julilili42/papers huggingface dataset:
Viability and MR detectability of iron labeled mesenchymal stem cells used for endoscopic injection into the porcine urethral sphincter
2015-07-05

Direct stem cell therapies for functionally impaired tissue require a sufficient number of cells in the target region and a method for verifying the fate of the cells in the subsequent time course. In vivo MRI of iron labeled mesenchymal stem cells has been suggested to comply with these requirements. The study was conducted to evaluate proliferation, migration, differentiation and adhesion effects as well as the obtained iron load of an iron labeling strategy for mesenchymal stem cells. After injection into the porcine urethral sphincter, the labeled cells were monitored for up to six months using MRI. Mesenchymal stem cells were labeled with ferucarbotran (60/100/200 μg/mL) and ferumoxide (200 μg/mL) for the analysis of migration and viability. Phantom MR measurements were made to evaluate effects of iron labeling. For short and long term studies, the iron labeled cells were injected into the porcine urethral sphincter and monitored by MRI. High resolution anatomical images of the porcine urethral sphincter were applied for detection of the iron particles with a turbo‐spin‐echo sequence and a gradient‐echo sequence with multiple T E values. The MR images were then compared with histological staining. The analysis of cell function after iron labeling showed no effects on proliferation or differentiation of the cells. Although the adherence increases with higher iron dose, the ability to migrate decreases as a presumed effect of iron labeling. The iron labeled mesenchymal stem cells were detectable in vivo in MRI and histological staining even six months after injection. Labeling with iron particles and subsequent evaluation with highly resolved three dimensional data acquisition allows sensitive tracking of cells injected into the porcine urethral sphincter for several months without substantial biological effects on mesenchymal stem cells. Copyright © 2015 John Wiley &amp; Sons, Ltd.
Retention Time Prediction Improves Identification in Nontargeted Lipidomics Approaches
2015-07-06

Identification of lipids in nontargeted lipidomics based on liquid-chromatography coupled to mass spectrometry (LC-MS) is still a major issue. While both accurate mass and fragment spectra contain valuable information, retention time (tR) information can be used to augment this data. We present a retention time model based on machine learning approaches which enables an improved assignment of lipid structures and automated annotation of lipidomics data. In contrast to common approaches we used a complex mixture of 201 lipids originating from fat tissue instead of a standard mixture to train a support vector regression (SVR) model including molecular structural features. The cross-validated model achieves a correlation coefficient between predicted and experimental test sample retention times of r = 0.989. Combining our retention time model with identification via accurate mass search (AMS) of lipids against the comprehensive LIPID MAPS database, retention time filtering can significantly reduce the rate of false positives in complex data sets like adipose tissue extracts. In our case, filtering with retention time information removed more than half of the potential identifications, while retaining 95% of the correct identifications. Combination of high-precision retention time prediction and accurate mass can thus significantly narrow down the number of hypotheses to be assessed for lipid identification in complex lipid pattern like tissue profiles.
Occult Hepatitis B Virus Infection in Nigerian Blood Donors and Hepatitis B Virus Transmission Risks
2015-07-06

High incidence of OBI is relevant in high endemic areas worldwide and is a general burden in blood safety. This study signifies the high prevalence of OBI and proposes blood donor samples in Nigeria should be pre-tested for OBI by nucleic acid testing (NAT) and/or anti-HBc prior to transfusion to minimize the HBV infection risk.
Interlaboratory study to evaluate the robustness of capillary electrophoresis‐mass spectrometry for peptide mapping
2015-07-06

A collaborative study on the robustness and portability of a capillary electrophoresis‐mass spectrometry method for peptide mapping was performed by an international team, consisting of 13 independent laboratories from academia and industry. All participants used the same batch of samples, reagents and coated capillaries to run their assays, whereas they utilized the capillary electrophoresis‐mass spectrometry equipment available in their laboratories. The equipment used varied in model, type and instrument manufacturer. Furthermore, different types of sheath‐flow capillary electrophoresis–mass spectrometry interfaces were used. Migration time, peak height and peak area of ten representative target peptides of trypsin‐digested bovine serum albumin were determined by every laboratory on two consecutive days. The data were critically evaluated to identify outliers and final values for means, repeatability (precision within a laboratory) and reproducibility (precision between laboratories) were established. For relative migration time the repeatability was between 0.05 and 0.18% RSD and the reproducibility between 0.14 and 1.3% RSD. For relative peak area repeatability and reproducibility values obtained were 3–12 and 9–29% RSD, respectively. These results demonstrate that capillary electrophoresis‐mass spectrometry is robust enough to allow a method transfer across multiple laboratories and should promote a more widespread use of peptide mapping and other capillary electrophoresis‐mass spectrometry applications in biopharmaceutical analysis and related fields.
Impella 5.0 Support in INTERMACS II Cardiogenic Shock Patients Using Right and Left Axillary Artery Access
2015-07-06

Abstract The catheter‐based I mpella 5.0 left ventricular assist device ( LVAD ) is a powerful and less invasive alternative for patients in cardiogenic shock. The use of this device as a primary mechanical circulatory support strategy in INTERMACS II patients should be evaluated. From A pril 2014 to A ugust 2014, eight Impella 5.0 devices were implanted in seven patients via the axillary artery access (six right and two left). We analyzed the outcome of the four patients in whom the I mpella 5.0 device was implanted for the purpose of primary stabilization of cardiogenic shock ( INTERMACS II ). The remaining three patients had a contraindication for a permanent LVAD and received the device for prolonged weaning from extracorporeal life support (ECLS) system. The implantation of the I mpella 5.0 was technically successful in all patients and resulted in the stabilization of the clinical situation. All four patients could be bridged to a long‐term device ( n = 3) or to cardiac recovery ( n = 1). In one patient, 2 days of ECLS support was necessary because of pump thrombosis after 31 days of Impella 5.0 support. One patient with bronchopneumonia had the Impella 5.0 exchanged from the right to the left axillary artery after 22 days of support because of the progressive loss of purge flow and the need for longer bridging to a permanent LVAD . The last patient was supported for giant‐cell myocarditis for 22 days and bridged to cardiac recovery. All patients were transferred to the intensive care unit with the I mpella device in place. In INTERMACS II situations, the implantation of the I mpella 5.0 via the right or left axillary access allowed additional time for decision making. Early patient mobilization, including walking with the Impella device in place, optimized the conditions for either weaning or the implantation of a permanent LVAD . This novel technique of left axillary approach leads to more flexibility in the case of anatomical‐ or device‐related contraindications to right‐side access, or when the device needs to be exchanged while continuous support is necessary.
Stronger Neural Modulation by Visual Motion Intensity in Autism Spectrum Disorders
2015-07-06

Theories of autism spectrum disorders (ASD) have focused on altered perceptual integration of sensory features as a possible core deficit. Yet, there is little understanding of the neuronal processing of elementary sensory features in ASD. For typically developed individuals, we previously established a direct link between frequency-specific neural activity and the intensity of a specific sensory feature: Gamma-band activity in the visual cortex increased approximately linearly with the strength of visual motion. Using magnetoencephalography (MEG), we investigated whether in individuals with ASD neural activity reflect the coherence, and thus intensity, of visual motion in a similar fashion. Thirteen adult participants with ASD and 14 control participants performed a motion direction discrimination task with increasing levels of motion coherence. A polynomial regression analysis revealed that gamma-band power increased significantly stronger with motion coherence in ASD compared to controls, suggesting excessive visual activation with increasing stimulus intensity originating from motion-responsive visual areas V3, V6 and hMT/V5. Enhanced neural responses with increasing stimulus intensity suggest an enhanced response gain in ASD. Response gain is controlled by excitatory-inhibitory interactions, which also drive high-frequency oscillations in the gamma-band. Thus, our data suggest that a disturbed excitatory-inhibitory balance underlies enhanced neural responses to coherent motion in ASD.
Embodied learning of a generative neural model for biological motion perception and inference
2015-07-06

Although an action observation network and mirror neurons for understanding the actions and intentions of others have been under deep, interdisciplinary consideration over recent years, it remains largely unknown how the brain manages to map visually perceived biological motion of others onto its own motor system. This paper shows how such a mapping may be established, even if the biologically motion is visually perceived from a new vantage point. We introduce a learning artificial neural network model and evaluate it on full body motion tracking recordings. The model implements an embodied, predictive inference approach. It first learns to correlate and segment multimodal sensory streams of own bodily motion. In doing so, it becomes able to anticipate motion progression, to complete missing modal information, and to self-generate learned motion sequences. When biological motion of another person is observed, this self-knowledge is utilized to recognize similar motion patterns and predict their progress. Due to the relative encodings, the model shows strong robustness in recognition despite observing rather large varieties of body morphology and posture dynamics. By additionally equipping the model with the capability to rotate its visual frame of reference, it is able to deduce the visual perspective onto the observed person, establishing full consistency to the embodied self-motion encodings by means of active inference. In further support of its neuro-cognitive plausibility, we also model typical bistable perceptions when crucial depth information is missing. In sum, the introduced neural model proposes a solution to the problem of how the human brain may establish correspondence between observed bodily motion and its own motor system, thus offering a mechanism that supports the development of mirror neurons.
Network Modeling for Functional Magnetic Resonance Imaging (fMRI) Signals during Ultra-Fast Speech Comprehension in Late-Blind Listeners
2015-07-06

In many functional magnetic resonance imaging (fMRI) studies blind humans were found to show cross-modal reorganization engaging the visual system in non-visual tasks. For example, blind people can manage to understand (synthetic) spoken language at very high speaking rates up to ca. 20 syllables/s (syl/s). FMRI data showed that hemodynamic activation within right-hemispheric primary visual cortex (V1), bilateral pulvinar (Pv), and left-hemispheric supplementary motor area (pre-SMA) covaried with their capability of ultra-fast speech (16 syllables/s) comprehension. It has been suggested that right V1 plays an important role with respect to the perception of ultra-fast speech features, particularly the detection of syllable onsets. Furthermore, left pre-SMA seems to be an interface between these syllabic representations and the frontal speech processing and working memory network. So far, little is known about the networks linking V1 to Pv, auditory cortex (A1), and (mesio-) frontal areas. Dynamic causal modeling (DCM) was applied to investigate (i) the input structure from A1 and Pv toward right V1 and (ii) output from right V1 and A1 to left pre-SMA. As concerns the input Pv was significantly connected to V1, in addition to A1, in blind participants, but not in sighted controls. Regarding the output V1 was significantly connected to pre-SMA in blind individuals, and the strength of V1-SMA connectivity correlated with the performance of ultra-fast speech comprehension. By contrast, in sighted controls, not understanding ultra-fast speech, pre-SMA did neither receive input from A1 nor V1. Taken together, right V1 might facilitate the "parsing" of the ultra-fast speech stream in blind subjects by receiving subcortical auditory input via the Pv (= secondary visual pathway) and transmitting this information toward contralateral pre-SMA.
Prevalence and risk factors associated with colonization and infection of extensively drug-resistantPseudomonas aeruginosa: a systematic review
2015-07-07

Pseudomonas aeruginosa is a Gram-negative human pathogen with extensively drug-resistant (XDR) strains emerging in hospitals across the globe. This systematic review is focused on the worldwide prevalence of XDR P. aeruginosa (XDR-PA) and on the risk factors associated with its colonization and infection, based on literature available through PubMed, Web of Science and BioMed Central databases. An overview of surveillance systems is provided as well as a synopsis on the prevalence of XDR-PA, showing an increase in recent reports. Risk factors independently associated with XDR-PA colonization or infections are described in four groups with reference to antimicrobial therapy, medical devices as well as patient- and hospital environment-related factors.
Genome mining and metabolic profiling of the rhizosphere bacterium Pseudomonas sp. SH-C52 for antimicrobial compounds
2015-07-07

The plant microbiome represents an enormous untapped resource for discovering novel genes and bioactive compounds. Previously, we isolated Pseudomonas sp. SH-C52 from the rhizosphere of sugar beet plants grown in a soil suppressive to the fungal pathogen Rhizoctonia solani and showed that its antifungal activity is, in part, attributed to the production of the chlorinated 9-amino-acid lipopeptide thanamycin (Mendes et al., 2011). To get more insight into its biosynthetic repertoire, the genome of Pseudomonas sp. SH-C52 was sequenced and subjected to in silico, mutational and functional analyses. The sequencing revealed a genome size of 6.3 Mb and 5579 predicted ORFs. Phylogenetic analysis placed strain SH-C52 within the Pseudomonas corrugata clade. In silico analysis for secondary metabolites revealed a total of six non-ribosomal peptide synthetase (NRPS) gene clusters, including the two previously described NRPS clusters for thanamycin and the 2-amino acid antibacterial lipopeptide brabantamide. Here we show that thanamycin also has activity against an array of other fungi and that brabantamide A exhibits anti-oomycete activity and affects phospholipases of the late blight pathogen Phytophthora infestans. Most notably, mass spectrometry led to the discovery of a third lipopeptide, designated thanapeptin, with a 22-amino-acid peptide moiety. Seven structural variants of thanapeptin were found with varying degrees of activity against P. infestans. Of the remaining four NRPS clusters, one was predicted to encode for yet another and unknown lipopeptide with a predicted peptide moiety of 8-amino acids. Collectively, these results show an enormous metabolic potential for Pseudomonas sp. SH-C52, with at least three structurally diverse lipopeptides, each with a different antimicrobial activity spectrum.
Case report of a patient with progressive multifocal leukoencephalopathy under treatment with dimethyl fumarate
2015-07-07

Progressive multifocal leukoencephalopathy can occur in patients with lymphocyte counts between 450 and 700/μl, produce only faint symptoms and is not excluded by negative JC-virus-polymerase chain reaction in cerebrospinal fluid. The incidence of progressive multifocal leukoencephalopathy may thus be underestimated and a more careful surveillance of patients would be necessary.
Genome-Wide Screens in Saccharomyces cerevisiae Highlight a Role for Cardiolipin in Biogenesis of Mitochondrial Outer Membrane Multispan Proteins
2015-07-07

A special group of mitochondrial outer membrane (MOM) proteins spans the membrane several times via multiple helical segments. Such multispan proteins are synthesized on cytosolic ribosomes before their targeting to mitochondria and insertion into the MOM. Previous work recognized the import receptor Tom70 and the mitochondrial import (MIM) complex, both residents of the MOM, as required for optimal biogenesis of these proteins. However, their involvement is not sufficient to explain either the entire import pathway or its regulation. To identify additional factors that are involved in the biogenesis of MOM multispan proteins, we performed complementary high-throughput visual and growth screens in Saccharomyces cerevisiae. Cardiolipin (CL) synthase (Crd1) appeared as a candidate in both screens. Our results indeed demonstrate lower steady-state levels of the multispan proteins Ugo1, Scm4, and Om14 in mitochondria from crd1Δ cells. Importantly, MOM single-span proteins were not affected by this mutation. Furthermore, organelles lacking Crd1 had a lower in vitro capacity to import newly synthesized Ugo1 and Scm4 molecules. Crd1, which is located in the mitochondrial inner membrane, condenses phosphatidylglycerol together with CDP-diacylglycerol to obtain de novo synthesized CL molecules. Hence, our findings suggest that CL is an important component in the biogenesis of MOM multispan proteins.
Coherent averaging
2015-07-07

We investigate in detail a recently introduced “coherent averaging scheme” in terms of its usefulness for achieving Heisenberg limited sensitivity in the measurement of different parameters. In the scheme, N quantum probes in a product state interact with a quantum bus. Instead of measuring the probes directly and then averaging as in classical averaging, one measures the quantum bus or the entire system and tries to estimate the parameters from these measurement results. Combining analytical results from perturbation theory and an exactly solvable dephasing model with numerical simulations, we draw a detailed picture of the scaling of the best achievable sensitivity with N , the dependence on the initial state, the interaction strength, the part of the system measured, and the parameter under investigation. In particular, we identify the situations allowing one to reach Heisenberg‐limited scaling of the sensitivity.
Learning from heterogeneous data sources: an application in spatial proteomics
2015-07-07

Abstract Sub-cellular localisation of proteins is an essential post-translational regulatory mechanism that can be assayed using high-throughput mass spectrometry (MS). These MS-based spatial proteomics experiments enable us to pinpoint the sub-cellular distribution of thousands of proteins in a specific system under controlled conditions. Recent advances in high-throughput MS methods have yielded a plethora of experimental spatial proteomics data for the cell biology community. Yet, there are many third-party data sources, such as immunofluorescence microscopy or protein annotations and sequences, which represent a rich and vast source of complementary information. We present a unique transfer learning classification framework that utilises a nearest-neighbour or support vector machine system, to integrate heterogeneous data sources to considerably improve on the quantity and quality of sub-cellular protein assignment. We demonstrate the utility of our algorithms through evaluation of five experimental datasets, from four different species in conjunction with four different auxiliary data sources to classify proteins to tens of sub-cellular compartments with high generalisation accuracy. We further apply the method to an experiment on pluripotent mouse embryonic stem cells to classify a set of previously unknown proteins, and validate our findings against a recent high resolution map of the mouse stem cell proteome. The methodology is distributed as part of the open-source Bioconductor pRoloc suite for spatial proteomics data analysis. Abbreviations LOPIT Localisation of Organelle Proteins by Isotope Tagging PCP Protein Correlation Profiling ML Machine learning TL Transfer learning SVM Support vector machine PCA Principal component analysis GO Gene Ontology CC Cellular compartment iTRAQ Isobaric tags for relative and absolute quantitation TMT Tandem mass tags MS Mass spectrometry
Grating enhanced apertureless near-field optical microscopy
2015-07-07

We examine the possibility of optimizing the emission and the near-field signal of apertureless silver and gold tips by using an optimized non-periodic grating. In this context, we consider the emission of a single quantum emitter in close proximity to optimized tips. Additionally, we study the far-field coupling efficiency of a tightly focused beam to the near-field of the tip. The gain in performance is compared with unstructured tips and the comparison with a pure plasmonic excitation of an unstructured tip is discussed. The optimized, structured tips show a significant enhancement of the total decay rate, as a result of standing plasmonic waves between the grating and the tip apex, leading to a resonant behavior. The resonances can be explained well with a Fabry-Pérot model. Furthermore, the total decay rate of an emitter near a structured tip can also be decreased as compared to an unstructured tip, when the grating is shifted from the optimal resonant position. The proposed scheme represents an interesting novel nano-antenna, for which the resonance as well as the directivity can be controlled by the grating.
Paternally InheritedIGF2Mutation and Growth Restriction
2015-07-08

In humans, mutations in IGF1 or IGF1R cause intrauterine and postnatal growth restriction; however, data on mutations in IGF2, encoding insulin-like growth factor (IGF) II, are lacking. We report an IGF2 variant (c.191C→A, p.Ser64Ter) with evidence of pathogenicity in a multigenerational family with four members who have growth restriction. The phenotype affects only family members who have inherited the variant through paternal transmission, a finding that is consistent with the maternal imprinting status of IGF2. The severe growth restriction in affected family members suggests that IGF-II affects postnatal growth in addition to prenatal growth. Furthermore, the dysmorphic features of affected family members are consistent with a role of deficient IGF-II levels in the cause of the Silver-Russell syndrome. (Funded by Bundesministerium für Bildung und Forschung and the European Union.).