pinecone/core-2020-05-10-deduplication huggingface dataset:
Performance of pairwise shape dissimilarity morphometrics on non-mammalian taxa (Insecta : Neuroptera : Mantispidae)

Morphometric dissimilarity metrics aim
to quantify the variation between compared specimens
such that inferences about their relatedness and alpha
taxonomy can be made. Recently, the technique has
developed metrics that purport to quantify shape dissimilarity
between specimens—employing the use of
least squares regression analysis. These metrics have
been well applied by studies in the hominin fossil
record with an arguably unsubstantiated backing for
the technique. Originally postulated was the log10 sem
metric which subsequently led to the standard error
test of the null hypothesis metric. Following this, the
standard deviation of logged ratios (SLR) metric arose
as a pairwise dissimilarity metric that constrains the
regression to a zero-intercept, that is, a significant
development in the robustness of the technique. This
metric was tested on extant primates in order to evaluate
its effectiveness alongside the two other metrics. It
was shown to be the most reliable for comparisons
between specimens of primates, but was unable to discriminate
between heterospecific and conspecific comparisons.
Arguably, an alternative model organism with
which to compare the technique is lacking. This study
considers shape dissimilarity metrics with respect to a
group of nonmammalian organisms (mantidflies) and
tests the metrics against three lines of evidence (morphology,
CO1-DNA, and geographic distribution) that
can delimit the species-level taxonomy for the group. It
is shown that the metrics are unable to discriminate
between pairwise comparisons of closely related species,
resulting in biologically erroneous groupings, and
contradicting the groupings derived from morphological,
CO1-DNA, and distributional comparisons. It is
thus asserted that the technique is unsuitable for use
in alpha taxonomy as an additional line of evidence in
mantidflies. It is further supposed that morphometrics
in general should be employed with caution in studies
of evolutionary history as phylogeny is not the only information
contained within morphometric data.National Research Foundation (NRF)http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1097-46872016-12-31hb2016Zoology and Entomolog
The comparative gastrointestinal morphology of Jaculus jaculus (Rodentia) and Paraechinus aethiopicus (Erinaceomorpha)

Jaculus jaculus (Lesser Egyptian jerboa) and Paraechinus aethiopicus (Desert
hedgehog) are small mammals which thrive in desert conditions and are found, amongst
others, in the Arabian Peninsula. J. jaculus is omnivorous while P. aethiopicus is
described as being insectivorous. The study aims to describe the gastrointestinal tract
(GIT) morphology of these animals which differ in diet and phylogeny. The GITs of J. jaculus (n=8) and P. aethiopicus (n=7) were weighed, photographed, and the length,
basal surface areas and luminal surface areas of each of the anatomically distinct
gastrointestinal segments were determined. The internal aspects of each area were
examined and photographed while representative histological sections of each area were
processed to wax and stained using haematoxylin and eosin. Both species had a simple
unilocular stomach which was confirmed as wholly glandular on histology sections. P.
aethiopicus had a relatively simple GIT which lacked a caecum. The caecum of J.
jaculus was elongated, terminating in a narrow cecal appendix which contained
lymphoid tissue on histological examination. The internal aspect of the proximal colon
revealed distinct V-shaped folds. Stomach content analysis of J. jaculus revealed mostly
plant and seed material and some insects, whereas P. aethiopicus samples showed plant
material in addition to insects, indicating omnivorous feeding tendencies in areas where
insects may be scarce.Harry Crossley Foundation and King Saud University, Vice deanship of Research Chairs.http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1097-46872017-05-31hb2016Mammal Research InstituteZoology and Entomolog
The Nematode Stoma: Homology of Cell Architecture with Improved Understanding by Confocal Microscopy of Labeled Cell Boundaries

Nematode stomas vary widely in the cuticular structures evolved for different feeding strategies, yet the arrangement of the epithelial cell classes that form these structures may be conserved. This article addresses several issues that have impeded the full acceptance of this hypothesis including controversies arising from the structure of the&nbsp;Caenorhabditis elegans&nbsp;stoma. We investigated fluorescent antibody labeling of cell boundaries in conjunction with confocal microscopy as an alternative to transmission electron microscopy (TEM), using MH27 to label apical junctions in&nbsp;C. elegans&nbsp;and two other species. Accurately spaced optical sections collected by the confocal microscope provide a three-dimensional array of pixels (voxels) that, using image-processing software, can be rotated and sectioned at accurately chosen thicknesses and locations. Ribbons of fluorescence clearly identify cell boundaries along the luminal cuticle in&nbsp;C. elegans&nbsp;and&nbsp;Zeldia punctata&nbsp;and less clearly in&nbsp;Bunonema&nbsp;sp. The patterns render cell classes and their relationships readily identifiable. In the&nbsp;C. elegans&nbsp;stoma they correct a misreading of serial TEMs that was not congruent with architecture in other nematodes—the row of marginal cells is now seen to be continuous as in other nematodes, rather than being interrupted by encircling&nbsp;pm1&nbsp;cells. Also impeding understanding, the reference to certain cell classes as ‘epithelial’ and others as “muscle” in the&nbsp;C. elegans&nbsp;literature is at variance with muscle expression in most other taxa. For consistent comparison among species, we propose that these cell class descriptors based on function be replaced by topological terms. With these and other confusing concepts and terminology removed, the homology of the cellular architecture among taxa becomes obvious. We provide a corrected description of the cell architecture of the&nbsp;C. elegans&nbsp;stoma and examples of how it is modified in other taxa with different feeding strategies
Relationship between the chondrocyte maturation cycle and the endochondral ossification in the diaphyseal and epiphyseal ossification centers

The chondrocyte maturation cycle and endochondral ossification were studied in human, fetal cartilage Anlagen and in postnatal meta-epiphyses. The relationship between the lacunar area, the inter-territorial fibril network variations, and calcium phosphorus nucleation in primary and secondary ossification centers were assessed using light microscopy and scanning electron microscopy (SEM) morphometry. The Anlage topographic, zonal classification was derived from the anatomical nomenclature of the completely developed long bone (diaphysis, metaphyses and epiphyses). A significant increase in the chondrocyte lacunar area was documented in the Anlage of epiphyseal zones 4 and 3 to zone 2 (metaphysis) and zone 1 (diaphysis), with the highest variation from zone 2 to zone 1. An inverse reduction in the intercellular matrix area and matrix interfibrillar empty space was also documented. These findings are consistent with the osmotic passage of free cartilage water from the interfibrillar space into the swelling chondrocytes, which increased the ion concentrations to a critical threshold for mineral precipitation in the matrix. The mineralized cartilage served as a scaffold for osteoblast apposition both in primary and secondary ossification centers and in the metaphyseal growth plate cartilage, though at different periods of bone Anlage development and with distinct patterns for each zone. All developmental processes shared a common initial pathway but progressed at different rates, modes and organization in diaphysis, metaphysis and epiphysis. In the ossification phase the developing vascular supply appeared to play a key role in determining the cortical or trabecular structure of the long bones
Imaging material properties of biological samples with a Force Feedback
  Microscope

Mechanical properties of biological samples have been imaged with a
\textit{Force Feedback Microscope}. Force, force gradient and dissipation are
measured simultaneously and quantitatively, merely knowing the AFM cantilever
spring constant. Our first results demonstrate that this robust method provides
quantitative high resolution force measurements of the interaction The little
oscillation imposed to the cantilever and the small value of its stiffness
result in a vibrational energy much smaller than the thermal energy, reducing
the interaction with the sample to a minimum. We show that the observed
mechanical properties of the sample depend on the force applied by the tip and
consequently on the sample indentation.
  Moreover, the frequency of the excitation imposed to the cantilever can be
chosen arbitrarily, opening the way to frequency-dependent studies in
biomechanics, sort of spectroscopic AFM investigations
Dynamic identification of H2 epitopes from Leishmania (Leishmania) amazonensis cysteine proteinase B with potential immune activity during murine infection

Peptides from the COOH-terminal extension of cysteine proteinase B from Leishmania (Leishmania) amazonensis (cyspep) can modulate immune responses in vertebrate hosts. With this hypothesis as base, we used the online analysis tool SYFPEITHI to predict seven epitopes from this region with potential to bind H2 proteins. We performed proliferation tests and quantified reactive T lymphocytes applying a cytometry analysis, using samples from draining lymph node of lesions from L. (L.) amazonensis-infected mice. To define reactivity of T cells, we used complexes of DimerX (H2 Db:Ig and H2 Ld:Ig) and the putative epitopes. Additionally, we applied surface plasmon resonance to verify real time interactions between the putative epitopes and DimerX proteins. Five peptides induced blastogenesis in BALB/c cells, while only two presented the same property in C57BL/6 mouse cells. In addition, our data indicate the existence of CD8+ T lymphocyte populations able to recognize each tested peptide in both murine strains. We observed an overlapping of results between the peptides that induced lymphocyte proliferation and those capable of binding to the DimerX in the surface plasmon resonance assays thus indicating that using these recombinant proteins in biosensing analyses is a promising tool to study real time molecular interactions in the context of major histocompatibility complex epitopes. The data gathered in this study reinforce the hypothesis that cyspep-derived peptides are important factors in the murine host infection by L. (L.) amazonensis.CAPES (1/2009) /FAPERJ (E-26/103.060/2008; E-26/110.257/2010)CNPq (509737/2010-2)Programa de Apoio à Pesquisa Estratégica em Saúde V (PAPES V) - CNPq/Fiocruz (300731/2010-8
Molecular imprinting science and technology : A survey of the literature for the years 2004 - 2011

This is the accepted version of the following article: Whitcombe, M. J., Kirsch, N. and Nicholls, I. A. (2014), Molecular imprinting science and technology: a survey of the literature for the years 2004–2011. J. Mol. Recognit., 27: 297–401, which has been published in final form at  http://onlinelibrary.wiley.com/doi/10.1002/jmr.2347/abstractThe file associated with this record is embargoed until 12 months after the date of publication. The final published version may be available through the links above.Herein, we present a survey of the literature covering the development of molecular imprinting science and technology over the years 2004-2011. In total, 3779 references to the original papers, reviews, edited volumes and monographs from this period are included, along with recently identified uncited materials from prior to 2004, which were omitted in the first instalment of this series covering the years 1930-2003. In the presentation of the assembled references, a section presenting reviews and monographs covering the area is followed by sections describing fundamental aspects of molecular imprinting including the development of novel polymer formats. Thereafter, literature describing efforts to apply these polymeric materials to a range of application areas is presented. Current trends and areas of rapid development are discussed. Copyright © 2014 John Wiley & Sons, Ltd.Peer-reviewedPost-prin
Effect of SXWS/WSXWS peptides on chemotaxis and adhesion of the macrophage-like cell line J774

WSXWS motif is a conserved amino acid sequence that is present in type I cytokine receptors. This motif that can be found both in the ligand binding chains and signal transducer molecule of the receptors with different amino acids at the position “X” plays a role in the receptor folding, ligand binding and signal transduction as well. Structural analysis proved that WSEWS motif of IL-6R is located in a highly accessible location in the protein. Structural properties and chemotaxis of a tetrapeptide library with SXWS sequence, where X was the 19 proteinogenic amino acids except cystein were systematically studied earlier. It has been proved that C-terminal amidation and the identity of amino acid X had a pronounced influence on the chemotactic properties but less of the structure of the peptides. Here, we present our findings on the effect of a tetrapeptide and a pentapeptide library with the sequence of SXWS and WSXWS on the chemotaxis and adhesion of J774 murine macrophage cell line. We studied the effect of the presence/absence of N-terminal tryptophan and the different amino acids at the X position on these physiological responses. Results indicated that amino acid X had a marked influence on chemotaxis, adhesion as well as on proliferation induced by (W)SXWS peptides. Elongation of SXWS sequence with a tryptophan at the N terminus also altered pronouncedly all the physiological responses of the cells studied. A good correlation could be observed between the chemotaxis and the proliferation and physicochemical parameters of the amino acid X
Optimization of protein–protein docking for predicting Fc–protein interactions

The antibody crystallizable fragment (Fc) is recognized by effector proteins as part of the immune system. Pathogens produce proteins that bind Fc in order to subvert or evade the immune response. The structural characterization of the determinants of Fc–protein association is essential to improve our understanding of the immune system at the molecular level and to develop new therapeutic agents. Furthermore, Fc-binding peptides and proteins are frequently used to purify therapeutic antibodies. Although several structures of Fc–protein complexes are available, numerous others have not yet been determined. Protein–protein docking could be used to investigate Fc–protein complexes; however, improved approaches are necessary to efficiently model such cases. In this study, a docking-based structural bioinformatics approach is developed for predicting the structures of Fc–protein complexes. Based on the available set of X-ray structures of Fc–protein complexes, three regions of the Fc, loosely corresponding to three turns within the structure, were defined as containing the essential features for protein recognition and used as restraints to filter the initial docking search. Rescoring the filtered poses with an optimal scoring strategy provided a success rate of approximately 80% of the test cases examined within the top ranked 20 poses, compared to approximately 20% by the initial unrestrained docking. The developed docking protocol provides a significant improvement over the initial unrestrained docking and will be valuable for predicting the structures of currently undetermined Fc–protein complexes, as well as in the design of peptides and proteins that target Fc.This work was supported by grant number BIO2013‐48213‐R from Spanish Government. M.A. is a recipient of an NHMRC Early Career\ud
Fellowship (GNT1054245). We acknowledge the computational resources provided by the Australian Government through the Victorian Life Sciences Computational Initiative under the National Computational Merit Allocation Scheme (project dq3). The authors gratefully\ud
acknowledge the contribution toward this study fromthe VictorianOperational Infrastructure Support Program received by the Burnet Institute.Peer ReviewedPostprint (author's final draft
Force spectroscopy reveals the presence of structurally modified dimers in transthyretin amyloid annular oligomers.

Toxicity in amyloidogenic protein misfolding disorders is thought to involve intermediate states of aggregation associated with the formation of amyloid fibrils. Despite their relevance, the heterogeneity and transience of these oligomers have placed great barriers in our understanding of their structural properties. Among amyloid intermediates, annular oligomers or annular protofibrils have raised considerable interest because they may contribute to a mechanism of cellular toxicity via membrane permeation. Here we investigated, by  using AFM force spectroscopy, the structural detail of amyloid annular oligomers  from transthyretin (TTR), a protein involved in systemic and neurodegenerative amyloidogenic disorders. Manipulation was performed in situ, in the absence of molecular handles and using persistence length-fit values to select relevant curves. Force curves reveal the presence of dimers in TTR annular oligomers that  unfold via a series of structural intermediates. This is in contrast with the manipulation of native TTR that was more often manipulated over length scales compatible with a TTR monomer and without unfolding intermediates. Imaging and force spectroscopy data suggest that dimers are formed by the assembly of monomers in a head-to-head orientation with a nonnative interface along their beta-strands. Furthermore, these dimers stack through nonnative contacts that may enhance the stability of the misfolded structure
Analysis of the binding loops configuration and surface adaptation of different crystallized single‐domain antibodies in response to various antigens

Monoclonal antibodies have revolutionized the biomedical field through their ubiquitous utilization in different diagnostics and therapeutic applications. Despite this widespread use, their large size and structural complexity have limited their versatility in specific applications. The antibody variable region that is responsible for binding antigen is embodied within domains that can be rescued individually as single-domain antibody (sdAb) fragments. Because of the unique characteristics of sdAbs, such as low molecular weight, high physicochemical stability, and the ability to bind antigens inaccessible to conventional antibodies, they represent a viable alternative to full-length antibodies. Consequently, 149 crystal structures of sdAbs, originating from human (VH), camelids (VHH), or sharks (VNAR), were retrieved from the Protein Data Bank, and their structures were compared. The 3 types of sdAbs displayed complementarity determining regions (CDRs) with different lengths and configurations. CDR3 of the VHH and VNAR domains were dominated by pleated and extended orientations, respectively. Although VNAR showed the smallest average molecular weight and molecular surface area compared with VHH and VH antibodies. However, the solvent accessible surface area measurements of the 3 tested sdAbs types were very similar. All the antihapten VHH antibodies showed pleated CDR3, which were sufficient to create a binding pocket to accommodate haptens (methotrexate and azo dyes) in terms of shape and electrostatic potential. The sdAbs that recognized lysozyme showed more diversity in their CDR3 orientation to enable them to recognize various topographies of lysozyme. Subsequently, the three sdAb classes were different in size and surface area and have shown distinguishable ability to optimize their CDR length and orientation to recognize different antigen classes
Direct mapping of melanoma cell – endothelial\ud
cell interactions

The most life-threatening aspect of cancer is metastasis; cancer patient mortality is\ud
mainly due to metastasis. Among all metastases, presence of brain metastasis is one with\ud
the poorest prognosis; the median survival time can be counted in months. Therefore,\ud
prevention or decreasing their incidence would be highly desired both by patients and\ud
physicians. Since the central nervous system (CNS) lacks classical lymphatic circulation,\ud
metastatic cells invading the CNS must breach the blood-brain barrier. The key step in\ud
this process is the establishment of firm adhesion between the cancer cell and the cerebral\ud
endothelial layer.\ud
Using the atomic force microscope, a high resolution force-spectrograph, our aim was\ud
to explore the connections among the cell morphology, cellular mechanics and biological\ud
function in the process of transendothelial migration of metastatic cancer cells. By\ud
immobilization of a melanoma cell to an atomic force microscope’s cantilever,\ud
intercellular adhesion was directly measured at quasi-physiological conditions. Hereby\ud
we present our latest results using this melanoma -decorated probe. Binding\ud
characteristics to a confluent layer of brain endothelial cells was directly measured by\ud
means of single cell force spectroscopy. Adhesion dynamics and strength was\ud
characterized and we present data about spatial distribution of elasticity and detachment\ud
strength.\ud
These results highlight the importance of cellular mechanics in brain metastasis\ud
formation and emphasize the enormous potential towards exploration of intercellular\ud
dynamics related processes
A survey of the year 2006 literature on applications of isothermal titration calorimetry

Isothermal titration calorimetry (ITC) is a fast and robust method to determine the energetics of association reactions in solution. The changes in enthalpy, entropy and heat capacity that accompany binding provide unique insights into the balance of forces driving association of molecular entities. ITC is used nowadays on a day-to-day basis in hundreds of laboratories. The method aids projects both in basic and practice-oriented research ranging from medicine and biochemistry to physical chemistry and material sciences. Not surprisingly, the range of studies utilizing ITC data is steadily expanding. In this review, we discuss selected results and ideas that have accumulated in the course of the year 2006, the focus being on biologically relevant systems. Theoretical developments, novel applications and studies that provide a deeper level of understanding of the energetic principles of biological function are primarily considered. Following the appearance of a new generation of titration calorimeters, recent papers provide instructive examples of the synergy between energetic and structural approaches in biomedical and biotechnological research