Miracle-dz/UniFAR-FTUs huggingface dataset:
Predicting functional effects of missense variants in voltage-gated sodium and calcium channels

A machine learning method can predict loss- versus gain-of-function effects of human genetic variants in disease-associated ion channels. Predicting ion channel variant phenotypes Ion channel variants have been associated with disease, predominantly neurological. Heyne et al. developed a tool to predict the functional effects of variants in disease-associated voltage-gated sodium and calcium ion channels using machine learning–based statistical models. Loss of function versus gain of function (LOF or GOF) was predicted separately from neutrality versus pathogenicity. Their model was trained to classify variant effects using protein sequences and structures containing missense variants with known or highly probable effects and validated against experimentally tested variants and in cohorts including individuals with epilepsy and autism. This work could have implications for ion channel and clinical genetics research. Malfunctions of voltage-gated sodium and calcium channels (encoded by SCNxA and CACNA1x family genes, respectively) have been associated with severe neurologic, psychiatric, cardiac, and other diseases. Altered channel activity is frequently grouped into gain or loss of ion channel function (GOF or LOF, respectively) that often corresponds not only to clinical disease manifestations but also to differences in drug response. Experimental studies of channel function are therefore important, but laborious and usually focus only on a few variants at a time. On the basis of known gene-disease mechanisms of 19 different diseases, we inferred LOF (n = 518) and GOF (n = 309) likely pathogenic variants from the disease phenotypes of variant carriers. By training a machine learning model on sequence- and structure-based features, we predicted LOF or GOF effects [area under the receiver operating characteristics curve (ROC) = 0.85] of likely pathogenic missense variants. Our LOF versus GOF prediction corresponded to molecular LOF versus GOF effects for 87 functionally tested variants in SCN1/2/8A and CACNA1I (ROC = 0.73) and was validated in exome-wide data from 21,703 cases and 128,957 controls. We showed respective regional clustering of inferred LOF and GOF nucleotide variants across the alignment of the entire gene family, suggesting shared pathomechanisms in the SCNxA/CACNA1x family genes.
Rubiacearum Americanarum Magna Hama Pars XLIV: Review of the Palicourea Pilosa Group, with Some New Species and a New Subspecies (Palicoureeae)

Abstract. Palicourea Aubl. (Rubiaceae) comprises a large group of Neotropical species, many of which were previously classified in Psychotria L. subg. Heteropsychotria Steyerm. Ongoing study of those species here clarifies the identity of Palicourea pilosa (Ruiz & Pav.) Borhidi, Palicourea hazenii (Standl.) Borhidi, and several similar species, and classifies them all in Palicourea subg. Montanae C. M. Taylor sect. Montanae ser. 4 subser. f. Twenty-five species found from southern Central America through western South America are studied here. The circumscription of Palicourea pilosa is narrowed, four new nomenclatural combinations are made in Palicourea, and 10 new species and one new subspecies are described.
Evaluating the ALERT algorithm for local outbreak onset detection in seasonal infectious disease surveillance data

Estimation of epidemic onset timing is an important component of controlling the spread of seasonal infectious dis-eases within community healthcare sites. The Above Local Elevated Respiratory Illness Threshold (ALERT) algorithm uses a threshold-based approach to suggest incidence levels that historically have indicated the transition from endemic to epidemic activity. In this paper, we present the first detailed overview of the computational approach underlying the algorithm. In the motivating example section, we evaluate the performance of ALERT in determining the onset of increased respiratory virus incidence using laboratory testing data from the Children’s Hospital of Colorado. At a threshold of 10 cases per week, ALERT-selected intervention periods performed better than the observed hospital site periods (2004/2005-2012/2013) and a CUSUM method. Additional simulation studies show how data properties may effect ALERT performance on novel data. We found that the conditions under which ALERT showed ideal performance generally included high seasonality and low off-season incidence.
Economic losses caused by tree species proportions and site type errors in forest management planning

The aim of this study was to estimate economic losses, which are caused by forest inventory errors of tree species proportions and site types. Our study data consisted of ground truth data and four sets of erroneous tree species proportions. They reflect the accuracy of tree species proportions in four remote sensing data sets, namely 1) airborne laser scanning (ALS) with 2D aerial image, 2) 2D aerial image, 3) 3D and 2D aerial image data together and 4) satellite data. Furthermore, our study data consisted of one simulated site type data set. We used the erroneous tree species proportions to optimise the timing of forest harvests and compared that to the true optimum obtained with ground truth data. According to the results, the mean losses of Net Present Value (NPV) because of erroneous tree species proportions at an interest rate of 3% varied from 124.4 â¬ ha to 167.7 â¬ ha. The smallest losses were observed using tree species proportions predicted using ALS data and largest using satellite data. In those stands, respectively, in which tree species proportion errors actually caused economic losses, they were 468 â¬ ha on average with tree species proportions based on ALS data. In turn, site type errors caused only small losses. Based on this study, accurate tree species identification seems to be very important with respect to operational forest inventory. â1â1â1
Evaluation of mass trapping for control of Mediterranean fruit fly, Ceratitis capitata (Wiedemann) (Diptera: Tephritidae) in Satsuma mandarin in Hatay province of Turkey

The Mediterranean fruit fly (Medfly), Ceratitis capitata (Wiedemann) (Diptera: Tephritidae), is one of the most important pests of citrus in Turkey. The objective of this study was to evaluate mass trapping for the control of Medfly in Satsuma mandarin in Hatay province of Turkey. The studies were conducted in 2011-2012 using eostrap® invaginada traps baited with % 95 Trimedlure impregnated in a polymeric plug-type dispenser. In the first year, 48 traps per 0.7 ha were placed in an experimental site from 1st August to December. In the second year, 23 traps per 0.7 ha were placed in the same site from 14 August to December. After two years of the study, the population density of medfly varied in each of the sampling year. In the first year, a total of 8968 medfly adults were caught by traps. The largest mean of catches per trap were recorded on 31 October (64.21), followed by 24 October (31.29), 17 October (22.48), 7 November (20.64), 3 October (17.60) and 10 October (16.71). In the second year, a total of 1307 medfly adults were caught by traps. The largest mean of the catches per trap were recorded on 25 September (7.35), followed by 13 November (5.83), 6 November (5.52), 18 September (5.43) and 30 October (4.26), respectively. The percentages of damage rates of medfly observed in both years. The damage rates of Medfly were 10.91 and 8.56 % in 2011 and 2012, respectively. In conclusion, the population density of medfly on satsuma mandarin increased in September and October due to high temperature. The mass trapping was not enough to control medfly on satsuma mandarin. Therefore, the mass trapping should be used with pesticides to decrease the population density of medfly during September and October in Hatay province of Turkey.
Inoculation of fowlpox viruses coexpressing avian influenza H5 and chicken IL-15 cytokine gene stimulates diverse host immune responses

Fowlpox virus (FWPV) has been used as a recombinant vaccine vector to express antigens from several important avian pathogens. Attempts have been made to improve vaccine strains induced-host immune responses by coexpressing cytokines. This study describes the construction of recombinant FWPV (rFWPV) strain FP9 and immunological responses in specific-pathogen-free (SPF) chickens, co-expressing avian influenza virus (AIV) H5 of A/Chicken/Malaysia/5858/2004, and chicken IL-15 cytokine genes. Expression of H5 (50 kD) was confirmed by western blotting. Anti-H5 antibodies, which were measured by the haemagglutinin inhibition test, were at the highest levels at Week 3 post-inoculation in both rFWPV/H5- and rFWPV/H5/IL-15-vaccinated chickens, but decreased to undetectable levels from Week 5 onwards. CD3+/CD4+ or CD3+/CD8+T cell populations, assessed using flow cytometry, were significantly increased in both WT FP9- and rFWPV/H5-vaccinated chickens and were also higher than in rFWPV/H5/IL-15- vaccinated chickens, at Week 2. Gene expression analysis using real time quantitative polymerase chain reaction (qPCR) demonstrated upregulation of IL-15 expression in all vaccinated groups with rFWPV/H5/IL-15 having the highest fold change, at day 2 (117±51.53). Despite showing upregulation, fold change values of the IL-18 expression were below 1.00 for all vaccinated groups at day 2, 4 and 6. This study shows successful construction of rFWPV/H5 co-expressing IL-15, with modified immunogenicity upon inoculation into SPF chickens.
Packet Radio Performance Over Slow Rayleigh Fading Channels

Expressions for the throughput and average packet delay for a Pure-ALOHA single-hop packet radio system operating in slow Rayleigh fading are derived. For noncoherent frequency-shift-keying (NCFSK), an exact closed form expression is presented. For coherent phase-shift-keying (CPSK) an excellent approximation for large packet sizes is derived. This approximation technique is valid in general for other modulation schemes and for other fading channel statistical characterizations. The packet length which maximizes the useful data throughput in slow Rayleigh fading is found. The results of this investigation indicate that a packet radio system can be designed with a modest link margin for fading and achieve identical throughput performance over a nonfading channel and a fading channel with only a small increase in average packet delay for the fading channel.
Changes in hematological biomarkers of Nellore cows at different reproductive stages

This study was conducted to evaluate changes in hematological biomarkers of Nellore cows at different reproductive stages. Fifteen multiparous cows with 4 ± 1 years of age and live weight of 400 ± 50 kg were used at different stages (non-pregnant, in the initial, middle and late pregnancy, at birth, one day postpartum, 30 and 60 days postpartum). Blood collections were performed every 30 days and assayed for the following hematological biomarkers: hemogram (red blood cells, globular volume, hemoglobin, mean corpuscular volume (MCV) and mean corpuscular hemoglobin concentration (MCHC)) and leukogram (total and differential counts). The erythrogram was influenced (p < 0.001) by the reproductive stages, with variation in the results obtained for the total red cell count, hemoglobin content, globular volume, MCV, MCHC and total plasma proteins. The reproductive stages influenced the leukocyte profile with variation in the total leukocyte count and in the absolute values of neutrophils, eosinophils, lymphocytes and monocytes. Hematological biomarkers of Nellore cows showed significant changes due to the physiological adjustments required in response to the metabolic requirements imposed in the final stage of pregnancy and in the beginning of lactation, ensuring the nutritional contribution in energy and oxygen transported through the blood.
ANÁLISE MOLECULAR DE Escherichia coli ISOLADAS DE CELULITE E MIÚDOS (FÍGADO E CORAÇÃO) DE FRANGOS SOB INSPEÇÃO SANITÁRIA

ABSTRACT. Vieira T.B. , Pereira V.L. de A. , Franco R.M. , Nascimento E.R. , Lopes M.Q. P., Gomes H.M. , de Araujo M.E. I. , Suffys P.N. & Tortelly R. [Molecular analysis of Escherichia coli isolated from cellulitis and offal (liver and heart) of broiler by Sanitary Inspection]. Analise molecular de Escherichia coli isoladas de celulite e miudos (figado e coracao) de frangos sob Inspecao Sanitaria. Revista Brasileira de Medicina Veterinaria, 35(3):247-252, 2013. Programa de Pos-Graduacao em Medicina Veterinaria (H.V.P.T.P.O.A.), Faculdade de Veterinaria, Universidade Federal Fluminense, Rua Vital Brazil Filho, 64, Santa Rosa, Niteroi, RJ 24230-360, Brasil. Email: thais.badini@hotmail.com In function of industrial production of broiler chickens, skin lesions, such as cellulitis, are becoming one of the biggest reasons for carcasses condemnation around the world. The objective of this study was isolate Escherichia coli from cellulitis and offal (liver and heart) of broilers, identify the isolates by RAPD-PCR and correlate them by molecular analysis to prove the septic character of the infection. During the Sanitary Inspection, 51 broiler chickens with characteristic lesions of cellulitis were removed from the slaughter line. These broilers were sent to Laboratory of Quality Control where the cellulitis lesions were measured and described macroscopically. Samples of skin and offal (heart and liver) of each broiler chicken were collected for microbiological examination. Isolates of E. coli were analyzed by RAPD-PCR and compared phylogenetically using the software BIONUMERICS 5.1. All lesions of cellulitis were visualized as cutaneous ulcer, changes in color (reddish-yellow) and irregular skin. In eight broilers were also observed thickening of the skin. At cutting, gelatinous fluid and yellowish patches were observed and, in some cases, there were involvement of adjacent muscle. 190 isolates of E. coli were obtained, 98 in cellulitis, 52, in liver and 40, in heart. The results of the RAPD-PCR, were compared by the software BIONUMERICS and grouped into 46 “clusters” with 80% or more similarity, with the lowest “cluster” containing two strains and the greater “cluster”, twelve. Of the 30 broilers in which were isolated E. coli in cellulitis lesions associated with offal (liver and / or heart), in 10, were obtained strains with more than 85% of similarity between isolates of cellulite and offal; in nine broilers, were obtained strains with more than 85% of similarity between E. coli isolates of the liver and heart, however these isolates showed no similarity to the isolates obtained from the cellulite; and 11, there were no correlation between the isolates. The detection of strains of E. coli with high genetic similarity in cellulitis and offal can mean that the partial removal of these lesions does not minimize the risk to public health.
Interference of Urochloa plantaginea on Morphophysiology and Yield Components of Black Beans

Among the factors which affect crop productivity, there are weeds which compete for environment resources. The objective of this work was to determine the periods of interference of alexandergrass on the morphophysiology and productivity components of black beans. The experiment was conducted in a complete randomized block design with four replications. The bean cultivar of the black type used was IPR Uirapuru, being the treatments separated in two models of interference: in the coexistence group, the crop of the bean lived with the alexandergrass by growing periods of 0, 7, 14, 21, 28, 35, 42 and throughout the cycledays after emergence and throughout the cycle; in the control group the crop was kept free of the infestation for the same periods described previously. At 42 DAE were evaluated the variables related to plant morphology and physiology (height of bean plants, number of trifoliate leaves, dry mass plant, number of grains pods, number od pods plants, stomatal conductance, internal CO2 concentration, photosynthetic activity, efficiency of carboxylation, efficient use of water, transpiration rate). Considering the results, it is possible to conclude that the critical period of interference prevention (CPIP) comprises 24 to 50 DAE, the period before the interference (PBI) was 24 DAE and the total period of interference prevention (TPIP) was 50 days and that the morphological and physiological variables of the plants were negatively affected in the coexistence with the alexandergrass when compared to the treatments kept free of weeds throughout the crop cycle.
Durability of environment-recruitment relationships in aquatic ecosystems: insights from long-term monitoring in a highly modified estuary and implications for management

The environment can strongly influence the survival of aquatic organisms and their resulting dynamics. Our understanding of these relationships, typically based on correlations, underpins many contemporary resource management decisions and conservation actions. However, such relationships can break down over time as ecosystems evolve. Even when durable, they may not be very useful for management if they exhibit high variability, context dependency, or non-stationarity. Here, we systematically review the literature to identify trends across environment-recruitment relationships for aquatic taxa from California’s San Francisco Bay and Sacramento-San Joaquin Delta Estuary. This is one of the most heavily modified aquatic ecosystems in North America, and home to numerous species of concern whose relationships with the environment inform regulatory actions and constraints. We retested 23 of these relationships spanning 9 species using data that have accumulated in the years since they were first published (9-40 additional years) to determine whether they persisted. Most relationships were robust (i.e., same or stronger in magnitude) to the addition of new data, but the ability to predict how a species will respond to environmental change did not generally improve with more data. Instead, prediction error generally increased over time and in some cases very quickly, suggesting a rapid regime shift. Our results suggest that more data alone will not necessarily improve the ability of these relationships to inform decision making. We conclude by synthesizing emerging insights from the literature on best practices for the analysis, use, and refinement of environment-recruitment relationships to inform decision making in dynamic ecosystems.
Structure of the human pro-myostatin precursor and determinants of growth factor latency

Myostatin, a key regulator of muscle mass in vertebrates, is biosynthesised as a latent precursor in muscle and is activated by sequential proteolysis of the pro-domain. To investigate the molecular mechanism by which pro-myostatin remains latent, we have solved the structure of unprocessed promyostatin and analysed the properties of the protein in its different forms. Crystal structures and SAXS analyses show that pro-myostatin adopts an open, V-shaped structure with a domain-swapped arrangement. The pro-mature complex, after cleavage of the furin site, has significantly reduced activity compared with mature growth factor and persists as a stable complex that is resistant to the natural antagonist follistatin. The latency appears to be conferred by a number of distinct features that collectively stabilise the interaction of the pro-domains with the mature growth factor, enabling a regulated step-wise activation process, distinct from the prototypical pro-TGF-β1. These results provide a basis for understanding the effect of missense mutations in pro-myostatin and pave the way for the design of novel myostatin inhibitors.
Long words in maximum entropy phonotactic grammars*

A phonotactic grammar assigns a well-formedness score to all possible surface forms. This paper considers whether phonotactic grammars should be probabilistic, and gives several arguments that they need to be. Hayes & Wilson (2008) demonstrate the promise of a maximum entropy Harmonic Grammar as a probabilistic phonotactic grammar. This paper points out a theoretical issue with maxent phonotactic grammars: they are not guaranteed to assign a well-defined probability distribution, because sequences that contain arbitrary repetitions of unmarked sequences may be underpenalised. The paper motivates a solution to this issue: include a *Struct constraint. A mathematical proof of necessary and sufficient conditions to avoid the underpenalisation problem are given in online supplementary materials.
Using the first European Breeding Bird Atlas for science and perspectives for the new Atlas

ABSTRACT Capsule: The first European Bird Census Council (EBCC) Atlas of European Breeding Birds has been widely used in scientific publications. Aims: To quantify how scientific publications have used data from the first European Bird Census Council (EBCC) Atlas of European Breeding Birds, what the topics of these studies have been, and to identify key aspects in which a second European Breeding Bird Atlas will provide new opportunities for basic and applied science. Methods: We searched Google Scholar to find papers published in scientific journals that cited the first atlas. We analysed the contents of a random selection of 100 papers citing this atlas and described the way these papers used information from it. Results: The first atlas has been cited in 3150 scientific publications, and can be regarded as a fundamental reference for studies about birds in Europe. It was extensively used as a key reference for the studied bird species. A substantial number of papers re-analysed atlas data to derive new information on species distribution, ecological traits and population sizes. Distribution and ecology were the most frequent topics of studies referring to the atlas, but this source of information was used in a diverse range of studies. In this context, climate change, impact of agriculture and habitat loss were, by order, the most frequently studied environmental pressures. Constraints in the atlas, such as the poor coverage in the east of Europe, the lack of information on distribution change and the coarse resolution were identified as issues limiting the use of the atlas for some purposes. Conclusions: This study demonstrates the scientific value of European-wide breeding bird atlases. A second atlas, with its almost complete coverage across Europe, the incorporation of changes in distribution between the two atlases and the inclusion of modelled maps at a resolution of 10 × 10 km will certainly become a key data source and reference for researchers in the near future.