bluuebunny/crossref_metadata_2025_split huggingface dataset:
Endoscopic ultrasound-guided gastroenterostomy for the management of gastric outlet obstruction: A large comparative study with long-term follow-up
Authors: Jaruvongvanich Veeravich , Mahmoud Tala , Abu Dayyeh Barham K. , Chandrasekhara Vinay , Law Ryan , Storm Andrew C. , Levy Michael J. , Vargas Eric J. , Marya Neil B. , Abboud Donna M. , Ghazi Rabih , Matar Reem , Rapaka Babusai , Buttar Navtej , Truty Mark J. , Aerts Maridi , Messaoudi Nouredin , Kunda Rastislav 
Published: November 2022

Abstract
Background and study aims Gastric outlet obstruction (GOO) is traditionally managed with surgical gastroenterostomy (surgical-GE) and enteral stenting (ES). Endoscopic ultrasound-guided gastroenterostomy (EUS-GE) is now a third option. Large studies assessing their relative risks and benefits with adequate follow-up are lacking. We conducted a comparative analysis of patients who underwent EUS-GE, ES, or surgical-GE for GOO.
Patients and methods In this retrospective comparative cohort study, consecutive patients presenting with GOO who underwent EUS-GE, ES, or surgical-GE at two academic institutions were reviewed and independently cross-edited to ensure accurate reporting. The primary outcome was need for reintervention. Secondary outcomes were technical and clinical success, length of hospital stay (LOS), and adverse events (AEs).
Results A total of 436 patients (232 EUS-GE, 131 ES, 73 surgical-GE) were included. The median duration of follow-up of the entire cohort was 185.5 days (interquartile range 55.25–454.25 days). The rate of reintervention in the EUS-GE group was lower than in the ES and surgical-GE groups (0.9 %, 12.2 %, and 13.7 %, P < 0.0001). Technical success was achieved in 98.3 %, 99.2 %, and 100 % (P = 0.58), and clinical success was achieved in 98.3 %, 91.6 %, and 90.4 % (P < 0.0001) in the EUS-GE, ES, and surgical-GE groups, respectively. The EUS-GE group had a shorter LOS (2 days vs. 3 days vs. 5 days, P < 0.0001) and a lower AE rate than the ES and surgical-GE groups (8.6 % vs. 38.9 % vs. 27.4 %, P < 0.0001).
Conclusion This large cohort study demonstrates the safety and palliation durability of EUS-GE as an alternative strategy for GOO palliation in select patients.
XantPhos Pd-G3 as an Efficient Catalyst: Microwave-Assisted C–S Cross-Coupling Reaction in DMF
Authors: Katla Rakhi , Katla Ramesh , Domingues Nelson L. C. 
Published: November 2022

AbstractBuchwald precatalyst (XantPhos Pd-G3) was employed for the first time in a C–S cross-coupling reaction involving 2-(4-bromophenyl)benzothiazole or 5-bromo-2,1,3-benzothiadiazole with various benzenethiols in DMF, K2CO3 as a base, under microwave irradiation at 80 °C, 200 W. Good to excellent yields of the desired products were obtained under microwave conditions. Other significant benefits of this synthetic approach are low catalyst loading, short reaction times, and eco-friendly conditions. Additionally, 29 compounds were successfully synthesized, some of which are new in this protocol.
Extracellular Vesicles: A New Promise for the Prevention of Bronchopulmonary Dysplasia
Authors: Bonadies Luca , De Vos Beatrice , Muraca Maurizio , Baraldi Eugenio 
Published: November 2022

Bronchopulmonary dysplasia (BPD) despite numerous efforts of neonatologists remains one of the most frequent and long-lasting chronic respiratory diseases consequent to extreme preterm birth. New clinical trials are exploring the possible use of mesenchymal stem cells (MSCs) and especially their products, extracellular vesicles (EVs), that overcome some of the possible issues related to the use of live cells. MSCs already reached clinical implementation; MSC-EVs, on the contrary, showed extremely promising results in the preclinical setting but are still waiting their first in human results that are likely to happen soon.
Key Points
Subacute Aortic Rupture Due to Mechanical Chest Compression with Indwelling Impella
Authors: Penov Kiril , Radakovic Dejan , Madrahimov Nodir , Aleksic Ivan 
Published: November 2022

AbstractMechanical cardiopulmonary resuscitation (CPR) devices like Lund University Cardiopulmonary Assist System (LUCAS) cause more skeletal and visceral injuries than standard CPR. A 62-year-old woman with ST-elevation myocardial infarction was resuscitated with LUCAS and Impella CP for refractory cardiogenic shock during percutaneous coronary intervention. She suffered delayed ascending aortic rupture necessitating supracommissural ascending aortic replacement plus triple bypass grafting. Prolonged mechanical CPR with concomitant Impella may lead to aortic rupture. The combined use of LUCAS and Impella may have disastrous consequences.
The effect of scent lures on detection is not equitable among sympatric species
Authors: Dart Marlin M. , Perkins Lora B. , Jenks Jonathan A. , Hatfield Gary , Lonsinger Robert C. 
Published: November 2022

Context Camera trapping is an effective tool for cost-efficient monitoring of species over large temporal and spatial scales and it is becoming an increasingly popular method for investigating wildlife communities and trophic interactions. However, camera trapping targeting rare and elusive species can be hampered by low detection rates, which can decrease the accuracy and precision of results from common analytical approaches (e.g., occupancy modeling, capture-recapture). Consequently, researchers often employ attractants to increase detection without accounting for how attractants influence detection of species among trophic levels. Aims We aimed to evaluate the influences of a commonly used non-species-specific olfactory lure (i.e. sardines) and sampling design on detection of four species (i.e. bobcat [Lynx rufus], coyote [Canis latrans], raccoon [Procyon lotor], and eastern cottontail [Sylvilagus floridanus]) that represented a range of foraging guilds in an agricultural landscape. Methods We set 180 camera stations, each for ∼28 days, during the summer of 2019. We set cameras with one of three lure treatments: (1) olfactory lure, (2) no olfactory lure, or (3) olfactory lure only during the latter half of the survey. We evaluated the influence of the lure at three temporal scales of detection (i.e. daily probability of detection, independent sequences per daily detection, and triggers per independent sequence). Key results The lure tended to positively influence detection of coyotes and raccoons but negatively influenced detection of bobcats and eastern cottontails. The influence of the lure varied among temporal scales of detection. Conclusions Scent lures can differentially influence detection of species within or among tropic levels, and the influence of a scent lure may vary among temporal scales. Implications Our results demonstrate the importance of evaluating the influence of an attractant for each focal species when using camera data to conduct multi-species or community analyses, accounting for variation in sampling strategies across cameras, and identifying the appropriate species-specific temporal resolution for assessing variation in detection data. Furthermore, we highlight that care should be taken when using camera data as an index of relative abundance (e.g. as is commonly done with prey species) when there is variation in the use of lures across cameras.
L’intelligence interculturelle en traduction
Authors: Le Poder Marie-Évelyne 
Published: November 2022

Résumé
Cet article aborde le concept de l’intelligence interculturelle en traduction à partir d’une étude de cas, concrètement la traduction de l’espagnol vers le français de la pièce de théâtre Bodas de sangre (« Noces de sang ») de Federico García Lorca. L’objectif principal consiste à analyser les références culturelles présentes dans le texte source et la façon dont elles ont été traduites dans le texte cible. Pour ce qui est des objectifs spécifiques, il s’agit de proposer une définition du concept de l’intelligence interculturelle au sens large d’abord, puis en rapport avec la traduction ; délimiter le concept de référence culturelle ; catégoriser les références culturelles du texte source ; examiner les procédés de traduction utilisés par les traducteurs pour recréer les références culturelles du texte source dans le texte cible.
CNN-GRU-Based intelligent online prediction of screw machine rotation speed for Earth pressure balance shield machine
Authors: Liu Xuan-Yu , Gan Xin-Yang , Shao Cheng , Wang Yu-Dong , Cong Qiu-Mei 
Published: November 2022

Abstract
During shield machine construction, the precise determination of control parameters is particularly important for construction safety. By effectively using construction big data and mining the information in it, accurate construction control parameters with geological adaptability can be obtained in real time. To this end, this study proposes an intelligent online prediction method for screw machine rotation speed of Earth pressure balanced (EPB) shield based on convolutional neural network gated recursive unit (CNN-GRU). Firstly, the construction data is processed with Pearson correlation coefficient, the 10-dimensional data of the current moment is selected as the input variable, and screw machine rotation speed at the next moment is chosen as the output. Next, CNN is used to extract features from the input variables to find a nonlinear relationship between the input and output. Then, in order to construct a complete screw machine rotation speed prediction model, the GRU is used to filter the features to establish a more accurate nonlinear relationship. Finally, the control effect of the method was verified by simulation experiments. The simulation results show that the proposed method can accurately predict the rotation speed of the screw machine online. The traditional control mode in shield tunnel construction can lead to unstable excavation surface due to time lag and inaccuracy. Meanwhile, once the excavation surface is unstable, soil collapse or uplift can lead to construction safety problems, while the the required construction data to the control room at the next moment can be quickly and accurately fed by the online prediction method proposed in this study, thereby effectively avoiding the above construction safety problems and having certain practical application value.
Atomic structure generation from reconstructing structural fingerprints
Authors: Fung Victor , Jia Shuyi , Zhang Jiaxin , Bi Sirui , Yin Junqi , Ganesh P 
Published: November 2022

Abstract
Data-driven machine learning methods have the potential to dramatically accelerate the rate of materials design over conventional human-guided approaches. These methods would help identify or, in the case of generative models, even create novel crystal structures of materials with a set of specified functional properties to then be synthesized or isolated in the laboratory. For crystal structure generation, a key bottleneck lies in developing suitable atomic structure fingerprints or representations for the machine learning model, analogous to the graph-based or SMILES representations used in molecular generation. However, finding data-efficient representations that are invariant to translations, rotations, and permutations, while remaining invertible to the Cartesian atomic coordinates remains an ongoing challenge. Here, we propose an alternative approach to this problem by taking existing non-invertible representations with the desired invariances and developing an algorithm to reconstruct the atomic coordinates through gradient-based optimization using automatic differentiation. This can then be coupled to a generative machine learning model which generates new materials within the representation space, rather than in the data-inefficient Cartesian space. In this work, we implement this end-to-end structure generation approach using atom-centered symmetry functions as the representation and conditional variational autoencoders as the generative model. We are able to successfully generate novel and valid atomic structures of sub-nanometer Pt nanoparticles as a proof of concept. Furthermore, this method can be readily extended to any suitable structural representation, thereby providing a powerful, generalizable framework towards structure-based generation.
Improving protein structure prediction using templates and sequence embedding
Authors: Wu Fandi , Jing Xiaoyang , Luo Xiao , Xu Jinbo 
Published: November 2022

Abstract

Motivation
Protein structure prediction has been greatly improved by deep learning, but the contribution of different information is yet to be fully understood. This article studies the impacts of two kinds of information for structure prediction: template and multiple sequence alignment (MSA) embedding. Templates have been used by some methods before, such as AlphaFold2, RoseTTAFold and RaptorX. AlphaFold2 and RosetTTAFold only used templates detected by HHsearch, which may not perform very well on some targets. In addition, sequence embedding generated by pre-trained protein language models has not been fully explored for structure prediction. In this article, we study the impact of templates (including the number of templates, the template quality and how the templates are generated) on protein structure prediction accuracy, especially when the templates are detected by methods other than HHsearch. We also study the impact of sequence embedding (generated by MSATransformer and ESM-1b) on structure prediction.

Results
We have implemented a deep learning method for protein structure prediction that may take templates and MSA embedding as extra inputs. We study the contribution of templates and MSA embedding to structure prediction accuracy. Our experimental results show that templates can improve structure prediction on 71 of 110 CASP13 (13th Critical Assessment of Structure Prediction) targets and 47 of 91 CASP14 targets, and templates are particularly useful for targets with similar templates. MSA embedding can improve structure prediction on 63 of 91 CASP14 (14th Critical Assessment of Structure Prediction) targets and 87 of 183 CAMEO targets and is particularly useful for proteins with shallow MSAs. When both templates and MSA embedding are used, our method can predict correct folds (TMscore &gt; 0.5) for 16 of 23 CASP14 FM targets and 14 of 18 Continuous Automated Model Evaluation (CAMEO) targets, outperforming RoseTTAFold by 5% and 7%, respectively.

Availability and implementation
Available at https://github.com/xluo233/RaptorXFold.

Supplementary information
Supplementary data are available at Bioinformatics online.
End-to-end learning of multiple sequence alignments with differentiable Smith–Waterman
Authors: Petti Samantha , Bhattacharya Nicholas , Rao Roshan , Dauparas Justas , Thomas Neil , Zhou Juannan , Rush Alexander M , Koo Peter , Ovchinnikov Sergey 
Published: November 2022

Abstract

Motivation
Multiple sequence alignments (MSAs) of homologous sequences contain information on structural and functional constraints and their evolutionary histories. Despite their importance for many downstream tasks, such as structure prediction, MSA generation is often treated as a separate pre-processing step, without any guidance from the application it will be used for.

Results
Here, we implement a smooth and differentiable version of the Smith–Waterman pairwise alignment algorithm that enables jointly learning an MSA and a downstream machine learning system in an end-to-end fashion. To demonstrate its utility, we introduce SMURF (Smooth Markov Unaligned Random Field), a new method that jointly learns an alignment and the parameters of a Markov Random Field for unsupervised contact prediction. We find that SMURF learns MSAs that mildly improve contact prediction on a diverse set of protein and RNA families. As a proof of concept, we demonstrate that by connecting our differentiable alignment module to AlphaFold2 and maximizing predicted confidence, we can learn MSAs that improve structure predictions over the initial MSAs. Interestingly, the alignments that improve AlphaFold predictions are self-inconsistent and can be viewed as adversarial. This work highlights the potential of differentiable dynamic programming to improve neural network pipelines that rely on an alignment and the potential dangers of optimizing predictions of protein sequences with methods that are not fully understood.

Availability and implementation
Our code and examples are available at: https://github.com/spetti/SMURF.

Supplementary information
Supplementary data are available at Bioinformatics online.
Role of genetic testing in young patients with idiopathic atrioventricular conduction disease
Authors: Auricchio Angelo , Demarchi Andrea , Özkartal Tardu , Campanale Daniela , Caputo Maria Luce , di Valentino Marcello , Menafoglio Andrea , Regoli Francois , Facchini Marco , Del Bufalo Alessandro , Foglia Pietro , Ferrari Nicola , Bomio Fulvio , Medeiros-Domingo Argelia , Moccetti Tiziano , Pedrazzini Giovanni B , Klersy Catherine , Conte Giulio 
Published: November 2022

AbstractAimsTo investigate the role of genetic testing in patients with idiopathic atrioventricular conduction disease requiring pacemaker (PM) implantation before the age of 50 years.Methods and resultsAll consecutive PM implantations in Southern Switzerland between 2010 and 2019 were evaluated. Inclusion criteria were: (i) age at the time of PM implantation: &lt; 50 years; (ii) atrioventricular block (AVB) of unknown aetiology. Study population was investigated by ajmaline challenge and echocardiographic assessment over time. Genetic testing was performed using next-generation sequencing panel, containing 174 genes associated to inherited cardiac diseases, and Sanger sequencing confirmation of suspected variants with clinical implication. Of 2510 patients who underwent PM implantation, 15 (0.6%) were young adults (median age: 44 years, male predominance) presenting with advanced AVB of unknown origin. The average incidence of idiopathic AVB computed over the 2010–2019 time window was 0.7 per 100 000 persons per year (95% CI 0.4–1.2). Most of patients (67%) presented with specific genetic findings (pathogenic variant) or variants of uncertain significance (VUS). A pathogenic variant of PKP2 gene was found in one patient (6.7%) with no overt structural cardiac abnormalities. A VUS of TRPM4, MYBPC3, SCN5A, KCNE1, LMNA, GJA5 genes was found in other nine cases (60%). Of these, three unrelated patients (20%) presented the same heterozygous missense variant c.2531G &gt; A p.(Gly844Asp) in TRPM4 gene. Diagnostic re-assessment over time led to a diagnosis of Brugada syndrome and long-QT syndrome in two patients (13%). No cardiac events occurred during a median follow-up of 72 months.ConclusionIdiopathic AVB in adults younger than 50 years is a very rare condition with an incidence of 0.7 per 100 000 persons/year. Systematic investigations, including genetic testing and ajmaline challenge, can lead to the achievement of a specific diagnosis in up to 20% of patients. Heterozygous missense variant c.2531G &gt; A p.(Gly844Asp) in TRPM4 gene was found in an additional 20% of unrelated patients, suggesting possible association of the variant with the disease.
Sense-B-noise: an enigmatic cause for inappropriate shocks in subcutaneous implantable cardioverter defibrillators
Authors: Haeberlin Andreas , Burri Haran , Schaer Beat , Koepfli Pascal , Grebmer Christian , Breitenstein Alexander , Reichlin Tobias , Noti Fabian 
Published: November 2022

AbstractAimsSubcutaneous implantable cardioverter defibrillators (S-ICDs) are well established. However, inappropriate shocks (IAS) remain a source of concern since S-ICDs offer very limited troubleshooting options. In our multicentre case series, we describe several patients who experienced IAS due to a previously unknown S-ICD system issue.Methods and resultsWe observed six patients suffering from this novel IAS entity. The IAS occurred exclusively in primary or alternate S-ICD sensing vector configuration (therefore called ‘Sense-B-noise’). IAS were caused by non-physiologic oversensing episodes characterized by intermittent signal saturation, diminished QRS amplitudes, and disappearance of the artefacts after the IAS. Noise/oversensing could not be provoked by manipulation, X-ray did not show evidence for lead/header issues and impedance measurements were within normal limits. The pooled experience of our centres implies that up to ∼5% of S-ICDs may be affected. The underlying root cause was discussed extensively with the manufacturer but remains unknown and is under further investigation.ConclusionSense-B-noise is a novel cause for IAS due to non-physiologic signal oversensing, arising from a previously unknown S-ICD system issue. Sense-B-noise may be suspected if episodes of signal saturation in primary or alternate vector configuration are present, oversensing cannot be provoked, and X-ray and electrical measurements appear normal. The issue can be resolved by reprogramming the device to secondary sensing vector.
New CNN-based tool to discriminate anthropogenic from natural low magnitude seismic events
Authors: Hourcade Céline , Bonnin Mickaël , Beucler Éric 
Published: November 2022

SUMMARY
With the deployment of high quality and dense permanent seismic networks over the last 15 yr comes a dramatic increase of data to process. In order to lower the threshold value of magnitudes in a catalogue as much as possible, the issue of discrimination between natural and anthropogenic events is becoming increasingly important. To achieve this discrimination, we propose the use of a convolutional neural network (CNN) trained from spectrograms. We built a database of labelled events detected in metropolitan France between 2020 and 2021 and trained a CNN with three-component 60 s spectrograms ranging frequencies from 1 to 50 Hz. By applying our trained model on independent French data, we reach an accuracy of 98.2 per cent. In order to show the versatility of the approach, this trained model is also applied on different geographical areas, a post-seismic campaign from NW France and data from Utah, and reaches an accuracy of 100.0 and 96.7 per cent, respectively. These tests tend to hypothesize that some features due to explosions compared to earthquakes are widely shared in different geographical places. In a first approach, we propose that it can be due to a contrast in the energy balance between natural and anthopogenic events. Earthquake seismic energies seem to be more continuous as a function of frequency (vertical bands features in a spectrogram) and conversely for explosions (horizontal strips).
A novel chaotic Runge Kutta optimization algorithm for solving constrained engineering problems
Authors: Yıldız Betül Sultan , Mehta Pranav , Panagant Natee , Mirjalili Seyedali , Yildiz Ali Riza 
Published: November 2022

Abstract
This study proposes a novel hybrid metaheuristic optimization algorithm named chaotic Runge Kutta optimization (CRUN). In this study, 10 diverse chaotic maps are being incorporated with the base Runge Kutta optimization (RUN) algorithm to improve their performance. An imperative analysis was conducted to check CRUN’s convergence proficiency, sustainability of critical constraints, and effectiveness. The proposed algorithm was tested on six well-known design engineering tasks, namely: gear train design, coupling with a bolted rim, pressure vessel design, Belleville spring, and vehicle brake-pedal optimization. The results demonstrate that CRUN is superior compared to state-of-the-art algorithms in the literature. So, in each case study, CRUN was superior to the rest of the algorithms and furnished the best-optimized parameters with the least deviation. In this study, 10 chaotic maps were enhanced with the base RUN algorithm. However, these chaotic maps improve the solution quality, prevent premature convergence, and yield the global optimized output. Accordingly, the proposed CRUN algorithm can also find superior aspects in various spectrums of managerial implications such as supply chain management, business models, fuzzy circuits, and management models.