Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantifying Rarity, Losses, and Risks for Native Fishes of the Lower Colorado River Basin: Implications for Conservation Listing

Abstract: We examined spatial distributions of fishes native to the lower basin of the Colorado River (25 species) at three scales to determine percent decline from historical distributions based on a regional biodiversity database. We cumulated records from 1843 to 1980 to develop a “historical distribution” for each species and used those occurrences recorded from 1981 to 1998 as “modern” records. We then contrasted historical and modern distributions to (1) quantify losses in spatial distribution; (2) determine how strongly these losses and fragmentation patterns corresponded to the perceived risk of extinction of each species, as represented by its status under the IUCN Red List of Endangered Species; and (3) update extinction risk rankings for 15 fishes endemic to the lower Colorado Basin according to the IUCN criteria. Based on presence and absence data, fish fauna of the lower Colorado Basin have suffered massive distributional losses. On average, ranges of extant species have diminished more than 45% relative to their historical distribution, and 35% of species have lost 50% or more of their occurrences. We provide nine new IUCN rankings and six updates to reflect more accurately the heightened imperilment of these species. Based on our new rankings, 7 of the 15 lower Colorado Basin endemics are critically endangered, 1 is endangered, 2 are vulnerable, and 1 is already extinct. We categorize the remaining 2 endemics as lower risk. This work demonstrates the utility of matching quantitative spatial metrics such as the scale‐area slope statistic to extinction risk criteria for species whose persistence is strongly influenced by spatial distribution.
Atlas-Based Segmentation of Degenerated Lumbar Intervertebral Discs From MR Images of the Spine

Intervertebral disc degeneration is an age-associated condition related to chronic back pain, while its consequences are responsible for over 90% of spine surgical procedures. In clinical practice, MRI is the modality of reference for diagnosing disc degeneration. In this study, we worked toward 2-D semiautomatic segmentation of both normal and degenerated lumbar intervertebral discs from T2-weighted midsagittal MR images of the spine. This task is challenged by partial volume effects and overlapping gray-level values between neighboring tissue classes. To overcome these problems three variations of atlas-based segmentation using a probabilistic atlas of the intervertebral disc were developed and their accuracies were quantitatively evaluated against manually segmented data. The best overall performance, when considering the tradeoff between segmentation accuracy and time efficiency, was accomplished by the atlas-robust-fuzzy c-means approach, which combines prior anatomical knowledge by means of a rigidly registered probabilistic disc atlas with fuzzy clustering techniques incorporating smoothness constraints. The dice similarity indexes of this method were 91.6% for normal and 87.2% for degenerated discs. Research in progress utilizes the proposed approach as part of a computer-aided diagnosis system for quantification and characterization of disc degeneration severity. Moreover, this approach could be exploited in computer-assisted spine surgery.
Advantages and challenges of using soil water isotopes to assess groundwater recharge dominated by snowmelt at a field study located in Canada

ABSTRACT Seasonal signals of stable isotopes in precipitation, combined with measurements of isotope ratios in soil water, can be used for quantitative estimation of groundwater recharge rates. This study investigates the applicability of using the piston flow principle and the peak shift displacement method to estimate actual groundwater recharge rates in a humid Nordic region located in the province of Quebec, Canada. Two different sites with and without vegetation (C1 and C2) in an unconfined aquifer were tested by measuring soil water isotope ratios (18O/16O and 2H/1H) and volumetric pore water content. Core samples were obtained along the vadose zone down to the groundwater table at the two sites (2.45 m for Site C1 and 4.15 m for Site C2). The peak shift method to estimate groundwater recharge rates was shown to be accurate only in certain specific conditions inherent to the soil properties and the topographical situation of the investigated sites. Indeed, at Site C2, recharge from the snowmelt could not be estimated because of heterogeneity in the lower part of the vadose zone. At this same site the later recharge after the snowmelt (in the period from late spring to early autumn) could be estimated accurately because the upper part of the vadose zone was homogeneous. Furthermore, at site C1, runoff/runon phenomena hampered calculations of actual infiltration and thus produced inaccurate results for recharge. These two different site effects (heterogeneity in the first site and runoff/runon in the other site) were identified as being limiting factors in the accurate assessment of actual recharge. This study therefore recommends the use of the peak shift method for (1) humid Nordic regions, (2) homogeneous and thick vadose zones, and (3) areas with few or limited site effects (runoff/runon).
Evolution of Open Source Software Projects: A Systematic Literature Review

Open Source Software (OSS) is continuouslygaining acceptance in commercial organizations. It is inthis regard that those organizations strive for a betterunderstanding of evolutionary aspects of OSS projects.The study of evolutionary patterns of OSS projects andcommunities has received substantial attention from theresearch community over the last decade. These effortshave resulted in an ample set of research results for whichthere is a need for up-to-date comprehensive overviews andliterature surveys. This paper reports on a systematic literature survey aimedat the identiﬁcation and structuring of research on evolutionof OSS projects. In this review we systematically selectedand reviewed 101 articles published in relevant venues. Thestudy outcome provides insight in what constitutes the maincontributions of the ﬁeld, identiﬁes gaps and opportunities,and distills several important future research directions.
Misconduct, Marginality and Editorial Practices in Management, Business and Economics Journals

Objectives The paper presents data on the two problems of misconduct and marginality in management, business and economics (MBE) journals and their practices to combat these problems. Design Data was collected in three phases. First, all publicly retracted papers in MBE journals were identified through keywords searches in 7 major databases (n = 1329 journals). Second, a focused survey was distributed to editors involved in such retractions (n = 64; response rate = 28%). Finally, a survey was administered to all active journals in the seven databases to collect data on editors’ perceptions and practices related to the two problems (n = 937, response rate = 31.8%). Frequency analyses, cross tabulations, and qualitative analyses of open answers were used to examine the data. Results 184 retracted papers in MBE journals were identified in 2005–2015 (no retraction was found before 2005). From 2005–2007 to 2012–2015, the number of retractions increased by a factor ten with an all-time high in 2015. The survey to journals with reported retractions illustrates how already a few cases of suspected misconduct put a strain on the editorial workload. The survey to all active journals revealed that 42% of the respondents had started to use software to screen all submitted papers, and that a majority recognized the problem of marginality, as indicated by salami-style submissions. According to some editors, reviewers easily spot such submissions whereas others argued that authors may submit thinly sliced papers in parallel to several journals, which means that this practice is only discovered post-publication. The survey question on ways to support creative contributions stimulated a rich response of ideas regarding editorial vision, engaged boards and developmental approaches. The study uses data from three specialized fields, but its findings may be highly relevant to many journals in the social sciences.
Chronic exposure to a predator or its scent does not inhibit male–male competition in male mice lacking brain serotonin

Although it is well-known that defective signaling of the 5-HT system in the brain and stressful stimuli can cause psychological disorders, their combined effects on male–male aggression and sexual attractiveness remain unknown. Our research aimed at examining such effects using tryptophan hydroxylase 2 (Tph2) knockout male mice vs. a rat- or rat scent-based chronic stress model. Tph2+/+ and Tph2−/− male mice were placed individually into the rat home cage (rat), a cage containing soiled rat bedding (rat scent) or a cage containing fresh bedding (control) for 5 h every other day for 56 consecutive days. In Tph2+/+ male mice, rat-exposure decreased male–male aggression and sexual attractiveness of urine odor relative to either rat scent-exposure or control; and rat scent-exposure decreased aggression rather than sexual attractiveness of urine odor compared with control. However, such dose-dependent and long-lasting behavioral inhibitory effects vanished in Tph2−/− male mice. RT-PCR assay further revealed that putative regulatory genes, such as AR, ERα and GluR4 in the prefrontal cortex, and TrkB-Tc and 5-HTR1A in the hippocampus, were down-regulated at the mRNA level in either rat- or rat scent-exposed Tph2+/+ male mice, but partially in the Tph2−/− ones. Hence, we suggest that the dose-dependent and long-lasting inhibitory effects of chronic predator exposure on male–male aggression, sexual attractiveness of urine odor, and mRNA expression of central regulatory genes might be mediated through the 5-HT system in the brain of male mice.
Macropinocytosis-Like HIV-1 Internalization in Macrophages Is CCR5 Dependent and Leads to Efficient but Delayed Degradation in Endosomal Compartments

ABSTRACT HIV-1 endocytosis by a macropinocytosis-like mechanism has been shown to lead to productive infection in macrophages. However, little is known of this pathway. In this study, we examined HIV-1 endocytosis using biochemical approaches and imaging techniques in order to better understand the mechanisms that allow for productive infection of these cells via the endosomal pathway. We show here that this macropinocytosis-like mechanism is not the sole pathway involved in HIV-1 endocytosis in macrophages. However, this pathway specifically requires CCR5 engagement at the cell surface, which in turn suggests that the virus and its coreceptor are present in the endosomal environment simultaneously. Furthermore, although we observed efficient viral degradation following endocytosis, analyses of HIV-1 transport through the endolysosomal pathway revealed that viral degradation is delayed following endosomal internalization, possibly allowing the virus to complete its fusion.
A robotic game to evaluate interfaces used to show and teach visual objects to a robot in real world condition

In this paper, we present a real world user study of 4 interfaces designed to teach new visual objects to a social robot. This study was designed as a robotic game in order to maintain the user's motivation during the whole experiment. Among the 4 interfaces 3 were based on mediator objects such as an iPhone, a Wiimote and a laser pointer. They also provided the users with different kind of feedback of what the robot is perceiving. The fourth interface was a gesture based interface with a Wizard-of-Oz recognition system added to compare our mediator interfaces with a more natural interaction. Here, we specially studied the impact the interfaces have on the quality of the learning examples and the usability. We showed that providing non-expert users with a feedback of what the robot is perceiving is needed if one is interested in robust interaction. In particular, the iPhone interface allowed non-expert users to provide better learning examples due to its whole visual feedback. Furthermore, we also studied the user's gaming experience and found that in spite of its lower usability, the gestures interface was stated as entertaining as the other interfaces and increases the user's feeling of cooperating with the robot. Thus, we argue that this kind of interface could be well-suited for robotic game.
Rejecting the attack: Source authentication for Wi-Fi management frames using CSI Information

Comparing to well protected data frames, Wi-Fi management frames (MFs) are extremely vulnerable to various attacks. Since MFs are transmitted without encryption or authentication, attackers can easily launch various attacks by forging the MFs. In a collaborative environment with many Wi-Fi sniffers, such attacks can be easily detected by sensing the anomaly RSS changes. However, it is quite difficult to identify these spoofing attacks without assistance from other nodes. By exploiting some unique characteristics (e.g., rapid spatial decorrelation, independence of Txpower, and much richer dimensions) of 802.11n Channel State Information (CSI), we design and implement CSITE, a prototype system to authenticate the Wi-Fi management frames on PHY layer merely by one station. Our system CSITE, built upon off-the-shelf hardware, achieves precise spoofing detection without collaboration and in-advance fingerprint. Several novel techniques are designed to address the challenges caused by user mobility and channel dynamics. To verify the performances of our solution, we conduct extensive evaluations in various scenarios. Our test results show that our design significantly outperforms the RSS-based method. We observe about 8 times improvement by CSITE over RSS-based method on the falsely accepted attacking frames.
Comparison of voice activity detection algorithms for VoIP

We discuss techniques for voice activity detection (VAD) for voice over Internet Protocol (VoIP). VAD aids in saving the bandwidth requirement of a voice session, thereby increasing the bandwidth efficiently. We compare the quality of speech, level of compression and computational complexity for three time-domain and three frequency-domain VAD algorithms. Implementation of time-domain algorithms is computationally simple. However, better speech quality is obtained with the frequency-domain algorithms. A comparison of the merits and demerits along with the subjective quality of speech after removal of silence periods is presented for all the algorithms. A quantitative measurement of speech quality for different algorithms is also presented.
Multilingual Reliability and “Semantic” Structure of Continuous Word Spaces

While continuous word vector representations enjoy increasing popularity, it is still poorly understood (i) how reliable they are for other languages than English, and (ii) to what extent they encode deep semantic relatedness such as paradigmatic relations. This study presents experiments with continuous word vectors for English and German, a morphologically rich language. For evaluation, we use both published and newly created datasets of morpho-syntactic and semantic relations. Our results show that (i) morphological complexity causes a drop in accuracy, and (ii) continuous representations lack the ability to solve analogies of paradigmatic relations.
Recent changes in the North Atlantic circulation

The three-dimensional ocean circulation is hardly observable but its quantification has greatly improved over the last two decades, due to moored array observations, deep float trajectories and satellite altimetry. Historical temperature and salinity data reveal changes on various periods in the North Atlantic: a global warming trend of the upper layers, quasi-decadal and multidecadal oscillations. The associated changes in the circulation are not yet clearly determined, but some hints from observations and models are presented.
A fast subspace channel estimation for STBC-based MIMO-OFDM systems

The subspace channel estimation technique is investigated for MIMO-OFDM systems with space-time block codes (STBC). The noise subspace computed from the correlation matrix of received signals requires a large number of symbols to converge. Using the block cyclic property of the channel matrix, we propose the cyclic repetition method (CRM) to generate many times of equivalent symbols for each OFDM symbol. With these equivalent symbols, the subspace channel estimation can perform very well within a few OFDM symbols. Computer simulations demonstrate the proposed CRM-based channel estimation has better performance than the conventional ones.
Photo-TaPE: user privacy preferences in photo tagging

Although they are used to expose pictures on the Web, users may not want to have a link between their identity and pictures without being able to modify them or control who accesses them. Photo tagging --- and more broadly face-recognition algorithms --- often escapes to the users' control and creates links between private situations and their public profile. To address this issue, we designed a geo-location aided system to let users declare their tagging preferences directly when the picture is taken. We present Photo-Tagging Preference Enforcement (Photo-TaPE) a system enforcing users tagging preferences without revealing their identity. By improving face-recognition efficiency, Photo-TaPE can guarantee the user tagging preferences in 67% of the cases and significantly reduces the processing time of face-recognition algorithms.
PubChem: a public information system for analyzing bioactivities of small molecules

PubChem (http://pubchem.ncbi.nlm.nih.gov) is a public repository for biological properties of small molecules hosted by the US National Institutes of Health (NIH). PubChem BioAssay database currently contains biological test results for more than 700 000 compounds. The goal of PubChem is to make this information easily accessible to biomedical researchers. In this work, we present a set of web servers to facilitate and optimize the utility of biological activity information within PubChem. These web-based services provide tools for rapid data retrieval, integration and comparison of biological screening results, exploratory structure–activity analysis, and target selectivity examination. This article reviews these bioactivity analysis tools and discusses their uses. Most of the tools described in this work can be directly accessed at http://pubchem.ncbi. nlm.nih. gov/assay/. URLs for accessing other tools described in this work are specified individually.
Quantification of correlational selection on thermal physiology, thermoregulatory behavior, and energy metabolism in lizards

Phenotypic selection is widely accepted as the primary cause of adaptive evolution in natural populations, but selection on complex functional properties linking physiology, behavior, and morphology has been rarely quantified. In ectotherms, correlational selection on thermal physiology, thermoregulatory behavior, and energy metabolism is of special interest because of their potential coadaptation. We quantified phenotypic selection on thermal sensitivity of locomotor performance (sprint speed), thermal preferences, and resting metabolic rate in captive populations of an ectothermic vertebrate, the common lizard, Zootoca vivipara. No correlational selection between thermal sensitivity of performance, thermoregulatory behavior, and energy metabolism was found. A combination of high body mass and resting metabolic rate was positively correlated with survival and negatively correlated with fecundity. Thus, different mechanisms underlie selection on metabolism in lizards with small body mass than in lizards with high body mass. In addition, lizards that selected the near average preferred body temperature grew faster that their congeners. This is one of the few studies that quantifies significant correlational selection on a proxy of energy expenditure and stabilizing selection on thermoregulatory behavior.
Homelessness and health

Homelessness is evolving into a national and international crisis. Within developed countries, homeless rates are now believed to approximate 1% of most urban populations. [1][1] In the 2001 Canadian census, 14 145 people were counted as living in a shelter. Of note, 1490 (0r 10%) people were under
Visualizing program slices

Program slicing is an automatic technique for determining which code in a program is relevant to a particular computation. Slicing has been applied in many areas, including program understanding, debugging, and maintenance. However, little attention has been paid to suitable interfaces for exploring program slices. We present an interface for program slicing that allows slicing at the statement procedure, or file level, and provides fast visual feedback on slice structure, integral to the interface is a global visualization of the program that shows the extent of a slice as it crosses procedure and file boundaries, and facilitates quick browsing of numerous slices. <<ETX>>
The Geography of Development

We develop a dynamic spatial growth theory with realistic geography. We characterize the model and its balanced-growth path and propose a methodology to analyze equilibria with different levels of migration frictions. Different migration scenarios change local market size, innovation incentives, and the evolution of technology. We bring the model to the data for the whole world economy at a 1° × 1° geographic resolution. We then use the model to quantify the gains from relaxing migration restrictions. Our results indicate that fully liberalizing migration would increase welfare about threefold and would significantly affect the evolution of particular regions of the world.
The Design and Implementation of Primitives in Column-Oriented Database Based on Multi-core Architecture

During the last decade, column-store databases have gained successes in OLAP, data mining. For current multi-core architecture, CPU and GPU, designing a set of primitives that exploit the potential parallelism efficiently is very important. In this article, we implement a set of fine-grained primitives for our column-store database gSQL. We gain an order of magnitude faster than My SQL. At the same time, we conclude that memory bandwidth and PCI-E bandwidth are the bottlenecks for the CPU and GPU primitives respectively. It is easy for the primitives to gain high bandwidth at the cost of increasing the temporary vector and we propose some solutions.
Detection and Classification of Grassland with Stellera chamaejasme through HJ-1A Hyperspectral Image in Northern Tibet

Stellera chamaejasme is the most typical invasive plant in North Tibet. Monitoring the distribution of the Stellera chamaejasme is the prerequisite for grassland quality evaluation or management. In this paper, the hyperspectral image of HJ-1A satellite (HJ-1A HSI) was used to monitor the Stellera chamaejasme in the northern region of Xainza. Linear Spectral Unmixing (LSU) algorithm was used to get the abundances of six landuse types(include grassland with Stellera chamaejasme) based on HSI. Feature extraction method of principle component analysis (PCA) was used to compress the HSI information into five bands. And then, maximum likelihood classifier(MLC) was applied to the six abundances and the first five principal components for getting the classification result. The result showed that the classification result of LSU-MLC was better than PCA5-MLC, the mapping accuracy of Stellera chamaejasme grassland based on both methods were all greater than 91%, the user accuracy was all greater than 66%. We concluded that HJ-1A HSI can be used to detect and classify Stellera chamaejasme in northern Tibet. In addition, we got the spatial distribution characteristics of Stellera chamaejasme by overlay analysis of classification result with the terrain factors: the Stellera chamaejasme mainly distributed in the area with elevation between 4500 and 4800m, slope less than 10 degrees and mostly in the Southwest aspect, where radiation and hydrothermal condition were favorable.