bluuebunny/crossref_metadata_2025 huggingface dataset:
Meta-Analysis and Potential Role of Preexisting Heterosubtypic Cellular Immunity Based on Variations in Disease Severity Outcomes for Influenza Live Viral Challenges in Humans
Authors: Pleguezuelos Olga , Robinson Stuart , Fernandez Ana , Stoloff Gregory A. , Caparrós-Wanderley Wilson
Published: June 2015

Influenza live viral challenges in humans are valuable models for testing the efficacy of vaccines and antiviral agents. Volunteers are treated with an investigational agent, and their clinical outcomes postchallenge are compared to those of placebo-treated volunteers. Despite using a common protocol, similar recruitment criteria, and similar doses of the same challenge strain, we noticed differences in disease severity outcomes between the placebo groups from different studies. We investigated whether these differences were significant and, if so, whether any pattern and its possible causes could be identified. We compared the clinical outcomes postchallenge in placebo groups from five clinical studies carried out between 2008 and 2013. Correlations between the prechallenge heterosubtypic cellular response (gamma interferon [IFN-γ]) and postchallenge clinical outcomes were also investigated in one study. Placebo groups from studies carried out between 2009 and 2010 attained significantly reduced (
P
< 0.05) symptom scores postchallenge compared to those of placebo groups from studies carried out in either 2008 or 2013. Also, in a 2010 study, the frequency of high-influenza heterosubtypic cellular responders prevaccination was significantly lower in the test group (FLU-v) than that in the placebo group (
P
= 0.04). Moreover, the increased preexisting heterosubtypic cellular response of the placebo group correlated with reductions in symptom score and viral shedding postchallenge (
P
≤ 0.023). Only postvaccination did the test group display an equivalent correlation. The last influenza pandemic coincided with a significant reduction in disease severity outcomes. This reduction also appears to correlate with increased preexisting influenza heterosubtypic cellular responses. (This study is registered at ClinicalTrials.gov under registration number NCT01226758.)
Evaluation of the Efficiency of the Sample Inactivation Reagent in the Abbott RealTi
m
e MTB Assay for Inactivation of Mycobacterium tuberculosis
Authors: Qi Chao , Wallis Carole , Pahalawatta Vihanga , Frank Andrea , Ramdin Neeshan , Viana Raquel , Abravaya Klara , Leckie Gregor , Tang Ning
Published: June 2015

The Abbott RealTi
m
e MTB assay is a nucleic acid amplification test (NAAT) for the detection of
Mycobacterium tuberculosis
complex DNA. The sample inactivation procedure used in the assay, consisting of one part sample treated with 3 parts inactivation reagent for 60 min, effectively reduced viscosity and inactivated
M. tuberculosis
in clinical specimens.
Field-Applicable Recombinase Polymerase Amplification Assay for Rapid Detection of Mycoplasma capricolum subsp. capripneumoniae
Authors: Liljander Anne , Yu Mingyan , O'Brien Elizabeth , Heller Martin , Nepper Julia F. , Weibel Douglas B. , Gluecks Ilona , Younan Mario , Frey Joachim , Falquet Laurent , Jores Joerg
Published: June 2015

Contagious caprine pleuropneumonia (CCPP) is a highly contagious disease caused by
Mycoplasma capricolum
subsp.
capripneumoniae
that affects goats in Africa and Asia. Current available methods for the diagnosis of
Mycoplasma
infection, including cultivation, serological assays, and PCR, are time-consuming and require fully equipped stationary laboratories, which make them incompatible with testing in the resource-poor settings that are most relevant to this disease. We report a rapid, specific, and sensitive assay employing isothermal DNA amplification using recombinase polymerase amplification (RPA) for the detection of
M. capricolum
subsp.
capripneumoniae
. We developed the assay using a specific target sequence in
M. capricolum
subsp.
capripneumoniae
, as found in the genome sequence of the field strain ILRI181 and the type strain F38 and that was further evidenced in 10 field strains from different geographical regions. Detection limits corresponding to 5 × 10
3
and 5 × 10
4
cells/ml were obtained using genomic DNA and bacterial culture from
M. capricolum
subsp.
capripneumoniae
strain ILRI181, while no amplification was obtained from 71 related
Mycoplasma
isolates or from the
Acholeplasma
or the
Pasteurella
isolates, demonstrating a high degree of specificity. The assay produces a fluorescent signal within 15 to 20 min and worked well using pleural fluid obtained directly from CCPP-positive animals without prior DNA extraction. We demonstrate that the diagnosis of CCPP can be achieved, with a short sample preparation time and a simple read-out device that can be powered by a car battery, in <45 min in a simulated field setting.
Rapid Diagnosis of Tuberculosis by Real-Time High-Resolution Imaging of Mycobacterium tuberculosis Colonies
Authors: Ghodbane Ramzi , Asmar Shady , Betzner Marlena , Linet Marie , Pierquin Joseph , Raoult Didier , Drancourt Michel
Published: June 2015

Culture remains the cornerstone of diagnosis for pulmonary tuberculosis, but the fastidiousness of
Mycobacterium tuberculosis
may delay culture-based diagnosis for weeks. We evaluated the performance of real-time high-resolution imaging for the rapid detection of
M. tuberculosis
colonies growing on a solid medium. A total of 50 clinical specimens, including 42 sputum specimens, 4 stool specimens, 2 bronchoalveolar lavage fluid specimens, and 2 bronchial aspirate fluid specimens were prospectively inoculated into (i) a commercially available Middlebrook broth and evaluated for mycobacterial growth indirectly detected by measuring oxygen consumption (standard protocol) and (ii) a home-made solid medium incubated in an incubator featuring real-time high-resolution imaging of colonies (real-time protocol). Isolates were identified by Ziehl-Neelsen staining and matrix-assisted laser desorption ionization–time of flight mass spectrometry. Use of the standard protocol yielded 14/50 (28%)
M. tuberculosis
isolates, which is not significantly different from the 13/50 (26%)
M. tuberculosis
isolates found using the real-time protocol (
P
= 1.00 by Fisher's exact test), and the contamination rate of 1/50 (2%) was not significantly different from the contamination rate of 2/50 (4%) using the real-time protocol (
P
= 1.00). The real-time imaging protocol showed a 4.4-fold reduction in time to detection, 82 ± 54 h versus 360 ± 142 h (
P
< 0.05). These preliminary data give the proof of concept that real-time high-resolution imaging of
M. tuberculosis
colonies is a new technology that shortens the time to growth detection and the laboratory diagnosis of pulmonary tuberculosis.
Cladophialophora bantiana as an Emerging Pathogen in Animals: Case Report of Equine Endometritis and Review of the Literature
Authors: Rantala Merja , Attia Stella , Koukila-Kähkölä Pirkko , de Hoog Sybren , Anttila Marjukka , Katila Terttu
Published: June 2015

We present an unusual equine endometritis case associated with
Cladophialophora bantiana
in a 15-year-old mare. The mare displayed infertility and uterine fluid accumulation with numerous black, hairy granules. Microscopically, the fluid revealed numerous septate, dark fungal hyphae and conidia in chains. Culture yielded
C. bantiana
(CBS 138271); the species was confirmed by internal transcribed spacer (ITS) sequencing. Treatment was unsuccessful.
C. bantiana
causes cerebral phaeohyphomycosis in humans, while animal cases are rare. Animal cases are reviewed.
Commentary: Whole-Genome Sequencing Data for Serotyping Escherichia coli—It's Time for a Change!
Authors: Jenkins Claire
Published: June 2015

The accessibility of whole-genome sequencing (WGS) presents the opportunity for national reference laboratories to provide a state-of-the-art public health surveillance service. The replacement of traditional serology-based typing ofEscherichia coliby WGS is supported by user-friendly, freely available data analysis Web tools. Anarticle in this issueof theJournal of Clinical Microbiology(K. G. Joensen, A. M. M. Tetzschner, A. Iguchi, F. M. Aarestrup, and F. Scheutz, J Clin Microbiol, 53:2410–2426, 2015,http://dx.doi.org/10.1128/JCM.00008-15) describes SerotypeFinder, an essential guide to serotypingE. coliin the 21st century.
Possible Human Papillomavirus 38 Contamination of Endometrial Cancer RNA Sequencing Samples in The Cancer Genome Atlas Database
Authors: Kazemian Majid , Ren Min , Lin Jian-Xin , Liao Wei , Spolski Rosanne , Leonard Warren J.
Published: June 2015

Viruses are causally associated with a number of human malignancies. In this study, we sought to identify new virus-cancer associations by searching RNA sequencing data sets from >2,000 patients, encompassing 21 cancers from The Cancer Genome Atlas (TCGA), for the presence of viral sequences. In agreement with previous studies, we found human papillomavirus 16 (HPV16) and HPV18 in oropharyngeal cancer and hepatitis B and C viruses in liver cancer. Unexpectedly, however, we found HPV38, a cutaneous form of HPV associated with skin cancer, in 32 of 168 samples from endometrial cancer. In 12 of the HPV38-positive (HPV38
+
) samples, we observed at least one paired read that mapped to both human and HPV38 genomes, indicative of viral integration into the host DNA, something not previously demonstrated for HPV38. The expression levels of HPV38 transcripts were relatively low, and all 32 HPV38
+
samples belonged to the same experimental batch of 40 samples, whereas none of the other 128 endometrial carcinoma samples were HPV38
+
, raising doubts about the significance of the HPV38 association. Moreover, the HPV38
+
samples contained the same 10 novel single nucleotide variations (SNVs), leading us to hypothesize that one patient was infected with this new isolate of HPV38, which was integrated into his/her genome and may have cross-contaminated other TCGA samples within batch 228. Based on our analysis, we propose guidelines to examine the batch effect, virus expression level, and SNVs as part of next-generation sequencing (NGS) data analysis for evaluating the significance of viral/pathogen sequences in clinical samples.

IMPORTANCE
High-throughput RNA sequencing (RNA-Seq), followed by computational analysis, has vastly accelerated the identification of viral and other pathogenic sequences in clinical samples, but cross-contamination during the processing of the samples remain a major problem that can lead to erroneous conclusions. We found HPV38 sequences specifically present in RNA-Seq samples from endometrial cancer patients from TCGA, a virus not previously associated with this type of cancer. However, multiple lines of evidence suggest possible cross-contamination in these samples, which were processed together in the same batch. Despite this potential cross-contamination, our data indicate that we have detected a new isolate of HPV38 that appears to be integrated into the human genome. We also provide general guidelines for computational detection and interpretation of pathogen-disease associations.
Cocrystal Structures of Antibody N60-i3 and Antibody JR4 in Complex with gp120 Define More Cluster A Epitopes Involved in Effective Antibody-Dependent Effector Function against HIV-1
Authors: Gohain Neelakshi , Tolbert William D. , Acharya Priyamvada , Yu Lei , Liu Tongyun , Zhao Pingsen , Orlandi Chiara , Visciano Maria L. , Kamin-Lewis Roberta , Sajadi Mohammad M. , Martin Loïc , Robinson James E. , Kwong Peter D. , DeVico Anthony L. , Ray Krishanu , Lewis George K. , Pazgier Marzena
Published: June 2015

Accumulating evidence indicates a role for Fc receptor (FcR)-mediated effector functions of antibodies, including antibody-dependent cell-mediated cytotoxicity (ADCC), in prevention of human immunodeficiency virus type 1 (HIV-1) acquisition and in postinfection control of viremia. Consequently, an understanding of the molecular basis for Env epitopes that constitute effective ADCC targets is of fundamental interest for humoral anti-HIV-1 immunity and for HIV-1 vaccine design. A substantial portion of FcR effector function of potentially protective anti-HIV-1 antibodies is directed toward nonneutralizing, transitional, CD4-inducible (CD4i) epitopes associated with the gp41-reactive region of gp120 (cluster A epitopes). Our previous studies defined the A32-like epitope within the cluster A region and mapped it to the highly conserved and mobile layers 1 and 2 of the gp120 inner domain within the C1-C2 regions of gp120. Here, we elucidate additional cluster A epitope structures, including an A32-like epitope, recognized by human monoclonal antibody (MAb) N60-i3, and a hybrid A32-C11-like epitope, recognized by rhesus macaque MAb JR4. These studies define for the first time a hybrid A32-C11-like epitope and map it to elements of both the A32-like subregion and the seven-layered β-sheet of the gp41-interactive region of gp120. These studies provide additional evidence that effective antibody-dependent effector function in the cluster A region depends on precise epitope targeting—a combination of epitope footprint and mode of antibody attachment. All together these findings help further an understanding of how cluster A epitopes are targeted by humoral responses.

IMPORTANCE
HIV/AIDS has claimed the lives of over 30 million people. Although antiretroviral drugs can control viral replication, no vaccine has yet been developed to prevent the spread of the disease. Studies of natural HIV-1 infection, simian immunodeficiency virus (SIV)- or simian-human immunodeficiency virus (SHIV)-infected nonhuman primates (NHPs), and HIV-1-infected humanized mouse models, passive transfer studies in infants born to HIV-infected mothers, and the RV144 clinical trial have linked FcR-mediated effector functions of anti-HIV-1 antibodies with postinfection control of viremia and/or blocking viral acquisition. With this report we provide additional definition of the molecular determinants for Env antigen engagement which lead to effective antibody-dependent effector function directed to the nonneutralizing CD4-dependent epitopes in the gp41-reactive region of gp120. These findings have important implications for the development of an effective HIV-1 vaccine.
Host Range Restriction of Epstein-Barr Virus and Related Lymphocryptoviruses
Authors: Mühe Janine , Wang Fred
Published: June 2015

Epstein-Barr-related herpesviruses, or lymphocryptoviruses (LCV), naturally infect humans and nonhuman primates (NHP), but their host range is not well characterized. Using LCV and B cells from multiple species of Hominidae and Cercopithecidae, we show that LCV can immortalize B cells from some nonnative species but that growth transformation is restricted to B cells from their own family of hominoids or Old World NHP, suggesting a high degree of LCV adaptation to their natural primate host.
The Human Adenovirus Type 5 E4orf4 Protein Targets Two Phosphatase Regulators of the Hippo Signaling Pathway
Authors: Mui Melissa Z. , Zhou Yiwang , Blanchette Paola , Chughtai Naila , Knight Jennifer F. , Gruosso Tina , Papadakis Andreas I. , Huang Sidong , Park Morag , Gingras Anne-Claude , Branton Philip E.
Published: June 2015

When expressed alone at high levels, the human adenovirus E4orf4 protein exhibits tumor cell-specific p53-independent toxicity. A major E4orf4 target is the B55 class of PP2A regulatory subunits, and we have shown recently that binding of E4orf4 inhibits PP2A
B55
phosphatase activity in a dose-dependent fashion by preventing access of substrates (M. Z. Mui et al., PLoS Pathog 9:e1003742, 2013,
http://dx.doi.org/10.1371/journal.ppat.1003742
). While interaction with B55 subunits is essential for toxicity, E4orf4 mutants exist that, despite binding B55 at high levels, are defective in cell killing, suggesting that other essential targets exist. In an attempt to identify additional targets, we undertook a proteomics approach to characterize E4orf4-interacting proteins. Our findings indicated that, in addition to PP2A
B55
subunits, ASPP-PP1 complex subunits were found among the major E4orf4-binding species. Both the PP2A and ASPP-PP1 phosphatases are known to positively regulate effectors of the Hippo signaling pathway, which controls the expression of cell growth/survival genes by dephosphorylating the YAP transcriptional coactivator. We find here that expression of E4orf4 results in hyperphosphorylation of YAP, suggesting that Hippo signaling is affected by E4orf4 interactions with PP2A
B55
and/or ASPP-PP1 phosphatases. Furthermore, knockdown of YAP1 expression was seen to enhance E4orf4 killing, again consistent with a link between E4orf4 toxicity and inhibition of the Hippo pathway. This effect may in fact contribute to the cancer cell specificity of E4orf4 toxicity, as many human cancer cells rely heavily on the Hippo pathway for their enhanced proliferation.

IMPORTANCE
The human adenovirus E4orf4 protein has been known for some time to induce tumor cell-specific death when expressed at high levels; thus, knowledge of its mode of action could be of importance for development of new cancer therapies. Although the B55 form of the phosphatase PP2A has long been known as an essential E4orf4 target, genetic analyses indicated that others must exist. To identify additional E4orf4 targets, we performed, for the first time, a large-scale affinity purification/mass spectrometry analysis of E4orf4 binding partners. Several additional candidates were detected, including key regulators of the Hippo signaling pathway, which enhances cell viability in many cancers, and results of preliminary studies suggested a link between inhibition of Hippo signaling and E4orf4 toxicity.
Spontaneous coronary artery dissection in men presenting with acute coronary syndrome, successfully managed by intravascular ultrasound-guided percutaneous coronary intervention
Authors: Thomas Bethan Nia , Aslam Sajid , Cullen James , Anantharaman Rajaram
Published: June 2015

Spontaneous coronary artery dissection is a rare cause of acute coronary syndrome. It is most commonly seen in young women, without atherosclerosis, in the peripartum period. Management options include conservative medical treatment, percutaneous coronary intervention or a surgical approach depending on the presentation, extent of dissection and luminal stenosis. We describe three unusual cases of spontaneous coronary artery dissection occurring in young/middle-aged men—the first in association with heavy mechanical work, the second in association with high levels of anxiety and emotional distress and the third in association with intense physical exercise. In each case we report the use of coronary angiography and intravascular ultrasound in the diagnosis of the condition, and their successful management using percutaneous coronary intervention.
Platypnoea-orthodeoxia syndrome: novel cause for a known condition
Authors: Takhar Rajendra , Biswas Rakesh , Arora Ashish , Jain Vipin
Published: June 2015

A 50-year-old man presented with dyspnoea while sitting, standing and walking but resolved completely in supine position. On cardiorespiratory examinations, fine crackles were noted over bibasal area. Chest X-ray showed bilateral reticulonodular shadows, restrictive pattern on spirometry, elevated alveolar arterial O2gradient on arterial blood gas. High-resolution CT of the thorax revealed pattern as ‘confident’ or ‘certain’ radiographic diagnosis of idiopathic pulmonary fibrosis (IPF). Bubble-contrast echocardiography in recumbent, sitting and upright positions revealed no intracardiac (right to left shunt) or intrapulmonary shunts. This case highlights the necessity of awareness of this syndrome in cases of interstitial lung diseases (ILDs) also. Although 188 cases have been described thus far of platypnoea-orthodeoxia syndrome (P-OS) of various aetiologies, to the best of our knowledge, it is the first ever case of P-OS in ILD/IPF. Both lung bases were predominantly affected in this patient, platypnoea and orthodeoxia were attributed to areas of low/zero ventilation/perfusion (V/Q) ratio (zone 1 phenomena) as no other obvious explanation was found.
Midgut malrotation with congenital peritoneal band: a rare cause of small bowel obstruction in adulthood
Authors: Low Soo Fin , Ngiu Chai Soon , Sridharan Radhika , Lee Yee Ling
Published: June 2015

Midgut malrotation commonly presents in the neonatal period, and rarely manifests its symptoms in adulthood with an estimated incidence of 0.2–0.5%. Nevertheless, the symptoms are non-specific with no strong pointers towards the clinical diagnosis. Consequently, the diagnosis is usually disclosed with imaging or surgery. We report a case of small bowel obstruction secondary to a congenital peritoneal band with underlying midgut malrotation in a 48-year-old man.
A trekker in Nepal with painful skin blisters
Authors: Pant Sushil , Keyes Linda E , Sharma Ramesh , Basnyat Buddha
Published: June 2015

The authors present a case of a 27-year-old woman trekker with painful, slightly itchy eruptions on the dorsum of both hands for 5 days. On examination, she had a papulovesicular rash with some haemorrhagic vesicles over the dorsum of her hands and thumbs.
Venous thromboembolism and subsequent risk of cancer in patients with liver disease: a population-based cohort study
Authors: Montomoli Jonathan , Erichsen Rune , Søgaard Kirstine Kobberøe , Körmendiné Farkas Dóra , Bloch Münster Anna-Marie , Sørensen Henrik Toft
Published: June 2015

Objective

Venous thromboembolism (VTE) may be a marker of occult cancer in the general population. While liver disease is known to increase the risk of VTE and cancer, it is unclear whether VTE in patients with liver disease is also a marker of occult cancer.

Design

A population-based cohort study.

Setting

Denmark.

Participants

We used population-based health registries to identify all patients with liver disease in Denmark with a first-time diagnosis of VTE (including superficial or deep venous thrombosis and pulmonary embolism) during 1980–2010. Patients with non-cirrhotic liver disease and patients with liver cirrhosis were followed as two separate cohorts from the date of their VTE.

Measures

For each cohort, we computed the absolute and relative risk (standardised incidence ratio; SIR) of cancer after VTE.

Results

During the study period, 1867 patients with non-cirrhotic liver disease and 888 with liver cirrhosis were diagnosed with incident VTE. In the first year following VTE, the absolute risk of cancer was 2.7% among patients with non-cirrhotic liver disease and 4.3% among those with liver cirrhosis. The SIR for the first 90 days of follow-up was 9.96 (95% CI 6.85 to 13.99) among patients with non-cirrhotic liver disease and 13.11 (95% CI 8.31 to 19.67) among patients with liver cirrhosis. After 1 year of follow-up, SIRs declined, but remained elevated in patients with non-cirrhotic liver disease (SIR=1.50, 95% CI 1.23 to 1.81) and patients with liver cirrhosis (SIR=1.95, 95% CI 1.45 to 2.57).

Conclusions

VTE may be a marker of occult cancer in patients with liver disease.
Perioperative dexamethasone administration in tonsillectomy patients: A three-cycle audit showing improvement using printed theatre lists
Authors: Bola Summy , Bartlett Annie , Williams Richard
Published: June 2015

Dexamethasone administration prior to tonsillectomy has been shown to reduce morbidity and is part of SIGN guideline 117. We conducted a three-cycle audit of 149 patients to ascertain how well guidelines were being met and introduce a sustainable method to improve compliance. A 3-month audit was conducted to ascertain how many tonsillectomy patients didn’t receive pre-operative dexamethasone. ENT secretaries were requested to add ‘Dex Please’ to tonsillectomy theatre lists. A 3-month re-audit was conducted; the intervention was only implemented in half of cases and so a reminding tool for the secretarial staff was administered before a third cycle. Initially, there was 73% compliance to SIGN guidelines, this improved to 87% in the second cycle. After the second intervention, all tonsillectomy theatre lists had the ‘Dex Please’ note and compliance to SIGN guidelines was 100%. There were five readmissions in the first cycle, three in the second and two in the third cycle. All readmissions were underdosed according to guidelines. Understanding there are regular staff rotations throughout many U.K. hospitals, we implemented a reliable method to increase compliance to guidelines which helped reduce post-operative readmission after tonsillectomy. This can be easily introduced to other institutions and for other perioperative requirements.
Mass gap in Yang's theory of gravity
Authors: Mielke Eckehard W.
Published: June 2015

The quantization of a curvature-squared model of gravity, in the affine form proposed by Yang, is reconsidered in the path integral formulation. Due to its inherent Weyl invariance, sharing this with internal Yang–Mills fields, it or some of its topological generalizations are still a possible route to quantum gravity. Instanton type solutions with double duality properties exhibit a "vacuum degeneracy", i.e. a bifurcation into distinct classical Einsteinian backgrounds. For linearized fields, this conclusively induces a mass gap in the graviton spectrum, a feature which is an open problem in the quantization of internal Yang–Mills fields.
MECHANICAL CHARACTERIZATION OF ANIMAL DERIVED GRAFTS FOR SURGICAL IMPLANTATION
Authors: PAVAN PIERO GIOVANNI , PACHERA PAOLA , TODROS SILVIA , TIENGO CESARE , NATALI ARTURO NICOLA
Published: June 2015

Bioprostheses obtained from animal models are often adopted in abdominal surgery for repair and reconstruction. The functionality of these prosthetic implants is related also to their mechanical characteristics that are analyzed here. This work illustrates a constitutive model to describe the short-term mechanical response of Permacol[Formula: see text] bioprostheses. Experimental tests were developed on tissue samples to highlight mechanical non-linear characteristics and viscoelastic phenomena. Uni-axial tensile tests were developed to evaluate the strength and strain stiffening. Incremental uni-axial stress relaxation tests were carried out at nominal strain ranging from 10% to 20% and to monitor the stress relaxation process up to 400[Formula: see text]s. The constitutive model effectively describes the mechanical behavior found in experimental testing. The mechanical response appears to be independent on the loading direction, showing that the tissue can be considered as isotropic. The viscoelastic response of the tissue shows a strong decay of the stress in the first seconds of the relaxation process. The investigation performed is aimed at a general characterization of the biomechanical response and addresses the development of numerical models to evaluate the biomechanical performance of the graft with surrounding host tissues.
Enhanced in vitro photocytotoxicity of water-soluble dendritic pheophorbide-a
Authors: Lee Eun Ji , Kong Hyoung Jun , Kim Young-Jin , Park Jong S. , Choi Myung-Seok
Published: June 2015

Photosensitizers can produce highly reactive singlet oxygen with exposure to visible light and are used in photodynamic therapy to treat a variety of tumors. We report on the synthesis of triethylene glycol dendron-conjugated pheophorbide-a5, a novel photosensitizer. The characteristic absorption bands (Soret and Q-bands, λmax = 405 and 670 nm, respectively) of 5 were appeared clearly in aqueous solution, due to the improved water-solubility of the dendron moiety. The value of singlet oxygen quantum yield of 5 (ΦΔ = 0.22) was higher than free pheophorbide-a (ΦΔ = 0.17) as reference in aqueous solution. Compound 5 also exhibited an enhanced in vitro phototoxicity than pheophorbide-a (PhA) in the concentration range of 1.0–5.0 μg/mL: cell viability in cells treated with 5 was reduced by ~20%, indicating a cell death rate of ~80%, while PhA treatment resulted in a cell death rate of only about 10%. These results indicate that 5 will likely be more efficient in PDT applications. Compared with free PhA, compound 5 showed highly enhanced singlet oxygen generation ability and in vitro photocytotoxicity.
Two Dimensional Finite Element Model to Study Calcium Distribution in Oocytes
Authors: Naik Parvaiz Ahmad , Pardasani Kamal Raj
Published: June 2015

Cytosolic free calcium concentration is a key regulatory factor and perhaps the most widely used means of controlling cellular function. Calcium can enter cells through different pathways which are activated by specific stimuli including membrane depolarization, chemical signals and calcium depletion of intracellular stores. One of the important components of oocyte maturation is differentiation of the Ca 2+ signaling machinery which is essential for egg activation after fertilization. Eggs acquire the ability to produce the fertilization-specific calcium signal during oocyte maturation. The calcium concentration patterns required during different stages of oocyte maturation are still not completely known. Also the mechanisms involved in calcium dynamics in oocyte cell are still not well understood. In view of above a two dimensional FEM model has been proposed to study calcium distribution in an oocyte cell. The parameters such as buffers, ryanodine receptor, SERCA pump and voltage gated calcium channel are incorporated in the model. Based on the biophysical conditions the initial and boundary conditions have been framed. The model is transformed into variational form and Ritz finite element method has been employed to obtain the solution. A program has been developed in MATLAB 7.10 for the entire problem and executed to obtain numerical results. The numerical results have been used to study the effect of buffers, RyR, SERCA pump and VGCC on calcium distribution in an oocyte cell.
Sedimentology of the Lower Cretaceous reservoirs of the Sea Lion Field, North Falkland Basin
Authors: Williams L. S.
Published: June 2015

The Sea Lion Field in the North Falkland Basin was discovered in 2010 by Well 14/10-2, which tested oil from Lower Cretaceous sands of the Sea Lion fan complex. Appraisal of the field involved the drilling of a further eight wells from which an extensive wireline-log data set and 455 m of core were acquired. This unique data set has allowed detailed study of the reservoir sedimentology and has significantly benefited reservoir characterization. The reservoirs are interpreted to be deposited in a deep-water lacustrine basin as base-of-slope to basin-floor fans fed by canyons or channel-feeder systems from the east. Deposition is considered to have been affected both by turbidity currents and by liquefied sediment gravity flows, such that reservoir facies are dominated by those associated with high- and low-density turbidites, mass-flow deposits, and, to a lesser extent, hybrid-event beds. In the absence of significant chronostratigraphic control, the description of the first-order reservoir architecture is primarily driven by seismic interpretation, whilst the core affords significant control of the internal architecture of individual fans. Several lines of evidence point towards the Sea Lion sands being derived from a coexisting, shallow-water system on the eastern margin of the basin. Palaeogeographical reconstruction links this shoreface system to a large, contemporaneous, southerly-prograding delta via wave reworking and longshore drift of delta-front sands. Evolution of this delta has played a significant role in the timing, positioning and emplacement of fans along the eastern margin of the North Falkland Basin. The overall impact of the core data set has been to improve confidence in the reservoir characterization and spatial distribution of facies within the reservoir model, and to narrow significantly the range of uncertainty, which has direct implications for field development planning.
Petroleum geochemistry of the Sea Lion Field, North Falkland Basin
Authors: Farrimond P. , Green A. , Williams L.
Published: June 2015

The Sea Lion Field, lying approximately 220 km north of the Falkland Islands in the northern rift of the North Falkland Basin, contains waxy oil in Lower Cretaceous reservoir sands. The oil is likely to be sourced from Lower Cretaceous lacustrine source rocks lying beneath the reservoir sands. A significant complication in interpreting the geochemical data for the Sea Lion oils comes from their overprinting by leaching of bitumen components (especially biomarkers) from immature organic-rich claystones that are interbedded with the reservoir. Accordingly, best estimates of maturity are obtained from gasoline-range and aromatic hydrocarbons. A higher maturity charge is seen in oils from some of the more western wells, consistent with their higher gas–oil ratios. Basin modelling has shown that the source rocks are more mature to the south of the Sea Lion Field, and the observed differences in oil maturity can be related to sourcing from different parts of this kitchen area and/or different stratigraphic intervals of the source-rock package. Gasoline-range hydrocarbons provide evidence for phase fractionation, with some oils having lost a more volatile fraction whilst others have received additional gas charge. A gas leg in the Beverley and Casper South reservoirs in Well 14/15-4Z appears to have been the original fluid charge, and has not displaced oil, although gas compositions suggest that gas was co-generated with oil, and subsequently separated into two phases, at least in some parts of the field.
Approaches to Temporal Expression Recognition in Hindi
Authors: Ramrakhiyani Nitin , Majumder Prasenjit
Published: June 2015

Temporal annotation of plain text is considered a useful component of modern information retrieval tasks. In this work, different approaches for identification and classification of temporal expressions in Hindi are developed and analyzed. First, a rule-based approach is developed, which takes plain text as input and based on a set of hand-crafted rules, produces a tagged output with identified temporal expressions. This approach performs with a strict F1-measure of 0.83. In another approach, a CRF-based classifier is trained with human tagged data and is then tested on a test dataset. The trained classifier identifies the time expressions from plain text and further classifies them to various classes. This approach performs with a strict F1-measure of 0.78. Next, the CRF is replaced by an SVM-based classifier and the same experiment is performed with the same features. This approach is shown to be comparable to the CRF and performs with a strict F1-measure of 0.77. Using the rule base information as an additional feature enhances the performances to 0.86 and 0.84 for the CRF and SVM respectively. With three different comparable systems performing the extraction task, merging them to take advantage of their positives is the next step. As the first merge experiment, rule-based tagged data is fed to the CRF and SVM classifiers as additional training data. Evaluation results report an increase in F1-measure of the CRF from 0.78 to 0.8. Second, a voting-based approach is implemented, which chooses the best class for each token from the outputs of the three approaches. This approach results in the best performance for this task with a strict F1-measure of 0.88. In this process a reusable gold standard dataset for temporal tagging in Hindi is also developed. Named the ILTIMEX2012 corpus, it consists of 300 manually tagged Hindi news documents.
Towards Machine Translation in Semantic Vector Space
Authors: Zhang Jiajun , Liu Shujie , Li Mu , Zhou Ming , Zong Chengqing
Published: June 2015

Measuring the quality of the translation rules and their composition is an essential issue in the conventional statistical machine translation (SMT) framework. To express the translation quality, the previous lexical and phrasal probabilities are calculated only according to the co-occurrence statistics in the bilingual corpus and may be not reliable due to the data sparseness problem. To address this issue, we propose measuring the quality of the translation rules and their composition in the semantic vector embedding space (VES). We present a recursive neural network (RNN)-based translation framework, which includes two submodels. One is the bilingually-constrained recursive auto-encoder, which is proposed to convert the lexical translation rules into compact real-valued vectors in the semantic VES. The other is a type-dependent recursive neural network, which is proposed to perform the decoding process by minimizing the semantic gap (meaning distance) between the source language string and its translation candidates at each state in a bottom-up structure. The RNN-based translation model is trained using a max-margin objective function that maximizes the margin between the reference translation and the n-best translations in forced decoding. In the experiments, we first show that the proposed vector representations for the translation rules are very reliable for application in translation modeling. We further show that the proposed type-dependent, RNN-based model can significantly improve the translation quality in the large-scale, end-to-end Chinese-to-English translation evaluation.
Conditional Random Fields for Korean Morpheme Segmentation and POS Tagging
Authors: Na Seung-Hoon
Published: June 2015

There has been recent interest in statistical approaches to Korean morphological analysis. However, previous studies have been based mostly on generative models, including a hidden Markov model (HMM), without utilizing discriminative models such as a conditional random field (CRF). We present a two-stage discriminative approach based on CRFs for Korean morphological analysis. Similar to methods used for Chinese, we perform two disambiguation procedures based on CRFs: (1) morpheme segmentation and (2) POS tagging. In morpheme segmentation, an input sentence is segmented into sequences of morphemes, where a morpheme unit is either atomic or compound. In the POS tagging procedure, each morpheme (atomic or compound) is assigned a POS tag. Once POS tagging is complete, we carry out a post-processing of the compound morphemes, where each compound morpheme is further decomposed into atomic morphemes, which is based on pre-analyzed patterns and generalized HMMs obtained from the given tagged corpus. Experimental results show the promise of our proposed method.
Src mediates endocytosis of TWIK-related acid-sensitive K+ 1 channels in PC12 cells in response to nerve growth factor
Authors: Matsuoka Hidetada , Inoue Masumi
Published: June 2015

TWIK-related acid-sensitive K+ (TASK) channels produce background K+ currents. We elucidated that TASK1 channels in rat adrenal medullary cells and PC12 cells are internalized in a clathrin-dependent manner in response to nerve growth factor (NGF). Here, the molecular mechanism for this internalization in PC12 cells was explored. The combination of enzyme inhibitors with tropomyosin receptor kinase A mutants revealed that the internalization was mediated by both phospholipase C and phosphatidylinositol 3-kinase pathways that converge on protein kinase C with the consequent activation of Src, a nonreceptor tyrosine kinase. The NGF-induced endocytosis of TASK1 channels did not occur in the presence of the Src inhibitor or with the expression of a kinase-dead Src mutant. Additionally, NGF induced a transient colocalization of Src with the TASK1 channel, but not the TASK1 mutant, in which tyrosine at 370 was replaced with phenylalanine. This TASK1 mutant showed no increase in tyrosine phosphorylation and markedly diminished internalization in response to NGF. We concluded that NGF induces endocytosis of TASK1 channels via tyrosine phosphorylation in its carboxyl terminus.
Fructose-induced increases in expression of intestinal fructolytic and gluconeogenic genes are regulated by GLUT5 and KHK
Authors: Patel Chirag , Douard Veronique , Yu Shiyan , Tharabenjasin Phuntila , Gao Nan , Ferraris Ronaldo P.
Published: June 2015

Marked increases in fructose consumption have been tightly linked to metabolic diseases. One-third of ingested fructose is metabolized in the small intestine, but the underlying mechanisms regulating expression of fructose-metabolizing enzymes are not known. We used genetic mouse models to test the hypothesis that fructose absorption via glucose transporter protein, member 5 (GLUT5), metabolism via ketohexokinase (KHK), as well as GLUT5 trafficking to the apical membrane via the Ras-related protein in brain 11a (Rab11a)-dependent endosomes are required for the regulation of intestinal fructolytic and gluconeogenic enzymes. Fructose feeding increased the intestinal mRNA and protein expression of these enzymes in the small intestine of adult wild-type (WT) mice compared with those gavage fed with lysine or glucose. Fructose did not increase expression of these enzymes in the GLUT5 knockout (KO) mice. Blocking intracellular fructose metabolism by KHK ablation also prevented fructose-induced upregulation. Glycolytic hexokinase I expression was similar between WT and GLUT5- or KHK-KO mice and did not vary with feeding solution. Gavage feeding with the fructose-specific metabolite glyceraldehyde did not increase enzyme expression, suggesting that signaling occurs before the hydrolysis of fructose to three-carbon compounds. Impeding GLUT5 trafficking to the apical membrane using intestinal epithelial cell-specific Rab11a-KO mice impaired fructose-induced upregulation. KHK expression was uniformly distributed along the villus but was localized mainly in the basal region of the cytosol of enterocytes. The feedforward upregulation of fructolytic and gluconeogenic enzymes specifically requires GLUT5 and KHK and may proactively enhance the intestine's ability to process anticipated increases in dietary fructose concentrations.
The Physiological, Biochemical, and Molecular Roles of Zinc Transporters in Zinc Homeostasis and Metabolism
Authors: Kambe Taiho , Tsuji Tokuji , Hashimoto Ayako , Itsumura Naoya
Published: June 2015

Zinc is involved in a variety of biological processes, as a structural, catalytic, and intracellular and intercellular signaling component. Thus zinc homeostasis is tightly controlled at the whole body, tissue, cellular, and subcellular levels by a number of proteins, with zinc transporters being particularly important. In metazoan, two zinc transporter families, Zn transporters (ZnT) and Zrt-, Irt-related proteins (ZIP) function in zinc mobilization of influx, efflux, and compartmentalization/sequestration across biological membranes. During the last two decades, significant progress has been made in understanding the molecular properties, expression, regulation, and cellular and physiological roles of ZnT and ZIP transporters, which underpin the multifarious functions of zinc. Moreover, growing evidence indicates that malfunctioning zinc homeostasis due to zinc transporter dysfunction results in the onset and progression of a variety of diseases. This review summarizes current progress in our understanding of each ZnT and ZIP transporter from the perspective of zinc physiology and pathogenesis, discussing challenging issues in their structure and zinc transport mechanisms.
A Fault Diagnosis Scheme for Aircraft Multibranches Wiring Network Based on Matching Algorithm
Authors: Liwen Wang , Lu Zhang , Meng Xu , Xudong Shi
Published: June 2015

This paper mainly describes a fault diagnosis scheme for aircraft multibranches wiring networks. The background theory is based on the matching algorithm with theoretical reflection waveform and realistic reflection waveform. Firstly, a numerical model with a comprehensive database was built to create the theoretical waveform of the measured wiring network. On the other hand, the realistic reflection waveform of the measured wiring network can be collected by reflectometry detection system. Then, the waveform matching algorithm and fault diagnosis algorithm were applied to detect the fault type and fault location in the measured wiring network. With all the steps above, the fault diagnosis scheme was designed and realized. Finally, a multibranches wiring network, which includes two branches, and one of its branches contains two subbranches with different types of faults, was built to verify the fault diagnosis scheme and the results show that the scheme is an effective way to diagnose faults in multibranches wiring network.
Significance of Theoretical Decomposition Enthalpies for Predicting Thermal Hazards
Authors: Mathieu Didier
Published: June 2015

Much effort is currently put into the development of models for predicting decomposition enthalpies measured using differential scanning calorimetry (DSC). As an alternative to the purely empirical schemes reported so far, this work relies on theoretical values obtained on the basis of simple assumptions. For nitroaromatic compounds (NACs) studied in sealed sample cells, our approach proves clearly superior to previous ones. In contrast, it correlates poorly with data measured in pin-hole sample cells. Progress might be obtained through a combination of the present approach with the usual Quantitative Structure-Property Relationships (QSPR) methodologies. This work emphasizes the significance of the theoretical decomposition enthalpy as a fundamental descriptor for the prediction of DSC values. In fact, the theoretical value provides a valuable criterion to characterize thermal hazards, as a complement to experimental decomposition temperatures.
Accelerated Compressed Sensing Based CT Image Reconstruction
Authors: Hashemi SayedMasoud , Beheshti Soosan , Gill Patrick R. , Paul Narinder S. , Cobbold Richard S. C.
Published: June 2015

In X-ray computed tomography (CT) an important objective is to reduce the radiation dose without significantly degrading the image quality. Compressed sensing (CS) enables the radiation dose to be reduced by producing diagnostic images from a limited number of projections. However, conventional CS-based algorithms are computationally intensive and time-consuming. We propose a new algorithm that accelerates the CS-based reconstruction by using a fast pseudopolar Fourier based Radon transform and rebinning the diverging fan beams to parallel beams. The reconstruction process is analyzed using a maximum-a-posterior approach, which is transformed into a weighted CS problem. The weights involved in the proposed model are calculated based on the statistical characteristics of the reconstruction process, which is formulated in terms of the measurement noise and rebinning interpolation error. Therefore, the proposed method not only accelerates the reconstruction, but also removes the rebinning and interpolation errors. Simulation results are shown for phantoms and a patient. For example, a 512 × 512 Shepp-Logan phantom when reconstructed from 128 rebinned projections using a conventional CS method had 10% error, whereas with the proposed method the reconstruction error was less than 1%. Moreover, computation times of less than 30 sec were obtained using a standard desktop computer without numerical optimization.
Long Time Decay Rate to a Bipolar Quantum Drift-Diffusion Model
Authors: Zhu Yingjie , Liang Bo , Peng Xiting
Published: June 2015

This paper is devoted to studying the long time behavior of solutions to a bipolar quantum hydrodynamic in one-dimensional space for general pressure functions. The model is usually applied to simulate some quantum effects in semiconductor devices. The decay rate for time variable is obtained by the entropy functional method and semidiscrete technique.