Miracle-dz/UniFAR-FTUs huggingface dataset:
Grass genomes.

For the most part, studies of grass genome structure have been limited to the generation of whole-genome genetic maps or the fine structure and sequence analysis of single genes or gene clusters. We have investigated large contiguous segments of the genomes of maize, sorghum, and rice, primarily focusing on intergenic spaces. Our data indicate that much (>50%) of the maize genome is composed of interspersed repetitive DNAs, primarily nested retrotransposons that insert between genes. These retroelements are less abundant in smaller genome plants, including rice and sorghum. Although 5- to 200-kb blocks of methylated, presumably heterochromatic, retrotransposons flank most maize genes, rice and sorghum genes are often adjacent. Similar genes are commonly found in the same relative chromosomal locations and orientations in each of these three species, although there are numerous exceptions to this collinearity (i.e., rearrangements) that can be detected at the levels of both the recombinational map and cloned DNA. Evolutionarily conserved sequences are largely confined to genes and their regulatory elements. Our results indicate that a knowledge of grass genome structure will be a useful tool for gene discovery and isolation, but the general rules and biological significance of grass genome organization remain to be determined. Moreover, the nature and frequency of exceptions to the general patterns of grass genome structure and collinearity are still largely unknown and will require extensive further investigation.
Trypsin‐immobilized fiber core in syringe needle for highly efficient proteolysis

In this report, a core‐changeable needle enzymatic reactor was developed for highly efficient proteolysis. A piece of enzyme‐immobilized fiber core was inserted into the needle of a syringe pump to form a flow‐through bioreactor. The novel in‐needle bioreactor could be regenerated by changing its fiber core. The feasibility and performance of the unique bioreactor were demonstrated by the tryptic digestion of BSA and lysozyme and the digestion time was significantly reduced to less than 5 s. The digests were identified by MALDI‐TOF MS with sequence coverages comparable to those obtained by the conventional in‐solution tryptic digestion. The present in‐needle bioreactor provides a promising platform for the high‐throughput protein identification.
[Circulating leptin and ghrelin in patients with chronic obstructive pulmonary disease].

OBJECTIVE To investigate the potential roles of leptin and ghrelin in malnutrition in patients with chronic obstructive pulmonary disease (COPD). METHODS Plasma leptin, total ghrelin and active ghrelin, TNF-alpha and IL-6 levels were determined in 53 patients with COPD and 26 control subjects. Body compositions were assessed by bioelectrical impedance analysis. RESULTS Plasma leptin levels were significantly lower in underweight patients than those in normal weight patients and in healthy controls [2.6 (2.0 - 4.4) vs. 6.1 (5.1 - 7.8) vs. 4.8 (3.3 - 6.1) ng/L]. The leptin level was associated positively with fat mass (r = 0.662, P = 0.000) and TNF-alpha (r = 0.431, P = 0.001) in the patients. By a stepwise multiple regression analysis, fat mass, TNF-alpha, presence of COPD, smoking and sex were found to affect leptin level (R(2) = 0.635). Both plasma total ghrelin levels and active ghrelin levels were significantly higher in underweight patients than those in normal weight patients and in healthy controls [total ghrelin: 1090 (860 - 2838) vs. 765 (651 - 941) vs. 844 (676 - 1045) ng/L; active ghrelin: 63 (50 - 97) vs. 47 (41 - 56) vs. 54 (41 - 60) ng/L]. Plasma total ghrelin and active ghrelin were associated negatively with BMI respectively (total ghrelin: r = -0.517, P = 0.000; active ghrelin: r = -0.417, P = 0.002). CONCLUSIONS Plasma leptin levels were decreased, while plasma total ghrelin and active ghrelin levels were elevated in underweight patients with COPD, and the levels were associated with nutritional parameters. The plasma levels of leptin and ghrelin may be a compensatory mechanism in malnutritional status of COPD. After adjustment for nutritional parameters, leptin levels were elevated in COPD patients and correlated to TNF-alpha. The result suggests that leptin may play a role in systemic inflammation of COPD.
Diagnostic Accuracy of Fecal Immunochemical Test in Patients at Increased Risk for Colorectal Cancer: A Meta-analysis

Importance The potential role of the fecal immunochemical test (FIT) for screening patients at increased risk for colorectal cancer (CRC) has not yet been elucidated. Objective To assess the diagnostic accuracy of FIT for CRC or advanced neoplasia (AN) in asymptomatic patients at above-average risk. Data Sources MEDLINE, EMBASE, Cochrane Library, and gray literature sources through August 2016. Study Selection Diagnostic studies evaluating the accuracy of FIT for CRC or AN in patients with a personal or familial history of CRC using colonoscopy as the reference standard. Data Extraction and Synthesis Two authors (A.K. and P.P.) independently extracted data and evaluated study quality using the Quality Assessment of Diagnostic Accuracy Studies–2 tool, and evaluated the quality of the body of evidence by means of GRADE (Grading of Recommendations Assessment, Development, and Evaluation). Hierarchical models were used to synthesize available evidence. Main Outcomes and Measures The primary outcome was the diagnostic performance of FIT for detecting CRC or AN. Results We included 12 studies (6204 participants). Seven studies were deemed at high or unclear risk of bias. The average sensitivity of FIT for CRC was 93% (95% CI, 53%-99%), and the average specificity was 91% (95% CI, 89%-92%), yielding a positive likelihood ratio (LR+) of 10.30 (CI 7.7-13.9) and a negative likelihood ratio (LR−) of 0.08 (95% CI, 0.01-0.75) (GRADE: very low). The average sensitivity of FIT for AN was 48% (95% CI, 39%-57%); and the average specificity was 93% (95% CI, 91%-94%), yielding an LR+ of 6.55 (95% CI, 5.0-8.5) and an LR− of 0.57 (95% CI, 0.48-0.67) (GRADE: very low). Subgroup analyses indicated that FIT cutoff values between 15- and 25-&mgr;g/g feces provided the best combination of sensitivity and specificity for the diagnosis of CRC (93% and 94%, respectively). Quantitative and 1-sample FIT showed adequate test performance, but data on other FIT brands and multiple samples were insufficient. Conclusions and Relevance The FIT has high overall diagnostic accuracy for CRC but moderate accuracy for AN in patients at above-average personal or familial risk. Heterogeneity and wide confidence intervals limit the trustworthiness of our findings.
Antibody response to low-molecular-weight antigens of Aspergillus fumigatus in allergic bronchopulmonary aspergillosis

Sera from patients with allergic bronchopulmonary aspergillosis (ABPA) or aspergilloma and normal sera were analyzed for specific antibodies by Western (immuno-) blotting with Aspergillus fumigatus antigens transferred electrophoretically onto polyvinylidene difluoride membranes. Western blot analysis demonstrated consistent reactivity of low-molecular-weight A. fumigatus antigens against ABPA sera but not against uncomplicated aspergilloma or normal sera. None of these low-molecular-weight components had any lectin-binding activity. Sera from patients with aspergilloma, however, frequently reacted with high-molecular-weight components of A. fumigatus. The majority of these high-molecular-weight antigenic components demonstrated concanavalin A-binding activity. The low-molecular-weight bands were discernible in Western blots with sera from all ABPA patients irrespective of disease activities, such as relapse, flare, or treatment. Antibodies detected by methods such as immunodiffusion or enzyme-linked immunosorbent assays demonstrated total antibody responses to most or all antigenic components, while Western blots demonstrated the reactivities of the individual components with the specific antibodies. Western blot analysis thus provided more information for immunodiagnosis of ABPA than other methods, especially when only crude antigens were available.
New Synthetic Glutathione Derivatives with Increased Antiviral Activities

A series of glutathione (GSH) derivatives with aliphatic chains of different lengths, coupled by peptides bound to the α-NH2 group of Glu, were synthesized. When added to several cell lines, the C6 (n-hexanoyl), C8 (n-octanoyl) and C12 (n-dodecanoyl) derivatives were toxic while the C2 (n-ethanoyl) and C4 (n-butanoyl) derivatives were not. Preliminary experiments were performed to investigate the potential antiviral activity of the C2 and C4 derivatives compared to GSH. The C4 derivative was the most potent and fully characterized. GSH-C4 is a poor substrate of GSH metabolizing enzymes; once oxidized by disulphide-bound formation, C4 is slowly reduced by GSH-reductase. GSH-C4 completely abrogated Sendai virus replication at 7.5 mM with an EC50 of 3.6 mM, compared to 7.5 mM for GSH. GSH-C4 completely inhibited herpes simplex virus (HSV-1) virus production in Vero cells at 10 mM, while the same dose of GSH caused only a 2.5 log10 reduction. Furthermore, the GSH-C4 treatment (7.5 mM) was able to markedly reduce the cytopathic effect of HSV-1 in Vero cells. Thus, GSH derivatives with increased hydrophobic properties are more effective antiviral agents against Sendai and HSV-1 viruses than GSH, suggesting their usefulness in antiviral therapy.
Bronchodilator effects of intravenous olprinone, a phosphodiesterase 3 inhibitor, with and without aminophylline in asthmatic patients.

AIMS There is no evidence demonstrating the clinical usefulness of phosphodiesterase (PDE) inhibitors in the treatment of asthma, although PDE3 and 4 inhibitors have received much attention for the treatment of bronchial asthma. We compared the bronchodilator effects of intravenously administered olprinone, a selective PDE3 inhibitor, and aminophylline, a nonselective PDE inhibitor, both alone and concomitantly. METHODS In 12 patients with mild stable asthma, we compared the acute bronchodilator effects of the following two drugs, alone and together using a double-blind crossover design: intravenous administration of olprinone, 30 micro g min-1; aminophylline, 2.25 mg min-1; and olprinone plus aminophylline over a total period of 150 min. RESULTS Mean maximal increase (95% confidence interval) in the FEV1 was 7.8% (2.4, 13.2), 17.1% (10.0, 24.2), 16.6% (11.2, 22.0), and 1.0% (-1.1, 3.1) during infusion of aminophylline, olprinone, aminophylline and olprinone, and saline, respectively. The magnitude of bronchodilatation produced by olprinone was greater than that by aminophylline. The combination of aminophylline and olprinone did not produce any greater bronchodilatation than olprinone alone. Olprinone alone or in combination with aminophylline lowered diastolic blood pressure, and increased heart rate. CONCLUSIONS These results suggest that the intravenous administration of PDE3 inhibitors exhibits a bronchodilatory effect. There are no additive or synergistic effects of administration of olprinone and aminophylline at the same time.
Depression symptom prevalence and demographic risk factors among U.S. women during the first 2 years postpartum.

OBJECTIVE To examine differences in depression symptom rates and severity and factors associated with depression ratings. PARTICIPANTS Cross-sectional sample of 1,359 American women who had delivered a single, live infant within the previous 2 years. DESIGN Data were collected using the Edinburgh Postnatal Depression Scale online to screen for depression symptoms as part of Listening to Mothers, a national survey sponsored by Childbirth Connection of New York City and administered by Harris Interactive between May and June 2002. RESULTS Evidence of continued mild and moderate-to-severe depression symptom rates throughout the first 2 years postpartum was found. Age, income, education, and employment had significant negative associations with depression symptom severity, and parity had a significant positive association with depression symptom severity. Race was not associated with depression symptom severity. CONCLUSIONS Long-term screening for childbearing women is justified based on the study findings. The ease in survey administration suggests potential for online depression screening by health care providers and researchers. Furthermore, risk factors identified from this large-scale national survey, specifically young maternal age, low income, low education, not being employed full time, and multiparity, merit evaluation in clinical practice and future research.
p16 expression as a surrogate marker for HPV‐related oropharyngeal carcinoma: A guide for interpretative relevance and consistency

Recent studies of oropharyngeal carcinoma have reported remarkable correlation between integrated human papillomavirus (HPV) viral detection and p16 protein overexpression in tumor cells. These findings led to calls for the substitution of p16 expression for the more demanding HPV testing in clinical practice. The rationale for such practice is largely driven by the simplicity, low cost, and the feasibility of the immunohistochemical (IHC) analysis. There are, however, several caveats that need to be fully considered. These include the subjective nature of IHC evaluation, the variable mechanisms of p16 expression in head and neck squamous cell carcinoma, and the lack of scoring and interpretive criteria. This perspective addresses the conceptual and practical issues associated with the p16 expression analysis and provides a broad outline for its application and evaluation in patients with oropharyngeal carcinoma. © 2011 Wiley Periodicals, Inc. Head Neck, 2012
Parosteal lymphoblastic lymphoma. A human counterpart of Abelson virus‐induced lymphosarcoma of mice

A 16‐year‐old girl with an unusual presentation of lymphoblastic lymphoma is described. The tumor originated as a paraspinal mass accompanied by lytic bone lesions in the pelvic bones. Neither an anterior mediastinal mass nor lymphadenopathy were noted. This pattern of disease is strikingly reminiscent of lymphomas induced in mice by the Abelson leukemia virus. This patient's lymphoma cells, unlike the usual lymphoblastic lymphoma cells, did not bear classical T‐lymphocyte surface markers. A permanent cell line was derived from her tumor. Sparse amounts of cytoplasmic μ‐immunoglobulin heavy chains were present in most of these cells, suggesting that the tumor originated in pre‐B‐lymphocytes. The phenotype of the cultured tumors cells is similar to Abelson virus‐transformed murine bone marrow cells. Tumor cells of this phenotype may originate in the bone marrow and spread subsequently in and around the involved bones. This pattern of disease is distinctly different from that of T‐cell lymphoblastic lymphoma, which typically presents in the mediastinum and cervical lymph nodes, and involves the bone marrow only as a late manifestation of advanced disease.
Benzoyl-coenzyme-A 3-monooxygenase, a flavin-dependent hydroxylase. Purification, some properties and its role in aerobic benzoate oxidation via gentisate in a denitrifying bacterium.

A new variant of aerobic benzoate degradation has been found in a denitrifying bacterium in which benzoyl-CoA is the first intermediate [Altenschmidt, U. , Oswald, B. , Steiner, E. , Herrmann, H. & Fuchs, G. (1993) New aerobic benzoate oxidation pathway via benzoyl-coenzyme A and 3-hydroxybenzoyl-coenzyme A in a denitrifying Pseudomonas sp, J. Bacteriol. 175, 4851-4858)]. The initial reaction is catalyzed by benzoate-CoA ligase (AMP-forming), converting benzoate into benzoyl-CoA. The next step is 3-hydroxylation of benzoyl-CoA to 3-hydroxybenzoyl-CoA catalyzed by a flavin-nucleotide-dependent monooxygenase, benzoyl-CoA 3-monooxygenase. This novel enzyme has been purified and studied. It is specific for NADPH and requires the presence of a flavin nucleotide for activity; both FAD or FMN function similarly well as cofactor. Only benzoyl-CoA, but not benzoate, is hydroxylated. The protein is a monomer of M(r) 65,000 and is induced when cells are grown aerobically with benzoate. 3-Hydroxybenzoyl-CoA is further hydroxylated para to the hydroxyl group affording 2,5-dihydroxybenzoate (gentisate). This reaction requires another monooxygenase, 3-hydroxybenzoyl-CoA 6-monooxygenase, which is unspecific specific with respect to the pyridine nucleotide. Cells contain a second 6-monooxygenase activity which acts on free 3-hydroxybenzoate. Based on these and other data, the outlines of the new aerobic benzoate pathway have been deduced. The proposed intermediates are benzoyl-CoA, 3-hydroxybenzoyl-CoA, gentisate, maleylpyruvate, fumarylpyruvate and fumarate plus pyruvate.
STEALing Lab Support in Digital Forensics Education

Digital forensics is still an emerging field of study where the best methods for gaining subject matter expertise are still unclear. This paper presents a worked example of pairing traditional learning methods with a highly adaptive laboratory environment in a university setting. The example environment and pedagogy presented here represent a unique collaborative relationship between academia, industry and government parties. Several learning styles have been employed at the university level to provide opportunities for conventional students to excel, meanwhile training and topical exploration opportunities exist for regional industry and government parties.
No Functional Involvement of 5‐Hydroxytryptamine1A Receptors in Nitric Oxide‐Dependent Dilatation Caused by Serotonin in the Human Forearm Vascular Bed

Summary The vascular effects of serotonin (5-hydroxytryptamine, 5-HT) are complex and heterogeneous. In human forearm, we showed that low doses of 5-HT cause marked but transient vasodilatation followed by a persistent vasodilator response. In in vitro and in animal experiments, 5-HT induced release of nitric oxide (NO) through stimulation of endothelial 5-HT,-like receptors. In the present study, we investigated involvement of the “NO pathway” and possible involvement of the 5-HT1A receptor subtype in 5-HT-induced persistent vasodilator response. In 8 healthy volunteers, we infused 5-HT (0.1, 0.3, and 1 ng/kg/min) and the selective 5-HT1A receptor agonist flesinoxan (15, 45, and 150 ng/kg/min) intraarterially (i.a.) with NG-monomethyl-L-arginine (L-NMMA 30 (μ/kg/min) or saline. Forearm blood flow (FBF) was measured by automated R-wave-triggered venous occlusion plethysmography. Forearm vascular resistance (FVR) was derived from simultaneously recorded i.a. blood pressure (BP) and FBF. 5-HT dose-dependently decreased FVR (p < 0.001). The persistent vasodilator response to 5-HT appears to be mediated by NO release, as suggested by its complete abolition by L-NMMA (p < 0.001). Flesinoxan decreased FVR slightly, but only at high doses (p < 0.05). The present findings indicate that 5-HT1A receptors are not functionally involved in 5-HT-mediated vasodilatation in human forearm.
p53 and K-ras mutations in pancreatic juice samples from patients with chronic pancreatitis.

BACKGROUND Mutations in p53 and ras genes are frequent in pancreatic carcinoma. Several ras mutations are consistently detected in the pancreatic juice from patients with chronic pancreatitis. The p53 gene mutations have been detected occasionally in chronic pancreatitis tissue. It was the aim of this study to evaluate the presence and clinical significance of p53 and ras mutations in clinical pancreatic juice samples from patients with chronic pancreatitis. METHODS Pancreatic juice was obtained from 66 patients with chronic pancreatitis and no evidence of pancreatic carcinoma (51 men, 15 women; age 17-86 years [mean 49.6 +/- 12.9]). Patients were followed prospectively for 26 +/- 3 (4-54) months. Detection of p53 gene mutations was by temperature gradient gel electrophoresis (TGGE) and single strand conformation polymorphism (SSCP) for exons 5-8. Analysis of ras mutations was performed by SSCP/polymerase chain reaction, restriction fragment length polymorphism/polymerase chain reaction. All mutations were confirmed by sequencing. RESULTS Five of 66 (7.5%) pancreatic juice samples contained p53 mutations, and ras mutations were detected in 6 cases (9%). Cytology was negative in all cases. No pancreatic carcinoma developed during follow-up and neither cancer cells nor preneoplastic lesions could be detected histologically in resected specimens. Although no correlation between p53 mutations and duration of pancreatitis or drinking habits was found, K-ras mutations correlated with both heavy smoking and severity of the disease. CONCLUSION p53 and ras mutations can be detected in a minority of pancreatic juice samples from patients with chronic pancreatitis in the absence of malignancy.
Using A3 thinking to improve the STAT medication process.

BACKGROUND Although the term STAT conveys a sense of urgency, it is sometimes used to circumvent a system that may be too slow to accomplish tasks in a timely manner. We describe a quality-improvement project undertaken by a US Department of Veterans Affairs (VA) hospital to improve the STAT medication process. METHODS We adapted A3 Thinking, a problem-solving process common in Lean organizations, to our problem. In the discovery phase, a color-coded flow map of the existing process was constructed, and a real-time STAT order was followed in a modified "Go to the Gemba" exercise. In the envisioning phase, the team brainstormed to come up with as many improvement ideas as possible, which were then prioritized based on the anticipated effort and impact. The team then identified initial experiments to be carried out in the experimentation phase; each experiment followed a standard Plan-Do-Study-Act cycle. RESULTS On average, the number of STAT medications ordered per month decreased by 9.5%. The average time from STAT order entry to administration decreased by 21%, and time from medication delivery to administration decreased by 26%. Improvements were also made in technician awareness of STAT medications and nurse notification of STAT medication delivery. CONCLUSIONS Adapting A3 Thinking for process improvement was a low-cost/low-tech option for a VA facility. The A3 Thinking process led to a better understanding of the meaning of STAT across disciplines, and promoted a collaborative culture in which other hospital-wide problems may be addressed in the future.