julilili42/papers huggingface dataset:
Systematics of the Hipposideros turpis complex and a description of a new subspecies from Vietnam
2011-12-06

ABSTRACT Hipposideros turpis is traditionally known as a species composed of three subspecies, H. t. turpis , H. t. alongensis and H. t. pendleburyi , distributed disjunctly in south‐west Japan, north‐east Vietnam and south‐west Thailand, respectively. Prior to the present study, the systematic status of forms within the species remained unclear. Using morphological (external, bacular, cranial and dental characters), genetic and echolocation data, we demonstrate that turpis , alongensis and pendleburyi represent three distinct species, and that these species are endemic to Japan, Vietnam and Thailand, respectively. They are very distinct genetically and do not even form a monophyletic group. We also prove that H. alongensis is composed of two subspecies, H. a. alongensis and H. a. sungi . The latter subspecies is described as new to science. To date, H. a. alongensis appears to be restricted to the Cat Ba Island of Cat Ba National Park, west Ha Long Bay, whereas H. a. sungi ssp. nov. is known from three localities in mainland northeast Vietnam. These two subspecies are distinguished by body size, molecular data and the frequency of the constant‐frequency component of their echolocation signals.
Membrane integration of a mitochondrial signal-anchored protein does not require additional proteinaceous factors
2011-12-06

The MOM (mitochondrial outer membrane) contains SA (signal-anchored) proteins that bear at their N-terminus a single hydrophobic segment that serves as both a mitochondrial targeting signal and an anchor at the membrane. These proteins, like the vast majority of mitochondrial proteins, are encoded in the nucleus and have to be imported into the organelle. Currently, the mechanisms by which they are targeted to and inserted into the OM (outer membrane) are unclear. To shed light on these issues, we employed a recombinant version of the SA protein OM45 and a synthetic peptide corresponding to its signal-anchor segment. Both forms are associated with isolated mitochondria independently of cytosolic factors. Interaction with mitochondria was diminished when a mutated form of the signal-anchor was employed. We demonstrate that the signal-anchor peptide acquires an α-helical structure in a lipid environment and adopted a TM (transmembrane) topology within artificial lipid bilayers. Moreover, the peptide's affinity to artificial membranes with OM-like lipid composition was much higher than that of membranes with ER (endoplasmic reticulum)-like lipid composition. Collectively, our results suggest that SA proteins are specifically inserted into the MOM by a process that is not dependent on additional proteins, but is rather facilitated by the distinct lipid composition of this membrane.
Comparison of synthetic maps from truncated jet-formation models with YSO jet observations
2011-12-06

\\n Context. Significant progress has been made in the last years in the understanding \\n of the jet formation mechanism through a combination of numerical \\n simulations and analytical MHD models for outflows characterized by the \\n symmetry of self-similarity. Analytical radially self-similar models \\n successfully describe disk-winds, but need several improvements. In a \\n previous article we introduced models of truncated jets from disks, i.e. \\n evolved in time numerical simulations based on a radially self-similar MHD \\n solution, but including the effects of a finite radius of the jet-emitting \\n disk and thus the outflow.\\n Aims. These models need now to be compared with available observational data. A \\n direct comparison of the results of combined analytical theoretical models \\n and numerical simulations with observations has not been performed as yet. \\n This is our main goal.\\n Methods. In order to compare our models with observed jet widths inferred from\\n recent optical images taken with the Hubble Space Telescope (HST) and \\n ground-based adaptive optics (AO) observations, we use a new set of tools \\n to create emission maps in different forbidden lines, from which we \\n determine the jet width as the full-width half-maximum of the emission.\\n Results. It is shown that the untruncated analytical disk outflow solution considered\\n here cannot fit the small jet widths inferred by observations of several \\n jets. Furthermore, various truncated disk-wind models are examined, whose \\n extracted jet widths range from higher to lower values compared to the \\n observations. Thus, we can fit the observed range of jet widths by tuning \\n our models.\\n Conclusions. We conclude that truncation is necessary to reproduce the observed jet \\n widths and our simulations limit the possible range of truncation radii. We \\n infer that the truncation radius, which is the radius on the disk mid-plane \\n where the jet-emitting disk switches to a standard disk, must be between \\n around 0.1 up to about 1 AU in the observed sample for the considered \\n disk-wind solution. One disk-wind simulation with an inner truncation \\n radius at about 0.11 AU also shows potential for reproducing the \\n observations, but a parameter study is needed.\\n
A Multicomponent Carba‐Betti Strategy to Alkylidene Heterodimers – Total Synthesis and Structure–Activity Relationships of Arzanol
2011-12-07

Abstract Using the synthesis of the heterodimeric phloroglucinyl pyrone arzanol as a benchmark reaction, a carba‐version of the Betti multicomponent reaction has been developed. Capitalizing on the fluorous activation of the phenolic component and the use of iminium ions as bivalent and “transmissive” aldehyde equivalents, the reaction has been used to colonize a biologically privileged but previously inaccessible area of chemical space and investigate the structure–activity relationships of arzanol towards a series of proinflammatory targets (mPGES‐1, 5‐LO).
2-Bromo-1,3-diisopropyl-4,5-dimethyl-1H-imidazol-3-ium dicyanidoargentate
2011-12-07

The title structure, (C(11)H(20)BrN(2))[Ag(CN)(2))], is built up from an approximately C(2v)-symmetric imidazolium cation and a nearly linear dicyanidoargentate anion [N-Ag-N = 176.6 (9)° and Ag-C-N = 178.8 (9) and 177.2 (11)°]. These two constituents are linked by a remarkably short inter-action between the Br atom of the imidazolium cation [C-Br = 1.85 (3) Å] and one N atom of the cyanidoargentate anion [Br⋯N = 2.96 (2) Å], which is much less than the sum of the van der Waals radii (3.40 Å). The crystal studied was twinned by merohedry.
CARBONATE GEOBODIES: HIERARCHICAL CLASSIFICATION AND DATABASE – A NEW WORKFLOW FOR 3D RESERVOIR MODELLING
2011-12-08

Quantitative data on geobodies are crucial for reservoir modelling. Although abundant quantitative data are available in the literature for siliciclastic depositional systems, equivalent data for carbonate systems are scarce. In this paper we introduce a new approach to the management of quantitative data on carbonate geobodies which is based on a hierarchical classification scheme. The classes to which a carbonate geobody are assigned are: (1) depo‐time (i.e. geological age); (2) depo‐system (i.e. type of carbonate platform); (3) depo‐zone (i.e. facies belt or zone); (4) depo‐shape (i.e. geometry of the geological body); (5) depo‐element (i.e. architectural elements present); and (6) depo‐facies (litho‐ and biofacies). This hierarchical classification is complemented by a set of rules for modifying depo‐shapes which refer to their spatial distribution and patterns of interaction. Based on this classification, an extensive database has been developed which can be used for 3D reservoir modelling. The database holds more than 600 case studies from outcrop analogues and the subsurface and also from satellite images of modern carbonate settings. The database can be used as the basis for a new workflow for reservoir modelling which uses multiple‐point statistics (MPS). MPS makes use of training images to capture and reproduce facies patterns and geometries during stochastic simulations. The application of this new approach is demonstrated by modelling a Cretaceous outcrop reservoir analogue from southern France. The use of MPS allows the generation of geologically realistic and complex facies distributions in the model based on the simplified training images.
Application times for the single-step/double-mix technique for impression materials in clinical practice.
2011-12-08

Hydrophilicity of unset impression materials underlies changes occurring during working time. Hence, the clinical application time when impression materials contact oral tissues after mixing may play a critical role in successful impressions. The aim of this study was to analyze the clinical time course of impression taking applying the single-step/double-mix technique. Application times of 86 impressions, comprising 265 prepared teeth and 46 implants, taken by 14 different clinicians at a university dental clinic were analyzed. The mean time from loading the impression tray until its final position in the patient's mouth (total application time) was 51.2 seconds; confidence intervals were 46.9 (lower limit) and 55.5 (upper limit). The number of registered teeth and implants did not influence the duration of impression taking. Related to wettability data, several polyvinyl siloxane impression materials show decreased hydrophilicity with respect to estimated application times. The authors suggest considering clinically relevant application times for impression taking in future in vitro studies on physicochemical characteristics of impression materials.
Administration of bortezomib before and after autologous stem cell transplantation improves outcome in multiple myeloma patients with deletion 17p
2011-12-09

Abstract In patients with multiple myeloma (MM), risk stratification by chromosomal abnormalities may enable a more rational selection of therapeutic approaches. In the present study, we analyzed the prognostic value of 12 chromosomal abnormalities in a series of 354 MM patients treated within the HOVON-65/GMMG-HD4 trial. Because of the 2-arm design of the study, we were able to analyze the effect of a bortezomib-based treatment before and after autologous stem cell transplantation (arm B) compared with standard treatment without bortezomib (arm A). For allanalyzed chromosomal aberrations, progression-free survival (PFS) and overall survival (OS) were at least equal or superior in the bortezomib arm compared with the standard arm. Strikingly, patients with del(17p13) benefited the most from the bortezomib-containing treatment: the median PFS in arm A was 12.0 months and in arm B it was 26.2 months (P = .024); the 3 year-OS for arm A was 17% and for arm B it was 69% (P = .028). After multivariate analysis, del(17p13) was an independent predictor for PFS (P &lt; .0001) and OS (P &lt; .0001) in arm A, whereas no statistically significant effect on PFS (P = .28) or OS (P = .12) was seen in arm B. In conclusion, the adverse impact of del(17p13) on PFS and OS could be significantly reduced by bortezomib-based treatment, suggesting that long-term administration of bortezomib should be recommended for patients carrying del(17p13). This trial is registered at the International Standard Randomised Controlled Trial Number Register as ISRCTN64455289.
Wound Fluid Diagnostics in Diabetic Foot Ulcers
2011-12-09

Wound fluid seems -at least theoreticallyeasily accessible and might open a new window to the local wound microenvironment that cannot be evaluated by the analysis of serum or plasma markers. Recently, this strategy has been supported by a first time wound fluid proteome analysis comparing acute and chronic wounds (Eming et al. 2010). Interestingly, there seem to be essential differences with respect to wound fluid protein composition when comparing acute and chronic wounds. The wound fluid proteome of healing tissue is characterised by proteins involved in tissue growth and protection from inflammatory activity, whereas non-healing wounds are characterised by a chronic inflammatory environment primarily consisting of leukocyte proteases and inflammatory mediators (Eming et al. 2010). This is particularly striking since the non-healing state in diabetic foot ulcers has previously been linked to persistent inflammatory activity (Acosta et al. 2008). Thus, the wound fluid of chronic wounds seems to be characterised by an altered wound micro-milieu and may, therefore, provide deeper insights into the causes of delayed wound healing.
High dose artesunate in combination with mefloquine: pharmacovigilance in the Venezuelan Amazon
2011-12-09

Forty-six patients in a remote health post of Amazonas, Venezuela, accidentally received artesunate in a dose of 10 mg/kg/day combined with mefloquine. This corresponds to the upper limit of the therapeutic range recommended by the WHO (2-10 mg/kg/day). Side effects were retrospectively investigated and a pharmacovigilance report was written. The main side effects were vomiting and diarrhea. Four patients developed complications with signs of dehydration. It is suggested to re-assess the therapeutic range of artesunate when given in combination with mefloquine and to establish a worldwide centralized antimalarial toxicity reporting system.
MicroRNA-520/373 family functions as a tumor suppressor in estrogen receptor negative breast cancer by targeting NF-κB and TGF-β signaling pathways
2011-12-12

MicroRNAs (miRNAs) as modulators of gene expression have been described to display both tumor-promoting and tumor-suppressive functions. Although their role has been studied in different tumor types, little is known about how they regulate nuclear factor κB (NF-κB) signaling in breast cancer. Here, we performed an unbiased whole genome miRNA (miRome) screen to identify novel modulators of NF-κB pathway in breast cancer. The screen identified 13 miRNA families whose members induced consistent effects on NF-κB activity. Among those, the miR-520/373 family inhibited NF-κB signaling through direct targeting of RELA and thus strongly reduced expression and secretion of the pro-inflammatory cytokines interleukin (IL)-6 and IL-8. With a combination of in vitro and in vivo approaches, we propose a metastasis-suppressive role of miR-520/373 family. miR-520c and miR-373 abrogated both in vitro cell invasion and in vivo intravasation of highly invasive MDA-MB-231 cells. However, knockdown of RELA did not affect their metastatic ability. mRNA profiling of MDA-MB-231 cells on overexpression of miR-520/373 members revealed a strong downregulation of transforming growth factor-β (TGF-β) signaling. Mechanistically, the metastasis-suppressive role of miR-520/373 can be attributed to direct suppression of TGFBR2, as the silencing of TGFBR2 phenocopied the effects of miR-520/373 overexpression on suppression of Smad-dependent expression of the metastasis-promoting genes parathyroid hormone-related protein, plasminogen activator inhibitor-1 and angiopoietin-like 4 as well as tumor cell invasion, in vitro and in vivo. A negative correlation between miR-520c and TGFBR2 expression was observed in estrogen receptor negative (ER(-)) breast cancer patients but not in the ER positive (ER(+)) subtype. Remarkably, decreased expression of miR-520c correlated with lymph node metastasis specifically in ER(-) tumors. Taken together, our findings reveal that miR-520/373 family has a tumor-suppressive role in ER(-) breast cancer by acting as a link between the NF-κB and TGF-β pathways and may thus contribute to the interplay of tumor progression, metastasis and inflammation.
Sensory signs in complex regional pain syndrome and peripheral nerve injury
2011-12-12

This study determined patterns of sensory signs in complex regional pain syndrome (CRPS) type I and II and peripheral nerve injury (PNI). Patients with upper-limb CRPS-I (n=298), CRPS-II (n=46), and PNI (n=72) were examined with quantitative sensory testing according to the protocol of the German Research Network on Neuropathic Pain. The majority of patients (66%-69%) exhibited a combination of sensory loss and gain. Patients with CRPS-I had more sensory gain (heat and pressure pain) and less sensory loss than patients with PNI (thermal and mechanical detection, hypoalgesia to heat or pinprick). CRPS-II patients shared features of CRPS-I and PNI. CRPS-I and CRPS-II had almost identical somatosensory profiles, with the exception of a stronger loss of mechanical detection in CRPS-II. In CRPS-I and -II, cold hyperalgesia/allodynia (28%-31%) and dynamic mechanical allodynia (24%-28%) were less frequent than heat or pressure hyperalgesia (36%-44%, 67%-73%), and mechanical hypoesthesia (31%-55%) was more frequent than thermal hypoesthesia (30%-44%). About 82% of PNI patients had at least one type of sensory gain. QST demonstrates more sensory loss in CRPS-I than hitherto considered, suggesting either minimal nerve injury or central inhibition. Sensory profiles suggest that CRPS-I and CRPS-II may represent one disease continuum. However, in contrast to recent suggestions, small fiber deficits were less frequent than large fiber deficits. Sensory gain is highly prevalent in PNI, indicating a better similarity of animal models to human patients than previously thought. These sensory profiles should help prioritize approaches for translation between animal and human research.
Efficient inference in matrix-variate Gaussian models with iid observation noise
2011-12-12

Inference in matrix-variate Gaussian models has major applications for multi-output prediction and joint learning of row and column covariances from matrix-variate data. Here, we discuss an approach for efficient inference in such models that explicitly account for iid observation noise. Computational tractability can be retained by exploiting the Kronecker product between row and column covariance matrices. Using this framework, we show how to generalize the Graphical Lasso in order to learn a sparse inverse covariance between features while accounting for a low-rank confounding covariance between samples. We show practical utility on applications to biology, where we model covariances with more than 100,000 di-mensions. We find greater accuracy in recovering biological network structures and are able to better reconstruct the confounders. 1
Results of the 2nd Scientific Workshop of the ECCO (III): Basic mechanisms of intestinal healing
2011-12-12

Abstract The second scientific workshop of the European Crohn's and Colitis Organization (ECCO) focused on the relevance of intestinal healing for the disease course of inflammatory bowel disease (IBD). The objective was to better understand basic mechanisms, markers for disease prediction, detection and monitoring of intestinal healing, impact of intestinal healing on the disease course of IBD as well as therapeutic strategies. The results of this workshop are presented in four separate manuscripts. This section describes basic mechanisms of intestinal healing, identifies open questions in the field and provides a framework for future studies.
Quantitative in vivo diffusion imaging of cartilage using double echo steady‐state free precession
2011-12-12

Abstract Single‐shot echo‐planar imaging techniques are commonly used for diffusion‐weighted imaging (DWI) but offer rather poor spatial resolution and field‐of‐view coverage for species with short T 2 . In contrast, steady‐state free precession (SSFP) has shown promising results for DWI of the musculoskeletal system, but quantification is generally hampered by its prominent sensitivity on relaxation times. In this work, a new and truly diffusion‐weighted (that is relaxation time independent) SSFP DWI technique is introduced using a double‐echo steady‐state approach. Within this framework (and this is in contrast to common SSFP DWI techniques using SSFP‐Echo) both primary echo paths of nonbalanced SSFP are acquired, namely the FID and the Echo. Simulations and in vitro measurements reveal that the ratio of the Echo/FID signal ratios of two double‐echo steady‐state scans acquired with and without diffusion sensitizing dephasing moments provides a highly relaxation independent quantity for diffusion quantification. As a result, relaxation‐independent high‐resolution (0.4 × 0.4 − 0.6 × 0.6 mm 2 in‐plane resolution) quantitative in vivo SSFP DWI is demonstrated for human articular cartilage using diffusion‐weighted double‐echo steady‐state scans in the knee and ankle joint at 3.0 T. The derived diffusion coefficients for cartilage ( D ∼ 1.0–1.5 μm 2 /ms) and synovial fluid ( D ∼ 2.6 μm 2 /ms) are in agreement with previous work. Magn Reson Med, 2012. © 2011 Wiley Periodicals, Inc.
A clustering optimization strategy to estimate species richness of Sebacinales in the tropical Andes based on molecular sequences from distinct DNA regions
2011-12-12

Fungi are believed to be diverse in the tropics, but because many groups are only known from their DNA sequences this hampers comparative diversity studies. We investigated mycorrhizal Sebacinales (Basidiomycota) of 67 individuals of Ericaceae and Orchidaceae in a tropical mountain ecosystem in Southern Ecuador to provide a first estimate of whether these fungi are particularly diverse in the Northern Andes. We partially sequenced the internal transcribed spacer (ITS) and large subunit (LSU) regions of the nuclear ribosomal DNA and analyzed them together with all Sebacinales sequences available from GenBank. The clustering optimization technique was used to determine clustering parameters that maximize the comparability between molecular operational taxonomic units (MOTUs) obtained from the distinct loci. Sampling effort and species richness were estimated with rarefaction-accumulation curves and non-parametric estimation using Chao2 and compared between Southern Ecuador and France. Clustering optimization indicated that a 1% LSU distance threshold corresponds to the commonly used 3% dissimilarity threshold for ITS, and that a clustering algorithm close to single-linkage clustering is optimal. The resulting clusters show that about 8-9% of observed Sebacinales MOTUs occur in the study area and that most of these MOTUs are endemic (74%). The widespread MOTUs from Southern Ecuador were also found in Panama, North America and Europe. The estimation of species richness revealed unsaturated sampling of Sebacinales in general and also in our study area. Our results suggest a high diversity of Sebacinales associated with Ericaceae and Orchidaceae at the study site in Southern Ecuador, but no hotspot of Sebacinales in comparison with other areas. © 2011 Springer Science+Business Media B.V.
Response-level probability effects on reaction time: Now you see them, now you don't
2011-12-12

Many reaction time (RT) experiments have tested for response-level probability effects. Their results have been mixed, which is surprising because psychophysiological studies provide clear evidence of motor-level changes associated with an anticipated response. A survey of the designs used in the RT studies reveals many potential problems that could conceal the effects of response probability. We report five new RT experiments testing for response-level probability effects with the most promising of the previous designs—that of Blackman (1972)—and with new designs. Some of these experiments yield evidence of response-level probability effects, but others do not. It appears that response-level probability effects are present primarily in simple tasks with a strong emphasis on response preparation, possibly because participants only expend effort on response preparation in these tasks.