Miracle-dz/UniFAR-FTUs huggingface dataset:
Investigation of acid phosphatase variants for the synthesis of phosphate monoesters

The major drawback of using phosphatases for transphosphorylation reactions lies in product depletion caused by the natural hydrolytic activity of the enzymes. Variants of PhoC‐Mm from Morganella morganii and NSAP‐Eb from Escherichia blattae were studied for their ability to maintain a high product level in the transphosphorylation of various primary alcohols. A single amino acid exchange delivered phosphatase variant PhoC‐Mm G92D, which was able to catalyze the phosphorylation of primary alcohols without any major hydrolysis of the formed phosphate esters. The mutation mostly improved the affinity of the enzyme for alcohols, while rate constants of transphosphorylation and hydrolysis were decreased, overall resulting in a superior catalytic efficiency in transphosphorylation compared to hydrolysis. The presence of residual substrate alcohol at a given concentration was crucial to suppress phosphate ester hydrolysis. The present work extends the synthetic applicability of phosphatase variants beyond the previously reported nucleosides and allows preparative‐scale production of various primary phosphate esters (yields up to 42%) with high enzyme productivity (TONs up to ∼66,000). Biotechnol. Bioeng. 2017;114: 2187–2195. © 2017 Wiley Periodicals, Inc.
Clonal relationship between infiltrating immunoglobulin G4 (IgG4)‐positive plasma cells in lacrimal glands and circulating IgG4‐positive lymphocytes in Mikulicz's disease

Mikulicz's disease (MD) is gaining acceptance as an immunoglobulin G4 (IgG4)‐related disease characterized by bilateral lacrimal and salivary gland swelling. The aetiology of MD and other IgG4‐related diseases is still unclear. The present work was performed to study the clonality of infiltrating IgG4‐positive plasma cells in lacrimal glands and circulating peripheral blood cells in patients with MD, and compare the clonal relationship between infiltrating and circulating IgG4 positive cells. Total cellular RNA was extracted from the lacrimal glands and peripheral blood in five MD patients. Reverse transcription polymerase chain reaction was performed with primers specific for activation‐induced cytidine deaminase (AID) and for Ig VH and IgG4. Sequences of Ig VH were compared with the structure of Ig VH of the lacrimal glands and the peripheral blood cells. AID was expressed to varying degrees in lacrimal glands of all MD patients. Most IgG4‐positive cells infiltrating lacrimal glands and in peripheral blood were polyclonal, although several clonally related pairs were detected. In one patient, two of the circulating IgG4 VH4‐59 clones shared identical CDR3 sequences with the clones within the lacrimal glands. In conclusion, while most tissue‐infiltrating and circulating IgG4‐positive cells in MD are polyclonal, some clonally related IgG4 positive cells exist between lacrimal gland and peripheral blood, accounting for the clinical features of MD as an IgG4‐related disease involving multiple organs.
Regulation of IL-1β–induced NF-κB by hydroxylases links key hypoxic and inflammatory signaling pathways

Significance Oxygen-sensing hydroxylases are a family of enzymes that control the cellular adaptive response to hypoxia. Hydroxylase inhibitors reduce inflammation in vivo; however, the anti-inflammatory mechanism of action remains unclear. IL-1β is a cytokine that potently promotes inflammation through activation of the transcription factor NF-κB. Here, we demonstrate that hydroxylase inhibition leads to a suppression of IL-1β–induced NF-κB activity and provide insight into the underlying mechanism involved. This work develops our understanding of how hydroxylase inhibition regulates IL-1β–induced inflammation and sheds light on our understanding of the association between hypoxic and inflammatory signaling pathways, underscoring the potential use of hydroxylase inhibitors for the treatment of inflammatory disease. Hypoxia is a prominent feature of chronically inflamed tissues. Oxygen-sensing hydroxylases control transcriptional adaptation to hypoxia through the regulation of hypoxia-inducible factor (HIF) and nuclear factor κB (NF-κB), both of which can regulate the inflammatory response. Furthermore, pharmacologic hydroxylase inhibitors reduce inflammation in multiple animal models. However, the underlying mechanism(s) linking hydroxylase activity to inflammatory signaling remains unclear. IL-1β, a major proinflammatory cytokine that regulates NF-κB, is associated with multiple inflammatory pathologies. We demonstrate that a combination of prolyl hydroxylase 1 and factor inhibiting HIF hydroxylase isoforms regulates IL-1β–induced NF-κB at the level of (or downstream of) the tumor necrosis factor receptor-associated factor 6 complex. Multiple proteins of the distal IL-1β–signaling pathway are subject to hydroxylation and form complexes with either prolyl hydroxylase 1 or factor inhibiting HIF. Thus, we hypothesize that hydroxylases regulate IL-1β signaling and subsequent inflammatory gene expression. Furthermore, hydroxylase inhibition represents a unique approach to the inhibition of IL-1β–dependent inflammatory signaling.
Effects of Silybum marianum on serum hepatitis C virus RNA, alanine aminotransferase levels and well‐being in patients with chronic hepatitis C

Background/Aims: Silybum marianum is a herbal preparation commonly used by subjects with chronic hepatitis C (CHC). The aims of this pilot study were to assess the efficacy and safety of S. marianum on serum hepatitis C virus (HCV) RNA, alanine aminotransferase levels and well‐being in patients with CHC.
Early treatment of multiple sclerosis: A Latin American Experts Meeting

Patients with clinically isolated syndrome (CIS) by definition do not have multiple sclerosis (MS) but are at risk of developing it. While studies show earlier immunomodulating drug use is effective, treatment must consider likely patient prognosis. In this paper we review current diagnosis, prognosis, and treatment literature for patients with CIS within Latin American clinical settings. Latin American MS experts, convened by ACINDES (The Civil Association for Research and Development in Health), reviewed current CIS (and early MS) literature and drew consensus conclusions. Three subgroups addressed separate questionnaires on CIS issues: prognosis, diagnosis, and treatment. MRI can contribute to predicting MS risk in patients with CIS; in Latin America, investigation of haplotype presence associated with CIS would be appropriate. McDonald's criteria and subsequent revisions enable earlier, more accurate MS diagnosis. Type A evidence exists supporting all leading immunomodulating MS drugs for effective treatment of CIS with a high risk of conversion to MS. In conclusion, patients with CIS are usually young, with often-limited symptomatic manifestations, and must be adequately prepared to receive preventive treatment. This consensus review should contribute to the dialogue between physicians and patients. Multiple Sclerosis 2009; 15: S1–S12. http://msj.sagepub. com
Parameters of oxidative stress, DNA damage and DNA repair in type 1 and type 2 diabetes mellitus

Objectives: (i) to determine the extent of oxidative stress and DNA damage and repair using a panel of selected markers in patients with type 1 and type 2 diabetes mellitus (T1DM, T2DM), (ii) to find their possible relationships with diabetes compensation and duration, and finally (iii) to test for the effect of functional polymorphisms in the 8-oxoguanin DNA glycosylase (rs1052133), catalase (rs1001179) and superoxide dismutase (rs4880) genes on respective intermediate phenotypes. Methods: A total of 207 subjects (23 children and 44 adults with T1DM, 52 adult patients with T2DM and 88 healthy adult control subjects) were enrolled in the study. The following markers of redox state were determined in participants: erythrocyte superoxide dismutase (Ery-SOD), whole blood glutathione peroxidase (WB-GPx), erythrocyte glutathione (Ery-GSH), plasma total antioxidant capacity (P-tAOC) and plasma malondialdehyde (P-MDA). Furthermore, the extent of DNA damage and repair was ascertained using the following parameters: DNA single strand breaks (DNAssb), DNA repair capacity (DNArc) and DNA repair index (DNRI). Results: Comparison of T1DM vs. T2DM patients revealed significantly higher Ery-GSH content (P < 0.0001) and significantly lower Ery-SOD activity (P = 0.0006) and P-tAOC level (P < 0.0001) in T1DM subjects. T2DM diabetics exhibited a significant increase in DNAssb (P < 0.0001) and significant decrease in both DNArc (P < 0.0001) and DNRI (P < 0.0001) compared with T1DM patients. Patient’s age (irrespective of DM type) significantly correlated with DNAssb (r = 0.48, P < 0.0001), DNArc (r = −0.67, P < 0.0001) and DNRI (r = −0.7, P < 0.0001). Allele frequencies of all studied polymorphisms did not exhibit any significant association with the investigated parameters. Conclusion: We demonstrated significant age- and DM type-related changes of oxidative DNA modification and capacity for its repair in subjects with T1DM and T2DM.
Acute Reversal of the Enhanced Insulin Action in Trained Athletes: Association with Insulin Receptor Changes

We studied the effect of aerobic training and detraining on insulin-stimulated glucose disposal and on erythrocyte insulin receptor binding. Seven endurancetrained athletes were studied at 12 h, 60 h, and 7 days after cessation of training and compared with three untrained, age- and weight-matched controls. The metabolic clearance rate of glucose as measured by the euglycemic clamp technique was 15.6 ± 1 . 8 ml/kg/min (mean ± SEM) in the trained subjects 12 h after the last bout of exercise compared with 7.8 ± 1.2 ml/kg/min in the untrained control group. When the trained subjects refrained from physical training, the metabolic clearance rate decreased to 10.1 ± 1 . 0 ml/kg/min at 60 h and further to 8.5 ± 0.5 ml/kg/min after 7 days of detraining. The percentage of specific insulin binding to young erythrocytes (density 1.089–1.092), isolated by density gradient centrifugation, decreased from 10.4 ± 0.9 at 12 h after the last exercise to 8.1 ± 0.7%/3 × 109 cells after 60 h of detraining (P < 0.001). The decrease in insulin binding to erythrocytes was almost entirely accounted for by a decrease in the number of insulin receptors. We conclude that the increase in peripheral insulin action seen in trained athletes is rapidly reversed, possibly by a mechanism separate from other phenomena associated with chronic training. The parallel findings of decreased in vivo insulin action and decreased insulin binding in young erythrocytes suggest that modulation of in vivo insulin response by detraining may be at least partially mediated by changes in insulin receptor number. Isolated young erythrocytes are better indicators of acute insulin receptor modulation than are whole cell preparations.
Cyclosporin A increases nitric oxide activity in vivo.

The use of cyclosporine is complicated by its vaso-constrictive actions. In vitro cyclosporine has been associated with both decreased endothelium-dependent vasodilatation and increased nitric oxide activity. We studied the interaction between cyclosporine and endothelium-derived nitric oxide in seven healthy volunteers. Using venous-occlusion plethysmography, we measured forearm blood flow during intra-arterial infusion of serotonin, which in the concentrations used is a selective agonist of endothelial nitric oxide release, or NG-monomethyl-L-arginine, a specific inhibitor of nitric oxide synthase, during coinfusion of saline or cyclosporine (75 micrograms/min), respectively. During coinfusion of cyclosporine, forearm blood flow increased on maximal serotonin infusion from 2.9 (SE, 0.2) to 8.1 (0.9) mL/100 mL per minute in forearm tissue, which was significantly higher than the increase during saline coinfusion (3.0[0.3] to 6.0 [0.5]; P < .05). Cyclosporine infusion during a "free" nitric oxide system had no effect on basal forearm blood flow, but in significantly decreased forearm blood flow (21.7[2.8]%; P < .05) during fixed nitric oxide activity. These data suggest that acute administration of cyclosporine enhances both basal and receptor-stimulated nitric oxide activity. The mechanism is not clear but may include cyclosporine-induced shear stress as well as direct effects of cyclosporine. The latter was supported by our observation that gene expression of the enzyme nitric oxide synthase III was enhanced by approximately 50% after coincubation with cyclosporine. In conclusion, the present observation demonstrates that nitric oxide constitutes an important regulating mechanism that protects against cyclosporine-associated vasoconstriction in vivo.
The Role of Palliative Resection for Asymptomatic Primary Tumor in Patients With Unresectable Stage IV Colorectal Cancer

BACKGROUND: The prognostic role of surgical resection of primary tumors is not well established in patients with asymptomatic unresectable stage IV colorectal cancer. OBJECTIVE: The aims of this study were to reveal the prognostic role of surgical resection of primary tumors and to define prognostic factors affecting long-term oncological outcomes in patients with asymptomatic unresectable synchronous metastases. DESIGN: This study was a retrospective analysis of prospectively collected data. PATIENTS: Between 2000 and 2008, a total of 416 patients with asymptomatic unresectable stage IV colorectal cancer were analyzed with propensity score matching. MAIN OUTCOME MEASURES: Prematching baseline characteristics were compared by bivariate analysis, and 113 pairs were selected after 1:1 matching with propensity scores estimated from logistic regression. The primary end point was overall survival. RESULTS: Among 416 patients, 218 (52.4%) underwent palliative resection of the primary tumor. Before propensity score matching, palliative resection resulted in a better survival rate than nonresection in univariate analysis (p < 0.001), but not in multivariate analysis (p = 0.08). After matching, the 5-year overall survival rate was significantly lower for patients with peritoneal metastasis and clinical M1b stage tumors in univariate analysis (p = 0.004 and p = 0.02). However, neither peritoneal metastasis nor clinical M1b stage showed any prognostic significance in multivariate analysis. The overall 5-year survival rate of the postmatching group was 4.9% and 3.5% in the palliative resection and nonresection groups. Consequently, palliative resection was not associated with a significant increase in survival compared with nonresection (p = 0.27). A subgroup analysis performed according to the site of metastasis also did not show any significant survival benefit of palliative resection after matching. LIMITATIONS: Selection bias and potential confounders were limitations of this study. CONCLUSIONS: Resection of the primary tumor in patients with asymptomatic unresectable stage IV colorectal cancer was not associated with an improvement in overall survival after propensity score matching.
DNA repair genes XPC, XPG polymorphisms: Relation to the risk of colorectal carcinoma and therapeutic outcome with oxaliplatin‐based adjuvant chemotherapy

Xeroderma pigmentosum complementation group C and G (XPC, XPG) play important roles in DNA damage repairing machinery. Genetic variations in the XPC and XPG may be associated with increased risk for colorectal carcinoma (CRC). In this study, we evaluated the relation between the XPC Lys939Gln, XPG Asp1104His polymorphisms, and CRC susceptibility in a population‐based case–control study, which included 1,028 CRC cases and 1,085 controls. Compared with the corresponding wild genotypes, we found that individuals with at least one copy of the XPC Lys939Gln (AC or CC genotype) and XPG Asp1104His (GC or CC genotype) had an increased risk for CRC. In addition, the variant genotypes of the XPC Lys939Gln AC/CC (P = 0.027) or XPG Asp1104His GC/CC (P = 0.003) reduced the elevation of preoperative carcinoembryonic antigen (CEA) level. Moreover a significantly longer progression‐free survival (PFS) after Oxaliplatin‐based adjuvant chemotherapy was observed in patients with XPG Asp1104His wide‐type GG genotype (n = 432, Log‐rank test: P = 0.033). Cox proportional hazards analyses demonstrated that variant genotypes of XPG Asp1104His [hazard ratio (HR) = 1.692, 95% confidence interval (95%CI): 1.202–2.383, P = 0.003] as well as pathology grade (HR = 2.545, 95%CI: 2.139–3.030, P < 0.001), and lymph node metastases (HR = 1.851, 95%CI: 1.306–2.625, P < 0.001) were predictive of shorter PFS for the CRC patients with Oxaliplatin‐based adjuvant chemotherapy. In conclusion, the current data suggested that XPC Lys939Gln and XPG Asp1104His polymorphisms might contribute to the identification of patients with increased risk for CRC. © 2011 Wiley Periodicals, Inc.
Fever in the wake of a stroke

We performed a prospective study of the frequency and cause of fever, defined as a rectal temperature of ≥ 101 °F detected within the first 5 days, in 104 consecutive adults admitted to a community/teaching hospital because of a nontraumatic stroke. Fever was documented in 23 patients. A source for the fever was identified in 19 patients and was attributed to a pulmonary insult, either aspiration chemical pneumonitis or an infectious pneumonia, in 13 of these patients. Patients who experienced lacunar infarcts did not develop fever. Fever occurring in the wake of a stroke should not be attributed to the vascular process, but should direct attention to inflammatory disorders of the lungs.
Parenting Practices as Mediators of Treatment Effects in an Early-Intervention Trial of Multidimensional Family Therapy

Background: Contemporary intervention models use research about the determinants of adolescent problems and their course of symptom development to design targeted interventions. Because developmental detours begin frequently during early-mid adolescence, specialized interventions that target known risk and protective factors in this period are needed. Methods: This study (n = 83) examined parenting practices as mediators of treatment effects in an early-intervention trial comparing Multidimensional Family Therapy (MDFT), and a peer group intervention. Participants were clinically referred, low-income, predominantly ethnic minority adolescents (average age 14). Assessments were conducted at intake, and six weeks after intake, discharge, and at 6 and 12 months following intake. Results: Previous studies demonstrated that MDFT was more effective than active treatments as well as services as usual in decreasing substance use and improving abstinence rates. The current study demonstrated that MDFT improves parental monitoring—a fundamental treatment target—to a greater extent than group therapy, and these improvements occur during the period of active intervention, satisfying state-of-the-science criteria for assessing mediation in randomized clinical trials. Conclusions and Scientific Significance: Findings indicate that change in MDFT occurs through improvements in parenting practices. These results set the foundation for examining family factors as mediators in other samples.
Phased Training for High-Reliability Occupations

Objective: The aim of this study was to assess whether the stress reduction effects of phased training culminating in repeated exposure to a stressful scenario generalize to new scenarios. Background: High-reliability occupations require personnel to operate in stressful situations involving complex environments, high degrees of uncertainty and time pressure, and severe consequences for mistakes. One method of training for such environments culminates in practice in high-fidelity, highly stressful simulations. For some domains, realism necessitates large-scale, difficult-to-modify physical simulations. This necessity often results in repeated exposure to one or very few scenarios. The literature gives reason to question whether the stress reduction effects of such exposure transfer to new scenarios. Method: Anxiety and cognitive difficulties were measured among firefighter trainees during three live-fire drills. For each trainee, two drills involved the same scenario, and the other involved a new scenario that was structurally similar to the repeated scenario. Results: As predicted, anxiety and cognitive difficulties decreased across repetitions of the same scenario. However, the reduction did not generalize to a new scenario, and a nontrivial portion of the sample showed signs of negative transfer. Conclusion: Repeated exposure to the same stressful scenario as the final phase of training has limited practical value for stress reduction. Methods for expanding the range of scenarios to which trainees are exposed or for increasing the value of the exposure are recommended. Application: The findings could help improve design of training programs for high-reliability occupations.
Using Panel Vendors for Recruitment Into a Web-Based Family Prevention Program: Methodological Considerations

Use of online panel vendors in research has grown over the past decade. Panel vendors are organizations that recruit participants into a panel to take part in web-based surveys and match panelists to a target audience for data collection. We used two panel vendors to recruit families (N = 411) with a 16- to 17-year-old teen to participate in a randomized control trial (RCT) of an online family-based program to prevent underage drinking and risky sexual behaviors. Our article addresses the following research questions: (1) How well do panel vendors provide a sample of families who meet our inclusion criteria to participate in a RCT? (2) How well do panel vendors provide a sample of families who reflect the characteristics of the general population? and (3) Does the choice of vendor influence the characteristics of families that we engage in research? Despite the screening techniques used by the panel vendors to identify families who met our inclusion criteria, 23.8% were found ineligible when research staff verified their eligibility by direct telephone contact. Compared to the general U.S. population, our sample had more Whites and more families with higher education levels. Finally, across the two panel vendors, there were no significant differences in the characteristics of families, except for mean age. The online environment provides opportunities for new methods to recruit participants in research studies. However, innovative recruitment methods need careful study to ensure the quality of their samples.
Effect of Substrate Concentration and Organic and Inorganic Compounds on the Occurrence and Rate of Mineralization and Cometabolism

Isopropyl N-phenylcarbamate (IPC) at 400 pg and 1 μg/ml was mineralized in samples of sewage, but only the lower concentration was mineralized in lake water samples in a 50-day period. IPC at 1 μg/ml disappeared from lake water, but it was converted to organic products. Mineralization of IPC at 400 pg/ml in lake water was enhanced by additions of inorganic nutrients or a mixture of nonchlorinated water pollutants but not by yeast extract or mixtures containing aromatic compounds or excretions of primary producers. The mineralization of 200 pg of 2,4-dichlorophenoxyacetate per ml of lake water was not affected by additions of low levels of yeast extract or compounds excreted by primary producers but was enhanced by low concentrations of mixtures of water pollutants. It is suggested that some chemicals that are found to be converted only to organic products, presumably by cometabolism, in tests using the concentrations commonly employed in laboratory evaluations may be mineralized at the lower concentrations prevailing in natural waters.