Miracle-dz/UniFAR-FTUs huggingface dataset:
Oligomerization Mechanisms of an H-NS Family Protein, Pmr, Encoded on the Plasmid pCAR1 Provide a Molecular Basis for Functions of H-NS Family Members

Enterobacterial H-NS-like proteins and Pseudomonas MvaT-like proteins share low homology at the amino acid sequence level, but both can function as xenogeneic silencers and are included in the H-NS family of proteins. H-NS family members have dimerization/oligomerization and DNA-binding domains connected by a flexible linker and form large nucleoprotein complexes using both domains. Pmr, an MvaT-like protein encoded on the IncP-7 carbazole-degradative plasmid pCAR1, is a key regulator of an interaction between pCAR1 and its host Pseudomonas putida KT2440. KT2440 has two transcribed genes that encode the MvaT-like proteins TurA and TurB. Our previous transcriptome analyses suggested that the functions of Pmr, TurA and TurB are non-equivalent, although the detailed underlying mechanisms remain unclear. In this study, we focused on the protein–protein interactions of Pmr, and assessed the homo-oligomerization capacity of various substituted and truncated Pmr derivatives by protein–protein cross-linking analysis. Six of the seven residues identified as important for homo-oligomerization in Pmr were located near the N-terminus, and the putative flexible linker or the region near that was not involved in homo-oligomerization, suggesting that Pmr homo-oligomerization is different from that of enterobacterial H-NS and that the functional mechanism differs between H-NS-like and MvaT-like proteins. In addition, we assessed homo- and hetero-oligomerization of Pmr by surface plasmon resonance analysis and found that the coupling ratio of TurB-Pmr oligomers is smaller than that of Pmr-Pmr or TurA-Pmr oligomers. These results raised the possibility that composition of the hetero-oligomers of Pmr, TurA, and TurB could explain why the different gene sets were affected by either pmr, turA, or turB disruption in our previous studies.
A Sociotechnical Framework for Governing Climate Engineering

Proposed ways of governing climate engineering have most often been supported by narrowly framed and unreflexive appraisals and processes. This article explores the governance implications of a Deliberative Mapping project that, unlike other governance principles, have emerged from an extensive process of reflection and reflexivity. In turn, the project has made significant advances in addressing the current deficit of responsibly defined criteria for shaping governance propositions. Three such propositions argue that (1) reflexive foresight of the imagined futures in which climate engineering proposals might reside is required; (2) the performance and acceptance of climate engineering proposals should be decided in terms of robustness, not optimality; and (3) climate engineering proposals should be satisfactorily opened up before they can be considered legitimate objects of governance. Taken together, these propositions offer a sociotechnical framework not simply for governing climate engineering but for governing responses to climate change at large.
Past-Tense Morphology and Phonological Deficits in Children With Dyslexia and Children With Language Impairment

The authors investigated past-tense morphology problems in children with dyslexia compared to those classically observed in children with oral language impairment (LI). Children were tested on a past-tense elicitation task involving regulars (look-looked), irregulars (take-took), and nonwords (murn-murned). Phonological skills were also assessed, using tests of nonsense word reading and phoneme elision. Analyses focused on whether children with dyslexia and LI showed overlapping patterns of morphological and phonological difficulties compared to controls with typical reading and language levels. Both the groups with LI and dyslexia had difficulty generating past tenses overall, although the deficit was less pronounced in dyslexia. Both groups also showed similar problems with phonological processing. The results have important implications for the theory that both language and reading problems involve oral language processing deficits. Specifically, our data support the theory that the phonological deficits observed in both dyslexia and LI are related to deficits in morphological processing. However, some important differences between dyslexia and LI are also discussed.
Significance of colonoscopy in patients with intestinal graft-versus-host disease after hematopoietic stem cell transplantation.

BACKGROUND AND STUDY AIMS Patients with intestinal graft-versus-host disease (GVHD) are generally in poor clinical condition. In this study we aimed to establish the clinical significance of endoscopic diagnosis of this condition, observing only the distal section of the large intestine. PATIENTS AND METHODS Endoscopic and pathological findings at colonoscopy were evaluated retrospectively in 12 patients who were diagnosed with intestinal GVHD after undergoing hematopoietic stem cell transplantation. RESULTS The main mucosal changes observed at endoscopy were granular change, edema, "spotty redness", and sloughing. These were clearly displayed after enhancement with Indigo carmine staining, and with insertion of the colonoscope only as far as the distal section of the large intestine. A histological diagnosis of intestinal GVHD was made in 50 % of the patients, whose intestinal epithelium specimens showed numerous apoptotic bodies. It was possible to perform total colonoscopy in two patients who were in relatively good condition clinically, but there were no remarkable differences in the endoscopic findings throughout the large intestine, from the terminal ileum to the rectum. In terms of clinical outcomes of the 12 patients, their prognosis was poor in that they all either went on to suffer from chronic GVHD or died. CONCLUSIONS Endoscopic and histological findings on distal colonoscopy are clinically significant in the diagnosis of intestinal GVHD, and limiting this examination to the distal section of the large intestine avoids causing further clinical deterioration in patients who are already in very poor general condition and the possibility of causing endoscopy-related complications.
Atelectatic children treated with intrapulmonary percussive ventilation via a face mask: Clinical trial and literature overview

Background: Persistent atelectasis in children is lacking a gold standard treatment. Intrapulmonary percussive ventilation (IPV) is presented as a promising chest physiotherapy technique in the treatment of atelectasis. This study aimed to follow the evolution of atelectasis resolution with noninvasive IPV in young children and to detect eventual adverse effects.
Prenatal and Postnatal Bisphenol A Exposure and Body Mass Index in Childhood in the CHAMACOS Cohort

Background: Bisphenol A (BPA), a widely used endocrine-disrupting chemical, has been associated with increased body weight and fat deposition in rodents. Objectives: We examined whether prenatal and postnatal urinary BPA concentrations were associated with body mass index (BMI), waist circumference, percent body fat, and obesity in 9-year-old children (n = 311) in the CHAMACOS longitudinal cohort study. Methods: BPA was measured in spot urine samples collected from mothers twice during pregnancy and from children at 5 and 9 years of age. Results: Prenatal urinary BPA concentrations were associated with decreased BMI at 9 years of age in girls but not boys. Among girls, being in the highest tertile of prenatal BPA concentrations was associated with decreased BMI z-score (β = –0.47, 95% CI: –0.87, –0.07) and percent body fat (β = –4.36, 95% CI: –8.37, –0.34) and decreased odds of overweight/obesity [odds ratio (OR) = 0.37, 95% CI: 0.16, 0.91] compared with girls in the lowest tertile. These findings were strongest in prepubertal girls. Urinary BPA concentrations at 5 years of age were not associated with any anthropometric parameters at 5 or 9 years, but BPA concentrations at 9 years were positively associated with BMI, waist circumference, fat mass, and overweight/obesity at 9 years in boys and girls. Conclusions: Consistent with other cross-sectional studies, higher urinary BPA concentrations at 9 years of age were associated with increased adiposity at 9 years. However, increasing BPA concentrations in mothers during pregnancy were associated with decreased BMI, body fat, and overweight/obesity among their daughters at 9 years of age.
The relationship between pre-morbid personality and challenging behaviour in people with dementia: A systematic review

It has been suggested that challenging behaviour in people with dementia reflects a person's pre-morbid personality traits and a number of studies have explored this hypothesis. However, inconsistencies in outcome between studies suggest a need to review the available evidence systematically. As a result, major bibliographic databases were searched for studies examining the relationship between pre-morbid personality and challenging behaviour in order to conduct a systematic review. We included all English language studies published in referenced journals that assessed pre-morbid personality via a valid comprehensive personality measure, and also explored a relationship with challenging behaviour in people with dementia. A total of 18 studies were identified that covered a wide range of challenging behaviours including ‘wandering’, affective states, aggression, anxiety and delusions/hallucinations. Studies were assessed for their methodological quality and statistical findings. Studies lacked representative samples, were affected by confounding variables and suffered from small sample sizes. However, 72% of the studies reported significant relationships between pre-morbid personality and behaviour. In terms of specific relationships, the strongest evidence was found for a positive relationship between pre-morbid neuroticism and mood, and aggression and overall behavioural acts, thus supporting the inclusion of personality as one factor in the formulation of behaviour (Ballard, C., O’Brien, J., James, I., & Swann, A. (2001). Dementia: Management of Behavioural and Psychological Symptoms. Oxford: Oxford University Press; Kitwood, T. (1993). Person and process in dementia: Editorial. International Journal of Geriatric Psychiatry, 1, 541–545).
Reappraising the Value of Urine Leukocyte Esterase Testing in the Age of Nucleic Acid Amplification

Background: The leukocyte esterase (LE) test has a limited role in the determination of empiric therapy for male patients screened for urethritis because of its poor positive predictive value in low (<5%) prevalence settings. The recent advent of nucleic acid amplification testing of first‐void urine (FVU) has dramatically increased the ease with which widespread screening for Chlamydia trachomatis and Neisseria gonorrhoeae can be performed, but the costs of such testing may be prohibitive. The LE test may therefore have a role in management of urethritis because of its high negative predictive value. Objectives: To determine the sensitivity, specificity, and positive and negative predictive value of LE testing for the diagnosis of N. gonorrhoeae and C. trachomatis in male FVU specimens in a low‐prevalence urban setting using a commercial polymerase chain reaction (PCR) as the gold standard. Methods: Data were obtained on men presenting to an urban sexually transmitted disease clinic over a 16‐month period. Patients were included if an FVU had been tested for the presence of LE using a rapid dipstick, read by an automated urine analyzer, and the sample (either an FVU or urethral swab) had then been processed for the detection of N. gonorrhoeae and C. trachomatis by PCR. Results: Of 301 assessable patients, there were 14 cases of gonorrhoea, 21 cases of chlamydia, and 1 case of dual infection detected by PCR. Most men (245/301; 81.4%) were asymptomatic, of whom 12 of 245 (4.9%) had an infection detected compared with 24 of 56 (42.9%) in the symptomatic men (P < 0.001). Using a “≥trace” cutoff, the overall value for the sensitivity of the LE test was 77.8% (95% confidence interval, 60.4‐89.3), specificity 80.8% (75.4‐85.2), positive predictive value 35.4% (25.2‐47.1), and negative predictive value 96.4% (92.8‐98.3). Conclusions: The negative predictive value of the LE test may be of use in determining which patients should proceed to specific diagnosis by nucleic amplification methods (e.g., PCR or ligase chain reaction). By limiting testing to patients with positive LE results, costs savings may be made, enabling the technology to be used in a wider community setting. The value of the LE test in higher prevalence populations with access to nucleic amplification testing remains to be established.
Complex Systems in Education: Scientific and Educational Importance and Implications for the Learning Sciences

The multidisciplinary study of complex systems in the physical and social sciences over the past quarter of a century has led to the articulation of important new conceptual perspectives and methodologies that are of value both to researchers in these fields as well as to professionals, policymakers, and citizens who must deal with challenging social and global problems in the 21st century. The main goals of this article are to (a) argue for the importance of learning these ideas at the precollege and college levels; (b) discuss the significant challenges inherent in learning complex systems knowledge from the standpoint of learning sciences theory and research; (c) discuss the "learnability issue" of complex systems conceptual perspectives and review a body of literature that has been exploring how learning sciences pedagogical approaches can lead to student learning of important dimensions of complex systems knowledge; (d) argue that the cognitive and sociocultural factors related to learning complex systems knowledge are relevant and challenging areas for learning sciences research; and (e) consider ways that concepts and methodologies from the study of complex systems raise important issues of theoretical and methodological centrality in the field of the learning sciences itself.
Quantum-critical relativistic magnetotransport in graphene

We study the thermal and electric transport of a fluid of interacting Dirac fermions using a Boltzmann approach. We include Coulomb interactions, a dilute density of charged impurities, and the presence of a magnetic field to describe both the static and the low-frequency response as a function of temperature T and chemical potential . In the quantum-critical regime T we find pronounced deviations from Fermi-liquid behavior, such as a collective cyclotron resonance with an intrinsic collision-broadened width and significant enhancements of the Mott and Wiedemann-Franz ratios. Some of these results have been anticipated by a relativistic hydrodynamic theory, whose precise range of validity and failure at large fields and frequencies we determine. The Boltzmann approach allows us to go beyond the hydrodynamic regime and to quantitatively describe the deviations from magnetohydrodynamics and the crossover to disorder-dominated Fermi-liquid behavior at large doping and low temperatures, as well as the crossover to the ballistic regime at high fields. Finally, we obtain the full frequency and doping dependence of the single universal conductivity Q which parametrizes the hydrodynamic response.
Subband-based speech recognition

In the framework of hidden Markov models (HMM) or hybrid HMM/artificial neural network (ANN) systems, we present a new approach towards automatic speech recognition (ASR). The general idea is to divide up the full frequency band (represented in terms of critical bands) into several subbands, compute phone probabilities for each subband on the basis of subband acoustic features, perform dynamic programming independently for each band, and merge the subband recognizers (recombining the respective, possibly weighted, scores) at some segmental level corresponding to temporal anchor points. The results presented in this paper confirm some preliminary tests reported earlier. On both isolated word and continuous speech tasks, it is indeed shown that even using quite simple recombination strategies, this subband ASR approach can yield at least comparable performance on clean speech while providing better robustness in the case of narrowband noise.
A Functionally Essential Domain of RFX5 Mediates Activation of Major Histocompatibility Complex Class II Promoters by Promoting Cooperative Binding between RFX and NF-Y

ABSTRACT Major histocompatibility complex class II (MHC-II) molecules occupy a pivotal position in the adaptive immune system, and correct regulation of their expression is therefore of critical importance for the control of the immune response. Several regulatory factors essential for the transcription of MHC-II genes have been identified by elucidation of the molecular defects responsible for MHC-II deficiency, a hereditary immunodeficiency disease characterized by regulatory defects abrogating MHC-II expression. Three of these factors, RFX5, RFXAP, and RFXANK, combine to form the RFX complex, a regulatory protein that binds to the X box DNA sequence present in all MHC-II promoters. In this study we have undertaken a dissection of the structure and function of RFX5, the largest subunit of the RFX complex. The results define two distinct domains serving two different essential functions. A highly conserved N-terminal region of RFX5 is required for its association with RFXANK and RFXAP, for assembly of the RFX complex in vivo and in vitro, and for binding of this complex to its X box target site in the MHC-II promoter. This N-terminal region is, however, not sufficient for activation of MHC-II expression. This requires an additional domain within the C-terminal region of RFX5. This C-terminal domain mediates cooperative binding between the RFX complex and NF-Y, a transcription factor binding to the Y box sequence of MHC-II promoters. This provides direct evidence that RFX5-mediated cooperative binding between RFX and NF-Y plays an essential role in the transcriptional activation of MHC-II genes.
Structural and functional characterization of TRI3 trichothecene 15‐O‐acetyltransferase from Fusarium sporotrichioides

Fusarium head blight is a devastating disease of cereal crops whose worldwide incidence is increasing and at present there is no satisfactory way of combating this pathogen or its associated toxins. There is a wide variety of trichothecene mycotoxins and they all contain a 12,13‐epoxytrichothecene skeleton but differ in their substitutions. Indeed, there is considerable variation in the toxin profile across the numerous Fusarium species that has been ascribed to differences in the presence or absence of biosynthetic enzymes and their relative activity. This article addresses the source of differences in acetylation at the C15 position of the trichothecene molecule. Here, we present the in vitro structural and biochemical characterization of TRI3, a 15‐O‐trichothecene acetyltransferase isolated from F. sporotrichioides and the “in vivo” characterization of Δtri3 mutants of deoxynivalenol (DON) producing F. graminearum strains. A kinetic analysis shows that TRI3 is an efficient enzyme with the native substrate, 15‐decalonectrin, but is inactive with either DON or nivalenol. The structure of TRI3 complexed with 15‐decalonectrin provides an explanation for this specificity and shows that Tri3 and Tri101 (3‐O‐trichothecene acetyltransferase) are evolutionarily related. The active site residues are conserved across all sequences for TRI3 orthologs, suggesting that differences in acetylation at C15 are not due to differences in Tri3. The tri3 deletion mutant shows that acetylation at C15 is required for DON biosynthesis even though DON lacks a C15 acetyl group. The enzyme(s) responsible for deacetylation at the 15 position of the trichothecene mycotoxins have not been identified.
Comparison of diffusion-weighted MRI and CT in acute stroke

Objective: To compare diffusion-weighted MRI (DWI) and CT with respect to accuracy of localizing acute cerebral infarction; sensitivity, specificity, and interrater reliability for identifying more than one-third middle cerebral artery (MCA) territory involvement; and correlation of acute lesion volume with final infarct volume. Method:— Nineteen consecutive stroke patients underwent CT and DWI within 7 hours of stroke onset and a follow-up DWI examination 36 hours after symptom onset, which served as the “gold standard” for lesion location and extent of MCA involvement. Each scan was evaluated for acute ischemic lesions by two experienced observers. After 30 days, T2-weighted MRI was obtained for assessment of the final infarct volume. Results: The acute CT and DWI scans were obtained on average 2.6 and 5.1 hours after symptom onset. On DWI the acute lesion was identified correctly in all instances and on CT it was identified correctly in 42 to 63% of patients. Sensitivity for detection of more than 33% MCA involvement was better for DWI (57 to 86%) than for CT (14 to 43%), whereas specificity was excellent for both. Interrater reliability was moderately good for both (kappa, 0.6 for DWI; 0.5 for CT). A positive correlation (r = 0.79; p = 0.001) existed between lesion volume on acute DWI and final infarct volume, whereas no correlation was found between CT volume and final infarct volume. Conclusion: When compared with CT, DWI was more accurate for identifying acute infarction and more sensitive for detection of more than 33% MCA involvement. In addition, lesion volume on acute DWI, but not on acute CT, correlated strongly with final infarct volume. Additional studies are required to demonstrate whether these advantages of DWI are clinically relevant in the management of patients with acute stroke.
On the Spectrum of an Operator Pencil with Applications to Wave Propagation in Periodic and Frequency Dependent Materials

We study wave propagation in periodic and frequency dependent materials when the medium in a frequency interval is characterized by a real-valued permittivity. The spectral parameter relates to the quasi momentum, which leads to spectral analysis of a quadratic operator pencil where frequency is a parameter. We show that the underlying operator has a discrete spectrum, where the eigenvalues are symmetrically placed with respect to the real and imaginary axis. Moreover, we discretize the operator pencil with finite elements and use a Krylov space method to compute eigenvalues of the resulting large sparse matrix pencil.