bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inference and Forecasting in the Age–Period–Cohort Model with Unknown Exposure with an Application to Mesothelioma Mortality
Authors: Martínez Miranda María Dolores , Nielsen Bent , Nielsen Jens Perch 
Published: February 2014

SummaryIt is of considerable interest to forecast future mesothelioma mortality. No measures for exposure are available so it is not straightforward to apply a dose–response model. It is proposed to model the counts of deaths directly by using a Poisson regression with an age–period–cohort structure, but without offset. Traditionally the age–period–cohort is viewed as suffering from an identification problem. It is shown how to reparameterize the model in terms of freely varying parameters, to avoid this problem. It is shown how to conduct inference and how to construct distribution forecasts.
Treatment of feline lymphoma using a 12‐week, maintenance‐free combination chemotherapy protocol in 26 cats
Authors: Limmer S. , Eberle N. , Nerschbach V. , Nolte I. , Betz D. 
Published: February 2014

AbstractThe aim of this prospective clinical trial was to investigate the efficacy and toxicity of a short‐term, maintenance‐free chemotherapy protocol in feline lymphoma. Twenty‐six cats with confirmed diagnosis of high‐/intermediate‐grade lymphoma were treated with a 12‐week protocol consisting of cyclic administration ofl‐asparaginase, vincristine, cyclophosphamide, doxorubicin and prednisolone. Complete (CR) and partial remission (PR) rates were 46 and 27%, respectively. Median duration of firstCRwas 394 days compared with a medianPRduration of 41 days. No factor was identified to significantly influence the likelihood to reachCR. Overall survival amounted to 78 days (range: 9–2230 days). Median survival inCRcats was 454 days and inPRcats was 82 days. Toxicosis was mainly low grade with anorexia seen most frequently. In cats achievingCR, maintenance‐free chemotherapy may be sufficient to attain long‐term remission and survival. Factors aiding in prognosticating the likelihood forCR, strategies enhancing response and targeting chemotherapy‐induced anorexia need to be identified in future.
Philippine English revisited
Authors: PEFIANCO MARTIN ISABEL 
Published: February 2014

ABSTRACTIn this paper, I argue that the Three Circles Model of Kachru, a profoundly influential and instructive model for approaching the varieties of Englishes across the world, might be re‐examined in the context of the Philippines, in order to better capture the sociolinguistic realities of Outer Circle speakers of English. Using the Philippines as an example, I hope to demonstrate that within the Outer Circle that is the Philippines, there are circles of English as well. While some educated Filipino scholars have rejected the dominance of American English in the Philippines, others remain ambivalent about the place of Philippine English in such domains such as English language teaching. And for a majority of the Filipinos, to whom English of whatever variety remains elusive and inaccessible, English is irrelevant. Thus, the situation for the Philippines is that there is an Inner Circle, an Outer Circle, and an Expanding circle of English. By presenting the Philippine experience of English through this framework of ‘circles within circles,’ I hope to offer a more nuanced position on the acceptability of Philippine English among Filipino users of the language.
English naming and code‐mixing in Thai mass media
Authors: SNODIN NAVAPORN SANPRASERT 
Published: February 2014

ABSTRACTThis paper examines the increasing role of English in the modern day mass media of Thailand, and the rapid increase in the use of English names and code‐mixing since the turn of the century. It provides a description of the present day phenomena of English naming and code‐mixing in both the broadcast and print media of Thailand. The paper also provides an assessment of the impact of English, which explains the adoption of English names or English‐Thai hybrids, and the assimilation of Western cultural dimensions by the indigenous population of Thailand, who use English as a foreign language. The intended audience of the mass media in this study are Thais. The data supports knowledge about the widespread use of English among users in the Expanding Circle, and about world Englishes as mixed codes that are used among people who share a common language, other than English, for their intranational communication.
Three‐dimensional x‐ray fluorescence mapping of a gold nanoparticle‐loaded phantom
Authors: Ren Liqiang , Wu Di , Li Yuhua , Wang Ge , Wu Xizeng , Liu Hong 
Published: February 2014

Purpose: X‐ray fluorescence (XRF) is a promising technique with sufficient specificity and sensitivity for identifying and quantifying features in small samples containing high atomic number (Z) materials such as iodine, gadolinium, and gold. In this study, the feasibility of applying XRF to early breast cancer diagnosis and treatment is studied using a novel approach for three‐dimensional (3D) x‐ray fluorescence mapping (XFM) of gold nanoparticle (GNP)‐loaded objects in a physical phantom at the technical level.Methods: All the theoretical analysis and experiments are conducted under the condition of using x‐ray pencil beam and a compactly integrated x‐ray spectrometer. The penetrability of the fluorescence x‐rays from GNPs is first investigated by adopting a combination of BR12 with 70 mm/50 mm in thickness on the excitation/emission path to mimic the possible position of tumor goldin vivo. Then, a physical phantom made of BR12 is designed to translate in 3D space with three precise linear stages and subsequently the step by step XFM scanning is performed. The experimental technique named as background subtraction is applied to isolate the gold fluorescence from each spectrum obtained by the spectrometer. Afterwards, the attenuations of both the incident primary x‐ray beam with energies beyond the gold K‐edge energy (80.725 keV) and the isolated gold Kα fluorescence x‐rays (65.99 −69.80 keV) acquired after background subtraction are well calibrated, and finally the unattenuated Kα fluorescence counts are used to realize mapping reconstruction and to describe the linear relationship between gold fluorescence counts and corresponding concentration of gold solutions.Results: The penetration results show that the goldKα fluorescence x‐rays have sufficient penetrability for this phantom study, and the reconstructed mapping results indicate that both the spatial distribution and relative concentration of GNPs within the designed BR12 phantom can be well identified and quantified.Conclusions: Although the XFM method in this investigation is still studied at the technical level and is not yet practical for routinein vivo mapping tasks with GNPs, the current penetrability measurements and phantom study strongly suggest the feasibility to establish and develop a 3D XFM system.
Suitability of markerless EPID tracking for tumor position verification in gated radiotherapy
Authors: Serpa Marco , Baier Kurt , Cremers Florian , Guckenberger Matthias , Meyer Juergen 
Published: February 2014

Purpose:To maximize the benefits of respiratory gated radiotherapy (RGRT) of lung tumors real‐time verification of the tumor position is required. This work investigates the feasibility of markerless tracking of lung tumors during beam‐on time in electronic portal imaging device (EPID) images of the MV therapeutic beam.Methods:EPID movies were acquired at ∼2 fps for seven lung cancer patients with tumor peak‐to‐peak motion ranges between 7.8 and 17.9 mm (mean: 13.7 mm) undergoing stereotactic body radiotherapy. The external breathing motion of the abdomen was synchronously measured. Both datasets were retrospectively analyzed inPortalTrack, an in‐house developed tracking software. The authors define a three‐step procedure to run the simulations: (1) gating window definition, (2) gated‐beam delivery simulation, and (3) tumor tracking. First, an amplitude threshold level was set on the external signal, defining the onset of beam‐on/‐off signals. This information was then mapped onto a sequence of EPID images to generate stamps of beam‐on/‐hold periods throughout the EPID movies in PortalTrack, by obscuring the frames corresponding to beam‐off times. Last, tumor motion in the superior‐inferior direction was determined on portal images by the tracking algorithm during beam‐on time. The residual motion inside the gating window as well as target coverage (TC) and the marginal target displacement (MTD) were used as measures to quantify tumor position variability.Results:Tumor position monitoring and estimation from beamˈs‐eye‐view images during RGRT was possible in 67% of the analyzed beams. For a reference gating window of 5 mm, deviations ranging from 2% to 86% (35% on average) were recorded between the reference and measured residual motion. TC (range: 62%–93%; mean: 77%) losses were correlated with false positives incidence rates resulting mostly from intra‐/inter‐beam baseline drifts, as well as sudden cycle‐to‐cycle fluctuations in exhale positions. Both phenomena can lead to considerable deviations (with MTD values up to a maximum of 7.8 mm) from the intended tumor position, and in turn may result in a marginal miss. The difference between tumor traces determined within the gating window against ground truth trajectory maps was 1.1 ± 0.7 mm on average (range: 0.4–2.3 mm).Conclusions:In this retrospective analysis of motion data, it is demonstrated that the system is capable of determining tumor positions in the plane perpendicular to the beam direction without the aid of fiducial markers, and may hence be suitable as an online verification tool in RGRT. It may be possible to use the tracking information to enable on‐the‐fly corrections to intra‐/inter‐beam variations by adapting the gating window by means of a robotic couch.
Towards clinical prostate ultrasound elastography using full inversion approach
Authors: Mousavi Seyed Reza , Sadeghi‐Naini Ali , Czarnota Gregory J. , Samani Abbas 
Published: February 2014

Purpose:Various types of cancers including prostate cancer are known to be associated with biological changes that lead to tissue stiffening. Digital rectal examination is based on manually palpating the prostate tissue via the rectum. This test lacks sufficient accuracy required for early diagnosis which is necessary for effective management of prostate cancer. To develop an effective prostate cancer diagnostic technique, the authors propose an imaging technique that maps the distribution of the relative prostate tissueˈs elasticity modulus. Unlike digital rectal examination, this technique is quantitative, capable of accurately detecting small prostate lesions that cannot be sensed by manual palpation, and its accuracy is independent of the physicianˈs experience.Methods:The proposed technique is a quasistatic elastography technique which uses ultrasound imaging to acquire tissue displacements resulting from transrectal ultrasound mechanical stimulation. The system involves a standard ultrasound imaging unit with accessibility to its radiofrequency data. The displacements are used as data for the tissue elasticity reconstruction. This reconstruction does not require tissue segmentation and is based on physics governing tissue mechanics. It is formulated using an inverse problem framework where elastic tissue deformation equations are fully inverted using an iterative scheme where each iteration involves stress calculation followed by elastic modulus updating until convergence is achieved.In silico and tissue mimicking phantom studies were conducted to validate the proposed technique, followed by a clinical pilot study involving two prostate cancer patients with whole‐mount histopathology analysis on prostatectomy specimens to confirm a cancer location.Results:The phantom studies demonstrated robustness and reasonably high accuracy of the proposed method. Obtained Youngˈs modulus ratios indicated reconstruction errors of less than 12%. Reconstructed elastic modulus images of the two clinical cases were compared to whole‐mount histopathology slides where cancerous areas were identified. This comparison indicated marked tissue stiffening in the cancer area with reasonably accurate consistency observed between cancerous lesions identified by histopathology and high stiffness areas of the elastography images.Conclusions:Results obtained from the phantom and patient studies indicate that the proposed method is reasonably accurate for detecting cancerous lesions. The proposed system does not require any additional hardware attachment for mechanical stimulation or data acquisition while the elasticity reconstruction algorithm can be easily implemented, leading to a low cost system that can be potentially utilized as an effective clinical tool for prostate cancer diagnosis.
Combination Therapy with Tamoxifen and Amphotericin B in Experimental Cutaneous Leishmaniasis
Authors: Trinconi Cristiana T. , Reimão Juliana Q. , Yokoyama-Yasunaka Jenicer K. U. , Miguel Danilo C. , Uliana Silvia R. B. 
Published: February 2014

ABSTRACT

Leishmaniasis chemotherapy remains very challenging. The high cost of active drugs, along with the severity of their side effects and the increasing failure rate of the current therapeutic schemes, calls for the discovery of new active drugs and schemes of treatment. The use of combination therapy has gained much attention in recent years as a possible strategy for overcoming the various shortcomings in the present arsenal. We recently described the effectiveness of tamoxifen in murine models of leishmaniasis, and here, we investigated the interactions between tamoxifen and amphotericin B, one of the most potent drugs used in leishmaniasis treatment. The
in vitro
interactions were indifferent for the association of tamoxifen and amphotericin B. The association was also assayed
in vivo
in
Leishmania amazonensis
-infected BALB/c mice and was found to yield at least additive effects at low doses of both drugs.
Role of Malic Enzyme during Fatty Acid Synthesis in the Oleaginous Fungus Mortierella alpina
Authors: Hao Guangfei , Chen Haiqin , Wang Lei , Gu Zhennan , Song Yuanda , Zhang Hao , Chen Wei , Chen Yong Q. 
Published: February 2014

ABSTRACT

The generation of NADPH by malic enzyme (ME) was postulated to be a rate-limiting step during fatty acid synthesis in oleaginous fungi, based primarily on the results from research focusing on ME in
Mucor circinelloides
. This hypothesis is challenged by a recent study showing that leucine metabolism, rather than ME, is critical for fatty acid synthesis in
M. circinelloides
. To clarify this, the gene encoding ME isoform E from
Mortierella alpina
was homologously expressed. ME overexpression increased the fatty acid content by 30% compared to that for a control. Our results suggest that ME may not be the sole rate-limiting enzyme, but does play a role, during fatty acid synthesis in oleaginous fungi.
Synergism of Glycoside Hydrolase Secretomes from Two Thermophilic Bacteria Cocultivated on Lignocellulose
Authors: Zhang Kundi , Chen Xiaohua , Schwarz Wolfgang H. , Li Fuli 
Published: February 2014

ABSTRACT

Two cellulolytic thermophilic bacterial strains, CS-3-2 and CS-4-4, were isolated from decayed cornstalk by the addition of growth-supporting factors to the medium. According to 16S rRNA gene-sequencing results, these strains belonged to the genus
Clostridium
and showed 98.87% and 98.86% identity with
Clostridium
stercorarium
subsp.
leptospartum
ATCC 35414
T
and
Clostridium
cellulosi
AS 1.1777
T
, respectively. The endoglucanase and exoglucanase activities of strain CS-4-4 were approximately 3 to 5 times those of strain CS-3-2, whereas the β-glucosidase activity of strain CS-3-2 was 18 times higher than that of strain CS-4-4. The xylanase activity of strain CS-3-2 was 9 times that of strain CS-4-4, whereas the β-xylosidase activity of strain CS-4-4 was 27 times that of strain CS-3-2. The enzyme activities in spent cultures following cocultivation of the two strains with cornstalk as the substrate were much greater than those in pure cultures or an artificial mixture of samples, indicating synergism of glycoside hydrolase secretomes between the two strains. Quantitative measurement of the two strains in the cocultivation system indicated that strain CS-3-2 grew robustly during the initial stages, whereas strain CS-4-4 dominated the system in the late-exponential phase. Liquid chromatography-tandem mass spectrometry analysis of protein bands appearing in the native zymograms showed that ORF3880 and ORF3883 from strain CS-4-4 played key roles in the lignocellulose degradation process. Both these open reading frames (ORFs) exhibited endoglucanase and xylanase activities, but ORF3880 showed tighter adhesion to insoluble substrates at 4, 25, and 60°C owing to its five carbohydrate-binding modules (CBMs).
Carbon Dioxide Fixation by Metallosphaera yellowstonensis and Acidothermophilic Iron-Oxidizing Microbial Communities from Yellowstone National Park
Authors: Jennings Ryan M. , Whitmore Laura M. , Moran James J. , Kreuzer Helen W. , Inskeep William P. 
Published: February 2014

ABSTRACT

The fixation of inorganic carbon has been documented in all three domains of life and results in the biosynthesis of diverse organic compounds that support heterotrophic organisms. The primary aim of this study was to assess carbon dioxide fixation in high-temperature Fe(III)-oxide mat communities and in pure cultures of a dominant Fe(II)-oxidizing organism (
Metallosphaera yellowstonensis
strain MK1) originally isolated from these environments. Protein-encoding genes of the complete 3-hydroxypropionate/4-hydroxybutyrate (3-HP/4-HB) carbon dioxide fixation pathway were identified in
M. yellowstonensis
strain MK1. Highly similar
M. yellowstonensis
genes for this pathway were identified in metagenomes of replicate Fe(III)-oxide mats, as were genes for the reductive tricarboxylic acid cycle from
Hydrogenobaculum
spp. (
Aquificales
). Stable-isotope (
13
CO
2
) labeling demonstrated CO
2
fixation by
M. yellowstonensis
strain MK1 and in
ex situ
assays containing live Fe(III)-oxide microbial mats. The results showed that strain MK1 fixes CO
2
with a fractionation factor of ∼2.5‰. Analysis of the
13
C composition of dissolved inorganic C (DIC), dissolved organic C (DOC), landscape C, and microbial mat C showed that mat C is from both DIC and non-DIC sources. An isotopic mixing model showed that biomass C contains a minimum of 42% C of DIC origin, depending on the fraction of landscape C that is present. The significance of DIC as a major carbon source for Fe(III)-oxide mat communities provides a foundation for examining microbial interactions that are dependent on the activity of autotrophic organisms (i.e.,
Hydrogenobaculum
and
Metallosphaera
spp.) in simplified natural communities.
Cerecidins, Novel Lantibiotics from Bacillus cereus with Potent Antimicrobial Activity
Authors: Wang Jian , Zhang Li , Teng Kunling , Sun Shutao , Sun Zhizeng , Zhong Jin 
Published: February 2014

ABSTRACT

Lantibiotics are ribosomally synthesized and posttranslationally modified antimicrobial peptides that are widely produced by Gram-positive bacteria, including many species of the
Bacillus
group. In the present study, one novel gene cluster coding lantibiotic cerecidins was unveiled in
Bacillus cereus
strain As 1.1846 through genomic mining and PCR screening. The designated
cer
locus is different from that of conventional class II lantibiotics in that it included seven tandem precursor
cerA
genes, one modification gene (
cerM
), two processing genes (
cerT
and
cerP
), one orphan regulator gene (
cerR
), and two immunity genes (
cerF
and
cerE
). In addition, one unprecedented quorum sensing component,
comQXPA
, was inserted between
cerM
and
cerR
. The expression of cerecidins was not detected in this strain of
B. cereus
, which might be due to repressed transcription of
cerM
. We constitutively coexpressed
cerA
genes and
cerM
in
Escherichia coli
, and purified precerecidins were proteolytically processed with the endoproteinase GluC and a truncated version of putative serine protease CerP. Thus, two natural variants of cerecidins A1 and A7 were obtained which contained two terminal nonoverlapping thioether rings rarely found in lantibiotics. Both cerecidins A1 and A7 were active against a broad spectrum of Gram-positive bacteria. Cerecidin A7, especially its mutant Dhb13A, showed remarkable efficacy against multidrug-resistant
Staphylococcus aureus
(MDRSA), vancomycin-resistant
Enterococcus faecalis
(VRE), and even
Streptomyces
.
Specific Microbial Attachment to Root Knot Nematodes in Suppressive Soil
Authors: Adam Mohamed , Westphal Andreas , Hallmann Johannes , Heuer Holger 
Published: February 2014

ABSTRACT

Understanding the interactions of plant-parasitic nematodes with antagonistic soil microbes could provide opportunities for novel crop protection strategies. Three arable soils were investigated for their suppressiveness against the root knot nematode
Meloidogyne hapla
. For all three soils,
M. hapla
developed significantly fewer galls, egg masses, and eggs on tomato plants in unsterilized than in sterilized infested soil. Egg numbers were reduced by up to 93%. This suggested suppression by soil microbial communities. The soils significantly differed in the composition of microbial communities and in the suppressiveness to
M. hapla
. To identify microorganisms interacting with
M. hapla
in soil, second-stage juveniles (J2) baited in the test soil were cultivation independently analyzed for attached microbes. PCR-denaturing gradient gel electrophoresis of fungal ITS or 16S rRNA genes of bacteria and bacterial groups from nematode and soil samples was performed, and DNA sequences from J2-associated bands were determined. The fingerprints showed many species that were abundant on J2 but not in the surrounding soil, especially in fungal profiles. Fungi associated with J2 from all three soils were related to the genera
Davidiella
and
Rhizophydium
, while the genera
Eurotium
,
Ganoderma
, and
Cylindrocarpon
were specific for the most suppressive soil. Among the 20 highly abundant operational taxonomic units of bacteria specific for J2 in suppressive soil, six were closely related to infectious species such as
Shigella
spp., whereas the most abundant were
Malikia spinosa
and
Rothia amarae
, as determined by 16S rRNA amplicon pyrosequencing. In conclusion, a diverse microflora specifically adhered to J2 of
M. hapla
in soil and presumably affected female fecundity.
A New Subfamily of Polyphosphate Kinase 2 (Class III PPK2) Catalyzes both Nucleoside Monophosphate Phosphorylation and Nucleoside Diphosphate Phosphorylation
Authors: Motomura Kei , Hirota Ryuichi , Okada Mai , Ikeda Takeshi , Ishida Takenori , Kuroda Akio 
Published: February 2014

ABSTRACT

Inorganic polyphosphate (polyP) is a linear polymer of tens to hundreds of phosphate (P
i
) residues linked by “high-energy” phosphoanhydride bonds as in ATP. PolyP kinases, responsible for the synthesis and utilization of polyP, are divided into two families (PPK1 and PPK2) due to differences in amino acid sequence and kinetic properties. PPK2 catalyzes preferentially polyP-driven nucleotide phosphorylation (utilization of polyP), which is important for the survival of microbial cells under conditions of stress or pathogenesis. Phylogenetic analysis suggested that the PPK2 family could be divided into three subfamilies (classes I, II, and III). Class I and II PPK2s catalyze nucleoside diphosphate and nucleoside monophosphate phosphorylation, respectively. Here, we demonstrated that class III PPK2 catalyzes both nucleoside monophosphate and nucleoside diphosphate phosphorylation, thereby enabling us to synthesize ATP from AMP by a single enzyme. Moreover, class III PPK2 showed broad substrate specificity over purine and pyrimidine bases. This is the first demonstration that class III PPK2 possesses both class I and II activities.