Miracle-dz/UniFAR-FTUs huggingface dataset:
Orientation of cosmic web filaments with respect to the underlying velocity field

The large-scale structure of the Universe is characterised by a web-like structure made of voids, sheets, filaments, and knots. The structure of this so-called cosmic web is dictated by the local velocity shear tensor. In particular, the local direction of a filament should be strongly aligned with e3, the eigenvector associated with the smallest eigenvalue of the tensor. That conjecture is tested here on the basis of a cosmological simulation. The cosmic web delineated by the halo distribution is probed by a marked point process with interactions (the Bisous model), detecting filaments directly from the halo distribution (P-web). The detected P-web filaments are found to be strongly aligned with the local e3: the alignment is within 30 degree for 80% of the elements. This indicates that large-scale filaments defined purely from the distribution of haloes carry more than just morphological information, although the Bisous model does not make any prior assumption on the underlying shear tensor. The P-web filaments are also compared to the structure revealed from the velocity shear tensor itself (V-web). In the densest regions, the P- and V-web filaments overlap well (90%), whereas in lower density regions, the P-web filaments preferentially mark sheets in the V-web.
Multilingual Translation Issues in Qualitative Research

Focus on the translation and validation of measurement instruments has left a gap in the discussion on how to construct multilingual qualitative tools, such as interviews. Traditional methods of forward and backward translation have been criticized for weak conceptual equivalence, a crucial issue when multiple language interview methods are used.Through a creative arts metaphor of weaving, the authors describe an alternative process of multicentric translation used in the development of an interview guide designed to explore the impact of transition on palliative care patients in six European countries. Four identified core constructs illuminate this multicentric process: Cohesion, Congruence, Clarity, and Courtesy. Mutual reciprocity between researcher and translator offers greater possibility for construction of nuance and meaning, particularly where cultural parameters influence the collection and meaning of sensitive data from vulnerable populations. The translator therefore becomes a collaborator in the research process, which strengthens the rigor of language-based inquiry.
Diversity of a major repetitive DNA sequence in diploid and polyploid Triticeae

About 90 members of a major tandemly repeated DNA sequence family originally described in rye as pSc119.2 have been isolated from 11 diploid and polyploid Triticeae species using primers from along the length of the sequence for PCR amplification. Alignment and similarity analysis showed that the 120-bp repeat unit family is diverse with single nucleotide changes and few insertions and deletions occurring throughout the sequence, with no characteristic genome or species-specific variants having developed during evolution of the extant genomes. Fluorescent in situ hybridization showed that each of the large blocks of the repeat at chromosomal sites harboured many variants of the 120-bp repeat. There were substantial copy number differences between genomes, with abundant sub-terminal sites in rye, interstitial sites in the B genome of wheat, and relatively few sites in the A and D genome. We conclude that sequence homogenization events have not been operative in this repeat and that the common ancestor of the Triticeae tribe had multiple sequences of the 120-bp repeat with a range of variation not unlike that seen within and between species today. This diversity has been maintained when sites are moved within the genome and in all species since their divergence within the Triticeae.
Phase Locking of Multiple Single Neurons to the Local Field Potential in Cat V1

The local field potential (LFP) is thought to reflect a temporal reference for neuronal spiking, which may facilitate information coding and orchestrate the communication between neural populations. To explore this proposed role, we recorded the LFP and simultaneously the spike activity of one to three nearby neurons in V1 of anesthetized cats during the presentation of drifting sinusoidal gratings, binary dense noise stimuli, and natural movies. In all stimulus conditions and during spontaneous activity, the average LFP power at frequencies >20 Hz was higher when neurons were spiking versus not spiking. The spikes were weakly but significantly phase locked to all frequencies of the LFP. The average spike phase of the LFP was stable across high and low levels of LFP power, but the strength of phase locking at low frequencies (≤10 Hz) increased with increasing LFP power. In a next step, we studied how strong stimulus responses of single neurons are reflected in the LFP and the LFP–spike relationship. We found that LFP power was slightly increased and phase locking was slightly stronger during strong compared with weak stimulus-locked responses. In summary, the coupling strength between high frequencies of the LFP and spikes was not strongly modulated by LFP power, which is thought to reflect spiking synchrony, nor was it strongly influenced by how strongly the neuron was driven by the stimulus. Furthermore, a comparison between neighboring neurons showed no clustering of preferred LFP phase. We argue that hypotheses on the relevance of phase locking in their current form are inconsistent with our findings. SIGNIFICANCE STATEMENT The local field potential (LFP) is hypothesized to play a vital role in the efficient communication between neuronal populations, as well as in the efficient coding of information. Underlying these roles is the assumption that spikes can be strongly and reliably locked to certain phases of oscillations in the LFP. Gamma oscillations are thought to be the best candidate mechanism exerting the hypothesized roles of the LFP. They occur most reliably in response to specific artificial stimuli, but are usually very weak in response to natural movies or images. The current study finds that spikes exhibited weak phase locking when the power of gamma oscillations is weak and thus casts doubt on a general relevance of phase locking for neural communication and coding.
Primary Ciliary Dyskinesia in Mice Lacking the Novel Ciliary Protein Pcdp1

ABSTRACT Primary ciliary dyskinesia (PCD) results from ciliary dysfunction and is commonly characterized by sinusitis, male infertility, hydrocephalus, and situs inversus. Mice homozygous for the nm1054 mutation develop phenotypes associated with PCD. On certain genetic backgrounds, homozygous mutants die perinatally from severe hydrocephalus, while mice on other backgrounds have an accumulation of mucus in the sinus cavity and male infertility. Mutant sperm lack mature flagella, while respiratory epithelial cilia are present but beat at a slower frequency than wild-type cilia. Transgenic rescue demonstrates that the PCD in nm1054 mutants results from the loss of a single gene encoding the novel primary ciliary dyskinesia protein 1 (Pcdp1). The Pcdp1 gene is expressed in spermatogenic cells and motile ciliated epithelial cells. Immunohistochemistry shows that Pcdp1 protein localizes to sperm flagella and the cilia of respiratory epithelial cells and brain ependymal cells in both mice and humans. This study demonstrates that Pcdp1 plays an important role in ciliary and flagellar biogenesis and motility, making the nm1054 mutant a useful model for studying the molecular genetics and pathogenesis of PCD.
A Mathematical Model of an In Vitro Experiment to Investigate Endothelial Cell Migration

Angiogenesis, the growth of new blood vessels from existing ones, is an important, yet not fully understood, process and is involved in diseases such as rheumatoid arthritis, diabetic retinopathy and solid tumour growth. Central to the process of angiogenesis are endothelial cells (EC), which line all blood vessels, and are capable of forming new capillaries by migration, proliferation and lumen formation. We construct a cell-based mathematical model of an experiment (Vernon, R.B. and Sage, E.H. (1999) “A novel, quantitative model for study of endothelial cell migration and sprout formation within three-dimensional collagen matrices”, Microvasc. Res. 57, 118–133) carried out to assess the response of EC to various diffusible angiogenic factors, which is a crucial part of angiogenesis. The model for cell movement is based on the theory of reinforced random walks and includes both chemotaxis and chemokinesis. Three-dimensional simulations are run and the results correlate well with the experimental data. The experiment cannot easily distinguish between chemotactic and chemokinetic effects of the angiogenic factors. We, therefore, also run two-dimensional simulations of a hypothetical experiment, with a point source of angiogenic factor. This enables directed (gradientdriven) EC migration to be investigated independently of undirected (diffusion-driven) migration.
Immunodominance of CD4 T Cells to Foreign Antigens Is Peptide Intrinsic and Independent of Molecular Context: Implications for Vaccine Design1

Immunodominance refers to the restricted peptide specificity of T cells that are detectable after an adaptive immune response. For CD4 T cells, many of the mechanisms used to explain this selectivity suggest that events related to Ag processing play a major role in determining a peptide’s ability to recruit CD4 T cells. Implicit in these models is the prediction that the molecular context in which an antigenic peptide is contained will impact significantly on its immunodominance. In this study, we present evidence that the selectivity of CD4 T cell responses to peptides contained within protein Ags is not detectably influenced by the location of the peptide in a given protein or the primary sequence of the protein that bears the test peptide. We have used molecular approaches to change the location of peptides within complex protein Ags and to change the flanking sequences that border the peptide epitope to now include a protease site, and find that immunodominance or crypticity of a peptide observed in its native protein context is preserved. Collectively, these results suggest immunodominance of peptides contained in complex Ags is due to an intrinsic factor of the peptide, based upon the affinity of that peptide for MHC class II molecules. These findings are discussed with regard to implications for vaccine design.
Influenza in children

Excess mortality associated with annual influenza epidemics is highest among persons over 65 y of age, and therefore influenza is often regarded as an illness of the elderly population. Ample evidence indicates, however, that the burden of influenza is also substantial in children, and that children have a central role in the spread of influenza in the community during epidemics. Vaccination of children against influenza could bring about substantial health benefits not only to children themselves but also to persons in other age groups.
Gastro-intestinal stromal tumours (GISTs) - the Pretoria experience and a literature review.

AIM To analyse the presentation and management of patients with gastrointestinal stromal tumours (GISTs) at Pretoria hospitals. DESIGN A retrospective study was done in which all available clinical records of primary c-KIT positive GISTs were analysed. SETTING Secondary and tertiary care institutions in Pretoria, including both private and public hospitals. Subjects. The population studied included all individuals treated at Pretoria hospitals from 17 July 2000 to 1 April 2009 who had a GIST confirmed with immunohistochemical c KIT staining. Patients with incomplete or inaccessible clinical records were excluded. Outcome measures. Patient demographics including gender, age and race; presenting symptoms and signs; results of special investigations; and treatment. RESULTS Fifty-four cases were identified for inclusion in the study. The age of the subjects ranged from 15 to 83 years. The male-to-female ratio was 1.5:1. The organ most commonly affected was the stomach, and abdominal pain and weight loss were the most common presenting symptoms. Seventy-six per cent of the patients were treated surgically, and 24% received Imatinib. CONCLUSION GISTs often present late with non-specific symptoms, and are frequently discovered incidentally. Large tumours tend to be malignant.
PscI is a type III secretion needle anchoring protein with in vitro polymerization capacities

The export of bacterial toxins across the bacterial envelope requires the assembly of complex, membrane‐embedded protein architectures. Pseudomonas aeruginosa employs type III secretion (T3S) injectisome to translocate exotoxins directly into the cytoplasm of a target eukaryotic cell. This multi‐protein channel crosses two bacterial membranes and extends further as a needle through which the proteins travel. We show in this work that PscI, proposed to form the T3S system (T3SS) inner rod, possesses intrinsic properties to polymerize into flexible and regularly twisted fibrils and activates IL‐1β production in mouse bone marrow macrophages in vitro. We also found that point mutations within C‐terminal amphipathic helix of PscI alter needle assembly in vitro and T3SS function in cell infection assays, suggesting that this region is essential for an efficient needle assembly. The overexpression of PscF partially compensates for the absence of the inner rod in PscI‐deficient mutant by forming a secretion‐proficient injectisome. All together, we propose that the polymerized PscI in P. aeruginosa optimizes the injectisome function by anchoring the needle within the envelope‐embedded complex of the T3S secretome and – contrary to its counterpart in Salmonella – is not involved in substrate switching.
AN UNEXPECTED DISCOVERY IN THE RICH OPEN CLUSTER NGC 6819 USING XMM-NEWTON

We present the first study of the X-ray population of the intermediate-age rich open cluster NGC 6819 using the XMM-Newton Observatory. In the past decade, Chandra X-ray observations have shown a relationship between the X-ray population of globular clusters and their internal dynamics and encounter frequency. We investigate the role dynamics possibly play in the formation of X-ray sources in NGC 6819, and compare our results with known properties of field and globular cluster X-ray populations. We implement a multi-wavelength approach to studying the X-ray sources, utilizing X-ray and UV data from XMM observations along with the wealth of photometry and radial-velocity data from the WIYN Open Cluster Study and the CFHT Open Cluster Survey. Within the cluster half-light radius, we detect 12 X-ray sources down to a luminosity of 1030 erg s−1 for cluster members. The sources include a candidate quiescent low-mass X-ray binary (qLMXB), a candidate cataclysmic variable, and two active binary systems. The presence of a qLMXB in an open cluster is previously unexpected given the known relationships between luminous X-ray sources and encounter frequency in globular clusters, and most likely has a dynamical origin.
Risk factors for sudden infant death syndrome following the prevention campaign in New Zealand: a prospective study.

OBJECTIVES To identify the risk factors for sudden infant death syndrome (SIDS) following a national campaign to prevent SIDS. METHODS For 2 years (October 1, 1991 through September 30, 1993) data were collected by community child health nurses on all infants born in New Zealand at initial contact and at 2 months. RESULTS There were 232 SIDS cases in the postneonatal age group (2.0/1000 live births) and these were compared with 1200 randomly selected control subjects. Information was available for 127 cases (54.7%) and 922 (76.8%) of controls. The previously identified modifiable risk factors were examined. The prevalence of prone sleeping position of the infant was very low (0.7% at initial contact and 3. 0% at 2 months), but was still associated with an increased risk of SIDS. In addition, the side sleeping position was also found to have an increased risk of SIDS compared with the supine sleeping position (at 2 months: adjusted odds ratio (OR) = 6.57; 95% confidence interval (CI) = 1.71, 25.23). Maternal smoking was found to be the major risk factor for SIDS. Bed sharing was also associated with an increased risk of SIDS. There was an interaction between maternal smoking and bed sharing on the risk of SIDS. Compared with infants not exposed to either bed sharing or maternal smoking, the adjusted OR for infants of mothers who smoked was 5.01 (95% CI = 2.01, 12.46) for bed sharing at the initial contact and 5.02 (95% CI = 1.05, 24. 05) for bed sharing at 2 months. In this study breastfeeding was not associated with a statistically significant reduction in the risk of SIDS. The other risk factors for SIDS identified were: unmarried mother, leaving school at a younger age, young mother, greater number of previous pregnancies, late attendance for antenatal care, smoking in pregnancy, male infant, Maori ethnicity, low birth weight, and shorter gestation. CONCLUSIONS After adjustment for potential confounders, prone and side sleeping positions, maternal smoking, and the joint exposure to bed sharing and maternal smoking were associated with statistically significant increased risk of SIDS. A change from the side to the supine sleeping position could result in a substantial reduction in SIDS. Maternal smoking is common in New Zealand and with the reduction in the prevalence of prone sleeping position is now the major risk factor in this country. However, smoking behavior has been difficult to change. Bed sharing is also a major factor but appears only to be a risk to infants of mothers who smoke. Addressing bed sharing among mothers who smoke could reduce SIDS by at least one third. Breastfeeding did not appear to offer a statistically significant reduction in SIDS risk after adjustment of potential confounders, but as breastfeeding rates are comparatively good in New Zealand, this result should be interpreted with caution as the power of this study to detect a benefit is small.
Ventromedial nucleus of hypothalamus is related to the development of cancer-induced anorexia: in vivo microdialysis study.

UNLABELLED Based on reports that increased hypothalamic ventromedial nucleus (VMN)-serotonin (5-HT) is associated with cancer anorexia and recent findings in our laboratory that low levels of dopamine (DA) in the VMN are associated with prolonged inter meal intervals thus decreased food intake, and reports that setting up satiation is concomitant with descending levels of DA in the rostromedial hypothalamus, we hypothesized that an elevated 5-HT to low DA ratio in the VMN modulates food intake in cancer anorexia. METHODS In Expt 1: A microdialysis cannula guide was placed stereotactically into the VMN of methylcholanthrene (MCA) sarcoma tumor-bearing (TB) Fischer rats and in non-tumor-bearing (NTB) and pair-fed (PF) controls. When TB rats manifested anorexia by a decrease in food intake, VMN-5-HT, its metabolite 5-hydroxyindolacetic acid (5-HIAA), and DA with its metabolite 3,4,-dihydroxyphenylacetic acid (DOPAC) were measured by in vivo microdialysis using HPLC during baseline, in response to food, and after feeding. In Expt 2: TB rats had tumor removed and VMN microdialysis performed 7 days later. RESULTS Increased 5-HT release and turnover, and significantly reduced DA release with increased DOPAC occurred in TB vs NTB or PF rats. When food was offered, intake in TB rats was significantly lower than in NTB control rats. During eating, VMN-5-HT rose and peaked significantly earlier in TB vs NTB rats, while DA release was significantly reduced. With eating, the 5-HT and DA metabolism became reduced in all rats. Seven days after surgical removal of the tumor, 24 h food intake had increased to the level of controls; and when food was offered during microdialysis, intake in TB rats increased (ns relative to control), but was not yet normal. VMN microdialysis showed that 5-HT was normal at baseline, as well as during and after eating, while DA remained depressed. The metabolic turnover of 5-HT and DA was significantly lower in TB-r and PF vs NTB rats. We conclude that increased 5-HT/DA ratio is related to the development of cancer-induced anorexia.
Behavioural and cortisol response of pigs and sheep during transport

Furthermore, it made use of umbilical girth, which was difficult to measure in the donkeys. The equation of Eley and French (1993) for adult donkeys also consistently overestimated the liveweights of the Moroccan donkeys. Hard working donkeys, particularly in areas where the feed supply is irregular, are more likely to be in poor than in good body condition. Unfortunately Eley and French (1993) did not provide information on the liveweight or body condition of the animals they sampled. However, if, as is probable, their equation was produced from donkeys in good body condition, doing little work, it would be expected to overestimate the liveweight of donkeys in generally poorer condition, such as those in the present study. It is also likely that there were differences in the age distributions of the adult populations sampled to produce the prediction equations in the UK and Morocco, although it is doubtful whether they would have greatly influenced the effectiveness of the equation. Surveys of working donkeys in other Mediterranean countries (Egypt, Tunisia and Turkey) by the International Donkey Protection Trust (Bliss 1989, Svendsen 1991) have indicated that the average life span of a working donkey in these areas is rarely over 12 years. The age range of the sample of donkeys measured in the present study suggests that in Morocco too the life span of donkeys is short, in comparison with the average life span of British donkeys of 37 years reported by Bliss (1989) and of Zimbabwean donkeys of about 20 years (E. M. Nengomasha, personal communication). Although the equations derived in the present study for adult and young donkeys performed well on the data, this is to be expected because the equations were derived from measurements pertaining to those particular donkeys. The ultimate validation, therefore, must rest on testing other samples of working donkeys in other parts of the world. Acknowledgements. The authors are grateful for the financial support given by the International Donkey Protection Trust, and the British Overseas Development Administration, and the technical assistance of the Society for the Protection of Animals Abroad in Morocco, which made this work possible. They thank M. Bakkoury, A. Belemlih and A. Prentis for their assistance in Morocco, A. E. Hunter for statistical advice and P. R. Lawrence for making the nomogram.
Hepadnavirus Envelope Topology: Insertion of a Loop Region in the Membrane and Role of S in L Protein Translocation

ABSTRACT A unique feature of the large hepadnavirus envelope protein (L) is its mixed transmembrane topology, resulting from partial posttranslational translocation of the pre-S domain. Using protease protection analysis, we demonstrate for duck hepatitis B virus an essential role for the small envelope protein (S) in this process, providing the first experimental evidence for an S translocation channel. Further analysis revealed that the presumed cytoplasmic loop between TM1 and TM2 in the C-terminal S domain is membrane embedded and protrudes to the particle surface. These data suggest that some L molecules form a highly folded, potentially spring-loaded topology with five membrane-spanning regions and a membrane-traversing pre-S chain.