Parameterizable consensus connectomes from the Human Connectome Project: the Budapest Reference Connectome Server v3.0

Connections of the living human brain, on a macroscopic scale, can be mapped by a diffusion MR imaging based workflow. Since the same anatomic regions can be corresponded between distinct brains, one can compare the presence or the absence of the edges, connecting the very same two anatomic regions, among multiple cortices. Previously, we have constructed the consensus braingraphs on 1015 vertices first in five, then in 96 subjects in the Budapest Reference Connectome Server v1.0 and v2.0, respectively. Here we report the construction of the version 3.0 of the server, generating the common edges of the connectomes of variously parameterizable subsets of the 1015-vertex connectomes of 477 subjects of the Human Connectome Project’s 500-subject release. The consensus connectomes are downloadable in CSV and GraphML formats, and they are also visualized on the server’s page. The consensus connectomes of the server can be considered as the “average, healthy” human connectome since all of their connections are present in at least k subjects, where the default value of \(k=209\), but it can also be modified freely at the web server. The webserver is available at http://connectome.pitgroup.org.     

Larval host records of butterflies in Japan

Using Japanese literature, we created a consolidated list of host records of butterflies in Japan. The list used the host records described in eight major illustrated reference books, two checklists, and 14 other pieces of literature. The presence of larvae on plants, the observation of larvae eating plants or insects in the field were considered as host records. We collected all species recorded in Japan. Scientific, family, and Japanese names of butterflies were consolidated using the BINRAN database (http://binran.lepimages.jp/). Scientific and Japanese names of host plants were based on the YList database (http://ylist.info/). If scientific names of host plants were not found in YList, we used scientific names based on The Plant List (http://www.theplantlist.org/). Family names of host plants were based on the Catalogue of Life database (http://www.catalogueoflife.org/). Scientific, family, and Japanese names of host insects were based on the MOKUROKU database (http://konchudb.agr.agr.kyushu-u.ac.jp/mokuroku/) for Hymenoptera and the catalogue of the Paraneoptera of Japan published by the Entomological Society of Japan for Hemiptera. We also provided the references of each host record and the original names described in the referred literature. Two datasets, HostDB and ReferenceDB, were created to include 3600 records of butterfly larval hosts in Japan, along with scientific and Japanese names of each species and a literature list. These datasets will be useful for basic and applied biological studies of butterflies. Data files are stored in the Ecological Research Data Archives (http://db.cger.nies.go.jp/JaLTER/ER_DataPapers/) and available from http://hostbj.lepumus.net/. These datasets are published under the Creative Commons License Attribution-ShareAlike 4.0 (CC BY-SA, https://creativecommons.org/licenses/by-sa/4.0/).     

A new species of Larsia Fittkau, 1962 (Diptera: Chironomidae: Tanypodinae) from phytotelmata of Aechmea distichantha Lemaire, 1853 (Bromeliaceae) in Argentina

A new species of Larsia Fittkau, 1962 Fittkau, E.J. (1962), ‘Die Tanypodinae (Diptera: Chironomidae) (Die Tribus Anatopyniini, Macropelopiini und Pentaneurini)’, Abhandlungen zur Larvalsystematik der Insekten, 6, 1–453. [Google Scholar], viz. Larsia angusticornis sp. n., is described and adults and immatures are figured. The study is based on larvae collected from phytotelmata of the bromeliad Aechmea distichantha Lemaire, 1853 Lemaire, A.C. (1853), Le Jardin Fleuriste; Journal General des Progres et des Interets Horticoles et Botaniques, 3: pl. 269. [Google Scholar] in northeastern Argentina that were reared to the adult stage. The pupa bears thoracic horns unusual for the genus, which distinguish this new species from other Larsia species.

http://zoobank.org/urn:lsid:zoobank.org:pub:41DFD96D-98E2-4FFC-9CDE-C290BCA84D45     

Metabolic syndrome is associated to high-sensitivity cardiac troponin T elevation

Introduction: Metabolic syndrome (MetS) and high-sensitivity cardiac troponin T (hs-TnT) are associated with higher risk for cardiovascular diseases (CVD). Our aim was to assess the relation between hs-TnT elevation and MetS in a general population sample.

Materials and methods: Individuals participating in an annual health survey program between 2010 and 2016 were included in the study. Blood samples including hs-TnT levels were collected. The study population was divided into three groups based on hs-TnT levels – undetectable (<5?ng/L), intermediate (5–14?ng/L) and elevated (>14?ng/L).

Results: A total of 5994 subjects were included in the study, the mean age was 48.5 and 4336 (72%) were males. Compared with subjects with undetectable hs-TnT the prevalence of MetS was higher in those with detectable and elevated levels – 392 (10%) vs. 270 (15%) and 51 (33%), respectively (p?<?0.001). In a multivariate model adjusted for age, gender and multiple co-morbidities, the number of MetS components and presence of MetS were significantly associated with an increased risk for detectable hs-TnT levels (OR?=?1.02 {for each component}; 95% CI [1.00–1.05], p?=?0.04) and (OR?=?1.13; 95% CI [1.07–1.2], p?<?0.001) respectively. Only the waist, glucose and hypertension components of the MetS were significantly associated with elevated troponin.

Conclusions: The MetS and its distinct components have a cumulative impact on hs-TnT levels in apparently healthy subjects.     

Comet assay for assessment of DNA damage in greenhouse workers exposed to pesticides

Purpose: The main goal of the present study was to determine DNA damage in pesticide-exposed greenhouse workers and pesticides non-exposed controls.

Materials and methods: The DNA damage was measured by alkaline comet assay method (pH?>?13) in 41 greenhouse workers and 45 non-exposed individuals as the control. Pesticide exposure was assessed by duration of working in the greenhouse and pesticide application in the greenhouse time. DNA damage was estimated by arbitrary unit and damage frequency.

Results: Arbitrary unit and damage frequency were consistently significantly higher in greenhouse workers than those of the controls (p?=?0.001). In terms of gender in greenhouse, DNA damage of female workers was significantly higher than those in male workers (p?<?0.05). We found significant correlation between DNA damage and working hours spent. Multiple linear regression analysis showed that working hours in the greenhouse as an indication of pesticide exposure were significantly associated with the DNA damage, which can be attributed to the genotoxic potential of the pesticide mixture.

Conclusions: The comet assay is sensitive to detect the damage exposed to chronic effect of pesticides in greenhouse workers. Significant DNA damage was obtained for the exposed group, which was associated with the pesticide exposure.     

siMBa—a simple graphical user interface for the Bayesian phylogenetic inference program MrBayes

MrBayes is a program that uses a Bayesian framework for inferring phylogenetic relationships. As MrBayes is a command-line-driven program, users acquainted to programs with graphical user interfaces will not find it easy to operate, especially as it requires a complex input format for the data to be analysed. We thus developed siMBa (simple MrBayes), a simple graphical user interface for MrBayes. This tool gives the user interactive control over most of the parameters and also facilitates the input of a multiple sequence alignment, as any widely used format can be used. siMBa is coded in Perl using the Tk module. Executables are provided for Windows, Linux, and Macintosh. The Perl codes, along with executables for different operating system, are freely available to download from [http://www.thines-lab.senckenberg.de/simba].     

The scent of your enemy is my friend? The acquisition of large carnivore scent by a smaller carnivore

Scent marking is critical to intraspecific communication in many mammal species, but little is known regarding its role in communication among different species. We used 4 years of motion-triggered video to document the use of scent marking areas—termed “community scrapes”—by pumas (Puma concolor) (http://www.momo-p.com/showdetail-e.php?movieid=momo160812pc01a) and other carnivore species. We found that gray foxes (Urocyon cinereoargenteus) routinely rubbed their cheeks on puma scrapes (http://www.momo-p.com/showdetail-e.php?movieid=momo160812uc01a), and tested a series of hypotheses to determine its function. We found that gray foxes selected puma scrapes over other objects, and cheek rubbing by foxes was also correlated with how recently a puma had visited the scrape, suggesting that foxes were intent upon accumulating fresh puma scent. Cheek rubbing by foxes was not correlated with their breeding season or with how recently another fox had visited the site. Finally we found a cascading pattern in the occurrence of pumas, coyotes (Canis latrans) and gray foxes at community scrapes, suggesting that gray foxes may use puma scent to deter predation. This is the first published study to find evidence of a subordinate species using the scent of a dominant species to communicate with heterospecifics. The behavioral cascade we found in scent marking patterns also suggests that scent marking could be a mechanism that impacts the distribution and abundance of species. Additional videos pertaining to this article include http://www.momo-p.com/showdetail-e.php?movieid=momo160812uc02a, and http://www.momo-p.com/showdetail-e.php?movieid=momo160812uc03a.     

Indoor Air as a Source of VOC Contamination in Shallow Soils Below Buildings

US EPA and many state regulatory agency guidance documents recommend below-foundation vapor sampling as a key element of site investigations to determine if vapor migration from underlying soil into buildings is a completed exposure pathway (USEPA, 2002 US EPA (U.S. Environmental Protection Agency). Draft Guidance for Evaluating the Vapor Intrusion to Indoor Air Pathway from Groundwater and Soils (Subsurface Vapor Intrusion Guidance). November2002.  [Google Scholar]; WIDHFS, 2003 WIDHFS (Wisconsin Department of Health and Family Services). Chemical Vapor Intrusion and Residential Indoor Air, Guidance for Environmental Consultants and Contractors. June202004. Available at http://dhfs.wisconsin.gov/eh/Air/fs/VI_prof.htm (accessed) [Google Scholar]; San Diego County, 2004 San Diego County Department of Environmental Health. Site Assessment and Mitigation (SAM) Manual. June202004. http://www.sdcounty.ca.gov/deh/lwq/sam/vapor_risk_assessment_2000.html (accessed) [Google Scholar]; PADEP, 2004 PADEP (Pennsylvania Department of Environmental Protection). Land Recycling Program Technical Guidance Manual-Section IV.A.4. June202004. Vapor Intrusion into Buildings from Groundwater and Soil under Act 2 Statewide Health Standard. Document Number 253-0300-100. http://www.dep.state.pa.us/eps/default.asp (accessed) [Google Scholar]). If volatile organic compounds (VOCs) are detected below the building foundation, then VOC migration from the subsurface is assumed to be occurring, and further investigation is needed to determine the extent of the VOC impact. These guidance documents are predicated on the assumption that VOCs detected in below-foundation samples have originated from deeper within the subsurface. However, detection of VOCs in below-foundation vapor samples alone is not sufficient to conclude that the VOCs are migrating from the subsurface upward towards a building. VOCs detected in below-foundation vapor samples can originate from indoor sources, migrating down through the slab by diffusion or advection. Commonly referenced conceptual models for vapor intrusion address VOC migration from the subsurface into buildings but do not consider the potential for VOC migration from buildings into the subsurface (USEPA, 2002 US EPA (U.S. Environmental Protection Agency). Draft Guidance for Evaluating the Vapor Intrusion to Indoor Air Pathway from Groundwater and Soils (Subsurface Vapor Intrusion Guidance). November2002.  [Google Scholar]; Johnson and Ettinger, 1991 Johnson, P. C. and Ettinger, R. A. 1991. Heuristic model for the intrusion rate of contaminant vapors into buildings. Environ. Sci. Technol., 25(8): 1445–1452. [CSA][CROSSREF][Crossref], [Web of Science ®] [Google Scholar]; Parker, 2003 Parker, J. C. 2003. Modeling volatile chemical transport, biodecay, and emission to indoor air. Ground Water Mon. Remed., 23(1): 107–120. [CSA][Crossref], [Web of Science ®] [Google Scholar]). The advective and diffusive forces that lead to the migration of VOCs from the subsurface into buildings are equally likely to result in the migration of VOCs from buildings into the subsurface when pressure or concentration gradients support such migration. In this paper we present: i) pressure gradient measurements indicating bi-directional advective flow across building foundations, ii) simple modeling indicating that indoor sources of VOCs may cause subsurface impacts through advection across the building foundation, and iii) field data from a site where indoor sources rather than subsurface contamination were the source of VOCs detected in below-foundation vapor samples.     

Anatomy,relationships and distribution of Taiwanassiminea affinis (Böttger) (Caenogastropoda: Assimineidae), with a reassessment of Cyclotropis Tapparone-Canefri

Assiminea affinis (Mousson ms) Böttger, 1887 Böttger, O. (1887) Aufzählung der zur Gattung Assiminea Fleming gehörigen Arten. Jahrbücher der Deutschen Malakozoologischen Gesellschaft 14, 147–234, pl. 6. [Google Scholar](=A. queenslandica [Pilsbry ms] Thiele, 1927 Thiele, J. (1927) Über die Schneckenfamilie Assimineidae. Zoologische Jahrbücher, Abteilung für Systematik, Ökologie und Geographie der Tiere 53, 114–146, pl. 1. [Google Scholar]), a previously unrecognised Australian assimineid species, is described anatomically and allocated to the genus Taiwanassiminea Kuroda and Habe, 1950 Kuroda, T. & Habe, T. (1950) Nomenclatural notes. Illustrated Catalogue of Japanese Shells 1, 16. [Google Scholar], first described from Taiwan. This is the first record of the genus from Australia. Taiwanassiminea affinis is found in slightly brackish waters in the upper tidal reaches of the larger rivers from northern Queensland to the Shoalhaven River in the southern half of New South Wales. The terrestrial Cyclotropis Tapparone-Canefri, 1883, which has somewhat similar shell and radular characters, is redefined and several species (Assiminea bedaliensis Rensch, 1934; Paludinella javana Thiele, 1927 Thiele, J. (1927) Über die Schneckenfamilie Assimineidae. Zoologische Jahrbücher, Abteilung für Systematik, Ökologie und Geographie der Tiere 53, 114–146, pl. 1. [Google Scholar]; Assiminea lentula, A. riparia and A. sororcula, all Benthem Jutting, 1963 Benthem Jutting, W.S.S. van. (1963) Non-marine Mollusca of west New Guinea Part 1, Mollusca from fresh and brackish waters. Nova Guinea, Zoology 20, 409–521. [Google Scholar]) previously included in Cyclotropis are transferred to Taiwanassiminea.     

A new species of Stenochironomus Kieffer, 1919 from the Atlantic Rainforest in southern Brazil (Diptera: Chironomidae)

Stenochironomus falcifer sp. n. is described and figured based on the characters of a male adult. The species was collected in Malaise traps in the Serra Furada State Park (PAESF), in Santa Catarina State, southern Brazil. It can be separated from all other species of Stenochironomus Kieffer, 1919 Kieffer, J.J. (1919), ‘Chironomiden der Nördlichen Polarregion’, Entomologische Mitteilungen, 8, 40–48. [Google Scholar] by its unique thorax pigmentation, with two dark patches on the lateral vittae, brownish postnotum and dark stripes on the scutum, and also by the combination of a narrow, parallel-sided anal point, inferior volsella with a stout apical seta, rounded posterior margin of the tergite IX and green metallic eyes.

http://zoobank.org/urn:lsid:zoobank.org:act:3646E02D-7E3F-487A-BED1-A7937AFF8040     

On a new species of Euchondrus Boettger, 1883 from Syria (Pulmonata: Enidae)

A new species of Euchondrus, Euchondrus adwani n. sp., is described from Syria. It is morphologically similar to E. desertorum Rochanaburananda in Forcart, 1981 Forcart, L. (1981): Neubeschreibungen von Landschnecken aus Palästina. Basteria, 45, 97–108. [Google Scholar], which is endemic to the Negev desert.

http://www.zoobank.org/urn:lsid:zoobank.org:pub:C030F4D1-D722-4186-BA7B-EACCF9BFA563     

Paternal care behaviors of Japanese giant salamander <Emphasis Type="Italic">Andrias japonicus</Emphasis> in natural populations

Parental care among salamanders is typically provided by females. A rare case of parental care by male salamanders appears to occur in Cryptobranchidae. Yet, paternal behaviors have rarely been reported from natural populations of any Cryptobranchid salamanders, and their adaptive significance is poorly understood. The present study aimed to examine paternal care behaviors in a fully aquatic Japanese giant salamander (Andrias japonicus) in situ. At the beginning of the summer breeding season, large males, called den-masters, occupy burrows along stream banks for breeding and nesting. We videotaped post-breeding behaviors of two den-masters that stayed with the eggs, one in a natural and the other in an artificial nest in natural streams. We identified three behaviors, tail fanning, agitating and egg eating, to be parental care. Tail fanning provides oxygenated water for the eggs. We found that the den-master in the artificial nest, where dissolved oxygen level was lower, displayed tail fanning more frequently. Agitating the eggs with its head and body likely prevents yolk adhesions. The den-masters selectively ate whiter eggs that appeared to be dead or infected with water mold. This behavior, which we termed hygienic filial cannibalism, likely prevents water mold from spreading over healthy eggs. Digital video images relating to this article are available at http://www.momo-p.com/showdetail-e.php?movieid=momo140906aj01a, http://www.momo-p.com/showdetail-e.php?movieid=momo140906aj02a, http://www.momo-p.com/showdetail-e.php?movieid=momo140906aj03a and http://www.momo-p.com/showdetail-e.php?movieid=momo140906aj04a.     

Computing folding pathways between RNA secondary structures

Given an RNA sequence and two designated secondary structures A, B, we describe a new algorithm that computes a nearly optimal folding pathway from A to B. The algorithm, RNAtabupath, employs a tabu semi-greedy heuristic, known to be an effective search strategy in combinatorial optimization. Folding pathways, sometimes called routes or trajectories, are computed by RNAtabupath in a fraction of the time required by the barriers program of Vienna RNA Package. We benchmark RNAtabupath with other algorithms to compute low energy folding pathways between experimentally known structures of several conformational switches. The RNApathfinder web server, source code for algorithms to compute and analyze pathways and supplementary data are available at http://bioinformatics.bc.edu/clotelab/RNApathfinder.     

First record of the genus Gynecaptera Skorikov, 1935 (Hymenoptera: Bradynobaenidae: Apterogyninae) from Saudi Arabia,with description of a new species

In the present study, the genus Gynecaptera Skorikov, 1935 Skorikov, A. S. (1935): Zur Mutilliden-Fauna Zentralasiens. Trudy tadzhikskoi basy Akademii Nauk. SSSR, 5, 257–349 + 7 plates. [Google Scholar] is recorded from the Arabian Peninsula for the first time, with a nocturnal new species, G. arabica Soliman &; Gadallah, which has been collected from the Riyadh region in Saudi Arabia and which is described and illustrated.

http://www.zoobank.org/urn:lsid:zoobank.org:pub:F7ACB779-3750-4DC6-B29B-B7F290E7C7B4     

A new species of Paratheuma (Araneae: Dictynidae) from Southwestern Asia and transfer of the genus

The marine spider genus Paratheuma Bryant, 1940 Bryant, E. B. (1940): Cuban spiders in the Museum of Comparative Zoology. Bulletin of the Museum of Comparative Zoology, 86, 247–532. [Google Scholar] is recorded in southwestern Asia for the first time, and a new species, P. enigmatica sp. n. is described from southern and southeastern Iran on the basis of both sexes. Based on morphological and molecular evidence, the genus is transferred from Desidae to Litisedinae, Dictynidae.

http://www.zoobank.org/urn:lsid:zoobank.org:pub:BC5B70CB-E6C9-4624-8BE8-22FF14AF6DC7     

Interspecific responses of wild African carnivores to odour of 3-mercapto-3-methylbutanol,a component of wildcat and leopard urine

The scent of 3-mercapto-3-methylbutanol (3-M-3-MB), a volatile component of leopard (Panthera pardus) and domestic cat (Felis silvestris catus) urine, released at about 10 ng/s from slow-release dispensers, elicited scent-marking from African civet (Civettictis civetta), small-spotted genet (Genetta genetta) and slender mongoose (Galerella sanguinea), as well as African wildcat (F. s. cafra). A female leopard was apparently repelled by the scent. The scent-marking and scent-rubbing by species other than African wildcats and leopards were unexpected and have important implications for the design of studies to investigate chemical communication between wild mammals and the use of camera traps to estimate animal numbers. Videos showing the behaviours referred to in this article are available at; http://www.momo-p.com/showdetail-e.php?movieid=momo161223fs01a; http://www.momo-p.com/showdetail-e.php?movieid=momo161223gs01a; http://www.momo-p.com/showdetail-e.php?movieid=momo161223gg01a.     

An Efficient Alternative Route To 3,6-Disubstituted-Furo[2,3-d]Pyrimidin-2-One Analogues

Copper(I)-catalyzed 5-endo-dig cyclizations of 5-(alkyn-1-yl)uracil derivatives had given poor yields of substituted furo[2 Robins, M. J. and Barr, P. J. 1983. Nucleic acid related compounds. 39. Efficient conversion of 5-iodo to 5-alkynyl and derived 5-substituted uracil bases and nucleosides. J. Org. Chem, 48: 1854–1862. [CSA][CROSSREF][Crossref], [Web of Science ®] , [Google Scholar], 3 De Clercq, E., Descamps, J., Balzarini, J., Giziewicz, J., Barr, P. J. and Robins, M. J. 1983. Nucleic acid related compounds. 40. Synthesis and biological activities of 5-alkynyluracil nucleosides. J. Med. Chem, 26: 661–666. [PUBMED][INFOTRIEVE][CSA][CROSSREF][Crossref], [PubMed], [Web of Science ®] , [Google Scholar]]pyrimidin-2-ones unless the uracil ring was substituted at N1 with alkyl or glycosyl groups. This limited flexibility for the synthesis of analogues with varied substituents at N3 and/or C6 of the furo[2 Robins, M. J. and Barr, P. J. 1983. Nucleic acid related compounds. 39. Efficient conversion of 5-iodo to 5-alkynyl and derived 5-substituted uracil bases and nucleosides. J. Org. Chem, 48: 1854–1862. [CSA][CROSSREF][Crossref], [Web of Science ®] , [Google Scholar], 3 De Clercq, E., Descamps, J., Balzarini, J., Giziewicz, J., Barr, P. J. and Robins, M. J. 1983. Nucleic acid related compounds. 40. Synthesis and biological activities of 5-alkynyluracil nucleosides. J. Med. Chem, 26: 661–666. [PUBMED][INFOTRIEVE][CSA][CROSSREF][Crossref], [PubMed], [Web of Science ®] , [Google Scholar]]pyrimidin-2-one core has been overcome with 5-(3-hydroxyalkyn-1-yl)uracil compounds with no substituent at N1. Manipulation of the side-chain hydroxyl group gives access to additional furo[2,3-d]pyrimidin-2-one analogues.