bluuebunny/crossref_metadata_2025_split huggingface dataset:
Is it Possible to Implement a Rare Disease Case-Finding Tool in Primary Care? A UK-Based Pilot Study
Authors: Buendia Orlando , Shankar Sneha , Mahon Hadley , Toal Connor , Menzies Lara , Ravichandran Pradeep , Roper Jane , Taghar Jag , Benfredj Rudy , Evans Will 
Published: August 2021

Abstract
Introduction:This study implemented MendelScan, a primary care rare disease case-finding tool, into a UK National Health Service (NHS) population. Rare disease diagnosis is challenging due to disease complexity and low physician awareness. The 2021 UK Rare Diseases Framework highlights a global need for faster diagnosis to improve clinical outcomes as a key priority.Methods & Results:A UK primary care locality with 68,705 patients was examined. MendelScan encodes diagnostic/screening criteria for multiple rare diseases, mapping clinical terms to appropriate SNOMED CT codes (UK primary care standardised clinical terminology) to create digital algorithms. These algorithms were applied to a pseudo-anonymised structured data extract of the electronic health records (EHR) in this locality to "flag" at-risk patients who may require further evaluation. All flagged patients then underwent internal clinical review (a doctor reviewing each EHR flagged by the algorithm, removing all cases with a clear diagnosis that explains the clinical features that led to the patient being flagged); for those that passed this review, a report was returned to their GP. 55 of 76 disease criteria flagged at least one patient. 227 (0.33%) of the total 68,705 of EHR were flagged; 18 EHR were already diagnosed with the disease (The highlighted EHR has a diagnostic code for the same RD it was screened for. e.g Behcet’s disease algorithm identifying an EHR with a SNOMED CT code Behcet's disease). 75/227 (33%) EHR passed our internal review. Thirty-six reports were returned to the GP. Feedback was available for 28/36 of the reports sent. GP categorised nine reports as "Reasonable possible diagnosis" (advance for investigation), six reports as "diagnosis has already been excluded", ten reports as "patient has a clear alternative aetiology", and three reports as "Other" (patient left study locality, unable to re identify accurately). All the 9 cases considered as "reasonable possible diagnosis" had a further actionable evaluation.Conclusions:This pilot demonstrates that implementing such a tool is feasible at a population level. The case-finding tool identified credible cases which were subsequently referred for further investigation. Future work includes performance-based validation studies of diagnostic algorithms and the scalability of the tool.
The Genomic Basis of the Genetic Differentiation and Local Adaptive Evolution of Pampus Echinogaster based on SLAF-seq
Authors: Li Yuan , Lou Fangrui , Li Hai , Wang Rui , Cai Zizi , Zhang Ran , Weng Youzhu , Lin Longshan , Zhuang Xuan 
Published: August 2021

Abstract
Background: Factors such as climate change (especially ocean warming) and overfishing have led to a decline in the supply of Pampus echinogaster and a trend of decreasing age. Exploring the genetic structure and local adaptive evolutionary mechanisms is crucial for the management of P. echinogaster. Results: This population genomic study of nine geographical populations of P. echinogaster in China was conducted by specific-locus amplified fragment sequencing (SLAF-seq). A total of 935,215 SLAF tags were obtained, and the average sequencing depth of the SLAF tags was 20.80×. After filtering, a total of 46,187 high-consistency genome-wide single nucleotide polymorphisms (SNPs) were detected. Based on all SNPs, the overall genetic diversity among the nine P. echinogaster populations was high. The Shantou population had the lowest genetic diversity, and the Tianjin population had the highest. Meanwhile, the population genetic structure based on all SNPs revealed significant gene exchange and insignificant genetic differentiation between the nine P. echinogaster populations. Based on pairwise genetic differentiation (FST), we further screened 1,852 outlier SNPs that might have been affected by habitat selection and annotated SLAF tags containing these 1,852 outlier SNPs using Blast2GO. The annotation results showed that the genomic sequences at the outlier SNPs were mainly related to material metabolism, ion transport, breeding, stress response, and inflammatory reactions, which may be related to the adaptation of P. echinogaster to different environmental conditions (such as water temperature and salinity) in different sea areas.Conclusions: The high genetic similarity of nine P. echinogaster populations may have been caused by the population expansion after the last glacial period, the lack of balance between migration and genetic drift, and the long-distance diffusion of eggs and larvae. We suspected that variation of these genes associated with material metabolism, ion transfer, breeding, stress reactions, and inflammatory reactions were critical for adaptation to spatially heterogeneous temperatures in natural P. echinogaster populations.
Cyphellostereum Ushima Sp. Nov. (Hygrophoraceae, Agaricales) Described from Amami-Oshima Island (Kagoshima Prefecture, Ryukyu Islands), Japan, with Ultrastructural Observations of its Rhizonema Photobiont Filaments Penetrated Longitudinally by a Central Haustorium
Authors: Masumoto Hiroshi , Degawa Yousuke 
Published: August 2021

Abstract
We collected a resupinate fungus lichenized with filamentous Rhizonema cyanobacteria in Amami-Oshima Island, Japan. Microscopic observations and molecular phylogenetic analyses of both the basidioma and the lichenized thallus indicated affinities within Cyphellostereum, the first record of this basidiomycete genus from Japan. Its unique combination of structural characters and ITS rDNA sequences suggest a new species, described here as C. ushima. Light and transmission electron microscopic observations revealed tubular intracellular haustoria penetrating longitudinally within the cyanobacterial cells, a feature typically seen in the related genus Dictyonema, but unusual in Cyphellostereum. The generic circumscription of Cyphellostereum was therefore emended to include features of C. ushima and other recently described species that deviate from the conventional definition of the genus. Ultrastructural details of symbiont interactions are provided for the first time in this genus. We also succeeded in cultivating the fungus from hyphae regenerated from thallus fragments, and include a brief description of those results.TreeBASE reviewer access URL:http://purl.org/phylo/treebase/phylows/study/TB2:S28437?x-access-code=84d2007afb05bd743f34101ac2d97dac&format=html
Construction of Yeast One-hybrid Library and Screening of Transcription Factors Regulating LhMYB12-Lat Expression in Asiatic Hybrid Lilies (Lilium spp.)
Authors: Cao Yuwei , Bi Mengmeng , Yang Panpan , Song Meng , He Guoren , Wang Jing , Yang Yue , Xu Leifeng , Ming Jun 
Published: August 2021

Abstract
Background: Anthocyanins, which belong to flavonoids, are widely colored among red-purple pigments in the Asiatic hybrid lilies (Lilium spp.). Transcription factor (TFs) LhMYB12-Lat, identified as the major kernel protein, regulating the anthocyanin biosynthesis pathway in ‘Tiny Padhye’ of Tango series cultivars, which the pigmentation density is high in the lower half of tepals and this patterning is of exceptional ornamental value. However, the research on mechanism of regulating the spatial and temporal expression differences of LhMYB12-Lat, which belongs to the R2R3-MYB subfamily, is still not well established. To explore the molecular mechanism of directly related regulatory proteins of LhMYB12-Lat in the anthocyanin pigmentation, the yeast one-hybrid (Y1H) cDNA library was constructed and characterized. Results: In this study, we describe a yeast one-hybrid library to screen transcription factors that regulate LhMYB12-Lat gene expression in Lilium, with the library recombinant efficiency of over 98%. The lengths of inserted fragments ranged from 400-2000 bp, and the library capacity reached 1.6 × 106 CFU of cDNA insert, which is suitable to fulfill subsequent screening. Finally, seven prey proteins, including BTF3, MYB4, IAA6-like, ERF4, ARR1, ERF WIN1-like, and ERF061 were screened by the recombinant bait plasmid and verified by interaction with the LhMYB12-Lat promoter. Among them, ERF, AUX/IAA, and BTF3 may participate in the negative regulation of the anthocyanin biosynthesis pathway in Lilium.Conclusion: A yeast one-hybrid library of lily was successfully constructed in the tepals for the first time. Seven candidate TFs of LhMYB12-Lat were screened, which may provide a theoretical basis for the study of floral pigmentation.
Exploration the Role of a Clinical Supervisor to Improve the Professional Skills of Medical Students in IRAN: A Content Analyze Study
Authors: Keshavarzi Mohammad Hasan , Azandehi Salimeh khalili , Koohestani Hamidreza , Moghadam Hamid Reza Baradaran Attar , Ghorbani Ali Asghar , Hayat Ali Asghar 
Published: August 2021

Abstract
Background Clinical supervision is a supporter for learners and paves the way for effective and efficient learning in clinical settings. This study aimed to explain the responsibilities of clinical supervisors in clinical education wards to improve the professional skills of medical students.Methods: In this qualitative study, we used the conventional content analysis approach. The sample consisted of 16 faculty members of Iranian universities of medical sciences and medical graduates. Purposeful sampling and semi-structured interviews were used to collect data. The Granheim and Landman method (2004) was used to analyze the data.Results: From the analysis of interviews, 2 themes, 8 categories, and 18 subcategories were obtained. "Clinical supervisor responsibilities” as a theme includes the categories: “Creating motivation in learner”, “Learner's need recognition”, “Performance evaluation”, “Creating learning opportunities”, and “Professional ethics education”. And, the sub-categories were: “Creating a supportive atmosphere”, “Task assignment” ,”Understanding training needs”, “Understanding individual needs”, “Periodic evaluation”, “Proper feedback’, “Reduce work stress”, “Learner engagement’ , “Learning Facilitation”, “Attention to the patient's treatment”, and “Ethical observance in relation to patients”. As the second theme "Clinical supervisor characteristics” included the categories of: “Scientific competence”, “Leading role”, and “Ethical model”. Their sub-categories are clustered as: “Knowledge of educational concepts”, “Mastery of professional concepts”, “Effective communication skills”, “Understanding managerial concepts”, “High resilience”, “Career commitment “, and “ social commitment ”. Conclusions The clinical supervisor will improve the professional skills of medical students, which will improve the quality of services provided, train efficient graduates, and provide a safe and relaxing environment that leads to patient satisfaction.
Gigahertz free-space electro-optic modulators based on Mie resonances
Authors: Benea-Chelmus Ileana-Cristina , Mason Sydney , Meretska Maryna , Elder Delwin , Kazakov Dmitry , Shams-Ansari Amirhassan , Dalton Larry , Capasso Federico 
Published: August 2021

Abstract
Electro-optic modulators from non-linear χ(2) materials are essential for sensing, metrology and telecommunications because they link the optical domain with the microwave domain. At present, most geometries are suited for fiber applications. In contrast, architectures that modulate directly free-space light at gigahertz (GHz) speeds have remained very challenging, despite their dire need for active free-space optics, in diffractive computing or for optoelectronic feedback to free-space emitters. They are typically bulky or suffer from much reduced interaction lengths. Here, we employ an ultrathin array of sub-wavelength Mie resonators that support quasi bound states in the continuum (BIC) as a key mechanism to demonstrate electro-optic modulation of free-space light with high efficiency at GHz speeds. Our geometry relies on hybrid silicon-organic nanostructures that feature low loss (Q = 550 at λres = 1594 nm) while being integrated with GHz-compatible coplanar waveguides. We maximize the electro-optic effect by using high-performance electro-optic molecules (whose electro-optic tensor we engineer in-device to exploit r33 = 100 pm/V) and by nanoscale optimization of the optical modes. We demonstrate both DC tuning and high speed modulation up to 5 GHz (fEO,-3 dB = 3 GHz) and shift the resonant frequency of the quasi-BIC by Δλres =11 nm, surpassing its linewidth. We contrast the properties of quasi-BIC modulators by studying also guided mode resonances that we tune by Δλres=20 nm. Our approach showcases the potential for ultrathin GHz-speed free-space electro-optic modulators.
A Log-Exponential Shrinkage Technique for De-Noising of Ultrasound Images for Breast Cancer
Authors: Singh Mayank Kumar , Saini Indu , Sood Neetu 
Published: August 2021

Abstract
Ultrasound in diagnostic imaging is well known for its safety and accessibility. But its efficiency for diagnosis is always limited by the presence of noise. So, in this study, a Log-Exponential shrinkage technique is presented for denoising of ultrasound images. A Combinational filter was designed for the removal of additive noise without losing any details. The speckle noise after homomorphic transformation follows Gaussian distribution and the conventional median estimator has very low accuracy for Gaussian distribution. The scale parameter calculated from the sub-band coefficients after homomorphic transformation was utilized to design the estimator. For shrinkage of wavelet coefficients, a multi-scale thresholding function was designed, with better flexibility. The proposed technique was tested for both medical and standard images. A significant improvement was observed in the estimation of speckle noise variance. For quantitative evaluation of the proposed technique with existing denoising methods, Mean Squared Error (MSE), Structural Similarity Index (SSIM), and Peak Signal to Noise Ratio (PSNR) were used. At the highest noise variance, the minimum improvement achieved by the proposed denoising technique in PSNR, SSIM, and MSE was 10.65%, 23.21%, and 30.46% respectively.
Silicon Mediated Changes in Growth and Photosynthetic Pigment of Wheat Plant Under Salt Stress
Authors: Singh Pooja , Kumar Vikram , Sharma Jyoti , Sharma Asha 
Published: August 2021

Abstract
Purpose Salinity is a most important environmental stress which adversely affects the crop production and yield. In recent years, Silicon (Si) is gaining an increased attention in the field of stress management. Wheat (Triticum aestivum L.) is one of the moderately prone crops to different abiotic stresses which instantly damage the crop yield under stress condition. This work demonstrates the positive impact of Si on growth and photosynthetic pigments in wheat under saline conditions.Methods In this research work, two genotypes of wheat i.e. KRL 210 and WH 1105, were grown-up in soil under different salt stress concentration. There were different treatments under which they grown included T0= Control without salt stress (0 dS m-1) , T1= Sodium silicate without salt stress (2 mM) , T2= Control with salt stress (4 dS m-1) T3= Control with salt stress (8 dS m-1) T4= Control with salt stress (12 dS m-1) T5= Sodium silicate with salt stress (4dS m -1 + 2mM Si) T6= Sodium silicate with salt stress (8dS m-1 +2 mM Si) T7= Sodium silicate with salt stress (12dS m-1 +2mM Si). At vegetative stage, both the wheat genotypes were compared with their growth parameters and photosynthetic pigments.Results Plant biomass, shoot-root length and photosynthetic pigments (chlorophyll- a, b, carotenoid & total chlorophyll) of wheat decreased under salt stress when increased up to 12 dS m-1 NaCl concentration. However, in salt stressed wheat plants, plant biomass increased by the Si application. Supplementation of Si improved the plant length as well as chlorophyll pigments which were decreased by the high salt concentration in plants. Silicon was found more effective in salt stressed condition than in alone with control.Conclusion So, it was determined that the Si application aided the wheat genotypes in alleviating salinity and enhancing their biomass and photosynthetic pigments which were declined in salt stress condition.
Personalized Multi-Drug Combinations in Breast Cancer Treatment Using Individual Pattern of Perturbed Gene Expression and Drug Signatures
Authors: Mokhtari Majid , Khoshbakht Samane , Akbari Mohammad Esmaeil , Moraveji Sayyed Sajjad , Masoudi-Nejad Ali 
Published: August 2021

Abstract
The greatest challenge in recent years in cancer treatment has been drug screening. Few platforms presented reliable solutions for personalized drug validation and safety testing. Here, we constructed a personalized drug combination protocol as the primary input to such platforms. We used public data from whole-genome expression profiles of 6173 breast cancer patients, 312 healthy individuals, and 691 drugs. We developed an individual pattern of perturbed gene expression (IPPGE) for each patient. A protocol was designed to extract personalized drug combinations by comparing the IPPGE and drug signatures. We tried to use the concept of drug repurposing, which searches for the new benefits of the existing medicines that may perturb the desired genes. The potential for treatment effectiveness was more significant for drug combinations extracted from specialized and nonspecialized cancer medicines than specialized medicines. Thus, effective treatments can be provided through the approach of drug repurposing and combination drug therapy. Implications The protocol allows personalized drug combinations to be extracted from hundreds of drugs and thousands of drug combinations. This can be used as a methodological interface between drug repurposing and combination drug therapy in cancer treatment.
HIV Care in Times of COVID-19 – Rapid Treatment Start Seems as Vital and Cost-Effective Approach in Central and Eastern Europe
Authors: KOWALSKA Justyna D. , WOJCIK Grzegorz , RUTKOWSKI Jakub , SIEWASZEWICZ Ewa 
Published: August 2021

Abstract
Background: In times of SARS-CoV-2 epidemic it is essential to deliver specialist HIV care with a maximum effectiveness, but minimum epidemiological risk. Therefore, we aimed to determine whether rapid linkage tocare definedas starting combined antiretroviral therapy (cART) at the day of first visit in HIV clinic is a cost-effective approach.Methods:The analysis used Markov's lifetime model presented in our previous study. The input data used in the model were updated in terms of costs, life expectancy tables and patient’s characteristics. This analysis used information from the previous model about the additional cost of treatment and QALY lost in the life horizon for people newly infected with HIV. Number of new infected persons was estimated on the basis of available data.Results:Input data were available for 344 MSM patients who registered in HIV specialist care between 2016 and 2017. Estimated QALY loss due to no rapid treatmentin case of no taking (taking) into account viral load equal 0·018 (0·022), 0·039 (0·047), 0·131 (0·158) respectively in low, medium and high-risk transmission groups. RapidcART initiation was dominant regardless of the chosenscenarios. Conclusions:Taking into account HIV transmission in cost–effectiveness analysis indicates that rapid-initiation of HIV treatment is profitable.
Deep Neural Networks Evolve Human-like Attention Distribution during Goal-directed Reading Comprehension
Authors: Zou Jiajie , Ding Nai 
Published: August 2021

Abstract
Attention is a key mechanism for information selection in both biological brains and many state-of-the-art deep neural networks (DNNs). Here, we investigate whether humans and DNNs allocate attention in comparable ways when seeking information in a text passage to answer a question. We analyze 3 transformer-based DNNs that reach human-level performance when trained to perform the reading comprehension task. We find that the DNN attention distribution quantitatively resembles human attention distribution measured by eye tracking: Human readers fixate longer on words that are more relevant to the question-answering task, demonstrating that attention is modulated by the top-down reading goal, on top of lower-level visual layout and textual features. Further analyses reveal that the attention weights in DNNs are also influenced by both the top-down reading goal and lower-level textual features, with the shallow layers more strongly influenced by lower-level textual features and the deep layers attending more to task-relevant words. Additionally, deep layers’ attention to task-relevant words gradually emerges when pre-trained DNN models are fine-tuned to perform the reading comprehension task, which coincides with the improvement in task performance. These results demonstrate that DNNs can naturally evolve human-like attention distribution through task optimization. The results suggest that human attention during goal-directed reading comprehension is a consequence of task optimization and the attention weights in DNN are of biological significance.
Predictive Power of Extubation Failure Diagnosed by Cough Strength: A Systematic Review and Meta-Analysis
Authors: Duan Jun , Zhang Xiaofang , Song Jianping 
Published: August 2021

Abstract
Background: The predictive power of extubation failure diagnosed by cough strength is various in different studies. We aimed to summarize the diagnostic power of extubation failure tested by cough strength. Methods: A comprehensive on-line search was performed to select any potentially eligible studies that evaluated the predictive power of extubation failure tested by cough strength. A manual research was also performed to identify additional studies. Data were extracted to calculate the pooled sensitivity, specificity, positive likelihood ratio (LR), negative LR, diagnostic odds ratio (DOR), and area under the receiver operating characteristic curves (AUC) to evaluate predictive power of extubation failure. I2 was used to test the heterogeneity and deek’s funnel plot was used to detect the publication bias.Results: A total of 35 studies involving 7515 patients were included. Of them, 1113 patients (14.8%) experienced extubation failure. Twenty studies involving 2787 patients assessed cough strength by measure of cough peak flow (CPF) to predict extubation failure. The pooled sensitivity, specificity, positive LR, negative LR, DOR, and AUC were 0.77 (95%CI: 0.72-0.80), 0.75 (0.69-0.80), 2.84 (2.36-3.42), 0.34 (0.29-0.39), 9.16 (6.14-13.67), and 0.81 (0.77-0.84), respectively. Twenty studies involving 5508 patients assessed cough strength by measurement of a semiquantitative cough strength scale (SCSS) to predict extubation failure. The pooled sensitivity, specificity, positive LR, negative LR, DOR, and AUC were 0.54 (95%CI: 0.43-0.65), 0.82 (0.73-0.88), 2.48 (1.92-3.21), 0.63 (0.54-0.74), 4.61 (3.03-7.01), and 0.74 (0.70-0.78), respectively. Conclusions: Cough strength can be measured by CPF and SCSS. The CPF has good predictive power to diagnose extubation failure and SCSS has moderate predictive power.