Miracle-dz/UniFAR-FTUs huggingface dataset:
Counter-selection recombineering of the baculovirus genome: a strategy for seamless modification of repeat-containing BACs

Recombineering is employed to modify large DNA clones such as fosmids, BACs and PACs. Subtle and seamless modifications can be achieved using counter-selection strategies in which a donor cassette carrying both positive and negative markers inserted in the target clone is replaced by the desired sequence change. We are applying counter-selection recombineering to modify bacmid bMON14272, a recombinant baculoviral genome, as we wish to engineer the virus into a therapeutically useful gene delivery vector with cell targeting characteristics. Initial attempts to replace gp64 with Fusion (F) genes from other baculoviruses resulted in many rearranged clones in which the counter-selection cassette had been deleted. Bacmid bMON14272 contains nine highly homologous regions (hrs) and deletions were mapped to recombination between hr pairs. Recombineering modifications were attempted to decrease intramolecular recombination and/or increase recombineering efficiency. Of these only the use of longer homology arms on the donor molecule proved effective permitting seamless modification. bMON14272, because of the presence of the hr sequences, can be considered equivalent to a highly repetitive BAC and, as such, the optimized method detailed here should prove useful to others applying counter-selection recombineering to modify BACs or PACs containing similar regions of significant repeating homologies.
Jets from black hole X-ray binaries: testing, refining and extending empirical models for the coupling to X-rays

In this paper we study the relation of radio emission to X-ray spectral and variability properties for a large sample of black hole X-ray binary systems. This is done to test, refine and extend – notably into the timing properties – the previously published ‘unified model’ for the coupling of accretion and ejection in such sources. In 14 outbursts from 11 different sources we find that in every case the peak radio flux, on occasion directly resolved into discrete relativistic ejections, is associated with the bright hard to soft state transition near the peak of the outburst. We also note the association of the radio flaring with periods of X-ray flaring during this transition in most, but not all, of the systems. In the soft state, radio emission is in nearly all cases either undetectable or optically thin, consistent with the suppression of the core jet in these states and ‘relic’ radio emission from interactions of previously ejected material and the ambient medium. However, these data cannot rule out an intermittent, optically thin, jet in the soft state. In attempting to associate X-ray timing properties with the ejection events we find a close, but not exact, correspondence between phases of very low integrated X-ray variability and such ejections. In fact the data suggest that there is not a perfect one-to-one correspondence between the radio, X-ray spectral or X-ray timing properties, suggesting that they may be linked simply as symptoms of the underlying state change and not causally to one another. We further study the sparse data on the reactivation of the jet during the transition back to the hard state in decay phase of outbursts, and find marginal evidence for this in one case only. In summary we find no strong evidence against the originally proposed model, confirming and extending some aspects of it with a much larger sample, but note that several aspects remain poorly tested.
Robust online Hamiltonian learning

In this work we combine two distinct machine learning methodologies, sequential Monte Carlo and Bayesian experimental design, and apply them to the problem of inferring the dynamical parameters of a quantum system. We design the algorithm with practicality in mind by including parameters that control trade-offs between the requirements on computational and experimental resources. The algorithm can be implemented online (during experimental data collection), avoiding the need for storage and post-processing. Most importantly, our algorithm is capable of learning Hamiltonian parameters even when the parameters change from experiment-to-experiment, and also when additional noise processes are present and unknown. The algorithm also numerically estimates the Cramer–Rao lower bound, certifying its own performance.
A first look into SCADA network traffic

Supervisory Control and Data Acquisition (SCADA) networks are commonly deployed to aid the operation of critical infrastructures, such as water distribution facilities. These networks provide automated processes that ensure the correct functioning of these infrastructures, in a operation much similar to those of management operations found in traditional Internet Protocol (IP), in particular the Simple Network Management Protocol (SNMP). In this paper we provide a first look into characteristics of SCADA traffic, with the goal of building an empirical foundation for future research, and investigate to what extent the SCADA traffic patterns are similar to SNMP.
Research digest

Children with a parent who suffers from depression are at raised risk for the disorder themselves. Relatively little is known about the development of psychological vulnerability to depression through childhood, particularly during infancy and early childhood. This paper describes results from a longitudinal prospective study of the development of children, studied from birth to 16 years, of mothers who experienced postnatal depression; it highlights the roles of the developing mother-child relationship, and of physiological functioning and social relationships in the development of adolescent vulnerability.
Brain tumor segmentation and its area calculation in brain MR images using K-mean clustering and Fuzzy C-mean algorithm

This paper deals with the implementation of Simple Algorithm for detection of range and shape of tumor in brain MR images. Tumor is an uncontrolled growth of tissues in any part of the body. Tumors are of different types and they have different Characteristics and different treatment. As it is known, brain tumor is inherently serious and life-threatening because of its character in the limited space of the intracranial cavity (space formed inside the skull). Most Research in developed countries show that the number of people who have brain tumors were died due to the fact of inaccurate detection. Generally, CT scan or MRI that is directed into intracranial cavity produces a complete image of brain. This image is visually examined by the physician for detection & diagnosis of brain tumor. However this method of detection resists the accurate determination of stage & size of tumor. To avoid that, this project uses computer aided method for segmentation (detection) of brain tumor based on the combination of two algorithms. This method allows the segmentation of tumor tissue with accuracy and reproducibility comparable to manual segmentation. In addition, it also reduces the time for analysis. At the end of the process the tumor is extracted from the MR image and its exact position and the shape also determined. The stage of the tumor is displayed based on the amount of area calculated from the cluster.
Comparative Analysis of the Japanese Version of the Revised Impact of Event Scale: A Study of Firefighters

Abstract Introduction: The Impact of Event Scale Revised (IES-R) has been used in various epidemiological studies to assess the prevalence of post-traumatic stress disorder (PTSD). Previous studies using the IES-R Japanese version to assess the mental health of firefighters were based on the premise that firefighters had experienced a traumatic event(s) as a matter of course. However, use of the IES-R-J does not indicate whether or not a traumatic event was experienced. The purpose of this study is to clarify the differences between: (1) IES-R-J high and low score groups; and (2) those who report symptoms similar to those of PTSD with and without having been being exposed to a traumatic event. Methods: Questionnaire packets distributed to all 157 workers in a Japanese fire station included the IES-R, the Japan Brief Job Stress Questionnaire, a questionnaire regarding traumatic event experiences, and demographic questions. Participants who scored ≥25 points on the IES-R-J scale were defined as the PTSD high risk (HR) group; those with scores <25 points as the PTSD low risk (LR) group. Results: One hundred thirty-one of the 157 subjects (83.4%) responded to the questionnaire; three were excluded from the analysis because of missing data. The mean total IES-R-J score was 14.9 ±15.2. Twenty-eight subjects scored in the PTSD HR group (≥25); 100 scored in the LR group (<25). A total of 54 (42.2%) participants had experienced a traumatic event; 57.8% had not. In the HR group, 14 subjects had experienced a traumatic event and 14 had not. Participants who had experienced a traumatic event reported a higher incidence of intrusion/re-experience symptoms than did those who had not experienced a traumatic event. The level of social support significantly affected the risk for PTSD. Firefighters who scored ≥25 on the IES-R-J and, thus, considered to be at high risk for the development of PTSD, were less confident about their health, experienced more job stressors and had less social support than did those whose IES-R-J scores were <25. Having experienced a traumatic event was reported by only 42% of all the participants and by only 50% of those in the high risk PTSD group. Conclusions: Although the IES-R is an easily-administered tool useful in epidemiological studies evaluating psychological stress, it is recommended that the questionnaire be amended to include a question regarding the existence of a threatened experience or event and to analyze the data using positive and negative predictive value methodology.
Evolving Molecular Epidemiological Profile of Human Immunodeficiency Virus 1 in the Southwest Border of China

Background We have previously reported in Xishuangbanna (Banna) Dai Autonomous Prefecture, a well-developed tourist destination in the southwest border of China, that HIV-1 transmitted dominantly through heterosexual contact with less divergent genotypes and few drug resistant mutations [1]. Due to the rapid increase of newly diagnosed HIV-1 cases per year in Banna in recent years, it’s important to evaluate the evolution of HIV-1 molecular epidemiology for the better understanding of ongoing HIV-1 outbreak in this region. Methodology/Principal Findings By sequencing of HIV-1 pol genes and phylogenetic analysis, we conducted a molecular epidemiologic study in 352 HIV-1-seropositive highly active antiretroviral treatment (HAART)-naïve individuals newly diagnosed at the Banna Center for Disease Control and Prevention between 2009 and 2011. Of 283 samples (84.1% taken from heterosexually acquired adults, 10.6% from needle-sharing drug users, 2.8% from men who have sex with men, 0.4% from children born from HIV-1-infected mothers, and 2.1% remained unknown) with successful sequencing for pol gene, we identified 108 (38.2%) HIV-1 subtype CRF08_BC, 101 (35.7%) CRF01_AE, 49 (17.3%) CRF07_BC, 5 (1.8%) C/CRF57_BC, 3 (1.1%) B’, 1 (0.4%) B/CRF51_01B, and 16 (5.7%) unique recombinants forms. Among these infected individuals, 104 (36.7%) cases showed drug resistant or resistance-relevant mutations, and 4 of them conferring high-level resistance to 3TC/FTC, EFV/NVP or NFV. Phylogenetic analysis revealed 21 clusters (2–7 sequences) with only 21.2% (60/283) sequences involved. Conclusion/Significance In contrast to our previous findings, CRF08_BC, replaced CRF01_AE, became the dominant genotype of HIV-1 in Banna prefecture. The viral strains with drug resistance mutations were detected frequently in newly diagnosed HIV-1-infected individuals in this region.
The fibrinogen but not the Factor VIII content of transfused plasma determines its effectiveness at reducing bleeding in coagulopathic mice

The evidence supporting plasma transfusion as a means to restore hemostatic control and prevent or treat bleeding is weak, leading to uncertainties as to which proteins affect the therapeutic quality of plasma. Some regulators focus on coagulation Factor (F)VIII activity, but whether this measure reflects overall transfusable plasma efficacy is questionable. We developed a mouse model of coagulopathy in which bleeding outcomes were responsive to plasma transfusion and addressed the relative contributions of FVIII and fibrinogen (Fg) to plasma quality.
Expanding role of chemotherapy in lung cancer.

Lung cancer is a major cause of mortality worldwide, with an estimated annual incidence of over 1.2 million cases and overall mortality of over 1.1 million cases [1]. In the United States alone in 2003, an estimated 171 900 new cases of lung cancer will be diagnosed, and this disease will cause an estimated 157 200 deaths [2]. Estimates of cancer incidence and mortality in Europe in 2000 predicted 375 000 new cases of lung cancer and 347 000 deaths due to this disease [3]. In Europe, the mortality rates are rising in women, due to the increasing tobacco use [4]. The overall 5-year survival rates of patients with lung cancer have only modestly increased over the last 25 years, remaining at approximately 14% [5]. This disappointing figure may have several explanations including age at diagnosis (median 69 years), the high frequency of co-morbidities, and the absence of significantly relevant improvement of the three major therapeutic modalities, i.e. surgery, radiotherapy and chemotherapy. Nevertheless, the emergence of some new drugs and concepts has broadened the perspectives of lung cancer management.
The fungicide procymidone alters sexual differentiation in the male rat by acting as an androgen-receptor antagonist in vivo and in vitro

Procymidone is a dicarboximide fungicide structurally related to the well-characterized fungicide vinclozolin. Vinclozolin metabolites bind to mammalian androgen receptors (AR) and act as AR antagonists, inhibiting androgen-dependent gene expression in vivo and in vitro by inhibiting AR-binding to DNA. The current study was designed to determine if procymidone acted as an AR antagonist in vitro and to describe the dosage levels of procymidone that alter sexual differentiation in vivo. In vitro, procymidone inhibited androgen from binding the human AR (hAR) in COS (monkey kidney) cells transfected with hAR at 3.16 μM. In vitro, procymidone acted as an androgen antagonist, inhibiting dihydrotestosterone (DHT)-induced transcriptional activation at 0.2 μM in CV-1 cells (cotransfected with the hAR and a MMTV-luciferase reporter gene). In vivo, maternal procymidone exposure at 0, 25, 50, 100, or 200 mg kg−1 day−1 during gestation and early lactation (gestational day 14 to postnatal day 3) altered reproductive development of male offspring at all dosage levels tested. Male offspring exhibited shortened anogenital distance (at 25 mg kg−1 day−1 and above), permanent nipples, reduced weight of several androgen-dependent tissues (levator ani and bulbocavernosus muscles, prostate, seminal vesicles, Cowper's gland and glans penis), and malformations (hypospadias, cleft phallus, exposed os penis, vaginal pouch, hydronephrosis, occasional hydroureter, epididymal granulomas, and ectopic, undescended testes). In addition, perinatal procymidone treatment had a marked effect on the histology of the lateral and ventral prostatic and seminal vesicular tissues of the offspring (at 50 mg kg−1 day−1 and above). These effects consisted of fibrosis, cellular infiltration, and epithelial hyperplasia. This constellation of effects is similar to that produced by perinatal exposure to vinclozolin. However, procymidone appears to be slightly less potent in inducing malformations than vinclozolin by a factor of about two. In summary, the antiandrogenic activity of procymidone was demonstrated in vivo and in vitro in cell lines transfected with hAR. Since the role of androgens in mammalian sexual differentiation is highly conserved, it is likely that humans would be adversely affected by procymidone in a predictable manner if the human fetus was exposed to sufficient levels during critical stages of intrauterine and neonatal life.
Social support by four categories of work colleagues: Relationships between activities, stress and satisfaction

An approach to the study of social support at work is presented emphasizing nature and type of social support. One hundred employees in a range of occupations rated the frequency of engaging in 12 types of social and work-related activity with each of four work colleagues varying in degree of intimacy. They also rated levels of job satisfaction and work stress. The results confirm the usefulness of this approach and also suggest that type of work relationship is associated with different sorts of socially supportive activities, and that these affect stress but not satisfaction. These findings were discussed in terms of the interaction between type of support given, source of support, and outcome.
An H.264/AVC full-mode intra-frame encoder for 1080HD video

We present a high-performance hardware architecture for H.264/AVC full-mode intra-frame encoding. We propose a novel method to alleviate performance bottleneck caused by the long data dependency loop among 4times4 blocks. Synthesized into a TSMC 0.13 mum CMOS cell library, our design takes 212 K gates to run at 138 MHz and is able to real-time encode 1080HD (1920times1088) video sequences at 30 frames per second (fps). Compared with all state-of-the-art designs, our design needs lower working frequency, supports high resolution up to 1080HD and achieves better bit-rate saving.
Virtual Transmission Method, A New Distributed Algorithm to Solve Sparse Linear Systems

In this paper, we propose a new distributed numerical algorithm which could work naturally on the parallel computer with arbitrary number of processors. This algorithm is named virtual transmission method (VTM), which is inspired by the behavior of transmission line from the electrical engineering. VTM is a scalable, distributed and global-iterative-local-direct algorithm to solve the large sparse linear system whose coefficient matrix is symmetric-positive-definite (SPD). As a distributedly-iterative algorithm, VTM is proved to be convergent. VTM requires simple hardware and could be easily implemented on any kind of parallel computer, including the manycore microprocessor, and all the traditional serial solvers could be assembled into VTM without any change. Numerical experiments show that VTM is an efficient and accurate algorithm. Accompanied with VTM, we bring in a new technique to partition the symmetric linear system, which is named electric vertex splitting technique (EVS). We present the conformal splitting existence theorem to assure that this splitting technique is feasible to partition any SPD linear system.
Multicasting for cascaded fault-tolerant Wireless Networked Control Systems in noisy industrial environments

This paper studies a Wireless Networked Control System based on IEEE's 802.11b Wi-Fi standard protocol consisting of two identical workcells with zero meter inter-cell distance. It is first shown how to improve system performance and increase the amount of noise that the system can tolerate without violating delay requirements or dropping control packets. Different noise models were studied. It was proved that increasing the short retry threshold increases system tolerance to noise. It was then shown through OPNET simulations that the two cell model is fault-tolerant at the controller level when either unicasting or multicasting is used. However, for the system to operate correctly in the presence of noise, multicasting had to be used.
Simulations of organic aerosol concentrations during springtime in theGuanzhong Basin, China

Abstract. The organic aerosol (OA) concentration is simulated in the Guanzhong Basin, China from 23 to 25 April 2013 utilizing the WRF-CHEM model. Two approaches are used to predict OA concentrations: (1) a traditional secondary organic aerosol (SOA) module; (2) a non-traditional SOA module including the volatility basis-set modeling method in which primary organic aerosol (POA) is assumed to be semivolatile and photochemically reactive. Generally, the spatial patterns and temporal variations of the calculated hourly near-surface ozone and fine particle matters agree well with the observations in Xi'an and surrounding areas. The model also yields reasonable distributions of daily PM2.5 and elemental carbon (EC) compared to the filter measurements at 29 sites in the basin. Filter-measured organic carbon (OC) and EC are used to evaluate OA, POA, and SOA using the OC ∕ EC ratio approach. Compared with the traditional SOA module, the non-traditional module significantly improves SOA simulations and explains about 88 % of the observed SOA concentration. Oxidation and partitioning of POA treated as semivolatile constitute the most important pathway for the SOA formation, contributing more than 75 % of the SOA concentrations in the basin. Residential emissions are the dominant anthropogenic OA source, constituting about 50 % of OA concentrations in urban and rural areas and 30 % in the background area. The OA contribution from transportation emissions decreases from 25 % in urban areas to 20 % in the background area, and the industry emission OA contribution is less than 6 %.
Political homophily on social network sites and users' poll skepticism

Although many studies have investigated citizens' attitudes toward polls and the political consequences, there have been no studies examining the effects of social network site (SNS) users' opinion environments on their poll skepticism. Based on prior studies on poll skepticism, we examine the relationship between perceived SNS opinion environments, poll skepticism, perceived concerns over the negative influence of the polls, and voting intention in an upcoming election. Using the survey data of the 2012 South Korean General Election, this study found that if the published polls are against respondents' political position, their homophilous SNS opinion environments promote poll skepticism, and augmented poll skepticism leads to concerns over the negative influence of the polls on other voters, which in turn increases voting intention.
Field Independence in Concept Attainment

Concept-attainment tasks in which the stimulus materials are composed of several perceptual attributes appear to require differentiation of the stimulus complex or the cognitive capacity of field independence. High and low field-independent females were compared on performance of a concept-attainment task. The high field-independent Ss were significantly more efficient as measured by number of choices to solution, number of incorrect verbalizations, and thoroughness with which attributes were tested. These Ss also demonstrated greater readiness to accept the irrelevance of attribute values of an initial exemplar of the concept. General intelligence was ruled out as a possible explanation of these differences.
Efficacy of Veno-Venous Extracorporeal Membrane Oxygenation in Severe Acute Respiratory Failure

Purpose The objective of this study was to evaluate our institutional experience with veno-venous (VV) extracorporeal membrane oxygenation (ECMO) in patients with severe acute respiratory failure (ARF). Materials and Methods From January 2007 to August 2013, 31 patients with severe ARF that was due to various causes and refractory to mechanical ventilation with conventional therapy were supported with VV ECMO. A partial pressure of arterial oxygen (PaO2)/inspired fraction of oxygen (FiO2) <100 mm Hg at an FiO2 of 1.0 or a pH <7.25 due to CO2 retention were set as criteria for VV ECMO. Results Overall, 68% of patients survived among those who had received VV ECMO with a mean PaO2/FiO2 of 56.8 mm Hg. Furthermore, in trauma patients, early use of ECMO had the best outcome with a 94% survival rate. Conclusion VV ECMO is an excellent, life-saving treatment option in patients suffering from acute and life-threatening respiratory failure due to various causes, especially trauma, and early use of VV ECMO therapy improved outcomes in these patients.