bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Effect of Micro- and Nanoscale Surface Topographies on Silk on Human Corneal Limbal Epithelial Cell Differentiation
Authors: Kang Kai B. , Lawrence Brian D. , Gao X. Raymond , Guaiquil Victor H. , Liu Aihong , Rosenblatt Mark I. 
Published: February 2019

AbstractWe previously reported that micro- and nano-scale topographic pitch created on silk films mimic features of the corneal basement membrane by providing biophysical cues to direct corneal epithelial cell adherence and migration. However, the effect of these topographical features on corneal limbal epithelial cell differentiation has not been explored. We hypothesize in the current study that various topographical pitch created on silk may affect corneal epithelial stem cell differentiation and alter the expression of genes involved in cell differentiation and self-renewal. We patterned silk films with different topographic pitch via soft lithography and observed human corneal limbal epithelial cell behavior. Colony forming assay demonstrated increased colony forming efficiency on patterned silk films. Cells cultured on nanoscale patterned silk films also expressed lower levels of putative keratocyte differentiation markers and higher levels of putative limbal stem cell markers. RNA-Seq analysis further implicated the involvement of pathways related to stem cell differentiation and self-renewal, including Notch, ERK/MAPK and Wnt/β-catenin signaling. We conclude that patterned silk film substrates can be used as scaffolds and provide biophysical cues to corneal limbal stem cells that may maintain corneal epithelial stem cells at a less differentiated state.
Unique skull network complexity of Tyrannosaurus rex among land vertebrates
Authors: Werneburg Ingmar , Esteve-Altava Borja , Bruno Joana , Torres Ladeira Marta , Diogo Rui 
Published: February 2019

AbstractLike other diapsids,Tyrannosaurus rexhas two openings in the temporal skull region. In addition, like in other dinosaurs, its snout and lower jaw show large cranial fenestrae. InT.rex, they are thought to decrease skull weight, because, unlike most other amniotes, the skull proportion is immense compared to the body. Understanding morphofunctional complexity of this impressive skull architecture requires a broad scale phylogenetic comparison with skull types different to that of dinosaurs with fundamentally diverging cranial regionalization. Extant fully terrestrial vertebrates (amniotes) provide the best opportunities in that regard, as their skull performance is known from life. We apply for the first time anatomical network analysis to study skull bone integration and modular constructions in tyrannosaur and compare it with five representatives of the major amniote groups in order to get an understanding of the general patterns of amniote skull modularity. Our results reveal that the tyrannosaur has the most modular skull organization among the amniotes included in our study, with an unexpected separation of the snout in upper and lower sub-modules and the presence of a lower adductor chamber module. Independent pathways of bone reduction in opossum and chicken resulted in different degrees of cranial complexity with chicken having a typical sauropsidian pattern. The akinetic skull of opossum, alligator, and leatherback turtle evolved in independent ways mirrored in different patterns of skull modularity. Kinetic forms also show great diversity in modularity. The complex tyrannosaur skull modularity likely represents a refined mosaic of phylogenetic and ecological factors with food processing being probably most important for shaping its skull architecture. Mode of food processing primarily shaped skull integration among amniotes, however, phylogenetic patterns of skull integration are low in our sampling. Our general conclusions on amniote skull integrity are obviously preliminary and should be tested in subsequent studies. As such, this study provides a framework for future research focusing on the evolution of modularity on lower taxonomic levels.
Crystal structure of the dog allergen Can f 6 and structure-based implications of its cross-reactivity with the cat allergen Fel d 4
Authors: Yamamoto Kenji , Ishibashi Osamu , Sugiura Keisuke , Ubatani Miki , Sakaguchi Masaya , Nakatsuji Masatoshi , Shimamoto Shigeru , Noda Masanori , Uchiyama Susumu , Fukutomi Yuma , Nishimura Shigenori , Inui Takashi 
Published: February 2019

AbstractSeveral dog allergens cause allergic reactions in humans worldwide. Seven distinct dog allergens, designated Canis familiaris allergen 1 to 7 (Can f 1–Can f 7), have been identified thus far. Can f 6 shows high sequence similarity and cross-reactivity with Fel d 4 and Equ c 1, major cat and horse allergens, respectively. This study was conducted on the allergenic epitopes of Can f 6 based on its structural characterization. We demonstrated that sera from 18 out of 38 (47%) dog-sensitized patients reacted to recombinant Can f 6 protein (rCan f 6). We then determined the crystal structure of rCan f 6 by X-ray crystallography, which exhibited a conserved tertiary structural architecture found in lipocalin family proteins. Based on the tertiary structure and sequence similarities with Fel d 4 and Equ c 1, we predicted three IgE-recognizing sites that are possibly involved in cross-reactivity. Substituting three successive amino acids in these sites to triple alanine decreased IgE reactivity to the allergen. However, the degree of reduction in IgE reactivity largely depended on the site mutated and the serum used, suggesting that Can f 6 is a polyvalent allergen containing multiple epitopes and Can f 6-reactive sera contain varied amounts of IgE recognising individual Can f 6 epitopes including those predicted in this study. We also demonstrated that the predicted epitopes are partly involved in IgE cross-reactivity to Fel d 4. Interestingly, the effect of the mutation depended on whether the protein was structured or denatured, indicating that the bona fide tertiary structure of Can f 6 is essential in determining its IgE epitopes.
Pulsed photo-ionization spectroscopy of traps in as-grown and neutron irradiated ammonothermally synthesized GaN
Authors: Gaubas E. , Čeponis T. , Meškauskaite D. , Mickevičius J. , Pavlov J. , Rumbauskas V. , Grigonis R. , Zajac M. , Kucharski R. 
Published: February 2019

AbstractGaN-based structures are promising for production of radiation detectors and high-voltage high-frequency devices. Particle detectors made of GaN are beneficial as devices simultaneously generating of the optical and electrical signals. Photon-electron coupling cross-section is a parameter which relates radiation absorption and emission characteristics. On the other hand, photon-electron coupling cross-section together with photo-ionization energy are fingerprints of deep centres in material. In this work, the wafer fragments of the GaN grown by ammonothermal (AT) technology are studied to reveal the dominant defects introduced by growth procedures and reactor neutron irradiations in a wide range, 1012–1016 cm−2, of fluences. Several defects in the as-grown and irradiated material have been revealed by using the pulsed photo-ionization spectroscopy (PPIS) technique. The PPIS measurements were performed by combining femtosecond (40 fs) and nanosecond (4 ns) laser pulses emitted by optical parametric oscillators (OPO) to clarify the role of electron-phonon coupling. Variations of the operational characteristics of the tentative sensors, made of the AT GaN doped with Mg and Mn, under radiation damage by reactor neutrons have been considered.
Increased adiposity, inflammation, metabolic disruption and dyslipidemia in adult male offspring of DOSS treated C57BL/6 dams
Authors: Temkin Alexis M. , Bowers Robert R. , Ulmer Candice Z. , Penta Kayla , Bowden John A. , Nyland Jennifer , Baatz John E. , Spyropoulos Demetri D. 
Published: February 2019

AbstractEvidence indicates that obesity can be promoted by chemical ‘obesogens’ that drive adiposity, hunger, inflammation and suppress metabolism. Dioctyl sodium sulfosuccinate (DOSS), a lipid emulsifier and candidate obesogen in vitro, is widely used in processed foods, cosmetics and as stool softener medicines commonly used during pregnancy. In vivo testing of DOSS was performed in a developmental origins of adult obesity model. Pregnant mice were orally administered vehicle control or DOSS at times and doses comparable to stool softener use during human pregnancy. All weaned offspring consumed only standard diet. Adult male but not female offspring of DOSS-treated dams showed significantly increased body mass, overall and visceral fat masses, and decreased bone area. They exhibited significant decreases in plasma adiponectin and increases in leptin, glucose intolerance and hyperinsulinemia. Inflammatory IL-6 was elevated, as was adipose Cox2 and Nox4 gene expressions, which may be associated with promoter DNA methylation changes. Multiple significant phospholipid/sterol lipid increases paralleled profiles from long-term high-fat diet induced obesity in males. Collectively, developmental DOSS exposure leads to increased adult adiposity, inflammation, metabolic disorder and dyslipidemia in offspring fed a standard diet, suggesting that pharmaceutical and other sources of DOSS taken during human pregnancy might contribute to long-term obesity-related health concerns in offspring.
Antimicrobial peptides from Rana [Lithobates] catesbeiana: Gene structure and bioinformatic identification of novel forms from tadpoles
Authors: Helbing Caren C. , Hammond S. Austin , Jackman Shireen H. , Houston Simon , Warren René L. , Cameron Caroline E. , Birol Inanç 
Published: February 2019

AbstractAntimicrobial peptides (AMPs) exhibit broad-spectrum antimicrobial activity, and have promise as new therapeutic agents. While the adult North American bullfrog (Rana [Lithobates] catesbeiana) is a prolific source of high-potency AMPs, the aquatic tadpole represents a relatively untapped source for new AMP discovery. The recent publication of the bullfrog genome and transcriptomic resources provides an opportune bridge between known AMPs and bioinformatics-based AMP discovery. The objective of the present study was to identify novel AMPs with therapeutic potential using a combined bioinformatics and wet lab-based approach. In the present study, we identified seven novel AMP precursor-encoding transcripts expressed in the tadpole. Comparison of their amino acid sequences with known AMPs revealed evidence of mature peptide sequence conservation with variation in the prepro sequence. Two mature peptide sequences were unique and demonstrated bacteriostatic and bactericidal activity against Mycobacteria but not Gram-negative or Gram-positive bacteria. Nine known and seven novel AMP-encoding transcripts were detected in premetamorphic tadpole back skin, olfactory epithelium, liver, and/or tail fin. Treatment of tadpoles with 10 nM 3,5,3′-triiodothyronine for 48 h did not affect transcript abundance in the back skin, and had limited impact on these transcripts in the other three tissues. Gene mapping revealed considerable diversity in size (1.6–15 kbp) and exon number (one to four) of AMP-encoding genes with clear evidence of alternative splicing leading to both prepro and mature amino acid sequence diversity. These findings verify the accuracy and utility of the bullfrog genome assembly, and set a firm foundation for bioinformatics-based AMP discovery.
Psychische Auswirkungen der Frühgeburt auf die
Eltern
Authors: Weigl Tobias 
Published: February 2019

ZusammenfassungDie Frühgeburt ihres Kindes erleben Eltern meist als ein belastendes Ereignis. In
seiner Doktorarbeit ging der Autor der Frage nach, welche psychischen
Auswirkungen dies auf die Mütter und Väter hat. In diesem Artikel schildert er,
wie sich die aktuelle Versorgungssituation darstellt und welche Empfehlungen
sich daraus für den Umgang der Hebamme mit betroffenen Eltern ergeben.
Kleinzelliges Lungenkarzinom
Authors: Reinmuth Niels , Hoffmann Hans 
Published: February 2019

ZusammenfassungDas kleinzellige Lungenkarzinom stellt eine besonders aggressive Tumorentität dar und ist durch schnellen Progress, sehr frühe Metastasierung und schlechte Prognose charakterisiert. Nur wenige Patienten werden in einem frühen Erkrankungsstadium diagnostiziert, bei dem in ausgewählten Fällen eine chirurgische Resektion diskutiert werden kann. Chemotherapie und Strahlentherapie sind initial häufig effektiv. Allerdings erleiden die meisten Patienten im metastasierten Stadium nach zunächst gutem Ansprechen auf eine platinhaltige Chemotherapie einen Progress mit dann nur limitierten Therapieoptionen.
Knochensarkome
Authors: Hardes Jendrik , Gosheger Georg , Budny Timo 
Published: February 2019

ZusammenfassungKnochensarkome sind im Gegensatz zu den häufig auftretenden benignen Knochentumoren und tumorähnlichen Knochenläsionen sehr selten und verursachen daher häufig diagnostische und therapeutische Schwierigkeiten. Dieser Beitrag hat zum Ziel, dem Leser die Diagnostik und zumeist multimodale Therapie der häufigsten Knochensarkome wie Osteosarkom, Ewing-Sarkom und Chondrosarkom näherzubringen.
Koloskopie bei querschnittsgelähmten Patienten
Authors: Mangold Martin , Mangold Hermann 
Published: February 2019

ZusammenfassungSchicksalsschläge wie plötzliche Unfälle mit folgenschweren Verletzungen zerstören Lebenspläne und Träume. Nicht alle gehen damit so mutig und willensstark um wie die Sportlerin Kristina Vogel. Querschnittsgelähmte Patienten in Spezialkliniken zu versorgen bedeutet für Ärzte und Pflegende auch, sich intensiv mit der Behandlungs- und Pflegesituation auseinanderzusetzen. Oftmals verbringen die Patienten viele Monate ihres Lebens im Krankenhaus und anschließend in der Rehabilitationseinrichtung. Das erfordert eine besondere Beziehungsgestaltung.Auch Mitarbeiter in der Endoskopie müssen sich einstellen auf die besondere Situation, rückenmarksverletzte Patienten zu behandeln. Dazu gehören ein größeres Untersuchungszeitfenster sowie geeignete Hilfsmittel zur unterstützenden Lagerung gelähmter Arme und/oder Beine.Oft wissen die Patienten selbst sehr gut, was ihnen hilft und was nicht. Sie einzubeziehen in die unmittelbare Untersuchungsvorbereitung muss ein pflegerisches Selbstverständnis sein im Bemühen um einen würdevollen Umgang mit rückenmarksverletzten Menschen.
EFSUMB Recommendations for Gastrointestinal Ultrasound Part 3: Endorectal, Endoanal and Perineal Ultrasound
Authors: Nuernberg Dieter , Saftoiu Adrian , Barreiros Ana , Burmester Eike , Ivan Elena , Clevert Dirk-André , Dietrich Christoph , Gilja Odd , Lorentzen Torben , Maconi Giovanni , Mihmanli Ismail , Nolsoe Christian , Pfeffer Frank , Rafaelsen Søren , Sparchez Zeno , Vilmann Peter , Waage Jo 
Published: February 2019

AbstractThis article represents part 3 of the EFSUMB Recommendations and Guidelines for Gastrointestinal Ultrasound (GIUS). It provides an overview of the examination techniques recommended by experts in the field of endorectal/endoanal ultrasound (ERUS/EAUS), as well as perineal ultrasound (PNUS). The most important indications are rectal tumors and inflammatory diseases like fistula and abscesses in patients with or without inflammatory bowel disease (IBD). PNUS sometimes is more flexible and convenient compared to ERUS. However, the technique of ERUS is quite well established, especially for the staging of rectal cancer. EAUS also gained ground in the evaluation of perianal diseases like fistulas, abscesses and incontinence. For the staging of perirectal tumors, the use of PNUS in addition to conventional ERUS could be recommended. For the staging of anal carcinomas, PNUS can be a good option because of the higher resolution. Both ERUS and PNUS are considered excellent guidance methods for invasive interventions, such as the drainage of fluids or targeted biopsy of tissue lesions. For abscess detection and evaluation, contrast-enhanced ultrasound (CEUS) also helps in therapy planning.
Pyrroles as Dienes in (4+3) Cycloadditions
Authors: Hu Fan , Ng Jerome , Chiu Pauline 
Published: February 2019

This short review summarizes the examples to date of successful (4+3) cycloadditions, including formal (4+3) cycloadditions, where pyrrole derivatives reacted as the diene component, to provide aza-bridged bicyclic and polycyclic adducts.1	Introduction2	Unsubstituted Pyrroles as Dienes in (4+3) Cycloadditions3	C-Substituted Pyrroles as Dienes in (4+3) Cycloadditions4	Intramolecular Pyrrole (4+3) Cycloadditions5	Conclusions
Sharpening Up Your Spectra: Broadband Homonuclear Decoupling in HSQC by Real-Time Pure Shift Acquisition
Authors: Kiraly Peter , Morris Gareth , Quanxiu Liu , Nilsson Mathias 
Published: February 2019

Structure elucidation using NMR spectroscopy has become a vital part of the toolkit of modern synthetic chemistry. Characterisation of final products, quality control of production, analysis of complex mixtures in synthetic method development, and structure elucidation of isolated natural products are examples where NMR spectroscopy is a part of daily routine. The two factors that usually limit the applicability of NMR are resolution and sensitivity. The experimental method described in this Account, real-time pure shift acquisition, yields heteronuclear correlation spectra such as HSQC that offer significant improvements in both resolution and sensitivity, at negligible cost to the analyst. The advantages that real-time pure shift acquisition enjoys over conventional experiments are discussed and illustrated with selected examples including carbohydrate and alkaloid mixtures. Advanced data acquisition and processing techniques that reduce experiment time and are easily combined with pure shift NMR methods are also described.1	Introduction2	Simultaneous Sensitivity and Resolution Enhancement Using Real-Time Acquisition in HSQC3	Processing Pure Shift Data4	Pulse Sequences for Real-Time Pure Shift HSQC5	Conclusions and Future Perspectives
Does Postmenstrual Age Affect Medical Patent Ductus Arteriosus Treatment Success in Preterm Infants?
Authors: Kaur Sharandeep , Stritzke Amelie , Soraisham Amuchou Singh 
Published: February 2019

Objective Patent ductus arteriosus (PDA) is the most common cardiovascular problem of prematurity. Our objective was to examine the effect of postmenstrual age (PMA) on response to medical PDA treatment.
Study Design This retrospective cohort study included infants ≤ 32 weeks' gestational age (GA) who received nonsteroidal anti-inflammatory drugs (NSAIDs) for PDA treatment. Response was positive if echocardiogram showed closed or small PDA or no further treatment was required. Baseline characteristics between responders and nonresponders were compared. Multivariable logistic regression analysis with generalized estimating equations was used to analyze the association between PMA and response.
Results A total of 183 infants with a mean GA of 26.4 ± 2.2 weeks and birth weight of 870 ± 313 g received 257 courses of NSAIDs. Positive response rate to the first course was 65.6%. Two and three courses were given in 62 and 12 infants, with response rates of 48.4 and 50%, respectively. Surgical ligation of PDA occurred in 30 (16.4%) infants. Multivariable logistic regression analysis with generalized estimating equations revealed that PMA was not associated with a positive response (adjusted odds ratio [aOR]: 0.88; 95% confidence interval [CI]: 0.71–1.10). GA at birth remained the most influential factor (aOR: 1.33; 95% CI: 1.02–1.73).
Conclusion GA rather than PMA is the strongest predictor for a positive response in medical PDA treatment.
18.15.8 Tetraheterosubstituted Methanes with a Carbon—Halogen Bond (Update 2018)
Authors: Kleoff M. , Omoregbee K. , Zimmer R. 
Published: February 2019

AbstractIn this chapter, recent methods for the preparation and elaboration of various substituted halomethanes are summarized. In addition to updates on classical methods, recently developed procedures employing new fluorinating agents, such as Togni’s reagents, are also presented. These methods are also put in the context of the synthesis of biologically active compounds.
Plasma Renin Activity Is a Predictive Biomarker of Blood Pressure Response in European but not in African Americans With Uncomplicated Hypertension
Authors: Mehanna Mai , Wang Zhiying , Gong Yan , McDonough Caitrin W , Beitelshees Amber L , Gums John G , Chapman Arlene B , Schwartz Gary L , Bailey Kent R , Johnson Julie A , Turner Stephen T , Cooper-DeHoff Rhonda M 
Published: February 2019

Abstract

BACKGROUND
Interindividual variability in blood pressure (BP) response to antihypertensives has been reported. Although plasma renin activity (PRA) is a potential biomarker for personalizing antihypertensive therapy in European American (EA) and African American (AA) hypertensives, clinical utility of PRA-guided prescribing is incompletely understood.

METHODS
Using systematic-phased approach, PRA’s clinical utility was assessed. After categorizing by baseline PRA, clinic systolic BP (SBP) responses to metoprolol and chlorthalidone were compared in 134 EAs and 102 AAs enrolled in the Pharmacogenomics Evaluation of Antihypertensive Responses-2 (PEAR-2) trial. Receiver operating characteristic (ROC) analysis was conducted in EAs. Data from PEAR-2 AAs were used to estimate an optimal PRA cut point using multivariable linear regression models. The derived cut point in AAs was tested in a meta-analysis of 2 independent AA cohorts, and its sensitivity and specificity were assessed.

RESULTS
EAs with PRA &lt; 0.65 ng/ml/hour had a greater decrease in SBP to chlorthalidone than metoprolol (by –15.9 mm Hg, adjusted P &lt; 0.0001), whereas those with PRA ≥ 0.65 ng/ml/hour had a greater decrease in SBP to metoprolol than chlorthalidone (by 3.3 mm Hg, adjusted P = 0.04). Area under ROC curve (0.69, P = 0.0001) showed that PRA can predict SBP response among EAs. However, we observed no association between PRA and SBP response in PEAR-2 AAs. Among independent AA cohorts, those with PRA ≥ 1.3 ng/ml/hour (PEAR-2-derived cut point) responded better to atenolol/candesartan than hydrochlorothiazide (meta-analysis P = 0.01). However, sensitivity of the derived cut point was 10%.

CONCLUSIONS
PRA at the previously established 0.60–0.65 ng/ml/hour cut point is an effective predictive biomarker of BP response in EAs. However, we were unable to identify PRA cut point that could be used to guide antihypertensive selection in AAs.

TRIAL REGISTRATION
NCT01203852, NCT00246519, NCT00005520.
Biological sequence modeling with convolutional kernel networks
Authors: Chen Dexiong , Jacob Laurent , Mairal Julien 
Published: February 2019

Abstract

Motivation
The growing number of annotated biological sequences available makes it possible to learn genotype-phenotype relationships from data with increasingly high accuracy. When large quantities of labeled samples are available for training a model, convolutional neural networks can be used to predict the phenotype of unannotated sequences with good accuracy. Unfortunately, their performance with medium- or small-scale datasets is mitigated, which requires inventing new data-efficient approaches.

Results
We introduce a hybrid approach between convolutional neural networks and kernel methods to model biological sequences. Our method enjoys the ability of convolutional neural networks to learn data representations that are adapted to a specific task, while the kernel point of view yields algorithms that perform significantly better when the amount of training data is small. We illustrate these advantages for transcription factor binding prediction and protein homology detection, and we demonstrate that our model is also simple to interpret, which is crucial for discovering predictive motifs in sequences.

Availability and implementation
Source code is freely available at https://gitlab.inria.fr/dchen/CKN-seq.

Supplementary information
Supplementary data are available at Bioinformatics online.