bluuebunny/crossref_metadata_2025_split huggingface dataset:
Aspergillus flavus pangenome (AflaPan) uncovers novel aflatoxin and secondary metabolite associated gene clusters
Authors: Gangurde Sunil S. , Korani Walid , Bajaj Prasad , Wang Hui , Fountain Jake C. , Agarwal Gaurav , Pandey Manish K. , Abbas Hamed K. , Chang Perng-Kuang , Holbrook C. Corley , Kemerait Robert C. , Varshney Rajeev K. , Dutta Bhabesh , Clevenger Josh P. , Guo Baozhu 
Published: February 2024

Abstract

Background
Aspergillus flavus is an important agricultural and food safety threat due to its production of carcinogenic aflatoxins. It has high level of genetic diversity that is adapted to various environments. Recently, we reported two reference genomes of A. flavus isolates, AF13 (MAT1-2 and highly aflatoxigenic isolate) and NRRL3357 (MAT1-1 and moderate aflatoxin producer). Where, an insertion of 310 kb in AF13 included an aflatoxin producing gene bZIP transcription factor, named atfC. Observations of significant genomic variants between these isolates of contrasting phenotypes prompted an investigation into variation among other agricultural isolates of A. flavus with the goal of discovering novel genes potentially associated with aflatoxin production regulation. Present study was designed with three main objectives: (1) collection of large number of A. flavus isolates from diverse sources including maize plants and field soils; (2) whole genome sequencing of collected isolates and development of a pangenome; and (3) pangenome-wide association study (Pan-GWAS) to identify novel secondary metabolite cluster genes.
Results
Pangenome analysis of 346 A. flavus isolates identified a total of 17,855 unique orthologous gene clusters, with mere 41% (7,315) core genes and 59% (10,540) accessory genes indicating accumulation of high genomic diversity during domestication. 5,994 orthologous gene clusters in accessory genome not annotated in either the A. flavus AF13 or NRRL3357 reference genomes. Pan-genome wide association analysis of the genomic variations identified 391 significant associated pan-genes associated with aflatoxin production. Interestingly, most of the significantly associated pan-genes (94%; 369 associations) belonged to accessory genome indicating that genome expansion has resulted in the incorporation of new genes associated with aflatoxin and other secondary metabolites.
Conclusion
In summary, this study provides complete pangenome framework for the species of Aspergillus flavus along with associated genes for pathogen survival and aflatoxin production. The large accessory genome indicated large genome diversity in the species A. flavus, however AflaPan is a closed pangenome represents optimum diversity of species A. flavus. Most importantly, the newly identified aflatoxin producing gene clusters will be a new source for seeking aflatoxin mitigation strategies and needs new attention in research.
Digital quantum simulation of gravitational optomechanics with IBM quantum computers
Authors: Rufo Pablo Guillermo Carmona , Mazumdar Anupam , Bose Sougato , Lestayo Carlos Sabín 
Published: February 2024

Abstract
We showcase the digital quantum simulation of the action of a Hamiltonian that governs the interaction between a quantum mechanical oscillator and an optical field, generating quantum entanglement between them via gravitational effects. This is achieved by making use of a boson-qubit mapping protocol and a digital gate decomposition that allow us to run the simulations in the quantum computers available in the IBM Quantum platform. We present the obtained results for the fidelity of the experiment in two different quantum computers, after applying error mitigation and post-selection techniques. The achieved results correspond to fidelities over 90%, which indicates that entanglement was indeed generated through the simulation of a quantum gravitational field.
Leveraging Transcriptomics-Based Approaches to Enhance Genomic Prediction: Integrating SNPs and gene-networks for Cotton Fibre Quality Improvement
Authors: Khalilisamani Nima , Li Zitong , Pettolino Filomena A. , Moncuquet Philippe , Reverter Antonio , MacMillan Colleen Pauline 
Published: February 2024

Abstract
The cotton genome (Gossypium hirsutum) contains ~ 80K protein-coding genes, making precision breeding for complex traits a challenge. This study tested biology-informed approaches to improve genomic prediction (GP) accuracy for cotton fibre traits to help accelerate precision breeding of valuable traits. The study’s foundational approach was the use of RNA-seq data from key time points during fibre development, namely fibre cells undergoing primary, transition, and secondary wall development. The test approaches included using a range of summary statistics from RNA-seq analysis such as gene Differential Expression (DE). The three test approaches included DE genes overall, target pairwise DE lists informed by gene functional annotation, and finally, gene-network-clusters created based on Partial Correlation and Information Theory (PCIT) as the prior information in Bayesian GP models. The most promising improvements in GP accuracy were at the level of ~ 5% increase by using PCIT-based gene-network clusters as the prior knowledge network neighbours of key genes, and for the traits of cotton fibre Elongation and Strength. These results indicate that there is scope to help improve precision breeding of target traits by incorporating biology-based inference into GP models, and points to specific approaches to achieve this.
An Exploratory Study on Spatiotemporal Clustering of Suicide in Korean Adolescents
Authors: Choi Won-Seok , Roh Beop-rae , Jon Duk-In , Ryu Vin , Oh Yunhye , Hong Hyun Ju 
Published: February 2024

Abstract

Background
This study aimed to determine the existence of spatiotemporal clustering in adolescent suicides in Korea and to identify any differences between clustered and non-clustered suicide cases using novel statistical methods.
Methods
From 2016 to 2020, the dates and locations, including specific addresses from which the latitude and longitude of all student suicides (aged 9–18 years) in Korea were obtained through Student Suicide Reports. Sociodemographic characteristics of the adolescents who died by suicide were collected, and the individual characteristics of each student who died by suicide were reported by teachers using the Strengths and Difficulties Questionnaire (SDQ). Density-Based Spatial Clustering of Applications with Noise (DBSCAN) analysis was used to assess the clustering of suicides.
Results
We identified 23 clusters through the data analysis of 652 adolescent suicides using DBSCAN. By comparing the size of each cluster, we identified 63 (9.7%) spatiotemporally clustered suicides among adolescents, and the temporal range of these clusters was 7–59 days. The suicide cluster group had a lower economic status than the non-clustered group. There were no significant differences in other characteristics between the two groups.
Conclusions
This study attempts to define the spatiotemporal clustering of suicides using a novel analytical method. Although clustering has been identified in adolescent suicides in Korea, the specificity of clustered suicides is limited. An enhanced understanding of the underlying mechanisms driving clustered suicides among adolescents has the potential to contribute to adolescent suicide prevention efforts.
Left colectomy for diverticular disease - systematic review and meta-analysis comparing robotic and laparoscopic resections
Authors: Eltyeb Hazim A , Mohamedahmed Ali Yasen Y , Mills Graham A , Khan Jim 
Published: February 2024

Abstract
Backgroud:
Diverticular disease affects approximately 50% of the population aged ≥ 60 and above. Twenty-five % will require surgical intervention. We aimed to compare the outcomes of left colonic resectionfor sigmoid diverticular disease by robotic and laparoscopic approaches. Our primary aim was to conduct a meta-analysis and to investigate conversion to open, stoma and complication rates between the two approaches.
Methodology:
A systematic review was performed according to the PRISMA guidelines. A meta-analysis was conducted using RevMan Version 5.4 software. Dichotomous outcomes were pooled with a random-effect model to estimate risk and odds ratios (OR). Prospero (reg # CRD42023440509).
Results:
Eight studies were thought to fulfil the eligibility criteria: 1,892 patients (49.2%) had robotic surgery, and 1,952 patients (50.84%) underwent a laparoscopic approach. There were fewer conversions to open surgery in the robotic group when compared to the laparoscopic group, [P < 0.00001] less rate of post-operative ileus [P = 0.005], less length of stay [mean difference (MD) - 0.18 P = 0.003] and fewer morbidities [P = 0.002]. There were similar rates of stoma formation [4.7%, P = 1.00], anastomotic leak [2.6% P = 0.85] and mortality [0.3% versus 0.2%, P = 0.59]. Although not significant, a shorter operative time in the robotic approach [P = 0.47].
Conclusion:
Compared to laparoscopic left colectomy, robotic surgery is feasible, with a reduction in conversion to open rate, reduced morbidity, less ileus and similar rates of stoma formation, anastomotic leak and mortality. Further high-quality research needs to be done to investigate this further.
Mobile outreach clinics for improving health care services accessibility in vulnerable populations of the Diffa Region in Niger: A descriptive study.
Authors: Rabiou Lawali Mahaman , Oumarou Batoure , Mor Diaw , Abdou Maman , Ibrahim Camara , Tamuzi Jacques Lukenze , Katoto Patrick D. M. C. , Wiysonge Charles S. , Anya Blanche-Philomene Melanga 
Published: February 2024

Abstract

Background
Niger is a large country with many distant locations that can be difficult to access because the Sahara Desert covers 80% of the country's land. In Niger, just 49% of residents have access to a health centre within 5 km of their house. Health care may be difficult to access in the Diffa region of Niger, as non-state armed groups strike on a regular basis and floods cause a high rate of vulnerability. This study looked at how mobile clinics can improve healthcare accessibility for vulnerable populations in the Diffa region.
Methods
This was a descriptive cross-sectional, population-based study conducted over the period from 15 August 2022 to 15 October 2022, using three months’ mobile outreach clinic to improve health outcomes in five districts of the Diffa region, including Bosso, Diffa, Goudoumaria, Mainé Soroa, and N’guigmi.
Results
During the three months of mobile outreach clinic, 42251 people were sensitized and 12004 were treated. A total of 18,708 vaccine doses were delivered to children aged 0–11 months, with Maine Soroa, Goudoumaria, Bosso, Diffa, and N’guigmi districts accounting for 29.24%, 24.62%, 18.54%, 18.05%, and 9.5%, respectively. In the same line, Goudoumaria, Bosso, and Maine Soroa districts recorded relatively high antenatal clinic (ANC) attendance percentages of 27.85%, 25.62%, and 21.89%, respectively. Furthermore, mobile clinic outreach provided a variety of healthcare treatments, both curative and preventative. Mobile Clinic 2 increased vaccine dose received among children aged 0–11 months by 1.11% (95%CI: 0.15%-2.06%, P = 0.023) when compared to Mobile Clinic 1. In the same line, mobile clinic showed a statistically significant increase of ANC between the three clinical rotations (P = 0001), showing an increased ANC update over time.
Conclusion
This study found that mobile outreach clinic can play an important role in improving healthcare access for vulnerable populations in the Diffa region. However, well-designed, and frequent mobile clinic outreach should be planned and included in the country's public health policy.
Two – Dimensional Reynolds Equation for Squeeze film lubrication between wide parallel rectangular plates with the effect of Magnetic field and Micro – Polar fluid
Authors: S Asha B. , M Shivakumar H. , N Hanumagowda B. , H Brinda , R Vasanth K 
Published: February 2024

Abstract
This investigation aims to provide a thorough mathematical analysis to examine the behavior of squeezing films that consist of a micropolar fluid lubricant. These films are situated between wide, parallel, rectangular plates while being subjected to a transverse magnetic field. Hydromagnetic flow theory is used to analyze the impact of MHD considerations on squeezing with micropolar fluids on smooth surfaces. The modified Reynolds equation is the fundamental equation applied to explain the behaviour of fluids in thin films, and it is responsible for estimating the pressure distribution of the film area. The effects of the MHD and micropolar lubricant on the bearing characteristics are discussed. Lubrication characteristics are determined as functions of micropolar fluid, Hartmann number, fluid gap number, coupling number, and aspect ratio parameters. When compared to a classical case, the magnetic field and micropolar fluid provide more significant bearing characteristics. As the Hartmann number, fluid gap number, and coupling number are increased, the improved characteristics become more evident.
Test Scenario Generation from Nested ConcurrentActivity Diagrams
Authors: Shirole Mahesh , Kumar Rajeev 
Published: February 2024

Abstract
UML is a de-facto standard for system and test cases design, yet test scenariogeneration for concurrent systems is challenging due to constructs such as forkjoinand their nesting. Systematically exploring complete interleaving space ofsuch test scenarios is an exponential task. Existing activity diagram test scenariogeneration algorithms explore a restricted interleaving space, which maybe insufficient to uncover most concurrency errors. Therefore, in this work, weuse evolutionary search for exploring wider interleaving space from concurrentactivity diagrams. The naive evolutionary search yields many infeasible interleavingpaths, therefore, we design evolutionary search operators, traversals andfitness functions, using graph-theoretic domain knowledge, for optimizing functionvalues with constraint satisfaction for feasible interleaving paths. We presentevolutionary and hybrid evolutionary search algorithms for generating concurrenttest scenarios from activity diagrams. We have observed, empirically, that evolutionarysearch satisfies 5-50% interleavings activity path coverage at the costof higher convergence time. However, such high convergence time is significantlyreduced in the range of 40-50% using hybrid evolutionary search with the samecoverage.
Comparative Evaluation of the Encapsulating Lens on the Depreciation of the Lumen of High Power Pcleds in Tropical Conditions
Authors: CHAKRABORTY ARINDAM , Datta Swarnabha , Mukherjee Chiradeep , Ganguly Rajiv , Mitra Monojit 
Published: February 2024

Abstract

With the current technological growth, the demand for lighting has increased in indoor as well as outdoor application. To meet such huge expectations, Light emitting diodes (LEDs) are inclining towards energy-efficient illumination. However, the useful life of commercially available LEDs is an important parameter. Gradually after passage of time, depreciation in lumen output of LEDs is observed. There are several factors responsible for such degradation in output. One of the reasons is due to bulging of encapsulating lens used on high power pcLEDs. This research discusses the role of encapsulating wafer on LEDs discussing the useful lifetime characteristics of high power pcLEDs. This is an emerging field that combines physics, materials science, device technology and industry. We discuss the effect of lens through systematic observations and calculations are made from the lumen depreciation characteristic graph.
Total Knee Replacement In A Patient Of Pseudogout: A Rare Case Report
Authors: Meena R P , Karir Ekaansh , Meena Umesh Kumar , Kumar Anand 
Published: February 2024

Abstract
TKR in patients suffering from pesudogout of the knee is a rare phenomenon.Crystalline arthropathies are characterized by the deposition of crystals within a synovial membrane or joint cavity. The patient had bilateral knee pain for 5 years associated with swelling and hypertension for 2 years and was recently diagnosed with hepatitis B. The patient had no other relevant history.
The patient was provisionally diagnosed with B/L osteoarthritis of the knee. Since the patient was willing to undergo surgery for only one joint, total knee replacement was performed on the left knee joint, and a biopsy was sent for investigation, which revealed pesudogout. The patient was started on NSAIDS. Postoperatively, the patient recovered 90% of his normal ROM and developed no complications. These findings show that patients with arthritis due to pseudogout can be treated with total knee arthroplasty surgeries.
3D Printing of Ceffe-Infused Scaffolds for Tailored Nipple-Like Cartilage Development
Authors: Ding Jinghao , Wei Chuanzhi , Xu Yong , Dai Wufei , Chen Ru 
Published: February 2024

Abstract

The reconstruction of a stable, nipple-shaped cartilage graft that precisely matches the natural nipple in shape and size on the contralateral side is a clinical challenge. While 3D printing technology can efficiently and accurately manufacture customized complex structures, it faces limitations due to inadequate blood supply, which hampers the stability of nipple-shaped cartilage grafts produced using this technology. To address this issue, we employed a biodegradable biomaterial, Poly(lactic-co-glycolic acid) (PLGA), loaded with Cell-Free Fat Extract (Ceffe). Ceffe has demonstrated the ability to promote angiogenesis and cell proliferation, making it an ideal bio-ink for bioprinting precise nipple-shaped cartilage grafts. We utilized the Ceffe/PLGA scaffold to create a porous structure with a precise nipple shape. This scaffold exhibited favorable porosity and pore size, ensuring stable shape maintenance and satisfactory biomechanical properties. Importantly, it could release Ceffe in a sustained manner. Our in vitro results confirmed the scaffold's good biocompatibility and its ability to promote angiogenesis, as evidenced by supporting chondrocyte proliferation and endothelial cell migration and tube formation. Furthermore, after 8 weeks of in vivo culture, the Ceffe/PLGA scaffold seeded with chondrocytes regenerated into a cartilage support structure with a precise nipple shape. Compared to the pure PLGA group, the Ceffe/PLGA scaffold showed remarkable vascular formation, highlighting the beneficial effects of Ceffe. These findings suggest that our designed Ceffe/PLGA scaffold with a nipple shape represents a promising strategy for precise nipple-shaped cartilage regeneration, laying a foundation for subsequent nipple reconstruction.
Did The Regulation of Abortion Affect Stability of Marriage? The Effect of State Abortion Restrictions on Marital Dissolution
Authors: Deng Haihan 
Published: February 2024

Abstract

I estimate the effects of abortion restrictions from gestational limits, parental involvement for minors, and length of mandated waiting period on state divorce rate and change of marital status for individual to test whether the abortion regulation affects stability of marriage. From the state-level analysis, I found liberalized abortion restrictions are associated with higher state divorce rates. From the individual-level analysis, the effect only appears to be significant for younger groups and is the opposite direction of implication when compared to the state-level analysis. Furthermore, a new insight from the individual-level analysis suggests that additional abortion restrictions might stress younger couples and therefore increase their risks of divorce, even if some of the policies do not directly apply to them. Moreover, this paper also shows that having more children tends to strengthen the stability of marriage and reduces the risk of divorce, which is consistent with previous studies, as well as presenting additional supportive evidence.
JEL classification: J12, K36
The GLCCI1/STAT3 pathway: A novel pathway involved in diabetic cognitive dysfunction and the therapeutic effect of salidroside
Authors: Niu Lin , Xu Min , Liu Wenqiang , Li Fuzhi , Wang Teng , Sun Die , Yao Tiefeng , Li Wanze , Yang Zhengzhong , Liu Xuezheng , Zuo Zhongfu 
Published: February 2024

Abstract
Diabetic cognitive dysfunction (DCD) is a complication of diabetes that seriously affects quality of life. Glucocorticoid-induced transcript 1 (GLCCI1) has been found to be involved in inflammation, apoptosis and autophagy in various diseases. However, the distribution of GLCCI1 in the brain and its role in DCD have not yet been revealed. In addition, the potential therapeutics effects of salidroside (SAL), a phenyl propyl glycoside compound known for its neuroprotective effects in treating DCD are unknow. In the present study, we found that GLCCI1 was localized in hippocampal neurons. C57BL/6J mice with DCD presented downregulation of GLCCI1 and Bcl-2 and upregulation of p-STAT3, Bax, Caspase-3 and Cleaved Caspase-3. Overexpression of GLCCI1 or SAL administration relieved DCD, reversed the changes in the expression of these cytokines, and alleviated morphological alterations in hippocampal neurons. Interestingly, SAL alleviated DCD and attenuated the expression of GLCCI1 and p-STAT3, showing similar effects as GLCCI1 overexpression. These findings suggest that the GLCCI1/STAT3 axis plays a crucial role in DCD and is involved in SAL-mediated attenuation of DCD.
A Machine Learning Method for Early Stewardship of Invasive Mechanical Ventilation in Patients with Sepsis
Authors: Liu Wanjun , Xiao Wenyan , Zhang Jin , Hu Juanjuan , Huang Shanshan , Liu Yu , Hua Tianfeng , Yang Min 
Published: February 2024

Abstract
Background
Heterogeneity among mechanically ventilated patients with sepsis makes it challenging to define appropriate treatments. This study aimed to establish a method for identifying high-risk patients in this vulnerable population. To this end, unsupervised machine learning models were used to analyze a large volume of real-world clinical data for determining prognosis in these patients at an early stage.
Methods
The Intensive Care Medical Information Database IV (MIMIC-IV; version 2.0) was used to generate training and test sets. Three datasets were used for further validation: the Intensive Care Medical Information Database III (MIMIC-III, version 1.4), Philips eICU Collaborative Research Database (eICU-CRD; version 2.0), and a local set from the Second Affiliated Hospital of Anhui Medical University.
Results
In the training, test, MIMIC-III, eICU-CRD, and local sets, approximately 9571, 1595, 4821, 6624, and 110 patients, respectively, diagnosed with sepsis who received invasive mechanical ventilation (IMV) on the first day of intensive care unit (ICU) admission were found. Three unique clinical phenotypes were derived based on the training set and were named phenotypes I, II, and III according to the order of clustering results. Patients with phenotype I had a 28-day mortality rate higher than 30% and characteristically presented with concurrent respiratory and circulatory dysfunction, whereas patients with other phenotypes had a better prognosis.
Conclusions
This retrospective exploratory study identified three unique phenotypes in patients with sepsis undergoing mechanical ventilation. These three phenotypes were distinctive and suggested that patients assigned phenotype I are a high-risk group, warranting focused attention during the early ICU stage.