bluuebunny/crossref_metadata_2025_split huggingface dataset:
An extension to artifact‐free projection overlaps
Authors: Lin Jianyu 
Published: April 2015

Purpose:In multipinhole single photon emission computed tomography, the overlapping of projections has been used to increase sensitivity. Avoiding artifacts in the reconstructed image associated with projection overlaps (multiplexing) is a critical issue. In our previous report, two types of artifact‐free projection overlaps, i.e., projection overlaps that do not lead to artifacts in the reconstructed image, were formally defined and proved, and were validated via simulations. In this work, a new proposition is introduced to extend the previously defined type‐II artifact‐free projection overlaps so that a broader range of artifact‐free overlaps is accommodated. One practical purpose of the new extension is to design a baffle window multipinhole system with artifact‐free projection overlaps.Methods:First, the extended type‐II artifact‐free overlap was theoretically defined and proved. The new proposition accommodates the situation where the extended type‐II artifact‐free projection overlaps can be produced with incorrectly reconstructed portions in the reconstructed image. Next, to validate the theory, the extended‐type‐II artifact‐free overlaps were employed in designing the multiplexing multipinhole spiral orbit imaging systems with a baffle window. Numerical validations were performed via simulations, where the corresponding 1‐pinhole nonmultiplexing reconstruction results were used as the benchmark for artifact‐free reconstructions. The mean square error (MSE) was the metric used for comparisons of noise‐free reconstructed images. Noisy reconstructions were also performed as part of the validations.Results:Simulation results show that for noise‐free reconstructions, the MSEs of the reconstructed images of the artifact‐free multiplexing systems are very similar to those of the corresponding 1‐pinhole systems. No artifacts were observed in the reconstructed images. Therefore, the testing results for artifact‐free multiplexing systems designed using the extended type‐II artifact‐free overlaps numerically validated the developed theory.Conclusions:First, the extension itself is of theoretical importance because it broadens the selection range for optimizing multiplexing multipinhole designs. Second, the extension has an immediate application: using a baffle window to design a special spiral orbit multipinhole imaging system with projection overlaps in the orbit axial direction. Such an artifact‐free baffle window design makes it possible for us to image any axial portion of interest of a long object with projection overlaps to increase sensitivity.
Optical eye tracking system for real‐time noninvasive tumor localization in external beam radiotherapy
Authors: Via Riccardo , Fassi Aurora , Fattori Giovanni , Fontana Giulia , Pella Andrea , Tagaste Barbara , Riboldi Marco , Ciocca Mario , Orecchia Roberto , Baroni Guido 
Published: April 2015

Purpose:External beam radiotherapy currently represents an important therapeutic strategy for the treatment of intraocular tumors. Accurate target localization and efficient compensation of involuntary eye movements are crucial to avoid deviations in dose distribution with respect to the treatment plan. This paper describes an eye tracking system (ETS) based on noninvasive infrared video imaging. The system was designed for capturing the tridimensional (3D) ocular motion and provides an on‐line estimation of intraocular lesions position based on a priori knowledge coming from volumetric imaging.Methods:Eye tracking is performed by localizing cornea and pupil centers on stereo images captured by two calibrated video cameras, exploiting eye reflections produced by infrared illumination. Additionally, torsional eye movements are detected by template matching in the iris region of eye images. This information allows estimating the 3D position and orientation of the eye by means of an eye local reference system. By combining ETS measurements with volumetric imaging for treatment planning [computed tomography (CT) and magnetic resonance (MR)], one is able to map the position of the lesion to be treated in local eye coordinates, thus enabling real‐time tumor referencing during treatment setup and irradiation. Experimental tests on an eye phantom and seven healthy subjects were performed to assess ETS tracking accuracy.Results:Measurements on phantom showed an overall median accuracy within 0.16 mm and 0.40° for translations and rotations, respectively. Torsional movements were affected by 0.28° median uncertainty. On healthy subjects, the gaze direction error ranged between 0.19° and 0.82° at a median working distance of 29 cm. The median processing time of the eye tracking algorithm was 18.60 ms, thus allowing eye monitoring up to 50 Hz.Conclusions:A noninvasive ETS prototype was designed to perform real‐time target localization and eye movement monitoring during ocular radiotherapy treatments. The device aims at improving state‐of‐the‐art invasive procedures based on surgical implantation of radiopaque clips and repeated acquisition of X‐ray images, with expected positive effects on treatment quality and patient outcome.
Solar and Temperature Treatments Affect the Ability of Human Rotavirus Wa To Bind to Host Cells and Synthesize Viral RNA
Authors: Romero-Maraccini Ofelia C. , Shisler Joanna L. , Nguyen Thanh H. 
Published: April 2015

ABSTRACT
Rotavirus, the leading cause of diarrheal diseases in children under the age of five, is often resistant to conventional wastewater treatment and thus can remain infectious once released into the aquatic environment. Solar and heat treatments can inactivate rotavirus, but it is unknown how these treatments inactivate the virus on a molecular level. To answer this question, our approach was to correlate rotavirus inactivation with the inhibition of portions of the virus life cycle as a means to identify the mechanisms of solar or heat inactivation. Specifically, the integrity of the rotavirus NSP3 gene, virus-host cell interaction, and viral RNA synthesis were examined after heat (57°C) or solar treatment of rotavirus. Only the inhibition of viral RNA synthesis positively correlated with a loss of rotavirus infectivity; 57°C treatment of rotavirus resulted in a decrease of rotavirus RNA synthesis at the same rate as rotavirus infectivity. These data suggest that heat treatment neutralized rotaviruses primarily by targeting viral transcription functions. In contrast, when using solar disinfection, the decrease in RNA synthesis was responsible for approximately one-half of the decrease in infectivity, suggesting that other mechanisms, including posttranslational, contribute to inactivation. Nevertheless, both solar and heat inactivation of rotaviruses disrupted viral RNA synthesis as a mechanism for inactivation.
Symbiosis Island Shuffling with Abundant Insertion Sequences in the Genomes of Extra-Slow-Growing Strains of Soybean Bradyrhizobia
Authors: Iida Takayuki , Itakura Manabu , Anda Mizue , Sugawara Masayuki , Isawa Tsuyoshi , Okubo Takashi , Sato Shusei , Chiba-Kakizaki Kaori , Minamisawa Kiwamu 
Published: April 2015

ABSTRACT

Extra-slow-growing bradyrhizobia from root nodules of field-grown soybeans harbor abundant insertion sequences (ISs) and are termed highly reiterated sequence-possessing (HRS) strains. We analyzed the genome organization of HRS strains with the focus on IS distribution and symbiosis island structure. Using pulsed-field gel electrophoresis, we consistently detected several plasmids (0.07 to 0.4 Mb) in the HRS strains (NK5, NK6, USDA135, 2281, USDA123, and T2), whereas no plasmids were detected in the non-HRS strain USDA110. The chromosomes of the six HRS strains (9.7 to 10.7 Mb) were larger than that of USDA110 (9.1 Mb). Using MiSeq sequences of 6 HRS and 17 non-HRS strains mapped to the USDA110 genome, we found that the copy numbers of ISRj1, ISRj2, ISFK1, IS
1632
, ISB27, ISBj8, and IS
1631
were markedly higher in HRS strains. Whole-genome sequencing showed that the HRS strain NK6 had four small plasmids (136 to 212 kb) and a large chromosome (9,780 kb). Strong colinearity was found between 7.4-Mb core regions of the NK6 and USDA110 chromosomes. USDA110 symbiosis islands corresponded mainly to five small regions (S1 to S5) within two variable regions, V1 (0.8 Mb) and V2 (1.6 Mb), of the NK6 chromosome. The USDA110
nif
gene cluster (
nifDKENXSBZHQW-fixBCX
) was split into two regions, S2 and S3, where ISRj1-mediated rearrangement occurred between
nifS
and
nifB
. ISs were also scattered in NK6 core regions, and ISRj1 insertion often disrupted some genes important for survival and environmental responses. These results suggest that HRS strains of soybean bradyrhizobia were subjected to IS-mediated symbiosis island shuffling and core genome degradation.
Long-Term Fungal Inhibition by Pisum sativum Flour Hydrolysate during Storage of Wheat Flour Bread
Authors: Rizzello Carlo Giuseppe , Lavecchia Anna , Gramaglia Valerio , Gobbetti Marco 
Published: April 2015

ABSTRACTIn order to identify antifungal compounds from natural sources to be used as ingredients in the bakery industry, water/salt-soluble extracts (WSE) from different legume flour hydrolysates obtained by the use of a fungal protease were assayed againstPenicillium roquefortiDPPMAF1. The agar diffusion assays allowed the selection of the pea (Pisum sativum) hydrolysate as the most active. As shown by the hyphal radial growth rate, the WSE had inhibitory activity towards several fungi isolated from bakeries. The MIC of the WSE was 9.0 mg/ml. Fungal inhibition was slightly affected by heating and variations in pH. The antifungal activity was attributed to three native proteins (pea defensins 1 and 2 and a nonspecific lipid transfer protein [nsLTP]) and a mixture of peptides released during hydrolysis. The three proteins have been reported previously as components of the defense system of the plant. Five peptides were purified from WSE and were identified as sequences encrypted in leginsulin A, vicilin, provicilin, and the nsLTP. To confirm antifungal activity, the peptides were chemically synthesized and tested. Freeze-dried WSE were used as ingredients in leavened baked goods. In particular, breads made by the addition of 1.6% (wt/wt) of the extract and fermented by baker's yeast or sourdough were characterized for their main chemical, structural, and sensory features, packed in polyethylene bags, stored at room temperature, and compared to controls prepared without pea hydrolysate. Artificially inoculated slices of a bread containing the WSE did not show contamination by fungi until at least 21 days of storage and behaved like the bread prepared with calcium propionate (0.3%, wt/wt).
Can staff and patient perspectives on hospital safety predict harm-free care? An analysis of staff and patient survey data and routinely collected outcomes
Authors: Lawton Rebecca , O'Hara Jane Kathryn , Sheard Laura , Reynolds Caroline , Cocks Kim , Armitage Gerry , Wright John 
Published: April 2015

BackgroundPatients have the potential to provide feedback on the safety of their care. Recently, tools have been developed that ask patients to provide feedback on those factors that are known to contribute to safety, therefore providing information that can be used proactively to manage safety in hospitals. The aim of this study was to investigate whether the safety information provided by patients is different from that provided by staff and whether it is related to safety outcomes.MethodData were collected from 33 hospital wards across 3 acute hospital Trusts in the UK. Staff on these wards were asked to complete the four outcome measures of the Hospital Survey of Patient Safety Culture, while patients were asked to complete the Patient Measure of Safety and the friends and family test. We also collated publicly reported safety outcome data for ‘harm-free care’ on each ward. This patient safety thermometer measure is used in the UK NHS to record the percentage of patients on a single day of each month on every ward who have received harm-free care (ie, no pressure ulcers, falls, urinary tract infections and hospital acquired new venous thromboembolisms). These data were used to address questions about the relationship between measures and the extent to which patient and staff perceptions of safety predict safety outcomes.ResultsThe friends and family test, a single item measure of patient experience was associated with patients’ perceptions of safety, but was not associated with safety outcomes. Staff responses to the patient safety culture survey were not significantly correlated with patient responses to the patient measure of safety, but both independently predicted safety outcomes. The regression models showed that staff perceptions (adjusted r2=0.39) and patient perceptions (adjusted r2=0.30) of safety independently predicted safety outcomes. When entered together both measures accounted for 49% of the variance in safety outcomes (adjusted r2=0.49), suggesting that there is overlap but some unique variance is also explained by these two measures. Based on responses to the Patient Measure of Safety it was also possible to identify differences between the acute Hospital Trusts.DiscussionThe findings suggest that although the views of patients and staff predict some overlapping variance in patient safety outcomes, both also offer a unique perspective on patient safety, contributing independently to the prediction of safety outcomes. These findings suggest that feedback from patients about the safety of the care that they receive can be used, in addition to data from staff to drive safety improvements in healthcare.Trial registration numberISRCTN07689702.
A retrospective study of patients with follicular lymphoma (FL): identification of in situ FL or FL-like B cells of uncertain significance in lymph nodes resected at the time of previous surgery for carcinomas
Authors: Morita Kohei , Nakamine Hirokazu , Nakai Tokiko , Takano Masato , Takeda Maiko , Enomoto Yasunori , Yoshii Yumi , Kanno Masatoshi , Ohbayashi Chiho 
Published: April 2015

Background and aimsIn situ follicular lymphoma (iFL)/intrafollicular neoplasia and follicular lymphoma (FL)-like B cells of uncertain significance represent proliferation of Bcl-2/t(14;18)-positive B cells solely in the germinal centres. The condition is interpreted as an early event in the multi-step lymphomagenesis of FL. The aim of this study is to examine the issue more specifically.MethodsWe reviewed medical history of FL patients in whom thoracoabdominal surgery with lymphadenectomy had been performed for management of carcinomas. These previously resected lymph nodes as well as the current FL nodes were analysed by immunohistochemistry, fluorescent in situ hybridisation, and PCR amplification with direct sequencing.ResultsWe studied four such FL patients from a total of 150 patients with FL; all had iFL in the previously resected lymph nodes. Clonal relation was verified and suggested in one case each. The time from lymphadenectomy to the diagnosis of FL was 23–120 months. There appeared to be a reverse correlation between the rate of Bcl-2-positive follicle proliferation and the time from surgery to diagnosis of FL.ConclusionsAlthough the rate for development of FL in individuals having iFL has been reported to be low from prospective studies, the present data indicate that follow-up studies for a longer period is necessary; the rate of Bcl-2-positive follicle proliferation could be a factor to predict development of FL in prospective studies. Such a retrospective study may contribute to elucidate mechanism(s) involved in lymphomagenesis of FL.
Identification and quantification of factors affecting neonatal immunological transfer in dairy calves in the UK
Authors: MacFarlane J. A. , Grove‐White D. H. , Royal M. D. , Smith R. F. 
Published: April 2015

The object of the study was to quantify the prevalence of failure of passive transfer in UK dairy farms and to identify variables that had a significant impact on the rate of immunological transfer. In a six‐month study of 444 calvings from seven UK dairy farms, 26 per cent of calves failed to receive adequate immunoglobulin transfer as judged by a plasma total protein (pTP) concentration less than 5.6 g/dl. Colostrum immunoglobulin concentration, indirectly measured using Brix refractometry, showed wide variations with samples ranging from 10.3 to 34.7 Brix units. Thirty‐seven per cent of samples were below the suggested cut‐off Brix score for colostrum quality of 22 per cent. Potential associations between covariates and plasma protein concentration were investigated using multiple linear regression models. The covariate with the greatest impact on the pTP concentration was the farm on which the calf was born (P<0.05). A significant but small association was demonstrated between colostrum immunoglobulin concentration and calf pTP concentration (P<0.01). Multiple linear regression models suggested that the time of colostrum collection after calving, parity of the dam, and the individual farm were associated with the Brix measurements (P<0.05). This study suggested that veterinary review of colostrum protocols on farm with emphasis on prompt collection and dosing after calving remains a simple and effective measure to improve passive transfer and thus calf health on UK dairy farms.
Os papéis dos espaços livres públicos na estruturação territorial e no projeto de parcelamento: a experiência de ensino na PUC-Campinas
Authors: Silva Jonathas Magalhães Pereira da , Benfatti Denio , Moreira Tomás A. , Pera Caroline K. L. 
Published: April 2015

<p>Considerando as práticas contemporâneas de ensino no Projeto e no Planejamento Urbano e Regional, o presente texto objetiva compartilhar a experiência de ensino desenvolvida nos anos de 2009 a 2012 na FAU/PUC-Campinas. Apresentam-se os procedimentos e posturas atitudinais adotadas em sala de aula, explicitando as etapas de desenvolvimento, os argumentos e os resultados obtidos. Por meio da sistematização da experiência pedagógica, objetiva-se a construção de um diálogo interdisciplinar que explicite avanços na consideração dos sistemas de espaços livres de edificação no processo de planejamento e estruturação territorial. Busca-se com o exercício proposto identificar e questionar os processos contemporâneos de ocupação territorial condicionados por uma lógica em que o transporte individual é dominante e pela ausência de uma estruturação territorial prévia aos projetos de parcelamento de solo. A disciplina não quer se limitar a instrumentalizar o aluno para a prática profissional, mas sim provocar uma prática reflexiva baseada na construção de argumentos que se revelem em desenhos, considerando as diferentes escalas, os interesses de diferentes agentes, as contradições existentes e a história da disciplina. O desenho da paisagem é utilizado aqui como instrumento de reflexão que contesta a realidade e cria argumentos para novas configurações espaciais urbanas. </p>
O Programa Minha Casa Minha Vida e seus resultados formais em Uberaba (MG): residencial Tancredo Neves
Authors: Maluf Carmem Silvia , Donoso Verônica Garcia , Valicente Mariana , Oliveira Júnior João Batista De 
Published: April 2015

<p>Este artigo propõe a discussão do Programa Minha Casa Minha Vida, suas consequências e transformações cíclicas no espaço urbano, com foco na análise da morfologia urbana resultante do loteamento residencial Tancredo Neves, localizado no município de Uberaba (MG). O mesmo possui algumas características únicas, diferenciando-se dos demais conjuntos, desde o público até a utilização imprópria da Área de Preservação Permanente (APP) por parte dos moradores. Os resultados obtidos por esta análise reforçam a importância do poder público na promoção da habitação, identifica a recorrente reprodutibilidade de modelos habitacionais, além de mostrar como essa proliferação de unidades habitacionais impacta a morfologia urbana, trazendo consigo questionáveis consequências para a paisagem.</p>
Polygenic Overlap Between C-Reactive Protein, Plasma Lipids, and Alzheimer Disease
Authors: Desikan Rahul S. , Schork Andrew J. , Wang Yunpeng , Thompson Wesley K. , Dehghan Abbas , Ridker Paul M , Chasman Daniel I. , McEvoy Linda K. , Holland Dominic , Chen Chi-Hua , Karow David S. , Brewer James B. , Hess Christopher P. , Williams Julie , Sims Rebecca , O’Donovan Michael C. , Choi Seung Hoan , Bis Joshua C. , Ikram M. Arfan , Gudnason Vilmundur , DeStefano Anita L. , van der Lee Sven J. , Psaty Bruce M. , van Duijn Cornelia M. , Launer Lenore , Seshadri Sudha , Pericak-Vance Margaret A. , Mayeux Richard , Haines Jonathan L. , Farrer Lindsay A. , Hardy John , Ulstein Ingun Dina , Aarsland Dag , Fladby Tormod , White Linda R. , Sando Sigrid B. , Rongve Arvid , Witoelar Aree , Djurovic Srdjan , Hyman Bradley T. , Snaedal Jon , Steinberg Stacy , Stefansson Hreinn , Stefansson Kari , Schellenberg Gerard D. , Andreassen Ole A. , Dale Anders M. 
Published: April 2015

Background—
Epidemiological findings suggest a relationship between Alzheimer disease (AD), inflammation, and dyslipidemia, although the nature of this relationship is not well understood. We investigated whether this phenotypic association arises from a shared genetic basis.

Methods and Results—

Using summary statistics (
P
values and odds ratios) from genome-wide association studies of >200 000 individuals, we investigated overlap in single-nucleotide polymorphisms associated with clinically diagnosed AD and C-reactive protein (CRP), triglycerides, and high- and low-density lipoprotein levels. We found up to 50-fold enrichment of AD single-nucleotide polymorphisms for different levels of association with C-reactive protein, low-density lipoprotein, high-density lipoprotein, and triglyceride single-nucleotide polymorphisms using a false discovery rate threshold <0.05. By conditioning on polymorphisms associated with the 4 phenotypes, we identified 55 loci associated with increased AD risk. We then conducted a meta-analysis of these 55 variants across 4 independent AD cohorts (total: n=29 054 AD cases and 114 824 healthy controls) and discovered 2 genome-wide significant variants on chromosome 4 (rs13113697; closest gene,
HS3ST1
; odds ratio=1.07; 95% confidence interval=1.05–1.11;
P
=2.86×10
−8
) and chromosome 10 (rs7920721; closest gene,
ECHDC3
; odds ratio=1.07; 95% confidence interval=1.04–1.11;
P
=3.38×10
−8
). We also found that gene expression of
HS3ST1
and
ECHDC3
was altered in AD brains compared with control brains.

Conclusions—
We demonstrate genetic overlap between AD, C-reactive protein, and plasma lipids. By conditioning on the genetic association with the cardiovascular phenotypes, we identify novel AD susceptibility loci, including 2 genome-wide significant variants conferring increased risk for AD.