julilili42/papers huggingface dataset:
How to tackle the molecular species inventory for an industrialized nation—lessons from the first phase of the German Barcode of Life initiative GBOL (2012–2015)
2016-03-17

Biodiversity loss is mainly driven by human activity. While concern grows over the fate of hot spots of biodiversity, contemporary species losses still prevail in industrialized nations. Therefore, strategies were formulated to halt or reverse the loss, driven by evidence for its value for ecosystem services. Maintenance of the latter through conservation depends on correctly identified species. To this aim, the German Federal Ministry of Education and Research is funding the GBOL project, a consortium of natural history collections, botanic gardens, and universities working on a barcode reference database for the country’s fauna and flora. Several noticeable findings could be useful for future campaigns: (i) validating taxon lists to serve as a taxonomic backbone is time-consuming, but without alternative; (ii) offering financial incentives to taxonomic experts, often citizen scientists, is indispensable; (iii) completion of the libraries for widespread species enables analyses of environmental samples, but the process may not hold pace with technological advancements; (iv) discoveries of new species are among the best stories for the media; (v) a commitment to common data standards and repositories is needed, as well as transboundary cooperation between nations; (vi) after validation, all data should be published online via the BOLD to make them searchable for external users and to allow cross-checking with data from other countries.
On the observability of bow shocks of Galactic runaway OB stars
2016-03-17

Massive stars that have been ejected from their parent cluster and supersonically sailing away through the interstellar medium (ISM) are classified as exiled. They generate circumstellar bow-shock nebulae that can be observed. We present two-dimensional, axisymmetric hydrodynamical simulations of a representative sample of stellar wind bow shocks from Galactic OB stars in an ambient medium of densities ranging from &lt;it&gt;n&lt;/it&gt;&lt;inf&gt;ISM&lt;/inf&gt; = 0.01 up to 10.0 cm− 3. Independently of their location in the Galaxy, we confirm that the infrared is the most appropriated waveband to search for bow shocks from massive stars. Their spectral energy distribution is the convenient tool to analyse them since their emission does not depend on the temporary effects which could affect unstable, thin-shelled bow shocks. Our numerical models of Galactic bow shocks generated by high-mass ( &amp;ap; 40 M&lt;inf&gt;&amp;odot;&lt;/inf&gt;) runaway stars yield H α fluxes which could be observed by facilities such as the SuperCOSMOS H-Alpha Survey. The brightest bow-shock nebulae are produced in the denser regions of the ISM. We predict that bow shocks &lt;it&gt;in the field&lt;/it&gt; observed at H α by means of Rayleigh-sensitive facilities are formed around stars of initial mass larger than about 20 M&lt;inf&gt;&amp;odot;&lt;/inf&gt;. Our models of bow shocks from OB stars have the emission maximum in the wavelength range 3 ≤ λ ≤ 50 μm which can be up to several orders of magnitude brighter than the runaway stars themselves, particularly for stars of initial mass larger than 20 M&lt;inf&gt;&amp;odot;&lt;/inf&gt;.
Quantifying semantic animacy: How much are words alive?
2016-03-17

ABSTRACT The main goal of this study, which comprised two experimental tasks and three normative studies, was to describe the underlying distribution of semantic animacy, with the focus on Serbian and English. Animacy was measured using three normative techniques. The cognitive effects of obtained measures were tested in two experiments conducted in both Serbian and English: a visual lexical decision task and a semantic categorization task. Results suggest that semantic animacy is a graded property. A high correlation between Serbian and English measures suggests that semantic animacy might be language independent, most likely because of its biological grounding. As for its behavioral correlates, animacy does not affect lexical decision times but it does codetermine the categorization speed: the category decision gradually slows as a function of the degree of animacy. These results were consistent across two languages under research scrutiny. We thus conclude that animacy is a continuous aspect of meaning.
PLA2G6 Mutations Related to Distinct Phenotypes: A New Case with Early-onset Parkinsonism
2016-03-17

Background: PLA2G6-associated neurodegeneration (PLAN) is a recessive neurodegenerative disorder characterized by three distinct phenotypes: infantile neuroaxonal dystrophy (INAD), atypical neuroaxonal dystrophy (atypical NAD), and PLA2G6-related dystonia–parkinsonism. Methods: A consanguineous index case from Turkey was diagnosed with early-onset Parkinsonism at the Istanbul Faculty of Medicine. She and her unaffected brother were subjected to whole-genome sequencing. Results: In this report, we describe a 33-year-old index case with parental consanguinity and early-onset Parkinsonism. Whole-genome sequencing of this individual revealed that a homozygous p.R747W mutation in PLA2G6 segregates with the disease in this family Discussion: This result supports the importance of prioritizing this gene in mutational analysis of autosomal recessive Parkinsonism, and confirms the clinical heterogeneity of PLAN.
Comparison of laboratory parameters of a mountain bike specific performance test and a simulated race performance in the field
2016-03-17

Previous studies have described the need for a tailored performance test to predict mountain bike performance. This test should improve characterisation of intensive and intermittent physiological demands of mountain biking. Therefore, the aim of the study was to identify mountain bike related parameters that can more accurately explain the variance of mountain bike performance. Ten competitive mountain bike riders (age: 34 Â± 8.7 years; VI‡O 2 peak: 69 Â± 11.1 mlÂ·min âˆ’1 Â·kg âˆ’1 ) participated in the following tests: (a) an incremental bicycle ergometer test to determine their individual anaerobic threshold (IAT) and maximal oxygen consumption (VI‡O 2 peak), (b) an isometric strength test, (c) a second bicycle ergometer test consisting of time trials with maximal effort during 10-s, 1-min and 5-min trials and (d) a simulated race in the field. The laboratory parameters were scaled by body weight and subsequently compared with the mean power scaled by body weight and the race time using univariate correlations ( r power ; r time ) . The incremental test parameters of individual anaerobic threshold ( r power = 0.70; r time = âˆ’0.74) and VI‡O 2 peak ( r power = 0.85; r time = âˆ’0.86) showed strong correlations with the mean power output during the race and the race time. This result also applies for PO of the laboratory time trials during 1 min ( r power = 0.69; r time = âˆ’0.68) and 5 min ( r power = 0.63; r time = âˆ’0.82). PO of the 10-s time trial ( r power = 0.20; r time = âˆ’ 0.44), as well as maximal muscle strength ( r power = âˆ’0.13; r time = âˆ’0.24), were weakly correlated. In conclusion, power outputs of the 1- and 5-min time trials showed similar correlations with race performance compared with traditional aerobic parameters. These findings underline that traditional aerobic parameters of an incremental test, as well as power output during short high intensive intervals, should be considered when analysing mountain bike performance. Â
High‐sensitivity HLA class I peptidome analysis enables a precise definition of peptide motifs and the identification of peptides from cell lines and patients’ sera
2016-03-18

The characterization of peptides bound to human leukocyte antigen (HLA) class I is of fundamental importance for understanding CD8+ T cell‐driven immunological processes and for the development of immunomodulatory therapeutic strategies. However, until now, the mass spectrometric analysis of HLA‐bound peptides has typically required billions of cells, still resulting in relatively few high‐confidence peptide identifications. Capitalizing on the recent developments in mass spectrometry and bioinformatics, we have implemented a methodology for the efficient recovery of acid‐eluted HLA peptides after purification with the pan‐reactive antibody W6/32 and have identified a total of 27 862 unique peptides with high confidence (1% false discovery rate) from five human cancer cell lines. More than 93% of the identified peptides were eight to 11 amino acids in length and contained signatures that were in excellent agreement with published HLA binding motifs. Furthermore, by purifying soluble HLA class I complexes (sHLA) from sera of melanoma patients, up to 972 high‐confidence peptides could be identified, including melanoma‐associated antigens already described in the literature. Knowledge of the HLA class I peptidome should facilitate multiplex tetramer technology‐based characterization of T cells, and allow the development of patient selection, stratification and immunomodulatory therapeutic strategies.
Dynamic recrystallisation of ice aggregates during co-axial viscoplastic deformation: a numerical approach
2016-03-18

ABSTRACT Results of numerical simulations of co-axial deformation of pure ice up to high-strain, combining full-field modelling with recrystallisation are presented. Grain size and lattice preferred orientation analysis and comparisons between simulations at different strain-rates show how recrystallisation has a major effect on the microstructure, developing larger and equi-dimensional grains, but a relatively minor effect on the development of a preferred orientation of c -axes. Although c -axis distributions do not vary much, recrystallisation appears to have a distinct effect on the relative activities of slip systems, activating the pyramidal slip system and affecting the distribution of a -axes. The simulations reveal that the survival probability of individual grains is strongly related to the initial grain size, but only weakly dependent on hard or soft orientations with respect to the flow field. Dynamic recrystallisation reduces initial hardening, which is followed by a steady state characteristic of pure-shear deformation.
Structure‐Based Virtual Screening for Dopamine D2 Receptor Ligands as Potential Antipsychotics
2016-03-18

Abstract Structure‐based virtual screening using a D 2 receptor homology model was performed to identify dopamine D 2 receptor ligands as potential antipsychotics. From screening a library of 6.5 million compounds, 21 were selected and were subjected to experimental validation. From these 21 compounds tested, ten D 2 ligands were identified (47.6 % success rate, among them D 2 receptor antagonists, as expected) that have additional affinity for other receptors tested, in particular 5‐HT 2A receptors. The affinity ( K i values) of the compounds ranged from 58 n m to about 24 μ m . Similarity and fragment analysis indicated a significant degree of structural novelty among the identified compounds. We found one D 2 receptor antagonist that did not have a protonatable nitrogen atom, which is a key structural element of the classical D 2 pharmacophore model necessary for interaction with the conserved Asp(3.32) residue. This compound exhibited greater than 20‐fold binding selectivity for the D 2 receptor over the D 3 receptor. We provide additional evidence that the amide hydrogen atom of this compound forms a hydrogen bond with Asp(3.32), as determined by tests of its derivatives that cannot maintain this interaction.
Comparison of small animal CT contrast agents
2016-03-18

Non‐invasive in vivo small animal computed tomography (CT) imaging provides high resolution bone scans but cannot differentiate between soft tissues. For most applications injections of contrast agents (CAs) are necessary. Aim of this study was to uncover the advantages and disadvantages of commercially available CT CAs (ExiTron nano 12 000 and 6000, eXIA 160 and 160XL, Fenestra VC and LC) regarding their pharmacokinetics, toxicological side‐effects and the influence of anesthesia on the biodistribution, based on an injection volume of 100 μL/25 g body weight. The pharmacokinetics of the CAs were determined for up to five days. The CA‐induced toxicological/physiological side‐effects were evaluated by determining blood counts, liver enzymes, thyroxine and total protein values, pro‐inflammatory mediators (messenger ribonucleic acid (mRNA)), histology and immunohistochemistry. ExiTron nano 12 000 and 6000 yielded a long‐term contrast enhancement (CE) in the liver and spleen for up to five days. Some of the evaluated CAs did not show any CE at all. Anesthesia did not impair the CAs' biodistribution. The CAs differentially affected the body weight, blood counts, liver enzymes, thyroxine and total protein values. ExiTron nano 12 000 and 6000 induced histiocytes in the liver and spleen. Moreover, ExiTron nano 12 000 and eXIA 160 enhanced tumor necrosis factor (TNF) mRNA expression levels in the kidneys. Thus, we recommend ExiTron nano 12 000 and 6000 when multiple injections should be avoided. We recommend careful selection of the employed CA in order to achieve an acceptable CE in the organs of interest and to avoid influences on the animal physiology. Copyright © 2016 John Wiley &amp; Sons, Ltd.
In vivo assessment of riluzole as a potential therapeutic drug for spinocerebellar ataxia type 3
2016-03-18

Abstract Spinocerebellar ataxia type 3 ( SCA 3) is an autosomal dominantly inherited neurodegenerative disorder for which no curative therapy is available. The cause of this disease is the expansion of a CAG repeat in the so‐called ATXN 3 gene leading to an expanded polyglutamine stretch in the ataxin‐3 protein. Although the function of ataxin‐3 has been defined as a deubiquitinating enzyme, the pathogenic pathway underlying SCA 3 remains to be deciphered. Besides others, also the glutamatergic system seems to be altered in SCA 3. The antiglutamatergic substance riluzole has thus been suggested as a potential therapeutic agent for SCA 3. To assess whether riluzole is effective in the treatment of SCA 3 in vivo , we used a phenotypically well‐characterized conditional mouse model previously generated by us. Treatment with 10 mg/kg riluzole in the drinking water was started when mice showed impairment in rotarod performance. Post‐symptomatic treatment with riluzole carried out for a period of 10 months led to reduction of the soluble ataxin‐3 level and an increase in ataxin‐3 positive accumulations, but did not improve motor deficits measured by rotarod. There was also no positive effect on home cage behavior or body weight. We even observed a pronounced reduction of calbindin expression in Purkinje cells in riluzole‐treated mice. Thus, long‐term treatment with riluzole was not able to alleviate disease symptoms observed in transgenic SCA 3 mice and should be considered with caution in the treatment of human patients. image Assessing riluzole as a potential treatment for spinocerebellar ataxia type 3 (SCA3) had no beneficial, but rather a worsening effect on our transgenic SCA3 mouse model. We hypothesize that: Riluzole treatment enhanced glutamate release in ATXN3 ‐expressing cells leading to an increased Ca 2+ influx resulting in Purkinje cell damage shown by loss of calbindin expression.
Regional and directional compliance of the healthy aorta: anex vivostudy in a porcine model
2016-03-18

The aorta appears to be a complex organ with distinct regional and directional differences in compliance and wall strength that is designed to effectively absorb the kinetic energy of cardiac systole and to cushion the momentum of systolic impact. Under normotensive conditions and a preconditioned physiological morphology, the aortic wall works in the steep part of the logarithmic strain-stress function; under hypertensive conditions and pathological morphology, the wall reacts in an non-compliant manner. The high longitudinal compliance and low failure stress of the ascending aorta and subsequent pathological changes may be the main determinants of the recurrent patho-anatomy of Type A aortic dissection.
Evaluation of Presumably Disease Causing SCN1A Variants in a Cohort of Common Epilepsy Syndromes
2016-03-18

We identified 8 known missense mutations, previously reported as pathogenic, in a total of 17 unrelated epilepsy patients (17/448; 3.80%). Our re-evaluation indicates that 7 out of these 8 variants (p.R27T; p.R28C; p.R542Q; p.R604H; p.T1250M; p.E1308D; p.R1928G; NP_001159435.1) are not pathogenic. Only the p.T1174S mutation may be considered as a genetic risk factor for epilepsy of small effect size based on the enrichment in patients (P = 6.60 x 10-4; OR = 0.32, fishers exact test), previous functional studies but incomplete penetrance. Thus, incorporation of previous studies in genetic counseling of SCN1A sequencing results is challenging and may produce incorrect conclusions.
Heritability, evolvability, phenotypic plasticity and temporal variation in sperm‐competition success of Drosophila melanogaster
2016-03-18

Abstract Sperm‐competition success ( SCS ) is seen as centrally important for evolutionary change: superior fathers sire superior sons and thereby inherit the traits that make them superior. Additional hypotheses, that phenotypic plasticity in SCS and sperm ageing explain variation in paternity, are less considered. Even though various alleles have individually been shown to be correlated with variation in SCS , few studies have addressed the heritability, or evolvability, of overall SCS . Those studies that have addressed found low or no heritability and have not examined evolvability. They have further not excluded phenotypic plasticity, and temporal effects on SCS , despite their known dramatic effects on sperm function. In Drosophila melanogaster , we found that both standard components of sperm competition, sperm defence and sperm offence, showed nonsignificant heritability across several offspring cohorts. Instead, our analysis revealed, for the first time, the existence of phenotypic plasticity in SCS across an extreme environment (5% CO 2 ), and an influence of sperm ageing. Evolvability of SCS was substantial for sperm defence but weak for sperm offence. Our results suggest that the paradigm of explaining evolution by sperm competition is more complex and will benefit from further experimental work on the heritability or evolvability of SCS , measuring phenotypic plasticity, and separating the effects of sperm competition and sperm ageing.
Echinoid test damage by a stingray predator
2016-03-19

Stingrays (Order: Myliobatiformes) are well-known predators that feed on a variety of marine species including crustaceans, teleosts, molluscs and annelids. Here, a predatory attack by a stingray on the large spatangoid echinoid Meoma ventricosa (Lamarck) is reported from the shallow-water carbonate platform of San Salvador, Bahamas. A single stingray was observed feeding on a large adult specimen of M. ventricosa near Sand Dollar Beach, San Salvador Island. The partially crushed and partially eviscerated test of the attacked echinoid was collected from the feeding site. In addition, a crushed test of a freshly killed, smaller irregular clypeasteroid echinoid Leodia sexiesperforata (Leske) was also recovered at the same site. In both cases, the test was broken across the test plates and not along plate boundaries. Meoma ventricosa showed major plate loss on the oral side; however, bite traces and spine loss were not observed in the damaged areas. Similarly, L. sexiesperforata showed no evidence of spine removal; however, bite marks were identifiable. The observed test damage in both taxa is morphologically distinct and could be potentially identifiable in the fossil record.
Quality assurance in the analysis of growth hormone and insulin-like growth factor I in disorders of the somatotropic axis
2016-03-19

Abstract Background: Reliable laboratory analysis is fundamental to diagnostics, therapy, and follow-up of growth disturbance and secretory dysfunction of growth hormone (GH) and insulin-like growth factor I (IGF-I). Currently available commercial assays have their limitations, as they show large variations in hormone concentrations measured. Methods: The recommendations of an expert workshop with practicing endocrinologists from the fields of pediatrics and internal medicine and with laboratory physicians, with reference to the outcome of the interdisciplinary consensus conference in Keswick (Virginia, USA) in 2009, were used. Results: Among the quality criteria stipulated by the workshop participants are the use of uniform reference standards, documentation of analytical conditions (such as calibrators, binding epitopes, cross-reactivity, and methods for removal from the binding protein), batch-to-batch consistency, and low inter-assay variability. The participants recommended developing assay-specific thresholds and reference intervals based on large and well-defined reference populations. It is furthermore recommended to delineate the assay quality, particularly with reference to clinically important cutoffs. Conclusions: The manufacturers of diagnostic assays should be obliged to regularly monitor and report the implementation of quality criteria. Only assays that are evaluated according to uniform quality standards and that are employed clinically permit informed diagnostic and therapy of patients with GH secretory dysfunction, preventing avoidable burden on both patients and paying authorities.
A distal 140 kyr sediment record of Nile discharge and East African monsoon variability
2016-03-21

Abstract. Clay mineral assemblages in a sediment core from the distal Nile discharge plume off Israel have been used to reconstruct the late Quaternary Nile sediment discharge into the eastern Mediterranean Sea (EMS). The record spans the last ca. 140 kyr. Smectite abundances indicate the influence of the Blue Nile and the Atbara River that have their headwaters in the volcanic rocks of the Ethiopian Highlands. Kaolinite abundances indicate the influence of wadis, which contribute periodically to the suspension load of the Nile. Due to the geographical position, the climate and the sedimentary framework of the EMS is controlled by two climate systems. The long-term climate regime was governed by the African monsoon that caused major African humid periods (AHPs) with enhanced sediment discharge at 132 to &lt; 126 (AHP 5), 116 to 99 (AHP4), and 89 to 77 ka (AHP3). They lasted much longer than the formation of the related sapropel layers S5 (&gt; 2 kyr), S4 (3.5 kyr), and S3 (5 kyr). During the last glacial period (Marine Isotope Stages (MISs) 4–2), the long-term changes in the monsoonal system were superimposed by millennial-scale changes in an intensified midlatitude glacial system. This climate regime caused short but pronounced drought periods in the Nile catchment, which are linked to Heinrich events and alternate with more humid interstadials. The clay mineral record further implies that feedback mechanisms between vegetation cover and sediment discharge of the Nile are detectable but of minor importance for the sedimentary record in the southeastern Mediterranean Sea during the investigated African humid periods.
Signal processing in urodynamics: towards high definition urethral pressure profilometry
2016-03-21

With its advanced sensing capabilities, the novel microtip catheter collects an unprecedented amount of urethral pressure data. Through sequential signal processing steps, physicians are provided with detailed information on the pressure distribution in and around the urethra. Therefore, HD-UPP overcomes many current limitations of conventional UPP and offers the opportunity to evaluate urethral structures, especially the sphincter, in context of the correct anatomical location. This could enable the development of focal therapy approaches in the treatment of SUI.