bluuebunny/crossref_metadata_2025_split huggingface dataset:
Update on eating disorders and disordered eating behaviors in metabolic bariatric surgery patients
Authors: Conceição Eva , Mitchell James E. , Sarwer David B. 
Published: September 2024

Purpose of review
Recent literature suggests a potential causal link between metabolic bariatric surgery (MBS) and an increased risk of eating disorders. However, the available literature offers unclear results regarding the definition of eating problems among MBS patients, their potential impact on weight outcomes, and the efficacy of adjunctive treatment.

Recent findings
Although eating disorders may be rare phenomena after surgery, disordered eating behaviors are more common and tend to be more consistently associated with suboptimal weight loss. There also appear to be clear problems when using Diagnostic and Statistical Manual of Mental Disorders 5th edition (DSM-5) criteria to assess eating disorders among MBS patients, particularly for restrictive eating, binge-eating episodes, and the core psychopathology of eating disorders. Finally, preoperative interventions appear to offer effects limited to the presurgery period, and the evidence for the efficacy of postoperative interventions remains limited. Glucagon-like peptide-1 receptor agonists (GLP-1 RAs) offer promising benefits for weight loss and the treatment of binge-eating problems, but their potential risks must be carefully managed.

Summary
Recognizing the diverse presentations of these problems among individuals undergoing MBS is crucial. Clinical attention should focus on intensive specialized care during the postoperative period for those who develop eating-related problems.
Additions to the list of arthropods of Reunion Island
Authors: Nibouche Samuel , Sadeyen Joëlle , Dervin Sébastien , Gauche Mirana , Merion Sabine , Minatchy Janice , Fontaine Romuald , Reynaud Philippe , Michel Bruno 
Published: September 2024

AbstractContribution to the inventory of arthropods of Reunion IslandThis work is a synthesis of new taxa for the Reunion Island identified between 1963 and 2022 and not published to date. The collections were carried out mainly by researchers and technicians from CIRAD or FDGDON. Sampling mainly targeted at crop pests and their natural enemies. The list includes 101 taxa new for Reunion. The Hymenoptera and Hemiptera are the most represented orders.
A novel combination therapy for ER+ breast cancer suppresses drug resistance via an evolutionary double-bind
Authors: Emond Rena , West Jeffrey , Grolmusz Vince , Cosgrove Patrick , Nath Aritro , Anderson Alexander R.A. , Bild Andrea H. 
Published: September 2024

AbstractChemotherapy remains a commonly used and important treatment option for metastatic breast cancer. A majority of ER+ metastatic breast cancer patients ultimately develop resistance to chemotherapy, resulting in disease progression. We hypothesized that an “evolutionary double-bind”, where treatment with one drug improves the response to a different agent, would improve the effectiveness and durability of responses to chemotherapy. This approach exploits vulnerabilities in acquired resistance mechanisms. Evolutionary models can be used in refractory cancer to identify alternative treatment strategies that capitalize on acquired vulnerabilities and resistance traits for improved outcomes. To develop and test these models, ER+ breast cancer cell lineages sensitive and resistant to chemotherapy are grown in spheroids with varied initial population frequencies to measure cross-sensitivity and efficacy of chemotherapy and add-on treatments such as disulfiram combination treatment. Different treatment schedules then assessed the best strategy for reducing the selection of resistant populations. We developed and parameterized a game-theoretic mathematical model from this in vitro experimental data, and used it to predict the existence of a double-bind where selection for resistance to chemotherapy induces sensitivity to disulfiram. The model predicts a dose-dependent re-sensitization (a double-bind) to chemotherapy for monotherapy disulfiram.
Kontextual: Reframing analysis of spatial omics data reveals consistent cell relationships across images
Authors: Ameen Farhan , Robertson Nick , Lin David M. , Ghazanfar Shila , Patrick Ellis 
Published: September 2024

AbstractState-of-the-art spatial proteomic and transcriptomic technologies can deeply pheno-type cells in their native tissue environment, providing a high throughput means to effectively quantify spatial relationships between diverse cell populations. However, the experimental design choice of which regions of a tissue will be imaged can greatly impact the interpretation of spatial quantifications. That is, spatial relationships identified in one region of interest may not be interpreted consistently across other regions. To address this challenge, we introduce Kontextual, a method which considers alternative frames of reference for contextualising spatial relationships. These contexts may represent landmarks, spatial domains, or groups of functionally similar cells which are consistent across regions. By modelling spatial relationships between cells relative to these contexts, Kontextual produces robust spatial quantifications that are not confounded by the region selected. We demonstrate in spatial proteomics and spatial transcriptomics datasets that modelling spatial relationships this way is biologically meaningful. We also demonstrate how this approach can be used in a classification setting to improve prediction of patient prognosis.
Development and Validation of Collaborative Robot-assisted Cutting Method for Iliac Crest Flap Raising: Randomized Crossover Trial
Authors: Becker Paulina , Li Yao , Drobinsky Sergey , Egger Jan , Xie Kunpeng , Rashad Ashkan , Radermacher Klaus , Röhrig Rainer , de la Fuente Matías , Hölzle Frank , Puladi Behrus 
Published: September 2024

AbstractThe current gold standard of computer-assisted jaw reconstruction includes raising microvascular bone flaps with patient-specific 3D-printed cutting guides. The downsides of cutting guides are invasive fixation, periosteal denudation, preoperative lead time and missing intraoperative flexibility. This study aimed to investigate the feasibility and accuracy of a robot-assisted cutting method for raising iliac crest flaps compared to a conventional 3D-printed cutting guide.In a randomized crossover design, 40 participants raised flaps on pelvic models using conventional cutting guides and a robot-assisted cutting method. The accuracy was measured and compared regarding osteotomy angle deviation, Hausdorff Distance (HD) and Average Hausdorff Distance (AVD). Duration, workload and usability were further evaluated.The mean angular deviation for the robot-assisted cutting method was 1.9±1.1° (mean±sd) and for the 3D-printed cutting guide it was 4.7±2.9° (p<0.001). The HD resulted in a mean value of 1.5±0.6mm (robot) and 2.0±0.9mm (conventional) (p<0.001). For the AVD, this was 0.8±0.5mm (robot) and 0.8±0.4mm (conventional) (p=0.320). Collaborative robot-assisted cutting is an alternative to 3D-printed cutting guides in experimental static settings, achieving slot design benefits with less invasiveness and higher intraoperative flexibility. In the next step, the results should be tested in a dynamic environment with a moving phantom and on the cadaver.
Religion and COVID 19 Pandemic for better or for worse?
Authors: Ranasinghe Sameera Upashantha , Ranasinghe Lakshitha Iroshan , Pathiraja Indika 
Published: September 2024

AbstractCOVID-19 has negative repercussions on psychological aspects of the individual. Provision of personalized assistance to each individual is a task which cannot be fulfilled by the health system. In this context religion remains to be an effective tool. A qualitative study was conducted to find the spiritual practices and coping mechanisms of COVID-19 infected people(N=15, mean age =46.3 years) in Kurunegala district. Data collection was conducted using in-depth interviews and thematic analysis was conducted. The main themes found were Fatalism and perceived risk of COVID 19, Adherence to health care guidelines despite fatalistic beliefs, Religious coping in COVID 19, Spiritual practices for coping with stress/ distress and Fatalism as a positive force for self-care. It is imperative to manage the pandemic with the assistance of religion and spiritual practices.
Humoral Immunity after mRNA Omicron JN.1 Vaccination
Authors: Happle Christine , Hoffmann Markus , Kempf Amy , Nehlmeier Inga , Stankov Metodi V. , Hampel Noemi Calderon , Witte Torsten , Pöhlmann Stefan , Behrens Georg M. N. , Dopfer-Jablonka Alexandra 
Published: September 2024

AbstractIn late June 2024, the European Medicines Agency (EMA) recommended market authorization for a monovalent COVID-19 mRNA-vaccine based on JN.1 spike. We assessed immune responses in n=42 health-care workers (median age 47 years, interquartile range, IQR 19·5 years, 48% male), who in August 2024 were vaccinated with 30 μg of the updated mRNA omicron JN.1 vaccine (bretovameran, BioNTech/Pfizer, Mainz, Germany). Humoral immune responses were analyzed directly prior to and 13 days after vaccination.The omicron JN.1 vaccination resulted in a significant 1·2-fold increase of anti-S IgG and 1·2-fold increase of omicron anti-S IgG (p<0·0001). To assess plasma neutralisation capacity, we employed a pseudovirus particle (pp) neutralisation assay including S proteins of seven SARS-CoV-2 lineages. Baseline response rates were 100% for XBB.1.5pp, 90% for JN.1ppand KP.2pp, 82% for KP.2.3pp, 92% for KP.3pp, and 72% for LB.1pp. Before JN.1 vaccination, particles bearing KP sublineage S proteins were slightly less efficiently neutralised compared with JN.1pp(median change, 1·2-fold to 2·6-fold), while LB.1ppneutralisation was 3-fold reduced, indicating antibody evasion. After vaccination, the response rates increased significantly for all pseudoviruses except XBB.1.5ppand KP.3pp. Thus, we observed a significant increase in neutralisation of JN.1pp, KP.2pp, KP.2.3pp, and LB.1pp, showing a median change of 2.2-fold, 3.8-fold, 3.3-fold, and 4.9-fold, respectively.In summary, bretovameran increased anti-S IgG and strengthened neutralising responses against circulating SARS-CoV-2-variants, except for KP.3. We wish to point out that our study population exhibited high pre-vaccination omicron-related hybrid immunity and may not be representative of other populations. Our data supports the notion that the new mRNA vaccine against omicron JN.1 most likely increases protection against hospitalization and post-COVID sequelae caused by most current variants.
Structure and inhibition mechanisms ofMycobacterium tuberculosisessential transporter efflux protein A
Authors: Khandelwal Nitesh Kumar , Gupta Meghna , Gomez James E. , Barkho Sulyman , Guan Ziqiang , Eng Ashley Y. , Kawate Tomo , Balasubramani Sree Ganesh , Sali Andrej , Hung Deborah T. , Stroud Robert M. 
Published: September 2024

AbstractA broad chemical genetics screen inMycobacterium tuberculosis (Mtb)to identify inhibitors of established or previously untapped targets for therapeutic development yielded compounds (BRD-8000.3 and BRD-9327) that inhibit the essential efflux pump EfpA. To understand the mechanisms of inhibition by these compounds, we determined the structures of EfpA with inhibitors bound at 2.7 -3.4 Å resolution. Our structures reveal different mechanisms of inhibition for the two inhibitors. BRD-8000.3 binds in a tunnel making contact with the lipid bilayer and extending toward the central cavity to displace the fatty acid chain of a lipid molecule bound in the apo structure, suggesting its blocking of an access route for a natural lipidic substrate, in contrast to its uncompetitive mechanism for the small molecule substrate ethidium bromide which likely enters through an alternative tunnel. Meanwhile, BRD-9327 binds in the outer vestibule without complete blockade of the substrate path to the outside, suggesting its possible inhibition of the dynamical motion necessary for “alternate access” to the two different sides of the membrane, as is characteristic of major facilitator superfamily (MFS) transporters. Both inhibitors may have a role in inhibiting the “alternate access” mechanism that could account for the uncompetitive nature of their efflux of some substrates. Our results explain the basis of the synergy of these inhibitors and their potential for combination in a multi drug strategy for anti-tuberculosis therapy. They also potentially point to a possible function for this essential efflux pump as a lipid transporter. The structures provide a foundation for rational modification of these inhibitors to increase potency.
The Autonomous Cognitive Examination: Machine-Learning Based Cognitive Examination
Authors: Howard Calvin W. , Johnson Amy , Barotono Sheena , Faust Katharina , Peedicail Joseph , Ng Marcus 
Published: September 2024

Structured AbstractINTRODUCTIONThe rising prevalence of dementia necessitates a scalable solution to cognitive screening and diagnosis. Digital cognitive assessments offer a solution but lack the extensive validation of older paper-based tests. Creating a digital cognitive assessment which recreates a paper-based assessment could have the strengths of both tests.METHODSWe developed the Autonomous Cognitive Examination (ACoE), a fully remote and automated digital cognitive assessment which recreates the assessments of paper-based tests. We assessed its ability to reproduce entire cognitive screens in a comparison cohort (n = 35), and the ability to reproduce overall diagnoses with an additional validation cohort (n = 11).RESULTSThe ACoE reproduced overall cognitive assessments with excellent agreement (intraclass correlation coefficient = 0.89) and reproduced overall diagnoses with excellent fidelity (area under the curve = 0.96).DISCUSSIONThe ACoE may reliably reproduce the evaluations of the ACE-3, which may help in accessible evaluation of patient cognition. Assessment in larger population of patients with specific diseases will be necessary to determine usefulness.
Disrupted developmental signaling induces novel transcriptional states
Authors: Patel Aleena , Gonzalez Vanessa , Menon Triveni , Shvartsman Stanislav Y. , Burdine Rebecca , Avdeeva Maria 
Published: September 2024

Signaling pathways induce stereotyped transcriptional changes as stem cells progress into mature cell types during embryogenesis. Signaling perturbations are necessary to discover which genes are responsive or insensitive to pathway activity. However, gene regulation is additionally dependent on cell state-specific factors like chromatin modifications or transcription factor binding. Thus, transcriptional profiles need to be assayed in single cells to identify potentially multiple, distinct perturbation responses among heterogeneous cell states in an embryo. In perturbation studies, comparing heterogeneous transcriptional states among experimental conditions often requires samples to be collected over multiple independent experiments. Datasets produced in such complex experimental designs can be confounded by batch effects. We present Design-Aware Integration of Single Cell ExpEriments (DAISEE), a new algorithm that models perturbation responses in single-cell datasets with a complex experimental design. We demonstrate that DAISEE improves upon a previously available integrative non-negative matrix factorization framework, more efficiently separating perturbation responses from confounding variation. We use DAISEE to integrate newly collected single-cell RNA-sequencing datasets from 5-hour old zebrafish embryos expressing optimized photoswitchable MEK (psMEK), which globally activates the extracellular signal-regulated kinase (ERK), a signaling molecule involved in many cell specification events. psMEK drives some cells that are normally not exposed to ERK signals towards other wild type states and induces novel states expressing a mixture of transcriptional programs, including precociously activated endothelial genes. ERK signaling is therefore capable of introducing profoundly new gene expression states in developing embryos.Significance StatementSignaling perturbations produce heterogeneous transcriptional responses that must be measured at the single-cell level. Data integration techniques allow us to model these responses which, however, can be confounded by batch effects. We present a computational tool (DAISEE) for extracting the common and perturbation-specific features of single-cell datasets representing multiple experimental conditions while achieving efficient batch effect correction. DAISEE outperforms its predecessor and will enable accurate analysis of a broad range of single-cell datasets. DAISEE applied to new single-cell RNA sequencing data from zebrafish embryos shows that gain-of-function signaling perturbations can induce novel states. Our analysis suggests that a wild type endothelial cell-specification program can be activated in abnormal developmental contexts when the extracellular signal-regulated kinase (ERK) pathway is deregulated.
Application of barcode sequencing to increase the throughput and complexity ofPlasmodium falciparumgenetic screening
Authors: Muhwezi Allan , Ghorbal Mehdi , Sanderson Theo , Ivanova Maria , Ansari Rizwan , Harper Sarah , Wong Wesley , Schulte Reiner , Girling Gareth , Schwach Frank , Bushell Ellen , Beaver Charlotte , Billker Oliver , Rayner Julian C. 
Published: September 2024

SummaryAll the pathology and symptoms associated with malaria are caused by the growth ofPlasmodiumparasites inside human red blood cells. This process, which in the case of the major human malaria pathogenPlasmodium falciparumtakes place over a 48-hour period, involves multiple tightly regulated developmental transitions. Understanding theP. falciparumgenes that regulate these key processes could lead to the identification of targets for new drugs. However, while large-scale sequencing efforts have led to a good understanding of theP. falciparumgenome and how it evolves over time and space, a disconnect remains between the amount of genome sequence data available and the amount of data describing what exactly the genes contained within it do – the phenotype. We have generated a panel of 66P. falciparumlines carrying individual gene knockouts tagged with unique DNA barcodes. We then used these lines in a series of assays that combine flow cytometry, cell sorting and DNA barcode quantification using next generation sequencing (Barcode Sequencing or BarSeq) to phenotype key aspects of the parasite life cycle such as growth, replication capacity and cell cycle progression. This approach both yields new data about individual gene function, and outlines a new approach where barcodedP. falciparumlines are used in pooled BarSeq-based assays to generate more precise phenotype data at scale.
Transcription termination and antitermination are critical for the fitness and function of the integrative and conjugative element Tn916
Authors: Wirachman Erika S. , Grossman Alan D. 
Published: September 2024

ABSTRACTPremature expression of genes in mobile genetic elements can be detrimental to their bacterial hosts. Tn916, the founding member of a large family of integrative and conjugative elements (ICEs; aka conjugative transposons), confers tetracycline-resistance and is found in several Gram-positive bacterial species. We identified a transcription terminator near one end of Tn916that functions as an insulator that prevents expression of element genes when Tn916is integrated downstream from an active host promoter. The terminator blocked expression of Tn916genes needed for unwinding and rolling circle replication of the element DNA, and loss of the terminator caused a fitness defect for the host cells. Further, we identified an element-encoded antiterminator (namedcanTfor conjugation-associated antitermination) that is essential for transcription of Tn916genes after excision of the element from the host chromosome. We found that the antiterminator is orientation-specific, functions with heterologous promoters and terminators, is processive and is most likely acis-acting RNA. Insulating gene expression in conjugative elements that are integrated in the chromosome is likely a key feature of the interplay between mobile genetic elements and their hosts and appears to be critical for the function and evolution of the large family of Tn916-like elements.AUTHOR SUMMARYHorizontal gene transfer allows bacteria to rapidly acquire new traits that can enhance their adaptability to different conditions. Integrative and conjugative elements (ICEs) are mobile genetic elements that reside integrated in a bacterial chromosome and can transfer to another cell via cell-to-cell contact through the element-encoded secretion system. ICEs often confer beneficial traits to their hosts, including antibiotic resistances, symbiotic/pathogenic determinants, metabolic capabilities, and anti-phage defense systems. Tn916, the first-described ICE, was identified based on its ability to transfer tetracycline resistance in the pathogenEnterococcus faecalis, and is found in several Gram-positive species. Once transferred into a new cell, Tn916integrates into AT-rich sequences, sometimes downstream from a host promoter. We found that Tn916has a transcription terminator near one end of the element that blocks transcription from an upstream host promoter, thereby protecting cells from detrimental effects of premature expression of element genes. Further, we found that Tn916has a transcription antitermination system that is essential for expression of element genes after excision from the host chromosome. Our findings highlight the complex layers of transcriptional regulation that have evolved in ICEs, impacting host cell viability and the spread of the element.
Mapping the ultrastructural topology of the corynebacterial cell surface
Authors: Isbilir Buse , Yeates Anna , Alva Vikram , Bharat Tanmay A.M. 
Published: September 2024

AbstractCorynebacterium glutamicumis a diderm bacterium extensively used in the industrial-scale production of amino acids. Corynebacteria belong to the bacterial familyMycobacteriaceae, which is characterized by a highly unusual cell envelope with an outer membrane consisting of mycolic acids. Despite the occurrence of this distinctive cell envelope in several bacterial pathogens, includingCorynebacterium diphtheriae, Mycobacterium tuberculosis, andMycobacterium leprae, its ultrastructural and molecular details remain elusive.To address this, we investigated the cell envelope ofC. glutamicumusing electron cryotomography and cryomicroscopy of focused ion beam-milled cells. Our high-resolution images allowed us to accurately map the different components of the cell envelope into the tomographic density. Our data reveal thatC. glutamicumhas a variable cell envelope, with the outermost layer comprising the surface (S-)layer, which decorates the mycomembrane in a patchy manner. We further isolated and resolved the structure of the S-layer at 3.1 Å resolution using single particle electron cryomicroscopy. Our structure shows that the S-layer ofC. glutamicumis composed of a hexagonal array of the PS2 protein, which interacts directly with the mycomembrane via a coiled coil-containing anchoring segment. Bioinformatic analyses revealed that the PS2 S-layer is sparsely yet exclusively present within theCorynebacteriumgenus and absent in other genera of theMycobacteriaceaefamily, suggesting distinct evolutionary pathways in the development of their cell envelopes.Our structural and cellular data collectively provide a high-resolution topography of the unusualC. glutamicumcell surface, features of which are shared by many pathogenic and microbiome-associated bacteria, as well as by several industrially significant bacterial species. This study, therefore, provides a strong experimental framework for understanding cell envelopes that contain mycolic acids.