bluuebunny/crossref_metadata_2025 huggingface dataset:
Switchable disposable passive RFID vapour sensors from inkjet printed electronic components integrated with PDMS as a stimulus responsive material
Authors: Belsey K. E. , Parry A. V. S. , Rumens C. V. , Ziai M. A. , Yeates S. G. , Batchelor J. C. , Holder S. J.
Published: March 2017

Passive RFID sensors are capable of detecting a number of volatile organic compound vapors dependent upon the solubility parameters of the solvent and their vapor pressure.
Real-time and label-free impedimetric analysis of the formation and drug testing of tumor spheroids formed via the liquid overlay technique
Authors: Lei Kin Fong , Lin Bo-Yuan , Tsang Ngan-Ming
Published: March 2017

Tumor spheroids formed via the liquid overlay technique were quantitatively monitored by impedance measurement across the interdigitated electrodes.
New amphiphilic polycarbonates with side functionalized cholesteryl groups as biomesogenic units: synthesis, structure and liquid crystal behavior
Authors: Xu Xiaoxu , Liu Xiaofeng , Li Qun , Hu Jianshe , Chen Qifan , Yang Liqun , Lu Yanhua
Published: March 2017

In this study, a series of new side cholesterol-functionalized amphipathic copolymers based on an aliphatic polycarbonate backbone were synthesized and characterized.
Nickel nanoparticles supported on nitrogen-doped honeycomb-like carbon frameworks for effective methanol oxidation
Authors: Wang Juan , Zhao Qi , Hou Hongshuai , Wu Yifei , Yu Weizhen , Ji Xiaobo , Shao Lidong
Published: March 2017

Nitrogen-doped honeycomb-like carbon framework supported nickel nanoparticles synthesized by a low-cost and scalable method for effective methanol oxidation.
Swallowing Exercises in Patients Post-Stroke: What Is the Current Evidence?
Authors: Rangarathnam Balaji , McCullough Gary H.
Published: March 2017

The act of swallowing is “multidimensional” and involves contributions from several neuroanatomical structures. A stroke affecting any of these areas is likely to cause some amount of physiologic impairment in deglutition. This paper explores current and emerging evidence for rehabilitative exercises for physiological impairments in deglutition due to stroke. Evidence is more emerging than current. However, focus on task specificity and muscle load, along with the use of resistance that can be measured in an increasing number of ways, is encouraging. Results are supporting exercises at specific increments of maximum values using exercises that are as task-specific as possible. Clinical trials on patients post-stroke are challenging and require scrutiny toward diagnosis, age, severity, and type of dysphagia, as well as judicious use of controls. More research is needed to define effective exercise programs for swallowing impairments post-stroke.
Superluminal wave propagation in a non‐Foster negative capacitor loaded transmission line
Authors: Niang A. , de Lustrac A. , Burokur S.N.
Published: March 2017

Superluminal wave propagation phenomenon achieved from a periodic structure in which a transmission line (TL) is loaded with non‐Foster negative capacitors is presented. The loading decreases the effective capacitance and the effective permittivity of the dielectric substrate of the TL. An experimental investigation of the superluminal phase and group velocity in the non‐Foster loaded TL is reported. The phase and group velocities are extracted from measured S‐parameters. To do so, three non‐Foster negative capacitors operating over [50–350 MHz] frequency band are integrated in a TL. Superluminal broadband effects are obtained from 50 to 220 MHz. The negative capacitors loaded TL paves the way to innovative broadband leaky wave antennas, active metamaterial surfaces and cloaking devices.
Rainfall and grazing: not the only barriers to arid-zone conifer recruitment
Authors: Zimmer Heidi C. , Florentine Singarayer K. , Enke Rita , Westbrooke Martin
Published: March 2017

An understanding of the drivers of infrequent recruitment is fundamental in managing for species persistence. Callitris glaucophylla Joy Thomps. & L.A.S. Johnson (white cypress-pine) is a slow-growing, long-lived conifer, with a distribution that extends across arid Australia. Arid populations of C. glaucophylla are endangered in New South Wales, and are characterised by infrequent recruitment. We examined recruitment patterns of C. glaucophylla in differential grazing exclosures (excluding rabbits, excluding large herbivores or excluding both) and in unfenced areas. More recruitment occurred in rabbit-proof exclosures, compared with nearby large herbivore and control exclosures, although some rabbit-proof exclosures recorded no recruitment. Increases in recruitment at several long-term exclosures were associated with wet periods, as was recruitment at some unfenced sites. Apart from grazing and rainfall, recruitment was related to mature tree size and stand density (probably because of their influence on seed availability). These endangered arid C. glaucophylla woodlands are all that remains of a once extensive distribution, and are habitat for a suite of threatened species. Reduction in grazing pressure, particularly from rabbits, is clearly critical to maintain recruitment in these remnant populations. Chances of recruitment appear to be enhanced in low-density stands, around large trees, and in dune blow outs – fencing should focus on these areas.
Novel Dual BODIPY-Carbazole Conjugates with Various Linkers
Authors: Zong Qiao , Zhao Hongbin , Zhou Weinan , Zhang Wentao , Liao Junxu , Yang Nianfa
Published: February 2017

Four dual BODIPY-carbazole conjugates (BDPa–d, BODIPY is 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene), with various π bridges, including none, phenyl, thiophene, and furan, were designed and synthesized. The results suggest that the π bridges have significant effect on the thermal, photophysical, and electrochemical properties of the conjugates. BDPc and BDPd, with a five-membered heterocycle as a π bridge possessing more coplanar molecular geometry, exhibit broader and red-shifted absorption with an obvious charge transfer shoulder peak, as well as red-shifted emission. UV-visible absorption spectroscopy and cyclic voltammetry results show that the extension of the π-conjugated system leads to a reduction in the optical gap with a decrease of the LUMO level. All conjugates display remarkable Stokes shifts (107–216 nm) and low fluorescence quantum yields. BDPc and BDPd, which essentially possess broad and intense absorption, and suitable HOMO–LUMO energy levels, are potential candidates for light-harvesting and photovoltaic applications.
Habitat use and selection by takin in the Qinling Mountains, China
Authors: Yan Wen-Bo , Zeng Zhi-Gao , Gong Hui-Sheng , He Xiang-Bo , Liu Xin-Yu , Si Kai-Chuang , Song Yan-Ling
Published: February 2017

Context Understanding habitat use and selection by threatened ungulates is a crucial prerequisite to prioritise management areas and for developing effective conservation strategies. Aims The aim of our research was to determine the habitat use and selection of takins (Budorcas taxicolor) in the middle range of the Qinling Mountains, China. Methods The study was conducted from August 2013 to August 2015. Global positioning system (GPS) radio-tracking was used to monitor 10 collared takins to gain their location information. The Manly–Chesson selectivity index and Bonferroni-adjusted 95% confidence intervals were applied to determine which habitats were selected. Key results Habitat use and selection by takins showed obvious individual differences. At the landscape scale, all of the four most common habitat types were preferred by takins. However, all takins avoided artificially planted larch forest, and farmland and village. Available habitats within the home ranges also mostly included the four common habitat types. At the home-range scale, all individuals had significant habitat selectivity during the entire tracking period and each season. The habitat use and selection within the home range varied obviously with season and showed sexual differences to a certain extent. Conclusions The habitat selection by takins is scale-dependent. At the landscape scale, takins are most likely to occur at sites covered by forest. At both landscape and home-range scales, our results indicated that takins need more diverse forest habitats, but none of the four most common forest habitats is essential for survival of this species. Implications The present work has provided more insight into the habitat use and habitat selection of takins in mountainous forest landscapes. Many measures such as maintaining a diversity of forest habitats, avoiding habitat alteration by invasion of exotic plants, and increasing the area of available habitats by relocating the villages from within to outside of the reserve are recommended to conserve this large species.
APMP supplementary comparison report of absorbed dose rate in tissue for beta radiation (BIPM KCDB: APMP.RI(I)-S2)
Authors: Kato M , Kurosawa T , Saito N , Kadni T B , Kim I J , Kim B C , Yi C -Y , Pungkun V , Chu C -H
Published: March 2017

The supplementary comparison of absorbed dose rate in tissue for beta radiation (APMP.RI(I)-S2) was performed with five national metrology institutes in 2013 and 2014. Two commercial thin window ionization chambers were used as transfer instruments and circulated among the participants. Two of the NMIs measured the calibration coefficients of the chambers in reference fields produced from Pm-147, Kr-85 and Sr-90/Y-90, while the other three measured those only in Sr-90/Y-90 beta-particle field. The degree of equivalence for the participants was determined and this comparison verifies the calibration capabilities of the participating laboratories. In addition, most of the results of this comparison are consistent with another international comparison (EUROMET.RI(I)-S2) reported before this work.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.

The final report has been peer-reviewed and approved for publication by the CCRI, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Report of the CCQM-K123: trace elements in biodiesel fuel
Authors: Kuroiwa T , Zhu Y , Inagaki K , Long S E , Christopher S J , Puelles M , Borinsky M , Hatamleh N , Murby J , Merrick J , White I , Saxby D , Sena R C , Almeida M D , Vogl J , Phukphatthanachai P , Fung W H , Yau H P , Okumu T O , Kang'iri J N , Télle J A S , Campos E Z , Galv´n E C , Kaewkhomdee N , Taebunpakul S , Thiengmanee U , Yafa C , Tokman N , Tunç M , Can S Z
Published: March 2017

The CCQM-K123 key comparison was organized by the Inorganic Analysis Working Group (IAWG) of CCQM to assess and document the capabilities of the national metrology institutes (NMIs) or the designated institutes (DIs) to measure the mass fractions of sodium, calcium, potassium, magnesium phosphorous and sulfur in biodiesel fuel (BDF). National Metrology Institute of Japan (NMIJ) and National Institute of Standards and Technology (NIST) acted as the coordinating laboratories.

Results were submitted by 11 NMIs and DIs. Most of the participants used inductively coupled plasma-mass spectrometry (ICP-MS), isotope dilution technique with ICP-MS and inductively coupled plasma-optical emission spectrometry (ICP-OES) with microwave acid digestion.

Accounting for relative expanded uncertainty, comparability of measurement results for each of Na, Ca, K, Mg and P was successfully demonstrated by the participants. Concerning S, the variation in results between participants, particularly those using IDMS methods was observed. According to the additional evaluation and investigation, the revised results were overlapping between IDMS measurements at the k = 2 level. However, this KC does not support S measurements.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.

The final report has been peer-reviewed and approved for publication by the CCQM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Pilot Study EURAMET.AUV.V-P1: Bilateral comparison on magnitude of the complex charge sensitivity of accelerometers from 10 Hz to 10 kHz
Authors: Bartoli Claire , Hermawanto Denny
Published: March 2017

The results of a Pilot Study EURAMET.AUV.V-P1 between LNE (France) and RCM-LIPI (Indonesia) are reported. This bilateral comparison of sinusoidal vibration was organized after the implementation of various improvements at RCM-LIPI following a previous (unpublished) comparison that had revealed discrepancies in their results at frequencies above 5 kHz.

The results of this Pilot Study, using the same accelerometers as the earlier comparison, demonstrate that the discrepancies at high frequencies have been resolved. For both the back-to-back and the single-ended accelerometers tested, the sensitivities of the RCM-LIPI and the LNE over the frequency range from 10 Hz to 10 kHz now agree within their declared uncertainties.

Main text

To reach the main text of this paper, click on Final Report.

The final report has been peer-reviewed and approved for publication by the CCAUV.
Phosphoregulation of Tau modulates inhibition of kinesin-1 motility
Authors: Stern Jamie L. , Lessard Dominique V. , Hoeprich Gregory J. , Morfini Gerardo A. , Berger Christopher L.
Published: March 2017

Microtubule-based axonal transport is tightly regulated by numerous pathways, ensuring appropriate delivery of specific organelle cargoes to selected subcellular domains. Highlighting the importance of this process, pathological evidence has linked alterations in these pathways to the pathogenesis of several neurodegenerative diseases. An important regulator of this system, the microtubule-associated protein Tau, has been shown to participate in signaling cascades, modulate microtubule dynamics, and preferentially inhibit kinesin-1 motility. However, the cellular means of regulating Tau’s inhibition of kinesin-1 motility remains unknown. Tau is subject to various posttranslational modifications, including phosphorylation, but whether phosphorylation regulates Tau on the microtubule surface has not been addressed. It has been shown that tyrosine 18 phosphorylated Tau regulates inhibition of axonal transport in the disease state. Tyrosine 18 is both a disease- and nondisease-state modification and is therefore an attractive starting point for understanding control of Tau’s inhibition of kinesin-1 motility. We show that pseudophosphorylation of tyrosine 18 reduces 3RS-Tau’s inhibition of kinesin-1 motility. In addition, we show that introduction of negative charge at tyrosine 18 shifts Tau’s previously described static–dynamic state binding equilibrium toward the dynamic state. We also present the first evidence of Tau’s static–dynamic state equilibrium under physiological conditions.
Ecological data from observer programmes underpin ecosystem-based fisheries management
Authors: Gilman Eric , Weijerman Mariska , Suuronen Petri
Published: February 2017

Data required from fisheries monitoring programmes substantially expand as management authorities transition to implement elements of ecosystem-based fisheries management (EBFM). EBFM extends conventional approaches of managing single fishery effects on individual stocks of target species by taking into account the effects, within a defined ecosystem, of local to regional fisheries on biodiversity, from genotypes to ecological communities. This includes accounting for fishery effects on evolutionary processes, associated and dependent species, habitats, trophic food web processes, and functionally linked systems. Despite seemingly insurmountable constraints, through examples, we demonstrate how data routinely collected in most observer programmes and how minor and inexpensive expansions of observer data fields and collection protocols supply ecological data underpinning EBFM. Observer data enable monitoring bycatch, including catch and mortality of endangered, threatened and protected species, and assessing the performance of bycatch management measures. They provide a subset of inputs for ecological risk assessments, including productivity–susceptibility analyses and multispecies and ecosystem models. Observer data are used to monitor fishery effects on habitat and to identify and protect benthic vulnerable marine ecosystems. They enable estimating collateral sources of fishing mortality. Data from observer programmes facilitate monitoring ecosystem pressure and state indicators. The examples demonstrate how even rudimentary fisheries management systems can meet the ecological data requirements of elements of EBFM.
Using Wikipedia to Predict Election Outcomes
Authors: Smith Benjamin K. , Gustafson Abel
Published: February 2017

This study seeks to improve election forecasting by supplementing polling data with online information-seeking behavior trends as an indicator of public opinion. Aggregate trends of demonstrations of interest or engagement have been shown to accurately predict behavior trends and reflect public opinion. Further, because traditional poll-based predictions are inherently undermined by self-reporting biases and the intention-behavior disconnect, we can expect that information-seeking trends on widely used social media—as an autonomous and unobtrusive indicator of relative levels of public opinion—can help correct for some of this error and explain unique, additional variance in election results. We advance the literature by using data from Wikipedia pageviews along with polling data in a synthesized model based on the results of the 2008, 2010, and 2012 US Senate general elections. Results show that Wikipedia pageviews data significantly add to the ability of poll- and fundamentals-based projections to predict election results up to 28 weeks prior to Election Day, and benefit predictions most at those early points, when poll-based predictions are weakest.
Identifying Perceptions of Health Professionals Regarding Deathbed Visions and Spiritual Care in End-of-Life Care
Authors: Chang Sung Ok , Ahn Soo Yeon , Cho Myung-Ok , Choi Kyung Sook , Kong Eun Suk , Kim Chun-Gill , Kim Hee Kyung , Lee Young Whee , Song Misoon , Kim Nam Cho
Published: March 2017

The final hours before death can be the most significant time for the dying. Adequate preparation for death can help reduce patients’ fears. Research on end-of-life experiences suggests that deathbed visions are not uncommon, but many doctors and nurses find this a difficult subject to approach. A 2-round Delphi method was used to gain a reliable consensus on deathbed visions from experts in end-of-life care. A purposive sample of nurses (n = 18) and doctors (n = 13) was invited from across hospitals and nursing homes to participate in this study. In this Delphi evaluation, the health professionals’ perceptions of the deathbed visions experienced by patients were identified, as well as how these phenomena should be integrated into spiritual care. The research found that healthcare professionals who are experts in end-of-life care tend to remain at the end-of-life care setting while acknowledging human spirituality as part of a peaceful death. However, they tend to not make conclusions about how death visions should be classified. This Delphi study was an attempt to identify a consensus on spiritual care including deathbed visions in end-of-life care among healthcare professionals.
Releasing potential power of terpene synthases by a robust precursor supply platform
Authors: Bian Guangkai , Han Yichao , Hou Anwei , Yuan Yujie , Liu Xinhua , Deng Zixin , Liu Tiangang
Published: February 2017

Approximately 76,000 discovered makes terpenoids the largest family of natural products in nature with widespread applications. The wide-spectrum of structural diversity of the terpenoids were largely due to the variable skeletons generated by terpene synthases. The number of terpene skeletons found in nature, however, were so much more than those conceivably generated from known terpene synthases and the limited characterized terpene synthases also make no chance for some useful terpenoids overproduction in microbe. Here, we first demonstrated that the promiscuous synthasesin vivocan produce more variable terpenoid products by converting precursors of different lengths (C10, C15, C20, C25). This discovery was prompted by the development of an efficientin vivoplatform by combining the two promiscuous terpene synthases and three prenyltransferases to generate 50 terpenoids, at least 3 ring systems of which were completely new. Furthermore, protein engineering was further integrated to enhance product diversity. Clearly, the work is expected to dramatically reshape the terpenoid research by widening the flexibility of the terpene synthases for the fresh discovery or creation of the new terpenoid compounds by skeleton reframing.
Laminar organization of encoding and memory reactivation in the parietal cortex
Authors: Wilber Aaron A. , Skelin Ivan , McNaughton Bruce L.
Published: February 2017

Egocentric neural coding has been observed in parietal cortex (PC), but its topographical and laminar organization is not well characterized. We used multi-site recording to look for evidence of local clustering and laminar consistency of linear and angular velocity encoding in multi-neuronal spiking activity (MUA) and in the high-frequency (300-900 Hz) component of the local field potential (HF-LFP), believed to reflect local spiking activity. Rats were trained to run many trials on a large circular platform, either to LED-cued goal locations or as a spatial sequence from memory. Tuning to specific self-motion states was observed consistently, and exhibited distinct cortical depth-invariant coding properties. These patterns of collective local and laminar activation during behavior were reactivated in compressed form during post-experience sleep, and temporally coupled to hippocampal sharp wave ripples. Thus, PC neuron motion encoding is consistent across cortical laminae, and this consistency is maintained during memory reactivation.

Highlights

Parietal cortex MUA encodes specific movements coherently across laminae.

This organizational scheme is maintained during subsequent memory reactivation

MUA and HF-LFP showed similar self-motion tuning and memory reactivation dynamics

This establishes the utility of MUA and HF-LFP for human memory reactivation studies
An alternative STAT signaling pathway acts in antiviral immunity inCaenorhabditis elegans
Authors: Tanguy Mélanie , Véron Louise , Stempor Przemyslaw , Ahringer Julie , Sarkies Peter , Miska Eric A.
Published: February 2017

Across metazoans, innate immunity is vital in defending organisms against viral infection. In mammals, antiviral innate immunity is orchestrated by interferon signaling, activating the STAT transcription factors downstream of the JAK kinases to induce expression of antiviral effector genes. In the nematodeC. elegans, which lacks the interferon system, the major antiviral response so far described is RNA interference but whether additional gene expression responses are employed is not known. Here we show that, despite the absence of both interferon and JAK, theC. elegansSTAT homologue STA-1 orchestrates antiviral immunity. Intriguingly, mutants lacking STA-1 show increased resistance to antiviral infection. Using gene expression analysis and chromatin immunoprecipitation we show that, in contrast to the mammalian pathway, STA-1 acts as a transcriptional repressor. Thus STA-1 might act to suppress a constitutive antiviral response in the absence of infection. Using a reverse genetic screen we identify the SID-3 as a kinase upstream of STA-1 in the response to infection. Together, our work identifies a novel STAT regulatory cascade controlling its activity in antiviral resistance, illustrating the complex evolutionary trajectory displayed by innate immune signaling pathways across metazoan organisms.
Evidence-based gene models for structural and functional annotations of the oil palm genome
Authors: Kuang Lim Chan , Tatarinova Tatiana V. , Rosli Rozana , Amiruddin Nadzirah , Azizi Norazah , Halim Mohd Amin Ab , Nik Mohd Sanusi Nik Shazana , Nagappan Jayanthi , Ponomarenko Petr , Triska Martin , Solovyev Victor , Firdaus-Raih Mohd , Sambanthamurthi Ravigadevi , Murphy Denis , Low Eng Ti Leslie
Published: February 2017

The advent of rapid and inexpensive DNA sequencing has led to an explosion of data that must be transformed into knowledge about genome organization and function. Gene prediction is customarily the starting point for genome analysis. This paper presents a bioinformatics study of the oil palm genome, including a comparative genomics analysis, database and tools development, and mining of biological data for genes of interest. We annotated 26,087 oil palm genes integrated from two gene-prediction pipelines, Fgenesh++ and Seqping. As case studies, we conducted comprehensive investigations on intronless, resistance and fatty acid biosynthesis genes, and demonstrated that the current gene prediction set is of high quality. 3,672 intronless genes were identified in the oil palm genome, an important resource for evolutionary study. Further scrutiny of the oil palm genes revealed 210 candidate resistance genes involved in pathogen defense. Fatty acids have diverse applications ranging from food to industrial feedstock, and we identified 42 key genes involved in fatty-acid biosynthesis in oil palm mesocarp and kernel. These results provide an important resource for studies on plant genomes and a theoretical foundation for marker-assisted breeding of oil palm and related crops.
Predicting bioprocess targets of chemical compounds through integration of chemical-genetic and genetic interaction networks
Authors: Simpkins Scott W. , Nelson Justin , Deshpande Raamesh , Li Sheena C. , Piotrowski Jeff S. , Wilson Erin H. , Gebre Abraham A. , Okamoto Reika , Yoshimura Mami , Costanzo Michael , Yashiroda Yoko , Ohya Yoshikazu , Osada Hiroyuki , Yoshida Minoru , Boone Charles , Myers Chad L.
Published: March 2017

Chemical-genetic interactions – observed when the treatment of mutant cells with chemical compounds reveals unexpected phenotypes – contain rich functional information linking compounds to their cellular modes of action. To systematically identify these interactions, an array of mutants is challenged with a compound and monitored for fitness defects, generating a chemical-genetic interaction profile that provides a quantitative, unbiased description of the cellular function(s) perturbed by the compound. Genetic interactions, obtained from genome-wide double-mutant screens, provide a key for interpreting the functional information contained in chemical-genetic interaction profiles. Despite the utility of this approach, integrative analyses of genetic and chemical-genetic interaction networks have not been systematically evaluated. We developed a method, called CG-TARGET (Chemical Genetic Translation via A Reference Genetic nETwork), that integrates large-scale chemical-genetic interaction screening data with a genetic interaction network to predict the biological processes perturbed by compounds. CG-TARGET compared favorably to a baseline enrichment approach across a variety of benchmarks, achieving similar accuracy while substantially improving the ability to control the false discovery rate of biological process predictions. We applied CG-TARGET to a recent screen of nearly 14,000 chemical compounds inSaccharomyces cerevisiae, integrating this dataset with the globalS. cerevisiaegenetic interaction network to prioritize over 1500 compounds with high-confidence biological process predictions for further study. Upon investigation of the compatibility of chemical-genetic and genetic interaction profiles, we observed that one-third of observed chemical-genetic interactions contributed to the highest-confidence biological process predictions and that negative chemical-genetic interactions overwhelmingly formed the basis of these predictions. We present here a detailed characterization of the CG-TARGET method along with experimental validation of predicted biological process targets, focusing on inhibitors of tubulin polymerization and cell cycle progression. Our approach successfully demonstrates the use of genetic interaction networks in the functional annotation of compounds to biological processes.
Clay-induced DNA double-strand breaks underlay genetic diversity, antibiotic resistance and could be a molecular basis for asbestos-induced cancer
Authors: González-Tortuero Enrique , Rodríguez-Beltran Jerónimo , Radek Renate , Blázquez Jesús , Rodríguez-Rojas Alexandro
Published: February 2017

Some natural clays and synthetic nanofibres present in the environment have a severe impact on human health. After several decades of research, the molecular mechanism of how asbestos induce cancers is not well understood. Different fibres, including asbestos, can penetrate the membrane and introduce DNA in both, bacterial and eukaryotic cells. Incubating Escherichia coli with sepiolite, a clayey material, and asbestos under friction forces, both fibres cause double-strand breaks in bacteria. Since antibiotics and clays are used together in animal husbandry, the mutagenic effect of these fibres might constitute a pathway to antibiotic resistance due to the friction provided by peristalsis of the gut from farm animals in addition to the previously proposed horizontal gene transfer. Moreover, we raise the possibility that the same mechanism could generate bacteria diversity in natural scenarios with a role in the evolution of species. Finally, we provide a new model on how asbestos may promote mutagenesis and cancer based on the observed mechanical genotoxicity.
Inferring individual-level processes from population-level patterns in cultural evolution
Authors: Kandler Anne , Wilder Bryan , Fortunato Laura
Published: February 2017

Our species is characterized by a great degree of cultural variation, both within and between populations. Understanding how group-level patterns of culture emerge from individual-level behaviour is a long-standing question in the biological and social sciences. We develop a simulation model capturing demographic and cultural dynamics relevant to human cultural evolution, focusing on the interface between population-level patterns and individual-level processes. The model tracks the distribution of variants of cultural traits across individuals in a population over time, conditioned on different pathways for the transmission of information between individuals. From these data we obtain theoretical expectations for a range of statistics commonly used to capture population-level characteristics (e.g. the degree of cultural diversity). Consistent with previous theoretical work, our results show that the patterns observed at the level of groups are rooted in the interplay between the transmission pathways and the age structure of the population. We also explore whether, and under what conditions, the different pathways can be distinguished based on their group-level signatures, in an effort to establish theoretical limits to inference. Our results show that the temporal dynamic of cultural change over time retains a stronger signature than the cultural composition of the population at a specific point in time. Overall, the results suggest a shift in focus from identifying the one individual-level process that likely produced the observed data to excluding those that likely did not. We conclude by discussing the implications for empirical studies of human cultural evolution.
BECon: A tool for interpreting DNA methylation findings from blood in the context of brain
Authors: Edgar Rachel , Jones Meaghan J , Meaney Michael J , Turecki Gustavo , Kobor Michael S
Published: February 2017

Tissue differences are one of the largest contributors to variability in the human DNA methy-lome. Despite the tissue specific nature of DNA methylation, the inaccessibility of human brain samples necessitates the frequent use of surrogate tissues such as blood, in studies of associations between DNA methylation and brain function and health. Results from studies of surrogate tissues in humans are difficult to interpret in this context, as the connection between blood-brain DNA methylation is tenuous and not well documented. Here we aimed to provide a resource to the community to aid interpretation of blood based DNA methylation results in the context of brain tissue. We used paired samples from 16 individuals from three brain regions and whole blood, run on the Illumina 450K Human Methylation Array to quantify the concordance of DNA methylation between tissues. From these data we have made available metrics on: the variability of CpGs in our blood and brain samples, the concordance of CpGs between blood and brain, and estimations of how strongly a CpG is affected by cell composition in both blood and brain through the web application BECon (Blood-Brain Epigenetic Concordance;https://redgar598.shinyapps.io/BECon/). We anticipate that BECon will enable biological interpretation of blood based human DNA methylation results, in the context of brain.
Community evolution increases plant productivity at low diversity
Authors: van Moorsel Sofia J. , Hahl Terhi , Wagg Cameron , De Deyn Gerlinde B. , Flynn Dan F.B. , Zuppinger-Dingley Debra , Schmid Bernhard
Published: February 2017

Species extinctions from local communities can negatively affect ecosystem functioning. Ecological mechanisms underlying these impacts are well studied but the role of evolutionary processes is rarely assessed. Using a long-term field experiment, we tested whether natural selection in plant communities increased the effects of biodiversity on productivity. We re-assembled communities with 8-year co-selection history adjacent to communities with identical species composition but no history of co-selection (“naïve communities”). Monocultures and in particular mixtures of two to four co-selected species were more productive than their corresponding naïve communities over four years in soils with or without co-selected microbial communities. At the highest diversity level of eight plant species, no such differences were observed. Our findings suggest that plant community evolution can lead to rapid increases in ecosystem functioning at low diversity but may take longer at high diversity. This effect was not modified by treatments that simulated additional co-evolutionary processes between plants and soil organisms.
Multiplexed confocal and super-resolution fluorescence imaging of cytoskeletal and neuronal synapse proteins
Authors: Guo Syuan-Ming , Veneziano Remi , Gordonov Simon , Li Li , Park Demian , Kulesa Anthony B. , Blainey Paul C. , Cottrell Jeffrey R. , Boyden Edward S. , Bathe Mark
Published: February 2017

Neuronal synapses contain dozens of protein species whose expression levels and localizations are key determinants of synaptic transmission and plasticity. The spectral properties of fluorophores used in conventional microscopy limit the number of measured proteins to four species within a given sample. The ability to perform high-throughput confocal or super-resolution imaging of many proteins simultaneously without limitation in target number imposed by this spectral limit would enable large-scale characterization of synaptic protein networks in situ. Here, we introduce PRISM: Probe-based Imaging for Sequential Multiplexing, a method that sequentially utilizes either high affinity Locked Nucleic Acid (LNA) or low affinity DNA probes to enable diffraction-limited confocal and PAINT-based super-resolution imaging. High-affinity LNA probes offer high-throughput, confocal-based imaging compared with PAINT, which uses low affinity probes to realize localization-based super-resolution imaging. Simultaneous immunostaining of all targets is performed prior to imaging, followed by sequential LNA/DNA probe exchange that requires only minutes under mild wash conditions. We apply PRISM to quantify the co-expression levels and nanometer-scale organization of one dozen cytoskeletal and synaptic proteins within individual neuronal synapses. Our approach is scalable to dozens of target proteins and is compatible with high-content screening platforms commonly used to interrogate phenotypic changes associated with genetic and drug perturbations in a variety of cell types.
Elastic Multi-Scale Mechanisms: Computation and Biological Evolution
Authors: Diaz Ochoa Juan G.
Published: February 2017

Explanations based on low level interacting elements are valuable and powerful since they contribute to identify the key mechanisms of biological functions. However, many dynamic systems based on low level interacting elements with unambiguous, finite and complete information of initial states generate future states that cannot be predicted, implying an increase of complexity and open-ended evolution (oee). Such systems are like Turing machines, that overlap with dynamical systems that cannot halt. We argue that organisms find halting conditions by distorting these mechanisms, creating conditions for a constant creativity that drives evolution. We introduce a modulus of elasticity to measure the changes in these mechanisms in response to changes in the computed environment. We test this concept in a population of predators and predated cells with chemotactic mechanisms and demonstrate how the selection of a given mechanism depends on the entire population. We finally explore this concept in different frameworks and postulate that the identification of predictive mechanisms is only successful with small elasticity modulus.
The reactivation of reprogramming factors within human blastocysts by using ATP contribute to human blastocyst development
Authors: Takemura Takashi , Okabe Midori
Published: February 2017

Scientists worldwide have been unable to replicate the stimulus-triggered acquisition of pluripotency (STAP) cells and/or the STAP phenomenon. However, investigations into STAP cells and/or the STAP phenomenon by RIKEN CDB in Japan found that ATP (adenosine 5’-triphosphate disodium salt hydrate) can upregulate Oct3/4 (POU5F1: POU domain, class 5, transcription factor 1) and Nanog mRNA expression in mouse hepatocytes.

On the other hand, no studies have investigated whether ATP can contribute to human blastocyst development. Here we show the reactivation of reprogramming factors within human blastocysts by appropriate ATP treatment (1 mM for 2 days) can contribute to human blastocyst development.

In conclusion, although ATP treatment could not replicate STAP cells and/or the STAP phenomenon by scientists worldwide, appropriate ATP treatment (1 mM for 2 days) in cultured human blastocysts with totipotency would be helpful for infertility women.
Bacterial tail anchors can target to the mitochondrial outer membrane
Authors: Bal Güleycan Lutfullahoğlu , Keskin Abdurrahman , Seferoğlu Ayşe Bengisu , Dunn Cory D.
Published: February 2017

During the generation and evolution of the eukaryotic cell, a proteobacterial endosymbiont was refashioned into the mitochondrion, an organelle that appears to have been present in the ancestor of all present-day eukaryotes. Mitochondria harbor proteomes derived from coding information located both inside and outside the organelle, and the rate-limiting step toward the formation of eukaryotic cells may have been development of an import apparatus allowing protein entry to mitochondria. Currently, a widely conserved translocon allows proteins to pass from the cytosol into mitochondria, but how proteins encoded outside of mitochondria were first directed to these organelles at the dawn of eukaryogenesis is not clear. Because several proteins targeted by a carboxyl-terminal tail anchor (TA) appear to have the ability to insert spontaneously into the mitochondrial outer membrane (OM), it is possible that self-inserting, tail-anchored polypeptides obtained from bacteria might have formed the first gate allowing proteins to access mitochondria from the cytosol. Here, we tested whether bacterial TAs are capable of targeting to mitochondria. In a survey of proteins encoded by the proteobacteriumEscherichia coli, predicted TA sequences were directed to specific subcellular locations within the yeastSaccharomyces cerevisiae. Importantly, TAs obtained from DUF883 family members ElaB and YqjD were abundantly localized to and inserted at the mitochondrial OM. Our results support the notion that eukaryotic cells are able to utilize membrane-targeting signals present in bacterial proteins obtained by lateral gene transfer, and our findings make plausible a model in which mitochondrial protein translocation was first driven by tail-anchored proteins.
Thermal transients excite neurons through universal intramembrane mechano-electrical effects
Authors: Plaksin Michael , Kimmel Eitan , Shoham Shy
Published: February 2017

Modern advances in neurotechnology rely on effectively harnessing physical tools and insights towards remote neural control, thereby creating major new scientific and therapeutic opportunities. Specifically, rapid temperature pulses were shown to increase membrane capacitance, causing capacitive currents that explain neural excitation, but the underlying biophysics is not well understood. Here, we show that an intramembrane thermal-mechanical effect wherein the phospholipid bilayer undergoes axial narrowing and lateral expansion accurately predicts a potentially universal thermal capacitance increase rate of ~0.3%/°C. This capacitance increase and concurrent changes in the surface charge related fields lead to predictable exciting ionic displacement currents. The new theory’s predictions provide an excellent agreement with multiple experimental results and indirect estimates of latent biophysical quantities. Our results further highlight the role of electro-mechanics in neural excitation; they may also help illuminate sub-threshold and novel physical cellular effects, and could potentially lead to advanced new methods for neural control.
Comparing arenavirus infection patterns in experimentally and naturally infected rodent hosts
Authors: Mariën Joachim , Borremans Benny , Gryseels Sophie , Vanden Broecke Bram , Becker-Ziaja Beate , Makundi Rhodes , Massawe Apia , Reijniers Jonas , Leirs Herwig
Published: February 2017

Infectious diseases of wildlife are typically studied using data on antibody and pathogen presence/level. In order to interpret these data, it is necessary to know the course of antibodies and pathogen presence/levels after infection. Such data are typically collected using experimental infection studies in which host individuals are inoculated in the laboratory and sampled over an extended period, but because laboratory conditions are controlled and much less variable than natural conditions, the immune response and pathogen dynamics may differ. Here, we compared Morogoro arenavirus infection patterns between naturally and experimentally infected multimammate mice (Mastomys natalensis). Longitudinal samples were collected during three months of bi-weekly trapping in Morogoro, Tanzania, and antibody titer and viral RNA presence were determined to assess whether the natural temporal patterns are similar to those previously observed in the laboratory. A good match with laboratory data was found for 52% of naturally infected individuals, while most of the mismatches can be explained by the presence of chronically infected individuals (35%), maternal antibodies (10%) and an antibody detection limit (25%). These results suggest that while laboratory data are useful for interpreting field samples, there can still be differences due to conditions that were not tested in the laboratory.

Important notice

This is a pre-print version of the manuscript, made available through bioRxiv.org. Note that this manuscript has not yet been peer-reviewed, and has been submitted to a peer-reviewed journal.
Constraint-based modeling identifies new putative targets to fight colistin-resistantA. baumanniiinfections
Authors: Presta Luana , Bosi Emanuele , Mansouri Leila , Dijkshoorn Lenie , Fani Renato , Fondi Marco
Published: February 2017

Acinetobacter baumanniiis a clinical threat to human health, causing major infection outbreaks worldwide. As new drugs against Gram-negative bacteria do not seem to be forthcoming, and due to the microbial capability of acquiring multi-resistance, there is an urgent need for novel therapeutic targets. Here we have derived a list of new potential targets by means of metabolic reconstruction and modelling ofA. baumanniiATCC 19606. By integrating constraint-based modelling with gene expression data, we simulated microbial growth in normal and stressful conditions (i.e. following antibiotic exposure). This allowed us to describe the metabolic reprogramming that occurs in this bacterium when treated with colistin (the currently adopted last-line treatment) and identify a set of genes that are primary targets for developing new drugs againstA. baumannii, including colistin-resistant strains. It can be anticipated that the metabolic model presented herein will represent a solid and reliable resource for the future treatment ofA. baumanniiinfections.
A unifying mechanism for the biogenesis of prokaryotic membrane proteins co-operatively integrated by the Sec and Tat pathways
Authors: Tooke Fiona J. , Babot Marion , Chandra Govind , Buchanan Grant , Palmer Tracy
Published: February 2017

The vast majority of polytopic membrane proteins are inserted into the cytoplasmic membrane of prokaryotes by the general secretory (Sec) pathway. However, a subset of monotopic proteins that contain non-covalently-bound redox cofactors depend on the twin-arginine translocase (Tat) machinery for membrane integration. Recently actinobacterial Rieske iron-sulfur cluster-containing proteins were identified as an unusual class of membrane proteins that require both the Sec and Tat pathways for the insertion of their three transmembrane domains (TMDs). The Sec pathway inserts the first two TMDs of these proteins co-translationally, but releases the polypeptide prior to the integration of TMD3 to allow folding of the cofactor-containing domain and its translocation by Tat. Here we have investigated features of theStreptomyces coelicolorRieske polypeptide that modulate its interaction with the Sec and Tat machineries. Mutagenesis of a highly conserved loop region between Sec-dependent TMD2 and Tat-dependent TMD3 shows that it plays no significant role in coordinating the activities of the two translocases, but that a minimum loop length of approximately eight amino acids is required for the Tat machinery to recognise TMD3. Instead we show that a combination of relatively low hydrophobicity of TMD3, coupled with the presence of C-terminal positively-charged amino acids, results in abortive insertion of TMD3 by the Sec pathway and its release at the cytoplasmic side of the membrane. Bioinformatic analysis identified two further families of polytopic membrane proteins that share features of dual Sec-Tat-targeted membrane proteins. A predicted heme-molybdenum cofactor-containing protein with five TMDs, and a polyferredoxin also with five predicted TMDs, are encoded across bacterial and archaeal genomes. We demonstrate that membrane insertion of representatives of each of these newly-identified protein families is dependent on more than one protein translocase, with the Tat machinery recognising TMD5. Importantly, the combination of low hydrophobicity of the final TMD and the presence of multiple C-terminal positive charges that serve as critical Sec-release features for the actinobacterial Rieske protein also dictate Sec release in these further protein families. Therefore we conclude that a simple unifying mechanism governs the assembly of dual targeted membrane proteins.