Miracle-dz/UniFAR-FTUs huggingface dataset:
Calibrating a flow model in an irrigation network: Case study in Alicante, Spain

The usefulness of models depends on their validation in a calibration process, ensuring that simulated flows and pressure values in any line are really occurring and, therefore, becoming a powerful decision tool for many aspects in the network management ( i.e., selection of hydraulic machines in pumped systems, reduction of the installed power in operation, analysis of theoretical energy recovery). A new proposed method to assign consumptions patterns and to determine flows over time in irrigation networks is calibrated in the present research. As novelty, the present paper proposes a robust calibration strategy for flow assignment in lines, based on some key performance indicators (KPIF) coming from traditional hydrological models: Nash-Sutcliffe coefficient (non-dimensional index), root relative square error (error index) and percent bias (tendency index). The proposed strategy for calibration was applied to a real case in Alicante (Spain), with a goodness of fit considered as “very good” in many indicators. KPIF parameters observed present a satisfactory goodness of fit of the series, considering their repeatability. Average Nash-Sutcliffe coefficient value oscillated between 0.30 and 0.63, average percent bias values were below 10% in all the range, and average root relative square error values varied between 0.65 and 0.80.
Treatment of 5-azacytidine as DNA demethylating agent in Jatropha curcas L.

The role of DNA methylation (the most well-known epigenetic regulation mechanism found in many plant species) was investigated in the development of Jatropha curcas L. using the DNA demethylating agent, 5-azacytidine (AzaC). The treatments were performed in the greenhouse and as a separate embryo culture experiment. The results showed that plants responded to AzaC by both accelerating and inhibiting growth and development. Some plants exhibited observable morphological abnormalities, such as stem bending, reduced plant height and increased stem branching. The most severe effect in the treated plants was the significant failure of root development, which was lethal. The efficiency of AzaC was confirmed by methylation sensitive amplification polymorphism (MSAP) analysis of the treated plants. The MSAP fingerprints showed changes in DNA methylation at the nucleotide level. The cDNA-amplified fragment length polymorphism (cDNA-AFLP) analysis revealed differential gene expression in the treated plants compared to the untreated control plants in both the greenhouse and embryo culture experiments. The differential sequences matched with some known genes. However, the majority of differential sequences were found to be retroelement derivatives. Reverse transcription polymerase chain reaction (RT-PCR) analysis of four major DNA methyltransferase genes indicated that only the DRM and Dnmt2 genes were up-regulated in AzaC-treated J. curcas plants. This study demonstrated the important role of DNA methylation in the normal development of J. curcas. The cDNA-AFLP and RT-PCR results led to the hypothesis that AzaC inhibits DNA methylation in particular regions during the first stage of plant development and is involved in the movement of the transposable element in the genome which in turn causes phenotypic abnormalities and activates RNA-dependent DNA methylation pathways. However, this hypothesis requires further intensive study.
The ETS transcription factor pointed is essential for germ line survival in "Drosophila melanogaster"

Stem cells reside in a specialized microenvironment or niches that maintain them in an undifferentiated state and that regulate their proliferation. Drosophila ovarian germline stem cell niche shapes during larval development and is composed of support cells -often in contact with stem cells-, signaling molecules communicating the cells within the niche and the extracellular matrix. At these stages soma-germline interactions are critical to control the formation of the niche and to tightly regulate the proliferation of the primordial germ cells (PGC) to assure that every niche receives a supply of 2-3 Germline stem cells (GSCs). We have mapped and characterized a new mutation that prevents germline survival. Adult flies homozygous for the mutation are viable but sterile, as their reproductive system is agametic (absence of germ cells). Interestingly, because other somatic cell types proliferate normally when mutated, our mutation disrupts germline cells viability specifically. PGC development initiates properly as embryonic mutant gonads form organs of normal size and shape. However, at larval stages the number of PGCs is significantly reduced as they start dying by apoptosis. Thus, the somatic niche of the GSCs forms normally but devoid of germ cells. The agametic phenotype is due to a fortuitous mutation on the 3R arm chromosome. We have mapped the mutation to an intronic region near the 5? UTR of the ETS transcription factor PointedC/E. We also demonstrate that Pnt regulates PGC survival non-autonomously, as it is expressed in the somatic cells of the niche and this expression rescues the agametic phenotype. Our results show for the first time that the pointed locus plays a major role in controlling the survival and proliferation of the PGCs and suggest that the balance in pnt isoforms is critical for this function.
Reproducibility of R-fMRI Metrics on the Impact of Different Strategies for Multiple Comparison Correction and Sample Sizes

Concerns regarding reproducibility of resting-state functional magnetic resonance imaging (R-fMRI) findings have been raised. Little is known about how to operationally define R-fMRI reproducibility and to what extent it is affected by multiple comparison correction strategies and sample size. We comprehensively assessed two aspects of reproducibility, test-retest reliability and replicability, on widely used R-fMRI metrics in both between-subject contrasts of sex differences and within-subject comparisons of eyes-open and eyes-closed (EOEC) conditions. We noted permutation test with Threshold-Free Cluster Enhancement (TFCE), a strict multiple comparison correction strategy, reached the best balance between family-wise error rate (under 5%) and test-retest reliability / replicability (e.g., 0.68 for test-retest reliability and 0.25 for replicability of amplitude of low-frequency fluctuations (ALFF) for between-subject sex differences, 0.49 for replicability of ALFF for within-subject EOEC differences). Although R-fMRI indices attained moderate reliabilities, they replicated poorly in distinct datasets (replicability < 0.3 for between-subject sex differences, < 0.5 for within-subject EOEC differences). By randomly drawing different sample sizes from a single site, we found reliability, sensitivity and positive predictive value (PPV) rose as sample size increased. Small sample sizes (e.g., < 80 (40 per group)) not only minimized power (sensitivity < 2%), but also decreased the likelihood that significant results reflect “true” effects (PPV < 0.26) in sex differences. Our findings have implications for how to select multiple comparison correction strategies and highlight the importance of sufficiently large sample sizes in R-fMRI studies to enhance reproducibility.
LCR-activated expression of cloned K+ channel genes in mammalian cells.

The human p-globin LCR confers high levels of expression on cis linked cDNAs and genes under control of the p-globin promoter, and certain genes under control of their native promoter elements. This heterologous expression is copy-number-dependent and position-independent in the nucleii of erythroid specific cells. Mouse erythroleukemia (MEL) cells have been established as being electrophysiologically quiet with respect to K+ channels and suitable for patchclamp analysis. Furthermore, the MEL-cell line has been utilized as an erythroid-spedfic host for the stable expression of mammalian delayed rectifier (RCKl), transient (A-type) (RatSW and hPCN2) and inward rectifier type (IRKl) voltage-activated K+ channel cDNAs under control of the (3-globin promoter. Parallel work has allowed the characterisation of a novel human delayedrectifier type K+ channel (hCDRl) from human chromosomal DNA, and an analysis of the hCDRl gene promoter region has been initiated. Furthermore, a 5.2kb Bg/n-generated DNA fragment (hCDR15.2) containing the full hCDRl coding-region and 2.4kb of upstream chromosomal sequence was isolated. hCDR15.2 has been linked to the human p-giobin LCR and activation of native hCDRl promoter elements in MEL-cell nuclei! and subsequent detection of expressed hCDRl homotetramers was achieved by patch-damp analysis. Finally, the establishment of a gene-activation library for the functional expression of novel and existing K+ channel genes has been attempted. A rabbit genomic DNA cosmid library was constructed with firstly a Ikb (nanolocus) LCR cassette shown to confer 30-40% full LCR activity and secondly a full LCR (6.5kb) based vector. 14 different nanolocus-based rabbit genomic cosmid library dones, shown to be homologues of voltage-activated K+ channel sequences, were isolated. No detectable expression was observed from any of these clones after stable integration into MEL-cell nudeii. Transcriptional silencing and insulation have been discussed as probable reasons for the lack of detectable expression from these 14 dones. AdmowledgemenÊs I would like to especially thank Prof. W. J. Brammar and Dr. I d Conley for their support, guidance, enthusiasm and helpful input to my work. I would also like to thank the rest of the staff of die ICI Joint Laboratory for dieir help and moral support during my time at Leicester. Many thanks also go to Dr. Noel Davies (Dept. Physiology, Leicester University) for his collaboration with all the electrophysiology that is presented in dûs thesis.
Multidirectional Changes in the Blood Cholesterol in Mammals of Different Species during Pregnancy and Lactation

The aim of this review is to summarize the data on cholesterol variations in animals of different species during pregnancy and lactation period. The physiological hypercholesterolemia of late pregnancy in many species, including rats, heterozygous Watanable heritable hyperlipidemic rabbits, dogs, sheep, goats, deer and pregnant women are not common. The concentration of serum cholesterol in some mammals (e.g. rabbits, guinea pigs, buffaloes, cows, baboon and monkey) gradually decreased to the end of pregnancy. Why cholesterol is increased in some mammals during pregnancy and it decreases in other animals? Its changes are necessary or not for female organism? In this review, we have demonstrated the need for physiological changes of cholesterol in animals during the breeding season. We have tried to summarize the factors that are responsible for the cholesterol level fluctuations in females of different species at certain stages of the reproductive cycles.
New records of Trichoptera in the Balkan Peninsula and Romania, with description of new Rhyacophila sibling species by speciation traits

Processing of light collected Balkan material supplemented with sweep-netted Rhyacophila Pictet, 1834 from Bosnia-Herzegovina and Romania has resulted in 40 new species records with the description of three new species: Rhyacophila olahorum sp. n. , R. neretva sp. n. and R. nurga sp. n. from the Rhyacophila orghidani and Rhyacophila pascoei new species complexes. With 18 fi gures.
Prognostic value of myeloid antigens expression in childhood acute lymphoblastic leukemia

Background: Leukemic blasts in acute lymphoblastic leukemia (ALL) may have immunological features of both lymphoid and myeloid lineages known as aberrant myeloid antigens expression in ALL, which are explained as abnormal genetic program of leukemic cells that lead to lineage infidelity. In this study, CD13, CD14, and CD33 (which are the most frequent myeloid antigens associated with aberrant antigens expression in ALL) were investigated. Objectives: To evaluate the occurrence of aberrant myeloid antigens expression in childhood ALL and its effects on complete remission and other parameters. Materials and Methods: This study was conducted on 31 pediatric patients with newly diagnosed de novo ALL (27 B-ALL, 4 T-ALL) in Children Welfare Teaching Hospital/Medical City of Baghdad; diagnosis of ALL based on morphology and cytochemistry, CD13, CD14, CD33 were investigated as myeloid antigens using four-color flow cytometry. Results: Five cases of ALL (16.13%) out of 31 cases were confirmed to have aberrant myeloid antigens expression (CD13 was expressed in all five cases, CD33 was expressed in three cases, and CD14 was not expressed in any of these five cases). Complete remission was achieved in 90.30% (28 patients) and all cases with aberrant myeloid antigens expression achieved complete remission; however, despite this, there was no significant difference in complete remission between myeloid-positive (MY+) and myeloid-negative (MY−) cases, P > 0.05. Regarding other parameters, there were significant statistical differences in lactate dehydrogenase (LDH), hemoglobin value, and bone marrow (B.M.) blasts percent at diagnosis between MY+ and MY− cases, P< 0.05; however, there was no significant differences in leukocytes count, platelets count, peripheral blood blast percent at diagnosis, age, and gender, P > 0.05. Conclusions: The most frequent aberrant myeloid antigens expression in childhood ALL is CD13 and less frequently is CD33 while CD14 showed no expression; myeloid antigens expression in ALL may have better prognosis as they have lower B.M. blast percent and LDH value.
Effect of Algal Bio-fertilizer on the Vigna radiata: A Critical Review

The continuous increasing demand of food crops and decrease in productivity due to continuous use of chemical fertilizer has not only resulted in decline of crop yield, loss of fertility and degradation of soil but has also led us one step back in achieving sustainable agriculture. The use of algal bio-fertilizer provides an effective, eco-friendly and non-polluting approach in improving the productivity of crop by both nitrogen fixation and photosynthesis. Algal bio-fertilizers improve soil structure and increase yield productivity even if applied in a small area. The application of algal bio-fertilizers in plants has resulted in increase in root, shoot length with number of leaves and hence overall growth of the plant has been increased. India being one of the largest producer and consumer of pulses requires abundant amount of pulse production to fulfil the demands of ever growing populations which can be achieved by using algal bio-fertilizers. This paper briefly underlines the usage of algal bio-fertilizers as an important tool for sustainability and alternative usage against the chemical fertilizers.
Utility of mitochondrial‐encoded cytochrome c oxidase I gene for phylogenetic analysis and species identification of the planktonic diatom genus Skeletonema

Small subunit (SSU) and large subunit (LSU) rDNA sequences have been commonly used to delineate the taxonomy and biogeography of the planktonic diatom genus Skeletonema, but the genes occur as multiple copies and are therefore not suitable for barcoding purposes. Here, we analyzed phylogenetic relationships of Skeletonema using the mitochondrial‐encoded cytochrome c oxidase I gene (cox1), as well as partial LSU rDNA (D1–D3) and SSU rDNA, to identify the factors that define species and to evaluate the utility of these three markers for this taxon. Twelve Skeletonema species were divided into six clades, I–VI, each of which comprised the same species by the three markers: clades I (S. japonicum, S. grethae, S. pseudocostatum, and S. tropicum), II (S. menzelii), III (S. dohrnii and S. marinoi), IV (S. costatum, S. potamos, and S. subsalsum), V (S. grevillei), and VI (S. ardens). However, the branching order among these clades was incongruent among the markers. In clade III, six S. marinoi strains had identical cox1 sequences. These S. marinoi strains branched along with S. dohrnii, except for strains from the Gulf of Naples, with high support in cox1. Species delimitation between S. dohrnii and S. marinoi was therefore not supported. In clade IV, S. costatum and S. subsalsum were robustly clustered, with S. potamos as a sister clade in the cox1 tree, not in the LSU and SSU trees. In clade II, cox1 also confirmed that S. menzelii includes three subclades potentially distinguishable from each other by morphological features. Cox1 proved to be the most useful marker for the identification of Skeletonema species because it gave a tree with highly supported clades, has sufficient variation within and among species, encodes a protein in a single copy, and requires relatively few primers.
Clinical implication of occult hepatitis B infection

Occult hepatitis B infection (OBI) can be found in three different clinical groups of patients according to the documentation of the history of hepatitis B virus (HBV) exposure. They are patients with definite history of apparently self-limiting acute hepatitis B infection, patients with known chronic hepatitis B (CHB) infection with loss of hepatitis B surface antigen (HBsAg) (HBsAg seroclearance) and patients without prior history of hepatitis B infection. The second group likely contributes the largest group of patient population in OBI. These patients have same rate of development of end-staged liver disease including cirrhosis-related complications and hepatocellular carcinoma (HCC) if HBsAg seroclearance occurs when there is pre-existing cirrhosis or at the age older than 50 years. Nevertheless, majority of the patients with OBI usually have normal liver biochemistry and histology. The intrahepatic HBV DNA is detectable in almost all the patients whereas the covalently closed circular (ccc)DNA and pre-genomic RNA levels are usually very low. With regard to the clinical implications, HBV transmission from the blood products of occult hepatitis B donors is possible as demonstrated in animal and human experiments, although the actual HBV transmission rate in human is quite low especially in anti-HBs positive recipients. HBV can also be transmitted to the recipients through organ transplantation especially liver transplantation from occult hepatitis B donors. OBI may be an accelerating risk factor for development of HCC in patients with chronic hepatitis C infection and patients with alcoholic liver disease. Importantly, OBI may also contribute to a great extent in patients with cryptogenic cause of HCC. In another scenario, patients with OBI may have severe hepatitis B reactivation with a surge of viral replication and hence clinical hepatitis and mortality. This phenomenon is more commonly seen in patients receiving immunosuppressive therapy especially anti-CD monoclonal antibody. Patients receiving haematopoetic stem cell transplantation also carry a high risk of hepatitis B reactivation. Prompt antiviral therapy at the time of detectable HBV DNA upon interval monitoring is very effective in controlling hepatitis B viral replication and therefore is associated with a hepatitis-free recovery.
The Establishment and Characteristics of Dominant Syntrophic Propionate Oxidation Bacteria and Sulfate-Reducing Bacteria in a Mixed Culture

The anaerobic bio-treatment of lower COD/SO42- ratio wastewater constitutes a bottle-aqneck due to the limited carbon source. In this type of environment, interactions between acidogenic fermentation bacteria and methane-producing bacteria (MPB) are aided by syntrophic fatty acid oxidation bacteria present in the functional niche; MPB and sulfate-reducing bacteria (SRB) compete with each other due to the availability of sulfate. Therefore, introduction of syntrophic fatty acid oxidation bacteria into an SRB dominated culture can achieve maximum utilization of the substrate, weakening the competition of MPB. In this study, the mixed culture of dominant syntrophic propionate oxidation bacteria (SPOB) and SRB was established and characterized at 35°C. The dominant SPOB and SRB were enriched in a continuous flow stirred-tank reactor and in batch experiments, respectively. Subsequently, an equal proportion of the enriched sludge was mixed and incubated in conical flasks with propionate as the sole substrate. Six parallel experiments (SP1–SP6) were conducted and two of them (SP2 and SP4) were chosen. The results revealed that the sulfate removal efficiencies of SP2 and SP4 were 91.83% and 93.03%, respectively. Furthermore, the outcome of the microbial analysis showed that the dominant microbial communities included Uncultured Smithella spp. , Uncultured Desulfobacteraceae bacterium and sequences related to members of the family Desulfovibrio. Excess propionate was mainly syntrophically decomposed via sulfate reduction. Findings from this study could provide valuable information for the establishment of new processes and the regulation of parameters in the treatment of lower COD/SO42- ratio wastewater.
Isolation and identification of catechol degrading bacteria

This research involves the isolation, identification, determination of bacterial growth, degradation rate and enzyme activity of catechol dioxygenase in bacteria. Eight bacteria were isolated from 3 locations: the oxidation pool, refinery pool and soil at the PETRONAS Oil Refinery Plant in Kerteh, Terengganu, Malaysia. Out of the eight isolated bacteria, seven were Gram negative and one Gram positive, bacilli. Two bacteria were chosen based on correlation from the screening results of spread plate method and optical density method. Both bacteria were identified as Pseudomonas pickettii (88.3%) and Agrobacterium radiobacter (99.8%) via the API Kit 20NE. Based on the growth profile of bacteria, the growth rate of A.radiobacter was higher than P. pickettii , with 0.045 h - ¹ compared to 0.011 h - ¹ . A.radiobacter showed higher degradation rate than P.pickettii , with 1.037 mgL - ¹ h - ¹ for A.radiobacter and 0.910 mgL - ¹ h - ¹ for P.pickettii . Enzyme assay of catechol 1,2-dioxygenase and catechol 2,3-dioxygenase was conducted on both bacteria and the result was a higher enzyme activity in A.radiobacter than P.pickettii . Enzyme activity and specific activity of catechol 1,2-dioxygenase in A.radiobacter was 0.085 µmol min - ¹ mL - ¹ and 0.167 µmol min - ¹ mg - ¹ respectively while P. pickettii was 0.042 µmol min - ¹ mL - ¹ and 0.115 µmol min - ¹ mg - ¹ . Enzyme activity and specific activity of catechol 2,3-dioxygenase in A.radiobacter was 0.002 µmol min - ¹ mL - ¹ and 0.004 µmol min - ¹ mg - ¹ respectively while P. pickettii was 0.001 µmol min - ¹ mL - ¹ and 0.003 µmol min - ¹ mg - ¹ . The overall results of this study showed that A.radiobacter is a better candidate of the two bacteria in degrading catechol.