ANOVA to Compare Three Methods to Track COVID-19 in Nine Countries / ANOVA en la comparación de tres métodos para rastrear COVID-19 en nueve países

ABSTRACT A new coronavirus denominated first 2019-nCoV and later SARS-CoV-2 was found in Wuhan, China in December of 2019. This paper compares three mathematical methods: nonlinear regression, SIR, and SEIR epidemic models, to track the covid-19 disease in nine countries affected by the SARS-CoV-2 virus, to help epidemiologists to know the disease trajectory, considering initial data in the pandemic, mainly 100 days from the beginning. To evaluate the results obtained with the three methods one-way ANOVA is applied. The average of predicted infected cases with SARS-CoV-2, obtained with the mentioned methods was: for United States of America 1,098,508, followed by Spain with 226,721, Italy with 202,953, France with 183,897 United Kingdom with 182,190, Germany with 159,407, Canada with 58,696, Mexico with 50,366 and Argentina with 4,860 in average. The one-way ANOVA does not show a significant difference among the results of the projected infected cases by SARS-CoV-2, using nonlinear regression, SIR, and SEIR epidemic methods. The above could mean that initially any method can be used to model the pandemic course.

RESUMEN Un nuevo coronavirus denominado primero 2019-nCoV y más tarde SARS-CoV-2 fue encontrado en Wuhan, China en diciembre de 2019. El objetivo de este trabajo es comparar tres métodos matemáticos: regresión no lineal, modelos epidemiológicos SIR y SEIR, para rastrear la enfermedad del COVID-19 en nueve países infectados por el virus SARS-CoV-2, con el propósito de ayudar al epidemiólogo a conocer el curso de la pandemia, considerando principalmente sus primeros 100 días. Para evaluar los resultados obtenidos de la aplicación de los tres métodos, se aplicó ANOVA de una vía. El número promedio de casos infectados con SARS-CoV-2, obtenidos con los tres métodos descritos son: para Estados Unidos 1,098,508, seguido de España con 226,721, Italia con 202,953, Francia con 183,897 Reino Unido con 182,190, Alemania con 159,407, Canadá con 58,696, México con 50,366 y Argentina con 4,860 en promedio. El ANOVA de una vía no muestra diferencias significativas entre los resultados de los casos infectados proyectados por SARS-CoV-2, utilizando la regresión no lineal y los métodos SIR and SEIR. Lo anterior podría señalar que cualquiera de los tres métodos estudiados puede modelar el curso de la pandemia en las condiciones descritas para cada uno.

The Bark Beetle Dendroctonus rhizophagus (Curculionidae: Scolytinae) Has Digestive Capacity to Degrade Complex Substrates: Functional Characterization and Heterologous Expression of an α-Amylase.

Dendroctonus-bark beetles are natural agents contributing to vital processes in coniferous forests, such as regeneration, succession, and material recycling, as they colonize and kill damaged, stressed, or old pine trees. These beetles spend most of their life cycle under stem and roots bark where they breed, develop, and feed on phloem. This tissue is rich in essential nutrients and complex molecules such as starch, cellulose, hemicellulose, and lignin, which apparently are not available for these beetles. We evaluated the digestive capacity of Dendroctonusrhizophagus to hydrolyze starch. Our aim was to identify α-amylases and characterize them both molecularly and biochemically. The findings showed that D. rhizophagus has an α-amylase gene (AmyDr) with a single isoform, and ORF of 1452 bp encoding a 483-amino acid protein (53.15 kDa) with a predicted signal peptide of 16 amino acids. AmyDr has a mutation in the chlorine-binding site, present in other phytophagous insects and in a marine bacterium. Docking analysis showed that AmyDr presents a higher binding affinity to amylopectin compared to amylose, and an affinity binding equally stable to calcium, chlorine, and nitrate ions. AmyDr native protein showed amylolytic activity in the head-pronotum and gut, and its recombinant protein, a polypeptide of ~53 kDa, showed conformational stability, and its activity is maintained both in the presence and absence of chlorine and nitrate ions. The AmyDr gene showed a differential expression significantly higher in the gut than the head-pronotum, indicating that starch hydrolysis occurs mainly in the midgut. An overview of the AmyDr gene expression suggests that the amylolytic activity is regulated through the developmental stages of this bark beetle and associated with starch availability in the host tree.

SEOM clinical guideline on hereditary colorectal cancer (2019).

In the last 2 decades, clinical genetics on hereditary colorectal syndromes has shifted from just a molecular characterization of the different syndromes to the estimation of the individual risk of cancer and appropriate risk reduction strategies. In the last years, new specific therapies for some subgroups of patients have emerged as very effective alternatives. At the same time, germline multigene panel testing by next-generation sequencing (NGS) technology has become the new gold standard for molecular genetics.

Correction to: Stabilized Human Cystatin C, Variant L47C/G69C, is a Better Reporter than the Wild-type Inhibitor for Characterizing the Thermodynamics of Binding to Cysteine Proteases.

The original publication of this article contained a number of grammatical errors. Unfortunately, an incorrect version of the file that did not include some final language editing was inadvertently published online. The original article has been corrected.

Stabilized Human Cystatin C Variant L47C/G69C Is a Better Reporter Than the Wild-Type Inhibitor for Characterizing the Thermodynamics of Binding to Cysteine Proteases.

Human cystatin C (HCC) binds and inhibits all types of cysteine proteases from the papain family, including cathepsins (a group of enzymes that participate in a variety of physiological processes), which are some of its natural targets. The affinities of diverse proteases for HCC, expressed as equilibrium binding constants (Kb), range from 106 to 1014 M-1. Isothermal titration calorimetry (ITC) is one of the most useful techniques to characterize the thermodynamics of molecular associations, making it possible to dissect the binding free energy into its enthalpic and entropic components. This information, together with the structural changes that occur during the different associations, could enable better understanding of the molecular basis of affinity. Notwithstanding the high sensitivity of modern calorimeters, ITC requires protein concentrations in at least the 10-100 µM range to obtain reliable data, and it is known that HCC forms oligomers in this concentration range. We present herein a comparative study of the structural, thermal stability, and oligomerization properties of HCC and its stabilized variant (sHCC) L47C/G69C (which possesses an additional disulfide bridge) as well as their binding thermodynamics to the protease chymopapain, analyzed by ITC. The results show that, because sHCC remains monomeric, it is a better reporter than wild-type HCC to characterize the thermodynamics of binding to cysteine proteases.

Novel clinical and molecular findings in Spanish patients with naevoid basal cell carcinoma syndrome.

BACKGROUND: Naevoid basal cell carcinoma syndrome (NBCCS) is an autosomal dominant disorder characterized by developmental alterations and multiple basal cell carcinomas. Mutations in PTCH1, which encodes a membrane receptor for Sonic Hedgehog, are associated with the development of the disease. Most of them produce a truncated protein, which is unable to suppress Smoothened protein and continuously activates the downstream pathway. OBJECTIVES: We aimed to characterize 22 unrelated Spanish patients with NBCCS, the largest cohort with Gorlin syndrome reported to date in Spain. METHODS: Genomic analysis of PTCH1 was performed in patients with NBCCS and controls, and mutations were analysed using bioinformatics tools. RESULTS: We report for the first time two young patients, one each with uterus didelphys and ganglioneuroma, within the context of NBCCS. One patient showing a severe phenotype of the disease had developed basal cell carcinomas since childhood. Sanger sequencing of PTCH1 in this cohort identified 17 novel truncating mutations (11 frameshift, five nonsense and one mutation affecting an exon-intron splice site) and two novel missense mutations that were predicted to be pathogenic. The patients showed great clinical variability and inconsistent genotype-phenotype correlation, as seen in relatives carrying similar mutations. CONCLUSIONS: This study contributes to increase the pool of clinical manifestations of NBCCS, as well as increasing the number of pathogenic mutations identified in PTCH1 predisposing to the condition. The inconsistencies found between phenotype and genotype suggest the involvement of other modifying factors, genetic, epigenetic or environmental.

Clinical guideline seom: hereditary colorectal cancer.

Genetic mutations have been identified as the cause of inherited cancer risk in some colon cancer; these mutations are estimated to account for only 5-6 % of colorectal cancer (CRC) cases overall. Up to 25-30 % of patients have a family history of CRC that suggests a hereditary component, common exposures among family members, or a combination of both. Cancers in people with a hereditary predisposition typically occur at an earlier age than in sporadic cases. A predisposition to CRC may include a predisposition to other cancers, such as endometrial cancer. We describe genetics, current diagnosis and management of CRC hereditary syndromes pointing to a multidisciplinary approach to achieve the best results in patients and family outcomes.

Multifocal-motor-neuropathy-like disease associated with Infliximab treatment in a patient with Crohn's disease.

Multifocal motor neuropathy is an immune-mediated disorder characterized by motor-conduction block in nerve-conduction studies. It is recognized that anti-TNF-α therapies are associated with immune-mediated conditions as adverse events. We report a case of multifocal-motor-neuropathy-like disease associated with the use of Infliximab in a patient with Crohn's disease. The diagnosis was based on neurophysiological evaluation and complete screening tests. Clinical and laboratory findings were not compatible with other potential causes. There was a mild response to the IVIg treatment, and once Infliximab treatment was withdrawn, the patient made slow but substantial progress in his motor function, with partial improvement of motor conduction blocks in the last neurophysiological evaluation. We believe there is a causal relationship between anti-TNF-α treatment and the disorder in this patient. There are few well-documented reports of this association. To our knowledge, our case is the first occurring in a patient with Crohn's disease.

Detailed characterization of MLH1 p.D41H and p.N710D variants coexisting in a Lynch syndrome family with conserved MLH1 expression tumors.

Lynch syndrome (LS) is an autosomal dominant cancer-susceptibility disease caused by inactivating germline mutations in mismatch repair (MMR) genes. Variants of unknown significance (VUS) are often detected in mutational analysis of MMR genes. Here we describe a large family fulfilling Amsterdam I criteria carrying two rare VUS in the MLH1 gene: c.121G > C (p.D41H) and c.2128A > G (p.N710D). Collection of clinico-pathological data, multifactorial analysis, in silico predictions, and functional analyses were used to elucidate the clinical significance of the identified MLH1 VUS. Only the c.121G > C variant cosegregated with LS-associated tumors in the family. Diagnosed colorectal tumors were microsatellite unstable although immunohistochemical staining revealed no loss of MMR proteins expression. Multifactorial likelihood analysis classified c.2128A > G as a non-pathogenic variant and c.121G > C as pathogenic. In vitro functional tests revealed impaired MMR activity and diminished expression of c.121G > C. Accordingly, the N710 residue is located in the unconserved MLH1 C-terminal domain, whereas D41 is highly conserved and located in the ATPase domain. The obtained results will enable adequate genetic counseling of c.121G > C and c.2128A > G variant carriers and their families. Furthermore, they exemplify how cumulative data and comprehensive analyses are mandatory to refine the classification of MMR variants.

[Validation of genetic polymorphisms associated to the toxicity of chemotherapy in colorectal cancer patients]. / Validación de polimorfismos genéticos asociados a toxicidad al tratamiento quimioterápico en pacientes de cáncer colorrectal.

OBJECTIVE: To validate the associations previously found in three cohorts of patients from the General University Hospital Gregorio Marañón, between the polymorphisms rs1128503, rs2032582 and rs1045642 of the ABCB1 gene and the hand-foot syndrome and diarrhea in colorectal cancer patients treated with chemotherapy regimes containing Capecitabine and 5-Fluorouracil, respectively, and between the polymorphisms rs2297595 of the DPYD gene and nausea/vomiting, rs11615 of ERCC1 and neutropenia, and rs28399433 CYP2A6 and neutropenia, in colorectal cancer patients treated with FOLFOX or XELOX as adjuvant therapy. METHOD: Colorectal cancer patients treated with chemotherapy regimes, containing Capecitabine (n = 157), 5-Fluorouracil (n = 99) were included in the study, as well as patients treated with XELOX or FOLFOX (n = 83) as adjuvant therapy. The patients included were recruited from the Doce de Octubre University Hospital and from the Gregorio Marañón General University Hospital, and signed the informed consent form. DNA was obtained from blood samples. Genotyping was carried out with SNaPshot. Contingency tables were created for analyzing the associations between the genotypes and the adverse reactions. RESULTS: None of the associations previously identified was replicated in the validation cohort. CONCLUSIONS: Pharmacogenetic studies with a limited sample size must be validated with bigger cohorts, if possible by means of multicentre studies, reducing the variables to the maximum and should never be used in clinical practice without validation.

OBJETIVO: Validar las asociaciones, encontradas previamente en tres cohortes de pacientes del Hospital General Universitario Gregorio Marañón, entre los polimorfismos rs1128503, rs2032582 y rs1045642 del gen ABCB1 con síndrome manopie y diarrea en pacientes de cáncer colorrectal tratados con regímenes que contenían capecitabina y 5-Fluorouracilo, respectivamente, y entre los polimorfismos rs2297595 del gen DPYD con nauseas/vómitos, rs11615 ERCC1 y neutropenia, y rs28399433 CYP2A6 y neutropenia en pacientes de cáncer colorrectal tratados con FOLFOX o XELOX en adyuvancia. MÉTODO: Se incorporaron al estudio pacientes de cáncer colorrectal tratados con regímenes quimioterápicos que contenían capecitabina (n = 157), 5-fluorouracilo (n = 99) y pacientes tratados en adyuvancia con XELOX o FOLFOX (n = 83). Los pacientes participantes fueron reclutados en el Hospital Universitario Doce de Octubre y en el Hospital General Universitario Gregorio Marañón tras firmar consentimiento informado. Se extrajo ADN a partir de muestras de sangre. Los genotipados se realizaron mediante SNaPshot. Se realizaron tablas de contingencia para analizar las asociaciones entre genotipos y reacciones adversas. RESULTADOS: Ninguna de las asociaciones previamente identificadas fue replicada en la cohorte de validación. CONCLUSIONES: Los estudios farmacogenéticos con un tamaño muestral limitado deben ser validados en cohortes más numerosas, a ser posible en estudios multicéntricos, reduciendo al máximo las variables y nunca deben ser utilizados en clínica sin validar.

Association of BRCA1 germline mutations in young onset triple-negative breast cancer (TNBC).

BACKGROUND: BRCA1-associated breast cancers have been associated to a triple-negative phenotype. The prevalence of BRCA1 germline mutations in young onset TNBC based on informativeness of family history has not been reported. PATIENTS AND METHODS: From January 2008 to May 2009 were collected blood and tumor samples from patients with TNBC younger than 50 years and without a family history of breast and ovarian cancer in first- and second-degree relatives. Analysis of BRCA1 germline mutations was made. Age at diagnosis and informativeness of family history (presence of female in first- and second-degree relatives alive until age 45) was collected in all cases. Immunohistochemistry of basal-like features was performed centrally in all available tumors. RESULTS: Seven pathogenic mutations were detected in 92 patients (7.6 %), two of them in patients younger than 35 years (28.6 %) (Fisher's exact test, p = 0.631). Three non-classified variants were detected (3.2 %). Family history was informative in two patients with a pathogenic mutation (28.6 %) and not informative in five (71.4 %) (Fisher's exact test, p = 0.121). Of the seven patients with a pathogenic mutation, four had a basal-like phenotype. CONCLUSION: Patients with apparently sporadic TNBC younger than 50 years and a non-informative family history are candidates for germline genetic testing of BRCA1.

[Consensus on hereditary cancer between the Spanish Oncology Society and the primary care societies]. / Consenso en cáncer hereditario entre la Sociedad Española de Oncología Médica y las sociedades de atención primaria.

INTRODUCTION: It is believed that 5% of all cancers are hereditary, on being caused by mutations in the germinal line in cancer susceptibility genes. The hereditary pattern in the majority of cases is autosomal dominant. Genetic tests are only recommended to individuals whose personal or family history is highly suggestive of a hereditary cancer. The appropriate assessment of these individuals and their families must be performed in Cancer Genetic Counselling Units (UCGC). MATERIAL AND METHODS: Representatives of the Spanish Medical Oncology Society (Sociedad Española de Oncología Médica [SEOM]) and the three primary care scientific societies: Spanish Society of Family and Community Medicine (Sociedad Española de Medicina de Familia y Comunitaria [SEMFyC]), Spanish Society of Primary Care Physicians (Sociedad Española de Médicos de Atención Primaria [SEMERGEN]) and the Spanish Society of General and Family Doctors (Sociedad Española de Médicos Generales y de Familia [SEMG]), met to prepare this consensus document on hereditary cancer. The consensus identified the three main aspects: how to identify subjects at risk of hereditary cancer; how to refer to a UCGC; and the usefulness of the assessment and genetic studies. RESULTS: A document, with the text fully agreed by all the participants, has been prepared. It contains a summary of the principal characteristics of the care for individuals with hereditary cancer. It shows how to; identify them, assess them, refer them to a UCGC. How to assess their genetic risk, perform genetic studies, as well as prevention measures and reduction of the risk is also presented. CONCLUSIONS: This consensus document is a landmark in the relationships with several Scientific Societies that represent the professionals who provide care to individuals with cancer and their families, and will help to improve care in hereditary cancer in Spain.

Phenotypic characterization of hereditary epithelial ovarian cancer based on a tissue microarray study.

The pathologic and immunohistochemical features of familial epithelial ovarian cancers are not well understood. We have carried out a comprehensive immunohistochemical study of familial ovarian carcinomas from women with and without BRCA1 or BRCA2 mutations, in order to identify specific and/or common features among these different familial case groups (BRCA1, BRCA2 and non-BRCA1/2) and to identify markers of diagnostic value that might help to select more specific treatments. 73 familial primary ovarian carcinomas were analyzed for the expression of 40 antibodies involved in different genetic pathways using a tissue microarray. Serous carcinomas comprised the majority of all three familial case groups. On the other hand, BRCA1 and BRCA2 carcinomas have similar histopathologic features; i.e. they are often high-grade and are usually diagnosed at a more advanced FIGO stage than non-BRCA1/2 carcinomas. In our series, BRCA1 carcinomas had better clinical evolution and they also more frequently over-expressed PR and P53 than BRCA2 and non-BRCA1/2 carcinomas. Unsupervised cluster analysis and survival analysis identified ERCC1 as a potential marker of better clinical outcome for hereditary epithelial ovarian cancer.

Effects of exposure to calves persistently infected with bovine viral diarrhea virus type 1b and subsequent infection with Mannheima haemolytica on clinical signs and immune variables: model for bovine respiratory disease via viral and bacterial interaction.

The objective was to determine effects of an intratracheal Mannheimia haemolytica challenge after 72-h exposure to bovine viral diarrhea virus type 1b (BVDV1b) persistently infected (PI) calves on serum antibody production, white blood cell count (WBC), cytokine concentrations, and blood gases in feedlot steers. Twenty-four steers (initial BW = 314 +/- 31 kg) were randomly allocated to 1 of 4 treatments (6 steers/treatment) arranged as a 2 x 2 factorial. Treatments were 1) steers not exposed to steers PI with BVDV nor challenged with M. haemolytica (control; CON); 2) steers exposed to 2 steers PI with BVDV for 72 h (BVD); 3) steers intratracheally challenged with M. haemolytica (MH); and 4) steers exposed to 2 steers PI with BVDV for 72 h and challenged with M. haemolytica (BVD+MH). There were 12 h between exposure to PI steers and challenge with M. haemolytica. Rectal temperature was increased (P < 0.001) for MH and BVD+MH during the initial 24 h after the M. haemolytica challenge. For MH and BVD+MH, total WBC count was increased (P < 0.01) at 36 h post M. haemolytica challenge compared with CON, whereas in BVD steers, WBC count was decreased (P < 0.01). Total lymphocyte count was increased (P = 0.004) during the initial 72 h post BVDV exposure for the BVD and BVD+MH groups compared with MH and CON, and this difference remained at 96 h post M. haemolytica challenge. An increased (P < 0.001) total neutrophil count was observed during the initial 36 h for the MH group and at 72 h for the BVD+MH challenge group. Interleukin 1beta, IL-6, and tumor necrosis factor alpha (TNFalpha) concentrations were greater (P

Surgical management of hereditary colorectal cancer: surgery based on molecular analysis and family history.

The importance of colorectal cancer (CRC) is increasing. A proportion show a hereditary component, as in Lynch syndrome and Familial Adenomatous Polyposis, and a recently defined entity as well, namely, Familial Colorectal Cancer type X. The high probability to develop CRC in these groups may, at the time of recognition, change surgical management, including its timing or even the surgical technique. In some cases prophylactic surgery can play an important role. The possibility of using tools that allow recognition of the aforementioned syndromes, including microsatellite instability, immunohistochemistry for DNA mismatch repair system proteins, and especially their mutations, is on the basis of therapeutic strategies that differ from those employed in sporadic CRC cases.

Seasonal distribution and modeling of diesel particulate matter in the Southeast US.

The fine and ultra fine size of diesel particulate mater (DPM) are of great health concern and significantly contribute to the overall cancer risk. In addition, diesel particles may contribute a warming effect on the planet's climate. The composition of these particles is composed principally of elemental carbon (EC) with adsorbed organic compounds, sulfate, nitrate, ammonia, metals, and other trace elements. The purpose of this study was to depict the seasonality and modeling of particulate matter in the Southeastern US produced by the diesel fueled sources (DFSs). The modeling results came from four one-month cases including March, June, September, and December to represent different seasons in 2003 by linking Models-3/CMAQ and SMOKE. The 1999 National Emissions Inventory Version 3 (NEI99) was used in this analysis for point, area, and non-road sources, whereas the National Mobile Inventory Model (NMIM) was used to create the on-road emissions. Three urban areas, Atlanta, Birmingham, and Nashville were selected to analyze the DPM emissions and concentrations. Even though the model performance was not very strong, it could be considered satisfactory to conduct seasonal distribution analysis for DPM. Important hourly DPM seasonality was observed in each city, of which higher values occurred at the morning traffic rush hours. The EC contributions of primary DPM were similar for all three sites (approximately 74%). The results showed that there is no significant daily seasonality of DPM contribution to PM(2.5) for any of these three cities in 2003. The annual DPM contribution to total PM(2.5) for Atlanta, Nashville, and Birmingham were 3.7%, 2.5%, and 2.2%, respectively.

Determination of beryllium by electrothermal atomic absorption spectrometry using tungsten surfaces and zirconium modifier.

Electrothermal atomization of beryllium from graphite and tungsten surfaces was compared with and without the use of various chemical modifiers. Tungsten proved to be the best substrate, giving the more sensitive integrated atomic absorption signals of beryllium. Tungsten platform atomization with zirconium as a chemical modifier was used for the determination of beryllium in several NIST SRM certified reference samples, with good agreement obtained between the results found and the certified values. The precision of the measurements (at 10 microgL(-1)), the limit of detection (3sigma), and the characteristic mass of beryllium were 2.50%, 0.009 microgL(-1) and 0.42 pg, respectively.