bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multi-Objective Optimization of VBHF in Deep Drawing Based on the Improved QO-Jaya Algorithm
Authors: Jiang Xiangyu , Hong Zhaoxi , Feng Yixiong , Tan Jianrong 
Published: January 2024

AbstractBlank holder force (BHF) is a crucial parameter in deep drawing, having close relation with the forming quality of sheet metal. However, there are different BHFs maintaining the best forming effect in different stages of deep drawing. The variable blank holder force (VBHF) varying with the drawing stage can overcome this problem at an extent. The optimization of VBHF is to determine the optimal BHF in every deep drawing stage. In this paper, a new heuristic optimization algorithm named Jaya is introduced to solve the optimization efficiently. An improved “Quasi-oppositional” strategy is added to Jaya algorithm for improving population diversity. Meanwhile, an innovated stop criterion is added for better convergence. Firstly, the quality evaluation criteria for wrinkling and tearing are built. Secondly, the Kriging models are developed to approximate and quantify the relation between VBHF and forming defects under random sampling. Finally, the optimization models are established and solved by the improved QO-Jaya algorithm. A VBHF optimization example of component with complicated shape and thin wall is studied to prove the effectiveness of the improved Jaya algorithm. The optimization results are compared with that obtained by other algorithms based on the TOPSIS method.
High-sensitivity flip chip blue Mini-LEDs miniaturized optical instrument for non-invasive glucose detection
Authors: Ye Zhi Ting , Tseng Shen Fu , Tsou Shang Xuan , Tsai Chun Wei 
Published: January 2024

AbstractThe colorimetric detection of glucose typically involves a peroxidase reaction producing a color, which is then recorded and analyzed. However, enzyme detection has difficulties with purification and storage. In addition, replacing enzyme detection with chemical methods involves time-consuming steps such as centrifugation and purification and the optical instruments used for colorimetric detection are often bulky and not portable. In this study, ammonium metavanadate and sulfuric acid were used to prepare the detection solution instead of peroxidase to produce color. We also analyzed the effect of different concentrations of detection solution on absorbance sensitivity. Finally, a flip chip blue Mini-LEDs miniaturized optical instrument (FC blue Mini-LEDs MOI) was designed for glucose detection using optics fiber, collimating lenses, a miniaturized spectrometer, and an FC Blue Mini-LEDs with a center wavelength of 459 nm. While detecting glucose solutions in the concentration range of 0.1–10 mM by the developed MOI, the regression equation of y = 0.0941x + 0.1341, R2 of 0.9744, the limit of detection was 2.15 mM, and the limit of quantification was 7.163 mM. Furthermore, the preparation of the detection solution only takes 10 min, and the absorbance sensitivity of the optimized detection solution could be increased by 2.3 times. The detection solution remained stable with only a 0.6% decrease in absorbance compared to the original after storing it in a refrigerated environment at 3 °C for 14 days. The method proposed in this study for detecting glucose using FC blue light Mini-LEDs MOI reduces the use of peroxidase. In addition, it has a wide detection range that includes blood as well as non-invasive saliva and tear fluids, providing patients with a miniaturized, highly sensitive, and quantifiable glucose detection system.
The RING Domain of Rice HEI10 is Essential for Male, But Not Female Fertility
Authors: Tan Qian , Zhang Xu , Luo Qian , Xu Yi-Chun , Zhang Jie , Liang Wan-Qi 
Published: January 2024

AbstractHEI10 is a conserved E3 ubiquitin ligase involved in crossover formation during meiosis, and is thus essential for both male and female gamete development. Here, we have discovered a novel allele of HEI10 in rice that produces a truncated HEI10 protein missing its N-terminal RING domain, namely sh1 (shorter hei10 1). Unlike previously reported hei10 null alleles that are completely sterile, sh1 exhibits complete male sterility but retains partial female fertility. The causative sh1 mutation is a 76 kb inversion between OsFYVE4 and HEI10, which breaks the integrity of both genes. Allelic tests and complementation assays revealed that the gamete developmental defects of sh1 were caused by disruption of HEI10. Further studies demonstrated that short HEI10 can correctly localise to the nucleus, where it could interact with other proteins that direct meiosis; expressing short HEI10 in hei10 null lines partially restores female fertility. Our data reveal an intriguing mutant allele of HEI10 with differential effects on male and female fertility, providing a new tool to explore similarities and differences between male and female meiosis.
Prop3D: A flexible, Python-based platform for machine learning with protein structural properties and biophysical data
Authors: Draizen Eli J. , Readey John , Mura Cameron , Bourne Philip E. 
Published: January 2024

Abstract
Background
Machine learning (ML) has a rich history in structural bioinformatics, and modern approaches, such as deep learning, are revolutionizing our knowledge of the subtle relationships between biomolecular sequence, structure, function, dynamics and evolution. As with any advance that rests upon statistical learning approaches, the recent progress in biomolecular sciences is enabled by the availability of vast volumes of sufficiently-variable data. To be useful, such data must be well-structured, machine-readable, intelligible and manipulable. These and related requirements pose challenges that become especially acute at the computational scales typical in ML. Furthermore, in structural bioinformatics such data generally relate to protein three-dimensional (3D) structures, which are inherently more complex than sequence-based data. A significant and recurring challenge concerns the creation of large, high-quality, openly-accessible datasets that can be used for specific training and benchmarking tasks in ML pipelines for predictive modeling projects, along with reproducible splits for training and testing.

Results
Here, we report ‘’, a platform that allows for the creation, sharing and extensible reuse of libraries of protein domains, featurized with biophysical and evolutionary properties that can range from detailed, atomically-resolved physicochemical quantities (e.g., electrostatics) to coarser, residue-level features (e.g., phylogenetic conservation). As a community resource, we also supply a ‘’ protein dataset, obtained by applying our approach to CATH. We have developed and deployed the framework, both in the cloud and on local HPC resources, to systematically and reproducibly create comprehensive datasets via the Highly Scalable Data Service (HSDS). Our datasets are freely accessible via a public HSDS instance, or they can be used with accompanying Python wrappers for popular ML frameworks.

Conclusion
and its associated dataset can be of broad utility in at least three ways. Firstly, the workflow code can be customized and deployed on various cloud-based compute platforms, with scalability achieved largely by saving the results to distributed HDF5 files via HSDS. Secondly, the linked dataset provides a hand-crafted, already-featurized dataset of protein domains for 20 highly-populated CATH families; importantly, provision of this pre-computed resource can aid the more efficient development (and reproducible deployment) of ML pipelines. Thirdly, ’s construction explicitly takes into account (in creating datasets and data-splits) the enigma of ‘data leakage’, stemming from the evolutionary relationships between proteins.
Integrated analysis strategy of genome-wide functional gene mining reveals DKK2 gene underlying meat quality in Shaziling synthesized pigs
Authors: He Shuaihan , Wang Yubei , Luo Yabiao , Xue Mingming , Wu Maisheng , Tan Hong , Peng Yinglin , Wang Kejun , Fang Meiying 
Published: January 2024

Abstract
Background
Shaziling pig is a well-known indigenous breed in China who has superior meat quality traits. However, the genetic mechanism and genomic evidence underlying meat quality characteristics of Shaziling pigs are still unclear. To explore and investigate the germplasm characteristics of Shaziling pigs, we totally analyzed 67 individual’s whole genome sequencing data for the first time (20 Shaziling pigs [S], 20 Dabasha pigs [DBS], 11 Yorkshire pigs [Y], 10 Berkshire pigs [BKX], 5 Basha pigs [BS] and 1 Warthog).

Results
A total of 2,538,577 SNPs with high quality were detected and 9 candidate genes which was specifically selected in S and shared in S to DBS were precisely mined and screened using an integrated analysis strategy of identity-by-descent (IBD) and selective sweep. Of them, dickkopf WNT signaling pathway inhibitor 2 (DKK2), the antagonist of Wnt signaling pathway, was the most promising candidate gene which was not only identified an association of palmitic acid and palmitoleic acid quantitative trait locus in PigQTLdb, but also specifically selected in S compared to other 48 Chinese local pigs of 12 populations and 39 foreign pigs of 4 populations. Subsequently, a mutation at 12,726-bp of DKK2 intron 1 (g.114874954 A > C) was identified associated with intramuscular fat content using method of PCR–RFLP in 21 different pig populations. We observed DKK2 specifically expressed in adipose tissues. Overexpression of DKK2 decreased the content of triglyceride, fatty acid synthase and expression of relevant genes of adipogenic and Wnt signaling pathway, while interference of DKK2 got contrary effect during adipogenesis differentiation of porcine preadipocytes and 3T3-L1 cells.

Conclusions
Our findings provide an analysis strategy for mining functional genes of important economic traits and provide fundamental data and molecular evidence for improving pig meat quality traits and molecular breeding.
Virome analysis of Desmodus rotundus tissue samples from the Amazon region
Authors: Albuquerque Nádia K. , Silva Sandro P. , Aragão Carine F. , Cunha Tânia Cristina A. S. , Paiva Francisco A. S. , Coelho Taciana F. S. B. , Cruz Ana Cecília R. 
Published: January 2024

Abstract
Background
Bats are renowned for harboring a high viral diversity, their characteristics contribute to emerging infectious diseases. However, environmental and anthropic factors also play a significant role in the emergence of zoonotic viruses. Metagenomic is an important tool for investigating the virome of bats and discovering new viruses.

Results
Twenty-four families of virus were detected in lung samples by sequencing and bioinfomatic analysis, the largest amount of reads was focused on the Retroviridae and contigs assembled to Desmodus rotundus endogenous retrovirus, which was feasible to acquire complete sequences. The reads were also abundant for phages.

Conclusion
This lung virome of D. rotundus contributes valuable information regarding the viral diversity found in bats, which is useful for understanding the drivers of viral cycles and their ecology in this species. The identification and taxonomic categorization of viruses hosted by bats carry epidemiological significance due to the potential for viral adaptation to other animals and humans, which can have severe repercussions for public health. Furthermore, the characterization of endogenized viruses helps to understanding the host genome and the evolution of the species.
Spotting disease disrupts the microbiome of infected purple sea urchins, Strongylocentrotus purpuratus
Authors: Shaw Chloe G. , Pavloudi Christina , Crow Ryley S. , Saw Jimmy H. , Smith L. Courtney 
Published: January 2024

Abstract
Background
Spotting disease infects a variety of sea urchin species across many different marine locations. The disease is characterized by discrete lesions on the body surface composed of discolored necrotic tissue that cause the loss of all surface appendages within the lesioned area. A similar, but separate disease of sea urchins called bald sea urchin disease (BSUD) has overlapping symptoms with spotting disease, resulting in confusions in distinguishing the two diseases. Previous studies have focus on identifying the underlying causative agent of spotting disease, which has resulted in the identification of a wide array of pathogenic bacteria that vary based on location and sea urchin species. Our aim was to investigate the spotting disease infection by characterizing the microbiomes of the animal surface and various tissues.

Results
We collected samples of the global body surface, the lesion surface, lesioned and non-lesioned body wall, and coelomic fluid, in addition to samples from healthy sea urchins. 16S rRNA gene was amplified and sequenced from the genomic DNA. Results show that the lesions are composed mainly of Cyclobacteriaceae, Cryomorphaceae, and a few other taxa, and that the microbial composition of lesions is the same for all infected sea urchins. Spotting disease also alters the microbial composition of the non-lesioned body wall and coelomic fluid of infected sea urchins. In our closed aquarium systems, sea urchins contracted spotting disease and BSUD separately and therefore direct comparisons could be made between the microbiomes from diseased and healthy sea urchins.

Conclusion
Results show that spotting disease and BSUD are separate diseases with distinct symptoms and distinct microbial compositions.

Graphical abstract
Survey of prothioconazole sensitivity in Fusarium pseudograminearum isolates from Henan Province, China, and characterization of resistant laboratory mutants
Authors: Zhou Feng , Jiao Yan , Han Aohui , Zhou Xiaoli , Kong Jiamei , Hu Haiyan , Liu Runqiang , Li Chengwei 
Published: January 2024

Abstract
Background
Fusarium crown rot (FCR) is one of the most significant diseases limiting crop production in the Huanghuai wheat-growing region of China. Prothioconazole, a triazole sterol 14α-demethylation inhibitor (DMI) fungicide developed by the Bayer Crop Protection Company, is mainly registered for the prevention and control of wheat powdery mildew and stripe rust (China Pesticide Information Network). It is known to exhibit high activity against F. pseudograminearum, but further research, particularly regarding the potential for fungicide resistance, is required before it can be registered for the control of FCR in China.

Results
The current study found that the baseline sensitivity of 67 field isolates of F. pseudograminearum collected between 2019 and 2021 ranged between 0.016–2.974 μg/mL, with an average EC50 value of 1.191 ± 0.720 μg/mL (mean ± SD). Although none of the field isolates exhibited signs of resistance, three highly resistant mutants were produced by repeated exposure to prothioconazole under laboratory conditions. All of the mutants were found to exhibit significantly reduced growth rates on potato dextrose agar (PDA), as well as reduced levels of sporulation, which indicated that there was a fitness cost associated with the resistance. However, inoculation of wounded wheat coleoptiles revealed that the pathogenicity of the resistant mutants was little affected or actually increased. Molecular analysis of the genes corresponding to the prothioconazole target protein, FpCYP51 (FpCYP51A, FpCYP51B, and FpCYP51C), indicated that the resistant mutants contained three conserved substitutions (M63I, A205S, and I246V) that were present in the FpCYP51C sequence of all three mutants, as well as several non-conserved substations in their FpCYP51A and FpCYP51B sequences. Expression analysis revealed that the presence of prothioconazole (0.1 μg/mL) generally resulted in reduced expression of the three FpCYP51 genes, but that the three mutants exhibited more complex patterns of expression that differed in comparison to their parental isolates. The study found no evidence of cross-resistance between prothioconazole and any of the fungicides tested including three DMI fungicides tebuconazole, prochloraz, and flutriafol.

Conclusions
Taken together these results not only provide new insight into the resistant mechanism and biological characteristics associated with prothioconazole resistance in F. pseudograminearum, but also strong evidence that prothioconazole could provide effective and sustained control of FCR, especially when applied in combination with other fungicides.
Identification of difficult laryngoscopy using an optimized hybrid architecture
Authors: Liu XiaoXiao , Flanagan Colin , Li Gang , Lei Yiming , Zeng Liaoyuan , Fang Jingchao , Guo Xiangyang , McGrath Sean , Han Yongzheng 
Published: January 2024

Abstract
Background
Identification of difficult laryngoscopy is a frequent demand in cervical spondylosis clinical surgery. This work aims to develop a hybrid architecture for identifying difficult laryngoscopy based on new indexes.

Methods
Initially, two new indexes for identifying difficult laryngoscopy are proposed, and their efficacy for predicting difficult laryngoscopy is compared to that of two conventional indexes. Second, a hybrid adaptive architecture with convolutional layers, spatial extraction, and a vision transformer is proposed for predicting difficult laryngoscopy. The proposed adaptive hybrid architecture is then optimized by determining the optimal location for extracting spatial information.

Results
The test accuracy of four indexes using simple model is 0.8320. The test accuracy of optimized hybrid architecture using four indexes is 0.8482.

Conclusion
The newly proposed two indexes, the angle between the lower margins of the second and sixth cervical spines and the vertical direction, are validated to be effective for recognizing difficult laryngoscopy. In addition, the optimized hybrid architecture employing four indexes demonstrates improved efficacy in detecting difficult laryngoscopy.

Trial registration
Ethics permission for this research was obtained from the Medical Scientific Research Ethics Committee of Peking University Third Hospital (IRB00006761-2015021) on 30 March 2015. A well-informed agreement has been received from all participants. Patients were enrolled in this research at the Chinese Clinical Trial Registry (http://www.chictr.org.cn, identifier: ChiCTR-ROC-16008598) on 6 June 2016.
Evaluation of autoimmune liver disease natural history in patients referred to Middle East Liver Diseases (MELD) center
Authors: Nejad Seyed Erfan Mehdi , Heiat Mohammad , Javanbakht Mohammad , Alavian Seyed Moayed , Haris Mohammad Ali Abyazi 
Published: January 2024

Abstract
Background
Autoimmune liver diseases (AILD) are increasing and common forms of chronic liver disease (CLD) with different clinical responses and characteristics which can result in cirrhosis. This study aimed to investigate the natural history and characteristics of AILD in an Iranian population.

Methods
Patients with AILD [Autoimmune Hepatitis (AIH), Primary Biliary Cholangitis (PBC), Primary Sclerosing Cholangitis (PSC) and Overlap Syndrome (OS)] referred to Middle East Liver Diseases (MELD) center, Tehran, Iran, between January 2002 and December 2022 were included in this retrospective cohort study. The main features of natural history (the trends of liver functional tests (LFT), Auto-Antibodies, response to treatment and cirrhotic status) along with demographic data were studied.

Results
Two hundred sixty-five patients (160 (60.4%) AIH, 37 (14.0%) PBC, 20 (7.5%) PSC, 48 (18.1%) overlap syndrome) with a median follow-up time of 5 years (IQR 4 to 8 years) were included. Baseline laboratory tests revealed that patients with AIH exhibit elevated transaminase levels. However, patients suffering from PBC and PSC displayed increased alkaline phosphatase levels. Conversely, in overlap syndrome patients, both transaminases and alkaline phosphatase were observed at high levels. Autoantibodies represented themselves as important diagnostic markers for the AIH and PBC but not for PSC. The complete response occurred in 112 (70%) of and 28 (58.4%) patients with AIH and overlap syndrome respectively and 21 patients 11 (6.9%) of AIH and 10 (20.8%) of overlap syndrome) were non-responders. Other patients in these two categories were considered as insufficient responders. On the other side, 32 (91.9%) and 8 (40%) of patients with PBC and PSC biochemically responded to Ursodeoxycholic Acid (UDCA). Unpredictably, cirrhosis regression was observed in some AIH and PBC patients.

Conclusion
Appropriate medication management for AILD patients may leads to regression from cirrhosis and improvement of manifestations; while discontinuation of medication may cause relapses. However, patient suffering from PSC showed limited response to treatment.
Pharmacotherapy for primary biliary cholangitis: an assessment of medication candidacy and rates of treatment
Authors: MacDonald Nicholas , Loh Rebecca , Fenkel Jonathan M. , Sass David A. , Halegoua-DeMarzio Dina 
Published: January 2024

Abstract
Background
Ursodeoxycholic acid is the preferred first-line therapy for primary biliary cholangitis. Alternative therapies, such as obeticholic acid, are recommended for patients who cannot tolerate ursodeoxycholic acid or who have an inadequate response to ursodeoxycholic acid monotherapy. Prior investigations have suggested that as many as 30% of patients with primary biliary cholangitis may have never received treatment with ursodeoxycholic acid. No prior investigations have examined usage rates of obeticholic acid in the treatment of primary biliary cholangitis.

Methods
All patients with an ICD-10 diagnosis of primary biliary cholangitis who had any records within the health system were included. A review of medical records was performed to confirm the diagnosis of primary biliary cholangitis and determine which medications had been prescribed for treatment, as well as candidacy for second-line therapies.

Results
A total of 495 patients met inclusion criteria. Notably, 95% of patients were taking ursodeoxycholic acid for treatment of their primary biliary cholangitis, with 67% of patients having disease that was well-controlled on ursodeoxycholic acid monotherapy. In total, 8% of patients were taking obeticholic acid (either as combination or monotherapy). Only 3% would benefit from the addition of a second line therapy but had not yet been offered medication. Only 3% of patients were not on any medication for management of their primary biliary cholangitis.

Conclusions
Ursodeoxycholic acid is a readily available and generally well-tolerated medication that should be offered to all patients with primary biliary cholangitis as first-line therapy. While prior investigations have suggested that up to 30% of patients with primary biliary cholangitis may never have received treatment for the disorder, the present study suggests that patients are generally being managed according to guidelines. Moreover, a significant proportion of patients with primary biliary cholangitis will qualify for second line therapies and prescribers should be aware of the indications to use these medications.