MIRRAGGE – Minimum Information Required for Reproducible AGGregation Experiments

Reports on phase separation and amyloid formation for multiple proteins and aggregation-prone peptides are recurrently used to explore the molecular mechanisms associated with several human diseases. The information conveyed by these reports can be used directly in translational investigation, e.g., for the design of better drug screening strategies, or be compiled in databases for benchmarking novel aggregation-predicting algorithms. Given that minute protocol variations determine different outcomes of protein aggregation assays, there is a strong urge for standardized descriptions of the different types of aggregates and the detailed methods used in their production. In an attempt to address this need, we assembled the Minimum Information Required for Reproducible Aggregation Experiments (MIRRAGGE) guidelines, considering first-principles and the established literature on protein self-assembly and aggregation. This consensus information aims to cover the major and subtle determinants of experimental reproducibility while avoiding excessive technical details that are of limited practical interest for non-specialized users. The MIRRAGGE table (template available in Supplementary Information) is useful as a guide for the design of new studies and as a checklist during submission of experimental reports for publication. Full disclosure of relevant information also enables other researchers to reproduce results correctly and facilitates systematic data deposition into curated databases.This work was supported by (i) the European Regional Development Fund (ERDF) through the COMPETE 2020—Operacional Programme for Competitiveness and Internationalisation (POCI), Portugal 2020, and by Portuguese funds through FCT—Fundação para a Ciência e a Tecnologia (FCT/MCTES) in the framework of grants POCI-01-0145-FEDER-031173, POCI-01-0145-FEDER-007274, POCI-01-0145-FEDER-031323 (“Institute for Research and Innovation in Health Sciences”), UID/Multi/04046/2013 (BioISI) and PTDC/NEUNMC/2138/2014 (to CMG). SV was funded by the Spanish Ministry of Economy and Competitiveness (BIO2016-78310-R) and by ICREA (ICREA-Academia 2015). ZG and ZB were funded by Slovak research agentures VEGA 02/0145/17, 02/0030/18 and APVV-18-0284. RS was funded by VEGA 02/0163/19. DEO was funded by the Lundbeck Foundation (grant no. R276-2018-671) and the Independent Research Foundation Denmark | Natural Sciences (grant no. 8021-00208B). AP research was supported by UK Dementia Research Institute (RE1 3556) and by ARUK (ARUK-PG2019B-020)

Examination of Late Palaeolithic archaeological sites in northern Europe for the preservation of cryptotephra layers

We report the first major study of cryptotephra (non-visible volcanic ash layers) on Late Palaeolithic archaeological sites in northern Europe. Examination of 34 sites dating from the Last Termination reveals seven with identifiable cryptotephra layers. Preservation is observed in minerogenic and organic deposits, although tephra is more common in organic sediments. Cryptotephra layers normally occur stratigraphically above or below the archaeology. Nearby off-site palaeoclimate archives (peat bogs and lakes <0.3 km distant) were better locations for detecting tephra. However in most cases the archaeology can only be correlated indirectly with such cryptotephras. Patterns affecting the presence/absence of cryptotephra include geographic position of sites relative to the emitting volcanic centre; the influence of past atmospherics on the quantity, direction and patterns of cryptotephra transport; the nature and timing of local site sedimentation; sampling considerations and subsequent taphonomic processes. Overall, while tephrostratigraphy has the potential to improve significantly the chronology of such sites many limiting factors currently impacts the successful application

The RESET project: constructing a European tephra lattice for refined synchronisation of environmental and archaeological events during the last c. 100 ka

This paper introduces the aims and scope of the RESET project (. RESponse of humans to abrupt Environmental Transitions), a programme of research funded by the Natural Environment Research Council (UK) between 2008 and 2013; it also provides the context and rationale for papers included in a special volume of Quaternary Science Reviews that report some of the project's findings. RESET examined the chronological and correlation methods employed to establish causal links between the timing of abrupt environmental transitions (AETs) on the one hand, and of human dispersal and development on the other, with a focus on the Middle and Upper Palaeolithic periods. The period of interest is the Last Glacial cycle and the early Holocene (c. 100-8 ka), during which time a number of pronounced AETs occurred. A long-running topic of debate is the degree to which human history in Europe and the Mediterranean region during the Palaeolithic was shaped by these AETs, but this has proved difficult to assess because of poor dating control. In an attempt to move the science forward, RESET examined the potential that tephra isochrons, and in particular non-visible ash layers (cryptotephras), might offer for synchronising palaeo-records with a greater degree of finesse. New tephrostratigraphical data generated by the project augment previously-established tephra frameworks for the region, and underpin a more evolved tephra 'lattice' that links palaeo-records between Greenland, the European mainland, sub-marine sequences in the Mediterranean and North Africa. The paper also outlines the significance of other contributions to this special volume: collectively, these illustrate how the lattice was constructed, how it links with cognate tephra research in Europe and elsewhere, and how the evidence of tephra isochrons is beginning to challenge long-held views about the impacts of environmental change on humans during the Palaeolithic. © 2015 Elsevier Ltd.RESET was funded through Consortium Grants awarded by the Natural Environment Research Council, UK, to a collaborating team drawn from four institutions: Royal Holloway University of London (grant reference NE/E015905/1), the Natural History Museum, London (NE/E015913/1), Oxford University (NE/E015670/1) and the University of Southampton, including the National Oceanography Centre (NE/01531X/1). The authors also wish to record their deep gratitude to four members of the scientific community who formed a consultative advisory panel during the lifetime of the RESET project: Professor Barbara Wohlfarth (Stockholm University), Professor Jørgen Peder Steffensen (Niels Bohr Institute, Copenhagen), Dr. Martin Street (Romisch-Germanisches Zentralmuseum, Neuwied) and Professor Clive Oppenheimer (Cambridge University). They provided excellent advice at key stages of the work, which we greatly valued. We also thank Jenny Kynaston (Geography Department, Royal Holloway) for construction of several of the figures in this paper, and Debbie Barrett (Elsevier) and Colin Murray Wallace (Editor-in-Chief, QSR) for their considerable assistance in the production of this special volume.Peer Reviewe

Genomic characterization of enterohaemolysin-encoding haemolytic Escherichia coli of animal and human origin

Enterohaemolysin (Ehx) and alpha-haemolysin are virulence-associated factors (VAFs) causing the haemolytic phenotype in . It has been shown that chromosomally and plasmid-encoded alpha-haemolysin are characteristic of specific pathotypes, virulence-associated factors and hosts. However, the prevalence of alpha- and enterohaemolysin does not overlap in the majority of pathotypes. Therefore, this study focuses on the characterization of the haemolytic population associated with multiple pathotypes in human and animal infectious diseases. Using a genomics approach, we investigated characteristic features of the enterohaemolysin-encoding strains to identify factors differentiating enterohaemolysin-positive from alpha-haemolysin-positive populations. To shed light on the functionality of Ehx subtypes, we analysed Ehx-coding genes and inferred EhxA phylogeny. The two haemolysins are associated with a different repertoire of adhesins, iron acquisition or toxin systems. Alpha-haemolysin is predominantly found in uropathogenic (UPEC) and predicted to be chromosomally encoded, or nonpathogenic and undetermined pathotypes and typically predicted to be plasmid-encoded. Enterohaemolysin is mainly associated with Shiga toxin-producing (STEC) and enterohaemorrhagic (EHEC) and predicted to be plasmid-encoded. Both types of haemolysin are found in atypical enteropathogenic (aEPEC). Moreover, we identified a new EhxA subtype present exclusively in genomes with VAFs characteristic of nonpathogenic . This study reveals a complex relationship between haemolytic of diverse pathotypes, providing a framework for understanding the potential role of haemolysin in pathogenesis

Computer evaluation of the body posture of the young soccer players selected biomechanical parameters

Wstęp. Postawa ciała uwarunkowana jest napięciem odpowiednich grup mięśni, które decydują o określonym ułożeniu poszczególnych segmentów ciała człowieka. Coraz częściej wśród dzieci i młodzieży pojawiają się różnego rodzaju wady postawy ciała, które mogą być spowodowane czynnikami funkcjonalnymi. Jedną z przyczyn ich powstawania może być asymetria obciążeń, jaka często występuje w treningu specjalistycznym. Materiał i metody. Materiał badawczy stanowią wyniki pomiarów 24 piłkarzy nożnych w wieku 15 lat. Badania obejmowały ocenę postawy ciała, cechy antropometryczne oraz pomiary momentów sił prostowników i zginaczy stawu kolanowego. Pomiar statycznego momentu siły mięśniowej przeprowadzono na specjalnym stanowisku pomiarowym firmy OPIW. Do oceny postawy ciała wykorzystano sprzężony z komputerem posturometr S. Wyniki i wnioski. Kryterium oceny pomiaru kręgosłupa w płaszczyźnie czołowej była wartość kąta Cobba. Na tej podstawie stwierdzono występowanie skoliozy lub śladowej skoliozy lewostronnej u 29,3% badanych piłkarzy. W grupie ogółu badanych stwierdzono nieznaczną dominację prostowników i zgi- naczy prawej kończyny dolnej nad lewą. Ta sama tendencja występuje u osób bez skoliozy. U zawodników z bocznym skrzywieniem kręgosłupa dominują mięśnie prostujące i zginające staw kolanowy kończyny lewej. Ważnym kryterium oceny dozowanych obciążeń treningowych piłkarzy nożnych w obrębie prawej i lewej strony ciała może być badanie postawy ciała i momentów sił obydwu kończyn dolnych. Pozwoli to na ewentualne zniwelowanie nieprawidłowości w stosowanych metodach treningowych, które mogą być przyczyną problemów zdrowotnych sportowców.Introduction. Body posture is determined by muscular tone of the particular muscles that decide about the specific position of the human body segments. This feature is influenced by a tension of muscle groups, which determine the position of separate human body segments. Varius types of spinal abnormalities are caused by functional factors. Material and method. 24 soccer players in the age of 15 were examined. The study included body posture, anthropometric features, the force moments of knee joint flexors and extensors. The static measurements of the muscles’ force moment were evaluated on the special measurement post, made by OPIW Company. The body posture was assessed by means of computer aided posturometer S. Results and conclusions. The value of Cobb angle was the evaluation criterion for the spine measurement in the frontal plane. On that basis the scoliosis or the weak symptoms of left side scoliosis in 29,3% examined players were registered. A slight domination of the right lower limb extensors and flexors over left limb was observed in the research group. The same tendency is observed in the group without scoliosis. The opposite strength arrangement i.e. the domination of flexors and extensors bending left limb knee joint, was found in players with scoliosis. The examination of body posture and force moments of two limbs can be an important evaluation criterion of dosed training loads in soccer players within the area of both left and right body sections. It will help avoiding incorrectness in the applied methods, which may cause athletes’ health problems

Morphological structure and characteristics of judo contestants' feet

W pracy poddano analizie budowę morfologiczną oraz charakterystykę stóp zawodników uprawiających dżudo. Do opracowania wykorzystano pomiary antropometryczne 58 mężczyzn. Budowę ciała oceniono, za pomocą typologii Williama Sheldona oraz wskaźnika względnej masy ciała BMI (wskaźnik masy ciała). Posługując się podosla)pem, wyznaczono Itąty Alfe, Beta, Clarice'a i Gamma, charakteryzujące wybrane parametry stóp.The analysis of morphological structure and characteristics of judo contestants' feet, was carried out. The anthropometric data of 58 men were collected. The body build was evaluated on the basis of William Sheldon typology and the body mass index (BMI). The podoscope was used to determine Alfa, Beta, Clarice's, and Gamma angles that characterize the specific feet parameters

Body composition examined by use of the bioelectrical impedance analysis in adolescent teenagers

Początki badań składu ciała sięgają drugiej połowy XIX wieku. Od tego czasu obserwuje się intensywny i wielokierunkowy rozwój metod pomiarów umożliwiających zrozumienie procesów fizjologicznych i biochemicznych oraz wspomagających leczenie chorób, takich jak otyłość lub anoreksja. Jedną z bardziej popularnych jest nieinwazyjna analiza bioimpedancji elektrycznej (BIA – Bioelectrical Impedance Analysis). Materiał i metoda. W artykule wykorzystano wyniki badań longitudinalnych dziewcząt (N = 91) i chłopców (N = 89) w wieku 13–15 lat. Zmierzono wysokość, masę ciała oraz skład ciała za pomocą aparatu BIA 101S. Określono: procentową zawartość tłuszczu, masy komórkowej i masy pozakomórkowej. Wyznaczono wskaźnik masy ciała (BMI – Body Mass Index) i obliczono stosunek masy ciała szczupłego do masy tłuszczu oraz masy komórkowej do masy pozakomórkowej. Statystyczną analizę wyników przeprowadzono za pomocą programu Statistica 9.0. Wyniki. W analizowanym przedziale wieku większe tempo rozwoju masy ciała w odniesieniu do jego wysokości wpływa na kształtowanie masywniejszej sylwetki u badanej młodzieży. Powiększenie masywności budowy płci męskiej dotyczy przede wszystkim rozwoju masy ciała szczupłego, zwłaszcza masy komórkowej. U dziewcząt w analizowanym okresie ontogenezy wzrost masywności ciała wynika z większych przyrostów masy tłuszczu.The examinations of the body components is known since 19th century. Such analysis is important e.g. for the treatment of anorexia and obesity. One of the most popular methods is the Bioelectrical Impedance Analysis (BIA) – non-invasive and effective way to determine the human body composition. Material and method. In this paper, the results of longitudinal measurements of girls (N = 91) and boys (N = 89), aged 13 to 15, were analyzed. The body height, mass and tissue composition were measured by means of BIA 101S Apparatus (% fat, % body cell mass, % extracellular mass). Body Mass Index (BMI) and the ratio of the lean body mass to fat mass, as well as the body cell mass to extracellular mass, were calculated. The statistical analysis was performed by means Statistica 9.0. Results. Within the analysed age range, the higher pace of the body mass development, in relation to the body height, causes more massive posture of examined youths. The increase of body massiveness in boys is connected mainly with the development of lean body mass, in particular, the cell mass. In girls in the analysed ontogenetic period, the increase of body massiveness results from the greater increase of fat mass

Anthropometric characteristics and lower limb power of professional female volleyball players

Success in performing professional sport is determined by many factors. Motor skills, psychological conditions and somatic structure are important. The aim of this research was to investigate detailed anthropometrical characteristics of highly skilled female volleyball players and their non-sporting peers. Additionally, the diversity of those features based on court position was examined. The sample consisted of first league female volleyball players (N=17), while 50 students from the University School of Physical Education served as reference group. The 35 anthropometric measurements, complemented by a biomechanical evaluation of lower limb power using the counter movement jump (CMJ), were examined. The values of height, length, width and body circumference were significantly higher for female volleyball players than those obtained from the reference group. The female volleyball players revealed a balanced mesomorphic somatotype. Stature differed and was related to court position. In comparison to the attackers and setters, the receivers, middle and libero players were characterised by better CMJ. This knowledge could enable coaches to individualise and determine suitable training methods, depending on the somatic predisposition of an athlete, which will reduce the risk of injury.Key words: Anthropometry; Body composition; Counter movement jump; Volleyball

Algorithms for automated detection of hook effect-bearing amplification curves

Amplification curves from quantitative Real-Time PCR experiments typically exhibit a sigmoidal shape. They can roughly be divided into a ground or baseline phase, an exponential amplification phase, a linear phase and finally a plateau phase, where in the latter, the PCR product concentration no longer increases. Nevertheless, in some cases the plateau phase displays a negative trend, e.g. in hydrolysis probe assays. This cycle-to-cycle fluorescence decrease is commonly referred to in the literature as the hook effect. Other detection chemistries also exhibit this negative trend, however the underlying molecular mechanisms are different.In this study we present two approaches to automatically detect hook effect-like curvatures based on linear (hookreg) and nonlinear regression (hookregNL). As the hook effect is typical for qPCR data, both algorithms can be employed for the automated identification of regular structured qPCR curves. Therefore, our algorithms streamline quality control, but can also be used for assay optimization or machine learning. Keywords: Hook effect, QPCR, TaqMan, EvaGreen, SybrGreen, Linear, Nonlinear, RDML, Automatio