bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modular DAS demodulation system based on ultra-weak fibre Bragg grating
Authors: Luo Z.H. , Yang Z. , Lu B. , Xu B. , Huang J.L. 
Published: October 2022

Abstract
Aiming at the requirements of low power consumption,
miniaturization, and massive data processing, a modular distributed
optical fibre acoustic sensing (DAS) demodulation system based on
ultra-weak fibre Bragg grating (UW-FBG) is proposed. A highly
integrated circuit and embedded system is used for the time-domain
positioning and data acquisition of the gratings. Field programmable
gate array (FPGA) demodulates the phase changes of each sensing
section in real time. The demodulation outputs are uploaded through
a Gigabit Ethernet connection. Through innovative software and
hardware design, the demodulation system power consumption is less
than 20 W, and the device volume is
250 mm× 180 mm× 45 mm, and the output
data size is about 2.6% of the conventional methods. All the
outputs are then tested on a piezoelectric transducer (PZT)
platform. Results show that the background noise within
5 Hz–1280 Hz range is 2.16 pε/√(Hz), and
the strain sensitivity reaches
484 pε/√(Hz)@200 Hz. The correlation
coefficient of voltage and phase is 0.9991, which shows good
linearity. Combined with a common commercial laptop to demodulate
the micro-vibration signals, this system could provide a
cost-effective scheme for acquiring acoustic-level micro-vibration
signals and on-line field monitoring.
Boosts in leaf-level photosynthetic capacity aid Pinus ponderosa recovery from wildfire
Authors: Bryant Kelsey N , Stenzel Jeffrey , Mathias Justin , Kwon Hyojung , Kolden Crystal A , Lynch Laurel , Hudiburg Tara 
Published: October 2022

Abstract
Forests mitigate climate change by sequestering massive amounts of carbon, but recent increases in wildfire activity are threatening carbon storage. Currently, our understanding of wildfire impacts on forest resilience and the mechanisms controlling post-fire recovery remains unresolved due to a lack of empirical data on mature trees in natural settings. Here, we quantify the physiological mechanisms controlling carbon uptake immediately following wildfire in mature individuals of ponderosa pine (Pinus ponderosa), a wide-spread and canopy-dominant tree species in fire-prone forests. While photosynthetic capacity was lower in burned than unburned trees due to an overall depletion of resources, we show that within the burned trees, photosynthetic capacity increases with the severity of damage. Our data reveal that boosts in the efficiency of carbon uptake at the leaf-level may compensate for whole-tree damage, including the loss of leaf area and roots. We further show that heightened photosynthetic capacity in remaining needles on burned trees may be linked with reduced water stress and leaf nitrogen content, providing pivotal information about post-fire physiological processes. Our results have implications for Earth system modeling efforts because measurements of species-level physiological parameters are used in models to predict ecosystem and landscape-level carbon trajectories. Finally, current land management practices do not account for physiological resilience and recovery of severely burned trees. Our results suggest premature harvest may remove individuals that may otherwise survive, irrevocably altering forest carbon balance.
Mapping global hotspots and trends of water quality (1992–2010): a data driven approach
Authors: Desbureaux Sebastien , Mortier Frederic , Zaveri Esha , van Vliet Michelle T H , Russ Jason , Rodella Aude Sophie , Damania Richard 
Published: October 2022

AbstractClean water is key for sustainable development. However, large gaps in monitoring data limit our understanding of global hotspots of poor water quality and their evolution over time. We demonstrate the value added of a data-driven approach (here, random forest) to provide accurate high-frequency estimates of surface water quality worldwide over the period 1992–2010. We assess water quality for six indicators (temperature, dissolved oxygen, pH, salinity, nitrate-nitrite, phosphorus) relevant for the sustainable development goals. The performance of our modeling approach compares well to, or exceeds, the performance of recently published process-based models. The model’s outputs indicate that poor water quality is a global problem that impacts low-, middle- and high-income countries but with different pollutants. When countries become richer, water pollution does not disappear but evolves. Water quality exhibited a signif icant change between 1992 and 2010 with a higher percentage of grid cells where water quality shows a statistically significant deterioration (30%) compared to where water quality improved (22%).
CoaDTI: multi-modal co-attention based framework for drug–target interaction annotation
Authors: Huang Lei , Lin Jiecong , Liu Rui , Zheng Zetian , Meng Lingkuan , Chen Xingjian , Li Xiangtao , Wong Ka-Chun 
Published: October 2022

Abstract

Motivation
The identification of drug–target interactions (DTIs) plays a vital role for in silico drug discovery, in which the drug is the chemical molecule, and the target is the protein residues in the binding pocket. Manual DTI annotation approaches remain reliable; however, it is notoriously laborious and time-consuming to test each drug–target pair exhaustively. Recently, the rapid growth of labelled DTI data has catalysed interests in high-throughput DTI prediction. Unfortunately, those methods highly rely on the manual features denoted by human, leading to errors.

Results
Here, we developed an end-to-end deep learning framework called CoaDTI to significantly improve the efficiency and interpretability of drug target annotation. CoaDTI incorporates the Co-attention mechanism to model the interaction information from the drug modality and protein modality. In particular, CoaDTI incorporates transformer to learn the protein representations from raw amino acid sequences, and GraphSage to extract the molecule graph features from SMILES. Furthermore, we proposed to employ the transfer learning strategy to encode protein features by pre-trained transformer to address the issue of scarce labelled data. The experimental results demonstrate that CoaDTI achieves competitive performance on three public datasets compared with state-of-the-art models. In addition, the transfer learning strategy further boosts the performance to an unprecedented level. The extended study reveals that CoaDTI can identify novel DTIs such as reactions between candidate drugs and severe acute respiratory syndrome coronavirus 2-associated proteins. The visualization of co-attention scores can illustrate the interpretability of our model for mechanistic insights.

Availability
Source code are publicly available at https://github.com/Layne-Huang/CoaDTI.
Interaction-based transcriptome analysis via differential network inference
Authors: Leng Jiacheng , Wu Ling-Yun 
Published: October 2022

Abstract
Gene-based transcriptome analysis, such as differential expression analysis, can identify the key factors causing disease production, cell differentiation and other biological processes. However, this is not enough because basic life activities are mainly driven by the interactions between genes. Although there have been already many differential network inference methods for identifying the differential gene interactions, currently, most studies still only use the information of nodes in the network for downstream analyses. To investigate the insight into differential gene interactions, we should perform interaction-based transcriptome analysis (IBTA) instead of gene-based analysis after obtaining the differential networks. In this paper, we illustrated a workflow of IBTA by developing a Co-hub Differential Network inference (CDN) algorithm, and a novel interaction-based metric, pivot APC2. We confirmed the superior performance of CDN through simulation experiments compared with other popular differential network inference algorithms. Furthermore, three case studies are given using colorectal cancer, COVID-19 and triple-negative breast cancer datasets to demonstrate the ability of our interaction-based analytical process to uncover causative mechanisms.
An Adaptive MAC Protocol Based on Time-Domain Interference Alignment for UWANs
Authors: Zhao Nan , Yao Nianmin , Gao Zhenguo 
Published: October 2022

Abstract
The spatial and temporal uncertainty caused by large propagation delays is a fundamental feature of Underwater Acoustic Networks (UWANs), which seriously affects the performance of the UWANs and also brings challenges to the design of MAC protocols. In this paper, we develop an adaptive MAC protocol based on deep reinforcement learning for UWANs, called ARL-MAC protocol, to intelligently allocate time slots for nodes. Firstly, we design a reward mechanism based on the idea of Time-Domain Interference Alignment (TDIA). We determine the reward according to the combination of the node action and the feedback corresponding to the action. Then, we propose a flexible training mechanism to deal with the ever-changing underwater environment, which improves the fairness of time slot allocation. In addition, we introduce the Deep Recurrent Q-Network (DRQN) algorithm to solve the partially observable information issue. Finally, we evaluate the ARL-MAC protocol with the different number of nodes and changing network environment. Simulation results reveal that the ARL-MAC protocol outperforms other MAC protocols for UWANs in terms of throughput, collision rate and service fairness.
Relationships and resilience at work and at home
Authors: Ali Hebatallah Naim , Gittell Jody Hoffer , Deng Sien , Stults Cheryl D. , Martinez Meghan , Pertsch Suzanne , Weger Lauren , Dillon Ellis C. 
Published: October 2022

Background
The COVID-19 pandemic has been an unusually comprehensive crisis that has taken a toll on people in their roles both at work and at home, giving rise to a new normal.

Purpose
Relational coordination theory shows how communicating and relating for the purpose of task integration drives positive outcomes for workers, their clients, and their employers. The ecological theory of work–family spillover shows how relational dynamics from work spillover into family life, and vice versa. We build upon these two theories to understand how relationships at work impact work–life balance and worker well-being, especially in times of crisis.

Methodology
This study was based on surveys of clinicians affiliated with a large California health system during the COVID-19 pandemic. Mediation and multilevel logistic regression models were used to assess how relational coordination among colleagues impacts well-being (job satisfaction and lack of burnout) through its effects on work–life balance (schedule control and personal time).

Results
A 1-point increase in relational coordination tripled clinician odds of having schedule control (OR = 3.33, p < .001) and nearly doubled the odds of having adequate personal time (OR = 1.83, p < .001). A 1-point increase in relational coordination nearly quadrupled odds of being satisfied with their job (OR = 3.92, p < .001) and decreased odds of burnout by 64% (OR = 0.36, p < .001). The impact of relational coordination on worker well-being was mediated by greater schedule control and personal time.

Conclusion
Relational coordination among colleagues impacts worker well-being by enabling greater control over one’s schedule and more personal time, thus creating a positive spillover from work to home in times of crisis.

Practice Implications
In times of crisis, leaders should prioritize relational coordination among colleagues in order to support their resilience both at work and at home.
PER3 plays anticancer roles in the oncogenesis and progression of breast cancer via regulating MEK/ERK signaling pathway
Authors: Liu Yinfeng , Wu Zizheng , Li Yanli , Zhang Jing , Gao Yang , Yuan Guanli , Han Meng 
Published: October 2022

Background:
The study aimed at exploring the expression of period circadian regulator 3 (PER3), a major member of the circadian clock gene family, and its biological function in breast cancer.

Methods:
PER3-silencing and PER3-overexpression cell lines were established by transfecting with pGenesil1-PER3 and Lenti-blast-PER3 vector, respectively.

Results:
The results showed that the expression of PER3 was downregulated in breast cancer tissues and cell lines (p < 0.001), and its low expression was significantly correlated with advanced tumor stage (p = 0.031) and advanced T stage (p = 0.018). Cell functional experiments indicated that the silencing of PER3 elevated the ability of breast cancer cells to proliferate, invade, and metastasize in vitro (p < 0.05), whereas overexpression of PER3 had an inhibitory effect on these malignant phenotype of breast cancer cells (p < 0.05). Moreover, the activation of MEK/ERK signaling pathway was evidently inhibited by silencing of PER3, as evidenced by decreased expression levels of p-MEK and p-ERK1/2 proteins in breast cancer cells (p < 0.05). PER3-silencing and PER3-overexpression cells were treated with PD98059 (an inhibitor of MEK/ERK signaling) and TPA (an activator of MEK/ERK signaling), respectively. It was observed that PER3 silencing-mediated malignant phenotype in breast cancer cells was markedly suppressed by PD98059 treatment. Instead, TPA exposure reversed the inhibitory effects of PER3 overexpression on DNA synthesis, proliferation, migration, and invasion of breast cancer cells.

Conclusion:
These findings suggested that PER3 function as a tumor suppressor in the development and progression of breast cancer and its anticancer roles might be dependent on the MEK/ERK signaling pathway.
The strategy of diminishing age gap effect on different donor-recipient combinations in living donor kidney transplantation
Authors: Kuo Fang-Cheng , Wu Tsai-Hun , Loong Che-Chuan , Lin Niang-Cheng , Ou Shuo-Ming , Chen Cheng-Yen 
Published: October 2022

Background:
The disparity between kidney donation and the number of uremic patients on the waiting list has increased the demand for older live-donor kidneys (OLK). However, the donor-recipient age gap may have an impact on the recipient’s outcome.

Methods:
Patients who underwent living donor kidney transplantation at our institute between 2005 and 2019 were enrolled and categorized into four donor-recipient groups according to age (≥50 years and <50 years). The Estimated Post-Transplant Survival (EPTS) score was used to quantify the recipient’s condition. Adjusted models analyzed recipient outcomes and related risks among the four groups.

Results:
Of the 154 pairs of live donors and recipients, OLK did not influence overall or death-censored graft survival. The four donor-recipient combinations had similar recipient outcomes, except it slightly worsened in the “old donor to young recipient” group. The EPTS score (adjusted HR, 1.02; 95% CI, 1.01-1.04; p = 0.014) and rejection (adjusted HR, 4.26; 95% CI, 1.36-13.37; p = 0.013) were significant risk factors for overall and death-censored graft survival, respectively. Recipients with pretransplant diabetes or prior solid organ transplantation could have amplified risk effects. The main causes of graft loss were death in older recipients and chronic rejection in younger recipients.

Conclusion:
OLK is safe for young recipients. Nevertheless, adequate immunosuppression should be maintained to prevent rejection and subsequent graft loss, especially for those receiving second kidney transplantation. In contrast, older recipients should avoid overt immunosuppression and control their comorbidities, such as diabetes-related complications to improve their long-term outcomes.
Eptifibatide-induced acute profound thrombocytopenia: A case report
Authors: Alamin Mohammed A. , Al-Mashdali Abdulrahman , Al Kindi Dawoud I. , Elshaikh Elkhansa A. , Othman Fahmi 
Published: October 2022

Rationale:
Eptifibatide is an antiplatelet agent used in the medical management of acute coronary syndrome. Although multiple studies did not reveal a significant association between eptifibatide and the development of thrombocytopenia, recent case reports brought attention to this relatively rare side effect.

Patient concerns:
We report a 61 years old male with acute coronary syndrome who underwent primary coronary intervention.

Diagnosis and intervention:
The patient developed acute profound thrombocytopenia following eptifibatide administration. Following prompt offending drug discontinuation, the platelet counts recovered, without clinical sequelae or the need for platelet transfusion. Dual antiplatelet therapy with aspirin and clopidogrel was resumed after platelet count normalization.

Outcomes:
The patient had a normal platelet count and no bleeding events on follow-up after three months upon discharge.

Conclusion:
Eptifibatide, a glycoprotein IIa/IIIb inhibitor used in the management of acute coronary syndrome, can induce acute, profound thrombocytopenia that can have significant morbidity in patients. This case highlights this relatively rare side effect and the importance of monitoring blood counts and observing for any signs of bleeding or thrombosis that might occur in such patients.
IL2RA is a prognostic indicator and correlated with immune characteristics of pancreatic ductal adenocarcinoma
Authors: Fan Liwen , Wang Xinyu , Chang Qing , Wang Yue , Yang Wenjie , Liu Linlin 
Published: October 2022

Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive and incurable cancer with a dismal prognosis. In this study, we aimed to explore potential predictors for the prognosis and immunological characteristics of PDAC.
Estimation of stromal and immune cells in malignant tumors, using expression data (ESTIMATE) method was applied to calculate the immune and stromal scores of 206 PDAC samples from GSE71729. R package of “limma” was utilized to identify differentially expressed genes (DEGs). Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analyses were conducted for functional exploration. Protein-protein interaction (PPI) network and Univariate Cox analysis were conducted to select key prognostic genes of PDAC. Gene set enrichment analysis (GSEA) was applied to investigate the roles of IL2RA in PDAC. Single sample GSEA (ssGSEA) was performed to evaluate the immunological characteristics of PDAC samples. Wilcoxon rank sum test was conducted to compare the difference of immunological characteristics of PDAC samples between low IL2RA and high IL2RA. Spearman correlation analysis was used to explore the correlations of IL2RA expression and immune checkpoint genes.
A total of 747 DEGs were identified between low and high immune/stromal groups. Functional exploration revealed upregulated DEGs were associated with immune-related activities, whereas downregulated DEGs were involved in inflammatory-related activities. IL2RA was selected as the critical gene by overlapping the hub genes in PPI network and prognostic genes. Significantly, IL2RA expression was significantly elevated in PDAC and patients with higher IL2RA expression had worse prognoses. The immunological and oncogenic roles of IL2RA in PDAC were evidenced by GSEA. Furthermore, PDAC samples with high IL2RA expression exhibited increased immune infiltration and better immunotherapy responses. IL2RA expression was positively correlated with PDCD1, CD274, CTLA4, IDO1, TDO2, and TIGT.
Higher expression of IL2RA predicts worse survival outcomes and increased immune infiltration in PDAC. PDAC patients with high IL2RA expression might potentially benefit from immunotherapy.
Surgical operation combined with bronchoscopy in the treatment of fungal empyema: 5 cases report
Authors: Xin Shunxin , Wu Yongyong , He Zhongliang , He Xueming , Wang Lei , Qi Yaoli 
Published: October 2022

Rationale:
Fungal empyema is a chronic refractory disease. It is difficult to control thoracic infection, and it is faced with the problem of recurrence. How to control the infection and reduce the probability of recurrence is a difficult problem. Surgical operation combined with endobronchial therapy was used to control infection, seal the fistula and eliminate residual cavity and achieved good results.

Patient concerns:
A total of 5 patients with fungal empyema were treated from 2019 to 2021, aged 27 to 72 years, with an average age of 54.8 ± 7.6 years. Two cases were on the left side and 3 cases on the right side.

Diagnosis:
While meeting the diagnostic criteria of empyema, the diagnosis of fungus in pus culture or the discovery of fungus in deep tissue pathology confirmed the diagnosis of fungal empyema in the 5 cases.

Interventions:
Through surgical operations combined with bronchoscopy and individualized treatment, the infection was controlled, the fistulas were blocked, and the pus cavity was filled.

Outcomes:
After 11 to 30 months of follow-up, the muscle flap in the abscess cavity was mildly atrophied, and there was no recurrence of empyema. Three patients who completed the second-stage operation had their chest tubes removed and returned to normal life. The 2 patients who did not complete the second-stage operation had no recurrence of thoracic infection and no recurrence of cough or fever, and their quality of life was greatly improved.

Lessons:
Surgical operation combined with bronchoscopy is a reliable method for the treatment of fungal empyema, which can find and plug the fistula more efficiently and eliminate the residual cavity by surgery to avoid recurrence. Therefore, it is a recommended treatment method.
Vitamin D supplementation for patients with alopecia areata: A protocol for systematic review and meta-analysis
Authors: Zhu Baohua , Zhang Lan , Wang Jun , Tan Guiyuan 
Published: October 2022

Background:
Several studies have reported an association between low Vitamin D (VD) levels and Alopecia areata (AA), and suggested VD preparations as a potential therapy. VD has immunomodulatory function closely associated with a variety of skin diseases, but there is no conclusive evidence to support VD supplementation for patients with AA. Therefore, we will conduct a meta-analysis to collect and evaluate the efficacy and safety of VD supplementation in the treatment of AA.

Methods:
We will search the following databases according to the developed strategy: Cochrane Library, PubMed, Web of Science, EMBASE, Scopus, Google scholar for Randomized controlled trials related to VD supplementation for AA. The retrieval time is from the establishment of each database to July 2022. Two reviewers will independently complete the literature search and screening, risk of bias assessment and data extraction. Severity of Alopecia Tool, Alopecia Density and Extent, Lesional area and senstivity (score) will be the primary results. RevMan V.5.3 will be used for data analysis and synthesis. For dichotomous outcomes and the continuous outcomes, we will calculate risk ratio with 95% Confidence intervals and mean differences or standardized mean differences with 95% Confidence intervals respectively. The reporting bias will be investigated using funnel plots, and the asymmetry of the funnel plots will be explained using the Harbord modified test or the Egger’s regression test.

Results:
The results of the study expect to provide a high-quality, evidence-based recommendation on VD supplementation in the treatment of AA for clinicians.

Conclusions:
The study will provide scientific and useful evidence for better use of VD supplementation in treating AA.