Miracle-dz/UniFAR-FTUs huggingface dataset:
Particularities of Real-Time Polymerase Chain Reaction Technique ( RT-PCR ) in the Monitoring of Chronic Myeloid Leukemia Patients – A Brief Overview

Chronic myeloid leukemia (CML) is a myeloproliferative disorder, characterized by a specific chromosomal aberration, the Philadelphia [Ph] chromosome. The Ph chromosome is the result of a reciprocal translocation between the long arms of chromosomes 9 and 22, t (9;22)(q34;q11). The molecular consequence of this translocation is a novel fusion gene, BCR-ABL, which encodes a constitutively active tyrosine kinase, implicated in pathophysiology and development of CML [1,2]. Imatinib mesylate currently the golden standard for front line treatment of CML, is a selective inhibitor of the BCR-ABL tyrosine kinase activity. Responses to imatinib occur at hematologic, cytogenetic and molecular levels. IM therapy now allows the majority of patients with CML to reach CCyR a confirmed good prognostic indicator [3]. In different studies, 87% of patients in chronic, 17% of patients in accelerated, and 7% of patients in blast phases reached the important clinical aim of Ph negativity [3-5]. Ph chromosome status is usually assessed by classical bone marrow cytogenetics and this method has the limitation of poor sensitivity. Patients who reveal 10 leukemic cells at the time of diagnosis, in CCyR may still have as many as 10 leukemic cells in their body. Once a patient has achieved CCyR, monitoring of residual cells is usually performed by estimating the BCR-ABL transcripts on a molecular level using quantitative real-time polymerase chain reaction (QRT-PCR). A 2-log reduction in BCR-ABL transcripts correlates with Ph negativity in CCyR. Patients achieving a 3log reduction in BCR-ABL transcripts are defined as having a major molecular response (MMR), a surrogate marker closely correlating with the probability of disease free survival [8]. Patients failing to achieve this 3-log response, at any time during therapy, had significantly shorter progression-free survival [6]. After a 5 to 6 log reduction, BCR-ABL transcripts can no longer be detected by QRT-PCR and patients are designated as having complete molecular response (CMR). But even with the most sensitive QRT-PCR assay, CMR is consistent with the persistence in the patient’s body of up to 10 or 10 leukemic cells [7]. Due to the proliferation of such residual cells a significant fraction of those patients who have responded on a deep molecular level, lose this response and progress to advanced phase disease. The clinical advantage of the extremely sensitive method of QRT-PCR is to be alerted by rising transcript levels at a very early time point, usually weeks or even months before the onset of clinical symptoms, allowing early terapeutic intervention with a beneficial impact on survival.
Effect of sleep deprivation on the human metabolome

Significance Sleep restriction and circadian clock disruption are associated with metabolic disorders including obesity and diabetes; this association can be studied by using the powerful tool of metabolomics. By using liquid chromatography/MS metabolomics, we have characterized plasma metabolites that were significantly affected by acute sleep deprivation (mainly lipids and acylcarnitines), all increasing during sleep deprivation. Observed increased levels of serotonin, tryptophan, and taurine may explain the antidepressive effect of sleep deprivation and deserve further study. Clear daily rhythms were observed in most metabolites, with 24 h wakefulness mainly reducing the amplitude of these rhythms. Our results further the understanding of sleep/wake regulation and the associated metabolic processes, and will be vital when using metabolic profiling to identify robust biomarkers for disease states and drug efficacy. Sleep restriction and circadian clock disruption are associated with metabolic disorders such as obesity, insulin resistance, and diabetes. The metabolic pathways involved in human sleep, however, have yet to be investigated with the use of a metabolomics approach. Here we have used untargeted and targeted liquid chromatography (LC)/MS metabolomics to examine the effect of acute sleep deprivation on plasma metabolite rhythms. Twelve healthy young male subjects remained in controlled laboratory conditions with respect to environmental light, sleep, meals, and posture during a 24-h wake/sleep cycle, followed by 24 h of wakefulness. Two-hourly plasma samples collected over the 48 h period were analyzed by LC/MS. Principal component analysis revealed a clear time of day variation with a significant cosine fit during the wake/sleep cycle and during 24 h of wakefulness in untargeted and targeted analysis. Of 171 metabolites quantified, daily rhythms were observed in the majority (n = 109), with 78 of these maintaining their rhythmicity during 24 h of wakefulness, most with reduced amplitude (n = 66). During sleep deprivation, 27 metabolites (tryptophan, serotonin, taurine, 8 acylcarnitines, 13 glycerophospholipids, and 3 sphingolipids) exhibited significantly increased levels compared with during sleep. The increased levels of serotonin, tryptophan, and taurine may explain the antidepressive effect of acute sleep deprivation and deserve further study. This report, to our knowledge the first of metabolic profiling during sleep and sleep deprivation and characterization of 24 h rhythms under these conditions, offers a novel view of human sleep/wake regulation.
Blood-derived dermal langerin+ dendritic cells survey the skin in the steady state

Langerin is a C-type lectin receptor that recognizes glycosylated patterns on pathogens. Langerin is used to identify human and mouse epidermal Langerhans cells (LCs), as well as migratory LCs in the dermis and the skin draining lymph nodes (DLNs). Using a mouse model that allows conditional ablation of langerin+ cells in vivo, together with congenic bone marrow chimeras and parabiotic mice as tools to differentiate LC- and blood-derived dendritic cells (DCs), we have revisited the origin of langerin+ DCs in the skin DLNs. Our results show that in contrast to the current view, langerin+CD8− DCs in the skin DLNs do not derive exclusively from migratory LCs, but also include blood-borne langerin+ DCs that transit through the dermis before reaching the DLN. The recruitment of circulating langerin+ DCs to the skin is dependent on endothelial selectins and CCR2, whereas their recruitment to the skin DLNs requires CCR7 and is independent of CD62L. We also show that circulating langerin+ DCs patrol the dermis in the steady state and migrate to the skin DLNs charged with skin antigens. We propose that this is an important and previously unappreciated element of immunosurveillance that needs to be taken into account in the design of novel vaccine strategies.
Increased incidence of cytogenetic abnormalities in chorionic villus samples from pregnancies established by in vitro fertilization and embryo transfer (IVF–ET)

We studied 201 pregnancies that were established by in vitro fertilization and embryo transfer (IVF–ET) and compared the frequency of cytogenetic abnormalities with that found in a large control population matched for indication group (advanced maternal age) and time of sampling. A total of 252 IVF–ET fetuses were cytogenetically analysed by either chorionic villus sampling (CVS; n = 80) or amniocentesis (n = 172). Eleven chromosome abnormalities were found in the CVS group (13·8 per cent); among them, a 45, X/46, X, dic(q11)/46, X, del(Y)(q11) mosaic that was found in an IVF pregnancy established by intracytoplasmic sperm injection (ICSI), four cases of trisomy 21, and three cases of trisomy 7 confined to the placenta. The results indicate a statistically significant three‐to five‐fold increase in both confined placental abnormalities (P<0·008) and true fetal chromosome anomalies (P<0·04). In the amniocentesis group, identical rates (1·7 per cent) of chromosome abnormalities were found in the IVF–ET and control groups. It is concluded that late first trimester, but not early second trimester, IVF–ET pregnancies are characterized by an increased frequency of cytogenetic abnormalities found at prenatal diagnosis.
Arithmetic Spectrum Applied to Fault Detection for Combinational Networks

A method for the derivation of fault signatures for the detection of faults in single-output combinational networks is described. The approach uses the arithmetic spectrum instead of the Rademacher-Walsh spectrum. It is a form of data compression that serves to reduce the volume of the response data at test time. The price which is paid for the reduction in the storage requirements is that some of the knowledge of exact fault location is lost. The derived signatures are short and easily tested using very simple test equipment. The test circuitry could be included on the chip since the overhead involved is comparatively small. The test procedure requires a high-speed counter cycling at maximum speed through selected subsets of all input combinations. Hence, the network under test is exercised at speed, and a number of dynamic errors that are not testable by means of conventional test-set approaches will be detected. >
Detecting de novo mutations in intellectual disability.

Copy number variation (CNV) is a common source of genetic variation that has been implicated in many genomic disorders. This has resulted in the widespread application of genomic microarrays as a first-tier diagnostic tool for CNV detection. More recently, whole-exome sequencing (WES) has been proven successful for the detection of clinically relevant point mutations and small insertion-deletions exome wide. We evaluate the utility of short-read WES (SOLiD 5500xl) to detect clinically relevant CNVs in DNA from 10 patients with intellectual disability and compare these results to data from two independent high-resolution microarrays. Eleven of the 12 clinically relevant CNVs were detected via read-depth analysis of WES data; a heterozygous single-exon deletion remained undetected by all algorithms evaluated. Although the detection power of WES for small CNVs currently does not match that of high-resolution microarray platforms, we show that the majority (88%) of rare coding CNVs containing three or more exons are successfully identified by WES. These results show that the CNV detection resolution of WES is comparable to that of medium-resolution genomic microarrays commonly used as clinical assays. The combined detection of point mutations, indels, and CNVs makes WES a very attractive first-tier diagnostic test for genetically heterogeneous disorders. INTRODUCTION Whole-exome sequencing (WES) has revolutionized Mendelian disease gene identification by providing a powerful tool for exome-wide detection of singlenucleotide variants (SNVs) and small insertions and deletions (InDels) [Bainbridge et al., 2013; Bamshad et al., 2011; Gilissen et al., 2012; Hanchard et al., 2013; Ng et al., 2010; O’Roak et al., 2012]. In addition, WES is being introduced as a diagnostic procedure for genetically heterogeneous diseases in a number of laboratories [de Ligt et al., 2012; Hanchard et al., 2013; Rauch et al., 2012]. Structural variation such as copy number variants (CNVs), also contributes to these disorders [Cooper et al., 2011; Lupski, 2009; Stankiewicz and Lupski, 2010], and is currently not routinely assessed from WES data. The identification of CNVs, in addition to SNVs and InDels, would increase the versatility of WES as a genome-wide variant detection method in research and diagnostics. It would reduce the number of genomic assays required per patient to reach a diagnosis and create new possibilities to analyze the combined effects of SNVs and structural variation within an individual [Kurotaki et al., 2005]. Genomic microarray platforms based on either single-nucleotide polymorphisms (SNPs) or comparative genomic hybridization (CGH) have proven highly successful as a robust, high-throughput method for CNV detection [Boone et al., 2010; Pinkel et al., 1998; Schaaf et al., 2011; Vissers et al., 2003]. Advances in technology have resulted in an increase in the number of probes being included on a single array
Cowpea Mosaic Virus 32- and 60-Kilodalton Replication Proteins Target and Change the Morphology of Endoplasmic Reticulum Membranes

ABSTRACT Cowpea mosaic virus (CPMV) replicates in close association with small membranous vesicles that are formed by rearrangements of intracellular membranes. To determine which of the viral proteins are responsible for the rearrangements of membranes and the attachment of the replication complex, we have expressed individual CPMV proteins encoded by RNA1 in cowpea protoplasts by transient expression and in Nicotiana benthamiana plants by using the tobacco rattle virus (TRV) expression vector. The 32-kDa protein (32K) and 60K, when expressed individually, accumulate in only low amounts but are found associated with membranes mainly derived from the endoplasmic reticulum (ER). 24K and 110K are freely soluble and accumulate to high levels. With the TRV vector, expression of 32K and 60K results in rearrangement of ER membranes. Besides, expression of 32K and 60K results in necrosis of the inoculated N. benthamiana leaves, suggesting that 32K and 60K are cytotoxic proteins. On the other hand, during CPMV infection 32K and 60K accumulate to high levels without causing necrosis.
The Respiratory Syncytial Virus Polymerase Has Multiple RNA Synthesis Activities at the Promoter

Respiratory syncytial virus (RSV) is an RNA virus in the Family Paramyxoviridae. Here, the activities performed by the RSV polymerase when it encounters the viral antigenomic promoter were examined. RSV RNA synthesis was reconstituted in vitro using recombinant, isolated polymerase and an RNA oligonucleotide template representing nucleotides 1–25 of the trailer complement (TrC) promoter. The RSV polymerase was found to have two RNA synthesis activities, initiating RNA synthesis from the +3 site on the promoter, and adding a specific sequence of nucleotides to the 3′ end of the TrC RNA using a back-priming mechanism. Examination of viral RNA isolated from RSV infected cells identified RNAs initiated at the +3 site on the TrC promoter, in addition to the expected +1 site, and showed that a significant proportion of antigenome RNAs contained specific nucleotide additions at the 3′ end, demonstrating that the observations made in vitro reflected events that occur during RSV infection. Analysis of the impact of the 3′ terminal extension on promoter activity indicated that it can inhibit RNA synthesis initiation. These findings indicate that RSV polymerase-promoter interactions are more complex than previously thought and suggest that there might be sophisticated mechanisms for regulating promoter activity during infection.
Common SCN10A variants modulate PR interval and heart rate response during atrial fibrillation.

AIMS SCN10A encodes the sodium channel Nav1.8 implicated by genome-wide association studies as a modulator of atrioventricular conduction (PR interval). In a cohort of patients with atrial fibrillation (AF), we examined whether there was an association between common variants in SCN10A and both the PR interval during normal sinus rhythm and the heart rate response during AF. METHODS AND RESULTS Patients prospectively enrolled in the Vanderbilt AF registry with electrocardiograms in normal sinus rhythm and/or AF within 1 year of enrollment were genotyped for two common SCN10A variants rs6795970 and rs12632942. Both variants were associated with the PR interval duration in a gene-dose effect on unadjusted analysis; after adjustment for the covariates age, gender, body mass index, hypertension, congestive heart failure, and medication usage, the association remained for rs6795970 only (P = 0.012, partial R(2) = 0.0139). On unadjusted analysis, heart rate response during AF was associated with rs6795970 (P = 0.035, partial R(2) = 0.015), but not with rs12632942 (P = 0.89), and neither association was significant after adjustment for covariates. CONCLUSION The common variant rs6795970 in SCN10A is associated with the PR interval duration among healthy patients and those with AF. In addition, this single nucleotide polymorphism trended towards an association with heart rate response during AF indicating the importance of this common SCN10A polymorphism as a marker of atrioventricular conduction.
Caspase-mediated Apoptotic Effects of Ebenus boissieri Barbey Extracts on Human Cervical Cancer Cell Line HeLa

Background: Ebenus boissieri Barbey is an Antalya, Turkey-endemic plant belonging to Fabaceae family. The aerial parts and the roots of E. boissieri Barbey were used in this study. Objective: In the present study, we have examined the apoptotic effects of hydroalcoholic extracts of E. boissieri Barbey in human cervical cancer cell line HeLa. Materials and Methods: To determine the cytotoxic effect, cells were treated with various concentrations of extracts for 24, 48, and 72 h incubation periods. Cytotoxic effects were examined by Cell Titer 96 aqueous nonradioactive cell proliferation assay and the results were corrected by live/dead viability/cytotoxicity assay and trypan blue exclusion assay. Apoptotic effects were studied with multicaspase kit. Tumor necrosis factor-alpha (TNF-α) and interferon gamma (IFN-γ) release were also measured by enzyme-linked immunosorbent assay. Results: According to the results, E. boissieri Barbey extract caused significant increase in caspase levels. Thus, we suggest that the extract induces cells to undergo apoptosis. Especially, there was a sharp induction in caspase-3 activity. Levels of both TNF-α and IFN-γ in extract-treated groups were significantly and dose dependently exalted as compared to their relative controls. Conclusion: The effects of the extract on caspase-3, TNF-α, and IFN-γ levels mediate the plausible mechanism of apoptosis induction in HeLa. To the best of our knowledge, this is the first report indicating any pharmacological properties of E. Boissieri on HeLa cells. Abbreviations used: Tumor necrosis factor-alpha (TNF-α); Interferon gamma (IFN-γ); 3-(4, 5 dimethylthiazol-2-yl)-5-(3- carboxymethoxy-phenyl)-2-(4-sulfonyl)-2H-tetrazolium (MTS); Phosphate-Buffered Saline (PBS); Fetal Bovine Serum (FBS); para-Nitroanilin pNA; Enzyme-Linked ImmunoSorbent Assay (ELISA); Sodium Dodesyl sulphate –Polyacrilamide gel electrophoresis (SDS-PAGE); Tris-Buffered Saline (TBS); Hydocloric acid (HCl); Standart Error of Mean (SEM); National Cancer Institute (NCI); half maximal inhibitory concentration (IC50)
Biochemical simulations: stochastic, approximate stochastic and hybrid approaches

Computer simulations have become an invaluable tool to study the sometimes counterintuitive temporal dynamics of (bio-)chemical systems. In particular, stochastic simulation methods have attracted increasing interest recently. In contrast to the well-known deterministic approach based on ordinary differential equations, they can capture effects that occur due to the underlying discreteness of the systems and random fluctuations in molecular numbers. Numerous stochastic, approximate stochastic and hybrid simulation methods have been proposed in the literature. In this article, they are systematically reviewed in order to guide the researcher and help her find the appropriate method for a specific problem.
OPTICAL SPECTROSCOPY AND VELOCITY DISPERSIONS OF GALAXY CLUSTERS FROM THE SPT-SZ SURVEY

We present optical spectroscopy of galaxies in clusters detected through the Sunyaev–Zel'dovich (SZ) effect with the South Pole Telescope (SPT). We report our own measurements of 61 spectroscopic cluster redshifts, and 48 velocity dispersions each calculated with more than 15 member galaxies. This catalog also includes 19 dispersions of SPT-observed clusters previously reported in the literature. The majority of the clusters in this paper are SPT-discovered; of these, most have been previously reported in other SPT cluster catalogs, and five are reported here as SPT discoveries for the first time. By performing a resampling analysis of galaxy velocities, we find that unbiased velocity dispersions can be obtained from a relatively small number of member galaxies (≲ 30), but with increased systematic scatter. We use this analysis to determine statistical confidence intervals that include the effect of membership selection. We fit scaling relations between the observed cluster velocity dispersions and mass estimates from SZ and X-ray observables. In both cases, the results are consistent with the scaling relation between velocity dispersion and mass expected from dark-matter simulations. We measure a ∼30% log-normal scatter in dispersion at fixed mass, and a ∼10% offset in the normalization of the dispersion–mass relation when compared to the expectation from simulations, which is within the expected level of systematic uncertainty.
4-Biphenylaldehyde and 9-anthraldehyde: two fluorescent substrates for determining P450 enzyme activities in rat and human

1. 4-Biphenylaldehyde (4-BA) and 9-anthraldehyde (9-AA) were examined as substrates for cytochrome P450 (CYPs) enzymes in rat and human. Both aldehydes were oxidized by CYPs to fluorescent carboxylic acids, which can be assayed with a high sensitivity by an easy fluorimetric method. 2. With liver microsomes from control and induced rats, the oxidation of both 9-AA and 4-BA followed simple Michaelis-Menten kinetics. Only microsomes from rats pretreated with phenobarbital (a strong inducer of P4502B1/2) could increase (about threefold) the oxidation rates (V max) of both aldehydes above the control values, which were 6.7 ± 1.1 and 3.3 ± 0.6 nmol min − 1 mg − 1 protein for 4-BA and 9-AA, respectively. On the other hand, the K m 's, which were similar for both aldehydes (about 25 µM), did not change significantly with any inducer. The use of purified rat CYP1A1, 2E1, 2B1 and 2C11 in a reconstituted system showed that only 2B1 and 2C11 could oxidize both substrates with a high turnover. 3. In human liver microsomes, the oxidation rates of these aldehydes (1.6 ± 0.2 and 0.42 ± 0.1 nmol min − 1 mg − 1 protein for 4-BA and 9-AA, respectively) were lower than those of rat but with similar K m 's(20-26 µm). 4. The oxidation of these aldehydes was also determined with cDNA-expressed CYP1A1, 1A2, 2A6, 2B6, 2C9, 2D6, 2E1 and 3A4 and with a characterized bank of 14 human liver microsomes. In a reconstituted system, only CYP2B6, 2A6, 3A4 and with a lower turnover 2C9 oxidized both substrates. 5. Among the CYP marker activities of the 14 human samples, good correlations were only observed between CYP3A-dependent 6 β -testosterone hydroxylase and the oxidation of 4-BA (r = 0.74) or 9-AA (r = 0.80) and between the oxidation of 4-BA versus 9-AA (r = 0.74). Weak correlations were also found between the 2B6-linked S-mephenytoin N- demethylase and the oxidation of 4-BA (r = 0.58) or 9-AA (r = 0.65). 6. Inhibition experiments revealed that the oxidation of these aldehydes was inhibited by ketoconazole, 8-methoxypsoralene and sulphophenazole, selective inhibitors for P4503A6, 2A6 and 2C9, respectively. 7. In summary, based on the use of cDNA-expressed CYPs, correlation analysis and chemical inhibition, the metabolism in human liver microsomes of these aldehydes appears primarily catalysed by CYP3A, although CYP2A6, 2B6 and 2C9 may play a role. 9-AA and particularly 4-BA, owing to the high rate of its metabolism, may be two novel useful fluorescent probe substrates for assaying CYP activities in various species.