Miracle-dz/UniFAR-FTUs huggingface dataset:
Polymerase chain reaction detection of nonviable bacterial pathogens

Polymerase chain reaction (PCR) methodologies for detection of pathogens in environmental samples are currently available. However, positive amplification products for any set of primers only signal that the appropriate target nucleic acid sequences were present in the sample. The presence of the amplification products does not imply that the target organisms were viable. Here we show that PCR will detect nonviable cells, as long as intact target nucleic acid sequences are available. In an environmental water sample, nucleic acids degraded quickly and were not detectable by PCR after 3 weeks even when stored at 4 degrees C. However, these data show that there is a window of opportunity for PCR analyses to result in false positives with respect to viable cells. We further show that care must be taken in the way samples are stored for future PCR amplifications and that filter sterilization of media is not acceptable for long-term preservation of samples for PCR.
Carbon gain and water use in pinyon pine-juniper woodlands of northern New Mexico: field versus phytotron chamber measurements.

We compared phytotron chamber- and field-obtained gas exchange parameters from a semiarid pinyon pine-juniper (Pinus edulis Engelm.-Juniperus monosperma (Engelm.) Sarg. ) community in northern New Mexico, an ecosystem where carbon gain could be limited by both water and nitrogen availability. In both species, variations in rates of photosynthesis with xylem pressure potential (Psi) and minimum Psi for positive carbon gain were similar in the field and phytotron chamber studies. Rates of maximum photosynthesis were greater in pinyon pine than in juniper in both the field and phytotron chamber studies. Pinyon pine showed a greater response to increases in Psi than juniper, although juniper was able to continue photosynthetic activity at lower values of Psi than pinyon pine. There were significant differences in instantaneous water use efficiency (WUE) measured in the field and the phytotron chamber, although relative rankings of the species and their responses to Psi were similar. In the field experiments, WUE of N-fertilized plants was marginally greater in pinyon pine than juniper during the wet season, and in both the field and phytotron chamber experiments instantaneous values of WUE were greater in juniper during dry seasons or during drying cycles. However, delta(13)C values suggested that pinyon pine had greater seasonally integrated values of WUE, perhaps because this species ceases stomatal activity during dry seasons. Field data showed significant interactions between N and WUE, as well as between Psi and the degree of response to N, however, there were insufficient data to derive predictive equations because of the limited range of environmental conditions encountered in the field.
Endocytosis of Hepatic Lipase and Lipoprotein Lipase into Rat Liver Hepatocytes in Vivo Is Mediated by the Low Density Lipoprotein Receptor-related Protein*

In isolated cell studies, the internalization and degradation of hepatic lipase (HL) has been linked to its binding to the low density lipoprotein receptor-related protein (LRP). We have utilized the receptor-associated protein (RAP), a universal inhibitor of high affinity ligand binding to LRP, to evaluate the participation of LRP in the endocytosis of HL and lipoprotein lipase (LPL). We isolated a total endosome fraction from rat livers after a 30-min infusion of recombinant RAP, administered as a glutathione S-transferase conjugate (GST-RAP). GST-RAP infusion had no effect on the concentration of HL in liver homogenates, but its concentration in blood plasma increased progressively by 20%, and enrichment over homogenate of HL in endosomes was reduced by 50% as compared with infusion of GST alone. The concentrations of LPL in liver and plasma were 1.4 and 0.5%, respectively, those of HL, but endosomal enrichment of the two enzymes was similar (∼10-fold). GST-RAP infusion had no effect on the concentration of LPL in liver but increased its concentration in blood plasma by 250% and reduced its endosomal enrichment by 95% or greater. GST-RAP infusion also reduced endosomal enrichment of LRP by 40%, but enrichment of several other endocytic receptors was unaffected. Endosomal enrichment of several membrane trafficking proteins associated with the endocytic pathway in hepatocytes was unaffected by GST-RAP with the exception of early endosome endosome antigen 1, which was reduced by 85%. We conclude that HL is partially and LPL almost exclusively taken up into rat hepatocytes after binding to the endocytic receptor LRP.
Evaluation of molecular typing for epidemiological study of Chlamydia trachomatis genital infections

Molecular typing and serotyping were compared for 150 Chlamydia trachomatis strains isolated from genital sources, belonging to 10 different serovars. Because of the general agreement of the two methods, molecular omp1 genotyping was applied to the epidemiological study of C. trachomatis isolates from genital infections in Bordeaux (France), during a 29-month period. The most prevalent omp1 genotypes were E (51.7%), F (17.3%), D (8.8%), and G (8.4%). Restriction enzyme analysis allowed identification of a serovar D variant (Dv), whereas serovar E strains were homogeneous.
A new thrombectomy catheter device (AngioJet) for the disruption of thrombi: An in vitro study.

In this study we examined a new thrombectomy catheter device. Different kinds of in vitro generated thrombi and cadaver thrombi were disrupted in test tubes. The mean disruption rate (and disruption time for 1 g of thrombus) was 225 +/- 65 mg/sec (5 +/- 2 sec) for whole-blood, 117 +/- 60 mg/sec (12 +/- 9 sec) for fibrin, 41 +/- 18 mg/sec (30 +/- 18 sec) for mixed, 70 +/- 42 mg/sec (17 +/- 5 sec) for unorganized, 45 +/- 8 mg/sec (22 +/- 4 sec) for partly, and 5 +/- 1 mg/sec (216 +/- 29 sec) for completely organized cadaver thrombi (P < 0.05). More than 99% of fragmented particles of whole-blood thrombi were 0-12 microm in diameter. The particle size of fibrin, mixed, and cadaver thrombi was similar, with 25%-40% of particles between 0-12 microm, 55%-71% >12-24 microm, and 2%-7% >24 microm. The device may be effectively used in the therapy of massive pulmonary embolism or acute peripheral and coronary artery syndromes when medical thrombolysis is contraindicated and organization of thrombus is absent. Further studies need to be performed to investigate the potential effects of particle microembolization. Cathet. Cardiovasc. Intervent. 47:381-389, 1999.
Adventitial Expression of Recombinant Endothelial Nitric Oxide Synthase Gene Reverses Vasoconstrictor Effect of Endothelin-1

The present study was designed to determine the effect of recombinant endothelial nitric oxide synthase (eNOS) gene expression on reactivity of canine basilar arteries to endothelin-1 (ET-1). Experiments were performed ex vivo. The arteries were exposed (30 minutes at 37°C) to adenoviral vectors encoding eNOS gene (AdCMVeNOS) or β-galactosidase reporter gene (AdCMVβ-Gal). Twenty-four hours after transduction, transgene expression was evident mainly in the vascular adventitia. Rings of control (nontransduced), AdCMVβ-Gal- and AdCMVeNOS-transduced arteries with and without endothelium were suspended for isometric tension recording. Levels of guanosine 3′,5′ -cyclic monophosphate (cGMP) were measured by radioimmunoassay. During contractions to uridine 5′-triphosphate, ET-1 (10−10 to 3×10−9 mol/L) caused further increase in tension in control and AdCMVβ-Gal-transduced arteries. In contrast, ET-1 caused concentration-dependent relaxations of AdCMVeNOS-transduced arteries. The relaxations to ET-1 in AdCMVeNOS-transduced arteries were endothelium-independent They were abolished by NG-nitro-L-argininemethyl ester or by chemical treatment of adventitia with paraformaldehyde before gene transfer. ET-1 (10−9 mol/L) significantly increased intracellular cGMP levels in AdCMVeNOS-transduced arteries without endothelium. In arteries transduced with AdCMVeNOS, higher concentrations (10−9 to 3×10−8 mol/L) of ET-2 also caused relaxations, whereas ET-3 and sarafotoxin, a selective ETB receptor agonist, did not produce any relaxations. The relaxations to ET-1 in AdCMVeNOS-transduced arteries were strongly reduced by BQ-123 (10−7 mol/L), an ETA receptor antagonist, but were not affected by BQ-788 (3×10−7 mol/L), an ETB receptor antagonist These results suggest that genetically modified adventitia can produce nitric oxide and cause relaxations in response to ET-1 via activation of ETA receptors. Our findings support a novel concept that successful transfer and expression of recombinant eNOS gene can lead to a qualitative change in responsiveness to vasoconstrictor substances.
Evidence on the cost-effectiveness of lifelong antiretroviral therapy for prevention of mother-to-child transmission of HIV: implications for resource-limited countries in sub-Saharan Africa

ABSTRACT Introduction: The 2016 World Health Organization (WHO) consolidated guideline recommends lifelong antiretroviral therapy (ART) for all HIV-infected pregnant and breastfeeding women for preventing mother-to-child HIV transmission (PMTCT). Ambiguity remains about the cost-effectiveness of this strategy in resource-limited developing countries. Areas covered: We reviewed model-based studies on the cost-effectiveness of lifelong ART (formerly Option B+) relative to previous WHO guidelines for PMTCT. Our search using PubMed, Medline and Google Scholar for articles on Option B+ resulted in the final inclusion of seven studies published between 2012 and 2016. The Consolidated Health Economic Evaluation Reporting Standards (CHEERS) checklist was used to assess the quality of reporting. Outcomes of interest, which included infant infections averted, maternal quality and length of life, and the Incremental Cost Effectiveness Ratio (ICER), were used in comparing cost-effectiveness. Expert commentary: Despite most model-based studies favouring lifelong ART (Option B+) in terms of its cost-effectiveness in comparison to Options A and B, inclusiveness of the evidence remains weak for generalization. This is largely because setting specificity for providing lifelong ART to all pregnant and breastfeeding women may differ significantly in each setting. Consequently, future cost-effectiveness studies should be robust, setting-specific, and endeavor to assess the willingness and ability to pay of each setting.
Typing of Pseudomonas aeruginosa strains in Norwegian cystic fibrosis patients.

OBJECTIVES Typing of Pseudomonas aeruginosa isolates from Norwegian cystic fibrosis (CF) patients with chronic Pseudomonas lung infection in order to see whether cross-infection might have occurred. METHODS Isolates from 60 patients were collected during the years 1994-98, and typed by pulsed field gel electrophoresis. RESULTS Seventy-one strains were identified. One large cluster of identical strains included 27 patients, and 13 smaller clusters of 2-4 patients were found (26 patients). Seven patients had a strain not shared by other patients (private strains). Harboring the main cluster strain was significantly associated with participation in summer camps and training courses (P = 0.004, chi-squared test). There were no associations with regular admissions to hospital (intravenous antibiotic courses) or smaller social gatherings of short duration. Small clusters and private strains were not associated with any of the risk factors. All strains were sensitive to colistin. The minimal inhibitory concentrations were generally lower in Norwegian P. aeruginosa strains compared with isolates from Danish patients. CONCLUSIONS Our results indicate that cross-infection with P. aeruginosa between cystic fibrosis patients has occurred.
Protective Effects of Rutin on Acute Lung Injury Induced by Oleic Acid in Rats

The purpose of this study was to explore the protective effects of different doses of rutin with the antioxidant and anti-inflammatory properties on acute lung injury (ALI) induced by oleic acid (OA) in rats. Thirty-five Sprague-Dawley male rats were randomly separated into five groups comprising control, rutin 150 mg, OA, rutin 75 mg + OA and rutin 150 mg + OA. In the rutin 75 mg + OA and rutin 150 mg + OA groups, the lung malondialdehyde level (MDA) was significantly lower than that of the OA group. In the rutin 75 mg + OA and and rutin 150 mg + OA groups, the lung GPx (glutathione peroxidase), CAT (catalase) and SOD (superoxide dismutase) activities and GSH (glutathione) levels were significantly higher than those of the OA group, and significantly lower than those of the control group. iNOS expressions in the interstitial parts of the lungs were significantly lower than those of the OA group. The iNOS expression was lower in the 150 mg + OA group compared to the rutin 75 mg + OA group. It was concluded that on the ALI induced by OA, rutin had protective effects through the antioxidant and antiinflammatory properties and that the treatment of rutin as a supportive treatment in ALI was found to be practically useful.
Randomized trial of a whole-system ayurvedic protocol for type 2 diabetes.

CONTEXT Though complementary and alternative medicine (CAM) treatments are popular, evidence to support their application to diabetes care is scarce. Previous CAM diabetes research has generally focused on single modalities, but CAM practitioners more commonly prescribe complex, multimodality interventions. OBJECTIVES The aims of this study were to determine the feasibility and clinical impact of a whole-system, Ayurvedic intervention for newly diagnosed people with type 2 diabetes. DESIGN Patients were randomly assigned to either an experimental or control arm. SETTING Group model health maintenance organization. PARTICIPANTS We recruited 60 adult patients with baseline glycosylated hemoglobin (HbA1c) values between 6.0 and 8.0. INTERVENTION Treatment for the experimental group included exercise, an Ayurvedic diet, meditation instruction, and an Ayurvedic herb supplement (MA 471). Control patients attended standard diabetes education classes with primary care clinician follow-up. MEASUREMENTS Clinical outcomes were assessed at 3 and 6 months and included HbA1c, fasting glucose, lipids, blood pressure, and weight. RESULTS Ninety-two percent of randomized patients completed the study, and there were no significant adverse study-related events. Using analysis of co-variance (ANCOVA), we found no significant differences for clinical outcomes at 6 months between on-study patient groups, though trends favored the Ayurvedic group. When we included a factor measuring how much baseline HbA1c exceeded the mean (6.5%), however, we found statistically significant improvements in the Ayurvedic group for HbA1c (P = .006), fasting glucose (P = .001), total cholesterol (P = .05), low-density lipoprotein (LDL) cholesterol (P = .04), and weight (P = .035). CONCLUSIONS These results suggest that the Ayurvedic intervention may benefit patients with higher baseline HbA1c values, warranting further research.
Membrane Topology of an ATP-gated Ion Channel (P2X Receptor)*

Western blots of Xenopus oocyte membrane preparations showed that the apparent molecular mass of the wild type P2X2 receptor (about 65 kDa) was reduced by pretreatment with endoglycosidase H. Mutagenesis of one or more of three potential asparagines (N182S, N239S, and N298S) followed by Western blots showed that each of the sites was glycosylated in the wild type receptor. Functional channels were formed by receptors lacking any single asparagine, but not by channels mutated in two or three positions. Artificial consensus sequences (N-X-S/T) introduced into the N-terminal region (asparagine at position 9, 16, or 26) were not glycosylated. Asparagines were glycosylated when introduced at the C-terminal end of the first hydrophobic domain (positions 62 and 66) and at the N-terminal end of the second hydrophobic domain (position 324). A protein in which the C terminus of one P2X2 subunit was joined to the N terminus of a second P2X2 subunit (from a concatenated cDNA) had twice the molecular mass of the P2X2 receptor subunit, and formed fully functional channels. The experiments provide direct evidence for the topology originally proposed for the P2X receptor, with intracellular N and C termini, two membrane-spanning domains, and a large extracellular loop.
Validity of the QuickDASH in patients with shoulder-related disorders undergoing surgery.

STUDY DESIGN Validity study. OBJECTIVE To determine the validity of the shortened version of the Disabilities of the Arm, Shoulder and Hand questionnaire (QuickDASH) in comparison to the full DASH in patients undergoing total shoulder arthroplasty (TSA) and rotator cuff repair (RCR). BACKGROUND The QuickDASH is a shorter version of the DASH that may reduce respondent burden while retaining similar measurement properties. METHODS One hundred thirty-two patients undergoing TSA or RCR were assessed at baseline and at 3 and 6 months postoperatively. The patients completed the DASH, American Shoulder and Elbow Surgeons Standardized Shoulder Assessment Form self-report section, and the Western Ontario Rotator Cuff index, and were tested to determine their shoulder range of motion and isometric strength. The differences between scores on the DASH and QuickDASH across the scale range were evaluated using the Bland-Altman technique. Item difficulty, correlations with other patient-reported outcome measures, and physical impairments were used to assess validity. Known group validity was assessed by examining differentiation of work status. Responsiveness was assessed through standardized response means. RESULTS QuickDASH scores were slightly higher than DASH scores, with a mean difference of 1 to 1.3 points for the TSA group and 1 to 3 points for the RCR group tested preoperatively, and at 3 months and 6 months postoperatively, although limits of agreement were wide (ranging from -10 to 13 across all estimates). The QuickDASH items were distributed across the full DASH, when ranked by item difficulty, for both patient groups. The correlation between the QuickDASH and DASH was almost perfect (r>0.92). Correlations between the DASH/QuickDASH and other patient-reported outcome measures ranged from moderate to very large (American Shoulder and Elbow Surgeons Standardized Shoulder Assessment Form self-report section, r=0.47-0.85; Western Ontario Rotator Cuff index, r=0.83-0.91), whereas correlations to impairments were small to moderate. Correlation estimates varied by less than 0.07, depending on whether the DASH or QuickDASH was used, suggesting equivalent construct validity. Both the DASH and QuickDASH discriminated between working and nonworking patients, with similar group differences and statistical significance (P<.01). The QuickDASH and DASH showed similar responsiveness between presurgery and 6-month follow-up (standardized response mean, 1.1 following TSA and 0.8 following RCR). CONCLUSION When substituting the QuickDASH for the full DASH, similar score estimates, discrimination of clinically relevant subgroups, and responsiveness can be expected across patients following TSA and RCR.
Algorithms for Weighted Sums of Squares Decomposition of Non-negative Univariate Polynomials

It is well-known that every non-negative univariate real polynomial can be written as the sum of two polynomial squares with real coefficients. When one allows a weighted sum of finitely many squares instead of a sum of two squares, then one can choose all coefficients in the representation to lie in the field generated by the coefficients of the polynomial. In this article, we describe, analyze and compare both from the theoretical and practical points of view, two algorithms computing such a weighted sums of squares decomposition for univariate polynomials with rational coefficients. The first algorithm, due to the third author relies on real root isolation, quadratic approximations of positive polynomials and square-free decomposition but its complexity was not analyzed. We provide bit complexity estimates, both on runtime and output size of this algorithm. They are exponential in the degree of the input univariate polynomial and linear in the maximum bitsize of its complexity. This analysis is obtained using quantifier elimination and root isolation bounds. The second algorithm, due to Chevillard, Harrison, Joldes and Lauter, relies on complex root isolation and square-free decomposition and has been introduced for certifying positiveness of polynomials in the context of computer arithmetics. Again, its complexity was not analyzed. We provide bit complexity estimates, both on runtime and output size of this algorithm, which are polynomial in the degree of the input polynomial and linear in the maximum bitsize of its complexity. This analysis is obtained using Vieta's formula and root isolation bounds. Finally, we report on our implementations of both algorithms. While the second algorithm is, as expected from the complexity result, more efficient on most of examples, we exhibit families of non-negative polynomials for which the first algorithm is better.
Isolated liver transplantation in infants with end‐stage liver disease due to short bowel syndrome

Infants with short bowel syndrome (SBS) and associated liver failure are often referred for combined liver/intestinal transplantation. We speculated that in some young children, nutritional autonomy would be possible with restoration of normal liver function. Features we believed to predict nutritional autonomy include history of at least 50% enteral tolerance, age less than 2 yr, and no underlying intestinal disease. This report documents our experience with liver transplantation alone in children with liver failure associated with SBS. Twenty‐three children with SBS and end‐stage liver disease, considered to have good prognostic features for eventual full enteral adaptation, underwent isolated liver transplantation. Median age was 11 months (range, 6.5 to 48 months). Median pretransplant weight was 7.4 kg (range, 5.2 to 15 kg). All had growth retardation and advanced liver disease. Bowel length ranged from 25 to 100 cm. Twenty‐three children underwent 28 isolated liver transplants. There were 14 whole livers and 14 partial grafts (five living donors). Seventeen patients are alive at a median follow‐up of 57 months (range, 6 to 121 months). Actuarial patient and graft survival rates at 1 yr are 82% and 75% and at 5 yr are 72% and 60%, respectively. Four deaths resulted from sepsis, all within 4 months of transplantation, and 1 death resulted from progressive liver failure. Two allografts developed chronic rejection; both children were successfully retransplanted with isolated livers. Of 17 surviving patients, three require supplemental intravenous support; the remaining 14 have achieved enteral autonomy, at a median of 3 months (range, 1 to 72 months) after transplantation. Linear growth is maintained and, in many, catch‐up growth is evident. Median change in z score for height is 0.57 (range, −4.47 to 2.68), and median change in z score for weight is 0.42 (range, −1.65 to 3.05). In conclusion, Isolated liver transplantation in children with liver failure as a result of SBS, who have favorable prognostic features for full enteral adaptation, is feasible with satisfactory long‐term survival. Liver Transpl 12:1062–1066, 2006. © 2006 AASLD.