bluuebunny/crossref_metadata_2025_split huggingface dataset:
Shear-wave velocity determination by combining data from passive and active source field investigations in Kumamoto city, Japan
Authors: Manakou Maria , Roumelioti Zafeiria , Riga Evi 
Published: October 2023

AbstractWe present the 1D subsoil structure and local site effects at KUMA strong ground motion station in Kumamoto City, Japan. We analyze data from a field campaign conducted in the framework of the Blind Prediction BP1 test of the 6th IASPEI/IAEE International Symposium: Effects of Surface Geology on Seismic Motion. In parallel with other participants of the BP1 test, we process data from passive and active source measurements aiming to determine the shear-wave velocity, Vs, structure and the site response at KUMA station. Passive measurements are associated to five microtremor arrays. In each array, seven seismometers have been deployed in a common-center triangle shape, recording microtremors simultaneously for 1 to 2 h. The vertical component of microtremors was analyzed using the spatial autocorrelation (SPAC) method. Cross-correlation coefficients were computed for all station pairs available for each array. By fitting the average SPAC’s coefficients to the first-kind zero-order Bessel function, J0, and assuming that microtremors primarily comprise fundamental mode Rayleigh waves, phase velocity dispersion curves were determined. Phase velocity values for frequencies > 15 Hz were obtained from data of a close-by active source geophone profile. We integrated the data with those of the passive measurements and obtained an experimental phase velocity dispersion curve. The resulting curve shows low velocity variation, from 150 to 200 m/s, in the surface layers, whereas significant dispersion appears in frequencies below 2.5 Hz. By inverting this curve, we achieved to determine the 1D shear-wave velocity structure at KUMA station. Site response characteristics were determined by applying the Horizontal-to-Vertical-Spectral-Ratios method. Significantly amplified peaks in the frequency range between 0.3 to 1.5 Hz dominate HVSR spectral ratios. These peaks correspond to resonant frequencies of soils and originate from different impedance contrasts within the substratum of the site.
Graphical Abstract
A plagiarism paperdemic: determining plagiarism among COVID-19 articles in infectious disease journals between 2020 and 2021
Authors: Menshawey Rahma , Menshawey Esraa , Mitkees Ahmed , Mahamud Bilal A. 
Published: October 2023

Abstract
Background
The COVID-19 pandemic has caused drastic changes in the publishing framework which allowed for the quick review and rapid publication of manuscripts in order to quickly share vital information about this new viral pandemic to the general public and scientists. Alarms have been raised for the potential for misconduct in COVID-19 research. The purpose of this study is to determine the presence of plagiarism in COVID-19 papers across infectious disease journals.

Methods
COVID-19 related research and review articles published in infectious disease journals were collected. Each manuscript was optimized and uploaded to Turnitin, which is a similarity checking tool. Similarity reports were manually checked for events of true plagiarism using an 80% threshold, performed via human judgment.

Results
In this cross-sectional study, 41.61% (n = 129) of manuscripts were deemed plagiarized out of a total of 310 papers that were analyzed. Plagiarism was identified in 35.07% of reviews (n = 47), and 46.6% of original research (n = 82). Among the plagiarized papers, the median number of copied sentences was 3 IQR 4. The highest recorded similarity report was 60%, and the highest number of copied sentences was 85. The discussion section of these articles was the most problematic area, with the average number of copied sentences in that section being 6.25 ± 10.16. The average time to judge all manuscripts was 2.45 ± 3.09 min. Among all the plagiarized papers, 72.09% belonged to papers where the similarity report was ≤ 15% (n = 93). No significant differences were found with regards to plagiarism events among the quartiles.

Conclusions
Plagiarism is prevalent in COVID-19 publications. All similarity reports should be supplemented with human judgment.
Predicting acute kidney injury with an artificial intelligence-driven model in a pediatric cardiac intensive care unit
Authors: Fragasso Tiziana , Raggi Valeria , Passaro Davide , Tardella Luca , Lasinio Giovanna Jona , Ricci Zaccaria 
Published: October 2023

Abstract
Background
Acute kidney injury (AKI) is among the most common complications following cardiac surgery in adult and pediatric patients, significantly affecting morbidity and mortality. Artificial Intelligence (AI) with Machine Learning (ML) can be used to predict outcomes. AKI diagnosis anticipation may be an ideal target of these methods. The scope of the study is building a Machine Learning (ML) train model with Random Forest (RF) algorithm, based on electronic health record (EHR) data, able to forecast AKI continuously after 48 h in post-cardiac surgery children, and to test its performance.
Four hundred nineteen consecutive patients out of 1115 hospital admissions were enrolled in a single-center retrospective study. Patients were younger than 18 years and admitted from August 2018 to February 2020 in a pediatric cardiac intensive care unit (PCICU) undergoing cardiac surgery, invasive procedure (hemodynamic studies), and medical conditions with complete EHR records and discharged after 48 h or more.

Results
Thirty-six variables were selected to build the algorithm according to commonly described cardiac surgery-associated AKI clinical predictors. We evaluated different models for different outcomes: binary AKI (no AKI vs. AKI), severe AKI (no-mild vs severe AKI), and multiclass classification (maximum AKI and the most frequent level of AKI, mode AKI). The algorithm performance was assessed with the area under the curve receiver operating characteristics (AUC ROC) for binary classification, with accuracy and K for multiclass classification. AUC ROC for binary AKI was 0.93 (95% CI 0.92–0.94), and for severe AKI was 0.99 (95% CI 0.98–1). Mode AKI accuracy was 0.95, and K was 0.80 (95% CI 0.94–0.96); maximum AKI accuracy was 0.92, and K was 0.71 (95% CI 0.91–0.93). The importance matrix plot demonstrated creatinine, basal creatinine, platelets count, adrenaline support, and lactate dehydrogenase for binary AKI with the addition of cardiopulmonary bypass duration for severe AKI as the most relevant variables of the model.

Conclusions
We validated a ML model to detect AKI occurring after 48 h in a retrospective observational study that could help clinicians in individuating patients at risk of AKI, in which a preventive strategy can be determinant to improve the occurrence of renal dysfunction.
Mapping alterations in the local synchrony of the cerebral cortex in schizophrenia
Authors: Pujol Jesus , Pujol Nuria , Mané Anna , Martínez-Vilavella Gerard , Deus Joan , Pérez-Sola Víctor , Blanco-Hinojo Laura 
Published: October 2023

Abstract

Background
Observations from different fields of research coincide in indicating that a defective gamma-aminobutyric acid (GABA) interneuron system may be among the primary factors accounting for the varied clinical expression of schizophrenia. GABA interneuron deficiency is locally expressed in the form of neural activity desynchronization. We mapped the functional anatomy of local synchrony in the cerebral cortex in schizophrenia using functional connectivity MRI.

Methods
Data from 86 patients with schizophrenia and 137 control subjects were obtained from publicly available repositories. Resting-state functional connectivity maps based on Iso-Distant Average Correlation measures across three distances were estimated detailing the local functional structure of the cerebral cortex.

Results
Patients with schizophrenia showed weaker local functional connectivity (i.e., lower MRI signal synchrony) in (i) prefrontal lobe areas, (ii) somatosensory, auditory, visual, and motor cortices, (iii) paralimbic system at the anterior insula and anterior cingulate cortex, and (iv) hippocampus. The distribution of the defect in cortical area synchrony largely coincided with the synchronization effect of the GABA agonist alprazolam previously observed using identical functional connectivity measures. There was also a notable resemblance between the anatomy of our findings and cortical areas showing higher density of parvalbumin (prefrontal lobe and sensory cortices) and somatostatin (anterior insula and anterior cingulate cortex) GABA interneurons in humans.

Conclusions
Our results thus provide detail of the functional anatomy of synchrony changes in the cerebral cortex in schizophrenia and suggest which elements of the interneuron system are affected. Such information could ultimately be relevant in the search for specific treatments.
The Cross-sectional and Longitudinal Association Between Thyroid Function and Depression: A Population-Based Study
Authors: Roa Dueñas Oscar Hernando , Hofman Amy , Luik Annemarie I , Medici Marco , Peeters Robin P , Chaker Layal 
Published: October 2023

Abstract

Context
An association of thyroid function with mood disorders has been widely suggested, but very few studies have examined this association longitudinally.

Objective
We assessed the cross-sectional and longitudinal association between thyroid function and depression in a population-based cohort.

Methods
A total of 9471 individuals were included in cross-sectional analyses, of whom 8366 had longitudinal data. At baseline, we assessed thyroid function using serum samples (thyrotropin [TSH], free thyroxine (FT4), and thyroid peroxidase antibodies) and depressive symptoms using the Centre for Epidemiologic Studies Depression (CES-D) scale. Incident depressive events (n = 1366) were continuously followed up with the CES-D and clinical interviews. We analyzed the cross-sectional association of thyroid function and thyroid disease with depressive symptoms using linear and logistic regression, and the longitudinal association with Cox proportional hazard models for depressive events.

Results
Lower TSH levels and lower and higher FT4 levels were cross-sectionally associated with more depressive symptoms with a B value of −0.07 per 1 unit increase of natural log-transformed TSH (95% CI −0.11; −0.04). Furthermore, hypothyroidism was cross-sectionally associated with less depressive symptoms and hyperthyroidism with more depressive symptoms. Longitudinally, there was a U-shaped association between FT4 and incident depressive events but only in euthyroid participants.

Conclusion
We show a cross-sectional association between thyroid (dys)function with depressive symptoms, and a U-shaped association between FT4 and incident depressive events in euthyroid individuals. Our findings suggest an association of thyroid function with the risk of developing depression, albeit small. Reverse causation and additional underlying factors may also contribute to the association.
Chronic Immune-Mediated Demyelinating Neuropathies
Authors: Gable Karissa 
Published: October 2023

ABSTRACTOBJECTIVEThis article is an overview of chronic demyelinating neuropathies and highlights the phenotypic categorization, diagnosis, and treatment of chronic immune-mediated neuropathies. The clinical and diagnostic characteristics of other chronic demyelinating neuropathies that are common mimics of immune-mediated neuropathies are also discussed.LATEST DEVELOPMENTSThe underlying pathophysiology of chronic demyelinating neuropathies is heterogeneous, and components of both humoral and cellular immune responses are thought to play a role in the immune-mediated types of chronic demyelinating neuropathy. The role of the humoral response is highlighted with a specific focus on the relatively recent discovery of antibody-mediated antinodal and paranodal demyelinating neuropathies. Additionally, new diagnostic criteria for some of the chronic demyelinating neuropathies, as well as ways to differentiate chronic inflammatory demyelinating polyradiculoneuropathy from other chronic demyelinating polyneuropathies, are discussed.ESSENTIAL POINTSChronic demyelinating neuropathies can present with overlapping clinical characteristics with seemingly subtle variations. It is clinically important to differentiate these types of neuropathies because the treatment and management can vary and affect prognosis.
Pseudo dual-energy CT-derived iodine mapping using single-energy CT data based on a convolution neural network
Authors: Yuasa Yuki , Shiinoki Takehiro , Fujimoto Koya , Tanaka Hidekazu 
Published: October 2023

Objective: The objectives of this study are: (1) to develop a convolutional neural network model that yields pseudo high-energy CT (CTpseudo_high) from simple image processed low-energy CT (CTlow) images, and (2) to create a pseudo iodine map (IMpseudo) and pseudo virtual non-contrast (VNCpseudo) images for thoracic and abdominal regions. Methods: Eighty patients who underwent dual-energy CT (DECT) examinations were enrolled. The data obtained from 55, 5, and 20 patients were used for training, validation, and testing, respectively. The ResUnet model was used for image generation model and was trained using CTlow and high-energy CT (CThigh) images. The proposed model performance was evaluated by calculating the CT values, image noise, mean absolute errors (MAEs), and histogram intersections (HIs). Results: The mean difference in the CT values between CTpseudo_high and CThigh images were less than 6 Hounsfield unit (HU) for all evaluating patients. The image noise of CTpseudo_high was significantly lower than that of CThigh. The mean MAEs was less than 15 HU, and HIs were almost 1.000 for all the patients. The evaluation metrics of IM and VNC exhibited the same tendency as that of the comparison between CTpseudo_high and CThigh images. Conclusions: Our results indicated that the proposed model enables to obtain the DECT images and material-specific images from only single-energy CT images. Advances in knowledges: We constructed the CNN-based model which can generate pseudo DECT image and DECT-derived material-specific image using only simple image-processed CTlow images for the thoracic and abdominal regions.
Does the availability of prior mammograms improve radiologists’ observer performance?—a scoping review
Authors: Akwo Judith D. , Trieu Phuong , Lewis Sarah 
Published: October 2023

Objective:The objective of this review was to examine the impact of previous mammogram availability on radiologists’ performance from screening populations and experimental studies.Materials and Methods:A search of the literature was conducted using five databases: MEDLINE, PubMed, Web of Science, ScienceDirect, and CINAHL as well as Google and reference lists of articles. Keywords were combined with “AND” or “OR” or “WITH” and included “prior mammograms, diagnostic performance, initial images, diagnostic efficacy, subsequent images, previous imaging, and radiologist’s performance”. Studies that assessed the impact of previous mammogram availability on radiologists’ performance were reviewed. The Standard for Reporting Diagnostic Accuracy guidelines was used to critically appraise individual sources of evidence.Results:A total of 15 articles were reviewed. The sample of mammogram cases used across these studies varied from 36 to 1,208,051. Prior mammograms did not affect sensitivity [with priors: 62–86% (mean = 73.3%); without priors: 69.4–87.4% (mean = 75.8%)] and cancer detection rate, but increased specificity [with priors: 72–96% (mean = 87.5%); without priors: 63–87% (mean = 80.5%)] and reduced false-positive rates [with priors: 3.7 to 36% (mean = 19.9%); without priors 13.3–49% (mean = 31.4%)], recall rates [with priors: 3.8–57% (mean = 26.6%); without priors: [4.9%–67.5% (mean = 37.9%)], and abnormal interpretation rate decreased by 4% with priors. Evidence for the associations between the availability of prior mammograms and positive-predictive value, area under the curve (AUC) from the receiver operating characteristic curve (ROC) and localisation ROC AUC, and positive-predictive value of recall is limited and unclear.Conclusion:Availability of prior mammograms reduces recall rates, false-positive rates, abnormal interpretation rates, and increases specificity without affecting sensitivity and cancer detection rate.
Bactericidal activity of newly synthesized antimicrobial peptides against methicillin-resistant staphylococcus aureus and biofilm-forming methicillin-resistant staphylococcus aureus
Authors: Salama Ali 
Published: October 2023

Background: The emergence of multidrug-resistant bacteria (MDRB) poses a significant global challenge for healthcare professionals. Methicillin-resistant Staphylococcus aureus (MRSA), a prominent pathogen responsible for both hospital-acquired (nosocomial) and community-acquired infections, is particularly difficult to treat. Existing treatment options, such as vancomycin, linezolid, or clindamycin, have limitations. Therefore, there is a need for innovative approaches to combat infections caused by drug-resistant organisms. Methods: In this study, we synthesized a novel ultra-short antimicrobial peptide composed of three units of tryptophan and three units of lysine. We evaluated the effectiveness of this peptide against MRSA and MRSA that forms biofilms. Results: Encouraging results demonstrated that the peptide effectively killed both MRSA and biofilm-forming MRSA, while exhibiting low toxicity to human red blood cells. Additionally, our novel peptide showed excellent synergistic effects when combined with vancomycin against MRSA. Furthermore, when combined with levofloxacin and clarithromycin, our peptide exhibited synergistic effects against biofilm-forming MRSA. Conclusions: In conclusion, this study presents a novel ultra-short antimicrobial peptide (USAMP) that holds potential as a new generation of antibiotics to combat globally prevalent drug-resistant bacteria.
plastiC: A pipeline for recovery and characterization of plastid genomes from metagenomic datasets
Authors: Cameron Ellen S. , Blaxter Mark L. , Finn Robert D. 
Published: October 2023

The use of culture independent molecular methods, often referred to as metagenomics, have revolutionized the ability to explore and characterize microbial communities from diverse environmental sources. Most metagenomic workflows have been developed for identification of prokaryotic and eukaryotic community constituents, but tools for identification of plastid genomes are lacking. The endosymbiotic origin of plastids also poses challenges where plastid metagenomic assembled genomes (MAGs) may be misidentified as low-quality bacterial MAGs. Current tools are limited to classification of contigs as plastid and do not provide further assessment or characterization of plastid MAGs. plastiC is a workflow that allows users to identify plastid genomes in metagenome assemblies, assess completeness, and predict taxonomic association from diverse environmental sources. plastiC is a Snakemake workflow available at https://github.com/Finn-Lab/plastiC. We demonstrate the utility of this workflow with the successful recover of algal plastid MAGs from publicly available lichen metagenomes.
Complication rates associated with traction removal of percutaneous endoscopic gastrostomy tubes
Authors: Melling Georgina , Farley Joshua 
Published: October 2023

Background: percutaneous endoscopic gastrostomy (PEG) tubes are removed and/or replaced for reasons such as tube malfunction, degradation, patient's device preference, and when stopping enteral feeding. Aims: to identify the types and rate of complications associated with traction removal of a PEG tube and if this is associated with the size of the PEG or length of time it had been in situ prior to removal. Methods: This retrospective study looked at the tube removal/replacement reports written by the Enteral Feeding Nursing Service over an 8-year period at a large teaching hospital trust in the north of England. Findings: the PEG tube removal reports of 127 patients were reviewed. Five types of complication were identified, categorised as retained bumper (5.5%); intraperitoneal placement of new device (3.17%); misplacement of replacement device into colon (a consequence of the insertion procedure not the removal of the PEG) (0.78%): gastrocutaneous fistula (0.78%); and inability to remove the tube (1.57%). The complication of retained bumpers was associated with an average length of time in situ prior to removal of the PEG tube of 29 months. In the cases of intraperitoneal placement, the PEG tube had been in situ for an average of 6 months. Nurses were unable to remove the PEG tube on two occasions; each had been in situ for approximately 4 years prior to attempted removal. Conclusion: the complication rates are low following removal of a PEG tube using a traction pull. There was no clear correlation between length of time in situ or tube size and complication rate.
Climate variability and water-related infectious diseases in Pacific Island Countries and Territories, a systematic review
Authors: Hosking Rose , Smurthwaite Kayla , Hales Simon , Richardson Alice , Batikawai Suliasi , Lal Aparna 
Published: October 2023

BackgroundClimate induced changes in water-related infectious disease (WRID) transmission are a growing public health concern. The effects of climate on disease vary regionally, as do key socioeconomic modifiers. Regional syntheses are necessary to develop public health tools like risk maps and early warning systems at this scale. There is a high burden of WRID in the Pacific Island Countries and Territories (PICTs). There has been significant work on this topic in the PICTs, however, to date, there has been no regional systematic review of climate variability and WRID.MethodsWe searched the PubMed, Web of Science and Scopus scientific databases in September 2022 using a combination of disease, climate, and country terms. We included studies that evaluated the association between climate or weather variability and a WRID in the PICTs using a quantitative epidemiological design. We assessed risk of bias using validated tools. We analysed spatiotemporal publication patterns, synthesised the outcomes of studies in relation to the international literature and identified missing evidence.Results & discussionWe identified 45 studies of climate and malaria, dengue, diarrhoea, leptospirosis, and typhoid, which represent major WRIDs of concern in the Pacific Islands. More than half of the studies were set in Papua New Guinea or Fiji. The number of studies published each year increased exponentially over time from the 1980s to present. We found few comparable outcomes per disease and setting across epidemiological studies which limited the potential for meta-analysis. However, we identified consistent increased incidence of diarrhoea, dengue, leptospirosis, and typhoid following extreme weather events, highlighting the necessity for adequate water, sanitation, and hygiene access across the PICTs. Additionally, there were consistent positive associations between temperature and dengue incidence in New Caledonia, highly seasonal malaria in PNG, increased diarrhoea incidence with high and low rainfall, and positive associations between leptospirosis and rainfall. These findings are biologically plausible and consistent with the international literature. Future work on this topic in the PICTs can take advantage of increasingly available health and climate data to consolidate the field across a greater diversity of settings and apply these findings to strengthening climate resilient health systems.RegistrationThis review is registered with the international prospective register of systematic reviews (PROSPEROCRD42022353853), in accordance with PRISMA guidelines.