bluuebunny/crossref_metadata_2025 huggingface dataset:
Colorimetric assay of Hg2+ based on the inhibition of peroxidase mimetic activity of gold nanoclusters induced by Hg2+
Authors: Jiang Xueding , Xu Weicheng , Chen Xin , Liang Yong
Published: February 2019

In this paper, we report a highly sensitive and selective colorimetric assay for Hg2+ detection in aqueous solutions.
Pyrazolo[4,3-e][1,2,4]triazolo[1,5-c]pyrimidines to develop functionalized ligands to target adenosine receptors: fluorescent ligands as an example
Authors: Federico Stephanie , Margiotta Enrico , Paoletta Silvia , Kachler Sonja , Klotz Karl-Norbert , Jacobson Kenneth A. , Pastorin Giorgia , Moro Stefano , Spalluto Giampiero
Published: February 2019

A series of adenosine receptor antagonists bearing a reactive linker was developed.
The influence of 2D nanomaterials on electron transfer across molecular thin films
Authors: Kong Na , Zhang Shuang , Liu Jing , Wang Jianmei , Liu Zhen , Wang Hongbin , Liu Jingquan , Yang Wenrong
Published: February 2019

Design and formation of electron transfer pathways across self-assembled monolayers by the hydrophobic attachment of BN-NH2 and MoS2 nanosheets.
Nondestructive, longitudinal measurement of collagen scaffold degradation using computed tomography and gold nanoparticles
Authors: Finamore Tyler A. , Curtis Tyler E. , Tedesco James V. , Grandfield Kathryn , Roeder Ryan K.
Published: February 2019

Gold nanoparticles and computed tomography were used synergistically to enable nondestructive, longitudinal, and volumetric measurement of collagen scaffold degradation.
Molecular-salt hybrids; integration of ammonia borane into lithium halides
Authors: Cascallana-Matías Irene , Breternitz Joachim , Baker Annabelle , Davis Hallam , Cussen Edmund J. , Gregory Duncan H.
Published: February 2019

New hybrids release hydrogen on decomposition and demonstrate Li-ion conductivity >100 times higher than the component salts.
Oxidant-templating fabrication of pure polypyrrole hydrogel beads as a highly efficient dye adsorbent
Authors: Ye Xi , Xu Qingchi , Xu Jun
Published: February 2019

Pure polypyrrole (PPY) hydrogel bead is a type of dye adsorbent with good adsorbing capacity.
Numerical Monte Carlo simulations of charge transport across the surface of dye and cocatalyst modified spherical nanoparticles under conditions of pulsed or continuous illumination
Authors: Tkaczibson Kevin , Ardo Shane
Published: February 2019

Solar fuel constructs consisting of discrete light-absorbers and distinct redox-active electrocatalysts are well suited for numerical modeling of their charge-transfer processes.
A promising europium-based down conversion material: organic–inorganic perovskite solar cells with high photovoltaic performance and UV-light stability
Authors: Rahman Naveed Ur , Khan Wasim Ullah , Khan Shaukat , Chen Xiaojie , Khan Javid , Zhao Juan , Yang Zhiyong , Wu Mingmei , Chi Zhenguo
Published: February 2019

A europium-based down conversion material enables perovskite solar cells with simultaneous improvement in photovoltaic performance and device stability.
Designed synthesis of a p-Ag2S/n-PDI self-assembled supramolecular heterojunction for enhanced full-spectrum photocatalytic activity
Authors: Yang Jun , Miao Hong , Li Wenlu , Li Huiquan , Zhu Yongfa
Published: February 2019

An efficient full-spectrum responsive p-Ag2S/n-PDI heterojunction was successfully constructed. The excellent activity was mainly attributed to the more effective separation of electron-hole pairs.
Transition metal-doped ultrathin RuO2 networked nanowires for efficient overall water splitting across a broad pH range
Authors: Wang Juan , Ji Yujin , Yin Rongguan , Li Youyong , Shao Qi , Huang Xiaoqing
Published: February 2019

Although water splitting has been successfully achieved in recent years, the design of highly efficient bifunctional catalysts applicable across a broad pH range, especially in harsh acidic conditions, remains full of challenges.
Interaction between GDF5 gene polymorphisms and environment factors increased the risk of knee osteoarthritis: a case–control study
Authors: Zhang Sujie , Wang Juan , Ji Hongliang , Jia Helei , Guan Dongsheng
Published: February 2019

Using a case–control design, we assessed the association between single nucleotide polymorphisms (SNPs) of growth and differentiation factor 5 (GDF5)/rs143383 gene and interaction with environments and knee osteoarthritis (KOA). We recruited 288 KOA patients from the First Clinical College, Henan University of Chinese Medicine between June 2017 and May 2018. There was significant difference in genotype distribution between case group and control group (χ2 = 22.661, P=0.000). The minor C allele was significantly higher in the case group than that in the control group (20.5 vs 8.1%, P=0.000, odds ratio (OR) = 1.62, 95% confidence interval (CI): 1.29–2.03). Significant differences were also observed in other gene models. For age, all models show significant differences (P<0.05) for those whose age was more than 60 years, and no significant difference was observed for those under 60 years. For non-smoking group, there were significant differences between case group and control group, and for smoker, significance level was found in TT compared with CC and allele gene models. Patients with drinking and Bbody mass index (MI )≥ 24 also showed significant relationship between rs143383 and osteoarthritis (OA) under the following models: TT vs CC (P=0.000, P=0.018), TT/CT vs CC (P=0.043), TT vs CT/CC (P=0.000, P=0.009), and T vs C (P=0.024, P=0.000). Other gene models indicated no significance (P>0.05). Our results revealed a possible genetic association between GDF5 and KOA, and the TT genotype of rs143383 increased the risk of KOA in Chinese Han population. The interaction between GDF5 gene and drinking, smoking, and obesity further increased the risk of KOA.
Behavioral state-dependent lateralization of dorsal dentate gyrus c-Fos expression in mice
Authors: Jordan Jake T. , Shanley M. Regis , Pytte Carolyn L.
Published: February 2019

Hemispheric lateralization is a fundamental organizing principle of nervous systems across taxonomic groups with bilateral symmetry. The mammalian hippocampus is lateralized anatomically, physiologically, and chemically; however, functional asymmetries are not yet well understood. Imaging studies in humans have implicated the left and right hippocampus in specialized processing. However, it is not clear if lateralized activity occurs in the rodent hippocampus. c-Fos imaging in animals provides a measure of neuronal activity with a resolution at the level of single cells. The aim of the present study was to determine whether lateralized activity-dependent c-Fos expression occurs in the rodent hippocampus. To understand functional lateralization of hippocampal processing, we compared interhemispheric expression of c-Fos in the dentate gyrus (DG), a structure involved in encoding new experiences, in mice that ran on a wheel, encoded a novel object, or remained in home cages. We found that wheel running (WR) induced the greatest amount of DG c-Fos expression in both hemispheres, with no difference between hemispheres. Object exploration (OB) resulted in left-lateralized DG c-Fos expression, whereas control (CON) mice were not lateralized. We then sought to determine whether differential consideration of hemispheres might influence the conclusions of a study by simulating common cell quantitation methods. We found that different approaches led to different conclusions. These data demonstrate lateralization of neuronal activity in the mouse DG corresponding to the experience of the animal and show that differentially considering hemisphere leads to alternative conclusions.
L’haleine et les capteurs d’odeurs
Authors: Pajot-Augy Édith
Published: February 2019

Grâce à leurs capacités olfactives développées, des animaux sont capables de détecter des odeurs associées à certaines pathologies. Récemment, des nez électroniques, consistant en des réseaux de senseurs artificiels générant une signature caractéristique aux odorants présents, par exemple dans l’haleine, permettent à l’heure actuelle de diagnostiquer des pathologies variées, à des stades précoces, et de façon fiable et non invasive. Pour bénéficier de la capacité intrinsèque et naturellement optimisée du système olfactif animal à détecter et discriminer des traces d’odorants, des dispositifs hybrides bioélectroniques sont également en développement pour le diagnostic médical. Ces divers senseurs olfactifs sont en plein essor avec des résultats prometteurs.
Trois chercheurs, dont un Français, récompensés pour leurs travaux sur les lasers
Authors: Mordon Serge R.
Published: February 2019

Six ans après le physicien Serge Haroche, un autre Français, qui détient aussi la nationalité américaine, reçoit le prix Nobel de physique. Gérard Mourou, né en 1944 à Albertville (France), est professeur émérite à l’École polytechnique (Palaiseau, France) et ancien professeur à l’université du Michigan (Ann Arbor, États-Unis). Il partage la moitié du prix Nobel avec Donna Strickland, de l’université de Waterloo (Ontario, Canada). Née en 1959 à Guelph, au Canada, elle était alors étudiante à l’époque de ces travaux portant sur les lasers. Elle est la troisième femme seulement à être récompensée en physique, après Marie Curie en 1903 et Maria Goeppert-Mayer en 1963. L’autre moitié de cette récompense prestigieuse revient à l’Américain Arthur Ashkin, 96 ans, de l’université Cornell (Ithaca, État de New York, États-Unis). Arthur Ashkin est désormais la personne la plus âgée à voir été lauréat d’un prix Nobel, toutes catégories confondues. Ces trois chercheurs ont un point commun : ils manipulent la lumière et leurs recherches ont abouti à de nouvelles utilisations des lasers en médecine.
Avant-propos
Authors: Jouault Thierry
Published: February 2019

Pour éclairer la série que nous vous proposons, il nous a semblé important de rappeler les règles définissant ce que sont les organismes-modèles ainsi que la réglementation en vigueur quant à leur utilisation en recherche biomédicale. Les études in vitro ou ex vivo, sur cellules ou tissus, ou les analyses in silico ne permettent pas d’aborder des problématiques complexes. Elles sont certes utiles pour des analyses mécanistiques, mais ne permettent pas l’étude de réponses biologiques intégrées qui nécessitent l’analyse d’un organisme entier. Ces organismes sont soumis à une réglementation stricte. Elle les distingue selon qu’ils sont vertébrés ou invertébrés. Si les mammifères modélisent nombre de pathologies humaines, certains organismes simples permettent également de mener ce type d’études et de répondre à des questions liées à la génétique. Leur intérêt est leur rapidité et leur capacité de reproduction qui facilitent les expérimentations. Le poisson zèbre en est un bon exemple avec les nombreuses versions de morphants qui ont été développés et qui ont permis de révéler les conséquences d’altérations génomiques sur un phénotype particulier. Cet organisme-modèle est donc particulièrement utilisé pour l’étude de pathologies monogéniques ou pour déterminer le rôle d’un gène dans l’étiologie de diverses pathologies. La transparence du poisson zèbre rend de plus les investigations plus faciles. Caenorhabditis elegans est également un excellent modèle d’organisme simple et qui, contrairement au poisson zèbre, ne relève pas de la réglementation concernant l’expérimentation animale. Son utilisation est ainsi, comme pour les insectes, plus aisée.

Connaître les différences entre les organismes-modèles, leurs avantages et leurs limites, et les règles dictant leur utilisation est donc primordial pour la réalisation d’expérimentations qui restent nécessaires à l’acquisition de nouvelles connaissances dans le domaine de la biologie et de la santé.
Körperliche Aktivität und deren Effekte auf das Burn-out-Syndrom – Ein systematisches Review
Authors: Dreher Matthias , Dößereck Nils , Lachtermann Ella
Published: February 2019

Das vorliegende Review legt dar, dass regelmäßige körperliche Aktivität einen positiven Einfluss auf die Burn-out-Symptomatik hat. Mittels einer systematischen Literaturrecherche wurden die möglichen Effekte untersucht und die Evidenz mithilfe des Standard Index of Convergence (SIC) bewertet. Der SIC lag in den Längsschnittstudien bei SIC (3)=− 1, während er in den Interventionsstudien bei SIC (6)=− 0,50 lag. Daher ist jeweils von einer moderat starken Evidenz auszugehen, dass körperliche Aktivität einen positiven gesundheitlichen Effekt auf das Burn-out-Syndrom hat. Aufgrund der Heterogenität der Erhebungstools und der Studienlage ist es notwendig, weitere qualitativ hochwertige Studien zur Burn-out-Thematik durchzuführen, um repräsentative Aussagen zu gewährleisten. Unabhängig von den positiven präventiven und therapeutischen Effekten ist die regelmäßige körperliche Aktivität ein grundlegender, jedoch kein alleiniger Ansatzpunkt, um der Erschöpfungssymptomatik vorzubeugen und entgegenzuwirken. Eine ausgewogene Life-Balance (privates Umfeld, berufliches Umfeld und Hygiene der Grundbedürfnisse) ist daher unerlässlich.
Prevention of Cervical Cancer
Authors: Hillemanns Peter , Friese Klaus , Dannecker Christian , Klug Stefanie , Seifert Ulrike , Iftner Thomas , Hädicke Juliane , Löning Thomas , Horn Lars , Schmidt Dietmar , Ikenberg Hans , Steiner Manfred , Freitag Ulrich , Siebert Uwe , Sroczynski Gaby , Sauerbrei Willi , Beckmann Matthias , Gebhardt Marion , Friedrich Michael , Münstedt Karsten , Schneider Achim , Kaufmann Andreas , Petry K. , Schäfer Axel , Pawlita Michael , Weis Joachim , Mehnert Anja , Fehr Mathias , Grimm Christoph , Reich Olaf , Arbyn Marc , Kleijnen Jos , Wesselmann Simone , Nothacker Monika , Follmann Markus , Langer Thomas , Jentschke Matthias
Published: February 2019

Aims Annual opportunistic screening for cervical carcinoma has been done in Germany since 1971. The creation of this S3 guideline meets an important need, outlined in the National Cancer Plan, with regard to screening for cervical cancer, as this guideline aims to provide important information and support for planned organized screening for cervical cancer in Germany.

Methods With the financial support of German Cancer Aid, 21 professional societies developed evidence-based statements and recommendations (classified using the GRADE system) for the screening, management and treatment of precancerous conditions of the cervix. Two independent scientific institutes compiled systematic reviews for this guideline.

Recommendations The second part of this short summary deals with the triage, treatment and follow-up care of cervical dysplasia. With regard to those women who do not participate in screening, the guideline authors recommend sending out repeat invitation letters or an HPV self-collection kit. Colposcopy should be carried out for further investigation if cytology findings are Pap II-p and HPV test results are positive or if the results of an HPV 16 or HPV 18 screening test are positive. A single abnormal Pap smear should be triaged and investigated using HPV testing or p16/Ki67 dual staining.
Kosteneffektivität – Welche Auswirkungen haben Wartelisten bei
Operationen?
Authors: Thiem Helena
Published: February 2019

Ribera A et al. The impact of waiting for intervention on costs and
effectiveness: the case of transcatheter aortic valve replacement. Eur J Health
Econ 2018; 19: 945–956

Hohe Kosten innovativer Operations- und Behandlungsmethoden können trotz eines
Zusatznutzens den Zugang für die Patienten erschweren. Eine zeitliche
Verzögerung kann dabei negative Auswirkungen auf die Mortalität und
Lebensqualität der Betroffenen haben. Aufschluss über mögliche klinische wie
ökonomische Folgen von Beschränkungen des Zugangs zu wirksamen Innovationen
soll eine Analyse der Kosteneffektivität am Beispiel von Patienten mit
Aortenklappenstenose geben.
Iron-Catalysed Aerobic Oxidative C–C Bond Cleavage of Ketones for the Synthesis of Primary Amides
Authors: Zhan Haosheng , Hu Zhiwei , Tao Weihua , Ling Min , Cao Wei , Lin Jing , Liu Zhenhua , Wang Yu , Fang Zhongxue
Published: February 2019

An iron-catalysed aerobic oxidative C–C bond cleavage of ketones for the synthesis of primary amides has been developed using TEMPO and oxygen as an oxidant. This reaction tolerates a wide range of substrates, and primary amides are obtained in good to excellent yields. Substrates with long-chain alkyl substituents could also be selectively cleaved and converted into the corresponding amides.
ATP- and ADP-Induced Rat Platelet Aggregation: Significance of Plasma in ATP-Induced Aggregation
Authors: Haskel Ethan J , Agarwal Kailash C , Parks Robert E
Published: February 2019

ATP caused platelet aggregation in rat platelet-rich plasma (PRP) but in contrast strongly inhibited ADP-induced human platelet aggregation. ADP-induced aggregation of rat platelets suspended in human plasma was strongly inhibited by ATP, whereas human platelets in rat plasma were aggregated by ADP. The ATP analog β,γ-methylene ATP which is not dephosphorylated did not induce aggregation in rat PRP. Adenosine, AMP, 2- chloroadenosine, α,β-methylene ADP and β,γ-methylene ATP each inhibited ATP-induced aggregation of platelets in rat PRP to a similar extent as ADP-induced aggregation. A solution containing creatine kinase and creatine phosphate (which converts ADP to ATP) rapidly reversed both ADP- and ATP-induced aggregation in rat PRP; preincubation with this solution completely inhibited rat platelet aggregation induced by both ADP and ATP. Adenosine-8-14C-triphosphate ([14C]-ATP) conversion to [14C]-ADP was about five-fold faster in rat plasma than in human plasma. Addition of creatine phosphate to rat PRP strongly inhibited ATP-induced aggregation, while creatine or creatine kinase slightly potentiated aggregation by ATP. Creatine phosphate, creatine, or creatine kinase individually had minimal and varying effects on ADP-induced rat platelet aggregation. These results suggest that the observed phenomenon of ATP-induced aggregation in rat PRP is caused by a higher activity of creatine kinase in rat plasma than in human plasma, which converts the added ATP to ADP, a potent aggregator.
Relative Activities of Heparin Fractions Obtained by Gel Chromatography
Authors: Graham David T , Pomeroy Alan R
Published: February 2019

In order to investigate the reported heterogeneity of commercial heparin injections, lung and mucous preparations were fractionated by gel chromatography according to molecular size. Eluent pools were characterized by measuring electrophoretic mobility, anticoagulant activity using a reactivation assay and an anti-Xa assay, lipolytic activity and the protamine neutralization value. The only biological activity to show a marked relationship with the molecular size of the heparin fraction was the anti-Xa activation activity. This effect was more pronounced with the mucous heparins than with the lung heparin preparation studied.
Microsurgical Resection of Cerebellopontine Angle Meningioma
Authors: Cândido Duarte N. C. , Passos Gustavo A. R. , Rassi Marcio S. , de Oliveira Jean Gonçalves , Borba Luis A. B.
Published: February 2019

Meningiomas of the cerebellopontine angle (CPA) are the second most frequent lesions related to this region (around 10–15%),1 being the vestibular schwannomas the first (around 85%). This lesions arise from the dura of the petrosal surface of the temporal bone, lateral to the trigeminal nerve (Fig. 1). Variable attachment sites and directions of growth make different clinical presentations and operative challenges. This pathologies can be classified accordingly to they're extension related to the internal acoustic meatus in: postmeatal, premeatal, and large meningiomas with pre- and postmeatal extension (Fig. 2). We present an operative video performed by the senior author (L.A.B.B.). A 64-year-old woman with 3 months of complaint of left facial pain on the V2 territory of the trigeminal nerve and diplopia secondary to VI nerve paresis. Magnetic resonance imaging (MRI) scans demonstrated a large homogeneous enhancing lesion at the left CPA, extending pre- and postmeatal and from the tentorium cerebeli to the jugular foramen region, highly suggestive of CPA meningioma. Surgery was offered to the patient as a first option. In our point of view, neurophysiological monitoring with somatosensory and motor evoked potentials is mandatory while dealing with such large tumors around the CPA. The surgery was performed after a standard retrosigmoid craniotomy, with careful dissection and debulking while devascularizing the tumor from its petrosal attachment. Near-total resection was achieved and the patient had a remarkable postoperative outcome with improvement of the diplopia and facial pain with preservation of VII and VIII nerves function. The pathology demonstrated a grade 1 meningioma.

The link to the video can be found at: https://youtu.be/UVVyEhq8Fu0.
The Ultimate Skull Base Maneuver Does Not Involve Removing Bone: Quantifying the Benefits of the Interfascial Dissection
Authors: Effendi Sabih T. , Momin Eric N. , Basma Jaafar , Michael L Madison , Duckworth Edward A.M.
Published: February 2019

Introduction Several adjunctive osteal skull base maneuvers have been proposed to increase surgical exposure of the anterolateral approach. However, one of the easiest methods does not involve bone: the interfascial temporalis muscle dissection.

Methods Sequential dissections were performed bilaterally on five fixed silicone-injected cadaver heads. The amount of sphenoid drilling, scalp retraction, and brain retraction was standardized in all specimens. For each approach, surgical angles were measured for four deep targets: the tip of the anterior clinoid process, the internal carotid artery terminus, the origin of the posterior communicating artery, and the anterior communicating artery. Five surgical angles were measured for each target.

Results There were increases on the order of 20% in the anteroposterior (AP)-mid, AP–lateral, and mediolateral–anterior angles for all deep targets with interfascial approach versus a myocutaneous flap. An orbitozygomatic osteotomy additionally increased almost all the angles, but incrementally less so.

Conclusion An interfascial dissection increases the surgical exposure to a larger degree than additional osteotomies for several surgically relevant working angles. The addition of an orbitozygomatic osteotomy affords a particular benefit for the suprachiasmatic region. Increased adoption of interfascial mobilization or the temporalis muscle—an easily performed and low-risk maneuver—during anterolateral craniotomies may obviate the need for more involved skull base drilling.
Approaching the Sella through the Nonpneumatized Sphenoid in Pediatric Patients
Authors: Oviedo Parisa , Levy Michael L. , Nation Javan
Published: February 2019

Objective The purpose of this study is to specifically assess pediatric patients with nonpneumatized sphenoid sinuses who have undergone transsphenoidal resections of skull base tumors and assess the complications and outcomes.

Methods Data was collected by a retrospective chart review done on children ages 7 and under who underwent endoscopic tumor resection and had a partially or completely nonpneumatized sphenoid sinus on preoperative computed tomography imaging. Surgical data collected included surgical corridor, gross total versus subtotal resection, repair method, use of septal flap, intraoperative and postoperative cerebrospinal fluid leak, and estimated blood loss.

Results Six patients were identified that fit our inclusion criteria who underwent surgery between November 2015 and April 2018 (3 males, 3 females; average age = 4.28 years). Tumor pathologies include three craniopharyngiomas, Rathke cleft cyst, meningocele, and neuroblastoma. All cases involved varying percentages of sphenoid sinus pneumatization. All cases except one craniopharyngioma and the neuroblastoma required removal of cancellous bone to access pathology. Degree of sphenoid pneumatization tended to be greater with age and resulted in less intraoperative bleeding. The two youngest patients with completely nonpneumatized sphenoid sinuses lost 61.73 and 17.52% of their total blood volume intraoperatively. Procedures were able to be adequately performed and pathology completely addressed with minimal postoperative complications and no postoperative CSF leaks.

Conclusions Intraoperative challenges including hemorrhage are likely in nonpneumatized patients, and thus surgeons should be prepared with adequate vascular access and blood products. Hemorrhage and total blood volume loss are increased in the younger patients with no sphenoid pneumatization. Despite the additional challenges, a nonpneumatized sphenoid sinus is not a contraindication for an endoscopic resection in the pediatric population.
On a Plasminogen Activator from Human Plasma
Authors: Diaz Batista A , Hernandez Solana G , Corral Almonte J F
Published: February 2019

A plasminogen activating substance was purified from the dialysates of the eluates of glass adsorbed kallikrein from fresh human plasma, by chromatography on QAE-Sephadex A-50 and gel filtration in Sephadex G-25. The preparation was concentrated by lyophilization. Its electrophoretic mobility was found to be similar to that of prealbumin. Its molecular weight appeared to be 15000–18000 daltons. The analysis of aminoacids of this activator showed that it contains a high proportion of acid amino acids. The purified activator showed esterase activity, fibrinolytic activity and kininogenase activity on heated human plasma. These activities were respectively equivalent to 150 μM BAEe/mg protein, 19 × 103 units of streptokinase/μg protein and 250 μg bradykinin/mg protein.
The VvBAP1 gene is identified as a potential inhibitor of cell death in grape berries
Authors: Cao Shifeng , Xiao Zeyu , Jiranek Vladimir , Tyerman Stephen D.
Published: February 2019

Cell death (CD) in Vitis vinifera L grape berries, exemplified in Shiraz, occurs late in ripening influencing yield, berry and wine quality. Here we isolated and functionally characterised a BON1-associated gene, VvBAP1 from Shiraz berries, encoding a small protein with a C2 domain. VvBAP1 transcript increased during fruit development from veraison to harvest, and was significantly inhibited by drought stress 92 days after flowering when CD normally begins. This was correlated with high CD in Shiraz berries. The agrobacterium-mediated transient expression of VvBAP1 in tobacco leaves led to a decrease in electrolyte leakage and downregulated a marker gene (Hsr203J) for cell death. Expressing VvBAP1 in yeast (Saccharomyces cerevisiae) also alleviated cell death induced by hydrogen peroxide (H2O2). Overexpression of VvBAP1 in Arabidopsis increased resistance to H2O2 and reduced CD due to higher expression of genes involved in anti-oxidative responses. Arabidopsis overexpressing VvBAP1 displayed higher tolerance to drought accompanied by upregulation of antioxidant-related gene expression. VvBAP1 complemented an Arabidopsis bap1 knockout by abolishing its CD phenotypes. These results indicate that VvBAP1 may play a role in alleviating CD in grape berries and its downregulation under drought stress may be responsible for the generally observed increase in CD within the berry.
The content of immunomodulatory glycoepitopes in seminal plasma glycoproteins of fertile and infertile men
Authors: Kałuża Anna , Ferens-Sieczkowska Mirosława , Olejnik Beata , Kołodziejczyk Justyna , Zimmer Mariusz , Kratz Ewa Maria
Published: February 2019

According to a concept of fetoembryonic defence, protein–carbohydrate interaction may be involved in the regulation of maternal immunity that prevents rejection of allograft spermatozoa, embryo and fetus. In the present study we focussed on the evaluation of the expression of glycoepitopes that may be of crucial importance in this process: LewisY (LeY) and LewisX (LeX) as well as terminal sialylation. Polyacrylamide gel electrophoresis with sodium dodecyl sulphate was used to separate seminal plasma samples of fertile (n=10) and infertile (n=103) men; these were then probed with lectins specific to fucose (Lotus tetragonolobus agglutinin and Ulex europaeus agglutinin) and sialic acid (Sambucus nigra agglutinin and Maackia amurensis agglutinin). Differential expression of α2,3-bound sialic acid was found in six out of seven analysed bands, whereas differences in the other analysed glycoepitopes were found in fewer numbers of bands. Mass spectrometry analysis focussed on the identification of proteins carrying glycans with immunomodulatory epitopes, including fibronectin, lactoferrin, clusterin, zinc-α2-glycoprotein, prostate acid phosphatase and prostate-specific antigen; these should be submitted to further detailed analysis.
Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs
Authors: Limasset Antoine , Flot Jean-François , Peterlongo Pierre
Published: February 2019

Motivation

Short-read accuracy is important for downstream analyses such as genome assembly and hybrid long-read correction. Despite much work on short-read correction, present-day correctors either do not scale well on large datasets or consider reads as mere suites of k-mers, without taking into account their full-length sequence information.

Results

We propose a new method to correct short reads using de Bruijn graphs and implement it as a tool called Bcool. As a first step, Bcool constructs a compacted de Bruijn graph from the reads. This graph is filtered on the basis of k-mer abundance then of unitig abundance, thereby removing most sequencing errors. The cleaned graph is then used as a reference on which the reads are mapped to correct them. We show that this approach yields more accurate reads than k-mer-spectrum correctors while being scalable to human-size genomic datasets and beyond.

Availability and implementation

The implementation is open source, available at http://github.com/Malfoy/BCOOL under the Affero GPL license and as a Bioconda package.

Supplementary information

Supplementary data are available at Bioinformatics online.
pldist: ecological dissimilarities for paired and longitudinal microbiome association analysis
Authors: Plantinga Anna M , Chen Jun , Jenq Robert R , Wu Michael C
Published: February 2019

Motivation

The human microbiome is notoriously variable across individuals, with a wide range of ‘healthy’ microbiomes. Paired and longitudinal studies of the microbiome have become increasingly popular as a way to reduce unmeasured confounding and to increase statistical power by reducing large inter-subject variability. Statistical methods for analyzing such datasets are scarce.

Results

We introduce a paired UniFrac dissimilarity that summarizes within-individual (or within-pair) shifts in microbiome composition and then compares these compositional shifts across individuals (or pairs). This dissimilarity depends on a novel transformation of relative abundances, which we then extend to more than two time points and incorporate into several phylogenetic and non-phylogenetic dissimilarities. The data transformation and resulting dissimilarities may be used in a wide variety of downstream analyses, including ordination analysis and distance-based hypothesis testing. Simulations demonstrate that tests based on these dissimilarities retain appropriate type 1 error and high power. We apply the method in two real datasets.

Availability and implementation

The R package pldist is available on GitHub at https://github.com/aplantin/pldist.

Supplementary information

Supplementary data are available at Bioinformatics online.
Protein model quality assessment using 3D oriented convolutional neural networks
Authors: Pagès Guillaume , Charmettant Benoit , Grudinin Sergei
Published: February 2019

Motivation

Protein model quality assessment (QA) is a crucial and yet open problem in structural bioinformatics. The current best methods for single-model QA typically combine results from different approaches, each based on different input features constructed by experts in the field. Then, the prediction model is trained using a machine-learning algorithm. Recently, with the development of convolutional neural networks (CNN), the training paradigm has changed. In computer vision, the expert-developed features have been significantly overpassed by automatically trained convolutional filters. This motivated us to apply a three-dimensional (3D) CNN to the problem of protein model QA.

Results

We developed Ornate (Oriented Routed Neural network with Automatic Typing)—a novel method for single-model QA. Ornate is a residue-wise scoring function that takes as input 3D density maps. It predicts the local (residue-wise) and the global model quality through a deep 3D CNN. Specifically, Ornate aligns the input density map, corresponding to each residue and its neighborhood, with the backbone topology of this residue. This circumvents the problem of ambiguous orientations of the initial models. Also, Ornate includes automatic identification of atom types and dynamic routing of the data in the network. Established benchmarks (CASP 11 and CASP 12) demonstrate the state-of-the-art performance of our approach among single-model QA methods.

Availability and implementation

The method is available at https://team.inria.fr/nano-d/software/Ornate/. It consists of a C++ executable that transforms molecular structures into volumetric density maps, and a Python code based on the TensorFlow framework for applying the Ornate model to these maps.

Supplementary information

Supplementary data are available at Bioinformatics online.
UnfairDuelMerge: Merging with Even Fewer Moves
Authors: Mergen Sergio L S
Published: February 2019

The merging problem consists of forming an ordered sequence with n elements from two ordered sequences with n1 and n2 elements (where n=n1+n2). One recent development in in-place merging is a minimum storage algorithm (DuelMerge) that requires half the number of moves in average, when compared to other partition-based algorithms. The reduction is achieved by limiting the exchange to blocks with equal sizes, and using a particularly suited exchange method. The algorithm proposed in this paper (UnfairDuelMerge) reduces the number of moves even further, by limiting the exchange to blocks where the left side is one element larger than the right side, and using the floating hole technique to perform the exchange. As its predecessor, the algorithm is stable, in-place and the merge is asymptotically performed with a O(nlognn) runtime. A formal description of the method is provided, as well as an analysis of stability, memory cost and time complexity. Experimental results show that the proposed algorithm outperforms other partition-based solutions when applied directly to merge ordered sequences and when used within MergeSort.
Modular hierarchical and power-law small-world networks bear structural optima for minimal first passage times and cover time
Authors: Maier Benjamin F , Huepe Cristián , Brockmann Dirk
Published: February 2019

Networks that are organized as a hierarchy of modules have been the subject of much research, mainly focusing on algorithms that can extract this community structure from data. The question of why modular hierarchical (MH) organizations are so ubiquitous in nature, however, has received less attention. One hypothesis is that MH topologies may provide an optimal structure for certain dynamical processes. We revisit a MH network model that interpolates, using a single parameter, between two known network topologies: from strong hierarchical modularity to an Erdős–Rényi random connectivity structure. We show that this model displays a similar small-world effect as the Kleinberg model, where the connection probability between nodes decays algebraically with distance. We find that there is an optimal structure, in both models, for which the pair-averaged first passage time (FPT) and mean cover time of a discrete-time random walk are minimal, and provide a heuristic explanation for this effect. Finally, we show that analytic predictions for the pair-averaged FPT based on an effective medium approximation fail to reproduce these minima, which implies that their presence is due to a network structure effect.
Clinical impact of native T1 mapping for detecting myocardial impairment in takotsubo cardiomyopathy
Authors: Aikawa Yukio , Noguchi Teruo , Morita Yoshiaki , Tateishi Emi , Kono Atsushi , Miura Hiroyuki , Komori Yoshiaki , Asaumi Yasuhide , Fukuda Tetsuya , Yasuda Satoshi
Published: February 2019

Aims

To investigate the clinical impact of T1 mapping for detecting myocardial impairment in takotsubo cardiomyopathy (TTC) over time.

Methods and results

In 23 patients with the apical ballooning type of TTC, the following 3T magnetic resonance (MR) examinations were performed at baseline and 3 months after TTC onset: T2-weighted imaging, T2 mapping, native T1 mapping, extracellular volume fraction (ECV), and late gadolinium enhancement. Eight healthy controls underwent the same MR examinations. Serial echocardiography was performed daily for ≥7 days and monthly until 3 months after onset. The median time from onset to MR examination was 7 days. During the acute phase, patients had, relative to controls, higher native T1 (1438 ± 162 vs. 1251 ± 90 ms, P < 0.001), ECV (35 ± 5% vs. 29 ± 4%, P < 0.001), and T2 (90 ± 34 vs. 68 ± 12 ms, P < 0.001) for the entire heart. Per-region analysis showed that higher native T1 and T2 in the basal region were correlated with lower left ventricular ejection fraction (r = −0.599, P = 0.004 and r = −0.598, P = 0.003, respectively). Receiver operator characteristic analysis showed that the area under the curve for native T1 (0.96) was significantly larger than that for T2 (0.86; P = 0.005) but similar to that for ECV (0.92; P = 0.104). At 3-month follow-up, native T1, ECV, and T2 in the apical region remained significantly elevated in all patients with TTC. The number of left ventricular (LV) segments with elevated native T1 (cut-off value 1339 ms) was significantly correlated with prolonged LV wall motion recovery time (r = 0.494, P = 0.027).

Conclusion

Characterization of myocardium with native T1 mapping is a promising method for predicting LV wall motion restoration in TTC.
Famine on the Coast: The Royal Navy and the Relief of Ireland, 1846–1847
Authors: McLean David
Published: February 2019

While the significance of private charity, local organisation and government policy have all been evaluated with respect to Irish famine relief, the role of the Royal Navy in distributing food and assisting ashore has been overlooked within the existing historical literature. Operating from its base at Cork and receiving provisions from Plymouth and Portsmouth, the navy battled against Atlantic storms throughout the winter of 1846–7, and for months thereafter, to supply coastal food depots. It had also to confront a growing lawlessness which placed merchant craft at sea and the movement of aid on shore in peril. Yet the navy was not only a vital means of transport. To assist with medical care, the Admiralty sent surgeons to Ireland who reported at length on the extent of starvation and the worst effects of disease—an initiative which brought the Admiralty into conflict with the authorities in Dublin. Furthermore, naval activities had always to be co-ordinated with the Treasury in London, which had overall responsibility for Irish relief yet often far less understanding of the practicalities of distribution along the south and west coasts of Ireland. The unexplored archival material used allows an original perspective on the efforts made to alleviate the worst effects of Black ’47 and the calamity which overwhelmed so much of Ireland.
The association between self-harm and area-level characteristics in Northern Ireland: an ecological study
Authors: Griffin Eve , Bonner Brendan , Dillon Christina B , O’Hagan Denise , Corcoran Paul
Published: February 2019

Background

Factors contributing to suicidal behaviour are complex and multi-faceted. This study took an ecological approach to examine the association between area-level factors and rates of self-harm in Northern Ireland.

Methods

Data on self-harm presentations to emergency departments (EDs) were obtained from the Northern Ireland Self-harm Registry. The study included residents of Northern Ireland aged 16–64 years. Deprivation was measured using the Northern Ireland Multiple Deprivation Measure 2017. Population density and social fragmentation were calculated using measures from the 2011 census. Associations between area-level factors and self-harm rates were explored using negative binomial regression.

Results

Between 2013 and 2015, 14 477 individuals aged 16–64 years presented to EDs in Northern Ireland following self-harm. The rate of self-harm was 472 per 100 000 and was higher for male residents (478 vs. 467). Self-harm rates were highest in urban areas—680 per 100 000 in Belfast City and 751 per 100 000 in Derry City. Rates of self-harm in Northern Ireland were more than four times higher in the most deprived areas. A positive association with rates of self-harm held for the deprivation domains of employment, crime, education, health and income. There was a moderate association with population density. Some gender differences emerged, with associations with male rates of self-harm more pronounced.

Conclusion

These findings indicate that self-harm rates are highest for those residing in highly deprived areas, where unemployment, crime and low level of education are challenges. Community interventions tailored to meet the needs of specific areas may be effective in reducing suicidal behaviour.
The Application of a Self-Labeling Approach among Military-Connected Adolescents in a Public School Setting
Authors: Kranke Derrick , Barmak Shant , Weiss Eugenia , Dobalian Aram
Published: February 2019

The contextual factors and individual responses to the labeling of military-connected adolescents as “being in a military family” is an understudied yet important phenomenon. Minimal research construes the experience of being in a military family as a label applied to military-connected populations by people in society. However, social environmental factors associated with school setting among military-connected adolescents being in a military family have common components to the process of self-labeling. This article seeks to explore the concept and application of self-labeling by (a) providing a literature review of self-labeling among military-connected adolescents and (b) relying on modified labeling theory to identify any consistencies or potential nuances. The analysis of the process is strictly hypothetical, but could help to account for widely varying responses, sequence of events, and underlying reasons for the behaviors among some military-connected adolescents identified in the literature review and in light of the U.S. protracted military involvement in Iraq and Afghanistan. Authors conclude by highlighting the need for future research to assess the adequacy of this self-labeling framework to ensure the healthy development of military-connected youths.
To jump or not to jump? A multicentre propensity-matched study of sequential vein grafting of the heart
Authors: Skov Jens K , Kimose Hans-Henrik , Greisen Jacob , Jakobsen Carl-Johan
Published: February 2019

OBJECTIVES

In this propensity-matched study we investigated the outcome after grafting with either a single vein or a sequential vein grafting strategy. Outcomes were primarily risk of reintervention and death in the short, intermediate and long term (10 years).

MATERIALS

In the period from 2000 to 2016, data from 24 742 patients undergoing coronary artery bypass grafting were extracted from the Western Denmark Heart Registry, where data are registered perioperatively. We used a propensity-matched study in which the study groups were matched on parameters primarily from the EuroSCORE. The numbers of patients in both groups after matching were 3380.

RESULTS

Single grafts resulted in significantly more postoperative bleeding and were more time-consuming. No differences were seen regarding in-hospital events such as stroke, acute myocardial infarction, dialysis or arrhythmias. After 30 days, patients in the jump graft group showed an increased rate of reintervention due to ischaemia after adjusting for confounding factors [hazard ratio (HR) 2.08, 95% confidence interval 1.01–4.34]. In addition, after adjusting for known confounders, sequential grafts were found to increase the risk of mortality at 6 months (HR 1.51, 95% confidence limits 1.07–2.11) and 5 years (HR 1.23, 95% confidence limits 1.04–1.46).

CONCLUSIONS

This propensity-matched analysis suggested, although discretely, that a jump graft as a grafting strategy is associated with a slightly increased risk of mortality and early graft failure and that a single grafting strategy to the coronary arteries should be preferred when feasible.
Variations in 𝔸1 on a Theme of Mohan Kumar
Authors: Wendt Matthias
Published: February 2019

For every prime $p$, Mohan Kumar constructed examples of stably free modules of rank $p$ on suitable $p+1$-dimensional smooth affine varieties. This note discusses how to detect the corresponding unimodular rows by an explicit motivic cohomology group. Using the recent developments in the $\mathbb{A}^1$-obstruction classification of vector bundles, this provides an alternative proof of non-triviality of Mohan Kumar’s stably free modules. The reinterpretation of Mohan Kumar’s examples also allows to produce interesting examples of stably trivial torsors for other algebraic groups.
Data-driven modeling of diabetes care teams using social network analysis
Authors: Ostovari Mina , Steele-Morris Charlotte-Joy , Griffin Paul M , Yu Denny
Published: February 2019

Objective

We assess working relationships and collaborations within and between diabetes health care provider teams using social network analysis and a multi-scale community detection.

Materials and Methods

Retrospective analysis of claims data from a large employer over 2 years was performed. The study cohort contained 827 patients diagnosed with diabetes. The cohort received care from 2567 and 2541 health care providers in the first and second year, respectively. Social network analysis was used to identify networks of health care providers involved in the care of patients with diabetes. A multi-scale community detection was applied to the network to identify groups of health care providers more densely connected. Social network analysis metrics identified influential providers for the overall network and for each community of providers.

Results

Centrality measures identified medical laboratories and mail-order pharmacies as the central providers for the 2 years. Seventy-six percent of the detected communities included primary care physicians, and 97% of the communities included specialists. Pharmacists were detected as central providers in 24% of the communities.

Discussion

Social network analysis measures identified the central providers in the network of diabetes health care providers. These providers could be considered as influencers in the network that could enhance the implication of promotion programs through their access to a large number of patients and providers.

Conclusion

The proposed framework provides multi-scale metrics for assessing care team relationships. These metrics can be used by implementation experts to identify influential providers for care interventions and by health service researchers to determine impact of team relationships on patient outcomes.