bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel concept of photosynthetic soft membranes: a numerical study
Authors: Falciani Gabriele , Bergamasco Luca , Bonke Shannon A. , Sen Indraneel , Chiavazzo Eliodoro 
Published: February 2023

AbstractWe focus on a novel concept of photosynthetic soft membranes, possibly able to allow the conversion of solar energy and carbon dioxide (CO$$_2$$

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) into green fuels. The considered membranes rely on self-assembled functional molecules in the form of soap films. We elaborate a multi-scale and multi-physics model to describe the relevant phenomena, investigating the expected performance of a single soft photosynthetic membrane. First, we present a macroscale continuum model, which accounts for the transport of gaseous and ionic species within the soap film, the chemical equilibria and the two involved photocatalytic half reactions of the CO$$_2$$

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reduction and water oxidation at the two gas–surfactant–water interfaces of the soap film. Second, we introduce a mesoscale discrete Monte Carlo model, to deepen the investigation of the structure of the functional monolayers. Finally, the morphological information obtained at the mesoscale is integrated into the continuum model in a multi-scale framework. The developed tools are then used to perform sensitivity studies in a wide range of possible experimental conditions, to provide scenarios on fuel production by such a novel approach.
Multi-round recycling of green waste for the production of iron nanoparticles: synthesis, characterization, and prospects in remediation
Authors: Rónavári Andrea , Balázs Margit , Szilágyi Árpád , Molnár Csaba , Kotormán Márta , Ilisz István , Kiricsi Mónika , Kónya Zoltán 
Published: February 2023

AbstractDue to the widespread applications of metal nanoparticles (NPs), green synthesis strategies have recently advanced, e.g., methods that utilize extracts made from different plant wastes. A particularly innovative approach to reducing large amounts of available household/agricultural green wastes is their application in nanoparticle generation. Regarding this, the aim of our work was to examine the possibility of upgrading green nanoparticle syntheses from an innovative economic and environmental point of view, namely by investigating the multiple recyclabilities of green tea (GT), coffee arabica (CA), and Virginia creeper (Parthenocissus quinquefolia) (VC) waste residues for iron nanoparticle (FeNPs) synthesis. The plant extracts obtained by each extraction round were analyzed individually to determine the amount of main components anticipated to be involved in NPs synthesis. The synthesized FeNPs were characterized by X-ray powder diffraction and transmission electron microscopy. The activity of the generated FeNPs in degrading chlorinated volatile organic compounds (VOC) and thus their future applicability for remediation purposes were also assessed. We have found that VC and especially GT residues could be reutilized in multiple extraction rounds; however, only the first extract of CA was suitable for FeNPs’ generation. All of the obtained FeNPs could degrade VOC with efficiencies GT1-Fe 91.0%, GT2-Fe 83.2%, GT3-Fe 68.5%; CA1-Fe 76.2%; VC1-Fe 88.2%, VC2-Fe 79.7%, respectively, where the number (as in GT3) marked the extraction round. These results indicate that the adequately selected green waste material can be reutilized in multiple rounds for nanoparticle synthesis, thus offering a clean, sustainable, straightforward alternative to chemical methods.Graphical abstract
Model performance and interpretability of semi-supervised generative adversarial networks to predict oncogenic variants with unlabeled data
Authors: Ren Zilin , Li Quan , Cao Kajia , Li Marilyn M. , Zhou Yunyun , Wang Kai 
Published: February 2023

Abstract
Background
It remains an important challenge to predict the functional consequences or clinical impacts of genetic variants in human diseases, such as cancer. An increasing number of genetic variants in cancer have been discovered and documented in public databases such as COSMIC, but the vast majority of them have no functional or clinical annotations. Some databases, such as CiVIC are available with manual annotation of functional mutations, but the size of the database is small due to the use of human annotation. Since the unlabeled data (millions of variants) typically outnumber labeled data (thousands of variants), computational tools that take advantage of unlabeled data may improve prediction accuracy.

Result
To leverage unlabeled data to predict functional importance of genetic variants, we introduced a method using semi-supervised generative adversarial networks (SGAN), incorporating features from both labeled and unlabeled data. Our SGAN model incorporated features from clinical guidelines and predictive scores from other computational tools. We also performed comparative analysis to study factors that influence prediction accuracy, such as using different algorithms, types of features, and training sample size, to provide more insights into variant prioritization. We found that SGAN can achieve competitive performances with small labeled training samples by incorporating unlabeled samples, which is a unique advantage compared to traditional machine learning methods. We also found that manually curated samples can achieve a more stable predictive performance than publicly available datasets.

Conclusions
By incorporating much larger samples of unlabeled data, the SGAN method can improve the ability to detect novel oncogenic variants, compared to other machine-learning algorithms that use only labeled datasets. SGAN can be potentially used to predict the pathogenicity of more complex variants such as structural variants or non-coding variants, with the availability of more training samples and informative features.
SigB modulates expression of novel SigB regulon members via Bc1009 in non-stressed and heat-stressed cells revealing its alternative roles in Bacillus cereus
Authors: Yeak Kah Yen Claire , Tempelaars Marcel , Wu Jia Lun , Westerveld Wouter , Reder Alexander , Michalik Stephan , Dhople Vishnu M. , Völker Uwe , Pané-Farré Jan , Wells-Bennik Marjon H. J. , Abee Tjakko 
Published: February 2023

AbstractBackgroundTheBacillus cereusSigma B (SigB) dependent general stress response is activated via the two-component RsbKY system, which involves a phosphate transfer from RsbK to RsbY. It has been hypothesized that the Hpr-like phosphocarrier protein (Bc1009) encoded bybc1009in the SigB gene cluster may play a role in this transfer, thereby acting as a regulator of SigB activation. Alternatively, Bc1009 may be involved in the activation of a subset of SigB regulon members.ResultsWe first investigated the potential role ofbc1009to act as a SigB regulator but ruled out this possibility as the deletion ofbc1009did not affect the expression ofsigBand other SigB gene cluster members. The SigB-dependent functions of Bc1009 were further examined inB. cereusATCC14579 via comparative proteome profiling (backed up by transcriptomics) of wt, Δbc1009and ΔsigBdeletion mutants under heat stress at 42 °C. This revealed 284 proteins displaying SigB-dependent alterations in protein expression levels in heat-stressed cells, including a subgroup of 138 proteins for which alterations were also Bc1009-dependent. Next to proteins with roles in stress defense, newly identified SigB and Bc1009-dependent proteins have roles in cell motility, signal transduction, transcription, cell wall biogenesis, and amino acid transport and metabolism. Analysis of lethal stress survival at 50 °C after pre-adaptation at 42 °C showed intermediate survival efficacy ofΔbc1009cells, highest survival of wt, and lowest survival ofΔsigBcells, respectively. Additional comparative proteome analysis of non-stressed wt and mutant cells at 30 °C revealed 96 proteins with SigB and Bc1009-dependent differences in levels: 51 were also identified under heat stress, and 45 showed significant differential expression at 30 °C. This includes proteins with roles in carbohydrate/ion transport and metabolism. Overlapping functions at 30 °C and 42 °C included proteins involved in motility, and ΔsigBand Δbc1009cells showed reduced motility compared to wt cells in swimming assays at both temperatures.ConclusionOur results extend theB. cereusSigB regulon to > 300 members, with a novel role of SigB-dependent Bc1009 in the activation of a subregulon of  > 180 members, conceivably via interactions with other transcriptional regulatory networks.
Dissecting the microbial community structure of internal organs during the early postmortem period in a murine corpse model
Authors: Liu Ruina , Zhang Kai , Li Huan , Sun Qinru , Wei Xin , Li Huiyu , Zhang Siruo , Fan Shuanliang , Wang Zhenyuan 
Published: February 2023

Abstract
Background
Microorganisms distribute and proliferate both inside and outside the body, which are the main mediators of decomposition after death. However, limited information is available on the postmortem microbiota changes of extraintestinal body sites in the early decomposition stage of mammalian corpses.

Results
This study investigated microbial composition variations among different organs and the relationship between microbial communities and time since death over 1 day of decomposition in male C57BL/6 J mice by 16S rRNA sequencing. During 1 day of decomposition, Agrobacterium, Prevotella, Bacillus, and Turicibacter were regarded as time-relevant genera in internal organs at different timepoints. Pathways associated with lipid, amino acid, carbohydrate and terpenoid and polyketide metabolism were significantly enriched at 8 h than that at 0.5 or 4 h. The microbiome compositions and postmortem metabolic pathways differed by time since death, and more importantly, these alterations were organ specific.

Conclusion
The dominant microbes differed by organ, while they tended toward similarity as decomposition progressed. The observed thanatomicrobiome variation by body site provides new knowledge into decomposition ecology and forensic microbiology. Additionally, the microbes detected at 0.5 h in internal organs may inform a new direction for organ transplantation.
A comparison of SARS-CoV-2 rapid antigen testing with realtime RT-PCR among symptomatic and asymptomatic individuals
Authors: Sabat Jyotsnamayee , Subhadra Subhra , Rath Sonalika , Ho Lal Mohan , Satpathy Tanushree , Pattnaik Dipankar , Pati Sanghamitra , Turuk Jyotirmayee 
Published: February 2023

Abstract
Background
Identification of SARS-CoV-2 positive patients with rapid and cost-effective test methods is the key for isolating infected individuals, interrupting the transmission chain, and thus, containment of the CoVID-19 disease. In this regard, Rapid Antigen Test (RAT) plays an important role at point of care testing but the low sensitivity attributing towards escape of positive cases is reported as a major disadvantage of RAT which led us to evaluate a RAT kit among symptomatic and asymptomatic individuals suspected of CoVID-19.

Methods
We analyzed 329 parallel nasopharyngeal swabs for RAT (Zydus Cadila, India) at the point of collection in a hospital-based facility and RealTime RT-PCR in the laboratory. The performance parameters were analyzed by evaluating the specificity, sensitivity, Negative Predictive Value (NPV), Positive Predictive Value (PPV), and Kappa coefficient.

Results
The sensitivity and specificity were found to be 75.17% and 98.89% respectively. Positive Predictive value was 98.25% and the negative predictive value was 82.79%. The accuracy between the two techniques was found to be 88.14% with a kappa coefficient of 0.756 (SE: 0.036 and CI at 95%: 0.686 to 0.826) with a good strength of agreement (0.61–0.80) between the two testing techniques. Among the false-negative cases, 22 (59.5%) were asymptomatic having the Cycle Threshold (Ct) range 27 to 32.9 including 12 cases with a history of close contact with the known positive cases (i.e. household contact). The remaining 15 cases (40.5%) were symptomatic having low to moderate Ct values.

Conclusion
It is observed from the results that the false negative result for symptomatic individuals is a matter of concern as it was noted in 4 cases of our study subjects who required hospitalisation later. Also the positives among asymptomatic contacts are important from epidemiological point of view for isolation and curtailing the infection from spreading in a community. These results support the fact that RAT showing sensitivity below 80% can be used for mass screening purposes with provision for additional testing in case of false negative with symptomatic individuals. Also false-negative results should be interpreted cautiously considering the epidemiological link as well as the clinical condition of the patients.
Disease severity in hospitalized COVID-19 patients: comparing routine surveillance with cohort data from the LEOSS study in 2020 in Germany
Authors: Koppe Uwe , Schilling Julia , Stecher Melanie , Rüthrich Maria Madeleine , Marquis Adine , Diercke Michaela , Haselberger Martina , Koll Carolin E. M. , Niebank Michaela , Ruehe Bettina , Borgmann Stefan , Grabenhenrich Linus , Hellwig Kerstin , Pilgram Lisa , Spinner Christoph D. , Paerisch Thomas ,   the LEOSS study group, Spinner Christoph D. , Rüthrich Maria Madeleine , Lanznaster Julia , Borgmann Stefan , Hellwig Kerstin , Vehreschild Maria , Hohmann Christian , Hanses Frank , Wille Kai , Jensen Bjoern-Erik , Hower Martin , Rieg Siegbert , vom Dahl Juergen , Rupp Jan , Roemmele Christoph , Isberner Nora , Rothfuss Katja , Eberwein Lukas , Jung Norma , Westhoff Timm , Dolff Sebastian , Strauss Richard , Voigt Ingo , von Bergwelt-Baildon Michael , Merle Uta , Degenhardt Christian , Beutel Gernot , Walter Lorenz , Göpel Siri , Gruener Beate , Rauschning Dominic , Trauth Janina , Milovanovic Milena , de With Katja , Markart Philipp , Rueddel Jessica , Friedrichs Anette , Kielstein Jan , Tometten Lukas , Heigener David , Wojtecki Lars , Schubert Joerg , Guggemos Wolfgang , Roeseler Stefani , Neufang Mark 
Published: February 2023

Abstract
Introduction
Studies investigating risk factors for severe COVID-19 often lack information on the representativeness of the study population. Here, we investigate factors associated with severe COVID-19 and compare the representativeness of the dataset to the general population.

Methods
We used data from the Lean European Open Survey on SARS-CoV-2 infected patients (LEOSS) of hospitalized COVID-19 patients diagnosed in 2020 in Germany to identify associated factors for severe COVID-19, defined as progressing to a critical disease stage or death. To assess the representativeness, we compared the LEOSS cohort to cases of hospitalized patients in the German statutory notification data of the same time period. Descriptive methods and Poisson regression models were used.

Results
Overall, 6672 hospitalized patients from LEOSS and 132,943 hospitalized cases from the German statutory notification data were included. In LEOSS, patients above 76 years were less likely represented (34.3% vs. 44.1%). Moreover, mortality was lower (14.3% vs. 21.5%) especially among age groups above 66 years. Factors associated with a severe COVID-19 disease course in LEOSS included increasing age, male sex (adjusted risk ratio (aRR) 1.69, 95% confidence interval (CI) 1.53–1.86), prior stem cell transplantation (aRR 2.27, 95% CI 1.53–3.38), and an elevated C-reactive protein at day of diagnosis (aRR 2.30, 95% CI 2.03–2.62).

Conclusion
We identified a broad range of factors associated with severe COVID-19 progression. However, the results may be less applicable for persons above 66 years since they experienced lower mortality in the LEOSS dataset compared to the statutory notification data.
Point of care obstetric ultrasound knowledge retention among mid-wives following a training program: a prospective cohort pilot study
Authors: Mubuuke Aloysius G. , Nassanga Rita 
Published: February 2023

Abstract
Background
Obstetric ultrasound has become a routine part of antenatal care in many parts of the world including low income settings. However, there is a shortage of radiologists and sonographers to perform routine obstetric scans in many areas especially in the rural settings of low income countries, despite having equipment available to do this. As a result, Point of care ultrasound (POCUS) has been suggested to bridge this gap by training other health workers such as midwives to perform basic obstetric ultrasound as part of their clinical care.

Methods
It was a prospective cohort pilot study in which trained midwives in point of care obstetric ultrasound were followed up at 6 months post training to assess their knowledge retention. Eleven trained midwives were purposively selected and followed up for knowledge retention. These were trained for 6 weeks and were given a knowledge assessment immediately after training, then given an assessment at 6 months following training. Data was analyzed using SPSS. Wilcoxon signed rank test was used to compare assessments and perceived knowledge as well as Spearman correlation to test the relationship between the number of scans performed and exam assessments, knowledge and exam assessments, and number of scans and knowledge.

Results
There were eleven midwives, all female with an average age of 42.3 years. The mean exam score (out of 50) was 44.2 at the end of the training and 42.9 at 6-months follow up. The midwives demonstrated higher perceived knowledge at the end of the training when compared to the 6-months follow up. However, this perceived higher knowledge was not statistically significant when correlated with the exam scores either at the end of the training or at the follow up of 6 months.

Conclusion
This pilot study has demonstrated that training midwives in point of care obstetric ultrasound can result into acceptable levels of knowledge retention that assist the midwives to apply this knowledge when making routine clinical decisions in relation to pregnant women.
Suprachoroidal triamcinolone acetonide for the treatment of macular edema associated with retinal vein occlusion: a pilot study
Authors: Ali Boushra M. , Azmeh Arwa M. , Alhalabi Nawras M. 
Published: February 2023

Abstract
Background
Suprachoroidal Drug Delivery has emerged in recent years as a novel promising approach, which may help address the clinical unmet needs in the management of Retinal Vein Occlusion (RVO) associated Macular Edema (ME). In this study, we aim to evaluate the feasibility in regard of the potential efficacy and safety of suprachoroidal injection of Triamcinolone Acetonide (TA) using a microinjector as a mono-treatment of ME due to RVO.

Methods
This trial included 16 eyes of 16 patients with RVO associated ME presenting to the department of ophthalmology, Al Mouwasat university hospital, Syria. 4 mg of preserved TA was injected suprachoroidally 4 mm away from the inferotemporal limbus using a patient-customized microinjector. After injection, patients were followed after 1 week then monthly for 3 months.
Primary outcome measures included the percentage of participants with best-corrected visual acuity (BCVA) gain≥15 letters and increased intraocular pressure (IOP) ≥ 20 mmHg in months 1,2, and 3, secondary measures included mean change from baseline BCVA, central subfield thickness (CST), and IOP through each of the follow-up points in addition to other measures.

Results
After injection, BCVA gain≥15 letters occurred in 68.7, 62.5, 50, 50% of patients at week 1 and through months 1,2 and 3 respectively, the mean BCVA improved significantly by 16.4, 16, 14.4, and 11.9 letters (p-value< 0.0005) at week 1 and months 1,2 and 3 respectively. This visual gain was associated with a significant reduction of CST by 290.94 ± 181.76 (week-1) (p-value< 0.0005), 274.31 ± 184.60 (month-1) (p-value< 0.0005), 183.50 ± 165.61 (month-2) (p-value = 0.006) and 137,75 ± 156.25 μm (month-3) (p-value = 0.038). We reported one case of increased IOP ≥ 20 mmHg in the first month that decreased in the second month. The mean change of IOP readings was not statistically significant, with an increase ranging from 0.75 mmHg after the first week (p-value = 0.09) and 0.5 mmHg after 3 months (p-value = 0.72).

Conclusion
This study suggests that suprachoroidal TA could be well tolerated and efficacious as a mono-treatment of RVO associated ME. Future clinical trials are required to confirm its longer-term safety and efficacy and to compare this efficacy with the other therapeutic options.

Trial registration
This study was retrospectively registered at clinicaltrials.gov (ID: NCT05038072) on 08/09/2021.
This article was published as a preprint on 22/06/2022. https://doi.org/10.21203/rs.3.rs-1701105/v1.
Development of an implantable collamer lens sizing model: a retrospective study using ANTERION swept-source optical coherence tomography and a literature review
Authors: Kim Taein , Kim Su Jeong , Lee Bo Young , Cho Hye Jin , Sa Beom Gi , Ryu Ik Hee , Kim Jin Kuk , Lee In Sik , Han Eoksoo , Kim Hyungsu , Yoo Tae Keun 
Published: February 2023

Abstract
Background
Optimal sizing for phakic intraocular lens (EVO-ICL with KS-AquaPort) implantation plays an important role in preventing postoperative complications. We aimed to formulate optimal lens sizing using ocular biometric parameters measured with a Heidelberg anterior segment optical coherence tomography (AS-OCT) device.

Methods
We retrospectively analyzed 892 eyes of 471 healthy subjects treated with an intraocular collamer lens (ICL) and assigned them to either the development (80%) or validation (20%) set. We built vault prediction models using the development set via classic linear regression methods as well as partial least squares and least absolute shrinkage and selection operator (LASSO) regression techniques. We evaluated prediction abilities based on the Bayesian information criterion (BIC) to select the best prediction model. The performance was measured using Pearson’s correlation coefficient and the mean squared error (MAE) between the achieved and predicted results.

Results
Measurements of aqueous depth (AQD), anterior chamber volume, anterior chamber angle (ACA) distance, spur-to-spur distance, crystalline lens thickness (LT), and white-to-white distance from ANTERION were highly associated with the ICL vault. The LASSO model using the AQD, ACA distance, and LT showed the best BIC results for postoperative ICL vault prediction. In the validation dataset, the LASSO model showed the strongest correlation (r = 0.582, P < 0.001) and the lowest MAE (104.7 μm).

Conclusion
This is the first study to develop a postoperative ICL vault prediction and lens-sizing model based on the ANTERION. As the measurements from ANTERION and other AS-OCT devices are not interchangeable, ANTERION may be used for optimal ICL sizing using our formula. Because our model was developed based on the East Asian population, further studies are needed to explore the role of this prediction model in different populations.