Miracle-dz/UniFAR-FTUs huggingface dataset:
‘Universal’ primers for PCR‐sequencing of grass chloroplastic acetyl‐CoA carboxylase domains involved in resistance to herbicides

Summary Primers were designed to amplify two regions involved in sensitivity to herbicides inhibiting the plastidic acetyl-CoA carboxylase (ACCase) from grasses (Poaceae). The first primer pair amplified a 551-bp amplicon containing a variable Ile/Leu codon at position 1781 in Alopecurus myosuroides sequence. The second primer pair amplified a 406-bp amplicon containing four variable codons (Trp/Cys, Ile/Asn, Asp/Gly, Gly/Ala) at positions 2027, 2041, 2078 and 2096, respectively, in A. myosuroides sequence. Both primer pairs amplified the targeted fragments from genes encoding plastidic ACCases, but not from the very similar genes encoding cytosolic ACCases. Clear DNA sequences were obtained from fresh or dried plant material from the field, and from 29 various grass species. Sequences revealed that the gene encoding plastidic ACCase in Poa annua and Festuca rubra contained a Leu1781 codon, in agreement with both species being inherently tolerant to herbicides inhibiting ACCase. Sequencing confirmed the hybrid origin of P. annua. Compared with ACCase enzyme assay, polymerase chain reaction is faster, can be performed from a single plant and suppresses the need for radioactive experiments. It can be completed with basic molecular biology laboratory equipment. It is the tool of choice for diagnosing resistance caused by alteration(s) of the plastidic ACCase.
Physico-chemical characteristics and nutraceutical distribution of crude palm oil and its fractions

Crude palm oil (CRPO) was dry fractionated at 25 °C to get crude palm olein (CRPOL, 77%) and crude palm stearin (CRPS, 23%). Low and high melting crude palm stearin (LMCRPS 14.3% and HMCRPS 8.7%) were separated by further fractionation of CRPS with acetone. The physico-chemical parameters and nutraceutical distribution showed variation in different fractions. The CRPO contained 514.7 mg·Kg −1 of β-carotene and 82.6%, 16.1%, 12.5% and 3.1% of it was distributed in CRPOL, CRPS, LMCRPS and HMCRPS respectively. The distribution of phytosterols in fraction was 1870.2, 1996.8, 1190.9, 1290.4 and 115.4 mg·Kg −1 for CRPO, CRPOL, CRPS, LMCRPS and HMCRPS respectively. Total tocopherol composition was 535.5, 587.1, 308.0, 305.6 and 36.2 mg·Kg −1 for CRPO, CRPOL, CRPS, LMCRPS and HMCRPS respectively. The results show that the fractionation of CRPO may be helpful in the preparation of nutraceutical-rich fractions.
Effects of the Extent and Duration of Seasonal Flood Pool Inundation on Recruitment of Threadfin Shad, White Crappies, and Largemouth Bass in Hugo Reservoir, Oklahoma

Abstract Our objective was to determine the effects of the extent and duration of seasonal flooding (meters above normal pool) on recruitment indices for threadfin shad Dorosoma petenense, white crappies Pomoxis annularis, and largemouth bass Micropterus salmoides in Hugo Reservoir, Oklahoma. We used simple linear regression to examine the relations between seasonal pool elevation exceedence duration (number of days for which elevation exceeded target values) and (1) mean monthly (June–September) estimates of age-0 threadfin shad abundance in midwater trawls; (2) white crappie abundance estimates from May and June trawl samples and November trap-net samples; and (3) fall electrofishing samples of age-0 largemouth bass. Due to the large number of relations tested, we could not discount the possibility that a significant positive relation between threadfin shad trawl catches in July–September and winter exceedence duration (≥123.8 m) occurred by chance. No relation was found between elevation and age-0 whit.
Cellular origin of ionizing radiation‐induced NF‐κB activation in vivo and role of NF‐κB in ionizing radiation‐induced lymphocyte apoptosis

Purpose: To investigate the cellular origin of ionizing radiation (IR)‐induced NF‐κB activation in vivo and the role of NF‐κB in IR‐induced lymphocyte apoptosis. Materials and methods: NF‐κB activities were analysed by gel shift/supershift assay in isolated murine T‐ and B‐cells, macrophages (Mϕ) and tissues from normal and T‐ and B‐cell‐deficient Rag1 mice with or without exposure to IR. IR‐induced lymphocyte apoptosis was determined by analysis of 3,3′‐dihexyloxacarbocyanine iodide (DiOC6) uptake, annexin‐V staining and the sub‐G0/1 population, or by TUNEL assay. Results: The results showed that IR activated NF‐κB in lymphocytes, including both T‐ and B‐cells, but failed to do so in Mϕ. Furthermore, T‐ and B‐cell‐deficient Rag1 mice exposed to IR exhibited a significant reduction in NF‐κB activation as compared with normal mice. Although NF‐κB1 (p50) gene knockout or NF‐κB decoy oligonucleotide treatment specifically inhibited IR‐induced lymphocyte NF‐κB activation, they had no significant effect on IR‐induced lymphocyte apoptosis. Conclusions: This finding suggests that lymphocytes are the main cellular origin of IR‐induced NF‐κB activation in vivo. However, NF‐κB activation has no significant effect on IR‐induced lymphocyte apoptosis.
Comment

We congratulate Fan, Peng, and Huang (FPH hereafter) on their interesting, innovative, and important contribution on microarray normalization. In addition to proposing new methodology that addresses several important open problems, FPH also present new asymptotic theory that both validates their approach and provides insight into the normalization process. Such theoretical work has been sparse in the microarray literature, probably because of the nonstandard way in which the number of parameters is large relative to the number of observations. We appreciate the opportunity to comment on this article. Normalization is the process of removing systematic background noises of gene expression measurements in microarray experiments. Typically, this is done slide-by-slide before conducting a significance analysis of individual gene effects. However, some authors advocate combining normalization and significance analysis to account for the variability of estimators used in the normalization process (Huang, Wang, and Zhang 2003; Huang and Zhang 2003). We revisit this issue later on in this comment. For now, we note that techniques for normalization and significance analysis share a number of similarities for both cDNA and oligonucleotide microarrays. Hence some of the concepts in FPH on cDNA arrays are also applicable to oligonucleotide arrays. However, there are sufficient structural differences between the two kinds of arrays that significant work is needed before these concepts can be applied to the oligonucleotide setting. Thus we restrict our comments primarily to cDNA arrays. We first briefly outline the key contributions of FPH, then discuss a few useful extensions. We briefly discuss a connection to marginal asymptotics for controlling false discovery rates (FDR) in significance analysis, then give a few comments on computational issues before presenting our closing comments.
Comment

Chatterjee, Chen, Maas, and Carroll (hereafter CCMC) have identified an important class of problems associated with big data’s potential for increasing scientific understanding and we congratulate them on their insightful development. The limitations for scientific inference of big observational datasets on their own are well known, and CCMC focus instead on the use of big databases as sources of auxiliary information that can be used to enhance inference from smaller studies in which important variables not in the big data have been measured. More specifically, they deal with situations in which only summary information from the big database is available, and not individual micro data. As they observe, this is a familiar topic in survey methodology, for example, where calibration of survey data to census or administrative data is concerned. It has also been considered in other fields such as econometrics, where macro or aggregate data are used to enhance inference from micro data on individuals (e.g., Imbens and Lancaster). In the article, CCMC use a constrained semiparametric maximum likelihood (CML) approach that is equivalent to a form of empirical likelihood (EL). In the following sections, we discuss how setting the problems more explicitly within an empirical likelihood framework allows an improvement to the synthetic CML (SCML) estimator in the article as well as straightforward extensions to other situations. In addition, we show that estimators from the CML/EL approach dominate generalized regression (GR) estimators.
Notes on Early Land Plants Today. 66. Nomenclatural notes on Acrobolbaceae

The liverwort family Acrobolbaceae Hodgson (1962: 117) is primarily distributed in the Southern Hemisphere and is currently described as containing three subfamilies and seven genera with approximately 60 accepted species names. The subfamily Acrobolboideae (or Acrobolbaceae s. str. ) has historically contained the genera Acrobolbus Gottsche et al . (1844: 5) , Marsupidium Mitt. in Hooker (1867: 751), and Tylimanthus Mitt. in Hooker (1867: 751).
Missing Treatments

This article analyzes the problem of identifying a treatment effect with imperfect observability of the treatment received by the population. Imperfect observability may be due to item/survey nonresponse or to noncompliance with randomly assigned treatments. I derive sharp worst-case bounds that are a function of the available prior information on the distribution of missing treatments. Under the assumption of monotone treatment response, I show that prior information on the distribution of missing treatments is not necessary to get sharp informative bounds. I illustrate the results with an empirical analysis of drug use and employment using data from the National Longitudinal Survey of Youth.
Investigations of subterranean bacteria in deep crystalline bedrock and their importance for the disposal of nuclear waste

The diversity and distribution of bacteria in subterranean environments have been found to be extensive and to depend on the prevailing environmental conditions. In 1987, microbiology became a part of the Swedish scientific program for the safe disposal of high level nuclear waste (HLW). The goal of the microbiology program is to understand how subterranean bacteria will interact with the performance of a future HLW repository. It concerns several major processes that directly or indirectly may exert influence on waste canister corrosion and the mobility of radionuclides. Uptake and transport of radionuclides by bacteria seem to be negligible components for radionuclide migration, but the effect from bacterial production of complexing agent remains to be evaluated. Also, bacterial production and consumption of gases will influence radionuclide transport due to gas bubbles. Many important radionuclides are immobile at reduced conditions and mobile at oxidized conditions. Bacterial activity can, therefore, .
Telegraphic Reviews

This book addresses, through the collected contributions of experts from a variety of scienti c disciplines, the issue of simplicity in modeling. Many of the authors are econometricians. The contributions originate from a conference on “Simplicity and Scienti c Inference” held in Tilburg, The Netherlands, in January 1997 sponsored by the Center for Economic Research. Every experienced data analyst has, at least at an informal level, an appreciation of the fact that a model should be kept simple, although fewer would be able to pinpoint exactly what simplicity means, why it should be pursued, and how it should be attained. The contributions in this book directly address these issues by attempting to de ne and quantify such concepts as simplicity, complexity, and parsimony and by exploring the connections between simplicity, goodness of  t, empirical modeling, and prediction. The lively and informative exposition of several points of view (at times con icting) will make this book pleasurable reading not only for philosophers of science and epistemologists, but also for those data analysts interested in formalizing the foundations that guide and shape their modeling practices.
Fungi isolated from phyllosphere of fodder galega (Galega orientalis)

The object of the experiment was fodder galega ( Galega orientalis Lam.) cultivated in 2001-2003 as field crop on three plots: 1. without fertilization, 2. 40 kg P 2 O 5 × ha -1 and 80 kg K 2 O × ha -1 , 3. 80 kg P 2 O 5 × ha -1 and 160 kg K 2 O × ha -1 . During the dry and warm vegetation season of 2002 almost two times fewer isolates were obtained from the leaves than in 2003 that was the most abundant in fungi. Yeasts-like fungi (30% of the total number of isolates) and saprotrophic fungi with dominated species: Acremonium strictum (8.5%), genus Epicoccum (7.8%), Humicola (9.5%) and Penicillium (18.9%) were the fungi most frequently populating the leaves of galega. The share of pathogens in the total number of isolates obtained from the phyllosphere was 10.6%. They were represented by fungi of Ascochyta spp. , Botrytis cinerea , genus Fusarium, Phoma medicaginis and Sclerotinia sclerotiorum . Reduction by 1.9 to 4.6% in the number of fungi isolated from the phyllosphere of galega without fertilization as compared to galega cultivated in combinations with fertilization was recorded. Generally, the smallest number of pathogens was recovered from galega fertilized with 40 kg P 2 O 5 × ha -1 and 80 kg K 2 O × ha -1 . B. cinerea most frequently populated galega in combination without fertilization, genus Fusarium fungi in combination without fertilization and with fertilization with 80 kg P 2 O 5 × ha -1 and 160 kg K 2 O × ha -1 , while Ascochyta spp. were isolated from galega with fertilization only.
Comment

Mahmoud, M. A. , Parker, P. A. , Woodall, W. H. , and Hawkins, D. M. (2007), “A Change Point Method for Linear Profile Data,” Quality and Reliability Engineering International, 23, 247–268. [265] Rice, J. A. , and Wu, C. O. (2001), “Nonparametric Mixed Effects Models for Unequally Sampled Noisy Curves,” Biometrics, 57, 253–259. [266] Seifert, B. , Brockmann, M. , Engel, J., and Gasser, T. (1994), “Fast Algorithms for Nonparametric Estimation,” Journal of Computational and Graphical Statistics, 3, 192–213. [270] Shi, M. , Weiss, R. E. , and Taylor, J. M. G. (1996), “An Analysis of Paediatric CD4 Counts for Acquired Immune Deficiency Syndrome Using Flexible Random Curves,” Applied Statistics, 45, 151–163. [266] Walker, E. , and Wright, S. P. (2002), “Comparing Curves Using Additive Models,” Journal of Quality Technology, 34, 118–129. [266] Wang, Y. (1998), “Smoothing Spline Models With Correlated Random Errors,” Journal of the American Statistical Association, 93, 341–348. [267] Williams, J. D. , Birch, J. B. , Woodall, W. H. , and Ferry, N. M. (2007), “Statistical Monitoring of Heteroscedastic Dose-Response Profiles From HighThroughput Screening,” Journal of Agricultural, Biological, and Environmental Statistics, 12, 216–235. [265] Williams, J. D. , Woodall, W. H. , and Birch, J. B. (2007), “Statistical Monitoring of Nonlinear Product and Process Quality Profiles,” Quality and Reliability Engineering International, 23, 925–941. [265,266,273] Woodall, W. H. (2000), “Controversies and Contradictions in Statistical Process Control,” Journal of Quality Technology, 32, 341–350. [265] Woodall, W. H. , Spitzner, D. J., Montgomery, D. C. , and Gupta, S. (2004), “Using Control Charts to Monitor Process and Product Quality Profiles,” Journal of Quality Technology, 36, 309–320. [265] Wu, H. , and Zhang, J. (2002), “Local Polynomial Mixed-Effects Models for Longitudinal Data,” Journal of the American Statistical Association, 97, 883–897. [266-268,270,271,275] Zhang, D. , Lin, X. , Raz, J., and Sowers, M. (1998), “Semiparametric Stochastic Mixed Models for Longitudinal Data,” Journal of the American Statistical Association, 93, 710–719. [267] Zou, C. , Tsung, F. , and Wang, Z. (2007), “Monitoring General Linear Profiles Using Multivariate EWMA Schemes,” Technometrics, 49, 395–408. [265, 266,273] (2008), “Monitoring Profiles Based on Nonparametric Regression Methods,” Technometrics, 50, 512–526. [265,271,273,274] Zou, C. , Zhang, Y. , and Wang, Z. (2006), “Control Chart Based on ChangePoint Model for Monitoring Linear Profiles,” IIE Transactions, 38, 1093– 1103. [265]
The sequence of a 16691bp segment of Saccharomyces cerevisiae chromosome IV identifies the DUN1, PMT1, PMT5, SRP14 and DPR1 genes, and five new open reading frames

As part of the European BIOTECH programme, the nucleotide sequence of a 16691bp fragment from the left arm of chromosome IV of Saccharomyces cerevisiae has been deduced. Analysis of the sequence reveals the presence of 13 open reading frames (ORFs) larger than 100 codons. Five of these were previously identified as genes DUN1, PMT1, PMT5, SRP14 and DPR1. One putative protein, D2371p, contains an ATP‐GTP binding site, and shares homology to the ArsA component of an Escherichia coli arsenical pump. No significant homology to any known protein has been found for the other ORFs. D2378p contains a zinc finger domain. The nucleotide sequence has been deposited at EMBL, with Accession Number X95644.
Chloroplasts autophagy during senescence of individually darkened leaves

We recently reported that autophagy plays a role in chloroplasts degradation in individually-darkened senescing leaves. Chloroplasts contain approximately 80% of total leaf nitrogen, mainly as photosynthetic proteins, predominantly ribulose 1, 5-bisphosphate carboxylase/oxygenase (Rubisco). During leaf senescence, chloroplast proteins are degraded as a major source of nitrogen for new growth. Concomitantly, while decreasing in size, chloroplasts undergo transformation to non-photosynthetic gerontoplasts. Likewise, over time the population of chloroplasts (gerontoplasts) in mesophyll cells also decreases. While bulk degradation of the cytosol and organelles is mediated by autophagy, the role of chloroplast degradation is still unclear. In our latest study, we darkened individual leaves to observe chloroplast autophagy during accelerated senescence. At the end of the treatment period chloroplasts were much smaller in wild-type than in the autophagy defective mutant, atg4a4b-1, with the number of chloroplasts decreasing only in wild-type. Visualizing the chloroplast fractions accumulated in the vacuole, we concluded that chloroplasts were degraded by two different pathways, one was partial degradation by small vesicles containing only stromal-component (Rubisco containing bodies; RCBs) and the other was whole chloroplast degradation. Together, these pathways may explain the morphological attenuation of chloroplasts during leaf senescence and describe the fate of chloroplasts.
Biologia de Mahanarva fimbriolata em gramíneas forrageiras

Under controlled conditions, six forage grasses (Setaria anceps cv. 'Kazungula' and Brachiaria brizantha cv. 'Marandu'; and codified genotypes BB33, BB39; BBS 5 and BBS8), along with a control check (sugarcane cv. 'SP80-1842') were evaluated as to Mahanarva fimbriolata resistance. The following parameters have been evaluated: nymphal phase duration and mortality, sex ratio, pre-oviposition period, number of eggs per female, longevity, viability and embryonic period. The highest mortalities and longer nymphal periods occurred on BBS 8, cv. 'Marandu' and cv. 'Kazungula'. BBS5 also caused high nymph mortality, however with the shortest nymphal period. The lowest longevity and fecundity values were detected for BBS5 and BBS8, whereas the sugarcane control check revealed the highest one. As to embryonic phase viability, BBS 8 originated the highest values and BBS 5, the lowest ones. Among the tested plants, BBS 8 along with the cv. 'Marandu', proved to be the most resistant genetic material, both through antibiosis and/or nonpreference for feeding mechanism.
The four dimensions of cereal aphids

For most of this century, aphids have been known to infest cereals, but their potential importance does not seem to have been fully appreciated until the early 1950s when they were found to be vectors of barley yellow dwarf virus (Bruehl, 1961). Although this discovery initiated a great deal of research in many countries, especially in North America, very little was done, or thought necessary to be done, in Britain. In 1968, however, some of this complacency was lost when the large numbers of aphids found on the cereals in this country indicated how little was known about them and their effects. Aphids are part of a complex four-dimensional continuum of time and space, and this paper briefly describes some of the results obtained since 1969.
Two new species of Agauopsis (Halacaridae, Acari) from Southeastern Brazil

Mites belonging to two new species of Agauopsis (Halacaridae, Acari) were obtained from seaweed, coarse sand and coarse shell debris taken from several sites in Northern Coast of Sao Paulo State. Agauopsis legionium sp. nov., which belongs to the brevipalpus group and Agauopsis itassussensis sp. nov., closely related to A. okinavensis Bartsch, 1986 are described.
Comment

in Sensitivity of Blood Pressure to Aldosterone,” Hypertension, 63, 1212–1218. [160] Winn, J. (2003), “VariationalMessage Passing and ItsApplication,” PhD thesis, University of Cambridge. [158,159] Winn, J., and Bishop, C. M. (2005), “Variational Message Passing,” Journal of Machine Learning Research, 6, 661–694. [158,159] Yu, Z. , Eckert, G. J., Liu, H. , Pratt, J. H. , and Tu, W. (2013), “Adiposity has Unique Influence on the Renin-Aldosterone Axis and Blood Pressure in Black Children,” Journal of Pediatrics, 163, 1317–1322. [160]
A Collaborative Inquiry between a Person-Centered Therapist and a Client: Working with an emerging dissociated “self” Part One: Adult Mary/Young Mary—One self, two parts / Eine gemeinsame Untersuchung eines personzentrierten Therapeuten und einer Klientin: Arbeit an einem auftauchenden dissoziierten

Abstract This is my account of a therapeutic journey which started with two adults, a counselor named Rob and myself, the student. On the way, however, we were to encounter a young child. The journey was not to be an easy one; it would hold many challenges for both of us and events which readers may see as strange or even bizarre. During this time a special therapeutic relationship was to develop and mature, its very existence being built on the elements of trust and safety.
Feeding Habits of Wild and Hatchery-Reared Pacific Threadfin, Polydactylus sexfilis (Family Polynemidae), in Hawaií

As part of a marine restocking study in Hawaií, an assessment of the dietary acclimation of hatchery-reared Pacific threadfin, Polydactylus sexfilis, in the natural environment was undertaken. Successful acclimation of cultured threadfin was determined by comparing dietary similarities between stocked and wild threadfin. The diets of both were primarily composed of crustaceans and strongly overlapped (> 0.80). Relative prey weights did not differ significantly between cultured and wild threadfin (Mann-Whitney, p > 0.05). Evidence of an ontogenetic shift in diet was apparent where larger prey items such as crabs and fishes became more common, and smaller prey such as amphipods became less common with successively larger threadfin size classes. A trial was carried out to reduce the initial acclimation period of hatchery-reared fish by conditioning them with live shrimp as food for several days before release. Conditioned threadfin had a significantly higher frequency of wild shrimp in the diet up to 5 days post-release than the control group (X 2 = 5.35, p = 0.02). Further research testing the frequency and duration of the treatment period may result in maximizing the initial survival of cultured fish in the field while minimizing the cost of shrimp production.