The early Pliocene Titiokura Formation: stratigraphy of a thick, mixed carbonate-siliciclastic shelf succession in Hawke's Bay Basin, New Zealand

This paper presents a systematic stratigraphic description of the architecture of the early Pliocene Titiokura Formation (emended) in the Te Waka and Maungaharuru Ranges of western Hawke's Bay, and presents a facies, sequence stratigraphic, and paleoenvironmental analysis of the sedimentary succession. The Titiokura Formation is of early Pliocene (Opoitian-Waipipian) age, and unconformably overlies Mokonui Formation, which is a regressive late Miocene and early Pliocene (Kapitean to early Opoitian) succession. In the Te Waka Range and the southern parts of the Maungaharuru Range, the Titiokura Formation comprises a single limestone sheet 20-50 m thick, with calcareous sandstone parts. In the vicinity of Taraponui Trig, and to the northeast, the results of 1:50 000 mapping show that the limestone gradually partitions into five members, which thicken markedly to the northeast to total thicknesses of c. 730 m, and concomitantly become dominated by siliciclastic sandstone. The members (all new) from lower to upper are: Naumai Member, Te Rangi Member, Taraponui Member, Bellbird Bush Member, and Opouahi Member. The lower four members are inferred to each comprise an obliquity-controlled 41 000 yr 6th order sequence, and the Opouahi Member at least two such sequences. The sequences typically have the following architectural elements from bottom to top: disconformable sequence boundary that formed as a transgressive surface of erosion; thin transgressive systems tracts (TSTs) with onlap and backlap shellbeds, or alternatively, a single compound shellbed; downlap surface; and very thick (70-200 m) highstand (HST) and regressive systems tracts (RST) composed of fine sandstone. The sequences in the Opouahi Member have cryptic TSTs, sandy siltstone to silty sandstone HSTs, and cross-bedded, differentially cemented, fine sandstone RSTs; a separate variant is an 11 m thick bioclastic limestone (grainstone and packstone) at the top of the member that crops out in the vicinity of Lake Opouahi. Lithostratigraphic correlations along the crest of the ranges suggest that the Titiokura Formation, and its correlatives to the south around Puketitiri, represent a shoreline-to-shelf linked depositional system. Carbonate production was focused around a rocky seascape as the system onlapped basement in the south, with dispersal and deposition of the comminuted carbonate on an inner shelf to the north, which was devoid of siliciclastic sediment input. The rates of both subsidence and siliciclastic sediment flux increased rapidly to the northeast of the carbonate "platform", with active progradation and offlap of the depositional system into more axial parts of Hawke's Bay Basin

The ice-breaker effect: Singing mediates fast social bonding

It has been proposed that singing evolved to facilitate social cohesion. However, it remains unclear whether bonding arises out of properties intrinsic to singing or whether any social engagement can have a similar effect. Furthermore, previous research has used one-off singing sessions without exploring the emergence of social bonding over time. In this semi-naturalistic study, we followed newly formed singing and non-singing (crafts or creative writing) adult education classes over seven months. Participants rated their closeness to their group and their affect, and were given a proxy measure of endorphin release, before and after their class, at three timepoints (months 1, 3 and 7). We show that although singers and non-singers felt equally connected by timepoint 3, singers experienced much faster bonding: singers demonstrated a significantly greater increase in closeness at timepoint 1, but the more gradual increase shown by non-singers caught up over time. This represents the first evidence for an ‘ice-breaker effect’ of singing in promoting fast cohesion between unfamiliar individuals, which bypasses the need for personal knowledge of group members gained through prolonged interaction. We argue that singing may have evolved to quickly bond large human groups of relative strangers, potentially through encouraging willingness to coordinate by enhancing positive affect

A characteristics framework for Semantic Information Systems Standards

Semantic Information Systems (IS) Standards play a critical role in the development of the networked economy. While their importance is undoubted by all stakeholders—such as businesses, policy makers, researchers, developers—the current state of research leaves a number of questions unaddressed. Terminological confusion exists around the notions of “business semantics”, “business-to-business interoperability”, and “interoperability standards” amongst others. And, moreover, a comprehensive understanding about the characteristics of Semantic IS Standards is missing. The paper addresses this gap in literature by developing a characteristics framework for Semantic IS Standards. Two case studies are used to check the applicability of the framework in a “real-life” context. The framework lays the foundation for future research in an important field of the IS discipline and supports practitioners in their efforts to analyze, compare, and evaluate Semantic IS Standard

A study of patent thickets

Report analysing whether entry of UK enterprises into patenting in a technology area is affected by patent thickets in the technology area

Bayesian multiple-instance motif discovery with BAMBI: inference of recombinase and transcription factor binding sites

Finding conserved motifs in genomic sequences represents one of essential bioinformatic problems. However, achieving high discovery performance without imposing substantial auxiliary constraints on possible motif features remains a key algorithmic challenge. This work describes BAMBI—a sequential Monte Carlo motif-identification algorithm, which is based on a position weight matrix model that does not require additional constraints and is able to estimate such motif properties as length, logo, number of instances and their locations solely on the basis of primary nucleotide sequence data. Furthermore, should biologically meaningful information about motif attributes be available, BAMBI takes advantage of this knowledge to further refine the discovery results. In practical applications, we show that the proposed approach can be used to find sites of such diverse DNA-binding molecules as the cAMP receptor protein (CRP) and Din-family site-specific serine recombinases. Results obtained by BAMBI in these and other settings demonstrate better statistical performance than any of the four widely-used profile-based motif discovery methods: MEME, BioProspector with BioOptimizer, SeSiMCMC and Motif Sampler as measured by the nucleotide-level correlation coefficient. Additionally, in the case of Din-family recombinase target site discovery, the BAMBI-inferred motif is found to be the only one functionally accurate from the underlying biochemical mechanism standpoint. C++ and Matlab code is available at http://www.ee.columbia.edu/~guido/BAMBI or http://genomics.lbl.gov/BAMBI/

Hard X-ray Bursts Detected by the IBIS Telescope Onboard the INTEGRAL Observatory in 2003-2004

All of the observations performed with the IBIS telescope onboard the INTEGRAL observatory during the first one and a half years of its in-orbit operation (from February 10, 2003, through July 2, 2004) have been analyzed to find X-ray bursts. IBIS/ISGRI detector lightcurves total count rate in the energy range 15-25 keV revealed 1077 bursts of durations from ~5 to ~500 s detected with a high statistical significance (only one event over the entire period of observations could be detected by a chance with a probability of 20%). Apart from the events associated with cosmic gamma-ray bursts (detected in the field of view or passed through the IBIS shield), solar flares, and activity of the soft gamma repeater SGR1806-20, we were able to localize 105 bursts and, with one exception, to identify them with previously known persistent or transient X-ray sources (96 were identified with known X-ray bursters). In one case, the burst source was a new burster in a low state. We named it IGR J17364-2711. Basic parameters of the localized bursts and their identifications are presented in the catalog of bursts. Curiously enough, 61 bursts were detected from one X-ray burster - GX 354-0. The statistical distributions of bursts in duration, maximum flux, and recurrence time have been analyzed for this source. Some of the bursts observed with the IBIS/ISGRI telescope were also detected by the JEM-X telescope onboard the INTEGRAL observatory in the standard X-ray energy range 3-20 keV.Comment: 30 pages, 9 figure

Quantum Dots Do Not Affect the Behaviour of Mouse Embryonic Stem Cells and Kidney Stem Cells and Are Suitable for Short-Term Tracking

Quantum dots (QDs) are small nanocrystals widely used for labelling cells in order to enable cell tracking in complex environments in vitro, ex vivo and in vivo. They present many advantages over traditional fluorescent markers as they are resistant to photobleaching and have narrow emission spectra. Although QDs have been used effectively in cell tracking applications, their suitability has been questioned by reports showing they can affect stem cell behaviour and can be transferred to neighbouring cells. Using a variety of cellular and molecular biology techniques, we have investigated the effect of QDs on the proliferation and differentiation potential of two stem cell types: mouse embryonic stem cells and tissue-specific stem cells derived from mouse kidney. We have also tested if QDs released from living or dead cells can be taken up by neighbouring cells, and we have determined if QDs affect the degree of cell-cell fusion; this information is critical in order to assess the suitability of QDs for stem cell tracking. We show here that QDs have no effect on the viability, proliferation or differentiation potential of the two stem cell types. Furthermore, we show that the extent of transfer of QDs to neighbouring cells is <4%, and that QDs do not increase the degree of cell-cell fusion. However, although the QDs have a high labelling efficiency (>85%), they are rapidly depleted from both stem cell populations. Taken together, our results suggest that QDs are effective cell labelling probes that are suitable for short-term stem cell tracking

Business networks and localization effects for new Swedish technology-based firms’ innovation performance

This study examines the business networks and localization effects for new technology-based firms (NTBFs) in the context of innovation performance (the number of patents and product differentiation). In this regard, the study includes 28 variables. A survey was conducted in 2016 with 401 Swedish NTBFs that were small and young (the employment mean was 1.80 and the average age of each firm was 28.3\ua0months). The biggest category of NTBFs was knowledge-intensive high-technology services, followed by medium high-technology manufacturing, and high-technology manufacturing. Hypotheses on how business networks and localization are related to innovation performance were tested using principal component analysis, correlation analysis, and regression analysis. The results show that the primary significant factor for innovation performance regarding business networks and localization dimensions are professional network services, while industrial and regional areas also have a positive relationship on product differentiation. Our study also shows that innovation performance enhances firms’ abilities to access external financing through professional network services (e.g., venture capital companies)

Complete Sequencing of the blaNDM-1-Positive IncA/C Plasmid from Escherichia coli ST38 Isolate Suggests a Possible Origin from Plant Pathogens

The complete sequence of the plasmid pNDM-1_Dok01 carrying New Delhi metallo-β-lactamase (NDM-1) was determined by whole genome shotgun sequencing using Escherichia coli strain NDM-1_Dok01 (multilocus sequence typing type: ST38) and the transconjugant E. coli DH10B. The plasmid is an IncA/C incompatibility type composed of 225 predicted coding sequences in 195.5 kb and partially shares a sequence with blaCMY-2-positive IncA/C plasmids such as E. coli AR060302 pAR060302 (166.5 kb) and Salmonella enterica serovar Newport pSN254 (176.4 kb). The blaNDM-1 gene in pNDM-1_Dok01 is terminally flanked by two IS903 elements that are distinct from those of the other characterized NDM-1 plasmids, suggesting that the blaNDM-1 gene has been broadly transposed, together with various mobile elements, as a cassette gene. The chaperonin groES and groEL genes were identified in the blaNDM-1-related composite transposon, and phylogenetic analysis and guanine-cytosine content (GC) percentage showed similarities to the homologs of plant pathogens such as Pseudoxanthomonas and Xanthomonas spp., implying that plant pathogens are the potential source of the blaNDM-1 gene. The complete sequence of pNDM-1_Dok01 suggests that the blaNDM-1 gene was acquired by a novel composite transposon on an extensively disseminated IncA/C plasmid and transferred to the E. coli ST38 isolate

Non-Integrative Lentivirus Drives High-Frequency cre-Mediated Cassette Exchange in Human Cells

Recombinase mediated cassette exchange (RMCE) is a two-step process leading to genetic modification in a specific genomic target sequence. The process involves insertion of a docking genetic cassette in the genome followed by DNA transfer of a second cassette flanked by compatible recombination signals and expression of the recombinase. Major technical drawbacks are cell viability upon transfection, toxicity of the enzyme, and the ability to target efficiently cell types of different origins. To overcome such drawbacks, we developed an RMCE assay that uses an integrase-deficient lentivirus (IDLV) vector in the second step combined with promoterless trapping of double selectable markers. Additionally, recombinase expression is self-limiting as a result of the exchangeable reaction, thus avoiding toxicity. Our approach provides proof-of-principle of a simple and novel strategy with expected wide applicability modelled on a human cell line with randomly integrated copies of a genetic landing pad. This strategy does not present foreseeable limitations for application to other cell systems modified by homologous recombination. Safety, efficiency, and simplicity are the major advantages of our system, which can be applied in low-to-medium throughput strategies for screening of cDNAs, non-coding RNAs during functional genomic studies, and drug screening