Miracle-dz/UniFAR-FTUs huggingface dataset:
Glutamine Synthetase/Glutamine:a-Ketogluta rate Aminotransferase inChloroplasts fromtheMarineAlgaCaulerpa

Theenzymic capacities forammonia assimilation into aminoacids have beeninvestigated inchloroplasts fromthesiphonous green algaCaulerpa simpliciuscula (Turner) C.Ag. Theresults showthatthese chloroplasts differ fromthose ofhigher plants inhaving present simultaneously the enzymic capacities topermit assimilation ofammonia bytwopathways. Glutamine synthetase (EC6.3.1.2) activity atlevels upto4jumoles permg chlorophyll perhourwerefound insoluble extracts ofthechloroplasts. Glutamine(amide):a-ketoglutarate aminotransferase (oxidoreductase ferredoxin) (EC1.4.7.1) activity atlevels upto1.4pmoles permgchlorophyll perhourwasdetected byincubation ofphotosynthetically active chloroplasts either inlight orwithreduced ferredoxin. Together these enzymes provide thecapacity fortheconventional pathway ofammonium assimilation inchloroplasts viaglutamine. Asimilar level ofaglutamate dehydrogenase withanunusually lowKmforammonia which hasbeendescribed previously inthese chloroplasts provides thesecond potential pathway. Chloroplasts isolated fromsiphonous greenalgae havebeen shownrecently tosynthesize adifferent, andoften wider, array of photosynthetic products from''CO2 thanhigher plant chloroplasts (7,19). Inthis theyresemble thechloroplasts isolated fromAcetabularia where asimilar range ofproducts issynthesized bythe isolated organelle (17). Inthis paperthestudies ofthemetabolic competence ofchloroplasts fromsiphonous greenalgae areextended toinclude thepathways ofassimilation ofammoniuminto amino acids. Inchloroplasts ofhigher plants ammoniumisincorporated into aminoacids viathetwoenzymic steps, glutamine synthetase (EC 6.3.1.2) followed byGOGAT2(Jo). Ithasbeensuggested that the situation inchloroplasts isolated fromthemarine algaCaulerpa simpliciuscula isdifferent, since theyhavebeenfoundtocontain highlevels ofanNADP-dependent glutamate dehydrogenase, withanabnormally lowapparent Kmforammoniaof0.4to0. 7 mM (5). Thisenzymecouldprovide analternative meansof ammoniumincorporation into aminoacids inthese algae. GOGAT activity hasbeendemonstrated bothinphotosynthetic organisms whicharemoreadvanced inevolution thanC.simpliciuscula andalso inthose whicharemoreprimitive (10,11). We wouldexpect that GOGAT activity should alsobepresent inC.
Phylogenetic Position and Genetic Diversity of Neridae - Polychaeta Based on Molecular Data from 16S r RNA Sequences

Molecular phylogenetic analysis and genetic diversity distance among two species of marine polychaetes relationship was investigated based on 16S rRNA sequences. Data set be analysed by using Clustal W and MEGA likelihood methods. Genetic differentiation (D) among populations was higher in the Pseudonereis variegata and Namalycastis indica D: 0.64. The differences among the D values of all populations forms were significant by ANOCOVA; F= 0.784, P = 0.676). Our investigation showed how 28.16 such simple statistical summaries of huge DNA sequences data can enable to identify the structural signature of genome as well as to classify phylogenetic relationships amongst different species reflected in the differentiation of genetic diversity distributions within their DNA sequences.
Misdiagnosis of Myocardial Infarction Related to Limitations of the Current Regulatory Approach to Define Clinical Decision Values for Cardiac Troponin

Background— Misdiagnosis of acute myocardial infarction (AMI) may significantly harm patients and may result from inappropriate clinical decision values (CDVs) for cardiac troponin (cTn) owing to limitations in the current regulatory process. Methods and Results— In an international, prospective, multicenter study, we quantified the incidence of inconsistencies in the diagnosis of AMI using fully characterized and clinically available high-sensitivity (hs) cTn assays (hs-cTnI, Abbott; hs-cTnT, Roche) among 2300 consecutive patients with suspected AMI. We hypothesized that the approved CDVs for the 2 assays are not biologically equivalent and might therefore contribute to inconsistencies in the diagnosis of AMI. Findings were validated by use of sex-specific CDVs and parallel measurements of other hs-cTnI assays. AMI was the adjudicated diagnosis in 473 patients (21%). Among these, 86 patients (18.2%) had inconsistent diagnoses when the approved uniform CDV was used. When sex-specific CDVs were used, 14.1% of female and 22.7% of male AMI patients had inconsistent diagnoses. Using biologically equivalent CDV reduced inconsistencies to 10% (P<0.001). These findings were confirmed with parallel measurements of other hs-cTn assays. The incidence of inconsistencies was only 7.0% for assays with CDVs that were nearly biologically equivalent. Patients with inconsistent AMI had long-term mortality comparable to that of patients with consistent diagnoses (P=NS) and a trend toward higher long-term mortality than patients diagnosed with unstable angina (P=0.05). Conclusions— Currently approved CDVs are not biologically equivalent and contribute to major inconsistencies in the diagnosis of AMI. One of 5 AMI patients will receive a diagnosis other than AMI if managed with the alternative hs-cTn assay. Clinical Trial Registration— URL: http://www.clinicaltrials. gov. Unique identifier: NCT00470587.
Use of sewage sludge as supplementary diet for the carp, Cyprinus carpio (L)

Sewage sludge - a common urban refuse was tried as supplementary feed for the fish {Cyprinus carpio L average weight 4.9 g) @ 0, 50, 75 and 100%. The fish was raised on the experimental diet in plastic containers of 65 1 capacity for 60 days. Common carp fed on 100% sewage sludge failed to indicate appreciable growth. However, partial replacement (50%) was favourable and resulted in high growth (4.58 g). Fish reared with 50% sewage sludge supplemented diet also attained high (9.12%) protein level (wet weight basis) as compared to control (9.05%) and other treatments. The bacterial load in the selected body tissues was well below the safe levels prescribed by WHO for human consumption. The values of total coliforms, faecal coliforms, E. coli and streptococci ranged between 0-7, 0-3, 0-1 and 0-3 MPN/g respectively in fish skin and muscles
INTER-SUBUNIT CONTACTS OF THE PROTEASOMAL ALPHA-SUBUNITS AS DETERMINANTS OF PARALOG GROUPS

Summary Motivation: Assignment of the proteasomal subunits to paralog groups has been initially based on phylogenetic analysis of amino acid sequences. The aim of the current work was to analyse the capability of the inter-subunit contact regions of the proteasomal subunits to determine the orderly arrangement of the alpha-subunits in the ring. This was because these regions are essential for the self-assembly of the proteasomes, and, hence, for the determination of the paralog groups. Results. Based on the data on amino acid sequences and the known 3D structures of some proteasomes, we marked the positions of the alpha-subunits involved in inter-subunit contacts (the contact position, CP). There was a good match between the clustering based on the CPs and the one that was based on the complete sequences. Thus, we demonstrated that the CPs contain the information required for distinguishing the paralog groups.
Phylogenetic study of the Schismatoglottis Nervosa Complex (Araceae: Schismatoglottideae)

The Schismatoglottis Nervosa Complex (Araceae: Schismatoglottideae) currently comprises 10 species: Schismatoglottis adoceta S.Y. Wong, S. elegans A.Hay, S. liniae S.Y. Wong, S. tessellata S.Y. Wong, S. ulusarikeiensis S.Y. Wong, S. matangensis S.Y. Wong, S. simonii S.Y. Wong, S. turbata S.Y. Wong, and S. nervosa Ridl. , occurring in Borneo, with each endemic to a specific locality and most to a particular geology; and one species (S. brevicuspis Hook.f.) widespread in Peninsular Malaysia and Sumatera, where it is restricted to granites. Based on analysis of the matK region, a preliminary biogeographical hypothesis for the origins and subsequent taxagenesis of the Nervosa Complex is presented. This study also provides insight into possible evolution of localised mesophytic endemics in everwet, humid, and perhumid megathermal Sundaic forests. Two clades are resolved: one north of, and another south of, the Lupar Divide.
Reliability in Transformation of the Basidiomycete Coprinopsis cinerea

Transformation of the basidiomycete Coprinopsis cinerea makes use of unicellular haploid asexual spores called oidia. Protoplasts of oidia are generated by a cellulase/chitinase enzyme mix. Protoplasts and DNAs are incubated together in 25 mM Ca2+ and 5% PEG (polyethylene glycol) 4000 on ice and more PEG is added (23% final concentration) after a ‘heat shock’ step at RT (room temperature). Upon regeneration on selective media, transformation rates of several hundreds of clones might be obtained per 1 μg DNA and 107 protoplasts. Although the technique has been invented 25 years ago by Binninger et al. (1), there are reoccurring pitfalls in the method that can cause failure. Successful transformation needs a good amount of skilful knowhow about the fungus and the method. Here we present our experiences with C. cinerea transformations, call attention to potential flaws and to optimal handlings in fungal cultivation, harvesting, protoplasting, transformation, and subsequent regeneration of the fungus.
Use of quantitative real time PCR for a genome-wide study of AYWB phytoplasma gene expression in plant and insect hosts.

Phytoplasmas are obligate parasites of plants and insects and cause significant crop yield losses worldwide. A number of microarray gene expression studies have been performed to understand better the effects of phytoplasma infection on plant physiology. However, little effort has been made for the study of changes in gene expression patterns of the pathogen itself. Quantitative real time PCR in combination with the delta delta Ct method has been shown to be a relatively inexpensive and simple alternative to microarrays. We employed this method to explore whether it is possible to apply this technique for reliable gene expression quantification of phytoplasmas on a large scale. In our experimental setup, 242 genes of aster yellows phytoplasma strain witches’ broom (AY-WB) were tested for differences in expression in plant and insect host environments, and were shown to be predominantly expressed in the plant or insect hosts. In silico operon prediction corroborated the experimental data. Our findings suggest that the delta delta Ct method can be used to study the physiology of this pathogen.
INCIDENCE OF FUSARIUM MYCOTOXINS ON DIFFERENT OAT CULTIVARS UNDER NATURAL AND ARTIFICIAL INFECTION CONDITIONS

Evaluation of the genetic variability of the oat resources regarding resistance to Fusarium sp. and the accumulation of mycotoxins has been achieved within the European project "Avena-genetic resources for quality in human consumption" (AVEQ-AGRI GEN RES 06.11.03.2007- 28.02.011) in two out of ten work packages. Testing of the oat genotypes was effectuated under artificial infection conditions with different species of Fusarium in three locations from Europe (Romania, Czech Republic, Germany). In the experimental field of Suceava Genebank in 2008, 11 modern cultivars originating from different parts of Europe were used as inoculated and noninoculated standards to determine the infection with Fusarium sp. and the presence of different mycotoxins types. Analysis of accumulated mycotoxins in these standard cultivars was achieved using LC-MS/MS method in Eurofins laboratory Contaminants WEJ GmbH, Hamburg, Germany. The infected panicles with Fusarium head blight (FHB) were visually assessed using the 1-9 scale (1 - no infection, 9 - all spikelets and panicles infected). Quantification of the obtained results on the analysis of mycotoxins and the estimations concerning the infection on panicles and grains in inoculated and noninoculated standard genotypes from genebank experimental field were achieved through identification of Fusarium mycotoxins distribution, the differences between the concentrations of mycotoxins and correlations between concentrations of mycotoxins and infection with Fusarium head blight (FHB) and Fusarium damaged kernels (FDK - score 3).
Cancer Embryonic Stem Cell-like Attractors alongside Deficiency of Regulatory Restraints of Cell-Division and Cell-Cycle

The attractive conception of cancerattractors has recently been proposed, but it remains hypothetic and awaiting for experimental confirmation. Further, it is essential to elucidate how cell cycle and cell division may smoothly integrate with it. It is well-known that many cancers show with embryonic stem cell-like signatures. Based on publicly available gene expression profiling data, one unique pattern for cancer embryonic stem cell-like attractors was identified alongside deficiency of Mi-2/NuRD and its partner’s chromatin remodel systems (CRS) critical for germline-reactivated cancers, and particularly extendable to deficiency of regulatory components of cell-cycle and cell-division. Moreover, our results of Gene Expression Dynamics Inspector (GEDI) assays exemplified with the state of cell attractors of fruitfly l(3)mbt brain tumor reveals that cancer embryonic stem cell-like attractors might fall in between those of two-cell embryos and onset of differentiation states. Such stem–like attractors were further explored for its dynamics feature. The high-transcript abundance (HTA) within Self Organization Maps (SOMs) decrease during the progression of differentiation in wild-type animals and this trend can be significantly antagonized with a mutation in Polycomb homolog mes-2/E(Z) (enhancer of zeste homolog 2 (EZH2)) in Caenorhabditis elegans. Finally such features may contribute to a better understanding of carcinogenesis under cancer embryonic stem celllike attractors theory and provide novel angles for cancer therapeutic interventions.
Ranking water quality variables using feature selection algorithms to improve generalization capability of artificial neural networks

Artificial neural networks (ANNs) have been recently used intensively in the water resource management and planning. As the demand on the clean water increases, the estimation of important parameters using ANNs to evaluate the surface water quality has become an importance practice. In this study, feature selection methods, which are important tools in data mining, are used to shed light into a further understanding in the correlation between measured parameters of water quality variables and dissolved oxygen level. The aim is to enhance the generalization ability of ANNs in prediction of dissolved oxygen level. Three different feature selection methods are utilized to discern the inherent correlation in the water quality variables in a given data set collected from Melen River, Turkey. Results show that, a small set of variable can be identified, which effectively improves the generalization ability of ANNs. Key words: Water quality, artificial neural networks, Melen river, ranking.
Biogeography and Phytogeny of the Crocinae (Neuroptera: Nemopteridae)

The biogeography of the world fauna of Crocinae (Neuroptera: Nemopteridae) is outlined. 47 species in 17 genera are known, and larvae of 21 species have been described. A theory is proposed to explain the present-day distribution of the subfamily. The relationships between the various crocine genera, and their evolutionary progress, are discussed on the basis of a set of characters which have emerged from this study, and from the work of HOLZEL (1975b).
PHYSIOLOGICAL RESPONSES TO INTERVAL TRAINING SESSIONS AT VELOCITIES ASSOCIATED WITH &OV0312;O2MAX

Previous research has indicated that short-duration, high-intensity work intervals performed at velocities associated with maximal oxygen uptake (v&OV0312;O2max) combined with active recovery intervals may be effective in eliciting improvements in endurance performance. This study was designed to characterize selected physiological responses to short-duration (≤60 seconds) interval work performed at velocities corresponding to 100% of v&OV0312;O2max. Twelve men participated in 3 randomized trials consisting of treadmill running using work (W)/recovery (R) intervals of 15 seconds W/15 seconds R (15/15); 30 seconds W/15 seconds R (30/15); and 60 seconds W/15 seconds R (60/15). Work intervals were performed at 100% of v&OV0312;O2max, whereas R intervals were performed at 50% of v&OV0312;O2max. A fourth trial consisting of continuous work (C) at 100% of v&OV0312;O2max was also performed. All subjects completed the 15/15 and 30/15 trials; however, only 5 of the 12 completed the 60/15 trial. The percentage of &OV0312;O2max (mean ± SD) during 15/15 (71.6 ± 4.2%) was significantly lower (p ≤ 0.05) than the percentages during 30/15 (84.6 ± 4.0%), 60/15 (89.2 ± 4.2%), or C (87.9 ± 5.0%). Similar results were found for heart rate and perceived exertion. Blood lactate concentrations following exercise were significantly lower (p ≤ 0.05) in 15/15 (7.3 ± 2.4 mmol·L−1) than in the other trials. No significant differences (p > 0.05) existed among 30/15 (11.5 ± 1.8 mmol·L−1), 60/15 (12.5 ± 1.8 mmol·L−1) or C (12.1 ± 1.8 mmol·L−1). High intensity, short-duration 2:1 W/R intervals appear to produce responses that may benefit both aerobic and anaerobic energy system development. A 4:1 W/R ratio may be an upper limit for individuals in the initial phases of interval training.
Overcoming obstacles to nonhomologous end joining repair of chromosome double strand breaks

STEVEN ANDREW ROBERTS: Overcoming Obstacles to Nonhomologous End Joining Repair of Chromosome Double Strand Breaks (under the direction of Dale Ramsden) Protein occlusions and oxidative nucleotide damages that flank chromosome double strand breaks are serious obstacles to nonhomologous end joining (NHEJ) since they each directly impact a specific step of this repair pathway. Because NHEJ requires the Ku heterodimer (a ring protein requiring 360 of access for binding) to recognize DNA ends, this pathway would seem particularly sensitive to DNA end-occlusions. Endassociated nucleotide damages would also seemly present a significant obstacle to NHEJ as they specifically inhibit XRCC4-LigaseIV, and their proximity to DNA ends precludes their removal by traditional base excision repair enzymes. Surprisingly, NHEJ is able to overcome these obstacles. I have shown that despite the potential steric conflicts, Ku readily binds protein-occluded DNA ends. Moreover, this very protein, predicted to be inhibited by end-associated protein obstructions, may specifically limit NHEJ’s need for ATP-dependent chromatin remodeling as Ku readily evicts weakly bound DNA-associated proteins and peels DNA from strongly positioned nucleosomes. In the case of end-associated nucleotide damages, NHEJ employs a large repertoire of processing factors, some displaying unique activity, to specifically remove, repair, or bypass these complex lesions. My work identifies a new part of this repertoire:
Adipocyte Turnover: Relevance to Human Adipose Tissue

atmospheric 14 C into DNA. RESULTS—Occurrence of hyperplasia (negative morphology value) or hypertrophy (positive morphology value) was independent of sex and body weight but correlated with fasting plasma insulin levels and insulin sensitivity, independent of adipocyte volume (-coefficient 0.3, P 0.0001). Total adipocyte number and morphology were negatively related (r 0.66); i.e., the total adipocyte number was greatest in pronounced hyperplasia and smallest in pronounced hypertrophy. The absolute number of new adipocytes generated each year was 70% lower (P 0.001) in hypertrophy than in hyperplasia, and individual values for adipocyte generation and morphology were strongly related (r 0.7, P 0.001). The relative death rate (10% per year) or mean age of adipocytes (10 years) was not correlated with morphology. CONCLUSIONS—Adipose tissue morphology correlates with insulin measures and is linked to the total adipocyte number independently of sex and body fat level. Low generation rates of adipocytes associate with adipose tissue hypertrophy, whereas high generation rates associate with adipose hyperplasia. Diabetes 59:105–109, 2010
THE EFFECTS OF UV-A, UV-B AND UV-C ON PROTEIN AND ASCORBATE CONTENT, LIPID PEROXIDATION AND BIOSYNTHESIS OF SCREENING COMPOUNDS IN BRASSICA NAPUS

The role of the antioxidant defense system was studied in Brassica napus, and subjected todifferent supplementary bands of ultraviolet radiation (UV-A, UV-B and UV-C). This study showed thatUV-B and UV-C induced oxidative stress as evidenced by an increase in lipid peroxidation and totalascorbate content. Under UV-B and UV-C treatments, flavonoids and anthocyanins were increasedsignificantly compared with control and UV-A treated plants. These compounds act as internal filtersand also have an antioxidant activity against active oxygen species such as H2O2. Results of this researchshowed that the protein content increased under UV-B and UV-C. These increments are probably relatedto the synthesis of defense proteins such as HSP, the expression of genes that are encoding theantioxidant enzymes, or those which contribute in UV-absorbing compound synthesis pathways such asPAL, CHS and CHI.
Untangling the Systematics of Salt Marsh Dodders: Cuscuta pacifica, a New Segregate Species from Cuscuta salina (Convolvulaceae)

Abstract The salt marsh dodders, Cuscuta salina, have been historically delimited as a morphologically variable assemblage of inbreeding forms that parasitize hosts growing in alkaline or saline habitats from western North America. This morphological diversity has been traditionally classified into three varieties: salina, major, and papillata. A morphometric analysis of floral characters and a molecular study using both plastid and nuclear DNA sequences strongly support the segregation of a new species, Cuscuta pacifica Costea and M. A. R. Wright, from C. salina. The new species corresponds to a lineage that includes varieties major and papillata, whereas C. salina is limited essentially to its type variety. Cuscuta pacifica and C. salina are sister species that have only a small area of parapatry in lower California, where they are ecologically and reproductively separated. Cuscuta salina occurs mostly in inland vernal pools and salt flats of Arizona, California, Nevada, Utah, Baja California, and Sonora, and grows primarily on Frankenia and Suaeda. Cuscuta pacifica can be found in salt marshes from the southcentral Pacific coast of California north into British Columbia, parasitic especially on Salicornia and Jaumea carnosa. Cuscuta salina var. papillata (Yunck.) Costea and M. A. R. Wright, parasitic on hosts that grow in coastal interdunes, falls within the range of variation of C. pacifica, where it is transferred.