Miracle-dz/UniFAR-FTUs huggingface dataset:
In vitro Micropropagation of Tinospora cordifolia (Willd.) Miers ex Hook. F. & Thoms - An Important Medicinal Plant

A protocol was established for rapid clonal propagation medicinal plant, Tinospora cordifolia (TC), through in vitro culture using nodal explants. Best shoot induction was observed on MS medium with 4.36 µM KIN produces 2.320.1 cm length with 1.80.1 numbers of shoots with 70% response when compared with other Cytokinins BA and 2iP. After a month of shoot induced culture, creates a phenolic exudation problem in shoot formation, media had discoloration and explants were browning and the buds were break so, further analysis protocols were found by treating with different substances from that, silver nitrate (20%) with KIN (4.36 µM) gives 100% response with 3.011.0 cm length of shoots with 2.010.1 numbers of shoots within 16 days. Nodal explants of TC were cultured on MS medium with various concentrations of BA alone and in combination with NAA or IAA for shoot proliferation. From that, BA (8.82 µM) alone showed better growth response and produced 4.810.2 numbers of shoots with an average length of 3.10.1 cm after 20 days. Small shootlet were transferred to shoot elongation medium with 8.82 µM of BA alone. An average length of 4.820.4 cm with 4.610.2 numbers of shoots produced, 76% of response. The elongated shootlets transferred to half strength MS medium and 6.43 µM of IBA with 3% sucrose produce 5.20.2 rootlets per plant with average root length of 3.20.1 cm after 27 days. Rooted plantlets were transplanted ex vitro. Approximately 80% of plantlets survived.
Integrative construction of regulatory region networks in 127 human reference epigenomes by matrix factorization

Despite large experimental and computational efforts aiming to dissect the mechanisms underlying disease risk, mapping cis-regulatory elements to target genes remains a challenge. Here, we introduce a matrix factorization framework to integrate physical and functional interaction data of genomic segments. The framework was used to predict a regulatory network of chromatin interaction edges linking more than 20,000 promoters and 1.8 million enhancers across 127 human reference epigenomes, including edges that are present in any of the input datasets. Our network integrates functional evidence of correlated activity patterns from epigenomic data and physical evidence of chromatin interactions. An important contribution of this work is the representation of heterogeneous data with different qualities as networks. We show that the unbiased integration of independent data sources suggestive of regulatory interactions produces meaningful associations supported by existing functional and physical evidence, correlating with expected independent biological features.
Life at Low Reynolds Number

Editor’s note: This is a reprint (slightly edited) of a paper of the same title that appeared in the book Physics and Our World: A Symposium in Honor of Victor F. Weisskopf, published by the American Institute of Physics (1976). The personal tone of the original talk has been preserved in the paper, which was itself a slightly edited transcript of a tape. The figures reproduce transparencies used in the talk. The demonstration involved a tall rectangular transparent vessel of corn syrup, projected by an overhead projector turned on its side. Some essential hand waving could not be reproduced.
Species relationships in the genus Helichrysum Mill. (Asteraceae) based onmorphological characters in Iran

The present study considers phenetic and cladistic analyses of 20 populations belong to 19 Helichrysum species, trying to reveal their morphological variations and inter-specific relationships in Iran. To evaluate the species relationships, cluster analyses and principal component analysis were done. Statistical analyses indicated that characters as maximum basal leaf width, maximum stem leaf width, involucre form, achene length and achenial papillae, bud prop, longitudinal plicate in phyllary and stem branched had the most important role as diagnostic characters in intera- genus variation. In general two clusters provided, H. makranicum (Rech. f. & Esfand.) Rech. f. due absence rest buds placed in first cluster and remaining species formed the second cluster. In the second cluster, H. araxinum Takht. ex Kirp. , H. athanaton Georgiadou & Rech. f. , H. artemisioides Boiss. & Hausskn. and H. davisianum Rech. f. with slim stems formed the first sub cluster and H. plicatum DC. , H. polyphyllum Ledeb. , H. pseudoplicatum Nab. - by having phyllaries with longitudinal plicate-, H.psychrophilum Boiss. , H. graveolens (M. B.) Sweet. , H. armenium DC. , H. aucheri Boiss. , H. glandoliferum Schultz. Bip. , H. globiferum DC. , H. leucocephalum Boiss. , H. oligocephalum DC. , H. oocephalum Boiss. , H. pallasii (Spreng.) Ledeb. , and H. rubicundum (C. Kooch) Bornm. , populations -with wide rosette leaf- have been placed together in second sub cluster.
There is no Diophantine D(−1)$D(-1)$ ‐quadruple

A set of positive integers with the property that the product of any two of them is the successor of a perfect square is called Diophantine D(−1)$D(-1)$ ‐set. Such objects are usually studied via a system of generalized Pell equations naturally attached to the set under scrutiny. In this paper, an innovative technique is introduced in the study of Diophantine D(−1)$D(-1)$ ‐quadruples. The main novelty is the uncovering of a quadratic equation relating various parameters describing a hypothetical D(−1)$D(-1)$ ‐quadruple with integer entries. In combination with extensive computations, this idea leads to the confirmation of the conjecture according to which there is no Diophantine D(−1)$D(-1)$ ‐quadruples.
Effects of taphonomic deformation on geometric morphometric analysis of fossils: a study using the dicynodont Diictodon feliceps (Therapsida, Anomodontia)

Taphonomic deformation, the distortion of fossils as a result of geological processes, poses problems for the use of geometric morphometrics in addressing paleobiological questions. Signal from biological variation, such as ontogenetic trends and sexual dimorphism, may be lost if variation from deformation is too high. Here, we investigate the effects of taphonomic deformation on geometric morphometric analyses of the abundant, well known Permian therapsid Diictodon feliceps. Distorted Diictodon crania can be categorized into seven typical styles of deformation: lateral compression, dorsoventral compression, anteroposterior compression, “saddle-shape” deformation (localized collapse at cranial mid-length), anterodorsal shear, anteroventral shear, and right/left shear. In simulated morphometric datasets incorporating known “biological” signals and subjected to uniform shear, deformation was typically the main source of variance but accurate “biological” information could be recovered in most cases. However, in empirical datasets, not only was deformation the dominant source of variance, but little structure associated with allometry and sexual dimorphism was apparent, suggesting that the more varied deformation styles suffered by actual fossils overprint biological variation. In a principal component analysis of all anomodont therapsids, deformed Diictodon specimens exhibit significant dispersion around the “true” position of this taxon in morphospace based on undistorted specimens. The overall variance associated with deformation for Anomodontia as a whole is minor, and the major axes of variation in the study sample show a strong phylogenetic signal instead. Although extremely problematic for studying variation in fossil taxa at lower taxonomic levels, the cumulative effects of deformation in this study are shown to be random, and inclusion of deformed specimens in higher-level analyses of morphological disparity are warranted. Mean morphologies of distorted specimens are found to approximate the morphology of undistorted specimens, so we recommend use of species-level means in higher-level analyses when possible.
Detection and Quantification of Listeria monocytogenes in Ready-to-eat Vegetables, Frozen Vegetables and Sprouts Examined by Culture Methods and Real-time PCR

In this study, a total of 175 samples of ready-to-eat vegetables, frozen vegetables and sprouted seeds originating in 10 states of the European Union and from 32 manufacturers were collected during a period of one year and examined for the presence of Listeria monocytogenes using standard culture methods and qPCR. In addition to these methods, isolation of Listeria monocytogenes was also carried out following a unified sample preparation for combined downstream use in culture and qPCR analysis. Standard culture and culture preceded by unified sample preparation, showed that L. monocytogenes was present in 6.9% and 11.4% of analyzed samples, respectively, in low numbers. Application of qPCR revealed only 2.3% of samples to be positive for L. monocytogenes in small quantities (less than 10 cells/gram). A statistically significant higher occurrence of L. monocytogenes was seen in frozen vegetables compared to ready to eat vegetables (p<0.01; Fisher’s exact post-hoc tests with Bonferroni’s correction) or sprouts (p<0.05; Fisher’s exact post-hoc tests with Bonferroni’s correction). Therefore, temperature abuse in food containing pieces of frozen vegetables without any processing such as cooking, may pose health risks, especially for sensitive individuals such as pregnant women, children, the elderly, and immunocompromised individuals.
Genomic signatures of globally enhanced gene duplicate accumulation in the megadiverse higher Diptera fueling intralocus sexual conflict resolution

Gene duplication is an important source of evolutionary innovation. To explore the relative impact of gene duplication during the diversification of major insect model system lineages, we performed a comparative analysis of lineage-specific gene duplications in the fruit fly Drosophila melanogaster (Diptera: Brachycera), the mosquito Anopheles gambiae (Diptera: Culicomorpha), the red flour beetle Tribolium castaneum (Coleoptera), and the honeybee Apis mellifera (Hymenoptera). Focusing on close to 6,000 insect core gene families containing maximally six paralogs, we detected a conspicuously higher number of lineage-specific duplications in Drosophila (689) compared to Anopheles (315), Tribolium (386), and Apis (223). Based on analyses of sequence divergence, phylogenetic distribution, and gene ontology information, we present evidence that an increased background rate of gene duplicate accumulation played an exceptional role during the diversification of the higher Diptera (Brachycera), in part by providing enriched opportunities for intralocus sexual conflict resolution, which may have boosted speciation rates during the early radiation of the megadiverse brachyceran subclade Schizophora.
Biometric and chemical characteristics of sugarcane varieties for use as forage in limiting soil water conditions

ABSTRACT This study aimed to evaluate the biometric and chemical characteristics of five sugarcane varieties (RB 863129, RB 867515, RB 92579, RB 943365, and RB 98710) grown in a semi-arid climate for use as forage. The experiment was designed as randomized blocks, in a 5 × 2 factorial arrangement (five sugarcane varieties and two evaluation times, 407 and 483 days). Response variables included dry matter productivity, morphological characteristics, chemical composition, digestibility, and ratios among neutral detergent fiber (NDF), Brix, and [. ]
Rett Syndrome Induced Pluripotent Stem Cell-derived Neurons Exhibit Electrophysiological Aberrations

Induced pluripotent stem (iPS) cells generated from patients hold great promise for studying diseases that affect the central nervous system, as differentiation into the neuronal lineage creates a limitless supply of affected cells for disease study. Rett syndrome (RTT) is a neurodevelopmental autism spectrum disorder primarily caused by mutations in the methylCpG-binding protein 2 (MECP2) gene. Due to the inaccessibility of patient neurons, most of what is known about underlying phenotypes has been described using mouse models. iPS cells provide a potential solution, but reprogramming of patient cells is hampered by low efficiency, and early methods of identifying iPS cells involve transgenic techniques that are not translatable to human patient samples. The first part of this thesis describes the generation and characterization of a pluripotency reporter to address this issue. The EOS lentiviral reporter allows real-time observation of pluripotency changes during reprogramming, and is a useful tool for more efficient isolation of reprogrammed cell lines. Further, the EOS selection system can be used in a disease context to reproducibly mark and maintain disease-specific iPS cell lines for future use in disease modelling. Though iPS cells have been used to study RTT in vitro, extensive assessments of neuron function and electrophysiology have not yet been performed. In iii the second part of this thesis, iPS cell lines generated from a RTT mouse model were tested for their ability to model disease in vitro. Directed differentiation of multiple Mecp2-deficient and wild-type iPS cell lines to glutamatergic neurons revealed neurons that lack Mecp2 have a smaller soma size, diminished sodium currents, and are less excitable, firing fewer, prolonged action potentials that are smaller in magnitude. This deficiency in intrinsic excitability was accompanied by a dysfunction at excitatory glutamatergic synapses, which together recapitulate changes previously observed in the Mecp2-deficient mouse brain. Having accumulated counts and recordings from hundreds of neurons with consistent responses among lines, the iPS cell system is a representative model of the neuronal and synaptic defects in RTT. These results illustrate the requirement of MeCP2 in normal neuronal function, and suggest altered neuronal homeostasis or aberrant network circuitry may underlie RTT pathogenesis.
Network-Based Coexpression Analysis Identifies Functional and Prognostic Long Noncoding RNAs in Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC) is a primary liver cancer associated with a growing incidence and extremely high mortality. However, the pathogenic mechanism is still not fully understood. In the present study, we identified 1,631 upregulated and 1,515 downregulated genes and found that cell cycle and metabolism-related pathways or biological processes highly dysregulated in HCC. To assess the biological importance of these DEGs, we carried out weighted gene coexpression network analysis (WGCNA) to identify the functional modules potentially involved in HCC pathogenesis or progression. The five modules were detected with Dynamic Tree Cut algorithm, and GO enrichment analysis revealed that these modules exhibited different biological processes or signaling pathways, such as metabolism-related pathways, cell proliferation-related pathways, and molecules in tumor microenvironment. Moreover, we also observed two immune cells, namely, cytotoxic cells and macrophage enriched in modules grey and brown, respectively, while T helper cell-2 (Th2) was enriched in module turquoise. Among the WGCNA network, four hub long noncoding RNAs (lncRNAs) were identified to be associated with HCC prognostic outcomes, suggesting that coexpression network analysis could uncover lncRNAs with functional importance, which may be associated with prognostic outcomes of HCC patients. In summary, this study demonstrated that network-based analysis could identify some functional modules and some hub-lncRNAs, which may be critical for HCC pathogenesis or progression.
Overgrazing-induced legacy effects may permit Leymus chinensis to cope with herbivory

There is growing evidence that herbivory-induced legacy effects permit plants to cope with herbivory. However, herbivory-induced defense strategies in plants against grazing mammals have received little attention. To further understand the grazing-induced legacy effects on plants, we conducted a greenhouse experiment with Leymus chinensis experiencing different grazing histories. We focused on grazing-induced legacy effects on above-ground spatial avoidance and below-ground biomass allocation. Our results showed that L. chinensis collected from the continuous overgrazing plot (OG) exhibited higher performance under simulated grazing in terms of growth, cloning and colonizing ability than those collected from the 35-year no-grazing plot (NG). The enhanced adaptability of OG was attributed to increased above-ground spatial avoidance, which was mediated by larger leaf angle and shorter height (reduced vertical height and increased leaf angle contributed to the above-ground spatial avoidance at a lower herbivory stubble height, while reduced tiller natural height contributed to above-ground spatial avoidance at a higher herbivory stubble height). Contrary to our prediction, OG pre-allocated less biomass to the rhizome, which does not benefit the herbivory tolerance and avoidance of L. chinensis; however, this also may reflect a tolerance strategy where reduced allocation to rhizomes is associated with increased production of ramets.
Effect of plant-parasitic nematodes on rhizosphere interactions in oaks

1 Zusammenfassung . 2 Chapter One: Introduction. 3 1.1 Nematodes . 3 1.2 Plant-parasitic nematodes . 5 1.3 Multitrophic interactions in the rhizosphere of forest trees . 8 1.4 Carbon dynamics in forest trees and their rhizosphere . 9 1.5 Objectives of the study . 11 Chapter Two: Materials and Methods . 12 2. Microcutting investigations . 12 2.1 The genetic, nutrient allocation and growth responses of oaks to plantparasitic nematodes . 13 2.1.1 Materials . 13 2.1.2 Experimental design . 16 2.1.3 Stable isotope labelling . 17 2.1.4 Sampling. 18 2.2 Interrelationships between plant-parasitic nematodes and beneficial rhizosphere microorganisms . 19 2.2.1. Materials . 20 2.2.2 Experimental design . 20 2.2.3 Sampling. 21 2.3 Rhizopshere carbon dynamics modulated by plant-parasitic nematodes and fungivorous Collembola . 22 2.3. 1 Materials . 22 2.3. 2 Experimental design and labelling . 23 2.3. 3 Pulse labelling of oaks . 24 2.3. 4 Sampling. 24
2-(Benzo[d]thiazol-2-yl) phenyl-4-nitrophenyl alkyl/aryl substituted phosphoramidates: Synthesis, characterization and antimicrobial activity evaluation

GRAPHICAL ABSTRACT ABSTRACT A series of new 2-(benzo[d]thiazol-2-yl) phenyl-4-nitrophenyl alkyl/aryl substituted phosphoramidate derivatives (7a-j) of biological interest are synthesized in two steps via an in situ process without the isolation of the intermediate. 2-(Benzo[d]thiazol-2-yl) phenol (3) was treated with 4-nitrophenyl phosphorodichloridate(4) to obtain the monochloro intermediate, 2-(benzo[d]thiazol-2-yl)phenyl (4-nitrophenyl) phosphorochloridate(5). It was subsequently reacted with various amines, 6(a-j) to afford the desired title products. IR, NMR (1H, 13C and 31P), mass spectral and elemental analysis are used to characterize the structures of the newly synthesized compounds. The antibacterial and antifungal activities are determined by the growth of inhibition of bacteria and fungi of the title compounds at two concentrations, 50 and 100 µg/mL, and minimum inhibitory concentrations to the active compounds. The compounds 7e, 7f and 7j exhibited promising inhibition activity against bacterial strains and 7c, 7e and 7i against A. niger and C. albicans and MIC values are in the range of 10.0–15.0 µg/mL.
Synthesis of Hsv Epitope Peptides with Acid Sensitive Asp-Pro Bond

Peptides from Herpes Simplex virus type I glycoprotein-D,containing the Asp-Pro bond were synthesised by SPPS using benzyl or cyclohexyl (cHex) protection at the Asp/Glu side chains. Increased stability of the cHex group was demonstrated during the treatment with TMSOTf-thioanisole/TFA. This observation was successfully utilised to prepare partly protected 9-mer peptides and their 18-mer derivatives by fragment condensation both in solution and on solid support
Research Note. New data on plant parasitic nematode Longidorus distinctus Lamberti, Choleva & Agostinelli, 1983 (Nematoda: Longidoridae) from Poland

Summary During a survey on the occurrence of the plant parasitic nematodes of the family Longidoridae in Poland, 925 soil samples were taken. Longidorus distinctus was present in 10 (1.08 %) of these samples. In this Research Note we provide: 1) distribution map of these populations, 2) morphometric data, 3) sequence data for D2-D3 28S rDNA and (partial)18S-ITS1 -5.8S(partial) markers and 4) LdistFOR primer (5′-GGCTGTAAAGATATATGCGT-3’) effective in obtaining ITS1 sequence for the species. Morphometric similarities and dissimilarities with data on other published populations are discussed.
miRNA detection and analysis from high-throughput small RNA sequencing data

Small RNAs (sRNAs) are a broad class of short regulatory non-coding RNAs. microRNAs (miRNAs) are a special class of -21-22 nucleotide sRNAs which are derived from a stable hairpin-like secondary structure. miRNAs have critical gene regulatory functions and are involved in many pathways including developmental timing, organogenesis and development in both plants and animals. Next generation sequencing (NGS) technologies, which are often used for identifying miRNAs, are continuously evolving, generating datasets containing millions of sRNAs, which has led to new challenges for the tools used to predict miRNAs from such data. There are several tools for miRNA detection from NGS datasets, which we review in this thesis, identifying a number of potential shortcomings in their algorithms. In this thesis, we present a novel miRNA prediction algorithm, miRCat2. Our algorithm is more robust to variations in sequencing depth due to the fact that it compares aligned sRNA reads to a random uniform distribution to detect peaks in the input dataset, using a new entropy-based approach. Then it applies filters based on the miRNA biogenesis on the read alignment and on the computed secondary structure. Results show that miRCat2 has a better specificity-sensitivity trade-off than similar tools, and its predictions also contains a larger percentage of sequences that are downregulated in mutants in the miRNA biogenesis pathway. This con�rms the validity of novel predictions, which may lead to new miRNA annotations, expanding and contributing to the field of sRNA research.