Miracle-dz/UniFAR-FTUs huggingface dataset:
Compatibility Evaluation of Clustering Algorithms for Contemporary Extracellular Neural Spike Sorting

Deciphering useful information from electrophysiological data recorded from the brain, in-vivo or in-vitro, is dependent on the capability to analyse spike patterns efficiently and accurately. The spike analysis mechanisms are heavily reliant on the clustering algorithms that enable separation of spike trends based on their spatio-temporal behaviors. Literature review report several clustering algorithms over decades focused on different applications. Although spike analysis algorithms employ only a small subset of clustering algorithms, however, not much work has been reported on the compliance and suitability of such clustering algorithms for spike analysis. In our study, we have attempted to comment on the suitability of available clustering algorithms and performance capacity when exposed to spike analysis. In this regard, the study reports a compatibility evaluation on algorithms previously employed in spike sorting as well as the algorithms yet to be investigated for application in sorting neural spikes. The performance of the algorithms is compared in terms of their accuracy, confusion matrix and accepted validation indices. Three data sets comprising of easy, difficult, and real spike similarity with known ground-truth are chosen for assessment, ensuring a uniform testbed. The procedure also employs two feature-sets, principal component analysis and wavelets. The report also presents a statistical score scheme to evaluate the performance individually and overall. The open nature of the data sets, the clustering algorithms and the evaluation criteria make the proposed evaluation framework widely accessible to the research community. We believe that the study presents a reference guide for emerging neuroscientists to select the most suitable algorithms for their spike analysis requirements.
Quarter-Century (1993–2018) Nesting Trends in the Peripheral Populations of Three Sea Turtle Species at Ishigakijima Island, Japan

Abstract. Three sea turtle species (loggerhead [Caretta caretta], green [Chelonia mydas], and hawksbill [Eretmochelys imbricata] turtles) have nesting sites at Ishigakijima Island, which is located in the southwestern part of Japan. This island is known as the geographic southern (low-latitude) limit of north Pacific loggerhead turtles' nesting sites and close to the northern (high-latitude) limit of northwest Pacific green and hawksbill turtles' nesting sites. Our 26-yr nesting survey (1993–2018) revealed that the number of nesting events of loggerhead turtles decreased (with a temporal increment between 2006 and 2008), while the other study reported that the entire Japanese loggerhead nesting population continued to increase substantially from 2006 to, at least, 2012. In contrast, the green turtle population increased gradually, with fluctuations. Hawksbill turtles had several nests annually. The sea surface temperature during the nesting season was significantly related to the annual number of nesting events in loggerhead turtles but not in green and hawksbill turtles. Thus, warming temperature may have caused a reduction in the nesting population of loggerhead turtles at Ishigakijima Island, which is the southern limit of their nesting distribution.
Canopy cover and drought influence the landscape epidemiology of an amphibian chytrid fungus

Batrachochytrium dendrobatidis (Bd) is a globally distributed fungal pathogen of amphibians that has caused amphibian population declines. Prevalence and infection intensity of Bd should vary spatially across heterogeneous landscapes because survival of the pathogen depends on environmental conditions including humidity and temperature. Wetland temperatures should vary with forest canopy cover, but few studies have examined the relationship between Bd prevalence and canopy cover. We sampled anurans for Bd at 33 wetlands in Illinois across a canopy cover gradient during the severe drought of 2012 and during more typical weather in 2013. We hypothesized that anurans from closed canopy wetlands would have higher Bd prevalence than anurans from open canopy wetlands because high canopy cover would prevent temperatures from exceeding Bd's critical maximum temperature as often. We used occupancy modeling to examine how Bd prevalence varied spatially in relation to environmental covariates, and to determine if we.
The Utilization of Fats of Different Melting Points Added to Broiler Feed

Abstract CERTAIN fats have been shown by a number of investigators to enhance the value of chick rations. For this reason, they are being widely used in commercial feeds. For the most part, the fats used are low melting tallows and greases which improve the physical texture of feed as well as its nutritive qualities. These fats must be melted and added in liquid form to obtain uniform distribution, a factor which complicates the manufacture of feed. Hardened fats, particularly hydrogenated tallow, can be handled more readily and would be convenient fats for use in feeds, if they can be readily utilized by animals. There was some doubt in this respect since Carver and Johnson (1953) have shown that stearic acid was not well utilized by the chick when added at one or two percent levels to a semipurified diet. Hydrogenated tallow contains approximately 75 percent stearic acid in the glyceride …
Integration of Machine Learning Improves the Prediction Accuracy of Molecular Modelling for M. jannaschii Tyrosyl-tRNA Synthetase Substrate Specificity

Design of enzyme binding pocket to accommodate substrates with different chemical structure is a great challenge. Traditionally, thousands even millions of mutants have to be screened in wet-lab experiment to find a ligand-specific mutant and large amount of time and resources is consumed. To accelerate the screening process, here we propose a novel workflow through integration of molecular modeling and data-driven machine learning method to generate mutant libraries with high enrichment ratio for recognition of specific substrate. M. jannaschii tyrosyl-tRNA synthetase (Mj. TyrRS) is used as an example system to give a proof of concept since the sequence and structure of many unnatural amino acid specific Mj. TyrRS mutants have been reported. Based on the crystal structures of different Mj. TyrRS mutants and Rosetta modeling result, we find D158G/P is the critical residue which influences the backbone disruption of helix with residue 158-163. Our results show that compared with random mutation, Rosetta modeling and score function calculation can elevate the enrichment ratio of desired mutants by 2-fold in a test library having 687 mutants, while after calibration by machine learning model trained using known data of Mj. TyrRS mutants and ligand, the enrichment ratio can be elevated by 11-fold. This molecular modeling and machine learning-integrated workflow is anticipated to significantly benefit to the Mj. tyrRS mutant screening and substantially reduce the time and cost of web-lab experiment. Besides, this novel process will have broad application in the field of computational protein design. CCS Concepts • Applied computing • Life and medical sciences • Computational biology • Molecular structural biology
Exploring the Histone Acetylation Cycle in the Protozoan Model Tetrahymena thermophila

The eukaryotic histone acetylation cycle is composed of three classes of proteins, histone acetyltransferases (HATs) that add acetyl groups to lysine amino acids, bromodomain (BRD) containing proteins that are one of the most characterized of several protein domains that recognize acetyl-lysine (Kac) and effect downstream function, and histone deacetylases (HDACs) that catalyze the reverse reaction. Dysfunction of selected proteins of these three classes is associated with human disease such as cancer. Additionally, the HATs, BRDs, and HDACs of fungi and parasitic protozoa present potential drug targets. Despite their importance, the function and mechanisms of HATs, BRDs, and HDACs and how they relate to chromatin remodeling (CR) remain incompletely understood. Tetrahymena thermophila (Tt) provides a highly tractable single-celled free-living protozoan model for studying histone acetylation, featuring a massively acetylated somatic genome, a property that was exploited in the identification of the first nuclear/type A HAT Gcn5 in the 1990s. Since then, Tetrahymena remains an under-explored model for the molecular analysis of HATs, BRDs, and HDACs. Studies of HATs, BRDs, and HDACs in Tetrahymena have the potential to reveal the function of HATs and BRDs relevant to both fundamental eukaryotic biology and to the study of disease mechanisms in parasitic protozoa.
Increased Temporal Lobe Beta Activity in Boys With Attention-Deficit Hyperactivity Disorder by LORETA Analysis

Aim: Attention-deficit hyperactivity disorder (ADHD) is a common childhood neuropsychiatric disorder that affects 6.1 million US children. The mechanism of ADHD is currently unclear. Differences in ADHD presentations between boys and girls are well-established. In the present study, we used quantitative electroencephalography (EEG) to investigate the brain area and EEG bands of boys with ADHD. Methods: This study enrolled 40 boys with ADHD and 40 age-matched controls without ADHD. Low-resolution electromagnetic tomography (LORETA) and instantaneous frequency were used to analyze EEG data to reveal the mechanisms underlying ADHD in boys. Results: We found that the instantaneous frequencies in the T3 and T4 EEG channels in boys with ADHD were significantly higher than those in the controls. The beta band showed significant difference in current density between the ADHD and control groups. In the entire brain area, the bilateral inferior and middle temporal gyrus exhibited the most significant difference between the ADHD and control groups in the EEG beta band. Connectivity analysis revealed an increase in connectivity between the left middle frontal gyrus and fusiform gyrus of the temporal lobe in boys with ADHD. Conclusions: LORETA is a promising tool for analyzing EEG signals and can be used to investigate the mechanism of ADHD. Our results reveal that the inferior temporal gyrus, middle temporal gyrus, and fusiform gyrus of the temporal lobe are potentially involved in the pathogenesis of ADHD in boys. In comparison with other imaging methods, such as magnetic resonance imaging, EEG is easy to perform, fast, and low cost. Our study presents a new approach for investigating the pathogenesis of ADHD in boys.
Application of Surgical Lead Management and Reconfigurable Coil Technology to Reduce RF Heating of DBS Implants during MRI at 3T Under Variant Body Compositions

Patients with active implants such as deep brain stimulation (DBS) devices, have limited access to magnetic resonance imaging (MRI) due to risks of RF heating. With an aging population, the prevalence of neurodegenerative and vascular disease increases; and so does the indication for MRI exams in patients with such implants. In response to this growing need for MRI, many groups have investigated strategies to mitigate the RF heating of the implants. These efforts, however, have relied either on simulations with homogenous body models or simplified phantom experiments (box shaped phantom with single tissue). It is well established, however, that the shape and heterogeneity of human body affects the distribution of MRI electric fields, which by proxy, alters the RF heating of an implant inside the body. In this contribution, we applied numerical simulations and phantom experiments to examine the effectiveness of RF heating mitigation strategies under variant patient body compositions, focusing on two recently proposed techniques: (a) surgical modification of DBS lead trajectories inside the body, and (b) use of a patient-adjustable reconfigurable MRI coil, both aiming to reduce the coupling of implanted leads and MRI electric fields. Our results demonstrated that both techniques perform well under variant body compositions.
Effect of culture medium and genotype on germination of hybrid oil palm zygotic embryos.

Nutritional requirements for germination of mature zygotic embryos of four genotypes of Elaeis guineensis Jacq. Dura◊ Pisifera were assessed. A factorial experiment was conducted with four genotypes from separate crossing events and three culture media to show Interactions between genotypes and culture media on seedling germination (p < 0.05). The highest frequency of normal seedling germination was facilitated by 1/2 Murashige and Skoog (MS) medium (29.2%), followed by MS (15.0%) and Blaydes (12.9%). Speed of shoot formation followed a similar trend. Roots were induced most rapidly in 1/2 MS medium, followed by Blaydes and then MS. Root induction was similar in 1/2 MS medium (2.29%) and Blaydes medium (1.25%) but only significantly higher than in MS (0.00%).
Toxoplasma gondii Mechanisms of Entry Into Host Cells

Toxoplasma gondii, the causative agent of toxoplasmosis, is an obligate intracellular protozoan parasite. Toxoplasma can invade and multiply inside any nucleated cell of a wide range of homeothermic hosts. The canonical process of internalization involves several steps: an initial recognition of the host cell surface and a sequential secretion of proteins from micronemes followed by rhoptries that assemble a macromolecular complex constituting a specialized and transient moving junction. The parasite is then internalized via an endocytic process with the establishment of a parasitophorous vacuole (PV), that does not fuse with lysosomes, where the parasites survive and multiply. This process of host cell invasion is usually referred to active penetration. Using different cell types and inhibitors of distinct endocytic pathways, we show that treatment of host cells with compounds that interfere with clathrin-mediated endocytosis (hypertonic sucrose medium, chlorpromazine hydrochloride, and pitstop 2 inhibited the internalization of tachyzoites). In addition, treatments that interfere with macropinocytosis, such as incubation with amiloride or IPA-3, increased parasite attachment to the host cell surface but significantly blocked parasite internalization. Immunofluorescence microscopy showed that markers of macropinocytosis, such as the Rab5 effector rabankyrin 5 and Pak1, are associated with parasite-containing cytoplasmic vacuoles. These results indicate that entrance of T. gondii into mammalian cells can take place both by the well-characterized interaction of parasite and host cell endocytic machinery and other processes, such as the clathrin-mediated endocytosis, and macropinocytosis.
Ancestral reconstructions decipher major adaptations of ammonia oxidizing archaea upon radiation into moderate terrestrial and marine environments

Unlike all other archaeal lineages, ammonia oxidizing archaea (AOA) of the phylum Thaumarchaea are widespread and abundant in all moderate and oxic environments on Earth. The evolutionary adaptations that led to such unprecedented ecological success of a microbial clade characterized by highly conserved energy and carbon metabolisms have, however, remained underexplored. Here we reconstructed the genomic content and growth temperature of the ancestor of all AOA as well as the ancestors of the marine and soil lineages based on 39 available complete or nearly complete genomes of AOA. Our evolutionary scenario depicts an extremely thermophilic autotrophic, aerobic ancestor from which three independent lineages of a marine and two terrestrial groups radiated into moderate environments. Their emergence was paralleled by (I) a continuous acquisition of an extensive collection of stress tolerance genes mostly involved in redox maintenance and oxygen detoxification, (II) an expansion of regulatory capacities in transcription and central metabolic functions and (III) an extended repertoire of cell appendages and modifications related to adherence and interactions with the environment. Our analysis provides insights into the evolutionary transitions and key processes that enabled the conquest of the diverse environments in which contemporary AOA are found.
The evolution of seasonal migration and the slow-fast continuum of life history in birds

Seasonal migration is a widespread adaptation in environments with predictable periods of resource abundance and scarcity. Migration is frequently associated with high mortality, suggesting that migratory species live on the “fast” end of the slow-fast continuum of life history. However, few interspecific comparative studies have tested this assumption and prior assessments have been complicated by environmental variation among breeding locations. We evaluate how migration distance influences the tradeoff between reproduction and survival in 45 species of mostly passerine birds that breed sympatrically in North American boreal forests but migrate to a diversity of environments and latitudes for the northern winter. We find, after accounting for mass and phylogeny, that longer distance migrations to increasingly amenable winter environments are correlated with reduced annual reproductive output, but also result in increased adult survival compared to shorter-distance migrations. Non-migratory boreal species have life history parameters more similar to long-distance migrants than to shorter-distance migrants. These results suggest that long-distance migration and other highly specialized strategies for survival in seasonal environments impose selection pressures that both confer and demand high adult survival rates. That is, owing to the reproductive cost of long-distance migration, this strategy can only persist if balanced by high adult survival. Our results reveal migratory distance as a fundamental life history parameter that predicts, and is inextricable from, the balance of survival and reproduction. Our study further provides evolutionary context for understanding the annual cycle demography of migratory species and the strategies long-distance migrants use to maximize survival on their journeys.
Immunohistochemical Identification of Placental Bed Biopsies and the Implications for the Inclusion of Specimens when Studying the Spiral Artery Response to Pregnancy

Objectives: To determine if a cytokeratin marker facilitates the detection of trophoblast and refines the identification of placental bed biopsies compared to standard techniques.Methods: Placental bed biopsies, n = 320, were taken at caesarean section from 148 women. Using standard histology, tissue sections were examined under light microscopy for trophoblast. Morphological features of spiral arteries were recorded. Biopsies in which no trophoblast was identified were stained for cytokeratin and reexamined under light microscopy.Results: In 148 (48%) of the biopsies, trophoblast was not identified using standard methods. Eighty-nine of these were stained for cytokeratin and 35 (39%) were found to contain trophoblast. In the placental bed, extravillous trophoblast distribution is not uniform, the morphology is diverse, giant cells are not predominant, and glandular tissue is often abundant although attenuated. Spiral artery morphology can be variable in the same biopsy.Conclusions: The identification of .
Micropropagation of Three Pyrus Rootstocks

Explants of three rootstock selections Pyrus calleryana Dcne 'Oregon Pear Rootstock (OPR) 157', P. betulifolia Bunge 'OPR 260', and P. communis L. 'Old Home' x 'Farmingdale 230' ('OH x F 230') were initiated from forced branches of field-grown trees. 'OPR 260' and 'OH x F 230' shoots cultured on Cheng medium with IBA proliferated better than those on NAA. NAA and IBA at concentrations >0.5 μM inhibited shoot multiplication. Overall, the best micropropagation medium for 'OPR 260' and 'OH x F 230' was Cheng medium with 8 μM BA and 0.5 μM IBA. Shoot multiplication of 'OPR 157' was best on 8 μM BA and better on low NAA (0.5 μM) or no auxin than on IBA. 'OH x F 230' rooted easily (>80%) with all IBA and NAA treatments. The best rooting treatment (42.9%) for 'OPR 260' was 10 μM IBA in darkness for 1 week; for 'OPR 157' (23.9%), it was a 15-second dip in 10 mM NAA. Only rooted plantlets survived 4 weeks of greenhouse acclimatization. Chemical names used: N 6 -benzyladenine (BA); indole-3-butyric acid (IBA); napthaleneacetic acid (NAA). adaptable to the northern United States; P. calleryana and P. betulifolia are more suited to warmer climates such as California and southern Oregon. All three selections are graft- compatible with many pear cultivars and with Cydonia oblonga L. (quince). Propagation of these genotypes has not been easy and, there- fore, has limited their availability. Tissue culture methods are available for many pear species and cultivars (Berardi et al., 1993; Cheng, 1978; Dolcet-Sanjuan et al., 1990; Nicolodi and Pieber, 1989; Singha, 1980; Stimart and Harbage, 1989). Differences exist among the various genotypes for both basal medium and growth regulators. Our objec- tives were to evaluate Cheng and woody plant media (WPM) containing a range of BA, NAA, and IBA concentrations as potential media for shoot multiplication of 'OPR 157', 'OPR 260', and 'OH x F 230'. Following shoot multiplica- tion, four in vitro and one ex vitro rooting treatment were tested. Shoots from rooting treatment were evaluated further for their abil- ity to acclimate to greenhouse conditions.
Describing undiscovered insect diversity: an introduction to collected papers describing 150 new taxa

The number of species on earth is estimated to be 8.7 million, with 87% of them to be discovered and described (Mora et al. 2011). The total of 8.7 million seems to be an underestimate, because for Animalia alone, over 1.5 million species have been described (Zhang 2011b). The most successful group, the Insecta, accounts for almost two-thirds of all animals. Zootaxa has been a major force in facilitating the descriptions of undiscovered animal species in the world—publishing about 20% of all new species indexed in Zoological Record each year (Zhang 2011a). In the first week since the publication of the ICZN amendment allowing e-only publication (ICZN 2012), Zootaxa has published 484 new taxa. In this special volume highlighting undiscovered global diversity of insects, Zootaxa publishes 150 new taxa (143 species + 7 genera) of 12 insect orders in 44 papers by authors from different parts of the world (Table 1).
Teaching NeuroImages: Spindle coma following cerebral herniation and pontine infarction

A 67-year-old woman presented with bilateral subdural hematomas. After hematoma evacuation, she was unresponsive with extensor posturing and preserved brainstem reflexes. MRI (figure 1) revealed extensive posterior circulation infarction including the mid-pons, thought secondary to herniation and vascular compression. EEG (figure 2) revealed an unreactive background resembling normal N2 sleep (including spindles, K-complexes, and vertex waves) for >24 hours, diagnostic of spindle coma.1 Conditions implicated in spindle coma tend to disrupt the ascending arousal system at the brainstem and hypothalamic level, but spare the thalamus.1,2 Underlying etiology, extent of injury, and EEG reactivity provide more prognostic insight than spindle coma alone.1,2
Le potentiel d'oxydoréduction et sa prise en compte dans les procédés d'utilisation des bactéries lactiques

Le potentiel d'oxydoreduction (Eh) est un parametre intrinseque a tout milieu biologique. Il peut intervenir a differents niveaux sur la cellule microbienne : expression des genes, metabolisme, physiologie et donc modifier potentiellement son aptitude a la croissance et a la production de molecules participant aux caracteristiques finales des produits fermentes. En fonction des types de produits, il existerait un Eh optimal pour le developpement des flores et d'une balance aromatique equilibree. Il apparait donc important de definir des criteres de mesure des aptitudes reductrices des differentes souches de bacteries utilisees en industrie. Ce type de demarche a permis de differencier les potentialites de bacteries lactiques et de ferments commerciaux.