bluuebunny/crossref_metadata_2025 huggingface dataset:
Schizophrenia versus Healthy Controls Classification based on fMRI 4D Spatiotemporal Data
Authors: Huan Pham Tieu Hoang , Wu Yihren , Ikuta Toshikazu , John Majnu
Published: January 2025

A wide array of machine learning approaches have been employed for differentiating patients with mental health disorders from healthy controls using neuroimaging data. However, almost all such methods have been applied on inputs based on connectivity matrices or features derived from the neuroimaging data. Only a few papers recently have considered such classification based on the original voxel-based spatiotemporal data. In this paper, we report the performance of a few cutting edge machine learning algorithms on voxel-based fMRI data to classify healthy controls and patients with schizophrenia. The methods that we employed included convolutional neural networks, convolutional recurrent neural networks with long short-term memory and a transfer learning approach for classification based on Wasserstein generative adversarial networks. In order to reduce the computational burden to fit in with available hardware, we had to reduce the original 4-dimensional data to 3-dimensional inputs for almost all architectures. Our results indicate that the relatively simpler architecture based on convolutional neural networks showed reasonable unambiguity in grouping patients from healthy controls. In contrast, the performance of the other two more complex architectures that we employed were comparatively poorer.
Genome- and Transcriptome-wide association meta-analysis reveals new insights into genes affecting coronary and peripheral artery disease
Authors: Rode Michael , Rosolowski Maciej , Horn Katrin , Henger Sylvia , Teren Andrej , Wirkner Kerstin , Thiery Joachim , Loeffler Markus , Pott Janne , Kirsten Holger , Scholz Markus
Published: January 2025

Background

A low ankle-brachial Index (ABI) is an established condition for peripheral artery disease (PAD) and cardiovascular disease risk. The search for genetic determinants of the ankle-brachial index (ABI) is important to better understand molecular patho-mechanisms of PAD and its commonalities with cardiovascular diseases (CVD), supporting development of new drug targets and tailored preventive or therapeutic measures.

Methods

To search for genetic factors contributing to ankle-brachial index, we integrated genome-wide (GWAMA) and transcriptome-wide association analysis (TWAMA) of two German cohorts, the population-based LIFE-Adult cohort and LIFE-Heart, a cohort of patients with suspected or confirmed coronary artery disease. Pathway analysis of identified genes was used to explore biological mechanisms potentially involved in ABI pathophysiology. Finally, we analysed co-associations of known CAD or carotid plaque associations with ABI to detect possible genetic commonalities.

Results

By our GWAMA, we identified four new gene loci associated with ABI that are also linked with coronary artery diseases (CAD) (6q26:LPAand 11q14.1:DLG2) or cholesterol levels (12q21.31:TMTC2and Xp21.1:DMD). Furthermore, we replicated a known ABI locus on cytoband 9p21.3 (CDKN2B) and four loci associated with PAD. In our TWAMA, we identified 145 blood transcripts associated with ABI at FDR 5% level. Gene set enrichment analysis of all TWAMA results revealed the inflammation-related pathwaysinterferon gamma response,neutrophil degranulation, andinterferon alpha responseas the top three upregulated pathways in patients with lower ABI. Among overlapping genes between blood TWAMA and tissue-specific genetically regulated gene-expression association analysis, 24 genes showed consistent effect directions at nominal significance, with lower ABI-associated genes relating to stress response and vascular integrity, while higher ABI-associated genes linked to cellular homeostasis and metabolism.

Conclusions

In our integrated genome- and transcriptome-wide meta-analysis, we identified novel and confirmed known candidate genes and pathways associated with ABI. Association signals partly overlap with those of other cardiovascular traits such as CAD and carotid plaque formation. The integration of gene-expression data, validated known and added new molecular insight how inflammatory signaling can contribute to atherosclerosis and vascular dysfunction. These findings pave the way for improved understanding of the molecular underpinnings of PAD and inform future strategies for targeted prevention and therapy.
Projected Cost-beneficial Impact of the Selective Cytopheretic Device in Pediatric Acute Kidney Injury Requiring Kidney Replacement Therapy
Authors: Kleinman Nathan , Kammerer Jennifer , Iyer Sai Prasad N. , Goldstein Stuart L. , Kleinman Alec , Chung Kevin K. , Thakar Charuhas V.
Published: January 2025

Rationale & Objective

The Selective Cytopheretic Device for Pediatrics (SCD-PED) is a cell-directed extracorporeal therapy approved by US FDA for pediatric patients with acute kidney injury (AKI) due to sepsis or a septic condition, requiring antibiotics and continuous renal replacement therapy (CRRT). This study aimed to estimate hospitalization costs and outcomes of SCD-PED therapy by leveraging the Kids’ Inpatient Database (KID) and SCD-PED studies.

Study Design

Publicly available hospitalization cost data were combined with clinical metrics from prior SCD-PED studies to assess the impact of SCD-PED on inpatient hospital costs among pediatric patients receiving CRRT.

Setting & Population

The SCD-PED was evaluated in two multicenter pediatric studies, involving 16 and 6 patients, respectively. Pediatric patients with AKI and multi-organ dysfunction receiving CRRT as part of standard care were included. The KID subset comprised hospitalizations with CRRT, a length of stay (LOS) up to 60 days, mortality and severity level 4, an AKI diagnosis, and total parenteral nutrition (TPN) procedures.

Interventions

Patients received SCD-PED therapy for up to 7 or 10 days or until CRRT termination.

Outcomes

Outcomes analyzed included hospital LOS, mortality, vasopressor use, mechanical ventilation, sepsis diagnosis, number of SCD-PED devices used, and hospitalization cost estimates.

Model, Perspective, & Timeframe

A regression-based economic cost model compared costs between SCD-PED therapy and theoretical controls, adjusted to 2024 US dollars.

Results

Modeled hospitalization costs were $457,092 in the KID cohort and $389,451 in the ppCRRT cohort. Median hospital LOS was lower in the SCD-PED group (28 days vs. 31 days), resulting in lower estimated costs ($320,304) and an estimated savings of $69,146 per hospitalization.

Limitations

Small sample sizes and single-arm design with no prospective control arm. Reported costs are estimates based on models.

Conclusions

The SCD-PED shows potential for survival benefit and cost-benefit in critically ill children with AKI requiring CRRT, including those with sepsis.
Kinetic mechanism for fidelity of CRISPR-Cas9 variants
Authors: Hecht Andrew D. , Igoshin Oleg A.
Published: January 2025

CRISPR-Cas9 is a nuclease creating DNA breaks at sites with sufficient complementarity to the RNA guide. Notably, Cas9 does not require exact RNA-DNA complementarity and can cleave off-target sequences. Various high-accuracy Cas9 variants have been developed, but the precise mechanism of how these variants achieve higher accuracy remains unclear. Here, we develop a kinetic model of Cas9 substrate selection and cleavage. We parameterize the model using datasets available in the literature, including both high-throughput substrate binding and cleavage data and Förster resonance energy transfer measurements of the Cas9 HNH domain transitions. Based on the observed transition statistics, we predict that the Cas9 substrate recognition and cleavage mechanism must allow for HNH domain transitions independent of substrate binding. Additionally, we show that the enhancement in Cas9 substrate specificity must be due to changes in kinetics rather than changes in substrate binding affinities. Furthermore, the fitted model produces quantitatively realistic cleavage error predictions for substrates with protospacer adjacent motif (PAM)-distal mismatches. Finally, we use our model to identify kinetic parameters for HNH domain transitions that can be perturbed to enable high-accuracy cleavage while maintaining cleavage speeds. Our results refine the biophysical mechanism of Cas9 cleavage to inform future routes for its engineering.
Improved transfection methods of primary cultured astrocytes for observation of cytoskeletal structures
Authors: Ikoma Chieko , Inoue Kodai , Kasai Kouta , Tsukuda Satoko , Tamura Akiko , Nakata Shihoko , Iwata Yuto , Tamagawa Takumi , Nakayama Ayako , Takano Kazunori , Shigetomi Eiji , Koizumi Shuichi , Nakagawa Hiroyuki , Terasaki Asako G
Published: January 2025

Astrocytes are the predominant type of glia in the central nervous system and have long branched stem processes and peripheral astrocyte processes (PAPs) contacting neurons and other glial cells. In many cell types, cell morphology and motility depend on actin cytoskeleton. However, a common astrocyte culture method in serum-containing medium generated undesired fibroblast-like cells; thus, the roles of cytoskeletal proteins in astrocyte morphology and motility have not been well studied. Previously, we reported a culture method of chicken astrocytes forming structures similar to stem processes and PAPs. In the current study, we improved transfection methods retaining astrocyte morphology at low cell density, suitable for observing the behavior of proteins. Immunostaining and live imaging of plasma membrane-actin linking protein ezrin (a PAP marker) and another actin-binding protein lasp-2 (highly expressed in cultured astrocytes) demonstrated that our cultured astrocytes had microvillus protrusions, filopodia, lamellipodia, and focal adhesion-like elliptical structures, and the two proteins accumulated in different substructures. Our developed methods offer significant advantages for analyzing how astrocytes form stem processes and PAPs to access target cells.
Culicoidesallergens expressed in insect cells induce sulfidoleukotriene release in peripheral blood leukocytes from horses affected with insect bite hypersensitivity
Authors: Jonsdottir S , Stefansdottir SB , Mirkovitch J , Ziegler A , Torsteinsdottir S , Marti E
Published: January 2025

Introduction

Insect bite hypersensitivity (IBH) is an IgE mediated dermatitis in horses caused by bites ofCulicoidesspp. The allergens are salivary gland proteins from these insects and nine major allergens fromCulicoides obsoletushave been identified and expressed inE. coli. However, proteins expressed in procaryotic systems have limitations in cellular assays, particularly in functional assays assessing the allergen-induced release of mediatorsin vitro, such as sulfidoleukotrienes (sLT) from basophils. Aims of the study were to produce functionalCulicoidesallergens in insect cells, to assess their allergenicity using a sLT release assay and to relate the sLT release with IgE sensitization to the respective allergens using ELISA.

Methods

Eight majorCulicoides obsoletusallergens (Cul o 1P, Cul o 2P, Cul o 3, Cul o 5, Cul o 7, Cul o 8, Cul o 9 and Cul o 11) were expressed in insect cells and purified. sLT release from peripheral blood leukocytes (PBL) following stimulation with the eightCulicoidesallergens was measured in 28 IBH-affected and 24 healthy control horses. Allergen-specific serum IgE levels was determined by ELISA.

Results

The eight major allergens were successfully expressed in insect cells and purified. All allergens induced a significantly higher sLT release from PBL of IBH-affected horses compared to healthy controls. There was a high correlation and substantial to excellent agreement between sLT release and serum IgE levels for sixCulicoidesallergens, while for two the agreement was moderate. Positivity rates in IBH horses were usually higher in IgE serology but more false positive results were obtained. The allergens performing best in both assays were Cul o 3, Cul o 8 and Cul o 9, with very high specificity and good sensitivity.

Discussion

Insect cell expressedCulicoidesrecombinant allergens are functionally relevant and will open new opportunities for the study of Culicoides hypersensitivity not only in horses, but also potentially in human patients or other species. They will also greatly improve IBH diagnostics using cellular assays as well as IgE serology.
Disulfide bonds are required for cell division, cell envelope biogenesis and antibiotic resistance proteins in mycobacteria
Authors: Mejia-Santana Adrian , Collins Rebecca , Doud Emma H. , Landeta Cristina
Published: January 2025

Mycobacteria, includingMycobacterium tuberculosis—the etiological agent of tuberculosis—have a unique cell envelope critical for their survival and resistance. The cell envelope’s assembly and maintenance influence permeability, making it a key target against multidrug-resistant strains. Disulfide bond (DSB) formation is crucial for the folding of cell envelope proteins. The DSB pathway in mycobacteria includes two enzymes, DsbA and VKOR, required for survival. Using bioinformatics and cysteine profiling proteomics, we identified cell envelope proteins dependent on DSBs. We validated viain vivoalkylation that key proteins like LamA (MmpS3), PstP, LpqW, and EmbB rely on DSBs for stability. Furthermore, chemical inhibition of VKOR results in phenotypes similar to those of Δvkor. Thus, targeting DsbA-VKOR systems could compromise both cell division and mycomembrane integrity. These findings emphasize the potential of DSB inhibition as a novel strategy to combat mycobacterial infections.
Microfluidic Co-Culture for Modeling Human Joint Inflammation in Osteoarthritis Research
Authors: Mirazi Hosein , Wood Scott T.
Published: January 2025

Here we present a microfluidic model that allows for co-culture of human osteoblasts, chondrocytes, fibroblasts, and macrophages of both quiescent (M0) and pro-inflammatory (M1) phenotypes, maintaining initial viability of each cell type at 24 h of co-culture. We established healthy (M0-based) and diseased (M1-based) joint models within this system. An established disease model based on supplementation of IFN-γ and LPS in cell culture media was used to induce an M1 phenotype in macrophages to recapitulate inflammatory conditions found in OA. Cell viability was assessed using NucBlue™ Live and NucGreen™ Dead fluorescent stains, with mean viability of 83.9% ± 14% and 83.3% ± 12% for healthy and diseased models, respectively, compared with 93.3% ± 4% for cell in standard monoculture conditions. Cytotoxicity was assessed via a lactate dehydrogenase (LDH) assay and showed no measurable increase in LDH release into the culture medium under co-culture conditions, indicating that neither model promotes a loss of cell membrane integrity due to cytotoxic effects. Cellular metabolic activity was assessed using a PrestoBlue™ assay and indicated increased cellular metabolic activity in co-culture, with levels 5.9 ± 3.2 times mean monolayer cell metabolic activity levels in the healthy joint model and 5.3 ± 3.4 times mean monolayer levels in the diseased model. Overall, these findings indicate that the multi-tissue nature ofin vivohuman joint conditions can be recapitulated by our microfluidic co-culture system at 24 h and thus this model serves as a promising tool for studying the pathophysiology of rheumatic diseases and testing potential therapeutics.
PICRUSt2-MPGA: an update to the reference database used for functional prediction within PICRUSt2
Authors: Wright Robyn J. , Langille Morgan. G.I.
Published: January 2025

PICRUSt2 is a bioinformatic tool that predicts microbial functions in amplicon sequencing data using a database of annotated reference genomes. We have constructed an updated database for PICRUSt2 that has substantially increased the number of bacterial (19,493 to 26,868) and archaeal (406 to 1,002) genomes as well as the number of functional annotations present. The previous PICRUSt2 database relied on many timely and computationally intensive manual processes that made it difficult to update. To make PICRUSt2 great again (MPGA), we constructed a new streamlined process to allow regular upgrades to the PICRUSt2 database on an ongoing basis. Additionally, we have shown that this updated database contains genomes that more closely match study sequences from a range of different environments. The genomes contained in the database therefore better represent these environments and this leads to an improvement in the predicted functional annotations obtained from PICRUSt2.

Availability

PICRUSt2 source code is freely available athttps://github.com/picrust/picrust2and athttps://anaconda.org/bioconda/picrust2. The PICRUSt2-MPGA database comes pre-installed with PICRUSt2 from version 2.6.0 onwards. Step-by-step instructions for making the updated database are athttps://github.com/picrust/picrust2/wiki/Updating-the-PICRUSt2-database. All code used for the analyses and figures in this manuscript is athttps://github.com/R-Wright-1/picrust2_mpga_application_note.

Funding and acknowledgements

This work was supported by an NSERC Discovery Grant (2016-05039) and was enabled in part by the Digital Research Alliance of Canada (alliancecan.ca).

We thank Dr. Gavin Douglas for invaluable insight and assistance with troubleshooting and several PICRUSt2 users for their time testing and giving feedback on an early version of the PICRUSt2 update.
Survival and Spread of EngineeredMycobacterium smegmatisand Associated Mycobacteriophage in Soil Microcosms
Authors: Fleeharty Megan S. , Carline Kate B.R. , Tchadi Bilalay V. , Shockey Bjorn B. , Holley Emma C. , Saha Margaret S.
Published: January 2025

The inoculation of microbes into soil environments has numerous applications for improving soil quality and crop health; however, the ability of exogenous and engineered microbes to survive and spread in soil remains uncertain. To address this challenge, we assayed the survival and spread ofMycobacterium smegmatis, engineered with either plasmid transformation or genome integration, as well as its mycobacteriophage Kampy, in both sterilized and non-sterilized soil microcosms over a period of 49 days. While engineeredM. smegmatisand Kampy persisted in all soil microcosms, there was minimal evidence of spread to 5 cm away from the inoculation site. There was a higher prevalence of Kampy observed in sterilized soil than non-sterilized soil, suggesting a detrimental effect of the native soil biotic and viral community on the ability of this phage to proliferate in the soil microcosm. Additionally, higher abundance of the genome-integrated bacteria relative to the plasmid-carrying bacteria as well as evidence for loss of plasmid over the duration of the experiment suggest a burden associated with bacteria harboring plasmids, although plasmids were still retained across 49 days. To our knowledge, this is the first study to simultaneously measure the persistence and spread of bacteria and their associated phage in both sterilized and non-sterilized soil microcosms, employing bacteria with plasmid-based and genome-integrated engineered circuits. As such, this study provides a novel understanding of challenges associated with the deployment of bioengineered microbes into soil environments.

Importance

Healthy soil is essential to sustain life, as it provides habitable land, enables food production, promotes biodiversity, sequesters and cycles nutrients, and filters water. Given the prevalence of soil degradation, treatment of soil with microbes that promote soil and crop health could improve global soil sustainability; furthermore, the application of bioengineering and synthetic biology to these microbes allows fine-tunable and robust control of gene-of-interest expression. These solutions require the successful deployment of bacteria into the soil, an environment in which abundant competition and often limited nutrients can result in bacterial death or dormancy. This study employsMycobacterium smegmatisas a chassis alongside its bacteriophage Kampy in soil microcosms to assess the ability of non-native microbes to survive and spread in soil. Insights from this experiment highlight important challenges which must be overcome for successful deployment of engineered microbes in the field.
Epidermal stem cell-derived extracellular vesicles induce fibroblasts mesenchymal-epidermal transition to alleviate hypertrophic scar via the miR-200s/ZEBs axis
Authors: Zhen Miao , Xie Juntao , Yang Rui , Liu Lijuan , Liu Hengdeng , He Xuefeng , Gao Suyue , Zhu Junyou , Li Jingting , Shu Bin , Wang Peng
Published: January 2025

Hypertrophic scar (HS) is a prevalent yet unresolved wound healing complication characterized by persistent hyperactive and proliferative fibroblasts, leading to excessive extracellular matrix (ECM) synthesis and collagen contraction. Our previous studies have identified epidermal stem cells (ESCs) as critical for wound healing and HS remodeling, with its extracellular vesicles (EVs) playing a vital role. However, the specific mechanisms remain unclear. In this study, we first discovered that ESC-EVs could effectively induce the mesenchymal-epidermal transition (MET) of HS fibroblasts (HSFs) and inhibit their biological activity. Furthermore, by next-generation sequencing and multiplexed CRISPR/Cas9 system, we elucidated that this therapeutic effect is mediated by the miR-200 family (miR-200s) encapsulated in ESC-EVs, which targeted and inhibited ZEB1 and ZEB2 in HSFs. This vital role and mechanism have been thoroughly validated in both in vitro cell experiments and in vivo rat tail HS (RHS) models. These findings not only shed light on a previously unidentified mechanism of ESC-EVs for HS, but also provide potential novel targets and strategies for its precise treatment.
The Swiss national program for the surveillance of influenza A viruses in pigs and humans: genetic variability and zoonotic transmissions from 2010 – 2022
Authors: Lechmann J. , Szelecsenyi A. , Bruhn S. , Harisberger M. , Wyler M. , Bachofen C. , Hadorn D. , Tobler K. , Krauer F. , Fraefel C. , Cabecinhas A. R. Gonçalves
Published: January 2025

Influenza A viruses (IAV) are likely candidates for pandemics. This report summarizes the results of the Swiss national program for surveillance of influenza viruses in pigs and transmissions to humans between 2010 and 2022. Challenges and optimization options in the program are discussed.

Nasal swabs or lung tissue samples from pigs with influenza-like signs (e.g. fever, cough) were screened by real-time RT-PCR for swine influenza virus (SIV) genomes, including that of the 2009 pandemic strain A(H1N1)pdm09; positive samples were subtyped for H1, N1, H3 and N2 by RT-PCR and Sanger sequencing. In parallel, humans with influenza-like symptoms and recent contact with diseased pigs were asked to self-sample themselves with a nasal swab. Human swabs were tested for IAV, and positive swabs further subtyped to identify potential cross-species transmission between swine and humans.

In the pigs, SIV was detected in 375 of 674 farm visits. H1N1 is the only subtype detected in Swiss pigs so far. The (H1N1)pdm09 strain (HA clade 1A) was only detected in seven out of 375 SIV positive farm visits. Phylogenetic analyses from partial hemagglutinin (HA) and neuraminidase (NA) genome sequences indicate that the remaining pigs were infected with the Eurasian avian lineage (HA clade 1C), which is predominant in swine in Europe. The Swiss H1N1 strains form distinct clusters within HA clades 1C.2.1 and 1C.2.2 and seem to evolve comparably slowly. Infection of humans with SIV was identified in five cases. Sequence analysis assigned the five viruses to the Eurasian avian lineage (C), clades 1C.2.1 and 1C.2.2. There was no evidence for sustained human-to-human transmission.

Although no critical IAV variants seem to have emerged so far in Switzerland, further surveillance of influenza viruses at the swine-human interface is of major importance.
Prognostic value of admission H3.1 nucleosome levels in sepsis-associated acute kidney injury: a secondary analysis of the SISPCT randomised clinical trial
Authors: Neumann Caroline , Bloos Frank , Hla Teddy Tun Win , Bygott Thomas , Bogatsch Holger , Kiehntopf Michael , Börner Friedemann , Press Adrian T , Bauer Michael , Retter Andrew ,   SepNet Critical Care Trials Group
Published: January 2025

Background

NETosis is a key innate immune defence mechanism where neutrophils release extracellular traps (NETs). However, excessive NET formation may damage organs during sepsis. We investigated the association between NETs and sepsis outcomes, including mortality and acute kidney injury (AKI).

Methods

We analysed levels of H3.1 nucleosomes in 971 patients with severe sepsis and septic shock from the SISPCT trial (Effect of Sodium Selenite Administration and Procalcitonin-Guided Therapy on Mortality in Patients With Severe Sepsis or Septic Shock). We evaluated associations between H3.1 levels and mortality and the need for renal replacement therapy using multivariable Cox regression and receiver operating characteristic analyses.

Results

We analysed 971 critically ill patients with complete data including admission H3.1 levels. 443 patients (45.6%) presented with sepsis, 520 (53.6%) had septic shock, and eight patients had an unknown diagnosis as defined by Sepsis-3. Admission H3.1 levels were higher in patients with septic shock than with sepsis (median 921.84 vs 432.71 ng/mL; p<0.001). Admission H3.1 levels were higher in non-survivors, and in a univariate Cox analysis, each log-10 increase in H3.1 was associated with a hazard ratio of 1.86 (95% confidence interval 1.41–2.47, p<0.05). H3.1 was also higher in patients requiring renal replacement therapy with septic shock vs sepsis (1832 ng/mL vs 801.4 ng/mL, p=0.01) and demonstrated a dose-response relationship with the severity of AKI.

Conclusion

Elevated levels of H3.1 nucleosomes at admission are independently associated with mortality and severe kidney dysfunction requiring renal replacement therapy.

Trial registration

Clinicaltrials.govIdentifier,NCT00832039.
Cognitive Costs and Gait Parameters During Single- and Dual-Task Conditions: A Comparative Study in Individuals With and Without Non-Specific Neck Pain
Authors: Moustafa Ibrahim M. , Abu-Ghosh Shorouk , Ahbouch Amal , Zadeh Shima Abdollah Mohammad , Kim Meeyoung , Khowailed Iman
Published: January 2025

Background

The high incidence of non-specific neck pain (NSNP) among students, commonly associated with prolonged sedentary behavior and extensive use of electronic devices, highlights the need to assess its impact on cognitive and motor functions. This study aims to evaluate the effects of NSNP on dual-task performance by analyzing gait parameters and cognitive performance during both single-task and dual-task conditions.

Methods

Forty-five participants with NSNP and forty-five age-matched controls were assessed using an optical motion-capture system. Participants underwent gait assessments during both single-task (without cognitive load) and dual-task conditions, in which the cognitive tasks involved simple mathematical computations.

Results

Results revealed that, under single-task conditions, differences in gait parameters between groups were not statistically significant. However, under dual-task conditions, participants with NSNP exhibited significant impairments in gait parameters and higher cognitive costs (p < 0.05). Correlation analysis indicated that pain intensity was significantly associated with cognitive cost and gait parameter alterations during dual-task conditions (p < 0.05).

Conclusions

These findings suggest that NSNP significantly elevates the cognitive effort required during dual tasking. These finding emphasizes on the need for interventions to alleviate neck pain and improve both physical and cognitive health.
A mathematical model of H5N1 influenza transmission in US dairy cattle
Authors: Rawson Thomas , Morgenstern Christian , Knock Edward S. , Hicks Joseph , Pham Anh , Morel Guillaume , Murillo Aurelio Cabezas , Sanderson Mike , Forchini Giovanni , FitzJohn Richard , Hauck Katharina , Ferguson Neil
Published: January 2025

We present a stochastic metapopulation transmission model that simulates the spread of H5N1 avian influenza through individual dairy cows in 35,974 dairy herds in the continental United States. Transmission is enabled through the movement of cattle between herds, as indicated from Interstate Certificates of Veterinary Inspection (ICVI) data. We estimate the rates of under-reporting by state and present the anticipated rates of positivity for cattle tested at the point of exportation over time. We investigate the likely impact of intervention methods to date on the underlying epidemiological dynamics, demonstrating that current interventions have had insufficient impact, preventing only a mean 175.2 reported outbreaks. Our model predicts that the majority of the disease burden is, as of January 2025, concentrated within West Coast states, due to the network of cattle movements and distribution of the respective dairy populations. We quantify the extent of uncertainty in the scale of the epidemic, highlighting the most pressing data streams to capture, and which states are most expected to see outbreaks emerge next, with Arizona and Wisconsin at greatest risk. Our model suggests that dairy herd outbreaks will continue to be a significant public health challenge in 2025, and that more urgent, farm-focused, biosecurity interventions and targeted surveillance schemes are sorely needed.
Bodily Self-Dysfunction in Psychosis: Altered Neural and Spinal Response to Self-produced Sensations
Authors: Salamone Paula C. , Enmalm Adam , Kaldewaij Reinoud , Åman Marie , Medley Charlotte , Pietrzak Michal , Olausson Håkan , Capusan Andrea Johansson , Boehme Rebecca
Published: January 2025

Psychosis is often characterized by disturbances in the sense of self, with patients frequently misattributing self-produced sensations to external sources. While somatic hallucinations and misperceptions are common, the underlying disruptions in basic bodily self-processing remain unclear.

We aimed to investigate alterations in bodily self-processing, including touch and interoception, in psychosis using a multimodal, multi-method approach.

A total of 70 participants were included (35 patients diagnosed with psychotic disorders [DSM-IV F20-29], 35 age-and sex-matched controls).

Participants performed self-/other-touch-tasks and interoceptive assessments during functional magnetic resonance imaging (fMRI), evoked potentials (EP) measurements, and/or behavioral and psychophysical tests.

Primary outcomes included neural and behavioral responses to self-and externally-generated sensations (touch and heartbeat). Brain activation (fMRI), spinal responses (EPs), heartbeat perception and processing (EPs), and behavioral measures were analyzed, with preregistered hypotheses.

Patients demonstrated heightened neural activity during touch tasks, including increased right superior temporal gyrus activation during self-touch and heightened activity in a right temporoparietal cluster during social touch. Tactile self-other distinction impairments were evident at the spinal cord level (EPs). Behaviorally, patients showed reduced differentiation in tactile thresholds for self-vs. other-touch. Interoceptive impairments included diminished cortical responses to heartbeat signals (EPs), lower interoceptive accuracy (heartbeat detection), and reduced self-reported interoceptive sensitivity.

These findings reveal pervasive sensory and self-related disturbances in psychotic disorders. Impairments in differentiating self-and externally-evoked responses, detectable as early as the spinal cord level, may contribute to higher-order symptoms of psychosis.
The Language & Memory Test: International feasibility study of an unsupervised digital test of cognition for neurologic populations
Authors: Leavitt Victoria M. , Simani Leila , Koch Marcus , Morrow Sarah A. , Heuer Lauren , Roozbeh Mahrooz , Roozbeh Mehrdad , Traynor Sean
Published: January 2025

Background

Current cognitive outcomes are insufficient to monitor subtle change over time in neurologic populations. Challenging cognitive tests (i.e., cognitive “stress test”) unaffected by practice effects and learning are ideal for monitoring and tracking change. Here we describe the Language & Memory Test (LMT), an unsupervised digital test we developed to measure rapid naming, visuospatial memory, and fine motor dexterity, that takes approximately 4 minutes to complete.

Objective

Conduct feasibility study of the LMT in adults recruited across three countries; in English and non-English speaking participants; employing in-person, remote, and unsupervised administration modalities.

Methods

We investigated retest reliability, usability / tolerability, and equivalence across centers, administration modalities, and English / non-English speakers. We also evaluated performance across adult age groups: 18-40, 41-60, and 61+ years.

Results

The LMT was administered 555 times to 440 individuals ages 18-84 years in Canada, Iran, and the United States. Our sample was geographically and racially/ethnically diverse. Participants included a control sample of adults (n=115) and adults with a diagnosed neurologic disease (n=325). Of those invited to complete the LMT, 95.3% agreed; 99% of those who began the test completed it. Retest reliability was acceptable for finger tapping (Cronbach’sα=0.942) and language (α=0.872), and marginally acceptable for memory 1 (α=0.604). Equivalence varied across administration modalities, centers/countries, settings, and English / non-English speakers. Expected age-related performance decrements were shown for all three subtests.

Conclusions

The LMT shows promise as a culturally adaptable tool for use in diverse neurologic populations.
Variant Scientists in Genomic Medicine: Survey of Demographics, Training, Duties, and Professional Development
Authors: Dickson Alexa , Cone Kelsey R. , Fortini Barbara K. , Goldstein Jennifer , Thompson Michelle L. , Wilke Matheus V.M.B. , Hurst Anna C.E. , Schroeder Molly C. , Polonis Katarzyna , Bowling Kevin M.
Published: January 2025

Purpose

Genomic testing has proven utility in disease diagnostics, guiding clinical management and improving outcomes. Use of high throughput sequencing by clinical laboratories has generated opportunities and challenges in data analysis resulting in the emergence of a laboratory role termed Variant Scientist. The aim of this study was to characterize this laboratory role.

Methods

We developed a thirty-item survey to collect information describing the current demographic landscape, salary ranges, work environments, training options, and professional development of Variant Scientists. The survey was disseminated to individuals conducting variant analysis in the United States from November 6, 2023, to March 15, 2024.

Results

Survey responders (n=87) are predominantly female (78%), age 40 or less (64%), hold advanced degrees (92%), and report four or more years of experience (75%). Responders report involvement in a diverse set of laboratory tasks and received relevant training on the job (78%). This workforce is satisfied with their career path (70%) and reports adequate support from employers. They note that resources and recognition from professional organizations are currently lacking.

Conclusions

Variant Scientists are a group of diverse genetics professionals that are highly educated and perform a variety of complex tasks within a clinical genomics laboratory.
Post-Ictal Sleep Changes in Human Focal Epilepsy
Authors: Kremen Vaclav , Cao Yurui , Gerla Vaclav , Mivalt Filip , Sladky Vladimir , St.Louis Erik , Bower Mark , Brinkmann Ben , Miller Kai , VanGompel Jamie , Cook Mark , Denison Tim , Leyde Kent , Worrell Gregory A.
Published: January 2025

Bidirectional interactions between sleep, seizures, and epilepsy remain incompletely understood. Evidence from animal models and people with focal epilepsy suggest that seizures may engage mechanisms of memory consolidation to reinforce and strengthen synaptic connections within the pathological networks that generates seizures, termed seizure-related consolidation (SRC). Human studies of SRC, however, are limited by small sample size and restricted observations of post-ictal sleep. Using continuous local field potential (LFP) recordings from novel investigational devices implanted in 11 people with drug-resistant focal epilepsy living in their natural environments, we used automated methods to create accurate sleep-wake and seizure catalogs for investigating the interplay between seizures and sleep. Our findings demonstrate that post-ictal slow-wave sleep duration, slow-wave LFP spectral power and waveform slope are increased compared to inter-ictal nights without preceding seizures. The most significant changes localize to the epileptogenic networks generating the subjects’ habitual seizures. These results reveal parallels between SRC and physiological memory consolidation, providing new insights into the role of post-ictal sleep in epilepsy and underscoring the potential of targeting post-ictal sleep for therapeutic interventions in drug-resistant focal epilepsy.
Combined mitral and tricuspid TEER with a single TriClip steerable guide catheter: A single-center study
Authors: Papadopoulos Georgios E. , Ninios Ilias , Evangelou Sotirios , Ioannides Andreas , Ninios Vlasis
Published: January 2025

Structured Abstract

Background

Combined M- and T-TEER typically involves two separate systems, complicating logistics and increasing procedural risks. This study aims to evaluate the safety and efficacy of combined mitral (M-TEER) and tricuspid (T-TEER) transcatheter edge-to-edge repair using a single TriClip® steerable guide catheter (SGC).

Methods

Patients with moderate-to-severe (3+) or severe (4+) degenerative (DMR) or functional (FMR) mitral regurgitation and massive/torrential or severe functional tricuspid regurgitation (TR), classified as New York Heart Association (NYHA) class III or IV, who underwent combined M- and T-TEER with the same TriClip SGC between January 2022 and December 2024, were included. The primary objectives included procedural outcomes, MR and TR severity reduction, and NYHA class improvement.

Results

Among 42 patients (64% female; median age: 77 years [IQR: 9]], the implantation success rate was 100%, with mean device and procedure times of 39.2 ± 6.9 and 71.2 ± 9.6 minutes, respectively. There were no in-hospital or 30-day major adverse events (MAEs), except for 2 patients (4.8%) with tricuspid single leaflet device attachment (SLDA), and 1 patient (2.4%) who underwent atrial septal defect (ASD) closure. Over a median follow-up period of 0.91 years, 3 (7.1%) patients were hospitalized for heart failure, with zero mortality. At 1-year follow-up, all patients achieved NYHA class ≤II, along with MR ≤2+ and 34 (81%) patients had only trivial/mild TR.

Conclusions

Combined M-TEER and T-TEER using the same TriClip SGC demonstrated exceptional safety and efficacy, along with significant functional and echocardiographic improvements.
Improving wearable-based seizure prediction by feature fusion using growing network
Authors: Hasija Tanuj , Kuschel Maurice , Jackson Michele , Dailey Stephanie , Menne Henric , Reinsberger Claus , Vieluf Solveig , Loddenkemper Tobias
Published: January 2025

Abstract

The unpredictability of seizures is one of the most compromising features reported by people with epilepsy. Non-stigmatizing and easy-to-use wearable devices may provide information to predict seizures based on physiological data. We propose a patient-agnostic seizure prediction method that identifies group-level patterns across data from multiple patients. We employ supervised long-short-term networks (LSTMs) and add unsupervised deep canonically correlated autoencoders (DCCAE) and 24-hour patterns using time-of-day information. We fuse features from these three techniques using a growing neural network, allowing incremental learning. Our method with all three features improves prediction accuracy over the baseline LSTM by 7.3%, from 74.4% to 81.7%, averaged across all patients, and outperforms the LSTM in 84% of patients. Compared to the all-at-once fusion, the growing network improves the accuracy by 9.5%. We analyze the impact of preictal data duration, wearable data quality, and clinical variables on the prediction performance.
Collective biosynthesis of plant spirooxindole alkaloids through enzyme discovery and engineering
Authors: Chu Danni , Wang Hongkui , Nie Zhiwen , Li Kang-li , Cao Jiaqing , Yang Meijing , Yin Qin , Gu Yang , Jiang Yindi
Published: January 2025

Collective synthesis is a well-established strategy to produce natural product collections from common intermediates. Extending this concept to enzymatic systems, collective biosynthesis offers a sustainable approach to diverse molecular collections but faces distinct challenges, including incomplete pathway knowledge and narrow substrate specificity of biosynthetic enzymes. Here, we overcome these limitations through enzyme discovery and protein engineering to achieve collective biosynthesis of spirooxindole alkaloids, an important class of natural products with diverse biological activities. We identified two key enzymes that catalyze enzymatic epimerization, working sequentially with a previously discovered cytochrome P450 enzyme to fully elucidate the biosynthetic pathway of pentacyclic spirooxindole alkaloids. Structure-guided engineering expanded substrate scope, enabling collective biosynthesis of 12 tetracyclic and pentacyclic spirooxindole natural products. We also generated new-to-nature fluorinated and deuterated derivatives through precursor-directed biosynthesis. This work provides crucial insights into plant spirooxindole alkaloid biosynthesis while establishing a powerful approach for sustainable production of complex natural products.
Structural insights into Salinosporamide A mediated inhibition of the human 20S proteasome
Authors: Sülzen Hagen , Fajtova Pavla , O’Donoghue Anthony J , Boura Evzen , Silhan Jan
Published: January 2025

The 20S proteasome, a critical component of the ubiquitin-proteasome system, plays a central role in regulating protein degradation in eukaryotic cells. Marizomib (MZB), a natural γ-lactam-β-lactone compound derived fromSalinispora tropica, is a potent 20S proteasome covalent inhibitor with demonstrated anticancer properties. Its broad-spectrum inhibition of all three proteasome subunits and ability to cross the blood-brain barrier has made it a promising therapeutic candidate for glioblastoma. Here, we present the cryo-EM structure of the human 20S proteasome in complex with MZB at 2.55 Å resolution. This structure reveals the binding mode of MZB to all six catalytic subunits within the two β-rings of the 20S proteasome, providing a detailed molecular understanding of its irreversible inhibitory mechanism. These findings explain the therapeutic potential of MZB at the molecular level and highlight marine-derived natural products in targeting the proteasome for anticancer treatment.
Allostery links hACE2 binding, pan-variant neutralisation and helical extension in the SARS-CoV-2 Spike protein
Authors: Colyer Alice , Wolf Esther , Lento Cristina , Ustav Mart , Sljoka Adnan , Wilson Derek J.
Published: January 2025

The SARS-CoV-2 spike protein is highly antigenic, with epitopes in three distinct regions of the receptor binding domain (RBD) alone that have known mechanisms of neutralization. In previous work, we predicted a fourth RBD epitope based on allosteric conformational perturbations measured by hydrogen-deuterium exchange mass spectrometry (HDX-MS) upon complexation with the canonical spike protein target, human angiotensin-converting enzyme 2 (hACE2). We subsequently identified a pan-neutralizing antibody (ICO-hu104) with the predicted epitope, however, as the epitope was somewhat distant from the hACE2 binding interface, and our previous work limited to the spike RBD, the neutralization mechanism was unclear. Using HDX-MS, we investigated the binding of ICO-hu104 to the full-length SARS-CoV-2 spike protein from Wuhan, Delta and Omicron variants. We demonstrate that binding of ICO-hu104 at its epitope results in an increase in deuterium uptake in the distant HR1 domain for variants of concern, which in a biological context could be indicative of destabilisation of the helices within this region, promoting S1 shedding or failure of helical extension during S2-mediated fusion. This is supported by our computational modelling, highlighting propagation of allosteric effects to the S2 coiled-coil region. Collectively, this work demonstrates an alternative neutralization mechanism for ICO-hu104 which is distinct from its first-generation predecessors and thus opens alternative avenues targeting non-RBD epitopes through assessment of allosteric perturbations.

Highlights

HDX-MS reveals decreased deuterium uptake within the HR1 region of S2 for SARS-CoV-2 spike protein for variants of concern when bound to ICO-hu104.

Computational modelling validates high allosteric coupling between ICO-hu104 epitope and HR1 region.

Suggests an alternative neutralization mechanism from its predecessor ICO-hu23, whereby destabilisation of helices within the HR1 region promotes S1 shedding and/or failure of helical extension during S2-mediated fusion.

Graphical abstract
A single mutation in the ‘DSL’ motif of acyl carrier protein can prevent itsin vivomodification byE. coliHolo-acyl carrier protein synthase (AcpS)
Authors: Dhembla Chetna , Sadhukhan Debodyuti , Prem Rashima , Vaish Shivangi , Verma Shalini , Kundu Suman , Sundd Monica
Published: January 2025

E. coliexpression system is the method of choice to obtain high yields of a pure protein. However, there is always a chance that an overexpressed protein shares structural or sequence homology with the substrate of anE. colienzyme. In such cases, the expressed protein may be partially or fully converted into the product. A notable example is the expression of acyl carrier proteins (ACP) inE. coli. Since most type II ACPs of the fatty acid synthesis pathway (FAS) have a conserved helix II, the carrier proteins are recognized as a substrate by Holo-acyl carrier protein synthase (AcpS). Thus, most ACPs express as partially or fully loaded proteins inE. coli. This undesirable modification is a concern when the objective is to obtain milligram amounts of apo-ACP. Here, using an approach combining mutagenesis, enzyme activity, and NMR, we probed for residues in ACP that can prevent thisin vivomodification, without affecting Sfp (Surfactin synthetase activating enzyme) function. Taking cues from theE. coliACP-AcpS structure (PDB 5VCB), charge neutralization mutations were designed at five different positions inEcACP that participate in ion-pair interaction with AcpS. Three of the mutants expressed solely as apo-ACP inE. coli viz.D35N, E41A and E47A/E48A. However, only the D35N mutant could be converted into holo-/acyl-ACP using Sfpin vitro, establishing mutagenesis as a viable strategy to prevent undesired modificationsin vivo. As proof of principle, the mutation was applied to two unrelated ACPs that express primarily as modified proteins inE. coli-Mus musculusmitochondrial FAS ACP (MmACP) andSalmonellaTyphimurium invasion acyl carrier protein (IacP). Single D35N mutation of the ACPs prevented theirin vivomodification by AcpS, and the mutants were efficiently converted into holo-ACP by Sfpin vitro. These results demonstrate that D35N mutagenesis is a useful strategy to express apo-ACP inE. coliand is applicable across all type II ACPs. Furthermore, we show that holo-IacP and holo-MmACP are not recognized as substrates by AcpH (E. coliAcyl carrier protein hydrolase), and therefore they express predominantly as modified proteins inE. coli.