Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of Reference Genes for Quantitative Real-Time PCR in Oil Palm Elite Planting Materials Propagated by Tissue Culture

Background The somatic embryogenesis tissue culture process has been utilized to propagate high yielding oil palm. Due to the low callogenesis and embryogenesis rates, molecular studies were initiated to identify genes regulating the process, and their expression levels are usually quantified using reverse transcription quantitative real-time PCR (RT-qPCR). With the recent release of oil palm genome sequences, it is crucial to establish a proper strategy for gene analysis using RT-qPCR. Selection of the most suitable reference genes should be performed for accurate quantification of gene expression levels. Results In this study, eight candidate reference genes selected from cDNA microarray study and literature review were evaluated comprehensively across 26 tissue culture samples using RT-qPCR. These samples were collected from two tissue culture lines and media treatments, which consisted of leaf explants cultures, callus and embryoids from consecutive developmental stages. Three statistical algorithms (geNorm, NormFinder and BestKeeper) confirmed that the expression stability of novel reference genes (pOP-EA01332, PD00380 and PD00569) outperformed classical housekeeping genes (GAPDH, NAD5, TUBULIN, UBIQUITIN and ACTIN). PD00380 and PD00569 were identified as the most stably expressed genes in total samples, MA2 and MA8 tissue culture lines. Their applicability to validate the expression profiles of a putative ethylene-responsive transcription factor 3-like gene demonstrated the importance of using the geometric mean of two genes for normalization. Conclusions Systematic selection of the most stably expressed reference genes for RT-qPCR was established in oil palm tissue culture samples. PD00380 and PD00569 were selected for accurate and reliable normalization of gene expression data from RT-qPCR. These data will be valuable to the research associated with the tissue culture process. Also, the method described here will facilitate the selection of appropriate reference genes in other oil palm tissues and in the expression profiling of genes relating to yield, biotic and abiotic stresses.
Permanent Neonatal DM in Monozygotic Twins with p.C109Y Mutation in INS Gene: First Report from Saudi Arabia

Insulin gene mutation (INS) is the second most common cause of permanent neonatal diabetes (PNDM). We present the 1st cases of Saudi monozygotic twins with permanent neonatal diabetes mellitus who had simultaneous onset of disease due to p.C109Y (p.Cys109Tyr, c.326G>A) heterozygous missense mutation in exon 3 of the insulin (INS) gene. The twin patients had the same mutation while their parents are unaffected with normal genetic testing suggesting that this mutation had raised de novo. This p.C109Y mutation affects a highly conserved cysteine residue which is crucial for protein folding. Subjects with this form of diabetes will need lifelong insulin therapy.
Register and thread structure optimization for GPUs

GPUs are an increasingly popular implementation platform for a variety of general purpose applications from mobile and embedded devices to high performance computing. The CUDA and OpenCL parallel programming models enable easy utilization of the GPU's resources. However, tuning GPU applications' performance is a complex and labor intensive task. Software programmers employ a variety of optimization techniques to explore tradeoffs between the thread parallelism and performance of a single thread. However, prior techniques ignore register allocation, a significant factor in single thread performance and, indirectly affects the number of simultaneously active threads. In this paper, we show that joint optimization of register allocation and thread structure has great potential to significantly improve performance. However, the design space for this joint optimization can be large; therefore, we develop performance metrics appropriate for evaluation within a compiler's inner loop and efficient design space exploration techniques that use the metrics to narrow the search space. Across a range of GPU applications, we achieve average performance speedup of 1.33X (up to 1.73X) with design space exploration 355X faster than the exhaustive search.
Estimating long‐term treatment effects in observational data: A comparison of the performance of different methods under real‐world uncertainty

In the presence of time‐dependent confounding, there are several methods available to estimate treatment effects. With correctly specified models and appropriate structural assumptions, any of these methods could provide consistent effect estimates, but with real‐world data, all models will be misspecified and it is difficult to know if assumptions are violated.
Response by Banerjee et al to Letter Regarding Article, "Cognitive Impairment Before Intracerebral Hemorrhage Is Associated With Cerebral Amyloid Angiopathy".

We thank Cao et al for their interest in our work on the associations of preexisting cognitive impairment in patients with intracerebral hemorrhage.1 We agree that the association between preexisting cognitive impairment and cortical superficial siderosis (cSS) suggests that cSS might directly cause cortical injury or dysfunction through specific toxic effects of iron species or hemosiderin deposition. However, we think that the magnitude and direction of the associations between strictly lobar microbleeds (odds ratio, 2.47; 95% confidence interval, 0.95–6.37) and lobar intracerebral hemorrhage (odds ratio, 2.29; 95% confidence interval, 0.99–5.31) are also likely to be important for cognitive function although they did not reach statistical significance because of our relatively small sample …
Microstructure-induced giant elastic nonlinearity of threshold origin: Mechanism and experimental demonstration

There are known numerous examples of strong physical nonlinearity of elastic microinhomogeneous materials caused by the presence of a small amount of a “soft” component (cracks, intergrain contacts, bubbles, etc.). The dimensionless parameter B/A of quadratic nonlinearity for such materials can be on the order of 102–103 in contrast to values on the order of unity typical of ideal crystals, homogeneous amorphous solids or liquids. The sign of this nonlinearity is such that all those materials become stiffer as pressure increases. We consider an extension of this “soft-rigid paradigm” of the nonlinearity increase by accounting for threshold-type properties intrinsic to some inclusions. We show that the nonlinearity in this case can additionally be orders of magnitude higher. We present an example of such a material which unlike “normal” media becomes softer with increasing pressure. Its quasistatic negative parameter B/A reaches ∼(0.5–1)·105, which to our knowledge is a record value.
Of Meat and Men: Sex Differences in Implicit and Explicit Attitudes Toward Meat

Modern attitudes to meat in both men and women reflect a strong meat-masculinity association. Sex differences in the relationship between meat and masculinity have not been previously explored. In the current study we used two IATs (implicit association tasks), a visual search task, and a questionnaire to measure implicit and explicit attitudes toward meat in men and women. Men exhibited stronger implicit associations between meat and healthiness than did women, but both sexes associated meat more strongly with ‘healthy’ than ‘unhealthy’ concepts. As ‘healthy’ was operationalized in the current study using terms such as “virile” and “powerful,” this suggests that a meat-strength/power association may mediate the meat-masculinity link readily observed across western cultures. The sex difference was not related to explicit attitudes to meat, nor was it attributable to a variety of other factors, such as a generally more positive disposition toward meat in men than women. Men also exhibited an attention bias toward meats, compared to non-meat foods, while females exhibited more caution when searching for non-meat foods, compared to meat. These biases were not related to implicit attitudes, but did tend to increase with increasing hunger levels. Potential ultimate explanations for these differences, including sex differences in bio-physiological needs and receptivity to social signals are discussed.
Effects of chemical pretreatment on aerobic digestion and fertilizer value

In order to meet the stringent requirement of sludge disposal and to increase sludge digestibility, the pretreatment technologies were studied, including alkaline hydrolysis, ultrasonic treatment and the different combinations of these two methods. Based on COD solubilization, the combination pretreatment was more effective than a single treatment, especially the combination of simultaneous alkaline and ultrasonic treatment, in which SCOD concentration and COD solubilization got to 6700mg/l and 40%, respectively. In the subsequent aerobic digestion, it was obvious that the performance of digester B (fed with the sludge pretreated by NaOH) was better than that of digester A (fed with raw sludge) in terms of COD and SS removal. At 5 days, TSS removal rate reached 47% in the digester B, which was 71% of final TSS removal rate. It revealed that the pretreatment process can shorten the retention time of aerobic digestion. And after aerobic digestion, the contents of some heavy metals (Mo, As, Cr, Pb, Ti and Hg) were not detected in the sludge, which suggested that it was feasible to apply the stabilized sludge to agriculture. Biological assays reported that the pretreated sludge followed by aerobic digestion could promote the growth of seedling stem remarkably compared to the aerobically digested sludge without pretreatment.
Goal-directed Hemostatic Resuscitation of Trauma-induced Coagulopathy: A Pragmatic Randomized Clinical Trial Comparing a Viscoelastic Assay to Conventional Coagulation Assays

Background:Massive transfusion protocols (MTPs) have become standard of care in the management of bleeding injured patients, yet strategies to guide them vary widely. We conducted a pragmatic, randomized clinical trial (RCT) to test the hypothesis that an MTP goal directed by the viscoelastic assay thrombelastography (TEG) improves survival compared with an MTP guided by conventional coagulation assays (CCA). Methods:This RCT enrolled injured patients from an academic level-1 trauma center meeting criteria for MTP activation. Upon MTP activation, patients were randomized to be managed either by an MTP goal directed by TEG or by CCA (ie, international normalized ratio, fibrinogen, platelet count). Primary outcome was 28-day survival. Results:One hundred eleven patients were included in an intent-to-treat analysis (TEG = 56, CCA = 55). Survival in the TEG group was significantly higher than the CCA group (log-rank P = 0.032, Wilcoxon P = 0.027); 20 deaths in the CCA group (36.4%) compared with 11 in the TEG group (19.6%) (P = 0.049). Most deaths occurred within the first 6 hours from arrival (21.8% CCA group vs 7.1% TEG group) (P = 0.032). CCA patients required similar number of red blood cell units as the TEG patients [CCA: 5.0 (2–11), TEG: 4.5 (2–8)] (P = 0.317), but more plasma units [CCA: 2.0 (0–4), TEG: 0.0 (0–3)] (P = 0.022), and more platelets units [CCA: 0.0 (0–1), TEG: 0.0 (0–0)] (P = 0.041) in the first 2 hours of resuscitation. Conclusions:Utilization of a goal-directed, TEG-guided MTP to resuscitate severely injured patients improves survival compared with an MTP guided by CCA and utilizes less plasma and platelet transfusions during the early phase of resuscitation.
DETERMINATION OF STRUCTURAL AND PHOTOELECTRIC CHARACTERISTICS OF ZnO POLYCRYSTALLINЕ THIN FILMS AND ZnO NANOROD ARRAYS OBTAINED BY SPRAY PYROLYSIS

ZnO polycrystalline thin films and ZnO nanorod arrays were obtained by the spray pyrolysis method at a substrate temperature of 450 °C. By analyzing the XRD diffractograms, the hexagonal crystal structure of the ZnO films and ZnO nanorods was determined. On the other hand, the grain size of the films and nanorods was determined using the Debye-Scherrer equation. The optical properties of the films and nanorods were determined by measuring the dependence of the transmission on the wavelength of the light. Also, the optical band gap of 3.28 eV for the ZnO films and 3.21 eV for the ZnO nanorods was estimated. The photoconductivity spectrum of thin films and nanorods was recorded in the visible light range and their photoconductivity was studied when they were illuminated by X-rays, where the incident X-rays increase the conductivity of thin films of nanorods. The surface morphologies of the ZnO films and the ZnO nanorods, as well as the grain size of the film and the dimensions of the nanorods, were studied by a scanning electron microscope.
Interactive comment on “ Estimation of fossil-fuel CO 2 emissions using satellite measurements of “ proxy ” species ” by Igor B . Konovalov et al

Referee’s comment: One major issue seems to be the (lack of) distinction between NOx emissions and NO2 observations. It seems that the authors use NOx emission data (reported "as NOx", "as N", "as NO2"? ) in conjunction with NO2 measurements. They should explain how the uncertainty in the NO/NO2 partitioning (which can change with season and local time) influences their results, and it should be made clear to the reader that the difference between NOx emissions and NO2 observations is not problematic in this context (if this is actually the case). This is important, e.g., in the
Journal of Rheumatic Diseases and Treatment Case Report : Open Access

C l i n M e d International Library Citation: Cavoli GL, Bono L, Tortorici C, Giammarresi C, Cavoli TVL, et al. (2017) Scleroderma Renal Crisis. J Rheum Dis Treat 3:046. doi.org/10.23937/2469-5726/1510046 Received: November 22, 2016: Accepted: February 11, 2017: Published: February 14, 2017 Copyright: © 2017 Cavoli GL, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. DOI: 10.23937/2469-5726/1510046
Some Life-History Traits of the Adriatic Brown Trout, Salmo farioides Karaman, 1938 (Salmonidae) from the Morača River (Montenegro)

The length–weight relationship, condition factor, sex ratio and fecundity of the Adriatic brown trout, Salmo farioides, were studied in specimens from the upper part of the Morača River during the pre-spawning period. A total of 253 fish were examined; the ratio of matured males to females was estimated as 1:0.5. The length–weight relationship showed a positive allometric growth only in juveniles (age 0+) and isometric growth pattern in the other groups. The absolute fecundity ranged from 137 to 1455 eggs, while the relative fecundity from 210 to 596 (mean 310.89) eggs per 100 grams of body weight. The minimum size at first sexual maturity was 13.7 cm total length in females, and 11.4 cm total length in males. Estimates of the average K ranged from 1.03 in juveniles 0+, to 1.10 in mature males.
International Immunonutrition Workshop Session 5 : Early programming of the immune system and the role of nutrition Allergic disease : understanding how in utero events set the scene

Events and exposures in pregnancy can have critical effects on fetal development with lasting implications for subsequent health and disease susceptibility. There is growing interest in how modern environmental changes influence fetal immune development and contribute to the recent epidemic of allergy and other immune disorders. Rising rates of allergic disease in early infancy, together with pre-symptomatic differences in immune function at birth, suggest that antenatal events play a predisposing role in the development of disease. A number of environmental exposures in pregnancy can modify neonatal immune function including diet, microbial exposure and maternal smoking, and there is emerging evidence from animal models that these factors may have epigenetic effects on immune gene expression and disease susceptibility. Furthermore, functional genetic polymorphisms also alter individual vulnerability to the effects of these environmental exposures, highlighting the complexity of gene–environmental interactions in this period. All these observations underscore the need for ongoing research to understand the pathogenesis and rising incidence of disease in the hope of better strategies to reverse this.
Physical-Chemical Properties of Molybdenum Films Prepared with Magnetron Sputtering

The methods for evaluating the quality of the protective coating to the size etching of quartz glass with hydrofluoric acid were proposed. Molybdenum coating is generated with the installation NIKA 2012 TN by magnetron sputtering. Quartz glass with a roughness of Ra less than 1 nm was used. Discontinuity of coating was determined by the method of electron microscopy and energy dispersive analysis. Mathematical modeling of the hydrofluoric acid diffusion process performend via the molybdenum film was implemented. X-ray analysis of the coating was carried out to determine the residual internal stresses. We concluded that the studied phenomena affect the quality of the glass surface after etching.
Multiple organ dysfunction during resuscitation is not postinjury multiple organ failure.

HYPOTHESIS Multiple organ dysfunction (MOD) within 48 hours of injury is a reversible physiologic response to tissue injury and resuscitation. DESIGN A prospective 10-year inception cohort study ending September 2003. SETTING Regional academic level I trauma center. PATIENTS One thousand two hundred seventy-seven consecutive trauma patients at risk for postinjury multiple organ failure (MOF). Inclusion criteria were being 16 years and older, being admitted to the trauma intensive care unit, having an Injury Severity Score higher than 15, and surviving more than 48 hours after injury. Isolated head injuries were excluded. INTERVENTIONS None. MAIN OUTCOME MEASURES Development of postinjury MOD as defined by a Denver MOF score of 4 or higher within 48 hours of injury and MOF as defined by a Denver MOF score of 4 or higher more than 48 hours after injury. RESULTS Postinjury MOD and MOF were diagnosed in 209 (16%) and 300 (23%) patients, respectively. Age, Injury Severity Score, and 12-hour blood transfusion requirements were significantly higher among patients who developed MOD and MOF. Of the 209 patients who developed MOD, 134 (64%) progressively developed MOF while 75 (36%) had MOD resolve within 48 hours. CONCLUSION Multiple organ dysfunction during resuscitation is a reversible response to severe injury and often resolves during the resuscitation period.
FROG characterisation of SOA-based wavelength conversion using XPM in conjunction with shifted filtering up to line rates of 80 GHz

The work we present here builds on recent work where we obtained 80 Gb/s error free performance using cross phase modulation (XPM) in an SOA in conjunction with a blue shifted bandpass filter. Here we present a detailed characterisation of this wavelength conversion scheme using a Frequency Resolved Optical Gating (FROG) measurement scheme for both red and blue shifted filtering. This type of characterisation has not been provided before to the best of our knowledge and is an important analysis firstly to achieve a full understanding of the gain and phase dynamics exploited by the wavelength conversion scheme presented and secondly to design a filter so that an optimum performance can be obtained
Quantum e ® ects in the understanding of consciousness

*Center for Consciousness Studies The University of Arizona, Tucson, Arizona 85721, USA Center for Psychological Studies Nova Southeastern University, Ft. Lauderdale, FL 33314, USA Institute for Neuro-Immune Medicine Nova Southeastern University, Ft. Lauderdale, FL 33314, USA Graduate School for Computer and Information Sciences Nova Southeastern University, Ft. Lauderdale, FL 33314, USA Department of Oncology University of Alberta, Edmonton, Alberta T6G1Z2, Canada ||Department of Physics University of Alberta, Edmonton, Alberta T6G2E1, Canada
HLA-A is a Predictor of Hepatitis B e Antigen Status in HIV-Positive African Adults

Outcomes of chronic infection with hepatitis B virus (HBV) are varied, with increased morbidity reported in the context of human immunodeficiency virus (HIV) coinfection. The factors driving different outcomes are not well understood, but there is increasing interest in an HLA class I effect. We therefore studied the influence of HLA class I on HBV in an African HIV-positive cohort. We demonstrated that virologic markers of HBV disease activity (hepatitis B e antigen status or HBV DNA level) are associated with HLA-A genotype. This finding supports the role of the CD8+ T-cell response in HBV control, and potentially informs future therapeutic T-cell vaccine strategies.
Land application of sewage biosolids: are Canadian trace metal guidelines/regulations over-protective for crop production?

Canadian trace metal guidelines/regulations are more restrictive of sewage biosolids land application than those in some other jurisdictions. Reviews of: research involving long-term and larger than recommended biosolids applications to land; information about trace metal sorption in biosolids and soils; and recent biosolids analyses all indicate that Canadian guidelines/regulations are more protective than necessary for high quality agricultural crop production. Canadian guidelines/regulations for land application should be revised to focus on best management practices for beneficial use of the valuable nutrients and organic matter in biosolids rather than on trace metals as at present.
A Jensen Modified Sharpe Ratio to Improve Portfolio Performance

The main purpose of this paper is to reconcile my previous work on the modified Jensen alpha1 methodology with the Stochastic Portfolio Theory as presented in Fernholz (2002). From the standard stochastic model, inclusion of the alpha enhanced method will show that it is possible to perform better than a market average or index fund (be it ranked by capitalization, Sharpe ratio or constant weights). The alpha feedback process will not only improve performance, it will also give the ability, to a certain degree, to better control a portfolio. No attempt is made to make an exhaustive proof of every assertion in this paper as the goal is not to produce an academic paper but to show that Stochastic Portfolio Theory (SPT), just as the Capital Asset Pricing Model (CAPM), can be used as stepping stones to higher portfolio performance. On the other hand, every attempt will be made to follow as closely as possible the mathematical notation as used in most of the academic papers I’ve read on this subject (see references for a partial listing). This paper at first presents an overview of the stochastic differential equation model as used in SPT. Then, the alpha accelerator is added to the portfolio process in order to improve performance. It is followed by a description of the trading environment and procedure implementation. Acknowledgements: Special thanks go to Murielle Northon for her support and to Murielle Gagné for keeping me on track while writing this paper. © Guy Roland Fleury, November 10, 2008. e-mail: rolandfleury@sympatico.ca ____________ 1 Alpha Power: Adding More Alpha to Portfolio Return. Available free from: http:/www.pimck. com/gfleury