bluuebunny/crossref_metadata_2025 huggingface dataset:
Multivariate analysis of multimodal brain structure predicts individual differences in risk and intertemporal preference
Authors: Bergström Fredrik , Schu Guilherme , Lee Sangil , Lerman Caryn , Kable Joseph W.
Published: July 2024

Large changes to brain structure (e.g., from damage or disease) can explain alterations in behavior. It is therefore plausible that smaller structural differences in healthy samples can be used to better understand and predict individual differences in behavior. Despite the brain’s multivariate and distributed structure-to-function mapping, most studies have used univariate analyses of individual structural brain measures. Here we used a multivariate approach in a multimodal data set composed of volumetric, surface-based, diffusion-based, and functional resting-state MRI measures to predict reliable individual differences in risk and intertemporal preferences. We show that combining twelve brain structure measures led to better predictions across tasks than using any individual measure, and by examining model coefficients, we visualize the relative contribution of different brain measures from different brain regions. Using a multivariate approach to brain structure-to-function mapping that combines across many brain structure properties, along with reliably measured behavior phenotypes, may increase out-of-sample prediction accuracies and insight into neural underpinnings. Furthermore, this methodological approach may be useful to improve predictions and neural insight across basic, translational, and clinical research fields.
Quantitative Analysis of Miniature Synaptic Calcium Transients Using Positive Unlabeled Deep Learning
Authors: Beaupré Frédéric , Bilodeau Anthony , Wiesner Theresa , Leclerc Gabriel , Lemieux Mado , Nadeau Gabriel , Castonguay Katrine , Fan Bolin , Labrecque Simon , Hložek Renée , De Koninck Paul , Gagné Christian , Lavoie-Cardinal Flavie
Published: July 2024

Ca2+imaging methods are widely used for studying cellular activity in the brain, allowing detailed analysis of dynamic processes across various scales. Enhanced by high-contrast optical microscopy and fluorescent Ca2+sensors, this technique can be used to reveal localized Ca2+fluctuations within neurons, including in sub-cellular compartments, such as the dendritic shaft or spines. Despite advances in Ca2+sensors, the analysis of miniature Synaptic Calcium Transients (mSCTs), characterized by variability in morphology and low signal-to-noise ratios, remains challenging. Traditional threshold-based methods struggle with the detection and segmentation of these small, dynamic events. Deep learning (DL) approaches offer promising solutions but are limited by the need for large annotated datasets. Positive Unlabeled (PU) learning addresses this limitation by leveraging unlabeled instances to increase dataset size and enhance performance. This approach is particularly useful in the case of mSCTs that are scarce and small, associated with a very small proportion of the foreground pixels. PU learning significantly increases the effective size of the training dataset, improving model performance. Here, we present a PU learning-based strategy for detecting and segmenting mSCTs. We evaluate the performance of two 3D deep learning models, StarDist-3D and 3D U-Net, which are well established for the segmentation of small volumetric structures in microscopy datasets. By integrating PU learning, we enhance the 3D U-Net’s performance, demonstrating significant gains over traditional methods. This work pioneers the application of PU learning in Ca2+imaging analysis, offering a robust framework for mSCT detection and segmentation. We also demonstrate how this quantitative analysis pipeline can be used for subsequent mSCTs feature analysis. We characterize morphological and kinetic changes of mSCTs associated with the application of chemical long-term potentiation (cLTP) stimulation in cultured rat hippocampal neurons. Our data-driven approach shows that a cLTP-inducing stimulus leads to the emergence of new active dendritic regions and differently affects mSCTs subtypes.
Azole resistance: Patterns of amino acid substitutions inCandidasterol 14α-demethylase
Authors: Prasad Rao R. Shyama , Pinto Larina , Shastry Rajesh P. , Dakal Tikam Chand , Suravajhala Prashanth N. , Sashindran V. K. , Ghate Sudeep D.
Published: July 2024

The emergence of azole-resistantCandidainfections is a major concern. A key mechanism is the gain of resistance through amino acid substitutions in the sterol 14α-demethylase, the main target of azole drugs. While numerous resistant substitutions are known, the pattern of such substitutions is unclear. We hypothesized that the resistant substitutions occur disproportionately at the azole-binding sites. We compiled 2,222 instances of azole-resistant substitutions from the literature and performed extensive computational sequence analyses. Altogether there were 169 known substitutions at 133 sites in sterol 14α-demethylases of sevenCandidaspecies, whereasC. albicansalone had 120 substitutions at 97 sites. Just 10 sites and 18 substitutions (such as Y132F/H, K143R, D116E, and G464S) accounted for 75% of the total instances. Only about 48% of the sites were present within the previously recognized hotspot regions, while just 33% of the known azole-interacting residues had known resistant substitutions, most of them with only a few instances. The literature data on azole-resistant substitutions inCandidaappear to be highly biased as a few substitutions such as Y132F/H and K143R were preferentially sought and reported with over 1000 instances, while there were also numerous reports of “resistant” substitutions in azole-susceptibleCandidaisolates. Our study provides interesting perspectives into azole resistance.
Photopharmacological activation of adenosine A1receptor signaling suppresses seizures in a mouse model for temporal lobe epilepsy
Authors: Spanoghe Jeroen , Boon Paul , Vergaelen Marijke , Colvenaer Maren De , Mariman Tina , Vonck Kristl , Carrette Evelien , Wadman Wytse , Craey Erine , Larsen Lars E. , Sprengers Mathieu , Missinne Jeroen , Calenbergh Serge Van , Bundel Dimitri De , Smolders Ilse , Raedt Robrecht
Published: July 2024

Up to 30% of epilepsy patients suffer from drug-resistant epilepsy (DRE). The search for innovative therapies is therefore important to close the existing treatment gap in these patients. The adenosinergic system possesses potent anticonvulsive effects, mainly through the adenosine A1receptor (A1R). However, clinical application of A1R agonists is hindered by severe systemic side effects. To achieve local modulation of A1Rs, we employed a photopharmacological approach using a caged version of the A1R agonist N6-cyclopentyladenosine, termed cCPA. We performed the firstin vivostudy with intracerebroventricularly (ICV) administered cCPA to investigate the potential to uncage sufficient amounts of cCPA in the hippocampus by local illumination in order to suppress hippocampal excitability and seizures in mice. Using hippocampal evoked potential recordings, we showed a reduction in hippocampal neurotransmission after photo-uncaging of cCPA, similar to that obtained with ICV injection of CPA. Furthermore, in the intrahippocampal kainic acid mouse model for DRE, photo-uncaging of CPA in the epileptic hippocampus resulted in a strong suppression of seizures. Finally, we demonstrated that intrahippocampal photo-uncaging of CPA resulted in less impairment of motor performance in the rotarod test compared to ICV administration of CPA. These results provide a proof of concept for photopharmacological A1R modulation as an effective precision treatment for DRE.
Near-complete telomere-to-telomerede novogenome assemblies of Egyptian clover (Trifolium alexandrinum)
Authors: Sato Mitsuhiko P. , Arafa Ramadan A. , Rakha Mohamed , Emeran Amero A. , Isobe Sachiko , Shirasawa Kenta
Published: July 2024

Egyptian clover (Trifolium alexandrinumL.), also known as berseem clover, is an important forage crop to semi-arid conditions that was domesticated in ancient Egypt and introduced and well adapted to numerous countries. Despite its agricultural importance, genomic research on Egyptian clover has been limited to developing efficient modern breeding programs. In the present study, we constructed near-complete telomere-to-telomere-level genome assemblies for two Egyptian clover cultivars, Helaly and Fahl. Initial assemblies were established by using highly-fidelity long-read technology. To extend sequence contiguity, we developed a gap-targeted sequencing (GAP-Seq) method, in which contig ends are targeted for sequencing to obtain long reads bridging two contigs. The total length of the resultant chromosome-level assemblies was 547.7 Mb for Helaly and 536.3 Mb for Fahl. These differences in sequence length can be attributed to the expansion of DNA transposons. Population genomic analysis using single-nucleotide polymorphisms revealed 38 highly conserved genomic regions within Helaly. Growth- and stress response-associated gene ontologies were enriched in the 38 regions, indicating that these genes may determine the unique characteristics of Helaly. Comprehensive genomic resources can provide valuable insights into genetic improvements in Egyptian clover and legume genomics.
Synergically enhanced anti-tumor immunity ofin vivoCAR by circRNA vaccine boosting
Authors: Wang Yanyan , Lin Liangru , Wang Xinyue , Li Jing , Yin Jie , Gao Fei , Liao Xinyuan , Zhang Chenchen , Yin Qimeng , Zhao Chengzhi , Lin Jinzhong , Xu Yichi , Qiu Min , Luo Dan , Qu Liang
Published: July 2024

Chimeric Antigen Receptor (CAR) T cell therapy has shown promise in treating hematologic malignancies. However, it is limited to individualized cell therapy and faces challenges, including high costs, extended preparation time, and limited efficacy against solid tumors. Here, we generated circular RNAs (circRNAs) encoding Chimeric Antigen Receptor (CAR) transmembrane proteins, referred to as circRNACAR, which mediated remarkable tumor killing in both T cells and macrophages. In addition, macrophages exhibited efficient phagocytosis of tumor cells and pro-inflammatory polarization induced by circRNACARin vitro. We demonstrated that circRNACAR, delivered with immunocyte-tropic lipid nanoparticles (LNPs), significantly inhibited tumor growth, improved survival rates and induced a pro-inflammatory tumor microenvironment in mice. Importantly, the combination of circRNAAnti-HER2-CARand circRNA-based cancer vaccines encoding the corresponding transmembrane HER2 antigen, termed circRNAHER2, exhibited synergistically enhanced anti-tumor activity. This proof-of-concept study demonstrated that the combination of circRNA-basedin vivoCAR and vaccines, termedin vivoCAR-VAC, holds the potential to become an upgraded off-the-shelf immunotherapy.
Comparing Raman and NanoSIMS for heavy water labeling of single cells
Authors: Schaible George A. , Cliff John B. , Crandall Jennifer A. , Bougoure Jeremy J. , Atwood Joseph , Hatzenpichler Roland
Published: July 2024

Stable isotope probing (SIP) experiments in conjunction with Raman microspectroscopy (Raman) or nano-scale secondary ion mass spectrometry (NanoSIMS) are frequently used to explore single cell resolved metabolic activity in pure cultures as well as complex microbiomes. Despite the increasing popularity of these techniques, no study has yet compared results from isotope incorporation measurements using both Raman and NanoSIMS directly on the same cell. This knowledge gap creates uncertainty about the comparability of single cell SIP data generated independently using these techniques. In this study, we conducted a comparative analysis of 543Escherichia colicells grown in M9 minimal medium in the absence or presence of heavy water (2H2O) at single cell resolution using correlative Raman and NanoSIMS measurements. For the first time, we were able to establish the extent of data equivalence, allowing for comparisons between the two approaches. Utilizing the dataset from this study, we examined the effectiveness of preprocessing techniques and optimal wavenumbers for analyzing Raman spectra, along with identifying the ideal masses for NanoSIMS analysis of cells incubated in the presence of2H2O. We make recommendations for approaches to analyzing and comparing data using both or either of these techniques. We anticipate that the findings presented herein will enhance the comparability of studies employing either technique and ultimately contribute to the establishment of a standardized framework within the field.

Importance

Accurate and reliable measurements of cellular properties are fundamental to understanding the function and activity of microbes. This study addresses to what extent Raman microspectroscopy and nano-scale secondary ion mass spectrometry (NanoSIMS) measurements of single cell anabolic activity can be compared. For the first time, we study the relationship of the incorporation of a stable isotope (2H through incorporation of2H2O) as determined by the two techniques and calculate a correlation coefficient to support the use of either technique when analyzing cells incubated with2H2O. The ability to discern between the comparative strengths and limitations of these techniques is invaluable in refining experimental protocols, enhancing data comparability between studies, data interpretation, and ultimately advancing the quality and reliability of outcomes in microbiome research.
The regulatory functions of ESX-1 substrates, EspE and EspF, are separable from secretion
Authors: Prest Rebecca J. , Korotkov Konstantin V. , Champion Patricia A.
Published: July 2024

Pathogenic mycobacteria are a significant global health burden. The ESX-1 secretion system is essential for mycobacterial pathogenesis. The secretion of ESX-1 substrates is required for phagosomal lysis, which allows the bacteria to enter the macrophage cytoplasm, induce a Type I IFN response, and spread to new host cells. EspE and EspF are dual- functioning ESX-1 substrates. Inside the mycobacterial cell, they regulate transcription of ESX- 1-associated genes. Following secretion, EspE and EspF are essential for lytic activity. The link between EspE/F secretion and regulatory function has not been investigated. We investigated the relationship between EspE and EspF using molecular genetics inMycobacterium marinum,a non-tuberculous mycobacterial species that serves as an established model for ESX-1 secretion and function inM. tuberculosis.Our data support that EspE and EspF, which require each other for secretion, directly interact. Disruption of the predicted protein-protein interaction abrogates hemolytic activity and secretion but does not impact their gene regulatory activities in the mycobacterial cell. In addition, we predict a direct protein-protein interaction between the EsxA/EsxB heterodimer and EspF. Our data support that the EspF/EsxA interaction is also required for hemolytic activity and EspE secretion. Our study sheds light on the intricate molecular mechanisms governing the interactions between ESX-1 substrates, regulatory function and ESX-1 secretion, moving the field forward.

Importance

Tuberculosis (TB), caused byMycobacterium tuberculosis,is a historical and pervasive disease responsible for millions of deaths annually. The rise of antibiotic and treatment-resistant TB, as well as the rise of infection by non-tuberculous mycobacterial species, calls for better understanding of pathogenic mycobacteria. The ESX-1 secreted substrates EspE and EspF are required for mycobacterial virulence, and may be responsible for phagosomal lysis. This study focuses on the mechanism of EspE and EspF secretion from the mycobacterial cell.
Multiple stressor effects on organic carbon degradation and microbial community composition in urban river sediments in a mesocosm experiment
Authors: Baikova Daria , Hadžiomerović Una , Pimentel Iris Madge , Buchner Dominik , Vermiert Anna-Maria , A.M.  , Rehsen Philipp M. , Brauer Verena S. , Meckenstock Rainer U.
Published: July 2024

Microorganisms in river sediments are the primarily responsible organisms for the turnover of dissolved organic carbon (DOC) in these systems and therefore are key players for river ecosystem functioning. Rivers are increasingly threatened by multiple stressors such as salinization and temperature rise, but little is known about how microbial DOC-degradation responds to these stressors and whether this function recovers after stressor release. Here, we investigated the direct and indirect effects of salinity and temperature increase and decrease on microbial communities and their ability to degrade DOC in river sediments using the outdoor experimental mesocosm systemExStream. Composition of sediment microbial communities was determined at the end of acclimatization, stressor, and recovery phase using 16S rRNA gene sequencing. At the same time points, DOC degradation rates were quantified in additional microcosm incubations based on isotopic changes of CO2 with the help of reverse stable isotope labelling. Our results showed that raising the salinity by 154.1 mg Cl-L-1and temperature by 3.5 °C did not affect DOC degradation during the stressor phase but significantly increased DOC degradation in the recovery phase after stressors were released. Likewise, microbial community composition stayed constant during acclimation and stressor phase, but became more diverse in the recovery phase. The results indicate that microbial community composition and functioning were resistant towards both stressors, but responded to stressor release due to indirect effects of stressor increase and release on the riverine food web.

Graphical abstract
Plastid translocon recycling in dinoflagellates demonstrates the portability of complex plastids between hosts
Authors: Lewis William H , Paris Giulia , Beedessee Girish , Koreny Ludek , Flores Victor , Dendooven Tom , Gallet Benoit , Yee Daniel , Lam Simon , Decelle Johan , Luisi Ben F , Waller Ross F
Published: July 2024

The plastids of photosynthetic organisms on land are predominantly ‘primary plastids’ derived from an ancient endosymbiosis of a cyanobacterium. Conversely, marine photosynthetic diversity is dominated by plastids gained by subsequent endosymbioses of photosynthetic eukaryotes, so-called ‘complex plastids’. The plastids of major eukaryotic lineages including cryptophytes, haptophytes, stramenopiles, dinoflagellates and apicomplexans, were originally all posited to derive from a single secondary endosymbiosis of a red alga—the ‘chromalveloate’ hypothesis1. Subsequent phylogenetic resolution of eukaryotes indicated that separate events of plastid acquisition must have occurred to account for this distribution of plastids2,3. The number of such events, however, and the donor organisms for the new plastid endosymbioses are still not resolved. A perceived bottleneck of endosymbiotic plastid gain is the development of protein targeting from the hosts into new plastids, and this supposition has often driven hypotheses towards minimising the number of plastid-gain events to explain plastid distribution in eukaryotes. But how plastid protein-targeting is established for new endosymbionts is often unclear, which makes it difficult to assess the likelihood of plastid transfers between lineages. Here we show that Kareniaceae dinoflagellates, that possess complex plastids known to be derived from haptophytes, acquired all the necessary protein import machinery from these haptophytes. Furthermore, cryo-electron tomography revealed that no additional membranes were added to the Kareniaceae complex plastid during serial endosymbiosis, suggesting that the haptophyte-derived import processes were sufficient. Our analyses suggests that complex red plastids are preadapted for horizontal transmission, potentially explaining their widespread distribution in aquatic algal diversity.
Effectiveness of integrating cervical cancer prevention strategies into HIV care programmes: A mixed-methods systematic review protocol
Authors: Govindsamy Kimeshnee , Noll Susanne , Blose Ntombifuthi , Amponsah-Dacosta Edina
Published: July 2024

Introduction

Cervical cancer, which is the fourth most frequently diagnosed cancer among women globally, remains a significant health burden despite being preventable and treatable, exposing gaps in accessing prevention and control services. Adolescent girls and young women (AGYW) face heightened risk of persistent HPV infection, a primary cause of cervical cancer. The overlap of cervical cancer and HIV exacerbates public health challenges, especially in resource-limited areas, urging intensified efforts in bolstering prevention and control measures. Integrating HPV vaccination, cervical cancer screening, treatment of precancerous lesions and educational interventions into HIV care programs shows promise in effectively addressing this dual burden.

Methods

To evaluate the effectiveness of integrating cervical cancer prevention strategies within HIV care programs, a mixed-methods systematic review will be conducted. A comprehensive Boolean search for literature published between 2006 to present and indexed in PubMed, Cochrane Library, EBSCO Host, Web of Science, Scopus, and Google Scholar will be conducted, without imposing any language restrictions. This review will be conducted in alignment with the Joanna Briggs guidelines on systematic reviews together with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Data from eligible studies will be extracted and synthesized, and their quality assessed.

Discussion

There is limited understanding of the effectiveness of integrating cervical cancer prevention and HIV care in the real-world setting. While some studies touch on integration, focus tends to be on cervical cancer screening alone, neglecting vaccination, treatment of precancerous lesions, and education programs. Previous reviews on this focus are outdated, surpassing six years. This systematic review aims to fill these evidence gaps by thoroughly evaluating the challenges and opportunities associated with integrating the full complement of HPV prevention strategies and HIV care programs. The anticipated findings could enhance service delivery models aimed at reducing cervical cancer incidence and mortality among AGYW living with HIV.

Trial registration

Systematic review registration: PROSPERO registration number: CRD42024535821.
Anti-integrin αvβ6 antibodies predict pouchitis in patients with ulcerative colitis after restorative proctocolectomy with ileal pouch-anal anastomosis
Authors: Nakanishi Risa , Kuwada Takeshi , Shiokawa Masahiro , Nishikawa Yoshihiro , Ota Sakiko , Yamazaki Hajime , Yanaidani Takafumi , Sawada Kenji , Hirata Ayako , Yasuda Muneji , Takimoto Ikuhisa , Chikugo Koki , Yokode Masataka , Muramoto Yuya , Matsumoto Shimpei , Matsumori Tomoaki , Uza Norimitsu , Chiba Tsutomu , Seno Hiroshi
Published: July 2024

Background

Pouchitis is the most common complication of restorative proctocolectomy (RPC) with ileal pouch-anal anastomosis (IPAA) in patients with ulcerative colitis (UC). We previously reported the presence of anti-integrin αvβ6 antibodies in the serum of patients with UC. This study investigated the association between anti-integrin αvβ6 antibodies and the development of pouchitis in patients with UC.

Methods

Serum levels of anti-integrin αvβ6 antibodies were measured by enzyme-linked immunosorbent assay in 16 patients with UC who underwent RPC with IPAA. Integrin αvβ6 expression in the colonic, terminal ileal, and pouch epithelium was examined using immunohistochemistry and western blot analysis.

Results

Anti-integrin αvβ6 antibody levels in patients with UC were significantly decreased at 3, 9, and 12 months after RPC (P < 0.05). However, in patients who developed pouchitis, antibody levels remained high. The antibody levels at the time of RPC were significantly higher in patients who developed pouchitis compared to those who did not. Kaplan–Meier analysis revealed a significantly higher incidence of pouchitis in patients with antibody levels above the cutoff at the time of RPC. Although integrin αvβ6 was not expressed in the terminal ileal epithelium at the time of RPC, expression became positive in the pouch epithelium of patients with pouchitis.

Conclusions

The anti-integrin αvβ6 antibody levels in patients with UC were decreased after RPC, but remained high in patients who developed pouchitis. The antibody levels at the time of RPC may serve as a potential prognostic biomarker for predicting the risk of pouchitis in patients with UC.
Antimicrobial resistance ofStaphylococcusspp. from human specimens submitted to diagnostic laboratories in South Africa, 2012–2017
Authors: Sigudu Themba Titus , Qekwana Daniel Nenene , Oguttu James Wabwire
Published: July 2024

Background

Antimicrobial drug resistance is of public health importance due to its potential to reduce treatment options and increase healthcare expenditure. There is, however, a paucity of studies that have examined antimicrobial resistance in countries with poor to moderate income. The present study examined the patterns and predictors of antimicrobial resistance in Staphylococcus isolates collected from humans at diagnostic laboratories in South Africa between 2012 and 2017.

Method and materials

A cross-sectional study design using retrospective data of 404 217 diagnostic laboratory records of staphylococcal isolates collected between 2012 and 2017 was adopted in this study. Isolates were assessed for antimicrobial drug resistance against 24 antimicrobials. Descriptive statistics, and binary logistic regression models were used to analyse the data. Significance was assessed at < 0.05.

Results

The highest resistance was observed against Cloxacillin (70.3%), while the lowest resistance was against Colistin (0.1%). A significant (p < 0.05) decreasing trend in AMR was observed over the study period, while a significant increasing temporal trend (p < 0.05) was observed for MDR over the same period. A Significant (p < 0.05) association was observed between specimen type, species of organism, and year of isolation with AMR outcome. Significant (p < 0.05) associations were observed between specimen type and season, with MDR.

Discussion and recommendations

The observed high levels of AMR and the increasing temporal trend in MDR is of public health concern. Clinicians should consider these findings when deciding on therapeutic options. Continued monitoring of AMR amongStaphylococcusspp. and judicious use of antimicrobials in human medicine should be promoted.
Using a mixed-reality headset to elicit and track clinically relevant movement in the clinic
Authors: Calame Dylan , Lester Evan , Chiu Phil , Seeberger Lauren
Published: July 2024

Background

21st century neurology will require scalable and quantitative tools that can improve neurologic evaluations over telehealth and expand access to care. Commercially available mixed-reality headsets allow for simultaneous presentation of stimuli via holograms projected into the real world and objective and quantitative measurement of hand movement, eye movement, and phonation.

Methods

We created 6 tasks designed to mimic standard neurologic assessments and administered them to a single participant via the Microsoft HoloLens 2 mixed-reality headset. The tasks assessed postural hand tremor, finger tapping, pronation and supination of hands, hand and eye tracking of a center-out task, hand and eye tracking of a random motion task, and vocal assessment.

Findings

We show the utility of the HoloLens for commonly used neurological exams. First, we demonstrate that headset-derived holograms can project hand movements and objects in 3D space, providing a method to accurately and reproducibly present test stimuli to reduce test-test variability. Second, we found that participant hand movements closely matched holographic stimuli using a variety of metrics calculated on recorded movement data. Third, we showed that the HoloLens can record and playback exam tasks for visual inspection, sharing with other medical providers, and future analysis. Fourth, we showed that vocal recordings and analysis could be used to profile vocal characteristics over time. Together, this demonstrates the versatility of mixed reality headsets and possible applications for neurological assessment.

Interpretation

Administering components of the neurologic exam via a self-contained and commercially available mixed-reality headset has numerous benefits including detailed kinematic quantification, reproducible stimuli presentation from test to test, and can be self-administered expanding access to neurological care and saving hospital time and money.

Funding

This work was supported by grants from the National Institutes of Health (NIH) (F30AG063468) (E.L.), (F31NS113395) (D.J.C), and the Pilot Grant Award from the University of Colorado Movement Disorders Center (D.J.C).
The Association of NICU Strain with Neonatal Mortality and Morbidity
Authors: Salazar Elizabeth G. , Passarella Molly , Formanowski Brielle , Rogowski Jeannette , Edwards Erika , Phibbs Ciaran , Lorch Scott A.
Published: July 2024

Objective

To examine the association of admission NICU strain with neonatal mortality and morbidity.

Study Design

2008-2021 South Carolina cohort using linked vital statistics and discharge data of 22-44 weeks GA infants, born at hospitals with ≥ level 2 unit and ≥5 births of infants <34 weeks GA/year. The exposure was tertiles of admission NICU strain, defined as the sum of infants <44 weeks GA with a congenital anomaly plus all infants born <33 weeks GA at midnight on the day of birth. We used Poisson generalized linear mixed models to examine the association of exposure to strain with the primary outcome of a composite of mortality and term and preterm morbidities adjusting for patient and hospital characteristics.

Results

We studied 64,647 infants from 30 hospitals. High strain was associated with increased risk of mortality and morbidity adjusting for patient/hospital factors (aIRR 1.07, 95% CI 1.01 – 1.12).

Conclusion

NICU strain is associated with increased adverse outcomes.
Central Nervous System Complications in Miliary Pulmonary Tuberculosis: A Systematic Review Of Published Case Reports And Case Series
Authors: Garg Ravindra Kumar , Paliwal Vimal Kumar , Srivastava Anand , Garg Rajiv , Bhattacharya Sandeep , Jain Amita , Rizvi Imran
Published: July 2024

Background

This systematic review aims to evaluate central nervous system involvement in context of miliary pulmonary tuberculosis.

Methods

We included studies on central nervous system infections associated with miliary pulmonary tuberculosis involving human subjects in any language. Patients with disseminated tuberculosis involving two non-contiguous organs were excluded. Databases searched included PubMed, Scopus, Embase, and Google Scholar. Case reports, case series, and observational studies with confirmed diagnoses were included. The review follows PRISMA guidelines and is registered with PROSPERO (CRD42024542130).

Results

The review included 158 records describing 161 patients. The mean age was 32.7 years, with 53.4% females. Key comorbid conditions included human immunodeficiency virus positivity (6.8%), immunosuppressive therapy (9.9%), and chronic kidney disease (2.5%). Common clinical features were fever (58.4%), headache or vomiting (41.6%), and altered sensorium (26.7%). Frequent neuroimaging abnormalities were miliary or multiple brain tuberculomas (66.5%), basal exudates (7.5%), vertebral tuberculosis (7.5%), cerebral infarcts (6.8%), and spinal cord tuberculoma or abscess (6.2%). Paradoxical manifestations occurred in one-third of cases, including new or enlarged brain lesions (22.4%) and paradoxical cerebral infarcts (2.5%). Cerebrospinal fluid findings were normal or unavailable in 45.3% of cases. Positive diagnostic tests included smear, culture, polymerase chain reaction, or GeneXpert in 25% of cases, with 5% showing drug resistance. Improvement was seen in 80.8% of patients, while 9.9% either died or did not improve.

Conclusion

This review highlights diverse central nervous system involvement in miliary pulmonary tuberculosis, including tuberculous meningitis and spinal cord lesions, with common paradoxical manifestations and significant patient improvement with following treatment.
Autoencoder to Identify Sex-Specific Sub-phenotypes in Alzheimer’s Disease Progression Using Longitudinal Electronic Health Records
Authors: Meng Weimin , Xu Jie , Huang Yu , Wang Cankun , Song Qianqian , Ma Anjun , Song Lixin , Bian Jiang , Ma Qin , Yin Rui
Published: July 2024

Alzheimer’s Disease (AD) is a complex neurodegenerative disorder significantly influenced by sex differences, with approximately two-thirds of AD patients being women. Characterizing the sex-specific AD progression and identifying its progression trajectory is a crucial step to developing effective risk stratification and prevention strategies. In this study, we developed an autoencoder to uncover sex-specific sub-phenotypes in AD progression leveraging longitudinal electronic health record (EHR) data from OneFlorida+ Clinical Research Consortium. Specifically, we first constructed temporal patient representation using longitudinal EHRs from a sex-stratified AD cohort. We used a long short-term memory (LSTM)-based autoencoder to extract and generate latent representation embeddings from sequential clinical records of patients. We then applied hierarchical agglomerative clustering to the learned representations, grouping patients based on their progression sub-phenotypes. The experimental results show we successfully identified five primary sex-based AD sub-phenotypes with corresponding progression pathways with high confidence. These sex-specific sub-phenotypes not only illustrated distinct AD progression patterns but also revealed differences in clinical characteristics and comorbidities between females and males in AD development. These findings could provide valuable insights for advancing personalized AD intervention and treatment strategies.
Library size can undermine accurate molecular and phenotypic subtyping in spatial transcriptomics data
Authors: Fisher Natalie C , Malla Sudhir B , Jamieson Nigel B , Dunne Philip D
Published: July 2024

In an era where transcriptomics-based subtyping, phenotyping and mechanistic understanding is increasingly being driven by state-of-the-art spatially resolved transcriptomic (ST) technologies, it is imperative that researchers, journals, and funders do all they can to ensure that as a community we are interpreting these exciting data as accurately as possible with awareness of their limitations. In this short report, we highlight one potential bias in ST data that could undermine accurateinterpretationof transcriptional signatures, providing the field with an opportunity to identify and avoid this issue prior to release of new mechanistic findings. This issue is particularly relevant for platforms that produce some of the most granular and high-resolution spatial information at single cell (and sub-cellular) resolution, with the compromise of a reduced transcriptome panel of genes (Figure 1A).
Discovery and mechanism of K63-linkage-directed deubiquitinase activity in USP53
Authors: Wendrich Kim , Gallant Kai , Recknagel Sarah , Petroulia Stavroula , Führer Siska , Bezstarosti Karel , O’Dea Rachel , Demmers Jeroen , Gersch Malte
Published: July 2024

Ubiquitin-specific proteases (USPs) are the largest class of human deubiquitinases (DUBs) and comprise its phylogenetically most distant members USP53 and USP54, which are annotated as catalytically inactive pseudo-enzymes. Conspicuously, mutations in the USP domain ofUSP53cause familial intrahepatic cholestasis. Here we report the discovery that USP53 and USP54 are in fact active DUBs with high specificity for K63-linked polyubiquitin. We demonstrate how USP53 patient mutations abrogate catalytic activity, implicating loss of DUB activity inUSP53-mediated pathology. Depletion of USP53 increases K63-linked ubiquitination of tricellular junction components. Assays with substrate-bound polyubiquitin reveal that USP54 cleaves within K63-linked chains, whereas USP53 can deubiquitinate a substrate in a K63-linkage-dependent manner. Biochemical and structural analyses uncover underlying K63-specific S2-ubiquitin-binding sites within their catalytic domains. Collectively, our work revises the annotation of USP53 and USP54, provides chemical reagents and a mechanistic framework to broadly investigate K63-polyubiquitin chain length decoding, and establishes K63-linkage-directed deubiquitination as novel DUB activity.
RNA genome expansion up to 64 kb in nidoviruses is host constrained and associated with new modes of replicase expression
Authors: Neuman Benjamin W. , Smart Alexandria , Vaas Josef , Bartenschlager Ralf , Seitz Stefan , Gorbalenya Alexander E. , Caliskan Neva , Lauber Chris
Published: July 2024

Positive-strand RNA viruses of the orderNidoviraleswith genomes larger than ∼20 kb, including the largest known 36.7 kb RNA genome in vertebrate viruses, encode a proofreading exoribonuclease (ExoN). Here, we assemble 76 genome sequences of invertebrate nidoviruses from >500.000 published transcriptome experiments and triple the number of known nidoviruses with >36 kb genomes, including the largest known 64 kb RNA genome. We classify multi-cistronic ExoN-encoding nidoviruses into five groups, according to canonical and non-canonical modes of viral polymerase expression by ribosomes and genome segmentation. The largest group employing the canonical mode comprises invertebrate and vertebrate nidoviruses, including coronaviruses, with genomes ranging from 20-to-36 kb. Four groups with non-canonical expression modes include giant invertebrate nidoviruses with 31-to-64 kb genomes, some of which utilize dual ribosomal frameshifting that we validate experimentally. Thus, expansion of giant RNA virus genomes, the vertebrate/invertebrate host division, and the control of viral replicase expression are interconnected.
Hedgehog-Hippo pathway interactions promote T cell exclusion from the tumor microenvironment in basal cell carcinoma
Authors: Stockmaier Georg , Varkhande Suraj , Krenn Peter W , Dang Hieu-hoa , Sharma Anshu , Elmer Dominik P , Steiner Markus , Zaborsky Nadja , Neureiter Daniel , Greil Richard , Horejs-Hoeck Jutta , Fortelny Nikolaus , Gratz Iris K , Aberger Fritz
Published: July 2024

Basal cell carcinoma (BCC) is the most common non-melanoma skin cancer driven primarily by genetic activation of the Hedgehog/GLI (HH/GLI) signaling pathway. BCC also displays a high mutational burden, with frequent co-occurrence of mutations in the TP53, NOTCH, N-MYC, and Hippo/YAP pathways, though the impact of these mutations on HH/GLI-driven tumorigenesis remains poorly understood. This study examines the interaction between the HH/GLI and Hippo/YAP signaling pathways in the pathogenesis of BCC and the establishment of an immunosuppressive tumor microenvironment (TME). The study used 3D human organotypic skin models and humanized mouse models to demonstrate that co-activation of HH/GLI and Hippo/YAP in epidermal cells suppresses T cell chemotaxis. Transcriptome analysis revealed a significant downregulation of chemotactic and inflammatory genes, particularly under combined GLI-YAP activation. Analysis of primary human BCC biopsies confirmed these findings and demonstrated a marked suppression of T cell chemo-attractants, including CCL22 and CCL27. Spatial profiling of immune cells in BCC tissues revealed preferential exclusion of CD8+ T cells from the TME, which correlated with high HH/GLI and Hippo/YAP activity. Further, functional assays in humanized mice showed that the GLI-YAP interaction controls immune cell distribution by inhibiting T cell recruitment and migration into the skin. These findings suggest that cooperation between oncogenic HH/GLI and Hippo/YAP signaling contributes to the development of an immunosuppressive TME in BCC by disrupting local chemokine signaling. Understanding these mechanisms provides a basis for the development of targeted combination therapies to enhance the efficacy of existing treatments, such as Smoothened (SMO) inhibitors and immune checkpoint blockers, by promoting T cell infiltration and activation within the TME.
Phase I study on the pharmacokinetics of intravaginal, self-administered artesunate vaginal pessaries among women in Kenya
Authors: Mungo Chemtai , Sorgi Katherine , Misiko Brenda , Cheserem Cynthia , Rahangdale Lisa , Githongo George , Ogollah Cirilus , Omoto Jackton , Plesa Mihaela , Zamboni William
Published: July 2024

Cervical cancer remains a significant global health issue, especially in low- and middle-income countries (LMICs), where access to prevention and treatment is limited and women are at a higher risk of cervical cancer. Artesunate, a widely available drug used to treat malaria, has shown promise in treating human papillomavirus (HPV)-associated anogenital lesions including high-grade cervical precancer, in a recent Phase I studies in the United States. Data on the pharmacokinetics of artesunate following intravaginal use, and its implications on malaria resistance, are lacking.

Objectives

The primary objective of this study is to investigate the pharmacokinetics of Artesunate (AS) and its active metabolite, dihydroartemisinin (DHA) following intravaginal use at the dosing and frequency intended for cervical precancer treatment. A secondary objective is to assess safety among study participants.

Methods

We are conducting a single-arm, phase I trial with a sample size of 12 female volunteers. Participants will self-administer artesunate vaginal pessaries in the study clinic daily for 5 consecutive days. Participants will have their blood drawn prior to receiving the first dose of artesunate on day one of the study and then will receive 8 blood draws on study day five, prior to artesunate administration and at 15 minutes, 30 minutes, 1 hour, 2 hours, 4 hours, 6 hours, and 8 hours after pessary administration. Pharmacokinetic parameters of artesunate and DHA will be calculated by way of quantitative analysis of with determination of maximum concentration (Cmax), time to Cmax (Tmax), area under the serum concentration versus time curve (AUC), apparent clearance, and elimination half-life (t1/2).
Structural basis for Vipp1 membrane binding: From loose coats and carpets to ring and rod assemblies
Authors: Junglas Benedikt , Kartte David , Kutzner Mirka , Hellmann Nadja , Ritter Ilona , Schneider Dirk , Sachse Carsten
Published: July 2024

Vipp1 (also known as IM30) is essential in most oxygenic photoautotrophic organisms. It is involved in membrane remodeling and fusion and is critical for thylakoid membrane biogenesis and maintenance. Vipp1 has recently been identified as a member of the ESCRT-III superfamily of membrane remodeling proteins, albeit it still is elusive how Vipp1 interacts with and finally remodels membranes. Here we present a series of cryo-EM structures of cyanobacterial Vipp1 interacting with bacterial membranes: first, we solved seven structures between 5 and 7 Å resolution of three unique helical and four types of stacked-ring assemblies engulfing membranes, and, second, using sub-tomogram averaging, we determined three ∼20 Å resolution structures compatible with previously observed carpet structures at three different membrane curvatures. By analyzing ten additional unique structures of N-terminally truncated Vipp1, we could show that helix α0 is essential for membrane tubulation and forms the membrane anchoring domain of Vipp1. Using a conformation-restrained Vipp1 mutant, we were able to reduce the structural plasticity of Vipp1 assemblies in the presence of lipids and determined two structures of Vipp1 at 3.0 Å resolution, resolving the molecular details of membrane anchoring and intersubunit contacts of helix α0. Our data reveal the molecular details of how Vipp1 interacts with membranes, showing membrane curvature-dependent structural transitions from carpets to rings and rods, some of which are capable of inducing and/or stabilizing high local membrane curvature triggering membrane fusion.

Bacterial ESCRT-III family member Vipp1 forms membrane-bound coats, carpets, ring complexes, stacked-ring assemblies and helical tubes capable of internalizing lipids and inducing high membrane curvature.
Structural plasticity of bacterial ESCRT-III protein PspA in higher-order assemblies
Authors: Junglas Benedikt , Hudina Esther , Schönnenbeck Philipp , Ritter Ilona , Heddier Anja , Santiago-Schübel Beatrix , Huesgen Pitter F. , Schneider Dirk , Sachse Carsten
Published: July 2024

Eukaryotic members of theendosome sorting complex required for transportIII (ESCRT-III) family have been shown to form diverse oligomeric assemblies. The bacterialphage shock protein A(PspA) has recently been identified as a bacterial member of the ESCRT-III superfamily, and monomeric PspA homo-oligomerizes to form large rod-shaped assemblies. As observed for eukaryotic ESCRT-III, PspA forms different tubular assemblies with varying diameters. Using electron cryo-microscopy (cryo-EM), we determined a total of 61 PspA structures and observed in molecular detail how structural plasticity of PspA rods is mediated by conformational changes at three hinge regions in the monomer and by the fixed as well as changing molecular contacts between protomers. Moreover, we reduced and increased the structural plasticity of PspA rods by removing the loop connecting helices α3/α4 and the addition of nucleotides, respectively. Based on our analysis of PspA-mediated membrane remodeling, we suggest that the observed mode of structural plasticity is a prerequisite for the biological function of ESCRT-III superfamily members.

A series of cryo-EM structures of PspA rods with induced diameter modulations reveals the molecular basis of structural plasticity.
Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins
Authors: Vakirlis Nikolaos , Kupczok Anne
Published: July 2024

Species-specific genes, also known as orphans, are ubiquitous across life's domains. In prokaryotes, species-specific orphan genes (SSOGs) are mostly thought to originate in external elements such as viruses followed by horizontal gene transfer, whereas the scenario of native origination, through rapid divergence or de novo, is mostly dismissed. However, quantitative evidence supporting either scenario is lacking. Here, we systematically analyzed genomes from 4644 human gut microbiome species and identified more than 600,000 unique SSOGs, representing an average of 2.6% of a given species’ pangenome. These sequences are mostly rare within each species yet show signs of purifying selection. Overall, SSOGs use optimal codons less frequently, and their proteins are more disordered than those of conserved genes (i.e., non-SSOGs). Importantly, across species, the GC content of SSOGs closely matches that of conserved ones. In contrast, the ∼5% of SSOGs that share similarity to known viral sequences have distinct characteristics, including lower GC content. Thus, SSOGs with similarity to viruses differ from the remaining SSOGs, contrasting an external origination scenario for most of them. By examining the orthologous genomic region in closely related species, we show that a small subset of SSOGs likely evolved natively de novo and find that these genes also differ in their properties from the remaining SSOGs. Our results challenge the notion that external elements are the dominant source of prokaryotic genetic novelty and will enable future studies into the biological role and relevance of species-specific genes in the human gut.