bluuebunny/crossref_metadata_2025_split huggingface dataset:
An energy charge sensor for balancing RNA polymerase recycling and hibernation
Authors: Wahl Markus , Pei Hao-Hong , Hilal Tarek , Chen Zhuo , Huang Yong-Heng , Gao Yuan , Said Nelly , Loll Bernhard , Rappsilber Juri , Belogurov Georgiy , Artsimovitch Irina 
Published: July 2020

Abstract
Cellular RNA polymerases can become trapped on DNA or RNA, threatening genome stability and limiting free enzyme pools, or enter dormancy. How RNA polymerase recycling into active states is achieved and balanced with quiescence remains elusive. We structurally analyzed Bacillus subtilis RNA polymerase bound to the NTPase HelD. HelD has two long arms: a Gre cleavage factor-like coiled-coil inserts deep into the RNA polymerase secondary channel, dismantling the active site and displacing RNA; a unique helical protrusion inserts into the main channel, prying β and β’ subunits apart and dislodging DNA, aided by the δ subunit. HelD release depends on ATP, and a dimeric structure resembling hibernating RNA polymerase I suggests that HelD can induce dormancy at low energy levels. Our results reveal an ingenious mechanism by which active RNA polymerase pools are adjusted in response to the nutritional state.
Dynamic Memristor-based Reservoir Computing for High-Efficiency Spatiotemporal Signal Processing
Authors: Zhong Yanan , Tang Jianshi , Li Xinyi , Gao Bin , Qian He , Wu Huaqiang 
Published: July 2020

Abstract
Reservoir computing (RC) is a highly efficient network for processing spatiotemporal signals due to its low training cost compared to standard recurrent neural networks. The design of different reservoir states plays a very important role in the hardware implementation of RC system. Recent studies have used the device-to-device variation to generate different reservoir states; however, this method is not well controllable and reproducible. To solve this problem, we report a dynamic memristor-based RC system. By applying a controllable mask process, we reveal that even a single dynamic memristor can generate rich reservoir states and realize the complete reservoir function. We further build a parallel RC system that can efficiently handle spatiotemporal tasks including spoken-digit and handwritten-digit recognitions, in which high classification accuracies of 99.6% and 97.6% have been achieved, respectively. The performance of dynamic memristor-based RC system is almost equivalent to the software-based one. Besides, our RC system does not require additional read operations, which can make full use of the device nonlinearity and further improve the system efficiency. Our work could pave the road towards high-efficiency memristor-based RC systems to handle more complex spatiotemporal tasks in the future.
Identification of a Six-Gene Signature Predicting Overall Survival for Oxaliplatin and 5-Fluorouracil Resistant Colon Cancer and Potential Drug-Repurposing
Authors: Yang Feng , Cai Shaoyi , Su Riya , Ling Li , Tao Liang , Wang Qin 
Published: July 2020

Abstract
Background: Oxaliplatin (L-OHP) and 5-fluorouracil (5-FU) resistance in colorectal cancer (CRC) is a major medical problem. Therefore, detailed mechanisms and predictive markers are urgently needed. The aim of this study was to identify key pathways, a robust prognostic gene signature and potential drug-repurposing. Methods: In order to confirm the predictive markers and detailed molecular mechanisms of L-OHP and 5-Fu chemoresistant CRC, we performed weighted correlation network analysis (WGCNA), an unsupervised analysis method, to identify the chemoresistant CRC significantly related genes. Then, the gene prognostic model was conducted by Univariate Cox regression and Lasso penalized Cox regression analysis. Subsequently, the time-dependent receiver operating characteristic (ROC) and Kaplan-Meier survival curve were performed to assess the prognostic capacity of the model. Simultaneously, pathway enrichment was done to identify the key pathways involved in chemoresistant CRC. Moreover, we explored how the hub genes interacted with key pathways and transcription factors. Then, we found the potential drug target by the subcellular location fo hub genes. Finally, we identified the potential drug-repurposing by virtual screening for chemoresistant CRC according to ZINC 15 database. Results: We identified the key pathways using KEGG over-representation test and Gene Set Enrichment Analysis (GSEA): Ribosome KEGG pathway. Moreover, six hub-genes prognostic model was conducted by Univariate Cox regression and Lasso penalized Cox regression analysis. Additionally, the detailed interactions among the pathway and hub genes (RBM6, PNN, LEF1, ANO1, PAFAH1B3 and BHLHE41) were examined by protein-protein interaction (PPI) network and shortest-pathway analysis. Furthermore, ANO1 was considered the potential drug target based on the subcellular location and ZINC000018043251 was verified the potential drug by virtual screening Conclusions: Our study identified a novel six-gene resistant signature for CRC prognosis prediction and the molecular details of these interactions between hub genes (RBM6, PNN, LEF1, ANO1, PAFAH1B3 and BHLHE41) and Ribosome key pathways. Furthermore, ZINC000018043251 was verified the potential drug for ANO1 by virtual screening, which might help to improve the outcome of CRC patients.
Combining External Medical Knowledge for improving Obstetric Intelligent Diagnosis
Authors: Zhang Kunli , Cai Linkun , Song Yu , Liu Tao , Zhao Yueshu 
Published: July 2020

Abstract
Background: Data-driven medical health information processing has become a new development trend in obstetrics. Electronic medical records (EMRs) are the basis of evidence-based medicine and important information source for intelligent diagnosis. To obtain diagnostic results, doctors combine clinical experience and medical knowledge in their diagnosis process. External medical knowledge provides strong support for diagnosis. Therefore, how to make full use of EMRs and medical knowledge in intelligent diagnosis is worth studying.Methods: As an EMR usually contains multiple types of diagnostic results, the intelligent diagnosis can be treated as a multi-label classification task. We propose a novel neural network model called Knowledge-aware Hierarchical Diagnosis Model (KHDM) in which Chinese obstetric EMRs and external medical knowledge can be synchronously and effectively used for intelligent diagnostics. In the KHDM, EMRs and external knowledge documents are integrated by the attention mechanism contained in the hierarchical deep learning framework. In this way, we enrich the language model with curated knowledge documents, combining the advantages of both to make a knowledge-aware diagnosis.Results: We evaluate our model on a real-world Chinese obstetric EMR dataset show that KHDM achieves an accuracy of 0.8929, which exceeds that of the most advanced classification benchmark methods.Conclusion: In this paper, an improved model combining medical knowledge and an attention mechanism is proposed, which is based on the problem of the diversity of diagnostic results in Chinese EMRs. KHDM can effectively integrate domain knowledge to greatly improve the accuracy of diagnosis, and we also verify the model's interpretability advantage.
Efficient Protection of Probiotics for Delivery to the gastric tract by Cellulose Sulphate Encapsulation
Authors: Gunzburg Walter Henry , Aung Myo Myint , Toa Pauline , Ng Shirelle , Read Eliot , Tan Wee Jin , Brandtner Eva Maria , Dangerfield John , Salmons Brian 
Published: July 2020

Abstract
Gut microbiota in humans and animals play an important role in health, aiding in digestion, regulation of the immune system and protection against pathogens. Changes or imbalances in the gut microbiota (dysbiosis) have been linked to a variety of local and systemic diseases, and there is growing evidence that restoring the balance of the microbiota can restore health. This can be achieved by oral delivery of members of the microbiome (including probiotics) or by fecal microbiome transplantation. In order to provide their health promoting effects, microbiota must survive (i) transport and storage (i.e. shelf life) and (ii) transit through the highly acid conditions in the stomach and bile salts in the small intestine. We have developed a cell encapsulation technology based on the natural polymer, cellulose sulphate (CS) that protects members of the microbiota from stomach acid and bile.
Barriers in Implementing the Dying Patient Law: The Israeli Experience - A Qualitative Study
Authors: Zigdon Avi , Nissanholtz-Gannot Rachel 
Published: July 2020

Abstract
Background Coping with end-of-life issues is a major challenge for governments and health systems. Despite progress in legislation, many barriers exist to its full implementation. This study is aimed at identifying these end-of-life barriers in relation to Israel.Methods Qualitative in-depth interviews using professionals and decision makers in the health-care and related systems (n=37) were carried out, along with two focus groups based on brainstorming techniques consisting of nurses (n=10) and social workers (n=10). Data was managed and analyzed using Naralyzer software.Results Qualitative analysis showed identification of six primary barriers: 1) law, procedures, and forms; 2) clinical aspects; 3) human aspects; 4) knowledge and skills of medical teams; 5) communication; and 6) resource allocation. These were further divided into 44 sub area barriers.Conclusions This study highlights the role of the family doctor in end-of-life by training physicians in decision-making workshops and increasing their knowledge in the field of palliative medicine. Effectively channeling resources, knowledge, and support for medical teams, by accounting for the structure and response of the units for home treatment will improve patient's access to information on and support for end-of-life laws, as well as reduce legislative barriers in other countries that face the same issues.
Health-Care Organization For The Management and Surveillance of SARS-CoV-2 Infection in Children During Pandemic in Italy
Authors: Nunziata Francesco , Bruzzese Eugenia , Poeta Marco , Pierri Luca , Catzola Andrea , Ciccarelli Gian Paolo , Vassallo Edoardo , Montella Emma , Vecchio Andrea Lo , Guarino Alfredo 
Published: July 2020

Abstract
Background: In comparison with adults, severe acute respiratory syndrome (SARS-CoV-2) infection in children has a milder course. The management of children with suspected or confirmed coronavirus disease (COVID-19) needs to be appropriately targeted. Methods: We designed a hub-and-spoke system involving a Hub Centre to provide relevant healthcare information, based on the use of telemedicine and stringent admission criteria. Result: Between March and April 2020, the Hub Centre managed a total of 119 children (62 males, 52%; median age, 5.5 years; interquartile range [IQR], 2; 10) with suspected or confirmed COVID-19. Of the 119 children, 90 were managed in cooperation with family paediatricians and 29 with hospital-based physicians. In total, 8 (6.7%) children were hospitalised, with a median length of hospital stay of 10 days (IQR, 8.5 days; range, 4–22 days). Conclusion: case-by-case management allows a global evaluation in which the clinical condition is one determinant in medical decision-making along with the use of isolation to prevent the spread of COVID-19 among family members and cohabitants, and biocontainment measures. Large centres could coordinate paediatric COVID-19 cases through telemedicine, taking advantage of the generally milder presentation in children but also considering their dependence on adults and risk of infection spreading.
Differences in Objectively Measured Daily Physical Activity Patterns Related to Depressive Symptoms in Community Dwelling Women - mPED Trial
Authors: Figueroa Caroline , Vittinghof Eric , Aguilera Adrian , Fukuoka Yoshimi 
Published: July 2020

Abstract
Background:Physical activity(PA) has been identified as an effective depression treatment.However, knowledge on how variation in day-to-day PA relates to depression is lacking. Purpose:The purposes of this cross-sectional analysis were to 1) compare overall objectively measured baseline daily steps and duration of moderate to vigorous PA (MVPA) and 2) examine differences in steps and MVPA on days of the week between women with high and low depressive symptoms, enrolled in the mobile phone based physical activity education (mPED) trial.Methods:The Center for Epidemiological Studies Depression Scale was used to categorize low and high depressive symptom groups.We used linear mixed-effects models to examine the associations between steps and MVPA and depression-status both overall and by day of the week,adjusting for selected demographic variables and their interactions with day of the week.Results:275 women were included in the final analysis, of which 217 had low and 58 had high depressive symptoms. We found that day of the week modified the associations of depression with both daily steps and MVPA. Women with high depressive symptoms were characterized by reduced activity at the end of the week (Friday: 832 fewer steps, 95% CI:116 to 1548, p=0.023; 8.9 lower MVPA, 95% CI:2.2 to 15.5, p=0.009), whereas women with low depression showed an increase in physical activity.Conclusions:Day of the week might be an important target for personalization of physical activity interventions. Future work should evaluate potential causes of alterations in daily activity patterns in depression.Trial RegistrationClinicalTrials.gov#:NCTO1280812registered January 21, 2011
Intestinal Protozoan Infections Shape Fecal Bacterial Microbiota in Children from Guinea-Bissau.
Authors: Huth Sebastian von , Thingholm Louise B. , Kofoed Poul-Erik , Bang Corinna , Rühlemann Malte C. , Franke Andre , Holmskov Uffe 
Published: July 2020

Abstract
Background: Intestinal parasitic infections, caused by helminths and protozoa, are globally distributed and major causes of worldwide morbidity. The gut microbiota may modulate parasite virulence and host response upon infection. The complex interplay between parasites and the gut microbiota is poorly understood, partly due to sampling difficulties in remote areas with high parasite prevalence and burden. Results: In a large study of children in Bissau, Guinea-Bissau, we found high prevalence of intestinal parasites, including hookworms, Entamoeba spp. and Giardia lamblia. By high-quality sequencing of the 16S rRNA gene of fecal samples stored on filter paper from a total of 1,204 children, we demonstrate that the bacterial microbiota is more or less unaltered by helminth infections, whereas it is shaped by the presence of both pathogenic and non-pathogenic protozoa, including Entamoeba spp. and Giardia lamblia. Within-sample (alpha) diversity remains largely unaffected, whereas overall community composition (beta diversity) is significantly affected by infection with both nonpathogenic Entamoeba coli (R2=0.0131, P= 0.0001) and Endolimax nana (R2=0.00902, P= 0.0001), and by pathogenic Entamoeba histolytica (R2=0.0164, P= 0.0001) and Giardia lamblia (R2=0.00676, P= 0.0001). Heavy infection load with multiple parasite species induces more pronounced shifts in microbiota community than mild ones. A total of 31 bacterial genera across all four major gut bacterial phyla associates with protozoan infection, including increased abundance of Prevotella, Campylobacter and two Clostridium clades (IV and WIVb), and decreased abundance of Collinsella (associated with irritable bowel syndrome), Lactobacillus, Ruminococcus, Veillonella and one Clostridium clade (XVIII). Further, we demonstrate that filter papers are usable for storage of samples at room temperature in large-scale studies where immediate freezing is not possible with minor alterations of microbiota composition. Conclusion: In the present largest-to-date study, we demonstrate that the fecal bacterial microbiota is shaped by intestinal parasitic infection, with most pronounced associations for protozoan species. Our results provide insights into the interplay between the microbiota and intestinal parasites, which are useful to understand infection outcome and design further studies aimed at optimizing treatment strategies.
A Research of the Predictive Values of E2F Factors in Colorectal Cancer
Authors: Zhang Jiang , Yang Xiudeng , Zhang Zhixue , Xiang Lili 
Published: July 2020

Abstract
Background: E2F family of transcription factors are related to cell cycle and apoptosis with activate or repress function on human cancer. Their critical role in colorectal cancer (CRC), including colon adenocarcinoma (COAD) and rectum adenocarcinoma (READ), were widely investigated with contradictory and ambiguous results. Methods: In this study, we explored the expressions of these eight E2F genes and their predictive values on the overall survive (OS) and disease-free survival (DFS) in CRC patients by means of bioinformatic databases, such as ONCOMINE, GEPIA, DAVIA and cBioPortal.Results: We found that the transcriptional levels of E2F1/2/3/5/7/8 were significantly higher in CRC patients than that in normal samples, while the E2F4/6 showed no significantly difference from GEPIA database. The transcriptional levels of all eight E2F factors showed no correlation with four tumor stages, except for the E2F3 is significantly varied in COAD patients. Survival analysis based on GEPIA database indicated that lower E2F3 and E2F4 mRNA expressions were significantly associated with the OS of the COAD patients.Conclusions: This study manifested that the E2F1/2/3/5/7/8 are potential biomarkers of CRC patients, and E2F3 could be used as the predictive factor of tumor stage in COAD patients. E2F3 and E2F4 might be the prognostic markers for COAD patients.
Initial Diastolic Dysfunction is a Powerful Predictor of 5-year Mortality in Peripheral Arterial Disease Patients undergoing Percutaneous Transluminal Angioplasty
Authors: Kim Kyung-Hee , Rha Seung Woon , Choi Byoung Geol , Byun Jae-Kyung , Kim Woohyeun , Choi Cheol Ung , Seo Hong-Seog 
Published: July 2020

Abstract
Background

Peripheral arterial disease (PAD) and heart failure share common risks and are associated with increased morbidity and mortality. However, it is unknown whether cardiac function can be an independent predictor of long-term mortality in patients with PAD.
Methods

In total, 902 patients who underwent percutaneous transluminal angioplasty for PAD were enrolled. The patients were categorized into three groups according to the left ventricular ejection fraction (LVEF): reduced EF (< 40%, n = 62); mid-range EF (40–49%, n = 76); and preserved EF (≥ 50%, n = 764). Echocardiographic (EF, ratio of mitral inflow velocity to annular velocity E/eʹ ≥ 15, and others) and clinical parameters were tested using stepwise logistic regression analysis to determine independent predictors of 5-year mortality.
Results

A higher proportion of patients with reduced EF had ischemic heart disease than those with preserved EF (77.4% vs. 56.8%, p < 0.001). Up to 5 years, patients with reduced EF and mid-range EF showed a higher incidence of total death than those with normal EF. However, there was no difference in the incidence of myocardial infarction, stroke, and revascularization among the three groups. After multivariable adjustment, the ratio of E/eʹ ≥ 15 was the only strong predictor of total mortality (hazard ratio, 6.14; 95% confidence interval, 3.7–10.1;p < 0.01).
Conclusion

Patients with PAD and reduced EF undergoing PTA had a higher incidence of total death during the 5-year follow-up. Initial tissue Doppler E/eʹ ≥ 15, a non-invasive estimate of left atrial filling pressure, was the only independent predictor of long-term mortality.
MAGAN: Mask Attention Generative Adversarial Network for Liver Tumor CT Image Synthesis
Authors: Liu Yang , Meng Lu , Zhong Jianping 
Published: July 2020

Abstract
Background: For deep learning, the size of the dataset greatly affects the final training effect. However, in the field of computer-aided diagnosis, medical image datasets are often limited and even scarce.Methods: We aim to synthesize medical images and enlarge the size of the medical image dataset. In the present study, we synthesized the liver CT images with a tumor based on the mask attention generative adversarial network (MAGAN). We masked the pixels of the liver tumor in the image as the attention map. And both the original image and attention map were loaded into the generator network to obtain the synthesized images. Then the original images, the attention map, and the synthesized images were all loaded into the discriminator network to determine if the synthesized images were real or fake. Finally, we can use the generator network to synthesize liver CT images with a tumor.Results: The experiments showed that our method outperformed the other state-of-the-art methods, and can achieve a mean peak signal-to-noise ratio (PSNR) as 64.72dB.Conclusions: All these results indicated that our method can synthesize liver CT images with tumor, and build large medical image dataset, which may facilitate the progress of medical image analysis and computer-aided diagnosis.
Differential Diagnosis of Multiple Primary and Intra-lung Metastasis of Lung Cancer by Multiple Gene Detection
Authors: Liuyang Xu , Jin Chen , Yupeng Zeng , Pan Ji , Shuaishuai Zhuo , Xiao Li , Zhang Zhihong 
Published: July 2020

Abstract
Objective

To study the differential diagnosis of MPLC and IM by detecting the different lesions of the same patient. To explore the differences in prognosis between MPLC and IM, and to explore the factors affecting the prognosis of multi-focal lung cancer.
Methods

Fifty patients with multi-focal lung cancer were screened, and the relevant clinical information was noted; the patients were diagnosed by ACCP standard. Mutations of the lesions were detected by ARMS-PCR, and the detected genes included EGFR, ALK, ROS1, MET, KRAS, RET, HER-2, BRAF, NRAS and PIK3CA. The results of genetic testing were compared with those of ACCP standard diagnosis.
Results

We analyzed a total of 101 tumors from 50 patients. Classification based on gene testing contradicted the clinicopathologic diagnosis in 10 (20%) of the comparisons, identifying independent primaries in 6 cases diagnosed as metastasis and metastases in 4 cases diagnosed as independent primaries. Another 7(14%) tumor pairings were assigned an “equivocal” result based on gene testing. The results of gene testing of the remaining 33(66%) tumor pairings were consistent with the clinicopathologic diagnosis. The mutant heat map indicated that IM patients have a higher rate of mutation consistency than MPLC patients.
Conclusion

Multi-gene detection of multi-focal lung cancer has a certain auxiliary effect on the differential diagnosis of MPLC and IM, which can complement the clinical standards, but also has some limitations.