Efficacy of ramucirumab combination chemotherapy as second-line treatment in patients with advanced adenocarcinoma of the stomach or gastroesophageal junction after exposure to checkpoint inhibitors and chemotherapy as first-line therapy.

FOLFOX plus nivolumab represents a standard of care for first-line therapy of advanced gastroesophageal cancer (aGEC) with positive PD-L1 expression. The efficacy of second-line VEGFR-2 inhibition with ramucirumab (RAM) plus chemotherapy after progression to immunochemotherapy remains unclear. Medical records of patients with aGEC enrolled in the randomized phase II AIO-STO-0417 trial after treatment failure to first-line FOLFOX plus nivolumab and ipilimumab were retrospectively analyzed. Patients were divided into two groups based on second-line therapy: RAM plus chemotherapy (RAM group) or treatment without RAM (control group). Eighty three patients were included. In the overall population, progression-free survival (PFS) in the RAM group was superior to the control (4.5 vs 2.9 months). Responders (CR/PR) to first-line immunochemotherapy receiving RAM containing second-line therapy had prolonged OS from start of first-line therapy (28.9 vs 16.5 months), as well as second-line OS (9.6 vs 7.5 months), PFS (5.6 vs 2.9 months) and DCR (53% vs 29%) compared to the control. PD-L1 CPS ≥1 was 42% and 44% for the RAM and the control, respectively. Patients with CPS ≥1 in the RAM group showed better tumor control (ORR 25% vs 10%) and improved survival (total OS 11.5 vs 8.0 months; second-line OS 6.5 vs 3.9 months; PFS 4.5 vs 1.6 months) compared to the control. Prior exposure to first-line FOLFOX plus dual checkpoint inhibition followed by RAM plus chemotherapy shows favorable response and survival rates especially in patients with initial response and positive PD-L1 expression and has the potential to advance the treatment paradigm in aGEC.

[Palliative Treatment of Metastatic Rectal Cancer]. / Palliative Systemtherapie des metastasierten Rektumkarzinoms.

Palliative treatment of metastatic rectal cancer (mCRC) has developed considerably in recent years, with new therapeutic strategies such as induction and maintenance therapies, the establishment of targeted therapies and molecularly defined strategies in defined subgroups such as MSI-H-patients. The following article presents evidence based therapeutic options and algorithms.

Blood-Based Targeted Metabolomics Discriminate Patients with Alcoholic Liver Cirrhosis from Those with Non-Cirrhotic Liver Damage: An Explorative Study.

BACKGROUND: Early detection of liver cirrhosis is crucial for secondary prevention of complications. However, noninvasive blood-based patient monitoring tools are lacking. In this explorative study, we conducted a targeted metabolomic analysis in order to identify possible serum markers indicating alcoholic liver cirrhosis (aLiC) with or without hepatocellular carcinoma (HCC). METHODS: Venous blood of 30 individuals was collected: healthy controls ("Con", n = 12), patients with aLiC without and with HCC ("aLiC": n = 6 and "aLiC + HCC": n = 6), and patients with other liver diseases ("oLiD": n = 6). A targeted metabolomic analysis was conducted using the AbsoluteIDQ® p180 Kit (Biocrates Life Sciences®, Innsbruck, Austria). Statistical analysis was performed by applying a one-way ANOVA on all subgroups followed by a t test for pairwise comparison of subgroups and logistic regression analysis. RESULTS: ANOVA revealed 29 metabolites that significantly discriminate between the different cohorts. Among these analytes, 25 were significantly altered in Con versus aLiC, as indicated by t test, most importantly SM C18:1 (p < 0.001), SM C20:2 (p = 0.001), SM (OH) C22:2 (p < 0.001), lysoPC a C20:4 (p < 0.001), and PC aa C36:5 (p < 0.001). To a similar extent, the metabolites discriminated also between the oLiD and aLiC but less between the Con or oLiD and aLiC + HCC cohorts. Most of these analytes were either lyso- and phosphatidylcholines or sphingomyelins. Results were not significant for comparison of Con versus oLiD and aLiC versus aLiC + HCC. CONCLUSION: Decreased lyso- and phosphatidylcholine as well as sphingomyelin species in venous blood could help to detect liver cirrhosis in patients with non-cirrhotic liver disease.

A 17-billion-solar-mass black hole in a group galaxy with a diffuse core.

Quasars are associated with and powered by the accretion of material onto massive black holes; the detection of highly luminous quasars with redshifts greater than z = 6 suggests that black holes of up to ten billion solar masses already existed 13 billion years ago. Two possible present-day 'dormant' descendants of this population of 'active' black holes have been found in the galaxies NGC 3842 and NGC 4889 at the centres of the Leo and Coma galaxy clusters, which together form the central region of the Great Wall--the largest local structure of galaxies. The most luminous quasars, however, are not confined to such high-density regions of the early Universe; yet dormant black holes of this high mass have not yet been found outside of modern-day rich clusters. Here we report observations of the stellar velocity distribution in the galaxy NGC 1600--a relatively isolated elliptical galaxy near the centre of a galaxy group at a distance of 64 megaparsecs from Earth. We use orbit superposition models to determine that the black hole at the centre of NGC 1600 has a mass of 17 billion solar masses. The spatial distribution of stars near the centre of NGC 1600 is rather diffuse. We find that the region of depleted stellar density in the cores of massive elliptical galaxies extends over the same radius as the gravitational sphere of influence of the central black holes, and interpret this as the dynamical imprint of the black holes.

Shaping convex edges in borosilicate glass by single pass perforation with an Airy beam.

We demonstrate curved modifications with lengths of up to 2 mm within borosilicate glass produced by single 1030 nm picosecond laser shots with an Airy beam profile. Plasma ignition in the sidelobes of the beam as well as surface damage prove to be the crucial limitations for confined bulk energy deposition on a curved trajectory. A combined experimental and numerical analysis reveals optimum laser parameters for confined bulk energy deposition. This way, we achieved single pass perforation of a 525 µm thick glass sheet and separation by a subsequent etching step, resulting in a well-defined convex edge down to a radius of curvature of 774 µm.

Large scale ab initio modeling of structurally uncharacterized antimicrobial peptides reveals known and novel folds.

Antimicrobial resistance within a wide range of infectious agents is a severe and growing public health threat. Antimicrobial peptides (AMPs) are among the leading alternatives to current antibiotics, exhibiting broad spectrum activity. Their activity is determined by numerous properties such as cationic charge, amphipathicity, size, and amino acid composition. Currently, only around 10% of known AMP sequences have experimentally solved structures. To improve our understanding of the AMP structural universe we have carried out large scale ab initio 3D modeling of structurally uncharacterized AMPs that revealed similarities between predicted folds of the modeled sequences and structures of characterized AMPs. Two of the peptides whose models matched known folds are Lebocin Peptide 1A (LP1A) and Odorranain M, predicted to form ß-hairpins but, interestingly, to lack the intramolecular disulfide bonds, cation-π or aromatic interactions that generally stabilize such AMP structures. Other examples include Ponericin Q42, Latarcin 4a, Kassinatuerin 1, Ceratotoxin D, and CPF-B1 peptide, which have α-helical folds, as well as mixed αß folds of human Histatin 2 peptide and Garvicin A which are, to the best of our knowledge, the first linear αßß fold AMPs lacking intramolecular disulfide bonds. In addition to fold matches to experimentally derived structures, unique folds were also obtained, namely for Microcin M and Ipomicin. These results help in understanding the range of protein scaffolds that naturally bear antimicrobial activity and may facilitate protein design efforts towards better AMPs.

ConKit: a python interface to contact predictions.

SUMMARY: Recent advances in protein residue contact prediction algorithms have led to the emergence of many new methods and a variety of file formats. We present ConKit , an open source, modular and extensible Python interface which allows facile conversion between formats and provides an interface to analyses of sequence alignments and sets of contact predictions. AVAILABILITY AND IMPLEMENTATION: ConKit is available via the Python Package Index. The documentation can be found at http://www.conkit.org . ConKit is licensed under the BSD 3-Clause. CONTACT: hlfsimko@liverpool.ac.uk or drigden@liverpool.ac.uk. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Flexible femtosecond inscription of fiber Bragg gratings by an optimized deformable mirror.

The period of fiber Bragg gratings is adapted by shaping the wavefronts of ultrashort laser pulses applied in a phase mask inscription technique. A specially designed deformable mirror, based on a dielectric substrate to withstand high peak powers, is utilized to deform the wavefront. A shift of about 11 nm is demonstrated for a Bragg wavelength around 1550 nm.

A population response analysis approach to assign class II HLA-epitope restrictions.

Identification of the specific HLA locus and allele presenting an epitope for recognition by specific TCRs (HLA restriction) is necessary to fully characterize the immune response to Ags. Experimental determination of HLA restriction is complex and technically challenging. As an alternative, the restricting HLA locus and allele can be inferred by genetic association, using response data in an HLA-typed population. However, simple odds ratio (OR) calculations can be problematic when dealing with large numbers of subjects and Ags, and because the same epitope can be presented by multiple alleles (epitope promiscuity). In this study, we develop a tool, denominated Restrictor Analysis Tool for Epitopes, to extract inferred restriction from HLA class II-typed epitope responses. This automated method infers HLA class II restriction from large datasets of T cell responses in HLA class II-typed subjects by calculating ORs and relative frequencies from simple data tables. The program is validated by: 1) analyzing data of previously determined HLA restrictions; 2) experimentally determining in selected individuals new HLA restrictions using HLA-transfected cell lines; and 3) predicting HLA restriction of particular peptides and showing that corresponding HLA class II tetramers efficiently bind to epitope-specific T cells. We further design a specific iterative algorithm to account for promiscuous recognition by calculation of OR values for combinations of different HLA molecules while incorporating predicted HLA binding affinity. The Restrictor Analysis Tool for Epitopes program streamlines the prediction of HLA class II restriction across multiple T cell epitopes and HLA types.

Exploring the speed and performance of molecular replacement with AMPLE using QUARK ab initio protein models.

AMPLE clusters and truncates ab initio protein structure predictions, producing search models for molecular replacement. Here, an interesting degree of complementarity is shown between targets solved using the different ab initio modelling programs QUARK and ROSETTA. Search models derived from either program collectively solve almost all of the all-helical targets in the test set. Initial solutions produced by Phaser after only 5 min perform surprisingly well, improving the prospects for in situ structure solution by AMPLE during synchrotron visits. Taken together, the results show the potential for AMPLE to run more quickly and successfully solve more targets than previously suspected.

Crystal structure of the nipah virus phosphoprotein tetramerization domain.

The Nipah virus phosphoprotein (P) is multimeric and tethers the viral polymerase to the nucleocapsid. We present the crystal structure of the multimerization domain of Nipah virus P: a long, parallel, tetrameric, coiled coil with a small, α-helical cap structure. Across the paramyxoviruses, these domains share little sequence identity yet are similar in length and structural organization, suggesting a common requirement for scaffolding or spatial organization of the functions of P in the virus life cycle.

Discrete nonplanar reflections from an ultrashort pulse written volume Bragg grating.

In this Letter, we present a direct writing technique for two-dimensional periodic volume Bragg gratings (VBGs) in fused silica based on the phase mask technology, ultrashort laser pulses, and three-beam interference. An algorithm to predict the grating pattern and its diffraction behavior under collimated, spectral broad illumination is developed. The predicted data are in good agreement with the measurements.

Integrated single grating compressor for variable pulse front tilt in simultaneously spatially and temporally focused systems.

A Ti:Al(3)O(2) multipass chirped pulse amplification system is outfitted with a single-grating, simultaneous spatial and temporal focusing (SSTF) compressor platform. For the first time, this novel design has the ability to easily vary the beam aspect ratio of an SSTF beam, and thus the degree of pulse-front tilt at focus, while maintaining a net zero-dispersion system. Accessible variation of pulse front tilt gives full spatiotemporal control over the intensity distribution at the focus and could lead to better understanding of effects such as nonreciprocal writing and SSTF-material interactions.

Aquaponics in schools: Hands-on learning about healthy eating and a healthy planet.

Our food system is giving rise to a growing social, health and environmental crisis. Much of the food consumed in the United Kingdom is cheap, nutrient-poor and highly processed, leading to under-consumption of essential foods such as grains, beans, vegetables and fruit. This has contributed to a rise in diet-related diseases, with approximately 22% of primary school leavers being overweight or obese. Food production is unsustainable with agriculture responsible for 10% of the UK's greenhouse gas emissions and intensive farming practices have led to a significant loss of soil carbon and a decline in biodiversity. COVID-19 increased inequalities in our food system. Therefore, there is an urgent need for interventions to counteract these adverse social, health and environmental impacts. Education can play a crucial role as an intervention to address challenges in the food system. We tested an innovative school initiative using portable aquaponic pods and aligned to the national curriculum, to engage pupils in food production and foster learning about sustainability, climate change and healthy eating. The evaluation, based on teacher surveys, aquapod chart data, student blogs and postcards and feedback from the development team, revealed positive impacts on students' environmental awareness, as well as sustainability and practical food production knowledge. However, the programme encountered logistical challenges and we therefore highlight future improvements to produce a curriculum programme that can be delivered at scale to enhance food education and empower pupils to drive the agenda on tackling food sustainability and climate change.

Perioperative Atezolizumab Plus Fluorouracil, Leucovorin, Oxaliplatin, and Docetaxel for Resectable Esophagogastric Cancer: Interim Results From the Randomized, Multicenter, Phase II/III DANTE/IKF-s633 Trial.

PURPOSE: This trial evaluates the addition of the PD-L1 antibody atezolizumab (ATZ) to standard-of-care fluorouracil, leucovorin, oxaliplatin, and docetaxel (FLOT) as a perioperative treatment for patients with resectable esophagogastric adenocarcinoma (EGA). METHODS: DANTE started as multicenter, randomized phase II trial, which was subsequently converted to a phase III trial. Here, we present the results of the phase II proportion, focusing on surgical pathology and safety outcomes on an exploratory basis. Patients with resectable EGA (≥cT2 or cN+) were assigned to either four preoperative and postoperative cycles of FLOT combined with ATZ, followed by eight cycles of ATZ maintenance (arm A) or FLOT alone (arm B). RESULTS: Two hundred ninety-five patients were randomly assigned (A, 146; B, 149) with balanced baseline characteristics between arms. Twenty-three patients (8%) had tumors with microsatellite instability (MSI), and 58% patients had tumors with a PD-L1 combined positive score (CPS) of ≥1. Surgical morbidity (A, 45%; B, 42%) and 60-day mortality (A, 3%; B, 2%) were comparable between arms. Downstaging favored arm A versus arm B (ypT0, 23% v 15% [one-sided P = .044]; ypT0-T2, 61% v 48% [one-sided P = .015]; ypN0, 68% v 54% [one-sided P = .012]). Histopathologic complete regression rates (pathologic complete response or TRG1a) were higher after FLOT plus ATZ (A, 24%; B, 15%; one-sided P = .032), and the difference was more pronounced in the PD-L1 CPS ≥10 (A, 33%; B, 12%) and MSI (A, 63%; B, 27%) subpopulations. Complete margin-free (R0) resection rates were relatively high in both arms (A, 96%; B, 95%). The incidence and severity of adverse events were similar in both groups. CONCLUSION: Within the limitations of the exploratory nature of the data, the addition of ATZ to perioperative FLOT is safe and improved postoperative stage and histopathologic regression.

Highly polarized all-fiber thulium laser with femtosecond-laser-written fiber Bragg gratings.

We demonstrate and characterize a highly linearly polarized (18.8 dB) narrow spectral emission (<80 pm) from an all-fiber Tm laser utilizing femtosecond-laser-written fiber Bragg gratings. Thermally-dependent anisotropic birefringence is observed in the FBG transmission, the effects of which enable both the generation and elimination of highly linearly polarized output. To our knowledge, this is the first detailed study of such thermal anisotropic birefringence in femtosecond-written FBGs.

Femtosecond laser-induced apodized Bragg grating waveguides.

We report on the inscription of apodized Bragg grating waveguides (BGWs) in fused silica using a modulated high repetition rate fs laser system. Tailoring of the grating's coupling strength is facilitated by appropriately substructuring the modulation of the inscribing laser radiation. The proposed alteration delivers an unchanged constant mean refractive index entailing homogeneous guiding properties along the entire waveguide. The BGWs fabricated using a Gaussian apodized modulation profile exhibit a 10 dB improvement in sideband suppression compared to waveguide gratings written with a uniform modulation profile.

Utility of a three-gene transcriptomic signature in the diagnosis of tuberculosis in a low-endemic hospital setting.

BACKGROUND: Host transcriptomic blood signatures have demonstrated diagnostic potential for tuberculosis (TB), requiring further validation across different geographical settings. Discriminating TB from other diseases with similar clinical manifestations is crucial for the development of an accurate immunodiagnostic tool. In this exploratory cohort study, we evaluated the performance of potential blood-based transcriptomic signatures in distinguishing TB disease from non-TB lower respiratory tract infections in hospitalised patients in a TB low-endemic country. METHOD: Quantitative real-time polymerase chain reaction qPCR) was used to evaluate 26 previously published genes in blood from 31 patients (14 TB and 17 lower respiratory tract infection cases) admitted to Oslo University Hospital in Norway. The diagnostic accuracies of differentially expressed genes were determined by receiver operating characteristic curves. RESULTS: A significant difference (p < .01) in the age distribution was observed between patients with TB (mean age, 40 ± 15 years) and lower respiratory tract infection (mean age 59 ± 12 years). Following adjustment for age, ETV7, GBP1, GBP5, P2RY14 and BLK were significantly differentially expressed between patients with TB and those with LRI. A general discriminant analysis generated a three-gene signature (BAFT2, ETV7 and CD1C), which diagnosed TB with an area under the receiver operating characteristic curve (AUC) of 0.86 (95% CI, 0.69 - 1.00), sensitivity of 69.23% (95% CI, 38.57%-90.91%) and specificity of 94.12% (95% CI, 71.31%-99.85%). CONCLUSION: The three-genes signature may have potential to improve diagnosis of TB in a hospitalised low-burden setting. However, the influence of confounding variables or covariates such as age requires further evaluation in larger studies.

Cladding mode coupling in highly localized fiber Bragg gratings II: complete vectorial analysis.

Highly localized fiber Bragg gratings can be inscribed point-by-point with focused ultrashort pulses. The transverse localization of the resonant grating causes strong coupling to cladding modes of high azimuthal and radial order. In this paper, we show how the reflected cladding modes can be fully analyzed, taking their vectorial nature, orientation and degeneracies into account. The observed modes' polarization and intensity distributions are directly tied to the dispersive properties and show abrupt transitions in nature, strongly correlated with changes in the coupling strengths.

MrParse: finding homologues in the PDB and the EBI AlphaFold database for molecular replacement and more.

Crystallographers have an array of search-model options for structure solution by molecular replacement (MR). The well established options of homologous experimental structures and regular secondary-structure elements or motifs are increasingly supplemented by computational modelling. Such modelling may be carried out locally or may use pre-calculated predictions retrieved from databases such as the EBI AlphaFold database. MrParse is a new pipeline to help to streamline the decision process in MR by consolidating bioinformatic predictions in one place. When reflection data are provided, MrParse can rank any experimental homologues found using eLLG, which indicates the likelihood that a given search model will work in MR. Inbuilt displays of predicted secondary structure, coiled-coil and transmembrane regions further inform the choice of MR protocol. MrParse can also identify and rank homologues in the EBI AlphaFold database, a function that will also interest other structural biologists and bioinformaticians.