Miracle-dz/UniFAR-FTUs huggingface dataset:
Human bocavirus in children with acute gastroenteritis in Albania

Human Bocavirus (HBoV) has been recently identified in association with acute viral gastroenteritis (AGE). The objective of this work was to investigate the prevalence of HBoV in children with AGE in Albania. Stool specimens collected from 142 children were analyzed by amplification of partial NP1 and Vp1/Vp2 genes. HBoV was detected in 13 samples (9.1%), 12 HBoV‐1 and one HBoV‐2. All HBoV‐positive patients were co‐infected with rotavirus and/or adenovirus, a finding which might indicate that there is no clear causal association of this agent with diarrhea. Further investigation is needed to assess the pathogenic role of HBoV in childhood diarrhea. J. Med. Virol. 88:906–910, 2016. © 2015 Wiley Periodicals, Inc.
Cherenkov radiation fluence estimates in tissue for molecular imaging and therapy applications

Cherenkov radiation has recently emerged as an interesting phenomenon for a number of applications in the biomedical sciences. Its unique properties, including broadband emission spectrum, spectral weight in the ultraviolet and blue wavebands, and local generation of light within a given tissue, have made it an attractive new source of light within tissue for molecular imaging and phototherapy applications. While several studies have investigated the total Cherenkov light yield from radionuclides in units of [photons/decay], further consideration of the light propagation in tissue is necessary to fully consider the utility of this signal in vivo. Therefore, to help further guide the development of this novel field, quantitative estimates of the light fluence rate of Cherenkov radiation from both radionuclides and radiotherapy beams in a biological tissue are presented for the first time. Using Monte Carlo simulations, these values were found to be on the order of 0.01–1 nW cm−2 per MBq g−1 for radionuclides, and 1–100 μW cm−2 per Gy s−1 for external radiotherapy beams, dependent on the given waveband, optical properties, and radiation source. For phototherapy applications, the total light fluence was found to be on the order of nJ cm−2 for radionuclides, and mJ cm−2 for radiotherapy beams. The results indicate that diagnostic potential is reasonable for Cherenkov excitation of molecular probes, but phototherapy may remain elusive at such exceedingly low fluence values. The results of this study are publicly available for distribution online at www.dartmouth. edu/optmed/.
[Comparison of phenotypic methods for the detection of beta-lactamases MBL in strains from the Enterobacteriaceae family and non-fermentative bacilli isolated from clinical specimens].

INTRODUCTION Bacterial resistance is growing because of treatment a broad spectrum antibio- tics. Gram-negative pathogens which producing carbapenemase are a one of major problem in many hospitals. Rapid detection those strains provide an early inhibition of infection and control the expansion of microorganisms. The aim of work was to characterize the frequency of appearance MBLs in specific groups of Gram-negative bacilli which are resistant or intermediate to at least one of carbapenems. METHODS Bacterial isolates were collected from Baby Jesus Clinical Hospital from 2003 to 2009. Pathogens were isolated from urine, blood, fluids, swab of the wound, pharyngeal swab. They were identified by the ID 32 E (bioMérieux, France) and Vitek2. Antimicrobial resistance was marked by the ATB G-5 and ATB UR (bioMérieux, France). Detection of metalo-beta-lactamases was tested by disk diffusion test recommended by the EUCAST. The DDS test using imipenem, ceftazidime, ethylenediaminetetraacetic acid (EDTA) and 2-mercaptopropionic acid (2-MPA). Positive test was reading as enlargement of inhibition zone about imipenem- or ceftazidime-impregnated disk. RESULTS Of the 88 isolates, 32 come fromEnterobacteriaceae and 56 from non-fermentative bacilli. All strains were tested of production of MBL by disk diffusion test. This method used two inhibitors: ethylenediaminetetraacetic acid and 2-mercaptopropionic acid. As a result of EDTA there was 45 MBL positive strains. In apply 2-MPA there was 55 MBL positive strains. Both the EDTA and 2-MPA disk test showing the highest percentage of positive result in Enterobacter cloacae, Serratia marcescens, Pseudomonas aeruginosa and Pseudomonas putida. CONCLUSIONS Resistance to carbapenems in the non-fermentative bacilli occurs more often than in the Enterobacteriaceae. Method with 2-mercaptopropionic acid was more effective to detect metallo-beta-lactamases than EDTA. Concerns especially bacilli from Enterobacteriaceae.
Applying the transtheoretical model to eating behaviour change: challenges and opportunities

Abstract This review provides a rigorous investigation of the question of whether the transtheoretical model (TTM) (or stages of change model) is applicable to eating behaviour change. The TTM is currently the most popular of a number of stage theories being used to examine health behaviour change. Stage theories specify an ordered set of ‘stages of readiness to change’ into which people can be classified and identify the factors that can facilitate movement from one stage to the next. If eating behaviour change follows a stage process, then nutritionists could identify the predominant stage or stages in a population and focus resources on those issues most likely to move people to the next stage (e.g. from no intention of changing, to thinking about changing). In addressing this question, the review draws on the defining characteristics of stage theories as clarified by Weinstein et al. (1998), provides an in-depth coverage of methodological considerations, and a detailed summary table of dietary studies applying the TTM. Specific recommendations are made for improving the accuracy of dietary stage classifications. Among the key conclusions are: (1) dietary studies using the TTM have been hampered by a focus on nutritional outcomes such as dietary fat reduction, rather than clearly understood food behaviours (e.g. five servings of fruit and vegetables per day); (2) accurate stage classification systems are possible for food-based goals, but major misclassification problems occur with nutrient-based goals; (3) observation of an association between stage and dietary intake is not sufficient to demonstrate the validity of the model for dietary behaviour; (4) there is a need for valid questionnaires to measure all aspects of the TTM, and more research on the whole model, particularly the ‘processes of change’, rather than on single constructs such as ‘stage’ (5) cross-sectional studies generally support the predicted patterns of between-stage differences in decisional balance, self-efficacy, and processes of change; (6) studies which test the key hypothesis that different factors are important in distinguishing different stages are rare, as are prospective studies and stage-matched interventions. Only such studies can conclusively determine whether the TTM is applicable to eating behaviour. Since the ultimate test of the TTM will be the effectiveness of stage-matched dietary interventions, the review ends by exploring the requirements for such studies.
Biodynamique d'une couverture pedologique dans la region de botucatu (bresil-sp)

Nous avons etudie l'organisation spatio-temporelle d'une couverture pedologique developpee sur gres (groupe bauru) et basalte (formation serra geral) dans la region de botucatu (sp), bresil. L'objectif du travail a ete de decrire et de comprendre les structures de cette couverture pedologique et leur dynamique. Les principaux resultats du travail mene a botucatu concernent: 1) la genese et l'evolution des structures microagregees (ovoides et polyedriques) et macroagregees polyedriques des latosolos (ferralsols) et des terras roxas estruturadas (nitosols); 2) le role fondamental de la macrofaune du sol (principalement fourmis atta et termites) dans l'organisation et dans la biodynamique de ces sols; 3) l'evolution des structures et des mecanismes a travers la mise en evidence des fronts de transformation; 4) la reconstitution de l'histoire de cette couverture pedologique.
Immediate Localized CDKN1A (p21) Radiation Response after Damage Produced by Heavy-Ion Tracks

Abstract Jakob, B. , Scholz, M. and Taucher-Scholz, G. Immediate Localized CDKN1A (p21) Radiation Response after Damage Produced by Heavy-Ion Tracks. Using confocal microscopy on immunofluorescence-stained cells, we have investigated the response of CDKN1A (p21), one of the key proteins involved in the DNA damage response pathway, after irradiation with accelerated lead or chromium ions. Each traversal of an accelerated ion leads to the formation of a single, bright focus of the CDKN1A protein in the nuclei of human fibroblasts within 2 min after irradiation at 4°C. This immediate, localized CDKN1A response is specific for particle irradiation with a high linear energy transfer (LET), whereas X irradiation, after a period of induction, yields a diffusely spread pattern, in line with the differences in the microscopic dose deposition pattern of both radiation types. The particle-induced CDKN1A foci persist for several hours until they become diffuse and vanish. These findings suggest that CDKN1A accumulates at the sites of primary DNA damage, possibly mediated by the interaction with proteins involved in DNA repair. Here, for the first time, an immediate biological response confined to the radial extension of low-energy particle tracks (∼1 μm) is directly visualized and correlated to ion traversals. This indicates that particle irradiation represents an ideal tool to study the processing of biological damage induced in defined subnuclear regions.
Optical Image Quality and Visual Performance for Patients With Keratitis

Purpose: To evaluate the optical image quality, using 2 optical devices (an aberrometer and a double-pass device), and visual performance [contrast sensitivity function (CSF)] in patients with keratitis and after resolution of the disease. Methods: Twenty subjects with keratitis (18 patients with unilateral keratitis and 2 patients with bilateral keratitis) were included in this study. We also took measurements in healthy fellow eyes for comparison. Ten patients were studied before and after the resolution of keratitis. Objective data were gathered by aberrometry (ocular higher order, spherical, and coma aberrations) and the Strehl ratio, a parameter derived from the double-pass device that included information on diffraction, ocular aberrations, and scattering. The CSF was also measured for all the patients. Results: Ocular higher order, spherical, and coma aberrations in keratitis eyes were significantly (P < 0.05) higher than those in healthy fellow eyes. The Strehl ratio indicates a worse optical quality for keratitis eyes being significantly (P < 0.05) lower than the Strehl ratio for healthy fellow eyes. CSF for keratitis eyes was also significantly lower than that for the healthy eyes (P < 0.05). Data for keratitis eyes after the resolution of the disease showed a significant increase in the optical function and visual performance but, after treatment, continued to suffer significant (P < 0.05) impairment in the optical quality of the affected eyes compared with the healthy fellow eyes. Conclusions: Devices to measure optical image quality and the CSF enable the characterization of the optical quality and visual performance in patients with keratitis, showing a significant decline in optical quality and visual performance during keratitis and an improvement after the resolution of the pathology.
Dose convolution filter: incorporating spatial dose information into tissue response modeling.

PURPOSE A model is introduced to integrate biological factors such as cell migration and bystander effects into physical dose distributions, and to incorporate spatial dose information in plan analysis and optimization. METHODS The model consists of a dose convolution filter (DCF) with single parameter sigma. Tissue response is calculated by an existing NTCP model with DCF-applied dose distribution as input. The authors determined sigma of rat spinal cord from published data. The authors also simulated the GRID technique, in which an open field is collimated into many pencil beams. RESULTS After applying the DCF, the NTCP model successfully fits the rat spinal cord data with a predicted value of sigma = 2.6 +/- 0.5 mm, consistent with 2 mm migration distances of remyelinating cells. Moreover, it enables the appropriate prediction of a high relative seriality for spinal cord. The model also predicts the sparing of normal tissues by the GRID technique when the size of each pencil beam becomes comparable to sigma. CONCLUSIONS The DCF model incorporates spatial dose information and offers an improved way to estimate tissue response from complex radiotherapy dose distributions. It does not alter the prediction of tissue response in large homogenous fields, but successfully predicts increased tissue tolerance in small or highly nonuniform fields.
Profiling the RNA editomes of wild-type C. elegans and ADAR mutants

RNA editing increases transcriptome diversity through post-transcriptional modifications of RNA. Adenosine deaminases that act on RNA (ADARs) catalyze the adenosine-to-inosine (A-to-I) conversion, the most common type of RNA editing in higher eukaryotes. Caenorhabditis elegans has two ADARs, ADR-1 and ADR-2, but their functions remain unclear. Here, we profiled the RNA editomes of C. elegans at different developmental stages of wild-type and ADAR mutants. We developed a new computational pipeline with a “bisulfite-seq-mapping-like” step and achieved a threefold increase in identification sensitivity. A total of 99.5% of the 47,660 A-to-I editing sites were found in clusters. Of the 3080 editing clusters, 65.7% overlapped with DNA transposons in noncoding regions and 73.7% could form hairpin structures. The numbers of editing sites and clusters were highest at the L1 and embryonic stages. The editing frequency of a cluster positively correlated with the number of editing sites within it. Intriguingly, for 80% of the clusters with 10 or more editing sites, almost all expressed transcripts were edited. Deletion of adr-1 reduced the editing frequency but not the number of editing clusters, whereas deletion of adr-2 nearly abolished RNA editing, indicating a modulating role of ADR-1 and an essential role of ADR-2 in A-to-I editing. Quantitative proteomics analysis showed that adr-2 mutant worms altered the abundance of proteins involved in aging and lifespan regulation. Consistent with this finding, we observed that worms lacking RNA editing were short-lived. Taken together, our results reveal a sophisticated landscape of RNA editing and distinct modes of action of different ADARs.
Deleterious effects of mild simulated overwintering temperatures on survival and potential fecundity of rose-galling Diplolepis wasps (Hymenoptera: Cynipidae).

Prepupae of the rose galling Diplolepis spinosa from areas with relatively cold winters in southern Canada, and Diplolepis variabilis from a milder locale in western Canada, were used to test the hypothesis that mild winter temperatures are detrimental to the survival and potential fecundity of insects. Prepupae of D. spinosa held within or removed from their galls were exposed to simulated overwintering temperatures (-22, 0, 5, or 10 degrees C) for approximately four months before measuring their survival, body size, and potential fecundity. Similar studies were conducted using prepupae of D. variabilis that were removed from their gall and subjected to 0 degrees C or 10 degrees C treatments. Diplolepis spinosa, with or without their galls, averaged 66% more mortality at 10 degrees C than at 0 degrees C. Female D. spinosa that survived the 10 degrees C treatment had 32% fewer eggs than those held at 0 degrees C. In contrast, there was no difference in survival or numbers of eggs between D. variabilis held at 0 degrees C and 10 degrees C. Body size of adult females and size of eggs did not differ among temperature treatments for either species. We conclude that mild overwintering temperatures may be detrimental for insects by raising their metabolism, and consequently reducing energetic reserves needed for development to the adult stage and subsequent production of eggs the following spring.
Indoor transformer stations as predictors of residential ELF magnetic field exposure

Transformer stations in apartment buildings may offer a possibility to conduct epidemiological studies that involve high exposure to extremely low frequency magnetic fields (MF), avoid selection bias and minimize confounding factors. To validate exposure assessment based on transformer stations, measurements were performed in thirty buildings in three Finnish cities. In each building, spot measurements in all rooms and a 24‐h recording in a bedroom were performed in one apartment above a transformer station (AAT), in one first floor (FF) reference apartment, and one reference apartment on upper floors (UF). The apartment mean of spot measurements was 0.62 µT in the AATs, 0.21 µT in the FF and 0.11 µT in the UF reference apartments The 24‐h apartment mean (estimated from the spot measurements and the bedroom 24‐h recording) was 0.2 µT or higher in 29 (97%) AATs, in 7 (25%) FF and in 3 (10 %) UF reference apartments. The corresponding numbers for the 0.4 µT cut‐off point were 19 (63%), 4 (14%), and 1 (3.3%). The higher MF level in the FF reference apartments indicates that they should not be considered “unexposed” in epidemiological studies. If such apartments are excluded, a transformer station under the floor predicts 24‐h apartment mean MF with a sensitivity of 0.41 (or 0.58) and a specificity of 0.997 (or 0.97), depending on the MF cut‐off point (0.2 or 0.4 µT). The results indicate that apartments can be reliably classified as high and low MF field categories based on the known location of transformer stations. Bioelectromagnetics 29:213–218, 2008. © 2007 Wiley‐Liss, Inc.
MIR‐137 Suppresses Growth and Invasion, is Downregulated in Oligodendroglial Tumors and Targets CSE1L

MicroRNA‐137 (miR‐137) expression has been reported to be decreased in astrocytic tumors in two expression profiling studies but its role in the pathogenesis of oligodendroglial tumors is still limited. In this study, we demonstrate that miR‐137 expression is significantly downregulated in a cohort of 35 oligodendroglial tumors and nine glioma cell lines compared with normal brains. Lower miR‐137 expression is associated with shorter progressive‐free survival and overall survival. Restoration of miR‐137 expression in an oligodendroglial cells TC620, and also glioblastoma cells of U87 and U373 significantly suppressed cell growth, anchorage‐independent growth, as well as invasion. Demethylation and deacetylation treatments resulted in upregulation of miR‐137 expression in TC620 cells. In silico analysis showed that CSE1 chromosome segregation 1‐like (yeast) (CSE1L) is a potential target gene of miR‐137. Luciferase reporter assay demonstrated that miR‐137 negatively regulates CSE1L by interaction between miR‐137 and complementary sequences in the 3′ UTR of CSE1L. Immunohistochemistry revealed that CSE1L is upregulated in oligodendroglial tumors. Knockdown of CSE1L resulted in similar outcomes as overexpressing miR‐137 in oligodendroglioma cells and glioblastoma cells. Overall, our data suggest that miR‐137 regulates growth of glioma cells and targets CSE1L, providing further understanding in the tumorigenesis of gliomas.
Neurofilament spacing, phosphorylation, and axon diameter in regenerating and uninjured lamprey axons

It has been postulated that phosphorylation of the carboxy terminus sidearms of neurofilaments (NFs) increases axon diameter through repulsive electrostatic forces that increase sidearm extension and interfilament spacing. To evaluate this hypothesis, the relationships among NF phosphorylation, NF spacing, and axon diameter were examined in uninjured and spinal cord‐transected larval sea lampreys (Petromyzon marinus). In untransected animals, axon diameters in the spinal cord varied from 0.5 to 50 μm. Antibodies specific for highly phosphorylated NFs labeled only large axons (>10 μm), whereas antibodies for lightly phosphorylated NFs labeled medium‐sized and small axons more darkly than large axons. For most axons in untransected animals, diameter was inversely related to NF packing density, but the interfilament distances of the largest axons were only 1.5 times those of the smallest axons. In addition, the lightly phosphorylated NFs of the small axons in the dorsal columns were widely spaced, suggesting that phosphorylation of NFs does not rigidly determine their spacing and that NF spacing does not rigidly determine axon diameter. Regenerating neurites of giant reticulospinal axons (GRAs) have diameters only 5–10% of those of their parent axons. If axon caliber is controlled by NF phosphorylation via mutual electrostatic repulsion, then NFs in the slender regenerating neurites should be lightly phosphorylated and densely packed (similar to NFs in uninjured small caliber axons), whereas NFs in the parent GRAs should be highly phosphorylated and loosely packed. However, although linear density of NFs (the number of NFs per micrometer) in these slender regenerating neurites was twice that in their parent axons, they were highly phosphorylated. Following sectioning of these same axons close to the cell body, axon‐like neurites regenerated ectopically from dendritic tips. These ectopically regenerating neurites had NF linear densities 2.5 times those of uncut GRAs but were also highly phosphorylated. Thus, in the lamprey, NF phosphorylation may not control axon diameter directly through electrorepulsive charges that increase NF sidearm extension and NF spacing. It is possible that phosphorylation of NFs normally influences axon diameter through indirect mechanisms, such as the slowing of NF transport and the formation of a stationary cytoskeletal lattice, as has been proposed by others. Such a mechanism could be overridden during regeneration, when a more compact, phosphorylated NF backbone might add mechanical stiffness that promotes the advance of the neurite tip within a restricted central nervous system environment. © 1996 Wiley‐Liss, Inc.
Histone Deacetylase 6 (HDAC6) Promotes the Pro-survival Activity of 14-3-3ζ via Deacetylation of Lysines within the 14-3-3ζ Binding Pocket*

Background: 14-3-3ζ promotes cell survival by interacting with a network of proteins. However, its regulation remains poorly understood. Results: Proteomics identified several acetyl-lysines on 14-3-3ζ, two of which are regulated by HDAC6 and impact 14-3-3ζ activity. Conclusion: HDAC6 controls 14-3-3ζ binding via deacetylation of lysines within its binding pocket. Significance: These findings provide a novel mechanism linking HDAC6 to the pro-survival activity of 14-3-3ζ. The phospho-binding protein 14-3-3ζ acts as a signaling hub controlling a network of interacting partners and oncogenic pathways. We show here that lysines within the 14-3-3ζ binding pocket and protein-protein interface can be modified by acetylation. The positive charge on two of these lysines, Lys49 and Lys120, is critical for coordinating 14-3-3ζ-phosphoprotein interactions. Through screening, we identified HDAC6 as the Lys49/Lys120 deacetylase. Inhibition of HDAC6 blocks 14-3-3ζ interactions with two well described interacting partners, Bad and AS160, which triggers their dephosphorylation at Ser112 and Thr642, respectively. Expression of an acetylation-refractory K49R/K120R mutant of 14-3-3ζ rescues both the HDAC6 inhibitor-induced loss of interaction and Ser112/Thr642 phosphorylation. Furthermore, expression of the K49R/K120R mutant of 14-3-3ζ inhibits the cytotoxicity of HDAC6 inhibition. These data demonstrate a novel role for HDAC6 in controlling 14-3-3ζ binding activity.