bluuebunny/crossref_metadata_2025_split huggingface dataset:
The NCEP and ERA-Interim reanalysis temperature and humidity errors and their relationships with atmospheric boundary layer in the Tibetan Plateau
Authors: Che Junhui , Zhao Ping 
Published: January 2023

The lack of sounding observations in the western Tibetan Plateau (TP), the highest terrain in the world, has resulted in few efforts to evaluate the quality of the atmospheric reanalysis results in this region. Using the sounding observations from the Third Tibetan Plateau Atmospheric Scientific Experiment during 2013–2015, the NCEP and ERA-Interim reanalysis temperature and humidity fields in the TP are evaluated and the characteristics of the reanalysis Atmospheric Boundary Layer (ABL) height are utilized to explain the reasons for the differences in temperature and humidity between the western and eastern TP. The results show that the NCEP and ERA-Interim reanalysis temperature and humidity products generally have larger errors at low level (such as 500 hPa) in the western TP (WTP) than in the eastern one (ETP) at 12:00 UTC. However, this difference is small at 00:00 UTC. Further analysis reveals that the temporal and spatial variations of temperature and humidity errors at low level are closely associated with the differences in the terrain and ABL between the western and eastern TP. In the early morning when the ABL height is low over the TP, the 500 hPa pressure level in both the WTP and ETP is significantly above the top of ABL, with weak spatial variations of temperature and humidity errors. However, in the late afternoon when there is a larger increase in ABL height over the WTP than over the ETP, the 500 hPa pressure level is located inside the ABL in the WTP and is still above the ABL in the ETP, which causes significant regional differences in these errors.
Assessment of choroidal structural changes in patients with pre- and early-stage clinical diabetic retinopathy using wide-field SS-OCTA
Authors: Xu Fabao , Li Zhiwen , Yang Xueying , Gao Yang , Li Zhiwei , Li Guihua , Wang Shaopeng , Ning Xiaolin , Li Jianqiao 
Published: January 2023

PurposeTo investigate the micro-vascular changes in choroidal structures in patients with pre- and early-stage clinical diabetic retinopathy (DR) using wide-field Swept-Source Optical Coherence Tomography Angiography (SS-OCTA).MethodThis observational cross-sectional study included 131 eyes of 68 subjects that were divided into healthy controls (group 1, n = 46), pre-DR (group 2, n = 43), early-stage DR (group 3, n = 42) cohorts. All participants that underwent SS-OCTA examination were inpatients in the department of Ophthalmology and the department of Endocrinology, Qilu Hospital, Shandong University, and Department of Ophthalmology, Aier Eye Hospital, Jinan, from July 11, 2021 to March 17, 2022. The choroidal vascularity index (CVI), choroidal thickness (ChT) and central macular thickness (CMT) in the whole area (diameter of 12 mm) and concentric rings with different ranges (0–3, 3–6, 6–9, and 9–12 mm) were recorded and analyzed from the OCTA image.ResultCompared with healthy eyes, decreases in CVI and ChT were found in the eyes of patients with pre-or early-stage DR. The changes were more significant in the peripheral choroid, with the most prominent abnormalities in the 9-12mm area (P &lt; 0.001). However, there was no obvious difference in the average CMT value. Furthermore, CVI and ChT were significantly correlated with the duration of diabetes in the range of 6–9 and 9–12 mm (Ps &lt; 0.05; Correlation coefficient = -0.549, -0.395, respectively), with the strongest correlation (Ps &lt; 0.01; Correlation coefficient = -0.597, -0.413, respectively) observed at 9–12 mm.ConclusionThe CVI and ChT values of diabetic patients are significantly lower than in healthy controls, especially in patients with early-stage DR. In addition, the peripheral choroidal capillaries are more susceptible to early DM-induced injury than in the central area.
Burden in primary informal caregivers of children and adolescents with type 1 diabetes: Is it associated with depression, family dysfunction, and glycemic control?
Authors: Balcázar-Hernández Lourdes , Huerta-Martínez Hebert , Garrido Magaña Eulalia , Nishimura-Meguro Elisa , Jiménez Márquez Abigail , Rivera-Hernández Aleida 
Published: January 2023

ObjectiveThe requirement of a chronic treatment and the increase in life expectancy in children with type 1 diabetes (T1D) leads to the possibility of caregiver burden. The aim of our study was to evaluate the burden in primary informal caregivers (PIC) of children and adolescents with type 1 diabetes and its association with depression, family dysfunction, and glycemic control.Materials and methodsA retrospective study was performed in PIC of children and adolescents with T1D. Zarit Burden Interview Scale (ZBIS) was used to evaluate caregiver burden. Beck Depression Inventory (BDI-II) was used to evaluate depression in PIC, and the Family APGAR questionnaire was used to evaluate the family functionality.ResultsA total of 100 PIC of children and adolescents with T1D were included. Caregiver burden was found in 33% of caregivers. The total score of the Zarit scale was 41 (34–49); 19% had mild caregiver burden, and 14% had severe caregiver burden. According to the BDI-II, 82% had minimal depression, 11% mild depression, 5% moderate depression, and 2% severe depression. Family function was good in 69%; 13% had moderate dysfunction, and 18% had severe dysfunction. A positive correlation between caregiver burden and BDI-II score (r = 0.84; p = 0.001) and the grade of depression (r = 0.87; p = 0.001) was found. A logistic regression model showed that BDI-II score was associated with caregiver burden (OR 1.14; 95% CI 1.061–1.23; p = 0.001). A BDI-II cut off of 9 or more had a sensibility and specificity of 58% and 28%, respectively, for caregiver burden [AUC 0.751 (0.64–0.85); p = 0.001]. A BDI-II score ≥9 was a predictor of caregiver burden (OR 3.4; 95% CI 1.4–8.1; p = 0.008).ConclusionCaregiver burden is present in more than one third of the PIC of patients with T1D and is associated with depression. A BDI-II score ≥9 is a predictor of caregiver burden which may be a point to take into account in the integral approach to the patient with T1D and his or her family nucleus.
Circulating levels and the bioactivity of miR-30b increase during pubertal progression in boys
Authors: Mørup Nina , Stakaitis Rytis , Main Ailsa Maria , Golubickaite Ieva , Hagen Casper P. , Juul Anders , Almstrup Kristian 
Published: January 2023

BackgroundPuberty marks the transition from childhood to adulthood and is initiated by activation of a pulsatile GnRH secretion from the hypothalamus. MKRN3 functions as a pre-pubertal break on the GnRH pulse generator and hypothalamic expression and circulating levels of MKRN3 decrease peri-pubertally. In rodents, microRNA miR-30b seems to directly target hypothalamic MKRN3 expression – and in boys, circulating levels of miR-30b-5p increase when puberty is pharmacologically induced. Similarly, miR-200b-3p and miR-155-5p have been suggested to inhibit expression of other proteins potentially involved in the regulation of GnRH secretion. Here we measure circulating levels of these three miRNAs as boys progress through puberty.Materials and MethodsForty-six boys from the longitudinal part of the Copenhagen Puberty Study were included. All boys underwent successive clinical examinations including estimation of testis size by palpation. miR-30b-5p, miR-200b-3p, and miR-155-5p were measured in serum by RT-qPCR using a kit sensitive to the phosphorylation status of the miRNAs. Thirty-nine boys had miRNA levels measured in three consecutive samples (pre-, peri-, and post-pubertally) and seven boys had miR-30b-5p levels measured in ten consecutive samples during the pubertal transition.ResultsWhen circulating levels of miR-30b-5p in pre- and peri-pubertal samples were compared with post-pubertal levels, we observed a significant increase of 2.3 and 2.2-fold (p-value&lt;6.0×10-4), respectively, and a larger fraction of miR-30b-5p appeared to be phosphorylated post-pubertally indicating an increase in its bioactivity. We also observed a negative correlation between circulating levels of miR-30b-5p and MKRN3. The inter-individual variation in circulating miR-30b levels was substantial and we could not define a clinical threshold for miR-30b-5p suggestive of imminent puberty. Also, miR-155-5p showed significantly increasing levels from the peri- to the post-pubertal stage (p=3.0×10-3), whereas miR-200b-3p did not consistently increase.ConclusionBoth circulating levels of miR-30b-5p and its bioactivity increase during the pubertal transition in boys supporting its role in the activation of the HPG axis at the onset of physiologically normal puberty.
Characterizing urban growth and land surface temperature in the western himalayan cities of India using remote sensing and spatial metrics
Authors: Gupta Rajman , Sharma Mani , Singh Garima , Joshi Rajendra Kr 
Published: January 2023

Urban heat islands (UHI) are developing due to increasing urbanization and loss of vegetation in major cities in India. Increased urbanization modifies the urban microclimate that leads to significant land-use changes resulting in surface conversion and heat release, which poses serious risks to human health, environment and the ecosystem of the Himalayan ecosystem. Hence, mitigating UHI becomes important and requires a better understanding of underlying associated biophysical processes. In the study an attempt has been made to demonstrate the impact of urbanization on land surface temperature (LST) in Shimla and Dehradun, capitals of the Western Himalayan states, India using satellite data and spatial metrics. The process was analyzed using urban coverage patterns obtained from Landsat 5, 7, and 8 and corresponding sensors from TM, ETM+, and OLI. The Built-up and Non-Built-up areas were extracted and the biophysical parameters NDVI, NDBI, NDWI and LST were calculated to capture different features of urban growth. The result indicated, that the built-up area increased from 32.19 km2 (2000) to 68.37 km2 (2016) in Dehradun and from 12.38 km2 (2000) to 29.47 km2 (2016) in Shimla during the study period, resulting in an increase in NDBI and LST and Reduction and NDVI and NDWI. Results showed that temperature hotspots were largest in urban areas, followed by vegetation and water bodies. A significant correlation (p &lt; 0.05) was observed between LST and biophysical parameters -NDVI, NDBI, NDWI. Spatial metrics at the class and landscape levels show that increased urban growth from 2000 to 2016 has made the landscape fragmented and more heterogeneous. The Identified trends and changes in landscape patterns and their impact on heterogeneous urban areas suggest that the study is feasible to estimate LST, NDVI, NDBI and NDWI with reasonable accuracy that will likely have influence on policy interventions.
Climate change enhanced the positive contribution of human activities to net ecosystem productivity from 1983 to 2018
Authors: Liu Min , Bai Xiaoyong , Tan Qiu , Luo Guangjie , Zhao Cuiwei , Wu Luhua , Chen Fei , Li Chaojun , Yang Yujie , Ran Chen , Luo Xuling , Zhang Sirui 
Published: January 2023

IntroductionAccurate assessment of the net ecosystem productivity (NEP) is very important for understanding the global carbon balance. However, it remains unknown whether climate change (CC) promoted or weakened the impact of human activities (HA) on the NEP from 1983 to 2018.MethodsHere, we quantified the contribution of CC and HA to the global NEP under six different scenarios based on a boosted regression tree model and sensitivity analysis over the last 40 years.Results and discussionThe results show that (1) a total of 69% of the areas showed an upward trend in the NEP, with HA and CC controlled 36.33 and 32.79% of the NEP growth, respectively. The contribution of HA (HA_con) far exceeded that of CC by 6.4 times. (2) The CO2 concentration had the largest positive contribution (37%) to NEP and the largest influence area (32.5%). It made the most significant contribution to the NEP trend in the range of 435–440 ppm. In more than 50% of the areas, the main loss factor was solar radiation (SR) in any control area of the climate factors. (3) Interestingly, CC enhanced the positive HA_con to the NEP in 44% of the world, and in 25% of the area, the effect was greater than 50%. Our results shed light on the optimal range of each climatic factor for enhancing the NEP and emphasize the important role of CC in enhancing the positive HA_con to the NEP found in previous studies.
Phenotypic and genetic parameters of circadian rhythms from core body temperature profiles and their relationships with beef steers’ production efficiency profiles during successive winter feeding periods
Authors: Durunna Obioha , Carroll Jeffery A. , Dailey Jeff W. , Damiran Daalkhaijav , Larson Kathy A. , Timsit Edouard , Parsons Rex , Manafiazar Ghader , Lardner Herbert A. 
Published: January 2023

This 2-year study evaluated differences in circadian parameters obtained from measures of core body temperatures using telemetric reticulo-rumen and rectal devices during two winter feeding regimes in western Canada. The study also estimated phenotypic correlations and genetic parameters associated with circadian parameters and other production traits in each feeding regime. Each year, 80 weaned steer calves (initial age: 209 ± 11 days; BW: 264 ± 20 kg) from the same cohort were tested over two successive regimes, Fall-Winter (FW) and Winter-Spring (WS) at Lanigan, Saskatchewan, Canada. The steers received forage-based rations in both regimes where the individual feed intake was measured with automatic feeding units. During the trial, the reticulo-rumen (RTMP) and rectal (RCT) temperatures were simultaneously measured every 5 min using telemetric devices. These were used to calculate the circadian parameters (Midline Estimating Statistic Of Rhythms, amplitude, and acrophase/peak time) for both temperature measures. Growth and efficiency performance traits were also determined for all steers. Each steer was assigned into inefficient, neutral, and efficient classes based on the SD of the residual feed intake (RFI), residual gain (RG), and residual intake and gain (RIG) within each year and feeding regime. Higher (p &lt; 0.0003) RTMP and rectal temperature MESORs were observed in the Fall-Winter compared to the Winter-Spring regime. While the two test regimes were different (p &lt; 0.05) for the majority of the RTMP or RCT temperature parameters, they did not differ (p &gt; 0.10) with the production efficiency profiles. The heritability estimates were higher in FW (0.78 ± 0.18 vs. 0.56 ± 0.26) than WS (0.50 ± 0.18 vs. 0.47 ± 0.22) for the rumen and rectal MESORs, respectively. There were positive genetic correlations between the two regimes for the RTMP (0.69 ± 0.21) and RCT (0.32 ± 0.59). There was a negative correlation (p &lt; 0.001) between body temperature and ambient temperature. The high heritability estimates and genetic correlations for rumen and rectal temperature parameters demonstrate their potential as beef genetic improvement tools of economic traits associated with the parameters. However, there are limited practical implications of using only the core-body temperature as a proxy for production efficiency traits for beef steers during winter.
PseU-ST: A new stacked ensemble-learning method for identifying RNA pseudouridine sites
Authors: Zhang Xinru , Wang Shutao , Xie Lina , Zhu Yuhui 
Published: January 2023

Background: Pseudouridine (Ψ) is one of the most abundant RNA modifications found in a variety of RNA types, and it plays a significant role in many biological processes. The key to studying the various biochemical functions and mechanisms of Ψ is to identify the Ψ sites. However, identifying Ψ sites using experimental methods is time-consuming and expensive. Therefore, it is necessary to develop computational methods that can accurately predict Ψ sites based on RNA sequence information.Methods: In this study, we proposed a new model called PseU-ST to identify Ψ sites in Homo sapiens (H. sapiens), Saccharomyces cerevisiae (S. cerevisiae), and Mus musculus (M. musculus). We selected the best six encoding schemes and four machine learning algorithms based on a comprehensive test of almost all of the RNA sequence encoding schemes available in the iLearnPlus software package, and selected the optimal features for each encoding scheme using chi-square and incremental feature selection algorithms. Then, we selected the optimal feature combination and the best base-classifier combination for each species through an extensive performance comparison and employed a stacking strategy to build the predictive model.Results: The results demonstrated that PseU-ST achieved better prediction performance compared with other existing models. The PseU-ST accuracy scores were 93.64%, 87.74%, and 89.64% on H_990, S_628, and M_944, respectively, representing increments of 13.94%, 6.05%, and 0.26%, respectively, higher than the best existing methods on the same benchmark training datasets.Conclusion: The data indicate that PseU-ST is a very competitive prediction model for identifying RNA Ψ sites in H. sapiens, M. musculus, and S. cerevisiae. In addition, we found that the Position-specific trinucleotide propensity based on single strand (PSTNPss) and Position-specific of three nucleotides (PS3) features play an important role in Ψ site identification. The source code for PseU-ST and the data are obtainable in our GitHub repository (https://github.com/jluzhangxinrubio/PseU-ST).
Exploring causal correlations between inflammatory cytokines and systemic lupus erythematosus: A Mendelian randomization
Authors: Xiang Mengmeng , Wang Yilun , Gao Zhanyan , Wang Jie , Chen Qian , Sun Zhan , Liang Jun , Xu Jinhua 
Published: January 2023

ObjectivesPrevious studies have reported that a few inflammatory cytokines have associations with systemic lupus erythematosus (SLE)—for example, IL-6, IL-17, and macrophage inflammatory protein (MIP). This Mendelian randomization was conducted to further assess the causal correlations between 41 inflammatory cytokines and SLE.MethodsThe two-sample Mendelian randomization utilized genetic variances of SLE from a large publicly available genome-wide association study (GWAS) (7,219 cases and 15,991 controls of European ancestry) and inflammatory cytokines from a GWAS summary containing 8,293 healthy participants. Causalities of exposures and outcomes were explored mainly using inverse variance weighted method. In addition, multiple sensitivity analyses including MR-Egger, weighted median, simple mode, weighted mode, and MR-PRESSO were simultaneously applied to strengthen the final results.ResultsThe results indicated that cutaneous T cell-attracting chemokine (CTACK) and IL-17 may be suggestively associated with the risk of SLE (odds ratio, OR: 1.21, 95%CI: 1.04–1.41, p = 0.015; OR: 1.37, 95%CI: 1.03–1.82, p = 0.029). In addition, cytokines including beta nerve growth factor, basic fibroblast growth factor, IL-4, IL-6, interferon gamma-induced protein 10, monokine induced by interferon-gamma, MIP1b, stromal cell-derived factor-1 alpha, and tumor necrosis factor-alpha are suggested to be the consequences of SLE disease (Beta: 0.035, p = 0.014; Beta: 0.021, p = 0.032; Beta: 0.024, p = 0.013; Beta: 0.019, p = 0.042; Beta: 0.040, p = 0.005; Beta: 0.046, p = 0.001; Beta: 0.021, p = 0.029; Beta: 0.019, p = 0.045; Beta: 0.029, p = 0.048).ConclusionThis study suggested that CTACK and IL-17 are probably the factors correlated with SLE etiology, while a couple of inflammatory cytokines are more likely to be involved in SLE development downstream.
New methods for the quantification of mixed chimerism in transplantation
Authors: Picard Christophe , Frassati Coralie , Cherouat Nicem , Maioli Sandrine , Moskovtchenko Philippe , Cherel Mathilde , Chiaroni Jacques , Pedini Pascal 
Published: January 2023

BackgroundQuantification of chimerism showing the proportion of the donor in a recipient is essential for the follow-up of hematopoietic stem cell transplantation but can also be useful to document an immune tolerance situation after solid organ transplantation. Historically, chimerism has been quantified from genomic DNA, but with technological advances, chimerism from donor-derived cell-free DNA seems particularly relevant in solid organ transplantation.MethodsThe reference method was until recently the short tandem repeat technique, but new innovative techniques as digital PCR (dPCR) and NGS, have revolutionized the quantification of chimerism, such as the so-called microchimerism analysis. After a short review of chimerism methods, a comparison of chimerism quantification data for two new digital PCR systems (QIAcuity™ dPCR (Qiagen®) and QuantStudio Absolute Q (ThermoFisher®) and two NGS-based chimerism quantification methods (AlloSeq HCT™ (CareDx®) and NGStrack™ (GenDX®)) was performed.ResultsThese new methods were correlated and concordant to routinely methods (r²=0.9978 and r²=0.9974 for dPCR methods, r²=0.9978 and r²=0.9988 for NGS methods), and had similar high performance (sensitivity, reproductibility, linearity).ConclusionFinally, the choice of the innovative method of chimerism within the laboratory does not depend on the analytical performances because they are similar but mainly on the amount of activity and the access to instruments and computer services.
Water model determines thermosensitive and physicochemical properties of poly(N-isopropylacrylamide) in molecular simulations
Authors: Quoika Patrick K. , Kamenik Anna S. , Fernández-Quintero Monica L. , Zacharias Martin , Liedl Klaus R. 
Published: January 2023

Poly (N-isopropylacrylamide) (PNIPAM) is a famous representative of thermosensitive polymers. Thermosensitive polymers undergo a phase transition with lower critical solution temperature. Commonly, their phase behavior is linked to a conformational collapse above a certain temperature. This thermosensitive conformational transition is called Coil-Globule transition. In contrast, most other polymers usually show inverse temperature behavior, i.e., an upper critical solution temperature, corresponding to a Globule-Coil transition. Besides their numerous possible applications, thermosensitive polymers are of interest for fundamental research, because of similarities to macromolecular conformational transitions, e.g., protein folding. The counter-intuitive behavior of thermosensitive polymers is commonly associated with solvation effects. Thus, an accurate description of the solvent is crucial for the investigation of thermosensitive polymers in molecular simulations. Here, we investigate the influence of the in silico water model on the thermosensitive Coil-Globule transition in molecular dynamics simulations. To this end, we performed extensive atomistic simulations of the syndiotactic PNIPAM 20-mer at multiple temperatures with eight different water models–four of which are 3-point water models (TIP3P-type) and four are 4-point water models (TIP4P-type). We found that the thermosensitive Coil-Globule transition is strongly influenced by the water model in the simulations. Depending on the water model, the conformational ensemble of the polymer is shifted significantly, which leads to dramatically different results: The estimated transition temperature may span between 255 and 350 K. Consequently, depending on the description of the solvent, the physicochemical and mechanical properties of these polymers, e.g., the polymer-solvent affinity and persistence length, vary. These divergent results originate from the strength of interactions between polymer and solvent, but also on the bulk state of the solvent. Both these quantities vary between water models. We found that the Lennard-Jones interaction parameter ϵ of the water model correlates with the transition temperature of the polymer. Indeed, the quadrupole moment of the water model shows an even higher correlation with this quantity. Our results suggest a connection between the phase diagram of the solvent and the thermosensitive transition of the polymer.