Miracle-dz/UniFAR-FTUs huggingface dataset:
Automation and Evaluation of the SOWH Test with SOWHAT

The Swofford-Olsen-Waddell-Hillis (SOWH) test evaluates statistical support for incongruent phylogenetic topologies. It is commonly applied to determine if the maximum likelihood tree in a phylogenetic analysis is significantly different than an alternative hypothesis. The SOWH test compares the observed difference in likelihood between two topologies to a null distribution of differences in likelihood generated by parametric resampling. The test is a well-established phylogenetic method for topology testing, but is is sensitive to model misspecification, it is computationally burdensome to perform, and its implementation requires the investigator to make multiple decisions that each have the potential to affect the outcome of the test. We analyzed the effects of multiple factors using seven datasets to which the SOWH test was previously applied. These factors include bootstrap sample size, likelihood software, the introduction of gaps to simulated data, the use of distinct models of evolution for data simulation and likelihood inference, and a suggested test correction wherein an unresolved “zero-constrained” tree is used to simulate sequence data. In order to facilitate these analyses and future applications of the SOWH test, we wrote SOWHAT, a program that automates the SOWH test. We find that inadequate bootstrap sampling can change the outcome of the SOWH test. The results also show that using a zero-constrained tree for data simulation can result in a wider null distribution and higher p-values, but does not change the outcome of the SOWH test for most datasets. These results will help others implement and evaluate the SOWH test and allow us to provide recommendation for future applications of the SOWH test. SOWHAT is available for download from https://github.com/josephryan/SOWHAT.
Approximate Hypergraph Partitioning and Applications

We show that any partition-problem of hypergraphs has an O(n) time approximate partitioning algorithm and an efficient property tester. This extends the results of Goldreich, Goldwasser and Ron who obtained similar algorithms for the special case of graph partition problems in their seminal paper (1998). The partitioning algorithm is used to obtain the following results: ldr We derive a surprisingly simple O(n) time algorithmic version of Szemeredi's regularity lemma. Unlike all the previous approaches for this problem which only guaranteed to find partitions of tower-size, our algorithm will find a small regular partition in the case that one exists; ldr For any r ges 3, we give an O(n) time randomized algorithm for constructing regular partitions of r-uniform hypergraphs, thus improving the previous O(n2r-1) time (deterministic) algorithms. The property testing algorithm is used to unify several previous results, and to obtain the partition densities for the above problems (rather than the partitions themselves) using only poly(1/isin) queries and constant running time.
Influence of steeping conditions (time, temperature, and particle size) on antioxidant properties and sensory attributes of some white and green teas

Abstract The influence of commonly used steeping times and temperatures, as well as leaf size on the antioxidant activity and sensory attributes of tea were studied. Five unblended white and green tea samples from China and Malawi, infused in hot (70 °C and 90 °C; 7 min) or cold water (room temperature: 15, 30, 60, or 120 min) either as whole leaves or as milled, were analyzed. Total phenolic and flavonoid contents as well as antioxidant power (ABTS assay) were measured. The results show that the maximum extraction efficiency occurs with cold water for 120 min and with hot water at 90 °C and that only in the case of teas from whole, large leaves, the extraction was greater in cold than in hot infusions. Moreover, tea infusions prepared from milled leaves have the greatest antioxidant activity. In the sensory evaluation of some of the tea infusions, white teas were perceived more fragrant than green ones and were judged as the most favorite by the majority of the judges, especially for the brew prepared in cold water from whole leaves; all infusions obtained from the milled leaves in fact have a more bitter and astringent taste.
Face Classification in Schizophrenia: Evidence for a Sensitivity to Distinctiveness

The face-processing skills of people with schizophrenia were compared with those of a group of unimpaired individuals. Participants were asked to make speeded face-classification decisions to faces previously rated as being typical or distinctive. The schizophrenic group responded more slowly than the unimpaired group; however, both groups demonstrated the customary sensitivity to the distinctiveness of the face stimuli. Face-classification latencies made to typical faces were shorter than those made to distinctive faces. The implication of this finding with the schizophrenic group is discussed with reference to accounts of face-processing deficits attributed to these individuals.
On linear H∞ equalization of communication channels

As an alternative to existing techniques and algorithms, we investigate the merit of the H/sup /spl infin// approach to the linear equalization of communication channels. We first give the formulation of all causal H/sup /spl infin// equalizers using the results of and then look at the finite delay ease. We compare the risk-sensitive H/sup /spl infin// equalizer with the MMSE equalizer with respect to both the average and the worst-case BER performances and illustrate the improvement due to the use of the H/sup /spl infin// equalizer.
The experience of acculturative stress-related growth from immigrants’ perspectives

Previous literature has mainly focused on the positive effects of stress associated with disability and illness, called stress-related growth. Little research has explored positive changes as a result of acculturative stress among a group of immigrants. In particular, older Asian immigrants may experience a high level of stress related to acculturation because they may face more challenges to adapt to and navigate a new culture. This study was designed to capture the characteristics of stress-related growth associated with acculturative stress. Using in-depth interviews among 13 older Korean immigrants, three main themes associated with the stress-coping strategies were identified: (a) the development of mental toughness, (b) engagement in meaningful activities, and (c) promotion of cultural understanding. These themes indicate that by following the stressful acculturation process, participants developed a better understanding of the new culture, engaged in various leisure activities, and enhanced mental strength. This finding provides information on how immigrants deal with acculturative stress and have positive psychological changes, which results in a sense of happiness and psychological well-being.
Global 8.4‐GHz VLBI observations of JVAS B0218+357

In this paper we present new observations of the gravitational lens system JVAS B0218+357 made with a global very long baseline interferometry (VLBI) network at a frequency of 8.4 GHz. Our maps have an rms noise of 30 μJy beam - 1 and with these we have been able to image much of the extended structure of the radio jet in both the A and B images at high resolution (∼1 mas). The main use of these maps will be to enable us to further constrain the lens model for the purposes of H 0 determination. We are able to identify several subcomponents common to both images with the expected parity reversal, including one which we identify as a counter-jet. We have not been successful in detecting either the core of the lensing galaxy or a third image. Using a model of the lensing galaxy we have back-projected both of the images to the source plane and find that they agree well. However, there are small, but significant, differences which we suggest may arise from multi-path scattering in the interstellar medium (ISM) of the lensing galaxy. We also find an exponent of the radial mass distribution of β 1.04, in agreement with lens modelling of published 15-GHz VLBI data. Polarization maps of each image are presented which show that the distributions of polarization across images A and B are different. We suggest that this results from Faraday rotation and associated depolarization in the lensing galaxy.
Evaluation of the Ecotoxicity of Sediments from Yangtze River Estuary and Contribution of Priority PAHs to Ah Receptor-Mediated Activities

In this study, in vitro bioassays were performed to assess the ecotoxicological potential of sediments from Yangtze River estuary. The cytotoxicity and aryl hydrocarbon receptor (AhR)-mediated toxicity of sediment extracts with rainbow trout (Oncorhynchus mykiss) liver cells were determined by neutral red retention and 7-ethoxyresorufin-O-deethylase assays. The cytotoxicity and AhR-mediated activity of sediments from the Yangtze River estuary ranged from low level to moderate level compared with the ecotoxicity of sediments from other river systems. However, Yangtze River releases approximately 14 times greater water discharge compared with Rhine, a major river in Europe. Thus, the absolute pollution mass transfer of Yangtze River may be detrimental to the environmental quality of estuary and East China Sea. Effect-directed analysis was applied to identify substances causing high dioxin-like activities. To identify unknown substances contributing to dioxin-like potencies of whole extracts, we fractionated crude extracts by open column chromatography. Non-polar paraffinic components (F1), weakly and moderately polar components (F2), and highly polar substances (F3) were separated from each crude extract of sediments. F2 showed the highest dioxin-like activities. Based on the results of mass balance calculation of chemical toxic equivalent concentrations (TEQs), our conclusion is that priority polycyclic aromatic hydrocarbons indicated a low portion of bio-TEQs ranging from 1% to 10% of crude extracts. Further studies should be conducted to identify unknown pollutants.
Intertidal Area Disappears Under Sea Level Rise: 250 Years of Morphodynamic Modeling in San Pablo Bay, California

Anticipated sea level rise (SLR) threatens intertidal areas and associated ecosystems in estuaries worldwide. There is a need to develop validated modeling tools to assess the impact of SLR on estuarine morphodynamics. This study explores the morphological impact of SLR on a channel‐shoal system in San Pablo Bay, a subembayment of San Francisco Bay, California, using a 3‐D, process‐based modeling approach (Delft3D) including density currents and wave action. The Bay underwent considerable morphologic development in response to variations in fluvial sediment load and discharge associated with a period of hydraulic mining for gold and later damming in the watershed. The availability of a unique 150‐year, 30‐year sequenced, bathymetric data set provided a rare opportunity for model validation. We investigate a 250‐year period of morphodynamic evolution including a 150‐year hindcast and a 100‐year forecast with different SLR scenarios. The model shows significant skill in hindcasting volumes and patterns of bathymetric development during both net depositional (1856–1951) and erosional (1951–onward) periods. Forecasts show that SLR alters the Bay's erosional trend to a depositional trend again. Despite increased sediment trapping rates, the intertidal mudflats drown under all modeled SLR scenarios (42, 84, and 167 cm by end of the 21st century). Our work highlights the potential of using process‐based models to assess the morphodynamic impact of SLR. The study also suggests that SLR can greatly increase the loss of intertidal area when landward migration is not possible. Sustainable management strategies are required to safeguard these valuable intertidal habitats.
Relationships between Personal and Collective Place Identity and Well-Being in Mountain Communities

The aim was to investigate the relationships between landscape-related personal and collective identity and well-being of residents living in a Swedish mountain county (N = 850). It was shown that their most valued mountain activities were viewing and experiencing nature and landscape, outdoor recreation, rest and leisure, and socializing with friends/family. Qualitative analyses showed that the most valued aspects of the sites were landscape and outdoor restoration for personal favorite sites, and tourism and alpine for collective favorite sites. According to quantitative analyses the stronger the attachment/closeness/belonging (emotional component of place identity) residents felt to favorite personal and collective sites the more well-being they perceived when visiting these places. Similarly, the more remembrance, thinking and mental travel (cognitive component of place identity) residents directed to these sites the more well-being they perceived in these places. In both types of sites well-being was more strongly predicted by emotional than cognitive component of place-identity. All this indicates the importance of person-place bonds in beneficial experiences of the outdoors, over and above simply being in outdoor environments.
Significance for Wildlife Management of the late Quaternary Biogeography of Mountain Goats (Oreamnos Americanus) in the Pacific Northwest, U.S.A.

Management policy of the U.S. National Park Service regarding mountain goats (Oreamnos americanus) in Olympic National Park, Washington, is founded in part on the argument that alpine environments there evolved through the late Quaternary without mountain goats. Descendants of mountain goats artificially introduced to park lands in the 1920s are being experimentally sterilized and translocated to control population size. The potential that Oreamnos sp. colonized and inhabited the Olympic Mountains during the late Quaternary is, however, great. Prehistoric and historic extralimital records of mountain goats in Oregon and northern California, the Wisconsin glacial and floral histories, and the modern distributions of other alpine and subalpine mammalian taxa suggest the Puget lowland served as a biogeographic filter rather than a barrier for mammalian taxa during periods of maximum glacial extent. Extirpation of isolated mountain goat populations on mountains of Oregon, California, and Washington apparently.
Performance Study on a CSMA/CA-Based MAC Protocol for Multi-User MIMO Wireless LANs

A multi-antenna access point (AP) can communicate simultaneously with multiple clients, however, this multi-user MIMO (MU-MIMO) capability is underutilized in conventional 802.11 wireless LANs (WLANs). To address this problem, researchers have recently developed a CSMA/CA-based MAC protocol to support concurrent transmissions from different clients. In this paper, we propose an analytical model to characterize the saturation throughput and mean access delay of this CSMA/CA-based MAC protocol operating in an MU-MIMO WLAN. We also consider and model a distributed opportunistic transmission scheme, where clients are able to contend for the concurrent transmission opportunities only when their concurrent rates exceed a threshold. Comparisons with simulation results show that our analytical model provides a close estimation of the network performance. By means of the developed model, we evaluate the throughput and delay performance with respect to different network parameters, including the backoff window sizes, the number of AP's antennas, the network size, and the threshold of the opportunistic transmission scheme. Performance optimization over key parameters is also conducted for the transmission schemes.
Recombinant adeno-associated virus 2-mediated antiangiogenic prevention in a mouse model of intraperitoneal ovarian cancer.

PURPOSE In the present study, we sought to determine the potential of sustained transgene expression by a single i.m. administration of recombinant adeno-associated virus 2 (rAAV) encoding angiostatin and endostatin in inhibiting i.p. ovarian cancer growth and dissemination in a preclinical mouse model. EXPERIMENTAL DESIGN Cohorts of female athymic nude mice received either no virus or 1.2 x 10(11) particles of rAAV encoding green fluorescence protein or endostatin plus angiostatin, i.m. Three weeks later, the mice were i.p. injected with 10(6) human epithelial ovarian cancer cell line SKOV3.ip1. As a measure of effectiveness of the therapy, tumor weight, abdominal distension, ascites volume and vascular endothelial growth factor level, and tumor weight were determined. Immunohistochemistry was done to determine tumor cell apoptosis and endothelial cell proliferation following the therapy. Tumor-free survival was recorded as the end point. RESULTS Results indicated a significant tumor-free survival (P < 0.003) following therapy with rAAV encoding endostatin and angiostatin compared with untreated or rAAV-green fluorescence protein-treated mice. Ascites volume in rAAV endostatin and angiostatin-treated mice was significantly lower than naive mice and contained less hemorrhage and tumor conglomerates. The level of vascular endothelial growth factor in the ascites of antiangiogenic vector treated mice was also significantly less compared with the untreated mice. Immunohistochemical analyses indicated increased tumor cell apoptosis and decreased blood vasculature following rAAV endostatin and angiostatin treatment. CONCLUSION The results indicate that antiangiogenic genetic prevention from stable systemic levels of angiostatin and endostatin by i.m. administration of rAAV can be used for the treatment of i.p. ovarian cancer growth and dissemination.
Bridging the transmission gap: An end to an important mystery of attachment research?

Abstract The authors provide a context for this special section by arguing that the attachment relationships of infancy fulfil an evolutionary role in ensuring that the brain structures that come to subserve social cognition are appropriately organised and prepared to equip the individual for the collaborative existence with other people for which his or her brain was designed. Processes as fundamental as gene expression or changes in receptor densities can be seen as direct functions of the extent of understanding of mental states provided by the caregiving environment. If the attachment relationship is indeed a major organiser of brain development, it is even more important to understand the processes that underpin the transgenerational transmission of attachment patterns. The contributions of the papers in the special section to understanding the role of reflective function in the development of attachment and social cognition are reviewed, and the implications for the development of both theory and practice are explored.
Wavelet Adaptive Backstepping Control for a Class of Nonlinear Systems

This paper proposes a wavelet adaptive backstepping control (WABC) system for a class of second-order nonlinear systems. The WABC comprises a neural backstepping controller and a robust controller. The neural backstepping controller containing a wavelet neural network (WNN) identifier is the principal controller, and the robust controller is designed to achieve L2 tracking performance with desired attenuation level. Since the WNN uses wavelet functions, its learning capability is superior to the conventional neural network for system identification. Moreover, the adaptation laws of the control system are derived in the sense of Lyapunov function and Barbalat's lemma, thus the system can be guaranteed to be asymptotically stable. The proposed WABC is applied to two nonlinear systems, a chaotic system and a wing-rock motion system to illustrate its effectiveness. Simulation results verify that the proposed WABC can achieve favorable tracking performance by incorporating of WNN identification, adaptive backstepping control, and L2 robust control techniques
Leading the Herd to Greener Pastures: When Trade Imitation is the Most "Profitable" Form of Flattery

We find that relatively large institutional trade packages that are spread across multiple brokers and multiple days contain information about market fundamentals. We show that fund managers executing these packages are leaders, in the sense that other managers subsequently follow with packages on the same side in the same securities. This following behavior, or herding, is rational to the extent that early followers profit from their trades. Although some leaders subsequently reverse their positions, the price effects associated with these initial trades are not reversed, establishing that leaders’ and followers’ trades enhance price discovery.
The effect of graded spinal cord injury on the extrapyramidal and pyramidal motor evoked potentials of the rat.

This study investigated the differential effects of graded spinal cord injury on the rat extrapyramidal motor evoked potential (exp-MEP) and pyramidal motor evoked potential (pyr-MEP) and the prognostic value of these effects in predicting postinjury motor performance in the rat model. In 20 rats subjected to graded spinal injury (10-100 g-cm), there was a differential injury threshold for ablation of exp-MEP and pyr-MEP. All peaks of the pyr-MEP were extinguished in the animals subjected to impact forces of 50 g-cm and above (n = 12). In contrast, the exp-MEP was completely abolished in only two animals at injuries of 80 g-cm or above. A residual exp-MEP response persisted in the remaining 18 animals. Motor performance was monitored in 16 additional animals for up to 1 week after spinal injury. The pyr-MEP was abolished in 100% of the rats subjected to a 50-g-cm injury (n = 7), whereas the exp-MEP persisted up to the highest impact forces (80 g-cm). Hind leg paralysis was present in the five rats where the pyr-MEP was extinguished but with persistence of the exp-MEP. An 80% reduction in the amplitude of the pyr-MEP in four animals resulted in mild ataxia with motor improvement at the end of a week. An increase or a 70% loss in pyr-MEP peak amplitude resulted in no clinical motor deficits (n = 5). These findings demonstrate that the exp-MEP and pyr-MEP are differentially affected by spinal cord injury and that an alteration in the postinjury pyrMEP is an accurate prognosticator of motor function. These findings have significant implications for the evaluation of potential therapeutic modalities in the rat spinal injury model.