Miracle-dz/UniFAR-FTUs huggingface dataset:
Clinical laboratory comparison of lysis-centrifugation and BACTEC radiometric blood culture techniques

The lysis-centrifugation technique (ISOLATOR; E. I. du Pont de Nemours & Co., Wilmington, Del.) and the radiometric blood culture technique (BACTEC; Johnston Laboratories, Inc., Cockeysville, Md.) were compared on 1,000 blood cultures. A total of 16 ml of blood was distributed: 8 ml into an ISOLATOR 7.5 microbial tube and 4 ml each into BACTEC 7C and 8B bottles. The concentrate from the ISOLATOR tubes was inoculated under a laminar-flow hood onto two sheep blood agar plates (one incubated in CO2 and one incubated anaerobically), one chocolate agar plate, and one brain heart infusion agar plate. Of 91 blood specimens obtained that yielded clinically significant organisms, 52 were positive by both systems, 27 were positive by the ISOLATOR system only, and 12 were positive by the BACTEC system only. From the positive blood specimens, 97 clinically significant organisms were isolated: 57 by both systems, 27 by the ISOLATOR system only, and 13 by the BACTEC system only. Of the 57 organisms detected by both systems, 28 were detected simultaneously, 13 were detected earlier by the ISOLATOR system, and 16 were detected earlier by the BACTEC system. Isolated colonies were obtained earlier by the ISOLATOR system in 40 cases and by the BACTEC system in 5 cases. Organisms determined to be contaminants by thorough chart review were isolated from 138 ISOLATOR tubes. In 98 instances, these were represented by one colony of Staphylococcus epidermidis, alpha-hemolytic streptococci, or diphtheroids. The ability to determine CFU per milliliter with the ISOLATOR system did not help differentiate clinically significant organisms from contaminants.
Molecular cloning of a GABA receptor subunit from Laodelphax striatella (Fallén) and patch clamp analysis of the homo‐oligomeric receptors expressed in a Drosophila cell line

A cDNA encoding a γ‐aminobutyric acid (GABA) receptor subunit was cloned from the small brown planthopper Laodelphax striatella. The L. striatella GABA receptor subunit was found to have high amino acid sequence similarity to the bd‐type splice variant of the Drosophila GABA receptor Rdl subunit and several other GABA receptor subunits, with identities of over 70%. The cDNA was inserted into the expression vector pAc5.1‐lac‐Hygro. Clonal cell lines stably expressing homo‐oligomeric L. striatella GABA receptors were generated by transfecting the vector into D.mel‐2 cells. Expression of functional GABA receptors in the cell lines was demonstrated by whole‐cell patch clamp recordings. GABA induced inward currents with an EC50 value of 29 µM and a Hill coefficient of 1.7. The GABA‐evoked responses reversed close to the Nernst equilibrium potential for chloride ions. The amplitudes of agonist‐induced currents were found to be in the order muscimol (100 µM) ≥ GABA (100 µM) > isoguvacine (100 µM) > cis‐4‐aminocrotonic acid (CACA) (100 µM) > 5‐(4‐piperidyl)‐3‐isoxazolol (4‐PIOL) (1 mM). Antagonists such as fipronil (100 nM), 4′‐ethynyl‐4‐n‐propylbicycloorthobenzoate (EBOB) (100 nM), dieldrin (100 nM) and SR95531 (gabazine) (1 µM) suppressed GABA‐induced currents. The functional expression of a GABA receptor from an agricultural pest presents a unique opportunity to discover new molecules active at this important target site.
Alprazolam and Exposure Alone and Combined in Panic Disorder with Agoraphobia

A cross-national randomised trial of alprazolam for chronic panic disorder with agoraphobia was run. Compared with previous trials it had three new features: an exposure therapy contrast group, a six-month treatment-free follow-up, and a low rate of early placebo drop-outs (‘non-evaluables’). The dose of alprazolam was high (5 mg/day). The 154 patients had eight weeks of: alprazolam and exposure (combined treatment); or alprazolam and relaxation (a psychological placebo); or placebo and exposure; or placebo and relaxation (double placebo). Drug taper was from weeks 8 to 16. Follow-up was to week 43. Results were similar at both sites. Treatment integrity was good. All four treatment groups, including double placebo, improved well on panic throughout. On non-panic measures, by the end of treatment, both alprazolam and exposure were effective, but exposure had twice the effect size of alprazolam. During taper and follow-up, gains after alprazolam were lost, while gains after exposure were maintained. Combining alprazolam with exposure marginally enhanced gains during treatment, but impaired improvement thereafter. The new features put previous trials in a fresh light. By the end of treatment, though gains on alprazolam were largely as in previous studies, on phobias and disability they were half those with exposure. Relapse was usual after alprazolam was stopped, whereas gains persisted to six-month follow-up after exposure ceased. Panic improved as much with placebo as with alprazolam or exposure.
Molecular detection of p16 promoter methylation in the serum of recurrent colorectal cancer patients

We previously proved that p16 promoter methylation present in the tumors of colorectal cancer patients can be detected in the serum of those same patients using methylation‐specific PCR (MSP). To seek the possibility that this technique could be applied to the monitoring of cancer recurrence, we examined the p16 methylation using MSP. We detected tumor DNA in the serum of 31 of 45 (69%) patients with recurrent colorectal cancer. No methylation was found in serum DNA of 50 patients with colorectal cancers whose corresponding tumor DNA had no methylation in p16 promoter. These results suggested that MSP might be a sensitive and useful method to detect recurrent colorectal cancer in serum. © 2003 Wiley‐Liss, Inc.
Integration of human papillomavirus type-16 and type-18 is a very early event in cervical carcinogenesis

Aim: Human papillomavirus (HPV) integration is a critical event in cervical carcinogenesis. The aim of this study was to explore the physical status of HPV-16 and HPV-18 during the progression of cervical precancerous lesions. Methods: A series of 101 HPV-16 or HPV-18 positive cervical neoplasms (32 cervical intraepithelial neoplasia (CIN) cases and 69 cervical carcinoma (CC) cases) were evaluated. The physical status of both types of HPV was assessed from paraffin-embedded formaldehyde-fixed surgical specimens by real-time PCR. Results: For HPV-16, integrated DNA was observed in 5 (83.3%) of 6 CIN I cases, 10 (90.9%) of 11 CIN II/III cases, 29 (82.9%) of 35 FIGO (International Federation of Gynecology and Obstetrics) stage I CC cases and 16 (94.1%) of 17 FIGO stages II∼IV CC cases. For HPV-18, integrated DNA was observed in 3 (50%) of 6 CIN I cases, 5 (55.6%) of 9 CIN II/III cases, 9 (64.3%) of 14 FIGO stage I CC cases, and 1 (33.3%) of 3 FIGO stages II∼IV CC cases. The mixed form of HPV DNA was the most prevalent physical state in HPV-16. There was no significant difference between the physical state of HPV-16 and HPV-18 DNA with regard to the various grades of cervical lesions. Conclusions: These data imply that integration of HPV-16 and HPV-18 DNA into the host genome occurs in the very early stage of cervical neoplastic progression. These early events may play an initiating role in the malignant transformation of HPV-16- and HPV-18-related low-grade lesions into high-grade dysplasia and invasive carcinoma.
Role of GenoType® Mycobacterium Common Mycobacteria/Additional Species Assay for Rapid Differentiation Between Mycobacterium tuberculosis Complex and Different Species of Non-Tuberculous Mycobacteria

Background: Mycobacterium tuberculosis complex (MTBC) and non-tuberculous mycobacteria (NTM) may or may not have same clinical presentations, but the treatment regimens are always different. Laboratory differentiation between MTBC and NTM by routine methods are time consuming and cumbersome to perform. We have evaluated the role of GenoType® Mycobacterium common mycobacteria/additional species (CM/AS) assay for differentiation between MTBC and different species of NTM in clinical isolates from tuberculosis (TB) cases. Materials and Methods: A total of 1080 clinical specimens were collected from January 2010 to June 2012. Diagnosis was performed by Ziehl-Neelsen staining followed by culture in BacT/ALERT 3D system (bioMerieux, France). A total of 219 culture positive clinical isolates (BacT/ALERT® MP cultures) were selected for differentiation by p-nitrobenzoic acid (PNB) sensitivity test as and BIO-LINE SD Ag MPT64 TB test considering as the gold standard test. Final identification and differentiation between MTBC and different species of NTM were further confirmed by GenoType® Mycobacterium CM/AS assay (Hain Lifescience, Nehren, Germany). Results: Out of 219 BacT/ALERT® MP culture positive isolates tested by PNB as 153 MTBC (69.9%) and by GenoType® Mycobacterium CM/AS assay as 159 (72.6%) MTBC and remaining 60 (27.4%) were considered as NTM species. The GenoType® Mycobacterium CM/AS assay was proved 99.3% sensitive and 98.3% specific for rapid differentiation of MTBC and NTM. The most common NTM species were; Mycobacterium fortuitum 20 (33.3%) among rapid growing mycobacteria and Mycobacterium intracellulare 11 (18.3%) among slow growing mycobacteria. Conclusion: The GenoType® Mycobacterium assay makes rapid and accurate identification of NTM species as compared with different phenotypic and molecular diagnostic tool and helps in management of infections caused by different mycobacteria.
Sulfatase-1 overexpression indicates poor prognosis in urothelial carcinoma of the urinary bladder and upper tract

Urothelial carcinoma (UC), arising from the urothelium of the urinary tract, can occur in the upper (UTUC) and the urinary bladder (UBUC). A representative molecular aberration for UC characteristics and prognosis remains unclear. Data mining of Gene Expression Omnibus focusing on UBUC, we identified sulfatase-1 (SULF1) upregulation is associated with UC progression. SULF1 controls the sulfation status of heparan sulfate proteoglycans and plays a role in tumor growth and metastasis, while its role is unexplored in UC. To first elucidate the clinical significance of SULF1 transcript expression, real-time quantitative RT-PCR was performed in a pilot study of 24 UTUC and 24 UBUC fresh samples. We identified that increased SULF1 transcript abundance was associated with higher primary tumor (pT) status. By testing SULF1 immunoexpression in independent UTUC and UBUC cohorts consisted of 340 and 295 cases, respectively, high SULF1 expression was significantly associated with advanced pT and nodal status, higher histological grade and presence of vascular invasion in both UTUC and UBUC. In multivariate survival analyses, high SULF1 expression was independently associated with worse DSS (UTUC hazard ratio [HR] = 3.574, P < 0.001; UBUC HR = 2.523, P = 0.011) and MeFS (UTUC HR = 3.233, P < 0.001; UBUC HR = 1.851, P = 0.021). Furthermore, depletion of SULF1 expression by using RNA interference leaded to impaired cell proliferative, migratory, and invasive abilities in vitro. In addition, we further confirmed oncogenic role of SULF1 with gain-of function experiments. In conclusion, our findings implicate the oncogenic role of SULF1 expression in UC, suggesting SULF1 as a prognostic and therapeutic target of UC.
Entrepreneurial Risk and Diversification through Trade

Demand shocks have been shown to be an important determinant of firm sales' variation across different markets. The key insight of this paper is that, in presence of incomplete financial markets, firms can reduce demand risk through geographical diversification. I first develop a general equilibrium trade model with monopolistic competition, characterized by stochastic demand and risk-averse entrepreneurs, who exploit the imperfect correlation of demand across countries to lower the variance of their total sales. Despite its complexity, I provide a novel analytical characterization of the firms problem and show that both entry and trade flows to a market are affected by its risk-return profile, which in turn depends on the multilateral covariance of the country's demand with all other markets. Moreover, I show that welfare gains from trade can be significantly higher than the gains predicted by standard models which neglect firm level risk. After a trade liberalization, risk-averse firms boost exports to countries that offer better diversification benefits. Hence, in these markets foreign competition becomes stronger, lowering the price level more. Therefore, countries with better risk-return profiles gain more from international trade, while riskier markets reap lower gains. I then use data on Portuguese firm-level international trade flows, from 1995 to 2005, to provide evidence that exporters behave in a way consistent with my model's predictions. Finally, policy counterfactuals reveal that, for the median country in the sample, the risk diversification channel increases welfare gains from trade by 15% relative to traditional models with risk neutrality.
How appropriate are global models for long-run poverty assessment?

The major shift in global food prices between 2008 and 201 has left the world with a significantly higher level of food prices and therefore it has also raised an important question of the long-run impacts of high food prices on global poverty. While short run-impacts have been assessed satisfactorily by a number of researchers who found higher food prices to be generally raising poverty, the long-run impacts are less clear for numerous difficulties that stand in the way of such analyses. These obstacles are mainly represented by our current lack of understanding how households respond to change in relative prices and incomes by changing their consumption, savings, household business production and labor force participation. While most of the difficulties in assessing long-run price impacts on households could be approximated by a global or national CGE model, it is currently not clear how well the use of a representative agent and the imperfectly estimated behavioral parameters approximate the behavior of actual households and what are the implications of the discrepancies between the representative and actual household on poverty assessment. We support our assessment by three recent panel survey data sets for three low-income countries (Pakistan 2008–2010, Uganda 2005–2010, and Vietnam 2006–2008), all of which span the time of the recent food price crisis. In each of the surveys, we observe the actual decisions taken by households during the crisis which include detailed changes in household consumption, farm production, hours worked and the changes in the overall household incomes. Strictly following a non-parametric approach, we look at various sub-samples of the surveyed populations in order to measure the impacts of various price and income variables on households. For example, to measure the welfare impact of consumption substitution without the effects of income change, by considering a sub-sample of population which experienced little change in real.
Increasing Retention of New Graduate Nurses: A Systematic Review of Interventions by Healthcare Organizations

With the nursing shortage and the high incidence of turnover among new graduate nurses (NGNs) within the first year of employment, there is an increased need to investigate the effectiveness of retention strategies aimed at retraining NGNs. The purpose of this articled was to determine which organizational strategies increase the retention rates of NGNs. A systematic review of the research literature was conducted to examine published studies that focused on a retention strategy implemented to influence NGNs to stay in their place of employment. Data were extracted, and the quality of each study was assessed. Sixteen published studies were included in this review. Of these, 13 did not use true experimental study designs. Based on the studies with the strongest designs, the highest retention rates were associated with retention strategies that used a preceptor program model that focused on the NGN as well as a program length of 3 to 6 months. Evidence for the effectiveness of implementation strategies is limited; however, it is apparent from all the studies reviewed that implementing a retention strategy is effective for increasing retention rates of NGNs.
Assessment of 1p/19q status by fluorescence in situ hybridization assay: A comparative study in oligodendroglial, mixed oligoastrocytic and astrocytic tumors.

BACKGROUND Due to overlapping histomorphological features, difference in clinical behavior and treatment response, establishing potential molecular markers to facilitate diagnosis of various genetic subtypes of diffuse gliomas is essential. AIM To analyze 1p/19q status in diffuse gliomas and correlate it with epidermal growth factor receptor (EGFR) and p53 protein expression. MATERIALS AND METHODS 1p/19q status in 43 cases was evaluated by fluorescence in situ hybridization assay. Glial fibrillary acidic protein (GFAP), EGFR and p53 were assessed by immunohistochemistry. RESULTS Glial fibrillary acidic protein immunopositivity was observed in oligodendrogliomas within minigemistocytes and gliofibrillary oligodendrocytes as perinuclear homogenous blobs. It also highlighted the intermingled reactive astrocytes. Astrocytomas and the astrocytic component of oligoastrocytomas showed a diffuse fibrillary type of staining. 1p and/or 19q loss was seen in 65% (13/20) of oligodendrogliomas and 66.6% (5/9) of mixed oligoastrocytomas. There was one case each of pediatric oligodendroglioma and mixed oligoastrocytoma, none of which showed 1p/19q loss. None of the astrocytomas including two pediatric cases showed this alteration (P < 0.05). p53 was expressed in 57.1% of astrocytomas (8/14), 33% of mixed oligoastrocytomas (3/9) and 10% of oligodendrogliomas (2/20). Majority of oligodendrogliomas (85%; 17/20) and oligodendroglial areas in mixed oligoastrocytomas (77.7%; 7/9) showed a membranous lace-like immunopositivity with EGFR. In contrast, all astrocytomas (Grade II and III) were EGFR negative. CONCLUSION Loss of 1p/19q is strongly associated with oligodendroglial phenotype, while astrocytic tumors are more likely to show p53 over-expression. p53 expression and 1p/19q status appear to be mutually exclusive.
Characterization of the Genus Bifidobacterium by Automated Ribotyping and 16S rRNA Gene Sequences

In order to characterize the genus Bifidobacterium, ribopatterns and approximately 500 bp (Escherichia coli positions 27 to 520) of 16S rRNA gene sequences of 28 type strains and 64 reference strains of the genus Bifidobacterium were determined. Ribopatterns obtained from Bifidobacterium strains were divided into nine clusters (clusters I–IX) with a similarity of 60%. Cluster V, containing 17 species, was further subdivided into 22 subclusters with a similarity of 90%. In the genus Bifidobacterium, four groups were shown according to Miyake et al.: (i) the Bifidobacterium longum infantis‐longum‐suis type group, (ii) the B. catenulatum‐pseudocatenulatum group, (iii) the B. gallinarum‐saeculare‐pullorum group, and (iv) the B. coryneforme‐indicum group, which showed higher than 97% similarity of the 16S rRNA gene sequences in each group. Using ribotyping analysis, unique ribopatterns were obtained from these species, and they could be separated by cluster analysis. Ribopatterns of six B. adolescentis strains were separated into different clusters, and also showed diversity in 16S rRNA gene sequences. B. adolescentis consisted of heterogeneous strains. The nine strains of B. pseudolongum subsp. pseudolongum were divided into five subclusters. Each type strain of B. pseudolongum subsp. pseudolongum and B. pseudolongum subsp. globosum and two intermediate groups, which were suggested by Yaeshima et al., consisted of individual clusters. B. animalis subsp. animalis and B. animalis subsp. lactis could not be separated by ribotyping using EcoRI. We conclude that ribotyping is able to provide another characteristic of Bifidobacterium strains in addition to 16S rRNA gene sequence phylogenetic analysis, and this information suggests that ribotyping analysis is a useful tool for the characterization of Bifidobacterium species in combination with other techniques for taxonomic characterization.
Attenuated UV Radiation Alters Volatile Profile in Cabernet Sauvignon Grapes under Field Conditions

This study aimed to explore the effect of attenuated UV radiation around grape clusters on the volatile profile of Cabernet Sauvignon grapes (Vitis vinifera L. cv.) under field conditions. Grape bunches were wrapped with two types of polyester films that cut off 89% (film A) and 99% (film B) invisible sunlight of less than 380 nm wavelength, respectively. Solar UV radiation reaching the grape berry surface was largely attenuated, and an increase in the concentrations of amino acid-derived benzenoid volatiles and fatty acid-derived esters was observed in the ripening grapes. Meanwhile, the attenuated UV radiation significantly reduced the concentrations of fatty acid-derived aldehydes and alcohols and isoprenoid-derived norisoprenoids. No significant impact was observed for terpenes. In most case, these positive or negative effects were stage-dependent. Reducing UV radiation from the onset of veraison to grape harvest, compared to the other stages, caused a larger alteration in the grape volatile profile. Partial Least Square Discriminant Analysis (PLS-DA) revealed that (E)-2-hexenal, 4-methyl benzaldehyde, 2-butoxyethyl acetate, (E)-2-heptenal, styrene, α-phenylethanol, and (Z)-3-hexen-1-ol acetate were affected most significantly by the attenuated UV radiation.
Opportunities for improving the use of an ecosystem services approach in land-use planning: experiences of professionals in Florida

This research explores the use of an Ecosystem Services (ES) approach as a land-use planning tool, its perceived benefits and challenges, and opportunities for improvement. For this study, in-depth interviews were used with 21 professionals who had been involved in projects in which ecosystem services were valuated, quantified, and/ or described in Florida. Three categories of obstacles are identified that hinder the integration of an ES approach in land-use planning. These categories are 1) method complexity; 2) communication of results; and, 3) support for ES efforts. Based on the interviewees' experiences, options to address these challenges are proposed.
Pathological role of osteoclast costimulation in arthritis-induced bone loss

Abnormal T cell immune responses induce aberrant expression of inflammatory cytokines such as TNF-α, leading to osteoclastmediated bone erosion and osteoporosis in autoimmune arthritis. However, the mechanism underlying enhanced osteoclastogenesis in arthritis is not completely understood. Here we show that TNF-α contributes to inflammatory bone loss by enhancing the osteoclastogenic potential of osteoclast precursor cells through inducing paired Ig-like receptor-A (PIR-A), a costimulatory receptor for receptor activator of NF-κB (RANK). In fact, bone erosion and osteoporosis, but not inflammation, caused by aberrant TNF-α expression were ameliorated in mice deficient in Fc receptor common γ subunit or β2-microglobulin, in which the expression of PIR-As and PIR-A ligands is impaired, respectively. These results establish the pathological role of costimulatory receptors for RANK in bone loss in arthritis and may provide a molecular basis for the future therapy of inflammatory diseases.