Predicting the secondary structure of proteins using Machine Learning algorithms

The functions of proteins in living organisms are related to their 3-D structure, which is known to be ultimately determined by their linear sequence of amino acids that together form these macromolecules. It is, therefore, of great importance to be able to understand and predict how the protein 3D-structure arises from a particular linear sequence of amino acids. In this paper we report the application of Machine Learning methods to predict, with high values of accuracy, the secondary structure of proteins, namely alpha-helices and beta-sheets, which are intermediate levels of the local structure

Iliac artery false aneurysm twelve years after allograft nephrectomy

We report a case of a non-infected right external iliac artery false aneurysm. The patient was a 44 year-old woman on chronic peritoneal dialysis had had an allograft nephrectomy 12 years before and who presented with acute abdominal pain. Ultrasound and CT-scan showed a saccular aneurysm arising from the right external iliac artery. A large false aneurysm was identified during surgery, from donor arterial vessel remaining in situ after graft nephrectomy. Resection of the false aneurysm, with ligation of the right external iliac artery and interposition of a femorofemoral graft was successfully performed, with an uneventful post-operative recovery. False aneurysms after renal allograft nephrectomy are very rare. To our knowledge, this is the longest reported period of time between na nephrectomy and clinical evidence of a false aneurysm.info:eu-repo/semantics/publishedVersio

Fungal peritonitis in peritoneal dialysis patients: is previous antibiotic therapy an essential condition?

The aim of this study was to analyse the clinical and microbiological features of fungal peritonitis, in chronic peritoneal dialysis patients, focusing on non-traditional risk factors for this feared complication. From 2001 to 2004, five episodes of fungal peritonitis were diagnosed in five different patients, accounting for 4.5% of all peritonitis cases seen during this period. Candida spp. were the most frequent isolates. In all cases, peritoneal dialysis catheter removal and switching to haemodialysis were necessary. In these five cases of fungal peritonitis only one was preceded by antibiotic use, within the previous 3 months, the classical risk factor for fungal peritonitis. Identifying predisposing factors usually not taken into account, may lead to an early diagnosis and to a better understanding of fungal peritonitis pathogenesis.info:eu-repo/semantics/publishedVersio

Entre consumos suntuários e comuns: a posse de objetos exóticos entre alguns habitantes do Porto (séculos XVI – XVII)

O estudo da documentação referente aos doadores da Misericórdia do Porto entre os séculos XVI e XVII, através dos objetos exóticos patentes nos respectivos testamentos e inven- tários – estes últimos provenientes de uma área que se estende de Macau ao Brasil –, permite discernir uma panóplia de objetos que mudaram a cultura material dos portuenses em contato com os territórios da expansão portuguesa. Um levantamento sistemático permitiu já rastrear, até o ano de 1699, 257 doadores, dos quais se apresentarão aqui apenas alguns, referentes a benfeitores que, não obstante possuírem bens móveis nesse âmbito, não são dados como tendo estado nos territórios de expansão transoceânica. Argumentar-se-á que essa circulação de objetos não foi exclusiva das elites nobiliárquicas, nem dos grandes centros urbanos, pelo que a sua difusão atingiu maiores proporções do que aquelas que a historiografia tem admitido até agora. A cidade em observação neste estudo – o Porto dos séculos XVI e XVII – estava longe de ser das maiores da Europa nesse período, quer em dimensão territorial, quer em efetivos populacionais, embora se situasse numa região de demografia pujante, que canalizou os seus excedentes desde cedo para a emigração interna e externa – o Entre Douro e Minho. Como teremos ocasião de verificar, fidalgos e nobres possuíam bens exóticos, mas estes encontravam-se também entre mercadores e até artesãos mais desafogados. Por outro lado, nem todos os objetos provenientes dos espaços da expansão transoceânica devem ser conotados com bens de luxo.The study of the sources referring to the donors of the Misericórdia of the city of Porto during the sixteenth and seventeenth centuries has revealed the presence of numerous exotic objects in their last wills and inventories. A survey has traced 257 donors until 1699, some of them having died in an area that extends from Macao to Brazil. Only a small number of cases shall be presented here, pertaining to benefactors who, in spite of owning objects of transoceanic origin, seem to have remained in mainland Portugal. It shall be argued that the circulation of objects has not been exclusive either to the elites of the nobility or to the large urban centres, their diffusion having been on a larger scale than what has been admitted until now. The city under scrutiny in this study – Porto during the sixteenth and seventeenth centuries – was not one of the bigger cities in this period, either in what respects to size or population, although it was located in an area of flourishing demography, that channelled its surplus population early on to internal and external emigration. Fidalgos and noblemen owned exotic goods, but these were to be found among merchants and even well-to-do artisans. On the other hand, not all objects originating from the areas of transoceanic expansion should be considered as luxury goods.info:eu-repo/semantics/publishedVersio

Search for dark matter produced in association with bottom or top quarks in √s = 13 TeV pp collisions with the ATLAS detector

A search for weakly interacting massive particle dark matter produced in association with bottom or top quarks is presented. Final states containing third-generation quarks and miss- ing transverse momentum are considered. The analysis uses 36.1 fb−1 of proton–proton collision data recorded by the ATLAS experiment at √s = 13 TeV in 2015 and 2016. No significant excess of events above the estimated backgrounds is observed. The results are in- terpreted in the framework of simplified models of spin-0 dark-matter mediators. For colour- neutral spin-0 mediators produced in association with top quarks and decaying into a pair of dark-matter particles, mediator masses below 50 GeV are excluded assuming a dark-matter candidate mass of 1 GeV and unitary couplings. For scalar and pseudoscalar mediators produced in association with bottom quarks, the search sets limits on the production cross- section of 300 times the predicted rate for mediators with masses between 10 and 50 GeV and assuming a dark-matter mass of 1 GeV and unitary coupling. Constraints on colour- charged scalar simplified models are also presented. Assuming a dark-matter particle mass of 35 GeV, mediator particles with mass below 1.1 TeV are excluded for couplings yielding a dark-matter relic density consistent with measurements

Global burden of 288 causes of death and life expectancy decomposition in 204 countries and territories and 811 subnational locations, 1990–2021: a systematic analysis for the Global Burden of Disease Study 2021

BACKGROUND Regular, detailed reporting on population health by underlying cause of death is fundamental for public health decision making. Cause-specific estimates of mortality and the subsequent effects on life expectancy worldwide are valuable metrics to gauge progress in reducing mortality rates. These estimates are particularly important following large-scale mortality spikes, such as the COVID-19 pandemic. When systematically analysed, mortality rates and life expectancy allow comparisons of the consequences of causes of death globally and over time, providing a nuanced understanding of the effect of these causes on global populations. METHODS The Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2021 cause-of-death analysis estimated mortality and years of life lost (YLLs) from 288 causes of death by age-sex-location-year in 204 countries and territories and 811 subnational locations for each year from 1990 until 2021. The analysis used 56 604 data sources, including data from vital registration and verbal autopsy as well as surveys, censuses, surveillance systems, and cancer registries, among others. As with previous GBD rounds, cause-specific death rates for most causes were estimated using the Cause of Death Ensemble model-a modelling tool developed for GBD to assess the out-of-sample predictive validity of different statistical models and covariate permutations and combine those results to produce cause-specific mortality estimates-with alternative strategies adapted to model causes with insufficient data, substantial changes in reporting over the study period, or unusual epidemiology. YLLs were computed as the product of the number of deaths for each cause-age-sex-location-year and the standard life expectancy at each age. As part of the modelling process, uncertainty intervals (UIs) were generated using the 2·5th and 97·5th percentiles from a 1000-draw distribution for each metric. We decomposed life expectancy by cause of death, location, and year to show cause-specific effects on life expectancy from 1990 to 2021. We also used the coefficient of variation and the fraction of population affected by 90% of deaths to highlight concentrations of mortality. Findings are reported in counts and age-standardised rates. Methodological improvements for cause-of-death estimates in GBD 2021 include the expansion of under-5-years age group to include four new age groups, enhanced methods to account for stochastic variation of sparse data, and the inclusion of COVID-19 and other pandemic-related mortality-which includes excess mortality associated with the pandemic, excluding COVID-19, lower respiratory infections, measles, malaria, and pertussis. For this analysis, 199 new country-years of vital registration cause-of-death data, 5 country-years of surveillance data, 21 country-years of verbal autopsy data, and 94 country-years of other data types were added to those used in previous GBD rounds. FINDINGS The leading causes of age-standardised deaths globally were the same in 2019 as they were in 1990; in descending order, these were, ischaemic heart disease, stroke, chronic obstructive pulmonary disease, and lower respiratory infections. In 2021, however, COVID-19 replaced stroke as the second-leading age-standardised cause of death, with 94·0 deaths (95% UI 89·2-100·0) per 100 000 population. The COVID-19 pandemic shifted the rankings of the leading five causes, lowering stroke to the third-leading and chronic obstructive pulmonary disease to the fourth-leading position. In 2021, the highest age-standardised death rates from COVID-19 occurred in sub-Saharan Africa (271·0 deaths [250·1-290·7] per 100 000 population) and Latin America and the Caribbean (195·4 deaths [182·1-211·4] per 100 000 population). The lowest age-standardised death rates from COVID-19 were in the high-income super-region (48·1 deaths [47·4-48·8] per 100 000 population) and southeast Asia, east Asia, and Oceania (23·2 deaths [16·3-37·2] per 100 000 population). Globally, life expectancy steadily improved between 1990 and 2019 for 18 of the 22 investigated causes. Decomposition of global and regional life expectancy showed the positive effect that reductions in deaths from enteric infections, lower respiratory infections, stroke, and neonatal deaths, among others have contributed to improved survival over the study period. However, a net reduction of 1·6 years occurred in global life expectancy between 2019 and 2021, primarily due to increased death rates from COVID-19 and other pandemic-related mortality. Life expectancy was highly variable between super-regions over the study period, with southeast Asia, east Asia, and Oceania gaining 8·3 years (6·7-9·9) overall, while having the smallest reduction in life expectancy due to COVID-19 (0·4 years). The largest reduction in life expectancy due to COVID-19 occurred in Latin America and the Caribbean (3·6 years). Additionally, 53 of the 288 causes of death were highly concentrated in locations with less than 50% of the global population as of 2021, and these causes of death became progressively more concentrated since 1990, when only 44 causes showed this pattern. The concentration phenomenon is discussed heuristically with respect to enteric and lower respiratory infections, malaria, HIV/AIDS, neonatal disorders, tuberculosis, and measles. INTERPRETATION Long-standing gains in life expectancy and reductions in many of the leading causes of death have been disrupted by the COVID-19 pandemic, the adverse effects of which were spread unevenly among populations. Despite the pandemic, there has been continued progress in combatting several notable causes of death, leading to improved global life expectancy over the study period. Each of the seven GBD super-regions showed an overall improvement from 1990 and 2021, obscuring the negative effect in the years of the pandemic. Additionally, our findings regarding regional variation in causes of death driving increases in life expectancy hold clear policy utility. Analyses of shifting mortality trends reveal that several causes, once widespread globally, are now increasingly concentrated geographically. These changes in mortality concentration, alongside further investigation of changing risks, interventions, and relevant policy, present an important opportunity to deepen our understanding of mortality-reduction strategies. Examining patterns in mortality concentration might reveal areas where successful public health interventions have been implemented. Translating these successes to locations where certain causes of death remain entrenched can inform policies that work to improve life expectancy for people everywhere. FUNDING Bill & Melinda Gates Foundation