Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular basis for serum resistance in Neisseria gonorrhoeae

The molecular basis for resistance to killing by normal human serum (NHS) exhibited by certain strains of Neisseria gonorrhoeae represents a composite of numerous phenomena. These include (i) the absence in human serum of bactericidal antibody directed against specific epitopes, the most important of which reside in lipooligosaccharide (LOS) antigens (11, 52, 59); and (ii) phenotypic shifting of LOS epitope expression (41, 59), such as may occur especially in vivo (10). This may result in the loss of epitopes that serve as appropriate receptors (bactericidal or lytic epitopes) for bactericidal antibodies and complement. Alternatively, new epitopes may be acquired in vivo, which may obscure underlying lytic epitopes, thereby preventing recognition of these by human bactericidal antibodies. In addition, (iii) blocking antibodies, directed at outer membrane protein antigens, modulate or down-regulate bacterial killing, mainly by preventing binding of bactericidal antibodies to lytic epitopes (26, 49). Finally, and least well understood, (iv) there is a partial failure to form the C5 convertase necessary for full development of membrane attack complexes (MACs or C5b-9 [11, 12]) but also a failure of MACs that do form to fully insert through the gonococcal outer membrane (22, 27). In addition, less C3 may bind to serum-resistant organisms, and C3 that does bind may not be hemolytically active (51).
Novel Avian Influenza A(H7N9) Virus in Tree Sparrow, Shanghai, China, 2013

In spring 2013, influenza A(H7N9) virus was isolated from an apparently healthy tree sparrow in Chongming Dongping National Forest Park, Shanghai City, China. The entire gene constellation of the virus is similar to that of isolates from humans, highlighting the need to monitor influenza A(H7N9) viruses in different species.
Regulation of megakaryocytopoiesis

Megakaryocytopoiesis is the cellular developmental process prior to the release of platelets into the circulation. Regulation of megakaryocytopoiesis is a complex phenomenon that begins with commitment of hematopoietic stem cells to the replication and maturation of progenitor cells through endomitosis and megakaryocyte differentiation [1‐4]. Platelet production is determined by the number and size of megakaryocytes in the marrow and may be regulated at two levels: at early stages of cell proliferation resulting in increased megakaryocyte numbers, and at later stages by endoreplication which increases DNA content and the size of megakaryocytes [5].
Kendrick mass defect spectrum: a compact visual analysis for ultrahigh-resolution broadband mass spectra.

At currently achievable Fourier transform ion cyclotron resonance broadband mass spectrometry resolving power (m/deltam50% > 350,000 for 200 < m/z < 1,000), it would be necessary to spread out a conventional mass spectrum over approximately 200 m in order to provide visual resolution of the most closely resolved peaks. Fortunately, there are natural gaps in a typical mass spectrum, spaced 1 Da apart, because virtually no commonly encountered elemental compositions yield masses at those values. Thus, it is possible to break a broadband mass spectrum into 1-Da segments, rotate each segment by 90 degrees, scale each segment according to its mass defect (i.e., difference between exact and nominal mass), and then compress the spacing between the segments to yield a compact display. For hydrocarbon systems, conversion from IUPAC mass to "Kendrick" mass (i.e., multiplying each mass by 14.00000/14.01565) further simplifies the display by rectilinearizing the peak patterns. The resulting display preserves not only the "coarse" spacings (e.g., approximately 1 Da between odd and even masses, corresponding to either even vs odd number of nitrogens or 12C(c) vs 12C(c-1)13C1 elemental compositions of the same molecule; approximately 2-Da separations, corresponding to a double bond or ring; approximately 14 Da separations, corresponding to one CH2 group) but also the "fine structure" (i.e., different mass defects for different elemental compositions) across each 1-Da segment. The method is illustrated for experimental electrospray ionization FTICR ultrahigh-resolution mass spectra of a petroleum crude oil. Several thousand elemental compositions may be resolved visually in a single one-page two-dimensional display, and various compound families-class (NnOoSs), type (Z in C(c)H2(c+z)NnOoSs), and alkylation series-may be identified visually as well.
Interdimer processing mechanism of procaspase‐8 activation

The execution of apoptosis depends on the hierarchical activation of caspases. The initiator procaspases become autoproteolytically activated through a less understood process that is triggered by oligomerization. Procaspase‐8, an initiator caspase recruited to death receptors, is activated through two cleavage events that proceed in a defined order to generate the large and small subunits of the mature protease. Here we show that dimerization of procaspase‐8 produces enzymatically competent precursors through the stable homophilic interaction of the procaspase‐8 protease domain. These dimers are also more susceptible to processing than individual procaspase‐8 molecules, which leads to their cross‐cleavage. The order of the two interdimer cleavage events is maintained by a sequential accessibility mechanism: the separation of the large and small subunits renders the region between the large subunit and prodomain susceptible to further cleavage. In addition, the activation process involves an alteration in the enzymatic properties of caspase‐8; while procaspase‐8 molecules specifically process one another, mature caspases only cleave effector caspases. These results reveal the key steps leading to the activation of procaspase‐8 by oligomerization.
The acute effect of stretching on the passive stiffness of the human gastrocnemius muscle tendon unit

Passive stretching is commonly used to increase limb range of movement prior to athletic performance but it is unclear which component of the muscle–tendon unit (MTU) is affected by this procedure. Movement of the myotendinous junction (MTJ) of the gastrocnemius medialis muscle was measured by ultrasonography in eight male participants (20.5 ± 0.9 years) during a standard stretch in which the ankle was passively dorsiflexed at 1 deg s−1 from 0 deg (the foot at right angles to the tibia) to the participants' volitional end range of motion (ROM). Passive torque, muscle fascicle length and pennation angle were also measured. Standard stretch measurements were made before (pre‐) and after (post‐) five passive conditioning stretches. During each conditioning stretch the MTU was taken to the end ROM and held for 1 min. Pre‐conditioning the extension of the MTU during stretch was taken up almost equally by muscle and tendon. Following conditioning, ROM increased by 4.6 ± 1.5 deg (17%) and the passive stiffness of the MTU was reduced (between 20 and 25 deg) by 47% from 16.0 ± 3.6 to 10.2 ± 2.0 Nm deg−1. Distal MTJ displacement (between 0 and 25 deg) increased from 0.92 ± 0.06 to 1.16 ± 0.05 cm, accounting for all the additional MTU elongation and indicating that there was no change in tendon properties. Muscle extension pre‐conditioning was explicable by change in length and pennation angle of the fascicles but post‐conditioning this was not the case suggesting that at least part of the change in muscle with conditioning stretches was due to altered properties of connective tissue.
PINK1-Phosphorylated Mitofusin 2 Is a Parkin Receptor for Culling Damaged Mitochondria

Where Parkin Parks Damaged mitochondria are removed from cells in a process known as mitophagy. Failure of this quality-control mechanism contributes to Parkinson's disease. When damaged mitochondria lose membrane depolarization, the protein kinase, PINK1, accumulates on the mitochondrial surface, recruits Parkin, and promotes mitophagy. Chen and Dorn (p. 471) describe another component of this process, mitofusin 2, which appears to function as the receptor for Parkin on the surface of damaged mitochondria. The Parkinson’s disease factors PINK1 and Parkin interact with mitofusin 2 on damaged mitochondria. Senescent and damaged mitochondria undergo selective mitophagic elimination through mechanisms requiring two Parkinson’s disease factors, the mitochondrial kinase PINK1 (PTEN-induced putative kinase protein 1; PTEN is phosphatase and tensin homolog) and the cytosolic ubiquitin ligase Parkin. The nature of the PINK-Parkin interaction and the identity of key factors directing Parkin to damaged mitochondria are unknown. We show that the mitochondrial outer membrane guanosine triphosphatase mitofusin (Mfn) 2 mediates Parkin recruitment to damaged mitochondria. Parkin bound to Mfn2 in a PINK1-dependent manner; PINK1 phosphorylated Mfn2 and promoted its Parkin-mediated ubiqitination. Ablation of Mfn2 in mouse cardiac myocytes prevented depolarization-induced translocation of Parkin to the mitochondria and suppressed mitophagy. Accumulation of morphologically and functionally abnormal mitochondria induced respiratory dysfunction in Mfn2-deficient mouse embryonic fibroblasts and cardiomyocytes and in Parkin-deficient Drosophila heart tubes, causing dilated cardiomyopathy. Thus, Mfn2 functions as a mitochondrial receptor for Parkin and is required for quality control of cardiac mitochondria.
Variability in cross-dialectal production and perception of contrasting phonemes: the case of the alveolar-retroflex contrast in Beijing and Taiwan Mandarin

The alveolar-retroflex contrast is a critical feature in Mandarin and is often used to differentiate Beijing Mandarin from other dialects of Mandarin like Taiwan Mandarin. While a number of linguistic and sociolinguistic factors have been found to affect the alveolar-retroflex contrast, leading to variation in Taiwan Mandarin, a consistent alveolar-retroflex distinction is described for Beijing Mandarin in the literature on Mandarin phonology. With a series of map tasks, this dissertation examines whether the production of alveolar-retroflex contrast in both dialects is subject to the effects of vowel context and focal prominence. With a discrimination task and a goodness rating task, the categorical and gradient modes of alveolar-retroflex perception in different vowel contexts are investigated for listeners of both dialects. Results of the production study indicate that the acoustic characterization of Beijing vs. Taiwan Mandarin alveolar-retroflex contrast varies by vowel and by how each contrasting phoneme is realized in a particular vowel context. Focal prominence is found to result in longer syllable durations but not increased spectral distinctiveness between the alveolar and retroflex sibilants. The findings are discussed with respect to enhancement theory. The perception study found that Beijing and Taiwan listeners have different perceptual boundaries along the acoustic continuum, with a lower cutoff frication frequency required for the retroflex percepts for Beijing listeners. Listeners’ alveolar-retroflex boundaries shift to lower frequencies in the rounded vowel context to normalize for vowel coarticulatory effects. Discrepant within-category sensitivity was found in that while both Beijing and Taiwan listeners perceive all retroflex variants as equally good, Beijing listeners consider the endpoint variant of the alveolar as the best category exemplar. The findings are discussed within the frameworks of quantal theory and exemplar theory as well as with respect to the hyperspace effect in perception. Together, the results show that linguistic (i.e., vowel context) and sociolinguistic (i.e., dialect) factors collectively and variably affect the production and perception of the Mandarin alveolar-retroflex contrast.
Virtual Unreality of Videogames

Beginning with an objection raised to the excessive attention promotion gives to the aspect of "realism" in videogames, I chose to describe instead how excessive realism may be counterproductive. I identify and focus on what game designers wish to obtain from their products, then proceed to introduce and explain the concept of "virtual unreality of videogames". A number of examples and counter-examples serve to describe important principles used by game designers to build what I have called virtual unreality.
FormulaBuilder: a tool for graph-based modelling and generation of formulae

In this paper we present the FormulaBuilder, a flexible tool for graph-based modelling and generation of formulae. The FormulaBuilder allows easy and intuitive creation of formulae by using basic components called Formula Building Blocks (FBBs) and arranging them as graphs according to the syntactic structure of a formula. Such a graph can then be validated and used to generate the corresponding formula on the basis of a specific syntax which is chosen from a list of syntaxes supported by the FormulaBuilder.An important application of the FormulaBuilder is the formal specification of properties that describe the requirements of a system. Such property specifications are usually needed by verification tools like model checkers, that help software engineers to detect errors in a specified system. The FormulaBuilder allows users to model property specifications as formula graphs by using commonly-occurring specification patterns.
A critical look at community based tourism

Community based tourism (CBT) could be one way of creating a more sustainable tourism industry. This article critically reviews the CBT approach in light of fieldwork in a North Queensland tourism destina- tion. The literature on CBT has three major failings from a community development perspective. Firstly, it tends to take a functional approach to community involvement; secondly, it tends to treat the host community as a homogeneous bloc; and thirdly, it neglects the structural constraints to local control of the tourism industry. Attention to these issues could contribute to a more sustainable and equitable tourism industry.
The effects of behavioral parental education application reducing parenting stress among parents children with ADHD

The present quasi-experimental study was performed to evaluate the efficacy of Behavioural Parent Training Program (BPTP) in reducing parental stress. The sample for this study consists of 60 parents of children with ADHD was randomly assigned to experimental and control groups. The experimental group received the Barkley’s parent training program. All participants completed the Parental Stress Index /Short Form (PSI/SF) at four different time points. A Mixed Model ANOVA using the SPSS 19.0 was used in data analysis. The results from mixed model ANOVA reflected that mean changes in parental stress were significantly different between two groups. In addition, Post hoc analysis revealed a statistically significant decrease in parental stress only for the experimental group. The present study in line with some previous studies provides some preliminary evidence that supports the effectiveness of Barkley’s parent training program to reduce parental stress for Iranian parents with ADHD children. The implications of the study findings and limitations of the research method along with recommendations for future studies are discussed. Keywords: AHDA children; Barkley’s parent training program; parental stress, parents
More Choice, Higher Turnout? The Impact of Consideration Set Size and Homogeneity on Political Participation

Abstract Central to the emerging scholarship on how political supply influences electoral behavior is the claim that more choice leads to higher turnout. However, empirical tests of this proposition have been limited to the aggregate level. This article examines the relationship between the properties of electoral choice sets, as perceived by the voters, and electoral participation. Following recent advances in choice research, the article distinguishes between an awareness set, consisting of all choice options known to the voter, and a consideration set which includes only those alternatives that are seriously considered by the voter. We hypothesize that the cardinality, ideological homogeneity and distinctiveness of individual consideration sets are positively associated with electoral participation. The expectation is tested with individual-level data from three waves of the European Elections Study. Our results suggest that the relationship between the structure of political supply and participation is complex: while the number of choice alternatives in the consideration set is positively associated with turnout, the ideological diversity of choice options suppresses electoral participation.
The signaling pathways of Epstein-Barr virus-encoded latent membrane protein 2A (LMP2A) in latency and cancer

Epstein-Barr virus (EBV) is a ubiquitous virus with infections commonly resulting in a latency carrier state. Although the exact role of EBV in cancer pathogenesis remains not entirely clear, it is highly probable that it causes several lymphoid and epithelial malignancies, such as Hodgkin’s lymphoma, NK-T cell lymphoma, Burkitt’s lymphoma, and nasopharyngeal carcinoma. EBV-associated malignancies are associated with a latent form of infection, and several of these EBV-encoded latent proteins are known to mediate cellular transformation. These include six nuclear antigens and three latent membrane proteins. Studies have shown that EBV displays distinct patterns of viral latent gene expression in these lymphoid and epithelial tumors. The constant expression of latent membrane protein 2A (LMP2A) at the RNA level in both primary and metastatic tumors suggests that this protein might be a driving factor in the tumorigenesis of EBV-associated malignancies. LMP2A may cooperate with the aberrant host genome, and thereby contribute to malignant transformation by intervening in signaling pathways at multiple points, especially in the cell cycle and apoptotic pathway. This review summarizes the role of EBV-encoded LMP2A in EBV-associated viral latency and cancers. We will focus our discussions on the molecular interactions of each of the conserved motifs in LMP2A, and their involvement in various signaling pathways, namely the B-cell receptor blockade mechanism, the ubiquitin-mediated (Notch and Wnt) pathways, and the MAPK, PI3-K/Akt, NK-κB and STAT pathways, which can provide us with important insights into the roles of LMP2A in the EBV-associated latency state and various malignancies.
Optimization model of the predictive head orientation for humanoid robots

Most studies on humanoid robot locomotion focus on the dynamic stability of the robot and movements of the limbs. The role of the head during locomotion is one aspect that has received relatively little focus. In humans, the head plays a very important role of stabilizing in space and anticipating walking direction. In order to generate realistic humanoid motion, this is a vital aspect that must be taken into account. In this study, we propose a generalized framework for modeling human like head-body behavior during locomotion. We developed a dynamic model of the head and body orientation in which the head orientation is actively controlled and the trunk is coupled to it by a rotational spring-damper like term. Least-squares optimization was used to determine the parameters of this model from recorded human experimental data. The results were evaluated against novel recordings and provided a good prediction of human behavior. Our approach is an effective way to create human-like motions for anthropomorphic agents such as humanoid robots, and provides a good mathematical basis for extension to other aspects of human movements.
The case for addressing primary resistance mutations to non-nucleoside reverse transcriptase inhibitors to treat children born from mothers living with HIV in sub-Saharan Africa

The prevalence of human immunodeficiency virus (HIV) drug resistance mutations (DRMs) was estimated in 25 untreated infants who were living with HIV‐1, younger than 13 months and living in Senegal. Antiretroviral DRMs were detected in 8 of 25 (32%) children. Non‐nucleoside reverse transcriptase inhibitor (NNRTI) DRMs were present in all (100%) children whose viruses harboured DRMs: K103N in 43%; Y181C, K101E and V106M each in 29%; and Y188L in 14%. The D67N thymidine‐analogue mutation was observed in only two children whose mothers had received chemoprophylaxis of mother‐to‐child transmission (MTCT). The proportion of children whose viruses harboured DRMs was then 6.5‐fold higher in children whose mother–child couples had received nevirapine (NVP)‐based chemoprophylaxis than in other couples without prophylaxis [7 of 13 (53.8%) vs. 1 of 12 (8.3%)]. These findings point to the absolute need to address primary resistance mutations in case of virological failure in young children treated by antiretroviral drugs, and to make more effective treatment regimens available to NVP‐exposed infants living with HIV‐1 in Senegal.
Evacuation in Cancun During Hurricane Gilbert

This paper describes the evacuation of the population of Cancun, Mexico during Hurricane Gilbert, and identifies some of the correlates of their evacuation behavior. The information was collected during a post-disaster visit conducted one week after impact (September 13, 1988) and as part of a survey a year later of a random sample of 431 persons 18 years old and older who resided in Cancun at the time of the disaster. One-fourth of the respondents evacuated. The majority of the evacuees found shelter in the homes of friends, neighbors, and relatives and were gone from their homes a week or less. Socio-demographic variables such as the number of persons in the household, gender, age, and marital status were not very useful predictors of evacuation behavior. Lower socioeconomic status (SES) and higher numbers of family contacts did not increase the probability of evacuation. The findings underscore the importance of calculations of risk for understanding evacuation behavior. The environmental context and physical characteristics of residences are significant variables impacting on the perceptions of risk and on subsequent evacuation behavior.
Evidence for non-conservative current-induced forces in the breaking of Au and Pt atomic chains

This experimental work aims at probing current-induced forces at the atomic scale. Specifically it addresses predictions in recent work regarding the appearance of run-away modes as a result of a combined effect of the non-conservative wind force and a ‘Berry force’. The systems we consider here are atomic chains of Au and Pt atoms, for which we investigate the distribution of break down voltage values. We observe two distinct modes of breaking for Au atomic chains. The breaking at high voltage appears to behave as expected for regular break down by thermal excitation due to Joule heating. However, there is a low-voltage breaking mode that has characteristics expected for the mechanism of current-induced forces. Although a full comparison would require more detailed information on the individual atomic configurations, the systems we consider are very similar to those considered in recent model calculations and the comparison between experiment and theory is very encouraging for the interpretation we propose.