Miracle-dz/UniFAR-FTUs huggingface dataset:
Somatic mutations and intraclonal variations in the rearranged Vk genes of B‐non‐Hodgkin's lymphoma cell lines

Abstract: Three established Burkitt's lymphoma (BL) cell lines (Daudi, Raji and DG‐75) and three B‐non‐Hodgkin's lymphoma (B‐NHL) of other types (Pfeiffer, Farage and Toledo) were analyzed with respect to the presence of somatic point mutations in their rearranged immunoglobulin Vk genes. Two of the Vk sequences of BL and two of those of the B‐NHL were heavily mutated (up to 11%), when compared with their closest germline variable region counterparts (“clonal mutations”). Only one of the six cell lines contained an unmutated germline Vk sequence. The clonal mutations have features characteristic of the mutation machinery operating in the course of the T‐dependent immune response, such as a preference of mutations in purine bases, more transitions than transversions and targeting to CDR and to known “hotspot” motifs. Sequence variations among different Vk PCR clones isolated from each of the cell lines (“intraclonal mutations”) showed that the Vk of Toledo exhibited about 5‐fold higher mutation frequency (MF) than the background level of Taq polymerase error (˜0.12% mut/bp). Similarly, the MF of Vk of two of the BL cell lines was 3–4‐fold higher than the Taq polymerase misincorporation rate. In contrast, the mutation frequencies of the Vk of DG‐75, Farage and Pfeiffer did not significantly exceed the level of Taq polymerase error.
Oxygen abundances in the most oxygen‐rich spiral galaxies

Oxygen abundances in the spiral galaxies expected to be richest in oxygen are estimated. The new abundance determinations are based on the recently discovered ff relation between auroral and nebular oxygen-line fluxes in high-metallicity H II regions. We find that the maximum gas-phase oxygen abundance in the central regions of spiral galaxies is 12+log(O/H) ∼ 8.75. This value is significantly lower (by a factor of ≥5) than the previously accepted value. The central oxygen abundance in the Milky Way is similar to that in other large spirals.
Evidence of Programmed Cell Death in Post-Phloem Transport Cells of the Maternal Pedicel Tissue in Developing Caryopsis of Maize1

We present cellular- and ultracellular-level studies here to show developmental programmed cell death (PCD) of placento-chalazal (P-C) cell layers in maternal pedicel tissue in developing caryopses of normal seed (Mn1) and in the invertase-deficient miniature (mn1) seed mutant in maize (Zea mays). PCD was evidenced by loss of nuclei and all subcellular membranous organizations in many P-C layers. The terminal deoxynucleotidyl transferase-mediated X-dUTP nick-end labeling (TUNEL) stain that is diagnostic of apoptotic-like PCD identified spatially and temporally two distinctive subdomains, which coincided with nucellar and integumental P-C layers based on their developmental origins. The early phase of PCD in the nucellar P-C was TUNEL negative and was specific to only the fertilized caryopses, indicating that the signaling for PCD in these maternal cells originated in the zygotic tissues. In fact, the initiation of PCD coincided with endosperm cellularization and was rapidly and coordinately completed prior to the beginning of the major storage phase in endosperm. Cell shape in these cell layers was also influenced by the genotype of filial endosperm. The later phase of PCD was restricted to the integumental P-C layers underneath the nucellar cells and was TUNEL positive in both genotypes. The two subdomains of the P-C layers were also distinguishable by unique cell wall-associated phenolic compounds. Based on collective evidence, we infer that the nucellar PCD may have osmolytic etiology and may lead to activation of the post-phloem transport function of the P-C layer, whereas the integumental PCD was senescent related, in particular, protecting the maturing seed against microbes that may be transported from the maternal tissue.
The Solidification Behavior of Slags: Phenomena Related to Mold Slags

The solidification behavior of slags is a complex subject due to the varied chemical compositions of steelmaking slags. However, recent experimental developments, using the fact that slags that do not contain significant quantities of transition metal oxides are transparent, has allowed the development of opti-cal techniques to observe slag solidification behavior. While “curiosity based research” was the initiator of such studies, it has quickly become apparent that observation of the phenomenon of slag solidification has lead to a much deeper understanding of the role of slag solidification behavior in the process of the continuous casting of steel. In this paper findings from observation of slag solidification will be discussed with reference to developments in continuous casting.
Unions and the Adoption of High Performance Work Systems: Does Employment Security Play a Role?

Previous research on the association between unionization and the adoption of high performance work systems (HPWSs) has yielded inconsistent results. Using data from a 2004 multi-industry survey of firms operating in the Republic of Ireland, the authors examine the relationship between employee union membership rates and relative use of HPWSs. They also test arguments that employment security may affect the receptiveness of unions to such HR practices. The results indicate that as union representation increased, there was a significant decrease in the use of high performance work systems. Evidence also suggests that providing employment security significantly ameliorated this negative impact.
The crucial role of plant mitochondria in orchestrating drought tolerance.

BACKGROUND Around the world, the frequency and intensity of droughts is increasing as a result of global climate change, with important consequences for the growth and survival of agricultural and native plant species. Understanding how plants respond to water stress is thus crucial for predicting the impacts of climate change on the crop productivity and ecosystem functioning. In contrast to the large number of studies assessing drought impacts on photosynthesis, relatively little attention has been devoted to understanding how mitochondrial respiratory metabolism is altered under water stress conditions. SCOPE This review provides an overview of the impacts of water stress on mitochondrial respiration (R), combining studies at the whole-plant, individual organ, cellular and organelle levels. To establish whether there are clear patterns in the response of in vivo R to water stress, a wide range of root, leaf and whole-plant studies are reviewed. It is shown that water stress almost always inhibits R in actively growing roots and whole plants. However, in fully expanded, mature leaves the response is more variable, with water stress reducing R in near two-thirds of reported studies, with most of the remainder showing no change. Only a few studies reported increases in leaf R under severe water stress conditions. The mechanisms responsible for these variable responses are discussed. Importantly, the fact is highlighted that irrespective of whether drought increases or decreases respiration, overall the changes in R are minor compared with the large decreases in photosynthetic carbon gain in response to drought. Based on recent work highlighting the link between chloroplast and mitochondrial functions in leaves, we propose a model by which mitochondrial R enables survival and rapid recovery of productivity under water stress conditions. Finally, the effects of water stress on mitochondrial function, protein abundance and overall metabolism are reviewed.
Solutions to the Computer Networking Challenges of the Distribution Smart Grid

Communication networks play a crucial role in the context of Smart Grids since they enable a broad set of appealing facilities, from both producers and consumers side, to be effectively delivered. So far, several standards (e.g., IEC 61850-5) have been presented aiming to detail the specific requirements for such networks on the Smart Grid domain. However, the definitions proposed by these standards are confined to a reduced part of the grid: the primary substation. This situation prevents electrical distribution networks from fully exploiting the Smart Grid concept as a whole (i.e., provide truly distributed energy resources). The purpose of this paper is to (1) provide a further insight qualitative analysis of the yet-unexplored communication requirements raised by the electrical distribution Smart Grid, and (2) propose novel solutions targeted at creating link layer networks spanning a given electrical distribution area to allow faster and more reliable communication. Specifically, these solutions are devoted to extend all standards and communication mechanisms already defined for primary substations, to the whole grid by considering the electrical distribution grid as a collection of virtual substations. Furthermore, collected experiences throughout the implementation of this proposal envisage some alternatives to boost the performance of this protocol in terms of reliability and latency.
Prevalence of sexually transmitted infections including HIV in street-connected adolescents in western Kenya

Purpose The objectives of this study were to characterise the sexual health of street-connected adolescents in Eldoret, Kenya, analyse gender disparity of risks, estimate the prevalence of sexually transmitted infections (STIs), and identify factors associated with STIs. Methods A cross-sectional study of street-connected adolescents ages 12–21 years was conducted in Eldoret, Kenya. Participants were interviewed and screened for Chlamydia trachomatis, Neisseria gonorrhoeae, Trichomonas vaginalis, herpes simplex virus-2, syphilis and HIV. Descriptive statistics and logistic regression were used to identify factors associated with having any STI. Results Of the 200 participants, 81 (41%) were female. 70.4% of females and 60.5% of males reported sexual activity. Of those that participated in at least one STI test, 28% (55/194) had ≥1 positive test, including 56% of females; 14% (28/194) had >1 positive test. Twelve females and zero males (6% overall, 14.8% of females) were HIV positive. Among females, those with HIV infection more frequently reported transactional sex (66.7% vs 26.1%, p=0.01), drug use (91.7% vs 56.5%, p=0.02), and reported a prior STI (50.0% vs 14.7%, p<0.01). Having an adult caregiver was less likely among those with HIV infection (33.3% vs 71.0%, p=0.04). Transactional sex (AOR 3.02, 95% CI (1.05 to 8.73)), a previous STI (AOR 3.46 95% CI (1.05 to 11.46)) and ≥2 sexual partners (AOR 5.62 95% (1.67 to 18.87)) were associated with having any STI. Conclusions Street-connected adolescents in Eldoret, Kenya are engaged in high-risk sexual behaviours and females in particular have a substantial burden of STIs and HIV. There is a need for STI interventions targeted to street-connected youth.
Production and Characterization of Activated Carbon from Banana Empty Fruit Bunch and Delonix regia Fruit Pod

Activated carbon was produced from banana empty fruit bunch (BEFB) and Delonix regia fruit pod (DRFP) through single step chemical activation process. As both the lignocellulosic wastes showed maximum weight loss at temperatures lower than 500°C, they were carbonized at 450°C (BEFP) and 400°C (DRFP) respectively after impregnating with H3PO4 and KOH. Highest yield of 41.09% was recorded in DRFP treated with H3PO4 followed by other treatments. The KOH treated DRFP recorded maximum bulk density of 0.46 g/ml followed by H3PO4 treated DRFP. The BEFP carbons displayed lower attrition values than DRFP carbons. While the H3PO4 treated DRFP carbon sample showed higher surface area, the untreated DRFP registered higher pore volume. However BET surface area was comparatively low in both the substrates. FT-IR analysis of H3PO4, KOH and untreated carbon sample, though did not show much difference in surface functional groups, showed shifts in bands and changes in wave numbers and absorbance between the untreated and treated samples indicating chemical transformations during pyrolysis. While highest iodine removal was observed in KOH treated BEFP and DRFP samples, methylene blue reduction was high in H3PO4, KOH and untreated BEFP carbon samples.
Substrate competition in postischemic myocardium. Effect of substrate availability during reperfusion on metabolic and contractile recovery in isolated rat hearts.

Normal myocardium can derive energy for contraction and relaxation from oxidative metabolism of a variety of substrates. This investigation examined the influence of substrate availability early during reperfusion on the substrate pattern of oxidative metabolism and recovery of contractile function. For this purpose, isovolumically beating isolated rat hearts, perfused retrogradely with erythrocyte-supplemented buffer containing 0.4 mmol/L palmitate and 11 mmol/L glucose, were subjected to 40 minutes of no-flow ischemia. Hearts were reperfused with medium containing selected concentrations of palmitate and glucose. The substrate pattern for oxidative metabolism was determined on the basis of myocardial release of 14CO2 after equilibration of the hearts during the initial 15 minutes of reperfusion with either [1-14C]palmitate or [U-14C]glucose. In continuously perfused control hearts, glucose oxidation was largely inhibited by palmitate. During postischemic reperfusion, oxidation of glucose was increased by 59% (P < .05) and 467% (P <.01) in hearts reperfused after the ischemic period with 11 mmol/L glucose plus 0.4 or 1.2 mmol/L palmitate, respectively. Oxidation of palmitate was concomitantly reduced during reperfusion at low (0.4 mmol/L) but not at high (1.2 mmol/L) palmitate concentration. Compared with hearts reperfused with medium containing 0.4 mmol/L palmitate as sole substrate, hearts reperfused with medium containing 11 mmol/L glucose with 0.4 mmol/L palmitate exhibited lower left ventricular diastolic pressure (69 +/- 5 versus 90 +/- 3 mm Hg [mean +/- SEM], P < .05), less release of creatine kinase (31 +/- 5 versus 59 +/- 7 U/g wet wt, P < .05), and better recovery of left ventricular pressure development (26 +/- 9 versus 6 +/- 4 mm Hg, P < .05). Omission of palmitate or increasing the palmitate concentration to 1.2 mmol/L did not significantly alter postischemic myocardial contracture and enzyme release. The findings support the view that glucose oxidation early during reperfusion may be crucial for functional recovery. The results further indicate that interaction of substrates of oxidative metabolism is altered in severely injured postischemic myocardium. Inhibition of glucose oxidation by fatty acids was partially reversed during reperfusion.
Behavioral flexibility is associated with changes in structure and function distributed across a frontal cortical network in macaques

One of the most influential accounts of central orbitofrontal cortex– that it mediates behavioral flexibility – has been challenged by the finding that discrimination reversal in macaques –the classic test of behavioral flexibility –is unaffected when lesions are made by excitotoxin injection rather than aspiration. This suggests the critical brain circuit mediating behavioral flexibility in reversal tasks lies beyond the central orbitofrontal cortex. To determine its identity a group of nine macaques were taught discrimination reversal learning tasks and its impact on grey matter was measured. Magnetic resonance imaging scans were taken before and after learning and compared with scans from two control groups each comprising ten animals. One control group learned similar discrimination tasks but which lacked any reversal component and the other control group engaged in no learning. Grey matter changes were prominent in posterior orbitofrontal cortex/anterior insula but also were found in three other frontal cortical regions: lateral orbitofrontal cortex (12o), cingulate cortex, and lateral prefrontal cortex. In a second analysis, neural activity in posterior orbitofrontal cortex/anterior insula was measured at rest and its pattern of coupling with the other frontal cortical regions was assessed. Activity coupling increased significantly in the reversal learning group in comparison to controls. In a final set of experiments we used similar structural imaging procedures and analyses to demonstrate that aspiration lesion of central orbitofrontal cortex, of the type known to affect discrimination learning, affected structure and activity in the same frontal cortical circuit. The results identify a distributed frontal cortical circuit associated with behavioral flexibility.
Long‐term results of corpus cavernosum autoinjection therapy for chronic erectile dysfunction

Summary. Between May 1985 and March 1992, 172 patients suffering from chronic erectile dysfunction (21–70 years old) underwent constant corpus cavernosum autoinjection therapy (CAT) with a standardized papaverine‐phentolamine mixture (16385 injections). Thereafter 41 patients continued CAT with the single agent papaverine (1257 injections). On the basis of both these 17642 protocol auto‐injections, and over 6 years of experience with intracavernosal autoinjection therapy we conclude that, especially with the papaverine‐phentolamine mixture, CAT constitutes an effective therapy (full rigidity in 95.8%) with tolerable side‐effects for chronic erectile dysfunction when preceded by careful patient selection and thorough multi‐disciplinary evaluation. This is especially so in the case of arterial and/or neurogenic aetiology of the erectile dysfunction. In addition, the contraindications must be strictly observed, the treatment and technique fully explained, and a regular follow‐up instituted. CAT is generally well accepted by the patients and their partners (98.8% /97.6%) and has distinct positive effects on self‐esteem (77.8%), performance anxiety (84.4%), and partnership (79.5%). The most serious side‐effect was prolonged erection (25 out of 17642 injections). In 6 patients reversible fibrotic changes near the tunica albuginea were observed.
Cell wall glycosphingolipids of Sphingomonas paucimobilis are CD1d‐specific ligands for NKT cells

The current consensus on characterization of NKT cells is based on their reactivity to the synthetic glycolipid, α‐galactosylceramide (α‐GalCer) in a CD1d‐dependent manner. Because of the limited availability of α‐GalCer, there is a constant search for CD1d‐presented ligands that activate NKT cells. The α‐anomericity of the carbohydrate is considered to be an important requisite for the CD1d‐specific activation of NKT cells. The gram‐negative, lipopolysaccharide‐free bacterium Sphingomonas paucimobilis is known to contain glycosphingolipids (GSL) with α‐anomeric sugars attached to the lipid chain. Here, we report that GSL extracted from this bacterium are able to stimulate NKT cells in a CD1d‐specific manner. In addition, soluble CD1d–Ig dimers loaded with this lipid extract specifically bind to NKT cells (but not conventional T cells). Further studies on the S. paucimobilis GSL could potentially lead to other natural sources of CD1d‐specific ligands useful for NKT cell analyses and aimed at identifying novel therapies for a variety of disease states.
A Hybrid Feature Selection Method for Microarray Classification

—Gene expression data is widely used in disease analysis and cancer diagnosis. However, since gene expression data could contain thousands of genes simultaneously, successful microarray classification is rather difficult. Feature selection is an important pre-treatment for any classification process. Selecting a useful gene subset as a classifier not only decreases the computational time and cost, but also increases classification accuracy. In this study, we applied both the information gain and correlation-based feature selection method as filter approaches, and an improved binary particle swarm optimization as a wrapper approach to implement feature selection; selected gene subsets were used to evaluate the performance of classification. Experimental results show that by employing the proposed method fewer gene subsets needed to be selected and better classification accuracy could be obtained.
COSTS OF PLASTICITY IN FORAGING CHARACTERISTICS OF THE CLONAL PLANT RANUNCULUS REPTANS

Abstract In clonal plants, evolution of plastic foraging by increased lengths of leaves and internodes under unfavourable conditions may be constrained by costs and limits of plasticity. We studied costs and limits of plasticity in foraging characteristics in 102 genotypes of the stoloniferous herb Ranunculus reptans. We grew three replicates of each genotype with and three without competition by the naturally co-occuring grass Agrostis stolonifera. We used regression and correlation analyses to investigate potential costs of plasticity in lengths of leaves and stolon internodes, developmental instability costs of these traits, and a developmental range limit of these traits. We used randomization procedures to control for spurious correlations between parameters calculated from the same data. Under competition the number of rosettes, rooted rosettes, and flowers was 58%, 40%, and 61% lower, respectively, than in the absence of competition. Under competition lengths of leaves and stolon internodes were 14% and 6% smaller, respectively, than in the absence of competition. We detected significant costs of plasticity in stolon internode length in the presence of competition when fitness was measured in terms of the number of rosettes and the number of flowers (selection gradients against plasticity were 0.250 and 0.214, respectively). Within-environment variation (SD) in both foraging traits was not positively correlated with the corresponding plasticity, which indicates that there were no developmental instability costs. More plastic genotypes did not have less extreme trait values than less plastic genotypes for both foraging traits, which indicates that there was no developmental range limit. We conclude that in R. reptans costs of plasticity more strongly constrain evolution of foraging in the horizontal plane (i.e., stolon internode length) than in the vertical plane (i.e., leaf length). Editor: C. Boggs
Survival Outcomes of Primary Intraocular Lymphoma: A Single-institution Experience

Objectives:We report the clinical outcomes of 22 patients with primary intraocular lymphoma (PIOL) treated over a 15-year period. Materials and Methods:Patients with confirmed PIOL by central pathology review treated from 1994 to 2010 with isolated ocular (N=13) or central nervous system (CNS) plus ocular involvement (N=9) were included. Intraocular and CNS failure-free survival, relapse-free survival, and overall survival outcomes were analyzed. Results:Median follow-up was 29.0 (range, 10.2 to 96.4) months. Sixteen patients (9 with isolated ocular, 7 with ocular and CNS disease) received combined modality therapy (CMT) consisting of systemic chemotherapy (usually high-dose methotrexate based) and orbital +/− whole-brain radiation. Two patients were treated with chemotherapy and 4 with local ocular therapy alone. Among patients with isolated ocular versus CNS involvement, CNS failure-free survival was 79% versus 57%, and intraocular failures were 62% versus 78% at 24 months. Median relapse-free survival was 34.0 versus 21.3 months (P=0.368), and overall survival 43.4 versus 30.3 months (P=0.744), respectively. Three patients treated with CMT (2 with isolated ocular and 1 with CNS involvement) with >1-year follow-up alive at the time of analysis never relapsed, and one remains disease-free >4.5 years after treatment. Conclusions:In this series of patients with PIOL+/− CNS disease, CNS and intraocular relapse were common. A trend toward better survival was seen among patients with isolated ocular presentation, and a limited number of long-term disease-free survivors seen after CMT.