Miracle-dz/UniFAR-FTUs huggingface dataset:
Radiation-Use Efficiency in Summer Rape

The radiation-use efficiency (RUE) is a parameter that represents a crop canopy's ability to convert intercepted solar energy to dry matter. The RUE is used in simulation models and can vary with crop type and environment. The objective was to examine the effects of varying row width and seeding rate on the amount of intercepted photosynthetically active radiation (IPAR) and the RUE in summer rape (Brassica napus L.). 'Westar' summer rape was seeded at rates of 1.5, 3.0, 6.0, and 12.0 kg ha -1 in rows spaced 15 or 30 cm apart. Plant sampling was done at key growth stages, and the leaf and pod areas and total plant dry weights were determined. After flowering, plants intercepted more PAR when grown in 15-cm-wide rows than 30-cm-wide rows. For both row widths, as seeding rate increased from 1.5 to 12.0 kg ha -1 , IPAR increased. The RUE was greater for plants grown in 15-cm-wide rows than for those grown in 30-cm rows ; however, RUE decreased with increasing seeding rate. The mean RUE value was 233 g MJ -1 PAR. When the pod area was added to the leaf area, the IPAR increased and the RUE decreased.
BLOS1 mediates kinesin switch during endosomal recycling of LDL receptor

Low-density lipoprotein receptor (LDLR) in hepatocytes plays a key role in normal clearance of circulating LDL and in whole body cholesterol homeostasis. The trafficking of LDLR is highly regulated in clathrin-dependent endocytosis, endosomal recycling and lysosomal degradation. Current studies have been focusing on its endocytosis and degradation. However, the detailed molecular and cellular mechanisms underlying its endosomal recycling are largely unknown. We found that BLOS1, a shared subunit of BLOC-1 and BORC, is involved in LDLR endosomal recycling. Loss of BLOS1 leads to less membrane LDLR and impairs LDL clearance from plasma in hepatocyte-specific BLOS1 knockout mice. BLOS1 interacts with kinesin-3, and that BLOS1 acts as a new adaptor for kinesin-2 to coordinate kinesin-3 and kinesin-2 during the long-range transport of recycling endosomes (REs) to plasma membrane along microtubule tracks to overcome hurdles at microtubule intersections. These findings provide new insights into RE’s anterograde transport and the pathogenesis of dyslipidemia.
Sex-Specific Cross Tissue Meta-Analysis Identifies Immune Dysregulation in Women With Alzheimer’s Disease

In spite of evidence of females having a greater lifetime risk of developing Alzheimer’s Disease (AD) and greater apolipoprotein E4-related (apoE4) AD risk compared to males, molecular signatures underlying these findings remain elusive. We took a meta-analysis approach to study gene expression in the brains of 1,084 AD patients and age-matched controls and whole blood from 645 AD patients and age-matched controls. Gene-expression, network-based analysis and cell type deconvolution approaches revealed a consistent immune signature in the brain and blood of female AD patients that was absent in males. Machine learning-based classification of AD using gene expression from whole blood in addition to clinical features revealed an improvement in classification accuracy upon stratifying by sex, achieving an AUROC of 0.91 for females and 0.80 for males. These results help identify sex and apoE4 genotype-specific transcriptomic signatures of AD and underscore the importance of considering sex in the development of biomarkers and therapeutic strategies for AD.
EFFECT OF INOCULATION ROUTE ON BACTERIAL INFECTION OF TISSUES AND DEVELOPMENT OF HISTOPATHOLOGIC LESIONS IN MICE INFECTED WITH COXIELLA BURNETII

ii CHAPTER 1: LITERATURE REVIEW . 1 History of Coxiella burnetii . 1 Bacteriology . 2 Epidemiology . 7 Human Disease . 8 Animal Disease . 12 Diagnostics . 13 Treatment and Control . 15 Animal Models . 17 Future Directions for Coxiella Research . 19 References . 20 CHAPTER 2: EFFECT OF INOCULATION ROUTE ON BACTERIAL INFECTION OF TISSUES AND DEVELOPMENT OF HISTOPATHOLOGIC LESIONS IN MICE INFECTED WITH COXIELLA BURNETII . 28 Introduction . 28 Materials and Methods . 30 Animals. 30 Microorganism . 30 Statistical Analyses . 36 Results . 37 Experiment 1: Evaluation of IP versus IN Inoculation Route . 37 Experiment 2: Long-term Infection Following Intranasal Inoculation of C. 41 burnetii. 41 Discussion. 42 References . 48 CHAPTER 3: EFFECT OF AGE AND CHEMICALLY INDUCED IMMUNOSUPPRESSION IN MICE . 50 Introduction . 50 Materials and Methods . 53 Assays for Detection of C. burnetii . 55 Statistical Analyses . 56 Results . 57 Clinical Signs and Gross Pathology . 57 Histopathology . 58 Discussion. 65 References . 69 CHAPTER 4: EVALUATION OF DOXYCYCLINE THERAPY IN TREATING . 71
Computationally replicating the Smith et al. (2015) positive-negative mode linking functional connectivity and subject measures

Understanding brain functionality and predicting human behavior based on functional brain activity is a major goal of neuroscience. Numerous studies have been conducted to investigate the relationship between functional brain activity and attention, subject characteristics, autism, psychiatric disorders, and more. By modeling brain activity data as networks, researchers can leverage the mathematical tools of graph and network theory to probe these relationships. In their landmark study, Smith et al. (2015) analyzed the relationship of young adult connectomes and subject measures, using data from the Human Connectome Project (HCP). Using canonical correlation analysis (CCA), Smith et al. found that there was a single prominent CCA mode which explained a statistically significant percentage of the observed variance in connectomes and subject measures. They also found a strong positive correlation of 0.87 between the primary CCA mode connectome and subject measure weights. In this study, we computationally replicate the findings of the original study in both the HCP 500 and HCP 1200 subject releases. The exact computational replication in the HCP 500 dataset was a success, validating our analysis pipeline for extension studies. The extended replication in the larger HCP 1200 dataset was partially successful and demonstrated a dominant primary mode.
A splicing isoform of GPR56 mediates microglial synaptic refinement via phosphatidylserine binding

Developmental synaptic remodeling is important for the formation of precise neural circuitry and its disruption has been linked to neurodevelopmental disorders such as autism and schizophrenia. Microglia prune synapses, but integration of this synapse pruning with overlapping and concurrent neurodevelopmental processes remains elusive. Adhesion G protein-coupled receptor ADGRG1/GPR56 controls multiple aspects of brain development in a cell type-specific manner: in neural progenitor cells, GPR56 regulates cortical lamination, whereas in oligodendrocyte progenitor cells, GPR56 controls developmental myelination and myelin repair. Here, we show that microglial GPR56 maintains appropriate synaptic numbers in several brain regions in a time- and circuit-dependent fashion. Phosphatidylserine (PS) on pre-synaptic elements binds GPR56 in a domain-specific manner, and microglia-specific deletion of Gpr56 leads to increased synapses as a result of reduced microglial engulfment of PS+ pre-synaptic inputs. Remarkably, a particular alternatively spliced isoform of GPR56 is selectively required for microglia-mediated synaptic pruning. Our present data provide a ligand- and isoform-specific mechanism underlying microglial GPR56-mediated synapse pruning in the context of complex neurodevelopmental processes.
Zika virus-based immunotherapy enhances long-term survival of rodents with brain tumors through upregulation of memory T-cells

Zika virus (ZIKV) exhibits a tropism for brain tumor cells and has been used as an oncolytic virus to target brain tumors in mice with modest effects on extending median survival. Recent studies have highlighted the potential for combining virotherapy and immunotherapy to target cancer. We postulated that ZIKV could be used as an adjuvant to enhance the long-term survival of mice with malignant glioblastoma and generate memory T-cells capable of providing long-term immunity against cancer remission. To test this hypothesis mice bearing malignant intracranial GL261 tumors were subcutaneously vaccinated with irradiated GL261 cells previously infected with the ZIKV. Mice also received intracranial injections of live ZIKV, irradiated ZIKV, or irradiated GL261 cells previously infected with ZIKV. Long-term survivors were rechallenged with a second intracranial tumor to examine their immune response and look for the establishment of protective memory T-cells. Mice with subcutaneous vaccination plus intracranial irradiated ZIKV or intracranial irradiated GL261 cells previously infected with ZIKV exhibited the greatest extensions to overall survival. Flow cytometry analysis of immune cells within the brains of long-term surviving mice after tumor rechallenge revealed an upregulation in the levels of T-cells, including CD4+ and tissue-resident memory CD4+ T-cells, in comparison to long-term survivors that were mock-rechallenged, and in comparison to naïve untreated mice challenged with intracranial gliomas. These results suggest that ZIKV can serve as an adjuvant to subcutaneous tumor vaccines that enhance long-term survival and generate protective tissue-resident memory CD4+ T-cells.
Genome-wide chromatin binding of transcriptional corepressor Topless-related 1 in Arabidopsis

Timely and specific regulation of gene expression is critical for plant responses to environmental and developmental cues. Transcriptional coregulators have emerged as important factors in gene expression control, although they lack DNA-binding domains and the mechanisms by which they are recruited to and function at the chromatin are poorly understood. Plant Topless-related 1 (TPR1), belonging to a family of transcriptional corepressors found across eukaryotes, contributes to immunity signaling in Arabidopsis thaliana and wild tobacco. We performed chromatin immunoprecipitation and sequencing (ChIP-seq) on an Arabidopsis TPR1-GFP expressing transgenic line to characterize genome-wide TPR1-chromatin associations. The analysis revealed ∼1400 genes bound by TPR1, with the majority of binding sites located at gene upstream regions. Among the TPR1 bound genes, we find not only regulators of immunity but also genes controlling growth and development. To support further analysis of TPR1-chromatin complexes and other transcriptional corepressors in plants, we provide two ways to access the processed ChIP-seq data and enable their broader use by the research community.
Lumbricid Prey and Potential Herpetofaunal Predators of the Invading Terrestrial Flatworm Bipalium adventitium (Turbellaria: Tricladida: Terricola)

Abstract Bipalium adventitium Hyman, an exotic terrestrial planarian invading North America, is an aggressive predator on earthworms. The spread and ecological impact of this flatworm will be determined in part by the its interactions with potential predators and prey. In laboratory trials, we tested the ability of B. adventitium to prey upon earthworms of different species and sizes. We also tested the predatory responses of six salamander species and two snake species to the flatworms. Bipalium adventitium attacked and ate members of all earthworm species offered and attacked earthworms over 100 times their mass. However, flatworm predatory success was related to the relative size of the prey. The largest prey eaten in our study was 12.1 times the mass of the flatworm that killed it. When attacking, B. adventitium often used a previously undescribed behavior of capping the anterior end of the earthworm, causing subdued escape behavior. None of the amphibians and reptiles tested as predators treated B. adventitium as a regular prey item. Only a few salamanders (2%) struck and ate a flatworm, with most salamanders and all snakes showing little interest in the planarian. Salamanders that consumed flatworms showed no apparent long-term ill effects.
Response of Palmer Amaranth (Amaranthus palmeri) Accessions to Glyphosate, Fomesafen, and Pyrithiobac1

Field studies were conducted at Fayetteville, Arkansas, to determine whether 47 Palmer amaranth accessions from different areas of the southern United States varied in response to postemergence applications of the registered rates of the isopropylamine salt of glyphosate (840 g ae/ha), fomesafen (420 g ai/ha), and pyrithiobac (70 g ai/ha). Glyphosate controlled all Palmer amaranth accessions at least 99% 21 d after treatment (DAT). Palmer amaranth control with fomesafen was equivalent for all accessions and at least 96% 21 DAT. Percent dry weight reductions were at least 92 and 94% for glyphosate and fomesafen, respectively. Palmer amaranth control with pyrithiobac was variable and ranged from 20 to 94% 21 DAT, but differences could not be attributed to accession origin. Herbicides with alternate modes of action from pyrithiobac should be utilized for Palmer amaranth control in regions where pyrithiobac has been used continuously. Nomenclature: Fomesafen, glyphosate, pyrithiobac, Palmer amaranth, Amaranthus palmeri (S.) Wats. #3 AMAPA. Additional index words: Accession, dry weight reductions, ecotype, herbicide response variability. Abbreviations: ALS, acetolactate synthase (EC 4.1.3.18); DAE, days after emergence; DAT, days after treatment.
An integrated mosquito small RNA genomics resource reveals dynamic evolution and host responses to viruses and transposons

Although mosquitoes are major transmission vectors for pathogenic arboviruses, viral infection has little impact on mosquito health. This immunity is due in part to mosquito RNA interference (RNAi) pathways that generate antiviral small interfering RNAs (siRNAs) and Piwi-interacting RNAs (piRNAs). RNAi also maintains genome integrity by potently repressing mosquito transposon activity in the germline and soma. However, viral and transposon small RNA regulatory pathways have not been systematically examined together in mosquitoes. Therefore, we developed an integrated Mosquito Small RNA Genomics (MSRG) resource that analyzes the transposon and virus small RNA profiles in mosquito cell cultures and somatic and gonadal tissues across four medically important mosquito species. Our resource captures both somatic and gonadal small RNA expression profiles within mosquito cell cultures, and we report the evolutionary dynamics of a novel Mosquito-Conserved piRNA Cluster Locus (MCpiRCL) composed of satellite DNA repeats. In the larger culicine mosquito genomes we detected highly regular periodicity in piRNA biogenesis patterns coinciding with the expansion of Piwi pathway genes. Finally, our resource enables detection of crosstalk between piRNA and siRNA populations in mosquito cells during a response to virus infection. The MSRG resource will aid efforts to dissect and combat the capacity of mosquitoes to tolerate and spread arboviruses.
A note on the statistical evidence for an influence of geomagnetic activity on Northern Hemisphere seasonal-mean stratospheric temperatures using the Japanese 55-year Reanalysis

Abstract. We employ JRA-55 (Japanese 55-year Reanalysis), a recent second-generation global reanalysis providing data of high quality in the stratosphere, to examine whether a distinguishable effect of geomagnetic activity on Northern Hemisphere stratospheric temperatures can be detected. We focus on how the statistical significance of stratospheric temperature differences may be robustly assessed during years with high and low geomagnetic activity. Two problems must be overcome. The first is the temporal autocorrelation of the data, which is addressed with a correction of the t statistics by means of the estimate of the number of independent values in the series of correlated values. The second is the problem of multiplicity due to strong spatial autocorrelations, which is addressed by means of a false discovery rate (FDR) procedure. We find that the statistical tests fail to formally reject the null hypothesis, i.e. no significant response to geomagnetic activity can be found in the seasonal-mean Northern Hemisphere stratospheric temperature record.
Glottalisation and word linking as resources for multi-unit turn construction in German talk-in-interaction: Initial observations

In spoken German, glottal stops are frequently inserted before word initial vowels (ʔewig) and at morphological boundaries (ʔurʔalt). As part of a conversation analytic investigation into glottalisation in naturally occurring German, this pilot study is concerned with a specific conversational context in which variation between glottalisation and direct linking from the end of one word to the beginning of the next are routinely employed. The context in question is multi-unit turn construction. It is found that in the pilot study corpus vowel-fronted TCUs that continue an action-in-progress are frequently preceded by glottalisation; vowelfronted TCUs that implement a new action, but are being integrated into an ongoing turn, are typically linked across from preceding TCUs. This finding contradicts a potential hypothesis that action boundaries are always accompanied by phonetic ones. Instead, the participants in these data implement the opposite pattern: where there is an action boundary they delete the phonetic one, possibly in order to design their talk as continuing phonetically when sequentially it is not. These findings suggest that linguistic practices are not the result of interactional structure, but instead are resources for its implementation.
Trocas gasosas em folhas de sol e sombreadas de cajueiro anão em diferentes regimes hídricos

Resumo - Foram analisadas as variacoes sazonais nas taxas de trocas gasosas em lâminas foliares, sombreadas e a pleno sol, de cajueiro anao precoce (Anacardium occidentale L.), quando submetidas aos regimes de irrigacao e de sequeiro. Os clones CCP 76 e BRS 189 foram mensalmente avaliados quanto ao seu desempenho fisiologico em relacao a condutância estomatica (g s ), as taxas transpiratorias (E) e fotossinteticas (A), a temperatura foliar e a relacao entre as concentracoes interna e externa de CO 2 (C i /C e ). O experimento foi conduzido entre setembro de 2006 e agosto de 2007, na estacao experimental da Embrapa Agroindustria Tropical, localizada no municipio de Paraipaba, Ceara. As variaveis A, g s , E e C i /C e fo ram afetadas apenas em funcao da epoca do ano e dos tipos de folhas. A maior influencia nos fatores fisiologicos analisados ocorreu devido as condicoes em que as folhas estavam submetidas (sol ou sombra) e aos fatores meteorologicos e nao a supressao da irrigacao. Isto, possivelmente porque os resultados aqui obtidos estejam mais bem relacionados com as fases fenologicas da cultura do que com os tratamentos, demonstrando assim o conspicuo efeito fisiologico da forca dos drenos e da irradiância nessas plantas. Palavras-chave - Anacardium occidentale. Estresse hidrico. Ecofisiologia vegetal.
FATTY ACIDS AND HYDROXY FATTY ACIDS IN THREE SPECIES OF FRESHWATER EUSTIGMATOPHYTES

The monocarboxylic fatty acids and hydroxy fatty acids of three species of freshwater microalgae—Vischeria punctata Vischer, Vischeria helvetica (Vischer et Pascher) Taylor, and Eustigmatos vischeri (Hulbert) Taylor, all from the class Eustigmatophyceae— were examined. Each species displayed a very similar distribution of fatty acids, the most abundant of which were 20:5n‐3, 16:0, and 16:1n‐7; C18 polyunsaturated fatty acids were minor components. These fatty acid distributions closely resemble those found in marine eustigmatophytes but are quite distinct from those found in most other algal classes. These microalgae also contain long‐chain saturated and unsaturated monohydroxy fatty acids. Two distinct types of hydroxy fatty acids were found: a series of saturated α‐hydroxy acids ranging from C24 to C30 with a shorter series of monounsaturated α‐hydroxy acids ranging from C26 to C30 together with a series of saturated β‐hydroxy acids ranging from C26 to C30. The latter have not previously been reported in either marine or freshwater microalgae, although C30 to C34 midchain (ω‐18)‐hydroxy fatty acids have been identified in hydrolyzed extracts from marine eustigmatophytes of the genus Nannochloropsis, and C22 to C26 saturated and monounsaturated α‐hydroxy fatty acids have been found in three marine chlorophytes. These findings have provided a more complete picture of the lipid distributions within this little studied group of microalgae as well as a range of unusual compounds that might prove useful chemotaxonomic markers. The functions of the hydroxy fatty acids are not known, but a link to the formation of the lipid precursors of highly aliphatic biopolymers is suggested.
Venomics and antivenomics of the poorly studied Brazil’s lancehead, Bothrops brazili (Hoge, 1954), from the Brazilian State of Pará

ABSTRACT Background: The Brazil’s lancehead, Bothrops brazili, is a poorly studied pit viper distributed in lowlands of the equatorial rainforests of southern Colombia, northeastern Peru, eastern Ecuador, southern and southeastern Venezuela, Guyana, Suriname, French Guiana, Brazil, and northern Bolivia. Few studies have been reported on toxins isolated from venom of Ecuadorian and Brazilian B. brazili. The aim of the present study was to elucidate the qualitative and quantitative protein composition of B. brazili venom from Pará (Brazil), and to carry out a comparative antivenomics assessment of the immunoreactivity of the Brazilian antibothropic pentavalent antivenom [soro antibotrópico (SAB) in Portuguese] against the venoms of B. brazili and reference species, B. jararaca. Methods: We have applied a quantitative snake venomics approach, including reverse-phase and two-dimensional electrophoretic decomplexation of the venom toxin arsenal, LC-ESI-MS mass profiling and peptide-centric MS/MS proteomic analysis, to unveil the overall protein composition of B. brazili venom from Pará (Brazil). Using third-generation antivenomics, the specific and paraspecific immunoreactivity of the Brazilian SAB against homologous (B. jararaca) and heterologous (B. brazili) venoms was investigated. Results: The venom proteome of the Brazil’s lancehead (Pará) is predominantly composed of two major and three minor acidic (19%) and two major and five minor basic (14%) phospholipase A2 molecules; 7-11 snake venom metalloproteinases of classes PI (21%) and PIII (6%); 10-12 serine proteinases (14%), and 1-2 L-amino acid oxidases (6%). Other toxins, including two cysteine-rich secretory proteins, one C-type lectin-like molecule, one nerve growth factor, one 5'-nucleotidase, one phosphodiesterase, one phospholipase B, and one glutaminyl cyclase molecule, represent together less than 2.7% of the venom proteome. Third generation antivenomics profile of the Brazilian pentabothropic antivenom showed paraspecific immunoreactivity against all the toxin classes of B. brazili venom, with maximal binding capacity of 132.2 mg venom/g antivenom. This figure indicates that 19% of antivenom's F(ab')2 antibodies bind B. brazili venom toxins. Conclusion: The proteomics outcome contribute to a deeper insight into the spectrum of toxins present in the venom of the Brazil’s lancehead, and rationalize the pathophysiology underlying this snake bite envenomings. The comparative qualitative and quantitative immunorecognition profile of the Brazilian pentabothropic antivenom toward the venom toxins of B. brazili and B. jararaca (the reference venom for assessing the bothropic antivenom's potency in Brazil), provides clues about the proper use of the Brazilian antibothropic polyvalent antivenom in the treatment of bites by the Brazil’s lancehead.