bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development and Application of Reverse Transcription Loop‐Mediated Isothermal Amplification for Detecting Live Shewanella putrefaciens in Preserved Fish Sample
Authors: Li Chenghua , Ying Qi , Su Xiurong , Li Taiwu 
Published: April 2012

Abstract:  Given that live Shewanella putrefaciens is one of the major causes of spoilage for aquatic products even in chill storage, the rapid and accurate detection process is the first priority. In the present study, a novel reverse transcription loop‐mediated isothermal amplification (RT‐LAMP) detecting assay was developed by targeting internal transcribed spacer (ITS) sequence between 16S and 23S rRNA. At the same time, a new procaryotic mRNA isolation strategy was also established by introducing a polyA tail to RNA during cDNA synthesis step. Under the optimal reaction time (60 min) and temperature (64.1 °C), S. putrefaciens could be specially identified from a variety of other tested bacteria by RT‐LAMP. The sensitivity analysis showed that RT‐LAMP could be identified as lower as 5.4 copies per reaction, which is over 200‐fold higher than that of standard PCR (1.08 × 103 copies per reaction). The method could be effectively identified S. putrefaciens in artificially contaminated or spoilaged fish samples with dose‐dependent manners. To our knowledge, this is the first report using RT‐LAMP assay to detect live S. putrefaciens in fish.Practical Application:  The study provided a rapid and accurate detection method for live bacteria in aquatic food and established a new procaryotic mRNA isolation strategy at the same time, which will be useful for food preservation.
Mathematical Modeling of Growth of Non‐O157 Shiga Toxin‐Producing Escherichia coli in Raw Ground Beef
Authors: Huang Lihan , Tu Shu‐I , Phillips John , Fratamico Pina 
Published: April 2012

Abstract:  The objective of this study was to investigate the growth of Shiga toxin‐producing Escherichia coli (STEC, including serogroups O45, O103, O111, O121, and O145) in raw ground beef and to develop mathematical models to describe the bacterial growth under different temperature conditions. Three primary growth models were evaluated, including the Baranyi model, the Huang 2008 model, and a new growth model that is based on the communication of messenger signals during bacterial growth. A 5 strain cocktail of freshly prepared STEC was inoculated to raw ground beef samples and incubated at temperatures ranging from 10 to 35 °C at 5 °C increments. Minimum relative growth (<1 log10 cfu/g) was observed at 10 °C, whereas at other temperatures, all 3 phases of growth were observed. Analytical results showed that all 3 models were equally suitable for describing the bacterial growth under constant temperatures. The maximum cell density of STEC in raw ground beef increased exponentially with temperature, but reached a maximum of 8.53 log10 cfu/g of ground beef. The specific growth rates estimated by the 3 primary models were practically identical and can be evaluated by either the Ratkowsky square‐root model or a Bělehrádek‐type model. The temperature dependence of lag phase development for all 3 primary models was also developed. The results of this study can be used to estimate the growth of STEC in raw ground beef at temperatures between 10 and 35 °C.Practical Application:  Incidents of foodborne infections caused by non‐O157 Shiga toxin‐producing Escherichia coli (STEC) have increased in recent years. This study reports the growth kinetics and mathematical modeling of STEC in ground beef. The mathematical models can be used in risk assessment of STEC in ground beef.
Cytotoxicity of All‐Trans‐Retinal Increases Upon Photodegradation†
Authors: Różanowska Małgorzata , Handzel Kinga , Boulton Michael E. , Różanowski Bartosz 
Published: April 2012

AbstractAll‐trans‐retinal (AtRal) can accumulate in the retina as a result of excessive exposure to light. The purpose of this study was to compare cytotoxicity of AtRal and photodegraded AtRal (dAtRal) on cultured human retinal pigment epithelial cells in dark and upon exposure to visible light. AtRal was degraded by exposure to visible light. Cytotoxicity was monitored by imaging of cell morphology, propidium iodide staining of cells with permeable plasma membrane and measurements of reductive activity of cells. Generation of singlet oxygen photosensitized by AtRal and dAtRal was monitored by time‐resolved measurements of characteristic singlet oxygen phosphorescence. Photodegradation of AtRal resulted in a decrease in absorption of visible light and accumulation of the degradation products with absorption maximum at ∼330 nm. Toxicity of dAtRal was concentration‐dependent and was greater during irradiation with visible light than in dark. DAtRal was more cytotoxic than AtRal both in dark and during exposure to visible light. Photochemical properties of dAtRal indicate that it may be responsible for the maximum in the action spectra of retinal photodamage recorded in animals. In conclusion, photodegradation products of AtRal may impose a significant threat to the retina and therefore their roles in retinal pathology need to be explored.
Laparoendoscopic single‐site surgery for urachal remnants
Authors: Iida T , Kawa G , Takizawa N , Kawabata T , Komai Y , Kinoshita H , Matsuda T 
Published: April 2012

AbstractIntroductionUrachal remnants are relatively rare but may potentially cause various symptoms and an increased risk for developing adenocarcinoma. Open or laparoscopic surgery is usually used for their resection. Laparoendoscopic single‐site surgery has been recently applied in several surgical procedures. This report describes two cases of vesicourachal diverticulum treated by resection using laparoendoscopic single‐site surgery.Materials and Surgical TechniqueIn each case, laparoendoscopic single‐site surgery was performed transperitoneally via one port at a subumbilical semicircular incision. Except for a flexible camera and SILS Port, traditional, non‐flexible laparoscopic instruments were used. After the induction of general anesthesia, the patient was placed in a supine position (or lithotomy position). A 2.0‐cm incision was made semicircumferentially following the natural subumbilical folds. After the umbilical ligament was cut under direct vision, a SILS Port was placed at the incision. The urachus was liberated distally down to the roof of the urinary bladder using 0° 5‐mm flexible camera. Vesicourachal diverticulum with a bladder cuff was completely excised under the supporting view of cystoscopy. Both patients' perioperative days were uneventful.DiscussionOur findings suggest that the laparoendoscopic single‐site surgery procedure is safe, minimally invasive and cosmetically acceptable. Therefore, this procedure is an excellent option for the radical resection of urachal remnants.
Novel organotypic culture model of cholangiocarcinoma progression
Authors: Campbell Deanna J. W. , Dumur Catherine I. , Lamour Nadia F. , DeWitt Jennifer L. , Sirica Alphonse E. 
Published: April 2012

Aim:  Recent studies have suggested that increased α‐smooth muscle‐actin positive myofibroblastic cells (α‐SMA positive CAF) in the desmoplastic stroma may relate to a more aggressive cancer and worse survival outcomes for intrahepatic cholangiocarcinoma (ICC) patients. To facilitate investigating cellular and molecular interactions between α‐SMA positive CAF and cholangiocarcinoma cells related to ICC progression, we developed a novel 3‐D organotypic culture model of cholangiocarcinoma that more accurately mimics the stromal microenvironment, gene expression profile and select pathophysiological characteristics of desmoplastic ICC in vivo.Methods:  This unique model was established by co‐culturing within a type I collagen gel matrix, a strain of cholangiocarcinoma cells (derived from an ICC formed in syngeneic rat liver following bile duct inoculation of spontaneously‐transformed rat cholangiocytes) with varying numbers of clonal α‐SMA positive CAF established from the same tumor type.Results:  Cholangiocarcinoma cells and α‐SMA positive CAF in monoculture each exhibited cell‐specific biomarker gene expression profiles characteristic of stromal myofibroblastic cell versus malignant cholangiocyte cell types. In comparison, the gene expression profile and histopathological characteristics exhibited by the organotypic co‐culture closely resembled those of whole tissue samples of the parent orthotopic ICC. We further showed α‐SMA positive CAF to significantly enhance cholangiocarcinoma cell “ductal‐like” growth and cancer cell migration/invasiveness in vitro, as well as to promote upregulated expression of select genes known to be associated with ICC invasion.Conclusion:  This novel organotypic model provides an important new resource for studying the effects of microenvironment on cholangiocarcinoma progression in vitro and may have potential as a preclinical model for identifying molecularly targeted therapies.
Modulation of the Myxoma Virus Plaque Phenotype by Vaccinia Virus Protein F11
Authors: Irwin Chad R. , Evans David H. 
Published: April 2012

ABSTRACT

Vaccinia virus (VACV) produces large plaques consisting of a rapidly expanding ring of infected cells surrounding a lytic core, whereas myxoma virus (MYXV) produces small plaques that resemble a focus of transformed cells. This is odd, because bioinformatics suggests that MYXV carries homologs of nearly all of the genes regulating
Orthopoxvirus
attachment, entry, and exit. So why does MYXV produce foci? One notable difference is that MYXV-infected cells produce few of the actin microfilaments that promote VACV exit and spread. This suggested that although MYXV carries homologs of the required genes (A33R, A34R, A36R, and B5R), they are dysfunctional. To test this, we produced MYXV recombinants expressing these genes, but we could not enhance actin projectile formation even in cells expressing all four VACV proteins. Another notable difference between these viruses is that MYXV lacks a homolog of the F11L gene. F11 inhibits the RhoA-mDia signaling that maintains the integrity of the cortical actin layer. We constructed an MYXV strain encoding F11L and observed that, unlike wild-type MYXV, the recombinant virus disrupted actin stress fibers and produced plaques up to 4-fold larger than those of controls, and these plaques expanded ∼6-fold faster. These viruses also grew to higher titers in multistep growth conditions, produced higher levels of actin projectiles, and promoted infected cell movement, although neither process was to the extent of that observed in VACV-infected cells. Thus, one reason for why MYXV produces small plaques is that it cannot spread via actin filaments, although the reason for this deficiency remains obscure. A second reason is that leporipoxviruses lack vaccinia's capacity to disrupt cortical actin.
Differential Impact of Interferon Regulatory Factor 7 in Initiation of the Type I Interferon Response in the Lymphocytic Choriomeningitis Virus-Infected Central Nervous System versus the Periphery
Authors: Christensen Jeanette Erbo , Fenger Christina , Issazadeh-Navikas Shohreh , Krug Anna , Liljestrøm Peter , Goriely Stanislas , Paludan Søren Riis , Finsen Bente , Christensen Jan Pravsgaard , Thomsen Allan Randrup 
Published: April 2012

ABSTRACTInterferon (IFN) regulatory factors (IRFs) are a family of transcription factors involved in regulating type I IFN genes and other genes participating in the early antiviral host response. To better understand the mechanisms involved in virus-induced central nervous system (CNS) inflammation, we studied the influence of IRF1, -3, -7, and -9 on the transcriptional activity of key genes encoding antiviral host factors in the CNS of mice infected with lymphocytic choriomeningitis virus (LCMV). A key finding is that neither IRF3 nor IRF7 is absolutely required for induction of a type I IFN response in the LCMV-infected CNS, whereas concurrent elimination of both factors markedly reduces the virus-induced host response. This is unlike the situation in the periphery, where deficiency of IRF7 almost eliminates the LCMV-induced production of the type I IFNs. This difference is seemingly related to the local environment, as peripheral production of type I IFNs is severely reduced in intracerebrally (i.c.) infected IRF7-deficient mice, which undergo a combined infection of the CNS and peripheral organs, such as spleen and lymph nodes. Interestingly, despite the redundancy of IRF7 in initiating the type I IFN response in the CNS, the response is not abolished in IFN-β-deficient mice, as might have been expected. Collectively, these data demonstrate that the early type I IFN response to LCMV infection in the CNS is controlled by a concerted action of IRF3 and -7. Consequently this work provides strong evidence for differential regulation of the type I IFN response in the CNS versus the periphery during viral infection.
First-Order Structure Function Analysis of Statistical Scale Invariance in the AIRS-Observed Water Vapor Field
Authors: Pressel Kyle G. , Collins William D. 
Published: April 2012

AbstractThe power-law scale dependence, or scaling, of first-order structure functions of the tropospheric water vapor field between 58°S and 58°N is investigated using observations from the Atmospheric Infrared Sounder (AIRS). Power-law scale dependence of the first-order structure function would indicate that the water vapor field exhibits statistical scale invariance. Directional and directionally independent first-order structure functions are computed to assess the directional dependence of derived first-order structure function scaling exponents (H) for a range of scales from 50 to 500 km. In comparison to other methods of assessing statistical scale invariance, the methodology used here requires minimal assumptions regarding the homogeneity of the spatial distribution of data within regions of analysis. Additionally, the methodology facilitates the evaluation of anisotropy and quantifies the extent to which the structure functions exhibit scale invariance.The spatial and seasonal dependence of the computed scaling exponents are explored. Minimum scaling exponents at all levels are shown to occur proximate to the equator, while the global maximum is shown to occur in the middle troposphere near the tropical–subtropical margin of the winter hemisphere.From a detailed analysis of AIRS maritime scaling exponents, it is concluded that the AIRS observations suggest the existence of two scaling regimes in the extratropics. One of these regimes characterizes the statistical scale invariance the free troposphere with H approximately = 0.55 and a second that characterizes the statistical scale invariance of the boundary layer with H approximately = ⅓.
Psychiatric advance statements: An Indian experience
Authors: Kumar TC Ramesh , John Sujit , Gopal Subhashini , Mohan Greeshma , Joseph Jainey ,   PAS study group, Rangaswamy Thara 
Published: April 2012

Background: The psychiatric advance statement (PAS) is a document that outlines the preferences of patients in their future treatment. Formulating and writing a PAS has not been studied in low- and middle-income (LAMI) countries. Aim: To study the feasibility of writing a PAS in an Indian population. Methods: Patients’ diagnosed with schizophrenia or schizoaffective psychosis attending the outpatient clinic at the Schizophrenia Research Foundation (SCARF) or its community centres in 2011 were screened using the study criteria. After obtaining informed consent, stratified sampling was used to derive the final sample. Results: Most patients consented to participate in the study (122/123 patients). Following interviews with research assistants, 93 patients were assessed to have the capacity to write a PAS and 92 completed one. The patients were mostly able to complete the PAS on their own. Major themes included choice of treatment facility, type of treatment and nomination of others to take decisions on their behalf. A third of the sample were either from rural areas or not exclusively urban. At the time of the study, about 45% of the sample was rated as being symptomatic. Conclusion: Psychotic patients with a long-term illness, a third of them from non-urban areas, were able to write a valid PAS.
Durkheim, Wittgenstein and the Norms of Thought
Authors: Keucheyan Razmig 
Published: April 2012

AbstractIn their respective fields of philosophy and sociology, Ludwig Wittgenstein and E´mile Durkheim are known for having associated two types of norms usually considered to be distinct: social norms and cognitive norms. They shared the same idea that the rules which govern the activity of the mind – for examples the laws of logic – are fundamentally linked to those which subtend social activity. For Wittgenstein and Durkheim, cognitive norms are thus a type of social norm.The objective of this article is to compare the way in which Wittgenstein and Durkheim thematise the relationship between social norms and cognitive norms. It begins by clarifying the author’s understanding of ‘‘cognitive norms’’. It then presents Durkheim’s and Wittgenstein’s analyses of these norms, and it finally attempts to define some of the similarities and differences existing between their approaches to this problem.
States of Violence and Infatuation in Politics: The Idea of Right at the Heart of Their Excesses
Authors: Douailler Stéphane 
Published: April 2012

AbstractThe idea of the political state as a cluster of stability amidst chaos entails an inflation of legal ties that bind the immoderation of the chaos through an immoderate set of laws. This paper suggests an examination of the opposite approach, one attempted by Alexandre Kojève during the Second World War: an investigation of the practice of disassociation. By presenting four loose figures (the judge, the leader, the father, the master) in his book La notion d’autorité, Kojève pursued his quest for a disinterested operator in Esquisse d’une phénoménologie du droit, where he described its emergence out of the void created by anthropogenic desire in the natural world. As an outcome of this approach, history-laden figures such as the judge, leader, father or master, are replaced by the admission and promotion of the random human being. The quest for other figures starts here: the paper evokes, for example, the case of the misanthrope.
Investigation of compressor correction quantities for automotive applications
Authors: Leufven Oskar , Eriksson Lars 
Published: April 2012

Turbo performance is represented using maps, measured for one set of inlet conditions. Corrections are then applied to scale the performance to other inlet conditions. A turbo compressor for automotive applications experiences large variations in inlet conditions, and the use of two-stage charging increases these variations. The variations are the motivation for analysing the correction quantities and their validity. A novel surge-avoidance strategy is found in the correction equations, where the result is that a reduction in inlet pressure can increase the surge margin of eight studied maps. The method for investigating the applicability of the strategy is general. An experimental analysis of the applicability of the commonly used correction factors, used when estimating compressor performance for varying inlet conditions, is presented. A set of experimental measurements from an engine test cell and from a gas stand shows a small but clearly measurable trend, with decreasing compressor pressure ratio for decreasing compressor inlet pressure. A method is developed, enabling measurements to be analysed with modified corrections. An adjusted shaft speed correction quantity is proposed, also incorporating the inlet pressure in the shaft speed correction. The resulting decrease in high-altitude engine performance, due to compressor limitations, is quantified and shows a reduction in altitude of 200–600 m, for when engine torque has to be reduced due to limited compressor operation.
Challenges in estimating percent inclusion of alternatively spliced junctions from RNA-seq data
Authors: Kakaradov Boyko , Xiong Hui Yuan , Lee Leo J , Jojic Nebojsa , Frey Brendan J 
Published: April 2012

Abstract
Transcript quantification is a long-standing problem in genomics and estimating the relative abundance of alternatively-spliced isoforms from the same transcript is an important special case. Both problems have recently been illuminated by high-throughput RNA sequencing experiments which are quickly generating large amounts of data. However, much of the signal present in this data is corrupted or obscured by biases resulting in non-uniform and non-proportional representation of sequences from different transcripts. Many existing analyses attempt to deal with these and other biases with various task-specific approaches, which makes direct comparison between them difficult. However, two popular tools for isoform quantification, MISO and Cufflinks, have adopted a general probabilistic framework to model and mitigate these biases in a more general fashion. These advances motivate the need to investigate the effects of RNA-seq biases on the accuracy of different approaches for isoform quantification. We conduct the investigation by building models of increasing sophistication to account for noise introduced by the biases and compare their accuracy to the established approaches.
We focus on methods that estimate the expression of alternatively-spliced isoforms with the percent-spliced-in (PSI) metric for each exon skipping event. To improve their estimates, many methods use evidence from RNA-seq reads that align to exon bodies. However, the methods we propose focus on reads that span only exon-exon junctions. As a result, our approaches are simpler and less sensitive to exon definitions than existing methods, which enables us to distinguish their strengths and weaknesses more easily. We present several probabilistic models of of position-specific read counts with increasing complexity and compare them to each other and to the current state-of-the-art methods in isoform quantification, MISO and Cufflinks. On a validation set with RT-PCR measurements for 26 cassette events, some of our methods are more accurate and some are significantly more consistent than these two popular tools. This comparison demonstrates the challenges in estimating the percent inclusion of alternatively spliced junctions and illuminates the tradeoffs between different approaches.
Implementation and evaluation of a new TCP loss recovery architecture
Authors: Kang Moonsoo , Park Hosung , Mo Jeonghoon 
Published: April 2012

Abstract
In this article, we propose a novel loss recovery algorithm of transmission control protocol (TCP) using packet transmission order, which shows a steady loss recovery ability even though packet loss rate increases. This leads to a significant throughput increase of TCP with heavy packet loss. We have verified the performance increase of the new TCP under various environments such as a wireless network, and multimedia transmission through simulation. Moreover, we implemented the proposed idea in Linux and conducted some experiments in a real environment. Even though the experiment results did not perfectly agree with the simulation results, we obtained a similar throughput increase to that of the simulation.