bluuebunny/crossref_metadata_2025_split huggingface dataset:
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: April 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. An easy-to-use and flexible toolbox for this purpose is lacking.
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, and the Gompertz model 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
We have developed the first comprehensive toolbox to characterize and forecast time-series data using simple phenomenological growth models. As a contagion process takes off, the tools presented in this tutorial 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.
surviveR: a flexible shiny application for patient survival analysis
Authors: Sessler Tamas , Quinn Gerard P. , Wappett Mark , Rogan Emily , Sharkey David , Ahmaderaghi Baharak , Lawler Mark , Longley Daniel B. , McDade Simon S. 
Published: April 2023

Abstract
Motivation
Kaplan-Meier (KM) survival analyses based on complex patient stratifications due to the burgeoning volumes of genomic, molecular and phenotypic data, are an increasingly important aspect of the biomedical researcher’s toolkit. Commercial statistics/graphing packages for such analyses are functionally limited, whereas open-source tools have a high barrier-to-entry in terms of understanding of methodologies and computational expertise. We developed surviveR to address this unmet need for a survival analysis tool that can enable users with limited computational expertise to conduct routine but complex analyses.
Results
We developed surviveR, a cloud-based Shiny app, to address this unmet need for easy-to-use web-based tool that can draw and analyse Kaplan-Meier survival graphs. Integrated customization options allows user with limited computational expertise to easily filter patients to enable custom cohort generation, automatically calculates log-rank test and Cox hazard ratios, as well as providing multiple options for integrating continuous data types, such as RNA or protein expression measurements for survival plotting. We further demonstrate the utility through exemplifying its application to a clinically relevant colorectal cancer patient dataset.
Conclusion
surviveR is a cloud-based web application available at https://generatr.qub.ac.uk/app/surviveR, that can be used by non-experts users to perform complex custom survival analysis.
Efficacy of fractional CO2 laser in combination with stromal vascular fraction (SVF) compared with fractional CO2 laser alone in the treatment of burn scars: a randomized controlled clinical trial
Authors: Roohaninasab Masoumeh , Khodadad Fariba , Sadeghzadeh-Bazargan Afsaneh , Atefi Najmolsadat , Zare Sona , Jafarzadeh Alireza , Rahimi Seyyedeh Tahereh , Nouri Maryam , Nilforoushzadeh Mohammad Ali , Behrangi Elham , Goodarzi Azadeh 
Published: April 2023

Abstract
Background
The appearance of skin scars is known as one of the main side effects of skin burns. Stromal vascular fraction (SVF), as a rich source of cell populations with tissue regeneration properties, plays an important role in the healing of skin lesions. Fractional CO2 lasers, have occupied a special place in treating skin lesions, particularly skin scars, since their introduction. Our study aimed to compare the combination of SVF and fractional CO2 laser with fractional CO2 laser alone in the treatment of burn scars.
Method
This double-blind clinical trial study was conducted on 10 patients with burn scars that were treated three times with a fractional CO2 laser at site of burn lesions, and one of the two areas studied was randomly injected with SVF. Two months after completion of the procedure, patients' scars were assessed using the Vancouver Scar Scale (VSS), biometric criteria, and physician and patient satisfaction ratings.
Results
The results confirmed a significant improvement in VSS, cutometry, R7 criteria, complete density sonography, and skin density sonography in the fractional CO2 laser- treated group. The VSS criteria, epidermal thickness sonography, complete density sonography, and skin density sonography in the group treated with the combination of fractional CO2 laser and SVF also showed significant improvement. The VSS criteria, and melanin index of Mexameter in the group treated with SVF in combination with fractional CO2 laser were significantly better than the group treated with fractional CO2 laser alone. Also, physician and patient satisfaction in the group treated with SVF injection in combination with fractional CO2 laser was significantly higher than the other group.
Conclusion
The results confirm the efficacy of SVF injection in combination with fractional CO2 laser in the treatment of burn scars and can be considered as a treatment option for better management of these lesions.
The study protocol was registered at Iranian Registry of Clinical Trials with code: IRCT20210515051307N1, Registration date: 2021-11-14, URL: https://www.irct.ir/trial/56337.
Intra-Articular Delivery of an Indoleamine 2,3-Dioxygenase Galectin-3 Fusion Protein for Osteoarthritis Treatment in Male Lewis Rats
Authors: Partain Brittany D. , Bracho-Sanchez Evelyn , Farhadi Shaheen A. , Yarmola Elena G. , Keselowsky Benjamin G. , Hudalla Gregory A. , Allen Kyle D. 
Published: April 2023

Abstract
Objective: Controlling joint inflammation can improve osteoarthritis (OA) symptoms; however, current treatments often fail to provide long-term effects. We have developed an indoleamine 2,3-dioxygenase and galectin-3 fusion protein (IDO-Gal3). IDO converts tryptophan to kynurenines, directing the local environment toward an anti-inflammatory state; Gal3 binds carbohydrates and extends IDO’s joint residence time. In this study, we evaluated IDO-Gal3’s ability to alter OA-associated inflammation and pain-related behaviors in a rat model of established knee OA.
Methods: Joint residence was first evaluated with an analog Gal3 fusion protein (NanoLuc™ and Gal3, NL-Gal3) that produces luminescence from furimazine. OA was induced in male Lewis rats via a medial collateral ligament and medial meniscus transection (MCLT+MMT). At 8 weeks, NL or NL-Gal3 were injected intra-articularly (n=8 per group), and bioluminescence was tracked for 4 weeks. Next, IDO-Gal3’s ability to modulate OA pain and inflammation was assessed. Again, OA was induced via MCLT+MMT in male Lewis rats, with IDO-Gal3 or saline injected into OA-affected knees at 8 weeks post-surgery (n=7 per group). Gait and tactile sensitivity were then assessed weekly. At 12 weeks, intra-articular levels of IL6, CCL2, and CTXII were assessed.
Results: The Gal3 fusion increased joint residence in OA and contralateral knees (p<0.0001). In OA-affected animals, IDO-Gal3 improved tactile sensitivity (p=0.002), increased walking velocities (p≤0.033), and improved vertical ground reaction forces (p≤0.04). Finally, IDO-Gal3 decreased intra-articular IL6 levels within the OA-affected joint (p=0.0025).
Conclusion: Intra-articular IDO-Gal3 delivery provided long-term modulation of joint inflammation and pain-related behaviors in rats with established OA.
Catalysis sans catalyst loss: The origins of prolonged stability of graphene-metal-graphene sandwich architecture for oxygen reduction reactions
Authors: Abdelhafiz Ali Ali A. , Choi Jiil , Zhao Bote , Cho Jinwon , Ding Yong , Soule Luke , Jang Seung Soon , Liu Meilin , Alamgir Faisal 
Published: April 2023

AbstractOver the past several decades, the design of highly active and cost-effective catalysts and electrocatalyst has been the subject of intense research efforts.to However, there has been significantly less deliberate emphasis on rationally designing a catalyst system with a prolonged stability. A major obstacle comes from the ambiguity behind how catalyst degrades. Several degradation mechanisms have been proposed in literature, such as catalyst particles detachment of the substrate, metal atom dissolution, agglomeration, Ostwald ripening, or corrosion of the carbon support, but with a lack of systematic studies, the causal relations between degradation and these proposed mechanisms remain ambiguous. Here, we report a systematic study of a catalyst system comprising of small particles and single atoms of Pt sandwiched between graphene layers, GR/Pt/GR where Pt-specific catalysis occurs through “chemically transparent” outer Gr layer(s). Experimental and computational analyses unravel the degradation mechanism of the studied electrocatalyst architecture for oxygen reduction reaction in acidic medium. Catalyst suffers from atomic dissolution under ORR harsh acidic and oxidizing operation voltages. Single atoms trapped in point defects within the top graphene layer on their way hopping through towards the surface of GR/Pt/GR architecture. Trapping mechanism renders individual Pt atoms as single atom catalyst sites catalyzing ORR for thousands of cycles before washed away in the electrolyte. The GR/Pt/GR catalysts also compare favorably to state-of-the-art commercial Pt/C catalysts and demonstrates a rational design of a hybrid nanoarchitecture with a prolonged stability for thousands of operation cycles. The proposed Gr/metal/Gr architecture is not only applicable to other electrocatalytic reactions but can have several applications in sensors and biomedical fields.
Environmental injustice in estimated cancer risk from airborne toxics exposure across United States communities
Authors: Hurbain Patrick , Strickland Matthew , Liu Yan , Li Dingsheng 
Published: April 2023

Abstract
US Census Bureau data was matched to estimated cancer risk by US EPA from 2011 to 2018 to explore environmental justice on a national level with census tract resolution for a wide range of airborne toxins. Spearman correlations showed modest associations between various socio-demographic status factors and estimated cancer risk. Multiple linear regressions analyses showed increases in the numbers of minorities relative to White individuals were positively associated with increased estimated cancer risk in urban areas (p <0.05), but only for high proportions of Blacks in suburban and rural areas. Urban tracts suffer from highest estimated cancer risks were concentrated among the communities with population of higher density of minority and lack of education. While in general environmental justice seems improved across the examined years, equity is far from achieved and future work in identifying the sources of environmental injustice could help in achieving a more just environment.
A Non-Invasive Approach to the Resistive Switching Physical Model of Ultra-Thin Organic-Inorganic Dielectric-based ReRAM
Authors: Martinez Alba , Cho Byung Jin , Kim Min Ju 
Published: April 2023

Abstract
The extremely reduced thickness of the recently introduced ultra-thin (< 5 nm) organic-inorganic hybrid dielectric-based ReRAM hinders their processability through material characterization techniques. But the attractiveness of these devices as the next-generation non-volatile memory requires a deep understanding of the resistive switching (RS) dynamics in the hybrid dielectric layer. Moreover, the poor uniformity in key switching parameters still persistent in ReRAMs impedes any trends to be clearly defined through electrical characterization. This work uses electrical manipulation through a ramped-pulse series (RPS) method to improve the voltage and resistance fluctuations in the reset process of ultra-thin Al/Hf-hybrid/Ni devices at different pulse voltage amplitude, pulse width, and temperature conditions. By analyzing the electrical behavior of the device under these conditions, a novel and detailed physical model describing the operating mechanism is proposed. The coexistence in the conductive filament (CF) of a hybrid metallic portion composed of \(\text{A}\text{l}\) and \({\text{H}\text{f}}_{3}{\text{A}\text{l}}_{2}\), and an oxygen vacancy portion is confirmed. Our model emphasizes the vacancies contribution in the RS, where majority of them are generated during the CF forming process and participate to different degrees in the filament rupture of the RPS and no-RPS-processed devices via Joule heating, drift, and Fick forces. Additionally, switching failure events are explained based on the presence of an \({\text{A}\text{l}}_{2}{\text{O}}_{3}\) interlayer in the Al/Hf-hybrid interface.
A Priori Prediction of Breast Cancer Response to Neoadjuvant Chemotherapy using Quantitative Ultrasound, Texture Derivative and Molecular Subtype
Authors: Sannachi Lakshmanan , Osapoetra Laurentius O. , DiCenzo Daniel , Halstead Schontal , Wright Frances , Look-Hong Nicole , Slodkowska Elzbieta , Gandhi Sonal , Curpen Belinda , Kolios Michael C. , Oelze Michael , Czarnota Gregory J. 
Published: April 2023

Abstract
The purpose of this study was to investigate the performances of the tumor response prediction prior to neoadjuvant chemotherapy based on quantitative ultrasound, tumour core-margin, texture derivative analyses, and molecular parameters in a large cohort of patients (n = 208) with locally advanced breast cancer and combined them to best determine tumour responses with machine learning approach. Two multi-features response prediction algorithms using a k-nearest neighbour and support vector machine were developed with leave-one out and hold-out cross-validation methods to evaluate the performance of the response prediction models. In a leave-one out approach, the quantitative ultrasound-texture analysis based model attained a good classification performance with 80% of accuracy and AUC of 0.83. Including molecular subtype in the model improve the performance to 83% of accuracy and 0.87 of AUC. Due to limited number of sample in the training process, a model developed with a hold-out approach exhibited slightly higher bias error in classification performance. The most relevant features selected in predicting the response groups are core-to-margin, texture derivative, and molecular subtype. These results imply that that tumour-margin, baseline texture-derivative analysis methods combined with molecular subtype can be potentially used for the prediction of ultimate treatment response in patients prior to neoadjuvant chemotherapy.
Preparation of biomass yam solar absorber and its application in solar evaporation
Authors: Ting Li , Juan Jia , Wang Yanqing , Hanxue Sun , Li Jiyan , Zhaoqi Zhu , Liang weidong 
Published: April 2023

Abstract
Solar evaporation system has become a research hotspot in the field of photothermal conversion technology in recent years because of its high photothermal conversion efficiency and practicality of promotion. Biomass solar absorbers have excellent solar absorption properties and high solar-water vapor conversion, but they have the limitations of long feedstock production cycle and high carbonization temperature. As a kind of biomass materials, yam is not only inexpensive, but also has a short production cycle and rich pore structures. Therefore, in this paper, a yam based solar absorber with rich pore structure was prepared, and the photothermal conversion efficiency of the absorber was further investigated. The yam was treated with freeze-dried method and carbonized at different temperatures to obtain yam solar absorbers. Then find the thermal stability and porosity of solar absorber gradually rise as the treatment temperature increasing. The solar absorption rate of the carbonized yam was close to 90% in the near UV-visible region. Solar-water vapor control experiments with different treatments of the solar absorber of the yam were carried out in simulated solar-driven interface steam generation system (SISGS). The absorber treated at 200°C in the sun was found to have the best performance with a solar-water vapor conversion of about 90% and a water evaporation rate of 1.3164 kg m− 2 h− 1.
New Values of Normal Ankle Strength and Its Importance for Rehabilitation and Return to Play
Authors: Fonseca Lucas da , Inojossa Thiago , Maciel Eduardo , Netto Cesar de Cesar , Mansur Nacime , Astur Diego 
Published: April 2023

Abstract
Background: the isokinetic test has been broadly used to assess the functional results after the rehabilitation of musculoskeletal injuries. Particular in the ankle, most studies are related to injuries of the lateral ligaments and the Achilles tendon, without the knowledge of normative values. This study aimed to comprehensively evaluate the ankle isokinetic strength profile.
Methods: 200 ankles were evaluated using the Biodex 3 System for the movements of eversion, inversion, extension, and plantar flexion. Healthy individuals with an active life and without previous injuries were widely assessed. The Maximum Torque, Agonist / Antagonist Ratio, Limb Simmetry Index, among others and their relationships with demographic variables were also evaluated. Different statistical analyzes were performed for each parameters and ratios.
Results: the mean age was 38.5 years and the BMI was 25.8 in 69 men and 31 women. In 78 participants, the dominant ankle was the right one. The non-dominant side was consistently stronger in every moviment. The mean values ​​obtained for the torque in each movement were 29.9 N/m for eversion, 34.8 N/m for inversion, 48.6 N/m for extension, and 140.2 N/m for flexion. Such parameters for men and women were also obtained and there was no correlation between age or BMI with maximum torque. The evertors/inverters ratio was 88.8% and the extensor/flexor ratio was 36.1%. The Muscular Deficiency Index and Limb Simmetry Index showed a balance between the sides for each movement, with an average global difference of less than 10% between them (eversion 8.66; inversion 4.2; extension 3.41 and flexion 5.18).
Conclusion: the sample was considered homogeneous, which allows to propose a new profile of normative values ​​for the isokinetic strength of the ankle. Values ​​of torque forces and agonist/antagonist balances have been accomplished. The results have implications for rehabilitation protocols and return-to-sport criteria.
Prevalence and clinical correlates of suicide attempts in first episode, never treated major depressive disorder patients with comorbid autoimmune thyroiditis
Authors: Luo Yinli , Peng Pu , Zhou Yanan , Wang Yuan , Zhang Xiangyang , Wang Yizhuo 
Published: April 2023

Abstract
Backgrounds: Autoimmune thyroiditis (AIT) is closely associated with major depressive disorder (MDD). However, its association with suicide attempts (SA) in this population remains unexplored. The study aimed to assess the prevalence and correlates of SA in first-episode drug-naïve (FEDN) MDD patients with AIT.
Methods: We recruited 1718 FEDN MDD outpatients and assessed depressive, anxiety, and psychotic symptoms by the Hamilton Rating Scale for Depression (HAMD), the Hamilton Rating Scale for Anxiety, and the Positive and Negative Syndrome Subscale positive subscale, respectively. The serum levels of free triiodothyronine, free thyroxine, thyroid stimulating hormone (TSH), anti-thyroglobulin, thyroid peroxidases antibody (TPOAb), and several other metabolic parameters were assessed. Multiple logistic regression model was applied to identify the correlates of SA in AIT MDD patients. The Area Under the Curve (AUC) was used to test the performance of this model.
Results: The prevalence of SA was higher in AIT patients than in non-AIT patients (34% vs 14%, p<0.001). The presence of AIT independently doubled the risk of SA (OR, 1.88, 95%CI, 1.42-2.50, p<0.001). Anxiety (OR, 3.09, 95%CI, 1.76-5.42, p<0.001), HAMD score (OR, 1.19, 95%CI, 1.09-1.31, p<0.001), TPOAb (OR, 1.002, 95%CI, 1.001-1.002, p<0.001), and TSH (OR, 1.20, 95%CI, 1.10-1.32, p<0.001) were independently associated with SA in MDD patients with AIT. The combination of the four variables well distinguished SA patients from non-SA patients (AUC value:0.80).
Conclusions: Taken together, AIT was closely associated with SA. Regular thyroid examination may help detect SA in MDD patients.