bluuebunny/crossref_metadata_2025 huggingface dataset:
Enhancing Uploads of Health Data in the Electronic Health Record – The Role of Framing and Length of Privacy Information
Authors: von Kalckreuth Niklas , Feufel Marks A
Published: October 2024

Background

The German electronic health record (EHR) aims to enhance patient care and reduce costs, but users often worry about data security. In this article, we propose and test communication strategies to mitigate privacy concerns and increase EHR uploads.

Objective

We explore whether presenting a privacy fact sheet (PFS) before interacting with the EHR increases users’ willingness to upload medical reports. Our study examines the effects of PFS framing and length on this decision.

Methods

In an online user study with 227 German participants, we used a realistic EHR click dummy and varied the PFS in terms of length (short vs. long) and framing (EHR-centered vs. patient-centered).

Results

The results show that a PFS has a positive effect on uploading (OR 4.276, P=.015). Although there was no effect regarding the length of a PFS, a patient-centered framing increased uploads compared to an EHR-centered framing (OR 4.043,P=.003).

Conclusion

Displaying PFSs at the beginning of an upload process is a cost-effective intervention to boost EHR adoption and increase diagnoses uploads. Specifically, the effectiveness of the PFS depends more on how information is framed rather than its length. Willingness to upload medical data is key to EHR success and its benefits, like better treatment and lower costs.
Anti-tumor activity of camptothecin analog conjugate of a RSPO4-based peptibody targeting LGR4/5/6 in preclinical models of colorectal cancer
Authors: Toh Yukimatsu , Wu Ling , Tu Jianghua , Liang Zhengdong , Aldana Adela M. , Wen Jake J. , Li Li , Pan Sheng , Julie Rowe H. , Hensel Martha E. , Hodo Carolyn L. , Finch Rick A. , Carmon Kendra S. , Liu Qingyun J.
Published: October 2024

Antibody-drug conjugates (ADCs) have emerged as a major modality of targeted cancer therapy, yet no ADC has been approved specifically for colorectal cancer (CRC). LGR4/5/6 (leucine-rich repeat containing, G protein-coupled receptor 4, 5, 6) are three related receptors that are expressed at high levels together or alternately in nearly all cases of CRC. ADCs targeting LGR5 have been shown to have robust anti-tumor potency, but not all CRC cells express LGR5 and LGR5-positive tumor cells may lose LGR5 expression due to cancer cell plasticity. R-spondin 4 (RSPO4) is a natural protein ligand of LGR4/5/6 with high affinity for all three receptors. We fused a mutant form of RSPO4 furin domain that retains high affinity binding to LGR4/5/6 to human IgG1 Fc to create a peptibody designated R462. Conjugation of R462 with a camptothecin analog designated CPT2 at eight drugs per peptibody led to the generation of R462-CPT2 that showed highly potent cytotoxic activity in vitro in CRC cell lines expressing any of LG4/5/6. In cell line xenograft and PDX models of CRC, R462-CPT2 demonstrated robust anti-tumor effect. Importantly, R462-CPT2 showed no major adverse effect at therapeutically effective dose levels. These results strongly support the use of RSPO ligand drug-conjugates that target LGR4/5/6 simultaneously for the treatment of CRC.
Endogenous SNAP-tagging of Munc13-1 for monitoring synapse nanoarchitecture
Authors: Kowald Maria , Bachollet Sylvestre P. J. T. , Benseler Fritz , Steinecker Maria , Boll Moritz , Kaushik Sofia , Soykan Tolga , Sun Siqi , Birke Ramona , Ilic Dragana , Brose Nils , Hörnberg Hanna , Lehmann Martin , Rizzoli Silvio O. , Broichhagen Johannes , Lipstein Noa
Published: October 2024

ABSTRACT

Synaptic function is governed by highly regulated protein machineries, whose abundance and spatial localization change continually. Studies to determine the dynamic changes in synaptic proteins nanoarchitecture typically rely on immunolabeling, or on the expression of fluorescent proteins. The former employs chemical fluorophores and signal amplification, but requires fixation. The latter enables monitoring of proteins in live microscopy, but uses suboptimal fluorophores. Self-labeling tags have been introduced to combine the advantages of these two approaches, and here we introduce a knock-in mouse line where the essential presynaptic protein Munc13-1 is endogenously fused to the self-labeling SNAP tag. We demonstrate efficient Munc13-1-SNAP labeling in fixed neurons and brain sections by various SNAP dyes, as well as by a novel far-red and cell impermeable compound, SBG-SiR-d12. We introduce and characterize SBG-SiR-d12 here as a highly-efficient dye for SNAP-tag labeling of extracellular epitopes, and of intracellular proteins in fixed and permeabilized tissue. Finally, we show that Munc13-1-SNAP can be labeled in living neurons and monitored through live-cell imaging using confocal- and super resolution microscopy. We conclude that the Unc13aSNAPmouse line is a useful tool for the analysis of presynaptic nanoarchitectural dynamics, with a potential for wide adoption.
Multiple neural pathways to successful visual short-term memory across the adult lifespan
Authors: Jansen Michelle G. , Salami Alireza , Martínez Fernando Ruiz , Mitchell Daniel J. , Oosterman Joukje M. ,   Cam-CAN, Geerligs Linda
Published: October 2024

Cognitive task performance can be supported through multiple neural pathways, a concept referred to as brain degeneracy. We used a novel approach to consider brain degeneracy during a visual short-term memory task (VSTM) across the adult lifespan in the Cam-CAN study (n = 113, 23-87 years old). Our main goal was to identify subgroups of participants whose VSTM performance was characterized by distinct brain activation patterns. First, we identified seven brain modules that responded similarly to the VSTM task and resembled previously identified functional networks (adjusted mutual information [aMI] = 0.45). Subsequently, latent profile analysis revealed four distinct subgroups of participants. Each subgroup was characterized by different recruitment patterns of these brain modules, predominantly in the frontal control module (FCM), visual module (VM), and default mode module (DMM). Subgroups did not differ in demographics or task performance. However, associations between brain activity and performance varied across subgroups, particularly in the FCM, suggesting that individuals may use different cognitive operations to perform the VSTM task. Further analyses revealed group differences in white matter integrity, mostly in the uncinate fasciculus, suggested that individual differences in structural brain properties may shape the different brain activation patterns. Altogether, our study contributes to our understanding of how multiple neural pathways could underlie cognitive performance.
Torsional Mechanics of Circular DNA
Authors: Singh Gundeep , Hong Yifeng , Inman James T. , Sethna James P. , Wang Michelle D.
Published: October 2024

Circular DNA found in the cell is actively regulated to an underwound state, with their superhelical density close toσ∼ - 0.06. While this underwound state is essential to life, how it impacts the torsional mechanical properties of DNA is not fully understood. In this work, we performed simulations to understand the torsional mechanics of circular DNA and validated our results with single-molecule measurements and analytical theory. We found that the torque generated atσ∼ - 0.06 is near but slightly below that required to melt DNA, significantly decreasing the energy barrier for proteins that interact with melted DNA. Furthermore, supercoiled circular DNA experiences force (tension) and torque that are equally distributed through the DNA contour. We have also extended a previous analytical framework to show how the plectonemic twist persistence length depends on the intrinsic bending persistence length and twist persistence length. Our work establishes a framework for understanding DNA supercoiling and torsional dynamics of circular DNA.
Coalescence-Driven Local Crowding Promotes Liquid-to-Solid-Like Phase Transition in a Homogeneous and Heterogeneous Droplet Assembly
Authors: Patel Chinmaya Kumar , Mallik Abhradip , Rath Deb Kumar , Kumar Rajesh , Mukherjee Tushar Kanti
Published: October 2024

Liquid-to-solid-like phase transition (LSPT) of disordered proteinsviametastable liquid-like droplets is a well-documented phenomenon in biology and linked to many pathological conditions including neurodegenerative diseases. However, very less is known about the early microscopic events and transient intermediates involved in the irreversible protein aggregation of functional globular proteins. Herein, using a range of microscopic and spectroscopic techniques, we show that the LSPT of a functional globular protein, human serum albumin (HSA) is exclusively driven by spontaneous coalescence of liquid-like droplets involving various transient intermediates in a temporal manner. We show that inter-droplet communication via coalescence is essential for both nucleation and growth of amorphous aggregates within individual droplets, which subsequently transform to amyloid-like fibrils. Immobilized droplets neither show any nucleation nor any growth upon aging. Moreover, we found that exchange of materials with the dilute dispersed phase has negligible influence on the LSPT of HSA. Notably, binding of small ligands modulates the feasibility and kinetics of LSPT of HSA, suggesting a possible regulatory mechanism that cells utilize to control the dynamics of LSPT. Further, using a dynamic heterogeneous droplet assembly of two functional proteins, HSA and transferrin (Tf), we show an intriguing phenomenon within the fused droplets where both liquid-like and solid-like phases co-exist within the same droplet, which eventually transform to a mixed fibrillar assembly. These microscopic insights not only highlight the importance of inter-droplet interactions behind the LSPT of biomolecules but also showcase its adverse effect on the structure and function of other functional proteins in a crowded and heterogeneous protein assembly.
Optimal Prescriptive Treatments for Ovarian Cancer with Genetic Data
Authors: Mertzios Alkiviadis , Gjika Matea , Xu Xidan , Guha Samayita , Bardhan Neelkanth M. , Kumar Subodha , Belcher Angela , Perakis Georgia
Published: October 2024

Among the cancers affecting the female population, Ovarian Cancer (OC), while being relatively rare, is the leading cause of gynecological cancer-related deaths, with overall 5-year survival rates of approximately 50% for all stages combined. This is because of the challenges associated with the diagnosis, resulting in detection at advanced stages of OC, coupled with the slow progress in effective treatment options since the approval of platinum-based chemotherapy in the late 1970s. There has been a relative lack of sophisticated methods based on Machine Learning (ML) models that use genetic data for better prediction of Ovarian Cancer outcomes and result in more effective treatment recommendations. Therefore, there is an unmet clinical need to create models that allow physicians to make informed decisions based on all available data, including patient demographic, social, health, and genomic data. Hence, we develop new techniques for leveraging genetic information in prescribing optimal treatments for patients with OC, using a publicly available dataset from the Prostate, Lung, Colorectal and Ovarian Cancer (PLCO) trial. Our approach is able to transform genotype sequencing information into a simple tabular form that can then be used as the input to any ML model. Coupled with the recorded treatment regimen and clinical parameters of matched patients from the genetic dataset, we estimate the treatment effect in terms of mortality prediction and use it to prescribe the optimal treatment for any given patient. By including the genetic features engineered through our proposed method, our models have a higher accuracy than the models without genetic information embedded. The increase in predictive accuracy demonstrates the improved efficacy of our method in the predictive setting. Furthermore, in the prescriptive setting, the models including genetic features output different treatment choices for patients, showing the impact of their inclusion. This is further highlighted by the feature importance of the genetic features such as mutations in the FAT3, BRCA1, BRCA2, and NF1 genes, where they rank highly with a tighter aggregation of the top features, relative to the sharp drop-off in feature importance after the top feature in the models without genetic data. Taken together, in summary, our models will allow oncologists to make more informed and accurate decisions, incorporating a patient’s genetic data with all other available clinical information, which has the potential for improved prognosis and better long-term survival outcomes for Ovarian Cancer patients.
Genomic ascertainment to quantify prevalence and cancer risk in adults with pathogenic and likely pathogenic germline variants in RASopathy genes
Authors: Kim Jung , Ney Gina , Frone Megan N. , Haley Jeremy S. , Mirshahi Uyenlinh L. , Astiazaran-Symonds Esteban , Shandrina Mariya , Urban Gretchen , Rao H. Shanker , Stahl Rick , Golden Alicia , Yohe Marielle E. , Gross Andrea M. , Ding Yi , Carey David J. , Gelb Bruce D. , Stewart Douglas R.
Published: October 2024

Purpose

Genomic ascertainment of electronic health record-linked exome data in two large biobanks was used to quantify germline pathogenic/likely pathogenic (P/LP) variant prevalence, cancer prevalence, and survival in adults with non-NF1RAS/mitogen-activated protein kinase genes (RASopathies).

Patients and Methods

Germline RASopathy variants were examined from adult participants in UK Biobank (UKBB; n=469,802), Geisinger MyCode (n=167,050) and Mount Sinai BioMe(n=30,470). Variants were classified as per American College of Medical Genetics/Association for Molecular Pathology criteria and reviewed by a RASopathy variant expert. Heterozygotes harbored a RASopathy pathogenic/likely pathogenic variant; controls harbored wild type or benign/likely benign RASopathy variation. To distinguish germline variants from clonal hematopoiesis, benign tissues were Sanger sequenced. Tumor phenotype and demographic data were retrieved from MyCode and UKBB.

Results

Pathogenic variants in Noonan syndrome-associated genes (excluding known Noonan syndrome with multiple lentigines variants) were the most common with an estimated prevalence that ranged between 1:1,772–1:3,330 in the three cohorts. Pathogenic variants in cardiofaciocutaneous syndrome-associated genes had an estimated prevalence of 1:41,762– 1:55,683 in two cohorts. Pathogenic variants inSPRED1(Legius syndrome) were more frequent in UKBB (1:19,567 [95%CI: 1:13,150–1:29,116]) compared to MyCode (1:41,762 [95%CI: 1:15,185–1:130,367]). InSPRED1-heterozygotes, cancer prevalence was significantly increased in UKBB (OR:3.8 [95% CI: 2.48–8.64]; p=1.2×10-3) but not in the MyCode cohort. Pathogenic variants inHRAS(Costello syndrome) were not identified. In MyCode and UKBB cohorts, there was no significant increase in cancer prevalence in individuals with Noonan-,CBL-and CFC syndrome-associated pathogenic variants.

Conclusion

Genomic ascertainment from two large biobanks did not show evidence of elevated cancer risk in adult Noonan syndrome heterozygotes. There may be an increased cancer risk for adultSPRED1heterozygotes.
Recent advances in the clinical applications of machine learning in proton therapy
Authors: Wildman Vanessa L. , Wynne Jacob F. , Kesarwala Aparna H. , Yang Xiaofeng
Published: October 2024

The present systematic review is an effort to explore the different clinical applications and current implementations of machine/deep learning in proton therapy. It will assist as a reference for scientists, researchers, and other health professionals who are working in the field of proton radiation therapy and need up-to-date knowledge regarding recent technological advances. This review utilized Pubmed and Embase to search for and identify research studies of interest published between 2019 and 2024. This systematic literature review utilized PubMed and Embase to search for and identify studies pertinent to machine learning in proton therapy. The time period of 2019 to 2024 was chosen to capture the most recent signficant advances. An initial search on PubMed was made with the search strategy “‘proton therapy’, ‘machine learning’, ‘deep learning’”, with filters including only research articles from 2019 to 2024, returning 84 results. Next, “(“proton therapy”) AND (“machine learning” OR “deep learning”)” was searched on Embase, retrieving 546 results. When filtered between 2019 to 2024 and to only research articles, 250 results were retrieved on Embase. Reviews, editorials, technical notes, and articles in any language other than English were excluded from the broad search on both databases. Filtering by title, papers were chosen based on two inclusion factors: explicit application to, or mention of, proton therapy, and inclusion of a machine learning algorithm. Assessing by abstract, works irrelevant to specific aspects of the proton therapy workflow in the scope of the review were excluded. Upon assessing and evaluating full texts for quality, studies were excluded that lacked a clear explanation of model architecture. If multiple studies of the same architecture applied to the same workflow step were identified, chronologically only the most recent advancement in application was included. An additional 5 studies that met all inclusion criteria were identified from references of chosen papers. In total, 38 relevant studies have been summarized and incorporated into this review. This is the first systematic review to comprehensively cover all current and potential areas of application of machine learning to the proton therapy clinical workflow.
An evaluation of combined objective neurophysiologic markers to aid assessment of prolonged disorders of consciousness (PDoC)
Authors: du Bois N. , Hill J. , Korik A. , Hoad D. , Bradley L. , Judge S. , Vaughan T. M. , Wolpaw J. R. , Coyle D.
Published: October 2024

Objective

Clinical assessments of individuals with Cognitive-Motor Dissociation (CMD) following brain injury are challenging and prone to errors. This prompts investigation of objective, movement-independent neurophysiological markers using electroencephalography (EEG)-based Brain-Computer Interface (BCI) technology. The current pilot study involving adults with prolonged disorders of consciousness (PDoC) investigated the combination of Motor-Imagery BCI (MI-BCI) training and auditory evoked Event Related Potentials (ERPs) using an oddball paradigm to produce complementary biomarkers to improve evaluation of awareness in PDoC.

Approach

EEG data (16 channels) were collected from participants with Unresponsive Wakefulness Syndrome (UWS,n= 2), Minimally Conscious State (MCS,n= 3), and Locked-In Syndrome (LIS,n= 4). The MI-BCI involved assessing sensorimotor rhythm modulation, motor-imagery training with and without auditory feedback, and motor-imagery responses to closed questions over 12 sessions each lasting ∼1hour. The oddball protocol was also deployed in 2-3 of those sessions, with ∼10 days between first and last, featuring auditory stimuli, comprising two 5-minute sets of standard, deviant beeps plus novel sounds, in a structured ratio. We expected those with the lowest levels of awareness would have reduced ERP components, with highest latencies to peak, as well as lowest accuracy in the motor imagery BCI protocol – and that trends across these metrics would be observed across the three patient groups based on their clinical diagnoses.

Main results

Significant differences in mean N1 component latencies and mean MI Decoding Accuracies (DA, for significant runs) occurred between groups – with shorter N1 latencies for the LIS and MCS groups than for the UWS group (LIS vs. UWS and MCS vs. UWS,p< 0.001), and higher DA for the LIS group compared to MCS and UWS (p< 0.001). Mean DA were found to have a significant negative correlation with mean N1 latencies (two-tailed,p= 0.017).

Significance

The results indicate that neurophysiological markers from the concomitant application of an MI-BCI and auditory-oddball paradigm can augment standard clinical assessments by providing objective measures that produce robust evidence of awareness in people with PDoC.
REVISITING TUBERCULOSIS (TB) DIAGNOSIS: THE PROSPECT OF URINE LIPOARABINOMANNAN (LAM) ASSAY AS A DIAGNOSTIC TOOL IN PEOPLE LIVING WITH HIV
Authors: Adedokun Ayodele Isaac , Bala Gaius , Elehamer Nafisa M.K. , Yohanna Raphael , Oyelabi Boluwatife Deborah , Gana Samuel Eniola
Published: October 2024

Background

Tuberculosis (TB), since its discovery has become a global health burden, continuously spreading across the nations of the earth with increased mortality. Its effect on human immunodeficiency virus (HIV) progression and immune cell deterioration cannot be overlooked. The widespread use of traditional and molecular TB diagnostic methods has been hindered by several factors. Nonetheless, the development of a rapid, sensitive, timely, non-invasive diagnostic protocol could revolutionize the diagnostic era and halt the spread of this infectious agent. It could also help in the early diagnosis of the infection in poorly developed areas. The detection efficacy of urine lipoarabinomannan assay as a prospect in tuberculosis diagnosis in HIV-positive patients was assessed in this study. Urine samples were collected into a wide- mouthed universal container from HIV-positive patients with signs and symptom of tuberculosis and HIV advanced disease. Alere Determine urine lateral flow - LAM test was used for the detection of LAM antigen in urine samples of HIV-positive patients. The CD4 count of the HIV- positive patients was also documented.

Results

A total of 85 HIV-positive subjects were included in the analysis based on the inclusion criteria. Urinary LAM was reactive in 29 (34.1%) of 85 HIV-positive patients and non-reactive in 56 (69.1%). The majority of the participants had a CD4+count < 200 cells/µL 60 (70.6%) while others had CD4+count ≥ to 200 cells/µL 25 (29.4%). There was no statistically significant difference between CD4 count and LAM positivity. Most of the affected age groups in the study were 31-45 years, and females had preponderance in comparison to male subjects.

Conclusions

The use of urinary LAM in HIV-positive patients is a helpful tool for TB screening. It also has a promising ability for early TB diagnosis in the study group and other TB-associated disease conditions in resource-deprived settings. For the general populace, further research is required to certify its sensitivity and specificity.
Danicamtiv reduces myosin’s working stroke but enhances contraction by activating the thin filament
Authors: Scott Brent , Greenberg Lina , Squarci Caterina , Campbell Kenneth S. , Greenberg Michael J.
Published: October 2024

Heart failure is a leading cause of death worldwide, and even with current treatments, the 5-year transplant-free survival rate is only ∼50-70%. As such, there is a need to develop new treatments for patients that improve survival and quality of life. Recently, there have been efforts to develop small molecules for heart failure that directly target components of the sarcomere, including cardiac myosin. One such molecule, danicamtiv, recently entered phase II clinical trials; however, its mechanism of action and direct effects on myosin’s mechanics and kinetics are not well understood. Using optical trapping techniques, stopped flow transient kinetics, andin vitroreconstitution assays, we found that danicamtiv reduces the size of cardiac myosin’s working stroke, and in contrast to studies in muscle fibers, we found that it does not affect actomyosin detachment kinetics at the level of individual crossbridges. We demonstrate that danicamtiv accelerates actomyosin association kinetics, leading to increased recruitment of myosin crossbridges and subsequent thin filament activation at physiologically-relevant calcium concentrations. Finally, we computationally model how the observed changes in mechanics and kinetics at the level of single crossbridges contribute to increased cardiac contraction and improved diastolic function compared to the related myotrope, omecamtiv mecarbil. Taken together, our results have important implications for the design of new sarcomeric-targeting compounds for heart failure.

SIGNIFICANCE STATEMENT

Heart failure is a leading cause of death worldwide, and there is a need to develop new treatments that improve outcomes for patients. Recently, the myosin-binding small molecule danicamtiv entered clinical trials for heart failure; however, its mechanism at the level of single myosin crossbridges is not well understood. We determined the molecular mechanism of danicamtiv and showed how drug-induced molecular changes can mechanistically increase heart contraction. Moreover, we demonstrate fundamental differences between danicamtiv and the related myosin-binding small molecule omecamtiv mecarbil that explain the improved diastolic function seen with danicamtiv. Our results have important implications for the design of new therapeutics for heart failure.
Randomization based evaluation of distinct topological and cancer expression characteristics of mutually acting gene pairs
Authors: Dalgıç Ertuğrul , Çelebi-Çınar Muazzez , Vural-Özdeniz Merve , Konu Özlen
Published: October 2024

Small scale molecular network patterns and motifs are crucial for systems level understanding of cellular information transduction. A subgroup of such patterns consists of only 2 molecules, which we named as mutually acting pairs. Using randomizations, we statistically explored such gene pair designs, i.e. mutually positive (PP) or negative (NN) and positive-negative (PN) pairs, in two comprehensive and distinct large-scale molecular networks from literature; the human protein signaling network (PSN) and the human gene regulatory network (GRN). While the numbers of NN and PN pairs were significantly higher, the number of PP pairs was significantly lower than randomly expected values. Genes participating in mutual pairs were more connected than other genes. The connectivity of mutual gene pairs differed between the two networks. NN genes were more connected than PP and PN in GRN for all types of degree values, including in, out, positive or negative connections, but less connected for in-degree and more connected for out-degree values in PSN. They also had significantly high number of intersections with each other and PN pairs than randomly expected values, indicating potential cooperative mechanisms. The three mutual interaction designs we examined had distinct RNA and protein expression correlation characteristics. NN protein pairs were uniquely over-represented across normal tissue samples, whose negative correlations were lost across cancer tissue samples. PP and PN pairs showed non-random positive RNA or protein expression correlation across normal or cancer tissue samples. Moreover, we developed an online tool, i.e., MGPNet, for further user specific analysis of mutual gene pairs. For example, we identified SNCA with significantly enriched negatively correlated NN pairs with ubiquitin-proteasome members only in normal tissues. Unique non-random characteristics of mutual gene/protein pairs identified in two different comprehensive human molecular networks could provide valuable information for a better understanding of molecular design principles between normal and cancer states.
Natural disturbances and connectivity shape the seasonal variability of aquatic macroinvertebrate communities across Europe
Authors: Chalmandrier Loic , Cunillera-Montcusi David , Lopez-Rojo Naiara , Canedo-Arguelles Miguel , Csabai Zoltan , Foulquier Arnaud , Jabot Franck , Milisa Marko , Mykra Heikki , Paril Petr , Pernecker Balint , Polovic Luka , Sarremejane Romain , Snare Henna , Soria Maria , Datry Thibault , Bonada Nuria , Munoz Francois
Published: October 2024

Understanding the joint influence of natural disturbance, spatial connectivity and biogeography on biodiversity is essential to forecast its responses to climate change. Macroinvertebrate communities in drying river networks constitute an ideal study system to understand the interplay of these ecological processes. We analyze the taxonomic and functional structure of macroinvertebrate communities sampled across 126 reaches with perennial and intermittent streamflow, surveyed in six drying river networks (DRN) across Europe, six times over one year.

Drying frequency decreased community richness and functional diversity of communities, whereas spatio-temporal connectivity increased community richness in intermittent reaches. Communities experiencing a high drying frequency increased the proportion of taxa with K-strategies and drying resistance traits. Communities experiencing a long drying duration compensated by high spatio-temporal connectivity had more taxa with a r-strategy and high dispersal ability. Perennial communities varied from taxa-poor communities of r-strategists in spring and autumn and taxa-rich communities of K-strategists in summer and had a constant functional diversity throughout the year. When drying frequency increased, communities showed a similar pattern except in autumn when they shifted towards species-poor communities of K-strategists. Functional diversity then peaked in summer. Community trait structure and in particular optimal drying resistance traits changed across biogeographical scales. It opposed communities from mountainous DRN (with more r-strategies and high dispersal ability) to non-mountainous DRN (with more K-strategies).

Drying frequency, drying duration, and spatio-temporal connectivity drive divergent community structures, suggesting the presence of an ecological threshold that explains the variability of disturbed ecosystems across broad spatial scales. These factors also shaped seasonal community variations, particularly after summer, with intermittent communities influenced by stochastic recolonization events in spring and autumn. Spatial-temporal connectivity proved crucial for maintaining diversity in communities subjected to intense drying. Lastly, the effectiveness of drying resistance traits was dependent on the biogeographical and environmental conditions of drying river networks.
Disordered proteins: microphases or associative polymers?
Authors: Girard Martin
Published: October 2024

We develop a surrogate model for low complexity disordered proteins, which allows us to generate sequences with quantifiable disorder. We investigate properties of these sequences, and show that the sequence dependence of the radius of gyration only arises in the vicinity of the polymer collapse transition. Microphase propensity of the sequence is shown to be a reliable predictor, outperforming state of the art methods, in the crossover region. We show that predictions of associative polymer theory arises only as a limiting case, and discuss its applicability.
Discovery of new and variantPotyvirusesinAsparagalesplants from a Dutch urban botanic garden
Authors: Dekker Rob J. , Rauwerda Han , de Leeuw Wim C. , van Olst Marina , Ensink Wim A. , van Leeuwen Selina , Meijs Claartje , Baksi Moezammin M.M. , Breit Timo M. , Jonker Martijs J.
Published: October 2024

Although viruses play an important role in human health and plant health, most viruses are still undetected. One of the reasons is that they may evolve in distinct natural habitats that are not yet extensively sampled for virus analysis. An example of such a habitat is urban botanic gardens. We analyzed 25Asparagalesplants with a mild to severe disease phenotype from a Dutch urban botanic garden for the presence of known an unknown virus types and virus variants by smallRNA-seq and RNA-seq. We found in all samples evidence for (past)Potyviridaepresence, mostly Ornithogalum virus (OV) and Ornithogalum mosaic virus (OrMV), as well as a new Iris mild mosaic virus variant (IMMV) and a yet unknown species of Potyvirus. Also, presence of a new Betaflexivirus, a new Polerovirus and a new Phenuivirus were detected. Most analyzed plants harbored multiple viruses, 18 out of 25 plants showed evidence for three to seven viruses and 12 out of 13 viruses were present in four to 11 samples. In this study, we describe the characteristics of a newly discovered Potyvirus and identify several variants of known potyviruses. We place these findings in the context of known viruses. However, we were unable to link these potyviruses to any specific disease phenotype.
Novel amylase genes enable utilisation of resistant starch by bifidobacteria relevant to early-life microbiome development
Authors: Millar Molly E. , Abele Miriam , Harris Hannah C. , Koev Todor T. , Telatin Andrea , Kiu Raymond , Van Sinderen Douwe , Khimyak Yaroslav Z. , Ludwig Christina , Hall Lindsay J. , Warren Frederick J.
Published: October 2024

Bifidobacteriumspecies and strains are key members of the gut microbiota, appearing soon after birth and persisting into adulthood. Resistant starch is an important dietary substrate for adult-associated bifidobacteria, where its fermentation supports host health. However, little is known about how different starch structures interact with bifidobacteria across various ages and ecological niches. To address this, we carried out detailed growth kinetics screening ofBifidobacteriumreference strains and unique isolates from breast-fed infants, testing their metabolic interaction with a variety of starch structures.1H NMR metabolomics as well as analysis of CAZyme profiles from genomes were generated for eachBifidobacterium-starch combination. For a subset of resistant starch-utilising isolates, we integrated multi-omics approaches to attain further mechanistic interaction insights. Our results revealed that bifidobacterial starch hydrolysis capabilities are closely associated with their CAZyme profiles and appear to be connected to the niche they occupy. Notably, in one isolate ofBifidobacterium pseudolongum, we identified a novel gene cluster containing three multi-functional amylase enzymes complemented by several starch binding modules which were significantly upregulated in response to resistant starch. This gene cluster was also found in the genomes of bifidobacterial isolates from weaning infants and adults. These findings provide new insights into their participation in the maturation process of the infant gut microbiota. Uncovering mechanisms of metabolic interaction between starch structures and bifidobacteria underscores the importance of this ecological function and potential health implications.
The biological consequences of knockout of genes involved in the synthesis and metabolism of H2S inDrosophila melanogaster
Authors: Shilova V.Y. , Chuvakova L.N. , Garbuz D.G. , Rezvykh A.P. , Funikov S.Y. , Davletshin A.I. , Sorokina S. , Nikitina E.A. , Gorenskaya O. , Evgen’ev M.B. , Zatsepina O.G.
Published: October 2024

Here, we describe the effect of knockout (KO) of two key genes (cbs,cse) responsible for H2S synthesis in the transsulfuration pathway as well as the inactivation of sulfurtransferase gene (dtst1) encoding single domain rhodanese onDrosophila melanogastergenome expression and several life-history traits. The analysis of H2S production in the KO flies showed its minimal level in the strain with double KO (CBS-/-; CSE-/-) while flies with triple KO (CBS-/-;CSE-/-;dTST1-/-) exhibited higher H2S level and improvements in lifespan. The transcriptomic analysis of fly bodies from the double KO strain with maximum disturbances of fitness components revealed a profound increase in the expression of genes involved in the functioning of the excretory system. Besides, double and triple KO flies exhibited drastic changes in Malpighian tubules’ appearance. Inactivation of genes related to H2S metabolism resulted in altered expression of numerous loci involved in mitochondrial function. While KO of thedtst1gene did not affect the genome expression, the triple KO flies exhibited more changes in the whole-body transcriptome than double KO flies. Reduced fecundity in double knockouts correlates with pronounced changes in ovarian transcriptome data. Surprisingly, the knockout of thedtst1gene affected the flies’ memory.
2.6-Å resolution cryo-EM structure of a class Ia ribonucleotide reductase trapped with mechanism-based inhibitor N3CDP
Authors: Westmoreland Dana E. , Feliciano Patricia R. , Kang Gyunghoon , Cui Chang , Kim Albert , Stubbe JoAnne , Nocera Daniel G. , Drennan Catherine L.
Published: October 2024

Ribonucleotide reductases (RNRs) reduce ribonucleotides to deoxyribonucleotides using radical-based chemistry. For class Ia RNRs, the radical species is stored in a separate subunit (β2) from the subunit housing the active site (α2), requiring the formation of a short-lived α2β2 complex and long-range radical transfer (RT). RT occurs via proton-coupled electron transfer (PCET) over a long distance (~32-Å) and involves the formation and decay of multiple amino acid radical species. Here, we use cryogenic-electron microscopy and a mechanism-based inhibitor 2′-azido-2′-deoxycytidine-5′-diphosphate (N3CDP) to trap a wild-type α2β2 complex ofE. coliclass Ia RNR. We find that one α subunit has turned over and that the other is trapped, bound to β in a mid-turnover state. Instead of N3CDP in the active site, forward RT has resulted in N2loss, migration of the third nitrogen from the ribose C2′ to C3′ positions, and attachment of this nitrogen to the sulfur of cysteine-225. To the best of our knowledge, this is the first time an inhibitor has been visualized as an adduct to an RNR. Additionally, this structure reveals the positions of PCET residues following forward RT, complementing the previous structure that depicted a pre-turnover PCET pathway and suggesting how PCET is gated at the α–β interface. This N3CDP-trapped structure is also of sufficient resolution (2.6 Å) to visualize water molecules, allowing us to evaluate the proposal that water molecules are proton acceptors and donors as part of the PCET process.

Significance Statement

Several FDA-approved cancer drugs target human ribonucleotide reductase (RNR), a radical enzyme that produces the requisite deoxyribonucleotides for DNA biosynthesis and repair. Human RNR is a class Ia enzyme that requires radical transfer (RT) from a β2 subunit to an α2 subunit on every round of turnover. Long-range RT is both a remarkable feature and an Achilles heel, given that inhibitors can intercept the radical species. Here we present a cryogenic electron microscopy (cryo-EM) structure of the best studied class Ia RNR, the enzyme fromE. coli, in which α2 and β2 subunits have been trapped together using a mechanism-based inhibitor. This structure provides insight into both the mechanism of RNR inhibition and the mechanism of long-range RT.
DNA Polymerase Locks Replication Fork Under Stress
Authors: Jia Xiaomeng , Inman James T. , Singh Anupam , Patel Smita S. , Wang Michelle D.
Published: October 2024

Replication of DNA requires the parental DNA to be unwound to allow the genetic information to be faithfully duplicated by the replisome. While this function is usually shared by a host of proteins in the replisome, notably DNA polymerase (DNAP) and helicase, the consequence of DNAP synthesizing DNA while decoupled from helicase remains not well understood. The unwinding of downstream DNA poses significant stress to DNAP, and the interaction between DNAP and the replication fork may affect replication restart. In this work, we examined the consequences of DNAP working against the stress of the DNA replication fork. We found that prolonged exposure of DNAP to the stress of the replication fork inactivates replication. Surprisingly, replication inactivation was often accompanied by a strong DNAP interaction with the leading and lagging strands at the fork, locking the fork in place. We demonstrated that fork locking is a consequence of DNAP forward translocation, and the exonuclease activity of DNAP, which allows DNAP to move in reverse, is essential in protecting the fork from inactivation. Furthermore, we found the locking configuration is not reversible by the subsequent addition of helicase. Collectively, this study provides a deeper understanding of the DNAP-fork interaction and mechanism in keeping the replication fork active during replication stress.
Unprecedented sighting of coral populations and associated fauna in the High Sedimentation Waters of Puerto Velero, Atlántico, Colombia
Authors: Moreno-Tilano Jorge , Sanabria Ramirez Irene Lucia , Neme Rafik
Published: October 2024

The marine coastal zone of Atlántico, Colombia, faces significant anthropogenic impact due to sediment and organic matter from the Magdalena River. This study reports the presence of two distinct coral patches in Puerto Velero, Atlántico, an area previously considered unfavorable for coral growth. Located at depths of 1-6 meters, these patches harbor a variety of marine species, extending the known distribution of 15 species in the Colombian Caribbean. Despite high sedimentation rates, the larger coral colonies show resilience, surviving mass mortality events and diseases. These findings highlight the adaptive capacity of corals in adverse conditions, emphasizing the importance of systematic monitoring and conservation efforts to understand their response to environmental changes and support marine biodiversity in the Colombian Caribbean.
Associations between Neonicotinoid, Pyrethroid, and Organophosphate Insecticide Metabolites and Neurobehavioral Performance in Ecuadorian Adolescents
Authors: Yen Jessica , Yang Kun , Tu Xin M. , Kayser Georgia , Skomal Ana , Gahagan Sheila , Suarez-Torres Jose , Hong Suzi , Moore Raeanne C. , Suarez-Lopez Jose R.
Published: October 2024

Abstract

Background

Organophosphate and pyrethroid insecticides can affect children’s neurodevelopment and increase inflammation. Limited evidence exists among adolescents and on whether inflammation may mediate pesticide–neurobehavior associations. We examined the associations between insecticide metabolite concentrations and neurobehavior among adolescents in Ecuadorian agricultural communities.

Methods

We included 520 participants aged 11-17 years. We measured urinary insecticide metabolites (mass spectrometry) and neurobehavior (NEPSY-II). Associations were adjusted for socio-demographic and anthropometric characteristics. The associations of insecticide mixtures with neurobehavior were evaluated using PLS regression, and mediation by inflammatory biomarkers (TNF-α, IL-6, CRP, SAA, sICAM-1, sVCAM-1 and sCD-14) was conducted.

Results

Among organophosphates, para-nitrophenol (PNP) and 3,5,6-Trichloro-2-pyridinol (TCPy) were inversely associated with Social Perception (score difference per 50% increase [β50%] = -0.26 [95%CI: - 1.07, -0.20] and -0.10 [-0.22, 0.01], respectively). PNP and TCPy also had significant inverse associations with Attention/Inhibitory Control at concentrations >60thpercentile (β50%= -0.26 [95%CI: -0.51, -0.01] and β50%= -0.22 [95%CI: -0.43, -0.00], respectively). The pyrethroid, 3-phenoxybenzoic acid (3-PBA), was inversely associated with Language (β50%= -0.13 [95%CI: -0.19, -0.01]) and had a negative quadratic association with Attention/Inhibitory Control. The neonicotinoid 5-Hydroxy imidacloprid (OHIM) was positively associated with Memory/Learning (β50%= 0.20 [95%CI: 0.04, 0.37]). Mixtures of all insecticides were significantly negatively related to all domains, except for Memory/Learning, which was positively associated. No mediation by inflammatory markers on these associations was observed.

Conclusions

Concurrent organophosphate, pyrethroid, and the mixtures of all metabolites were associated with lower performance in all domains except for Memory/Learning. Neonicotinoids were positively associated with Memory/Learning and Social Perception scores.
Comparing neuromodulation targets to reduce cigarette craving and withdrawal: A randomized clinical trial
Authors: Petersen Nicole , Apostol Michael R , Jordan Timothy , Ngo Thuc Doan , Kearley Nicholas W , London Edythe D , Leuchter Andrew F
Published: October 2024

Importance: Cigarette smoking remains the leading preventable cause of death worldwide, leading to development of new therapeutics, such as repetitive transcranial magnetic stimulation (rTMS). Objective: To optimize treatment, we compared three TMS targets to evaluate the effects on cigarette craving and withdrawal, and on within- and between-network connectivity of the default mode, salience, and executive control networks. Design: Data were collected using a repeated-measures, crossover trial. Investigators were not blinded, nor were participants, who were aware of the location of the stimulating magnet but not which locations were designated as the control and experimental sites. Setting: Data were collected in a neuromodulation clinic within an academic medical center. Participants: Participants were men and women (44%) aged 21-45 (M = 33.3 years), who met DSM-5 criteria for tobacco use disorder and endorsed daily smoking for at least one year. Interventions: TMS was delivered to three neuroanatomical targets: dorsolateral prefrontal cortex (dlPFC), superior frontal gyrus (SFG), and posterior parietal cortex (PPC). Area v5 of the visual cortex served as an active control site. Participants were scanned with resting-state fMRI and completed behavioral assessments before and after TMS. Main Outcomes and Measures: Self-reports of craving, withdrawal, and negative affect were obtained, and resting-state functional connectivity of three canonical networks (executive control, default mode, and salience networks) was measured. Results: Seventy-two participants completed at least one data collection session, and 57 completed all 4, yielding 61, 60, 62, and 66 complete stimulation sessions to the dlPFC, SFG, PPC, and v5, respectively. Stimulation to the SFG significantly reduced craving (95% CI, 0.0476-7.9559) and withdrawal (95% CI, 0.9225-8.1063) more than control stimulation. Effect sizes were larger in men (up D = 0.59) than in women (up to D =0.30). Neither PPC nor control site stimulation significant effects on craving, withdrawal, or negative affect. Functional connectivity analyses revealed that SFG stimulation did not produce significant changes to the networks examined, whereas dlPFC stimulation led to increased connectivity between somatomotor, default mode, and dorsal attention networks. Conclusions and Relevance: The SFG appears to be a viable target for smoking-cessation treatment, especially for men, with possible advantages over dlPFC.