Multidisciplinary studies on a sick-leader syndrome-associated mass stranding of sperm whales (Physeter macrocephalus) along the Adriatic coast of Italy

Mass strandings of sperm whales (Physeter macrocephalus) are rare in the Mediterranean Sea. Nevertheless, in 2014 a pod of 7 specimens stranded alive along the Italian coast of the Central Adriatic Sea: 3 individuals died on the beach after a few hours due to internal damages induced by prolonged recumbency; the remaining 4 whales were refloated after great efforts. All the dead animals were genetically related females; one was pregnant. All the animals were infected by dolphin morbillivirus (DMV) and the pregnant whale was also affected by a severe nephropathy due to a large kidney stone. Other analyses ruled out other possible relevant factors related to weather conditions or human activities. The results of multidisciplinary post-mortem analyses revealed that the 7 sperm whales entered the Adriatic Sea encountering adverse weather conditions and then kept heading northward following the pregnant but sick leader of the pod, thereby reaching the stranding site. DMV infection most likely played a crucial role in impairing the health condition and orientation abilities of the whales. They did not steer back towards deeper waters, but eventually stranded along the Central Adriatic Sea coastline, a real trap for sperm whales

Acute Delta Hepatitis in Italy spanning three decades (1991–2019): Evidence for the effectiveness of the hepatitis B vaccination campaign

Updated incidence data of acute Delta virus hepatitis (HDV) are lacking worldwide. Our aim was to evaluate incidence of and risk factors for acute HDV in Italy after the introduction of the compulsory vaccination against hepatitis B virus (HBV) in 1991. Data were obtained from the National Surveillance System of acute viral hepatitis (SEIEVA). Independent predictors of HDV were assessed by logistic-regression analysis. The incidence of acute HDV per 1-million population declined from 3.2 cases in 1987 to 0.04 in 2019, parallel to that of acute HBV per 100,000 from 10.0 to 0.39 cases during the same period. The median age of cases increased from 27 years in the decade 1991-1999 to 44 years in the decade 2010-2019 (p < .001). Over the same period, the male/female ratio decreased from 3.8 to 2.1, the proportion of coinfections increased from 55% to 75% (p = .003) and that of HBsAg positive acute hepatitis tested for by IgM anti-HDV linearly decreased from 50.1% to 34.1% (p < .001). People born abroad accounted for 24.6% of cases in 2004-2010 and 32.1% in 2011-2019. In the period 2010-2019, risky sexual behaviour (O.R. 4.2; 95%CI: 1.4-12.8) was the sole independent predictor of acute HDV; conversely intravenous drug use was no longer associated (O.R. 1.25; 95%CI: 0.15-10.22) with this. In conclusion, HBV vaccination was an effective measure to control acute HDV. Intravenous drug use is no longer an efficient mode of HDV spread. Testing for IgM-anti HDV is a grey area requiring alert. Acute HDV in foreigners should be monitored in the years to come

Neue computationelle Methoden für die Automatische Zuordnung von Kreuzsignalen in Lösungs- und Festkörper-NMR Proteinspektren.

0\. Title Page and Table of Contents 1\. General Introduction 10 1.1 Nuclear Magnetic Resonance (NMR) 10 1.2 Solution NMR 16 1.3 Solid-state NMR 24 1.4 ARIA 32 1.5 Overview of the thesis 48 2\. Material und Methods 50 2.1 ARIA calculations 50 2.2 SOLARIA calculations 52 3\. Influence of chemical shift tolerances on NMR structure calculations using ARIA protocols for assigning NOE data 54 3.1 Introduction 54 3.2 Cesta.py: a pre-calculation analysis of the influence of chemical shift tolerances on peak annotation 52 3.3 Results and discussion 61 3.4 Conclusions 73 4\. Quantitative study of the effects of chemical shift tolerances and rates of SA cooling on structure calculation from automatically assigned NOE data 76 4.1 Introduction 76 4.2 Results and discussion 77 4.3 Conclusions 92 5\. SOLARIA: a protocol for automated cross-peak assignment and structure calculation for solid-state NMR 94 5.1 Introduction 94 5.2 Computational aspects 95 5.3 Results and discussion 99 5.4 Conclusions and perspectives 105 6\. Summary 108 6.1 Summary of the work and future perspectives 108 6.2 Zusammenfassung 111 Bibliography 116In the last few years, protein structure determination by solution NMR has benefited enormously from the introduction of software packages for automatically assigning NOESY spectra of small proteins. However, experience shows that more robust protocols are required to tackle the problem of structure calculation of larger proteins or protein complexes. Also, new challenges such as the automation of protein structure determination by MAS solid-state NMR need to be addressed. This first part of this work represents a thorough study of the influence of the input conditions on the performance of such programmes, using the ARIA protocol (Ambiguous Restraints for Iterative Assignment) as an example. The second section is focused on automated structure calculations using solid-state NMR data. In Chapters 3 and 4, the influence of three important parameters, the chemical shift tolerances D, the cut-off nmax for the assignment possibilities of a peak and the number of simulated annealing cooling steps, was extensively investigated. A large number of structure calculations on datasets from five proteins were performed in which these three parameters were systematically varied. In the course of this study, the dependence of the average number of assignment options per peak (nav) and of the number of rejected peaks on D and nmax was studied and rationalised by mathematical relations. It turned out that these functions might be employed as a diagnostic tool to detect macroscopic anomalies in datasets, and, most importantly, to guide the choice of Dand nmax prior to structure calculation. A Python script, named Cesta.py, was created and made freely available for rapidly evaluating these diagnostic functions prior to structure calculations. In Chapter 5, a modification of the ARIA procedure is described, which is specifically designed to assign cross-peaks of solid-state NMR PDSD spectra. This new software, SOLARIA, accepts also typical solid-state 13C-13C and 13C-15N correlations in the input peak lists and exploits the characteristic 13C-labelling scheme of the samples to simplify the assignment of the cross-peaks. PDSD spectra are notably affected by extensive resonance overlap and large line widths, which prevent an accurate measurement of the chemical shifts. To compensate for this, generous values of the tolerances D have to be chosen, which leads to high numbers of assignment options per peak. Furthermore, PDSD spectra lack a clear dependence of measured volumes on inter-nuclear distances. Such a problem was circumvented in SOLARIA by the use of unusually large, uniform boundaries for all distance restraints, which reduces, however, their effectiveness in restraining the structure. The quality of the structures of the SH3 domain calculated by SOLARIA expressed as root-mean-square deviation to the X-ray reference varied from 1.3 Å, when inter-molecular cross-peaks were manually removed, to 2.2 Å, when they were included in the calculation. This is the first example of protein structure determination by automated assignment of MAS NMR spectra of solid protein samples. The automation of cross-peak assignment resulted in a dramatic speed- up of the whole procedure and, most importantly, provided a way to handle unassigned, ambiguous cross-peaks in MAS NMR spectra.In den letzten Jahren hat die Proteinstrukturbestimmung mittels NMR von der Einführung von Softwarepaketen für die automatische Zuordnung von NOESY Spektren und die Strukturberechnung kleiner Proteine stark profitiert. Robustere Protokolle sind jedoch notwendig, um das Problem der Strukturberechnung von größeren Proteinen und von Proteinkomplexen anzugehen. Zusätzlich ergeben sich mit der Automatisierung von Strukturbestimmung durch MAS NMR neue Herausforderungen, zu deren Bewältigung neue Lösungswege beschritten werden müssen. Der erste Teil dieser Arbeit stellt eine Untersuchung des Einflusses der Eingabeparameter auf die Leistung solcher Programme anhand des Beispiels des ARIA-Protokolls dar. Der zweite Teil beschäftigt sich mit der Automatisierung von Proteinstrukturbestimmung mittels Festkörper-NMR Daten. In den Kapiteln 3 und 4 wird der Einfluss dreier wichtiger Parameter, der Toleranzen Dfür die chemischen Verschiebungen, des Höchstwertes nmax für die Zuordnungsmöglichkeiten eines Kreuzsignals und der Kühlungsgeschwindigkeit während des Simulated Annealing, untersucht. Dazu wurden viele Strukturberechnungen angesetzt, in denen diese Parameter systematisch geändert wurden. Dabei wurde die Abhängigkeit von D und nmax der Durchschnittsanzahl der Zuordnungsmöglichkeiten pro Kreuzsignal und der Anzahl der verworfenen Kreuzsignale untersucht und durch Formeln beschrieben. Diese Untersuchungen zeigten, dass solche Funktionen als diagnostisches Werkzeug benutzt werden können, um makroskopische Anomalien zu erkennen, und, was noch wichtiger ist, bei der Auswahl von D und nmax vor der Strukturberechnung zu helfen. Ein frei herunterladbares Python Script, Cesta.py, wurde erstellt, um diese diagnostischen Funktionen vor der Strukturberechnung schnell auszuwerten. Im Kapitel 5 wird eine Abwandlung des ARIA-Verfahrens beschrieben, die besonders dafür geeignet ist, Kreuzsignale in PDSD Festkörper-NMR-Spektren zuzuordnen. Dieses neue Software, SOLARIA, akzeptiert auch typische Festkörper-Korrelationen in den Kreuzsignallisten und nutzt das charakteristische Markierungsmuster der Proben, um die Zuordnung zu vereinfachen. PDSD Spektren zeigen bekanntlich eine höhere Überlagerung von Resonanzen und große Linienbreiten, die eine genaue Messung der chemischen Verschiebungen erschweren. Um Zuordnungsfehler zu vermeiden, müssen große Werte für die D-Toleranzen gewählt werden, welche zu einer großen Anzahl von Zuordnungsmöglichkeiten führen. Dazu mangelt es PDSD Spektren an einer deutlichen Abhängigkeit der gemessenen Volumina von internuklearen Abständen. Dieses Problem wurde in SOLARIA dadurch gelöst, dass außergewöhnlich große und gleiche Grenzen für alle Abstandsschranken benutzt werden, die jedoch ihre Nützlichkeit, die Struktur zu definieren, mindern. SOLARIA lieferte genaue Strukturen von der SH3 domäne, mit mittlerer quadratischer Differenz zu der Röntgen-Referenzstruktur von 1.3 Å, wenn die intermolekularen Kreuzsignale manuell verworfen wurden, oder 2.2 Å, wenn sie in die Rechnung einbezogen wurden. Das ist das erste Beispiel von Strukturbestimmung eines Proteins im Festkörper mittels automatischer Zuordnung von MAS-NMR Spektren. Die Automatisierung der Kreuzsignalzuordnung führte zu einer erheblichen Beschleunigung des gesamten Verfahrens und, was noch wichtiger ist, ermöglichte die Zuordnung von sehr mehrdeutigen Kreuzsignale, die man manuell nicht zuordnen konnte

Hangi Duyu?: Duyu Eğitimine Yönelik Kısa Bir Kılavuz

Duyarlı olmak, sağ duyulu olmak… Bunlar, duyuların yönelimimiz için önemini vurgulayan günlük ifadelerden sadece birkaçıdır. Tüketim tercihlerimizi ve yaşam tarzımızı nasıl tanımladığımızı duyularımızın yönlendirmesi belirler. Günümüzde, duyusal uyaranlardan gelen algıların duyguların, bilincin ve sinir sisteminin gelişimi üzerinde kaçınılmaz bir etkisi olduğunu biliyoruz. Bu algılar ana rahmindeyken bile, yani hayatımızın en erken evrelerinden itibaren, mevcuttur. Duyularımız aracılığıyla sürekli olarak içinde bulunduğumuz çevreden ve kültürden kesintisiz bir duyumlar dizisi alırız. Bu duyumlar beynimizdeki ve belleğimizdeki bağlantıları tanımlar ve şekillendirir

Evaluation of the exposure of the Mediterranean biodiversity to marine litter: the ASI – plastic busters MPAs projects connection

A number of marine species in the Mediterranean are threatened by the presence of several pressure factors, which include climate change, collisions with vessels, entanglement and ingestion of marine litter, especially plastic. Risk reduction policies can only be conceived starting from an accurate analysis of the exposure to such pressure factors. To estimate spatial abundance of both marine species and plastic litter and to assess the exposure risk, a two-stage analysis approach was applied, using aerial survey data from the ACCOBAMS Survey Initiative (ASI), in synergy with the Plastic Busters MPAs (PB MPAs) project. First, a detection function was fitted to observation data to obtain detection probabilities for individuals, then a Generalized Additive Model (GAM) was employed to estimate the spatial distribution of relative abundance, based on survey observations. A bivariate Local Indicator of Spatial Association (LISA) was then applied to the maps of relative abundance to derive risk maps of exposure of marine species to marine litter. The maps, obtained with a spatial resolution of about 10 km, allow us to identify areas with the highest neighboring abundance of taxa and marine litter, in particular for the MPAs studied by the PB MPAs project, which include the North-Western Mediterranean (Pelagos Sanctuary and Tuscan Archipelago), the Ionian and Aegean Sea (Zakynthos), and the Strait of Sicily (Cabrera Archipelago)

Update on Helicobacter pylori research. Malignancies.

No abstract available

Table_1_Evaluation of the exposure of the Mediterranean biodiversity to marine litter: the ASI – plastic busters MPAs projects connection.docx

A number of marine species in the Mediterranean are threatened by the presence of several pressure factors, which include climate change, collisions with vessels, entanglement and ingestion of marine litter, especially plastic. Risk reduction policies can only be conceived starting from an accurate analysis of the exposure to such pressure factors. To estimate spatial abundance of both marine species and plastic litter and to assess the exposure risk, a two-stage analysis approach was applied, using aerial survey data from the ACCOBAMS Survey Initiative (ASI), in synergy with the Plastic Busters MPAs (PB MPAs) project. First, a detection function was fitted to observation data to obtain detection probabilities for individuals, then a Generalized Additive Model (GAM) was employed to estimate the spatial distribution of relative abundance, based on survey observations. A bivariate Local Indicator of Spatial Association (LISA) was then applied to the maps of relative abundance to derive risk maps of exposure of marine species to marine litter. The maps, obtained with a spatial resolution of about 10 km, allow us to identify areas with the highest neighboring abundance of taxa and marine litter, in particular for the MPAs studied by the PB MPAs project, which include the North-Western Mediterranean (Pelagos Sanctuary and Tuscan Archipelago), the Ionian and Aegean Sea (Zakynthos), and the Strait of Sicily (Cabrera Archipelago).</p

Multiethnic PDX models predict a possible immune signature associated with TNBC of African ancestry

PURPOSE: Triple-negative breast cancer (TNBC) is an aggressive subtype most prevalent among women of Western Sub-Saharan African ancestry. It accounts for 15-25% of African American (AA) breast cancers (BC) and up to 80% of Ghanaian breast cancers, thus contributing to outcome disparities in BC for black women. The aggressive biology of TNBC has been shown to be regulated partially by breast cancer stem cells (BCSC) which mediate tumor recurrence and metastasis and are more abundant in African breast tumors. METHODS: We studied the biological differences between TNBC in women with African ancestry and those of Caucasian women by comparing the gene expression of the BCSC. From low-passage patient derived xenografts (PDX) from Ghanaian (GH), AA, and Caucasian American (CA) TNBCs, we sorted for and sequenced the stem cell populations and analyzed for differential gene enrichment. RESULTS: In our cohort of TNBC tumors, we observed that the ALDH expressing stem cells display distinct ethnic specific gene expression patterns, with the largest difference existing between the GH and AA ALDH+ cells. Furthermore, the tumors from the women of African ancestry [GH/AA] had ALDH stem cell (SC) enrichment for expression of immune related genes and processes. Among the significantly upregulated genes were CD274 (PD-L1), CXCR9, CXCR10 and IFI27, which could serve as potential drug targets. CONCLUSIONS: Further exploration of the role of immune regulated genes and biological processes in BCSC may offer insight into developing novel approaches to treating TNBC to help ameliorate survival disparities in women with African ancestry