bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human transporter de-oligomerization regulates copper uptake into cells
Authors: Chen Tai-Yen , Wen Meng-Hsuan , Chen Huanhuan , Yan Guangjie , Zhang Yuteng , Chen Wenkai , Dokholyan Martin , Wang Jian , Dokholyan Nikolay 
Published: December 2024

Abstract

Copper is an essential element involved in various biochemical processes, such as mitochondrial energy production and antioxidant defense, but improper regulation can lead to cellular toxicity and disease. Copper Transporter 1 (CTR1) plays a key role in copper uptake and maintaining cellular copper homeostasis. Although CTR1 endocytosis was previously thought to reduce copper uptake when levels are high, it was unclear how rapid regulation is achieved. Using single-molecule localization microscopy and single-molecule neighbor density assays, we discovered that excess copper induces monomerization of the wild-type trimeric CTR1 prior to endocytosis, a response blocked in the endocytosis-deficient CTR1 (M150L) mutant. This monomerization rapidly halts copper uptake and prevents copper overload. These findings reveal changes in protein oligomerization as a new paradigm of metal transport regulation, linking CTR1's structural changes to its endocytosis and copper homeostasis.
Discovery and language model-guided design of hyperactive transposase
Authors: Güell Marc , Ivančić Dimitrije , Agudelo Alejandro , Lindstrom-Vautri Jonathan , Jaraba-Wallace Jessica , Gallo Maria , Ragel Alejandro , Higueras Irene , Billeci Federico , Sanvicente Marta , Petazzi Paolo , Ferruz Noelia , Sánchez-Mejías Avencia , Das Ravi 
Published: December 2024

Abstract

The PiggyBac transposase gene writing system has been efficiently used across biotechnological applications, however its diversity and biochemical potential remain largely unexplored. By developing a eukaryotic transposon mining pipeline, we expand the known diversity by two orders of magnitude and experimentally validate a subset of highly divergent PiggyBacs. We then fine tune a protein language model to further expand PiggyBac sequence space and discover transposons with improved activity, compatible with T-cell engineering and Cas9-guided programmable transposition. Our work illustrates how combining bioprospecting and AI-driven sequence exploration can accelerate the discovery of novel eukaryotic gene writing tools.
Design of robust networks via reinforcement learning prompt the emergence of multilayer backbones
Authors: Li Daqing , Zhu Bingyu , Zhu Tianchen , Gao Jianxi , Havlin Shlomo 
Published: December 2024

Abstract

Network robustness design is a significant engineering task in complex systems including urban planning, communication programming, and chip designing. With the embedded vulnerability of complex networks, the relationship between network topology and its robustness remains unknown, presenting a significant challenge in designing robust networks. Existing approaches—ranging from empirical manual designs, statistically-driven rules to optimization via Monte Carlo simulations, struggle to meet the design demands of large-scale networks under multidimensional attacks. Here, we introduce a general framework for designing robust networks based on AI reinforcement learning. This framework establishes an interactive environment between network attack strategies and design models, enabling the learning of effective robustness design strategies against specific attacks. Our framework enables efficient design of robust large-scale networks for a given cost, surpassing existing methods. Notably, we find that during the design process, the network may develop suitable multilayer backbones that mitigate its current vulnerability, offering insight into higher-order relations in real-world networks. Our approach can be adopted to various network design scenarios, which provides an integrative intelligent solution for designing robust complex systems.
Association of KRAS and TERT Genetic Variants with Opioid Dependence in a Large Clinical Cohort
Authors: Cuomo Raphael E. 
Published: December 2024

Abstract

Introduction:
The present exploratory study seeks to showcase an approach to uncover potential genetic associations predisposing individuals to opioid dependence, in which a large clinical database is utilized to compare results of testing for genetic variants with clinical diagnoses of opioid dependence.
Methods
Employing a STROBE-compliant study design, this research leveraged the UC Health Data Warehouse, an OMOP CDM-compliant database with EHR data from six University of California academic health centers. Utilizing SQL queries embedded in Python scripts with the Spark framework, the study extracted genetic data, focusing on individuals tested for specific genetic variants.
Results
Rates of detection for nine genes were evaluated between 222 patients with opioid dependence and 20141 patients without, revealing significantly decreased odds of opioid dependence for individuals with the TERT gene (OR = 0.61, p = 0.010) and significantly increased odds for individuals with the KRAS gene (OR = 1.45, p = 0.014). Significant associations persisted after adjusting for demographics.
Conclusions
The discovery of KRAS and TERT associations with opioid dependence in our study highlights the intricate genetic landscape of this condition. This study, in triangulation with findings from GWAS and other designs, may pave the way for more personalized approaches to prevention and treatment of opioid dependence.
Understanding the plant food spectrum at the Jiangzhuang site of the Liangzhu culture (5300–4300 BP) through a starch grain analysis of human dental calculus
Authors: Yin Yitong , Zou Huilin , Gan Huiyuan , Zhu Xiaoting , Tao Dawei 
Published: December 2024

Abstract

The Liangzhu culture (5,300-4,300 BP) is an important archaeological culture in late Neolithic period in the lower reaches of the Yangtze River, which has entered the stage of an early state. To better understand ancient societies of the Liangzhu culture, the comprehensive studies on the subsistence of the Liangzhu culture is necessary. Until date, many multidisciplinary studies have been conducted on the Liangzhu culture, including archaeobotanical research, which mainly focused on the core area of the Liangzhu culture, and relatively limited archaeobotanical studies were conducted in the non-core area of the Liangzhu culture including the eastern Jianghuai region, where the Jiangzhuang site is located. In this study, a starch grain analysis was conducted on human dental calculus samples belonging to the Liangzhu period from the Jiangzhuang site. A variety of starch grains were extracted from these dental calculus samples, including crops of rice (Oryza sativa) and millets, and wild plants such as Triticeae, Coix sp., Fabaceae, acorns, and roots/tubers, which revealed diverse plant-based consumption by Jiangzhuang inhabitants. Significantly, some newly recognized edible plant species revealed by the starch residue entrapped in the human dental calculus broaden the understanding of plant food spectrum during the Liangzhu period at the Jiangzhuang site. This research reveals broad-spectrum plant consumption in a large settlement located in the non-core area of the Liangzhu culture, and provides new evidence for comprehensive understanding of subsistence patterns in different regions of the Liangzhu culturedistribution area.
Comparing the Performance of IRI-2020 and AfriTEC Ionospheric Models Over East Africa In Case Of Ethiopia During Disturbed Time
Authors: Bagaje Melaku Belayneh 
Published: December 2024

Abstract

This study evaluates the performance of IRI-2020 and AfriTEC ionospheric models in predicting Total Electron Content (TEC) variations during geomagnetically disturbed time over East Africa in the case of Ethiopia. In equatorial places like Ethiopia, the geomagnetic disturbance of the ionosphere can cause significant changes during disturbed time, which could lead to inaccurate position and timing data in satellite navigation and communication systems. For Ethiopian sectoral radio long-distance transmission, it is significant that the electron density can fluctuate diurnally, monthly and seasonally due to variations in the height and peak density of the F-region. To minimize this problem, we use the IRI-2020 model, the AfriTEC model, and GPS-TEC data. The IRI-2020 model data predicted from the instant run version, the AfriTEC model data predicated MatLab toolbox, and GPS-derived TEC data were obtained from the IGS network of ground-based dual-frequency GPS receivers from five Ethiopian sectors. By using geomagnetic parameters from Omniweb data sources, particularly the DST index ranging from -70 to 20 nT for 2016. The results show a consistent daily and monthly correlation between the estimated TEC from both models and the GPS-TEC, with notable seasonal variations. While the models demonstrated good agreement across all seasons, discrepancies were observed in December and June. Seasonal equinox and solstice periods were particularly analyzed, with AfriTEC showing an overestimation of TEC by 3 to 50 TECU in April, yet having a lower root mean square error (RMSE) of 0.36 compared to IRI-2020. Finally, the diurnal, monthly, seasonal statistical RMSE values indicate that the IRI-2020 RMSE is a maximum error and the AfriTEC RMSE is the minimum error value. Therefore, the evidence shows that the AfriTEC ionospheric model gives a better prediction of the TEC at Ethiopian sectors and shows its superior performance in capturing ionospheric behavior during disturbed periods.
Light Use Efficiency (LUE) based bimonthly Gross Primary Productivity (GPP) for global grasslands at 30 m spatial resolution (2000-2022)
Authors: Isik Mustafa Serkan , Parente Leandro , Consoli Davide , Sloat Lindsey , Mesquita Vinicius , Ferreira Laerte Guimaraes , Sabbatini Simone , Stanimirova Radost , Teles Nathália , Robinson Nathaniel , Junior Ciniro Costa , Hengl Tomislav 
Published: December 2024

Abstract

The paper describes production of a high spatial resolution (30 m) bimonthly Light Use Efficiency (LUE) based Gross Primary Productivity (GPP) data set representing grasslands for the period 2000 to 2022. The data set is based on using reconstructed global complete consistent bimonthly Landsat archive (400TB of data), combined with 1 km MOD11A1 temperature data and 1o CERES Photosynthetically Active Radiation (PAR). First, the LUE model was implemented by taking the biome-specific productivity factor (maximum LUE parameter) as a global constant, producing a global bimonthly (uncalibrated) productivity data for the complete land mask. Second, the GPP 30 m bimonthly maps were derived for the global grassland annual predictions and calibrating the values based on the maximum LUE factor of 0.86 gCm-2d-1MJ-1. The results of validation of the produced GPP estimates based on more than 500 eddy covariance flux towers show an R2 between 0.48-0.71 and RMSE bellow ~2.3 gCm-2d-1 for all land cover classes; for grasslands the RMSE was 1.53 gCm-2d-1. The final time-series of maps (uncalibrated and grassland GPP) are available as bimonthly (daily estimates in units of gCm-2d-1) and annual (daily average accumulated by 365 days in units of gCm-2yr-1 ) in Cloud-Optimized GeoTIFF (~23TB in size) as open data (CC-BY license). The recommended uses of data include: trend analysis e.g. to determine where are the largest losses in GPP and which could be an indicator of potential land degradation, crop yield mapping and for modeling GHG fluxes at finer spatial resolution. Produced maps will be made available via the SpatioTemporal Asset Catalog (http://stac.openlandmap.org) and Google Earth Engine upon publication. In the meantime, beta versions of the product can be accessed through the Global Pasture Watch Early Access data program (https://survey.alchemer.com/s3/7859804/Pasture-Early-Adopters), which provides data in exchange for feedback.
From eco-industrial parks to circular-industrial parks: developing new industrial parks for new business models
Authors: coussa Alexandre 
Published: December 2024

Abstract

This study introduces the understudied concept of circular industrial parks (CIPs), which extend the commonly acknowledged initial role of eco-industrial parks (EIPs) in waste management and energy efficiency. CIPs give a new perspective on EIPs literature by integrating circular business models (CBMs) related to broader aspects of the circular economy (CE), while promoting collaboration with local communities to enhance social, environmental, and economic outcomes. By applying the Sustainable Value Framework (SVF) and the UNIDO EIPs framework, this study provides a comprehensive analysis of how CIPs create value, the strategic stakes for practitioners and policy makers, and a roadmap for their development. The study concludes that CIPs have the potential to drive CE at the local level differently from traditional EIPs and provides actionable strategies for practitioners and policymakers to facilitate their success. They enable the clustering of businesses committed to CE and facilitate the development of new CBMs by providing space for collaboration, innovation, resilience and improved infrastructure for energy and resource use at costs that would be difficult to achieve independently. CIPs also increase the visibility of CBMs within their region and strengthen the role of CE by serving as local hubs for the distribution of resources and goods. This research contributes to the academic and practical understanding of CIPs and opens avenues for further exploration and field studies. While further field studies are needed, CIPs are seen as powerful catalysts for CE and industrial symbiosis.
Intuition & the Expert Neuroscience Nurse
Authors: Evans Vicki 
Published: December 2024

Abstract
Personal knowledge is a process whereby practice and research evolve simultaneously. Therefore, knowledge evolves with practice. It is a personal process, thus it creates a difficulty when identifying appropriate research methods of objectivity and analysis. Many researchers discount intuition as it is not an analytical process and cannot be studied. Rather, it is associated and absorbed through experience. Expert nurses integrate both intuitive knowledge and scientific development of intuitive skills, thereby enhancing the quality of practice. Today, scholars are beginning to understand the importance and value of expert intuition, especially in the neuroscience arena. It is this personal knowledge and intuition of expert neuroscience nurses that is the focus of this paper.
Perencanaan Manajemen Kewirausahaan Pesantren: Studi Kasus pada SMA Madina Citra Insani Boarding School Kota Samarinda
Authors: Intitsal Amiratul Fadilah , Khojir Khojir 
Published: December 2024

Manajemen kewirausahaan pesantren didefinisikan sebagai kegiatan yang mengatur dan mengelola wirausaha di antara anggota masyarakat pesantren dengan tujuan meningkatkan produktivitas dan kreativitas para santri. SMA Madina Citra Insani Boarding School Kota Samarinda memiliki ciri khas dalam pengelolaan kewirausahaan yang melibatkan partisipasi aktif komunitas sekolah. Jenis penelitian ini adalah studi kasus dengan pendekatan penelitian kualitatif. Sumber data dalam penelitian ini ialah kepala sekolah, Waka Kesiswaan, pengelola unit usaha, dan pengurus osis. Teknik pengumpulan data menggunakan teknik observasi, wawancara semi terstruktur, dan dokumentasi. Teknik analisis data menggunakan model Miles, Huberman, dan Saldana yang meliputi tahap pengumpulan data/penyediaan data, kondensasi data, penyajian data dan pengambilan kesimpulan. Sedangkan uji keabsahan data menggukan teknik triangulasi. Hasil penelitian didapatkan Planning program kewirausahaan setiap usaha dirancang dengan cermat untuk memastikan keselarasan dengan kebutuhan santri seperti menyediakan produk yang halal dan sehat, serta kelengkapan santri dan kebutuhan guru seperti usaha tanam saham. Perencanaan ini di lakukannya rapat bersama kepala sekolah dan karyawan sekolah untuk pembentukan unit usaha dengan adanya peluang yang akan di buka di sekolah, selanjutnya di pilih penanggung jawab setiap unit usaha yang di bentuk di sekolah.
Optimization of water distribution networks using simulated annealing (SA) with variable neighbourhood search (VNS): a case study in the city of Malard
Authors: Jandaghi Hossein , Haghgoo Ahmad , Tavakoli Moghadam Mahtab 
Published: December 2024

ABSTRACT

Water distribution networks (WDNs) are essential for modern cities, as effective design can reduce construction costs and ensure reliable service. As cities expand, optimizing these large networks becomes increasingly complex. In this work, we introduce a novel approach by combining simulated annealing (SA) with variable neighbourhood search (VNS) into a single heuristic algorithm for WDN optimization, marking the first use of the SA-VNS method in this context. Additionally, we apply Taguchi's design of experiments (DOE) to tune the parameters of the SA-VNS algorithm specifically for water networks. We tested our new algorithm on four standard benchmark networks and a real-world WDN, including a case study of a large city. Our results demonstrate that the SA-VNS algorithm outperforms existing methods in terms of cost, speed, and overall effectiveness, making this research a significant advancement in both heuristic methods and parameter-tuning techniques for WDN optimization.
Assessing the suitability of water for irrigation purposes using irrigation water quality indices in the Irob catchment, Tigray, Northern Ethiopia
Authors: Abadi Haile Tadelle , Alemayehu Tewodros , Berhe Berihu Abadi 
Published: December 2024

ABSTRACT

Irrigation alleviates poverty in arid and semi-arid regions, such as Ethiopia, necessitating a water suitability assessment. This study evaluates irrigation water quality in the Irob catchment, Northern Ethiopia. It differs by using combined parameters of the irrigation water quality index (IWQI) for comprehensive assessment beyond standard comparisons. Eighteen water samples were collected and analyzed using ultraviolet spectrometry, titration, and atomic absorption spectrometry. The evaluation considered electrical conductivity (EC), total dissolved solids (TDS), total hardness (TH), sodium adsorption ratio, sodium percentage, residual sodium carbonate, permeability index, magnesium ratio, Kelley's index, potential salinity, and the IWQI. The findings revealed that 22.2, 38.9, 88.8, 66.7, 83.3, 66.7, 100, 72.2, and 55.6% of samples exceeded recommended standards for EC, TDS, TH, permeability index, manganese, cobalt, copper, cadmium, and nickel, respectively. Most water quality parameters meet standards, but improved irrigation management is crucial to reduce risks. The IWQI indicates that 22.2% of water samples have minor restrictions, while 77.8% have no restrictions. This method provides key insights for evaluating irrigation water quality in similar hydrogeological and environmental conditions, particularly in semi-arid and arid regions. The findings enhance the understanding of sustainable water quality, supporting local authorities in developing resilient irrigation strategies for regional agricultural sustainability.
Acute Suppurative Thyroiditis Caused by Gemella Morbillorum: A Case Report
Authors: Brunetti Alessandro , Cipri Claudia , Sartor Assunta , Bergamin-Bracale Anna Maria , Manso Jacopo , Vescini Fabio 
Published: December 2024

Background:
Acute suppurative thyroiditis (AST) is a rare form of thyroid inflammation
prevalently of bacterial origin that usually affects subjects with risk factors such as immunodeficiency,
sepsis, and neck fistulas. The most prevalent pathogens associated with AST are gram--
positive aerobic bacteria, followed by gram-negatives, while infections by anaerobic germs are exceptionally
rare. Gemella morbillorum is a facultative anaerobic gram-positive bacterium that commonly
populates the upper respiratory tract. Infections by Gemella Morbillorum have been previously
documented in different regions (i.e., lung, brain, bone, liver), but never in the thyroid.

Case presentation:
An 18-year-old male with no previous medical history presented to the emergency
department complaining of a rapidly enlarging painful neck mass in left anterior latero-cervical
region progressively worsening over the last two weeks, accompanied by dysphagia and fever.
Blood tests showed the presence of thyroiditis (suppressed TSH with increased free thyroxine,
elevated inflammation markers and neutrophilic leucocytosis). Neck ultrasonography and CT
showed a large abscess involving the left thyroid lobe and extending to the ipsilateral laterocervical
region, suggesting the diagnosis of AST. Prompt antibiotic therapy was started and subsequent
surgical drainage of the abscess was performed, resulting in a rapid clinical recovery and the restoration
of normal thyroid function. The bacterial culture of the abscess showed exclusively the presence
of Gemella morbillorum.

Conclusion:
We present the first documented case of AST caused by Gemella morbillorum in an
otherwise healthy young man. Although rare, AST in immunocompetent patients is possible;
prompt diagnosis and treatment of this condition are fundamental to avoid severe complications.
GSTP Polymorphism of GSTP1 (rs1695) and its Potential Association with Dental Caries in the Tamil Population
Authors: Sivakumar Kaniha , Subbiah Usha 
Published: December 2024

Background:
Dental caries result from the demineralization of enamel or dentin
caused by acids produced by cariogenic oral bacteria. The Glutathione S-transferase
P1 (GSTP1) is a prominent member of the GST family, and it exhibits several genetic
polymorphisms, with rs1695 being the most common variant.

Aim:
Our study is to investigate the relationship between GSTP1 rs1695 polymorphism
and the susceptibility to dental caries.

Objective:
The study focused on understanding the relationship between GSTP1 rs1695
polymorphisms and susceptibility to dental caries in the Tamil population.

Methods:
SNPs in the GSTP1 missense variant rs1695 (A/G) were analysed by PCR
RFLP. The study group included 100 dental caries with (DMFT >5) and 100 healthy controls
(DMFT=0). Further analysis of the impact of the GSTP1 wild-type gene with the
rs1695 variant on mRNA's secondary structure was conducted using in silico prediction
tools.

Results:
The results showed a significant frequency distribution of the heterozygous AG
genotype (P<0.05). While the genotypic distribution of GSTP1 remained consistent with
Hardy-Weinberg equilibrium (HWE) in the control group (p-value > 0.05), it deviated
from HWE in the caries group. The free energy of the thermodynamic ensemble for the
rs1695 variant was calculated to be -186.20 kcal/mol. This lower free energy, compared
to the wild-type, indicates that the variant is more stable.

Conclusion:
Our findings indicate that GSTP1 rs1695 variants could enhance susceptibility
to dental caries by suggesting genetic load as a possible risk factor. However, additional
functional research and larger studies are required to confirm these results.