Miracle-dz/UniFAR-FTUs huggingface dataset:
Chlamydomonas reinhardtii Genome Project. A Guide to the Generation and Use of the cDNA Information1

The National Science Foundation-funded Chlamydomonas reinhardtii genome project involves (a) construction and sequencing of cDNAs isolated from cells exposed to various environmental conditions, (b) construction of a high-density cDNA microarray, (c) generation of genomic contigs that are nucleated around specific physical and genetic markers, (d) generation of a complete chloroplast genome sequence and analyses of chloroplast gene expression, and (e) the creation of a Web-based resource that allows for easy access of the information in a format that can be readily queried. Phases of the project performed by the groups at the Carnegie Institution and Duke University involve the generation of normalized cDNA libraries, sequencing of cDNAs, analysis and assembly of these sequences to generate contigs and a set of predicted unique genes, and the use of this information to construct a high-density DNA microarray. In this paper, we discuss techniques involved in obtaining cDNA end-sequence information and the ways in which this information is assembled and analyzed. Descriptions of protocols for preparing cDNA libraries, assembling cDNA sequences and annotating the sequence information are provided (the reader is directed to Web sites for more detailed descriptions of these methods). We also discuss preliminary results in which the different cDNA libraries are used to identify genes that are potentially differentially expressed.
Synthesis and biological activity of tuftsin, its analogue and conjugates containing muramyl dipeptides or nor‐muramyl dipeptides

Several conjugates of muramyl dipeptide (MDP) or nor‐muramyl dipeptide (nor‐MDP) with tuftsin were synthesized. Conjugates 8a–f were prepared by acylation of protected tuftsin with the isoglutamine carboxyl group of MDP or nor‐MDP 2a–f. Also tuftsin analogue 6 (H‐Thr‐Lys‐Pro‐Arg(NO2)‐OH) was obtained. All synthesized compounds were investigated at the Medical University of Gdansk. The biological activity of the examined compounds was estimated using in vitro cultures of human monocytes and lymphocytes. The substances displayed cytotoxic effects, as was revealed in the viability tests performed. The effects were most probably mediated by the induction of an oxidative burst in monocytes and the stimulation of redox enzymes in lymphocytes. In addition, the analogues turned out to be efficient stimulators of TNFα and IL6 secretion by monocytes and lymphocytes. Nevertheless, the secretion of cytokines did not affect the viability of the leukocyte population used in the experiments.
A rapid test for B-type natriuretic peptide correlates with falling wedge pressures in patients treated for decompensated heart failure: a pilot study.

OBJECTIVES To determine if changes in B-type natriuretic peptide (BNP) levels can accurately reflect acute changes in pulmonary capillary wedge pressure during treatment of decompensated heart failure. BACKGROUND Tailored therapy of decompensated congestive heart failure with hemodynamic monitoring is controversial. Other than the expense and complications of Swan-Ganz catheters, its use in titration of drug therapy has no conclusive end point. Because BNP reflects both elevated left ventricular pressure and neurohormonal modulation and has a short half-life, we hypothesized that levels of BNP would decline in association with falling wedge pressures. Final BNP levels would perhaps signify a new set point of neuromodulation. METHODS AND RESULTS Twenty patients with decompensated New York Heart Association (NYHA) class III-IV congestive heart failure (CHF) undergoing tailored therapy were studied. BNP levels were drawn every 2 to 4 hours for the first 24 hours (active treatment phase) and then every 4 hours for the next 24 to 48 hours (stabilization period). Hemodynamic data was recorded simultaneously. In 15 patients whose wedge pressure responded to treatment in the first 24 hours, there was a significant drop in BNP levels (55%) versus nonresponders (8%). There was a significant correlation between percent change in wedge pressure from baseline per hour and the percent change of BNP from baseline per hour (r = 0.79, P <.05). When the wedge pressure was kept at a stable, low level during the stabilization phase, BNP levels continued to fall another 37% (937 +/- 140 pg/mL at 24 hours to 605 +/- 128 pg/mL). Patients who died (n = 4) had higher final BNP levels (1,078 +/- 123 pg/mL v 701 +/- 107 pg/mL). CONCLUSIONS The data suggest that rapid testing of BNP may be an effective way to improve the in-hospital management of patients admitted with decompensated CHF. Although BNP levels will not obviate the need for invasive hemodynamic monitoring, it may be a useful adjunct in tailoring therapy to these patients.
Cell‐based DNA demethylation detection system for screening of epigenetic drugs in 2D, 3D, and xenograft models

Aberrant DNA methylation that results in silencing of genes has remained a significant interest in cancer research. Despite major advances, the success of epigenetic therapy is elusive due to narrow therapeutic window. A wide variety of naturally occurring epigenetic agents and synthetic molecules that can alter methylation patterns exist, however, their usefulness in epigenetic therapy remains unknown. This underlines the need for effective tumor models for large‐scale screening of drug candidates with potent hypomethylation activity. In this study, we present the development of a cell‐based DNA demethylation detection system, which is amenable for high content screening of epigenetic drugs in two‐dimensional and three‐dimensional cell culture models. Additionally, the detection system also supports the in vivo monitoring of demethylation efficacy of potential lead compounds from in vitro screens in tumor xenografts. The described detection system not only permits the continuous monitoring of demethylation but also of the induced cytostatic/cytotoxic drug effects in live cells, as a function of time. The detection system is fluorescence based and exploits the dominant ability of DNA methylation to inhibit gene transcription, and utilizes FLJ32130 gene, which is silenced on account of promoter hypermethylation in human colorectal cancer. The described work will provide the researchers with an efficient tool for epigenetic drug screens on a high throughput platform and would therefore benefit academic and industrial drug discovery. © 2016 International Society for Advancement of Cytometry
Itraconazole Formulation Studies of the Melt-Extrusion Process with Mixture Design

Abstract Itraconazole is a poorly water soluble compound. One method to increase the aqueous solubility of itraconazole is through formation of a solid dispersion. The purpose of this study is to develop a 40% w/w itraconazole formulation through solid dispersion formation, using hydroxypropyl-β-cyclodextrin (HP-β-CD) and hydroxypropylmethylcellulose (HPMC) as mixture components. The solid dispersion was obtained by melt-extrusion using a twin-screw corotating melt extruder. A D-optimal mixture design was applied for the development of the optimal itraconazole formulation. The itraconazole fraction varied between 20% w/w and 50% w/w in the mixture design and the HPMC and HP-β-CD fractions varied between 10% w/w and 60% w/w. The itraconazole formulation was optimized by producing clear extrudates, minimizing the torque, and maximizing the glass transition temperature and the apparent itraconazole solubility in 0.1 N HCl. Regression models were developed for the torque, glass transition temperature, and apparent solubility of itraconazole. High itraconazole fraction in the mixture promoted a better melt processing (minimizes torque). High HPMC fraction (>33% w/w) resulted in clear extrudates, indicating a solid dispersion and resulted in high glass transition temperature of the melt. High HP-β-CD fraction resulted in increased apparent itraconazole solubility in 0.1 N HCl. The optimal itraconazole formulation consisted of 45% w/w HPMC and 15% HP-β-CD w/w.
Expression of Two Members of the pMGA Gene Family of Mycoplasma gallisepticum Oscillates and Is Influenced by pMGA-Specific Antibodies

ABSTRACT Certain monoclonal antibodies and polyclonal antisera directed to pMGA, the major protein of Mycoplasma gallisepticum, were tested for the ability to influence the surface phenotype of the cell population which resulted from their inclusion in growth medium. The polyclonal antiserum and one monoclonal antibody (MAb 66) resulted in an alteration of surface phenotype; specifically, populations of cells grown either on plates or in broth cultures which contained these reagents ceased the expression of pMGA and instead expressed an antigenically unrelated new polypeptide (p82). Upon the removal of antibody, the progeny of these cells regained pMGA expression and produced antigenically sectored colonies. The basis of this switch between pMGA+ and pMGA− states was shown to be transcriptional. The p82 polypeptide, the expression of which resulted from growth of cells in antibodies, was another member of the pMGA gene family and was located just downstream from the pMGA gene normally expressed by the M. gallisepticum cells used. Collectively the results of this work suggest that this organism has evolved an unusual means of altering the antigenic composition of its surface in response to antibodies or to other environmental cues.
Feeding behaviour of sheep fed lucerne v. grass hays with controlled post-ingestive consequences.

Understanding what determines feeding behaviour in herbivores is essential to optimise the use of forages in breeding systems. Herbivores can evaluate foods by associative learning of their pre-ingestive characteristics (taste, odour, etc.) and their post-ingestive consequences. Post-ingestive consequences are acknowledged as influencing intake and food choices, but the role of pre-ingestive characteristics is still being debated. Our experiment was designed to test their separate effects on daily dry matter intake (DMI), intake patterns and short-term choices in sheep by crossing the nature of the hay orally consumed (o) ad libitum, lucerne (L) or grass (G), with the nature of the hay introduced into the rumen (r), L or G, at a rate of half the total amount of hay received the day before. We applied four treatments, Go/Gr, Go/Lr, Lo/Gr and Lo/Lr, to test the effects of (i) post-ingestive consequences with similar pre-ingestive characteristics (Go/Gr v. Go/Lr; Lo/Gr v. Lo/Lr) and (ii) pre-ingestive characteristics with similar post-ingestive consequences at the end of the feeding period (Go/Lr v. Lo/Gr). Six rumen-fistulated sheep underwent all the treatments over 11-day periods in a latin square design. Eating time was restricted to 6 h/day, intraruminal introductions were performed just before food offer and choice tests were conducted after food removal. For similar pre-ingestive characteristics, DMI increased when L hay was introduced into the rumen rather than G (P < 0.05), possibly owing to a lower fill effect of L due to its lower NDF content and higher rumen degradability. The increased DMI resulted from longer eating time when G was orally consumed (149 v. 192 min, P < 0.05), whereas it resulted from higher intake rate with L (4.8 v. 6.1 g/min, P < 0.05). For similar post-ingestive consequences at the end of the feeding period (Go/Lr and Lo/Gr), DMI were similar (P > 0.05). Pre-ingestive characteristics or palatability per se did not therefore influence daily intake, although they influenced eating patterns. Pre-ingestive characteristics also greatly influenced short-term choices in favour of the hay that was not previously consumed, independently of any post-ingestive influence. This study confirms the effects of post-ingestive consequences on daily intake, but demonstrates that these variations are obtained by different behavioural adjustments under the influence of pre-ingestive characteristics. Preference for novelty, regardless of post-ingestive consequences, thus suggests that sheep may seek a diverse diet more for pleasure than for functional purposes, with implications for animal welfare.
Topic Modeling for Classification of Clinical Reports

Electronic health records (EHRs) contain important clinical information about patients. Efficient and effective use of this information could supplement or even replace manual chart review as a means of studying and improving the quality and safety of healthcare delivery. However, some of these clinical data are in the form of free text and require pre-processing before use in automated systems. A common free text data source is radiology reports, typically dictated by radiologists to explain their interpretations. We sought to demonstrate machine learning classification of computed tomography (CT) imaging reports into binary outcomes, i.e. positive and negative for fracture, using regular text classification and classifiers based on topic modeling. Topic modeling provides interpretable themes (topic distributions) in reports, a representation that is more compact than the commonly used bag-of-words representation and can be processed faster than raw text in subsequent automated processes. We demonstrate new classifiers based on this topic modeling representation of the reports. Aggregate topic classifier (ATC) and confidence-based topic classifier (CTC) use a single topic that is determined from the training dataset based on different measures to classify the reports on the test dataset. Alternatively, similarity-based topic classifier (STC) measures the similarity between the reports' topic distributions to determine the predicted class. Our proposed topic modeling-based classifier systems are shown to be competitive with existing text classification techniques and provides an efficient and interpretable representation.
c-Ski Acts as a Transcriptional Co-repressor in Transforming Growth Factor-β Signaling through Interaction with Smads*

Smads are intracellular signaling mediators of the transforming growth factor-β (TGF-β) superfamily that regulates a wide variety of biological processes. Among them, Smads 2 and 3 are activated specifically by TGF-β. We identified c-Ski as a Smad2 interacting protein. c-Ski is the cellular homologue of thev-ski oncogene product and has been shown to repress transcription by recruiting histone deacetylase (HDAC). Smad2/3 interacts with c-Ski through its C-terminal MH2 domain in a TGF-β-dependent manner. c-Ski contains two distinct Smad-binding sites with different binding properties. c-Ski strongly inhibits transactivation of various reporter genes by TGF-β. c-Ski is incorporated in the Smad DNA binding complex, interferes with the interaction of Smad3 with a transcriptional co-activator, p300, and in turn recruits HDAC. c-Ski is thus a transcriptional co-repressor that links Smads to HDAC in TGF-β signaling.
SET DOMAIN GROUP25 Encodes a Histone Methyltransferase and Is Involved in FLOWERING LOCUS C Activation and Repression of Flowering1[W][OA]

Covalent modifications of histone lysine residues by methylation play key roles in the regulation of chromatin structure and function. In contrast to H3K9 and H3K27 methylations that mark repressive states of transcription and are absent in some lower eukaryotes, H3K4 and H3K36 methylations are considered as active marks of transcription and are highly conserved in all eukaryotes from yeast (Saccharomyces cerevisiae) to Homo sapiens. Paradoxically, protein complexes catalyzing H3K4 and H3K36 methylations are less-extensively characterized in higher eukaryotes, particularly in plants. Arabidopsis (Arabidopsis thaliana) contains 12 SET DOMAIN GROUP (SDG) proteins phylogenetic classified to Trithorax Group (TrxG) and thus potentially involved in H3K4 and H3K36 methylations. So far only some genes of this family had been functionally characterized. Here we report on the genetic and molecular characterization of SDG25, a previously uncharacterized member of the Arabidopsis TrxG family. We show that the loss-of-function mutant sdg25-1 has an early flowering phenotype associated with suppression of FLOWERING LOCUS C (FLC) expression. Recombinant SDG25 proteins could methylate histone H3 from oligonucleosomes and mutant sdg25-1 plants showed weakly reduced levels of H3K36 dimethylation at FLC chromatin. Interestingly, sdg25-1 transcriptome shared a highly significant number of differentially expressed genes with that of sdg26-1, a previously characterized mutant exhibiting late-flowering phenotype and elevated FLC expression. Taken together, our results provide, to our knowledge, the first demonstration for a biological function of SDG25 and reveal additional layers of complexity of overlap and nonoverlap functions of the TrxG family genes in Arabidopsis.
Absolute Myocardial Blood Flow and Flow Reserve Assessed by Gated SPECT with Cadmium–Zinc–Telluride Detectors Using 99mTc-Tetrofosmin: Head-to-Head Comparison with 13N-Ammonia PET

Recent advances in SPECT technology including cadmium–zinc–telluride (CZT) semiconductor detector material may pave the way for absolute myocardial blood flow (MBF) measurements by SPECT. The aim of the present study was to compare K1 uptake rate constants as surrogates of absolute MBF and myocardial flow reserve index (MFRi) in humans as assessed with a CZT SPECT camera versus PET. Methods: Absolute MBF was assessed in 28 consecutive patients undergoing adenosine stress–rest myocardial perfusion imaging (MPI) by 99mTc-tetrofosmin CZT SPECT and 13N-ammonia PET, and MFR was calculated as a ratio of hyperemic over resting MBF. Results from both MPI methods were compared, and correlation coefficients were calculated. The diagnostic accuracy of CZT MFRi to predict an abnormal MFR defined as PET MFR less than 2 was assessed using a receiver-operator-characteristic curve. Results: Median MBF at rest was comparable between CZT and PET (0.89 [interquartile range (IQR), 0.77–1.00] vs. 0.92 [IQR, 0.78–1.06] mL/g/min; P = not significant) whereas it was significantly lower at stress in CZT than PET (1.11 [IQR, 1.00–1.26] vs. 2.06 [IQR, 1.48–2.56] mL/g/min; P < 0.001). This resulted in median MFRi values of 1.32 (IQR, 1.13–1.52) by CZT and 2.36 (IQR, 1.57–2.71) by PET (P < 0.001). The receiver-operator-characteristic curve revealed a cutoff for CZT MFRi at 1.26 to predict an abnormal PET MFR yielding an accuracy of 75%. Conclusion: The estimation of absolute MBF index values by CZT SPECT MPI with 99mTc-tetrofosmin is technically feasible, although hyperemic values are significantly lower than from PET with 13N-ammonia, resulting in a substantial underestimation of MFR. Nevertheless, CZT MFRi may confer diagnostic value.
Emission Permits as a Monetary Policy Tool: Is it Feasible? Is it Ethical?

The price of emission permits is deemed too low to mitigate climate change. In three studies, policy approaches to pricing carbon in a market setting are examined. First, the emission permit market is analyzed comparatively to how the ethanol mandate impacted prices in the corn market. This leads to the realization that the marketization of carbon is more like a currency than a physical commodity. The next study examines emission permits as a monetary policy tool. Emissions correlate GDP output, thus central banks can use emission permits as forward guidance, as a means to optimize the price for climate change mitigation, and as an alternative to interest rates. Opinions of thought leaders are used to question the acceptability of emission permits as a monetary policy tool. The final study is an ethical analysis using deontology, utilitarianism and virtue ethics within a pragmatic philosophical context, analyzing carbon as a monetary policy tool. In order for carbon as a monetary policy tool to be considered ethically acceptable, it must satisfy the temporal, spatial and institutional dilemmas of climate change articulated in Stephen Gardiner’s Perfect Moral Storm. Under this ethical standard, it is found that using carbon as a monetary policy tool can help address these concerns, but not solve them alone. This research is presented using transdisciplinary methods which provide a unique and holistic approach to policy formation not yet presented in the literature. This research is relevant to policy makers in central banking, the IMF and World Bank.
IoT based smart health care system using CNT electrodes (for continuous ECG monitoring)

As the world population is growing at a rapid pace, the demand for better health care facilities is increasing steadily. It has been observed that many health problems are unpredictable; especially heart diseases; hence it is important to monitor heart continuously. Earlier it was not always possible to monitor the patient continuously and for longer durations, but thanks to the latest developments in the domain of Information and Communications Technology (ICT), that facilitate the acquirement, transmission, interpretation and reception of various bio-signals, from permanent or mobile sites. The developments in the sphere of sensing technologies, wireless communication, embedded systems, nano-electronics, etc make it feasible to build intelligent systems to monitor bio-signals especially heart signals (ECG) of the patient; and further with the help of necessary protocols, the information can be promptly sent to the doctor, hospitals, etc. Thanks to the concept of Internet-of-Things (IoT), which provides necessary help in emergency situations. Nanomaterials are now being used in a big way because of their several advantages over the conventional materials. So, getting together the concept of IoT and nanomaterials will restructure the field of health-care, promising economic, technological and social benefits.
Comparative effectiveness research and genomic medicine: An evolving partnership for 21st century medicine

The American Recovery and Reinvestment Act has provided resources for comparative effectiveness research that will lead to evidence-based decisions about health and health care choices. Some have voiced concerns that evidence-based comparative effectiveness research principles are only relevant to “average” patients and not as much to individuals with unique combinations of genes, exposures and disease outcomes, intrinsic to genomic medicine. In this commentary, we argue that comparative effectiveness research and genomic medicine not only can and should coexist but also they will increasingly benefit from each other. The promise and success of genomic medicine will depend on rigorous comparative effectiveness research to compare outcomes for genome-based applications in practice to traditional non–genome-based approaches. In addition, the success of comparative effectiveness research will depend on developing new methods and clinical research infrastructures to integrate genome-based personalized perspectives into point of care decisions by patients and providers. There is a need to heal the apparent schism between genomic medicine and comparative effectiveness research to enhance knowledge-driven practice of medicine in the 21st century.