Miracle-dz/UniFAR-FTUs huggingface dataset:
The In Vitro Interaction of Streptococcus pyogenes with Human Pharyngeal Cells Induces a Phage-Encoded Extracellular DNase

ABSTRACT The role lysogenic bacteriophage play in the pathogenesis of the host bacterium is poorly understood. In a previous study, we found that streptococcal coculture with human pharyngeal cells resulted in the induction of lysogenic bacteriophage as well as the phage-associated streptococcal pyrogenic exotoxin C (SpeC). In this study, we have determined that in addition to SpeC induction, a number of other streptococcal proteins are also released by the bacteria during coculture with pharyngeal cells. Among these, we identified and characterized a novel 27-kDa secreted protein. Sequence analysis of this novel protein demonstrated it to be encoded by the same lysogenic bacteriophage which harbors speC. Protein sequence analysis revealed varied homologies with several streptococcal DNases. Further biochemical characterization of the recombinantly expressed protein verified it to be a divalent cation-dependent streptococcal phage-encoded DNase (Spd1). Although functionally distinct, SpeC and Spd1 are associated by a number of parameters, including genetic proximity and transcriptional regulation. Finally, we speculate on the induction of phage-encoded DNase (Spd1) enhancing the fitness of both bacteria and phage.
Generalisation of the limiting distribution of program sizes in tree-based genetic programming and analysis of its effects on bloat

Recent research [1] has found that standard sub-tree crossover with uniform selection of crossover points, in the absence of fitness pressure, pushes a population of GP trees towards a Lagrange distribution of tree sizes. However, the result applied to the case of single arity function plus leaf node combinations, e.g., unary, binary, ternary, etc trees only. In this paper we extend those findings and show that the same distribution is also applicable to the more general case where the function set includes functions of mixed arities. We also provide empirical evidence that strongly corroborates this generalisation. Both predicted and observed results show a distinct bias towards the sampling of shorter programs irrespective of the mix of function arities used. Practical applications and implications of this knowledge are investigated with regard to search efficiency and program bloat. Work is also presented regarding the applicability of the theory to the traditional 90%-function 10%-terminal crossover node selection policy.
Patterns of retrograde amnesia for recent and remote incidental spatial learning in rats

A non‐navigational test of incidental spatial learning was used to determine whether hippocampal damage causes temporally‐graded retrograde amnesia (TGRA) for allocentric‐spatial information. Rats were exposed to two identical objects in a circular open field for 7 min on seven consecutive days. In the 1–3 days after the last day of familiarization, rats received neurotoxic lesions of the hippocampal formation (HPC) or sham lesions. Another two groups received the same lesions 3 weeks after familiarization. The rats were then placed back in the open field with one object displaced, and the time spent in each of the quadrants as well as time spent exploring the objects was recorded. Rats that received HPC lesions 3 weeks but not 1–3 days after familiarization showed evidence of preserved remote spatial memory; however, their remote memory was expressed through different behavior than control rats. Rats with HPC lesions spent more time with the displaced object than with the object that remained in the same place, whereas control rats spent more time in the quadrant where the displaced object used to be. These results suggest that remote spatial memories may be preserved with a sufficiently long familiarization‐to‐surgery interval before HPC lesions, but that the nature of these memories may differ in quantity and/or quality from those of intact rats. © 2009 Wiley‐Liss, Inc.
Urban Scale Shifts since the Bronze Age: Upsweeps, Collapses, and Semiperipheral Development

This is a study of the growth and decline of cities for the purpose of identifying those events in which they significantly increased in size. Significant changes in the scale of cities are important for understanding the long-term trend toward more complex and hierarchical human societies. We report the results of an inventory of cycles, upsweeps, and collapses of settlements in five separate interpolity systems. Upsweeps are instances in which the largest settlement in a world system significantly increases in size. Collapses occur when the size of the largest settlement greatly decreases and stays down for a significant period of time rather than rebounding. We use regional interpolity systems (world systems) rather than single polities or settlements as our unit of analysis. Because the accurate designation of sweeps requires interval scale measures, we are limited to those regions and time periods for which quantitative estimates of largest settlement sizes are regularly available. We find a total of 18 upsweeps and five downsweeps, and only two instances of prolonged systemwide settlement collapse. We also investigate whether or not the rate of cycles has increased over the long run, and we find that cycles of city growth and decline have not accelerated. We also find a greater rate of urban cycles in the Western (Central) System than in the East Asian System, which supports the usual notion that the Western city system was less stable than the Eastern city system.
Rising Burden of Obesity in Asia

Overweight and obesity have reached epidemic proportions in many Asian countries. These countries also face a grave burden of obesity-related disorders such as diabetes, hypertension, and cardiovascular diseases, which develop at a younger age than in Western populations. These disorders are also manifested in childhood. The major causative factors are related to the lifestyle changes occurring due to rapid socioeconomic transition. Asian populations show several differences in genetic factors when compared with the white population, and they also have lower cut points for environmental risk factors. National programmes targeting public awareness, education and improved structural facilities to facilitate healthy lifestyle are the keys to alleviate the economic and health care burden of the obesity-related disorders.
Surface acoustic wave (SAW) biosensors

This paper reports an overview of biosensor technologies employing surface acoustic wave (SAW) principles for detection of biomarkers. First, the field of biosensors will be introduced in a broader framework through a general survey of the most popular transduction mechanisms in current biosensor research. Secondly, SAW based piezoelectric transduction mechanism along with device design approaches will be discussed. In this discussion, modeling, fabrication, optimization and characterization of SAW biosensors designed in CMOS technology will be laid out. An assortment of design novelties [1]–[3] such as circular architecture, embedded heaters, acoustic absorbers and their corresponding performance improvements will be introduced. In conclusion, we will list major research areas to be explored in developing sensitive biosensors by reflecting on problems encountered in improving sensitivity, selectivity, and specificity of such sensors throughout our CMOS-SAW biosensor research.
Dynamic Range-Aware Uplink Transmit Power Control in LTE Networks: Establishing an Operational Range for LTE's Open-Loop Transmit Power Control Parameters  $(\alpha, P_{0})$

While setting LTE's open-loop transmit power control parameters α (the path loss correction factor) and P0 (a cell/UE specific parameter), an important metric to be considered is the dynamic receive power range at the receiving base station. We consider the dynamic receive power range to be crucial, since very high dynamic receive power ranges cause signal suppression in the base station's analog-to-digital converter, which (in turn) lowers the network's quality of service in the uplink. In this work, we derive a closed-form expression for a base stations' dynamic receive power range and justify an upper limit for the same. We show that the dynamic receive power limitation along with an uplink coverage limitation leads to a confined set of suitable parameters (α, P0) called the operational range. Considering a cell's operational range ensures that signal suppression at the base station is kept at an acceptable level and that the uplink coverage condition is fulfilled.
Energy-Aware Scheduling of Distributed Systems

Scheduling of tasks on a multi-machine system to reduce the makespan, while satisfying the precedence constraints between the tasks, is known to be an NP-hard problem. We propose a new formulation and show that energy-aware scheduling is a generalization of the minimum makespan scheduling problem. Taking the system graph and program graph as inputs, we propose three different algorithms for energy-aware scheduling, each of them having its own strengths and limitations. The first is a genetic algorithm (Plain GA) that searches for an energy reducing schedule. The second (CA+GA) uses cellular automata (CA) to generate low energy schedules, while using a genetic algorithm (GA) to find good rules for the CA. The third (EAH) is a heuristic which gives preference to high-efficiency machines in allocation. We have tested our algorithms on well-known program graphs and compared our results with other state-of-the-art scheduling algorithms, which confirms the efficacy of our approach. Our work also gives insight into the time-energy trade-offs in scheduling.
Activation of the Complement Pathway: Comparison of Normal Pregnancy, Preeclampsia, and Systemic Lupus Erythematosus During Pregnancy

ABSTRACT: To evaluate a flare of systemic lupus erythematosus (SLE) during pregnancy and to differentiate it from diseases of pregnancy, serological parameters are often utilized. However, there are conflicting reports regarding the merit of conventional measurements of complement and activation products. While in normal pregnancy the levels of serum C3, C4, and CH50 gradually rise, a decline in these levels occurs during the course of pregnancy in selected SLE patients. There is controversy regarding whether such falls represent decreases in the overall synthesis of complement or activation, the former theory being supported by a report of normal levels of the C1s‐C1 inhibitor complex. During normal pregnancies, increases of complement split products, such as plasma C3a, may occur, and these correlate positively with elevations of C3. In pregnancies complicated by lupus, increases of C3a are often accompanied by a decline in total C3 and CH50. In a minority of non‐SLE patients, preeclampsia has been associated with elevations of a variety of complement split products. Ba, C3a, C4d, SC5b‐9, indicating activation of both the classical and alternative pathways. The CH50 levels tend to remain normal in these patients. In contrast, elevations of complement split products frequently accompany disease flares in patients with SLE. A high ratio of CH50/Ba may differentiate patients with preeclampsia from those with active SLE. A decline in conventional measures of C3, C4, or CH50 which is accompanied by elevations of complement split products appears to differentiate a lupus flare from non‐SLE diseases of pregnancy.
A picture book reading intervention in day care and home for children from low-income families.

The effects of an interactive book reading program were assessed with children from low-income families who attended subsidized day-care centers in New York. The children entered the program with language development in standard English vocabulary and expression that was about 10 months behind chronological age on standardized tests. Children were pretested and assigned randomly within classrooms to 1 of 3 conditions: (a) a school plus home condition in which the children were read to by their teachers and their parents, (b) a school condition in which children were read to only by teachers, and (c) a control condition in which children engaged in play activities under the supervision of their teachers. Training of adult readers was based on a self-instructional video
Stochastic heat equations with general multiplicative Gaussian noises: Hölder continuity and intermittency

This paper studies the stochastic heat equation with multiplicative noises of the form uW, where W is a mean zero Gaussian noise and the differential element uW is interpreted both in the sense of Skorohod and Stratonovich. The existence and uniqueness of the solution are studied for noises with general time and spatial covariance structure. Feynman-Kac formulas for the solutions and for the moments of the solutions are obtained under general and different conditions. These formulas are applied to obtain the Holder continuity of the solutions. They are also applied to obtain the intermittency bounds for the moments of the solutions.
Research of intelligent word segmentation and information retrieval

Chinese information retrieval process is somewhat different from the English information retrieval process. In consideration of the existing problems and difficulties of Chinese language information processing, Hibernate search was introduced to exploit information retrieval engine in this paper. A Chinese language analyzer based on the word stock was adopted to process Chinese language information, therefore this analyzer could advance with the times by updating the word stock at any time. However, ambiguity errors caused by the Chinese language analyzer always interfered with the degree of accuracy of the result. During the time of information retrieval, a secondary word segmentation algorithm was used in order to improve Chinese language information retrieval precision. The result list given in this paper had shown that the intelligent Chinese segmentation algorithm had improved the system performance well.
Time Domain Analysis for Electromagnetic Pulses Reflected from a Conductive Half Space

The preceding work is extended to the analysis of the pulse reflected from a lossy interface with an incident angle not smaller than the Brewster angle. The comparison between our results for vertical polarization and the published ones is made and a good agreement is shown. The variation trends of the shapes of reflected pulses with an incident angle are presented and discussed both for horizontal and vertical polarizations. The physical interpretation is addressed for the waveform of the reflected pulse. Some meaningful conclusions are drawn
From sounds to movement and back: how movement shapes internal representation of musical rhythms

The perception of beat and meter when listening to musical rhythms is an extremely commonability that allows people to synchronize to music. The rhythms are spontaneously structuredby the listener into beat and meter, i.e., multiple periodic levels, even if the acoustic input isnot strictly periodic. However, how musical rhythms are embodied in brain structures remainsunclear. Using EEG to record beat- and meter-related steady-state evoked potentials, we inves-tigated how body movements involving motor, proprioceptive and vestibular systems shape theinternal representation of an ambiguous polyrhythm (i.e. a rhythm that can be perceived in dif-ferent meters). We recorded the EEGwhile participants listened to such ambiguous polyrhythm,before and after a body movement training session aiming to disambiguate the perception ofthis rhythm by favoring the ternary meter. We found that brain activities recorded beforethe movement session faithfully followed the structure of the sound envelope, with no selectiveenhancement at specific frequencies. In contrast, the steady-state evoked potentials recordedduring the listening session performed after the body movement training were significantly en-hanced at frequencies corresponding to the ternary metric interpretation to which they movedduring the movement training. These results provide evidence that movement shapes selectivelythe perception and neural representations of rhythm as captured with EEG. Moreover, theseresults help to progress in our understanding of the neural dynamics underlying auditorymotorintegration, as captured in the context of musical rhythm.
In Vitro Activities of Isavuconazole and Comparator Antifungal Agents Tested against a Global Collection of Opportunistic Yeasts and Molds

ABSTRACT Isavuconazole is a new broad-spectrum triazole with a favorable pharmacokinetic and safety profile. We report the MIC distributions for isavuconazole and 111 isolates of Candida (42 Candida albicans, 25 Candida glabrata, 22 Candida parapsilosis, 14 Candida tropicalis, and 8 Candida krusei isolates), as determined by Clinical and Laboratory Standards Institute (CLSI) and European Committee on Antimicrobial Susceptibility Testing (EUCAST) broth microdilution (BMD) methods. Also, the relative activities of isavuconazole, itraconazole, fluconazole, posaconazole, voriconazole, and the three echinocandins were assessed against a recent (2011) global collection of 1,358 isolates of Candida spp. , 101 of Aspergillus spp. , 54 of non-Candida yeasts, and 21 of non-Aspergillus molds using CLSI BMD methods. The overall essential agreement (EA) (±2 log2 dilutions) between the CLSI and EUCAST methods was 99.1% (EA at ±1 log2 dilution, 90.1% [range, 80.0 to 100.0%]). The activities of isavuconazole against the larger collection of Candida spp. and Aspergillus spp. were comparable to those of posaconazole and voriconazole; the MIC90 values for isavuconazole, posaconazole, and voriconazole against Candida spp. were 0.5, 1, and 0.25 μg/ml and against Aspergillus spp. were 2, 1, and 1 μg/ml, respectively. Isavuconazole showed good activities against Cryptococcus neoformans (MIC90, 0.12 μg/ml) and other non-Candida yeasts (MIC90, 1 μg/ml) but was less potent against non-Aspergillus molds (MIC90, >8 μg/ml). Isavuconazole MIC values for three mucormycete isolates were 4, 1, and 2 μg/ml, whereas all three were inhibited by 1 μg/ml posaconazole. Isavuconazole demonstrates broad-spectrum activity against this global collection of opportunistic fungi, and the CLSI and EUCAST methods can be used to test this agent against Candida, with highly comparable results.
Implications of Authoritarianism for Young Adulthood: Longitudinal Analysis of College Experiences and Future Goals

Longitudinal data were used to explore links between right-wing authoritarianism (RWA) and young adult development. Analyses demonstrated that 4 years of college were related to reductions in RWA and that high-RWA participants who majored in the liberal arts had lower grade point averages. No grade effects were found for students in the professional schools. Explanations centered on the difficulty that high-RWA students might have with the ambiguous nature of liberal arts knowledge (e.g., hermeneutics, conflicting theories and data). In terms of goals after graduation, men and women high on authoritarianism had different expectations. Men scoring high on RWA focused on career goals, whereas high-RWA women experienced career confusion and expected marriage to entail increased responsibilities without personal rewards. Both genders high on RWA were also uninterested in exploring aspects of identity. Although focused on young adulthood, this study suggests that links exist between developmental theory in general and authoritarianism.
Characterization of the nonallelic homologous recombination hotspot PRS3 associated with type‐3 NF1 deletions

Nonallelic homologous recombination (NAHR) is the major mechanism underlying recurrent genomic rearrangements, including the large deletions at 17q11.2 that cause neurofibromatosis type 1 (NF1). Here, we identify a novel NAHR hotspot, responsible for type‐3 NF1 deletions that span 1.0 Mb. Breakpoint clustering within this 1‐kb hotspot, termed PRS3, was noted in 10 of 11 known type‐3 NF1 deletions. PRS3 is located within the LRRC37B pseudogene of the NF1‐REPb and NF1‐REPc low‐copy repeats. In contrast to other previously characterized NAHR hotspots, PRS3 has not developed on a preexisting allelic homologous recombination hotspot. Furthermore, the variation pattern of PRS3 and its flanking regions is unusual since only NF1‐REPc (and not NF1‐REPb) is characterized by a high single nucleotide polymorphism (SNP) frequency, suggestive of unidirectional sequence transfer via nonallelic homologous gene conversion (NAHGC). By contrast, the previously described intense NAHR hotspots within the CMT1A‐REPs, and the PRS1 and PRS2 hotspots underlying type‐1 NF1 deletions, experience frequent bidirectional sequence transfer. PRS3 within NF1‐REPc was also found to be involved in NAHGC with the LRRC37B gene, the progenitor locus of the LRRC37B‐P duplicons, as indicated by the presence of shared SNPs between these loci. PRS3 therefore represents a weak (and probably evolutionarily rather young) NAHR hotspot with unique properties. Hum Mutat 33:372–383, 2012. © 2011 Wiley Periodicals, Inc.
Signal Conditioning for the Kalman Filter: Application to Satellite Attitude Estimation with Magnetometer and Sun Sensors

Most satellites use an on-board attitude estimation system, based on available sensors. In the case of low-cost satellites, which are of increasing interest, it is usual to use magnetometers and Sun sensors. A Kalman filter is commonly recommended for the estimation, to simultaneously exploit the information from sensors and from a mathematical model of the satellite motion. It would be also convenient to adhere to a quaternion representation. This article focuses on some problems linked to this context. The state of the system should be represented in observable form. Singularities due to alignment of measured vectors cause estimation problems. Accommodation of the Kalman filter originates convergence difficulties. The article includes a new proposal that solves these problems, not needing changes in the Kalman filter algorithm. In addition, the article includes assessment of different errors, initialization values for the Kalman filter; and considers the influence of the magnetic dipole moment perturbation, showing how to handle it as part of the Kalman filter framework.
Self configuring services for extensible networks: a routing integrated approach

During the last decades the original Internet architecture evolved dramat¬ ically with new functionality being added to the network layer to support a wide range of emerging applications. Network services such as firewalls, congestion control, media gateways, and traffic engineering all require a net¬ work that not only forwards packets based on the destination address, but also performs packet processing on nodes interior to the network. In an effort to support such application-specific packet handling requirements, router manufacturers have started to embed programmable elements into routers for providing network service functionality in a more flexible way. However, de¬ ploying new services in an existing network is usually a manual and time consuming process requiring the installation of code on multiple routers dis¬ tributed all over the network. Given the complexity of how services can be composed, the only feasible approach is to automate this process. For this reason, it is crucial to have a suitable service infrastructure built on top ofthe raw processing capabilities to enable programmability of each node. This thesis presents a service framework that allows router resources to be programmed and coordinated in such a way that the underlying network provides the anticipated services on behalf of applications. We have devel¬ oped the ANCS (Active Network Control Software), which can be seen as an additional control layer in an active network environment that offers a gener¬ ic service abstraction and automates the configuration of processing resourc¬ es to form network services. Our system accepts processing demands from applications, maps their processing requirements onto the available network resources, and configures appropriate resources on network nodes.