bluuebunny/crossref_metadata_2025_split huggingface dataset:
Production of indigo by recombinant bacteria
Authors: Linke Julia A. , Rayat Andrea , Ward John M. 
Published: March 2023

AbstractIndigo is an economically important dye, especially for the textile industry and the dyeing of denim fabrics for jeans and garments. Around 80,000 tonnes of indigo are chemically produced each year with the use of non-renewable petrochemicals and the use and generation of toxic compounds. As many microorganisms and their enzymes are able to synthesise indigo after the expression of specific oxygenases and hydroxylases, microbial fermentation could offer a more sustainable and environmentally friendly manufacturing platform. Although multiple small-scale studies have been performed, several existing research gaps still hinder the effective translation of these biochemical approaches. No article has evaluated the feasibility and relevance of the current understanding and development of indigo biocatalysis for real-life industrial applications. There is no record of either established or practically tested large-scale bioprocess for the biosynthesis of indigo. To address this, upstream and downstream processing considerations were carried out for indigo biosynthesis. 5 classes of potential biocatalysts were identified, and 2 possible bioprocess flowsheets were designed that facilitate generating either a pre-reduced dye solution or a dry powder product. Furthermore, considering the publicly available data on the development of relevant technology and common bioprocess facilities, possible platform and process values were estimated, including titre, DSP yield, potential plant capacities, fermenter size and batch schedule. This allowed us to project the realistic annual output of a potential indigo biosynthesis platform as 540 tonnes. This was interpreted as an industrially relevant quantity, sufficient to provide an annual dye supply to a single industrial-size denim dyeing plant. The conducted sensitivity analysis showed that this anticipated output is most sensitive to changes in the reaction titer, which can bring a 27.8% increase or a 94.4% drop. Thus, although such a biological platform would require careful consideration, fine-tuning and optimization before real-life implementation, the recombinant indigo biosynthesis was found as already attractive for business exploitation for both, luxury segment customers and mass-producers of denim garments.
Graphical Abstract
Prospective insight into the role of benzyl propylene glycoside as a modulator of the cGAS-STING signaling pathway in the management of nonalcoholic fatty pancreas animal model
Authors: Albadawy Reda , Hasanin Amany Helmy , Agwa Sara H. A. , Hamady Shaimaa , Mohamed Reham Hussein , Gomaa Eman , Othman Mohamed , Yahia Yahia A. , Ghani Amani Mohamed Abdel , Matboli Marwa 
Published: March 2023

Abstract
Background
Nonalcoholic fatty pancreatitis (NAFP) is one of the metabolic syndrome manifestations that need further studies to determine its molecular determinants and find effective medications. We aimed to investigate the potential effect of benzyl propylene glycoside on NAFP management via targeting the pancreatic cGAS-STING pathway-related genes (DDX58, NFκB1 & CHUK) and their upstream regulator miRNA (miR-1976) that were retrieved from bioinformatics analysis.

Methods
The rats were fed either normal chow or a high-fat high-sucrose diet (HFHS), as a nutritional model for NAFP. After 8 weeks, the HFHS-fed rats were subdivided randomly into 4 groups; untreated HFHS group (NAFP model group) and three treated groups which received 3 doses of benzyl propylene glycoside (10, 20, and 30 mg/kg) daily for 4 weeks, parallel with HFHS feeding.

Results
The molecular analysis revealed that benzyl propylene glycoside could modulate the expression of the pancreatic cGAS-STING pathway-related through the downregulation of the expression of DDX58, NFκB1, and CHUK mRNAs and upregulation of miR-1976 expression. Moreover, the applied treatment reversed insulin resistance, inflammation, and fibrosis observed in the untreated NAFP group, as evidenced by improved lipid panel, decreased body weight and the serum level of lipase and amylase, reduced protein levels of NFκB1 and caspase-3 with a significant reduction in area % of collagen fibers in the pancreatic sections of treated animals.

Conclusion
benzyl propylene glycoside showed a potential ability to attenuate NAFP development, inhibit pancreatic inflammation and fibrosis and reduce the pathological and metabolic disturbances monitored in the applied NAFP animal model. The detected effect was correlated with modulation of the expression of pancreatic (DDX58, NFκB1, and CHUK mRNAs and miR-1976) panel.
Thrive or survive: prokaryotic life in hypersaline soils
Authors: Vera-Gargallo Blanca , Hernández Marcela , Dumont Marc G. , Ventosa Antonio 
Published: March 2023

Abstract
Background
Soil services are central to life on the planet, with microorganisms as their main drivers. Thus, the evaluation of soil quality requires an understanding of the principles and factors governing microbial dynamics within it. High salt content is a constraint for life affecting more than 900 million hectares of land, a number predicted to rise at an alarming rate due to changing climate. Nevertheless, little is known about how microbial life unfolds in these habitats. In this study, DNA stable-isotope probing (DNA-SIP) with 18O-water was used to determine for the first time the taxa able to grow in hypersaline soil samples (ECe = 97.02 dS/m). We further evaluated the role of light on prokaryotes growth in this habitat.

Results
We detected growth of both archaea and bacteria, with taxon-specific growth patterns providing insights into the drivers of success in saline soils. Phylotypes related to extreme halophiles, including haloarchaea and Salinibacter, which share an energetically efficient mechanism for salt adaptation (salt-in strategy), dominated the active community. Bacteria related to moderately halophilic and halotolerant taxa, such as Staphylococcus, Aliifodinibius, Bradymonadales or Chitinophagales also grew during the incubations, but they incorporated less heavy isotope. Light did not stimulate prokaryotic photosynthesis but instead restricted the growth of most bacteria and reduced the diversity of archaea that grew.

Conclusions
The results of this study suggest that life in saline soils is energetically expensive and that soil heterogeneity and traits such as exopolysaccharide production or predation may support growth in hypersaline soils. The contribution of phototrophy to supporting the heterotrophic community in saline soils remains unclear. This study paves the way toward a more comprehensive understanding of the functioning of these environments, which is fundamental to their management. Furthermore, it illustrates the potential of further research in saline soils to deepen our understanding of the effect of salinity on microbial communities.
Using the RE-AIM framework to evaluate the feasibility of a parent-focused intervention targeting childhood obesity
Authors: Briatico Daniel , Reilly Kristen C. , Tucker Patricia , Irwin Jennifer D. , Johnson Andrew M. , Pearson Erin S. , Bock Dirk E. , Burke Shauna M. 
Published: March 2023

Abstract
Background
Childhood obesity remains a serious public health concern. Community-based childhood obesity treatment interventions have the potential to improve health behaviors and outcomes among children, but require thorough evaluation to facilitate translation of research into practice. The purpose of the current study was to determine the feasibility of a community-based, parent-focused childhood obesity intervention (“C.H.A.M.P. Families”) using the RE-AIM framework, an evaluation tool for health interventions.

Methods
A single-group, non-randomized, repeated measures feasibility study was conducted. Participants (n = 16 parents/caregivers of 11 children with obesity) completed a 13-week parent-focused education intervention. The intervention consisted of three main components: (a) eight group-based (parent-only) education sessions; (b) eight home-based (family-centered) activities; and (c) two group-based follow-up support sessions for parents and children. The five dimensions of RE-AIM—reach, effectiveness, adoption, implementation, and maintenance—were assessed using various measures and data sources (e.g., child, parent/caregiver, costing, census) obtained throughout the study period. Outcome variables were measured at baseline, mid-intervention, post-intervention, and at a 6-month follow-up.

Results
Overall, the C.H.A.M.P. Families intervention reached approximately 0.09% of eligible families in London, Ontario. Despite the small number, participants were generally representative of the population from which they were drawn, and program participation rates were high (reach). Findings also suggest that involvement in the program was associated with improved health-related quality of life among children (effectiveness/individual-level maintenance). In addition, the intervention had high fidelity to protocol, attendance rates, and cost-effectiveness (implementation). Lastly, important community partnerships were established and maintained (adoption/setting-level maintenance).

Conclusions
Based on a detailed and comprehensive RE-AIM evaluation, the C.H.A.M.P. Families intervention appears to be a promising parent-focused approach to the treatment of childhood obesity.

Trial registration
ISRCTN Registry, Study ID ISRCTN 10752416. Registered 24 April 2018.
De novo design of a novel AIE fluorescent probe tailored to autophagy visualization via pH manipulation
Authors: Huang Xueyan , Chen Fei , Ma Yeshuo , Zheng Fan , Fang Yanpeng , Feng Bin , Huang Shuai , Zeng Hongliang , Zeng Wenbin 
Published: March 2023

Abstract

Background
Macroautophagy is an essential cellular self-protection mechanism, and defective autophagy has been considered to contribute to a variety of diseases. During the process, cytoplasmic components are transported via autophagosomes to acidic lysosomes for metabolism and recycling, which represents application niches for lysosome-targeted fluorescent probes. Additionally, in view of the complexity of the autophagy pathway, it entails more stringent requirements for probes suitable for monitoring autophagy. Meanwhile, aggregation-induced emission (AIE) fluorescent probes have been impressively demonstrated in the biomedical field, which bring fascinating possibilities to the autophagy visualization.

Methods
We reported a generalizable de novo design of a novel pH-sensitive AIE probe ASMP-AP tailored to lysosome targeting for the interpretation of autophagy. Firstly, the theoretical calculation was carried out followed by the investigation of optical properties. Then, the performance of ASMP-AP in visualizing autophagy was corroborated by starvation or drugs treatments. Furthermore, the capability of ASMP-AP to monitor autophagy was demonstrated in ex vivo liver tissue and zebrafish in vivo.

Results
ASMP-AP displays a large stokes shift, great cell permeability and good biocompatibility. More importantly, ASMP-AP enables a good linear response to pH, which derives from the fact that its aggregation state can be manipulated by the acidity. It was successfully applied for imaging autophagy in living cells and was proved capable of monitoring mitophagy. Moreover, this novel molecular tool was validated by ex vivo visualization of activated autophagy in drug-induced liver injury model. Interestingly, it provided a meaningful pharmacological insight that the melanin inhibitor 1-phenyl-2-thiourea (PTU)-induced autophagy was clearly presented in wild-type zebrafish.

Conclusions
ASMP-AP offers a simple yet effective tool for studying lysosome and autophagy. This is the first instance to visualize autophagy in zebrafish using a small-molecule probe with AIE characters, accurate lysosome targeting and simultaneous pH sensitivity. Ultimately, this novel fluorescent system has great potential for in vivo translation to fuel autophagy research.

Graphical Abstract
Online payment fraud: from anomaly detection to risk management
Authors: Vanini Paolo , Rossi Sebastiano , Zvizdic Ermin , Domenig Thomas 
Published: March 2023

AbstractOnline banking fraud occurs whenever a criminal can seize accounts and transfer funds from an individual’s online bank account. Successfully preventing this requires the detection of as many fraudsters as possible, without producing too many false alarms. This is a challenge for machine learning owing to the extremely imbalanced data and complexity of fraud. In addition, classical machine learning methods must be extended, minimizing expected financial losses. Finally, fraud can only be combated systematically and economically if the risks and costs in payment channels are known. We define three models that overcome these challenges: machine learning-based fraud detection, economic optimization of machine learning results, and a risk model to predict the risk of fraud while considering countermeasures. The models were tested utilizing real data. Our machine learning model alone reduces the expected and unexpected losses in the three aggregated payment channels by 15% compared to a benchmark consisting of static if-then rules. Optimizing the machine-learning model further reduces the expected losses by 52%. These results hold with a low false positive rate of 0.4%. Thus, the risk framework of the three models is viable from a business and risk perspective.
Experiences and results from using a novel clinical feedback system in routine stoma care nurse follow-up of patients with an ostomy: a longitudinal study
Authors: Indrebø Kirsten Lerum , Aasprang Anny , Olsen Torill Elin , Andersen John Roger 
Published: March 2023

Abstract
Background
A faecal or urinary ostomy may be lifesaving. However, it involves significant bodily change, and the adjustment process to life with an ostomy includes a broad spectre of physical and psychosocial challenges. Thus, new interventions are needed to improve adaptation to living with an ostomy. This study aimed to examine experiences and outcomes using a new clinical feedback system with patient-reported outcome measures in ostomy care.

Methods
In this longitudinal explorative study, 69 ostomy patients were followed by a stoma care nurse in an outpatient clinic, using a clinical feedback system postoperatively at 3, 6 and 12 months. The patients responded electronically to the questionnaires before each consultation. The Generic Short Patient Experiences Questionnaire was used to measure patient experiences and satisfaction with follow-up. The Ostomy Adjustment Scale (OAS) measured adjustment to life with an ostomy, and the Short Form-36 (SF-36) assessed the patient's health-related quality of life. Longitudinal regression models with time as an explanatory (categorical) variable were used to analyse changes. The STROBE guideline was applied.

Results
The patients were satisfied with their follow-up (96%). Especially, they felt they received sufficient and individualised information, were involved in treatment decisions, and benefited from the consultations. The OAS subscale scores for 'daily activities', 'knowledge and skills' and 'health' improved over time (all p < 0.05), as did the physical and mental component summary scores of the SF-36 (all p < 0.05). Effect sizes of changes were small (0.20–0.40). Sexuality was the most challenging factor reported.

Conclusions
The clinical feedback system could be helpful because outpatient follow-ups for ostomy patients may be more tailored when clinicians use clinical feedback systems. However, further development and testing are needed.
Renal, splenic, and mesenteric artery thrombosis in the setting of cytomegalovirus infection of an immunocompromised patient: a case report
Authors: Tariang Blah Garyll Ryan , Pradeep Megha , Harshil C. Shah , Singh Rajnish 
Published: March 2023

AbstractWe present a case report of an immunocompromised adult with cytomegalovirus infection and APLA positivity complicated by multiple large arterial thrombi. This is a rare presentation as most of the cases reported earlier have been of venous thrombosis, thus demonstrating propensity of CMV to induce arterial thrombosis either directly or indirectly.
IncepTCN: A new deep temporal convolutional network combined with dictionary learning for strong cultural noise elimination of controlled-source electromagnetic data
Authors: Li Guang , Wu Shouli , Cai Hongzhu , He Zhushi , Liu Xiaoqiong , Zhou Cong , Tang Jingtian 
Published: March 2023

When the controlled-source electromagnetic (CSEM) data are contaminated by intense cultural noise and the signal-to-noise ratio (S/N) is lower than 0 dB, the existing denoising methods can hardly achieve good results. To overcome the problem, a new strong-noise elimination method called inception-temporal convolutional network-shift-invariant sparse coding (IncepTCN-SISC) is developed based on deep learning and dictionary learning. First, a novel deep neural network model called IncepTCN is created based on the inception block and temporal convolutional network (TCN). Then, IncepTCN is used to recognize strong-noise segments in the observed signal, which are then discarded. Finally, a dictionary-learning method based on shift-invariant convolutional coding is used to denoise the remaining weak-noise segments. A series of simulated and field data experiments indicate that the new proposed IncepTCN network has obvious advantages in accuracy and efficiency compared with alternative methods. The average recognition accuracy of IncepTCN is 96.5%, which is 25.5%, 3.2%, 1.1%, and 2.0% higher than that of the fuzzy C-means clustering, convolutional neural network (CNN), residual network (ResNet), and the nonimproved TCN, respectively. In addition, the test results of unfamiliar data indicate that the generalization ability of IncepTCN is significantly better than the CNN, ResNet, and nonimproved TCN. This IncepTCN-SISC method can improve the S/N of CSEM data from −5.0 dB to 3.1 dB or from 5.0 dB to 31.9 dB and solve the denoising problem of noisy data below 0 dB to a certain extent. After IncepTCN-SISC processing, the initially distorted apparent resistivity curves become smooth, and the result is better than dictionary learning. This method is intelligent without any manual intervention and is suitable for batch processing of CSEM data.
Substance use, risk behaviours and well-being after admission to a quasi-residential abstinence-based rehabilitation programme: 4-year follow-up
Authors: MacKenzie Nina , Smith Daniel J. , Lawrie Stephen M. , M. Rome Andrew , McCartney David 
Published: March 2023

Background
Tackling Scotland's drug-related deaths and improving outcomes from substance misuse treatments, including residential rehabilitation, is a national priority.

Aims
To analyse and report outcomes up to 4 years after attendance at a substance misuse residential rehabilitation programme (Lothians and Edinburgh Abstinence Programme).

Method
In total, 145 participants were recruited to this longitudinal quantitative cohort study of an abstinence-based residential rehabilitation programme based on the therapeutic community model; 87 of these participants were followed up at 4 years. Outcomes are reported for seven subsections of the Addiction Severity Index-X (ASI-X), together with frequency of alcohol use, heroin use, injecting drug use and rates of abstinence from substances of misuse.

Results
Significant improvement in most outcomes at 4 years compared with admission scores were found. Completing the programme was associated with greater rates of abstinence, reduced alcohol use and improvements in alcohol status score (Mann–Whitney U = 626, P = 0.013), work satisfaction score (U = 596, P = 0.016) and psychiatric status score (U = 562, P = 0.007) on the ASI-X, in comparison with non-completion. Abstinence rates improved from 12% at baseline to 48% at 4 years, with the rate for those completing the programme increasing from 14.5% to 60.7% (χ2(2, 87) = 9.738, P = 0.002). Remaining abstinent from substances at follow-up was associated with better outcomes in the medical (U = 540, P < 0.001), psychiatric (U = 273.5, P < 0.001) and alcohol (U = 322.5, P < 0.001) subsections of the ASI-X.

Conclusions
Attending this abstinence-based rehabilitation programme was associated with positive changes in psychological and social well-being and harm reduction from substance use at 4-year follow-up, with stability of change from years 1 to 4.
Data-driven inference of complex system dynamics: A mini-review
Authors: Gao Ting-Ting , Yan Gang 
Published: March 2023

Abstract
Our ability to observe the network topology and nodes' behaviors of complex systems has significantly advanced in the past decade, giving rise to a new and fast-developing frontier—inferring the underlying dynamical mechanisms of complex systems from the observation data. Here we explain the rationale of data-driven dynamics inference and review the recent progress in this emerging field. Specifically, we classify the existing methods of dynamics inference into three categories, and describe their key ideas, representative applications and limitations. We also discuss the remaining challenges that are worth the future effort.
Association Between Hospital Postoperative Troponin Use and Patient Outcomes After Vascular Surgery
Authors: Azizi Paymon M. , Wijeysundera Duminda N. , Wijeysundera Harindra C. , Austin Peter C. , Jerath Angela , Kayssi Ahmed , Ko Dennis T. 
Published: March 2023

BACKGROUND:
Acute myocardial injury after noncardiac surgery, which is most often symptomatically silent, is associated with increased mortality and morbidity. However, it is not known if routine postoperative troponin testing will affect patient outcomes.

METHODS:
We assembled a cohort of patients who underwent carotid endarterectomy or abdominal aortic aneurysm repair in Ontario, Canada, from 2010 to 2017. Hospitals were categorized into high, medium, and low troponin testing intensity based on the proportion of patients who received postoperative troponin testing. Cox proportional hazards modeling was used to assess the association between hospital-specific testing intensity and 30-day and 1-year major adverse cardiovascular events (MACEs) while adjusting for patient-, surgery-, and hospital-level factors.

RESULTS:
The cohort consisted of 18,467 patients from 17 hospitals. Mean age was 72 years, and 74.0% were men. Rates of postoperative troponin testing were 77.5%, 35.8%, and 21.6% in the high-, medium-, and low-testing intensity hospitals, respectively. At 30 days, 5.3%, 5.3%, and 6.5% of patients in high-, medium-, and low-testing intensity hospitals experienced MACE, respectively. Higher troponin testing rate was associated with lower adjusted hazard ratios (HRs) for MACE at 30 days (0.94; 95% confidence interval [CI], 0.89–0.98) and at 1 year (0.97; 95% CI, 0.94–0.99) for each 10% increase in hospital troponin rate. Hospitals with high-testing intensity had higher rates of postoperative cardiology referrals, cardiovascular testing, and rates of new cardiovascular prescriptions.

CONCLUSIONS:
Patients undergoing vascular surgery at hospitals with higher postoperative troponin testing intensity experienced fewer adverse outcomes than patients who had surgery at hospitals with lower testing intensity.