Miracle-dz/UniFAR-FTUs huggingface dataset:
Architecture of the DNA polymerase B-proliferating cell nuclear antigen (PCNA)-DNA ternary complex

DNA replication in archaea and eukaryotes is executed by family B DNA polymerases, which exhibit full activity when complexed with the DNA clamp, proliferating cell nuclear antigen (PCNA). This replication enzyme consists of the polymerase and exonuclease moieties responsible for DNA synthesis and editing (proofreading), respectively. Because of the editing activity, this enzyme ensures the high fidelity of DNA replication. However, it remains unclear how the PCNA-complexed enzyme temporally switches between the polymerizing and editing modes. Here, we present the three-dimensional structure of the Pyrococcus furiosus DNA polymerase B-PCNA-DNA ternary complex, which is the core component of the replisome, determined by single particle electron microscopy of negatively stained samples. This structural view, representing the complex in the editing mode, revealed the whole domain configuration of the trimeric PCNA ring and the DNA polymerase, including protein–protein and protein–DNA contacts. Notably, besides the authentic DNA polymerase-PCNA interaction through a PCNA-interacting protein (PIP) box, a novel contact was found between DNA polymerase and the PCNA subunit adjacent to that with the PIP contact. This contact appears to be responsible for the configuration of the complex specific for the editing mode. The DNA was located almost at the center of PCNA and exhibited a substantial and particular tilt angle against the PCNA ring plane. The obtained molecular architecture of the complex, including the new contact found in this work, provides clearer insights into the switching mechanism between the two distinct modes, thus highlighting the functional significance of PCNA in the replication process.
A novel closed-form estimator for 3D source localization using angle of arrivals and gain ratio of arrivals

This paper presents a new closed-form solution for 3D source localization using the hybrid measurements of angles of arrival and gain ratios of arrival. Under the small Gaussian noise condition, we linearize the hybrid measurement equations to obtain a weighted least-squares solution and then the mean-square error matrix of the proposed method is derived. Theoretical analysis and simulations show that the proposed estimator can achieve the Cramer-Rao bound over the small error region.
A map-based visual analysis method for patterns discovery of mobile learning in education with big data

Big data in education relate closely to a wealth of activities from the teachers, students and parents, as well as a substantial resources of knowledge that can be represented in hierarchical structures. The activities have characteristic of geolocation which can be projected onto a map, while the resources of knowledge can also be converted into the map. A map-based management and visual analysis method will largely benefit the users and the researchers from taking advantages of the big data in education. In this paper, we propose a novel map based method to manage and analyze the big data of mobile learning in education. With this method, the activities of users scattered among the space are reorganized on a geographic map with location changes in time series, and the resources are geo-tagged with the information from the developers or adopters, which are converted to a map style according to their hierarchical structures even when the users' information are unavailable. We first present the basic framework to organize the data by a map-based technology, and then a platform is proposed to perform the visual analysis. The method is adapt to the construction of massive online learning system and the mobile learning system of Central China Normal University to serve a national wide big data cloud learning program.
Performance Analysis of COOPERATIVEOFDM Systems

Orthogonal frequency division multiplexing (OFDM) is becoming the chosen modulation technique for wireless communications. OFDM can provide high data rate, large spectrum efficiency with sufficient robustness to radio channel impairments. Cooperative diversity in wireless communication is a promising technique to mitigate multi-path fading, which results in a fluctuation in the amplitude of the received signal. This work combines the features of both OFDM and cooperative communication thereby achieving a better system performance in terms of the bit error rate.
Use of the serum-opacity reaction in the typing of group-A streptococci.

Summary A large collection of group-A streptococci was examined for the production of opacity in horse serum and for the presence of M and T antigens. Opacity production is a constant character of certain M types and is consistently absent from the rest. Testing for opacity production is a valuable addition to the serological typing procedure especially if it is carried out first. It has proved useful in (1) reducing the number of tests with M antisera that have to be set up and (2) drawing attention to errors in M typing due to the presence of cross-reacting precipitins in typing sera. The serological specificity of the opacity factor corresponds to that of the M antigen. Inhibition of opacity production therefore provides a useful alternative method of typing strains that form the opacity factor. M antisera for opacity-producing serotypes are often of poor quality and difficult to prepare. In these circumstances, the opacity inhibition test has proved useful for preliminary identification of new M types of streptococci.
History and principles of patient navigation

In 1971 President Richard Nixon declared a war on cancer and signed the National Cancer Act. During the past several decades since this declaration, the nation has made extraordinary progress toward a far better understanding of the molecular, cellular, and genetic changes resulting in cancer. We have also seen significant declines in overall and site-specific cancer mortality1. This decline in mortality has been attributed to improved cancer prevention, screening, and detection measures as well as the application of more effective and more targeted cancer treatments. However, some Americans (such as the poor, uninsured, and underinsured) have not shared sufficiently in this progress as measured by higher mortality, lower survival, and 5-year cancer survival2, 3. These findings suggest that there is a disconnect between the nation’s discovery and delivery enterprises; a disconnect between what we know and what we do (Fig 1). Figure 1 Discovery-Delivery Disconnect Disparities occur when beneficial medical interventions are not shared by all. Moreover, health disparities arise from a complex interplay of economic, social, and cultural factors. The model presented in (Fig. 2) illustrates the overlapping factors of poverty, culture, and social injustice as principal causes of health disparities. These causal factors impact on all aspects of the healthcare continuum from prevention, detection, diagnosis, treatment, and survival to the end of life. Disparities occur principally in individuals or populations who experience one or more of the following circumstances: insufficient resources, risk-promoting lifestyle and behavior, and social inequities. Approaches to reducing or eliminating disparities must necessarily take these factors into consideration. Figure 2 Causes of Health Disparities
Absence of Erythrogenesis and Vasculogenesis in Plcg1-deficient Mice*

Mice nullizygous for Plcg1 cease growing at early to mid-gestation. An examination of carefully preserved wild-type embryos shows clear evidence of erythropoiesis, but erythropoiesis is not evident in Plcg1 nullizygous embryos at the same stage. The analyses of embryonic materials demonstrate that in the absence of Plcg1, erythroid progenitors cannot be detected in the yolk sac or embryo body by three different assays, burst-forming units, colony-forming units, and analysis for the developmental marker Ter119. However, non-erythroid granulocyte/macrophage colonies are produced by Plcg1 null embryos. Further analysis of these embryos demonstrates significantly diminished vasculogenesis in Plcg1 nullizygous embryos based on the lack of expression of the endothelial marker platelet endothelial cell adhesion molecule-1. In addition,Plcg1 nullizygous embryos express a greatly reduced level of vascular endothelial growth factor receptor-2/Flk-1, consistent with significantly impaired vasculogenesis and erythropoiesis. Interestingly, these early embryos do express phospholipase C-γ2, however, it is unable to substitute for the absence of phospholipase C-γ1, which can be detected in its tyrosine-phosphorylated state.
Overlapped Cell Image Segmentation Based on Distance Transform

In micro cell images, several cells overlapped with each other often appears which causes difficulty to automatic cell estimation. How to separate overlapped cells to individual cells becomes the prerequisite of analyzing the micro cell images. In this paper, by introducing the theory of distance transform combining with watershed algorithm, a new algorithm of overlapped cell segmentation is proposed. This algorithm adopts distance transform to turn the position information of pixels to grey level information, and then adopts the watershed algorithm to realize the search and segmentation of the adhesion border of cell. The main characteristic of this method is that it can reduce the requisition of the quality of image, such as grey difference or noise level and so on. At the same time, it can calculate fast with high accuracy and steady result. So it is suitable for most overlapped cell images segmentation
cation and molecular characterization of fi ve putative toxins from the venom gland of the snake Philodryas chamissonis ( Serpentes : Dipsadidae ) F elix

Philodryas chamissonis is a rear-fanged snake endemic to Chile. Its bite produces mild to moderate symptoms with proteolytic and anti-coagulant effects. Presently, the composition of the venom, as well as, the biochemical and structural characteristics of its toxins, remains unknown. In this study, we cloned and reported the first full-length sequences of five toxin-encoding genes from the venom gland of this species: Type III snake venom metalloprotease (SVMP), snake venom serine protease (SVSP), Cysteinerich secretory protein (CRISP), a and b subunits of C-type lectin-like protein (CLP) and C-type natriuretic peptide (NP). These genes are highly expressed in the venom gland and their sequences exhibited a putative signal peptide, suggesting that these are components of the venom. These putative toxins had different evolutionary relationships with those reported for some front-fanged snakes, being SVMP, SVSP and CRISP of P. chamissonis closely related to the toxins present in Elapidae species, while NP was more related to those of Viperidae species. In addition, analyses suggest that the a and b subunits of CLP of P. chamissonis might have a a-subunit scaffold in common with Viperidae species, whose highly variable C-terminal region might have allowed the diversification in a and b subunits. Our results provide the first molecular description of the toxins possibly implicated in the envenomation of prey and humans by the bite of P. chamissonis. © 2015 Elsevier Ltd. All rights reserved.
Limitations of monastral blue as a vascular label: Rapid rate of clearance is age‐dependent, and interactions with anesthetics depress arterial blood pressure in rats

Monastral blue (MB) has been described as an inexpensive, nontoxic vascular label. Discrepancies as to its rate of removal from circulation and physiological side effects prompted this study in which retention time of MB in the vascular system and effects of MB upon arterial blood pressure with different anesthetics (halothane, isoflurane, and pentobarbital) were measured in rats. Arterial pressure was monitored during intravenous infusion of MB with or without Evans blue, an albumin label. Localized areas of leakage were created by injecting 30 μL of 10−4 M histamine into abdominal dermis at −2, 0, 5, 7, 10, and 15 minutes from infusion of MB. Mean arterial pressure decreased by 25–30% after MB infusion when halothane or isoflurane was used, but not with pentobarbital. Sites which leaked at 10 and 15 minutes did not usefully label with MB, although Evans blue‐labelled albumin appeared in the interstitium. Younger, lighter rats (125–200 vs. 200–250 gm) retained MB longer in circulation, and had a shorter duration of MB‐induced hypotension. Spectrophotometric analysis of rat serum showed rapid elimination of MB from the vascular system, with a half‐life of 3.5 ± 1.9 minutes. While MB remains a useful vascular label, its rapid removal from the circulation and its hypotensive effect must be recognized. © 1992 Wiley‐Liss, Inc.
Prevention by blockade of angiotensin subtype1‐receptors of the development of genetic hypertension but not its heritability

1 We determined whether early inhibition of angiotensin II subtype1 (AT1) receptors by the newly synthesized nonpeptidic antagonist, A‐81988, can attenuate the development of hypertension in spontaneously hypertensive rats (SHR) and if the altered blood pressure phenotype can be passed on to the subsequent generation, not exposed to the antagonist. 2 Pairs of SHR were mated while drinking tap water or A‐81988 in tap water, and the progeny was maintained on the parental regimen until 14 weeks of age. At this stage, A‐81988‐treated rats showed lower systolic blood pressure and body weight values (136 ±5 versus 185 ±4 mmHg and 247 ±4 versus 283±4 g in controls, P<0.01), while heart rate was similar. In addition, mean blood pressure was reduced (101 ±7 versus 170 ±7 mmHg in controls, P < 0.01), and the pressor responses to intravenous or intracerebroventricular angiotensin II were inhibited by 27 and 59%, respectively. Heart/body weight ratio was smaller in A‐81988‐treated rats (3.2±0.1 versus 3.8±0.1 in controls, P<0.01). 3 The antihypertensive and antihypertrophic effect of A‐81988 persisted in rats removed from therapy for 7 weeks (systolic blood pressure: 173 ±4 versus 220 ±4 mmHg, heart/body weight ratio: 3.4 ±0.1 versus 4.1 ±0.1 in controls at 21 weeks of age, P < 0.01 for both comparisons), whereas the cardiovascular hypertensive phenotype was fully expressed in the subsequent generation that was maintained without treatment. 4 These results indicate that chronic blockade of angiotensin AT1‐receptors attenuates the development of hypertension in SHR but it does not prevent the transmission of hypertension to the following generation. Thus, heritability of the SHR's hypertensive trait is not affected by pharmacological manipulation of the cardiovascular phenotype.
Automated readability index.

Abstract : Inasmuch as the utility of technical manuals is influenced to a marked extent by their reading difficulty or readability, the Automated Readability Index was devised to provide an easy, automated method of collecting data from which textual material can be evaluated in terms of readability. Whereas most readability formulae include separate factors related to (1) word difficulty and (2) sentence difficulty, the Automated Readability Index provides for the mechanical tabulation of the required data on passages as they are typed on a standard typewriter. Impulses from the typewriter activate counters which record the number of letters, words and sentences contained in the passage. From this, the average word length and average sentence length are computed. Appropriate weightings of these factors result in an index reflecting the readability of the passage. This index is in close agreement with other indices of readability.
Precise binding of single‐stranded DNA termini by human RAD52 protein

The human RAD52 protein, which exhibits a heptameric ring structure, has been shown to bind resected double strand breaks (DSBs), consistent with an early role in meiotic recombination and DSB repair. In this work, we show that RAD52 binds single‐stranded and tailed duplex DNA molecules via precise interactions with the terminal base. When probed with hydroxyl radicals, ssDNA–RAD52 complexes exhibit a four‐nucleotide repeat hypersensitivity pattern. This unique pattern is due to the interaction of RAD52 with either a 5′ or a 3′ terminus of the ssDNA, is sequence independent and is phased precisely from the terminal nucleotide. Hypersensitivity is observed over ∼36 nucleotides, consistent with the length of DNA that is protected by RAD52 in nuclease protection assays. We propose that RAD52 binds DNA breaks via specific interactions with the terminal base, leading to the formation of a precisely organized ssDNA–RAD52 complex in which the DNA lies on an exposed surface of the protein. This protein–DNA arrangement may facilitate the DNA–DNA interactions necessary for RAD52‐mediated annealing of complementary DNA strands.
Distributed output encoding for multi-class pattern recognition

Fingerspelling recognition and handshape recognition are two examples of real-world, multi-class recognition problems consisting of 26 and 78 classes respectively. While it is theoretically possible to solve any multi-class problem with a single "smart" classifier the complexity of such a classifier is usually prohibitively high. This paper looks at several approaches to solving a numerous multi-class recognition problem and discusses in detail a method involving coded output. Experiments are conducted using biomechanical data from a human hand as input, but work is continuing concerning the extraction of this data from multi-view hand images alone. Code generation is discussed and results are presented for several different coded output cases including the Hamming, Golay, and several hybrid codes. Conclusions show that the recognition accuracy increases proportionally to code length.
Assessing Corporate Reputational Damage of Data Breaches: An Empirical Analysis

Corporate reputation represents a core asset of companies and research has shown that better reputation can have positive effects such as increased revenues and sales. On the other hand, companies may suffer reputational damage that can result from internal or external and potentially unforeseen events such as operational losses. In this paper, we present an empirical analysis of how unforeseen IT security incidents have an impact on corporate reputation. With a focus on data breaches, i.e. situations in which internal information has been lost or stolen, we have conducted an event study providing evidence that newly published data breach has a negative effect on firm value. While this finding confirms existing research in this field, we also applied a method that aims at isolating the related reputation effects in the context of data breaches. Thereby, our results provide new insights into how IT security incidents do negatively impact corporate reputation.
Insects found in birds nests from Argentina: cytogenetic studies in Cimicidae (Hemiptera) and its taxonomical and phylogenetic implications

The Cimicidae (Hemiptera) are known to be blood ectoparasites primarily on birds and bats. Three species of the subfamily Haematosiphoninae are known from Argentina: Acanthocrios furnarii, Ornithocoris toledoi, and Psitticimex uritui; all feed on diverse avian hosts. The chromosome number and male meiosis of A. furnarii, and P. uritui from new Argentinean samples are analyzed and compared with previous data. The sample of A. furnarii described by Ueshima (1966) with 2n = 32 + XY (male), strikingly differs from the present results (2n = 10 + XY, male). The diploid number of P. uritui agree with the previously reported by Ueshima (1966), 2n = 28 + X 1 X 2 Y (male). Taxonomical implications about the identity of A. furnarii are discussed and the mechanisms of the karyotype evolution of species belonging to Haematosiphoninae are proposed.
A unique Ni2+ -dependent and methylglyoxal-inducible rice glyoxalase I possesses a single active site and functions in abiotic stress response.

The glyoxalase system constitutes the major pathway for the detoxification of metabolically produced cytotoxin methylglyoxal (MG) into a non-toxic metabolite D-lactate. Glyoxalase I (GLY I) is an evolutionarily conserved metalloenzyme requiring divalent metal ions for its activity: Zn(2+) in the case of eukaryotes or Ni(2+) for enzymes of prokaryotic origin. Plant GLY I proteins are part of a multimember family; however, not much is known about their physiological function, structure and metal dependency. In this study, we report a unique GLY I (OsGLYI-11.2) from Oryza sativa (rice) that requires Ni(2+) for its activity. Its biochemical, structural and functional characterization revealed it to be a monomeric enzyme, possessing a single Ni(2+) coordination site despite containing two GLY I domains. The requirement of Ni(2+) as a cofactor by an enzyme involved in cellular detoxification suggests an essential role for this otherwise toxic heavy metal in the stress response. Intriguingly, the expression of OsGLYI-11.2 was found to be highly substrate inducible, suggesting an important mode of regulation for its cellular levels. Heterologous expression of OsGLYI-11.2 in Escherichia coli and model plant Nicotiana tabacum (tobacco) resulted in improved adaptation to various abiotic stresses caused by increased scavenging of MG, lower Na(+) /K(+) ratio and maintenance of reduced glutathione levels. Together, our results suggest interesting links between MG cellular levels, its detoxification by GLY I, and Ni(2+) - the heavy metal cofactor of OsGLYI-11.2, in relation to stress response and adaptation in plants.
Natural co-infection of Solanum tuberosum crops by the Potato yellow vein virus and potyvirus in Colombia

The Potato yellow vein virus (PYVV), a Crinivirus with an RNA tripartite genome, is the causal agent of the potato yellow vein disease, reported in Colombian since 1950, with yield reductions of up to 50%. Co-infection of two or more viruses is common in nature and can be associated with differences in virus accumulation and symptom expression. No evidence of mixed infection between PYVV and other viruses has been reported. In this study, eight plants showing yellowing PYVV symptoms: four Solanum tuberosum Group Phureja (P) and four Group Andigena (A), were collected in Cundinamarca, Colombia to detect mixed infection in the isolates using next generation sequencing (NGS). The Potato virus Y (PVY) complete genome (similar to N strain) and the Potato virus V (PVV) partial genomes were detected using NGS and re-confirmed by RT-PCR. Preliminary field screening in a large sample showed that PYVV and PVY co-infect potato plants with a prevalence of 21% within the P group and 23% within the A group. This is the first report of co-infection of PYVV and potyvirus in Colombia and with the use of NGS. Considering that potyviruses enhance symptom severity and/or yield reductions in mixed infections, our results may be relevant for disease diagnosis, breeding programs and tuber certification.