Miracle-dz/UniFAR-FTUs huggingface dataset:
The effects of maternal size on clutch traits in a tropical invariant-clutch lizard, Carlia rubrigularis (Scincidae)

Species with an invariant or "fixed" clutch offer a unique opportunity to examine how variation in maternal size relates to key reproductive traits, such as egg size. Theoretical models of offspring size suggest selection should operate to optimize egg size and reproductive output. However, because invariant-clutch species are unable to allocate surplus resources to additional eggs (or offspring) they may exhibit different relationships than those anticipated under theoretical expectations. To test this, I examined relationships between maternal size-egg size in Carlia rubrigularis, an invariant-clutch producing scincid lizard from tropical Australia. C. rubrigularis exhibited relative clutch masses that were lower than variant clutch size species, but which were similar to other invariant clutch size species. However, maternal size (snout-vent length and post-oviposition mass) was correlated with several clutch traits (egg mass, egg width and egg volume), but females in better condition did not produce relatively heavier eggs. These results suggest mechanistic hypotheses may best explain the observed maternal size-egg size relationships in C. rubrigularis.
Clines in Africa: does size vary in the same way among widespread sub‐Saharan monkeys?

We characterize and compare patterns of clinal size variation among diverse widespread sub‐Saharan monkeys with the aim of identifying commonalities and differences in biogeographical variation. Thus, we accurately quantify nonlinear clines in representatives of the main lineages of widespread sub‐Saharan terrestrial and arboreal monkeys, and provide a crude numerical estimate of the strength of similarities across taxonomic groups.
Physiological relevance of successive hydroxylations of toluene by toluene para-monooxygenase of Ralstonia pickettii PKO1

We have recently found that toluene para-monooxygenase (TpMO) of Ralstonia pickettii PKO1 (encoded by tbuA1UBVA2C) performs successive hydroxylations of benzene (Appl. Environ. Microbiol. 70: 3814, 2004) as well as hydroxylates toluene to a mixture of 90% p-cresol and 10% m-cresol which are then further oxidized to 100% 4-methylcatechol (J. Bacteriol. 186: 3117, 2004) whereas it was thought previously that TpMO forms 100% m-cresol and is not capable of successive hydroxylations. Here we propose a modification of the degradation pathway originally described by Olsen et al. (J. Bacteriol. 176: 3749, 1994) that now relies primarily on TpMO for conversion of toluene to 4-methylcatechol (instead of m-cresol) since both m-cresol and p-cresol are shown here to be good substrates for Escherichia coli expressing TpMO (Vmax/Km=0.046, 0.036, and 0.055 mL min−1 mg−1 protein for the oxidation of toluene, m-cresol, and p-cresol, respectively). In light of the broader activity of TpMO, phenol hydroxylase (encoded by tbuD) appears to facilitate conversion of any m-cresol or p-cresol formed from toluene oxidation by TpMO to 4-methylcatechol; hence, the cell has a redundant method for making this important intermediate 4-methylcatechol. Further, it is suggested that the physiological relevance of the 10% m-cresol formed from toluene oxidation by TpMO is needed for induction of the meta cleavage operon tbuWEFGKIHJ to enable full metabolism of toluene since p-cresol (and o-cresol) do not induce the meta-cleavage pathway. Therefore both the successive hydroxylation of toluene by TpMO and the product distribution are of physiological relevance to the cell.
Genetic analysis of durable adult plant stripe rust resistance in durum wheat cultivars

The deployment of combinations of resistance genes in commercial cultivars is necessary to achieve sustained disease control. Old American durum cultivars Wells and Leeds as well as Australian cultivars Yallaroi and Wollaroi are susceptible to Australian Puccinia striiformis f. sp. tritici pathotypes 110 E143A+ and 134 E16A+ at the seedling stage. These cultivars produced low stripe rust responses at the adult plant stage since their release and therefore were chosen for genetic analysis. Genetic analyses of adult plant stripe rust resistance using Wells/Bansi and Leeds/Bansi F3 populations indicated the involvement of two independent genes each in Wells and Leeds. These genes produced intermediate adult plant stripe rust responses when present singly. Absence of segregation among F3 lines derived from crosses of older north American cultivars Leeds and Wells with Australian cultivars Wollaroi and Yallaroi indicated the presence of common gene(s) for stripe rust resistance. Common parentage of these cultivars supported this conclusion and suggested narrow genetic base of stripe rust resistance among Australian and old American durum wheat cultivars. The effectiveness of both old and modern cultivars over two and four decades, respectively, indicated durable nature of the genes carried by these cultivars.
OOGAMOUS REPRODUCTION, WITH TWO‐STEP AUXOSPORULATION, IN THE CENTRIC DIATOM THALASSIOSIRA PUNCTIGERA (BACILLARIOPHYTA) 1

Thalassiosira species are common components of marine planktonic communities worldwide and are used intensively as model experimental organisms. However, data on life cycles and sexuality within the genus are fragmentary. A clone of the cosmopolitan marine diatom Thalassiosira punctigera Cleve emend. Hasle was isolated from the North Sea and oogamous sexual reproduction was observed in culture. Cells approximately 45 μm and smaller became sexualized. Oogonia were produced preferentially and spermatogenesis was infrequent. Unfertilized oogonia always aborted and their development was apparently arrested at prophase of meiosis I. Further progression through meiosis and auxospore formation occurred only after a sperm had penetrated into the oocyte. Many cells of the new large‐celled generation (approximately 90–120 μm in size) immediately became sexualized again but only oogonia were produced. A few of the large oogonia became auxospores and produced initial cells 132–153 μm in diameter. The second step of auxosporulation probably involved fertilization of large‐celled oocytes by the sperm of the small‐celled spermatogonangia that were still present in the culture. An F1 clone obtained after selfing within the small‐celled auxosporulation size range was investigated. Like the parent clone, the F1 clone was homothallic but no auxosporulation was observed: spermatogonangia were unable to produce viable sperm, apparently because of inbreeding depression. Aggregation and interaction of oogonia were documented, and may be relevant for understanding the mechanisms of signaling and recognition between sexualized cells and the evolution of sexuality in pennate diatoms.
In Situ Estimation of Carbon Balance of In Vitro Sweetpotato and Tomato Plantlets Cultured with Varying Initial Sucrose Concentrations in the Medium

The effects of initial sucrose (suc) concentrations in the medium (S0) on the carbon balance and growth of sweetpotato (Ipomoea batatas (L.) Lam. 'Beniazuma') and tomato (Lycopersicon esculentum Mill. 'HanaQueen') plantlets were studied under controlled environmental conditions. Plantlets were cultured with 0, 7.5, 15, or 30 g·L -1 of S0 under high photosynthetic photon flux (160 to 200 µmol·m -2 ·s -1 ) and CO2 enriched (1400 to 2050 µmol·mol -1 ) conditions. Net photosynthetic rate per leaf area (Pl) decreased and dry weight per plantlet (Wd) increased with increasing S0, but did not differ significantly between S0 of 7.5 to 30 g·L -1 for sweetpotato or 15 to 30 g·L -1 for tomato. Carbon influxes and effluxes of the plantlets by metabolism of medium suc and/or photosynthesis, and respiration were estimated based on measurements of in situ and steady state CO2 exchange rates and sugar uptake during culture. At S0 from 7.5 to 30 g·L -1 , photosynthesis was responsible for 82% to 92% and 60% to 67% of carbohydrate assimilation for sweetpotato and tomato, respectively. Estimated carbon balances of plantlets based on the estimated and actual increases of moles of carbon in plant tissue demonstrated that in situ estimation of carbon balance was reasonably accurate for sweetpotato at S0 of 0 to 15 g·L -1 and for tomato at S0 of 0 g·L -1 and that the actual contribution of photosynthesis for tomato at high S0 might be lower than the values estimated in the present experiment. Results showed that initial suc concentration affected the relative contribution of photosynthesis on their carbon balances and that the responses were species specific. The failure of validation at S0 in a range specific to each species suggested the need for further study on carbon metabolism of in vitro plantlets cultured with sugar in the medium. uptake and photosynthesis is necessary to enhance plantlet growth with a minimal input of energy and other resources, thereby maxi- mizing the biomass production efficiency. Reducing suc concentra- tion in the medium and increasing photosynthetic photon flux (PPF)
Metabolic responses in zebrafish (Danio rerio) exposed to zinc and cadmium by nuclear magnetic resonance -based metabolomics

ABSTRACT Heavy metals are common marine and soil pollutants that are mainly the result of industrial activity, and are a threat to the environment and human health. In this study, 1H nuclear magnetic resonance (NMR)-based metabolomics was applied to adult Danio rerio to monitor the metabolic change as a response to ZnCl2 and CdCl2 exposure at different concentrations for 72 h. NMR spectroscopy was used to identify and quantify the metabolites extracted from D. rerio. The metabolite profiles of the control and heavy metal exposed group were classified by partial least squares – discriminant analysis (PLS-DA) analysis, and potential contaminant-specific biomarkers were suggested. For the ZnCl2-exposed zebrafish, the levels of ATP, aspartate and NAD+ were increased, whereas the levels of formate, inosine, hypoxanthine and succinate decreased. In addition, the CdCl2-exposed zebrafish showed an increase in the levels of ATP and formate and a decrease in the levels of glutamate, inosine and glutathione. Overall, Zn and Cd may lead to neurotoxicity, disturbances in the energy metabolism and oxidative stress. Our finding demonstrated that the application of NMR-based metabolomics might be useful for detecting the toxicity caused by sub-lethal concentrations of heavy metal contaminants in the environment.
Assessment of richness estimation methods on macroinvertebrate communities of mountain ponds in Castilla y Leon (Spain)

Complete inventories of the fauna at a given place, for a specific community or geographical area are often exceedingly hard to get. In recent years a number of estimation techniques have emerged that can be used to extrapolate from these samples to the true number of species in an area. These estimation models are based on different mathematical approaches and can be classified as either species accumulation curves or nonparametric estimators (Brose et al. , 2003, Ecology , 84 , 2364–2377). In this paper, we have tested the performance of some of the richness estimators on nineteen mountain ponds in Castilla y Leon (Spain) in order to provide guidance on their potential use in future researches. We collected benthic macroinvertebrate of these ponds from the littoral zone with a pond net by kicking and sweeping. Ten-second samples were collected in each pond up to a total time of 3 to 5 minutes per pond, depending on the pond size. In addition, two of the ponds, were sampled in 2004, 2006 and 2007 providing a three-year time series. The results of this study showed that Jackknife 2 was the best of the evaluated methods based on all chosen criteria and also performed well across all studied ponds. Jackknife 1, Chao 1 and Chao 2 also presented good results and they were inferior to Jackknife 2 mainly because of the requirement for larger sub-sample sizes.
Comprehensive Visualization of Longitudinal Patient Data for the Dermatological Oncological Tumor Board

In multidisciplinary oncological team meetings for patient-speciﬁc treatment decision-making, so-called tumor boards, usually one physician introduces a patient case verbally and proposes an initial therapy recommendation. This is followed by a short collaborative discussion of the recommendation’s suitability. While patient-related image data, such as CT and MR scans, are displayed during the discussion, clinical patient data must be memorized from the introduction or repeatedly inquired by the participating domain experts. To support physicians in this concern, we propose a comprehensive visualization of longitudinal patient-speciﬁc information entities during case introduction and discussion. Our visual approach advances over existing work by simultaneously providing an overview of the current patient status as well as of previous therapy measures and their effects on the status. The latter assists in relating the currently proposed recommendation to the previous treatment measures and the related patient status. The visualization has been designed in close collaboration with dermatologists and oncologists aiming at a comprehensive yet easily comprehensible presentation of relevant patient-data and minimal user interaction. The usability and clinical relevance of the prototypical implementation of our visual approach have been evaluated in a qualitative user study with ﬁve domain experts based on real anonymized data of melanoma patients.
Costs of utilizing healthcare services in Chakaria, a rural area in Bangladesh

their access to critical healthcare and other basic needs. Episodes of illness and ill health may result in substantial medical expenses and trigger impoverishment of households. Cost of healthcare services may deter or delay patients, especially the poor, from seeking appropriate care. Affordability or perceived costs of care are signi cant factors in uencing healthcare behaviour such as choice of the provider and time of care.
Digital Window @ Vassar Digital Window @ Vassar

We propose an algorithm that constructs relationships among any number of seed words. A relationship consists of a set of iteratively-generated paths of similar words, where each path links one seed word to another. The similar words are generated using Word2Vec word embeddings and the cosine similarity measure. By examining the eﬀectiveness of the proposed algorithm in the mental health domain, we ﬁnd that the algorithm eﬀectively returns meaningful relationships and has the potential to be used for hypothesis generation and information extraction
Molecular cloning of neuronally expressed mouse βPix isoforms

Pix, a Pak-interacting exchange factor, is known to be involved in the regulation of Cdc42/Rac GTPases and Pak kinase activity. In this study, we cloned the cDNAs encoding two betaPix isoforms from mouse brain cDNA library. Both of the cloned genes, designated betaPix-b and betaPix-c (GenBank Accession Nos. AF247654 and AF247655, respectively), have a novel insert region consisting of 59 amino acid residues. In betaPix-c, 75 amino acid residues are deleted in the proline-rich region at the carboxyl-terminus of betaPix. In situ hybridization studies with insert region-specific probe in rat embryo show that insert region-containing isoforms are expressed mainly in the central nervous system. Moreover, temporal expression pattern of isoforms is correlated with the active neurogenesis period in the cerebral cortex and cerebellum. These results strongly suggest that betaPix isoforms may play important roles in the cellular events required for brain development such as neuronal migration.
Inhibitory effect of caffeic acid and its derivatives on human liver cytochrome P450 3A4 activity

Effects of caffeic acid (CAF) and its derivatives on human liver CYP3A4 activity were evaluated by using diazepam as a substrate. It was found that CAF inhibited CYP3A4 activity by uncompetitive inhibition with IC50 0.72 µM, whereas ester and amide analogues inhibited CYP3A4 by competitive inhibition with IC50 value of 0.31, 0.37, 0.46, 0.49, 0.53, 0.58, 0.75 and 0.82 µM for ethyl 1- (3’,4’-dihydroxyphenyl) propen amide (EDPA), phenmethyl 1- (3’,4’-dihydroxyphenyl) propen amide (PMDPA), phenethyl 1(3’,4’-dihydroxyphenyl) propen amide (PEDPA), phenylethyl 1- (3’,4’-dihydroxyphenyl) propenate (PC), ethyl 1- (3’,4’-dihydroxyphenyl) propenate (EC), octyl 1- (3’,4’-dihydroxyphenyl) propen amide (ODPA), octyl 1- (3’,4’-dihydroxyphenyl) propenate (OC) and phenylmethyl 1- (3’,4’-dihydroxyphenyl) propenate (BC), respectively. The K i values of CAF, PMDPA, EC, PC, ODPA, PEDPA, OC, EDPA and BC were 0.24, 0.29, 0.49, 0.56, 0.57, 0.59, 0.62, 0.62 and 1.03 µM, respectively. However, CAF and its derivatives had high potential to inhibit CYP3A4. Therefore, consumption of herbal medicine containing CAF and its derivatives that are concomitant with other medications should be cautiously monitored.
Automated System for Detection of Vehicle Features

: Automation is the process of detecting traffic rule violation and recognition of the vehicle. Violating the traffic rule is also a problem of great concern, with so many violations taking place, it would be humanely impossible to scrutinize each and every violation and bring the defaulter to justice. The above problem can be basically broken down into three parts. The first would be to detect the vehicle which has violated the traffic rule, which is an independent problem in itself. The second part would be to recognize the vehicle on the basis of extraction of the number plate. The third would be to identify different features of the vehicle like the color of the vehicle, its class and further the corresponding model which would help in the precise recognition of the vehicle. In this paper, we have concentrated our efforts on the third part of the problem. Algorithms have been developed and implemented for independent recognition of the vehicle on the basis of its class, model and color. Karhunen-Loeve transform in combination with Support Vector Machines has been used to obtain information about class of the vehicle. An algorithm has been developed and implemented to detect the color of the vehicle by means of modification of the color map of the image and by using RGB histograms. Finally Scale Invariant Feature Transform (SIFT and PCA-SIFT) has been made use of foridentifying the vehicle model. Very high recognition rates is being obtained in all the cases.
Genetics of polygalacturonase activity in relation to shelf life governing traits in tomato (Solanum lycopersicum L.)

Gene effects for polygalacturonase activity and other shelf life governing traits in tomato were studied in 45 cross combinations involving 10 parental lines. Studies revealed that the additive gene actions play a greater role for the inheritance of polygalacruronase activity, fruit firmness, pericarp thickness and shelf life. Component analysis of these traits suggested that polygalaturonase activity and pericarp thickness is under the control of partial dominance, whereas number of locules was under the control of over dominance genes. Combining ability analysis revealed that the lines CLN 5915-206 D4-2-2-0 and CLN 14663were good general combiners for incorporating lower polygalacturonase activity, higher whole fruit firmness, pericarp thickness, lower number of locules and better shelf life. The combination CLN 1462A x CLN 14663 could be commercially utilized for improving the shelf life of tomato fruits as this combination recorded significant estimates of specific combining ability (sca) in desirable direction for all the traits under study except for number of locules. Heritability in narrow sense was observed to be moderate for all the traits studied, which suggested that line breeding or family selection methods might be employed for developing pure lines having lower polygalacturonase activity and longer shelf life of tomato fruits.
Efficacy of quality protein maize in meeting energy and essential amino acid requirements in broiler chicken production

Quality protein maize (QPM), with almost double lysine and tryptophan in protein, is no different from regular maize (RM) in terms of quantity of energy and protein. The objective of the study was to assess whether QPM can substitute RM as an efficient energy source as well as requirement of essential amino acids in poultry feed. Experiments were conducted to determine apparent metabolizable energy (AME), digestible amino acid values, and utilization pattern of QPM and RM in chickens. AME of QPM was similar to RM. Lysine and threonine digestibilities were significantly (P≤0.05) higher in QPM than RM. Dietary replacement of RM by QPM at 50% or higher level significantly improved the body-weight gain. The overall feed conversion ratio (0–40 days) improved significantly in QPM compared to RM at 50% replacement level or higher. Abdominal fat content decreased by 40% and breast meat yield increased by 4.91% by dietary replacement of RM with QPM at 100% level. The protein concentration in serum increased linearly by increasing the level of replacement of RM by QPM. Serum cholesterol decreased significantly in the dietary group where RM was replaced by QPM at 100% level. Neither dressed weight nor giblet weight was influenced by replacement of RM by QPM or supplementing lysine to RM-based diet. However, the breast weight increased and abdominal fat content decreased significantly where RM was replaced by QPM at 50% level or higher. Our findings clearly indicated that feeding value of QPM was higher than RM in broiler chickens.
Genetic homogeneity of vegetatively propagated Clinacanthus nutans (Acanthaceae)

Clinacanthus nutans is a medicinal Asian plant often propagated by stem cuttings but little is known about the genetic relationships between existing accessions and the extent of homogeneity. In this study, we examined the genetic homogeneity in 12 C. nutans samples from Malaysia, Thailand and Vietnam reproduced by vegetative propagation from different regions between and within countries, and compared it to sexually propagated Andrographis paniculata (same family), related Clinacanthus siamensis (same family) and an out-group (different family) using restriction fragment length polymorphism (RFLP), random amplified polymorphic DNA (RAPD) and microsatellite markers. There was a high genetic similarity between C. nutans accessions from all countries, with identical genetic profiles even though they were geographically distant. C. nutans clustered closely with C. siamensis and was distant from A. paniculata and the out-group. Genetic similarity for C. nutans was almost double that of A. paniculata, but the combined clustering analysis revealed higher diversity in C. nutans. These results provide fundamental knowledge in future planting decisions and options, and also facilitate further germplasm conservation of C. nutans and other vegetatively propagated medicinal species. Key words: Clinacanthus nutans, Andrographis paniculata, Clinacanthus siamensis, Acanthaceae, genetic variation, vegetative propagation, sexual reproduction.
A Candidate SNP in the Bovine SP110 Gene is not Associated with Susceptibility to Tuberculosis in Cattle

The human SP110 nuclear body protein (SP110) gene and the orthologous murine Intracellular pathogen resistance 1 (Ipr1) have been reported to be related with susceptibility to tuberculosis. In addition, a recent study reported that SNP c.587A>G (N196S) in the bovine SP110 gene is associated with susceptibility to Mycobacterium avium subsp. paratuberculosis infection in dairy cattle. The objective of the present study was to analyze the putative association between SNP c.587A>G in SP110 gene and susceptibility to Mycobacterium bovis infection in cattle. A total of 158 cows (50 infected and 108 non-infected) from a multibreed sample were included in the study. Neither SNP c.587A>G alleles nor genotypes showed significant association with susceptibility to Mycobacterium bovis infection in the analyzed cattle population. Nevertheless, other SNPs in this gene must be analyzed in order to rule out the implication of SP110 gene in susceptibility to bovine tuberculosis.