bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic profiling of tumours using both circulating free DNA and circulating tumour cells isolated from the same preserved whole blood sample
Authors: Rothwell Dominic G. , Smith Nigel , Morris Daniel , Leong Hui Sun , Li Yaoyong , Hollebecque Antoine , Ayub Mahmood , Carter Louise , Antonello Jenny , Franklin Lynsey , Miller Crispin , Blackhall Fiona , Dive Caroline , Brady Ged
Published: November 2015

Molecular information obtained from cancer patients' blood is an emerging and powerful research tool with immense potential as a companion diagnostic for patient stratification and monitoring. Blood, which can be sampled routinely, provides a means of inferring the current genetic status of patients' tumours via analysis of circulating tumour cells (CTCs) or circulating tumour DNA (ctDNA). However, accurate assessment of both CTCs and ctDNA requires all blood cells to be maintained intact until samples are processed. This dictates for ctDNA analysis EDTA blood samples must be processed with 4 h of draw, severely limiting the use of ctDNA in multi‐site trials. Here we describe a blood collection protocol that is amenable for analysis of both CTCs and ctDNA up to four days after blood collection. We demonstrate that yields of circulating free DNA (cfDNA) obtained from whole blood CellSave samples are equivalent to those obtained from conventional EDTA plasma processed within 4 h of blood draw. Targeted and genome‐wide NGS revealed comparable DNA quality and resultant sequence information from cfDNA within CellSave and EDTA samples. We also demonstrate that CTCs and ctDNA can be isolated from the same patient blood sample, and give the same patterns of CNA enabling direct analysis of the genetic status of patients' tumours.

In summary, our results demonstrate the utility of a simple approach that enabling robust molecular analysis of CTCs and cfDNA for genotype‐directed therapies in multi‐site clinical trials and represent a significant methodological improvement for clinical benefit.
How Partners Experience Personality Change After Traumatic Brain Injury – Its Impact on Their Emotions and their Relationship
Authors: Bodley-Scott Sarah E. M. , Riley Gerard A.
Published: November 2015

Objective: The aim of this qualitative study was to explore how spouses/partners experience social, emotional and behavioural changes in persons following traumatic brain injury (TBI), with a particular focus on their emotional impact and the effect on the couple relationship.

Method: Interpretative phenomenological analysis (IPA) of interview data explored five women's experiences of these changes in their partners following TBI.

Results: Themes describe the direct emotional impact of living with the changes as well as the emotional impact of attempts to manage and make sense of the changes (identity change, managing the changes and making sense of the changes). The impact on the couple relationship is described under the themes of feeling love and receiving love. Changes led three of the participants to experience their partner as having been replaced by a new person; they actively disliked this new person; they felt unable to love the new person in the same way as the old person; and their love was defined in terms of a caring relationship, rather than a spousal relationship.

Conclusions: The study provides insight into why social, emotional and behavioural changes might be so consistently associated with reduced emotional wellbeing and lower levels of relationship quality and satisfaction.
Single Center Outcomes of Status Epilepticus at a Paediatric Intensive Care Unit
Authors: Shah Samir , Shah Namrata , Johnson Robert , West Alina Nico , Prasad Narayan
Published: November 2015

Background:Status epilepticus (SE) is a frequent admission diagnosis to paediatric intensive care units (PICUs) and is associated with variable outcomes. We have audited our experience of patients presenting in SE at a Canadian PICU to determine unfavorable outcome variables.Methods:Charts of patients <18 years of age presenting in SE to a tertiary care PICU over a 10-year period were audited. Data were analyzed at three care-points: transport, the emergency department (ED) and the PICU. Patient outcome before PICU discharge was categorized as “favorable” for return to pre-status functioning level or “unfavorable” for new deficit/death. Student’st-test andthe Kruskal-Wallis test were used for analysis of normal and skewed continuous variables, respectively, and either Chi-square test or Fisher’s exact test for categorical variables.Results:189 patients (54% males) were identified with a median age of 1.9 years. Idiopathic SE had the highest incidence; infectious/vascular etiologies were associated with more unfavorable outcomes. Progression to refractory SE in the ED had a higher incidence of death (p<0.05). Patients with an unfavorable outcome had a higher incidence of apnea during transport (p=0.01), longer hospital stays (p<0.05), need for therapeutic coma (p=0.01), longer duration of therapeutic coma (p<0.05), need for mechanical ventilation (p<0.05), and recurrent or refractory seizures during inpatient stay (p<0.05). Multivariate analysis of unfavorable outcomes of patients in SE presenting to the PICU included renal failure, cerebral edema, apnea during transport, refractory seizures, and recurrent seizures.Conclusions:Refractory seizures in children presenting with SE are associated with worsened outcomes in the PICU.
Conceiving a national head and neck cancer screening programme
Authors: Gogarty D S , Shuman A , O'Sullivan E M , Sheahan P , Kinsella J , Timon C , O'Neill J P
Published: November 2015

Background:

This study was undertaken to determine the optimum approach to screening for head and neck cancer based on international experiences.

Objective:

To determine whether or not head and neck cancer is suitable for screening, and, if so, what the ideal approach should be.

Methods:

An electronic search of online databases up to and including May 2014 was conducted. Key search terms included ‘head and neck’, ‘cancer’, ‘screening’, ‘larynx’, ‘oropharynx’ and ‘oral’.

Results:

Subset analysis of high-risk cohorts showed statistically significant improvements in early detection of head and neck cancer via screening.

Conclusion:

Current levels of public awareness regarding head and neck cancers are suboptimal, despite increased incidence and mortality. Scheduled and opportunistic screening, coupled with efforts to enhance education and health behaviour modification, are highly recommended for pre-defined, high-risk, targeted populations. This can enable early detection and therefore improve morbidity and mortality.
Occurrence, distribution and behaviour of Bryde's whales (Cetacea: Mysticeti) off south-east Brazil
Authors: Gonçalves Leandra Regina , Augustowski Mabel , Andriolo Artur
Published: November 2015

Bryde's whales are among the lesser known balaenopterids found in Brazilian waters, as well as globally. At the beginning of this project, only occasional sightings of this species were identified off the coast of São Paulo State. In this paper, we present the results of our investigations into the occurrence and behaviour of Bryde's whales along the São Paulo coast, both inside and outside the Marine State Park of Laje de Santos, as a contribution to biological and behavioural knowledge of Bryde's whales under the conservation scope. Sighting surveys were conducted from January 2003 to July 2005 in coastal and oceanic areas. During the survey, 42 sightings were made, totalling 71 individuals, between the isobaths of 20 and 3000 m. Sightings and individual rates were higher in coastal areas during the summer season. Different kinds of behaviour were observed in coastal and oceanic areas. At the 1200 m isobath, notable social interactions were observed in which four adult individuals performed breaching – the first report of this behavioural pattern for Brazil. Results suggest that Bryde's whales possibly use coastal areas for feeding and may migrate to oceanic areas for breeding, thus providing important aspects that must be considered for the proper management of Marine Protected Areas and for oceanic areas, especially considering the intensive and continuous increase of oil and gas exploitation activities in those areas. Data reported here, therefore, constitute a significant contribution in Bryde's whale research and to cetacean conservation efforts in Brazil.
The biology and functional morphology of the predatory septibranch Cardiomya costellata (Deshayes, 1833) (Bivalvia: Anomalodesmata: Cuspidariidae) from the Acores: survival at the edge
Authors: Morton Brian
Published: November 2015

This is the first comprehensive anatomical study of a representative of the septibranch Cuspidariidae. Particular interest in Cardiomya costellata is related to the fact that only two species of such predatory septibranchs have been recorded from the remote Açorean Archipelago and, here, individuals of both taxa are half the shell length of conspecifics throughout the species’ North-eastern Atlantic range. The shell of C. costellata is thin, fragile and rostrate. This latter attribute allows the inhalant siphon (as in other cuspidarioids) to be extended towards potential prey to effect their capture. How this extension is effected has been described but, herein, the hydrodynamic forces needed to achieve this are put into a firmer anatomical context. Uniquely amongst the Anomalesmata, cuspidarioids have, previously, been regarded as dioecious. This is not the case for C. costellata, which is a protandric consecutive hermaphrodite. The gonads and reproductive strategy of this species are compared with those of the spheniopsid Grippina coronata that is representative of a second cuspidarioid family of deeper water predators and which is a simultaneous hermaphrodite brooding self-fertilized embryos in the gonadial follicles with their release being post mortem. Some evidence suggests that in the Açores, the possible crustacean prey of C. costellata are also smaller than their mainland conspecifics, which, when viewed in the overall context of the predator's biology and anatomy, might explain its poor success in the oligotrophic waters of these mid-Atlantic islands.
A Dalit Paradigm: A new narrative in South Asian historiography
Authors: JANGAM CHINNAIAH
Published: November 2015

This is the meaning of Negro History Week. It is not so much a Negro History Week as it is a History Week. We should emphasize not Negro History, but the Negro in history. What we need is not a history of selected races or nations, but the history of the world void of national bias, race hate, and religious prejudice. There should be no indulgence in undue eulogy of the Negro. The case of the Negro is well taken care of when it is shown how he has influenced the development of civilization.1
Developing Brief Opportunistic Interactions: practitioners facilitate patients to identify and change health risk behaviours at an early preventive stage
Authors: Docherty Barbara , Sheridan Nicolette , Kenealy Timothy
Published: November 2015

Aim

To identify shortcomings in existing models of patient behaviour change, and present the development and testing of a novel approach using practitioner facilitation and person-focussed conversations that identifies and addresses behaviours at an earlier stage than current models.

Background

Systematic strategies used by health professionals to change patient behaviours began with motivational interviewing and brief intervention approaches for serious addictive behaviours. Practitioners typically presume they should drive the process of patient behaviour change. Attempts to transfer these approaches to primary care, and a broader range of health risk behaviours, have been less successful. The TADS programme (Tobacco, Alcohol and Other Drugs, later Training and Development Services) began teaching motivational interviewing and brief interventions to practitioners in New Zealand in 1996. Formal and informal evaluations showed that practitioners used screening tools that patients rejected and that led to incomplete disclosure, used language that did not engage patients, failed to identify the behaviours patients wished to address and therefore misdirected interventions.

Methods

Iterative development of new tools with input from patients and primary care clinicians.

Findings

The TADS programme developed a questionnaire whose results remained private to the patient, which enabled the patient to identify personal behaviours that they might choose to change (the TADS Personal Assessment Choice Tool). This was assisted by a brief conversation that facilitated and supported any change prioritised by the patient (the TADS Brief Opportunistic Interaction). The need for this approach, and its effectiveness, appeared to be similar across adults, youth, different ethnic groups and people in different socio-economic circumstances. Behaviours patients identified were often linked to other health risk behaviours or early-stage mental health disorders that were not easily detected by practitioner-driven screening or inquiry. The long-term effectiveness of this approach in different populations in primary health care settings requires further evaluation.
Crossing Mexico (1620–1621): Franciscan Nuns and Their Journey to the Philippines
Authors: Owens Sarah E.
Published: November 2015

In 1620, almost a hundred years after the Virgin of Guadalupe is said to have appeared to Juan Diego on the Hill of Tepeyac, a small group of Spanish nuns paid a visit to the chapel dedicated to Our Lady of Guadalupe. Like many others before and after them they stopped at the shrine on their way to Mexico City. The Franciscan nuns were traveling from Toledo to Manila and were about to cross Mexico to board the yearly Manila Galleon at the port of Acapulco.
Landschaft der Herzen III
Authors: Becker-Glauch Wulf
Published: November 2015

Zusammenfassung. Landschaft der Herzen–mitten im Krieg und auf dem Rückzug ein menschliches Zeugnis der Kunst von Reinhard und Irmgard Becker-Glauch als Halt zum Durchhalten des Stabsgefreiten und Hoffnung auf Frieden. Die Kunst begleitet und sucht ihren Ausdruck im einzelnen Menschen, der für viele, besonders die Kameraden, spricht. Bei all dem Unheil der Nazizeit und des 2. Weltkrieges vergisst man zu Recht, dass menschliches Verhalten möglich war, denn es war unauffällig. Landschaft der Herzen III geht auf dessen Voraussetzungen bei meinem Bruder Reinhard im christlichen Elternhaus und im humanistischen Gymnasium ein. Es werden vor allem Gedichte des 14 – 16-jährigen über Zeit, Ewigkeit und Tod vorgestellt und seine Erzählung Grenzen als Zeichen deutsch-polnischer Freundschaft im Jahre 1940 sowie Briefe aus der Vorgeschichte der Erzählung. Eingeschoben ist ein kleiner Beitrag zu Gedichten über Deutschland von Klopstock, Hölderlin und R. A. Schröder u. a.
A Big Five Facet Analysis of a Paranoid Personality	Disorder
Authors: Furnham Adrian , Crump John
Published: November 2015

Abstract. Around 4,100 British adults completed the NEO-PI-R ( Costa & McCrae, 1985 ), which measures the Big Five Personality factors at the Domain and the Facet level, as well as the Hogan Development Survey ( Hogan & Hogan, 2009 ) measure of Paranoid Personality Disorder called Sceptical. This study sought to validate this measure by comparing NEO facet correlational results with other studies. The Sceptical score from the HDS was the criterion variable in the correlations and multiple regressions. Sceptical people were Disagreeable, Neurotic, and Conscientious. Facet analysis showed them low on Trust, Compliance, and Straightforwardness but high on Depression and Angry Hostility. Limitations of the study are discussed.
An Ionospheric Index to Predict Earthquakes Falls Short
Authors: Wheeling Kate
Published: November 2015

Scientists disagree about the validity of the spatial scintillation index, a tool that aims to forecast earthquakes based on atmospheric disturbances.
Low-Altitude Clouds Play an Important Role in a Changing Climate
Authors: Strelich Lily
Published: November 2015

Scientists uncover the mechanics behind tropical marine low cloud cover and its influence on models of anthropogenic climate change.
Climate Change Is a Conservative Issue, British Minister Says
Authors: Showstack Randy
Published: November 2015

The UK foreign minister argues for dealing with climate change with market-based solutions. Asked separately about this approach, a U.S. cabinet secretary supports the general goal.
Ice Loss Benefits Adélie Penguins—For Now
Authors: Sullivan Cody
Published: November 2015

New research that may presage effects of climate change on this species looks back 22,000 years, finding robust growth in the East Antarctic population as melting followed the last ice age.
PPARγ regulated CIDEA affects pro-apoptotic responses in glioblastoma
Authors: Chatterjee A , Mondal P , Ghosh S , Mehta VS , Sen E
Published: November 2015

Refractoriness of glioblastoma multiforme (GBM) to current treatment paradigms has necessitated identification of new targets to better the existing therapeutic strategies. One such target is peroxisome proliferator-activated receptor gamma (PPARγ) – a transcription factor involved in regulation of lipid metabolism and inflammation. Expression of PPARγ, a known regulator of cell death-inducing DFFA-like effector (CIDEA), is modulated by hypoxia inducible factor (HIF-1α). While the involvement of CIDEA in lipid metabolism is known, its role in malignancies remains largely unknown. An elevated PPARγ and low CIDEA level was observed in GBM tumors as compared with surrounding non-neoplastic tissue. As reciprocal relation exists between PPAR and HIF-1α: and as HIF-1α is a key component in glioma progression, their role in regulating CIDEA expression in glioblastoma was investigated. Although HIF-1α inhibition had no effect on CIDEA expression, pharmacological inhibition of PPARγ elevated CIDEA levels. PPARγ mediated upregulation of CIDEA was accompanied by decreased recruitment of NFκB and SP1 to their predicted binding sites on CIDEA promoter. Ectopic expression of CIDEA triggered apoptosis, activated JNK, decreased HIF-1α activation and increased PPARγ levels in glioma cells. While CIDEA overexpression induced actin cytoskeletal disruption, cell cycle arrest, release of pro-inflammatory cytokine IL-6 in a JNK-dependent manner; CIDEA mediated apoptotic cell death, decreased STAT3 phosphorylation and increased p53 acetylation was JNK independent. This study highlights for the first time the existence of (i) PPARγ-CIDEA regulatory loop in glioma and (ii) novel function of CIDEA as regulator of glioma cell survival.
Sperm Associated Antigen 6 (SPAG6) Regulates Fibroblast Cell Growth, Morphology, Migration and Ciliogenesis
Authors: Li Wei , Mukherjee Abir , Wu Jinhua , Zhang Ling , Teves Maria E. , Li Hongfei , Nambiar Shanti , Henderson Scott C. , Horwitz Alan R. , Strauss III Jerome F. , Fang Xianjun , Zhang Zhibing
Published: November 2015

MammalianSpag6is the orthologue of ChlamydomonasPF16, which encodes a protein localized in the axoneme central apparatus and regulates flagella/cilia motility. MostSpag6-deficient mice are smaller in size than their littermates. Because SPAG6 decorates microtubules, we hypothesized that SPAG6 has other roles related to microtubule function besides regulating flagellar/cilia motility. Mouse embryonic fibroblasts (MEFs) were isolated fromSpag6-deficient and wild-type embryos for these studies. Both primary and immortalizedSpag6-deficient MEFs proliferated at a much slower rate than the wild-type MEFs and they had a larger surface area. Re-expression of SPAG6 in theSpag6-deficient MEFs rescued the abnormal cell morphology.Spag6-deficient MEFs were less motile than wild-type MEFs, as shown by both chemotactic analysis and wound-healing assays.Spag6-deficient MEFs also showed reduced adhesion associated with a non-polarized F-actin distribution. Multiple centrosomes were observed in theSpag6-deficient MEF cultures. The percentage of cells with primary cilia was significantly reduced compared to the wild-type MEFs and someSpag6-deficient MEFs developed multiple cilia. Furthermore, SPAG6 selectively increased expression of acetylated tubulin, a microtubule stability marker. TheSpag6-deficient MEFs were more sensitive to paclitaxel, a microtubule stabilizer. Our studies reveal new roles for SPAG6 in modulation of cell morphology, proliferation, migration and ciliogenesis.
Plasma proteomic analysis of active and torpid greater mouse-eared bats (Myotis myotis)
Authors: Hecht Alexander M. , Braun Beate C. , Krause Eberhard , Voigt Christian C. , Greenwood Alex D. , Czirják Gábor Á.
Published: November 2015

Hibernation is a physiological adaptation to overcome extreme environmental conditions. It is characterized by prolonged periods of torpor interrupted by temporary arousals during winter. During torpor, body functions are suppressed and restored rapidly to almost pre-hibernation levels during arousal. Although molecular studies have been performed on hibernating rodents and bears, it is unclear how generalizable the results are among hibernating species with different physiology such as bats. As targeted blood proteomic analysis are lacking in small hibernators, we investigated the general plasma proteomic profile of European Myotis myotis and hibernation associated changes between torpid and active individuals by two-dimensional gel electrophoresis. Results revealed an alternation of proteins involved in transport, fuel switching, innate immunity and blood coagulation between the two physiological states. The results suggest that metabolic changes during hibernation are associated with plasma proteomic changes. Further characterization of the proteomic plasma profile identified transport proteins, coagulation proteins and complement factors and detected a high abundance of alpha-fetoprotein. We were able to establish for the first time a basic myotid bat plasma proteomic profile and further demonstrated a modulated protein expression during torpor in Myotis myotis, indicating both novel physiological pathways in bats in general and during hibernation in particular.
Nopaline-type Ti plasmid of Agrobacterium encodes a VirF-like functional F-box protein
Authors: Lacroix Benoît , Citovsky Vitaly
Published: November 2015

During Agrobacterium-mediated genetic transformation of plants, several bacterial virulence (Vir) proteins are translocated into the host cell to facilitate infection. One of the most important of such translocated factors is VirF, an F-box protein produced by octopine strains of Agrobacterium, which presumably facilitates proteasomal uncoating of the invading T-DNA from its associated proteins. The presence of VirF also is thought to be involved in differences in host specificity between octopine and nopaline strains of Agrobacterium, with the current dogma being that no functional VirF is encoded by nopaline strains. Here, we show that a protein with homology to octopine VirF is encoded by the Ti plasmid of the nopaline C58 strain of Agrobacterium. This protein, C58VirF, possesses the hallmarks of functional F-box proteins: it contains an active F-box domain and specifically interacts, via its F-box domain, with SKP1-like (ASK) protein components of the plant ubiquitin/proteasome system. Thus, our data suggest that nopaline strains of Agrobacterium have evolved to encode a functional F-box protein VirF.
Slit2N Inhibits Transmission of HIV-1 from Dendritic Cells to T-cells by Modulating Novel Cytoskeletal Elements
Authors: Shrivastava Ashutosh , Prasad Anil , Kuzontkoski Paula M. , Yu Jinlong , Groopman Jerome E.
Published: November 2015

Dendritic cells are among the first cells to encounter sexually acquired human immunodeficiency virus (HIV-1), in the mucosa and they can transmit HIV-1 to CD4+ T-cells via an infectious synapse. Recent studies reveal that actin-rich membrane extensions establish direct contact between cells at this synapse and facilitate virus transmission. Genesis of these contacts involves signaling through c-Src and Cdc42, which modulate actin polymerization and filopodia formation via the Arp2/3 complex and Diaphanous 2 (Diaph2). We found that Slit2N, a ligand for the Roundabout (Robo) receptors, blocked HIV-1-induced signaling through Arp2/3 and Diaph2, decreased filopodial extensions on dendritic cells and inhibited cell-to-cell transmission of HIV-1 in a Robo1-dependent manner. Employing proteomic analysis, we identified Flightless-1 as a novel, Robo1-interacting protein. Treatment with shRNAs reduced levels of Flightless-1 and demonstrated its role in efficient cell-to-cell transfer of HIV-1. These results suggest a novel strategy to limit viral infection in the host by targeting the Slit/Robo pathway with modulation of cytoskeletal elements previously unrecognized in HIV-1 transmission.
An Efficient Site-Specific Method for Irreversible Covalent Labeling of Proteins with a Fluorophore
Authors: Liu Jiaquan , Hanne Jeungphill , Britton Brooke M. , Shoffner Matthew , Albers Aaron E. , Bennett Jared , Zatezalo Rachel , Barfield Robyn , Rabuka David , Lee Jong-Bong , Fishel Richard
Published: November 2015

Fluorophore labeling of proteins while preserving native functions is essential for bulk Förster resonance energy transfer (FRET) interaction and single molecule imaging analysis. Here we describe a versatile, efficient, specific, irreversible, gentle and low-cost method for labeling proteins with fluorophores that appears substantially more robust than a similar but chemically distinct procedure. The method employs the controlled enzymatic conversion of a central Cys to a reactive formylglycine (fGly) aldehyde within a six amino acid Formylglycine Generating Enzyme (FGE) recognition sequence in vitro. The fluorophore is then irreversibly linked to the fGly residue using a Hydrazinyl-Iso-Pictet-Spengler (HIPS) ligation reaction. We demonstrate the robust large-scale fluorophore labeling and purification of E.coli (Ec) mismatch repair (MMR) components. Fluorophore labeling did not alter the native functions of these MMR proteins in vitro or in singulo. Because the FGE recognition sequence is easily portable, FGE-HIPS fluorophore-labeling may be easily extended to other proteins.
Resequencing of the common marmoset genome improves genome assemblies and gene-coding sequence analysis
Authors: Sato Kengo , Kuroki Yoko , Kumita Wakako , Fujiyama Asao , Toyoda Atsushi , Kawai Jun , Iriki Atsushi , Sasaki Erika , Okano Hideyuki , Sakakibara Yasubumi
Published: November 2015

The first draft of the common marmoset (Callithrix jacchus) genome was published by the Marmoset Genome Sequencing and Analysis Consortium. The draft was based on whole-genome shotgun sequencing and the current assembly version is Callithrix_jacches-3.2.1, but there still exist 187,214 undetermined gap regions and supercontigs and relatively short contigs that are unmapped to chromosomes in the draft genome. We performed resequencing and assembly of the genome of common marmoset by deep sequencing with high-throughput sequencing technology. Several different sequence runs using Illumina sequencing platforms were executed and 181 Gbp of high-quality bases including mate-pairs with long insert lengths of 3, 8, 20 and 40 Kbp were obtained, that is, approximately 60× coverage. The resequencing significantly improved the MGSAC draft genome sequence. The N50 of the contigs, which is a statistical measure used to evaluate assembly quality, doubled. As a result, 51% of the contigs (total length: 299 Mbp) that were unmapped to chromosomes in the MGSAC draft were merged with chromosomal contigs and the improved genome sequence helped to detect 5,288 new genes that are homologous to human cDNAs and the gaps in 5,187 transcripts of the Ensembl gene annotations were completely filled.
Evolution of opercle shape in cichlid fishes from Lake Tanganyika - adaptive trait interactions in extant and extinct species flocks
Authors: Wilson Laura A. B. , Colombo Marco , Sánchez-Villagra Marcelo R. , Salzburger Walter
Published: November 2015

Phenotype-environment correlations and the evolution of trait interactions in adaptive radiations have been widely studied to gain insight into the dynamics underpinning rapid species diversification. In this study we explore the phenotype-environment correlation and evolution of operculum shape in cichlid fishes using an outline-based geometric morphometric approach combined with stable isotope indicators of macrohabitat and trophic niche. We then apply our method to a sample of extinct saurichthyid fishes, a highly diverse and near globally distributed group of actinopterygians occurring throughout the Triassic, to assess the utility of extant data to inform our understanding of ecomorphological evolution in extinct species flocks. A series of comparative methods were used to analyze shape data for 54 extant species of cichlids (N = 416) and 6 extinct species of saurichthyids (N = 44). Results provide evidence for a relationship between operculum shape and feeding ecology, a concentration in shape evolution towards present along with evidence for convergence in form and significant correlation between the major axes of shape change and measures of gut length and body elongation. The operculum is one of few features that can be compared in extant and extinct groups, enabling reconstruction of phenotype-environment interactions and modes of evolutionary diversification in deep time.
Self-regulation of charged defect compensation and formation energy pinning in semiconductors
Authors: Yang Ji-Hui , Yin Wan-Jian , Park Ji-Sang , Wei Su-Huai
Published: November 2015

Current theoretical analyses of defect properties without solving the detailed balance equations often estimate Fermi-level pinning position by omitting free carriers and assume defect concentrations can be always tuned by atomic chemical potentials. This could be misleading in some circumstance. Here we clarify that: (1) Because the Fermi-level pinning is determined not only by defect states but also by free carriers from band-edge states, band-edge states should be treated explicitly in the same footing as the defect states in practice; (2) defect formation energy, thus defect density, could be pinned and independent on atomic chemical potentials due to the entanglement of atomic chemical potentials and Fermi energy, in contrast to the usual expectation that defect formation energy can always be tuned by varying the atomic chemical potentials; and (3) the charged defect compensation behavior, i.e., most of donors are compensated by acceptors or vice versa, is self-regulated when defect formation energies are pinned. The last two phenomena are more dominant in wide-gap semiconductors or when the defect formation energies are small. Using NaCl and CH3NH3PbI3 as examples, we illustrate these unexpected behaviors. Our analysis thus provides new insights that enrich the understanding of the defect physics in semiconductors and insulators.
Design and Synthesis of Near-infrared Fluorescent Probes for Imaging of Biological Nitroxyl
Authors: Tan Yi , Liu Ruochuan , Zhang Huatang , Peltier Raoul , Lam Yun-Wah , Zhu Qing , Hu Yi , Sun Hongyan
Published: November 2015

Nitroxyl (HNO), the reduced and protonated form of nitric oxide (NO), has recently been identified as an interesting and important signaling molecule in biological systems. However, research on its biosynthesis and bioactivities are hampered by the lack of versatile HNO detection methods applicable to living cells. In this report, two new near-infrared (NIR) probes were designed and synthesized for HNO imaging in living cells. One of the probes was found to display high sensitivity towards HNO, with up to 67-fold of fluorescence increment after reaction with HNO. The detection limit was determined to be as low as 0.043 μM. The probe displayed high selectivity towards HNO over other biologically related species including metal ions, reactive oxygen species, reactive nitrogen species and reactive sulfur species. Furthermore, the probe was shown to be suitable for imaging of exogenous and endogenous HNO in living cells. Interestingly, the probe was found to be mainly localized in lysosomes. We envision that the new NIR probe described here will serve as a useful tool for further elucidation of the intricate roles of HNO in living cells.
Introduction
Authors: Vione Davide , Calza Paola
Published: November 2015

This section gives a general overview of the topics and will introduce the contents that will be expanded in the following chapters. Particular attention is paid to the basic principles of photophysics and environmental photochemistry and to the depiction of photosensitisers and photoinduced transients in surface waters.
Excitation–Emission Matrices of Fluorescence – EEMF – for the Characterization of Organic Matter of Surface Waters
Authors: Coelho Christian , Guyot Ghislain
Published: November 2015

Excitation Emission Matrices – EEMs – are three-dimensional representations of the total emissive light in terms of intensity and diversity of emission wavelengths one sample can gather when irradiated in a fixed range of excitation wavelength, generally between 200 nm and 700 nm. Excitation Emission Matrices of Fluorescence – EEMF – is an analytical tool of choice when investigating chromophoric complex systems made of several chemical compounds, such as those of dissolved organic matter – DOM – in surface waters.The characterization of DOM via EEMF is non invasive and easily implementable in field sampling, making it more and more used. Additionally, EEMF can provide information on chemical composition of DOM, dissociate autochthonous from allochthonous organic matter production, visualize biological activities and investigate colloidal and particulate organic matter. Transept sampling approaches along watersheds enable DOM dynamics to be studied as well as biotic (macrophyte inputs, phytoplankton blooms) and abiotic processes (photoprocesses, mineralization, water fluxes). When EEMF is coupled to data processing algorithms, like PARAFAC, hidden features from the temporal and spatial variability of DOM composition in surface waters can be revealed.In order to go deeper in the study of the molecular composition of fluorophores in DOM samples, EEMF could also be coupled with orthogonal analytical tools like ultra-high resolution mass spectrometry or nuclear magnetic resonance. Such a strategy should, in the future, enable a set of chemical moieties or families responsible for DOM's cycling and reactivity to be targeted and strengthen the powerfulness of EEMF by increasing our knowledge on the fluorescent fingerprint gathered in a single EEM.
New Analytical Approaches for the Detection of Micropollutants in Natural Waters: Identification of 3,5-Dichloro-4-Hydroxybenzene Sulfonic Acid as an Unknown Persistent Pollutant
Authors: Wang Qian , Lutz Marlon , Reichert Matthew , Becker Daniel P. , Chiarelli M. Paul
Published: November 2015

The analysis of emerging contaminants in natural water sources has been based primarily on the analysis of “known unknowns”. These are compounds whose identities are known and several of their chemical or physical properties are tabulated in a database. Here we present an analytical strategy for the determination of pollutants with unknown structures based on liquid chromatography and full scan tandem mass spectrometry with detection based on structural features that suggest the potential toxicity of the unknown. We are using precursor ion scanning for m/z 35 and m/z 37 ions that are specific for chlorine-containing compounds. Precursor ion scanning for chloride ions is carried out over consecutive, narrow mass ranges using several injections. The identification of unknown compounds is facilitated by accurate mass and product ion determinations of the chlorinated compounds detected during precursor ion analyses. Ultimately, the unknown chlorinated compound is identified by comparing its spectroscopic characteristics and retention time with analytical standards suggested to have the same empirical formula as the unknown. This experimental strategy is demonstrated by the identification of a dichlorinated sulfonic acid (3,5-dichloro-4-hydroxybenzenesulfonic acid) that has been detected in several branches of the Chicago River and Chicago wastewater effluent.
Photocatalytic Degradation of Irgarol in Water by Photo-Fenton Reactions
Authors: Eissa Fawzy , El-Hoda Zidan Nour , Sakugawa Hiroshi
Published: November 2015

The degradation behavior of the pesticide Irgarol 1051 in pure (Milli-Q) and river water samples in response to photolysis and Fenton reactions was investigated and the hydroxyl radical (•OH) formation rate was determined. Irgarol photolysis was found to occur at a much slower rate in both types of water in terms of the half-life (t1/2) and degradation rate constant (k). Prolongation of photolysis did not lead to complete degradation, even after 480 min. Conversely, Irgarol was rapidly degraded in pure water at pH 3 after 12 and 16 min of irradiation via the photo-Fenton reaction (Fe2+/H2O2/UV-Vis) and photo-Fenton-like reaction (Fe3+/H2O2/UV-Vis), respectively, because of the generation of additional •OH. Irgarol was also completely degraded by the Fe2+/H2O2/UV-Vis and Fe3+/H2O2/UV-Vis reactions in river water at pH 3 after 60 min, while it disappeared after 180 min of irradiation by the Fe2+/H2O2/UV-Vis reaction at pH 5. The photodegradation rates of Irgarol in pure and river water were consistent with the •OH generation rates in both types of water. Mineralization of 96.9 and 92.9% of the Irgarol was achieved in pure water at pH 3 after 16 h of irradiation by the Fe3+/H2O2/UV-Vis and Fe2+/H2O2/UV-Vis systems, respectively. Overall, these results indicate that photo-Fenton reactions are useful for treating Irgarol-contaminated water.
How Physicochemical Properties of Drugs Affect Their Metabolism and Clearance
Authors: Karlgren Maria , Bergström Christel A. S.
Published: November 2015

In this chapter the transport proteins and enzymes of importance for drug clearance are discussed. The primary organ for drug metabolism is the liver and to reach the intracellular compartment of hepatocytes, orally administered drugs must cross both the intestinal wall and the cell membrane of the liver cells. Transport proteins present in the cellular membrane may facilitate or hinder the compounds crossing these cellular barriers and hence will influence to what extent compounds will reach the enzymes. Here, the enzymes and transport proteins of importance for drug clearance are discussed. The molecular features of importance for drug interactions with transport proteins and enzymes are analyzed and the possibility to predict molecular features vulnerable to enzymatic degradation is discussed. From detailed analysis of the current literature it is concluded that for interaction, both with transport proteins and enzymes, lipophilicity plays a major role. In addition to this property, molecular properties such as hydrogen bond acceptors and donors, charge, aromaticity and molecular size can be used to distinguish between routes of clearance.
Metabolomics-Based Approaches to Determine Drug Metabolite Profiles
Authors: Christopher Lisa J. , Iyer Ramaswamy , Josephs Jonathan L. , Humphreys W. Griffith
Published: November 2015

Analytical technology forms the backbone of all absorption, distribution, metabolism and excretion (ADME)-related research and by far the most important single analytical technology is mass spectrometry (MS). The introduction of routine use high resolution high-resolution (HR) mass spectrometers over the last decade has provided an opportunity to greatly improve and enhance ADME scientists' abilities to conduct both qualitative and quantitative profiling of drug metabolites. Two of the most challenging tasks in metabolite identification by LC/MS are: (1) the rapid assignment of full scan and MS/MS spectra obtained from in vitro samples during the candidate optimization phase; and (2) the comprehensive detection and structural elucidation of all drug-related metabolites, including those that could be considered trace, either arising from predictable or unpredictable biotransformations in the presence of large amounts of complex interference ions from endogenous components. HR-MS can play a unique role in both of these key activities as well as other workflows in the ADME-related realm. This chapter will consider the utility of HR-MS in multiple aspects of drug metabolite detection in candidate optimization and characterization.
Three-dimensional multilayered fibrous constructs for wound healing applications
Authors: Reis Tiago C. , Castleberry Steven , Rego Ana M. B. , Aguiar-Ricardo Ana , Hammond Paula T.
Published: November 2015

Electrical driven self-organization of electrospun fibers is used to create topographically bioinspired three-dimensional multilayered constructs, with tunable morphological and physicochemical properties for ideal wound dressings.
The diameter-dependent photoelectrochemical performance of silicon nanowires
Authors: Zhang Bing-Chang , Wang Hui , He Le , Duan Chun-Yang , Li Fan , Ou Xue-Mei , Sun Bao-Quan , Zhang Xiao-Hong
Published: November 2015

We demonstrate the first systematic study of the diameter-dependent photoelectrochemical performance of single silicon nanowires within a broad size range from 200 to 2000 nm.
Base catalysed decomposition of anthracene endoperoxide
Authors: Klaper M. , Wessig P. , Linker T.
Published: November 2015

Anthracene endoperoxide (EPO) decomposes even under very mild basic conditions to anthraquinone (AQ) and hydrogen peroxide by an interesting mechanism, proposed herein.
Nickel cobalt phosphides quasi-hollow nanocubes as an efficient electrocatalyst for hydrogen evolution in alkaline solution
Authors: Feng Yi , Yu Xin-Yao , Paik Ungyu
Published: November 2015

Nickel cobalt phosphides quasi-hollow nanocubes for efficient HER in alkaline solution are synthesized using Ni–Co Prussian blue analogue as templates.
Silicon based radicals, radical ions, diradicals and diradicaloids
Authors: Chandra Mondal Kartik , Roy Sudipta , Roesky Herbert W.
Published: November 2015

Diradical (cAAC˙)2SiCl2 is isolated in two polymorphic forms. The crystals of one of the polymorphs are stable in open air for over a week.
Synthesis and characterisation of Li11RE18M4O39−δ: RE = Nd or Sm; M = Al, Co or Fe
Authors: Chen Yao-Chang , Reeves-McLaren Nik , Tan Chaou C. , Bingham Paul A. , Forder Susan D. , West Anthony R.
Published: November 2015

Four new phases of general formula, Li11RE18M4O39−δ: REM = NdAl, NdCo, SmCo, SmFe, have been synthesised and characterised.
Functionalized alkynyl-chlorogermanes: hydrometallation, Ge–Cl bond activation, Ge–H bond formation and chlorine-tert-butyl exchange via a transient germyl cation
Authors: Honacker Christian , Qu Zheng-Wang , Tannert Jens , Layh Marcus , Hepp Alexander , Grimme Stefan , Uhl Werner
Published: November 2015

An Al–Cl functionalized germane with an activated Ge–Cl bond showed atBu/Cl exchangeviaa transient germyl cation.
The synthesis of symmetrical disulfides by reacting organic halides with Na2S2O3·5H2O in DMSO
Authors: Abbasi Mohammad , Mohammadizadeh Mohammad Reza , Saeedi Narges
Published: November 2015

Symmetrical disulfides were prepared by heating organic halides with Na2S2O3 in DMSO in high yields and good purities.
Highly dispersible and magnetically recyclable poly(1-vinyl imidazole) brush coated magnetic nanoparticles: an effective support for the immobilization of palladium nanoparticles
Authors: Pourjavadi Ali , Safaie Niloofar , Hosseini Seyed Hassan , Bennett Craig
Published: November 2015

A heterogeneous recoverable catalyst was prepared via the complexation of palladium onto the surface of magnetic nanoparticles coated by a poly(1-vinyl imidazole) brush.
Regulation of collagen expression using nanoparticle mediated inhibition of TGF-β activation
Authors: Li Binbin , Clemons Tristan D. , Agarwal Vipul , Kretzmann Jessica , Bradshaw Michael , Toshniwal Priyanka , Smith Nicole M. , Li Shipu , Fear Mark , Wood Fiona M. , Swaminathan Iyer K.
Published: November 2015

Polymeric nanoparticle for delivery of an effective anti-fibrotic agent in anin vitromodel of scarring.
Catalytic oxidation of cyclohexane by substituted metalloporphyrins: experimental and molecular simulation
Authors: Feng Ze , Xie Yujia , Hao Fang , Liu Pingle , Luo He'an
Published: November 2015

The metalloporphyrins and metalloporphyrin intermediates with lower energy gap have stronger ability to activate the oxygen and cyclohexane respectively.
Novel composite membranes of triazole modified graphene oxide and polybenzimidazole for high temperature polymer electrolyte membrane fuel cell applications
Authors: Yang Jingshuai , Liu Chao , Gao Liping , Wang Jin , Xu Yixin , He Ronghuan
Published: November 2015

Novel acid-doped membranes possessing improved proton conductivity and enhanced mechanical properties were prepared from polybenzimidazole and triazole modified graphene oxide.
Potential responses to neutral thiophenols of polymeric membrane electrodes and their applications in potentiometric biosensing
Authors: Li Long , Qin Wei
Published: November 2015

Unexpected potential responses to electrically neutral thiophenols of anion-exchanger doped polymeric membranes have been observed and applied in potentiometric biosensing of horseradish peroxidase.
A highly sensitive multi-catalytic sensing system for organophosphorus and organochlorine pesticides based on the peroxidase-like activity of ferric ions
Authors: Xu Yan , Yu Tao , Wu Xiao-Qiong , Shen Jiang-Shan , Zhang Hong-Wu
Published: November 2015

A novel and highly sensitive multi-catalytic sensing system was successfully developed for OPs and organochlorine pesticides, on the basis of the color reaction of TMB catalyzed by Fe3+ ions.
Solvent free one-pot multi-component synthesis of β-azaarene substituted ketones via a Sn-catalyzed C(sp3)–H functionalization of 2-alkylazaarenes
Authors: Chavan Santosh S. , Pathan Mohsinkhan Y. , Mulla Shafeek A. R.
Published: November 2015

A tin-catalyzed solvent free one-pot multi-component cascade reaction strategy for the efficient synthesis of β-azaarene substituted ketones via an aldol–Michael addition/C(sp3)–H functionalization of 2-alkylazaarenes has been developed.
Experimental and theoretical studies of triisopropanolamine as an inhibitor for aluminum alloy in 3% NaCl solution
Authors: Ren Xiaolei , Xu Shenying , Chen Siyi , Chen Nanxi , Zhang Shengtao
Published: November 2015

Molecular structure of triisopropanolamine.
Synthesis of enzyme-embedded metal–organic framework nanocrystals in reverse micelles
Authors: Chulkaivalsucharit Poommarat , Wu Xiaoling , Ge Jun
Published: November 2015

Reverse micelles were utilized to prepare enzyme-incorporated metal–organic framework (MOF) nanocrystals with ultrahigh enzymatic activity.
Evolution from small sized Au nanoparticles to hollow Pt/Au nanostructures with Pt nanorods and a mechanistic study
Authors: Ma Ying , Xu Li , Chen Wei , Zou Chao , Yang Yun , Zhang Lijie , Huang Shaoming
Published: November 2015

A facile method for synthesizing hollow Au/Pt nanostructures is reported; this strategy involves using small sized Au nanoparticles (NPs) as seeds and KI as growth modifier.
Friedel–Crafts alkylation of heteroarenes and arenes with indolyl alcohols for construction of 3,3-disubstituted oxindoles
Authors: Wang Xiaoxiao , Liu Jian , Xu Lubin , Hao Zhihui , Wang Liang , Xiao Jian
Published: November 2015

An intriguing camphorsulfonic acid catalyzed Friedel–Crafts alkylation of arenes with indolyl alcohols has been developed featuring mild reaction conditions, wide substrate scope and high yields.
Tribochemistry-induced direct fabrication of nondestructive nanochannels on silicon surface
Authors: Guo Jian , Xiao Chen , Peng Bei , Qian Linmao
Published: November 2015

A maskless, straightforward and crystal plane-independent nanofabrication approach is proposed to produce nondestructive nanochannels on monocrystalline silicon through tribochemical reaction.
A novel NIR long phosphorescent phosphor:SrSnO3:Bi2+
Authors: Qin Xixi , Li Yang , Wu Dakun , Wu Yiling , Chen Ruchun , Ma Zhijun , Liu Shijian , Qiu Jianrong
Published: November 2015

A novel phosphor with near-infrared (NIR) long persistent luminescence, SrSnO3:Bi2+was successfully synthesized by traditional solid-state reaction.