Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Signatures Integral to Natural Reprogramming in the Pigment Epithelium Cells after Retinal Detachment in Pleurodeles waltl

The reprogramming of retinal pigment epithelium (RPE) cells into retinal cells (transdifferentiation) lies in the bases of retinal regeneration in several Urodela. The identification of the key genes involved in this process helps with looking for approaches to the prevention and treatment of RPE-related degenerative diseases of the human retina. The purpose of our study was to examine the transcriptome changes at initial stages of RPE cell reprogramming in adult newt Pleurodeles waltl. RPE was isolated from the eye samples of day 0, 4, and 7 after experimental surgical detachment of the neural retina and was used for a de novo transcriptome assembly through the RNA-Seq method. A total of 1019 transcripts corresponding to the differently expressed genes have been revealed in silico: the 83 increased the expression at an early stage, and 168 increased the expression at a late stage of RPE reprogramming. We have identified up-regulation of classical early response genes, chaperones and co-chaperones, genes involved in the regulation of protein biosynthesis, suppressors of oncogenes, and EMT-related genes. We revealed the growth in the proportion of down-regulated ribosomal and translation-associated genes. Our findings contribute to revealing the molecular mechanism of RPE reprogramming in Urodela.
A Modeling Study of Summertime East Pacific Wind-Induced Ocean–Atmosphere Exchange in the Intraseasonal Oscillation

Abstract Intraseasonal precipitation variability over the northeast Pacific warm pool during June–October in the National Center for Atmospheric Research Community Atmosphere Model 2.0. 1 with a relaxed Arakawa–Schubert convection parameterization is found to be strongly sensitive to wind-induced variations in surface latent heat flux. A control simulation with interactive surface fluxes produces northeast Pacific warm pool intraseasonal wind and precipitation variations that are of similar magnitude and structure to those associated with the observed intraseasonal oscillation (ISO). Periods of low-level westerly intraseasonal wind anomalies are associated with enhanced surface latent heat fluxes and enhanced precipitation, as in observations. Variations in surface wind speed primarily control the surface flux anomalies. A simulation in which eastern North Pacific oceanic latent heat fluxes are fixed produces intraseasonal precipitation variations that are significantly weaker than those in the control sim.
Sequence Stratigraphy and Depositional Setting of the Tiber Delta: Integration of High-resolution Seismics, Well Logs, and Archeological Data

ABSTRACT Using archeological evidence, radiocarbon data, well logs, and high-resolution seismic profiles, we applied sequence-stratigraphic analysis to sediments deposited during the last glacio-eustatic cycle on the Tyrrhenian continental margin embracing the Tiber River months. These sediments form a high-frequency sequence of fifth order that has developed over the last 20,000 yr since the last lowstand, hereafter referred to as the Tiber Depositional Sequence (TDS). The TDS is still evolving and lies on a Type 1 sequence boundary that has been identified both on the shelf and below the present delta plain. This sequence consists of lowstand, transgressive, and highstand systems tracts. The lowstand deposits are not present on the shelf but are found on the continental slope, where they constitute the last progradation set of the continental margin. A network of gullies, active when the river mouth was at the shelf break, is present within the lowstand deposits. The transgressive-systems-tract (TST) deposits lie directly on the basal unconformity. Landwards the TST is represented by a retrogradational parasequence set of fluvial, coastal barrier-lagoon, and lagoonal delta facies. Seaward, on the shelf, these parasequences merge into a seismically transparent deposit that forms a condensed section. The flooding surfaces that bound the parasequences are marked by peat layers that were dated by 14C. The radiometric ages were used to draw a carve of sea-level rise for the last 11,000 yr. The top of the transgressive systems tract (maximum flooding surface) is represented by the last peat layer, which was formed about 4700-5000 yr BP and buried 4-5 m below the present upper delta plain. The highstand systems tract is made up of deposits of the present Tiber wave-dominated delta, i.e., upper and lower delta plain, delta front, and prodelta slope. The aligned beach ridges mark the position of the prograding coastline, which for the last 2500 yr can be dated by archeological and historical data. The recent very fast progradation of the Tiber delta, during the last 500 years, is consistent with historical data on floods of the city of Rome and the suspended load of the Tiber River.
Effects of sorghum-based diets with phytase superdosing on broiler performance

Objective: The objective of this study was to evaluate the effects of sorghum-based diets with or without phytase superdosing on broiler performance. Materials and Methods: A 42-d grow-out trial with 1,500 male broiler chicks that were a day old (Ross 708) was conducted. The experiment included 30 pens of 50 birds, with 10 replicate pens per treatment. The 3 dietary treatments were as follows: T1—corn-based diet with 550 phytase units (FTU)/kg phytase (standard), T2—sor-ghum-based diet with 550 FTU/kg phytase, and T3—sor-ghum-based diet with 2,000 FTU/kg phytase (superdose). The diets were formulated to be isocaloric, isonitrogenous, and to contain the same levels of available phosphorus and calcium (Ca) across all treatments. Birds were fed ad libitum following a phase-feeding program. Cumulative BW, BW gain, feed intake, and adjusted feed conversion ratio were calculated. One-way ANOVA followed by Fisher’s LSD was used for statistical analysis. Significant differences were considered when P -values were less than 0.05, and trends were considered when P -values were between 0.1 and 0.05. Results and Discussion: No differences in feed intake were observed ( P > 0.05). At 14 d of age, birds fed T3 tended to gain around 6% more weight (0.368 vs. 0.346 kg) and be 3% more efficient (1.23 vs. 1.27 kg:kg) than birds fed T1 ( P < 0.10). Similarly, by 21 d, birds fed the T3 diet were 2% more efficient (1.284 vs. 1.313 kg:kg; P < 0.05) and tended to gain 4% more weight than T1 birds (0.799 vs. 0.767 kg; P < 0.10). Also, at 28 d, birds fed T3 were 1.7% more efficient than those fed T1 (1.301 vs. 1.324 kg:kg; P
A Mechanism for the Interannual Variation of Summer Northeast Asian Blocking High

Based on the spatial spectral functions describing the atmospheric circulation variation retrieved with observational data, the mechanism for the interannual variation of summer Northeast Asian Blocking High were studied with improved high truncated spectral model. The results showed that when the external thermal forcing distributes as El Nino pattern, there are wave-wave interaction of wave 2 in zonal direction and wave-mean flow interactions between wave 2 and wave 3 in meridianal direction and mean flow of wave 1 in meridianal direction. Under such case, there is positive abnormity over Northeast Asia on 500 hPa geopotential height field, which provides advantage atmospheric circulation background for the frequently occurring of Northeast Asia Blocking High during summer. When the external thermal forcing distributes as La Nina pattern, there exist wave-wave interaction between wave 1 in zonal direction and wave-mean flow interactions between wave 2 and wave 4 in meridianal direction and mean flow of wave 2 in meridianal direction. Under such case, there is negative abnormity over Northeast Asia on 500hPa geopotential height field, which restrains the occurring of Northeast Asia Blocking High during summer.
Cydonia oblonga Miller fruit extract exerts an anti-obesity effect in 3T3-L1 adipocytes by activating the AMPK signaling pathway

BACKGROUND/OBJECTIVES The fruit of Cydonia oblonga Miller (COM) is used traditionally in Mediterranean region medicine to prevent or treat obesity, but its mechanism of action is still unclear. Beyond a demonstrated anti-obesity effect, the fruit was tested for the mechanism of adipogenesis in 3T3-L1 preadipocytes. MATERIALS/METHODS 3T3-L1 preadipocytes were cultured for 8 days with COM fruit extract (COME) at different concentrations (0–600 µg/mL) with adipocyte differentiation medium. The cell viability was measured using an MTT assay; triglyceride (TG) was stained with Oil Red O. The expression levels of the adipogenesis-related genes and protein expression were analyzed by reverse transcription polymerase chain reaction and Western blotting, respectively. RESULTS COME inhibited intracellular TG accumulation during adipogenesis. A COME treatment in 3T3-L1 cells induced upregulation of the adenosine monophosphate-activated protein kinase (AMPK)α phosphorylation and downregulation of the adipogenic transcription factors, such as sterol regulatory element-binding protein 1c, peroxisome proliferator-activated receptor γ, and CCAAT/enhancer binding protein α. The COME treatment reduced the mRNA expression of fatty acyl synthetase, adenosine triphosphate-citrate lyase, adipocyte protein 2, and lipoprotein lipase. It increased the mRNA expression of hormone-sensitive lipase and carnitine palmitoyltransferase I in 3T3-L1 cells. CONCLUSIONS COME inhibits adipogenesis via the AMPK signaling pathways. COME may be used to prevent and treat obesity.
Calcite precipitation in landfills: an essential product of waste stabilization

Abstract Routine monitoring of landfill leachates has been extended to include characterization of suspended solids recovered by filtration. Calcite is consistently identified as a suspended solid, with less frequent reports of quartz and clays (kaolinite, illite, chlorite). Morphologically, calcite occurs as discrete grains, coatings on quartz sand and as microconcretions. Preliminary stable isotope data for seven samples generally show positive δ13C values (relative to PDB) up to +3.5‰ and δ18O values between -5 and -8‰, consistent with an origin through precipitation from leachate. Geochemical modelling of leachate compositions for the same samples indicates that the leachates are saturated with respect to calcite, and that the degree of supersaturation decreases for older samples. Mass balance considerations show that the proportions of methane and carbon dioxide observed for landfill gas do not reflect the amount of bicarbonate that is potentially available from the anaerobic decomposition of putrescible waste. Overall, putrescible waste has the potential to form a maximum of 1.9 g of calcite for every gram of waste, although values less than this are likely to be achieved in practice. From these differing lines of evidence, there can be no doubt that calcite precipitation should be expected to take place within landfill systems as an essential part of the waste degradation and stabilization process, and should be considered in modelling both gas evolution and carbon emissions.
The Trauma of Secularisation in Afrikaans Reformed Churches

On 18 July 2018, a column was published in a South African newspaper, Beeld, in which the authors present the results of interviews conducted with members of Afrikaans Reformed Churches in South Africa. The interviewees reported the trauma they had experienced with the church changing its symbols, which the interviewees experienced as “secularisation. ” Where the church is regarded as a place congregants visit for support in times of uncertainty and anxiety, in this case it has become the source of trauma. Interviewees expressed trauma wherever the following occurred: 1) well-known liturgies, symbols, and songs are replaced with “worldly” ones; 2) electronic music replaces the organ; 3) the pulpit is removed; 4) the pastor becomes an entertainer; and 5) office bearers dress casually. This column was also published in affiliated Afrikaans newspapers Die Burger and Volksblad, which provoked massive reaction in letters to the newspapers. This article reports on the reaction from writers under the following headings: 1) feelings of discomfort and estrangement from the church; 2) feelings of lost holiness; 3) concerns that a sacred space has been violated; 4) anger because symbols as powerful expressions of faith connecting one to God, have been removed from the church; 5) ageing church-goers are being blamed for keeping the church from renewing; 6) accusations that liturgy pointing to the Word of God is being changed; 7) warnings that the church exists by virtue of being different from the world. The article concludes by situating the trauma presented by the letter writers in the tension between tradition and modernity, a tension that is reportedly experienced at present at high levels in Afrikaans Reformed Churches.
Effects of a phytogenic feed additive on growth performance, feed intake, and carcass traits of beef steers

Objective: This study examined the effects of a commercial phytogenic feed additive (PFA) on growth performance, feed efficiency, carcass traits, liver abscesses, and the immune response of growing and finishing steers. Materials and Methods: Forty-five crossbred Angus steers (initial BW = 272 ± 20.5 kg) housed in individual pens (4.9 × 1.8 m) were used in a randomized complete block design in a 110-d growing and 120-d finishing experiment. Steers were blocked by BW and allocated to 1 of 3 treatments: control (without PFA and monensin), PFA at 500 mg/steer daily, or monensin at 300 mg/steer daily. Steers were fed a TMR ad libitum once daily and weighed on d 32, 59, and 110 in the growing phase but only at the beginning and the end of the finishing phase. Results and Discussion: During growing, DMI did not differ, whereas final BW (trend; 415 vs. 403 kg) and ADG (numerically; 1.31 vs. 1.20 kg/d) were greater with PFA than control but did not differ from monensin (BW = 422 kg and ADG = 1.38 kg/d). Gain: feed was greater with monensin (0.173) than with PFA (0.161) and for the control (0.156). During finishing, ADG, G:F, and carcass traits did not differ, whereas DMI and acute proteins were lesser with monensin than with PFA and for the control.
Research on Shear Strength Parameters of the Silty Fine Sand and the Rounded Gravel Layers in Nanning City

The silty fine sand and rounded gravel layers are widely distributed in Nanning City, China. Due to the low clay content, the silty fine sand and rounded gravel layers are prone to disturbance during sampling and transportation, which affects the shear strength test results. The reasonable determination of their shear strength is significant and imperative to the project. The rail transit project in Nanning is under large-scale construction. This work obtained the shear strength of the silty fine sand and the rounded gravel layers by conducting laboratory tests on undisturbed samples from deep foundation pits, combined with large-scale direct shear in situ tests. In addition, geotechnical investigation reports for typical projects in Nanning City were compiled, and the test data for the silty fine sand and the rounded gravel layers were comparatively analyzed using the empirical value. The results show that the shear strength test values of the fine sand layer are consistent with the current standard empirical values, and empirical values can be used for reference. The shear strength test value of the rounded gravel layer has significantly improved compared to the current standard empirical value, with a cohesion (c) value of 0–6.8 kPa and an increase in internal friction angle (φ) of 0%–12.5%. It is recommended to determine the shear strength of the rounded gravel layer based on the actual situation.
Reconstructing relative transmission rates in Bayesian phylodynamics: Two-fold transmission advantage of Omicron in Berlin, Germany during December 2021

Abstract Phylodynamic methods have lately played a key role in understanding the spread of infectious diseases. During the coronavirus disease (COVID-19) pandemic, large scale genomic surveillance has further increased the potential of dynamic inference from viral genomes. With the continual emergence of novel severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) variants, explicitly allowing transmission rate differences between simultaneously circulating variants in phylodynamic inference is crucial. In this study, we present and empirically validate an extension to the BEAST2 package birth–death skyline model (BDSKY), BDSKY\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} $\lambda $\end{document}, which introduces a scaling factor for the transmission rate between independent, jointly inferred trees. In an extensive simulation study, we show that BDSKY\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} $\lambda $\end{document} robustly infers the relative transmission rates under different epidemic scenarios. Using publicly available genome data of SARS-CoV-2, we apply BDSKY\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} $\lambda $\end{document} to quantify the transmission advantage of the Omicron over the Delta variant in Berlin, Germany. We find the overall transmission rate of Omicron to be scaled by a factor of two with pronounced variation between the individual clusters of each variant. These results quantify the transmission advantage of Omicron over the previously circulating Delta variant, in a crucial period of pre-established non-pharmaceutical interventions. By inferring variant- as well as cluster-specific transmission rate scaling factors, we show the differences in transmission dynamics for each variant. This highlights the importance of incorporating lineage-specific transmission differences in phylodynamic inference.
Investigating the factors of selecting audit clients: Evidence from an emerging market

This study investigates the insights and criteria audit partners use to select prospective clients in an emerging market. We use questionnaires to solicit responses from a sample of auditors at the partner/manager level in Big and non-Big 4 audit firms with international affiliations in an emerging economy. Descriptive statistical tools including the chi-square test and multiple logistic regression analysis are used for the analysis. This study finds that auditor reputation enhancement and corporate governance effectiveness are significantly associated with the acceptance of listed companies and that the higher financial reporting quality of listed companies and the need to promote audit and assurance services are significant factors affecting such decisions. Audit firms tend to select parents or subsidiaries because of the expected effective audits and reduced misstatement and litigation risks and audit firm industry expertise is needed to mitigate expected client risks to significantly affect the selection of clients with prior-year audit qualifications. Fraud is significantly associated with the selection of clients with prior violations reported by government monitoring bodies. This study is among the few empirical studies in emerging economies that provide insights from practicing auditors on a set of comprehensive attributes that affect the selection of audit clients. The findings have implications for audit partners and firms, auditees, and the audit profession in selecting clients that fit the firm’s and profession’s vision of audit branding and reputation
Joint fiber and MEC deployment for sparsely populated areas

The deployment of multi-access edge computing (MEC) networks gives rise to the MEC placement problem, which deals with finding the right server locations to reduce the cost and guarantee network performance. Multiple papers have been presented to solve this problem, but they are usually oriented to urban areas where short distances and high-quality network infrastructure are assumed. When this problem must be solved for sparsely populated areas, like rural environments, the connectivity is not always granted and the deployment of such connectivity using fiber technologies should be included in the problem. In contrast to urban areas, where the density of users is high and therefore the main problem is capacity, in sparsely populated areas, the problem lies in how to cost-effectively plan the MEC sites and the interconnecting network while meeting the delay constraints of the services offered through that network. This paper proposes a technique to solve the MEC placement problem considering the joint deployment of the optical network required to interconnect the base stations and the MEC servers. It consists of a three-phase scheme, which combines a spanning tree topology, for fiber deployment, with the use of mixed integer linear programming (MILP) formulations to minimize MEC servers and MEC data centers (MEC-DCs). We have applied the technique in a case study for a province in Spain (Valladolid, $8110\;{{\rm km}^2}$), obtaining a reduction of around 50% of the total cost when compared to a previous work. In addition, a clustering method is proposed to improve the scalability of the model for large scenarios. A simulation study is also presented to demonstrate the performance of the proposal assuming a ${94}{,}{226}\;{{\rm km}^2}$ region (Castilla y León) with 1576 base stations.
Hawaii Rainfall Anomalies and El Niño

Abstract An analysis of composite, seasonal rainfall anomalies in Hawaii shows that deficient rainfall tends to occur frequently in winter and spring of the year following an El Nino. The reliability of the El Nino composite has been tested using a Monte Carlo simulation technique. Upper-air circulation patterns during the recent three El Nino events are discussed in relation to drought winters in Hawaii. The more eastward elongated subtropical jet stream in the North Pacific and the thermally induced local Hadley circulation in the central North Pacific, characteristics of El Nino winters, are unfavorable for rainfall in Hawaii.