bluuebunny/crossref_metadata_2025 huggingface dataset:
Photoprotective melanin is maintained within keratinocytes in a storage lysosome
Authors: Neto Matilde V. , Hall Michael J. , Charneca João , Escrevente Cristina , Seabra Miguel C. , Barral Duarte C.
Published: February 2024

In the skin, melanin is synthesized by melanocytes within melanosomes, and transferred to keratinocytes. After being phagocytosed by keratinocytes, melanin polarizes to supranuclear caps that protect against the genotoxic effects of ultraviolet radiation. We provide evidence that melanin-containing phagosomes undergo a canonical maturation process, with the sequential acquisition of early and late endosomal markers. Subsequently, these phagosomes fuse with active lysosomes, leading to the formation of a melanin-containing phagolysosome that we named melanokerasome. Melanokerasomes achieve juxtanuclear positioning via lysosomal trafficking regulators Rab7 and RILP. Mature melanokerasomes exhibit lysosomal markers, elude connections with the endo/phagocytic pathway, are weakly degradative, retain undigested cargo and are likely tethered to the nuclear membrane. We propose that they represent a lysosomal-derived storage compartment that has exited the lysosome cycle, akin to the formation of lipofuscin in aged cells and dysfunctional lysosomes in lysosomal storage and age-related diseases. This storage lysosome allows melanin to persist for long periods, where it can exert its photoprotective effect efficiently.
Decoding cell identity with multi-scale explainable deep learning
Authors: Zhu Jun , Zhang Zeyang , Xiang Yujia , Xie Beini , Dong Xinwen , Xie Linhai , Zhou Peijie , Yao Rongyan , Wang Xiaowen , Li Yang , He Fuchu , Zhu Wenwu , Zhang Ziwei , Chang Cheng
Published: February 2024

Cells are the fundamental structural and functional units of life. Studying the definition and composition of different cell types can help us understand the complex mechanisms underlying biological diversity and functionality. The increasing volume of extensive single-cell omics data makes it possible to provide detailed characterisations of cell types. Recently, there has been a rise in deep learning-based approaches that generate cell type labels solely through mapping query data to reference data. However, these approaches lack multi-scale descriptions and interpretations of identified cell types. Here, we propose Cell Decoder, a biological prior knowledge informed model to achieve multi-scale representation of cells. We implemented automated machine learning and post-hoc analysis techniques to decode cell identity. We have shown that Cell Decoder compares favourably to existing methods, offering multi-view interpretability for decoding cell identity and data integration. Furthermore, we have showcased its applicability in uncovering novel cell types and states in both human bone and mouse embryonic contexts, thereby revealing the multi-scale heterogeneity inherent in cell identities.
Deep computer vision reveals the mediation of thermal-melanism and body size by precipitation and sex in a threatened alpine butterfly,Parnassius smintheus
Authors: Shirey Vaughn , Goswami Rhea , Latronica Greg , Goudarzi Arshan , Neupane Naresh , Breed Greg A. , Ries Leslie
Published: February 2024

Insect morphologies are strongly tied to selective forces, yet due to variation in these forces and finite resources, insects must strategically invest in select morphologies while deprioritizing others. Melanism and body size may be one such potential trade-off that insects navigate and these two factors are important for fecundity, dispersal, thermoregulation, anti-desiccation, and immunity. In this work, we examined how sex and environmental factors mediate a potential body-size/melanism trade-off in the cold-adapted butterflyParnassius smintheus(Lepidoptera: Papilionidae). We used deep computer vision approaches and museum specimen photography to process over 1,000 images of the species. We found that body-size and melanism are strongly mediated by temperature and elevation (thermal-melanism hypothesis) and that precipitation mediates these slopes for males and females differently. Notably, under the wettest conditions, females exhibit stronger concordance with the thermal-melanism hypothesis while the relationship for males is inverted, suggesting increased competition among males in cold-wet environments. Our results highlight the importance of considering sex when examining how the environment influences intraspecific morphological variation, especially under projected scenarios of global climate change.
DeleteomeTools: Utilizing a compendium of yeast deletion strain transcriptomes to identify co-functional genes
Authors: Neal Maxwell L. , Choudhry Sanjeev K. , Aitchison John D.
Published: February 2024

We introduce DeleteomeTools, an R package that leverages the Deleteome compendium of yeast single-gene deletion transcriptomes to predict gene function. Primarily, the package provides functions for identifying similarities between the transcriptomic signatures of deletion strains, thereby associating genes of interest with others that may be functionally related. We describe how our software predicted a novel relationship between the yeast nucleoporin Nup170 and the Ctf18-RFC complex, which was confirmed experimentally, revealing a previously unknown link between nuclear pore complexes and the DNA replication machinery. To assess the package’s broader predictive capabilities, we performed a systematic evaluation that tested how well it predicted Gene Ontology (GO) annotations already applied to the subset of genes deleted in Deleteome strains. We show that our package predicted a majority of reported GO:biological processannotations with semantic similarities ranging from moderate to identical. We also discuss how our strategy for quantifying similarity between deletion strains, which relies on differential expression signatures, differs from other approaches that use global expression profiles and why it has the potential to identify functional relationships that might otherwise go undetected.
Statistical modelling of seafood fraud in the Canadian supply chain
Authors: Phillips Jarrett D. , De Vuono-Fraser Fynn A.
Published: February 2024

Abstract

Seafood misrepresentation, encompassing product adulteration, mislabelling, and substitution, among other fraudulent practices, has been rising globally over the past decade, greatly impacting both the loss of important fish species and the behaviour of human consumers alike. While much effort has been spent attempting to localise the extent of seafood mislabelling within the supply chain, strong associations likely existing among key players have prevented timely management and swift action within Canada and the USA in comparison to European nations. To better address these shortcomings, herein frequentist and Bayesian logistic Generalised Linear Models (GLMs) are developed in R and Stan for estimation, prediction and classification of product mislabelling in Metro Vancouver, British Columbia, Canada. Obtained results based on odds ratios and probabilities paint a grim picture and are consistent with general trends found in past studies. This work paves the way to rapidly assess the current state of knowledge surrounding seafood fraud nationally and on a global scale using established statistical methodology.
Complementary human gene interaction maps from radiation hybrids and CRISPRi
Authors: Smith Desmond J.
Published: February 2024

The only comprehensive genetic interaction map of the human genome was constructed using increased gene copy number in radiation hybrid (RH) cells. More recently, interactions restricted to essential genes were identified using loss-of-function alleles made by CRISPRi technology. Here, the two maps are compared to understand their similarities and differences. Both maps overlapped significantly with a database of protein-protein interactions. However, interactions in the RH and CRISPRi datasets had no significant overlap, even though the participating genes overlapped significantly. In addition, the RH map showed highly significant similarity with an interaction map constructed from genome-wide association studies (GWASs), while the CRISPRi map did not. This study reveals the different aspects of the genetic interaction landscape illuminated by gain- and loss-of-function alleles.
Genetic architecture and adaptation of Ladakh highlanders of trans-Himalayas
Authors: Kumar Lomous , Rajpal Richa , Ahlawat Bhavna , Pasupuleti Nagarjuna , Konar Snigdha , Dwivedi Aparna , Kumar Sachin , Spalzin Sonam , Rabyang Stanzen , Thangaraj Kumarasamy , Rai Niraj
Published: February 2024

Trans-Himalayan Ladakh has witnessed complex cultural movements and demographic changes since the Neolithic period, which is still continue despite the harsh, inhospitable and cold climate. Although geographically isolated from mainland South Asia, Ladakh has historic trade routes and is well connected and accessible to travelers from Tibet and Central Asia. Despite its rich cultural heritage, a detailed description of the genetic landscape of the Ladakh region is completely lacking, particularly with regard to genome-wide analysis and larger sample sizes. Therefore, in the current study, we genotyped 80 individuals from Kargil and Leh districts of the Union Territory of Ladakh, India. Here, we performed a comprehensive genetic analysis based on allele frequency and haplotype sharing. Our analysis revealed the presence of two distinct genetic lineages in the region with quite distinct genetic composition. The population of Leh Region is more similar to East Asian and Southeast Asian populations. In contrast, the population of the Kargil Region (LDKLA) is more similar to Indo-European populations. Demographic modeling suggests that the Leh group shares a genetic history with Tibetans, while the Kargil group showed great affinities with Kashmiri Muslims, Gujjars and Nepalese Brahmins, and both showed recent admixture. Both groups have experienced a founder event around during 11th to 22nd generations ago, the duration of which coincided with the Mughal invasion. The genome-wide scan for a signal of positive selection revealed genetic signatures of high-altitude adaptation (EPAS1andELMO2) in the Leh population, while in the Kargil population the key gene signatures were associated with immunity and female fertility.
Effect of Urinary tract infection on the outcome of the Allograft in patients with Renal transplantation
Authors: Gangula Rahul Sai , Eswarappa Mahesh , Reddy Rajashekar , Siddaiah Gireesh Mathihally , Konana Gurudev , Reddy Hamsa , Prabhu Pooja Prakash , Mohammad Yousuff , Anish Lia Sara
Published: February 2024

Background

Urinary Tract Infections (UTIs) are the second most common cause of graft dysfunction, accounting for significant morbidity, and are associated with poor graft and patient survival. This study aimed to determine the association between post-renal transplant UTI and graft outcomes.

Methods

We examined the effect of UTIs on graft outcomes in patients who underwent renal transplantation surgery between January 2010 and December 2022. The study population included 349 renal transplantations, of which 74 experienced 140 UTI events. Based on the number of UTI episodes, patients were categorized into three groups

Results

Of the 349 recipients, 275 (74.4%) had no UTI, 47 (18.8%) had nonrecurrent UTIs (NR-UTIs), and 27 (6.8%) had Recurrent UTIs (R-UTIs). NR-UTIs were associated with very poor graft survival compared with no UTI (Hazard Ratio [HR], 2.312; 95% Confidence Interval [CI], 1.410–3.791; P=0.001). This relationship persisted even after adjusting for confounding factors in Multivariable Cox regression analysis (HR, 2.318; 95% CI, 1.414–3.800; P=0.001). Although R-UTIs appeared to result in poor patient survival, the difference was not significant (vs No UTI, HR, 1.517; 95% CI, 0.983–2.342; P=0.060). There appeared to be higher patient survival in R-UTIs but was not significant (vs NR-UTI, HR, 1.316; 95% CI, 0.486–3.564; P=0.589). R-UTIs were more likely to be associated with Multi-drug Resistant Gram-negative organisms (Klebsiella pneumonia or Escherichia coli) with resistance to Nitrofurantoin (RR, 2.753; 95% CI, 1.257–6.032; P=0.01) and Carbapenem (RR, 2.064; 95% CI, 0.988–4.314; P=0.05).

Conclusion

NR-UTIs were associated with poorer graft and patient outcomes than no UTI.
Simple Models Versus Deep Learning in Detecting Low Ejection Fraction From The Electrocardiogram
Authors: Hughes J. Weston , Somani Sulaiman , Elias Pierre , Tooley James , Rogers Albert J. , Poterucha Timothy , Haggerty Christopher M. , Ouyang David , Ashley Euan , Zou James , Perez Marco V.
Published: February 2024

Importance

Deep learning methods have recently gained success in detecting left ventricular systolic dysfunction (LVSD) from electrocardiogram waveforms. Despite their impressive accuracy, they are difficult to interpret and deploy broadly in the clinical setting.

Objective

To determine whether simpler models based on standard electrocardiogram measurements could detect LVSD with similar accuracy to deep learning models.

Design

Using an observational dataset of 40,994 matched 12-lead electrocardiograms (ECGs) and transthoracic echocardiograms, we trained a range of models with increasing complexity to detect LVSD based on ECG waveforms and derived measurements. We additionally evaluated models in two independent cohorts from different medical centers, vendors, and countries.

Setting

The training data was acquired from Stanford University Medical Center. External validation data was acquired from Cedars-Sinai Medical Center and the UK Biobank.

Exposures

The performance of models based on ECG waveforms in their detection of LVSD, as defined by ejection fraction below 35%.

Main outcomes

The performance of the models as measured by area under the receiver operator characteristic curve (AUC) and other measures of classification accuracy.

Results

The Stanford dataset consisted of 40,994 matched ECGs and echocardiograms, the test set having an average age of 62.13 (17.61) and 55.20% Male patients, of which 9.72% had LVSD. We found that a random forest model using 555 discrete, automated measurements achieves an area under the receiver operator characteristic curve (AUC) of 0.92 (0.91-0.93), similar to a deep learning waveform model with an AUC of 0.94 (0.93-0.94). Furthermore, a linear model based on 5 measurements achieves high performance (AUC of 0.86 (0.85-0.87)), close to a deep learning model and better than NT-proBNP (0.77 (0.74-0.79)). Finally, we find that simpler models generalize better to other sites, with experiments at two independent, external sites.

Conclusion

Our study demonstrates the value of simple electrocardiographic models which perform nearly as well as deep learning models while being much easier to implement and interpret.
Community-level Knowledge, Attitudes, and Practices regarding Cardiovascular Diseases and Modifiable Risk Factors in India
Authors: Singh Kavita , Kondal Dimple , Mohan Deepa , Gandral Mareesha , Rajan Sheril , Mohan Viswanathan , Ali Mohammed K , Venkat Narayan KM , Huffman Mark D. , Prabhakaran Dorairaj , Tandon Nikhil
Published: February 2024

Background

Assessment of knowledge, attitudes, and practices (KAP) regarding cardiovascular diseases (CVD) and cardiovascular risk factors (CVRF) is critical to inform CVD prevention strategies, but limited community-level data exist from developing countries.

Methods and Results

We conducted a telephone-based survey nested in the on-going CARRS cohort in Delhi and Chennai, India between January 2021 to February 2021. We randomly selected people with CVRF, but no established CVD and those with existing CVD from the CARRS cohort and assessed their 1) knowledge of CVD symptoms and risk factors, 2) attitude towards non-physician health workers (NPHW) facilitated care and text-messages for healthy lifestyle, and 3) practices regarding monitoring of CVRF. We performed logistic regression analyses to investigate the factors associated with KAP. We interviewed 502 participants (283 with CVRF and 219 with CVD); 45.8% were female, and mean age (SD) was 48.1 (11.2) years. The knowledge of heart attack symptoms, stroke symptoms, and CVRF (>75% correct answers) were: 12.9%, 20.7%, and 17.3%, respectively. Individuals with CVRF had 2.5 times lower knowledge of CVD symptoms compared to those with existing CVD. Acceptability of NPHW-facilitated care and text-messages for healthy lifestyle was 60% and 84%, respectively.

Conclusions

The knowledge of CVD symptoms and risk factors is below optimal levels, particularly among individuals at high risk of CVD, unskilled workers, those with lower levels of education and income. Innovative use of NPHW along with mHealth tools could potentially offer solutions to reduce the burden of CVD.
Benzodiazepine Initiation and the Risk of Falls or Fall-Related Injuries in Older Adults Following Acute Ischemic Stroke
Authors: Sun Shuo , Lomachinsky Victor , Smith Louisa H. , Newhouse Joseph P. , Westover M. Brandon , Blacker Deborah , Schwamm Lee , Haneuse Sebastien , Moura Lidia M.V.R.
Published: February 2024

Background

Benzodiazepine use in older adults following acute ischemic stroke (AIS) is common, yet short-term safety concerning falls or fall-related injuries remains unexplored.

Methods

We emulated a hypothetical randomized trial of benzodiazepine use during the acute post stroke recovery period to assess incidence of falls or fall related injuries in older adults. Using linked data from the Get With the Guidelines Registry and Mass General Brigham’s electronic health records, we selected patients aged 65 and older admitted for Acute Ischemic Stroke (AIS) between 2014 and 2021 with no documented prior stroke and no benzodiazepine prescriptions in the previous 3 months. Potential for immortal-time and confounding biases was addressed via separate inverse-probability weighting strategies.

Results

The study included 495 patients who initiated inpatient benzodiazepines within three days of admission and 2,564 who did not. After standardization, the estimated 10-day risk of falls or fall-related injuries was 694 events per 1000 (95% confidence interval CI: 676-709) for the benzodiazepine initiation strategy and 584 events per 1000 (95% CI: 575-595) for the non-initiation strategy. Subgroup analyses showed risk differences of 142 events per 1000 (95% CI: 111-165) and 85 events per 1000 (95% CI: 64-107) for patients aged 65 to 74 years and for those aged 75 years or older, respectively. Risk differences were 187 events per 1000 (95% CI: 159-206) for patients with minor (NIHSS≤ 4) AIS and 32 events per 1000 (95% CI: 10-58) for those with moderate-to-severe AIS.

Conclusions

Initiating inpatient benzodiazepines within three days of AIS is associated with an elevated 10-day risk of falls or fall-related injuries, particularly for patients aged 65 to 74 years and for those with minor strokes. This underscores the need for caution with benzodiazepines, especially among individuals likely to be ambulatory during the acute and sub-acute post-stroke period.
The cost of arteriovenous fistula placement in patients with chronic end-stage renal disease in Ouagadougou (Burkina Faso) 2020
Authors: Toure Amadou Oury , Yanne Tapsoba , Bocoum Fadima Yaya , Kouanda Seni
Published: February 2024

End-stage renal disease (ESRD) is a late diagnosis. Its prevalence is rapidly increasing worldwide. Although various management techniques exist, they all require access routes. The arteriovenous fistula (AVF) is the vascular access of choice for regular and prolonged hemodialysis sessions. Studies have shown that an AVF saves patients money. In our context, we found no data in the literature on the cost of AVF and the lump-sum cost. The aim of this study was to determine the average costs of AVF and lump-sum costs, and to describe patients’ coping strategies in relation to these costs.

Methods

We conducted a cross-sectional study in the three public hemodialysis units of the city of Ouagadougou, Burkina Faso. Hemodialysis patients suffering from chronic renal failure, hospitalized or not, minors or adults having given their consent (assent) were included in the study.

Results

A total of 290 patients ranging in age from 12 to 82 years participated in the study. Almost half the patients (47.5%) had no income. More than half the patients had undergone fistula repair privately. Hypertension and diabetes were the pathologies most frequently associated with end-stage renal disease in this study, with 77% and 16.90% respectively. The average cost of a fistula was 260,798 Fcfa, while the average cost of a package was 506,459 Fcfa. To cope with these costs, some patients resorted to selling goods (means of subsistence) in 4.83%, borrowing, bartering and others begging.

Conclusion

The average cost of arteriovenous fistula and the fixed fee for haemodialysis remain an economic barrier for patients and families to haemodialysis in Burkina Faso. More than half of all patients have their fistulas done in the private sector, which costs twice as much as the public sector. Training providers working in public haemodialysis units to perform arteriovenous fistula is necessary to reduce this cost for patients.
Regulatory divergences in dosage compensation cause hybrid male inviability inCaenorhabditis
Authors: Li Yongbin , Gao Yimeng , Ma Jiaonv , Gao Yifan , Zhou Wangyan , Zhang Hantang , Shao Wenhua , Liu Zhijin , Zhao Zhongying , Liu Xiao
Published: February 2024

The genetic basis of Haldane’s rule, such as hybrid male incompatibility in XX systems, has long remained elusive. Here, we found that crosses ofCaenorhabditis nigonimales withC. briggsaefemales result in insufficient expression ofCbr-xol-1, an X-linked master switch responsible for sex determination, consequently activating aberrant dosage compensation in males, and ultimately leading to embryonic inviability. Three compensatory divergences result in comparablexol-1expression levels between the parental species but lethalCbr-xol-1underexpression in hybrid male embryos: 1) a less activeCbr-xol-1promoter than itsC. nigoniortholog; 2) loss of an X-linkedxol-1paralog inC. briggsae; and 3) pseudogenization of aC. briggsaeautosomal repressor ofxol-1. Our results define an evolutionary scenario of sexual incompatibility leading to hybrid male inviability.
Convergent within-host evolution alters key virulence factors in aKlebsiella pneumoniaeclone during a large hospital outbreak
Authors: Zaborskytė Greta , Hjort Karin , Lytsy Birgitta , Sandegren Linus
Published: February 2024

Bacterial pathogens adapt to host niches because of within-host selective pressures, and this evolutionary process provides valuable insights into host-pathogen interactions. However, genetic changes underlying adaptive phenotypes are difficult to identify from data generated by genome-wide association studies of unrelated bacterial clones. Here, we followed the evolution of a singleKlebsiella pneumoniaeclone in 110 patients during a 5-year nosocomial outbreak by combining comparative genomics with phenotypic characterization. Strong positive within-patient selection targeted key virulence factors in isolates from infection sites. The clone repeatedly lost acute virulence primarily via alterations in capsule and lipopolysaccharide, changed regulation of iron uptake, and increased biofilm formation. These phenotypes represent likely niche adaptations, mainly to the urinary tract, and some were associated with trade-offs during gastrointestinal colonization. The substantial convergent evolution reflects the trajectories undertaken by high-risk clones ofK. pneumoniaeand other pathogens adapting during acute and chronic infections.
A real-time, high-performance brain-computer interface for finger decoding and quadcopter control
Authors: Willsey Matthew S. , Shah Nishal P. , Avansino Donald T. , Hahn Nick V. , Jamiolkowski Ryan M. , Kamdar Foram B. , Hochberg Leigh R. , Willett Francis R. , Henderson Jaimie M.
Published: February 2024

People with paralysis express unmet needs for peer support, leisure activities, and sporting activities. Many within the general population rely on social media and massively multiplayer video games to address these needs. We developed a high-performance finger brain-computer-interface system allowing continuous control of 3 independent finger groups with 2D thumb movements. The system was tested in a human research participant over sequential trials requiring fingers to reach and hold on targets, with an average acquisition rate of 76 targets/minute and completion time of 1.58 ± 0.06 seconds. Performance compared favorably to previous animal studies, despite a 2-fold increase in the decoded degrees-of-freedom (DOF). Finger positions were then used for 4-DOF velocity control of a virtual quadcopter, demonstrating functionality over both fixed and random obstacle courses. This approach shows promise for controlling multiple-DOF end-effectors, such as robotic fingers or digital interfaces for work, entertainment, and socialization.
Old, broad-leaved stands support both high biodiversity and carbon storage in German forests
Authors: Springer K. , Manning P. , Boesing A.L. , Ammer C. , Fiore-Donno A.M. , Fischer M. , Goldmann K. , Le Provost G. , Overmann J. , Ruess L. , Schöning I. , Seibold S. , Sikorski J. , Neyret M.
Published: February 2024

Ecosystems worldwide face threats related to human-driven degradation, climate change, and biodiversity loss. Addressing these challenges requires management strategies that combine biodiversity conservation with climate change mitigation. Here, we aimed to identify local-scale management actions that promote biodiversity at multiple trophic levels while also promoting carbon storage and sequestration. We combined data on the diversity of nine taxonomic groups (plants, birds, moths, Mollusca, soil fungi, active soil bacteria, Cercozoan and Endomyxan soil protists, Oomycotan soil protists, and nematodes), with above- and belowground carbon storage in 150 temperate forest plots in three regions of Germany. These were dominated by European beech, pine, spruce and oak. We investigated the relationships between multiple forest structure and management variables, biodiversity and carbon storage and sequestration in forest plots with different management types. Carbon storage was 32% higher in uneven-aged than even-aged forests and increased with mean tree diameter, while carbon sequestration in trees was 15% higher in even-aged than uneven-aged stands. Mean tree diameter was positively related to overall biodiversity, especially bird species richness and the richness of forest specialist birds. Oak and beech-dominated stands harboured higher biodiversity than stands dominated by conifers (especially Pine). One exception to this was the richness of plant species and forest specialist plants, which were highest in spruce plantations. Surprisingly, deadwood input did not significantly affect the diversity of any taxonomic group in this study. By showing that older forests with a high proportion of uneven-aged broad-leafed trees, or oak-dominated forests, can promote both biodiversity and carbon storage, our results could help inform sustainable local-scale forest management in Central Europe that promotes both biodiversity conservation and carbon storage. These findings can form the basis of further larger-scale studies investigating such relations at larger spatial scales to inform landscape-level recommendations for sustainable multifunctional forest management.
Effort Drives Saccade Selection
Authors: Koevoet Damian , Van Zantwijk Laura , Naber Marnix , Mathôt Sebastiaan , Van der Stigchel Stefan , Strauch Christoph
Published: February 2024

What determines where to move the eyes? We recently showed that pupil size, a well-established marker of effort, also reflects the effort associated with making a saccade ('saccade costs'). Here we demonstrate saccade costs to critically drive saccade selection: when choosing between any two saccade directions, the least costly direction was consistently preferred. Strikingly, this principle even held during search in natural scenes in two additional experiments. When increasing cognitive demand experimentally through an auditory counting task, participants made fewer saccades and especially cut costly directions. This suggests that the eye-movement system and other cognitive operations consume similar resources that are flexibly allocated among each other as cognitive demand changes. Together, we argue that eye-movement behavior is tuned to adaptively minimize saccade-inherent effort.
CD81-guided heterologous EVs present heterogeneous interactions with breast cancer cells
Authors: Gurrieri Elena , Carradori Giulia , Roccuzzo Michela , Pancher Michael , Peroni Daniele , Belli Romina , Trevisan Caterina , Notarangelo Michela , Huang Wen-Qiu , Carreira Agata SA , Quattrone Alessandro , Jenster Guido , Ten Hagen Timo L.M. , D’Agostino Vito Giuseppe
Published: February 2024

Extracellular vesicles (EVs) are cell-secreted particles conceived as natural vehicles for intercellular communication. The intrinsic biocompatibility, stability in biofluids, and heterogeneous molecular cargo of EVs promise advancements in targeted therapy applications. However, predicting cell-targeting spectrum and cargo delivery are fundamental challenges for exploiting EVs or hybrid formulations. In this work, we combined cell-based and biochemical approaches to understand if secreted EVs show predictable EV-cell interactions and consequent cargo delivery. We exploited the tetraspanin CD81 to encode full-length recombinant proteins with a C-terminal GFP reporter encompassing or not Trastuzumab light chains targeting the HER2 receptor. These fusion proteins participated in vesicular trafficking dynamics and accumulated on secreted EVs when transiently over-expressed in HEK293T cells. Despite the presence of GFP, secreted EV populations retained a HER2 receptor-binding capacity and were used in EV-cell interaction assays. In time-frames where the global GFP spot distribution did not change between HER2-positive (SK-BR-3) or –negative (MDA-MB-231) breast cancer cell lines, the HER2 manipulation in isogenic cells remarkably affected the tropism of heterologous EVs. In this line, secreted doxorubicin-EVs, which showed improved efficacy compared to the free drug, had a reduced cell-killing activity on SK-BR-3 with a knocked-out HER2 receptor. Interestingly, the fusion protein-corresponding transcripts also present as full-length mRNAs in recombinant EVs could reach orthotopic breast tumors in JIMT-1-xenografted mice, as detected by ddPCR in tissue biopsies, improving our sensitivity in detecting bioavailable cargoes. These data show multiple mechanisms underlying EV-cell interactions and prioritize the profiling of surfaceomes for better comprehension of cell engagement and design new generations of EV-based nanovehicles.
Assessment of salivary microRNA by RT-qPCR: Challenges in data interpretation for clinical diagnosis
Authors: Van Der Hofstadt Marc , Cardinal Anna , Lepeltier Morgane , Boulestreau Jérémy , Ouedraogo Alimata , Kahli Malik , Champigneux Pierre , Molina Laurence , Molina Franck , Ngoc Van Thi Nhu
Published: February 2024

Salivary microRNAs (miRNAs) have been recently revealed as the next generation of non-invasive biomarkers for the diagnostics of diverse diseases. However, their short and highly homologous sequences make their quantification by RT-qPCR technique highly heterogeneous and study dependent, thus limiting their implementation for clinical applications. In this study, we evaluated the use of a commercial RT-qPCR kit for quantification of salivary miRNAs for clinical diagnostics.

Methods

Saliva was sampled from ten healthy volunteers for a time course analysis. A panel of six miRNA targets (with different sequence homologies) were analysed by one of the most commonly used commercially available RT-qPCR kit. Sensitivity and specificity of the tested miRNA assays were corroborated using synthetic miRNAs. The reliability of all tested assays to differentiate miRNA expression profiles were analysed, to statistically discriminate background noise from intrinsic individual signals.

Results

Significant variabilities in expression profiles of six miRNAs from ten healthy participants were revealed, yet the poor specificity of the assays offered insufficient performance to associate these differences to biological context. Indeed, as the limit of quantification (LOQ) concentrations are from 2-4 logs higher than that of the limit of detection (LOD), the majority of the analysis for salivary miRNAs felt outside the quantification region. Most importantly, a remarkable number of crosstalk reactions exhibiting considerable OFF target signal intensities was detected, indicating their poor specificity and limited reliability. However, the spike-in of synthetic miRNA increased the capacity to discriminate endogenous salivary miRNA at the LOQ concentrations from those that were significantly lower.

Conclusions

Our results demonstrate that comparative analyses for salivary miRNA expression profiles by this commercial RT-qPCR kit are most likely associated to technical limitations rather than to biological differences. In particular, assessment of fundamental parameters including LOD, LOQ and crosstalk of each assay is strictly necessary to interpret observed variations. The standardization of rigorous sample handling and experimental design according to technical parameters of each assay plays a crucial role in reducing data inconsistencies across studies. However, further technological breakthroughs are still required to overcome discrepancies in order to accelerate the translation of salivary miRNAs for clinical applications.
Kinase activity of histone chaperone APLF maintains steady state of centrosomes in mouse embryonic stem cells
Authors: Rajam Sruthy Manuraj , Varghese Pallavi Chinnu , Shirude Mayur Balkrishna , Syed Khaja Mohieddin , Devarajan Anjali , Natarajan Kathiresan , Dutta Debasree
Published: February 2024

Our recent studies revealed the role of mouse Aprataxin PNK-like Factor (APLF) in development. Nevertheless, the comprehensive characterization of mouse APLF remains entirely unexplored. Based on domain deletion studies, here we report that mouse APLF’s Acidic Domain and Fork Head Associated (FHA) domain can chaperone histones and repair DNA like the respective human orthologs. Immunofluorescence studies in mouse embryonic stem cells showed APLF co-localized with γ-tubulin within and around the centrosomes and govern the number and integrity of centrosomes via PLK4 phosphorylation. Enzymatic analysis established mouse APLF as a kinase. Docking studies identified three putative ATP binding sites within the FHA domain. Site-directed mutagenesis showed that R37 residue is indispensable for the kinase activity of APLF thereby regulating the centrosome number. These findings might assist us comprehend APLF in different pathological and developmental conditions and reveal non-canonical kinase activity of proteins harbouring FHA domains that might impact multiple cellular processes.
Peripheral mutations underlie promiscuous transport of quaternary ammonium antiseptics by Small Multidrug Resistance transporters
Authors: Burata Olive E. , O’Donnell Ever , Hyun Jeonghoon , Lucero Rachael M. , Thomas Junius E. , Gibbs Ethan M. , Reacher Isabella , Carney Nolan A. , Stockbridge Randy B.
Published: February 2024

The mechanistic basis of transport promiscuity in multidrug exporters is not well understood. We examine this question using the Small Multidrug Resistance (SMR) transporters. We engineer a selective SMR protein to promiscuously export quaternary ammonium antiseptics, similar to multidrug exporters in this family. Using combinatorial mutagenesis and deep sequencing, we identify the necessary and sufficient molecular determinants of this new activity. Using x-ray crystallography, electrophysiology, and a novel proteoliposome-based antiseptic transport assay, we tease apart the mechanistic roles that these residues play in transport polyspecificity. We find that substrate preference changes not through modification of the residues that directly interact with the substrate, but through mutations peripheral to the binding pocket. Our new molecular insights into substrate promiscuity among the SMRs can be applied to understand multidrug export and the evolution of novel transport functions more generally.
Striatal dopamine contributions to skilled motor learning
Authors: Phillips Chris D. , Myers Courtney C. , Leventhal Daniel K. , Burgess Christian R.
Published: February 2024

Coordinated multi-joint limb and digit movements - “manual dexterity” - underlie both specialized skills (e.g., playing the piano) and more mundane tasks (e.g., tying shoelaces). Impairments in dexterous skill cause significant disability, as occurs with motor cortical injury, Parkinson’s Disease, and a range of other pathologies. Clinical observations, as well as basic investigations, suggest that cortico-striatal circuits play a critical role in learning and performing dexterous skills. Furthermore, dopaminergic signaling in these regions is implicated in synaptic plasticity and motor learning. Nonetheless, the role of striatal dopamine signaling in skilled motor learning remains poorly understood. Here, we use fiber photometry paired with a genetically encoded dopamine sensor to investigate striatal dopamine release as mice learn and perform a skilled reaching task. Dopamine rapidly increases during a skilled reach and peaks near pellet consumption. In dorsolateral striatum, dopamine dynamics are faster than in dorsomedial and ventral striatum. Across training, as reaching performance improves, dopamine signaling shifts from pellet consumption to cues that predict pellet availability, particularly in medial and ventral areas of striatum. Furthermore, performance prediction errors are present across the striatum, with reduced dopamine release after an unsuccessful reach. These findings show that dopamine dynamics during skilled motor behaviors change with learning and are differentially regulated across striatal subregions.
Temporal dynamics of BMP/Nodal ratio drive tissue-specific gastrulation morphogenesis
Authors: Emig Alyssa A , Hansen Megan , Grimm Sandra , Coarfa Cristian , Lord Nathan D , Williams Margot Kossmann
Published: February 2024

Anteroposterior (AP) elongation of the vertebrate body plan is driven by convergence and extension (C&E) gastrulation movements in both the mesoderm and neuroectoderm, but how or whether molecular regulation of C&E differs between tissues remains an open question. Using a zebrafish explant model of AP axis extension, we show that C&E of the neuroectoderm and mesoderm can be uncoupledex vivo, and that morphogenesis of individual tissues results from distinct morphogen signaling dynamics. Using precise temporal manipulation of BMP and Nodal signaling, we identify a critical developmental window during which high or low BMP/Nodal ratios induce neuroectoderm- or mesoderm-driven C&E, respectively. Increased BMP activity similarly enhances C&E specifically in the ectoderm of intact zebrafish gastrulae, highlighting thein vivorelevance of our findings. Together, these results demonstrate that temporal dynamics of BMP and Nodal morphogen signaling activate distinct morphogenetic programs governing C&E gastrulation movements within individual tissues.

SUMMARY STATEMENT

Using zebrafish embryo and explant models, we demonstrate that temporal dynamics of morphogen signaling ratios distinguish between tissue-specific morphogenetic programs during vertebrate body plan formation.
Disease Characteristics Influence the Privacy Calculus to adopt Electronic Health Records: A randomized controlled trial in Germany
Authors: von Kalckreuth Niklas , Feufel Markus
Published: February 2024

Background

The electronic health record (EHR) is integral to improving healthcare efficiency and quality. Its successful implementation hinges on patient willingness to use it, particularly in Germany where concerns about data security and privacy significantly influence usage intention. Little is known, however, about how specific characteristics of medical data influence patients’ intention to use the EHR.

Objective

This study aims to validate the Privacy Calculus Model (PCM) in the EHR context and to assess how personal and disease characteristics, namely disease-related stigma and disease time course, affect PCM predictions.

Methods

An online survey was conducted to empirically validate the PCM for EHR, incorporating a case vignette varying in disease-related stigma (high/low) and time course (acute/chronic), with 241 German participants. The data were analyzed using SEM-PLS.

Results

The model explains R²=71.8% of the variance in intention to use. The intention to use is influenced by perceived benefits, data privacy concerns, trust in the provider, and social norms. However, only the disease’s time course, not stigma, affects this intention. For acute diseases, perceived benefits and social norms are influential, whereas for chronic diseases, perceived benefits, privacy concerns, and trust in the provider influence intention.

Conclusions

The PCM validation for EHRs reveals that personal and disease characteristics shape usage intention in Germany. This suggests the need for tailored EHR adoption strategies that address specific needs and concerns of patients with different disease types. Such strategies could lead to a more successful and widespread implementation of EHRs, especially in privacy-conscious contexts.
Neuropsychology of chronic back pain managed with long-term opioid use
Authors: Baliki Marwan N , Vigotsky Andrew D. , Rached Gaelle , Jabakhanji Rami , Huang Lejian , Branco Paulo , Cong Olivia , Griffith James , Wasan Ajay D. , Schnitzer Thomas J. , Apkarian A. Vania
Published: February 2024

Chronic pain is commonly treated with long-term opioids, but the neuropsychological outcomes associated with stable long-duration opioid use remain unclear. Here, we contrasted the psychological profiles, brain activity, and brain structure of 70 chronic back pain patients on opioids (CBP+O, average opioid exposure 6.2 years) with 70 patients managing their pain without opioids. CBP+O exhibited moderately worse psychological profiles and small differences in brain morphology. However, CBP+O had starkly different spontaneous brain activity, dominated by increased mesocorticolimbic and decreased dorsolateral-prefrontal activity, even after controlling for pain intensity and duration. These differences strongly reflected cortical opioid and serotonin receptor densities and mapped to two antagonistic resting-state circuits. The circuits’ dynamics were explained by mesocorticolimbic activity and reflected negative affect. We reassessed a sub-group of CBP+O after they briefly abstained from taking opioids. Network dynamics, but not spontaneous activity, reflected exacerbated signs of withdrawal. Our results have implications for the management and tapering of opioids in chronic pain.
White matter microstructural changes in adult-onset idiopathic focal cervical dystonia using ultra-strong diffusion gradient MRI
Authors: MacIver CL , Jones DK , Green K , Szewczyk-krolikowski K , Doring A , Tax CMW , Peall KJ
Published: February 2024

Background and Objectives

Adult-onset idiopathic focal cervical dystonia (AOIFCD) involves loss of co-ordinated contraction of the cervical musculature, resulting in pain, impaired function and in some individuals, an associated head tremor. Existing neuroimaging studies have implicated key motor networks. However, measures used to date lack specificity in detailing the underlying pathophysiological differences.

Methods

A cohort of individuals diagnosed with AOIFCD and an age- and sex-matched control group were prospectively recruited. All participants underwent MRI using structural and diffusion sequences with multiple b-values up to 30,000 s/mm2, coupled with motor and non-motor clinical phenotyping. Tractography was performed assessing whole tract median values, while tractometry was used for along tract analysis. Key white matter motor pathways were assessed initially using general measures (DTI/DKI: FA-fractional anisotropy; MD-mean diffusivity; MK-mean kurtosis; AK-axial kurtosis; RK-radial kurtosis) with subsequent microstructural white matter modelling approaches (NODDI: ODI-orientation distribution index, NDI-neurite density index, FWF-free water fraction; and standard model:f-intra-axonal signal fraction, Da-intra axonal diffusivity, Depar-extra axonal parallel diffusivity, Deperp-extra axonal perpendicular diffusivity,p2-orientation coherence) and unconstrained high b-value zero-order spherical harmonic signal (R0, related to intra-axonal signal) to assess differences within these tracts. Subgroup analyses were undertaken comparing those with and without associated head tremor to the control cohort.

Results

50 AOIFCD and 30 healthy control participants underwent structural brain MRI, with 46 AOIFCD and 30 healthy controls included for analysis (33 without head tremor, 13 with head tremor). Significant differences were observed in the anterior thalamic radiations (lower mid tract FA, RK,fandp2and higher ODI), thalamopremotor tracts (mid tract higher MK and lower NDI, and distal tract lower ODI and higherf) and striatopremotor tracts (proximal lowerfand R0). These measures correlated with symptom severity across the spectrum with clinical measures, including psychiatric symptoms, sleep quality, pain and cognitive functioning.

Discussion

Overall, localised microstructural differences were identified within tracts linking the prefrontal cortex and premotor cortex with basal ganglia regions, suggesting microstructural aberrances of motor system modulatory pathways, particularly in relation to intra-axonal and fibre orientation dispersion measures.
Reliance on vision for walking balance is related to somatosensory deficits in individuals with cerebral palsy
Authors: Sansare Ashwini , Reimann Hendrik , Bodt Barry , Arcodia Maelyn , Verma Khushboo , Jeka John , Lee Samuel C.K.
Published: February 2024

Aim

To investigate the relationship between somatosensory deficits, specifically ankle and hip joint position sense, two-point discrimination, and vibration on the (1) responses to visual perturbations during walking and (2) response improvements to visual perturbations while receiving a sensory-centric treatment, i.e., stochastic resonance (SR) stimulation, in individuals with and without cerebral palsy (CP).

Methods

Twenty-eight individuals (14 CP, 14 age-and sex-matched controls) walked in a virtual reality cave while receiving visual perturbations. We applied SR to the ankle and hip joints. Data analysis consisted of bivariate correlations, and multiple regression analysis (MRA) using all four sensory tests as predictors with the responses to visual perturbation and the improvements in the responses when SR is applied as outcomes.

Results

We found significant and strong correlations between performance on sensory tests and the responses to visual perturbations, and improvements in the responses with SR. Only one predictor could be entered into the MRA, indicating that performance on any of the sensory tests could predict the responses to visual perturbation and the improvements with SR.

Interpretation

Individuals with sensory deficits are more responsive to sensory-centric interventions. This study is an initial step in identifying potential “responders” to sensory therapies in individuals with CP.