Miracle-dz/UniFAR-FTUs huggingface dataset:
Habitat use by caridean shrimps in lowland rivers

Caridean shrimps are an important component of lowland river ecosystems and their distributions may be affected by river regulation. We studied the mesoscale distributions of Paratya australiensis, Caridina mccullochi and Macrobrachium australiense in five lowland rivers of the Murray–Darling Basin, south-eastern Australia. We distinguished habitat patches according to water-current velocity and channel location – still littoral (SL), slow-current-velocity littoral (SCVL) and moderate-current-velocity channel (MCVC) – and investigated ontogenetic shifts in habitat use. We sampled seven reaches for shrimp in March 2003 and December 2003 using a modified backpack electrofisher. Paratya australiensis occurred in all habitats but was mostly associated with SL. All life stages of C. mccullochi utilised SL and SCVL, and only a few adults were collected from areas with greater than slow current velocity. The habitat preference of M. australiense changed with development: larvae only occurred in SL, but adults and berried females strongly preferred MCVC. Low flows and slow water currents are characteristic of lowland rivers in southern Australia during summer and autumn (December–April), the period during which shrimps’ larval development and juvenile recruitment occurs. Caridina mccullochi and M. australiense may rely on still and slow-current-velocity habitats during larval development and juvenile recruitment and to facilitate upstream movements.
Computing all s-t bridges and articulation points simplified

Given a directed graph $G$ and a pair of nodes $s$ and $t$, an $s$-$t$ bridge of $G$ is an edge whose removal breaks all $s$-$t$ paths of $G$. Similarly, an $s$-$t$ articulation point of $G$ is a node whose removal breaks all $s$-$t$ paths of $G$. Computing the sequence of all $s$-$t$ bridges of $G$ (as well as the $s$-$t$ articulation points) is a basic graph problem, solvable in linear time using the classical min-cut algorithm. When dealing with cuts of unit size ($s$-$t$ bridges) this algorithm can be simplified to a single graph traversal from $s$ to $t$ avoiding an arbitrary $s$-$t$ path, which is interrupted at the $s$-$t$ bridges. Further, the corresponding proof is also simplified making it independent of the theory of network flows.
AvE: Assistance via Empowerment

One difficulty in using artificial agents for human-assistive applications lies in the challenge of accurately assisting with a person's goal(s). Existing methods tend to rely on inferring the human's goal, which is challenging when there are many potential goals or when the set of candidate goals is difficult to identify. We propose a new paradigm for assistance by instead increasing the human's ability to control their environment, and formalize this approach by augmenting reinforcement learning with human empowerment. This task-agnostic objective preserves the person's autonomy and ability to achieve any eventual state. We test our approach against assistance based on goal inference, highlighting scenarios where our method overcomes failure modes stemming from goal ambiguity or misspecification. As existing methods for estimating empowerment in continuous domains are computationally hard, precluding its use in real time learned assistance, we also propose an efficient empowerment-inspired proxy metric. Using this, we are able to successfully demonstrate our method in a shared autonomy user study for a challenging simulated teleoperation task with human-in-the-loop training.
Investigating and Exploiting Image Resolution for Transfer Learning-based Skin Lesion Classification

Skin cancer is among the most common cancer types. Dermoscopic image analysis improves the diagnostic accuracy for detection of malignant melanoma and other pigmented skin lesions when compared to unaided visual inspection. Hence, computer-based methods to support medical experts in the diagnostic procedure are of great interest. Fine-tuning pre-trained convolutional neural networks (CNNs) has been shown to work well for skin lesion classification. Pre-trained CNNs are typically trained with natural images of a fixed image size significantly smaller than captured skin lesion images and consequently dermoscopic images are downsampled for fine-tuning. However, useful medical information may be lost during this transformation. In this paper, we explore the effect of input image size on skin lesion classification performance of fine-tuned CNNs. For this, we resize dermoscopic images to different resolutions, ranging from 64 x 64 to 768 x 768 pixels and investigate the resulting classification performance of three well-established CNNs, namely DenseNet-121, ResNet-18, and ResNet-50. Our results show that using very small images (of size 64 x 64 pixels) degrades the classification performance, while images of size 128 x 128 pixels and above support good performance with larger image sizes leading to slightly improved classification. We further propose a novel fusion approach based on a three-level ensemble strategy that exploits multiple fine-tuned networks trained with dermoscopic images at various sizes. When applied on the ISIC 2017 skin lesion classification challenge, our fusion approach yields an area under the receiver operating characteristic curve of 89.2% and 96.6% for melanoma classification and seborrheic keratosis classification, respectively, outperforming state-of-the-art algorithms.
Big-bang nucleosynthesis with sub-GeV massive decaying particles

We consider the effects of the injections of energetic photon and electron (or positron) on the big-bang nucleosynthesis. We study the photodissociation of light elements in the early Universe paying particular attention to the case that the injection energy is sub-GeV and derive upper bounds on the primordial abundances of the massive decaying particle as a function of its lifetime. We also discuss a solution of the 7Li problem in this framework.
A Unified Framework for Analyzing and Detecting Malicious Examples of DNN Models

Deep Neural Networks are well known to be vulnerable to adversarial attacks and backdoor attacks, where minor modifications on the input can mislead the models to give wrong results. Although defenses against adversarial attacks have been widely studied, research on mitigating backdoor attacks is still at an early stage. It is unknown whether there are any connections and common characteristics between the defenses against these two attacks. In this paper, we present a unified framework for detecting malicious examples and protecting the inference results of Deep Learning models. This framework is based on our observation that both adversarial examples and backdoor examples have anomalies during the inference process, highly distinguishable from benign samples. As a result, we repurpose and revise four existing adversarial defense methods for detecting backdoor examples. Extensive evaluations indicate these approaches provide reliable protection against backdoor attacks, with a higher accuracy than detecting adversarial examples. These solutions also reveal the relations of adversarial examples, backdoor examples and normal samples in model sensitivity, activation space and feature space. This can enhance our understanding about the inherent features of these two attacks, as well as the defense opportunities.
Protective effects of Echinacea purpurea in an acetic acid induced rat model of colitis

In order to investigate putative protective effects of Echinacea purpurea on colonic inflammation, we determined Adenosine deaminase (ADA) and superoxide dismutase (SOD) activities, malondialdehyde (MDA) levels and protein carbonyl contents were determined in colonic tissues of rats in the colitis and colitis plus Echinacea purpurea (at different doses 50,100 mg/kg) given rats. Besides, histopathology of colon tissues were evaluated. In the Echinacea treatment groups (50 and 100 mg/kg doses) ADA activities were significantly decreased as compared to acetic acid group, but there was no statistically significant between two treatment groups (p>0.05). Echinacea treatment also was decreased MDA levels at two doses according to colitis group (p 0.05). Slightly decreased protein carbonyl contents and elevated SOD activities were shown in the two Echinacea therapy groups as compared to acetic acid induced colitis group. But these were not statistically significant (p>0.05). Similar observations were recorded for these parameters in the extracts of colonic tissue specimens. The results revealed that pretreatment to colitic rats with Echinacea purpurea at doses of 50 and 100 mg/kg, partially attenuated the colonic damage induced by acetic acid. In conclusion, the preventive effects of Echinacea purpurea in the acetic acid model of rat colitis is probably related to its antioxidant properties, due to its flavonoid content. Abbreviations: ADA=Adenosine deaminase, SOD= superoxide dismutase, MDA= malondialdehyde, IBD= Inflammatory bowel diseases, UC= ulcerative colitis, ROS= reactive oxygen species, NO= nitric oxide, US= United States, NBT= nitrobluetetrazolium, TBA= thiobarbituric acid, SPSS=Statistical Package for Social Sciences.
Asynchronous Multi Agent Active Search

Active search refers to the problem of efficiently locating targets in an unknown environment by actively making data-collection decisions, and has many applications including detecting gas leaks, radiation sources or human survivors of disasters using aerial and/or ground robots (agents). Existing active search methods are in general only amenable to a single agent, or if they extend to multi agent they require a central control system to coordinate the actions of all agents. However, such control systems are often impractical in robotics applications. In this paper, we propose two distinct active search algorithms called SPATS (Sparse Parallel Asynchronous Thompson Sampling) and LATSI (LAplace Thompson Sampling with Information gain) that allow for multiple agents to independently make data-collection decisions without a central coordinator. Throughout we consider that targets are sparsely located around the environment in keeping with compressive sensing assumptions and its applicability in real world scenarios. Additionally, while most common search algorithms assume that agents can sense the entire environment (e.g. compressive sensing) or sense point-wise (e.g. Bayesian Optimization) at all times, we make a realistic assumption that each agent can only sense a contiguous region of space at a time. We provide simulation results as well as theoretical analysis to demonstrate the efficacy of our proposed algorithms.
SUBCULTURES OF PRIMARY RAT FIBROBLASTS

Cultures of fibroblasts from newborn rats and successive subcultures of these cells were treated with 4-nitroquinoline -l-oxide to induce DNA repair. DNA from the cultures was examined by velocity sedimentation in alkaline sucrose gradients immediately after drug treatment and after a post-treatment incubation period of 3 h. Early passage cells were able to repair the damage that appeared as single strand breaks, however, by the seventh subculture this activity was not apparent. Measurements of repair synthesis showed a partial loss of this capacity with successive subculture. The results fit a model in which 4NQO causes two kinds of DNA modification, one of which is alkali labile and appears as a single-strand break. Both modifications are subject to excision repair, but each is recognized initially by a specific endonuclease. In the late passage cells, the endonuclease specific for the alkali labile modification is absent. It has been well documented that the capacity for
Crown conductance and tree and stand transpiration in a second growth **Abies amabilis** forest

We measured whole-tree sap flow in a 43-year-old Abies amabilis (Dougl. ex Loud.) Dougl. ex J. Forbes n Tsuga heterophylla (Raf.) Sarg. forest in western Washington, U.S.A. We calculated whole-tree crown conductance to water vapor (gcrown) by substituting the sap flow data and meteorological measurements into the inverted PenmannMonteith equation. Individual tree sap flow and crown conductance varied widely with tree size, with the smallest tree sampled having average gcrown (on a ground-area basis) of 0.57 mms n1 and transpiring up to 4.9 kgday n1 , while the largest tree measured had an average gcrown of 7.20 mms n1 and lost as much as 98 kgday n1 . Crown conductance responded linearly and positively to radiation, and had a negative exponential response to vapor pressure deficit. These response patterns were utilized to construct an empirical model of gcrown that explained from 52 to 73% (average 66%) of the variation in gcrown. The dominant and codominant trees in the stand transpired for longer periods during the day than trees in the smaller size classes, and contributed disproportionately to total stand transpiration. Daily total sap flow for individual trees was strongly correlated with tree basal area; we used the relationship between these variables to estimate daily stand transpiration. Stand transpiration calculated for 28 days between August 6 and October 12, 1993, ranged from 0.01 to 3.52 mmday n1 . Stand transpiration increased curvilinearly with increasing average daily vapor pressure deficit, reflecting the negative response of gcrown to vapor pressure deficit.
Spatial and Temporal Variation in Reproductive Rates of the Red-Shouldered Hawk in Suburban and Rural Ohio

Abstract. We measured the reproductive rate of Red-shouldered Hawks (Buteo lineatus) nesting in suburban southwestern Ohio and in a rural forested region in Hocking Hills, southeastern Ohio, from 1997 to 2005. In the suburban region, the reproductive rate varied greatly from nest to nest, less so from year to year, indicating that some nest areas consistently produced more young than others. The most productive 25% of nest areas produced 44% of all the nestlings in the study, whereas the least productive 25% of nest areas produced only 7% of all nestlings. In the rural area, the reproductive rate varied significantly from year to year, less so from nest area to nest area. Overall reproductive rates in the two study areas differed only in 2000. We suggest that differences among the nest areas in reproductive rate likely indicate differences in habitat quality of individual nest areas, whereas differences among years likely reflect regional factors that influence nesting birds, such as weather.
Past as prologue: Approaches to the study of confirmation in science

In the 1970s, quantitative science studies were being pursued by sociologists, historians, and information scientists. Philosophers were part of this discussion, but their role would diminish as sociology of science asserted itself. An antiscience bias within the sociology of science became evident in the late 1970s, which split the science studies community, notably causing the “citationists” to go their own way. The main point of contention was whether science was a rational, evidence-based activity. To reverse the antiscience trend, it will be necessary to revive philosophical models of science, such as Bayesian confirmation theory or explanatory coherence models, where theory-experiment agreement plays a decisive role. A case study from the history of science is used to illustrate these models, and bibliometric and text-based methods are proposed as a source of data to test these models.
DEV114108 2912..2912

The ability to image cells live and in situ as they proliferate and differentiate has proved to be an invaluable asset to biologists investigating developmental processes. Here, we describe a Spectrum of Fates approach that allows the identification of all the major neuronal subtypes in the zebrafish retina simultaneously. Spectrum of Fates is based on the combinatorial expression of differently coloured fluorescent proteins driven by the promoters of transcription factors that are expressed in overlapping subsets of retinal neurons. Here, we show how a Spectrum of Fates approach can be used to assess various aspects of neural development, such as developmental waves of differentiation, neuropil development, lineage tracing and hierarchies of fates in the developing zebrafish
Compensatory growth and reduced maturation in second sea winter farmed Atlantic salmon following starvation in February and March

Starvation of second sea winter farmed Atlantic salmon through February and March reduced body weight by 0.10% day−1 or 6.0% during the starvation period, whereas fed fish increased body weight by 0.10 day−1 or 5.9%. When fed again during 41 days in April and May, the starved group increased weight by 22.7% (0.55% day−1) compared with a 11.4% (0.28% day−1) gain in the unrestricted control. Ultrasound determination of sex and maturity in late May showed that the incidence of maturation was reduced by 48% among females and 32% among males in the starved group, compared with the unrestricted group.
Body spot coloration of a nocturnal sit-and-wait predator visually lures prey

Many nocturnal spiders have paired conspicuous yellow ventral spots that contrast against their black and brown abdomens. A previous experiment, manipulating the coloration of the spots of the spider Neoscona punctigera, suggested that the spots lure prey. We conducted a field experiment in which we placed spider dummies that either mimicked an adult female N. punctigera in coloration, size, and shape (standard dummies) or mimicked N. punctigera but with the coloration of their ventral spots manipulated onto orb webs in the field at night and monitored them with infrared video cameras. Spectrophotometry confirmed that the coloration of the dummies resembled spider bodies, with the exception of the spots of the gray spotted dummies, where chromatic and achromatic contrast differences from spider spots were found. We used entirely yellow dummies to assess whether the spots represent a compromise between prey attraction and predator avoidance. We found that the standard dummies, mimicking adult female N. punctigera in coloration, size, and shape, attracted more prey than the dummies with gray spots, the entirely black dummies, and webs without spiders. The entirely yellow dummies attracted fewer prey than the standard dummies. These results show that the coloration of nocturnal spider ventral spots lures prey, although whether chromatic or achromatic cues are used could not be identified. The entirely yellow dummies did not lure more prey than standard dummies, so the spots are unlikely to represent a compromise between prey attraction and predator avoidance, in contrast to the coloration of certain diurnal orb web spiders.
Regional leptomeningeal collateral score by computed tomographic angiography correlates with 3-month clinical outcome in acute ischemic stroke

PURPOSE: The aim of the study is to assess the correlation between regional leptomeningeal collateral (rLMC) Scores calculated on computed tomography (CT) angiography following acute anterior circulation ischemic stroke, with 3-month clinical outcome measured as modified Rankin Scale (mRS) and Barthel Index (BI). MATERIALS AND METHODS: A total of thirty patients were studied as per the exclusion and inclusion criteria and after informed consent. Multi-phase CT angiography was carried out within 24 h of stroke onset, and collateral scoring was done using rLMC score along with Alberta stroke programme early CT (ASPECT) scoring. At 3 months, patients were followed up to evaluate the clinical outcome using mRS and BI. Statistical analysis was performed to find out the correlation between rLMC score, ASPECT score, and clinical outcome and for association with demographic parameters and stroke risk factors. RESULTS: A strong correlation was noted between ASPECT and rLMC scores (P < 0.001) and between rLMC scores and clinical outcome at 3 months (mRS and BI). Correlation with mRS (P < 0.001) was nearly as strong as that of BI on follow-up (P < 0.001). The ASPECT score also was a predictor of clinical outcome and showed correlation with mRS (P < 0.001) and BI (P < 0.001). No significant association was found between various stroke risk factors and demographic parameters with rLMC scores. The rLMC scoring system showed substantial inter-rater reliability with Kappa = 0.7. CONCLUSIONS: rLMC score in CT angiography correlates with ASPECT Score and clinical outcome at 3 months. Hence, this scoring system can be used for collateral quantification as may be of use in predicting short-term clinical outcomes.
Preplant release of Nesidiocoris tenuis and supplementary tactics for control of Tuta absoluta and Bemisa tabaci in greenhouse tomato

An early release system developed for Nesidiocoris tenuis Reuter (Heteroptera: Miridae) could provide a good control of Tuta absoluta (Meyrick) (Lepidoptera: Gelechiidae) in tomato. Tuta absoluta and the whitefly Bemisia tabaci Gennadius (Hemiptera: Aleyrodidae) often appear simultaneously in tomato crops and this might affect control capacity. Therefore, the new approach needs to be tested in a situation with both pests present. In addition, Bacillus thuringiensis Berliner and Trichogramma achaeae Nagaraja & Nagarkatti (Hymenoptera: Trichogrammatidae) have been shown to be effective against T. absoluta and could be a supplement to N. tenuis. Two experiments were carried out to evaluate the potential of this approach and its combination with supplementary control agents against T. absoluta. In the first experiment four treatments were compared (T. absoluta, B. tabaci, T. absoluta + N. tenuis, and T. absoluta + B. tabaci + N. tenuis) and N. tenuis was able to control T. absoluta and B. tabaci either alone or together. In the second experiment, five treatments were compared: T. absoluta, T. absoluta + N. tenuis, T. absoluta + N. tenuis + T. achaeae, T. absoluta + N. tenuis + B. thuringiensis, and T. absoluta + N. tenuis + T. achaeae + B. thuringiensis. Nesidiocoris tenuis again proved capable of significantly reducing T. absoluta populations, and the implementation of additional agents did not increase its effectiveness.
Hepatitis B virus drug resistance: mechanism and clinical implications for the prevention of treatment failure

Hepatitis B virus (HBV) infection remains a major public health problem worldwide. Recently, the research efforts to identify new inhibitors enabled the development of antiviral agents to treat patients chronically infected by HBV. In clinical practice, the use of nucleoside analogs, which inhibit viral polymerase activity, induces suppression of viral replication accompanied by an improvement in biochemical and histological conditions in most patients. However, many clinical studies revealed the emergence of drug-resistant mutants during extended treatment. This review focuses on the mechanism of HBV drug-resistant mutant selection and on the clinical implications of HBV drug resistance for the prevention of treatment failure.