bluuebunny/crossref_metadata_2025 huggingface dataset:
Dosimetric evaluation of simplified intensity-modulated radiation therapy for thoracic tumors
Authors: Tian Wei , Zhou Pixiao , Guo Fen , Wen Yu , Dong Wen , Wang Hongming , Wu Zhijun , Du Yangfeng , Xiao Zemin
Published: February 2025

To evaluate the feasibility of multi-parameters combined simplified intensity-modulated radiation therapy (sIMRT) planning in thoracic tumors and provide guidance for clinical practice. A total of 34 patients with thoracic tumors who underwent radiotherapy during 2019 to 2020 in our hospital were retrospectively analyzed. The same experienced medical physicist designed the sIMRT planning. The sIMRT planning limited the maximum number of segments per beam-field, the minimum segment area, and the minimum number of segment monitor units (MU), remaining consistent with the conventional intensity-modulated radiation therapy (IMRT). Comparative analysis of the difference in the irradiation dose to the tumor target area, and organs at risk, and delivery validate between 2 groups. The sIMRT slightly increased the tumor target area irradiation dose, but the homogeneity index was similar when compared with IMRT (P > .05). The sIMRT planning significantly reduced the low dose-volume area of the lungs (left lung, V
5: 2.5%; right lung, V
5: 3.1%; V
10: 1.8%; lungs, V
5: 3.2%; V
10: 1.5%, P < .05) and significantly increased the high dose-volume area of the lungs, heart, and esophagus, while meeting the clinical dose-restriction requirements. Moreover, the planning delivery validation showed that significantly reduced the treatment time (6.5 ± 1.9 minutes vs 8.8 ± 2.0 minutes, P < .0001) and total MU (386.3 ± 109.4 MU vs 406.3 ± 107.9 MU, P < .05). This simplified sIMRT method can meet the requirements of thoracic tumors radiotherapy planning, and has higher time effectiveness. In the future, it needs to be further explored in clinical practice.
The ‘art’ of communication therapy
Authors: Dawson Camilla , Wheeler Jo
Published: February 2025

Purpose of review

An overview of research exploring communication rehabilitation published between 2022 and 2024. There is limited research in the field so this timely review offers the clinician an insight into the available literature and the gaps that exist.

Recent findings

The review identified four main themes related to communication and speech rehabilitation; articulation and intelligibility, measures of function following surgical interventions, therapeutic interventions and their variability and quality of life outcomes.

Clinicians may benefit from identifying organizational, institutional, cultural, practical and data driven influences on their clinical interventions and capacity to provide person-centred communication rehabilitation. There is an ongoing need to move beyond measurement of compromise and impairment-based interventions, to explore how enhancing communicative competence using multiple rehabilitative interventions from the Speech and Language Therapist may improve holistic outcomes for people with head and neck cancer.
The Tormented Soul
Authors: Hellwig Karen
Published: February 2025

This article explores depression in older adults, addressing types of depression, risk factors, signs and symptoms, prevention strategies, treatments, and the critical role of home care clinicians. It concludes with a discussion on the tragic issue of suicide among older adults, including its risk factors, prevention, and management.
TeamSTEPPS® in Home Health
Authors: Sevier Matt
Published: February 2025

TeamSTEPPS is a patient safety model that uses a collection of tools and best practices to optimize team performance. It has been widely adopted in the inpatient setting but clinician autonomy has been a barrier in its use. A home healthcare agency began using TeamSTEPPS® and found that it has a positive impact on nurse retention through the use of situational awareness and mutual support tools. Small improvements were made in OASIS outcomes and 30-day hospital readmissions through the use of handoffs and huddles.
Cultural Stigmatization in Home Care Nursing
Authors: Mensah-Nti Anna
Published: February 2025

This concept analysis explores cultural stigmatization and its impact on home care, using Walker and Avant's eight-step method and reviewing 49 peer-reviewed articles. Cultural stigmatization is identified as a key barrier, causing discrimination and negatively affecting patient outcomes. The home care implications of addressing cultural stigmatization include interventions that address clinician biases, enhance cultural sensitivity, and reduce stereotypes to improve care quality. These implications highlight the need for targeted strategies to address cultural stigmatization in home care settings, ensuring equitable and effective services for all patients.
Drivers of Bronchodilator Use in Bronchiolitis
Authors: Rivera-Sepulveda Andrea , Maul Timothy , Jurlina Anna , Blake Kathryn V. , Davis Matthew M. , Alexander Kenneth
Published: February 2025

Objectives:

This study aims to evaluate patient characteristics associated with bronchodilator (BD) use at various stages of bronchiolitis illness and evaluate corresponding patient outcomes in the emergency department (ED).

Methods:

This retrospective, cross-sectional study involves secondary data analysis from a sample of 932 children ages 3 to 24 months who received a diagnosis of bronchiolitis during an ED visit (1057 cases). Predictor variables included demographics, past medical history, family history, physical findings, medication use, and disposition. Outcomes included BD use for bronchiolitis symptoms in the pre-ED and ED settings, and associated care outcomes in the ED. Predictors of BD use in the ED with statistical significance were incorporated in a predictive multivariable logistic regression model with a training-validation split of 70% to 30%.

Results:

Children with prior BD use were significantly more likely than children without such history to receive BD treatment during their current bronchiolitis illness before the ED [odds ratio (OR): 23.7, 95% CI: 14.4-39], in the ED (OR: 2.6, 95% CI: 1.76-3.77), and as a prescription upon discharge from the ED (OR: 3.7, 95% CI: 2.49-5.58). In multivariable regression analyses, older age, parental asthma history, and wheezes and retractions on ED physical examination were significantly associated with BD use in the ED (P<0.05). The area under the curve for the validation model with these variables was 0.826 (95% CI: 0.794-0.858).

Conclusions:

Prior BD use was associated with subsequent use during the current illness, during ED care, and subsequent prescription, forming a cyclical pattern. A perceived bronchospastic phenotype of bronchiolitis may influence clinical practice in ED settings.
Thoracoabdominal Normothermic Regional Perfusion: Real-world Experience and Outcomes of DCD Liver Transplantation
Authors: Bababekov Yanik J. , Ha Anna H. , Nydam Trevor L. , Goncalves Carlos , Choudhury Rashikh , Shinsako JoLynn , Baimas-George Maria , Reynolds David M. , Yoshida Cassidy , Racke Caroline A. , Grewal Han , Pomposelli Sophia , Rodriguez Ivan E. , Hoffman Jordan R.H. , Schold Jesse D. , Kaplan Bruce , Pomfret Elizabeth A. , Pomposelli James J.
Published: February 2025

Background.

Donation after circulatory death liver transplantation (DCD LT) is underused given historical outcomes fraught with ischemic cholangiopathy (IC). We aimed to assess 6-mo IC in LT from DCD via normothermic regional perfusion (NRP) compared with DCD via static cold storage (SCS).

Methods.

A retrospective review of adult Maastricht-III DCD liver donors and recipients at the University of Colorado Hospital from January 1, 2017, to August 27, 2024, was performed. The 6-mo IC rate was compared between NRP and SCS. Secondary outcomes included biochemical assessments of accepted versus declined NRP liver allografts and allograft and patient survival for NRP and SCS groups.

Results.

One hundred sixty-two DCD LTs (SCS = 79; NRP = 97) were performed and 150 recipients (SCS = 74; NRP = 86) reached 6-mo follow-up. Six-month IC was lower for NRP compared with SCS (1.2% versus 9.5%, P = 0.03). The Donor Risk Index (2.44 [2.02–2.82] versus 2.17 [1.97–2.30], P = 0.002) and UK DCD Risk Score (4.2 ± 2.9 versus 3.2 ± 2.3, P = 0.008) were higher for NRP versus SCS. The Liver Graft assessment Following Transplantation score was less for NRP compared with SCS (–3.3 versus –3.1, P < 0.05). There were several differences in median biochemical parameters during NRP between accepted and declined livers, including higher terminal biliary bicarbonate (22.7 [20.9–29.1] versus 10.8 [7.6–13.1] mEq/L, P = 0.004). There were no significant differences in 12-mo allograft or patient survival for NRP versus SCS.

Conclusions.

NRP is a disruptive innovation that improves the utilization of DCD livers. Despite higher-risk donor-recipient pairing for NRP compared with SCS, we demonstrate a decrease in IC for NRP. These data facilitate benchmarking of thoracoabdominal NRP DCD LT and support further protocol development.
DETECTION AND ANTIBIOTIC RESISTANCE OF SALMONELLA ISOLATES FROM SELECTED POULTRY FARMS IN DAR ES SALAAM, TANZANIA.
Authors: Mwambene Saxon Joseph , Mtenga Adelard B. , Chengula Augustino A. , Hoza Abubakar S.
Published: February 2025

Introduction

Salmonella, one of the most frequent foodborne bacteria, is linked to 155,000 annual mortality and 93.8 million foodborne illnesses. Rampant use of antibiotic agents to combat Salmonellosis in poultry has contributed to the emergence of resistance against commonly used antibiotics.

Methodology

A cross-section study was conducted between January and June 2023. Purposive sampling was used to select farms, poultry faecal droppings were collected to determine the occurrence of multidrug-resistant (MDR) Salmonella spp. Samples were examined for the presence of Salmonella by standard microbiological techniques. Conventional biochemical tests and molecular methods such as PCR and partial DNA sequencing were used for the identification of Salmonella isolates. Antimicrobial susceptibility testing was performed to identify Salmonella isolates resistant to seven commonly used classes of antibiotics.

Results

The overall Salmonella spp isolated from faecal droppings from the selected farms was 6.04% (n=48). Of the PCR-confirmed isolates, 64.3% (n=18) were resistant to more than two classes of antibiotics and hence considered MDR. The highest resistance was observed with ampicillin (92.9%), followed by tetracycline (69%), ciprofloxacin (42.9%), sulfonamide (42.9%), gentamicin (35.7%), and azithromycin (28.9%). All the isolates were susceptible to chloramphenicol (100%). Twenty-eight (28) isolates were sequenced and only sixteen (16) sequences met the criteria for phylogenetic analysis. All the sixteen (16) Sequences clustered together with Salmonella enterica sub spp. enterica with accession number EU348369 which was isolated from chickens, pigs, and foods.

Conclusion

The observed high level of antibiotic resistance found in this study could be attributed to the unwarranted use of antibiotics. To limit the use of antibiotics in poultry farming at the farm level, immediate action is needed including advocating for prudent use of antibiotics in poultry production systems by strengthening extension services to poultry farmers and use of farm biosecurity.
Multi-omics dissection of Parkinson’s patients in subgroups associated with motor and cognitive severity
Authors: Athieniti Efi , Afxenti Sotiroula , Minadakis George , Spyrou George M.
Published: February 2025

Heterogeneity in the severity of Parkinson’s disease (PD) inhibits the effective interpretation of clinical trial outcomes. Multi-omics analysis may help explain the pathological mechanisms underlying disease progression and reveal biomarkers of clinical severity. We performed Multi-Omics Factor Analysis (MOFA) on whole blood RNA, miRNA and Cerebrospinal fluid (CSF) and blood plasma proteomics from the Parkinson’s Progression Marker Initiative (PPMI), to identify molecular factors correlated with motor (MDS-UPDRS3) and cognitive (Semantic Fluency Test, SFT) function. Three molecular factors significantly correlated with the MDS-UPDRS3 score and two with SFT, which remained significant after adjusting for age, sex, and medication dose. We used the identified factors to stratify patients into subgroups with distinct motor and cognitive severity. The severe motor clusters showed deregulation of cytotoxic natural killer cell mechanisms in peripheral blood, and changes to proteins associated with the endoplasmic reticulum in CSF. The severe cognitive clusters showed changes in complement and synaptic dysfunction. Our analysis capitalizes on multi-omics data integration to enrich our understanding of the mechanisms driving motor and cognitive decline in PD, to support precision medicine.
Monocyte control of organismal energy homeostasis
Authors: Martins Rui , Blankenhaus Birte , Braza Faouzi , Ventura Pedro , Singh Sumnima , Weis Sebastian , Mesquita Miguel , Pires Maria , Pagnotta Sara , Wu Qian , Cardoso Silvia , Jentho Elisa , Figueiredo Ana , Faisca Pedro , Novoa Ana , Morais Vanessa , Wculek Stefanie , Sancho David , Mallo Moises , Soares Miguel P.
Published: February 2025

Multicellular organisms rely on inter-organ communication networks to maintain vital parameters within a dynamic physiological range. Macrophages are central to this homeostatic control system, sensing deviations of those parameters and responding accordingly to support tissue function and organismal homeostasis. Here we demonstrate that dysregulation of iron metabolism in parenchyma cells, imposed by the deletion of ferritin H chain, is sensed by monocyte-derived macrophages. In response, macrophages derived from circulating monocytes support tissue function, energy metabolism and thermoregulation, as demonstrated in bone marrow chimeric and parabiotic mice. This salutary effect is contingent on a transcriptional program, controlled in macrophages by the transcription factor A mitochondria. This transcriptional response acts in a non-cell autonomous manner to support the mitochondria of parenchyma cells, irrespectively of mitochondrial transfer. In conclusion, monocyte-derived macrophages cross-regulate Fe and energy metabolism to support tissue function and organismal homeostasis.
Are reads required? High-precision variant calling from bacterial genome assemblies
Authors: Wick Ryan R , Judd Louise M , Stinear Timothy P , Monk Ian R
Published: February 2025

Accurate nucleotide variant calling is essential in microbial genomics, particularly for outbreak tracking and phylogenetics. This study evaluates variant calls derived from genome assemblies compared to traditional read-based variant-calling methods, using seven closely related Staphylococcus aureus isolates sequenced on Illumina and Oxford Nanopore Technologies platforms. By benchmarking multiple assembly and variant-calling pipelines against a ground truth dataset, we found that read-based methods consistently achieved high accuracy. Assembly-based approaches performed well in some cases but were highly dependent on assembly quality, as errors in the assembly led to false-positive variant calls. These findings underscore the need for improved assembly techniques before the potential benefits of assembly-based variant calling - such as reduced computational requirements and simpler data management - can be realised.
Immunosuppressive myeloid cells induce mesenchymal-like breast cancer stem cells by a mechanism involving membrane-bound TGF-β1.
Authors: Boyer Thomas , Blaye Celine , Chalopin Domitille , Madery Mathilde , Boucher Jonathan , Moisand Alexandra , Giraud Julie , Theodoly-Lannes Audrey , Peyraud Florent , Seeneevassen Lornella , Klein Clement , Mebroukine Samy , Auriol Sophie , Chaibi Assia , Zouine Atika , Alizadeh Darya , McGrogan Gaetan , Lamarthee Baptiste , Bonnotte Bernard , Bonneil Eric , Roux Philippe P , Varon Christine , Domblides Charlotte , Larmonier Nicolas
Published: February 2025

Suppressive myeloid cells play a central role in cancer escape from anti-tumor immunity. Beyond their immunosuppressive function, these cells are capable of exerting multiple other pro-tumoral activities, including the promotion of cancer cell survival, invasion and metastasis. The ability of some myeloid subsets to induce cancer stemness has recently emerged. Here we demonstrated that human immunosuppressive myeloid cells, generated in vitro or isolated from breast cancer patients, promoted the acquisition of mesenchymal-like breast cancer stemness properties. This cancer-stemness-inducing function was restricted to a myeloid subset expressing the glycoprotein CD52. Single cell transcriptomic- and surface proteome-based interactome analysis pointed towards membrane-bound TGF-β1 as a potential factor involved in cancer stemness induction. Functional inhibition of the TGF-β1 pathway blocked the emergence of cancer stem cells induced by suppressive myeloid cells. These results therefore identified the underlying mechanisms of a new tumor-promoting function of immunosuppressive myeloid cells, which may potentially be targeted.
Measuring Genomic Data with PFP
Authors: Liptak Zsuzsanna , Masillo Francesco , Lucá Simone
Published: February 2025

Prefix free parsing [Boucher et al., Alg. Mol. Biol., 2019], is a highly effective heuristic for computing text indexes for very large amounts of biological data. The algorithm constructs a data structure, the prefix-free parse (PFP) of the input, consisting of a dictionary and a parse, which is then used to speed up computation of the final index. In this paper, we study the size of the PFP, which we refer to as π, and show that it is a powerful theoretical tool in its own right. To show this, we present two use cases. We first study the application of π as a repetitiveness measure of the input text, and compare it to other currently used repetitiveness measures, including z, r, and δ. We then turn to the use of π as a measure for pangenome openness. In both applications, our results are similar to existing measures, but our tool, in almost all cases, is more efficient than those computing the other measures, both in terms of time and space, sometimes by an order of magnitude. We close the paper with the first systematic study of the parameter choice for PFP (window size w and modulus p). This gives rise to interesting open questions. Availability and implementation: The source code is available at https://github.com/simolucaa/piPFP, the accession codes for all the datasets used at https://github.com/simolucaa/piPFP_experiments.
Generative and integrative modeling for transcriptomics with formalin fixed paraffin embedded material
Authors: Mucaki Eliseos J , Zhang Wenhan , Saha Aryamaan , Trebinjac Sabina , Nofech-Mozes Sharon , Rakovitch Eileen , Dumeaux Vanessa , Hallett Michael T
Published: February 2025

Formalin-fixed paraffin embedded (FFPE) samples are challenging to profile using existing high-throughput sequencing technologies, including RNA-seq. This difficulty primarily arises from the degradation of nucleic acids, a problem that becomes particularly acute with samples stored for extended periods. FFPE-derived RNA-seq (fRNA-seq) data have a high rate of transcript dropout, a property shared with single cell RNA-seq. Transcript counts also have high variance and are prone to extreme values. We introduce the PaRaffin Embedded Formalin-FixEd Cleaning Tool (PREFFECT), a probabilistic framework for the analysis of fRNA-seq data. PREFFECT uses generative models to fit distributions to observed expression counts while adjusting for technical and biological variables. The framework can exploit multiple expression profiles generated from matched tissues for a single sample (e.g., a tumor and morphologically normal tissue) in order to stabilize profiles and impute missing counts. PREFFECT can also leverage sample-sample adjacency networks that assist graph attention mechanisms to identify the most informative correlations in the data. We demonstrate how PREFFECT uses this information to more accurately compute downstream analyses such as sample clustering in several datasets.
SAEG: A Novel Deep Learning Architecture for Somatic Alterations
Authors: Iglesias-Martinez Luis Fernando , Wester Dan Yang , Kolch Walter
Published: February 2025

Somatic alterations, like mutations and copy number changes, driver oncogenesis and cancer progression. Their inhibition has been exploited in the clinic, with several targeted therapies approved for patients with specific mutations or amplifications. However, the response rate of these treatments remains low. The causes are several, ranging from clonal heterogeneity to off target binding. For this reason, CRISPR assays have been developed to study the exact effect of a gene's deletion. Still, the results from them are puzzling with the same alterations responding different to knockout even in the same cellular context. For this reason, we have developed SAEG, a novel deep learning architecture for somatic alterations in cancer. Our architecture is able to model mutations and copy number alterations and protein-protein interactions to predict if a cell will be susceptible to a gene knockout. SAEG outperforms other models and we show that it learns patterns that can be traced back to the biochemical and biological properties of genes and amino acids.
Branching architecture limits the rate of somatic mutation accumulation in trees
Authors: Johannes Frank
Published: February 2025

Trees are long-lived plants that develop complex, highly branched shoot systems as they grow. Their extended lifespan allows somatic mutations to accumulate along these branching structures, ultimately becoming fixed in reproductive and vegetative tissues such as leaves, flowers, and fruits. Mature trees can easily sustain tens of thousands of terminal branches, each potentially carrying mutated gametes. To avoid mutational meltdown and inbreeding depression, long-lived plants appear to have evolved mechanisms that slow mutation accumulation per unit time. How this is achieved remains unclear. Here, we show that branching architecture can limit mutation accumulation to the same extent as reducing the mutation rate itself. Tree structures that maximize branch path sharing during development constrain mutational diversity in the crown. These architectural factors can drive differences in mutation burden by orders of magnitude, even when mutation rates and terminal branch numbers are identical. Building on these insights, we show that current estimates of somatic mutation rates in trees are actually upward biased by a factor that scales with the topological characteristics of the tree. These results raise the deeper question whether somatic mutation rate differences, recently detected among tree species, reflect variation in branching strategies rather than variation in the rates themselves. It is possible that specific branching architectures have evolved not only to optimize resource allocation and structural stability but also to limit mutational load.
Most Upf1-associated mRNAs have short poly(A) tails, lack a premature termination codon and are targeted by NMD.
Authors: Gouhier Toni , Saveanu Cosmin , Badis Gwenael
Published: February 2025

Nonsense-mediated mRNA decay (NMD) is a conserved eukaryotic surveillance pathway known to degrade mRNAs containing premature termination codons (PTCs). A distance long enough between the stop codon and the poly(A)-binding protein (Pab1) is required for mRNA recognition by the NMD factors Upf1, Upf2 and Upf3. Using Nanopore direct RNA sequencing, we show that PTC-containing NMD targets account for only 6% of Upf1-associated RNA and have long poly(A) tails, indicating that Upf1-binding occurs prior to RNA deadenylation. Conversely, most Upf1-associated mRNAs have short poly(A) tails, lack a PTC and correspond to highly expressed genes. A short poly(A) tail is thus an important feature of NMD targets, redefining the scope of this RNA degradation pathway. We propose a model in which loss of Pab1-binding to short poly(A)-tailed mRNAs impairs translation termination and dictates the recruitment of the NMD machinery, uncovering a hitherto unknown role of NMD in the degradation of these transcripts.
A breast tissue-specific epigenetic clock provides accurate chronological age predictions and reveals de-correlation of age and DNA methylation in tumor-adjacent and tumor samples
Authors: Garma Leonardo Daniel , Pernas Sonia , Baz David Vicente , Garcia Campelo Rosario , Terrasa Josefa , Colomer Ramon , Jimenez Desiree , Vera Garcia Ruch , Bermejo Begona , Gonzalez Santiago Santiago , Quintela-Fandino Miguel
Published: February 2025

Epigenetic clocks have been widely used to estimate biological age across various tissues, but their accuracy in breast tissue remains suboptimal. Pan-tissue models such as Horvath's and Hannum's clocks, perform poorly in predicting chronological age in breast tissue, underscoring the need for a tissue-specific approach. In this study, we introduce a Breast Tissue-specific Epigenetic Clock (BTEC), developed using DNA methylation data from 553 healthy breast tissue samples across seven different studies. BTEC significantly outperformed pan-tissue clocks, demonstrating superior correlation with chronological age (r=0.88) and lower prediction errors (MAE=3.27 years) without requiring for dataset-specific regressions adjustments. BTEC's chronological age predictions for tumor-adjacent samples showed distortions, with an average deviation of -1.76 years, which was even more pronounced in tumor samples, where the average difference between predicted and chronological age was -12.29 years. When analyzed by molecular subtype, the distortion was greater in the more aggressive HER2+ and TNBC tumors compared to HR+ tumors. The probes used by BTEC were associated with known oncogenes, genes involved in estrogen metabolism, cadherin binding and fibroblast growth factor binding. Despite the general rejuvenation observed in tumor tissue compared to normal breast, the correlation between BTEC's predictions and cancer-related survival indicated that TNBC tumors with increased epigenetic ages had significant lower survival.
Artificial Neural Network Reveals the Role of Transport Proteins in Rhodopseudomonas palustris CGA009 During Lignin Breakdown Product Catabolism
Authors: Chowdhury Niaz B , Kathol Mark , Shahreen Nabia , Saha Rajib
Published: February 2025

Rhodopseudomonas palustris, a versatile bacterium with diverse biotechnological applications, can effectively breakdown lignin, a complex and abundant polymer in plant biomass. This study investigates the metabolic response of R. palustris when catabolizing various lignin breakdown products (LBPs), including the monolignols p coumaryl alcohol, coniferyl alcohol, sinapyl alcohol, p coumarate, sodium ferulate, and kraft lignin. Transcriptomics and proteomics data were generated for those specific LBP breakdown conditions and used as features to train machine learning models, with growth rates as the target. Three models, namely Artificial Neural Networks (ANN), Random Forest (RF), and Support Vector Machine (SV), were compared, with ANN achieving the highest predictive accuracy for both transcriptomics (94%) and proteomics (96%) datasets. Permutation feature importance analysis of the ANN models identified the top twenty genes and proteins influencing growth rates. Combining results from both transcriptomics and proteomics, eight key transport proteins were found to significantly influence the growth of R. palustris on LBPs. Re-training the ANN using only these eight transport proteins achieved predictive accuracies of 86% and 76% for proteomics and transcriptomics, respectively. This work highlights the potential of ANN-based models to predict growth-associated genes and proteins, shedding light on the metabolic behavior of R. palustris in lignin degradation under aerobic and anaerobic conditions.
3D Bioprinting of Kidney Tissue Using a Photocrosslinkable Hydrogel Derived from Decellularized Extracellular Matrix
Authors: Kim Keekyoung , Shin Jaemyung , Tabatabaei Rezaei Nima , Choi Subin
Published: February 2025

Three-dimensional bioprinting has emerged as a promising strategy in tissue engineering, aiming to fabricate functional tissue constructs for organ regeneration. A critical challenge in this field is the development of organ-specific bioinks that can provide a microenvironment conducive to cellular growth and differentiation. In this study, we successfully developed a photocrosslinkable bioink by methacrylating decellularized porcine kidney extracellular matrix. The decellularization process effectively removed all cellular components while preserving the native kidney extracellular matrix composition. The resulting methacrylated decellularized extracellular matrix bioink exhibited optimal rheological properties, making it well-suited for digital light processing based stereolithography and piston-driven extrusion bioprinting. Human embryonic kidney cells encapsulated in the bioink showed high viability and a strong proliferative capacity, indicating potential for tissue-specific maturation over time. This work demonstrates the feasibility of utilizing kidney-specific decellularized extracellular matrix-based bioinks, providing a platform for engineering renal tissue constructs for therapeutic applications.
Matrix tropism influences endometriotic cell attachment patterns
Authors: Theriault Hannah Simone , Kimmel Hannah Rosene Conover , Nunes Alison C , Paxhia Allison , Hashim Sarah , Clancy Kathryn B.H. , Underhill Gregory H. , Harley Brendan A.C.
Published: February 2025

Due to the extended period for clinical diagnosis, the etiology of endometriotic lesion initiation is not well understood or characterized. Endometriotic lesions are most often found on pelvic tissues and organs, especially the ovaries. To investigate the role of tissue tropism on ovarian endometrioma initiation, we adapted a well-characterized polyacrylamide microarray system to investigate the role of tissue-specific extracellular matrix and adhesion motifs on endometriotic cell attachment, morphology, and size. We report the influence of cell origin (endometriotic vs. non-endometriotic), substrate stiffness mimicking aging and fibrosis, and the role of multicellular (epithelial-stromal) cohorts on cell attachment patterns. We identify multiple ovarian-specific attachment motifs that significantly increase endometriotic (vs. non-endometriotic) cell cohort attachment that could be implicated in early disease etiology.
Glioma-induced DNMT3A-dependent reduction of DNA methylation in microglia promotes a transient anti-tumoral phenotype.
Authors: Cheray Mathilde , Murgoci Adriana-Natalia , Fragkopoulou Adamantia , Rodrigues Carlos F.D. , Skandik Martin , Osman Ahmed M. , Hong Christine , Vazquez-Cabrera Guillermo , Friess Lara , Carlson Lena-Maria , Kanatani Shigeaki , Li Yue , Damdimopoulos Anastasius , Uhlen Per , Kamme Fredrik , Blomgren Klas , Joseph Bertrand
Published: February 2025

Glioblastoma, aggressive primary brain tumors with a dismal prognosis, promote the recruitment of microglia, brain resident innate immune cells, and ultimately their activation toward a tumor-supportive phenotype that increases gliomal proliferation and invasion capability. Here, we report that upon stimulation by glioma cells, microglia transit via a reactive state holding anti-tumoral properties coupled to reduced DNMT3A chromatin occupancy and DNA demethylation that promote microglial pro-inflammatory gene expressions. We find that upon repression of Dnmt3a expression in microglia, those cells maintain anti-tumoral attributes in vitro and in vivo. In a syngeneic immunocompetent glioblastoma mouse model, brain delivery of antisense oligonucleotide targeting Dnmt3a expression led to reduced tumor growth. Taken together, our results reveal the involvement of DNA demethylation in the control of glioma cells-induced microglia activation and indicate that microglial DNMT3A is a potentially therapeutic target to treat brain neoplasms such as glioblastoma that include a microglial component.
Hydrodynamic Radius Determination of Tau and AT8 Phosphorylated Tau Mutants: A Combined Simulation and Experimental Study
Authors: Lohberger Cynthia , Marien Jules , Bridot Clarisse , Prevost Chantal , Allegro Diane , Tatoni Mario , Landrieu Isabelle , Smett-nocca Caroline , Sacquin-Mora Sophie , Barbier Pascale
Published: February 2025

This study investigates the effect of multiple phosphorylations of the Intrinsically Disordered Protein (IDP) tau on its hydrodynamic radius (Rh). Hyperphosphorylated tau is notably implicated in Alzheimer's disease The kinases responsible for adding phosphate groups are highly involved in the regulation of biological processes such as cell division, cell signalling, and apoptosis and, particularly, in the development of Alzheimer's disease, especially those recognized by the AT8 antibody. The main objective of this work is to understand how phosphorylation at the AT8 site affects the conformation and dynamics of the tau protein through the study of its hydrodynamic radius. To achieve this, we used a tau protein mutant with all phosphorylation sites mutated to alanine except those recognized by the AT8 antibody to achieve a specific phosphorylation pattern. The phosphorylation of this mutant was performed, firstly, by incubation with cyclin A kinase to obtain a first phosphorylated state, termed p-state 1 (serines at positions 202 and 205 and threonine at position 212 are phosphorylated), and secondly by incubation with CDK2/cyclin A kinase followed by GSK3β kinase to obtain a phosphorylated state termed call p-state 2 (serines 198 and 208 are phosphorylated in addition to the three previously described). The Rh of each sample was measured experimentally by dynamic light scattering (DLS) and analytical ultracentrifugation (AUC), and simulated using a new simulation model, pCALVADOS, combining the CALVADOS 2 model for IDPs with parameters for phosphorylated residues. We find that both wild- type tau and AT8-phosphorylated Tau mutants exhibit a relatively monodisperse distribution in solution suggesting that phosphorylations do not significantly alter the overall size of the conformational ensemble of tau. Our calculations of Local Curvatures and Local Flexibilities confirm that the mutations made on the tau sequence to perform selective phosphorylations do not significantly impact local dynamics, which is corroborated by several experimental results. We also identify a local stiffening and extension of the AT8 epitope that is proportional to the number of phosphorylations. Interestingly, phosphorylations do not just affect the immediate AT8 area. We also report contact losses at a distance, with a noticeable directionality pointing towards the N-terminal end of the monomer, which could have functional implications for the phosphorylated Tau protein. The study paves the way for future research on the structure-function relationship of Tau and the role of phosphorylation in neurodegenerative diseases.
LivecellX: A Deep-learning-based, Single-Cell Object-Oriented Framework for Quantitative Analysis in Live-Cell Imaging
Authors: Ni Ke , Yu Gaohan , Zheng Zhiqian , Poe Dante , Khurana Yajushi , Zhang Sijie , Zhou Shiman , Wang Weikang , Xing Jianhua
Published: February 2025

Analyzing single-cell dynamics is crucial for understanding developmental biology, cancer biology, and other complex biological processes. This analysis depends on accurately detecting and tracking individual cells across both spatial and temporal scales, with live-cell imaging serving as a key tool. However, extracting reliable dynamic information from live-cell imaging data remains a significant challenge. The task involves constructing long single-cell trajectories and representing dynamic behaviors through multi-dimensional features. Despite recent advances in deep learning-driven segmentation, pre-trained and fine-tuned models often fail to achieve perfect segmentation in live-cell imaging scenarios. The extended duration of live-cell imaging further amplifies segmentation errors, complicating the maintenance of precise and consistent segmentation. To address these challenges, we introduce LivecellX, a comprehensive framework for live-cell imaging data analysis. LivecellX provides an integrated solution for segmentation, tracking, and dynamic analysis by adopting a single-cell, object-oriented architecture. This architecture not only enhances segmentation and tracking accuracy but also simplifies the extraction of trajectory dynamics, making it easier for users to analyze complex biological processes. Central to Live-cellX is the Correct Segmentation Network (CSN), a context-aware, multi-scale machine learning architecture designed to correct segmentation inaccuracies. To effectively apply CSN to large datasets, we developed trajectory-level algorithms that systematically address specific segmentation issues. To ensure robustness and user accessibility, we developed an asynchronous graphical user interface (GUI) based on Napari, allowing seamless interaction with the data both interactively and programmatically at any stage of the analysis. By combining automated methods with interactive correction capabilities, Live-cellX provides a comprehensive solution for precise, large-scale live-cell imaging analysis, empowering researchers to obtain more accurate biological insights.
Emergent 3D genome reorganization from the stepwise assembly of transcriptional condensates
Authors: Chowdhary Surabhi , Paracha Sarah , Dyer Lucas , Pincus David
Published: February 2025

Transcriptional condensates are clusters of transcription factors, coactivators, and RNA Pol II associated with high-level gene expression, yet how they assemble and function within the cell remains unclear. Here we show that transcriptional condensates form in a stepwise manner to enable both graded and three-dimensional (3D) gene control in the yeast heat shock response. Molecular dissection revealed a condensate cascade. First, the transcription factor Hsf1 clusters upon partial dissociation from the chaperone Hsp70. Next, the coactivator Mediator partitions following further Hsp70 dissociation and Hsf1 phosphorylation. Finally, Pol II condenses, driving the emergent coalescence of HSR genes. Molecular analysis of a series of Hsf1 mutants revealed graded, rather than switch-like, transcriptional activity. Separation-of-function mutants showed that condensate formation can be decoupled from gene activation. Instead, fully assembled HSR condensates promote adaptive 3D genome reconfiguration, suggesting a role of transcriptional condensates beyond gene activation.
A NATIONAL SURVEY SHOWS A DILEMMA TOWARDS SBP PROPHYLAXIS AMONG US-BASED HEPATOLOGY PROFESSIONALS
Authors: DiazGranados Deborah , O'Leary Jacqueline G , Yamuzala Madhumita , Rogal Shari , Bajaj Jasmohan
Published: February 2025

Background: Spontaneous bacterial peritonitis prophylaxis (SBPPr)-related practices are evolving, with recent studies showing almost half of potential subjects not being initiated on it. Aim: Determine practice dilemmas regarding SBPPr among US-based hepatology providers. Method: A questionnaire regarding primary and secondary SBPPr using quantitative and qualitative (open-ended) approaches was sent to US-based hepatology providers electronically. Results: 113 clinicians (86% physicians, 73% academic centers) responded. 54% started Primary and 72% secondary SBPPr in 50% of eligible patients. However, the issues related to antimicrobial resistance (AMR) and ineffectiveness lead to SBPPr usage variations and restrictions on a patient-specific basis. Most respondents (>70%) would withdraw/not initiate SBPPr with data regarding ineffectiveness and harms. Open-ended answers showed that most believed newer trials to reduce reliance on weaker older evidence are needed. Conclusion: A survey of US-based hepatologists demonstrates a major dilemma between usual care of SBPPr versus not initiating/withdrawing SBPPr that needs newer randomized trials.
Comprehensive analysis of myeloid reporter mice
Authors: Wang Yidan , Dowling Samuel D , Rodriguez Vanessa , Maciuch Jessica , Mayer Meghan , Therron Tyler A , Shaw Tovah N , Gurra Miranda G , Shah Caroline L , Makinde Hadijat-Kubura M , Ginhoux Florent , Voehringer David , Harrington Cole A , Lawrence Toby , Grainger John R , Cuda Carla M , Winter Deborah R , Perlman Harris R
Published: February 2025

Macrophages are a pivotal cell type within the synovial lining and sub-lining of the joint, playing a crucial role in maintaining homeostasis of synovium. Although fate-mapping techniques have been employed to differentiate synovial macrophages from other synovial myeloid cells, no comprehensive study has yet been conducted within the mouse synovial macrophage compartment. In this study, we present, for the first time, lineage tracing results from 18 myeloid-specific fate-mapping models in mouse peripheral blood (PB) and synovial tissue. The identification of synovial macrophages and monocyte-lineage cells through flow cytometry was further validated using cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) datasets. These findings provide a valuable methodological tool for researchers to select appropriate models for studying the function of synovial myeloid cells and serve as a reference for investigations in other tissue types.
Accurate and Reproducible Whole-Genome Genotyping for Bacterial Genomic Surveillance with Nanopore Sequencing Data
Authors: Prior Karola , Becker Karsten , Brandt Christian , Cabal Rosel Adriana , Dabernig-Heinz Johanna , Kohler Christian , Lohde Mara , Ruppitsch Werner , Schuler Franziska , Wagner-Lichtenegger Gabriel E. , Mellmann Alexander
Published: February 2025

Despite recent advances in error rate reduction, until recently Oxford Nanopore Technology (ONT) sequences lacked the accuracy required for fine scale bacterial genomic analysis. Here, recent software improvements of ONT and the ONT-cgMLST-Polisher within the SeqSphere+ software were evaluated. We used short- (Illumina) and long-read ONT sequences of 80 multidrug-resistant bacteria (MDROs) for benchmarking. Illumina reads were assembled with SKESA. For ONT, Dorado SUP model 4.3 or 5.0 basecalled reads were assembled with Flye and then polished with Medaka v1.12 m4.3 or Medaka v2.0 bacterial methylation model. In addition, the ONT-cgMLST-Polisher was run over all assemblies. The ground truth (GT) hybrid assemblies were created using Hybracter v0.10.0. Sixteen out of the 80 isolates, representing four species, were sent to six laboratories for a ring trial. The 80 MDROs basecalled with SUP m4.3 had an average cgMLST allele distance (AD) to the GT of 4.94 with Medaka v1.12 and 1.78 with Medaka v2.0, respectively. After further polishing the Medaka 2.0 data with the ONT-cgMLST-Polisher, the AD dropped to 0.09. Using data basecalled with SUP m5.0 with Medaka 2.0 further reduced the AD significantly to 0.04. While the ring trial data basecalled with Dorado SUP m4.3 showed more variability and insufficient results for some samples, model 5.0 data resulted in average ADs of 0.36 and 0.17 without and with the ONT-cgMLST-Polisher, respectively. In conclusion, recent ONT Dorado and Medaka models combined with the ONT-cgMLST-Polisher improved ONT sequencing accuracy and made it sufficiently reproducible for genomic surveillance of bacteria.
Utilization of Youth-Friendly Reproductive Health Services and Associated Factors among Secondary School Students in Addis Ababa, Ethiopia.
Authors: Huluka Yitbarek Biru , Dasa Tamirat Tesfaye
Published: February 2025

Abstract Introduction: Due to disparities in data gathering and dissemination between nations, it is challenging to provide exact statistics. However, the global scope of reproductive health problems within schools is substantial, with numerous problems influencing the development and well-being of young people. Objective: This study aimed to assess the utilization of youth-friendly reproductive health services (YFRHS) by secondary school students in Yeka Sub-City, Addis Ababa, Ethiopia. Method: To examine the YFRHS among secondary school students in Yeka Sub-City, Addis Ababa, an institution-based cross-sectional survey was conducted between June and July 2024. A total of 415 students from 15 secondary schools who were chosen randomly participated in this study. A standard, well-structured, self-administered questionnaire was used to collect the data. After cleaning, coding, and importing into EpiData version 4.6.0.2, data were exported to SPSS Windows version 27. Factors related to YFRHS use were identified using binary logistic regression analysis. In multivariable logistic regression, every factor in the bivariate analyses, with a p-value less than 0.25 in the bivariate analyses was included. The strength of relationship was evaluated using the adjusted odds ratio and a 95% CI, with a P value ≤ 0.05 was taken into consideration to announce the statistical significance. Results: Youth-friendly reproductive health services (YFRHS) utilization in this study was 18.8% (95% CI: 0.154, 0.227). This study found that having a sexual partner Adjusted Odd Ratio (AOR) (AOR: 3.8 (1.7, 8.4)), having a conversation with parents (AOR: 2.2 (1.2, 4.02)), having YFRHS facilities nearby (AOR: 5.1 (2.5, 10.3)), and believing that seeking behavior improves youth health (AOR: 4.6 (1.5, 14.04)) were all significantly associated with reproductive health utilization. Conclusion: Among school-aged youth, one in five used youth-friendly reproductive health services. Reproductive health use was significantly associated with having a sexual partner, having a favorable perspective on whether seeking behavior benefits youth health, having discussions with parents, and having YFRHS facilities in the living area. Key Wor ds: Reproductive Health, youths, secondary school, Yeka Sub-City, Ethiopia
Contact networks of small mammals highlight potential transmission foci of Lassa mammarenavirus.
Authors: Simons David , Goyal Ravi , Bangura Umaru , Gibb Rory , Rushton Ben , Sondufu Dianah , Lamin Joyce , Koninga James , Jimmy Momoh , Dawson Mike , Lahai Joseph , Ansumana Rashid , Fichet-Calvet Elisabeth , Watson-Jones Deborah , Kock Richard , Jones Kate E
Published: February 2025

Lassa fever, caused by Lassa mammarenavirus (LASV), is an endemic zoonosis in several West African countries. Human infections primarily result from transmission from rodent hosts, with the primary reservoir species being Mastomys natalensis, a synanthropic rodent. In Sierra Leone, small-mammal communities are structured along land use gradients, and this structure is hypothesized to influence the risk of Lassa fever outbreaks in human populations. However, whether anthropogenic habitats facilitate significant LASV transmission among small mammals is not well understood. To address this, we conducted rodent sampling over 43,266 trap nights, detecting 684 rodents and shrews in the Lassa fever-endemic Eastern Province of Sierra Leone. We reconstructed small-mammal contact networks to investigate whether contact rates and network structures differed by land use to identify settings more conducive to viral transmission. We found that small-mammal communities were larger in villages and agricultural settings than in forests, but contact rates were similar across habitats. Network structures differed by land use, with villages exhibiting more disconnected networks compared to agricultural settings. Notably, intra-specific contact among M. natalensis was more likely in agricultural environments than in villages, suggesting that land use type influences LASV transmission dynamics. Overall, LASV seroprevalence was 5.7% across the small-mammal communities, with LASV antibodies detected in nine rodent and shrew species. These findings underscore the importance of expanding rodent surveillance across various habitats to understand habitat-specific pathogen transmission dynamics. A more systematic approach to LASV surveillance in villages and agricultural settings will help identify key host species driving pathogen dynamics.