Miracle-dz/UniFAR-FTUs huggingface dataset:
Extracellular Proteins in Pea Root Tip and Border Cell Exudates1[OA]

Newly generated plant tissue is inherently sensitive to infection. Yet, when pea (Pisum sativum) roots are inoculated with the pea pathogen, Nectria haematococca, most newly generated root tips remain uninfected even though most roots develop lesions just behind the tip in the region of elongation. The resistance mechanism is unknown but is correlated spatially with the presence of border cells on the cap periphery. Previously, an array of >100 extracellular proteins was found to be released while border cell separation proceeds. Here we report that protein secretion from pea root caps is induced in correlation with border cell separation. When this root cap secretome was proteolytically degraded during inoculation of pea roots with N. haematococca, the percentage of infected root tips increased from 4% ± 3% to 100%. In control experiments, protease treatment of conidia or roots had no effect on growth and development of the fungus or the plant. A complex of >100 extracellular proteins was confirmed, by multidimensional protein identification technology, to comprise the root cap secretome. In addition to defense-related and signaling enzymes known to be present in the plant apoplast were ribosomal proteins, 14-3-3 proteins, and others typically associated with intracellular localization but recently shown to be extracellular components of microbial biofilms. We conclude that the root cap, long known to release a high molecular weight polysaccharide mucilage and thousands of living cells into the incipient rhizosphere, also secretes a complex mixture of proteins that appear to function in protection of the root tip from infection.
Endoscopic management of unresectable malignant gastroduodenal obstruction with a nitinol uncovered metal stent: A prospective Japanese multicenter study.

AIM To determine the safety and efficacy of endoscopic duodenal stent placement in patients with malignant gastric outlet obstruction. METHODS This prospective, observational, multicenter study included 39 consecutive patients with malignant gastric outlet obstruction. All patients underwent endoscopic placement of a nitinol, uncovered, self-expandable metal stent. The primary outcome was clinical success at 2 wk after stent placement that was defined as improvement in the Gastric Outlet Obstruction Scoring System score relative to the baseline. RESULTS Technical success was achieved in all duodenal stent procedures. Procedure-related complications occurred in 4 patients (10.3%) in the form of mild pneumonitis. No other morbidities or mortalities were observed. The clinical success rate was 92.3%. The mean survival period after stent placement was 103 d. The mean period of stent patency was 149 d and the patency remained acceptable for the survival period. Stent dysfunction occurred in 3 patients (7.7%) on account of tumor growth. CONCLUSION Endoscopic management using duodenal stents for patients with incurable malignant gastric outlet obstruction is safe and improved patients' quality of life.
A New Shiga Toxin 2 Variant (Stx2f) fromEscherichia coli Isolated from Pigeons

ABSTRACT We have isolated Shiga toxin (Stx)-producing Escherichia coli (STEC) strains from the feces of feral pigeons which contained a new Stx2 variant gene designatedstx2f. This gene is most similar tosltIIva of patient E. coli O128:B12 isolate H.I. 8. Stx2f reacted only weakly with commercial immunoassays. The prevalence of STEC organisms carrying the stx2fgene in pigeon droppings was 12.5%. The occurrence of a new Stx2 variant in STEC from pigeons enlarges the pool of Stx2 variants and raises the question whether horizontal gene transfer to E. coli pathogenic to humans may occur.
Climate change, plant migration, and range collapse in a global biodiversity hotspot: the Banksia (Proteaceae) of Western Australia

Climate change has already altered global patterns of biodiversity by modifying the geographic distributions of species. Forecasts based on bioclimatic envelop modeling of distributions of species suggests greater impacts can be expected in the future, but such projections are contingent on assumptions regarding future climate and migration rates of species. Here, we present a first assessment of the potential impact of climate change on a global biodiversity hotspot in southwestern Western Australia. Across three representative scenarios of future climate change, we simulated migration of 100 Banksia (Proteaceae) species at a rate of 5 km decade−1 and compared projected impacts with those under the commonly applied, but acknowledged as inadequate, assumptions of ‘full‐’ and ‘no‐migration. ’ Across all climate × migration scenarios, 66% of species were projected to decline, whereas only 6% were projected to expand or remain stable. Between 5% and 25% of species were projected to suffer range losses of 100% by 2080, depending mainly on climate scenario. Species losses were driven primarily by changes in current precipitation regimes, with the greatest losses of species projected to occur in a transition zone between wet coastal areas and interior arid regions and which is projected to become more arid in the future. Because the ranges of most species tended to collapse in all climate scenarios, we found that climate change impacts to flora of southwestern Western Australia may be large, even under optimistic assumptions regarding migration abilities. Taken together, our results suggest that the future of biodiversity in southwestern Western Australia may lie largely in the degree to which this hotspot experiences increased drought and in the ability of species to tolerate such decreases in precipitation. More broadly, our study is among a growing number of theoretical studies suggesting the impacts of future climate change on global biodiversity may be considerable.
Characterizing antireflection coatings on textured monocrystalline silicon with Spectroscopic Ellipsometry

Mono-crystalline silicon is chemically textured and coated with a silicon nitride surface anti-reflection (AR) film to improve light trapping and device efficiency in photovoltaic applications. The thickness and optical properties of the AR coating determine the effective suppression of reflected light. However, optical characterization of films on chemically textured surfaces is challenging due to the low reflectance. We present new measurement geometries and modeling methodology using Spectroscopic Ellipsometry (SE) to determine film thickness and optical properties of thin AR coatings on textured mono-crystalline silicon. Special measurement geometries are used to collect specular reflected light from the etched silicon pyramid facets. Both apexial and lateral measurement geometries are demonstrated, where the latter requires a special sample stage to tilt and rotate the sample to detect the specular reflected light from the pyramid facets. Measurement considerations are discussed including probe-beam incident angle, sample tilt and rotational angles. Effects of pyramid surface-coverage are also discussed in relation to the proposed measurement geometries. Previous modeling attempts using Effective Medium Approximation (EMA) theory showed inconsistent results when comparing apexial and lateral measurements of the same sample surface. In this work, results from a scattering-corrected modeling approach provide improved consistency for a series of SiNx coatings on textured monocrystalline silicon for both lateral and apexial measurement geometries.
Cyclooxygenase 2—implications on maintenance of gastric mucosal integrity and ulcer healing: controversial issues and perspectives

Cyclooxygenase (COX), the key enzyme for synthesis of prostaglandins, exists in two isoforms (COX-1 and COX-2). COX-1 is constitutively expressed in the gastrointestinal tract in large quantities and has been suggested to maintain mucosal integrity through continuous generation of prostaglandins. COX-2 is induced predominantly during inflammation. On this premise selective COX-2 inhibitors not affecting COX-1 in the gastrointestinal tract mucosa have been developed as gastrointestinal sparing anti-inflammatory drugs. They appear to be well tolerated by experimental animals and humans following acute and chronic (three or more months) administration. However, there is increasing evidence that COX-2 has a greater physiological role than merely mediating pain and inflammation. Thus gastric and intestinal lesions do not develop when COX-1 is inhibited but only when the activity of both COX-1 and COX-2 is suppressed. Selective COX-2 inhibitors delay the healing of experimental gastric ulcers to the same extent as non-COX-2 specific non-steroidal anti-inflammatory drugs (NSAIDs). Moreover, when given chronically to experimental animals, they can activate experimental colitis and cause intestinal perforation. The direct involvement of COX-2 in ulcer healing has been supported by observations that expression of COX-2 mRNA and protein is upregulated at the ulcer margin in a temporal and spatial relation to enhanced epithelial cell proliferation and increased expression of growth factors. Moreover, there is increasing evidence that upregulation of COX-2 mRNA and protein occurs during exposure of the gastric mucosa to noxious agents or to ischaemia-reperfusion. These observations support the concept that COX-2 represents (in addition to COX-1) a further line of defence for the gastrointestinal mucosa necessary for maintenance of mucosal integrity and ulcer healing.
Prévision du nombre de passagers entrant dans un réseau de transport multimodal en cas d'évènements atypiques, à l'aide de méthodes d'apprentissage automatique

Cet article traite de la prevision du nombre de passagers entrant dans un reseau de transport multimodal en cas d'evenements atypiques. Nous proposons une approche issue de l'apprentissage profond, au travers d'un reseau de neurones recurrent. Cette approche a ete comparee a la methode des forets aleatoires (Random Forest en anglais), largement utilisee en apprentissage statistique pour resoudre des problemes de regression. Nous avons teste trois variantes du reseau de neurones recurrents (Gated Recurrent Unit, GRU) qui peuvent etre decrites comme suit : "Un modele local qui considere independamment les differentes series temporelles propres a chaque station". Un modele global, qui est un modele multi-entrees/multi-sorties qui predit simultanement toutes les series temporelles des differentes stations". Un modele qui combine l'information obtenue de maniere globale et locale a propos des differentes series temporelles des stations.
[Arthrosonography and biomarkers in the evaluation of destructive knee cartilage osteoarthrosis].

INTRODUCTION Knee osteoarthrosis (OA) is a degenerative disease with progressive loss of cartilage of joints and bone destruction. During this process, the release of fragments of connective tissue matrix is detected in the biological fluids such as human cartilage glycoprotein (YKL-40), cartilage oligomeric matrix protein (COMP) and collagen type I C terminal telopeptid (CTX-I). OBJECTIVE The aim of the study was to determine the degree of connection cartilage thickness measured by ultrasound with serum concentrations of biomarkers YKL-40, COMP and CTX-I in patients with primary knee OA. METHODS The analysis included 88 patients with the diagnosis of knee OA. Ultrasound examination of knees were done by two rheumatologists. The analysis of serum samples determined the concentration of COMP, YKL-40 and CTX-I by the ELISA method. RESULTS The average age of patients was 69.97 +/- 9.37 years and the duration of knee OA 6.46 +/- 6.73 years. The average cartilage thickness of the femoral condyle was 1.33 +/- 0.20 mm; of the medial condyle (MC) (front access) 1.30 +/- 0.23 mm, (rear access) 1.30 +/- 0.29 mm and lateral condyli (LC) (front access) 1.39 +/- 0.27 mm. The average cartilage thickness of MC (front access) was 1.27 mm (0.98-1.42 mm), (rear access) 1.27 mm (0.84-1.46 mm) and LC (front access) 1.36 mm (1.01-1.57 mm) (p = 0.002). There was a significant connection in the negative direction between the patients' age and the cartilage thickness of MC (front and rear access) and LC (front access) (r = -0.253; p = 0.017). There was a significant negative direction of interrelationship between the cartilage thickness of MC (front access) (r = -0.259; p = 0.015) and LC (front access) and the disease duration (r = -0.259; p = 0.015). In patients with knee OA lasting for 5 years the measured cartilage thickness was 1.27 mm (1.16-1.49 mm), and 0.99 mm (0.94-1.23 mm) (p = 0.007) in those lasting for 20 years. There was a significant relationship in a negative direction between the concentration of YKL-40 and cartilage thickness of MC (front access) (r = -0.249; p = 0.019). CONCLUSION The progressive loss of cartilage during the long-term evolution of osteoarthrosis is most extensive in the femoral MC. The increased serum levels of YKL-40 can be a good indicator of joint cartilage destruction.
Segmenting speech into words.

Four experiments employed a listening for mispronuciations task to determine how listeners perceive an ordered series of words from a continuous, phonetically ambiguous stimulus. In experiments 1,2, and 3, listeners' reaction times to detect mispronuciations were obtained in phonological sequences that could be perceived as either one or two words (e.g., "cargo" or "car go" mispronounced "carko"). In experiment 1, segmentation of the acoustic signal as one or two words was guided by the theme of a short story. For example, the sentence "They saw the carko on the ferry" was spliced into two stories--one about a shipment of cargo, and one about a car about to go on a ferryboat. The results showed significantly faster reaction times--by about 300 ms--when the mispronunciation was perceived as occurring in the second syllable of a word. In experiment 2, alternate segmentation of the same acoustic signal were constrained by the grammatical nature of the first few words in a sentence. Subjects were presented with sentences such as "The doctor said that nosetrops will help the cold" or "the doctor said he knows trops will help the cold. " By means of tape splicing, the final portions of the two sentences in each pair were acoustically identical. Reaction times were again found to be faster--by about 150 ms--when the mispronunciation was perceived as occuring in the second or third syllable of a word, rather than at the beginning of a word. Experiment 3 replicated these results using naturally recorded sentences having normal prosody. The results of experiments 1-3 demonstrated that prior context determines how syllables are recognized as words and that a mispronounced second syllable is detected faster than a mispronounced word-initial syllable. It was argued that mispronunciations are detected more quickly in second syllables because the intended word has been accessed from its first syllable. This hypothesis was further supported in experiment 4. When subjects read each sentence before hearing it, so that all syllables were equally (and perfectly) predictable, mispronunications were detected equally fast in first and second syllables.
Improving thromboprophylaxis: performance measures and practical strategies.

1288. 20. Sobieraj DM.Development and implementation of a program to assess medical patients’ need for venous thromboembolism prophylaxis. Am J Health Syst Pharm. 2008;65(18):1755–1760. 21. Bauer JB, Chun DS, Karpinski TA.Pharmacist-led program to improve venous thromboembolism prophylaxis in a community hospital. Am J Health Syst Pharm. 2008;65(17):1643–1647. 2009 Society of Hospital Medicine DOI 10.1002/jhm.564 Published online in wiley InterScience (www.interscience.wiley.com). S30 Journal of Hospital Medicine Vol 4 No 8 Supplement 2 October 2009
Improving the Accuracy of Specimen Labeling

Accurate specimen identification is a challenge in all hospitals. A mislabeled specimen can lead to devastating consequences for a patient. In an effort to decrease the risk of potential harm caused by labeling errors, Children's Hospitals and Clinics of Minnesota successfully implemented a Zero Tolerance Laboratory Specimen Labeling process. After months of studying, charting, networking, and communicating with all stakeholders the new process led to a 75% reduction in laboratory specimen labeling errors. Over 70% of all information used by a clinician to diagnose and treat a patient comes from the laboratory.1 Ensuring that specimens are correctly identified at the point of collection is essential for accurate diagnostic information. Patient and/or specimen misidentification can be serious, resulting in misdiagnosis and mistreatment.2,3 A misidentification event creates multiple victims: the patient whose treatment was based on the provided results, the patient whose sample it actually was who may have gone untreated, and the healthcare workers who were directly involved with the patient or the specimen. There are also financial and emotional costs from this type of error. While the financial toll can be calculated, the emotional toll on the patients, their families, and healthcare workers who experience its impact is not easily quantifiable. METHOD In April 2003, a multidisciplinary team from Children's Hospitals and Clinics of Minnesota performed a Failure Mode and Effects Analysis (FMEA). 4 The team was composed of representatives from the following departments: the clinical laboratory, pathology, process improvement, nursing, and risk management. FMEA analysis identifies potential flaws before an… ABBREVIATIONS: FMEA = Failure Mode and Effects Analysis.
Growth standards for twins from birth to four years.

SummaryGrowth standards for twins are presented for weight, height, and head circumference, based on a sample repeatedly measured from birth to four years of age. The results give the means, SDs, and selected centiles for the size attained at each age, the amount of gain between ages, and the size differences within twin pairs. Sex differences in growth rate were evident at several ages; males grew more rapidly during the first 6 months, whereas females grew more rapidly during the third year. Comparing high and low birth-weight twins, the mean weight gain was the same for both groups during the first two years, and the weight differential remained constant also, but there was an increasing degree of overlap between the two weight distributions. By age 4, over 20% of the low birth-weight twins were larger than the average high birth-weight twins.Compared to singletons, the twins' size deficit was greatest at birth but there was a marked recovery in the first six months, followed by only gradual changes th.
Pre-transplant immune factors may be associated with BK polyomavirus reactivation in kidney transplant recipients

BK polyomavirus (BKPyV) reactivation in kidney transplant recipients can lead to allograft damage and loss. The elements of the adaptive immune system that are permissive of reactivation and responsible for viral control remain incompletely described. We performed a prospective study evaluating BKPyV-specific T-cell response, humoral response and overall T-cell phenotype beginning pre-transplant through one year post-transplant in 28 patients at two centers. We performed an exploratory analysis of risk factors for the development of viremia and viruria as well as compared the immune response to BKPyV in these groups and those who remained BK negative. 6 patients developed viruria and 3 developed viremia. BKPyV-specific CD8+ T-cells increased post-transplant in viremic and viruric but not BK negative patients. BKPyV-specific CD4+ T-cells increased in viremic, but not viruric or BK negative patients. Anti-BKPyV IgG antibodies increased in viruric and viremic patients but remained unchanged in BK negative patients. Viremic patients had a greater proportion of CD8+ effector cells pre-transplant and at 12 months post-transplant. Viremic patients had fewer CD4+ effector memory cells at 3 months post-transplant. Exploratory analysis demonstrated lower CD4 and higher total CD8 proportions, higher anti-BKPyV antibody titers and the cause of renal failure were associated BKPyV reactivation. In conclusion, low CD4, high CD8 and increased effector CD8 cells were found pre-transplant in patients who became viremic, a phenotype associated with immune senescence. This pre-transplant T-cell senescence phenotype could potentially be used to identify patients at increased risk of BKPyV reactivation.
Outsourcing in-service education in Japan : Challenges and issues

This paper examines a four-month program of pedagogical training for Japanese Teachers of English (JTEs) in Canada based on a yardstick provided for communicative language teaching (CLT) in-service education and training (INSET) programs for teachers who teach English as a foreign language (EFL). In particular, with the purpose of determining the overall effectiveness of the Canadian pedagogical program and offering recommendations for future ones, this study examines three dimensions of the four-month program: the program planning dimension, the program execution dimension, and the cultural dimension. Three paradigms are used to compare cultural and educational differences between Japan and Canada: the interpretation-based versus transmission-based culture paradigm (Wedell, 2003), the collectionist versus integrationist educational paradigm (Holliday, 1994a), and the routine/uncertain culture versus non-routine/certain culture paradigm (Sato, 2002). This qualitative study indicates that while the program meets almost all of the recommended criteria, especially in the execution dimension, a more thorough knowledge of Japanese educational culture and a re-examination of some assumptions on which the program is constructed may be useful to program planners and trainers in helping JTEs overcome barriers to incorporating CLT practices into their lessons.
H∞ controller design for a class of switched linear discrete-time system with polytopic uncertainties

In this article, a new parameter-dependent stability criterion for switched linear discrete-time systems with polytopic uncertainties is provided to correct an error occurring in previous work, and the parameter-dependent idea is extended to ℓ2 gain analysis problem. Particularly, a less conservative result is proposed by introducing additional slack matrices. Furthermore, the ℋ∞ control problem is investigated. Due to the online calculation characteristic of parameter-dependent controller, a controller structure with less computation cost is of interest. Aside from the controller with the same form as in some existing results involving matrix multiplication and inversion operators, another simple structure of controller formulated by a convex combination of a set of matrices is proposed, which can reduce the online computation cost significantly. A numerical example and results of simulation performed on the model of two-mass-spring mechanical system are provided to illustrate the theoretical findings within this article.
Indinavir Population Pharmacokinetics in Plasma and Cerebrospinal Fluid

ABSTRACT Plasma and cerebrospinal fluid (CSF) indinavir concentrations were measured by high-performance liquid chromatography. The median concentration in plasma exceeded that in CSF 10-fold. The modeled CSF curve was flat at 155 nM, and the estimated ratio of the areas under the CSF and plasma concentration-time curves was 6%. We conclude that CSF indinavir concentrations are lower than levels in plasma but exceed the clinical 95% inhibitory concentration range.