Miracle-dz/UniFAR-FTUs huggingface dataset:
Approximating the coalescent under facultative sex

Genome studies of facultative sexual species are providing insight into the evolutionary consequences of mixed reproductive modes. However, it is unclear if the evolutionary history of facultative sexuals’ genomes can be captured by standard population genetic models; in particular, whether they can be approximated by Wright–Fisher dynamics while assuming a rescaled effective population size Ne. Here, I determine when the gene genealogies of diploid facultative sexuals, which can either reproduce by sex or parthenogenesis, can be approximated by the standard coalescent, and further derive coalescent–based estimates of Ne. When sex is frequent (occurring at a frequency much greater than 1/N, for N the actual population size), the underlying genealogy can be approximated by the standard coalescent and Ne is approximately equal to N. When sex is very rare (at frequency much lower than 1/N), Ne can be defined for two alleles, which is independent of N and is instead influence by the frequencies of sex and mitotic gene conversion. However, the genealogy of more than two alleles does not approximate to the standard coalescent, so a general Ne cannot be defined for the entire population under rare sex. These results clarify the conditions for when the genetic history of facultative sexual populations can be captured by standard models, and sheds light on the best sampling strategies to investigate their evolutionary history.
Improving Phosphorous Uptake Efficiency and Quality of Maize Through Optimization of Basal Application

Phosphorous (P) dearth in alkaline calcareous soils of Pakistan renders P unavailable for plant uptake. Consequently, affects grain yield and is major constraint to achieve desired yield potential of field grown maize (Zea mays L.). The objectives of this study were to enhance phosphorus use efficiency (PUE) by determining thresholds of basal applied P. Treatments comprised of five rates of basal applied P viz. 0, 30, 60, 90, 120, and 150 kg ha-1. The experiment was laid out in randomized complete block design (RCBD) with a net plot size of 2.7 m × 5 m, during autumn season 2013. Improved agronomic attributes; i.e., plant height, cob length, grains per cob, grain-pith ratio, 1000-grain weight, biomass and grain yield were observed at 120 kg P ha-1. Likewise, higher agronomic use efficiency of P, grain P content and total P uptake were recorded. Conclusively, application of P at 120 and 150 kg ha-1 would improve grain yield and quality of maize over control. However, 120 kg P ha-1 manifested more promising results than 150 kg P ha-1.
In Vitro Inhibitory Activity of Dayak Onion (Eleutherine bulbosa Mill.) Essential Oil Against Klebsiella pneumoniae

Background: The cases of Klebsiella pneumoniae infec on in West Java province is s ll high. Klebsiella pneu- moniae bacterium can produce the Extended Spectrum Beta Lactamase enzyme leading to an bio cs resistant, so it is important to look for natural and inexpensive an bio c alterna ves; one of which is Dayak onion plant (Eleutherine bulbosa Mill). The content found in Dayak onion is believed to inhibit the growth of Klebsiella pneu- moniae bacteria. This study aims to determine the effec veness of Dayak onion essen al oil on the growth of Klebsiella pneumoniae bacteria. Methods: This study was an experimental study with a post-test control group design using the culture of Kleb- siella pneumoniae on the media Muller Hinton Agar in 7 groups. Groups 1 to 5 (K1 to K5) were given sequen ally Dayak Onion essen al oil solu on in 10% DMSO solvent with concentra ons of 50%, 25%, 12.5%, 6.25%, and 3.125%. Group 6 (K6) was posi ve control (+) with 5 μg Levofloxacin, and Group 7 (K7) was Nega ve (-) with 10% DMSO. The treatment results were measured by the diameter of the host zone and the collected data were analyzed using One-way ANOVA with appropriate Post hoc analysis. Results: The results showed that that there are differences in each group to inhibit the growth of bacteria (p <0.005). K1 are higher than K2, K3, K4, K5, and K7 with increasing concentra ons showed greater inhibi on. Levofloxacin (K6) showed the highest inhibitory power. Conclusion: The results showed that that there are differences in each group to inhibit the growth of bacteria (p <0.005). K1 are higher than K2, K3, K4, K5, and K7 with increasing concentra ons showed greater inhibi on. Levofloxacin (K6) showed the highest inhibitory power.
Principles of tactile search over the body

Although we experience complex patterns over our entire body, how we selectively perceive multi-site touch over our bodies remains poorly understood. Here, we characterized tactile search behavior over the body using a tactile analog of the classic visual search task. Participants judged whether a target stimulus (e.g., 10-Hz vibration) was present or absent on the upper or lower limbs. When present, the target stimulus could occur alone or with distractor stimuli (e.g., 30-Hz vibrations) on other body locations. We varied the number and spatial configurations of the distractors as well as the target and distractor frequencies and measured the impact of these factors on search response times. First, we found that response times were faster on target-present trials compared to target-absent trials. Second, response times increased with the number of stimulated sites, suggesting a serial search process. Third, search performance differed depending on stimulus frequencies. This frequency-dependent behavior may be related to perceptual grouping effects based on timing cues. We constructed models to explore how the locations of the tactile cues influenced search behavior. Our modeling results reveal that, in isolation, cues on the index fingers make relatively greater contributions to search performance compared to stimulation experienced on other body sites. Additionally, co-stimulation of sites within the same limb or simply on the same body side preferentially influence search behavior. Our collective findings identify some principles of attentional search that are common to vision and touch, but others that highlight key differences that may be unique to body-based spatial perception. New & Noteworthy Little is known about how we selectively experience multi-site touch over the body. Using a tactile analog of the classic visual search paradigm, we show that tactile search behavior for flutter cues is generally consistent with a serial search process. Modeling results reveal the preferential contributions of index finger stimulation and two-site interactions involving ipsilateral and within-limb patterns. Our results offer initial evidence for spatial and temporal principles underlying tactile search behavior over the body.
“Zebrafish as an animal model for food safety research: trends in the animal research”

ABSTRACT Toxicity studies in mammals continue to be the most appropriate model for predicting risk in humans, but they tend to be expensive and time-consuming. In the aftermath of the genetic sequencing of zebrafish (Danio rerio), this species is highly genetically homologous to humans. The use of the zebrafish model to assess food toxicity is already a reality as it is capable of biological processes difficult to reproduce in vitro. Studies of complex mechanisms of absorption, distribution, metabolism, and excretion as well as cellular and tissue interactions are of great information value resulting in time, space and cost savings, when compared to studies with rodents. This review addresses the relevance of zebrafish model in food safety research, both in the use of ingredients and approved and generally recognized as safe food additives as well as for establishing levels of safe food contaminant residues present in the environment. Toxicological screening using the zebrafish model integrate the evaluation of teratogenicity, cardiotoxicity, hepatotoxicity, genotoxicity, neurotoxicity, endocrine toxicity, reproductive and behavioral aspects. These are important endpoints for food safety assessment, which take substantially less time than in mammalian tests. Furthermore, it serves well as a screening test follow-up for validating favorable results in murine models, hence accelerating the risk assessment process of products submitted for approval and registration, prioritizing safe compounds and reducing unnecessary costs in subsequent mammalian studies. In conclusion, the zebrafish model can be a useful tool for food safety tests; however, additional studies are needed to further validate this model for registration of new food ingredients and additives.
The demographic pattern of infection with chronic wasting disease in reindeer at an early epidemic stage

Infection patterns linked to age and sex are crucial to predict the population dynamic effects of diseases in long-lived species. How such demographic patterns of infection arise is often multifactorial, although the cause is commonly seen as a combination of immune status as well as variation in pathogen exposure. Prion diseases are particularly interesting, as they do not trigger an adaptive immune response; hence, differences in pathogen exposure linked to behavior could be the prime determinant of the pattern of infection. In cervids, the fatal prion disease, chronic wasting disease (CWD), is spreading geographically, with economic and cultural consequences in affected areas in North America, and all infected individuals eventually die from disease-associated sequelae if they live long enough. Understanding the causes of the demographic pattern of infection with CWD is therefore urgent but is limited by the fact that reported data primarily come from related deer species in North America. The recent (detected 2016) emergence of CWD among wild alpine reindeer (Rangifer tarandus) in Norway with a different social organization, that is, no home range behavior and no matrilineal female groups, offers an opportunity to advance our understanding of how behavior influences the infection patterns. Testing of 1081 males and 1278 females detected 19 animals positive for abnormal prion protein in brain and/or lymphatic tissues. No calves and only one male yearling were infected, with the remaining positives being adults (representing 1.5% of adult males and 0.5% of adult females). We found a strong sex-biased infection pattern in reindeer (with infection 2.7 times more likely in adult males), which is similar to the results reported in mule deer and white-tailed deer. The hazard of being detected as positive increased with age in males. There was no close genetic relatedness among positive animals. The results were consistent with the within-group contact of males being a possible major route of transmission. We discuss the demographic pattern of infection with CWD in view of the lack of stable home range behavior and other key behavioral traits of reindeer relevant to understanding pathogen exposure in general.
Lipid-Mediated Insertion of Toll-Like Receptor (TLR) Ligands for Facile Immune Cell Engineering

Cell-based immunotherapies have tremendous potential to treat many diseases, such as activating immunity in cancer or suppressing it in autoimmune diseases. Most cell-based cancer immunotherapies in the clinic provide adjuvant signals through genetic engineering to enhance T cell functions. However, genetically encoded signals have minimal control over dosing and persist for the life of a cell lineage. These properties make it difficult to balance increasing therapeutic efficacy with reducing toxicities. Here, we demonstrated the potential of phospholipid-coupled ligands as a non-genetic system for immune cell engineering. This system provides simple, controlled, non-genetic adjuvant delivery to immune cells via lipid-mediated insertion into plasma membranes. Lipid-mediated insertion (depoting) successfully delivered Toll-like receptor (TLR) ligands intracellularly and onto cell surfaces of diverse immune cells. These ligands depoted into immune cells in a dose-controlled fashion and did not compete during multiplex pairwise loading. Immune cell activation could be enhanced by autocrine and paracrine mechanisms depending on the biology of the TLR ligand tested. We determined that depoted ligands can functionally persist on plasma membranes for up to four days in naïve and activated T cells, enhancing their activation, proliferation, and skewing cytokine secretion. Depoted ligands provide a persistent yet non-permanent adjuvant signal to immune cells that may minimize the intensity and duration of toxicities compared to permanent genetic delivery. Altogether, these findings demonstrate potential for lipid-mediated insertion (depoting) as a universal cell engineering approach with unique, complementary advantages to other cell engineering methods.
Cranial morphology and phylogenetic relationships of the Middle Permian pareiasaur Embrithosaurus schwarzi from the Karoo Basin of South Africa

Pareiasaurs were globally distributed, abundant, herbivorous parareptiles of the Middle to Late Permian, with the basal-most members found in the Middle Permian of South Africa. These basal taxa were particularly abundant and went extinct at the end of the Gaudalupian (Capitanian) at the top of the Tapinocephalus Assemblage Zone. Currently four taxa are recognized in this group: Bradysaurus seeleyi, B. baini, Nochelesaurus alexanderi and Embrithosaurus schwarzi, but they are all poorly understood. We here present the first detailed cranial description and updated diagnosis for Embrithosaurus schwarzi. No cranial autapomorphies were identified. However, Embrithosaurus schwarzi is a distinct taxon in this group, based on its unique dentition and using a combination of cranial features. It has nine marginal cusps on all maxillary and mandibular teeth, and wider maxillary teeth than in the co-occurring taxa, due to the marginal cusps being arranged more regularly around the crown, and the apex of the crown lacking the long, central, three-cusped trident. Our updated phylogenetic analysis recovers the four Middle Permian South African taxa as a monophyletic group for the first time, which we call Bradysauria, comprising a clade including Embrithosaurus, Bradysaurus baini and a polytomy including Nochelesaurus and Bradysaurus seeleyi.
Effect of Xueshuantong on Serum D-dimer and High Sensitivity C-reactive Protein in Patients with Actue Cerebral Infarction

Objective: To observe the effect of xueshuangtong on serum D-dimer and high sensitivity C-reactive protein in patients with ACI. Methods: Sixty-eight patients with ACI were randomly divided into two groups. One group received conventional treatment(control group) and the other received additional intravenous drip 0.5 g of xueshuantong per day besides conventional medications(treatment group). Serum concentrations of D-dimer and hs-CRP in the two groups were measured before the treatment and on 3 rd, 7 th and 14 th day respectively after treatment. Results: Compared with control group, the serum levels of D-dimer and hs-CRP in treatment group decreased significantly on the 3rd, 7th and 14th day after treatment(P 0.05), while scores of MESSS and BI in treatment group improved obviously on 7 th and 14 th day after treatment(P 0.05). The markedly effective rate and the total effective rate of treatment group were significantly than those of control group(P 0.05). Conclusion: Xueshuangtong may reduce serum levels of D-dimer and hs-CRP and have neurprotection role. The results showed that Xueshuangtong may represent an effective treatment of ACI.
Genetic differentiation and diversity of sugarbeet germplasm resistant to the sugarbeet root maggot

Abstract Germplasm lines with resistance to the sugarbeet root maggot (SBRM) have been developed and released to the public, providing a means to generate hybrids with resistance against the most devastating insect pest of sugarbeet in North America. Effective use of this germplasm, however, requires knowledge of relative strengths of SBRM resistance between lines and knowledge of the diversity and genetic relationships between germplasm. Therefore, field studies comparing SBRM resistance of four released SBRM-resistant germplasm lines (F1015, F1016, F1024 and F1043), a SBRM-resistant parent (PI 179180) and an unreleased SBRM-resistant population (F1055) were performed, and genetic analysis of the diversity and relationships between SBRM-resistant germplasm and their available parents was conducted using simple sequence repeat (SSR) markers. Under natural SBRM infestations, resistant germplasm exhibited significantly less SBRM damage than a susceptible control, with similar, high levels of resistance in F1016, F1024, F1043, F1055 and PI 179180 and lower resistance in F1015. SSR analysis revealed genetic similarities between F1016, F1024 and F1055, while F1015 and F1043 were genetically distinct from these lines. Among resistant genotypes, F1015 and F1043 exhibited greatest and least within-line genetic diversity, indicating greater and lesser inbreeding for F1043 and F1015, respectively. Similarities in damage ratings and genetics for F1016, F1024 and F1055 indicate that these lines are likely to be equally effective at introducing SBRM resistance into elite populations and in combining ability. In contrast, F1043, with its unique parentage and genetic dissimilarity from other resistant lines, provides a genetically distinct, but similarly effective, source of SBRM resistance.
Association between 677C/T polymorphism of methylenetetrahydrofolate reductase gene and type 2 diabetes with macrovascular complications in Shanghai

Objective To explore the relationship between 677C/T polymorphism of methy lenetetrahydrofolate reductase (MTHFR) gene and diabetic macrovascular complications (including cerebral infarction and coronary heart disease) in Shanghai.Methods Among 416 Chinese subjects, 216 were in macrovascular disease group 〔the atherosclerosis (AS) group〕 which included cerebral infarction (CI) subgroup consisting of 111 subjects (50 cases with and 61 without diabetes) and coronary heart disease (CHD) subgroup consisting of 105 subjects (48 with and 57 without diabetes); 100 subjects were in diabetes group without macrovascular disease (DM); and 100 normal subjects in control group (C). Genotypes were determined by PCR/restriction enzyme digestion and the relationship between 677C/T polymorphism and diabetic macrovascular complications was studied by population based association analysis. Results The frequencies of MTHFR TT genotype and T allele were significantly higher in macrovascular disease group. Logistic regression analysis showed that MTHFR gene was a potential contributor to AS. Comparison of genotype frequencies between diabetic and non diabetic subgroups in macrovascular disease group revealed no difference. Significant difference of high density lipoprotein cholesterol and diastolic blood pressure between different genotype subgroups was observed within some macrovascular disease groups after stratification by sex and diabetes. Conclusion MTHFR contributes to the development of macroangiopathy (cerebral infarction and coronary heart disease) whether associated with type 2 diabetes or not in Shanghai district.
The left angular gyrus is causally involved in information buffering and context formation: evidence from a narrative reading task

The role of the left angular gyrus (Ag) in semantic processing remains unclear. In this study, we used transcranial magnetic stimulation (TMS) to test the hypothesis that the left Ag supports the information buffering processes necessary for context-dependent semantic integration (narrative reading task). We applied online TMS to the left Ag to disrupt the buffering processes while female and male human participants integrated information between two paragraphs of text presented sequentially (i.e., context and target conditions). We assessed the effect of TMS on the left Ag by recording reading times for target conditions during the reading task and by asking participants to retrieve contextual information given the target condition as cue in a successive memory task. TMS applied over the left Ag during the reading task impaired the retrieval of contextual information in the memory task without affecting reading times. These results suggest that the Ag supports information buffering and context formation. This study provides the first evidence of a causal role of the left Ag in language tasks that require context-dependent semantic integration. Significance statement The present study offers novel insights into the processes that are associated with the left angular gyrus (Ag) activation during context-dependent naturalistic language processing. We used TMS while human participants read written narratives to interfere with online language integration. We measured how TMS over the left Ag was affecting reading times and retrieval of integrated narrative representations. We were able to show that the left Ag is causally involved in information buffering and context formation.
Role of a versatile peptide motif in controlling Hox nuclear export and autophagy in the Drosophila fat body

Hox proteins are major regulators of embryonic development, acting in the nucleus to regulate the expression of their numerous downstream target genes. By analyzing deleted forms of the Drosophila Hox protein Ultrabithorax (Ubx), we revealed the presence of an unconventional Nuclear Export Signal (NES) that overlaps with the highly conserved hexapeptide (HX) motif. This short linear motif was originally described as mediating the interaction with the PBC proteins, a generic and crucial class of Hox transcriptional cofactors in development and cancer. Here we show that the HX motif is involved in the interaction with the major CRM1/Embargoed exportin protein. This novel role was found in several Drosophila and human Hox proteins. We provide evidence that HX-dependent Hox nuclear export is tightly regulated in the Drosophila fat body to control the onset of autophagy. Our results underline the high molecular versatility of a unique short peptide motif for controlling context-dependent activity of Hox proteins at both transcriptional and non-transcriptional levels.
Characterization of the complete mitochondrial genome of lesser grain borer Rhyzopertha dominica Fabricius (Insecta: Coleoptera: Bostrichidae) from Jingziguan

Abstract The lesser grain borer, Rhyzopertha dominica (Fabricius) is a primary pest of starch-containing stored products worldwide. Here, we report characterization of mitogenome of R. dominica and its phylogenetic position. Rhyzopertha dominica complete mitochondrial genome (GenBank accession number MN527959) from Jingziguan town consisted of a circular DNA molecule of 15,862 bp (with 74.36% A + T content). The mitogenome comprised of 13 protein-coding genes (PCGs), and 22 tRNA and two rRNA genes. PCGs had typical ATN (Met) initiation codons and were terminated by typical TAN stop codons.