Miracle-dz/UniFAR-FTUs huggingface dataset:
Arabidopsis gene expression changes during cyst nematode parasitism revealed by statistical analyses of microarray expression profiles.

With the availability of microarray technology, the expression profiles of thousands of genes can be monitored simultaneously to help determine the mechanisms of these biological processes. We conducted Affymetrix GeneChip microarray analyses of the Arabidopsis-cyst nematode interaction and employed a statistical procedure to analyze the resultant data, which allowed us to identify significant gene expression changes. Quantitative real-time RT-PCR assays were used to confirm the microarray analyses. The results of the expression profiling revealed 128 genes with altered steady-state mRNA levels following infection by the sugar beet cyst nematode (Heterodera schachtii; BCN), in contrast to only 12 genes that had altered expression following infection by the soybean cyst nematode (H. glycines; SCN). The expression of these 12 genes also changed following infection by BCN, i.e. we did not identify any genes regulated exclusively by SCN. The identification of 116 genes whose expression changes during successful cyst nematode parasitism by BCN suggests a potential involvement of these genes in the infection events starting with successful syncytium induction. Further characterization of these genes will permit the formulation of testable hypotheses to explain successful cyst nematode parasitism.
Survival of ganglion cells which form the retino-retinal projection during optic nerve regeneration in the frog

Abstract During optic nerve regeneration in the frog, axons transiently grow along the opposite optic nerve forming a retino-retinal projection. In the present study, we crushed the left optic nerve in the frog Litoria (Hyla) moorei and later applied horseradish peroxidase (HRP) or diamidino yellow (DY) to the right optic nerve. In one series, retinae were examined 3 days after application of the tracer. The retino-retinal projection was found to be maximal at 5 weeks, fell significantly by 7 weeks, and returned to close-to-normal levels by 24 weeks. In a second series, we applied DY at 5 weeks as before but did not sacrifice the frogs until 7 weeks. Numbers of labeled ganglion cells were not significantly different from those frogs in the first series labeled and examined at 5 weeks. We conclude that ganglion cells giving rise to the retino-retinal projection had not died in appreciable numbers, presumably being sustained by collateral axons in the brain.
Full-dose intraoperative radiotherapy with electrons in breast surgery: broadening the indications.

HYPOTHESIS Although postoperative fractionated radiotherapy (PFR) remains the standard method for conservative treatment of breast carcinomas, widespread experience in the use of full-dose intraoperative radiotherapy with electrons (ELIOT) merits its application in novel clinical situations, although long-term results of ongoing clinical trials have not been fully reported. DESIGN Retrospective case series. SETTING Division of breast surgery in a comprehensive cancer center. PATIENTS From June 1999 to September 2003 ELIOT was used as the sole radiotherapy in 355 patients with unifocal invasive carcinoma who were candidates for breast-conserving surgery and most of whom were participating in an ongoing institutional trial. In a group of patients in whom PFR was not considered safe or feasible (because of previous mantle field irradiation for Hodgkin disease, cosmetic breast augmentation, severe cardiopathy, large hypertrophic scarring from skin burns, vitiligo, and geographic or social obstacles), ELIOT was performed outside of the ongoing trial. RESULTS No particular adverse effects, unusual acute reactions, late sequelae, and local or systemic events were noted in these patients after a mean follow-up of 27.3 months. CONCLUSIONS In appropriated selected patients, when it is critical to perform PFR after breast-conserving therapy, a single dose of ELIOT may be considered to avoid mastectomy, reduce potential treatment toxicity, improve quality of life, and resolve logistic problems. The long-term results of ongoing clinical trials will further delineate patients in whom ELIOT may replace PFR.
Opposite effects of Agrimonia pilosa Ledeb aqueous extracts on blood coagulation function.

BACKGROUND Agrimonia pilosa Ledeb (APL) has showed anticoagulant and antithrombotic activities in some studies, whereas its actual effects on blood coagulation are still unclear. This study was designed to observe the in vitro effects of APL aqueous extracts on blood coagulation, as well as to investigate the underlying mechanisms. METHODS Studies were divided into four groups: 0, 4, 20, and 80 g/L of APL aqueous extracts mixed with plasma or whole blood samples. Clotting time of whole blood, plasma coagulation tests, activities of plasma coagulation factors, plasma calcium ion, platelet aggregation test, and platelet fibrinogen receptor as well as the blood viscosity were measured. RESULTS It was observed that the APL aqueous extracts in 4 g/L significantly prolonged the whole blood clotting time and activated partial thromboplastin time, shortened prothrombin time, decreased activities of coagulation factor VIII, IX and XI, and levels of platelet aggregation and fibrinogen receptor expression. However, coagulation factor VII activity, and blood viscosity were increased after the extracts treatment. And the effects of APL extracts were in a concentration-dependent manner (0-80 g/L). CONCLUSIONS The results suggest that APL aqueous extracts have a total anticoagulant activity, whereas they exhibit opposite effects of greater anticoagulant activity than pro-coagulant activity.
Tertiary endosymbiosis driven genome evolution in dinoflagellate algae.

Dinoflagellates are important aquatic primary producers and cause "red tides. " The most widespread plastid (photosynthetic organelle) in these algae contains the unique accessory pigment peridinin. This plastid putatively originated via a red algal secondary endosymbiosis and has some remarkable features, the most notable being a genome that is reduced to 1-3 gene minicircles with about 14 genes (out of an original 130-200) remaining in the organelle and a nuclear-encoded proteobacterial Form II Rubisco. The "missing" plastid genes are relocated to the nucleus via a massive transfer unequaled in other photosynthetic eukaryotes. The fate of these characters is unknown in a number of dinoflagellates that have replaced the peridinin plastid through tertiary endosymbiosis. We addressed this issue in the fucoxanthin dinoflagellates (e.g., Karenia brevis) that contain a captured haptophyte plastid. Our multiprotein phylogenetic analyses provide robust support for the haptophyte plastid replacement and are consistent with a red algal origin of the chromalveolate plastid. We then generated an expressed sequence tag (EST) database of 5,138 unique genes from K. brevis and searched for nuclear genes of plastid function. The EST data indicate the loss of the ancestral peridinin plastid characters in K. brevis including the transferred plastid genes and Form II Rubisco. These results underline the remarkable ability of dinoflagellates to remodel their genomes through endosymbiosis and the considerable impact of this process on cell evolution.
Keap1 facilitates p62-mediated ubiquitin aggregate clearance via autophagy

The accumulation of ubiquitin-positive protein aggregates has been implicated in the pathogenesis of neurodegenerative diseases, heart disease and diabetes. Emerging evidence indicates that the autophagy lysosomal pathway plays a critical role in the clearance of ubiquitin aggregates, a process that is mediated by the ubiquitin binding protein p62. In addition to binding ubiquitin, p62 also interacts with LC3 and transports ubiquitin conjugates to autophagosomes for degradation. The exact regulatory mechanism of this process is still largely unknown. Here we report the identification of Keap1 as a binding partner for p62 and LC3. Keap1 inhibits Nrf2 by sequestering it in the cytosol and preventing its translocation to the nucleus and activation of genes involved in the oxidative stress response. In this study, we found that Keap1 interacts with p62 and LC3 in a stress-inducible manner, and that Keap1 colocalizes with LC3 and p62 in puromycin-induced ubiquitin aggregates. Moreover, p62 serves as a bridge between Keap1 and ubiquitin aggregates and autophagosomes. Finally, genetic ablation of Keap1 leads to the accumulation of ubiquitin aggregates, increased cytotoxicity of misfolded protein aggregates, and defective activation of autophagy. Therefore, this study assigns a novel positive role of Keap1 in upregulating p62-mediated autophagic clearance of ubiquitin aggregates.
Comparison of gastric lesions in dogs and cats with and without gastric spiral organisms.

OBJECTIVES To determine prevalence of gastric spiral organisms (GSO) in dogs and cats that were clinically normal or had primary gastrointestinal disease and to compare histologic lesions of the stomach in dogs and cats with and without GSO. ANIMALS 21 dogs and 10 cats that were clinically normal and 56 dogs and 33 cats with gastrointestinal disease. DESIGN Case-control study. RESULTS Unevenness of the gastric mucosal surface was detected, using endoscopic techniques in 20 and 25% of clinically normal and abnormal dogs, respectively. On histologic examination, GSO were located on the mucosal surface within or beneath the mucus, in gastric pits, and within glandular lumina in 86 and 90% of clinically normal dogs and cats, respectively, and in 61 and 64% of clinically abnormal dogs and cats, respectively. Prevalence of GSO infection in dogs and cats that were clinically abnormal was not higher than in those that were clinically normal. Infection was detected in stomachs of > 60% of dogs and cats 1 year old or less. Helicobacter pylori was not isolated from any specimen; however, specimens in which GSO were found had positive results on a urease test. CLINICAL IMPLICATIONS Prevalence of GSO infection was high in clinically normal and abnormal dogs and cats, some of which were young. This should be considered during assessment of clinically normal animals with GSO as they can be a potential reservoir for infection in human beings.
Predictors of influenza vaccination uptake among adults with a history of heart attack

Background: Influenza vaccination can reduce morbidity and mortality caused by cardiovascular diseases. This study sought to evaluate influenza vaccination coverage among adults with a history of heart attack and to determine which variables were associated with vaccine uptake. Design: A descriptive study was conducted using individual data from adults aged ≥ 40 years included in the year 2006/7 Spanish Health Survey and comparing subjects with a history of heart attack with those who had not suffered this event. Methods: The number of participants surveyed was 20,060. Subjects were classified as heart attack sufferers if they answered affirmatively to the question: "Has your doctor told you that you have suffered a heart attack? " To assess influenza vaccination status we considered the response to the question, "Did you have a 'flu shot in the latest campaign? ". Independent variables included sociodemographic, health-related, lifestyles and periodic control of cardiovascular risk factors. Results: A total of 716 adults reported having suffered a heart attack. The coverage among sufferers was 67.9% as against 35% for non sufferers. The variables that were significantly associated with a higher likelihood of receiving the vaccine among sufferers were: higher age; male gender, no smoking habit, "Physician visits in the preceding four weeks"; and, "Blood pressure control in the preceding three months". Conclusions: Influenza vaccination coverage among subjects who have suffered a heart attack is below desirable levels. Multiple strategies focused on providers and patients are needed to improve influenza vaccination coverage among these high risk subjects, particularly now with the emerging H1N1 pandemic.
Item and Scale Differential Functioning of the Mini-Mental State Exam Assessed Using the Differential Item and Test Functioning (DFIT) Framework

Objectives:To illustrate the application of the Differential Item and Test Functioning (DFIT) method using English and Spanish versions of the Mini-Mental State Examination (MMSE). Subjects:Study participants were 65 years of age or older and lived in North Manhattan, New York. Of the 1578 study participants who were administered the MMSE 665 completed it in Spanish. Measures:The MMSE contains 20 items that measure the degree of cognitive impairment in the areas of orientation, attention and calculation, registration, recall and language, as well as the ability to follow verbal and written commands. Research Design:After assessing the dimensionality of the MMSE scale, item response theory person and item parameters were estimated separately for the English and Spanish sample using Samejima's 2-parameter graded response model. Then the DFIT framework was used to assess differential item functioning (DIF) and differential test functioning (DTF). Results:Nine items were found to show DIF; these were items that ask the respondent to name the correct season, day of the month, city, state, and 2 nearby streets, recall 3 objects, repeat the phrase no ifs, no ands, no buts, follow the command, “close your eyes,” and the command, “take the paper in your right hand, fold the paper in half with both hands, and put the paper down in your lap. ” At the scale level, however, the MMSE did not show differential functioning. Conclusions:Respondents to the English and Spanish versions of the MMSE are comparable on the basis of scale scores. However, assessments based on individual MMSE items may be misleading.
Delirium superimposed on dementia is associated with prolonged length of stay and poor outcomes in hospitalized older adults.

BACKGROUND Current literature does not identify the significance of underlying cognitive impairment and delirium in older adults during and 30 days following acute care hospitalization. OBJECTIVE Describe the incidence, risk factors, and outcomes associated with incident delirium superimposed on dementia. DESIGN A 24-month prospective cohort study. SETTING Community hospital. PATIENTS A total of 139 older adults (>65 years) with dementia. METHODS This prospective study followed patients daily during hospitalization and 1 month posthospital. Main measures included dementia (Modified Blessed Dementia Rating score, Informant Questionnaire on Cognitive Decline in the Elderly), daily mental status change, dementia stage/severity (Clinical Dementia Rating, Global Deterioration Scale), delirium (Confusion Assessment Method), and delirium severity (Delirium Rating Scale-Revised-98). All statistical analysis was performed using SAS 9.3, and significance was an α level of 0.05. Logistic regression, analysis of covariance, or linear regression was performed controlling for age, gender, and dementia stage. RESULTS The overall incidence of new delirium was 32% (44/139). Those with delirium had a 25% short-term mortality rate, increased length of stay, and poorer function at discharge. At 1 month follow-up, subjects with delirium had greater functional decline. Males were more likely to develop delirium, and for every 1 unit increase in dementia severity (Global Deterioration Scale), subjects were 1.5 times more likely to develop delirium. CONCLUSIONS Delirium prolongs hospitalization for persons with dementia. Thus, interventions to increase early detection of delirium have the potential to decrease the severity and duration of delirium and to prevent unnecessary suffering and costs from the complications of delirium and unnecessary readmissions to the hospital.
Effects of Interdisciplinary Team Care Interventions on General Medical Wards: A Systematic Review.

IMPORTANCE Improving the quality of health care for general medical patients is a priority, but the organization of general medical ward care receives less scrutiny than the management of specific diseases. Optimizing teams' performance improves patient outcomes in other settings, and interdisciplinary practice is a major target for improvement efforts. However, the effect of interdisciplinary team interventions on general medical ward care has not been systematically reviewed. OBJECTIVES To describe the range of objective patient outcomes used in studies of general medical ward interdisciplinary team care, and to evaluate the performance of interdisciplinary interventions against them. EVIDENCE REVIEW We searched EMBASE, MEDLINE, and PsycINFO from January 1, 1998, through December 31, 2013, for interdisciplinary team care interventions in adult general medical wards using an objective patient outcome measure. Reference lists of included articles were also searched. The last search was conducted on January 29, 2014, and the narrative and statistical analysis was conducted through December 1, 2014. Study quality was assessed using the Cochrane Effective Practice and Organization of Care group's tool. FINDINGS Thirty of 6934 articles met the selection criteria. The studies included 66,548 patients, with a mean age of 63 years. Nineteen of 30 (63%) studies reported length of stay, readmission, or mortality rate as their primary outcome, or did not specify the primacy of their outcomes. The most commonly reported objective patient outcomes were length of stay (23 of 30 [77%]), complications of care (10 of 30 [33%]), in-hospital mortality rate (8 of 30 [27%]), and 30-day readmission rate (8 of 30 [27%]). Of 23 interventions, 16 (70%) had no effect on length of stay, 12 of 15 (80%) did not reduce readmissions, and 14 of 15 (93%) did not affect mortality. Five of 10 (50%) interventions reduced complications of care. In an exploratory quantitative analysis, the interventions did not consistently reduce the relative risk of early readmission or early mortality, or the weighted mean difference in length of stay. All studies had a medium or high risk of bias. CONCLUSIONS AND RELEVANCE Current evidence suggests that interdisciplinary team care interventions on general medical wards have little effect on traditional measures of health care quality. Complications of care or preventable adverse events may merit inclusion as quality indicators for general medical wards. Future study should clarify how best to implement interdisciplinary team care interventions and establish quality metrics that are credible to both health care professionals and patients in this setting.
A report on occurrence of Leptonema from Andhra Pradesh

T current investigation was carried out to evaluate oxidative stress serum biomarkers and antioxidant concentrations in pneumonic goat. Thirty goats of different age and sex belonging to private farms in Giza governorate were used in this study. All goats were exposed to complete and comprehensive clinical examination (rectal temperature, pulse and respiratory rates) which revealed significant increase (p≤0.05) in pneumonic goats. The animals were divided into two equal groups: Apparently healthy (15), diseased (15). Blood samples were collected from both groups in clean test tubes to determine various serum biomarkers as enzymatic activates of superoxidase dismutase (SOD), glutathione peroxidase (GPX) in erythrocyte haemolysate, catalase (CAT), vitamin C, vitamin E and selected biochemical parameters as (Albumin (Alb), aspartate aminotransaminase (AST), alanine aminotransaminase (ALT), urea and creatinine). The levels of superoxidase dismutase, glutathione peroxidase were significant higher (p≤0.05) in pneumonic goats than healthy while vitamins C, E were significant decrease (p≤0.05) in pneumonic goats. Serum biochemical analysis revealed significant decrease (p≤0.05) in Albumin with significant increase (p≤0.05) in ALT, AST and creatinine levels in pneumonic goats. It can be concluded that pneumonia served to produce oxidative stress in the goat with increased activities of antioxidant enzymes to facing excessive production of free radicals. For healthier status in small ruminant antioxidant supplementation is very important as supportive treatment in diseased cases and preventive aid in healthy cases. Antioxidants play a critical role in protection of animal from oxidative stress and ensuring rapid curing in diseased cases.
Aspergillus tubingensis: a major filamentous fungus found in the airways of patients with lung disease.

The black Aspergillus group comprises A. niger and 18 other species, which are morphologically indistinguishable. Among this species subset, A. tubingensis, described in less than 30 human cases before 2014, is primarily isolated from ear, nose, and throat samples. Recently, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry has emerged as a powerful technique to identify microbes in diagnostic settings. We applied this method to identify 1,720 filamentous fungi routinely isolated from clinical samples our laboratory over a two-year study period. Accordingly, we found 85 isolates of A. niger, 58 of A. tubingensis, and six other black Aspergillus (4 A. carbonarius and 2 A. japonicus). A. tubingensis was the fifth most frequent mold isolated in our mycology laboratory, primarily isolated from respiratory samples (40/58 isolates). In this study, we mainly aimed to describe the clinical pattern of Aspergillus tubingensisWe analyzed the clinical features of the patients in whom A. tubingensis had been isolated from 40 respiratory samples. Thirty patients suffered from cystic fibrosis, chronic obstructive pulmonary disease or other types of chronic respiratory failure. Strikingly, 20 patients were experiencing respiratory acute exacerbation at the time the sample was collected. Antifungal susceptibility testing of 36 A. tubingensis isolates showed lower amphotericin B MICs (P < 10(-4)) and higher itraconazole and voriconazole MICs (P < 10(-4) and P = . 0331, respectively) compared with 36 A. niger isolates. Further studies are required to better establish the role that this fungus plays in human diseases, especially in the context of cystic fibrosis and chronic pulmonary diseases.
Levels of TGFbeta1 in gingival crevicular fluid during a 21-day experimental model of gingivitis.

OBJECTIVE TGFbeta1 is a multifunctional growth factor with both pro- and anti-inflammatory properties. This study aimed to determine levels of TGFbeta1 in gingival crevicular fluid (GCF), serum and plasma in the early stages of gingival inflammation. DESIGN A 21-day experimental model of gingivitis employing a split mouth design with a soft vinyl splint used to cover test teeth during brushing. SUBJECTS Ten healthy volunteers (mean age 21 years; five males and five females). METHODS GCF and blood (with and without EDTA) was collected on days 0, 7, 14 and 21. GCF volumes were measured on a precalibrated Periotron 8000TM. Clinical indices of gingival inflammation and plaque levels were obtained after GCF sampling. Normal brushing resumed after GCF collection on day 21 and final samples were collected on day 35. TGFbeta1 and alkaline phosphatase (ALP) levels were determined using enhanced chemiluminescent methods. RESULTS Clinical indices and GCF volumes increased at test sites during the 21-day test period. Concentrations of TGFbeta1 and ALP in GCF (test and control), serum and plasma did not change throughout the study (P > 0.3). However, total amounts of TGFbeta1 (pg sample-1) and ALP (mu IU sample-1) in GCF increased at test sites and were significantly higher than baseline values at days 7, 14 and 21 (P < 0.04). Control sites showed no variation in TGFbeta1 or ALP levels throughout the study period (P > 0.35). All parameters at test sites returned to control levels at day 35 (P > 0.3). CONCLUSION The data indicate that GCF TGFbeta1 levels increase early in plaque-induced inflammation. Whether the biological consequence of this site-specific increase is pro- or anti-inflammatory in nature remains to be elucidated.