BeliefBank: Adding Memory to a Pre-Trained Language Model for a Systematic Notion of Belief

Although pretrained language models (PTLMs) contain significant amounts of world knowledge, they can still produce inconsistent answers to questions when probed, even after specialized training. As a result, it can be hard to identify what the model actually “believes” about the world, making it susceptible to inconsistent behavior and simple errors. Our goal is to reduce these problems. Our approach is to embed a PTLM in a broader system that also includes an evolving, symbolic memory of beliefs – a BeliefBank – that records but then may modify the raw PTLM answers. We describe two mechanisms to improve belief consistency in the overall system. First, a reasoning component – a weighted MaxSAT solver – revises beliefs that significantly clash with others. Second, a feedback component issues future queries to the PTLM using known beliefs as context. We show that, in a controlled experimental setting, these two mechanisms result in more consistent beliefs in the overall system, improving both the accuracy and consistency of its answers over time. This is significant as it is a first step towards PTLM-based architectures with a systematic notion of belief, enabling them to construct a more coherent picture of the world, and improve over time without model retraining

Application of shotgun metagenomics sequencing and targeted sequence capture to detect circulating porcine viruses in the Dutch-German border region

Porcine viruses have been emerging in recent decades, threatening animal and human health, as well as economic stability for pig farmers worldwide. Next-generation sequencing (NGS) can detect and characterize known and unknown viruses but has limited sensitivity when an unbiased approach, such as shotgun metagenomics sequencing, is used. To increase the sensitivity of NGS for the detection of viruses, we applied and evaluated a broad viral targeted sequence capture (TSC) panel and compared it to an unbiased shotgun metagenomic approach. A cohort of 36 pooled porcine nasal swab and blood serum samples collected from both sides of the Dutch-German border region were evaluated. Overall, we detected 46 different viral species using TSC, compared to 40 viral species with a shotgun metagenomics approach. Furthermore, we performed phylogenetic analysis on recovered influenza A virus (FLUAV) genomes from Germany and revealed a close similarity to a zoonotic influenza strain previously detected in the Netherlands. Although TSC introduced coverage bias within the detected viruses, it improved sensitivity, genome sequence depth and contig length. In-depth characterization of the swine virome, coupled with developing new enrichment techniques, can play a crucial role in the surveillance of circulating porcine viruses and emerging zoonotic pathogens

NH3-SCR catalysts for heavy-duty diesel vehicles: Preparation of CHA-type zeolites with low-cost templates

Computer-assistance allows selecting the most adequate low-cost organic structure directing agents (OSDAs) for the crystallization of Al-rich CHA-type zeolites. The host-guest stabilization energies of tetraethylammonium (TEA), methyltriethylammonium (MTEA) and dimethyldiethylammonium (DMDEA), in combination with Na, were first theoretically evaluated. This “ab-initio” analysis reveals that two TEA show a serious steric hindrance in a cha cavity, whereas two MTEA would present excellent host-guest confinements. The synthesis of Al-rich CHA-type zeolites has been accomplished using TEA and MTEA. Electron diffraction and high-resolution transmission electron microscopy reveal large CHA-domains with narrow faulted GME-domains in the CHA-type material synthesized with TEA, confirming the better OSDA-directing roles of MTEA cations towards the cha cavity, in good agreement with DFT calculations. Cu-exchanged Al-rich CHA-type samples achieved with MTEA and TEA show excellent catalytic activity and hydrothermal stability for the selective catalytic reduction (SCR) of NOx with ammonia under conditions relevant for future heavy duty diesel conditions.This work has been supported by Umicore and by the Spanish Government-MCIU through RTI2018-101033-B-I00 (MCIU/AEI/FEDER, UE) and PID2020-112590GB-C21 (AEI/FEDER, UE). T.W. acknowledges financial support by the Swedish Research Council (Grant No. 2019-05465). E.B. acknowledges the Spanish Government-MCIU for a FPI scholarship (PRE2019-088360). P.F. thanks ITQ for a contract. The Electron Microscopy Service of the UPV is acknowledged for their help in sample characterization. The computations were performed on the Tirant III cluster of the Servei d'Informàtica of the University of Valencia

First implementation of a new cross-disciplinary observation strategy for heavy precipitation events from formation to flooding

Heavy Precipitation Events (HPE) are the result of enormous quantities of water vapor being transported to a limited area. HPE rainfall rates and volumes cannot be fully stored on and below the land surface, often leading to floods with short forecast lead times that may cause damage to humans, properties, and infrastructure. Toward an improved scientific understanding of the entire process chain from HPE formation to flooding at the catchment scale, we propose an elaborated event-triggered observation concept. It combines flexible mobile observing systems out of the fields of meteorology, hydrology and geophysics with stationary networks to capture atmospheric transport processes, heterogeneous precipitation patterns, land surface and subsurface storage processes, and runoff dynamics. As part of the Helmholtz Research Infrastructure MOSES (Modular Observation Solutions for Earth Systems), the effectiveness of our observation strategy is illustrated by its initial implementation in the Mueglitz river basin (210 km$^2$), a headwater catchment of the Elbe in the Eastern Ore Mountains with historical and recent extreme flood events. Punctual radiosonde observations combined with continuous microwave radiometer measurements and back trajectory calculations deliver information about the moisture sources, and initiation and development of HPE. X-band radar observations calibrated by ground-based disdrometers and rain gauges deliver precipitation information with high spatial resolution. Runoff measurements in small sub-catchments complement the discharge time series of the operational network of gauging stations. Closing the catchment water balance at the HPE scale, however, is still challenging. While evapotranspiration is of less importance when studying short-term convective HPE, information on the spatial distribution and on temporal variations of soil moisture and total water storage by stationary and roving cosmic ray measurements and by hybrid terrestrial gravimetry offer prospects for improved quantification of the storage term of the water balance equation. Overall, the cross-disciplinary observation strategy presented here opens up new ways toward an integrative and scale-bridging understanding of event dynamics

Complete genome sequence of Spirosoma linguale type strain (1).

Spirosoma linguale Migula 1894 is the type species of the genus. S. linguale is a free-living and non-pathogenic organism, known for its peculiar ringlike and horseshoe-shaped cell morphology. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is only the third completed genome sequence of a member of the family Cytophagaceae. The 8,491,258 bp long genome with its eight plasmids, 7,069 protein-coding and 60 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project

Probing the SELEX Process with Next-Generation Sequencing

Background SELEX is an iterative process in which highly diverse synthetic nucleic acid libraries are selected over many rounds to finally identify aptamers with desired properties. However, little is understood as how binders are enriched during the selection course. Next-generation sequencing offers the opportunity to open the black box and observe a large part of the population dynamics during the selection process. Methodology We have performed a semi-automated SELEX procedure on the model target streptavidin starting with a synthetic DNA oligonucleotide library and compared results obtained by the conventional analysis via cloning and Sanger sequencing with next-generation sequencing. In order to follow the population dynamics during the selection, pools from all selection rounds were barcoded and sequenced in parallel. Conclusions High affinity aptamers can be readily identified simply by copy number enrichment in the first selection rounds. Based on our results, we suggest a new selection scheme that avoids a high number of iterative selection rounds while reducing time, PCR bias, and artifacts

Beweis von Schwefel‐non‐Innocence in [CoII(Dithiacyclam)]2+‐vermittelten, katalytischen Sauerstoff‐Reduktions‐Reaktionen

In vielen Metallenzymen sind Schwefel-enthaltende Liganden an Elektronen-Transfer-Reaktionen beteiligt. In dem hier diskutierten biomimetischen Ansatz wird der Einfluss einer Schwefelkoordination auf eine Kobalt-katalysierte Sauerstoff-Reduktionsreaktion (ORR) demonstriert. Ein Vergleich des ORR-Vermögens eines vierfach Stickstoff-koordinierten [Co(Cyclam]2+-Komplexes (1; Cyclam=1,5,8,11-Tetraaza-cyclotetradecan) und dessen Schwefel-Analogons [Co(S2N2-Cyclam)]2+ (2; S2N2-Cyclam=1,8-Dithia-5,11-diazacyclotetradecan) zeigt verbesserte katalytische Eigenschaften mit dem in die Ligandensphäre am Kobalt eingeführten Chalkogen. Isolierung und Charakterisierung der Intermediate, die sich im Zuge der Sauerstoffaktivierung an den Kobalt(II)-Zentren von 1 und 2 bilden, identifizieren eine Beteiligung des Schwefels am O2-Reduktionsprozess als entscheidenden Faktor für die verbesserten Eigenschaften von 2 bei der katalytischen ORR.Peer Reviewe