bluuebunny/crossref_metadata_2025_split huggingface dataset:
OsCCRL1 is Essential for Phenylpropanoid Metabolism in Rice Anthers
Authors: Zhang Lisha , Zheng Lintao , Wu Jingwen , Liu Yang , Liu Weichi , He Guanghua , Wang Nan 
Published: February 2023

AbstractPhenylpropanoid metabolism and timely tapetal degradation are essential for anther and pollen development, but the underlying mechanisms are unclear. In the current study, to investigate this, we identified and analyzed the male-sterile mutant, osccrl1 (cinnamoyl coA reductase-like 1), which exhibited delayed tapetal programmed cell death (PCD) and defective mature pollen. Map-based cloning, genetic complementation, and gene knockout revealed that OsCCRL1 corresponds to the gene LOC_Os09g32020.2, a member of SDR (short-chain dehydrogenase/reductase) family enzyme. OsCCRL1 was preferentially expressed in the tapetal cells and microspores, and localized to the nucleus and cytoplasm in both rice protoplasts and Nicotiana benthamiana leaves. The osccrl1 mutant exhibited reduced CCRs enzyme activity, less lignin accumulation, delayed tapetum degradation, and disrupted phenylpropanoid metabolism. Furthermore, an R2R3 MYB transcription factor OsMYB103/OsMYB80/OsMS188/BM1, involved in tapetum and pollen development, regulates the expression of OsCCRL1. Finally, the osmyb103 osccrl1 double mutants, exhibited the same phenotype as the osmyb103 single mutant, further indicating that OsMYB103/OsMYB80/OsMS188/BM1 functions upstream of OsCCRL1. These findings help to clarify the role of phenylpropanoid metabolism in male sterility and the regulatory network underlying the tapetum degradation.
SALON ontology for the formal description of sequence alignments
Authors: Benítez-Hidalgo Antonio , Aldana-Montes José F. , Navas-Delgado Ismael , Roldán-García María del Mar 
Published: February 2023

Abstract
Background
Information provided by high-throughput sequencing platforms allows the collection of content-rich data about biological sequences and their context. Sequence alignment is a bioinformatics approach to identifying regions of similarity in DNA, RNA, or protein sequences. However, there is no consensus about the specific common terminology and representation for sequence alignments. Thus, automatically linking the wide existing knowledge about the sequences with the alignments is challenging.

Results
The Sequence Alignment Ontology (SALON) defines a helpful vocabulary for representing and semantically annotating pairwise and multiple sequence alignments. SALON is an OWL 2 ontology that supports automated reasoning for alignments validation and retrieving complementary information from public databases under the Open Linked Data approach. This will reduce the effort needed by scientists to interpret the sequence alignment results.

Conclusions
SALON defines a full range of controlled terminology in the domain of sequence alignments. It can be used as a mediated schema to integrate data from different sources and validate acquired knowledge.
ncDENSE: a novel computational method based on a deep learning framework for non-coding RNAs family prediction
Authors: Chen Kai , Zhu Xiaodong , Wang Jiahao , Hao Lei , Liu Zhen , Liu Yuanning 
Published: February 2023

Abstract
Background
Although research on non-coding RNAs (ncRNAs) is a hot topic in life sciences, the functions of numerous ncRNAs remain unclear. In recent years, researchers have found that ncRNAs of the same family have similar functions, therefore, it is important to accurately predict ncRNAs families to identify their functions. There are several methods available to solve the prediction problem of ncRNAs family, whose main ideas can be divided into two categories, including prediction based on the secondary structure features of ncRNAs, and prediction according to sequence features of ncRNAs. The first type of prediction method requires a complicated process and has a low accuracy in obtaining the secondary structure of ncRNAs, while the second type of method has a simple prediction process and a high accuracy, but there is still room for improvement. The existing methods for ncRNAs family prediction are associated with problems such as complicated prediction processes and low accuracy, in this regard, it is necessary to propose a new method to predict the ncRNAs family more perfectly.

Results
A deep learning model-based method, ncDENSE, was proposed in this study, which predicted ncRNAs families by extracting ncRNAs sequence features. The bases in ncRNAs sequences were encoded by one-hot coding and later fed into an ensemble deep learning model, which contained the dynamic bi-directional gated recurrent unit (Bi-GRU), the dense convolutional network (DenseNet), and the Attention Mechanism (AM). To be specific, dynamic Bi-GRU was used to extract contextual feature information and capture long-term dependencies of ncRNAs sequences. AM was employed to assign different weights to features extracted by Bi-GRU and focused the attention on information with greater weights. Whereas DenseNet was adopted to extract local feature information of ncRNAs sequences and classify them by the full connection layer. According to our results, the ncDENSE method improved the Accuracy, Sensitivity, Precision, F-score, and MCC by 2.08$$\%$$
%
, 2.33$$\%$$
%
, 2.14$$\%$$
%
, 2.16$$\%$$
%
, and 2.39$$\%$$
%
, respectively, compared with the suboptimal method.

Conclusions
Overall, the ncDENSE method proposed in this paper extracts sequence features of ncRNAs by dynamic Bi-GRU and DenseNet and improves the accuracy in predicting ncRNAs family and other data.
Leaf wettability and leaf angle affect air-moisture deposition in wheat for self-irrigation
Authors: Hakeem Sadia , Ali Zulfiqar , Saddique Muhammad Abu Bakar , Merrium Sabah , Arslan Muhammad , Habib-ur-Rahman Muhammad 
Published: February 2023

Abstract
Background
Climate change and depleting water sources demand scarce natural water supplies like air moisture to be used as an irrigation water source. Wheat production is threatened by the climate variability and extremes climate events especially heat waves and drought. The present study focused to develop the wheat plant for self-irrigation through optimizing leaf architecture and surface properties for precise irrigation.

Methods
Thirty-four genotypes were selected from 1796 genotypes with all combinations of leaf angle and leaf rolling. These genotypes were characterized for morpho-physiological traits and soil moisture content at stem-elongation and booting stages. Further, a core set of ten genotypes was evaluated for stem flow efficiency and leaf wettability.

Results
Biplot, heat map, and correlation analysis indicated wide diversity and traits association. The environmental parameters indicated substantial amount of air moisture (> 60% relative humidity) at the critical wheat growth stages. Leaf angle showed negative association with leaf rolling, physiological and yield traits, adaxial and abaxial contact angle while leaf angle showed positive association with the stem flow water. The wettability and air moisture harvesting indicated that the genotypes (coded as 1, 7, and 18) having semi-erect to erect leaf angle, spiral rolling, and hydrophilic leaf surface (<90o) with contact angle hysteresis less than 10o had higher soil moisture content (6-8%) and moisture harvesting efficiency (3.5 ml).

Conclusions
These findings can provide the basis to develop self-irrigating, drought-tolerant wheat cultivars as an adaptation to climate change.
Promoter activity and transcriptome analyses decipher functions of CgbHLH001 gene (Chenopodium glaucum L.) in response to abiotic stress
Authors: Zhou Zixin , Wang Juan , Yu Qinghui , Lan Haiyan 
Published: February 2023

Abstract
Background
Our previous studies revealed that CgbHLH001 transcription factor (TF) played an important role in abiotic stress tolerance, suggesting that its promoter was a potential target in response to stress signals. In addition, the regulatory mechanism of CgbHLH001 TF is still limited.

Results
In the present study, a 1512 bp of 5’-flanking sequence of CgbHLH001 gene was identified, and the sequence carried quite a few of cis-acting elements. The gene promoter displayed strong activity and was induced by multiple abiotic stress. A series of 5’-deletions of the promoter sequence resulted in a gradual decrease in its activity, especially, the 5’ untranslated region (UTR) was necessary to drive promoter activity. Further, CgbHLH001 promoter drove its own gene overexpression ectopically at the transcriptional and translational levels, which in turn conferred the stress tolerance to transgenic Arabidopsis. Transcriptome analysis showed that salt stress induced a large number of genes involved in multiple biological regulatory processes. Differentially expressed genes (DEGs) that mediate phytohormone signal transduction and mitogen-activated protein kinase (MAPK) signaling pathway were widely induced and mostly upregulated under salt stress, and the transcription levels in PbHLH::bHLH-overexpressing transgenic lines were higher than that of 35S::bHLH overexpression.

Conclusions
The CgbHLH001 promoter exhibited a positive response to abiotic stress and its 5’ UTR sequence enhanced the regulation of gene expression to stress. A few important pathways and putative key genes involved in salt tolerance were identified, which can be used to elucidate the mechanism of salt tolerance and decipher the regulatory mechanism of promoters to develop an adaptation strategy for desert halophytes.
Non-invasive assessment of Pulse Wave Transit Time (PWTT) is a poor predictor for intraoperative fluid responsiveness: a prospective observational trial (best-PWTT study)
Authors: Fukui Kimiko , Wirkus Johannes M. , Hartmann Erik K. , Schmidtmann Irene , Pestel Gunther J. , Griemert Eva-Verena 
Published: February 2023

Abstract
Background
Aim of this study is to test the predictive value of Pulse Wave Transit Time (PWTT) for fluid responsiveness in comparison to the established fluid responsiveness parameters pulse pressure (ΔPP) and corrected flow time (FTc) during major abdominal surgery.

Methods
Forty patients undergoing major abdominal surgery were enrolled with continuous monitoring of PWTT (LifeScope® Modell J BSM-9101 Nihon Kohden Europe GmbH, Rosbach, Germany) and stroke volume (Esophageal Doppler Monitoring CardioQ-ODM®, Deltex Medical Ltd, Chichester, UK). In case of hypovolemia (difference in pulse pressure [∆PP] ≥ 9%, corrected flow time [FTc] ≤ 350 ms) a fluid bolus of 7 ml/kg ideal body weight was administered. Receiver operating characteristics (ROC) curves and corresponding areas under the curve (AUCs) were used to compare different methods of determining PWTT. A Wilcoxon test was used to discriminate fluid responders (increase in stroke volume of ≥ 10%) from non-responders. The predictive value of PWTT for fluid responsiveness was compared by testing for differences between ROC curves of PWTT, ΔPP and FTc using the methods by DeLong.

Results
AUCs (area under the ROC-curve) to predict fluid responsiveness for PWTT-parameters were 0.61 (raw c finger Q), 0.61 (raw c finger R), 0.57 (raw c ear Q), 0.53 (raw c ear R), 0.54 (raw non-c finger Q), 0.52 (raw non-c finger R), 0.50 (raw non-c ear Q), 0.55 (raw non-c ear R), 0.63 (∆ c finger Q), 0.61 (∆ c finger R), 0.64 (∆ c ear Q), 0.66 (∆ c ear R), 0.59 (∆ non-c finger Q), 0.57 (∆ non-c finger R), 0.57 (∆ non-c ear Q), 0.61 (∆ non-c ear R) [raw measurements vs. ∆ = respiratory variation; c = corrected measurements according to Bazett’s formula vs. non-c = uncorrected measurements; Q vs. R = start of PWTT-measurements with Q- or R-wave in ECG; finger vs. ear = pulse oximetry probe location]. Hence, the highest AUC to predict fluid responsiveness by PWTT was achieved by calculating its respiratory variation (∆PWTT), with a pulse oximeter attached to the earlobe, using the R-wave in ECG, and correction by Bazett’s formula (AUC best-PWTT 0.66, 95% CI 0.54–0.79). ∆PWTT was sufficient to discriminate fluid responders from non-responders (p = 0.029). No difference in predicting fluid responsiveness was found between best-PWTT and ∆PP (AUC 0.65, 95% CI 0.51–0.79; p = 0.88), or best-PWTT and FTc (AUC 0.62, 95% CI 0.49–0.75; p = 0.68).

Conclusion
ΔPWTT shows poor ability to predict fluid responsiveness intraoperatively. Moreover, established alternatives ΔPP and FTc did not perform better.

Trial registration
Prior to enrolement on clinicaltrials.gov (NC T03280953; date of registration 13/09/2017).
A quantitative clinical evaluation of simultaneous reconstruction of attenuation and activity in time-of-flight PET
Authors: Zhang Haiqiong , Wang Jingnan , Li Nan , Zhang Yue , Cui Jie , Huo Li , Zhang Hui 
Published: February 2023

AbstractBackgroundThe maximum likelihood activity and attenuation (MLAA) reconstruction algorithm has been proposed to jointly estimate tracer activity and attenuation at the same time, and proven to be a promising solution to the CT attenuation correction (CT-AC) artifacts in PET images. This study aimed to perform a quantitative evaluation and clinical validation of the MLAA method.MethodsA uniform cylinder phantom filled with18F-FDG solution was scanned to optimize the reconstruction parameters for the implemented MLAA algorithm. 67 patients who underwent whole-body18F-FDG PET/CT scan were retrospectively recruited. PET images were reconstructed using MLAA and clinical standard OSEM algorithm with CT-AC (CT-OSEM). The mean and maximum standardized uptake values (SUVmean and SUVmax) in regions of interest (ROIs) of organs, high uptake lesions and areas affected by metal implants and respiration motion artifacts were quantitatively analyzed.ResultsIn quantitative analysis, SUVs in patient’s organ ROIs between two methods showedR2ranging from 0.91 to 0.98 andkranging from 0.90 to 1.06, and the average SUVmax and SUVmean differences between two methods were within 10% range, except for the lung ROI, which was 10.5% and 16.73% respectively. The average SUVmax and SUVmean differences of a total of 117 high uptake lesions were 7.25% and 7.10% respectively. 20 patients were identified to have apparent respiration motion artifacts in the liver in CT-OSEM images, and the SUVs differences between two methods measured at dome of the liver were significantly larger than measured at middle part of the liver. 10 regions with obvious metal artifacts were identified in CT-OSEM images and the average SUVmean and SUVmax differences in metal implants affected regions were reported to be 52.90% and 56.20% respectively.ConclusionsPET images reconstructed using MLAA are clinically acceptable in terms of image quality as well as quantification and it is a useful tool in clinical practice, especially when CT-AC may cause respiration motion and metal artifacts. Moreover, this study also provides technical reference and data support for the future iteration and development of PET reconstruction technology of SUV accurate quantification.
Risk factors for early neurologic deterioration in single small subcortical infarction without carrier artery stenosis: predictors at the early stage
Authors: Jin Di , Yang Jing , Zhu Hui , Wu Yuexia , Liu Haichao , Wang Qi , Zhang Xiaoyun , Dong Yanhua , Luo Bin , Shan Yong , Zhang Lvming , Wang Peifu , Du Jichen 
Published: February 2023

AbstractObjectivesThis study aimed to assess the epidemiological features and explore the potential risk factors for early neurological deterioration (END) in patients with acute single small subcortical infarction (SSSI) who underwent antiplatelet therapy without carotid artery stenosis.Materials & methodsPatients with SSSI, as confirmed by cranial magnetic resonance imaging (MRI), who were hospitalized within 48 h after the onset of symptoms were enrolled. END was mainly defined as increment in the National Institutes of Health Stroke Scale (NIHSS) score of ≥ 2 points or any new neurological deficit. Poor functional outcome was defined as modified Rankin Scale (mRS) score of > 2 points at 3-month after the onset. The association of END with multiple indicators was assessed at the early stage of admission using multivariate logistic regression analysis, and adjusted odds ratios (aORs) were calculated.ResultsA total of 280 patients were enrolled from June 2020 to May 2021, of whom, END occurred in 44 (15.7%) patients (median age, 64 years; 70.5% male), while END occurred during sleep in 28 (63.6%) patients. History of hypertension (aOR: 4.82,p = 0.001), infarction in internal capsule (aOR: 3.35,p = 0.001), and elevated level of low-density lipoprotein cholesterol (LDL-C; aOR: 0.036,p = 0.0016) were significantly associated with the risk of END. Patients with END (aOR: 5.74,p = 0.002), history of diabetes (aOR: 2.61,p = 0.020), and higher NIHSS scores at discharge (per 1-score increase, aOR: 1.29,p = 0.026) were associated with the poor functional outcome at 3-month after the onset.ConclusionPatients with a history of hypertension, infarction in internal capsule or a higher level of LDL-C were found to be at a higher risk of END.
Mental health professionals and telehealth in a rural setting: a cross sectional survey
Authors: Nelson David , Inghels Maxime , Kenny Amanda , Skinner Steve , McCranor Tracy , Wyatt Stephen , Phull Jaspreet , Nanyonjo Agnes , Yusuff Ojali , Gussy Mark 
Published: February 2023

Abstract
Background
Telehealth usage has been promoted in all settings but has been identified as a panacea to issues of access and equity in the rural context. However, uptake and widespread integration of telehealth across all parts of the health system has been slow, with a myriad of barriers documented, including in rural settings. The crisis of the COVID-19 pandemic, saw barriers rapidly overturned with the unprecedented and exponential rise in telehealth usage. The uniqueness of the crisis forced telehealth adoption, but as the urgency stabilises, pandemic learnings must be captured, utilised, and built upon in a post-pandemic world. The aim of this study was to document staff experiences and perceptions of delivering rural psychological therapies via telehealth during the pandemic and to capture learnings for future rural telehealth delivery.

Methods
An online cross-sectional survey that explored mental health professional’s experiences, use, and perceptions of telehealth before and after pandemic-enforced changes to service delivery.

Results
Sixty-two respondents completed the questionnaire (response rate 68%). Both the delivery of telehealth via telephone and online video conferencing significantly increased during the pandemic (66% vs 98%, p < .001 for telephone and 10% vs 89%, p < 0.001 for online video). Respondents indicated that client’s access to services and attendance had improved with telehealth use but their attention and focus during sessions and non-verbal communication had been negatively affected. The challenges for older adults, people with learning and sensory disabilities, and residents in remote areas with poorer mobile/internet connectivity were identified. Despite these challenges, none of the respondents indicated a preference to return to fully face-to-face service delivery with most (86%) preferring to deliver psychological therapies fully or mostly via telehealth.

Conclusions
This study addresses three major gaps in knowledge: the experience of delivering local telehealth solutions to address rural mental health needs, the provision of strong rural-specific telehealth recommendations, and the dearth of rural research emanating from the United Kingdom. As the world settles into a living with COVID-19 era, the uniqueness of the rural telehealth context may be forgotten as urban myopia continues to dominate telehealth policy and uptake. It is critical that rural resourcing and digital connectivity are addressed.
Identification of gene profiles related to the development of oral cancer using a deep learning technique
Authors: Tapak Leili , Ghasemi Mohammad Kazem , Afshar Saeid , Mahjub Hossein , Soltanian Alireza , Khotanlou Hassan 
Published: February 2023

Abstract
Background
Oral cancer (OC) is a debilitating disease that can affect the quality of life of these patients adversely. Oral premalignant lesion patients have a high risk of developing OC. Therefore, identifying robust survival subgroups among them may significantly improve patient therapy and care. This study aimed to identify prognostic biomarkers that predict the time-to-development of OC and survival stratification for patients using state-of-the-art machine learning and deep learning.

Methods
Gene expression profiles (29,096 probes) related to 86 patients from the GSE26549 dataset from the GEO repository were used. An autoencoder deep learning neural network model was used to extract features. We also used a univariate Cox regression model to select significant features obtained from the deep learning method (P < 0.05). High-risk and low-risk groups were then identified using a hierarchical clustering technique based on 100 encoded features (the number of units of the encoding layer, i.e., bottleneck of the network) from autoencoder and selected by Cox proportional hazards model and a supervised random forest (RF) classifier was used to identify gene profiles related to subtypes of OC from the original 29,096 probes.

Results
Among 100 encoded features extracted by autoencoder, seventy features were significantly related to time-to-OC-development, based on the univariate Cox model, which was used as the inputs for the clustering of patients. Two survival risk groups were identified (P value of log-rank test = 0.003) and were used as the labels for supervised classification. The overall accuracy of the RF classifier was 0.916 over the test set, yielded 21 top genes (FUT8-DDR2-ATM-CD247-ETS1-ZEB2-COL5A2-GMAP7-CDH1-COL11A2-COL3A1-AHR-COL2A1-CHORDC1-PTP4A3-COL1A2-CCR2-PDGFRB-COL1A1-FERMT2-PIK3CB) associated with time to developing OC, selected among the original 29,096 probes.

Conclusions
Using deep learning, our study identified prominent transcriptional biomarkers in determining high-risk patients for developing oral cancer, which may be prognostic as significant targets for OC therapy. The identified genes may serve as potential targets for oral cancer chemoprevention. Additional validation of these biomarkers in experimental prospective and retrospective studies will launch them in OC clinics.