bluuebunny/crossref_metadata_2025_split huggingface dataset:
The rpl23 gene and pseudogene are hotspots of illegitimate recombination in barley chloroplast mutator seedlings
Authors: Lencina F. , Landau A. M. , Petterson M. E. , Pacheco M. G. , Kobayashi K. , Prina A. R. 
Published: July 2019

AbstractPreviously, through a TILLING (Targeting Induced Local Lesions in Genomes) approach applied on barley chloroplast mutator (cpm) seedlings a high frequency of polymorphisms in the rpl23 gene was detected. All the polymorphisms corresponded to five differences already known to exist in nature between the rpl23 gene located in the inverted repeats (IRs) and the rpl23 pseudogene located in the large single copy region (LSC). In this investigation, polymorphisms in the rpl23 gene were verified and besides, a similar situation was found for the pseudogene in cpm seedlings. On the other hand, no polymorphisms were found in any of those loci in 40 wild type barley seedlings. Those facts and the independent occurrence of polymorphisms in the gene and pseudogene in individual seedlings suggest that the detected polymorphisms initially arose from gene conversion between gene and pseudogene. Moreover, an additional recombination process involving small recombinant segments seems to occur between the two gene copies as a consequence of their location in the IRs. These and previous results support the hypothesis that the CPM protein is a component of the plastome mismatch repair (MMR) system, whose failure of the anti-recombination activity results in increased illegitimate recombination between the rpl23 gene and pseudogene.
A Nanoparticle-Based Approach for the Detection of Extracellular Vesicles
Authors: Islam Md. Khirul , Syed Parvez , Lehtinen Laura , Leivo Janne , Gidwani Kamlesh , Wittfooth Saara , Pettersson Kim , Lamminmäki Urpo 
Published: July 2019

AbstractThe analysis of extracellular vesicles (EVs) typically requires tedious and time-consuming isolation process from bio-fluids. We developed a nanoparticle-based time resolved fluorescence immunoassay (NP-TRFIA) that uses biotinylated antibodies against the proteins of tetraspanin family and tumor-associated antigens for capturing EVs from urine samples and cell culture supernatants without the need for isolation. The captured-EVs were detected either with Eu3+-chelate or Eu3+-doped nanoparticle-based labels conjugated either to antibodies against the tetraspanins or lectins targeting the glycan moieties on EVs surface. The NP-TRFIA demonstrated specific capturing and detection of EVs by antibodies and lectins. Lectin-nanoparticle based assays showed 2–10 fold higher signal-to-background ratio compared with lectin-chelate assays. The nanoparticle assay concept allowed surface glycosylation profiling of the urine derived-EVs with lectins. It was also applied to establish an assay showing differential expression of tumor-associated proteins on more aggressive (higher ITGA3 on DU145- and PC3-EVs) compared to less aggressive (higher EpCAM on LNCaP-EVs) PCa- cell lines derived-EVs. This NP-TRFIA can be used as a simple tool for analysis and characterization of EVs in urine and cell culture supernatants. Such approach could be useful in identification of disease-specific markers on the surface of patient-derived urinary EVs.
Changes in DXA-derived lean mass and MRI-derived cross-sectional area of the thigh are modestly associated
Authors: Tavoian Dallin , Ampomah Kwasi , Amano Shinichi , Law Timothy D. , Clark Brian C. 
Published: July 2019

AbstractDual-energy X-ray absorptiometry (DXA) derived measures of lean mass demonstrate strong associations with magnetic resonance imaging (MRI) derived measures of muscle volume (MV) in cross-sectional studies, however, few studies have compared changes in response to an intervention. The purpose of this study was to determine the accuracy of DXA at detecting changes in lean mass, using MRI-derived MV as a reference standard. 10 male and 16 female subjects (29.2 ± 9.5 years) underwent DXA and MRI scans before and after a 10-week resistance training intervention. DXA thigh lean mass was compared to MRI mid-thigh MV, and percent change in size was compared between MRI and DXA. There was a strong correlation between measures cross-sectionally (r = 0.89) in agreement with previous investigations. However, there was a modest correlation of percentage change over time between methods (r = 0.49). Bland-Altman plots revealed that the amount of random error increased as the magnitude of the change from baseline increased. DXA measures of change in lean mass were modestly associated with MRI measures of change in MV. While there are several advantages to using DXA for the measurement of lean mass, the inability to accurately detect changes over time calls into question its use in clinical trials.
The composition of the aphid fauna (Insecta, Hemiptera) of the Royal Botanic Gardens, Kew
Authors: Wieczorek Karina , Fulcher Tim K. , Chłond Dominik 
Published: July 2019

AbstractAt least a dozen species of aphids (Insecta, Hemiptera) of non-native origin have expanded their range in Europe, however the importance of botanic gardens in this phenomenon has not been studied previously in detail. As a case study, investigations on the species composition and host range of Aphidomorpha in the Royal Botanic Gardens, Kew, London, United Kingdom, were conducted over a period of twelve days, in June 2017. The inventory study was carried out in the collection of living plants, both in the gardens and the glasshouses and nurseries. In total, 94 taxa of Aphidomorpha are identified (one phylloxerid, one adelgid and 92 species of aphids). 20 species are regarded as alien to the European aphid fauna and among them nine are believed to be the first published records for Kew. 20 species are regarded as serious pests, capable of virus transmission. The list of host plants includes 155 taxa from 89 genera and 49 families.Ericolophium holsti(Takahashi), species of Asiatic origin associated withRhododendronspp., was found for the first time in the field in the UK. Changes in the species composition of the aphid fauna in reference to the Eastop’s studies in 1960s were discussed.
Population density and water balance influence the global occurrence of hepatitis E epidemics
Authors: Carratalà Anna , Joost Stéphane 
Published: July 2019

AbstractIn developing countries, the waterborne transmission of hepatitis E virus (HEV), caused by HEV genotypes 1 (HEV-1) and 2 (HEV-2), leads to the onset of large recurrent outbreaks. HEV infections are of particular concern among pregnant women, due to very high mortality rates (up to 70%). Unfortunately, good understanding of the factors that trigger the occurrence of HEV epidemics is currently lacking; therefore, anticipating the onset of an outbreak is yet not possible. In order to map the geographical regions at higher risk of HEV epidemics and the conditions most favorable for the transmission of the virus, we compiled a dataset of HEV waterborne outbreaks and used it to obtain models of geographical suitability for HEV across the planet. The main three variables that best predict the geographical distribution of HEV outbreaks at global scale are population density, annual potential evapotranspiration and precipitation seasonality. At a regional scale, the temporal occurrence of HEV outbreaks in the Ganges watershed is negatively correlated with the discharge of the river (r = −0.77). Combined, our findings suggest that ultimately, population density and water balance are main parameters influencing the occurrence of HEV-1 and HEV-2 outbreaks. This study expands the current understanding of the combination of factors shaping the biogeography and seasonality of waterborne viral pathogens such as HEV-1 and HEV-2, and contributes to developing novel concepts for the prediction and control of human waterborne viruses in the near future.
Understanding how birds rebuild fat stores during migration: insights from an experimental study
Authors: Araújo Pedro M. , Viegas Ivan , Rocha Afonso D. , Villegas Auxiliadora , Jones John G. , Mendonça Liliana , Ramos Jaime A. , Masero José A. , Alves José A. 
Published: July 2019

AbstractMechanisms underlying fat accumulation for long-distance migration are not fully understood. This is especially relevant in the context of global change, as many migrants are dealing with changes in natural habitats and associated food sources and energy stores. The continental Black-tailed godwit Limosa limosa limosa is a long-distance migratory bird that has undergone a considerable dietary shift over the past few decades. Historically, godwits fed on an animal-based diet, but currently, during the non-breeding period godwits feed almost exclusively on rice seeds. The latter diet may allow building up of their fuel stores for migration by significantly increasing de novo lipogenesis (DNL) activity. Here, we performed an experiment to investigate lipid flux and the abundance of key enzymes involved in DNL in godwits, during fasting and refueling periods at the staging site, while feeding on rice seeds or fly larvae. Despite no significant differences found in enzymatic abundance (FASN, ME1, ACC and LPL) in stored fat, experimental godwits feeding on rice seeds presented high rates of DNL when compared to fly-larvae fed birds (~35 times more) and fasted godwits (no DNL activity). The increase of fractional DNL in godwits feeding on a carbohydrate-rich diet can potentially be enhanced by the fasting period that stimulates lipogenesis. Although requiring further testing, these recent findings provide new insights into the mechanisms of avian fat accumulation during a fasting and refueling cycle and associated responses to habitat and dietary changes in a migratory species.
Intermittent restraint stress induces circadian misalignment in the mouse bladder, leading to nocturia
Authors: Ihara Tatsuya , Nakamura Yuki , Mitsui Takahiko , Tsuchiya Sachiko , Kanda Mie , Kira Satoru , Nakagomi Hiroshi , Sawada Norifumi , Kamiyama Manabu , Shigetomi Eiji , Shinozaki Youichi , Yoshiyama Mitsuharu , Nakao Atsuhito , Koizumi Schuichi , Takeda Masayuki 
Published: July 2019

AbstractIntermittent stress disrupts the circadian rhythm in clock genes such as Per2 only in peripheral organs without any effect on the central circadian clock in the suprachiasmatic nucleus. Here, the effect of restraint stress (RS) on circadian bladder function was investigated based on urination behavior and gene expression rhythms. Furthermore, PF670462 (PF), a Per2 phosphorylation enzyme inhibitor, was administered to investigate the effects on circadian bladder re-alignment after RS. Two-hour RS during the light (sleep) phase was applied to mice (RS mice) for 5 days. The following parameters were then examined: urination behaviors; clock gene expression rhythms and urinary sensory-related molecules such as piezo type mechanosensitive ion channel component 1 (Piezo1), transient receptor potential cation channel subfamily V member 4 (TRPV4), and Connexin26 (Cx26) in the bladder mucosa; Per2 expression in the excised bladder of Per2luciferase knock-in mice (Per2::luc); in vivo Per2 expression rhythms in the bladder of Per2::luc mice. Control mice did not show altered urination behavior in the light phase, whereas RS mice exhibited a higher voiding frequency and lower bladder capacity. In the bladder mucosa, RS mice also showed abrogated or misaligned Piezo1, TRPV4, Connexin26, and clock gene expression. The rhythmic expression of Per2 was also altered in RS mice both in excised- and in vivo bladder, compared with control mice. After PF administration, voiding frequency was reduced and bladder capacity was increased during the light phase in RS mice; the in vivo Per2 expression rhythm was also fully restored. Therefore, RS can alter circadian gene expression in the bladder during the light phase and might cause nocturia via changes in circadian bladder function due the dysregulation of clock genes. Amending the circadian rhythm therapeutically could be applied for nocturia.
Needle-based storage-phosphor detector radiography is superior to a conventional powder-based storage phosphor detector and a high-resolution screen-film system in small patients (budgerigars and mice)
Authors: Tebrün Wiebke , Ludewig Eberhard , Köhler Claudia , Böhme Julia , Pees Michael 
Published: July 2019

AbstractThis method comparison study used radiographs of 20 mice and 20 budgerigars to investigate comparability between computed radiography (CR) and high-resolution screen-film systems and study the effects of reduced radiation doses on image quality of digital radiographs of small patients. Exposure settings used with the mammography screen-film system (SF) were taken as baseline settings. A powder-based storage-phosphor system (CRP) and a needle-based storage-phosphor system (CRN) were used with the same settings (D/100%) and half the detector dose (D/50%). Using a scoring system four reviewers assessed five criteria per species covering soft tissue and bone structures. Results were evaluated for differences between reviewers (interobserver variability), systems and settings (intersystem variability, using visual grading characteristic analysis). Correlations were significant (p ≤ 0.05) for interobserver variability in 86.7% of the cases. Correlation coefficients ranged from 0.206 to 0.772. For mice and budgerigars, the CRN system was rated as superior to the SF and CRP system for most criteria, being significant in two cases each. Comparing the SF and CRP system, the conventional method scored higher for all criteria, in one case significantly. For both species and both digital systems, dose reduction to 50% resulted in significantly worse scores for most criteria. In summary, the needle-based storage-phosphor technique proved to be superior compared to the conventional storage-phosphor and mammography screen-film system. Needle-based detector systems are suitable substitutes for high-resolution screen–film systems when performing diagnostic imaging of small patients. Dose reduction to 50% of the corresponding dose needed in high-resolution film-screen systems cannot be recommended.
On the dynamic instability of Arctic sea ice
Authors: Chavas Jean-Paul , Grainger Corbett 
Published: July 2019

AbstractThe last few decades have seen a significant decline in Arctic sea ice, generating concerns about both its causes and its longer-term implications. In this paper, we introduce an empirical technique to examine the dynamics of Arctic sea ice extent. Using quantile autoregression, we find that the negative effect of atmospheric CO2 is stronger in the upper tail of the ice distribution. We also document that Arctic sea ice dynamics have become more unstable over the last three decades, especially during the summer. The rising summer instability occurs across quantiles, indicating that it is due to the joint effects of rising atmospheric CO2 and nonlinear feedbacks (and not due to outside shocks). While we do not find evidence of “critical slowing”, we see the increasing instability as a cause for concern. We also use the model to predict the evolution of Arctic sea ice extent under alternative CO2 concentration scenarios.
A nanoscale, multi-parametric flow cytometry-based platform to study mitochondrial heterogeneity and mitochondrial DNA dynamics
Authors: MacDonald Julie A. , Bothun Alisha M. , Annis Sofia N. , Sheehan Hannah , Ray Somak , Gao Yuanwei , Ivanov Alexander R. , Khrapko Konstantin , Tilly Jonathan L. , Woods Dori C. 
Published: July 2019

AbstractMitochondria are well-characterized regarding their function in both energy production and regulation of cell death; however, the heterogeneity that exists within mitochondrial populations is poorly understood. Typically analyzed as pooled samples comprised of millions of individual mitochondria, there is little information regarding potentially different functionality across subpopulations of mitochondria. Herein we present a new methodology to analyze mitochondria as individual components of a complex and heterogeneous network, using a nanoscale and multi–parametric flow cytometry-based platform. We validate the platform using multiple downstream assays, including electron microscopy, ATP generation, quantitative mass-spectrometry proteomic profiling, and mtDNA analysis at the level of single organelles. These strategies allow robust analysis and isolation of mitochondrial subpopulations to more broadly elucidate the underlying complexities of mitochondria as these organelles function collectively within a cell.
Stochastic profile of Epstein-Barr virus in nasopharyngeal carcinoma settings
Authors: Cordeiro Marcos Tadeu Andrade , García Jesús E. , González-López Verónica Andrea , Londoño Sergio Luis Mercado 
Published: July 2019

We build a profile of the Epstein-Barr virus (EBV) by means of genomic sequences obtained from patients with nasopharyngeal carcinoma (NPC). We consider a set of sequences coming from the NCBI free source and we assume that this set is a collection of independent samples of stochastic processes related by an equivalence relation. Given a collection {(Xjt)t∈ℤ}pj=1 of p independent discrete time Markov processes with finite alphabet A and state space S, we state that the elements (i, s) and (j, r) in {1, 2,…, p} × S are equivalent if and only if they share the same transition probability for all the elements in the alphabet. The equivalence allows to reduce the number of parameters to be estimated in the model avoiding to delete states of S to achieve that reduction. Through the equivalence relationship, we build the global profile for all the EBV in NPC sequences, this model allows us to represent the underlying and common stochastic law of the set of sequences. The equivalence classes define an optimal partition of {1, 2,…, p} × S, and it is in relation to this partition that we define the profile of the set of genomic sequences.
The Effect of Dehydroepiandrosterone (DHEA) Supplementation on IVF or ICSI: A Meta-Analysis of Randomized Controlled Trials
Authors: Xu Lin , Hu Chunxia , Liu Qun , Li Yaxuan 
Published: July 2019

Abstract
Introduction A systematic review and meta-analysis were conducted to evaluate the efficacy of dehydroepiandrosterone (DHEA) supplementation in patients with diminished ovarian reserve (DOR) and/or poor ovarian response (POR) who were undergoing in vitro fertilization or intracytoplasmic sperm injection (IVF/ICSI).
Patients and Methods We searched the PubMed, EMBASE, Web of Science, and Cochrane Library electronic databases for literature published until July 2018. The analysis included randomized controlled trials (RCTs) of the effects of DHEA versus placebo on IVF or ICSI. Two independent reviewers extracted information from the reports and evaluated the quality of the studies. Overall, we identified nine prospective RCTs involving 833 patients.
Results Compared to the controls, patients treated with DHEA exhibited increases in the number of retrieved oocytes (mean difference, 0.91; 95% confidence interval [CI], 0.23 – 1.59; p = 0.009), clinical pregnancy rate (relative risk [RR] = 1.27; 95% CI, 1.01 – 1.61; p = 0.04), and live birth rate (RR, 1.76; 95% CI, 1.17 – 2.63; p = 0.006). However, there was no intergroup difference in the miscarriage rate (RR, 0.37; 95% CI, 0.12 – 1.13; p = 0.08).
Conclusion DHEA supplementation improved the outcomes of IVF/ICSI in women with DOR or POR.
Expertenempfehlung zur Anwendung der hyperthermen intrathorakalen Chemotherapie (HITOC) in Deutschland
Authors: Ried Michael , Eichhorn Martin , Winter Hauke , Grützner Uwe , Lindner Michael , Hatz Rudolf A. , Haager Benedikt , Passlick Bernward , Galetin Thomas , Lopez-Pastorini Alberto , Stoelben Erich , Hofmann Hans-Stefan 
Published: July 2019

Zusammenfassung
Hintergrund Die hypertherme intrathorakale Chemotherapie (HITOC) wird bereits seit einigen Jahren in mehreren thoraxchirurgischen Kliniken angewendet. Diese Expertenempfehlung soll nun basierend auf der klinischen Erfahrung und der vorhandenen Literatur grundlegende Empfehlungen für eine standardisierte Durchführung der HITOC liefern.
Material und Methode Im Zeitraum von Oktober bis Dezember 2018 wurden Empfehlungen zur Anwendung der HITOC in Deutschland durch eine Gruppe von Experten aus 5 thoraxchirurgischen Kliniken erarbeitet. Die Auswahl der Experten mit den meisten Operationen mit HITOC erfolgte anhand einer deutschlandweiten HITOC-Umfrage aus dem Jahr 2017. Die Empfehlungen basieren auf den klinischen Erfahrungen sowie wissenschaftlichen Arbeiten bzw. Daten der einzelnen Kliniken und einer aktuellen Literaturrecherche zur HITOC.
Ergebnis Die Empfehlungen wurden durch alle 5 teilnehmenden Kliniken in einer Konsensusumfrage bewertet. Hieraus ergaben sich 6 Schwerpunkte mit insgesamt 17 Empfehlungen. Bei jeder Empfehlung wurde eine Konsensstärke in Prozent berechnet. Eine 100%ige Konsensstärke wurde bei der Nomenklatur (HITOC), der technischen Durchführung, dem Chemotherapeutikum, dem perioperativen Management, den Schutzmaßnahmen und den Indikationen erreicht. Als Basis-Chemotherapeutikum für die HITOC wird von allen Experten Cisplatin empfohlen, da hier die meisten klinischen Erfahrungen und Daten vorliegen. Die Dosierung von Cisplatin wird in mg/m2 Körperoberfläche (KOF) angegeben und sollte zwischen 150 und 175 mg/m2 KOF betragen. Die zusätzliche Angabe des Perfusionsvolumens (ca. 4 – 5 l) scheint für den intrathorakalen Konzentrationsgradienten eine Rolle zu spielen und sollte mit beachtet werden.
Schlussfolgerung Diese Expertenempfehlungen zeigen eine standardisierte und einheitliche Durchführung der HITOC. Hierdurch sollen postoperative Komplikationen durch die HITOC vermindert und eine bessere Vergleichbarkeit der Ergebnisse ermöglicht werden.
Movement Disorders in Children: An Observational Study in a Tertiary Care Center in North India
Authors: Pandey Chandra Shekhar , Kumar Rashmi , Malhotra Hardeep Singh , Kohli Neera , Kumar Chandrakanta , Verma Sanjeev Kumar 
Published: July 2019

AbstractMovement disorders (MDs) are disorders of pathological movements that cannot be fully initiated, modulated, or interrupted voluntarily. Spectrum and etiology of MDs are likely to vary with geographical location, but there are few studies on pediatric MDs from India, and severity of the disease is not well documented. Response to treatment of MDs is often unpredictable. Objective of the study was to describe the relative prevalence, types, severity, etiology, and response to treatment of pediatric MDs as seen at a public teaching hospital in northern India. Over a period of 1 year, consecutive children with MDs seen in outpatient department (OPD) or wards were enrolled, after excluding cerebral palsy and musculoskeletal disorders. Detailed history, examination, treatment, and outcome were recorded. Severity was rated according to Battini's scale at initial contact and each follow-up. Neuroimaging and relevant investigations were done for etiology. Serial 2-minute video recordings were obtained. Out of 93 patients enrolled, the most common MDs were dystonia (24.7%), tremors (22.4%), ataxia (19.6%), and chorea (12.9%). Tics, hemiballismus, and myoclonus were also seen and 4% could not be classified. Mixed MDs were seen in 9.7%. Etiologies of MDs were infectious (acute encephalitis syndrome, tuberculous meningitis, subacute sclerosing panencephalitis, and rheumatic chorea) or nutritional (infantile tremor syndrome) in 46%. Genetic neurodegenerations accounted for a significant proportion (15.1%). Improvement occurred in majority (63.4%) of patients. Etiology of MDs was largely specific to this part of the world, related to infectious and nutrition causes. In the absence of complex genetic investigations, many cases were left with unknown etiology.