Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomics of Peripheral T-Cell Lymphoma and Its Implications for Personalized Medicine

Peripheral T-cell lymphoma (PTCL) is a rare, heterogenous group of mature T-cell neoplasms that comprise 10–15% of non-Hodgkin lymphoma cases in the United States. All subtypes of PTCL, except for ALK+ anaplastic T-cell lymphoma, are associated with poor prognosis, with median overall survival (OS) rates of 1–3 years. The diagnosis of PTCL is mainly based on clinical presentation, morphologic features, and immunophenotypes. Recent advances in genome sequencing and gene expression profiling have given new insights into the pathogenesis and molecular biology of PTCL. An enhanced understanding of its genomic landscape holds the promise of refining the diagnosis, prognosis, and management of PTCL. In this review, we examine recently discovered genetic abnormalities identified by molecular profiling in 3 of the most common types of PTCL: RHOAG17V and epigenetic regulator mutations in angioimmunoblastic T-cell lymphoma, ALK expression and JAK/STAT3 pathway mutations in anaplastic T-cell lymphoma, and T-follicular helper phenotype and GATA3/TBX21 expression in PTCL-not otherwise specified. We also discuss the implications of these abnormalities for clinical practice, new/potential targeted therapies, and the role of personalized medicine in the management of PTCL.
mTORC1 Enhances Early Phase Ribosome Processivity

During translation elongation, the ribosome serially adds amino acids to a growing polypeptide over many rounds of catalysis. The ribosome remains bound to mRNAs over these multiple catalytic cycles, requiring high processivity. Despite its importance to translation, relatively little is known about how mRNA sequences or signaling pathways might enhance or reduce ribosome processivity. Here, we describe a metric for ribosome processivity, the ribosome density index (RDI), which is readily calculated from ribosomal profiling data. We show that ribosome processivity is not strongly influenced by open-reading frame (ORF) length or codon optimality. However, we do observe that ribosome processivity exists in two phases and that the early phase of ribosome processivity is enhanced by mTORC1, a key translational regulator. By showing that ribosome processivity is regulated, our findings suggest an additional layer of control that the cell can exert to govern gene expression.
Study of the Interaction between Bacteriophage T4 asiA and Escherichia coli ς70, Using the Yeast Two-Hybrid System: Neutralization of asiA Toxicity to E. coli Cells by Coexpression of a Truncated ς70 Fragment

ABSTRACT The interaction of T4 phage-encoded anti-sigma factor, asiA, andEscherichia coli ς70 was studied by using the yeast two-hybrid system. Truncation of ς70 to identify the minimum region involved in the interaction showed that the fragment containing amino acid residues proximal to the C terminus (residues 547 to 603) was sufficient for complexing to asiA. Studies also indicated that some of the truncated C-terminal fragments (residues 493 to 613) had higher affinity for asiA as judged by the increased β-galactosidase activity. It is proposed that the observed higher affinity may be due to the unmasking of the binding region of asiA on the sigma protein. Advantage was taken of the increased affinity of truncated ς70 fragments to asiA in designing a coexpression system wherein the toxicity of asiA expression in E. coli could be neutralized and the complex of truncated ς70 and asiA could be expressed in large quantities and purified.
BIOBASED ANTIBIOTICS FROM BASIDIOS: A CASE STUDY ON THE IDENTIFICATION AND MANIPULATION OF A GENE CLUSTER INVOLVED IN PLEUROMUTILIN BIOSYNTHESIS FROM CLITOPILUS PASSECKERIANUS

With bacteria becoming resistant to antibiotics, there is a growing need to find new sources of antibiotics. Our work has focussed on the organism Clitopilus passeckerianus which produces a natural antibiotic, pleuromutilin. Recently, a derivative of pleuromutilin, retapamulin (developed by GSK) was approved for use in humans. Clinical trials have demonstrated its efficacy against certain Gram-positive bacteria including MRSA. We have developed all the tools to manipulate this important organism, and will present results on transformation, gene manipulation and enhancement, as well as gene isolation and mapping. These tools have allowed us to isolate the pleuromutilin gene cluster. Using the molecular tools we have been able to identify all genes involved, their roles, and perhaps most importantly, the ability to manipulate to elevate levels of antibiotic production and deliberately alter products produced. These results demonstrate that we are able to manipulate and control the Clitopilus genome. This provides a molecular toolbox which makes it possible to identify and manipulate individual genes of this fungus, and leading to some major new drugs which are not compromised by antibiotic-resistant strains of bacteria. The results will open up major opportunities for other previously intractable systems and antibiotics in fungi.
Recognition of mechanical sphygmomanometer dial value based on Hough transform

This paper presents an effective method to recognize mechanical sphygmomanometer dial value based on Hough transform. The edges of image are detected by using the canny operator on the binarized image. Geometric features in the image are obtained based on Hough transform, which includes the center of the dial and the vertex of the pointer. After connecting the center of the dial and the vertex of the pointer, a pointer line segment is obtained, and then an accurate dial value is effectively computed according to the deflection angle of the line segment. Experiments show that the method in this paper has wide applicability and can be used to display the waveform of numerical changes more accurately in the video.
The response of heterotrophic activity and carbon cycling to nitrogen additions and warming in two tropical soils

Nitrogen (N) deposition is projected to increase significantly in tropical regions in the coming decades, where changes in climate are also expected. Additional N and warming each have the potential to alter soil carbon (C) storage via changes in microbial activity and decomposition, but little is known about the combined effects of these global change factors in tropical ecosystems. In this study, we used controlled laboratory incubations of soils from a long‐term N fertilization experiment to explore the sensitivity of soil C to increased N in two N‐rich tropical forests. We found that fertilization corresponded to significant increases in bulk soil C concentrations, and decreases in C loss via heterotrophic respiration (P< 0.05). The increase in soil C was not uniform among C pools, however. The active soil C pool decomposed faster with fertilization, while slowly cycling C pools had longer turnover times. These changes in soil C cycling with N additions corresponded to the responses of two groups of microbial extracellular enzymes. Smaller active C pools corresponded to increased hydrolytic enzyme activities; longer turnover times of the slowly cycling C pool corresponded to reduced activity of oxidative enzymes, which degrade more complex C compounds, in fertilized soils. Warming increased soil respiration overall, and N fertilization significantly increased the temperature sensitivity of slowly cycling C pools in both forests. In the lower elevation forest, respired CO2 from fertilized cores had significantly higher Δ14C values than control soils, indicating losses of relatively older soil C. These results indicate that soil C storage is sensitive to both N deposition and warming in N‐rich tropical soils, with interacting effects of these two global change factors. N deposition has the potential to increase total soil C stocks in tropical forests, but the long‐term stability of this added C will likely depend on future changes in temperature.
The effect of neem (Azadirachta indica A. Juss) oil on oviposition, development and reproductive potentials of Sesamia calamistis Hampson (Lepidoptera: Noctuidae) and Eldana saccharina Walker (Lepidoptera: Pyralidae)

Abstract 1 The effect of different treatments of neem oil (0, 0.075, 0.1 and 0.15 mL/plant) and their persistence (0, 5 and 10 days after application; DAA) on the oviposition behaviour and the bionomics of the noctuid Sesamia calamistis and the pyralid Eldana saccharina were tested in laboratory and greenhouse experiments.
ANALYSIS OF CHROMOSOMAL DNA CONTENT IN PACIFIC RED ABALONE HALIOTIS RUFESCENS BY FLUORESCENCE IMAGE ANALYSIS

Abstract The fluorescence fading and chromosome imaging method were used together to analyze chromosomal DNA contents (haploid set) in Pacific red abalone Haliotis rufescens (Archaeogastropoda: Haliotidae). The fluorescence intensity was measured each 1.6 sec in H. rufescens chromosomes (2 n = 36) stained with DAPI. The fluorescence of each chromosomal type was recorded using color digital images of 24 bits. These kind of images allowed converting the RGB (true color) images to pseudocolor images to quantify the fluorescence intensity by means of 256 levels of brightness. Algorithms built with MATLAB software were used to determine the area under the curve (fading function). Therefore, estimates of DNA contents in individual chromosome types were obtained. Their DNA contents were related with chromosomal sizes (P < 0.001). The DNA values found showed a range from 0.1106 ± 0.0045 pg (chromosome # 1) to 0.0890 ± 0.0060 pg (chromosome # 18). The genome size calculated for H. rufescens by sum of all chromosomal DNA contents was 1.77 ± 0.005 pg. This study describes an alternative imaging method to analyze the chromosome morphology and chromosomal DNA contents in molluscs, and represents an alternative approach to the lack of cell lines required in flow cytogenetics.
Studies on the nutritive value of silage with particular reference to the effects of energy and nitrogen supplementation in growing heifers

Summary Four digestibility and balance experiments were carried out in which 33 growing heifers were fed basal diets of low dry matter silage offered ad libitum, supplemented with various levels of barley and/or groundnut meal or urea. Voluntary intake of the silages was low although apparent digestibility of D.M. was high (66–75%). There was a significant linear negative relationship between the intake of D.M. as supplement and silage D.M. intake. Apparent digestibility of crude fibre in the silages was high (74–83%). It was depressed significantly by addition of barley but not by addition of groundnut. There was a highly significant linear relationship between the digestibility of D.M. and G.B. in the mixed silage concentrate diets used. Metabolizable energy (M.E.) values for the silages varied from 2·04 to 2·52 Mcal/kg (8·5–10·5 MJ/kg) D.M. Supplementation with barley at approximately 1% of live weight, increased M.E. values of the mixed diets to 2·57–2·85 Mcal/kg (10·8–11·9 MJ/kg) D.M. Additional N had little effect on these values. Nitrogen retention was significantly increased in all experiments by barley supplementation. It was further significantly increased by groundnut in three experiments and by urea in one experiment. Multiple regression analysis showed that N retention was significantly related to both M.E. intake and intake of absorbed N, and to M.E. intake and intake of supplementary N. Apparent availabilities of Ca and Mg in silage based diets were low and the availability of Na varied with Na intake. Supplementation with either energy or nitrogen increased apparent availability and retention of Mg but did not exert consistent effects on availability or retention of Ca or Na. There was a highly significant linear relationship between ingested and digested Na but not for Ca or Mg. There was a highly significant linear relationship between absorbed and retained Ca and Mg, but not for Na. Animals fed second cut silages had rather low blood glucose levels and higher than normal levels of blood ketones.
Isolation and amplification of genomic DNA from barks of Cinnamomum spp.

Cinnamomum verum Presl (syn. C. zeylanicum Blume), the cinnamon of commerce, is an important aromatic tree spice having wide applications in perfumery, flavoring, beverages, and medicine. Adulteration of cinnamon with the cheaper and inferior barks of C. aromaticum and C. malabatrum is a problem. Morphological distinction of the barks is difficult; in the case of powdered barks, the situation is even worse. DNA-based molecular tools are preferred under these circumstances. Isolation of high quality DNA is a prerequisite for molecular studies, but barks contain polysaccharides, polyphenols, and secondary metabolites that hamper DNA isolation. Since attempts at isolating DNA using existing protocols and commercial DNA isolation kits (Qiagen) have failed, a reliable and efficient protocol for the isolation and amplification of genomic DNA from the dried barks of 3 species of Cinnamomum (true cinnamon plus 2 spurious species), very recalcitrant materials, was perfected by trial and error. The yield of genomic DNA ranged from 5 to 8.1 µg g-1 of dried bark and the absorbance values at 260 nm and 280 nm gave a ratio higher than 1.8, indicating the good quality of DNA. The isolated DNA was PCR-amplified using 3 RAPD primers, 1 barcoding locus (rbcL) primer, and restriction digested (EcoR V and Hind III). Complete restriction digestion and PCR amplification of the isolated DNA confirmed the good quality of the results and supported the efficacy of this protocol to yield DNA that can be utilized in further molecular analysis.
Comparing Oprm1 Gene Promoter Methylation in the Lymphocytes of Male Rats Addicted to Nicotine, Morphine, Methadone, and Buprenorphine

Background: Addiction is a polygenic disorder caused by genetic and environmental factors. The opioid material can act as an epigenetic element, like DNA methylation. Objectives: The present study aimed to examine the effect of epigenetic drugs such as nicotine, morphine, methadone, and buprenorphine on the methylation of two CpG sites in promoter of Oprm1 gene in male Wistar rats. Materials & Methods: In this case-control study, 48 male Wistar rats with Mean±SD (200±30) g were divided into 6 groups: These are five groups only The control (intact) group, nicotine (0.4 mg/kg, SC injection for 5 days), morphine (10 mg/kg on days 1-3 and 20 mg/kg on days 4-6 and 40 mg/kg, IP injection on days 7-9), methadone (0.5 mg/kg, IP injection for 15 days), buprenorphine (0.05 mg/kg, SC injection for 6 days) and finally saline for each respected group. After the treatment, genomic DNA was extracted from the whole blood of the rats. Then, the extracted DNA was treated with sodium bisulfate. To identify the selected methylated areas of Oprm1 promoter sites (CpG-107 and CpG+33), we used methylation-specific PCR (MSP). Results: Our results showed no methylation in the two CpG sites of Oprm1 promoter in all of the treated groups. Conclusion: Addiction with nicotine, morphine, methadone, and buprenorphine in doses and duration used in this study was not associated with the methylation of the Oprm1 promoter sites in the male Wistar rats.
PriorityBucket: A Multipath-QUIC Scheduler on Accelerating First Rendering Time in Page Loading

Page load time is a web performance metric that directly impacts user experience. It measures the time it takes to fully load a web page after making a request. However, as the first visual feedback of a web page, first rendering time is also a key metric to satisfy the users. In this paper, we focus on speeding up the first rendering time in page loading from the perspective of protocol improvements. We observe that by prioritizing the streams that make up the critical rendering path in Multipath-QUIC (MPQUIC), the first rendering time can be effectively reduced. Therefore, we propose PriorityBucket - an MPQUIC scheduler that provides stream prioritization in the transport layer. By comparing to the existing schedulers of MPQUIC, we show its effectiveness in reducing the first rendering time and page load time of web pages in different path heterogeneity using the Chrome browser. Results show that PriorityBucket can reduce the first rendering time and page load time up to 34% and 35% respectively in high path heterogeneity when loading Bing.
Acetylcholine Receptors

Using 125iodine-labeled α-bungarotoxin (α-BGT-125I) and quantitative radioautography, we have studied the time-course of the change in acetylcholine (ACh) receptor distribution and density occurring in rat diaphragm after denervation. In innervated fibers, ACh receptors are localized at the neuromuscular junction and the extrajunctional receptor density is less than five receptors per square micrometer. The extrajunctional receptor density begins to increase between 2 and 3 days after denervation and increases approximately linearly to 1695 receptors/µm2 at 14 days, subsequently decreasing to 529 receptors/µm2 at 45 days. We have isolated plasma membranes from rat leg muscles at various times after denervation and find that the change in concentration of ACh receptors in the membranes measured by α-BGT-125I binding and scintillation counting follows a time-course similar to the change in ACh receptor density measured radioautographically. Furthermore, we have correlated extrajunctional ACh receptor density measured by radioautography with extrajunctional ACh sensitivity measured by iontophoretic application of ACh and intracellular recording and find that the log of ACh receptor density is related to 0.53 times the log of ACh sensitivity. These results are discussed in terms of the electrophysiological experiments on the ACh receptor and the recent, more biochemical approaches to the study of ACh receptor control and function.
P21 Regulates TGF-β1–Induced Pulmonary Responses via a TNF-α–Signaling Pathway

Transforming growth factor (TGF)-β1 is an essential regulatory cytokine that has been implicated in the pathogenesis of diverse facets of the injury and repair responses in the lung. The types of responses that it elicits can be appreciated in studies from our laboratory that demonstrated that the transgenic (Tg) overexpression of TGF-β1 in the murine lung causes epithelial apoptosis followed by fibrosis, inflammation, and parenchymal destruction. Because a cyclin-dependent kinase inhibitor, p21, is a key regulator of apoptosis, we hypothesized that p21 plays an important role in the pathogenesis of TGF-β1–induced tissue responses. To test this hypothesis we evaluated the effect of TGF-β1 on the expression of p21 in the murine lung. We also characterized the effects of transgenic TGF-β1 in mice with wild-type and null mutant p21 loci. These studies demonstrate that TGF-β1 is a potent stimulator of p21 expression in the epithelial cells and macrophages in the murine lung. They also demonstrate that TGF-β1–.
Cultural Differences in Prisoners’ Dilemma Game Experiments: Evidence from a Meta-Analysis

This study examines the effect of cultural norms on cooperative behavior in the repeated prisoner’s dilemma game. 111 treatments are collected from 45 experimental studies comprising more than 6000 participants and conducted in 13 different countries. The findings suggest that there is no significant difference in cooperative behavior between individualistic and collectivistic countries when cultural norms are measured at the country level. Rather, cooperative behavior is affected mainly by methodological factors of the experiment.
A Comparative Bayes tactic for mate assessment and choice

Models of mate choice tactics have assumed that females randomly encounter males when collecting information and the information is perfect. Empirical observations of four bird species show that females selectively visit males and repeat visits to males before mating. This suggests that the assumptions of previous models have been too restrictive. An alternative model of information gathering and mate choice, which relaxes the assumptions of random encounters and perfect information, is presented. In this Comparative Bayes model, the decision of when and from whom to collect information is made using Bayesian estimates of each male's quality. Predictions from the model are that: (1) the occurrence of mate assessment will increase as initial uncertainty about the quality of males increases, as the cost of gathering information decreases, and as the signal perceived by the female becomes a better representation of males' actual qualities; (2) the occurrence of repeat visits to males will be highest when signals from males are of medium reliability; and (3) the decision of which male to assess will depend on the estimated qualities of males, prior certainty about each male's quality, the reliability of each male's signal, and the costs of assessment. Simulations compare the fitness outcomes of the Comparative Bayes tactic to other mate choice tactics. The fitness from the Comparative Bayes tactic is significantly higher than from the fixed threshold tactic and than from the best-of-n tactic when the cost of assessment is low.
A molecular clock in endosymbiotic bacteria is calibrated using the insect hosts

The primary endosymbionts of aphids are maternally inherited bacteria that live only within specialized host cells. Phylogenetic analysis of the 16S ribosomal DNA sequences of aphid endosymbionts reveals that they are a monophyletic group with a phylogeny completely concordant with that of their hosts, implying long-term cospeciation. Here we show that rates of base substitution are similar in the 16.S ribosomal DNA of different endosymbiont lineages. In addition, we calibrate these rates by assigning age estimates for ancestral aphid hosts to the corresponding endosymbionts. The resulting rate estimates (1—2% per 50 Ma) are among the most reliable available for prokaryotes. They are very near values previously conjectured by using more tenuous assumptions for dating divergence events in eubacteria. Rates calibrated using dates inferred from fossil aphids imply that Asian and American species of the aphid tribe Melaphidina diverged by the early Eocene; this result confirms an earlier hypothesis based on biogeographic evidence. Based on these rate estimates, the minimum age of this endosymbiotic association and the age of aphids as a whole is estimated at 160-280 Ma.
Do Returns to Schooling Differ by Race and Ethnicity?

Using data from the U.S. Decennial Census and the National Longitudinal Surveys, we find little evidence of differences in the return to schooling across racial and ethnic groups, even with attempts to control for ability and measurement error biases. While our point estimates are relatively similar across racial and ethnic groups, our conclusion is driven in part by relatively large standard errors. That said, we find no evidence that returns to schooling are lower for African Americans or Hispanics than for non-minorities. As a result, policies that increase education among the lowskilled have a good possibility of increasing economic well-being and reducing inequality. More generally, our analysis suggests further research is needed to better understand the nature of measurement error and ability bias across subgroups in order to fully understand potential heterogeneity in the return to schooling across the population.