Considerations and consequences of allowing DNA sequence data as types of fungal taxa.

Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.

Estimates of cancer burden in Trentino-Alto Adige.

AIMS AND BACKGROUND: The Trentino-Alto Adige region is composed of two autonomous provinces (Trento and Bolzano), each with its own cancer registry. The registries' total coverage is 100% of the regional population. The main difference between the two provinces in terms of cancer epidemiology is related to the prostate cancer incidence and survival, with higher values in Bolzano. This paper provides an update until 2015 of the basic epidemiological indicators for seven major cancers for the entire region. METHODS: The indicators were estimated by means of the MIAMOD method, a statistical back-calculation approach to derive incidence and prevalence figures starting from mortality and relative survival data. Mortality data were provided by ISTAT for the period 1970-2002 while survival was modeled on the basis of published data from the Italian cancer registries. RESULTS: The estimates for 2012 show that breast cancer was the most common cancer in women and prostate cancer was most common in men. Incidence and mortality were decreasing for cervix cancer and stomach cancer in both genders during the whole study period. The lung cancer incidence and mortality were decreasing in men but increasing in women. The colorectal cancer incidence rose in both genders while the mortality was decreasing in women. The incidence of skin melanoma increased in both sexes, while the mortality remained very low. The breast cancer incidence was increasing up to 2015 while the mortality was declining since 1986. The prostate cancer incidence increased up to 2006, thereafter the rates stabilized while mortality started to decrease in the early 2000s. The highest mortality rates were estimated for lung cancer in men and breast cancer in women. CONCLUSIONS: Lifestyle plays an important role in cancer trends, as does organized screening for early detection of cervix, breast and colorectal cancer. The provincial data on risk factor distribution and adherence to and coverage of organized screening are satisfactory and their optimization may allow additional benefits in terms of public health.

Changes in the incidence of thyroid cancer between 1991 and 2005 in Italy: a geographical analysis.

BACKGROUND: The incidence of thyroid cancer (TC) has been increasing over the last 30 years in several countries, with some of the worldwide highest TC incidence rates (IRs) reported in Italy. The objectives of this study were to evaluate by histological subtypes the geographical heterogeneity of the incidence of TC in Italy and to analyze recent time trends for papillary thyroid carcinoma (PTC) in different cancer registries (CRs). METHODS: The study included cases of TC (<85 years of age) reported to 25 Italian CRs between 1991 and 2005. Age-standardized IRs were computed for all histological subtypes of TC according to CRs. Estimated annual percent change and joinpoint regression analysis were used for analysis of PTC. RESULTS: In women, IRs of PTC ranged between 3.5/100,000 in Latina and 8.5/100,000 in Sassari for the period 1991-1995 (a 2.4-fold difference) and between 7.3/100,000 in Alto Adige and 37.5/100,000 in Ferrara for 2001-2005 (a 5.1-fold difference). In men, IRs ranged between 0.7/100,000 in Latina and 3.4/100,000 in Sassari for the period 1991-1995 (a 4.9-fold difference) and between 2.0/100,000 (Alto Adige, Trento) and 10.6/100,000 in Ferrara for 2001-2005 (a 5.3-fold difference). In both sexes, IRs significantly higher than the pooled estimates emerged for the most recent period in the majority of CRs located within the Po River plain and in Latina, but they were lower in the Alpine belt. For women, CRs reported higher IRs than pool estimates showed, between 1991 to 2005, a significantly more marked annual percent change (+12%) than other CRs (+7%). For men the corresponding estimates were +11% and +8%. CONCLUSIONS: The distribution of PTC does not lend support to a role of environmental radiation exposure due to the Chernobyl fallout, iodine deficiency, or (volcanic) soils. Between 1991 and 2005, wide geographic variations in the incidence of PTC and heterogeneous upward trends emerged, suggesting that the heterogeneity was a relatively recent phenomenon; this appeared to be mainly explained by variations, at a local level, in medical surveillance.

Cancer incidence in people with AIDS in Italy.

People with HIV/AIDS (PWHA) have increased risk of some cancers. The introduction of highly active antiretroviral therapies (HAART) has improved their life expectancy, exposing them to the combined consequences of aging and of a prolonged exposure to cancer risk factors. The aim of this study was to estimate incidence rates (IR) in PWHA in Italy, before and after the introduction of HAART, after adjusting for sex and age through direct standardization. An anonymous record linkage between Italian AIDS Registry (21,951 cases) and Cancer Registries (17.3 million, 30% of Italian population) was performed. In PWHA, crude IR, sex- and age-standardized IR and age-specific IR were estimated. The standardized IR for Kaposi sarcoma and non-Hodgkin lymphoma greatly declined in the HAART period. Although the crude IR for all non-AIDS-defining cancers increased in the HAART period, standardized IR did not significantly differ in the 2 periods (352 and 379/100,000, respectively). Increases were seen only for cancer of the liver (IR ratio = 4.6, 95% CI: 1.3-17.0) and lung (IR ratio = 1.8, 95% CI: 1.0-3.2). Age-specific IRs for liver and lung cancers, however, largely overlapped in the 2 periods pointing to the strong influence of the shift in the age distribution of PWHA on the observed upward trends. In conclusion, standardized IRs for non-AIDS-defining cancers have not risen in the HAART period, even if crude IRs of these cancers increased. This scenario calls, however, for the intensification of cancer-prevention strategies, notably smoking cessation and screening programs, in middle-aged HIV-patients.

Incidence of primary liver cancer in Italy between 1988 and 2002: an age-period-cohort analysis.

We conducted in Italy a study to evaluate trends of primary liver cancer (PLC) and to disentangle the period from birth-cohort effects on PLC incidence. Cases aged<80 years and diagnosed between 1988 and 2002 in 20 areas covered by population-based Cancer Registries were included. Age-standardised incidence rates and age-period-cohort effects were estimated. In 1998-2002, incidence rates of PLC were 21.1/100,000 men and 6.0/100,000 women. In both genders, incidence rates increased slightly between 1988-1992 and 1993-1997 but did not rise thereafter. Amongst men, PLC risk increased in every cohort born after 1913 and the rise became steeper for cohorts born in 1948. In women, an upward trend appeared only in the cohorts born after 1953. Incidence of PLC over the last two decades in Italy did not substantially change but huge geographical variability emerged, mainly due to different times and modalities of spread of hepatitis C virus.

Estimated and observed cancer incidence in Italy: a validation study.

AIMS AND BACKGROUND: The study aimed to validate model-based incidence estimates by means of observed incidence rates provided by Italian cancer registries, for five major cancer sites (stomach, colon and rectum, lung, breast and prostate cancers) and for all cancers together. METHODS: Recent incidence rates observed by Italian population-based cancer registries were extracted from the data base of the Italian Association of Cancer Registries. Regional estimates of incidence rates for the same cancers were obtained by the MIAMOD method. Observed and estimated crude incidence rates and incidence trends were compared for the period of diagnosis 1985-2000. Eight Italian cancer registries and seven regions were selected for the analysis since they had incidence data available during the entire selected period. RESULTS AND CONCLUSIONS: An excellent agreement between estimated and observed crude incidence rates was found for all single cancer sites, regarding absolute incidence levels and time trends. A partial exception was breast, where empirical data showed a sudden increase in the last three years of observation, perhaps due to organized screenings in some Italian regions, and not captured by statistical models. Substantial underestimation of model-based incidence rates was found for all cancers combined, where the difference tended to increase with calendar year, up to a maximum of 20% in recent years. The greatest part of the discrepancy can be attributed to multiple cancers, which were included in cancer registries statistics but were not accounted for in MIAMOD estimates.

Cancers of the male genital organs: prostate and testis.

The present paper presents the temporal trend analysis of prostate and testis cancers within the Italian Network of Cancer Registries (pool AIRT) for the period 1986-1997. As regards prostate cancer (27,477 incident cases and 11,189 deaths analysed), incidence showed a strong increasing trend, particularly evident in the period 1991-1994, during which standardised rates increased on an average of 12.1% every year. Mortality showed a slight, but significant, decreasing trend. Testis cancer (1,808 incident cases and 185 deaths) incidence increased significantly from 1986 to 1997 and mortality was stable.

Incidence of AIDS-defining cancers after AIDS diagnosis among people with AIDS in Italy, 1986-1998.

A record linkage was carried out between the Italian National Registry of AIDS and 19 cancer registries. The aim was to evaluate the 1986 through 1998 trends in incidence rate (IR) of AIDS-defining cancers (ADCs) among persons with AIDS (PWA) in Italy overall and according to various characteristics. A steady decrease in IRs was found for Kaposi sarcoma (KS) in men between 1986-1992 (2.5 per 100 person-years [py]) and 1997-1998 (1.0 per 100 py). Conversely, the first decrease in IRs of KS in women (from 0.9 to 0.6 per 100 py) and of non-Hodgkin lymphoma in both genders (from 1.7 to 0.7 per 100 py) was seen between 1993-1996 and 1997-1998, thus pointing to a favorable impact of highly active antiretroviral therapies. The decline was consistent across different age and HIV transmission groups, but it was more marked in PWA with a CD4 count >50 cells/microL than in PWA with more severe immune suppression. As a proportion of AIDS cases, invasive cervical cancer increased from 1.5% in 1993-1996 to 2.4% in 1997-1998, but IRs after AIDS could not be evaluated. On account of the marked decline of KS in men in 1997-1998, the overall burden of ADCs in Italy became similar in both genders.