Miracle-dz/UniFAR-FTUs huggingface dataset:
Predictability of stemflow in a species‐rich tropical forest

Numerous studies investigated the influence of abiotic (meteorological conditions) and biotic factors (tree characteristics) on stemflow generation. Although these studies identified the variables that influence stemflow volumes in simply structured forests, the combination of tree characteristics that allows a robust prediction of stemflow volumes in species‐rich forests is not well known. Many hydrological applications, however, require at least a rough estimate of stemflow volumes based on the characteristics of a forest stand. The need for robust predictions of stemflow motivated us to investigate the relationships between tree characteristics and stemflow volumes in a species‐rich tropical forest located in central Panama. Based on a sampling setup consisting of ten rainfall collectors, 300 throughfall samplers and 60 stemflow collectors and cumulated data comprising 26 rain events, we derive three main findings. Firstly, stemflow represents a minor hydrological component in the studied 1‐ha forest patch (1.0% of cumulated rainfall). Secondly, in the studied species‐rich forest, single tree characteristics are only weakly related to stemflow volumes. The influence of multiple tree parameters (e.g. crown diameter, presence of large epiphytes and inclination of branches) and the dependencies among these parameters require a multivariate approach to understand the generation of stemflow. Thirdly, predicting stemflow in species‐rich forests based on tree parameters is a difficult task. Although our best model can capture the variation in stemflow to some degree, a critical validation reveals that the model cannot provide robust predictions of stemflow. A reanalysis of data from previous studies in species‐rich forests corroborates this finding. Based on these results and considering that for most hydrological applications, stemflow is only one parameter among others to estimate, we advocate using the base model, i.e. the mean of the stemflow data, to quantify stemflow volumes for a given study area. Studies in species‐rich forests that wish to obtain predictions of stemflow based on tree parameters probably need to conduct a much more extensive sampling than currently implemented by most studies. Copyright © 2015 John Wiley & Sons, Ltd.
K o - OCR Relationships in Soil

The relationships between K o and OCR are investigated for primary loading - unloading - reloading conditions. The study reviews laboratory data from over 170 different soils and presents an approach common to clays, silts and sands. Simple empirical methods for predicting K o for normally consolidated and overconsolidated soils are evaluated. The validity of the methods is supported by statistical analyses. On the basis of the findings, only the effective stress friction angle (O') and prior stress history (OCR and OCRmax) are needed to predict approximate values of K o .
Outpatient hip and knee arthroplasty: how is it utilized?

1 Department of Orthopedic Surgery, Clinical Orthopaedic Research Hvidovre (CORH), Copenhagen University Hospital Hvidovre, Copenhagen, Denmark; 2 Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Science, University of Oxford, Oxford, UK; 3 Department of Orthopedics, Sahlgrenska University Hospital, Gothenburg, Sweden; 4 Department of Orthopedic Surgery, Rush University Medical Center, Chicago, Illinois, USA Correspondence: kirgromov@gmail.com Submitted 2023-09-19. Accepted 2023-10-01.
AlexandrusPS: A User-Friendly Pipeline for the Automated Detection of Orthologous Gene Clusters and Subsequent Positive Selection Analysis

Abstract The detection of adaptive selection in a system approach considering all protein-coding genes allows for the identification of mechanisms and pathways that enabled adaptation to different environments. Currently, available programs for the estimation of positive selection signals can be divided into two groups. They are either easy to apply but can analyze only one gene family at a time, restricting system analysis; or they can handle larger cohorts of gene families, but require considerable prerequisite data such as orthology associations, codon alignments, phylogenetic trees, and proper configuration files. All these steps require extensive computational expertise, restricting this endeavor to specialists. Here, we introduce AlexandrusPS, a high-throughput pipeline that overcomes technical challenges when conducting transcriptome-wide positive selection analyses on large sets of nucleotide and protein sequences. The pipeline streamlines 1) the execution of an accurate orthology prediction as a precondition for positive selection analysis, 2) preparing and organizing configuration files for CodeML, 3) performing positive selection analysis using CodeML, and 4) generating an output that is easy to interpret, including all maximum likelihood and log-likelihood test results. The only input needed from the user is the CDS and peptide FASTA files of proteins of interest. The pipeline is provided in a Docker image, requiring no program or module installation, enabling the application of the pipeline in any computing environment. AlexandrusPS and its documentation are available via GitHub (https://github.com/alejocn5/AlexandrusPS).
Alzheimer's disease‐induced phagocytic microglia express a specific profile of coding and non‐coding RNAs

Abstract INTRODUCTION Alzheimer's disease (AD) is a neurodegenerative disease and the main cause of dementia in the elderly. AD pathology is characterized by accumulation of microglia around the beta‐amyloid (Aβ) plaques which assumes disease‐specific transcriptional signatures, as for the disease‐associated microglia (DAM). However, the regulators of microglial phagocytosis are still unknown. METHODS We isolated Aβ‐laden microglia from the brain of 5xFAD mice for RNA sequencing to characterize the transcriptional signature in phagocytic microglia and to identify the key non‐coding RNAs capable of regulating microglial phagocytosis. Through spatial sequencing, we show the transcriptional changes of microglia in the AD mouse brain in relation to Aβ proximity. RESULTS Finally, we show that phagocytic messenger RNAs are regulated by miR‐7a‐5p, miR‐29a‐3p and miR‐146a‐5p microRNAs and segregate the DAM population into phagocytic and non‐phagocytic states. DISCUSSION Our study pinpoints key regulators of microglial Aβ clearing capacity suggesting new targets for future therapeutic approaches.
A note on estimating finite difference interblock hydraulic conductivity values for transient unsaturated flow problems

Nine different methods of weighting interblock hydraulic conductivity values used for modeling one-dimensional water transfer in homogeneous unsaturated soil are tested for their influence upon the accuracy of the finite difference solution. On the basis of these results the most suitable weighting relation is selected. In a first stage the numerical results obtained by the models using the various conductivity weighting formulas are compared with the quasi-analytical solution developed by Philip for a clay soil. In a second stage the models are used to simulate a laboratory experiment carried out on a sandy soil. In both cases, rather drastic boundary conditions are applied. It appears clearly from these tests that the weighting errors are of critical influence on the accuracy of solution. As proposed in this note, the geometric mean taken over two adjacent hydraulic conductivity values is the only weighting method that generates little weighting error. The latter weighting relation is found to be preferable in terms of flexibility, precision, and feasibility.
Two Types of Strong Northeast Asian Summer Monsoon

The characteristics of a strong northeast Asian summer monsoon (NEASM) with and without (A and B type, respectively) a basinwide warming in the Indian Ocean during the preceding winter are examined for the period of 1979-2006. In the case of the A type, strong El Nino-like sea surface temperature (SST) decays very rapidly from the preceding winter (December-February) to the following summer (June-August), which may be due to a feedback process of the warm Indian Ocean. In addition, the A-type strong NEASM is more associated with a weak western North Pacific summer monsoon than the B-type strong NEASM. On the other hand, for the B type an El Nino-like SST during the preceding winter is a persistent influence into the following summer. A striking difference can be found in the atmospheric teleconnection pattern from the tropics to the midlatitudes over the Indo-Pacific region, that is, the Pacific-Japan-like pattern versus a pronounced Rossby wave train pattern. This may result from the difference in location of the maximum center of rainfall anomalies over the tropical northwestern Pacific between the two types of strong NEASM. The authors argue that Indian Ocean basin warming plays a role in modifying the convective system over the subtropical western Pacific, resulting in changes in atmospheric teleconnections between the two types of strong NEASM. The weak NEASM, in which the anomalous rainfall pattern resembles that of the A-type strong NEASM except for the sign, is also discussed.
Leptospirosis in the Rural Areas of Guilan Province (2004-2005)

Introduction: Leptospirosis is a worldwide disease which affects wild and domestic animals as well as human beings, and has become a major public health problem throughout the world, particularly in the tropics and temperate regions, especially in costal region of northern par tap Iran. It is caused by the pathogenic Leptospira sp. strains that are often responsible for nervous system abnormalities. The disease varies from subclinical infection to a severe illness with multi organ involvement. Rodents and domestic animals are the reservoir of this disease. Rural inhabitants are mainly farmers, therefore all of them could be affected with direct contact by animals and working on farms, since most of them are working specially in warm seasons and bare-footed with paying no attention to any basic advice. In this research, we wanted to determine the incidence rate of Leptospira between the rural inhabitants, and detect the serum titers of the patients. Materials and Methods: This study carried out on 552 people in a selected area of Guilan Province based on the stratified sampling criteria. All of these rural inhabitants who were cultivators and animal husbandmen were volunteers for this research. All samples were tested through MAT (Microscopic Agglutination Test) method, then positive serums and different titers were all reported. Results: 21% of the population had positive serum reaction to different strains of Leptospira spp. and according to the results, 21% and 22% of men and women had positive serum reaction respectively. Prevalence of disease is more visible in the 30-50-year-old rural inhabitants. Area L. icterohaemorrhagiae is the majority of different strains of leptospira spp with the serum titers ranged from 1:100(54% of cases) to The prevalence of leptospirosis among cultivators is higher than others. Conclusion: According to the findings, we could say that leptospirosis exists in Guilan province, but since this test has been performed on limited people in this province, and since the tropic and temperate climate in this province is seen in the most time of the year, then it is necessary to do this test in all parts of this province.
ASSESSING THE EFFICIENCY OF SUBSURFACE CONSTRUCTED WETLANDS PLANTED WITH DIFFERENT MACROPHYTES IN REMOVING HEAVY METALS FROM WASTEWATER

This study was undertaken to assess the efficiency of macrophyte plants in removing heavy metal in municipal wastewater using laboratory scale quarry dust vertical constructed subsurface wetlands. Plants used were Typha latifolia, Phragmites australis and Polygonam spp. The control treatment was not vegetated. The parameters evaluated were the concentration of lead, cadmium and zinc in the influent and effluent sewage after different retention periods in the wetland. At the end of experiment the macrophytes were harvested and the concentration of the heavy metals in shoots and roots determined. Polygonam spp. absorbed highest amounts of Zinc while Phragmites australis absorbed the highest amount of lead and cadmium. The roots had a higher concentration of the heavy metals than the shoots. Planted beds differed in the removal rates of the heavy metals which were found to be dependent on the plant species. The percentage removal of the heavy metals from the raw sewage by the vegetated system was 87%, 83% and 84% for lead, cadmium and zinc respectively after a retention period of 8 days. The control surprisingly showed a percentage removal in excess of 60%, indicating that the removal of heavy metals was mainly accomplished by the quarry dust medium. The concentrations of the three heavy metals in the effluent sewage were all below the maximum allowable concentrations for discharge into the environment. The constructed wetlands were therefore effective in reducing the heavy metals concentrations from the raw sewage to tolerable levels.
Magnetism of the Mid-Ordovician Tramore Volcanics, SE Ireland, and the Question of a Wide Proto-Atlantic Ocean

Useful evidence regarding a Proto-Atlantic (Iapetus) ocean may be obtained from paleomagnetic comparisons across sutures in presumed hybrid blocks such as Newfoundland, Britain and Ireland. Usually this involves Lower Paleozoic results that may be further compared with data from larger cratonic units, e.g. Europe and North America. Towards these ends the first paleomagnetic results are reported for an igneous suite comprising andesite sills and flows, pillow lavas, tuffs, mafic intrusives and rhyolite collected from a 20-km wide coastal section near Tramore, Co. Waterford, Eire. From associated fossil evidence the rocks range in age from Lower Caradoc to somewhat earlier (Llanvirn? ) Ordovician time, or a mean age of about 460 Myr. Although at 12 out of the 28 sites studied the remanence of the samples after demagnetization was too weak to measure, or was randomly or anomalously directed, the mean vectors of the remaining 16 sites (76 samples) after AF or thermal treatment and geological tilt correction became well grouped in sharp misalignment with the present Earth's field direction. At most sites the vector groupings of the samples improved upon demagnetization. These results indicate long-term stability of the remanence. At the 6 oldest stable sites this remanence is of reversed polarity and is nearly antiparallel to the (normal) mean direction of the 10 youngest sites, giving an overall north pole at 11S, 162W (dp, dm=10, 13; N=16 sites). Confidence that the magnetization reflects a midOrdovician field direction is based on 1) a strongly positive fold test demonstrating that this magnetization pre-dates the Caledonian folding, 2) the presence of both polarities, and 3) the other long-term stability evidence cited. The Tramore pole significantly diverges from most published midto late Ordovician paleomagnetic poles for the British Isles, including the Mweelrea ignimbrites in western Ireland. The data support a 30 rotation of the British Isles relative to the geomagnetic field during the Ordovician. The 30 angular difference between the Tramore and Mweelrea poles can be reconciled only through relative rotation between the two sampling localities in a sense that places them on opposite margins of a mid-Ordovician ProtoAtlantic ocean. Application of these Irish paleomagnetic results to the plate tectonic model of Phillips, Stillman and Murphy yields a unique rotation pivot for post mid-Ordovician closure of a Proto-Atlantic ocean 3,300+2,200 km wide. Ordovician paleomagnetic comparisons across the North Atlantic suggest that a total Proto-Atlantic reconstruction is premature.
Measuring Negative and Positive Thoughts in Children: An Adaptation of the Children's Automatic Thoughts Scale (CATS) Sanne M. HogendoornLidewij H. WoltersLeentje Vervoort • Pier J. M. PrinsFrits BoerEmelie KooijElse de Haan

The Author(s) 2010. This article is published with open access at Springerlink.com Abstract The aim of this study is to describe the factor structure and psychometric properties of an extended ver- sion of the Children's Automatic Thoughts Scale (CATS), the CATS-Negative/Positive (CATS-N/P). The CATS was originally designed to assess negative self-statements in children and adolescents. However, positive thoughts also play a major role in childhood disorders such as anxiety and depression. Therefore, positive self-statements were added to the CATS. The CATS-N/P was administered to a community sample of 554 children aged 8-18 years. The results of a confirmatory factor analysis revealed that the positive self-statements formed a separate and psycho- metrically sound factor. Internal and short-term test-retest reliability was good. Boys reported more hostile and positive thoughts than girls; and younger children reported more negative thoughts concerning physical threat, social threat, and failure than older children. In conclusion, the results of the current study support the use of the CATS-N/ P for the measurement of positive and negative thoughts in children. The application of the CATS-N/P can facilitate further research on cognitive factors in different childhood disorders.
Nonnegative Matrix Factorization for identification of unknown number of sources emitting delayed signals

Factor analysis is broadly used as a powerful unsupervised machine learning tool for reconstruction of hidden features in recorded mixtures of signals. In the case of a linear approximation, the mixtures can be decomposed by a variety of model-free Blind Source Separation (BSS) algorithms. Most of the available BSS algorithms consider an instantaneous mixing of signals, while the case when the mixtures are linear combinations of signals with delays is less explored. Especially difficult is the case when the number of sources of the signals with delays is unknown and has to be determined from the data as well. To address this problem, in this paper, we present a new method based on Nonnegative Matrix Factorization (NMF) that is capable of identifying: (a) the unknown number of the sources, (b) the delays and speed of propagation of the signals, and (c) the locations of the sources. Our method can be used to decompose records of mixtures of signals with delays emitted by an unknown number of sources in a nondispersive medium, based only on recorded data. This is the case, for example, when electromagnetic signals from multiple antennas are received asynchronously; or mixtures of acoustic or seismic signals recorded by sensors located at different positions; or when a shift in frequency is induced by the Doppler effect. By applying our method to synthetic datasets, we demonstrate its ability to identify the unknown number of sources as well as the waveforms, the delays, and the strengths of the signals. Using Bayesian analysis, we also evaluate estimation uncertainties and identify the region of likelihood where the positions of the sources can be found.
Optimization of stabilized anaerobic landfill leachate treatment using ozonation with metallic compound using response surface methodology

Malaysia encounters a consistent rise in the generation of solid waste and leachate on a daily basis. It should also be noted that leachate has a low degree of biodegradability (BOD5/chemical oxygen demand [COD]), as shown by its BOD5/COD ratio. Its high toxicity levels significantly threaten the environment, water bodies, and human well‐being. High concentrations of COD, color, and ammoniacal nitrogen (NH3‐N) in leachate prevent this wastewater from being allowed to be discharged directly into the water body. Therefore, an effective process to remove the pollutant is desired. The aims of this study are to investigate the performance of ozonation with two metallic compounds, ZrCl4 and SnCl4, and optimize their performance using response surface methodology (RSM). In this study, the performance of ozonation with ZrCl4 (O3/ZrCl4) recorded better pollutant removals compared with the ozonation with tin tetrachloride (O3/SnCl4), as seen in the removals of 99.8%, 93.5%, and 46.3% for color, COD, and NH3‐N, respectively. These removals were achieved by following the experimental model (optimum experiment condition) generated by RSM at O3 dosage of 31 g/m3, COD and ZrCl4 dosage ratio (COD, mg/L/ZrCl4, mg/L) of 1:1.35, with the pH solution of 8.78 and reaction time of 89 min. The R2 of each parameter for this model was recorded as 0.999 (COD), 0.999 (color), and 0.998 (NH3‐N), respectively. These data indicated that the model is well fitted as the predicted data by statistical calculation and in good agreement with the actual data.
An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors Results and Discussion

Transcription factors (TFs) play key roles in both development and stress responses. By integrating into and rewiring original systems, novel TFs contribute significantly to the evolution of transcriptional regulatory networks. Here, we report a high-confidence transcriptional regulatory map covering 388 TFs from 47 families in Arabidopsis. Systematic analysis of this map revealed the architectural heterogeneity of developmental and stress response subnetworks and identified three types of novel network motifs that are absent from unicellular organisms and essential for multicellular development. Moreover, TFs of novel families that emerged during plant landing present higher binding specificities and are preferentially wired into developmental processes and these novel network motifs. Further unveiled connection between the binding specificity and wiring preference of TFs explains the wiring preferences of novel-family TFs. These results reveal distinct functional and evolutionary features of novel TFs, suggesting a plausible mechanism for their contribution to the evolution of multicellular organisms. Novel genes can rapidly integrate into existing networks and effectively drive the evolution of phenotypes (Chen et al. 2010, 2013). By turning gene transcription on or off at a specific time in a given space, transcription factors (TFs) and transcriptional regulatory networks play key roles in both development and stress responses. After diverging from other kingdoms more than one billion years ago, plants have evolved a sophisticated and distinctive system to precisely regulate development and to rapidly respond to environmental changes. Particularly during plant landing, many novel TF families emerged, contributing to more complex morphogenesis and adaption to a dramatically changed environment (Lang et al. 2010; Zhang, Jin, et al. 2011; Jin et al. 2014), providing an intriguing case to investigate how novel TFs contribute to the evolution of transcriptional regulatory systems. However, the absence of a large-scale, high-quality transcriptional regulatory network in plants hinders the full understanding of the contribution of novel TFs to the evolution of transcriptional regulatory systems. The identification of numerous validated regulatory interactions across the vast scientific literature concerning studies in Arabidopsis, the most widely used model plant, offers a unique opportunity to build a high-confidence transcriptional regulatory network (Aerts et al. 2008). In this study, we cu-rated a literature-derived transcriptional regulatory map for Arabidopsis and revealed the heterogeneity of developmental and stress response subnetworks and the wiring preference of novel TFs in transcriptional regulatory systems. These results provide insight into the fate determination of novel TFs, suggesting a plausible mechanism for the contribution of novel …