Miracle-dz/UniFAR-FTUs huggingface dataset:
AVIAN LIFE-HISTORY EVOLUTION HAS AN EMINENT PAST: DOES IT HAVE A BRIGHT FUTURE?

A has an eminent past (Moreau 1944; Lack 1948, 1954, 1968; Skutch 1949), because birds played a critical role in the early development of life-history theory (Partridge and Harvey 1988). Those early investigators focused on clutch-size variation and described not only broad pa erns of worldwide variation in clutch sizes, but also outlined a variety of hypotheses to explain that variation, including food limitation, nest predation, and adult mortality (Moreau 1944, Lack 1948, Skutch 1949). Despite the early description of broad geographical pa erns and alternative hypotheses, subsequent a ention focused on north-temperate systems and food limitation. Life-history evolution continues to be an area of active investigation among ornithologists, but I believe progress has been retarded because we remain fi xed on three historical foci: (1) clutch-size evolution, (2) food limitation, and (3) north-temperate systems (and possibly an even narrower subset of northern strategies given a common focus on hole-nesting birds). Those focal points can be traced to the strong infl uence of David Lack on life-history studies in birds (i.e. Lack 1948, 1954, 1968). Lack energized an important fi eld of investigation and made signifi cant historical contributions to thinking about components of those issues. Yet, we o en remain transfi xed on those three foci and conduct tests at the wrong level (i.e. a proximate level) to understand evolution of life-history variation. Recognizing the pitfalls of those issues and moving beyond them is needed for a progressive future in avian life-history theory.
Prestimulus hemodynamic activity in dorsal attention network is negatively associated with decision confidence in visual perception.

Attention is thought to improve most aspects of perception. However, we recently showed that, somewhat surprisingly, endogenous attention can also lead to low subjective perceptual ratings (Rahnev et al., 2011). Here we investigated the neural basis of this effect and tested whether spontaneous fluctuations of the attentional state can lead to low confidence in one's perceptual decision. We measured prestimulus functional magnetic resonance imaging activity in the dorsal attention network and used that activity as an index of the level of attention involved in a motion direction discrimination task. Extending our previous findings, we showed that low prestimulus activity in the dorsal attention network, which presumably reflected low level of attention, was associated with higher confidence ratings. These results were explained by a signal detection theoretic model in which lack of attention increases the trial-by-trial variability of the internal perceptual response. In line with the model, we also found that low prestimulus activity in the dorsal attention network was associated with higher trial-by-trial variability of poststimulus peak activity in the motion-sensitive region MT+. These findings support the notion that lack of attention may lead to liberal subjective perceptual biases, a phenomenon we call "inattentional inflation of subjective perception. "
Learning Concept Drift with a Committee of Decision Trees

Concept drift occurs when a target concept changes over time. We present a new method for learning shifting target concepts during concept drift. The method, called Concept Drift Committee (CDC), uses a weighted committee of hypotheses that votes on the current classification. When a committee member’s voting record drops below a minimum threshold, the member is forced to retire. A new committee member then takes the open place on the committee. The algorithm is compared to a leading algorithm on several benchmarks. The results indicate that using a committee to track drift has several advantages over traditional window-based approaches.
Efficient Scheduling of Complete Exchange on Clusters

One of the performance limitations of clusters is their message passing capability, while complete exchange is known to be the severest communication pattern on all types of message passing machines. In this paper, we focus on the practical issues of designing high-speed complete exchange algorithms on a commodity cluster interconnected by a non-blocking crossbar switch. Four complete exchange algorithms, including, shift exchange, pairwise exchange, group shuffle exchange and synchronous shuffle exchange algorithms are implemented and tested on a cluster platform. To avoid node and link contention, these algorithms schedule the communication at the packet-level. They aim at fully utili zing the available communication bandwidth both in the links and switch and avoiding the Head-Of-Line problem which would stall the pipelines and decrease the overall efficiency. Both the analytical and measured results show that the synchronous shuffle exchange algorithm can achieve the best performance. It can reach 97% of the available bandwidth in our tests; while the group shuffle exchange performs almost as good as the synchronous shuffle exchange algorithm but scales better when it works on an input-buffered switch. Both shift and pairwise exchanges become inefficient when exchanging small messages, as they cannot fill up those network pipelines effectively. Performance studies of the four algorithms on both input-buffered and shared-buffered switches are also reported.
Daily travel behavior: lessons from a week-long survey for the extraction of human mobility motifs related information

Multi-agent models for simulating the mobility behavior of the urban population are gaining momentum due to increasing computing power. Such models pose high demands in terms of input data in order to be reliably able to match real world behavior. To run the models a synthetic population mirroring typical mobility demand needs to be generated based on real world observations. Traditionally this is done using travel diary surveys, which are costly (and hence have relatively low sample size) and focus mainly on trip choice rather than on activities for an entire day. Thus in this setting the generation of synthetic populations either relies on resampling identical activity chains or on imposing independence of various trips occurring during the day. Both assumptions are not realistic. Using Call Detail Records (CDRs) it has been found that individual daily movement uses only a small number of movement patterns. These patterns, termed motifs, appear stably in many different cities, as has been shown for both CDR data as well as travel diaries. In this paper the relation between these motifs and other mobility related quantities like the distribution of travel distances and times as well as mode choice is investigated. Additionally transition probabilities both for motifs (relevant for multi-day simulations) and mode transitions are discussed. The main finding is that while some of the characteristics seem to be unrelated to motifs, others such as mode choice exhibit strong correlations which could improve the provision of synthetic populations for multi-agent models. Thus the results in this paper are seen as one step further towards the creation of realistic (with respect to mobility behavior) synthetic populations for multi-agent models in order to analyze the performance of multi-modal transportation systems or disease spreading in urban areas.
The AT-hook motif-encoding gene METABOLIC NETWORK MODULATOR 1 underlies natural variation in Arabidopsis primary metabolism

Regulation of primary metabolism is a central mechanism by which plants coordinate their various responses to biotic and abiotic challenge. To identify genes responsible for natural variation in primary metabolism, we focused on cloning a locus from Arabidopsis thaliana that influences the level of TCA cycle metabolites in planta. We found that the Met.V. 67 locus was controlled by natural variation in METABOLIC NETWORK MODULATOR 1 (MNM1), which encoded an AT-hook motif-containing protein that was unique to the Brassicales lineage. MNM1 had wide ranging effects on plant metabolism and displayed a tissue expression pattern that was suggestive of a function in sink tissues. Natural variation within MNM1 had differential effects during a diurnal time course, and this temporal dependency was supported by analysis of T-DNA insertion and over-expression lines for MNM1. Thus, the cloning of a natural variation locus specifically associated with primary metabolism allowed us to identify MNM1 as a lineage-specific modulator of primary metabolism, suggesting that the regulation of primary metabolism can change during evolution.
Predicting binocular visual field sensitivity from monocular visual field results.

PURPOSE To compare methods of predicting binocular visual field sensitivity of patients with glaucoma from monocular visual field data. METHODS Monocular and binocular visual fields were obtained for 111 patients with varying degrees of glaucomatous damage in one or both eyes, using the Humphrey 30-2 full-threshold procedure. Four binocular sensitivity prediction models were evaluated: BEST EYE, predictions based on individual values for the most sensitive eye, defined by mean deviation (MD); AVERAGE EYE, predictions based on the average sensitivity between eyes at each visual field location; BEST LOCATION, predictions based on the highest sensitivity between eyes at each visual field location; and BINOCUIAR SUMMATION, predictions based on binocular summation of sensitivity between eyes at each location. Differences between actual and predicted binocular sensitivities were calculated for each model. RESULTS The average difference between predicted and actual binocular sensitivities was close to zero for the BINOCULAR SUMMATION and BEST LOCATION models, with 95% of all predictions being within +/-3 dB of actual binocular sensitivities. The best eye (MD) prediction had an average error of 1.5 dB (95% confidence limits [CL], +/-3.7 dB). The average eye prediction was the poorest, with an average error of 3.7 dB (95% CL, +/-4.6 dB). CONCLUSIONS The BINOCULAR SUMMATION and BEST LOCATION models provided better predictions of binocular visual field sensitivity than the other two models, with a statistically significant difference in performance. The small difference in performance between the BINOCULAR SUMMATION and BEST LOCATION models was not statistically significant. For evaluations of functional visual field influences on task performance, daily activities, and related quality-of-life issues, either the BINOCULAR SUMMATION or BEST LOCATION model provides good estimates of binocular visual field sensitivity.
Application of wireless communication technology in the construction of intelligent community wireless network system

At present community intelligent system in China has such problems as serious waste and high failure rate. Above problems can be solved by the application of ZigBee technology. All relatively independent subsystems which are connected by RS485 bus in the current intelligent are accessed to network system platform which is built by using Zigbee technology and is based on RS485 interface. As to each system of intelligent community, the function of subsystem is realized by wireless network connection. There is no wiring in intelligent community system, which not only reduces the cost but also avoids the influence of thunder and lightning. The signal transmission is stable. Application of this technology fills the blank of intelligent community wireless network connection in China.
Online distributed network traffic signal control using the cell transmission model

This paper considers the solution of the adaptive network traffic signal control problem under a fully distributed architecture. To achieve a system-wide optimal solution, the problem is modeled as a large-scale mixed integer linear program with the traffic dynamics being captured by the cell transmission model. To achieve an online distributed solution to the considered problem, the loosely connected structure of transportation networks is exploited to decompose the problem in both space and time. The proposed solution methodology involves two main phases. In the first phase, binary decision variables are relaxed and the resulting linear program is distributedly solved via the alternating direction method of multipliers. The second phase involves distributed rounding of the obtained relaxed solution. Simulation results demonstrate the effectiveness of the proposed approach in providing close to optimal, online solutions.
Experiments with LSA scoring: optimal rank and basis

values of the SVD approximation rank k. In Se tion 4, I present results from a similar experiment on mat hing question with answers, within the ontext of the Frequently Asked Question Organizer (FAQO), a prototype system for te hni al support that I developed. In Se tion 5, I summarize related work, and dis uss the signi(cid:12) an e of these results.
Swimming behaviour and ascent paths of brook trout in a corrugated culvert

Culverts may restrict fish movements under some hydraulic conditions such as shallow flow depths or high velocities. Although swimming capacity imposes limits to passage performance, behaviour also plays an important role in the ability of fish to overcome velocity barriers. Corrugated metal culverts are characterized by unsteady flow and existence of low‐velocity zones, which can improve passage success. Here, we describe swimming behaviour and ascent paths of 148 wild brook trout in a 1.5‐m section of a corrugated metal culvert located in Raquette Stream, Québec, Canada. Five passage trials were conducted in mid‐August, corresponding to specific mean cross‐sectional flow velocities ranging from 0.30 to 0.63 m/s. Fish were individually introduced to the culvert and their movements recorded with a camera located above the water. Lateral and longitudinal positions were recorded at a rate of 3 Hz in order to identify ascent paths. These positions were related to the distribution of flow depths and velocities in the culvert. Brook trout selected flow velocities from 0.2 to 0.5 m/s during their ascents, which corresponded to the available flow velocities in the culvert at the low‐flow conditions. This however resulted in the use of low‐velocity zones at higher flows, mainly located along the walls of the culvert. Some fish also used the corrugations for sheltering, although the behaviour was marginal and did not occur at the highest flow condition. This study improves knowledge on fish behaviour during culvert ascents, which is an important aspect for developing reliable and accurate estimates of fish passage ability.
Cooperative Spectrum Sensing in Cognitive Radios With Incomplete Likelihood Functions

This paper investigates the problem of cooperative spectrum sensing in cognitive radios with unknown parameters in the likelihood function. We first derive the optimal likelihood ratio test (LRT) statistic based on the Neyman-Pearson (NP) criterion at the fusion center for hard (one-bit), soft (infinite precision) and quantized (multi-bit) local decisions. This NP-based LRT detector is feasible only if primary signal statistics and channel parameters are known. This assumption may not be realistic in cognitive radio systems. Thus, we propose a linear composite hypothesis testing approach which estimates the unknown parameters, and further simplify it so that it does not even require these estimates. Under the scenarios of: i) unknown primary signal and channel statistics; and ii) unknown primary signal statistics but known channel statistics, we apply the proposed test and also, for case ii), derive the locally most powerful (LMP) detector for weak signals. For performance analysis and threshold setting, we derive the distributions of the linear test and LMP statistics under the signal-absent hypothesis. Our simulation results show that the linear test performs very closely to the optimal LRT while not requiring the primary statistics. As a result, this method enhances robustness in cooperative spectrum sensing to uncertainties in channel gains and signal statistics.
Software Defined Networking for Heterogeneous Networks

In this paper, motivated by the vision that future internets will comprise infrastructure--based and infrastructure--less networks, we explore the use of the Software-Defined Networking (SDN) paradigm in these so-called ''heterogeneous'' networked environments. To make the case for SDN in heterogeneous networks, we examine an application scenario in which SDN is a key enabling technology. We also identify the additional requirements imposed by the SDN paradigm and discuss the research challenges they raised.
Optimizing stem cell functions and antibacterial properties of TiO2 nanotubes incorporated with ZnO nanoparticles: experiments and modeling

To optimize mesenchymal stem cell differentiation and antibacterial properties of titanium (Ti), nano-sized zinc oxide (ZnO) particles with tunable concentrations were incorporated into TiO2 nanotubes (TNTs) using a facile hydrothermal strategy. It is revealed here for the first time that the TNTs incorporated with ZnO nanoparticles exhibited better biocompatibility compared with pure Ti samples (controls) and that the amount of ZnO (tailored by the concentration of Zn(NO3)2 in the precursor) introduced into TNTs played a crucial role on their osteogenic properties. Not only was the alkaline phosphatase activity improved to about 13.8 U/g protein, but the osterix, collagen-I, and osteocalcin gene expressions was improved from mesenchymal stem cells compared to controls. To further explore the mechanism of TNTs decorated with ZnO on cell functions, a response surface mathematical model was used to optimize the concentration of ZnO incorporation into the Ti nanotubes for stem cell differentiation and antibacterial properties for the first time. Both experimental and modeling results confirmed (R2 values of 0.8873–0.9138 and 0.9596–0.9941, respectively) that Ti incorporated with appropriate concentrations (with an initial concentration of Zn(NO3)2 at 0.015 M) of ZnO can provide exceptional osteogenic properties for stem cell differentiation in bone cells with strong antibacterial effects, properties important for improving dental and orthopedic implant efficacy.
Extrapharyngeal group A Streptococcus infection: diagnostic accuracy and utility of rapid antigen testing

Background. Antigen tests have been well-studied and are widely used in pediatric practice for rapid detection of group A Streptococcus (GAS) infections in the throat, but they have not been examined sufficiently for the detection of infection of skin sites, such as the perineal region or impetiginous lesions. Methods. During the 3-year period 1999 to 2002, we evaluated 239 patients with suspected GAS skin infection, in 5 pediatric practices, using 3 Dacron swabs for each site. The first swab was tested in the pediatric office laboratory with an antigen detection kit. For the first 91 patients, the Abbott Test Pack Plus antigen detection test (ADT) was used. The Abbott Signify Strep A ADT was used to test subsequent patients. The second swab was tested with BD Directigen 1-2-3 ADT in the hospital laboratory. The third swab was placed in modified Stuart’s transport medium for comparison of recovery of GAS from culture in broth or on agar. A positive culture served as the reference standard. Test performance and test accuracy were determined for each ADT. Results. Of the 247 ADTs and cultures performed on 239 patients, 91 with suspected skin infection were tested with the Test Pack Plus test, 149 with the Signify Strep A test and 247 with the Directigen test. Eighty-six (35%) cultures were positive, 73 from perineal sites (54 rectal, 13 vaginal, 6 penile) and 13 from impetiginous lesions. There was 100% concordance for the 86 cultures positive for GAS in a comparison between dry Dacron swabs and swabs that had been placed in modified Stuart’s transport medium. Test Pack Plus and Signify Strep A ADTs had similar performance characteristics for skin infections: sensitivity, 92 and 88%; specificity, 99 and 97%; positive predictive value, 96 and 94%; and negative predictive value, 97 and 93%. Directigen ADT had sensitivity 78%, specificity 100%, positive predictive value 100% and negative predictive value 89%. Accuracy for the tests varied from 92 to 97%. Conclusion. Tests designed to detect GAS carbohydrate antigen in patients with pharyngitis can be used rapidly and accurately to detect GAS antigen in patients with cutaneous lesions suspected of GAS infection.
Left-to-Right Tree-to-String Decoding with Prediction

Decoding algorithms for syntax based machine translation suffer from high computational complexity, a consequence of intersecting a language model with a context free grammar. Left-to-right decoding, which generates the target string in order, can improve decoding efficiency by simplifying the language model evaluation. This paper presents a novel left to right decoding algorithm for tree-to-string translation, using a bottom-up parsing strategy and dynamic future cost estimation for each partial translation. Our method outperforms previously published tree-to-string decoders, including a competing left-to-right method.
Automated intrusion recovery for web applications

In this dissertation, we develop recovery techniques for web applications and demonstrate that automated recovery from intrusions and user mistakes is practical as well as effective. Web applications play a critical role in users' lives today, making them an attractive target for attackers. New vulnerabilities are routinely found in web application software, and even if the software is bug-free, administrators may make security mistakes such as misconfiguring permissions; these bugs and mistakes virtually guarantee that every application will eventually be compromised. To clean up after a successful attack, administrators need to find its entry point, track down its effects, and undo the attack's corruptions while preserving legitimate changes. Today this is all done manually, which results in days of wasted effort with no guarantee that all traces of the attack have been found or that no legitimate changes were lost. To address this problem, we propose that automated intrusion recovery should be an integral part of web application platforms. This work develops several ideas-retroactive patching, automated UI replay, dependency tracking, patch-based auditing, and distributed repair-that together recover from past attacks that exploited a vulnerability, by retroactively fixing the vulnerability and repairing the system state to make it appear as if the vulnerability never existed. Repair tracks down and reverts effects of the attack on other users within the same application and on other applications, while preserving legitimate changes. Using techniques resulting from these ideas, an administrator can easily recover from past attacks that exploited a bug using nothing more than a patch fixing the bug, with no manual effort on her part to find the attack or track its effects. The same techniques can also recover from attacks that exploit past configuration mistakes-the administrator only has to point out the past request that resulted in the mistake. We built three prototype systems, WARP, POIROT, and AIRE, to explore these ideas. Using these systems, we demonstrate that we can recover from challenging attacks in real distributed web applications with little or no changes to application source code; that recovery time is a fraction of the original execution time for attacks with a few affected requests; and that support for recovery adds modest runtime overhead during the application's normal operation. Thesis Supervisor: Nickolai Zeldovich Title: Associate Professor