bluuebunny/crossref_metadata_2025 huggingface dataset:
Confidence-Enhanced Semi-supervised Learning for Mediastinal Neoplasm Segmentation1
Authors: Fu Xiaotong , Zhang Shuying , Zhou Jing , Ji Ying
Published: July 2024

Automated segmentation of mediastinal neoplasms in preoperative computed tomography (CT) scans is critical for accurate diagnosis. Though convolutional neural networks (CNNs) have proven effective in medical imaging analysis, the segmentation of mediastinal neoplasms, which vary greatly in shape, size, and texture, presents a unique challenge due to the inherent local focus of convolution operations. To address this limitation, we propose a confidence-enhanced semi-supervised learning framework for mediastinal neoplasm segmentation. Specifically, we introduce a confidence-enhanced module that improves segmentation accuracy over indistinct tumor boundaries by assessing and excluding unreliable predictions simultaneously, which can greatly enhance the efficiency of exploiting unlabeled data. Additionally, we implement an iterative learning strategy designed to continuously refine the estimates of prediction reliability throughout the training process, ensuring more precise confidence assessments. Quantitative analysis on a real-world dataset demonstrates that our model significantly improves the performance by leveraging unlabeled data, surpassing existing semi-supervised segmentation benchmarks. Finally, to promote more efficient academic communication, the analysis code is publicly available athttps://github.com/fxiaotong432/CEDS.

Author summary

In clinical practice, computed tomography (CT) scans can aid in the detection and evaluation of mediastinal tumors. The early detection of mediastinal tumors plays a crucial role in formulating appropriate treatment plans and improving patient survival rates. To reduce the high cost of manual annotation, researchers have attempted to employ convolutional neural networks (CNNs) for efficient automatic segmentation. However, the significant challenges arise due to the considerable variation in shape, size, and texture of mediastinal tumors, posing difficulties for the segmentation task. In this study, we introduce a confidence-enhanced module with a semi-supervised learning framework. By evaluating the model’s prediction confidence and selecting high-confidence predictions, we improve the efficiency and quality of data utilization. This approach demonstrates the achievement of accurate mediastinal tumor segmentation with only a minimal amount of labeled data. Our research not only provides an effective technical approach for automatic segmentation of mediastinal tumors but also opens up new possibilities for optimizing strategies in semi-supervised learning methods.
Non-floral scent sources of orchid bees: observations and significance
Authors: Henske Jonas , De Dijn Bart P. E. , Eltz Thomas
Published: July 2024

Males of the neotropical orchid bees collect environmental volatiles to concoct complex species-specific perfumes that are later used in sexual communication. While perfumes are typically seen as being derived from floral sources, these bees also collect scents from non-floral resources such as decaying wood or tree wounds, even though reports of these sources remain scarce. Here we report observations of male orchid bees collecting scent at 21 different non-floral sources in Central and South America. MaleEufriesea coruscathat were marked at one of them, a woundedProtium raveniisecreting odoriferous sap/resin, returned repeatedly over periods of up to 19 days. Chemical analyses of hind-leg contents suggest that this single non-floral source accounted for a substantial fraction (>50%) of the species-specific perfume. This and other findings strengthen the view that non-floral scent sources play a central role in orchid bee perfume biology. Moreover, at the sameProtiumwe also observed femaleEuglossaspp. harvesting resin for nest construction. The collection of substances by both euglossine male and female bees at the same source strengthens the notion that the evolution of male perfume signaling was promoted by a sensory bias for resinous nest construction materials in females.
Evaluating the Anti-Tumor Efficacy and Safety of AEV01 in Glioblastoma and Hepatocellular Carcinoma: AnIn VitroandIn VivoApproach
Authors: Biswas Indrani , Precilla S Daisy , Kumar Aravinda , Sekhar MM , Medasani Renu , TS Anitha
Published: July 2024

Gliomas and hepatocellular carcinoma (HCC) are aggressive cancers with poor prognoses, often leading to less than a year of survival. Therapeutic resistance underscores the need for novel therapeutic strategies. AEV01, derived fromPicrorhiza kurroa, has shown promise as a potential anticancer agent. In this context, the current study aimed to evaluate the anti-tumor efficacy and safety profile of AEV01 bothin vitroandin vivoin glioblastoma and HCC models. Briefly, cytotoxicity and apoptosis were assessed using MTT assays and AO/EtBr staining, while ELISA and immunofluorescence measured inflammatory markers, TP53 and CD36 expression.In vivo, ELISA was performed against the inflammatory and tumor suppressor markers while, histopathological analysis assessed tumor morphology and organ toxicity. AEV01 exhibited dose-dependent cytotoxicity against U-87 MG glioblastoma and HepG2 liver cancer cells, with optimal concentrations at 400 µg and 300 µg respectively. Treatment downregulated inflammatory markers, CD36 expression and concomitantly increased TP53 expression. Xenograft models depicted similar results, with reduced tumor markers expression, reduced tissue architecture, and no significant organ toxicity. Thus, AEV01 demonstrated potent anti-tumor activity with a favorable safety profile, suggesting its potential as a novel therapeutic agent for gliomas and HCC, warranting further clinical investigation.
Multi trait assessment of wheat variety mixtures performance and stability: mixtures for the win!
Authors: Stefan Laura , Strebel Silvan , Camp Karl-Heinz , Christinat Sarah , Fossati Dario , Städeli Christian , Levy Häner Lilia
Published: July 2024

In the current quest for a more sustainable, environment-friendly agriculture, variety mixtures are often suggested as a practical option to increase the stability of food production systems. Their effects on yield have been extensively researched, yet clear conclusions remain elusive, notably in terms of mechanistic processes and optimal variety combinations. Furthermore, in the case of wheat, yield is not the only component in the equation: grain quality is crucial for the bread value chain, yet the effects of variety mixtures on wheat quality and its stability have rarely been investigated. To that end, we conducted a multi-year, multi-site wheat variety mixture experiment investigating the role of variety mixtures on the performance and stability of five traits linked to grain yield and quality, and the mechanisms underlying these effects. Eight varieties were grown in pure stands and 2-variety mixtures, following a full diallel design. We considered the responses of grain yield, protein content, thousand kernel weight, hectoliter weight, and Zeleny sedimentation value. Results showed that mixtures generally outperformed pure stands in terms of global performance and stability for the 5 parameters. We particularly noticed an increase in quality stability and in Zeleny sedimentation value in mixtures, showing the potential of mixtures to improve crop quality. Moreover, we highlighted the important role of light interception for increased mixtures benefits. A more detailed investigation into individual mixture performances led us to some practical rules for optimal variety combinations: we advise combining varieties with similar heights and phenologies but different tillering abilities and yield potential. This study thus shows that variety mixtures represent a promising solution to sustainably increase the stability of wheat yield and quality. With practical recommendations, our results could benefit farmers but also processors and bakers, and promote the adoption of wheat variety mixtures.
Nuclease-Resistant L-DNA Tension Probes Enable Long-Term Force Mapping of Single Cells and Cell Consortia
Authors: Sethi Soumya , Xu Tao , Sarkar Aritra , Drees Christoph , Jacob Claire , Walther Andreas
Published: July 2024

DNA-based tension probes with precisely programmable force response provide important insights into cellular mechanosensing. However, their degradability in cell culture limits their use for long-term imaging, for instance, when cells migrate, divide, and differentiate. This is a critical limitation for providing insights into mechanobiology for these longer-term processes. Here, we present DNA-based tension probes that are entirely designed based on the stereoisomer of biological D-DNA, i.e., L-DNA. We demonstrate that L-DNA tension probes are essentially indestructible by nucleases and provide days-long imaging without significant loss in image quality. We also show their superiority already for short imaging times commonly used for classical D-DNA tension probes. We showcase the potential of these resilient probes to image minute movements, and for generating long term force maps of single cells and for the first time, of collectively migrating cell populations.
Systematic profiling of the acetyl lysine machinery reveals a role for MAPKAPK2 in bromodomain inhibitor resistance
Authors: Tchara Pata-Eting Kougnassoukou , Loehr Jérémy , Germain Lucas , Steinhart Zachary , Gonzalez-Badillo Beatriz , Lashgari Anahita , Chartier François J.M. , Tucholska Monika , Picaud Sarah , Knight James D.R. , Angers Stéphane , Bisson Nicolas , Goding Colin R. , Audet-Walsh Étienne , Filippakopoulos Panagis , Gingras Anne-Claude , Lambert Jean-Philippe
Published: July 2024

Bromodomain (BRD)-containing proteins are chemically tractable multi-domain scaffolding molecules involved in acetyl lysine (Kac) signaling. BRD inhibitors have shown promise in clinical oncology, including melanomas; however, their narrow therapeutic windows and issues with resistance in pre-clinical models highlight the need to better understand the functions of and interconnection between BRD-containing proteins. Here, we use complementary interaction-mapping techniques (affinity purification and proximity-dependent biotinylation) to map the interactions of 39 of the 42 BRD-containing proteins and 110 additional proteins that physically or functionally associate with them. We uncover 3,892 novel interactions and reveal the intricate connectivity of the Kac machinery. Chemical inhibition of multiple BRD classes revealed that inhibiting BETs—but not mSWI/SNF or CREBBP/EP300 proteins—dramatically rewired the interactome. Finally, we identified MAPKAPK2 activity as a critical determinant of BET inhibitor sensitivity in melanoma through its impact on chromatin composition remodeling.

In Brief

Kougnassoukou Tcharaet al. generate a static protein interaction map of the human acetyl lysine machinery by coupling two complementary functional proteomics approaches (FLAG affinity purification and proximity-dependent biotinylation) to mass spectrometry. They also investigate network changes upon bromodomain inhibition, and describe a novel resistance mechanism mediated by the p38 stress signaling pathway that causes significant metabolic changes.

Highlights

Two complementary interaction proteomics analyses of the human acetyl lysine machinery were performed.

Novel target- and compound-specific impacts of bromodomain inhibitors were identified.

MAPKAPK2was identified as a novel resistance gene to BET bromodomain inhibitors in melanoma.

BET bromodomain inhibition leads to metabolic adaptation in melanoma.
Neural microstates in real-world behaviour captured on the smartphone
Authors: Kock Ruchella , Ghosh Arko
Published: July 2024

Microstates are periods of quasi-stability in large-scale neural networks, and they are ubiquitous spanning sleep, rest and behaviour. One possibility is that the temporal and spatial features of these states vary from person to person contributing to inter-individual behavioural differences. Another possibility is that the microstates support momentary behavioural needs and as a result their properties may vary with behavioural fluctuations in the same person. Here, we leverage the history of smartphone touchscreen interaction dynamics and combined smartphone and EEG recordings (N = 61), to address if and how microstates contribute to real-world behaviour. We find that microstates measured when at rest correlated with the history (∼30 days) of smartphone interaction dynamics captured in the real world, indicating their role in the behaviour. During smartphone behaviour, the configuration of microstates varied over time. However, this variance was largely unrelated to the rich behavioural dynamics, as in similar temporal and spatial features were observed during rapid and slow smartphone interactions. We show that in the real world microstates do not respond to the fluctuations of the ongoing behaviour. Still, as microstates measured at rest are correlated to the inter-individual behavioural differences captured on the smartphone, we propose that microstates exert a top-down influence to broadly orchestrate real-world behaviour.
Enhanced restoration of visual code after targeting on bipolar cells compared to retinal ganglion cells with optogenetic therapy
Authors: Rodgers Jessica , Hughes Steven , Ebrahimi Aghileh , Allen Annette E , Storchi Riccardo , Lindner Moritz , Peirson Stuart N , Badea Tudor , Hankins Mark W , Lucas Robert J
Published: July 2024

Optogenetic therapy is a promising vision restoration method where light sensitive opsins are introduced to the surviving inner retina following photoreceptor degeneration. The cell type targeted for opsin expression will likely influence the quality of restored vision. However, a like-for-like pre-clinical comparison of visual responses evoked following equivalent opsin expression in the two major targets, ON bipolar (ON BCs) or retinal ganglion cells (RGCs), is absent. We address this deficit by comparing stimulus-response characteristics at single unit resolution in retina and dorsal lateral geniculate nucleus (dLGN) of retinally degenerate mice genetically engineered to express the opsin ReaChR inGrm6-orBrn3c-expressing cells (ON BC vs RGCs respectively). For both targeting strategies, we find ReaChR-evoked responses have equivalent sensitivity and can encode contrast across different background irradiances. Compared to ON BCs, targeting RGCs decreased response reproducibility and resulted in more stereotyped responses with reduced diversity in response polarity, contrast sensitivity and temporal frequency tuning. Recording ReaChR-driven responses in visually intact retinas confirmed that RGC-targeted ReaChR expression disrupts visual feature selectivity of individual RGCs. Our data show that while both approaches restore visual responses with impressive fidelity, ON BC targeting produces a richer visual code better approaching that of wildtype mice.
Phosphorylation at serine 214 correlates with tau seeding activity in an age-dependent manner in two mouse models for tauopathies and is required for tau transsynaptic propagation
Authors: Martinez Pablo , Jury-Garfe Nur , Patel Henika , You Yanwen , Perkins Abigail , You Yingjan , Lee-Gosselin Audrey , Vidal Ruben , Lasagna-Reeves Cristian A.
Published: July 2024

Pathological aggregation and propagation of hyperphosphorylated and aberrant forms of tau are critical features of the clinical progression of Alzheimer’s disease and other tauopathies. To better understand the correlation between these pathological tau species and disease progression, we profiled the temporal progression of tau seeding activity and the levels of various phospho- and conformational tau species in the brains of two mouse models of human tauopathies. Our findings indicate that tau seeding is an early event that occurs well before the appearance of AT8-positive NFT. Specifically, we observed that tau phosphorylation in serine 214 (pTau-Ser214) positively correlates to tau seeding activity during disease progression in both mouse models. Furthermore, we found that the histopathology of pTau-Ser214 appears much earlier and has a distinct pattern and compartmentalization compared to the pathology of AT8, demonstrating the diversity of tau species within the same region of the brain. Importantly, we also observed that preventing the phosphorylation of tau at Ser214 significantly decreases tau propagation in mouse primary neurons, and seeding activity in aDrosophilamodel of tauopathy, suggesting a role for this tau phosphorylation in spreading pathological forms of tau. Together, these results suggest that the diverse spectrum of soluble pathological tau species could be responsible for the distinct pathological properties of tau and that it is critical to dissect the nature of the tau seed in the context of disease progression.
Host selection in European ectomycorrhizal Basidiomycetes affects their estimated spore volumes
Authors: Izumi Hironari
Published: July 2024

Many ectomycorrhizal fungi show selective associations with certain host tree taxa. Their significance has been demonstrated in the vegetative growth of the fungi, such as structuring the fungal community of the mycorrhizal roots. On the other hand, our understanding of the effects of host selection on reproductive traits such as pore production is very limited. Using two independently published descriptions of host associations and spore dimensions, the differences in spore volumes depending on the associated host taxa were examined in species belonging to 10 ectomycorrhizal genera. The species inSuilluswere the most host-selective while those inInocybewere generalist. Some species inSuillus, Lactarius, Russula, andHebelomaproduced significantly (P<0.05) larger spores when they associated with certain host taxa or groups, including Pinaceae or broad-leaved hosts. However, such differences were not found inLeccinumandTricholoma. The ecological/evolutionary processes to facilitate host selection through spore volumes were discussed.
Enabling Packaging Integration of Paper-based Electrical Gas Sensors for the Monitoring of Spoilage in Fresh Spinach
Authors: Naik Atharv , Lee Hong Seok , Herrington Jack , Barandun Giandrin , Flock Genevieve , Güder Firat , Gonzalez-Macia Laura
Published: July 2024

Gas sensors present an alternative to traditional off-package food quality assessment, due to their high sensitivity and fast response without the need of sample pre-treatment. The safe integration of gas sensors into packaging without compromising sensitivity, response rate, and stability, however, remains a challenge. Such packaging integration of spoilage sensors is crucial towards preventing food waste and transitioning towards more sustainable supply chains. Here, we demonstrate a wide-ranging solution to enable the use of gas sensors for the continuous monitoring of food spoilage, building upon our previous work on Paper-based Electrical Gas Sensors (PEGS). By comparing various materials commonly used in the food industry, we analyze the optimal membrane to encapsulate PEGS for packaging integration. Focusing on spinach as a high-value crop, we assess the feasibility of PEGS to monitor the gases released during its spoilage at low and room temperatures. Finally, we integrate the sensors with wireless communication and batteryless electronics, creating a user-friendly system to evaluate the spoilage of spinach, operated by a smartphone via Near Field Communication (NFC). The work reported here provides an alternative approach that surpasses traditional on-site and in-line monitoring, ensuring comprehensive monitoring of food shelf life.
A spectrum of clinically-identified cysteine mutations in fibulin-3 (EFEMP1) highlight its disulfide bonding complexity and potential to induce stress response activation
Authors: Collier Gracen E. , Hulleman John D.
Published: July 2024

Fibulin-3 (FBLN3), also known as EFEMP1, is a secreted extracellular matrix (ECM) glycoprotein that contains forty cysteine residues. These cysteines, which are distributed across one atypical and five canonical calcium-binding epidermal growth factor (EGF) domains, are important for regulating FBLN3 structure, secretion, and presumably function. As evidence of this importance, a rare homozygous p.C55R mutation in FBLN3 negates its function, alters disulfide bonding, and causes marfanoid syndrome. Additional studies suggest that heterozygous premature stop codon mutations in FBLN3 may also cause similar, albeit less severe, connective tissue disorders. Interestingly, a series of twenty-four cysteine mutations in FBLN3 have been identified in the human population and published in the Clinical Variation (ClinVar) and gnomAD databases. We tested how seven of these cysteine mutants (five loss-of-cysteine variants: C42Y, C190R, C218R, C252F, and C365S, two gain-of-cysteine variants: R358C, Y369C) and two newly developed mutations (G57C and Y397C) altered FBLN3 secretion, disulfide bonding, MMP2 zymography, and stress response activation Surprisingly, we found a wide variety of biochemical behaviors: i) loss-of-cysteine variants correlated with an increased likelihood of disulfide dimer formation, ii) N-terminal mutations were less likely to disrupt secretion, and were less prone to aggregation, iii) in contrast to wild-type FBLN3, multiple, but not all variants failed to induce MMP2 levels in cell culture, and iv) C-terminal mutations (either loss or gain of cysteines) were more prone to significant secretion defects, intracellular accumulation/misfolding, and stress response activation. These results provide molecular and biochemical insight into FBLN3 folding, secretion, and function for many cysteine mutations found in the human population, some of which may increase the likelihood of subclinical connective tissue or other FBLN3-associated haploinsufficiency diseases.
Malaria Cell Image Classification via Majority Voting Ensembling aided Label Contrastive Learning
Authors: Kundu Shreyan , Talukdar Rahul , Roy Nirban , Das Semanti , Basu Soumili , Mukhopadhyay Souradeep , Mallik Biswadip Basu
Published: July 2024

The plasmodium group single-celled parasite that causes malaria is contagious. A female Anopheles mosquito with the infection is most frequently the one spreading it. Over 40of the world’s population is at danger; 219 million illnesses and around 435,000 deaths were recorded in 2017 alone. Even with many sophisticated evaluation tools, microscopists in resourceconstrained settings still struggle to improve the accuracy of diagnosis. Cell picture classification using deep learning avoids making incorrect diagnosis conclusions. This research aims to increase diagnostic accuracy by classifying malarial-infected cells using majority voting ensembling in conjunction with triplet loss aided label contrastive learning. The outcomes of the experiment demonstrate how well our method works with microscopic cell images in terms of accuracy, precision, recall, and other parameters.
The Molecular Evolution of the SARS-COV-2 Spike Protein: Study of Amino Acid Substitutions and Types
Authors: Moradian Mike M , Baghoomian Ania , Sweredoski Michael , Ivan Tobias , Ramjit Ruan
Published: July 2024

The molecular evolution of SARS-COV-2 has been challenging to predict. Emergence of the Omicron Variant of Concern (VOC) and its sublineages indicated that SARS-COV-2 could evolve more rapidly than previously thought. We analyzed the mutation and amino acid substitution patterns in the spike (S) protein of SARS-COV-2 VOCs to assess how they evolved in response to the selective pressure exerted by both natural immunity and vaccination.

Our results indicate less evolutionary constraint on the first part of the S protein, allowing more amino acid substitutions, especially in the NTD, RBD, and subdomain 1. Omicron lineages introduced mutations in the FP and HR1 domains for the first time. The NTD, subdomain 1, and FP domains allowed more radical amino acid substitutions, followed by RBD and HR1, possibly due to their function. There were up to nine conservative and one radical substitutions in the amino acids interacting with the Human ACE2 receptor in the RBM of the Omicron sublineages only, a remarkable departure from the previous VOCs.

We show that the molecular evolution of SARS-COV-2 S protein was relatively limited up to the Omicron lineage. The selective pressure from previous VOCs and global vaccination potentially accelerated the emergence of the highly transmissible Omicron lineage. This antigenic drift in Omicron is fueled by a high rate of radical amino acid substitutions in the S1 domains, resulting in positive selection with a high potential to change due to adaptive evolution. However, the conservative nature of changes in the RBM may signal a relative stabilization.
Transiently boosting Vγ9+Vδ2+ γδ T cells early in Mtb coinfection of SIV-infected juvenile macaques does not improve Mtb host resistance
Authors: Larson Erica C. , Ellis Amy L. , Rodgers Mark A. , Gubernat Abigail K. , Gleim Janelle L. , Moriarty Ryan V. , Balgeman Alexis J. , de Menezes Yonne T. , Ameel Cassaundra L. , Fillmore Daniel J. , Pergalske Skyler M. , Juno Jennifer A. , Maiello Pauline , Chishti Harris B. , Lin Philana Ling , Godfrey Dale I. , Kent Stephen J. , Pellicci Daniel G. , Ndhlovu Lishomwa C. , O’Connor Shelby L. , Scanga Charles A.
Published: July 2024

Children living with HIV have a higher risk of developing tuberculosis (TB), a disease caused by the bacteriumMycobacterium tuberculosis(Mtb). Gamma delta (γδ) T cells in the context of HIV/Mtb coinfection have been understudied in children, despitein vitroevidence suggesting γδ T cells assist with Mtb control. We investigated whether boosting a specific subset of γδ T cells, phosphoantigen-reactive Vγ9+Vδ2+ cells, could improve TB outcome using a nonhuman primate model of pediatric HIV/Mtb coinfection. Juvenile Mauritian cynomolgus macaques (MCM), equivalent to 4–8-year-old children, were infected intravenously (i.v.) with SIV. After 6 months, MCM were coinfected with a low dose of Mtb and then randomized to receive zoledronate (ZOL), a drug that increases phosphoantigen levels, (n=5; i.v.) at 3- and 17-days after Mtb accompanied by recombinant human IL-2 (s.c.) for 5 days following each ZOL injection. A similarly coinfected MCM group (n=5) was injected with saline as a control. Vγ9+Vδ2+ γδ T cell frequencies spiked in the blood, but not airways, of ZOL+IL-2-treated MCM following the first dose, however, were refractory to the second dose. At necropsy eight weeks after Mtb, ZOL+IL-2 treatment did not reduce pathology or bacterial burden. γδ T cell subset frequencies in granulomas did not differ between treatment groups. These data show that transiently boosting peripheral γδ T cells with ZOL+IL-2 soon after Mtb coinfection of SIV-infected MCM did not improve Mtb host defense.
Parametrically guided design of beta barrels and transmembrane nanopores using deep learning
Authors: Kim David E. , Watson Joseph L. , Juergens David , Majumder Sagardip , Sonigra Ria , Gerben Stacey R. , Kang Alex , Bera Asim K. , Li Xinting , Baker David
Published: July 2024

Francis Crick’s global parameterization of coiled coil geometry has been widely useful for guiding design of new protein structures and functions. However, design guided by similar global parameterization of beta barrel structures has been less successful, likely due to the deviations from ideal barrel geometry required to maintain inter-strand hydrogen bonding without introducing backbone strain. Instead, beta barrels have been designed using 2D structural blueprints; while this approach has successfully generated new fluorescent proteins, transmembrane nanopores, and other structures, it requires expert knowledge and provides only indirect control over the global shape. Here we show that the simplicity and control over shape and structure provided by parametric representations can be generalized beyond coiled coils by taking advantage of the rich sequence-structure relationships implicit in RoseTTAFold based design methods. Starting from parametrically generated barrel backbones, both RFjoint inpainting and RFdiffusion readily incorporate backbone irregularities necessary for proper folding with minimal deviation from the idealized barrel geometries. We show that for beta barrels across a broad range of beta sheet parameterizations, these methods achieve high in silico and experimental success rates, with atomic accuracy confirmed by an X-ray crystal structure of a novel barrel topology, and de novo designed 12, 14, and 16 stranded transmembrane nanopores with conductances ranging from 200 to 500 pS. By combining the simplicity and control of parametric generation with the high success rates of deep learning based protein design methods, our approach makes the design of proteins where global shape confers function, such as beta barrel nanopores, more precisely specifiable and accessible.

Significance

De novo beta barrel proteins have previously been designed using “blueprint” based methods which require expert knowledge of the rules of folding and provide only indirect control of the overall barrel shape by specifying structural features such as glycine kinks and beta bulges. The barrel shape can be directly modeled using global parametric methods, but to date such methods have not succeeded in generating folded proteins, likely due to the absence of such structural features. Here, we describe methods that combine the simplicity and control of parametric barrel specification with the high success rates of deep learning based protein design methods to successfully design new beta barrel folds of different and pre-specified sizes, including both soluble designs and transmembrane nanopores.
Pulsed inhibition of corticospinal excitability by the thalamocortical sleep spindle
Authors: Hassan Umair , Okyere Prince , Masouleh Milad Amini , Zrenner Christoph , Ziemann Ulf , Bergmann Til Ole
Published: July 2024

Thalamocortical sleep spindles, i.e., oscillatory bursts at ∼12-15 Hz of waxing and waning amplitude, are a hallmark feature of non-rapid eye movement (NREM) sleep and believed to play a key role in sleep-dependent memory reactivation and consolidation. Generated in the thalamus and projecting to neocortex and hippocampus, they are phasically modulated by neocortical slow oscillations (<1 Hz) and in turn phasically modulate hippocampal sharp-wave ripples (>80 Hz). This hierarchical cross-frequency nesting may enable phase-dependent plasticity in the neocortex, and spindles have thus been considered windows of plasticity in the sleeping brain. However, the assumed phasic excitability modulation had not yet been demonstrated for spindles. Utilizing a recently developed real-time spindle detection algorithm, we applied spindle phase-triggered transcranial magnetic stimulation (TMS) to the primary motor cortex (M1) hand area and measured motor evoked potentials (MEP) to characterize corticospinal excitability during sleep spindles. We found a net suppression of MEP amplitudes during spindles, driven by selective inhibition during the falling flank of the spindle oscillation, but no inhibition during its peak, rising flank, and trough. Importantly, this phasic inhibition occurred on top of the general sleep-related inhibition observed during spindle-free NREM sleep and did not extend into the immediate refractory post-spindle periods. We conclude that spindles exert asymmetric “pulsed inhibition” of corticospinal excitability, which is assumedly relevant for processes of phase-dependent plasticity. These findings and the developed real-time spindle targeting methods will enable future studies to uncover the causal role of spindles in synaptic plasticity and systems memory consolidation.
High throughput method for simultaneous screening of membrane permeability and toxicity for discovery of new cryoprotective agents
Authors: Ahmadkhani Nima , Benson James D. , Eroglu Ali , Higgins Adam Z.
Published: July 2024

Vitrification is the most promising method for cryopreservation of complex structures such as organs and tissue constructs. However, this method requires multimolar concentrations of cell-permeant cryoprotective agents (CPAs), which can be toxic at such elevated levels. The selection of CPAs for organ vitrification has been limited to a few chemicals; however, there are numerous chemicals with properties similar to commonly used CPAs. In this study, we developed a high-throughput method that significantly increases the speed of cell membrane permeability measurement, enabling ~100 times faster permeability measurement than previous methods. The method also allows assessment of CPA toxicity using the same 96-well plate. We tested five commonly used CPAs and 22 less common ones at both 4 °C and room temperature, with 23 of them passing the screening process based on their favorable toxicity and permeability properties. Considering its advantages such as high throughput measurement of membrane permeability along with simultaneous toxicity assessment, the presented method holds promise as an effective initial screening tool to identify new CPAs for cryopreservation.

Significance

Cryoprotective agent (CPA) toxicity is the most limiting factor impeding cryopreservation of critically needed tissues and organs for transplantation and medical research. This limitation is in part due to the challenge of rapidly screening compounds to identify candidate molecules that are highly membrane permeable and non-toxic at high concentrations. Such a combination would facilitate rapid CPA permeation throughout the sample, enabling ice-free cryopreservation with minimal toxicity. This study presents a method for rapidly assessing the cell membrane permeability and toxicity of candidate CPAs, identifies several novel high-permeability low-toxicity CPAs for further testing, and lays the groundwork for additional high throughput screening to discover novel CPAs with the potential to improve cryopreservation of complex tissues and organs.
Specialization restricts the evolutionary paths available to yeast sugar transporters
Authors: Crandall Johnathan G. , Zhou Xiaofan , Rokas Antonis , Hittinger Chris Todd
Published: July 2024

Functional innovation at the protein level is a key source of evolutionary novelties. The constraints on functional innovations are likely to be highly specific in different proteins, which are shaped by their unique histories and the extent of global epistasis that arises from their structures and biochemistries. These contextual nuances in the sequence-function relationship have implications both for a basic understanding of the evolutionary process and for engineering proteins with desirable properties. Here, we have investigated the molecular basis of novel function in a model member of an ancient, conserved, and biotechnologically relevant protein family. These Major Facilitator Superfamily sugar porters are a functionally diverse group of proteins that are thought to be highly plastic and evolvable. By dissecting a recent evolutionary innovation in an α-glucoside transporter from the yeast Saccharomyces eubayanus, we show that the ability to transport a novel substrate requires high-order interactions between many protein regions and numerous specific residues proximal to the transport channel. To reconcile the functional diversity of this family with the constrained evolution of this model protein, we generated new, state-of-the-art genome annotations for 332 Saccharomycotina yeast species spanning approximately 400 million years of evolution. By integrating phylogenetic and phenotypic analyses across these species, we show that the model yeast α-glucoside transporters likely evolved from a multifunctional ancestor and became subfunctionalized. The accumulation of additive and epistatic substitutions likely entrenched this subfunction, which made the simultaneous acquisition of multiple interacting substitutions the only reasonably accessible path to novelty.
Secretome analysis of oligodendrocytes and precursors reveals their roles as contributors to the extracellular matrix and potential regulators of inflammation
Authors: Godoy Marlesa I , Pandey Vijaya , Wohlschlegel James A , Zhang Ye
Published: July 2024

Oligodendrocytes form myelin that ensheaths axons and accelerates the speed of action potential propagation. Oligodendrocyte progenitor cells (OPCs) proliferate and replenish oligodendrocytes. While the myelin-forming role of oligodendrocytes and OPCs is well-established, potential additional roles of these cells are yet to be fully explored. Here, we analyzed the secreted proteome of oligodendrocytes and OPCs in vitro to determine whether these cell types are major sources of secreted proteins in the central nervous system (CNS). Interestingly, we found that both oligodendrocytes and OPCs secret various extracellular matrix proteins. Considering the critical role of neuroinflammation in neurological disorders, we evaluated the responses and potential contributions of oligodendrocytes and OPCs to this process. By characterizing the secreted proteomes of these cells after pro-inflammatory cytokine treatment, we discovered the secretion of immunoregulators such as C2 and B2m. This finding sheds new light on the hitherto underappreciated role of oligodendrocytes and OPCs in actively modulating neuroinflammation. Our study provides a comprehensive and unbiased proteomic dataset of proteins secreted by oligodendrocyte and OPC under both physiological and inflammatory conditions. It revealed the potential of these cells to secrete matrix and signaling molecules, highlighting their multifaceted function beyond their conventional myelin-forming roles.
A ONECUT1 regulatory, non-coding region in pancreatic development and diabetes
Authors: Merz Sarah , Senee Valerie , Philippi Anne , Oswald Franz , Shaigan Mina , Fuehrer Marita , Drewes Cosima , Allgoewer Chantal , Oellinger Rupert , Heni Martin , Boland Anne , Deleuze Jean-Francois , Birkhofer Franziska , Gusmao Eduardo G , Wagner Martin , Hohwieler Meike , Breunig Markus , Rad Roland , Siebert Reiner , Messerer David Alexander Christian , Gesteira Costa Filho Ivan , Alvarez Fernando , Julier Cecile , Heller Sandra , Kleger Alexander
Published: July 2024

In a patient with permanent neonatal syndromic diabetes clinically similar to cases with ONECUT1 biallelic mutations, we identified a disease-causing deletion located upstream of ONECUT1. Through genetic, genomic and functional studies we identified a crucial regulatory region acting as an enhancer of ONECUT1 specifically during pancreatic development. This enhancer region contains a low-frequency variant showing strong association with type 2 diabetes and other glycemic traits, thus extending the contribution of this region to common forms of diabetes. Clinical relevance is provided by experimentally tailored therapy options for patients carrying ONECUT1 coding or regulatory mutations.
Polygenic proxies of age-related plasma protein levels reveal TIMP2 role in cognitive performance
Authors: Anastasi Federica , Genius Patricia , Rodriguez-Fernandez Blanca , Yang Chengran , Gorijala Priyanka , Timsina Jigyasha , Hernández-Villamizar Felipe , Lorenzini Luigi , del Campo Marta , Sánchez-Benavides Gonzalo , Minguillon Carolina , Navarro Arcadi , Cruchaga Carlos , Suárez-Calvet Marc , Vilor-Tejedor Natalia
Published: July 2024

Several studies have identified blood proteins that influence brain aging performance in mice, yet translating these findings to humans remains challenging. Here we found that higher predicted plasma levels of Tissue Inhibitor of Metalloproteinases 2 (TIMP2) were significantly associated with improved global cognition and memory performance in humans. We first identified 12 proteins with aging or rejuvenating effects on murine brains through a systematic review. Using protein quantitative trait loci data for these proteins, we computed polygenic scores as proxies for plasma protein levels and validated their prediction accuracy in two independent cohorts. Association models between genetic proxies and cognitive performance highlighted the significance of TIMP2, also when the models were stratified by sex,APOE-ε4, and Aβ42 status. This finding aligns with TIMP2’s brain-rejuvenating role in murine models, suggesting it as a promising therapeutic target for brain aging and age-related brain diseases in humans.
Association of home and neighbourhood conditions with anxiety and depression symptoms during the COVID-19 lockdown: Findings from the ALSPAC study
Authors: Pinkney Connor , Kirkbride James B. , Boyd Andrew , Zammit Stanley , Newbury Joanne B.
Published: July 2024

Background

The first COVID-19 lockdown in the UK was initially hailed as a great leveller. However, given that people were restricted to their homes and immediate neighbourhoods, there were stark inequalities in how different people experienced lockdown. Nevertheless, evidence on the associations of home and neighbourhood conditions in mental health during lockdown is sparce.

Methods

Using data from the Avon Longitudinal Study of Parents and Children (ALSPAC), a UK population-based cohort, we examined associations of home and neighbourhood conditions with anxiety and depression symptoms at two points during the first UK lockdown in 2020 (23/03/20-15/06/20). Questionnaires were sent to the ALSPAC cohort at two timepoints (T1: April; T2: May/June), including validated measures of mental health, and questions about current home conditions and behaviours, including access to nature, garden access, house type, and household composition. Neighbourhood conditions were obtained via a novel linkage, and included neighbourhood deprivation, population density, social fragmentation, and greenspace. Main associations were examined using linear regression. Potential confounders were identified using a directed acyclic graph and included ethnicity, family psychiatric history, maternal social class, financial difficulties before lockdown, and previous anxiety and depression at age 18.

Findings

At T1, reduced access to nature (B=1.06, 95% CI=0.68-1.45, p<0.001) and neighbourhood deprivation (B=0.25, 95% CI=0.02-0.48) were associated with anxiety. Furthermore, reduced access to nature (B=0.99, 95% CI=0.57-1.40, p<0.001), no garden access (B=0.62, 95% CI=0.04-1.20, p=0.037), living alone (B=1.53, 95% CI=0.63-2.43, p=0.001), and neighbourhood deprivation (B=0.27, 95% CI=0.02-0.52, p=0.033) were associated with depression. Associations were similar, but often weaker, at T2. For example, there was strong evidence of associations only for access nature with anxiety (B=0.74, 95% CI=0.25-1.23, p=0.004); and for access to nature (B=1.06, 95% CI=0.50-1.61, p=0.001) and living alone (B=1.19, 95% CI=0.25-2.13, p=0.013) with depression.

Interpretation

Disadvantaged home and neighbourhood conditions, especially reduced access to nature and neighbourhood deprivation, were associated with more anxiety and depression symptoms during the first UK lockdown. In the case of future pandemics, mitigation efforts should be tailored to reduce the burden on mental health for those most vulnerable. However, the causality of these observational findings is uncertain.
Trends in hospitalisations for lower respiratory tract infection after the COVID-19 pandemic in adults with chronic respiratory disease
Authors: Sabaté-Elabbadi Alexandre , Brolon Lucie , Brun-Buisson Christian , Guillemot Didier , Fartoukh Muriel , Watier Laurence
Published: July 2024

Introduction

COVID-19 pandemic has modified the epidemiology of lower respiratory tract infections (LRTI), particularly in patients presenting a chronic respiratory disease (CRD). LRTI incidence substantially decreased at the start of the COVID-19 pandemic. However, studies focusing on the post-pandemic period are missing. We aimed to evaluate the impact of the pandemic and post-pandemic periods on hospital admissions for LRTI, with a focus on patients with CRD.

Methods

From July 2013 to June 2023, monthly numbers of adult hospitalisations for LRTI (excluding SARS-CoV-2) were extracted from the anonymized French National Hospital Discharge Database. They were modelled by regressions with autocorrelated errors. Three periods were defined: (1) early pandemic and successive lockdowns (April 2020 to May 2021); (2) gradual lifting of restrictions and widespread SARS-CoV-2 vaccination (June 2021 to June 2022); (3) withdrawal of restriction measures (July 2022 to July 2023). Analyses were computed for the entire series, by gender, age, severity, and pre-existing CRD

Results

Before the pandemic, LRTI hospitalisations showed a winter seasonal pattern with a rising trend. Pre-pandemic incidence was 96 (90.5 to 101.5) per 100,000 population. Compared with the pre-pandemic period, seasonality was no longer present and significant reductions were estimated in the first two periods: −43.64% (−50.11 to −37.17) and −32.97% (−39.88 to −26.05), respectively. A rebound with a positive trend and a seasonal pattern was observed in period 3. Similar results were observed for CRD patients with no significant difference with pre-pandemic levels in the last period (−9.21%; −20.9% to 1.67%), albeit with differential changes according to the type of CRD.

Conclusions

COVID-19 pandemic containment measures contributed to significant changes in LRTI incidence, with a rapid increase and return to a seasonal pattern after their gradual lifting, particularly in patients with CRD.
Stress and Sleep Duration in Immune and Neuroendocrine Patterning. An Analytical Triangulation in ELSA
Authors: Hamilton Odessa S. , Steptoe Andrew
Published: July 2024

Background. Proinflammatory and neuroendocrine mediators are implicated in disease aetiopathogenesis. Stress increases concentrations of immune-neuroendocrine biomarkers through a complex network of brain-body signalling pathways. Suboptimal sleep further modulates these processes by altering major effector systems that sensitise the brain to stress. Given the ubiquitous, impactful nature of material deprivation, we tested for a synergistic association of financial stress and suboptimal sleep with these molecular processes.Methods. With data drawn from the English Longitudinal Study of Ageing (ELSA), associations were tested on 4,940 participants (∼66±9.4 years) across four-years (2008-2012). Through analytical triangulation, we tested whether financial stress (>60% insufficient resources) and suboptimal sleep (≤5/≥9 hours) were independently and interactively associated with immune-neuroendocrine profiles, derived from a latent profile analysis (LPA) of C-reactive protein, fibrinogen, white blood cell counts, hair cortisol, and insulin-like growth factor-1.Results. A three-class LPA model offered the greatest parsimony. After adjustment for genetic predisposition, sociodemographics, lifestyle, and health, financial stress was associated with short-sleep cross-sectionally (RRR=1.45; 95%CI=1.18-1.79;p<0.001) and longitudinally (RRR=1.31; 95%CI=1.02-1.68;p=0.035), and it increased risk of belonging to thehigh-riskbiomarker profile by 42% (95%CI=1.12-1.80;p=0.004). Suboptimal sleep was not related to future risk ofhigh-riskprofile membership, nor did it moderate financial stress-biomarker profile associations.Discussion. Results advance psychoneuroimmunological knowledge by revealing how immune-neuroendocrine markers cluster in older cohorts and respond to financial stress over time. Financial stress associations with short-sleep are supported. The null role of suboptimal sleep, as exposure and mediator, in profile membership, provides valuable insight into the dynamic role of sleep in immune-neuroendocrine processes.