Miracle-dz/UniFAR-FTUs huggingface dataset:
Associative database of protein sequences

MOTIVATION We present a new concept that combines data storage and data analysis in genome research, based on an associative network memory. As an illustration, 115 000 conserved regions from over 73 000 published sequences (i.e. from the entire annotated part of the SWISSPROT sequence database) were identified and clustered by a self-organizing network. Similarity and kinship, as well as degree of distance between the conserved protein segments, are visualized as neighborhood relationship on a two-dimensional topographical map. RESULTS Such a display overcomes the restrictions of linear list processing and allows local and global sequence relationships to be studied visually. Families are memorized as prototype vectors of conserved regions. On a massive parallel machine, clustering and updating of the database take only a few seconds; a rapid analysis of incoming data such as protein sequences or ESTs is carried out on present-day workstations. AVAILABILITY Access to the database is available at http://www.bioinf. mdc-berlin.de/unter2.html++ + CONTACT (hanke,lehmann,reich)@mdc-berlin.de; bork@embl-heidelberg.de
Maize Homologs of CCoAOMT and HCT, Two Key Enzymes in Lignin Biosynthesis, Form Complexes with the NLR Rp1 Protein to Modulate the Defense Response1

Maize caffeoyl CoA O-methyltransferase and hydroxycinnamoyltransferase proteins, which are key enzymes in lignin biosynthesis, form a complex with NLR Rp1 protein to regulate the hypersensitive defense response. Disease resistance (R) genes encode nucleotide binding Leu-rich-repeat (NLR) proteins that confer resistance to specific pathogens. Upon pathogen recognition they trigger a defense response that usually includes a so-called hypersensitive response (HR), a rapid localized cell death at the site of pathogen infection. Intragenic recombination between two maize (Zea mays) NLRs, Rp1-D and Rp1-dp2, resulted in the formation of a hybrid NLR, Rp1-D21, which confers an autoactive HR in the absence of pathogen infection. From a previous quantitative trait loci and genome-wide association study, we identified genes encoding two key enzymes in lignin biosynthesis, hydroxycinnamoyltransferase (HCT) and caffeoyl CoA O-methyltransferase (CCoAOMT), adjacent to the nucleotide polymorphisms that were highly associated with variation in the severity of Rp1-D21-induced HR. We have previously shown that the two maize HCT homologs suppress the HR conferred by Rp1-D21 in a heterologous system, very likely through physical interaction. Here, we show, similarly, that CCoAOMT2 suppresses the HR induced by either the full-length or by the N-terminal coiled-coil domain of Rp1-D21 also likely via physical interaction and that the metabolic activity of CCoAOMT2 is unlikely to be necessary for its role in suppressing HR. We also demonstrate that CCoAOMT2, HCTs, and Rp1 proteins can form in the same complexes. A model is derived to explain the roles of CCoAOMT and HCT in Rp1-mediated defense resistance.
Insights on the Impact of Arbuscular Mycorrhizal Symbiosis on Tomato Tolerance to Water Stress1[OPEN]

Arbuscular mycorrhizal symbiosis can improve tolerance to severe water stress conditions in tomato plants. Arbuscular mycorrhizal (AM) fungi, which form symbioses with the roots of the most important crop species, are usually considered biofertilizers, whose exploitation could represent a promising avenue for the development in the future of a more sustainable next-generation agriculture. The best understood function in symbiosis is an improvement in plant mineral nutrient acquisition, as exchange for carbon compounds derived from the photosynthetic process: this can enhance host growth and tolerance to environmental stresses, such as water stress (WS). However, physiological and molecular mechanisms occurring in arbuscular mycorrhiza-colonized plants and directly involved in the mitigation of WS effects need to be further investigated. The main goal of this work is to verify the potential impact of AM symbiosis on the plant response to WS. To this aim, the effect of two AM fungi (Funneliformis mosseae and Rhizophagus intraradices) on tomato (Solanum lycopersicum) under the WS condition was studied. A combined approach, involving ecophysiological, morphometric, biochemical, and molecular analyses, has been used to highlight the mechanisms involved in plant response to WS during AM symbiosis. Gene expression analyses focused on a set of target genes putatively involved in the plant response to drought, and in parallel, we considered the expression changes induced by the imposed stress on a group of fungal genes playing a key role in the water-transport process. Taken together, the results show that AM symbiosis positively affects the tolerance to WS in tomato, with a different plant response depending on the AM fungi species involved.
Patellar taping, the theory versus the evidence: a review

AbstractAlthough taping of the patella is a cheap and easy clinical procedure used on patients with patellofemoral pain, the reasons for its success have not yet been established. The original rationale was that taping could realign the patella, enhance the contraction of the vastus medialis oblique muscle, and as a consequence alleviate the patient's pain. This paper reviews the literature available on this technique to ascertain whether the theories for its success can be substantiated by objective evidence.
Comparison of a fludarabine and melphalan combination‐based reduced toxicity conditioning with myeloablative conditioning by radiation and/or busulfan in acute myeloid leukemia in Japanese children and adolescents

The relative efficacy of allogeneic hematopoietic cell transplantation (allo‐HCT) after reduced toxicity conditioning (RTC) compared with standard myeloablative conditioning (MAC) in pediatric patients with acute myeloid leukemia (AML) has not been studied extensively. To address whether RTC is a feasible approach for pediatric patients with AML in remission, we performed a retrospective investigation of the outcomes of the first transplant in patients who had received an allo‐HCT after RTC or standard MAC, using nationwide registration data collected between 2000 and 2011 in Japan.
Série de treinamento intervalado de alta intensidade como índice de determinação da tolerância à acidose na predição da performance anaeróbia de natação

The aim of the present study was to determine the acidosis tolerance through one high intensity interval swim serie and to relate with anaerobic threshold speed (ATS), blood lactate peak concentration ([Lac]peak), anaerobic work capacity (AWC), stroke rate (SR), stroke length (SL) and stroke index (SI) in swimming 100 m performance prediction. Ten swimmers performed six maximal swims along 100 m by crawl style with 6 minutes for a rest. Blood samples were taken 5 minutes before each swim for lactate analyses ([Lac)]. Through the division of the [Lac] for the time to complete the 6 swims, was determined acidosis tolerance (AT). The numbers of strokes in the six efforts were taken for SR, SL and SI determination. A maximal 100 m swim was considered as performance parameter (P100) and blood samples were taken for blood lactate peak concentration determination ([Lac]peak). Three progressive efforts along 400 m were accomplished for ATS determination corresponding to 3.5 mM lactate fixed concentration; 200 and 400 m maximal efforts were accomplished for AWC determination by linear regression (linear coefficient). The results showed significant correlations (p < 0.05) of AT with ATS (r = 0.77), [Lac]peak (r = 0.81), SL (r = 0.85) and SI (r = 0.84). Moreover, P100 was correlated with ATS (r = 0.88), AT (r = 0.95), [Lac]peak (r = 0.77), SL (r = 0.97) and SI (r = 0.96). It was concluded that AT determined through a high intensity training series appears to be useful to anaerobic fitness determination and 100 m swim performance prediction, besides suffer SL and SI influence.
Delayed hypersensitivity reactions to sulphonamides: syndromes, pathogenesis and management.

Sulphonamide antibiotics are a commonly used, and important, group of antibiotics in veterinary dermatology. However, many of the commonly used sulphonamides such as sulphamethoxazole, sulpha-diazine, or sulphasalazine are associated with idiosyncratic drug reactions in dogs. This paper will review the clinical syndromes, pathogenesis of sulphonamide hypersensitivity reactions and current methods for predicting these occurrences.
Optimierter Radioextraktionsassay zur quantitativen Bestimmung der Aktivität von Diaminooxidase (DAO) in humanem Serum und Plasma

Patients intolerant to histamine-containing foods (histamine intolerance) frequently suffer from diminished histamine degradation based on deficiency or reduced activity of the enzyme diamine oxidase (DAO). Here, we present an easy-to-use, commercially available test kit for the quantification of DAO activity in blood. Radiolabeled putrescine is added as a substrate to 100 μl of plasma or serum. DAO converts one amino group to an aldehyde. The resulting molecule spontaneously reacts to cyclic Δ 1 -pyrroline which can be extracted selectively by ethylacetate. With an optimized buffer system, we could improve the yield of extractable reactants four-fold compared to previous systems. A calibration curve with DAO from porcine kidney is used for quantification. Intraassay variation is < 10% (3.5 - 14%,n = 20), interassay variation is < 15% (4 - 21%, n = 10). Mean recovery of DAO added to samples was 104% (86 - 123%, n = 20). Results are available within three hours. DAO activity in samples was stable at 4 °C for one week, storage at -20 °C with repeated freeze cycles did not affect activity. This assay is a reliable tool for the determination of blood DAO activity and is a helpful tool in the diagnosis of non-allergic food hypersensitivities. Due to the good stability of DAO, blood samples may be drawn in the doctors office and shipped to the diagnostic lab.
How do I interpret a p value?

A p‐value is a number between 0 and 1 that is extremely useful in interpreting research results. Using comparison of the means of two samples as an example, a p‐value <0.05 suggests that there is enough evidence to presume a real difference between groups from which the samples were drawn (that the “null hypothesis” can be rejected). We say that the difference between the means is statistically significant. However, it isn't iron clad proof and there is still a chance that there is really no difference. Furthermore, a statistically significant difference may not be clinically significant if it is not enough to appreciably affect patient outcomes. We describe the theory behind p‐values and some common errors in interpretation.
Palliative care of patients with motor neurone disease

Abstract As there is no curative treatment for motor neurone disease (MND), palliative care is appropriate from the time of diagnosis with the aim of managing the symptoms and problems faced by the patient, and their family, allowing the maintenance of quality of life. This will involve a multidisciplinary assessment considering all the aspects of care – physical, psychological, social and spiritual – of both the person with MND and their close family/carers. The care provided may include the consideration of many ethical dilemmas, especially as death approaches and careful discussion and team involvement is essential. This paper provides recommendations for the appropriate management and support of patients with MND so that they are able to die peacefully.
Translokationsnachweis bei Lymphomen in der Pathologie

Der Nachweis von Translokationen ist heute integrativer Bestandteil der hamatopathologischen Diagnostik. Ihr Nachweis in Non-Hodgkin Lymphomen nahm in den letzten Jahren stark an Bedeutung zu, da neben ihrer diagnostischen Wertigkeit zunehmend auch ihre prognostische und pradiktive Voraussagekraft erkannt wurde. Der Nachweis dieser Translokationen kann dank verfeinerten Aufarbeitungsprozessen der Gewebe nicht mehr nur an Frischmaterial, sondern auch an Formalin fixierten und Paraffin eingebetteten, selbst entkalkten Biopsien nachgewiesen werden. Zum Einsatz kommen zwei molekulare Untersuchungs-Techniken: Hybridisierungs- (Southern blot, FISH) und Genamplifikationsmethoden (PCR, RT-PCR). Trotz der zahlreichen bekannten Translokationen fand bis jetzt nur ein kleiner Anteil den Eingang in die Routine-Diagnostik. Gemas der Haufigkeit der entsprechenden Lymphome sind Translokationen besonders in B-Zell Lymphomen gut untersucht, wahrend in T-Zell Lymphomen nur einige wenige charakterisiert wurden. Der nachfolge.
Transcatheter embolization with bucrylate (in 100 patients)

Since 1974 we have been investigating the role of transcatheter embolization with bucrylate. During this period of time we have learned a great deal about the use of bucrylate for such purposes. Because of its unique properties, which can be varied to some degree by angiographic techniques, the tissue adhesive can be used successfully as an embolic material in a wide spectrum of difficult clinical situations. The material, however, is not easy to use and we have experienced some complications in its use. In order to minimize these complications, one must have knowledge of the inherent risks when one embolizes a particular region. In the stomach, one must be concerned with infarction; in arteriovenous malformations, with pulmonary embolization, and in the spleen, with the development of an abscess (Drawing 6). [See figure in the PDF file] Control of the embolization procedure is crucial to a successful outcome. This control can be achieved by: A. Selective catheter positioning. B. Opacification of the tiss.
A Palmitic Acid Elongase Affects Eicosapentaenoic Acid and Plastidial Monogalactosyldiacylglycerol Levels in Nannochloropsis1

A heterokont palmitic acid desaturase initiates the production of eicosapentaenoic acid in the endoplasmic reticulum of Nannochloropsis, which is specifically used for monogalactosyldiacylglycerol assembly in the secondary plastid. Nannochloropsis species are oleaginous eukaryotes containing a plastid limited by four membranes, deriving from a secondary endosymbiosis. In Nannochloropsis, thylakoid lipids, including monogalactosyldiacylglycerol (MGDG), are enriched in eicosapentaenoic acid (EPA). The need for EPA in MGDG is not understood. Fatty acids are de novo synthesized in the stroma, then converted into very-long-chain polyunsaturated fatty acids (FAs) at the endoplasmic reticulum (ER). The production of MGDG relies therefore on an EPA supply from the ER to the plastid, following an unknown process. We identified seven elongases and five desaturases possibly involved in EPA production in Nannochloropsis gaditana. Among the six heterokont-specific saturated FA elongases possibly acting upstream in this pathway, we characterized the highly expressed isoform Δ0-ELO1. Heterologous expression in yeast (Saccharomyces cerevisiae) showed that NgΔ0-ELO1 could elongate palmitic acid. Nannochloropsis Δ0-elo1 mutants exhibited a reduced EPA level and a specific decrease in MGDG. In NgΔ0-elo1 lines, the impairment of photosynthesis is consistent with a role of EPA-rich MGDG in nonphotochemical quenching control, possibly providing an appropriate MGDG platform for the xanthophyll cycle. Concomitantly with MGDG decrease, the level of triacylglycerol (TAG) containing medium chain FAs increased. In Nannochloropsis, part of EPA used for MGDG production is therefore biosynthesized by a channeled process initiated at the elongation step of palmitic acid by Δ0-ELO1, thus acting as a committing enzyme for galactolipid production. Based on the MGDG/TAG balance controlled by Δ0-ELO1, this study also provides novel prospects for the engineering of oleaginous microalgae for biotechnological applications.
Connecting the Molecular Structure of Cutin to Ultrastructure and Physical Properties of the Cuticle in Petals of Arabidopsis1[OPEN]

GPAT6 and DCR play different roles in structuring the cell wall-cuticle continuum. The plant cuticle is laid down at the cell wall surface of epidermal cells in a wide variety of structures, but the functional significance of this architectural diversity is not yet understood. Here, the structure-function relationship of the petal cuticle of Arabidopsis (Arabidopsis thaliana) was investigated. Applying Fourier transform infrared microspectroscopy, the cutin mutants long-chain acyl-coenzyme A synthetase2 (lacs2), permeable cuticle1 (pec1), cyp77a6, glycerol-3-phosphate acyltransferase6 (gpat6), and defective in cuticular ridges (dcr) were grouped in three separate classes based on quantitative differences in the ν(C=O) and ν(C-H) band vibrations. These were associated mainly with the quantity of 10,16-dihydroxy hexadecanoic acid, a monomer of the cuticle polyester, cutin. These spectral features were linked to three different types of cuticle organization: a normal cuticle with nanoridges (lacs2 and pec1 mutants); a broad translucent cuticle (cyp77a6 and dcr mutants); and an electron-opaque multilayered cuticle (gpat6 mutant). The latter two types did not have typical nanoridges. Transmission electron microscopy revealed considerable variations in cuticle thickness in the dcr mutant. Different double mutant combinations showed that a low amount of C16 monomers in cutin leads to the appearance of an electron-translucent layer adjacent to the cuticle proper, which is independent of DCR action. We concluded that DCR is not only essential for incorporating 10,16-dihydroxy C16:0 into cutin but also plays a crucial role in the organization of the cuticle, independent of cutin composition. Further characterization of the mutant petals suggested that nanoridge formation and conical cell shape may contribute to the reduction of physical adhesion forces between petals and other floral organs during floral development.
Phospholipase C2 Affects MAMP-Triggered Immunity by Modulating ROS Production1

Arabidopsis Phospholipase C2 (PLC2) participates in a branch of microbe-associated molecular pattern-triggered immunity that involves reactive oxygen species-regulated processes. The activation of phosphoinositide-specific phospholipase C (PI-PLC) is one of the earliest responses triggered by the recognition of several microbe-associated molecular patterns (MAMPs) in plants. The Arabidopsis (Arabidopsis thaliana) PI-PLC gene family is composed of nine members. Previous studies suggested a role for PLC2 in MAMP-triggered immunity, as it is rapidly phosphorylated in vivo upon treatment with the bacterial MAMP flg22. Here, we analyzed the role of PLC2 in plant immunity using an artificial microRNA to silence PLC2 expression in Arabidopsis. We found that PLC2-silenced plants are more susceptible to the type III secretion system-deficient bacterial strain Pseudomonas syringae pv tomato (Pst) DC3000 hrcC− and to the nonadapted pea (Pisum sativum) powdery mildew Erysiphe pisi. However, PLC2-silenced plants display normal susceptibility to virulent (Pst DC3000) and avirulent (Pst DC3000 AvrRPM1) P. syringae strains, conserving typical hypersensitive response features. In response to flg22, PLC2-silenced plants maintain wild-type mitogen-activated protein kinase activation and PHI1, WRKY33, and FRK1 immune marker gene expression but have reduced reactive oxygen species (ROS)-dependent responses such as callose deposition and stomatal closure. Accordingly, the generation of ROS upon flg22 treatment is compromised in the PLC2-defficient plants, suggesting an effect of PLC2 in a branch of MAMP-triggered immunity and nonhost resistance that involves early ROS-regulated processes. Consistently, PLC2 associates with the NADPH oxidase RBOHD, suggesting its potential regulation by PLC2.
Quantitative Assessment of Postural Stability and Balance Between Persons with Lower Limb Amputation and Normal Subjects by using Dynamic Posturography

Quantitative Assessment of Postural Stability and Balance Between Persons with Lower Limb Amputation and Normal Subjects by using Dynamic Posturography Background. The amputation of lower limb constitutes a major handicap which involves a functional and professional incapacity. Balance has been reported to be a better predictor of an individual's engagement in physical, daily, and social activities among persons with amputations. Aim. To study quantitatively the postural stability between persons with amputation and normal subjects by using dynamic posturography. Also, to determine whether differences in balance confidence exist between persons with amputations due to trauma or vascular causes, as well as between below knee (BK) or above knee (AK) amputations. Subjects and Methods. Twenty one patients with lower limb amputations who were ambulant with prostheses and 20 age-matched healthy individuals as control group were be randomly selected. The patients with BK and AK amputations due to trauma and vascular causes were included. All subjects were clinically evaluated along with brief neurological examination. The postural stability and balance were studied by using computerized dynamic posturography. Results. A significant reduction was observed for composite equilibrium score of persons with amputation as compared with control group (p < 0.05). Moreover, significant reduction was observed for composite equilibrium score of vascular causes as compared with trauma causes in persons with amputation (p < 0.05). However, Non-significant difference was observed for composite equilibrium score in BK amputation as compared with AK amputation (p > 0.05). Conclusion. Our data suggest that lower limb persons with amputation have low balance confidence compared to normal subjects and the balance is lower among individuals who had amputations due to vascular causes than trauma causes. This may be explained by impairment due to amputation as well as reduction of muscle strength and endurance in residual limb.
Identification and Characterization of Daurichromenic Acid Synthase Active in Anti-HIV Biosynthesis1

Daurichromenic acid, an anti-HIV meroterpenoid, is biosynthesized by a novel flavoprotein oxidase localized in the specialized epidermal organ, the glandular scales of Rhododendron dauricum. Daurichromenic acid (DCA) synthase catalyzes the oxidative cyclization of grifolic acid to produce DCA, an anti-HIV meroterpenoid isolated from Rhododendron dauricum. We identified a novel cDNA encoding DCA synthase by transcriptome-based screening from young leaves of R. dauricum. The gene coded for a 533-amino acid polypeptide with moderate homologies to flavin adenine dinucleotide oxidases from other plants. The primary structure contained an amino-terminal signal peptide and conserved amino acid residues to form bicovalent linkage to the flavin adenine dinucleotide isoalloxazine ring at histidine-112 and cysteine-175. In addition, the recombinant DCA synthase, purified from the culture supernatant of transgenic Pichia pastoris, exhibited structural and functional properties as a flavoprotein. The reaction mechanism of DCA synthase characterized herein partly shares a similarity with those of cannabinoid synthases from Cannabis sativa, whereas DCA synthase catalyzes a novel cyclization reaction of the farnesyl moiety of a meroterpenoid natural product of plant origin. Moreover, in this study, we present evidence that DCA is biosynthesized and accumulated specifically in the glandular scales, on the surface of R. dauricum plants, based on various analytical studies at the chemical, biochemical, and molecular levels. The extracellular localization of DCA also was confirmed by a confocal microscopic analysis of its autofluorescence. These data highlight the unique feature of DCA: the final step of biosynthesis is completed in apoplastic space, and it is highly accumulated outside the scale cells.