Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of Laccase-like Multicopper Oxidases (LMCOs) in Arabidopsis thaliana

Laccase-like multicopper oxidases (LMCOs) have repeatedly been associated with the process of lignification in plants, and previous work suggested that these enzymes might be acting as specific marker for highly localized, small-scale lignification events in tissues not typically thought of as lignified. However, plant LMCOs typically occur as members of gene families and different family members can display disparate enzyme activities and overlapping patterns of expression in bulk tissues. This study used reporter genes and knockout mutants to document the involvement of a specific Arabidopsis thaliana LMCO family member (At2g30210 ) in early root development, specifically with development of endodermal tissues. Expression of the gene product was found to be under the control of sucrose levels, but the gene also responded to fluctuations in salt concentrations. The expression patterns of this gene were consistent with its involvement in the formation of suberin in the Casparian strip of root endodermis. An additional LMCO (At5g58910) displayed a more generalized expression in the radicles emergent seedlings. Additional members of the Arabidopsis LMCO family (At2g29130, At5g01190, and At5g05390) were also investigated with reporter gene constructs and knockout mutants. Expression of these LMCOs was associated with lignifying xylem, and the genes had over-lapping expression. Single knockout mutants did not display obvious phenotypes, suggesting that the gene products might have degenerate functionality that could compensate for loss of a single LMCO function.
Investigating the combined burden of transcription and quality control errors in yeast

The Rtf1 subunit of the Paf1 complex is required for specific conserved transcription-coupled histone modifications, including histone H2B lysine 123 monoubiquitylation. In Saccharomyces cerevisiae, deletion of RTF1 is lethal in the absence of Rkr1, a ubiquitin-protein ligase involved in the destruction of nonstop proteins, which arise from mRNAs lacking stop codons or translational read-through into the poly(A) tail. To understand the combined requirement for H2B ubiquitylation and protein quality control in yeast, I performed a transposon-based mutagenesis screen to identify suppressors of rtf1Δ rkr1Δ lethality. I found that mutations in the genes encoding RNA Polymerase III subunit Rpc17, sister chromatid cohesion protein Chl1, or the protein chaperone Hsp104 could rescue viability. Of these genes, the role of Hsp104 in yeast is best understood. Hsp104 plays a role in prion propagation, including the maintenance of [PSI+], which contributes to the synthesis of nonstop proteins. I demonstrate that rtf1Δ and rkr1Δ are synthetically lethal only in the presence of [PSI+]. The deletion, inactivation, and overexpression of HSP104 or the overexpression of prion-encoding genes URE2 and LSM4 clear [PSI+] and rescue rtf1Δ rkr1Δ lethality. In addition, the presence of [PSI+] decreases the fitness of rkr1Δ strains. I investigated whether the loss of RTF1 exacerbates an overload in nonstop proteins in rkr1Δ [PSI+] strains but, using reporter plasmids, found that rtf1Δ decreases nonstop protein levels, indicating that excess nonstop proteins may not be the cause of synthetic lethality. Although the mechanism of suppression is not yet clear, mutations in CHL1 suppress this rtf1Δ-specific defect by increasing nonstop protein levels. In addition, I have performed experiments to identify substrates and interacting partners for Rkr1 and these results have further indicated a role of Rkr1 in protein quality control. My data suggest that the loss of Rtf1-dependent histone modifications increases a burden on quality control in rkr1Δ [PSI+] cells. Importantly, my research indicates an essential connection between these conserved processes of transcription and quality control.
Multiple ecological processes underpin the eruptive dynamics of small mammals: House mice in a semi‐arid agricultural environment

Abstract Mouse plagues are a regular feature of grain‐growing regions, particularly in southern and eastern Australia, yet it is not clear what role various ecological processes play in the eruptive dynamics generating these outbreaks. This research was designed to assess the impact of adding food, water, and cover in all combinations on breeding performance, abundance, and survival of mouse populations on a typical cereal growing farm in northwestern Victoria. Supplementary food, water, and cover were applied in a 2 × 2 × 2 factorial design to 240 m sections of internal fence lines between wheat or barley crops and stubble/pasture fields over an 11‐month period to assess the impact on mouse populations. We confirmed that mice were eating the additional food and were accessing the water provided. We did not generate an outbreak of mice, but there were some significant effects from the experimental treatments. Additional food increased population size twofold and improved apparent survival. Both water and cover improved breeding performance. Food and cover increased apparent survival. Our findings confirm that access to food, water, and cover are necessary for outbreaks, but are not sufficient. There remain additional factors that are important in generating mouse plagues, particularly in a climatically variable agricultural environment.
Feeding Preferences and Dietary Specialisation among Obligate Coral-Feeding Butterflyfishes

[Extract] Coral reef fishes have long been known to exhibit highly specialised patterns of habitat use (e.g., Fautin, 1985; Munday et al., 1997; Gardiner and Jones, 2005), but are generally considered to be highly versatile in their feeding (Ross, 1986; Bellwood et al., 2006c), opportunistically consuming a wide range of different prey. One striking example of this is the range of fishes (including algal farming damselfishes) that abandon their normal feeding habitats to take advantage of ephemeral, lipid-rich prey, feeding on corals eggs during annual mass spawning by scleractinian corals (Pratchett et al., 2001; McCormick, 2003). There is however, increasing realisation that coral reef fishes can be extremely specialised when it comes to diet. The broad trophic groups once used to categorise reef fishes (e.g., planktivores, herbivores, carnivores and omnivores) are increasingly being sub-divided to capture important differences in ecosystem function (Graham et al., 2006; Hoey and Bellwood, 2011), while some studies simply recognise that individual species have unique and important functional roles (e.g., Bellwood et al., 2003, 2006b). Many species have extremely specialised diets or feeding habits, such as Holacanthus angelfishes that feed almost exclusively on sponges, and mainly on just one species (Randall and Hartman, 1968) or tube-lip wrasses (Labroides and Labrichthys) that consume coral mucous from small wounds that they inflict on specific coral types (Cole et al., 2008).
Natural bioluminescence as a genetic marker for ophiuroid species

Bioluminescence is the emission of visible light by living organisms. This amazing property is used in various research fields such as genetics, molecular biology, chemistry, etc. The aim of this work was to gather evidence that bioluminescence could also be used as a genetic marker in various luminescent species. Previous studies with the brittlestar Amphipholis squamata have shown that bioluminescence is an excellent marker for intraspecific genetic variability. The method, using maximum luminous capabilities induced by KCl 200mM depolarization, presents numerous advantages over other genetic markers (RAPDs, microsatellites, RFLP, etc.): it is cheaper, faster and easier to use. Since bioluminescence is a frequent phenomenon in brit- tlestars, the same method was used to compare variability between six different species: Amphipholis squa- mata, Amphiura filiformis, A. arcystata, Ophiopsila aranea, O. californica and a new species of Amphiodia. Our results show that Amphiodia and both Ophiopsila species could be clearly isolated, each in a separated cluster, according to their luminous capabilities. These differences could be explained by physiological prop- erties. On the other hand, an important intraspecific variability was observed for two species (A. squamata and A. filiformis). We propose that natural bioluminescence is a good marker to study inter- and intraspecific vari- ability, providing useful functional information for physiological and population studies.
Effect of ratio of enzymes to substrate on amino acid patterns released from proteins in vitro.

: Using an in vitro procedure, with both plant (gluten and edestin) and animal proteins (egg white and casein) as ratio of protein substrate to enzymes (pepsin, trypsin, erepsin) was increased in progressive stages, there was a change in the amino acids released; the proportions of some amino acids progressively increased, others progressively decreased while still others remained constant. The pattern of amino acids released was distinct for each protein and as substrate increased relative to enzymes, certain amino acids essential for the human increased with some proteins and decreased with others which suggests nutritional implications. The variations in amino acids released with changes in ratio of substrate to enzymes was not a random effect but an apparent orderly process. The phenomenon is termed "variable ratio effect".
Phenotypic and genotypic characterisation of Aeromonas isolates

In the present study 62 Aeromonas strains, isolated from different sources, were characterised by biochemical tests (Biolog system) and amplified 16S rDNA restriction analysis (ARDRA), previously proposed as a useful tool to identify Aeromonas species. Fifteen type strains and one reference strain were also analysed. The Biolog system ascribed most of the local isolates to A. media and A. veronii bv. sobria. Sixteen isolates were recorded as Aeromonas spp. ARDRA subdivided all analysed strains in 13 clusters. None of our isolates were attributed to A. sobria, A. schubertii, or to Aeromonas unnamed HG11 with both approaches. However, discrepancies were found between Biolog and 16S ARDRA species attribution of isolates. Moreover, total DNA restriction profile analysis on a selected group of isolates showed a low similarity among strains with identical ARDRA profiles. Therefore, sets of our data suggest that a single approach cannot be adequate for the identification of Aeromonas new isolates at the species rank and point out the need to apply a polyphasic approach, integrating phenotypic, phylogenetic (16S rDNA sequencing) and genomic (i.e. DNA/DNA hybridisation values) data, to define the taxonomic status of the genus Aeromonas.
Embryological stages of the marine turtle Lepidochelys olivacea (Eschscholtz)

Embryos of the Pacific Ridley Turtle, Lepidochelys olivacea , obtained from eggs from the Pacific Coast of Costa Rica and Panama, developing on a beach and others incubated in the laboratory respectlvely, were exarnined and evaluated in terms of development by means of an lndex of Morphological Development (IMD); selected morphological characters and measurements were used to diagnose 31 different developmental stages from gastrula to neonate.
Inferring a duplication and speciation history from a gene tree (2)

Fig. 1. A gene family evolutionary scenario is represented by the reconciliation of the gene tree (dotted lines) and the species tree (blue lines). “WHAT DO WE DO IF WE DON’T KNOW THE SPECIES TREE? ” Given a gene tree T , we study the following two problems: 1. DS-recognition problem: can T be explained by a history involving only duplication and speciation events? Such a gene tree is called a “DS-tree”. 2. Gene losses minimisation problem: what is the minimum number of losses needed to be inserted in T to transform it into a DS-tree?
Continued Circulation of DENV-2 (Genotype IV) in Delhi, India

Background: Dengue is one of the rapidly emerging arboviral infection in many parts of the world including India. The metropolitan city, Delhi is one of the worst affected areas by dengue. In the last two decades, it has serotype(s)/genotype(s) NS1 reverse transcription polymerase chain reaction (RT-PCR) partial nucleotide sequencing for capsid-premembrane (CprM) gene Results: Serotypic and genotypic analysis revealed cases of DENV-2 (genotype IV) 58.33%, DENV-3 (genotype III) 33.33% and DENV-1 (genotype III) 8.33%. Presence of DENV-2 (genotype IV) in majority of the cases (58.33%) indicated its pre-dominance. Multiple sequence alignment and phylogenetic analysis revealed the presence of a new strain of DENV-2 (genotype IV); Short Communication differentiated from pre-existing strain by the substitutions; Ala102Val in capsid and Ile49Val in premembrane protein. Conclusion: This study reports, continued circulation of DENV-2 (genotype IV) in 2014. The results also indicated circulation of a new strain of DENV-2, similar to Hyderabad isolate “1392” (JX475906), along with the pre-existing strain. It is proposed that, this strain has been introduced recently and circulating at low key in the capital.
Development of the Clinical Corpus with Disease Name Annotation

高度な人工知能研究のためには,その材料となるデータが必須となる. 医療,特に 臨床に関わる分野において,人工知能研究の材料となるデータは主に自然言語文を 含む電子カルテである. このようなデータを最大限に利用するには,自然言語処理 による情報抽出が必須であり,同時に,情報抽出技術を開発するためのコーパスが 必要となる. 本コーパスの特徴は,45,000テキストという我々の知る限りもっとも 大規模なデータを構築した点と,単に用語のアノテーションや用語の標準化を行っ ただけでなく,当該の疾患が実際に患者に生じたかどうかという事実性をアノテー ションした点の 2点である. 本稿では病名や症状のアノテーションを対象に,この 医療コーパス開発についてその詳細を述べる. 人工知能研究のための医療コーパス 開発について病名や症状のアノテーションを中心にその詳細を述べる. 本稿の構成 は以下の通りである. まず,アノテーションの基準について,例を交えながら,概 念の定義について述べる. 次に,実際にアノテーターが作業した際の一致率などの 指標を算出し,アノテーションのフィージビリティについて述べる. 最後に,構築 したコーパスを用いた病名抽出システムについて報告する. 本稿のアノテーション 仕様は,様々な医療テキストや医療表現をアノテーションする際の参考となるであ ろう. キーワード:電子カルテ,医療テキスト,症例報告,病名,ICD-10,医療情報
High focused Evaluation of Atherosclerotic risk profile in Retinal Thrombosis: Vascular events Incidence, Sex involvement and Interventional outcomes assessed by Ophthalmologists and internists Network – HEART VISION study protocol

Background and objectives: Retinal vein occlusion (RVO), one of the most relevant causes of vision loss, still represents an open issue in ophthalmology and vascular medicine. Its epidemiology and management approach have not been clearly characterized yet, with several grey zones requiring investigation. Significance of RVO on cardiovascular prognosis is also unclear. “High focused Evaluation of Atherosclerotic risk profile in Retinal Thrombosis: Vascular events Incidence, Sex involvement and Interventional outcomes assessed by Ophthalmologists and internists Network” (HEART VISION) is a longitudinal, prospective, multi-center study which aims at determining the epidemiology, potentially modifiable risk factors and the determinants of RVO in an Italian-based cohort. Methods: Enrollment of all the eligible patients presenting to recruiting centers ( i.e . ophthalmology emergency room and thrombosis centers) with suspect of RVO. At baseline, all patients will undergo an opthalmologic evaluation and further investigations about cardiovascular co- morbidities and risk factors. Recruited patients will be followed for a 2-year period. Outcome measures: Data about adverse cardiovascular events and eye-related outcomes will be recorded. Discussion: HEART VISION will present data on prevalence and will inform on the prognosis of RVO in an Italian-based cohort. Char acterization and prospective evaluation of these patients will be useful in developing novel strategies for management of RVO and their cardiovascular-related risk factors. Ethics and dissemination: This study protocol
Functional electrical stimulation reduces pain and shoulder subluxation in chronic post-stroke patients?

Background: Shoulder subluxation is a common complication of cerebral vascular accident (stroke) and the use of Functional Electrical Stimulation (FES) within the rehabilitation process is extremely important. Objective: To analyze the therapeutic effects of FES in the treatment of chronic shoulder subluxation in post-stroke patients. Method: This is a case study of patients with radiologically subluxation confirmed, who were randomly divided into two groups: Control Group (CG) and Treatment Group (TG). Patients were assessed before and after treatment and at the 2-month follow-up. The assessment consisted of the modified Ashworth scale; passive goniometry; Fugl-Meyer scale; McGill pain questionnaire and evaluation of shoulder subluxation by radiography. The CG did not receive physiotherapeutic intervention; and TG underwent 20 sessions of motor kinesiotherapy and FES associated with functional exercises with a total duration of 1 hour, three times a week, for 7 weeks. The data were analyzed descriptively. Results: The mean age of CG participants was 82.5 ± 1.5 years and of the TG was 70.5 ± 13.5 years. All of them were retired, sedentary, non-smokers/alcoholics and had hemiparesis on the left side. There was an approximate increase of 10o for most joint movements of the shoulder, improvement in McGill scale scores and reduction of shoulder subluxation in TG patients. Conclusion: FES associated with functional movements was effective in reducing the degree of subluxation of the shoulder joint and decreased pain in subjectsin the chronic phase of the post-stroke.
Die Fibrinagar-Elektrophorese

Zusammenfassung Es wird eine neue Methode beschrieben, die Fibrinagar-Elektrophorese, die sowohl zum Nachweis von Proteinasen als auch von Proteinase-Inhibitoren und Proteinase-Aktivatoren geeignet ist. Die Kombination der Fibrinagar-Elektrophorese mit der Immuno-Elektrophorese erleichtert die Charakterisierung und Identifizierung bestimmter, biologisch wirksamer Proteine. Die vielseitige Verwendbarkeit der Methode wird an einigen Beispielen erörtert: Charakterisierung von Plasmin, Trypsin und Chymotrypsin und ihrer Inhibitoren im Serum, Nachweis des fibrinolytischen Systems im Serum und Unterscheidung von spontan wirksamer und durch Streptokinase aktivierbarer Fibrinolyse.
Update on the safety and efficacy of commercial ultrasound contrast agents in cardiac applications

Ultrasound contrast agents (UCAs) are currently used throughout the world in both clinical and research settings. The concept of contrast-enhanced ultrasound imaging originated in the late 1960s, and the first commercially available agents were initially developed in the 1980s. Today's microbubbles are designed for greater utility and are used for both approved and off-label indications. In October 2007, the US Food and Drug Administration (FDA) imposed additional product label warnings that included serious cardiopulmonary reactions, several new disease-state contraindications, and a mandated 30 min post-procedure monitoring period for the agents Optison and Definity. These additional warnings were prompted by reports of cardiopulmonary reactions that were temporally related but were not clearly attributable to these UCAs. Subsequent published reports over the following months established not only the safety but also the improved efficacy of clinical ultrasound applications with UCAs. The FDA consequently updated the product labeling in June 2008 and reduced contraindications, although it continued to monitor select patients. In addition, a post-marketing program was proposed to the sponsors for a series of safety studies to further assess the risk of UCAs. Then in October 2011, the FDA leadership further downgraded the warnings after hearing the results of the post-marketing data, which revealed continued safety and improved efficacy. The present review focuses on the use of UCAs in today's clinical practice, including the approved indications, a variety of off-label uses, and the most recent data, which affirms the safety and efficacy of UCAs.
BloodSpot: a database of gene expression profiles and transcriptional programs for healthy and malignant haematopoiesis

Research on human and murine haematopoiesis has resulted in a vast number of gene-expression data sets that can potentially answer questions regarding normal and aberrant blood formation. To researchers and clinicians with limited bioinformatics experience, these data have remained available, yet largely inaccessible. Current databases provide information about gene-expression but fail to answer key questions regarding co-regulation, genetic programs or effect on patient survival. To address these shortcomings, we present BloodSpot (www.bloodspot.eu), which includes and greatly extends our previously released database HemaExplorer, a database of gene expression profiles from FACS sorted healthy and malignant haematopoietic cells. A revised interactive interface simultaneously provides a plot of gene expression along with a Kaplan–Meier analysis and a hierarchical tree depicting the relationship between different cell types in the database. The database now includes 23 high-quality curated data sets relevant to normal and malignant blood formation and, in addition, we have assembled and built a unique integrated data set, BloodPool. Bloodpool contains more than 2000 samples assembled from six independent studies on acute myeloid leukemia. Furthermore, we have devised a robust sample integration procedure that allows for sensitive comparison of user-supplied patient samples in a well-defined haematopoietic cellular space.
CARDIOPROTECTIVE EFFECT OF DATE PALM AGAINST DOXORUBICIN-INDUCED CARDIOTOXICITY

Objective: Doxorubicin (Dox), an anthracycline antibiotic, has been widely used to treat cancer, principally hematological malignancies, and solid tumors. The administration of Dox is a topic of concern in the medical community, as it frequently related to dose-dependent cardiotoxicity. Therefore, the present study was designed to investigate the protective potential of date palm fruit extract on Dox-induced cardiotoxicity.Methods: A total of 40 female albino rats were used in this study and classified into four groups including control, date palm fruit extract, Dox, and treated date palm fruit extract groups.Results: Dox produced a significant increase in creatine kinase-MB and lactate dehydrogenase activities. It also decreased the activities of cardiac glutathione peroxidase and superoxide dismutase but increase levels of cardiac malondialdehyde and also of urinary 8-hydroxy-2-deoxyguanosine. Myocardial toxicity of Dox also appeared in the elevation of serum total cholesterol, triglycerides, and low-density lipoprotein cholesterol levels, while level of high-density lipoprotein cholesterol decreased. Histopathological studies revealed alteration of cardiac tissue structure by Dox. Treatment with date palm fruit extract restored the aforementioned parameters.Conclusion: Date palm fruit exhibits a cardioprotective influence on the heart tissue against toxicity induced by Dox.
Segmental Schwannomatosis of the Upper Extremity

Schwannomatosis is characterized by the development of multiple schwannomas without evidence of vestibular tumors. Segmental schwannomatosis is defined as being limited to 1 limb or 5 or fewer contiguous segments of the spine. We report a case of a 38-year-old male with multiple, painful masses of the right upper extremity with associated numbness and paresthesia in the ulnar and radial nerve distribution. An open, microsurgical approach provided definitive diagnosis and treatment. Twenty-one cases of segmental schwannomatosis of the upper extremity have been reported in the literature, making this case the 22nd. It is 1 of 5 cases of segmental schwannomatosis to have simultaneous tumors in the forearm and hand. We are the first to report multiple schwannomas of the ulnar and ulnar sensory nerve and the second to report multiple schwannomas of the radial sensory nerve. We additionally review the literature regarding pathogenesis, diagnosis, and treatment of this uncommon tumor.