The extinct, giant giraffid Sivatherium giganteum: skeletal reconstruction and body mass estimation

Sivatherium giganteum is an extinct giraffid from the Plio–Pleistocene boundary of the Himalayan foothills. To date, there has been no rigorous skeletal reconstruction of this unusual mammal. Historical and contemporary accounts anecdotally state that Sivatherium rivalled the African elephant in terms of its body mass, but this statement has never been tested. Here, we present a three-dimensional composite skeletal reconstruction and calculate a representative body mass estimate for this species using a volumetric method. We find that the estimated adult body mass of 1246 kg (857—1812 kg range) does not approach that of an African elephant, but confirms that Sivatherium was certainly a large giraffid, and may have been the largest ruminant mammal that has ever existed. We contrast this volumetric estimate with a bivariate scaling estimate derived from Sivatherium's humeral circumference and find that there is a discrepancy between the two. The difference implies that the humeral circumference of Sivatherium is greater than expected for an animal of this size, and we speculate this may be linked to a cranial shift in centre of mass

Photographic identification of individuals of a free-ranging, small terrestrial vertebrate

This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.Recognition of individuals within an animal population is central to a range of estimates about population structure and dynamics. However, traditional methods of distinguishing individuals, by some form of physical marking, often rely on capture and handling which may affect aspects of normal behavior. Photographic identification has been used as a less-invasive alternative, but limitations in both manual and computer-automated recognition of individuals are particularly problematic for smaller taxa (<500 g). In this study, we explored the use of photographic identification for individuals of a free-ranging, small terrestrial reptile using (a) independent observers, and (b) automated matching with the Interactive Individual Identification System (I3S Pattern) computer algorithm. We tested the technique on individuals of an Australian skink in the Egernia group, Slater’s skink Liopholis slateri, whose natural history and varied scale markings make it a potentially suitable candidate for photo-identification. From ‘photographic captures’ of skink head profiles, we designed a multichoice key based on alternate character states and tested the abilities of observers — with or without experience in wildlife survey — to identify individuals using categorized test photos. We also used the I3S Pattern algorithm to match the same set of test photos against a database of 30 individuals. Experienced observers identified a significantly higher proportion of photos correctly (74%) than those with no experience (63%) while the I3S software correctly matched 67% as the first ranked match and 83% of images in the top five ranks. This study is one of the first to investigate photo identification with a free-ranging small vertebrate. The method demonstrated here has the potential to be applied to the developing field of camera-traps for wildlife survey and thus a wide range of survey and monitoring applications

In vivo and ex vivo range of motion in the fire salamander Salamandra salamandra

Joint range of motion (RoM) analyses are fundamental to our understanding of how an animal moves throughout its ecosystem. Recent technological advances allow for more detailed quantification of this RoM (e.g. including interaction of degrees of freedom) both in ex vivo joints and in vivo experiments. Both types of data have been used to draw comparisons with fossils to reconstruct locomotion. Salamanders are often used as analogues for early tetrapod locomotion; testing such hypotheses requires an in-depth analysis of salamander joint RoM. Here, we provide a detailed dataset of the ex vivo ligamentous rotational joint RoM in the hindlimb of the fire salamander Salamandra salamandra, using a new method for collecting and visualising joint RoM. We also characterise in vivo joint RoM used during walking, via scientific rotoscoping and compare the in vivo and ex vivo data. In summary, we provide (1) a new method for joint RoM data experiments and (2) a detailed analysis of both in vivo and ex vivo data of salamander hindlimbs, which can be used for comparative studies

Spherical frame projections for visualising joint range of motion, and a complementary method to capture mobility data

Quantifying joint range of motion (RoM), the reachable poses at a joint, has many applications in research and clinical care. Joint RoM measurements can be used to investigate the link between form and function in extant and extinct animals, to diagnose musculoskeletal disorders and injuries or monitor rehabilitation progress. However, it is difficult to visually demonstrate how the rotations of the joint axes interact to produce joint positions. Here, we introduce the spherical frame projection (SFP), which is a novel 3D visualisation technique, paired with a complementary data collection approach. SFP visualisations are intuitive to interpret in relation to the joint anatomy because they ‘trace’ the motion of the coordinate system of the distal bone at a joint relative to the proximal bone. Furthermore, SFP visualisations incorporate the interactions of degrees of freedom, which is imperative to capture the full joint RoM. For the collection of such joint RoM data, we designed a rig using conventional motion capture systems, including live audio-visual feedback on torques and sampled poses. Thus, we propose that our visualisation and data collection approach can be adapted for wide use in the study of joint function

Clustering and Precipitation Processes in Microalloyed Aluminium Alloys(APFIM/FIM)

Recent progress in understanding the origins of hardening in Al-1.7Cu-0.01Sn (at. %) and Al-1.1Cu-1.7Mg-(0.1Ag, 0.3-0.5Si) (at. %) microalloyed alloys is presented. The results of systematic studies involving atom probe field ion microscopy in conjunction with transmission electron microscopy indicate that the precipitation processes depend to a considerable degree upon the nature of pre-precipitate clustering reactions which occur early in the decomposition of the solid solution. Furthermore, it is shown that the presence of these co-clusters can influence significantly the alloy properties

A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains

BACKGROUND: Noncoding RNA species play a diverse set of roles in the eukaryotic cell. While much recent attention has focused on smaller RNA species, larger noncoding transcripts are also thought to be highly abundant in mammalian cells. To search for large noncoding RNAs that might control gene expression or mRNA metabolism, we used Affymetrix expression arrays to identify polyadenylated RNA transcripts displaying nuclear enrichment. RESULTS: This screen identified no more than three transcripts; XIST, and two unique noncoding nuclear enriched abundant transcripts (NEAT) RNAs strikingly located less than 70 kb apart on human chromosome 11: NEAT1, a noncoding RNA from the locus encoding for TncRNA, and NEAT2 (also known as MALAT-1). While the two NEAT transcripts share no significant homology with each other, each is conserved within the mammalian lineage, suggesting significant function for these noncoding RNAs. NEAT2 is extraordinarily well conserved for a noncoding RNA, more so than even XIST. Bioinformatic analyses of publicly available mouse transcriptome data support our findings from human cells as they confirm that the murine homologs of these noncoding RNAs are also nuclear enriched. RNA FISH analyses suggest that these noncoding RNAs function in mRNA metabolism as they demonstrate an intimate association of these RNA species with SC35 nuclear speckles in both human and mouse cells. These studies show that one of these transcripts, NEAT1 localizes to the periphery of such domains, whereas the neighboring transcript, NEAT2, is part of the long-sought polyadenylated component of nuclear speckles. CONCLUSION: Our genome-wide screens in two mammalian species reveal no more than three abundant large non-coding polyadenylated RNAs in the nucleus; the canonical large noncoding RNA XIST and NEAT1 and NEAT2. The function of these noncoding RNAs in mRNA metabolism is suggested by their high levels of conservation and their intimate association with SC35 splicing domains in multiple mammalian species

Results of 1992 seismic reflection experiment in Lake Baikal

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/95684/1/eost9857.pd

Improved Imputation of Common and Uncommon Single Nucleotide Polymorphisms (SNPs) with a New Reference Set

Statistical imputation of genotype data is an important technique for analysis of genome-wide association studies (GWAS). We have built a reference dataset to improve imputation accuracy for studies of individuals of primarily European descent using genotype data from the Hap1, Omni1, and Omni2.5 human SNP arrays (Illumina). Our dataset contains 2.5-3.1 million variants for 930 European, 157 Asian, and 162 African/African-American individuals. Imputation accuracy of European data from Hap660 or OmniExpress array content, measured by the proportion of variants imputed with R^2^&#x3e;0.8, improved by 34%, 23% and 12% for variants with MAF of 3%, 5% and 10%, respectively, compared to imputation using publicly available data from 1,000 Genomes and International HapMap projects. The improved accuracy with the use of the new dataset could increase the power for GWAS by as much as 8% relative to genotyping all variants. This reference dataset is available to the scientific community through the NCBI dbGaP portal. Future versions will include additional genotype data as well as non-European populations

Pilot Trial on the Use of Etanercept and Methylprednisolone as Primary Treatment for Acute Graft-versus-Host Disease

AbstractClinical and preclinical data indicate that tumor necrosis factor (TNF)–α is an important mediator of acute graft-versus-host disease (aGVHD) after allogeneic bone marrow transplantation. We completed a study using etanercept, a fusion protein capable of neutralizing TNF-α, for the initial treatment of aGVHD. Etanercept (25 mg subcutaneously) was administered twice weekly for 16 doses, along with methylprednisolone (2 mg/kg) and tacrolimus for biopsy-proven aGVHD. Twenty patients with a median age of 47 years (range, 8–63 years) were enrolled. Fourteen patients with grade II aGVHD (11 family donors and 3 unrelated donors) and 6 patients with grade III aGVHD (3 family donors and 3 unrelated donors) were treated. Twelve patients completed 16 doses of therapy, and 8 received 5 to 15 doses. Reasons for not completing all doses of etanercept included progression of aGVHD (n = 4), relapsed leukemia (n = 2), progression of pulmonary and central nervous system lesions (n = 1), and perforated duodenal ulcer (n = 1). Fifteen (75%) of 20 patients had complete resolution of aGVHD within 4 weeks of therapy. Increasing levels of soluble TNF receptor 1 plasma concentration during the first 4 weeks of therapy indicated progression of aGVHD in 5 patients. In contrast, for 15 responding patients, soluble TNF receptor 1 plasma concentration levels returned to baseline. These data demonstrate the feasibility of using cytokine blockade in the early treatment of aGVHD