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Long-read sequencing has recently transformed metagenomics, enhancing strain-level pathogen characterization, enabling accurate and complete metagenome-assembled genomes, and improving microbiome taxonomic classification and profiling. These advancements are not only due to improvements in sequencing accuracy, but also happening across rapidly changing analysis methods. In this Review, we explore long-read sequencing’s profound impact on metagenomics, focusing on computational pipelines for genome assembly, taxonomic characterization and variant detection, to summarize recent advancements in the field and provide an overview of available analytical methods to fully leverage long reads. We provide insights into the advantages and disadvantages of long reads over short reads and their evolution from the early days of long-read sequencing to their recent impact on metagenomics and clinical diagnostics. We further point out remaining challenges for the field such as the integration of methylation signals in sub-strain analysis and the lack of benchmarks.

Complete, telomere-to-telomere (T2T) genome assemblies promise improved analyses and the discovery of new variants, but many essential genomic resources remain associated with older reference genomes. Thus, there is a need to translate genomic features and read alignments between references. Here we describe a method called levioSAM2 that performs fast and accurate lift-over between assemblies using a whole-genome map. In addition to enabling the use of several references, we demonstrate that aligning reads to a high-quality reference (for example, T2T-CHM13) and lifting to an older reference (for example, Genome reference Consortium (GRC)h38) improves the accuracy of the resulting variant calls on the old reference. By leveraging the quality improvements of T2T-CHM13, levioSAM2 reduces small and structural variant calling errors compared with GRC-based mapping using real short- and long-read datasets. Performance is especially improved for a set of complex medically relevant genes, where the GRC references are lower quality.

Long-read sequencing technologies substantially overcome the limitations of short-reads but have not been considered as a feasible replacement for population-scale projects, being a combination of too expensive, not scalable enough or too error-prone. Here we develop an efficient and scalable wet lab and computational protocol, Napu, for Oxford Nanopore Technologies long-read sequencing that seeks to address those limitations. We applied our protocol to cell lines and brain tissue samples as part of a pilot project for the National Institutes of Health Center for Alzheimer’s and Related Dementias. Using a single PromethION flow cell, we can detect single nucleotide polymorphisms with F1-score comparable to Illumina short-read sequencing. Small indel calling remains difficult within homopolymers and tandem repeats, but achieves good concordance to Illumina indel calls elsewhere. Further, we can discover structural variants with F1-score on par with state-of-the-art de novo assembly methods. Our protocol phases small and structural variants at megabase scales and produces highly accurate, haplotype-specific methylation calls.

Advancements in sequencing technologies and assembly methods enable the regular production of high-quality genome assemblies characterizing complex regions. However, challenges remain in efficiently interpreting variation at various scales, from smaller tandem repeats to megabase rearrangements, across many human genomes. We present a PanGenome Research Tool Kit (PGR-TK) enabling analyses of complex pangenome structural and haplotype variation at multiple scales. We apply the graph decomposition methods in PGR-TK to the class II major histocompatibility complex demonstrating the importance of the human pangenome for analyzing complicated regions. Moreover, we investigate the Y-chromosome genes, DAZ1/DAZ2/DAZ3/DAZ4, of which structural variants have been linked to male infertility, and X-chromosome genes OPN1LWand OPN1MWlinked to eye disorders. We further showcase PGR-TK across 395 complex repetitive medically important genes. This highlights the power of PGR-TK to resolve complex variation in regions of the genome that were previously too complex to analyze.

The challenge in pavement management is to ensure that the correct treatment is applied to each segment of road at the appropriate time. Although pavement management systems assist with such predictions, pavement engineers further investigate and, ultimately, decide on the timing and type of treatment to be applied. While it is understandable that these might differ to some extent, large disparities between the two are coming under increased scrutiny. In order to assist with this challenge, this research develops a model for the prediction of pavement treatment types using multi-classification machine learning algorithms. The model attempts to predict what particular treatment type (reseal, overlay or rehabilitation) would be undertaken, based on available inventory and condition data. It also highlights the categories of data that were most influential in the prediction. The model was over 82% accurate in predicting the untreated segments and 80% accurate in predicting the treated segments.

Tae Wan Kim, John Hooker, and Thomas Donaldson make an attempt, in recent articles, to solve the alignment problem. As they define the alignment problem, it is the issue of how to give AI systems moral intelligence. They contend that one might program machines with a version of Kantian ethics cast in deontic modal logic. On their view, machines can be aligned with human values if such machines obey principles of universalization and autonomy, as well as a deontic utilitarian principle. Programming machines to do so might be useful, in their view, for applications such as future autonomous vehicles. Their proposal draws both on traditional logic-based and contemporary connectionist approaches, to fuse factual information with normative principles. I will argue that this approach makes demands of machines that go beyond what is currently feasible, and may extend past the limits of the possible for AI. I also argue that a deontological ethics for machines should place greater stress on the formula of humanity of the Kantian categorical imperative. On this principle, one ought never treat a person as a mere means. Recognition of what makes a person a person requires ethical insight. Similar insight is needed to tell treatment as a means from treatment as a mere means. The resources in Kim, Hooker, and Donaldson’s approach is insufficient for this reason. Hesitation regarding deployment of autonomous machines is warranted in light of these alignment concerns.

The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure that includes long palindromes, tandem repeats and segmental duplications1–3. As a result, more than half of the Y chromosome is missing from the GRCh38 reference sequence and it remains the last human chromosome to be finished4,5. Here, the Telomere-to-Telomere (T2T) consortium presents the complete 62,460,029-base-pair sequence of a human Y chromosome from the HG002 genome (T2T-Y) that corrects multiple errors in GRCh38-Y and adds over 30 million base pairs of sequence to the reference, showing the complete ampliconic structures of gene families TSPY, DAZand RBMY; 41 additional protein-coding genes, mostly from the TSPYfamily; and an alternating pattern of human satellite 1 and 3 blocks in the heterochromatic Yq12 region. We have combined T2T-Y with a previous assembly of the CHM13 genome4and mapped available population variation, clinical variants and functional genomics data to produce a complete and comprehensive reference sequence for all 24 human chromosomes.

Genetic variant calling from DNA sequencing has enabled understanding of germline variation in hundreds of thousands of humans. Sequencing technologies and variant-calling methods have advanced rapidly, routinely providing reliable variant calls in most of the human genome. We describe how advances in long reads, deep learning, de novo assembly and pangenomes have expanded access to variant calls in increasingly challenging, repetitive genomic regions, including medically relevant regions, and how new benchmark sets and benchmarking methods illuminate their strengths and limitations. Finally, we explore the possible future of more complete characterization of human genome variation in light of the recent completion of a telomere-to-telomere human genome reference assembly and human pangenomes, and we consider the innovations needed to benchmark their newly accessible repetitive regions and complex variants.

The exponential increase in sequencing data calls for conceptual and computational advances to extract useful biological insights. One such advance, minimizers, allows for reducing the quantity of data handled while maintaining some of its key properties. We provide a basic introduction to minimizers, cover recent methodological developments, and review the diverse applications of minimizers to analyze genomic data, including de novo genome assembly, metagenomics, read alignment, read correction, and pangenomes. We also touch on alternative data sketching techniques including universal hitting sets, syncmers, or strobemers. Minimizers and their alternatives have rapidly become indispensable tools for handling vast amounts of data.

La nefrotoxicidad y la hematotoxicidad después de la terapia con péptidos marcados con radionúclidos (PRRT) se han descrito en múltiples estudios usando diferentes actividades acumulativas, número de ciclos o péptidos marcados con radionúclidos. Aunque los tumores neuroendocrinos (NET) altamente diferenciados con metástasis tienen una larga supervivencia libre de progresión, pueden progresar. Analizamos los efectos secundarios a largo plazo en un esquema de tratamiento homogéneo en pacientes con PRRT y su impacto en el futuro tratamiento oncológico en caso de progresión.

Structural variants are associated with cancers and developmental disorders, but challenges with estimating population frequency remain a barrier to prioritizing mutations over inherited variants. In particular, variability in variant calling heuristics and filtering limits the use of current structural variant catalogs. We present STIX, a method that, instead of relying on variant calls, indexes and searches the raw alignments from thousands of samples to enable more comprehensive allele frequency estimation.

Einleitung: Die COVID-19-Pandemie hatte starke Auswirkungen auf die Arbeit von traumatologischen Teams. Ziel der Studie war es, die Inzidenz der Schockräume (SR) und die Traumamechanismen vor und während der Pandemie in einem Traumazentrum der Stufe I zu vergleichen. Ziel der Arbeit: Die Beobachtung der Auswirkungen der COVID-19-Pandemie auf das Aufkommen von Schwerverletzten im Sinne der SR-Inzidenz vor und während der Pandemie. Material und Methoden: Krankenakten aller SR-Patienten von März 2019 bis Februar 2021 wurden analysiert. Inzidenz- und Traumamechanismen der 12 Monate vor und der 12 Monate während der Pandemie wurden verglichen. Traumaverteilung und -grad wurden mittels AIS und ISS beschrieben, und das Heimatland der Patienten wurde erfasst. Ergebnisse: Die SR-Fälle gingen von 694 vor der COVID-19-Pandemie auf 477 Fälle während der Pandemie zurück (Inzidenzrate 0,69). Der stärkste Rückgang der Traumata war bei Sportverletzungen (0,55) zu verzeichnen, gefolgt von Suizidversuchen (0,63), Verkehrsunfällen (0,71) und Freizeitunfällen (0,76). Die Rate der Patienten mit schweren Verletzungen (ISS ≥ 16) war vergleichbar mit 40 % vor der Pandemie und 44 % während der Pandemie. Der Anteil an SR-Patienten aus dem Heimatland erhöhte sich von 63 auf 84 %. Die Zahl ausländischer Patienten wurde während der Pandemie signifikant reduziert (257 vs. 77). Diskussion: Die SR-Inzidenz ging während der Pandemie durch die verhängten Lockdowns während der Winterhochsaison signifikant zurück. Die Rate der ausländischen SR-Patienten hat sich während der Pandemie verändert, während die Rate der Schwerverletzten stabil geblieben ist. Graphic abstract:

We performed a phase 1 clinical trial to evaluate outcomes in patients receiving donor-derived CD19-specific chimeric antigen receptor (CAR) T cells for B-cell malignancy that relapsed or persisted after matched related allogeneic hemopoietic stem cell transplant. To overcome the cost and transgene-capacity limitations of traditional viral vectors, CAR T cells were produced using the piggyBac transposon system of genetic modification. Following CAR T-cell infusion, 1 patient developed a gradually enlarging retroperitoneal tumor due to a CAR-expressing CD4+ T-cell lymphoma. Screening of other patients led to the detection, in an asymptomatic patient, of a second CAR T-cell tumor in thoracic para-aortic lymph nodes. Analysis of the first lymphoma showed a high transgene copy number, but no insertion into typical oncogenes. There were also structural changes such as altered genomic copy number and point mutations unrelated to the insertion sites. Transcriptome analysis showed transgene promoter–driven upregulation of transcription of surrounding regions despite insulator sequences surrounding the transgene. However, marked global changes in transcription predominantly correlated with gene copy number rather than insertion sites. In both patients, the CAR T-cell–derived lymphoma progressed and 1 patient died. We describe the first 2 cases of malignant lymphoma derived from CAR gene–modified T cells. Although CAR T cells have an enviable record of safety to date, our results emphasize the need for caution and regular follow-up of CAR T recipients, especially when novel methods of gene transfer are used to create genetically modified immune therapies. This trial was registered at www.anzctr.org.au as ACTRN12617001579381.

Long-read sequencing technologies have now reached a level of accuracy and yield that allows their application to variant detection at a scale of tens to thousands of samples. Concomitant with the development of new computational tools, the first population-scale studies involving long-read sequencing have emerged over the past 2 years and, given the continuous advancement of the field, many more are likely to follow. In this Review, we survey recent developments in population-scale long-read sequencing, highlight potential challenges of a scaled-up approach and provide guidance regarding experimental design. We provide an overview of current long-read sequencing platforms, variant calling methodologies and approaches for de novo assemblies and reference-based mapping approaches. Furthermore, we summarize strategies for variant validation, genotyping and predicting functional impact and emphasize challenges remaining in achieving long-read sequencing at a population scale.

Germline variation and somatic alterations contribute to the molecular profile of cancers. We combine RNA with whole genome sequencing across 1,218 cancer patients to determine the extent germline structural variants (SVs) impact expression of nearby genes. For hundreds of genes, recurrent and common germline SV breakpoints within 100 kb associate with increased or decreased expression in tumors spanning various tissues of origin. A significant fraction of germline SV expression associations involves duplication of intergenic enhancers or 3′ UTR disruption. Genes altered by both somatic and germline SVs include ATRXand CEBPA. Genes essential in cancer cell lines include BARD1and IRS2. Genes with both expression and germline SV breakpoint patterns associated with patient survival include GCLM. Our results capture a class of phenotypic variation at work in the disease setting, including genes with cancer roles. Specific germline SVs represent potential cancer risk variants for genetic testing, including those involving genes with targeting implications.

An increasingly important scenario in population genetics is when a large cohort has been genotyped using a low-resolution approach (e.g., microarrays, exome capture, short-read WGS), from which a few individuals are resequenced using a more comprehensive approach, especially long-read sequencing. The subset of individuals selected should ensure that the captured genetic diversity is fully representative and includes variants across all subpopulations. For example, human variation has historically focused on individuals with European ancestry, but this represents a small fraction of the overall diversity. Addressing this, SVCollector identifies the optimal subset of individuals for resequencing by analyzing population-level VCF files from low-resolution genotyping studies. It then computes a ranked list of samples that maximizes the total number of variants present within a subset of a given size. To solve this optimization problem, SVCollector implements a fast, greedy heuristic and an exact algorithm using integer linear programming. We apply SVCollector on simulated data, 2504 human genomes from the 1000 Genomes Project, and 3024 genomes from the 3000 Rice Genomes Project and show the rankings it computes are more representative than alternative naive strategies. When selecting an optimal subset of 100 samples in these cohorts, SVCollector identifies individuals from every subpopulation, whereas naive methods yield an unbalanced selection. Finally, we show the number of variants present in cohorts selected using this approach follows a power-law distribution that is naturally related to the population genetic concept of the allele frequency spectrum, allowing us to estimate the diversity present with increasing numbers of samples.

The COVID-19 pandemic has sparked an urgent need to uncover the underlying biology of this devastating disease. Though RNA viruses mutate more rapidly than DNA viruses, there are a relatively small number of single nucleotide polymorphisms (SNPs) that differentiate the main SARS-CoV-2 lineages that have spread throughout the world. In this study, we investigated 129 RNA-seq data sets and 6928 consensus genomes to contrast the intra-host and inter-host diversity of SARS-CoV-2. Our analyses yielded three major observations. First, the mutational profile of SARS-CoV-2 highlights intra-host single nucleotide variant (iSNV) and SNP similarity, albeit with differences in C > U changes. Second, iSNV and SNP patterns in SARS-CoV-2 are more similar to MERS-CoV than SARS-CoV-1. Third, a significant fraction of insertions and deletions contribute to the genetic diversity of SARS-CoV-2. Altogether, our findings provide insight into SARS-CoV-2 genomic diversity, inform the design of detection tests, and highlight the potential of iSNVs for tracking the transmission of SARS-CoV-2.

Probing epigenetic features on DNA has tremendous potential to advance our understanding of the phased epigenome. In this study, we use nanopore sequencing to evaluate CpG methylation and chromatin accessibility simultaneously on long strands of DNA by applying GpC methyltransferase to exogenously label open chromatin. We performed nanopore sequencing of nucleosome occupancy and methylome (nanoNOMe) on four human cell lines (GM12878, MCF-10A, MCF-7 and MDA-MB-231). The single-molecule resolution allows footprinting of protein and nucleosome binding, and determination of the combinatorial promoter epigenetic signature on individual molecules. Long-read sequencing makes it possible to robustly assign reads to haplotypes, allowing us to generate a fully phased human epigenome, consisting of chromosome-level allele-specific profiles of CpG methylation and chromatin accessibility. We further apply this to a breast cancer model to evaluate differential methylation and accessibility between cancerous and noncancerous cells.

The optimization of road maintenance on large road networks over long analysis periods is an extremely complex problem. Different approaches to the problem have been investigated and methods such as dynamic programming, integer programming, and genetic algorithms have shown promise in providing near-optimal solutions. One of the general approaches to the road maintenance optimization problem uses a sequential approach in which feasible candidate treatment strategies are first generated for each road segment. These strategies can then be evaluated using benefit cost analysis principles and the most promising strategies can be used in the network optimization phase. A key challenge in this approach is the tendency for the candidate treatment strategy set to increase exponentially as the modeling period increases. This leads at best to long modeling times, and at worst to computational instability. This paper presents a fast, approximate alternative to the conventional decision tree-based approach to strategy generation. The method involves the use of a specified “trigger horizon” to control the number of years a triggered treatment can be postponed. The proposed method is shown to have a more gradual increase in the number of strategies generated as the modeling period increases. The method is also shown to provide overall network costs that are within 2% for an unconstrained budget, and 11% for a constrained budget scenario, of the cost generated by the more comprehensive but slower, less stable, decision tree-based methods.

Somatic mosaicism, manifesting as single nucleotide variants (SNVs), mobile element insertions, and structural changes in the DNA, is a common phenomenon in human brain cells, with potential functional consequences. Using a clonal approach, we previously detected 200–400 mosaic SNVs per cell in three human fetal brains (15–21 wk postconception). However, structural variation in the human fetal brain has not yet been investigated. Here, we discover and validate four mosaic structural variants (SVs) in the same brains and resolve their precise breakpoints. The SVs were of kilobase scale and complex, consisting of deletion(s) and rearranged genomic fragments, which sometimes originated from different chromosomes. Sequences at the breakpoints of these rearrangements had microhomologies, suggesting their origin from replication errors. One SV was found in two clones, and we timed its origin to ∼14 wk postconception. No large scale mosaic copy number variants (CNVs) were detectable in normal fetal human brains, suggesting that previously reported megabase-scale CNVs in neurons arise at later stages of development. By reanalysis of public single nuclei data from adult brain neurons, we detected an extrachromosomal circular DNA event. Our study reveals the existence of mosaic SVs in the developing human brain, likely arising from cell proliferation during mid-neurogenesis. Although relatively rare compared to SNVs and present in ∼10% of neurons, SVs in developing human brain affect a comparable number of bases in the genome (∼6200 vs. ∼4000 bp), implying that they may have similar functional consequences.

Improved identification of structural variants (SVs) in cancer can lead to more targeted and effective treatment options as well as advance our basic understanding of the disease and its progression. We performed whole-genome sequencing of the SKBR3 breast cancer cell line and patient-derived tumor and normal organoids from two breast cancer patients using Illumina/10x Genomics, Pacific Biosciences (PacBio), and Oxford Nanopore Technologies (ONT) sequencing. We then inferred SVs and large-scale allele-specific copy number variants (CNVs) using an ensemble of methods. Our findings show that long-read sequencing allows for substantially more accurate and sensitive SV detection, with between 90% and 95% of variants supported by each long-read technology also supported by the other. We also report high accuracy for long reads even at relatively low coverage (25×–30×). Furthermore, we integrated SV and CNV data into a unifying karyotype-graph structure to present a more accurate representation of the mutated cancer genomes. We find hundreds of variants within known cancer-related genes detectable only through long-read sequencing. These findings highlight the need for long-read sequencing of cancer genomes for the precise analysis of their genetic instability.

The current version of the human reference genome, GRCh38, contains a number of errors including 1.2 Mbp of falsely duplicated and 8.04 Mbp of collapsed regions. These errors impact the variant calling of 33 protein-coding genes, including 12 with medical relevance. Here, we present FixItFelix, an efficient remapping approach, together with a modified version of the GRCh38 reference genome that improves the subsequent analysis across these genes within minutes for an existing alignment file while maintaining the same coordinates. We showcase these improvements over multi-ethnic control samples, demonstrating improvements for population variant calling as well as eQTL studies.

Genomic benchmark datasets are essential to driving the field of genomics and bioinformatics. They provide a snapshot of the performances of sequencing technologies and analytical methods and highlight future challenges. However, they depend on sequencing technology, reference genome, and available benchmarking methods. Thus, creating a genomic benchmark dataset is laborious and highly challenging, often involving multiple sequencing technologies, different variant calling tools, and laborious manual curation. In this review, we discuss the available benchmark datasets and their utility. Additionally, we focus on the most recent benchmark of genes with medical relevance and challenging genomic complexity.

To provide a validated method to confidently identify exon-containing copy-number variants (CNVs), with a low false discovery rate (FDR), in targeted sequencing data from a clinical laboratory with particular focus on single-exon CNVs.

The material and device performance of GaN layers on large diameter (150mm-200mm) engineered substrates was assessed. Vertical Schottky diode structures and lateral P-N junction gated field effect transistors were used as the device test vehicles. Vertical devices formed by substrate removal exhibited rectifying behavior and reasonable blocking performance, while lateral transistors exhibited excellent gate control and high current density.

Copper Oxide and Nickel Oxide were deposited and investigated for their electrical and optical properties as a wide bandgap p-type oxide semiconductor. Heterojunctions of CuxOy/b-Ga2O3 were fabricated with a rectification ratio of 2.5x104 at +-2 V. NiO films were deposited using both RF sputtering and atomic layer deposition methods, resulting in rectifying heterojunctions in both cases. A 3.6 eV bandgap was measured upon a 500 degC post-deposition anneal for the sputtered films.

The SK-BR-3 cell line is one of the most important models for HER2+ breast cancers, which affect one in five breast cancer patients. SK-BR-3 is known to be highly rearranged, although much of the variation is in complex and repetitive regions that may be underreported. Addressing this, we sequenced SK-BR-3 using long-read single molecule sequencing from Pacific Biosciences and develop one of the most detailed maps of structural variations (SVs) in a cancer genome available, with nearly 20,000 variants present, most of which were missed by short-read sequencing. Surrounding the important ERBB2oncogene (also known as HER2), we discover a complex sequence of nested duplications and translocations, suggesting a punctuated progression. Full-length transcriptome sequencing further revealed several novel gene fusions within the nested genomic variants. Combining long-read genome and transcriptome sequencing enables an in-depth analysis of how SVs disrupt the genome and sheds new light on the complex mechanisms involved in cancer genome evolution.

To compare the diagnostic performance of frequency-selective non-linear blending and conventional linear blending contrast-enhanced CT for the diagnosis of acute (AC) and gangrenous (GC) cholecystitis.

Homeostasis is a fundamental principle of biological systems. A paradigm of immune homeostasis is the remarkably constant number of naive T and B lymphocytes in the body that continuously circulate through the secondary lymphoid organs to maximize immune surveillance. Whether the dynamics and distribution of the systemic naive lymphocyte pool is affected following organ-specific infection is not known. Here we show that, following infection of mice with an enteric helminth, naive T and B lymphocytes accumulate in the T helper type 2-reactive mesenteric lymph node while they are concurrently depleted from non-draining peripheral lymph nodes. This systemic redistribution of naive lymphocytes is sustained into the chronic phase of the infection, requires lymphotoxin beta receptor-dependent signals and is associated with a reduced ability of parasitized animals to mount antigen-specific cellular and humoral immune responses to heterologous immunization or infection at peripheral sites. Our data suggest that the function of the homeostatic naive lymphocyte pool can be modulated by its systemic distribution following infection and may provide a novel concept underlying compromised immune responsiveness at peripheral sites in helminth-infected individuals.

From the perspective of zoological institutions reintroduction projects offer many possibilities to link conservation and research programmes. An example of the multi‐layered and diverse contributions that zoological institutions in general and, specifically, Vienna Zoo, Austria, can make is the reintroduction of the Northern bald ibis Geronticus eremitain central Europe. The involvement of zoological institutions ranges from the provision of eggs or birds for release trials, to financial and advocacy support, including with government agencies and non‐governmental organizations. Through involvement at a steering level at the coordinative association ‘Förderverein Waldrappteam’ and as a partner in the EU LIFE+ reintroduction project, Vienna Zoo directly contributes to the shape of the reintroduction project for this Critically Endangered species, and provides much more than technical and infrastructural support. The reintroduction of the Northern bald ibis is broadly in line with the reintroduction guidelines of the International Union for Conservation of Nature. This project provides added benefits not only through its work to prevent the illegal hunting of migratory birds but also the production and dissemination of scientific research. Reintroduction projects provide zoological institutions with many possibilities to link conservation and research programmes. Vienna Zoo (Austria) has contributed in multi‐layered and diverse ways to the reintroduction of Northern bald ibis Geronticus eremitain central Europe. Involvement ranges from the provision of eggs or birds for release trials, to financial and advocacy support, including with government agencies and non‐governmental organizations. Through involvement at a steering‐committee level (‘Förderverein Waldrappteam’) and a partner in the EU LIFE+ project, Vienna Zoo directly contributes to the shape of the programme. This report, at the midterm of a 6 year project, describes the techniques developed for human‐led migrations and the progress made towards establishing three breeding colonies of Northern bald ibis north of the Alps with a tradition of migration to a wintering area in southern Tuscany. This work has also contributed to the prevention of illegal hunting and dissemination of scientific research. (Photo: Pablo Przesang, 2015)

High voltage (>4000 V) GaN lateral photoconductive semiconductor switches (PCSSs) were developed and characterized. The epitaxial structure consisted of 1.4 um of semi-insulating GaN grown on a SiC substrate. Intrinsic mode operation, where above bandgap light is used to trigger the PCSS, results in the highest amount of photocurrent. These PCSSs can also be triggered in extrinsic mode, where sub-bandgap illumination excites carriers from extrinsic defect levels, but this results in a significantly lower photocurrent. Triggering at near bandgap with 10 V applied, the on-state photocurrent is over eight magnitudes higher than the dark off-state leakage, indicating extremely high responsivity. A 293 nm picosecond pulse width laser was used to determine the rise time of the PCSS to be [?]160 ps. Various geometry devices were fabricated, and the low voltage on-state current obeyed a linear trend as a function of perimeter/gap optically while optically gating the PCSS, which is analogous to the width/length of a metal oxide semiconductor field effect transistor. Off-state breakdown voltages >4000 V were achieved and were likely limited by the thickness of the GaN epitaxial layer.

Temperature dependent current-voltage characteristics and Schottky barrier height are reported for 65 nm thick TiN films deposited by atomic layer deposition on (-201) b-Ga2O3 and compared with those of reference Pt Schottky contacts. Using thermionic emission theory, a thermionic emission model for both the Pt and TiN Schottky contacts to (-201) b-Ga2O3 was determined. Both contacts had comparable barrier heights of about 1 eV and near-unity ideality factor values, independent of temperature. The TiN contact had about an order of magnitude lower reverse current at room temperature, however, at high temperature the reverse current of the Pt contact was substantially lower (0.27 mA/cm2).

Deep reactive-ion etching (DRIE) of high aspect ratio structures in 4H-SiC is demonstrated. Electroplated nickel is used as the etch mask and patterned with openings ranging from 2-10 um. Etch depths of 51 to 57 um are obtained after a 2 hour reactive ion etch with SF6/O2 inductively coupled plasma for 2-6 um mask openings. Thus, aspect ratios (depth: mask opening) of 25.5 to 9.5 are achieved. Sidewall morphology is shown as a function of helium back side cooling with close to vertical sidewalls obtained with less cooling.

A tri-layer plasma enhanced CVD (PECVD) process for SiN deposition was developed to effectively passivate AlGaN/GaN high electron mobility transistors (HEMTs). A combination of thin, pre-gate SiN film deposited at high frequency (13.56 MHz) to minimize N-ion surface bombardment caused by low frequency ions, and a thick, post-gate bilayer SiN film designed to suppress on-state conductance degradation were demonstrated. By combining an annealed, 10.5 nm thick pre-gate SiN film with a bilayer post-gate SiN film, a trilayer PECVD SiN film with a total thickness of 122 nm was developed which maintained mobility, reduced on-resistance, improved drain-source current density, minimized degradation in dynamic on-state conductance upon off-state drain voltage stress, and minimized additional tensile stress.

Organisms use endogenous clocks to anticipate regular environmental cycles, such as days and tides. Natural variants resulting in differently timed behaviour or physiology, known as chronotypes in humans, have not been well characterized at the molecular level. We sequenced the genome of Clunio marinus, a marine midge whose reproduction is timed by circadian and circalunar clocks. Midges from different locations show strain-specific genetic timing adaptations. We examined genetic variation in five C. marinusstrains from different locations and mapped quantitative trait loci for circalunar and circadian chronotypes. The region most strongly associated with circadian chronotypes generates strain-specific differences in the abundance of calcium/calmodulin-dependent kinase II.1 (CaMKII.1) splice variants. As equivalent variants were shown to alter CaMKII activity in Drosophila melanogaster, and C. marinus(Cma)-CaMKII.1 increases the transcriptional activity of the dimer of the circadian proteins Cma-CLOCK and Cma-CYCLE, we suggest that modulation of alternative splicing is a mechanism for natural adaptation in circadian timing.