Miracle-dz/UniFAR-FTUs huggingface dataset:
Late Pleistocene leopards as a bone accumulator: taphonomic results from S’Espasa cave and other Iberian key sites

Abstract The Pleistocene faunal accumulations documented in caves have commonly been attributed to the activity of humans or carnivores. According to the palaeontological and archaeological literature, cave hyena (Crocuta spelaea) was the main known bone accumulator in karstic environments. However, in recent times, the role of leopards as bone accumulators has been revealed, and recent research has identified this behaviour in the Iberian Pleistocene. Moreover, there are other caves where leopard could have been claimed as an accumulator such as S’Espasa. In this work we present its taphonomic study. This cave was compared with the actualistic studies of leopards. Besides, the site of S’Espasa was compared with the other leopard dens in the Iberian Peninsula. These sites present faunal assemblages composed mainly by leopard (Panthera pardus) and Iberian wild goat (Capra pyrenaica), the bones of this ungulate present a similar pattern of bone modification by carnivores, skeletal survival rate, and bone breakage. These features indicate that goats could have been accumulated by leopards. With the data from this work and the previous ones, we try to establish a pattern that will help in the future to identify other accumulations created by this big cat.
Evidence of suboscine song plasticity in response to traffic noise fluctuations and temporary road closures

Abstract This study investigates how noise reduction (road closure) mitigates the effect of traffic noise on the acoustic communication of the Eastern wood pewee (Contopus virens) (EAWP), a suboscine passerine. Songs were passively recorded at sites where the traffic pattern of the nearest road was either relatively constant or reduced on a weekly basis during a 36 h road closure. Five song attributes, low frequency traffic noise amplitude (LAeq) measured within 20 s of each song, and full-spectrum background noise levels (LAeq) characteristic of each territory were measured and analysed in order to better understand how EAWP respond to variation in traffic noise levels. EAWP adjusted its spectral song attributes by increasing song tonality to improve transmission in immediate response to fluctuations in traffic noise. The results suggest that song adjustments are responses to traffic noise levels at the time of their song, instead of the average background noise level measured per territory. This study provides a better understanding of how suboscine communication is affected by traffic noise, as well as the potential mitigating effect of noise reduction for animal acoustic communication.
Magnicamarosporium diospyricola sp. nov. (Sulcatisporaceae) from Thailand

A new species of Magnicamarosporium, M. diospyricola was found on dead or dying twigs of a dicotyledonous plant in southern Thailand. The new species is distinct from other species in Sulcatisporaceae, as it has dematiaceous dictyosporous conidia. It differs from Magnicamarosporium iriomotense in its smaller conidiomata and conidia. Bayesian inference and maximum likelihood analysis of combined LSU, SSU, ITS, and TEF1-α sequence data indicate that M. diospyricola is a well-resolved species, sister to M. iriomotense, in the family Sulcatisporaceae. The morphology and phylogenetic placement of the new species are discussed in this paper.
Bioluminescent detection of tick-borne encephalitis virus in native ticks

A one-step bioluminescent immunoassay for tick-borne encephalitis virus (TBEV) in natural ticks based on the hybrid protein 14D5a-Rm7 was developed. Recombinant Ca2+-dependent coelenterazine-binding protein was shown to be a more convenient substrate form for the Rm7 domain than coelenterazine. Over 600 samples of natural ticks were analyzed and shown to have essential differences in the discrimination factor D for TBEV-positive (2.77 ± 0.81) and TBEV-negative (1.15 ± 0.28) samples.
Genetic variation within and among populations of fairy shrimp, Streptocephalus texanus, from southeastern Utah

Abstract To estimate levels of gene flow over short distances (less than a few kilometers) in the fairy shrimp, Streptocephalus texanus, mitochondrial DNA sequences (part of the cytochrome oxidase locus) were examined in 98 individuals from 13 populations near Moab, Utah. Populations were arranged linearly along two transects on slickrock ridges, and one isolated population about 2–3 km from the others. We found six haplotypes, differing from one another by 1 to 23 nucleotides. Nucleotide diversity among the nine populations from the MiVida ridge was 0.0019 with no isolation by distance. The three populations from the Sand Flat ridge were fixed for the same haplotype, not found in other populations. The isolated population (loop B pool) contained two haplotypes, one of which was very different from others in the study. The general pattern was little differentiation among populations separated by less than about 1 km, with more differentiation at greater distances. This is consistent with passive dispersal of cysts by wind over short distances, and rare long-distance dispersal.
The threshold of binocularity: natural image statistics explain the reduction of visual acuity in peripheral vision

Visual acuity is greatest in the centre of the visual field, peaking in the fovea and degrading significantly towards the periphery. The rate of decay of visual performance with eccentricity depends strongly on the stimuli and task used in measurement. While detailed measures of this decay have been made across a broad range of tasks, a comprehensive theoretical account of this phenomenon is lacking. We demonstrate that the decay in visual performance can be attributed to the efficient encoding of binocular information in natural scenes. The efficient coding hypothesis holds that the early stages of visual processing attempt to form an efficient coding of ecologically valid stimuli. Using Independent Component Analysis to learn an efficient coding of stereoscopic images, we show that the ratio of binocular to monocular components varied with eccentricity at the same rate as human stereo acuity and Vernier acuity. Our results demonstrate that the organisation of the visual cortex is dependent on the underlying statistics of binocular scenes and, strikingly, that monocular acuity depends on the mechanisms by which the visual cortex processes binocular information. This result has important theoretical implications for understanding the encoding of visual information in the brain.
Efficacy of 10% w/v fipronil spot-on against tick (Rhipicephalus sanguineus) infestation on Cats

The efficacy of 10% w/v fipronil spot-on for treatment and prevention of Rhipicephalus sanguineus infestation on cats was examined. Twelve cats were randomly allocated into two groups which were the treatment and control groups. The treatment group received 10% fipronil spot-on at a dosage of 6.7 mg/kg on day 0. A group of 60 R. sanguineus was released to feed on each cat on days -7, -2, 3, 7, 14, 21, and 28. The ticks were counted and removed on days -4, 3, 6, 10, 17, 24, and 31. The infested ticks on the cats were also counted but not removed on day 0. Geometric mean number of tick infestation in the control group ranged from 20.83 to 26.17 ticks per cat, or the attachment rate of 34.72 to 43.62% and the mean attachment rate of 39.41%. Geometric mean number of tick infestation in the treatment group on the days before fipronil was applied on the cats ranged from 24.50 to 25.83 ticks per cat, or the attachment rate of 40.83 to 43.06% and the mean attachment rate of 41.95%. Percentages of the efficacy of fipronil used in this study were 99.24, 100, 100, 100, 99.18 and 99.24% on days 3, 6, 10, 17, 24, and 31, respectively. There were statistically significant differences between the geometric mean numbers of tick infestation between the control and treatment groups on days 3, 6, 10, 17, 24, and 31.
The effects of dominance, linkage, and gene flow on local adaptation and differentiation

In dieser Dissertation im Bereich der mathematischen Populationsgenetik untersuchen wir das Zusammenspiel der evolutionaren Krafte Selektion, Rekombination und Migration sowie deren gemeinsame Wirkung auf die genetische Konstitution, auf das Ausmas der lokalen Anpassung und auf den Grad der Differenzierung einer Population. Alle hier prasentierten Arbeiten behandeln eine geografisch strukturierte Population mit zwei gekoppelten Genorten und jeweils zwei Allelen. Diese Genorte sind lokal unterschiedlicher Selektion ausgesetzt, wobei wir Interaktionen zwischen den Genorten (Epistasie) und Neumutationen vernachlassigen. Wir nehmen an, dass die (unendlich grose) Population auf zwei Deme aufgeteilt ist, welche durch Genfluss verbunden sind. Als wichtigen Spezialfall behandeln wir das sogenannte Kontinent-Insel-Modell. Fur die verwendeten deterministischen Modelle bestimmen wir das Gleichgewichts- und Stabilitatsverhalten fur zahlreiche wichtige Falle. Wir zeigen analytisch, dass wir in geografisch strukturierten Populationen, welche lokal unterschiedlichen Umweltbedingungen ausgesetzt sind, Clusters von gekoppelten, vorteilhaften Allelen erwarten. Weiters bestimmen wir die Abhangigkeit der lokaler Anpassung und der Differenzierung (FST und QST) von Dominanz, Rekombination und Migration.
Efficacy of three essential oils and their nano-particles against Sitophilus granarius under laboratory and store conditions

The effect of three essential oils and their nano-preparations (castor, mustard and purslane) were tested against the granary weevil Sitophilus granarius under laboratory and stored conditions. Purslane oil (bulk and nano) had strong insecticidal efficacy and was significantly highly effective tested oil against granary weevil with 86.64, 75.21, 55.32, and 18.61% mortality obtained at 5, 2.5, 1.25 and 0.63% concentrations, respectively. While, the mortality values reached 95.61, 73.51, 58.39 and 20.61% when the adults were exposed to 0.5, 0.25, 0.13, 0.06 concentrations of nano-purslane, respectively. Castor oil had moderate effect and mustard was the least one. Nano-purslane was highly significantly more effective as sterilizer against adult weevils in comparison with other tested nano-oils. The mean number of eggs/female recorded 3.0 ± 3.8, 22.0 ± 7.8 and 28.8 ± 7.9 eggs/female in case of purslane, castor and mustard, respectively in comparison to control (198 ± 4.9 eggs/female). After 125 days of storage, the percentage of emerged weevils were 21 and 7% in case of purslane oil (bulk and nano), respectively comparing with untreated control (98%).
Characterization of a H4K20me2 methyl-binding domain in the Fanconi anemia protein FANCD2

Fanconi anemia (FA) is a rare genetic disease that results on early onset bone marrow failure, congenital defects, and increased cancer susceptibility. It is caused by mutation in any one of twenty two genes, whose protein products work in conjunction as part of the FA-BRCA pathway, a DNA repair pathway that specifically repairs DNA interstrand crosslinks (ICLs). One of the key steps in pathway activation is the monoubiquitination of the FANCD2 protein. Upon pathway activation, FANCD2 is recruited to sites of DNA damage, where is interacts with downstream repair protiens to promote DNA repair via homologous recombination (HR). How FANCD2 recognizes DNA damage in condensed compact chromatin, however, has remained unknown. Here, we uncover a FANCD2 methyl-binding domain, which specifically binds for H4K20me2 in order to recruit FANCD2 to sites on DNA damage and promote homologous recombination, support cell survival and maintain genomic integrity.
Deposition of Au x Ag1 − x / Au y Ag1 − y Multilayers and Multisegment Nanowires

Au x Ag 1-x /Au y Ag 1-y multilayers and multisegment nanowires were deposited from a single solution containing KAu(CN) 2 , KAg(CN) 2 , and Na 2 CO 3 (pH 13). Cyclic voltammograms for deposition from solutions containing Au(CN) - 2 and Ag(CN) - 2 show the characteristic deposition peaks for gold and silver. The composition of the deposited alloys is dependent on the deposition potential (or current) and solution chemistry. Multisegment nanowires were prepared by sequential deposition at -0.7 and -1.2 V from solutions containing Au(CN)2 and Ag(CN) - 2 solution in porous Al 2 O 3 templates. The different segments deposited at -0.7 and -1.2 V are clearly distinguished by scanning electron microscopy and optical microscopy under blue light illumination.
Characterization of ubiquitin-binding domain in C1orf124 protein

Ubiquitin has recently been discovered to have a key role in a variety of biological processes. In parallel, different protein domains were identified with the ability to bind different ubiquitin species. Ubiquitin-binding zinc-finger 4 (UBZ4) family was recently revealed using bioinformatical analysis. UBZ4 is a C2HC Zn-finger found in all eukaryotic lineages; most of the UBZ4-containing proteins appear to play a role in the DNA damage response. Iterative alignment with known UBZ4 revealed 13 members of putative family. C1orf124 protein was chosen to analyse its ubiquitin binding abilities. I have showed that C1orf124 protein binds monoubiquitin and polyubiquitin chains. Pull down assay showed that interaction is achieved through hydrophobic patch surrounding Ile44 on ubiquitin and Asp residue in-between second Zn-binding dyad of UBZ4 domain.
Scandinavian Oncophorus (Bryopsida, Oncophoraceae): species, cryptic species, and intraspecific variation

Scandinavian members of the acrocarpous moss genus Oncophorus were revised after field observations had suggested unrecognized diversity. Based on molecular (nuclear: internal transcribed spacers 1 and 2, ITS; plastid: trn G UCC G2 intron, trn G, rps 4 gene + trn S- rps 4 spacer, rps 4) and morphological evidence, four morphologically distinguishable species are recognized, Oncophorus elongatus (I.Hagen) Hedenas, O. integerrimus Hedenas sp. nov. (syn. O. virens var. elongatus Limpr.), O. virens (Hedw.) Brid. , and O. wahlenbergii Brid. ( O. sardous Herzog, syn. nov.). Oncophorus elongatus was earlier recognized, but much of its variation was hidden within O. wahlenbergii . Its circumscription is here expanded to include plants with long leaves having mostly denticulate or sharply denticulate upper margins and with long and narrow marginal cells in the basal portion of the sheathing leaf lamina. The new species O. integerrimus sp. nov. differs from O. virens in having more loosely incurved leaves and entire or almost entire upper leaf margins. Besides these characters, the species in the respective pairs differ in quantitative features of the leaf lamina cells. Several cryptic entities were found, in several cases as molecularly distinct as some of the morphologically recognizable species, and phylogeographic structure is present within O. elongatus and O. virens .
On the Difficulty of Unbiased Alpha Divergence Minimization

Several approximate inference algorithms have been proposed to minimize an alpha-divergence between an approximating distribution and a target distribution. Many of these algorithms introduce bias, the magnitude of which is poorly understood. Other algorithms are unbiased. These often seem to suffer from high variance, but again, little is rigorously known. In this work we study unbiased methods for alpha-divergence minimization through the Signal-to-Noise Ratio (SNR) of the gradient estimator. We study several representative scenarios where strong analytical results are possible, such as fully-factorized or Gaussian distributions. We find that when alpha is not zero, the SNR worsens exponentially in the dimensionality of the problem. This casts doubt on the practicality of these methods. We empirically confirm these theoretical results.
Value of Plasma NGAL and Creatinine on First Day of Admission in the Diagnosis of Cardiorenal Syndrome Type 1

Background The presence of acute kidney injury in the setting of acute heart failure (AHF) or acute decompensated heart failure (ADHF) is a very common occurrence and was termed cardiorenal syndrome 1 (CRS1). Neutrophil gelatinase-associated lipocalin (NGAL) in the blood and urine is one of the earliest biomarkers of acute kidney injury due to ischemia or renal toxicity. This study was aimed to evaluate the diagnostic efficacy of plasma NGAL in the diagnosis of CRS1. Methods There were 139 patients with AHF or ADHF in the department of Cardiovascular Resuscitation and Interventional Cardiology at Ho Chi Minh City 115 People Hospital from September 2018 to March 2019. This was a prospective cohort study. Results There were 48 cases (rate 34.5%) with CRS1, mean age was 66.12 ± 15.77 and men accounted for 50.4%. There were no significant differences of vital signs at admission, diagnosis, and EF-based heart failure between CRS1 and non-CRS1 groups. The urea, creatinine on first day (creatinine D1) and third day (creatinine D3), NT-proBNP, and NGAL levels were higher in the CRS1 group than the non-CRS1 group, p < 0.05. The optimal cutoff plasma NGAL for diagnosing CRS1 was >353.23 ng/ml, area under curve (AUC) 0.732 (95% CI 0.65–0.80, p < 0.001), sensitivity 74.47%, specificity 68.48%, positive predictive value 54.7%, and negative predictive value 84%. Multivariable logistic regression analysis eGFRCKDEPID1 remained the strongest independent predictor of CRS1. Building the optimal regression model (without eGFRCKDEPID1) by the BMA (Bayesian model average) method with two variables NGAL and Creatinine D1, we had the equation: odds ratio = ey while y = −2.39 + 0.0037 × NGAL + 0.17 × Creatinine D1. The nomogram (without eGFRCKDEPID1) was designed to predict the likelihood of CRS1 with AUC 0.79. Conclusions The combination of plasma NGAL and creatinine D1 on the first day at admission had a high accuracy of predictive model for CRS1.
Forensic post-mortem interval (PMI) estimates: variation in fly developmental times of individuals

Immature stages of flies are paramount in establishing the post-mortem interval (PMI) in forensic practice. My focus is on differences in developmental time that can be influenced by genetic differences or individual life history traits, which latter may be interpreted as life history decisions. Data of a calliphorid fly species (Lucilia ampullacea) are presented: one female produced 300 eggs within an hour and the individual developmental time varied subsequently to a great extent – when the first flies emerged from their puparia there were still first instar larvae in the food (pig liver) provided. In conclusion the estimated PMI must be based on a wide range of collected flies (not simply the oldest or largest or widest individual), since a limited sample can be one extremity of a potentially bell shaped (Gaussian) frequency distribution of developmental times — unrepresentative sampling will bias the PMI in an unpredictable way. One possible solution can be to use large, randomized samples and their body measurement means.
Transcriptomic approach of the response to metals in the hydrothermal mussel Bathymodiolus azoricus

Bathymodiolus azoricus is an endemic bivalve from hydrothermal vents in the Mid-Atlantic ridge, which is known to accumulate different types of metals in various tissues at high concentrations, and has therefore been granted model species for exotoxicology. The objective of this work is to describe the mechanisms of metal tolerance and detoxification as they occur in natural populations and during experimental exposures, using both chemical (metal quantification) and transcriptomic (qPCR and microarrays) approaches to understand how environmental factors influence gene expression response in B. azoricus and to identify potential biomarkers useful for ecotoxicological studies in extreme environments. Bioaccumulation of different metals (Cd, Cu, Fe, Pb,…) was measured on individuals from contrasted vent sites, revealing specific population patterns and tissue differences for this species that could be related to processes of organotropism. Our results also suggest that the symbiotic bacteria in gills may be involved in metal tolerance and detoxification. Similar variation trends are observed in the relative expression of candidate genes involved in response to metal stress, e.g. metallothioneins, superoxide dismutase, ferritin, and phytochelatin, revealing contrasted responses at population and tissue level, and reflecting differences in physiological status not directly correlated with the accumulation of metals. In addition, global scale microarray analysis allowed us to identify the principal biological pathways representative of each population and tissues.
Liana avoidance strategies in trees: Combined attributes increase efficiency

We investigated the importance of specific tree attributes: height, exfoliating bark, smooth bark, and fast growth to determine whether single or multiple attributes were more important in liana colonization on trees. Specifically we asked: Does the presence of multiple liana-shedding attributes in trees reduce the number of lianas on a tree? We sampled the number of lianas on each tree and recorded tree attributes in three ecologically distinct sites in southeast Brazil. Data were analyzed using model selection by Akaike Information Criterion, in which the number of lianas on a tree was the response variable and tree attributes were explanatory variables. We found that a combination of two attributes in trees was sufficient to deter liana infestation, whereas only one attribute had zero probability of deterring lianas across all sites. Taller trees bear more lianas, probably because of their well-lit canopies, but tree height was always associated with other attributes: slow growth in rain forest, exfoliating bark in seasonal forest, and rough bark in savanna woodland. We conclude that the presence of two attributes is sufficient to reduce liana infestation on a tree.
Succession of embryonic and intestinal bacterial communities of Atlantic salmon

Host-associated microbiota undergoes continuous transition to achieve a stable community, and these modifications are immediately initiated from the birth of the host. In the present study, the succession of early life (eyed egg, embryo, and hatchling stages) and intestinal (the whole intestine at the early freshwater stages and the distal intestine at the late freshwater and seawater stages) bacterial communities of Atlantic salmon (Salmo salar; a prominent farmed fish) were studied using a 16S rRNA gene (V3 region) amplicon sequencing technique. Stage-specific bacterial community compositions and the progressive transitions of the communities were evident in both the early life and the intestine. The embryonic communities were relatively less diverse, but after hatching the diversity increased significantly. A marked transition of the intestinal communities also occurred during the development. The most abundant functional pathways associated with the different stages were not affected by the transition of the community composition A perceptible transition in the community composition occurred during the development of Atlantic salmon. The transition generally did not alter the core functions of the community. Hatching and transfer to seawater are the key events that affect the bacterial diversity and community composition. The contribution of host-derived factors and environment in shaping the bacterial communities need to be confirmed through further studies.