Miracle-dz/UniFAR-FTUs huggingface dataset:
The homeotic gene long sterile lemma (G1) specifies sterile lemma identity in the rice spikelet

The mechanism of floral organ specification is principally conserved in angiosperms, as demonstrated by the ABC model. By contrast, mechanisms that regulate the development of organs or structures specific to a group of species remain unclear. Grasses have unique inflorescence units, comprising spikelets and florets. In the genus Oryza (rice), the single spikelet consists of a fertile floret subtended by a lemma and a palea, two sterile lemmas, and rudimentary glumes. Each sterile lemma is a tiny glume-like organ with a smooth surface. Here, we have examined a long sterile lemma1 (g1) mutant, in which the sterile lemma is enlarged like the lemma. Detailed phenotypic analysis reveals that the large sterile lemma in the g1 mutant appears to be caused by homeotic transformation of the sterile lemma into a lemma, suggesting that G1 is involved in the repression of lemma identity to specify the sterile lemma. Gene isolation reveals that G1 is a member of a plant-specific gene family that encodes proteins with a previously uncharacterized domain, named here ALOG (Arabidopsis LSH1 and Oryza G1). G1 mRNA is expressed in sterile lemma primordia throughout their development, and G1 protein is localized in the nucleus. A trans-activation assay using the yeast GAL4 system suggests that G1 is involved in transcriptional regulation. Repression of lemma identity by G1 is consistent with a hypothesis proposed to explain the morphological evolution of rice spikelets. We also show that a wild rice species, Oryza grandiglumis, that forms large sterile lemmas has serious mutations in the G1 gene.
Prolonged morphine treatment targets delta opioid receptors to neuronal plasma membranes and enhances delta-mediated antinociception.

Opioid receptors are known to undergo complex regulatory changes in response to ligand exposure. In the present study, we examined the effect of morphine on the in vitro and in vivo density and trafficking of delta opioid receptors (deltaORs). Prolonged exposure (48 hr) of cortical neurons in culture to morphine (10 microm) resulted in a robust increase in the internalization of Fluo-deltorphin, a highly selective fluorescent deltaOR agonist. This effect was mu-mediated because it was entirely blocked by the selective mu opioid receptor antagonist d-Phe-Cys-Tyr-d-Trp-Orn-Thr-Pen-Thr-NH(2) and was reproduced using the selective mu agonist fentanyl citrate. Immunogold electron microscopy revealed a marked increase in the cell surface density of deltaORs in neurons exposed to morphine, indicating that the increase in Fluo-deltorphin internalization was caused by increased receptor availability. Prolonged morphine exposure had no effect on deltaOR protein levels, as assessed by immunocytochemistry and Western blotting, suggesting that the increase in bioavailable deltaORs was caused by recruitment of reserve receptors from intracellular stores and not from receptor neosynthesis. Complementary in vivo studies demonstrated that chronic treatment of adult rats with morphine (5-15 mg/kg, s.c., every 12 hr) similarly augmented targeting of deltaORs to neuronal plasma membranes in the dorsal horn of the spinal cord. Furthermore, this treatment markedly potentiated intrathecal d-[Ala(2)]deltorphin II-induced antinociception. Taken together, these results demonstrate that prolonged stimulation of neurons with morphine markedly increases recruitment of intracellular deltaORs to the cell surface, both in vitro and in vivo. We propose that this type of receptor subtype cross-mobilization may widen the transduction repertoire of G-protein-coupled receptors and offer new therapeutic strategies.
Dosing Adjustments in Postpartum Patients Maintained on Buprenorphine or Methadone

Scant scientific attention has been given to examining the need for agonist medication dose changes in the postpartum period. Study objectives were: 1) to determine the need for medication dose adjustments in participants stabilized on buprenorphine or methadone 3 weeks before and 4 weeks after delivery, and 2) to evaluate the need for methadone dose adjustments during the first 7 days in participants transferred from buprenorphine to methadone at 5 weeks postpartum. Participants were opioid-dependent pregnant women who had completed a randomized, double-blind, double-dummy, flexible dosing comparison of buprenorphine to methadone. Participants received a stable dose of methadone (N = 10) or buprenorphine (N = 8) before and 4 weeks after delivery. Buprenorphine-maintained participants were transferred to methadone at 5 weeks postpartum. There were no significant differences predelivery and/or postdelivery between the buprenorphine and methadone conditions in the mean ratings of dose adequacy, “liking,” “hooked,” and “craving” of heroin or cocaine. Patient response to the conversion from buprenorphine to methadone seems variable. Buprenorphine-maintained participants required dose changes postpartum only after they transferred to methadone. Regardless of type of medication, postpartum patients should be monitored for signs of overmedication.
Null Models For Cultural And Social Evolution

Analogies between biological and cultural evolution date back to Darwin, yet the analogies have remained loose. Neutral evolution, known to be important in biology, has been proposed as a null model for cultural change, but has not developed into tests for selection on cultural features. Using inference in timeseries of alternative word forms and grammatical constructions, I demonstrate a cultural analog of natural selection on a background of netural evolution. Social evolution, on the other hand, implies selection in a social environment and therefore cannot be described with a neutral model. I propose a model of pure frequency-dependent selection as a generic null model for social evolution, and use the model to illustrate diverse effects of social selection. I derive a non-linear form of frequency-dependent selection from a mechanistic model of mate choice and show unintuitive consequences for evolutionary dynamics. I infer complex forms of frequency dependent selection—including positive and negative frequency-dependent selection at different frequencies—from data regarding the copying of baby names, the fashions of dog breeds, and the use of rare languages, and discuss the implications for cultural diversity. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Biology First Advisor Joshua B. Plotkin Second Advisor Paul D. Sniegowski
ORF57 Overcomes the Detrimental Sequence Bias of Kaposi's Sarcoma-Associated Herpesvirus Lytic Genes

ABSTRACT Kaposi's sarcoma-associated herpesvirus (KSHV) encodes ORF57, which enhances the expression of intronless KSHV genes on multiple posttranscriptional levels. However, it remains elusive how ORF57 recognizes viral RNAs. Here, we demonstrate that ORF57 also increases the expression of the multiple intron-containing K15 gene. The nucleotide bias of the K15 cDNA revealed an unusual high AT content. Thus, we optimized the K15 cDNA by raising the frequency of GC nucleotides, yielding an ORF57-independent version. To further prove the importance of the sequence bias of ORF57-dependent RNAs, we grouped KSHV mRNAs according to their AT content and found a correlation between AT-richness and ORF57 dependency. More importantly, latent genes, which have to be expressed in the absence of ORF57, have a low AT content and are indeed ORF57 independent. The nucleotide composition of K15 resembles that of HIV gag, which cannot be expressed unless RNA export is facilitated by the HIV Rev protein. Interestingly, ORF57 can partially rescue HIV Gag expression. Thus, the KSHV target RNAs of ORF57 and HIV gag RNA may share certain motifs based on the nucleotide bias. A bioinformatic comparison between wild-type and sequence-optimized K15 revealed a higher density for hnRNP-binding motifs in the former. We speculate that binding of particular hnRNPs to KSHV lytic transcripts is the prerequisite for ORF57 to enhance their expression. IMPORTANCE The mostly intronless genes of KSHV are only expressed in the presence of the viral regulator protein ORF57, but how ORF57 recognizes viral RNAs remains elusive. We focused on the multiple intron-containing KSHV gene K15 and revealed that its expression is also increased by ORF57. Moreover, sequences in the K15 cDNA mediate this enhancement. The quest for a target sequence or a response element for ORF57 in the lytic genes was not successful. Instead, we found the nucleotide bias to be the critical determinant of ORF57 dependency. Based on the fact that ORF57 has only a weak affinity for nucleic acids, we speculate that a cellular RNA-binding protein provides the sequence preference for ORF57. This study provides evidence that herpesviral RNA regulator proteins use the sequence bias of lytic genes and the resulting composition of the viral mRNP to distinguish between viral and cellular mRNAs.
Strong Effects of Temperature on the Early Life Stages of a Cold Stenothermal Fish Species, Brown Trout (Salmo trutta L.)

Temperature is the main abiotic factor that influences the life cycle of poikilotherms. The present study investigated the thermal tolerance and phenotypic plasticity of several parameters (development time, morphometric measures, bioenergetics) for both embryos and fry of a cold stenothermal fish species, brown trout (Salmo trutta L.) in order to allow for a holistic evaluation of the potential effects of temperature. Five temperatures (4°C, 6°C, 8°C, 10°C, and 12°C) were tested, and the effects of temperature were analyzed at three stages: hatching, emergence, and first food intake. A mean of 5,440 (S.E. ± 573) eggs, coming from seven females and seven males (seven families) captured close to Linkebeek (Belgium), were used for each temperature. Maximum survival of well-formed fry at first food intake and better use of energy budget were found at 6°C and 8°C, temperatures at which the possible contribution to the next generation should therefore be greatest. At 12°C, the experimental population fell dramatically (0.9% survival rate for well-formed fry at first food intake), and fry had almost no yolk sac at first food intake. The present results on survival at 12°C are in accordance with predictions of a sharp decrease in brown trout numbers in France over the coming decades according to climate change projections (1°C to 5°C temperature rise by 2100 for France). At 10°C, there was also a lower survival rate (55.4% at first food intake). At 4°C, the survival rate was high (76.4% at first food intake), but the deformity rate was much higher (22% at first food intake) than at 6°C, 8°C, and 10°C. The energetic budget showed that at the two extreme temperatures (4°C and 12°C) there was less energy left in the yolk sac at first food intake, suggesting a limited ability to survive starvation.
Comparative analysis among DSP and FPGA-based control capabilities in PWM power converters

PWM power converters are close to be mature for standard diffusion. New FPGA technologies could now realise at best the digital control key-points: flexible performance and time to market. The paper deals with the new digital control properties of FPGA-based techniques. On the basis of reference structures, a comparative analysis is carried-out trading-off dynamic performances and immunity to PWM environment. All possible sampled control or DSP techniques are firstly analysed and compared to each other. A breakthrough concept for FPGAs is defined, definitely solving for PWM feedback immunity by practical over-sampling and parallel processing while improving dynamic performances. Simulation tests and the application of dead-beat control clearly point-out the respective dynamic properties.
Anti-hyperglycemic Effects of Saffron and its Active Constituents, Crocin and Safranal, in Alloxan-Induced Diabetic Rats

Background: Saffron is the dried stigmata of the flowers of saffron (Crocus sativus L., Iridaceae). Saffron and its major active constituents, crocin (crocetin glycoside), crocetin and safranal, have a variety of pharmacological effects including high antioxidant properties and crocetin has insulin sensitizing effect possibly due to its antioxidant activity. Oral crocin is not absorbed and is hydrolyzed and absorbed as the active metabolite crocetin in the rat intestines. Objective: Study of the saffron, crocin and safranal effects on the blood levels of fasting glucose, HbA1c (glycosylated hemoglobin) and liver/kidney function tests in alloxan-diabetic rats. Methods: The effects of 6 weeks' daily oral administration of saffron methanolic extract, crocin and safranal on the fasting blood glucose, HbA1c, insulin, creatinine and SGOT and SGPT levels after single alloxan intraperitoneal injection at a dose of 125 mg/kg in rats were evaluated. Results: Alloxan injection resulted in significant increase of fasting blood glucose and HbA1c levels but decreased blood insulin levels significantly. Saffron methanolic extract (80 and 240 mg/kg), crocin (50 and 150 mg/kg) and safranal (0.25 and 0.5 ml/kg) significantly reduced the fasting blood glucose and HbA1c levels but significantly increased the blood insulin levels without any significant effects on the blood SGOT, SGPT and creatinine levels in the diabetic rats compared with the control diabetic rats. Conclusion: The results suggest that saffron may have anti-hyperglycemic and blood insulin level elevating effects without hepatic and renal toxicities in the alloxan diabetic rats. Further, crocin, crocetin and safranal may be involved in these effects of saffron.
Digital Avulsion With Compromised Vascularization: Study of 23 Cases in Children

Background Avulsion of a digit has not always been an indication for replantation because of extensive injuries. The advent of microsurgery changed this, permitting avulsed digit replantations with varying rates of success. The aim of this study was to analyze surgical management of finger avulsion injuries of an exclusively pediatric series. Methods A retrospective study of children with finger avulsion injuries and compromised arterial circulation degloving or amputation, treated primarily in our institution between 1997 and 2007. Factors that could affect the outcome included demographic and clinical data, description of the lesion using Urbaniak's and Tamai's classification, technical data related to surgery, and results of revascularization were collected. Results Twenty-three children with 23 digital injuries were identified as digital avulsions with compromised vascularization. The mean age was 11 years and 8 months (range, 2 to 15 y). Four cases involved devascularization classified as Urbaniak 2 and the other 19 cases involved amputation or complete degloving, classified as Urbaniak 3. In 7 cases, replantation was not performed because of the extent of the lesions (all were classified as Urbaniak 3). The complete survival rate when revascularization or replantation was attempted was 25%. One case required a new procedure 6 days after the first surgery with a trans-P2 amputation. Injuries classified as Urbaniak 2 had an overall survival rate of 75% and injuries classified Urbaniak 3 had an overall survival rate of 5.3%. Conclusions The global rate of survival after revascularization or replantation of avulsed fingers in children seemed to be poor. Urbaniak classification is an important prognostic factor with a good prognosis for lesions classified as Urbaniak 2 and a very poor prognosis for lesions classified as Urbaniak 3.
Ethnic differences in the distribution of CYP3A5 gene polymorphisms

The genetic polymorphism affecting the CYP3A5 enzyme is responsible for interindividual and interethnic variability in the metabolism of CYP3A5 substrates. The full extent of the CYP3A5 genetic polymorphism was analysed in French Caucasian, Gabonese and Tunisian populations using a polymerase chain reaction-single strand conformational polymorphism (PCR-SSCP) strategy. In the three populations, eight, 17 and ten single nucleotide polymorphisms (SNPs), respectively, were identified, among which nine correspond to rare new mutations. Also identified were 16 alleles including eight new allelic variants. Significant differences were observed in the distribution of these alleles. Particularly, the frequency of the CYP3A5*3C null allele in French Caucasians (81.3%) and in Tunisians (80.0%) is higher than in the Gabonese population (12.5%) (p < 0.001). Considering the CYP3A5 genotypes of the tested individuals, only 10.4% of French Caucasians and 30.0% of Tunisians were identified as CYP3A5 expressors. In contrast, 90.0% of Gabonese subjects appear to express the CYP3A5 protein.
Gender differences in HIV-related stigma in Kenya

Stigma associated with HIV/AIDS directly and indirectly drives HIV transmission. We examined how factors associated with HIV-related stigma differed by gender, using data from the 2008–2009 Kenya Demographic and Health Survey (KDHS). Descriptive, bivariate and multinomial logistic regression analyses were conducted on selected HIV-related stigma indicators for men and women. Bivariate analyses showed significant gender differences in the overall HIV Stigma index with a higher proportion of women than men presented at the highest stigma level (4.9% vs 2.7%, p < 0.01). Women were more likely to express higher stigmatic attitudes for all components of stigma measured than men. Multivariate analyses showed that HIV-related knowledge had significant inverse dose-response for both men and women. For instance, compared to women in the first HIV-related knowledge quartile, a 1 unit increase in HIV-related knowledge among women at the third HIV-related knowledge quartile was expected to lead to a 63.8% decrease in HIV-related stigma (95% CI [0.21, 0.63]) for women with high stigma, 57.8% decrease for similar women with medium stigma (95% CI [0.33, 0.55]) and 28.4% decrease for those with low stigma (95% CI [0.57, 0.90]). Acceptance with the statement “a husband is justified to hit or beat his wife if she refuses to have sex with him” was a significant risk factor for expression of stigmatising attitudes at all levels for women (High: OR = 1.49, 95% CI [1.02, 2.17]), Medium: OR = 1.47, 95% CI [1.18, 1.82], Low: OR = 1.38, 95% CI [1.10, 1.73]) and men at medium stigma (OR = 2.02, 95% CI [1.38, 2.95]). Other notable gender differences were found in employment, marital status, ethnicity, region of residence, wealth and media exposure. Our results showed that women in the general Kenyan population had higher stigmatic attitudes than men. This was associated with differences in risk factor profile and confirmed previous literature on complexity of social-cultural factors associated with HIV-related stigma.
Care of post-traumatic spinal cord injury patients in India: An analysis

Background: The spinal cord injured patients if congregated early in spinal units where better facilities and dedicated expert care exist the outcome of treatment and rehabilitation, can be improved. The objective of this study is to find out the various factors responsible for a delay in the presentation of spinal injury patients to the specialized spinal trauma units and to suggest steps to improve the quality of care of the spinal trauma patients in the Indian setup. Materials and Methods: Sixty patients of traumatic spinal cord injury admitted for rehabilitation between August 2005 and May 2006 were enrolled into the study and their data was analyzed. Results: Eighty-five per cent of the spinal cord injured patients were males and the mean age was 34 years (range 13-56 years). Twenty-nine (48.33%) of the spinal injuries occurred due to fall from height. There was an average of 45 days (range 0-188 days) of delay in presentation to a specialized spinal unit and most of the time the cause for the delay was unawareness on the part of patients and/or doctors regarding specialized spinal units. In 38 (62.5%) cases the mode of transportation of the spinal cord injured patient to the first visited hospital was by their own conveyance and the attendants of the patients did not have any idea about precautions essential to prevent neurological deterioration. Seventeen (28.33%) patients were given injection solumedrol with conservative treatment, 35 (60%) patients were given only conservative treatment and seven patients were operated (11.66%) upon at initially visited hospital. Of the seven patients operated five were fixed with posterior Harrington instrumentation (71.42%) and two (28.57%) were operated by short segment posterior pedicle screw fixation. None of the patients were subjected to physiotherapy-assisted transfers or wheel chair skills or even basic postural training, proper bladder/ bowel training program and sitting balance. Conclusion: Awareness on the part of the general population, attendants of the patients, clinical and paraclinical team regarding spinal cord injury needs to be addressed. Safe mode of transportation of spinal cord injured patient and early presentation at tertiary spinal care center with comprehensive spinal trauma care team should be stressed upon.
General Equilibrium Under Convex Portfolio Constraints and Heterogeneous Risk Preferences

This paper characterizes the equilibrium in a continuous time financial market populated by heterogeneous agents who differ in their rate of relative risk aversion and face convex portfolio constraints. The model is studied in an application to margin constraints and found to match real world observations about financial variables and leverage cycles. It is shown how margin constraints increase the market price of risk and decrease the interest rate by forcing more risk averse agents to hold more risky assets, producing a higher equity risk premium. In addition, heterogeneity and margin constraints are shown to produce both pro- and counter-cyclical leverage cycles. Beyond two types, it is shown how constraints can cascade and how leverage can exhibit highly non-linear dynamics. Finally, empirical results are given, documenting a novel stylized fact which is predicted by the model, namely that the leverage cycle is both pro- and counter-cyclical.
Inequality Implications of EMU Membership: A Reassessment

A growing number of studies have concluded that the European Economic and Monetary Union (EMU) has exacerbated inequalities in income, wealth and society. Furthermore, the endogeneity of income inequality is now becoming recognised as an important part of the cost-benefit analysis of euro currency adoption. Yet the nature, significance and scale of different monetary (and market) integration channels in operation in EMU remain uncertain. In this contribution we employ static and dynamic panel data methodologies to investigate the intra-national household inequality implications, both realised and expected over coming years. Our analysis reveals that the within-country inequality outcomes differ significantly for core and non-core country-groups in EMU, which have so far realised very different distributional costs and benefits from the integration process. These are crucial issues for policy-makers, not just for EMU member states, but for other countries as well, especially the European Union (EU) countries that are expected to adopt the euro currency in the future. This is so in terms of their attempts to look for, design and implement policies, which alleviate within-country inequality.