bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plasmodium falciparum drug resistance-associated mutations in isolates from children living in endemic areas of Burkina Faso
Authors: Casimire Tarama Wendlamita , Harouna Soré , Mafama Siribié , Siaka Débé , Réné Kinda , Adama Ganou , Gérard Nonkani , Farida Tiendrebeogo , Winnie Bantango , Kassoum Yira , Aladari Sagnon , Sonia Ilboudo , Esther Hien Yéri , Moussa Guelbéogo Wandaogo , NFale Sagnon , Yves Traoré , Didier Menard , Adama Gansané 
Published: March 2023

Abstract
Introduction. Artemisinin-based combinations (ACT) are the current frontline curative therapy for uncomplicated malaria in Burkina Faso. Sulfadoxine-pyrimethamine (SP) is used for the preventive treatment of pregnant women (IPTp) while SP plus amodiaquine (SP-AQ) is recommended for children under five in seasonal malaria chemoprevention (SMC). This study aimed to assess the proportions of mutations in the Pfdhfr, Pfdhps, and Pfmdr1 genes from isolates collected during household surveys in Burkina Faso.
Methods. Dried blood spots from Plasmodium falciparum-positive cases at three sites (Orodara, Gaoua, and Banfora) collected during the peak of transmission were analyzed for mutations in Pfcrt (codons 72-76, 93, 97, 145, 218, 343, 350 and 353), Pfmdr-1 (codons 86, 184, 1034, 1042 and 1246) dhfr (codons 51, 59, 108, 164) and dhps (at codons 431, 436, 437, 540, 581, 613) genes using deep sequencing of multiplexed PCR amplicons.
Results. Of the 377 samples analyzed, 346 (91.7%), 369 (97.9%), 368 (97.6%), and 374 (99.2%) were successfully sequenced for Pfcrt, Pfmdr-1, dhfr, and dhps, respectively. Most of the samples had a Pfcrt wild-type allele (89.3%). The 76T mutation was below 10%. The most frequent Pfmdr-1 mutation was detected at codon 184 (Y>F, 30.9%). The single mutant genotype (NFSND) predominated (66.7%), followed by the wild-type genotype (NYSND, 30.4%). The highest dhfr mutations were observed at codon 59R (69.8%), followed by codons 51I (66.6%) and 108N (14.7%). The double mutant genotype (ACIRSI) predominated (52.4%). For mutation in the dhps gene, the highest frequency was observed at codon 437K (89.3%), followed by codons 436A (61.2%), and 613S (14.4%). The double mutant genotype (IAKKAA) and the single mutant genotype (ISKKAA) were predominant (37.7 % and 37.2 %, respectively). The most frequent dhfr/dhps haplotypes were the triple mutant ACIRSI/IAKKAA (23%), the wild-type ACNCSI/ISKKAA (19%) and the double mutant ACIRSI/ISKKAA (14%). A septuple mutant ACIRNI/VAKKGA was observed in 2 isolates from Gaoua (0.5%).
Conclusion. The efficacy of ACT partner drugs and drugs used in IPTp and SMC does not appear to be affected by the low proportion of highly resistant mutants observed in this study. Continued monitoring, including molecular surveillance, is critical for decision-making on effective treatment policy in Burkina Faso.
A MATLAB toolbox to fit and forecast growth trajectories using phenomenological growth models: Application to epidemic outbreaks
Authors: Chowell Gerardo , Bleichrodt Amanda , Dahal Sushma , Tariq Amna , Roosa Kimberlyn , Hyman James M. , Luo Ruiyan 
Published: March 2023

Abstract
Background
Simple dynamic modeling tools can be useful for generating real-time short-term forecasts with quantified uncertainty of the trajectory of diverse growth processes unfolding in nature and society, including disease outbreaks.
Results
In this tutorial-based primer, we introduce and illustrate a user-friendly MATLAB toolbox for fitting and forecasting time-series trajectories using phenomenological dynamic growth models based on ordinary differential equations. This toolbox is accessible to various audiences, including students training in time-series forecasting, dynamic growth modeling, parameter estimation, parameter uncertainty and identifiability, model comparison, performance metrics, and forecast evaluation, as well as researchers and policymakers who need to conduct short-term forecasts in real-time. The models included in the toolbox capture exponential and sub-exponential growth patterns that typically follow a rising pattern followed by a decline phase, a common feature of contagion processes. Models include the 2-parameter generalized-growth model, which has proved useful to characterize and forecast the ascending phase of epidemic outbreaks, as well as the 3-parameter generalized logistic-growth model and the Richards model, which have demonstrated competitive performance in forecasting single peak outbreaks.
The toolbox provides a tutorial for forecasting time-series trajectories that include the full uncertainty distribution, derived through parametric bootstrapping, which is needed to construct prediction intervals and evaluate their accuracy. Functions are available to assess forecasting performance across different models, estimation methods, error structures in the data, and forecasting horizons. The toolbox also includes functions to quantify forecasting performance using metrics that evaluate point and distributional forecasts, including the weighted interval score.
Conclusions
As a contagion process takes off, the tools in the presented toolbox can facilitate policymaking to guide the implementation of control strategies and assess the impact of interventions. The toolbox functionality is demonstrated through various examples, including a tutorial video, and is illustrated using weekly data on the monkeypox epidemic in the USA.
Coordinated transcriptional waves and changes in abundant lncRNAs define the inflammatory response of primary microglial culture
Authors: Linial Michal , Zohar Keren , Lezmi Elyad , Reichert Fanny , Eliyahu Tsiona , Rotshenker Shlomo , Weinstock-Rosin Marta 
Published: March 2023

Abstract
The primary role of microglia is to maintain homeostasis by effectively responding to various disturbances. Activation of transcriptional programs determines the microglia's response to external stimuli. In this study, we stimulated murine neonatal microglial cells with benzoyl ATP (bzATP) and lipopolysaccharide (LPS) and monitored their ability to release pro-inflammatory cytokines. When cells are exposed to bzATP, a purinergic receptor agonist, a short-lived wave of transcriptional changes occurs. However, only combining bzATP and LPS led to a sustainable and robust response. The transcriptional profile is dominated by induced cytokines (e.g., IL1-a and IL1-b), chemokines, and their membrane receptors. Several abundant long noncoding RNAs (lncRNAs) are induced by bzATP/LPS, including Ptgs2os2, Bc1, and Morrbid, that function in inflammation and cytokine production. Analyzing the observed changes through TNF and NF-kB pathways confirmed that neonatal glial cells exhibit a distinctive expression program in which inflammatory-related genes are upregulated by orders of magnitude. The observed capacity of the microglial culture to activate a robust inflammatory response is useful for studying neurons under stress, brain injury, and aging. We propose the use of a primary neonatal microglia culture as a responsive in vitro model for testing drugs that may interact with inflammatory signaling and the ncRNA regulatory network.
Ten Years Follow-up of Dilatation of Aortic Structures in Fallot type Anomalies
Authors: Kim Woojung , Kwak Jae Gun , Cho Sungkyu , Kim Woong-Han 
Published: March 2023

Abstract
Objectives
Dilatation of the aortic root structures or ascending aorta is often observed in patients with Fallot type anomalies. We tried to find how fast the aortic structures dilate and how to manage this phenomenon.
Methods
Among 801 patients who underwent corrective surgery of Fallot type anomalies, [tetralogy of Fallot (TOF) and Fallot type of double outlet right ventricle (DORV)] from 2004 to 2020, 66 patients who had follow-up cardiac computed tomography angiography (CT) images at least over 5-year interval after the initial CT study were enrolled in this retrospective study. We analyzed the diameters and aortic cross-sectional area/height ratio (AH) of aortic annulus, sinus of Valsalva, sinotubular junction and ascending aorta between initial and follow-up CTs. "Dilatation” was defined as a z-score over 2 in each aortic structure.
Results
The median age at initial and follow-up CTs were 5.9 years (Interquartile range (IQR): 0.4~12.4) and 15.9 years (IQR: 9.3~23.4), respectively. The median CT interval (initial ~ latest CT) was 9.5 years (IQR: 6.6~12.0). Sinus of Valsalva was the aortic structure that dilated the most rapidly (0.94 mm/year) and significantly (32.8 mm at follow-up CT) across the study period. The AH ratio increased significantly in the four aortic structures. Patient’s age was significantly associated with higher AH in follow-up CT. Aortic dilatation was found in 74.2% at initial CT and 86.4% at follow-up CT.
Conclusions
In Fallot type anomalies, the AH ratio of aortic root structures significantly increased over about 9.5 years. The number of the patients diagnosed within the range of aortic dilatation also increased. Shorter interval for regular follow-up should be considered for these young patients because it could reach a significant dilatation in their mid-20s according to our observation in this study.
Investigation of the composition and morphology of raw materials from the Aral Sea region
Authors: Kurbanov Davron , Mylsamy Savithri , Zhou Biao , Babayev Zabibulla , Bazarbayev Rustam , Allaniyazov Atabek , Balakumar S. , Zeng Guanggen , Yakubov Komiljon , Karazhanov Smagul 
Published: March 2023

Abstract
Clay and Clay-based minerals have fascinated attention because of their unique properties and a vast range of applications in innumerable industrial fields. In order to assess the potential applications, six different processed local kaolin-based raw minerals were collected from the Aral Sea region of Uzbekistan, and the total mineralogical properties have been investigated. The result reveals that some significant differences occurred based on the elemental percentage of silica and alumina in all the mineral samples. The presence of corundum, quartz, and kaolinite structural phases of the mineral was determined by XRD studies. At the same time, the FTIR and Raman studies expose the primary peaks which are associated with the functional groups of Al-OH, Al-O, and Si-O in higher-frequency stretching and lower-frequency bending modes. The elemental and chemical compositional (XRF and XPS) analysis demonstrates the presence of major elements (Al, Si, Na, Fe, Ti) in the raw mineral and other metal contaminations (Mg, Ca, S, Cr, Zr). The SEM analysis demonstrates the morphological natureof kaolinite-based raw minerals that can be exploited for industrial purposes.
Radioprotective effects of quercetin and curcumin on hepatotoxicity and nephrotoxicity in male Albino rats
Authors: Ali Said A. , Yassen Noha N. , Azzoz Rady M. , Soliman Saeed M. , Khalil Wafaa M. , El-Hady Amr M. Abd 
Published: March 2023

Abstract
The present study aimed to assess the radioprotective effects of curcumin in combination with quercetin against radiation-induced changes in some histopathological, immunohistochemical, and biophysical parameters. The current study rats had been grouped into control, curcumin, quercetin, gamma irradiated (8 Gy fractionated dose), curcumin pretreated irradiated, quercetin pretreated irradiated, and both curcumin and quercetin pretreated irradiated groups. Gamma radiation exposure resulted in hepatic and renal damage. Administration of curcumin along with quercetin before gamma radiation exposure reduced the liver and kidney damage caused by radiation, demonstrating the radioprotective effects of both curcumin and quercetin antioxidants through free radicals scavenging effects, P53, and TNF-α inhibition, and structural changes measured by Fourier Transform Infrared (FTIR). The cellular damage by gamma radiation is greatly mitigated by administration of curcumin and quercetin before radiation exposure.
Development of a Tumour Metabolism and Immune Microenvironment-Based Prognostic Model for Prognosis and Anti-Cancer Drug Response in Lung Adenocarcinoma
Authors: Xue Fei , Wang Hao , Jiang Tao , Wu Xuanpeng , Chen Nanzheng , Wu Qifei 
Published: March 2023

Abstract
Lung cancer remains the leading cause of cancer-related mortality worldwide, adenocarcinoma stands out as the most prevalent and lethal form. Tumour metabolism plays an important role in malignancy progression. The current stage-based approach falls short in accurately predicting survival and guiding clinical decision-making for patients with lung adenocarcinoma. For our study, we employed data from the TCGA-LUAD cohort as our training dataset, with validation cohorts derived from GSE30219, GSE42127, and GSE72094. Hypoxia, glycolysis, fatty acid metabolism and immune genes were extracted from GSEA and ImmPort database. To develop the model, we carried out univariate Cox regression and LASSO regression analyses, allowing us to classify patients into the low-risk group (LRG) and high-risk group (HRG). The patients categorized into HRG and LRG showed a significant variation in overall survival (OS), HR is 2.21, and an AUC of 0.713, 0.717, and 0.659 for predicting OS at 1, 3, and 5 years, correspondingly. The GSE72094 dataset exhibited an HR of 2.01, with the AUCs for predicting survival at 1, 3, and 5 years being 0.676, 0.669, and 0.465, respectively. In the GSE30219, the AUCs were 0.562, 0.633, and 0.644, while the HR was 2.14. However, the model in the GSE42127 dataset was not able to differentiate between OS in the HRG and LRG, with AUCs of 0.779, 0.565, and 0.578 and an HR of 1.33. The model demonstrated independent predictability of overall survival in LUAD patients and was found to be closely associated with several immune microenvironmental characteristics. Additionally, it was effective in predicting anti-cancer drug sensitivity, with low-risk patients exhibiting a better response to chemotherapy and targeted therapy. Our tumour metabolism risk score based on hypoxia, glycolysis, fatty acid metabolism and immune genes can serve as a valuable prognostic tool and aid in guiding treatment decisions for individuals with LUAD.
Excluding external iliac node irradiation during neoadjuvant radiotherapy decreases lower intestinal toxicity without compromising efficacy in T4b rectal cancer patients with tumours involving the anterior structures
Authors: Li Anchuan , Mao Miaobin , Chen Runfan , Chi Pan , Huang Ying , Xu Benhua 
Published: March 2023

Abstract
Background
This study aimed to explore the impact of excluding the external iliac node (EIN) from the clinical target volume (CTV) during preoperative radiotherapy in T4b rectal cancer with anterior structure invasion.
Methods
We identified 132 patients with T4b rectal cancer involving the anterior structures who received radiotherapy followed by surgery between May 2010 and June 2019. Twenty-nine patients received EIN irradiation (EIN group), and 103 did not (NEIN group). Failure patterns, survival and toxicities were compared between the two groups. Multivariate Cox proportional hazard regression was used to analyse the factors affecting survival.
Results
A total of 132 patients with a median age of 55 years were included in the analysis, 94.7% patients were diagnosed as cN+. Distant failure occurred first in 24 patients (18.2%), and total distant metastasis were noted in 31 patients (23.5%). 11 patients (8.3%) developed locoregional recurrence, 10 (9.7%) patients were in the NEIN group, and 1 (3.4%) was in the EIN group (P = 0.34). The EIN region failure rate was seen in 1patient (1.0%) in the NEIN group and no patients in the EIN group. The locoregional recurrence-free survival (LRFS), distant metastasis-free survival (DMFS), overall survival (OS) and progression-free survival (PFS) rates were 96.3% vs. 90.5%, 82.1% vs.73.7%, 75.9% vs. 78.0% and 72.4% vs. 68.3% (all P > 0.05) for the EIN group and NEIN group, respectively. For patients with cN+, NEIN irradiation consistently did not decrease the LRFS, DMFS, OS and PFS compare to the EIN group. EIN irradiation failed to be an independent prognostic factor for LRFS, DMFS, OS and PFS. The incidence of grade 3–4 acute toxicity in the lower intestine was significantly higher in the EIN group than in the NEIN group (13.8% vs. 1.9%, P = 0.02). The Dmax (4479cGy vs. 5039cGy), V35 (45.8cc vs. 91.1cc) and V45 (11.4cc vs. 51.0cc) of the small bowel was decreased in the NEIN group compared to the EIN group.
Conclusions
Exclusion of the EIN from the CTV in T4b rectal cancer with anterior structure invasion could reduce lower intestinal toxicity without compromising oncological outcomes. These results need further evaluation in future studies.
Exploration of different parameter optimization algorithms within the context of ACTS software framework
Authors: Garg Rocky Bala , Gray Heather , Hofgard Elyssa , Tompkins Lauren 
Published: March 2023

Abstract

Particle track reconstruction, in which the trajectories of charged particles are determined, is a critical and time consuming component of the full event reconstruction chain. The underlying software is complex and consists of a number of mathematically intense algorithms, each dealing with a particular tracking sub-process.
These algorithms have many input parameters that need to be supplied in advance. However, it is difficult to determine the configuration of these parameters that produces the best
performance. Currently, the input parameter values are decided on the basis of prior experience or by the use of brute force techniques.
A parameter optimization approach that is able to automatically tune these parameters for high performance is greatly desirable.
In the current work, we explore various machine learning based optimization methods to devise a suitable technique to optimize parameters in the complex
track reconstruction environment. These methods are evaluated on the basis of a metric that targets high efficiency while keeping
the duplicate and fake rates small. We focus on derivative free optimization approaches that can be applied to problems involving
non-differentiable loss functions. For our studies, we consider the tracking algorithms defined within A Common Tracking
Software (ACTS) framework. We test our methods using simulated data from ACTS software corresponding to the ACTS Generic detector and the ATLAS ITk detector geometries.
Slowly walking down to the more food: Relative “number” discrimination in African spurred tortoises (Centrochelys sulcata)
Authors: Tomonaga Masaki , Haraguchi Daiki , Wilkinson Anna 
Published: March 2023

Abstract
Numerical discrimination is thought to be highly adaptive as it allows an organism to select greater amounts of food or larger social groups. The processes underlying this ability are well understood in mammals with two systems being posited to control behavior, the approximate number system, which uses the ratios between numbers and the object file system which tracks individual small numbers. Much less in known in reptiles, the work that is available suggests that chelonia may use the ratios between the numbers to discriminate numerical values. This experiment examined the effect of ratio and number size on relative numerical discrimination in African spurred tortoises (Centrochelys XXXulcate). To assess this, tortoises were presented with trays containing favored food in all possible number combinations between 1 and 7. The tortoise had to approach the tray it perceived as having the larger number, if correct, the tortoise received one piece of reinforcement. Each tortoise received 36 pairings of each stimulus combination. The results revealed that numerical discrimination was influenced by the ratio between the numbers, with performance improving as the ratio between the numbers increased. This suggests that the approximate number system may be controlling their behavior. However, the opposite tendency was observed for the larger numbers, suggesting that an object-file system may also be involved in numerical discrimination.
Organizational Ecology Theory: Review Past for Directing the Future Development
Authors: Chen Xiaomei , Wu Xiaojie , Wang Xiuqiong 
Published: March 2023

AbstractResearch on organizational ecology theory (OET) focuses on the effects of environmental constraints and competition within and between populations to explain the expansion and decline of organizational populations. While OET utilization has gained tremendous momentum over the past four decades, the literature remains fragmented. The integration of existing OET studies is important and timely. Thus, following a systematic process, we select 332 papers identified from the Web of Science database and perform a document-level bibliographic coupling analysis that explores the OET literature through clustering algorithms. This analysis reveals four thematic clusters within OET applications: (1) the antecedents of organizational vital rates (founding, mortality, change), (2) the structure of organizational populations and communities, (3) the intrapopulation and interpopulation evolutionary processes, and (4) the consequences of the intrapopulation and interpopulation evolutionary processes. Then, we supplement this in-depth analysis with a review of the literature, which enhances our understanding of the research themes related to OET applications, helping to develop an integrative framework and formulate new research questions that support the development of this promising theory. Therefore, this review suggests avenues for a more productive route to coherent theoretical and methodological development and promising topics for OET research.
Data-Driven Personas Creation Based on the CHARLS Database: Analyzing the Interaction Design of Mobility Aid for the Chinese Elderly with Difficulty in Indoor transferring
Authors: Zhang Xiaochen , Pan Ziyi , Huang Qianbo , Xiao Jia Xin , Luh Ding-Bang 
Published: March 2023

Abstract
China has entered into a light aging society and is gradually moving into the moderate aging society stage. A portion of the elderly with indoor transferring difficulties has become the core user of mobility aid design. In order to construct a persona for this relevant population, the data of the elderly in various fields in the CHARLS database from 2018 was sorted, and a hierarchical clustering analysis was conducted using 12 variables of 119 samples. Based on the overall variability of sample variables, the elderly with indoor transferring difficulties in China were classified according to the similarity of their characteristic data. The results of the hierarchical clustering analysis indicated that the elderly with indoor transferring difficulties in China can be divided into seven clusters. By sorting and refining the data of each cluster, seven data-driven personas containing their characteristic labels were obtained. By utilizing the cluster characteristics, the design direction of the mobility aid was determined, and a summary was made of the mobility aid 's functional features and corresponding interactive solutions for the physical needs of the elderly with indoor transferring difficulties in China.