GENCODE: reference annotation for the human and mouse genomes in 2023

GENCODE produces high quality gene and transcript annotation for the human and mouse genomes. All GENCODE annotation is supported by experimental data and serves as a reference for genome biology and clinical genomics. The GENCODE consortium generates targeted experimental data, develops bioinformatic tools and carries out analyses that, along with externally produced data and methods, support the identification and annotation of transcript structures and the determination of their function. Here, we present an update on the annotation of human and mouse genes, including developments in the tools, data, analyses and major collaborations which underpin this progress. For example, we report the creation of a set of non-canonical ORFs identified in GENCODE transcripts, the LRGASP collaboration to assess the use of long transcriptomic data to build transcript models, the progress in collaborations with RefSeq and UniProt to increase convergence in the annotation of human and mouse protein-coding genes, the propagation of GENCODE across the human pan-genome and the development of new tools to support annotation of regulatory features by GENCODE. Our annotation is accessible via Ensembl, the UCSC Genome Browser and https://www.gencodegenes.org.

Ensembl 2022

Ensembl (https://www.ensembl.org) is unique in its flexible infrastructure for access to genomic data and annotation. It has been designed to efficiently deliver annotation at scale for all eukaryotic life, and it also provides deep comprehensive annotation for key species. Genomes representing a greater diversity of species are increasingly being sequenced. In response, we have focussed our recent efforts on expediting the annotation of new assemblies. Here, we report the release of the greatest annual number of newly annotated genomes in the history of Ensembl via our dedicated Ensembl Rapid Release platform (http://rapid.ensembl.org). We have also developed a new method to generate comparative analyses at scale for these assemblies and, for the first time, we have annotated non-vertebrate eukaryotes. Meanwhile, we continually improve, extend and update the annotation for our high-value reference vertebrate genomes and report the details here. We have a range of specific software tools for specific tasks, such as the Ensembl Variant Effect Predictor (VEP) and the newly developed interface for the Variant Recoder. All Ensembl data, software and tools are freely available for download and are accessible programmatically.

First results of a regenerative transcatheter heart valve implant from autologous tissue in a long-term animal model

Background

The perfect heart valve replacement remains to be found regarding longevity, freedom of anticoagulation and availability in each size.

Purpose

Examination of a new technique for a regenerative, immunocompatible, transcatheter pulmonary valve implant from autologous pericardium was performed in an adult sheep model.

Methods

For each valve implant a pericardial patch was harvested by left antero-lateral mini-thoracotomy, placed on one of two slightly different shaped moulds either made of acrylic glass (AG) or printed in a 3D Printer (3D) and transferred into a container filled with a biological crosslinking agent at a non-toxic concentration to stabilize the given shape. After a median of 3 days (d) they were unpacked, sewn into a self-expandable nitinol stent with a diameter of 26 or 30mm and implanted via the jugular vein into pulmonary valve position of the same animal using a custom-made delivery system (1). Three groups (Gr) were planned: Gr 1) 4 animals with at least 6 d of crosslinking and AG mould; Gr 2) 5 animals with at least 3 d of crosslinking and AG mould; Gr 3) 6 animals with at least 3 d crosslinking and 3D mould. Follow ups (FU) were performed every 3 months (mo) evaluating valve function by intracardiac echocardiography (ICE) and cardiac MRI for up to 20.5 mo. All experiments were approved and conducted according to German federal law.

Results

In 11 of 13 animals minimally-invasive implantation was successful. One animal died because of ventricular fibrillation, in the other the implant dislocated into the right ventricle, so it had to be sacrificed. Direct post-implantation valve insufficiency was evaluated in 9 animals using ICE or angiography. In Gr 1 insufficiency was non-existent (n=2), in Gr 2 moderate or severe (n=2) and in Gr 3 non-existent or mild (n=5). Long term function as shown in figure 1 decreased rapidly in Gr 1 and 2 with median MRI regurgitation fractions (RF) in Gr 1 of 31% at 3 mo (n=3), 41% at 6 mo (n=3), 48% at 9 mo (n=2), 47% at 12 mo (n=3) and in Gr 2 of 43% at 3 and 54% at 6 mo (n=1) after implantation. Median RF in Gr 3 was small with 9% at 3 mo (n=4), 8% at 6 mo (n=3), 8% at 9 mo (n=3), 12% at 13 mo (n=3), 8% at 17 mo (n=2) and 20.5 mo (n=2). We never witnessed valve stenosis in any group at any point in time.

Conclusion

Gr 3 showed promising results regarding long time function of the implant which encourages further research with higher validity. The reason for failing of Gr 1 and 2 remains a topic of discussion. Regardless, valuable experience was gained in crafting and conducting the implantation of this new regenerative heart valve implant.

Funding Acknowledgement

Type of funding sources: Public grant(s) – National budget only. Main funding source(s): EXIST research transfer program of the federal ministry of education and research

Color, composition, and thermal environment of Kuiper Belt object (486958) Arrokoth

The outer Solar System object (486958) Arrokoth (provisional designation 2014 MU₆₉) has been largely undisturbed since its formation. We studied its surface composition using data collected by the New Horizons spacecraft. Methanol ice is present along with organic material, which may have formed through irradiation of simple molecules. Water ice was not detected. This composition indicates hydrogenation of carbon monoxide-rich ice and/or energetic processing of methane condensed on water ice grains in the cold, outer edge of the early Solar System. There are only small regional variations in color and spectra across the surface, which suggests that Arrokoth formed from a homogeneous or well-mixed reservoir of solids. Microwave thermal emission from the winter night side is consistent with a mean brightness temperature of 29 ± 5 kelvin.

Aloenxertos ósseos e enxerto sintético de hidroxiapatita em falha óssea ulnar em galinhas (Gallus gallus domesticus), aspectos radiográficos e histológicos

RESUMO Dos atendimentos ortopédicos realizados em aves no HCV-UFRGS, 86% são fraturas, sendo aproximadamente 30% delas cominutivas com perda óssea expressiva, justificando a importância da utilização de enxertos em fraturas de aves. O objetivo deste trabalho foi avaliar dois aloenxertos e enxerto sintético de hidroxiapatita em defeito ósseo de galinhas. Utilizaram-se 30 galinhas separadas em três grupos: aloenxerto congelado em ultra-freezer (GUF), aloenxerto congelado em nitrogênio líquido (GNL) e enxerto sintético de hidroxiapatita deficiente em cálcio (GHA). Nos três grupos, os enxertos foram aplicados com placas e parafusos bloqueados de 2mm na ulna direita das aves, avaliando-se a evolução por meio de exames radiográficos até serem completados 90 dias de pós-operatório e o resultado final mediante exame histológico. A média e desvio-padrão relacionando o tempo de consolidação óssea radiográfica foi: GNL 61,67±21,79 dias (90% de consolidação), GUF 47,14±13,50 dias (70% de consolidação) e GHA 70±18,17 dias (60% de consolidação). Houve diferença significativa no tempo de consolidação óssea entre o GUF e o GHA. Histologicamente, os enxertos do GUF foram os que estavam em consolidação mais avançada. Os aloenxertos do GNL foram superiores no preenchimento de falha óssea ulnar de galinhas.

1 kHz fixed-target serial crystallography using a multilayer monochromator and an integrating pixel detector

Reliable sample delivery and efficient use of limited beam time have remained bottlenecks for serial crystallography (SX). Using a high-intensity polychromatic X-ray beam in combination with a newly developed charge-integrating JUNGFRAU detector, we have applied the method of fixed-target SX to collect data at a rate of 1 kHz at a synchrotron-radiation facility. According to our data analysis for the given experimental conditions, only about 3 000 diffraction patterns are required for a high-quality diffraction dataset. With indexing rates of up to 25%, recording of such a dataset takes less than 30 s.

Prebiotic Chemistry of Pluto

We present the case for the presence of complex organic molecules, such as amino acids and nucleobases, formed by abiotic processes on the surface and in near-subsurface regions of Pluto. Pluto's surface is tinted with a range of non-ice substances with colors ranging from light yellow to red to dark brown; the colors match those of laboratory organic residues called tholins. Tholins are broadly characterized as complex, macromolecular organic solids consisting of a network of aromatic structures connected by aliphatic bridging units (e.g., Imanaka et al., 2004; Materese et al., 2014, 2015). The synthesis of tholins in planetary atmospheres and in surface ices has been explored in numerous laboratory experiments, and both gas- and solid-phase varieties are found on Pluto. A third variety of tholins, exposed at a site of tectonic surface fracturing called Virgil Fossae, appears to have come from a reservoir in the subsurface. Eruptions of tholin-laden liquid H₂O from a subsurface aqueous repository appear to have covered portions of Virgil Fossae and its surroundings with a uniquely colored deposit (D.P. Cruikshank, personal communication) that is geographically correlated with an exposure of H₂O ice that includes spectroscopically detected NH₃ (C.M. Dalle Ore, personal communication). The subsurface organic material could have been derived from presolar or solar nebula processes, or might have formed in situ. Photolysis and radiolysis of a mixture of ices relevant to Pluto's surface composition (N₂, CH₄, CO) have produced strongly colored, complex organics with a significant aromatic content having a high degree of nitrogen substitution similar to the aromatic heterocycles pyrimidine and purine (Materese et al., 2014, 2015; Cruikshank et al., 2016). Experiments with pyrimidines and purines frozen in H₂O-NH₃ ice resulted in the formation of numerous nucleobases, including the biologically relevant guanine, cytosine, adenine, uracil, and thymine (Materese et al., 2017). The red material associated with the H₂O ice may contain nucleobases resulting from energetic processing on Pluto's surface or in the interior. Some other Kuiper Belt objects also exhibit red colors similar to those found on Pluto and may therefore carry similar inventories of complex organic materials. The widespread and ubiquitous nature of similarly complex organic materials observed in a variety of astronomical settings drives the need for additional laboratory and modeling efforts to explain the origin and evolution of organic molecules. Pluto observations reveal complex organics on a small body that remains close to its place of origin in the outermost regions of the Solar System.

Initial results from the New Horizons exploration of 2014 MU69, a small Kuiper Belt object

The Kuiper Belt is a distant region of the outer Solar System. On 1 January 2019, the New Horizons spacecraft flew close to (486958) 2014 MU₆₉, a cold classical Kuiper Belt object approximately 30 kilometers in diameter. Such objects have never been substantially heated by the Sun and are therefore well preserved since their formation. We describe initial results from these encounter observations. MU₆₉ is a bilobed contact binary with a flattened shape, discrete geological units, and noticeable albedo heterogeneity. However, there is little surface color or compositional heterogeneity. No evidence for satellites, rings or other dust structures, a gas coma, or solar wind interactions was detected. MU₆₉'s origin appears consistent with pebble cloud collapse followed by a low-velocity merger of its two lobes.

Detection of ammonia on Pluto's surface in a region of geologically recent tectonism

We report the detection of ammonia (NH3) on Pluto's surface in spectral images obtained with the New Horizons spacecraft that show absorption bands at 1.65 and 2.2 μm. The ammonia signature is spatially coincident with a region of past extensional tectonic activity (Virgil Fossae) where the presence of H2O ice is prominent. Ammonia in liquid water profoundly depresses the freezing point of the mixture. Ammoniated ices are believed to be geologically short lived when irradiated with ultraviolet photons or charged particles. Thus, the presence of NH3 on a planetary surface is indicative of a relatively recent deposition or possibly through exposure by some geological process. In the present case, the areal distribution is more suggestive of cryovolcanic emplacement, however, adding to the evidence for ongoing geological activity on Pluto and the possible presence of liquid water at depth today.

[Antagonistic function of the heart muscle : Part II: Clinical implications]

In the hypertrophic heart the myostructural afterload in the form of endoepicardial networks is predominant, which enhances myocardial hypertrophy. The intrinsic antagonism is derailed. Likewise, the connective tissue scaffold, i.e. the stromatogenic afterload, is enriched in the response to the derailment of antagonism in a hypertrophic heart up to regional captivation of the heart musculature. Due to the selective susceptibility of the auxotonic, contracting oblique transmural myocardial network for low dose negative inotropic medication, this promises to attenuate progress in myocardial hypertrophy. Volume reduction surgery is most effective in reducing wall stress as long as the myocardium is not critically fettered by fibrosis. The use of external mechanical circulatory support is then effective if the heart is supported in its resting mode, which means around a middle width and at minimal amplitude of motion. The takotsubo cardiomyopathy might possibly reflect an isolated, extreme stimulation of the intrinsic antagonism as a response to hormonally induced sensitization of the myocardium to catecholamine. A particular significant conclusion with respect to the diseased heart is that clinical diagnostics need new impulses with a focus on the analysis of local motion patterns and on myocardial stiffness reflecting disease-dependent antagonistic intensity. This would become a relevant diagnostic marker if corresponding (noninvasive) measurement techniques would become available.

Ensaio biomecânico para determinação do diâmetro de barra conectora de polimetilmetacrilato em fixador esquelético externo tipo Ia no úmero de suínos

RESUMO Fraturas ósseas podem ser corrigidas com a utilização de fixadores esqueléticos externos (FEE), método de estabilização bastante comum. Para tanto, têm-se utilizado barras conectoras de polimetilmetacrilato (PMMA) sem critério de diâmetro, as quais podem quebrar, se ficarem muito delgadas, ou ocasionar incômodo, quando muito pesadas e volumosas. O objetivo deste trabalho foi testar, por meio de ensaio biomecânico de compressão axial e flexão, qual é o diâmetro ideal da barra conectora de PMMA, correlacionado com o diâmetro ósseo para utilização em FEE tipo Ia. Utilizaram-se 24 úmeros para se realizarem medidas de comprimento, diâmetro, circunferência e ensaios biomecânicos. Após, foram confeccionadas barras de 1,5 vezes a média do diâmetro ósseo (grupo I), do mesmo diâmetro ósseo (grupo II) e de 0,5 vezes o diâmetro (grupo III). Com os resultados obtidos ao se compararem os valores dos ossos com os dos grupos II e III, verificou-se que as barras conectoras do grupo II mostraram-se mais resistentes do que o tecido ósseo no ensaio de compressão. No ensaio de flexão, os ossos resistiram mais quando comparados aos grupos II e III, sendo 4,3 vezes mais resistentes do que o grupo III nesse mesmo ensaio mecânico. Os resultados permitem um direcionamento para confecção de barras considerando-se o diâmetro ósseo como referência.

Comparison of lipases for in vitro models of gastric digestion: lipolysis using two infant formulas as model substrates

The aim of this study was to find a lipase suitable as a surrogate for Human Gastric Lipase (HGL), since the development of predictive gastrointestinal lipolysis models are hampered by the lack of a lipase with similar digestive properties as HGL. Three potential surrogates for HGL; Rhizopus Oryzae Lipase (ROL), Rabbit Gastric Lipase (RGL) and recombinant HGL (rHGL), were used to catalyze the in vitro digestion of two infant formulas (a medium-chain triacylglyceride enriched formula (MC-IF) and a predominantly long-chain triacylglyceride formula (LC-IF)). Digesta were withdrawn after 0, 5, 15, 30, 60 min of gastric digestion and after 90 or 180 min of intestinal digestion with or without the presence of pancreatic enzymes, respectively. The digesta were analyzed by scanning electron microscopy and gas chromatography to quantify the release of fatty acids (FAs). Digestions of both formulas, catalyzed by ROL, showed that the extent of gastric digestion was higher than expected from previously published in vivo data. ROL was furthermore insensitive to FA chain length and all FAs were released at the same pace. RGL and rHGL favoured the release of MC-FAs in both formulas, but rHGL did also release some LC-FAs during digestion of MC-IF, whereas RGL only released MC-FAs. Digestion of a MC-IF by HGL in vivo showed that MC-FAs are preferentially released, but some LC-FAs are also released. Thus of the tested lipase rHGL replicated the digestive properties of HGL the best and is a suitable surrogate for HGL for use in in vitro gastrointestinal lipolysis models.

Addition of Amide Proton Transfer Imaging to FDG-PET/CT Improves Diagnostic Accuracy in Glioma Grading: A Preliminary Study Using the Continuous Net Reclassification Analysis

BACKGROUND AND PURPOSE

Amide proton transfer imaging has been successfully applied to brain tumors, however, the relationships between amide proton transfer and other quantitative imaging values have yet to be investigated. The aim was to examine the additive value of amide proton transfer imaging alongside [¹⁸F] FDG-PET and DWI for preoperative grading of gliomas.

MATERIALS AND METHODS

Forty-nine patients with newly diagnosed gliomas were included in this retrospective study. All patients had undergone MR imaging, including DWI and amide proton transfer imaging on 3T scanners, and [¹⁸F] FDG-PET. Logistic regression analyses were conducted to examine the relationship between each imaging parameter and the presence of high-grade (grade III and/or IV) glioma. These parameters included the tumor-to-normal ratio of FDG uptake, minimum ADC, mean amide proton transfer value, and their combinations. In each model, the overall discriminative power for the detection of high-grade glioma was assessed with receiver operating characteristic curve analysis. Additive information from minimum ADC and mean amide proton transfer was also evaluated by continuous net reclassification improvement. P < .05 was considered significant.

RESULTS

Tumor-to-normal ratio, minimum ADC, and mean amide proton transfer demonstrated comparable diagnostic accuracy in differentiating high-grade from low-grade gliomas. When mean amide proton transfer was combined with the tumor-to-normal ratio, the continuous net reclassification improvement was 0.64 (95% CI, 0.036-1.24; P = .04) for diagnosing high-grade glioma and 0.95 (95% CI, 0.39-1.52; P = .001) for diagnosing glioblastoma. When minimum ADC was combined with the tumor-to-normal ratio, the continuous net reclassification improvement was 0.43 (95% CI, -0.17-1.04; P = .16) for diagnosing high-grade glioma, and 1.36 (95% CI, 0.79-1.92; P < .001) for diagnosing glioblastoma.

CONCLUSIONS

Addition of amide proton transfer imaging to FDG-PET/CT may improve the ability to differentiate high-grade from low-grade gliomas.

The EIGER detector for low-energy electron microscopy and photoemission electron microscopy

EIGER is a single-photon-counting hybrid pixel detector developed at the Paul Scherrer Institut, Switzerland. It is designed for applications at synchrotron light sources with photon energies above 5 keV. Features of EIGER include a small pixel size (75 µm × 75 µm), a high frame rate (up to 23 kHz), a small dead-time between frames (down to 3 µs) and a dynamic range up to 32-bit. In this article, the use of EIGER as a detector for electrons in low-energy electron microscopy (LEEM) and photoemission electron microscopy (PEEM) is reported. It is demonstrated that, with only a minimal modification to the sensitive part of the detector, EIGER is able to detect electrons emitted or reflected by the sample and accelerated to 8-20 keV. The imaging capabilities are shown to be superior to the standard microchannel plate detector for these types of applications. This is due to the much higher signal-to-noise ratio, better homogeneity and improved dynamic range. In addition, the operation of the EIGER detector is not affected by radiation damage from electrons in the present energy range and guarantees more stable performance over time. To benchmark the detector capabilities, LEEM experiments are performed on selected surfaces and the magnetic and electronic properties of individual iron nanoparticles with sizes ranging from 8 to 22 nm are detected using the PEEM endstation at the Surface/Interface Microscopy (SIM) beamline of the Swiss Light Source.

The EIGER detector for low-energy electron microscopy and photoemission electron microscopy

EIGER is a single-photon-counting hybrid pixel detector developed at the Paul Scherrer Institut, Switzerland. It is designed for applications at synchrotron light sources with photon energies above 5 keV. Features of EIGER include a small pixel size (75 µm × 75 µm), a high frame rate (up to 23 kHz), a small dead-time between frames (down to 3 µs) and a dynamic range up to 32-bit. In this article, the use of EIGER as a detector for electrons in low-energy electron microscopy (LEEM) and photoemission electron microscopy (PEEM) is reported. It is demonstrated that, with only a minimal modification to the sensitive part of the detector, EIGER is able to detect electrons emitted or reflected by the sample and accelerated to 8-20 keV. The imaging capabilities are shown to be superior to the standard microchannel plate detector for these types of applications. This is due to the much higher signal-to-noise ratio, better homogeneity and improved dynamic range. In addition, the operation of the EIGER detector is not affected by radiation damage from electrons in the present energy range and guarantees more stable performance over time. To benchmark the detector capabilities, LEEM experiments are performed on selected surfaces and the magnetic and electronic properties of individual iron nanoparticles with sizes ranging from 8 to 22 nm are detected using the PEEM endstation at the Surface/Interface Microscopy (SIM) beamline of the Swiss Light Source.

Facet tropism and facet joint orientation: risk factors for the development of early biochemical alterations of lumbar intervertebral discs

OBJECTIVE

To assess the glycosaminoglycan (GAG) content of lumbar intervertebral discs (IVD) in healthy volunteers with facet tropism (FT) and sagittal facet joint (FJ) orientation using glycosaminoglycan chemical exchange saturation transfer imaging (gagCEST).

METHOD

Seventy-five lumbar IVDs of twenty-five young, healthy volunteers without any history of lumbar spine pathologies (13 female; 12 male; mean age: 28.0 ± 4.4 years; range: 21-35 years) were examined with a 3T MRI scanner. Orientation of FT and FJ were assessed for L3/4, L4/5 and L5/S1 using standard T2 weighted images. Biochemical gagCEST imaging was used to determine the GAG content of each nucleus pulposus (NP) and annulus fibrosus (AF).

RESULTS

Significantly higher gagCEST values of NP were found in volunteers without FT and normal FJ orientation compared to volunteers with FT and sagittal FJ orientation >45° (P < 0.0001). GagCEST values were significantly higher in volunteers without FT compared to volunteers with moderate or severe FT (moderate FT: P < 0.0001; severe FT: P = 0.0033). Volunteers with normal FJ orientation showed significantly higher gagCEST values compared to those with sagittal FJ orientation >45° (P < 0.001). We found a significant, negative correlation between gagCEST values and higher angels in sagittal FJ orientation (rho = -0.459; P < 0.0001).

CONCLUSION

GagCEST analysis indicated lower GAG values of NP in young volunteers with FT and sagittal orientated FJ, indicating that FT and sagittal orientation of the FJ represent risk factors for the development of early biochemical alterations of lumbar IVDs.

The small satellites of Pluto as observed by New Horizons

The New Horizons mission has provided resolved measurements of Pluto's moons Styx, Nix, Kerberos, and Hydra. All four are small, with equivalent spherical diameters of ~40 kilometers for Nix and Hydra and ~10 kilometers for Styx and Kerberos. They are also highly elongated, with maximum to minimum axis ratios of ~2. All four moons have high albedos (~50 to 90%) suggestive of a water-ice surface composition. Crater densities on Nix and Hydra imply surface ages of at least 4 billion years. The small moons rotate much faster than synchronous, with rotational poles clustered nearly orthogonal to the common pole directions of Pluto and Charon. These results reinforce the hypothesis that the small moons formed in the aftermath of a collision that produced the Pluto-Charon binary.

Towards hybrid pixel detectors for energy-dispersive or soft X-ray photon science

JUNGFRAU (adJUstiNg Gain detector FoR the Aramis User station) is a two-dimensional hybrid pixel detector for photon science applications at free-electron lasers and synchrotron light sources. The JUNGFRAU 0.4 prototype presented here is specifically geared towards low-noise performance and hence soft X-ray detection. The design, geometry and readout architecture of JUNGFRAU 0.4 correspond to those of other JUNGFRAU pixel detectors, which are charge-integrating detectors with 75 µm × 75 µm pixels. Main characteristics of JUNGFRAU 0.4 are its fixed gain and r.m.s. noise of as low as 27 e(-) electronic noise charge (<100 eV) with no active cooling. The 48 × 48 pixels JUNGFRAU 0.4 prototype can be combined with a charge-sharing suppression mask directly placed on the sensor, which keeps photons from hitting the charge-sharing regions of the pixels. The mask consists of a 150 µm tungsten sheet, in which 28 µm-diameter holes are laser-drilled. The mask is aligned with the pixels. The noise and gain characterization, and single-photon detection as low as 1.2 keV are shown. The performance of JUNGFRAU 0.4 without the mask and also in the charge-sharing suppression configuration (with the mask, with a `software mask' or a `cluster finding' algorithm) is tested, compared and evaluated, in particular with respect to the removal of the charge-sharing contribution in the spectra, the detection efficiency and the photon rate capability. Energy-dispersive and imaging experiments with fluorescence X-ray irradiation from an X-ray tube and a synchrotron light source are successfully demonstrated with an r.m.s. energy resolution of 20% (no mask) and 14% (with the mask) at 1.2 keV and of 5% at 13.3 keV. The performance evaluation of the JUNGFRAU 0.4 prototype suggests that this detection system could be the starting point for a future detector development effort for either applications in the soft X-ray energy regime or for an energy-dispersive detection system.

Retrospective evaluation of low long-term efficacy of antiepileptic drugs and ketogenic diet in 39 patients with CDKL5-related epilepsy

OBJECTIVE

Mutations in the CDKL5 gene cause an early-onset epileptic encephalopathy. To date, little is known about effective antiepileptic treatment in this disorder.

METHOD

Accordingly, the aim of this retrospective study was to explore the role of different antiepileptic drugs (AEDs) and the ketogenic diet (KD) in the treatment of this rare genetic disorder. We evaluated the efficacy in 39 patients with CDKL5 mutations at 3, 6 and 12 months after the introduction of each treatment. One patient was lost to follow-up after 6 and 12 months.

RESULTS

The responder rate (>50% reduction in seizure frequency) to at least one AED or KD was 69% (27/39) after 3 months, 45% (17/38) after 6 months and 24% (9/38) after 12 months. The highest rate of seizure reduction after 3 months was reported for FBM (3/3), VGB (8/25), CLB (4/17), VPA (7/34), steroids (5/26), LTG (5/23) and ZNS (2/11). Twelve patients (31%) experienced a seizure aggravation to at least one AED. Most patients showed some but only initial response to various AEDs with different modes of actions.

SIGNIFICANCE

Considering both age-related and spontaneous fluctuation in seizure frequency and the unknown impact of many AEDs or KD on cognition, our data may help defining realistic treatment goals and avoiding overtreatment in patients with CDKL5 mutations. There is a strong need to develop new treatment strategies for patients with this rare mutation.

Radiation hardness assessment of the charge-integrating hybrid pixel detector JUNGFRAU 1.0 for photon science

JUNGFRAU (adJUstiNg Gain detector FoR the Aramis User station) is a two-dimensional hybrid pixel detector for photon science applications in free electron lasers, particularly SwissFEL, and synchrotron light sources. JUNGFRAU is an automatic gain switching, charge-integrating detector which covers a dynamic range of more than 10(4) photons of an energy of 12 keV with a good linearity, uniformity of response, and spatial resolving power. The JUNGFRAU 1.0 application-specific integrated circuit (ASIC) features a 256 × 256 pixel matrix of 75 × 75 μm(2) pixels and is bump-bonded to a 320 μm thick Si sensor. Modules of 2 × 4 chips cover an area of about 4 × 8 cm(2). Readout rates in excess of 2 kHz enable linear count rate capabilities of 20 MHz (at 12 keV) and 50 MHz (at 5 keV). The tolerance of JUNGFRAU to radiation is a key issue to guarantee several years of operation at free electron lasers and synchrotrons. The radiation hardness of JUNGFRAU 1.0 is tested with synchrotron radiation up to 10 MGy of delivered dose. The effect of radiation-induced changes on the noise, baseline, gain, and gain switching is evaluated post-irradiation for both the ASIC and the hybridized assembly. The bare JUNGFRAU 1.0 chip can withstand doses as high as 10 MGy with minor changes to its noise and a reduction in the preamplifier gain. The hybridized assembly, in particular the sensor, is affected by the photon irradiation which mainly shows as an increase in the leakage current. Self-healing of the system is investigated during a period of 11 weeks after the delivery of the radiation dose. Annealing radiation-induced changes by bake-out at 100 °C is investigated. It is concluded that the JUNGFRAU 1.0 pixel is sufficiently radiation-hard for its envisioned applications at SwissFEL and synchrotron beam lines.

Spectrometer for shot-to-shot photon energy characterization in the multi-bunch mode of the free electron laser at Hamburg

The setup and first results from commissioning of a fast online photon energy spectrometer for the vacuum ultraviolet free electron laser at Hamburg (FLASH) at DESY are presented. With the use of the latest advances in detector development, the presented spectrometer reaches readout frequencies up to 1 MHz. In this paper, we demonstrate the ability to record online photon energy spectra on a shot-to-shot base in the multi-bunch mode of FLASH. Clearly resolved shifts in the mean wavelength over the pulse train as well as shot-to-shot wavelength fluctuations arising from the statistical nature of the photon generating self-amplified spontaneous emission process have been observed. In addition to an online tool for beam calibration and photon diagnostics, the spectrometer enables the determination and selection of spectral data taken with a transparent experiment up front over the photon energy of every shot. This leads to higher spectral resolutions without the loss of efficiency or photon flux by using single-bunch mode or monochromators.

The diurnal cycle of water ice on comet 67P/Churyumov-Gerasimenko

Observations of cometary nuclei have revealed a very limited amount of surface water ice, which is insufficient to explain the observed water outgassing. This was clearly demonstrated on comet 9P/Tempel 1, where the dust jets (driven by volatiles) were only partially correlated with the exposed ice regions. The observations of 67P/Churyumov-Gerasimenko have revealed that activity has a diurnal variation in intensity arising from changing insolation conditions. It was previously concluded that water vapour was generated in ice-rich subsurface layers with a transport mechanism linked to solar illumination, but that has not hitherto been observed. Periodic condensations of water vapour very close to, or on, the surface were suggested to explain short-lived outbursts seen near sunrise on comet 9P/Tempel 1. Here we report observations of water ice on the surface of comet 67P/Churyumov-Gerasimenko, appearing and disappearing in a cyclic pattern that follows local illumination conditions, providing a source of localized activity. This water cycle appears to be an important process in the evolution of the comet, leading to cyclical modification of the relative abundance of water ice on its surface.

Improved diagnostics targeting c-MET in non-small cell lung cancer: expression, amplification and activation?

BACKGROUND

Several c-MET targeting inhibitory molecules have already shown promising results in the treatment of patients with Non-small Cell Lung Cancer (NSCLC). Combination of EGFR- and c-MET-specific molecules may overcome EGFR tyrosine kinase inhibitor (TKI) resistance. The aim of this study was to allow for the identification of patients who might benefit from TKI treatments targeting MET and to narrow in on the diagnostic assessment of MET.

METHODS

222 tumor tissues of patients with NSCLC were analyzed concerning c-MET expression and activation in terms of phosphorylation (Y1234/1235 and Y1349) using a microarray format employing immunohistochemistry (IHC). Furthermore, protein expression and MET activation was correlated with the amplification status by Fluorescence in Situ Hybridization (FISH).

RESULTS

Correlation was observed between phosphorylation of c-MET at Y1234/1235 and Y1349 (spearman correlation coefficient rs = 0.41; p < 0.0001). No significant correlation was shown between MET expression and phosphorylation (p > 0.05). c-MET gene amplification was detected in eight of 214 patients (3.7%). No significant association was observed between c-MET amplification, c-MET protein expression and phosphorylation.

CONCLUSION

Our data indicate, that neither expression of c-MET nor the gene amplification status might be the best way to select patients for MET targeting therapies, since no correlation with the activation status of MET was observed. We propose to take into account analyzing the phosphorylation status of MET by IHC to select patients for MET targeting therapies. Signaling of the receptor and the activation of downstream molecules might be more crucial for the benefit of therapeutics targeting MET receptor tyrosine kinases than expression levels alone.

Regional distribution of body fat in relation to DNA methylation within the LPL, ADIPOQ and PPARγ promoters in subcutaneous adipose tissue

Obesity may be related to differential DNA methylation and thus to differential expression of key genes in adipose tissue metabolism, such as LPL, ADIPOQ and PPARγ. Using subcutaneous adipose tissue (SAT) from 59 individuals of the European Prospective Investigation into Cancer and Nutrition–Potsdam study, we performed quantitative DNA methylation analysis within the promoters of LPL (LPL-CG1 and -CG2), ADIPOQ (ADIPOQ-CG1 and-CG2) and PPARγ (PPARγ-CG1). We then studied DNA methylation in relation to SAT gene expression, body composition measured using whole-body magnetic resonance imaging, body mass index (BMI), waist circumference (WC) and long-term changes in BMI and WC. For LPL-CG1 and LPL-CG2, higher methylation levels were associated with lower LPL expression, but with higher past WC gain. LPL-CG1 was also positively associated with BMI, WC, and visceral and subcutaneous fat mass. ADIPOQ-CG1 or -CG2 methylation exhibited no association with ADIPOQ expression or with anthropometric parameters. PPARγ-CG1 methylation was significantly higher in individuals with higher visceral fat mass. Among the investigated sites, LPL-CG1 methylation showed the strongest association with gene expression and regional body fat distribution, thereby possibly linking the degree of obesity with major metabolic processes in SAT.

Cometary science. The organic-rich surface of comet 67P/Churyumov-Gerasimenko as seen by VIRTIS/Rosetta

The VIRTIS (Visible, Infrared and Thermal Imaging Spectrometer) instrument on board the Rosetta spacecraft has provided evidence of carbon-bearing compounds on the nucleus of the comet 67P/Churyumov-Gerasimenko. The very low reflectance of the nucleus (normal albedo of 0.060 ± 0.003 at 0.55 micrometers), the spectral slopes in visible and infrared ranges (5 to 25 and 1.5 to 5% kÅ(-1)), and the broad absorption feature in the 2.9-to-3.6-micrometer range present across the entire illuminated surface are compatible with opaque minerals associated with nonvolatile organic macromolecular materials: a complex mixture of various types of carbon-hydrogen and/or oxygen-hydrogen chemical groups, with little contribution of nitrogen-hydrogen groups. In active areas, the changes in spectral slope and absorption feature width may suggest small amounts of water-ice. However, no ice-rich patches are observed, indicating a generally dehydrated nature for the surface currently illuminated by the Sun.