bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pan-Renal Cell Carcinoma classification and survival prediction from histopathology images using deep learning
Authors: Tabibu Sairam , Vinod P. K. , Jawahar C. V. 
Published: July 2019

AbstractHistopathological images contain morphological markers of disease progression that have diagnostic and predictive values. In this study, we demonstrate how deep learning framework can be used for an automatic classification of Renal Cell Carcinoma (RCC) subtypes, and for identification of features that predict survival outcome from digital histopathological images. Convolutional neural networks (CNN’s) trained on whole-slide images distinguish clear cell and chromophobe RCC from normal tissue with a classification accuracy of 93.39% and 87.34%, respectively. Further, a CNN trained to distinguish clear cell, chromophobe and papillary RCC achieves a classification accuracy of 94.07%. Here, we introduced a novel support vector machine-based method that helped to break the multi-class classification task into multiple binary classification tasks which not only improved the performance of the model but also helped to deal with data imbalance. Finally, we extracted the morphological features from high probability tumor regions identified by the CNN to predict patient survival outcome of most common clear cell RCC. The generated risk index based on both tumor shape and nuclei features are significantly associated with patient survival outcome. These results highlight that deep learning can play a role in both cancer diagnosis and prognosis.
Study on intracellular delivery of liposome encapsulated quantum dots using advanced fluorescence microscopy
Authors: Bruun Kristina , Hille Carsten 
Published: July 2019

AbstractQuantum dots increasingly gain popularity for in vivo applications. However, their delivery and accumulation into cells can be challenging and there is still lack of detailed information. Thereby, the application of advanced fluorescence techniques can expand the portfolio of useful parameters for a more comprehensive evaluation. Here, we encapsulated hydrophilic quantum dots into liposomes for studying cellular uptake of these so-called lipodots into living cells. First, we investigated photophysical properties of free quantum dots and lipodots observing changes in the fluorescence decay time and translational diffusion behaviour. In comparison to empty liposomes, lipodots exhibited an altered zeta potential, whereas their hydrodynamic size did not change. Fluorescence lifetime imaging microscopy (FLIM) and fluorescence correlation spectroscopy (FCS), both combined with two-photon excitation (2P), were used to investigate the interaction behaviour of lipodots with an insect epithelial tissue. In contrast to the application of free quantum dots, their successful delivery into the cytosol of salivary gland duct cells could be observed when applying lipodots. Lipodots with different lipid compositions and surface charges did not result in considerable differences in the intracellular labelling pattern, luminescence decay time and diffusion behaviour. However, quantum dot degradation after intracellular accumulation could be assumed from reduced luminescence decay times and blue-shifted luminescence signals. In addition to single diffusing quantum dots, possible intracellular clustering of quantum dots could be assumed from increased diffusion times. Thus, by using a simple and manageable liposome carrier system, 2P-FLIM and 2P-FCS recording protocols could be tested, which are promising for investigating the fate of quantum dots during cellular interaction.
Temperature dependent persistent luminescence: Evaluating the optimum working temperature
Authors: Du Jiaren , De Clercq Olivier Q. , Poelman Dirk 
Published: July 2019

AbstractDevelopment of persistent luminescent materials has drawn continuous attention in recent years in view of their potential applications in the fields of security night-vision signage, in vivo bio-imaging and optical data storage. Currently, the normative evaluation of a new persistent luminescent material is focused on the light emission spectrum, the afterglow decay curve and the total duration time of the persistent luminescence. In this paper, we investigate the temperature dependent persistent luminescence in some well-known persistent phosphors and relate this to their thermoluminescence properties. The concept of the optimum working temperature is proposed as a new means for evaluating persistent phosphors. It is shown that there is a clear relation between the efficient temperature range of the afterglow output and the thermoluminescence glow curve. The experimental work is supported by simulations of thermoluminescence and afterglow characteristics. The concept of the optimum working temperature for persistent phosphors can be used as an evaluative criterion for applications in various working environments.
Studying hydrogen bonding and dynamics of the acetylate groups of the Special Pair of Rhodobacter sphaeroides WT
Authors: Gräsing Daniel , Dziubińska-Kühn Katarzyna M. , Zahn Stefan , Alia A. , Matysik Jörg 
Published: July 2019

AbstractAlthough the cofactors in the bacterial reaction centre of Rhodobacter sphaeroides wild type (WT) are arranged almost symmetrically in two branches, the light-induced electron transfer occurs selectively in one branch. As origin of this functional symmetry break, a hydrogen bond between the acetyl group of PL in the primary donor and His-L168 has been discussed. In this study, we investigate the existence and rigidity of this hydrogen bond with solid-state photo-CIDNP MAS NMR methods offering information on the local electronic structure due to highly sensitive and selective NMR experiments. On the time scale of the experiment, the hydrogen bond between PL and His-L168 appears to be stable and not to be affected by illumination confirming a structural asymmetry within the Special Pair.
Distinct epigenetic profiles in children with perinatally-acquired HIV on antiretroviral therapy
Authors: Shiau Stephanie , Strehlau Renate , Wang Shuang , Violari Avy , Do Catherine , Patel Faeezah , Liberty Afaaf , Krupska Izabela , Arpadi Stephen M. , Foca Marc , Coovadia Ashraf , Abrams Elaine J. , Tycko Benjamin , Terry Mary Beth , Kuhn Louise 
Published: July 2019

AbstractPerinatally-acquired HIV has persistent effects on long-term health outcomes, even after early treatment. We hypothesize that epigenetic indicators, such as DNA methylation, may elucidate cellular processes that explain these effects. Here, we compared DNA methylation profiles in whole blood from 120 HIV-infected children on antiretroviral therapy (ART) and 60 frequency age-matched HIV-uninfected children aged 4–9 years in Johannesburg, South Africa. Using an individual CpG site approach, we found 1,309 differentially-methylated (DM) CpG sites between groups, including 1,271 CpG sites that were hyper-methylated in the HIV-infected group and 38 CpG sites that were hypo-methylated in the HIV-infected group. Six hyper-methylated CpG sites were inEBF4, which codes for a transcription factor involved in B-cell maturation. The top hypomethylated site was in the promoter region ofNLRC5, encoding a transcription factor that regulates major histocompatibility complex (MHC) class I molecule expression. Using a differentially-methylated region (DMR) approach, we found 315 DMRs between groups, including 28 regions encompassing 686 CpG sites on chromosome 6. A large number of the genes identified in both the CpG site and DMR approaches were located in the MHC region on chromosome 6, which plays an important role in the adaptive immune system. This study provides the first evidence that changes in the epigenome are detectable in children with perinatally-acquired HIV infection on suppressive ART started at an early age.
Ancient origins of low lean mass among South Asians and implications for modern type 2 diabetes susceptibility
Authors: Pomeroy Emma , Mushrif-Tripathy Veena , Cole Tim J. , Wells Jonathan C. K. , Stock Jay T. 
Published: July 2019

AbstractLiving South Asians have low lean tissue mass relative to height, which contributes to their elevated type 2 diabetes susceptibility, particularly when accompanied by obesity. While ongoing lifestyle transitions account for rising obesity, the origins of low lean mass remain unclear. We analysed proxies for lean mass and stature among South Asian skeletons spanning the last 11,000 years (n = 197) to investigate the origins of South Asian low lean mass. Compared with a worldwide sample (n = 2,003), South Asian skeletons indicate low lean mass. Stature-adjusted lean mass increased significantly over time in South Asia, but to a very minor extent (0.04 z-score units per 1,000 years, adjusted R2 = 0.01). In contrast stature decreased sharply when agriculture was adopted. Our results indicate that low lean mass has characterised South Asians since at least the early Holocene and may represent long-term climatic adaptation or neutral variation. This phenotype is therefore unlikely to change extensively in the short term, so other strategies to address increasing non-communicable disease rates must be pursued.
Analysis of lncRNA-miRNA-mRNA Interactions in Hyper-proliferative Human Pulmonary Arterial Smooth Muscle Cells
Authors: Chinnappan Mahendran , Gunewardena Sumedha , Chalise Prabhakar , Dhillon Navneet K. 
Published: July 2019

AbstractWe previously reported enhanced proliferation of smooth muscle cells on the combined exposure of HIV proteins and cocaine leading to the development of HIV-pulmonary arterial hypertension. Here, we attempt to comprehensively understand the interactions between long noncoding RNAs (lncRNAs), mRNAs and micro-RNAs (miRNAs) to determine their role in smooth muscle hyperplasia. Differential expression of lncRNAs, mRNAs and miRNAs were obtained by microarray and small-RNA sequencing from HPASMCs treated with and without cocaine and/or HIV-Tat. LncRNA to mRNA associations were conjectured by analyzing their genomic proximity and by interrogating their association to vascular diseases and cancer co-expression patterns reported in the relevant databases. Neuro-active ligand receptor signaling, Ras signaling and PI3-Akt pathway were among the top pathways enriched in either differentially expressed mRNAs or mRNAs associated to lncRNAs. HPASMC with combined exposure to cocaine and Tat (C + T) vs control identified the following top lncRNA-mRNA pairs, ENST00000495536-HOXB13, T216482-CBL, ENST00000602736-GDF7, and, TCONS_00020413-RND1. Many of the down-regulated miRNAs in the HPASMCs treated with C + T were found to be anti-proliferative and targets of up-regulated lncRNAs targeting up-regulated mRNAs, including down-regulation of miR-185, -491 and up-regulation of corresponding ENST00000585387. Specific knock down of the selected lncRNAs highlighted the importance of non-coding RNAs in smooth muscle hyperplasia.
A zebrafish drug screening platform boosts the discovery of novel therapeutics for spinal cord injury in mammals
Authors: Chapela Diana , Sousa Sara , Martins Isaura , Cristóvão Ana Margarida , Pinto Patrícia , Corte-Real Sofia , Saúde Leonor 
Published: July 2019

AbstractSpinal cord injury (SCI) is a complex condition, with limited therapeutic options, that results in sensory and motor disabilities. To boost discovery of novel therapeutics, we designed a simple and efficient drug screening platform. This innovative approach allows to determine locomotor rescue properties of small molecules in a zebrafish (Danio rerio) larval spinal cord transection model. We validated our screening platform by showing that Riluzole and Minocycline, two molecules that are in clinical trials for SCI, promote rescue of the locomotor function of the transected larvae. Further validation of the platform was obtained through the blind identification of D-Cycloserine, a molecule scheduled to enter phase IV clinical trials for SCI. Importantly, we identified Tranexamic acid and further showed that this molecule maintains its locomotor recovery properties in a rodent female contusion model. Our screening platform, combined with drug repurposing, promises to propel the rapid translation of novel therapeutics to improve SCI recovery in humans.
SMAC, a computational system to link literature, biomedical and expression data
Authors: Pirrò Stefano , Gadaleta Emanuela , Galgani Andrea , Colizzi Vittorio , Chelala Claude 
Published: July 2019

AbstractHigh-throughput technologies have produced a large amount of experimental and biomedical data creating an urgent need for comprehensive and automated mining approaches. To meet this need, we developed SMAC (SMart Automatic Classification method): a tool to extract, prioritise, integrate and analyse biomedical and molecular data according to user-defined terms. The robust ranking step performed on Medical Subject Headings (MeSH) ensures that papers are prioritised based on specific user requirements. SMAC then retrieves any related molecular data from the Gene Expression Omnibus and performs a wide range of bioinformatics analyses to extract biological insights. These features make SMAC a robust tool to explore the literature around any biomedical topic. SMAC can easily be customised/expanded and is distributed as a Docker container (https://hub.docker.com/r/hfx320/smac) ready-to-use on Windows, Mac and Linux OS. SMAC’s functionalities have already been adapted and integrated into the Breast Cancer Now Tissue Bank bioinformatics platform and the Pancreatic Expression Database.
Stumbling reactions in hypo and hyper gravity – muscle synergies are robust across different perturbations of human stance during parabolic flights
Authors: Holubarsch Janek , Helm Michael , Ringhof Steffen , Gollhofer Albert , Freyler Kathrin , Ritzmann Ramona 
Published: July 2019

AbstractThe control of bipedal stance and the capacity to regain postural equilibrium after its deterioration in variable gravities are crucial prerequisites for manned space missions. With an emphasize on natural orthograde posture, computational techniques synthesize muscle activation patterns of high complexity to a simple synergy organization. We used nonnegative matrix factorization to identify muscle synergies during postural recovery responses in human and to examine the functional significance of such synergies for hyper-gravity (1.75 g) and hypo-gravity (0.25 g). Electromyographic data were recorded from leg, trunk and arm muscles of five human exposed to five modes of anterior and posterior support surface translations during parabolic flights including transitional g-levels of 0.25, 1 and 1.75 g. Results showed that in 1 g four synergies accounted for 99% of the automatic postural response across all muscles and perturbation directions. Each synergy in 1 g was correlated to the corresponding one in 0.25 and 1.75 g. This study therefore emphasizes the similarity of the synergy organization of postural recovery responses in Earth, hypo- and hyper-gravity conditions, indicating that the muscle synergies and segmental strategies acquired under terrestrial habits are robust and persistent across variable and acute changes in gravity levels.
Momentum-forbidden dark excitons in hBN-encapsulated monolayer MoS2
Authors: Uchiyama Yosuke , Kutana Alex , Watanabe Kenji , Taniguchi Takashi , Kojima Kana , Endo Takahiko , Miyata Yasumitsu , Shinohara Hisanori , Kitaura Ryo 
Published: July 2019

AbstractEncapsulation by hexagonal boron nitride (hBN) has been widely used to address intrinsic properties of two-dimensional (2D) materials. The hBN encapsulation, however, can alter properties of 2D materials through interlayer orbital hybridization. In this paper, we present measurements of temperature dependence of photoluminescence intensity from monolayer MoS2 encapsulated by hBN flakes. The obtained temperature dependence shows an opposite trend to that of previously observed in a monolayer MoS2 on a SiO2 substrate. This is caused by the existence of stable momentum-forbidden dark excitons in the hBN-encapsulated MoS2. Ab-initio band-structure calculations have shown that orbital hybridization between MoS2 and hBN leads to upward shift of Γ-valley of MoS2, which results in lowering of energy of the momentum-forbidden dark excitons. This work shows an important implication that the hBN-encapsulated structures used to address intrinsic properties of two-dimensional crystals can alter basic properties of encapsulated materials.
C2O and C3O in low-mass star-forming regions
Authors: Urso R. G. , Palumbo M. E. , Ceccarelli C. , Balucani N. , Bottinelli S. , Codella C. , Fontani F. , Leto P. , Trigilio C. , Vastel C. , Bachiller R. , Baratta G. A. , Buemi C. S. , Caux E. , Jaber Al-Edhari A. , Lefloch B. , López-Sepulcre A. , Umana G. , Testi L. 
Published: July 2019

Context.C2O and C3O belong to the carbon chain oxides family. Both molecules have been detected in the gas phase towards several star-forming regions, and to explain the observed abundances, ion-molecule gas-phase reactions have been invoked. On the other hand, laboratory experiments have shown that carbon chain oxides are formed after energetic processing of CO-rich solid mixtures. Therefore, it has been proposed that they are formed in the solid phase in dense molecular clouds after cosmic ion irradiation of CO-rich icy grain mantles and released in the gas phase after their desorption.Aims.In this work, we contribute to the understanding of the role of both gas-phase reactions and energetic processing in the formation of simple carbon chain oxides that have been searched for in various low-mass star-forming regions.Methods.We present observations obtained with the Noto-32m and IRAM-30 m telescopes towards star-forming regions. We compare these with the results of a gas-phase model that simulates C2O and C3O formation and destruction, and laboratory experiments in which both molecules are produced after energetic processing (with 200 keV protons) of icy grain mantle analogues.Results.New detections of both molecules towards L1544, L1498, and Elias 18 are reported. The adopted gas phase model is not able to reproduce the observed C2O/C3O ratios, while laboratory experiments show that the ion bombardment of CO-rich mixtures produces C2O/C3O ratios that agree with the observed values.Conclusions.Based on the results obtained here, we conclude that the synthesis of both species is due to the energetic processing of CO-rich icy grain mantles. Their subsequent desorption because of non-thermal processes allows the detection in the gas-phase of young star-forming regions. In more evolved objects, the non-detection of both C2O and C3O is due to their fast destruction in the warm gas.
Laboratory rotational spectroscopy of isotopic acetone, CH313C(O)CH3and13CH3C(O)CH3, and astronomical search in Sagittarius B2(N2)
Authors: Ordu Matthias H. , Zingsheim Oliver , Belloche Arnaud , Lewen Frank , Garrod Robin T. , Menten Karl M. , Schlemmer Stephan , Müller Holger S. P. 
Published: July 2019

Context.Spectral lines of minor isotopic species of molecules that are abundant in space may also be detectable. Their respective isotopic ratios may provide clues about the formation of these molecules. Emission lines of acetone in the hot molecular core Sagittarius B2(N2) are strong enough to warrant a search for its singly substituted13C isotopologs.Aims.We want to study the rotational spectra of CH313C(O)CH3and13CH3C(O)CH3and search for them in Sagittarius B2(N2).Methods.We investigated the laboratory rotational spectrum of isotopically enriched CH313C(O)CH3between 40 GHz and 910 GHz and of acetone between 36 GHz and 910 GHz in order to study13CH3C(O)CH3in natural isotopic composition. In addition, we searched for emission lines produced by these species in a molecular line survey of Sagittarius B2(N) carried out with the Atacama Large Millimeter/submillimeter Array (ALMA). Discrepancies between predictions of the main isotopic species and the ALMA spectrum prompted us to revisit the rotational spectrum of this isotopolog.Results.We assigned 9711 new transitions of CH313C(O)CH3and 63 new transitions of13CH3C(O)CH3in the laboratory spectra. More than 1000 additional transitions were assigned for the main isotopic species. We modeled the ground state data of all three isotopologs satisfactorily with the ERHAM program. We find that models of the torsionally excited statesv12 = 1 andv17 = 1 of CH3C(O)CH3improve only marginally. No transitrrrion of CH313C(O)CH3is clearly detected toward the hot molecular core Sgr B2(N2). However, we report a tentative detection of13CH3C(O)CH3with a12C/13C isotopic ratio of 27 that is consistent with the ratio previously measured for alcohols in this source. Several dozens of transitions of both torsional states of the main isotopolog are detected as well.Conclusion.Our predictions of CH313C(O)CH3and CH3C(O)CH3are reliable into the terahertz region. The spectrum of13CH3C(O)CH3should be revisited in the laboratory with an enriched sample. The torsionally excited statesv12 = 1 andv17 = 1 of CH3C(O)CH3were not reproduced satisfactorily in our models. Nevertheless, transitions pertaining to both states could be identified unambiguously in Sagittarius B2(N2).
Prävalenz von Komorbiditäten bei Lymphödemerkrankungen
Authors: Reißhauer Anett , Schuester Leon , Kling Annelies , Liebl Max Emanuel 
Published: July 2019

Zusammenfassung
Hintergrund Komorbiditäten sind Erkrankungen, die nebeneinander auftreten, entweder voneinander unabhängig, oder als Folgeerkrankung einer Indexerkrankung. Bekannte Ursachen oder Risikofaktoren für Lymphödeme (LÖ) sind u. a. maligne Erkrankungen und ihre Behandlung, Adipositas, chronisch-venöse Insuffizienz und das Lipödem. Bekannte Folgeerkrankungen sind u. a. Erysipele sowie Haut- und Nagelpilzerkrankungen. Ziel ist die Erhebung der Prävalenz von Komorbiditäten bei Lymphödem-Erkrankungen.
Methoden Retrospektive Analyse von 457 konsekutiven Fällen der Sprechstunde für Lymphödemerkrankungen der Hochschulambulanz einer Universitätsklinik hinsichtlich der Prävalenz von Komorbiditäten.
Ergebnisse n=391 Fälle kamen zur Auswertung, getrennt nach Ödemgenese, darunter n=51 primäre Lymphödeme (pL) (Verdacht und gesichert, davon 8 gesicherte syndromale Erkrankungen) und n=340 sekundäre Lymphödeme (sL). Das Geschlechterverhältnis in der Stichprobe war 9:1 (w:m). Während die pL-PatientInnen einen BMI vergleichbar der altersentsprechenden Referenzgruppe der Allgemeinbevölkerung aufweisen, zeigen PatientInnen mit sL einen durchschnittlichen BMI von 33,8 und einen Anteil von 64% adipöser Patientinnen (21% mit BMI über 40). Die Prävalenz rezidivierender Erysipele ist mit 7,8 bzw. 7,9% zwischen pL und sL vergleichbar häufig. Weitere Prävalenzen wie Diagnosen aus dem muskuloskeletalen Bereich (ICD-Kapitel XIII/„M“) zeigten sich in der Stichprobe in altersgerechter Verteilung. Eine besonders hohe Prävalenz zeigen in der Gruppe der sL Schilddrüsenerkrankungen (30%), dabei überwiegend die Schilddrüsenunterfunktion.
Diskussion Nur z. T. kann das Patientenalter und Geschlecht die Prävalenzen der Komorbiditäten erklären. Auffällig beim sekundären LÖ ist die Prävalenz der Adipositas, die als Kofaktor bei der Entstehung und als aggravierender Faktor bekannt ist. Von Interesse ist auch die vergleichbare Prävalenz von Erysipelen zwischen den primären und sekundären Lymphödemen. Offenbar spielt die Genese des LÖ für die Entstehung eines Erysipels keine Rolle. Bislang kaum beschrieben, aber höchst auffällig ist die hohe Prävalenz von Schilddrüsenerkrankungen, insbesondere der Hypothyreose, bei sekundären LÖ.
Der schwierige Weg zum Frau-Sein
Authors: Saucke Elsbeth 
Published: July 2019

ZusammenfassungGynäkologische Störungen in der Pubertät lassen sich mit Homöopathie oft leicht behandeln. Die erfolgreiche Behandlung kann eine Pathologisierung mit entsprechender Dauermedikation verhindern. Ich möchte Ihnen 3 Fälle erfolgreicher Behandlung von Dysmenorrhö, Amenorrhö bzw. Körperwahrnehmungsstörung vorstellen. Die gebrauchten Arzneimittel waren Cyclamen, Pulsatilla, Natrium muriaticum, Calcium carbonicum.