The braingraph.org database of high resolution structural connectomes and the brain graph tools

Based on the data of the NIH-funded Human Connectome Project, we have computed structural connectomes of 426 human subjects in five different resolutions of 83, 129, 234, 463 and 1015 nodes and several edge weights. The graphs are given in anatomically annotated GraphML format that facilitates better further processing and visualization. For 96 subjects, the anatomically classified sub-graphs can also be accessed, formed from the vertices corresponding to distinct lobes or even smaller regions of interests of the brain. For example, one can easily download and study the connectomes, restricted to the frontal lobes or just to the left precuneus of 96 subjects using the data. Partially directed connectomes of 423 subjects are also available for download. We also present a GitHub-deposited set of tools, called the Brain Graph Tools, for several processing tasks of the connectomes on the site http://braingraph.org.     

Reproducibility of the Structural Brain Connectome Derived from Diffusion Tensor Imaging

Rationale

Disruptions of brain anatomical connectivity are believed to play a central role in several neurological and psychiatric illnesses. The structural brain connectome is typically derived from diffusion tensor imaging (DTI), which may be influenced by methodological factors related to signal processing, MRI scanners and biophysical properties of neuroanatomical regions. In this study, we evaluated how these variables affect the reproducibility of the structural connectome.

Methods

Twenty healthy adults underwent 3 MRI scanning sessions (twice in the same MRI scanner and a third time in a different scanner unit) within a short period of time. The scanning sessions included similar T1 weighted and DTI sequences. Deterministic or probabilistic tractography was performed to assess link weight based on the number of fibers connecting gray matter regions of interest (ROI). Link weight and graph theory network measures were calculated and reproducibility was assessed through intra-class correlation coefficients, assuming each scanning session as a rater.

Results

Connectome reproducibility was higher with data from the same scanner. The probabilistic approach yielded larger reproducibility, while the individual variation in the number of tracked fibers from deterministic tractography was negatively associated with reproducibility. Links connecting larger and anatomically closer ROIs demonstrated higher reproducibility. In general, graph theory measures demonstrated high reproducibility across scanning sessions.

Discussion

Anatomical factors and tractography approaches can influence the reproducibility of the structural connectome and should be factored in the interpretation of future studies. Our results demonstrate that connectome mapping is a largely reproducible technique, particularly as it relates to the geometry of network architecture measured by graph theory methods.     

The braingraph.org database with more than 1000 robust human connectomes in five resolutions

The human brain is the most complex object of study we encounter today. Mapping the neuronal-level connections between the more than 80 billion neurons in the brain is a hopeless task for science. By the recent advancement of magnetic resonance imaging (MRI), we are able to map the macroscopic connections between about 1000 brain areas. The MRI data acquisition and the subsequent algorithmic workflow contain several complex steps, where errors can occur. In the present contribution we describe and publish 1064 human connectomes, computed from the public release of the Human Connectome Project. Each connectome is available in 5 resolutions, with 83, 129, 234, 463 and 1015 anatomically labeled nodes. For error correction we follow an averaging and extreme value deleting strategy for each edge and for each connectome. The resulting 5320 braingraphs can be downloaded from the https://braingraph.org site. This dataset makes possible the access to this graphs for scientists unfamiliar with neuroimaging- and connectome-related tools: mathematicians, physicists and engineers can use their expertize and ideas in the analysis of the connections of the human brain. Brain scientists and computational neuroscientists also have a robust and large, multi-resolution set for connectomical studies.Supplementary InformationThe online version contains supplementary material available at 10.1007/s11571-021-09670-5.     

An analysis of a ‘community-driven’ reconstruction of the human metabolic network

Following a strategy similar to that used in baker’s yeast (Herrgård et al. Nat Biotechnol 26:1155–1160, 2008). A consensus yeast metabolic network obtained from a community approach to systems biology (Herrgård et al. 2008; Dobson et al. BMC Syst Biol 4:145, 2010). Further developments towards a genome-scale metabolic model of yeast (Dobson et al. 2010; Heavner et al. BMC Syst Biol 6:55, 2012). Yeast 5—an expanded reconstruction of the Saccharomyces cerevisiae metabolic network (Heavner et al. 2012) and in Salmonella typhimurium (Thiele et al. BMC Syst Biol 5:8, 2011). A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella typhimurium LT2 (Thiele et al. 2011), a recent paper (Thiele et al. Nat Biotechnol 31:419–425, 2013). A community-driven global reconstruction of human metabolism (Thiele et al. 2013) described a much improved ‘community consensus’ reconstruction of the human metabolic network, called Recon 2, and the authors (that include the present ones) have made it freely available via a database at http://humanmetabolism.org/ and in SBML format at Biomodels (http://identifiers.org/biomodels.db/MODEL1109130000). This short analysis summarises the main findings, and suggests some approaches that will be able to exploit the availability of this model to advantage.     

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.     

Discovery of the subfamily Microtypinae (Hymenoptera: Braconidae) in Egypt,with the description of a new species

The subfamily Microtypinae Szépligeti, 1908 Szépligeti, G. (1908): Braconiden aus der Sammlung des ungarischen National-Museums. 2. Annales Historico-Naturales Musei Nationalis Hungarici, 6, 397–427. [Google Scholar] (Hymenoptera: Braconidae) is recorded for the first time for Egypt. The present study is based on specimens collected from Gebel Elba, Wadi Allaqi, St. Catherine, and Fayoum, as well as specimens deposited in various entomological collections in Egypt. Four species belonging to the genus Microtypus Ratzeburg, 1848 (M. algiricus Szépligeti, 1908 Szépligeti, G. (1908): Braconiden aus der Sammlung des ungarischen National-Museums. 2. Annales Historico-Naturales Musei Nationalis Hungarici, 6, 397–427. [Google Scholar]; M. desertorum Shestakov, 1932 Shestakov, A. (1932): Zur Kenntnis der asiatischen Braconiden. Zoologische Annalen (Würzburg), 99, 255–263. [Google Scholar]; M. vanharteni van Achterberg, 2010 Achterberg, C. van (2010): Order Hymenoptera, family Braconidae. Genus Microtypus Ratzeburg (Hymenoptera: Braconidae: Microtypinae). Arthropod Fauna of the United Arab Emirates, 3, 381–387. [Google Scholar] and M. aegypticus sp. n.) are reported for the first time from Egypt.

http://www.zoobank.org/urn:lsid:zoobank.org:pub:022282A1-183F-4E0C-9F88-A53C42735532     

Studies on the Reaction Conditions of DOPA Production with Alcaligenes faecalis.

The effects of several factors on the enzymatic production of 3,4-dihydroxyphenyl-l-alanine (DOPA) and 3,4-dimethoxyphenyl-l-alanine (DMPA) by transamination reaction were investigated using wet cells of Alcaligenes faecalis IAM 1015. In addition, some experiments for the cultural conditions for transaminase production were performed. DOPA and DMPA were obtained in 80 and 90% yields, respectively, using the mixture of l-glutamate and l-aspartate as amino donors. Accumulation of DMPA in the culture under the growing state of the bacteria was also confirmed.     

The genus Antillophos Woodring, 1928 (Gastropoda: Buccinidae) from the China seas,with description of a new species

The species of genus Antillophos Woodring, 1928 Woodring, W.P. (1928) Miocene Mollusks from Bowden, Jamaica. 2. Gastropods and Discussion of Results. Contributions to the Geology and Paleontology of the West Indies. Carnegie Institute of Washington, Washington D.C. [Google Scholar] from the China seas are studied. Six species, Antillophos liui n. sp., Antillophos lucubratonis Fraussen & Poppe, 2005 Fraussen, K. & Poppe, G.T. (2005) Revision of Phos and Antillophos (Buccinidae) from the Central Philippines. Visaya 1, 76–115. [Google Scholar], Antillophos monsecourorum Fraussen & Poppe, 2005 Fraussen, K. & Poppe, G.T. (2005) Revision of Phos and Antillophos (Buccinidae) from the Central Philippines. Visaya 1, 76–115. [Google Scholar], Antillophos pyladeum (Kato, 1995 Kato, S. (1995) Discussion of the genus Phos. Hitaciobi 70, 15–20. [Google Scholar]), Antillophos roseatus (Hinds, 1844 Hinds, R.B. (1844) Mollusca. In: Hinds, R.B. (Ed.) The Zoology of the Voyage of H.M.S. Sulphur During the years 1836–1842. 2. Smith, Elder and Co., London, pp. 1–72. [Google Scholar]) and Antillophos sp., are described and illustrated.

http://zoobank.org/urn:lsid:zoobank.org:pub:51481997-A841-4F37-8E15-B753DC99CB4D     

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     

Revision of the Clytra subfasciata species group (Coleoptera: Chrysomelidae: Cryptocephalinae: Clytrini)

The Clytra subfasciata species group is proposed, to comprise Clytra subfasciata Lacordaire, 1848 Lacordaire, J. T. (1848): Monographie des coléoptères subpentamères de la famille des phytophages. Tome second. Mémoires de la Société Royale des Sciences de Liége, 5, 1–890 pp. [Google Scholar], C. hajeki Medvedev &; Kantner, 2002 Medvedev, L. N., &; Kantner, F. (2002): Some new and poorly know Clytrinae (Coleoptera, Chrysomelidae) of the Old World. Entomologica Basiliensia, 24, 259–269. [Google Scholar] and C. kadleci sp. n. (Yemen). The species of the group are characterised by the peculiar shape of the aedeagus, with a dorsal plate separated from the rest of aedeagus by a deep narrow slit. Colour photographs of habitus and drawings of genitalia are provided for all three species.

http://www.zoobank.org/urn:lsid:zoobank.org:pub:F6706A76-CD49-4A5A-A109-A6E6C23514A5     

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     

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     

Going going gone: the loss of a reef building gastropod (Mollusca: Caenogastropoda: Vermetidae) in the southeast Mediterranean Sea

A new harvestman species, Rilaena artvinensis sp. n. (Opiliones: Phalangiidae), is described and illustrated based on males collected in north-eastern Anatolia, Turkey. The new species is similar to R. buresi (?ilhavý, 1965 ?ilhavý, V. (1965): Die Weberknechte der Unterordnung Eupnoi aus Bulgarien; zugleich eine Revision europäischer Gattungen der Unterfamilien Oligolophinae und Phalangiinae (Arachnoidea, Opilionidea). Acta Entomologica Bohemoslovaca, 62, 369–406. [Google Scholar]) and R. lenkoranica Snegovaya, 2007 Snegovaya, N. Y. (2007): Two new harvestman species from Lenkoran, Azerbaijan (Arachnida: Opiliones: Phalangiidae). Bulletin of the British Arachnological Society, 14, 88–92. [Google Scholar]. The differences between these species are elaborated.

http://www.zoobank.org/urn:lsid:zoobank.org:pub:A53452BB-A85D-4BE8-8A6B-D0FC3421AFE3     

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/).     

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.     

Reconstruction of ancestral RNA sequences under multiple structural constraints

Background

Secondary structures form the scaffold of multiple sequence alignment of non-coding RNA (ncRNA) families. An accurate reconstruction of ancestral ncRNAs must use this structural signal. However, the inference of ancestors of a single ncRNA family with a single consensus structure may bias the results towards sequences with high affinity to this structure, which are far from the true ancestors.

Methods

In this paper, we introduce achARNement, a maximum parsimony approach that, given two alignments of homologous ncRNA families with consensus secondary structures and a phylogenetic tree, simultaneously calculates ancestral RNA sequences for these two families.

Results

We test our methodology on simulated data sets, and show that achARNement outperforms classical maximum parsimony approaches in terms of accuracy, but also reduces by several orders of magnitude the number of candidate sequences. To conclude this study, we apply our algorithms on the Glm clan and the FinP-traJ clan from the Rfam database.

Conclusions

Our results show that our methods reconstruct small sets of high-quality candidate ancestors with better agreement to the two target structures than with classical approaches. Our program is freely available at: http://csb.cs.mcgill.ca/acharnement.

     

Intervention or Inversion: Australian Indigenous Justice and the Politics of Cultural Incompatibility

Australian Indigenous affairs are underscored by a central tension between the rights of Indigenous peoples to self-determination, and assimilation policy premised on cultural homogeneity. This tension is most evident between the Northern Territory Government-commissioned Anderson and Wild (2007 Anderson, P. and Wild, R. Ampe akelyernemane meke mekarle: Little children are sacred. Report to the Northern Territory board of inquiry into the protection of Aboriginal children from sexual abuse. Darwin: Northern Territory Government.  [Google Scholar]) report, entitled Ampe akelyernemane meke mekarle: Little children are sacred, which recommends the continuation of community-led programs in response to childhood sexual abuse in Indigenous communities, and the Commonwealth's Northern Territory National Emergency Response Act 2007 (NTNER), commonly known as ‘the intervention’, which Altman and Hinkson (2007 Altman, J. and Hinkson, M. 2007. Coercive reconciliation: Stabilise, normalise, exit Aboriginal Australia, Melbourne: Arena Publications.  [Google Scholar]) claim represents a ‘coercive’ attempt to dismantle Indigenous rights to manage their affairs. In her critique of cultural incompatibility (culturalism), McConaghy (2000 McConaghy, C. 2000. Rethinking Indigenous education: Culturalism, colonialism and the politics of knowing, Flaxton: Post Pressed.  [Google Scholar]) observes that radicalism, or cultural difference policy in oppositional histories of power and control, seeks to invert colonial power relations. Instead, argues McConaghy, radicalism (much like assimilation) reinstitutes colonial relations of dominance. I draw on culturalism to explore the tension between Indigenous self-determination (a form of inversion), represented within the Little children are sacred report, and intervention, as a model not for coercive assimilation but for cultural integration (Sutton 2001a Sutton, P. 2001a. The politics of suffering: Indigenous policy in Australia since the 1970s. Anthropological Forum, 11: 125–173. [Taylor & Francis Online] [Google Scholar]; Pearson 2007 Pearson, N. 2007. The urgent quest for a radical political centre. The Age, 1 September Insight 11 [Google Scholar]). I propose that cultural inversion, as a justificatory model for addressing dysfunction within Indigenous communities, displaces the needs and rights of individuals for mainstream intervention.