Miracle-dz/UniFAR-FTUs huggingface dataset:
Ignoring Imperfect Detection in Biological Surveys Is Dangerous: A Response to ‘Fitting and Interpreting Occupancy Models'

In a recent paper, Welsh, Lindenmayer and Donnelly (WLD) question the usefulness of models that estimate species occupancy while accounting for detectability. WLD claim that these models are difficult to fit and argue that disregarding detectability can be better than trying to adjust for it. We think that this conclusion and subsequent recommendations are not well founded and may negatively impact the quality of statistical inference in ecology and related management decisions. Here we respond to WLD's claims, evaluating in detail their arguments, using simulations and/or theory to support our points. In particular, WLD argue that both disregarding and accounting for imperfect detection lead to the same estimator performance regardless of sample size when detectability is a function of abundance. We show that this, the key result of their paper, only holds for cases of extreme heterogeneity like the single scenario they considered. Our results illustrate the dangers of disregarding imperfect detection. When ignored, occupancy and detection are confounded: the same naïve occupancy estimates can be obtained for very different true levels of occupancy so the size of the bias is unknowable. Hierarchical occupancy models separate occupancy and detection, and imprecise estimates simply indicate that more data are required for robust inference about the system in question. As for any statistical method, when underlying assumptions of simple hierarchical models are violated, their reliability is reduced. Resorting in those instances where hierarchical occupancy models do no perform well to the naïve occupancy estimator does not provide a satisfactory solution. The aim should instead be to achieve better estimation, by minimizing the effect of these issues during design, data collection and analysis, ensuring that the right amount of data is collected and model assumptions are met, considering model extensions where appropriate.
Query Expansion for Microblog Retrieval

The extreme brevity of Microblog posts (such as ‘tweets’) exacerbates the well-known vocabulary mismatch problem when retrieving tweets in response to user queries. In this study, we explore various query expansion approaches as a way to address this problem. We use the Web as a source of query expansion terms. We also tried a variation of a standard pseudo-relevance feedback method. Results on the TREC 2011 Microblog test data (TWEETS11 corpus) are very promising – significant improvements are obtained over a baseline retrieval strategy that uses no query expansion. Since many of the TREC queries were oriented towards the news genre, we also tried using only news sites (BBC and NYTIMES) in the hope that these would be a cleaner, less noisy source for expansion terms. This turned out to be counter-productive.
Regulation by blue light and heat shock of gene transcription in the fungus Phycomyces: proteins required for photoinduction and mechanism for adaptation to light

The gene hspA for the heat‐shock protein HSP100 is induced by blue light and heat shock in the zygomycete fungus Phycomyces blakesleeanus. We have investigated the molecular details of the regulation of hspA gene transcription. We have cloned 1.9 kb of hspA upstream DNA sequence and identified many DNA segments possibly involved in heat‐shock and blue‐light regulation. We have identified several gene products required for hspA photoactivation and found that they are also required for mycelial photoresponses, a suggestion for a common signal transduction pathway. In addition, we have found that beta‐carotene, or a chemical derivative, is required for hspA gene photoactivation. The activation of hspA after blue light‐exposure or a heat shock is transient, suggesting the adaptation to the stimulus. The adaptation of hspA photoactivation seems to be the result of a novel mechanism causing a light‐dependent loss of gene transcription. We propose that a reduction in the amount of MADA, a putative flavin‐binding zinc‐finger protein, in light‐exposed mycelia may cause a reduced hspA photoactivation, providing a simple explanation for adaptation to light.
Handwriting automaticity: the search for performance thresholds

Evidence is accumulating that handwriting has an important role in written composition. In particular, handwriting automaticity appears to relate to success in composition. This relationship has been little explored in British contexts and we currently have little idea of what threshold performance levels might be. In this paper, we report on two linked studies that attempted to identify performance levels in handwriting automaticity for children at two ages, below which their success in writing composition might be considered to be at risk. We conclude by suggesting interpolated levels for children at different ages, although we recognise the tentative nature of these suggestions.
How dynamic are IP addresses?

This paper introduces a novel algorithm, UDmap, to identify dynamically assigned IP addresses and analyze their dynamics pattern. UDmap is fully automatic, and relies only on application-level server logs. We applied UDmap to a month-long Hotmail user-login trace and identified a significant number of dynamic IP addresses - more than 102 million. This suggests that the fraction of IP addresses that are dynamic is by no means negligible. Using this information in combination with a three-month Hotmail email server log, we were able to establish that 95.6% of mail servers setup on the dynamic IP addresses in our trace sent out solely spam emails. Moreover, these mail servers sent out a large amount of spam - amounting to 42.2% of all spam emails received by Hotmail. These results highlight the importance of being able to accurately identify dynamic IP addresses for spam filtering. We expect similar benefits to arise for phishing site identification and botnet detection. To our knowledge, this is the first successful attempt to automatically identify and understand IP address dynamics.
Dynamic Reconfiguration Method for Web Service Based on Policy

A more challenging problem for Web Service reconfiguration is to reconfigure services dynamically on demand. This paper proposes the dynamic reconfiguration method for Web Service. A policy based framework supports three levels reconfiguration strategies that separate reconfiguration from application. This framework includes three conceptual layers: change instruction, reconfiguration management, and application management. The reconfiguration is implemented in two phases by two layers: semantic analysis phase, and reconfiguration policy specification phase. The semantic analysis base on OWL-S is provided. A policy based on reasoning model addresses the dynamical reconfiguration in which systems can be controlled at a meta-level without changing their underlying implementation. Five issues concerned with consistency, policy conflict, security, fault tolerance, and configure schedule during period of dynamic reconfiguration are applied in our dynamical reconfiguration to guarantee the consistency, policy application, security, fault tolerance and time consume.
The Role of Osteoblasts in the Hematopoietic Microenvironment

Hematopoietic stem cell differentiation occurs in direct proximity to osteoblasts within the bone marrow cavity. Despite this striking affiliation, surprisingly little is known about the precise cellular and molecular impact of osteoblasts on the bone marrow microenvironment. Recently, it has been proposed that human osteoblasts support the growth of primitive human hematopoietic cells in vitro and possibly in vivo. Evidence to support this hypothesis is reviewed as follows: the influence of osteoblasts on osteoclast development; the participation of osteoblasts in long‐term bone marrow cultures; the production of positive hematopoietic regulatory molecules by osteoblasts; the production of cell‐cycle inhibitory factors by osteoblasts, and cell‐cell interactions between early hematopoietic cells and osteoblasts.
Body Dissatisfaction and Characteristics of Disordered Eating Among Black and White Early Adolescent Girls and Boys

Multiple measures of body dissatisfaction and behaviors associated with disordered eating were studied in 258 White girls, 223 White boys, 106 Black girls, and 82 Black boys. All participants were unpaid volunteers between the ages of 12 and 15 attending six middle schools in Delaware and Maryland. On two self-ideal figure drawing discrepancy measures and four attitude measures of body dissatisfaction, girls had greater dissatisfaction than boys, and Whites had greater body dissatisfaction than Blacks. Racial differences among girls were more common than among boys. Similar results were found for measures of behaviors associated with disordered eating. Gender and racial differences generally paralleled those reported in college populations but were considerably larger than those typically reported in older populations. The majority of Black girls and boys, like the majority of White girls and boys, were dissatisfied with the size of their bodies.
Preparing Offspring for a Dangerous World: Potential Costs of Being Wrong

Adaptive maternal responses to stressful environments before young are born can follow two non-exclusive pathways: either the mother reduces current investment in favor of future investment, or influences offspring growth and development in order to fit offspring phenotype to the stressful environment. Inducing such developmental cues, however, may be risky if the environment changes meanwhile, resulting in maladapted offspring. Here we test the effects of a predator-induced maternal effect in a predator-free postnatal environment. We manipulated perceived predation-risk for breeding female great tits by exposing them to stuffed models of either a predatory bird or a non-predatory control. Offspring were raised either in an environment matching the maternal one by exchanging whole broods within a maternal treatment group, or in a mismatching environment by exchanging broods among the maternal treatments. Offspring growth depended on the matching of the two environments. While for offspring originating from control treated mothers environmental mismatch did not significantly change growth, offspring of mothers under increased perceived predation risk grew faster and larger in matching conditions. Offspring of predator treated mothers fledged about one day later when growing under mismatching conditions. This suggests costs paid by the offspring if mothers predict environmental conditions wrongly.
Dysfunctional Eating in an Australian Community Sample: The Role of Emotion Regulation, Impulsivity, and Reward and Punishment Sensitivity

This study aimed to examine the role of emotion regulation and reinforcement sensitivity in dysfunctional eating behaviours. Two hundred twenty‐eight adults from the Australian community completed self‐report inventories assessing the variables. Dysfunctional restrained eaters differed from those who did not engage in restrained eating in terms of their emotion regulation, impulsivity, and sensitivity to reward. Difficulties in emotion regulation, low impulsivity, and sensitivity to reward predicted engagement in restrained eating. Emotional eaters significantly differed from those who did not engage in dysfunctional levels of emotional eating in terms of their emotion regulation, impulsivity, and sensitivity towards reward, and difficulties in emotion regulation predicted emotional eating. Finally, dysfunctional external eaters differed from non‐dysfunctional external eaters in terms of their emotion regulation, impulsivity, sensitivity towards reward, as well as sensitivity towards punishment, and difficulties with emotion regulation and sensitivity towards reward predicted external eating. These findings highlight the importance of the inclusion of emotional functioning in models of development and maintenance of eating disorders, and support the potential implementation of treatment interventions that address emotion regulation and include strategies to cope with impulsivity and reinforcement sensitivities.
The Meaning of Weaning: Influence of the Weaning Period on Behavioral Development in Mice

Maternal care during the first week postpartum has long-term consequences for offspring development in rodents. However, mother-infant interactions continue well beyond this period, with several physiological and behavioral changes occurring between days 18 and 28 PN. In the present study, we investigate the long-term effects on offspring behavior of being weaned at day 21 PN versus day 28 PN. We found that male and female offspring engage in higher initial levels of social interaction if weaned at day 28 PN, as well as sexually dimorphic changes in exploratory behavior. Females who were themselves weaned earlier also appeared to wean their own pups earlier. Sex-specific effects of weaning age were found on levels of oxytocin and vasopressin V1a receptor density in the hypothalamus, central nucleus of the amygdala and nucleus accumbens. These results indicate that altering weaning age in mice may be a useful model for investigating the development of sexual dimorphism in neurobiology and behavior.
Application of a disease‐specific, quality‐of‐life measure (QoL‐AGHDA) in growth hormone‐deficient adults and a random population sample in Sweden: validation of the measure by Rasch analysis

Growth hormone deficiency (GHD) in adults has been associated with impaired health status and quality of life (QoL) in several studies using generic measures, and in a few studies using recently developed disease‐specific measures. Theoretically, disease‐specific measures may be more sensitive and succinct than generic measures, and hence prove convenient for general use in clinical practice. The present study sought to validate the scaling properties of the disease‐specific QoL‐AGHDA measure through the implementation of Rasch analysis. The study also sought to compare, by using the QoL‐AGHDA, the QoL of a relatively large Swedish cohort of adults with untreated GHD with that of a reference population also from Sweden.
A Phase II Clinical Trial of CPI-613 in Patients with Relapsed or Refractory Small Cell Lung Carcinoma

Background Small cell lung cancer (SCLC) is a common lung cancer which presents with extensive stage disease at time of diagnosis in two-thirds of patients. For treatment of advanced disease, traditional platinum doublet chemotherapy induces response rates up to 80% but with few durable responses. CPI-613 is a novel anti-cancer agent that selectively inhibits the altered form of mitochondrial energy metabolism in tumor cells. Methods We evaluated CPI-613 with a single-arm, open-label phase II study in patients with relapsed or refractory SCLC. CPI-613 was given at a dose of 3,000 mg/m2 on days 1 and 4 of weeks 1–3 of 4 week cycle. The primary outcome was response rate as assessed by CT imaging using RECIST v1.1 criteria. Secondary outcomes were progression-free survival (PFS), overall survival (OS), and toxicity. Twelve patients were accrued (median age 57yo) who had previously received between 1 and 4 lines of chemotherapy (median 1) for SCLC with a treatment-free interval of less than 60 days in 9 of the 12 patients. Results No complete or partial responses were seen. Ten patients (83%) progressed as best response and 2 (17%) were not evaluable for response. Median time to progression was 1.7 months (range 0.7 to 1.8 months). Eleven patients (92%) died with median overall survival of 4.3 months (range 1.2 to 18.2 months). The study was closed early due to lack of efficacy. Of note, three out of three patients who progressed after CPI-613 and were subsequently treated with standard topotecan then demonstrated treatment response with survival for 18.2, 7.4, and 5.1 months. We conducted laboratory studies which found synergy in-vitro for CPI-613 with topotecan. Conclusions Single agent CPI-613 had no efficacy in this study. Further study of CPI 613 in combination with a topoisomerase inhibitor is warranted.
Modularity of Directed Networks: Cycle Decomposition Approach

The problem of decomposing networks into modules (or clusters) has gained much attention in recent years, as it can account for a coarse-grained description of complex systems, often revealing functional subunits of these systems. A variety of module detection algorithms have been proposed, mostly oriented towards finding hard partitionings of undirected networks. Despite the increasing number of fuzzy clustering methods for directed networks, many of these approaches tend to neglect important directional information. In this paper, we present a novel random walk based approach for finding fuzzy partitions of directed, weighted networks, where edge directions play a crucial role in defining how well nodes in a module are interconnected. We will show that cycle decomposition of a random walk process connects the notion of network modules and information transport in a network, leading to a new, symmetric measure of node communication. walk process, for which we will prove that although being time-reversible it inherits all necessary information about directions and modular structure of the original network. Finally, we will use this measure to introduce a communication graph, for which we will show that although being undirected it inherits all necessary information about modular structures from the original network.
Analysis and control of DAB based DC-AC multiport converter with small DC link capacitor

Multiport Converter gets growing applications due to its advantages of flexible control mode, high power density, bidirectional power delivery capability etc. In this paper, a DAB based partial isolated DC-AC multiport power converter, which combines photovoltaic panel, battery storage and grid connection is studied. Modulation method, analysis for power transmission and control design are provided. And for the proposed converter topology, a new method for DC link 100Hz ripple power compensation is proposed which can reduce DC link ripple voltage with smaller capacitor. Simulation results are presented to demonstrate the validity of the proposed control strategy.
Bus encoding for low-power high-performance memory systems

High-performance memory buses consume large energy as they include termination networks, BiCMOS and/or open-drain output. This paper introduces power reduction techniques for memory systems deliberating on burst-mode transfers over the high-speed bus specifications such as Low Voltage BiCMOS (LVT), Gunning Transfer Logic (GTL+) and Stub Series Termination Logic (SSTL_2) which are widely used. The reduction techniques take both the static and the dynamic power consumption into account because most high-performance bus drivers and end-termination networks dissipate significant static power as well. Extensive performance analysis is conducted through mathematical analysis and trace data-driven simulations. We had reduction of 14% with random data and up to 67.5% with trace data.
Computing Word Similarity and Identifying Cognates with Pair Hidden Markov Models

We present a system for computing similarity between pairs of words. Our system is based on Pair Hidden Markov Models, a variation on Hidden Markov Models that has been used successfully for the alignment of biological sequences. The parameters of the model are automatically learned from training data that consists of word pairs known to be similar. Our tests focus on the identification of cognates --- words of common origin in related languages. The results show that our system outperforms previously proposed techniques.
Combinatorial property testing (a survey)

We consider the question of determining whether a given object has a predetermined property or is \far" from any object having the property. Speciically, objects are modeled by functions, and distance between functions is measured as the fraction of the domain on which the functions diier. We consider (randomized) algorithms which may query the function at arguments of their choice, and seek algorithms which query the function at relatively few places. We focus on combinatorial properties, and speciically on graph properties. The two standard representations of graphs { by adjacency matrices and by incidence lists { yield two diierent models for testing graph properties. In the rst model, most appropriate for dense graphs, distance between N-vertex graphs is measured as the fraction of edges on which the graphs disagree over N 2. In the second model, most appropriate for bounded-degree graphs, distance between N-vertex d-degree graphs is measured as the fraction of edges on which the graphs disagree over dN. To illustrate the two models, we survey results regarding the complexity of testing whether a graph is Bipartite. For a constant distance parameter, a constant number of queries suuce in the rst model, whereas e (p N) queries are necessary and suucient in the second model.
Commissioning of the ATLAS offline software with cosmic rays

The ATLAS experiment of the LHC is now taking its first data by collecting cosmic ray events. The full reconstruction chain including all sub-systems (inner detector, calorimeters and muon spectrometer) is being commissioned with this kind of data for the first time. Detailed analysis are being performed in order to provide ATLAS with its first alignment and calibration constants and to study the combined muon performance. Combined monitoring tools and event displays have also been developed to ensure good data quality. A simulation of cosmic events according to the different detector and trigger setups has also been provided to verify it gives a good description of the data.
Music and felt emotions: How systematic pitch level variations affect the experience of pleasantness and arousal

Pitch is a fundamental musical factor; however, findings about its contribution to the elicitation of emotions are contradictory. The purpose of this work was to assess the effect of systematic pitch variations on self-reports of felt valence and arousal. In a within-subject design, 49 subjects listened to four 1-minute classical piano excerpts, each presented at three different pitch levels (one octave lower than the original version, the original version and one octave higher than the original version). Compared to excerpts both without octave modification and in the +1 octave variant, pleasantness of excerpts in the -1 octave variant was significantly lower. This main effect was stronger for women than men and, importantly, was modulated by the specific characteristics of the stimuli. There was also a significant, yet smaller, negative relationship between pitch level and arousal, moderated by gender: Compared to higher pitch, lower pitch was associated with higher arousal in men only. Regarding the complex outcomes of this study, future studies should investigate to which extent our findings can be generalized to other musical works. The ultimate goal might be to demonstrate how pitch level interacts with other musical features and listeners’ characteristics in eliciting diverse affective experiences.
A concern-based approach to dy namic software evolution

The problem we are trying to tackle in this research is that of the availability of critical applications while they are being updated. We are investigating how dynamic aspects can be used to evolve some concerns of a running application. Our approach targets a three steps process: first, an application is statically refactored so that evolvable concerns are cleanly separated, second, concerns are handled by a reflective infrastructure, and third, a runtime API to this infrastructure makes it possible to update the separated concerns one at a time.