Miracle-dz/UniFAR-FTUs huggingface dataset:
The impact of rainfall on drinking water quality in Antananarivo, Madagascar

Low-income cities that are subject to high population pressure and vulnerable to climate events often have a low capacity to continuously deliver safe drinking water. Here we report the findings of a 32-year investigation of the temporal dynamics of indicators of drinking water quality in the city of Antananarivo, where we assess the long-term evolution of supplied water quality and characterize the interactions between climate conditions and the full-scale supply system. A total of 25,467 water samples were collected every week at different points in the supplied drinking water system. Samples were analyzed for total coliforms (TC), Escherichia coli (EC), intestinal Enterococci (IE), and spores of Clostridia (SSRC). Nine-hundred-eighty-one samples that were identified as positive for one or more indicators were unevenly distributed across the series. The breakpoint method identified four periods when the time series displayed changes in the level and profile of contamination (i) and the monthly pattern of contamination (ii), with more direct effects of rainfall on the quality of supplied drinking water. The modeling showed significantly different lags among indicators of bacteria occurrence after cumulative rainfall, which range from 4 to 8 weeks. Among the effects of low-income urbanization, a rapid demographic transition and urban watershed degradation are progressively affecting the quality of supplied water and resulting in the more direct effects of rainfall events.
Hodgkin Lymphoma and Cutaneous T-Cell Lymphoma Sharing the PCM1-JAK2 Fusion and a Common T-Cell Clone.

The 2016 revision to the WHO classification of myeloid neoplasms and acute leukemia added myeloid or lymphoid neoplasms with PCM1-JAK2 as provisional entities. The t(8;9)(p22;p24.1) translocation was first described in a patient in 1990, and this cytogenetic abnormality was subsequently found to result in a PCM1-JAK2 fusion gene in 2005. Approximately 50 patients with lymphoid or myeloid neoplasms associated with t(8;9)(p22;p24.1) PCM1-JAK2 have been reported, and these neoplasms have had an array of presenting diagnoses. Common features associated with this translocation are a male predominance, hepatosplenomegaly, and eosinophilia. Diagnoses reported include Philadelphia chromosome–negative myeloproliferative neoplasms, myelodysplastic or myeloproliferative neoplasms, B-cell lymphoblastic leukemia, and rarely, T-cell lymphoma. One of the initial reports in the literature describing the t(8;9)(p22; p24) translocation was found in the cutaneous T-cell lymphoma of a patient who initially was reported to have lymphomatoid papulosis, followed by a diagnosis of Hodgkin disease, with evidence that all three of these diseases were derived from a common T-cell clone. Here, we report what we believe is the second patient harboring the PCM1-JAK2 fusion with a history of cutaneous T-cell lymphoma who was later diagnosed with classic Hodgkin lymphoma. Additional immunophenotypic and molecular studies indicate that these are not two separate diseases but different manifestations of the same disease.
Soil Moisture Response to Short-Term Inorganic Fertilization on Tef (Eragrostis tef (Zucc.) Trotter) Crop Varieties in Northern Ethiopia

Little is known about soil nutrient practice effects on soil moisture under cereal cropping systems. The objective of this research was to evaluate soil moisture content (SMC) response to short-term nitrogen (N) and phosphorus (P) fertilizer rates applied on tef crop varieties and their interactions. A rain-fed fertilizer experiment using tef varieties as the test crop was conducted for two years (2012-2013) in the Chromic Cambisols of northern Ethiopia. The experimental design was laid down in randomized complete block design with three replications. Two treatment factors, namely, fertilizer (four N + P rates) and variety (three tef varieties), were tested. Soil samples were taken at different tef crop growth stages or days after sowing time (DAS) to determine SMC using the gravimetric method. Data were analyzed at a probability level of 0.05. The fertilizer treatments significantly affected the SMC determined at the different tef growth stages and cropping seasons. The highest SMC was determined at 33 DAS (51 m3·m−3), but SMC decreased with increasing fertilizer rates. A higher SMC response to local tef variety than improved variety was found across all the growth stages and cropping seasons. There were also significant differences in SMC among the treatment interactions determined at the different growth stages and across the years. The paired mean differences in SMC due to the treatments between the two years were strongly correlated (r > 0.90, P=0.001). For SMC response being effective to fertilizer and its interaction effect with variety, it is suggested that soil management practices that improve moisture such as organic sources should be integrated with the inorganic fertilizer in the conditions of Chromic Cambisols in northern Ethiopia.
A wideband low-noise variable-gain BiCMOS transimpedance amplifier

A new monolithic variable gain transimpedance amplifier is described. The circuit is realized in BiCMOS technology and has measured gain of 98 k/spl Omega/, bandwidth of 128 MHz, input noise current spectral density of 1.17 pA//spl radic/(Hz) and input signal-current handling capability of 3 mA. >
The WD40-repeat protein WDR-48 promotes the stability of the deubiquitinating enzyme USP-46 by inhibiting its ubiquitination and degradation

Ubiquitination is a reversible post-translational modification that has emerged as a critical regulator of synapse development and function. However, the mechanisms that regulate the deubiquitinating enzymes (DUBs) responsible for the removal of ubiquitin from target proteins are poorly understood. We have previously shown that the DUB ubiquitin-specific protease 46 (USP-46) removes ubiquitin from the glutamate receptor GLR-1 and regulates its trafficking and degradation in Caenorhabditis elegans. We found that the WD40-repeat proteins WDR-20 and WDR-48 bind and stimulate the catalytic activity of USP-46. Here, we identified another mechanism by which WDR-48 regulates USP-46. We found that increased expression of WDR-48, but not WDR-20, promotes USP-46 abundance in mammalian cells in culture and in C. elegans neurons in vivo. Inhibition of the proteasome increased USP-46 abundance, and this effect was nonadditive with increased WDR-48 expression. We found that USP-46 is ubiquitinated and that expression of WDR-48 reduces the levels of ubiquitin–USP-46 conjugates and increases the t1/2 of USP-46. A point-mutated WDR-48 variant that disrupts binding to USP-46 was unable to promote USP-46 abundance in vivo. Finally, siRNA-mediated knockdown of wdr48 destabilizes USP46 in mammalian cells. Together, these results support a model in which WDR-48 binds and stabilizes USP-46 protein levels by preventing the ubiquitination and degradation of USP-46 in the proteasome. Given that a large number of USPs interact with WDR proteins, we propose that stabilization of DUBs by their interacting WDR proteins may be a conserved and widely used mechanism that controls DUB availability and function.
Fitness effects of Hepatozoon blood parasites in selected lizard species

Recent findings show that parasites play a major role in host populations’ ecology and dynamics. The phylum Apicomplexa is a very interesting and diverse group of obligate unicellular blood parasites, with a vast distribution. Their study has become progressively more important as documented works reveal that emergent diseases caused by Apicomplexa pose serious health risks both for animals and humans. In many Apicomplexans, pathogenicity is still poorly understood, such as in the haemogregarine genus Hepatozoon, the most widespread Apicomplexan parasite detected in reptiles, especially in lacertids. Although in a broad sense haemogregarines seem to have a low impact on their natural reptilian hosts, the fitness impact of harbouring parasites of the genus Hepatozoon is still controversial. In order to understand the impact of Hepatozoon in three species of lacertids, we conducted three studies in which we assessed the influence of Hepatozoon infections on different host traits and fitness indicators. In two studies, we applied the Phytohaemagglutinin skin-testing (PHA) technique for estimating host immune response, and scored the number of circulating blood cells. In addition, one of these experiments incorporated two performance tests, sprinting speed and bite force, considered to be key traits for host survival and increased fitness. The aim of the last study was to investigate possible changes in host behavior induced by these parasites, by assessing lizards’ flight-initiation distance from a simulated predator. Differences in prevalence between localities and species were remarkable across the three studies. However, parasite intensity revealed no consistent pattern with host size, with very different results between studies. For all experiments no sex effects were detected, while the impact on body condition was found to be different among studies. Hepatozoon presence appeared to have little or no impact on the immune response of the lizards, and no significant correlation was found between immune reaction or parasitemia load and haematological pathologies. Increased parasitism was correlated with maximum bite force but only due to an overall relationship with size, while no effects of Hepatozoon parasites were detected on locomotor performance or escape behaviour. Overall our results showed that all parasites belong to the same genetic lineage, exhibiting a very widespread nature. Broadly, results from these experiments suggest that Hepatozoon presence has little or no impact on their hosts, which has seen by the lack of significant effects on important host traits including immune response, bite force and sprinting speed. These studies contribute to increase the knowledge on the impact of Hepatozoon parasites in lizards, and highlight the importance of further investigations to determine the real impact of these widespread hemoparasites in other aspects of host life history, which is essential information prior to making conservation efforts.
Agroinfiltration-based efficient transient protein expression in leguminous plants.

Transient protein expression is an effective tool to rapidly unravel novel gene functions, such as transcriptional activity of promoters and sub-cellular localization of proteins. However, transient expression is not applicable to some species and varieties because of insufficient expression levels. We recently developed one of the strongest agroinfiltration-based transient protein expression systems for plant cells, termed 'Tsukuba system. ' About 4 mg/g fresh weight of protein expression in Nicotiana benthamiana was obtained using this system. The vector pBYR2HS, which contains a geminiviral replication system and a double terminator, can be used in various plant species and varieties, including lettuces, eggplants, tomatoes, hot peppers, and orchids. In this study, we assessed the applicability of the Tsukuba system to several species of legumes, including Lotus japonicus, soybean Glycine max, and common bean Phaseolus vulgaris. The GFP protein was transiently expressed in the seedpods of all examined legume species, however, protein expression in leaves was observed only in P. vulgaris. Taken together, our system is an effective tool to examine gene function rapidly in several legume species based on transient protein expression.
Biochar and high-carbon wood ash effects on soil and vegetation in a boreal clearcut

Additions of fire residues in the form of charcoal and wood ash may better emulate natural disturbance processes in managed boreal forests. We examined the effects of a poplar (Populus) wood biochar and a high-carbon wood ash on soil and vegetation in a 3-year experiment in northwestern Ontario, Canada. Both soil amendments increased soil pH and soil Ca levels; high-carbon wood ash also increased soil Cu, Zn, B, S, and Pb. Amendments had large effects on plant community composition, favoring a subset of ruderal species including raspberry (Rubus idaeus L.) and goldenrod (Solidago canadensis L.). The addition of high-carbon wood ash resulted in declines in growth of planted white spruce (Picea glauca (Moench) Voss); a path analysis suggests that this was due to the effects of toxic elements rather than the indirect effects of competition. We conclude that high-carbon wood ash, while qualifying as a type of biochar and having some beneficial effects on soil properties, can enhance toxic metals in boreal forest soils, with negative consequences to early tree growth. Differences in plant species responses to biochars and the potential for toxicity effects and indirect effects mediated by plant competition will require screening and field trials of potential biochars prior to their use in operational forestry and forest restoration.
A novel zebrafish intestinal tumor model reveals a role for cyp7a1-dependent tumor-liver crosstalk in tumor's adverse effects on host

The nature of host organs and genes that underlie tumor-induced physiological disruption on host remains ill-defined. Here, we establish a novel zebrafish intestinal tumor model that is optimized for addressing this issue, and find that hepatic cyp7a1, the rate-limiting factor for synthesizing bile acids (BAs), is such a host gene. Inducing krasG12D by Gal4 specifically expressed in the posterior intestine resulted in formation of an intestinal tumor classified as dysplasia. The local intestinal tumor caused systemic detrimental effects on host including liver inflammation, hepatomegaly, growth defects, and organismal death. Whole-organismal level gene expression analysis and metabolite measurements revealed that the intestinal tumor reduced total BAs levels via down-regulation of hepatic cyp7a1. Genetically rescuing cyp7a1 expression in the liver restored the BAs synthesis and ameliorated tumor-induced liver inflammation, but not other tumor-dependent phenotypes. Thus, we found a previously unknown role of cyp7a1 as the host gene that links the intestinal tumor, hepatic cholesterol-BAs metabolism, and liver inflammation in tumor-bearing fish. Our model provides an important basis to discover host genes responsible for tumor-induced phenotypes and to uncover mechanisms underlying how tumors adversely affect host organisms.
Phosphorus fractionation in grasses with different resource-acquisition characteristics in natural grasslands of South America

Abstract The natural grasslands in South America have soils with low phosphorus (P) availability (1.0 to 7.5 mg kg−1), possibly altering the absorption and accumulation of P in grasses. We evaluated the chemical fractionation of P in the leaves of the most important grasses present in these grasslands to better understand the mechanisms involved in the storage of P. The grasses studied were Axonopus affinis and Paspalum notatum (fast tissue cycling and high nutrient demand) and Andropogon lateralis and Aristida laevis (slow tissue cycling and low nutrient demand). They were grown in pots filled with an Ultisol with two levels of P: control, and addition of 50 mg P kg–1. The main P fractions were the inorganic soluble (44%) and P in RNA (26%). Addition of P increased the total P concentration, following the order A. affinis (140%) > P. notatum (116%) > A. lateralis (81%) > A. laevis (21%). In conclusion, the species A. affinis and P. notatum responded to P fertilization with high variation and accumulating P in less-structural chemical forms, such as inorganic P. The species A. lateralis and A. laevis showed low variation in the concentration of P forms, with higher P concentrations in structural forms.
Growth response and carcass characteristics of broiler chickens fed diets supplemented with garlic ( Allium sativum )

This study was conducted to determine the effects of garlic (Allium sativum) as a phytogenic feed additive (PFA) on growth and carcass characteristics of broiler chicken. One hundred and fifty day old Marshal Strains of broiler chicken were assigned to five dietary treatments with thirty birds in a Completely Randomized Design with the following inclusion levels of Treatment 1, 0.0% of garlic (without oral antibiotics medication for birds), Treatment 2, 0.0% garlic (with the use of antibiotics for the birds), T3 – 0.2% of garlic, T4 – 0.4% of garlic, T5 – 0.8% of garlic. The thirty chicks were subdivided into 3 replicates of 10 birds each. Feed and water were offered ad libitum and mortality was recorded as it occurred. Data were obtained on the growth performance parameters such as body weight, feed intake and liveability while feed conversion ratio was calculated. Carcass parameters measured were live weight, bled weight, eviscerated weight, dressed weight, primal cuts (thigh, drumstick, breast and wing) and internal organs (Gizzard, Liver, and Heart). The result of the growth performance showed that there were significant differences (P 0.05) in the values of the organs (liver, heart and gizzard) and the primal cuts. This study revealed that the inclusion of garlic (Allium sativum) in the diets of broiler chicken has no detrimental effect on growth performance, organ weight and primal cut values of the experimental birds but improved the average body weight and liveability of the birds at the inclusion level of 0.4% /100kg of feed.Keywords: Broiler, Phytogenic, Allium sativum, marshal strain, growth performance, carcass characteristics
Genetic diversity, admixture, and hatchery influence in Brook Trout (Salvelinus fontinalis) throughout western New York State

Abstract Although Brook Trout are distributed across most of eastern North America, population numbers have declined in many regions due to habitat loss, climate change, and competition with non‐native species. In New York State, Brook Trout habitat has been substantially reduced, with many areas showing complete extirpation of Brook Trout populations, predominantly in the western portion of the state. Small, fragmented populations are at risk of genetic diversity loss, inbreeding depression, and reduced fitness, leading to a greater potential for local extirpation. Genetic monitoring is a practical tool that can facilitate further conservation‐decision making regarding small populations. In this study, we used 12 microsatellite loci to examine 3,436 sampled Brook Trout, representing 75 sites from the Allegheny, Erie/Niagara, Genesee, Oswego, Lake Ontario, and Susquehanna drainage basins throughout western New York State. Three Brook Trout hatchery strains were also genetically characterized to evaluate the degree of hatchery introgression between wild populations and hatchery strains stocked in the region. Overall, estimates of genetic diversity varied widely: Allelic richness ranged from 2.23 to 7.485, and expected heterozygosity ranged from 0.402 to 0.766. As observed for Brook Trout in other regions, we found a high degree of genetic differentiation among populations, with all comparisons except one showing significant F ST values. Hatchery introgression was found to be minimal, with estimates ranging from 1.96% to 3.10% of wild individuals exhibiting membership proportions to a hatchery strain cluster exceeding 10% (q ≥ 0.10). Results from this investigation can be used to prioritize management efforts for Brook Trout in western New York State and act as a baseline to monitor future population trends.
Computational model demonstrates that Ndc80-associated proteins strengthen kinetochore-microtubule attachments in metaphase

Chromosome segregation is mediated by spindle microtubules that attach to kinetochore via dynamic protein complexes, such as Ndc80, Ska, Cdt1 and ch-TOG during mitotic metaphase. While experimental studies have previously shown that these proteins and protein complexes are all essential for maintaining a stable kinetochore-microtubule interface, their exact roles in this process remains elusive. In this study, we employed experimental and computational methods in order to characterize how these proteins can strengthen kMT attachments in both non load-bearing and load-bearing conditions, typical of prometaphase and metaphase, respectively. Immunofluorescence staining of Hela cells showed that the levels of Ska and Cdt1 significantly increase from prometaphase to metaphase. Our new computational model showed that, by incorporating binding and unbinding of each protein complex, coupled with a biased diffusion mechanism, the displacement of a possible complex formed by Ndc80-Ska-Cdt1 is significantly higher than that formed by Ndc80 alone or Ndc80-Ska. In addition, when we use Ndc80/ch-TOG in the model, rupture force and time of attachment of the kMT interface increases. These results support the hypothesis that Ndc80-associated proteins strengthen kMT attachments and that it is the interplay between kMT protein complexes in metaphase that ensures stable attachments.
Prolonged ovarian storage of mature Drosophila oocytes dramatically increases meiotic spindle instability

More than 95% of fertilized Drosophila oocytes from outbred stocks develop fully regardless of maternal age, in contrast to human oocytes, which frequently generate non-viable aneuploid embryos. Since Drosophila oocytes are normally stored only briefly prior to ovulation, unlike their human counterparts, we investigated the effects of storage on oocyte quality. Using a novel system to acquire oocytes held for known periods, we analyzed by ribosome profiling how translation and cellular function change over time. Oocyte developmental capacity decays in a precise temperature-dependent manner over 1-4 weeks, due to a progressive inability to complete meiosis. Meiotic metaphase genes, the Fmr1 translational regulator, and the small heat shock protein chaperones Hsp26 and Hsp27 are preferentially translated during storage, and oocytes lacking Hsp26 and Hsp27 age prematurely. However translation falls generally 2.3-fold with age despite constant mRNA levels, and this inability to maintain translational equilibrium correlates with oocyte functional decline. These findings show that meiotic chromosome segregation in Drosophila oocytes is uniquely sensitive to prolonged quiescence, and suggest that the extended storage of mature human oocytes contributes to their chromosome instability. If so, then these problems may be more amenable to intervention than previously supposed.
Structure-activity relationship of flavin analogs that target the FMN riboswitch

The flavin mononucleotide (FMN) riboswitch is an emerging target for the development of novel RNA-targeting antibiotics. We previously discovered an FMN derivative —5FDQD— that protects mice against diarrhea-causing Clostridium difficile bacteria. Here, we present the structure-based drug design strategy that led to the discovery of this fluoro-phenyl derivative with antibacterial properties. This approach involved the following stages: (1) structural analysis of all available free and bound FMN riboswitch structures; (2) design, synthesis and purification of derivatives; (3) in vitro testing for productive binding using two chemical probing methods; (4) in vitro transcription termination assays; (5) resolution of the crystal structures of the FMN riboswitch in complex with the most mature candidates. In the process, we delineated principles for productive binding to this riboswitch, thereby demonstrating the effectiveness of a coordinated structure-guided approach to designing drugs against RNA. GRAPHICAL ABSTRACT Exploring the chemical structure landscape of FMN riboswitch binders.