bluuebunny/crossref_metadata_2025 huggingface dataset:
Complement Is Activated by IgG Hexamers Assembled at the Cell Surface
Authors: Diebolder Christoph A. , Beurskens Frank J. , de Jong Rob N. , Koning Roman I. , Strumane Kristin , Lindorfer Margaret A. , Voorhorst Marleen , Ugurlar Deniz , Rosati Sara , Heck Albert J. R. , van de Winkel Jan G. J. , Wilson Ian A. , Koster Abraham J. , Taylor Ronald P. , Ollmann Saphire Erica , Burton Dennis R. , Schuurman Janine , Gros Piet , Parren Paul W. H. I.
Published: March 2014

Hexing Complement

Complement activation is an immediate and potent immune defense mechanism, but how immunoglobulin G (IgG) antibodies activate complement at the molecular level is poorly understood. Using high-resolution crystallography,

Diebolder
et al.

(p.
1260
) show that human IgGs form hexameric structures by interacting with neighboring IgG molecules, and the complex then activates complement. Thus, IgG molecules and the complement system can coexist in the blood because complement activation will only be triggered after IgG senses a surface antigen and starts to aggregate.
Where Do Batteries End and Supercapacitors Begin?
Authors: Simon Patrice , Gogotsi Yury , Dunn Bruce
Published: March 2014

Electrochemical measurements can distinguish between different types of energy storage materials and their underlying mechanisms.
The Future Is Flat in White House's 2015 Spending Request
Authors: Malakoff David
Published: March 2014

Major U.S. science agencies would see essentially flat or declining spending under the 2015 budget request that President Barack Obama sent to Congress on 4 March.
Postexposure Protection of Macaques from Vaginal SHIV Infection by Topical Integrase Inhibitors
Authors: Dobard Charles , Sharma Sunita , Parikh Urvi M. , West Rolieria , Taylor Andrew , Martin Amy , Pau Chou-Pong , Hanson Debra L. , Lipscomb Jonathan , Smith James , Novembre Francis , Hazuda Daria , Garcia-Lerma J. Gerardo , Heneine Walid
Published: March 2014

Postexposure protection of macaques from SHIV infection by a gel containing integrase inhibitors.
Intestinal Inhibition of the Na
+
/H
+
Exchanger 3 Prevents Cardiorenal Damage in Rats and Inhibits Na
+
Uptake in Humans
Authors: Spencer Andrew G. , Labonte Eric D. , Rosenbaum David P. , Plato Craig F. , Carreras Christopher W. , Leadbetter Michael R. , Kozuka Kenji , Kohler Jill , Koo-McCoy Samantha , He Limin , Bell Noah , Tabora Jocelyn , Joly Kristin M. , Navre Marc , Jacobs Jeffrey W. , Charmot Dominique
Published: March 2014

An inhibitor of intestinal NHE3 reduces absorption of dietary sodium in rats and humans and prevents salt-induced cardiorenal injury in nephrectomized rats.
Identification of OppA2 Linear Epitopes as Serodiagnostic Markers for Lyme Disease
Authors: Signorino Giacomo , Arnaboldi Paul M. , Petzke Mary M. , Dattwyler Raymond J.
Published: March 2014

Laboratory diagnosis of Lyme disease is based on the serological detection of antibodies against the etiologic agentBorrelia burgdorferi. Current diagnostics are insensitive at detecting early infection, when treatment is most effective. This deficiency results from the limited number ofB. burgdorferiantigens expressed in early infection and the use of an insensitive two-tier paradigm, put in place to deal with insufficient specificity associated with the use of whole-protein antigens and/or bacterial lysates as serodiagnostic targets. Whole-protein antigens contain epitopes that are unique toB. burgdorferias well as cross-reactive epitopes found in other bacteria. One method for overcoming the limitations imposed by cross-reactive epitopes is the use of short peptides containing epitopes unique toB. burgdorferias antigen targets. This eliminates nonspecific epitopes. Using overlapping peptide libraries, we performed epitope mapping of linear epitopes in oligopeptide permease A2 (OppA2), a member of the oligopeptide permease (Opp) family of peptide transporters, expressed during earlyB. burgdorferiinfection. We identified 9 epitopes, synthesized peptides containing these epitopes, and screened those using panels of blood from patients with early Lyme disease, rheumatoid arthritis (RA), or syphilis or from healthy individuals. Two of the peptides, OppA2 (191-225) (amino acids comprising the peptide are shown in parentheses) and OppA2 (381-400), are highly conserved among the three major pathogenicBorreliaspecies responsible for most Lyme disease cases in North America and Europe. They detected antibodies in Lyme disease patient sera with sufficient sensitivity and specificity to indicate that they could have value in a serological assay for Lyme disease.
Identification of Coagulase-Negative Staphylococci from Bovine Intramammary Infection by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry
Authors: Tomazi Tiago , Gonçalves Juliano Leonel , Barreiro Juliana Regina , Braga Patrícia Aparecida de Campos , Prada e Silva Luis Felipe , Eberlin Marcos Nogueira , dos Santos Marcos Veiga
Published: March 2014

Coagulase-negative staphylococci (CoNS) are among the main pathogens causing bovine intramammary infection (IMI) in many countries. However, one of the limitations related to the specific diagnosis of CoNS is the lack of an accurate, rapid, and convenient method that can differentiate the bacterial species comprising this group. The aim of this study was to evaluate the ability of matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) to accurately identify CoNS species in dairy cow IMI. In addition, the study aimed to determine the frequency of CoNS species causing bovine IMI. A total of 108 bacterial isolates were diagnosed as CoNS by microbiological cultures from two milk samples collected from 21 dairy herds; the first sample was collected at the cow level (i.e., 1,242 composite samples from all quarters), while the second sample was collected at the mammary quarter level (i.e., 1,140 mammary samples collected from 285 cows). After CoNS isolation was confirmed by microbiological culture for both samples, all CoNS isolates (n= 108) were genotypically differentiated by PCR restriction fragment length polymorphism (RFLP) analysis of a partialgroELgene sequence and subjected to the MALDI-TOF MS identification procedure. MALDI-TOF MS correctly identified 103 (95.4%) of the CoNS isolates identified by PCR-RFLP at the species level. Eleven CoNS species isolated from bovine IMI were identified by PCR-RFLP, and the most prevalent species wasStaphylococcus chromogenes(n= 80; 74.1%). In conclusion, MALDI-TOF MS may be a reliable alternative method for differentiating CoNS species causing bovine IMI.
Detection of Nonhemagglutinating Influenza A(H3) Viruses by Enzyme-Linked Immunosorbent Assay in Quantitative Influenza Virus Culture
Authors: van Baalen C. A. , Els C. , Sprong L. , van Beek R. , van der Vries E. , Osterhaus A. D. M. E. , Rimmelzwaan G. F.
Published: March 2014

To assess the efficacy of novel antiviral drugs against influenza virus in clinical trials, it is necessary to quantify infectious virus titers in respiratory tract samples from patients. Typically, this is achieved by inoculating virus-susceptible cells with serial dilutions of clinical specimens and detecting the production of progeny virus by hemagglutination, since influenza viruses generally have the capacity to bind and agglutinate erythrocytes of various species through their hemagglutinin (HA). This readout method is no longer adequate, since an increasing number of currently circulating influenza A virus H3 subtype (A[H3]) viruses display a reduced capacity to agglutinate erythrocytes. Here, we report the magnitude of this problem by analyzing the frequency of HA-deficient A(H3) viruses detected in The Netherlands from 1999 to 2012. Furthermore, we report the development and validation of an alternative method for monitoring the production of progeny influenza virus in quantitative virus cultures, which is independent of the capacity to agglutinate erythrocytes. This method is based on the detection of viral nucleoprotein (NP) in virus culture plates by enzyme-linked immunosorbent assay (ELISA), and it produced results similar to those of the hemagglutination assay using strains with good HA activity, including A/Brisbane/059/07 (H1N1), A/Victoria/210/09 (H3N2), other seasonal A(H1N1), A(H1N1)pdm09, and the majority of A(H3) virus strains isolated in 2009. In contrast, many A(H3) viruses that have circulated since 2010 failed to display HA activity, and infectious virus titers were determined only by detecting NP. The virus culture ELISA described here will enable efficacy testing of new antiviral compounds in clinical trials during seasons in which nonhemagglutinating influenza A viruses circulate.
Quantification of Deaminase Activity-Dependent and -Independent Restriction of HIV-1 Replication Mediated by APOBEC3F and APOBEC3G through Experimental-Mathematical Investigation
Authors: Kobayashi Tomoko , Koizumi Yoshiki , Takeuchi Junko S. , Misawa Naoko , Kimura Yuichi , Morita Satoru , Aihara Kazuyuki , Koyanagi Yoshio , Iwami Shingo , Sato Kei
Published: March 2014

APOBEC3F and APOBEC3G cytidine deaminases potently inhibit human immunodeficiency virus type 1 (HIV-1) replication by enzymatically inserting G-to-A mutations in viral DNA and/or impairing viral reverse transcription independently of their deaminase activity. Through experimental and mathematical investigation, here we quantitatively demonstrate that 99.3% of the antiviral effect of APOBEC3G is dependent on its deaminase activity, whereas 30.2% of the antiviral effect of APOBEC3F is attributed to deaminase-independent ability. This is the first report quantitatively elucidating how APOBEC3F and APOBEC3G differ in their anti-HIV-1 modes.
Association between Cellular Immune Activation, Target Cell Frequency, and Risk of Human Immunodeficiency Virus Type 1 Superinfection
Authors: Blish Catherine A. , Dogan Ozge C. , Jaoko Walter , McClelland R. Scott , Mandaliya Kishorchandra , Odem-Davis Katherine , Richardson Barbra A. , Overbaugh Julie
Published: March 2014

We performed a case-control study of women at risk of HIV-1 superinfection to understand the relationship between immune activation and HIV-1 acquisition. An increase in the frequency of HIV-1 target cells, but not in other markers of T cell activation, was associated with a 1.7-fold increase in the odds of superinfection. This suggests that HIV-1 acquisition risk is influenced more by the frequency of target cells than by the generalized level of immune activation.
Attenuation of Human Enterovirus 71 High-Replication-Fidelity Variants in AG129 Mice
Authors: Meng Tao , Kwang Jimmy
Published: March 2014

In a screen for ribavirin resistance, a novel high-fidelity variant of human enterovirus 71 (EV71) with the single amino acid change L123F in its RNA-dependent RNA polymerase (RdRp or 3D) was identified. Based on the crystal structure of EV71 RdRp, L123 locates at the entrance of the RNA template binding channel, which might form a fidelity checkpoint. EV71 RdRp-L123F variants generated less progeny in a guanidine resistance assay and virus populations with lower mutation frequencies in cell culture passage due to their higher replication fidelity. However, compared with wild-type viruses, they did not show growth defects.
In vivo
infections further revealed that high-fidelity mutations L123F and G64R (previously reported) negatively impacted EV71 fitness and greatly reduced viral pathogenicity alone or together in AG129 mice. Interestingly, a variant with double mutations, RG/B4-G64R/L123F (where RG/B4 is an EV71 genotype B4 virus constructed by reverse genetics [RG])showed higher fidelity
in vitro
and less virulence
in vivo
than any one of the above two single mutants. The 50% lethal dose (LD
50
) of the double mutant increased more than 500 times compared with the LD
50
of wild-type RG/B4 in mice. The results indicated that these high-fidelity variants exhibited an attenuated pathogenic phenotype
in vivo
and offer promise as a live attenuated EV71 vaccine.

IMPORTANCE
The error-prone nature of the RNA-dependent RNA polymerase (RdRp) of RNA viruses during replication results in quasispecies and aids survival of virus populations under a wide range of selective pressures. Virus variants with higher replication fidelity exhibit lower genetic diversity and attenuated pathogenicity
in vivo
. Here, we identified a novel high-fidelity mutation L123F in the RdRp of human enterovirus 71 (EV71). We further elucidated that EV71 variants with the RdRp-L123F mutation and/or the previously identified high-fidelity mutation RdRp-G64R were attenuated in an AG129 mouse model. As EV71 has emerged as a serious worldwide health threat, especially in developing countries in the Asia-Pacific region, we urgently need EV71 vaccines. Learning from the poliovirus vaccination, we prefer live attenuated EV71 vaccines to inactivated EV71 vaccines in order to effectively control EV71 outbreaks at low cost. Our results imply a new means of attenuating EV71 and reducing its mutation rate at the same time.
Preferential Packing of Acidic Glycosidases and Proteases into
Bacteroides
Outer Membrane Vesicles
Authors: Elhenawy Wael , Debelyy Mykhaylo O. , Feldman Mario F.
Published: March 2014

Outer membrane vesicles (OMV) are spherical membranous structures released from the outer membrane (OM) of Gram-negative bacteria. OMV have been proposed to play several different roles during both pathogenesis and symbiosis. Despite the fact that OMV were described several decades ago, their biogenesis is a poorly characterized process. Whether OMV are produced by an active mechanism or by passive disintegration of the OM is a still matter of controversy.
Bacteroides fragilis
and
Bacteroides thetaiotaomicron
are important members of the human microbiota. In this work, we determined and compared the protein compositions of OM and OMV from
B. fragilis
and
B. thetaiotaomicron
. SDS-PAGE analysis of both fractions revealed dramatically different protein profiles. Proteomic analysis of OM and OMV in
B. fragilis
identified more than 40 proteins found exclusively in OMV and more than 30 proteins detectable only in the OM. The OMV-specific proteome showed a high prevalence of glycosidases and proteases, some of which were shown to be active
in vitro
. Similar results were obtained for
B. thetaiotaomicron
. Most of the OMV-exclusive proteins were acidic. Based on these results, we propose that these species possess machinery devoted to selectively pack acidic proteins into the OMV. These OMV equipped with hydrolytic enzymes could help in securing nutrients for the benefit of the whole bacterial community present in the microbiota, uncovering a novel function for bacterial OMV.

IMPORTANCE
The members of genus
Bacteroides
are key players in the symbiosis between the human host and the gut microbiota. It is known for its ability to degrade a wide variety of glycans that are not substrates for human glycosidases. The cleaved glycans can be utilized by
Bacteroides
and other microbiota members, resulting in the production of short-chain fatty acids that are beneficial for the host. Although members of the genus
Bacteroides
are known to secrete different hydrolases, their secretion pathways remain uncharacterized. In this article, we show that
B. fragilis
and
B. thetaiotaomicron
preferentially pack a large number of hydrolases in outer membrane vesicles (OMV). Most of these hydrolases are acidic and were detected exclusively in OMV. This suggests the presence of a molecular mechanism in
Bacteroides
responsible for the selection of OMV proteins based on their charge. We propose that OMV contribute to the establishment and balance of the gut microbiota.
Mycoplasma pneumonia-associated mucositis
Authors: Varghese Cyril , Sharain Korosh , Skalski Joseph , Ramar Kannan
Published: March 2014

We present a case of a young man with severe mucositis following an upper respiratory tract infection limited to the ophthalmic and oral mucosa while sparing the rest of the skin, genitalia and perianal regions. Investigations revealed that the mucositis was a rare extrapulmonary manifestation ofMycoplasma pneumoniaeinfection. He had progressive vision-threatening symptoms despite antibiotics and best supportive care and thus was treated with intravenous corticosteroids, immunoglobulins, temporary ocular amniotic membrane grafts and tarsorrhaphy. The patient made an almost complete recovery over 6 weeks.
Holy Saturday asthma
Authors: O'Connor Terence M , Cusack Ruth , Landers Sarah , Bredin Charles Patrick
Published: March 2014

A 61-year-old man complained of cough and dyspnoea after exposure to colophony-containing solder fumes at work. A histamine challenge test confirmed airway hyper-responsiveness, and colophony-challenge demonstrated a 16.7% drop in peak expiratory flow rate (PEFR), supporting a diagnosis of colophony-induced occupational asthma. At review, the patient presented with cough, dyspnoea and wheeze that occurred acutely when exposed to the fumes from burning incense during Easter Saturday services, necessitating his departure from the church. Inhalation challenge tests using two blends of incense used at his church (Greek and Vatican) led to identical symptoms and a significant reduction in forced expiratory volume in 1 s 15 min after exposure and PEFRs up to 48 h after exposure, indicating an early and late phase asthmatic reaction. This is the first report of coexistent colophony and incense-induced asthma. The similarities in chemical structures between abietic acid in colophony and boswellic acid in incense suggest a common mechanism.
Public hospital quality report awareness: evidence from National and Californian Internet searches and social media mentions, 2012
Authors: Huesch Marco D , Currid-Halkett Elizabeth , Doctor Jason N
Published: March 2014

Objectives

Publicly available hospital quality reports seek to inform consumers of important healthcare quality and affordability attributes, and may inform consumer decision-making. To understand how much consumers search for such information online on one Internet search engine, whether they mention such information in social media and how positively they view this information.

Setting and design

A leading Internet search engine (Google) was the main focus of the study. Google Trends and Google Adwords keyword analyses were performed for national and Californian searches between 1 August 2012 and 31 July 2013 for keywords related to ‘top hospital’, best hospital’, and ‘hospital quality’, as well as for six specific hospital quality reports. Separately, a proprietary social media monitoring tool was used to investigate blog, forum, social media and traditional media mentions of, and sentiment towards, major public reports of hospital quality in California in 2012.

Primary outcome measures

(1) Counts of searches for keywords performed on Google; (2) counts of and (3) sentiment of mentions of public reports on social media.

Results

National Google search volume for 75 hospital quality-related terms averaged 610 700 searches per month with strong variation by keyword and by state. A commercial report (Healthgrades) was more commonly searched for nationally on Google than the federal government's Hospital Compare, which otherwise dominated quality-related search terms. Social media references in California to quality reports were generally few, and commercially produced hospital quality reports were more widely mentioned than state (Office of Statewide Healthcare Planning and Development (OSHPD)), or non-profit (CalHospitalCompare) reports.

Conclusions

Consumers are somewhat aware of hospital quality based on Internet search activity and social media disclosures. Public stakeholders may be able to broaden their quality dissemination initiatives by advertising on Google or Twitter and using social media interactively with consumers looking for relevant information.
Randomised Evaluation of modified Valsalva Effectiveness in Re-entrant Tachycardias (REVERT) study
Authors: Appelboam Andrew , Reuben Adam , Mann Clifford , Lobban Trudie , Ewings Paul , Benger Jonathan , Vickery Jane , Barton Andrew , Gagg James
Published: March 2014

Introduction

The Valsalva manoeuvre (VM) is a recommended first-line physical treatment for patients with re-entrant supraventricular tachycardia (SVT), but is often ineffective in standard practice. A failed VM is typically followed by treatment with intravenous adenosine, which patients often find unpleasant. VM effectiveness might be improved by a modification to posture which exaggerates the manoeuvre's vagal response and reduces the need for further emergency treatment.

Methods and analysis

This is a multicentre randomised controlled clinical trial in 10 UK emergency departments (EDs). It compares a standard VM with a modified VM incorporating leg elevation and a supine posture after a standardised strain in stable adult patients presenting to the ED with SVT. The primary outcome measure is return to sinus rhythm on a 12-lead ECG. Secondary outcome measures include the need for treatment with adenosine or other antiarrhythmic treatments and the time patients spend in the ED. We plan to recruit approximately 372 patients, with 80% power to demonstrate an absolute improvement in cardioversion rate of 12%. An improvement of this magnitude through the use of a modified VM would be of significant benefit to patients and healthcare providers, and justify a change to standard practice.

Ethics and dissemination

The study has been approved by the South West—Exeter Research Ethics Committee (REC reference 12/SW/0281). The trial will be published in an international peer reviewed journal. Study findings will be sent to the European and International resuscitation councils to inform future revisions of arrhythmia management guidelines.

Results

The trial will also be disseminated at international conferences and to patients through the Arrhythmia Alliance, a patient support charity.

Registration

The study is registered with Current Controlled Trials (ISRCTN67937027) and has been adopted by the National Institute for Health Research (NIHR) Clinical Research Network.
External quality assessment: best practice
Authors: James David , Ames Darren , Lopez Berenice , Still Rachel , Simpson Wiliam , Twomey Patrick
Published: March 2014

There is a requirement for accredited laboratories to participate in external quality assessment (EQA) schemes, but there is wide variation in understanding as to what is required by the laboratories and scheme providers in fulfilling this. This is not helped by a diversity of language used in connection with EQA; Proficiency testing (PT), EQA schemes, and EQA programmes, each of which have different meanings and offerings in the context of improving laboratory quality.

We examine these differences, and identify what factors are important in supporting quality within a clinical laboratory and what should influence the choice of EQA programme. Equally as important is how EQA samples are handled within the laboratory, and how the information provided by the EQA programme is used.

EQA programmes are a key element of a laboratory's quality assurance framework, but laboratories should have an understanding of what their EQA programmes are capable of demonstrating, how they should be used within the laboratory, and how they support quality. EQA providers should be clear as to what type of programme they provide – PT, EQA Scheme or EQA Programme.
Phase separation in the Langmuir–Blodgett films of p-quaterphenyl mixed with two different matrices
Authors: Nath Jayasree , Pal Ajitesh , Deb Subrata , Mishra Bijay Kumar , Nath Ranendu Kumar
Published: March 2014

The phase behavior of two components p-quaterphenyl (QP) and polymethyl methacrylate (PMMA)/heptadecanoic acid (HA)) in the Langmuir monolayer was characterized. The surface pressure versus area per molecule isotherms revealed that the area per molecule systematically changed with increasing mole fractions of QP, indicating that repulsive types of interactions were involved between the QP and the matrix molecules (PMMA/HA), leading to the phase separation which in turn stimulated the aggregate formation. Absorption spectroscopy, complemented with scanning electron microscopy (SEM), confirmed the aggregation of QP molecules in the mixed films.
MODIS NDVI time series clustering under dynamic time warping
Authors: Zhang Zheng , Tang Ping , Huo Lianzhi , Zhou Zengguang
Published: March 2014

For MODIS NDVI time series with cloud noise and time distortion, we propose an effective time series clustering framework including similarity measure, prototype calculation, clustering algorithm and cloud noise handling. The core of this framework is dynamic time warping (DTW) distance and its corresponding averaging method, DTW barycenter averaging (DBA). We used 12 years of MODIS NDVI time series to perform annual land-cover clustering in Poyang Lake Wetlands. The experimental result shows that our method performs better than classic clustering based on ordinary Euclidean methods.
Continuous Variable Quantum Information: Gaussian States and Beyond
Authors: Adesso Gerardo , Ragy Sammy , Lee Antony R.
Published: March 2014

The study of Gaussian states has arisen to a privileged position in continuous variable quantum information in recent years. This is due to vehemently pursued experimental realisations and a magnificently elegant mathematical framework. In this paper, we provide a brief, and hopefully didactic, exposition of Gaussian state quantum information and its contemporary uses, including sometimes omitted crucial details. After introducing the subject material and outlining the essential toolbox of continuous variable systems, we define the basic notions needed to understand Gaussian states and Gaussian operations. In particular, emphasis is placed on the mathematical structure combining notions of algebra and symplectic geometry fundamental to a complete understanding of Gaussian informatics. Furthermore, we discuss the quantification of different forms of correlations (including entanglement and quantum discord) for Gaussian states, paying special attention to recently developed measures. The paper is concluded by succinctly expressing the main Gaussian state limitations and outlining a selection of possible future lines for quantum information processing with continuous variable systems.
Recursion rules for the hypergeometric zeta function
Authors: Byrnes Alyssa , Jiu Lin , Moll Victor H. , Vignat Christophe
Published: March 2014

The hypergeometric zeta function is defined in terms of the zeros of the Kummer function M(a, a+b; z). It is established that this function is an entire function of order 1. The classical factorization theorem of Hadamard gives an expression as an infinite product. This provides linear and quadratic recurrences for the hypergeometric zeta function. A family of associated polynomials is characterized as Appell polynomials and the underlying distribution is given explicitly in terms of the zeros of the associated hypergeometric function. These properties are also given a probabilistic interpretation in the framework of beta distributions.
The strike-fed sandy coast of Southern Brazil
Authors: Dillenburg Sergio R. , Barboza Eduardo G.
Published: March 2014

The Holocene barrier along the southern Brazilian coast is most likely the most continuous barrier structure in the world. This coast is characterized by a Holocene barrier extending for 760 km, interrupted by only six discontinuities, which are associated with narrow lagoonal inlets and river mouths. This coast is marked by a huge availability of sand, a gently sloping continental shelf, and incident waves of moderate to high energy. Together, these factors constitute ideal conditions for the formation of coastal barriers. During periods of low sea-levels, the continental shelf in front of the La Plata estuary was fed by immature fluvial sands delivered by the Paraná River, which were transported to the southern Brazilian coast by a predominantly northward littoral drift. Based on forecasts of sea-level rise, it will take decades or centuries for change to occur in the progradation of the regressive barriers along the coastal embayments. During the last centuries and millennia (Middle to Late Holocene), the evolution of this coast has been controlled by the variations in wave energy along the coast.
Plagiogranites from the mantle section of the Oman Ophiolite: models for early crustal evolution
Authors: Rollinson Hugh
Published: March 2014

Plagiogranites intrusive into the harzburgites of the mantle section of the Oman Ophiolite are compositionally distinct from plagiogranites in the crustal section of the ophiolite and are relatively enriched in MgO, Cr and Ni and in the incompatible trace elements K, Th, U, Ta, La and Ce. These geochemical features are used to explain the origin of the plagiogranites and it is suggested that they are the product of three-component mixing between melts from mafic, crustal and mantle sources. There is geochemical evidence to show that the plagiogranites interacted with their mantle host, although the geochemical signature of this interaction appears to be different from that produced during two-component mixing between a slab melt and the mantle wedge. This mantle interaction makes the Oman mantle plagiogranites a helpful analogue for understanding the extent to which Archaean tonalite–trondhjemite–granodiorite (TTGs) interacted with the mantle during their genesis. However, it is shown that the high Mg# in Archaean TTGs may be masked by later hornblende fractionation, obscuring the originally high Mg# of parental TTG magmas and reopening the possibility that Archaean TTGs might be slab melts.
Late Cretaceous Conglomerates of the Qahlah Formation, north Oman
Authors: Abbasi Iftikhar A. , Salad Hersi O. , Al-Harthy A.
Published: March 2014

Conglomerate sequences over 700 m thick were deposited subsequent to ophiolite emplacement during Late Cretaceous time in north Oman. The conglomerates were deposited by streams draining the allochthonous ophiolite and Hawasina complex after their obduction onto autochthonous Mesozoic and older Oman shelf sequences and subsequent uplift. The conglomerates belong to the Qahlah Formation of Late Cretaceous age, which is sandwiched between the Semail Ophiolite/Hawasina complex and Maastrichtian–Palaeogene carbonate rocks. The siliciclastics of the Qahlah Formation are the first sediments deposited over the obducted oceanic crust sequence of ophiolite and Hawasina lithologies. In five locations studied in north Oman, the thickness of the formation varies from 140 m to over 700 m and comprises interbedded conglomerate, sandstone and siltstone. The sediments were deposited in isolated segmented depressions each characterized by its source terrain depending on lithologies exposed in the source area. Lithofacies associations, clast sorting and grain roundness suggest deposition in stream-dominated alluvial fans. Clasts in the conglomerates range from subangular to subrounded pebbles to boulders with both grain and matrix (sandstone) support. Cross-bedded fining-upwards sequences in channelized conglomerate and sandstone suggest deposition by high-energy flows in the proximal to distal reaches of alluvial fans. High proportions of chert and ophiolite fragments in the conglomerates suggest rapid erosion of obducted oceanic crust. The presence of
Loftusia
-bearing carbonate beds and bivalve-bearing conglomerate beds in different sections indicates occasional interruption of alluvial deposition by marine transgressions.
Petroleum systems in the Middle East
Authors: Alsharhan A. S.
Published: March 2014

Since the start of the twentieth century more than 550 commercially significant oil and gas fields have been discovered in the Middle East. Most of the fields have more than one pay zone and produce from shallow-water carbonates and clastics that range in age from Infracambrian to Oligo-Miocene. A providential juxtaposition of source-reservoir-seal, migration history and trapping mechanism has lead to the entrapment of hydrocarbons throughout the Phanerozoic strata of the Middle East. Each occurrence shares some characteristics but each also has unique features. The geographic occurrence of hydrocarbons in the region reflects the original facies variations across the depositional shelf and basin and the tectonic history of basement faults and halokinetic activity. The evaluation and integration of these critical variables, together with an appreciation of the maturation, migration history and trapping mechanisms, drives the search for new fields. The continued discovery of new fields proves that the region has not yielded all its treasure and stimulates future exploration. Although evidence for orogenic deformation is lacking in the Middle East, epeirogenic warping is common. The latter is attributed to the reactivation of basement faults, and evaporite structures and flow at depth. A prominent sedimentary and erosional break, locally marked by eroded Hercynian unconformities, followed an important Late Palaeozoic epeirogenic uplift. Similarly, Mesozoic sedimentary fill is broken by a major change in tectonic and depositional regimes, and numerous unconformities thought to be primarily controlled by high-frequency fluctuations in eustatic sea level and a low uniform rate of tectonic movement. Late Cretaceous and Tertiary events followed the collision and partial subduction of the east and southeastern margin of the Arabian Plate and involved vertical epeirogenic uplift of the resulting folded and thrusted gravity features. Vast areas of the Middle East Basin have yet to be extensively drilled. Although the long-lived stability of the shelf has influenced the development of the giant oil pools, and to some extent reduced the potential for stratigraphic traps, it has not eliminated the potential for smaller structures and the exploration for new oil and gas reserves. Future exploration is expected to focus on the discovery of smaller structures and subtle traps revealed by analysis of existing geological data and special seismic processing. Exploration will involve extensive regional and local geological–sedimentological studies, 3D or 4D seismic surveys and drilling progrmmes, and proposed better petroleum system model(s) for each basin (or sub-basin).
North Oman fault geometries in outcrops, analogues and subsurface
Authors: Richard Pascal , Bazalgette Loic , Al-Kindi Mohammed
Published: March 2014

North Oman offers a rare opportunity for making outcrop observations of faults developed in carbonate formations that are also producing reservoirs in the subsurface. It is possible to look in great detail at fault geometries and associated fault damage zones, both in map view and cross-sections. These observations allow the establishment of geometrical concepts and rules to be established that allow the interpretation of seismic faults and the building of coherent static models. This paper highlights how the combination of the input from outcrops, a database of sandbox analogue models and high quality seismic data enables the development of conceptual geometrical models of faults. These conceptual geometrical models support interpretation and modelling strategies and workflows for the construction of geo-cellular models. In the first part of this paper, the challenge faced by the geo-modeller is described. A description of the vertical segmentation of faults in cross-section is provided. A summary of these observations is sketched as a series of 3D block diagrams. Finally, the mechanisms of fault initiation and growth through time reviewed to highlight the particular 3D segmented nature of faults in carbonate.
Pn
-velocity structure beneath Arabia–Eurasia Zagros collision and Makran subduction zones
Authors: Al-Lazki Ali I. , Al-Damegh Khaled S. , El-Hadidy Salah Y. , Ghods Abdolreza , Tatar Mohammad
Published: March 2014

We use
Pn
-tomography to map lithospheric mantle velocity and anisotropy at the Arabia–Eurasia plate boundary, namely Makran and Zagros. We use catalogue events recorded by Oman, UAE, Saudi Arabia and Iran networks, the International Seismological Centre and the National Earthquake Information Center. Events of 1.8–16 degree distances were used for this
Pn
-tomography. In this study we show that the northeastern Arabia plate is characterized by cold and stable lithospheric mantle. Contrastingly, Eurasia is underlain by hot unstable lithospheric mantle. The Arabia–Eurasia lithospheric suture follows the Zagros collision surface suture within
c.
70 km lateral proximity. At the southernmost Zagros collision, the Arabia lithosphere is inferred to extend further NE beneath Lut Block. This may be indicative of extended subduction of Arabia beneath Eurasia in southernmost Zagros. We find that eastern Makran shows typical subduction characteristics, with inferred oceanic lithosphere underlying the eastern Oman Sea and hot unstable lithospheric mantle below overriding Helmand Block. Contrastingly, the western Makran subduction zone including Arabia and Eurasia continental sides is underlain by a low-
Pn
-velocity anomaly, indicative of hot unstable lithospheric mantle. Surface evidence show that western, southern and eastern boundaries of western Makran low-
Pn
-velocity anomaly may represent a Late Neogene reactivated Precambrian terrane boundary in north Oman.
Structure of the northern Oman Mountains from the Semail Ophiolite to the Foreland Basin
Authors: Cooper D. J. W. , Ali M. Y. , Searle M. P.
Published: March 2014

The northern Oman Mountains record the Late Cretaceous emplacement of the Semail Ophiolite and associated subduction trench and deeper-water sediments into a foredeep on the downwarped Arabian continental margin. In-sequence piggy-back thrusting was modified by later thrust sheets of Permian–Mesozoic continental slope sediments that breached the overlying allochthonous stack. Sections through these culminations show asymmetries linked to deep-seated faults perpendicular to the margin edge which created offsets (promontories) that influenced detachment. Seismic profiles across the foredeep indicate an unconformity at the top of the Mesozoic carbonate platform, the product of early flexural uplift, onlapped by sediments. A second onlap phase is linked with rapid subsidence during final emplacement of the allochthon. Passive margin conditions resumed during Maastrichtian time, conformable along the axis of the foredeep. A Paleocene–Eocene (Pabdeh) foredeep was initiated in the northern mountains, recorded on seismic profiles with another onlapping sequence. Subsidence and infill persisted into the Oligocene when compression, linked with the Zagros collision, resulted in uplift and en echelon folding, probably due to the reactivation of deep-seated faults. Post-Miocene erosion of one culmination exposed the cap of a gypsum/anhydrite intrusion. The origin remains uncertain, but derivation from the Neoproterozoic to Cambrian Ara Group salt is preferred.
Silencing of hypoxia-inducible factor-1α gene attenuates chronic ischemic renal injury in two-kidney, one-clip rats
Authors: Wang Zhengchao , Zhu Qing , Li Pin-Lan , Dhaduk Romesh , Zhang Fan , Gehr Todd W. , Li Ningjun
Published: March 2014

Overactivation of hypoxia-inducible factor (HIF)-1α is implicated as a pathogenic factor in chronic kidney diseases (CKD). However, controversy exists regarding the roles of HIF-1α in CKD. Additionally, although hypoxia and HIF-1α activation are observed in various CKD and HIF-1α has been shown to stimulate fibrogenic factors, there is no direct evidence whether HIF-1α is an injurious or protective factor in chronic renal hypoxic injury. The present study determined whether knocking down the HIF-1α gene can attenuate or exaggerate kidney damage using a chronic renal ischemic model. Chronic renal ischemia was induced by unilaterally clamping the left renal artery for 3 wk in Sprague-Dawley rats. HIF-1α short hairpin (sh) RNA or control vectors were transfected into the left kidneys. Experimental groups were sham+control vector, clip+control vector, and clip+HIF-1α shRNA. Enalapril was used to normalize blood pressure 1 wk after clamping the renal artery. HIF-1α protein levels were remarkably increased in clipped kidneys, and this increase was blocked by shRNA. Morphological examination showed that HIF-1α shRNA significantly attenuated injury in clipped kidneys: glomerular injury indices were 0.71 ± 0.04, 2.50 ± 0.12, and 1.34 ± 0.11, and the percentage of globally damaged glomeruli was 0.02, 34.3 ± 5.0, and 6.3 ± 1.6 in sham, clip, and clip+shRNA groups, respectively. The protein levels of collagen and α-smooth muscle actin also dramatically increased in clipped kidneys, but this effect was blocked by HIF-1α shRNA. In conclusion, long-term overactivation of HIF-1α is a pathogenic factor in chronic renal injury associated with ischemia/hypoxia.
Adaptation of naturally paced saccades
Authors: Gray Michael J. , Blangero Annabelle , Herman James P. , Wallman Josh , Harwood Mark R.
Published: March 2014

In the natural environment, humans make saccades almost continuously. In many eye movement experiments, however, observers are required to fixate for unnaturally long periods of time. The resulting long and monotonous experimental sessions can become especially problematic when collecting data in a clinical setting, where time can be scarce and subjects easily fatigued. With this in mind, we tested whether the well-studied motor learning process of saccade adaptation could be induced with a dramatically shortened intertrial interval. Observers made saccades to targets that stepped left or right either ∼250 ms or ∼1,600 ms after the saccade landed. In experiment I, we tested baseline saccade parameters to four different target amplitudes (5°, 10°, 15°, and 20°) in the two timing settings. In experiments II and III, we adapted 10° saccades via 2° intrasaccadic steps either backwards or forwards, respectively. Seven subjects performed eight separate adaptation sessions (2 intertrial timings × 2 adaptation direction × 2 session trial lengths). Adaptation proceeded remarkably similarly in both timing conditions across the multiple sessions. In the faster-paced sessions, robust adaptation was achieved in under 2 min, demonstrating the efficacy of our approach to streamlining saccade adaptation experiments. Although saccade amplitudes were similar between conditions, the faster-paced condition unexpectedly resulted in significantly higher peak velocities in all subjects. This surprising finding demonstrates that the stereotyped “main sequence” relationship between saccade amplitude and peak velocity is not as fixed as originally thought.
Serum metabolomics identifies citrulline as a predictor of adverse outcomes in an equine model of gut-derived sepsis
Authors: Steelman Samantha M. , Johnson Philip , Jackson Amy , Schulze James , Chowdhary Bhanu P.
Published: March 2014

Acute laminitis is an inflammatory disease of the equine foot that often occurs secondarily to sepsis or systemic inflammation associated with gastrointestinal disease. It has been suggested that laminitis is similar to multiple organ dysfunction syndrome in humans, although in horses the weight-bearing laminar epithelium of the foot appears to be the tissue most sensitive to insult and the first “organ” to fail. Metabolomics performed on serum samples collected before (Con) and after (Lmn) experimental induction of gastrointestinal-associated sepsis in six horses detected 1,177 metabolites of both mammalian and bacterial origin in equine serum. Network and correlation analyses suggested a dysregulation of fatty acid metabolism in the Lmn group, as well as an accumulation of organic acids such as lactate. Furthermore, concentrations of the amino acid citrulline were decreased in Lmn samples from all study animals, suggesting that citrulline might be useful as a biomarker to identify critically ill animals that are at risk of developing laminitis. We therefore established normal ranges of plasma citrulline concentrations in a separate group of horses ( n = 36) and tested the ability of citrulline to predict adverse outcomes (laminitis or death) in critically ill horses ( n = 23). Plasma citrulline was significantly lower in critically ill horses that went on to experience adverse outcomes ( n = 6). Further study is required to accurately determine a diagnostic cutoff, but the present data are suggestive of the predictive value of citrulline as a biomarker for laminar failure in equine sepsis.
Tripled Fixed Point Theorems for Mixed Monotone Kannan Type Contractive Mappings
Authors: Borcut Marin , Păcurar Mădălina , Berinde Vasile
Published: March 2014

We present new results on the existence and uniqueness of tripled fixed points for nonlinear mappings in partially ordered complete metric spaces that extend the results in the previous works: Berinde and Borcut, 2011, Borcut and Berinde, 2012, and Borcut, 2012. An example and an application to support our new results are also included in the paper.
Asymptotic Behaviors of the Eigenvalues of Schrödinger Operator with Critical Potential
Authors: Jia Xiaoyao , Zhao Yan , Zhai Haoyu
Published: March 2014

We study the asymptotic behaviors of the discrete eigenvalue of Schrödinger operatorP(λ)=P0+λVwithP0=-Δ+qθ/r2.We obtain the leading terms of discrete eigenvalues ofP(λ)when the eigenvalues tend to 0. In particular, we obtain the asymptotic behaviors of eigenvalues when(P0−α)−1has singularity atα=0.
Molecular Patterns of Neurodevelopmental Preconditioning: A Study of the Effects of Antenatal Steroid Therapy in a Protein-Restriction Mouse Model
Authors: Velayo Clarissa , Ito Takuya , Dong Yupeng , Endo Miyuki , Sugibayashi Rika , Funamoto Kiyoe , Iida Keita , Yaegashi Nobuo , Kimura Yoshitaka
Published: March 2014

Introduction. Prenatal programming secondary to maternal protein restriction renders an inherent susceptibility to neural compromise in neonates and any addition of glucocorticosteroids results in further damage. This is an investigation of consequent global gene activity due to effects of antenatal steroid therapy on a protein restriction mouse model. Methods. C57BL/6N pregnant mice were administered control or protein restricted diets and subjected to either 100 μg/Kg of dexamethasone sodium phosphate with normosaline or normosaline alone during late gestation (E10–E17). Nontreatment groups were also included. Brain samples were collected on embryonic day 17 and analyzed by mRNA microarray analysis. Results. Microarray analyses presented 332 significantly regulated genes. Overall, neurodevelopmental genes were overrepresented and a subset of 8 genes allowed treatment segregation through the hierarchical clustering method. The addition of stress or steroids greatly affected gene regulation through glucocorticoid receptor and stress signaling pathways. Furthermore, differences between dexamethasone-administered treatments implied a harmful effect during conditions of high stress. Microarray analysis was validated using qPCR. Conclusion. The effects of antenatal steroid therapy vary in fetuses according to maternal-fetal factors and environmental stimuli. Defining the key regulatory networks that signal either beneficial or damaging corticosteroid action would result in valuable adjustments to current treatment protocols.