Characterization and sequence analysis of the lsg (LOS synthesis genes) locus from Haemophilus influenzae type b

Analysis of the lsg (LOS synthesis genes) cluster in Escherichia coli strain K12 and mutations in the lsg locus in Haemophilus influenzae type b indicated the presence of 3 regions responsible for sequential modifications of E. coli lipopolysaccharide (LPS). Sequencing of the lsg region yielded 7,435 bp that encompassed 7 complete and 1 partial open reading frames (ORFs 1-8). The predicted product of ORF1 had homology to the consensus sequence of cytochrome b proteins (21% identity, 51% similarity) and to other transmembrane proteins. The products of ORF5 and ORF6 share overall 23% identity and 49% similarity with each other. The ORF6 protein had high homology with the product of ORF275 of the E. coli rfb gene cluster (40% identity, 58% similarity), whose function is not known. Multiple sequence alignment of the ORF5 and ORF6 proteins with the RfbB, RfbJ and RfbX proteins revealed conserved motifs over the N-terminal half region of all these proteins. The products of ORF7 and ORF8 are homologous with Azotobacter vinelandii MolA protein (30% identity, 51% similarity) and MolB protein (26% identity, 48% similarity), respectively. The promoter regions of ORF1, 7 and 8 were determined by primer extension analysis and found to be similar to bacterial σ70-dependent promoters. ORF7 and ORF8 are transcribed into diverse orientation. At least 5 of the encoded proteins have been identified using coupled E. coli transcription/translation system and labeling with [35S]-methionine. We conclude that the genetic organization of the lsg biosynthesis pathway involves multiple operons that lead to the assembly of an H. influenzae LOS structure.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/67077/2/10.1177_096805199400100305.pd

Brucelose humana em operários de um frigorífico no município de Salvador, Bahia, Brasil

Human Brucellosis, from the point of view of its serologic, occupational and clinic aspects, was studied in a slaughter-house personnel at the Salvador city, State of Bahia, Brazil. Sorologic test showed 10.58% frequency, as a characteristic aspect of work time. So, 55.55% of positive cases were more than 5 years old at the same activity, with the type of work as a remarkable aspect. At hog and gut sectors, a positivity of 33.33% and 30.00% was found. Clinical symptoms, beside his subjectivity and the fashion that it was performed in a apparently health community, were much more frequent between the positive ones. The necessity of to know the amount of population exposed risk is emphasized, as a possibility of detection of real brucellosis prevalence at the region.Estuda-se a brucelose humana sob o ponto de vista sorológico, ocupacional e clínico, em operários de frigorífico do município de Salvador-Bahia, Brasil. Foi encontrada freqüência de 10,58% de indivíduos com sorologia positiva, ficando bem caracterizada a importância do tempo de trabalho. Dos positivos, 55,55% tinham mais de 5 anos na mesma ocupação, destacando-se o tipo de trabalho. Assim nas seções de suínos e triparia, encontrou-se 33,33% e 30,00% de positivos, respectivamente. Os sintomas clínicos, apesar da subjetividade, reforçado pelo fato do estudo ter sido realizado em comunidade aparentemente sadia, foram bem mais freqüentes nos positivos. Ressaltou-se a necessidade de se conhecer a população exposta ao risco de contrair a infecção para, através de uma amostra representativa, se detectar a real prevalência da brucelose na região

Detection Of Metabolic Syndrome Features Among Childhood Cancer Survivors: A Target To Prevent Disease

Along with the growing epidemic of obesity, the risk of atherosclerosis, cardiovascular disease morbidity, and mortality are increasing markedly. Several risk factors for cardiovascular disease, such as visceral obesity, glucose intolerance, arterial hypertension, and dyslipidemia commonly cluster together as a condition currently known as metabolic syndrome. Thus far, insulin resistance, and endothelial dysfunction are the primary events of the metabolic syndrome. Several groups have recommended clinical criteria for the diagnosis of metabolic syndrome in adults. Nonetheless, in what concerns children and adolescents, there are no unified definitions, and modified adult criteria have been suggested by many authors, despite major problems. Some pediatric disease states are at risk for premature cardiovascular disease, with clinical coronary events occurring very early in adult life. Survivors of specific pediatric cancer groups, particularly acute lymphocytic leukemia, central nervous system tumors, sarcomas, lymphomas, testicular cancer, and following bone marrow transplantation, may develop metabolic syndrome traits due to: hormonal deficiencies (growth hormone deficiency, thyroid dysfunction, and gonadal failure), drug or radiotherapy damage, endothelial impairment, physical inactivity, adipose tissue dysfunction, and/or drug-induced magnesium deficiency. In conclusion, some primary and secondary prevention remarks are propose in order to reduce premature cardiovascular disease risk in this particular group of patients. © 2008 Siviero-Miachon et al, publisher and licensee Dove Medical Press Ltd.44825836Adan, L., Trivin, C., Sainte-Rose, C., GH deficiency caused by cranial irradiation during childhood: Factors and mukers in young adults (2001) J Clin Endocrinol Metab, 86, pp. 5245-5251Ahmet, A., Blaser, S., Stephens, D., Weight gain in craniopharyngioma -a model for hypothalamic obesity (2006) J Pediatr Endocrinol Metab, 19, pp. 121-128Alberti, K.G.M.M., Zimmet, P.Z., World Health Organisation (WHO)-Definition, diagnosis and classification of diabetes mellitus and its complications. Part 1: Diagnosis and classification of diabetes mellitus provisional report of a WHO consultation (1998) Diabet Med, 15, pp. 539-553National Cholesterol Education Program: Report of the Expert Panel on Blood Cholesterol Levels in Children and Adolescents (1992) Pediatrics, 89 (PART 2), pp. 525-584. , American Academy of PediatricsType 2 diabetes in children and adolescents (2000) Diabetes Care, 23, pp. 381-389. , American Diabetes AssociationArgüelles, B., Barrios, V., Buño, M., Anthropometric parameters and their relationship to serum growth hormone-binding protein and leptin levels in children with acute lymphoblastic leukemia: A prospective study (2000) Eur J Endocrinol, 143, pp. 243-250Baker, K.S., Ness, K.K., Steinberger, J., Diabetes, hypertension, and cardiovascular events in survivors of hematopoietic cell transplantation: A report from the Bone Marrow Transplantation Survivor Study (2007) Blood, 109, pp. 1765-1772Balkau, B., Charles, M.A., European Group for the Study of Insulin Resistance (EGIR) - Comment on the provisional report from the WHO consultation. European Group for the Study of Insulin Resistance (1999) Diabet Med, 16, pp. 442-443Barker, D.J., Fetal origins of coronary heart disease (1995) BMJ, 311, pp. 171-174Brydøy, M., Fosså, S.D., Dahl, O., Gonadal dysfunction and fertility problems in cancer survivors (2007) Acta Oncol, 46, pp. 480-489Bülow, B., Link, Y., Ahren, B., Survivors of childhood acute lymphoblastic leukaemia, with radiation-induced GH deficiency, exhibit hyperleptinaemia and impaired insulin sensitivity, unaffected by 12 months of GH treatment (2004) Clin Endocrinol (Oxf), 61, pp. 683-691Chatterjee, R., Palla, K., MeGarrigle, H.H., Syndrome "X" in adult female recipients of bone marrow transplantation for haematological malignancies (2005) Bone Marrow Transplant, 35, pp. 209-210Colao, A., Di Somma, C., Rota, F., Common carotid intima-media thickness in growth hormone (GH)-deficient adolescents: A prospective study after GH withdrawal and restarting GH replacement (2005) J Clin Endocrinol Metab, 90, pp. 2659-2665Cook, S., Weitzman, M., Auinger, P., Prevalence of a metabolic syndrome phenotype in adolescents: Findings from the third National Health and Nutrition Examination Survey, 1988-1994 (2003) Arch Pediatr Adolesc Med, 157, pp. 821-827Cruz, M.L., Weigensberg, M.J., Huang, T.T., The metabolic syndrome in overweight Hispanic youth and the role of insulin sensitivity (2004) J Clin Endocrinol Metab, 89, pp. 108-113Dalton, V.K., Rue, M., Silverman, L.B., Height and weight in children treated for acute lymphoblastic leukemia: Relationship to CNS treatment (2003) J Clin Oncol, 21, pp. 2953-2960DeFerranti, S.D., Gauvreau, K., Ludwig, D.S., Prevalence of the metabolic syndrome in American adolescents (2004) Circulation, 110, pp. 2494-2497Einhom, D., Reaven, G.M., Cobin, R.H., The American College of Endocrinology - American College of Endocrinology position statement on the insulin resistance syndrome (2003) Endocr Pract, 9, pp. 237-252Florin, T.A., Fryer, G.E., Miyoshi, T., Physical inactivity in adult survivors of childhood acute lymphoblastic leukemia: A report from the Childhood Cancer Survivor Study (2007) Cancer Epidenziol Biomarkers Prev, 16, pp. 1356-1363Genuth, S., Alberti, K.G., Bennett, P., Follow-up report on the diagnosis of diabetes mellitus. The Expert Committee on the Diagnosis and Classification of Diabetes Mellitus (2003) Diabetes Care, 26, pp. 3160-3167Gleeson, H.K., Shalet, S.M., The impact of cancer therapy on the endocrine system in survivors of childhood brain tumors (2004) Endocr Relat Cancer, 11, pp. 589-602Grundy SM, Brewer Jr HB, Cleeman JI, et al. 2004. Definition of metabolic syndrome. Report of the National Heart, Lung, and Blood Institute/American Heart Association Conference on Scientific Issues Related to Definition. Circulation, 109:433-8Guo, C.Y., Halton, J.M., Barr, R.D., Hypomagnesemia associated with chemotherapy in patients treated for acute lymphoblastic leukemia: Possible mechanisms (2004) Oncol Rep, 11, pp. 185-189Gurney, J.G., Ness, K.K., Sibley, S.D., Metabolic syndrome and growth hormone deficiency in adult survivors of childhood acute lymphoblastic leukemia (2006) Cancer, 107, pp. 1303-1312Harish, K., Dharmalingam, M., Himanshu, M., Study protocol: Insulin and its role in cancer (2007) BMC Endocr Disord, 7, p. 10Harz, K.J., Müller, H.L., Waldeck, E., Obesity in patients with craniopharyngioma: Assessment of food intake and movement counts indicating physical activity (2003) J Clin Endocrinol Metab, 88, pp. 5227-5231Heikens, J., Ubbink, M.C., Van der Pal, H.P.J., Long term survivors of childhood brain cancer have an increased risk for cardiovascular disease (2000) Cancer, 88, pp. 2116-2121Hickman, T.B., Briefel, R.R., Carroll, M.D., Distributions and trends of serum lipid levels among United States children and adolescents ages 4-19 years: Data from the Third National Health and Nutrition Examination Survey (1998) Prev Med, 27, pp. 879-890Higgins, K., Noon, C., Cartwright, V., Features of the metabolic syndrome present in bone marrow transplantation in adulthood (2004) Bone Marrow Transplant, 33 (SUPPL. 1), pp. S216-S217Hodgkinson, E., Neville-Webbe, H.L., Coleman, R.E., Magnesium depletion in patients receiving cisplatin-based chemotherapy (2006) Clin Oncol (R Coll Radiol), 18, pp. 710-718Hoffman, K.E., Derdak, J., Bernstein, D., Metabolic syndrome traits in long-term survivors of pediatric sarcoma (2008) Pediatr Blood Cancer, 50, pp. 341-346Hsu, I.R., Kim, S.P., Kabir, M., Metabolic syndrome, hyperinsulinemia, and cancer (2007) Am J Clin Nutr, 86, pp. S867-S871Hu, G., Qiao, Q., Tuomilehto, J., Prevalence of the metabolic syndrome and its relation to all-cause and cardiovascular mortality in nondiabetic European men and women (2004) Arch Intern Med, 164, pp. 1066-1076. , for the DECODE Study Group(2006) The IDF consensus worldwide definition of the metabolic syndrome, , http://www.idf.org/webdata/docs/IDF_Meta_def_final.pdf, online, Accessed on January 10, 2008. URLJaniszewski, P.M., Oeffinger, K.C., Church, T.S., Abdominal obesity, liver fat, and muscle composition in survivors of childhood acute lymphoblastic leukemia (2007) J Clin Endocrinol Metab, 92, pp. 3816-3821Jarfelt, M., Lannering, B., Bosaeus, I., Body composition in young adult survivors of childhood acute lymphoblastic leukaemia (2005) Eur J Endocrinol, 153, pp. 81-89Jones, K.L., The dilemma of the metabolic syndrome in children and adolescents: Disease or distraction? (2006) Pediatr Diabetes, 7, pp. 311-321Kavey RE, Allada V, Daniels SR, et al. 2006. Cardiovascular risk reduction in high-risk pediatric patients: a scientific statement from the American Heart Association Expert Panel on Population and Prevention Sciencethe Councils on Cardiovascular Disease in the Young, Epidemiology and Prevention, Nutrition, Physical Activity and Metabolism, High Blood Pressure Research, Cardiovascular Nursing, and the Kidney in Heart Diseaseand the Interdisciplinary Working Group on Quality of Care and Outcomes Research: endorsed by the American Academy of Pediatrics. Circulation, 114:2710-38Kourti, M., Tragiannidis, A., Makedou, A., Metabolic syndrome in children and adolescents with acute lymphoblastic leukemia after the completion of chemotherapy (2005) J Pediatr Hematol/Oncol, 27, pp. 499-501Link, K., Moëll, C., Garwicz, S., Growth hormone deficiency predicts cardiovascular risk in young adults treated for acute lymphoblastic leukemia in childhood (2004) J Clin Endocrinol Metab, 89, pp. 5003-5012Lustig, R.H., Autonomic dysfunction of the β-Cell and the pathogenesis of obesity (2003) Rev Endocr Metab Disord, 4, pp. 23-32Lustig, R.H., Post, S.R., Srivannaboon, K., Risk factors for the development of obesity in children surviving brain tumors (2003) J Clin Endocrinol Metab, 88, pp. 611-616Mertens, A.C., Yasui, Y., Neglia, J.P., Late mortality experience in five-year survivors of childhood and adolescent cancer: The Childhood Cancer Survivor Study (2001) J Clin Oncol, 19, pp. 3163-3172Mohamed-Ali, V., Pinkney, J.H., Coppack, S.W., Adipose tissue as an endocrine and paracrine organ (1998) Int J Obes, 22, pp. 1145-1158Moser, E.C., Noordijk, E.M., Carde, P., Late non-neoplastic events in patients with aggressive non-Hodgkin's lymphoma in four randomized European Organisation for Research and Treatment of Cancer trials (2005) Clin Lymphoma Myeloma, 6, pp. 122-130National Center for Health Statistics. 2000 CDC Growth Charts: United States [updated 2007 February 12cited 2007 November 08] [online]. Accessed on January 10, 2008. URL: http://www.cdc.gov/ growthcharts[NCEP-ATP III] National Cholesterol Education Program Adult Treatment Panel III - Expert panel on the detection, evaluation, and treatment of high blood cholesterol in adults. 2001. Executive summary of the Third Report of the National Cholesterol Education Program Expert Panel on Detection, Evaluation, and Treatment of High Blood Cholesterol in Adults (Adult Treatment Panel III). JAMA, 285:2486-97National High Blood Pressure Education Program Working Group on Hypertension Control in Children and Adolescents. 1996. Update on the 1987 Task Force Report on High Blood Pressure in Children and Adolescents: a working group report from the National High Blood Pressure Education Program. Pediatrics, 98:649-58National High Blood Pressure Education Program Working Group on High Blood Pressure in Children and Adolescents. 2004. Fourth report of the Task Force on the Diagnosis, Evaluation and Treatment of High Blood Pressure in Children. Pediatrics, 114:555-76Neville, K.A., Cohn, R.J., Steinbeck, K.S., Hyperinsulinemia, impaired glucose tolerance, and diabetes mellitus in survivors of childhood cancer: Prevalence and risk factors (2006) J Clin Endocrinol Metab, 91, pp. 4401-4407Nuver, J., Smit, A.J., Postma, A., The metabolic syndrome in long-term cancer survivors, an important target for secondary preventive measures (2002) Cancer Treat Ver, 28, pp. 195-214Nuver, J., Smit, A.J., Wolffenbuttel, B.H., The metabolic syndrome and disturbances in hormone levels in long-term survivors of disseminated testicular cancer (2005) J Clin Oncol, 23, pp. 3718-3725Oeffinger, K.C., Buchanan, G.R., Eshelman, D.A., Cardiovascular risk factors in young adult survivors of childhood acute lymphoblastic leukemia (2001) J Pediatr Hematol/Oncol, 23, pp. 424-430Oeffinger, K.C., Mertens, A.C., Sklar, C.A., Obesity in adult survivors of childhood acute lymphoblastic leukemia: A report from the Childhood Cancer Survivor Study (2003) J Clin Oncol, 21, pp. 1359-1365Oeffinger, K.C., Are survivors of acute lymphoblastic leukemia (ALL) at increased risk of cardiovascular disease? (2008) Pediatr Blood Cancer, 50, pp. 462-467Pollak, M.N., Insulin, insulin-like growth factors, insulin resistance, and neoplasia (2007) Am J Clin Nutr, 86, pp. S820-S821Razzouk, B.I., Rose, S.R., Hongeng, S., Obesity in survivors of childhood acute lymphoblastic leukemia and lymphoma (2007) J Clin Oncol, 25, pp. 1183-1189Reaven, G.M., Banting lecture 1988: Role of insulin resistance in human disease (1988) Diabetes, 37, pp. 1595-1607Reilly, J.J., Kelly, A., Ness, P., Premature adiposity rebound in children treated for acute lymphoblastic leukemia (2001) J Clin Endocrinol Metab, 86, pp. 2775-2778Ross, J.A., Oeffinger, K.C., Davies, S.M., Genetic variation in the leptin receptor gene and obesity in survivors of childhood acute lymphoblastic leukemia: A report from the Childhood Cancer Survivor Study (2004) J Clin Oncol, 22, pp. 3558-3562Roth C, Wilken B, Hanefeld F, et al. 1998. Hyperphagia in children with craniopharyngioma is associated with hyperleptinaemia and a failure in the downregulation of appetite. Eur J Endocrinol, 138-89-91Rutter, M.M., Rose, R.S., Long-term endocrine sequelae of childhood cancer (2007) Curr Opin Pediatr, 19, pp. 480-487Saini, A., Al-Shanti, N., Stewart, C.E., Waste management - cytokines, growth factors and cachexia (2006) Cytokine Growth Factor Rev, 17, pp. 475-486Sarti, C., Gallagher, J., The metabolic syndrome: Prevalence, CHD risk, and treatment (2006) J Diabetes Compl, 20, pp. 121-132Shalitin, S., Phillip, M., Stein, J., Endocrine dysfunction and parameters of the metabolic syndrome after bone marrow transplantation during childhood and adolescence (2006) Bone Marrow Transplant, 37, pp. 1109-1117Shoelson, S.E., Lee, J., Goldfine, A.B., Inflammation and insulin resistance (2006) J Clin Invest, 116, pp. 1793-1801Siviero-Miachon, A.A., Spinola-Castro, A.M., Tosta-Hernandez, P.D.C., Leptin assessment in acute lymphocytic leukemia survivors: Role of cranial radiotherapy? (2007) J Ped Hematol/Oncol, 29, pp. 776-782Sklar, C.A., Mertens, A.C., Walter, A., Changes in body mass index and prevalence of overweight in survivors of childhood acute lymphoblastic leukemia: Role of cranial irradiation (2000) Med Pediatr Oncol, 35, pp. 91-95Sklar, C.A., Mertens, A.C., Mitby, P., Premature menopause in survivors of childhood cancer: A report from the Childhood Cancer Survivor Study (2006) J Natl Cancer Inst, 98, pp. 890-896Soares, D.V., Spina, L.D., de Lima, Oliveira Brasil, R.R., Carotid artery intima-media thickness and lipid profile in adults with growth hormone deficiency after long-term growth hormone replacement (2005) Metabolism, 54, pp. 321-329Srinivasan, S., Ogle, G.D., Garnett, S.P., Features of the metabolic syndrome after childhood craniopharyngioma (2004) J Clin Endocrinol Metab, 89, pp. 81-86Szczepaniska-Kostro, J., Tolwinska, J., Urban, M., Cardiac mass and function, carotid artery intima media thickness, homocysteine and lipoprotein levels in children and adolescents with growth hormone deficiency (2004) J Pediatr Endocrinol Metab, 17, pp. 1405-1413Talvensaari, K.K., Lanning, M., Tapanainen, P., Long-term survivors of childhood cancer have an increased risk of manifesting the metabolic syndrome (1996) J Clin Endocrinol Metab, 81, pp. 3051-3055Taskinen, M., Lipsanen-Nyman, M., Tiitinen, A., Insufficient growth hormone secretion is associated with metabolic syndrome after allogeneic stem cell transplantation in childhood (2007) J Pediatr Hematol/ Oncol, 29, pp. 529-534Trimis, G., Moschovi, M., Papassotiriou, I., Early indicators of dysmetabolic syndrome in young survivors of acute lymphoblastic leukemia in childhood as a target for preventing disease (2007) J Ped Hematol/ Oncol, 29, pp. 309-314Waychenberg, B.L., Subcutaneous and visceral adipose tissue: Their relation to the metabolic syndrome (2000) Endocr Rev, 21, pp. 697-738Weiss, R., Dziura, J., Burgett, T.S., Obesity and the metabolic syndrome in children and adolescents (2004) N Engl J Med, 350, pp. 2362-2374Zimmet P, Alberti G, Kaufinan F, et al. on behalf of the International Diabetes Federation Task Force on Epidemiology and Prevention of Diabetes. 2007. The metabolic syndrome in children and adolescents. Lancet, 369:2059-61Zhou JR, Blackburn GL, Walker WA. 2007. Symposium introduction: metabolic syndrome and the onset of cancer. Am J Clin Nutr, 86: S817-S81

Sex determining region Y-box 2 (SOX2) is a potential cell-lineage gene highly expressed in the pathogenesis of squamous cell carcinomas of the lung

Background: Non-small cell lung cancer (NSCLC) represents the majority (85%) of lung cancers and is comprised mainly of adenocarcinomas and squamous cell carcinomas (SCCs). The sequential pathogenesis of lung adenocarcinomas and SCCs occurs through dissimilar phases as the former tumors typically arise in the lung periphery whereas the latter normally arise near the central airway. Methodology/Principal Findings:We assessed the expression of SOX2, an embryonic stem cell transcriptional factor that also plays important roles in the proliferation of basal tracheal cells and whose expression is restricted to the main and central airways and bronchioles of the developing and adult mouse lung, in NSCLC by various methodologies. Here, we found that SOX2 mRNA levels, from various published datasets, were significantly elevated in lung SCCs compared to adenocarcinomas (all p<0.001). Moreover, a previously characterized OCT4/SOX2/NANOG signature effectively separated lung SCCs from adenocarcinomas in two independent publicly available datasets which correlated with increased SOX2 mRNA in SCCs. Immunohistochemical analysis of various histological lung tissue specimens demonstrated marked nuclear SOX2 protein expression in all normal bronchial epithelia, alveolar bronchiolization structures and premalignant lesions in SCC development (hyperplasia, dysplasia and carcinoma in situ) and absence of expression in all normal alveoli and atypical adenomatous hyperplasias. Moreover, SOX2 protein expression was greatly higher in lung SCCs compared to adenocarcinomas following analyses in two independent large TMA sets (TMA set I, n = 287; TMA set II, n = 511 both p<0.001). Furthermore, amplification of SOX2 DNA was detected in 20% of lung SCCs tested (n = 40) and in none of the adenocarcinomas (n = 17). Conclusions/Significance: Our findings highlight a cell-lineage gene expression pattern for the stem cell transcriptional factor SOX2 in the pathogenesis of lung SCCs and suggest a differential activation of stem cell-related pathways between squamous cell carcinomas and adenocarcinomas of the lung. © 2010 Yuan et al.published_or_final_versio

Joint association of polymorphism of the FGFR4 gene and mutation TP53 gene with bladder cancer prognosis

The impact of the fibroblast growth factor receptor 4 (FGFR4) Gly388Arg polymorphism on bladder cancer is unknown. We found no clear correlations between the FGFR4 genotype and risk of bladder cancer or pathological parameters. Neither the polymorphism nor TP53 mutation status was an independent predictor of prognosis, but they might act jointly on the disease-specific survival of patients

Naming the pain in requirements engineering : Contemporary problems, causes, and effects in practice

Requirements Engineering (RE) has received much attention in research and practice due to its importance to software project success. Its interdisciplinary nature, the dependency to the customer, and its inherent uncertainty still render the discipline difficult to investigate. This results in a lack of empirical data. These are necessary, however, to demonstrate which practically relevant RE problems exist and to what extent they matter. Motivated by this situation, we initiated the Naming the Pain in Requirements Engineering (NaPiRE) initiative which constitutes a globally distributed, bi-yearly replicated family of surveys on the status quo and problems in practical RE. In this article, we report on the qualitative analysis of data obtained from 228 companies working in 10 countries in various domains and we reveal which contemporary problems practitioners encounter. To this end, we analyse 21 problems derived from the literature with respect to their relevance and criticality in dependency to their context, and we complement this picture with a cause-effect analysis showing the causes and effects surrounding the most critical problems. Our results give us a better understanding of which problems exist and how they manifest themselves in practical environments. Thus, we provide a first step to ground contributions to RE on empirical observations which, until now, were dominated by conventional wisdom only.Peer reviewe

Putative role of the adenosine A3 receptor in the antiproliferative action of N6-(2-isopentenyl)adenosine

We tested a panel of naturally occurring nucleosides for their affinity towards adenosine receptors. Both N6-(2-isopentenyl)adenosine (IPA) and racemic zeatin riboside were shown to be selective human adenosine A3 receptor (hA3R) ligands with affinities in the high nanomolar range (Ki values of 159 and 649 nM, respectively). These values were comparable to the observed Ki value of adenosine on hA3R, which was 847 nM in the same radioligand binding assay. IPA also bound with micromolar affinity to the rat A3R. In a functional assay in Chinese hamster ovary cells transfected with hA3R, IPA and zeatin riboside inhibited forskolin-induced cAMP formation at micromolar potencies. The effect of IPA could be blocked by the A3R antagonist VUF5574. Both IPA and reference A3R agonist 2-chloro-N6-(3-iodobenzyl)adenosine-5′-N-methylcarboxamide (Cl-IB-MECA) have known antitumor effects. We demonstrated strong and highly similar antiproliferative effects of IPA and Cl-IB-MECA on human and rat tumor cell lines LNCaP and N1S1. Importantly, the antiproliferative effect of low concentrations of IPA on LNCaP cells could be fully blocked by the selective A3R antagonist MRS1523. At higher concentrations, IPA appeared to inhibit cell growth by an A3R-independent mechanism, as was previously reported for other A3R agonists. We used HPLC to investigate the presence of endogenous IPA in rat muscle tissue, but we could not detect the compound. In conclusion, the antiproliferative effects of the naturally occurring nucleoside IPA are at least in part mediated by the A3R

Analysis of Clinical Phenotypes through Machine Learning of First-Line H. pylori Treatment in Europe during the Period 2013–2022: Data from the European Registry on H. pylori Management (Hp-EuReg)

The segmentation of patients into homogeneous groups could help to improve eradication therapy effectiveness. Our aim was to determine the most important treatment strategies used in Europe, to evaluate first-line treatment effectiveness according to year and country. Data collection: All first-line empirical treatments registered at AEGREDCap in the European Registry on Helicobacter pylori management (Hp-EuReg) from June 2013 to November 2022. A Boruta method determined the “most important” variables related to treatment effectiveness. Data clustering was performed through multi-correspondence analysis of the resulting six most important variables for every year in the 2013–2022 period. Based on 35,852 patients, the average overall treatment effectiveness increased from 87% in 2013 to 93% in 2022. The lowest effectiveness (80%) was obtained in 2016 in cluster #3 encompassing Slovenia, Lithuania, Latvia, and Russia, treated with 7-day triple therapy with amoxicillin–clarithromycin (92% of cases). The highest effectiveness (95%) was achieved in 2022, mostly in Spain (81%), with the bismuth–quadruple therapy, including the single-capsule (64%) and the concomitant treatment with clarithromycin–amoxicillin–metronidazole/tinidazole (34%) with 10 (69%) and 14 (32%) days. Cluster analysis allowed for the identification of patients in homogeneous treatment groups assessing the effectiveness of different first-line treatments depending on therapy scheme, adherence, country, and prescription year