Miracle-dz/UniFAR-FTUs huggingface dataset:
Emerging Views on the CTD Code

The C-terminal domain (CTD) of RNA polymerase II (Pol II) consists of conserved heptapeptide repeats that function as a binding platform for different protein complexes involved in transcription, RNA processing, export, and chromatin remodeling. The CTD repeats are subject to sequential waves of posttranslational modifications during specific stages of the transcription cycle. These patterned modifications have led to the postulation of the “CTD code” hypothesis, where stage-specific patterns define a spatiotemporal code that is recognized by the appropriate interacting partners. Here, we highlight the role of CTD modifications in directing transcription initiation, elongation, and termination. We examine the major readers, writers, and erasers of the CTD code and examine the relevance of describing patterns of posttranslational modifications as a “code. ” Finally, we discuss major questions regarding the function of the newly discovered CTD modifications and the fundamental insights into transcription regulation that will necessarily emerge upon addressing those challenges.
HIV-1 Capsid-Targeting Domain of Cleavage and Polyadenylation Specificity Factor 6

ABSTRACT The antiviral factor CPSF6-358 restricts human immunodeficiency virus type 1 (HIV-1) infection through an interaction with capsid (CA), preventing virus nuclear entry and integration. HIV-1 acquires resistance to CPSF6-358 through an N74D mutation of CA that impairs binding of the antiviral factor. Here we examined the determinants within CPSF6-358 that are necessary for CA-specific interaction. Residues 314 to 322 include amino acids that are essential for CPSF6-358 restriction of HIV-1. Fusion of CPSF6 residues 301 to 358 to rhesus TRIM5α is also sufficient to restrict wild-type but not N74D HIV-1. Restriction is lost if CPSF6 residues in the amino acid 314 to 322 interaction motif are mutated. Examination of the CA targeting motif in CPSF6-358 did not reveal evidence of positive selection. Given the sensitivity of different primate lentiviruses to CPSF6-358 and apparent conservation of this interaction, our data suggest that CPSF6-358-mediated targeting of HIV-1 could provide a broadly effective antiviral strategy.
Association between nonsteroidal anti-inflammatory drugs and upper gastrointestinal tract bleeding/perforation: an overview of epidemiologic studies published in the 1990s.

BACKGROUND In the last decades, studies have estimated the upper gastrointestinal tract bleeding/perforation (UGIB) risk associated with individual nonsteroidal anti-inflammatory drugs (NSAIDs). Later analyses have also included the effect of patterns of NSAID use, risk factors for UGIB, and modifiers of NSAID effect. METHODS Systematic review of case-control and cohort studies on serious gastrointestinal tract complications and nonaspirin NSAIDs published between 1990 and 1999 using MEDLINE. Eighteen original studies were selected according to predefined criteria. Two researchers extracted the data independently. Pooled relative risk estimates were calculated according to subject and exposure characteristics. Heterogeneity of effects was tested and reasons for heterogeneity were considered. RESULTS Advanced age, history of peptic ulcer disease, and being male were risk factors for UGIB. Nonsteroidal anti-inflammatory drug users with advanced age or a history of peptic ulcer had the highest absolute risks. The pooled relative risk of UGIB after exposure to NSAIDs was 3.8 (95% confidence interval, 3.6-4.1). The increased risk was maintained during treatment and returned to baseline once treatment was stopped. A clear dose response was observed. There was some variation in risk between individual NSAIDs, though these differences were markedly attenuated when comparable daily doses were considered. CONCLUSIONS The elderly and patients with a history of peptic ulcer could benefit the most from a reduction in NSAID gastrotoxicity. Whenever possible, physicians may wish to recommend lower doses to reduce the UGIB risk associated with all individual NSAIDs, especially in the subgroup of patients with the greatest background risk.
Molecular detection of thyroglobulin mRNA transcripts in peripheral blood of patients with thyroid disease by RT-PCR

The sensitive detection of circulating tumour cells in patients with differentiated thyroid cancer may precede the detection of relapse by other diagnostic studies – such as serum thyroglobulin – and thus may have important therapeutic and prognostic implications. We performed reverse transcription-polymerase chain reaction (RT-PCR) on blood samples from patients diagnosed with thyroid disease using two different RT-PCR sensitivities. Additionally, tissue specificity of TG mRNA-expression was determined using RNA extracts from 27 different human tissues. The lower limit of detection was 50–100 TG mRNA producing cells/ml blood using a ‘normal’ RT-PCR sensitivity and 10–20 cells/ml blood using a ‘high’ sensitivity. With the normal sensitivity TG mRNA was detected in 9/13 patients with thyroid cancer and metastasis, 63/137 patients with a history of thyroid cancer and no metastasis, 21/85 with non-malignant thyroid disease and 9/50 controls. With the high sensitivity TG mRNA was detected in 11/13 patients with thyroid cancer and metastasis, 111/137 patients with a history of thyroid cancer and no metastasis, 61/85 with non-malignant thyroid disease and 41/50 controls. Interestingly, using the normal RT-PCR sensitivity TG mRNA transcripts are specific for thyroid tissue and detectable in the peripheral blood of controls and patients with thyroid disease, which correlates with a diagnosis of metastasized thyroid cancer. However, with a high RT-PCR sensitivity, TG mRNA expression was found not to be specific for thyroid tissue and was not correlated with a diagnosis of thyroid cancer in patients. As a consequence, to date TG mRNA detected by RT-PCR in the peripheral blood cannot be recommended as a tumour marker superior to TG serum-level. © 2000 Cancer Research Campaign
Grensk Culture in Eastern Belarus: The Current State of Research

The article deals with the main range of problems of Grensk culture in the Final Palaeolithic and Mesolithic in the Upper Dnieper region. At present, the understanding of the ways and mechanisms of the formation and the time of habitation of members of this ancient culture are rather debatable. Interpretations of the sources have resulted in two completely different research approaches in terms of methodology, bringing together supporters of the indigenous (U. Budzko, V. Kapytsin, A. Kalechyts, G. Sinitsyna, etc) or migration (L. Zaliznyak, U. Ksiandzou, A. Sorokin, etc) ways of the emergence and the development of Grensk culture. It is impossible to understand the essence of the ‘Grensk question’ without considering the nature of its origin, the problem looked at in this article. Key words: Final Palaeolithic and Mesolithic, Grensk culture, eastern Belarus, Upper Dnieper region, asymmetrical shouldered points, Ienevo culture, Pesochny Rov culture. DOI: http://dx.doi. org/10.15181/ab.v25i0. 1828
Randomized evaluation of anticoagulation versus antiplatelet therapy after coronary stent implantation in high-risk patients: the multicenter aspirin and ticlopidine trial after intracoronary stenting (MATTIS).

BACKGROUND Although the association of ticlopidine and aspirin has been shown to be superior to anti-vitamin K agents and aspirin after coronary stent implantation in low-risk patients, the latter combination has remained an unproven reference regimen for high-risk patients until recently. METHODS AND RESULTS We randomized 350 high-risk patients within 6 hours after stent implantation to receive during 30 days either aspirin 250 mg and ticlopidine 500 mg/d (A+T group) or aspirin 250 mg/d and oral anticoagulation (A+OAC group) targeted at an international normalized ratio of 2.5 to 3. The primary composite end point was defined as the occurrence of cardiovascular death, myocardial infarction, or repeated revascularization at 30 days. Patients were eligible if (1) the stent(s) were implanted to treat abrupt closure after PTCA; (2) the angiographic result after implantation was suboptimal; (3) a long segment was stented (>45 mm and/or >/=3 stents); or (4) the largest balloon inflated in the stent had a nominal diameter of </=2.5 mm. The primary cardiac end point was reached for 10 patients (5.6%) in the A+T group and 19 (11%) in the A+OAC group (relative risk [RR], 1. 9; 95% CI, 0.9 to 4.1; P=0.07). Major vascular and bleeding complications were less frequent in the A+T group (3 patients, 1.7%) than in the A+OAC group (12 patients, 6.9%) (RR, 4.1; 95% CI, 1.2 to 14.3; P=0.02). CONCLUSIONS High-risk patients should be treated with A+T rather than A+OAC after coronary stenting because the bleeding and vascular complications are significantly reduced and there is a marked trend suggesting a decrease in cardiac events.
Pre-post effect sizes should be avoided in meta-analyses

Aims The standardised mean difference (SMD) is one of the most used effect sizes to indicate the effects of treatments. It indicates the difference between a treatment and comparison group after treatment has ended, in terms of standard deviations. Some meta-analyses, including several highly cited and influential ones, use the pre-post SMD, indicating the difference between baseline and post-test within one (treatment group). Methods In this paper, we argue that these pre-post SMDs should be avoided in meta-analyses and we describe the arguments why pre-post SMDs can result in biased outcomes. Results One important reason why pre-post SMDs should be avoided is that the scores on baseline and post-test are not independent of each other. The value for the correlation should be used in the calculation of the SMD, while this value is typically not known. We used data from an ‘individual patient data’ meta-analysis of trials comparing cognitive behaviour therapy and anti-depressive medication, to show that this problem can lead to considerable errors in the estimation of the SMDs. Another even more important reason why pre-post SMDs should be avoided in meta-analyses is that they are influenced by natural processes and characteristics of the patients and settings, and these cannot be discerned from the effects of the intervention. Between-group SMDs are much better because they control for such variables and these variables only affect the between group SMD when they are related to the effects of the intervention. Conclusions We conclude that pre-post SMDs should be avoided in meta-analyses as using them probably results in biased outcomes.
Whole blood viscosity assessment issues IV: Prevalence in acute phase inflammation

Background: Hyperviscosity syndrome has been suggested as not simply an acute reaction. Yet, erythrocyte sedimentation rate is associated with whole blood viscosity and it is an indirect acute phase inflammation marker. Aims: This work investigates the prevalence of hyperviscosity in acute phase inflammation. Materials and Methods: Archived clinical pathology data for the period of 1999 to 2008 were utilized. 40,632-cases tested for C-reactive protein and/or erythrocyte sedimentation rate from five alternate years, which were concomitantly tested for haematocrit and total proteins, were extracted. The prevalence of abnormal viscosity associated with positive results of C-reactive protein and erythrocyte sedimentation rate were evaluated. Results: Hyperviscosity is infrequently associated with positive C-reactive protein (2.9%) and erythrocyte sedimentation rate (2.7%) sub-populations, and are not statistically different from their respective negative sub-populations. Normoviscosity is significantly more prevalent in the positive sub-populations (p < 0.01). Further analyses indicate that prevalence of acute phase inflammation is statistically significantly less in hyperviscosity compared to normoviscosity sub-population (p < 0.00001). Actual blood viscosity level increases with level of inflammation though. Conclusion: The study demonstrates that although blood viscosity level may increase with inflammation, hyperviscosity is not frequent in, or sensitive to acute phase inflammation. It portends that whole blood viscosity is not unspecific as acute phase inflammation markers. It calls for clinicians to consider utilizing whole blood viscosity in disease conditions where stasis is implicated, in which it is specific and valuable. It would also benefit to establish whether hyperviscosity is a chronic phase inflammation marker.
Release of repetitive nuclear RNA into the cytoplasm in liver of rats fed 3'-methyl-4-dimethylaminoazobenzene.

Metabolically active 3.5S RNA bound to nonhistone chro mosomal proteins is one of the low-molecular-weight nuclear RNA's present in rat liver. The nucleotide sequences of this RNA are copied from repetitive DNA and are found in the chromatin of liver from normal rats. In rats fed 3'-methyl-4dimethylaminoazobenzene (3'-MeDAB) for 1, 3, or 10 weeks, approximately 17% of the nucleotide sequences of this RNA is released into the cytoplasm of the liver cells as parts of larger RNA molecules. With continuous feeding of the azocarcinogen, additional sequences of this nuclear RNA are released from the nuclei. After 16 weeks of feeding, approximately 35% of the total nucleotide sequences of this RNA is found in the cyto plasm. No release of this nuclear RNA into the cytoplasm was observed in control animals fed noncarcinogenic aminoazobenzene. The process initiated by the azocarcinogen which leads to the appearance in the cytoplasm of the nucleotide sequences of this RNA is irreversible, and it continues even when the feeding of the azocarcinogen was interrupted after 10 weeks. Toxic effects of the azocarcinogen in the liver cells result in temporary changes in the cell population of the liver. In our system, the largest changes were observed after 10 weeks of feeding 3'-MeDAB when many of the hepatocytes were larger than normal and when the majority of the hepato cytes had enlarged nuclei and an altered appearance of the chromatin. With continuous feeding of 3'-MeDAB, the changes in liver morphology characteristic for animals fed 3'-MeDAB for 10 weeks become less pronounced, and the liver of animals fed 3'-MeDAB for 17 weeks resembled morphologically the liver of control animals. The release of the nucleotide se quences does not appear to be related directly to the morpho logical changes in the liver observed during the early stages of the feeding of 3'-MeDAB.
Application of satellite radar interferometry (PSINSAR) in analysis of secondary surface deformations in mining areas case studies from Czech Republic and Poland

Secondary deformations are ground movements occurring in areas of ceased underground mining. These are associated with delayed readjustment of rock mass resulting in subsidence, discontinuous deformations (sinks, cracks, etc.) due to destruction of underground, usually shallow, workings, and elevation of ground surface in response of rock mass to rising groundwater levels following the end of mine water drainage. Comparative analysis of secondary deformations in two former mining areas in the first period after cessation of underground hard coal mining is the subject of this study. We used ERS-1/2 and Envisat satellite radar interferometry data processed with PSInSAR technique and GIS to map vertical (in satellite’s line of sight, LOS) movements of the surface and analyse them in relation to location of coal fields and underground water table rise. In the study, two areas have been compared, the Ostrava city in the Czech part of the Upper Silesian Basin and the Wałbrzych Coal Basin in Poland. The results of analyses based on the results of PSInSAR processing between 1995 and 2000 for the Wałbrzych site indicate uplift (up to +12 mm/year) in closed parts of coal fields and subsidence (up to –8 mm/year) in areas of declining mining. Results of PSInSAR analysis over the Ostrava site indicate decaying subsidence after mine closures in the rate of up to -6 mm/year during 1995-2000. Residual subsidence and gentle uplift have been partly identified at surroundings of closed mines in Ostrava from 2003-2010 Envisat data. In Wałbrzych gentle elevation has been determined from 2002 to 2009 in areas previously subsiding. ARTICLE INFO
Removing ECG Artifact from the Surface EMG Signal Using Adaptive Subtraction Technique

Background: The electrocardiogram artifact is a major contamination in the electromyogram signals when electromyogram signal is recorded from upper trunk muscles and because of that the contaminated electromyogram is not useful. Objective: Removing electrocardiogram contamination from electromyogram signals. Methods: In this paper, the clean electromyogram signal, electrocardiogram artifact and electrocardiogram signal were recorded from leg muscles, the pectoralis major muscle of the left side and V4, respectively. After the pre-processing, contaminated electromyogram signal is simulated with a combination of clean electromyogram and electrocardiogram artifact. Then, contaminated electromyogram is cleaned using adaptive subtraction method. This method contains some steps; (1) QRS detection, (2) formation of electrocardiogram template by averaging the electrocardiogram complexes, (3) using low pass filter to remove undesirable artifacts, (4) subtraction. Results: Performance of our method is evaluated using qualitative criteria, power spectrum density and coherence and quantitative criteria signal to noise ratio, relative error and cross correlation. The result of signal to noise ratio, relative error and cross correlation is equal to 10.493, 0.04 and %97 respectively. Finally, there is a comparison between proposed method and some existing methods. Conclusion: The result indicates that adaptive subtraction method is somewhat effective to remove electrocardiogram artifact from contaminated electromyogram signal and has an acceptable result.
Fourier series and estimation on the circle with applications to synchronous communication-I: Analysis

A wide variety of continuous- and discrete-time estimation problems on the circle S^1 are considered with the aid of Fourier series analysis. Measurement and diffusion update equations are derived for the conditional expectation of certain functions of the parameter to be estimated, and we investigate the use of Fourier series to obtain easily implemented optimal estimation equations. A variety of important examples--phase tracking, frequency demodulation, and phase demodulation in the presence of oscillator instabilities, additive noise, Rayleigh fading, or any combination of these--are considered.
LC-MS identification and preparative HPLC isolation of Frankenia pulverulenta phenolics with antioxidant and neuroprotective capacities in PC12 cell line

Abstract Context: Frankenia pulverulenta L. (Frankeniaceae) is a medicinal species with carminative, analgesic and antiviral properties. However, phytochemical investigations, antioxidant and neuroprotective capacities of this plant remain unclear. Objective: This work assesses the phenolic composition of F. pulverulenta shoot and root and evaluates their antioxidant and neuroprotective capacities. Materials and methods: Successive fractionation of F. pulverulenta shoot and root using 6 solvents were used. Antioxidant capacity of these fractions was assessed through four in vitro tests (DPPH, ABTS, Fe-chelating activity and ORAC). Phenolic identification, purification as well as neuroprotective activity of ethyl acetate (EtOAc) fraction and purified molecules were assessed. Results: Among the tested fractions, EtOAc shoot and root fractions possessed considerable phenolic contents (383 and 374 mg GAE/g E, respectively) because of their important ORAC (821 and 1054 mg of TE/g E), DPPH (586 and 750 mg of TE/g) and ABTS (1453 and 1319 mg of TE/g) results. Moreover, gallic acid, quercetin, quercetin galloyl glucoside, trigalloyl hexoside, procyanidin dimers and sulfated flavonoids were identified by LC-DAD-ESI-MS for the first time in this species. The relevant cytoprotective capacity (at 300 μg/mL) against β-amyloid peptide induced toxicity in PC12 cells of EtOAc fractions were corroborated with the chemical composition. In addition, purified molecules were tested for their ORAC and neuroprotective activity. Quercetin showed the best ORAC value (33.55 mmol TE/g polyphenols); nevertheless, procyanidin dimer exhibited an exceptionally efficient neuroprotective activity (100% of viability at 50 μg/mL). Discussion and conclusions: These findings suggest that this halophyte is a promising source of antioxidant and neuroprotective molecules for pharmaceutical purposes.
Diurnal, seasonal, and sex patterns of heart rate in grip-restrained African giant rats (Cricetomys gambianus, Waterhouse)

This study was carried out to determine heart rate (HR) values, including diurnal, seasonal, and sex patterns, in the African giant rat (Cricetomys gambianus, Waterhouse). HR was measured using stethoscope in grip‐restrained African giant rats of either sex (103 bucks and 98 does), live‐trapped from a tropical Savannah, and caged individually in the laboratory during the harmattan (cold‐dry), hot‐dry, and rainy seasons over a 3‐year period. The HR fluctuated between 90 and 210 beats per minute (bpm) throughout the study period. Diurnal changes in HR (mean ± SEM) during the hot‐dry and rainy seasons were nonsignificant (P > 0.05), but the morning and afternoon values differed (P < 0.01) during the cold‐dry season. The HR varied (P < 0.05) among seasons, with peak, nadir, and moderate values recorded during the cold‐dry (165.8 ± 0.51 bpm), hot‐dry (153.1 ± 0.74 bpm), and rainy (163.4 ± 0.70 bpm) seasons, respectively. Mean HR of bucks was lower than that of does during the cold‐dry (P < 0.0001) and hot‐dry (P < 0.01) seasons, but sex difference during the rainy season was insignificant (P > 0.05). Overall, mean HR was lower (P < 0.0001) in bucks (158.8 ± 0.53 bpm) than in does (164.8 ± 0.53 bpm). In conclusion, values of HR in African giant rats are shown for the first time. Season, sex, and daytime influenced the HR, and should be considered during clinical evaluations of the rats.
Constructing prototypes from large databases

This paper illustrates the use of the model, established in previous papers, enabling to construct different kinds of measures of comparison according to wished properties, as well as to classify the existing measures according to their properties. So, this model helps to choose (or to construct) an appropriate measure for the considered problem. This paper especially looks into the list of measures of comparison in the construction of fuzzy prototypes and then in prototype-based reasoning.
The intrinsic resistance of Escherichia coli to various antimicrobial agents requires ppGpp and σs

We have examined the effect of a wide range of antimicrobial compounds (antibiotics and biocides) on the growth of various strains of Escherichia coli which vary in their ability to produce ppGpp and σs. We conclude that strains able to synthesize ppGpp, either in a RelA‐ or SpoT‐dependent manner, possess a greater resistance to antimicrobial compounds compared with strains that cannot produce ppGpp. Investigation of an E. coli strain, unable to produce σs, and an isogenic parent strain, suggests that there is a requirement for this sigma factor in increased expression of intrinsic resistance. We propose that ppGpp is required to induce production of σs, which in turn directs gene expression of intrinsic resistance determinants.