Miracle-dz/UniFAR-FTUs huggingface dataset:
Cell Wall Modifications in Arabidopsis Plants with Altered α-l-Arabinofuranosidase Activity[C][W]

Although cell wall remodeling is an essential feature of plant growth and development, the underlying molecular mechanisms are poorly understood. This work describes the characterization of Arabidopsis (Arabidopsis thaliana) plants with altered expression of ARAF1, a bifunctional α-l-arabinofuranosidase/β-d-xylosidase (At3g10740) belonging to family 51 glycosyl-hydrolases. ARAF1 was localized in several cell types in the vascular system of roots and stems, including xylem vessels and parenchyma cells surrounding the vessels, the cambium, and the phloem. araf1 T-DNA insertional mutants showed no visible phenotype, whereas transgenic plants that overexpressed ARAF1 exhibited a delay in inflorescence emergence and altered stem architecture. Although global monosaccharide analysis indicated only slight differences in cell wall composition in both mutant and overexpressing lines, immunolocalization experiments using anti-arabinan (LM6) and anti-xylan (LM10) antibodies indicated cell type-specific alterations in cell wall structure. In araf1 mutants, an increase in LM6 signal intensity was observed in the phloem, cambium, and xylem parenchyma in stems and roots, largely coinciding with ARAF1 expression sites. The ectopic overexpression of ARAF1 resulted in an increase in LM10 labeling in the secondary walls of interfascicular fibers and xylem vessels. The combined ARAF1 gene expression and immunolocalization studies suggest that arabinan-containing pectins are potential in vivo substrates of ARAF1 in Arabidopsis.
Predictive value of sputum gram stain for the determination of appropriate antibiotic therapy in ventilator-associated pneumonia.

BACKGROUND Ventilator-associated pneumonia (VAP) is diagnosed in about 30% to 50% of critically ill postsurgical and trauma patients. Early appropriate antibiotic therapy has been associated with improved survival rates. The diagnosis, however, continues to be a challenge. We routinely employ clinical pulmonary infection scores to warrant a bronchoalveolar lavage (BAL) quantitative culture to subsequently diagnose VAP. Presumptive antibiotic therapy for the first 48 to 72 hours is based on the sputum Gram stain, obtained at the time of BAL. This study was conducted to analyze the predictive value of sputum Gram stain for selecting appropriate early antibiotic therapy for VAP as confirmed by a BAL quantitative culture (>10 CFU/mL considered diagnostic). METHODS The retrospective analysis included 124 consecutive intensive care unit patients with 186 identified episodes of presumed VAP from December 2002 to June 2006. VAP episodes were identified by a clinical pulmonary infection score > or =6, availability of a sputum Gram stain, and a corresponding quantitative culture result from a BAL sample. RESULTS The overall correlation between Gram stain and subsequent organism identified on the BAL quantitative culture was only fair with a kappa score of 0.314. The best predictive value calculated was for the category of negative Gram stain. However, in 10 of 45 episodes where the sputum Gram stain did not identify a predominant organism, the BAL culture isolated pathogenic strains. Pseudomonas sp. was the most common bacteria isolated from the BAL samples. CONCLUSIONS Irrespective of sputum Gram stain, presumptive triple antibiotic coverage should be instituted to provide dual antibiotic coverage for gram-negative bacilli, and vancomycin for gram-positive cocci. Additionally, identification of no organisms in the sputum Gram stain should still prompt broad-spectrum antibiotic coverage until the final results of the BAL quantitative culture are available.
Sentiment analysis of public complaints using lexical resources between Indonesian sentiment lexicon and Sentiwordnet

Public complaints were one of the kinds of public participation and awareness to public service implementation. Information from public complaints can be used by the government to improve public satisfaction. In addition, the government can obtain public sentiment from public complaints either on media social or the official government site. Many kinds of research on sentiment analysis have been done, either used statistical method approach, semantic method approach or both. Statistical method approach was widely used. While semantic method approach being the hot topic recently. On semantic method approach, lexical resource was an important component to classily sentiment on text. Namely Sentiwordnet and Indonesian sentiment lexicon. Currently, Indonesian lexical resources for sentiment analysis has grown. But the lexicon doesn't have polarity score that can be measure emotion on text like Sentiwordnet. Sentiwordnet has been widely used on research in English. In this research, we apply Sentiwordnet to classify sentiment on Indonesian public complaints with accuracy 47% either on media Twitter and 56.85% on the official government website's data. Furthermore, we compare it with Indonesian sentiment lexical and get the accuracy 65.4% on media Twitter and 81.4% on the of Ticial government website
Immortalization of Porcine 11β-Hydroxysteroid Dehydrogenase Type 1-Transgenic Liver Cells Using SV40 Large T Antigen

Cortisol is a steroid hormone essential to the maintenance of homeostasis that is released in response to stress and low blood glucose concentration. Cortisol is converted from cortisone by 11β-hydroxysteroid dehydrogenase type 1 (HSD11B1). It has been reported that too much cortisol or overexpression of HSD11B1 induces obesity and the insulin resistance that accompanies metabolic syndrome in rodent adipose tissue. In our previous study, HSD11B1-transgenic (TG) fibroblasts were established, and a porcine model was generated by SCNT using those fibroblasts. Hepatocytes overexpressing HSD11B1 were obtained from livers of this porcine model and cultured in vitro. However, the primary hepatocytes were found to have a short life span or low proliferation rate. To overcome these problems, the SV40 large T antigen was transduced into primary HSD11B1-TG hepatocytes, and those cells were immortalized. Immortalized HSD11B1-TG hepatocytes showed restored morphology, more rapid proliferation rate, and more expression of HSD11B1 than primary hepatocytes. As well, these cells kept the hepatic characteristics such as gluconeogenic response to cortisone and increased expression of hepatic makers. The immortalized HSD11B1-TG hepatocytes may be useful for studying traits and potential therapeutic drugs for treatment of metabolic disorders induced by overexpression of HSD11B1.
Isolation and Characterization of Specialized Lambda Transducing Bacteriophage Carrying the metBJF Methionine Gene Cluster

Secondary attachment site lysogens of ΔattλΔppc-argECBH strains of Escherichia coli with λcI857 integrated into the bfe gene (88 min) were isolated. Of 20 such lysogens examined, 2 produce lysates with transducing phage containing the metBJF gene cluster (87 min). Reintroduction of the ppc-argECBH chromosome segment (which lies between the bfe and met genes) into these strains virtually abolishes the production of met transducing phage. All of the phage examined have lost essential genes from the left arm of the λ chromosome. Approximately 85% of the phage appear to have the same genetic composition, containing the metBJF gene cluster, but not the closely linked gene cytR, and having lost phage genes G and J. Analytical CsCl density gradient centrifugation of five representatives of this major class of phage shows four of them to have identical densities (lighter than λ), while the fifth cannot be resolved from λ. The four apparently identical phage were isolated from three separate lysates, which suggests the existence of preferred sites for illegitimate recombination on the bacterial and phage chromosomes. Three specialized transducing phage that carry cytR in addition to metB, metJ, and metF have also been studied. Each of these viruses has a different amount of phage deoxyribonucleic acid. Two of them have less deoxyribonucleic acid than λ, whereas the third has about the same amount. The metB, metF, and cytR genes of the transducing phage have been shown to function in vivo. The phage-borne metB and metF genes are subject to metJ-mediated repression.
Interferons and Ribavirin Effectively Inhibit Norwalk Virus Replication in Replicon-Bearing Cells

ABSTRACT The development of effective therapies for noroviral gastroenteritis has been hampered by the absence of a cell culture system. Recently, we reported the generation of Norwalk virus (NV) replicon-bearing cells in BHK21 and Huh-7 cells and demonstrated that alpha interferon (IFN-α) effectively inhibited the replication of NV in these cells. In continuing studies for screening potential antinoroviral agents, we tested IFN-γ and ribavirin for their effects on NV replication in the cells. Like IFN-α, IFN-γ inhibited the replication of NV in the replicon-bearing cells, showing the reduction of the NV genome and proteins in a dose-dependent manner. The effective dose for reducing 50% (ED50) of the NV genome and protein was calculated to be approximately 40 units/ml. When ribavirin was applied to the cells, it effectively reduced the NV genome and protein with the ED50 calculated as approximately 40 μM. The combination of IFN-α and ribavirin showed additive effects on the inhibition of NV replication. With the addition of guanosine to the ribavirin treatment, moderately reversed antiviral effects were observed, suggesting that the ribavirin effect may be associated with the depletion of GTP in the cells. Sequencing analysis of the conserved polymerase regions of NV in the ribavirin-treated (100 μM) and nontreated groups showed that the mutation rates were similar and indicated that ribavirin did not induce catastrophic mutations. The NV replicon-bearing cells provide an excellent tool for screening potential antinoroviral agents, and our results indicated that IFNs and ribavirin may be good therapeutic options for noroviral gastroenteritis.
The evaluation of 20 MHz ultrasonography, computed tomography scans as compared to direct microscopy for periodontal system assessment.

AIM To identify by ultrasonography (DermaScan C, Cortex Technology1) the reference points necessary to monitor the horizontal bone resorbtion and to assess the accuracy of the measurements by comparing with Cone Beam Computed Tomography images, having direct microscopic section measurements as a gold standard. MATERIAL AND METHODS We performed the examinations on the lingual side of the alveolar bone of 4 pig mandibles. We tried to identify the enamel-cementum junction, the root, the periodontal space at the appearance of the tooth from the alveolar bone, the edge of cortical bone at its coronary limit (in order to assess the horizontal bone resorption). We measured the distance between the enamel-cementum junction and the coronal edge of cortical bone. RESULTS There was a strong positive correlation between the alveolar bone level measured with the 3 techniques. Correlation parametric R2 tests were statistically significant for DermaScan measurements compared to microscopy ones (p<0.0001). Linear regression showed statistically significant correlations for alveolar bone level measurements made by CBCT compared to microscopy (p<0.05). CONCLUSIONS The cementum-enamel junction may be identified on ultrasonic images with high accuracy according to the tooth anatomical convexities, therefore this method can be used for monitoring the periodontium.
Modélisation des cultures européennes au sein de la biosphère : phénologie, productivité et flux de CO2

L'extension des surfaces cultivees et l'intensification de leur gestion, en reponse a la demande croissante en produits agricoles, transforment les proprietes des continents depuis plusieurs centaines d'annees. Or les surfaces continentales sont un maillon des grands cycles hydrologique, energetique et de carbone de la planete. Les cultures occupent actuellement 35% de la superficie de l'Europe de l'Ouest. Leur fonctionnement specifique (selection genetique, semis, irrigation, fertilisation, recolte. . . ) n'etait jusqu'a recemment pas pris en compte dans les modeles de biosphere, mais leur effet sur ces cycles est important et incertain. Cette these vise a quantifier la contribution des cultures au bilan de carbone europeen. On poursuit et evalue l'amelioration, a l’echelle de l’Europe, de la representation des surfaces cultivees dans le modele de biosphere ORCHIDEE associe au modele de cultures STICS. La comparaison des simulations d’ORCHIDEE-STICS aux indices de vegetation satellitaires montre que le cycle saisonnier des cultures est mieux simule. Par consequent on simule plus realistement la productivite annuelle moyenne des cultures et sa variabilite inter-annuelle et spatiale observees dans les statistiques agricoles. La chute de productivite comme lors de l'ete caniculaire de 2003 est a l'origine d'une source de carbone pour l'atmosphere qui a annule une partie des benefices du puits biospherique europeen. La source estimee avec ORCHIDEE-STICS est en bon accord avec les estimations atmospheriques inverses et contribue a augmenter d'un quart les emissions de CO2 par les activites humaines en Europe. Ce travail montre l'importance et quantifie l'effet de mieux prendre en compte les cultures dans un modele de biosphere sur les composantes du bilan carbone de la vegetation, a l'echelle europeenne. Il ouvre la voie a de nombreuses etudes de l'effet non seulement biogeochimique mais aussi biophysique des surfaces cultivees sur le systeme climatique.
The influence of body position and differential ventilation on lung dimensions and atelectasis formation in anaesthetized man

The effects of body position and anaesthesia with mechanical ventilation on thoracic dimensions and atelectasis formation were studied by means of computerized tomography in 14 patients. Induction of anaesthesia in the supine position reduced the cross‐sectional area for both lungs and caused atelectasis formation in dependent lung regions in 4/5 patients. Conventional ventilation with positive end‐expiratory pressure (PEEP) increased thoracic dimensions and reduced, but did not eliminate, the atelectatic areas. The vertical diameters of both lungs were smaller in the lateral position as compared to the supine position (16.7 vs 10.4 cm in the left lung and 17.3 vs 12.8 cm in the right lung). The lateral positioning also caused a large reduction of the atelectatic area in the non‐dependent lung. Differential ventilation with selective PEEP to the dependent lung eliminated (3/8 patients) or reduced (5/8 patients) dependent lung atelectasis. It can be concluded that lung geometry is altered in the lateral position: the shape of the lung makes the vertical diameter of each lung less in the lateral position, compared to the supine position. The atelectatic areas are mainly located in the dependent lung in the lateral position, and these atelectatic areas could be further reduced by selective PEEP to this lung.
Fine mapping and molecular cloning of mutations in the herpes simplex virus DNA polymerase locus

Mutations in five phenotypically distinct mutants derived from herpes simplex virus type 1 strain KOS which lie in or near the herpes simplex virus DNA polymerase (pol) locus have been fine mapped with the aid of cloned fragments of mutant and wild-type viral DNAs to distinct restriction fragments of 1.1 kilobase pairs (kbp) or less. DNA sequences containing a mutation or mutations conferring resistance to the antiviral drugs phosphonoacetic acid, acyclovir, and arabinosyladenine of pol mutant PAAr5 have been cloned as a 27-kbp Bg+II fragment in Escherichia coli. These drug resistance markers have been mapped more finely in marker transfer experiments to a 1.1-kbp fragment (coordinates 0.427 to 0.434). In intratypic marker rescue experiments, temperature-sensitive (ts), phosphonoacetic acid resistance, and acyclovir resistance markers of pol mutant tsD9 were mapped to a 0.8-kbp fragment at the left end of the EcoRI M fragment (coordinates 0.422 to 0.427). The ts mutation of pol mutant tsC4 maps within a 0.3-kbp sequence (coordinates 0.420 to 0.422), whereas that of tsC7 lies within the 1.1-kbp fragment immediately to the left (coordinates 0.413 to 0.420). tsC4 displays the novel phenotype of hypersensitivity to phosphonoacetic acid; however, the phosphonoacetic acid hypersensitivity phenotype is almost certainly not due to the mutation(s) conferring temperature sensitivity. The ts mutation of mutant tsN20--which does not affect DNA polymerase activity--maps to a 0.5-kbp fragment at the right-hand end of the EcoRI M fragment (coordinates 0.445 to 0.448). The mapping of the mutations in these five mutants further defines the limits of the pol locus and separates mutations differentially affecting catalytic functions of the polymerase.
Recognizing Sudden Cardiac Arrest May Require More Than Two Questions during Telephone Triage: Developing a Complementary Checklist.

OBJECTIVE To develop decision-support tools to identify patients experiencing sudden cardiac arrest (SCA). METHODS Eighty calls related to SCA were content analyzed, and the contextual patterns that emerged were organized into a checklist. Two researchers independently analyzed the recorded calls and compared their findings. Eighteen dispatchers scored 20 cases (which included SCA and non-SCA cases) both with and without the checklist. Correct responses for each case and agreement among dispatchers have been reported. RESULTS Eighty audio files (total time, 96 min) were analyzed, and a total of 602 codes were extracted from the text and recordings. The caller's tone of voice and presence or absence of background voices, calling for an ambulance and giving the dispatcher the address promptly, and description of the primary complaint and respirations accounted for 38%, 39%, and 23% of all codes, respectively. A 15-item complementary checklist has been developed. The mean percentages of correct responses were 66.9%+27.96% prior to the use of checklist and 80.05%+10.84% afterwards. Results of the independent t test for checklist scores showed that statistically significant differences were present between the SCA and non-SCA cases (t=5.88, df=18, p=0.000). CONCLUSION Decision support tools can potentially increase the recognition rate of SCA cases, and therefore produce a higher rate of dispatcher-directed CPR.
Effect of a bronchial provocation test with house‐dust mite on blood eosinophilia, eosinophil cationic protein, soluble interleukin‐2 receptor, and interleukin‐6 in asthmatic children

Eighteen children with perennial asthma and allergy to house‐dust mite (HDM) underwent a bronchial challenge with HDM. Before and 24 h after the test, a venous blood sample was taken to determine levels of eosinophils, eosinophil cationic protein (ECP), soluble interleukin‐2 receptor (IL‐2R), and interleukin‐6 (IL‐6). A histamine challenge was performed before and 24 h after the HDM challenge. All subjects showed an immediate asthmatic reaction (IAR). A definite late asthmatic reaction (LAR) was observed in 15 children, a probable LAR in two, and no LAR in one. Because of persistent bronchial obstruction (FEV1>70%), eight children were unable to perform a histamine challenge 24 h after the allergen challenge. These were the children with the lowest prechallenge provocation dose (PD20) of histamine. In the other 10 children, the mean PD20 histamine decreased after the HDM challenge (mean PD20 before was 0.56 mg/ml; after challenge it was 0.14 mg/ml; P= 0.007). After the HDM challenge, an increase was detected in the mean values of blood eosinophils (mean before was 446/mm3; mean after was 733/mm3; P= 0.002), ECP (mean before was 26.3 μg/1; mean after was 34.3 μg/1; P<0.040), and IL‐2R (mean before was 116.35 U/ml; mean after was 128.52 U/ml; P<0.040). On the other hand, IL‐6 remained unchanged after the HDM challenge (mean before was 9.47 pg/1; mean after was 9.70 pg/1; P= 0.360). Furthermore, as compared with a group of normal, age‐matched children (n =18), asthmatic children were found to have higher prechallenge levels of ECP (mean: 10.3 μg/1 compared with 26.3 μg/1) (P>0.001) and IL‐2R (mean: 80.30 U/ml compared with 116.35 U/ml) (P =0.009), but not of IL‐6 (mean: 11.34 pg/1 compared with 9.47 pg/1) (P = 0.436).
Device and technology implications of the Internet of Things

We live in an interconnected world. Computing power once reserved for server rooms now resides in our pockets. Tablets now outsell PCs. As marked as these changes have been, we are now entering a new era of vastly greater connectivity, where people interact with the world around them in entirely new ways. The Internet of Things is in its infancy, so predictions of precisely what it will become are dangerous, but several things are clear. First, the leaf nodes of the network will share some device and technology properties in terms of cost and computing capability, but also analog and wireless functionality. These nodes will interact with people and with the cloud. The “little data” of these interactions needs to integrate seamlessly with the “big data” of the world around them. The trust, security and service components of these interactions lead to further device and technology requirements. This talk looks at the trends and discusses some likely paths forward.
Effect of a probiotic on liver aminotransferases in nonalcoholic fatty liver disease patients: a double blind randomized clinical trial.

OBJECTIVE The present pilot trial was carried out to evaluate the effects of an acute treatment with a mixture containing 500 million of Lactobacillus bulgaricus and Streptococcus thermophilus per day in patients with non alcoholic fatty liver disease (NAFLD). RESEARCH METHODS A sample of 30 patients with NAFLD (diagnosed by liver biopsy) was enrolled and 28 patients were analyzed in a double blind randomized clinical trial. Patients were randomized to one of the following treatments during 3 months: group I, treated with one tablet per day with 500 million of Lactobacillus bulgaricus and Streptococcus thermophilus and group II, treated with one placebo tablet (120 mg of starch). RESULTS In group I, alanine amino transferase (ALT: 67.7 +/- 25.1 vs. 60.4 +/- 30.4 UI/L; p < 0.05), aspartate aminotransferase activity (AST: 41.3 +/- 15.5 vs. 35.6 +/- 10.4 UI/L; p < 0.05) and gammaglutamine transferase levels (gammaGT: 118.2 +/- 63.1 vs. 107.7 +/- 60.8 UI/L; p < 0.05) decreased. In group II, all liver function parameters remained unchanged (ALT: 60.7 +/- 32.1 vs. 64.8 +/- 35.5 UI/L; p < 0.05), aspartate aminotransferase activity (AST: 31.7 +/- 13.1 vs. 36.4 +/- 13.8 UI/L; ns) and gammaglutamine transferase levels (gammaGT: 82.1 +/- 55.1 vs. 83.6 +/- 65.3 UI/L; ns). Anthropometric parameters and cardiovascular risk factors remained unchanged after treatment in both groups. CONCLUSION A tablet of 500 million of Lactobacillus bulgaricus and Streptococcus thermophilus, with a randomized clinical design, improved liver aminotransferases levels in patients with NAFLD.