bluuebunny/crossref_metadata_2025 huggingface dataset:
The minor chicken class I gene BF1 is deleted between short imperfect direct repeats in the B14 and typical B15 major histocompatibility complex (MHC) haplotypes
Authors: Rocos Nicolas I. E. , Coulter Felicity J. , Tan Thomas C. J. , Kaufman Jim
Published: July 2023

The chicken major histocompatibility complex (MHC, also known as the BF-BL region of the B locus) is notably small and simple with few genes, most of which are involved in antigen processing and presentation. There are two classical class I genes, of which only BF2 is well and systemically expressed as the major ligand for cytotoxic T lymphocytes (CTLs). The other class I gene, BF1, is believed to be primarily a natural killer (NK) cell ligand. Among most standard chicken MHC haplotypes examined in detail, BF1 is expressed tenfold less than BF2 at the RNA level due to defects in the promoter or in a splice site. However, in the B14 and typical B15 haplotypes, BF1 RNA was not detected, and here, we show that a deletion between imperfect 32 nucleotide direct repeats has removed the BF1 gene entirely. The phenotypic effects of not having a BF1 gene (particularly on resistance to infectious pathogens) have not been systematically explored, but such deletions between short direct repeats are also found in some BF1 promoters and in the 5′ untranslated region (5′UTR) of some BG genes found in the BG region of the B locus. Despite the opposite transcriptional orientation of homologous genes in the chicken MHC, which might prevent the loss of key genes from a minimal essential MHC, it appears that small direct repeats can still lead to deletion.
Bioprospection of the bacterial β-myrcene-biotransforming trait in the rhizosphere
Authors: Soares-Castro Pedro , Soares Filipa , Reis Francisca , Lino-Neto Teresa , Santos Pedro M.
Published: July 2023

The biocatalysis of β-myrcene into value-added compounds, with enhanced organoleptic/therapeutic properties, may be performed by resorting to specialized enzymatic machinery of β-myrcene-biotransforming bacteria. Few β-myrcene-biotransforming bacteria have been studied, limiting the diversity of genetic modules/catabolic pathways available for biotechnological research. In our model Pseudomonas sp. strain M1, the β-myrcene catabolic core-code was identified in a 28-kb genomic island (GI). The lack of close homologs of this β-myrcene-associated genetic code prompted a bioprospection of cork oak and eucalyptus rhizospheres, from 4 geographic locations in Portugal, to evaluate the environmental diversity and dissemination of the β-myrcene-biotransforming genetic trait (Myr+).

Soil microbiomes were enriched in β-myrcene-supplemented cultures, from which β-myrcene-biotransforming bacteria were isolated, belonging to Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Sphingobacteriia classes. From a panel of representative Myr+ isolates that included 7 bacterial genera, the production of β-myrcene derivatives previously reported in strain M1 was detected in Pseudomonas spp., Cupriavidus sp., Sphingobacterium sp., and Variovorax sp. A comparative genomics analysis against the genome of strain M1 found the M1-GI code in 11 new Pseudomonas genomes. Full nucleotide conservation of the β-myrcene core-code was observed throughout a 76-kb locus in strain M1 and all 11 Pseudomonas spp., resembling the structure of an integrative and conjugative element (ICE), despite being isolated from different niches.

Furthermore, the characterization of isolates not harboring the Myr+-related 76-kb locus suggested that they may biotransform β-myrcene via alternative catabolic loci, being thereby a novel source of enzymes and biomolecule catalogue for biotechnological exploitation.

Key points

• The isolation of 150 Myr+bacteria hints the ubiquity of such trait in the rhizosphere.

• The Myr+trait is spread across different bacterial taxonomic classes.

• The core-code for the Myr+trait was detected in a novel ICE, only found in Pseudomonas spp.
A step forward to the optimized HlyA type 1 secretion system through directed evolution
Authors: Pourhassan Zohreh N. , Cui Haiyang , Muckhoff Neele , Davari Mehdi D. , Smits Sander H. J. , Schwaneberg Ulrich , Schmitt Lutz
Published: July 2023

Secretion of proteins into the extracellular space has great advantages for the production of recombinant proteins. Type 1 secretion systems (T1SS) are attractive candidates to be optimized for biotechnological applications, as they have a relatively simple architecture compared to other classes of secretion systems. A paradigm of T1SS is the hemolysin A type 1 secretion system (HlyA T1SS) from Escherichia coli harboring only three membrane proteins, which makes the plasmid-based expression of the system easy. Although for decades the HlyA T1SS has been successfully applied for secretion of a long list of heterologous proteins from different origins as well as peptides, but its utility at commercial scales is still limited mainly due to low secretion titers of the system. To address this drawback, we engineered the inner membrane complex of the system, consisting of HlyB and HlyD proteins, following KnowVolution strategy. The applied KnowVolution campaign in this study provided a novel HlyB variant containing four substitutions (T36L/F216W/S290C/V421I) with up to 2.5-fold improved secretion for two hydrolases, a lipase and a cutinase.

Key points

• An improvement in protein secretion via the use of T1SS

• Reaching almost 400 mg/L of soluble lipase into the supernatant

• A step forward to making E. coli cells more competitive for applying as a secretion host

Graphical Abstract
Multi-Instrumental Analysis Toward Exploring the Diabetic Foot Infection Microbiota
Authors: Złoch Michał , Maślak Ewelina , Kupczyk Wojciech , Pomastowski Paweł
Published: July 2023

The polymicrobial nature of diabetic foot infection (DFI) makes accurate identification of the DFI microbiota, including rapid detection of drug resistance, challenging. Therefore, the main objective of this study was to apply matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI TOF MS) technique accompanied by multiply culture conditions to determine the microbial patterns of DFIs, as well as to assess the occurrence of drug resistance among Gram-negative bacterial isolates considered a significant cause of the multidrug resistance spread. Furthermore, the results were compared with those obtained using molecular techniques (16S rDNA sequencing, multiplex PCR targeting drug resistance genes) and conventional antibiotic resistance detection methods (Etest strips). The applied MALDI-based method revealed that, by far, most of the infections were polymicrobial (97%) and involved many Gram-positive and -negative bacterial species—19 genera and 16 families in total, mostly Enterobacteriaceae (24.3%), Staphylococcaceae (20.7%), and Enterococcaceae (19.8%). MALDI drug-resistance assay was characterized by higher rate of extended-spectrum beta-lactamases (ESBLs) and carbapenemases producers compared to the reference methods (respectively 31% and 10% compared to 21% and 2%) and revealed that both the incidence of drug resistance and the species composition of DFI were dependent on the antibiotic therapy used. MALDI approach included antibiotic resistance assay and multiply culture conditions provides microbial identification at the level of DNA sequencing, allow isolation of both common (eg. Enterococcus faecalis) and rare (such as Myroides odoratimimus) bacterial species, and is effective in detecting antibiotic-resistance, especially those of particular interest—ESBLs and carbapenemases.
Changes in serial multiparametric MRI and FDG-PET/CT functional imaging during radiation therapy can predict treatment response in patients with head and neck cancer
Authors: Trada Yuvnik , Keall Paul , Jameson Michael , Moses Daniel , Lin Peter , Chlap Phillip , Holloway Lois , Min Myo , Forstner Dion , Fowler Allan , Lee Mark T.
Published: July 2023

Objectives

To test if tumour changes measured using combination of diffusion-weighted imaging (DWI) MRI and FDG-PET/CT performed serially during radiotherapy (RT) in mucosal head and neck carcinoma can predict treatment response.

Methods

Fifty-five patients from two prospective imaging biomarker studies were analysed. FDG-PET/CT was performed at baseline, during RT (week 3), and post RT (3 months). DWI was performed at baseline, during RT (weeks 2, 3, 5, 6), and post RT (1 and 3 months). The ADCmean from DWI and FDG-PET parameters SUVmax, SUVmean, metabolic tumour volume (MTV), and total lesion glycolysis (TLG) were measured. Absolute and relative change (%∆) in DWI and PET parameters were correlated to 1-year local recurrence. Patients were categorised into favourable, mixed, and unfavourable imaging response using optimal cut-off (OC) values of DWI and FDG-PET parameters and correlated to local control.

Results

The 1-year local, regional, and distant recurrence rates were 18.2% (10/55), 7.3% (4/55), and 12.7% (7/55), respectively. ∆Week 3 ADCmean (AUC 0.825, p = 0.003; OC ∆ > 24.4%) and ∆MTV (AUC 0.833, p = 0.001; OC ∆ > 50.4%) were the best predictors of local recurrence. Week 3 was the optimal time point for assessing DWI imaging response. Using a combination of ∆ADCmean and ∆MTV improved the strength of correlation to local recurrence (p ≤ 0.001). In patients who underwent both week 3 MRI and FDG-PET/CT, significant differences in local recurrence rates were seen between patients with favourable (0%), mixed (17%), and unfavourable (78%) combined imaging response.

Conclusions

Changes in mid-treatment DWI and FDG-PET/CT imaging can predict treatment response and could be utilised in the design of future adaptive clinical trials.

Clinical relevance statement

Our study shows the complementary information provided by two functional imaging modalities for mid-treatment response prediction in patients with head and neck cancer.

Key Points

•FDG-PET/CT and DWI MRI changes in tumour during radiotherapy in head and neck cancer can predict treatment response.

•Combination of FDG-PET/CT and DWI parameters improved correlation to clinical outcome.

•Week 3 was the optimal time point for DWI MRI imaging response assessment.
Sugar and low/no-calorie-sweetened beverage consumption and associations with body weight and waist circumference changes in five European cohort studies: the SWEET project
Authors: Buso Marion E. C. , Brouwer-Brolsma Elske M. , Naomi Novita D. , Ngo Joy , Soedamah-Muthu Sabita S. , Mavrogianni Christina , Harrold Joanne A. , Halford Jason C. G. , Raben Anne , Geleijnse Johanna M. , Manios Yannis , Serra-Majem Luis , Feskens Edith J. M.
Published: July 2023

Purpose

Results of prospective studies investigating associations between low/no-calorie sweeteners (LNCS) and body weight-related outcomes are inconclusive. We conducted dose–response and theoretical replacement individual patient data meta-analyses using harmonised prospective data to evaluate associations between sugar-sweetened beverage (SSB) consumption, low/no-calorie sweetened beverage (LNCB) consumption, and changes in body weight and waist circumference.

Methods

Individual participant data were obtained from five European studies, i.e., Lifelines Cohort Study, NQplus study, Alpha Omega Cohort, Predimed-Plus study, and Feel4diabetes study, including 82,719 adults aged 18–89 with follow-up between 1 and 9 years. Consumption of SSB and LNCB was assessed using food-frequency questionnaires. Multiple regression analyses adjusting for major confounders and including substitution models were conducted to quantify associations in individual cohorts; random-effects meta-analyses were performed to pool individual estimates.

Results

Overall, pooled results showed weak adverse associations between SSB consumption and changes in body weight (+ 0.02 kg/y, 95%CI 0.00; 0.04) and waist circumference (+ 0.03 cm/y, 95%CI 0.01; 0.05). LNCB consumption was associated with higher weight gain (+ 0.06 kg/y, 95%CI 0.04; 0.08) but not with waist circumference. No clear associations were observed for any theoretical replacements, i.e., LNCB or water for SSB or water for LNCB.

Conclusion

In conclusion, this analysis of five European studies found a weak positive association between SSB consumption and weight and waist change, whilst LNCB consumption was associated with weight change only. Theoretical substitutions did not show any clear association. Thus, the benefit of LNCBs as an alternative to SSBs remains unclear.
Bayesian coarsening: rapid tuning of polymer model parameters
Authors: Weeratunge Hansani , Robe Dominic , Menzel Adrian , Phillips Andrew W. , Kirley Michael , Smith-Miles Kate , Hajizadeh Elnaz
Published: July 2023

A protocol based on Bayesian optimization is demonstrated for determining model parameters in a coarse-grained polymer simulation. This process takes as input the microscopic distribution functions and temperature-dependent density for a targeted polymer system. The process then iteratively considers coarse-grained simulations to sample the space of model parameters, aiming to minimize the discrepancy between the new simulations and the target. Successive samples are chosen using Bayesian optimization. Such a protocol can be employed to systematically coarse-grained expensive high-resolution simulations to extend accessible length and time scales to make contact with rheological experiments. The Bayesian coarsening protocol is compared to a previous machine-learned parameterization technique which required a high volume of training data. The Bayesian coarsening process is found to precisely and efficiently discover appropriate model parameters, in spite of rough and noisy fitness landscapes, due to the natural balance of exploration and exploitation in Bayesian optimization.
Characteristics of disk halo size and its correlation with lenticule quality in small incision lenticule extraction for moderate to high myopia
Authors: Zhao Yu , Zhao Wuxiao , Wang Jifang , Zhang Zhe , Zhou Xingtao , Zhao Jing
Published: July 2023

Purpose

To investigate changes in disk halo size after small incision lenticule extraction (SMILE) and the correlation between halo size and lenticule quality in moderate to high myopia.

Methods

Thirty eyes of 30 consecutive patients (mean age, 24.9 ± 4.5 years; mean spherical equivalent, −6.85 ± 1.18 D) undergoing SMILE were included in this prospective study. Lenticule surface quality was accessed with a scanning electron microscopy by a scoring system. Halo size was measured preoperatively and at 1, 3, and 6 months postoperatively. Multiple linear regression analysis was performed to explore associations between halo size and a range of factors, including lenticule quality.

Results

Disk halo size increased slightly at 1 month and then recovered continually from 3 to 6 months postoperatively, with no difference between halo size during the preoperative period and at 6 months postoperatively (P > 0.05). One month after SMILE, halo size (1 cd/m2, 5 cd/m2) was associated only with uncorrected distance visual acuity (P ≤ 0.004). A halo size of 5 cd/m2 at 3 months postoperatively correlated with the anterior surface quality of the lenticule (P = 0.046). At 6 months postoperatively, a halo size of 1 cd/m2 was associated only with the baseline, accounting for 11.9% of the variability (P = 0.041); no correlations were found for the halo size of 5 cd/m2.

Conclusions

Disk halo size after SMILE was enlarged at an early stage postoperatively and subsequently declined to the baseline level during a 6-month follow-up. The quality of the lenticule surface influenced halo size changes in the early phase.
Differential expression of genes during recovery of Nicotiana tabacum from tomato leaf curl Gujarat virus infection
Authors: Namgial T. , Singh A. K. , Singh N. P. , Francis A. , Chattopadhyay D. , Voloudakis A. , Chakraborty S.
Published: July 2023

Main conclusion

Nicotiana tabacum exhibits recovery response towards tomato leaf curl Gujarat virus. Transcriptome analysis revealed the differential expression of defense-related genes. Genes encoding for cysteine protease inhibitor, hormonal- and stress-related to DNA repair mechanism are found to be involved in the recovery process.

Elucidating the role of host factors in response to viral infection is crucial in understanding the plant host–virus interaction. Begomovirus, a genus in the family Geminiviridae, is reported throughout the globe and is known to cause serious crop diseases. Tomato leaf curl Gujarat virus (ToLCGV) infection in Nicotiana tabacum resulted in initial symptom expression followed by a quick recovery in the systemic leaves. Transcriptome analysis using next-generation sequencing (NGS) revealed a large number of differentially expressed genes both in symptomatic as well as recovered leaves when compared to mock-inoculated plants. The virus infected N. tabacum results in alteration of various metabolic pathways, phytohormone signaling pathway, defense related protein, protease inhibitor, and DNA repair pathway. RT-qPCR results indicated that Germin-like protein subfamily T member 2 (NtGLPST), Cysteine protease inhibitor 1-like (NtCPI), Thaumatin-like protein (NtTLP), Kirola-like (NtKL), and Ethylene-responsive transcription factor ERF109-like (NtERTFL) were down-regulated in symptomatic leaves when compared to recovered leaves of ToLCGV-infected plants. In contrast, the Auxin-responsive protein SAUR71-like (NtARPSL) was found to be differentially down-regulated in recovered leaves when compared to symptomatic leaves and the mock-inoculated plants. Lastly, Histone 2X protein like (NtHH2L) gene was found to be down-regulated, whereas Uncharacterized (NtUNCD) was up-regulated in both symptomatic as well as recovered leaves compared to the mock-inoculated plants. Taken together, the present study suggests potential roles of the differentially expressed genes that might govern tobacco’s susceptibility and/or recovery response towards ToLCGV infection.
Preferences of German and Swiss melanoma patients for toxicities versus melanoma recurrence during adjuvant treatment (GERMELATOX-A-trial)
Authors: Kähler Katharina C. , Hüning S. , Nashan D. , Meiss F. , Rafei-Shamsabadi D. A. , Rissmann H. , Colapietro C. , Livingstone E. , Maul L. V. , Heppt M. , Hassel J. C. , Gutzmer R. , Loquai C. , Heinzerling L. , Sachse M. M. , Bohne A. S. , Moysig L. , Peters W. , Rusch J. , Blome C.
Published: July 2023

Purpose

Adjuvant treatment with immune checkpoint inhibitors like PD1-antibodies (ICI) ± CTLA4-antibodies (cICI) or targeted therapy with BRAF/MEK inhibitors (TT) in high-risk melanoma patients demonstrate a significant improvement in disease-free survival (DFS). Due to specific side effects, the choice of treatment is very often driven by the risk for toxicity.

This study addressed for the first time in a multicenter setting the attitudes and preferences of melanoma patients for adjuvant treatment with (c)ICI and TT.

Methods

In this study (“GERMELATOX-A”), 136 low-risk melanoma patients from 11 skin cancer centers were asked to rate side effect scenarios typical for each (c)ICI and TT with mild-to-moderate or severe toxicity and melanoma recurrence leading to cancer death. We asked patients about the reduction in melanoma relapse and the survival increase at 5 years they would require to tolerate defined side-effects.

Results

By VAS, patients on average valued melanoma relapse worse than all scenarios of side-effects during treatment with (c)ICI or TT. In case of severe side effects, patients required a 15% higher rate of DFS at 5 years for (c)ICI (80%) compared to TT (65%). For survival, patients required an increase of 5–10% for melanoma survival during (c)ICI (85%/80%) compared to TT (75%).

Conclusion

Our study demonstrated a pronounced variation of patient preferences for toxicity and outcomes and a clear preference for TT. As adjuvant melanoma treatment with (c)ICI and TT will be increasingly implemented in earlier stages, precise knowledge of the patient perspective can be helpful for decision making.
Is the presence of foraminal stenosis associated with outcome in lumbar spinal stenosis patients treated with posterior microsurgical decompression
Authors: Aaen Jørn , Banitalebi Hasan , Austevoll Ivar Magne , Hellum Christian , Storheim Kjersti , Myklebust Tor Åge , Anvar Masoud , Weber Clemens , Solberg Tore , Grundnes Oliver , Brisby Helena , Indrekvam Kari , Hermansen Erland
Published: July 2023

Background

We aim to investigate associations between preoperative radiological findings of lumbar foraminal stenosis with clinical outcomes after posterior microsurgical decompression in patients with predominantly central lumbar spinal stenosis (LSS).

Methods

The study was an additional analysis in the NORDSTEN Spinal Stenosis Trial. In total, 230 men and 207 women (mean age 66.8 (SD 8.3)) were included. All patients underwent an MRI including T1- and T2-weighted sequences. Grade of foraminal stenosis was dichotomized into none to moderate (0–1) and severe (2–3) category using Lee’s classification system. The Oswestry Disability Index (ODI), Zurich Claudication Questionnaire (ZCQ), and numeric rating scale (NRS) for back and leg pain were collected at baseline and at 2-year follow-up. Primary outcome was a reduction of 30% or more on the ODI score. Secondary outcomes included the mean improvement on the ODI, ZCQ, and NRS scores. We performed multivariable regression analyses with the radiological variates foraminal stenosis, Pfirrmann grade, Schizas score, dural sac cross-sectional area, and the possible plausible confounders: patients’ gender, age, smoking status, and BMI.

Results

The cohort of 437 patients presented a high degree of degenerative changes at baseline. Of 414 patients with adequate imaging of potential foraminal stenosis, 402 were labeled in the none to moderate category and 12 in the severe category. Of the patients with none to moderate foraminal stenosis, 71% achieved at least 30% improvement in ODI. Among the patients with severe foraminal stenosis, 36% achieved at least 30% improvement in ODI. A significant association between severe foraminal stenosis and less chance of reaching the target of 30% improvement in the ODI score after surgery was detected: OR 0.22 (95% CI 0.06, 0.83), p=0.03. When investigating outcome as continuous variables, a similar association between severe foraminal stenosis and less improved ODI with a mean difference of 9.28 points (95%CI 0.47, 18.09; p=0.04) was found. Significant association between severe foraminal stenosis and less improved NRS pain in the lumbar region was also detected with a mean difference of 1.89 (95% CI 0.30, 3.49; p=0.02). No significant association was suggested between severe foraminal stenosis and ZCQ or NRS leg pain.

Conclusion

In patients operated with posterior microsurgical decompression for LSS, a preoperative severe lumbar foraminal stenosis was associated with higher proportion of patients with less than 30% improvement in ODI.

Trial registration

The study is registered at ClinicalTrials.gov (22.11.2013) under the identifier NCT02007083.
Novel potentially pathogenic variants detected in genes causing intellectual disability and epilepsy in Polish families
Authors: Skoczylas S. , Jakiel P. , Płoszaj T. , Gadzalska K. , Borowiec M. , Pastorczak A. , Moczulska H. , Malarska M. , Eckersdorf-Mastalerz A. , Budzyńska E. , Zmysłowska A.
Published: July 2023

Background

Intellectual disability (ID) affects 1–3% of the world population. The number of genes whose dysfunctions cause intellectual disability is increasing. In addition, new gene associations are constantly being discovered, as well as specific phenotypic features for already identified genetic alterations are being described. The aim of our study was to search for pathogenic variants in genes responsible for moderate to severe intellectual disability and epilepsy, using a panel of targeted next-generation sequencing (tNGS) for diagnosis.

Methods

The group of 73 patients (ID, n=32; epilepsy, n=21; ID and epilepsy, n=18) was enrolled in the nucleus DNA (nuDNA) study using a tNGS panel (Agilent Technologies, USA). In addition, high coverage mitochondrial DNA (mtDNA) was extracted from the tNGS data for 54 patients.

Results

Fifty-two rare nuDNA variants, as well as 10 rare and 1 novel mtDNA variants, were found in patients in the study group. The 10 most damaging nuDNA variants were subjected to a detailed clinical analysis. Finally, 7 nuDNA and 1 mtDNA were found to be the cause of the disease.

Conclusions

This shows that still a very large proportion of patients remain undiagnosed and may require further testing. The reason for the negative results of our analysis may be a non-genetic cause of the observed phenotypes or failure to detect the causative variant in the genome. In addition, the study clearly shows that analysis of the mtDNA genome is clinically relevant, as approximately 1% of patients with ID may have pathogenic variant in mitochondrial DNA.
Twenty years of energy policy in Europe: achievement of targets and lessons for the future
Authors: Márquez-Sobrino Patricia , Díaz-Cuevas Pilar , Pérez-Pérez Belén , Gálvez-Ruiz David
Published: July 2023

The different energy transition efforts in the EU-27 countries are analysed, paying special attention to the achievement of set energy targets and the real influence on energy dependence and GHG reduction. Various methodologies were used, ranging from construction of timelines to geo-statistical analysis using Geographic Information Systems (GIS) and the implementation of machine learning techniques and models, using R. The results show how different modifications of the energy saving and efficiency targets, along with lower power consumption due to the COVID pandemic, resulted in that although most of the EU-27 countries have achieved their saving and efficiency targets, this has not been reflected in a real reduction in consumption (compared to 1990 levels). In addition, the fulfilment of the objectives has not resulted in a reduction in energy dependence, generating a false sense of security and satisfaction in the fulfilment of the targets. Concerning GHGs, almost all EU-27 countries decrease their GHG emissions per capita compared to 2000 (with the exception of Lithuania, Bulgaria, Croatia and Latvia), with this decrease being mainly related to the fulfilment of renewable energy targets in transport. The conclusion highlights the need to make greater efforts to achieve saving and efficiency in the near future; otherwise, higher power consumption via renewable energy sources, while helping meet future increases in energy demand, will not impact the reduction in energy dependence compared to current levels.

Graphical abstract

Achievement of energy transition targets. Contribution to the reduction in greenhouse gases and energy dependence.
Artificial Intelligence Application to Screen Abdominal Aortic Aneurysm Using Computed tomography Angiography
Authors: Spinella Giovanni , Fantazzini Alice , Finotello Alice , Vincenzi Elena , Boschetti Gian Antonio , Brutti Francesca , Magliocco Marco , Pane Bianca , Basso Curzio , Conti Michele
Published: July 2023

The aim of our study is to validate a totally automated deep learning (DL)-based segmentation pipeline to screen abdominal aortic aneurysms (AAA) in computed tomography angiography (CTA) scans. We retrospectively evaluated 73 thoraco-abdominal CTAs (48 AAA and 25 control CTA) by means of a DL-based segmentation pipeline built on a 2.5D convolutional neural network (CNN) architecture to segment lumen and thrombus of the aorta. The maximum aortic diameter of the abdominal tract was compared using a threshold value (30 mm). Blinded manual measurements from a radiologist were done in order to create a true comparison. The screening pipeline was tested on 48 patients with aneurysm and 25 without aneurysm. The average diameter manually measured was 51.1 ± 14.4 mm for patients with aneurysms and 21.7 ± 3.6 mm for patients without aneurysms. The pipeline correctly classified 47 AAA out of 48 and 24 control patients out of 25 with 97% accuracy, 98% sensitivity, and 96% specificity. The automated pipeline of aneurysm measurements in the abdominal tract reported a median error with regard to the maximum abdominal diameter measurement of 1.3 mm. Our approach allowed for the maximum diameter of 51.2 ± 14.3 mm in patients with aneurysm and 22.0 ± 4.0 mm in patients without an aneurysm. The DL-based screening for AAA is a feasible and accurate method, calling for further validation using a larger pool of diagnostic images towards its clinical use.
Automated Rib Fracture Detection on Chest X-Ray Using Contrastive Learning
Authors: Sun Hongbiao , Wang Xiang , Li Zheren , Liu Aie , Xu Shaochun , Jiang Qinling , Li Qingchu , Xue Zhong , Gong Jing , Chen Lei , Xiao Yi , Liu Shiyuan
Published: July 2023

To develop a deep learning-based model for detecting rib fractures on chest X-Ray and to evaluate its performance based on a multicenter study. Chest digital radiography (DR) images from 18,631 subjects were used for the training, testing, and validation of the deep learning fracture detection model. We first built a pretrained model, a simple framework for contrastive learning of visual representations (simCLR), using contrastive learning with the training set. Then, simCLR was used as the backbone for a fully convolutional one-stage (FCOS) objective detection network to identify rib fractures from chest X-ray images. The detection performance of the network for four different types of rib fractures was evaluated using the testing set. A total of 127 images from Data-CZ and 109 images from Data-CH with the annotations for four types of rib fractures were used for evaluation. The results showed that for Data-CZ, the sensitivities of the detection model with no pretraining, pretrained ImageNet, and pretrained DR were 0.465, 0.735, and 0.822, respectively, and the average number of false positives per scan was five in all cases. For the Data-CH test set, the sensitivities of three different pretraining methods were 0.403, 0.655, and 0.748. In the identification of four fracture types, the detection model achieved the highest performance for displaced fractures, with sensitivities of 0.873 and 0.774 for the Data-CZ and Data-CH test sets, respectively, with 5 false positives per scan, followed by nondisplaced fractures, buckle fractures, and old fractures. A pretrained model can significantly improve the performance of the deep learning-based rib fracture detection based on X-ray images, which can reduce missed diagnoses and improve the diagnostic efficacy.
Exploring the prevalence of undetected bradyarrhythmia in dementia with Lewy bodies
Authors: Heyman Isak , Persson Torbjörn , Haglund Mattias , Londos Elisabet
Published: July 2023

Purpose

To explore the prevalence of undetected bradyarrhythmia in a cohort of people with dementia with Lewy bodies.

Methods

Thirty participants diagnosed with dementia with Lewy bodies were enrolled from three memory clinics in southern Sweden between May 2021 and November 2022. None had a history of high-grade atrioventricular block or sick sinus syndrome. Each participant underwent orthostatic testing, cardiac [123I]metaiodobenzylguanidine scintigraphy and 24-h ambulatory electrocardiographic monitoring. Concluding bradyarrhythmia diagnosis was obtained until the end of December 2022.

Results

Thirteen participants (46.4%) had bradycardia at rest during orthostatic testing and four had an average heart rate < 60 beats per minute during ambulatory electrocardiographic monitoring. Three participants (10.7%) received a diagnosis of sick sinus syndrome, of whom two received pacemaker implants to manage associated symptoms. None received a diagnosis of second- or third-degree atrioventricular block.

Conclusion

This report showed a high prevalence of sick sinus syndrome in a clinical cohort of people with dementia with Lewy bodies. Further research on the causes and consequences of sick sinus syndrome in dementia with Lewy bodies is thus warranted.
Dynamic deformation monitoring and scenario simulation of the Xiaomojiu landslide in the Jinsha River Basin, China
Authors: Zhang Chenglong , Li Zhenhong , Ding Mingtao , Zhu Wu , Chen Bo , Zhuang Jianqi , Du Jiantao , Peng Jianbing
Published: July 2023

The Xiaomojiu landslide is a typical high-elevation, long-runout landslide located in the Jinsha River Corridor. In this study, sequential InSAR time-series estimation was used to calculate the line of sight (LOS) surface displacements with descending and ascending Sentinel-1 images, and it turned out that the cumulative LOS surface displacement of the landslide was up to −78.4 mm during the period from October 2017 to April 2021 with the maximum LOS surface displacement rate of −38.5 mm/year. The landslide body could be divided into five zones (A, B1, B2, B3, and C) according to its topographical characteristics together with the LOS surface displacement time series. Combining engineering geological characteristics, LOS cumulative surface displacements with site investigation suggest that the Xiaomojiu landslide is likely to be a precipitation-triggered ancient traction rock landslide at the accelerated deformation stage. A dynamic simulation of the Xiaomojiu landslide with the PFC3D software shows that it could take approximately 65 s for the Xiaomojiu landslide from start-up to acceleration to deceleration to build-up of a barrier lake, followed by a simulation from the barrier lake to outburst floods with the HEC-RAS software indicating that the maximum depth of the outburst floods could be 13.5 m (15%), 24.6 m (25%), 42.1 m (50%), and 50.3 m (75%) along Qinghai-Tibet Plateau Transportation Corridor (QTPTC). It is believed that the results of this study provide a reference for landslide prevention along the QTPTC and the Jinsha River.
Surgical Robotics for Intracerebral Hemorrhage Treatment: State of the Art and Future Directions
Authors: Wu Zhuojin , Chen Danyang , Pan Chao , Zhang Ge , Chen Shiling , Shi Jian , Meng Cai , Zhao Xingwei , Tao Bo , Chen Diansheng , Liu Wenjie , Ding Han , Tang Zhouping
Published: July 2023

Intracerebral hemorrhage (ICH) is a stroke subtype with high mortality and disability, and there are no proven medical treatments that can improve the functional outcome of ICH patients. Robot-assisted neurosurgery is a significant advancement in the development of minimally invasive surgery for ICH. This review encompasses the latest advances and future directions of surgical robots for ICH. First, three robotic systems for neurosurgery applied to ICH are illustrated. Second, the key technologies of robot-assisted surgery for ICH are introduced in aspects of stereotactic technique and navigation, the puncture instrument, and hematoma evacuation. Finally, the limitations of current surgical robots are summarized, and the possible development direction is discussed, which is named “multisensor fusion and intelligent aspiration control of minimally invasive surgical robot for ICH”. It is expected that the new generation of surgical robots for ICH will facilitate quantitative, precise, individualized, standardized treatment strategies for ICH.
Using stochastic frontier analysis instead of data envelopment analysis in modelling investment performance
Authors: Lamb John D. , Tee Kai-Hong
Published: July 2023

We introduce methods to apply stochastic frontier analysis (SFA) to financial assets as an alternative to data envelopment analysis, because SFA allows us to fit a frontier with noisy data. In contrast to conventional SFA, we wish to deal with estimation risk, heteroscedasticity in noise and inefficiency terms. We investigate measurement error in the risk and return measures using a simulation–extrapolation method and develop residual plots to test model fit. We find that shrinkage estimators for estimation risk makes a striking difference to model fit, dealing with measurement error only improves confidence in the model, and the residual plots are vital for establishing model fit. The methods are important because they allow us to fit a frontier under the assumption that the risks and returns are not known exactly.
Closing the Gap for Children with OCD: A Staged-Care Model of Cognitive Behavioural Therapy with Exposure and Response Prevention
Authors: Farrell Lara J. , Waters Allison M. , Storch Eric A. , Simcock Gabrielle , Perkes Iain E. , Grisham Jessica R. , Dyason Katelyn M. , Ollendick Thomas H.
Published: July 2023

Childhood obsessive–compulsive disorder (OCD) is among the most prevalent and disabling mental health conditions affecting children and adolescents. Although the distress and burden associated with childhood OCD are well documented and empirically supported treatments are available, there remains an unacceptable “treatment gap” and “quality gap” in the provision of services for youth suffering from OCD. The treatment gap represents the large number of children who never receive mental health services for OCD, while the quality gap refers to the children and young people who do access services, but do not receive evidence-based, cognitive behavioural therapy with exposure and response prevention (CBT-ERP). We propose a novel staged-care model of CBT-ERP that aims to improve the treatment access to high-quality CBT-ERP, as well as enhance the treatment outcomes for youth. In staged care, patients receive hierarchically arranged service packages that vary according to the intensity, duration, and mix of treatment options, with provision of care from prevention, early intervention, through to first and second-line treatments. Based on a comprehensive review of the literature on treatment outcomes and predictors of treatments response, we propose a preliminary staging algorithm to determine the level of clinical care, informed by three key determinants: severity of illness, comorbidity, and prior treatment history. The proposed clinical staging model for paediatric OCD prioritises high-quality care for children at all stages and levels of illness, utilising empirically supported CBT-ERP, across multiple modalities, combined with evidence-informed, clinical decision-making heuristics. While informed by evidence, the proposed staging model requires empirical validation before it is ready for prime time.
How did the Treatment Work for Robin? And for Dylan? Studying Individual Youth Treatment Mediators Using Single-Case Experimental Designs
Authors: Maric Marija , Kok Shawn I.
Published: July 2023

Study of individual treatment mechanisms in youth interventions facilitates evidence-based development, selection and implementation of treatment components that are most effective for each individual child. This position paper aims to bring together two important topics from the area of youth intervention research: mediators of treatment outcomes and single-case experimental design methodology. We start by outlining the benefits of studying within-person mechanisms and propose how statistical mediation analysis and single-case methods can be integrated to enable this type of research. Further, we review existing methodology for the study of individual youth treatment mechanisms and provide recommendations for the clinical practice research.
Cellulose acetate for a humidity-responsive self-actuator bilayer composite
Authors: Khoshtinat Shiva , Carvelli Valter , Marano Claudia
Published: July 2023

The use of stimuli-responsive polymers to produce environmentally responsive self-actuators continues to rise. Highly hygroscopic materials are attracting great interest for the design of humidity-responsive self-actuators. In this context, bilayer composites, formed by the coupling of a hygroscopic layer with a non-hygroscopic one, are relevant as they allow for the response to be tuned through the design of the composite layers. Therefore, the meticulous material characterization and the definition of descriptive models of their hygroscopic behavior are the primary steps towards the development of humidity-responsive self-actuators. This study is aimed at measuring and predicting the response of a bilayer composite made of a hygroscopic material layer and a layer of a non-hygroscopic material when subjected to changes in environmental humidity levels, to be used as a humidity-responsive self-actuator. A cellulose acetate was used as the hygroscopic material. Predictions for the induced hygroscopic deformation in the bilayer composite, based on two-physics finite element simulations, are compared to experimental measurements.
Rich scholar, poor scholar: inequalities in research capacity, “knowledge” abysses, and the value of unconventional approaches to research
Authors: Goyes David Rodriguez , Skilbrei May-Len
Published: July 2023

The dominance of modern rationality in knowledge production implies that the distribution of intellectual capital highly depends on the capacity to gather representative data and generate generalizable theses. Furthermore, as research becomes more formalized and dominated by large funding schemes, intellectual capital allocation is increasingly associated with high economic, labor force and institutional power. This phenomenon has consequences at the global level. As the United Nations Educational, Scientific and Cultural Organization (UNESCO) has documented, there are significant disparities between countries in research capacities, with a marked difference between “core” countries with semi-monopolies over sanctioned knowledge production and “peripheral” states primarily used as data mines. The core–periphery divide in research capacity brings about what decolonial theorists call knowledge abysses: the widespread idea that core countries are the ultimate knowledge producers and thus the legitimate guides in humanity’s road to “progress.” In that context, the democratization of knowledge and the prevention of neo-colonial dynamics require the development of cheaper and more accessible ways of collecting representative data. In this article, we make a call for innovations in methods that can serve to overcome this, and we illustrate possible avenues for achieving sound research without incurring high financial costs by describing and discussing our experiences in researching narco-violence in Colombia and prostitution in Russia with what we call the “taxi method.”
Specifying a principle of cryptographic justice as a response to the problem of going dark
Authors: Wilson Michael
Published: July 2023

Over the past decade, the Five Eyes Intelligence community has argued cryptosystems with end-to-end encryption (E2EE) are disrupting the acquisition and analysis of digital evidence. They have labelled this phenomenon the ‘problem of going dark’. Consequently, several jurisdictions have passed ‘responsible encryption’ laws that limit access to E2EE. Based upon a rhetorical analysis (Cunningham in Understanding rhetoric: a guide to critical reading and argumentation, BrownWalker Press, Boca Raton, 2018) of official statements about ‘going dark’, it is argued there is a need for a domain-specific principle of cryptographic justice to reorient the debate away from competing technocratic claims about the necessity, proportionality, and accountability of digital surveillance programs. This article therefore specifies a principle of cryptographic justice by adapting more general norms of information justice to decision-making about encryption law and policy. The resulting principle is that encryption laws and policies should be designed to empower the comparatively powerless to protect themselves from domination (i.e., morally arbitrary forms of surveillance). It is argued this principle can reorient decision-making about encryption law and policy towards consideration of how cryptography impacts systems-level power dynamics within information societies.
Thermal and Structural Response of Beam-end Shear Connections During a Large Compartment Fire Experiment
Authors: Dai Xu , Choe Lisa , Fischer Erica , Clifton G Charles
Published: July 2023

The role of steel connections is essential in structural fire design and analysis for steel-framed composite structures. The current structural design provisions provide strength reduction factors of load-carrying members and their end-connection elements at elevated temperatures, based on small-scale experiments under uniform heating conditions. The realistic thermal and structural evolution in member connections, especially as part of full-scale floor assemblies exposed to a large compartment fire, has not been well characterized. A large compartment fire experiment was recently conducted on a 9.1 m by 6.1 m composite floor assembly as part of a two-story steel-framed building. The test assembly had a total of ten shear-tab (fin-plate) connections subjected to combined fire and mechanical loading. This paper presents the measured thermal response of these connections to fire and comparison with the corresponding Eurocode 3 predictions with two methods (1) incorporating the beam bottom flange temperature at midspan and (2) the section factor method. The results show that the Eurocode 3 methods conservatively predict the maximum temperature during heating and the cooling rate but overestimate the high-temperature strength of connections when estimated using the section factor method, showing that the Eurocode 3 simplified approaches are not meant to provide the details of the failure mode for connections. This study suggests that estimating the strength of connections using strength reduction factors may not guarantee a safe structural fire design. In addition, this paper estimated the total axial force (from slab and beam) at the composite connection via using the strain gauge measurements close to the column bases which were not exposed to fire. It suggests realistic axial load and rotational demand on the shear connection due to restraints to thermal elongation or contraction of supported members should be considered in future design guidance as should designing and detailing the connections for ductility to withstand the inelastic deformation demands during the heating and the cooling phases.
Validation, Reliability, and Performance of Shear Strength Models for Unsaturated Soils
Authors: Pham Tuan A. , Sutman Melis , Medero Gabriela M.
Published: July 2023

Soil shear strength is the most fundamental property when designing structures in the ground and should be carefully assessed and understood. Several empirical models were introduced to predict the shear strength of unsaturated soils. However, there is uncertainty regarding the applicability and sensitivity of these prediction models. This paper presents a comprehensive verification study to assess the reliability and validity of the existing theoretical models. The results obtained from the prediction models are compared to measured data using thirty experimental data sets. A performance classification program is also conducted to assess the suitability of the analytical models for different soil types as well as over a wide range of matric suctions, saturation degrees, soil densities, soil plasticity, and clay activity. The impact of each single parameter is clarified by the microstructure studies, which also provides insight into the mechanics of unsaturated soils. The results indicated that the applicability of models is more appropriate for sandy soils rather than for clayey ones. The performance of shear strength models tends to decrease with an increase in matric suction, initial density, plasticity index, and clay activity. It is, therefore, recommended that the shear strength estimation models should be carefully selected depending on the soil type and properties. Besides, the analysed results pointed out that the choice to assume the factor $$\chi$$
χ
in the equation of Bishop equals the saturation degree is only suitable for medium-dense soils with low matric suction. This assumption is particularly not effective for clayey soils, or dense soils with high matric suction.