Miracle-dz/UniFAR-FTUs huggingface dataset:
Seasonal physiological and behavioural responses of a small bird in a hot, arid habitat

In arid-zones, fauna and flora have to deal with large seasonal shifts and/or extremes in temperature and/or moisture levels that will become more pronounced in the coming decades. Arid-zone species are sensitive to changes in temperature and rainfall, which underscores their suitability as model taxa for developing conceptual frameworks for predicting responses to climate change. I determined the physiological adjustments of an arid-zone endemic passerine, the rufous-eared warbler (Malcorus pectoralis; mass = 9 – 11 g), in the Karoo semi-desert of South Africa. I found that the resting metabolic rate (RMR) of the warblers was approximately 10% lower in summer compared to winter. I also demonstrated that whole-animal evaporative water loss (EWL) correlated with Ta in both summer and winter, but was significantly lower at high Ta’s in summer compared to winter (182.1 mg.hr vs. 293.1 mg.hr in summer and winter respectively at Ta = 41 °C). The EWL began to increase at approximately the same Ta in both seasons (Ta = 37.7 °C), which contrasted the significantly higher Ta at which the warblers began to pant (Tpant) during experiments in summer compared to winter (Ta = 38.6 °C vs. 36.9 °C respectively). Body temperatures (Tb) also showed strong dependence on Ta, with a similar, clear pattern of heterothermy (mean Tb ranged from 34.6 °C to 44.15 °C) in both seasons. However, in summer the warblers were able to remain calm, and tolerated higher Ta’s before their Tb’s increased to potentially detrimental levels compared to winter. The set 29 point Tb (mean Tb of the birds while at rest during BMR measurements) was significantly higher in summer compared to winter (Tb = 39.2 °C vs. 38.0 °C, respectively). These results illustrate the plastic responses rufous-eared warblers are capable of to increase heat tolerance in summer, and thus balance energy and water demands in an arid environment that exhibits wide seasonality in Ta, in addition to high summer Ta. Moreover, these findings emphasise the importance of identifying, as well as understanding the associated costs, of physiological responses to environmental variables. These data are also important for predicting biologically meaningful responses (and hence, vulnerability) of arid-zone avian communities to climactic shifts.
Sucrose: X-ray refinement and comparison with neutron refinement

BARTELL, L. S. , KUCHITSU, K. & DE NEUI, R. J. (1961). J. Chem. Phys. 35, 1211-1218. BEEVERS, C. A. , MCDONALD, T. R. R,. ROBERTSON, J. H. & STERN, F. (1952). Acta Cryst. 5, 689-690. BERMAN, H. (1970). Acta Cryst. B26, 290-299. BERMAN, H. , CHU, S. S. C. & JEFFREY, G. A. (1967). Science, 157, 1576-1577. BROWN, G. M. & LEVY, H. A. (1963). Science, 141,921-923. BROWN, G. M. & LEVY, H. A. (1964a). J. Phys. Radium, 25, 469-473. BROWN, G. M. & LEVY, H. A. (1964b). J. Phys. Radium, 25, 497-502. BROWN, G. M. & LEVY, H. A. (1965). Science, 147, 10381039. BUSING, W. R. & LEVY, H. A. (1964). Acta Cryst. 17, 142146. BUSING, W. R. & LEVY, H. A. (1967). Acta Cryst. 22, 457464. CHIDAMBARAM, R. & BROWN, G. M. (1972). Cryst. Struct. Commun. 1, 269-272. COPPENS, P. & HAMILTON, W. C. (1970). Acta Cryst. A26, 71-83. CRUICKSHANK, D. W. J. (1956). Acta Cryst. 9, 757-758. ELIEL, E. L. (1969). Svensk kem. Tidskr.81, No. 6-7, 22-27. FRIES, D. C. , RAO, S. T. & SUNDARALINGAM, M. (1971). Aeta Cryst. B27, 994-1005. FROST, A. & ROUSE, R. A. (1968). J. Amer. Chem. Soc. 90, 1965-1969. HANSON, J. C. , SIEKER, L. C. & JENSEN, L. H. (1973). Acta Cryst. B29, 797-808. HIROTA, E. & MORINO, Y. (1966). J. Chem Phys. 45, 23262327. HOOG, A. J. DE, BuYs, H. R. , ALTONA, C. & HAVINGA, E. (1969). Tetrahedron, 25, 3365-3375. JEFFREY, G. A. & PARK, Y. J. (1972). Acta Cryst. B28, 257267. JOHNSON, C. K. (1970). ORTEP. Report ORNL-3794, (2nd rev.), Oak Ridge National Laboratory, Oak Ridge, Tennessee. KLYNE, W. & PRELOG, V. (1960). Experientia, 16, 521-523. KOETZLE, T. F. & HAMILTON, W. C. (1972). Acta Cryst. B28, 2083-2090. KUCHITSU, K. (1968). J. Chem. Phys. 49, 4456-4462. LIDE, D. R. , JR (1960a). J. Chem Phys. 33, 1514-1518. LIDE, D. R. , JR (1960b). J. Chem. Phys. 33, 1519-1522. LIDE, D. R. , JR & CHRISTENSEN, D. (1961). J. Chem. Phys. 35, 1374-1378. NEUTRON DIFFRACTION COMMISSION (1969). Acta Cryst. A25, 391-392. NEWTON, M. D. , LATHAM, W. m. , HEHRE, W. J. & POPLE, J. A. (1970). J. Chem. Phys. 52, 4064-4072. PARK, Y. J., JEFFREY, G. A. & HAMILTON, W. C. (1971). Acta Cryst. B27, 2393-2401. ROHRER, D. C. (1972). Acta Cryst. A28, 425-433. SCHARPEN, L. & LAURIE, V. L. (1963). J. Chem. Phys. 39, 1732-1733. SEQUEIRA, A. , RAJAGOPAL, H. & CHIDAMBARAM, R. (1972). Acta Cryst. B28, 2514-2519. STRAHS, G. (1970). Advanc. Carbohydrate Chem. 25, 53-107. Structure Reports (1952). 16, 483-484. SUNDARALINGAM, M. (1965). J. Amer Chem. Soc. 87, 599605. SUNDARALINGAM, M. (1968). Biopolymers, 6, 189-213.
Stability-Indicating HPTLC Method for Determination of Duloxetine Hydrochloride in Bulk Drug and Tablet Formulation

A simple, accurate, precise, sensitive, selective, and stability-indicating high-performance thin-layer chromatographic method was developed and validated for determination of duloxetine hydrochloride both in bulk drug as well as in tablet formulation. The stationary phase used in our method consisted of HPTLC aluminum plates precoated with silica gel 60F-254, while, chloroform : methanol (8 : 2, v/v) was used as binary mobile phase. These chromatographic conditions eluted the drug effectively, and distinct compact spots were seen, (Rf, retardation factor, value (0.42 ± 0.20). Densitometric determination of duloxetine hydrochloride was carried out in the absorbance mode at a wavelength of 217 nm. The mean value of corelation coefficient; slope and intercept were 0.9962 ± 0.0015, 121.54 ± 0.61, and 987.3 ± 6.17, in the amount range of 600–2000 ng (nanogram) per spot, respectively. Stress testing validation were performed as per the guidelines of International Conference on Harmonization (ICH) and drug was subjected to stress conditions like acid-hydrolysis, alkali-hydrolysis, oxidation, and thermal degradation. As the method effectively separated the active drug from its degradation products, it can be employed as a stability-indicating assay method (SIAM) for identification and quantitative determination of duloxetine HCl in bulk drug and tablet dosage formulation.
Best practices for the visualization, mapping, and manipulation of R‐loops

R‐loops represent an abundant class of large non‐B DNA structures in genomes. Even though they form transiently and at modest frequencies, interfering with R‐loop formation or dissolution has significant impacts on genome stability. Addressing the mechanism(s) of R‐loop‐mediated genome destabilization requires a precise characterization of their distribution in genomes. A number of independent methods have been developed to visualize and map R‐loops, but their results are at times discordant, leading to confusion. Here, we review the main existing methodologies for R‐loop mapping and assess their limitations as well as the robustness of existing datasets. We offer a set of best practices to improve the reproducibility of maps, hoping that such guidelines could be useful for authors and referees alike. Finally, we propose a possible resolution for the apparent contradictions in R‐loop mapping outcomes between antibody‐based and RNase H1‐based mapping approaches.
Novel dual multiplex real-time RT-PCR assays for the rapid detection of SARS-CoV-2, influenza A/B, and respiratory syncytial virus using the BD MAX open system

ABSTRACT SARS-CoV-2 has spread rapidly, causing deaths worldwide. In this study, we evaluated the performance of the BD MAX Open System module for identifying viral pathogens, including SARS-CoV-2, in nasopharyngeal specimens from individuals with symptoms of upper respiratory tract infection. We developed and validated a rapid total nucleic acid extraction method based on real-time reverse transcription-polymerase chain reaction (RT-PCR) for the reliable, high-throughput simultaneous detection of common cold viral pathogens using the BD MAX Platform. The system was evaluated using 205 nasopharyngeal swab clinical samples. For assessment of the limit of detection (LoD), we used SARS-CoV-2, influenza A/B, and respiratory syncytial virus (RSV) RNA standards. The BD MAX dual multiplex real-time RT-PCR panel demonstrated a sensitivity comparable to that of the World Health Organization-recommended SARS-CoV-2 assay with an LoD of 50 copies/PCR. The LoD of influenza A/B and RSV was 100–200 copies/PCR. The overall percent agreement between the BD MAX panel and laboratory-developed RT-PCR test on 55 SARS-CoV-2-positive clinical samples was 100%. Among the 55 positive cases of COVID-19 analysed, no coinfection was detected. The BD MAX rapid multiplex PCR provides a highly sensitive, robust, and accurate assay for the rapid detection of SARS-CoV-2, influenza A/B, and RSV.
Preliminary adipose removal did not prevent diet-induced metabolic disorders in mice

Abstract Background: Obesity is a fundamental factor in metabolic disorders such as hyperlipidemia, insulin resistance, fatty liver, and atherosclerosis. However, effective preventive measures are still lacking. This study aimed to investigate different surgical protocols for removing partial adipose tissue before the onset of obesity and determine whether, and by which protocol, preliminary adipose removal could exert potent preventive effects against diet-induced metabolic disorders. Methods: Male low-density lipoprotein receptor (LDL-R) knockout (KO) mice were randomly divided into four groups and subjected to epididymal fat removal (Epi-FR) surgery, subcutaneous fat removal (suQ-FR) surgery, both subcutaneous and epididymal fat removal (Epi + suQ-FR) surgery, or sham-operation. After 1 week of recovery, all mice were given a high-fat diet (HFD) for 10 weeks to induce metabolic disorders. Results: In the Epi-FR group and the sham-operated group, the mean numbers of the residual subcutaneous fat were 28.59 mg/g and 18.56 mg/g, respectively. The expression of relative genes such as Pparg, Cebpa, Dgat2, Fabp4 and Cd36 in the residual subcutaneous fat increased 2.62, 3.90, 3.11, 2.06, 1.78 times in the Epi-FR group compared with that in the sham-operated group. Whereas in the other fat-removal groups, the residual fat depots had no significant change in either size or gene expression, as compared with those of the sham-operated group. Plasma lipid and glucose levels and insulin sensitivity, as detected by the glucose tolerance test, were not significantly alleviated in the three fat removal groups. Liver mass or lipid content was not attenuated in any of the three fat removal groups. The atherosclerosis burdens in the entire inner aorta and aortic root did not decrease in any of the three fat removal groups. Conclusions: Our data suggest that removal of epididymal adipose or subcutaneous adipose alone or in combination before the onset of obesity did not protect against hyperlipidemia, insulin resistance, fatty liver, or atherosclerosis in LDL-R KO mice fed with a HFD. Hence, adipose removal possibly does not represent a potential approach in preventing obesity-related metabolic disorders in the obesity-susceptible population.
Epidemiology of fowl adenovirus (FAdV) infections in South Korean chickens during 2013–2019 following introduction of FAdV-4 vaccines

ABSTRACT Fowl adenoviruses (FAdV) are important infectious pathogens responsible for causing substantial economic losses to the poultry industry worldwide. One hundred and forty-six FAdV strains were continuously collected and analysed from 2013 to 2019 to understand the epidemiological change and nature of the virus in South Korea from two different standpoints, before and after the release of multiple commercial FAdV-4 vaccines. Phylogenetic analysis of the hexon loop-1 gene sequences showed that 92 strains belonged to FAdV-C (63%), 35 strains to FAdV-E (24%), 18 strains to FAdV-D (12.3%), and one strain to FAdV-A (0.7%), respectively. We provide evidence that the dominant FAdV serotype has recently changed from FAdV-4 to FAdV-8b, as reflected in the proportion of each serotype in field cases in 2019 (18.5% and 77.8%, respectively). The newly emerged FAdV-8b cluster was significantly noticeable compared to the old FAdV clusters, indicating that the development of a vaccine for FAdV-8b may be necessary. Overall, this new insight into FAdV prevalence provides a foundation for strategic control and the development of efficient vaccines against FAdV cases in chickens in South Korea. RESEARCH HIGHLIGHTS The dominant FAdV serotype in South Korea shifted from FAdV-4 to FAdV-8b in 2013–2019. A new cluster of FAdV-8b has emerged in South Korea, indicating the development of new vaccines.
Current attitudes of veterinarians and producers regarding the use of local and systemic analgesia in beef and dairy cattle in the United States.

OBJECTIVE To survey cattle producers and veterinarians about the use of analgesia on US cattle operations. SAMPLE 1,187 members of the following database, electronic mailing lists, and social media groups: FarmProgress master file, American Association of Bovine Practitioners, Academy of Veterinary Consultants, National Milk Producers Federation Farm Evaluators, Dairy Moms Facebook group, and Dairy Girl Network Facebook group. PROCEDURES An online survey was developed to gather information about the frequency of local and systemic analgesia use for common painful procedures and diseases in cattle < 2, 2 to 12, and > 12 months old. Respondents also rated their extent of agreement with each of 10 statements related to pain management in cattle. The survey was available from June 11 to August 10, 2018. Descriptive data were generated. Logistic regression was used for comparisons among cattle age groups and respondents on the basis of their industry role. RESULTS In general, frequency of analgesia use increased as cattle age increased, regardless of the procedure or disease. The odds of analgesia use were lower for men, compared with women, and greater for veterinarians, compared with producers. Many respondents indicated they were cognizant of the benefits of analgesia use in cattle but perceived federal regulations and drug costs as impediments to the implementation of pain mitigation protocols on cattle operations. CONCLUSIONS AND CLINICAL RELEVANCE Results provided insight into current perceptions and use of analgesia in cattle, which can be used to guide implementation of pain mitigation protocols on US beef and dairy cattle operations.
Digital Tools to Support Family-Based Weight Management for Children: Mixed Methods Pilot and Feasibility Study

Background Family-based behavioral therapy is an efficacious approach to deliver weight management counseling to children and their parents. However, most families do not have access to in-person, evidence-based treatment. We previously developed and tested DRIVE (Developing Relationships that Include Values of Eating and Exercise), a home-based parent training program to maintain body weight among children at risk for obesity, with the intent to eventually disseminate it nationally alongside SafeCare, a parent support program that focuses on parent-child interactions. Currently the DRIVE program has only been tested independently of SafeCare. This study created the “mHealth DRIVE” program by further adapting DRIVE to incorporate digital and mobile health tools, including remotely delivered sessions, a wireless scale that enabled a child-tailored weight graph, and a pedometer. Telehealth delivery via mHealth platforms and other digital tools can improve program cost-effectiveness, deliver long-term care, and directly support both families and care providers. Objective The objective of this study was to examine preliminary acceptability and effectiveness of the mHealth DRIVE program among children and parents who received it and among SafeCare providers who potentially could deliver it. Methods Study 1 was a 13-week pilot study of a remotely delivered mHealth family-based weight management program. Satisfaction surveys were administered, and height and weight were measured pre- and post-study. Study 2 was a feasibility/acceptability survey administered to SafeCare providers. Results Parental and child satisfaction (mean of 4.9/6.0 and 3.8/5.0, respectively) were high, and children’s (N=10) BMI z-scores significantly decreased (mean –0.14, SD 0.17; P=.025). Over 90% of SafeCare providers (N=74) indicated that SafeCare families would benefit from learning how to eat healthily and be more active, and 80% of providers reported that they and the families would benefit from digital tools to support child weight management. Conclusions Pediatric mHealth weight management interventions show promise for effectiveness and acceptability by families and providers. Trial Registration Clinicaltrials.gov NCT03297541, https://clinicaltrials.gov/ct2/show/NCT03297541.
The organic output from mechanical–biological treatment plants as a source of microplastics: Mini-review on current knowledge, research methodology and future study perspectives

Plastic pollution is one of the biggest environmental problems facing the world. In recent years, microplastics, polymer particles from 1 µm to 5 mm, have been getting much attention. The presence of microplastics has already been confirmed in aquatic and marine ecosystems, soil, atmosphere, biota, and others. The organic output from mechanical–biological treatment (MBT) plants was added to the list of microplastics sources only recently. However, according to preliminary estimates, it may be the second-largest source of microplastics. This article presents an overview of already published investigations on this microplastics source and explains the supposed pathway of microplastics in the MBT plants. The main waste treatment processes that can affect the amount of microplastics in the organic output have been identified as shredding, sieving and, to a lesser extent, aerobic or anaerobic processing. This mini-review also includes methods used in the scientific literature for microplastics extraction, purification, and identification in organic-rich samples, their advantages and limitations. Particular attention is paid to the methods of identifying the small microplastics, less than 1 mm, since the methods for particles 1−5 mm have been more extensively studied. Furthermore, future research needs are highlighted.
A Network Analysis of Research Topics and Trends in End-of-Life Care and Nursing

This study identified the trends in end-of-life care and nursing through text network analysis. About 18,935 articles published until September 2019 were selected through searches on PubMed, Embase, Cochrane, Web of Science, and Cumulative Index to Nursing and Allied Health Literature. For topic modeling, Latent Dirichlet Allocation (K = 8) was applied. Most of the top ranked topic words for the degree and betweenness centralities were consistent with the top 1% through the semantic network diagram. Among the important keywords examined every five years, “care” was unrivaled. When analyzing the two- and three-word combinations, there were many themes representing places, roles, and actions. As a result of performing topic modeling, eight topics were derived as ethical issues of decision-making for treatment withdrawal, symptom management to improve the quality of life, development of end-of-life knowledge education programs, life-sustaining care plan for elderly patients, home-based hospice, communication experience, patient symptom investigation, and an analysis of considering patient preferences. This study is meaningful as it analyzed a large amount of existing literature and considered the main trends of end-of-life care and nursing research based on the core subject control and semantic structure.
Effects of codon usage on gene expression are promoter context dependent

Abstract Codon usage bias is a universal feature of all genomes. Although codon usage has been shown to regulate mRNA and protein levels by influencing mRNA decay and transcription in eukaryotes, little or no genome-wide correlations between codon usage and mRNA levels are detected in mammalian cells, raising doubt on the significance of codon usage effect on gene expression. Here we show that gene-specific regulation reduces the genome-wide codon usage and mRNA correlations: Constitutively expressed genes exhibit much higher genome-wide correlations than differentially expressed genes from fungi to human cells. Using Drosophila S2 cells as a model system, we showed that the effect of codon usage on mRNA expression level is promoter-dependent. Regions downstream of the core promoters of differentially expressed genes can repress the codon usage effects on mRNA expression. An element in the Hsp70 promoter was identified to be necessary and sufficient for this inhibitory effect. The promoter-dependent codon usage effects on mRNA levels are regulated at the transcriptional level through modulation of histone modifications, nucleosome densities and premature termination. Together, our results demonstrate that promoters play a major role in determining whether codon usage influences gene expression and further establish the transcription-dependent codon usage effects on gene expression.
Hydrogen passivation of deep levels in n–GaN

Differential postgrowth hydrogen passivation of deep levels in n–GaN grown by metal-organic chemical vapor deposition has been directly observed by means of both deep level transient spectroscopy and deep level optical spectroscopy. Two deep levels found at Ec−Et=0.62 and 1.35 eV show strong H passivation effects, with their concentrations decreasing by a factor of ⩾30 and ∼14, respectively. The decrease in the 0.62 eV trap concentration together with its correlation with the presence of Mg in n–GaN is consistent with Mg–H complex formation. A band of closely spaced deep levels observed at Ec−Et=2.64–2.80 eV narrows to Ec−Et=2.74–2.80 eV after hydrogenation, consistent with hydrogen complexing with VGa3− defects as anticipated by earlier theoretical results. Finally, a deep level at Ec−Et=3.22 eV likely related to background acceptors remains unaffected by hydrogen.