Miracle-dz/UniFAR-FTUs huggingface dataset:
Temporal metabolic profiling of the Quercus suber–Phytophthora cinnamomi system by middle-infrared spectroscopy

Summary The oomycete Phytophthora cinnamomi is an aggressive plant pathogen, detrimental to many ecosystems including cork oak (Quercus suber) stands, and can inflict great losses in one of the greatest ‘hotspots’ for biodiversity in the world. Here, we applied Fourier transform-infrared (FT-IR) spectroscopy combined with chemometrics to disclose the metabolic patterns of cork oak roots and P. cinnamomi mycelium during the early hours of the interaction. As early as 2 h post-inoculation (hpi), cork oak roots showed altered metabolic patterns with significant variations for regions associated with carbohydrate, glycoconjugate and lipid groups when compared to mock-inoculated plants. These variations were further extended at 8 hpi. Surprisingly, at 16 hpi, the metabolic changes in inoculated and mock-inoculated plants were similar, and at 24 hpi, the metabolic patterns of the regions mentioned above were inverted when compared to samples collected at 8 hpi. Principal component analysis of the FT-IR spectra confirmed that the metabolic patterns of inoculated cork oak roots could be readily distinguished from those of mock-inoculated plants at 2, 8 and 24 hpi, but not at 16 hpi. FT-IR spectral analysis from mycelium of P. cinnamomi exposed to cork oak root exudates revealed contrasting variations for regions associated with protein groups at 16 and 24 h post-exposure (hpe), whereas carbohydrate and glycoconjugate groups varied mainly at 24 hpe. Our results revealed early alterations in the metabolic patterns of the host plant when interacting with the biotrophic pathogen. In addition, the FT-IR technique can be successfully applied to discriminate infected cork oak plants from mock-inoculated plants, although these differences were dynamic with time. To a lesser extent, the metabolic patterns of P. cinnamomi were also altered when exposed to cork oak root exudates.
Highly Predictive Blacklists

We propose a radically different approach to source address blacklist formulation, which we call highly predictive blacklisting. We present a probabilistic attacker ranking algorithm for blacklist formulation for use in centralized collaborative log sharing infrastructures, such as the DShield.org security log repository. Our objective is not simply to identify a global list of proliﬁc attackers, which is among the most widely used strategies today. Rather, we construct a custom blacklist per contributor that reﬂects the most probable set of attackers that will attack the target contributor over a prediction window that may last several days into the future. Our attacker rank equation, inspired by hyperlink document link analysis, prioritizes candidate blacklist entries based on the how frequently they are observed by other peer contributors who share signiﬁcant attacker overlap with the target blacklist user. Through an examination of real DShield datasets we conduct a comparative assessment of the highly predictive blacklist strategy versus three competing blacklist formulation meth-ods. Our results show that highly predictive blacklist entries consistently yield much higher attacker hit rates for the vast majority of contributors in the repositories. In addition, the hit rate quality of these blacklists can last multiple days into the future. We discuss a practical implementation of our highly predictive blacklist algorithm, which we have posted to the DShield.org website for use by DShield log contributors.
Independent effects of habitat loss, habitat fragmentation and structural connectivity on forest‐dependent birds

Aim Habitat loss and fragmentation are amongst the greatest threats to biodiversity world‐wide. However, there is still little evidence on the relative influence of these two distinct processes on biodiversity, and no study, to date, has investigated the independent contribution of structural connectivity in addition to habitat loss and fragmentation. The aim of this study is to evaluate the independent effects of habitat loss (the decrease in total amount of habitat), habitat fragmentation per se (habitat subdivision) and structural connectivity (in the form of hedgerow networks) on the distribution of seven resident forest‐dependent birds in central Italy.
Genetic analysis of partial rust resistance in faba beans

Five parent populations of faba bean, differing in reaction to rust disease, were crossed to prepare a complete diallel of F1 hybrids. Detached leaves of the parents and F1 hybrids were challenged with 3 Australian rust populations and symptom development was monitored from 11 to 16 days after inoculation, using a disease score related to the percentage of leaf area covered with pustules, and a nominal value for pustule size. Additive gene action was very important in determining the response to rust disease, with ILB 3025 and ILB 3107 having similar low disease scores, Fiord and Acc 327 having high values, and Icarus an intermediate value. Cytoplasmic effects were also critical, with ILB 3025 having the most susceptible cytoplasm and ILB 3107 the most resistant, and this was most readily detected in terms of the size of the pustule. Heterosis conferred slightly lower disease scores and dominance was significant but of lesser importance than additive gene action, particularly for disease score. Rust population host gene action interactions were significant by the end of the observation period, but were much smaller than the main effects. The hybrid ILB 3107 ILB 3025 had less disease development than either parent, indicating the potential for developing more resistant cultivars using transgressive segregation. ILB 3107 shows particular promise for use as a female line as it had both nuclear and cytoplasmic factors to contribute to the development of resistant cultivars.
Evaluation of different cytokinins for in vitro multiplication of banana var. Robusta.

Tissue culture technique in multiplication of banan a is very efficient and widely applied. The technology will give high-quality, genetically similar plants, free of d iseases and nematodes. Much of the planting materia l used in commercial plantations, especially smallholder production, com es from mass micropropagation. The method of shoot tip culture has been most widely used in banana. However, use of a typical tissue culture protocol is applicable as th e technology is highly dependent on genotypes and a number of local variab les. In the present study, banana cultivar Robusta was subjected to different cytokinins amended in MS Basal medium. Cy tokinins showed differential effects in the micropr agation of Robusta cultivar. Among the different cytokinins te sted, BAP was found to be the best cytokinin at an optimum concentration 5mg/L.
RESEARCH REGARDING THE WATER CONSUMPTION OF TOMATOES, GREEN PEPPER AND CUCUMBERS CULTIVATED IN SOLARIUMS

In such conditions, saving water represents a very important aspect, both economically and socially. But in horticulture saving water must consider another very important aspect, that of providing food for a continuously growing population. So horticultors have the difficult task of obtaining big productions as well as saving water. Our research come to support the cultivators who grow tomatoes, green peppers and cucumbers in solariums. Determining precisely the water consumption of this species will create the possibility of avoiding both the excess and the lack of water of the tomatoes, green peppers and cucumbers grown in solariums, each of them having negative effects on production. Establishing the best water regime of this crop will lead to the application of optimum water quantities, at the right time and by the most efficient irrigation methods. This way, the cultivators will have the possibility of obtaining high productions, of superior quality, justified economically.
A New Enzyme, β-Diketone Hydrolase: a Component of a Poly(vinyl alcohol)-degrading Enzyme Preparation

Some soil bacteria degrade and assimilate poly(vinyl alcohol) (PVA), a water-soluble synthetic polymer.1 ~3) An enzyme activity responsible for the degradation of PVA molecules was found in a cultivation broth of a bacterial symbiotic mixed culture grown on a minimal medium containing PVA as a sole source of carbon and energy.2'4) Twodifferent enzymes have been isolated from the cultivation broth in a homogeneousstate, one is an oxidase5) and the other a hydrolase.6) The
Context-dependent gene expression programs promote lymphocyte development and function and suppress transformation

Coordinated orchestration of gene expression programs at the transcriptional, post-transcriptional, and posttranslational levels is essential for development and function of all cells, including lymphocytes. Normal tissue function also demands that the genome be faithfully passed from mother to daughter cell during the many rounds of cell division required to generate a mammalian organism. Genome integrity is maintained in part by integration of DNA damage signaling with cell cycle control. These mechanisms are especially critical for lymphocytes following V(D)J recombination, since V(D)J recombination involves genetic cutting and pasting of germline gene segments to form antigen receptors (AgRs). Using conditional deletion of the p53 tumor suppressor in mice, I found that p53 promotes genome stability in developmental stage-specific ways. Inactivation of p53 beginning in hematopoietic stem cells yields thymic tumors with aneuploidy; whereas deletion of p53 at the beginning of thymocyte development results in tumors bearing T cell AgR translocations. I also show that downregulation of the G1 phase cyclin D3 occurs in immature B and T cells in response to exogenously-induced DNA breaks through lineage-specific mechanisms. Further, this downregulation of D3 may be important for delaying S phase entry in response to DNA breaks, providing an additional mechanism to promote genome stability during lymphocyte development. Finally, I discovered novel roles of the HuR RNA-binding protein in regulating B cell function. Specifically, HuR is largely dispensable for B cell development and in vitro B cell function; however, it is crucial for the in vivo T cell-dependent immune response in mice, likely by facilitating the ability of B cells to interact with other immune cells in the follicular milieu. This work provides new insight into the lineageand developmental stage-specific ways in which complex gene expression programs contribute to the normal development and function of B and T lymphocytes, while suppressing malignant transformation. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Cell & Molecular Biology First Advisor Craig H. Bassing
Soils of South Africa

This is the first book in 70 years on soils of South Africa and is a significant scientific contribution on the understanding of South African soils. As the title suggests, this book's main objective is to give the reader a comprehensive view on the unique soils of South Africa, their distribution, properties, classification, genesis and land use. The author has developed his own grouping system with which all the soils from the South African soil classification system are grouped into fourteen distinctive soil groups. This totally new concept for South African soils and the key on how to do this is well thought out. This book compares well with any book written in the U.S.A. or Europe and is quite unique in the way the author strikes a relationship between animals and soils. There have been no previous attempts in the literature to illustrate the contribution of animals to soil formation so clearly as this book.
Is maximizing protection the same as minimizing loss? Efficiency and retention as alternative measures of the effectiveness of proposed reserves

We used two measures to compare the effectiveness of 52 conservation criteria in achieving conservation targets for forest types. The first measure was efficiency. Although widely used, efficiency assumes no loss or reduction of biodiversity features before conservation is implemented. This is invalid in many situations. Often, it is more realistic to assume gradual implementation accompanied by incremental, predictable reduction and loss of biodiversity features. We simulated future landscapes resulting from the annual interplay of loss and conservation of forest types. We then based our second measure, retention, on how well criteria scheduled conservation action to prevent targets being compromised. The simulations partly support predictions about the best criteria for scheduling implementation with continuing biodiversity loss. Retention was weakly related or unrelated to efficiency across 52 criteria. Although retention values were sensitive to changes in targets and rates of conservation and forest loss, one criterion consistently produced highest retention values.
Alternative phage-host interaction in Lactococcus lactis: the carrier state drives rapid evolution of phages

Lactococcus lactis is a lactic acid bacterium widely used as starter culture for the manufacture of fermented milk products like quark, buttermilk and cheese. Bacteriophage infection of starter cultures is one of the biggest causes of fermentation failure and, therefore, lactococcal phages have received great attention from the scientific community in the past decades. In this work we present evidence for the establishment of a carrier state life cycle (CSLC) by a bacteriophage belonging to the c2 species, in the model laboratory strain L. lactis MG1363. Our results show that infection of L. lactis MG1363 with a second, dissimilar, c2 bacteriophage can induce the CSLC phage to enter an active lytic life cycle. The viral progeny obtained after this infection is a mixed population of phages with differences in their genome sequences and host ranges, indicative of an extremely rapid evolution process. We discuss the possible implications of this phage-host interaction, both with respect to bacteriophage evolution and phage adaptation to different hosts. IMPORTANCE Our results broaden the current know-how on the yet poorly investigated phage-host interaction mechanism of CSLC, propose a new bacteriophage evolution mechanism, and demonstrate that the outcome of phage infections is possibly more intricate than presently acknowledged.
A rod-like bacterium is responsible for high molybdenum concentrations in the tropical sponge Halichondria phakellioides

The tropical marine sponge, Halichondria phakellioides, from Darwin Harbour contains high concentrations of molybdenum. A rod-like bacterium extracellular in sponge tissue was observed using transmission electron microscopy. Molybdenum was located within these bacteria, but not in sponge cells. This is the first report of the trace element molybdenum localised in a sponge bacterial symbiont. Many different bacterial symbionts were identified in the sponge by sequence analysis so the identity of the molybdenum-accumulating bacterium could only be inferred.
A versatile system to introduce clusters of genomic double-strand breaks in large cell populations

In vitro assays for clustered DNA lesions will facilitate the analysis of the mechanisms underlying complex genome rearrangements such as chromothripsis, including the recruitment of repair factors to sites of DNA double-strand breaks. We present a novel method generating localized DNA double-strand breaks using UV-irradiation with photomasks. The size of the damage foci and the spacing between lesions are fully adjustable, making the assay suitable for different cell types and targeted areas. We validated this set-up with genomically stable epithelial cells, normal fibroblasts, pluripotent stem cells and patient-derived primary cultures. Our method does not require a specialized device such as a laser, making it accessible to a broad range of users. Sensitization by BrdU incorporation is not required, which enables analyzing the DNA damage response in post-mitotic cells. Irradiated cells can be cultivated further, followed by time-lapse imaging or used for downstream biochemical analyses, thanks to the high-throughput of the system. Importantly, we showed genome rearrangements in the irradiated cells, providing a proof of principle for the induction of structural variants by localized DNA lesions.
Visualizing drug inhibitor binding interactions using microcrystal electron diffraction

Visualizing drug inhibitor binding interactions at the atomic level is important for both structure-based drug design and fragment-based screening methods. Rapid and uniform soaking with potentially less lattice defects make small macromolecular crystals attractive targets for studying ligand biding using 3D microcrystal electron diffraction (MicroED). However, so far no drug inhibitor binding interactions could unambiguously be resolved by electron diffraction. Here, we use MicroED to study the binding of a sulfonamide inhibitor to human carbonic anhydrase isoform II (HCA II). We show that MicroED data can efficiently be collected in-house on a conventional TEM from thin hydrated microcrystals after a brief soaking with the clinical drug inhibitor acetazolamide (AZM). The data are of high enough quality to unequivocally fit and resolve the inhibitor bound to the active site of the protein. We anticipate MicroED can play an important role in future drug discovery experiments, complementing existing methods in structural biology such as x-ray and neutron diffraction.
A simple and rapid colorimetric method for the determination of amylose in starch products

A method for the determination of the amylose content in starch has been developed which is based on the colorimetric measurement of the iodine complexes formed with amylose and amylopectin. The method requires measurement at only one wavelength and avoids the use of harsh dispersants for the starch. Dimethyl sulphoxide is used as the dispersant and a wavelength of 600 nm can be used for measurement of the amylose content of starches from different botanical sources. A linear relationship was obtained between absorbance and amylose concentration for mixtures of amylose and amylopectin standards, and this forms the basis of the determination. The method is rapid, simple, accurate and does not require the use of multi-component analysis of spectra, since a wavelength is chosen that suits the particular starch being analysed. It can be adapted to a micro-scale method if necessary.
Asynchrony between virus diversity and antibody selection limits influenza virus evolution

Seasonal influenza viruses create a persistent global disease burden by evolving to escape immunity induced by prior infections and vaccinations. New antigenic variants have a substantial selective advantage at the population level, but these variants are rarely selected within-host, even in previously immune individuals. Using a mathematical model, we show that the temporal asynchrony between within-host virus exponential growth and antibody-mediated selection could limit within-host antigenic evolution. If selection for new antigenic variants acts principally at the point of initial virus inoculation, where small virus populations encounter well-matched mucosal antibodies in previously infected individuals, there can exist protection against reinfection that does not regularly produce observable new antigenic variants within individual infected hosts. Our results provide a theoretical explanation for how virus antigenic evolution can be highly selective at the global level but nearly neutral within host. They also suggest new avenues for improving influenza control.
Answer to Reviewers

This article gives an overview of a unique measurement campaign that uses cutting-edge instrumentation with the intent of answering difficult and important questions for wind engineering. The dataset seems promising and the authors seem to have put a lot of thought into instrument choice, placement, analysis, etc. I have specific comments on the attached PDF. An overview of key comments is below: Technical – I would like to request a little more on (i) coastal internal boundary layers, including previous work/measurements where appropriate; (ii) the validity of assuming vr ==wind speed; (iii) acknowledgment of other coherence models in addition to davenport; (iv) can these data potentially be used to improve the way we model coherence rather than rely on axisting model for coherence for their very analysis? ; (v) if/how/when can any of these data be shared with other groups for collaborative research; (vi) a discussion on where we need to go in instrumentation development so you could get more and better data next time (your dataset is great in comparison to past efforts but obviously we have a long way to go); (vii) how do you anticipate modeling studies being able to complement this dataset? ; (viii) at the end, please provide some big-picture take-aways of how far this dataset can take us – for technology development in the context of wind plants, offshore turbine design and operation, coastal infrastructure, etc; (ix) why wasn’t the lidar data validated against the sonics at the beginning, just at the end? Other minor – while the article is well written and relatively easy to follow, it could benefit substantially from editing by a professional communications specialist (several sentences are a bit strange or have small mistakes); clean up on nomenclature, variable definition, figure improvements, etc are noted in the pdf.
Schistonchus (Aphelenchoididae) from Ficus (Moraceae) in Australia, with description of S. aculeata sp. n.

A checklist of Schistonchus collected from Ficus spp. in Australia and stored in the Waite Nematode Collection at the University of Adelaide is presented. Within Australia, Schistonchus contains 12 morphospecies and four nominal species, based on a combination of the following characters: body shape when heat-relaxed, position of excretory pore, length of post-uterine sac, spicule form, and number and position of caudal papillae. Up to four morphospecies of Schistonchus have been collected from one species of Ficus and, in several cases, one morphospecies of Schistonchus has been collected from more than one host fig species. A phylogenetic tree based on D2/D3 sequences showed that Australian collections of Schistonchus fall into two clades, suggestive of endemic and introduced lineages with host switching. Schistonchus aculeata sp. n. is described from F. aculeata and F. opposita and differentiated from other species of Schistonchus by having the excretory pore opening near the lips, a short post-uterine sac, rosethorn-shaped spicules, arcuate gubernaculum or thickening of dorsal wall, amoeboid sperm, and three pairs of caudal papillae (one pair adcloacal, one just posterior to mid-tail, and one near the tail tip), association with Kradibia spp. pollinating wasps and apparent biogeographical range. A key to the known species and morphospecies of Schistonchus from Australia is presented.