Miracle-dz/UniFAR-FTUs huggingface dataset:
Visual Comparative Omics of Fungi for Plant Biomass Deconstruction

Wood-decay fungi contain the cellular mechanisms to decompose such plant cell wall components as cellulose, hemicellulose, and lignin. A multi-omics approach to the comparative analysis of wood-decay fungi gives not only new insights into their strategies for decomposing recalcitrant plant biomass, but also an understanding of how to exploit these mechanisms for biotechnological applications. We have developed an analytical workflow, Applied Biomass Conversion Design for Efficient Fungal Green Technology (ABCDEFGT), to simplify the analysis and interpretation of transcriptomic and secretomic data. ABCDEFGT utilizes self-organizing maps for grouping genes with similar transcription patterns, and an overlay with secreted proteins. The key feature of ABCDEFGT is simple graphic outputs of genome-wide transcriptomic and secretomic topographies, which enables visual inspection without a priori of the omics data and facilitates discoveries of co-regulated genes and proteins. Genome-wide omics landscapes were built with the newly sequenced fungal species Pycnoporus coccineus, Pycnoporus sanguineus, and Pycnoporus cinnabarinus grown on various carbon sources. Integration of the post-genomic data revealed a global overlap, confirming the pertinence of the genome-wide approach. ABCDEFGT was evaluated by comparison with the latest clustering method for ease of output interpretation, and ABCDEFGT gave a better biological representation of fungal behaviors. The genome-wide multi-omics strategy allowed us to determine the potential synergy of particular enzymes decomposing cellulose, hemicellulose, and lignin such as Lytic Polysaccharide Monooxygenases, modular enzymes associated with a cellulose binding module1, and Class II Peroxidase isoforms co-regulated with oxido-reductases. Overall, ABCDEFGT was capable of visualizing genome-wide transcriptional and secretomic profiles for intuitive interpretations and is suitable for exploration of newly-sequenced organisms.
Online Signature Verification Based on Legendre Series Representation: Robustness Assessment of Different Feature Combinations

In this paper, orthogonal polynomials series are used to approximate the time functions associated to the signatures. The coefficients in these series expansions, computed resorting to least squares estimation techniques, are then used as features to model the signatures. Different combinations of several time functions (pen coordinates, incremental variation of pen coordinates and pen pressure), related to the signing process, are analyzed in this paper for two different signature styles, namely, Western signatures and Chinese signatures of a publicly available Signature Database. Two state-of-the-art classification methods, namely, Support Vector Machines and Random Forests are used in the verification experiments. The proposed online signature verification system delivers error rates comparable to results reported over the same signature datasets in a previous signature verification competition.
A Comparison of Tyrosine against Placebo, Phentermine, Caffeine, and d-Amphetamine During Sleep Deprivation

Abstract Sleep deprivation can impair alertness and cognitive and motor performance. We hypothesized that the amino acid tyrosine might reduce deleterious effects of sleep deprivation. Seventy-six healthy males, age 18-35 years, participated in a four-day protocol that included a habituation night, a baseline night, a 40.5 h period without sleep, and a recovery night. Tyrosine 150 mg/kg, caffeine 300 mg/70 kg, phentermine 37.5 mg, d-amphetamine 20 mg and placebo were administered in a double-blind, randomized fashion to compare their effects on the time it took to fall asleep, on endocrine responses during sleep deprivation, and on sleep quantity, quality and architecture as measured by polysomnography during recovery sleep. When given after 36 h without sleep, tyrosine had no significant effect on any parameter of sleep. d-amphetamine produced marked decrease in sleep drive but caused deleterious effects on many aspects of recovery sleep. Still, d-amphetamine was associated with increased alertness on the first recovery day. Phentermine and caffeine both decreased sleep drive during sleep deprivation, but phentermine impaired rapid-eye-movement (REM) recovery sleep. Tyrosine (when compared to placebo) had no effect on any sleep related measure, but it did stimulate prolactin release.
‘It's their word against mine’: young people's attitudes to the police complaints procedure in Northern Ireland

One of the central aims of the police reform process in Northern Ireland has been to increase the legitimacy of the policing structures and police officers amongst those who are served and policed by the Police Service of Northern Ireland (PSNI). To meet this aim, structures have been created to ensure that the PSNI is accountable to all sections of the community for its strategy and performance, and in monitoring the attitudes and behaviour of its officers. To that end, the Office of the Police Ombudsman for Northern Ireland (PONI), the Northern Ireland Policing Board and 26 District Policing Partnerships have been created. This paper aims to break ground by looking in some detail at young people's attitudes to and experiences of the workings of one of those new bodies, the Police Ombudsman, and to explore issues related to young people's willingness to engage with the PONI.
MULTI-EPOCH OBSERVATIONS OF HD 69830: HIGH-RESOLUTION SPECTROSCOPY AND LIMITS TO VARIABILITY

The main-sequence solar-type star HD 69830 has an unusually large amount of dusty debris orbiting close to three planets found via the radial velocity technique. In order to explore the dynamical interaction between the dust and planets, we have performed multi-epoch photometry and spectroscopy of the system over several orbits of the outer dust. We find no evidence for changes in either the dust amount or its composition, with upper limits of 5%–7% (1σ per spectral element) on the variability of the dust spectrum over 1 year, 3.3% (1σ) on the broadband disk emission over 4 years, and 33% (1σ) on the broadband disk emission over 24 years. Detailed modeling of the spectrum of the emitting dust indicates that the dust is located outside of the orbits of the three planets and has a composition similar to main-belt, C-type asteroids in our solar system. Additionally, we find no evidence for a wide variety of gas species associated with the dust. Our new higher signal-to-noise spectra do not confirm our previously claimed detection of H2O ice leading to a firm conclusion that the debris can be associated with the break-up of one or more C-type asteroids formed in the dry, inner regions of the protoplanetary disk of the HD 69830 system. The modeling of the spectral energy distribution and high spatial resolution observations in the mid-infrared are consistent with a ∼1 AU location for the emitting material.
Role of transforming growth factor beta in human disease.

In human tissues, normal homeostasis requires intricately balanced interactions between cells and the network of secreted proteins known as the extracellular matrix. These cooperative interactions involve numerous cytokines acting through specific cell-surface receptors. When the balance between the cells and the extracellular matrix is perturbed, disease can result. This is clearly evident in the interactions mediated by the cytokine transforming growth factor β (TGF-β). TGF-β is a member of a family of dimeric polypeptide growth factors that includes bone morphogenic proteins and activins. All of these growth factors share a cluster of conserved cysteine residues that form a common cysteine .
Cortico‐cortical connectivity of the human mid‐dorsolateral frontal cortex and its modulation by repetitive transcranial magnetic stimulation

Modulation of cortico‐cortical connectivity in specific neural circuits might underlie some of the behavioural effects observed following repetitive transcranial magnetic stimulation (rTMS) of the human frontal cortex. This possibility was tested by applying rTMS to the left mid‐dorsolateral frontal cortex (MDL‐FC) and subsequently measuring functional connectivity of this region with positron emission tomography (PET) and TMS. The results showed a strong rTMS‐related modulation of brain activity in the fronto‐cingulate circuit. These results were confirmed in a parallel experiment in the rat using electrical stimulation and field‐potential recordings. Future studies are needed to provide a direct link between the rTMS‐induced modulation of cortical connectivity and its effects on specific behaviours.
Heterologous expression of the Mycobacterium tuberculosis gene encoding antigen 85A in Corynebacterium glutamicum

By using appropriate Corynebacterium glutamicum-Escherichia coli shuttle plasmids, the gene encoding the fibronectin-binding protein 85A (85A) from Mycobacterium tuberculosis was expressed in C. glutamicum, also an actinomycete and nonsporulating gram-positive rod bacterium, which is widely used in industrial amino acid production. The 85A gene was weakly expressed in C. glutamicum under the control of the ptac promoter from E. coli, but it was produced efficiently under the control of the promoter of the cspB gene encoding PS2, one of the two major secreted proteins from C. glutamicum. The 85A protein was produced in various forms, with or without its own signal sequence and with or without the signal sequence and the NH2-terminal (18-amino-acid) mature sequence of PS2. Western blot analysis with monoclonal antibodies raised against the M. tuberculosis antigen 85 complex showed that recombinant 85A protein was present in the corynebacterial cell wall extract and also released in extracellular culture medium. NH2-terminal microsequencing of recombinant 85A secreted by C. glutamicum showed that signal peptide was effectively cleaved off at the predicted site. The recombinant 85A protein was biologically active in vitro, inducing significant secretion of Th1 T-cell cytokines, particularly interleukin-2 and gamma interferon, in spleen cell cultures from mice vaccinated with live Mycobacterium bovis BCG. Heterologous expression of mycobacterial antigens in C. glutamicum now offers a potent tool for further immunological characterization and large scale preparation of these recombinant proteins.
Finnish adolescents' attitudes towards wholegrain bread and healthiness.

BACKGROUND Wholegrain food may have an important role in the prevention of chronic diseases, and therefore its consumption should be increased. However, wholegrain products have a low consumption because of unfamiliar taste and poor understanding about the health benefits. Generally, adolescents unfamiliar with wholegrain bread dislike it. Food use in childhood correlates positively with practices in adult life, and therefore adolescents are an important target group for research. The aim was to study adolescents' attitudes towards wholegrain bread in a society where wholegrain products are widely used. RESULTS A qualitative focus group method (n = 61) and a quantitative procedure (n = 104) with 13-15-year-old secondary school students indicated that Finnish adolescents considered wholegrain breads healthier and more acceptable than refined breads. The motives for wholegrain bread consumption were taste, feeling of fillingness and weight control. Girls were more interested in bread healthfulness than boys (P < 0.01), and participants who showed a more positive attitude towards general health interest reported using more rye and wholegrain breads than participants with negative attitudes. CONCLUSION Adolescents familiar with the sensory properties and healthfulness of rye and wholegrain breads consumed them regularly and perceived them as pleasant and very acceptable.
Changes in the morphology and the distribution of rat intestinal eosinophils during infection with the nematode Nippostrongylus brasiliensis.

Increases in the numbers of eosinophil leukocytes present in the lamina propria of intestines infected with nematodes is a well described phenomenon, yet the role of these leukocytes and their actions in this situation are not yet fully understood. Morphologic changes in these cells occur with the course of the infection, as do alterations in their location within the gut; these findings may give important clues to the function of this prominent cell. We observed changes in intestinal eosinophils in the August rat during infection with the nematode Nippostrongylus brasiliensis and found, together with the well known increases in number infiltrating the lamina propria at Day 20 (three times the levels in normal animals), a distinct change in the morphology of individual cells which included increase of the cell's overall size and changes in shape, as well as a dissemination of cytoplasmic granules in relationship to the cell's nucleus. No ultrastructural evidence of extracellular degranulation or intact eosinophil cytoplasmic granules outside the bounds of cell cytoplasmic membranes was seen. This finding is important considering the light microscopic appearance of individual eosinophil granules apparently distributed extracellularly, and lying in the connective tissue of the lamina propria, a common histopathologic observation in eosinophilic conditions. Eosinophils within the lamina propria changed their location as the infection progressed, tending to move to line up along the subepithelial zones. In addition, eosinophils were observed both at the light and electron microscopic levels to be passing through the basement membrane and into the epithelial layer. This latter phenomenon was confirmed using confocal optical slicing where eosinophils were commonly observed on the luminal side of the nuclei of the gut epithelium. These observations strongly suggest that morphologic alterations occur in eosinophils in the lamina propria and these changes may be associated with functional alterations in these cells akin to the putative phenomenon of "activation. " Our findings indicate that eosinophils have the capacity to enlarge and extend their cytoplasmic processes between various components of the lamina propria and move toward the basement membrane during an active infection, as well as into, and possibly through, the intestinal epithelium. These findings emphasize the need for careful consideration of the changing morphologic status of eosinophils when investigating biologic changes associated with the activation of these cells in tissue inflammatory responses.
Differences in germinal centre and non-germinal center phenotype in gastric and intestinal diffuse large B-cell lymphomas

The gastrointestinal tract is the most common extranodal site of lymphoma, and the most common gastrointestinal lymphoma is diffuse large B-cell type (DLBCL). DLBCL can be separated into germinal centre (GCP) and non-germinal centre phenotypes (non-GCP) using CD10, BCL-6 and MUM1 immunohistochemistry, but primary gastrointestinal DLBCL has not been extensively studied. We investigated 48 cases of primary gastrointestinal DLBCL (33% involving the small intestine, 50% the stomach, 13% the large intestine and 4% the ileocecal junction) and found that most (88%) DLBCL in the intestines were of GCP, while only 58% of gastric DLBCL were of GCP. This difference in GCP and non-GCP in gastric vs. intestinal DLBCL may be due to variations in lymphomagenesis reflecting acquired vs. native mucosa-associated lymphoid tissue. There was no significant difference in either overall survival or disease-free survival between the germinal centre and non-germinal centre groups. The distribution of Helicobacter pylori in different gastric DLBCL phenotypes raises interesting questions about the pathogenesis of H. pylori-associated lymphomas.
Observations on So-Called Idiopathic Vocal Cord Paralysis

A series of 238 patients with laryngeal paralysis seen during a six-year period (1976–1982) were studied with serial 16-mm motion picture filmstrips. There were 39 cases in which no etiological disease process could be found responsible for the paralysis; these were called “idiopathic. ” In all 39 cases, both the superior and recurrent laryngeal nerves were paralyzed indicating that the lesion involved the central (nuclear) lower motor neurons of the dorsal and ventral nucleus ambiguus. The high incidence of upper respiratory infections suggests a viral etiology in many cases. The ability to separate a pure recurrent from a combined superior and recurrent laryngeal paralysis on morphological indirect endoscopic appearance has significant diagnostic and therapeutic implications.
Aspects of rating communicative interaction: Effects on reliability and agreement

Communication partner training can be effective in improving communication in aphasia. However, further research is needed on how to measure the outcome of such interventions. In this paper we discuss the phenomenon of reliability in assessments in relation to the results of analyses using a rating scale designed to measure the ability to support a person with aphasia in natural conversational interaction. The scale was used by four assessors to rate 45 video recordings. Calculations of reliability and agreement produced varying results but were mostly satisfactory. However, the results highlight how interaction between factors such as complexity of assessments; design of the rating scale; factors inherent in the individual assessor; and the statistical measures used to analyse the outcome may result in a conflict between aspects of validity and reliability. Interpretations of outcome obtained with rating scales thus need to be based on knowledge about factors influencing the results.
Lymphoma development in Sjögren's syndrome: novel p53 mutations.

OBJECTIVE Sjögren's syndrome (SS) is a chronic autoimmune disease characterized by lymphocytic infiltrations of the exocrine glands. Disease progression may lead to uncontrolled clonal proliferation of B lymphocytes and development of lymphoma. This study was undertaken to examine the possible involvement of the cell cycle checkpoint genes p53 and p21 in the pathophysiology of the syndrome. METHODS Protein expression of p53 and p21 was studied, by immunohistochemistry and Western blot analysis, in minor salivary gland (MSG) biopsy specimens from 7 patients with SS and 5 control subjects. In addition, sequence analysis of the p53 gene was performed on DNA samples obtained from MSG biopsy samples of the same 7 patients with SS and from 4 patients with SS and in situ non-Hodgkin's lymphoma (NHL). RESULTS The study revealed increased protein expression of p53 and p21 in MSG biopsy specimens from patients as compared with controls, while sequence analysis showed that the p53 gene was of the wild type. Furthermore, sequence analysis of the p53 gene from patients with SS and in situ NHL revealed 2 novel mutations in exon 5 of the p53 gene. These mutations are single-base substitutions and appear to be functional since exon 5 is included in the coding region of the p53 gene. CONCLUSION This is the first report on wild-type p53 gene activation in SS. Our findings indicate a probable role for the DNA damage response genes in the pathogenesis of this syndrome. The novel mutations of the p53 gene implicate dysregulation of this tumor suppressor gene as a possible mechanism for lymphoma development in SS.
Strategic Action In A Community Environment

In this article, the author proposes a synthetic approach to the analysis of institutional effects on EU policy making by combining a rationalist theory of action with a constructivist assumption on the social environment: Actors in European integration act strategically on the basis of individual specific policy preferences but do so in a community environment that affects their strategies and the collective interaction outcome. This synthetic approach draws on the work of Erving Goffman and is based on the "sequencing" of rationalist and constructivist propositions. Furthermore, this approach will be most salient when the institutional rules in question are constitutive and legitimate and resonate with national values and norms. Following the design of controlled competition, the author argues that this sequencing better explains the EU's decision to expand to the East than either rationalist or constructivist propositions alone.
‘Our fellow Africans make our lives hell’: the lives of Congolese and Nigerians living in Johannesburg

Abstract Xenophobia in post-apartheid South Africa has become a major issue. Much of the hostility is directed at Africans from countries north of Southern Africa who are often easily distinguishable due to their physical features, distinctive dress and inability to speak the indigenous languages. This article focuses on immigrants and asylum seekers from two countries, Nigeria and the Democratic Republic of Congo. Both groupings have experienced significant antagonism and prejudice from the local population, more especially from black South Africans. The article describes and analyses the interaction of the two groupings in question with the local populace and authorities. What is argued is that during the apartheid era the restrictions on black immigration meant that the number of black foreigners was limited. Since 1990, however, there has been a substantial increase in illegal and legal migration from Southern African countries and countries further north. This increase, in a context of growing unempl.
Development of concern for others.

The development of prosocial and reparative bebaviors was investigated by examining children's responses to distresses they caused and those they witnessed in others during the 2nd year of life. Prosocial behaviors (help, sharing, provision of comfort) emerged between the ages of 1 and 2, increasing in frequency and variety over this time period. These behaviors were linked to expressions of concern as well as efforts to understand and experience the other's plight. Children's reparative behaviors after they had caused distress also increased with age. Age changes in these early signs of moral development were accompanied by social-cognitive changes in self-recognition. In assessments at age 2, children were most responsive to distress in their mothers but also showed some sensitivity toward unfamiliar persons
New neurons: extraordinary evidence or extraordinary conclusion?

Gould et al . ([1][1]) reported that in the adult primate new neurons may be added to some neocortical association areas. This remarkable finding explicitly challenges previous work indicating that the production of new neurons in the primate neocortex is limited to the fetal period ([2][2]), and,
Meningococcal Group C Subgroup Determinant Detected by Immunofluorescence 1

Summary The presence or absence of a meningococcal Group C subgroup antigen (C1+) can be detected by immunofluorescence as readily as by a previously reported hemagglutination-inhibition method. When compared in strains isolated from cases and carriers, subgroup negative (C1-) strains seemed to occur more often in cases. The subgroup antigen is widely distributed geographically. The characterization of meningococci by its presence or absence may be of value in epidemiological studies.