bluuebunny/crossref_metadata_2025 huggingface dataset:
The Effect of Labeled/Unlabeled Prior Information for Masseter Segmentation
Authors: Rezaei Tabar Yousef , Ulusoy Ilkay
Published: June 2013

Several segmentation methods are implemented and applied to segment the facial masseter tissue from magnetic resonance images. The common idea for all methods is to take advantage of prior information from different MR images belonging to different individuals in segmentation of a test MR image. Standard atlas-based segmentation methods and probabilistic segmentation methods based on Markov random field use labeled prior information. In this study, a new approach is also proposed where unlabeled prior information from a set of MR images is used to segment masseter tissue in a probabilistic framework. The proposed method uses only a seed point that indicates the target tissue and performs automatic segmentation for the selected tissue without using labeled training set. The segmentation results of all methods are validated and compared where the influences of labeled or unlabeled prior information and initialization are discussed particularly. It is shown that if appropriate modeling is done, there is no need for labeled prior information. The best accuracy is obtained by the proposed approach where unlabeled prior information is used.
Diffuse Pulmonary Meningotheliomatosis Diagnosed by Transbronchial Lung Biopsy
Authors: Bernabeu Mora Roberto , Sánchez Nieto Juan Miguel , Hu Chunshao , Alcaraz Mateos Eduardo , Giménez Bascuñana Alberto , Rodríguez Rodríguez Manuel
Published: June 2013

Minute pulmonary meningothelial-like nodules (MPMNs) are usually unique lesions in the lung parenchyma. Diffuse pulmonary meningotheliomatosis, which is presented as multiple MPMNs, has been less frequently described. MPMNs are mainly asymptomatic and are diagnosed after lung surgery or during autopsy. We report on a patient with multiple and bilateral pulmonary nodules, some of which were cavitated, diagnosed with diffuse pulmonary meningotheliomatosis by transbronchial lung biopsy. Diffuse pulmonary meningotheliomatosis should be included in the differential diagnosis of bilateral lung nodules.
Seizure Risk Factors in Shunted Hydrocephalic Patients
Authors: Majed Masoud , Andrabi Yasir , Nejat Farideh , El Khashab Mostafa
Published: June 2013

Objective: There are controversies about seizure risk factors in shunted hydrocephalic patients which can be due to having merged two different types of seizure (preshunt and postshunt seizures) in previous studies. Also, it is not known whether a considerable change in ventricular size after shunting can be a risk factor of postshunt seizures. Methods: 150 hydrocephalic patients who underwent shunting from 2006 to 2011 in the Children's Hospital Medical Center in Tehran, Iran, were visited at least 1 year after shunting to assess risk factors of preshunt and postshunt seizures. Ventricular size was assessed by using a radiologic index of bifrontal ratio (BFR). Results: Preshunt seizures were higher in patients with postinfectious hydrocephalus and intraventricular hemorrhage. Early shunting, history of shunt complications and shunt infection, and a high number of shunt revisions were significant risk factors for developing postshunt seizures. The change in BFR after shunting was not a significant risk factor of postshunt seizures. Conclusion: The difference between risk factors of preshunt seizures and postshunt seizures shows that they are two different types of seizures with different natures. Preshunt seizures are hard to prevent as they are related to the underlying disease of the brain or the etiology of hydrocephalus. However, postshunt seizures are related to the shunt and might be decreased by preventing shunt complications.
Thymosin α1 Activates Complement Receptor-Mediated Phagocytosis in Human Monocyte-Derived Macrophages
Authors: Serafino Annalucia , Pica Francesca , Andreola Federica , Gaziano Roberta , Moroni Noemi , Moroni Gabriella , Zonfrillo Manuela , Pierimarchi Pasquale , Sinibaldi-Vallebona Paola , Garaci Enrico
Published: June 2013

Thymosin α1 (Tα1) is a naturally occurring thymic peptide used worldwide in clinical trials for the treatment of infectious diseases and cancer. The immunomodulatory activity of Tα1 on innate immunity effector cells has been extensively described, but its mechanism of action is not completely understood. We report that Tα1-exposed human monocyte-derived macrophages (MDMs) assume the typical activated morphology also exhibited by lipopolysaccharide-activated MDMs, but show a comparatively higher ability of internalizing fluorescent beads and zymosan particles. Tα1 exposure also promptly and dramatically stimulates MDM phagocytosis and killing of Aspergillus niger conidia starting as soon as 30 min after challenge. The effect is dose dependent and early coupled to low transcription of the proinflammatory cytokines tumor necrosis factor α and interleukin-6 and unmodified Toll-like receptor expression. The Tα1-stimulated phagocytosis is strictly dependent on the integrity of the microtubule network and protein kinase C activity and occurs by a variation in the classic zipper model, with recruitment of vinculin and actin at the phagosome exhibiting a punctate distribution. These findings indicate that, in human mature MDMs, Tα1 implements pathogen internalization and killing via the stimulation of the complement receptor-mediated phagocytosis. Our observations document that Tα1 is an early and potent activator of innate immunity and reinforce the concept of its pleiotropy.
GDF15 Is Related to Anemia and Hepcidin in Kidney Allograft Recipients
Authors: Malyszko Jolanta , Koc-Zorawska Ewa , Malyszko Jacek S. , Glowinska Irena , Mysliwiec Michal , Macdougall Iain C.
Published: June 2013

Anemia is more prevalent in renal transplant recipients than in GFR-matched chronic kidney disease patients. Hepcidin is a small defensin-like peptide whose production by hepatocytes is modulated in response to anemia, hypoxia or inflammation. Growth differentiation factor 15 (GDF15) was recently identified as a hepcidin-suppression factor that is expressed at high levels in patients with ineffective erythropoiesis. The aim of the study was to assess GDF15 levels with relation to iron parameters in 62 stable kidney allograft recipients maintained on triple immunosuppressive therapy. Methods: Complete blood count, urea, creatinine, and iron status were assessed by standard methods. We measured GDF15, hepcidin, hemojuvelin, IL-6 and NGAL with commercially available assays. Results: Mean levels of GDF15, NGAL, hepcidin and hemojuvelin were significantly higher in kidney allograft recipients when compared to the control group (p < 0.001 for all). GDF15 was significantly higher in patients with anemia according to the WHO definition when compared to their nonanemic counterparts (p < 0.05). GDF15 levels were not dependent on the type of immunosuppressive therapy. In univariate analysis GDF15 was related to kidney function (creatinine r = 0.39, p < 0.01, eGFR by MDRD r = -0.37, p < 0.01), urea (r = 0.39, p < 0.01), uric acid (r = 0.42, p < 0.01), hepcidin (r = -0.32, p < 0.01), IL-6 (r = 0.28, p < 0.05), hemoglobin (r = -0.32, p < 0.05), and NGAL (r = -0.35, p < 0.01). GDF15 was not related to serum iron, or ferritin. In multivariate analysis, hepcidin was found to be a predictor of GDF15. In conclusion, our preliminary data may suggest possible mutual relations between GDF15 and hepcidin in patients with kidney disease and that GDF15 might be involved in the pathogenesis of anemia in kidney allograft recipients. However, the role of inflammation should be also elucidated.
Hemodialysis-Induced Acute Myocardial Dyssynchronous Impairment in Children
Authors: Hothi Daljit K. , Rees Lesley , McIntyre Christopher W. , Marek Jan
Published: June 2013

In adults, recurrent hemodialysis (HD)-induced cardiac injury results in ischemic myocardial dysfunction. Uremic children, like adults, share the full complement of uremia-related cardiovascular abnormalities but without significant atheromatous coronary artery disease. The aim of this study was, to assess the impact of HD on left ventricular (LV) myocardial function in children. Method: We assessed all single-center chronic HD patients (n = 15, range 1-17 years) excluding those with overt cardiac disease. Regional LV function and mechanical synchronicity was measured echographically by two-dimensional segmental longitudinal, circumferential and radial myocardial strain. All patients were assessed pre-dialysis and at the end of dialysis. In addition, we scanned age-matched controls at rest. Results: The peak longitudinal strain was lower in uremic patients compared with controls with a significant fall during HD (mean peak strain -19.9 controls, -17.9 pre-HD, -15.3 end of HD, p < 0.05). Radial strain was lower in uremic patients and increased during HD. Circumferential strain was preserved in uremic patients and fell during HD. Intrasegmental deformation synchronicity was progressively worse pre-dialysis and end of dialysis compared with controls. Intradialytic peak longitudinal strain reduction was significantly associated with systolic blood pressure and ultrafiltrate volume (p < 0.05). Conclusion: Uremic children have impaired regional LV function, with a predisposition to longitudinal axis dysfunction and LV mechanical dyssynchrony, both of which are established markers of ischemic injury. This is further evidence for a characteristic cardiovascular phenotype in uremic patients that predisposes them to subclinical demand ischemia during dialysis.
Metastatic Castration-Resistant Prostate Cancer: Two Case Reports of Dramatic Response with Abiraterone Acetate in Patients Heavily Pretreated with Chemotherapy
Authors: Dupuy Laura , Long Jérôme , Ranchoup Yves
Published: June 2013

Metastatic castration-resistant prostate cancer (mCRPC) with visceral involvement requires new, effective and safe treatments after chemotherapy failure. The CYP17A1 inhibitor abiraterone acetate has been approved as a treatment for mCRPC, both after docetaxel chemotherapy and more recently for patients who are not responding to chemotherapy. In published studies, most patients previously treated with docetaxel had received a limited number of lines of chemotherapy and a small proportion of these patients presented with visceral metastases. We report two mCRPC patients with extensive visceral disease, who were heavily pretreated with chemotherapy. They experienced major responses to treatment with abiraterone acetate. For both patients, responses to abiraterone were noticeable within 1 month, encompassing a marked regression of visceral metastases and a decrease in prostate-specific antigen. The clinical benefit of abiraterone was maintained for at least 6 months and the treatment was well tolerated.
Influence of the Atmospheric Surface Layer on a Turbulent Flow Downstream of a Ship Superstructure
Authors: Luznik Luksa , Brownell Cody J. , Snyder Murray R. , Kang Hyung Suk
Published: June 2013

This paper describes a set of turbulence measurements at sea in the area of high flow distortion in the near-wake and recirculation zone behind a ship's superstructure that is similar in geometry to a helicopter hangar/flight deck arrangement found on many modern U.S. Navy ships. The instrumented ship is a 32-m-long training vessel operated by the United States Naval Academy that has been modified by adding a representative flight deck and hangar structure. The flight deck is instrumented with up to seven sonic anemometers/thermometers that are used to obtain simultaneous velocity measurements at various spatial locations on the flight deck, and one sonic anemometer at bow mast is used to characterize inflow atmospheric boundary conditions. Data characterizing wind over the deck at an incoming angle of 0° (head winds) and wind speeds from 2 to 10 m s−1 obtained in the Chesapeake Bay are presented and discussed. Turbulent statistics of inflow conditions are analyzed using the Kaimal universal turbulence spectral model for the atmospheric surface layer and show that for the present dataset this approach eliminates the need to account for platform motion in computing variances and covariances. Conditional sampling of mean flow and turbulence statistics at the flight deck indicate no statistically significant variations between unstable, stable, and neutral atmospheric inflow conditions, and the results agree with the published data for flows over the backward-facing step geometries.
Thymoquinone-induced reactive oxygen species causes apoptosis of chondrocytes via PI3K/Akt and p38kinase pathway
Authors: Yu Seon-Mi , Kim Song-Ja
Published: June 2013

Thymoquinone (TQ), a bioactive ingredient of the volatile oil of black seed ( Nigella sativa), has been shown to possess anti-neoplastic and anti-inflammatory effects on a variety of tumours. However, the precise mechanism of action is not clear in normal cells such as primary chondrocytes. So, we have investigated the effects of TQ on the apoptosis of chondrocytes with a focus on reactive oxygen species (ROS) production. In in vitro experiments, chondrocytes were cultured with increasing concentrations of TQ for 24 h or with 20 µmol/L TQ for the indicated time periods, and various experiments were performed to detect the apoptotic effects caused by TQ. The results showed that TQ significantly increases apoptosis. Apoptosis was dose- and time-dependently expressed, and the generation of ROS also dramatically increased in a dose-dependent manner. Pretreatment of N-acetyl-l-cysteine (NAC), an inhibitor of ROS, inhibited both TQ-induced apoptosis and ROS generation. Also, TQ up-regulated phosphorylation of phosphatidylinositol 3-kinase/Akt (PI3K/Akt) and mitogen-activated protein kinases ([MAPKs] p38kinase, ERK-1/-2, and JNKinase), and these effects were prevented by pretreatment of NAC. However, pretreatment with inhibitors of PI3K/Akt and MAPKs did not inhibit TQ-caused ROS generation. Among the inhibitors of PI3K/Akt, p38kinase, ERK-1/-2, and JNKinase, pretreatment with LY294002 and SB203580 abolished TQ-induced apoptosis, but PD98059 and SP600125 did not have any effect on TQ-caused apoptosis. These findings suggest that TQ-induced ROS generation regulates apoptosis by modulating PI3K/Akt and p38kinase pathways.
Identification and real-time expression analysis of selected Toxoplasma gondii in-vivoinduced antigens recognized by IgG and IgM in sera of acute toxoplasmosis patients
Authors: Amerizadeh Atefeh , Khoo Boon Yin , Teh Ai Ying , Golkar Majid , Abdul Karim Izzati Zahidah , Osman Sabariah , Yunus Muhammad Hafiznur , Noordin Rahmah
Published: June 2013

Background

Toxoplasma gondii is an obligate intracellular zoonotic parasite of the phylum Apicomplexa which infects a wide range of warm-blooded animals, including humans. In this study in-vivo induced antigens of this parasite was investigated using in-vivo induced antigen technology (IVIAT) and pooled sera from patients with serological evidence of acute infection.

Methods

The pooled sera was first pre-absorbed against three different preparations of antigens from in-vitro-grown cells of each T. gondii and E. coli XL1-Blue MRF’, subsequently it was used to screen T. gondii cDNA phage expression library. Positive clones from each group were subjected to quantitative real-time PCR expression analysis on mRNA of in-vivo and in-vitro grown parasites.

Results

A total of 29 reactive clones from each IgM and IgG immunoscreenings were found to have high homology to T. gondii genes. Quantitative real-time PCR expression analysis showed that 20 IgM-detected genes and 11 IgG-detected genes were up-regulated in-vivo relative to their expression levels in-vitro. These included genes encoding micronemes, sterol-regulatory element binding protein site, SRS34A, MIC2-associated protein M2AP, nucleoredoxin, protein phosphatase 2C and several hypothetical proteins. A hypothetical protein (GenBank accession no. 7899266) detected by IgG had the highest in-vivo over in-vitro fold change of 499.86; while another up-regulated hypothetical protein (GenBank accession no. 7898829) recognized by IgM showed high sensitivity (90%) and moderate specificity (70%) in detecting T. gondii antibodies when tested with 20 individual serum samples.

Conclusion

The highly up-regulated genes and the corresponding proteins, in particular the hypothetical proteins, may be useful in further studies on understanding the disease pathogenesis and as potential vaccine candidates.
The diagnostic value of ultrasonography in carpal tunnel syndrome: a comparison between diabetic and non-diabetic patients
Authors: Tsai Nai-Wen , Lee Lian-Hui , Huang Chi-Ren , Chang Wen-Neng , Wang Hung-Chen , Lin Yu-Jun , Lin Wei-Che , Lin Tsu-Kung , Cheng Ben-Chung , Su Yu-Jih , Kung Chia-Te , Chen Shu-Fang , Lu Cheng-Hsien
Published: June 2013

Background

To compare the value of ultrasonography for diagnosing carpal tunnel syndrome (CTS) in patients with and without diabetes mellitus (DM).

Methods

Eighty non-DM and 40 DM patients with electromyography-confirmed CTS were assessed and underwent high-resolution ultrasonography of the wrists. Cross-sectional area (CSA) and flattening ratio (FR) of the median nerve were measured at the carpal tunnel outlet (D) and wrist crease (W).

Results

The 80 non-DM and 40 DM patients had 81 and 59 CTS-hands, respectively. The CSA_D and CSA_W were significantly larger in the CTS-hands and DM-CTS-hands compared to the normal control (p < 0.001). However, there is no difference of CSA_D and CSA_W between DM and non-DM CTS patients. Receiver operating characteristics [ROC] curve analysis revealed that CSA_W ≥13 mm2was the most powerful predictor of CTS in DM (area under curve [AUC] = 0.72; sensitivity 72.9%, specificity 61.9%) and non-DM (AUC = 0.72; sensitivity 78.5%, specificity 53.2%) patients. The CSA positively correlated with the distal motor latency of the median compound motor action potential (CMAP), distal sensory latency of the median sensory nerve action potential (SNAP), and latency of the median F wave, but negatively correlated with the amplitude of the median CMAP, amplitude of the median SNAP, and sensory NCV of the median nerve. Stepwise logistic regression revealed that CSA_W (OR 1.21, 95% CI 1.07-1.38;p = 0.003) was independently associated with CTS in DM patients and any 1 mm2increase in CSA_W increased the rate of CTS by 28%.

Conclusions

The CSA of the median nerve at the outlet and wrist crease are significantly larger in CTS hands in both DM and non-DM patients compared to normal hands. The CSA of the median nerve by ultrasonography may be a diagnostic tool for evaluating CTS in DM and non-DM patients.
Improved accessibility of emergency obstetrics and newborn care(EmONC) services for maternal and newborn health: a community based project
Authors: Turab Ali , Ariff Shabina , Habib Muhammad A , Ahmed Imran , Hussain Masawar , Rashid Akhtar , Memon Zahid , Khan Mohammad I , Soofi Sajid , Bhutta Zulfiqar A
Published: June 2013

Background

Every year an estimated three million neonates die globally and two hundred thousand of these deaths occur in Pakistan. Majority of these neonates die in rural areas of underdeveloped countries from preventable causes (infections, complications related to low birth weight and prematurity). Similarly about three hundred thousand mother died in 2010 and Pakistan is among ten countries where sixty percent burden of these deaths is concentrated. Maternal and neonatal mortality remain to be unacceptably high in Pakistan especially in rural areas where more than half of births occur.

Method/Design

This community based cluster randomized controlled trial will evaluate the impact of an Emergency Obstetric and Newborn Care (EmONC) package in the intervention arm compared to standard of care in control arm. Perinatal and neonatal mortality are primary outcome measure for this trial. The trial will be implemented in 20 clusters (Union councils) of District Rahimyar Khan, Pakistan. The EmONC package consists of provision of maternal and neonatal health pack (clean delivery kit, emollient, chlorhexidine) for safe motherhood and newborn wellbeing and training of community level and facility based health care providers with emphasis on referral of complicated cases to nearest public health facilities and community mobilization.

Discussion

Even though there is substantial evidence in support of effectiveness of various health interventions for improving maternal, neonatal and child health. Reduction in perinatal and neonatal mortality remains a big challenge in resource constrained and diverse countries like Pakistan and achieving MDG 4 and 5 appears to be a distant reality. A comprehensive package of community based low cost interventions along the continuum of care tailored according to the socio cultural environment coupled with existing health force capacity building may result in improving the maternal and neonatal outcomes.

The findings of this proposed community based trial will provide sufficient evidence on feasibility, acceptability and effectiveness to the policy makers for replicating and scaling up the interventions within the health system

Trial registration

ClinicalTrial.govNCT01751945
Connexin-43 can delay early recurrence and metastasis in patients with hepatitis B-related hepatocellular carcinoma and low serum alpha-fetoprotein after radical hepatectomy
Authors: Wang Zu-Sen , Wu Li-Qun , Yi Xin , Geng Chao , Li Yu-Jun , Yao Ru-Yong
Published: June 2013

Background

We studied the relationships among Cx43, CD105, and VEGF in specimens of hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC) with different serum AFP levels with respect to recurrence and metastasis.

Methods

Expressions of Cx43, CD105, and VEGF in 234 HCC tissue specimens were examined using tissue microarray and immunohistochemistry. Cx43 mRNA expression was examined in 38 frozen HCC specimens using RT-PCR. Correlations between these expressions and tumor recurrence, metastasis, and prognosis were analyzed using Kaplan–Meier and Cox regression analyses.

Results

Cx43 expression correlated with early tumor recurrence (P = 0.001), disease-free survival (P = 0.026), and overall survival (P = 0.000) in patients with serum AFP < 400 ng/ml, but not in those with serum AFP ≥ 400 μg/L. Cx43 expression is an independent predictor of later recurrence and longer overall survival and is inversely correlated with expression of CD105 and VEGF (P = 0.018 and 0.023, respectively), histological differentiation (P = 0.002), vessel tumor embolism (P = 0.029), and focal number (P = 0.017). Immunohistochemistry showed that Cx43 expression in patients with low AFP was lower in patients with distant metastases than in those with no metastasis or those with liver metastasis. Patients with early recurrence expressed less Cx43 mRNA than did those with no recurrence (χ2 = 9.827, P = 0.002).

Conclusions

Cx43 expression can delay early HCC recurrence, metastasis, and poor prognosis after radical hepatectomy in patients with HBV-related HCC and low AFP.
Rhaphidophora korthalsii modulates peripheral blood natural killer cell proliferation, cytokine secretion and cytotoxicity
Authors: Yeap Swee Keong , Omar Abdul Rahman , Ho Wan Yong , Beh Boon Kee , Ali Abdul Manaf , Alitheen Noorjahan Banu
Published: June 2013

Background

Rhaphidophora korthalsii (Araceae) is a root-climber plant which has been widely used in Chinese traditional medicine for cancer and skin disease treatment. Previous reports have recorded its immunomodulatory effects on mice splenocyte and human peripheral blood. This study investigated the potential immunostimulatory effect of Rhaphidophora korthalsii on human PBMC enriched NK cell.

Methods

PBMC was exposed to various concentrations of R. korthalsii extract and the T and NK cell population in the control and extract treated PBMC were identified by immunophenotyping. Intracellular perforin and granzyme B expressions were detected by flow cytometry and extra-cellular Granzyme B, IFN-γ and TNF-α production in the isolated NK cells were determined by ELISA. The cytotoxicity of effector NK cell towards target K562 cell was assessed by CytoTox 96 assay.

Results

Rhaphidophora korthalsii methanol extract significantly increased PBMC NK cell population and intracellular perforin and granzyme B expressions. Moreover, the extract also enhanced the secretion of IFN-γ and TNF-α which subsequently enhanced the cytotoxicity of NK cell against the NK sensitive target K562 cell line. NK cell enriched with extract treated PBMC showed better activation than NK cell directly treated with the extract.

Conclusion

Our findings indicated a potential IL-2 free immunotherapy through direct and indirect R. korthalsii stimulation on NK cell activation.
Hypersusceptibility mechanism of Tenofovir-resistant HIV to EFdA
Authors: Michailidis Eleftherios , Ryan Emily M , Hachiya Atsuko , Kirby Karen A , Marchand Bruno , Leslie Maxwell D , Huber Andrew D , Ong Yee T , Jackson Jacob C , Singh Kamalendra , Kodama Eiichi N , Mitsuya Hiroaki , Parniak Michael A , Sarafianos Stefan G
Published: June 2013

Background

The K65R substitution in human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) is the major resistance mutation selected in patients treated with first-line antiretroviral tenofovir disoproxil fumarate (TDF). 4'-ethynyl-2-fluoro-2'-deoxyadenosine (EFdA), is the most potent nucleoside analog RT inhibitor (NRTI) that unlike all approved NRTIs retains a 3'-hydroxyl group and has remarkable potency against wild-type (WT) and drug-resistant HIVs. EFdA acts primarily as a chain terminator by blocking translocation following its incorporation into the nascent DNA chain. EFdA is in preclinical development and its effect on clinically relevant drug resistant HIV strains is critically important for the design of optimal regimens prior to initiation of clinical trials.

Results

Here we report that the K65R RT mutation causes hypersusceptibility to EFdA. Specifically, in single replication cycle experiments we found that EFdA blocks WT HIV ten times more efficiently than TDF. Under the same conditions K65R HIV was inhibited over 70 times more efficiently by EFdA than TDF. We determined the molecular mechanism of this hypersensitivity using enzymatic studies with WT and K65R RT. This substitution causes minor changes in the efficiency of EFdA incorporation with respect to the natural dATP substrate and also in the efficiency of RT translocation following incorporation of the inhibitor into the nascent DNA. However, a significant decrease in the excision efficiency of EFdA-MP from the 3’ primer terminus appears to be the primary cause of increased susceptibility to the inhibitor. Notably, the effects of the mutation are DNA-sequence dependent.

Conclusion

We have elucidated the mechanism of K65R HIV hypersusceptibility to EFdA. Our findings highlight the potential of EFdA to improve combination strategies against TDF-resistant HIV-1 strains.
Vaccination induced antibodies to recombinant avian influenza A virus M2 protein or synthetic M2e peptide do not bind to the M2 protein on the virus or virus infected cells
Authors: Swinkels Willem J C , Hoeboer Jeroen , Sikkema Reina , Vervelde Lonneke , Koets Ad P
Published: June 2013

Background

Influenza viruses are characterized by their highly variable surface proteins HA and NA. The third surface protein M2 is a nearly invariant protein in all Influenza A strains. Despite extensive studies in other animal models, this study is the first to describe the use of recombinant M2 protein and a peptide coding for the extracellular part of the M2 protein (M2e) to vaccinate poultry.

Methods

Four groups of layer chickens received a prime-boost vaccination with recombinant M2 protein, M2e, a tetrameric construct from M2e peptide bound to streptavidin and a control tetrameric construct formulated with Stimune adjuvant.

Results

We determined the M2-specific antibody (Ab) responses in the serum before vaccination, three weeks after vaccination and two weeks after booster, at days 21, 42 and 56 of age. The group vaccinated with the M2 protein in combination with Stimune adjuvant showed a significant Ab response to the complete M2 protein as compared to the other groups. In addition an increased Ab response to M2e peptide was found in the group vaccinated with the M2e tetrameric construct. None of the vaccinated animals showed seroconversion to AI in a commercial ELISA. Finally no Ab’s were found that bound to M2 expressed on in vitro AI infected MDCK cells.

Conclusion

Although Ab’s are formed against the M2 protein and to Streptavidin bound M2e peptide in a tetrameric conformation these Ab’s do not recognize of M2 on the virus or on infected cells.
A case of adenocarcinoma of the rete testis accompanied by focal adenomatous hyperplasia
Authors: Lin Xu-Yong , Yu Juan-Han , Xu Hong-Tao , Wang Liang , Fan Chui-Feng , Liu Yang , Wang En-Hua
Published: June 2013

Adenocarcinoma of the rete testis is very rare. There is still little knowledge about its etiology and pathogenesis. Herein, we present a case of rete testis adenocarcinoma in a 36-year-old Chinese male. The tumor was predominantly composed of irregular small tubules and papillary structures with cuboidal or polygonal cells. In peripheral area of the tumor, the remaining normal rete testis and adenomatous hyperplasia of the rete testis could also be seen, indicating the possible relationship between adenomatous hyperplasia and adenocarcinoma. In addition, the patient underwent a left hydrocelectomy because of the existence of hydrocele 3 years ago. But, it is unclear whether hydrocele and hydrocelectomy is its cause or just the early clinical presentation of the adenocarcinoma.

Virtual slides

The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/6757609119625499
Effect of plate working length on plate stiffness and cyclic fatigue life in a cadaveric femoral fracture gap model stabilized with a 12-hole 2.4 mm locking compression plate
Authors: Chao Peini , Conrad Bryan P , Lewis Daniel D , Horodyski MaryBeth , Pozzi Antonio
Published: June 2013

Background

There are several factors that can affect the fatigue life of a bone plate, including the mechanical properties of the plate and the complexity of the fracture. The position of the screws can influence construct stiffness, plate strain and cyclic fatigue of the implants. Studies have not investigated these variables in implants utilized for long bone fracture fixation in dogs and cats. The purpose of the present study was to evaluate the effect of plate working length on construct stiffness, gap motion and resistance to cyclic fatigue of dog femora with a simulated fracture gap stabilized using a 12-hole 2.4 mm locking compression plates (LCP). Femora were plated with 12-hole 2.4 mm LCP using 2 screws per fracture segment (long working length group) or with 12-hole 2.4 mm LCP using 5 screws per fracture segment (a short working length group).

Results

Construct stiffness did not differ significantly between stabilization techniques. Implant failure did not occur in any of the plated femora during cycling. Mean ± SD yield load at failure in the short plate working length group was significantly higher than in the long plate working length group.

Conclusion

In a femoral fracture gap model stabilized with a 2.4 mm LCP applied in contact with the bone, plate working length had no effect on stiffness, gap motion and resistance to fatigue. The short plate working length constructs failed at higher loads; however, yield loads for both the short and long plate working length constructs were within physiologic range.
Parallel-META: efficient metagenomic data analysis based on high-performance computation
Authors: Su Xiaoquan , Xu Jian , Ning Kang
Published: June 2013

Background

Metagenomics method directly sequences and analyses genome information from microbial communities. There are usually more than hundreds of genomes from different microbial species in the same community, and the main computational tasks for metagenomic data analyses include taxonomical and functional component examination of all genomes in the microbial community. Metagenomic data analysis is both data- and computation- intensive, which requires extensive computational power. Most of the current metagenomic data analysis softwares were designed to be used on a single computer or single computer clusters, which could not match with the fast increasing number of large metagenomic projects' computational requirements. Therefore, advanced computational methods and pipelines have to be developed to cope with such need for efficient analyses.

Result

In this paper, we proposed Parallel-META, a GPU- and multi-core-CPU-based open-source pipeline for metagenomic data analysis, which enabled the efficient and parallel analysis of multiple metagenomic datasets and the visualization of the results for multiple samples. In Parallel-META, the similarity-based database search was parallelized based on GPU computing and multi-core CPU computing optimization. Experiments have shown that Parallel-META has at least 15 times speed-up compared to traditional metagenomic data analysis method, with the same accuracy of the results http://www.computationalbioenergy.org/parallel-meta.html.

Conclusion

The parallel processing of current metagenomic data would be very promising: with current speed up of 15 times and above, binning would not be a very time-consuming process any more. Therefore, some deeper analysis of the metagenomic data, such as the comparison of different samples, would be feasible in the pipeline, and some of these functionalities have been included into the Parallel-META pipeline.
A computational procedure for identifying master regulator candidates: a case study on diabetes progression in Goto-Kakizaki rats
Authors: Piao Guanying , Saito Shigeru , Sun Yidan , Liu Zhi-Ping , Wang Yong , Han Xiao , Wu Jiarui , Zhou Huarong , Chen Luonan , Horimoto Katsuhisa
Published: June 2013

Background

We have recently identified a number of active regulatory networks involved in diabetes progression in Goto-Kakizaki (GK) rats by network screening. The networks were quite consistent with the previous knowledge of the regulatory relationships between transcription factors (TFs) and their regulated genes. To study the underlying molecular mechanisms directly related to phenotype changes, such as diseases, we also previously developed a computational procedure for identifying transcriptional master regulators (MRs) in conjunction with network screening and network inference, by effectively perturbing the phenotype states.

Results

In this work, we further improved our previous method for identifying MR candidates, by listing them in a more reliable manner, and applied the method to reveal the MR candidates for diabetes progression in GK rats from the active networks. Specifically, the active TF-gene pairs for different time periods in GK rats were first extracted from the networks by network screening. Another set of active TF-gene pairs was selected by network inference, by considering the gene expression signatures for those periods between GK and Wistar-Kyoto (WKY) rats. The TF-gene pairs extracted by the two methods were then further selected, from the viewpoints of the emergence specificity of TF in GK rats and the regulated-gene coverage of TF in the expression signature. Finally, we narrowed all of the genes down to only 5 TFs (Etv4, Fus, Nr2f1, Sp2, and Tcfap2b) as the candidates of MRs, with 54 regulated genes, by merging the selected TF-gene pairs.

Conclusions

The present method has successfully identified biologically plausible MR candidates, including the TFs related to diabetes in previous reports. Although the experimental verifications of the candidates and the present procedure are beyond the scope of this study, we narrowed down the candidates to 5 TFs, which can be used to perform the verification experiments relatively easily. The numerical results showed that our computational method is an efficient way to detect the key molecules responsible for biological phenomena.
Non-destructive characterisation and classification of ceramic artefacts using pEDXRF and statistical pattern recognition
Authors: Gajić-Kvaščev Maja D , Marić-Stojanović Milica D , Jančić-Heinemann Radmila M , Kvaščev Goran S , Andrić Velibor Dj
Published: June 2013

Background

Portable energy dispersive X-ray fluorescence (pEDXRF) spectrometry analysis was applied for the characterisation of archaeological ceramic findings from three Neolithic sites in Serbia. Two dimension reduction techniques, principal component analysis (PCA) and scattering matrices-based dimension reduction were used to examine the possible classification of those findings, and to extract the most discriminant features.

Results

A decision-making procedure is proposed, whose goal is to classify unknown ceramic findings based on their elemental compositions derived by pEDXRF spectrometry. As a major part of decision-making procedure, the possibilities of two dimension reduction methods were tested. Scattering matrices-based dimension reduction was found to be the more efficient method for the purpose. Linear classifiers designed based on the desired output allowed for 7 of 8 unknown samples from the test set to be correctly classified.

Conclusions

Based on the results, the conclusion is that despite the constraints typical of the applied analytical technique, the elemental composition can be considered as viable information in provenience studies. With a fully-developed procedure, ceramic artefacts can be classified based on their elemental composition and well-known provenance.
Role of platelet chemokines, PF-4 and CTAP-III, in cancer biology
Authors: Pilatova Katerina , Greplova Kristina , Demlova Regina , Bencsikova Beatrix , Klement Giannoula Lakka , Zdrazilova-Dubska Lenka
Published: June 2013

With the recent addition of anti-angiogenic agents to cancer treatment, the angiogenesis regulators in platelets are gaining importance. Platelet factor 4 (PF-4/CXCL4) and Connective tissue activating peptide III (CTAP-III) are two platelet-associated chemokines that modulate tumor angiogenesis, inflammation within the tumor microenvironment, and in turn tumor growth. Here, we review the role of PF-4 and CTAP-III in the regulation of tumor angiogenesis; the results of clinical trial using recombinant PF-4 (rPF-4); and the use of PF-4 and CTAP-III as cancer biomarkers.
The inverse correlations between methane content and elastic parameters of coal-bed methane reservoirs
Authors: Chen Xin-Ping , Huo Quanming , Lin Jiandong , Wang Yang , Sun Fenjin , Li Wuzhong , Li Guizhong
Published: June 2013

We investigated three coal-bed methane (CBM) reservoirs in which there exist, when we are careful about data quality and reduce environmental variations, inverse correlations between methane content and the elastic properties of the coal beds. Such inverse correlations may exist in general in high- and medium-rank CBM reservoirs. There is evidence that supports the generalization of such inverse correlations and factors that distort them. These distorting factors may prevent identification of such inverse correlations in certain CBM prospects; however, they cannot negate the underlying inverse correlations. Such inverse correlations may play a role in CBM amplitude versus offset (AVO) similar to the role played by Gassmann-Biot theory ( Gassmann, 1951 ; Biot, 1956 , 1962 ) in AVO technology for conventional gas reservoirs. This may lay the first brick for a theoretical basis of CBM AVO.
Globally optimal finite-difference schemes based on least squares
Authors: Liu Yang
Published: June 2013

Spatial finite-difference (FD) coefficients are usually determined by the Taylor-series expansion (TE) or optimization methods. The former can provide high accuracy on a smaller wavenumber or frequency zone, and the latter can give moderate accuracy on a larger zone. Present optimization methods applied to calculate FD coefficients are generally gradient-like or global optimization-like algorithms, and thus iterations are involved. They are more computationally expensive, and sometimes the global solution may not be found. I examined second-order spatial derivatives and computed the optimized spatial FD coefficients over the given wavenumber range using the least-squares (LS) method. The results indicated that the FD accuracy increased with increasing operator length and decreasing wavenumber range. Therefore, for the given error and operator length, globally optimal spatial FD coefficients can be easily obtained. Some optimal FD coefficients were given. I developed schemes to obtain optimized LS-based spatial FD coefficients by minimizing the relative error of space-domain dispersion relation for second-order derivatives and time-space-domain dispersion relation for the acoustic wave equation. I discovered that minimizing the relative error of the space-domain dispersion relation provides less phase velocity error for small wavenumbers, compared to minimizing the absolute error. I also found that minimizing the relative error of the time-space-domain dispersion relation can reduce relative errors of phase velocity. Accuracy analysis demonstrated the correctness and advantage of schemes. I gave three examples of 2D acoustic FD modeling for a homogeneous, a large velocity-contrast, and a heterogeneous model, respectively. LS-based spatial FD operators have variable lengths for different velocities. Modeling examples demonstrated that the proposed LS-based FD scheme can maintain the same modeling precision while using a shorter spatial FD operator length, thus reducing the computation cost relative to conventional TE-based FD schemes, particularly for the higher order.
Inversion of slingram electromagnetic induction data using a Born approximation
Authors: Kamm Jochen , Becken Michael , Pedersen Laust B.
Published: June 2013

We present an efficient approximate inversion scheme for near-surface loop-loop EM induction data (slingram) that can be applied to obtain 2D or 3D models on a normal desktop computer. Our approach is derived from a volume integral equation formulation with an arbitrarily conductive homogeneous half-space as a background model. The measurements are not required to fulfill the low induction number condition (low frequency and conductivity). The high efficiency of the method is achieved by invoking the Born approximation around a half-space background. The Born approximation renders the forward operator linear. The choice of a homogeneous half-space yields closed form expressions for the required electromagnetic normal fields. It also yields a translationally invariant forward operator, i.e., a highly redundant Jacobian. In connection with the application of a matrix-free conjugate gradient method, this allows for very low memory requirements during the inversion, even in three dimensions. As a consequence of the Born approximation, strong conductive deviations from the background model are underestimated. Highly resistive anomalies are in principle overestimated, but at the same time difficult to resolve with induction methods. In the case of extreme contrasts, our forward model may fail in simultaneously explaining all the data collected. We applied the method to EM34 data from a profile that has been extensively studied with other electromagnetic methods and compare the results. Then, we invert three conductivity maps from the same area in a 3D inversion.
31P NMR and IR Study of Highly Water-stable SrO–BaO–Nb2O5–P2O5 Glass and Glass-ceramics
Authors: Masai Hirokazu , Shirai Ryota , Yoshida Kazuki , Takahashi Yoshihiro , Ihara Rie , Fujiwara Takumi , Tokuda Yomei , Yoko Toshinobu
Published: June 2013

We describe the preparation of [(100 − y)/4](SrO–BaO–2Nb2O5)–yP2O5 (SBNPy) glasses and glass-ceramics with the Sr0.5Ba0.5Nb2O6 (SBN50) phase, using a conventional process, and the analysis of the chemical stability of the materials in water. The SBNPy glasses and glass-ceramics consist of orthophosphate (Q0) and pyrophosphate (Q1) units with strongly delocalized P=O bonds. Because of the presence of these phosphate units, the glasses and glass-ceramics obtained in this study show no weight changes, even after exposure to water at 70 °C for 100 h. We hypothesize that the lack of phosphate chains within the glass network is responsible for the superior water stability.
Optimal Stopping and Early Exercise: An Eigenfunction Expansion Approach
Authors: Li Lingfei , Linetsky Vadim
Published: June 2013

This paper proposes a new approach to solve finite-horizon optimal stopping problems for a class of Markov processes that includes one-dimensional diffusions, birth–death processes, and jump diffusions and continuous-time Markov chains obtained by time-changing diffusions and birth-and-death processes with Lévy subordinators. When the expectation operator has a purely discrete spectrum in the Hilbert space of square-integrable payoffs, the value function of a discrete optimal stopping problem has an expansion in the eigenfunctions of the expectation operator. The Bellman's dynamic programming for the value function then reduces to an explicit recursion for the expansion coefficients. The value function of the continuous optimal stopping problem is then obtained by extrapolating the value function of the discrete problem to the limit via Richardson extrapolation. To illustrate the method, the paper develops two applications: American-style commodity futures options and Bermudan-style abandonment and capacity expansion options in commodity extraction projects under the subordinate Ornstein-Uhlenbeck model with mean-reverting jumps with the value function given by an expansion in Hermite polynomials.
Introduction to the OR Forum Article: “Blotto Politics”
Authors: Pinker Edieal J.
Published: June 2013

Comment on “Blotto Politics” by Alan Washburn.
Carers’ perspectives on choosing a care home for a relative with dementia
Authors: Katz Jeanne , Holland Caroline , Mitchell Kate , Sheehan Bart , Gage Heather , Thein Nwe
Published: June 2013

This article describes findings from a project that explored what happens to people with dementia (PWDs) following discharge from a general hospital to a residential care home. In 15 out of 109 cases referred to a hospital psychiatric liaison team, admission to a residential care home was indicated during the hospital stay. This ‘last resort’ for families, following repeated hospital admissions and a deteriorating condition, was accepted when all involved agreed that it was in the best interests of the PWDs. Four months after the move, carers reflected on their criteria for choosing the home, their expectations and whether these were met. Carers’ own wellbeing improved and their mental distress reduced as the PWDs appeared settled and safer. However, the findings suggest a continuing key role for family carers of PWDs in care homes and emphasises the need for advocacy for PWDs without such support.
Beyond ‘average’ family life: a secondary analysis of atypicality in 1960s families
Authors: O’Connor Henrietta , Goodwin John
Published: June 2013

This article is based on data gathered in the 1960s, which included information on household composition and family formations. We explore different family formations and structures represented in this data and the meaning attached to issues around a number of ‘unusual’ family compositions encountered by the researchers at that time. We also examine the significance attached to atypical family units by both the respondents and the interviewers.
City present in city past: Rafael Chirbes’ cartographic imaginary
Authors: Compitello Malcolm Alan
Published: June 2013

This article examines Rafael Chirbes’ 1994 novel Los disparos del cazador in relationship to important transformations of Madrid’s built environment from the 1940s to the middle of the 1990s. Using as a point of departure the groundbreaking work of the geographer David Harvey on the relationships between cultural production and urban process, this article offers a model for analysis that bridges the gap between the humanities and social sciences and in so doing offers a reading that demonstrates how Chirbes’ text weaves a message of resistance into the fabric of his novel about urban change.