bluuebunny/crossref_metadata_2025 huggingface dataset:
A generalized framework for unsupervised learning and data recovery in computational fluid dynamics using discretized loss functions
Authors: Aulakh Deepinder Jot Singh , Beale Steven B. , Pharoah Jon G.
Published: June 2022

The authors present generalized finite-volume-based discretized loss functions integrated into pressure-linked algorithms for physics-based unsupervised training of neural networks (NNs). In contrast to automatic differentiation-based counterparts, discretized loss functions leverage well-developed numerical schemes of computational fluid dynamics (CFD) for tailoring NN training specific to the flow problems. For validation, neural network-based solvers (NN solvers) are trained by posing equations such as the Poisson equation, energy equation, and Spalart–Allmaras model as loss functions. The predictions from the trained NNs agree well with the solutions from CFD solvers while also providing solution time speed-ups of up to seven times. Another application of unsupervised learning is the novel hybrid loss functions presented in this study. Hybrid learning combines the information from sparse or partial observations with a physics-based loss to train the NNs accurately and provides training speed-ups of up to five times compared with a fully unsupervised method. Also, to properly utilize the potential of discretized loss functions, they are formulated in a machine learning (ML) framework (TensorFlow) integrated with a CFD solver (OpenFOAM). The ML-CFD framework created here infuses versatility into the training by giving loss functions access to the different numerical schemes of the OpenFOAM. In addition, this integration allows for offloading the CFD programming to OpenFOAM, circumventing bottlenecks from manually coding new flow conditions in a solely ML-based framework like TensorFlow.
A genome-wide association study (GWAS) identifies multiple loci linked with the natural variation for Al
Authors: Du Hanmei , Raman Harsh , Kawasaki Akitomo , Perera Geetha , Diffey Simon , Snowdon Rod , Raman Rosy , Ryan Peter R.
Published: June 2022

Acid soils limit yields of many important crops including canola (Brassica napus), Australia’s third largest crop. Aluminium (Al3+) stress is the main cause of this limitation primarily because the toxic Al3+ present inhibits root growth. Breeding programmes do not target acid-soil tolerance in B. napus because genetic variation and convincing quantitative trait loci have not been reported. We conducted a genome-wide association study (GWAS) using the BnASSYST diversity panel of B. napus genotyped with 35 729 high-quality DArTseq markers. We screened 352 B. napus accessions in hydroponics with and without a toxic concentration of AlCl3 (12 μM, pH 4.3) for 12 days and measured shoot biomass, root biomass, and root length. By accounting for both population structure and kinship matrices, five significant quantitative trait loci for different measures of resistance were identified using incremental Al3+ resistance indices. Within these quantitative trait locus regions of B. napus, 40 Arabidopsis thaliana gene orthologues were identified, including some previously linked with Al3+ resistance. GWAS analysis indicated that multiple genes are responsible for the natural variation in Al3+ resistance in B. napus. The results provide new genetic resources and markers to enhance that Al3+ resistance of B. napus germplasm via genomic and marker-assisted selection.
Virus finding tools: current solutions and limitations
Authors: Privitera Grete Francesca , Alaimo Salvatore , Ferro Alfredo , Pulvirenti Alfredo
Published: June 2022

Motivation

The study of the Human Virome remains challenging nowadays. Viral metagenomics, through high-throughput sequencing data, is the best choice for virus discovery. The metagenomics approach is culture-independent and sequence-independent, helping search for either known or novel viruses. Though it is estimated that more than 40% of the viruses found in metagenomics analysis are not recognizable, we decided to analyze several tools to identify and discover viruses in RNA-seq samples.

Results

We have analyzed eight Virus Tools for the identification of viruses in RNA-seq data. These tools were compared using a synthetic dataset of 30 viruses and a real one. Our analysis shows that no tool succeeds in recognizing all the viruses in the datasets. So we can conclude that each of these tools has pros and cons, and their choice depends on the application domain.

Availability

Synthetic data used through the review and raw results of their analysis can be found at https://zenodo.org/record/6426147. FASTQ files of real data can be found in GEO (https://www.ncbi.nlm.nih.gov/gds) or ENA (https://www.ebi.ac.uk/ena/browser/home). Raw results of their analysis can be downloaded from https://zenodo.org/record/6425917.
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

Long 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

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

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

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

Defining 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

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

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

Neutrophils 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

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

In 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

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

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

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

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 > 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.
Formation of S0s in extreme environments III: the role of environment in the formation pathways
Authors: Coccato Lodovico , Fraser-McKelvie Amelia , Jaffé Yara L , Johnston Evelyn J , Cortesi Arianna , Pallero Diego
Published: June 2022

It is well established that there are at least two main channels to form lenticular (or S0) galaxies. The first, which we name ‘faded spiral’ scenario, includes quenching events that led to consumption or removal of gas from a spiral progenitor. The second, which we call ‘merger’ scenario, includes merger-like events and interactions between galaxies. Each scenario leaves characteristic signatures in the newly formed lenticular galaxy. However, the conditions that trigger one mechanism over another are still unknown. This paper is the third of a series aimed at understanding the role of the environment in the formation of lenticular galaxies. In this study, we combine the kinematics, morphology, and properties of the stellar populations of 329 S0s from the SAMI and MaNGA surveys in order to highlight the role of the environment in the process. We divide the S0s into two classes (A and B) according to their global properties, that we can associate to the products of a faded spiral scenario (class A) or a merger scenario (class B). We then study how the various classes are distributed within different environments. Our study reveals that the ‘faded spiral’ pathway is the most efficient channel to produce S0s, and it becomes more efficient as the mass of the group or cluster or local density of galaxies increase. The merger pathway is also a viable channel, and its efficiency becomes higher with decreasing local density or environment mass.
The distribution and morphologies of Fornax Cluster dwarf galaxies suggest they lack dark matter
Authors: Asencio Elena , Banik Indranil , Mieske Steffen , Venhola Aku , Kroupa Pavel , Zhao Hongsheng
Published: June 2022

Due to their low surface brightness, dwarf galaxies are particularly susceptible to tidal forces. The expected degree of disturbance depends on the assumed gravity law and whether they have a dominant dark halo. This makes dwarf galaxies useful for testing different gravity models. In this project, we use the Fornax Deep Survey (FDS) dwarf galaxy catalogue to compare the properties of dwarf galaxies in the Fornax Cluster with those predicted by the Lambda cold dark matter (ΛCDM) standard model of cosmology and Milgromian dynamics (MOND). We construct a test particle simulation of the Fornax system. We then use the Markov Chain Monte Carlo (MCMC) method to fit this to the FDS distribution of tidal susceptibility η (half-mass radius divided by theoretical tidal radius), the fraction of dwarfs that visually appear disturbed as a function of η, and the distribution of projected separation from the cluster centre. This allows us to constrain the η value at which dwarfs should get destroyed by tides. Accounting for an r′-band surface brightness limit of 27.8 magnitudes per square arcsec, the required stability threshold is $\eta _{\textrm {destr}} = 0.25^{+0.07}_{-0.03}$ in ΛCDM and $1.88^{+0.85}_{-0.53}$ in MOND. The ΛCDM value is in tension with previous N-body dwarf galaxy simulations, which indicate that ηdestr ≈ 1. Our MOND N-body simulations indicate that ηdestr = 1.70 ± 0.30, which agrees well with our MCMC analysis of the FDS. We therefore conclude that the observed deformations of dwarf galaxies in the Fornax Cluster and the lack of low surface brightness dwarfs towards its centre are incompatible with ΛCDM expectations but well consistent with MOND.
Pentatricopeptide repeat protein MITOCHONDRIAL STABILITY FACTOR 3 ensures mitochondrial RNA stability and embryogenesis
Authors: Wang Chuande , Blondel Lisa , Quadrado Martine , Dargel-Graffin Céline , Mireau Hakim
Published: June 2022

Gene expression in plant mitochondria is predominantly governed at the post-transcriptional level and relies mostly on nuclear-encoded proteins. However, the protein factors involved and the underlying molecular mechanisms are still not well understood. Here, we report on the function of the MITOCHONDRIAL STABILITY FACTOR 3 (MTSF3) protein, previously named EMBRYO DEFECTIVE 2794 (EMB2794), and show that it is essential for accumulation of the mitochondrial NADH dehydrogenase subunit 2 (nad2) transcript in Arabidopsis (Arabidopsis thaliana) but not for splicing of nad2 intron 2 as previously proposed. The MTSF3 gene encodes a pentatricopeptide repeat protein that localizes in the mitochondrion. An MTSF3 null mutation induces embryonic lethality, but viable mtsf3 mutant plants can be generated through partial complementation with the developmentally regulated ABSCISIC ACID INSENSITIVE3 promoter. Genetic analyses revealed growth retardation in rescued mtsf3 plants owing to the specific destabilization of mature nad2 mRNA and a nad2 precursor transcript bearing exons 3 to 5. Biochemical data demonstrate that MTSF3 protein specifically binds to the 3′ terminus of nad2. Destabilization of nad2 mRNA induces a substantial decrease in complex I assembly and activity and overexpression of the alternative respiratory pathway. Our results support a role for MTSF3 protein in protecting two nad2 transcripts from degradation by mitochondrial exoribonucleases by binding to their 3′ extremities.
A calmodulin-like protein (CML10) interacts with cytosolic enzymes GSTU8 and FBA6 to regulate cold tolerance
Authors: Yu Shuhan , Wu Jiaxuan , Sun Yanmei , Zhu Haifeng , Sun Qiguo , Zhao Pengcheng , Huang Risheng , Guo Zhenfei
Published: June 2022

Calmodulin-like proteins (CMLs) are calcium (Ca2+) sensors involved in plant growth and development as well as adaptation to environmental stresses; however, their roles in plant responses to cold are not well understood. To reveal the role of MsCML10 from alfalfa (Medicago sativa) in regulating cold tolerance, we examined transgenic alfalfa and Medicago truncatula overexpressing MsCML10, MsCML10-RNAi alfalfa, and a M. truncatula cml10-1 mutant and identified MsCML10-interacting proteins. MsCML10 and MtCML10 transcripts were induced by cold treatment. Upregulation or downregulation of MsCML10 resulted in increased or decreased cold tolerance, respectively, while cml10-1 showed decreased cold tolerance that was complemented by expressing MsCML10, suggesting that MsCML10 regulates cold tolerance. MsCML10 interacted with glutathione S-transferase (MsGSTU8) and fructose 1,6-biphosphate aldolase (MsFBA6), and the interaction depended on the presence of Ca2+. The altered activities of Glutathione S-transferase and FBA and levels of ROS and sugars were associated with MsCML10 transcript levels. We propose that MsCML10 decodes the cold-induced Ca2+ signal and regulates cold tolerance through activating MsGSTU8 and MsFBA6, leading to improved maintenance of ROS homeostasis and increased accumulation of sugars for osmoregulation, respectively.
Full electroweak 𝒪(α) corrections to Higgs-boson production processes with beam polarization at the International Linear Collider
Authors: Quach Nhi My Uyen , Fujimoto Junpei , Kurihara Yoshimasa
Published: June 2022

We present the full ${{\cal O}}(\alpha )$ electroweak radiative corrections to the production of nine Higgs bosons with beam polarization at the International Linear Collider (ILC). The computation is performed with the help of GRACE-Loop. We compare the full ${{\cal O}}(\alpha )$ electroweak radiative corrections with the factorized initial-state radiation (ISR) effects to estimate the pure weak corrections. This reveals that the pure weak corrections are not negligible and should be taken into account for precision measurements of the Higgs-boson property at the ILC experiments.
Trade Credit and the Transmission of Unconventional Monetary Policy
Authors: Adelino Manuel , Ferreira Miguel A , Giannetti Mariassunta , Pires Pedro
Published: June 2022

We show that production networks are important for the transmission of unconventional monetary policy. Firms with bonds eligible for purchase under the European Central Bank’s Corporate Sector Purchase Program act as financial intermediaries by extending additional trade credit to their customers. The increase in trade credit is pronounced from core countries to periphery countries and for financially constrained customers. Customers then increase investment and employment in response to the increased trade financing, whereas suppliers expand their customer base, contributing to upstream industry concentration. Our findings suggest that trade credit redistributes the effects of monetary policy across regions and firms.
Attention to the other’s body sensations modulates the ventromedial prefrontal cortex
Authors: Tomasino Barbara , Canderan Cinzia , Bonivento Carolina , Rumiati Raffaella I
Published: June 2022

Theory of Mind (ToM) is involved in experiencing the mental states and/or emotions of others. A further distinction can be drawn between emotion and perception/sensation. We investigated the mechanisms engaged when participants’ attention is driven toward specific states. Accordingly, 21 right-handed healthy individuals performed a modified ToM task in which they reflected about someone’s emotion or someone’s body sensation, while they were in a functional magnetic resonance imaging scanner. The analysis of brain activity evoked by this task suggests that the two conditions engage a widespread common network previously found involved in affective ToM (temporo-parietal junction (TPJ), parietal cortex, dorso-lateral prefrontal cortex (DLPFC), medial- prefrontal cortex (MPFC), Insula). Critically, the key brain result is that body sensation implicates selectively ventromedial prefrontal cortex (VMPFC). The current findings suggest that only paying attention to the other’s body sensations modulates a self-related representation (VMPFC).
Borders, Politics, and Bounded Sympathy: How U.S. Television News Constructs Refugees, 1980–2016
Authors: Brown Hana E , Dromgold-Sermen Michelle S
Published: June 2022

This article problematizes a particular category in immigration politics: refugee. Drawing on a content analysis of 356 television news segments that aired on five major news networks between 1980 and 2016, we examine how the category “refugee” has been used in public discourse, to whom it has been applied, and the factors that shape characterizations of those who receive the label. While existing research finds that the media disproportionately associate the term “immigrant” with economic, criminal, and national security threats, we find that U.S. television news coverage associates the term “refugee” with sympathy. We find that these sympathetic portrayals are contingent upon and most common in stories about migrants in distant locales. When the news media cover individuals likely to settle or who are already settled in the United States, coverage takes a more negative tone. We also find evidence that U.S. border politics and foreign political interests affect which migrants receive the refugee label and how they are portrayed. We conclude with implications for the sociological study of classification and for immigration politics more generally.
Standardized ileal digestible amino acids and digestible energy contents in two modified soy protein concentrates and soybean meal fed to growing pigs
Authors: Huber Lee-Anne , Zhu Cuilan , Hansen Lauren , Kozole Cierra , Munoz Alfonso Cristhiam J , Mark Jessica , Moghaddam Kakhki Reza Akbari , Rho Youngji , Kiarie Elijah
Published: June 2022

Six ileal-cannulated barrows (28.0 ± 1.3 kg initial BW) were used in a replicated 3 × 3 Latin square design with one additional period (n = 7 or 6) to determine standardized ileal digestible (SID) AA and digestible energy of two modified soy protein concentrates [MSPC1 and MSPC2] and soybean meal (SBM). Pigs were fed one of three cornstarch-based diets with either MSPC1 or MSPC2 or SBM as the sole source of AA at a rate of 2.8 times the estimated maintenance energy requirement. In each period, pigs were adapted to diets for 7 d followed by 2 d of fecal collection and subsequently, 2 d of continuous ileal digesta collection for 8 h. The SID of AA was calculated using basal endogenous losses from a previous study for pigs fed a nitrogen-free diet. The digestible energy of the ingredients was calculated according to the difference method using a nitrogen-free diet that contained the same cornstarch:sucrose:oil ratio as the three test diets. The total Lys content was 33% and 38% greater for MSPC1 vs. MSPC2 and SBM, respectively. The SID of crude protein was greater for MSPC1 (96.9%) than for SBM (91.3%; P < 0.05), whereas an intermediate value was observed for MSPC2 (94.3% ± 1.2%). The SID of Ile (93.8%), Leu (93.6%), Lys (93.9%), Phe (96.7%), and Val (93.2%) were not different between MSPC1 and MSPC2 but greater than for SBM (88.8% ± 1.3%, 87.8% ± 1.2%, 84.5% ± 1.7%, 92.9% ± 1.0%, 86.5% ± 1.7% for Ile, Leu, Lys, Phe, and Val, respectively; P < 0.05). The SID of His and Thr was greater for MSPC1 than MSPC2 and SBM (P < 0.05), which were not different. The SID of Met was greater for MSPC1 and SBM vs. MSPC2 (P < 0.05). The SID of Arg was greater for MSPC1 than MSPC2 and SBM (P < 0.05), and greater for MSPC2 than SBM (P < 0.05). The digestible energy was greater for MSPC1 (4,677 kcal/kg) than MSPC2 and SBM (average; 3,896 ± 239 kcal/kg; P < 0.05), which were not different. Therefore, the MSPC1 was a better source of SID Lys and digestible energy than either MSPC2 or SBM and could be used as a highly digestible protein ingredient in swine rations.
Characteristics and Results of Hospital Admission Caused by Influenza Virus Infections in Children under 5 Years Old
Authors: Üzüm Özlem , Karadağ Öncel Eda , Demirçelik Yavuz , Örsdemir Hortu Hacer , Kanık Ali , Eliaçık Kayı , Yılmaz Çiftdoğan Dilek , Helvacı Mehmet
Published: June 2022

Aims

The influenza virus is an infectious disease with acute respiratory tract infections, caused secondary bacterial infections and death. In this study, we aimed to determine which predictors were associated with the need for high-flow nasal cannula oxygen therapy (HFNC) and transition to intensive care for influenza virus and also to compare single viral pathogens with multiple ones.

Methods

Inpatients under the age of 5 with influenza virus-related respiratory tract infections between November 2015 and March 2019 were included in the study. Demographic features, comorbidities, symptoms, secondary bacterial infection, need for HFNC and pediatric intensive care unit and respiratory support system, length of hospital stay, polymerase chain reaction tests were recorded.

Results

A total of 93 patients were included in the study. It was determined that 53.8% of the cases were male and 84.9% were under the age of 2. Comorbidities were present in 50.5% of the cases. Secondary bacterial pneumonia developed in 56.9% of the cases. Patients with secondary bacterial pneumonia had higher PICU need, HFNC need and hospital stay (p = 0.014, p ≤ 0.001 and p ≤ 0.001, respectively). Patients with comorbidity had longer hospital stays and a higher need for HFNC (p ≤ 0.001 and p = 0.001, respectively).

Conclusions

In this study, it was determined that especially comorbidity and secondary bacterial infection aggravated the clinical treatment of hospitalized patients. Therefore, it was concluded that patients with comorbidity should be followed closely and secondary bacterial pneumonia should be recognized and treated early.
Independent Predictors of Discontinuation of Diabetic Medication after Sleeve Gastrectomy and Gastric Bypass
Authors: Varban Oliver A , Bonham Aaron J , Carlin Arthur M , Ghaferi Amir A , Finks Jonathath F , Ehlers Anne P
Published: June 2022

BACKGROUND:

Both gastric bypass and sleeve gastrectomy can induce diabetes remission. However, deciding which procedure to perform is challenging, because remission rates and morbidity can vary, depending on patient factors as well as disease severity.

STUDY DESIGN:

Using a statewide bariatric-specific data registry, we evaluated all patients undergoing sleeve gastrectomy and gastric bypass between 2006 and 2019 who reported taking either oral diabetic medication alone or who were on insulin before surgery and who also had 1-year follow-up (n=11,664). Multivariate regression was used to identify independent predictors for discontinuation of oral diabetic medication or insulin, respectively, and risk-adjusted complication rates were compared between procedure types among each group.

RESULTS:

At 1-year after surgery, 85.7% of patients reported discontinuation of oral diabetic medication and 66.6% reported discontinuation of insulin. Gastric bypass was an independent predictor for insulin discontinuation (odds ratio 1.17; CI 1.01 to 1.35; p = 0.0329); however, procedure type was not associated with discontinuation of oral medication alone. Risk-adjusted complication rates were significantly higher after gastric bypass than after sleeve gastrectomy, regardless of whether the patient was taking oral diabetic medications alone or was on insulin (11.2% vs 4.8%, p < 0.0001 and 12.0% vs 7.4%, p < 0.0001, respectively).

CONCLUSIONS:

Patients requiring insulin experience higher rates of insulin discontinuation after gastric bypass, but also have significantly higher complication rates when compared to sleeve gastrectomy. However, if patients are on oral diabetic medication alone, rates of medication discontinuation at 1 year are greater than 85% and procedure type is not predictive. Disease severity is an important factor when deciding on the optimal procedure for diabetes.
Comparison Between Sporadic and Multiple Endocrine Neoplasia Type 1–Associated Insulinoma
Authors: Sada Alaa , Habermann Elizabeth B , Szabo Yamashita Thomas , Thompson Geoffrey B , Lyden Melanie L , Foster Trenton R , Dy Benzon M , Halfdanarson Thorvardur R , Vella Adrian , McKenzie Travis J
Published: June 2022

BACKGROUND:

The differences between sporadic and multiple endocrine neoplasia type 1 (MEN-1)–associated insulinoma are not well described. Herein, we compared demographics, neoplasm characteristics, presentation, and survival in patients with sporadic vs MEN-1 insulinomas including benign and malignant disease.

STUDY DESIGN:

A retrospective study identified insulinoma patients. MEN-1 was defined based on genetic testing or clinically in patients with 2 or more primary MEN-1 tumor types.

RESULTS:

A total of 311 patients were identified: 84% benign and 16% malignant. The incidence of malignancy was similar (18% vs 16%, MEN-1 vs sporadic, p = 0.76). Within malignant patients, the median (interquartile range) age was 33 (25 ,44) years in MEN-1 vs 54 (41, 70) years in sporadic insulinoma (p = 0.04). There was no difference in sex or tumor size between MEN-1 and sporadic malignant insulinoma (p > 0.05). Of the 260 patients with benign insulinoma, 7% had MEN-1 syndrome. MEN-1 patients presented with insulinoma at a younger age: median (interquartile range) age was 38 (24, 49) years vs 52 (43, 65) years (p < 0.01). Resection of benign insulinoma was performed in 78% of the MEN-1 and 94% of the sporadic group (p = 0.03). Resected benign tumors were larger in the MEN-1 group: 2.0 (1.65, 2.45) cm vs 1.5 (1.2, 2.0) cm, respectively (p = 0.03). Concurrent insulinomas were more common in MEN-1 (17% vs 2%; p < 0.01).

CONCLUSIONS:

MEN-1 patients present with insulinoma at younger age and have larger benign pancreatic lesions at the time of resection compared with sporadic neoplasms. Younger patients and those with multifocal pancreatic neuroendocrine tumor in the setting of endogenous hyperinsulinism should be evaluated for MEN-1.