Miracle-dz/UniFAR-FTUs huggingface dataset:
The relationship of 3' vitamin D receptor haplotypes to urinary supersaturation of calcium oxalate salts and to age at onset and familial prevalence of nephrolithiasis.

BACKGROUND Idiopathic hypercalciuria (IHc) and idiopathic hypocitraturia are frequently associated with calcium nephrolithiasis. We investigated the relationship of vitamin D receptor (VDR) polymorphisms (BsmI, TaqI and FokI) to urinary supersaturation of calcium oxalate salts in recurrent calcium oxalate stone formers with IHc and the clinical relevance of this relationship. METHODS The study included 110 Caucasian stone formers with IHc and 127 unrelated healthy controls without history of nephrolithiasis. Age at onset of nephrolithiasis, familial history score (FHS) and the ion activity product of calcium oxalate salts in urine (AP(CaOx)) were tabulated. BsmI, TaqI and FokI VDR polymorphisms were evaluated in all participants. RESULTS Patients and controls were classified as homozygous (bbTT and BBtt) or heterozygous in relation to BsmI and TaqI polymorphisms. Compared with BBtt patients, bbTT homozygous stone formers showed lower citrate excretion (1.91+/-0.89 vs 3.46+/-1.39 mmol/24 h, P = 0.004) and higher AP(CaOx) (2.02+/-0.51 vs 1.53+/-0.53, P = 0.006). Among controls, there were similar differences in citrate excretion and AP(CaOx) between the two groups, but they were not statistically significant. Compared with BBtt, bbTT patients showed lower mean age at onset of nephrolithiasis (29.7+/-12.1 vs 38.1+/-12.7 years, P = 0.008) and higher values of FHS (2.45+/-1.9 vs 0.83+/-0.7, P = 0.006). Similar results were obtained for individual BsmI and TaqI alleles. The analysis of FokI alleles was not informative. CONCLUSIONS Recurrent calcium oxalate stone formers with IHc and the bT VDR haplotype have more aggressive kidney stone diseases as indicated by a higher familial incidence and lower mean age at onset. This clinical severity is associated with the higher urinary supersaturation of calcium oxalate salts and abnormalities of renal citrate handling.
Programmed ribosomal frameshifting generates the Escherichia coli DNA polymerase III gamma subunit from within the tau subunit reading frame.

The Escherichia coli dnaX gene encodes both the tau and gamma subunits of DNA polymerase III holoenzyme in one reading frame. The 71.1 kDa tau and the shorter gamma share N-terminal sequences. Mutagenesis of a potential ribosomal frameshift signal located at codons 428-430 without changing the amino acid sequence of the tau product, eliminated detectable synthesis of the gamma subunit, suggesting that the reading frame is shifted at that sequence and gamma is terminated by a nonsense codon located in the -1 frame 3 nucleotides downstream of the signal. This seems to be the first known case of a frameshift which is used, along with the termination codon in the -1 frame, to terminate a peptide within a reading frame. [Mutagenesis of a dibasic peptide (lys-lys) at codons 498-499, the site at which a tau'-'LacZ fusion protein was cleaved in vitro (1) had no effect on gamma formation in vivo, suggesting that cleavage observed in vitro is not the mechanism of gamma formation in vivo. Images
Industrial policies for avoiding the middle-income trap: a new structural economics perspective*

Abstract Economic development is a process of structural transformation with continuous technological innovation and industrial upgrading, which increases labor productivity, and accompanied improvements in infrastructure and institution, which reduces transaction costs. The middle-income trap is a result of a middle-income country’s failure to have a faster labor productivity growth through technological innovation and industrial upgrading than high-income countries. Industrial policy is essential for the government of a middle-income country to prioritize the use of its limited resources to facilitate technological innovation and industrial upgrading by overcoming inherent externality and coordination issues in structural transformation. The industries in a middle-income country may be classified into five different types, depending on their distance to the global technology frontier: catching-up industries, leading-edge industries, comparative advantage-losing industries, short innovation cycle industries, and comparative advantage-defying strategic industries. Industrial policy should be designed accordingly.
Properties of Monolithic Silica Columns for HPLC

Monolithic silica columns and their use in high peak-capacity HPLC separations are reviewed. Monolithic silica columns can potentially provide higher overall performance than particle-packed columns based on the variable external porosity and variable through-pore size/skeleton size ratios. The high permeability of monolithic silica columns resulting from the high porosity is shown to be advantageous to generate large numbers of theoretical plates with long capillary columns. High permeability together with the high stability of the network structures of silica allows their use in high-speed separations required for a second-dimension column in two dimensional HPLC. Disadvantages of monolithic silica columns are also described.
A multiplex PCR mini-barcode assay to identify processed shark products in the global trade

Protecting sharks from overexploitation has become global priority after widespread population declines have occurred. Tracking catches and trade on a species-specific basis has proven challenging, in part due to difficulties in identifying processed shark products such as fins, meat, and liver oil. This has hindered efforts to implement regulations aimed at promoting sustainable use of commercially important species and protection of imperiled species. Genetic approaches to identify shark products exist but are typically based on sequencing or amplifying large DNA regions and may fail to work on heavily processed products in which DNA is degraded. Here, we describe a novel multiplex PCR mini-barcode assay based on two short fragments of the cytochrome oxidase I (COI) gene. This assay can identify to species all sharks currently listed on the Convention of International Trade of Endangered Species (CITES) and most shark species present in the international trade. It achieves species diagnosis based on a single PCR and one to two downstream DNA sequencing reactions. The assay is capable of identifying highly processed shark products including fins, cooked shark fin soup, and skin-care products containing liver oil. This is a straightforward and reliable identification method for data collection and enforcement of regulations implemented for certain species at all governance levels.
A simple taurocholate-induced model of severe acute pancreatitis in rats.

AIM To investigate gut barrier damage and intestinal bacteria translocation in severe acute pancreatitis (SAP), a simple rat model of SAP was induced and studied. METHODS Pancreatitis was induced by uniformly distributed injection of 3.8% Na taurocholate (1 mL/kg) beneath the pancreatic capsule. Rats in the control group were injected with normal saline in the identical location. RESULTS Serum amylase, plasma endotoxin, intestinal permeability, and pancreatitis pathology scores were all markedly higher in the pancreatitis group than in the control group (P < 0.01). The bacterial infection rate was significantly higher in the SAP group than in the control group (P < 0.01), observed in parallel by both bacterial culture and real-time polymerase chain reaction. Acute damage of the pancreas was observed histologically in SAP rats, showing interstitial edema, leukocyte infiltration, acinar cell necrosis and hemorrhage. The microstructure of the intestinal mucosa of SAP rats appeared to be destroyed with loose, shortened microvilli and rupture of the intercellular junction, as shown by electron microscopy. CONCLUSION Significant gut barrier damage and intestinal bacterial translocation were definitely observed with few potential study confounders in this SAP rat model, suggesting that it may be an appropriate animal model for study of gut barrier damage and bacterial translocation in SAP.
Predictors of quality of life for long-term cancer survivors with preexisting disabling conditions.

PURPOSE/OBJECTIVES To explore whether measures of resources, barriers, and health-promoting behaviors would add significantly to the prediction of health-related quality of life among survivors with disabilities that occurred prior to their cancer diagnosis once contextual factors were controlled for. DESIGN A descriptive correlational study. SETTING Adult cancer survivors with preexisting disabling conditions who had completed active treatment were recruited from throughout the United States. SAMPLE Most of the 145 respondents were breast cancer survivors with preexisting neuromuscular conditions such as polio and multiple sclerosis. The average time since cancer diagnosis was nine years. METHODS Respondents completed a mailed survey. MAIN RESEARCH VARIABLES Health-promoting behaviors, self-efficacy, barriers to health promotion, social support, functional limitations, cancer-related variables, depression, and quality of life. FINDINGS The sample reported poorer physical well-being than other cancer survivors without preexisting disabling conditions. Health-promoting behaviors and psychosocial factors, such as depressive symptoms and self-efficacy, added significantly to the prediction of physical, social, emotional, and functional components of health-related quality of life after contextual factors entered the equations. CONCLUSIONS The findings underscore the importance of providing this population with the means to promote their health to the greatest extent possible, given the multiple threats to their health status. IMPLICATIONS FOR NURSING Nurses may be able to help survivors with preexisting disabling conditions reduce the negative influence of poorer health status and functional limitations on quality of life by providing interventions that reduce depression and build perceived ability to engage in health-promoting behaviors.
Human and Swine Hosts Share Vancomycin-Resistant Enterococcus faecium CC17 and CC5 and Enterococcus faecalis CC2 Clonal Clusters Harboring Tn1546 on Indistinguishable Plasmids

ABSTRACT VRE isolates from pigs (n = 29) and healthy persons (n = 12) recovered during wide surveillance studies performed in Portugal, Denmark, Spain, Switzerland, and the United States (1995 to 2008) were compared with outbreak/prevalent VRE clinical strains (n = 190; 23 countries; 1986 to 2009). Thirty clonally related Enterococcus faecium clonal complex 5 (CC5) isolates (17 sequence type 6 [ST6], 6 ST5, 5 ST185, 1 ST147, and 1 ST493) were obtained from feces of swine and healthy humans. This collection included isolates widespread among pigs of European Union (EU) countries since the mid-1990s. Each ST comprised isolates showing similar pulsed-field gel electrophoresis (PFGE) patterns (≤6 bands difference; >82% similarity). Some CC5 PFGE subtype strains from swine were indistinguishable from hospital vancomycin-resistant enterococci (VRE) causing infections. A truncated variant of Tn1546 (encoding resistance to vancomycin) and tcrB (coding for resistance to copper) were consistently located on 150- to 190-kb plasmids (reppLG1). E. faecium CC17 (ST132) isolates from pig manure and two clinical samples showed identical PFGE profiles and contained a 60-kb mosaic plasmid (repInc18 plus reppRUM) carrying diverse Tn1546-IS1216 variants. The only Enterococcus faecalis isolate obtained from pigs (CC2-ST6) corresponded to a multidrug-resistant clone widely disseminated in hospitals in Italy, Portugal, and Spain, and both animal and human isolates harbored an indistinguishable 100-kb mosaic plasmid (reppRE25 plus reppCF10) containing the whole Tn1546 backbone. The results indicate a current intra- and international spread of E. faecium and E. faecalis clones and their plasmids among swine and humans.
Importance of Rub and Rinse in Use of Multipurpose Contact Lens Solution

Purpose. The introduction of contact lens multipurpose disinfection solution (MPDS) that can be used in conjunction with a “no-rub” regimen has simplified lens care requirements. Once adhered to a surface, microorganisms can become less susceptible to disinfection. The aim of the study was to evaluate the effect of various regimen steps on the efficacy of MPDS when used with silicone hydrogel and conventional lenses. Methods. Commercially available MPDSs containing polyquad or polyhexamethylene biguanide were used in conjunction with two types of silicone hydrogel (lotrafilcon B and galyfilcon A) and one type of conventional soft contact lenses (etafilcon A). Challenge microorganisms included Staphylococcus aureus ATCC 6538, Pseudomonas aeruginosa ATCC 9027, Serratia marcescens ATCC 13880, Fusarium solani ATCC 36031, Candida albicans ATCC 10231, or Acanthamoeba polyphaga Ros. The effect of regimen steps “rub and rinse,” “rinse-only,” or “no rub and no rinse” on the disinfection efficacy of test MPDSs was examined using the ISO 14729 Regimen Test procedure. Results. Overall, the greatest efficacy of MPDSs was observed when “rub and rinse” was performed before disinfection with each of the microorganisms tested, regardless of lens type. “No rub and no rinse” steps resulted in a greater load of microorganisms remaining on lenses compared with the other regimens (p < 0.05). When “rinse-only” was performed before disinfection, the MPDS containing polyquad performed generally better (p < 0.05) than MPDSs containing polyhexamethylene biguanide against bacteria. Significantly, less microorganisms were recovered from galyfilcon A than from other lenses (p < 0.05) when MPDSs were used with “rinse-only” step. Conclusions. This study has demonstrated that “rub and rinse” is the most effective regimen and should be recommended in conjunction with all multipurpose lens care solutions and all contact lens types, particularly with silicone hydrogel lenses.
Political attitudes and trade union membership in the Nordic countries

Do political attitudes influence the likelihood of employees being members of a trade union, and to what extent is this the case in the Nordic countries with their high aggregate levels of membership? In this article, I address these questions using European Social Survey data from 2012. The results show that left-wing political attitudes have the most impact on the likelihood of trade union membership in Sweden and to a lesser extent in Denmark. In Norway and Finland, there is no statistically significant impact. I argue that the impact of left-wing political attitudes on unionization in Sweden and Denmark reflects a conception among employees that trade unions are normative organizations.
Empirical Estimation of Elasticities and Their Use

Applied research in economics contains many papers that empirically estimate an elasticity (or a set of elasticities) and uses the estimate(s) for policy analyses. These estimates are typically based on an estimated relationship (such as a demand function). If the specific functional form used in the estimation yields a constant elasticity in the form of an estimated coefficient alone, that coefficient represents the elasticity. If, on the other hand, the formula for the elasticity involves other regressors and coefficients, empirical estimation of the elasticity is based on applying the calculus-based definition of elasticity to this expression. However, a di erential change in a variable is only an approximation to the actual discrete change for small changes, and the approximation can may be quite poor when large changes are considered. This paper advocates using the actual percentage change in the predicted value of the dependent variable when the variable with respect to which the elasticity is estimated changes by one percent. The example provided shows that the difference can be substantial when elasticities are estimated this way. An empirical illustration that uses and replicates a published study to calculate price elasticities in various ways. The study then considers the impact of large changes in prices to show that simply evaluating estimated functions gives substantially different results compared to using estimated elasticities. It is better to rely on estimated relationships and predict changes as finite changes in the predicted values. The approximation errors when elasticities are used can be substantial.
Veratryl alcohol oxidation by lignin peroxidase.

Lignin peroxidase (LiP) from the white rot fungus Phanerochaete chrysosporium catalyzes the H2O2-dependent oxidation of veratryl alcohol (VA), a secondary metabolite of the fungus, to veratryl aldehyde (VAD). The oxidation of VA does not seem to be simply one-electron oxidation by LiP compound I (LiPI) to its cation radical (VA.+) and the second by LiP compound II (LiPII) to VAD. Moreover, the rate constant for LiPI reduction by VA (3 x 10(5) M-1 s-1) is certainly sufficient, but the rate constant for LiPII reduction by VA (5.0 +/- 0.2 s-1) is insufficient to account for the turnover rate of LiP (8 +/- 0.4 s-1) at pH 4.5. Oxalate was found to decrease the turnover rate of LiP to 5 s-1, but it had no effect on the rate constants for LiP with H2O2 or LiPI and LiPII, the latter formed by reduction of LiPI with ferrocyanide, with VA. However, when LiPII was formed by reduction of LiPI with VA, an oxalate-sensitive burst phase was observed during its reduction with VA. This was explained by the presence of LiPII, formed by reduction of LiPI with VA, in two different states, one that reacted faster with VA than the other. Activity during the burst was sensitive to preincubation of LiPI with VA, decaying with a half-life of 0.54 s, and was possibly due to an unstable intermediate complex of VA. + and LiPII. This was supported by an anomalous, oxalate-sensitive, LiPII visible absorption spectrum observed during steady state oxidation of VA. The first order rate constant for the burst phase was 8.3 +/- 0.2 s-1, fast enough to account for the steady state turnover rate of LiP at pH 4.5. Thus, it was concluded that oxalate decreased the turnover of LiP by reacting with VA. + bound to LiPII. The VA. + concentration measured by electron spin resonance spectroscopy (ESR) was 2.2 microM at steady state (10 microM LiP, 250 microM H2O2, and 2 mM VA) and increased to 8.9 microM when measured after the reaction was acid quenched. Therefore, we assumed the presence of two states of VA. + bound to LiPII, one ESR-active and one ESR-silent. The ESR-silent species, which could be detected after acid quenching, would be responsible for the burst phase. Both of the VA. + species disappeared in the presence of 5 mM oxalate. The ESR-active species reached a maximum (3.5 microM) at 0.5 mM VA under steady state. From these studies, a mechanism for VA oxidation by LiP is proposed in which a complex of LiPII and VA. + reacts with an additional molecule of VA, leading to veratryl aldehyde formation.
Lamellar Keratectomy Using an Automated Microkeratome

Purpose: To evaluate the effectiveness of treating anterior corneal pathology by performing a superficial lamellar keratectomy with an automated microkeratome. Methods: Retrospective chart review of 10 eyes (8 patients) seen in a subspecialty referral practice for anterior segment disease. With the use of an automated microkeratome, a lamellar flap was created, which was then surgically excised. Results: Ten eyes of eight patients were followed for a mean of 5.4 months (range, 4 to 10 months). Subjective visual acuity and/or sensation of ocular irritation improved in 10 of 10 eyes. Mean improvement in Snellen best-corrected visual acuity was 1.8 lines (range, −1 to +3 lines). One patient lost 1 line of Snellen acuity due to progression of a posterior subcapsular cataract. Mean change in spherical equivalent was +0.5 diopters (range, −1.60 to +4.25 diopters), and mean improvement in corneal clarity (1 to 4 scale) was 1.8. Mean preoperative pachymetry was 589.0 μm (range, 507 to 741 μm). Mean postoperative pachymetry was 461.3 μm (range, 370 to 564 μm). Recurrence of pathology (band keratopathy and Salzmann’s nodular degeneration) occurred in two patients. In one patient, immunohistochemical staining of corneal tissue from the lamellar dissection confirmed the diagnosis of herpes simplex virus type 1 stromal keratitis, improving the course of postoperative care. Conclusion: Lamellar keratectomy with the use of an automated microkeratome is a safe and effective method for removing superficial anterior corneal opacities. For selected cases, it offers specific advantages over other surgical modalities. In particular, this procedure may induce far less hyperopic shift than would the equivalent amount of tissue removal by performing excimer laser phototherapeutic keratectomy.
The Pseudomonas fluorescens AlgG Protein, but Not Its Mannuronan C-5-Epimerase Activity, Is Needed for Alginate Polymer Formation

ABSTRACT Bacterial alginates are produced as 1-4-linked β-d-mannuronan, followed by epimerization of some of the mannuronic acid residues to α-l-guluronic acid. Here we report the isolation of four different epimerization-defective point mutants of the periplasmic Pseudomonas fluorescens mannuronan C-5-epimerase AlgG. All mutations affected amino acids conserved among AlgG-epimerases and were clustered in a part of the enzyme also sharing some sequence similarity to a group of secreted epimerases previously reported in Azotobacter vinelandii. An algG-deletion mutant was constructed and found to produce predominantly a dimer containing a 4-deoxy-l-erythro-hex-4-enepyranosyluronate residue at the nonreducing end and a mannuronic acid residue at the reducing end. The production of this dimer is the result of the activity of an alginate lyase, AlgL, whose in vivo activity is much more limited in the presence of AlgG. A strain expressing both an epimerase-defective (point mutation) and a wild-type epimerase was constructed and shown to produce two types of alginate molecules: one class being pure mannuronan and the other having the wild-type content of guluronic acid residues. This formation of two distinct classes of polymers in a genetically pure cell line can be explained by assuming that AlgG is part of a periplasmic protein complex.
The Myocardial Performance Index in Patients with Aortic Stenosis

Objectives: This study was designed to determine the effect of chronic afterload on a Doppler‐derived myocardial performance index (MPI) combining both systolic and diastolic left ventricular dysfunction. Methods: The study included 36 patients with a diagnosis of aortic stenosis and 36 normal subjects. Doppler‐derived myocardial performance index (MPI), defined as the sum of the isovolumic contraction time and isovolumic relaxation time divided by ejection time, was measured from the mitral valve inflow and left ventricular outflow velocity patterns and was then related to the aortic valve area, valve gradient, and other echocardiographic variables. Results: The values of the Doppler‐derived MPI in the patients with aortic stenosis were significantly higher than those in the controls (0.54 ± 0.20 vs 0.38 ± 0.04, respectively; P < 0.001). Transmitral deceleration time and the E/A ratio (r = 0.47 and r = 0.35, respectively; P < 0.05) were significant univariate correlates, and mitral deceleration time was the only significant correlate of MPI. However the index did not correlate with aortic valve area, peak and mean valve gradients, left ventricular mass, or age. Conclusions: Doppler‐derived MPI reflects severity of global left ventricular dysfunction in patients with aortic stenosis and may be of clinical value in this patient population.