Miracle-dz/UniFAR-FTUs huggingface dataset:
Baleen whale distribution, behaviour and overlap with anthropogenic activity in coastal regions of the New York Bight

ABSTRACT The New York Bight (NYB) is one of the busiest waterways along the US East Coast, and has recently seen an apparent increase in baleen whale presence. With growing anthropogenic pressures, a better understanding of their distribution and behaviour is needed. Encounter rates (sightings km−1) and behaviour of humpback (Megaptera novaeangliae), fin (Balaenoptera physalus) and minke (Balaenoptera acutorostrata) whales were obtained from dedicated non-systematic small vessel surveys conducted from May–November 2017–2019 in previously under-surveyed coastal areas of the NYB. Humpback whales were the most frequently sighted species, and their distribution in the NYB varied significantly by region and season. Within the mid-shelf region (10–60 km from shore), sightings of all species were generally concentrated spatially and temporally in mixed-species aggregations where feeding on sand lance (Ammodytes spp.) was observed. In the nearshore region (<10 km from shore), sightings of all species were more dispersed and typically occurred in close proximity to Atlantic menhaden (Brevoortia tyrannus). Humpback whales were commonly observed lunge feeding on these prey patches. The prevalence of foraging behaviour throughout the study area supports the hypothesis that the NYB may be an important supplementary feeding area for some species. Encounter rates were generally higher in areas overlapping with anthropogenic activity, suggesting that whales may be particularly vulnerable to anthropogenic impacts in the NYB. The observed species distribution patterns and importance of the NYB as a foraging habitat for baleen whales provides valuable information for the development of new baselines and best management practices within this heavily urbanized region.
The 3 T’s (Titan, Trailblazer, and Trustworthy) of Ed Latessa

ABSTRACT The words that typify Ed Latessa are titan, trailblazer, and trustworthy. His career has been driven by a desire to change American corrections to intertwine research into routine practices. Ed’s work embraces the principles of evidence-based practices and treatments. His devotion to these principles, even in a political era that embraced mass incarceration policies and practices, has been transformative. Being a titan, Ed has led the charge to change the field by widely disseminating information about evidence-based practices and treatments and working directly with all agencies regardless of government level to promote research findings into practice. As a trailblazer, Ed has been at the forefront of the evidence-based corrections and paved the way for its implementation. And, Ed, being the honest agent, has used research findings to enlighten the field, even when the field was going in a different direction. Ed has helped the field learn how to integrate research findings into effective practices, including giving attention to rehabilitation. Ed is known for his honesty and willingness to use research findings to make his points. This essay outlines how Ed’s passion, perseverance, and transformative leadership style has guided the field with ease and commitment.
Stability analysis of open-channel flows with secondary currents

Abstract This paper presents some results coming from a linear stability analysis of turbulent depth-averaged open-channel flows (OCFs) with secondary currents. The aim was to identify plausible mechanisms underpinning the formation of large-scale turbulence structures, which are commonly referred to as large-scale motions (LSMs) and very-large-scale motions (VLSMs). Results indicate that the investigated flows are subjected to a sinuous instability whose longitudinal wavelength compares very well with that pertaining to LSMs. In contrast, no unstable modes at wavelengths comparable to those associated with VLSMs could be found. This suggests that VLSMs in OCFs are triggered by nonlinear mechanisms to which the present analysis is obviously blind. We demonstrate that the existence of the sinuous instability requires two necessary conditions: (i) the circulation of the secondary currents $\omega$ must be greater than a critical value $\omega _c$; (ii) the presence of a dynamically responding free surface (i.e. when the free surface is modelled as a frictionless flat surface, no instabilities are detected). The present paper draws some ideas from the work by Cossu, Hwang and co-workers on other wall flows (i.e. turbulent boundary layers, pipe, channel and Couette flows) and somewhat supports their idea that LSMs and VLSMs might be governed by an outer-layer cycle also in OCFs. However, the presence of steady secondary flows makes the procedure adopted herein much simpler than that used by these authors.
Inmates’ empathy: relationship with childhood victimisation

Abstract Introduction Psychological trauma can occur at any time in life [1], and when it happens during childhood or adolescence, it may have negative repercussions on mental health that prevail in adult life [2]. The main objective of this study was to evaluate the relationship between childhood victimisation trauma experiences and empathy among incarcerated males. Materials and methods The sample was composed of 99 incarcerated males with ages between 18 and 73 years old (M = 37.96; SD = 11.6). Some of the participants were arrested for drug trafficking (n = 24, 24.2%), domestic violence (n = 10, 10.1%), homicide (n = 9, 9.1%), robbery (n = 7, 7.1%), theft (n = 5, 5.1%), and other types of crimes (e.g. kidnapping, attempted murder). Participants answered face-to-face to a sociodemographic questionnaire, to the Childhood Trauma Questionnaire (CTQ) [3] and the Interpersonal Reactivity Index (IRI) [4]. Results All the participants experienced all types of victimisation in their childhood: emotional abuse, physical abuse, emotional neglect, physical neglect, and sexual abuse. The experience of emotional neglect (M = 9.56; SD = 5.19) showed the highest incidence of child victimisation, and the other types of victimisation showed moderate rates. The analysis of the IRI confirmed high values of perspective taking (M = 16.70; SD = 4.00), empathic concern (M = 17.83; SD = 3.69), personal distress (M = 9.84; SD = 4.88), and fantasy (M = 13.09; SD = 4.39) among the participants. We found a positive and significant correlation between childhood trauma and interpersonal reactivity, specifically concerning the physical abuse (r = 0.22; p=.03) and the physical neglect (r = 0.24; p=.02) on childhood with the presence of personal distress on adulthood. Discussion and conclusions This study pointed out the emotional neglect as the most frequent victimisation in childhood, and this result is similar to previous studies [4,5]. Contrarily to some researches [6], our sample showed high general rates of empathy on inmates. It was also possible to verify that physical abuse and physical neglect during childhood, can influence the experience of distress in those incarcerated adults. Therefore, we conclude that the traumatic events of victimisation bring negative repercussions to adult life [2].
Study abroad in Turkey: the role of homestays on second language learning

ABSTRACT Study Abroad (SA) has often been referred as the ideal means to learn a second language due to the unique opportunities it brings to the learners. SA provides learners access to both formal and communicative learning contexts where they can interact with the members of the target language community. Existing studies identified various contextual and cultural factors that support or hinder language learning during study abroad programmes. This paper focuses on the affordances of the homestay environment in terms of L2 learning experiences in the Turkish SA context. Qualitative analysis of semi-structured interviews conducted with the sojourner students indicated that the socio-cultural setting students were exposed to during their time in Turkey played a key role in improving their self-assessed proficiency in Turkish and their understanding of the Turkish culture.
Epigenomic and transcriptomic analyses reveal early activation of the HPG axis in in vitro‐produced male dairy calves

In cattle, several calves born after IVP (“in vitro” embryo production) present similar birthweight to those generated after MOET (multiple ovulation and embryo transfer). However, the underlying molecular patterns in organs involved in the developmental process are unknown and could indicate physiological programming. The objectives of this study were: (1) to compare epigenomic and transcriptomic modifications in the hypothalamus, pituitary, gonadal and adrenal organs between 3 months old ovum pick‐up‐IVP and MOET male calves (n = 4 per group) and (2) to use blood epigenomic data to proxy methylation of the inner organs. Extracted gDNA and RNA were sequenced through whole‐genome bisulfite sequencing and RNA sequencing, respectively. Next, bioinformatic analyses determined differentially methylated cytosines (DMC) and differentially expressed genes (DEG) (FDR < 0.05) in IVP versus MOET samples and the KEGG pathways that were overrepresented by genes associated with DMC or DEG (FDR < 0.1). Pathways related to hypothalamus, pituitary, gonadal (HPG) axis activation (GnRH secretion in the hypothalamus, GnRH signaling in the pituitary, and steroidogenesis in the testicle) were enriched in IVP calves. Modeling the effect of the methylation levels and the group on the expression of all the genes involved in these pathways confirmed their upregulation in HPG organs in IVP calves. The application of the DIABLO method allowed the identification of 15 epigenetic and five transcriptomic biomarkers, which were able to predict the embryo origin using the epigenomic data from the blood. In conclusion, the use of an integrated epigenomic‐transcriptomic approach suggested an early activation of the HPG axis in male IVP calves compared to MOET counterparts, and the identification of potential biomarkers allowed the use of blood samples to proxy methylation levels of the relevant internal organs.
Stream Data Cleaning under Speed and Acceleration Constraints

Stream data are often dirty, for example, owing to unreliable sensor reading or erroneous extraction of stock prices. Most stream data cleaning approaches employ a smoothing filter, which may seriously alter the data without preserving the original information. We argue that the cleaning should avoid changing those originally correct/clean data, a.k. a. the minimum modification rule in data cleaning. To capture the knowledge about what is clean, we consider the (widely existing) constraints on the speed and acceleration of data changes, such as fuel consumption per hour, daily limit of stock prices, or the top speed and acceleration of a car. Guided by these semantic constraints, in this article, we propose the constraint-based approach for cleaning stream data. It is notable that existing data repair techniques clean (a sequence of) data as a whole and fail to support stream computation. To this end, we have to relax the global optimum over the entire sequence to the local optimum in a window. Rather than the commonly observed NP-hardness of general data repairing problems, our major contributions include (1) polynomial time algorithm for global optimum, (2) linear time algorithm towards local optimum under an efficient median-based solution, and (3) experiments on real datasets demonstrate that our method can show significantly lower L1 error than the existing approaches such as smoother.
Error Bounded Line Simplification Algorithms for Trajectory Compression: An Experimental Evaluation

Nowadays, various sensors are collecting, storing, and transmitting tremendous trajectory data, and it is well known that the storage, network bandwidth, and computing resources could be heavily wasted if raw trajectory data is directly adopted. Line simplification algorithms are effective approaches to attacking this issue by compressing a trajectory to a set of continuous line segments, and are commonly used in practice. In this article, we first classify the error bounded line simplification algorithms into different categories and review each category of algorithms. We then study the data aging problem of line simplification algorithms and distance metrics from the views of aging friendliness and aging errors. Finally, we present a systematic experimental evaluation of representative error bounded line simplification algorithms, including both compression optimal and sub-optimal methods, in terms of commonly adopted perpendicular Euclidean, synchronous Euclidean, and direction-aware distances. Using real-life trajectory datasets, we systematically evaluate and analyze the performance (compression ratio, average error, running time, aging friendliness, and query friendliness) of error bounded line simplification algorithms with respect to distance metrics, trajectory sizes, and error bounds. Our study provides a full picture of error bounded line simplification algorithms, which leads to guidelines on how to choose appropriate algorithms and distance metrics for practical applications.
Backward masking in mice requires visual cortex

The authors introduce a novel visual masking task and use recordings and optogenetics to reveal the role of visual cortex. Visual masking can reveal the timescale of perception, but the underlying circuit mechanisms are not understood. Here we describe a backward masking task in mice and humans in which the location of a stimulus is potently masked. Humans report reduced subjective visibility that tracks behavioral deficits. In mice, both masking and optogenetic silencing of visual cortex (V1) reduce performance over a similar timecourse but have distinct effects on response rates and accuracy. Activity in V1 is consistent with masked behavior when quantified over long, but not short, time windows. A dual accumulator model recapitulates both mouse and human behavior. The model and subjects’ performance imply that the initial spikes in V1 can trigger a correct response, but subsequent V1 activity degrades performance. Supporting this hypothesis, optogenetically suppressing mask-evoked activity in V1 fully restores accurate behavior. Together, these results demonstrate that mice, like humans, are susceptible to masking and that target and mask information is first confounded downstream of V1.
An innate immune activation state prior to vaccination predicts responsiveness to multiple vaccines

Many factors determine whether an individual responding to vaccination will generate an immune response that can lead to protection. Several studies have shown that the prevaccination immune state associate with the antibody response to vaccines. However, the generalizability and mechanisms that underlie this association remain poorly defined. Here, we sought to identify a common pre-vaccination signature and mechanisms that could predict the immune response across a wide variety of vaccines. We leveraged the “Immune Signatures Data Resource” created by the NIH Human Immunology Project Consortium (HIPC) to integrate data from 28 studies involving 13 different vaccines and associate the blood transcriptional status of 820 healthy young adults with their responses. An unsupervised analysis of blood transcriptional profiles across studies revealed three distinct pre-vaccination states, characterized by the differential expression of genes associated with a pro-inflammatory response, cell proliferation, and metabolism alterations downstream of NFκB and IRF7. Innate and adaptive immune cell subsetspecific genes were also associated with the three pre-vaccination states. Importantly, individuals whose pre-vaccination state was enriched in pro-inflammatory response genes known to be downstream of NFκB tended to have higher serum antibody responses one month after vaccination. A supervised analysis of the same data resulted in a single classifier, also enriched for NFκB regulated genes, that predicted the antibody response across most of the vaccines. Projection into single-cell RNA-sequencing data suggested that this pre-vaccination state was attributable to the signature of activation of non-classical monocytes and myeloid dendritic cells. Transcriptional signatures of recent exposure to bacterial and not viral infections were enriched in the high pro-inflammatory pre-vaccination state and also included NFκB regulated genes. The pro-inflammatory prevaccination state was highly reminiscent of the innate activation state triggered by TLR ligands or adjuvants. These results demonstrate that wide variations in the transcriptional state of the immune system in humans can be a key determinant of responsiveness to vaccination. They also define a transcriptional signature NFκB activation at baseline, that is associated with a greater magnitude of antibody response to 13 different vaccines, and suggest that modulation of the innate immune system by next-generation adjuvants targeting NFκB before vaccine administration may improve vaccine responsiveness.
Genotoxic Potential of Nanoparticles: Structural and Functional Modifications in DNA

The rapid advancement of nanotechnology enhances the production of different nanoparticles that meet the demand of various fields like biomedical sciences, industrial, material sciences and biotechnology, etc. This technological development increases the chances of nanoparticles exposure to human beings, which can threaten their health. It is well known that various cellular processes (transcription, translation, and replication during cell proliferation, cell cycle, cell differentiation) in which genetic materials (DNA and RNA) are involved play a vital role to maintain any structural and functional modification into it. When nanoparticles come into the vicinity of the cellular system, chances of uptake become high due to their small size. This cellular uptake of nanoparticles enhances its interaction with DNA, leading to structural and functional modification (DNA damage/repair, DNA methylation) into the DNA. These modifications exhibit adverse effects on the cellular system, consequently showing its inadvertent effect on human health. Therefore, in the present study, an attempt has been made to elucidate the genotoxic mechanism of nanoparticles in the context of structural and functional modifications of DNA.
Reading Minds, Reading Stories: Social-Cognitive Abilities Affect the Linguistic Processing of Narrative Viewpoint

Although various studies have shown that narrative reading draws on social-cognitive abilities, not much is known about the precise aspects of narrative processing that engage these abilities. We hypothesized that the linguistic processing of narrative viewpoint—expressed by elements that provide access to the inner world of characters—might play an important role in engaging social-cognitive abilities. Using eye tracking, we studied the effect of lexical markers of perceptual, cognitive, and emotional viewpoint on eye movements during reading of a 5,000-word narrative. Next, we investigated how this relationship was modulated by individual differences in social-cognitive abilities. Our results show diverging patterns of eye movements for perceptual viewpoint markers on the one hand, and cognitive and emotional viewpoint markers on the other. Whereas the former are processed relatively fast compared to non-viewpoint markers, the latter are processed relatively slow. Moreover, we found that social-cognitive abilities impacted the processing of words in general, and of perceptual and cognitive viewpoint markers in particular, such that both perspective-taking abilities and self-reported perspective-taking traits facilitated the processing of these markers. All in all, our study extends earlier findings that social cognition is of importance for story reading, showing that individual differences in social-cognitive abilities are related to the linguistic processing of narrative viewpoint.
The Relationship Between Central Auditory Tests and Neurocognitive Domains in Adults Living With HIV

Objective: Tests requiring central auditory processing, such as speech perception-in-noise, are simple, time efficient, and correlate with cognitive processing. These tests may be useful for tracking brain function. Doing this effectively requires information on which tests correlate with overall cognitive function and specific cognitive domains. This study evaluated the relationship between selected central auditory focused tests and cognitive domains in a cohort of normal hearing adults living with HIV and HIV– controls. The long-term aim is determining the relationships between auditory processing and neurocognitive domains and applying this to analyzing cognitive function in HIV and other neurocognitive disorders longitudinally. Method: Subjects were recruited from an ongoing study in Dar es Salaam, Tanzania. Central auditory measures included the Gap Detection Test (Gap), Hearing in Noise Test (HINT), and Triple Digit Test (TDT). Cognitive measures included variables from the Test of Variables of Attention (TOVA), Cogstate neurocognitive battery, and Kiswahili Montreal Cognitive Assessment (MoCA). The measures represented three cognitive domains: processing speed, learning, and working memory. Bootstrap resampling was used to calculate the mean and standard deviation of the proportion of variance explained by the individual central auditory tests for each cognitive measure. The association of cognitive measures with central auditory variables taking HIV status and age into account was determined using regression models. Results: Hearing in Noise Tests and TDT were significantly associated with Cogstate learning and working memory tests. Gap was not significantly associated with any cognitive measure with age in the model. TDT explained the largest mean proportion of variance and had the strongest relationship to the MoCA and Cogstate tasks. With age in the model, HIV status did not affect the relationship between central auditory tests and cognitive measures. Age was strongly associated with multiple cognitive tests. Conclusion: Central auditory tests were associated with measures of learning and working memory. Compared to the other central auditory tests, TDT was most strongly related to cognitive function. These findings expand on the association between auditory processing and cognitive domains seen in other studies and support evaluating these tests for tracking brain health in HIV and other neurocognitive disorders.