bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluating the global, regional, and national impact of syphilis: results from the global burden of disease study 2019
Authors: Chen Tao , Wan Bo , Wang Mingfang , Lin Su , Wu Yinlian , Huang Jiaofeng 
Published: July 2023

AbstractSyphilis is a global public health concern. This study aimed to assess the global and regional burden of syphilis from 1990 to 2019. Disease burden was evaluated using disability-adjusted life-years (DALYs) and prevalence. Data were extracted from the 2019 global burden of disease Study, an open database available for download. Age-standardized rates (ASR) and estimated annual percentage changes (EAPC) were calculated to evaluate the syphilis burden over time. In 2019, the total number of prevalent cases of syphilis was 49.71 million worldwide. The ASR of prevalence was stable from 1990 to 2019 with an EAPC of 0.00 (95% CI − 0.10–0.11). The number of DALYs caused by syphilis was 7.36 million in 2019, reflecting a reduction of 16.38% compared with that in 1990 (8.80 million). The ASR of DALYs exhibited a decreasing trend from 1990 to 2019 (EAPC =  − 1.01; 95% CI − 1.19 to − 0.84), with the highest rates observed in the younger age group (< 14 years old). In 2019, the highest ASR of DALYs was found in low sociodemographic index (SDI) regions (239.21/100,000), and the lowest in high SDI regions (3.14/100,000). Generally, the ASR of DALYs decreased as the SDI increased. The top three countries with the highest ASR of DALYs for syphilis were the Solomon Islands, Equatorial Guinea, and Liberia. While the global prevalence of syphilis remained persistently high from 1990 to 2019, there has been a recent decrease in the ASR of DALYs. Increased attention should be dedicated to younger populations and regions characterized by low SDIs.
E pluribus unum interpretable convolutional neural networks
Authors: Dimas George , Cholopoulou Eirini , Iakovidis Dimitris K. 
Published: July 2023

AbstractThe adoption of convolutional neural network (CNN) models in high-stake domains is hindered by their inability to meet society’s demand for transparency in decision-making. So far, a growing number of methodologies have emerged for developing CNN models that are interpretable by design. However, such models are not capable of providing interpretations in accordance with human perception, while maintaining competent performance. In this paper, we tackle these challenges with a novel, general framework for instantiating inherently interpretable CNN models, named E pluribus unum interpretable CNN (EPU-CNN). An EPU-CNN model consists of CNN sub-networks, each of which receives a different representation of an input image expressing a perceptual feature, such as color or texture. The output of an EPU-CNN model consists of the classification prediction and its interpretation, in terms of relative contributions of perceptual features in different regions of the input image. EPU-CNN models have been extensively evaluated on various publicly available datasets, as well as a contributed benchmark dataset. Medical datasets are used to demonstrate the applicability of EPU-CNN for risk-sensitive decisions in medicine. The experimental results indicate that EPU-CNN models can achieve a comparable or better classification performance than other CNN architectures while providing humanly perceivable interpretations.
Robust real-time imaging through flexible multimode fibers
Authors: Abdulaziz Abdullah , Mekhail Simon Peter , Altmann Yoann , Padgett Miles J. , McLaughlin Stephen 
Published: July 2023

AbstractConventional endoscopes comprise a bundle of optical fibers, associating one fiber for each pixel in the image. In principle, this can be reduced to a single multimode optical fiber (MMF), the width of a human hair, with one fiber spatial-mode per image pixel. However, images transmitted through a MMF emerge as unrecognizable speckle patterns due to dispersion and coupling between the spatial modes of the fiber. Furthermore, speckle patterns change as the fiber undergoes bending, making the use of MMFs in flexible imaging applications even more complicated. In this paper, we propose a real-time imaging system using flexible MMFs, but which is robust to bending. Our approach does not require access or feedback signal from the distal end of the fiber during imaging. We leverage a variational autoencoder to reconstruct and classify images from the speckles and show that these images can still be recovered when the bend configuration of the fiber is changed to one that was not part of the training set. We utilize a MMF 300 mm long with a 62.5 μm core for imaging $$10~\times ~10$$

10

×

10

cm objects placed approximately at 20 cm from the fiber and the system can deal with a change in fiber bend of 50$$^\circ$$

∘

and range of movement of 8 cm.
Drug resistance profiling of asymptomatic and low-density Plasmodium falciparum malaria infections on Ngodhe island, Kenya, using custom dual-indexing next-generation sequencing
Authors: Osborne Ashley , Phelan Jody E. , Kaneko Akira , Kagaya Wataru , Chan Chim , Ngara Mtakai , Kongere James , Kita Kiyoshi , Gitaka Jesse , Campino Susana , Clark Taane G. 
Published: July 2023

AbstractMalaria control initiatives require rapid and reliable methods for the detection and monitoring of molecular markers associated with antimalarial drug resistance in Plasmodium falciparum parasites. Ngodhe island, Kenya, presents a unique malaria profile, with lower P. falciparum incidence rates than the surrounding region, and a high proportion of sub-microscopic and low-density infections. Here, using custom dual-indexing and Illumina next generation sequencing, we generate resistance profiles on seventy asymptomatic and low-density P. falciparum infections from a mass drug administration program implemented on Ngodhe island between 2015 and 2016. Our assay encompasses established molecular markers on the Pfcrt, Pfmdr1, Pfdhps, Pfdhfr, and Pfk13 genes. Resistance markers for sulfadoxine-pyrimethamine were identified at high frequencies, including a quintuple mutant haplotype (Pfdhfr/Pfdhps: N51I, C59R, S108N/A437G, K540E) identified in 62.2% of isolates. The Pfdhps K540E biomarker, used to inform decision making for intermittent preventative treatment in pregnancy, was identified in 79.2% of isolates. Several variants on Pfmdr1, associated with reduced susceptibility to quinolones and lumefantrine, were also identified (Y184F 47.1%; D1246Y 16.0%; N86 98%). Overall, we have presented a low-cost and extendable approach that can provide timely genetic profiles to inform clinical and surveillance activities, especially in settings with abundant low-density infections, seeking malaria elimination.
Phytochemical profiling and cytotoxic potential of Arnebia nobilis root extracts against hepatocellular carcinoma using in-vitro and in-silico approaches
Authors: Kiran Asia , Altaf Awais , Sarwar Muhammad , Malik Arif , Maqbool Tahir , Ali Qurban 
Published: July 2023

AbstractHepatocellular carcinoma is the fifth most prevalent cancer worldwide. The emergence of drug resistance and other adverse effects in available anticancer options are challenging to explore natural sources. The current study was designed to decipher theArnebia nobilis(A. nobilis) extracts for detecting phytochemicals, in-vitro evaluation of antioxidative and cytotoxic potentials, and in-silico prediction of potent anticancer compounds. The phytochemical analysis revealed the presence of flavonoids, phenols, tannins, alkaloids, quinones, and cardiac glycosides, in the ethanol (ANE) and n-hexane (ANH) extracts ofA. nobilis.ANH extract exhibited a better antioxidant potential to scavenge DPPH, nitric oxide and superoxide anion radicals than ANE extract, which showed better potential only against H2O2radicals. In 24 h treatment, ANH extract revealed higher cytotoxicity (IC50value: 22.77 µg/mL) than ANH extract (IC50value: 46.74 µg/mL) on cancer (HepG2) cells without intoxicating the normal (BHK) cells using MTT assay. A better apoptotic potential was observed in ANH extract (49.10%) compared to ANE extract (41.35%) on HepG2 cells using the annexin V/PI method. GCMS analysis of ANH extract identified 35 phytocompounds, from which only 14 bioactive compounds were selected for molecular docking based on druggability criteria and toxicity filters. Among the five top scorers, deoxyshikonin exhibited the best binding affinities of − 7.2, − 9.2, − 7.2 and − 9.2 kcal/mol against TNF-α, TGF-βR1, Bcl-2 and iNOS, respectively, followed by ethyl cholate and 2-Methyl-6-(4-methylphenyl)hept-2-en-4-one along with their desirable ADMET properties. The phytochemicals of ANH extract could be used as a promising drug candidate for liver cancer after further validations.
Females occasionally create duets with males but they never sing solo-year-round singing behaviour in an Afrotropical songbird
Authors: Budka Michał , Uyeme John Emenike , Osiejuk Tomasz Stanisław 
Published: July 2023

AbstractOur knowledge of birdsong mainly comes from studies focused on male songs produced in a short breeding period, even though we know that sedentary species sing year-round, female song is quite widespread and many species sing collectively creating duets and choruses. In this study we focused on daily and seasonal changes in singing activity of an endemic, sedentary, duetting, Afrotropical songbird—the Bangwa forest warbler. We collected soundscape recordings in six recording locations and used singing activity index to examine how vocal activity of males and females varies daily and seasonally and how it correlates with the rainfall. We found that Bangwa forest warblers sing year-round, yet they do it more in wet than in dry season. The rapid increase of singing activity occurs after first rain, at the beginning of the rainy season. Males sing significantly more than females. Females never sing solo, however, in 13% of songs they create duets by joining male solos. The pattern of daily singing activity is sex-specific and seasonally variable, with two peaks (dawn and dusk) observed in males and only one in females (dawn). In Bangwa forest warbler male singing behaviour is similar to that of many songbirds, suggesting that territory defence and female attraction as main functions of singing. Females, which create duets and never sing solo may use songs in mate guarding, signalling commitment, resource defence or intersex territory defence. Duets observed year-round may suggest cooperative resource defence. Results of the study show that examining year-round singing behaviour is crucial to fully understand the evolution and functions of male and female songs.
Accuracy of a smart bottle in measuring fluid intake by American football players during pre-season training
Authors: Baker Lindsay B. , Alfred Shelby , Lee Khalil A. , Bonsignore Justina L. , Osterberg Kristin L. , Shepherd Brandon , De Chavez Peter John D. , Bentkovski Kobi 
Published: July 2023

AbstractRehydration is important for athlete performance and recovery. However, it can be challenging to follow appropriate fluid replacement practices due in part to difficulties in tracking fluid intake in real time. The purpose of this study was to determine the accuracy of a smart bottle in measuring fluid intake during exercise. Thirty male American football athletes drank from bottles equipped with a smart cap during outdoor pre-season practices (110 ± 30 min; 29.3 ± 3.0 °C; 75 ± 11% rh). The cap technology included optical sensors, microprocessors, batteries, and wireless connectivity that transmitted fluid volume data to a smartphone application in real-time. Reference measurements of fluid intake from the smart bottle were determined by gravimetry followed by conversion to volume using the density of the fluid consumed. There was no significant mean difference in fluid intake between the smart bottle and reference method (1220 ± 371 ml vs. 1236 ± 389 ml, p = 0.39 paired t test). Bland–Altman 95% limits of agreement between methods was − 212 to 180 ml. The smart bottle provided accurate measurements of fluid intake during exercise in real-world field conditions on a group level and within limits of agreement of − 212 to 180 ml (or approximately ± 15% of overall fluid intake) on an individual level.
Development and validation of a nomogram model for predicting chronic kidney disease after liver transplantation: a multi-center retrospective study
Authors: He Zenglei , Lin Yimou , Dong Siyi , Ke Qinghong , Zheng Shusen , Ling Qi 
Published: July 2023

AbstractChronic kidney disease (CKD) is a frequent complication after liver transplantation (LT) and associated with poor prognosis. In this study, we retrospectively analyzed 515 adult patients who underwent LT in our center. They were randomly divided into a training set (n = 360) and an internal test set (n = 155). Another 118 recipients in other centers served as external validation set. Univariate and multivariate COX regression analysis were used to determine risk factors. A nomogram model was developed to predict post-LT CKD. The incidence of post-LT CKD in our center was 16.9% (87/515) during a median follow-up time of 22.73 months. The overall survival of recipients with severe CKD (stage IV and V) were significantly lower than those with non or mild CKD (stage III) (p = 0.0015). A nomogram model was established based on recipient’s age, anhepatic phase, estimated glomerular filtration rate and triglyceride levels at 30 days after LT. The calibration curves for post-LT CKD prediction in the nomogram were consistent with the actual observation in both the internal and external validation set. In conclusion, severe post-LT CKD resulted in a significantly reduced survival in liver recipient. The newly established nomogram model had good predictive ability for post-LT CKD.
Multi-decadal variation of ENSO forecast skill since the late 1800s
Authors: Lou Jiale , Newman Matthew , Hoell Andrew 
Published: July 2023

AbstractDiagnosing El Niño-Southern Oscillation (ENSO) predictability within operational forecast models is hindered by computational expense and the need for initialization with three-dimensional fields generated by global data assimilation. We instead examine multi-year ENSO predictability since the late 1800s using the model-analog technique, which has neither limitation. We first draw global coupled model states from pre-industrial control simulations, from the Coupled Model Intercomparison Project Phase 6, that are chosen to initially match observed monthly sea surface temperature and height anomalies in the Tropics. Their subsequent 36-month model evolution are the hindcasts, whose 20th century ENSO skill is comparable to twice-yearly hindcasts generated by a state-of-the-art European operational forecasting system. Despite the so-called spring predictability barrier, present throughout the record, there is substantial second-year ENSO skill, especially after 1960. Overall, ENSO exhibited notably high values of both amplitude and skill towards the end of the 19th century, and again in recent decades.
Constrained tropical land temperature-precipitation sensitivity reveals decreasing evapotranspiration and faster vegetation greening in CMIP6 projections
Authors: Zhu Boyuan , Cheng Yongzhou , Hu Xuyue , Chai Yuanfang , Berghuijs Wouter R. , Borthwick Alistair G. L. , Slater Louise 
Published: July 2023

AbstractOver the tropical land surface, accurate estimates of future changes in temperature, precipitation and evapotranspiration are crucial for ecological sustainability, but remain highly uncertain. Here we develop a series of emergent constraints (ECs) by using historical and future outputs from the Coupled Model Inter-comparison Project Phase 6 (CMIP6) Earth System Models under the four basic Shared Socio-economic Pathway scenarios (SSP126, SSP245, SSP370, and SSP585). Results show that the temperature sensitivity to precipitation during 2015–2100, which varies substantially in the original CMIP6 outputs, becomes systematically negative across SSPs after application of the EC, with absolute values between −1.10 °C mm−1 day and −3.52 °C mm−1 day, and with uncertainties reduced by 9.4% to 41.4%. The trend in tropical land-surface evapotranspiration, which was increasing by 0.292 mm yr−1 in the original CMIP6 model outputs, becomes significantly negative (−0.469 mm yr−1) after applying the constraint. Moreover, we find a significant increase of 58.7% in the leaf area index growth rate.
Mendelian randomization uncovers a protective effect of interleukin-1 receptor antagonist on kidney function
Authors: Cho Jeong Min , Koh Jung Hun , Kim Seong Geun , Lee Soojin , Kim Yaerim , Cho Semin , Kim Kwangsoo , Kim Yong Chul , Han Seung Seok , Lee Hajeong , Lee Jung Pyo , Joo Kwon Wook , Lim Chun Soo , Kim Yon Su , Kim Dong Ki , Park Sehoon 
Published: July 2023

AbstractInterleukins (ILs), key cytokine family of inflammatory response, are closely associated with kidney function. However, the causal effect of various ILs on kidney function needs further investigation. Here we show two-sample summary-level Mendelian randomization (MR) analysis that examined the causality between serum IL levels and kidney function. Genetic variants with strong association with serum IL levels were obtained from a previous genome-wide association study meta-analysis. Summary-level data for estimated glomerular filtration rate (eGFR) were obtained from CKDGen database. As a main MR analysis, multiplicative random-effects inverse-variance weighted method was performed. Pleiotropy-robust MR analysis, including MR-Egger with bootstrapped error and weighted median methods, were also implemented. We tested the causal estimates from nine ILs on eGFR traits. Among the results, higher genetically predicted serum IL-1 receptor antagonist level was significantly associated with higher eGFR values in the meta-analysis of CKDGen and the UK Biobank data. In addition, the result was consistent towards eGFR decline phenotype of the outcome database. Otherwise, nonsignificant association was identified between other genetically predicted ILs and eGFR outcome. These findings support the clinical importance of IL-1 receptor antagonist-associated pathway in relation to kidney function in the general individuals, particularly highlighting the importance of IL-1 receptor antagonist.
Crosstalk between KIF1C and PRKAR1A in left atrial myxoma
Authors: Zhou Mengchen , Yao Yan , Wang Xiangyi , Zha Lingfeng , Chen Yilin , Li Yanze , Wang Mengru , Yu Chenguang , Zhou Yingchao , Li Qianqian , Cao Zhubing , Wu Jianfei , Shi Shumei , Jiang Dan , Long Deyong , Wang Jiangang , Wang Qing , Cheng Xiang , Liao Yuhua , Tu Xin 
Published: July 2023

AbstractCardiac myxoma (CM) is the most common benign cardiac tumor, and most CMs are left atrial myxomas (LAMs). Six variations of KIF1C, c.899 A > T, c.772 T > G, c.352 A > T, c.2895 C > T, c.3049 G > A, and c.*442_*443dup in left atrial myxoma tissues are identified by whole-exome sequencing (WES) and Sanger sequencing. RNA-seq and function experiments show the reduction of the expression of KIF1C and PRKAR1A caused by rare variations of KIF1C. KIF1C is observed to be located in the nucleus, bind to the promoter region of PRKAR1A, and regulate its transcription. Reduction of KIF1C decreases PRKAR1A expression and activates the PKA, which causes an increase in ERK1/2 phosphorylation and SRC-mediated STAT3 activation, a reduction of CDH1, TP53, CDKN1A, and BAX, and eventually promotes tumor formation both in vitro and in vivo. The results suggest that inhibition of KIF1C promotes the pathogenesis of LAM through positive feedback formed by the crosstalk between KIF1C and PRKAR1A.
Atlasing white matter and grey matter joint contributions to resting-state networks in the human brain
Authors: Nozais Victor , Forkel Stephanie J. , Petit Laurent , Talozzi Lia , Corbetta Maurizio , Thiebaut de Schotten Michel , Joliot Marc 
Published: July 2023

AbstractOver the past two decades, the study of resting-state functional magnetic resonance imaging has revealed that functional connectivity within and between networks is linked to cognitive states and pathologies. However, the white matter connections supporting this connectivity remain only partially described. We developed a method to jointly map the white and grey matter contributing to each resting-state network (RSN). Using the Human Connectome Project, we generated an atlas of 30 RSNs. The method also highlighted the overlap between networks, which revealed that most of the brain’s white matter (89%) is shared between multiple RSNs, with 16% shared by at least 7 RSNs. These overlaps, especially the existence of regions shared by numerous networks, suggest that white matter lesions in these areas might strongly impact the communication within networks. We provide an atlas and an open-source software to explore the joint contribution of white and grey matter to RSNs and facilitate the study of the impact of white matter damage to these networks. In a first application of the software with clinical data, we were able to link stroke patients and impacted RSNs, showing that their symptoms aligned well with the estimated functions of the networks.
The combined action of the intracellular regions regulates FGFR2 kinase activity
Authors: Lin Chi-Chuan , Wieteska Lukasz , Poncet-Montange Guillaume , Suen Kin Man , Arold Stefan T. , Ahmed Zamal , Ladbury John E. 
Published: July 2023

AbstractReceptor tyrosine kinases (RTKs) are typically activated through a precise sequence of intracellular phosphorylation events starting with a tyrosine residue on the activation loop (A-loop) of the kinase domain (KD). From this point the mono-phosphorylated enzyme is active, but subject to stringent regulatory mechanisms which can vary dramatically across the different RTKs. In the absence of extracellular stimulation, fibroblast growth factor receptor 2 (FGFR2) exists in the mono-phosphorylated state in which catalytic activity is regulated to allow rapid response upon ligand binding, whilst restricting ligand-independent activation. Failure of this regulation is responsible for pathologic outcomes including cancer. Here we reveal the molecular mechanistic detail of KD control based on combinatorial interactions of the juxtamembrane (JM) and the C-terminal tail (CT) regions of the receptor. JM stabilizes the asymmetric dimeric KD required for substrate phosphorylation, whilst CT binding opposes dimerization, and down-regulates activity. Direct binding between JM and CT delays the recruitment of downstream effector proteins adding a further control step as the receptor proceeds to full activation. Our findings underscore the diversity in mechanisms of RTK oligomerisation and activation.