bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plasma Short‐Chain Fatty Acids in Patients With Parkinson's Disease
Authors: Shin Chaewon , Lim Yunsook , Lim Hyewon , Ahn Tae‐Beom 
Published: March 2020

AbstractBackgroundShort‐chain fatty acids are exclusively produced by gut microbiota and are reduced in feces of patients with Parkinson's disease (PD). The objective of this study was to conduct a case–control study on peripheral concentration of short‐chain fatty acids based on evidence of pathologic changes in the blood–brain barrier in PD and the possible role of short‐chain fatty acids in blood–brain barrier permeability.MethodsThe plasma short‐chain fatty acid concentration was measured in 38 PD and 33 normal controls using gas chromatography. The clinical characteristics of patients with PD and controls were evaluated, and dietary information was obtained using a food frequency questionnaire. Short‐chain fatty acid concentrations were further compared after adjusting for age, sex, and significant food frequency questionnaire items.ResultsThe concentrations of acetate, propionate, and butyrate did not differ between patients with PD and controls in unadjusted comparison. Dietary intakes of fibers, carbohydrates, lipids (total and fatty acids), and proteins did not differ between groups. After correction of covariates, acetic acid concentration was higher in patients with PD than in controls (116.47 ± 16.83 vs 108.20 ± 18.37 μmol/L; P = 0.010). In correlation analyses, acetic acid concentration was positively correlated (R = 0.374, P = 0.021) with age, propionic acid concentration was negatively correlated with UPDRS part III score (R = −0.376, P = 0.020) and use of entacapone (R = −0.325, P = 0.047), and butyric acid concentration was correlated with monoamine oxidase inhibitor use (R = 0.382, P = 0.018) and anticholinergic use (R = −0.385, P = 0.024).ConclusionsPlasma short‐chain fatty acids were paradoxically increased in PD and were associated with disease severity and antiparkinsonian medications. Further studies are warranted to elucidate the relationships of gut dysbiosis and inflammation with plasma short‐chain fatty acids. © 2020 International Parkinson and Movement Disorder Society
A preliminary computational outputs versus experimental results: Application of sTRAP, a biophysical tool for the analysis of SNPs of transcription factor‐binding sites
Authors: Moradifard Shirin , Saghiri Reza , Ehsani Parastoo , Mirkhani Fatemeh , Ebrahimi‐Rad Mina 
Published: March 2020

AbstractBackgroundIn the human genome, the transcription factors (TFs) and transcription factor‐binding sites (TFBSs) network has a great regulatory function in the biological pathways. Such crosstalk might be affected by the single‐nucleotide polymorphisms (SNPs), which could create or disrupt a TFBS, leading to either a disease or a phenotypic defect. Many computational resources have been introduced to predict the TFs binding variations due to SNPs inside TFBSs, sTRAP being one of them.MethodsA literature review was performed and the experimental data for 18 TFBSs located in 12 genes was provided. The sequences of TFBS motifs were extracted using two different strategies; in the size similar with synthetic target sites used in the experimental techniques, and with 60 bp upstream and downstream of the SNPs. The sTRAP (http://trap.molgen.mpg.de/cgi-bin/trap_two_seq_form.cgi) was applied to compute the binding affinity scores of their cognate TFs in the context of reference and mutant sequences of TFBSs. The alternative bioinformatics model used in this study was regulatory analysis of variation in enhancers (RAVEN; http://www.cisreg.ca/cgi-bin/RAVEN/a). The bioinformatics outputs of our study were compared with experimental data, electrophoretic mobility shift assay (EMSA).ResultsIn 6 out of 18 TFBSs in the following genes COL1A1, Hb ḉᴪ, TF, FIX, MBL2, NOS2A, the outputs of sTRAP were inconsistent with the results of EMSA. Furthermore, no p value of the difference between the two scores of binding affinity under the wild and mutant conditions of TFBSs was presented. Nor, were any criteria for preference or selection of any of the measurements of different matrices used for the same analysis.ConclusionOur preliminary study indicated some paradoxical results between sTRAP and experimental data. However, to link the data of sTRAP to the biological functions, its optimization via experimental procedures with the integration of expanded data and applying several other bioinformatics tools might be required.
Broadband electrically tunable VO2‑Metamaterial terahertz switch with suppressed reflection
Authors: Schalch Jacob S. , Chi Yaojia , He Yulian , Tang Yahua , Zhao Xiaoguang , Zhang Xin , Wen Qiye , Averitt Richard D. 
Published: March 2020

AbstractDevices designed to dynamically control the transmission, reflection, and absorption of terahertz (THz) radiation are essential for the development of a broad range of THz technologies. A viable approach utilizes materials which undergo an insulator‐to‐metal transition (IMT), switching from transmissive to reflective upon becoming metallic. However, for many applications, it is undesirable to have spurious reflections that can scatter incident light and induce noise to the system. We present an electrically actuated, broadband THz switch which transitions from a transparent state with low reflectivity, to an absorptive state for which both the reflectivity and transmission are strongly suppressed. Our device consists of a patterned high‐resistivity silicon metamaterial layer that provides broadband reflection suppression by matching the impedance of free space. This is integrated with a VO2 ground plane, which undergoes an IMT by means of a DC bias applied to an interdigitated electrode. THz time domain spectroscopy measurements reveal an active bandwidth of 700 GHz with suppressed reflection and more than 90% transmission amplitude modulation with a low insertion loss. We utilize finite‐difference time domain (FDTD) simulations in order to examine the loss mechanisms of the device, as well as the sensitivity to polarization and incident angle. This device validates a general approach toward suppressing unwanted reflections in THz modulators and switches which can be easily adapted to a broad array of applications through straightforward modifications of the structural parameters.
Investigation of spectral performance for single‐scan contrast‐enhanced breast CT using photon‐counting technology: A phantom study
Authors: Ruth Veikko , Kolditz Daniel , Steiding Christian , Kalender Willi A. 
Published: March 2020

PurposeContrast‐enhanced imaging of the breast is frequently used in breast MRI and has recently become more common in mammography. The purpose of this study was to make single‐scan contrast‐enhanced imaging feasible for photon‐counting breast CT (pcBCT) and to assess the spectral performance of a pcBCT scanner by evaluating iodine maps and virtual non‐contrast (VNC) images.MethodsWe optimized the settings of a pcBCT to maximize the signal‐to‐noise ratio between iodinated contrast agent and breast tissue. Therefore, an electronic energy threshold dividing the x‐ray spectrum used into two energy bins was swept from 23.17 keV to 50.65 keV. Validation measurements were performed by placing syringes with contrast agent (2.5 mg/ml to 40 mg/ml) in phantoms with 7.5 cm and 12 cm in diameter. Images were acquired at different tube currents and reconstructed with 300 μm isotropic voxel size. Iodine maps and VNC images were generated using image‐based material decomposition. Iodine concentrations and CT values were measured for each syringe and compared to the known concentrations and reference CT values.ResultsMaximal signal‐to‐noise ratios were found at a threshold position of 32.59 keV. Accurate iodine quantification (average root mean square error of 0.56 mg/ml) was possible down to a concentration of 2.5 mg/ml for all tube currents investigated. The enhancement has been sufficiently removed in the VNC images, so they can be interpreted as unenhanced CT images. Only minor changes of CT values compared to a conventional CT scan were observed. Noise was increased by the decomposition by a factor of 2.62 and 4.87 (7.5 cm and 12 cm phantoms) but did not compromise the accuracy of the iodine quantification.ConclusionsAccurate iodine quantification and generation of VNC images can be achieved using contrast‐enhanced pcBCT from a single CT scan in the absence of temporal or spatial misalignment. Using iodine maps and VNC images, pcBCT has the potential to reduce dose, shorten examination and reading time, and to increase cancer detection rates.
Nursing diagnosis identification by nurses in burn wards: A descriptive cross‐sectional study
Authors: Khajehgoodari Mohammad , Lotfi Mojgan , Zamanzadeh Vahid , Valizadeh Leila , Khalilzad Parisa 
Published: March 2020

AbstractAimTo identify and document patients' care needs, it is vital to provide quality care services. This study was aimed to describe care needs derived from records of patients with burn and to evaluate whether nurses employed the North American Nursing Diagnosis Association classification to formulate patients' care needs.DesignA descriptive cross‐sectional study.MethodsIn this study using the convenient sampling method, 430 nursing records reviewed in the burn wards. Data were collected using Gordon's checklist. The validity of the checklist assessed by content validity and the reliability of them calculated with inter‐rater and internal consistency. Data analysed by SPSSv.24.ResultsThe mean number of diagnoses per record was 1.94. The most frequent diagnosis was in the domain of Safety/Protection and the top two prevalent nursing diagnoses in Sina hospital were a risk for infection and risk for falls. From all of the detected diagnostic, about 83% were determinedly not related to one of 247 labels of the North American Nursing Diagnosis Association. Given that nurses provide nursing care as requested by physicians and patient care needs are not assessed and recorded by them, it can be concluded that there was no nursing thinking behind their nursing care.
Conflicts over wildlife conservation: Learning from the reintroduction of beavers in Scotland
Authors: Coz Deborah M. , Young Juliette C. 
Published: March 2020

AbstractSpecies reintroductions have become a common conservation tool, but they can be controversial and may generate social conflicts.We examine the social dimension of beaver reintroduction in Scotland to understand the issue, the potential for, and impact of, conflict between groups or individuals with differing views on beavers and reintroductions.Using a literature review and semi‐structured interviews, we studied planned and unplanned beaver reintroductions to three contrasting landscapes in Scotland: in Knapdale, the reintroduction was planned and science‐led, whereas in Tayside and the Highlands, the reintroductions were accidental and/or illegal.Our results highlight the context dependency and complexity of reintroductions. Nationally, the reintroduction of beavers has not become a conflict. At the local scale, we found the Tayside situation to be a conflict with major consequences on the debate at the national scale. While there were no conflicts in the Highlands and Knapdale, the reintroduction remains controversial.The level of conflict depended on the reintroduction process, relationships between stakeholders and their perspectives on their role in nature, their perceptions of landscapes, and the potential issue of lack of control and uncertainty around reintroductions.Based on these findings, the study outlines lessons learned in terms of management, guidelines and implications for future species reintroductions. We argue that to prevent future conflicts over reintroductions, processes must go beyond addressing the effects of reintroduced species on the environment and people's perceptions and acceptance of these species. Reintroduction processes require engagement in effective discussions which involve all actual and potential stakeholders to agree on broad and long‐term conservation plans at the landscape scale.A freePlain Language Summarycan be found within the Supporting Information of this article.
A streamlined mass spectrometry–based proteomics workflow for large‐scale FFPE tissue analysis
Authors: Coscia Fabian , Doll Sophia , Bech Jacob Mathias , Schweizer Lisa , Mund Andreas , Lengyel Ernst , Lindebjerg Jan , Madsen Gunvor Iben , Moreira José MA , Mann Matthias 
Published: March 2020

AbstractFormalin fixation and paraffin‐embedding (FFPE) is the most common method to preserve human tissue for clinical diagnosis, and FFPE archives represent an invaluable resource for biomedical research. Proteins in FFPE material are stable over decades but their efficient extraction and streamlined analysis by mass spectrometry (MS)–based proteomics has so far proven challenging. Herein we describe a MS‐based proteomic workflow for quantitative profiling of large FFPE tissue cohorts directly from histopathology glass slides. We demonstrate broad applicability of the workflow to clinical pathology specimens and variable sample amounts, including low‐input cancer tissue isolated by laser microdissection. Using state‐of‐the‐art data dependent acquisition (DDA) and data independent acquisition (DIA) MS workflows, we consistently quantify a large part of the proteome in 100 min single‐run analyses. In an adenoma cohort comprising more than 100 samples, total workup took less than a day. We observed a moderate trend towards lower protein identification in long‐term stored samples (>15 years), but clustering into distinct proteomic subtypes was independent of archival time. Our results underscore the great promise of FFPE tissues for patient phenotyping using unbiased proteomics and they prove the feasibility of analyzing large tissue cohorts in a robust, timely, and streamlined manner. © 2020 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
The use of Mendelian randomisation to identify causal cancer risk factors: promise and limitations
Authors: Gala Harvinder , Tomlinson Ian 
Published: March 2020

AbstractThe use of observational analyses, such as classical epidemiological studies or randomised controlled trials (RCTs), to infer causality in cancer may be problematic due to both ethical reasons and technical issues, such as confounding variables and reverse causation. Mendelian randomisation (MR) is an epidemiological technique that uses genetic variants as proxies for exposures in an attempt to determine whether there is a causal link between an exposure and an outcome. Given that genetic variants are randomly assigned during meiosis according to Mendel's first and second laws of heritability, MR may be thought of as a ‘natural’ RCT and is therefore less vulnerable to the aforementioned problems. MR has the potential to help identify new, and validate or disprove previously implicated, modifiable risk factors in cancer, but it is not without limitations. This review provides a brief description of the history and principles of MR, as well as a guide to basic MR methodology. The bulk of the review then examines various limitations of MR in more detail, discussing some of the proposed solutions to these problems. The review ends with a brief section detailing the practical implementation of MR, with examples of its use in the study of cancer, and an assessment of its utility in identifying cancer predisposition traits. © 2020 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
Histology of pediatric classic Hodgkin lymphoma: From diagnosis to prognostic stratification
Authors: Pizzi Marco , Tazzoli Sara , Carraro Elisa , Chaviano Felicia , Massano Davide , Lovisa Federica , Mussolin Lara , Todesco Alessandra , Biffi Alessandra , d'Amore Emanuele S. , Pillon Marta , Rugge Massimo 
Published: March 2020

AbstractAimsClassic Hodgkin lymphoma (cHL) is a common malignancy of the pediatric age. Although clinical‐radiological features are routinely used for disease risk stratification, the role of tumor histology has yet to be defined. This study aimed to characterize the clinical‐pathological features of a large cohort of pediatric cHL specifically investigating the relevance of tumor histology for the prognostic stratification of patients.Methods and resultsThe study considered 96 clinically annotated cases of pediatric cHL treated according to the AIEOP‐LH2004 protocol. The following histological parameters were considered: (i) cHL variant; (ii) grade of nodular sclerosis (NS); (iii) staining for Bcl2 and p53, and expression of B‐cell (BCA) and T‐cell antigens (TCA) by Hodgkin/Reed‐Sternberg cells. The study population consisted of 51 males and 45 females (median age: 13.6 years) with five‐year overall and progression‐free survival of 94% and 81%, respectively. Most cases featured NS morphology (96%) with a prevalence of NS1 over NS2 grades. Two NS2 variants were recognized (sarcomatous/syncytial and fibrohistiocytic). A consistent subset of cases disclosed positivity for BCA (34%), TCA (26%), p53 (13%), and Bcl2 (19%). Clinical‐pathological correlations showed a more aggressive clinical course for NS2 over NS1 cases. The NS2 fibrohistiocytic variant was associated with the worst outcome. No other histological features correlated with prognosis.ConclusionsPediatric cHL is a clinically and histologically heterogeneous neoplasm. The majority of cases disclose NS morphology and aberrant phenotypes are frequently encountered. In the pediatric population, NS grading and NS2 subtyping bear significant prognostic impact.
Registration of TARS‐LH1 pinto bean germplasm with resistance to the leafhopper pest
Authors: Porch Timothy G. , Brisco‐McCann Elizabeth I. , Demosthene Gasner , Colbert Raphael W. , Beaver James S. , Kelly James D. 
Published: March 2020

AbstractLeafhoppers (Empoasca spp.) cause significant yield reductions in common bean (Phaseolus vulgaris L.) and are a particularly important constraint for organic producers. Genetic resistance would benefit both conventional and organic dry and snap bean production threatened by leafhopper damage. Improvement of Empoasca kraemeri leafhopper resistance in tropical germplasm has been successful, but resistance to Empoasca fabae in temperate germplasm has not been broadly pursued. TARS‐LH1 (Reg. no. GP‐306, PI 691505) is a pinto bean germplasm resistant to E. fabae and E. kraemeri. TARS‐LH1 has been adapted to both temperate and tropical growing environments and was developed through the introgression of leafhopper resistance from the Mesoamerican common bean race into the Durango common bean race. TARS‐LH1 also possesses drought tolerance and the I gene for resistance to Bean common mosaic virus, is a near‐commercial pinto bean seed type, and has produced seed yields greater than parental cultivars under leafhopper pressure. This germplasm was developed cooperatively by the USDA‐ARS, Michigan State University, the Ministry of Agriculture of Haiti, and the University of Puerto Rico, Mayaguez.
Radiosensitization effect of selenocystine on HeLa cells in vitro
Authors: Qian Shen , Xie Li‐xin , Li Guo‐bao , Zheng Sha‐sha , Li Na 
Published: March 2020

AbstractObjectivesTo study the effect of selenocystine (Selenocystine, SeC) on the radiosensitivity of human cervical cancer Hela cells, and to provide a new target for radiosensitivity of cervical cancer.MethodsSeC were added to the cervical cancer Hela cells, and then irradiate with 200 cGy/min X‐rays. The radiosensitization effect of SeC on cervical cancer Hela cells were confirmed with the experiments of cell growth inhibition, clone formation, flow cytometry and Western blotting to detect apoptosis.ResultsSeC were added to the Hela cells at different doses of 0, 5, 10, and 20 μmol/L and incubating for 24 hours, the cell growth inhibition rates were: 0%, 22.68%, 41.71%, 74.19%, and the calculated IC50 was 14.83 μmol/L. The growth inhibition rate of Hela cells was dose‐dependent with the concentration of SeC. The results of the colony formation experiments showed that the cell colony formation rates of the single X‐ray irradiation doses of 0, 2, 4, 6, and 8 Gy were 100%, 77.56%, 46.89%, 28.67%, and 10.89%, respectively. After adding 5μmol/L SeC under the same irradiation dose, the colony formation rate was reduced to 70.98%, 59.45%, 30.67%, 14.29%, 3.72%; 5μmol/L SeC combined with radiation therapy can shift the survival curve to the left, and the D0 and Dq values were significantly smaller than those in the radiation group, P < 0.05. Hela cell apoptosis were detected by the flow cytometry showed that when the single X‐ray irradiation dose was 0, 2, 4, 8 Gy, the apoptosis scores were: 2.51 ± 0.06, 6.76 ± 0.03, 14.51 ± 0.15, 21.41 ± 0.08; When 5 μmol/L SeC was added and then combined with X‐ray irradiation, and the irradiation dose was 0, 2, 4, 8Gy, the apoptosis score of each group was: 10.89 ± 0.36, 15.18 ± 0.21, 31.19 ± 0.08, 45.53 ± 0.28, SeC combined with X‐ray had an interaction effect on Hela cells, and the apoptosis rate increased (F = 21.52, P < 0.01). When Hela cells were treated with SeC and X‐rays, the expression of PARP protein and phosphorylated p53 protein was significantly increased compared with the control group.ConclusionsSeC may have a radiosensitizing effect on Hela cells, and its mechanism may be related to promoting apoptosis. SeC will be expected to become a new sensitization target for cervical cancer radiotherapy.
Stratified rank histograms for ensemble forecast verification under serial dependence
Authors: Bröcker Jochen , Ben Bouallègue Zied 
Published: March 2020

AbstractRank histograms are a popular way to assess the reliability of ensemble forecasting systems. If the ensemble forecasting system is reliable, the rank histogram should be flat, “up to statistical fluctuations.” There are two long‐noted challenges to this approach. Firstly, uniformity of the overall distribution is implied by but does not imply reliability; ideally the distribution of the ranks should be uniform even conditionally on different forecast scenarios. Secondly, the ranks are serially dependent in general, precluding the use of standard goodness‐of‐fit tests to assess the uniformity of rank distributions without any further precautions. The present paper deals with both these issues by drawing together the concept of stratified rank histograms, which have been developed to deal with the first issue, with ideas that exploit the reliability condition to manage the serial correlations, thus dealing with the second issue. As a result, tests for uniformity of stratified rank histograms are presented that are valid under serial correlations.