Miracle-dz/UniFAR-FTUs huggingface dataset:
On I-Optimal Designs for Generalized Linear Models: An Efficient Algorithm via General Equivalence Theory

The generalized linear model plays an important role in statistical analysis and the related design issues are undoubtedly challenging. The state-of-the-art works mostly apply to design criteria on the estimates of regression coefficients. It is of importance to study optimal designs for generalized linear models, especially on the prediction aspects. In this work, we propose a prediction-oriented design criterion, I-optimality, and develop an efficient sequential algorithm of constructing I-optimal designs for generalized linear models. Through establishing the General Equivalence Theorem of the I-optimality for generalized linear models, we obtain an insightful understanding for the proposed algorithm on how to sequentially choose the support points and update the weights of support points of the design. The proposed algorithm is computationally efficient with guaranteed convergence property. Numerical examples are conducted to evaluate the feasibility and computational efficiency of the proposed algorithm.
Inference in High-Dimensional Graphical Models

We provide a selected overview of methodology and theory for estimation and inference on the edge weights in high-dimensional directed and undirected Gaussian graphical models. For undirected graphical models, two main explicit constructions are provided: one based on a global method that maximizes the joint likelihood (the graphical Lasso) and one based on a local (nodewise) method that sequentially applies the Lasso to estimate the neighbourhood of each node. The proposed estimators lead to confidence intervals for edge weights and recovery of the edge structure. We evaluate their empirical performance in an extensive simulation study. The theoretical guarantees for the methods are achieved under a sparsity condition relative to the sample size and regularity conditions. For directed acyclic graphs, we apply similar ideas to construct confidence intervals for edge weights, when the directed acyclic graph is identifiable.
Review of the Current Knowledge on the Role of Stem Cell Transplantation in Neurorehabilitation

The management involving stem cell (SC) therapy along with physiotherapy offers tremendous chance for patients after spinal cord injury (SCI), traumatic brain injury (TBI), stroke, etc. However, there are still only a limited number of reports assessing the impact of stem cells (SCs) on the rehabilitation process and/or the results of the simultaneous use of SC and rehabilitation. Additionally, since there is still not enough convincing evidence about the effect of SCT on humans, e.g., in stroke, there have been no studies conducted concerning rehabilitation program formation and expected outcomes. It has been shown that bone marrow-derived mesenchymal stem cell (BMSCs) transplantation in rats combined with hyperbaric oxygen therapy (HBO) can promote the functional recovery of hind limbs after SCI. An anti-inflammatory effect has been shown. One case study showed that, after the simultaneous use of SCT and rehabilitation, an SCI patient progressed from ASIA Grade A to ASIA Grade C. Such promising data in the case of complete tetraplegia could be a breakthrough in the treatment of neurologic disorders in humans. Although SCT appears as a promising method for the treatment of neurological conditions, e.g., complete tetraplegia, much work should be done towards the development of rehabilitation protocols.
The Association between Toxoplasma gondii Infection and Risk of Parkinson's Disease: A Systematic Review and Meta-Analysis

Background Several studies have investigated the association between Toxoplasma gondii (T. gondii) infection and risk of Parkinson's disease (PD) with inconsistent results. Clarifying this relation might be useful for better understanding of the risk factors and the relevant mechanisms of PD, thus a meta-analysis was conducted to explore whether exposure to T. gondii is associated with an increased risk of PD. Methods We conducted this meta-analysis according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement. A rigorous literature selection was performed by using the databases of PubMed, Embase, Web of Science, Cochrane Library, and ScienceDirect. Odds ratio (OR) and corresponding 95% confidential interval (CI) were pooled by using fixed-effects models. Sensitivity analysis, publication bias test, and methodological quality assessment of studies were also performed. Results Seven studies involving 1086 subjects were included in this meta-analysis. Pooled data by using fixed-effects models suggested both latent infection (OR, 1.17; 95% CI, 0.86 to 1.58; P=0.314) and acute infection (OR, 1.13; 95% CI, 0.30 to 4.35; P=0.855) were not associated with PD risk. Stable and robust estimates were confirmed by sensitivity analysis. No publication bias was found by visual inspection of the funnel plot, Begg's, and Egger's test. Conclusions This meta-analysis does not support any possible association between T. gondii infection and risk of PD. Researches are still warranted to further explore the underlying mechanisms of T. gondii in the pathogenesis of PD and their causal relationship.
Information Theoretic Feature Transformation Learning for Brain Interfaces

Objective: A variety of pattern analysis techniques for model training in brain interfaces exploit neural feature dimensionality reduction based on feature ranking and selection heuristics. In the light of broad evidence demonstrating the potential sub-optimality of ranking-based feature selection by any criterion, we propose to extend this focus with an information theoretic learning-driven feature transformation concept. Methods: We present a maximum mutual information linear transformation and a nonlinear transformation framework derived by a general definition of the feature transformation learning problem. Empirical assessments are performed based on electroencephalographic data recorded during a four class motor imagery brain–computer interface (BCI) task. Exploiting the state-of-the-art methods for initial feature vector construction, we compare the proposed approaches with conventional feature selection-based dimensionality reduction techniques, which are widely used in brain interfaces. Furthermore, for the multi-class problem, we present and exploit a hierarchical graphical model-based BCI decoding system. Results: Both binary and multi-class decoding analyses demonstrate significantly better performances with the proposed methods. Conclusion: Information theoretic feature transformations are capable of tackling potential confounders of conventional approaches in various settings. Significance: We argue that this concept provides significant insights to extend the focus on feature selection heuristics to a broader definition of feature transformation learning in brain interfaces.
Learning partially ranked data based on graph regularization

Ranked data appear in many different applications, including voting and consumer surveys. There often exhibits a situation in which data are partially ranked. Partially ranked data is thought of as missing data. This paper addresses parameter estimation for partially ranked data under a (possibly) non-ignorable missing mechanism. We propose estimators for both complete rankings and missing mechanisms together with a simple estimation procedure. Our estimation procedure leverages a graph regularization in conjunction with the Expectation-Maximization algorithm. Our estimation procedure is theoretically guaranteed to have the convergence properties. We reduce a modeling bias by allowing a non-ignorable missing mechanism. In addition, we avoid the inherent complexity within a non-ignorable missing mechanism by introducing a graph regularization. The experimental results demonstrate that the proposed estimators work well under non-ignorable missing mechanisms.
Encoding of Wind Direction by Central Neurons in Drosophila

Wind is a major navigational cue for insects, but how wind direction is decoded by central neurons in the insect brain is unknown. Here, we find that walking flies combine signals from both antennae to orient to wind during olfactory search behavior. Movements of single antennae are ambiguous with respect to wind direction, but the difference between left and right antennal displacements yields a linear code for wind direction in azimuth. Second-order mechanosensory neurons share the ambiguous responses of single antenna and receive input primarily from the ipsilateral antenna. Finally, we identify a novel set of neurons, which we call wedge projection neurons, that integrate signals across the two antennae and receive input from at least three classes of second-order neurons to produce a more linear representation of wind direction. This study establishes how a feature of the sensory environment – the wind direction – is decoded by single neurons that compare information across two sensors.
Determination of the G+C mol% of DNA in a Novel Strain of Bifidobacterium bifidum by Reversed-Phase High Performance Liquid Chromatogrephy

A method was established to determine the G+C mol% of DNA in Bifidobacterium bifidum. Various bases were separated on a Kromasil C_(18) (5 μm, 250 mm×4. 6mm i. d. ) column by using KH_2PO_4 buffer (20 mmol·L~(-1), pH 5. 6)-methanol(90∶10) as mobile phase at a flow rate of 1 mL·min~(-1). The UV detection was set at 260 nm. The calculative value was identical with the documental value after the calculation by making use of peak areas.
Transformation of the Glycosides from Food Materials by Probiotics and Food Microorganisms

Glycosides are important functional materials in foods. Transformation, especially hydrolysis, of the sugar moieties tends to improve the functional properties of the administered glycosides in vivo. Various probiotic bacteria and edible food-grade fungi such as bifidobacteria, lactobacilli, leuconostocs, yeasts, and aspergilli are potential industrial microorganisms to transform glycosides of ginsenosides from ginseng, platycodin saponins from Platycodon grandiflorum, Trignoella foenum-graecum (TFG) saponins, and isoflavones from soybeans and Puerariae radix, respectively, by fermentation or enzymatic reaction. In this review, various transformation pathways bearing potential significance with respect to the changes in structure and function of the various glycosides from the food materials will be introduced. In conclusion, the proper combination of food microorganisms and transformation conditions will improve the functionality and the sensory value and reduce the cytotoxicity of the functional glycosides present in various functional food raw materials.
Leaf and Tiller Production of Prairie Grass (Bromus willdenowii Kunth) and Two Ryegrass (Lolium) Species

A detailed morphological study of three prairie grass cultivars (Bromus willdenowii Kunth) was conducted under ‘vegetative’ and ‘reproductive’ growth conditions (short and long photoperiods) and at different temperatures. Perennial ryegrass (Lolium perenne L.) and Westerwolds ryegrass (Lolium muhiflorum Lam.) were compared during vegetative growth. Prairie grass had higher leaf appearance rates (leaves per tiller per day) and lower site filling (tillers per tiller per leaf appearance interval) than the ryegrass species. Tillering rates (tillers per tiller per day) were also lower, except under vegetative conditions at 4°C. Low tiller number in prairie grass was not due to lack of tiller sites but a result of poor filling of these sites. Lower site filling occurred because of increased delays in appearance of the youngest axillary tiller and lack of axillary tillers emerging from basal tiller buds. In prairie grass, no tillers came from coleoptile buds while only occasionally did prophyll buds develop tillers. Low tiller number in prairie grass was compensated for by greater tiller weight. Prairie grass had more live leaves per tiller, greater area per leaf and a high leaf area per plant. Considerable variation between cultivars was found in prairie grass. The cultivar ‘Bellegarde’ had high leaf appearance, large leaves and rapid reproductive development, but had low levels of site filling, tillering rate, final tiller number and herbage quality during reproductive growth. ‘Primabel’ tended to have the opposite levels for these parameters, while ‘Grasslands Matua’ was intermediate and possibly provided the best balance of all plant parameters.
INSILICO INVESTIGATION OF MISSENSE MUTATIONS IN SUCCINATE DEHYDROGENASE COMPLEX 5 GENE USING DIFFERENT GENOMIC ALGORITHMS

Objective: Non-synonymous single nucleotide polymorphism (SNP) has a deleterious effect on the protein, thereby leading to a disease. Succinate dehydrogenase complex 5 (SDH5) gene, which encodes for a mitochondrial protein is responsible for the flavination of succinate dehydrogenase complex and also plays a major role in Krebs cycle. Mutations in this gene lead to the cancerous diseases such as paraganglioma and pheochromocytoma. The aim of this paper is to excavate the deleterious mutations in SDH5. Methods: The deleterious mutations in SDH5 are evaluated by assorted genomic algorithms and to find the drug binding affinity by docking the current drug against the mutated protein using molecular docking server. A total of 20 mutations were retrieved from SNP NCBI. The structural and the functional aspects of these 20 mutations were analyzed by using various genomics algorithms such as Sorting Intolerant From Tolerant, PolyPhen2.0, I-Mutant 2.0, SNPs, and gene ontology, protein analysis through evolutionary relationship, and prediction of human deleterious SNP, which helped us narrowing down our search to G78R and L80S as the deleterious missense mutations. The drug cyclophosphamide, used for the treatment of these cancerous diseases was considered for our study. Drug-protein interactions were studied using protein docking server. Binding efficiency of the cyclophosphamide drug with the most deleterious mutations were calculated. Result: G78R was found to be deleterious and confirmed that the mutation decrease the stability of the protein. Conclusion: Our findings lead to the better understanding of the deleterious mutations in SDH5, providing immense knowledge on the cancerous diseases, such as paraganglioma and pheochromocytoma, and drug docking mechanisms which will be extremely useful in the discovery of new treatments against such diseases.
The complete chloroplast genome sequence of a Korean indigenous ornamental plant Hydrangea serrata for. fertilis Nakai (Hydrangeaceae)

Abstract De novo assembly with whole genome sequencing data of Hydrangea serrata for. fertilis, a great ornamental landscape plant species worldwide, facilitated to generate the complete chloroplast genome sequence in this study. The complete sequence was a circular DNA molecule of 157 730 bp in length, containing the large single-copy (LSC) region of 86 789 bp, small single-copy (SSC) region of 18 711 bp and two inverted repeats (IRs) regions of 26 115 bp. The genome encoded 114 genes consisting of 80 protein-coding genes, 30 tRNA genes and four rRNA genes. Phylogenetic analysis with matK gene-coding sequences of 19 species in family Hydrangeaceae showed a close relationship of H. serrata for. fertilis Nakai with H. macrophylla.
Regulation of AtbZIP1 Gene Expression by T-DNA Insertion in Arabidopsis thaliana

bZIP transcription factor family is one of the largest groups of the plant transcription factor families and plays an important role in plant growth and adaption to the abiotic stresses.In this study,two AtbZIP1 mutant Arabidopsis (bzip1) were used with T-DNA inserted into two different sites,designated as SALK-556773 and SALK-660942,in order to identify different effects on AtbZIP1 gene expression by different T-DNA insertion sites.PCR and RT-PCR results revealed that T-DNA insertion in CDS region could effectively inhibit AtbZIP1 gene expression,while T-DNA insertion in 3'-UTR couldn't.The phenotype analysis further confirmed the differences and showed that T-DNA insertion in CDS region decreased plants' drought resistance,while in 3'-UTR couldn't.The phenotype assays also suggested that AtbZIP1 held pivotal roles in plant response to drought stress.
POLYCHAETA (ANNELIDA) OF THE NATUNA ISLANDS, SOUTH CHINA SEA

One-hundred and twenty-nine polychaete species in 38 families are reported from continental shelf sediments off the Natuna Islands, South China Sea. Less than half (52) of all species identified could be assigned Linnaean binomial names because of the poor state of taxonomy for most groups in the region. Diagnoses and/or remarks are provided for most taxa and voucher specimens of all identified taxa are deposited in Museums in Indonesia, Singapore and Australia. Among the Linnaean-named species, twenty-three are reported for the first time from the South China Sea. Twelve genera and one family (Hartmaniellidae) are also new records for the area. A preliminary assessment of biogeographical affinities indicated that of the 52 Linnaean-named species reported herein, six species (12%) appear to be restricted to the South China Sea, 17 species (33%) occur in both the South China Sea and neighbouring Indo-Malayan peninsula, and 41 species (79%) are Indo-West Pacific endemics. A few species appear to have a wider pantropical or cosmopolitan distribution, but these records in particular need to be verified.
Rival group scent induces changes in dwarf mongoose immediate behavior and subsequent movement

In many social species, groups of animals defend a shared territory against rival conspecifics. Intruders can be detected from a variety of cues, including fecal deposits, and the strength of response is expected to vary depending on the identity of the rival group. Previous studies examining differences in response to neighbor and stranger groups have focused on the immediate response to the relevant cues. Here, we investigated how simulated intrusions of rival groups affect both immediate responses and postinspection movement patterns. To do so, we used a fecal translocation experiment at latrine sites within the territories of dwarf mongoose Helogale parvula groups. Immediate responses were adjusted to the level of threat, with greater scent-marking behavior, time spent at the latrine, and group-member participation when groups were presented with fecal matter from out-group rivals relative to control (own group and herbivore) feces. Subsequent movement of the group was also affected by threat level, with a decrease in speed and distance covered following simulated intrusions by out-group rivals compared with control conditions. However, there were no significant differences in immediate responses or post-latrine movement patterns when comparing simulated neighbor and stranger intrusions. These results indicate that territorial intrusions can elicit not just an immediate change in behavior but more far-reaching consequences in terms of movement dynamics. They also raise the possibility that neighbor–stranger discrimination predictions are not necessarily as clear-cut as previously described.
An experimental analysis of the effects of plant and prey quality on the life history and behaviour of Dicyphus hesperus Knight (Hemiptera: Miridae), an omnivorous biological control agent

v Dedication vi Acknowledgements vii List of Tables xiv List of Figures xvi Chapter 1. Biological control using omnivores: the need for ecological theory in the study of Dicyphus hesperus Knight (Hemiptera: Miridae). 1 Biological control: History and definitions 1 What makes a good biological control agent? 3 Ecological theory and biological control 4 Optimal Foraging Theory 5 Optimal Oviposition Theory 7 Plant Vigor and Plant Stress Hypotheses 8 The study system 10 Research objective 19 References 20 Chapter 2. Does host plant quality affect the oviposition decisions of an omnivore? 29 Introduction 29 Materials and Methods 32 Insect and plant rearing 32 No-choice and choice preference trials 34 Egg mortality 35 Statistical analysis 36 Results 38 Discussion 39
Human impacts on two endemic cassowary species in Indonesian New Guinea

Abstract Cassowaries are important seed dispersers in tropical rainforests of New Guinea, but little is known about their population ecology or their responses to human disturbance. We used camera traps to measure the occurrence, local abundance, and activity patterns of northern cassowaries Casuarius unappendiculatus in lowland forests near Nimbokrang, Papua, and dwarf cassowaries Casuarius bennetti in the Arfak Mountains, West Papua. Our goals were to assess human impacts on cassowaries at multiple spatial scales and to measure their activity patterns over an elevational divide. At fine spatial scales local abundance of cassowaries was strongly reduced in areas frequented by humans. At larger spatial scales the distance to the nearest village or drivable road did not affect local abundance but altered the stage structure of the individuals detected, with a higher proportion of juveniles relative to adults. Local abundance of cassowaries was unrelated to site usage by introduced pigs. Both populations studied were strongly diurnal and their activity patterns were not significantly different. Efforts to control hunting remain critical to sustaining cassowaries and the seed dispersal services they provide.
Their Causes and Molecular Basis

■ Abstract Prion diseases are transmissible neurodegenerative conditions that include Creutzfeldt-Jakob disease (CJD) in humans and bovine spongiform encephalopathy (BSE) and scrapie in animals. Prions appear to be composed principally or entirely of abnormal isoforms of a host-encoded glycoprotein, prion protein. Prion propagation involves recruitment of host cellular prion protein, composed primarily of -helical structure, into a disease specific isoform rich in -sheet structure. The existence of multiple prion strains has been difficult to explain in terms of a protein-only infections agent, but recent studies suggest that strain specific phenotypes can be encoded by different prion protein conformations and glycosylation patterns. The ability of a protein to encode phenotypic information has important biological implications. The appearance of a novel human prion disease, variant CJD, and the clear experimental evidence that it is caused by exposure to BSE has highlighted the need to understand the molecular basis of prion propagation, pathogenesis, and the barriers limiting intermammalian transmission. It is unclear if a large epidemic of variant CJD will occur in the years ahead.