bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global Patterns of Resistance to Bt Crops Highlighting Pink Bollworm in the United States, China, and India
Authors: Tabashnik Bruce E , Carrière Yves 
Published: June 2019

Abstract
Crops genetically engineered to produce insecticidal proteins from Bacillus thuringiensis (Bt) have advanced pest control, but their benefits have been reduced by evolution of resistance in pests. The global monitoring data reviewed here reveal 19 cases of practical resistance to Bt crops, which is field-evolved resistance that reduces Bt crop efficacy and has practical consequences for pest control. Each case represents the responses of one pest species in one country to one Bt toxin. The results with pink bollworm (Pectinophora gossypiella) and Bt cotton differ strikingly among the world’s three leading cotton-producing nations. In the southwestern United States, farmers delayed resistance by planting non-Bt cotton refuges from 1996 to 2005, then cooperated in a program that used Bt cotton, mass releases of sterile moths, and other tactics to eradicate this pest from the region. In China, farmers reversed low levels of pink bollworm resistance to Bt cotton by planting second-generation hybrid seeds from crosses between Bt and non-Bt cotton. This approach yields a refuge of 25% non-Bt cotton plants randomly interspersed within fields of Bt cotton. Farmers adopted this tactic voluntarily and unknowingly, not to manage resistance, but apparently because of its perceived short-term agronomic and economic benefits. In India, where non-Bt cotton refuges have been scarce and pink bollworm resistance to pyramided Bt cotton producing Cry1Ac and Cry2Ab toxins is widespread, integrated pest management emphasizing shortening of the cotton season, destruction of crop residues, and other tactics is now essential.
Differences in physiological integration between invasive and noninvasive introduced clonal species of Carpobrotus
Authors: Roiloa Sergio R , Alpert Peter , Barreiro Rodolfo 
Published: June 2019

AbstractAimsClonal growth is associated with invasiveness in introduced plant species, but few studies have compared invasive and noninvasive introduced clonal species to investigate which clonal traits may underlie invasiveness. To test the hypothesis that greater capacity to increase clonal growth via physiological integration of connected ramets increases invasiveness in clonal plants, we compared the effects of severing connections on accumulation of mass in the two species of the creeping, succulent, perennial, herbaceous genus Carpobrotus that have been introduced on sand dunes along the Pacific Coast of northern California, the highly invasive species Carpobrotus edulis and the co-occurring, noninvasive species Carpobrotus chilensis.MethodsPairs of ramets from four mixed populations of the species from California were grown in a common garden for 3 months with and without severing the stem connecting the ramets. To simulate the effect of clones on soils in natural populations, the older ramet was grown in sand amended with potting compost and the younger in sand alone.Important FindingsSeverance decreased net growth in mass by ~60% in C. edulis and ~100% in C. chilensis, due mainly to the negative effect of severance on the shoot mass of the younger ramet within a pair. Contrary to the hypothesis, this suggests that physiological integration increases growth more in the less invasive species. However, severance also decreased allocation of mass to roots in the older ramet and increased it in the younger ramet in a pair, and the effect on the younger ramet was about twice as great in C. edulis as in C. chilensis. This indicates that the more invasive species shows greater phenotypic plasticity in response to physiological integration, in particular greater capacity for division of labor. This could contribute to greater long-term growth and suggests that the division of labor may be a trait that underlies the association between clonal growth and invasiveness in plants.
Sleep cycle of a fin whale based on reprocessing of old satellite observations
Authors: Viale Denise , Koechlin Laurent , Viale Carli 
Published: June 2019

AbstractReprocessing of old data from the satellite tracking of a fin whale in 1991 allowed us to detect new loops on its path and to show the significance of these loops. Originally, five loops on five consecutive days had been detected. The reprocessed data reveals at least 21 loops, plus many other phases of inertia, together with additional information on the whale’s position at the surface during these phases of inertia. Based on these new interpretations, we deduce a sleep cycle for this animal.RésuméMise en évidence à partir d’un suivi satellitaire d’une phase de sommeil quotidienne chez un baleinoptère.La fixation d’une balise Argos sur un rorqual (Balaenoptera physalus) donna lieu à un suivi satellitaire de septembre à novembre 1991, qui visait à démontrer notre hypothèse sur leurs déplacements migratoires. Notre suivi n’avait pas été assez long pour déterminer si le baleinoptère marqué sortait de Mediterranee mais il avait permis de mettre en évidence quelques phases d’inertie dans la vie de la baleine, identiques à celles observées dans les trajectoires de bouées dérivantes utilisées en océanographie physique.Nous avons repris ces anciennes données avec de nouveaux traitements. Outre la mise en évidence de l’adéquation de la trajectoire et du comportement de l’animal avec les caractéristiques hydrologiques et trophiques de chaque localisation, cela a permis de détecter une vingtaine de nouvelles boucles et des phases d’inertie dans la trajectoire de la baleine, et de les apparenter à des phases de sommeil. Pour cela il fallait démontrer quélles se répétaient chaque jour.
PIWI proteins as prognostic markers in cancer: a systematic review and meta-analysis
Authors: Mentis Alexios-Fotios A. , Dardiotis Efthimios , Papavassiliou Athanassios G. 
Published: June 2019

ABSTRACTBackgroundPIWI proteins, which interact with piRNAs, are implicated in stem cell and germ cell regulation, but have been detected in various cancers, as well.ObjectivesIn this systematic review, we explored, for the first time in the literature (to our knowledge), the association between prognosis in patients with cancer and intratumoral expression of PIWI proteins.Data sourcesPubMed, Embase and Web of Knowledge databases were searched for the relevant cohort studies.Study eligibility criteriaProspective or retrospective cohort studies investigating the association of intratumoral mRNA or protein expression of different types of PIWI proteins with survival, metastasis or recurrence of various types of cancers in the systematic review. Exclusion of cross-sectional studies, of studies on the prognostic value of genetic polymorphism of PIWI genes, of studies re-analyzed previously published databases, and of conference abstracts and non-English articles.ParticipantsTwenty-six studies with 4,299 participants were included in the systematic review.InterventionsPooled Hazard Ratios (HRs) and their 95% Confidence Intervals (CIs) were calculated for different PIWI proteins separately, by pooling of log of the calculated HRs using the random-effects model.Study appraisal and synthesis methodsData extraction was performed using a pre-designed form and quality of the studies was assessed using REMARK criteria. Heterogeneity assessed using the I2 index and the Cochran Q test. Publication bias assessed using funnel plots and Egger’s regression.ResultsThe pooled HR of mortality in high compared to low expression of HIWI, HILI and PIWIL4 was 1.87 (CI95%: 1.31-2.66, p < 0.05), 1.09 (CI95%: 0.58-2.07, p = 0.79) and 0.44 (CI95%: 0.25-0.76, p < 0.05), respectively. The pooled HR of recurrence in in high compared to low expression of HIWI and HILI was 1.72 (CI95%: 1.20-2.49, p < 0.05) and 1.98 (CI95%: 0.65-5.98, p = 0.23), respectively.LimitationsExclusion of studies not in English; Discrepancy between mRNA and protein levels, and the respective analytical methods; Only one cancer site – PIWI protein pair investigated in three or more studies.Conclusions and Implications of Key FindingsThe prognosis of cancer patients is worse with higher HIWI and lower PIWIL4 expression, although the results are highly variable for different cancers. The expression of these proteins can be used for personalized prognostication and treatment of individual patients.Systematic review registration numberNot registered.
TCR convergence in individuals treated with immune checkpoint inhibition for cancer
Authors: Looney Timothy , Topacio-Hall Denise , Lowman Geoffrey , Conroy Jeffrey , Morrison Carl , Oh David , Fong Lawrence , Zhang Li 
Published: June 2019

AbstractTumor antigen-driven selection may expand T cells having T cell receptors (TCRs) of shared antigen specificity but different amino acid or nucleotide sequence in a process known as TCR convergence. Substitution sequencing errors introduced by TCRβ (TCRB) repertoire sequencing may create artifacts resembling TCR convergence. Given the anticipated differences in substitution error rates across different next-generation sequencing platforms, the choice of platform could be consequential. To test this, we performed TCRB sequencing on the same peripheral blood mononuclear cells (PBMC) from individuals with cancer receiving anti-CTLA-4 or anti-PD-1 using an Illumina-based approach and an Ion Torrent-based approach. While both approaches found similar TCR diversity, clonality, and clonal overlap, we found that Illumina-based sequencing resulted in higher TCR convergence than with the Ion Torrent approach. Using the latter approach, we found that clonality and convergence independently predicted response and could be combined to improve the accuracy of a logistic regression classifier. These results demonstrate the importance of the sequencing platform in assessing TCRB convergence.
An S-cone circuit for edge detection in the primate retina
Authors: Patterson Sara S. , Kuchenbecker James A. , Anderson James R. , Bordt Andrea S. , Marshak David W. , Neitz Maureen , Neitz Jay 
Published: June 2019

AbstractMidget retinal ganglion cells (RGCs) are the most common RGC type in the primate retina. Their responses mediate both color and spatial vision, yet the specific links between midget RGC responses and visual perception are unclear. Previous research on the dual roles of midget RGCs has focused on those comparing long (L) vs. middle (M) wavelength sensitive cones. However, there is evidence for several other rare midget RGC subtypes receiving S-cone input, but their role in color and spatial vision is uncertain. Here, we confirm the existence of the single S-cone center OFF midget RGC circuit in the central retina of macaque monkey both structurally and functionally, by combining single cell electrophysiology with 3D electron microscopy reconstructions of the upstream circuitry. Like the well-studied L vs. M midget RGCs, the S-OFF midget RGCs have a center-surround receptive field consistent with a role in spatial vision. While spectral opponency in a primate RGC is classically assumed to contribute to hue perception, a role supporting edge detection is more consistent with the S-OFF midget RGC receptive field structure and studies of hue perception.
Cytological and genetic consequences for the progeny of a mitotic catastrophe provoked by Topoisomerase II deficiency
Authors: Ramos-Pérez Cristina , Dominska Margaret , Anaissi-Afonso Laura , Cazorla-Rivero Sara , Quevedo Oliver , Lorenzo-Castrillejo Isabel , Petes Thomas D , Machín Félix 
Published: June 2019

ABSTRACTTopoisomerase II (Top2) removes topological linkages between replicated chromosomes. Top2 inhibition leads to mitotic catastrophe (MC) when cells unsuccessfully try to split their genetic material between the two daughter cells. Herein, we have characterized the fate of these daughter cells in the budding yeast. Clonogenic and microcolony experiments, in combination with vital and apoptotic stains, showed that 75% of daughter cells become senescent in the short term; they are unable to divide but remain alive. Decline in cell vitality then occurred, yet slowly, uncoordinatedly when comparing pairs of daughters, and independently of the cell death mediator Mca1/Yca1. Furthermore, we showed that senescence can be modulated by ploidy, suggesting that gross chromosome imbalances during segregation may account for this phenotype. Indeed, we found that diploid long-term survivors of the MC are prone to genomic imbalances such as trisomies, uniparental disomies and terminal loss of heterozygosity (LOH), the latter affecting the longest chromosome arms.
Genetic determinants of lipids and cardiovascular disease outcomes: a wide-angled Mendelian randomization investigation
Authors: Allara Elias , Morani Gabriele , Carter Paul , Gkatzionis Apostolos , Zuber Verena , Foley Christopher N , Rees Jessica MB , Mason Amy M , Bell Steven , Gill Dipender , Butterworth Adam S , Angelantonio Emanuele Di , Peters James , Burgess Stephen 
Published: June 2019

ABSTRACTAimsTo systematically investigate causal relationships between circulating lipids and cardiovascular outcomes, using a Mendelian randomization approach.Methods and ResultsIn the primary analysis, we performed two-sample multivariable Mendelian randomization using data from participants of European ancestry. We also conducted univariable analyses using inverse-variance weighted and robust methods, and gene-specific analyses using variants that can be considered as proxies for specific lipid-lowering medications. We obtained associations with lipid fractions from the Global Lipids Genetics Consortium, a meta-analysis of 188,577 participants, and genetic associations with cardiovascular outcomes from 367,703 participants in UK Biobank.For LDL-cholesterol, in addition to the expected positive associations with coronary artery disease (CAD) risk (odds ratio per 1 standard deviation increase [OR], 1.45; 95% confidence interval [95%CI] 1.35-1.57) and other atheromatous outcomes (ischemic cerebrovascular disease and peripheral vascular disease), we found independent associations of genetically-predicted LDL-cholesterol with abdominal aortic aneurysm (OR 1.75; 95%CI 1.40-2.17), and aortic valve stenosis (OR 1.46; 95%CI 1.25-1.70). Genetically-predicted triglyceride levels were positively associated with CAD (OR 1.25; 95%CI 1.12-1.40), aortic valve stenosis (OR 1.29; 95%CI 1.04-1.61), and hypertension (OR 1.17; 95%CI 1.07-1.27), but inversely associated with venous thromboembolism (OR 0.79; 95%CI 0.67-0.93). The positive associations of genetically-predicted LDL-cholesterol and triglycerides with heart failure and aortic stenosis appeared to be mediated by CAD.ConclusionLowering LDL-cholesterol is likely to prevent abdominal aortic aneurysm and aortic stenosis, in addition to CAD and other atheromatous cardiovascular outcomes. Lowering triglycerides is likely to prevent CAD and aortic valve stenosis, but may increase risk of thromboembolism.
Characterization of Streptococcus pneumoniae phage-like element SpnCI reveals an enhanced virulent phenotype in the acute invertebrate infection model Galleria mellonella
Authors: McCullor Kimberly , Rahman Maliha , King Catherine , McShan W. Michael 
Published: June 2019

AbstractPhage-like elements are found in a multitude of streptococcal species, including pneumococcal strain Hungary19A-6 (SpnCI). The aim of our research was to investigate the role of phage-like element SpnCI in enhanced virulence and phenotypic modulation within Streptococcus pneumoniae. SpnCI was found to significantly enhance virulence within the invertebrate infection model Galleria mellonella. Infections with SpnCI led to a lower mean health score (1.6) and survival percentage (20%) compared to SpnCI null TIGR4 infections (3.85 mean health score and 50% survival). SpnCI remained integrated throughout growth, conferring greater sensitivity to UV irradiation. Change in transcriptional patterns occurred, including downregulation of operons involved with cell surface modelling in the SpnCI containing strain of TIGR4. Kanamycin-tagged SpnCI strain in Hungary19A-6 was inducible and isolated from lysate along with both annotated prophages. No phages were identified by PCR nor electron microscopy (EM) following induction of TIGR4 SpnCIΔstrA suggesting helper-phage dependence for dissemination. EM of lysate showed typical siphoviridae morphology with an average capsid size of 60 nm. Two of sixty capsids were found to be smaller, suggesting SpnCI disseminates using a similar mechanism described for Staphylococcus aureus phage-like element SaPI. SpnCI from lysate infected capsule null strain T4R but was incapable of infecting the encapsulated TIGR4 strain suggesting that capsule impedes phage infection. Our work demonstrates that SpnCI can modulate virulence, UV susceptibility, alter transcriptional patterns, and furthermore, can disseminate via infection within pneumococcus. Further research is necessary to elucidate how SpnCI modulates virulence and what genes are responsible for the enhanced virulence phenotype.ImportanceAlthough vaccines have limited the scope of pneumococcal infections, Streptococcus pneumoniae still remains an important human pathogen. Understanding novel elements, such as SpnCI, that enhance virulence can lead to the development of more targeted therapeutic and diagnostic tools within the clinical realm.
In-vivo targeted tagging of RNA isolates cell specific transcriptional responses to environmental stimuli and identifies liver-to-adipose RNA transfer
Authors: Darr J. , Lassi M. , Tomar Archana , Gerlini R. , Scheid F. , Hrabě de Angelis M. , Witting M. , Teperino R. 
Published: June 2019

AbstractBio-fluids contain various circulating cell-free RNA transcripts (ccfRNAs). The composition of these ccfRNAs varies between bio-fluids and constitute tantalizing biomarker candidates for several pathologies. ccfRNAs have also been demonstrated as mediators of cellular communication, yet little is known about their function in physiological and developmental settings and most works are limited to in-vitro studies. Here, we have developed iTAG-RNA, a novel method for the unbiased tagging of RNA transcripts in mice in-vivo. We used this method to isolate hepatocytes and kidney proximal epithelial cells-specific transcriptional response to a dietary challenge without interfering with the tissue architecture, and to identify multiple hepatocyte-secreted ccfRNAs in plasma. We also identified transfer of these hepatic derived ccfRNAs to adipose tissue, where they likely serve as a buffering mechanism to maintain cholesterol and lipid homeostasis. Our findings directly demonstrate in-vivo transfer of RNAs between tissues and highlight its implications for endocrine signaling and homeostasis.
DeepKinZero: Zero-Shot Learning for Predicting Kinase-Phosphosite Associations Involving Understudied Kinases
Authors: Deznabi Iman , Arabaci Busra , Koyutürk Mehmet , Tastan Oznur 
Published: June 2019

AbstractProtein phosphorylation is a key regulator of protein function in signal transduction pathways. Kinases are the enzymes that catalyze the phosphorylation of other proteins in a target specific manner. The dysregulation of phosphorylation is associated with many diseases including cancer. Although the advances in phosphoproteomics enable the identification of phosphosites at the proteome level, most of the phosphoproteome is still in the dark: more than 95% of the reported human phosphosites have no known kinases. Determining which kinase is responsible for phosphorylating a site remains an experimental challenge. Existing computational methods require several examples of known targets of a kinase to make accurate kinase specific predictions, yet for a large body of kinases, only a few or no target sites are reported. We present DeepKinZero, the first zero-shot learning approach to predict the kinase acting on a phosphosite for kinases with no known phosphosite information. DeepKinZero transfers knowledge from kinases with many known target phosphosites to those kinases with no known sites through a zero-shot learning model. The kinase specific positional amino acid preferences are learned using a bidirectional recurrent neural network. We show that DeepKinZero achieves significant improvement in accuracy for kinases with no known phosphosites in comparison to the baseline model and other methods available. By expanding our knowledge on understudied kinases, DeepKinZero can help to chart the phosphoproteome atlas.
Context-dependent activation of SIRT3 is necessary for anchorage-independent survival and metastasis of ovarian cancer cells
Authors: Kim Yeon Soo , Gupta-Vallur Piyushi , Jones Victoria M. , Worley Beth L. , Shimko Sara , Shin Dong-Hui , Crawford LaTaijah C. , Chen Chi-Wei , Aird Katherine M. , Abraham Thomas , Shepherd Trevor G. , Warrick Joshua I. , Lee Nam Y. , Phaeton Rebecca , Mythreye Karthikeyan , Hempel Nadine 
Published: June 2019

ABSTRACTCells must alter their antioxidant capacity for maximal metastatic potential. However, the antioxidant adaptations required for transcoelomic metastasis, which is the passive dissemination of cancer cells in the peritoneal cavity as seen in ovarian cancer, have largely remained unexplored. Contradicting the need for oxidant scavenging by tumor cells is the observation that expression of the nutrient stress sensor and regulator of mitochondrial antioxidant defenses, SIRT3, is suppressed in many primary tumors. We discovered that this mitochondrial deacetylase is however, upregulated in a context-dependent manner in cancer cells. SIRT3 activity and expression transiently increased following ovarian cancer cell detachment and in tumor cells derived from malignant ascites of high-grade serous adenocarcinoma patients. Mechanistically, SIRT3 prevents mitochondrial superoxide surges in detached cells by regulating the manganese superoxide dismutase SOD2. This mitochondrial stress response is under dual regulation by SIRT3. SIRT3 rapidly increases SOD2 activity as an early adaptation to cellular detachment, which is followed by SIRT3-dependent transcriptional increases in SOD2 during sustained anchorage-independence. In addition, SIRT3 inhibits glycolytic capacity in anchorage-independent cells thereby contributing to metabolic changes in response to detachment. While manipulation of SIRT3 expression has few deleterious effects on cancer cells in attached conditions, SIRT3 up-regulation and SIRT3-mediated oxidant scavenging following matrix detachment are required for anoikis resistance in vitro, and both SIRT3 and SOD2 are necessary for colonization of the peritoneal cavity in vivo. Our results highlight the novel context-specific, pro-metastatic role of SIRT3 in ovarian cancer.