Miracle-dz/UniFAR-FTUs huggingface dataset:
Neonatal Encephalopathic Cerebral Injury in South India Assessed by Perinatal Magnetic Resonance Biomarkers and Early Childhood Neurodevelopmental Outcome

Although brain injury after neonatal encephalopathy has been characterised well in high-income countries, little is known about such injury in low- and middle-income countries. Such injury accounts for an estimated 1 million neonatal deaths per year. We used magnetic resonance (MR) biomarkers to characterise perinatal brain injury, and examined early childhood outcomes in South India. Methods We recruited consecutive term or near term infants with evidence of perinatal asphyxia and a Thompson encephalopathy score ≥6 within 6 h of birth, over 6 months. We performed conventional MR imaging, diffusion tensor MR imaging and thalamic proton MR spectroscopy within 3 weeks of birth. We computed group-wise differences in white matter fractional anisotropy (FA) using tract based spatial statistics. We allocated Sarnat encephalopathy stage aged 3 days, and evaluated neurodevelopmental outcomes aged 3½ years using Bayley III. Results Of the 54 neonates recruited, Sarnat staging was mild in 30 (56%); moderate in 15 (28%) and severe in 6 (11%), with no encephalopathy in 3 (6%). Six infants died. Of the 48 survivors, 44 had images available for analysis. In these infants, imaging indicated perinatal rather than established antenatal origins to injury. Abnormalities were frequently observed in white matter (n = 40, 91%) and cortex (n = 31, 70%) while only 12 (27%) had abnormal basal ganglia/thalami. Reduced white matter FA was associated with Sarnat stage, deep grey nuclear injury, and MR spectroscopy N-acetylaspartate/choline, but not early Thompson scores. Outcome data were obtained in 44 infants (81%) with 38 (79%) survivors examined aged 3½ years; of these, 16 (42%) had adverse neurodevelopmental outcomes. Conclusions No infants had evidence for established brain lesions, suggesting potentially treatable perinatal origins. White matter injury was more common than deep brain nuclei injury. Our results support the need for rigorous evaluation of the efficacy of rescue hypothermic neuroprotection in low- and middle-income countries.
Matrix Metalloproteinase Expression Correlates with Virulence following Neurotropic Mouse Hepatitis Virus Infection

ABSTRACT The relationship(s) between viral virulence and matrix metalloproteinase (MMP) expression in the central nervous system (CNS) of mice undergoing lethal and sublethal infections with neurotropic mouse hepatitis virus was investigated. Lethal infection induced increased levels of MMP-3 and MMP-12 mRNAs as well as that of tissue inhibitor of matrix metalloproteinases 1 (TIMP-1) compared to sublethal infection. Increased induction of MMP, TIMP, and chemokine expression correlated with increased virus replication but not with inflammatory cell infiltration. Infection of immunosuppressed mice suggested that expression of most MMP, TIMP, and chemokine mRNA was induced primarily in CNS-resident cells. By contrast, MMP-9 protein activity was associated with the infiltration of neutrophils into the CNS. These data indicate an association between the magnitude of inflammatory gene expression within the CNS and viral virulence.
Cloning, sequencing and analysis of dnaK ‐dnaJ gene cluster of Bacillus megaterium

The DNA fragment of heat shock genes (hrcA‐grpE‐dnaK‐dnaJ) containing complete hrcA‐grpE‐dnaK operon and the transcription unit of dnaJ was cloned, sequensed and analyzed from Bacillus megaterium RF5. The sequence of hrcA, grpE and dnaJ were first time reported, and their coding products exibit 60%, 63% and 81% of identities to the homologs of B. subtilis. A σA‐type promoter of Gram‐positive bacteria (PA1) and a terminator were located upstream of the hrcA and downstream of dnaK, and a Controlling inverted repeat of chaperone expression element (CIRCE) was identified between PA1 and hrcA. Another σA‐type promoter (PA2) and a terminator were found upstream and downstream of dnaJ, indicating B. megaterium has a transcription unit containing a single gene dnaJ. The structure of dnaJ transcription unit is more similar to that of Listeria monocytogenes than other species of Bacillus. A partial protein‐based phylogenetic tree, derived from Gram‐positive bacteria using HrcA sequence, indicated a closer phylogenetic relationship between B. megaterium and Geobacillus species than other two Bacillus species. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Identification of highly significant sequence patterns in siRNAs for the optimal design of siRNA

siRNAs for gene silencing studies have a broad range of applications. Studies have addressed the design of siRNAs based on the target sequence patterns, such as the sequence AA around the ends of the siRNA or the avoidance of GGG in siRNA sequences. However, information from just these two patterns is not sufficient for effectively designing siRNA. Nine sequence patterns were identified as highly significantly correlated motifs in studies on oligonucleotides antisense activities. The correlation between the sequence patterns of the siRNA and the gene silencing ratio (GSR) by siRNA has not been described. Understanding this relationship may guide one to a systematic design of the most effective siRNAs. We designed a computer program to calculate the sequence patterns from our siRNA silencing database. Four statistical methods were used to identify the frequency and the distribution of the highly significant sequence patterns from the 1344 combinations for the three, four, and five nucleotide sequences. For the first time, 52 sequence patterns were identified as the highly significant patterns by ANOVA and Pearson correlation analyses with the GSR. These 52 patterns were further clustered into 18 groups. Information from this study may help in the optimized design of siRNA.
On Stolt stretch time migration

We implement Stolt-stretch time migration with an analytical formulation for the optimal stretch parameter and show how it improves the quality of imaging. By a cascaded f-k migration approach with this algorithm, we manage to obtain time migration results on real data comparable to Gazdag’s phase-shift method, with a high accuracy for steeply deeping events at a computational cost dramatically lowered.
Data-driven extraction of intonation contour classes

In this paper we introduce the first steps towards a new datadriven method for extraction of intonation events that does not require any prerequisite prosodic labelling. Provided with data segmented on the syllable constituent level it derives local and global contour classes by stylisation and subsequent clustering of the stylisation parameter vectors. Local contour classes correspond to pitch movements connected to one or several syllables and determine the local f0 shape. Global classes are connected to intonation phrases and determine the f0 register. Local classes initially are derived for syllabic segments, which are then concatenated incrementally by means of statistical language modelling of co-occurrence patterns. Due to its generality the method is in principal language independent and potentially capable to deal also with other aspects of prosody than intonation.
Changes over time in sexual behaviour among young people with different levels of educational attainment in Tanzania

HIV prevalence trends in Tanzania differ between socioeconomic groups. While HIV prevalence was initially higher among those with higher levels of educational attainment, it has fallen fastest among these groups. Among those with lower levels of education HIV prevalence has been stable. The behavioural dynamics underlying this phenomenon remain unclear, and a theory to guide interpretation of these trends and enable predictions of future patterns has not emerged.
Pheomelanin‐Based Coloration and the Ability to Cope with Variation in Food Supply and Parasitism

Although gene by environment interactions may play a key role in the maintenance of genetic polymorphisms, little is known about the ecological factors involved in these interactions. We investigated whether food supply and parasites can mediate covariation between the degree of adult pheomelanin‐based coloration, a heritable trait, and offspring body mass in the tawny owl (Strix aluco). We swapped clutches between nests to allocate genotypes randomly among environments. Three weeks after hatching, we challenged the immune system of 80 unrelated nestlings with either a phytohemagglutinin (PHA) or a lipopolysaccharide, surrogates of alternative parasites, and then fed them ad lib. or food‐restricted them during the following 6 days in the laboratory. Whatever the immune challenge, nestlings fed ad lib. converted food more efficiently into body mass when their biological mother was dark pheomelanic. In contrast, food‐restricted nestlings challenged with PHA lost less body mass when their biological mother was pale pheomelanic. Nestling tawny owls born from differently melanic mothers thus show differing reaction norms relative to food availability and parasitism. This suggests that dark and pale pheomelanic owls reflect alternative adaptations to food availability and parasites, factors known to vary in space and time.
Loss of Foxp3 Is Associated With CD30 Expression in the Anaplastic Large Cell Subtype of Adult T-cell Leukemia/Lymphoma (ATLL) in US/Caribbean Patients: Potential Therapeutic Implications for CD30 Antibody–mediated Therapy

Adult T-cell leukemia/lymphoma (ATLL) is caused by the HTLV-1 virus, endemic to Japan and the Caribbean, and is likely derived from cells with the T-regulatory phenotype. The malignant cells express IL2 receptor &agr; (CD25), and the majority express transcription factor Forkhead box P3 (Foxp3), in addition to T-cell markers. Occasional cases express CD30. Whereas Japanese cases are predominantly of the acute and chronic leukemic types, the less well-studied Caribbean cases are more often lymphomatous. We performed immunohistochemical analysis for CD25, Foxp3, and CD30 on samples from 42 US/Caribbean ATLL patients and correlated these markers with morphologic subtype and clinical characteristics. In the 16/42 patients who had successive biopsies, we determined the expression stability of these markers. Foxp3 was expressed in 26 of the 42 (62%) initial biopsies, and its intensity correlated with CD25 expression. It was more frequent in pleomorphic small-sized and medium-sized cell types than in large cell tumors but did not correlate with patients’ clinical attributes. Foxp3 expression and morphology were unchanged in successive biopsies in 13 of 16 patients. Four initial biopsies had features of anaplastic large cell T lymphomas, all of which were Foxp3−. Successive biopsies from 2 patients with pleomorphic medium cell variant showed diminishing expression of originally weak Foxp3 expression and de novo CD30 expression, whereas they showed morphologic progression to the anaplastic cell variant. A third patient’s second biopsy revealed progression from pleomorphic medium to anaplastic large cell morphology with loss of Foxp3, but it remained CD30−. Foxp3 expression correlates with pleomorphic small and medium cell types and may be lost with large cell transformation. The evolution of the latter type can be associated with the gain of CD30 expression; such ATLL tumors might respond to anti-CD30 monoclonal antibody therapies.
Atypical EMG activation patterns of the elbow extensors after complete C6 tetraplegia during isometric contractions: a case report

Atypical EMG activation patterns of the elbow extensors after complete C6 tetraplegia during isometric contractions: a case report S. Cremoux a , J. Tallet b , E. Berton a , F. Dal Maso b & D. Amarantini b c a ISM, Aix-Marseille Universite, Marseille, France b PRISSMH, Universite Paul Sabatier Toulouse 3, Toulouse, France c Departement de kinesiologie, Universite de Montreal, Montreal, Quebec, Canada
TOA/TDOA hybrid relative positioning system using UWB-IR

We developed a TOA/TDOA hybrid relative positioning system with UWB-IR technology. The proposed system reduces both the number of base stations and the wireless communication times in a positioning sequence. We evaluated the system performance over various distances between base stations by using computer simulations and experiments, assuming that the target nodes were outside the area surrounded by the base stations. For the experiments, we implemented the system with UWB transceivers that we developed. From the experimental results, we confirmed that the proposed system could detect the relative positions of the target nodes using two base stations 4 m apart and with a measured angle accuracy of 8.6 degrees.
"He would never just hit the sofa" A narrative of non-complaining among Dutch Mothers: a qualitative study of the influences of attitudes on work preferences and employment patterns of Dutch mothers

Working patterns among Dutch mothers differ remarkably. This variation makes the Netherlands an interesting case to study the origins of the labour participation pattern of women and mothers in particular. This article explores the influence of mothers’ work and gender attitudes and preferences on their diverse employment pattern through 39 semi-structured interviews with mothers living in Amsterdam. Previous studies have already addressed the question to what extent women’s attitudes correspond with their labour market behaviour. Yet, most of these studies are based on large surveys which lack the detail to study the intricacies of the relationship between attitudes, preferences and behaviour. This study shows that a woman’s employment behaviour is the result of a dynamic relationship between her personal work preferences and gender and work attitudes on the one hand, and her work experiences and cultural normative gender expectations on the other, rather than the outcome of a free choice. The study further reveals the prevalence of ‘a narrative of non-complaining’ among Dutch mothers regarding their spouses’ contribution to the home work. This finding may help to understand why the division of labour at home along gender lines persists.
Clifford group dipoles and the enactment of Weyl/Coxeter group W(E8) by entangling gates

Peres/Mermin arguments about no-hidden variables in quantum mechanics are used for displaying a pair (R, S) of entangling Clifford quantum gates, acting on two qubits. From them, a natural unitary realization of Coxeter/Weyl groups W (D5) and W (F4) emerges, which is also reflected into the splitting of the n-qubit Clifford group Cn into group dipoles C± n . The union of the three-qubit real Clifford group C 3 and the Toffoli gate ensures a orthogonal realization of the Weyl/Coxeter group W (E8), and of its relatives. Other concepts involved are complex reflection groups, BN pairs, unitary group designs and entangled states of the GHZ, W and chain families.
Calcium Imaging of Nerve-Mast Cell Signaling in the Human Intestine

Introduction: It is suggested that an altered microenvironment in the gut wall alters communication along a mast cell nerve axis. We aimed to record for the first time signaling between mast cells and neurons in intact human submucous preparations. Methods: We used the Ca2+ sensitive dye Fluo-4 AM to simultaneously image changes in intracellular calcium [Ca+2]i (%ΔF/F) in neurons and mast cells. Data are presented as median with interquartile ranges (25/75%). Results: We recorded nerve responses in 29 samples upon selective activation of 223 mast cells by IgE receptor cross linking with the antibody mAb22E7. Mast cells responded to mAb22E7 with a median [Ca+2]i increase of 20% (11/39) peaking 90 s (64/144) after the application. Only very few neurons responded and the median percentage of responding neuronal area was 0% (0/5.9). Mast cell activation remained in the presence of the fast sodium channel blocker tetrodotoxin. Specific neuronal activation by transmural electrical field stimulation (EFS) in 34 samples evoked instantaneously [Ca+2]i signals in submucous neurons. This was followed by a [Ca+2]i peak response of 8%ΔF/F (4/15) in 33% of 168 mast cells in the field of view. The mast cell response was abolished by the nerve blocker tetrododoxin, reduced by the Calcitonin Gene-Related Peptide receptor 1 antagonist BIBN-4096 and the Vasoactive Intestinal Peptide receptor antagonist PG97-269, but not by blockade of the neurokinin receptors 1–3. Conclusion: The findings revealed bidirectional signaling between mast cells and submucous neurons in human gut. In our macroscopically normal preparations a nerve to mast cell signaling was very prominent whereas a mast cell to nerve signaling was rather rare.
Nest Temperature Is Not Related to Egg Size in a Turtle with Temperature-Dependent Sex Determination

Abstract A recent hypothesis posits that temperature-dependent sex determination (TSD) in reptiles may be maintained if females can assess thermal conditions and lay eggs accordingly to produce the sex benefiting most from maternal investment. Specifically, females should lay large eggs in environments likely to produce the sex benefiting most from larger egg size. This relationship has been demonstrated in diamondback terrapins. To evaluate the generality of this hypothesis, we examined two components of this hypothesis using painted turtles (Chrysemys picta), a reptile with TSD. Vegetation cover around nests at oviposition significantly and negatively influenced nest temperatures during embryonic development, particularly during the period of sexual differentiation. However, no relationship existed between egg mass and either nest temperatures or vegetation cover around nests at oviposition. Therefore, large eggs were not laid in specific thermal microenvironments as a mechanism to match egg size with offspring sex ratio. These results do not support a general relationship between thermally based nest-site choice and maternal investment (egg mass) in reptiles with TSD.
Document image decoding approach to character template estimation

An approach to supervised training of document-specific character templates from sample page images and unaligned transcriptions is presented. The template estimation problem is formulated as one of constrained maximum likelihood parameter estimation within the document image decoding (DID) framework. This leads to a two-phase iterative training algorithm consisting of transcription alignment and aligned template estimation (ATE) steps. The ATE step is the heart of the algorithm and involves assigning template pixel colors to maximize likelihood while satisfying a template disjointness constraint. In one large-scale experiment, use of document-specific templates resulted in a character error rate that was about an order of magnitude less than that of a commercial omni-font OCR program.
Practical aspects of energy weighting in X-ray imaging

The technique of Energy Weighting takes advantage of the upcoming energy resolving properties of X-ray pixel detectors. It can improve the image quality (in terms of signal-to-noise ratio compared to integrating detectors) up to a factor of 1.5 as shown in [J. Giersch et al. (2003)]. The optimal weighting function depends on materials and thicknesses, but a good approximation is 1/E/sup 3/. In the presence of scattered radiation the usability of lower photon energies is limited. For this case we derived an adapted weighting function. Furthermore, we studied the influence of detector properties on the image quality improvement. Our results show that the energy bin size (i.e. number of energy channels) of the imaging system has a comparatively small impact on the benefit. Additionally, with optimised bin border positions, it is possible to achieve about 90% of maximum improvement with only three bins. To investigate the practical feasibility of Energy Weighting with present detectors, we used the Medipix2 in our X-ray setup. The Medipix2 is a photon counting hybrid pixel detector, which is in principle capable of energy sensitive X-ray measurements. By moving the thresholds together with the tube voltage we are able to take energy resolved images. Application of Energy Weighting results in SNR improvement in good agreement with theory. With Monte-Carlo simulations on computed tomography (CT) we are able to suppress spectral artifacts using Energy Weighting: an increased image quality without cupping artifacts can be achieved by applying the method after CT reconstruction for each energy bin.
Gene maps and location databases

A location database is defined in linear space by a vector of genetic and physical locations for each locus, which may be ordered by virtual sorting on composite location. This contrasts with an interval database defined in metric space, for which location must be inferred by list‐processing from numbered intervals which are assigned different ordinals in different tables and overlap other intervals in many ways. A location database has been used for all well‐studied experimental organisms. Principles for a human genome database may be derived from this experience.
Fuse or die: how to survive the loss of Dam in Vibrio cholerae

Dam methylates GATC sequences in γ‐proteobacteria genomes, regulating several cellular functions including replication. In Vibrio cholerae, which has two chromosomes, Dam is essential for viability, owing to its role in chr2 replication initiation. In this study, we isolated spontaneous mutants of V. cholerae that were able to survive the deletion of dam. In these mutants, homologous recombination and chromosome dimer resolution are essential, unless DNA mismatch repair is inactivated. Furthermore, the initiator of chr2 replication, RctB, is no longer required. We show that, instead, replication of chr2 is insured by spontaneous fusion with chr1 and piggybacking its replication machinery. We report that natural fusion of chr1 and chr2 occurred by two distinct recombination pathways: homologous recombination between repeated IS elements and site‐specific recombination between dif sites. Lastly, we observed a preferential fusion of the two chromosomes in their terminus of replication.
Influence of sensation seeking on response to alcohol versus placebo: implications for the acquired preparedness model.

OBJECTIVE Previous research has identified several aspects of behavioral undercontrol that are associated with heavy drinking and problems. Further, research on the acquired preparedness model (Smith and Anderson, 2001) has identified biased learning as a potential mechanism of these effects. Traits like sensation seeking have been linked to stronger positive and weaker negative expectancies, which, in turn, contribute to increased risk for heavy drinking and problems. Although expectancies are thought to represent potentially biased expectations about drinking outcomes, they may also reflect individual differences in alcohol response. The present study examined the strength of associations between sensation seeking and both expectancies (response to placebo) and subjective response under alcohol. METHOD Using a between-subjects design, young adult social drinkers (N = 236) were randomly assigned to receive alcohol (target breath alcohol concentration of .08%) or placebo, after which they reported on subjective experiences of stimulation and sedation. RESULTS Sensation seeking was significantly related to stimulant response, and the strength of this association did not differ by beverage condition (alcohol vs. placebo). CONCLUSIONS The findings argue against a pharmacological explanation for results of prior studies of the acquired preparedness model and support a biased learning interpretation of relations between sensation seeking and positive expectancies. Results also extend the findings on the acquired preparedness model to an implicit measure of positive alcohol expectancies (subjective response to placebo). Future studies using additional measures of implicit expectancies (e.g., Implicit Association Test) would be helpful in determining the relative strength of implicit and explicit expectancies as mediators within the acquired preparedness model.