Status of Divisions of the International Geologic Time Scale

Each chronostratigraphic unit of the International Geologic Time Scale will be defined at its base by a Global Stratotype Section and Point (GSSP) or Global Standard Stratigraphic Age (GSSA). Nearly 50 GSSPs and 10 GSSAs have now been ratified. Ideally, the GSSP coincides with events having a global correlation potential. The international stage divisions of some systems, such as the Jurassic or Neogene, are similar to traditional usage in European geology. However, in order to utilize global correlation horizons, the international stage divisions of other systems, such as the Ordovician or Permian, have required assembling new stage nomenclatures or hybrids of different regional stages. A reference table by the International Commission on Stratigraphy itemizes the current or potential GSSP and GSSA definitions of all international geologic time units.     

Introduction to an International Guide to Stratigraphic Classification,Terminology, and Usage

International Subcommission on Stratigraphic Classification [Report No. 7a; editor H. D. Hedberg]: Introduction to an International Guide to Stratigraphic Classification, Terminology, and Usage. Lethaia, Vol 5, pp. 283–295. Oslo, July 15th, 1972. The International Subcommission on Stratigraphic Classification (ISSC), a subcommission of the IUGS Commission on Stratigraphy, has been working for the last 15–20 years towards the preparation of an International Guide to Stratigraphic Classification, Terminology, and Usage. The purpose of the Guide is to promote international agreement on principles of stratigraphic classification and to establish internationally acceptable stratigraphic terminology and rules of stratigraphic procedure. The Introduction explains the background of its preparation.     

The new chronostratigraphic classification of the Ordovician System and its relations to major regional series and stages and to δ13C chemostratigraphy

The extensive work carried out during more than a decade by the International Subcommission on Ordovician Stratigraphy has resulted in a new global classification of the Ordovician System into three series and seven stages. Formal Global Boundary Stratotype Section and Points (GSSPs) for all stages have been selected and these and the new stage names have been ratified by the International Commission on Stratigraphy. Based on a variety of biostratigraphic data, these new units are correlated with chronostratigraphic series and stages in the standard regional classifications used in the UK, North America, Baltoscandia, Australia, China, Siberia and the Mediterranean‐North Gondwana region. Furthermore, based mainly on graptolite and conodont zones, the Ordovician is subdivided into 20 stage slices (SS) that have potential for precise correlations in both carbonate and shale facies. The new chronostratigraphic scheme is also tied to a new composite δ¹³C curve through the entire Ordovician.     

Integrated stratigraphy and 40Ar/39Ar chronology of early Middle Miocene sediments from DSDP Leg 42A,Site 372 (Western Mediterranean)

An integrated magneto-biostratigraphic framework is presented for Middle Miocene sediments of DSDP Site 372 located in the Western Mediterranean. Detailed biostratigraphic analysis shows a nearly complete sequence of early Middle Miocene calcareous plankton bioevents in the Mediterranean, including the LCO (Last Common Occurrence) of the nannofossil Sphenolithus heteromorphus which has been astronomically dated in the Ras il Pellegrin (RIP) section on Malta Island [Abels, H.A., Hilgen, F.J., Krijgsman, W., Kruk, R.W., Raffi, I., Turco, E., Zachariasse, W.J., 2005. Long-period orbital control on middle Miocene global cooling: integrated stratigraphy and astronomical tuning of the Blue Clay Formation on Malta, Paleoceanography, 20, PA4012. doi: 10.1029/2004PA001129. 11 pp]. Thermal demagnetization of discrete samples revealed a characteristic low-temperature component with dual polarities despite a weak paleomagnetic signal. The resultant magnetostratigraphic record, combined with the calcareous plankton biostratigraphy, is straightforwardly correlated to the geomagnetic polarity time scale (CK95) of Cande and Kent [Cande, S.C., Kent, D.V., 1995. Revised calibration of the Geomagnetic Polarity Time Scale for the Late Cretaceous and Cenozoic, J. Geophys. Res., 100, 6093–6095] and the Astronomical Tuned Neogene Time Scale (ATNTS04) of Lourens et al. [Lourens, L.J., Hilgen, F.J., Laskar, J., Shackleton, N.J., Wilson, D., 2004. The Neogene Period. In: Gradstein F.M., Ogg J.G., Smith A.G. (Eds.), A Geologic Time Scale, Cambridge Univ. Press, pp. 409–440]. The subchrons recorded in Site 372 succession range from C5Br up to C5AAr. To confirm the magnetostratigraphic calibration, ⁴⁰Ar/³⁹Ar dating was performed on feldspar of two volcanic ash layers. The radio-isotopic dating indicates a younger age for these two ash layers compared to the magnetostratigraphic calibrated ages according to the CK95 and ATNTS04 age models. However, if the astronomically calibrated age of 28.21 ± 0.04 Ma is used for the Fish Canyon standard (FCs), the age for the older ash layer exactly matches its ATNTS04 age. Ages for bioevents were calculated assuming constant sedimentation rates between magnetostratigraphic age-tie points. The S. heteromorphus LCO has an age of 13.54 Ma and 13.63 Ma according to CK95 and ATNTS04, respectively, which is consistent with the astronomical tuned age of 13.65 Ma determined at RIP section [Abels, H.A., Hilgen, F.J., Krijgsman, W., Kruk, R.W., Raffi, I., Turco, E., Zachariasse, W.J., 2005. Long-period orbital control on middle Miocene global cooling: integrated stratigraphy and astronomical tuning of the Blue Clay Formation on Malta, Paleoceanography, 20, PA4012. doi:10.1029/2004PA001129. 11 pp]. We therefore conclude that the magnetostratigraphic calibration of DSDP Site 372 is correct and that, for the time being, this site can be considered as a reference section for the early Middle Miocene of the Mediterranean region.     

The Ordovician-Silurian boundary: new data, new concerns

Despite International Union of the Geological Sciences (IUGS) ratification of the International Commission on Stratigraphy recommendation that the base of the Parakidograptus acuminatus zone be the base of the Silurian and that the boundary stratotype be at Dob's Linn, Scotland, numerous concerns continue to be expressed over the timing of the selection as well as the boundary and its stratotype. The richness of both graptolite and non-graptolite biostratigraphic data in numerous stratigraphic sections from many areas in China published at about the same time that the boundary and stratotype were approved formally and shortly after approval suggest the possibility that boundary designation may have been somewhat premature. The new data from China document clearly the major extinction of characteristic Late Ordovician taxa significantly below the presently accepted System boundary. The new data indicate that the re-radiation of graptolites after the extinction took place in the Glyptograptus persculptus zone, the graptolite zone subjacent to the P. acuminatus zone. New geochemical data from Dob's Linn reveal a change in chemistry in strata subjacent to the base of the G. persculptus zone that could be used as an aid in correlation. The new data suggest the possibility that the base of the G. persculptus zone, the relatively traditional base of the Silurian, could be as appropriate a System boundary as the base of the P. acuminatus zone.     

The Ordovician-Silurian boundary stratotype: consequences of its approval by the IUGS

Lespérance, Pierre J., Barnes, Christopher R., Berry, William B. N., Boucot, Arthur J. & Mu En-zhi 1987 07 15: The Ordovician-Silurian boundary stratotype: consequences of its approval by the IUGS.
The Ordovician-Silurian stratotype at Dob's Linn, Scotland is the second systemic boundary approved by the International Union of Geological Sciences (IUGS). A review of the internationally accepted criteria required of a stratotype shows that few of these are possessed by the Dob's Linn section. The strongest attribute of the section is the presence of zonal graptolites, although the boundary is recognized primarily on a single biological event (base of acuminatus Zone) for which the evolutionary relationships of the taxa are not established. In approving this boundary proposal in 1985, which received only simple majority support within the Ordovician-Silurian Boundary Working Group (OSBWG) and which fails to meet most of the accepted prerequisites for a stratotype, the International Commission on Stratigraphy (ICS) and the IUGS have established an unfortunate precedent. It follows that future systemic boundaries need not meet the accepted standards. It raises serious questions on the assessment and voting procedures of the International Commission on Stratigraphy and on the credence accorded the recommendations developed by the International Subcommission on Stratigraphic Classification of IUGS.     

Zur Biologie, Taxonomie und Chronologie der Conodonten

The actual state of knowledge concerning the conodont animal is critically reviewed. All soft tissue documented by the specimens of the conodont animal were interpreted by the British collectors as Craniota (Vertebrata) features. Opinions on the precise affinities, however, remain controverse: The alleged chorda could have been a gut, bilateral symmetry, myomery, apatitic biomineralisation occur also in Invertebrata, caudal fins do in Chaetognatha. Even the lobes in the capital area interpreted as sensory organs could have served as aiding organs for food intake. Therefore, the originally sensational findings are reduced to the core issue that the conodont animal had an eel-like body and at the blunt end of it, behind peculiar lobes, the mineralized conodont elements were arranged. As a consequence, a relationship to the Protochordata cannot be excluded. A systematic position of the conodont animal as possible Vertebrata is likely only if organized below the Ostracodermata which is particularly so because conodonts occur so early in the Cambrian. In the second part of the article conodonts are discussed as guide fossils. The comprehensive, empirically grown taxonomy of the single elements is the prerequisite for recognizing outstanding, high resolution stratigraphy. In comparison, a multielement taxonomy remains as long problematical, as it is based on assumed, mostly statistically reconstructed rather than on natural multielement apparatuses. Taxonomical and nomenclatorial operations built on assumed apparatus affinity can bear heavily on nomenclature and stratigraphy of platform elements. It can be shown at the example of the Devonian that the platform elements have provided particularly in the pelagic facies a Standard Conodont Zonation that covers time almost without any gaps. The basis for this is that platform single element species and their phylogenetic development are extra-well known. In a special paragraph, history and applicability of the Standard Zonation is discussed in details. Different conodont biofacies are developed between the pelagic realm where the Standard Zonation originated, and the coastal areas so that conodonts can indicate temporal and bathymetric relationships of the mother rocks. In addition alternative conodont zonations were introduced mainly for the shallow water. Because of their conspicuous stratigraphic significance in the Devonian, conodonts were employed by International Committees to redefine Series and Stage Boundaries. For the boundary selection species were utilized from phylognetic lineages as only from tight evolution their point of origination could be well identified and recognized in worldwide correlation. The GSSPs (Global Stratotype Section and Point) within the Devonian are discussed in detail. In recent times, attempts are made at calibrating the duration of conodont zones on the basis of their well known rate of evolution and high temporal resolution. These analyses have to be continued in order to demonstrate the absolute time relationship of condont zones in more and continuous detail. Currently the phyletically controlled Standard Conodont Zonation is the authoritative stratigraphic method in the Devonian. It has provided together with the GSSPs precise and valuable fix points for a Global Time Scale (GTS). In combination with additional stratigraphie methods the Standard Conodont Zonation may provide further refinements in the future.     

On-site diagnosis of Plasmodium falciparum, P. vivax, and P. malariae by using the Quantitative Buffy Coat system.

The Quantitative Buffy Coat (QBC) system was used for the detection and identification of malaria parasites in blood specimens from 570 residents of Oksibil, an isolated highland valley in the eastern Jayawijaya Mountains of Irian Jaya (Indonesian New Guinea). The availability of a battery-powered centrifuge and a fiberoptic Paralens enabled us to complete and interpret the assay in this remote environment. Of 322 QBC tubes examined for 2-4 min each, results of 295 (92%) concurred with findings on the matched Giemsa-stained thick smear (GTS). The 27 discrepant results included 13 QBC+/GTS- that, upon reexamination, were found to be GTS+. When using the corrected GTS results as the standard, the sensitivity and specificity of the QBC were 94% and 96%, respectively. Because electricity was available only 3 hr per day, it was decided to decrease the examination for an additional 248 QBC to a maximum of 90 sec per tube. This shortened inspection time resulted in a reduction of sensitivity to 53% but specificity was preserved at 89%. Forty-two of 45 conflicting results, QBC-/GTS+ from cases of light Plasmodium falciparum infections with < 1 trophozoite or gametocyte per field, were resolved by reexamination of the QBC in the laboratory. Tubes held at 4 C could be reexamined, without noticeable loss of fluorescence, for at least 6 wk after collection. Despite some difficulty in the identification of Plasmodium species, it was concluded that the QBC is an easy, sensitive method for the rapid diagnosis of malaria in the field and that it provides the inexperienced microscopist with an additional means for on-site identification of individuals needing treatment.     

Ontological analysis of gene expression data: current tools, limitations, and open problems

Independent of the platform and the analysis methods used, the result of a microarray experiment is, in most cases, a list of differentially expressed genes. An automatic ontological analysis approach has been recently proposed to help with the biological interpretation of such results. Currently, this approach is the de facto standard for the secondary analysis of high throughput experiments and a large number of tools have been developed for this purpose. We present a detailed comparison of 14 such tools using the following criteria: scope of the analysis, visualization capabilities, statistical model(s) used, correction for multiple comparisons, reference microarrays available, installation issues and sources of annotation data. This detailed analysis of the capabilities of these tools will help researchers choose the most appropriate tool for a given type of analysis. More importantly, in spite of the fact that this type of analysis has been generally adopted, this approach has several important intrinsic drawbacks. These drawbacks are associated with all tools discussed and represent conceptual limitations of the current state-of-the-art in ontological analysis. We propose these as challenges for the next generation of secondary data analysis tools.     

天津蓟县东营坊遗址出土的石制品

东营坊遗址位于天津蓟县境内。2007年,对该遗址进行抢救性发掘,发掘面积200m2,出土石制品90件。石制品原料系就地取材于遗址附近的河床或基岩;石制品类型包括石核、石片、石器和断块;剥片采用锤击法;石器以小型为主,包括刮削器和雕刻器,由硬锤直接加工而成,方向以正向居多。根据文化层底部哺乳动物化石的测年结果,遗址年代为旧石器时代中晚期过渡阶段或旧石器时代晚期早段。     

Molecular Biocomputing Suite: a word processor add-in for the analysis and manipulation of nucleic acid and protein sequence data.

In all fields of molecular biology, researchers are increasingly challenged by experiments planned and evaluated on the basis of nucleic acid and protein sequence data generally retrieved from public databases. Despite the wide spectrum of available Web-based software tools for sequence analysis, the routine use of these tools has disadvantages, particularly because of the elaborate and heterogeneous ways of data input, output, and storage. Here we present a Visual Basic-encoded Microsoft Word Add-In, the Molecular BioComputing Suite (MBCS), available at the BioTechniques Software Library (www.BioTechniques.com). The MBCS software aims to manage and expedite a wide range of sequence analyses and manipulations using an integrated text editor environment including menu-guided commands. Its independence of sequence formats enables MBCS to be used as a pivotal application between other software tools for sequence analysis, manipulation, annotation, and editing.     

DraGnET: Software for storing,managing and analyzing annotated draft genome sequence data

Background  

New "next generation" DNA sequencing technologies offer individual researchers the ability to rapidly generate large amounts of genome sequence data at dramatically reduced costs. As a result, a need has arisen for new software tools for storage, management and analysis of genome sequence data. Although bioinformatic tools are available for the analysis and management of genome sequences, limitations still remain. For example, restrictions on the submission of data and use of these tools may be imposed, thereby making them unsuitable for sequencing projects that need to remain in-house or proprietary during their initial stages. Furthermore, the availability and use of next generation sequencing in industrial, governmental and academic environments requires biologist to have access to computational support for the curation and analysis of the data generated; however, this type of support is not always immediately available.     

Indications of linkage and association of Gilles de la Tourette syndrome in two independent family samples: 17q25 is a putative susceptibility region

Gilles de la Tourette syndrome (GTS) is characterized by multiple motor and phonic tics and high comorbidity rates with other neurobehavioral disorders. It is hypothesized that frontal-subcortical pathways and a complex genetic background are involved in the etiopathogenesis of the disorder. The genetic basis of GTS remains elusive. However, several genomic regions have been implicated. Among them, 17q25 appears to be of special interest, as suggested by various independent investigators. In the present study, we explored the possibility that 17q25 contributes to the genetic component of GTS. The initial scan of chromosome 17 performed on two large pedigrees provided a nonparametric LOD score of 2.41 near D17S928. Fine mapping with 17 additional microsatellite markers increased the peak to 2.61 (P=.002). The original families, as well as two additional pedigrees, were genotyped for 25 single-nucleotide polymorphisms (SNPs), with a focus on three genes in the indicated region that could play a role in the development of GTS, on the basis of their function and expression profile. Multiple three-marker haplotypes spanning all three genes studied provided highly significant association results (P<.001). An independent sample of 96 small families with one or two children affected with GTS was also studied. Of the 25 SNPs, 3 were associated with GTS at a statistically significant level. The transmission/disequilibrium test for a three-site haplotype moving window again provided multiple positive results. The background linkage disequilibrium (LD) of the region was studied in eight populations of European origin. A complicated pattern was revealed, with the pairwise tests producing unexpectedly high LD values at the telomeric TBCD gene. In conclusion, our findings warrant the further investigation of 17q25 as a candidate susceptibility region for GTS.     

23rd International Symposium on Shiftwork and Working Time: Towards a Global Consensus

ABSTRACT

The Working Time Society (WTS), and the International Commission on Occupational Health (ICOH) Scientific Committee on Shiftwork and Working Time, are twin organisations focused on conducting research, and informing practice, regarding the impact of work hours in general, and shiftwork in particular, on the efficiency, productivity, safety, well-being, health, and biological rhythms, of employees. Every 2–3 years since 1969, the WTS and ICOH have conducted a series of international symposia in Europe, Asia, Australia, North America, and South America. The purpose of these symposia is to provide a forum for the exchange of knowledge, and the discussion of contested issues, with researchers, employee representatives, regulators, and employers. The most recent symposium in this series – the 23rd International Symposium on Shiftwork and Working Time, entitled “Toward a Global Consensus” – was held on 19–23 June 2017, at Yulara, Australia, near Uluru. Since 2004, Chronobiology International has released a special issue after each symposium, and that tradition continues with a special issue that includes 17 contributions based on a selection of the 128 papers that were presented at the most recent symposium. Here, we provide an overview of the papers that comprise the special issue, and we briefly comment on the implications of the findings for shiftworkers and their employers.     

UCSF ChimeraX: Structure visualization for researchers,educators, and developers

UCSF ChimeraX is the next‐generation interactive visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. ChimeraX brings (a) significant performance and graphics enhancements; (b) new implementations of Chimera's most highly used tools, many with further improvements; (c) several entirely new analysis features; (d) support for new areas such as virtual reality, light‐sheet microscopy, and medical imaging data; (e) major ease‐of‐use advances, including toolbars with icons to perform actions with a single click, basic “undo” capabilities, and more logical and consistent commands; and (f) an app store for researchers to contribute new tools. ChimeraX includes full user documentation and is free for noncommercial use, with downloads available for Windows, Linux, and macOS from https://www.rbvi.ucsf.edu/chimerax .     

New palaeoclimatology

A textbook in palaeoclimatology of manageable size and price has been badly needed for some time, and L. A. Frakes' Climates throughout Geologic Time meets at least the first requirement in another 'type-written book' from Elsevier. As usual one finds that simplified typesetting techniques and low overheads for illustrations have had no price-lowering effect as compared with books produced with more refined methods.     

Data standards, sense and stability: Scratchpads, the ICZN and ZooBank

The International Commission of Zoological Nomenclature has used the Scratchpads platform (currently being developed and maintained by ViBRANT) as the foundation for its redesigned website and as a platform for engaging with its users. The existing Scratchpad tools, with extensions to provide additional functions, have allowed for a major transformation in presentation of linked nomenclatural tools. Continued development of the new website will act as a springboard for the ICZN to participate more fully in the wider community of biodiversity informatics.     

沂源上崖洞石制品的研究

本文记述了１９８１年在山东省沂源县上崖洞发现的石制品,并仿制了有关类型的石器,进行切削、刮和钻孔试验,然后用电镜和体视显微镜（ＯＬＹＭＰＵＳ ＳＺＨ－１５１）观察其使用微痕。通过实验标本和上崖洞的石器二者对比观察和分析,认为本文所记述的石器主要用于切割和钻孔。根据洞内地层堆积,可以确定上岩洞石制品的时代晚期。