bluuebunny/crossref_metadata_2025_split huggingface dataset:
Morpho-Molecular Identification and First Report of Trichoderma Aggressivum is Causing Green Rot on White Button Mushroom in Iraq
Authors: Taha Abdulrasool Shallal , Jamel Dareen S. , Abdui-Razzak Ahmad K. 
Published: November 2023

Abstract
The aim of this study was to morphological isolation and identification of fungus associated with the fruits and culture media of the white mushroom Agaricus bisporus. The results of isolation and identification from the sampling areas included Baghdad, Babylon, and Diwaniyah. Besides, Sulaymaniyah governorates showed the association of seven species of fungi associated the fruiting body and culture media of the white mushroom A. bisporus represented by the two pathogens Cladobotryum spp. and Trichoderma spp. As well as, the competitive fungi of A. bisporus culture medium, such as Aspergillus spp. and Penicillium spp. and Phoma sp. and Rhizopus spp., and Ulocladium sp. The most common pathogenic fungus was Cladobotryum spp. with a frequency of 56.2%, followed by Trichoderma spp., with a frequency of 54.1%, which appeared in samples from two sampling areas. Conversely, species T. aggressivum recorded a frequency of 42.5%, which is the first record in Iraq on the fruits and media of white fungus. The fungus Aspergillus spp. showed the existence percentage reached 65.5%, which is the highest among the competing fungi, followed by Penicillium spp., with an existence percentage of 26.6%. Then, Rhizopus spp., Phoma sp., and Ulocladium sp. with a frequency of 16.6%, 10.4%, and 10.4%, respectively. The results of the pathogenicity of the fungus isolate Trichoderma spp. indicated that all the isolates tested for the pathogenicity of the fruiting bodies of the white mushroom A. bisporus led to the infection of the fruiting bodies and their transformation into brown color and damage. The isolates of the fungus T. aggressivum (isolate 1 and isolate 2) recorded a disease severity of 60.0% and 60.0%, respectively. While, at a temperature of 4 °C, the isolates of the fungus T. aggressivum (1 and 2) recorded a disease severity amounted to 40.0% and 50.0%, respectively, compared to the control treatment without fungus, where the disease severity amounted to 0.0%. The results of the molecular identification of the DNA of the T. aggressivum, which showed the highest pathogenicity of A. bisporus fruiting bodies, using the specialized primer ITSI/ITS4, as it gave bands with a molecular weight of 600 bp. These findings were compared with the GenBank with a high similarity for the fungus T. aggressivum and it has been deposited in the Gen Bank with the accession number (OQ109172).
The flowability and high-temperature resistance of manufactured sand concrete: An exploration for high-rise buildings
Authors: Ren Zhiping , Hua Jianmin , Wang Huichao , Hou Chunming , Du Fuxiang , Huang Lepeng , Huo Xiaowei 
Published: November 2023

Abstract
The depletion of natural concrete aggregates, e.g., river sands, is a gradual process, and hence, manufactured sand concrete (MSC) is widely used in various construction projects. The flowability and high-temperature resistance of MSC directly determine the transport of fresh concrete and the fire resistance of high-rise buildings. In this study, MSC with different superplasticizer contents and sand ratios was prepared and its flowability and high-temperature resistance were studied. Scanning electron microscopy (SEM) and mercury intrusion porosimetry (MIP) were used to characterize the microstructure and porosity of MSC. The flowability of MSC with higher than 0.75% superplasticizer content or lower than 43% sand ratio is suitable for super high-rise buildings according to GB/T 50081-2019. The mechanical properties of other MSC meet the C30 requirements except for the MSC with a sand ratio of 48%. And the relatively high superplasticizer content or low sand ratio can make the denser structure and lower porosity of MSC. In addition, the MSC with relatively high superplasticizer content and low sand ratio exhibits better resistance to high temperatures due to a denser structure. This study provides theoretical guidance for using MSC in high-rise buildings and studying fire performance.
Tungsten nanostructure growth by sputtering and redeposition in BCA-MD-KMC hybrid simulation
Authors: Ito Atsushi M , Takayama Arimichi , Nakamura Hiroaki 
Published: November 2023

Abstract
The formation mechanism of fibrous tungsten nanostructures, fuzz, induced by helium plasma irradiation on tungsten materials has been investigated. We have developed a BCA-MD-KMC hybrid simulation, which solves the injection process of helium atoms by the Binary Collision Approximation (BCA) method, the diffusion process of helium atoms in tungsten materials by the Kinetic Monte-Carlo (KMC) method, and the deformation of tungsten materials due to helium bubbles by the Molecular Dynamics (MD) method. In addition, the model used to calculate the recoiling of tungsten atoms in BCA was improved to account for the reduced binding energy of tungsten atoms on rough surfaces. Using the hybrid simulation, the height of the nanostructures reached about 50 nm. The main mechanism of nanostructure growth was that sputtering and redeposition caused transport of tungsten atoms perpendicular to the surface. The present simulation was able to represent not only the dependence that the nanostructure height increases in proportion to the square root of the helium fluence, but also the existence of incubation fluence before the growth starts.
Examining the influence of Scandium interlayer and parameters on the mechanical behaviour in FSW of AA 5754-H111 plate through response surface approach
Authors: Suresh Raj L , Manimaran G 
Published: November 2023

Abstract
Friction stir welding (FSW) was conducted on 5754-H111 aluminium alloy using a response surface methodology to examine the impact of process parameters on the efficiency of the weld. The key FSW parameters were the percentage of scandium inclusion in the interlayer, tool rotational speed, and tool travel speed. The significant responses were identified as the tensile strength of the weld and the hardness in the weld zone. An Al-Mg-Sc alloy was employed as an interlayer material between the 5754 plates to enhance the strength in the weld zone. The addition of Scandium had a more pronounced effect on the hardness of the stir zone. The tensile strength was increased by raising the tool’s rotational speed. The results showed that the maximum tensile strength of the joints was 225 MPa and the hardness was highest at 118 HV1 in the weld stir zone. The introduction of Scandium improved the joint strength by producing fine grains and Al3Sc precipitates. The welding speed had the least impact on the tensile properties of the joint among all the variables investigated.
Improved polarimetric analysis of human skin through stitching: advantages, limitations, and applications in dermatology
Authors: Jütte Lennart , Patel Harshkumar , Roth Bernhard 
Published: November 2023

Abstract
Polarimetry is a powerful tool for the analysis of the optical properties of materials and systems, such as human skin. However, in many polarimetric setups, the field of view is limited to a few square centimeters. In these cases, it is possible to resort to stitching techniques, which involve combining multiple Mueller matrix measurements obtained from different overlapping regions of the sample. In this paper, we propose a stitching technique for polarimetric data and discuss its advantages and limitations. We also describe the potential of image stitching for improving the accuracy and robustness of in vivo polarimetry in the presence of random patient movement. We conducted our research using a diverse set of samples which included porcine skin, human skin from arms and fingers, cold cuts of chicken and gelatine, alongside synthetically created sample data. Our results demonstrate the effectiveness of this technique for the application in dermatology. Each additional in vivo measurement enhances the field of view by approximately one third, thereby considerably augmenting the total observation area. We show that stitching enables for the polarimetric assessment of large skin patches which is useful for the diagnosis of inflammatory skin diseases.
Highly sensitive strain sensors based on dispensing technology for human–machine interaction
Authors: Chen Zhifu , Huang Liangsong , Zhang Peng , Li Yuxia , Bu Xiaofei , Chen Huake , Tan Jiapeng 
Published: November 2023

Abstract
Flexible strain sensors have stable and sensitive sensing performance under deformation conditions such as pressing, bending, and stretching. However, the preparation process of high-performance strain sensors is still very complex, which also limits the application and production of sensors. At the same time, most sensors are unstable and inefficient, so they cannot meet people’s expectations for high sensitivity and stability. In order to solve the above problems, this paper proposes a resistive strain sensor based on dispensing technology, with carbon black and polyurethane mixture as printing ink. Then, a sensor-sensitive layer with a right-angle serpentine structure is printed directly by air pressure extrusion. The sensor can detect changes at 0.1% strain and withstand 2400 tensile cycles while maintaining a sensitivity of 28.07 in the range of 0%–40%. In addition, the sensor can accurately and stably reflect the changes in different joints of the human body. At the same time, the data glove based on the strain sensor shows great application potential in the fields of gesture recognition and human–machine interaction.
Study on the matching rules and control mechanisms between flocculants and slurry settlement characteristics
Authors: Wang Wuchao , Fan Lei , Ni SongBo , Wei Jihong , Huang Yiping 
Published: November 2023

Abstract
In order to realise efficient, economic, low carbon and environmentally friendly slurry disposal, floc sedimentation velocity (S

f
), supernatant volume (V

s
), water content of bottom mud (W

b
), supernatant turbidity (N

s
) and pH value were determined by slurry sedimentation tests, specific resistance tests, and water quality analysis. Orthogonal tests were performed to analyze the matching rule and control mechanism between flocculants and the slurry settlement characteristics. The results show that polyaluminum chloride (PAC) and polyferric chloride (PFC) had a low dose and a fast sedimentation rate. The sedimentation effect of 20 ionic degree cationic polyacrylamide (CPAM-20) in organic flocculant is the best. Although flocculants can shorten the sedimentation time, excessive flocculants can also weaken the slurry separation effect. The sedimentation efficiency of organic flocculants is higher than that of inorganic flocculants, but it is easy to form foam on the supernatant surface. For the composite flocculants, the sensitivity sequence of S

f
, V

s
and W

b
is PAC>CPAM-20>PFC. PAC plays a controlling role in the sedimentation effect of the slurry.
Net zero emission buildings: a review of academic literature and national roadmaps
Authors: Þórólfsdóttir Elín , Árnadóttir Áróra , Heinonen Jukka 
Published: November 2023

Abstract
Addressing the growing issue of climate change demands active measures. With its significant carbon footprint, the building industry needs to make immediate efforts contributing to achieving the Paris Agreement’s objective of restricting global warming to 1.5 °C. This review focuses on net zero emission buildings (NZEBs) which are claimed to offer a viable option to significantly reduce greenhouse gas emissions from the built environment. The review covers both the recent academic literature on NZEBs, and the NZEB roadmaps from the member organizations of the World Green Building Council, focusing on those Green Building Councils actively working to implement NZEBs in their local contexts. By synthesizing a broad range of viewpoints and practices derived from academic literature and roadmaps, this review provides a holistic overview of the different perspectives to the current state of NZEBs and to their future. The review shows that NZEBs have the potential to provide significant environmental, economic, and social advantages, improving the built environment’s overall sustainability. The review also promotes a more thorough understanding over NZEBs that can facilitate collaborative policymaking and action amongst stakeholders.
Exploring non-linear modes of the subtropical Indian Ocean Dipole using autoencoder neural networks
Authors: Ibebuchi Chibuike Chiedozie 
Published: November 2023

Abstract
The subtropical Indian Ocean Dipole (SIOD) significantly influences climate variability, predominantly within parts of the Southern Hemisphere. This study applies an autoencoder—a type of artificial neural network (ANN)—known for its ability to capture intricate non-linear relationships in data through the process of encoding and decoding—to analyze the spatiotemporal characteristics of the SIOD. The encoded SIOD pattern(s) is compared to the conventional definition of the SIOD, calculated as the sea surface temperature (SST) anomaly difference between the western and eastern subtropical Indian Ocean. The analysis reveals two encoded patterns consistent with the conventional SIOD structure, predominantly represented by the SST dipole pattern south of Madagascar and off Australia’s west coast. During different analysis periods, distinct variability in the global SST patterns associated with the SIOD was observed. This variability underscores the SIOD’s dynamic nature and the challenges of accurately defining modes of variability with limited records. One of the ANN patterns has a substantial congruence match of 0.92 with the conventional SIOD pattern, while the other represents an alternate non-linear pattern within the SIOD. This implies the potential existence of additional non-linear SIOD patterns in the subtropical Indian Ocean, complementing the traditional model. When global temperature and precipitation are regressed onto the ANN temporal patterns and the conventional SIOD index, both appear to be associated with anomalous climate conditions over parts of Australia, with several other consistent global impacts. Nevertheless, due to the non-linear nature of the ANN patterns, their effects on local temperature and precipitation vary across different regions as compared to the conventional SIOD index. This study highlights that while the conventional SIOD pattern is consistent with the ANN-derived SIOD pattern, the climate system’s complexity and non-linearity might require ANN modeling to advance our comprehension of climatic modes.
KinScan: AI-based rapid profiling of activity across the kinome
Authors: Brahma Rahul , Shin Jae-Min , Cho Kwang-Hwi 
Published: November 2023

AbstractKinases play a vital role in regulating essential cellular processes, including cell cycle progression, growth, apoptosis, and metabolism, by catalyzing the transfer of phosphate groups from adenosing triphosphate to substrates. Their dysregulation has been closely associated with numerous diseases, including cancer development, making them attractive targets for drug discovery. However, accurately predicting the binding affinity between chemical compounds and kinase targets remains challenging due to the highly conserved structural similarities across the kinome. To address this limitation, we present KinScan, a novel computational approach that leverages large-scale bioactivity data and integrates the Multi-Scale Context Aware Transformer framework to construct a virtual profiling model encompassing 391 protein kinases. The developed model demonstrates exceptional prediction capability, distinguishing between kinases by utilizing structurally aligned kinase binding site features derived from multiple sequence alignment for fast and accurate predictions. Through extensive validation and benchmarking, KinScan demonstrated its robust predictive power and generalizability for large-scale kinome-wide profiling and selectivity, uncovering associations with specific diseases and providing valuable insights into kinase activity profiles of compounds. Furthermore, we deployed a web platform for end-to-end profiling and selectivity analysis, accessible at https://kinscan.drugonix.com/softwares/kinscan.
Ensemble-GNN: federated ensemble learning with graph neural networks for disease module discovery and classification
Authors: Pfeifer Bastian , Chereda Hryhorii , Martin Roman , Saranti Anna , Clemens Sandra , Hauschild Anne-Christin , Beißbarth Tim , Holzinger Andreas , Heider Dominik 
Published: November 2023

Abstract

Summary
Federated learning enables collaboration in medicine, where data is scattered across multiple centers without the need to aggregate the data in a central cloud. While, in general, machine learning models can be applied to a wide range of data types, graph neural networks (GNNs) are particularly developed for graphs, which are very common in the biomedical domain. For instance, a patient can be represented by a protein–protein interaction (PPI) network where the nodes contain the patient-specific omics features. Here, we present our Ensemble-GNN software package, which can be used to deploy federated, ensemble-based GNNs in Python. Ensemble-GNN allows to quickly build predictive models utilizing PPI networks consisting of various node features such as gene expression and/or DNA methylation. We exemplary show the results from a public dataset of 981 patients and 8469 genes from the Cancer Genome Atlas (TCGA).

Availability and implementation
The source code is available at https://github.com/pievos101/Ensemble-GNN, and the data at Zenodo (DOI: 10.5281/zenodo.8305122).
regioneReloaded: evaluating the association of multiple genomic region sets
Authors: Malinverni Roberto , Corujo David , Gel Bernat , Buschbeck Marcus 
Published: November 2023

Abstract

Motivation
Next-generation sequencing methods continue improving the annotation of genomes in part by determining the distribution of features such as epigenetic marks. Evaluating and interpreting the association between genomic regions and their features has become a common and challenging analysis in genomic and epigenomic studies.

Results
With regioneR we provided an R package allowing to assess the statistical significance of pairwise associations between genomic region sets using permutation tests. We now present the R package regioneReloaded that builds upon regioneR’s statistical foundation and extends the functionality for the simultaneous analysis and visualization of the associations between multiple genomic region sets. Thus, we provide a novel discovery tool for the identification of significant associations that warrant to be tested for functional interdependence.

Availability and implementation
regioneReloaded is an R package released under an Artistic-2.0 License. The source code and documentation are freely available through Bioconductor: http://www.bioconductor.org/packages/regioneReloaded.
Towards an accurate autism spectrum disorder diagnosis: multiple connectome views from fMRI data
Authors: Yang Jie , Xu Xiaowen , Sun Mingxiang , Ruan Yudi , Sun Chenhao , Li Weikai , Gao Xin 
Published: November 2023

Abstract
Functional connectome has revealed remarkable potential in the diagnosis of neurological disorders, e.g. autism spectrum disorder. However, existing studies have primarily focused on a single connectivity pattern, such as full correlation, partial correlation, or causality. Such an approach fails in discovering the potential complementary topology information of FCNs at different connection patterns, resulting in lower diagnostic performance. Consequently, toward an accurate autism spectrum disorder diagnosis, a straightforward ambition is to combine the multiple connectivity patterns for the diagnosis of neurological disorders. To this end, we conduct functional magnetic resonance imaging data to construct multiple brain networks with different connectivity patterns and employ kernel combination techniques to fuse information from different brain connectivity patterns for autism diagnosis. To verify the effectiveness of our approach, we assess the performance of the proposed method on the Autism Brain Imaging Data Exchange dataset for diagnosing autism spectrum disorder. The experimental findings demonstrate that our method achieves precise autism spectrum disorder diagnosis with exceptional accuracy (91.30%), sensitivity (91.48%), and specificity (91.11%).
Blood pressure reduction after renal denervation in patients with or without chronic kidney disease
Authors: Günes-Altan Merve , Schmid Axel , Ott Christian , Bosch Agnes , Pietschner Robert , Schiffer Mario , Uder Michael , Schmieder Roland E , Kannenkeril Dennis 
Published: November 2023

ABSTRACT

Background
Renal denervation (RDN) has emerged as an adjacent option for the treatment of hypertension. This analysis of the Erlanger registry aimed to compare the blood pressure (BP)-lowering effects and safety of RDN in patients with and without chronic kidney disease (CKD).

Methods
In this single-center retrospective analysis, 47 patients with and 127 without CKD underwent radiofrequency-, ultrasound- or alcohol-infusion-based RDN. Office and 24-h ambulatory BP and estimated glomerular filtration rate (eGFR) were measured at baseline, and after 6 and 12 months.

Results
A total of 174 patients with a mean age of 59.0 ± 10 years were followed up for 12 months. At baseline, mean eGFR was 55.8 ± 21 mL/min/1.73 m2 in patients with CKD and 87.3 ± 13 mL/min/1.73 m2 in patients without CKD. There was no significant eGFR decline in either of the groups during 12 months of follow-up. In patients without CKD, office systolic and diastolic BP were reduced by –15.3 ± 17.5/–7.9 ± 10.8 mmHg 6 months after RDN and by –16.1 ± 18.2/–7.7 ± 9.6 mmHg 12 months after RDN. In patients with CKD, office systolic and diastolic BP were reduced by –10.7 ± 24.0/–5.8 ± 13.2 mmHg 6 months after RDN and by –15.1 ± 24.9/–5.9 ± 12.9 mmHg 12 months after RDN. Accordingly, in patients without CKD, 24-h ambulatory systolic and diastolic BP were reduced by –7.2 ± 15.8/–4.9 ± 8.8 mmHg 6 months after RDN and by –9.0 ± 17.0/–6.2 ± 9.8 mmHg 12 months after RDN. In patients with CKD, 24-h systolic and diastolic BP were reduced by –7.4 ± 12.9/–4.2 ± 9.9 mmHg 6 months after RDN and by –8.0 ± 14.0/–3.6 ± 9.6 mmHg 12 months after RDN. There was no difference in the reduction of office and 24-h ambulatory BP between the two groups at any time point (all P &gt; .2). Similar results have been found for the 6 months data. With exception of rare local adverse events, we did not observe any safety signals.

Conclusion
According to our single-center experience, we observed a similar reduction in 24-h, day and night-time ambulatory BP as well as in-office BP in patients with and without CKD at any time point up to 12 months. We conclude that RDN is an effective and safe treatment option for patients with hypertension and CKD.