bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pheno-seq – linking visual features and gene expression in 3D cell culture systems
Authors: Tirier Stephan M. , Park Jeongbin , Preußer Friedrich , Amrhein Lisa , Gu Zuguang , Steiger Simon , Mallm Jan-Philipp , Krieger Teresa , Waschow Marcel , Eismann Björn , Gut Marta , Gut Ivo G. , Rippe Karsten , Schlesner Matthias , Theis Fabian , Fuchs Christiane , Ball Claudia R. , Glimm Hanno , Eils Roland , Conrad Christian 
Published: August 2019

AbstractPatient-derived 3D cell culture systems are currently advancing cancer research since they potentiate the molecular analysis of tissue-like properties and drug response under well-defined conditions. However, our understanding of the relationship between the heterogeneity of morphological phenotypes and the underlying transcriptome is still limited. To address this issue, we here introduce “pheno-seq” to directly link visual features of 3D cell culture systems with profiling their transcriptome. As prototypic applications breast and colorectal cancer (CRC) spheroids were analyzed by pheno-seq. We identified characteristic gene expression signatures of epithelial-to-mesenchymal transition that are associated with invasive growth behavior of clonal breast cancer spheroids. Furthermore, we linked long-term proliferative capacity in a patient-derived model of CRC to a lowly abundant PROX1-positive cancer stem cell subtype. We anticipate that the ability to integrate transcriptome analysis and morphological patho-phenotypes of cancer cells will provide novel insight on the molecular origins of intratumor heterogeneity.
Deeper Profiles and Cascaded Recurrent and Convolutional Neural Networks for state-of-the-art Protein Secondary Structure Prediction
Authors: Torrisi Mirko , Kaleel Manaz , Pollastri Gianluca 
Published: August 2019

AbstractProtein Secondary Structure prediction has been a central topic of research in Bioinformatics for decades. In spite of this, even the most sophisticated ab initio SS predictors are not able to reach the theoretical limit of three-state prediction accuracy (88–90%), while only a few predict more than the 3 traditional Helix, Strand and Coil classes. In this study we present tests on different models trained both on single sequence and evolutionary profile-based inputs and develop a new state-of-the-art system with Porter 5. Porter 5 is composed of ensembles of cascaded Bidirectional Recurrent Neural Networks and Convolutional Neural Networks, incorporates new input encoding techniques and is trained on a large set of protein structures. Porter 5 achieves 84% accuracy (81% SOV) when tested on 3 classes and 73% accuracy (70% SOV) on 8 classes on a large independent set. In our tests Porter 5 is 2% more accurate than its previous version and outperforms or matches the most recent predictors of secondary structure we tested. When Porter 5 is retrained on SCOPe based sets that eliminate homology between training/testing samples we obtain similar results. Porter is available as a web server and standalone program at http://distilldeep.ucd.ie/porter/ alongside all the datasets and alignments.
Pore Scale Visualization of Drainage in 3D Porous Media by Confocal Microscopy
Authors: do Nascimento Débora F. , Vimieiro Junior José R. , Paciornik Sidnei , Carvalho Marcio S. 
Published: August 2019

AbstractWe visualize the dynamics of immiscible displacement of a high viscosity wetting phase by a low viscosity non-wetting phase in a three-dimensional (3D) glass bead packing using confocal microscopy. Both phases were doped with two different fluorescent dyes, which enabled visualization of both phases simultaneously and quantification of the phase volumes without the need of image subtraction operations. The transient results show details of the displacement process and how pores are invaded by the non-wetting displacing phase. The static images at the end of the displacement process reveal how the trapped ganglia volume and morphology change with capillary number. The wetting phase is trapped as pendular rings spanning one to multiple pore necks. Details of the pore scale flow of oil wet media revealed with the experimental methods presented here can lead to better fundamental understanding of the physical processes and optimized enhanced oil recovery methods, CO2 sequestration and aquifer remediation.
Establishment and characterization of a fucosylated α-fetoprotein-specific monoclonal antibody: a potential application for clinical research
Authors: Egashira Yuriko , Suganuma Masatoshi , Kataoka Yukiko , Higa Yukiko , Ide Nobuyuki , Morishita Koichi , Kamada Yoshihiro , Gu Jianguo , Fukagawa Koji , Miyoshi Eiji 
Published: August 2019

AbstractThe Lens culinaris agglutinin (LCA)-reactive fraction of α-fetoprotein (AFP-L3) is a well-known cancer biomarker for hepatocellular carcinoma (HCC) with very high specificity. Because LCA recognizes only bi-antennary N-glycans with a core fucose, some of fucosylated AFP in HCC patients may not be detected. Then glycan antibodies, which recognize both specific glycan and protein, are desired for glycobiology. Here, we successfully established a novel glycan antibody for fucosylated AFP and demonstrated its potential clinical application. After immunization with a fucosylated AFP peptide, positive screening was performed for fucosylated AFP peptides using solid-phase enzyme-linked immunosorbent assay (ELISA). The newly developed antibody was designated: fucosylated AFP-specific mAb (FasMab). Western blot analysis showed that FasMab reacted with AFP produced by HepG2 cells, but not with AFP produced by α-1,6-fucosyltransferase deficient HepG2 cells. The specific binding of FasMab to fucosylated AFP was confirmed with ELISA as well as western blot analysis. A preliminary high sensitivity chemiluminescence enzyme immunoassay kit showed increased levels of fucosylated AFP in the sera of patients with HCC, but not in the sera of normal patients, or patients with chronic liver diseases. Thus, the novel glycan antibody, FasMab, is a promising tool to study fucosylated AFP with clinical and basic research applications.
Synthesis of Methane Hydrate from Ice Powder Accelerated by Doping Ethanol into Methane Gas
Authors: Chen Yen-An , Chu Liang-Kai , Chu Che-Kang , Ohmura Ryo , Chen Li-Jen 
Published: August 2019

AbstractClathrate hydrate is considered to be a potential medium for gas storage and transportation. Slow kinetics of hydrate formation is a hindrance to the commercialized process development of such applications. The kinetics of methane hydrate formation from the reaction of ice powder and methane gas doped with/without saturated ethanol vapor at constant pressure of 16.55 ± 0.20 MPa and constant temperature ranging from −15 to −1.0 °C were investigated. The methane hydrate formation can be dramatically accelerated by simply doping ethanol into methane gas with ultralow ethanol concentration (<94 ppm by mole fraction) in the gas phase. For ethanol-doped system 80.1% of ice powder were converted into methane hydrate after a reaction time of 4 h, while only 26.6% of ice powder was converted into methane hydrate after a reaction time of 24 h when pure methane gas was used. Furthermore, this trace amount of ethanol could also substantially suppress the self-preservation effect to enhance the dissociation rate of methane hydrate (operated at 1 atm and temperatures below the ice melting point). In other words, a trace amount of ethanol doped in methane gas can act as a kinetic promoter for both the methane hydrate formation and dissociation.
Phase-matched multi-layer based polarisation-independent spot-size converter for silicon nanowire
Authors: Jiang Weifeng , Rahman B. M. Azizur 
Published: August 2019

AbstractThe efficient coupling of optical power from a silicon nanowire (NW) to an optical fibre is challenging for both the quasi-TE and quasi-TM polarisations. Here, we propose a polarisation-independent spot-size converter (PI-SSC) based on phase-matched multi-layer waveguides for efficient coupling between a silicon NW and an optical fibre for both the polarisations. The fabrication process of the proposed PI-SSC is compatible with the complementary metal-oxide-semiconductor (CMOS) process. The optimisation for the proposed PI-SSC is studied by using a numerically efficient algorithm, combining a rigorous H-field based full-vectorial finite element method (VFEM) and the least squares boundary residual (LSBR) method. The simulation results show that using an eleven-layer based PI-SSC, the coupling losses between a silicon NW and a lensed fibre of radius 2 μm can be reduced to only 0.34 dB and 0.25 dB for the quasi-TE and quasi-TM polarisations, respectively. Furthermore, the output multi-layer is horizontally tapered, which further reduces the coupling loss for both the polarisations and the end face is easy to be polished.
The subgingival microbial community of feline periodontitis and gingivostomatitis: characterization and comparison between diseased and healthy cats
Authors: Rodrigues Marjory Xavier , Bicalho Rodrigo Carvalho , Fiani Nadine , Lima Svetlana Ferreira , Peralta Santiago 
Published: August 2019

AbstractPeriodontitis is a common and important health problem in domestic cats. The subgingival microbiota of cats diagnosed with chronic periodontitis (CP), aggressive periodontitis (AP), and feline chronic gingivostomatitis (FCGS) are not well characterized. Thus, the aim of the present study was to characterize and compare the periodontal microbiota of periodontally healthy cats versus cats diagnosed with CP, AP, and FCGS by using next-generation sequencing. In total, 44 domestic cats were enrolled, and 139 subgingival samples were subjected to 16S rRNA gene sequencing to investigate the microbiota composition of each periodontal group evaluated. Our results identified several key genera previously described in periodontal disease (e.g. Treponema and Filifactor) and in the oral microbiota (e.g. Moraxella and Capnocytophaga) of healthy cats. Phylogenetic beta diversity analysis showed that the microbiota of periodontally healthy cats were distinguishable from diseased cats. Even though most of the genera known to be associated with periodontal disease were also identified in healthy cats, they were present at significantly lower relative abundance. Remarkably, alpha diversity was found to be higher in the disease groups compared to healthy animals. These results suggest a pathological mechanism involving opportunistic behavior. Our findings corroborate those in the current literature regarding the complexity of the subgingival microbiota of the domestic cat and reveal both differences and similarities among periodontally healthy and diseased cats.
Construction of complete Tupaia belangeri transcriptome database by whole-genome and comprehensive RNA sequencing
Authors: Sanada Takahiro , Tsukiyama-Kohara Kyoko , Shin-I Tadasu , Yamamoto Naoki , Kayesh Mohammad Enamul Hoque , Yamane Daisuke , Takano Jun-ichiro , Shiogama Yumiko , Yasutomi Yasuhiro , Ikeo Kazuho , Gojobori Takashi , Mizokami Masashi , Kohara Michinori 
Published: August 2019

AbstractThe northern tree shrew (Tupaia belangeri) possesses high potential as an animal model of human diseases and biology, given its genetic similarity to primates. Although genetic information on the tree shrew has already been published, some of the entire coding sequences (CDSs) of tree shrew genes remained incomplete, and the reliability of these CDSs remained difficult to determine. To improve the determination of tree shrew CDSs, we performed sequencing of the whole-genome, mRNA, and total RNA and integrated the resulting data. Additionally, we established criteria for the selection of reliable CDSs and annotated these sequences by comparison to the human transcriptome, resulting in the identification of complete CDSs for 12,612 tree shrew genes and yielding a more accurate tree shrew genome database (TupaiaBase: http://tupaiabase.org). Transcriptome profiles in hepatitis B virus infected tree shrew livers were analyzed for validation. Gene ontology analysis showed enriched transcriptional regulation at 1 day post-infection, namely in the “type I interferon signaling pathway”. Moreover, a negative regulator of type I interferon, SOCS3, was induced. This work, which provides a tree shrew CDS database based on genomic DNA and RNA sequencing, is expected to serve as a powerful tool for further development of the tree shrew model.
Image processing approaches to enhance perivascular space visibility and quantification using MRI
Authors: Sepehrband Farshid , Barisano Giuseppe , Sheikh-Bahaei Nasim , Cabeen Ryan P. , Choupan Jeiran , Law Meng , Toga Arthur W. 
Published: August 2019

AbstractImaging the perivascular spaces (PVS), also known as Virchow-Robin space, has significant clinical value, but there remains a need for neuroimaging techniques to improve mapping and quantification of the PVS. Current technique for PVS evaluation is a scoring system based on visual reading of visible PVS in regions of interest, and often limited to large caliber PVS. Enhancing the visibility of the PVS could support medical diagnosis and enable novel neuroscientific investigations. Increasing the MRI resolution is one approach to enhance the visibility of PVS but is limited by acquisition time and physical constraints. Alternatively, image processing approaches can be utilized to improve the contrast ratio between PVS and surrounding tissue. Here we combine T1- and T2-weighted images to enhance PVS contrast, intensifying the visibility of PVS. The Enhanced PVS Contrast (EPC) was achieved by combining T1- and T2-weighted images that were adaptively filtered to remove non-structured high-frequency spatial noise. EPC was evaluated on healthy young adults by presenting them to two expert readers and also through automated quantification. We found that EPC improves the conspicuity of the PVS and aid resolving a larger number of PVS. We also present a highly reliable automated PVS quantification approach, which was optimized using expert readings.
Detection and genetic characterization of Giardia duodenalis in pigs from large-scale farms in Xinjiang, China
Authors: Jing Bo , Zhang Ying , Xu Chunyan , Li Dongfang , Xing Jinming , Tao Dayong , Zhang Longxian , Qi Meng , Wang Haiyan 
Published: August 2019

To study the presence of Giardia duodenalis in Xinjiang, northwest China, we collected 801 fecal specimens from seven large-scale pig farms and screened them using PCR targeting the SSU rRNA gene. Twenty-one (2.6%) of the specimens from five farms were G. duodenalis-positive, with a significant difference in prevalence among different farms (0–8.7%) (p < 0.01). Giardia duodenalis prevalence was highest in fattening pigs (5.4%, 7/129), followed by sows (3.2%, 7/222), post-weaning piglets (1.8%, 5/281), and pre-weaning piglets (1.2%, 2/169), but there was no significant difference in prevalence among the age groups (p > 0.05). Sequence analysis of the SSU rRNA gene revealed that the 21 G. duodenalis strains belonged to three assemblages: A (n = 2), B (n = 16), and E (n = 3). Assemblage B was the predominant assemblage and was widely distributed in all G. duodenalis-positive farms and age groups. All G. duodenalis-positive specimens were further assayed at the β-giardin (bg), glutamate dehydrogenase (gdh), and triosephosphate isomerase (tpi) genes, and two tpi, four gdh, and two bg sequences were identified. These data indicate that pigs may be a zoonotic risk and can potentially spread G. duodenalis infection from animals to humans.
A case of metastatic prostate cancer treated with metastasectomy
Authors: Miyata Yudai , Funahashi Yasuhito , Yamamoto Akiyuki , Sassa Naoto , Matsukawa Yoshihisa , Gotoh Momokazu 
Published: August 2019

AbstractIn general, metastatic prostate cancer is managed medically. Here we present a patient with metastatic prostate cancer who was treated by surgical resection in addition to medical therapies. Local therapies should be considered if metastatic lesions are limited, also in cases of metastatic prostate cancer.
Can Routine Data be used to Determine the Target Population of
Patients with Type 2 Diabetes in Early Benefit Assessments in
Germany?
Authors: Thoren Corinna ten , Schwalm Anja , Mostardt Sarah , Weber Dietmar , Ihle Peter , Altenhofen Lutz 
Published: August 2019

Abstract
Objectives Since 2011, early benefit assessment of all new drugs
launched in Germany is mandatory. The exact determination of the appropriate
target population (i. e. patients eligible for a drug) plays an
important role for subsequent price negotiations. In type 2 diabetes, the
size of the target population varies considerably between company dossiers
submitted for assessment. Our aim was to explore whether routine data from
all persons insured in German statutory health insurance (SHI) funds can be
used to derive information on the size of the target population with type 2
diabetes.
Methods We explored how the data available at the German Institute of
Medical Documentation and Information (DIMDI) can be used to obtain the
information required. A data-based concept was chosen and the selection
criteria were developed in a multidisciplinary project group. Before
finalizing the database query, the criteria were evaluated in a test
database and the database query was then repeatedly modified.
Results At the time of the design of our analysis in 2017, the most
recent data available at DIMDI were for 2013. The algorithm we developed for
identifying patients with type 2 diabetes and classifying them according to
their medication, based primarily on the combination of ICD and ATC codes,
enabled us to determine the size of target populations for different
indications in diabetes mellitus type 2.
Conclusion Our methodological approach seems to be suitable to
determine target populations in type 2 diabetes.
Reduction of Pyrrolizidine Alkaloid Levels in Comfrey (Symphytum officinale) Hairy Roots by RNAi Silencing of Homospermidine Synthase
Authors: Kruse Lars H. , Stegemann Thomas , Jensen-Kroll Julia , Engelhardt Annika , Wesseling Anne-Maria , Lippert Annemarie , Ludwig-Müller Jutta , Ober Dietrich 
Published: August 2019

AbstractComfrey is a medicinal plant, extracts of which are traditionally used for the treatment of painful inflammatory muscle and joint problems, because the plant contains allantoin and rosmarinic acid. However, its medicinal use is limited because of its toxic pyrrolizidine alkaloid (PA) content. PAs encompass more than 400 different compounds that have been identified from various plant lineages. To date, only the first pathway-specific enzyme, homospermidine synthase (HSS), has been characterized. HSS catalyzes the formation of homospermidine, which is exclusively incorporated into PAs. HSS has been recruited several times independently in various plant lineages during evolution by duplication of the gene encoding deoxyhypusine synthase (DHS), an enzyme of primary metabolism. Here, we describe the establishment of RNAi knockdown hairy root mutants of HSS in Symphytum officinale. A knockdown of HSS by 60 – 80% resulted in a significant reduction of homospermidine by ~ 86% and of the major PA components 7-acetylintermedine N-oxide and 3-acetylmyoscorpine N-oxide by approximately 60%. The correlation of reduced transcript levels of HSS with reduced levels of homospermidine and PAs provides in planta support for HSS being the central enzyme in PA biosynthesis. Furthermore, the generation of PA-depleted hairy roots might be a cost-efficient way for reducing toxic by-products that limit the medicinal applicability of S. officinale extracts.
Migratory Insertion Strategies for Dearomatization
Authors: Zeidan Nicolas , Lautens Mark 
Published: August 2019

Development of strategies for molecule functionalization by dearomatization has surged in the last two decades. The benefits of overcoming the resonance stabilization energy outweigh the cost; diverse compounds could be accessed in a short number of steps. One approach that has been of interest in recent years is the dearomatization of indoles and other (hetero)aromatic compounds by migratory insertion. The chiral σ-bond palladium intermediate could be reduced or trapped by a second functionalization. In this short review we will summarize the recently discovered reactions from our group and others in this field of metal-catalyzed dearomatizations by migratory insertion.1	Introduction2	Monofunctionalizations: Heck and Reductive Heck Reactions2.1	N-Tethered Heterocycles2.2	Non-N-tethered Heterocycles2.3	Non-heterocycles3	Dearomative Difunctionalizations: Interrupted Heck Reaction3.1	N-Tethered Heterocycles3.2	Non-N-tethered Heterocycles4	Conclusion
A versão femoral está associada a alterações na força dos músculos do quadril em mulheres com impacto femoroacetabular sintomático?
Authors: Marostica Adriano David , Pizzolatti André Luiz Almeida , Adam Guilherme Pradi , Codonho Daniel , Canella Richard Prazeres , Ganev Gerson Gandhi 
Published: August 2019

Resumo
Objetivo O objetivo deste estudo foi avaliar a associação da anteversão femoral e da força dos músculos do quadril em indivíduos com síndrome do impacto femoroacetabular.
Método Os ângulos de versão femoral descritos nas imagens de ressonância magnética articular e os testes isocinéticos foram avaliados retrospectivamente entre julho de 2016 e dezembro de 2017. Os critérios de inclusão foram: a) versão femoral avaliada pelo mesmo radiologista; b) ângulo α ≥ 55°; e c) ausência de dor limitante durante o teste isocinético. Os picos de torque em flexão/extensão, abdução/adução e rotação interna/externa foram avaliados a 30°/s em 5 repetições. A correlação entre a versão femoral e a força muscular foi avaliada por meio de regressão linear simples, com nível de significância estatística de 5%.
Resultados Um total de 37 mulheres atenderam aos critérios de inclusão. Foram avaliados 51 quadris sintomáticos. Não houve correlação da anteversão femoral nos picos de torque em flexão, extensão, abdução, adução, rotação externa e rotação interna.
Conclusão A anteversão femoral não foi correlacionada à força dos músculos do quadril em mulheres com impacto femoroacetabular sintomático.
Avaliação dos resultados clínicos e radiográficos da artroplastia total cimentada do quadril em 477 pacientes
Authors: Duarte Guydo Marques Horta , Alberti Luiz Ronaldo 
Published: August 2019

Resumo
Objetivo Avaliar os resultados da artroplastia total do quadril (ATQ) cimentada, com a utilização da técnica e prótese da escola Exeter.
Metódo Entre março de 2000 e dezembro de 2006, foram realizadas 504 ATQs em 477 pacientes, com diversos diagnósticos etiológicos, 260 à direita e 244 à esquerda, 27 bilaterais,. A idade média foi de 58,9 (17,7–86,8) anos, com mediana de 69,0 anos. O planejamento radiográfico foi feito utilizando-se gabaritos apropriados. O acesso cirúrgico foi o posterolateral com o paciente em decúbito lateral. Para a avaliação clínica, foi utilizado o escore do quadril de Harris (EQH). Na avaliação radiográfica, foi estudada a interface osso-cimento acetabular, nas três zonas de DeLee e Charnley e nas sete zonas de Gruen do lado femoral, a presença de migração distal do componente femoral, hipertrofia diafisária, e ossificação heterotópica.
Resultados O seguimento médio de 441 cirurgias (87,5%) foi de 7,2 (1,0–16,6) anos, com mediana de 7,1 anos. A incidência de complicações foi: luxação, 3,2%; infecção ,2,2%; tromboembolismo, 2,1%; disfunção de nervos periféricos 1,1%; hipertrofia diafisária, 1,5%; soltura do componente acetabular, 1,8%; migração distal do componente femoral entre 2,0 mm e 2,9 mm, 0,45%; 1 caso de soltura asséptica do componente femoral; e 1 caso de fratura da haste femoral. A pontuação média com o EQH foi de 92 pontos.
Conclusão A ATQ cimentada, com a metodologia utilizada, constituiu-se em uma opção eficaz para o tratamento deste grupo de pacientes, com resultados satisfatórios, com este tempo de seguimento.