bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome assembly of wild loquat (Eriobotrya japonica) and resequencing provide new insights into the genomic evolution and fruit domestication in loquat
Authors: Jing Danlong , Liu Xinya , He Qiao , Dang Jiangbo , Hu Ruoqian , Xia Yan , Wu Di , Wang Shuming , Zhang Yin , Xia Qingqing , Zhang Chi , Yu Yuanhui , Guo Qigao , Liang Guolu 
Published: December 2022

Abstract
Wild loquats (Eriobotrya japonica Lindl.) provide remarkable genetic resources for studying domestication and breeding improved varieties. Herein, we generate the first high-quality chromosome-level genome assembly of wild loquat, with 45 791 predicted protein-coding genes. Analysis of comparative genomics indicated that loquat shares a common ancestor with apple and pear, and a recent whole-genome duplication event occurred in loquat prior to its divergence. Genome resequencing showed that the loquat germplasms can be distinctly classified into wild and cultivated groups, and the commercial cultivars have experienced allelic admixture. Compared with cultivated loquats, the wild loquat genome showed very few selected genomic regions and had higher levels of genetic diversity. However, whole-genome scans of selective sweeps were mainly related to fruit quality, size, and flesh color during the domestication process. Large-scale transcriptome and metabolome analyses were further performed to identify differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) in wild and cultivated loquats at various fruit development stages. Unlike those in wild loquat, the key DEGs and DAMs involved in carbohydrate metabolism, plant hormone signal transduction, flavonoid biosynthesis, and carotenoid biosynthesis were significantly regulated in cultivated loquats during fruit development. These high-quality reference genome, resequencing, and large-scale transcriptome/metabolome data provide valuable resources for elucidating fruit domestication and molecular breeding in loquat.
SbMYB3 transcription factor promotes root-specific flavone biosynthesis in Scutellaria baicalensis
Authors: Fang Yumin , Liu Jie , Zheng Minmin , Zhu Sanming , Pei Tianlin , Cui Mengying , Chang Lijing , Xiao Hanwen , Yang Jun , Martin Cathie , Zhao Qing 
Published: December 2022

Abstract
Scutellaria baicalensis Georgi produces abundant root-specific flavones (RSFs), which provide various benefits to human health. We have elucidated the complete biosynthetic pathways of baicalein and wogonin. However, the transcriptional regulation of flavone biosynthesis in S. baicalensis remains unclear. We show that the SbMYB3 transcription factor functions as a transcriptional activator involved in the biosynthesis of RSFs in S. baicalensis. Yeast one-hybrid and transcriptional activation assays showed that SbMYB3 binds to the promoter of flavone synthase II-2 (SbFNSII-2) and enhances its transcription. In S. baicalensis hairy roots, RNAi of SbMYB3 reduced the accumulation of baicalin and wogonoside, and SbMYB3 knockout decreased the biosynthesis of baicalein, baicalin, wogonin, and wogonoside, whereas SbMYB3 overexpression enhanced the contents of baicalein, baicalin, wogonin, and wogonoside. Transcript profiling by qRT–PCR demonstrated that SbMYB3 activates SbFNSII-2 expression directly, thus leading to more abundant accumulation of RSFs. This study provides a potential target for metabolic engineering of RSFs.
Impact of fisheries footprint on an early warning indicator of resilience reduction in marine net primary productivity
Authors: Zhao Youzhu , Li Yangfan 
Published: December 2022

Abstract
Human activities and climate change have profound effects on marine ecosystems, leading to changes in ecosystem functionality and even reduced resilience. Hence, a systematic assessment of the marine ecosystem resilience and the drivers of resilience is needed. This study provides an approach to help measure the resilience of reduction marine ecosystems by calculating early warning signs of marine net primary productivity, while introducing fishing activities and environmental data in the study area to evaluate the factors affecting marine ecosystem resilience. The results showed that in 36.29% of the Chinese exclusive economic zone, resilience was likely to be significantly decreased. There was a non-linear relationship between fishing activities and indicators of resilience reduction, with pixels with high-intensity fishing activities being more susceptible to resilience reduction. Fishing regulations are urgently needed in areas where marine ecosystem resilience may be reducing. Effective management and protection of marine ecosystems require assessment of the spatial overlap between marine ecosystems states and human activities. This study provides a scientific basis for sustainable management of social-ecological systems by comparing high-precision fishing data to marine environmental data, thereby analysing marine ecosystem resilience through the use of early warning indicators.
The development of an automatic speech recognition model using interview data from long-term care for older adults
Authors: Hacking Coen , Verbeek Hilde , Hamers Jan P H , Aarts Sil 
Published: December 2022

AbstractObjectiveIn long-term care (LTC) for older adults, interviews are used to collect client perspectives that are often recorded and transcribed verbatim, which is a time-consuming, tedious task. Automatic speech recognition (ASR) could provide a solution; however, current ASR systems are not effective for certain demographic groups. This study aims to show how data from specific groups, such as older adults or people with accents, can be used to develop an effective ASR.Materials and methodsAn initial ASR model was developed using the Mozilla Common Voice dataset. Audio and transcript data (34 h) from interviews with residents, family, and care professionals on quality of care were used. Interview data were continuously processed to reduce the word error rate (WER).ResultsDue to background noise and mispronunciations, an initial ASR model had a WER of 48.3% on interview data. After finetuning using interview data, the average WER was reduced to 24.3%. When tested on speech data from the interviews, a median WER of 22.1% was achieved, with residents displaying the highest WER (22.7%). The resulting ASR model was at least 6 times faster than manual transcription.DiscussionThe current method decreased the WER substantially, verifying its efficacy. Moreover, using local transcription of audio can be beneficial to the privacy of participants.ConclusionsThe current study shows that interview data from LTC for older adults can be effectively used to improve an ASR model. While the model output does still contain some errors, researchers reported that it saved much time during transcription.
Been There, Done That: How Episodic and Semantic Memory Affects the Language of Authentic and Fictitious Reviews
Authors: Kronrod Ann , Gordeliy Ivan , Lee Jeffrey K 
Published: December 2022

AbstractThis article suggests a theory-driven approach to address the managerial problem of distinguishing between real and fake reviews. Building on memory research and linguistics, we predict that when recollecting an authentic experience in a product review, people rely to a greater extent on episodic memory. By contrast, when writing a fictitious review, people do not have episodic memory available to them. Therefore, they must rely to a greater extent on semantic memory. We suggest that reliance on these different memory types is reflected in the language used in authentic and fictitious reviews. We develop predictions about five linguistic features characterizing authentic versus fictitious reviews. We test our predictions via a multi-method approach, combining computational linguistics, experimental design, and machine learning. We employ a large-scale experiment to derive a dataset of reviews, as well as two datasets containing reviews from online platforms. We also test whether an algorithm relying on our theory-driven linguistic features is context independent, relative to other benchmark algorithms, and shows better cross-domain performance when tested across datasets. By developing a theory that extends memory and psycholinguistics research to the realm of word of mouth, this work contributes to our understanding of how authentic and fictitious reviews are created.
Association of optical, ultraviolet, and soft X-ray excess emissions in AGNs
Authors: Nour D , Sriram K 
Published: December 2022

ABSTRACT
Soft X-ray emission (0.5–2.0 keV) plays a pivotal role in regulating the optical and ultraviolet (UV) emission in the active galactic nuclei (AGNs). We collected a sample of 1811 AGNs from the SDSS database and obtained various parameters of Balmer lines, optical continuum, Mg ii line & UV continuum and studied their dependencies on soft X-ray luminosity. Based on the linear regression analysis, we found that FWHM$_{\rm {Mg\,\,\small {II}}}$ ∝ FWHM$_{\text{H}\beta }^{0.554}$ suggesting that UV emission is arising from a region relatively outside the broad-line region (BLR) associated to the Hβ emission and found a strong correlation between optical and UV luminosities (L$_{\rm {Mg\,\,\small {II}}}$ ∝ $L_{\rm {H}\beta }^{0.822}$). It was noticed that the dependency of optical continuum luminosities on soft excess changes with the redshift (LX ∝ L$^{0.596}_{5100\, \mathring{\rm A}}$ for z &lt; 0.5 and LX ∝ L$^{0.429}_{5100\, \mathring{\rm A}}$ for z &gt; 0.5). The full width at half-maximum components of Hβ and Mg ii core components were found to be virialized and is not affected by the soft excess emission whereas the wings of Mg ii display a dependency. We estimated a relation viz. LX ∝L$^{0.520}_{3000\, \mathring{\rm A}}$ FWHM$^{0.525}_{\rm {Mg\,\,\small {II}}}$ and found to be well in agreement with a proposed physical scenario. All the derived relations were used to understand the intermodulating association of the BLR and disc in the AGNs.
Neural networks: solving the chemistry of the interstellar medium
Authors: Branca L , Pallottini A 
Published: December 2022

ABSTRACT
Non-equilibrium chemistry is a key process in the study of the interstellar medium (ISM), in particular the formation of molecular clouds and thus stars. However, computationally, it is among the most difficult tasks to include in astrophysical simulations, because of the typically high (&gt;40) number of reactions, the short evolutionary time-scales (about 104 times less than the ISM dynamical time), and the characteristic non-linearity and stiffness of the associated ordinary differential equations system (ODEs). In this proof of concept work, we show that Physics Informed Neural Networks (PINN) are a viable alternative to traditional ODE time integrators for stiff thermochemical systems, i.e. up to molecular hydrogen formation (9 species and 46 reactions). Testing different chemical networks in a wide range of densities (−2 &lt; log n/cm−3 &lt; 3) and temperatures (1 &lt; log T/K &lt; 5), we find that a basic architecture can give a comfortable convergence only for simplified chemical systems: to properly capture the sudden chemical and thermal variations, a Deep Galerkin Method is needed. Once trained (∼103 GPUhr), the PINN well reproduces the strong non-linear nature of the solutions (errors $\lesssim 10{{\ \rm per\ cent}}$) and can give speed-ups up to a factor of ∼200 with respect to traditional ODE solvers. Further, the latter have completion times that vary by about $\sim 30{{\ \rm per\ cent}}$ for different initial n and T, while the PINN method gives negligible variations. Both the speed-up and the potential improvement in load balancing imply that PINN-powered simulations are a very palatable way to solve complex chemical calculation in astrophysical and cosmological problems.
Positive feedback, quenching, and sequential super star cluster (SSC) formation in NGC 4945
Authors: Bellocchi E , Martín-Pintado J , Rico-Villas F , Martín S , Jiménez-Sierra I 
Published: December 2022

ABSTRACT
We have used ALMA imaging (resolutions 0.1–0.4 arcsec) of ground and vibrationally excited lines of HCN and HC3N toward the nucleus of NGC 4945 to trace the protostellar phase in super star clusters (proto-SSC). Out of the 14 identified SSCs, we find that eight are in the proto-SSC phase showing vibrational HCN emission with five of them also showing vibrational HC3N emission. We estimate proto-SSC ages of 5–9.7 × 104 yr. The more evolved ones, with only HCN emission, are close to reach the zero-age main sequence (ZAMS; ages ≳105 yr). The excitation of the parental cloud seems to be related to the SSC evolutionary stage, with high (∼65 K) and low (∼25 K) rotational temperatures for the youngest proto and ZAMS SSCs, respectively. Heating by the H ii regions in the SSC ZAMS phase seems to be rather local. The youngest proto-SSCs are located at the edges of the molecular outflow, indicating SSC formation by positive feedback in the shocked regions. The proto-SSCs in NGC 4945 seem to be more evolved than in the starburst galaxy NGC 253. We propose that sequential SSC formation can explain the spatial distribution and different ages of the SSCs in both galaxies.
Predictive modeling of moonlighting DNA-binding proteins
Authors: Varghese Dana Mary , Nussinov Ruth , Ahmad Shandar 
Published: December 2022

Abstract
Moonlighting proteins are multifunctional, single-polypeptide chains capable of performing multiple autonomous functions. Most moonlighting proteins have been discovered through work unrelated to their multifunctionality. We believe that prediction of moonlighting proteins from first principles, that is, using sequence, predicted structure, evolutionary profiles, and global gene expression profiles, for only one functional class of proteins in a single organism at a time will significantly advance our understanding of multifunctional proteins. In this work, we investigated human moonlighting DNA-binding proteins (mDBPs) in terms of properties that distinguish them from other (non-moonlighting) proteins with the same DNA-binding protein (DBP) function. Following a careful and comprehensive analysis of discriminatory features, a machine learning model was developed to assess the predictability of mDBPs from other DBPs (oDBPs). We observed that mDBPs can be discriminated from oDBPs with high accuracy of 74% AUC of ROC using these first principles features. A number of novel predicted mDBPs were found to have literature support for their being moonlighting and others are proposed as candidates, for which the moonlighting function is currently unknown. We believe that this work will help in deciphering and annotating novel moonlighting DBPs and scale up other functions. The source codes and data sets used for this work are freely available at https://zenodo.org/record/7299265#.Y2pO3ctBxPY
A viral movement protein co-opts endoplasmic reticulum luminal-binding protein and calreticulin to promote intracellular movement
Authors: Huang Ying-Wen , Sun Chu-I , Hu Chung-Chi , Tsai Ching-Hsiu , Meng Menghsiao , Lin Na-Sheng , Dinesh-Kumar Savithramma P , Hsu Yau-Heiu 
Published: December 2022

Abstract
Intracellular movement is an important step for the initial spread of virus in plants during infection. This process requires virus-encoded movement proteins (MPs) and their interaction with host factors. Despite the large number of known host factors involved in the movement of different viruses, little is known about host proteins that interact with one of the MPs encoded by potexviruses, the triple-gene-block protein 3 (TGBp3). The main obstacle lies in the relatively low expression level of potexviral TGBp3 in hosts and the weak or transient nature of interactions. Here, we used TurboID-based proximity labeling to identify the network of proteins directly or indirectly interacting with the TGBp3 of a potexvirus, Bamboo mosaic virus (BaMV). Endoplasmic reticulum (ER) luminal-binding protein 4 and calreticulin 3 of Nicotiana benthamiana (NbBiP4 and NbCRT3, respectively) associated with the functional TGBp3-containing BaMV movement complexes, but not the movement-defective mutant, TGBp3M. Fluorescent microscopy revealed that TGBp3 colocalizes with NbBiP4 or NbCRT3 and the complexes move together along ER networks to cell periphery in N. benthamiana. Loss- and gain-of-function experiments revealed that NbBiP4 or NbCRT3 is required for the efficient spread and accumulation of BaMV in infected leaves. In addition, overexpression of NbBiP4 or NbCRT3 enhanced the targeting of BaMV TGBp1 to plasmodesmata (PD), indicating that NbBiP4 and NbCRT3 interact with TGBp3 to promote the intracellular transport of virion cargo to PD that facilitates virus cell-to-cell movement. Our findings revealed additional roles for NbBiP4 and NbCRT3 in BaMV intracellular movement through ER networks or ER-derived vesicles to PD, which enhances the spread of BaMV in N. benthamiana.
Varieties of Mobility Measures: Comparing Survey and Mobile Phone Data during the COVID-19 Pandemic
Authors: Kalleitner Fabian , Schiestl David W , Heiler Georg 
Published: December 2022

AbstractHuman mobility has become a major variable of interest during the COVID-19 pandemic and central to policy decisions all around the world. To measure individual mobility, research relies on a variety of indicators that commonly stem from two main data sources: survey self-reports and behavioral mobility data from mobile phones. However, little is known about how mobility from survey self-reports relates to popular mobility estimates using data from the Global System for Mobile Communications (GSM) and the Global Positioning System (GPS). Spanning March 2020 until April 2021, this study compares self-reported mobility from a panel survey in Austria to aggregated mobility estimates utilizing (1) GSM data and (2) Google’s GPS-based Community Mobility Reports. Our analyses show that correlations in mobility changes over time are high, both in general and when comparing subgroups by age, gender, and mobility category. However, while these trends are similar, the size of relative mobility changes over time differs substantially between different mobility estimates. Overall, while our findings suggest that these mobility estimates manage to capture similar latent variables, especially when focusing on changes in mobility over time, researchers should be aware of the specific form of mobility different data sources capture.
Validation of methods to identify people with idiopathic inflammatory myopathies using hospital episode statistics
Authors: Hannah Jennifer R , Gordon Patrick A , Galloway James , Rutter Megan , Peach Emily J , Rooney Michael , Stilwell Peter , Grainge Matthew J , Lanyon Peter C , Bythell Mary , Pearce Fiona A 
Published: December 2022

Abstract

Objective
Hospital episode statistics (HES) are routinely recorded at every hospital admission within the National Health Service (NHS) in England. This study validates diagnostic ICD-10 codes within HES as a method of identifying cases of idiopathic inflammatory myopathies (IIMs).

Methods
All inpatient admissions at one NHS Trust between 2010 and 2020 with relevant diagnostic ICD-10 codes were extracted from HES. Hospital databases were used to identify all outpatients with IIM, and electronic care records were reviewed to confirm coding accuracy. Total hospital admissions were calculated from NHS Digital reports. The sensitivity and specificity of each code and code combinations were calculated to develop an optimal algorithm. The optimal algorithm was tested in a sample of admissions at another NHS Trust.

Results
Of the 672 individuals identified by HES, 510 were confirmed to have IIM. Overall, the positive predictive value (PPV) was 76% and sensitivity 89%. Combination algorithms achieved PPVs between 89 and 94%. HES can also predict the presence of IIM-associated interstitial lung disease (ILD) with a PPV of 79% and sensitivity of 71%. The optimal algorithm excluded children (except JDM code M33.0), combined M33.0, M33.1, M33.9, M36.0, G72.4, M60.8 and M33.2, and included M60.9 only if it occurred alongside an ILD code (J84.1, J84.9 or J99.1). This produced a PPV of 88.9% and sensitivity of 84.2%. Retesting this algorithm at another NHS Trust confirmed a high PPV (94.4%).

Conclusion
IIM ICD-10 code combinations in HES have high PPVs and sensitivities. Algorithms tested in this study could be applied across all NHS Trusts to enable robust and cost-effective whole-population research into the epidemiology of IIM.
Positron Emission Tomography Assessments of Phosphodiesterase 10A in Patients With Schizophrenia
Authors: Kubota Manabu , Takahata Keisuke , Matsuoka Kiwamu , Sano Yasunori , Yamamoto Yasuharu , Tagai Kenji , Tarumi Ryosuke , Suzuki Hisaomi , Kurose Shin , Nakajima Shinichiro , Shiwaku Hiroki , Seki Chie , Kawamura Kazunori , Zhang Ming-Rong , Takahashi Hidehiko , Takado Yuhei , Higuchi Makoto 
Published: December 2022

Abstract

Background and hypothesis
Phosphodiesterase 10A (PDE10A) is a highly expressed enzyme in the basal ganglia, where cortical glutamatergic and midbrain dopaminergic inputs are integrated. Therapeutic PDE10A inhibition effects on schizophrenia have been reported previously, but the status of this molecule in the living patients with schizophrenia remains elusive. Therefore, this study aimed to investigate the central PDE10A status in patients with schizophrenia and examine its relationship with psychopathology, cognition, and corticostriatal glutamate levels.

Study design
This study included 27 patients with schizophrenia, with 5 antipsychotic-free cases, and 27 healthy controls. Positron emission tomography with [18F]MNI-659, a specific PDE10A radioligand, was employed to quantify PDE10A availability by measuring non-displaceable binding potential (BPND) of the ligand in the limbic, executive, and sensorimotor striatal functional subregions, and in the pallidum. BPND estimates were compared between patients and controls while controlling for age and gender. BPND correlations were examined with behavioral and clinical measures, along with regional glutamate levels quantified by the magnetic resonance spectroscopy.

Study results
Multivariate analysis of covariance demonstrated a significant main effect of diagnosis on BPND (p = .03). A posthoc test showed a trend-level higher sensorimotor striatal BPND in patients, although it did not survive multiple comparison corrections. BPND in controls in this subregion was significantly and negatively correlated with the Tower of London scores, a cognitive subtest. Striatal or dorsolateral prefrontal glutamate levels did not correlate significantly with BPND in either group.

Conclusions
The results suggest altered striatal PDE10A availability and associated local neural dysfunctions in patients with schizophrenia.