Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluating presence-absence models in ecology: the need to account for prevalence

1. Models for predicting the distribution of organisms from environmental data are widespread in ecology and conservation biology. Their performance is invariably evaluated from the percentage success at predicting occurrence at test locations. 2. Using logistic regression with real data from 34 families of aquatic invertebrates in 180 Himalayan streams, we illustrate how this widespread measure of predictive accuracy is affected systematically by the prevalence (i.e. the frequency of occurrence) of the target organism. Many evaluations of presence-absence models by ecologists are inherently misleading. 3. With the same invertebrate models, we examined alternative performance measures used in remote sensing and medical diagnostics. We particularly explored receiver-operating characteristic (ROC) plots, from which were derived (i) the area under each curve (AUC), considered an effective indicator of model performance independent of the threshold probability at which the presence of the target organism is accepted, and (ii) optimized probability thresholds that maximize the percentage of true absences and presences that are correctly identified. We also evaluated Cohen's kappa, a measure of the proportion of all possible cases of presence or absence that are predicted correctly after accounting for chance effects. 4. AUC measures from ROC plots were independent of prevalence, but highly significantly correlated with the much more easily computed kappa. Moreover, when applied in predictive mode to test data, models with thresholds optimized by ROC erroneously overestimated true occurrence among scarcer organisms, often those of greatest conservation interest. We advocate caution in using ROC methods to optimize thresholds required for real prediction. 5. Our strongest recommendation is that ecologists reduce their reliance on prediction success as a performance measure in presence-absence modelling. Cohen's kappa provides a simple, effective, standardized and appropriate statistic for evaluating or comparing presence-absence models, even those based on different statistical algorithms. None of the performance measures we examined tests the statistical significance of predictive accuracy, and we identify this as a priority area for research and development.
Isolation and characterization of tetramicrosatellite DNA markers in the Eurasian otter (Lutra lutra)

Eight new tetramicrosatellite loci for Eurasian otter ( Lutra lutra ) were designed. Polymorphism of these eight loci in 29 otter individuals was tested. The results indicated that the allele numbers of each of loci ranged from three to five and the observed heterozygosity from 0.483 to 0.828. These new loci can be useful for population genetic research on otters and help improve the resolution of individual identification using noninvasive method.
Emerging role for PLCβ1 MiRNA and disease

Nuclear inositides are independently regulated and their regulation is totally independent from the plasma membrane counterpart, suggesting that the nucleus constitutes a functionally distinct compartment of inositol lipids metabolism. This suggests that nuclear inositol lipids themselves can modulate nuclear processes as important as transcription and pre-mRNA splicing, growth, proliferation, cell cycle regulation and differentiation. Phospholipase C β1 (PLCβ1) is a key molecule for nuclear inositide signaling. Very recently it has been highlighted that the role of PLCβ1 during erythropoiesis is linked to that of miR-210. Moreover PLCβ1 signaling is linked to gene regulation and changes in microRNAs (miRNAs) occurs with PLCβ1 expression. Molecular targets of PLCβ1 have been found to be important during myogenesis and hematopoiesis. In addition, PLCβ1 signaling has been demonstrated to be impaired in diseases affecting both myogenic differentiation and affecting the hematopoietic system.
Cell‐Mediated Immune Response in MDMA Users After Repeated Dose Administration

Abstract: Acute administration of 3,4‐methylenedioxymethamphetamine (MDMA, “ecstasy”) produces time‐dependent immune dysfunction in humans. Recreational use of MDMA generally includes repeated drug consumption, often in association with other drugs, such as alcohol and cannabis. In the laboratory setting, repeated MDMA administration to healthy MDMA consumers produced a time‐dependent immune dysfunction similar to that observed with the ingestion of a single dose, and the first of the two administrations paralleled the time‐course of MDMA‐induced cortisol stimulation kinetics and MDMA plasma concentrations. A significant decrease in CD4 T‐helper cells with simultaneous increase in natural killer (NK) cell and a decrease in functional responsiveness of lymphocytes to mitogenic stimulation was observed. Response to the second dose was either long‐lasting compared with the first dose or disproportionate and did not show any parallelism with cortisol and MDMA plasma concentrations. This circumstance extended the critical period during which immunocompetence is highly impaired as a result of MDMA use. Accumulation of MDMA in the body of a poor metabolizer induced higher immunomodulatory effects with statistically significant differences in NK cell function compared with extensive metabolizers. When basal values of lymphocyte subsets were examined in a population of recreational MDMA users participating in different clinical trials, alterations in several immunological parameters were observed. The absolute number of lymphocytes, in particular T lymphocytes and CD4 T‐helper cell subsets, showed a trend toward reduced values, although cell counts were within normal limits. By contrast, NK cells in MDMA consumers were reduced to one‐third of those from healthy persons. A statistically significant decrease in affected immune parameters was recorded during a 2‐year observation period in a subgroup of recreational MDMA users. These permanent alterations in immunologic homeostasis may result in impairment of general health and subsequent increased susceptibility to infection and immune‐related disorders.
Organisation et régulation de l'expression des gènes de la Glyceraldéhyde-3-phosphate déshydrogénase, la Phosphoglycérate kinase et l'Erythrose-4-Phosphate déshydrogénase chez les protéobactéries de la subdivision [gamma]

Chez Escherichia coli, deux genes presentent une forte homologie de sequence avec les genes gap eucaryotes et bacteriens, qui codent la glyceraldehyde 3-phophate deshydrogenase (GAPDH), intervenant dans la glycolyse et la neoglucogenese. Le gene gapA code la GAPDH cellulaire, Le gene gapB code une proteine, qui presente· une activite erythrose 4-phosphate deshydrogenase (E4PDH). Ce gene epd (gapB) est localise en amont des genes pgk et fda, qui codent, respectivement, la phosphoglycerate kinase (PGK) et la fructose 1,6-diphosphate aldolase de classe II (FDA), impliquees egalement dans la glycolyse et la neoglucogenese. Cette organisation de genes est similaire a celle observee chez de nombreuses bacteries, dans lesquelles le gene gap actif est suivi du gene pgk. Nous avons entrepris une etude visant a caracteriser les mecanismes moleculaires permettant de reguler l'expression du gene epd (gapB) d'E. Coli. Nos travaux montrent que le gene epd (gapB) est transcrit a partir d'un promoteur unique, presentant des proprietes particulieres. [. ]Dans le but de caracteriser l'origine du gene epd, nous avons entrepris une etude systematique de l'organisation des genes gap et pgk et recherche la presence d'ORF epd dans les genomes sequences de bacteries. Seules certaines proteobacteries de la subdivision y presentent une ORF epd. L'ORF epd est toujours suivie d'une ORF. Pgk. De plus, chez toutes les proteobacteries de cette subdivision etudiees, l'ORF pgk precede une ORF fda. Cette organisation particuliere suggere que l'ORF epd ait evolue a partir d'une ORF gap ancestrale, tardivement dans l'evolution des bacteries. L'analyse de la sequence nucleotidique des tandems epd-pgk chez les enterobacteries montre que les modes de regulations transcriptionnelles et post-transcriptionnelles de ce tandem de genes sont conserves chez ces especes bacteriennes. Nous avons entrepris une etude de l'expression du tandem epd-pgk de V. Cholerae clone chez E. Coli. Dans cet organisme, les ORF epd et pgk ne sont pas co-transcrites, mais des promoteurs specifiques leur assurent une transcription independante. L'expression du gene epd de V. Cholerae est egalement limitee au niveau de l'initiation de la traduction. La region d'initiation de la traduction de tous les genes epd identifies met en evidence une conservation du faible ecartement entre la sequence SD et le codon d'initiation de la traduction. Ce faible ecartement semble jouer un role important dans la limitation de l'expression de ces genes, comme nous l'avons montre chez E. Coli, par mutagenese dirigee.
Bio-indicateurs de la fertilité des sols et la perception paysanne à l'Ouest du Niger

Objectif : Cette etude realisee a l’Ouest du Niger dans les Communes de Simiri et de Tamou a pour objectif d’identifier des bio-indicateurs des sols fertiles et des sols degrades selon la perception paysanne et des parametres environnementaux. Methodologie : des enquetes aupres des populations locales et des releves sur la strate herbacee ont ete realises. Resultats : Les resultats montrent qu’un sol est considere fertile par les paysans si le rendement en grains de mil est superieur a 800 kg/ha a Tamou et a 400 kg/ha a Simiri. De plus, les especes indicatrices de la fertilite des sols sont : Cenchrus biflorus (Simiri), Pennisetum pedicellatum et Diheteropogon hagerupii (Tamou). Cependant, Mitracarpus scaber (Simiri) et Sida cordifolia (Tamou) sont indicatrices des sols degrades. Conclusion et applicabilite des resultats : Cette etude realisee a l’Ouest du Niger a permis d’identifier des bioindicateurs de la degradation des sols. Ces resultats permettront aux paysans d’apprecier le niveau de fertilite des champs necessaire pour leur mise en jachere ou leur remise en culture. Ils constituent aussi un outil d’aide a la decision pour les decideurs dans la lutte contre la degradation des terres. Mots cle : Sol ; fertilite ; degradation ; indicateurs paysans ; Niger
Calmodulin-like proteins, CMLs: New players in plant defense regulation?

In natural ecosystems plants continuously face the presence of other living organisms such as pathogens and pests (Figure 1A) and this interaction is complex (Mithofer et al. 2009). Among others, plants have developed a sophisticated system to deal with challenges coming along with herbivores. Plants perceive herbivore-derived physical (mechanical wounding) and chemical cues, such as elicitors in insects’ oral secretions and in oviposition fluid, which are collectively referred to as herbivore-associated molecular patterns (HAMPs) (Mithofer et al. 2008). In order to defend themselves against insect herbivores, plants dramatically reshape their transcriptomes, proteomes, and metabolomes (Wu et al. 2010). Phytohormones, anti-herbivore secondary metabolites like alkaloids and proteins with antinutritional properties are produced by the plant to deal with diverse environmental stresses (Mithofer and Boland 2012). Those defensive compounds from the plant can act as toxins, target physiological processes in the insect and thus affect insect survival. One of the most popular examples is that of the alkaloid nicotine, which is produced in tobacco plants. Nicotine acts as an acetylcholine receptor agonist and is highly toxic to herbivores (Steppuhn et al. 2004; Mithofer and Boland 2012). Plant defense response against herbivory is tightly coordinated by a network of interacting phytohormones, in particular jasmonic acid (JA) dependent signaling pathways. Jasmonates represent a family of jasmonic acid derivatives that regulate plant response to biotic stress as well as growth and development. Jasmonic acid is synthesized from an unsaturated fatty acid, linolenic acid. Synthesis of JA is initiated with the three step conversion of linolenic acid to 12-oxo-phytodienoic acid (OPDA). OPDA then undergoes a reduction and three rounds of β-oxidation to form (+)-7-iso-JA. JA is further conjugated to the amino acid, isoleucine (Ile) to form the bioactive form JA-Ile, (+)-7iso-Jasmonoyl-L-isoleucine. Bioactive JA-Ile further binds to jasmonate receptor COI1. This F-box protein, coronatine insensitive 1 (COI1), is a component of the SCF E3 ubiquitin ligase complex and mediates jasmonate signaling by degradation of JA transcriptional repressor JAZ proteins. JAZ degradation relieves the repression of transcription factor MYC2 which in turn activates JA-responsive genes (Fonseca et al. 2009). Although much is known about downstream JA pathways, the initial recognition process in plant-herbivore interactions and the mediating signal transduction pathways connecting it to downstream defense induction are less understood.
Protocatechuate 3, 4-Dioxygenase from Nocardia erythropolis

Protocatechuate 3,4-dioxygenase was isolated from a gram-positive bacterium, Nocardia erythropolis, the enzyme participates in the phthalate ester metabolism in the bacterium. Cultural conditions for production of the enzyme, the purification procedure, and some properties of the enzyme were studied. A bouillon (beef) medium was the most effective among those tested for cell growth and enzyme formation. The effect was due to the ring closure type of creatine compounds. Protocatechuate 3,4-dioxygenase was purified from the cell-free extract ca. 1,400-fold and it gave a single band on polyacrylamide gel electrophoresis. The molecular weight was estimated to be ca. 150,000. The optimal pH and temperature were pH 8.0 and 40°C, respectively. The enzyme was stable in a pH range from 7.6 to 8.6 and below 42°C. The enzyme was inhibited by several metals such as Pb2+ , Cd2+ and Hg2+ . The enzyme was active on a wide range of o-dihydroxyphenyl compounds, in contrast to the high specificity of similar enzymes from g.
Gammarus fossarum Koch, 1835: redescription based on neotype material and notes on its local variation (Crustacea, Amphipoda)

Gammarus fossarum A redescription of Koch, 1835, is given, together with some notes on the variability in morphological characters of this species, both within one population and in different populations. It is proved through crosses that five morphologically different populations all belong to the same species, G. fossarum. The geographic variation of the various characters is discussed.
Modelos jerárquicos espacio temporales para mapear riesgos relativos de dengue, en el Municipio Girardot, Estado Aragua, Venezuela

Los modelos Bayesianos jerarquicos espaciotemporales han sido usados en el mapeo de enfermedades, estudios de contaminacion ambiental, contaminacion industrial, entre muchos otros. Bajo esta metodologia, los datos estan asociados con un punto en una localidad E y con un instante de tiempo t. El objetivo de este trabajo es modelar el riesgo relativo de contraer dengue en el municipio Girardot del estado Aragua, Venezuela, durante el periodo epidemiologico del ano 2009. Se proponen tres estructuras de modelos, un Binomial que toma en cuenta la variabilidad en el conteo de la ocurrencia de la enfermedad en las parroquias del municipio. Una segunda propuesta incluye un modelo Binomial como primer nivel de jerarquia, mas un segundo nivel que introduce el efecto espacial, el efecto temporal y la interaccion espacio-tiempo. Finalmente, un tercer modelo espacial que combina el modelo Poisson en el primer nivel de jerarquia para el numero de casos, y en el segundo nivel de jerarquia se relaciona el riesgo relativo con las covariables a traves de la funcion logaritmo mas un efecto aleatorio. Los datos fueron recopilados por semanas y clasificados de acuerdo a las parroquias del municipio. Se utilizo el criterio de informacion de deviancia (DIC) para seleccionar el mejor modelo, resultando el modelo Poisson el mas adecuado para representar el riesgo relativo de contraer dengue en la zona bajo estudio, confirmando que los patrones de alto riesgo se encuentran en las parroquias ubicadas al sur y suroeste del municipio Girardot, colindando algunas de ellas con el lago de Valencia.
Hubungan Jumlah Komplikasi Kronik Dengan Derajat Gejala Depresi Pada Pasien Diabetes Melitus Tipe 2 Di Poliklinik Rsup Dr. M. Djamil Padang

Abstrak Komplikasi akibat penyakit Diabetes Melitus (DM) dapat menyebabkan terjadinya perubahan psikologis, salah satunya adalah gejala depresi pada pasien DM. Tujuan penelitian ini adalah menentukan perbedaan jumlah komplikasi kronik pada setiap derajat depresi pada pasien DM tipe 2. Penelitian ini menggunakan desain analitik observasional yang dilaksanakan dari Maret sampai Mei 2014 di Poliklinik RSUP Dr. M. Djamil Padang. Sampel dalam penelitian ini terdiri dari 76 pasien DM. Jumlah komplikasi kronik diketahui dengan melihat rekam medik pasien, sedangkan derajat gejala depresi dinilai dengan wawancara menggunakan kuesioner Beck Depression Inventory (BDI) II. Hasil penelitian menunjukkan bahwa responden yang mengalami gejala depresi sebanyak 27 orang (35,5%). Derajat gejala depresi normal atau minimal sebanyak 64,5%, derajat ringan sebanyak 27,6% dan derajat sedang sebanyak 7,9%. Gejala depresi pada responden dengan satu komplikasi sebesar 6,9%, dengan dua komplikasi 42,4%, dengan tiga komplikasi 88,8 % dan empat komplikasi sebesar 60%. Setelah dilakukan analisis dengan uji Kruskal Wallis didapatkan bahwa terdapat perbedaan rerata jumlah komplikasi kronik pada setiap derajat depresi pada pasien DM tipe 2 (p < 0,001). Kata kunci: diabetes melitus tipe 2, gejala depresi, komplikasi kronik Abstract Complications due to diabetes disease can cause psychological changes, such as depression symptom. The objective of this study was to reveal the difference of the number of chronic complications on every single degree of depression in patients with type 2 diabetes. This was an analytic study that carried out from March to May 2014 in the polyclinic of RSUP Dr. M. Djamil Padang. The subject consisted of 76 diabetic patients. The number of chronic complications was identified by looking at the medical record of patients, whereas the degree of depressive symptom assessed by interview using a questionnaire BDI II. The results showed that respondents having depression symptom are made up by 27 people (35.5%). The amount of normal or minimal depression was 64.5%, mild depression is 27.6 %, and 7.9% for moderate depression. Depression symptoms on the respondents that having one complication is 6.9%, 42.4% for two complications, 88% for three complications and 60% for four complications. Kruskal Wallis test showed that there is the difference of the mean of chronic complication on every single degree of depression. Keywords: :type 2 diabetes mellitus, depression symptoms, chronic complications
Listening to the Noise: Model Improvement on the Basis of Variation Patterns in Tweets

In this paper, we take the view that the wide diversity in the language (use) found on Twitter can be explained by the fact that language use varies between users and from one use situation to another: what users are tweeting about and to what audience will influence the choices users make. We propose to model the language use of Twitter tribes, i.e. peer groups of users tweeting in different use situations. We argue that the use of tribal models can improve the modeling of the substantial variation present in Twitter (and other social media), and that the resulting models can be used in the normalization of text for NLP tasks. In our discussion of variation at the linguistic levels of orthography, spelling, and syntax, we give numerous examples of various types of variation, and indicate how tribal models could help process text in which such variation occurs. All examples are derived from our own experience with the Dutch part of Twitter, for which we could draw on a multi-billion word dataset.
Carp genetic resources for aquaculture in Asia

There are over 1 300 species of cyprinids in Asia, which form an important part of the worldA†s aquatic biodiversity. Aquaculture and capture fisheries involving cyprinids are a vital part of the livelihoods of many millions of people in this region. The production of carps from aquaculture in Asia constitutes over half of world finfish aquaculture production. Further growth in human populations will increase the demand for carps as food, but may also threaten wild populations. This publication focuses on carp genetic resources for aquaculture in major carp producing countries of Asia viz., Bangladesh, China, India, Indonesia, Thailand and Vietnam, describing the species of importance, our current knowledge of the genetics of these species and genetic improvement of these species for aquaculture.
On porcine pancreatic α-amylase action: kinetic evidence for the binding of two maltooligosaccharide molecules (maltose, maltotriose and o-nitrophenylmaltoside) by inhibition studies

Hydrolysis of small substrates (maltose, maltotriose and o-nitrophenylmaltoside) catalysed by porcine pancreatic α-amylase was studied from a kinetic viewpoint over a wide range of substrate concentrations. Nonlinear double-reciprocal plots are obtained at high maltose, maltotriose and o-nitrophenylmaltoside concentrations indicating typical substrate inhibition. These results are consistent with the successive binding of two molecules of substrate per enzyme molecule with dissociation constants Ks1 and Ks2. The Hill plot, log [ν/(V-ν)] versus log [S], is clearly biphasic and allows the dissociation constants of the ES1 and ES2 complexes to be calculated. Maltose and maltotriose are inhibitors of the amylase-catalysed amylose and o-nitrophenylmaltoside hydrolysis. The inhibition is of the competitive type. The (apparent) inhibition constant Kappi varies with the inhibitor concentration. These results are also consistent with the successive binding of at least two molecules of maltose or maltotriose per amylase molecule with the dissociation constants Ki1 and Ki2. These inhibition studies show that small substrates and large polymeric ones are hydrolysed at the same catalytic site(s). The values of the dissociation constants Ks1 and Ki1 of the maltose-amylase complexes are identical. According to the five-subsite energy profile previously determined, at low concentration, maltose (as substrate and as inhibitor) binds to the same two sites (4, 5) or (3, 4), maltotriose (as substrate and as inhibitor) and o-nitrophenyl-maltoside (as substrate) bind to the same three subsites (3, 4, 5). The dissociation constants Ks2 and Ki2 determined at high substrate and inhibitor concentration are consistent with the binding of the second ligand molecule at a single subsite. The binding mode of the second molecule of maltose (substrate) and o-nitrophenylmaltoside remains uncertain, very likely because of the inaccuracy due to simplifications in the calculations of the subsite binding energies. No binding site(s) outside the catalytic one has been taken into account in this model.
Reproductive ecology of Coula edulis Baill., source of a valuable non-timber forest product

The reproductive ecology of Coula edulis (Olacaceae), source of a highly valuable non-timber product for African populations, has been investigated on a large tree sample size in a Gabonese forest for a 3-year period, in order to propose options for its domestication. Reproduction is annual and the minimum tree diameter for flowering was 10.6 cm while the diameter for regular fructification was 23 cm. The annual diameter increment (ADI; mean = 0.22 cm year -1 ) was affected by crown exposure, but not by initial tree diameter or fruit production. Tree diameter influenced fruiting frequency and fruit production. There was a strong correlation between fruit production of 2011 and 2012 (Pearson's r = 0.85; P < 0.001), suggesting a high heritability of that trait. Phenotypical selection should be performed prior to any propagation activity. Moreover, as most of C. edulis fruits were sterile (64 %), we propose that sylvicultural strategies should be based on vegetative propagation.