleavage. Our results from analysis of this chimeric protein revealed that the p75NTRtransmembrane domain alone is insufficient to confer γ-secretase cleavage susceptibility. This is not completely unexpected, as there is evidence to suggest that other factors are crucial for selection/cleavage by the γ-secretase complex. We have established a system in which we can now attempt to dissect the structural basis for γ-secretase cleavage specificity and evolution.
Circumstances and factors of sleep-related sudden infancy deaths in Japan
Authors: Osawa Motoki , Ueno Yasuhiro , Ikeda Noriaki , Ikematsu Kazuya , Yamamoto Takuma , Irie Wataru , Kozawa Shuji , Kotani Hirokazu , Hamayasu Hideki , Murase Takehiko , Shingu Keita , Sugimoto Marie , Nagao Ryoko , Kakimoto Yu 
Published: May 2020

AbstractBackgroundSudden unexpected death in infancy (SUDI) comprises both natural and unnatural causes of death. However, a few epidemiological surveys have investigated SUDI in Japan.ObjectiveThis retrospective study was conducted to investigate the recent trends of circumstances and risk factors of sleep-related SUDI cases.MethodsForensic pathology sections from eight universities participated in the selection of subjects from 2013 to 2018. Data obtained from the checklist form were analyzed based on information at postmortem.ResultsThere were 259 SUDI cases consisting of 145 male infants and 114 female infants with a mean birth weight of 2888 ± 553 and 2750 ± 370 g, respectively. Deaths most frequently occurred among infants at 1 month of age (18%). According to population-based analyses, the odds ratio (95% confidence interval) of mother’s age ≤19 years was 11.1 (6.9–17.7) compared with ages 30–39. The odds ratio for the fourth- and later born infants was 5.2 (3.4–7.9) compared with the frequency of first-born infants. The most frequent time of day for discovery was between 7 and 8 o’clock. Co-sleeping was recorded for 61%, and the prone position was found for 40% of cases at discovery. Mother’s smoking habit exhibited an adds ratio of 4.5 (2.9–5.8).ConclusionThis study confirmed the trends that have been observed for sudden infant death syndrome; particularly, very high odds ratios were evident for teenage mothers and later birth order in comparison with those in other developed countries. The child of a young mother tended to die within 2 months of age. To our knowledge, this is the first report of an extensive survey of sleep-related SUDI in Japan.
Genetic variation associated with PPO-inhibiting herbicide tolerance in sorghum
Authors: Adhikari Pragya , Goodrich Emma , Fernandes Samuel B. , Lipka Alexander E. , Tranel Patrick , Brown Patrick , Jamann Tiffany M. 
Published: May 2020

AbstractHerbicide application is crucial for weed management in most crop production systems, but for sorghum herbicide options are limited. Sorghum is sensitive to residual protoporphyrinogen oxidase (PPO)- inhibiting herbicides, such as fomesafen, and a long re-entry period is required before sorghum can be planted after its application. Improving sorghum for tolerance to such residual herbicides would allow for increased sorghum production and the expansion of herbicide options for growers. To investigate the underlying mechanism of tolerance to residual fomesafen, a genome-wide association mapping study was conducted using the sorghum biomass panel (SBP) and field-collected data, and a greenhouse assay was developed to confirm the field phenotypes. A total of 26 significant SNPs (FDR<0.05), spanning a 215.3 kb region, were detected on chromosome 3. The ten most significant SNPs included two in genic regions (Sobic.003G136800, and Sobic.003G136900) and eight SNPs in the intergenic region encompassing the genes Sobic.003G136700, Sobic.003G136800, Sobic.003G137000, Sobic.003G136900, and Sobic.003G137100. The gene Sobic.003G137100 (PPXI), which encodes the PPO1 enzyme, one of the targets of PPO-inhibiting herbicides, was located 12kb downstream of the significant SNP S03_13152838. We found thatPPXIis highly conserved in sorghum and expression does not significantly differ between tolerant and sensitive sorghum lines. Our results suggest thatPPXImost likely does not underlie the observed herbicide tolerance. Instead, the mechanism underlying herbicide tolerance in the SBP is likely metabolism-based resistance, possibly regulated by the action of multiple genes. Further research is necessary to confirm candidate genes and their functions.
Network-based atrophy modelling in the common epilepsies: a worldwide ENIGMA study
Authors: Larivière Sara , Rodríguez-Cruces Raúl , Royer Jessica , Caligiuri Maria Eugenia , Gambardella Antonio , Concha Luis , Keller Simon S. , Cendes Fernando , Yasuda Clarissa , Bonilha Leonardo , Gleichgerrcht Ezequiel , Focke Niels K. , Domin Martin , Podewills Felix von , Langner Soenke , Rummel Christian , Wiest Roland , Martin Pascal , Kotikalapudi Raviteja , O’Brien Terence J. , Sinclair Benjamin , Vivash Lucy , Desmond Patricia M. , Alhusaini Saud , Doherty Colin P. , Cavalleri Gianpiero L. , Delanty Norman , Kälviäinen Reetta , Jackson Graeme D. , Kowalczyk Magdalena , Mascalchi Mario , Semmelroch Mira , Thomas Rhys H. , Soltanian-Zadeh Hamid , Davoodi-Bojd Esmaeil , Zhang Junsong , Lenge Matteo , Guerrini Renzo , Bartolini Emanuele , Hamandi Khalid , Foley Sonya , Weber Bernd , Depondt Chantal , Absil Julie , Carr Sarah J. A. , Abela Eugenio , Richardson Mark P. , Devinsky Orrin , Severino Mariasavina , Striano Pasquale , Tortora Domenico , Hatton Sean N. , Vos Sjoerd B. , Duncan John S. , Whelan Christopher D. , Thompson Paul M. , Sisodiya Sanjay M. , Bernasconi Andrea , Labate Angelo , McDonald Carrie R. , Bernasconi Neda , Bernhardt Boris C. 
Published: May 2020

SUMMARYEpilepsy is increasingly conceptualized as a network disorder. In this cross-sectional mega-analysis, we integrated neuroimaging and connectome analysis to identify network associations with atrophy patterns in 1,021 adults with epilepsy compared to 1,564 healthy controls from 19 international sites. In temporal lobe epilepsy, areas of atrophy co-localized with highly interconnected cortical hub regions, whereas idiopathic generalized epilepsy showed preferential subcortical hub involvement. These morphological abnormalities were anchored to the connectivity profiles of distinct disease epicenters, pointing to temporo-limbic cortices in temporal lobe epilepsy and fronto-central cortices in idiopathic generalized epilepsy. Indices of progressive atrophy further revealed a strong influence of connectome architecture on disease progression in temporal lobe, but not idiopathic generalized, epilepsy. Our findings were reproduced across individual sites and single patients, and were robust across different analytical methods. Through worldwide collaboration in ENIGMA-Epilepsy, we provided novel insights into the macroscale features that shape the pathophysiology of common epilepsies.
Chromatin Regulates Bipartite-Classified Small RNA Expression to Maintain Epigenome Homeostasis in Arabidopsis
Authors: Papareddy Ranjith K. , Páldi Katalin , Paulraj Subramanian , Kao Ping , Nodine Michael D. 
Published: May 2020

AbstractEukaryotic genomes are partitioned into euchromatic and heterochromatic domains to regulate gene expression and other fundamental cellular processes. However, chromatin is dynamic during growth and development, and must be properly re-established after its decondensation. Small interfering RNAs (siRNAs) promote heterochromatin formation in eukaryotes, but little is known about how chromatin regulates siRNA transcription. We demonstrated that thousands of transposable elements (TEs) produce exceptionally high levels of siRNAs inArabidopsis thalianaembryos. Depending on whether they are located in euchromatic or heterochromatic regions of the genome, bipartite-classified TEs generate siRNAs throughout embryogenesis according to two distinct patterns. siRNAs are transcribed in embryos and required to direct the re-establishment of DNA methylation on TEs from which they are derived in the new generation. Decondensed chromatin also permits the production of 24-nt siRNAs from heterochromatic TEs during post-embryogenesis, and siRNA production from bipartite-classified TEs is controlled by their chromatin states. Decondensation of heterochromatin in response to developmental, and perhaps environmental, cues promotes the transcription and function of siRNAs in plants. Our results indicate that chromatin-mediated siRNA transcription provides a cell-autonomous homeostatic control mechanism to reconstitute pre-existing chromatin states during growth and development including those that ensure silencing of TEs in the future germ line.