Miracle-dz/UniFAR-FTUs huggingface dataset:
Metabolic Pathways for Cytotoxic End Product Formation from Glutamate- and Aspartate-Containing Peptides byPorphyromonas gingivalis

ABSTRACT Metabolic pathways involved in the formation of cytotoxic end products by Porphyromonas gingivalis were studied. The washed cells of P. gingivalis ATCC 33277 utilized peptides but not single amino acids. Since glutamate and aspartate moieties in the peptides were consumed most intensively, a dipeptide of glutamate or aspartate was then tested as a metabolic substrate of P. gingivalis. P. gingivalis cells metabolized glutamylglutamate to butyrate, propionate, acetate, and ammonia, and they metabolized aspartylaspartate to butyrate, succinate, acetate, and ammonia. Based on the detection of metabolic enzymes in the cell extracts and stoichiometric calculations (carbon recovery and oxidation/reduction ratio) during dipeptide degradation, the following metabolic pathways were proposed. Incorporated glutamylglutamate and aspartylaspartate are hydrolyzed to glutamate and aspartate, respectively, by dipeptidase. Glutamate is deaminated and oxidized to succinyl-coenzyme A (CoA) by glutamate dehydrogenase and 2-oxoglutarate oxidoreductase. Aspartate is deaminated into fumarate by aspartate ammonia-lyase and then reduced to succinyl-CoA by fumarate reductase and acyl-CoA:acetate CoA-transferase or oxidized to acetyl-CoA by a sequential reaction of fumarase, malate dehydrogenase, oxaloacetate decarboxylase, and pyruvate oxidoreductase. The succinyl-CoA is reduced to butyryl-CoA by a series of enzymes, including succinate-semialdehyde dehydrogenase, 4-hydroxybutyrate dehydrogenase, and butyryl-CoA oxidoreductase. A part of succinyl-CoA could be converted to propionyl-CoA through the reactions initiated by methylmalonyl-CoA mutase. The butyryl- and propionyl-CoAs thus formed could then be converted into acetyl-CoA by acyl-CoA:acetate CoA-transferase with the formation of corresponding cytotoxic end products, butyrate and propionate. The formed acetyl-CoA could then be metabolized further to acetate.
Surgical Ventricular Restoration to Reverse Left Ventricular Remodeling

Heart failure is one of the major health care issues in the Western world. An increasing number of patients are affected, leading to a high rate of hospitalization and high costs. Even with administration of the best available medical treatment, mortality remains high. The increase in left ventricular volume after a myocardial infarction is a component of the remodeling process. Surgical Ventricular Restoration (SVR) has been introduced as an optional therapeutic strategy to reduce left ventricular volume and restore heart geometry. So far, it has been established that SVR improves cardiac function, clinical status, and survival in patients with ischemic, dilated cardiomyopathy and heart failure. Since its first description , SVR has been refined in an effort to standardize the procedure and to optimize the results. This review will discuss the rationale behind surgical reversal of LV remodeling, the SVR technique, its impact on cardiac function and survival, and future expectations.
Relational constraints in coalition formation

Relations on the set of economic agents are natural social constraints with respect to individusl and social behaviour of those agents. Although the society consists of a complex system of networks, such a relational structure is until now not used in general equilibrium theory. One of the main reasons is that such (finite) networks are determinants of social behaviour of the economic agents, which is not yet described very well in environ-ments with infinitely many agents. In this paper concepts are introduced that generate coalitions based on the positions of agents with respect to a given family of (relevant) networks. Our starting point therefore is a set of agents endowed with relations as the social characteristics of those agents. This will be called a relational structure. A coalitional structure can then be derived, using the instruments based on the mathematical notion of semi-ring as developed previously by Gilles (198~). The connection of a relational structure with standard economic general equilibrium theory is thus established.
Evaluation of pointing techniques for ray casting selection in virtual environments

Various techniques for object selection in virtual environments have been proposed over the years. Among them, the virtual pointer or ray-casting is one of the most popular method for object selection because it is easy and intuitive to use and allows the user to select objects that are far away. Variants of the virtual pointer metaphor include the Aperture, Flashlight, and Image plane method as categorized as such. In a monoscopic environment, these methods are essentially 2D interaction techniques, as the selection is made effectively on the image plane. Such a 2D based selection (or more generally, interaction) method has an added advantage in that it can find many good uses in 3D environments ranging from a simple 2D oriented subtask (object selection on a constrained surface, menu selection) to a situation where a whole 2D application (e.g. sketching tool, desktop manager) is embedded in the 3D environment. In this paper, we experimentally compare the performance of four different virtual pointer implementations, namely, the direct image plane selection, head-directed pointer, hand directed pointer and head-hand directed pointer. The experimental results revealed that the direct image plane selection produced the best performance among the four in terms of both task completion time and the pixel-level pointing error.
A functional magnetic resonance imaging study of bipolar disorder: state- and trait-related dysfunction in ventral prefrontal cortices.

BACKGROUND Abnormalities in prefrontal and anterior cingulate cortices are implicated in disturbances of attention, cognition, and impulse regulation in bipolar disorder. Acute episodes have been associated with dysfunction in these brain regions, and more enduring trait-related dysfunction has been implicated by volumetric and cellular abnormalities in these regions. The relative contributions of prefrontal regions to state and trait disturbances in bipolar disorder, however, have not been defined. We sought to characterize state- and trait-related functional impairment in frontal systems in bipolar disorder. METHODS Thirty-six individuals with bipolar disorder I (11 with elevated, 10 with depressed, and 15 with euthymic mood states) and 20 healthy control subjects matched for handedness and sex participated in an event-related functional magnetic resonance imaging study of the color-word Stroop to determine mean percentage of regional task-related signal change. RESULTS Signal increased during the Stroop task similarly across diagnostic groups in a distribution that included dorsal anterior cingulate and prefrontal cortices, consistent with previously reported activations in this task. Signal changes associated with specific mood states in bipolar disorder were detected in ventral prefrontal cortex, with a blunted increase in signal on the right side in the elevated mood group (P =.005) and an exaggerated increase in signal on the left side in the depressed group (P =.02) compared with the euthymic group. Patients (vs healthy controls) demonstrated blunted activation in a spatially distinct, rostral region of left ventral prefrontal cortex that was independent of mood state (P<.005). CONCLUSIONS Bipolar disorder is associated with a trait abnormality in left ventral prefrontal cortex. Additional ventral prefrontal abnormalities may be associated with specific acute mood states. The hemispheric laterality of the abnormality and the directions of signal change may relate to the valence of the mood episode.
The Lignoboost Process

A process for lignin removal from alkaline pulping liquors (black liquors) has been developed within the FRAM2 R&D Program (Future Resource Adapted Pulp Mill, part 2). The lignin product (Fig. 1) from a demonstration plant, owned and operated by Innventia (formerly STFI-Packforsk), was characterized and used in different combustion trials with good results – co-firing of lignin and bark in a fluidized bed boiler, co-firing with coal in a PFBC (Pressurized Fluidized Bed Combustion) boiler and firing of lignin in a full-scale lime kiln. The process development and operation of the demonstration plant has displayed good results. Runnability in the demonstration plant and the lignin quality have been both very good. The work done on the investment and operational costs showed great potential for improving the concept of economy, which is very promising. INTRODUCTION One way of exploiting the energy surplus of a modern kraft pulp mill is to extract lignin from the black liquor. This gives the pulp mill a great opportunity to develop new economical revenues when the new by-product, lignin, is commercialised or used within the pulp mill to reduce production costs. Lignin extraction has the additional advantage of providing an incremental capacity in the chemical recovery area, so that it can be used to off-load the recovery boiler or to avoid expansion, when pulp production is increased. One way to handle the bulk flow of produced lignin could be to use the dry lignin powder as a biofuel in the lime kiln and swap fossil fuel. Other ways could be to use lignin in other burners/boilers, where fossil fuel is normally used, boilers in which corrosion from chlorides is a problem or, generally, in fluidized bed boilers frequently used for biomass combustion. Processing of kraft lignin, precipitated from black liquor, to produce a solid biofuel with high energy density and low ash content, is an idea originating from the R&D Program entitled KAM (the Ecocyclic Pulp Mill), developed within the R&D Program
Silent Reading Fluency and Comprehension in Bilingual Children

This paper focuses on reading fluency by bilingual primary school students, and the relation of text fluency to their reading comprehension. Group differences were examined in a cross-sectional design across the age range when fluency is posed to shift from word-level to text-level. One hundred five bilingual children from primary grades 3, 4, and 5 were assessed for English word reading and decoding fluency, phonological awareness, rapid symbol naming, and oral language proficiency with standardized measures. These skills were correlated with their silent reading fluency on a self-paced story reading task. Text fluency was quantified using non-linear analytic methods: recurrence quantification and fractal analyses. Findings indicate that more fluent text reading appeared by grade 4, similar to monolingual findings, and that different aspects of fluency characterized passage reading performance at different grade levels. Text fluency and oral language proficiency emerged as significant predictors of reading comprehension.
Evaluation of the Quality of Four Root Canal Obturation Techniques Using Micro-Computed Tomography

Introduction One of the key factors in successful endodontic therapy is to adequately fill the root canals. The aim of this in vitro study was to compare the quality of four different root canal obturation techniques: cold lateral condensation (CLC), warm vertical condensation (WVC), Obtura II (OII) and Gutta Flow (GF) by using micro-computed tomography (micro CT). Materials and Methods A total of 20 extracted maxillary first molars prepared with ProTaper files, were randomly divided into four groups. Micro CT was used to measure the internal volume of root canals. Following application of AH26 sealer to canal obturation, new micro-CT images were taken and the volume percentage (VP) of voids, gutta-percha and sealer at different levels were calculated with CT software. Data was statistically analyzed using Kruskal-Wallis and Mann-Whitney U tests. Results The highest percentage of filling material was observed in GF group followed by OII with no statistically significant difference (P>0.05). These two groups had a significantly more acceptable filling than WVC and CLC groups (P<0.05). Voids were detected in all samples. There was a significant difference between the highest and the lowest percentage of voids in CLC (19.6%) and GF groups (6.7%), respectively. In the apical third, CLC and OII showed the highest and the lowest percentage of voids (5.5% and 2.6%) and the lowest and highest percentage of gutta-percha (76.52% and 94.26%), respectively. These differences were statistically significant (P<0.05). Conclusion None of the root canal filled teeth were gap-free. GF and CLC techniques showed the highest and lowest VP of obturation materials, respectively.
Acute Malaria Induces PD1+CTLA4+ Effector T Cells with Cell-Extrinsic Suppressor Function

In acute Plasmodium falciparum (P. falciparum) malaria, the pro- and anti-inflammatory immune pathways must be delicately balanced so that the parasitemia is controlled without inducing immunopathology. An important mechanism to fine-tune T cell responses in the periphery is the induction of coinhibitory receptors such as CTLA4 and PD1. However, their role in acute infections such as P. falciparum malaria remains poorly understood. To test whether coinhibitory receptors modulate CD4+ T cell functions in malaria, blood samples were obtained from patients with acute P. falciparum malaria treated in Germany. Flow cytometric analysis showed a more frequent expression of CTLA4 and PD1 on CD4+ T cells of malaria patients than of healthy control subjects. In vitro stimulation with P. falciparum-infected red blood cells revealed a distinct population of PD1+CTLA4+CD4+ T cells that simultaneously produced IFNγ and IL10. This antigen-specific cytokine production was enhanced by blocking PD1/PDL1 and CTLA4. PD1+CTLA4+CD4+ T cells were further isolated based on surface expression of PD1 and their inhibitory function investigated in-vitro. Isolated PD1+CTLA4+CD4+ T cells suppressed the proliferation of the total CD4+ population in response to anti-CD3/28 and plasmodial antigens in a cell-extrinsic manner. The response to other specific antigens was not suppressed. Thus, acute P. falciparum malaria induces P. falciparum-specific PD1+CTLA4+CD4+ Teffector cells that coproduce IFNγ and IL10, and inhibit other CD4+ T cells. Transient induction of regulatory Teffector cells may be an important mechanism that controls T cell responses and might prevent severe inflammation in patients with malaria and potentially other acute infections.
An experimental comparative study of web mining methods for recommender systems

An essential goal of the present web engineering is the development of efficient and competitive applications. This objective can be achieved by building recommender systems endowed with suitable web mining algorithms. Multiclassifiers are reliable data mining models that have been hardly used in the web system area. The paper presents a comparative study among different simple classifiers and multiclassifiers using a dataset from MovieLens recommender system. The aim of the work is to identify when the use of multiclassifiers in this type of systems is efficient.
Psychological Stress In First Year Medical Students In Response To The Dissection Of A Human Corpse

Objectives: Gross anatomy is one of the most important and time consuming subjects in the first preclinical part of medical school in Germany. In October 2007 186 students started the dissection course at Otto-von-Guericke-University Magdeburg. The objective of this study is to analyze the emotional aspect relating to the gross anatomy course. In order to address this issue, we investigated how medical students experience the first confrontation and the following exposure to the dead bodies and whether there are any differences between various groups (age, gender, experience) of students. Methods: The study was carried out with a group of 155 first year medical students (112 female, 43 male, 21.4±2.9 years). Self-composed questionnaires were used to distinguish between concerns related to dissection and individual experiences and anxiety because of deceasing or death. In order to detect the changes of attitudes towards the dissection course, one questionnaire was answered by participants in the beginning of the course and one in the end (n=94, 66 female, 28 male). Additionally, personality traits of the students were analyzed using two scales of the “Freiburger Persönlichkeitsinventar (FPI-R)”. Results: The self-composed questionnaires showed high reliability. For some students dissection was emotional stress; about 50% became anxious when coping the first confrontation, however, only 12% to large extent. Concerning the anxiety of dissection of individual body parts it was less for limbs, internal organs and skin and increased for head and genitals. Although hypothesized before, the correlation between age, extraversion, emotionality and the extent of anxiety were small. Almost 90% of the students approve the early beginning of the gross anatomy course. The follow-up study showed a marked decline of anxiety. Conclusion: Our results show that about 50% of the students started the course with emotional stress and about one-tenth of them were very worried about the confrontation with corpses. Furthermore, personality tests were shown to be only partly reliable for selecting affected people in advance. With regard to these results capabilities to provide support to the first year medical students should be discussed.
Collagen Content in Skin and Internal Organs of the Tight Skin Mouse: An Animal Model of Scleroderma

The Tight Skin mouse is a genetically induced animal model of tissue fibrosis caused by a large in-frame mutation in the gene encoding fibrillin-1 (Fbn-1). We examined the influence of gender on the collagen content of tissues in C57BL/6J wild type (+/+) and mutant Tight Skin (Tsk/+) mice employing hydroxyproline assays. Tissue sections were stained with Masson's trichrome to identify collagen in situ. Adult Tsk/+ mice skin contains ~15% more collagen, on average, than skin from +/+ mice of the same gender. The heart of Tsk/+ males had significantly more collagen than that of +/+ males. No significant gender differences were found in lungs and kidney collagen content. Overall, the collagen content of Tsk/+ males and +/+ males was higher than that of their Tsk/+ and +/+ female counterparts, respectively. Our data confirm increased deposition of collagen in skin and hearts of Tsk/+ mice; however, the effects of the Tsk mutation on collagen content are both tissue specific and gender specific. These results indicate that comparative studies of collagen content between normal and Tsk/+ mice skin and internal organs must take into account gender differences caused by expression of the androgen receptor.
The 2006 NESCent Phyloinformatics Hackathon: A Field Report

In December, 2006, a group of 26 software developers from some of the most widely used life science programming toolkits and phylogenetic software projects converged on Durham, North Carolina, for a Phyloinformatics Hackathon, an intense five-day collaborative software coding event sponsored by the National Evolutionary Synthesis Center (NESCent). The goal was to help researchers to integrate multiple phylogenetic software tools into automated workflows. Participants addressed deficiencies in interoperability between programs by implementing “glue code” and improving support for phylogenetic data exchange standards (particularly NEXUS) across the toolkits. The work was guided by use-cases compiled in advance by both developers and users, and the code was documented as it was developed. The resulting software is freely available for both users and developers through incorporation into the distributions of several widely-used open-source toolkits. We explain the motivation for the hackathon, how it was organized, and discuss some of the outcomes and lessons learned. We conclude that hackathons are an effective mode of solving problems in software interoperability and usability, and are underutilized in scientific software development.
CONVERGENCE OF REAL GDP PER CAPITA IN THE EU15 HOW DO THE ACCESSION COUNTRIES FIT IN

The EU15 countries’ real GDP per capita levels adjusted for purchasing power converged in 1960–2001. Convergence occurred in two spells, in 1960–73 and 1986–2001, with an interim period of stagnation. In this paper, we analyse both s and b convergence and discuss the impact of EU membership, trade and investment. We also analyse how seven accession countries fit into the historical picture of the EU15 area. The CEE countries are wellpositioned to catch up with the incumbent EU countries. After the mid-1990s, an increase in productivity and high investment rates have supported economic growth in the accession countries. Still, the experience of the EU15 countries shows that convergence cannot be taken for granted.
What Makes Human Cognition Unique? From Individual to Shared to Collective Intentionality

It is widely believed that what distinguishes the social cognition of humans from that of other animals is the belief–desire psychology of four–year–old children and adults (so–called theory of mind). We argue here that this is actually the second ontogenetic step in uniquely human social cognition. The first step is one year old children's understanding of persons as intentional agents, which enables skills of cultural learning and shared intentionality. This initial step is ‘the real thing’ in the sense that it enables young children to participate in cultural activities using shared, perspectival symbols with a conventional/normative/reflective dimension—for example, linguistic communication and pretend play—thus inaugurating children's understanding of things mental. Understanding beliefs and participating in collective intentionality at four years of age—enabling the comprehension of such things as money and marriage—results from several years of engagement with other persons in perspective–shifting and reflective discourse containing propositional attitude constructions.
Differential diagnosis of cyclin D 2 + mantle cell lymphoma ( MCL ) based on fluorescence in sit u hybridization ( FISH ) and quantitative real-time-PCR

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The Development of Prosocial Behavior in Adolescents

Learning transfer and prosocial behavior (PSB) are critical components of many outdoor education programs for adolescents. This study examined the effects of a theoretically grounded treatment curriculum designed to foster the transfer of learning of general and contextual PSB (also called expedition behavior) among adolescents enrolled on 14-day backpacking courses with the National Outdoor Leadership School. Results suggest that the treatment curriculum increased proximal learning of PSB more than courses that featured the traditional curriculum. Qualitative results suggested that students learned PSB primarily as a result of its relevance to the expedition environment, that it is most useful when working with or understanding others, and that it can be applied to multiple contexts post-course, including with family, at school, and with sport teams. Implications for designing a curriculum that fosters transfer and for developing PSB in participants are considered.