Miracle-dz/UniFAR-FTUs huggingface dataset:
Contrasting nitrogen and phosphorus budgets in urban watersheds and implications for managing urban water pollution

Significance Urban waters remain widely impaired by excess nutrients, despite substantial management efforts. We present a comparison of urban watershed nitrogen (N) and phosphorus (P) budgets. Household actions of lawn fertilization and pet ownership were responsible for the majority of watershed N and P inputs, respectively. N and P exhibited contrasting dynamics within watersheds. Watersheds exported most or all P inputs via stormwater runoff, likely contributing to surface water degradation. High apparent N retention likely resulted from unmeasured watershed N losses to the atmosphere and groundwater. These contrasting dynamics suggest that N management should emphasize reducing watershed inputs, whereas P management should focus on reducing watershed P inputs and transport from vegetated landscapes to streets and storm drains. Managing excess nutrients remains a major obstacle to improving ecosystem service benefits of urban waters. To inform more ecologically based landscape nutrient management, we compared watershed inputs, outputs, and retention for nitrogen (N) and phosphorus (P) in seven subwatersheds of the Mississippi River in St. Paul, Minnesota. Lawn fertilizer and pet waste dominated N and P inputs, respectively, underscoring the importance of household actions in influencing urban watershed nutrient budgets. Watersheds retained only 22% of net P inputs versus 80% of net N inputs (watershed area-weighted averages, where net inputs equal inputs minus biomass removal) despite relatively low P inputs. In contrast to many nonurban watersheds that exhibit high P retention, these urban watersheds have high street density that enhanced transport of P-rich materials from landscapes to stormwater. High P exports in storm drainage networks and yard waste resulted in net P losses in some watersheds. Comparisons of the N/P stoichiometry of net inputs versus storm drain exports implicated denitrification or leaching to groundwater as a likely fate for retained N. Thus, these urban watersheds exported high quantities of N and P, but via contrasting pathways: P was exported primarily via stormwater runoff, contributing to surface water degradation, whereas N losses additionally contribute to groundwater pollution. Consequently, N management and P management require different strategies, with N management focusing on reducing watershed inputs and P management also focusing on reducing P movement from vegetated landscapes to streets and storm drains.
Major Histocompatibility Complex Class I (FLA-E*01801) Molecular Structure in Domestic Cats Demonstrates Species-Specific Characteristics in Presenting Viral Antigen Peptides

ABSTRACT Feline immunodeficiency virus (FIV) infection in domestic cats is the smallest usable natural model for lentiviral infection studies. FLA-E*01801 was applied to FIV AIDS vaccine research. We determined the crystal structure of FLA-E*01801 complexed with a peptide derived from FIV (gag positions 40 to 48; RMANVSTGR [RMA9]). The A pocket of the FLA-E*01801 complex plays a valuable restrictive role in peptide binding. Mutation experiments and circular-dichroism (CD) spectroscopy revealed that peptides with Asp at the first position (P1) could not bind to FLA-E*01801. The crystal structure and in vitro refolding of the mutant FLA-E*01801 complex demonstrated that Glu63 and Trp167 in the A pocket play important roles in restricting P1D. The B pocket of the FLA-E*01801 complex accommodates M/T/A/V/I/L/S residues, whereas the negatively charged F pocket prefers R/K residues. Based on the peptide binding motif, 125 FLA-E*01801-restricted FIV nonapeptides (San Diego isolate) were identified. Our results provide the structural basis for peptide presentation by the FLA-E*01801 molecule, especially A pocket restriction on peptide binding, and identify the potential cytotoxic T lymphocyte (CTL) epitope peptides of FIV presented by FLA-E*01801. These results will benefit both the reasonable design of FLA-E*01801-restricted CTL epitopes and the further development of the AIDS vaccine. IMPORTANCE Feline immunodeficiency virus (FIV) is a viral pathogen in cats, and this infection is the smallest usable natural model for lentivirus infection studies. To examine how FLA I presents FIV epitope peptides, we crystallized and solved the first classic feline major histocompatibility complex class I (MHC-I) molecular structure. Surprisingly, pocket A restricts peptide binding. Trp167 blocks the left side of pocket A, causing P1D to conflict with Glu63. We also identified the FLA-E*01801 binding motif X (except D)-(M/T/A/V/I/L/S)-X-X-X-X-X-X-(R/K) based on structural and biochemical experiments. We identified 125 FLA-E*01801-restricted nonapeptides from FIV. These results are valuable for developing peptide-based FIV and human immunodeficiency virus (HIV) vaccines and for studying how MHC-I molecules present peptides.
The Dynamics of Liver Function Test Abnormalities after Malaria Infection: A Retrospective Observational Study

Abstract. Liver dysfunction has long been recognized as a clinical feature of malaria. We have observed delayed elevation in the transaminase portion of liver function tests (LFTs) after treatment in some participants undergoing induced blood stage malaria infection. We sought to determine whether similar LFT elevations occur after naturally acquired infection. We performed a retrospective audit of confirmed cases of Plasmodium falciparum and Plasmodium vivax in Queensland, Australia, from 2006 to 2016. All LFT results from malaria diagnosis until 28 days after diagnosis were collected with demographic and clinical information to describe longitudinal changes. The timing of peak LFT elevations was classified as early (0–3 days), delayed (4–11 days), or late (12–28 days) with respect to the day of diagnosis. Among 861 cases with LFT evaluated, an elevated bilirubin level was identified in 12.4% (N = 107/861), whereas elevated alanine transaminase (ALT) and aspartate transaminase levels were observed in 15.1% (N = 130/861) and 14.8% (N = 127/861) of cases, respectively. All peak bilirubin results occurred in the early period, whereas ALT elevations were biphasic, with elevations in the early and delayed periods, with 35.4% (N = 46/130) of cases delayed. Univariate and paired stepwise logistic regression analyses were performed to investigate factors associated with the incidence and timing of transaminase elevation. A raised ALT level at diagnosis was strongly associated with the timing of transaminase elevation. No other demographic, parasitic, or treatment factors were associated. Liver function test abnormalities are likely an inherent although variable aspect of human malaria, and individual-specific factors may confer susceptibility to hepatocyte injury.
A Miniaturized, Programmable Deep-Brain Stimulator for Group-Housing and Water Maze Use

Pre-clinical deep-brain stimulation (DBS) research has observed a growing interest in the use of portable stimulation devices that can be carried by animals. Not only can such devices overcome many issues inherent with a cable tether, such as twisting or snagging, they can also be utilized in a greater variety of arenas, including enclosed or large mazes. However, these devices are not inherently designed for water-maze environments, and their use has been restricted to individually-housed rats in order to avoid damage from various social activities such as grooming, playing, or fighting. By taking advantage of 3D-printing techniques, this study demonstrates an ultra-small portable stimulator with an environmentally-protective device housing, that is suitable for both social-housing and water-maze environments. The miniature device offers 2 channels of charge-balanced biphasic pulses with a high compliance voltage (12 V), a magnetic switch, and a diverse range of programmable stimulus parameters and pulse modes. The device's capabilities have been verified in both chronic pair-housing and water-maze experiments that asses the effects of nucleus reuniens DBS. Theta-burst stimulation delivered during a reference-memory water-maze task (but not before) had induced performance deficits during both the acquisition and probe trials of a reference memory task. The results highlight a successful application of 3D-printing for expanding on the range of measurement modalities capable in DBS research.
Archimedean lattices in the bound states of wave interacting particles

The possible periodic arrangements of droplets bouncing on the surface of a vibrated liquid are investigated. Because of the nature of the interaction through waves, the possible distance of binding of nearest neighbors is multi-valued. For large amplitude of the forcing, the bouncing becomes sub-harmonic and the droplets can have two different phases. This effect increases the possible distances of binding and the formation of various polygonal clusters is observed. From these elements it is possible to assemble crystalline structures related to the Archimedean tilings of the plane, the periodic tesselations which tile uniformly the 2D plane with convex polygons. Eight of the eleven possible configurations are observed. They are stabilized by the coupling of two sub-lattices of droplets of different phase, both contributing to sustain a common wave field.
Automated Diagnosis of Breast Cancer and Pre-invasive Lesions on Digital Whole Slide Images

Digital whole slide imaging has the potential to change diagnostic pathology by enabling the use of computeraided diagnosis systems. To this end, we used a dataset of 240 digital slides that are interpreted and diagnosed by an expert panel to develop and evaluate image features for diagnostic classification of breast biopsy whole slides to four categories: benign, atypia, ductal carcinoma in-situ and invasive carcinoma. Starting with a tissue labeling step, we developed features that describe the tissue composition of the image and the structural changes. In this paper, we first introduce two models for the semantic segmentation of the regions of interest into tissue labels: an SVM-based model and a CNN-based model. Then, we define an image feature that consists of superpixel tissue label frequency and co-occurrence histograms based on the tissue label segmentations. Finally, we use our features in two diagnostic classification schemes: a four-class classification, and an alternative classification that is one-diagnosis-at-a-time starting with invasive versus benign and ending with atypia versus ductal carcinoma in-situ (DCIS). We show that our features achieve competitive results compared to human performance on the same dataset. Especially at the critical atypia vs. DCIS threshold, our system outperforms pathologists by achieving an 83% accuracy.
Impaired swim bladder inflation in early life stage fathead minnows exposed to a deiodinase inhibitor, iopanoic acid

Inflation of the posterior and/or anterior swim bladder is a process previously demonstrated to be regulated by thyroid hormones. We investigated whether inhibition of deiodinases, which convert thyroxine (T4) to the more biologically active form, 3,5,3′‐triiodothyronine (T3), would impact swim bladder inflation. Two experiments were conducted using a model deiodinase inhibitor, iopanoic acid (IOP). First, fathead minnow embryos were exposed to 0.6, 1.9, or 6.0 mg/L or control water until 6 d postfertilization (dpf), at which time posterior swim bladder inflation was assessed. To examine anterior swim bladder inflation, a second study was conducted with 6‐dpf larvae exposed to the same IOP concentrations until 21 dpf. Fish from both studies were sampled for T4/T3 measurements and gene transcription analyses. Incidence and length of inflated posterior swim bladders were significantly reduced in the 6.0 mg/L treatment at 6 dpf. Incidence of inflation and length of anterior swim bladder were significantly reduced in all IOP treatments at 14 dpf, but inflation recovered by 18 dpf. Throughout the larval study, whole‐body T4 concentrations increased and T3 concentrations decreased in all IOP treatments. Consistent with hypothesized compensatory responses, deiodinase‐2 messenger ribonucleic acid (mRNA) was up‐regulated in the larval study, and thyroperoxidase mRNA was down‐regulated in all IOP treatments in both studies. These results support the hypothesized adverse outcome pathways linking inhibition of deiodinase activity to impaired swim bladder inflation. Environ Toxicol Chem 2017;36:2942–2952. Published 2017 Wiley Periodicals Inc. on behalf of SETAC. This article is a US government work and, as such, is in the public domain in the United States of America.
How vulnerable are the Indian banks: A cryptographers' view

With the advent of e-commerce and online banking it has become extremely important that the websites of the financial institutes (especially, banks) implement up-to-date measures of cyber security (in accordance with the recommendations of the regulatory authority) and thus circumvent the possibilities of financial frauds that may occur due to vulnerabilities of the website. Here, we systematically investigate whether Indian banks are following the above requirement. To perform the investigation, recommendations of Reserve Bank of India (RBI), National Institute of Standards and Technology (NIST), European Union Agency for Network and Information Security (ENISA) and Internet Engineering Task Force (IETF) are considered as the benchmarks. Further, the validity and quality of the security certificates of various Indian banks have been tested with the help of a set of tools (e.g., SSL Certificate Checker provided by Digicert and SSL server test provided by SSL Labs). The analysis performed by using these tools and a comparison with the benchmarks, have revealed that the security measures taken by a set of Indian banks are not up-to-date and are vulnerable under some known attacks.
Long-term consequences of adolescent cannabis use: Examining intermediary processes

ABSTRACT Background: In the United States, perceptions of marijuana’s acceptability are at an all-time high, risk perceptions among youth are low, and rates are rising among Black youth. Thus, it is imperative to increase the understanding of long-term effects of adolescent marijuana use and ways to mitigate adverse consequences. Objectives: To identify the midlife consequences of heavy adolescent marijuana use and the mechanisms driving effects among a Black, urban population. Methods: This study analyzed the propensity score-matched prospective data from the Woodlawn Study, a community cohort study of urban Black youth followed from ages 6–42. After matching the 165 adolescents who used marijuana heavily to 165 non-heavy/nonusers on background confounders to reduce selection effects (64.5% male), we tested the association of heavy marijuana use by age 16 with social, economic, and physical and psychological health outcomes in midlife and the ability of adult drug trajectories (marijuana, cocaine, and heroin use from ages 17–42) and school dropout to mediate effects. Results: Heavy adolescent marijuana use was associated with an increased risk of being poor and of being unmarried in midlife. Marijuana use also predicted lower income and greater anxious mood in midlife. Both adult drug use trajectories and school dropout significantly mediated socioeconomic effects but not marital or anxious mood outcomes. Conclusion: Heavy adolescent marijuana use seems to set Black, urban youth on a long-term trajectory of disadvantage that persists into midlife. It is critical to interrupt this long-term disadvantage through the prevention of heavy adolescent marijuana use, long-term marijuana and other drug use, and school dropout.
Peripherally administered orexin improves survival of mice with endotoxin shock

Sepsis is a systemic inflammatory response to infection, accounting for the most common cause of death in intensive care units. Here, we report that peripheral administration of the hypothalamic neuropeptide orexin improves the survival of mice with lipopolysaccharide (LPS) induced endotoxin shock, a well-studied septic shock model. The effect is accompanied by a suppression of excessive cytokine production and an increase of catecholamines and corticosterone. We found that peripherally administered orexin penetrates the blood-brain barrier under endotoxin shock, and that central administration of orexin also suppresses the cytokine production and improves the survival, indicating orexin’s direct action in the central nervous system (CNS). Orexin helps restore body temperature and potentiates cardiovascular function in LPS-injected mice. Pleiotropic modulation of inflammatory response by orexin through the CNS may constitute a novel therapeutic approach for septic shock. DOI: http://dx.doi. org/10.7554/eLife.21055. 001
c-Myc regulates the CDK1/cyclin B1 dependent-G2/M cell cycle progression by histone H4 acetylation in Raji cells

Overexpression of c-Myc is involved in the tumorigenesis of B-lineage acute lymphoblastic leukemia (B-ALL), but the mechanism is not well understood. In the present study, a c-Myc-knockdown model (Raji-KD) was established using Raji cells, and it was indicated that c-Myc regulates the expression of genes associated with cell cycle progression in G2/M-phase, cyclin D kinase (CDK)1 and cyclin B1, by modulating 60 kDa Tat-interactive protein (TIP60)/males absent on the first (MOF)-mediated histone H4 acetylation (AcH4), which was then completely restored by re-introduction of the c-Myc gene into the Raji-KD cells. The expression of CDK1 and cyclin B1 was markedly suppressed in Raji-KD cells, resulting in G2/M arrest. In comparison to Raji cells, the proliferation of Raji-KD cells was significantly reduced, and it was recovered via re-introduction of the c-Myc gene. In the tumorigenesis assays, the loss of c-Myc expression significantly suppressed Raji cell-derived lymphoblastic tumor formation. Although c-Myc also promotes Raji cell apoptosis via the caspase-3-associated pathway, CDK1/cyclin B1-dependent-G2/M cell cycle progression remains the major driving force of c-Myc-controlled tumorigenesis. The present results suggested that c-Myc regulates cyclin B1- and CDK1-dependent G2/M cell cycle progression by TIP60/MOF-mediated AcH4 in Raji cells.
A Dynamic Compensator for Parameter Varying Systems Subject to Actuator Limitations applied to a T-S Fuzzy System

Abstract We address the design of parameter-dependent dynamic output feedback controllers for discrete-time systems with time-varying parameters and subject to actuators saturations. The particularity of the proposed controller is that all its matrices are dependent of the varying parameters, differently from a previous proposed compensator that was partially dependent of the parameters. The proposed LMI stability and stabilization results are based on the use of a parameter dependent Lyapunov function and on the λ-contractivity of the associated level set to guarantee the local stability and some time performance. Two control strategies are addressed: avoiding saturation and allowing saturation, in both cases taking into account the realistic consideration of local validity of the plant model. The proposed numerical example shows the control design for a nonlinear system represented by a Takagi-Sugeno Fuzzy model.
Impact of Common Rater Variance on Construct Validity of Assessment Center Dimension Judgments

In an assessment center (AC), assessors generally rate an applicant's performance on multiple dimensions in just 1 exercise. This rating procedure introduces common rater variance within exercises but not between exercises. This article hypothesizes that this phenomenon is partly responsible for the consistently reported result that the AC lacks construct validity. Therefore, in this article, the rater effect is standardized on discriminant and convergent validity via a multitrait-multimethod design in which each matrix cell is based on ratings of different assessors. Two independent studies (N = 200, N = 52) showed that, within exercises, correlations decrease when common rater variance is excluded both across exercises (by having assessors rate only 1 exercise) and within exercises (by having assessors rate only 1 dimension per exercise). Implications are discussed in the context of the recent discussion around the appropriateness of the within-exercise versus the within-dimension evaluation method.
First record of Boccardia polybranchia (Haswell, 1885) (Polychaeta Spionida) from the Atlantic coast of Morocco

1 Laboratory of "Aliments, Environnement et santé", Faculty of Sciences and Technics Guéliz, Cadi Ayyad University, Marrakech, Morocco. 2 Equipe de Recherche Mer, Molécules, Santé EA 2160 Faculty of Sciences, West Catholic University, Angers, France. 3 Laboratory of "Biochimie, Nutrition et Valorisation des Ressources Naturelles", Department of Biology, Faculty of Sciences, Chouaib Doukkali University, El Jadida, Morocco. 4 Ecology Research Unit, Ecole Normale Supérieure, Cadi Ayyad University, Marrakech, Morocco.
Sources of Fecal Indicator Bacteria in Urban Streams and Ocean Beaches, Santa Barbara, California

Fecal indicator bacteria (FIB) indicative of fecal contamination in urban streams and recreational ocean beaches in Santa Barbara, California often exceed recreational water-quality standards. During low flow, FIB and human-specific Bacteroides concentrations in urban streams were associated with point discharges. FIB concentrations varied three-fold during diurnal sampling as a result of small variations in these discharges. During stormflow, FIB concentrations were higher than during low flow and varied over three orders of magnitude. FIB in stormflow were associated with non-point sources, and concentrations decreased as fecal contamination was washed from the urban watershed. Sources of fecal contamination to near-shore ocean water included surface discharges
Making a master filterer: Ontogeny of specialized filtering plates in silver carp (Hypophthalmichthys molitrix)

Filter feeding fishes possess several morphological adaptations necessary to capture and concentrate small particulate matter from the water column. Filter feeding teleosts typically employ elongated and tightly packed gill rakers with secondary bony or epithelial modifications that increase filtering efficiency. The gill rakers of Hypophthalmichthys molitrix, silver carp, are anatomically distinct from and more complex than the filtering apparatus of other teleostean fishes. The silver carp filtering apparatus is composed of biserial, fused filtering plates used to capture particles ranging in size from 4 to 80 μm. Early in ontogeny, at 15–25 mm standard length (SL), silver carp gill rakers are reminiscent of other more stereotypical teleostean rakers, characterized by individual lanceolate rakers that are tightly packed along the entirety of the branchial arches. At 30 mm SL, secondary epithelial projections and concomitant dermal ossification begin to stitch together individual gill rakers. During later juvenile stages, dermal bone further modifies the individual gill rakers and creates a bony scaffold that supports the now fully fused and porous epithelium. By adulthood, the stitching of bone and complete fusion of the overlying epithelium creates rigid filtering plates with morphologically distinct faces. The inner face of the plates is organized into a net‐like matrix while the outer face has a sponge‐like appearance comprised of differently sized pores. Here, we present morphological data from an ontogenetic series of the filtering apparatus within silver carp. These data inform hypotheses regarding both how these gill raker plates may have evolved from a more basal condition, as well as how this novel architecture allows this species to feed on exceedingly small phytoplankton, particles that represent a greater filtering challenge to the typical anatomy of the gill rakers of fishes.