bluuebunny/crossref_metadata_2025_split huggingface dataset:
A content-based dataset recommendation system for researchers—a case study on Gene Expression Omnibus (GEO) repository
Authors: Patra Braja Gopal , Roberts Kirk , Wu Hulin 
Published: August 2020

AbstractIt is a growing trend among researchers to make their data publicly available for experimental reproducibility and data reusability. Sharing data with fellow researchers helps in increasing the visibility of the work. On the other hand, there are researchers who are inhibited by the lack of data resources. To overcome this challenge, many repositories and knowledge bases have been established to date to ease data sharing. Further, in the past two decades, there has been an exponential increase in the number of datasets added to these dataset repositories. However, most of these repositories are domain-specific, and none of them can recommend datasets to researchers/users. Naturally, it is challenging for a researcher to keep track of all the relevant repositories for potential use. Thus, a dataset recommender system that recommends datasets to a researcher based on previous publications can enhance their productivity and expedite further research. This work adopts an information retrieval (IR) paradigm for dataset recommendation. We hypothesize that two fundamental differences exist between dataset recommendation and PubMed-style biomedical IR beyond the corpus. First, instead of keywords, the query is the researcher, embodied by his or her publications. Second, to filter the relevant datasets from non-relevant ones, researchers are better represented by a set of interests, as opposed to the entire body of their research. This second approach is implemented using a non-parametric clustering technique. These clusters are used to recommend datasets for each researcher using the cosine similarity between the vector representations of publication clusters and datasets. The maximum normalized discounted cumulative gain at 10 (NDCG@10), precision at 10 (p@10) partial and p@10 strict of 0.89, 0.78 and 0.61, respectively, were obtained using the proposed method after manual evaluation by five researchers. As per the best of our knowledge, this is the first study of its kind on content-based dataset recommendation. We hope that this system will further promote data sharing, offset the researchers’ workload in identifying the right dataset and increase the reusability of biomedical datasets.Database URL: http://genestudy.org/recommends/#/
PyDISH: database and analysis tools for heme porphyrin distortion in heme proteins
Authors: Kondo Hiroko X , Kanematsu Yusuke , Masumoto Gen , Takano Yu 
Published: August 2020

Abstract
Heme participates in a wide range of biological functions such as oxygen transport, electron transport, oxygen reduction, transcriptional regulation and so on. While the mechanism of each function has been investigated for many heme proteins, the origin of the diversity of the heme functions is still unclear and a crucial scientific issue. We have constructed a database of heme proteins, named Python-based database and analyzer for DIStortion of Heme porphyrin (PyDISH), which also contains some analysis tools. The aim of PyDISH is to integrate the information on the structures of hemes and heme proteins and the functions of heme proteins. This database will provide the structure–function relationships focusing on heme porphyrin distortion and lead to the elucidation of the origin of the functional diversity of heme proteins. In addition, the insights obtained from the database can be used for the design of protein function. PyDISH contains the structural data of more than 13 000 hemes extracted from the Protein Data Bank, including heme porphyrin distortion, axial ligands coordinating to the heme and the orientation of the propionate sidechains of heme. PyDISH also has information about the protein domains, including Uniprot ID, protein fold by CATH ID, organism, coordination distance and so on. The analytical tools implemented in PyDISH allow users to not only browse and download the data but also analyze the structures of heme porphyrin by using the analytical tools implemented in PyDISH. PyDISH users will be able to utilize the obtained results for the design of protein function.
Database URL: http://pydish.bio.info.hiroshima-cu.ac.jp/
ThRSDB: a database of Thai rice starch composition, molecular structure and functionality
Authors: Wanichthanarak Kwanjeera , Thitisaksakul Maysaya 
Published: August 2020

Abstract
As starch properties can affect end product quality in many ways, rice starch from Thai domesticated cultivars and landraces has been the focus of increasing research interest. Increasing knowledge in this area creates a high demand from the research community for better organized information. The Thai Rice Starch Database (ThRSDB) is an online database containing data extensively curated from original research articles on Thai rice starch composition, molecular structure and functionality. The key aim of the ThRSDB is to facilitate accessibility to dispersed rice starch information for, but not limited to, both research and industrial users. Currently, 373 samples from 191 different Thai rice cultivars have been collected from 39 published articles. The ThRSDB includes the search functions necessary for accessing data together with a user-friendly web interface and interactive visualization tools. We have also demonstrated how the collected data can be efficiently used to observe the relationships between starch parameters and rice cultivars through correlation analysis and Partial Least Squares Discriminant Analysis.
Database URL: http://thairicestarch.kku.ac.th
Reclassification of prosthesis–patient mismatch after transcatheter aortic valve replacement using predicted vs. measured indexed effective orifice area
Authors: Ternacle Julien , Guimaraes Leonardo , Vincent Flavien , Côté Nancy , Côté Mélanie , Lachance Dominique , Clavel Marie-Annick , Abbas Amr E , Pibarot Philippe , Rodés-Cabau Josep 
Published: August 2020

Abstract

Aims
The objective was to compare the incidence and impact on outcomes of measured (PPMM) vs. predicted (PPMP) prosthesis–patient mismatch following transcatheter aortic valve replacement (TAVR).

Methods and results
All consecutives patients who underwent TAVR between 2007 and 2018 were included. Effective orifice area (EOA) was measured by Doppler-echocardiography using the continuity equation and predicted according to the normal reference for each model and size of valve. PPM was defined using EOA indexed (EOAi) to body surface area as moderate if ≤0.85 cm2/m2 and severe if ≤ 0.65 cm2/m2 (respectively, ≤ 0.70 and ≤ 0.55 cm2/m2 if body mass index ≥ 30 kg/m2). The outcome endpoints were high residual gradient (≥20 mmHg) and the composite of cardiovascular mortality and hospital readmission for heart failure at 1 year. Overall, 1088 patients underwent a TAVR (55% male, age 79.1 ± 8.4 years, and STS score 6.6 ± 4.7%); balloon-expandable device was used in 83%. Incidence of moderate (10% vs. 27%) and severe (1% vs. 17%) PPM was markedly lower when defined by predicted vs. measured EOAi (P &lt; 0.001). Balloon-expandable device implantation (OR: 1.90, P = 0.029) and valve-in-valve procedure (n = 118; OR: 3.21, P &lt; 0.001) were the main factors associated with PPM occurrence. Compared with measured PPM, predicted PPM showed stronger association with high residual gradient. Severe measured or predicted PPM was not associated with clinical outcomes.

Conclusion
The utilization of the predicted EOAi reclassifies the majority of patients with PPM to no PPM following TAVR. Compared with measured PPM, predicted PPM had stronger association with haemodynamic outcomes, while both methods were not associated with clinical outcomes.
A case series on inflammatory cardiomyopathy and suspected cardiac sarcoidosis: role of cardiac PET in management
Authors: Kennel Peter J , Raza Farhan , Kim Jiwon , Singh Parmanand , Borczuk Alain , Krishnan Udhay , Karas Maria , Sobol Irina 
Published: August 2020

Abstract

Background
Presentation of life-threatening arrhythmias concomitantly with a new-onset non-ischaemic cardiomyopathy raises concern for an inflammatory cardiomyopathy such as cardiac sarcoidosis or cardiac manifestations of connective tissue disease. Comprehensive workup for specific aetiologies may be unrevealing except for signs of myocardial inflammation identified on cardiac positron emission tomography (PET). Here, we present five cases of such subjects and their clinical course.

Case summary
We collected clinical, imaging, pathological, and follow-up data of five subjects presenting with arrhythmias and unexplained new-onset cardiomyopathy. Mean age was 56.2 ± 5.8 years. Three subjects presented with ventricular tachycardia and two with atrial arrhythmias. Echocardiography showed a mean left ventricular ejection fraction of 37 ± 9%. Significant coronary artery disease was ruled out in all cases as the cause of the cardiomyopathy. All patients underwent cardiac magnetic resonance imaging (MRI) and PET scan at presentation and follow-up. In all patients, cardiac MRI revealed hyperenhancement in epicardial and mid-myocardial pattern in a non-coronary distribution, while PET scan revealed fluorodeoxyglucose (FDG) mismatch defects in multiple foci in a non-coronary distribution. Right ventricular biopsy was obtained in all patients and revealed interstitial fibrosis and cardiomyocyte hypertrophy. On median follow-up of 210 days, all subjects had improvement in both heart failure symptoms and arrhythmias and repeat PET in four out of five patients showed decreased inflammation.

Discussion
A high level of suspicion for inflammatory cardiomyopathy is needed in patients presenting with new unexplained cardiomyopathy and arrhythmias. A cardiac FDG-PET should be considered for diagnosis if cardiac inflammation is in the differential. This can inform further decisions regarding targeted immunomodulation therapy that may be helpful in this cohort.
Massive pulmonary embolism with intra-hospital cardiac arrest and full recovery of right ventricular function after veno-arterial extracorporeal membrane oxygenation therapy: a case report
Authors: Camen Stephan , Söffker Gerold , Kluge Stefan , Zengin Elvin 
Published: August 2020

Abstract

Background
Massive pulmonary embolism (PE) with shock constitutes a life-threatening disease, challenging physicians with the need for fast decision-making in an emergency situation. While thrombolytic treatment or thrombectomy are considered the treatment of choice in high-risk PE, these strategies might not be able to unload the right ventricle (RV) fast enough in some patients with severe cardiogenic shock.

Case summary
We present a case of a patient with massive bilateral central PE who presented in cardiogenic shock, rapidly deteriorating to cardiac arrest. After successful re-establishing spontaneous circulation, the patient remained highly unstable, necessitating a treatment strategy ensuring a quick stabilization of the circulation. Therefore, we decided to use veno-arterial extracorporeal membrane oxygenation (vaECMO) as a supportive strategy allowing for autolysis of the lung to dissolve the thrombi (bridge to recovery). We were able to wean the patient from vaECMO support within 4 days and documented a complete recovery of right ventricular in echocardiography before hospital discharge.

Discussion
The concept of vaECMO treatment alone might be a valuable alternative in selected patients with massive PE and cardiogenic shock, in whom thrombolytic therapy might not unload the RV fast enough.
One-stage off pump combined transapical aortic valve replacement and ascending aorta endografting
Authors: Gerosa Gino , Cibin Giorgia , Antonello Michele , D’Onofrio Augusto 
Published: August 2020

Abstract
An 84-year-old patient was referred for severe symptomatic aortic valve stenosis and focal chronic dissection of the ascending aorta. After multidisciplinary discussion, the patient was scheduled for combined transapical transcatheter aortic valve replacement and ascending aorta stent-grafting. The procedure was performed with a balloon aortic valvuloplasty followed by a custom-made stent graft implantation into the ascending aorta and then by balloon-expandable transapical transcatheter aortic valve replacement. The patient had an uneventful hospital stay. In conclusion, in selected high-risk patients, transapical combined ascending aorta stent-grafting and transcatheter aortic valve replacement are feasible and safe.
Social Origins, Shared Book Reading, and Language Skills in Early Childhood: Evidence from an Information Experiment
Authors: Barone Carlo , Fougère Denis , Pin Clément 
Published: August 2020

Abstract
Shared book reading (SBR) between parents and children is often regarded as a significant mediator of social inequalities in early skill development processes. We argue that socially biased gaps between parents in the awareness of the benefits of this activity for school success contribute to inequalities between children in access to this activity and in their language development. We test this hypothesis with a large-scale field experiment assessing the causal impact of an intervention targeting parents of pre-schoolers on both the frequency of SBR and the receptive vocabulary of children. Results indicate that low-educated parents are more reactive to this intervention, with significant effects on the language development of their children. We conclude that cognitive barriers and information gaps on the potential of informal learning activities at home fuel social inequalities in early childhood. At the same time, light-touch interventions removing these barriers are a cost-effective way of reducing these inequalities.
Two-year outcome after implantation of a full magnetically levitated left ventricular assist device: results from the ELEVATE Registry
Authors: Zimpfer Daniel , Gustafsson Finn , Potapov Evgenij , Pya Yuriy , Schmitto Jan , Berchtold-Herz Michael , Morshuis Michiel , Shaw Steven M , Saeed Diyar , Lavee Jacob , Heatley Gerald , Gazzola Carlo , Garbade Jens 
Published: August 2020

Abstract

Aims
The ELEVATE Registry was designed to study long-term outcomes with the Heartmate 3 (HM3), a fully magnetically levitated centrifugal ventricular assist device, in a real-world population following CE-mark approval.

Methods and results
A total of 540 patients, implanted in Europe and the Middle East were followed in ELEVATE. The registry included 463 patients receiving the HM3 as primary implant (Primary Implant Cohort), 19 patients underwent a pump upgrade from another device (Pump Exchange Cohort) and 58 patients who had experienced an outcome before having the possibility to sign the Informed Consent, for which only outcome data were collected (Anonymized Cohort). Data collection included demographics, survival, adverse events, EQ-5D Visual Analog Score quality of life (EQ-5D VAS QOL) questionnaire, and 6-min walk distance (6MWD). Mean age was 55.6 ± 11.7 years (89% male, 48% ischaemic cardiomyopathy). Seventy per cent of patients were in INTERMACS Profile 1–3 and 12.7% were on temporary mechanical circulatory support. Primary Implant Cohort survival was 83% after 2 years. In the Powered by Editorial Manager® and ProduXion Manager® from Aries Systems Corporation Primary Implant Cohort, strokes were observed in 10.2%, gastrointestinal bleedings in 9.7%, pump thrombosis in 1.5%, and outflow graft twists in 3.5%. Heartmate 3 implantation resulted in a significant and sustained improvement of functional capacity and QOL.

Conclusion
In a real-world population, cohort implanted with the HM3 left ventricular assist device we demonstrate good long-term survival, sustained improvement of functional capacity, and low rates of adverse events (including pump thrombosis).

ClinicalTrials.gov Identifier
NCT02497950
A simple and practical criterion for determining a failed His-bundle pacing
Authors: Liang Yanchun , Wang Na , Yu Haibo , Xu Baige , Yan Xiaolei , Wu Min , Gao Yang , Liu Rong , Xu Guoqing , Li Zhenhui , He Jiaqi , Wang Zulu , Han Yaling 
Published: August 2020

Abstract

Aims
To establish a simple criterion for determining a failed His-bundle pacing (HBP). This criterion states that if stimulus to QRS end interval is longer than His-bundle potential to QRS end interval (‘S-QRSend &gt; H-QRSend’) then a failed HBP can be determined.

Methods and results
We performed retrospective analysis on 737 pacing tests around His-bundle in 241 patients and prospective analysis on 400 tests in 123 patients. A successful HBP is defined as that whole His-bundle is captured with or without capture of adjacent ventricular myocardium, otherwise, a failed HBP was considered. The output criteria and effective refractory period criteria were used as the gold standards for determining a successful HBP. The gold standards are that if decreasing the pacing output or pacing cycle length to a certain level results in duration or morphology changes of QRS, then a successful HBP is ascertained. In retrospective analysis of patients with normal His-Purkinje conduction, a failed HBP was determined in 31% (154/492) of pacing tests according to ‘S-QRSend &gt; H-QRSend’; all of them were validated by the gold standards (specificity = 100%). In prospective study, a failed HBP was confirmed according to the simple criterion with 100% accuracy in 33% (79/241) pacing tests. This simple criterion was also suitable for patients with His-Purkinje conduction disease although cases with ‘S-QRSend &gt; H-QRSend’ rarely occurred.

Conclusion
A failed HBP can be easily and reliably determined solely by ‘S-QRSend &gt; H-QRSend’ in more than 30% pacing tests.
SETAP: epidemiology and prevention of stroke and transient ischaemic attack in Czech patients with atrial fibrillation
Authors: Táborský Miloš , Dušek Ladislav , Kautzner Josef , Vícha Marek , Aiglová Renata , Gloger Vít , Fedorco Marián , Duba Jaroslav , Dušek Lukáš , Jarkovský Jiří , Bezděková Monika , Skála Tomáš 
Published: August 2020

Abstract

Aims
The aim of this study is to analyse the prevalence, epidemiology, and anticoagulation prevention of stroke or transient ischaemic attack (TIA) in Czech patients with atrial fibrillation (AF).

Methods and results
Retrospective observational analysis of diagnoses, procedures, and treatment reported to the Czech National Registry of Reimbursed Healthcare Services between 2015 and 2018. Prevalence of AF in 2018 was 4.3% of Czech population and the prevalence of stroke/TIA in AF patients was 22.3% with annual incidence of 181.62 cases per 100 000 inhabitants. In 2018, CHA2DS2-ASc score ≥4 was present in 98% AF patients in secondary and 59% in primary prevention, respectively, while the anticoagulation treatment was used by 71–81% of them. Between 2015 and 2018, the percentage of AF patients treated with warfarin monotherapy in primary prevention decreased from 35% to 31%, with acetylsalicylic acid (ASA) monotherapy from 18% to 16% and non-vitamin K antagonist oral anticoagulants (NOACs) monotherapy increased from 7% to 11%. In secondary prevention, the percentage of warfarin monotherapy treatment decreased from 35% to 32%, with ASA monotherapy from 20% to 18% and with NOACs monotherapy increased from 9% to 15%.

Conclusion
This study followed all Czech patients with AF. The unadjusted prevalence and incidence of AF was higher compared with other countries and 2019 European Society of Cardiology Statistics. The study identified several gaps in standard of reimbursed care. 20–30% of AF patients with other risk factors were without any prevention medication and the share of ASA monotherapy in treated patients was 16–18%.
Complications related to elective generator replacement of the subcutaneous implantable defibrillator
Authors: van der Stuijt Willeke , Quast Anne-Floor B E , Baalman Sarah W E , de Wilde Koen C , Brouwer Tom F , Wilde Arthur A M , Knops Reinoud E 
Published: August 2020

Abstract

Aims
To guarantee uninterrupted function of the subcutaneous implantable cardioverter-defibrillator (S-ICD), the pulse generator needs to be surgically replaced before the battery is depleted. The risks related to this replacement substantially impact long-term outcome for S-ICD recipients, as the majority will undergo one or several of these procedures in their lifetime. We aim to describe the procedural characteristics of the replacement procedure and to provide an insight in the complications associated with these replacements.

Methods and results
In this retrospective analysis, data from replacement procedures and follow-up visits were collected from all patients who underwent elective S-ICD generator replacement in our tertiary centre from June 2014 until November 2019. Original device position was assessed using the PRAETORIAN score. Complications were defined as those requiring surgical intervention, systemic antibiotic treatment, or device extraction. Seventy-two patients were included, with a median follow-up of 1.9 years (IQR 0.6–3.3 years) after replacement. Battery depletion occurred after 5.9 ± 0.7 years. The pulse generator was repositioned in patients with a PRAETORIAN score ≥90 to minimize the defibrillation threshold. Although there was an increase in impedance compared to the implant procedure, first shock conversion rate during defibrillation testing was 91.4% with a success rate of 100% after multiple attempts. Two patients developed a complication after, respectively, 9 and 21 months, resulting in a complication rate of 1.4% per year.

Conclusion
With a median follow-up of 1.9 years, this study shows a low complication rate after S-ICD replacement, with a first shock conversion rate of 91.4%.
Direct antibacterial and antibiotic resistance modulatory activity of chalcones synthesized from the natural product 2-hydroxy-3,4,6-trimethoxyacetophenone
Authors: Freitas Thiago Sampaio de , Xavier Jayze da Cunha , Pereira Raimundo L S , Rocha Janaina E , Muniz Dédora F , da Silva Priscila T , da Hora João P , dos Santos Hélcio S , Bandeira Paulo N , Nogueira Carlos E S , Teixeira Alexandre M R , Coutinho Henrique D M 
Published: August 2020

ABSTRACT
Antibiotic for clinical use lose its effectiveness over time due to bacterial resistance. In this work, four chalcones with modifications in their ligands were synthesized from the natural product 2-hydroxy-3,4,6-trimethoxyacetophenone, characterized by nuclear magnetic resonance (NMR) and infrared spectroscopy, and tested in bacterial models to investigate the direct and modifiers effects of the antibiotic activity of these four novel chalcones. The tests followed the broth microdilution methodology to obtain the Minimum Inhibitory Concentration (MIC). The MIC/8 of the products were used in the resistance reversion test. The chalcone 2 showed the best result in terms of direct activity, with MIC 645 μg/mL for Staphylococcus aureus and 812 μg/mL for Escherichia coli. While, for the bacterial resistance reversal test, the chalcones presented several synergistic interactions, being that chalcone 4 had the best interaction with the tested antibiotics. It was found that the type of ligand, as well as its position in the ring, interferes in the modulation of the antibiotic activity. Our results show that chalcones are strong candidates to be used as antibacterial drug or in combination with antibiotics for the treatment of infections caused by multidrug-resistant (MDR) strains.