bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment and management of interfractional variations in daily diagnostic‐quality‐CT guided prostate‐bed irradiation after prostatectomy
Authors: Liu Feng , Ahunbay Ergun , Lawton Colleen , Allen Li X. 
Published: February 2014

Purpose:To quantify interfractional anatomic variations and limitations of the current practice of image‐guided radiation therapy (IGRT) for prostate‐bed patients and to study dosimetric benefits of an online adaptive replanning scheme that addresses the interfractional variations.Methods:Contours for the targets and organs at risk (OARs) from daily diagnostic‐quality CTs acquired with in‐room CT (CTVision, Siemens) were generated by populating the planning contours using an autosegmentation tool based on deformable registration (ABAS, Elekta) with manual editing for ten prostate‐bed patients treated with postoperative daily CT‐guided IMRT. Dice similarity coefficient (DSC) obtained by maximizing the overlap of contours for a structure between the daily and plan contours was used to quantify the organ deformation between the plan and daily CTs. Three interfractional‐variation‐correction schemes, the current standard practice of IGRT repositioning, a previously developed online adaptive RT (ART), and the full reoptimization, were applied to these daily CTs and a number of dose‐volume quantities for the targets and organs at risk were compared for their effectiveness to account for the interfractional variations.Results:Large interfractional organ deformations in prostate‐bed irradiation were seen. The mean DSCs for CTV, rectum, and bladder were 86.6 ± 5.1% (range from 61% to 97%), 77.3% ± 7.4% (range from 55% to 90%), and 75.4% ± 11.2% (range from 46% to 96%), respectively. The fractional and cumulative dose‐volume quantities for CTV and PTV: V100 (volume received at least 100% prescription dose), and rectum and bladder: V45Gy and V60Gy (volume received at least 45 or 60 Gy), were compared for the repositioning, adaptive, reoptimization, and original plans. The fractional and cumulative dosimetric results were nearly the same. The average cumulative CTV V100 were 88.0%, 98.4%, 99.2%, and 99.3% for the IGRT, ART, reoptimization, and original plans, respectively. The corresponding rectal V45Gy (V60Gy) were 58.7% (27.3%), 48.1% (20.7%), 43.8% (16.1%), and 44.9% (16.8%). The results for bladder were comparable among three schemes. Paired two‐tailed Wilcoxon signed‐rank tests were performed and it was found that ART and reoptimization provide better target coverage and better OAR sparing, especially rectum sparing.Conclusions:The interfractional organ motions and deformations during prostate‐bed irradiation are significant. The online adaptive replanning scheme is capable of effectively addressing the large organ deformation, resulting in cumulative doses equivalent to those originally planned.
Chimeric Plantibody Passively Protects Mice against Aerosolized Ricin Challenge
Authors: Sully Erin K. , Whaley Kevin J. , Bohorova Natasha , Bohorov Ognian , Goodman Charles , Kim Do H. , Pauly Michael H. , Velasco Jesus , Hiatt Ernie , Morton Josh , Swope Kelsi , Roy Chad J. , Zeitlin Larry , Mantis Nicholas J. 
Published: February 2014

ABSTRACTRecent incidents in the United States and abroad have heightened concerns about the use of ricin toxin as a bioterrorism agent. In this study, we produced, using a robust plant-based platform, four chimeric toxin-neutralizing monoclonal antibodies that were then evaluated for the ability to passively protect mice from a lethal-dose ricin challenge. The most effective antibody, c-PB10, was further evaluated in mice as a therapeutic following ricin exposure by injection and inhalation.
Demonstration of Plasmid-Mediated Drug Resistance in Mycobacterium abscessus
Authors: Matsumoto Cristianne Kayoko , Bispo Paulo José Martins , Santin Katiane , Nogueira Christiane Lourenço , Leão Sylvia Cardoso 
Published: February 2014

ABSTRACT

Plasmid-mediated kanamycin resistance was detected in a strain of
Mycobacterium abscessus
subsp.
bolletii
responsible for a nationwide epidemic of surgical infections in Brazil. The plasmid did not influence susceptibility to tobramycin, streptomycin, trimethoprim-sulfamethoxazole, clarithromycin, or ciprofloxacin. Plasmid-mediated drug resistance has not been described so far in mycobacteria.
Interlaboratory Reproducibility and Proficiency Testing within the Human Papillomavirus Cervical Cancer Screening Program in Catalonia, Spain
Authors: Ibáñez R. , Félez-Sánchez M. , Godínez J. M. , Guardià C. , Caballero E. , Juve R. , Combalia N. , Bellosillo B. , Cuevas D. , Moreno-Crespi J. , Pons L. , Autonell J. , Gutierrez C. , Ordi J. , de Sanjosé S. , Bravo I. G. 
Published: February 2014

ABSTRACT

In Catalonia, a screening protocol for cervical cancer, including human papillomavirus (HPV) DNA testing using the Digene Hybrid Capture 2 (HC2) assay, was implemented in 2006. In order to monitor interlaboratory reproducibility, a proficiency testing (PT) survey of the HPV samples was launched in 2008. The aim of this study was to explore the repeatability of the HC2 assay's performance. Participating laboratories provided 20 samples annually, 5 randomly chosen samples from each of the following relative light unit (RLU) intervals: <0.5, 0.5 to 0.99, 1 to 9.99, and ≥10. Kappa statistics were used to determine the agreement levels between the original and the PT readings. The nature and origin of the discrepant results were calculated by bootstrapping. A total of 946 specimens were retested. The kappa values were 0.91 for positive/negative categorical classification and 0.79 for the four RLU intervals studied. Sample retesting yielded systematically lower RLU values than the original test (
P
< 0.005), independently of the time elapsed between the two determinations (median, 53 days), possibly due to freeze-thaw cycles. The probability for a sample to show clinically discrepant results upon retesting was a function of the RLU value; samples with RLU values in the 0.5 to 5 interval showed 10.80% probability to yield discrepant results (95% confidence interval [CI], 7.86 to 14.33) compared to 0.85% probability for samples outside this interval (95% CI, 0.17 to 1.69). Globally, the HC2 assay shows high interlaboratory concordance. We have identified differential confidence thresholds and suggested the guidelines for interlaboratory PT in the future, as analytical quality assessment of HPV DNA detection remains a central component of the screening program for cervical cancer prevention.
Benchmarking of Methods for Genomic Taxonomy
Authors: Larsen Mette V. , Cosentino Salvatore , Lukjancenko Oksana , Saputra Dhany , Rasmussen Simon , Hasman Henrik , Sicheritz-Pontén Thomas , Aarestrup Frank M. , Ussery David W. , Lund Ole 
Published: February 2014

ABSTRACT

One of the first issues that emerges when a prokaryotic organism of interest is encountered is the question of what it is—that is, which species it is. The 16S rRNA gene formed the basis of the first method for sequence-based taxonomy and has had a tremendous impact on the field of microbiology. Nevertheless, the method has been found to have a number of shortcomings. In the current study, we trained and benchmarked five methods for whole-genome sequence-based prokaryotic species identification on a common data set of complete genomes: (i) SpeciesFinder, which is based on the complete 16S rRNA gene; (ii) Reads2Type that searches for species-specific 50-mers in either the 16S rRNA gene or the
gyrB
gene (for the
Enterobacteraceae
family); (iii) the ribosomal multilocus sequence typing (rMLST) method that samples up to 53 ribosomal genes; (iv) TaxonomyFinder, which is based on species-specific functional protein domain profiles; and finally (v) KmerFinder, which examines the number of cooccurring
k
-mers (substrings of
k
nucleotides in DNA sequence data). The performances of the methods were subsequently evaluated on three data sets of short sequence reads or draft genomes from public databases. In total, the evaluation sets constituted sequence data from more than 11,000 isolates covering 159 genera and 243 species. Our results indicate that methods that sample only chromosomal, core genes have difficulties in distinguishing closely related species which only recently diverged. The KmerFinder method had the overall highest accuracy and correctly identified from 93% to 97% of the isolates in the evaluations sets.
Coinfection of Fusobacterium nucleatum and Actinomyces israelii in Mastoiditis Diagnosed by Next-Generation DNA Sequencing
Authors: Salipante Stephen J. , Hoogestraat Daniel R. , Abbott April N. , SenGupta Dhruba J. , Cummings Lisa A. , Butler-Wu Susan M. , Stephens Karen , Cookson Brad T. , Hoffman Noah G. 
Published: February 2014

ABSTRACT

Some bacterial infections involve potentially complex mixtures of species that can now be distinguished using next-generation DNA sequencing. We present a case of mastoiditis where Gram stain, culture, and molecular diagnosis were nondiagnostic or discrepant. Next-generation sequencing implicated coinfection of
Fusobacterium nucleatum
and
Actinomyces israelii
, resolving these diagnostic discrepancies.
Loop-Mediated Isothermal Amplification Assay for Rapid Diagnosis of Malaria Infections in an Area of Endemicity in Thailand
Authors: Sattabongkot Jetsumon , Tsuboi Takafumi , Han Eun-Taek , Bantuchai Sirasate , Buates Sureemas 
Published: February 2014

ABSTRACT
The loop-mediated isothermal amplification (LAMP) method, developed by our group for diagnosis of four human malaria parasites, was evaluated on a large scale at a remote clinic in Thailand where malaria is endemic. A total of 899 febrile patients were analyzed in this study. LAMP was first evaluated in 219 patients, and the result was compared to those of two histidine-rich protein (HRP)-2 rapid diagnostic tests (RDTs) and microscopy as a gold standard. LAMP DNA extraction was conducted by a simple boiling method, and the test results were assessed visually. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were 95.7%, 100%, 100%, and 98%, respectively, for LAMP and 98.6%, 98%, 95.8%, and 99.3%, respectively, for RDTs. Since RDT-positive results were based on one out of two RDTs, the sensitivity of RDTs was slightly higher than that of LAMP. However, LAMP tended to be more specific than RDTs. LAMP next was evaluated in 680 patients, and the result was compared to that of microscopy as a gold standard. Sensitivity, specificity, PPV, NPV, and diagnostic accuracy of LAMP were 88.9%, 96.9%, 92.2%, 95.5%, and 94.6%, respectively. Nested PCR was used to confirm the discrepant results. Malaria LAMP in a remote clinic in Thailand achieved an acceptable result, indicating that LAMP malaria diagnosis is feasible in a field setting with limited technical resources. Additionally, the rapid boiling method for extracting DNA from dried blood spots proved to be simple, fast, and suitable for use in the field.
Clinical Implications of Evolutionary Patterns of Homologous, Full-Length Hepatitis B Virus Quasispecies in Different Hosts after Perinatal Infection
Authors: Liu Feng , Yu De-Min , Huang Su-Yuan , Yu Jia-Lun , Zhang Dong-Hua , Gong Qi-Ming , Zhang Xin-Xin 
Published: February 2014

ABSTRACTChronic hepatitis B virus (HBV) infection via perinatal transmission is common in the Asia-Pacific region, but related quasispecies (QS) characteristics are not yet defined. To investigate the homologous, full-length HBV QS after perinatal infection and their clinical implications, five pairs of mother-daughter patients with chronic HBV infection (one patient with liver cirrhosis, one with immune tolerance, and eight with chronic hepatitis) were included. Full-length HBV were amplified by PCR from serum samples before antiviral treatment and cloned; an average of 17 clones per sample were sequenced, and the QS complexities, diversities, and evolution patterns were analyzed. Full-length HBV sequence similarities within mother-daughter pairs were 91.3 to 98.3%. The QS complexities of full-length HBV were similar between mothers and daughters (median of 0.9734 compared to 0.9688,P> 0.05), as were the diversities (median of 3.396 × 10−3compared to 4.617 × 10−3substitutions/site,P> 0.05). However, the distribution patterns of QS complexities and diversities within specific genes were different, and QS genetic distances of the mothers were higher than those of daughters, both more evident in pairs with different antiviral responses and different immune phases or stages. The nucleotide substitution rate of full-length HBV was 14.388 × 10−5substitutions/site/year, whereas the preC/C gene rate was the highest. Mutations and indels were more common in clones from the mothers, which decreased the affinity of epitopes by 6- to 89-fold. The various genes from homologous HBV genomes evolved in different patterns despite numerically comparable full-length QS complexities and diversities. The different patterns may correlate with the immune stages of chronic HBV infection, which warrants further study.
New Automated Chemiluminescence Immunoassay for Simultaneous but Separate Detection of Human Immunodeficiency Virus Antigens and Antibodies
Authors: Alonso Roberto , López Roa Paula , Suárez Marisol , Bouza Emilio 
Published: February 2014

ABSTRACT
The recently launched Liaison XL Murex HIV Ab/Ag assay (DiaSorin S.p.A) uses chemiluminescence immunoassay technology for the combined qualitative determination of p24 antigen of HIV-1 and specific antibodies to both HIV-1 and HIV-2. We studied 571 serum samples from those submitted to our laboratory for HIV screening. The samples were divided into 3 subsets: subset A, 365 samples collected prospectively during 1 week; subset B, 158 samples from confirmed HIV-positive patients; and subset C, 48 samples with a positive screening result but a negative or indeterminate confirmatory test result. Our standard screening/confirmatory algorithm was used as a reference. In subset A (prospective), 5 samples were positive and 360 negative by the standard procedure. Liaison XL Murex HIV Ab/Ag correctly identified all 5 positive samples (100%) and 357 negative samples (99.2%). In subset B (confirmed positive), all 158 positive samples were in total agreement in both procedures. In subset C (screen positive only), Liaison XL Murex HIV Ab/Ag yielded accurate results in 42 out of 48 samples (87.5%). Global sensitivity and specificity for Liaison XL Murex HIV Ab/Ag (all subsets included) were 98.3% and 98.5%, respectively. Considering only nonselected prospective samples and confirmed positive samples (subsets A and B), the corresponding sensitivity and specificity values were 100% and 99.2%, respectively. The new fully automated HIV screening test showed high sensitivity and specificity compared to our standard algorithm. Its added advantage of being able to detect HIV-1 and HIV-2 antibodies and p24 antigen separately could prove useful in the diagnosis of early infections.
Rapid Detection of β-Lactamase-Hydrolyzing Extended-Spectrum Cephalosporins in Enterobacteriaceae by Use of the New Chromogenic βLacta Test
Authors: Morosini María Isabel , García-Castillo María , Tato Marta , Gijón Desirèe , Valverde Aránzazu , Ruiz-Garbajosa Patricia , Cantón Rafael 
Published: February 2014

ABSTRACT

The chromogenic βLacta test developed for the rapid detection of β-lactamase-hydrolyzing extended-spectrum cephalosporins in
Enterobacteriaceae
revealed good performance with extended-spectrum β-lactamase (ESBL) producers (97.5% true-positive results). However, false-negative results occurred with chromosomal AmpC hyperproducers and plasmid AmpC producers, whereas uninterpretable results were mostly due to VIM-1 carbapenemase producers and possibly low levels of expressed ESBLs.
Dendritic Cell-Lymphocyte Cross Talk Downregulates Host Restriction Factor SAMHD1 and Stimulates HIV-1 Replication in Dendritic Cells
Authors: Su Bin , Biedma Marina Elizabeth , Lederle Alexandre , Peressin Maryse , Lambotin Mélanie , Proust Alizé , Decoville Thomas , Schmidt Sylvie , Laumond Géraldine , Moog Christiane 
Published: February 2014

ABSTRACT
Human immunodeficiency virus type 1 (HIV-1) replication in dendritic cells (DCs) is restricted by SAMHD1. This factor is counteracted by the viral protein Vpx; Vpx is found in HIV-2 and simian immunodeficiency virus (SIV) from sooty mangabeys (SIVsm) or from macaques (SIVmac) but is absent from HIV-1. We previously observed that HIV-1 replication in immature DCs is stimulated by cocultivation with primary T and B lymphocytes, suggesting that HIV-1 restriction in DCs may be overcome under coculture conditions. Here, we aimed to decipher the mechanism of SAMHD1-mediated restriction in DC-lymphocyte coculture. We found that coculture with lymphocytes downregulated SAMHD1 expression and was associated with increased HIV-1 replication in DCs. Moreover, in infected DC-T lymphocyte cocultures, DCs acquired maturation status and secreted type 1 interferon (alpha interferon [IFN-α]). The blockade of DC-lymphocyte cross talk by anti-ICAM-1 antibody markedly inhibited the stimulation of HIV-1 replication and prevented the downregulation of SAMHD1 expression in cocultured DCs. These results demonstrate that, in contrast to purified DCs, cross talk with lymphocytes downregulates SAMHD1 expression in DCs, triggering HIV-1 replication and an antiviral immune response. Therefore, HIV-1 replication and immune sensing by DCs should be investigated in more physiologically relevant models of DC/lymphocyte coculture.

IMPORTANCE
SAMHD1 restricts HIV-1 replication in dendritic cells (DCs). Here, we demonstrate that, in a coculture model of DCs and lymphocytes mimicking early mucosal HIV-1 infection, stimulation of HIV-1 replication in DCs is associated with downregulation of SAMHD1 expression and activation of innate immune sensing by DCs. We propose that DC-lymphocyte cross talk occurring
in vivo
modulates host restriction factor SAMHD1, promoting HIV-1 replication in cellular reservoirs and stimulating immune sensing.
Mouse Dipeptidyl Peptidase 4 Is Not a Functional Receptor for Middle East Respiratory Syndrome Coronavirus Infection
Authors: Cockrell Adam S. , Peck Kayla M. , Yount Boyd L. , Agnihothram Sudhakar S. , Scobey Trevor , Curnes Nicole R. , Baric Ralph S. , Heise Mark T. 
Published: February 2014

ABSTRACT
Human dipeptidyl peptidase 4 (hDPP4) was recently identified as the receptor for Middle East respiratory syndrome coronavirus (MERS-CoV) infection, suggesting that other mammalian DPP4 orthologs may also support infection. We demonstrate that mouse DPP4 cannot support MERS-CoV infection. However, employing mouse DPP4 as a scaffold, we identified two critical amino acids (A288L and T330R) that regulate species specificity in the mouse. This knowledge can support the rational design of a mouse-adapted MERS-CoV for rapid assessment of therapeutics.
ON CONTEXT-FREE LANGUAGES OF SCATTERED WORDS
Authors: ÉSIK ZOLTÁN , OKAWA SATOSHI 
Published: February 2014

It is known that if a Büchi context-free language (BCFL) consists of scattered words, then there is an integer n, depending only on the language, such that the Hausdorff rank of each word in the language is bounded by n. Every BCFL is a Muller context-free language (MCFL). In the first part of the paper, we prove that an MCFL of scattered words is a BCFL iff the rank of every word in the language is bounded by an integer depending only on the language.Then we establish operational characterizations of the BCFLs of well-ordered and scattered words. We prove that a language is a BCFL consisting of well-ordered words iff it can be generated from the singleton languages containing the letters of the alphabet by substitution into ordinary context-free languages and the ⍵-power operation. We also establish a corresponding result for BCFLs of scattered words and define expressions denoting BCFLs of well-ordered and scattered words. In the final part of the paper we give some applications.
The Entrepreneur's Dilemma: Case of TMT Toughened Glass Pvt. Ltd.
Authors: Amitabh Manu 
Published: February 2014

TMT Toughened Glass Company is in the glass processing industry. This industry requires a high level of innovation and expertise to process glass which is a very fragile and unworkable material. Customers typically want complete and technically sound solutions to their security, structural, design and architectural needs where glass is a material of choice. Shiv Prasad, the Managing Director of TMT Toughened Glass Company Pvt. Ltd., likes to call himself a “Glass Fabricator” and has been the pioneer in finding innovative solutions to glass processing needs in India. Tempering is the core process in this. Manufacturers of float glass are the suppliers and real estate developers and builders, automobile manufacturers and industrial appliance manufacturers are its buyers. Growth in this industry has been fuelled by the economic boom in India. The industry is largely unregulated. The number of players in the industry has increased to 40 in the same period from a mere 10. While the demand in the glass processing industry is growing at a steady rate of 30%, the capacity is growing at a compound annual growth rate of almost 80%. Prasad's competence is in engineering and design innovation. The dilemma he faces is whether to carry on with his time-tested strategy of innovation led growth or follow what other industry players are doing. Prasad has the option of concentrating his resources on doing what he does best — finding innovative solutions to the glass processing needs of his customers. The central question for Prasad is how to ensure that TMT Toughened Glass outperforms others on a sustained basis. Out of several options, this case explores the option of expanding the product line to include processed glass for the passenger car segment.
COSMOS Service Centre: Service Recovery Using Distribution Channels
Authors: Singh Ramendra , Jyothi Amer , Sinha Ashish , Agarwal Babita , Patro Arun 
Published: February 2014

COSMOS is a technology solutions provider offering IT infrastructure, personal computing and access devices, global services, imaging, and printing for consumers and enterprises. The company uses a mix of distribution channels (both online and offline) to deliver its products and services. COSMOS uses authorized intermediaries to increase offline reach — both for sales and service. To offer seamless customer service, COSMOS has a complaints website for customer logs. COSMOS service centres have well defined processes and policies to guide them in service delivery. However, this has not helped the case of Amer (the case protagonist), a business graduate student, who has faced multiple issues in service recovery after the purchase of his laptop from COSMOS. Why is Amer facing this slew of problems because of the service failure from COSMOS? Is it because of the negligence of B'Devlop, the COSMOS Service Centre or are COSMOS's policies and processes flawed? Can COSMOS offer a permanent solution to Amer's problems? How can COSMOS rectify the situation and prevent it from recurring? What should be the service recovery strategies for the company, and its distribution channel members that have a direct interface with the customers? These are some of the key questions that the case highlights, and can bring up for discussion in the classroom.