Miracle-dz/UniFAR-FTUs huggingface dataset:
Mutational and secondary structural analysis of the basolateral sorting signal of the polymeric immunoglobulin receptor

The 17-juxtamembrane cytoplasmic residues of the polymeric immunoglobulin receptor contain an autonomous basolateral targeting signal that does not mediate rapid endocytosis (Casanova, J. E., G. Apodaca, and K. E. Mostov. Cell. 66:65-75). Alanine-scanning mutagenesis identifies three residues in this region, His656, Arg657, and Val660, that are most essential for basolateral sorting and two residues, Arg655 and Tyr668, that play a lesser role in this process. Progressive truncations suggested that Ser664 and Ile665 might also play a role in basolateral sorting. However, mutation of these residues to Ala or internal deletions of these residues did not affect basolateral sorting, indicating that these residues are probably not required for basolateral sorting. Two-dimensional NMR spectroscopy of a peptide corresponding to the 17-mer signal indicates that the sequence Arg658-Asn-Val-Asp661 has a propensity to adopt a beta-turn in solution. Residues COOH-terminal to the beta-turn (Arg662 to Arg669) seem to take up a nascent helix structure in solution. Substitution of Val660 with Ala destabilizes the turn, while mutation of Arg657 to Ala does not appear to affect the turn structure. Neither mutation detectably altered the stability of the nascent helix in the COOH-terminal portion of the peptide.
The first report of the vanC 1 gene in Enterococcus faecium isolated from a human clinical specimen

The vanC1 gene, which is chromosomally located, confers resistance to vancomycin and serves as a species marker for Enterococcus gallinarum. Enterococcus faecium TJ4031 was isolated from a blood culture and harbours the vanC1 gene. Polymerase chain reaction (PCR) assays were performed to detect vanXYc and vanTc genes. Only the vanXYc gene was found in the E. faecium TJ4031 isolate. The minimum inhibitory concentrations of vancomycin and teicoplanin were 2 µg/mL and 1 µg/mL, respectively. Real-time reverse transcription-PCR results revealed that the vanC1 and vanXYc genes were not expressed. Pulsed-field gel electrophoresis and southern hybridisation results showed that the vanC1 gene was encoded in the chromosome. E. faecalis isolated from animals has been reported to harbour vanC1 gene. However, this study is the first to report the presence of the vanC1 gene in E. faecium of human origin. Additionally, our research showed the vanC1 gene cannot serve as a species-specific gene of E. gallinarum and that it is able to be transferred between bacteria. Although the resistance marker is not expressed in the strain, our results showed that E. faecium could acquire the vanC1 gene from different species.
The conformational state of the nucleosome entry–exit site modulates TATA box-specific TBP binding

The TATA binding protein (TBP) is a critical transcription factor used for nucleating assembly of the RNA polymerase II machinery. TBP binds TATA box elements with high affinity and kinetic stability and in vivo is correlated with high levels of transcription activation. However, since most promoters use less stable TATA-less or TATA-like elements, while also competing with nucleosome occupancy, further mechanistic insight into TBP's DNA binding properties and ability to access chromatin is needed. Using bulk and single-molecule FRET, we find that TBP binds a minimal consensus TATA box as a two-state equilibrium process, showing no evidence for intermediate states. However, upon addition of flanking DNA sequence, we observe non-specific cooperative binding to multiple DNA sites that compete for TATA-box specificity. Thus, we conclude that TBP binding is defined by a branched pathway, wherein TBP initially binds with little sequence specificity and is thermodynamically positioned by its kinetic stability to the TATA box. Furthermore, we observed the real-time access of TBP binding to TATA box DNA located within the DNA entry–exit site of the nucleosome. From these data, we determined salt-dependent changes in the nucleosome conformation regulate TBP's access to the TATA box, where access is highly constrained under physiological conditions, but is alleviated by histone acetylation and TFIIA.
Improving network services resilience through automatic service node configuration generation

Network management is facing new challenges with the definition of the future Internet. Among those challenges, the management of network's heterogeneity represents a highly complex problem. The most popular proposals addressing this problem following RFC 3139 guidelines, translate from mid-level independent representations to the network's services and devices heterogeneous management interfaces and data models. However, the translation mechanisms defined so far, apart from being highly complex, perform inefficient mapping operations and depend on the administrator manual intervention to maintain and validate the mappings. The MiNSC framework was created to overcome the limitations of those translation mechanisms, providing a mid-level management abstraction based on the association of standard network management interfaces and standard network management information models. Supported through a distributed model, the MiNSC architecture improves network services resilience to node failures. This paper describes this new integrated management approach, illustrating and experimenting its functionalities for the DNS service configuration management, capable of automatic node's configuration replication and redeployment aiming to improve the service's resilience.
On the Thermonuclear Runaway in Type Ia Supernovae: How to Run Away?

Type Ia supernovae (SNe Ia) are thought to be thermonuclear explosions of massive white dwarfs (WDs). We present the first study of multidimensional effects during the final hours prior to the thermonuclear runaway that leads to the explosion. The calculations utilize an implicit, two-dimensional hydrodynamic code. Mixing and the ignition process are studied in detail. We find that the initial chemical structure of the WD is changed, but the material is not fully homogenized. In particular, the exploding WD sustains a central region with a low C/O ratio. This implies that the explosive nuclear burning will begin in a partially carbon-depleted environment. The thermonuclear runaway happens in a well-defined region close to the center. It is induced by compressional heat when matter is brought inward by convective flows. We find no evidence for multiple spot or strong off-center ignition. Convective velocities in the WD are on the order of 100 km s-1, which is well above the effective burning speeds in SNe Ia previously expected right after the runaway. In our calculations, the ignition occurs near the center. Then, for ≈ 0.5-1 s, the speed of the burning front will neither be determined by the laminar speed nor the Rayleigh-Taylor instabilities but by convective flows produced prior to the runaway. The consequences are discussed for our understanding of the detailed physics of the flame propagation, the deflagration to detonation transition, and the nucleosynthesis in the central layers. Our results strongly suggest the preconditioning of the progenitor as a key factor for our understanding of the diversity in SNe Ia.
Protocatechuic Aldehyde Attenuates Cisplatin-Induced Acute Kidney Injury by Suppressing Nox-Mediated Oxidative Stress and Renal Inflammation

Cisplatin is a classic chemotherapeutic agent widely used to treat different types of cancers including ovarian, head and neck, testicular and uterine cervical carcinomas. However, cisplatin induces acute kidney injury by directly triggering an excessive inflammatory response, oxidative stress, and programmed cell death of renal tubular epithelial cells, all of which lead to high mortality rates in patients. In this study, we examined the protective effect of protocatechuic aldehyde (PA) in vitro in cisplatin-treated tubular epithelial cells and in vivo in cisplatin nephropathy. PA is a monomer of Traditional Chinese Medicine isolated from the root of S. miltiorrhiza (Lamiaceae). Results show that PA prevented cisplatin-induced decline of renal function and histological damage, which was confirmed by attenuation of KIM1 in both mRNA and protein levels. Moreover, PA reduced renal inflammation by suppressing oxidative stress and programmed cell death in response to cisplatin, which was further evidenced by in vitro data. Of note, PA suppressed NAPDH oxidases, including Nox2 and Nox4, in a dosage-dependent manner. Moreover, silencing Nox4, but not Nox2, removed the inhibitory effect of PA on cisplatin-induced renal injury, indicating that Nox4 may play a pivotal role in mediating the protective effect of PA in cisplatin-induced acute kidney injury. Collectively, our data indicate that PA blocks cisplatin-induced acute kidney injury by suppressing Nox-mediated oxidative stress and renal inflammation without compromising anti-tumor activity of cisplatin. These findings suggest that PA and its derivatives may serve as potential protective agents for cancer patients receiving cisplatin treatment.
Geographic Routing in Large-Scale MANETs

In this paper, we propose and evaluate a geographic routing scheme, including an efficient position publish protocol and a routing protocol that can operate with imperfect information regarding the destination’s location, that scales to largemobile ad hoc networks (MANETs). The traffic generated by our position publish protocol fits within the transport capacity of MANET s with constant communication bandwidth allocated for routing overhead, even as the network size increases. The routing protocol gua rantees, with high probability, routes whose lengths are within a constant “stretch” factor of the shortest path from source to destination. The key idea underlying the scalability of the publish protocol is for each potential destination node to send location update s (with frequency decaying with distance) only to a subset of networ k nodes, structured as annular regions around it (the natural approach of updating circular regions in distance-dependent fashion d oes not scale). The routing protocol must therefore account for thefact that the source and/or relay nodes may not have estimates of the destination’s location (or may have stale estimates). S patial and temporal scaling of protocol parameters are chosen so as to guarantee scalability, route reliability and route stretch, and these analytical design prescriptions are verified using simulat ions.
On the Dynamics of Easterly Waves, Monsoon Depressions, and Tropical Depression Type Disturbances

The authors argue that certain aspects of the rotational, synoptic-scale disturbances of the wind field that are observed in ITCZ or monsoon trough regions can be understood by considering the linear response of a dry, initially resting atmosphere to a pulse of heating whose amplitude and spatial and temporal scales are characteristic of a large mesoscale convective system. The key points are that short Rossby waves have small intrinsic group and phase velocities, and that a heating pulse projects much more energy on the Rossby modes if it is located slightly off rather than on the equator. It follows that synoptic-scale Rossby waves, with characteristics broadly similar to those of observed disturbances, should be present in ofd equatorial regions of persistent deep convection, since large mesoscale convective systems tend to develop in such regions.
Proposal of a new staging system for intrahepatic cholangiocarcinoma: Analysis of surgical patients from a nationwide survey of the Liver Cancer Study Group of Japan

In the current American Joint Committee on Cancer/International Union Against Cancer staging system (seventh edition) for intrahepatic cholangiocarcinoma (ICC), tumor size was excluded, and periductal invasion was added as a new tumor classification‐defining factor. The objective of the current report was to propose a new staging system for ICC that would be better for stratifying the survival of patients based on data from the nationwide Liver Cancer Study Group of Japan database.
Global self-esteem, goal achievement orientations, and self-determined behavioural regulations in a physical education setting

Abstract We examined a theoretical model of global self-esteem that incorporated constructs from achievement goal and self-determination theories. The model hypothesized that self-determined or autonomous motives would mediate the influence of achievement goal orientation on global self-esteem. The adapted version of the Behavioural Regulation in Exercise Questionnaire (Mullan et al., 1997), the Perception of Success Questionnaire (Roberts & Balague, 1991), and Rosenberg's (1965) self-esteem scales were administered to 634 high school students aged 11 – 15 years. A structural equation model supported the hypotheses and demonstrated that autonomous motives mediated the effect of goal orientations on global self-esteem. The results suggest that generalized motivational orientations influence self-esteem by affecting autonomous motivation and is consistent with theory that suggests that experiences relating to intrinsic motivation are the mechanism by which global motivational orientations are translated into adaptive outcomes like self-esteem. The findings suggest that physical activity interventions that target autonomous motives in physical activity contexts are likely to enhance young people's general self-esteem.
Loss and loyalty: Change in political and gender identity among Clinton supporters after the 2016 U.S. presidential election

Abstract How do voters’ identities change after a candidate’s defeat? A longitudinal, within-subjects study used Hillary Clinton’s loss in the 2016 U.S. presidential election to explore social identity theory’s (SIT) tenet that threats to self-relevant groups motivate further connection to and affirmation of the group. Two independent samples (university students and adults on Mechanical Turk) were assessed before and after the 2016 U.S. presidential election. After Hillary Clinton’s defeat, those who reported voting for Clinton affirmed their political and gender identities in several ways, such as increasing their identification with Clinton. These ecologically valid results are consistent with SIT, and suggest supporters affirm their identities following a threat such as the defeat of their candidate during a high-stakes election. We discuss the implications of these findings within the context of the increasingly polarized U.S. electorate.
The Goldilocks Principle: Reading Children's Books with Explicit Memory Representations

We introduce a new test of how well language models capture meaning in children's books. Unlike standard language modelling benchmarks, it distinguishes the task of predicting syntactic function words from that of predicting lower-frequency words, which carry greater semantic content. We compare a range of state-of-the-art models, each with a different way of encoding what has been previously read. We show that models which store explicit representations of long-term contexts outperform state-of-the-art neural language models at predicting semantic content words, although this advantage is not observed for syntactic function words. Interestingly, we find that the amount of text encoded in a single memory representation is highly influential to the performance: there is a sweet-spot, not too big and not too small, between single words and full sentences that allows the most meaningful information in a text to be effectively retained and recalled. Further, the attention over such window-based memories can be trained effectively through self-supervision. We then assess the generality of this principle by applying it to the CNN QA benchmark, which involves identifying named entities in paraphrased summaries of news articles, and achieve state-of-the-art performance.
Can multimodal trip planning alter the travelers' mobility behavior? A cross-European study

The availability of multimodal information is expected to shift travelers to environmentally-friendly transport modes. A questionnaire study was conducted in three European regions, Catalonia (Spain), Berlin (Germany) and Trikala (Greece), among 95 travelers who were asked to use a specific multimodal trip planner in their everyday life. The travelers' attitudes towards the planner were positive and they expected it to be beneficial, offering them more possibilities to find the optimum route, enhancing their comfort and reducing their stress while travelling. Some decrease in the frequency of use of private car and increase in the frequency of use of public transport and walking before and while using the planner were found in two of the regions. Users did not expect a change in the number of journeys done by private car or public transport due to the usage of the planner. Although the findings have to be further verified, the present study indicates that the availability of information about environmentally-friendly transport modes via a multimodal trip planner, is rather not enough to achieve a shift of travelers to such modes. The adequate planning and integration of green transport services within a sustainable urban mobility plan and a supporting policy framework are also needed to achieve the greening of urban and interurban transport.
Unidirectional Expiratory Valve Method to Assess Maximal Inspiratory Pressure in Individuals without Artificial Airway

Introduction Maximal Inspiratory Pressure (MIP) is considered an effective method to estimate strength of inspiratory muscles, but still leads to false positive diagnosis. Although MIP assessment with unidirectional expiratory valve method has been used in patients undergoing mechanical ventilation, no previous studies investigated the application of this method in subjects without artificial airway. Objectives This study aimed to compare the MIP values assessed by standard method (MIPsta) and by unidirectional expiratory valve method (MIPuni) in subjects with spontaneous breathing without artificial airway. MIPuni reproducibility was also evaluated. Methods This was a crossover design study, and 31 subjects performed MIPsta and MIPuni in a random order. MIPsta measured MIP maintaining negative pressure for at least one second after forceful expiration. MIPuni evaluated MIP using a unidirectional expiratory valve attached to a face mask and was conducted by two evaluators (A and B) at two moments (Tests 1 and 2) to determine interobserver and intraobserver reproducibility of MIP values. Intraclass correlation coefficient (ICC[2,1]) was used to determine intraobserver and interobserver reproducibility. Results The mean values for MIPuni were 14.3% higher (-117.3 ± 24.8 cmH2O) than the mean values for MIPsta (-102.5 ± 23.9 cmH2O) (p<0.001). Interobserver reproducibility assessment showed very high correlation for Test 1 (ICC[2,1] = 0.91), and high correlation for Test 2 (ICC[2,1] = 0.88). The assessment of the intraobserver reproducibility showed high correlation for evaluator A (ICC[2,1] = 0.86) and evaluator B (ICC[2,1] = 0.77). Conclusions MIPuni presented higher values when compared with MIPsta and proved to be reproducible in subjects with spontaneous breathing without artificial airway.
Meta-stable brane configurations with seven NS5-branes

We present the intersecting brane configurations consisting of NS-branes, D4-branes (and anti D4-branes) and an O6-plane, of type IIA string theory corresponding to the meta-stable nonsupersymmetric vacua in four-dimensional supersymmetric SU(Nc) × SU(N′c) × SU(N″c) gauge theory with a symmetric tensor field, a conjugate symmetric tensor field and bifundamental fields. We also describe the intersecting brane configurations of type IIA string theory corresponding to the nonsupersymmetric meta-stable vacua in the above gauge theory with an antisymmetric tensor field, a conjugate symmetric tensor field, eight fundamental flavors and bifundamentals. These brane configurations consist of NS-branes, D4-branes (and anti D4-branes), D6-branes and O6-planes.
RADIO INTERFEROMETRIC OBSERVATIONS OF CANDIDATE WATER-MASER-EMITTING PLANETARY NEBULAE

We present Very Large Array observations of H2O and OH masers as well as radio continuum emission at 1.3 and 18 cm toward three sources previously cataloged as planetary nebulae (PNe) and in which single-dish detections of H2O masers have been reported: IRAS 17443−2949, IRAS 17580−3111, and IRAS 18061−2505. Our goal was to unambiguously confirm their nature as water-maser-emitting PNe, a class of objects of which only two bona fide members were previously known. We detected and mapped H2O maser emission toward all three sources, while OH maser emission is detected in IRAS 17443−2949 and IRAS 17580−3111 as well as in other two objects within the observed fields: IRAS 17442−2942 (unknown nature) and IRAS 17579−3121 (also cataloged as a possible PN). We found radio continuum emission associated only with IRAS 18061−2505. Our results confirm IRAS 18061−2505 as the third known case of a PN associated with H2O maser emission. The rest of the studied sources are not likely to trace PNe. The three known water-maser-emitting PNe have clear bipolar morphologies, which suggests that water maser emission in these objects is related to non-spherical mass-loss episodes. We speculate that these bipolar water-maser-emitting PNe would have “water-fountain” asymptotic giant branch (AGB) and post-AGB stars as their precursors. A note of caution is given for other objects that have been classified as OHPNe (objects with both OH maser and radio continuum emission that could be extremely young PNe) based on single-dish observations, since interferometric data of both OH masers and continuum are necessary for a proper identification as members of this class.