Miracle-dz/UniFAR-FTUs huggingface dataset:
Circular RNAs (circRNAs) in Health and Disease

Splicing events do not always produce a linear transcript. Circular RNAs (circRNAs) are a class of RNA that are emerging as key new members of the gene regulatory milieu, which are produced by back-splicing events within genes. In circRNA formation, rather than being spliced in a linear fashion, exons can be circularised by use of the 3′ acceptor splice site of an upstream exon, leading to the formation of a circular RNA species. circRNAs have been demonstrated across species and have the potential to present genetic information in new orientations distinct from their parent transcript. The importance of these RNA players in gene regulation and normal cellular homeostasis is now beginning to be recognised. They have several potential modes of action, from serving as sponges for micro RNAs and RNA binding proteins, to acting as transcriptional regulators. In accordance with an important role in the normal biology of the cell, perturbations of circRNA expression are now being reported in association with disease. Furthermore, the inherent stability of circRNAs conferred by their circular structure and exonuclease resistance, and their expression in blood and other peripheral tissues in association with endosomes and microvesicles, renders them excellent candidates as disease biomarkers. In this review, we explore the state of knowledge on this exciting class of transcripts in regulating gene expression and discuss their emerging role in health and disease.
Anti‐HIV‐1 limonoid: first isolation from Clausena excavata

A limonoid, clausenolide‐1‐ethyl ether (1) and two coumarins, dentatin (2) and nor‐dentatin (3), were isolated from Clausena excavata. Limonoid 1 was obtained from the crude ethanol extract of the rhizomes and the roots but had not previously been isolated from C. excavata and exhibited HIV‐1 inhibitory activity. Coumarins 2 and 3, with their structures related to an anti‐HIV‐1 substance, (+)‐calanolide A (4), were obtained from the crude chloroform extract of the rhizomes. Both induced toxicity to cells used in a syncytium assay for anti‐HIV‐1 activity. These compounds, 1–3, did not show any cytotoxic effect against KB and BC‐1 cell lines (IC50 value > 20 µg/mL). Copyright © 2003 John Wiley & Sons, Ltd.
A Long Duration Transient Resilient Pipeline Scheme

Single event transients (SETs) in combinational logic remain an important topic in the reliability domain. SETs were traditionally relatively short in comparison to the clock period. The majority of the countermeasures utilizes this property. However, advances in technology scaling will reverse the ratio for complementary metal-oxide semiconductor devices. Investigations show that SETs may last up to multiple clock cycles in the future. So-called long duration transients (LDTs) corrupt almost all available countermeasures. This paper presents a new methodology to tackle LDTs. Dual modular redundancy (DMR) is used to detect any corruption of the application logic. A new micro-rollback scheme expands the DMR architecture with fault correction capabilities. The concept is also capable of handling single event upsets and timing violations. The correction penalty is two clock cycles. The approach was implemented and verified in a Viterbi decoder architecture. The scheme utilizes a newly designed History Cell. The History Cell introduces an area overhead of 97% and a power overhead of 110%, compared to a standard cell DFF.
Political Science and the Crisis of Authoritarianism

Political science is a discipline in constant danger of fragmentation because of the centrifugal pulls of our subfields and the contradictions in our scientific and humanistic traditions. We are, however, periodically brought together by the need to respond to major developments that are reshaping the political universe. We are today confronted with a unifying challenge in the crisis of authoritarianism that is undermining the legitimacy of all types of authoritarian systems throughout the world, including the Marxist-Leninist regimes. The crisis will not necessarily produce democracies, but rather a variety of part-free, part-authoritarian systems which do not conform to our classical typologies. Although the crisis of authoritarianism stems from profound social, economic, and cultural trends, the outcome in each case will be decided by political responses. Political science, therefore, has the responsibility to lead intellectually other social sciences in analyzing the fundamental change in political life that involves the clash between individual political cultures and the world culture of modernization.
Beyond Numbers

This article considers the impact of electoral quotas for women. Most studies have either focused on whether particular policies increase the numbers of women elected or assessed the extent to which a greater number of women in the legislature produces more gender-sensitive legislation. However, little attention has been paid to the cultural changes that can result from adopting gender quotas. This article argues that, although increasing the number of women in legislatures may improve the attention to gender issues, broader processes are involved. Latin American women's activism and alliances have been critical in ensuring the expansion of women's rights and increasing the number of women elected. Quotas, and the debate surrounding their adoption, have provided an incentive for women's collective action and fostered the politicization of gender issues. An analysis of the impact of quotas, therefore, must recognize these broader impacts.
A Branch-and-Cut Algorithm to Design LDPC Codes without Small Cycles in Communication Systems

In a digital communication system, information is sent from one place to another over a noisy communication channel using binary symbols (bits). Original information is encoded by adding redundant bits, which are then used by low--density parity--check (LDPC) codes to detect and correct errors that may have been introduced during transmission. Error correction capability of an LDPC code is severely degraded due to harmful structures such as small cycles in its bipartite graph representation known as Tanner graph (TG). We introduce an integer programming formulation to generate a TG for a given smallest cycle length. We propose a branch-and-cut algorithm for its solution and investigate structural properties of the problem to derive valid inequalities and variable fixing rules. We introduce a heuristic to obtain feasible solutions of the problem. Our computational experiments show that our algorithm can generate LDPC codes without small cycles in acceptable amount of time for practically relevant code lengths.
Activation of pig oocytes using nitric oxide donors

Nitric oxide (NO) plays an important role in intracellular signaling, but its role during the activation of mammalian oocytes is little understood. In our study, in vitro matured pig oocytes were cultured with NO‐donors—S‐nitroso‐N‐acetylpenicillamine (SNAP) or sodium nitropruside (SNP). These treatments were able to induce parthenogenetic activation of pig oocytes matured in vitro. The specificity of this effect was confirmed by the activation of oocytes by exogenous endothelial nitric oxide synthase (eNOS) microinjected in the oocyte with its activator calmodulin. Relatively long exposure (10 hr) is needed for activation of pig oocytes with 2.0 mM SNAP. An active NOS is necessary for the NO‐dependent activation of pig oocytes because NOS inhibitors L‐NMMA or L‐NAME are able to inhibit activation of oocytes with NO‐donor SNAP. On the basis of our data, we conclude that the NO‐dependent activating stimulus seems inadequate because it did not induce the exocytosis of cortical granules. Also, the cleavage of parthenogenetic embryos was very low, and embryos did not develop beyond the stage of eight blastomeres. Mol. Reprod. Dev. 71: 115–122, 2005. © 2005 Wiley‐Liss, Inc.
Recombination at subtelomeres is regulated by physical distance, double‐strand break resection and chromatin status

Homologous recombination (HR) is a conserved mechanism that repairs broken chromosomes via intact homologous sequences. How different genomic, chromatin and subnuclear contexts influence HR efficiency and outcome is poorly understood. We developed an assay to assess HR outcome by gene conversion (GC) and break‐induced replication (BIR), and discovered that subtelomeric double‐stranded breaks (DSBs) are preferentially repaired by BIR despite the presence of flanking homologous sequences. Overexpression of a silencing‐deficient SIR3 mutant led to active grouping of telomeres and specifically increased the GC efficiency between subtelomeres. Thus, physical distance limits GC at subtelomeres. However, the repair efficiency between reciprocal intrachromosomal and subtelomeric sequences varies up to 15‐fold, depending on the location of the DSB, indicating that spatial proximity is not the only limiting factor for HR. EXO1 deletion limited the resection at subtelomeric DSBs and improved GC efficiency. The presence of repressive chromatin at subtelomeric DSBs also favoured recombination, by counteracting EXO1‐mediated resection. Thus, repressive chromatin promotes HR at subtelomeric DSBs by limiting DSB resection and protecting against genetic information loss.
What are the limitations on the flux of syntactic dependencies? Evidence from UD treebanks

The aim of this paper is to study some characteristics of dependency flux, that is the set of dependencies linking a word on the left with a word on the right in a given position. Based on an exploration of the whole set of UD treebanks (12M word corpus), we show that what we have called the flux weight, which measures center embeddings, is less than 3 in 99.62 % of the inter-word positions and is bounded by 6, which could be due to short-term memory limitations.
Angiosperm Phylogeny Group (APG) in jeopardy – Where have the flowers gone?

The Angiosperm Phylogeny Group (APG) is a loose assemblage of systematic botanists aiming to establish a stable, modern classification system of flowering plants strongly based on molecular phylogenetics. The group published three seminal papers starting in 1998. An update to be entitled "APG IV" is in preparation and due shortly. A survey was conducted among systematic botanists in the forefront of this project, the results of which were recently published. The author of this Opinion Piece comments on the concept, evaluation, and results of this survey, and on the advice provided by the initiators, in particular regarding the order Boraginales. Expert opinion should be favored over a general majority vote on suggestive questions of an uncoordinated survey conducted by a single "authority". Science is based on knowledge and on scholarly expertise, and should not be made a matter of popular votes and majority preferences.
The Effect of Changes in the Federal Reserve's Policy Rule on the Stochastic Structure Linking Reserves, Interest Rates, and Money

In October 1979 the Federal Reserve announced a fundamental reform in its monetary control procedures [2]. The alleged rationale for abandoning the old procedures, utilized more or less continuously since 1970, was to improve the Fed's control over the growth of the monetary aggregates-the so-called intermediate policy targets. As often accompanies political and social reform, the spectrum of criticism of the Fed's alteration in procedures was wide. This criticism ranged from the charge that the Fed had gone too far, or alternatively had regressed, to, ironically, the charge that nothing had changed. Such competing contentions are in this case largely generated by the lack of incontrovertible evidence that monetary control improved after 1979 and the considerable increase in the volatility of interest rates which ensued.
Fractionation of nucleic acids into single-stranded and double-stranded forms

We describe a rapid and efficient procedure for the fractionation of mixtures of nucleic acids (NA) into double-stranded (ds) and single-stranded (ss) forms regardless of the nature of the nucleic acid (DNA or RNA). The procedure is based on the differential binding of dsand ss-NA forms to silica particles in different lysis/binding buffers which have in common that they contain a high concentration of the chaotropic agent guanidinium thiocyanate (GuSCN). Previously we reported on a procedure (protocol Y) for the routine purification of total NA from clinical specimens (1). The method is based on the lysing and nuclease-inactivating properties of the chaotropic agent GuSCN together with the NA-binding properties of silica particles (or diatoms) in the presence of this agent. Comparison of different GuSCN-containing lysis/binding buffers with respect to the binding of different NA-types to silica particles revealed that only ds-forms were bound when using lysis/binding buffer L11 (see below) whereas both dsand ss-forms were bound in lysis/binding buffer L6 (1). This observation formed the basis for the development of a procedure (protocol R) for the fractionation of mixtures of ssand ds-NA. The procedure is summarised in Figure 1. A 50 μl specimen (containing a mixture of NA-types in TE buffer) was added to a mixture of 900 μl lysis/binding buffer L11 and 40 μl size-fractionated silica particles (SC) in an Eppendorf tube and subsequently homogenized by vortexing. After a 10 min binding step at room temperature, the tube was centrifuged (2 min at ∼12 000 g) which resulted in a silica/ds-NA pellet (‘initial silica pellet’) and a supernatant containing ss-NA. To recover ss-NA forms (protocol R-sup) 900 μl of the supernatant were added to a mixture of 400 μl binding buffer L10 (see below) and 40 μl SC. Thereafter the ss-NA was bound during a 10 min binding step at room temperature. The tube was subsequently centrifuged (15 s at ∼12 000 g), and the supernatant discarded (by suction). The resulting pellet was subsequently washed twice with 1 ml of washing buffer L2 (1), twice with 1 ml ethanol 70% (vol/vol) and once with 1 ml acetone. The silica pellet was dried (10 min at 56 C with open lid in an Eppendorf heating block) and eluted (10 min at 56 C; closed lid) in 50 μl TE buffer (10 mM Tris–HCl, 1 mM EDTA, pH 8.0). After centrifugation (2 min at ∼12 000 g) the supernatant contained the ss-NA fraction. To recover ds-NA forms (protocol R-pellet) from the initial silica-pellet, the remaining supernatant was discarded, and the silica pellet was washed twice with 1 ml lysis/binding buffer L11 to remove unbound ss-NA. The resulting silica pellet Figure 1. Outline of protocol R. Recovery of ds-NA takes place from the initial pellet (R-pellet), recovery of ss-NA takes place from the initial supernatant (R-sup). L11, L10, L6 and L2 are GuSCN containing buffers; SC is silica particle suspension. For details see text.
An impulse oscillometry system is less efficient than spirometry in tracking lung function improvements after intravenous antibiotic therapy in pediatric patients with cystic fibrosis

A literature search identified one retrospective study on the responsiveness of impulse oscillometry (IOS) in pediatric patients with cystic fibrosis. The aim of this prospective observational study was to assess this property in an adequately powered study after intravenous antibiotic therapy (IVAT) administered for an acute episode of pulmonary exacerbation. Spirometry and IOS were done on the same day as the start and the end of IVAT. Data from 34 patients’ of mean age 11.9 years (range, 5–17 years) were studied. The mean FEV1 at the start and at the end of the IVAT was 73.1 ± 23.8% (range, 23.4–122%) and 88.3 ± 21.3% (range, 29.4–131%), respectively. The mean relative change (mean ± SD) was 20.2 ± 14.2% for FEV1 (ΔFEV1), −21.9 ± 23.8% for reactance at 5 Hz (ΔX5) and –13.4 ± 18.9% for resistance at 5 Hz (Δ R5) (all P‐values <0.05). There was a weak but significant correlation between ΔFEV1 and ΔX5 (r =–0.473; p = 0.01). The magnitude of improvement of ΔX5 was not statistically different between patients with normal versus abnormal lung function at the start of IVAT. Furthermore, using ΔX5 alone as an outcome measure of IVAT efficiency resulted in a significant improvement in 44% of the patients, while it was 79% with ΔFEV1. These results indicate that IOS may track changes after IVAT, but that this improvement may be insufficiently evaluated using IOS alone. Pediatr Pulmonol. 2015; 50:1073–1081. © 2015 Wiley Periodicals, Inc.
Absence of PCR-detectable human papilloma virus in erythroplasia of Queyrat using a comparative control group

Objectives High-risk human papillomavirus (HPV) types have been linked with genital carcinomas. However, the exact relation between HPV and erythroplasia of Queyrat (EQ), for example, in-situ carcinoma of the glans and prepuce, is still unclear. Thw aim of this study was to detect the presence of lesional HPV-DNA in patients with EQ. Methods Paraffin-embedded biopsies were obtained from the glans or inner foreskin of 11 adult uncircumcised patients (mean age 67.7 years; range 57–79) with EQ. An equal number of randomly selected uncircumcised healthy control patients underwent a single brush cytology smear of the penile mucosa. Biopsy specimens and brushings were then assayed by a highly sensitive two-step nested PCR technique based on MY11/MY09 consensus primers and general GP5+/GP6+ PCR primers, followed by cycle sequencing. Statistical evaluation was performed using conditional logistic regression analysis. Results None of the EQ or control samples proved to be positive for the presence of HPV-DNA. Conclusions The findings do not support the hypothesis that there is a considerable risk of EQ development in patients with HPV infection. The prevalence of HPV infection in patients with EQ has rarely been investigated and available data are relatively scant and controversial. Therefore, the relation between HPV infection and the risk of progression of EQ into squamous cell carcinoma remains a matter of debate, and further investigations are needed in order to confirm the role of HPV in delineating this risk.
Parametric Control of National Economy within the Framework of Regional Customs Union

Econometric estimates were obtained in the form of a regression function of the main macroeconomic indicators, included in the terms of equilibrium of the macroeconomic markets of national economy (by example of the economy of the Republic of Kazakhstan) within the framework of its operation as a part of regional customs union and interaction with the rest of the world. Based on the checked for spurious regressions functions the econometric model was built for open small economy of the Republic of Kazakhstan and its sustainability indicator was evaluated. Macroeconomic analysis has been conducted on the basis of econometric models. Proposed and illustrated an approach of estimating the optimal values of economic policy instruments in the functioning of the national economy within the regional customs union and its interaction with the outside world.
Impact of a peer-delivered telephone intervention for women experiencing a breast cancer recurrence.

PURPOSE A first breast cancer recurrence creates considerable distress, yet few psychosocial interventions directed at this population have been reported. The Southwest Oncology Group conducted a phase III randomized trial to evaluate the effectiveness of a brief telephone intervention. PATIENTS AND METHODS Three hundred five women experiencing a first recurrence of breast cancer were randomly assigned to standard care or intervention. The intervention consisted of four to eight telephone calls delivered over a 1-month period. The calls were conducted by trained peer counselors at a breast cancer advocacy organization, the Y-ME National Breast Cancer Organization, and followed a standard curriculum. Psychosocial distress (Cancer Rehabilitation Evaluation System-Short Form [CARES-SF]) and depressive symptoms (Center for Epidemiologic Studies Depression Scale [CES-D]) outcomes were assessed at baseline and 3 and 6 months. The 3-month assessment was the primary end point and is the focus of this article. RESULTS Analysis revealed no differences in distress or depressive symptoms at 3 months between the intervention and control groups; at 3 months, 70% of control patients and 66% of intervention patients reported psychosocial distress, and 40% of control patients and 47% of intervention patients exhibited depressive symptoms. CONCLUSION Telephone peer counseling did not lead to better psychosocial outcomes. The persistent distress in these women supports the urgent need for the development and testing of more intensive or different supportive interventions for this group of patients.
Metaanalysis as an epidemiological tool and its application to studies of chromium.

Metaanalysis is a technique for combining the results of similar studies to arrive at a single estimate of effect or risk. It is of proven value in the field of clinical trials but its use as an epidemiological tool is less well established. The principal obstacles to the valid use of metaanalysis are lack of consistency in the design, conduct and analysis of studies, publication bias, and reporting bias. Metaanalysis has been used to question whether an excess of lung cancer is associated with postmodification production of chromates and whether tumors of any site other than the lung are associated with any level of chromium exposure. The metaanalysis of lung cancer postmodification did not show a statistically significant excess, but the combined studies lacked the statistical power to exclude the possibility of a continuing risk of moderate size. The data in the literature for tumors at sites other than the lung were too impaired by heterogeneity of reporting and reporting bias for metaanalysis to be applied with any validity. A more uniform approach to the planning and reporting of studies is essential if metaanalysis is to gain credibility as an epidemiological tool.
AGRONOMIC PERFORMANCE OF RADISH GENOTYPES UNDER DIFFERENT IRRIGATION DEPTHS

In radish production, the choice of proper genotypes and irrigation regime is of great importance to achieve success. In light of this, the current study aimed to evaluate the agronomic performance of a few radish genotypes under different irrigation strategies. The plants were grown in the city of Unaí MG, in Brazil, under field conditions, and during two cycles, one of 40 days (from February 28 to April 8, 2015) and other of 51 days (from May 9 to June 28, 2015). The experimental design was a randomized block design in a split-plot arrangement with four replications. The treatments consisted of four irrigation strategies (50, 75, 100, and 125% of crop evapotranspiration ETc) applied by a dripping irrigation system, while subplots consisted of three radish cultivars (Comet, Saxa, and Crimson Giant). We evaluated the following parameters: root system depth, leaf chlorophyll content, shoot fresh matter, diameter and length of tuberous root, number, and mass of commercial and non-commercial tuberous roots, and water use efficiency. All the radish genotypes showed no differences for agronomic characteristics. Under Brazilian Cerrado conditions, the most suitable irrigation strategy for radish crops is 100% of ETc.