Miracle-dz/UniFAR-FTUs huggingface dataset:
The crystal structure of the complex of replication protein A subunits RPA32 and RPA14 reveals a mechanism for single‐stranded DNA binding

Replication protein A (RPA), the eukaryote single‐stranded DNA‐binding protein (SSB), is a heterotrimer. The largest subunit, RPA70, which harbours the major DNA‐binding activity, has two DNA‐binding domains that each adopt an OB‐fold. The complex of the two smaller subunits, RPA32 and RPA14, has weak DNA‐binding activity but the mechanism of DNA binding is unknown. We have determined the crystal structure of the proteolytic core of RPA32 and RPA14, which consists of the central two‐thirds of RPA32 and the entire RPA14 subunit. The structure revealed that RPA14 and the central part of RPA32 are structural homologues. Each subunit contains a central OB‐fold domain, which also resembles the DNA‐binding domains in RPA70; an N‐terminal extension that interacts with the central OB‐fold domain; and a C‐terminal helix that mediate heterodimerization via a helix–helix interaction. The OB‐fold of RPA32, but not RPA14, possesses additional similarity to the RPA70 DNA‐binding domains, supporting a DNA‐binding role for RPA32. The discovery of a third and fourth OB‐fold in RPA suggests that the quaternary structure of SSBs, which in Bacteria and Archaea are also tetramers of OB‐folds, is conserved in evolution. The structure also suggests a mechanism for RPA trimer formation.
Standard (-1) divisors

In this paper we generalize the notion of (-1) curves to standard (-1) divisors for the blow up of n-dimensional projective space in several points. We generalize Noether's inequality, to prove that all standard (-1) divisors are in bijective correspondence with the orbit of the Weyl group action on one exceptional divisor. Moreover, we prove that the irreducibility condition from the definition of standard (-1) divisors can be replaced by the numerical condition of having positive intersection with all standard (-1) divisors of smaller degree via the Mukai pairing.
National-level risk assessment : A multi-country study of malware infections

The security of computers is a function of both their inherent vulnerability and the environment in which they operate. Much as with the public health of human populations, the “public health” of computer populations can be studied in terms of what factors influence their security. Using data collected from Microsoft Windows Malicious Software Removal Tool (MSRT) running on more than one billion machines, we conduct a multi-country analysis of malware infections and measures of economic development, educational achievement, Internet infrastructure, and cybersecurity preparedness. We find that while increases in these factors is often correlated with reduced infection rates, their significance and magnitude vary considerably. In contrast to past work, these variations suggest that policy interventions, such as efforts to increase the quality of home Internet connections, are likely to decrease infection rates in only some circumstances.
Age structure and public expenditures on children.

Data for U.S. states are used to examine the relationship between age structure and public expenditures on welfare and education. States with comparatively large child populations spend significantly less per child than states with smaller numbers of children. States with relatively large elderly populations spend slightly less on children. The effects of age structure on public expenditures on children are attributable to lower per capita incomes in states with higher dependency ratios. (EXCERPT)
Enhanced oxidative burst in immunologically activated but not elicited polymorphonuclear leukocytes correlates with fungicidal activity

Polymorphonuclear neutrophils (PMN) induced locally in immune mice by intraperitoneal injection of antigen exhibit enhanced fungicidal activity compared with PMN elicited with thioglycolate. The mechanism of the differences in these PMN populations was studied. Sublethal infection was used to produce immunity to Blastomyces dermatitidis. A correlation was sought between the ability of PMN to kill, or not kill, B. dermatitidis and the production of the oxidative burst, as measured by luminol-enhanced chemiluminescence (CL). Although elicited PMN cocultured with Candida albicans produced a burst of CL and were candidacidal, killing did not occur when PMN were cocultured with B. dermatitidis. Lack of killing of B. dermatitidis by elicited PMN correlated with lack of stimulation of a brisk oxidative burst. In contrast to elicited PMN, PMN induced by B. dermatitidis antigen responded to this fungus with a burst of CL and a significant reduction of inoculum CFU (80%). Furthermore, these PMN when cocultured with C. albicans produced an enhanced burst of CL, and killing was enhanced compared with that by elicited PMN, e.g., 86 versus 58%. The CL burst and killing of B. dermatitidis by antigen-induced PMN was abrogated in the presence of catalase, implying a critical role for hydrogen peroxide. Partial but significant depression of CL and killing in the presence of dimethyl sulfoxide, a hydroxyl radical scavenger, identified hydroxyl radical, or its metabolites, as a toxic product(s) responsible for a significant fraction of fungicidal activity. These results indicate that the metabolic activity and microbicidal activity of PMN can be altered (enhanced) at the site of an immunological reaction and thus could constitute an important factor in resistance.
PHOTOMETRIC FOLLOW-UP OBSERVATIONS OF THE TRANSITING NEPTUNE-MASS PLANET GJ 436b

This paper presents multiband photometric follow-up observations of the Neptune-mass transiting planet GJ 436b, consisting of five new ground-based transit light curves obtained in 2007 May. Together with one already published light curve, we have at hand a total of six light curves, spanning 29 days. The analysis of the data yields an orbital period P = 2.64386 ± 0.00003 days, midtransit time Tc [HJD] = 2454235.8355 ± 0.0001, planet mass Mp = 23.1 ± 0.9 M⊕ = 0.073 ± 0.003 MJup, planet radius Rp = 4.2 ± 0.2 R⊕ = 0.37 ± 0.01 RJup, and stellar radius Rs = 0.45 ± 0.02 R☉. Our typical precision for the midtransit timing for each transit is about 30 s. We searched the data for a possible signature of a second planet in the system through transit timing variations (TTV) and variation of the impact parameter. The analysis could not rule out a small, of the order of a minute, TTV and a long-term modulation of the impact parameter, of the order of +0.2 yr−1.
Violence against lesbians and gay men

Hate crimes against minority groups such as homosexuals present a particular challenge for the criminal justice system. This report discusses the prevalence of anti homosexual violence in Australia, its characteristics, and its impact on the victim. It also examines the cultural climate and social norms which encourage anti homosexual violence. Preventative measures are considered under the following headings: decriminalisation and anti discrimination legislation; education; the media; the criminal justice system; the police; research and statistics; and community prevention and education programs.
Possible Association between Parental Socioeconomic Status and Development of Autistic Traits among Children Screened 36 Months after Birth in the Norwegian Mother and Child Cohort Study Project paper

3 Introduction.3 Previous studies on the possible link between socioeconomic status and autism. 4 Aims of the study. 5 Materials and Methods. 5 MoBa and the ABC study. 5 The screening algorithm and the Social Communication Questionnaire – SCQ. 6 Diagnostic evaluation.7 Exposure and outcome variables. 8 Statistical analyses. 9 Possible selection bias in our study.10 Results. 10 SCQ-33 >=12 as outcome variable. 12 ASD-ST as outcome variable. 18 ASD as outcome variable.20 Investigation of possible selection bias.21 Discussion.25 Main results.25 Strengths and weaknesses.26 Conclusion.27 References.28
Joint Rate Allocation for Multiprogram Video Coding Using FGS

In this paper, we address the problem of joint rate allocation for scalable video coding (SVC) of multiple video programs using the fine granularity scalability (FGS), which is not specified by any current H.264/AVC profile. Most of the existing approaches are based on non-SVC platforms, where computationally expensive encoding or transcoding is demanded to adjust the bit-rate of each video program. Different from all these works, we develop a new statistical multiplexing system, where FGS is applied to compress the video programs. First, we propose an efficient look-ahead approach to distribute the base layer coding bit-rate. Second, a piecewise linear model is applied to accurately estimate the rate-distortion relationship in the FGS layers. Based on this model, a novel algorithm is designed to dynamically allocate the available bandwidth to different programs for rate adaptation in order to minimize the variation of quality of different video programs. Experiments are carried out to verify the performance of the proposed scheme by comparing it with existing methods. The results demonstrate the superiority of the proposed scheme and the quality difference between different programs is greatly reduced.
Recipient outcomes of salvage liver transplantation versus primary liver transplantation: A systematic review and meta‐analysis

Salvage liver transplantation (SLT), or liver transplantation after liver resection (LR), has been performed after primary LR for many years. However, the true outcomes and risks of SLT versus primary liver transplantation (PLT) remain unclear. We performed a systematic review and meta‐analysis to evaluate the survival rate of SLT recipients and the incidence of postoperative complications. Among 2799 screened references, 7 eligible studies were identified. The results of the meta‐analysis indicated no statistically significant differences in the overall survival rates of SLT and PLT: the pooled relative risk (RR) was 0.99 [95% confidence interval (CI) = 0.90‐1.09, P = 0.87] at 1 year, 0.97 (95% CI = 0.83‐1.13, P = 0.68) at 3 years, and 0.96 (95% CI = 0.81‐1.13, P = 0.61) at 5 years. As for postoperative complications, there were no statistically significant differences in the incidence of sepsis and biliary complications between SLT and PLT, but there was a significantly higher incidence of bleeding with SLT (RR = 2.84, 95% CI = 1.57‐5.13, P = 0.001). In conclusion, the overall survival associated with SLT is similar to that associated with PLT. Because of the limited organ donor pool, SLT might be an acceptable therapy for patients undergoing primary LR for hepatocellular carcinoma. Liver Transpl 18:1316–1323, 2012. © 2012 AASLD.
The Feeling Body: Affective Science Meets the Enactive Mind

In The Feeling Body, Giovanna Colombetti takes ideas from the enactive approach developed over the last twenty years in cognitive science and philosophy of mind and applies them for the first time to affective science -- the study of emotions, moods, and feelings. She argues that enactivism entails a view of cognition as not just embodied but also intrinsically affective, and she elaborates on the implications of this claim for the study of emotion in psychology and neuroscience. In the course of her discussion, Colombetti focuses on long-debated issues in affective science, including the notion of basic emotions, the nature of appraisal and its relationship to bodily arousal, the place of bodily feelings in emotion experience, the neurophysiological study of emotion experience, and the bodily nature of our encounters with others. Drawing on enactivist tools such as dynamical systems theory, the notion of the lived body, neurophenomenology, and phenomenological accounts of empathy, Colombetti advances a novel approach to these traditional issues that does justice to their complexity. Doing so, she also expands the enactive approach into a further domain of inquiry, one that has more generally been neglected by the embodied-embedded approach in the philosophy of cognitive science.
Furan in Commercially Processed Foods: Four-Year Field Monitoring and Risk Assessment Study in Korea

The aim of this study was to monitor and assess the risk associated with the presence of furan in various food products consumed in Korea. An optimized analytical method was used for the analysis of furan levels. The optimized solid-phase microextraction (SPME) fiber exposure conditions as follows for temperature, time, and amount of sample were 50°C, 20 min, and 5 g (ml), respectively. Furan was detected in all food samples tested, at levels ranging from 0.4 ng/g in canned crab to 814 ng/g in ground roasted coffee powder. The furan levels in coffee, canned fish, canned meats, sauce, soup, retort, canned vegetables, baby foods, nutritional/diet drinks, confectionary and biscuits and snacks, juice, jams, and canned fruit were (ng/g) 169, 56.1, 30.1, 21.1, 18.1, 15.6, 10.9, 10.6, 7.1, 5.4, 3.7, 3.2, and 2.9, respectively. Furan concentrations in baby food products were between 1 and 102.5 ng/g. The total exposure estimate of furan was determined to be 10.6 ng/kg/d (maximum, 20 ng/kg/d) for adults, and 17.4 ng/kg/d (maximum. 84.9 ng/kg/d) for babies. Exposure estimates found in this study are lower than those prescribed by the U.S. Food and Drug Administration (FDA).
A High-Performance 30-nm Gate-All-Around Poly-Si Nanowire Thin-Film Transistor With $\hbox{NH}_{3}$ Plasma Treatment

A novel 30-nm gate-all-around (GAA) polycrystalline-silicon (poly-Si) nanowire (NW) thin-film transistor (TFT) is reported for the first time. Owing to the NW and GAA structure, the channel electric potential is well controlled by the gate electrode. After NH3 plasma treatment for defects passivation, the values of 0.97 V, 224 mV/dec, and 0.895 V/V of threshold voltage, subthreshold swing, and drain-induced barrier lowering are achieved, respectively. A high driving current of 459 μA/μm and an ON-state/OFF-state current ratio of 5 × 107 are also obtained. These excellent characteristics indicate that the ultrasmall GAA NW poly-Si TFT would have the potential to be applied in the 3-D integrated-circuit or system-on-panel field.
Opinion Mining for Relating Subjective Expressions and Annual Earnings in US Financial Statements

Financial statements contain quantitative information and manager's subjective evaluation of firm's financial status. Using information released in U.S. 10-K filings. Both qualitative and quantitative appraisals are crucial for quality financial decisions. To extract such opinioned statements from the reports, we built tagging models based on the conditional random field (CRF) techniques, considering a variety of combinations of linguistic factors including morphology, orthography, predicate-argument structure, syntax, and simple semantics. Our results show that the CRF models are reasonably effective to find opinion holders in experiments when we adopted the popular MPQA corpus for training and testing. The contribution of our paper is to identify opinion patterns in multiword expressions (MWEs) forms rather than in single word forms. We find that the managers of corporations attempt to use more optimistic words to obfuscate negative financial performance and to accentuate the positive financial performance. Our results also show that decreasing earnings were often accompanied by ambiguous and mild statements in the reporting year and that increasing earnings were stated in assertive and positive way.
Automated pipeline for anatomical phenotyping of mouse embryos using micro-CT

The International Mouse Phenotyping Consortium (IMPC) plans to phenotype 20,000 single-gene knockout mice to gain an insight into gene function. Approximately 30% of these knockout mouse lines will be embryonic or perinatal lethal. The IMPC has selected three-dimensional (3D) imaging to phenotype these mouse lines at relevant stages of embryonic development in an attempt to discover the cause of lethality using detailed anatomical information. Rate of throughput is paramount as IMPC production centers have been given the ambitious task of completing this phenotyping project by 2021. Sifting through the wealth of data within high-resolution 3D mouse embryo data sets by trained human experts is infeasible at this scale. Here, we present a phenotyping pipeline that identifies statistically significant anatomical differences in the knockout, in comparison with the wild type, through a computer-automated image registration algorithm. This phenotyping pipeline consists of three analyses (intensity, deformation, and atlas based) that can detect missing anatomical structures and differences in volume of whole organs as well as on the voxel level. This phenotyping pipeline was applied to micro-CT images of two perinatal lethal mouse lines: a hypomorphic mutation of the Tcf21 gene (Tcf21-hypo) and a knockout of the Satb2 gene. With the proposed pipeline we were able to identify the majority of morphological phenotypes previously published for both the Tcf21-hypo and Satb2 mutant mouse embryos in addition to novel phenotypes. This phenotyping pipeline is an unbiased, automated method that highlights only those structural abnormalities that survive statistical scrutiny and illustrates them in a straightforward fashion.
Robots in Education

The new paradigm in engineering education demands hands-on training of the students using technology oriented projects. The roots of this approach can be traced back to the work of Seymour Papert in 1970s when he built a programmable turtle with a reflective light sensor (Papert, 1971). His ideas ultimately lead to the educational theory of constructionism (Papert, 1986 and Harel & Papert, 1991). According to this theory, students learn very effectively when they are involved in the creation of an external object that lives in the real world. Learners use this object to think with, and to relate ideas of, their subject of inquiry (Bourgoin, 1990). From an educational point of view, the theory of Papert can be linked to the constructivist theory of Jean Piaget (Paiget, 1972). According to this theory, learning comes from an active process of knowledge construction. This knowledge can be gained through real life experiences and linked to a learners’ previous knowledge. The concept of turtle was evolved further at MIT and became the famous Programmable Brick by Fred Martin who also developed new learning environments and methodologies based on this concept (Martin, 1988 and Martin 1994). The unusual idea put forward by the Brick, at least at the time of its invention, was the incorporation of the “design” work into the learning process. Students were not only users in this case, but were actively involved in the design process, while solving their problems (Martin, 1996a). The ‘Brick’ was later adopted and incorporated by the LEGO MINDSTORMS kit (RCX in 1998 and NXT made available in 2006). The use of the name “MINDSTROMS” can also be traced back to the book by Seymour Papert (Papert 1980). Versions of these Bricks for economically challenged communities have also been proposed recently (Sipitakiat, et al, 2004). The active learning methodology (Harmin and Toth, 2006) uses this philosophy of involving students in their own learning through class discussions and group problem solving and proves to be effective at least in certain cases. Robots have become a major player in this area and have been employed in improving the quality and level of student learning, ranging from primary schools to graduate level. As pointed out by Resnick and Martin (Resnick and Martin, 1990), “Creatures built from Electronic Bricks fall on the fuzzy boundary between animals and machines, forcing students to come to terms with how machines can be like animals, and vice versa”. In engineering courses incorporating connectionism approach, the students are asked to design and program a robot for a specific task. They also work in small teams and help and learn from each other. However it is important to know what is currently available to an educator so that he/she can develop the required skills, abilities, attitudes and values in students. In this article we identify some of the major research centres working in the area of education utilizing robots and discuss some of the robotic kits now available to educators. We also comment on the famous robotic competitions worldwide.
Mechanism of methacholine dose-response plateaus in normal subjects.

Normal subjects develop plateaus on dose-response curves produced from inhalation challenge tests with bronchoconstricting agonists. These plateaus occur after only mild degrees of airway narrowing despite the fact that, if unloaded, maximally activated airway smooth muscle (ASM) should be able to cause airway closure. Plateaus may develop because, despite maximal activation, the muscle load provided by lung parenchymal recoil and tidal swings in airway transmural pressure are sufficient to prevent further ASM shortening. Alternatively, progressive ASM activation may occur throughout the plateau, but progressive hyperinflation and/or parenchymal stiffening could increase parenchymal load and attenuate further airway narrowing. In the first case, maximal ASM activation causes the plateau and in the second case the plateau is caused by progressive activation balanced by progressive loading. To test which of these mechanisms is responsible for the plateau, we measured pulmonary resistance (RL) and the maximal, minimal, and mean pulmonary elastic recoil pressure (PELmax, PELmin, and PELmean) during tidal breathing throughout methacholine challenge in 10 normal subjects. PELmean served as our measure of ASM afterload. Subjects swallowed an esophageal balloon and inhaled doubling concentrations of methacholine (1 to 256 mg/ml). RL was measured after each dose, as was PEL. All subjects developed a plateau on the dose-response curve defined by < 25% change in RL over three successive doses. During the RL plateau, there was no significant further increase in PELmean, i.e., PELmean also plateaued. These data are consistent with the hypothesis that maximal activation of ASM is balanced by an equal afterload at the maximal dose-response plateau. Airway hyperresponsiveness could result from a failure of afterload to attenuate muscle shortening after maximal activation.
Interaction of myocyte enhancer factor 2 (MEF2) with a mitogen-activated protein kinase, ERK5/BMK1.

Myocyte enhancer factor 2 (MEF2) has been implicated in the complex hierarchical regulation of muscle-specific gene expression and differentiation. While the MyoD family members are able to initiate the skeletal muscle differentiation program, whether MEF2 is sufficient in directing skeletal muscle differentiation is still controversial. Furthermore, how MEF2 transactivates its target genes is not fully understood. It has been suggested that the interactions of MEF2 with other factors modify its transcriptional activity. Therefore, the identification of MEF2-interacting factors may be important in understanding the mechanism by which MEF2 activates its target genes. In this study, a mitogen-activated protein kinase (MAP kinase), ERK5/BMK1 was found to interact with MEF2 in a yeast two hybrid screen. The interaction was confirmed by a glutathione S -transferase-pull down assay and a co-immunoprecipitation study indicating that endogenous ERK5 and MEF2 interact with each other in vivo . The interacting domain of MEF2 was mapped to the N-terminus which contains the highly conserved MADS and MEF2 domains. Functionally, ERK5/BMK1 was able to phosphorylate MEF2 in vitro . Furthermore, when cotransfected with ERK5/BMK1, the transactivation capacity of MEF2 was enhanced. These results suggest that the functions of MEF2 could be regulated through ERK5/BMK1.