Miracle-dz/UniFAR-FTUs huggingface dataset:
RNA-Seq Analysis of Allele-Specific Expression, Hybrid Effects, and Regulatory Divergence in Hybrids Compared with Their Parents from Natural Populations

Hybridization is a prominent process among natural plant populations that can result in phenotypic novelty, heterosis, and changes in gene expression. The effects of intraspecific hybridization on F1 hybrid gene expression were investigated using parents from divergent, natural populations of Cirsium arvense, an invasive Compositae weed. Using an RNA-seq approach, the expression of 68,746 unigenes was quantified in parents and hybrids. The expression levels of 51% of transcripts differed between parents, a majority of which had less than 1.25× fold-changes. More unigenes had higher expression in the invasive parent (P1) than the noninvasive parent (P2). Of those that were divergently expressed between parents, 10% showed additive and 81% showed nonadditive (transgressive or dominant) modes of gene action in the hybrids. A majority of the dominant cases had P2-like expression patterns in the hybrids. Comparisons of allele-specific expression also enabled a survey of cis- and trans-regulatory effects. Cis- and trans-regulatory divergence was found at 70% and 68% of 62,281 informative single-nucleotide polymorphism sites, respectively. Of the 17% of sites exhibiting both cis- and trans-effects, a majority (70%) had antagonistic regulatory interactions (cis x trans); trans-divergence tended to drive higher expression of the P1 allele, whereas cis-divergence tended to increase P2 transcript abundance. Trans-effects correlated more highly than cis with parental expression divergence and accounted for a greater proportion of the regulatory divergence at sites with additive compared with nonadditive inheritance patterns. This study explores the nature of, and types of mechanisms underlying, expression changes that occur in upon intraspecific hybridization in natural populations.
Multidrug‐resistant hepatitis B virus resulting from sequential monotherapy with lamivudine, adefovir, and entecavir: Clonal evolution during lamivudine plus adefovir therapy

Whether multidrug‐resistant (MDR) hepatitis B virus (HBV) harbors mutations co‐located in the same HBV clones that confer reduced sensitivity to antiviral therapy remains uncertain. This study investigated the evolution of MDR HBV strains developed from sequential monotherapy with lamivudine (LAM), adefovir (ADV), and entecavir (ETV) during LAM plus ADV salvage therapy. Sera were obtained from six patients who had developed sequential resistance to LAM, ADV, and ETV before and during LAM plus ADV therapy. The HBV genomes from each patient were amplified, cloned, and sequenced. Among 6 sets of 20 clones obtained before salvage therapy, all clones harbored the rtM204V mutation, and ETV‐resistant mutations were detected with the rtM204V in 108 clones. The rtA181 mutation was not detected at baseline, but emerged in five patients during therapy. Among 9 sets of 20 clones obtained during salvage therapy, 39 clones harbored rtA181T/V ± rtN236T mutations, which were detected in the absence of rtM204 and ETV‐resistant mutations in 37 clones (94.9%). Only two clones (5.1%) harbored both rtA181T/V and ETV‐resistant mutations. The rtA181T/V mutation emerged after reversion from ETV‐resistant mutants to wild‐type HBV. Five patients achieved a partial virologic response to LAM plus ADV therapy. In conclusion, the majority of MDR mutations existed in different genomes. Suboptimal response to LAM plus ADV therapy may not result from the co‐localization of MDR HBV mutations in the same genome, but instead the low antiviral potency of these drugs. Thus, more potent antiviral drug combinations may be an effective salvage therapy for patients infected with MDR HBV. J. Med. Virol. 85:55–64, 2012. © 2012 Wiley Periodicals, Inc.
Ocular adnexal lymphoproliferative disease: a series of 73 cases

Background: This study involved 73 patients with lymphoproliferative lesions of the ocular adnexa. The lesions were categorized using the Revised European American Lymphoma classification of lymphoid tissues and analysed to determine the frequency and prognostic impact of tumour type, location, stage and patient's age and sex.
Yield and energy tradeoffs of an NVLatch design using radial sampling

Nonvolatile latches are increasingly popular with the advent of IoT design. We study the yield energy tradeoff of the backup mechanism of an STT-MTJ based nonvolatile latch. For the yield analysis, we rely on Hicks and Wheeling methodology for multi-cone radial sampling for the purpose of rare fail estimation. Yield is shown to be delimited by the Parallel-to-AntiParallel magnetic angle transitions. To accommodate for the slower cells, we note an increase in the average energy requirements for the backup mechanism. Simulations indicate an increase of 10%–40% for the average energy requirements to achieve an ideal yield requirement close to 99% for different number of components.
How Big is the Brain Drain?

The brain drain from developing countries has been lamented for many years, but knowledge of the empirical magnitude of the phenomenon is scant owing to the lack of systematic data sources. This paper presents estimates of emigration rates from 61 developing countries to OECD countries for three educational categories constructed using 1990 U.S. Census data, Barro and Lee`s data set on educational attainment, and OECD migration data. Although still tentative in many respects, these estimates reveal a substantial brain drain from the Caribbean, Central America, and some African and Asian countries.
Rational modification of protein stability by targeting surface sites leads to complicated results

The rational modification of protein stability is an important goal of protein design. Protein surface electrostatic interactions are not evolutionarily optimized for stability and are an attractive target for the rational redesign of proteins. We show that surface charge mutants can exert stabilizing effects in distinct and unanticipated ways, including ones that are not predicted by existing methods, even when only solvent-exposed sites are targeted. Individual mutation of three solvent-exposed lysines in the villin headpiece subdomain significantly stabilizes the protein, but the mechanism of stabilization is very different in each case. One mutation destabilizes native-state electrostatic interactions but has a larger destabilizing effect on the denatured state, a second removes the desolvation penalty paid by the charged residue, whereas the third introduces unanticipated native-state interactions but does not alter electrostatics. Our results show that even seemingly intuitive mutations can exert their effects through unforeseen and complex interactions.
Glycosyltransferases Involved in Biosynthesis of the Outer Core Region of Escherichia coli Lipopolysaccharides Exhibit Broader Substrate Specificities Than Is Predicted from Lipopolysaccharide Structures*

The waaJ, waaT, and waaR genes encode α-1,2-glycosyltransferases involved in synthesis of the outer core region of the lipopolysaccharide of Escherichia coli. They belong to the glycosyltransferase CAZy family 8, characterized by the GT-A fold, DXD motifs, and by retention of configuration at the anomeric carbon of the donor sugar. Each enzyme adds a hexose residue at the same stage of core oligosaccharide backbone extension. However, they differ in the epimers for their donor nucleotide sugars, and in their acceptor residues. WaaJ is a UDP-glucose: (galactosyl) LPS α-1,2-glucosyltransferase, whereas WaaR and WaaT have UDP-glucose:(glucosyl) LPS α-1,2-glucosyltransferase and UDP-galactose:(glucosyl) LPS α-1,2-galactosyltransferase activities, respectively. The objective of this work was to examine their ability to utilize alternate donors and acceptors. When expressed in the heterologous host, each enzyme was able to extend the alternate LPS acceptor in vivo but they retained their natural donor specificity. In vitro assays were then performed to test the effect of substituting the epimeric donor sugar on incorporation efficiency with the natural LPS acceptor of the enzyme. Although each enzyme could utilize the alternate donor epimer, activity was compromised because of significant decreases in kcat and corresponding increases in Km(donor). Finally, in vitro assays were performed to probe acceptor preference in the absence of the cellular machinery. The results were enzyme-dependent: while an alternate acceptor had no significant effect on the kinetic behavior of His6-WaaT, His6-WaaJ showed a significantly decreased kcat and increased Km(acceptor). These results illustrate the differences in behavior between closely related glycosyltransferase enzymes involved in the synthesis of similar glycoconjugates and have implications for glycoengineering applications.
Aberrant regulation and function of Src family tyrosine kinases: Their potential contributions to glutamate‐induced neurotoxicity

1. Excitotoxicity, a major cause of neuronal death in acute and chronic neurodegenerative diseases and conditions such as stroke and Parkinson’s disease, is initiated by overstimulation of glutamate receptors, leading to calcium overload in affected neurons. The sustained high concentration of intracellular calcium constitutively activates a host of enzymes, notably the calcium‐activated proteases calpains, neuronal nitric oxide synthase (nNOS) and NADPH oxidase (NOX), to antagonise the cell survival signalling pathways and induce cell death.
EBV PCR in the Diagnosis and Monitoring of Posttransplant Lymphoproliferative Disorder: Results of a Two‐Arm Prospective Trial

While EBV PCR is used in the management of PTLD, the optimal primer set, relative importance of intracellular versus free plasma EBV, and the baseline profile in an organ transplant population remains unclear. We performed a prospective 2‐arm trial utilizing an EBV PCR panel measuring LMP‐1, EBER‐1 and EBNA‐1 in both free plasma as well as intracellular whole blood. Control Arm A consisted of 31 lung transplant patients and Arm B consisted of 35 transplant patients being evaluated for possible PTLD. In Arm A, 1/31 (3%) patients developed a transient plasma EBV load. Thirteen of 31 (42%) had detectable intracellular EBV. In Arm B, 17 (49%) patients were diagnosed with PTLD. Thirteen (76%) had EBV‐positive PTLD with 12/13 (92%) having detectable EBV by PCR. The EBV PCR panel had a high sensitivity (92%), specificity (72%), positive predictive value (PPV) (71%) and negative predictive value (NPV) (93%) for diagnosing EBV‐positive PTLD and followed patients' clinical course well (p < 0.001). Comparing the individual PCR assays, plasma EBNA PCR was superior with high sensitivity (77%), specificity (100%), PPV (100%) and NPV (86%). We conclude that EBV PCR is a useful test for managing PTLD patients. While plasma EBNA PCR is the best single assay for diagnosing and monitoring PTLD, the complete PCR panel is superior for ruling out its presence.
Choice of Varieties by Sri Lanka Rice Farmers: Comparing Alternative Decision Models

Sri Lanka rice farmers are faced with a choice between traditional and high-yielding rice varieties. Three risky-choice models are compared to explain producer behavior. Forty farmers with typically small rice areas were studied. Choice criteria compared were multiple (two)-attribute utility maximization, single (profit)-attribute utility maximization, and expected profit maximization. Expected utility maximization performed better than expected profit maximization: single-attribute utility maximization outperformed the more complex multiattribute utility model. The importance of careful elicitation of subjective probability distributions is emphasized. Rice farmers appear to allocate their land between available technologies in an economically rational way.
Why 'Hold-Ups' Occur: The Self-Enforcing Range of Contractual Relationships

Court enforcement and private enforcement are not alternative contract enforcement mechanisms, but are used jointly by transactors to define the self-enforcing range of a contractual relationship. Within this framework contract terms economize on the limited amounts of private enforcement capital possessed by transactors, either by directly controlling transactor behavior or by shifting private enforcement capital between transactors to coincide with likely future market conditions. Hold-ups occur when market conditions change sufficiently to place the relationship outside the self-enforcing range. This probabilistic view of hold-ups is contrasted with opportunism more generally and with moral hazard behavior.
COMPARATIVE STUDY OF THE IRAN OIL NATIONALIZATION MOVEMENT AND THE NUCLEAR ENERGYWITHIN ROUZCRONCE AND KAPLUN' S THEORY

International system as one unity general which has the independent and distinctive entity from its founding units makes particular- behavioral constraints. The conservative entity of International system makes difficult changing in structure and hierarchy of power. In particular, big powers in the scale of the system which the structure of International system is shaped according to them, in order to maintain of existing conditions and regularity do not allow to emergence of other big powers that will cause to structural changes. Countries which has no ideological unity with International system and also pursue foreign, revolutionary or revisionist and indecent policy will encounter more structural constraints. The nationalization of the oil industry movement and Iran's nuclear energy programmed also pursue a revisionist strategy in a region and world-wide scale which face structural constraints.In this study, we want to answer this question that what strategy has been pursued vis-a-vis the nationalization of the oil industry and the nuclear file of Iran by important and international actors (united state, Russia and England)? We assume that Iran persist a revisionist strategy in own nationalization of the oil industry movement and nuclear energy programmed that face the dis approval westerns and structural constraints. The main- strategy of these three big powers is disapproval with the- nationalization of the oil industry and reaching of Iran to nuclear energy and bigs power severely oppose these two works And the approach of big powers (United Stats , England , and Russia)about the nationalization of oil industry and the process of access to nuclear energy follows a unit pattern ; United States and England are going to questioning and limiting Iran and Russia after getting concession and the provision of own benefits by Iran and at last , the resistance of Iran s society resulted in retreating of big powers in each both subject .
Early exercise boundary and option prices in Levy driven models

Pricing and hedging of European. American, barrier options and interest rate derivatives for wide classes of Levy driven models is consideref in situatins where qualitative and quantitative differences between gaussian and Levy modelling are most prominent, and the dependence on the choice of a family of Levy processes is analysed. Asymptotics of option prices near the barrier and expiry are calculated; for American options, two fast numerical methods are constructed. It is shown that for many classes of Levy processes, the early exercise boundary of the American put is separated from the strike by a non-vanishing margin, and as the riskless rate vanishes, the early exercise boundary tends to 0 uniformly over the interval [0, T). Implications for fitting of parameters are discussed.
Issues in the Hidden Economy-A Survey

This paper discusses a number of questions concerning the so-called hidden economy. What is the hidden economy? How big is it? Is it really growing? Does it matter? What should we do about it? The paper is not an exhaustive survey of the literature on the hidden economy. Its objective is more modest - namely to present an overview of the state of research, identify the major themes and issues and provide a framework for further work.
Twin-wave transmission with enhanced performance

We review recent progresses on the use of phase-conjugated twin waves (PCTWs) to enhance optical transmission performance in both nonlinear and linear regimes, including spectrally-efficient dual-PCTWs, real-valued OFDM signal with Hermitian symmetry, and positive-valued OFDM twins suitable for cost-effective IM/DD.
Kepler sheds new and unprecedented light on the variability of a blue supergiant: Gravity waves in the O9.5Iab star HD 188209⋆

Stellar evolution models are most uncertain for evolved massive stars. Asteroseismology based on high-precision uninterrupted space photometry has become a new way to test the outcome of stellar evolution theory and was recently applied to a multitude of stars, but not yet to massive evolved supergiants.Our aim is to detect, analyse and interpret the photospheric and wind variability of the O9.5 Iab star HD 188209 from Kepler space photometry and long-term high-resolution spectroscopy. We used Kepler scattered-light photometry obtained by the nominal mission during 1460 d to deduce the photometric variability of this O-type supergiant. In addition, we assembled and analysed high-resolution high signal-to-noise spectroscopy taken with four spectrographs during some 1800 d to interpret the temporal spectroscopic variability of the star. The variability of this blue supergiant derived from the scattered-light space photometry is in full in agreement with the one found in the ground-based spectroscopy. We find significant low-frequency variability that is consistently detected in all spectral lines of HD 188209. The photospheric variability propagates into the wind, where it has similar frequencies but slightly higher amplitudes. The morphology of the frequency spectra derived from the long-term photometry and spectroscopy points towards a spectrum of travelling waves with frequency values in the range expected for an evolved O-type star. Convectively-driven internal gravity waves excited in the stellar interior offer the most plausible explanation of the detected variability.
Competing Scenarios for European Fathers: Applying Sen's Capabilities and Agency Framework to Work—Family Balance

European policy and discourse create crosscurrents for fathers: the promotion of work-family balance (WFB) and more involved fathering versus work-focused competitiveness and productivity goals in globalized economies. Using Amartya Sen's capabilities and agency paradigm, the authors provide a theoretical framework for analyzing agency inequalities in WFB: the disjuncture between norms/values and practices and between policies and fathers' capabilities to exercise them. The authors apply the capability framework to comparative European data considering working times and desired working times, flexibility and autonomy in employment, as well as perceptions of economic security and job security. The authors find differences in fathers' capabilities and agency for WFB across countries representing different welfare regime configurations, most strikingly between old and new EU member states. The majority of the European fathers wanted to reduce working hours substantially despite possible reductions in pay, underscoring the value of the capabilities framework for understanding potential freedoms for achieving WFB.
Revision of Failed Unicompartmental Knee Arthroplasty

Little information has been published on the salvage of failed unicompartmental knee arthroplasty. The current authors examined the failure mechanisms, complexity of surgery, and complications in such revisions. Of 39 consecutive unicompartmental knee revisions, two patients died within 2 years of surgery, four had inadequate followup, and one was excluded because of infection before revision. Therefore, 30 patients (32 knees) were followed up a mean 53 months. The patients were a mean age of 59 years at the time of unicompartmental knee arthroplasty and were predominantly male (60%). Revisions were done 9 to 204 months after the unicompartmental knee arthroplasty. The predominant failure mechanism was polyethylene wear; however, nine failed because of loosening. The mean polyethylene thickness of the failed arthroplasties was 7.3 mm. Revision procedures were straightforward. Ten patients required local autograft but no allografts were used. Primary femoral components were used in all patients; 25 were cruciate-retaining. Fourteen patients had stemmed tibial components; eight had wedge augments. The mean range of motion after revision was 111°. Six patients had complications not requiring intervention. Three patients had rerevision surgery for polyethylene wear at 76, 77, and 102 months, respectively, two of whom required polyethylene insert and patellar component revision. The third patient also required tibial component revision for osteolysis. Although this is a small series, the simplicity of the procedure and the complications encountered compare favorably with those of total knee revision.
Occurrence of Escherichia coli and Enterococci in Cladophora (Chlorophyta) in Nearshore Water and Beach Sand of Lake Michigan

ABSTRACT Each summer, the nuisance green alga Cladophora (mostly Cladophora glomerata) amasses along Lake Michigan beaches, creating nearshore anoxia and unsightly, malodorous mats that can attract problem animals and detract from visitor enjoyment. Traditionally, elevated counts of Escherichia coli are presumed to indicate the presence of sewage, mostly derived from nearby point sources. The relationship between fecal indicator bacteria and Cladophora remains essentially unstudied. This investigation describes the local and regional density of Escherichia coli and enterococci in Cladophora mats along beaches in the four states (Wisconsin, Illinois, Indiana, and Michigan) bordering Lake Michigan. Samples of Cladophora strands collected from 10 beaches (n = 41) were assayed for concentrations of E. coli and enterococci during the summer of 2002. Both E. coli and enterococci were ubiquitous (up to 97% occurrence), with overall log mean densities (± standard errors) of 5.3 (± 4.8) and 4.8 (± 4.5) per g (dry weight). E. coli and enterococci were strongly correlated in southern Lake Michigan beaches (P < 0.001, R2 = 0.73, n = 17) but not in northern beaches (P = 0.892, n = 16). Both E. coli and enterococci survived for over 6 months in sun-dried Cladophora mats stored at 4°C; the residual bacteria in the dried alga readily grew upon rehydration. These findings suggest that Cladophora amassing along the beaches of Lake Michigan may be an important environmental source of indicator bacteria and call into question the reliability of E. coli and enterococci as indicators of water quality for freshwater recreational beaches.
Bayesian strategies for dynamic pricing in e‐commerce

E‐commerce platforms afford retailers unprecedented visibility into customer purchase behavior and provide an environment in which prices can be updated quickly and cheaply in response to changing market conditions. This study investigates dynamic pricing strategies for maximizing revenue in an Internet retail channel by actively learning customers' demand response to price. A general methodology is proposed for dynamically pricing information goods, as well as other nonperishable products for which inventory levels are not an essential consideration in pricing. A Bayesian model of demand uncertainty involving the Dirichlet distribution or a mixture of such distributions as a prior captures a wide range of beliefs about customer demand. We provide both analytic formulas and efficient approximation methods for updating these prior distributions after sales data have been observed. We then investigate several strategies for sequential pricing based on index functions that consider both the potential revenue and the information value of selecting prices. These strategies require a manageable amount of computation, are robust to many types of prior misspecification, and yield high revenues compared to static pricing and passive learning approaches. © 2006 Wiley Periodicals, Inc. Naval Research Logistics, 2007