Miracle-dz/UniFAR-FTUs huggingface dataset:
Random Subspace Ensemble Learning for Functional Near-Infrared Spectroscopy Brain-Computer Interfaces

The feasibility of the random subspace ensemble learning method was explored to improve the performance of functional near-infrared spectroscopy-based brain-computer interfaces (fNIRS-BCIs). Feature vectors have been constructed using the temporal characteristics of concentration changes in fNIRS chromophores such as mean, slope, and variance to implement fNIRS-BCIs systems. The mean and slope, which are the most popular features in fNIRS-BCIs, were adopted. Linear support vector machine and linear discriminant analysis were employed, respectively, as a single strong learner and multiple weak learners. All features in every channel and available time window were employed to train the strong learner, and the feature subsets were selected at random to train multiple weak learners. It was determined that random subspace ensemble learning is beneficial to enhance the performance of fNIRS-BCIs.
Root Architecture and Root:Shoot Allocation of Shrubs and Saplings in Two Lowland Tropical Forests: Implications for Life‐Form Composition 1

Entire root systems of saplings of five canopy species and of six shrub and treelet species growing in lowland mixed dipterocarp forest at Andulau, Brunei were excavated and measured. Referring to a prior study at Gigante, Panama, two‐way, fixed‐factor ANOVAs were used to compare life–forms and sites. Rooting depth and the proportion of root surface area in the upper 20 cm of soil did not differ significantly between life‐forms because some treelets/shrubs at Andulau were deep‐rooted; all saplings studied were deep‐rooted. The root:leaf area ratios of both saplings and treelets/ shrubs at Andulau were significantly higher than those at Gigante. We attribute this strong difference to the lower soil content of available nutrients at Andulau where rainfall shortage is less severe and regular than at Gigante. Available data on life‐form composition and mortality rates in large plots are consistent with our proposal that shallow‐rooted shrubs and treelets are more vulnerable to drought than deep‐rooted life‐forms. We suggest that future studies of water use partitioning, wood anatomy, leaf morphology, and associations with neighboring plants would benefit from an explicit examination of their relation to rooting depth.
Cystinosis: improved medical care and new insights into pathogenesis.

Background: Cystinosis is a rare inborn error of cystine transport, leading to accumulation of cystine within the lysosomes. To diagnose cystinosis and to monitor treatment with cysteamine, adequate measurements of intracellular cystine content are required. Historically, cystine has been measured in mixed leukocyte preparations (ML), although it preferentially accumulates in phagocytic blood cells (polymorphonuclear leukocytes (PMN) and monocytes). Therefore we have switched from cystine determinations in ML to PMN cells and compared the differences in intracellular cystine content in these two cell preparations. Methods: ML and PNM were isolated form freshly drawn blood. Cystine was measured as cysteine after reduction with sodium borohydride and derivatization with monobromobimane, followed by separation with automated HPLC. Results: Mean intracellular cystine content (nmol cystine/mg protein) was lower in ML compared to PMN cells in obligate heterozygotes (0.07 versus 0.27, p<0.001) and patients treated with cysteamine (0.15 versus 0.94, p<0.001). At the time of diagnosis cystine values of ML in two patients were within the reference interval, while it was clearly elevated in PMN and in cultured fibroblasts. After the switch from ML to PMN the dose of cysteamine had to be increased in 80% of patients under cysteamine therapy. Conclusions: We demonstrate that cystine must be measured in PMN leukocytes and not in ML preparation because using ML can lead to dismiss or delay of the diagnosis of cystinosis and inadequate adjustment of cysteamine dose. CHAPTER 2 30 bw.levtchenko 12-02-2006 15:13 Pagina 30
Plant-parasitic nematodes as invasive species: characteristics,uncertainty and biosecurity implications

Few species of plant-parasitic nematodes (PPN) are currently recognised as invasive but this is largely because of insufficient investigation and recognition. We compared the characteristics of PPN with those of invasive species generally, using the propagule pressure, abiotic and biotic factors (PAB) framework. Most PPN had many of the characteristics of invasive species and hence have the potential to become invasive. The most common characteristics included: adaptations for human mediated dispersal; multiple entry pathways; microscopic size; large number of propagules; high fecundity; many or cosmopolitan hosts; short lifecycle; ability to survive harsh or unfavourable conditions; ability to vary sex ratios; and ability to overcome host plant resistance. Information is lacking for many characteristics of many species and their impacts remain unquantified, which leaves some important unanswered questions and challenges for assessing PPN as invasive species. However many economically important PPN species have not been recognised as invasive, even when most of the known characteristics and data suggests they should be.
Effect of Environmental Temperature on Digestive Tract, Visceral Organ Size, Digestibility and Energy Metabolism in Rats Fed Different Levels of Pea Fibre

Abstract A study was performed to investigate the effect of environmental temperature (18°C or 28°C) and increasing levels of pea fibre in the diet on digestive tract, visceral organ size, digestibility and energy metabolism in rats. Thirty-six male Wistar rats, initial liveweight (LW) 77-79 g, were allocated to six groups and housed at either 18°C (three groups) or 28°C (three groups). Three wheat starch, fish meal and pea fibre-based diets were prepared to contain 100, 200 and 300 g pea fibre kg−1 (68, 110 and 157 g dietary fibre kg−1 DM) and 160 g protein (N × 6.25) kg−1. One group of rats at each temperature was fed one of the diets for four balance periods. Gas-exchange measurements were made and urine and faeces were quantitatively collected. Food to gain ratio was higher (P <.05) at 18°C than at 28°C and increased (P <.05) as the level of fibre was increased. The weight of the visceral organs from rats housed at 18°C was higher (P<.05) than at 28°C. The empty weight of the small intestine, caecum a.
Adult newborn granule cells confer emotional-state-dependent plasticity in memory retrieval

Achieving optimal behavior requires animals to flexibly retrieve prior knowledge. Here we show that adult newborn granule cells (anbGCs) mediate emotional-state-dependent plasticity of memory retrieval. We find that acute social reward (aSR) enhances memory retrieval by increasing the reactivation of engram cells, while acute social stress (aSS) weakens retrieval and reduces the reactivation. Such bidirectional regulation relies on the activation of distinct populations of anbGCs by aSR and aSS, triggering opposing modifications of dDG activity, which is sufficient to regulate and predict the performance of memory retrieval. Concordantly, in emotional disorder models, aSR-dependent memory plasticity is impaired, while the effect of aSS remains intact. Together, our data revealed that anbGCs mediate plasticity of memory retrieval, allowing animals to flexibly retrieve memory according to the current emotional state, and suggested the essential roles of anbGCs in translating emotional information to the regulation of memory expression.
Spatial Deconvolution of HER2-positive Breast Tumors Reveals Novel Intercellular Relationships

In the past decades, transcriptomic studies have revolutionized cancer treatment and diagnosis. However, tumor sequencing strategies typically result in loss of spatial information, critical to understand cell interactions and their functional relevance. To address this, we investigate spatial gene expression in HER2-positive breast tumors using Spatial Transcriptomics technology. We show that expression-based clustering enables data-driven tumor annotation and assessment of intra-and interpatient heterogeneity; from which we discover shared gene signatures for immune and tumor processes. We integrate and spatially map tumor-associated types from single cell data to find: segregated epithelial cells, interactions between B and T-cells and myeloid cells, co-localization of macrophage and T-cell subsets. A model is constructed to infer presence of tertiary lymphoid structures, applicable across tissue types and technical platforms. Taken together, we combine different data modalities to define novel interactions between tumor-infiltrating cells in breast cancer and provide tools generalizing across tissues and diseases.
Physical Properties of and Plant Responses to Rockwool-amended Media

Loose rockwool had a total porosity similar to peatmoss (92%, by volume) but with water retention capabilities similar to sand. Root media formulations containing loose rockwool were tested with seven plant species for plant response and nutrient uptake. The volume percent formulation, 20 rockwool : 10 peatmoss : 20 vermiculite : 45 pine bark : 5 perlite, was superior to formulations containing 10% or 30% rockwool. Plant response in this rockwool medium in bedding plant flats was superior to that in two high-performing commercial media for impatiens (Impatiens sultanii Hook), marigold (Tagetes patula L.), and petunia (Petunia hybrida Vilm) and equal to one com- mercial medium for tomato (Lycopersicon esculentum Mill.). However, response of chrysanthemum (Chrysanthemum × morifolium Ramat.), geranium (Pelargonium × hortorum Bailey), and poinsettia (Euphorbia pulcherrima Willd. ex Kl.) in 1.58-liter pots was inferior to both commercial media in one-half of the trials. Differential plant responses in the root media treatments did not relate directly to differences found to occur in plant nutrient composition. The high initial pH level of rockwool necessitated reduced application of limestone and increased application of calcium sulfate to offset Ca deficiency. Rockwool is an inert, rock-based fibrous material used in the insulation industry. Rock, coke, and other materials are liquified at 1600C, spun into fibers and used as "blowing wool insula- tion" or processed into various shapes with binders. Rectan- gular block forms manufactured with surfactant to increase wettability have been used successfully as root substrates for vegetable and cut flower production in Europe (Hamrick, 1985). Loose wool has been shown to have potential for container- grown plants both as a component in potting mixes (Hanan, 1983) and as a single component medium for geraniums (Lee and Goldsbury, 1988), pot chrysanthemums (Lee et al., 1987a), and poinsettia (Lee et al., 1987b). The objectives of this study 'were to examine the physical properties of rockwool and the plant growth response to media amended with loose rockwool. Materials and Methods
Mapping endothelial functional phenotype in cancer by unveiling the kinase and phosphatase drivers

Endothelial cells (EC) are state-dependent regulators of the tumor ecosystem: quiescent ECs promote homeostasis; proliferative ECs stimulate tumor growth. Tumors, in turn, promote pro-tumorigenic EC phenotype. We studied functional and phosphorylative transformations on EC state in cancer. Quiescent HUVECs cultured in breast cancer cell-conditioned media displayed marked elongation and impaired wound healing. Quantitative mass spectrometry identified phosphorylative regulators of this dysfunctional transformation. Growth factor receptor kinases showed decreased, rather than increased activity, suggesting that EC regulation in tumors can arise other than from classic growth-factor-mediated angiogenesis alone. Of the 152 kinases and phosphatases across 62 families, six were chosen for functional validation using pharmacologic inhibitors. Inhibiting Akt and Ptp1b restored EC regulatory state, warranting further investigation as therapeutic targets; Src inhibition, however, promoted the dysfunctional phenotype, suggesting caution for Src inhibitors as EC-regulating therapies. Mapping phosphorylative drivers reveals complex relationships between EC phenotype, transformation, and regulation, and may shed light on how existing cancer-targeting inhibitors affect tumor endothelium. Data are available via ProteomeXchange with identifier PXD020333.
Nuclear GSK-3β and Oncogenic KRas Promote Expansion of Terminal Duct Cells and the Development of Intraductal Papillary Mucinous Neoplasm

Intraductal papillary mucinous neoplasm (IPMN) represents one type of pancreatic ductal adenocarcinoma (PDA) precursor lesion, however its cell-of-origin remains unclear. Here we describe a new mouse model in which pancreas-specific Cre activation of a nuclear glycogen synthase kinase-3β transgene is combined with oncogenic KRas (referred to as KNGC). KNGC mice show accumulation of neoplastic ductal cells at 4-weeks that progressively develop into IPMN with low-grade dysplasia in advanced age. RNA-sequencing identified expression of several terminal duct cell lineage genes including Agr2 and Aqp5. Interestingly, Aqp5, a water channel, was found to be required for the development of IPMN lesions in KNGC mice. Staining of human IPMN samples indicates that these preneoplastic lesions also arise from expansion of the terminal duct population. Altogether, these data highlight the utility of the KNGC model for understanding the biology of IPMN and potential utility in defining predictive biomarkers of IPMN – PDA development. Statement of significance Understanding the cell-of-origin of IPMN is crucial to developing early detection methods that specifically target aggressive precursors of PDA. This work, using a novel mouse model, identifies Aqp5-modulated development of Agr2+ terminal ducts that could potentially serve as a clinical biomarker for IPMN.
Malaria prevention in the Buea health district in Cameroon: factors influencing Mosquito bed net use in households

Background : Insecticide treated bed nets (ITNs), though proven to be effective in preventing malaria will have little impact unless people sleep under them. Several studies have shown that owned ITNs are usually not used and that ITN use is influenced by several factors that vary between communities. Objective : To investigate the factors influencing the use of mosquito bed nets in households in the Buea Health District (BHD) in Cameroon. Material and Methods : A cross-sectional study with two-stage cluster sampling included 420 households from 35 sites. Questionnaires adapted from the Malaria Indicator Survey were used. CSPro 4.1 and Epi info 3.5. 3 were used to create database and analyze respectively. Results : ITN ownership in the BHD was high (92.6%; 95% CI: 89.6%-94.9%) but ITN use was less than average (41.2%; 95% CI: 39.2%-43.3%). ITN use was least likely in the age group 5-15 years (P<0.01), in educated individuals (P<0.01) and in households with less than one ITN for two persons (P<0.01). White ITNs were less likely to be used (P<0.01). Conclusion : There is a gap between ITN ownership and use in the malaria holoendemic BHD and ITN use is associated with age of individual, level of education, colour of ITNs and household net density. Use of the highly owned ITNs could be increased by targeting the least protected 5-15 years age group and schooling individuals; by promoting school-based education on ITN use. Keywords : Insecticide-treated nets, malaria, Buea Health District
tRNA-modifying enzyme mutations induce codon-specific mistranslation and protein aggregation in yeast

Protein synthesis rate and accuracy are essential for bona fide protein synthesis and proteome homeostasis (proteostasis), however the mRNA translation elongation factors that prevent protein mistranslation, misfolding and aggregation are poorly understood. To address this question, we evaluated the role of 70 yeast tRNA modifying enzyme genes on protein aggregation and used mass spectrometry to identify the aggregated and mistranslated proteins. We show that the mitochondrial tRNA-modifying enzyme Slm3 thiolates the cytoplasmic tRNAs at position 34 and that decreased levels of mcm5s2U34 in SLM3 mutants are compensated by increasing mcm5U34, ncm5U34 and ncm5Um34 levels. In the tRNA gene knockout strains, stress response proteins are overrepresented in protein aggregates and their genes are enriched in codons decoded by tRNAs lacking mcm5U34, mcm5s2U34, ncm5U34, ncm5Um34, modifications. Increased rates of amino acid misincorporation were detected in the yeast ELP1, SLM3 and TRM9 gene knockout mutants at protein sites that specifically mapped to the codons sites that are decoded by the hypomodified tRNAs, demonstrating that U34 tRNA modifications safeguard the proteome from translational errors, misfolding and cellular proteotoxic stress.
Sperm Competition and Its Evolutionary Consequences in the Insects

Ashot on goal does not ensure victory*. Likewise, insemination does not guaranteepaternity. When females store sperm fromseveral males, each male’s fitness dependson his ability to tilt the ensuing fertilizationcontest (sperm competition) in his favour.How males achieve this goal was the mainfocus of study for 30 years. Recently,however, there have been more questionsabout how females influence spermcompetition (cryptic female choice). Toanswer them, we need to know why femalesmate multiply. What are the fitness benefitsand consequent selection on femalemorphology, physiology and behaviour? In spite of the newfound popularity ofcryptic female choice, driven largely byBillEberhard’s book [1] and more recentwork on sexual conflict, the available dataare still limited. It is testimony to Simmons’hard-nosed empiricism that he pays moreattention to questions from the traditional‘male perspective’. The best chapter in the 1998 collection
Relationship of larval-stage growth and mortality to recruitment of striped bass,Morone saxatilis, in Chesapeake Bay

Variable recruitments of striped bass were hypothesized to be caused by factors influencing growth and survival of larvae. Eggs and larvae were collected in the Potomac River from 1987 to 1989 and in the Upper Chesapeake Bay in 1988 and 1989 to estimate abundances, larval growth and survival rates, and environmental variability. Larval batch dates, ages, and growth and mortality rates were estimated from analysis of otolith daily increments. A retrospective analysis of Potomae River ichthyoplankton data from 1974–1977 and 1980–1982 provided additional estimates of larval abundances and vital rates for comparative purposes. Significant correlations betweens vital rates (growth and mortality) and abundances of striped bass larvae, and the Maryland juvenile recruitment index indicated that recruitment level may be fixed during the larval stage. The ratio of mean daily growth and mortality rates (G:Z) of larvae in the Potomac River for 1987–1989 was highest in 1987 when the juvenile index was relatively high, and was lower in 1988 and 1989 when juvenile indices were low. In the Upper Bay, mean larval growth rate, survival rate, and the G:Z ratio were highest in 1989 when the juvenile index also was high. In both tributaries, abundances of late-stage larvae (8 mm SL) were correlated with juvenile-stage recruitment indices. The retrospective analysis provided additional evidence that Potomac River larval abundances and G:Z ratios were positively correlated with juvenile recruitment indices in the 1974–1977 and 1980–1982 periods. Conditions favoring striped bass larval abundance and potential recruitment differed between the Potomac River and the Upper Bay. In the Potomac, late-stage larval abundances coincided with late-season water temperatures that were relatively warm, low river discharges and high, late-season densities of zooplankton prey, which favored larval growth. In the Upper Bay, the high abundance of late-stage larvae in 1989 relative to 1988 was attributed to a higher egg production that was coincident with high zooplankton abundances.
Genetic changes in the bacterial community structure associated with protistan grazers

Besides controlling bacterial production, bacterivorous protists are thought to govern bacterial community structure. Experimental work has shown that both grazers and bacteria developed strategies that may influence the bacterial community structure. However, evidence from the natural environment is still lacking. Advances in molecular techniques now allow the profiling of natural bacterial assemblages. We used denaturing gradient gel electrophoresis (DGGE) to profile a bacterial community in a continuous flow system that was fed with living and detrital cyanobacterial cells. Although attempts were made to remove eukaryotic grazers, heterotrophic nanoflagellates were growing in the second stages of the system. Analysis of DGGE patterns by nonmetric multidimensional scaling showed a large change in the bacterial community structure coinciding with the peak in protist numbers. Our results show that DGGE analysis can be used to facilitate studies on the effect of protistan grazing on natural bacterial communities. [KEYWORDS: GRADIENT GEL-ELECTROPHORESIS; GRAZING-RESISTANT BACTERIA; 16S RIBOSOMAL-RNA; FRESH-WATER; DIVIDING CELLS; LAKE; BACTERIOPLANKTON; POPULATIONS; ASSEMBLAGES; PROTOZOA]
Comprehensive genotyping of Brazilian Cassava (Manihot esculenta Crantz) Germplasm Bank: insights into diversification and domestication

Cassava (Manihot esculenta Crantz) is a major staple root crop of the tropics, originating from the Amazonas region. In this study, 3,354 cassava landraces and modern breeding lines from the Embrapa Cassava Germplasm Bank (CGB) were characterized. All individuals were subjected to genotyping-by-sequencing (GBS), identifying 27,045 Single Nucleotide Polymorphisms (SNPs). Identity-by-state and population structure analyses revealed a unique set of 1,536 individuals and 10 distinct genetic groups with heterogeneous linkage disequilibrium (LD). On this basis, 1,300 to 4,700 SNP markers were selected for large quantitative trait loci (QTL) detection. Identified genetic groups were further characterized for population genetics parameters including minor allele frequency (MAF), observed heterozygosity (Ho), effective population size estimate and polymorphism information content (PIC). Selection footprints and introgressions of M. glaziovii were detected. Spatial population structure analysis revealed five ancestral populations related to distinct Brazilian ecoregions. Estimation of historical relationships among identified populations suggest earliest population split from Amazonas to Atlantic forest and Caatinga eco-regions and active gene flows. This study provides a thorough genetic characterization of ex situ germplasm resources from cassava center of origin, South America, with results shedding light on Brazilian cassava characteristics and its biogeographical landscape. These Findings support and facilitate the use of genetic resources in modern breeding programs including implementation of association mapping and genomic selection strategies. Key message Brazilian cassava diversity was characterized through population genetics and clustering approaches, highlighting contrasted genetic groups, and spatial genetic differentiation.