julilili42/papers huggingface dataset:
ToxDBScan: Large-Scale Similarity Screening of Toxicological Databases for Drug Candidates
2014-10-21

We present a new tool for hepatocarcinogenicity evaluation of drug candidates in rodents. ToxDBScan is a web tool offering quick and easy similarity screening of new drug candidates against two large-scale public databases, which contain expression profiles for substances with known carcinogenic profiles: TG-GATEs and DrugMatrix. ToxDBScan uses a set similarity score that computes the putative similarity based on similar expression of genes to identify chemicals with similar genotoxic and hepatocarcinogenic potential. We propose using a discretized representation of expression profiles, which use only information on up- or down-regulation of genes as relevant features. Therefore, only the deregulated genes are required as input. ToxDBScan provides an extensive report on similar compounds, which includes additional information on compounds, differential genes and pathway enrichments. We evaluated ToxDBScan with expression data from 15 chemicals with known hepatocarcinogenic potential and observed a sensitivity of 88 Based on the identified chemicals, we achieved perfect classification of the independent test set. ToxDBScan is publicly available from the ZBIT Bioinformatics Toolbox.
Tullock on the Football Pitch
2014-10-21

A simple Tullock contest model is used to predict levels of effort in English professional football (soccer). The effort of the teams is reflected in the numbers of fouls committed and the numbers of yellow and red cards awarded. Effort levels are found to be higher in matches between evenly talented teams, confirming the idea that asymmetries result in lower effort by participants. The results also suggest that teams’ effort levels are strategic complements.
Metabolic aspects of bacterial persisters
2014-10-22

Persister cells form a multi-drug tolerant subpopulation within an isogenic culture of bacteria that are genetically susceptible to antibiotics. Studies with different Gram negative and Gram positive bacteria have identified a large number of genes associated with the persister state. In contrast, the revelation of persister metabolism has only been addressed recently. We here summarize metabolic aspects of persisters, which includes an overview about the bifunctional role of selected carbohydrates as both triggers for the exit from the drug tolerant state and metabolites which persisters feed on. Also alarmones as indicators for starvation have been shown to influence persister levels via different signaling cascades involving the activation of toxin-antitoxin systems and other regulatory factors. Finally, recent data obtained by (13)C-isotopolog profiling demonstrated an active amino acid anabolism in Staphylococcus aureus cultures challenged with high drug concentrations. Understanding the metabolism of persister cells poses challenges but also paves the way for the development of anti-persister compounds.
XMM-Newtonstudy of 30 Doradus C and a newly identified MCSNR J0536−6913 in the Large Magellanic Cloud
2014-10-22

Aims: We present a study of the superbubble (SB) 30 Dor C and the newly\\nidentified MCSNR J0536-6913 in the LMC. Methods: All available XMM-Newton data\\n(exposure times of 420 ks EPIC-pn, 556 ks EPIC-MOS1, 614 ks EPIC-MOS2) were\\nused to characterise the thermal X-ray emission in the region. An analysis of\\nthe non-thermal X-rays is also presented and discussed in the context of\\nemission mechanisms previously suggested in the literature. These data are\\nsupplemented by X-ray data from Chandra, optical data from the MCELS, and radio\\ndata from ATCA and MOST. Results: The brightest thermal emission was found to\\nbe associated with a new supernova remnant, MCSNR J0536-6913. X-ray spectral\\nanalysis of MCSNR J0536-6913 suggested an ejecta-dominated remnant with lines\\nof O, Ne, Mg, and Si, and a total 0.3-10 keV luminosity of ~8E+34 erg/s. Based\\non derived ejecta abundance ratios, we determined the mass of the stellar\\nprogenitor to be either ~18 M_sun or as high as &gt;40 M_sun, though the spectral\\nfits were subject to assumptions (e.g., uniform temperature and well-mixed\\nejecta). The thermal emission from the SB exhibited enrichment by alpha-process\\nelements, evidence for a recent core-collapse SNR interaction with the SB\\nshell. We detected non-thermal X-ray emission throughout 30 Dor C, with the\\nbrightest regions being highly correlated with the H-alpha and radio shells. We\\ncreated a non-thermal spectral energy distribution for the north-eastern shell\\nof 30 Dor C which was best-fit with an exponentially cut-off synchrotron model.\\nConclusions: Thermal X-ray emission from 30 Dor C is very complex, consisting\\nof a large scale SB emission at the eastern shell wall with the brightest\\nemission due to MCSNR J0536-6913. The fact that the non-thermal spectral energy\\ndistribution of the SB shell was observed to roll-off is further evidence that\\nthe non-thermal X-rays from 30 Dor C are synchrotron in origin.\\n
Female, but not male, nematodes evolve under experimental sexual coevolution
2014-10-22

Coevolution between the sexes is often considered to be male-driven: the male genome is constantly scanned by selection for traits that increase relative male fertilization success. Whenever these traits are harmful to females, the female genome is scanned for resistance traits. The resulting antagonistic coevolution between the sexes is analogous to Red Queen dynamics, where adaptation and counteradaptation keep each other in check. However, the underlying assumption that male trait evolution precedes female trait counteradaptation has received few empirical tests. Using the gonochoristic nematode Caenorhabditis remanei , we now show that 20 generations of relaxed versus increased sexual selection pressure lead to female, but not to male, trait evolution, questioning the generality of a male-driven process.
Synthesis of aromatic glycoconjugates. Building blocks for the construction of combinatorial glycopeptide libraries
2014-10-22

New aromatic glycoconjugate building blocks based on the trifunctional 3-aminomethyl-5-aminobenzoic acid backbone and sugars linked to the backbone by a malonyl moiety were prepared via peptide coupling. The orthogonally protected glycoconjugates, bearing an acetyl-protected glycoside, were converted into their corresponding acids which are suitable building blocks for combinatorial glycopeptide synthesis.
Central Asia Active Fault Database
2014-10-22

The ongoing collision of the Indian subcontinent with Asia controls active tectonics and seismicity in Central Asia. This motion is accommodated by faults that have historically caused devastating earthquakes and continue to pose serious threats to the population at risk. Despite international and regional efforts to assess seismic hazards in Central Asia, little attention has been given to development of a comprehensive database for active faults in the region. To address this issue and to better understand the distribution and level of seismic hazard in Central Asia, we are developing a publically available database for active faults of Central Asia (including but not limited to Afghanistan, Tajikistan, Kyrgyzstan, northern Pakistan and western China) using ArcGIS. The database is designed to allow users to store, map and query important fault parameters such as fault location, displacement history, rate of movement, and other data relevant to seismic hazard studies including fault trench locations, geochronology constraints, and seismic studies. Data sources integrated into the database include previously published maps and scientific investigations as well as strain rate measurements and historic and recent seismicity. In addition, high resolution Quickbird, Spot, and Aster imagery are used for selected features to locate and measure offset of landforms associated with Quaternary faulting. These features are individually digitized and linked to attribute tables that provide a description for each feature. Preliminary observations include inconsistent and sometimes inaccurate information for faults documented in different studies. For example, the Darvaz-Karakul fault which roughly defines the western margin of the Pamir, has been mapped with differences in location of up to 12 kilometers. The sense of motion for this fault ranges from unknown to thrust and strike-slip in three different studies despite documented left-lateral displacements of Holocene and late Pleistocene landforms observed near the fault trace.
Paleoindian settlement of the high-altitude Peruvian Andes
2014-10-23

Mountain dwellers of the Pleistocene Humans colonized the inhospitable high Andes at least 11.5 thousand years ago. Rademaker et al. unearthed evidence of hunter-gatherer occupation at heights of almost 4500 m in Peru in two open-air sites. The sites contained more than 750 tools, including likely spearheads and scrapers. A nearby rockshelter with sooted ceilings and floor detritus may have been a campsite. The sites were probably used seasonally for hunting vicuña and other high-altitude prey. Science , this issue p. 466
The Interaction Between Sickle Cell Disease and HIV Infection: A Systematic Review
2014-10-23

Human immunodeficiency virus (HIV) and sickle cell disease (SCD) are regarded as endemic in overlapping geographic areas; however, for most countries only scarce data on the interaction between HIV and SCD and disease burden exist. HIV prevalence in SCD patients varies between 0% and 11.5% in published studies. SCD has been suggested to reduce disease progression of HIV into AIDS. Various interactions of antiretroviral therapy with SCD exist. Both SCD and HIV act as common risk factors for stroke, avascular necrosis, severe splenic dysfunction, pulmonary arterial hypertension, and sepsis, which may result in synergistic increase in risk of developing these diseases. No treatment guidelines regarding SCD with HIV coinfection were identified. Available evidence is mainly based on small clinical studies, thus making strong recommendations difficult. An increased effort to elucidate the precise interactions is warranted to better understand both diseases and effect more adequate treatment approaches, especially in view of their geographical coprevalence.
Covariation in the Human Masticatory Apparatus
2014-10-23

ABSTRACT Many studies have described shape variation of the modern human cranium in relation to subsistence; however, patterns of covariation within the masticatory apparatus (MA) remain largely unexplored. The patterns and intensity of shape covariation, and how this is related to diet, are essential for understanding the evolution of functional masticatory adaptations of the human cranium. Within a worldwide sample ( n = 255) of 15 populations with different modes of subsistence, we use partial least squares analysis to study the relationships between three components of the MA: upper dental arch, masseter muscle, and temporalis muscle attachments. We show that the shape of the masseter muscle and the shape of the temporalis muscle clearly covary with one another, but that the shape of the dental arch seems to be rather independent of the masticatory muscles. On the contrary, when relative positioning, orientation, and size of the masticatory components is included in the analysis, the dental arch shows the highest covariation with the other cranial parts, indicating that these additional factors are more important than just shape with regard to covariation within the MA. Covariation patterns among these cranial regions differ mainly between hunting–fishing and gathering–agriculture groups, possibly relating to greater masticatory strains resulting from a large meat component in the diet. High‐strain groups show stronger covariation between upper dental arch and masticatory muscle shape when compared with low‐strain groups. These results help to provide a clearer understanding of constraints and interlinkage of shape variation within the human MA and allow for more realistic modeling and predictions in future biomechanical studies. Anat Rec, 298:64–84, 2015. © 2014 Wiley Periodicals, Inc.
Do Himalayan treelines respond to recent climate change? An evaluation of sensitivity indicators
2014-10-23

Abstract. Climate warming is expected to induce treelines to advance to higher elevations. Empirical studies in diverse mountain ranges, however, give evidence of both advancing alpine treelines as well as rather insignificant responses. The inconsistency of findings suggests distinct differences in the sensitivity of global treelines to recent climate change. It is still unclear where Himalayan treeline ecotones are located along the response gradient from rapid dynamics to apparently complete inertia. This paper reviews the current state of knowledge regarding sensitivity and response of Himalayan treelines to climate warming, based on extensive field observations, published results in the widely scattered literature, and novel data from ongoing research of the present authors. Several sensitivity indicators such as treeline type, treeline form, seed-based regeneration, and growth patterns are evaluated. Since most Himalayan treelines are anthropogenically depressed, observed advances are largely the result of land use change. Near-natural treelines are usually krummholz treelines which are relatively unresponsive. Nevertheless, intense recruitment of treeline trees suggests a great potential for future treeline advance. Competitive abilities of seedlings within krummholz thickets and dwarf scrub heaths will be a major source of variation in treeline dynamics. Tree growth-climate relationships show mature treeline trees to be responsive to temperature change, in particular in winter and pre-monsoon seasons. High pre-monsoon temperature trends will most likely drive tree growth performance in W and central Himalaya. Ecological niche modelling suggests that bioclimatic conditions for a range expansion of treeline trees will be created during coming decades.
Rapid Induction of COOLing in Stroke Patients (iCOOL1): a randomised pilot study comparing cold infusions with nasopharyngeal cooling
2014-10-23

Abstract Introduction Induction methods for therapeutic cooling are under investigated. We compared the effectiveness and safety of cold infusions (CI) and nasopharyngeal cooling (NPC) for cooling induction in stroke patients. Methods A prospective, open-label, randomised (1:1), single-centre pilot trial with partially blinded safety endpoint assessment was conducted at the neurointensive care unit of Heidelberg University. Intubated stroke patients with an indication for therapeutic cooling and an intracranial pressure (ICP)/temperature brain probe were randomly assigned to CI (4°C, 2L at 4L/h) or NPC (60L/min for 1 h). Previous data suggested a maximum decrease of tympanic temperature for CI (2.1L within 35 min) after 52 min. Therefore the study period was 1 hour (15 min subperiods I-IV). The brain temperature course was the primary endpoint. Secondary measures included continuous monitoring of neurovital parameters and extracerebral temperatures. Statistical analysis based on repeated-measures analysis of variance. Results Of 221 patients screened, 20 were randomized within 5 months. Infusion time of 2L CI was 33 ± 4 min in 10 patients and 10 patients received NPC for 60 min. During active treatment (first 30 min), brain temperature decreased faster with CI than during NPC (I: -0.31 ± 0.2 versus -0.12 ± 0.1°C, P = 0.008; II: -1.0 ± 0.3 versus -0.49 ± 0.3°C, P = 0.001). In the CI-group, after the infusion was finished, the intervention no longer decreased brain temperature, which increased after 3.5 ± 3.3 min. Oesophageal temperature correlated best with brain temperature during CI and NPC. Tympanic temperature reacted similarly to relative changes of brain temperature during CI, but absolute values slightly differed. CI provoked three severe adverse events during subperiods II-IV (two systolic arterial pressure (SAP), one shivering) compared with four in the NPC-group, all during subperiod I (three SAP, one ICP). Classified as possibly intervention-related, two cases of ventilator failure occurred during NPC. Conclusions In intubated stroke patients, brain cooling is faster during CI than during NPC. Importantly, contrary to previous expectations, brain cooling stopped soon after CI cessation. Oesophageal but neither bladder nor rectal temperature is suited as surrogate for brain temperature during CI and NPC. Several severe adverse events in CI and in NPC demand further studying of safety. Trial registration ClinicalTrials.gov NCT01573117 . Registered 31 March 2012
The effects of direct and indirect speech on English discourse comprehension in aphasia
2014-10-23

The effects of direct and indirect speech on English discourse comprehension in aphasia Rimke Groenewold1,2,3, Roelien Bastiaanse1,3, Lyndsey Nickels2,3, Martijn Wieling1,4, Mike Huiskes1, Center for Language and Cognition Groningen, ARC Centre of Excellence in Cognition and its Disorders (CCD) and Department of Cognitive Science, Macquarie University, Sydney, Australia International Doctorate for Experimental Approaches to Language and Brain (IDEALAB), Universities of Groningen (NL), Newcastle (UK), Potsdam (GE), Trento (IT) & Macquarie University, Sydney (AU), Department of Quantitative Linguistics, University of Tubingen, Tubingen, Germany.
Synthesis, Structure, and Frequency‐Doubling Effect of Calcium Cyanurate
2014-10-24

Abstract Calcium cyanurate is synthesized by reacting calcium chloride with potassium cyanate following a solid‐state reaction. The formation of the new compound Ca 3 (O 3 C 3 N 3 ) 2 (CCY), which occurs by the cyclotrimerization of cyanate ions, was examined thermoanalytically and the crystal structure was determined by single‐crystal structure analysis. The structure of CCY is closely related to the structure of the well‐known oxoborate β‐BaB 2 O 4 (BBO). Second harmonic generation (SHG) measurements on crystal powders show a higher SHG efficiency for CCY than for BBO by about one order of magnitude.
Erythrocyte membrane fatty acid fluidity and risk of type 2 diabetes in the EPIC-Potsdam study
2014-10-24

A high lipophilic index, reflecting lower membrane fluidity, may be associated with a higher risk of type 2 diabetes. Our data corroborate the hypothesis that membrane fluidity may be an important mediator that links intake and metabolism of FAs to diabetes risk.
Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source
2014-10-24

Ammonium is the major nitrogen source in some plant ecosystems but is toxic at high concentrations, especially when available as the exclusive nitrogen source. Ammonium stress rapidly leads to various metabolic and hormonal imbalances that ultimately inhibit root and shoot growth in many plant species, including Arabidopsis thaliana (L.) Heynh. To identify molecular and genetic factors involved in seedling survival with prolonged exclusive NH4+ nutrition, a transcriptomic analysis with microarrays was used. Substantial transcriptional differences were most pronounced in (NH4)2SO4-grown seedlings, compared with plants grown on KNO3 or NH4NO3. Consistent with previous physiological analyses, major differences in the expression modules of photosynthesis-related genes, an altered mitochondrial metabolism, differential expression of the primary NH4+ assimilation, alteration of transporter gene expression and crucial changes in cell wall biosynthesis were found. A major difference in plant hormone responses, particularly of auxin but not cytokinin, was striking. The activity of the DR5::GUS reporter revealed a dramatically decreased auxin response in (NH4)2SO4-grown primary roots. The impaired root growth on (NH4)2SO4 was partially rescued by exogenous auxin or in specific mutants in the auxin pathway. The data suggest that NH4+-induced nutritional and metabolic imbalances can be partially overcome by elevated auxin levels.
Variational discretization of wave equations on evolving surfaces
2014-10-24

A linear wave equation on a moving surface is derived from Hamiltonâs principle of stationary action. The variational principle is discretized with functions that are piecewise linear in space and time. This yields a discretization of the wave equation in space by evolving surface finite elements and in time by a variational integrator, a version of the leapfrog or StÃ¶rmerâVerlet method. We study stability and convergence of the full discretization in the natural time-dependent norms under the same CFL condition that is required for a fixed surface. Using a novel modified Ritz projection for evolving surfaces, we prove optimal-order error bounds. Numerical experiments illustrate the behavior of the fully discrete method.
Instrumented Functional Reach Test Differentiates Individuals at High Risk for Parkinsonâ€™s Disease from Controls
2014-10-24

The functional reach (FR) test as a complex measure of balance including limits of stability has been proven to differentiate between patients with Parkinson's disease (PD) and controls (CO). Recently, it has been shown that the instrumentation of the FR (iFR) with a wearable sensor may increase this diagnostic accuracy. This cross-sectional study aimed at investigating whether the iFR has the potential to differentiate individuals with high risk for PD (HRPD) from CO, as the delineation of such individuals would allow for, e.g., early neuromodulation. Thirteen PD patients, 13 CO, and 31 HRPD were investigated. HRPD was defined by presence of an enlarged area of hyperechogenicity in the mesencephalon on transcranial sonography and either one motor sign or two risk and prodromal markers of PD. All participants were asked to reach with their right arm forward as far as possible and hold this position for 10 s. During this period, sway parameters were assessed with an accelerometer (Dynaport, McRoberts) worn at the lower back. Extracted parameters that differed significantly between PD patients and CO in our cohort [FR distance (shorter in PD), anterior-posterior and mediolateral acceleration (both lower in PD)] as well as JERK, which has been shown to differentiate HRPD from CO and PD in a previous study, were included in a model, which was then used to differentiate HRPD from CO. The model yielded an area under the curve of 0.77, with a specificity of 85%, and a sensitivity of 74%. These results suggest that the iFR can contribute to an assessment panel focusing on the definition of HRPD individuals.
Synthesis of Vicinal Diketoses by Using a Metathesis–Hydroxylation–Oxidation Sequence
2014-10-24

Abstract Symmetrical vicinal diuloses were prepared from 2,3:4,5‐di‐ O ‐isopropylidene‐ D ‐arabinose and ‐ L ‐arabinose by using methyltriphenylphosphonium bromide to convert both enantiomers into the corresponding 1,2‐dideoxy‐3,4:5,6‐di‐ O ‐isopropylidene‐ arabino ‐hex‐1‐enitols D‐5 and L‐5 . The metathesis reactions of D‐5 with itself and with L‐5 , respectively, by using the Hoveyda–Grubbs catalyst gave diastereomeric dec‐5‐enitols DD‐6 and DL‐6 , which were dihydroxylated with osmium tetroxide to give 1,2:3,4:7,8:9,10‐tetra‐ O ‐isopropylidene‐protected decitols DD‐7 and DL‐7 . Swern oxidation of the decitols afforded isopropylidene‐protected deco‐5,6‐diuloses DD‐8 and DL‐8 , which gave unprotected deco‐5,6‐diuloses DD‐9 and DL‐9 upon acidic cleavage of the isopropylidene groups. The structures of both diastereomers were confirmed by NMR spectroscopy and X‐ray crystal structure analysis.