bluuebunny/crossref_metadata_2025_split huggingface dataset:
Real world safety and exploratory efficacy of gene therapy for patients with 5q-Spinal Muscular Atrophy in a Brazilian cohort
Authors: Mendonca Rodrigo , Ortega Adriana , Matsui Ciro , Linden Vanessa Van Der , Kerstenetzky Marcelo , Grossklauss Luis Fernando , Lucas Elizabeth , Polido Graziela , Zanoteli Edmar 
Published: February 2023

Abstract

Spinal muscular atrophy (SMA) is a motor neuron disease associated with progressive muscle weakness, ventilatory failure, and reduced survival. Onasemnogene abeparvoves is the first gene replacement therapy (GT) approved to treat this condition. An observational retrospective study was conducted to assess adverse events and efficacy of GT in SMA patients. Forty-one patients with SMA (24 females, 58.5% and 33 SMA type 1, 80.1%) were included. The mean age at GT dosing was 18 (± 6.4) months. Thirty-six patients (87.8%) were under previous treatment with nusinersen, and 10 (24.4%) continued nusinersen after GT. Mean CHOP-INTEND increased 13 points after 6 months and this finding did not differ between groups according to nusinersen maintenance after GT (p = 0.949). Among SMA type 1 patients, 14 (46.6%) reached the ability to sit alone. Liver transaminases elevation at least two times higher than the upper limit of normal value occurred in 29 (70.7%) patients. Thrombocytopenia occurred in 13 (31.7%) patients, and one presented thrombotic microangiopathy. Older age (> 2 years) was associated with more prolonged use of corticosteroids (p = 0.021). GT is effective in SMA patients, combined nusinersen after GT does not present additional gain in motor function, and older age is associated with prolonged corticosteroid use.
Explainable prediction of catalysing enzymes from reactions using multilayer perceptrons
Authors: Probst Daniel 
Published: February 2023

Abstract
Assigning or proposing a catalysing enzyme given a chemical or biochemical reaction is of great interest to life sciences and chemistry alike. The exploration and design of metabolic pathways or the challenge of finding more sustainable enzyme-catalysed alternatives to traditional organic reactions are just two examples of tasks that require an association between reaction and enzyme. However, given the lack of large and balanced annotated data sets of enzyme-catalysed reactions, assigning an enzyme to a reaction still relies on expert-curated rules and databases. Here, we present a data-driven explainable human-in-the-loop machine learning approach to support and ultimately automate the association of a catalysing enzyme with a given biochemical reaction. In addition, the proposed method is capable of predicting enzymes as candidate catalysts for arbitrary organic reactions. Finally, the introduced explainability and visualisation methods can easily be generalised to support other machine-learning approaches involving chemical and biochemical reactions.
Iterative Decorrelation Analysis, Unit of Measure Preserving Transformations and Latent Biomarker Discovery
Authors: Tamez-Peña José Gerardo 
Published: February 2023

Abstract

Background Numerous biomarker discovery studies and exploratory clinical studies extract a large set of measurable variables, which often have varying degrees of correlation among them. This data collinearity can impact statistical model interpretation and hinder the discovery of potential associations between measured variables and the observed outcome. Exploratory Factor Analysis (EFA), Principal Component Analysis (PCA), and Machine-Learning (ML) can be used to discover latent variables associated with disease progression or outcome by computing transformation matrices, but the interpretation of unsupervised/supervised latent variables in high-dimensional datasets can be challenging. Results This study describe and reports the performance of the iterative decorrelation analysis algorithm (IDeA). The algorithm iteratively analyzes the correlation matrix of the data, updating the transformation coefficients until it reaches the desired correlation goal. The output of IDeA is a basis-transformation matrix that preserves the data dimensionality and unit of measure of the original observed variables. The main advantages of the IDeA basis transformations are sparsity and interpretability. The transformation does not alter uncorrelated features, thus statistical modeling and biomarker discovery in the new transformed basis can be a combination of novel latent variables and a sizable subset of unaltered variables. The algorithm was tested on five multidimensional/hyperdimensional and multimodal sets, demonstrating the effect of decorrelation parameters, interpretability, and latent biomarker discovery. Conclusions The iterative decorrelation approach provides a simple to use tool for researchers to explore the association between correlated features in hyperdimensional/multimodal settings and to decorrelate significant associations via latent variables that preserve the unit of measurement. An efficient computer implementation of IDeA is available in the FRESA.CAD R package (https://cran.r-project.org/web/packages/FRESA.CAD/index.html).
Measuring cumulus expansion of mammalian oocytes: comparing the reliability of methods and how artificial intelligence could automate the measurement
Authors: Raes Annelies , Azari-Dolatabad Nima , Athanasiou Georgios , Sadeghi Hafez , Andueza Sebastian Gonzalez , Arcos Josep Lluis , Cerquides Jesus , Pavani Krishna Chaitanya , Opsomer Geert , Pascottini Osvaldo Bogado , Smits Katrien , Velez Daniel Angel , Soom Ann Van 
Published: February 2023

Abstract
Cumulus expansion is an important indicator of oocyte maturation, often correlated with greater oocyte developmental capacity. Although multiple methods have been described to assess cumulus expansion, none of them is considered a gold standard. Additionally, these methods are subjective and time-consuming. Here, the reliability of three cumulus expansion measurement methods was evaluated and a deep learning model was created to automatically perform the measurement. Cumulus-oocyte complexes were compared before and after in vitro maturation by three independent observers using three methods: (1) measurement of the cumulus area, (2) measurement of three distances between the zona pellucida and outer cumulus, and (3) scoring cumulus expansion on a 5-point Likert scale. Inter- and intra-observer agreements were calculated using intraclass-correlation coefficients (ICC). The area method resulted in the best overall agreement with an ICC of 0.89 versus 0.54 and 0.30 for the 3-distance and scoring method, respectively. Therefore, the area method served as the base to create the deep learning model, which outperformed two observers while equivalent to the third. Measuring the area is the most reliable method to manually evaluate cumulus expansion, whilst deep learning automatically performs the calculation with human-level accuracy and could therefore be a valuable prospective tool for embryologists.
Direct operando observation and control of charge states in organic light-emitting diodes with a thermally activated delayed fluorescence material
Authors: Yumoto Shintaro , Katsumata Junya , Osawa Fumiya , Wada Yoshimasa , Suzuki Katsuaki , Kaji Hironori , Marumoto Kazuhiro 
Published: February 2023

Abstract
Organic light-emitting diodes (OLEDs) with thermally activated delayed fluorescence (TADF) materials have advantages such as high efficiency with low cost compared to OLEDs with conventional fluorescence and phosphorescence materials. To attain further high device performance, clarifying internal charge states in OLEDs at a microscopic viewpoint is crucial; however, only a few such studies have been performed. Here, we report a microscopic investigation into internal charge states in OLEDs with a TADF material by electron spin resonance (ESR) at a molecular level. We observed operando ESR signals of the OLEDs and identified their origins due to a hole-transport material PEDOT:PSS, gap states at an electron-injection layer, and a host material CBP in the light-emitting layer by performing density functional theory calculation and studying thin films used in the OLED. The ESR intensity varied with increasing applied bias before and after the light emission. We find leakage electrons in the OLED at a molecular level, which is suppressed by a further electron-blocking layer MoO3 between the PEDOT:PSS and light-emitting layer, resulting in the enhancement of luminance with a low-voltage drive. Such microscopic information and applying our method to other OLEDs will further improve the OLED performance from the microscopic viewpoint.
Identification and Classification of Pneumonia using CNN Model with Chest X- ray Image
Authors: Kumar Suraj , Prakash Shiva 
Published: February 2023

Abstract
Pneumonia is a bacterial, fungal, or viral infection that affects one or both lungs. It is a serious disease in which the air sacs in both lungs become clogged with pus and other substances. So, several frameworks and models have been built to properly assess such diseases, but there is still space for improvement. In this study, we used CXR images to train a CNN model to detect and classify Pneumonia disease in the lungs and also present how training accuracy and validation accuracy as well as training loss and validation loss vary when changing the size of the input image. The Kaggle CXR dataset is used, which was already created and pre-processed. The Convolutional Neural Network method is used in the research in close collaboration with some other data augmentation frameworks to enhance classification accuracy, which also will help to enhance training and validation accuracies, as well as characterize the precision of the Convolutional Neural Network model and achieve various results. The training and validation accuracy of our model are 0.9757 and 0.9568, respectively, and the training and validation loss are 0.0857 and 0.1399.
Living beyond loss: A qualitative investigation of caregivers' experiences after the death of their relatives with Amyotrophic Lateral Sclerosis
Authors: Volpato Eleonora , Banfi Paolo , Poletti Valentina , Pagnini Francesco 
Published: February 2023

Abstract

Background
The psychological experiences of a caregiver of an Amyotrophic Lateral Sclerosis (ALS) patient after the death of their loved one can vary greatly depending on the individual. Common experiences include grief, sadness, loneliness, guilt, and a sense of purposelessness.
Objectives
To investigate the prevalent emotional experiences encountered by caregivers and/or individuals who have provided care for ALS patients following their passing.
Methods
The present study used the Interpretative Phenomenological Approach (IPA) to qualitatively explore the accounts of 41 (Mean Age = 59.78; Men: 39.02%) bereaved caregivers of people affected by ALS.
Results
The results highlighted 5 superordinate themes (“Caregiver’s perception of his/her life”, “Caregiver’s feelings”, “Caregiver’s life after patient’s death”, “Caregiver’s disease description”, “Caregiver’s help resources”), 12 themes and 30 subthemes. In particular, it emerged that the transition from life before ALS (described as “a peaceful landscape” to caregiver life (mostly compared to colour “black” was lived as a “shock”, during which caregivers also had to change their needs (“Caregiver’s needs transformation”. On the other side, as literature confirmed, caregiver’s life after the patient’s death was both characterized by a sense of “re-birth” and “emptiness”, which could be filled by “psychological assistance” and different type of "social support".
Conclusions
Providing psychological support to caregivers of ALS patients after the death of their loved one is important for addressing their emotional needs, reducing isolation, and helping them navigate practical challenges and plans.
Retorting methods of silicon supply on growth stages of spring wheat (Triticum aestivum L.) through skipped irrigation system
Authors: Bukhari Muhammad Adnan , Ahmad Zahoor , Saqib Muhammad , Nasim Wajid , Iqbal Javid , Artyszak Arkadiusz , Baloch Mohammad Safdar , Siddiqui Manzer H. 
Published: February 2023

Abstract
Plants are exposed to various abiotic stressors in agricultural systems, especially drought stressors, which hinder plant growth and development. Two years field studies have been carried out on two wheat genotypes viz; chakwal-50 (drought tolerant) and sehar-06 (drought sensitive) under skipped irrigation systems via; three methods of silicon (Si) supply along with control treatment at Research Farm Area, Department of Agronomy, University of Agriculture, Faisalabad, Punjab-Pakistan, were focused to optimize method and time of exogenous Si supply under field environment. Irrigation was skipped at tillering growth stage (irrigation skipped at tillering = I1) and at anthesis growth stage (irrigations skipped at anthesis = I2) with controlled irrigation (no irrigation skipped = I0). When plants were grown under normal irrigation (I0 = no skipped irrigation) conditions with Si application at tillering, genotype Sehar-06 performed very well with maximum number of tillers (538 m− 2), number of fertile tillers (494 m− 2), spike length (12.13 cm), number of spikelet spike− 1 (21.97), number of grains spike− 1 (54.60), grain and biological yield (5.20 tha− 1 and 11.88 tha− 1, respectively) and harvest index (40.35%), compared to other irrigation treatments (I1 and I2) during both the years 2011-12 and 2012-13. However, genotype chakwal-50 produced highest BY (12.68 tha− 1) and GY (5.04 tha− 1) as compared to sehar-06 with utilization of silicon fertigation (soil applied) method at tillering. When irrigation was skipped at anthesis stage (I2), plants of chakwal-50 performed very well with maximum GY (5.20 tha− 1) as compared to sehar-06. Under normal irrigation (I0) along with Si tillering Sehar-06 gained more GY (5.13 tha− 1), as chakwal-50 is drought tolerant genotype and gave more GY (4.91 tha− 1) at anthesis through Si seed priming. Chakwal-50 produced more grain yield with exogenous Si application under fertigation method at tillering and followed by seed priming.
Accurate prediction algorithm of rolling force in slab gradient temperature rolling process
Authors: Zhang Yu , Yu Wei , Cheng Zhicheng , Cai Qingwu 
Published: February 2023

Abstract
The temperature gradient rolling (GTR) method effectively improves the problem of uneven deformation of surface and core in the rolling of extra-thick plate. Different from the traditional near uniform temperature rolling (UTR) process, there is a large temperature gradient in the thickness direction of the rolled piece during the GTR process, and the rolling force prediction model of uniform temperature rolling cannot be directly applied. Rolling force prediction model is one of the important process control models of plate mill and the basis of plate thickness control. However, there is few research for the method of rolling force predicting during GTR. In order to predict the change of stopping force in GTR process and control the rolling process better, the current paper proposed a simplified method based on the deformation resistance model, fitting of temperature distribution, differential method, and loop iteration. The precision of the method was examined by using a finite element model and plane strain experiment. The mean error between the method and FEM was less than 5%.
Two Novel coumarin-based fluorescent probes for the detection of Cu2+ and biological applications
Authors: Zhang Canxin , Huang Li , Wang Lizhen , Meng Xia , Zhou Jianhua , Duan Hongdong 
Published: February 2023

Abstract
Large accumulations of copper (Cu) ions in the human body may cause damage, including organ and brain damage. In recent years, studies have proven that a large accumulation of Cu ions can lead to Parkinson's disease and Alzheimer's disease, therefore it is great important to develop novel strategies for detecting trace Cu in environmental and biological samples. In this work, we designed two new coumarin-based colorimetric and fluorescent probes HQ1 and HQ2. These two probes could selectively respond to Cu2+ with obvious color and fluorescence changes, and the presence of other metal ions had no effect on these changes. The two probes also exhibited high sensitivity for Cu2+, with a detection limit as low as 1.81×10-8 M/ 1.57×10-8 M. Notably, the two probes showed potential practical applications and were successfully used for detecting Cu2+ in a test strip, A549 cells and living zebrafish larvae.
Food Web Structure in the Xingu River Rapids Prior to Operation of the Amazon’S Largest Hydropower Plant
Authors: Andrade Marcelo C , Keppeler Friedrich W , Zuluaga-Gómez Mario Alejandro , Conceição Jefferson W S , Lisboa Oliver P , Andrades Ryan , Winemiller Kirk , Giarrizzo Tommaso 
Published: February 2023

Abstract

Recent theoretical studies suggest that food webs are size-structured with top predators coupling different energy sources, but evidence for this hypothesis is still scarce, especially in highly diverse tropical rivers. Here, we explored the association between body size, trophic position, and the use of allochthonous and autochthonous basal production sources in the Volta Grande rapids of the Xingu River, a major clearwater tributary of the Amazon River, during the period prior to operation of the Belo Monte Hydropower Plant (BMHP). This section of the river contains a maze of channels with rocky shoals that support dozens of endemic fishes, mollusks and other aquatic taxa that may be impacted by flow regulation by the Pimental Dam located upstream. During the low-water season, we surveyed fish, crustaceans, mollusks, sponges, aquatic and terrestrial insects, zooplankton, and basal production sources to obtain tissue samples for analysis of stable isotope ratios of carbon (δ13C) and nitrogen (δ15N). Biomass of most aquatic organisms appears to be largely supported by riparian vegetation, highlighting the importance of the lateral connectivity between aquatic and terrestrial habitats. Unlike expected, we did not observe a gradual increase in coupling of energy pathways with increasing body size and trophic position. Findings provide a baseline for trophic ecology of this river under the natural flow regime for future impact assessments, and also indicated that more complex food web models, potentially including additional functional traits (e.g., gut length), are needed to describe resource and habitat use in highly diverse tropical ecosystems.
Metabolically versatile psychrotolerant bacterium Pseudomonas sp. ANT_H12B is an efficient producer of siderophores and accompanying metabolites (SAM) useful for agricultural purposes
Authors: Musialowski Marcin , Kowalewska Lucja , Stasiuk Robert , Krucon Tomasz , Debiec-Andrzejewska Klaudia 
Published: February 2023

Abstract

Background
Bacterial siderophores are chelating compounds with the potential for application in agriculture, due to their plant growth-promoting (PGP) properties, however, high production and purification costs are limiting factors for their wider application. Cost-efficiency of the production could be increased by omitting purification processes, especially since siderophores accompanying metabolites (SAM) often also possess PGP traits. In this study, the metabolism versatility of Pseudomonas sp. ANT_H12B was used for the optimization of siderophores production and the potential of these metabolites and SAM was characterized in the context of PGP properties.
Results
The metabolic diversity of ANT_H12B was examined through genomic analysis and phenotype microarrays. The strain was found to be able to use numerous C, N, P, and S sources, which allowed for the design of novel media suitable for the efficient production of siderophores in the form of pyoverdine (223.50 – 512.60μM). Moreover, depending on the culture medium, the pH of the siderophores and SAM solutions varied from acidic (pH<5) to alkaline (pH>8). In the germination test, siderophores and SAM were shown to have a positive effect on plants, with a significant increase in germination percentage observed in beetroot, pea, and tobacco. The PGP potential of SAM was further elucidated through GC/MS analysis, which revealed other compounds with PGP potential, such as indolic acetic acids, organic acids, fatty acids, sugars, and alcohols. These compounds not only improved seed germination but could also potentially be beneficial for plant fitness and soil quality.
Conclusions
Pseudomonassp. ANT_H12B was presented as an efficient producer of siderophores and SAM which exhibit PGP potential. It was also shown that omitting downstream processes could not only limit the costs of siderophores production but also improve their agricultural potential.
Observation and Analysis of Surge Impact Characteristics of Low-voltage Overhead Lines Caused by Natural Lightning
Authors: Yan Xu , Chen Shaodong , Ding Min , Lyu Weitao , Chen Chang , Zhang Yijun , Chen Lyewen , Li Yangbin 
Published: February 2023

Abstract
In this paper, the residual voltage of a surge impacting surge protective device (SPD) generated by the coupling of a 710 m low-voltage overhead line is observed and analyzed. Based on the observation results of 65 natural lightning returns, it is found that, with a duration of 97.3 µs, the peak value of the SPD’s residual voltage was 767.6 V. In addition, the peak current flowing through the SPD was 6.4 A, and the energy absorbed by the SPD was only 0.2 J. According to the different return stroke process and its superimposed M component, the surge impacting SPD was divided into three categories. The currents flowing through SPD of type A and type B were basically the same, but the residual voltage waveform differed, The surge impact was mainly in the return stroke process. Type C was quite different from the other two types: The surge impact was expanded in the form of superposition of M component in the return stroke process, the residual voltage duration and peak current flowing through SPD were about twice those of the other two types, and the energy absorbed by SPD was about 5.8 times. There was a certain correlation between the current peak value of the subsequent return stroke flowing through SPD and the ratio of lightning current peak value and distance, with the determination coefficient R2 reaching 0.71, while the correlation of the first return stroke was weak, the R2 being only 0.48.
Improvement of the properties of CrN Films on oxynitriding treated Vanadis 23 high-speed steel by the DC magnetron sputtering
Authors: Chang Shih-Hsien , Shiao Wen-Yu , Huang Kuo-Tsung 
Published: February 2023

Abstract
This study coated CrN films onto oxynitriding-treated Vanadis 23 high-speed steel using the DC magnetron sputtering process of the PVD technique. The experimental parameters include various deposition temperatures (275, 300, 325, and 350°C), a bias of -25 V, a power of 100 W, a gas flow rate of 45/30 (Ar/N2) sccm, and a deposition time of 2.5 h. The research results show that when the coatings were deposited at 325°C, the CrN coatings possessed an obvious columnar crystal structure, the highest hardness (13.4 GPa), and the highest elastic modulus (159.7 GPa). In addition, the CrN coating had the best wear properties (the lowest specific wear rates were 1.07×10− 6 and 1.33×10− 6 mm3·m− 1·N− 1 under the loads of 2 N and 4 N, respectively) and good corrosion resistance (corrosion current was 8.90×10− 5 A·cm− 2, and polarization resistance was 822.11 Ω·cm2 in a 3.5 wt% NaCl solution).