bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Participatory, Mixed Methods Approach to Define and Measure Partnership Synergy in Long‐standing Equity‐focused CBPR Partnerships
Authors: Coombe Chris M. , Chandanabhumma P. Paul , Bhardwaj Prachi , Brush Barbara L. , Greene‐Moton Ella , Jensen Megan , Lachance Laurie , Lee S.Y. Daniel , Meisenheimer Melanie , Minkler Meredith , Muhammad Michael , Reyes Angela G. , Rowe Zachary , Wilson‐Powers Eliza , Israel Barbara A. 
Published: August 2020

AbstractUnderstanding what contributes to success of community‐based participatory research (CBPR) partnerships is essential to ensuring their effectiveness in addressing health disparities and health inequities. Synergy, the concept of accomplishing more together than separately, is central to partnership effectiveness. However, synergy specific to long‐standing, equity‐focused CBPR partnerships has not been closely examined. To address this, we defined and developed measures of partnership synergy as one dimension of a participatory mixed methods study, Measurement Approaches to Partnership Success (MAPS), to develop a validated instrument to measure success in long‐standing CBPR partnerships. Framed by a conceptual model and scoping literature review, we conducted in‐depth interviews with a national panel of academic and community experts in CBPR and equity to develop partnership synergy measures. Items were refined through an iterative process, including a three‐stage Delphi process, comparison with existing measures, cognitive interviews, and pilot testing. Seven questionnaire items were developed to measure synergy arising from equitable partnerships bringing together diverse partners across power differences to promote equity. Defining and measuring synergy in the context of long‐standing partnership success is central to understanding the role of synergy in collaborative approaches to research and action and can strengthen CBPR partnerships to promote healthy communities and advance health equity.
A patient with novel MBOAT7 variant: The cerebellar atrophy is progressive and displays a peculiar neurometabolic profile
Authors: Farnè Marianna , Tedesco Giovanna M. , Bedetti Chiara , Mencarelli Amedea , Rogaia Daniela , Colavito Davide , Di Cara Giuseppe , Stangoni Gabriela , Troiani Stefania , Ferlini Alessandra , Prontera Paolo 
Published: August 2020

AbstractMutations in the MBOAT7 gene have been described in 43 patients, belonging to 18 families, showing nonspecific clinical features (intellectual disability [ID], seizures, microcephaly or macrocephaly, and mild to moderate cerebellar atrophy) that make the clinical diagnosis difficult. Here we report the first Italian patient, a 22.5‐year‐old female, one of the oldest reported, born to apparently consanguineous parents. She shows severe ID, macrocephaly, seizures, aggressive outbursts, hyperphagia. We also documented progressive atrophy of the cerebellar vermis, that appeared not before the age of 7. The whole‐exome sequencing of the trio identified a novel homozygous variant c.1057_1058delGCinsCA (p.Ala353His) in the MBOAT7 gene. The variant is considered to be likely pathogenic, since it is absent from population database and it lies in a highly conserved amino acid residue. This disorder has a neurometabolic pathogenesis, implicating a phospholipid remodeling abnormalities. A brain hydrogen‐magnetic resonance spectroscopy (H‐MRS) examination in our patient disclosed a peculiar neurometabolic profile in the cerebellar hemispheric region. This new finding could address the clinical suspicion of MBOAT7‐related disorder, among the wide range of genetic conditions associated with ID and cerebellar atrophy. Moreover, the documented progression of cerebellar atrophy and the worsening of the disease only after some years open to the possibility of a therapeutic window after birth.
Quantitating skill acquisition with optical ultrasound simulation
Authors: Clark Anna E , Shaw Caroline J , Bello Fernando , Chalouhi Gihad E , Lees Christoph C 
Published: August 2020

AbstractObjectiveTo investigate and compare the effect of simulator training on quantitative scores for ultrasound‐related skills for trainees with novice level ultrasound experience and expert ultrasound operators.MethodsThree novice (comprising of 11, 32, 23 participants) and one expert (10 participants) subgroups undertook an ultrasound simulation training session. Pre‐ and post‐training test scores were collected for each subgroup. Outcome measures were as follows: mean accuracy score for obtaining the correct anatomical plane, percentage of correctly acquired target planes, mean number of movements, time to achieve image, distance travelled by probe and accumulated angling of the probe.ResultsThe novices showed improvement in image acquisition after completion of the simulation training session with an improvement in the rate of correctly acquired target planes from 28–57% to 39–83%. This was not replicated in the experts. The novice’s individual ratios based on pre‐ vs. post‐training metrics improved between 1.7‐ and 4.3‐fold for number of movements, 1.9‐ and 6.7‐fold for distance, 2.0‐ and 5.2‐fold for time taken and 1.8‐ and 7.3‐fold for accumulated angling. Among the experts, there was no relationship between pre‐training simulator metrics and years of ultrasound experience.ConclusionsThe individual simulation metrics suggest the sessions were delivered at an appropriate level for basic training as novice trainees were able to show demonstrable improvements in both efficiency and accuracy on the simulator. Experts did not improve after the simulation modules, and the novice scores post‐training were similar to those of experts, suggesting the exercises were valid in testing ultrasound skills at novice but not expert level.
Hearing loss and microstructural integrity of the brain in a dementia‐free older population
Authors: Croll Pauline H. , Vernooij Meike W. , Reid Robert I. , Goedegebure André , Power Melinda C. , Rigters Stephanie C. , Sharrett A. Richey , de Jong Robert J. Baatenburg , Mosley Thomas H. , de Groot Marius , Lin Frank R. , Deal Jennifer A. 
Published: August 2020

AbstractIntroductionAs hearing loss has been identified as an important risk factor for dementia, we aimed to assess the association between hearing loss and microstructural integrity of the brain.MethodsA total of 1086 dementia‐free participants (mean age = 75.2 [standard deviation: 4.9], 61.4% female) of the population‐based Atherosclerosis Risk in Communities (ARIC) study underwent hearing assessment (2016–2017) and magnetic resonance imaging of the brain (2011–2013). Microstructural integrity was determined with diffusion tensor imaging. Multivariable linear regression was used to investigate associations between hearing loss and microstructural integrity of different brain regions and white matter (WM) tracts.ResultsHearing loss was associated with lower WM microstructural integrity in the temporal lobe, lower gray matter integrity of the hippocampus, and with lower WM microstructural integrity of the limbic tracts and the uncinate fasciculus.ConclusionOur results demonstrate that hearing loss is indepedently associated with lower microstructural integrity in brain regions that are important for different cognitive processes.
Refolding of Cold‐Denatured Barstar Induced by Radio‐Frequency Heating: A New Method to Study Protein Folding by Real‐Time NMR Spectroscopy
Authors: Pintér György , Schwalbe Harald 
Published: August 2020

AbstractThe C40A/C82A double mutant of barstar has been shown to undergo cold denaturation above the water freezing point. By rapidly applying radio‐frequency power to lossy aqueous samples, refolding of barstar from its cold‐denatured state can be followed by real‐time NMR spectroscopy. Since temperature‐induced unfolding and refolding is reversible for this double mutant, multiple cycling can be utilized to obtain 2D real‐time NMR data. Barstar contains two proline residues that adopt a mix of cis and trans conformations in the low‐temperature‐unfolded state, which can potentially induce multiple folding pathways. The high time resolution real‐time 2D‐NMR measurements reported here show evidence for multiple folding pathways related to proline isomerization, and stable intermediates are populated. By application of advanced heating cycles and state‐correlated spectroscopy, an alternative folding pathway circumventing the rate‐limiting cis‐trans isomerization could be observed. The kinetic data revealed intermediates on both, the slow and the fast folding pathway.
Oxidative Addition of Water, Alcohols, and Amines in Palladium Catalysis
Authors: Grünwald Annette , Heinemann Frank W. , Munz Dominik 
Published: August 2020

AbstractThe homolytic cleavage of O−H and N−H or weak C−H bonds is a key elementary step in redox catalysis, but is thought to be unfeasible for palladium. In stark contrast, reported here is the room temperature and reversible oxidative addition of water, isopropanol, hexafluoroisopropanol, phenol, and aniline to a palladium(0) complex with a cyclic (alkyl)(amino)carbene (CAAC) and a labile pyridino ligand, as is also the case in popular N‐heterocyclic carbene (NHC) palladium(II) precatalysts. The oxidative addition of protic solvents or adventitious water switches the chemoselectivity in catalysis with alkynes through activation of the terminal C−H bond. Most salient, the homolytic activation of alcohols and amines allows atom‐efficient, additive‐free cross‐coupling and transfer hydrogenation under mild reaction conditions with usually unreactive, yet desirable reagents, including esters and bis(pinacolato)diboron.
Fe(III)‐catalyzed degradation of persistent textile dyes by chlorine at slightly acidic conditions: the crucial role of Cl2●− radical in the degradation process and impacts of mineral and organic competitors
Authors: Meghlaoui Fatima Zohra , Merouani Slimane , Hamdaoui Oualid , Alghyamah Abdulaziz , Bouhelassa Mohammed , Ashokkumar Muthupandian 
Published: August 2020

AbstractIn this work, we have explored for the first time the potential application of trace‐Fe(III)/chlorine system as an innovative oxidation technology for the degradation of persistent textile dyes. Fe(III)/chlorine combination improved the dye removal by ~40% within 30 s, as compared with chlorination alone, mainly through a radical pathway induced by the catalytic activation of chlorine in the presence of Fe(III). A chemical probe method was used for identifying the main reactive species. Cl2●− was found to be the key species responsible of huge abatement of dyes in the Fe(III)/chlorine system, whereas ●OH and Cl● can participate with only ~5% in the overall removal efficiency. At pH 3, 77% of reactive green 12 (RG12) was removed after 30 s, and then the removal efficiency diminished to 60% at pH 4, 20% at pH 5, and ~10% at pH 6 and 7. However, the best implication of free radicals was achieved at pH 4, at which the degradation rate was 3.3 time higher than that of chlorination alone. The dye removal efficiency increased with an increase in chlorine and iron loads up to certain optimums, but detrimental effect was observed at higher dosage levels. An increase in the solution temperature notably accelerated the removal yield (i.e., 81% of RG12 was removed at 50°C against 67% at 30°C and 57% at 10°C). NO2− and HSO3− as well as the cationic surfactant Adogen 464 showed strongest inhibiting effect on the performance of the process. Based on these findings, the Fe(III)/chlorine process is highly efficient in removing dyes from wastewaters.
From bilingual to multilingual neural‐based machine translation by incremental training
Authors: Escolano Carlos , Costa‐Jussà Marta R. , Fonollosa José A. R. 
Published: August 2020

AbstractA common intermediate language representation in neural machine translation can be used to extend bilingual systems by incremental training. We propose a new architecture based on introducing an interlingual loss as an additional training objective. By adding and forcing this interlingual loss, we can train multiple encoders and decoders for each language, sharing among them a common intermediate representation. Translation results on the low‐resource tasks (Turkish‐English and Kazakh‐English tasks) show a BLEU improvement of up to 2.8 points. However, results on a larger dataset (Russian‐English and Kazakh‐English) show BLEU losses of a similar amount. While our system provides improvements only for the low‐resource tasks in terms of translation quality, our system is capable of quickly deploying new language pairs without the need to retrain the rest of the system, which may be a game changer in some situations. Specifically, what is most relevant regarding our architecture is that it is capable of: reducing the number of production systems, with respect to the number of languages, from quadratic to linear; incrementally adding a new language to the system without retraining the languages already there; and allowing for translations from the new language to all the others present in the system.
Genome mining and functional analysis of cytochrome P450 genes involved in insecticide resistance in Leucinodes orbonalis (Lepidoptera: Crambidae)
Authors: Kariyanna Bheeranna , Prabhuraj Aralimarad , Asokan Ramasamy , Ramkumar Govindaraju , Venkatesan Thiruvengadam , Gracy Ramasamy G. , Mohan Muthugounder 
Published: August 2020

AbstractGenome‐wide analysis of cytochrome P450 monooxygenase (CYP) genes from the advanced genome project of the Leucinodes orbonalis and the expression analysis provided significant information about the metabolism‐mediated insecticide resistance. A total of 72 putative CYP genes were identified from the genome and transcriptome of L. orbonalis. The genes were classified under 30 families and 46 subfamilies based on the standard nomenclature. In the present study, a novel CYP gene, CYP324F1, was identified and it has not been reported from any other living system so far. Biochemical assays showed enhanced titers (5.81–18.5‐fold) of O‐demethylase of CYP in five field‐collected populations. We selected 34 homologous CYP gene sequences, seemed to be involved in insecticide resistance for primer design and quantitative real‐time PCR studies. Among the many overexpressed genes (>10 fold), the expression levels of CYP324F1 and CYP306A1 were prominent across all the field populations as compared with the susceptible iso‐female line. Oral delivery of ds‐CYP324F1 and ds‐CYP306A1 directed against CYP324F1 and CYP306A1 to the larvae of one of the insecticide resistance populations caused reduced expression of these two transcripts in a dose‐dependent manner (53.4%–85.0%). It appears that the increased titer of O‐demethylase is the result of increased transcription level of CYP genes in resistant populations. The data provide insight for identifying the novel resistance management strategies against L. orbonalis.
Pan‐Genome‐Scale Network Reconstruction: Harnessing Phylogenomics Increases the Quantity and Quality of Metabolic Models
Authors: Correia Kevin , Mahadevan Radhakrishnan 
Published: August 2020

AbstractA genome‐scale network reconstruction (GENRE) is a knowledgebase for an organism and has various applications. Available genome sequences have risen in recent years, but the number of curated GENREs has not kept pace. Existing yeast GENREs contain significant commission and omission errors. Current practices limit the quantity and quality of GENREs. An open and transparent phylogenomic‐driven framework is outlined to address these issues. The method is demonstrated with 33 yeasts and fungi in Dikarya. A pan‐fungal metabolic network called FYRMENT (Fungal and Yeast Metabolic Network) (https://github.com/LMSE/FYRMENT) is created, and annotated with ortholog groups from AYbRAH (https://github.com/LMSE/AYbRAH). Metabolic models for lower‐level taxons are compiled. The fungal pan‐GENRE contains 1553 orthologs, 2759 reactions, 2251 metabolites. The GENREs have higher genomic and metabolic coverage than existing yeast and fungal GENREs created with other methods. Metabolic simulations show the maximum amino acid yields from glucose differs between yeast lineages, indicating metabolic networks have evolved. Curating genomes and reactions at higher taxonomic‐levels increases the quantity and quality of GENREs than conventional approaches. This approach can scale to other branches in the tree of life.
An instructional definition and assessment rubric for bioinformatics instruction
Authors: Tapprich William E. , Reichart Letitia , Simon Dawn M. , Duncan Garry , McClung William , Grandgenett Neal , Pauley Mark A. 
Published: August 2020

AbstractThe lack of an instructional definition of bioinformatics delays its effective integration into biology coursework. Using an iterative process, our team of biologists, a mathematician/computer scientist, and a bioinformatician together with an educational evaluation and assessment specialist, developed an instructional definition of the discipline: Bioinformatics is “an interdisciplinary field that is concerned with the development and application of algorithms that analyze biological data to investigate the structure and function of biological polymers and their relationships to living systems.” The field is defined in terms of its two primary foundational disciplines, biology and computer science, and its interdisciplinary nature. At the same time, we also created a rubric for assessing open‐ended responses to a prompt about what bioinformatics is and how it is used. The rubric has been shown to be reliable in successive rounds of testing using both common percent agreement (89.7%) and intraclass correlation coefficient (0.620) calculations. We offer the definition and rubric to life sciences instructors to help further integrate bioinformatics into biology instruction, as well as for fostering further educational research projects.
Bioscience education 2030 and beyond: Where will technology take the curriculum?
Authors: Poronnik Philip , Sellwood Matthew J. 
Published: August 2020

AbstractThis brief review explores the ever‐increasing role that technological affordances may play in the 21C biochemistry and molecular biology curriculum. We consider the need to develop digital and creative fluencies in our students and the importance of creativity and visualization in learning science. The potential of virtual reality (VR) platforms to complement these goals are discussed with a number of examples. Finally, we look into the future where to see how VR might fit into a future curriculum.
Developing critical thinking in STEM education through inquiry‐based writing in the laboratory classroom
Authors: Jeon Ah‐Jung , Kellogg David , Khan Mohammad Asif , Tucker‐Kellogg Greg 
Published: August 2020

AbstractLaboratory pedagogy is moving away from step‐by‐step instructions and toward inquiry‐based learning, but only now developing methods for integrating inquiry‐based writing (IBW) practices into the laboratory course. Based on an earlier proposal (Science 2011;332:919), we designed and implemented an IBW sequence in a university bioinformatics course. We automatically generated unique, double‐blinded, biologically plausible DNA sequences for each student. After guided instruction, students investigated sequences independently and responded through IBW writing assignments. IBW assignments were structured as condensed versions of a scientific research article, and because the sequences were double blinded, they were also assessed as authentic science and evaluated on clarity and persuasiveness. We piloted the approach in a seven‐day workshop (35 students) at Perdana University in Malaysia. We observed dramatically improved student engagement and indirect evidence of improved learning outcomes over a similar workshop without IBW. Based on student feedback, initial discomfort with the writing component abated in favor of an overall positive response and increasing comfort with the high demands of student writing. Similarly, encouraging results were found in a semester length undergraduate module at the National University of Singapore (155 students).
Do agenda 2030 and Sustainable Development Goals act at local and operational levels? Evidence from a case study in a large energy company in Italy
Authors: Battaglia Massimo , Annesi Nora , Calabrese Mario , Frey Marco 
Published: August 2020

AbstractThis paper investigates the relationship between the business orientation to sustainability read under the lens of viable systems, and the operational and local dimensions of the Sustainable Development Goals (SDGs). The study deals with the experience of an Italian company operating as a monopolist in the energy industry, and it focuses on three innovative power transmission lines built in the 2000s. All the construction processes are analysed in order to explore both the operational effects and local impacts from a sustainability perspective. Embedding sustainability in a company actively contributes to the SDGs and creates a new interpretive model.
Emerging radiotherapy technologies and trends in nasopharyngeal cancer
Authors: Tseng Michelle , Ho Francis , Leong Yiat Horng , Wong Lea Choung , Tham Ivan WK , Cheo Timothy , Lee Anne WM 
Published: August 2020

AbstractTechnology has always driven advances in radiotherapy treatment. In this review, we describe the main technological advances in radiotherapy over the past decades for the treatment of nasopharyngeal cancer (NPC) and highlight some of the pressing issues and challenges that remain. We aim to identify emerging trends in radiation medicine. These include advances in personalized medicine and advanced imaging modalities, standardization of planning and delineation, assessment of treatment response and adaptive re‐planning, impact of particle therapy, and role of artificial intelligence or automation in clinical care. In conclusion, we expect significant improvement in the therapeutic ratio of radiotherapy treatment for NPC over the next decade.
Improving survival of stage II‐III primary gastric signet ring cell carcinoma by adjuvant chemoradiotherapy
Authors: Li Yang , Zhu Zhikai , Ma Fuhai , Xue Liyan , Tian Yantao 
Published: August 2020

AbstractBackgroundThere is no consistent evidence about the appropriate treatment strategies for gastric signet ring cell carcinoma (GSRC) to improve prognosis. We conducted a population‐based study to examine the effects of combined modality therapies on survival outcomes using the Surveillance, Epidemiology, and End Results (SEER) data.MethodsAnalyses included stage II‐III primary GSRC patients who were diagnosed between 2006 and 2016. Therapies were categorized as gastrectomy group, adjuvant chemotherapy (CT) group, neoadjuvant radiotherapy (RT) group, and adjuvant chemoradiotherapy (CRT) group. Survival analyses were conducted by Kaplan‐Meier method and Cox proportional hazards models and subgrouped by gender, tumor site, stage at diagnosis, and number of lymph nodes removed.ResultsOf the 1717 cases of stage II‐III primary GSRC, the mean (SD) age was 59.6 (13.3) years, and over a half were male (52.8%). A total of 39.9% patients received adjuvant CRT and the 5‐year overall survival (OS) rate was 34.6%. The median OS of patients treated with adjuvant CRT was significantly longer than that of the gastrectomy group (33 months vs 24 months, aHR = 0.71, 95% CI: 0.59, 0.84). Although the crude model showed a significant association between adjuvant CT and total survival (cHR = 0.81, 95% CI: 0.68, 0.96), the effect measure turned null in the multivariable and sub‐group analysis. We did not find the significant effect of neoadjuvant RT.ConclusionsIn this study, GSRC patients with stage II‐III experienced improved overall survival after receiving adjuvant CRT, which provides several treatment implications. More clinical trials will be needed to verify the conclusion derived from this study.