Miracle-dz/UniFAR-FTUs huggingface dataset:
Hyena as a predator of small mammals? Taphonomic analysis from the site of Bois Roche, France

Abstract. Feeding behaviors may differ between past and current predators due to differences in the environments inhabited by these species at different times. We provide an example of this behavioral variability in spotted hyena (Crocuta crocuta), for which our analysis of a late Pleistocene micromammal assemblage indicates that hyenas preyed upon small rodents, a feeding habit that is rarely observed today among hyenas. The Bois Roche cave site is situated at the edge of a low bluff overlooking the floodplain of a small stream in Cherves-Richemont (Charente, France). The deposits are dated by electron spin resonance (ESR) to about 69.7 ± 4.1 Ka. Excavations at the site recovered fossil bones and teeth of large and small mammals, together with hyena coprolites. Water screening of the sediments produced large accumulations of rodent remains with low taxonomic diversity. Small mammal bones were recovered from hyena coprolites as well. Descriptions of small mammal bone modification, both from the sediments and coprolites, are reported here. The analysis yielded a distinct taphonomic pattern representative of large carnivores (over 30 kg), which differs from any other modern or fossil predator-accumulated microfaunal assemblage taphonomically analyzed to date. To our knowledge, previous studies of hyena diet have not recorded high concentrations of a single-rodent prey species. Weconclude that the lowspecies diversity of this small mammal assemblage most likely relates to a local abundance of the prey species due to an outbreak in the rodent population, rather than from specialist predator behavior and hunting technique.
A flicker of hope: Genomic data distinguish Northern Flicker taxa despite low levels of divergence

ABSTRACT Next-generation sequencing technologies are increasingly being employed to explore patterns of genomic variation in avian taxa previously characterized using morphology and/or traditional genetic markers. The hybridization dynamics of the Northern Flicker complex have received considerable attention, primarily due to the conspicuous plumage differences among these birds and the geographically extensive hybrid zone between the Red-shafted (Colaptes auratus cafer) and Yellow-shafted (Colaptes auratus auratus) flickers in the Great Plains region of North America. However, no traditional molecular techniques have been able to differentiate these 2 morphologically well-defined taxa from one another, or conclusively from the closely related Gilded Flicker (Colaptes chrysoides). Here, we use a next-generation sequencing approach to assess the genetic diversity and evolutionary history of these 3 taxa. We confirm the overall low levels of differentiation found using traditional molecular markers, but are able to distinguish between the 3 taxa for the first time, using a dataset of thousands of SNP loci distributed across the genome. Through demographic modeling and phylogenetic reconstructions, we find that Red-shafted and Yellow-shafted flickers are likely sister taxa, and that their divergence from the Gilded Flicker was comparatively older. The low level of divergence and lack of fixed differences in our dataset between Red-shafted and Yellow-shafted flickers, in particular, suggests whole-genome re-sequencing may be necessary to assess the dynamics of their hybridization and identify the genetic basis of their striking differences in plumage.
Development of a food-based index of dietary inflammatory potential for Koreans and its relationship with metabolic syndrome

BACKGROUND/OBJECTIVES Inflammation is known to be a risk factor for metabolic diseases. This study aimed to develop a Food-based Index of Dietary Inflammatory Potential (FBDI) and examine its association with metabolic biomarkers. SUBJECTS/METHODS This study analyzed the raw data from the 2012-2014 Korean Genome and Epidemiology Study data of 17,771 people. To analyze the relationship between foods consumed by Koreans and inflammation, we conducted a correlation analysis between 51 food groups and hs-CRP levels. The FBDI was developed from 17 food groups selected by multiple regression method. We examined whether FBDI was associated with metabolic markers (waist circumference, blood pressure, fasting glucose, triglyceride, and HDL-cholesterol) in the 6th Korea National Health and Nutrition Examination Survey (KNHANES). We used binary logistic regression analysis to examine the association. RESULTS The FBDI model included seven of the anti-inflammatory food groups and three of the pro-inflammatory food groups. The FBDI formula was calculated by multiplying the intake of food group by β-coefficients derived from the multiple regression model based on the correlation analysis. The FBDI was significantly associated with waist circumference (P < 0.001), blood pressure (P < 0.001), triglyceride level (P < 0.001), and HDL-cholesterol (P < 0.001) level among adults aged 20–64 years in the KNHANES. The prevalence of metabolic syndrome was 2.618 times higher in the group with the highest FBDI than in the group with the lowest one (95% confidence interval: 1.778–3.856, P for trend < 0.001). CONCLUSIONS This study established an FBDI reflecting food intake patterns of Koreans, which showed a significant relationship with the prevalence of metabolic syndrome.
Relationship between Soil Characteristics and Stand Structure of Robinia pseudoacacia L. and Pinus tabulaeformis Carr. Mixed Plantations in the Caijiachuan Watershed: An Application of Structural Equation Modeling

In order to study the multi-factor coupling relationships between typical Robinia pseudoacacia L. and Pinus tabulaeformis Carr. mixed plantations in the Caijiachuan basin of the Loess Plateau of Shanxi Province, West China, 136 sample plots were selected for building a structural equation model (SEM) of three potential variables: terrain, stand structure, and soil characteristics. Additionally, the indicators (also known as observed variables) were studied in this paper, including slope, altitude, diameter at breast height (DBH), tree height (TH), tree crown area, canopy density, stand density, leaf area index (LAI), soil moisture content, soil maximum water holding capacity (WHC), soil organic matter (SOM), total nitrogen (TN), total phosphorus (TP), ammonia-nitrogen (NH3-N), nitrate-nitrogen (NO3-N), and available phosphorus (AP). The results showed that terrain was the most important factor influencing soil moisture and nutrients, with a total impact coefficient of 1.303 and a direct path coefficient of 0.03, which represented mainly positive impacts; while correspondingly stand structure had a smaller negative impact on soil characteristics, with a total impact coefficient of −0.585 and a direct path coefficient of −0.01. The terrain also had a positive impact on the stand structure, with a total impact coefficient of 0.487 and a direct path coefficient of 0.63, indicating that the topography factors were more suitable for site conditions and both the stand structure and the soil moisture and nutrient conditions were relatively superior. By affecting the stand structure, terrain could restrict some soil, water, and nutrient functions of soil and water conservation. The influence coefficients of the four observed variables of DBH, stand density, soil water content, and organic matter, and potential variable topography reached 0.686, −0.119, 1.117, and 0.732, respectively; and the influence coefficients of soil moisture, organic matter and stand structure were −0.502 and −0.329, respectively. Therefore, besides observing the corresponding latent variables, the observed variables had a considerable indirect influence on other related latent variables. These relationships showed that the measures, such as changing micro-topography and adjusting stand density, should effectively maintain or enhance soil moisture and nutrient content so as to achieve improved soil and water conservation benefits in the ecologically important Loess Area.
Differential contributions of subthalamic beta rhythms and neural noise to Parkinson motor symptoms

Background Excessive beta oscillatory activity in the subthalamic nucleus (STN) is linked to Parkinson’s disease and associated motor symptoms. However, the relationship between beta activity and motor symptoms has been inconsistent, which may influence the efficacy of closed-loop deep brain stimulation. Hypothesis We hypothesized that this variability is due to the degree of neural noise in STN recordings. Recent evidence has shown that neural noise is influenced by multiple factors, such as development, aging and disease, and could confound measures of beta activity. In this work, we propose a model that disentangles beta oscillatory activity and neural noise in the STN power spectrum. Methods We investigated the impact of neural noise on estimations of beta activity and motor symptoms from data recorded bilaterally from the subthalamic nuclei of thirteen Parkinsonian patients. Results Results showed that the relationship between beta oscillatory amplitude and motor symptoms (bradykinesia and rigidity) significantly improved when neural noise was removed from the estimation of beta activity. Conclusion These findings emphasize the importance of modeling neural components independently for understanding physiological processes associated with Parkinson’s disease, and identifying better biomarkers for characterizing symptom severity. Subsequently, we predict that our findings can have a direct application for closed-loop deep brain stimulation on Parkinson’s Disease.
Neochondria gen. nov. (Rhodomelaceae, Rhodophyta), a segregate of Chondria, including N. ammophila sp. nov. and N. nidifica comb. nov.

Abstract: Using morphological and molecular evidence, we describe a new genus, Neochondria, based on specimens formerly identified as ‘Chondria tenuissima’ sensu Okamura in Japan. The generitype, Neochondria ammophila sp. nov., is not closely related to Chondria capillaris (Hudson) M.J. Wynne, the generitype of Chondria. The anatomy of Neochondria differs from that of Chondria by the development of adventitious elongate cells between the five major pericentral cells, forming densely compact layers surrounding the axial strand, even in the ultimate branchlets. We propose the new combination, Neochondria nidifica, based on Chondria nidifica Harvey from California, USA and Baja California, Mexico. Multigene analyses (rbcL, small subunit and cox1) and morphological observations demonstrated that N. ammophila and N. nidifica share a clade but preliminary results show that they may not belong in the tribe Chondrieae.
Brine shrimp cytotoxicity, phytochemical screening and larvicidal activities of plectranthus barbatus extracts

The genus Plectranthus (Lamiaceae) represents a large and widespread group of species with a diversity of traditional medicinal uses in the world. The new findings from Plectranthus barbatus ethanolic extracts revealed that cytotoxicity lethality based on Artemia salina Leach in roots are active with LC50=40.07 μg/mL followed by twigs and leaves with LC50= 66.12 μg/mL and 186. 33μg/mL respectively. All plant parts contained Saponins,Terpenoids and Glycosides as a mojor principal group of secondary metabolites. Extract from Leaves are more active in Anopheles gambiae with LC50=55.65 μg/mL followed by twigs and roots with LC50=465 μg/mL and LC50 636 μg/mL at 72hours exposure respectively. Twig extracts showed moderate effect on both A.gambiae and A.eagyptiae after 48hours and 72hours exposure time with 100% (MRC) Mortality Rate Concentration of >1000μg/mL. Correspondence to: Kidukuli AW, The Open University of Tanzania, Department of Physical Sciences, P.O. Box 31608. Dar es Salaam, Tanzania, Tel: +255 755 861 283; E-mail: kidukuli@yahoo.com
Evaluating fMRI-Based Estimation of Eye Gaze during Naturalistic Viewing

The collection of eye gaze information during functional magnetic resonance imaging (fMRI) is important for monitoring variations in attention and task compliance, particularly for naturalistic viewing paradigms (e.g., movies). However, the complexity and setup requirements of current in-scanner eye-tracking solutions can preclude many researchers from accessing such information. Predictive eye estimation regression (PEER) is a previously developed support vector regression-based method for retrospectively estimating eye gaze from the fMRI signal in the eye’s orbit using a 1.5-minute calibration scan. Here, we provide confirmatory validation of the PEER method’s ability to infer eye gaze on a TR-by-TR basis during movie viewing, using simultaneously acquired eye tracking data in five individuals (median angular deviation < 2°). Then, we examine variations in the predictive validity of PEER models across individuals in a subset of data (n=448) from the Child Mind Institute Healthy Brain Network Biobank, identifying head motion as a primary determinant. Finally, we accurately classify which of two movies is being watched based on the predicted eye gaze patterns (area under the curve = .90 ± .02) and map the neural correlates of eye movements derived from PEER. PEER is a freely available and easy-to-use tool for determining eye fixations during naturalistic viewing.
Monitoring tropical forest ungulates using camera‐trap data

Tropical forest ungulates are poorly known and, despite their ecological and conservation significance, there are few studies on their density and abundance. I estimated densities of lesser oriental chevrotain Tragulus kanchil in the Southern Cardamom National Park, south-west Cambodia using camera-trap encounter rates and fitting a random encounter model (REM) that does not require individual identification of animals. This represents the first use of REM on forest ungulates in mainland tropical Asia and provides the first density estimate for any chevrotain species in mainland South East Asia. Sixty-five camera-trap stations generated 501 encounters of lesser oriental chevrotain across >8200 camera-trap nights within a systematic random camera-trap grid of 200 km in the Southern Cardamom National Park. Density of lesser oriental chevrotain was estimated at between 57 and 98 ( X 81) individuals per km. The random deployment of camera-traps, a prerequisite of the REM, did not prevent the detection of the majority of grounddwelling large mammal species likely to be present in the study site. Despite its slow uptake by field conservationists, the REM may have potential for monitoring tropical ungulates particularly in dense evergreen forest where other methodologies, for example, distance-based line transect sampling are unsuitable.
Pathophysiology of immune-related complications in lysinuric protein intolerance

Pathophysiology of immune-related complications in Lysinuric Protein Intolerance Lysinuric Protein Intolerance (LPI, MIM #222700) is a rare autosomic disease caused by mutations in SLC7A7 gene. Hallmarks of LPI are malabsorption and deficient renal reabsorption of cationic amino acids, which drives a deficit in the functioning of the urea cycle due to the reduction levels of arginine and ornithine in plasma. Nevertheless LPI patients also develop immune and hematologic complications such as anemia, pulmonary alveolar proteinosis or hemophagocytic lymphohistiocytosis. However the molecular mechanism(s) and/or the initiation events that trigger the development of LPI immune and hematologic complications still remain unknown. Arginine has been demonstrated to be crucial for a correct immunity, and specifically, for a proper macrophage functioning. Then, we hypothesize that primary metabolic condition may be also contributing to the development of LPI immune and hematologic complications. Due to ablation of Slc7a7 is perinatally lethal in mouse; our group has generated the first tamoxifen-inducible KO mouse model (Slc7a7-/-) for the study of human LPI. Slc7a7-/- mouse model fulfilled human LPI metabolic disease: impaired renal reabsorption and intestinal malabsorption of cationic amino acids with consequent deficient functioning of the urea cycle. Urea cycle defect presented with increased levels of ammonia and glutamine in plasma and increased concentration of orotic acid in urine. In addition, Slc7a7-/- mice developed some of the immune-related complications reported in LPI patients: anemia, hyperferritinemia, pulmonary alveolar proteinosis and increased erythrophagocytosis. Furthermore we have characterized two novel traits in LPI; aberrant iron accumulation in macrophages, and defective erythropoiesis, which may be a plausible explanation for some of the LPI complications such as anemia, hyperferritinemia and increased erythrophagocytosis. Citrulline supplementation is commonly used to mitigate the defect in the urea cycle of LPI patients, and we corroborated that citrulline supplementation in the water drink improved the metabolic condition also in Slc7a7-/- animals. However, we also observed that by treating the metabolic disease, the immune and hematologic symptoms in Slc7a7-/- mice were improved as well. Moreover, Slc7a7-/- myeloid-specific ablated animals did not show any of the symptoms found in Slc7a7-/- mice, confirming the necessity of the metabolic condition for the development of the LPI immune-related complications. Thus, for the first time, we are describing a direct relationship between the primary metabolic dysfunction and the immune and hematologic complications in LPI.
The complete mitochondrial genome of the yellow coloured honeybee Apis mellifera (Insecta: Hymenoptera: Apidae) of New Zealand

Abstract The complete mitochondrial genome of the yellow coloured honeybee Apis mellifera from North Island, New Zealand was analyzed using next-generation sequencing. The mitochondrial genome was a 16,349bp circular molecule and was predicted to contain 13 protein-coding genes (PCGs), 22 tRNA genes and two rRNA genes. The initiation codon ATA was found in two genes, ATG in four genes, ATT in six genes, and ATC in one gene, while the termination codon TAA was observed in all the PCGs. Phylogenetic analysis using the sequence of 23 closely related taxa suggested a sister relationship with the Italian strain A. mellifera ligustica.
Variation in malaria infection and immune defence in invasive and endemic house sparrows

Biological invasions by exotic species impose substantial ecological, economic and social costs worldwide, being a major threat to biodiversity conservation. Because not all individuals introduced in the new environments become successful invaders, the identification of factors underlying variation in invasion success would be essential for evaluating invasion risk. Here, we test several host–parasite hypotheses accounting for invasion success of house sparrows Passer domesticus in Peru. According to the Enemy Release Hypothesis, invasive house sparrows from Peru showed lower prevalence and genetic diversity of haemosporidian parasites than sparrows from their natural range (Spain), indicating that the release from their natural parasites may have favoured the spread of sparrows in the new area of occurrence. We also showed that Peruvian sparrows had larger uropygial glands and higher anti‐bacterial activity in its secretion than sparrows from Spain, suggesting selection in defensive mechanisms driven by pathogens when colonizing new environments. Finally, we showed that uninfected sparrows had larger uropygial glands and higher anti‐bacterial activity than malaria‐infected house sparrows, implying that uropygial gland secretions may act as a defensive mechanism against haemosporidian infections. Alternatively, a condition‐dependent trade‐off exists between synthesis of uropygial secretion and immune response. These outcomes provide essential information for identifying potential invaders and designing interventions.
Genome-wide SNPs detection by genomic comparison between Dongxiang wild rice (Oryza rufipogon) and cultivated rice Nipponbare (Oryza sativa ssp. japonica)

Abstract Dongxiang wild rice (Oryza rufipogon, DXWR) exhibits valuable agronomic traits and represents a precious germplasm resource for rice breeding. The use of genetic markers can greatly speed up the breeding process and facilitate research on genetics and genomics. In our previous study, we identified insertion–deletion polymorphisms between DXWR and cultivated rice Nipponbare (Oryza sativa ssp. japonica), using whole-genome sequencing in DXWR. In this study, to further explore the genetic variations and enrich the available genetic markers of DXWR, we identified 1,089,478 single-nucleotide polymorphisms (SNPs) (corresponding to one SNP per 0.33 kb of the genome) by genomic comparison between DXWR and Nipponbare, using the genome sequencing data and bioinformatics approaches. Furthermore, the accuracy of the identified SNPs was also validated by polymerase chain reaction amplification and Sanger sequencing. This genome-wide SNPs identification greatly increases the number of genetic markers available for DXWR and provides new opportunities to exploit this valuable and endangered germplasm resource.
Development of bioinformatics methods for the analysis of large collections of transcription factor binding motifs : positional motif enrichment and motif clustering

Les facteurs transcriptionnels (TF) sont des proteines qui controlent l'expression des genes. Leurs motifs de liaison (TFBM, egalement appeles motifs) sont generalement representes sous forme de matrices de scores specifiques de positions (PSSM). L'analyse de motifs est utilisee en routine afin de decouvrir des facteurs candidats pour la regulation d'un jeu de sequences d'interet. L'avenement des methodes a haut debit a permis de detecter des centaines de motifs, qui sont disponibles dans des bases de donnees. Durant ma these, j'ai developpe deux nouvelles methodes et implemente des outils logiciels pour le traitement de collections massives de motifs: matrix-clustering regroupe les motifs par similarite; position-scan detecte les motifs presentant des preferences de position relativement a une coordonnee de reference. Les methodes que j'ai developpees ont ete evaluees sur base de cas d'etudes, et utilisees pour extraire de l'information interpretable a partir de differents jeux de donnees de Drosophila melanogaster et Homo sapiens. Les resultats demontrent la pertinence de ces methodes pour l'analyse de donnees a haut debit, et l'interet de les integrer dans des pipelines d'analyse de motifs.
Amylosporus guaraniticus sp. nov. (Wrightoporiaceae, Russulales) a new neotropical species from Paraguay

Amylosporus guaraniticus is described as a new species from Paraguay based on morphological characters and molecular evidence based on ITS and LSU markers. The species is characterized by its annual, pileate basidiomata, poroid hymenophore, a dimitic hyphal system with simple septate and double to multiple clamped generative hyphae and asperulated, amyloid basidiospores (4–6.5 × 3–4.5 μm). An identification key to Amylosporus species is presented.