Miracle-dz/UniFAR-FTUs huggingface dataset:
Mcm4,6,7 Uses a “Pump in Ring” Mechanism to Unwind DNA by Steric Exclusion and Actively Translocate along a Duplex*

Mcm4,6,7 is a ring-shaped heterohexamer and the putative eukaryotic replication fork helicase. In this study, we examine the mechanism of Mcm4,6,7. Mcm4,6,7 binds to only one strand of a duplex during unwinding, corresponding to the leading strand of a replication fork. Mcm4,6,7 unwinding stops at a nick in either strand. The Mcm4,6,7 ring also actively translocates along duplex DNA, enabling the protein to drive branch migration of Holliday junctions. The Mcm4,6,7 mechanism is very similar to DnaB, except the proteins translocate with opposite polarity along DNA. Mcm4,6,7 and DnaB have different structural folds and evolved independently; thus, the similarity in mechanism is surprising. We propose a “pump in ring” mechanism for both Mcm4,6,7 and DnaB, wherein a single-stranded DNA pump is situated within the central channel of the ring-shaped helicase, and unwinding is the result of steric exclusion. In this example of convergent evolution, the “pump in ring” mechanism was probably selected by eukaryotic and bacterial replication fork helicases in order to restrict unwinding to replication fork structures, stop unwinding when the replication fork encounters a nick, and actively translocate along duplex DNA to accomplish additional activities such as DNA branch migration.
Fully 4D list-mode reconstruction applied to respiratory-gated PET scans

18F-fluoro-deoxy-glucose (18F-FDG) positron emission tomography (PET) is one of the most sensitive and specific imaging modalities for the diagnosis of non-small cell lung cancer. A drawback of PET is that it requires several minutes of acquisition per bed position, which results in images being affected by respiratory blur. Respiratory gating techniques have been developed to deal with respiratory motion in the PET images. However, these techniques considerably increase the level of noise in the reconstructed images unless the acquisition time is increased. The aim of this paper is to evaluate a four-dimensional (4D) image reconstruction algorithm that combines the acquired events in all the gates whilst preserving the motion deblurring. This algorithm was compared to classic ordered subset expectation maximization (OSEM) reconstruction of gated and non-gated images, and to temporal filtering of gated images reconstructed with OSEM. Two datasets were used for comparing the different reconstruction approaches: one involving the NEMA IEC/2001 body phantom in motion, the other obtained using Monte-Carlo simulations of the NCAT breathing phantom. Results show that 4D reconstruction reaches a similar performance in terms of the signal-to-noise ratio (SNR) as non-gated reconstruction whilst preserving the motion deblurring. In particular, 4D reconstruction improves the SNR compared to respiratory-gated images reconstructed with the OSEM algorithm. Temporal filtering of the OSEM-reconstructed images helps improve the SNR, but does not achieve the same performance as 4D reconstruction. 4D reconstruction of respiratory-gated images thus appears as a promising tool to reach the same performance in terms of the SNR as non-gated acquisitions while reducing the motion blur, without increasing the acquisition time.
Social and Adaptive Functioning Scale 1 Running Head : SOCIAL AND ADAPTIVE FUNCTIONING SCALE The Development and Psychometric Properties of a Measure of Social and Adaptive Functioning for Children and Adolescents

Developed, piloted, and examined the psychometric properties of the Child and Adolescent Social and Adaptive Functioning Scale, a self-report measure designed to examine the social functioning of young people in the areas of school performance, peer relationships, family relationships, and home duties/self-care. The findings of confirmatory and exploratory factor analysis support a 4factor solution consistent with the hypothesized domains. Fit indices suggested that the 4correlated factor model represented a satisfactory solution for the data, with the covariation between factors being satisfactorily explained by a single, higher order factor reflecting social and adaptive functioning in general. The internal consistency and 12-month test-retest reliability of the total scale was acceptable. A significant, negative correlation was found between the CASAFS and a measure of depressive symptoms, showing that high levels of social functioning are associated with low levels of depression. Significant differences in CASAFS total and sub-scale scores were found between clinically depressed adolescents and a matched sample of non-clinical controls. Adolescents who reported elevated but sub-clinical levels of depression also reported lower levels of social functioning in comparison to non-clinical controls. Social and Adaptive Functioning Scale 3
Are partner and relationship characteristics associated with condom use in Zambian nonmarital relationships?

CONTEXT In Zambia, as in many other Sub-Saharan African countries, condom use is far below the level needed to alleviate serious threats to sexual and reproductive health. It is important to understand if and how partner and relationship characteristics are independently associated with condom use within nonmarital, noncohabiting relationships. METHODS Descriptive and logistic regression analyses of data on 657 nonmarital, noncohabiting relationships reported by male and female respondents in the 2000 Zambian Sexual Behavior Survey examined condom use in the 12 months preceding the survey. RESULTS Partner characteristics were not independently associated with condom use. Relationship characteristics that were significant largely differed by gender. Condom use within both male- and female-reported relationships was elevated if the male partner was five or more years older than the female (odds ratios, 2.1 and 3.7, respectively). Within male-reported relationships, having a partner from the same community was associated with a reduced likelihood of condom use (0.5); within female-reported relationships, the odds of condom use were elevated if sex had occurred only once (4.3). CONCLUSIONS Condom promotion programs and interventions in Africa must take into account the relationship characteristics of intended participants, paying special attention to gender differences.
Draft Genome Sequence of Rhodococcus ruber Strain BKS 20-38

ABSTRACT We report the 6.1-Mb genome sequence of Rhodococcus ruber strain BKS 20-38, isolated from the palm tree rhizosphere soil of Bhitarkanika National Park, Odhisha, India. The draft genome sequence of strain BKS 20-38 consists of 6,126,900 bp, with a G+C content of 69.72%, 5,716 protein-coding genes, and 49 RNAs.
Single‐Index Additive Vector Autoregressive Time Series Models

Abstract. We study a new class of nonlinear autoregressive models for vector time series, where the current vector depends on single‐indexes defined on the past lags and the effects of different lags have an additive form. A sufficient condition is provided for stationarity of such models. We also study estimation of the proposed model using P‐splines, hypothesis testing, asymptotics, selection of the order of the autoregression and of the smoothing parameters and nonlinear forecasting. We perform simulation experiments to evaluate our model in various settings. We illustrate our methodology on a climate data set and show that our model provides more accurate yearly forecasts of the El Niño phenomenon, the unusual warming of water in the Pacific Ocean.
SOME THEORIES ON RETAIL BUSINESS MICROLOCATION IN THE COMMUNITY OF WESTERN COUNTRIES

The discussion on locations of retail business has become one of the main topics on urban community study and planning in developed country. Based on the study of foreign experts, this paper draws some conclusions on locations of retail business, which include the relational theory of traffic patterns, interest gravitational area and microlocation, as well as the essential location elements of retail business.
Thirty Years of Computational Autopoiesis: A Review

Computational autopoiesisthe realization of autopoietic entities in computational mediaholds an important and distinctive role within the field of artificial life. Its earliest formulation by Francisco Varela, Humberto Maturana, and Ricardo Uribe was seminal in demonstrating the use of an artificial, computational medium to explore the most basic question of the abstract nature of living systemsover a decade in advance of the first Santa Fe Workshop on Artificial Life. The research program it originated has generated substantive demonstrations of progressively richer, lifelike phenomena. It has also sharply illuminated both conceptual and methodological problems in the field. This article provides an integrative overview of the sometimes disparate work in this area, and argues that computational autopoiesis continues to provide an effective framework for addressing key open problems in artificial life.
Retrieval induces reconsolidation of fear extinction memory

The nonreinforced expression of long-tem memory may lead to two opposite protein synthesis-dependent processes: extinction and reconsolidation. Extinction weakens consolidated memories, whereas reconsolidation allows incorporation of additional information into them. Knowledge about these two processes has accumulated in recent years, but their possible interaction has not been evaluated yet. Here, we report that inhibition of protein synthesis in the CA1 region of the dorsal hippocampus after retrieval of fear extinction impedes subsequent reactivation of the extinction memory trace without affecting its storage or that of the initial fear memory. Our results suggest that extinction memory is susceptible to a retrieval-induced process similar to reconsolidation in the hippocampus.
Aspect Oriented Middleware for Internet of Things: A State-of-the Art Survey of Service Discovery Approaches

Internet of Things refers to a paradigm consisting of a variety of uniquely identifiable day to day things communicating with one another to form a large scale dynamic network. The integration of these heterogeneous things in the constrained network is a challenging issue, for which service oriented and architecture based solutions are considered to be useful. The key element of any service oriented paradigm is service discovery which allows the client to get access to the right service at the right time to complete the requested tasks. This paper presented a comprehensive survey of major solutions for service and resource discovery detailing techniques and features used in existing systems. The survey presented the findings in tabular representation and outlined the proposed aspect oriented middleware framework for IoT highlighting context awareness and solving certain pitfalls in the existing service discovery approaches. The survey results might be helpful in deriving the limitations of the existing protocols in literature and identify future research opportunities in service discovery.
Efficient out-coupling of high-purity single photons from a coherent quantum dot in a photonic-crystal cavity

We demonstrate a single-photon collection efficiency of $(44.3\ifmmode\pm\else\textpm\fi{}2.1)%$ from a quantum dot in a low-Q mode of a photonic-crystal cavity with a single-photon purity of ${g}^{(2)}(0)=(4\ifmmode\pm\else\textpm\fi{}5)%$ recorded above the saturation power. The high efficiency is directly confirmed by detecting up to $962\ifmmode\pm\else\textpm\fi{}46$ kilocounts per second on a single-photon detector on another quantum dot coupled to the cavity mode. The high collection efficiency is found to be broadband, as is explained by detailed numerical simulations. Cavity-enhanced efficient excitation of quantum dots is obtained through phonon-mediated excitation and under these conditions, single-photon indistinguishability measurements reveal long coherence times reaching $0.77\ifmmode\pm\else\textpm\fi{}0.19$ ns in a weak-excitation regime. Our work demonstrates that photonic crystals provide a very promising platform for highly integrated generation of coherent single photons including the efficient out-coupling of the photons from the photonic chip.
High-Frequency Epigenetic Repression and Silencing of Retroviruses Can Be Antagonized by Histone Deacetylase Inhibitors and Transcriptional Activators, but Uniform Reactivation in Cell Clones Is Restricted by Additional Mechanisms

ABSTRACT Integrated retroviral DNA is subject to epigenetic gene silencing, but the viral and host cell properties that influence initiation, maintenance, and reactivation are not fully understood. Here we describe rapid and high-frequency epigenetic repression and silencing of integrated avian sarcoma virus (ASV)-based vector DNAs in human HeLa cells. Initial studies utilized a vector carrying the strong human cytomegalovirus (hCMV) immediate-early (IE) promoter to drive expression of a green fluorescent protein (GFP) reporter gene, and cells were sorted into two populations based on GFP expression [GFP(+) and GFP(−)]. Two potent epigenetic effects were observed: (i) a very broad distribution of GFP intensities among cells in the GFP(+) population as well as individual GFP(+) clones and (ii) high-frequency GFP reporter gene silencing in GFP(−) cells. We previously showed that histone deacetylases (HDACs) can associate with ASV DNA soon after infection and may act to repress viral transcription at the level of chromatin. Consistent with this finding, we report here that treatment with the histone deacetylase inhibitor trichostatin A (TSA) induces GFP activation in GFP(−) cells and can also increase GFP expression in GFP(+) cells. In the case of the GFP(−) populations, we found that after removal of TSA, GFP silencing was reestablished in a subset of cells. We used that finding to enrich for stable GFP(−) cell populations in which viral GFP reporter expression could be reactivated by TSA; furthermore, we found that the ability to isolate such populations was independent of the promoter driving the GFP gene. In such enriched cultures, hCMV IE-driven, but not the viral long terminal repeat-driven, silent GFP reporter expression could be reactivated by the transcriptional activator prostratin. Microscopy-based studies using synchronized cells revealed variegated reactivation in cell clones, indicating that secondary epigenetic effects can restrict reactivation from silencing. Furthermore we found that entry into S phase was not required for reactivation. We conclude that HDACs can act rapidly to initiate and maintain promoter-independent retroviral epigenetic repression and silencing but that reactivation can be restricted by additional mechanisms.
Microblog Retrieval for Post-Disaster Relief: Applying and Comparing Neural IR Models

Microblogging sites like Twitter and Weibo have emerged as important sourcesof real-time information on ongoing events, including socio-political events, emergency events, and so on. For instance, during emergency events (such as earthquakes, floods, terror attacks), microblogging sites are very useful for gathering situational information in real-time. During such an event, typically only a small fraction of the microblogs (tweets) posted are relevant to the information need. Hence, it is necessary to design effective methodologies for microblog retrieval, so that the relevant tweets can be automatically extracted from large sets of documents (tweets). In this work, we apply and compare various neural network-based IR models for microblog retrieval for a specific application, as follows. In a disaster situation, one of the primary and practical challenges in coordinating the post-disaster relief operations is to know about what resources are needed and what resources are available in the disaster-affected area. Thus, in this study, we focus on extracting these two specific types of microblogs or tweets namely need tweets and avail tweets, which are tweets which define some needs of the people and the tweets which offer some solutions or aid for the people, respectively.
Reappraisal of the human vestibular cortex by cortical electrical stimulation study

The cortical areas with vestibular input in humans were assessed by electrical stimulation in 260 patients with partial epilepsy who had undergone stereotactic intracerebral electroencephalogram recordings before surgery. Vestibular symptoms were electrically induced on 44 anatomical sites in 28 patients. The patients experienced illusions of rotation (yaw plane: 18, pitch plane: 6, roll plane: 6), translations (n = 6), or indefinable feelings of body motion (n = 8). Almost all vestibular sites were located in the cortex (41/44): in the temporal (n = 19), parietal (n = 14), frontal (n = 5), occipital (n = 2), and insular (n = 1) lobes. Among these sites, we identified a lateral cortical temporoparietal area we called the temporo–peri‐Sylvian vestibular cortex (TPSVC), from which vestibular symptoms, and above all rotatory sensations, were particularly easily elicited (24/41 cortical sites, 58.5%). This area extended above and below the Sylvian fissure, mainly inside Brodmann areas 40, 21, and 22. It included the parietal operculum (9/24 TPSVC sites) which was particularly sensitive for eliciting pitch plane illusions, and the mid and posterior part of the first and second temporal gyri (15/24 TPSVC sites) which preferentially caused yaw plane illusions. We suggest that the TPSVC could be homologous with the monkey's parietoinsular vestibular cortex.
n recognizing proportionality : Does the ability to solve issing value proportional problems presuppose the onception of proportional reasoning ?

This paper investigates the relationship between the ability of middle school students to solve missing value proportional problems and their facility in differentiating proportional relationships from non-proportional relationships. Students in lowand high-proficiency groups in mathematics took a ratio-and-proportion test involving two typical missing value proportional (MVP) and two recognizing proportionality (RP) problems. The findings revealed that while the students generally performed better on MVP problems than on RP problems, the two groups differed in their performance on MVP problems, but not on RP problems. Moreover, of those students from both the groups who successfully solved the two MVP problems, a significantly greater proportion of students in the high-proficiency group were unsuccessful in solving either of the two RP problems than those in the lowproficiency group. An analysis of performance differences between items within the same student group showed that the effect of differences in the structural components of RP problems to some extent contradicted the previous findings on the effect of differences in the structural components of MVP problems. It is hoped that these findings can shed light on what might be missing in the teaching and learning of proportional reasoning. © 2013 Elsevier Inc. All rights reserved.
Electrophysiological Study of Human Heart Muscle

Membrane potential changes in human ventricular and atrial muscle, excised from patients undergoing open-heart surgery, were recorded by micro-electrodes in vitro. Mean ventricular resting and action potentials were −87 mv. and 115 mv. , respectively. The mean atrial resting potential was −70 mv. , mean action potential 75 mv. Two forms of atrial action potential were found, one having conventional contour, the other with prominent spike and plateau. A disturbance in repolarization is believed to underlie the latter type of atrial potential cycle. The relation between the upstroke velocity of the action potential and the extracellular sodium concentration and membrane potential was shown to be similar to that in other mammalian cardiac tissue. The mean conduction velocity determined in ventricular fibers (1.3 M./sec.) was somewhat greater than that of the dog, and the possible relationship to hypertrophy of the cardiac fibers in the preparations studied is described. The effect of increased rate and anoxia in reducing the action potential duration is like that found in the hearts of other mammals. The conductance type of inhibition was produced by acetylcholine in spontaneously beating atrial tissue. The excitatory effect of epinephrine was preceded by a transitory inhibition. The basic mechanisms underlying the action potential, automaticity and transmitter effects, derived from investigation of other mammalian cardiac tissue are applicable to the human heart.
A simple tool for calculating egg shape, volume and surface area from digital images

The geometrical properties of eggs – such as volume and surface area – have uses ranging from ecological, physiological and morphological studies in birds, to predictions of chick condition in the poultry industry. Although measurements of an egg's length and breadth can be used to approximate its geometry, the coefficients used in these models are specific to the original test population, and intraspecific variation in egg shape means these methods cannot be used reliably beyond that population. Here I present a novel mathematical formula to describe the curvature of a bird's egg that can be used to calculate the shape, volume and surface area of an egg precisely from digital images. Using data from several species I demonstrate that the model has a greater level of accuracy than length- and breadth-based methods, and release the user-friendly tool for others to use for measuring eggs from digital images.
Quantitative PCR Analysis of Mitochondrial DNA Content in Patients with Mitochondrial Disease

Abstract: Molecular diagnosis of mitochondrial DNA disorder is usually focused on point mutations and large deletions. In the absence of detectable mtDNA mutations, abnormal amounts of mtDNA, either depletion or elevation, can be indicative of mitochondrial dysfunction. The amount of mitochondrial DNA (mtDNA), however, varies among individuals of different ages and among different tissues within the same individual. To establish a range of mtDNA levels, we analyzed 300 muscle and 200 blood specimens from patients suspected of having a mitochondrial disorder by real‐time quantitative polymerase chain reaction (PCR) method. Copy numbers were calculated from the standard curve and threshold cycle number using TaqMan probes; 6FAM 5′TTACCGGGCTCTGCCATCT3′‐TAMRA and VIC‐5′AGCAATAACAGGTCTGTGATG3′‐TAMRA for mtDNA and 18S rRNA gene (nDNA), respectively. The copy number ratio of mtDNA to nDNA was used as a measure of mtDNA content in each specimen. The mtDNA content in muscle increases steadily from birth to about 5 years of age; thereafter, it stays about the same. On the contrary, the mtDNA content in blood decreases with age. The amount of mtDNA in skeletal muscle is about 5‐20 times higher than that in blood. About 7% of patients had mtDNA levels in muscle below 20% of the mean of the age‐matched group, and about 10% of patients had muscle mtDNA levels 2‐ to 16‐fold higher than the mean of the age‐matched group. Patients with abnormal levels of mtDNA, either depletion or proliferation, had significant clinical manifestations characteristic of mitochondrial disease in addition to abnormal respiratory enzymes and mitochondrial cytopathies. Cardiomyopathy, lactic acidosis, abnormal brain MRI findings, hypotonia, developmental delay, seizures, and failure to thrive are general clinical pictures of patients with mtDNA depletion. The average age of patients with mtDNA depletion is 4.1 years, compared to 23.6 years in patients with mtDNA proliferation. Mutations in nuclear genes involved in mtDNA synthesis and deoxynucleotide pools are probably the cause of mtDNA depletion. Our results demonstrate that real time quantitative PCR is a valuable tool for molecular screening of mitochondrial diseases.