bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gluten‐induced cognitive impairment (“brain fog”) in coeliac disease
Authors: Yelland Gregory W 
Published: February 2017

AbstractMuch is known about the serious neurological effects of gluten ingestion in coeliac disease patients, such as sporadic ataxia and peripheral neuropathy, although the causal links to gluten are still under debate. However, such disorders are observed in only a small percentage of coeliac patients. Much less is known about the transient cognitive impairments to memory, attention, executive function, and the speed of cognitive processing reported by the majority of patients with coeliac disease. These mild degradations of cognitive functions, referred to as “brain fog,” are yet to be formally recognized as a medical or psychological condition. However, subtle tests of cognitive function are measurable in untreated patients with coeliac disease and improve over the first 12 months' therapy with a gluten‐free diet. Such deficits also occur in patients with Crohn's disease, particularly in association with systemic inflammatory activity. Thus, cognitive impairments associated with brain fog are psychologically and neurologically real and improve with adherence to a gluten‐free diet. There is not yet sufficient evidence to provide a definitive account of the mechanism by which gluten ingestion causes the impairments to cognitive function associated with brain fog, but current evidence suggests that it is more likely that the causal factor is not directly related to exposure to gluten.
Presumed primary immune‐mediated neutropenia in 35 dogs: a retrospective study
Authors: Devine L. , Armstrong P. J. , Whittemore J. C. , Sharkey L. , Bailiff N. , Huang A. , Rishniw M. 
Published: February 2017

ObjectivesTo describe, in a cohort of dogs with presumed primary immune‐mediated neutropenia, the presenting clinical characteristics, haematology results, bone marrow characteristics, therapies used (drugs and doses), clinical response to treatment, relapse and outcome at six months and one year.MethodsMulti‐institutional recruited retrospective descriptive case series with voluntary submissions. Presumed immune‐mediated neutropenia was diagnosed based on a neutrophil concentration <1·5×109 cells/L on a minimum of two complete blood counts, exclusion of other causes of neutropenia based on a diagnostic bone marrow aspirate or biopsy, and exclusion of secondary immune‐mediated neutropenia. Dogs meeting these diagnostic criteria between 2006 and 2013, and that had a haematocrit of ≥29% and minimum of two complete blood clounts performed after initiation of therapy, were included.ResultsInformation on 35 dogs was included. Neutropenia was less than 0·5×109 cells/L in most cases (21 dogs), 0·5 to ·99×109 cells/L in 11, and 1.0 to 1·49×109 cells/L in three. Eight dogs had thrombocytopenia, which was severe (<49·9×109 cells/L) in three. [Correction added on 23 May 2017, after first online publication: the cell numbers were incorrect due to errors in the conversion of cell measurements to international units. The numbers have been corrected throughout the article and Table 2.] Twenty‐three dogs had myeloid hyperplasia, 10 dogs had myeloid hypoplasia and two dogs had normal myelopoiesis. Neutropenia resolved in 32 of 33 dogs within two weeks of starting corticosteroid therapy and in all dogs within one month. Relapse of neutropenia occurred in 12 cases within one year.Clinical SignificanceInitial response of presumed primary immune‐mediated neutropenia cases to corticosteroid therapy can be excellent. Long‐term monitoring for relapse is warranted because 34% of cases relapsed during or after taper of immunosuppressive medications.
Early evolution of the land plant circadian clock
Authors: Linde Anna‐Malin , Eklund D. Magnus , Kubota Akane , Pederson Eric R. A. , Holm Karl , Gyllenstrand Niclas , Nishihama Ryuichi , Cronberg Nils , Muranaka Tomoaki , Oyama Tokitaka , Kohchi Takayuki , Lagercrantz Ulf 
Published: February 2017

Summary

While angiosperm clocks can be described as an intricate network of interlocked transcriptional feedback loops, clocks of green algae have been modelled as a loop of only two genes. To investigate the transition from a simple clock in algae to a complex one in angiosperms, we performed an inventory of circadian clock genes in bryophytes and charophytes. Additionally, we performed functional characterization of putative core clock genes in the liverwort Marchantia polymorpha and the hornwort Anthoceros agrestis.

Phylogenetic construction was combined with studies of spatiotemporal expression patterns and analysis of M. polymorpha clock gene mutants.

Homologues to core clock genes identified in Arabidopsis were found not only in bryophytes but also in charophytes, albeit in fewer copies. Circadian rhythms were detected for most identified genes in M. polymorpha and A. agrestis, and mutant analysis supports a role for putative clock genes in M. polymorpha.

Our data are in line with a recent hypothesis that adaptation to terrestrial life occurred earlier than previously expected in the evolutionary history of charophyte algae. Both gene duplication and acquisition of new genes was important in the evolution of the plant circadian clock, but gene loss has also contributed to shaping the clock of bryophytes.
Deletion‐bias in DNA double‐strand break repair differentially contributes to plant genome shrinkage
Authors: Vu Giang T. H. , Cao Hieu X. , Reiss Bernd , Schubert Ingo 
Published: February 2017

Summary

In order to prevent genome instability, cells need to be protected by a number of repair mechanisms, including DNA double‐strand break (DSB) repair. The extent to which DSB repair, biased towards deletions or insertions, contributes to evolutionary diversification of genome size is still under debate.

We analyzed mutation spectra in Arabidopsis thaliana and in barley (Hordeum vulgare) by PacBio sequencing of three DSB‐targeted loci each, uncovering repair via gene conversion, single strand annealing (SSA) or nonhomologous end‐joining (NHEJ). Furthermore, phylogenomic comparisons between A. thaliana and two related species were used to detect naturally occurring deletions during Arabidopsis evolution.

Arabidopsis thaliana revealed significantly more and larger deletions after DSB repair than barley, and barley displayed more and larger insertions. Arabidopsis displayed a clear net loss of DNA after DSB repair, mainly via SSA and NHEJ. Barley revealed a very weak net loss of DNA, apparently due to less active break‐end resection and easier copying of template sequences into breaks. Comparative phylogenomics revealed several footprints of SSA in the A. thaliana genome.

Quantitative assessment of DNA gain and loss through DSB repair processes suggests deletion‐biased DSB repair causing ongoing genome shrinking in A. thaliana, whereas genome size in barley remains nearly constant.
Overexpression of OsERF48 causes regulation of OsCML16, a calmodulin‐like protein gene that enhances root growth and drought tolerance
Authors: Jung Harin , Chung Pil Joong , Park Su‐Hyun , Redillas Mark Christian Felipe Reveche , Kim Youn Shic , Suh Joo‐Won , Kim Ju‐Kon 
Published: February 2017

SummaryThe AP2/ERF family is a plant‐specific transcription factor family whose members have been associated with various developmental processes and stress tolerance. Here, we functionally characterized the drought‐inducible OsERF48, a group Ib member of the rice ERF family with four conserved motifs, CMI‐1, ‐2, ‐3 and ‐4. A transactivation assay in yeast revealed that the C‐terminal CMI‐1 motif was essential for OsERF48 transcriptional activity. When OsERF48 was overexpressed in an either a root‐specific (ROXOsERF48) or whole‐body (OXOsERF48) manner, transgenic plants showed a longer and denser root phenotype compared to the nontransgenic (NT) controls. When plants were grown on a 40% polyethylene glycol‐infused medium under in vitro drought conditions, ROXOsERF48 plants showed a more vigorous root growth than OXOsERF48 and NT plants. In addition, the ROXOsERF48 plants exhibited higher grain yield than OXOsERF48 and NT plants under field‐drought conditions. We constructed a putative OsERF48 regulatory network by cross‐referencing ROXOsERF48 root‐specific RNA‐seq data with a co‐expression network database, from which we inferred the involvement of 20 drought‐related genes in OsERF48‐mediated responses. These included genes annotated as being involved in stress signalling, carbohydrate metabolism, cell‐wall proteins and drought responses. They included, OsCML16, a key gene in calcium signalling during abiotic stress, which was shown to be a direct target of OsERF48 by chromatin immunoprecipitation‐qPCR analysis and a transient protoplast expression assay. Our results demonstrated that OsERF48 regulates OsCML16, a calmodulin‐like protein gene that enhances root growth and drought tolerance.
Unravelling early events in the Taphrina deformans–Prunus persica interaction: an insight into the differential responses in resistant and susceptible genotypes
Authors: Svetaz Laura A. , Bustamante Claudia A. , Goldy Camila , Rivero Nery , Müller Gabriela L. , Valentini Gabriel H. , Fernie Alisdair R. , Drincovich María F. , Lara María V. 
Published: February 2017

AbstractLeaf peach curl is a devastating disease affecting leaves, flowers and fruits, caused by the dimorphic fungus Taphrina deformans. To gain insight into the mechanisms of fungus pathogenesis and plant responses, leaves of a resistant and two susceptible Prunus persica genotypes were inoculated with blastospores (yeast), and the infection was monitored during 120 h post inoculation (h.p.i.). Fungal dimorphism to the filamentous form and induction of reactive oxygen species (ROS), callose synthesis, cell death and defence compound production were observed independently of the genotype. Fungal load significantly decreased after 120 h.p.i. in the resistant genotype, while the pathogen tended to grow in the susceptible genotypes. Metabolic profiling revealed a biphasic re‐programming of plant tissue in susceptible genotypes, with an initial stage co‐incident with the yeast form of the fungus and a second when the hypha is developed. Transcriptional analysis of PRs and plant hormone‐related genes indicated that pathogenesis‐related (PR) proteins are involved in P. persica defence responses against T. deformans and that salicylic acid is induced in the resistant genotype. Conducted experiments allowed the elucidation of common and differential responses in susceptible versus resistant genotypes and thus allow us to construct a picture of early events during T. deformans infection.
Effects of diabetes mellitus on the clinical presentation and treatment response in tuberculosis
Authors: Leung Chi C. , Yew Wing W. , Mok Thomas Y.W. , Lau Kam S. , Wong Chi F. , Chau Chi H. , Chan Chi K. , Chang Kwok C. , Tam Greta , Tam Cheuk M. 
Published: February 2017

ABSTRACTBackground and objectiveWith the colliding global epidemics of diabetes mellitus (DM) and tuberculosis (TB), we studied the effects of DM on the presentation of TB and its response to treatment.MethodsConsecutive TB patients from 2006 to 2010 in a territory‐wide treatment programme offering 9‐month extended treatment for TB patients with DM were examined and followed up prospectively to assess their treatment response. Successful treatment completers were tracked through the TB registry and death registry for relapse, death or till 31 December 2014, whichever was the earliest.Results
DM was independently associated with more chest symptoms (adjusted OR (AOR): 1.13) and systemic symptoms (AOR: 1.30) but less with other site‐specific symptoms (AOR: 0.58) at TB presentation. There was more frequent pulmonary involvement (AOR: 1.69), with more extensive lung lesion (AOR: 1.25), lung cavity (AOR: 2.00) and positive sputum smear (AOR: 1.83) and culture (AOR: 1.38), but no difference in the proportion of retreatment cases or isoniazid and/or rifampicin resistance. After treatment initiation, there was higher overall incidence (AOR: 1.38) of adverse effects (mainly gastrointestinal symptoms, renal impairment and peripheral neuropathy but less fever and skin hypersensitivity reactions), more smear non‐conversion (AOR: 1.59) and culture non‐conversion (AOR: 1.40) at 2 months, and lower combined cure/treatment completion rate at 12 months (AOR: 0.79), but no difference in the relapse rate after having successfully completed treatment.Conclusion
DM adversely affected the clinical presentation and treatment response of TB, but there was no difference in the drug resistance and relapse rates.
Fully General Chao and Zelterman Estimators with Application to a Whale Shark Population
Authors: Farcomeni Alessio 
Published: February 2017

SummaryWe introduce generalized Chao and generalized Zelterman estimators which include individual, time varying and behavioural effects. Under mild assumptions in the presence of unobserved heterogeneity, the generalized Chao estimator asymptotically provides a lower bound for the population size and is unbiased otherwise. Corrected versions guarantee bounded estimates. To include the best set of predictors we propose the biased empirical focused information criterion bFIC. Simulations indicate that bFIC might give considerable improvements over other selection criteria in our context. We illustrate with an original application to size estimation of a whale shark (Rhincodon typus) population in South Ari Atoll, in the Maldives.
A mathematical model for estimating residual transmission risk of occult hepatitis B virus infection with different blood safety scenarios
Authors: Weusten Jos , van Drimmelen Harry , Vermeulen Marion , Lelie Nico 
Published: February 2017

BACKGROUNDIf anti‐hepatitis B core antibody testing is not mandated blood donors with occult hepatitis B infection (OBI) may transmit hepatitis B virus (HBV) to a recipient in spite of the use of nucleic acid amplification technology (NAT) or pathogen inactivation (PI).STUDY DESIGN AND METHODSWe developed a model to estimate OBI transmission risk based on three components: the probability distribution of the viral load (VL) in a randomly selected OBI donor, the probability that a given VL remains undetected, and the probability that this VL causes infection in the recipient. A subset of 217 South African OBI samples identified by individual donation (ID)‐NAT screening were quantified by replicate testing using an ID‐NAT assay (Ultrio Plus) against HBV DNA standard dilution series. The observed log VLs could be described by a Gumbel distribution. A correction was included to compensate for OBI samples missed by initial ID‐NAT screening.RESULTSThe model estimates that 3.3% of all OBI donations are undetected by ID‐NAT (Ultrio Plus) and cause infection by a blood component containing 20 mL plasma, going up to 8.7% when using minipools of 6 (MP6)‐NAT. For 200‐mL plasma transfusion these risks were estimated at 14 and 28%, respectively, while PI with modest (2 log) reduction capacity would reach 4.8% without NAT and 1.3 or 0.4% when combined with MP6‐ or ID‐NAT.CONCLUSIONThe model can be used to compare different screening and/or PI strategies in reducing viral transmission risk and could serve as a tool in evaluating efficacy of alternative blood safety scenarios.
A phantom study investigating the relationship between ground‐glass opacity visibility and physical detectability index in low‐dose chest computed tomography
Authors: Ichikawa Katsuhiro , Kobayashi Takeshi , Sagawa Motoyasu , Katagiri Ayako , Uno Yukiko , Nishioka Ryo , Matsuyama Jun 
Published: February 2017

In this study, the relationship between ground‐glass opacity (GGO) visibility and physical detectability index in low‐dose computed tomography (LDCT) for lung cancer screening was investigated. An anthropomorphic chest phantom that included synthetic GGOs with CT numbers of Hounsfield units (HU; high attenuation GGO: HGGO) and HU (low attenuation GGO: LGGO), and three phantoms for physical measurements were employed. The phantoms were scanned using 12 CT systems located in 11 screening centers in Japan. The slice thicknesses and CT dose indices () varied over 1.0–5.0 mm and 0.85–3.30 mGy, respectively, and several reconstruction kernels were used. Physical detectability index values were calculated from measurements of resolution, noise, and slice thickness properties for all image sets. Five radiologists and one thoracic surgeon, blind to one another's observations, evaluated GGO visibility using a five‐point scoring system. The physical detectability index correlated reasonably well with the GGO visibility ( for 6 mm HGGO and for 10 mm LGGO), and was nearly proportional to the CTDIvol. Consequently, the also correlated reasonably well with the GGO visibility ( for 6 mm HGGO and for 10 mm LGGO). As a result, the was nearly dominant in the GGO visibility for image sets with different reconstruction kernels and slice thicknesses, used in this study.PACS numbers: 81.70.Tx, 87.57.Q‐
Determining the optimal dosimetric leaf gap setting for rounded leaf‐end multileaf collimator systems by simple test fields
Authors: Yao Weiguang , Farr Jonathan B. 
Published: February 2017

Individual QA for IMRT/VMAT plans is required by protocols. Sometimes plans cannot pass the institute's QA criteria. For the Eclipse treatment planning system (TPS) with rounded leaf‐end multileaf collimator (MLC), one practical way to improve the agreement of planned and delivered doses is to tune the value of dosimetric leaf gap (DLG) in the TPS from the measured DLG. We propose that this step may be necessary due to the complexity of the MLC system, including dosimetry of small fields and the tongue‐and‐groove (T&G) effects, and report our use of test fields to obtain linac‐specific optimal DLGs in TPSs. More than 20 original patient plans were reoptimized with the linac‐specific optimal DLG value. We examined the distribution of gaps and T&G extensions in typical patient plans and the effect of using the optimal DLG on the distribution. The QA pass rate of patient plans using the optimal DLG was investigated. The dose‐volume histograms (DVHs) of targets and organs at risk were checked. We tested three MLC systems (Varian millennium 120 MLC, high‐definition 120 MLC, and Siemens 160 MLC) installed in four Varian linear accelerators (linacs) (TrueBEAM STx, Trilogy, Clinac 2300 iX, and Clinac 21 EX) and 1 Siemens linac (Artiste). With an optimal DLG, the individual QA for all those patient plans passed the institute's criteria (95% in DTA test or gamma test with ), even though most of these plans had failed to pass QA when using original DLGs optimized from typical patient plans or from the optimization process (automodeler) of Pinnacle TPS. Using either our optimal DLG or one optimized from typical patient plans or from the Pinnacle optimization process yielded similar DVHs.PACS number: 87.55Qr
Dosimetric effect due to the motion during deep inspiration breath hold for left‐sided breast cancer radiotherapy
Authors: Tang Xiaoli , Cullip Tim , Dooley John , Zagar Timothy , Jones Ellen , Chang Sha , Zhu Xiaofeng , Lian Jun , Marks Lawrence 
Published: February 2017

Deep inspiration breath‐hold (DIBH) radiotherapy for left‐sided breast cancer can reduce cardiac exposure and internal motion. We modified our in‐house treatment planning system (TPS) to retrospectively analyze breath‐hold motion log files to calculate the dosimetric effect of the motion during breath hold. Thirty left‐sided supine DIBH breast patients treated using AlignRT were studied. Breath‐hold motion was recorded — three translational and three rotational displacements of the treatment surface — the Real Time Deltas (RTD). The corresponding delivered dose was estimated using the beam‐on portions of the RTDs. Each motion was used to calculate dose, and the final estimated dose was the equally weighted average of the multiple resultant doses. Ten of thirty patients had internal mammary nodes (IMN) purposefully included in the tangential fields, and we evaluated the percentage of IMN covered by 40 Gy. The planned and delivered heart mean dose, lungs V20 (volume of the lungs receiving ), percentage of IMN covered by 40 Gy, and IMN mean dose were compared. The averaged mean and standard deviation of the beam‐on portions of the absolute RTDs were , , , , and , for vertical, longitudinal, lateral, yaw, roll, and pitch, respectively. The averaged planned and delivered mean heart dose were 99 and 101 cGy. Lungs V20 were 6.59% and 6.74%. IMN 40 Gy coverage was 83% and 77%, and mean IMN dose was 4642 and 4518 cGy. The averaged mean motion during DIBH was smaller than 1 mm and 1°, which reflects the relative reproducibility of the patient breath hold. On average, the mean heart dose and lungs V20 were reasonably close to what have been planned. IMN 40 Gy coverage might be modestly reduced for certain cases.PACS number: 87.55.km, 87.55.N
Implementation of an efficient Monte Carlo calculation for CBCT scatter correction: phantom study
Authors: Watson Peter G.F. , Mainegra‐Hing Ernesto , Tomic Nada , Seuntjens Jan 
Published: February 2017

Cone‐beam computed tomography (CBCT) images suffer from poor image quality, in a large part due to contamination from scattered X‐rays. In this work, a Monte Carlo (MC)‐based iterative scatter correction algorithm was implemented on measured phantom data acquired from a clinical on‐board CBCT scanner. An efficient EGSnrc user code (egs_cbct) was used to transport photons through an uncorrected CBCT scan of a Catphan 600 phantom. From the simulation output, the contribution from primary and scattered photons was estimated in each projection image. From these estimates, an iterative scatter correction was performed on the raw CBCT projection data. The results of the scatter correction were compared with the default vendor reconstruction. The scatter correction was found to reduce the error in CT number for selected regions of interest, while improving contrast‐to‐noise ratio (CNR) by 18%. These results demonstrate the performance of the proposed scatter correction algorithm in improving image quality for clinical CBCT images.PACS numbers: 87.10.Rt, 87.57.Q‐
Is 5 mm MMLC suitable for VMAT‐based lung SBRT? A dosimetric comparison with 2.5 mm HDMLC using RTOG‐0813 treatment planning criteria for both conventional and high‐dose flattening filter‐free photon beams
Authors: Subramanian Shanmuga V. , Subramani Vellaiyan , Swamy Shanmugam Thirumalai , Gandhi Arun , Chilukuri Srinivas , Kathirvel Murugesan 
Published: February 2017

The aim of this study is to assess the suitability of 5 mm millennium multileaf collimator (MMLC) for volumetric‐modulated arc therapy (VMAT)‐based lung stereotactic body radiotherapy (SBRT). Thirty lung SBRT patient treatment plans along with their planning target volumes (ranging from 2.01 cc to 150.11 cc) were transferred to an inhomogeneous lung phantom and retrospectively planned using VMAT technique, along with the high definition multileaf collimator (HDMLC) and MMLC systems. The plans were evaluated using Radiation Therapy Oncology Group (RTOG‐0813) treatment planning criteria for target coverage, normal tissue sparing, and treatment efficiency for both the MMLC and HDMLC systems using flat and flattening filter‐free (FFF) photon beams. Irrespective of the target volumes, both the MLC systems were able to satisfy the RTOG‐0813 treatment planning criteria without having any major deviation. Dose conformity was marginally better with HDMLC. The average conformity index (CI) value was found to be and for HDMLC and MMLC plans, respectively. For the 6 MV FFF beams, the plan was slightly more conformal, with the average CI values of and for the HDMLC and MMLC plans, respectively. The high dose spillage was the maximum for 2 cc volume set (3% for HDMLC and 3.1% for MMLC). In the case of low dose spillage, both the MLCs were within the protocol of no deviation, except for the 2 cc volume set. The results from this study revealed that VMAT‐based lung SBRT using 5 mm MMLC satisfies the RTOG‐0813 treatment planning criteria for the studied target size and shapes.PACS numbers: 87.53.Ly, 87.53D, 87.56.jk