bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evidence for social parasitism of early insect societies by Cretaceous rove beetles
Authors: Yamamoto Shûhei , Maruyama Munetoshi , Parker Joseph 
Published: December 2016

AbstractThe evolution of eusociality in ants and termites propelled both insect groups to their modern ecological dominance. Yet, eusociality also fostered the evolution of social parasitism—an adverse symbiosis, in which the superorganismal colonies formed by these insects are infiltrated by a profusion of invertebrate species that target nest resources. Predominant among these are the aleocharine rove beetles (Staphylinidae), a vast and ecologically diverse subfamily with numerous morphologically and behaviourally specialized socially parasitic lineages. Here, we report a fossil aleocharine,Mesosymbion compactusgen. et sp. nov., in Burmese amber (∼99 million years old), displaying specialized anatomy that is a hallmark of social parasites.Mesosymbioncoexisted in the Burmese palaeofauna with stem-group ants and termites that provide the earliest indications of eusociality in both insect groups. We infer that the advent of eusociality led automatically and unavoidably to selection for social parasitism. The antiquity and adaptive flexibility of aleocharines made them among the first organisms to engage in this type of symbiosis.
Acquired RAS or EGFR mutations and duration of response to EGFR blockade in colorectal cancer
Authors: Van Emburgh Beth O. , Arena Sabrina , Siravegna Giulia , Lazzari Luca , Crisafulli Giovanni , Corti Giorgio , Mussolin Benedetta , Baldi Federica , Buscarino Michela , Bartolini Alice , Valtorta Emanuele , Vidal Joana , Bellosillo Beatriz , Germano Giovanni , Pietrantonio Filippo , Ponzetti Agostino , Albanell Joan , Siena Salvatore , Sartore-Bianchi Andrea , Di Nicolantonio Federica , Montagut Clara , Bardelli Alberto 
Published: December 2016

AbstractBlockade of the epidermal growth factor receptor (EGFR) with the monoclonal antibodies cetuximab or panitumumab is effective in a subset of colorectal cancers (CRCs), but the emergence of resistance limits the efficacy of these therapeutic agents. At relapse, the majority of patients develop RAS mutations, while a subset acquires EGFR extracellular domain (ECD) mutations. Here we find that patients who experience greater and longer responses to EGFR blockade preferentially develop EGFR ECD mutations, while RAS mutations emerge more frequently in patients with smaller tumour shrinkage and shorter progression-free survival. In circulating cell-free tumour DNA of patients treated with anti-EGFR antibodies, RAS mutations emerge earlier than EGFR ECD variants. Subclonal RAS but not EGFR ECD mutations are present in CRC samples obtained before exposure to EGFR blockade. These data indicate that clonal evolution of drug-resistant cells is associated with the clinical outcome of CRC patients treated with anti-EGFR antibodies.
A large carnivorous mammal from the Late Cretaceous and the North American origin of marsupials
Authors: Wilson Gregory P. , Ekdale Eric G. , Hoganson John W. , Calede Jonathan J. , Vander Linden Abby 
Published: December 2016

AbstractMarsupial mammal relatives (stem metatherians) from the Mesozoic Era (252–66 million years ago) are mostly known from isolated teeth and fragmentary jaws. Here we report on the first near-complete skull remains of a North American Late Cretaceous metatherian, the stagodontid Didelphodon vorax. Our phylogenetic analysis indicates that marsupials or their closest relatives evolved in North America, as part of a Late Cretaceous diversification of metatherians, and later dispersed to South America. In addition to being the largest known Mesozoic therian mammal (node-based clade of eutherians and metatherians), Didelphodon vorax has a high estimated bite force and other craniomandibular and dental features that suggest it is the earliest known therian to invade a durophagous predator–scavenger niche. Our results broaden the scope of the ecomorphological diversification of Mesozoic mammals to include therian lineages that, in this case, were linked to the origin and evolution of marsupials.
Export of piRNA precursors by EJC triggers assembly of cytoplasmic Yb-body in Drosophila
Authors: Dennis Cynthia , Brasset Emilie , Sarkar Arpita , Vaury Chantal 
Published: December 2016

AbstractPIWI-interacting RNAs (piRNAs) are effectors of transposable element (TE) silencing in the reproductive apparatus. In Drosophila ovarian somatic cells, piRNAs arise from longer single-stranded RNA precursors that are processed in the cytoplasm presumably within the Yb-bodies. piRNA precursors encoded by the flamenco (flam) piRNA cluster accumulate in a single focus away from their sites of transcription. In this study, we identify the exportin complex containing Nxf1 and Nxt1 as required for flam precursor nuclear export. Together with components of the exon junction complex (EJC), it is necessary for the efficient transfer of flam precursors away from their site of transcription. Indeed, depletion of these components greatly affects flam intra-nuclear transit. Moreover, we show that Yb-body assembly is dependent on the nucleo-cytoplasmic export of flam transcripts. These results suggest that somatic piRNA precursors are thus required for the assembly of the cytoplasmic transposon silencing machinery.
Ecdysteroid-containing food supplements from Cyanotis arachnoidea on the European market: evidence for spinach product counterfeiting
Authors: Hunyadi Attila , Herke Ibolya , Lengyel Katalin , Báthori Mária , Kele Zoltán , Simon András , Tóth Gábor , Szendrei Kálmán 
Published: December 2016

AbstractPhytoecdysteroids like 20-hydroxyecdysone (“ecdysterone”) can exert a mild, non-hormonal anabolic/adaptogenic activity in mammals, and as such, are frequently used in food supplements. Spinach is well-known for its relatively low ecdysteroid content. Cyanotis arachnoidea, a plant native in China, is among the richest sources of phytoecdysteroids, and extracts of this plant are marketed in tons per year amounts via the internet at highly competitive prices. Here we report the investigation of a series of food supplements produced in Germany and claimed to contain spinach extracts. Twelve ecdysteroids including two new compounds were isolated and utilized as marker compounds. A comparative analysis of the products with Cyanotis and spinach extracts provides evidence that they were manufactured from Cyanotis extracts instead of spinach as stated. Based on the chromatographic fingerprints, 20-hydroxyecdysone 2- and 3-acetate are suggested as diagnostic markers for related quality control. This case appears to represent an unusual type of dietary supplement counterfeiting: undeclared extracts from alternative plants would supposedly ‘guarantee’ product efficacy.
Concordance between somatic copy number loss and down-regulated expression: A pan-cancer study of cancer predisposition genes
Authors: Wei Ran , Zhao Ming , Zheng Chun-Hou , Zhao Min , Xia Junfeng 
Published: December 2016

AbstractCancer predisposition genes (CPGs) are a class of cancer genes in which germline variants lead to increased risk of cancer. Research has revealed that copy number variation (CNV) may be linked to cancer susceptibility in CPGs. In this pan-cancer analysis, we explored the relationship between somatic CNV and gene expression changes in CPGs. Based on curated 827 human CPGs from literature, we firstly identified 729 CPGs with precise CNV information from 5067 tumor samples using TCGA CNV data. Among them, 128 CPGs tended to have more frequent copy number losses (CNLs) compared with copy number gains (CNGs). Then by correlating these CNV data with TCGA gene expression data, we obtained 49 CPGs with concordant CNLs and gene down-regulation. Intriguingly, five CPGs showed concordance between CNL and down-regulation in 50 or more tumor samples: MTAP (216 samples), PTEN (143), MCPH1 (86), SMAD4 (63), and MINPP1 (51), which may represent the recurrent driving force for gene expression change during oncogenesis. Moreover, network analysis revealed that these 49 CPGs were tightly connected. In summary, this study provides the first observation of concordance between CNLs and down-regulation of CPGs in pan-cancer, which may help better understand the CPG biology in tumorigenesis and cancer progression.
The minimum area requirements (MAR) for giant panda: an empirical study
Authors: Qing Jing , Yang Zhisong , He Ke , Zhang Zejun , Gu Xiaodong , Yang Xuyu , Zhang Wen , Yang Biao , Qi Dunwu , Dai Qiang 
Published: December 2016

AbstractHabitat fragmentation can reduce population viability, especially for area-sensitive species. The Minimum Area Requirements (MAR) of a population is the area required for the population’s long-term persistence. In this study, the response of occupancy probability of giant pandas against habitat patch size was studied in five of the six mountain ranges inhabited by giant panda, which cover over 78% of the global distribution of giant panda habitat. The probability of giant panda occurrence was positively associated with habitat patch area, and the observed increase in occupancy probability with patch size was higher than that due to passive sampling alone. These results suggest that the giant panda is an area-sensitive species. The MAR for giant panda was estimated to be 114.7 km2based on analysis of its occupancy probability. Giant panda habitats appear more fragmented in the three southern mountain ranges, while they are large and more continuous in the other two. Establishing corridors among habitat patches can mitigate habitat fragmentation, but expanding habitat patch sizes is necessary in mountain ranges where fragmentation is most intensive.
Real time optical Biopsy: Time-resolved Fluorescence Spectroscopy instrumentation and validation
Authors: Kittle David S. , Vasefi Fartash , Patil Chirag G. , Mamelak Adam , Black Keith L. , Butte Pramod V. 
Published: December 2016

AbstractThe Time-resolved fluorescence spectroscopy (TR-FS) has the potential to differentiate tumor and normal tissue in real time during surgical excision. In this manuscript, we describe the design of a novel TR-FS device, along with preliminary data on detection accuracy for fluorophores in a mixture. The instrument is capable of near real-time fluorescence lifetime acquisition in multiple spectral bands and analysis. It is also able to recover fluorescence lifetime with sub-20ps accuracy as validated with individual organic fluorescence dyes and dye mixtures yielding lifetime values for standard fluorescence dyes that closely match with published data. We also show that TR-FS is able to quantify the relative concentration of fluorescence dyes in a mixture by the unmixing of lifetime decays. We show that the TR-FS prototype is able to identify in near-real time the concentrations of dyes in a complex mixture based on previously trained data. As a result, we demonstrate that in complex mixtures of fluorophores, the relative concentration information is encoded in the fluorescence lifetime across multiple spectral bands. We show for the first time the temporal and spectral measurements of a mixture of fluorochromes and the ability to differentiate relative concentrations of each fluorochrome mixture in real time.
Internal luminescence efficiencies in InGaP/GaAs/Ge triple-junction solar cells evaluated from photoluminescence through optical coupling between subcells
Authors: Tex David M. , Imaizumi Mitsuru , Akiyama Hidefumi , Kanemitsu Yoshihiko 
Published: December 2016

AbstractIn-situ characterization is one of the most powerful techniques to improve material quality and device performance. Especially in view of highly efficient tandem solar cells this is an important issue for improving the cost-performance ratio. Optical techniques are suitable characterization methods, since they are non-destructing and contactless. In this work, we measured the power dependence of photoluminescence (PL) from the InGaP and GaAs subcells of an industry-standard triple-junction solar cell. High luminescence yields enhance the luminescence coupling, which was directly verified by time-resolved PL measurements. We present a new method to determine the internal luminescence efficiencies of InGaP and GaAs subcells with the aid of luminescence coupling. High luminescence efficiencies of 90% for GaAs and more than 20% for InGaP were found, which suggest that the material quality of the grown GaAs layer is excellent while the intrinsic luminescence limit of InGaP is still not reached even for high excitation conditions. The PL method is useful for probing the intrinsic material properties of the subcells in flat band condition, without influence of transport. Since no calibration of absolute PL is required, a fast screening of the material quality is possible, which should be extremely helpful for the solar cell industry.
Methionine sulfoxides in serum proteins as potential clinical biomarkers of oxidative stress
Authors: Suzuki Satoko , Kodera Yoshio , Saito Tatsuya , Fujimoto Kazumi , Momozono Akari , Hayashi Akinori , Kamata Yuji , Shichiri Masayoshi 
Published: December 2016

AbstractOxidative stress contributes to the pathophysiology of a variety of diseases, and circulating biomarkers of its severity remains a topic of great interest for researchers. Our peptidomic strategy enables accurate and reproducible analysis of circulating proteins/peptides with or without post-translational modifications. Conventional wisdom holds that hydrophobic methionines exposed to an aqueous environment or experimental handling procedures are vulnerable to oxidation. However, we show that the mass spectra intensity ratio of oxidized to non-oxidized methionine residues in serum tryptic proteins can be accurately quantified using a single drop of human serum and give stable and reproducible results. Our data demonstrate that two methionine residues in serum albumin (Met-111 and Met-147) are highly oxidized to methionine sulfoxide in patients with diabetes and renal failure and in healthy smokers versus non-smoker controls. This label-free mass spectrometry approach to quantify redox changes in methionine residues should facilitate the identification of additional circulating biomarkers suitable for predicting the development or progression of human diseases.
Antimicrobial growth promoters modulate host responses in mice with a defined intestinal microbiota
Authors: Brown Kirsty , Zaytsoff Sarah J. M. , Uwiera Richard R. E. , Inglis G. Douglas 
Published: December 2016

AbstractAntibiotics can promote growth in livestock (antimicrobial growth promoters, AGPs), however lack of knowledge regarding mechanisms has hampered the development of effective non-antibiotic alternatives. Antibiotics affect eukaryotic cells at therapeutic concentrations, yet effects of AGPs on host physiology are relatively understudied, partially due to the complexity of host-microorganism interactions within the gastrointestinal tract. To determine the direct effects of AGPs on the host, we generated Altered Schaedler Flora (ASF) mice, and administered chlortetracycline (CTC) and tylosin phosphate (TYL) in feed. Mice were challenged with Citrobacter rodentium to determine how AGPs alter host responses to physiological stress. Although CTC and TYL had inconsistent effects on the ASF taxa, AGPs protected mice from weight loss following C. rodentium inoculation. Mice treated with either CTC or TYL had lower expression of βd1 and Il17a in the intestine and had a robust induction of Il17a and Il10. Furthermore, AGP administration resulted in a lower hepatic expression of acute phase proteins (Saa1, Hp, and Cp) in liver tissue, and ameliorated C. rodentium-induced reductions in the expression of genes involved in lipogenesis (Hmgcl and Fabp1). Collectively, this indicates that AGPs directly affect host physiology, and highlights important considerations in the development of non-antibiotic alternatives.
Probing the role of cation-π interaction in the thermotolerance and catalytic performance of endo-polygalacturonases
Authors: Tu Tao , Li Yeqing , Su Xiaoyun , Meng Kun , Ma Rui , Wang Yuan , Yao Bin , Lin Zhemin , Luo Huiying 
Published: December 2016

AbstractUnderstanding the dynamics of the key pectinase, polygalacturonase, and improving its thermotolerance and catalytic efficiency are of importance for the cost-competitive bioconversion of pectic materials. By combining structure analysis and molecular dynamics (MD) simulations, eight mutagenesis sites having the potential to form cation-π interactions were identified in the widely used fungal endo-polygalacturonase PG63. In comparison to the wild-type, three single mutants H58Y, T71Y and T304Y showed improved thermostability (the apparentTms increased by 0.6−3.9 °C) and catalytic efficiency (by up to 32-fold). Chromatogram analysis of the hydrolysis products indicated that a larger amount of shorter sugars were released from the polygalacturonic acid by these three mutants than by the wild-type. MD analysis of the enzyme-substrate complexes illustrated that the mutants with introduced cation-π interaction have modified conformations of catalytic crevice, which provide an enviable environment for the catalytic process. Moreover, the lower plasticity of T3 loop 2 at the edge of the subsite tunnel appears to recruit the reducing ends of oligogalacturonide into the active site tunnel and initiates new hydrolysis reactions. This study demonstrates the importance of cation-π interaction in protein conformation and provides a realistic strategy to enhance the thermotolerance and catalytic performance of endo-polygalacturonases.
Magnetic separation of general solid particles realised by a permanent magnet
Authors: Hisayoshi K. , Uyeda C. , Terada K. 
Published: December 2016

AbstractMost existing solids are categorised as diamagnetic or weak paramagnetic materials. The possibility of magnetic motion has not been intensively considered for these materials. Here, we demonstrate for the first time that ensembles of heterogeneous particles (diamagnetic bismuth, diamond and graphite particles, as well as two paramagnetic olivines) can be dynamically separated into five fractions by the low field produced by neodymium (NdFeB) magnets during short-duration microgravity (μg). This result is in contrast to the generally accepted notion that ordinary solid materials are magnetically inert. The materials of the separated particles are identified by their magnetic susceptibility (χ), which is determined from the translating velocity. The potential of this approach as an analytical technique is comparable to that of chromatography separation because the extraction of new solid phases from a heterogeneous grain ensemble will lead to important discoveries about inorganic materials. The method is applicable for the separation of the precious samples such as lunar soils and/or the Hayabusa particles recovered from the asteroids, because even micron-order grains can be thoroughly separated without sample-loss.
RNA sequencing of chorionic villi from recurrent pregnancy loss patients reveals impaired function of basic nuclear and cellular machinery
Authors: Sõber Siim , Rull Kristiina , Reiman Mario , Ilisson Piret , Mattila Pirkko , Laan Maris 
Published: December 2016

AbstractRecurrent pregnancy loss (RPL) concerns ~3% of couples aiming at childbirth. In the current study, transcriptomes and miRNomes of 1st trimester placental chorionic villi were analysed for 2 RPL cases (≥6 miscarriages) and normal, but electively terminated pregnancies (ETP; n = 8). Sequencing was performed on Illumina HiSeq 2000 platform. Differential expression analyses detected 51 (27%) transcripts with increased and 138 (73%) with decreased expression in RPL compared to ETP (DESeq: FDR P < 0.1 and DESeq2: <0.05). RPL samples had substantially decreased transcript levels of histones, regulatory RNAs and genes involved in telomere, spliceosome, ribosomal, mitochondrial and intra-cellular signalling functions. Downregulated expression of HIST1H1B and HIST1H4A (Wilcoxon test, fc≤0.372, P≤9.37 × 10−4) was validated in an extended sample by quantitative PCR (RPL, n = 14; ETP, n = 24). Several upregulated genes are linked to placental function and pregnancy complications: ATF4, C3, PHLDA2, GPX4, ICAM1, SLC16A2. Analysis of the miRNA-Seq dataset identified no large disturbances in RPL samples. Notably, nearly 2/3 of differentially expressed genes have binding sites for E2F transcription factors, coordinating mammalian endocycle and placental development. For a conceptus destined to miscarriage, the E2F TF-family represents a potential key coordinator in reprogramming the placental genome towards gradually stopping the maintenance of basic nuclear and cellular functions.
Genetic diversity and population structure in Bactrocera correcta (Diptera: Tephritidae) inferred from mtDNA cox1 and microsatellite markers
Authors: Qin Yu-Jia , Buahom Nopparat , Krosch Matthew N. , Du Yu , Wu Yi , Malacrida Anna R. , Deng Yu-Liang , Liu Jia-Qi , Jiang Xiao-Long , Li Zhi-Hong 
Published: December 2016

AbstractBactrocera correcta is one of the most destructive pests of horticultural crops in tropical and subtropical regions. Despite the economic risk, the population genetics of this pest have remained relatively unexplored. This study explores population genetic structure and contemporary gene flow in B. correcta in Chinese Yunnan Province and attempts to place observed patterns within the broader geographical context of the species’ total range. Based on combined data from mtDNA cox1 sequences and 12 microsatellite loci obtained from 793 individuals located in 7 countries, overall genetic structuring was low. The expansion history of this species, including likely human-mediated dispersal, may have played a role in shaping the observed weak structure. The study suggested a close relationship between Yunnan Province and adjacent countries, with evidence for Western and/or Southern Yunnan as the invasive origin of B. correcta within Yunnan Province. The information gleaned from this analysis of gene flow and population structure has broad implications for quarantine, trade and management of this pest, especially in China where it is expanding northward. Future studies should concentrate effort on sampling South Asian populations, which would enable better inferences of the ancestral location of B. correcta and its invasion history into and throughout Asia.
Extraordinary behavioral entrainment following circadian rhythm bifurcation in mice
Authors: Harrison Elizabeth M. , Walbeek Thijs J. , Sun Jonathan , Johnson Jeremy , Poonawala Qays , Gorman Michael R. 
Published: December 2016

AbstractThe mammalian circadian timing system uses light to synchronize endogenously generated rhythms with the environmental day. Entrainment to schedules that deviate significantly from 24 h (T24) has been viewed as unlikely because the circadian pacemaker appears capable only of small, incremental responses to brief light exposures. Challenging this view, we demonstrate that simple manipulations of light alone induce extreme plasticity in the circadian system of mice. Firstly, exposure to dim nocturnal illumination (<0.1 lux), rather than completely dark nights, permits expression of an altered circadian waveform wherein mice in light/dark/light/dark (LDLD) cycles “bifurcate” their rhythms into two rest and activity intervals per 24 h. Secondly, this bifurcated state enables mice to adopt stable activity rhythms under 15 or 30 h days (LDLD T15/T30), well beyond conventional limits of entrainment. Continuation of dim light is unnecessary for T15/30 behavioral entrainment following bifurcation. Finally, neither dim light alone nor a shortened night is sufficient for the extraordinary entrainment observed under bifurcation. Thus, we demonstrate in a non-pharmacological, non-genetic manipulation that the circadian system is far more flexible than previously thought. These findings challenge the current conception of entrainment and its underlying principles, and reveal new potential targets for circadian interventions.