bluuebunny/crossref_metadata_2025 huggingface dataset:
Airway and head and neck high dependency unit: a single-centre experience
Authors: Bannister M , Trotter P , Jawad A , Veitch D Y
Published: July 2016

Objective:

Dedicated otolaryngology high dependency units are uncommon. This paper reports the first experiences of such a facility in the UK, assessing reason for admission, duration of stay, occupancy rate and need for care escalation. The study sought to assess the presence of similar units in the UK.

Methods:

A retrospective review of high dependency unit admissions over an 18-month period and a national survey of otolaryngology departments in the UK were conducted to establish the overall presence and location of similar high dependency units.

Results:

A total of 128 patients were admitted during the study period, mainly following surgery and because of airway compromise. The average duration of stay was 2–3 days (range, 1–12 days). The occupancy rate was 31.7 per cent. No patients required their care to be escalated to the intensive care unit. Seven similar high dependency units were identified in the UK.

Conclusion:

The care provided prevented the need for escalation of care to an intensive care unit. This challenges the need for patient management on intensive care units following major surgery or airway compromise for those not requiring assisted ventilation. High dependency units similar to ours are not widespread.
Pulmonicola cochleotrema (Digenea: Opisthotrematidae) in Antillean manatees (Trichechus manatus manatus) from the North-eastern region of Brazil
Authors: Borges João Carlos Gomes , Jung Larissa Molinari , Carvalho Vitor Luz , De Oliveira Moreira André Lucas , Attademo Fernanda Löffler Niemeyer , Ramos Rafael Antonio Nascimento , Alves Leucio Câmara
Published: July 2016

Currently, little is known about the helminth fauna in sirenian species. Therefore, the objective of this study was to assess the frequency of infection by Pulmonicola cochleotrema in Antillean manatees (Trichechus manatus manatus), in the North-eastern region of Brazil. Between the years of 1989 and 2014, 88 manatees found on the North-eastern Brazilian coast were clinically examined. They included animals that were found dead, animals maintained in captivity and specimens reintroduced into conservation areas. During their physical examination, helminths present in necropsied carcasses and in reintroduced animals were collected, as well as faecal samples. Parasites were detected in 7.95% (7/88) of the animals; all specimens collected being identified as P. cochleotrema. Only adult manatees were infected, and in two cases clinical signs were observed. This is the first report on the occurrence of P. cochleotrema in Antillean manatees in the states of Paraíba and Sergipe, in the North-eastern coast of Brazil.
Dimna's Trial andApologiain Kashifī'sAnvār-i Suhaylī. Morality's Place in the Corrupt Trial of a Rhetorical and Dialectical Genius.
Authors: VAN RUYMBEKE CHRISTINE
Published: July 2016

This essay challenges the received idea that Ibn al-Muqaffa‘, the eighth-century Arabic translator of the Kalīla-Dimna fables, added the Trial of Dimna, the sequel to the first story of the Lion and the Bull, in order to let morality win in the end. The analysis of this sequel's synopsis shows the absence of morality and how the ruler uses the judicial to manipulate public opinion and to redress his politically-damaged image. The essay also shows that the sequel's main purpose and use is to give a practical demonstration of the art of forensic rhetoric, casting Dimna as a pre-eminent and redoubtable sophist. TheAnvār-i Suhaylīversion, the fifteenth-century Persian rewriting by Vā’iz Kāshifī, on which the essay is based, also engages with the philosophical conundrum oftasdīq, which seems absent in the Arabic versions of the text.
OPTIMAL SAVINGS FOR RETIREMENT: THE ROLE OF INDIVIDUAL ACCOUNTS
Authors: Le Blanc Julia , Scholl Almuth
Published: July 2016

We employ a life-cycle model with income risk to analyze how tax-deferred individual accounts affect households' savings for retirement. We consider voluntary accounts as opposed to mandatory accounts with minimum contribution rates. We contrast add-on accounts with carve-out accounts that partly replace social security contributions. Quantitative results suggest that making add-on accounts mandatory has adverse welfare effects across income groups. Carve-out accounts generate positive welfare effects across all income groups, but gains are lower for low income earners. Default investment rules in individual accounts have a modest impact on welfare.
Chemical, biological, radiological or nuclear events: The humanitarian response framework of the International Committee of the Red Cross
Authors: Malich Gregor , Coupland Robin , Donnelly Steve , Nehme Johnny
Published: July 2016

Mounting an effective international humanitarian response to a chemical, biological, radiological or nuclear (CBRN) event, especially if the response is undertaken on an ad hoc basis, would be extremely difficult and would pose many risks to the responders. The International Committee of the Red Cross (ICRC) has created a competency-based capacity to respond to at least small-scale CBRN events, including a deployable capability to undertake operational activities. This involves informed assessments of CBRN risks, timely and competent decisions on how to respond, and effectively mobilizing appropriate resources to implement these decisions, through the creation of an emergency roster. In addition to the acquisition of technical expertise and material resources, the creation of such capacity requires the application of central processes, ensuring systematic management of CBRN response (including risk-based decision-making), standing operational procedures, and availability of and access to the necessary resources. Implementation of the ICRC's CBRN response framework as described in this article should be considered by any agency or other stakeholder preparing for international humanitarian assistance in CBRN events – especially if such events are related to armed conflict.
Former Academy Head Predicts Few Obstacles for Female Successor
Authors: Showstack Randy
Published: July 2016

Prior to retiring last week as president of the U.S. National Academy of Sciences, Ralph Cicerone said the academy is ready for its new leader to be a woman and a younger person.
Functional characterization of the 12p12.1 renal cancer-susceptibility locus implicates BHLHE41
Authors: Bigot Pierre , Colli Leandro M. , Machiela Mitchell J. , Jessop Lea , Myers Timothy A. , Carrouget Julie , Wagner Sarah , Roberson David , Eymerit Caroline , Henrion Daniel , Chanock Stephen J.
Published: July 2016

Genome-wide association studies have identified multiple renal cell carcinoma (RCC) susceptibility loci. Here, we use regional imputation and bioinformatics analysis of the 12p12.1 locus to identify the single-nucleotide polymorphism (SNP) rs7132434 as a potential functional variant. Luciferase assays demonstrate allele-specific regulatory activity and, together with data from electromobility shift assays, suggest allele-specific differences at rs7132434 for AP-1 transcription factor binding. In an analysis of The Cancer Genome Atlas data, SNPs highly correlated with rs7132434 show allele-specific differences in BHLHE41 expression (trend P value=6.3 × 10−7). Cells overexpressing BHLHE41 produce larger mouse xenograft tumours, while RNA-seq analysis reveals that constitutively increased BHLHE41 induces expression of IL-11. We conclude that the RCC risk allele at 12p12.1 maps to rs7132434, a functional variant in an enhancer that upregulates BHLHE41 expression which, in turn, induces IL-11, a member of the IL-6 cytokine family.
Correction: Corrigendum: Are viruses important in the plankton of highly turbid glacier-fed lakes?
Authors: Drewes Fabian , Peter Hannes , Sommaruga Ruben
Published: July 2016

Scientific Reports 6: Article number: 24608; published online: 20 April 2016; updated: 07 July 2016 In this Article, references 30 and 31 are not listed in the correct order. The correct references are listed below: 30. Knowles, B. et al. Lytic to temperate switching of viral communities. Nature 531, 466–470, doi: 10.
Toothbrushing, Blood Glucose and HbA1c: Findings from a Random Survey in Chinese Population
Authors: Su Lingyu , Liu Wenzhao , Xie Bingwu , Dou Lei , Sun Jun , Wan Wenjuan , Fu Xiaoming , Li Guangyue , Huang Jiao , Xu Ling
Published: July 2016

Both diabetes and periodontal disease are prevalent in China. Poor oral hygiene practice is the major cause of periodontal disease. An association between oral hygiene practice and blood glucose level was reported in individuals with diabetes, but not in the general population. We examined the association in a population-based random survey recruiting 2,105 adults without previously diagnosed diabetes in Chongqing city, China. Plasma glucose and hemoglobin A1c (HbA1c) were measured, and a 2-hour oral glucose tolerance test was conducted for each respondent. Self-reported toothbrushing frequency was used as a proxy for oral hygiene practice. In a linear model controlling for potential confounders (demographic characteristics, socio-economic status, lifestyle risk factors, BMI, dental visit frequency, etc.), urban residents who barely brushed their teeth had an increase of 0.50 (95% CI: 0.10–0.90) mmol/L in fasting plasma glucose, and an increase of 0.26% (0.04–0.47%) in HbA1c, relative to those brushing ≥twice daily; for rural residents, the effects were 0.26 (0.05–0.48) mmol/L in fasting plasma glucose and 0.20% (0.09–0.31%) in HbA1c. Individuals with better oral practice tended to have lower level of blood glucose and HbA1c. Establishing good oral health behavioral habits may be conducive to diabetes prevention and control in the general population.
S1PR2 variants associated with auditory function in humans and endocochlear potential decline in mouse
Authors: Ingham Neil J. , Carlisle Francesca , Pearson Selina , Lewis Morag A. , Buniello Annalisa , Chen Jing , Isaacson Rivka L. , Pass Johanna , White Jacqueline K. , Dawson Sally J. , Steel Karen P.
Published: July 2016

Progressive hearing loss is very common in the population but we still know little about the underlying pathology. A new spontaneous mouse mutation (stonedeaf, stdf ) leading to recessive, early-onset progressive hearing loss was detected and exome sequencing revealed a Thr289Arg substitution in Sphingosine-1-Phosphate Receptor-2 (S1pr2). Mutants aged 2 weeks had normal hearing sensitivity, but at 4 weeks most showed variable degrees of hearing impairment, which became severe or profound in all mutants by 14 weeks. Endocochlear potential (EP) was normal at 2 weeks old but was reduced by 4 and 8 weeks old in mutants and the stria vascularis, which generates the EP, showed degenerative changes. Three independent mouse knockout alleles of S1pr2 have been described previously, but this is the first time that a reduced EP has been reported. Genomic markers close to the human S1PR2 gene were significantly associated with auditory thresholds in the 1958 British Birth Cohort (n = 6099), suggesting involvement of S1P signalling in human hearing loss. The finding of early onset loss of EP gives new mechanistic insight into the disease process and suggests that therapies for humans with hearing loss due to S1P signalling defects need to target strial function.
Pathogenesis of Streptococcus urinary tract infection depends on bacterial strain and β-hemolysin/cytolysin that mediates cytotoxicity, cytokine synthesis, inflammation and virulence
Authors: Leclercq Sophie Y. , Sullivan Matthew J. , Ipe Deepak S. , Smith Joshua P. , Cripps Allan W. , Ulett Glen C.
Published: July 2016

Streptococcus agalactiae can cause urinary tract infection (UTI) including cystitis and asymptomatic bacteriuria (ABU). The early host-pathogen interactions that occur during S. agalactiae UTI and subsequent mechanisms of disease pathogenesis are poorly defined. Here, we define the early interactions between human bladder urothelial cells, monocyte-derived macrophages, and mouse bladder using uropathogenic S. agalactiae (UPSA) 807 and ABU-causing S. agalactiae (ABSA) 834 strains. UPSA 807 adhered, invaded and killed bladder urothelial cells more efficiently compared to ABSA 834 via mechanisms including low-level caspase-3 activation, and cytolysis, according to lactate dehydrogenase release measures and cell viability. Severe UPSA 807-induced cytotoxicity was mediated entirely by the bacterial β-hemolysin/cytolysin (β-H/C) because an β-H/C-deficient UPSA 807 isogenic mutant, UPSA 807ΔcylE, was not cytotoxic in vitro; the mutant was also significantly attenuated for colonization in the bladder in vivo. Analysis of infection-induced cytokines, including IL-8, IL-1β, IL-6 and TNF-α in vitro and in vivo revealed that cytokine and chemokine responses were dependent on expression of β-H/C that also elicited severe bladder neutrophilia. Thus, virulence of UPSA 807 encompasses adhesion to, invasion of and killing of bladder cells, pro-inflammatory cytokine/chemokine responses that elicit neutrophil infiltration, and β-H/C-mediated subversion of innate immune-mediated bacterial clearance from the bladder.
COG lobe B sub-complex engages v-SNARE GS15 and functions via regulated interaction with lobe A sub-complex
Authors: Willett Rose , Blackburn Jessica Bailey , Climer Leslie , Pokrovskaya Irina , Kudlyk Tetyana , Wang Wei , Lupashin Vladimir
Published: July 2016

The conserved oligomeric Golgi (COG) complex is a peripheral membrane protein complex which orchestrates tethering of intra-Golgi vesicles. We found that COG1-4 (lobe A) and 5–8 (lobe B) protein assemblies are present as independent sub-complexes on cell membranes. Super-resolution microscopy demonstrates that COG sub-complexes are spatially separated on the Golgi with lobe A preferential localization on Golgi stacks and the presence of lobe B on vesicle-like structures, where it physically interacts with v-SNARE GS15. The localization and specific interaction of the COG sub-complexes with the components of vesicle tethering/fusion machinery suggests their different roles in the vesicle tethering cycle. We propose and test a novel model that employs association/disassociation of COG sub-complexes as a mechanism that directs vesicle tethering at Golgi membranes. We demonstrate that defective COG assembly or restriction of tethering complex disassembly by a covalent COG1-COG8 linkage is inhibitory to COG complex activity, supporting the model.
Comparative genomic and functional analyses: unearthing the diversity and specificity of nematicidal factors in Pseudomonas putida strain 1A00316
Authors: Guo Jing , Jing Xueping , Peng Wen-Lei , Nie Qiyu , Zhai Yile , Shao Zongze , Zheng Longyu , Cai Minmin , Li Guangyu , Zuo Huaiyu , Zhang Zhitao , Wang Rui-Ru , Huang Dian , Cheng Wanli , Yu Ziniu , Chen Ling-Ling , Zhang Jibin
Published: July 2016

We isolated Pseudomonas putida (P. putida) strain 1A00316 from Antarctica. This bacterium has a high efficiency against Meloidogyne incognita (M. incognita) in vitro and under greenhouse conditions. The complete genome of P. putida 1A00316 was sequenced using PacBio single molecule real-time (SMRT) technology. A comparative genomic analysis of 16 Pseudomonas strains revealed that although P. putida 1A00316 belonged to P. putida, it was phenotypically more similar to nematicidal Pseudomonas fluorescens (P. fluorescens) strains. We characterized the diversity and specificity of nematicidal factors in P. putida 1A00316 with comparative genomics and functional analysis and found that P. putida 1A00316 has diverse nematicidal factors including protein alkaline metalloproteinase AprA and two secondary metabolites, hydrogen cyanide and cyclo-(l-isoleucyl-l-proline). We show for the first time that cyclo-(l-isoleucyl-l-proline) exhibit nematicidal activity in P. putida. Interestingly, our study had not detected common nematicidal factors such as 2,4-diacetylphloroglucinol (2,4-DAPG) and pyrrolnitrin in P. putida 1A00316. The results of the present study reveal the diversity and specificity of nematicidal factors in P. putida strain 1A00316.
Protease activated receptor 1 (PAR1) enhances Src-mediated tyrosine phosphorylation of NMDA receptor in intracerebral hemorrhage (ICH)
Authors: Duan Zhen-Zhen , Zhang Feng , Li Feng-Ying , Luan Yi-Fei , Guo Peng , Li Yi-Hang , Liu Yong , Qi Su-Hua
Published: July 2016

It has been demonstrated that Src could modulate NMDA receptor, and PAR1 could also affect NMDAR signaling. However, whether PAR1 could regulate NMDAR through Src under ICH has not yet been investigated. In this study, we demonstrated the role of Src-PSD95-GluN2A signaling cascades in rat ICH model and in vitro thrombin challenged model. Using the PAR1 agonist SFLLR, antagonist RLLFS and Src inhibitor PP2, electrophysiological analysis showed that PAR1 regulated NMDA-induced whole-cell currents (INMDA) though Src in primary cultured neurons. Both in vivo and in vitro results showed the elevated phosphorylation of tyrosine in Src and GluN2A and enhanced interaction of the Src-PSD95-GluN2A under model conditions. Treatment with the PAR1 antagonist RLLFS, AS-PSD95 (Antisense oligonucleotide against PSD95) and Src inhibitor PP2 inhibited the interaction among Src-PSD95-GluN2A, and p-Src, p-GluN2A. Co-application of SFLLR and AS-PSD95, PP2, or MK801 (NMDAR inhibitor) abolished the effect of SF. In conclusion, our results demonstrated that activated thrombin receptor PAR1 induced Src activation, enhanced the interaction among Src-PSD95-GluN2A signaling modules, and up-regulated GluN2A phosphorylation after ICH injury. Elucidation of such signaling cascades would possibly provide novel targets for ICH treatment.
Ionoacoustic tomography of the proton Bragg peak in combination with ultrasound and optoacoustic imaging
Authors: Kellnberger Stephan , Assmann Walter , Lehrack Sebastian , Reinhardt Sabine , Thirolf Peter , Queirós Daniel , Sergiadis George , Dollinger Günther , Parodi Katia , Ntziachristos Vasilis
Published: July 2016

Ions provide a more advantageous dose distribution than photons for external beam radiotherapy, due to their so-called inverse depth dose deposition and, in particular a characteristic dose maximum at their end-of-range (Bragg peak). The favorable physical interaction properties enable selective treatment of tumors while sparing surrounding healthy tissue, but optimal clinical use requires accurate monitoring of Bragg peak positioning inside tissue. We introduce ionoacoustic tomography based on detection of ion induced ultrasound waves as a technique to provide feedback on the ion beam profile. We demonstrate for 20 MeV protons that ion range imaging is possible with submillimeter accuracy and can be combined with clinical ultrasound and optoacoustic tomography of similar precision. Our results indicate a simple and direct possibility to correlate, in-vivo and in real-time, the conventional ultrasound echo of the tumor region with ionoacoustic tomography. Combined with optoacoustic tomography it offers a well suited pre-clinical imaging system.
Novel Alleviation Mechanisms of Aluminum Phytotoxicity via Released Biosilicon from Rice Straw-Derived Biochars
Authors: Qian Linbo , Chen Baoliang , Chen Mengfang
Published: July 2016

Replacing biosilicon and biocarbon in soil via biochar amendment is a novel approach for soil amelioration and pollution remediation. The unique roles of silicon (Si)-rich biochar in aluminum (Al) phytotoxicity alleviation have not been discovered. In this study, the alleviation of Al phytotoxicity to wheat plants (root tips cell death) by biochars fabricated from rice straw pyrolyzed at 400 and 700 °C (RS400 and RS700) and the feedstock (RS100) were studied using a slurry system containing typical acidic soils for a 15-day exposure experiment. The distributions of Al and Si in the slurry solution, soil and plant root tissue were monitored by staining methods, chemical extractions and SEM-EDS observations. We found that the biological sourced silicon in biochars served dual roles in Al phytotoxicity alleviation in acidic soil slurry. On one hand, the Si particles reduced the amount of soil exchangeable Al and prevented the migration of Al to the plant. More importantly, the Si released from biochars synchronously absorbed by the plants and coordinated with Al to form Al-Si compounds in the epidermis of wheat roots, which is a new mechanism for Al phytotoxicity alleviation in acidic soil slurry by biochar amendment. In addition, the steady release of Si from the rice straw-derived biochars was a sustainable Si source for aluminosilicate reconstruction in acidic soil.
Fabrication of water-soluble polymer-encapsulated As4S4 to increase oral bioavailability and chemotherapeutic efficacy in AML mice
Authors: Ma Qiang , Wang Chuan , Li Xiaojin , Guo Hua , Meng Jie , Liu Jian , Xu Haiyan
Published: July 2016

Realgar (As4S4) has been demonstrated to be effective for the treatment of acute myeloid leukemia (AML); it has the advantages of no drug resistance and oral administration. Nevertheless, its poor solubility has been an obstacle to its bioavailability, requiring high-dose administration over a long period. We investigated whether crushing realgar crystals to the nanoscale and encapsulating the particles in a water-soluble polymer in one step using hot-melt extrusion would increase the bioavailability of As4S4. Raw As4S4 (r-As4S4) and water-soluble polymer were processed via co-rotating twin screw extrusion. The resulting product (e-As4S4) was characterized by SEM, XRD, and DLS. The cytotoxicity and therapeutic effects of e-As4S4 were evaluated in vivo and in vitro. The results show that e-As4S4 dissolved rapidly in water, forming a stable colloid solution. The average size of e-As4S4 particles was 680 nm, which was reduced by more than 40-fold compared with that of r-As4S4. The bioavailability of e-As4S4 was up to 12.6-fold higher than that of r-As4S4, and it inhibited the proliferation of HL-60 cells much more effectively than did r-As4S4, inducing apoptosis and significantly reducing the infiltration of HL-60 cells into the bone marrow, spleen, and liver. This in turn prolonged the survival of AML mice.
Efficient Inhibition of Hepatitis B Virus Infection by a preS1-binding Peptide
Authors: Ye Xiaoli , Zhou Ming , He Yonggang , Wan Yanmin , Bai Weiya , Tao Shuai , Ren Yanqin , Zhang Xinxin , Xu Jianqing , Liu Jing , Zhang Junqi , Hu Kanghong , Xie Youhua
Published: July 2016

Entry inhibitors are promising novel antivirals against hepatitis B virus (HBV) infection. The existing potential entry inhibitors have targeted the cellular receptor(s). In this study, we aim to develop the first entry inhibitor that inhibits HBV infection via targeting viral particles. The preS1 segment of the large envelope glycoprotein of HBV is essential for virion attachment and infection. Previously, we obtained a preS1-binding short peptide B10 by screening a phage display peptide library using the N-terminal half of preS1 (residues 1 to 60, genotype C). We report here that by means of concatenation of B10, we identified a quadruple concatemer 4B10 that displayed a markedly increased preS1-binding activity. The main binding site of 4B10 in preS1 was mapped to the receptor binding enhancing region. 4B10 blocked HBV attachment to hepatic cells and inhibited HBV infection of primary human and tupaia hepatocytes at low nanomolar concentrations. The 4B10-mediated inhibition of HBV infection is specific as it did not inhibit the infection of vesicular stomatitis virus glycoprotein pseudotyped lentivirus or human immunodeficiency virus type 1. Moreover, 4B10 showed no binding activity to hepatic cells. In conclusion, we have identified 4B10 as a promising candidate for a novel class of HBV entry inhibitors.
Global alternans instability and its effect on non-linear wave propagation: dynamical Wenckebach block and self terminating spiral waves
Authors: Vandersickel Nele , Defauw Arne , Dawyndt Peter , Panfilov Alexander V.
Published: July 2016

The main mechanism of formation of reentrant cardiac arrhythmias is via formation of waveblocks at heterogeneities of cardiac tissue. We report that heterogeneity and the area of waveblock can extend itself in space and can result formation of new additional sources, or termination of existing sources of arrhythmias. This effect is based on a new form of instability, which we coin as global alternans instability (GAI). GAI is closely related to the so-called (discordant) alternans instability, however its onset is determined by the global properties of the APD-restitution curve and not by its slope. The APD-restitution curve relates the duration of the cardiac pulse (APD) to the time interval between the pulses and can easily be measured in an experimental or even clinical setting. We formulate the conditions for the onset of GAI, study its manifestation in various 1D and 2D situations and discuss its importance for the onset of cardiac arrhythmias.
Solar irradiance dictates settlement timing and intensity of marine mussels
Authors: Fuentes-Santos Isabel , Labarta Uxío , Álvarez-Salgado X. Antón , Fernández-Reiriz Mª José
Published: July 2016

Identifying the environmental factors driving larval settlement processes is crucial to understand the population dynamics of marine invertebrates. This work aims to go a step ahead and predict larval presence and intensity. For this purpose we consider the influence of solar irradiance, wind regime and continental runoff on the settlement processes. For the first time, we conducted a 5-years weekly monitoring of Mytilus galloprovincialis settlement on artificial suspended substrates, which allowed us to search for interannual variability in the settlement patterns. Comparison between the seasonal pattern of larval settlement and solar irradiance, as well as the well-known effect of solar irradiance on water temperature and food availability, suggest that solar irradiance indirectly influences the settlement process, and support the use of this meteorological variable to predict settlement occurrence. Our results show that solar irradiance allows predicting the beginning and end of the settlement cycle a month in advance: Particularly we have observed that solar irradiance during late winter indirectly drives the timing and intensity of the settlement onset, Finally, a functional generalise additive model, which considers the influence of solar irradiance and continental runoff on the settlement process, provides an accurate prediction of settlement intensity a fortnight in advance.
Tumour sampling method can significantly influence gene expression profiles derived from neoadjuvant window studies
Authors: Pearce Dominic A. , Arthur Laura M. , Turnbull Arran K. , Renshaw Lorna , Sabine Vicky S. , Thomas Jeremy S. , Bartlett John M. S. , Dixon J. Michael , Sims Andrew H.
Published: July 2016

Patient-matched transcriptomic studies using tumour samples before and after treatment allow inter-patient heterogeneity to be controlled, but tend not to include an untreated comparison. Here, Illumina BeadArray technology was used to measure dynamic changes in gene expression from thirty-seven paired diagnostic core and surgically excised breast cancer biopsies obtained from women receiving no treatment prior to surgery, to determine the impact of sampling method and tumour heterogeneity. Despite a lack of treatment and perhaps surprisingly, consistent changes in gene expression were identified during the diagnosis-surgery interval (48 up, 2 down; Siggenes FDR 0.05) in a manner independent of both subtype and sampling-interval length. Instead, tumour sampling method was seen to directly impact gene expression, with similar effects additionally identified in six published breast cancer datasets. In contrast with previous findings, our data does not support the concept of a significant wounding or immune response following biopsy in the absence of treatment and instead implicates a hypoxic response following the surgical biopsy. Whilst sampling-related gene expression changes are evident in treated samples, they are secondary to those associated with response to treatment. Nonetheless, sampling method remains a potential confounding factor for neoadjuvant study design.
mCSM-lig: quantifying the effects of mutations on protein-small molecule affinity in genetic disease and emergence of drug resistance
Authors: Pires Douglas E. V. , Blundell Tom L. , Ascher David B.
Published: July 2016

The ability to predict how a mutation affects ligand binding is an essential step in understanding, anticipating and improving the design of new treatments for drug resistance and in understanding genetic diseases. Here we present mCSM-lig, a structure-guided computational approach for quantifying the effects of single-point missense mutations on affinities of small molecules for proteins. mCSM-lig uses graph-based signatures to represent the wild-type environment of mutations and small-molecule chemical features and changes in protein stability as evidence to train a predictive model using a representative set of protein-ligand complexes from the Platinum database. We show our method provides a very good correlation with experimental data (up to ρ = 0.67) and is effective in predicting a range of chemotherapeutic, antiviral and antibiotic resistance mutations, providing useful insights for genotypic screening and to guide drug development. mCSM-lig also provides insights into understanding Mendelian disease mutations and as a tool for guiding protein design. mCSM-lig is freely available as a web server at http://structure.bioc.cam.ac.uk/mcsm_lig.
An electrochemical sensor based on fullerene nanorods for the detection of paraben, an endocrine disruptor
Authors: Rather Jahangir Ahmad , Al Harthi Abir Jumaa , Khudaish Emad A. , Qurashi Ahsanulhaq , Munam Abdul , Kannan Palanisamy
Published: July 2016

We have synthesized, characterized and immobilized C60NRs at GCE–Ph–NH2interface by N–H addition reaction across π-bonds of fullerene (C60). The ERC60NRs–NH–Ph–GCE sensor shows high electrocatalytic activity towards the detection of ethylparaben.
Thermoelectric plastics: from design to synthesis, processing and structure–property relationships
Authors: Kroon Renee , Mengistie Desalegn Alemu , Kiefer David , Hynynen Jonna , Ryan Jason D. , Yu Liyang , Müller Christian
Published: July 2016

Thermoelectric plastics are a class of polymer-based materials that combine the ability to directly convert heat to electricity, and vice versa, with ease of processing.
Flexible carbon nanofiber electrodes for a lead zirconate titanate nanogenerator
Authors: Bajaj Bharat , Hong Seonghwan , Jo Seong Mu , Lee Sungho , Kim Hyun Jae
Published: July 2016

The performance and stability of flexible carbon nanofiber (CNF) electrodes were investigated for a lead zirconate titanate (PZT) nanogenerator.
Correction: Brij-58 template synthesis of self-assembled thermostable lamellar crystalline zirconia via a reflux-hydrothermal hybrid method
Authors: Su Penghe , Gao Wenjun
Published: July 2016

Correction for ‘Brij-58 template synthesis of self-assembled thermostable lamellar crystalline zirconia via a reflux-hydrothermal hybrid method’ by Penghe Su et al., RSC Advances, 2015, 5, 36467–36471.
Adenine as an organocatalyst for the ring-opening polymerization of lactide: scope, mechanism and access to adenine-functionalized polylactide
Authors: Nogueira Guilherme , Favrelle Audrey , Bria Marc , Prates Ramalho João P. , Mendes Paulo J. , Valente Andreia , Zinck Philippe
Published: July 2016

Straightforward access to a bioconjugate is reportedviaadenine initiated ring-opening polymerization without a co-catalyst. The mechanism is elucidated by DFT.
6-endo-dig Cycloisomerization of N-Propargyl Aminoquinoxalines: A New Route to 1,4,8-Triazaphenanthrenes
Authors: Vallerotto Sara , Douaron Gael , Bernadat Guillaume , Ferrié Laurent , Figadère Bruno
Published: July 2016

We report the preparation of novel 1,4,8-triazaphenanthrenes and show that the target compounds are efficiently obtained from the corresponding 6-aminoquinoxalines after N-propargylation followed by copper-catalyzed 6-endo-dig cycloisomerization and aromatization. The cyclization was found to be completely regioselective.
Super-transient scaling in time-delay autonomous Boolean network motifs
Authors: D'Huys Otti , Lohmann Johannes , Haynes Nicholas D. , Gauthier Daniel J.
Published: July 2016

Autonomous Boolean networks are commonly used to model the dynamics of gene regulatory networks and allow for the prediction of stable dynamical attractors. However, most models do not account for time delays along the network links and noise, which are crucial features of real biological systems. Concentrating on two paradigmatic motifs, the toggle switch and the repressilator, we develop an experimental testbed that explicitly includes both inter-node time delays and noise using digital logic elements on field-programmable gate arrays. We observe transients that last millions to billions of characteristic time scales and scale exponentially with the amount of time delays between nodes, a phenomenon known as super-transient scaling. We develop a hybrid model that includes time delays along network links and allows for stochastic variation in the delays. Using this model, we explain the observed super-transient scaling of both motifs and recreate the experimentally measured transient distributions.
Negative magnetoresistance in indium antimonide whiskers doped with tin
Authors: Druzhinin A. , Ostrovskii I. , Khoverko Yu. , Liakh-Kaguy N.
Published: July 2016

Negative magnetoresistance of InSb whiskers with different impurity concentrations 4.4 × 1016–7.16 × 1017 cm−3 was studied in longitudinal magnetic field 0–14 T in the temperature range 4.2–77 K. The negative magnetoresistance reaches about 50% for InSb whiskers with impurity concentration in the vicinity to the metal–insulator transition. The negative magnetoresistance decreases to 35 and 25% for crystals with Sn concentration from the metal and dielectric side of the transition. The longitudinal magnetoresistance twice crosses the axis of the magnetic field induction for the lightly doped crystals. The behavior of the negative magnetoresistance could be explained by the existence of classical size effect, in particular boundary scattering in the subsurface whisker layer.
Quantum rotors in Pca21 lattice
Authors: Freiman Yu. A. , Grechnev Alexei
Published: July 2016

Analytical calculations of the potential barrier hindering rotation of the hydrogen molecules in the molecular field of neighboring molecules are performed for molecular solid hydrogen. The calculations are made for the four-sublattice Pca21 lattice which minimizes the electrostatic energy of classical quadrupoles on an hcp lattice.
First kind symmetric periodic solutions of the generalized van der Waals Hamiltonian
Authors: Alberti Angelo , Vidal Claudio
Published: July 2016

The aim of this paper is to prove the existence of a new symmetric family of periodic solutions of the generalized van der Waals Hamiltonian. In fact, we prove the existence of several families of first kind symmetric periodic solutions as continuation of circular orbits of the Kepler problem in the spatial case.
Research Update: Utilizing magnetization dynamics in solid-state thermal energy conversion
Authors: Boona Stephen R. , Watzman Sarah J. , Heremans Joseph P.
Published: July 2016

We review the spin-Seebeck and magnon-electron drag effects in the context of solid-state energy conversion. These phenomena are driven by advective magnon-electron interactions. Heat flow through magnetic materials generates magnetization dynamics, which can strongly affect free electrons within or adjacent to the magnetic material, thereby producing magnetization-dependent (e.g., remnant) electric fields. The relative strength of spin-dependent interactions means that magnon-driven effects can generate significantly larger thermoelectric power factors as compared to classical thermoelectric phenomena. This is a surprising situation in which spin-based effects are larger than purely charge-based effects, potentially enabling new approaches to thermal energy conversion.
Cooling rate dependence of structural order in Al90Sm10 metallic glass
Authors: Sun Yang , Zhang Yue , Zhang Feng , Ye Zhuo , Ding Zejun , Wang Cai-Zhuang , Ho Kai-Ming
Published: July 2016

The atomic structure of Al90Sm10 metallic glass is studied using molecular dynamics simulations. By performing a long sub-Tg annealing, we developed a glass model closer to the experiments than the models prepared by continuous cooling. Using the cluster alignment method, we found that “3661” cluster is the dominating short-range order in the glass samples. The connection and arrangement of “3661” clusters, which define the medium-range order in the system, are enhanced significantly in the sub-Tg annealed sample as compared with the fast cooled glass samples. Unlike some strong binary glass formers such as Cu64.5Zr35.5, the clusters representing the short-range order do not form an interconnected interpenetrating network in Al90Sm10, which has only marginal glass formability.
Features of exciton dynamics in molecular nanoclusters (J-aggregates): Exciton self-trapping (Review Article)
Authors: Malyukin Yu. V. , Sorokin A. V. , Semynozhenko V. P.
Published: July 2016

We present thoroughly analyzed experimental results that demonstrate the anomalous manifestation of the exciton self-trapping effect, which is already well-known in bulk crystals, in ordered molecular nanoclusters called J-aggregates. Weakly-coupled one-dimensional (1D) molecular chains are the main structural feature of J-aggregates, wherein the electron excitations are manifested as 1D Frenkel excitons. According to the continuum theory of Rashba-Toyozawa, J-aggregates can have only self-trapped excitons, because 1D excitons must adhere to barrier-free self-trapping at any exciton-phonon coupling constant g = εLR/2β, wherein εLR is the lattice relaxation energy, and 2β is the half-width of the exciton band. In contrast, very often only the luminescence of free, mobile excitons would manifest in experiments involving J-aggregates. Using the Urbach rule in order to analyze the low-frequency region of the low-temperature exciton absorption spectra has shown that J-aggregates can have both a weak (g < 1) and a strong (g > 1) exciton-phonon coupling. Moreover, it is experimentally demonstrated that under certain conditions, the J-aggregate excited state can have both free and self-trapped excitons, i.e., we establish the existence of a self-trapping barrier for 1D Frenkel excitons. We demonstrate and analyze the reasons behind the anomalous existence of both free and self-trapped excitons in J-aggregates, and demonstrate how exciton-self trapping efficiency can be managed in J-aggregates by varying the values of g, which is fundamentally impossible in bulk crystals. We discuss how the exciton-self trapping phenomenon can be used as an alternate interpretation of the wide band emission of some J-aggregates, which has thus far been explained by the strongly localized exciton model.
Communication: Energy transfer and reaction dynamics for DCl scattering on Au(111): An ab initio molecular dynamics study
Authors: Kolb Brian , Guo Hua
Published: July 2016

Scattering and dissociative chemisorption of DCl on Au(111) are investigated using ab initio molecular dynamics with a slab model, in which the top two layers of Au are mobile. Substantial kinetic energy loss in the scattered DCl is found, but the amount of energy transfer is notably smaller than that observed in the experiment. On the other hand, the dissociative chemisorption probability reproduces the experimental trend with respect to the initial kinetic energy, but is about one order of magnitude larger than the reported initial sticking probability. While the theory-experiment agreement is significantly improved from the previous rigid surface model, the remaining discrepancies are still substantial, calling for further scrutiny in both theory and experiment.
Lorentz force particle analyzer
Authors: Wang Xiaodong , Thess André , Moreau René , Tan Yanqing , Dai Shangjun , Tao Zhen , Yang Wenzhi , Wang Bo
Published: July 2016

A new contactless technique is presented for the detection of micron-sized insulating particles in the flow of an electrically conducting fluid. A transverse magnetic field brakes this flow and tends to become entrained in the flow direction by a Lorentz force, whose reaction force on the magnetic-field-generating system can be measured. The presence of insulating particles suspended in the fluid produce changes in this Lorentz force, generating pulses in it; these pulses enable the particles to be counted and sized. A two-dimensional numerical model that employs a moving mesh method demonstrates the measurement principle when such a particle is present. Two prototypes and a three-dimensional numerical model are used to demonstrate the feasibility of a Lorentz force particle analyzer (LFPA). The findings of this study conclude that such an LFPA, which offers contactless and on-line quantitative measurements, can be applied to an extensive range of applications. These applications include measurements of the cleanliness of high-temperature and aggressive molten metal, such as aluminum and steel alloys, and the clean manufacturing of semiconductors.
Secondary ion mass spectroscopy depth profiling of hydrogen-intercalated graphene on SiC
Authors: Michałowski Paweł Piotr , Kaszub Wawrzyniec , Merkulov Alexandre , Strupiński Włodek
Published: July 2016

For a better comprehension of hydrogen intercalation of graphene grown on a silicon carbide substrate, an advanced analytical technique is required. We report that with a carefully established measurement procedure it is possible to obtain a reliable and reproducible depth profile of bi-layer graphene (theoretical thickness of 0.69 nm) grown on the silicon carbide substrate by the Chemical Vapor Deposition method. Furthermore, we show that with depth resolution as good as 0.2 nm/decade, both hydrogen coming from the intercalation process and organic contamination can be precisely localized. As expected, hydrogen was found at the interface between graphene and the SiC substrate, while organic contamination was accumulated on the surface of graphene and did not penetrate into it. Such a precise measurement may prove to be invaluable for further characterization of 2D materials.
Electrical characteristics of SrTiO3/Al2O3 laminated film capacitors
Authors: Peng Yong , Yao Manwen , Chen Jianwen , Xu Kaien , Yao Xi
Published: July 2016

The electrical characteristics of SrTiO3/Al2O3 (160 nm up/90 nm down) laminated film capacitors using the sol-gel process have been investigated. SrTiO3 is a promising and extensively studied high-K dielectric material, but its leakage current property is poor. SrTiO3/Al2O3 laminated films can effectively suppress the demerits of pure SrTiO3 films under low electric field, but the leakage current value reaches to 0.1 A/cm2 at higher electric field (>160 MV/m). In this study, a new approach was applied to reduce the leakage current and improve the dielectric strength of SrTiO3/Al2O3 laminated films. Compared to laminated films with Au top electrodes, dielectric strength of laminated films with Al top electrodes improves from 205 MV/m to 322 MV/m, simultaneously the leakage current maintains the same order of magnitude (10−4 A/cm2) until the breakdown occurs. The above electrical characteristics are attributed to the anodic oxidation reaction in origin, which can repair the defects of laminated films at higher electric field. The anodic oxidation reactions have been confirmed by the corresponding XPS measurement and the cross sectional HRTEM analysis. This work provides a new approach to fabricate dielectrics with high dielectric strength and low leakage current.
Transport properties for carbon chain sandwiched between heteroatom-doped carbon nanotubes with different doping sites
Authors: Liu Wenjiang , Deng Xiaoqing , Cai Shaohong
Published: July 2016

The First-principles calculation is used to investigate the transport properties of a carbon chain connected with N-and/or B-doped caped carbon nanotube acting as electrodes. The I-V curves of the carbon chain are affected by the N/B doping sites, and rectifying behavior can be obtained distinctly when the carbon chain is just connected onto two doping atom sites (N- chain-B), and a weak rectification occurs when N (B) doping at other sites. Interestingly, the spin-filtering effects exist in the junction when it is doped at other sites, undoped system, or N-terminal carbon chains. However, no this behavior is found in N-chain-B and B-chain-B systems. The analysis on the transmission spectra, PDOS, LDOS, spin density, and the electron transmission pathways give an insight into the observed results for the system.
Source–sink plasmid transfer dynamics maintain gene mobility in soil bacterial communities
Authors: Hall James P. J. , Wood A. Jamie , Harrison Ellie , Brockhurst Michael A.
Published: July 2016

Significance

Bacterial adaptation through horizontal gene transfer is central to microbial evolution and, in the context of antibiotic resistance, represents a growing clinical threat. Conjugative plasmids are key mediators of genetic exchange both within and between species. Experimental studies have mostly focused on plasmid population dynamics in single-species populations, but between-species transfer could counteract purifying selection and maintain plasmids in hosts that would otherwise lose them. We show that plasmids can be lost from single-species populations, even when their genes are under selection, because beneficial genes are captured by the chromosome. In contrast, experiments and models show that, in a two-species community, between-species transfer maintains community-wide access to plasmids, promoting the spread of the ecologically and clinically important genes they carry.
Rationalizing spatial exploration patterns of wild animals and humans through a temporal discounting framework
Authors: Namboodiri Vijay Mohan K. , Levy Joshua M. , Mihalas Stefan , Sims David W. , Hussain Shuler Marshall G.
Published: July 2016

Significance

Understanding the movement patterns of wild animals is a fundamental question in ecology with implications for wildlife conservation. It has recently been hypothesized that random search patterns known as Lévy walks are optimal and underlie the observed power law movement patterns of wild foragers. However, as Lévy walk models assume that foragers do not learn from experience, they may not apply generally to cognitive animals. Here, we present a decision-theoretic framework wherein animals attempting to optimally learn from their environments will show near power law-distributed path lengths due to temporal discounting. We then provide experimental support for this framework in human exploration in a controlled laboratory setting and in animals foraging in the wild.
CCR7 expression alters memory CD8 T-cell homeostasis by regulating occupancy in IL-7– and IL-15–dependent niches
Authors: Jung Yong Woo , Kim Hyun Gyung , Perry Curtis J. , Kaech Susan M.
Published: July 2016

Significance

IL-7 and IL-15 have been shown to play crucial roles in maintaining the population of memory T cells, which are important in fighting against secondary infections, but how effector and memory T cells receive these cytokines is incompletely understood. We investigated the role of C-C receptor 7 (CCR7) in the development of memory T cells using CCR7-deficient mice. CCR7-deficient memory T cells showed an abnormal migratory pattern and increased survival, especially in the lungs and bone marrow, in an IL-15–dependent fashion compared with wild type memory cells. We conclude that the localization of memory T cells is important to “see” these cytokines for homeostasis.