bluuebunny/crossref_metadata_2025 huggingface dataset:
Perceived Mutual Understanding (PMU)
Authors: Burtscher Michael J. , Oostlander Jeannette
Published: October 2016

Abstract. Team cognition plays an important role in predicting team processes and outcomes. Thus far, research has focused on structured cognition while paying little attention to perceptual cognition. The lack of research on perceptual team cognition can be attributed to the absence of an appropriate measure. To address this gap, we introduce the construct of perceived mutual understanding (PMU) as a type of perceptual team cognition and describe the development of a respective measure – the PMU-scale. Based on three samples from different team settings ( NTotal = 566), our findings show that the scale has good psychometric properties – both at the individual as well as at the team-level. Item parameters were improved during a multistage process. Exploratory as well as confirmatory factor analyses indicate that PMU is a one-dimensional construct. The scale demonstrates sufficient internal reliability. Correlational analyses provide initial proof of construct validity. Finally, common indicators for inter-rater reliability and inter-rater agreement suggest that treating PMU as a team-level construct is justified. The PMU-scale represents a convenient and versatile measure that will potentially foster empirical research on perceptual team cognition and thereby contribute to the advancement of team cognition research in general.
Autoantibodies against CD80 in patients with COPD
Authors: Luo Xu Min , Liu Xin Yan , Tang Ji Hong , Yang Wei , Ni Zhen Hua , Chen Qing Ge , Wang Xiongbiao
Published: October 2016

Chronic obstructive pulmonary disease (COPD) is an inflammation disorder and possibly an autoimmune disease. The components of the autoimmune response in the circulatory system are of considerable interest to clinicians. Because aberrations of costimulation status have been noted in COPD, the presence of autoantibodies to B7 costimulatory factor CD80 were investigated in a cohort of patients. Recombinant rs1CD80 (lacking the transmembrane domain of CD80) was used for Western blot analysis and ELISA to investigate the presence of autoantibodies in sera of patients with stable COPD and in controls without COPD. Cytokines IL‐6 and IL‐8 were detected using ELISA. Western blot revealed a specific band reacting to rs1CD80 by diluting sera pool of patients, which indicated the existence of autoantibodies to CD80. The serum level of anti‐rs1CD80 was higher in patients with COPD than in controls(P=0.0185) and was positively correlated to the serum level of IL‐6 (r=0.797, P<0.001) and IL‐8 (r=0.608, P<0.001). There was a tendency that more higher level of anti‐rs1CD80, more severe COPD stage. The existence of autoantibodies to costimulatory factor CD80 may suggest a pathogenic role of costimulatory factors in COPD.
Structural characterization of antibiotic self-immunity tRNA synthetase in plant tumour biocontrol agent
Authors: Chopra Shaileja , Palencia Andrés , Virus Cornelia , Schulwitz Sarah , Temple Brenda R. , Cusack Stephen , Reader John
Published: October 2016

Antibiotic-producing microbes evolved self-resistance mechanisms to avoid suicide. The biocontrol Agrobacterium radiobacter K84 secretes the Trojan Horse antibiotic agrocin 84 that is selectively transported into the plant pathogen A. tumefaciens and processed into the toxin TM84. We previously showed that TM84 employs a unique tRNA-dependent mechanism to inhibit leucyl-tRNA synthetase (LeuRS), while the TM84-producer prevents self-poisoning by expressing a resistant LeuRS AgnB2. We now identify a mechanism by which the antibiotic-producing microbe resists its own toxin. Using a combination of structural, biochemical and biophysical approaches, we show that AgnB2 evolved structural changes so as to resist the antibiotic by eliminating the tRNA-dependence of TM84 binding. Mutagenesis of key resistance determinants results in mutants adopting an antibiotic-sensitive phenotype. This study illuminates the evolution of resistance in self-immunity genes and provides mechanistic insights into a fascinating tRNA-dependent antibiotic with applications for the development of anti-infectives and the prevention of biocontrol emasculation.
Insulin and TOR signal in parallel through FOXO and S6K to promote epithelial wound healing
Authors: Kakanj Parisa , Moussian Bernard , Grönke Sebastian , Bustos Victor , Eming Sabine A. , Partridge Linda , Leptin Maria
Published: October 2016

The TOR and Insulin/IGF signalling (IIS) network controls growth, metabolism and ageing. Although reducing TOR or insulin signalling can be beneficial for ageing, it can be detrimental for wound healing, but the reasons for this difference are unknown. Here we show that IIS is activated in the cells surrounding an epidermal wound in Drosophila melanogaster larvae, resulting in PI3K activation and redistribution of the transcription factor FOXO. Insulin and TOR signalling are independently necessary for normal wound healing, with FOXO and S6K as their respective effectors. IIS is specifically required in cells surrounding the wound, and the effect is independent of glycogen metabolism. Insulin signalling is needed for the efficient assembly of an actomyosin cable around the wound, and constitutively active myosin II regulatory light chain suppresses the effects of reduced IIS. These findings may have implications for the role of insulin signalling and FOXO activation in diabetic wound healing.
N-type organic electrochemical transistors with stability in water
Authors: Giovannitti Alexander , Nielsen Christian B. , Sbircea Dan-Tiberiu , Inal Sahika , Donahue Mary , Niazi Muhammad R. , Hanifi David A. , Amassian Aram , Malliaras George G. , Rivnay Jonathan , McCulloch Iain
Published: October 2016

Organic electrochemical transistors (OECTs) are receiving significant attention due to their ability to efficiently transduce biological signals. A major limitation of this technology is that only p-type materials have been reported, which precludes the development of complementary circuits, and limits sensor technologies. Here, we report the first ever n-type OECT, with relatively balanced ambipolar charge transport characteristics based on a polymer that supports both hole and electron transport along its backbone when doped through an aqueous electrolyte and in the presence of oxygen. This new semiconducting polymer is designed specifically to facilitate ion transport and promote electrochemical doping. Stability measurements in water show no degradation when tested for 2 h under continuous cycling. This demonstration opens the possibility to develop complementary circuits based on OECTs and to improve the sophistication of bioelectronic devices.
Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli
Authors: Kim Minseung , Rai Navneet , Zorraquino Violeta , Tagkopoulos Ilias
Published: October 2016

A significant obstacle in training predictive cell models is the lack of integrated data sources. We develop semi-supervised normalization pipelines and perform experimental characterization (growth, transcriptional, proteome) to create Ecomics, a consistent, quality-controlled multi-omics compendium for Escherichia coli with cohesive meta-data information. We then use this resource to train a multi-scale model that integrates four omics layers to predict genome-wide concentrations and growth dynamics. The genetic and environmental ontology reconstructed from the omics data is substantially different and complementary to the genetic and chemical ontologies. The integration of different layers confers an incremental increase in the prediction performance, as does the information about the known gene regulatory and protein-protein interactions. The predictive performance of the model ranges from 0.54 to 0.87 for the various omics layers, which far exceeds various baselines. This work provides an integrative framework of omics-driven predictive modelling that is broadly applicable to guide biological discovery.
Orbital disproportionation of electronic density is a universal feature of alkali-doped fullerides
Authors: Iwahara Naoya , Chibotaru Liviu F.
Published: October 2016

Alkali-doped fullerides show a wide range of electronic phases in function of alkali atoms and the degree of doping. Although the presence of strong electron correlations is well established, recent investigations also give evidence for dynamical Jahn–Teller instability in the insulating and the metallic trivalent fullerides. In this work, to reveal the interplay of these interactions in fullerides with even electrons, we address the electronic phase of tetravalent fulleride with accurate many-body calculations within a realistic electronic model including all basic interactions extracted from first principles. We find that the Jahn–Teller instability is always realized in these materials too. In sharp contrast to the correlated metals, tetravalent system displays uncorrelated band-insulating state despite similar interactions present in both fullerides. Our results show that the Jahn–Teller instability and the accompanying orbital disproportionation of electronic density in the degenerate lowest unoccupied molecular orbital band is a universal feature of fullerides.
In-vivo Dynamics of the Human Hippocampus across the Menstrual Cycle
Authors: Barth Claudia , Steele Christopher J , Mueller Karsten , Rekkas Vivien P. , Arélin Katrin , Pampel Andre , Burmann Inga , Kratzsch Jürgen , Villringer Arno , Sacher Julia
Published: October 2016

Sex hormones fluctuate during the menstrual cycle. Evidence from animal studies suggests similar subtle fluctuations in hippocampal structure, predominantly linked to estrogen. Hippocampal abnormalities have been observed in several neuropsychiatric pathologies with prominent sexual dimorphism. Yet, the potential impact of subtle sex-hormonal fluctuations on human hippocampal structure in health is unclear. We tested the feasibility of longitudinal neuroimaging in conjunction with rigorous menstrual cycle monitoring to evaluate potential changes in hippocampal microstructure associated with physiological sex-hormonal changes. Thirty longitudinal diffusion weighted imaging scans of a single healthy female subject were acquired across two full menstrual cycles. We calculated hippocampal fractional anisotropy (FA), a measure sensitive to changes in microstructural integrity, and investigated potential correlations with estrogen. We observed a significant positive correlation between FA values and estrogen in the hippocampus bilaterally, revealing a peak in FA closely paralleling ovulation. This exploratory, single-subject study demonstrates the feasibility of a longitudinal DWI scanning protocol across the menstrual cycle and is the first to link subtle endogenous hormonal fluctuations to changes in FA in vivo. In light of recent attempts to neurally phenotype single humans, our findings highlight menstrual cycle monitoring in parallel with highly sampled individual neuroimaging data to address fundamental questions about the dynamics of plasticity in the adult brain.
Locating the depth of magma supply for volcanic eruptions, insights from Mt. Cameroon
Authors: Geiger Harri , Barker Abigail K. , Troll Valentin R.
Published: October 2016

Mt. Cameroon is one of the most active volcanoes in Africa and poses a possible threat to about half a million people in the area, yet knowledge of the volcano’s underlying magma supply system is sparse. To characterize Mt. Cameroon’s magma plumbing system, we employed mineral-melt equilibrium thermobarometry on the products of the volcano’s two most recent eruptions of 1999 and 2000. Our results suggest pre-eruptive magma storage between 20 and 39 km beneath Mt. Cameroon, which corresponds to the Moho level and below. Additionally, the 1999 eruption products reveal several shallow magma pockets between 3 and 12 km depth, which are not detected in the 2000 lavas. This implies that small-volume magma batches actively migrate through the plumbing system during repose intervals. Evolving and migrating magma parcels potentially cause temporary unrest and short-lived explosive outbursts, and may be remobilized during major eruptions that are fed from sub-Moho magma reservoirs.
A Novel Genetic Variant in Long Non-coding RNA Gene NEXN-AS1 is Associated with Risk of Lung Cancer
Authors: Yuan Hua , Liu Hongliang , Liu Zhensheng , Owzar Kouros , Han Younghun , Su Li , Wei Yongyue , Hung Rayjean J. , McLaughlin John , Brhane Yonathan , Brennan Paul , Bickeboeller Heike , Rosenberger Albert , Houlston Richard S. , Caporaso Neil , Landi Maria Teresa , Heinrich Joachim , Risch Angela , Christiani David C. , Gümüş Zeynep H. , Klein Robert J. , Amos Christopher I. , Wei Qingyi
Published: October 2016

Lung cancer etiology is multifactorial, and growing evidence has indicated that long non-coding RNAs (lncRNAs) are important players in lung carcinogenesis. We performed a large-scale meta-analysis of 690,564 SNPs in 15,531 autosomal lncRNAs by using datasets from six previously published genome-wide association studies (GWASs) from the Transdisciplinary Research in Cancer of the Lung (TRICL) consortium in populations of European ancestry. Previously unreported significant SNPs (P value < 1 × 10−7) were further validated in two additional independent lung cancer GWAS datasets from Harvard University and deCODE. In the final meta-analysis of all eight GWAS datasets with 17,153 cases and 239,337 controls, a novel risk SNP rs114020893 in the lncRNA NEXN-AS1 region at 1p31.1 remained statistically significant (odds ratio = 1.17; 95% confidence interval = 1.11–1.24; P = 8.31 × 10−9). In further in silico analysis, rs114020893 was predicted to change the secondary structure of the lncRNA. Our finding indicates that SNP rs114020893 of NEXN-AS1 at 1p31.1 may contribute to lung cancer susceptibility.
Fast sintering of silver nanoparticle and flake layers by infrared module assistance in large area roll-to-roll gravure printing system
Authors: Park Janghoon , Kang Hyi Jae , Shin Kee-Hyun , Kang Hyunkyoo
Published: October 2016

We present fast sintering for silver (Ag) nanoparticle (NP) and flake layers printed using roll-to-roll (R2R) gravure printing. An infrared (IR) sintering module was applied to an R2R system to shorten the sintering duration of an R2R gravure-printed Ag layer. IR sintering of the conductive layer was improved by optimising the process condition. After printing of the Ag NP and Ag flake layers, additional IR sintering was performed in the R2R system. The lowest sheet resistance obtained in the Ag NP layer was 0.294 Ω/□, the distance between the substrate and lamp was 50-mm long, the IR lamp power was 500 W, and the sintering time was 5.4 s. The fastest sintering of 0.34 Ω/□ was achieved with 50-mm distance, 1,000-W IR lamp power, and 1.08-s sintering time. In the Ag flake layer, the lowest sheet resistance obtained was 0.288 Ω/□ with a 20-mm distance, 1,000-W IR lamp power, and 10.8-s sintering time. Meanwhile, the fastest sintering was obtained with a 3.83 Ω/□ sheet resistance, 20-mm distance, 1000-W IR lamp, and 1.08-s sintering time. Thus, the IR sintering module can easily be employed in an R2R system to obtain excellent layer sheet resistance.
Computational prediction shines light on type III secretion origins
Authors: Goldberg Tatyana , Rost Burkhard , Bromberg Yana
Published: October 2016

Type III secretion system is a key bacterial symbiosis and pathogenicity mechanism responsible for a variety of infectious diseases, ranging from food-borne illnesses to the bubonic plague. In many Gram-negative bacteria, the type III secretion system transports effector proteins into host cells, converting resources to bacterial advantage. Here we introduce a computational method that identifies type III effectors by combining homology-based inference with de novo predictions, reaching up to 3-fold higher performance than existing tools. Our work reveals that signals for recognition and transport of effectors are distributed over the entire protein sequence instead of being confined to the N-terminus, as was previously thought. Our scan of hundreds of prokaryotic genomes identified previously unknown effectors, suggesting that type III secretion may have evolved prior to the archaea/bacteria split. Crucially, our method performs well for short sequence fragments, facilitating evaluation of microbial communities and rapid identification of bacterial pathogenicity – no genome assembly required. pEffect and its data sets are available at http://services.bromberglab.org/peffect.
Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells
Authors: Hölzer Martin , Krähling Verena , Amman Fabian , Barth Emanuel , Bernhart Stephan H. , Carmelo Victor A. O. , Collatz Maximilian , Doose Gero , Eggenhofer Florian , Ewald Jan , Fallmann Jörg , Feldhahn Lasse M. , Fricke Markus , Gebauer Juliane , Gruber Andreas J. , Hufsky Franziska , Indrischek Henrike , Kanton Sabina , Linde Jörg , Mostajo Nelly , Ochsenreiter Roman , Riege Konstantin , Rivarola-Duarte Lorena , Sahyoun Abdullah H. , Saunders Sita J. , Seemann Stefan E. , Tanzer Andrea , Vogel Bertram , Wehner Stefanie , Wolfinger Michael T. , Backofen Rolf , Gorodkin Jan , Grosse Ivo , Hofacker Ivo , Hoffmann Steve , Kaleta Christoph , Stadler Peter F. , Becker Stephan , Marz Manja
Published: October 2016

The unprecedented outbreak of Ebola in West Africa resulted in over 28,000 cases and 11,000 deaths, underlining the need for a better understanding of the biology of this highly pathogenic virus to develop specific counter strategies. Two filoviruses, the Ebola and Marburg viruses, result in a severe and often fatal infection in humans. However, bats are natural hosts and survive filovirus infections without obvious symptoms. The molecular basis of this striking difference in the response to filovirus infections is not well understood. We report a systematic overview of differentially expressed genes, activity motifs and pathways in human and bat cells infected with the Ebola and Marburg viruses, and we demonstrate that the replication of filoviruses is more rapid in human cells than in bat cells. We also found that the most strongly regulated genes upon filovirus infection are chemokine ligands and transcription factors. We observed a strong induction of the JAK/STAT pathway, of several genes encoding inhibitors of MAP kinases (DUSP genes) and of PPP1R15A, which is involved in ER stress-induced cell death. We used comparative transcriptomics to provide a data resource that can be used to identify cellular responses that might allow bats to survive filovirus infections.
Intrinsic noise and deviations from criticality in Boolean gene-regulatory networks
Authors: Villegas Pablo , Ruiz-Franco José , Hidalgo Jorge , Muñoz Miguel A.
Published: October 2016

Gene regulatory networks can be successfully modeled as Boolean networks. A much discussed hypothesis says that such model networks reproduce empirical findings the best if they are tuned to operate at criticality, i.e. at the borderline between their ordered and disordered phases. Critical networks have been argued to lead to a number of functional advantages such as maximal dynamical range, maximal sensitivity to environmental changes, as well as to an excellent tradeoff between stability and flexibility. Here, we study the effect of noise within the context of Boolean networks trained to learn complex tasks under supervision. We verify that quasi-critical networks are the ones learning in the fastest possible way –even for asynchronous updating rules– and that the larger the task complexity the smaller the distance to criticality. On the other hand, when additional sources of intrinsic noise in the network states and/or in its wiring pattern are introduced, the optimally performing networks become clearly subcritical. These results suggest that in order to compensate for inherent stochasticity, regulatory and other type of biological networks might become subcritical rather than being critical, all the most if the task to be performed has limited complexity.
Antiestrogen Resistant Cell Lines Expressing Estrogen Receptor α Mutations Upregulate the Unfolded Protein Response and are Killed by BHPI
Authors: Mao Chengjian , Livezey Mara , Kim Ji Eun , Shapiro David J.
Published: October 2016

Outgrowth of metastases expressing ERα mutations Y537S and D538G is common after endocrine therapy for estrogen receptor α (ERα) positive breast cancer. The effect of replacing wild type ERα in breast cancer cells with these mutations was unclear. We used the CRISPR-Cas9 genome editing system and homology directed repair to isolate and characterize 14 T47D cell lines in which ERαY537S or ERαD538G replace one or both wild-type ERα genes. In 2-dimensional, and in quantitative anchorage-independent 3-dimensional cell culture, ERαY537S and ERαD538G cells exhibited estrogen-independent growth. A progestin further increased their already substantial proliferation in micromolar 4-hydroxytamoxifen and fulvestrant/ICI 182,780 (ICI). Our recently described ERα biomodulator, BHPI, which hyperactivates the unfolded protein response (UPR), completely blocked proliferation. In ERαY537S and ERαD538G cells, estrogen-ERα target genes were constitutively active and partially antiestrogen resistant. The UPR marker sp-XBP1 was constitutively activated in ERαY537S cells and further induced by progesterone in both cell lines. UPR-regulated genes associated with tamoxifen resistance, including the oncogenic chaperone BiP/GRP78, were upregulated. ICI displayed a greater than 2 fold reduction in its ability to induce ERαY537S and ERαD538G degradation. Progestins, UPR activation and perhaps reduced ICI-stimulated ERα degradation likely contribute to antiestrogen resistance seen in ERαY537S and ERαD538G cells.
The phasor-FLIM fingerprints reveal shifts from OXPHOS to enhanced glycolysis in Huntington Disease
Authors: Sameni Sara , Syed Adeela , Marsh J. Lawrence , Digman Michelle A.
Published: October 2016

Huntington disease (HD) is an autosomal neurodegenerative disorder caused by the expansion of Polyglutamine (polyQ) in exon 1 of the Huntingtin protein. Glutamine repeats below 36 are considered normal while repeats above 40 lead to HD. Impairment in energy metabolism is a common trend in Huntington pathogenesis; however, this effect is not fully understood. Here, we used the phasor approach and Fluorescence Lifetime Imaging Microscopy (FLIM) to measure changes between free and bound fractions of NADH as a indirect measure of metabolic alteration in living cells. Using Phasor-FLIM, pixel maps of metabolic alteration in HEK293 cell lines and in transgenic Drosophila expressing expanded and unexpanded polyQ HTT exon1 in the eye disc were developed. We found a significant shift towards increased free NADH, indicating an increased glycolytic state for cells and tissues expressing the expanded polyQ compared to unexpanded control. In the nucleus, a further lifetime shift occurs towards higher free NADH suggesting a possible synergism between metabolic dysfunction and transcriptional regulation. Our results indicate that metabolic dysfunction in HD shifts to increased glycolysis leading to oxidative stress and cell death. This powerful label free method can be used to screen native HD tissue samples and for potential drug screening.
Marangoni effect visualized in two-dimensions Optical tweezers for gas bubbles
Authors: Miniewicz A. , Bartkiewicz S. , Orlikowska H. , Dradrach K.
Published: October 2016

In the report we demonstrate how, using laser light, effectively trap gas bubbles and transport them through a liquid phase to a desired destination by shifting the laser beam position. The physics underlying the effect is complex but quite general as it comes from the limited to two-dimension, well-known, Marangoni effect. The experimental microscope-based system consists of a thin layer of liquid placed between two glass plates containing a dye dissolved in a solvent and a laser light beam that is strongly absorbed by the dye. This point-like heat source locally changes surface tension of nearby liquid-air interface. Because of temperature gradients a photo-triggered Marangoni flows are induced leading to self-amplification of the effect and formation of large-scale whirls. The interface is bending toward beam position allowing formation of a gas bubble upon suitable beam steering. Using various techniques (employing luminescent particles or liquid crystals), we visualize liquid flows propelled by the tangential to interface forces. This helped us to understand the physics of the phenomenon and analyze accompanying effects leading to gas bubble trapping. The manipulation of sessile droplets moving on the glass surface induced via controlled with laser light interface bending (i.e. “droplet catapult”) is demonstrated as well.
Zika virus infection during the period of maximal brain growth causes microcephaly and corticospinal neuron apoptosis in wild type mice
Authors: Huang Wen-Chin , Abraham Rachy , Shim Byoung-Shik , Choe Hyeryun , Page Damon T.
Published: October 2016

Zika virus (ZIKV) infection in pregnant women has been established as a cause of microcephaly in newborns. Here we test the hypothesis that neurodevelopmental stages when the brain is undergoing rapid growth are particularly vulnerable to the effects of ZIKV infection. We injected ZIKV intracranially into wild type C57BL/6 mice at two different time points: early postnatal development, when the brain is growing at its maximal rate, and at weaning, when the brain has largely reached adult size. Both time points showed widespread immunoreactivity for ZIKV and cleaved caspase 3 (CC3, a marker of apoptosis) throughout the brain. However, in early postnatal ZIKV injected mice, some brain areas and cell types display particularly large increases in apoptosis that we did not observe in older animals. Corticospinal pyramidal neurons, a cell type implicated in human microcephaly associated with ZIKV infection, are an example of one such cell type. Proliferating cells in the ventricular zone stem cell compartment are also depleted. These findings are consistent with the hypothesis that periods of rapid brain growth are especially susceptible to neurodevelopmental effects of ZIKV infection, and establish a valuable model to investigate mechanisms underlying neurodevelopmental effects of ZIKV infection and explore candidate therapeutics.
Islanding the power grid on the transmission level: less connections for more security
Authors: Mureddu Mario , Caldarelli Guido , Damiano Alfonso , Scala Antonio , Meyer-Ortmanns Hildegard
Published: October 2016

Islanding is known as a management procedure of the power system that is implemented at the distribution level to preserve sensible loads from outages and to guarantee the continuity in electricity supply, when a high amount of distributed generation occurs. In this paper we study islanding on the level of the transmission grid and shall show that it is a suitable measure to enhance energy security and grid resilience. We consider the German and Italian transmission grids. We remove links either randomly to mimic random failure events, or according to a topological characteristic, their so-called betweenness centrality, to mimic an intentional attack and test whether the resulting fragments are self-sustainable. We test this option via the tool of optimized DC power flow equations. When transmission lines are removed according to their betweenness centrality, the resulting islands have a higher chance of being dynamically self-sustainable than for a random removal. Less connections may even increase the grid’s stability. These facts should be taken into account in the design of future power grids.
New interpretation of the Gran Dolina-TD6 bearing Homo antecessor deposits through sedimentological analysis
Authors: Campaña I. , Pérez-González A. , Benito-Calvo A. , Rosell J. , Blasco R. , de Castro J. M. Bermúdez , Carbonell E. , Arsuaga J. L.
Published: October 2016

Gran Dolina is a cavity infilled by at least 25 m of Pleistocene sediments. This sequence contains the TD6 stratigraphic unit, whose records include around 170 hominin bones that have allowed the definition of a new species, Homo antecessor. This fossil accumulation was studied as a single assemblage and interpreted as a succession of several human home bases. We propose a complete stratigraphic context and sedimentological interpretation for TD6, analyzing the relationships between the sedimentary facies, the clasts and archaeo-palaeontological remains. The TD6 unit has been divided into three sub-units and 13 layers. Nine sedimentary facies have been defined. Hominin remains appear related to three different sedimentary facies: debris flow facies, channel facies and floodplain facies. They show three kinds of distribution: first a group of scattered fossils, then a group with layers of fossils in fluvial facies, and third a group with a layer of fossils in mixed fluvial and gravity flow facies. The results of this work suggest that some of these hominin remains accumulated in the cave by geological processes, coming from the adjacent slope above the cave or the cave entry, as the palaeogeography and sedimentary characteristics of these allochthonous facies suggest.
Versatile members of the DNAJ family show Hsp70 dependent anti-aggregation activity on RING1 mutant parkin C289G
Authors: Kakkar Vaishali , Kuiper E. F. Elsiena , Pandey Abhinav , Braakman Ineke , Kampinga Harm H.
Published: October 2016

Parkinson’s disease is one of the most common neurodegenerative disorders and several mutations in different genes have been identified to contribute to the disease. A loss of function parkin RING1 domain mutant (C289G) is associated with autosomal-recessive juvenile-onset Parkinsonism (AR-JP) and displays altered solubility and sequesters into aggregates. Single overexpression of almost each individual member of the Hsp40 (DNAJ) family of chaperones efficiently reduces parkin C289G aggregation and requires interaction with and activity of endogenously expressed Hsp70 s. For DNAJB6 and DNAJB8, potent suppressors of aggregation of polyglutamine proteins for which they rely mainly on an S/T-rich region, it was found that the S/T-rich region was dispensable for suppression of parkin C289G aggregation. Our data implies that different disease-causing proteins pose different challenges to the protein homeostasis system and that DNAJB6 and DNAJB8 are highly versatile members of the DNAJ protein family with multiple partially non-overlapping modes of action with respect to handling disease-causing proteins, making them interesting potential therapeutic targets.
Computational identification of putative lincRNAs in mouse embryonic stem cell
Authors: Liu Hui , Lyu Jie , Liu Hongbo , Gao Yang , Guo Jing , He Hongjuan , Han Zhengbin , Zhang Yan , Wu Qiong
Published: October 2016

As the regulatory factors, lncRNAs play critical roles in embryonic stem cells. And lincRNAs are most widely studied lncRNAs, however, there might still might exist a large member of uncovered lncRNAs. In this study, we constructed the de novo assembly of transcriptome to detect 6,701 putative long intergenic non-coding transcripts (lincRNAs) expressed in mouse embryonic stem cells (ESCs), which might be incomplete with the lack coverage of 5′ ends assessed by CAGE peaks. Comparing the TSS proximal regions between the known lincRNAs and their closet protein coding transcripts, our results revealed that the lincRNA TSS proximal regions are associated with the characteristic genomic and epigenetic features. Subsequently, 1,293 lincRNAs were corrected at their 5′ ends using the putative lincRNA TSS regions predicted by the TSS proximal region prediction model based on genomic and epigenetic features. Finally, 43 putative lincRNAs were annotated by Gene Ontology terms. In conclusion, this work provides a novel catalog of mouse ESCs-expressed lincRNAs with the relatively complete transcript length, which might be useful for the investigation of transcriptional and post-transcriptional regulation of lincRNA in mouse ESCs and even mammalian development.
AML1/ETO accelerates cell migration and impairs cell-to-cell adhesion and homing of hematopoietic stem/progenitor cells
Authors: Saia Marco , Termanini Alberto , Rizzi Nicoletta , Mazza Massimiliano , Barbieri Elisa , Valli Debora , Ciana Paolo , Gruszka Alicja M. , Alcalay Myriam
Published: October 2016

The AML1/ETO fusion protein found in acute myeloid leukemias functions as a transcriptional regulator by recruiting co-repressor complexes to its DNA binding site. In order to extend the understanding of its role in preleukemia, we expressed AML1/ETO in a murine immortalized pluripotent hematopoietic stem/progenitor cell line, EML C1, and found that genes involved in functions such as cell-to-cell adhesion and cell motility were among the most significantly regulated as determined by RNA sequencing. In functional assays, AML1/ETO-expressing cells showed a decrease in adhesion to stromal cells, an increase of cell migration rate in vitro, and displayed an impairment in homing and engraftment in vivo upon transplantation into recipient mice. Our results suggest that AML1/ETO expression determines a more mobile and less adherent phenotype in preleukemic cells, therefore altering the interaction with the hematopoietic niche, potentially leading to the migration across the bone marrow barrier and to disease progression.
Moku virus; a new Iflavirus found in wasps, honey bees and Varroa
Authors: Mordecai Gideon J , Brettell Laura E , Pachori Purnima , Villalobos Ethel M. , Martin Stephen J , Jones Ian M , Schroeder Declan C
Published: October 2016

There is an increasing global trend of emerging infectious diseases (EIDs) affecting a wide range of species, including honey bees. The global epidemic of the single stranded RNA Deformed wing virus (DWV), driven by the spread of Varroa destructor has been well documented. However, DWV is just one of many insect RNA viruses which infect a wide range of hosts. Here we report the full genome sequence of a novel Iflavirus named Moku virus (MV), discovered in the social wasp Vespula pensylvanica collected in Hawaii. The novel genome is 10,056 nucleotides long and encodes a polyprotein of 3050 amino acids. Phylogenetic analysis showed that MV is most closely related to Slow bee paralysis virus (SBPV), which is highly virulent in honey bees but rarely detected. Worryingly, MV sequences were also detected in honey bees and Varroa from the same location, suggesting that MV can also infect other hymenopteran and Acari hosts.
A novel proposal of a simplified bacterial gene set and the neo-construction of a general minimized metabolic network
Authors: Ye Yuan-Nong , Ma Bin-Guang , Dong Chuan , Zhang Hong , Chen Ling-Ling , Guo Feng-Biao
Published: October 2016

A minimal gene set (MGS) is critical for the assembly of a minimal artificial cell. We have developed a proposal of simplifying bacterial gene set to approximate a bacterial MGS by the following procedure. First, we base our simplified bacterial gene set (SBGS) on experimentally determined essential genes to ensure that the genes included in the SBGS are critical. Second, we introduced a half-retaining strategy to extract persistent essential genes to ensure stability. Third, we constructed a viable metabolic network to supplement SBGS. The proposed SBGS includes 327 genes and required 431 reactions. This report describes an SBGS that preserves both self-replication and self-maintenance systems. In the minimized metabolic network, we identified five novel hub metabolites and confirmed 20 known hubs. Highly essential genes were found to distribute the connecting metabolites into more reactions. Based on our SBGS, we expanded the pool of targets for designing broad-spectrum antibacterial drugs to reduce pathogen resistance. We also suggested a rough semi-de novo strategy to synthesize an artificial cell, with potential applications in industry.
HMG-CoAR expression in male breast cancer: relationship with hormone receptors, Hippo transducers and survival outcomes
Authors: Di Benedetto Anna , Mottolese Marcella , Sperati Francesca , Ercolani Cristiana , Di Lauro Luigi , Pizzuti Laura , Vici Patrizia , Terrenato Irene , Shaaban Abeer M. , Sundara-Rajan Sreekumar , Humphries Matthew P. , Barba Maddalena , Speirs Valerie , De Maria Ruggero , Maugeri-Saccà Marcello
Published: October 2016

Male breast cancer (MBC) is a rare hormone-driven disease often associated with obesity. HMG-CoAR is the central enzyme of the mevalonate pathway, a molecular route deputed to produce cholesterol and steroid-based hormones. HMG-CoAR regulates the oncogenic Hippo transducers TAZ/YAP whose expression was previously associated with shorter survival in MBC. 225 MBC samples were immunostained for HMG-CoAR and 124 were considered eligible for exploring its relationship with hormone receptors (ER, PgR, AR), Hippo transducers and survival outcomes. HMG-CoAR was positively associated with the expression of hormone receptors (ER, PgR, AR) and Hippo transducers. Overall survival was longer in patients with HMG-CoAR-positive tumors compared with their negative counterparts (p = 0.031). Five- and 10-year survival outcomes were better in patients whose tumors expressed HMG-CoAR (p = 0.044 and p = 0.043). Uni- and multivariate analyses for 10-year survival suggested that HMG-CoAR expression is a protective factor (HR 0.50, 95% CI: 0.25–0.99, p = 0.048 and HR 0.53, 95% CI: 0.26–1.07, p = 0.078). Results were confirmed in a sensitivity analysis by excluding uncommon histotypes (multivariate Cox: HR 0.45, 95% CI: 0.21–0.97, p = 0.043). A positive relationship emerged between HMG-CoAR, hormone receptors and TAZ/YAP, suggesting a connection between the mevalonate pathway, the hormonal milieu and Hippo in MBC. Moreover, HMG-CoAR expression may be a favorable prognostic indicator.
Semiconducting-polymer-dot based fluorescent probe for turn-on sensing of phytic acid
Authors: Wang Cong , Sun Junyong , Mei Han , Gao Feng
Published: October 2016

In this work, the synthesis of carboxyl functionalized semiconducting polymer dots (PFBT-COOH Pdots) is achieved by a co-precipitation method and a simple, selective and sensitive fluorescence probe for PA detection is designed.
Application of capillary ion chromatography and capillary ion chromatography coupled with mass spectrometry to determine methanesulfonate and inorganic anions in microliter sample volumes of Antarctic snow and ice
Authors: Rodriguez Estrella Sanz , Nation Meredith , Moy Andrew D. , Curran Mark A. J. , Haddad Paul R. , Nesterenko Pavel N. , Paull Brett
Published: October 2016

Development of low volume capillary ion chromatography to deliver anion records from Antarctic snow pit samples.
Light- or oxidation-triggered CO release from [MnI(CO)3(κ3-L)] complexes: reaction intermediates and a new synthetic route to [MnIII/IV2(μ-O)2(L)2] compounds
Authors: Sachs Ulf , Schaper Gerrit , Winkler Daniela , Kratzert Daniel , Kurz Philipp
Published: October 2016

The substitution of the carbonyl ligands of [MnI(CO)3(κ3-L)] complexes can be triggered in two different ways: by near-UV irradiation or by electrochemical oxidation of MnI to MnII.
An evaluation of credentials of a multicomponent reaction for the synthesis of isothioureas through the use of a holistic CHEM21 green metrics toolkit
Authors: Abou-Shehada S. , Mampuys P. , Maes B. U. W. , Clark J. H. , Summerton L.
Published: October 2016

Multicomponent reactions (MCRs) are considered green and material efficient methods for the synthesis of organic compounds, however very few studies have investigated the metrics of the upstream processes involved to achieve the starting materials used in these reactions.
Isobutylene-rich imidazolium ionomers for use in two-phase partitioning bioreactors
Authors: Bacon Stuart L. , Daugulis Andrew J. , Parent J. Scott
Published: October 2016

Imidazolium ionomer derivatives of an isobutylene-rich elastomer demonstrated superior absorption characteristics for target molecules of biological interest compared to their non-ionic parent material, while retaining biocompatibility with a range of suspended cell cultures.
Solvent- and halide-free synthesis of pyridine-2-yl substituted ureas through facile C–H functionalization of pyridine N-oxides
Authors: Rassadin Valentin A. , Zimin Dmitry P. , Raskil'dina Gulnara Z. , Ivanov Alexander Yu. , Boyarskiy Vadim P. , Zlotskii Semen S. , Kukushkin Vadim Yu.
Published: October 2016

A solvent- and halide-free atom-economical synthesis of practically useful pyridine-2-yl substituted ureas utilizes pyridine N-oxides and dialkylcyanamides.
Synthesis of lutetium(iii)–porphyrin complexes: old problems and new excellent conditions found
Authors: Kalota Bartosz , Mikus Agnieszka , Ostrowski Stanisław
Published: October 2016

A convenient high-yielding method for the preparation of very attractive lutetium(iii)–porphyrin complexes was developed (in sulfolane at reflux temperature, 0.5 h, up to 88%).
Synthesis of crinane utilizing an allylic sulfoxide for the construction of a hydroindole ring via vinylogous C–N bond formation
Authors: Raghavan Sadagopan , Ravi Anil
Published: October 2016

The synthesis of crinane is disclosed via intramolecular C–N bond formation by the displacement of an allylic sulfoxonium salt.
Methyl and phenyl substituent effects on the catalytic behavior of NHC ruthenium complexes
Authors: Perfetto Alessandra , Bertolasi Valerio , Costabile Chiara , Paradiso Veronica , Caruso Tonino , Longo Pasquale , Grisi Fabia
Published: October 2016

NHCs with different combinations of methyl and phenyl substituents produce ruthenium second generation catalysts with different RCM behavior.
Highly sensitive ratiometric fluorescence probes for nitric oxide based on dihydropyridine and potentially useful in bioimaging
Authors: Mahapatra Ajit Kumar , Ali Syed Samim , Maiti Kalipada , Mondal Sanchita , Maji Rajkishor , Manna Srimanta , Manna Saikat Kumar , Uddin Md. Raihan , Mandal Sukhendu
Published: October 2016

Hantzsch dihydropyridine-based ratiometric fluorescent NO probes, viz.PyNO and TPANO, were synthesized and characterized.
Electronic nature of zwitterionic alkali metal methanides, silanides and germanides – a combined experimental and computational approach
Authors: Li H. , Aquino A. J. A. , Cordes D. B. , Hase W. L. , Krempner C.
Published: October 2016

Zwitterionic group 14 complexes of the alkali metals of formula [E(SiMe2OCH2CH2OMe)3M], where E = C, Si or Ge and M = Li, Na or K, have been prepared, structurally characterized and their electronic nature was investigated by computational methods.
Comparison of Videostroboscopy to Stroboscopy Derived From High-Speed Videoendoscopy for Evaluating Patients With Vocal Fold Mass Lesions
Authors: Powell Maria E. , Deliyski Dimitar D. , Hillman Robert E. , Zeitels Steven M. , Burns James A. , Mehta Daryush D.
Published: October 2016

Purpose

Videostroboscopy (VS) uses an indirect physiological signal to predict the phase of the vocal fold vibratory cycle for sampling. Simulated stroboscopy (SS) extracts the phase of the glottal cycle directly from the changing glottal area in the high-speed videoendoscopy (HSV) image sequence. The purpose of this study is to determine the reliability of SS relative to VS for clinical assessment of vocal fold vibratory function in patients with mass lesions.

Methods

VS and SS recordings were obtained from 28 patients with vocal fold mass lesions before and after phonomicrosurgery and 17 controls who were vocally healthy. Two clinicians rated clinically relevant vocal fold vibratory features using both imaging techniques, indicated their internal level of confidence in the accuracy of their ratings, and provided reasons for low or no confidence.

Results

SS had fewer asynchronous image sequences than VS. Vibratory outcomes were able to be computed for more patients using SS. In addition, raters demonstrated better interrater reliability and reported equal or higher levels of confidence using SS than VS.

Conclusion

Stroboscopic techniques on the basis of extracting the phase directly from the HSV image sequence are more reliable than acoustic-based VS. Findings suggest that SS derived from high-speed videoendoscopy is a promising improvement over current VS systems.
Is data a toaster? Gender, sex, sexuality and robots
Authors: Cranny-Francis Anne
Published: October 2016

This article considers the development of robotics through the lens of Gender Studies, with a particular interest in exploring relationships of intimacy involving robots. The production of sex robots has prompted some ethicists to set up the Campaign Against Sex Robots, their position articulated in Kathleen Richardson’s, 2015 paper, “The Asymmetrical ‘Relationship’: Parallels Between Prostitution and the Development of Sex Robots”. It is notable that these sex robots are commonly referred to as sexbots or fembots, but there is seldom reference to a malebot, though makers suggest that they can or will be made. Others (notably the makers) see this technology as no different from a vibrator or dildo and suggest that it could be a way of dealing with aberrant and criminal sexual behaviours including paedophilia. Intimacy is more than sexual practice, of course, and the ability of humans to form emotional attachments to technology is well-documented. Consider, for example, Maja Mataric’s description of the relationships formed by families with their Roomba vacuum cleaner in the Robotics Primer (2007). This led to problems for the makers for whom it was less expensive to replace a broken machine than to fix it, but who were faced with demands from families that their Roomba be repaired and returned to them. This article addresses this debate, exploring a range of contributions from ethicists, roboticists, gender theorists and others, and making specific reference to the television programs, the Scandinavian series, Real Humans (2012) and its English version, Humans (2015), as well as to Jordan Wolfson’s recent artwork, Female Figure (2014). This article is published as part of a collection on gender studies.
The phase-contrast imaging instrument at the matter in extreme conditions endstation at LCLS
Authors: Nagler Bob , Schropp Andreas , Galtier Eric C. , Arnold Brice , Brown Shaughnessy B. , Fry Alan , Gleason Arianna , Granados Eduardo , Hashim Akel , Hastings Jerome B. , Samberg Dirk , Seiboth Frank , Tavella Franz , Xing Zhou , Lee Hae Ja , Schroer Christian G.
Published: October 2016

We describe the phase-contrast imaging instrument at the Matter in Extreme Conditions (MEC) endstation of the Linac Coherent Light Source. The instrument can image phenomena with a spatial resolution of a few hundreds of nanometers and at the same time reveal the atomic structure through X-ray diffraction, with a temporal resolution better than 100 fs. It was specifically designed for studies relevant to high-energy-density science and can monitor, e.g., shock fronts, phase transitions, or void collapses. This versatile instrument was commissioned last year and is now available to the MEC user community.
State-to-state differential cross sections for D2 + OH → D + DOH reaction: Influence of vibrational excitation of OH reactant
Authors: Zhao Bin , Sun Zhigang , Guo Hua
Published: October 2016

State-to-state differential cross sections (DCSs) are computed quantum mechanically in full dimensionality for the title reaction using a reactant-product decoupling scheme. The DCSs are calculated at three collision energies of 0.25, 0.28, and 0.34 eV, corresponding to the existing experimental results. In good agreement with experiment, the calculated DCSs are dominated by backward scattering, thanks to the direct rebound mechanism, and the DOH product has two quanta of OD stretching vibration in the newly formed OD bond. In addition, the vibrational excitation of the OH reactant is found to result in a very different but predictable vibrational distribution of the DOH product. It is further shown at the state-to-state level that the DCSs of the DOH(vOD, vb, vOH) product state from the OH(v = 1) reactant state resemble the ones of the DOH(vOD, vb, vOH-1) product state from the OH(v = 0) reactant state, thanks to the spectator nature of the OH moiety.