bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Modified Migrating Bird Optimization For University Course Timetabling Problem
Authors: Way Shen Lam , Asmuni Hishammuddin , Cheng Weng Fong 
Published: January 2015

University course timetabling problem is a dilemma which educational institutions are facing due to various demands to be achieved in limited resources. Migrating bird optimization (MBO) algorithm is a new meta-heuristic algorithm which is inspired by flying formation of migrating birds. It has been applied successfully in tackling quadratic assignment problem and credit cards fraud detection problem. However, it was reported that MBO will get stuck in local optima easily. Therefore, a modified migrating bird optimization algorithm is proposed to solve post enrolment-based course timetabling. An improved neighbourhood sharing mechanism is used with the aim of escaping from local optima. Besides that, iterated local search is selected to be hybridized with the migrating bird optimization in order to further enhance its exploitation ability. The proposed method was tested using Socha’s benchmark datasets. The experimental results show that the proposed method outperformed the basic MBO and it is capable of producing comparable results as compared with existing methods that have been presented in literature. Indeed, the proposed method is capable of addressing university course timetabling problem and promising results were obtained.
Age‐related changes to cardiac systolic and diastolic function during whole‐body passive hyperthermia
Authors: Lucas Rebekah A. I. , Sarma Satyam , Schlader Zachary J. , Pearson James , Crandall Craig G. 
Published: January 2015

New Findings
What is the central question of this study?
The effect of ageing on hyperthermia‐induced changes in cardiac function is unknown.

What is the main finding and its importance?
Using echocardiography, we show that during hyperthermia the systolic and diastolic function can be appropriately augmented to meet cardiac demand in healthy older adults, although overall age‐related impairments remain. One exception was late diastolic ventricular filling [i.e. E/A ratio and A/(A + E) ratio], which in the older adults was not further augmented during hyperthermia, unlike their young counterparts. To meet cardiac demand, therefore, healthy older adults appear to depend on an increased left ventricular systolic strain and proportion of their cardiac reserve.

The effect of ageing on hyperthermia‐induced changes in cardiac function is unknown. This study tested the hypothesis that hyperthermia‐induced changes in left ventricular systolic and diastolic function are attenuated in older adults when compared with young adults. Eight older (71 ± 5 years old) and eight young adults (29 ± 5 years old), matched for sex, physical activity and body mass index, underwent whole‐body passive hyperthermia. Mean arterial pressure (Finometer Pro), heart rate, forearm vascular conductance (venous occlusion plethysmography) and echocardiographic indices of diastolic and systolic function were measured during a normothermic supine period and again after an increase in internal temperature of ∼1.0 °C. Hyperthermia decreased mean arterial pressure and left ventricular end‐diastolic volumes and increased heart rate to a similar extent in both groups (P > 0.05). Ageing did not alter the magnitude of hyperthermia‐induced changes in indices of systolic (lateral mitral annular S′ velocity) or diastolic function (lateral mitral annular E′ velocity, peak early diastolic filling and isovolumic relaxation time; P > 0.05). However, with hyperthermia the global longitudinal systolic strain increased in the older group, but was unchanged in the young group (P = 0.03). Also, older adults were unable to augment late diastolic ventricular filling [i.e. E/A ratio and A/(A + E) ratio] during hyperthermia, unlike the young (P < 0.05). These findings indicate that older adults depend on a greater systolic contribution (global longitudinal systolic strain) to meet hyperthermic demand and that the atrial contribution to diastolic filling was not further augmented in older adults when compared with young adults.
Discovery of CLC transport proteins: cloning, structure, function and pathophysiology
Authors: Jentsch Thomas J. 
Published: January 2015

AbstractAfter providing a personal description of the convoluted path leading 25 years ago to the molecular identification of the Torpedo Cl− channel ClC‐0 and the discovery of the CLC gene family, I succinctly describe the general structural and functional features of these ion transporters before giving a short overview of mammalian CLCs. These can be categorized into plasma membrane Cl− channels and vesicular Cl−/H+‐exchangers. They are involved in the regulation of membrane excitability, transepithelial transport, extracellular ion homeostasis, endocytosis and lysosomal function. Diseases caused by CLC dysfunction include myotonia, neurodegeneration, deafness, blindness, leukodystrophy, male infertility, renal salt loss, kidney stones and osteopetrosis, revealing a surprisingly broad spectrum of biological roles for chloride transport that was unsuspected when I set out to clone the first voltage‐gated chloride channel.
Toward adaptive radiotherapy for head and neck patients: Uncertainties in dose warping due to the choice of deformable registration algorithm
Authors: Veiga Catarina , Lourenço Ana Mónica , Mouinuddin Syed , van Herk Marcel , Modat Marc , Ourselin Sébastien , Royle Gary , McClelland Jamie R. 
Published: January 2015

Purpose:The aims of this work were to evaluate the performance of several deformable image registration (DIR) algorithms implemented in our in‐house software (NiftyReg) and the uncertainties inherent to using different algorithms for dose warping.Methods:The authors describe a DIR based adaptive radiotherapy workflow, using CT and cone‐beam CT (CBCT) imaging. The transformations that mapped the anatomy between the two time points were obtained using four different DIR approaches available in NiftyReg. These included a standard unidirectional algorithm and more sophisticated bidirectional ones that encourage or ensure inverse consistency. The forward (CT‐to‐CBCT) deformation vector fields (DVFs) were used to propagate the CT Hounsfield units and structures to the daily geometry for “dose of the day” calculations, while the backward (CBCT‐to‐CT) DVFs were used to remap the dose of the day onto the planning CT (pCT). Data from five head and neck patients were used to evaluate the performance of each implementation based on geometrical matching, physical properties of the DVFs, and similarity between warped dose distributions. Geometrical matching was verified in terms of dice similarity coefficient (DSC), distance transform, false positives, and false negatives. The physical properties of the DVFs were assessed calculating the harmonic energy, determinant of the Jacobian, and inverse consistency error of the transformations. Dose distributions were displayed on the pCT dose space and compared using dose difference (DD), distance to dose difference, and dose volume histograms.Results:All the DIR algorithms gave similar results in terms of geometrical matching, with an average DSC of 0.85 ± 0.08, but the underlying properties of the DVFs varied in terms of smoothness and inverse consistency. When comparing the doses warped by different algorithms, we found a root mean square DD of 1.9% ± 0.8% of the prescribed dose (pD) and that an average of 9% ± 4% of voxels within the treated volume failed a 2%pD DD‐test (DD2%‐pp). Larger DD2%‐pp was found within the high dose gradient (21% ± 6%) and regions where the CBCT quality was poorer (28% ± 9%). The differences when estimating the mean and maximum dose delivered to organs‐at‐risk were up to 2.0%pD and 2.8%pD, respectively.Conclusions:The authors evaluated several DIR algorithms for CT‐to‐CBCT registrations. In spite of all methods resulting in comparable geometrical matching, the choice of DIR implementation leads to uncertainties in dose warped, particularly in regions of high gradient and/or poor imaging quality.
Marine defaunation: Animal loss in the global ocean
Authors: McCauley Douglas J. , Pinsky Malin L. , Palumbi Stephen R. , Estes James A. , Joyce Francis H. , Warner Robert R. 
Published: January 2015

Marine animals are disappearing, tooThe loss of animal species in terrestrial environments has been well documented and is continuing. Loss of species in marine environments has been slower than in terrestrial systems, but appears to be increasing rapidly. McCauleyet al.review the recent patterns of species decline and loss in marine environments. Though they note many worrying declines, they also highlight approaches that might allow us to prevent the type of massive defaunation that has occurred on land.Science, this issue10.1126/science.1255641
Reduced El Niño–Southern Oscillation during the Last Glacial Maximum
Authors: Ford Heather L. , Ravelo A. Christina , Polissar Pratigya J. 
Published: January 2015

A new tilt on predicting future ENSO variability
A new finding should improve the ability of climate models to predict the behavior of the El Niño–Southern Oscillation (ENSO) in a warmer future. Ford et al. looked at the distribution of surface and subsurface temperatures in the eastern and western equatorial Pacific 19,000 years ago and between 3000 and 6000 years ago. Temperatures fluctuated over a greater range during the older period. ENSO thus depended more on the tilt of the equatorial Pacific thermocline than on the east-to-west temperature gradient, as previously thought.

Science
, this issue p.
255
Long-Term Immunogenicity of an Inactivated Split-Virion 2009 Pandemic Influenza A H1N1 Virus Vaccine with or without Aluminum Adjuvant in Mice
Authors: Xu Wenting , Zheng Mei , Zhou Feng , Chen Ze 
Published: January 2015

ABSTRACTIn 2009, a global epidemic of influenza A(H1N1) virus caused the death of tens of thousands of people. Vaccination is the most effective means of controlling an epidemic of influenza and reducing the mortality rate. In this study, the long-term immunogenicity of influenza A/California/7/2009 (H1N1) split vaccine was observed as long as 15 months (450 days) after immunization in a mouse model. Female BALB/c mice were immunized intraperitoneally with different doses of aluminum-adjuvanted vaccine. The mice were challenged with a lethal dose (10× 50% lethal dose [LD50]) of homologous virus 450 days after immunization. The results showed that the supplemented aluminum adjuvant not only effectively enhanced the protective effect of the vaccine but also reduced the immunizing dose of the vaccine. In addition, the aluminum adjuvant enhanced the IgG antibody level of mice immunized with the H1N1 split vaccine. The IgG level was correlated to the survival rate of the mice. Aluminum-adjuvanted inactivated split-virion 2009 pandemic influenza A H1N1 vaccine has good immunogenicity and provided long-term protection against lethal influenza virus challenge in mice.
Mapping Antigenic Motifs in the Trypomastigote Small Surface Antigen from Trypanosoma cruzi
Authors: Balouz Virginia , Cámara María de los Milagros , Cánepa Gaspar E. , Carmona Santiago J. , Volcovich Romina , Gonzalez Nicolás , Altcheh Jaime , Agüero Fernán , Buscaglia Carlos A. 
Published: January 2015

ABSTRACTThe trypomastigote small surface antigen (TSSA) is a mucin-like molecule fromTrypanosoma cruzi, the etiological agent of Chagas disease, which displays amino acid polymorphisms in parasite isolates. TSSA expression is restricted to the surface of infective cell-derived trypomastigotes, where it functions as an adhesin and engages surface receptors on the host cell as a prerequisite for parasite internalization. Previous results have established TSSA-CL, the isoform encoded by the CL Brener clone, as an appealing candidate for use in serology-based diagnostics for Chagas disease. Here, we used a combination of peptide- and recombinant protein-based tools to map the antigenic structure of TSSA-CL at maximal resolution. Our results indicate the presence of different partially overlapping B-cell epitopes clustering in the central portion of TSSA-CL, which contains most of the polymorphisms found in parasite isolates. Based on these results, we assessed the serodiagnostic performance of a 21-amino-acid-long peptide that spans TSSA-CL major antigenic determinants, which was similar to the performance of the previously validated glutathioneS-transferase (GST)-TSSA-CL fusion molecule. Furthermore, the tools developed for the antigenic characterization of the TSSA antigen were also used to explore other potential diagnostic applications of the anti-TSSA humoral response in Chagasic patients. Overall, our present results provide additional insights into the antigenic structure of TSSA-CL and support this molecule as an excellent target for molecular intervention in Chagas disease.
Quest for Correlates of Protection against Tuberculosis
Authors: Bhatt Kamlesh , Verma Sheetal , Ellner Jerrold J. , Salgame Padmini 
Published: January 2015

ABSTRACTA major impediment to tuberculosis (TB) vaccine development is the lack of reliable correlates of immune protection or biomarkers that would predict vaccine efficacy. Gamma interferon (IFN-γ) produced by CD4+T cells and, recently, multifunctional CD4+T cells secreting IFN-γ, tumor necrosis factor (TNF), and interleukin-2 (IL-2) have been used in vaccine studies as a measurable immune parameter, reflecting activity of a vaccine and potentially predicting protection. However, accumulating experimental evidence suggests that host resistance againstMycobacterium tuberculosisinfection is independent of IFN-γ and TNF secretion from CD4+T cells. Furthermore, the booster vaccine MVA85A, despite generating a high level of multifunctional CD4+T cell response in the host, failed to confer enhanced protection in vaccinated subjects. These findings suggest the need for identifying reliable correlates of protection to determine the efficacy of TB vaccine candidates. This article focuses on alternative pathways that mediateM. tuberculosiscontrol and their potential for serving as markers of protection. The review also discusses the significance of investigating the natural human immune response toM. tuberculosisto identify the correlates of protection in vaccination.
Contribution of the BacT/Alert MB Mycobacterium Bottle to Bloodstream Infection Surveillance in Thailand: Added Yield for Burkholderia pseudomallei
Authors: Jorakate Possawat , Higdon Melissa , Kaewpan Anek , Makprasert Sirirat , Yuenprakhon Somkhit , Tawisaid Kittisak , Dejsirilert Surang , Whistler Toni , Baggett Henry C. 
Published: January 2015

ABSTRACT

Community-acquired bloodstream infections cause substantial morbidity and mortality worldwide, but microbiology capacity and surveillance limitations have challenged good descriptions of pathogen distribution in many regions, including Southeast Asia. Active surveillance for bloodstream infections has been conducted in two rural Thailand provinces for >7 years. Blood specimens were divided into two culture bottles, one optimized for aerobic growth (F bottle) and a second for enhanced growth of mycobacteria (MB bottle), and processed with the BactT/Alert 3D system. Because the routine use of MB culture bottles is resource intensive (expensive and requires prolonged incubation), we assessed the added yield of MB bottles by comparing the proportion of pathogens detected by MB versus that by F bottles from 2005 to 2012. Of 63,066 blood cultures, 7,296 (12%) were positive for at least one pathogen; the most common pathogens were
Escherichia coli
(28%),
Burkholderia pseudomallei
(11%),
Klebsiella pneumoniae
(9%), and
Staphylococcus aureus
(6%). Two bottles improved the yield overall, but the added yield attributable to the MB bottles was limited to a few pathogens. In addition to the detection of mycobacteria and some fungi, MB bottles improved the detection of
B. pseudomallei
(27% [MB] versus 8% [F];
P
< 0.0001), with added benefit if therapy was initiated prior to the blood culture. The targeted use of MB bottles is warranted for patients at risk for mycobacterial and fungal infections and for infection with
B. pseudomallei
, a common cause of septicemia in Thailand.
Multicenter Evaluation of the BioFire FilmArray Gastrointestinal Panel for Etiologic Diagnosis of Infectious Gastroenteritis
Authors: Buss Sarah N. , Leber Amy , Chapin Kimberle , Fey Paul D. , Bankowski Matthew J. , Jones Matthew K. , Rogatcheva Margarita , Kanack Kristen J. , Bourzac Kevin M. 
Published: January 2015

ABSTRACT

The appropriate treatment and control of infectious gastroenteritis depend on the ability to rapidly detect the wide range of etiologic agents associated with the disease. Clinical laboratories currently utilize an array of different methodologies to test for bacterial, parasitic, and viral causes of gastroenteritis, a strategy that suffers from poor sensitivity, potentially long turnaround times, and complicated ordering practices and workflows. Additionally, there are limited or no testing methods routinely available for most diarrheagenic
Escherichia coli
strains, astroviruses, and sapoviruses. This study assessed the performance of the FilmArray Gastrointestinal (GI) Panel for the simultaneous detection of 22 different enteric pathogens directly from stool specimens:
Campylobacter
spp.,
Clostridium difficile
(toxin A/B),
Plesiomonas shigelloides
,
Salmonella
spp.,
Vibrio
spp.,
Vibrio cholerae
,
Yersinia enterocolitica
, enteroaggregative
E. coli
, enteropathogenic
E. coli
, enterotoxigenic
E. coli
, Shiga-like toxin-producing
E. coli
(
stx
1
and
stx
2
) (including specific detection of
E. coli
O157),
Shigella
spp./enteroinvasive
E. coli
,
Cryptosporidium
spp.,
Cyclospora cayetanensis
,
Entamoeba histolytica
,
Giardia lamblia
, adenovirus F 40/41, astrovirus, norovirus GI/GII, rotavirus A, and sapovirus. Prospectively collected stool specimens (
n
= 1,556) were evaluated using the BioFire FilmArray GI Panel and tested with conventional stool culture and molecular methods for comparison. The FilmArray GI Panel sensitivity was 100% for 12/22 targets and ≥94.5% for an additional 7/22 targets. For the remaining three targets, sensitivity could not be calculated due to the low prevalences in this study. The FilmArray GI Panel specificity was ≥97.1% for all panel targets. The FilmArray GI Panel provides a comprehensive, rapid, and streamlined alternative to conventional methods for the etiologic diagnosis of infectious gastroenteritis in the laboratory setting. The potential advantages include improved performance parameters, a more extensive menu of pathogens, and a turnaround time of as short as 1 h.
Detection of a Transient R292K Mutation in Influenza A/H3N2 Viruses Shed for Several Weeks by an Immunocompromised Patient
Authors: Babady N. Esther , Laplante Jennifer M. , Tang Yi-Wei , St. George Kirsten 
Published: January 2015

ABSTRACTWe describe the case of an immunocompromised patient, positive for influenza A virus (H3N2), in whom the neuraminidase R292K mutation was transiently detected during oseltamivir treatment. The R292K mutation was identified by direct testing in 3 of 11 respiratory specimens collected throughout the patient's illness but in none of the cultures from those specimens.
Detection of Mycobacteria, Mycobacterium avium Subspecies, and Mycobacterium tuberculosis Complex by a Novel Tetraplex Real-Time PCR Assay
Authors: Sevilla Iker A. , Molina Elena , Elguezabal Natalia , Pérez Valentín , Garrido Joseba M. , Juste Ramón A. 
Published: January 2015

ABSTRACT

Mycobacterium tuberculosis
complex,
Mycobacterium avium
, and many other nontuberculous mycobacteria are worldwide distributed microorganisms of major medical and veterinary importance. Considering the growing epidemiologic significance of wildlife-livestock-human interrelation, developing rapid detection tools of high specificity and sensitivity is vital to assess their presence and accelerate the process of diagnosing mycobacteriosis. Here we describe the development and evaluation of a novel tetraplex real-time PCR for simultaneous detection of
Mycobacterium
genus,
M. avium
subspecies, and
M. tuberculosis
complex in an internally monitored single assay. The method was evaluated using DNA from mycobacterial (
n
= 38) and nonmycobacterial (
n
= 28) strains, tissues spiked with different CFU amounts of three mycobacterial species (
n
= 57), archival clinical samples (
n
= 233), and strains isolated from various hosts (
n
= 147). The minimum detectable DNA amount per reaction was 50 fg for
M. bovis
BCG and
M. kansasii
and 5 fg for
M. avium
subsp.
hominissuis
. When spiked samples were analyzed, the method consistently detected as few as 100 to 1,000 mycobacterial CFU per gram. The sensitivity and specificity values for the panel of clinical samples were 97.5 and 100% using a verified culture-based method as the reference method. The assays performed on clinical isolates confirmed these results. This PCR was able to identify
M. avium
and
M. tuberculosis
complex in the same sample in one reaction. In conclusion, the tetraplex real-time PCR we designed represents a highly specific and sensitive tool for the detection and identification of mycobacteria in routine laboratory diagnosis with potential additional uses.
Defining the Phylogenomics of Shigella Species: a Pathway to Diagnostics
Authors: Sahl Jason W. , Morris Carolyn R. , Emberger Jennifer , Fraser Claire M. , Ochieng John Benjamin , Juma Jane , Fields Barry , Breiman Robert F. , Gilmour Matthew , Nataro James P. , Rasko David A. 
Published: January 2015

ABSTRACT

Shigellae cause significant diarrheal disease and mortality in humans, as there are approximately 163 million episodes of shigellosis and 1.1 million deaths annually. While significant strides have been made in the understanding of the pathogenesis, few studies on the genomic content of the
Shigella
species have been completed. The goal of this study was to characterize the genomic diversity of
Shigella
species through sequencing of 55 isolates representing members of each of the four
Shigella
species:
S. flexneri
,
S. sonnei
,
S. boydii
, and
S. dysenteriae
. Phylogeny inferred from 336 available
Shigella
and
Escherichia coli
genomes defined exclusive clades of
Shigella
; conserved genomic markers that can identify each clade were then identified. PCR assays were developed for each clade-specific marker, which was combined with an amplicon for the conserved
Shigella
invasion antigen, IpaH3, into a multiplex PCR assay. This assay demonstrated high specificity, correctly identifying 218 of 221 presumptive
Shigella
isolates, and sensitivity, by not identifying any of 151 diverse
E. coli
isolates incorrectly as
Shigella
. This new phylogenomics-based PCR assay represents a valuable tool for rapid typing of uncharacterized
Shigella
isolates and provides a framework that can be utilized for the identification of novel genomic markers from genomic data.
Overlapping Local and Long-Range RNA-RNA Interactions Modulate Dengue Virus Genome Cyclization and Replication
Authors: de Borba Luana , Villordo Sergio M. , Iglesias Nestor G. , Filomatori Claudia V. , Gebhard Leopoldo G. , Gamarnik Andrea V. 
Published: January 2015

ABSTRACT

The dengue virus genome is a dynamic molecule that adopts different conformations in the infected cell. Here, using RNA folding predictions, chemical probing analysis, RNA binding assays, and functional studies, we identified new
cis
-acting elements present in the capsid coding sequence that facilitate cyclization of the viral RNA by hybridization with a sequence involved in a local dumbbell structure at the viral 3′ untranslated region (UTR). The identified interaction differentially enhances viral replication in mosquito and mammalian cells.