Miracle-dz/UniFAR-FTUs huggingface dataset:
RFL polymorphism of three fertility genes in Egyptian buffalo

There is a considerable interest in the application of molecular genetics technologies in the form of specific DNA markers that are associated with various productivity traits to promote more efficient and relatively easy selection and breeding of farm animals with an advantage for inheritable traits of production and reproduction. River buffalo is a species of great economic potential, especially in developing countries; it is the main source of meat and milk in Egypt. This study aimed to detect the genetic polymorphism of three genes; follicle-stimulating hormone receptor (FSHR), luteinizing hormone receptor (LHR) and estrogen receptor-α (ERα) genes which are considered candidate genes for fertility and reproduction performances. The genetic polymorphism detection of these genes in Egyptian buffaloes will enable us to identify and subsequently select the animals with high fertility performances- depending on these molecular markers- for breeding programs. Genomic DNA extracted from 100 healthy female buffaloes was amplified using primers that were designed from the cattle FSHR, LHR and ERα gene sequences. The amplified fragments of FSHR (306-bp), LHR (303-bp) and ERα (248-bp) were digested with AluI, HhaI and BglI restriction enzymes, respectively. The results showed that all tested buffaloes are genotyped as CC for FSHR and TT for LHR. Regarding to the ERα gene, 18% of the investigated buffaloes are genotypes as heterozygous AG and the remaining animals (82%) are genotyped as GG. To the best of our knowledge, this is the first published data on the genetic characterization and nucleotide sequences of fertility genes in Egyptian buffalo. The nucleotide sequences of Egyptian buffalo FSHRC, LHRT, ERαG and ERαA alleles were submitted to nucleotide sequences database NCBI/ Bankit/GenBank and have the accession numbers JX049145, JQ885687, JQ308795 and JQ308796, respectively.
Long-Term Post-Fire Effects on Spatial Ecology and Reproductive Output of Female Agassiz’s Desert Tortoises (Gopherus agassizii) at a Wind Energy Facility near Palm Springs, California, USA

We studied the long-term response of a cohort of eight female Agassiz’s desert tortoises (Gopherus agassizii) during the first 15 years following a large fire at a wind energy generation facility near Palm Springs, California, USA. The fire burned a significant portion of the study site in 1995. Tortoise activity areas were mapped using minimum convex polygons for a proximate post-fire interval from 1997 to 2000, and a long-term post-fire interval from 2009 to 2010. In addition, we measured the annual reproductive output of eggs each year and monitored the body condition of tortoises over time. One adult female tortoise was killed by the fire and five tortoises bore exposure scars that were not fatal. Despite predictions that tortoises would make the short-distance movements from burned to nearby unburned habitats, most activity areas and their centroids remained in burned areas for the duration of the study. The percentage of activity area burned did not differ significantly between the two monitoring periods. Annual reproductive output and measures of body condition remained statistically similar throughout the monitoring period. Despite changes in plant composition, conditions at this site appeared to be suitable for survival of tortoises following a major fire. High productivity at the site may have buffered tortoises from the adverse impacts of fire if they were not killed outright. Tortoise populations at less productive desert sites may not have adequate resources to sustain normal activity areas, reproductive output, and body conditions following fire.
Soil Carbon and Nutrient Recovery after High-Severity Wildfire in Mexico

Fire severity can increase above historical levels due to factors such as human-derived fire suppression and climate change. Studies about the effects of high-severity fires on soil carbon and nutrients in pine forest at tropical latitudes are still rare. We analyzed the changes in carbon (C), nitrogen (N), and phosphorus (P) contents in the organic layer and the top mineral soil layer in a post-fire chronosequence of Pinus douglasiana Martínez-dominated forest stands in central-western Mexico 8 yr, 28 yr, and 60 yr following a high-severity fire. We found that fire significantly affected the total C, N, and P contents in the organic layer, explained mainly by mass losses. We did not detect differences in C, N, and P contents (Mg ha−1) in the mineral soil, but C and N concentrations (mg g−1) increased with stand age. This can be explained by the high levels of tree mortality that occur during high-severity fires, depleting litter inputs to the soil. We observed a fast recovery of C, N, and P, perhaps resulting from the high capacity of Pinus douglasiana to regenerate following high-severity fires. This can be associated with high metabolic rates of forests in tropical latitudes, which, given their climate and soil conditions, favor higher rates of vegetation growth and, thus, faster rates of organic C inputs and soil organic C accumulation.ResumenLa severidad de los incendios podría aumentar por encima de los valores históricos como resultado de acciones humanas como la supresión de incendios y el cambio climático. Estudios sobre el efecto de los incendios de alta severidad sobre el carbono y los nutrientes almacenados en suelos de bosques de pino en latitudes tropicales, son escasos. En este estudio analizamos los cambios en los contenidos de carbono (C), nitrógeno (N) y fósforo (P) almacenados en la capa orgánica del suelo y en la capa superficial del suelo mineral, en una crono-secuencia post-incendio en bosques dominados por Pinus douglasiana Martínez, en el centro-occidente de México, 8 años, 28 años, y 60 años después de incendios severos. Los incendios afectaron significativamente los contenidos de C, N y P en la capa orgánica, explicado principalmente por la pérdida de masa. No hubo diferencias en los contenidos de C, N y P (Mg ha−1) en el suelo mineral, mientras que la concentración de C y N (mg g−1) se incrementó con la edad del rodal. Esto puede ser explicado por la alta mortalidad de árboles provocada por los incendios severos, lo que disminuyó la entrada de materia orgánica al suelo. Se registró una rápida recuperación de los contenidos de C, N y P probablemente como resultado de la alta capacidad de Pinus douglasiana para regenerar después de incendios severos. Lo anterior puede estar asociado con las altas tasas metabólicas de los bosques en latitudes tropicales, dadas las condiciones climáticas y de suelo que favorecen mayores tasas de crecimiento de la vegetación y de incorporación y acumulación de C en el suelo.
Linguist vs. Machine: Rapid Development of Finite-State Morphological Grammars

Sequence-to-sequence models have proven to be highly successful in learning morphological inflection from examples as the series of SIGMORPHON/CoNLL shared tasks have shown. It is usually assumed, however, that a linguist working with inflectional examples could in principle develop a gold standard-level morphological analyzer and generator that would surpass a trained neural network model in accuracy of predictions, but that it may require significant amounts of human labor. In this paper, we discuss an experiment where a group of people with some linguistic training develop 25+ grammars as part of the shared task and weigh the cost/benefit ratio of developing grammars by hand. We also present tools that can help linguists triage difficult complex morphophonological phenomena within a language and hypothesize inflectional class membership. We conclude that a significant development effort by trained linguists to analyze and model morphophonological patterns are required in order to surpass the accuracy of neural models.
Dietary and phylogenetic correlates of digestive trypsin activity in insect pests

Because food proteins are crucial for insect survival, growth, and fecundity, enzymes involved in their digestion have attracted the attention of fundamental entomologists studying the mechanisms and patterns of dietary specialization, and applied entomologists searching for more efficient modes of pest control. Most insects digest proteins using trypsin, an endopeptidase that cleaves polypeptide chains on the carboxyl side of arginine and lysine, two basic amino acids. As the most ancestral proteinase, trypsin is wide‐spread in the digestive tract of insects from various orders and with various feeding habits. The present review focuses on biochemical and molecular characteristics, mechanisms of regulation, and adaptive/non‐adaptive changes of trypsin activity in response to heterogeneous food environments in a phylogenetic context. Within‐ and among‐species variations in trypsin structure and regulation that contribute to better matching with specific food types are emphasized. We also discuss the relevance of these data for choosing an appropriate strategy for control of insect pests. Pest control strategies to reduce trypsin activity by interfering with substrate binding or trypsin synthesis and secretion have been suggested. Successful application of these procedures requires a multidisciplinary approach and knowledge about digestive physiology of the pest, as well as the structural characteristics of trypsins that determine their interaction with proteinaceous inhibitors and other food compounds, about patterns of developmental changes in trypsin gene expression, adaptive responses of insects to food composition, and various environmental effects on trypsin activity.
Updates on Vaccine Safety and Post-Licensure Surveillance for Adverse Events Following Immunization in South Korea, 2005–2017

Purpose Vaccine hesitancy is among the top ten threats to global health, and access to precise data on adverse events following immunization (AEFIs) is imperative to alleviate public concerns surrounding vaccines. This study aimed to present the overall trends of AEFIs reported in South Korea. Materials and Methods We evaluated the trends of AEFIs using the Korea Institute of Drug Safety & Risk Management-Korea Adverse Event Reporting System database between January 2005 and December 2017. AEFIs were classified into five categories to evaluate associations between vaccines and AEFIs through a case-non-case study: neurologic reactions, general systemic reactions, local reactions, allergic reactions, and others. Results Among 54378 reported adverse events (AEs) associated with all vaccines approved in South Korea, more than half (56.7%) occurred following influenza vaccination, followed by the pneumococcal (11.6%) and Bacillus Calmette-Guérin (BCG) vaccines (5.0%). After immunization with most vaccines, general systemic reactions were most common, followed by local and neurologic reactions. Adjusted reporting odds ratios were calculated for all neurologic, general, local, and allergic reactions: of all vaccines, rotavirus [neurologic 2.43, 95% confidence interval (CI), 2.25–2.62], BCG (general; 2.20, 95% CI, 1.91–2.53), BCG (local; 3.15, 95% CI, 2.69–3.68), and Japanese encephalitis (allergic 2.38, 95% CI, 1.98–2.87) vaccines showed the highest values. Conclusion The majority of reported AEFIs were non-serious and mostly general systemic reactions. Sufficient knowledge on the AEFIs would secure public confidence on the safety of vaccines, thereby reducing public health burden from vaccine-preventable diseases.
Indo‐Pacific population structure and evolutionary history of the coconut crab Birgus latro

Mitochondrial DNA variation was used to examine population structure in a widespread, marine‐dispersed species, Birgus latro. Crabs were collected from eight locations throughout the species' Indo‐Pacific distribution. Purified mtDNA from 160 individuals was cut with five restriction enzymes, revealing high haplotype diversity (0.96) and moderate nucleotide diversity (0.75%). Island populations from the Indian Ocean (Christmas I.) and Pacific Ocean were significantly different (GST= 0.37) and had distinct mtDNA lineages with a net sequence divergence of 1.4%. Pacific island populations had diverged in a manner consistent with isolation by distance, with only the most peripheral populations being significantly different. The results for mtDNA are largely concordant with those from allozymes, although estimates of gene flow between the Indian and Pacific Oceans were much lower when based on mtDNA. The mtDNA phylogeny also permitted a deeper examination of the evolutionary and demographic history of Birgus latro. Long‐term separation of populations is evident in the complete phylogenetic subdivision of mtDNA lineages between the Indian and Pacific Ocean populations sampled. The starlike phylogeny of alleles from the Pacific suggests a rapid population expansion in the Pacific during the Pleistocene. Including information about allele phylogeny, as well as distribution and frequency, obscured contemporary population structure, but provided unique insights into the evolutionary history of the species.
A critical role for trkB signaling in the adult function of parvalbumin interneurons and prefrontal network dynamics

Inhibitory interneurons expressing parvalbumin (PV) in the prefrontal cortex (PFC) are central to excitatory/inhibitory (E/I) balance, generation of gamma oscillations, and cognition. Dysfunction of PV interneurons disrupts information processing and cognitive behavior. Tyrosine receptor kinase B (trkB) signaling is known to regulate the differentiation and maturation of cortical PV interneurons during development, but is also suggested to be involved in the activity and network functions of PV interneurons in the adult brain. Using a novel viral strategy for cell-type and region-specific expression of a dominant negative trkB in adult mice, we show that reduced trkB signaling in PV interneurons in the PFC leads to pronounced morphological, physiological, and behavioral changes. Our results provide evidence for a critical role of trkB signaling in the function of PV interneurons in the adult brain, local network activities central to prefrontal circuit dynamics, and cognitive behavior.
Post-ictal generalized EEG suppression and seizure-induced mortality are reduced by enhancing dorsal raphe serotonergic neurotransmission

Sudden unexpected death in epilepsy (SUDEP) is the leading cause of death in patients with refractory epilepsy. A proposed risk marker for SUDEP is the duration of post-ictal generalized EEG suppression (PGES). The mechanisms underlying PGES are unknown. Serotonin (5-HT) has been implicated in SUDEP pathophysiology. Seizures suppress activity of 5-HT neurons in the dorsal raphe nucleus (DRN). We hypothesized that suppression of DRN 5-HT neuron activity contributes to PGES and increasing 5-HT neurotransmission or stimulating the DRN before a seizure would decrease PGES duration. Adult C57BL/6 and Pet1-Cre mice received EEG/EMG electrodes, a bipolar stimulating/recording electrode in the right basolateral amygdala, and either a microdialysis guide cannula or an injection of adeno-associated virus (AAV) allowing expression of channelrhodopsin2 plus an optic fiber into the DRN. Systemic application of the selective 5-HT reuptake inhibitor citalopram (20 mg/kg) decreased PGES duration from seizures induced during wake (n = 23) and NREM sleep (n = 13) whereas fluoxetine (20 mg/kg) pretreatment decreased PGES duration following seizures induced from wake (n = 11), but not NREM sleep (n = 9). Focal chemical (n = 6) or optogenetic (n = 8) stimulation of the DRN reduced PGES duration following kindled seizures and reduced morality following maximal electroshock seizures (n = 6) induced during wake. During PGES, animals exhibited immobility and suppression of EEG activity that was reduced by citalopram pretreatment. These results indicate that 5-HT and the DRN may regulate PGES and seizure-induced mortality. Highlights - PGES consistently follows seizures induced by amygdala stimulation in amygdala-kindled mice. - Seizure-induced dysregulation of 5-HT neurotransmission from the dorsal raphe nucleus may contribute to PGES. - Systemic administration of 5-HT enhancing drugs and stimulation of the DRN reduces PGES duration. - PGES is associated with post-ictal immobility in kindled mice that can be reduced by pretreatment with citalopram. - Recovery of EEG frequencies to baseline occurs in a stepwise manner with the lowest frequencies recovering first.
Notes: Inhibition of the Acetyl-CoA Carboxylase of Barley Chloroplasts by Cycloxydim and Sethoxydim

The effect of the three cyclohexane-1,3-dione derivatives cycloxydim, sethoxydim and clethodim on the incorporation of 14C-labelled acetate, malonate. acctyl-CoA or malonyl-CoA into fatty acids was studied in an enzyme preparation isolated from barley chloroplasts (Hordeum vulgare L. var. “Alexis”). The herbicides cycloxydim, clethodim and sethoxydim block the de novo fatty acid biosynthesis from [2-14C]acetatc and [1-14C]acetyl-CoA, whereas that of [2-14C]malonatc and [2-14C)malonyl-CoA is not affected. The data indicate that the mode of action of the cyclohexane-1,3-dione derivatives in the sensitive barley plant consists in the inhibition of de novo fatty acid biosynthesis by blocking the acetyl-CoA carboxylase (EC 6.4.1.2.).
Karyotypic study in some Iranian Iris species populations.

A karyotypic study was performed Iranian native Irises (I.songarica, I.aucheri, I.pseudocaucasica and I.sisyrinchium) populations. A number of mitotic cells at metaphase stage for each population were prepared. Chromosomes of suitable mitotic cells were counted and various parameters, including long arm (L), short arm (S), total length of chromosome (TL), relative length of chromosome (RL), arm ratio (AR), r-value, total chromosome volume (TCV) and centromeric index (CI), number of chloroplast, were measured. All populations were diploid with 2n=2x=44, 40, 32, 18 and they were differentiated by their karyotype formula and parameters. Chromosome length varied in the populations. The Irises I.songarica, I.aucheri, I.pseudocaucasica and I. sisyrinchium) populations under study occupied classes 1A and 2A of Stebbins’ karyotype classification, indicating the presence of a primitive symmetrical karyotype in these populations. The mean chromosome length ranged from 4.97 to 25.05 μm. Mean centromeric index (CI) of complements varied from 41.1 to 43.7%. The chromosome types were detected as mostly submetacentrics “Sm” and some subtelocentrics “St”. The results of factor analysis showed that the main elements of the first three main components determined 100% of the total variance. The first component was 50%, the second was 30% and the third components were 20% of the total variance. Highest positive correlation with the first component of the life form, and index showed the highest negative correlation with the short arms. The second component showed positively correlated with the percentage of the maximum size and the maximum negative correlation with inter chromosomal asymmetry index. The third component of the high correlation between distribution and descriptive statistics indicators showed the highest correlation with the length of the short arm. Results seemed to provide enough genetic evidence to identify each species and useful data to clarify the interspecific relationships among Iranian native Iris species.
High Incidence of Amoxicillin-Induced Crystal Nephropathy in Patients Receiving High Dose of Intravenous Amoxicillin

Background: Amoxicillin (AMX)-induced crystal nephropathy (AICN) is considered as a rare complication of high dose intravenous (IV) AMX administration. However, recently, its incidence seems to be increasing based on French pharmacovigilance centers. Occurrence of AICN has been observed mainly with IV administration of AMX and mostly under doses over 8 g/day. Given that pharmacovigilance data are based on declaration, the real incidence of AICN may be underestimated. Thus, the primary objective of the present study was to determine the incidence of AICN in the current practice. Materials and Methods: We conducted a retrospective study between 1 January 2015 and 31 December 2017 in Angers University Hospital. Inclusion criteria were age over 18 years-old and IV AMX administration of at least 8 g/day for more than 24 h. Patients admitted directly into the intensive care units were excluded. Medical records of patients that developed Kidney Disease:Improving Global Outcome (KDIGO) stage 2–3 acute kidney injury (AKI) were reviewed by a nephrologist and a specialist in pharmacovigilance. AICN was retained if temporality analysis was conclusive, after exclusion of other causes of AKI, in absence of other nephrotoxic drug administration. Results: A total of 1303 patients received IV AMX for at least 24 h. Among them, 358 (27.5%) were exposed to AMX doses of at least 8 g/day and were included. Patients were predominantly males (68.2%) with a mean age of 69.1 years-old. AMX was administered for a medical reason in 78.5% of cases. Patients received a median dose of AMX of 12 g/day (152.0 mg/kg/day). Seventy-three patients (20.4%) developed AKI, 42 (56.8%) of which were KDIGO stage 2 or 3. Among the latter, AICN diagnosis was retained in 16 (38.1%) patients, representing an incidence of 4.47% of total patients exposed to high IV AMX doses. Only female gender was associated with an increased risk of AICN. AMX dose was not significantly associated with AICN development. Conclusion: This study suggests a high incidence of AICN in patients receiving high IV AMX doses, representing one third of AKI causes in our study. Female gender appeared as the sole risk factor for AICN in this study.
MANAGEMENT AND CONSERVATION OF THE LARGE MACAWS IN THE WILD

Resumo. – Manejo e conservacao das grandes araras na natureza. – Araras e papagaios (Psittaciformes) representam um dos grupos de aves mais ameacados do mundo. Por seculos, araras foram capturadas por suas penas e para serem usadas como animais de estimacao. Os principais fatores que ameacam as araras sao a destruicao de habitat (perda e fragmentacao), caca clandestina ou captura para o comercio (penas, ovos, filhotes, adultos). Outros fatores importantes sao endogamia e distribuicao geografica restrita, especialmente para populacoes pequenas, especializacao da dieta e habitos, baixa taxa reprodutiva e grande tamanho corporal que os predispoe a extincao. O objetivo deste trabalho e resumir alguns dos estudos de campo conduzidos com grandes araras da America Central e do Sul durante os ultimos anos, e descrever as atuais atividades de manejo e conservacao conduzidas com araras azuis (Anodorhynchus hyacinthinus) no Pantanal Sul, atraves do Projeto Arara Azul.
Three-Event Energy Detection with Adaptive Threshold for Spectrum Sensing in Cognitive Radio Systems

Implementation of dynamic spectrum access (DSA) in cognitive radio (CR) systems requires the unlicensed secondary users (SU) to implement spectrum sensing to monitor the activity of the licensed primary users (PU). Energy detection (ED) is one of the most widely used methods for spectrum sensing in CR systems, and in this paper we present a novel ED algorithm with an adaptive sensing threshold. The three-event ED (3EED) algorithm for spectrum sensing is considered for which an accurate approximation of the optimal decision threshold that minimizes the decision error probability (DEP) is found using Newton’s method with forced convergence in one iteration. The proposed algorithm is analyzed and illustrated with numerical results obtained from simulations that closely match the theoretical results and show that it outperforms the conventional ED (CED) algorithm for spectrum sensing.