Miracle-dz/UniFAR-FTUs huggingface dataset:
Speed tuning in the macaque posterior parietal cortex

Neurons in the macaque posterior parietal cortex are known to encode the direction of self-motion. But do they also encode one’s speed? To test this, we performed neural recordings from area 7a while monkeys were passively translated or rotated at various speeds. Visual stimuli were delivered as optic flow fields and vestibular stimuli were generated by a motion platform. Under both conditions, the responses of a fraction of neurons scaled linearly with self-motion speed, and speed-selective neurons were not localized to specific layers or columns. We analyzed ensembles of simultaneously recorded neurons and found that the precision of speed representation was sufficient to support path integration over modest distances. Our findings describe a multisensory neural code for linear and angular self-motion speed in the posterior parietal cortex of the macaque brain, and suggest a potential role for this representation.
Corals in Healthy Populations Produce More Larvae Per Unit Cover

In coral reef conservation and management, the prevailing metric of reef health is percent coral cover, a measurement commonly used with the assumption that each unit of live coral tissue has equivalent ecological value. Here we show that the reproductive output of a coral population is not proportional to the cover of coral present. Instead, when compared to declining populations nearby, high cover coral populations produced up to four times more larvae per square centimeter of tissue, resulting in up to 200 times higher larval production per square meter of reef. Importantly, corals that produced more larvae did not produce smaller larvae, as predicted by resource allocation theory. Instead, higher fecundity corresponded to higher energetic lipid reserves in higher cover coral populations. In the wake of unprecedented global coral bleaching, our findings suggest that the largest reductions in coral reproduction may occur when corals are lost from previously healthy populations.
Gardenia jasminoides Encodes an Inhibitor-2 Protein for Protein Phosphatase Type 1

Protein phosphatase-1 (PP1) regulates diverse, essential cellular processes such as cell cycle progression, protein synthesis, muscle contraction, carbohydrate metabolism, transcription and neuronal signaling. Inhibitor-2 (I-2) can inhibit the activity of PP1 and has been found in diverse organisms. In this work, a Gardenia jasminoides fruit cDNA library was constructed, and the GjI-2 cDNA was isolated from the cDNA library by sequencing method. The GjI-2 cDNA contains a predicted 543 bp open reading frame that encodes 180 amino acids. The bioinformatics analysis suggested that the GjI-2 has conserved PP1c binding motif, and contains a conserved phosphorylation site, which is important in regulation of its activity. The three-dimensional model structure of GjI-2 was buite, its similar with the structure of I-2 from mouse. The results suggest that GjI-2 has relatively conserved RVxF, FxxR/KxR/K and HYNE motif, and these motifs are involved in interaction with PP1.
Transcriptome-based Gene Networks for Systems-level Analysis of Plant Gene Functions

Present day genomic technologies are evolving at an unprecedented rate, allowing interrogation of cellular activities with increasing breadth and depth. However, we know very little about how the genome functions and what the identified genes do. The lack of functional annotations of genes greatly limits the post-analytical interpretation of new high throughput genomic datasets. For plant biologists, the problem is much severe. Less than 50% of all the identified genes in the model plant Arabidopsis thaliana, and only about 20% of all genes in the crop model Oryza sativa have some aspects of their functions assigned. Therefore, there is an urgent need to develop innovative methods to predict and expand on the currently available functional annotations of plant genes. With open-access catching the ‘pulse’ of modern day molecular research, an integration of the copious amount of transcriptome datasets allows rapid prediction of gene functions in specific biological contexts, which provide added evidence over traditional homology-based functional inference. The main goal of this dissertation was to develop data analysis strategies and tools broadly applicable in systems biology research. Two user friendly interactive web applications are presented: The Rice Regulatory Network (RRN) captures an abiotic-stress conditioned gene regulatory network designed to facilitate the identification of transcription factor targets during induction of various environmental stresses. The Arabidopsis Seed Active Network (SANe) is a transcriptional regulatory network that encapsulates various aspects of seed formation, including embryogenesis, endosperm development and seed-coat formation. Further, an edge-set enrichment analysis algorithm is proposed that uses network density as a parameter to estimate the gain or loss in correlation of pathways between two conditionally independent coexpression networks. ©2017 by Chirag Gupta All Rights Reserved
Estimating specular roughness from polarized second order spherical gradient illumination

Measurement of spatially varying BRDFs of real world materials has been an active area of research in computer graphics with image-based measurements being the preferred approach in practice. In order to restrict the total number of measurements, existing techniques typically trade spatial variation for angular variation of the surface BRDF [Marschner et al. 1999]. Recently, Ma et al. [2007] introduced a technique for estimating high quality specular normals and albedo (Fig. 1, (a) & (b) respectively) of a specular object using polarized first order spherical gradient illumination conditions. In this work, we extend this technique to estimate per pixel specular roughness using polarized second order spherical gradients as a measure of the variance about the mean (reflection vector). We demonstrate that for isotropic BRDFs, only three spherical gradient illumination patterns related to the second order spherical harmonics are sufficient for a robust estimate of per pixel specular roughness (Fig. 1, (c)). Thus, we go further than previous work on image-based measurement of specular BRDFs that typically obtain sparse estimates of the spatial variation. Our technique also provides a direct estimate of the per pixel specular roughness and hence has the added advantage of not requiring any off-line numerical optimization that is typical of the measure and fit approach to BRDF modeling.
Antioxidant properties of aqueous and ethyl acetate extracts of some plants used as herbal tea in Tanzania

Objectives: The purpose of this study was to evaluate antioxidant activity of Rhus vulgaris, Sphaeranthus bullatus, Osyris lanceolata, Ocimum gratissimum, Cymbopogon citratus, Acacia nilotica, and Tylosema fassoglensis plants that have been used as herbal teas in Tanzania for treatment of various ailments including bacterial and fungal infections.Methods: Antioxidant activity of the aqueous (AQ) and ethyl acetate (ETA) plant extracts was assessed based on radical scavenging activity of the stable 1,1-diphenyl-2-picryl-hydrazyl (DPPH) on January 2017. Briefly, DPPH (0.2 mm) was obtained by dissolving 3.94 mg of DPPH in 50 ml of pure methanol. The stock solutions of the extracts were prepared in methanol. Serial dilution using 96 well plates was employed to determine radical scavenging activities of different concentrations.Results: All plants demonstrated free radical scavenging activity ranging from 5.36% to 87.75% in different concentrations with the highest activity of 87.75% observed in S. bullatus aqueous extracts in its 500 mg/ml at 60 minutes and the lowest scaveng-ing activity of 5.36% demonstrated by T. fassoglensis leaves ethyl acetate extracts in its 3.906 mg/ml. Scavenging activity was observed to change with polarity and time of reac-tion. Eighty five percent of AQ extracts exhibited the scavenging activity ranging from 80% to 87% at the concentration of 500 mg/ml compared to 39.3% that exhibited by ETA extracts at the same concentration. Total phenolic contents ranged from 57.7 ± 0.8 to 98.02 ± 1.1 mg GAE/g dry weight.Conclusion: The use of herbal tea from S.bullatus, O. lanceolata, T. fassoglensis, A. nilotica, R. vulgaris, C. citratus, and O. gratissimum has potential antioxidant benefits to human health, so it should be used to prepare herbal tea for management of diseases.
An analytical framework for understanding regulatory novelty accompanying allopolyploidization

Allopolyploidy is a prevalent process in plants, having important physiological, ecological, and evolutionary consequences. Massive, genome-wide transcriptomic rewiring in response to genomic merger and doubling has been demonstrated in many allopolyploid systems, encompassing a diversity of phenomena, including homoeolog expression bias, genome dominance, expression-level dominance, and revamping of co-expression networks. Here we present an analytical framework to reconcile these patterns of regulatory novelty as governed by distinct sets of intra-and inter-subgenome cis - trans relationships. This approach is a novel extension of classic allele-specific expression analysis to incorporate and distinguish the separate effects of parental regulatory interactions as well as further complications at the allopolyploid level. We demonstrated that the cis - trans framework devised not only offers new perspective on disentangling genetic from epigenetic and higher-order effects that impact gene expression, but also provides the conceptual basis and tools to unify recently presented models for both genome-wide expression dominance and biased fractionation in allopolyploids.
Enabling EMT: N-BLR promotes metastasis in colorectal cancer via regulation of epithelial-to-mesenchymal transition

Over the past twenty years, the advent of deep sequencing technology has revealed the pervasive and widespread nature of transcription across the human genome, with ~80% being transcribed at some point during development (1). Given that 200 nt) ncRNAs have emerged as major regulators of several key biological processes, including differentiation and oncogenesis (2,3).
Anticancer Effect of a Typhonium flagelliforme L. in Raji Cells Through Telomerase Expression

Cancer cells have a relatively high telomerase activity compared to normal cells, so the cancer cells have the ability to continue to proliferate and undergo mitosis uncontrolled. Telomerase is an enzyme which responsible for telomere length, a DNA segment that is at the end of eukaryotic cell chromosomes. Telomeres and telomerase play a role in the incidence of carcinogenesis. Natural materials such as taro mice ( Typhonium flagelliforme ) have potential as anticancer. The purpose of the study was to determine the effects of plant extracts of rat taro on the expression of telomerase in cancer cell Raji. The research method is experimental studies in some form cancerous cell culture cell line, Raji. Used as a control normal cells is Vero cell. The Culture medium used RPMI for Raji cell and M199 for Vero cell. The study consisted of three groups, control, doses of 1 ½ IC50 and IC50 doses. Expression of telomerase enzyme was measured by the Immunohystochemistry method (IHC). The results showed that the expression of telomerase in cancer cells showed values significantly higher than the normal cells (Vero). Giving mice taro plant extracts ( Typhonium flagelliforme ) were able to decrease the expression of telomerase significantly in both treatment doses. It was concluded that rodent tuber extract ( Typhonium flagelliforme Lodd) can reduce the expression of telomerase in Raji cells, so that the rodent tuber extract ( Typhonium flagelliforme Lodd) has potential as an anticancer through the expression of telomerase. Keywords : telomerase, IHC, Typhonium flagelliforme
Technological Advancement Development of a Fusarium graminearum AVymetrix GeneChip for proWling fungal gene expression in vitro and in planta

Recently the genome sequences of several Wlamentous fungi have become available, providing the opportunity for large-scale functional analysis including genome-wide expression analysis. We report the design and validation of the Wrst AVymetrix GeneChip microarray based on the entire genome of a Wlamentous fungus, the ascomycetous plant pathogen Fusarium graminearum. To maximize the likelihood of representing all putative genes (»14,000) on the array, two distinct sets of automatically predicted gene calls were used and integrated into the online F. graminearum Genome DataBase. From these gene sets, a subset of calls was manually annotated and a nonredundant extract of all calls together with additional EST sequences and controls were submitted for GeneChip design. Experiments were conducted to test the performance of the F. graminearum GeneChip. Hybridization experiments using genomic DNA demonstrated the usefulness of the array for experimentation with F. graminearum and at least four additional pathogenic Fusarium species. DiVerential transcript accumulation was detected using the F. graminearum GeneChip with treatments derived from the fungus grown in culture under three nutritional regimes and in comparison with fungal growth in infected barley. The ability to detect fungal genes in planta is surprisingly sensitive even without eVorts to enrich for fungal transcripts. The Plant Expression Database (PLEXdb, http:// www.plexdb.org) will be used as a public repository for raw and normalized expression data from the F. graminearum GeneChip. The F. graminearum GeneChip will help to accelerate exploration of the pathogen–host pathways that may involve interactions between pathogenicity genes in the fungus and disease response in the plant.
Comparison of Two Quantum Nearest Neighbor Classifiers on IBM’s Quantum Simulator

Today computers are used to store data in memory and then process them. In our big data era, we are facing the challenge of storing and processing the data simply due to their fast ever growing size. Quantum computation offers solutions to these two prominent issues quantum mechanically and beautifully. Through careful design to employ superposition, entanglement, and interference of quantum states, a quantum algorithm can allow a quantum computer to store datasets of exponentially large size as linear size and then process them in parallel. Quantum computing has found its way in the world of machine learning where new ideas and approaches are in great need as the classical computers have reached their capacity and the demand for processing big data grows much faster than the computing power the classical computers can provide today. Nearest neighbor algorithms are simple, robust, and versatile supervised machine learning algorithms, which store all training data points as their learned “model” and make the prediction of a new test data point by computing the distances between the query point and all the training data points. Quantum counterparts of these classical algorithms provide efficient and elegant ways to deal with the two major issues of storing data in memory and computing the distances. The purpose of our study is to select two similar quantum nearest neighbor algorithms and use a simple dataset to give insight into how they work, highlight their quantum nature, and compare their performances on IBM’s quantum simulator.
The evaluation of locally produced full-fat canola seed (Brassica napus) as an alternative protein source in the diets of slaughter ostriches (Struthio camelus var. domesticus)

ii Opsomming . iv Acknowledgements . vii Notes . x List of Figures . xi List of Tables . xiii List of abbreviations . xvi Chapter 1: General Introduction . 1 1.1 References . 2 Chapter 2: Literature Review . 5 2.
First Report and Distribution of the Papaya Mealybug, Paracoccus marginatus, in Kenya1

Abstract The papaya mealybug, Paracoccus marginatus Williams and Granara de Willink (Hemiptera: Pseudococcidae), a serious invasive pest affecting horticultural crops, was first reported in Kenya in 2016 at Kwale, Mombasa, and Kilifi Counties of the coastal region. A study was conducted to establish its identification, distribution and host ranges at the coastal region. This is the first report of P. marginatus distribution and crops attacked in Kenya. The papaya mealybug was found to infest papaya (Carica papaya), cassava (Manihot esculenta), chili pepper (Capsicum annuum), guava (Psidium guajava), mango (Mangifera indica), and eggplant (Solanum melongena) in this study. An average yield loss of 91% on papaya crop was reported in the affected farms. Only 7.2% of the farms surveyed were found to have management strategies in place against the papaya mealybug. Additional surveys should be conducted to determine pest migration and potential endemic or unintentionally introduced natural enemies.
Norovirus GII.17: The Emergence and Global Prevalence of a Novel Variant

A rare norovirus (NoV) genotype GII.17 has recently emerged and rapidly became pre- dominant in most East Asian countries in the winters of 2014–2015. In this study, we report the diversity of NoV GII.17 in detail; a total of 646 GII.17 sequences obtained dur- ing 1978–2015 were analyzed and subjected to meta-analysis. At least five major recom binant GII.17 clusters were identified. Each recombinant variant group appeared to have emerged following the time order: GII.P4-GII.17 (1978–1990), GII.P16-GII.17 (2001–2004), GII.P13-GII.17 (2004–2010), GII.Pe-GII.17 (2012–2015) and GII.P3-GII.17 (2011–2015). The newly emerged GII.P3-GII.17 variant, which exhibited significant sequence and structure variations, is evolving toward a unique lineage. Our results indicate that circulation of GII.17 appears to change every 3–5 years due to replacement by a newly emerged variant and that the evolution of GII.17 is sequentially promoted by inter-genotype recombina- tion, which contributes to the exchange between non-GII.17 and GII.17 RdRp genes and drives the evolution of GII.17 capsid genes.
The principle and application of new PCR Technologies

Polymerase chain reaction (PCR) is essentially a selective DNA amplification technique commonlyapplied for genetic testing and molecular diagnosis because of its high specificity and sensitivity.PCR technologies as the key of molecular biology, has realized that the qualitative detection of absolute quantitative has been changed. It has produced a variety of new PCR technologies, such as extreme PCR, photonic PCR, o-amplification at lower denaturation temperature PCR, nanoparticle PCR and so on. In this paper, the principle and application of PCR technologies are reviewed, and its development is prospected too.
Identification of an isoflavone glycoside hydrolyzing b-glucosidase in the seeds of the desert legume Prosopis cineraria

Legumes, in general, are rich in glycosidic isoflavone conjugates, whereby specific b-glucosidases act to release the free aglycones that could serve in plant-microbe interactions and defense. Prosopis cineraria is an important legume tree, bearing medicinally useful and edible pods, generally growing in extreme arid/semi-arid zones of Rajasthan. However, specific phytochemical-cum-metabolic profiles are lacking for the same. Therefore, the present investigation undertook phytochemical and metabolic screening of the pods/seeds of P. cineraria for the presence of putative isoflavonoids viz. genistein and daidzein, their glycosides and b-glucosidase(s) capable of catalyzing the glycoside hydrolysis. Extraction and identification of these two aglycone forms of the above isoflavonoids were performed with solvent partition chromatography and Fluorescent/High Performance Thin Layer Chromatography, respectively. Furthermore, optimization of the isoflavone conjugate-specific b-glucosidase activity with respect to pH optima, temperature and time were carried out. The partially purified enzyme showed a temperature optima of 50°C and pH optima of 4.5. The enzyme also demonstrated activity towards natural substrates daidzin and genistin which are glycosides of isoflavonoids daidzein and genistein respectively. The methanolic extracts of the seeds of P. cineraria indicated the presence of related isoflavonoids which needs to be further validated.
Development of mandibular arch in European sea bass, Dicentrarchus labrax (linneaus, 1758) from the hatchery "CENMAR", Croatia

The mandibular arch ossification process in Dicentrarchus labrax L. is described from day 15 to day 80 post hatching (DPH). Data on this aspect of larval development were presented for both the DPH and average standard length (Ls). Samples were collected in the hatchery "CENMAR" near Zadar, Croatia. Preparation techniques included fixation in buffered formalin, trypsin clearing and staining with alcian blue and alizarin red. At 15 DPH (Ls 5.0 mm), there were no bony elements in mandibular arch. Ethmoid plate represented roof of the splanchnocranium, while Meckel's cartilage, hyosymplectic and cartilaginous palato-qudrates formed lateral walls. Cartilaginous basibranchial, hyoid bar and branchial basket constituted the bottom of the oral cavity. The first noticed bony elements were maxillaries (20 DPH, Ls 5.9 mm), followed by premaxillaries and dentaries (25 DPH, Ls 7.9 mm) - all with dermal (membranous) ossification. Ossification of other mandibular arch elements (angular, quadrate, retroarticular, palatine end ectopterygoid bone) was noticed at 38 DPH, Ls 14.5 mm. Pharyngeal jaws and teeth on premaxillaries and dentaries were noticed at the same time. Ossification process of the above mentioned elements (particularly quadrate bone) seems to be finished at 80 DPH, Ls 32.2 mm. The results are discussed in view of the ontogeny process connected with vital requirements to environment.
Impact of High Temperature on Antioxidant Enzymes during Reproductive Phase in Rice Cultivars

Rice is the most diverse cereal crop in the world, it is poorly adapted to high temperature and flowering (anthesis) is the most heat sensitive stage (Farrel et al., 2006). Exposure of rice crop to heat stress at least during a part of its growth stage may drastically reduce the yield. High temperature at reproductive stage can decrease rice yield due to reduced pollen viability and increased spikelet sterility. At the cellular level, it has been observed in many crops that the level of active oxygen species (AOS) like superoxide radicle, hydrogen peroxide, single oxygen and hydroxyl radicle and antioxidant enzymes like superoxide dismutase, catalase and peroxidase increase when plants are exposed to high temperature (Bowler et al., 1992) and also when the plants undergo the shift from vegetative to reproductive stage (Gielis et al., 1999). The present study was undertaken to assess the contribution of different H2O2 scavenging enzymes in detoxification under two different stressful environment experienced by the same plants.
The introduction of Japanese knotweed, Reynoutria japonica, into North America1

This article presents the discovery of earliest known references to the cultivation of Japanese knotweed, Reynoutria japonica, in North America. As described in articles from 1868, 1872, and 1875 there were three distinct introductions of the plant in the 1860s, two from Europe and one from Japan. The European introductions consisted of the now widespread, seedless female clone introduced into commerce by Philipp von Siebold in the 1840s and a dwarf, seed-producing variety with reddish stems, probably also introduced by von Siebold. The introduction from Japan was sent by Thomas Hogg to his brother James's nursery in New York City and produced “an abundance of rose-colored fruits. ” Serendipitously, an herbarium specimen collected from Hogg's plant in 1873 was discovered in in 2006 and its examination strongly suggests that the introduction consisted of at least one male and one female plant. Thomas Hogg's independent introduction of the species from Japan could well explain the higher levels of genetic diversity displayed by Japanese knotweed populations in eastern North America compared to those in Europe.