Miracle-dz/UniFAR-FTUs huggingface dataset:
Cyclo-oxygenase-2 overexpression is a feature of early and well-differentiated hepatocellular carcinoma with a favourable prognosis

Aims: To determine the prognostic relevance of cyclo-oxygenase-2 (COX-2) expression in hepatocellular carcinoma (HCC) and its relationship to important clinicopathological parameters. Methods: A series of 196 patients with HCCs treated either by surgical resection (n = 106) or liver transplantation (n = 90) was investigated. Immunohistochemically confirmed COX-2 expression was correlated with a series of clinicopathologically relevant parameters as well as proliferative activity and apoptosis. Results: Overexpression of COX-2 correlated statistically with high histological tumour differentiation (p<0.001) and early TNM stage (p = 0.003). COX-2 overexpression was associated with lower apoptotic rates (p = 0.001), whereas proliferation activity did not differ significantly. In addition, COX-2 overexpression showed a significant correlation with favourable overall survival (p<0.001). In multivariate survival analysis, COX-2 expression qualified as an independent prognostic parameter (p = 0.030). Conclusions: Overexpression of COX-2 in HCC indicates early-stage cancer with less aggressive tumour behaviour and constitutes an independent prognostic factor.
Prevalence of Antibiotic-Resistant Escherichia coli in Drinking Water Sources in Hangzhou City

This study investigated the distribution of antibiotic resistant Escherichia coli (E. coli) and examined the possible relationship between water quality parameters and antibiotic resistance from two different drinking water sources (the Qiantang River and the Dongtiao Stream) in Hangzhou city of China. E. coli isolates were tested for their susceptibility to 18 antibiotics. Most of the isolates were resistant to tetracycline (TE), followed by ampicillin (AM), piperacillin (PIP), trimethoprim/sulfamethoxazole (SXT), and chloramphenicol (C). The antibiotic resistance rate of E. coli isolates from two water sources was similar; For E. coli isolates from the Qiantang River, their antibiotic resistance rates decreased from up- to downstream. Seasonally, the dry and wet season had little impact on antibiotic resistance. Spearman's rank correlation revealed significant correlation between resistance to TE and phenicols or ciprofloxacin (CIP), as well as quinolones (ciprofloxacin and levofloxacin) and cephalosporins or gentamicin (GM). Pearson's chi-square tests found certain water parameters such as nutrient concentration were strongly associated with resistance to some of the antibiotics. In addition, tet genes were detected from all 82 TE-resistant E. coli isolates, and most of the isolates (81.87%) contained multiple tet genes, which displayed 14 different combinations. Collectively, this study provided baseline data on antibiotic resistance of drinking water sources in Hangzhou city, which indicates drinking water sources could be the reservoir of antibiotic resistance, potentially presenting a public health risk.
Avoiding Imposters and Delinquents: Adversarial Crowdsourcing and Peer Prediction

We consider a crowdsourcing model in which $n$ workers are asked to rate the quality of $n$ items previously generated by other workers. An unknown set of $\alpha n$ workers generate reliable ratings, while the remaining workers may behave arbitrarily and possibly adversarially. The manager of the experiment can also manually evaluate the quality of a small number of items, and wishes to curate together almost all of the high-quality items with at most an $\epsilon$ fraction of low-quality items. Perhaps surprisingly, we show that this is possible with an amount of work required of the manager, and each worker, that does not scale with $n$: the dataset can be curated with $\tilde{O}\Big(\frac{1}{\beta\alpha^3\epsilon^4}\Big)$ ratings per worker, and $\tilde{O}\Big(\frac{1}{\beta\epsilon^2}\Big)$ ratings by the manager, where $\beta$ is the fraction of high-quality items. Our results extend to the more general setting of peer prediction, including peer grading in online classrooms.
Dispersal Between Two Patches in a Discrete Time SEIS Model

Dispersal and dormancy are two of the fundamental evolutionary mechanisms used by nature to support and generate ecological diver­ sity. In this investigation, we focus on the role of disease-enhanced or disease-suppressed dispersal on the dynamics of populations in a multi-patch system . Single patch systems, which are capable of sup­ porting simple and complex dynamics, are studied both analytically and numerically. The impact of disease and dispersal is also studied numerically. Our results are compared to those in the literature that focused on dispersal in disease free multipatch systems.
The Genetic Architecture of Seed Composition in Soybean Is Refined by Genome-Wide Association Scans Across Multiple Populations

Soybean oil and meal are major contributors to world-wide food production. Consequently, the genetic basis for soybean seed composition has been intensely studied using family-based mapping. Population-based mapping approaches, in the form of genome-wide association (GWA) scans, have been able to resolve loci controlling moderately complex quantitative traits (QTL) in numerous crop species. Yet, it is still unclear how soybean’s unique population history will affect GWA scans. Using one of the populations in this study, we simulated phenotypes resulting from a range of genetic architectures. We found that with a heritability of 0.5, ∼100% and ∼33% of the 4 and 20 simulated QTL can be recovered, respectively, with a false-positive rate of less than ∼6×10−5 per marker tested. Additionally, we demonstrated that combining information from multi-locus mixed models and compressed linear-mixed models improves QTL identification and interpretation. We applied these insights to exploring seed composition in soybean, refining the linkage group I (chromosome 20) protein QTL and identifying additional oil QTL that may allow some decoupling of highly correlated oil and protein phenotypes. Because the value of protein meal is closely related to its essential amino acid profile, we attempted to identify QTL underlying methionine, threonine, cysteine, and lysine content. Multiple QTL were found that have not been observed in family-based mapping studies, and each trait exhibited associations across multiple populations. Chromosomes 1 and 8 contain strong candidate alleles for essential amino acid increases. Overall, we present these and additional data that will be useful in determining breeding strategies for the continued improvement of soybean’s nutrient portfolio.
ECOLOGICAL DIVERGENCE ASSOCIATED WITH MATING SYSTEM CAUSES NEARLY COMPLETE REPRODUCTIVE ISOLATION BETWEEN SYMPATRIC MIMULUS SPECIES

Abstract Speciation often involves the evolution of numerous prezygotic and postzygotic isolating barriers between divergent populations. Detailed knowledge of the strength and nature of those barriers provides insight into ecological and genetic factors that directly or indirectly influenced their origin, and may help predict whether they will be maintained in the face of sympatric hybridization and introgression. We estimated the magnitude of pre- and postzygotic barriers between naturally occurring sympatric populations of Mimulus guttatus and M. nasutus. Prezygotic barriers, including divergent flowering phenologies, differential pollen production, mating system isolation, and conspecific pollen precedence, act asymmetrically to completely prevent the formation of F1 hybrids among seeds produced by M. guttatus (F1g), and reduce F1 hybrid production among seeds produced by M. nasutus (F1n) to only about 1%. Postzygotic isolation is also asymmetric: in field experiments, F1g but not F1n hybrids had significantly reduced germination rates and survivorship compared to parental species. Both hybrid classes had flower, pollen, and seed production values within the range of parental values. Despite the moderate degree of F1g hybrid inviability, postzygotic isolation contributes very little to the total isolation between these species in the wild. We also found that F1 hybrid flowering phenology overlapped more with M. guttatus than M. nasutus. These results, taken together, suggest greater potential for introgression from M. nasutus to M. guttatus than for the reverse direction. We also address problems with commonly used indices of isolation, discuss difficulties in calculating meaningful measures of reproductive isolation when barriers are asymmetric, and propose novel measures of prezygotic isolation that are consistent with postzygotic measures.
A Biophysical Indicator of Vaso-occlusive Risk in Sickle Cell Disease

Editor's Summary make their red blood cells just go with the flow. the test could pinpoint those who may benefit from such therapies, putting more patients on treatment regimens that. can objectively identify patients who are not responding well to treatment or transfusion. Conversely, et al by Wood It may never be possible to predict the exact timing of vaso-occlusion, but the ex vivo biophysical test proposed patient's response to therapy, such as a blood transfusion or small-molecule drugs. reliable markers like white blood cell count and hemoglobin S fraction. Wood and colleagues could also predict a biophysical marker helped the authors to successfully identify benign versus severe samples, without using less deoxygenation would result in a drop in flow velocity, which could be measured as a change in conductance. This oxygen reservoir. As sickle cells become deoxygenated, they adopt their stiff, sickle shape. In their device, such which were ''benign. '' The blood was flowed through a microfluidic device consisting of a channel coupled to an. collected blood from 29 patients: 23 of which were classified as having ''severe'' disease, and 6 of et al Wood severity. a new type of marker that could stratify sickle cell patients on the basis of disease −− biophysical changes in blood. therefore devised a microfluidic device that can mimic this vaso-occlusive event, allowing them to detect et al Wood cell disease can be detected through genetic and molecular tests, there is no objective biomarker of clinical outcome. S, that changes cells into a rigid sickle, or crescent, shape and causes blood flow to slow markedly. Although sickle hemoglobin hemoglobin. For those with sickle cell disease, red blood cells carry a mutated form of hemoglobin, called In healthy people, blood flows freely throughout the body, delivering oxygen to tissues via the molecule or Not … Going with the Flow
Influence of Gene Interaction on Complex Trait Variation with Multilocus Models

Although research effort is being expended into determining the importance of epistasis and epistatic variance for complex traits, there is considerable controversy about their importance. Here we undertake an analysis for quantitative traits utilizing a range of multilocus quantitative genetic models and gene frequency distributions, focusing on the potential magnitude of the epistatic variance. All the epistatic terms involving a particular locus appear in its average effect, with the number of two-locus interaction terms increasing in proportion to the square of the number of loci and that of third order as the cube and so on. Hence multilocus epistasis makes substantial contributions to the additive variance and does not, per se, lead to large increases in the nonadditive part of the genotypic variance. Even though this proportion can be high where epistasis is antagonistic to direct effects, it reduces with multiple loci. As the magnitude of the epistatic variance depends critically on the heterozygosity, for models where frequencies are widely dispersed, such as for selectively neutral mutations, contributions of epistatic variance are always small. Epistasis may be important in understanding the genetic architecture, for example, of function or human disease, but that does not imply that loci exhibiting it will contribute much genetic variance. Overall we conclude that theoretical predictions and experimental observations of low amounts of epistatic variance in outbred populations are concordant. It is not a likely source of missing heritability, for example, or major influence on predictions of rates of evolution.
Transfection and Stable Transformation of Adult Mouse Schwann Cells with SV-40 Large T Antigen Gene

Cultured Schwann cells derived from adult mouse dorsal root ganglia and peripheral nerves were transfected with a plasmid containing SV-40 large T antigen gene, and 25 colonies of stable transformants were obtained, one of which was expanded and recloned. This transfected cell line, designated MSI, expressed SV-40 large T antigen and showed continuous cell growth with a doubling time of 27 hours. The MSI cells had distinct Schwann cell phenotypes such as S-100 protein, laminin, 2',3'-cyclic nucleotide 3'-phosphodiesterase and P0 protein, as shown by immunofluorescence microscopy. When MSI cells were exposed to dibutyryl cyclic adenosine- 3',5'-monophosphate (dbc AMP), they extended long bipolar processes two- to ten-fold longer than those of untreated MSI cells and frequently formed whorl-like alignments similar to palisade formations or organoid patterns observed in human Schwannomas and neurofibromas. These results suggest that transformed Schwann cells can be a useful model for analyzing regulatory mechanisms of Schwann cells, neuron-Schwann cell interactions and experimental Schwann cell neoplasms in vitro.
Selection cooperation in multi-source cooperative networks

In a cooperative network with multiple potential relays and multiple simultaneous transmissions, we present selection cooperation wherein each source pairs with a single "best" relay. We analyze the outage probability of a simple and completely distributed selection scheme, requiring some feedback but no centralization, and show that it outperforms distributed space-time codes for networks with more than three relaying nodes. These gains are due to the more efficient use of power in networks using selection. We suggest two other more complex selection schemes based on increasing system intelligence and centralization, and show that for smaller network sizes their performance improvement over the simple selection scheme is not significant.
A morphological and phylogenetic revision of the Nectria cinnabarina species complex

The genus Nectria is typified by N. cinnabarina, a wood-inhabiting fungus common in temperate regions of the Northern Hemisphere. To determine the diversity within N. cinnabarina, specimens and cultures from Asia, Europe, and North America were obtained and examined. Their phylogeny was determined using sequences of multiple loci, specifically act, ITS, LSU, rpb1, tef1, and tub. Based on these observations, four species are recognised within the N. cinnabarina complex. Each species is delimited based on DNA sequence analyses and described and illustrated from specimens and cultures. The basionym for N. cinnabarina, Sphaeria cinnabarina, is lectotypified based on an illustration that is part of the protologue, and an epitype specimen is designated. Nectria cinnabarina s. str. is recircumscribed as having 2-septate ascospores and long stipitate sporodochia. Nectria dematiosa, previously considered a synonym of N. cinnabarina, has up to 2-septate ascospores and sessile sporodochia or no anamorph on the natural substrate. A third species, Nectria nigrescens, has up to 3-septate ascospores and short to long stipitate sporodochia. One newly described species, Nectria asiatica with a distribution restricted to Asia, has (0–)1-septate ascospores and short stipitate sporodochia. Young and mature conidia developing on SNA were observed for each species. Mature conidia of N. asiatica, N. cinnabarina, and N. nigrescens but not N. dematiosa bud when the mature conidia are crowded. On PDA the optimal temperature for growth for N. dematiosa is 20 °C, while for the other three species it is 25 °C. Based on our phylogenetic analyses, three subclades are evident within N. dematiosa. Although subtle culture and geographical differences exist, these subclades are not recognised as distinct species because the number of samples is small and the few specimens are insufficient to determine if morphological differences exist in the natural environment.
The Advanced Computing Systems Association Proceedings of the Workshop on Intrusion Detection and Network Monitoring Learning Program Behavior Profiles for Intrusion Detection Learning Program Behavior Prooles for Intrusion Detection

Prooling the behavior of programs can be a useful reference for detecting potential intrusions against systems. This paper presents three anomaly detection techniques for prooling program behavior that evolve from memorization to generalization. The goal of monitoring program behavior is to be able to detect potential intrusions by noting irregularities in program behavior. The techniques start from a simple equality matching algorithm for determining anomalous behavior, and evolve to a feed-forward backpropagation neural network for learning program behavior, and nally to an Elman network for recognizing recurrent features in program execution traces. In order to detect future attacks against systems , intrusion detection systems must be able to generalize from past observed behavior. The goal of this research is to employ machine learning techniques that can generalize from past observed behavior to the problem of intrusion detection. The performance of these systems is compared by testing them with data provided by the DARPA Intrusion Detection Evaluation program.
Reanalysis of carbamazepine and carbamazepine-epoxide pharmacokinetics after multiple dosing of extended release formulation.

PURPOSE To model and re-evaluate the pharmacokinetics of carbamazepine (CBZ) and CBZ-10, 11-epoxide (CBZ-E) after 5 day b.i. d. dosing with either Carbatrol (extended-release beads) or Tegretol-XR (an osmotic pump tablet, an Oros tablet) using compartmental method. METHODS Plasma concentration time profile data from 15 normal healthy adults received, in a randomized crossover fashion, Carbatrol (2 x 200 mg capsules), b.i. d. for 5 days and Tegretol-XR (400 mg), b.i. d. for 5 days were available for analysis from previous study. The compartmental kinetic parameters of CBZ and CBZ-E were simultaneously fitted by assuming: i) one compartment open model with zero order absorption with lag time, and first order elimination for CBZ and ii) one compartment open model with Michaelis-Menten formation with a sigmoidity factor, and first order elimination for CBZ-E. Time to 50% of CBZ plateau concentrations (TC50) was estimated and statistically compared between the two products. RESULTS There was a good agreement between simulated and observed plasma concentrations. For CBZ, the fitted parameters were: the first order elimination rate constant (K(10)) 0.024 and 0.022 hr(-1), t(1/2) 27.3 and 30.3 hr, volume of central compartment (V(1) ) 1.119 and 1.160 L/kg, for Carbatrol and Tegretol-XR, respectively. For CBZ-E, the fitted parameters were: the first order elimination rate constant (K (30) ) 0.128 and 0.157 hr (-1), t (1/2) 6.1 and 5.1 hr, volume of central compartment (V (3) ) 0.728 and 0.644 L/kg, V (max) 0.085 and 0.076 mg/hr/kg, K (m) 28.639 and 33.138 mg/mL, for Carbatrol and Tegretol-XR, respectively. The fitted pharmacokinetic parameters of CBZ and CBZ-E were generally consistent with published values from previous studies. A minimal rise in CBZ-E concentrations was observed during the first 12 hours, the finding of which has not been reported before. Consequently, the CBZ-E plasma profiles appear as sigmoid curves and have a different shape compared to those of the CBZ profiles. The inclusion of the sigmoidity factor allowed flexibility in the fitting and optimized the simulation results. When compared to published literature of single dose data, the investigation of CBZ and CBZ-E pharmacokinetics from this study suggested that autoinduction might occur by the fifth day of dosing and might partly contribute to the sigmoidal shape of CBZ-E profiles. CONCLUSION The fitted model well described the plasma profiles of both CBZ and CBZ-E. Carbatrol and Tegretol-XR were similar in their pharmacokinetics based on compartmental analysis.
Biosensing near the neutrality point of graphene

Using the charge neutrality point promises low-noise graphene electronic sensors. Over the past decade, the richness of electronic properties of graphene has attracted enormous interest for electrically detecting chemical and biological species using this two-dimensional material. However, the creation of practical graphene electronic sensors greatly depends on our ability to understand and maintain a low level of electronic noise, the fundamental reason limiting the sensor resolution. Conventionally, to reach the largest sensing response, graphene transistors are operated at the point of maximum transconductance, where 1/f noise is found to be unfavorably high and poses a major limitation in any attempt to further improve the device sensitivity. We show that operating a graphene transistor in an ambipolar mode near its neutrality point can markedly reduce the 1/f noise in graphene. Remarkably, our data reveal that this reduction in the electronic noise is achieved with uncompromised sensing response of the graphene chips and thus significantly improving the signal-to-noise ratio—compared to that of a conventionally operated graphene transistor for conductance measurement. As a proof-of-concept demonstration of the usage of the aforementioned new sensing scheme to a broader range of biochemical sensing applications, we selected an HIV-related DNA hybridization as the test bed and achieved detections at picomolar concentrations.
Floral features, pollination biology and breeding system of Chloraea membranacea Lindl. (Orchidaceae: Chloraeinae).

BACKGROUND AND AIMS The pollination biology of very few Chloraeinae orchids has been studied to date, and most of these studies have focused on breeding systems and fruiting success. Chloraea membranacea Lindl. is one of the few non-Andean species in this group, and the aim of the present contribution is to elucidate the pollination biology, functional floral morphology and breeding system in native populations of this species from Argentina (Buenos Aires) and Brazil (Rio Grande do Sul State). METHODS Floral features were examined using light microscopy, and scanning and transmission electron microscopy. The breeding system was studied by means of controlled pollinations applied to plants, either bagged in the field or cultivated in a glasshouse. Pollination observations were made on natural populations, and pollinator behaviour was recorded by means of photography and video. KEY RESULTS Both Argentinean and Brazilian plants were very consistent regarding all studied features. Flowers are nectarless but scented and anatomical analysis indicates that the dark, clavate projections on the adaxial labellar surface are osmophores (scent-producing glands). The plants are self-compatible but pollinator-dependent. The fruit-set obtained through cross-pollination and manual self-pollination was almost identical. The main pollinators are male and female Halictidae bees that withdraw the pollinarium when leaving the flower. Remarkably, the bees tend to visit more than one flower per inflorescence, thus promoting self-pollination (geitonogamy). Fruiting success in Brazilian plants reached 60·78 % in 2010 and 46 % in 2011. Some pollinarium-laden female bees were observed transferring pollen from the carried pollinarium to their hind legs. The use of pollen by pollinators is a rare record for Orchidaceae in general. CONCLUSIONS Chloraea membrancea is pollinated by deceit. Together, self-compatibility, pollinarium texture, pollinator abundance and behaviour may account for the observed high fruiting success. It is suggested that a reappraisal and re-analysis of important flower features in Chloraeinae orchids is necessary.