bluuebunny/crossref_metadata_2025_split huggingface dataset:
TACOS: a novel approach for accurate prediction of cell-specific long noncoding RNAs subcellular localization
Authors: Jeon Young-Jun , Hasan Md Mehedi , Park Hyun Woo , Lee Ki Wook , Manavalan Balachandran 
Published: June 2022

AbstractLong noncoding RNAs (lncRNAs) are primarily regulated by their cellular localization, which is responsible for their molecular functions, including cell cycle regulation and genome rearrangements. Accurately identifying the subcellular location of lncRNAs from sequence information is crucial for a better understanding of their biological functions and mechanisms. In contrast to traditional experimental methods, bioinformatics or computational methods can be applied for the annotation of lncRNA subcellular locations in humans more effectively. In the past, several machine learning-based methods have been developed to identify lncRNA subcellular localization, but relevant work for identifying cell-specific localization of human lncRNA remains limited. In this study, we present the first application of the tree-based stacking approach, TACOS, which allows users to identify the subcellular localization of human lncRNA in 10 different cell types. Specifically, we conducted comprehensive evaluations of six tree-based classifiers with 10 different feature descriptors, using a newly constructed balanced training dataset for each cell type. Subsequently, the strengths of the AdaBoost baseline models were integrated via a stacking approach, with an appropriate tree-based classifier for the final prediction. TACOS displayed consistent performance in both the cross-validation and independent assessments compared with the other two approaches employed in this study. The user-friendly online TACOS web server can be accessed at https://balalab-skku.org/TACOS.
TSNAPred: predicting type-specific nucleic acid binding residues via an ensemble approach
Authors: Nie Wenjuan , Deng Lei 
Published: June 2022

Abstract
Motivation: The interplay between protein and nucleic acid participates in diverse biological activities. Accurately identifying the interaction between protein and nucleic acid can strengthen the understanding of protein function. However, conventional methods are too time-consuming, and computational methods are type-agnostic predictions. We proposed an ensemble predictor termed TSNAPred and first used it to identify residues that bind to A-DNA, B-DNA, ssDNA, mRNA, tRNA and rRNA. TSNAPred combines LightGBM and capsule network, both learned on the feature derived from protein sequence. TSNAPred utilizes the sliding window technique to extract long-distance dependencies between residues and a weighted ensemble strategy to enhance the prediction performance. The results show that TSNAPred can effectively identify type-specific nucleic acid binding residues in our test set. What is more, it also can discriminate DNA-binding and RNA-binding residues, which has improved 5% to 10% on the AUC value compared with other state-of-the-art methods. The dataset and code of TSNAPred are available at: https://github.com/niewenjuan-csu/TSNAPred.
Pf-Phospho: a machine learning-based phosphorylation sites prediction tool for Plasmodium proteins
Authors: Gupta Priya , Venkadesan Sureshkumar , Mohanty Debasisa 
Published: June 2022

Abstract
Even though several in silico tools are available for prediction of the phosphorylation sites for mammalian, yeast or plant proteins, currently no software is available for predicting phosphosites for Plasmodium proteins. However, the availability of significant amount of phospho-proteomics data during the last decade and advances in machine learning (ML) algorithms have opened up the opportunities for deciphering phosphorylation patterns of plasmodial system and developing ML-based phosphosite prediction tools for Plasmodium. We have developed Pf-Phospho, an ML-based method for prediction of phosphosites by training Random Forest classifiers using a large data set of 12 096 phosphosites of Plasmodium falciparum and Plasmodium bergei. Of the 12 096 known phosphosites, 75% of sites have been used for training/validation of the classifier, while remaining 25% have been used as completely unseen test data for blind testing. It is encouraging to note that Pf-Phospho can predict the kinase-independent phosphosites with 84% sensitivity, 75% specificity and 78% precision. In addition, it can also predict kinase-specific phosphosites for five plasmodial kinases—PfPKG, Plasmodium falciparum, PfPKA, PfPK7 and PbCDPK4 with high accuracy. Pf-Phospho (http://www.nii.ac.in/pfphospho.html) outperforms other widely used phosphosite prediction tools, which have been trained using mammalian phosphoproteome data. It also has been integrated with other widely used resources such as PlasmoDB, MPMP, Pfam and recently available ML-based predicted structures by AlphaFold2. Currently, Pf-phospho is the only bioinformatics resource available for ML-based prediction of phospho-signaling networks of Plasmodium and is a user-friendly platform for integrative analysis of phospho-signaling along with metabolic and protein–protein interaction networks.
Perceptions of Dutch general practitioners towards eHealth for patients with type-2 diabetes: a qualitative study
Authors: Vonken Lieve , Hussein Hani , Crutzen Rik , Vluggen Stan 
Published: June 2022

Abstract

Background
eHealth provides a viable option to facilitate type-2 diabetes mellitus self-management and adherence. To this end, a web-based computer-tailored eHealth programme, My Diabetes Profile (MDP), was developed and implemented in Dutch diabetes care. To fully utilize the potential of eHealth, the reach of effective programmes like MDP should be maximized. Therefore, it is vital to explore perceptions of general practitioners (GPs) regarding eHealth and factors that influence GPs’ decision to adopt eHealth programmes.

Objective
To shed light on Dutch GPs’ perceptions towards eHealth in general and specifically, the adoption of MDP.

Methods
Interviews were conducted among a heterogeneous sample of 16 Dutch GPs. The interview guide, based on the Diffusion of Innovations Theory, addressed perceptions about eHealth in general, characteristics of MDP, organizational characteristics, and external influences on adoption. Audio-recordings were transcribed and analysed using deductive coding in NVivo.

Results
Nearly all GPs used some form of eHealth and listed many benefits and few drawbacks about eHealth. Sometimes, GPs were unaware of what eHealth encompassed; programmes resembling MDP were not mentioned. COVID-19 immensely increased eHealth uptake, especially for remote communication. Regarding MDP, the organizational and external influences on adoption were limited, while characteristics of the innovation were deemed more important. GPs expressed benefits of MDP (e.g. uncomplex, user-friendly, tailored) other than attributed to eHealth in general and fewer drawbacks.

Conclusion
While GPs’ opinions about eHealth and MDP were positive, the concept of MDP was relatively unfamiliar. Future research should focus on targeting GPs’ awareness of eHealth possibilities.
An alternative method to evaluate earthquake detection from synthetic Wood–Anderson seismograms: an application in Italy
Authors: Augliera Paolo 
Published: June 2022

SUMMARYDefining the regional variability of minimum magnitude for earthquake detection is crucial for planning seismic networks. Knowing the earthquake detection magnitude values is fundamental for the optimal location of new stations and to select the priority for reactivating the stations of a seismic network in case of a breakdown. In general, the assessment of earthquake detection is performed by analysing seismic noise with spectral or more sophisticated methods. Further, to simulate amplitude values at the recording sites, spectral methods require knowledge of several geophysical parameters including rock density, S-wave velocity, corner frequency, quality factor, site specific decay parameter and so on, as well as a velocity model for the Earth's interior. The simulation results are generally expressed in terms of Mw and therefore a further conversion must be done to obtain the values of local magnitude (ML), which is the parameter commonly used for moderate and small earthquakes in seismic catalogues. Here, the relationship utilized by a seismic network to determine ML is directly applied to obtain the expected amplitude [in mm, as if it were recorded by a Wood–Anderson (WA) seismometer] at the recording site, without any additional assumptions. The station detection estimates are obtained by simply considering the ratio of the expected amplitude with respect to the background noise, also measured in mm. The seismic noise level for the station is estimated starting from four waveforms (each signal lasting 1 min) sampled at various times of the day for a period of one week. The proposed method is tested on Italian seismic events occurring in 2019 by using the locations of 16.879 earthquakes recorded by 374 stations. The first results indicate that by evaluating the station noise level with 5-s windows, a representative sample of the variability in expected noise level is generated for every station, even if only 4 min of signal per day over a week of recordings is used. The method was applied to define the detection level of the Italian National Seismic Network (RSN). The RSN detection level represents a reference for the definition and application of guidelines in the field of monitoring of subsurface industrial activities in Italy. The proposed approach can be successfully applied to define the current performance of a local seismic network (managed by private companies) and to estimate the expected further improvements, requested to fulfil the guidelines with the installation of new seismic stations. This method has been tested in Italy and can be reproduced wherever the local magnitude ML, based on synthetic WA records, is used.
Coil embolization to treat pulmonary sequestration in the right upper lobe
Authors: Deng Yujiao , Fang Xin , Wu Bing 
Published: June 2022

Abstract
Although there have been a few case reports of pulmonary sequestration, it is primarily located in the lower lobe and left lung, rarely in the right upper lobe. Here, we report a case presented with haemoptysis. Computed tomography images revealed flake ground-glass shadows in the right upper lobe. Computed tomography angiography demonstrated an artery supplied the affected lesions stemmed from the aortic arch. We diagnosed and treated her with bronchial artery angiography with coil embolization. No complications were found after operation until now. Thus, CTA could help identify the abnormal blood vessels, and interventional therapy may be an effective alternative to surgery of pulmonary sequestration.
Recent improvement in operative techniques lead to lower pacemaker rate after Perceval implant
Authors: Fabre Olivier , Radutoiu Mihai , Carjaliu Ionut , Rebet Olivier , Gautier Laurence , Hysi Ilir 
Published: June 2022

Abstract
Central picture. Decrease in the pacemaker rate after Perceval implants in the last 5 years. The left Y-axis shows the percent of permanent cardiac pacemakers implanted. The right Y-axis (in green) shows the number of Perceval valves implanted.

OBJECTIVES
Our goal was to compare pacemaker rate usage following two different operating techniques for implanting the Perceval aortic valve replacement.

METHODS
In this retrospective, single-centre study, we studied patients with isolated or concomitant Perceval aortic valve replacement operated on first between April 2013 and January 2016, following traditional operating techniques, with patients operated on between January 2016 and December 2020, after the adoption of a modified protocol based on different annulus sizing, higher positioning of the valve and no ballooning after valve deployment was adopted. The operations were performed by 2 surgeons, and patients were followed-up for a period of 30 days.

RESULTS
A total of 286 patients, with a mean age of 77 (4.9) years, had Perceval valves implanted during the study period, of which 79% were isolated aortic valve procedures. Most patients (66.8%) underwent minimally invasive procedures. Cross-clamp time was 55.1 (17.6) min. The overall postoperative pacemaker insertion rate was 8.4%, which decreased decisively after the 2016 change in the implant protocol (16% vs 5.6%; P = 0.005), adjusted odds ratio of 0.31 (95% confidence interval: 0.13–0.74, P = 0.012). Univariable and multivariable analysis showed that larger valve size (P = 0.01) and ballooning (P = 0.002) were associated with higher risk of implanting a pacemaker. Postoperative 30-day mortality was of 4.5%.

CONCLUSIONS
Improvement in the operating techniques for implanting the Perceval valve may decrease the rate of pacemakers implanted postoperatively. Although further studies are needed to confirm these results, such a risk reduction may lead to wider use of Perceval valves in the future, potentially benefiting patients who are suitable candidates for minimally invasive surgery.
Neutrophils in homeostasis and tissue repair
Authors: Shim Hanjoo Brian , Deniset Justin F , Kubes Paul 
Published: June 2022

AbstractNeutrophils are the most abundant innate immune cell and are equipped with highly destructive molecular cargo. As such, these cells were long thought to be short-lived killer cells that unleash their full cytotoxic programs on pathogens following infection and on host bystander cells after sterile injury. However, this view of neutrophils is overly simplistic and as a result is outdated. Numerous studies now collectively highlight neutrophils as far more complex and having a host of homeostatic and tissue-reparative functions. In this review, we summarize these underappreciated roles across organs and injury models.
Classifying unstructured electronic consult messages to understand primary care physician specialty information needs
Authors: Ding Xiyu , Barnett Michael , Mehrotra Ateev , Tuot Delphine S , Bitterman Danielle S , Miller Timothy A 
Published: June 2022

Abstract

Objective
Electronic consultation (eConsult) content reflects important information about referring clinician needs across an organization, but is challenging to extract. The objective of this work was to develop machine learning models for classifying eConsult questions for question type and question content. Another objective of this work was to investigate the ability to solve this task with constrained expert time resources.

Materials and Methods
Our data source is the San Francisco Health Network eConsult system, with over 700 000 deidentified questions from the years 2008–2017, from gastroenterology, urology, and neurology specialties. We develop classifiers based on Bidirectional Encoder Representations from Transformers, experimenting with multitask learning to learn when information can be shared across classifiers. We produce learning curves to understand when we may be able to reduce the amount of human labeling required.

Results
Multitask learning shows benefits only in the neurology–urology pair where they shared substantial similarities in the distribution of question types. Continued pretraining of models in new domains is highly effective. In the neurology–urology pair, near-peak performance is achieved with only 10% of the urology training data given all of the neurology data.

Discussion
Sharing information across classifier types shows little benefit, whereas sharing classifier components across specialties can help if they are similar in the balance of procedural versus cognitive patient care.

Conclusion
We can accurately classify eConsult content with enough labeled data, but only in special cases do methods for reducing labeling effort apply. Future work should explore new learning paradigms to further reduce labeling effort.
An algebraic analysis of implication in non-distributive logics
Authors: Chajda Ivan , Emir Kadir , Fazio Davide , LÄnger Helmut , Ledda Antonio , Paseka Jan 
Published: June 2022

AbstractIn this paper, we introduce the concept of a (lattice) skew Hilbert algebra as a natural generalization of Hilbert algebras. This notion allows a unified treatment of several structures of prominent importance for mathematical logic, e.g. (generalized) orthomodular lattices, and MV-algebras, which admit a natural notion of implication. In fact, it turns out that skew Hilbert algebras play a similar role for (strongly) sectionally pseudocomplemented posets as Hilbert algebras do for relatively pseudocomplemented ones. We will discuss basic properties of closed, dense and weakly dense elements of skew Hilbert algebras and their applications, and we will provide some basic results on their structure theory.
On the transit spectroscopy features of warm Neptunes in the TOI-421 system, revealed with their 3D aeronomy simulations
Authors: Berezutsky A G , Shaikhislamov I F , Rumenskikh M S , Khodachenko M L , Lammer H , Miroshnichenko I B 
Published: June 2022

ABSTRACT
We simulate with a global 3D aeronomy code two warm Neptunes in the TOI-421 system and show that both planets experience significant escape of their upper atmospheres. The double shock structures, generated around the planets in course of their interaction with the stellar wind (SW) plasma flow are revealed. The calculations of stellar Ly α transit absorption by the planets reveal that it reaches a detectable level only for a moderate or strong SW, with a sufficiently high density. In this case, the energetic neutral atoms provide significant absorption at the high velocity blue wing of the Ly α line, whereas the corresponding transit light curves exhibit an early ingress and extended egress features. With the same code, we also modelled the absorption at the position of the 10 830 Å line of the metastable helium, showing that it can be detected only for the farthest planet of the considered two, if the helium abundance is comparable to the solar value.
Cometary dust analogues for physics experiments
Authors: Lethuillier A , Feller C , Kaufmann E , Becerra P , Hänni N , Diethelm R , Kreuzig C , Gundlach B , Blum J , Pommerol A , Kargl G , Laddha S , Denisova K , Kührt E , Capelo H L , Haack D , Zhang X , Knollenberg J , Molinski N S , Gilke T , Sierks H , Tiefenbacher P , Güttler C , Otto K A , Bischoff D , Schweighart M , Hagermann A , Jäggi N 
Published: June 2022

ABSTRACT
The CoPhyLab (Cometary Physics Laboratory) project is designed to study the physics of comets through a series of earth-based experiments. For these experiments, a dust analogue was created with physical properties comparable to those of the non-volatile dust found on comets. This ‘CoPhyLab dust’ is planned to be mixed with water and CO2 ice and placed under cometary conditions in vacuum chambers to study the physical processes taking place on the nuclei of comets. In order to develop this dust analogue, we mixed two components representative for the non-volatile materials present in cometary nuclei. We chose silica dust as a representative for the mineral phase and charcoal for the organic phase, which also acts as a darkening agent. In this paper, we provide an overview of known cometary analogues before presenting measurements of eight physical properties of different mixtures of the two materials and a comparison of these measurements with known cometary values. The physical properties of interest are particle size, density, gas permeability, spectrophotometry, and mechanical, thermal, and electrical properties. We found that the analogue dust that matches the highest number of physical properties of cometary materials consists of a mixture of either 60 per cent/40 per cent or 70 per cent/30 per cent of silica dust/charcoal by mass. These best-fit dust analogue will be used in future CoPhyLab experiments.
Cluster assembly and the origin of mass segregation in the STARFORGE simulations
Authors: Guszejnov Dávid , Markey Carleen , Offner Stella S R , Grudić Michael Y , Faucher-Giguère Claude-André , Rosen Anna L , Hopkins Philip F 
Published: June 2022

ABSTRACT
Stars form in dense, clustered environments, where feedback from newly formed stars eventually ejects the gas, terminating star formation and leaving behind one or more star clusters. Using the STARFORGE simulations, it is possible to simulate this process in its entirety within a molecular cloud, while explicitly evolving the gas radiation and magnetic fields and following the formation of individual, low-mass stars. We find that individual star-formation sites merge to form ever larger structures, while still accreting gas. Thus clusters are assembled through a series of mergers. During the cluster assembly process, a small fraction of stars are ejected from their clusters; we find no significant difference between the mass distribution of the ejected stellar population and that of stars inside clusters. The star-formation sites that are the building blocks of clusters start out mass segregated with one or a few massive stars at their centre. As they merge the newly formed clusters maintain this feature, causing them to have mass-segregated substructures without themselves being centrally condensed. The merged clusters relax to a centrally condensed mass-segregated configuration through dynamical interactions between their members, but this process does not finish before feedback expels the remaining gas from the cluster. In the simulated runs, the gas-free clusters then become unbound and breakup. We find that turbulent driving and a periodic cloud geometry can significantly reduce clustering and prevent gas expulsion. Meanwhile, the initial surface density and level of turbulence have little qualitative effect on cluster evolution, despite the significantly different star formation histories.
Tidal disruption of star clusters in galaxy formation simulations
Authors: Meng Xi , Gnedin Oleg Y 
Published: June 2022

ABSTRACT
We investigate the evolution of the tidal field experienced by massive star clusters using cosmological simulations of Milky Way-sized galaxies. Clusters in our simulations experience the strongest tidal force in the first few hundred Myr after formation, when the maximum eigenvalue of the tidal tensor reaches several times 104 Gyr−2. After about 1 Gyr the tidal field plateaus at a lower value, with the median λm ∼ 3 × 103 Gyr−2. The fraction of time clusters spend in high tidal strength (λm &gt; 3 × 104 Gyr−2) regions also decreases with their age from ∼20 per cent immediately after formation to less than 1 per cent after 1 Gyr. At early ages both the in situ and ex situ clusters experience similar tidal fields, while at older ages the in situ clusters in general experience stronger tidal field due to their lower orbits in host galaxy. This difference is reflected in the survival of clusters: we looked into cluster disruption calculated in simulation runtime and found that ex situ star clusters of the same initial mass typically end up with higher bound fraction at the last available simulation snapshot than the in situ ones.