bluuebunny/crossref_metadata_2025 huggingface dataset:
Infringing ‘use in the course of trade’: trade mark use and the essential function of a Trade mark
Authors: Sumroy Rob , Badger Carina
Published: October 2023

The recent Arsenal litigation discloses divergent views between the European 10.01

Court of Justice (ECJ) and certain of the English courts as to what protection a registered trade mark should confer on its owner under the Trade Mark Directive.1 In a brave new world of brands, where the exploitation of intellectual property is key, the legal uncertainty arising from such division is acutely unsatisfactory for rights owners in general and, in particular, for those First Council Directive 89/104/EEC of 21 December 1988.
The Political Economy of the World Trading System
Authors: Hoekman Bernard M , Kostecki Michel M
Published: October 2023

The Political Economy of the World Trading System is a comprehensive textbook account of the economics, institutional mechanics and politics of the world trading system. This third edition has been expanded and updated to cover developments in the World Trade Organisation (WTO) since its formation, including the Doha Round, presenting the essentials of trade negotiations and the WTO’s rules and disciplines. The authors focus in particular on the WTO’s role as the primary organisation through which trading nations manage their commercial interactions and the focal point for cooperation on policy responses to the rapidly changing global trading environment. It is the forum in which many features of the globalisation process are considered, and it currently faces an unprecedented set of challenges. The increasing importance of countries in Asia, Latin America and Africa in international trade relations, the revealed preference towards regionalism, intensification of trade conflicts, the role of business groups and NGOs in trade policy formation and negotiations, and pressures for more leadership in an institution threatened by paralysis are examples of issues that are discussed in some detail; all are critical for the operation of the system and for international business in the coming decade. This edition also includes numerous real-world examples to illustrate how the WTO impinges on business, workers and households, written from the perspective of managers and business associations. An insider’s view of the institutional history of the WTO allows the authors to use a variety of conceptual tools to analyse the working of the WTO in a non-technical manner. Suggestions for Further Reading at the end of each chapter and an extensive bibliography make the volume suitable both for introductory and postgraduate courses on international economics and business, international relations, and international economic law.
Law And Economics In European Merger Control
Authors: Schwalbe Ulrich , Zimmer Daniel
Published: October 2023

Law and Economics in European Merger Control provides a thorough introduction to the economic theory underlying the regulation of mergers. The central economic concepts of efficiency and welfare are introduced and their role in the foundations of competition law is explained. Market structures of perfect competition, monopoly and oligopoly are analysed and the methods for delineating and evaluating the effects of mergers on markets are explained. Having examined the economic context, the book then proceeds to offer an exhaustive analysis of the application of economic theory in the practice of merger regulation in Europe. Through an analysis of more than 300 competition cases the book critiques the current state of EC competition law against its economic aims, and offers views for the future development of the law. It also sets out an account of the European Commission's search for a 'more economic approach' to competition law, and analyses the policy's successes and failures.
Outcomes and Complications Associated With the Learning Curve for Endoscopic Cervical Foraminotomy
Authors: Baumann Anthony N. , Callaghan Megan E. , Walley Kempland C. , Anastasio Albert T. , Muralidharan Aditya , Talaski Grayson , Rocos Brett
Published: October 2023

Study Design.

A systematic review and meta-analysis.

Objective.

The objective of this study is to examine the impact of the learning curve for endoscopic cervical foraminotomy for clinical outcomes and patient safety.

Summary of Background Data.

Endoscopic cervical foraminotomy is a minimally invasive surgical technique emerging in the literature for surgical management of cervical radiculopathy without the use of open incision. The adoption of endoscopic cervical foraminotomy may be hindered by the learning curve, although no review and meta-analysis exists to date on the topic.

Materials and Methods.

A systematic review and meta-analysis was performed using PubMed, CINAHL, and MEDLINE from database inception until July 11, 2023. Inclusion criteria were articles that examined endoscopic cervical foraminotomy, reported outcomes, and/or complications for endoscopic cervical spine surgery relevant to the learning curve and had full-text. A random effects meta-analysis was performed for outcomes and complications.

Results.

A total of three articles (n=203 patients) were included from 792 articles initially retrieved. The learning curves from four surgeons were examined with a FWM 21 procedures until the competency phase. There was no significant difference in the postoperative hospitalization length (P=0.669), postoperative recovery room time (P=0.415), intraoperative blood loss (P=0.064), and total complication rates (10.9% vs. 1.2%, P=0.139) between endoscopic cervical foraminotomy procedures performed in the learning phase as compared with the competency phase of the learning curve. There was a significant decrease in operative time from the learning phase to the competency phase (P=0.005).

Conclusion.

Competency was achieved on the learning curve for endoscopic cervical foraminotomy after about 21 procedures. There is no significant difference in postoperative hospitalization time, postoperative recovery room time, intraoperative blood loss, and complication rates between the learning phase and the competency phase of the learning curve for endoscopic cervical foraminotomy, noting the relatively small sample size of this study that may underpower this finding.
Prospective clinical trial of EUS–guided choledochoduodenostomy without fistula dilation for malignant distal biliary obstruction
Authors: Koga Takehiko , Hijioka Susumu , Nagashio Yoshikuni , Maruki Yuta , Maehara Kosuke , Murashima Yumi , Kawasaki Yuki , Takeshita Kotaro , Yamada Natsumi , Yoshinari Motohiro , Hisada Yuya , Harai Shota , Kitamura Hidetoshi , Kawahara Shun , Ohba Akihiro , Morizane Chigusa , Ishida Yusuke , Hirai Fumihito , Okusaka Takuji
Published: October 2023

Background and Objectives

During EUS–guided choledochoduodenostomy (EUS-CDS), fistula dilation before stent insertion is associated with adverse events (AEs), such as bile leakage and peritonitis. We hypothesized that EUS-CDS without fistula dilation using a novel self-expandable metal stent (SEMS) with a thin delivery system could overcome this problem, and we conducted this study to evaluate its feasibility and safety.

Methods

This was an open-label, single-arm, phase II study at a single institution. We planned EUS-CDS without fistula dilation using a fully covered SEMS with a 5.9-Fr delivery system for unresectable malignant distal biliary obstruction. The primary outcome was overall technical success. Secondary outcomes were technical success without fistula dilation, procedure time, functional success, time to recurrent biliary obstruction, and AEs. The planned sample size was 25 patients.

Results

In total, 24 patients were included in this study. In 21 patients, EUS-CDS was performed as primary drainage. The overall technical success rate was 100% (24 of 24 patients). The technical success rate without fistula dilation was 96% (23 of 24). The median procedure time was 16 min (range, 10–66 min). The functional success rate was 96% (23 of 24). The median time to recurrent biliary obstruction was 148 days (95% confidence interval, 29–266 days). There were no procedure-related AEs. Furthermore, computed tomography immediately after the procedure showed no leakage of contrast medium into the abdominal cavity in any patient.

Conclusions

EUS–guided choledochoduodenostomy without fistula dilation using a fully covered SEMS with a 5.9-Fr delivery system is feasible with a high probability and can be achieved quickly while effectively preventing bile leakage and peritonitis.
Comparison of Magnetic Resonance Imaging and Endoscopic Ultrasound in the Sizing of Intraductal Papillary Mucinous Neoplasia of the Pancreas
Authors: Hesse Felix , Ritter Jessica , Hapfelmeier Alexander , Braren Rickmer , Phillip Veit
Published: October 2023

Objectives

Because IPMNs are potentially malignant, surveillance of IPMN is recommended by magnetic resonance imaging (MRI) and endoscopic ultrasound (EUS). The aim of the study was the evaluation of the concordance between EUS and MRI regarding cyst size.

Methods

Retrospective data analysis was done for patients with IPMN in whom EUS and MRI were performed simultaneously (≤60 days). The measured cyst size of both procedures was compared by Bland-Altman plots. Agreement of cyst localization and dilation of main pancreatic duct was assessed using kappa statistics.

Results

Fifty-nine cases were evaluated (median age, 71 years; 65% female; median time interval between both investigations, 17 days). The mean difference of IPMN maximal diameter between EUS and MRI was 0.55 mm with a prediction interval of −9.20 to +10.29 mm for 95% of the expected differences. There was strong interobserver agreement regarding cyst localization (κ = 0.669, P = 1.06e−13) and the width of main pancreatic duct (<5, 5–9, and ≥10 mm; κ = 0.676 caput, κ = 0.823 corpus).

Conclusions

We found a clinically relevant difference in cyst size comparing EUS and MRI. Therefore, alternating EUS and MRI for follow-up of the “worrisome feature” size growth is not reasonable.
Association of Longitudinal Mobility Levels in the Hospital and Injurious Inpatient Falls
Authors: Hoyer Erik , Young Daniel , Ke Victor , Zhang Jia Yi , Colantuoni Elizabeth , Farley Holley , Dahbura Anton , Ghobadi Kimia
Published: October 2023

Falls are one of the most common adverse events in hospitals, and patient mobility is a key risk factor. In hospitals risk assessment tools are used to identify patient-centered fall risk factors and guide care plans, but these tools have limitations. To address these issues, we examined daily patient mobility levels prior to injurious falls using the Johns Hopkins Highest Level of Mobility (JH-HLM), which quantifies key patient mobility milestones from low-level to community distances of walking. We aimed to identify longitudinal characteristics of patient mobility prior to a fall to help identify fallers before the event. Conducting a retrospective matched case-control analysis, we compared mobility levels in the days leading up to an injurious fall between fallers and non-fallers. We observed that patients who suffered an injurious fall, on average, spent 28% of their time pre-fall at a low mobility level (JH-HLM levels 1 to 4), compared to non-fallers who spent 19% of their time at a low mobility level (Mean Absolute Difference: 9%; 95% CI 1% to 16%, p = 0.026; Relative Difference: 44%). This suggests that assessing a patient’s mobility levels over time can help identify those at an increased risk for falls and enable hospitals to manage mobility problems more effectively.
Artificial Intelligence–based Quantification of Pleural Plaque Volume and Association With Lung Function in Asbestos-exposed Patients
Authors: Groot Lipman Kevin B.W. , Boellaard Thierry N. , de Gooijer Cornedine J. , Bogveradze Nino , Hong Eun Kyoung , Landolfi Federica , Castagnoli Francesca , Vakhidova Nargiza , Smesseim Illaa , van der Heijden Ferdi , Beets-Tan Regina G.H. , Wittenberg Rianne , Bodalal Zuhir , Burgers Jacobus A. , Trebeschi Stefano
Published: October 2023

Purpose:

Pleural plaques (PPs) are morphologic manifestations of long-term asbestos exposure. The relationship between PP and lung function is not well understood, whereas the time-consuming nature of PP delineation to obtain volume impedes research. To automate the laborious task of delineation, we aimed to develop automatic artificial intelligence (AI)–driven segmentation of PP. Moreover, we aimed to explore the relationship between pleural plaque volume (PPV) and pulmonary function tests.

Materials and Methods:

Radiologists manually delineated PPs retrospectively in computed tomography (CT) images of patients with occupational exposure to asbestos (May 2014 to November 2019). We trained an AI model with a no-new-UNet architecture. The Dice Similarity Coefficient quantified the overlap between AI and radiologists. The Spearman correlation coefficient (r) was used for the correlation between PPV and pulmonary function test metrics. When recorded, these were vital capacity (VC), forced vital capacity (FVC), and diffusing capacity for carbon monoxide (DLCO).

Results:

We trained the AI system on 422 CT scans in 5 folds, each time with a different fold (n = 84 to 85) as a test set. On these independent test sets combined, the correlation between the predicted volumes and the ground truth was r = 0.90, and the median overlap was 0.71 Dice Similarity Coefficient. We found weak to moderate correlations with PPV for VC (n = 80, r = −0.40) and FVC (n = 82, r = −0.38), but no correlation for DLCO (n = 84, r = −0.09). When the cohort was split on the median PPV, we observed statistically significantly lower VC (P = 0.001) and FVC (P = 0.04) values for the higher PPV patients, but not for DLCO (P = 0.19).

Conclusion:

We successfully developed an AI algorithm to automatically segment PP in CT images to enable fast volume extraction. Moreover, we have observed that PPV is associated with loss in VC and FVC.
Asuc_0142 of Actinobacillus succinogenes 130Z is the l-aspartate/C4-dicarboxylate exchanger DcuA
Authors: Cho Young Bin , Park Ji Won , Unden Gottfried , Kim Ok Bin
Published: October 2023

Anaerobic bacteria often use antiporters DcuB (malate/succinate antiport) or DcuA (l-aspartate/succinate antiport) for the excretion of succinate during fumarate respiration. The rumen bacterium

Actinobacillus succinogenes

is able to produce large amounts of succinate by fumarate respiration, using the DcuB-type transporter DcuE for l-malate/succinate antiport. Asuc_0142 was annotated as a second DcuB-type transporter. Deletion of Asuc_0142 decreased the uptake rate for l-[14C]aspartate into

A. succinogenes

cells. Properties of transport by heterologously expressed Asuc_0142 were investigated in an

Escherichia coli

mutant deficient of anaerobic C4DC transporters. Expression of Asuc_0142 resulted in high uptake activity for l-[14C]fumarate or l-[14C]aspartate, but the former showed a strong competitive inhibition by l-aspartate. In

E. coli

loaded with l-[14C]aspartate, [14C]succinate or [14C]fumarate, extracellular C4DCs initiated excretion of the intracellular substrates, with a preference for l-aspartateex/succinatein or l-aspartateex/fumaratein antiport. These findings indicate that Asuc_0142 represents a DcuA-type transporter for l-aspartate uptake and l-aspartateex/C4DCin antiport, differentiating it from the DcuB-type transporter DcuE for l-malateex/succinatein antiport. Sequence analysis and predicted structural characteristics confirm structural similarity of Asuc_0142 to DcuA, and Asuc_0142 was thus re-named as DcuAAs. The bovine rumen fluid contains l-aspartate (99.6 µM), whereas fumarate and l-malate are absent. Therefore, bovine rumen colonisers depend on l-aspartate as an exogenous substrate for fumarate respiration.

A. succinogenes

encodes HemG (protoporphyrinogen oxidase) and PyrD (dihydroorotate dehydrogenase) for haem and pyrimidine biosynthesis. The enzymes require fumarate as an electron acceptor, suggesting an essential role for l-aspartate, DcuAAs, and fumarate respiration for

A. succinogenes

growing in the bovine rumen.
A time-resolved multi-omics atlas of transcriptional regulation in response to high-altitude hypoxia across whole-body tissues
Authors: Yan Ze , Yang Ji , Wei Wen-Tian , Zhou Ming-Liang , Mo Dong-Xin , Wan Xing , Ma Rui , Wu Mei-Ming , Huang Jia-Hui , Liu Ya-Jing , Lv Feng-Hua , Li Meng-Hua
Published: October 2023

High-altitude hypoxia acclimatization requires whole-body physiological regulation in highland immigrants, but the underlying genetic mechanism has not been clarified. Here we used sheep as an animal model for plain-to-plateau transplantation. We generated multi-omics data including time-resolved bulk RNA-Seq, ATAC-Seq and single-cell RNA-Seq from multiple tissues as well as phenotypic data from 20 bio-indicators. We characterized transcriptional changes of all genes in each tissue, and examined multi-tissue temporal dynamics and transcriptional interactions among genes. In particular, we identified critical functional genes regulating the short response to hypoxia in each tissue (e.g.,PARGin the cerebellum andHMOX1in the colon). We further identified TAD-constrainedcis-regulatory elements, which suppressed the transcriptional activity of most genes under hypoxia. Phenotypic and transcriptional evidence indicated that antenatal hypoxia could improve hypoxia tolerance in offspring. Furthermore, we provided time-series expression data of candidate genes associated with human mountain sickness (e.g.,BMPR2) and high-altitude adaptation (e.g.,HIF1A). Our study provides valuable resources and insights for future hypoxia-related studies in mammals.
COMPARATIVE PHYTOCHEMICAL ANALYSIS OF TWO ALPINIA SPECIES FROM ZINGEBERACEAE FAMILY
Authors: Rabita N. , Palanisamy K.
Published: October 2023

The traditional applications of the rhizomes of two Alpinia species,Alpinia galangaandAlpinia nigra, both of which belong to the Zingiberaceae family, are widely recognized. Alpinia has been concentrating on its biological defenses against terrible diseases including cancer and devastating viral infections. In order to develop the diagnostic keys for these significant medications based on the phytochemical analysis, the current research work was done to conduct a detailed comparative phytochemical investigation of the two species.Alpinia galangaandAlpinia nigrawere the focus of this study’s evaluation of their phytochemical components. Alkaloids, saponins, quinones, terpenoids, steroids, tannins, flavonoids, cardiac glycosides, and coumarins were all investigated in our experiments to see if they were present within the two species. The primary chemical compounds found inAlpinia galangaandAlpinia nigrathat may be significant from a pharmacological perspective are highlighted in this article. A qualitative phytochemical study of plant extracts revealed that most of the substances, such as quinones, terpenoids, tannins, steroids, flavonoids, cardiac glycosides, and coumarins, were present.
Metabolic and behavioral alterations associated with viral vector-mediated toxicity in the paraventricular hypothalamic nucleus
Authors: Savani Rohan , Park Erin , Busannagari Nidhi , Lu Yi , Kwon Hyokjoon , Wang Le , Pang Zhiping P.
Published: October 2023

Objective

Combining adeno-associated virus (AAV)-mediated expression of Cre recombinase with genetically modified floxed animals is a powerful approach for assaying the functional role of genes in regulating behavior and metabolism. Extensive research in diverse cell types and tissues using AAV-Cre has shown it can save time and avoid developmental compensation as compared to using Cre driver mouse line crossings. We initially sought to study the impact of ablation of corticotropin-releasing hormone (CRH) in the paraventricular hypothalamic nucleus (PVN) using intracranial AAV-Cre injection in adult animals.

Methods

In this study, we stereotactically injected AAV8-hSyn-Cre or a control AAV8-hSyn-GFP both Crh-floxed and wild-type mouse PVN to assess behavioral and metabolic impacts. We then used immunohistochemical markers to systematically evaluate the density of hypothalamic peptidergic neurons and glial cells.

Results

We found that delivery of one specific preparation of AAV8-hSyn-Cre in the PVN led to the development of obesity, hyperphagia, and anxiety-like behaviors. This effect occurred independent of sex and in both floxed and wild-type mice. We subsequently found that AAV8-hSyn-Cre led to neuronal cell death and gliosis at the site of viral vector injections. These behavioral and metabolic deficits were dependent on injection into the PVN. An alternatively sourced AAV-Cre did not reproduce the same results.

Conclusions

Our findings reveal that delivery of a specific batch of AAV-Cre could lead to cellular toxicity and lesions in the PVN that cause robust metabolic and behavioral impacts. These alterations can complicate the interpretation of Cre-mediated gene knockout and highlight the need for rigorous controls.
Aggression: A gut reaction? The effects of the gut microbiome on aggression
Authors: Uzan-Yulzari Atara , Turjeman Sondra , Getselter Dmitriy , Rautava Samuli , Isolauri Erika , Khatib Soliman , Elliott Evan , Koren Omry
Published: October 2023

Recent research has unveiled conflicting evidence regarding the link between aggression and the gut microbiome. In our investigation, we meticulously examined the behavioral patterns of four groups of mice – wild-type, germ-free (GF), mice treated with antibiotics, and recolonized GF mice – to gain mechanistic insights into the impact of the gut microbiome on aggression. We discovered a significant correlation between diminished microbiome and increased aggression. Importantly, this behavioral shift could be restored when a WT microbiota was reinstated. Microbiota manipulation also significantly altered brain function, particularly in aggression-associated genes, and urine metabolite profiles. Notably, our study extends beyond the murine model, shedding light on clinical implications of early-life antibiotic exposure. We found that fecal microbiome transplants from 1mo old infants prescribed antibiotics during their first days of life led to a marked increase in aggression in recipient mice. This research demonstrates that the microbiota modulates aggression and underscores its importance in the realm of behavioral science.

One-Sentence Summary

The antibiotic-altered gut microbiome is implicated in increased aggression. It also leads to altered brain function, particularly in genes linked to aggression, and urine metabolite profiles showing a multi-system response to microbiota disruption.
High-fidelity (repeat) consensus sequences from short reads using combined read clustering and assembly
Authors: Mann Ludwig , Balasch Kristin , Schmidt Nicola , Heitkam Tony
Published: October 2023

Background

Despite the many cheap and fast ways to generate genomic data, good and exact genome assembly is still a problem, with especially the repeats being vastly underrepresented and often misassembled. As short reads in low coverage are already sufficient to represent the repeat landscape of any given genome, many read cluster algorithms were brought forward that provide repeat identification and classification. But how can trustworthy, reliable and representative full-length repeat consensuses be derived from unassembled genomes?

Results

Here, we combine methods from repeat identification and genome assembly to derive these robust consensuses. We test several use cases, such as (1) consensus building from clustered short reads of non-model genomes, (2) from genome-wide amplification setups, and (3) specific repeat-centred questions, such as the linked vs. unlinked arrangement of ribosomal genes. In all our use-cases, the derived consensuses are robust and representative. To evaluate overall performance, we compare our high-fidelity repeat consensuses to RepeatExplorer2-derived contigs and check, if they represent real transposable elements as found in long reads. Our results demonstrate that it is possible to generate useful, reliable and trustworthy consensuses from short reads by a combination from read cluster and genome assembly methods in an automatable way.

Conclusion

We anticipate that our workflow opens the way towards more efficient and less manual repeat characterization and annotation, benefitting all genome studies, but especially those of non-model organisms.
Species Composition and Distribution of Anopheles gambiae Complex Circulating in Kinshasa
Authors: Zanga Josue , Metelo Emery , Mvuama Nono , Nsabatien Victoire , Mvudi Vanessa , Banzulu Degani , Mansiangi Osée , Bamba Maxwel , Basosila Narcisse , Agossa Rodrigue , Wumba Roger
Published: October 2023

Understanding the distribution ofAnophelesspecies in a region is an important task in the planning and implementation of malaria control programmes. This study was proposed to evaluate the composition and distribution of cryptic species of the main malaria vector,Anopheles gambiaecomplex, circulating in different districts of Kinshasa.

To study the distribution of members of theAn.gambiaecomplex,Anopheleswere sampled by CDC light trap and larva collection across the four districts of Kinshasa city between July 2021 and June 2022. After morphological identification, an equal proportion ofAnopheles gambiaes.l. sampled per site were subjected to polymerase chain reaction (PCR) for identification of crypticAn.gambiaecomplex species.

TheAnopheles gambiaecomplex was widely identified in all sites across the city of Kinshasa, with a significant difference in mean density, captured by CDC light, inside and outside households in Kinshasa (p=0.002). Two species of this complex circulate in Kinshasa:Anopheles gambiae(82.1%) andAnopheles coluzzii(17.9%). In all study sites,Anopheles gambiaewas the most prevalent species.Anopheles coluzziiwas very prevalent in Tshangu district. No hybrids (Anopheles coluzzii/Anopheles gambiae) were identified.

Two cryptic species of theAnopheles gambiaecomplex circulate in Kinshasa.Anopheles gambiaes.s., present in all districts andAnopheles coluzzii, with a limited distribution. Studies on the ecology of the larval sites are essential to better understand the factors influencing the distribution of members of theAn. gambiaecomplex in this megalopolis.
Marine protection enhances the resilience of biological communities on temperate rocky reefs
Authors: Sanabria-Fernandez Jose A. , Alday Josu G.
Published: October 2023

Conservation science faces the urgent challenge of halting the biodiversity loss caused by the biological crisis of the present era. To achieve this, conservation science requires cutting-edge tools to focus on vital properties of ecosystems, such as the resilience. Resilience informs about the cost of recovering biological communities. Here, we developed a metric to quantify the communities ecological recovery cost based on the multidimensional distance between unprotected and partially protected communities from totally protected communities in Cabo de Gata Marine Reserve. Our results show that the biological community composed of fish, macroinvertebrates and cryptic fish, and macroalgae species in unprotected zones requires a higher ecological recovery cost than in partially protected zones when moving towards a fully protected community. This research contributes to monitoring marine the effectiveness of marine protection from a resilience perspective, with the goal of promoting the use of the recovery cost metric for building resilient coastal ecosystems.
Influenza vaccine effectiveness against hospitalized SARS-CoV-2 infection
Authors: Lee Yung-Chun , Liu Lufeiya , Yuan Liyang , Risk Malcolm , Heinrich Kevin , Witteveen-Lane Martin , Hayek Salim , Malosh Ryan , Pop-Busui Rodica , Jiang Bian , Shen Chen , Chesla Dave , Kennedy Richard , Xu Shi , Sims Matthew , Homayouni Ramin , Zhao Lili
Published: October 2023

Abstract

Background

Some studies conducted before the Delta and Omicron variant-dominant periods have indicated that influenza vaccination provided protection against COVID-19 infection or hospitalization, but these results were limited by small study cohorts and a lack of comprehensive data on patient characteristics. No studies have examined this question during the Delta and Omicron periods (08/01/2021 to 2/22/2022).

Methods

We conducted a retrospective cohort study of influenza-vaccinated and unvaccinated patients in the Corewell Health East(CHE, formerly known as Beaumont Health), Corewell Health West(CHW, formerly known as Spectrum Health) and Michigan Medicine (MM) healthcare system during the Delta-dominant and Omicron-dominant periods. We used a test-negative, case-control analysis to assess the effectiveness of the influenza vaccine against hospitalized SARS-CoV-2 outcome in adults, while controlling for individual characteristics as well as pandameic severity and waning immunity of COVID-19 vaccine.

Results

The influenza vaccination has shown to provided some protection against SARS-CoV-2 hospitalized outcome across three main healthcare systems. CHE site (odds ratio [OR]=0.73, vaccine effectiveness [VE]=27%, 95% confidence interval [CI]: [18-35], p<0.001), CHW site (OR=0.85, VE=15%, 95% CI: [6-24], p<0.001), MM (OR=0.50, VE=50%, 95% CI: [40-58], p <0.001) and overall (OR=0.75, VE=25%, 95% CI: [20-30], p <0.001).

Conclusion

The influenza vaccine provides a small degree of protection against SARS-CoV-2 infection across our study sites.
Epitope mapping of SARS-CoV-2 RBDs by hydroxyl radical protein footprinting reveals the importance of including negative antibody controls
Authors: Larsen Daniel Nyberg , Kaczmarek Jakub Zbigniew , Palarasah Yaseelan , Graversen Jonas Heilskov , Højrup Peter
Published: October 2023

Understanding protein-protein interaction is essential when designing drugs or investigating biological processes. A variety of techniques can be employed in order to map the regions on proteins that are involved in binding eg., CryoEM, X-ray spectroscopy, linear epitope mapping, or mass spectrometry-based methods. The most commonly utilized mass spectrometry-based techniques are cross-linking and hydrogen-deuterium exchange (HDX). An alternative technique for identifying residues on the three-dimensional structure of proteins, that are involved in binding, can be hydroxyl radical protein footprinting (HRPF). However, this method is currently hampered by high initial cost and complex experimental setup. Here we set out to present a generally applicable method using Fenton chemistry for mapping of epitopes in a standard mass spectrometry laboratory. Furthermore, the described method illustrates the importance of controls on several levels when performing mass spectrometry-based epitope mapping. In particular, the inclusion of a negative antibody control has not previously been widely utilized in epitope mapping by HRPF analysis. In order to limit the number of false positives, we further introduced quantification by TMT labelling, thereby allowing for direct comparison between sample conditions and biological triplicates. Lastly, up to six technical replicates were incorporated in the experimental setup in order to achieve increased depth of the final analysis.

Both binding and opening of regions on receptor-binding domain (RBD) from SARS-CoV-2 Spike Protein, Alpha, and Delta variants, were observed. The negative control antibody experiment combined with the high overlap between biological triplicates resulted in the exclusion of 40% of the significantly changed regions, including both binding and opening regions. The final identified binding region was mapped to a three-dimensional structure and agrees with the literature for neutralizing antibodies towards SARS-CoV-2 Spike Protein.

The presented method is straightforward to implement for the analysis of HRPF in a generic MS-based laboratory. The high reliability of the data was achieved by increasing the number of technical and biological replicates combined with negative antibody controls.
A pooled-sample draft genome assembly provides insights into host plant-specific transcriptional responses of a Solanaceae-specializing pest,Tupiocoris notatus(Hemiptera: Miridae)
Authors: Goldberg Jay K , Allan Carson W. , Copetti Dario , Matzkin Luciano M. , Bronstein Judith
Published: October 2023

The assembly of genomes from pooled samples of genetically heterogenous samples of conspecifics remains challenging. In this study we show that high-quality genome assemblies can be produced from samples of multiple wild-caught individuals. We sequenced DNA extracted from a pooled sample of conspecific herbivorous insects (Hemiptera: Miridae:Tupiocoris notatus) acquired from a greenhouse infestation in Tucson, Arizona (in the range of 30-100 individuals; 0.5 mL tissue by volume) using PacBio highly accurate long reads (HiFi). The initial assembly contained multiple haplotigs (>85% BUSCOs duplicated), but duplicate contigs could be easily purged to reveal a highly complete assembly (95.6% BUSCO, 4.4% duplicated) that is highly contiguous by short-read assembly standards (N50 = 675 kb; Largest contig = 4.3 Mb). We then used our assembly as the basis for a genome-guided differential expression study of host-plant specific transcriptional responses. We found thousands of genes (N = 4982) to be differentially expressed between our new data from individuals feeding onDatura wrightii(Solanaceae) and existing RNA-seq data fromNicotiana attenuata(Solanaceae) fed individuals. We identified many of these genes as previously documented detoxification genes such as glutathione-S-transferases, cytochrome P450s, UDP-glucosyltransferases. Together our results show that long-read sequencing of pooled samples can provide a cost-effective genome assembly option for small insects and provide insights into the genetic mechanisms underlying interactions between plants and herbivorous pests.
Colloidal aggregation confounds cell-based Covid-19 antiviral screens
Authors: Glenn Isabella S. , Hall Lauren N. , Khalid Mir M. , Ott Melanie , Shoichet Brian K.
Published: October 2023

Colloidal aggregation is one of the largest contributors to false-positives in early drug discovery and chemical biology. Much work has focused on its impact on pure-protein screens; here we consider aggregations role in cell-based infectivity assays in Covid-19 drug repurposing. We began by investigating the potential aggregation of 41 drug candidates reported as SARs-CoV-2 entry inhibitors. Of these, 17 formed colloidal-particles by dynamic light scattering and exhibited detergent-dependent enzyme inhibition. To evaluate antiviral efficacy of the drugs in cells we used spike pseudotyped lentivirus and pre-saturation of the colloids with BSA. The antiviral potency of the aggregators was diminished by at least 10-fold and often entirely eliminated in the presence of BSA, suggesting antiviral activity can be attributed to the non-specific nature of the colloids. In confocal microscopy, the aggregates induced fluorescent puncta of labeled spike protein, consistent with sequestration of the protein on the colloidal particles. Addition of either non-ionic detergent or of BSA disrupted these puncta. These observations suggest that colloidal aggregation is common among cell-based anti-viral drug repurposing, and perhaps cell-based assays more broadly, and offers rapid counter-screens to detect and eliminate these artifacts, allowing the community invest resources in compounds with true potential as a Covid-19 therapeutic.
Genome-wide evidence of the role of Paf1C in transcription elongation and histone H2B monoubiquitination inArabidopsis
Authors: Blanco-Touriñán Noel , Pérez-Alemany Jaime , Bourbousse Clara , Latrasse David , Ait-Mohamed Ouardia , Benhamed Moussa , Barneche Fredy , Blázquez Miguel A. , Gallego-Bartolomé Javier , Alabadí David
Published: October 2023

The evolutionarily conserved Paf1 complex (Paf1C) participates in transcription, and research in animals and fungi suggests that it facilitates RNAPII progression through chromatin remodeling. To obtain evidence that Paf1C acts in transcription elongation inArabidopsis, we examined the genomic distribution of the ELF7 and VIP3 subunits of Paf1C. The occupancy of both subunits was confined to thousands of gene bodies and positively correlated with RNAPII occupancy and the level of gene expression, supporting a role as a transcription elongation factor. We found that monoubiquitinated histone H2B, which marks most transcribed genes, was strongly reduced genome-wide inelf7seedlings. Genome-wide profiling of RNAPII revealed that inelf7mutants, RNAPII occupancy was reduced throughout the gene body and at the transcription end site of Paf1C-targeted genes, suggesting a direct role for the complex in transcription elongation. Overall, our observations suggest that there is a direct functional link between Paf1C activity, mono-ubiquitination of histone H2B, and the transition of RNPII to productive elongation. However, for several genes, Paf1C may also act independently of H2Bub deposition or occupy these genes more stably than H2Bub marking, possibly reflecting the dynamic nature of Paf1C association and H2Bub turnover during transcription.
Association of the LIfestyle for BRAin Health Score and Brain Vascular Damage in a Community-Dwelling Adults Cohort
Authors: Li Hang , Zhou Qi , Cai Xueli , Wang Yicong , Yang Yingying , Wang Suying , Meng Xia , Jing Jing , Liu Dandan , Zhang Yanli , Wang Yongjun , Pan Yuesong , Wang Yilong
Published: October 2023

OBJECTIVE

To investigate the association of brain vascular damage and the LIfestyle for BRAin Health (LIBRA) dementia risk scores.

METHODS

This cross-sectional study was based on the baseline survey from a population-based prospective cohort study. The Polyvascular Evaluation for Cognitive Impairment and Vascular Events (PRECISE) study recruited community-dwelling adults aged 50–75 years based on cluster sampling from Lishui city in China. Eleven modifiable risk or protective factors for dementia collected at baseline survey were combined in the LIBRA score. Eligible participants were scanned by a 3.0T Magnetic resonance imaging scanner. Intracranial atherosclerosis and cerebral small vessel disease (CSVD) burden were assessed.

RESULTS

In a total of 3059 individuals, the mean (SD) age was 61.2 (6.7) years; 1630 (53.5%) being women. Compared with the first tertile, subjects with the third tertile of LIBRA score were associated with increased odds of the presence of intracranial atherosclerotic plaque (adj. OR 2.22, 95% CI 1.75 to 2.82,P<0.001). A similar association was observed for intracranial atherosclerotic burden (adj. cOR 2.26, 95% CI 1.79 to 2.87,P<0.001). Whereas, subjects with the third tertile of LIBRA score were not associated with the presence of CSVD (adj. OR 1.05, 95% CI 0.86 to 1.29,P=0.63) or higher CSVD burden (adj. cOR 1.06, 95% CI 0.87 to 1.29,P=0.55). Multivariable binary logistic regression analysis for the association between the LIBRA score and the presence of coexistent atherosclerotic plaque and CSVD was also significant adjusting for the nonmodifiable factors age, sex, education, married or cohabiting status, socioeconomic status, and history of stroke (adj. OR 1.70, 95% CI 1.21 to 2.39,P= 0.002).

CONCLUSIONS

In this study, LIBRA scores were positively associated with the presence and burden of intracranial atherosclerosis, coexistence of atherosclerotic plaque and CSVD. These findings suggested that modifiable dementia score maybe useful in identifying individuals at high risk of brain vascular damage.
Fluid Uptake Pathways Are Differentially Modified in Rice (Oryza sativaL.) in Response to Drought and Salinity
Authors: Chowdery Rukaya Amin , Shashidhar H E , Mathew M K
Published: October 2023

Salinity and drought adversely affect rice production globally. Here we have examined physiological responses to drought and salinity across four rice cultivars with varying sensitivity to these stresses. The salt tolerant Pokkali restricts fluid entry to limit Na+uptake under saline stress, while the drought-tolerant ARB6 needs to enhance fluid uptake under drought. Surprisingly, Pokkali does reasonably well when subjected to drought as does ARB6 under saline stress - in contrast to the stress-sensitive but high yielding varieties IR-20 and Jaya. Both tolerant varieties use long roots to mine water under deficit conditions, increasing aerenchyma and suberization of the exodermis to provide oxygen to deep-reaching roots. Major alterations in patterns of suberization in both exodermis and endodermis are undertaken, the patterns being dramatically different under the two stresses. Genes implicated in suberin biosynthesis also showed variation in transcript levels under stress, corresponding with the observed suberization patterns. Osmolyte accumulation drives uptake of water under deficit conditions, while restricting fluid flow to symplastic routes minimizes Na+entry. Overall, the morphological and physiological responses of the tolerant varieties ensure adequate fluid flow through the transpiration stream without excessive salt uptake, thereby promoting growth under both drought and salinity.
Associations between Maternal Sucrose-stimulated Salivary pH and Early Childhood Caries Diagnosis and Severity: An Observational Study
Authors: Okuji David , Lin Amy , Odusanwo Olutayo , Wu Yinxiang
Published: October 2023

Background

Multiple studies indicate that maternal sucrose-stimulated salivary pH has the potential to signal higher risk for diagnoses of early childhood caries and severity categories from the vertical transmission of bacteria from mother to child.

Aim

This study primarily investigated the relationship between maternal sucrose-stimulated salivary pH and child caries diagnosis and severity. It secondarily validated associations between 1) child and maternal sucrose-stimulated salivary pH, and 2) child sucrose-stimulated salivary pH and caries diagnosis and severity.

Design

Salivary pH levels were measured from 440 mother-child dyads. Early childhood caries diagnoses and severity levels were recorded. The analysis of variance test identified the associations between child and maternal sucrose-stimulated salivary pH and regression models were derived to show that maternal and child salivary pH were estimators for children’s caries diagnosis and severity.

Results

Maternal salivary pH <= 5.6, compared to maternal salivary pH = 7, had 7.58 times higher odds for the child’s ECC diagnosis and 5.61 times higher odds for moderate-extensive caries severity. Similar results were found for child salivary pH <= 5.6, compared to child salivary pH = 7. Maternal and child salivary pH were positively associated. When maternal salivary pH, compared to child salivary pH, was included with age, gender, and race/ethnicity as predictors for early childhood caries, the median interquartile ranges for sensitivity increased from 58.8 to 64.7 percent and specificity decreased from 84.6 to 80.8 percent.

Conclusion

Dentists should understand that both maternal and child sucrose-stimulated salivary pH can signal the diagnosis and severity of early childhood caries.
Human DDX6 regulates translation and decay of inefficiently translated mRNAs
Authors: Weber Ramona , Wohlbold Lara , Chang Chung-Te
Published: October 2023

Recent findings indicate that the translation elongation rate influences mRNA stability. One of the factors that has been implicated in this link between mRNA decay and translation speed is the yeast DEAD-box helicase Dhh1p. Here, we demonstrated that the human ortholog of Dhh1p, DDX6, triggers deadenylation-dependent decay of inefficiently translated mRNAs in human cells. DDX6 interacts with the ribosome through the Phe-Asp-Phe (FDF) motif in its RecA2 domain. Furthermore, RecA2-mediated interactions and ATPase activity are both required for DDX6 to destabilize inefficiently translated mRNAs. Using ribosome profiling and RNA sequencing, we identified two classes of endogenous mRNAs that are regulated in a DDX6-dependent manner. The identified targets are either translationally regulated or regulated at the steady-state-level and either exhibit signatures of poor overall translation or of locally reduced ribosome translocation rates. Transferring the identified sequence stretches into a reporter mRNA caused translation- and DDX6-dependent degradation of the reporter mRNA. In summary, these results identify DDX6 as a crucial regulator of mRNA translation and decay triggered by slow ribosome movement and provide insights into the mechanism by which DDX6 destabilizes inefficiently translated mRNAs.
Functional and structural analysis of a cyclization domain in a cyclic β-1,2-glucan synthase
Authors: Tanaka Nobukiyo , Saito Ryotaro , Kobayashi Kaito , Nakai Hiroyuki , Kamo Shogo , Kuramochi Kouji , Taguchi Hayao , Nakajima Masahiro , Masaike Tomoko
Published: October 2023

Cyclic β-1,2-glucan synthase (CGS) is a key enzyme in production of cyclic β-1,2-glucans (CβGs) which are involved in bacterial infection or symbiosis to host organisms. Nevertheless, a mechanism of cyclization, the final step in the CGS reaction, has not been fully understood. Here we performed functional and structural analyses of the cyclization domain of CGS alone fromThermoanaerobacter italicus(TiCGSCy). We first found that β-glucosidase-resistant compounds are produced by TiCGSCywith linear β-1,2-glucans as substrates. The1H-NMR analysis revealed that these products are CβGs. Next, action pattern analyses using β-1,2-glucooligosaccharides revealed a unique reaction pattern: exclusive transglycosylation without hydrolysis and a hexasaccharide as the minimum length of the substrate. Nevertheless, longer substrate β-1,2-glucooligosaccharides are preferred, being consistent with the fact that CGSs generally produce CβGs with degrees of polymerization of around 20. Finally, the overall structure of the cyclization domain of TiCGSCywas found to be similar to those of β-1,2-glucanases in phylogenetically different groups. Meanwhile, the identified catalytic residues indicated clear difference in the reaction pathways between these enzymes. Therefore, we propose a novel reaction mechanism of TiCGSCy. Thus, we propose that the present group of CGSs should be defined as a new glycoside hydrolase family, GHxxx.

Statements and Declarations

Competing Interests: The authors declare no competing interests.

Key Points

It was clearly evidenced that cyclization domain alone produces cyclic β-1,2-glucans.

The domain exclusively catalyzes transglycosylation without hydrolysis.

The present catalytic domain should be defined as a new glycoside hydrolase family.