Optimized model-based reconstruction algorithms in computed tomography imaging for better depiction of liver lesions

Die Computertomographie spielt im Staging und der Nachsorge maligner Erkrankungen eine zentrale Rolle, insbesondere für die Evaluation möglicher Metastasen, welche oft prognosebestimmend sind. Häufigster Ort für Metastasen ist die Leber, eine frühe Diagnose dieser Metastasen senkt die Mortalität. Verbesserte Rekonstruktionsverfahren, die Bildrauschen reduzieren und den Kontrast stärken, steigern die Sensitivität und Spezifität in der Detektion von Metastasen. Zu diesen neuartigen Methoden zählen modellbasierte iterative Rekonstruktionsverfahren. In dieser Studie wurde die Auswirkung auf die Bildqualität durch ein solches Verfahren, Forward Projected Model-Based Iterative Reconstruction SoluTion Low Contrast Detectability (FIRST) Low Contrast Detectability (LCD), im Vergleich zu einem gängigen iterativen Rekonstruktionsalgorithmus getestet. Dazu wurden gering kontrastierte Leberläsionen verschiedener Dignität bei Patienten mit zugrunde liegendem Malignom retrospektiv eingeschlossen und mit dem neuen Algorithmus in drei verschiedenen Einstellungen („Standard“, „Mild“, „Strong“) erneut rekonstruiert. Es erfolgte eine objektive Analyse des Leber-zu-Läsion-Kontrastes und des Kontrast-zu-Rauschen-Verhältnisses (CNR) dieser Läsionen mittels Auswertung repräsentativer Regions of Interest. Alle Läsionen wurden hinsichtlich ihrer Abgrenzbarkeit von zwei erfahrenen Radiologen auf einer absteigenden Vier-Punkte-Skala bewertet. Die Ergebnisse wurden mit der Originalrekonstruktion (AIDR 3D) verglichen. Bei 82 eingeschlossenen und ausgewerteten Läsionen aus 57 Untersuchungen galten 37 als wahrscheinlich maligne. In der AIDR 3D-Rekonstruktion erreichten die Läsionen im Mittel einen Kontrast von 40,47 HU, einen CNR von 1,28 und eine visuelle Bewertung von 2,34. Mit FIRST-Standard verbesserte sich der Kontrast auf 42,94 HU (p < 0,001), der CNR auf 8,81 (p < 0,001) und der visuelle Score stieg auf 2,49 (p = 0,004). FIRST-Mild zeigte einen Kontrast von 45,84 HU (p < 0,001), einen CNR von 9,55 (p < 0,001) und einen visuellen Score von 2,59 (p < 0,001). FIRST-Strong hatte den besten visuellen Score der FIRST-Rekonstruktionen mit 2,46 (p = 0,033), der Kontrast lag bei 41,74 HU (p = 0,04) und der CNR bei 8,73 (p < 0,001). Mit dieser neuen Rekonstruktionsmethode zeigt sich eine objektive Verbesserung der Läsionsdarstellung, bei insgesamt schlechterer visueller Bewertung der Läsionen. Weitere Untersuchungen sind notwendig, um die Anwendbarkeit im klinischen Alltag zu überprüfen.Computed tomography plays a central role in staging and follow-up of malignant diseases, in particular for the evaluation of metastases, which are often determinant for prognosis. The most common location for metastases is the liver, an early diagnosis of these metastases decreases mortality. Improved reconstruction methods, that reduce image noise and increase contrast, can improve sensitivity and specificity in the detection of metastases. Among these new methods are model-based iterative reconstruction methods. In this study we compared the effects of such a method, Forward Projected Model-Based Iterative Reconstruction SoluTion Low Contrast Detectability (FIRST) Low Contrast Detectability (LCD), to a current iterative reconstruction algorithm. For this purpose, poorly contrasted liver lesions of different dignities in patients with an underlying malignancy were retrospectively included and reconstructed with the new algorithm in three different settings (“Standard”, “Mild”, “Strong”). An objective analysis of liver-to-lesion contrast and contrast-to-noise ratio (CNR) of these lesions was performed by evaluation of representative regions of interest. All lesions were rated regarding their delimitability by two experienced radiologists on a descending four-point Likert scale. The results were compared with the original reconstruction (AIDR 3D). In 82 included and evaluated lesions from 57 examinations, 37 were found to be likely malignant. In AIDR 3D reconstruction the lesions reached an average contrast of 40.47 HU, a CNR of 1.28 and a visual score of 2.34. With FIRST-Standard, contrast improved to 42.94 HU (p < 0.001), CNR to 8.81 (p < 0.001) and the visual score rose to 2.49 (p = 0.004). FIRST-Mild showed a contrast of 45.84 HU (p < 0.001), a CNR of 9.55 (p < 0.001) and a visual score of 2.59 (p < 0.001). FIRST-Strong had the best visual score of all FIRST reconstructions with 2.46 (p = 0.033), contrast was 41.74 HU (p = 0.04) and CNR 8.73 (p < 0.001). With these new reconstruction methods, a better objective depiction of lesions, albeit with poorer visual assessment is shown. Further studies are necessary to test the applicability in everyday clinical practice

Population turnover in remote oceania shortly after initial settlement

Ancient DNA from Vanuatu and Tonga dating to about 2,900–2,600 years ago (before present, BP) has revealed that the “First Remote Oceanians” associated with the Lapita archaeological culture were directly descended from the population that, beginning around 5000 BP, spread Austronesian languages from Taiwan to the Philippines, western Melanesia, and eventually Remote Oceania. Thus, ancestors of the First Remote Oceanians must have passed by the Papuan-ancestry populations they encountered in New Guinea, the Bismarck Archipelago, and the Solomon Islands with minimal admixture [1]. However, all present-day populations in Near and Remote Oceania harbor >25% Papuan ancestry, implying that additional eastward migration must have occurred. We generated genome-wide data for 14 ancient individuals from Efate and Epi Islands in Vanuatu from 2900–150 BP, as well as 185 present-day individuals from 18 islands. We find that people of almost entirely Papuan ancestry arrived in Vanuatu by around 2300 BP, most likely reflecting migrations a few hundred years earlier at the end of the Lapita period, when there is also evidence of changes in skeletal morphology and cessation of long-distance trade between Near and Remote Oceania [2, 3]. Papuan ancestry was subsequently diluted through admixture but remains at least 80%–90% in most islands. Through a fine-grained analysis of ancestry profiles, we show that the Papuan ancestry in Vanuatu derives from the Bismarck Archipelago rather than the geographically closer Solomon Islands. However, the Papuan ancestry in Polynesia—the most remote Pacific islands—derives from different sources, documenting a third stream of migration from Near to Remote Oceania

Social stratification without genetic differentiation at the site of Kulubnarti in Christian Period Nubia

Relatively little is known about Nubia’s genetic landscape prior to the influence of the Islamic migrations that began in the late 1st millennium CE. Here, we increase the number of ancient individuals with genome-level data from the Nile Valley from three to 69, reporting data for 66 individuals from two cemeteries at the Christian Period (~650–1000 CE) site of Kulubnarti, where multiple lines of evidence suggest social stratification. The Kulubnarti Nubians had ~43% Nilotic-related ancestry (individual variation between ~36–54%) with the remaining ancestry consistent with being introduced through Egypt and ultimately deriving from an ancestry pool like that found in the Bronze and Iron Age Levant. The Kulubnarti gene pool – shaped over a millennium – harbors disproportionately female-associated West Eurasian-related ancestry. Genetic similarity among individuals from the two cemeteries supports a hypothesis of social division without genetic distinction. Seven pairs of inter-cemetery relatives suggest fluidity between cemetery groups. Present-day Nubians are not directly descended from the Kulubnarti Nubians, attesting to additional genetic input since the Christian Period.K.A.S. was supported by a Doctoral Dissertation Research Improvement Grant from the National Science Foundation (BCS-1613577). D.R. was funded by NSF HOMINID grant BCS-1032255; NIH (NIGMS) grant GM100233; the Allen Discovery Center program, a Paul G. Allen Frontiers Group advised program of the Paul G. Allen Family Foundation; the John Templeton Foundation grant 61220; and the Howard Hughes Medical Institute

The genomic history of the Iberian Peninsula over the past 8000 years

We assembled genome-wide data from 271 ancient Iberians, of whom 176 are from the largely unsampled period after 2000 BCE, thereby providing a high-resolution time transect of the Iberian Peninsula.We document high genetic substructure between northwestern and southeastern hunter-gatherers before the spread of farming.We reveal sporadic contacts between Iberia and North Africa by ~2500 BCE and, by ~2000 BCE, the replacement of 40% of Iberia's ancestry and nearly 100% of its Y-chromosomes by people with Steppe ancestry.We show that, in the Iron Age, Steppe ancestry had spread not only into Indo-European-speaking regions but also into non-Indo-European-speaking ones, and we reveal that present-day Basques are best described as a typical Iron Age population without the admixture events that later affected the rest of Iberia. Additionally, we document how, beginning at least in the Roman period, the ancestry of the peninsula was transformed by gene flow from North Africa and the eastern Mediterranean

Ancient DNA and deep population structure in sub-Saharan African foragers

Multiple lines of genetic and archaeological evidence suggest that there were major demographic changes in the terminal Late Pleistocene epoch and early Holocene epoch of sub-Saharan Africa(1-4). Inferences about this period are challenging to make because demographic shifts in the past 5,000 years have obscured the structures of more ancient populations(3,5). Here we present genome-wide ancient DNA data for six individuals from eastern and south-central Africa spanning the past approximately 18,000 years (doubling the time depth of sub-Saharan African ancient DNA), increase the data quality for 15 previously published ancient individuals and analyse these alongside data from 13 other published ancient individuals. The ancestry of the individuals in our study area can be modelled as a geographically structured mixture of three highly divergent source populations, probably reflecting Pleistocene interactions around 80-20 thousand years ago, including deeply diverged eastern and southern African lineages, plus a previously unappreciated ubiquitous distribution of ancestry that occurs in highest proportion today in central African rainforest hunter-gatherers. Once established, this structure remained highly stable, with limited long-range gene flow. These results provide a new line of genetic evidence in support of hypotheses that have emerged from archaeological analyses but remain contested, suggesting increasing regionalization at the end of the Pleistocene epoch. DNA analysis of 6 individuals from eastern and south-central Africa spanning the past approximately 18,000 years, and of 28 previously published ancient individuals, provides genetic evidence supporting hypotheses of increasing regionalization at the end of the Pleistocene.info:eu-repo/semantics/publishedVersio

Ancient genomes indicate population replacement in Early Neolithic Britain

The roles of migration, admixture and acculturation in the European transition to farming have been debated for over 100 years. Genome-wide ancient DNA studies indicate predominantly Aegean ancestry for continental Neolithic farmers, but also variable admixture with local Mesolithic hunter-gatherers. Neolithic cultures first appear in Britain circa 4000 bc, a millennium after they appeared in adjacent areas of continental Europe. The pattern and process of this delayed British Neolithic transition remain unclear. We assembled genome-wide data from 6 Mesolithic and 67 Neolithic individuals found in Britain, dating 8500–2500 bc. Our analyses reveal persistent genetic affinities between Mesolithic British and Western European hunter-gatherers. We find overwhelming support for agriculture being introduced to Britain by incoming continental farmers, with small, geographically structured levels of hunter-gatherer ancestry. Unlike other European Neolithic populations, we detect no resurgence of hunter-gatherer ancestry at any time during the Neolithic in Britain. Genetic affinities with Iberian Neolithic individuals indicate that British Neolithic people were mostly descended from Aegean farmers who followed the Mediterranean route of dispersal. We also infer considerable variation in pigmentation levels in Europe by circa 6000 bc

The galaxy evolution probe

The Galaxy Evolution Probe (GEP) is a NASA Astrophysics Probe concept designed to address key questions about star formation and supermassive black hole growth in galaxies over cosmic time. GEP will achieve its goals with large mid- and far-infrared imaging and spectroscopic surveys. ..

Reconstructing the Deep Population History of Central and South America

We report genome-wide ancient DNA from 49 individuals forming four parallel time transects in Belize, Brazil, the Central Andes, and the Southern Cone, each dating to at least 9,000 years ago. The common ancestral population radiated rapidly from just one of the two early branches that contributed to Native Americans today. We document two previously unappreciated streams of gene flow between North and South America. One affected the Central Andes by 4,200 years ago, while the other explains an affinity between the oldest North American genome associated with the Clovis culture and the oldest Central and South Americans from Chile, Brazil, and Belize. However, this was not the primary source for later South Americans, as the other ancient individuals derive from lineages without specific affinity to the Clovis-associated genome, suggesting a population replacement that began at least 9,000 years ago and was followed by substantial population continuity in multiple regions

The Beaker phenomenon and the genomic transformation of northwest Europe

From around 2750 to 2500 bc, Bell Beaker pottery became widespread across western and central Europe, before it disappeared between 2200 and 1800 bc. The forces that propelled its expansion are a matter of long-standing debate, and there is support for both cultural diffusion and migration having a role in this process. Here we present genome-wide data from 400 Neolithic, Copper Age and Bronze Age Europeans, including 226 individuals associated with Beaker-complex artefacts. We detected limited genetic affinity between Beaker-complex-associated individuals from Iberia and central Europe, and thus exclude migration as an important mechanism of spread between these two regions. However, migration had a key role in the further dissemination of the Beaker complex. We document this phenomenon most clearly in Britain, where the spread of the Beaker complex introduced high levels of steppe-related ancestry and was associated with the replacement of approximately 90% of Britain’s gene pool within a few hundred years, continuing the east-to-west expansion that had brought steppe-related ancestry into central and northern Europe over the previous centuries

A genetic history of the pre-contact Caribbean

Humans settled the Caribbean about 6,000 years ago, and ceramic use and intensified agriculture mark a shift from the Archaic to the Ceramic Age at around 2,500 years ago1,2,3. Here we report genome-wide data from 174 ancient individuals from The Bahamas, Haiti and the Dominican Republic (collectively, Hispaniola), Puerto Rico, Curaçao and Venezuela, which we co-analysed with 89 previously published ancient individuals. Stone-tool-using Caribbean people, who first entered the Caribbean during the Archaic Age, derive from a deeply divergent population that is closest to Central and northern South American individuals; contrary to previous work4, we find no support for ancestry contributed by a population related to North American individuals. Archaic-related lineages were >98% replaced by a genetically homogeneous ceramic-using population related to speakers of languages in the Arawak family from northeast South America; these people moved through the Lesser Antilles and into the Greater Antilles at least 1,700 years ago, introducing ancestry that is still present. Ancient Caribbean people avoided close kin unions despite limited mate pools that reflect small effective population sizes, which we estimate to be a minimum of 500–1,500 and a maximum of 1,530–8,150 individuals on the combined islands of Puerto Rico and Hispaniola in the dozens of generations before the individuals who we analysed lived. Census sizes are unlikely to be more than tenfold larger than effective population sizes, so previous pan-Caribbean estimates of hundreds of thousands of people are too large5,6. Confirming a small and interconnected Ceramic Age population7, we detect 19 pairs of cross-island cousins, close relatives buried around 75 km apart in Hispaniola and low genetic differentiation across islands. Genetic continuity across transitions in pottery styles reveals that cultural changes during the Ceramic Age were not driven by migration of genetically differentiated groups from the mainland, but instead reflected interactions within an interconnected Caribbean world1,8.This work was supported by a grant from the National Geographic Society to M. Pateman to facilitate analysis of skeletal material from The Bahamas and by a grant from the Italian ‘Ministry of Foreign Affairs and International Cooperation’ (Italian archaeological, anthropological and ethnological missions abroad, DGPSP Ufficio VI). D.R. was funded by NSF HOMINID grant BCS-1032255, NIH (NIGMS) grant GM100233, the Paul Allen Foundation, the John Templeton Foundation grant 61220 and the Howard Hughes Medical Institute.Peer reviewe