Miracle-dz/UniFAR-FTUs huggingface dataset:
Ohana: detecting selection in multiple populations by modelling ancestral admixture components

One of the most powerful and commonly used methods for detecting local adaptation in the genome is the identification of extreme allele frequency differences between populations. In this paper, we present a new maximum likelihood method for finding regions under positive selection. The method is based on a Gaussian approximation to allele frequency changes and it incorporates admixture between populations. The method can analyze multiple populations simultaneously and retains power to detect selection signatures specific to ancestry components that are not representative of any extant populations. We evaluate the method using simulated data and compare it to related methods based on summary statistics. We also apply it to human genomic data and identify loci with extreme genetic differentiation between major geographic groups. Many of the genes identified are previously known selected loci relating to hair pigmentation and morphology, skin and eye pigmentation. We also identify new candidate regions, including various selected loci in the Native American component of admixed Mexican-Americans. These involve diverse biological functions, like immunity, fat distribution, food intake, vision and hair development.
Cognitive Maps and Urban Travel

The authors present an examination of the relationship between cognitive maps and travel behavior in urban environments. They discuss transportation-related issues such as the cognition of transportation networks, path selection, wayfinding and navigation. They examine problems of selecting paths to destinations through the use of existing transportation networks. The authors discuss concerns relating to the role of trip purpose in path selection, looking at how different purposes spawn different path or route selection strategies. The authors conclude with a look at how cognitive maps, cognitive mapping, and travel choice modeling interact.
TSST: an Expert System for Temporary Soil Stabilization on Commercial and Residential Building Sites in Malaysia

Urban development has been particularly rapid in Malaysia. An adverse environmental effect of urban growth in Malaysia has been the frequent occurrence of excessive soil losses from construction sites. According to Malaysian regulations, construction activities require an erosion and sediment control plan duly approved by the Department of Drainage and Irrigation before starting activities. An erosion and sediment control plan is for the local authority to effectively manage construction projects with particular emphasis on minimizing soil erosion during construction activities. The selection of temporary soil stabilization technique is an important, but complex and time-consuming, task that has to deal with a huge amount of data, domain regulations, and expert knowledge in terms of environmental protection, water pollution prevention, and soil erosion mitigation. An expert system has been successfully applied in various domains including environmental science. In this paper, an expert system – TSST – developed by using Microsoft Visual Basic was introduced. TSST to be used for selection of temporary soil stabilization technique at housing and new township development projects was designed based on the legal process in Malaysia. TSST primarily aims to provide an educational and support system for engineers and decision-makers during construction activities in terms of having the least negative impact around the area. It displays an erosion and sediment control plan in report form. When the use of TSST in such a plan becomes widespread, it is highly possible that it will benefit in terms of having more accurate and objective decisions on construction projects that are mainly focused on erosion and sediment control measures.
On the influence of local dispersion in solute transport through formations with evolving scales of heterogeneity

The aim of the present study is to determine the longitudinal dispersion coefficient DL for transport in formations of long‐range permeability fields by considering both large‐scale advection and local‐scale dispersion; the nonergodicity of the plume will be considered throughout the work. The scope is twofold: (1) to analyze the mutual role played by both the “macroscale” and the local scales of heterogeneity in determining the overall transport properties and (2) to check the validity of the results obtained in the past, in particular concerning the occurrence of anomalous transport. The results are obtained through the Lagrangean formulation of transport, by the means of a few simplifying assumptions. Two models of permeability K variations are considered: (1) a stationary Y = ln K with unbounded integral scale and (2) a formation of Y of stationary increments. For both cases, the longitudinal macrodispersion coefficient DL always grows with time when local‐scale dispersion is present, indicating that transport is always anomalous for the random fields examined. The results are in variance with those obtained in the past by considering nonergodic transport but neglecting the local‐scale dispersion [e.g., Dagan, 1994; Bellin et al., 1996] and in qualitative agreement to those obtained by adopting the ergodic assumption [e.g., Neuman, 1990; Glimm and Sharp, 1991], which, however, predicted higher rates of growth of DL with time. We conclude that the interplay between large‐scale, advective displacement and local‐scale dispersion has a fundamental impact on the occurrence of anomalous transport in long‐range correlated permeability random fields.
On the tropospheric measurements of ozone by the Stratospheric Aerosol and Gas Experiment II (SAGE II, version 6.1) in the tropics

Tropospheric measurements of ozone from SAGE II (version 6.1) in the tropics have been analyzed using 12 years of data (1985–1990, 1994–1999). The seasonally averaged vertical profiles of the ozone mixing ratio in the upper troposphere have been presented for the first time from satellite measurements. These profiles show qualitative similarities with corresponding seasonal mean ozonesonde profiles at northern and southern tropical stations and are about 40–50% less than the sonde values. Despite this systematic offset, the measurements appear to be consistent with a zonal wave one pattern in the upper tropospheric column ozone and with the recently predicted summertime ozone enhancement over the Middle East. These results thus affirm the usefulness of the occultation method in studying tropospheric ozone.
Sensitivity of mean transit time estimates to model conditioning and data availability

Mean transit times (MTTs) can give useful insights into the internal processes of hydrological systems. However, varying model conditioning assumptions and data availability can limit the use of MTT, particularly in terms of comparing the results of studies using different assumptions and data records of varying lengths. We present a systematic analysis of sensitivity of MTT estimates to different methods of artificially extending the data record, varying model warm‐up period lengths and varying sampling intervals for a small upland catchment in the Scottish Highlands. The analysis was based on Cl− data in conjunction with the convolution integral model using the gamma distribution as transit time distribution. It could be shown that three out of four different methods to artificially extend the data record and to generate a warm‐up period give mostly equivalent results. The required minimum warm‐up period length to reliably estimate MTT for a 3‐year period of data was observed to be about 2 years or 3 times the MTT, implying that ∼95% of the tracer signal entering the stream at day 1 of the warm‐up period has to be recovered by the end of the warm‐up period in order to avoid significant deviations from the best available MTT estimates. It was furthermore found that sampling intervals of up to 4 weeks can produce MTT estimates within about 0·25 times the best available MTT estimate, albeit with potentially increased process misrepresentation in terms of the gamma distribution parameter α. Copyright © 2011 John Wiley & Sons, Ltd.
Chemical characterization of water-soluble organic carbon aerosols at a rural site in the Pearl River Delta, China, in the summer of 2006

[1] Online measurements of water-soluble organic carbon (WSOC) aerosols were made using a particle-into-liquid sampler (PILS) combined with a total organic carbon (TOC) analyzer at a rural site in the Pearl River Delta region, China, in July 2006. A macroporous nonionic (DAX-8) resin was used to quantify hydrophilic and hydrophobic WSOC, which are defined as the fractions of WSOC that penetrated through and retained on the DAX-8 column, respectively. Laboratory calibrations showed that hydrophilic WSOC (WSOCHPI) included low-molecular aliphatic dicarboxylic acids and carbonyls, saccharides, and amines, while hydrophobic WSOC (WSOCHPO) included longer-chain aliphatic dicarboxylic acids and carbonyls, aromatic acids, phenols, organic nitrates, cyclic acids, and fulvic acids. On average, total WSOC (TWSOC) accounted for 60% of OC, and WSOCHPO accounted for 60% of TWSOC. Both WSOCHPI and WSOCHPO increased with photochemical aging determined from the NOx/NOy ratio. In particular, the average WSOCHPO mass was found to increase by a factor of five within a timescale of ∼10 hours, which was substantially larger than that of WSOCHPI (by a factor of 2–3). The total increase in OC mass with photochemical aging was associated with the large increase in WSOCHPO mass. These results, combined with the laboratory calibrations, suggest that significant amounts of hydrophobic organic compounds (likely containing large carbon numbers) were produced by photochemical processing. By contrast, water-insoluble OC (WIOC) mass did not exhibit significant changes with photochemical aging, suggesting that chemical transformation of WIOC to WSOC was not a dominant process for the production of WSOC during the study period.
Foreshock activity related to enhanced aftershock production

Foreshock activity sometimes precedes the occurrence of large earthquakes, but the nature of this seismicity is still debated, and whether it marks transient deformation and/or slip nucleation is still unclear. We here study at the worldwide scale how foreshock occurrence affects the postseismic phase and find a significant positive correlation between foreshock and aftershock activities: earthquakes preceded by accelerating seismicity rates produce 40% more aftershocks on average, and the length of the aftershock zone after 20 days is 20% larger. These observations cannot be reproduced by standard earthquake clustering models that predict the accelerating pattern of foreshock occurrence but not its impact on aftershock activity. This strongly suggests that slow deformation transients, possibly related to episodic creep, could initiate prior to the main shock and extend past the coseismic phase, resulting in compound ruptures that include a very long period (up to tens of days) component.
Notes on the occurrence of Gampsocoris Fuss, 1852 (Hemiptera: Heteroptera: Berytidae) in Poland

In Poland the genus Gampsocoris Fuss, 1852 is represented by two species: G. punctipes (Germar, 1822) and G. culicinus Seidenstücker, 1948. The paper presents new localities of both species, including the second record of G. culicinus in Poland. Additional information on their biology is provided. A possible immigration route of G. culicinus into Polish territory is discussed.
Sun‐coupled climate connection between eastern Asia and northern Atlantic

Few of annually resolved proxy temperature records are reported to coincide with centennial‐to‐millennial‐scale solar oscillations. Here we show that the warm season temperature inferred from the layer thickness of a stalagmite from Beijing in Eastern Asia is consistent with oscillations in total solar irradiance inferred from cosmogenic 10Be and 14C. On the other hand, this climate record is remarkably consistent with Northern Atlantic drift ice cycles that were identified to be controlled by the sun through the entire Holocene. The synchronism between the two independent sun‐linked climate records therefore suggests that the sun may directly couple hemispherical climate changes on centennial to millennial scales.
Two-and three-photon processes in photoinitiators for 3D laser printing

The performance of a photoinitiator is key to control efficiency and resolution in 3D laser nanoprinting. Upon light absorption, a cascade of competing excited states and photoreactions leads to the radical formation that initiates free radical polymerization. Here we investigate 7-diethylamino-3-thenoylcoumarin (DETC), one of the most efficient photoinitiators for two-photon polymerization (TPP). Depending on the presence of a co-initiator, DETC causes radical generation either with two-photon or with a unique three-photon excitation, but the mechanism for these processes is not well understood. Here we show that the unique three-photon based radical formation of DETC in the absence of a co-initiator results from the excitation of special highly excited triplet states followed by multiple bond scission possibilities generating radicals. In contrast, photoinitiation in the presence of a co-initiator proceeds via intermolecular electron transfer or hydrogen atom transfer after the photosensitization of the photoinitiator to the lowest triplet excited state. Our quantum mechanical calculations explain the different pathways for the multiphoton activation mechanism of DETC and its radical formation, which enables the rational design of efficient photoinitiators to increase the speed and sensitivity of 3D laser nanoprinting.
Recommender system in a non-stationary context: recommending job ads in pandemic times

HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés. Recommender system in a non-stationary context: recommending job ads in pandemic times Guillaume Bied, Solal Nathan, Elia Pérennes, Victor Alfonso Naya, Philippe Caillou, Bruno Crépon, Christophe Gaillac, Michèle Sebag
New equations for determining the formation constants of an aquifer from pumping test data

New equations are given, based on an extended theory, that take into account the following factors: the compressibility and anisotropy of the main aquifer; the partial penetration of the abstraction well; the depth at which the drawdown in an observation well is measured; the existence of a low-permeability layer, hereafter called ‘the aquitard,’ above the aquifer; and the saturated and unsaturated zones above the water table. A practical method of evaluating the formation constants for an aquifer from pumping test data is fully discussed. Type curves based on the new equations are used to analyze data from a pumping test in the thick Bunter sandstone formation of Shropshire (Great Britain). A correction for the water derived from storage within the abstraction well is found to be necessary.
Drug Metabolism Exposure of Rats to Multiple Oral Doses of Dichloroacetate Results in Upregulation of Hepatic GSTs and NQO1

Dichloroacetate is an investigational drug that is used in the treatment of various congenital and acquired disorders of energy metabolism. Although DCA is generally well-tolerated, some patients experience peripheral neuropathy, a side effect more common in adults than children. Repetitive DCA dosing causes downregulation of its metabolizing enzyme, GSTZ1, which is also critical in the detoxification of maleylacetoacetate and maleylacetone. GSTZ1 (-/-) knockout mice show upregulation of GSTs and antioxidant enzymes as well as an increase in GSSG:GSH, suggesting GSTZ1 deficiency causes oxidative stress. We hypothesized that DCA-mediated depletion of GSTZ1 causes oxidative stress and used the rat to examine induction of GSTs and antioxidant enzymes after repeated DCA exposure. We determined the expression of A, M, P, and O-class GSTs, NAD(P)H quinone dehydrogenase 1 (NQO1), gamma-glutamylcysteine ligase complex (GCLC), and glutathione synthetase (GSS). GSH and GSSG levels were measured by LC/MS/MS. Enzyme activity was measured in hepatic cytosol using 1-chloro-2,4-dinitrobenzene (CDNB), 1,2-dichloro-4-nitrobenzene (DCNB), and 2,6-dichloroindophenol (DCPIP) as substrates. In comparison to acetate-treated controls, DCA dosing increased the relative expression of GSTA1/A2 irrespective of rodent age, whereas only adults displayed higher levels of GSTM1 and GSTO1. NQO1 expression and activity were higher in juveniles after DCA dosing. GSH concentrations were increased by DCA in adults but the GSH:GSSG ratio was not changed. Levels of GCLC and GSS were higher and lower, respectively, in adults treated with DCA. We conclude that DCA-mediated depletion of GSTZ1 causes oxidative stress and promotes the induction of antioxidant enzymes that may vary if loss of the expression and activity of GSTZ1 in rat tissues following multiple DCA dosages that mimicked therapy resulted in similar effects. We hypothesized that the DCA-mediated downregulation of GSTZ1 causes oxidative stress through increased maleylacetone and reactive oxygen species. We used a rat model to assess the induction of hepatic GSTs and antioxidant enzymes following repeated administration of a “therapeutic” dose of DCA to juvenile (4-week) and adult (52-week) Sprague Dawley rats, which have been used in previous work to study the neurotoxic effects of DCA (Calcutt et al. , 2009). equation to determine the Michaelis constant (K m ) and maximal velocity (V max ). Group comparisons were performed using a two-tailed Student’s t-test (corrected for multiplicity by the Holm-Sidak method) or a two-way ANOVA. Statistical significance was defined as p < 0.05.
SOOD: Towards Semi-Supervised Oriented Object Detection (Supplementary Material)

1. Details of Partially Labeled Data Sets We randomly sample 10%, 20%, and 30% data from DOTA-v1.5-train [5] to form partially labeled data sets. Besides, the 20% set is a subset of the 30% set, and the 10% set is a subset of the 20% set. To maintain the characteristic of the original data, we ensure the partially labeled sets have similar data distributions with DOTA-v1.5-train, as shown in Fig. 1. In this manner, these splits can well reflect the effectiveness of different semi-supervised object detection methods.
Transcriptomic Evaluation of Stress Vulnerability Network using Single Cell RNA-Seq in mouse Prefrontal Cortex

Increased vulnerability to stress is a major risk factor for the manifestation of several mood disorders, including major depressive disorder (MDD). Despite MDD’s status as a significant donor to global disability, the complex integration of genetic and environmental factors that contribute to the behavioral display of such disorders has made a thorough understanding of related etiology elusive. Recent developments suggest that a brain-wide network approach is needed, taking into account the complex interplay of cell types spanning multiple brain regions. Single cell RNA-sequencing technologies can provide transcriptomic profiling at the single-cell level across heterogenous samples. Furthermore, we have previously used local field potential oscillations and machine learning to identify an electrical brain network that is indicative of a predisposed vulnerability state. Thus, this study combined single cell RNA-sequencing (scRNA-Seq) with electrical brain network measures of the stress-vulnerable state, providing a unique opportunity to access the relationship between stress network activity and transcriptomic changes within individual cell types. We found especially high numbers of differentially expressed genes between animals with high and low stress vulnerability brain network activity in astrocytes and glutamatergic neurons but we estimated that vulnerability network activity depends most on GABAergic neurons. Furthermore, we found that genes significantly upregulated in animals with higher vulnerability brain network activity across multiple cell types included upregulation of microglia activity, mitochondrial and metabolic pathways, and those with lower vulnerability network activity included pathways involved in synapse regulation.
Little Ben Sandstone, Maitai Group (Permian): nature and extent in the Hollyford-Eglinton region, South Island, New Zealand

Abstract The Upper Permian Matai Group and its constituent formations of the Nelson Regional Syncline may be extended across the Alpine Fault into the Key Summit Regional Syncline, southern South Island. The Bryneira Group and its constituent formations are in most respects indistinguishable from the Maitai, and their usage should be discontinued in favour of the senior synonym. Little Ben Sandstone (previously mapped in Southland and Otago as Key Summit Sandstone) comprises distinctive green, quartz-deficient, vol-canogenic strata which are exposed extensively in the Eglinton-Hollyford region. Stratigraphy, field sedimentology, petrography (sedimentary and metamorphic), and chemistry of Little Ben rocks are described. It is suggested that Little Ben sediments were derived from a basaltic-andesitic volcanic arc and were deposited by mass flow processes in coalescing submarine fans flanking the arc.
Identification of novel coloboma candidate genes through conserved gene expression analyses across four vertebrate species

Ocular coloboma (OC) is a failure of complete optic fissure closure during embryonic development and presents as a tissue defect along the proximal distal axis of the ventral eye. It is classed as part of the clinical spectrum of structural eye malformations with microphthalmia and anophthalmia, collectively abbreviated to MAC. Despite deliberate attempts to identify causative variants in MAC, many patients remain without a genetic diagnosis. To reveal potential candidate genes, we utilised transcriptomes experimentally generated from embryonic eye tissues derived from human, mouse, zebrafish, and chicken at stages coincident with optic fissure closure. Our in-silico analyses found 10 genes with optic fissure specific enriched expression: ALDH1A3, BMPR1B, EMX2, EPHB3, NID1, NTN1, PAX2, SMOC1, TENM3, and VAX1. In situ hybridization revealed that all 10 genes were broadly expressed ventrally in the developing eye, but that only PAX2 and NTN1 were expressed in cells at the edges of the optic fissure margin. Of these conserved optic fissure genes, EMX2, NID1, and EPHB3 have not previously been associated with human MAC cases. Targeted genetic manipulation in zebrafish embryos using CRISPR/Cas9 caused the developmental MAC phenotype for emx2 and ephb3. We scrutined available whole genome sequencing datasets from MAC patients and identified a range of variants with plausible causality. In combination our data suggest that expression of genes involved in ventral eye development are conserved across a range of vertebrate species, and that EMX2, NID1, and EPHB3 are candidate loci that should be adopted into clinical diagnostic screens for patients with structural eye malformations.