Miracle-dz/UniFAR-FTUs huggingface dataset:
Genealogy of the nuclear β-fibrinogen intron 7 in Lissotriton boscai (Caudata, Salamandridae): concordance with mtDNA and implications for phylogeography and speciation

The power of phylogeographic inference resides in its ability to integrate information from multiple sources in an iterative hypothesis-testing framework. In this paper, we build upon previous mtDNA-based hypotheses about the evolutionary history of the Iberian newt Lissotriton boscai using sequences of the highly variable nuclear β-fibrinogen intron 7. In addition to the nuclear sequences, we produced new mtDNA data across the species range to delineate contact zones and test the congruence between nuclear and mitochondrial datasets at the same level of spatial organization. Through a combination of phylogenetic, phylogeographic continuous diffusion, and genetic landscape modelling analyses, we infer the evolutionary history of the species. We found notable congruence between nuclear and mtDNA datasets, which confirms deep and consistent differentiation between two major lineages that originated in the Miocene. Additionally, we found a new nuclear haplogroup with no mtDNA counterpart, roughly circumscribed to the Iberian Sistema Central mountains, and extensive areas of nuclear admixture across mtDNA lineages. We describe potential historical dispersal routes from an ancestral hypothetical refugium in the western end of the Sistema Central in central Portugal and highlight how deep phylogeographic breaks do not necessarily indicate cryptic speciation events.
Karyotypes of Three Species of Lepidoptera Including an Investigation of B-chromosomes in Pieris

Chromosome banding techniques have been used to compare the karyotypes of Pieris rapae and P. napi. The basic complements (both n=25) are very similar but clear differences are present and these are discussed in detail. (A brief comparison is made with Pieris brassicae, n=15). Cytological techniques have confirmed the presence of a constriction (primary centromere) in the Pieris species and also in a member of the Satyridae (Pyronia tithonas, n=29). Supernumerary B-chromosomes were discovered in both P. rapae and P. napi. Hitherto these have been reported only in the Japanese races of these species and in a small number of Finnish P. rapae individuals and it has usually been as sumed that they are absent from populations in the rest of the world. The characteristics of the B-chromosomes differ both numerically and struc turally between the two species and the variations are discussed. 282 T. R. L. Bigger Cytologia 41 No phenotypic differences exist between individuals with and without B chromosomes.
The impact of host-microbe interactions on murine colonic secretomotor function

The impact of host-microbe interactions on murine colonic secretomotor function Author(s) Lomasney, Kevin W. Publication date 2014 Original citation Lomasney, K. W. 2014. The impact of host-microbe interactions on murine colonic secretomotor function. PhD Thesis, University College Cork. Type of publication Doctoral thesis Rights © 2014, Kevin W. Lomasney. http://creativecommons.org/licenses/by-nc-nd/3.0/
SYMPOSIUM OVERVIEW Endocrine Modulation of Reproduction 1

STEVENS, J. T. , HUGHES, C. L. , KELCE, W. R. , HESS, R. A. , AND DASTON, G. P. (1995). Fundam. AppL ToxicoL 29, 1-17. The ability of foreign compounds to affect the functioning of various endocrine systems is currently thought responsible for a wide variety of effects. The presentations in this Symposium reviewed the evidence for and against the involvement of endocrine systems in several different aspects of reproduction. The mechanism behind the ability of a triazine herbicide to cause enhanced appearance of mammary tumors in one strain of female rats is reviewed by Stevens. The data suggest that enhanced aging, not direct mammary modulation, is responsible. Dietary phytoestrogens, the mediators of their actions, their effects in various biological systems, and the relationships between phytoestrogen producers and consumers are all provocatively and succinctly reviewed by Hughes. Kelce presents the strategy used to dissect the mode and mechanisms of action of a fungicide that opened a new awareness in reproductive toxicology: the possibility of xenobiotics being antiandrogens. Finally, to heighten our understanding of the interplay among hormonal systems in vivo, Hess reviews the data that show that androgens are not the only hormones important in the development of the male reproductive system: the pituitary is shown to play a critical role at specific stages of development The breadth of these presentations, and the implications of their findings, should make us pause and realize how much there is still to discover about the interaction between the reproductive system and anthropogenic compounds, o
Strategies for whole-exome sequencing analysis in a case series study of familial male infertility

Abstract Background Infertility is one of the common health issues around the world. The prevalence of male factor infertility among infertile couples is approximately 30%-35%, of which genetic factors account for 15%. The family-based whole-exome sequencing (WES) approach can accurately detect novel variants. However, selecting an appropriate sample for data generation using WES has proven to be challenging in familial male infertility studies. The aim of this study was to identify types of pathogenic male infertility in cases of familial asthenozoospermia. Case Two families with multiple cases were recruited for the purpose of WES. The study population included two affected cases in pedigree I and three affected cases in pedigree II. Two different variant callers (SAMtools and GATK) with a single-sample calling strategy (SSCS) and a multiple-sample calling strategy (MSCS), were applied to identify variant sites. Conclusion In this study, we represented the results for variant prioritization of WES data without sequencing fertile siblings in the same pedigree by applying two different pipelines (homozygosity and linkage-based strategy). Using the aforementioned strategies, we prioritized annotated variants and generated a logical shortlist of private variants for each pedigree.
Extraction of Low Methoxyl Pectin from Fresh Sunflower Heads by Subcritical Water Extraction

Subcritical water extraction (SWE) of pectin from fresh sunflower heads was optimized using the response surface methodology (RSM). The optimal conditions for the maximum yield of pectin (6.57 ± 0.6%) were found to be a pressure of 8 bar, temperature of 120 °C, time of 20 min, and liquid–solid ratio (LSR) of 7 mL/g. The degree of esterification (DE) of pectin was analyzed by titrimetry and Fourier transform infrared (FTIR) methods, which was low methoxyl pectin. The molecular weight (Mw), galacturonic acid (GalA) content, and surface tension of pectin were 11.50 kDa, 82%, and 45.38 mN/m (1.5% w/v), respectively. Moreover, thermogravimetric (TG) and differential scanning calorimetry (DSC) analysis confirmed that pectin had excellent thermal stability. FTIR and 1H NMR spectra confirmed its structure. This study demonstrated that SWE could be used as a productive and environmentally friendly method for extracting pectin from fresh sunflower heads.
Modification, Expression, and Purification of Hyperactive Antifreeze Proteins from Insect Tenebrio Molitor

Antifreeze proteins (AFPs), also known as thermal hysteresis proteins, can protect organisms from damage caused by freezing by lowering the freezing point of fluids. AFPs can bind to small ice crystals, inhibit ice growth, and change the morphology of ice crystals. The difference between the freezing temperature and the melting temperature is termed thermal hysteresis (TH). There are different types of AFPs, such as fish AFPs (type I, II, III, and IV) and insect AFPs. These AFPs can also be classified by their thermal hysteresis activity: moderately active AFPs and hyperactive AFPs. Previous research groups successfully constructed AFP (type I, and type III) multimers, and the thermal hysteresis measurement showed that the size of multimers can affect TH activities. However, how the TH of insect AFPs will be affected by multimerization is still unknown, since they already have much higher thermal hysteresis activities than fish AFPs in nature. Making active multimers of insect AFPs can be harder than type I and type III fish AFPs because of their highly disulfide-bonded structure. The aim of this thesis is to construct trimers of Tenebio molitor (TmAFP) by adding a foldon domain. The foldon domain has been added separately to N-teminus and C-terminus of TmAFP. Cold finger purification was utilized for the protein purification process. The purified proteins were then run on protein gels, demonstrating that trimers of TmAFP were successfully made, for both the N-terminus and the C-terminus foldon domains; the TmAFPs were active, indicating proper folding.
Geographies of the COVID-19 pandemic

The spread of the novel coronavirus (SARS-CoV-2) has resulted in the most devastating global public health crisis in over a century. At present, over 10 million people from around the world have contracted the Coronavirus Disease 2019 (COVID-19), leading to more than 500,000 deaths globally. The global health crisis unleashed by the COVID-19 pandemic has been compounded by political, economic, and social crises that have exacerbated existing inequalities and disproportionately affected the most vulnerable segments of society. The global pandemic has had profoundly geographical consequences, and as the current crisis continues to unfold, there is a pressing need for geographers and other scholars to critically examine its fallout. This introductory article provides an overview of the current special issue on the geographies of the COVID-19 pandemic, which includes 42 commentaries written by contributors from across the globe. Collectively, the contributions in this special issue highlight the diverse theoretical perspectives, methodological approaches, and thematic foci that geographical scholarship can offer to better understand the uneven geographies of the Coronavirus/COVID-19.
Transarterial Chemoembolization Combined With Apatinib for Advanced Hepatocellular Carcinoma: A Propensity Score Matching Analysis

Background: Apatinib is a powerful inhibitor of vascular endothelial growth factor receptor-2. This study was aimed to investigate whether apatinib could improve the efficacy of transarterial chemoembolization (TACE) in patients with advanced hepatocellular carcinoma (HCC). Methods: Between June 2015 and September 2018, 357 patients with HCC at Barcelona Clinic Liver Cancer stage C who received the treatment of TACE combining with apatinib (TACE–apatinib) or TACE-alone were included. Propensity score matching (PSM) analysis was used to reduce the patient selection bias. Results: Ninety pairs of patients were chosen after the PSM analysis. The disease control rates of tumor and a-fetoprotein response in the TACE–apatinib group were significantly higher than that of the TACE-alone group before and after the PSM analysis (P < 0.05). Before the PSM analysis, the median time of tumor progression (TTP) and the overall survival (OS) in the TACE–apatinib group were significantly greater than those of the TACE-alone group (TTP: 9.0 months vs. 3.0 months, P < 0.001; OS: 14.0 months vs. 7.0 months, P < 0.001). After the PSM analysis, the median TTP and OS in the TACE–apatinib group was also significantly greater than that of the TACE-alone group (TTP: 7.0 months vs. 3.0 months, P < 0.001; OS: 13.0 months vs. 8.0 months, P < 0.001); the uni- and multivariate analysis revealed that TACE–apatinib was a protective factor for OS. Fourteen patients emerged with grade 3 apatinib-related adverse events. Conclusion: The efficacy of TACE–apatinib for patients with advanced HCC was inspiring, and the side effects of apatinib were tolerable.
Elevated Percentage of CD3+ T-Cells and CD4+/CD8+ Ratios in Multiple System Atrophy Patients

α-synuclein is involved in the pathogenesis of multiple system atrophy (MSA) and can be regulated by peripheral immune activation (PIA). We aimed to clarify the correlations between PIA and the prevalence of MSA and to analyze the role of PIA in the progression of the disease. A total of 321 patients with probable MSA and 321 age- and gender-matched healthy controls were included in this study. Lymphocyte subsets, including CD3+, CD4+, and CD8+ cells, and the levels of immunoglobulins IgG, IgM, and IgA were evaluated. The proportions of CD3+ and CD4+ T-lymphocytes were significantly increased in MSA patients compared with those of normal controls. In addition, the ratio of CD4+ to CD8+ cells was significantly increased in male MSA patients and IgG concentrations were decreased in female MSA patients. Furthermore, the concentrations of IgM in female MSA patients were dynamically different at various disease stages and gradually decreased from the early stage until the end stage of the disease (p = 0.029). Other detected immunological indexes were not significantly different during the entire disease course. In this study, high proportions of CD3+ and CD4+ T-lymphocytes and decreased IgG levels were associated with an increased risk for MSA in a Chinese patient population. In addition, PIA may be involved in the progression of MSA.
Potential lignocellulolytic Trichoderma for bioconversion of oil palm empty fruit bunches.

An experiment was conducted to evaluate the lignocellulolytic potential of Trichoderma spp. for bioconversion of oil palm empty fruit bunches (EFB). Thirty five Trichoderma isolates were tested for in-vitro lignocellulolytic activity by assaying their ability to develop dark brown zone and clearing zone on tannic acid, carboxymethyl cellulose (CMC) and avicel-amended media. Most of the isolates were found to synthesize polyphenol oxidase, endoglucanase and cellobiohydrolase enzymes on tannic acid, CMC and avicel-amended media, respectively. Five best selected isolates (T2, T15, T17, T20 and T35) were further tested for in-vitro bioconversion of oil palm EFB. All five isolates could decrease carbon content and increase nitrogen concentration at 3 to 6 weeks of incubation; thus, leading to a significant decrease in C/N ratio. The decrease in C/N ratio of the isolates, T. harzianum and T. koningii were higher than other isolates, exhibiting the potential for rapid bioconversion of lignocellulosic EFB.
Polymorphisms in Genes Affecting Interferon-γ Production and Th1 T Cell Differentiation Are Associated With Progression to Chagas Disease Cardiomyopathy

Background: Chagas disease, caused by the protozoan Trypanosoma cruzi, is endemic in Latin America. Thirty percent of infected individuals develop chronic Chagas cardiomyopathy (CCC), an inflammatory dilated cardiomyopathy that is the most important clinical consequence of T. cruzi infection, while the others remain asymptomatic (ASY). IFN-γ and IFN-γ-producing Th1-type T cells are increased in peripheral blood and CCC myocardium as compared to ASY patients, while the Th1-antagonizing cytokine IL-10 is more expressed in ASY patients. Importantly IFN-γ-producing Th1-type T cells are the most frequent cytokine-producing T cell subset in CCC myocardium, while expression of Th1-antagonizing cytokines IL-10 and IL-4 is unaltered. The control of IFN-γ production by Th1-type T cells may be a key event for progression toward CCC. A genetic component to disease progression was suggested by the familial aggregation of cases and the association of gene polymorphisms with CCC development. We here investigate the role of gene polymorphisms (SNPs) in several genes involved in the control of IFN-γ production and Th1 T cell differentiation in CCC development. Methods: We studied a Brazilian population including 315 CCC cases and 118 ASY subjects. We assessed 35 Tag SNPs designed to represent all the genetic information contained in the IL12B, IL10, IFNG, and IL4 genes. Results: We found 2 IL12 SNPs (rs2546893, rs919766) and a trend of association for a IL10 SNP (rs3024496) to be significantly associated with the ASY group. these associations were confirmed by multivariate analysis and allele tests. The rs919766C, 12rs2546893G, and rs3024496C alleles were associated to an increase risk to CCC development. Conclusions: Our data show that novel polymorphisms affecting IL12B and IL10, but not IFNG or IL4 genes play a role in genetic susceptibility to CCC development. This might indicate that the increased Th1 differentiation and IFN-γ production associated with CCC is genetically controlled.
Histopathological study and pulmonary classification of bovine lesions

The partial or total seizures of carcasses or organs by veterinary services during inspection constitute a real constraint for butchers from the economical point of view. Results of a study carried within two years in Tiaret slaughterhouse (west of Algeria) and within three years in Batna slaughterhouse (east of Algeria) have shown a high frequency of pathological pulmonary lesions in 870 bovine lungs that were inspected. 744 lungs were concerned by these lesions. The seasonal impact of the lesions has been highly marked. The hydatid cyst was the most frequently observed lesion with 330 cases (42.64%) followed by pulmonary emphysema with 111 cases (14.35%) and pulmonary congestion with 61 cases (7.89%). According to the localization of these lesions, we have noted that the right lung was the most affected (92.60%) than the left one, and the cranial lobes were more attacked (76.90%) than the caudal ones (71.45%).
Characterization of PF-6142, a Novel, Non-Catecholamine Dopamine Receptor D1 Agonist, in Murine and Nonhuman Primate Models of Dopaminergic Activation

Selective activation of dopamine D1 receptors remains a promising pro-cognitive therapeutic strategy awaiting robust clinical investigation. PF-6142 is a key example from a recently disclosed novel series of non-catechol agonists and partial agonists of the dopamine D1/5 receptors (D1R) that exhibit pharmacokinetic (PK) properties suitable for oral delivery. Given their reported potential for functionally biased signaling compared to known catechol-based selective agonists, and the promising rodent PK profile of PF-6142, we utilized relevant in vivo assays in male rodents and male and female non-human primates (NHP) to evaluate the pharmacology of this new series. Studies in rodents showed that PF-6142 increased locomotor activity and prefrontal cortex acetylcholine release, increased time spent in wakefulness, and desynchronized the EEG, like known D1R agonists. D1R selectivity of PF-6142 was supported by lack of effect in D1R knock-out mice and blocked response in the presence of the D1R antagonist SCH-23390. Further, PF-6142 improved performance in rodent models of NMDA receptor antagonist-induced cognitive dysfunction, such as MK-801-disrupted paired-pulse facilitation, and ketamine-disrupted working memory performance in the radial arm maze. Similarly, PF-6142 reversed ketamine-induced deficits in NHP performing the spatial delayed recognition task. Of importance, PF-6142 did not alter the efficacy of risperidone in assays predictive of antipsychotic-like effect in rodents including pre-pulse inhibition and conditioned avoidance responding. These data support the continued development of non-catechol based D1R agonists for the treatment of cognitive impairment associated with brain disorders including schizophrenia.
Interfacial tuning of chiral magnetic interactions for large topological Hall effects in LaMnO3/SrIrO3 heterostructures

Deliberate control of interface symmetry boosts chiral magnetism in spin-orbit–coupled oxide heterostructures. Chiral interactions in magnetic systems can give rise to rich physics manifested, for example, as nontrivial spin textures. The foremost interaction responsible for chiral magnetism is the Dzyaloshinskii-Moriya interaction (DMI), resulting from inversion symmetry breaking in the presence of strong spin-orbit coupling. However, the atomistic origin of DMIs and their relationship to emergent electrodynamic phenomena, such as topological Hall effect (THE), remain unclear. Here, we investigate the role of interfacial DMIs in 3d–5d transition metal-oxide-based LaMnO3/SrIrO3 superlattices on THE from a chiral spin texture. By additively engineering the interfacial inversion symmetry with atomic-scale precision, we directly link the competition between interfacial collinear ferromagnetic interactions and DMIs to an enhanced THE. The ability to control the DMI and resulting THE points to a pathway for harnessing interfacial structures to maximize the density of chiral spin textures useful for developing high-density information storage and quantum magnets for quantum information science.
Geometric Affordance Perception: Leveraging Deep 3D Saliency With the Interaction Tensor

Agents that need to act on their surroundings can significantly benefit from the perception of their interaction possibilities or affordances. In this paper we combine the benefits of the Interaction Tensor, a straight-forward geometrical representation that captures multiple object-scene interactions, with deep learning saliency for fast parsing of affordances in the environment. Our approach works with visually perceived 3D pointclouds and enables to query a 3D scene for locations that support affordances such as sitting or riding, as well as interactions for everyday objects like the where to hang an umbrella or place a mug. Crucially, the nature of the interaction description exhibits one-shot generalization. Experiments with numerous synthetic and real RGB-D scenes and validated by human subjects, show that the representation enables the prediction of affordance candidate locations in novel environments from a single training example. The approach also allows for a highly parallelizable, multiple-affordance representation, and works at fast rates. The combination of the deep neural network that learns to estimate scene saliency with the one-shot geometric representation aligns well with the expectation that computational models for affordance estimation should be perceptually direct and economical.