bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel RT-QPCR-based assay for the relative quantification of residue specific m6A RNA methylation
Authors: Castellanos-Rubio Ainara , Santin Izortze , Olazagoitia-Garmendia Ane , Romero-Garmendia Irati , Jauregi-Miguel Amaia , Legarda Maria , Bilbao Jose Ramon 
Published: March 2019

AbstractN6-methyladenosine (m6A) is the most common and abundant RNA modification. Recent studies have shown its importance in the regulation of several biological processes, including the immune response, and different approaches have been developed in order to map and quantify m6A marks. However, site specific detection of m6A methylation has been technically challenging, and existing protocols are long and tedious and often involve next-generation sequencing. Here, we describe a simple RT-QPCR based approach for the relative quantification of candidate m6A regions that takes advantage of the diminished capacity of BstI enzyme to retrotranscribe m6A residues. Using this technique, we have been able to confirm the recently described m6A methylation in the 3′UTR of SOCS1 and SOCS3 transcripts. Moreover, using the method presented here, we have also observed alterations in the relative levels of m6A in specific motifs of SOCS genes in celiac disease patients and in pancreatic β-cells exposed to inflammatory stimuli.
Transcriptome analysis of the curry tree (Bergera koenigii L., Rutaceae) during leaf development
Authors: Shivakumar Vikram S. , Johnson Gabriel , Zimmer Elizabeth A. 
Published: March 2019

AbstractThe curry tree (Bergera koenigii L.) is a widely cultivated plant used in South Asian cooking. Next-generation sequencing was used to generate the transcriptome of the curry leaf to detect changes in gene expression during leaf development, such as those genes involved in the production of oils which lend the leaf its characteristic taste, aroma, and medicinal properties. Using abundance estimation (RSEM) and differential expression analysis, genes that were significantly differentially expressed were identified. The transcriptome was annotated with BLASTx using the non-redundant (nr) protein database, and Gene Ontology (GO) terms were assigned based on the top BLAST hit using Blast2GO. Lastly, functional enrichment of the assigned GO terms was analyzed for genes that were significantly differentially expressed. Of the most enriched GO categories, pathways involved in cell wall, membrane, and lignin synthesis were found to be most upregulated in immature leaf tissue, possibly due to the growth and expansion of the leaf tissue. Terpene synthases, which synthesize monoterpenes and sesquiterpenes, which comprise much of the curry essential oil, were found to be significantly upregulated in mature leaf tissue, suggesting that oil production increases later in leaf development. Enzymes involved in pigment production were also significantly upregulated in mature leaves. The findings were based on computational estimates of gene expression from RNA-seq data, and further study is warranted to validate these results using targeted techniques, such as quantitative PCR.
Effects of iron spin transition on the electronic structure, thermal expansivity and lattice thermal conductivity of ferropericlase: a first principles study
Authors: Song Yalan , He Kaihua , Sun Jian , Ma Chaojie , Wan Miao , Wang Qingbo , Chen Qili 
Published: March 2019

AbstractThe effects of the spin transition on the electronic structure, thermal expansivity and lattice thermal conductivity of ferropericlase are studied by first principles calculations at high pressures. The electronic structures indicate that ferropericlase is an insulator for high-spin and low-spin states. Combined with the quasiharmonic approximation, our calculations show that the thermal expansivity is larger in the high-spin state than in the low-spin state at ambient pressure, while the magnitude exhibits a crossover between high-spin and low-spin with increasing pressure. The calculated lattice thermal conductivity exhibits a drastic reduction upon the inclusion of ferrous iron, which is consistent with previous experimental studies. However, a subsequent enhancement in the thermal conductivity is obtained, which is associated with the spin transition. Mechanisms are discussed for the variation in thermal conductivity by the inclusion of ferrous iron and the spin transition.
Forest litter and shrubs act as an understory filter for the survival of Quercus mongolica seedlings in Mt. Kwan-ak, South Korea
Authors: Song Uhram 
Published: March 2019

AbstractForest succession fromPinustoQuercushas often been observed in temperate forest, although the succession mechanism is not clearly understood. This study investigated factors that affect the succession of forests from pine to oak, using forest vegetation inventory data at plots at Kwan-ak mountain in Korea. Analyses of understory canopy coverage, light intensity, and tree numbers and ages inP. densifloraforests indicate thatQ. mongolicacan only invade these forests before understory shrub establishment. The results from analyses of all environmental factors indicate that similar adverse effects from environmental factors occur in establishedP. densifloraandQ. mongolicaforests that inhibitQ. mongolicaseedling survival. However, the observed survival rate ofQ. mongolicaseedlings underP. densifloraduring winter were much higher thanQ. mongolicaseedlings underQ. mongolicatrees, and it is due to accumulated snow overQ. mongolicaforest litter which breaks or inhibits the emergence ofQ. mongolicaseedlings. Protecting seedlings with plastic cups significantly increased the survival rate which confirms that forest floor litter acts as a filter for the regeneration and succession ofQ. mongolicaforests. This paper thus concludes that understory shrubs and forest litter affect the succession dynamics ofP. densifloraandQ. mongolicaforests.
Measurement of Glomerular Filtration Rate using Quantitative SPECT/CT and Deep-learning-based Kidney Segmentation
Authors: Park Junyoung , Bae Sungwoo , Seo Seongho , Park Sohyun , Bang Ji-In , Han Jeong Hee , Lee Won Woo , Lee Jae Sung 
Published: March 2019

AbstractQuantitative SPECT/CT is potentially useful for more accurate and reliable measurement of glomerular filtration rate (GFR) than conventional planar scintigraphy. However, manual drawing of a volume of interest (VOI) on renal parenchyma in CT images is a labor-intensive and time-consuming task. The aim of this study is to develop a fully automated GFR quantification method based on a deep learning approach to the 3D segmentation of kidney parenchyma in CT. We automatically segmented the kidneys in CT images using the proposed method with remarkably high Dice similarity coefficient relative to the manual segmentation (mean = 0.89). The GFR values derived using manual and automatic segmentation methods were strongly correlated (R2 = 0.96). The absolute difference between the individual GFR values using manual and automatic methods was only 2.90%. Moreover, the two segmentation methods had comparable performance in the urolithiasis patients and kidney donors. Furthermore, both segmentation modalities showed significantly decreased individual GFR in symptomatic kidneys compared with the normal or asymptomatic kidney groups. The proposed approach enables fast and accurate GFR measurement.
Streptococcus pneumoniae Cell Wall-Localized Trigger Factor Elicits a Protective Immune Response and Contributes to Bacterial Adhesion to the Host
Authors: Cohen Aviad , Troib Shani , Dotan Shahar , Najmuldeen Hastyar , Yesilkaya Hasan , Kushnir Tatyana , Shagan Marilou , Portnoi Maxim , Nachmani Hannie , Benisty Rachel , Tal Michael , Ellis Ronald , Chalifa-Caspi Vered , Dagan Ron , Nebenzahl Yaffa Mizrachi 
Published: March 2019

AbstractTrigger factor (TF) has a known cytoplasmic function as a chaperone. In a previous study we showed that pneumococcal TF is also cell-wall localized and this finding combined with the immunogenic characteristic of TF, has led us to determine the vaccine potential of TF and decipher its involvement in pneumococcal pathogenesis. Bioinformatic analysis revealed that TF is conserved among pneumococci and has no human homologue. Immunization of mice with recombinant (r)TF elicited a protective immune response against a pneumococcal challenge, suggesting that TF contributes to pneumococcal pathogenesis. Indeed, rTF and an anti-rTF antiserum inhibited bacterial adhesion to human lung derived epithelial cells, indicating that TF contributes to the bacterial adhesion to the host. Moreover, bacteria lacking TF demonstrated reduced adhesion, in vitro, to lung-derived epithelial cells, neural cells and glial cells. The reduced adhesion could be restored by chromosomal complementation. Furthermore, bacteria lacking TF demonstrated significantly reduced virulence in a mouse model. Taken together, the ability of rTF to elicit a protective immune response, involvement of TF in bacterial adhesion, conservation of the protein among pneumococcal strains and the lack of human homologue, all suggest that rTF can be considered as a future candidate vaccine with a much broader coverage as compared to the currently available pneumococcal vaccines.
Widespread shifts in the coastal biota of northern California during the 2014–2016 marine heatwaves
Authors: Sanford Eric , Sones Jacqueline L. , García-Reyes Marisol , Goddard Jeffrey H. R. , Largier John L. 
Published: March 2019

AbstractDuring 2014–2016, severe marine heatwaves in the northeast Pacific triggered well-documented disturbances including mass mortalities, harmful algal blooms, and declines in subtidal kelp beds. However, less attention has been directed towards understanding how changes in sea surface temperature (SST) and alongshore currents during this period influenced the geographic distribution of coastal taxa. Here, we examine these effects in northern California, USA, with a focus on the region between Point Reyes and Point Arena. This region represents an important biogeographic transition zone that lies <150 km north of Monterey Bay, California, where numerous southern species have historically reached their northern (poleward) range limits. We report substantial changes in geographic distributions and/or abundances across a diverse suite of 67 southern species, including an unprecedented number of poleward range extensions (37) and striking increases in the recruitment of owl limpets (Lottia gigantea) and volcano barnacles (Tetraclita rubescens). These ecological responses likely arose through the combined effects of extreme SST, periods of anomalous poleward flow, and the unusually long duration of heatwave events. Prolonged marine heatwaves and enhanced poleward dispersal may play an important role in longer-term shifts in the composition of coastal communities in northern California and other biogeographic transition zones.
Integrated analysis of relapsed B-cell precursor Acute Lymphoblastic Leukemia identifies subtype-specific cytokine and metabolic signatures
Authors: Schroeder Michael P. , Bastian Lorenz , Eckert Cornelia , Gökbuget Nicola , James Alva Rani , Tanchez Jutta Ortiz , Schlee Cornelia , Isaakidis Konstandina , Häupl Björn , Baum Katharina , Migueles Lozano Oscar Arturo , Kouidri Khouloud , Pan Kuan-Ting , Urlaub Henning , Schwartz Stefan , Burmeister Thomas , von Stackelberg Arend , Hoelzer Dieter , Pfeiffer Heike , Rieger Michael A. , Göllner Stefanie , Oellerich Thomas , Horstman Martin , Schrappe Martin , Wolf Jana , Kirschner-Schwabe Renate , Brüggemann Monika , Müller-Tidow Carsten , Serve Hubert , Neumann Martin , Baldus Claudia D. 
Published: March 2019

AbstractRecent efforts reclassified B-Cell Precursor Acute Lymphoblastic Leukemia (BCP-ALL) into more refined subtypes. Nevertheless, outcomes of relapsed BCP-ALL remain unsatisfactory, particularly in adult patients where the molecular basis of relapse is still poorly understood. To elucidate the evolution of relapse in BCP-ALL, we established a comprehensive multi-omics dataset including DNA-sequencing, RNA-sequencing, DNA methylation array and proteome MASS-spec data from matched diagnosis and relapse samples of BCP-ALL patients (n = 50) including the subtypes DUX4, Ph-like and two aneuploid subtypes. Relapse-specific alterations were enriched for chromatin modifiers, nucleotide and steroid metabolism including the novel candidates FPGS, AGBL and ZNF483. The proteome expression analysis unraveled deregulation of metabolic pathways at relapse including the key proteins G6PD, TKT, GPI and PGD. Moreover, we identified a novel relapse-specific gene signature specific for DUX4 BCP-ALL patients highlighting chemotaxis and cytokine environment as a possible driver event at relapse. This study presents novel insights at distinct molecular levels of relapsed BCP-ALL based on a comprehensive multi-omics integrated data set including a valuable proteomics data set. The relapse specific aberrations reveal metabolic signatures on genomic and proteomic levels in BCP-ALL relapse. Furthermore, the chemokine expression signature in DUX4 relapse underscores the distinct status of DUX4-fusion BCP-ALL.
The source effect as a natural function of disgust in interpersonal context and its impairment in mental disorders
Authors: Lenk Maria , Ritschel Gerhard , Abele Marion , Roever Peggy , Schellong Julia , Joraschky Peter , Weidner Kerstin , Croy Ilona 
Published: March 2019

AbstractDisgust affects interpersonal relationships and regulates hygienic, sexual and distance behaviour. Its intensity in the interpersonal context depends on the character of the relationship. Strangers normally evoke more disgust than intimates (known as the source effect). General disgust sensitivity is increased in various mental diseases. It is unclear how disgust in the interpersonal context is affected and whether the source effect is preserved. 460 inpatients with mental disorders and 463 healthy subjects answered a newly developed Questionnaire (DIRQ) that covers disgust in the interpersonal context on content categories (hygiene, physical proximity, sexuality) and on source categories (self, partner, parent, stranger). Mental disorders were diagnosed with structured interviews. Healthy controls exhibited a pronounced source effect, with strangers evoking more disgust than intimates. In patients, this source effect was reduced (Cohen’s d = 0.3), especially for sexual disgust, while general disgust sensitivity was increased (d = 0.5). High disgust in patients was best predicted by a history of sexual abuse and by the presence of post-traumatic stress disorder. In conclusion, mentally impaired patients show increased and trauma-associated disgust sensitivity. Their downregulation of sexual disgust in intimate relationships is hindered, which may have a boundary protective function but might also fuel difficulties engaging in relationships or intimacy.
Honey bee-collected pollen is a potential source of Ascosphaera apis infection in managed bumble bees
Authors: Pereira Kleber de Sousa , Meeus Ivan , Smagghe Guy 
Published: March 2019

AbstractThe trade of bumble bees started in the early nineties for pollinator-dependent greenhouse plants. Nowadays, its rearing and transport have received public attention, since managed bees can transfer pathogens to wild bee populations. Therefore, guaranteeing pathogen-free bumble bees is fundamental. The major protein source used in rearing facilities is honey bee-collected pollen. This can carry pathogens, however to date, solid data on the risk of this food source to the health of bumble bees is lacking. Here we performed a large pathogen screening of non-irradiated honey bee-collected pollen to discover particles infective to Bombus terrestris. We identified seven parasites (Apicystis bombi, Ascosphaera apis, Crithidia mellificae, Nosema ceranae, Paenibacillus larvae and two parasites resembling Nosema thomsoni and Microsporidium sp. Oise) and four viruses (CBPV, DWV, IAPV and SBV) in 17 pollen batches from two major European pollen source regions (Spain and Romania). Ascosphaera apis was capable of infecting bumble bees; the larvae showed similar symptoms to chalkbrood disease reported in honey bees. Bumble bee breeding facilities need to be cautious about the potential presence of this disease, which was originally reported in honey bees. Thorough diagnostic and control methods are needed, as risk of spillover to wild bee species is possible.
Growth-inhibition of cell lines derived from B cell lymphomas through antagonism of serotonin receptor signaling
Authors: Kolan Shrikant S. , Lidström Tommy , Mediavilla Tomás , Dernstedt Andy , Degerman Sofie , Hultdin Magnus , Björk Karl , Marcellino Daniel , Forsell Mattias N. E. 
Published: March 2019

AbstractA majority of lymphomas are derived from B cells and novel treatments are required to treat refractory disease. Neurotransmitters such as serotonin and dopamine influence activation of B cells and the effects of a selective serotonin 1A receptor (5HT1A) antagonist on growth of a number of B cell-derived lymphoma cell lines were investigated. We confirmed the expression of 5HT1A in human lymphoma tissue and in several well-defined experimental cell lines. We discovered that the pharmacological inhibition of 5HT1A led to the reduced proliferation of B cell-derived lymphoma cell lines together with DNA damage, ROS-independent caspase activation and apoptosis in a large fraction of cells. Residual live cells were found ‘locked’ in a non-proliferative state in which a selective transcriptional and translational shutdown of genes important for cell proliferation and metabolism occurred (e.g., AKT, GSK-3β, cMYC and p53). Strikingly, inhibition of 5HT1A regulated mitochondrial activity through a rapid reduction of mitochondrial membrane potential and reducing dehydrogenase activity. Collectively, our data suggest 5HT1A antagonism as a novel adjuvant to established cancer treatment regimens to further inhibit lymphoma growth.
Genome-wide Identification of Tebufenozide Resistant Genes in the smaller tea tortrix, Adoxophyes honmai (Lepidoptera: Tortricidae)
Authors: Uchibori-Asano Miwa , Jouraku Akiya , Uchiyama Toru , Yokoi Kakeru , Akiduki Gaku , Suetsugu Yoshitaka , Kobayashi Tetsuya , Ozawa Akihito , Minami Saki , Ishizuka Chiharu , Nakagawa Yoshiaki , Daimon Takaaki , Shinoda Tetsuro 
Published: March 2019

AbstractThe smaller tea tortrix, Adoxophyes honmai, has developed strong resistance to tebufenozide, a diacylhydrazine-type (DAH) insecticide. Here, we investigated its mechanism by identifying genes responsible for the tebufenozide resistance using various next generation sequencing techniques. First, double-digest restriction site-associated DNA sequencing (ddRAD-seq) identified two candidate loci. Then, synteny analyses using A. honmai draft genome sequences revealed that one locus contained the ecdysone receptor gene (EcR) and the other multiple CYP9A subfamily P450 genes. RNA-seq and direct sequencing of EcR cDNAs found a single nucleotide polymorphism (SNP), which was tightly linked to tebufenozide resistance and generated an amino acid substitution in the ligand-binding domain. The binding affinity to tebufenozide was about 4 times lower in in vitro translated EcR of the resistant strain than in the susceptible strain. RNA-seq analyses identified commonly up-regulated genes in resistant strains, including CYP9A and choline/carboxylesterase (CCE) genes. RT-qPCR analysis and bioassays showed that the expression levels of several CYP9A and CCE genes were moderately correlated with tebufenozide resistance. Collectively, these results suggest that the reduced binding affinity of EcR is the main factor and the enhanced detoxification activity by some CYP9As and CCEs plays a supplementary role in tebufenozide resistance in A. honmai.
Custom fabrication and mode-locked operation of a femtosecond fiber laser for multiphoton microscopy
Authors: Davoudzadeh Nima , Ducourthial Guillaume , Spring Bryan Q. 
Published: March 2019

AbstractSolid-state femtosecond lasers have stimulated the broad adoption of multiphoton microscopy in the modern laboratory. However, these devices remain costly. Fiber lasers offer promise as a means to inexpensively produce ultrashort pulses of light suitable for nonlinear microscopy in compact, robust and portable devices. Although encouraging, the initial methods reported in the biomedical engineering community to construct home-built femtosecond fiber laser systems overlooked fundamental aspects that compromised performance and misrepresented the significant financial and intellectual investments required to build these devices. Here, we present a practical protocol to fabricate an all-normal-dispersion ytterbium (Yb)-doped femtosecond fiber laser oscillator using commercially-available parts (plus standard optical components and extra-cavity accessories) as well as basic fiber splicing and laser pulse characterization equipment. We also provide a synthesis of established protocols in the laser physics community, but often overlooked in other fields, to verify true versus seemingly (partial or noise-like) mode-locked performance. The approaches described here make custom fabrication of femtosecond fiber lasers more accessible to a wide range of investigators and better represent the investments required for the proper laser design, fabrication and operation.
Association between HOMA-IR and Frailty among U.S. Middle-aged and Elderly Population
Authors: Peng Po-Sen , Kao Tung-Wei , Chang Pi-Kai , Chen Wei-Liang , Peng Po-Jui , Wu Li-Wei 
Published: March 2019

AbstractPrevious literatures revealed that homeostasis model assessment-estimated insulin resistance (HOMA-IR) was one of the cardio-metabolic risk factors. This study was conducted to access the association between HOMA-IR and frailty in the United States of America (U.S.) middle-aged and elderly high-risk insulin-resistant population. In the National Health and Nutrition Examination Survey (NHANES III) from 1988 to 1994, the study included 3,893 participants. In order to exam the association between HOMA-IR and frailty in the middle-aged and elderly population through the regression model adjusted for multiple covariates, we divided the participants into middle aged group (Age <65 years) and elderly group (Age > = 65 years) in this study. Each group was then divided into tertiles depending on their HOMA-IR levels. Higher level of HOMA-IR was significantly associated with frailty in the elderly group, but this association was not seen in the middle-aged population. These results demonstrated that the HOMA-IR level can be a novel risk assessment of frailty in elderly high-risk insulin-resistant individuals (Age > = 65 years).
Thermal tolerance and range expansion of invasive foraminifera under climate changes
Authors: Titelboim Danna , Almogi-Labin Ahuva , Herut Barak , Kucera Michal , Asckenazi-Polivoda Sarit , Abramovich Sigal 
Published: March 2019

AbstractThe Eastern Mediterranean is experiencing a large-scale invasion of alien tropical species from the Red Sea. This “Lessepsian invasion” began with the opening of the Suez Canal and is promoted by the ongoing oceanic warming. The environmental differences between the Red Sea and the Mediterranean act as a buffer allowing the invasion of certain species. This provides an opportunity to study the differences in temperature sensitivity between two sibling species of the cosmopolitian foraminifera Amphistegina. Both species are very common in the Red Sea. Whilest, only one is a successful invader and the other is absent in the Eastern Mediterranean. Here we show that the two species are different in their temperature sensitivity, which explains their selective invasion into the Mediterranean. These differences demonstrate that in respect to climate change resilient marine species can be distinguished by their ability to compensate for temperature changes by adjusting their physiological performance and by having tolerance to a wider temperature range. Moreover, we demonstrate that selective filtering mechanisms during invasion can prefer species that are more resilient to colder rather than expected warmer temperatures.