Miracle-dz/UniFAR-FTUs huggingface dataset:
Evidence of Recombination in Mixed-Mating-Type and α-Only Populations of Cryptococcus gattii Sourced from Single Eucalyptus Tree Hollows

ABSTRACT Disease caused by the pathogenic yeast Cryptococcus gattii begins with the inhalation of an infectious propagule. As C. gattii is heavily encapsulated, this propagule is most likely to be a basidiospore. However, most C. gattii strains are infertile in laboratory crosses, and population studies indicate that recombination and dispersal are very restricted. In addition, strains of the α mating type predominate, which would not be expected in a mating population. C. gattii comprises four genetically distinct molecular genotypes, designated VGI to VGIV. C. gattii molecular type VGI has a strong association with Eucalyptus camaldulensis and can be found in high numbers in E. camaldulensis hollows. Previous work on isolates obtained from E. camaldulensis suggested that environmental populations of C. gattii are highly fragmented, have limited ability to disperse, and are confined to individual tree hollows. In the current study, we examined large numbers of isolates from three separate hollows for evidence of recombination. In two hollows, the α and a mating types were present in approximately equal numbers. The third hollow had α cells only and was from a region where a isolates have never been found. Statistical analysis of multilocus genotypes revealed recombining subpopulations in the three Eucalyptus hollows. Recombination was equally present in the α-a and α-only populations. This is consistent with recent studies that have found evidence suggestive of α-α mating in C. gattii and Cryptococcus neoformans and raises the possibility this may be a widespread phenomenon, allowing these fungi to recombine despite a paucity of a mating partners.
First-trimester placental vascular development in multiparous women differs from that in nulliparous women

Abstract Objective: Multiparas differ from nulliparas by delivering larger babies with larger placentas and by having a lower risk of developing placental syndromes. We postulate that these differences result from a different initial course of placental vascular development. Study design: We measured placental flow index (FI), vascularization index (VI) and placental volume by 3D power Doppler and obtained blood samples at 8, 10 and 12 weeks pregnancy in 34 healthy nulliparous and 16 multiparous women with an uneventful pregnancy. Results: Between 8 and 12 weeks multiparas differed from nulliparas in a more rapid initial rise in FI, a higher angiopoietin-2 (ang2) level at eight weeks and no decline in the VEGF/sVEGF-R ratio. Nevertheless, at 12 weeks the FI and placental volume were indistinguishable between both study groups. Conclusions: These results combining serially measured placental vascularization, placental volume and circulating angiogenetic factors show initial differences in placental development, that howeve, did not maintain till the end of first trimester. The results support the concept that early placental vascular development differs between nulliparas and multiparas. Nevertheless, it is unclear whether these differences contribute to the development later on in pregnancy of intergroup differences in birthweight and incidence of placental syndromes.
Diferencias en el comportamiento defensores públicos en el contexto de la Reforma Procesal Penal chilena

La Defensoria Penal Publica chilena es el organismo encargado de proveer servicios de defensa penal en el contexto de la nueva justicia nacional (Reforma Procesal Penal). Para ello, o bien contrata abogados en forma directa (abogados institucionales) o bien licita los servicios a estudios juridicos, quienes a su vez contratan abogados para el efecto (abogados licitados). A fines del ano 2004 hubo un cambio en el mecanismo de licitacion, pasando de pagar un precio por tipo de salida de cada causa penal a pagar un precio unico por la misma. En este trabajo se analiza si dicho cambio afecto el comportamiento de los abogados licitados. En forma adicional, se analiza si el desempeno de los abogados licitados es distinto de los abogados institucionales.
Evaluation of “pupils' laptop” initiative in secondary education in Greece: Analyzing the qualitative results of a survey on teachers

In 2009 a project regarding the distribution of laptop computers to pupils of first grade in Greek secondary schools was implemented. Four years later a survey took place to evaluate the results of this intervention on teaching and learning. The survey was implemented both on teachers as well as on pupils who participated in the project with the utilization of respectively two questionnaires, one for each target group. Within the teachers' questionnaire some questions were intentionally selected to be open ended in order to acquire not only quantitative data but certain qualitative too, that might help to better understand the outcomes. In this paper the qualitative data from the teachers' responds are analyzed and presented in an attempt to clarify and support the quantitative results. Additionally the main results of the quantitative survey for each target group are presented, combined to each other and discussed with the perspective that qualitative data analysis is offering. The outcomes of this evaluation highlight interesting points regarding both the strategy that was adopted in the deployment of the project as well as for the lessons learned from the intervention and the actual use of the laptops within the classroom.
User-friendly web application for bibliographic material processing

Purpose – The purpose of this paper is implementation of a software system for bibliographic material processing which does not require knowledge about any format for bibliographic data input. This means that the input can be done not only by librarians, but also by other persons such as authors of bibliographic units, students, employees, etc.Design/methodology/approach – An object‐oriented methodology for developing information systems by means of computer‐aided software engineering (CASE) tools and software components is used. The software architecture is multi‐layered and web‐based. The implementation is done in Java environment.Findings – The result is a web application by which users can catalogue bibliographic material without being familiar with the corresponding format. Nevertheless, the bibliographic record is formed in accordance with the given format for bibliographic material processing (MARC21, UNIMARC, etc.). Research limitations/implications – Automatic generating of screen forms for the ch.
Dehalococcoides mccartyi gen. nov., sp. nov., obligately organohalide-respiring anaerobic bacteria relevant to halogen cycling and bioremediation, belong to a novel bacterial class, Dehalococcoidia classis nov., order Dehalococcoidales ord. nov. and family Dehalococcoidaceae fam. nov., within the ph

Six obligately anaerobic bacterial isolates (195(T), CBDB1, BAV1, VS, FL2 and GT) with strictly organohalide-respiring metabolisms were obtained from chlorinated solvent-contaminated aquifers, contaminated and uncontaminated river sediments or anoxic digester sludge. Cells were non-motile with a disc-shaped morphology, 0.3-1 µm in diameter and 0.1-0.2 µm thick, and characteristic indentations on opposite flat sides of the cell. Growth occurred in completely synthetic, reduced medium amended with a haloorganic electron acceptor (mostly chlorinated but also some brominated compounds), hydrogen as electron donor, acetate as carbon source, and vitamins. No other growth-supporting redox couples were identified. Aqueous hydrogen consumption threshold concentrations were <1 nM. Growth ceased when vitamin B(12) was omitted from the medium. Addition of sterile cell-free supernatant of Dehalococcoides-containing enrichment cultures enhanced dechlorination and growth of strains 195 and FL2, suggesting the existence of so-far unidentified stimulants. Dechlorination occurred between pH 6.5 and 8.0 and over a temperature range of 15-35 °C, with an optimum growth temperature between 25 and 30 °C. The major phospholipid fatty acids were 14 : 0 (15.7 mol%), br15 : 0 (6.2 mol%), 16 : 0 (22.7 mol%), 10-methyl 16 : 0 (25.8 mol%) and 18 : 0 (16.6 mol%). Unusual furan fatty acids including 9-(5-pentyl-2-furyl)-nonanoate and 8-(5-hexyl-2-furyl)-octanoate were detected in strains FL2, BAV1 and GT, but not in strains 195(T) and CBDB1. The 16S rRNA gene sequences of the six isolates shared more than 98 % identity, and phylogenetic analysis revealed an affiliation with the phylum Chloroflexi and more than 10 % sequence divergence from other described isolates. The genome sizes and G+C contents ranged from 1.34 to 1.47 Mbp and 47 to 48.9 mol% G+C, respectively. Based on 16S rRNA gene sequence comparisons, genome-wide average nucleotide identity and phenotypic characteristics, the organohalide-respiring isolates represent a new genus and species, for which the name Dehalococcoides mccartyi gen. nov., sp. nov. is proposed. Isolates BAV1 ( = ATCC BAA-2100 = JCM 16839 = KCTC 5957), FL2 ( = ATCC BAA-2098 = DSM 23585 = JCM 16840 = KCTC 5959), GT ( = ATCC BAA-2099 = JCM 16841 = KCTC 5958), CBDB1, 195(T) ( = ATCC BAA-2266(T) = KCTC 15142(T)) and VS are considered strains of Dehalococcoides mccartyi, with strain 195(T) as the type strain. The new class Dehalococcoidia classis nov., order Dehalococcoidales ord. nov. and family Dehalococcoidaceae fam. nov. are described to accommodate the new taxon.
Neonatal respiratory distress syndrome.

EDITOR,-Professor Southall and colleagues' question the comments of the working group on the management of neonatal respiratory distress syndrome regarding parameters of oxygenation.2 We write in support of the provisional and practical suggestion of an arterial oxygen saturation (Sao2) range of 85-93% and suggest that much of the data quoted by Southall et al is not applicable to this clinical setting. Professor Southall and colleagues suggest an upper limit for Sao2 of96% and quote four studies in support of this choice. In two of these papers,3 4 the majority of the patients were not preterm and were receiving treatment for other conditions, mainly congenital heart disease. These infants constitute a very different population from those suffering from respiratory distress syndrome. Our own study of 477 measurements made in clinical practice using Ohmeda Biox oximeters on a population under 33 weeks' gestation found that if the saturation value was 93% or below the arterial oxygen tension (Pao2) was never greater than 12 kPa.5 To maintain the Pao2 below 10 kPa, which is the upper limit suggested by the working party, requires a saturation of 92% or less. Certainly, when using an Ohmeda oximeter, an upper limit of 93% seems very reasonable. When discussing a lower limit for Sao2, Professor Southall recommends 95%, based on a study of well preterm infants.6 These infants bear little relation to the sick, low birthweight infants who, until very recently had experienced a physiological, umbilical venous oxygen tension (Po2) of approximately 4-5-6-0 kPa. With regard to the adverse effects of hypoxia, there is no firm evidence which defines the optimal range for any of the indices of oxygenation. There are almost no modem data relating levels of oxygenation to outcome; the papers quoted by Professor Southall regarding hypoxia describe physiological responses to lower levels of oxygenation and not outcome. Limited by the lack of scientific data, the working party have had to make reasonable and, equally important, practical recommendations. We feel that there is little evidence to support a range of 94 to 96% and in addition would be surprised to find any neonatal unit able to maintain the Sao2 within such narrow limits. With the marked fluctuations in oxygenation seen in preterm infants receiving intensive care, it would be difficult to make sufficiently frequent adjustments in ventilator settings to comply with these limits. Based on our own data we currently employ the range 86 to 94%, similar to that mentioned in the working party report and look forward to further studies to give us more guidance on this difficult question.
Loss of an MDR Transporter in Compact Stalks of Maize br2 and Sorghum dw3 Mutants

Agriculturally advantageous reduction in plant height is usually achieved by blocking the action or production of gibberellins. Here, we describe a different dwarfing mechanism found in maize brachytic2 (br2) mutants characterized by compact lower stalk internodes. The height reduction in these plants results from the loss of a P-glycoprotein that modulates polar auxin transport in the maize stalk. The sorghum ortholog of br2 is dwarf3 (dw3), an unstable mutant of long-standing commercial interest and concern. A direct duplication within the dw3 gene is responsible for its mutant nature and also for its instability, because it facilitates unequal crossing-over at the locus.
Hardware Trojan Insertion by Direct Modification of FPGA Configuration Bitstream

In this work, we have demonstrated the feasibility of hardware Trojan insertion in circuits mapped on FPGAs by direct modification of the FPGA configuration bitstream. The main challenge of this attack proved to be the lack of sufficient information in the public domain about the bitstream format and the internal architecture and configurability of the FPGA. Nevertheless, we were able to show that under certain constraints on the functionality, size and placement of the Trojan on the FPGA, it is possible to modify the configuration bitstream by a software program to insert a hardware Trojan in the design. The main strength of the attack lies in the fact that since the modification is at the configuration bitstream level, it bypasses all predeployment design validation mechanisms. We also propose some techniques to prevent the demonstrated attack. We hope that this work will raise awareness among FPGA users about the potency of the threat posed by this relatively simple attack and its improved variants.
A SIMPLE QUESTIONNAIRE TO DETECT HYPERMOBILITY: AN ADJUNCT TO THE ASSESSMENT OF PATIENTS WITH DIFFUSE MUSCULOSKELETAL PAIN

The aim of the study was to develop a simple and reproducible self‐reporting questionnaire that identifies individuals with hypermobility. Two hundred and twelve consecutive hypermobile female new attendees to the hypermobility clinic at two London teaching hospitals and a random selection of 57 healthy volunteers completed a 10‐part questionnaire. Questions were selected from clinical experience (RG), and assessed musculoskeletal symptoms and past and present physical agility. Of the 212 cases, 30 were hypermobile with no other underlying disorder and 182 fulfilled the 1998 Brighton criteria for benign joint hypermobility syndrome (BJHS). Odds ratios for the presence of hypermobility were calculated for each question. Six questions were found to be significant and the model of ‘best fit’ for sensitivity and specificity contained five of these. To demonstrate the reproducibility of the five‐part questionnaire a second cohort of 170 hypermobile cases with BJHS and 50 controls was surveyed. Analysis demonstrated that a positive answer to any two questions in the five‐part questionnaire gave the highest combined sensitivity and specificity for detecting hypermobility. The sensitivity and specificity was 84% and 89% respectively in the first cohort and reproduced with values of 84% and 80% in the second cohort. Overall the questionnaire correctly identified 84% of all cases and controls. This simple and reproducible questionnaire for detecting hypermobility could be of particular use as an adjunct in the clinical assessment of chronic, diffuse pain syndromes where hypermobility is often missed yet is potentially treatable.
Differential expression and localisation of gasdermin‐like (GSDML), a novel member of the cancer‐associated GSDMDC protein family, in neoplastic and non‐neoplastic gastric, hepatic, and colon tissues

Aim: Gasdermin‐like (GSDML) is a novel member of the cancer associated gasdermin‐domain containing (GSDMDC) protein family. The GSDMDC family has been linked to cancer development and progression, and this is the first study analysing the expression and intracellular localisation of GSDML. Methods: GSDML gene transcription was analysed using quantitative real‐time RT‐PCR. Anti‐peptide antibodies against GSDML were developed in rabbits, and an in vitro transcription‐translation reaction was used to verify specificity. The Protein‐G affinity purified antibodies were used in immunohistochemistry and immunoblotting on hepatocellular, gastric, and colorectal carcinomas and non‐lesional tissues. Results: The GSDML gene was transcribed in human gastric, liver and colon cell lines, carcinomas and non‐lesional tissues. The GSDML protein was localised to the cytoplasm of cells in both tumour and non‐lesional tissues. The GSDML protein splicing variants range in molecular weight from 35 to 50 kDa, and the expression profile varies between tumour and non‐tumour. A distinctive vesicular staining pattern was exhibited by GSDML in the apical region of gastric chief cells and colonic surface mucous cells, and the basal region of neuroendocrine cells. Conclusion: GSDML may be a secretory or metabolic product involved in a secretory pathway, and changes in the regulation of GSDML splicing variant transcription and translation may be seen in the development and/or progression of gastrointestinal and hepatic cancers.
Das Defizit an verkehrspsychologischer Strategie. Gruende fuer den Misserfolg der deutschen Verkehrspolitik

Verkehrspolitik und -planung in Deutschland folgt in Bund und Laendern und auch in den meisten Gemeinden dem gleichen Muster: Fortsetzung des autoorientierten Ausbaus der Verkehrsinfrastruktur (Strassen, Parkraum) und nur sehr zoegerlicher Ausbau bei den Alternativen (Fussverkehrssystem, Radverkehrssystem, oeffentlicher Verkehr einschliesslich Car-Sharing, Gueterbahn). Teilweise wird im Umweltverbund die Angebotsqualitaet sogar weiter verschlechtert, durch Stilllegung von Bahnstrecken, Bahnhoefen und Gueterverkehrsstellen, Ausduennung des Fahrplans. Noch groesser sind die Versaeumnisse im Bereich der Kommunikation. Marketing und Werbung auf dem Gebiet der Verkehrsinfrastruktur und fuer Verkehrssicherheit erfolgen fast ausschliesslich durch Autoindustrie und Autolobby und gestalten sich daher ueberwiegend gewinnorientiert, Alternativen zum Individualverkehr bleiben folglich die Ausnahme. So wird auf fatale Weise die Innovationsfaehigkeit der Verkehrspolitik blockiert. Kreative Psychologen koennten hier helfen, bessere Strategien zu entwickeln. (A) Titel in Englisch: The lack of psychological strategy. Reasons for the poor success of German transportation policy.
Immunoglobulins and measles antibodies in optic neuritis.

Abstract Patients with optic neuritis have been separated into two groups by the presence or absence of oligoclonal immunoglobulin G (IgG) (demonstrable by agar-gel electrophoresis) in the cerebrospinal fluid. Patients with oligoclonal IgG had mean serum concentration of measles-virus hemolysis-inhibiting antibodies about seven times higher, whereas no difference between the groups was seen in mean serum titers of hemagglutination-inhibiting and of nucleocapsid complement-fixing antibodies. Significantly reduced ratios of serum to cerebrospinal-fluid measles virus antibody were found in 12 of 21 patients with oligoclonal IgG but in only one of 20 without oligoclonal IgG, although either adenovirus hemagglutination enhancement or poliovirus neutralization-enhancement antibody ratios or both were normal. These findings indicate the occurrence of a local measles-virus antibody response within the central nervous system in some patients with optic neuritis and oligoclonal IgG in cerebrospinal fluid. The immun.
Multimodal Affect Recognition in Virtual Worlds: Avatars Mirroring User's Affect

Virtual worlds enable users' interactions through avatars. Avatars embody individual characteristics from their owners and exhibit those characteristics outward to the community. Motivated by the role of avatars in interpersonal communication, we integrated a generic real-time multimodal affect recognition hub as an input within an online virtual world to make an avatar mirror its owner's affect. Affect vectors (determined by pleasure, arousal, and dominance coordinates) in a continuous affective space are applied to characterize the user's affective state in real time.
Denervation alters mRNA levels of repair‐associated genes in a rabbit medial collateral ligament injury model

Previous experiments revealed that denervation impairs healing of the MCL. This suggested the hypothesis that denervation would decrease repair‐associated mRNA levels in the injured MCL when compared with normally innervated injured MCL. Adult, skeletally mature female rabbits were assigned to one of four groups: unoperated control, femoral nerve transection alone (denervated controls), MCL partial tear or denervated MCL partial tear. At three days, two weeks, six weeks or sixteen weeks post‐surgery, cohorts of 6 rabbits from each experimental group were killed. Ligaments were harvested, RNA extracted and RT‐PCR was performed using rabbitspecific primers. In the denervated injury group, mRNA levels for the angiogenesis‐associated gene MMP‐13, matrix components Collagen I and III, growth factor TGF‐β and angiogenesis inhibitors TIMP‐3, and TSP‐1 had all increased by two‐weeks post‐injury, in comparison to the non‐denervated injury group (p ≤ 0.01). An increased level of TSP‐1 mRNA was also detected in the denervated injured group at sixteen weeks post injury (p ≤ 0.01). Contrary to the initial hypothesis, denervation led to increased mRNA levels for many relevant molecules during the early stages of MCL healing. Thus, inappropriate timing of over‐expression of some molecules may potentially contribute to the decreased quality of the scar tissue, particularly molecules such as TSP‐1. Neuronal derived factors strongly influence the in vivo metabolic activity of ligament and scar fibroblasts in the initial phases of healing. © 2006 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res
Specific role for cathepsin S in the generation of antigenic peptides in vivo

To address the role of different proteases in degradation of antigen destined for MHC class II‐restricted presentation, we generated cathepsin‐deficient mice carrying a transgenic B cell receptor (BCR) specific for hen egg lysozyme (HEL). We demonstrate that degradation of HEL in B lymphocytes is highly processive and does not result in discrete processing intermediates. Moreover, degradation of HEL does not require initial unlocking of the antigen by any of the cathepsins tested. Using mass spectrometry and microsequencing, we show that all major cathepsins (CatS, CatL, CatB, and CatD) digest HEL in vitro with considerable redundancy, although some preferential cleavages are evident. These observations have a functional correlate: when triggered by cathepsin S‐deficient antigen‐presenting cells, T cells that recognize different HEL epitopes fail to present two HEL‐derived epitopes, while a third epitope is presented independently of the activity of cysteine proteases. We conclude that the proteolytic processing machinery is redundant, and that several proteases can substitute for each other to degrade a given antigen. However, a certain degree of proteolytic specificity is demonstrable for the generation of particular epitopes, notably by CatS.