Miracle-dz/UniFAR-FTUs huggingface dataset:
Rescue, ecology and conservation of a rediscovered island endemic fern (Anogramma ascensionis): ex situ methodologies and a road map for species reintroduction and habitat restoration.

Last seen in 1958, the Ascension Island endemic fern, Anogramma ascensionis, was listed as extinct on the 2003 IUCN Red List. However, a 2009 survey rediscovered four plants on Green Mountain. Spores were collected and cultured in vitro at the Royal Botanic Gardens, Kew, where a living collection of thousands of gametophytes and hundreds of sporophytes has been developed. To gain further insights into the biology of this species and the potential implications of in vitro multiplication for conservation purposes, samples were characterized from the karyological point of view. Chromosome analysis of root tips has confirmed that the species is tetraploid, and flow cytometry assessments have revealed that haploid gametophytes produce diploid sporophytes, which confirms natural fertilization. In addition, an rbcL sequence from A. ascensionis has been generated and compared with those published for other Anogramma spp. , suggesting a close relationship with A. chaerophylla from Brazil. Further surveys of Green Mountain have reported the presence of 40 A. ascensionis sporophytes in total. Vegetation community analyses have suggested that the present population may be confined to suboptimal habitats. We therefore propose that, prior to the dramatic transformation of the vegetation on the island as a result of the invasion of alien species (particularly Adiantum spp.), A. ascensionis may have flourished in more humid and shaded parts of the mountain. A multidisciplinary approach involving in vitro culture, invasive species clearance and controlled translocation is discussed as the future roadmap for the conservation of this critically endangered fern. Our experiences have also highlighted lessons more broadly applicable to the conservation of extremely rare species elsewhere in the world, especially on remote island systems. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 174, 461–477.
Optical coherent discrimination of peptides and plasma proteins

Cette these presente l'application du controle coherent pour la discrimination et l'identification des biomolecules dans la phase condensee. Les experiences de controle coherent sont effectuees dans le cadre de la discrimination optimale dynamique (ODD), qui est basee sur la modification de phase d’impulsions femtosecondes dans l’ultraviolet profond. L'objectif principal de ce travail est de demontrer que la fluorescence intrinseque des acides amines naturellement presents dans les proteines peut etre utilisee comme indicateur pour leur dosage, ce qui permet d'eliminer l'utilisation de tout autre marqueur fluorescent supplementaire. Dans la premiere partie, nous utilisons l'ODD pour moduler selectivement l’extinction de la fluorescence des paires de dipeptides contenant du tryptophane: alanine-tryptophane, cyclo(glycine-tryptophane) et cyclo(leucine-tryptophane). Dans la deuxieme partie, nous etendons l'approche ODD par l’application d'impulsions UV modulees en phase pour des proteines du plasma sanguin. Ces experiences montrent que notre approche pourrait etre developpee plus loin pour l'identification des proteines directement dans le plasma humain.
Multiparametric assessment of apical versus septal pacing study using Cardiac Magnetic Imaging

Evaluation of left ventricular torsion using cardiac MRI. Validation of feature tracking. Ainslie MP, Reid A, Miller C, Clark D, Francis L, Schmitt M. Journal of cardiovascular magnetic resonance. 2015. 17 (suppl 1): O47. MAPS; acute safety data of the St Jude accenttendril IPG system during prolonged max power CMR scanning. Ainslie M, Reid A, Miller C, Clark D, Brown B, Fox D, Davidson N, Trafford A, Schmitt M. Journal of cardiovascular magnetic resonance. 2015. 17 (Suppl 1): M6. Multiparametric CMR Assessment of RV apical versus septal pacing study (MAPS)Preliminary acute hemodynamic findings. Ainslie M, Miller C, Brown B, Fox D, Davidson N, Trafford A, Schmitt M. Heart 2013; 99: suppl 2 A50. Multiparametric CMR assessment of RV apical versus septal Pacing Study (MAPS) preliminary acute hemodynamic findings. Ainslie M, Miller CA, Brown B, Davidson N, Fox DJ, Schmitt M. Journal of Cardiovascular Magnetic Resonance. 2013; 15(suppl 1):O85.
Los vínculos entre la investigación sobre agrotóxicos y multinacionales agroindustriales: el caso del glifosato

aDepartamento Tratamiento y Transferencia de Información, Facultad de Información y Comunicación, Universidad de la República. Montevideo, Uruguay. bLaboratorio de Desarrollo Sustentable y Gestión Ambiental del Territorio, Geografía, Instituto de Ecología y Ciencias Ambientales, Facultad de Ciencias, Universidad de la República. Montevideo, Uruguay. cDepartamento de Sistemas Ambientales, Facultad de Agronomía, Universidad de la República, Montevideo, Uruguay. dDepartment of Environmental Science, Policy and Management, University of California, Berkeley, California, USA. Autor correspondencia: exequiel.fontans@fic.edu. uy, achkar@fcien.edu. uy.
Lamiaceae plant extracts and isolated compounds demonstrate activity against HIV/AIDS

Background: Lamiaceae plants are traditionally used in African countries to treat viral and microbial ailments. Several Lamiaceae species are specifically used by traditional medicine practitioners to manage HIV/AIDS and associated opportunistic infections. The aim of this study was to evaluate the inhibitory properties of extracts of several Lamiaceae plants against HIV-1 protease (PR), reverse transcriptase (RT) and virus expression in a chronic infection model in order to contribute some scientific evidence for the apparently successful traditional use against HIV/AIDS. Methods: Crude extracts were prepared from the leaves of fourteen Lamiaceae plants. These extracts were first tested for inhibitory activities against HIV-1 enzymes (PR and RT). Cytotoxicity was also investigated in TZM-bl cells and human peripheral blood mononuclear cells (PBMCs). Extracts that inhibited HIV-1 enzymes were screened for their ability to suppress HIV-1 replication in a chronically infected monocytic U1 cell line at non-cytotoxic concentrations because the enzyme inhibitory activity suggested a possible viral prevention mechanism. Results: Phorbol 12-myristate 13-acetate (PMA)-induced HIV-1 expression, as determined by HIV-1 p24 antigen ELISA, was significantly (p<0.05) reduced in U1 cells by Ocimum serratum, Salvia apiana and Stachys byzantina extracts at non-cytotoxic CHAPTER 3 Lamiaceae plant extracts suppress HIV-1 expression in chronically infected monocytic cells © University of Pretoria CHAPTER 3 INHIBITION OF HIV-1 REPLICATION 43 | P a g e concentrations. The same extracts inhibited HIV-1 PR and RT. CC50 values of the three extracts ranged from 33.6 to >100 μg/ml which translates to low toxicity. Conclusions: This study provides evidence that O. serratum, S. apiana and S. byzantina extracts inhibit HIV-1 replication, presumably by blocking HIV-1 enzymes PR and RT, and supports the traditional use of these plants in the treatment of HIV/AIDS.
Regulation and transcriptional role of CRTC1 during activity in neurons

Author(s): DeSalvo, Martina | Advisor(s): Martin, Kelsey C | Abstract: Long term memory is mediated by long-lasting forms of synaptic plasticity that require new gene transcription for their persistence. Previous work has shown that neuronal CREB-regulated transcriptional coactivator 1 (CRTC1) plays a crucial role during learning and memory by regulating activity-dependent gene expression. We have shown that CRTC1 undergoes synapse-to-nucleus translocation to regulate transcription of CREB target genes in response to neuronal activity. In this thesis, we investigate the regulation and retrograde transport of CRTC1 in neurons and examine the nuclear role of CRTC1 in activity-dependent gene transcription. Our first goal was to identify the mechanisms by which CRTC1 responds to activity. We describe key synaptic processes necessary to trigger dephosphorylation of three serine residues that are required for dynein-mediated transport of CRTC1 to the nucleus. Our second goal was to understand the role of CRCT1 as a transcriptional coactivator. We use a combination of ChIP-seq, ATAC-seq and RNA-seq to understand how CRTC1 binding to CREB and other transcription factors correlates with changes in chromatin accessibility and transcription of activity-induced genes. Finally, we summarize a series of projects that attempt to elucidate how regulation of CRTC1’s phosphorylation code may influence its function in neurons. These studies highlight the complexities of CRTC1 as an intrinsically disordered protein with 50 phosphorylated residues and a variety of potential interacting partners.
Genetic variation on confiscated pangolin of Sumatra, Jawa, and Kalimantan based on control region mitochondrial DNA.

diperdagangkan secara terjadinya penurunan populasi Tujuan penelitian ini adalah untuk melihat tingkat kualitas keragaman genetik trenggiling serta mengetahui asal usul satwa sitaan berdasarkan analisis molekuler. Sebagai kontrol asal usul trenggiling sitaan digunakan sampel alam berdasarkan sebaran populasi yang diketahui pasti yang berasal dari Jawa, Kalimantan, dan Sumatera. Analisis molekuler menggunakan daerah non coding control region (D-loop) mitokondrial DNA (mtDNA). Hasil analisis dari pohon filogeni menunjukkan bahwa dari 44 sampel trenggiling sitaan terindikasi berasal dari Kalimantan sebanyak 24 individu, asal Sumatera tujuh individu, dan dari populasi Jawa 13, sementara rataan jarak genetik (d) antara Kalimantan-Jawa d= 0,0121±0,0031; Kalimantan-Sumatera d= 0,0123±0,0038; dan Sumatera-Jawa d= ABSTRACT High levels of illegal trading on Java pangolin ( Manis javanica, Desmarest. 1822 ) for the basic ingredient of Traditional Chinese Medicine have caused sharp decline in its wild population. The purposes of this study were to assess the level of quality and genetic diversity, and to identify the origin of the confiscated individuals by molecular analysis. The original species used as a control were obtained from known areas in Java, Kalimantan, and Sumatera. Molecular analysis was carried out using non-coding region control region (D-loop) of mitochondrial DNA (mtDNA). The results of phylogenic tree analysis showed that 44 confiscated pangolins were from Kalimantan (24 individuals), from Sumatra (seven individuals), and from Java (13 individuals). As many as 19 haplotypes were found on the basis of their base substitutions consisting of nine from Kalimantan, seven from Java and three from Sumatra. Average genetic distance (d) between those from Kalimantan-Java was d = 0.0121 ± 0.0031; those from Borneo-Sumatra was d = 0.0123 ± 0.0038 and those from Sumatra-Java was d = 0.0075 ± 0.038, respectively. Overall genetic distance between populations was d = 0.0148 ± 0.0035, with the nucleotide diversity (ð) of 0.0146. These results indicate that over 50% of pangolins seized came from Kaimantan, and Kalimantan populations show a separate group with Java and Sumatra with boostrap 98%.
Shed female caribou antlers extend records of calving activity on the Arctic National Wildlife Refuge by millennia

Caribou (Rangifer tarandus) have among the longest annual migrations of any terrestrial mammal as they move from winter ranges to spring calving grounds. Biomonitoring records indicate broad consistencies in calving geography across the last several decades, but how long have herds used particular calving grounds? Furthermore, how representative are modern patterns of calving geography to periods that pre-date recent climatic perturbations and increased anthropogenic stresses? While modern ecological datasets are not long enough to address these questions, bones from past generations of caribou lying on the tundra provide unique opportunities to study historical calving geography. This is possible because female caribou shed their antlers within days of giving birth, releasing a skeletal indicator of calving. Today, the Coastal Plain of the Arctic National Wildlife Refuge (Alaska) is a key calving ground for the Porcupine Caribou Herd (PCH). To test the duration across which caribou have used this area as a calving ground, we radiocarbon dated three highly weathered female antlers collected from tundra surfaces on the Coastal Plain. Calibrated radiocarbon dates indicate that these antlers were shed between ~1,600 and more than 3,000 calendar years ago. The antiquity of these shed antlers provides the first physical evidence of calving activity on the PCH calving grounds from previous millennia, substantiating the long ecological legacy of the Coastal Plain as a caribou calving ground. Comparisons to published lake core records also reveal that dates of two of the antlers correspond to periods with average summer temperatures that were warmer than has been typical during the last several decades of biomonitoring. This finding expands the range of climatic settings in which caribou are known to use the current PCH calving grounds and suggests that the Coastal Plain of the Arctic Refuge may remain an important caribou calving ground during at least portions of predicted future warming. Discarded skeletal materials provide opportunities to assess the historical states of living populations, including aspects of reproductive biology and migration. Particularly in high-latitude settings, these insights can extend across millennia and offer rare glimpses into the past that can inform current and future management policies.
Combination of platelet-to-lymphocyte ratio and D-dimer for the identification of cardiogenic cerebral embolism in non-valvular atrial fibrillation

Background Non-valvular atrial fibrillation (NVAF) is the most common cause of cardiogenic cerebral embolism (CCE). However, the underlying mechanism between cerebral embolism and NVAF is indefinite, and there is no effective and convenient biomarker to identify potential risk of CCE in patients with NVAF in clinic. The present study aims to identify risk factors for interpreting the potential association of CCE with NVAF and providing valuable biomarkers to predict the risk of CCE for NVAF patients. Methods 641 NVAF patients diagnosed with CCE and 284 NVAF patients without any history of stroke were recruited in the present study. Clinical data including demographic characteristics, medical history, and clinical assessments, were recorded. Meanwhile, Blood cell counts, lipid profiles, high-sensitivity C-reactive protein, and coagulation function-related indicators were measured. Least absolute shrinkage and selection operator (LASSO) regression analysis was utilized to build a composite indicator model based on the blood risk factors. Results (1) CCE patients had significantly increased neutrophil-to-lymphocyte ratio, platelet-to-lymphocyte ratio (PLR), and D-dimer levels as compared with patients in the NVAF group, and these three indicators can distinguish CCE patients from ones in the NVAF group with an area under the curve (AUC) value of over 0.750, respectively. (2) Using the LASSO model, a composite indicator, i.e., the risk score, was determined based on PLR and D-dimer and displayed differential power for distinguishing CCE patients from NVAF patients with an AUC value of over 0.934. (3) The risk score was positively correlated with the National Institutes of Health Stroke Scale and CHADS2 scores in CCE patients. (4) There was a significant association between the change value of the risk score and the recurrence time of stroke in initial CCE patients. Conclusions The PLR and D-dimer represent an aggravated process of inflammation and thrombosis in the occurrence of CCE after NVAF. The combination of these two risk factors can contribute to identifying the risk of CCE for patients with NVAF with an accuracy of 93.4%, and the greater in change of composite indicator, the shorter in the recurrence of CCE for NVAF patients.
Diversity and evolutionary biology of tropical flowers

1. Introduction 2. Floral organisation (bauplan, groundplan) 3. Floral construction (architecture, gestalt) 4. Floral adaptations to different pollinators (floral styles) 5. Special differentiations associated with pollinator attraction 6. Special differentiations associated with the breeding system 7. The process of anthesis 8. Floral structure: biology of selected systematic groups in the tropics 9. Aspects of flower evolution 10. Prospects Index.
Development of a simplified NASBA protocol for detecting viable cells of the citrus pathogen Xanthomonas citri subsp. citri under different treatments

Nucleic acid sequence based amplification (NASBA) is a method of amplifying RNA, for the detection of RNA viruses and human pathogenic bacteria. Recently, NASBA has also been employed for the detection of plant diseases caused by viruses and quarantine bacteria. A major citrus pathogen, Xanthomonas citri subsp. citri (Xcc), causal agent of citrus bacterial canker, is being studied in depth due to its economic importance, with recent focus concentrating on its viability and survival under different stress conditions and control treatments. In this work, a NASBA protocol using primers for gumD mRNA has been developed to assess the viability of this pathogen under different bacteriocidal treatments. This method is rapid, specific and sensitive, and is able to detect viable bacterial cells, using a hybridization device which allows the visualization of the results in only 30 min. The usefulness of the method has been confirmed with bacterial suspensions subjected to different heat treatments and to sodium orthophenylphenate.
Genomic sequencing and molecular characteristics of a very virulent strain of infectious bursal disease virus isolated in China.

[Objective] The paper was to determine the genomic sequence of a very virulent strain of infectious bursal disease virus(IBDV),and study its molecular characteristics. [Method] A very virulent strain(vvIBDV)(HLJ-0504) of infectious bursal disease virus(IBDV) with special characters was isolated in China and its genome was sequenced. [Result] Sequence analysis showed that segment A of HLJ-0504 was derived from vvIBDV,while segment B was from a distinct ancestor.The morbidity and mortality of HLJ-0504 was 100% and 86.7%to SPF chickens,respectively. [Conclusion] vvIBDV with distinct segment B were still circulating and the evolution of IBDV was diversified in China.Besides,it is hard to imagine that the virulence of IBDV is determined solely by segment A or B.
The Woman That Never Evolved

This work argues that evolutionary theorists' emphasis on sexual competition among males for access to females overlooks selection pressures on females themselves. In an account of what female primates themselves actually do to secure their own reproductive advantage, Sarah Hrdy demolishes myths about sexually passive, "coy", compliant and exclusively nurturing females. Her account of the great range of behaviours in many species of primates, in many circumstances, expands the concept of female nature to include the range of selection pressures on females, and reminds the reader of the complexity and dynamism of the evolutionary story.
Advanced delivery and therapeutic applications of RNAi

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The effects of heat stress and nutritional status on metabolism and intestinal integrity in growing pigs

Heat stress (HS) negatively affects pig performance variables and is thus a costly industry issue. It is unknown whether or not HS directly or indirectly (via reduced feed intake) is responsible for the suboptimal production. To account for differences in nutrient intake, we utilized an ad-libitum thermal neutral control group and a pair-fed thermal neutral control group of pigs. In these experiments, pigs in HS conditions had increased body temperatures, reduced feed intake, and lighter body weights compared to controls. Presumably, this production difference may also includes a difference in body composition as HS pigs have increased circulating insulin levels, decreased basal lipolysis, and increased adipose tissue lipogenesis compared to bioenergetic controls. In addition, HS pigs had increased markers of protein catabolism. Heat stress pigs also had compromised intestinal integrity, but this appears to be due to be confounded by reduced nutrient intake, as pair-fed controls had similar intestinal dysfunction characteristics. In conclusion, heat stress directly and indirectly (via reduced feed intake) affects post-absorptive metabolism and intestinal integrity and both variables probably contribute to decreased growth parameters in young pigs.
Genetic variation for sexual dimorphism in flower size within and between populations of gynodioecious Thymus vulgaris

There has been very little empirical study of quantitative genetic variation in flower size in sexually dimorphic plant species, despite the frequent occurrence of flower size differences between sexual phenotypes. In this study we quantify the nature of quantitative flower size variation in females and hermaphrodites of gynodioecious Thymus vulgaris. In a field study, females had significantly smaller flowers than hermaphrodites, and the degree of flower size dimorphism varied significantly among populations. To quantify the genetic basis of flower size variation we sampled maternal progeny from 10 F0 females in three populations (across the range of variation in flower size in the field), performed controlled crosses on F1 offspring in the glasshouse and grew F2 progeny to flowering in uniform field conditions. A significant population * sex interaction was again observed, hence the degree of sexual dimorphism shows genetic variation among populations. A significant family * sex interaction was also observed, indicating that the degree of sexual dimorphism shows genetic variation among families. Females showed significantly greater variation among populations and among families than hermaphrodites. Female flower size varied significantly depending on the degree of stamen abortion, with morphologically intermediate females having flowers more similar to hermaphrodites than to other females. The frequency of female types that differ in the degree of stamen abortion varied among populations and families and mean family female flower size increased as the proportion of intermediate female types increased across families. Variation in the degree of flower size dimorphism thus appears to be a result of variation in the degree of stamen abortion in females, the potential causes of which are discussed.