bluuebunny/crossref_metadata_2025 huggingface dataset:
Orbicularis Oculi Transpalpebral Pedicle Flap for the Repair of Laminar Resorption Associated With Osteo-Odonto-Keratoprosthesis
Authors: Hong Sheng Chiong , Trinh Tanya , Martin Peter , Chorny Alexander , Moloney Greg
Published: November 2024

Osteo-odonto-keratoprosthesis (OOKP) is a surgical procedure reserved for severe end-stage corneal blindness with a dry, keratinized ocular surface. Late resorption of bone has been described as a complication of this procedure. We present a novel surgical technique to repair laminar resorption associated with OOKP using transpalpebral split-pedicle orbicularis oculi flaps. The technique comes with the advantages of not needing additional bone grafts, and provides the alveo-bonemucosa complex with additional tissue bulk and blood supply.
Intraoperative liquid biopsy as a tool for detecting R1 resection during pancreatoduodenectomy in patients with pancreatic carcinoma: the CETUPANC trial (part II)
Authors: Padillo-Ruiz Javier , Garcia Carlos , Suarez Gonzalo , Blanco Gerardo , Muñoz-Bellvis Luis , Justo Iago , García-Domingo Maria I. , Ausania Fabio , Muñoz-Forner Elena , Serrablo Alejandro , Martin Elena , Díez Luis , Cepeda Carmen , Marin Luis , Alamo Jose , Bernal Carmen , Pereira Sheila , Calero Francisco , Laga Imán , Paterna Sandra , Cugat Esteban , Fondevila Constantino , López-Guerra Diego , Gallego-Jiménez Inmaculada , Borrero-Martín Juan José , Gomez-Bravo Miguel Ángel , Tinoco Jose , Sabater Luis
Published: November 2024

Introduction:

A positive surgical margin (R1 resection) is a relevant risk factor for local recurrence in patients with pancreatic ductal adenocarcinoma of the pancreas (PDAC). An intraoperative liquid biopsy (ILB) based on tumor cell mobilization could help to detect R1 resection intraoperatively.

Objective:

To evaluate the potential role of the intraoperative circulating tumor cells (CTCs) and cluster mobilization on the R0/R1 detection.

Methods:

Sixty-three patients with resectable PDAC of the head of the pancreas were prospective enrolled under the CETUPANC trial. Open pancreaticoduodenectomy (PD) was done in all patients. Intraoperative CTCs and clusters were determined during PD.

Results:

The overall rate of R1 resection was 34.9% (22/63 patients). Multivariate analysis showed that factors associated with R1 resection (AUC=0.920) were the presence of undifferentiated G3 tumor (P=0.017), microscopic vascular invasion (P=0.016), and the intraoperative increase of both free CTCs and clusters in portal vein determination from the beginning to the end of the surgery (P=0.002 and P=0.005, respectively). A specific logistic regression model, including delta end to baseline CTCs and cluster mobilization to achieve a combined cut-off to detect R1 detection was calculated (AUC=0.799). The obtained R1-index based on ILB had 84% of sensitivity and 68% of specificity to detect R1 resection.

Conclusions:

The ILB based on the intraoperative mobilization of CTCs and clusters from the beginning to the end of the PD was a predictive factor to detect R1 resection in patients with PDAC.
The Difficulties of Treating Complement-3–Mediated Glomerulopathy
Authors: Ghani Maham , Alisan Bedir , Barmas-Alamdari Daniel , Attieh Rose Mary , Jhaveri Kenar D.
Published: November 2024

Background:

C3 glomerulopathy (C3G) is a rare disease affecting the complement alternative pathway, categorized into dense deposit disease and C3 glomerulonephritis. Dense deposit disease predominantly affects younger individuals, while C3 glomerulonephritis tends to manifest in older populations. The diseases are characterized by dysregulation of the complement alternative pathway, leading to the deposition of complement components in the glomeruli and subsequent renal dysfunction. Notably, the incidence of C3G in the United States is low, with 1–3 cases per 1,000,000 and a prevalence of 5 cases per 1,000,000.

Areas of Uncertainty:

Numerous uncertainties persist in comprehending the etiology and pathophysiology of C3G. While biomarkers such as C3 nephritic factor, autoantibodies, and relevant genetic mutations have been identified, their pathogenicity and clinical utility remain unclear. Standard workups involve complement assays and autoantibody panels, yet the definitive diagnostic test remains a kidney biopsy. Nuanced challenges lie in deciphering the sensitivity and specificity of these diagnostic tools, especially in the presence of phenotypical variations among individuals.

Therapeutic Advancement:

Current therapeutic approaches, albeit lacking robust evidence, encompass a spectrum ranging from supportive care to targeted B-cell therapy and immunosuppression with mycophenolate mofetil and glucocorticoids. For severe and refractory cases, the monoclonal antibody eculizumab, targeting C5 in the complement cascade, is recommended. These treatments, while offering some relief, pose challenges related to their cost and obtaining insurance approval. Exploratory avenues delve into the potential of plasma exchange and innovative treatments such as oral complement inhibitors, reflecting the ongoing quest for effective therapeutic modalities. Trials investigating various complement inhibitors underscore the dynamic landscape of therapeutic advancements in C3G management.

Conclusion:

In conclusion, the article highlights the complexities of C3G management. The need for further understanding, large-scale trials, and ongoing investigations into disease etiology and pathophysiology is emphasized.
Correlation Between Self-reported or Supervised Physical Activity in Noncommunicable Diseases and Comorbidities During COVID-19 Pandemic: A Systematic Review
Authors: Dixit Snehil , Srivastava Saumya , Reddy Ravi Shankar , Faghy MA , Tedla Jaya Shanker , Kakaraparthi Venkata Nagaraj , Gular Kumar , Gupta Kanishk
Published: November 2024

Objective

The aim of the study is to systematically identify the protective and ameliorative effects of physical activity among people with noncommunicable diseases such as diabetes, cancer, chronic respiratory disease, chronic vascular disease, hypertension, and existing comorbidities during the coronavirus disease (COVID-19) pandemic.

Methods

The trial is registered in the PROSPERO registry and used the PICO (population, intervention, comparison, and outcomes) strategy to perform the search strategy. Assessors analyzed related studies in the MEDLINE, PROQUEST, PubMed, Cochrane Library, CINAHL, Embase, Google Scholar, Physiotherapy Evidence, and Science Direct databases between December 2022 and January 2023. Researchers independently conducted a quality assessment of each study using a predeveloped quality assessment tool adapted from established tools for quantitative studies.

Results

Eighteen trials were included (chronic vascular disease–7, diabetes–4, hypertension–1, cancer–3, and chronic respiratory disease–3). The total number of individuals included in the systematic review was 780,003, and the total with or without COVID-19 was 188,435. Qualitative rating by the Newcastle-Ottawa Score for cross-sectional and cohort studies and the Physiotherapy Evidence Database scale revealed fair to good evidence for physical activity as a tool to reduce complications.

Conclusions

There is evidence that exercise can protect people with noncommunicable diseases during the COVID-19 pandemic.

Registration: Registered with Prospero registry
Understanding the Preferred Learning Styles of Urogynecology Patients
Authors: Kunycky Christina , Bernard Adele , Willis-Gray Marcella , Geller Elizabeth J.
Published: November 2024

Importance

Patient comprehension is paramount to treatment option counseling in urogynecology. This study investigates how patients prefer to receive information in a learning environment.

Objective

This study aimed to understand the learning preferences of patients presenting to a urogynecology clinic.

Methods

We conducted a cross-sectional survey study of patients presenting to an outpatient academic urogynecology clinic. The primary objective was to identify patient learning styles using the Visual, Aural, Read/write, Kinesthetic (VARK) Learning Style Questionnaire. Secondary objectives included determining predictive characteristics of learning styles such as age, race, education level, socioeconomic status, and the patient's self-identified learning style.

Results

Of 125 participants, most were multimodal (60%) preferring a combination of learning styles. Twenty percent of patients were categorized as kinesthetic learners, 10% reading/writing, 7% aural, and 2% visual. Forty-three percent correctly identified their learning styles, and an additional 26% partially identified their learning styles. When assessing predictors of learning style, visual and kinesthetic learners were younger. Aural learners had a higher proportion of Black and Latina representation. Visual and reading/writing learners all had at least some college education.

Conclusions

Among patients presenting to a urogynecology clinic, a range of learning preferences was identified, with the majority of patients having a preference for multimodal learning with the majority accurately identifying 1 or more modalities of their learning styles. Given the high rate of multimodal learning, health care providers should consider having multiple modalities in which information can be provided to urogynecology patients.
Clinical and Histopathological Findings in HIV-positive to HIV-positive Kidney Transplant Recipients
Authors: Wearne Nicola , Botha Francois , Manning Kathryn , Price Brendon , Barday Zunaid , Post Frank A. , Freercks Robert , Bertels Laurie , Mtingi-Nkonzombi Lungiswa , Muller Elmi
Published: November 2024

Background.

The spectrum of histological findings in transplanted kidneys from HIV-positive donors to HIV-positive recipients is relatively unexplored. This study describes the type and timing of histological diagnoses observed in this unique cohort.

Methods.

Adequate biopsies were analyzed at implantation and posttransplant between September 2008 and May 2022. Histological disease spectrum, distributions over time, and relevant clinical characteristics and management were reported for both for-cause and protocol biopsies.

Results.

Twenty-four implantation biopsies from 31 deceased donors and 179 allograft biopsies (100 for-cause, 79 protocol) from 50 recipients were analyzed. Most rejection episodes occurred in the first year posttransplant. Eighteen recipients (36%) had at least 1 episode of biopsy-confirmed acute/chronic T cell–mediated rejection (TCMR) or active antibody-mediated rejection (AMR). Protocol biopsies showed no active AMR or acute/chronic TCMR. However, 9 of 79 biopsies identified borderline/suspicious TCMR. Common nonrejection diagnoses were interstitial fibrosis and tubular atrophy, ascending pyelonephritis, and calcineurin inhibitor toxicity. Classic and suspected HIV-associated nephropathy (HIVAN) were identified in 3 and 6 patients, respectively. Protocol biopsies diagnosed 1 case of classic HIVAN and 6 cases of suspected HIVAN. AMR most adversely affected kidney function and significantly contributed to graft failure.

Conclusions.

The histological findings in this cohort of HIV-positive kidney transplant recipients who received grafts from unmatched HIV-positive donors revealed a spectrum of abnormalities. Protocol biopsies added to surveillance on borderline rejection and assisted in the recognition of HIVAN. Confirmed rejection occurred in 18 recipients (36%). Understanding the factors contributing to this may assist in the optimization of immunosuppressive protocols in the future.
Increased Systemic Immune-Inflammatory Index and Association with Occult Nodal Disease in Non-Small Cell Lung Cancer
Authors: Khan Arsalan A , Shah Savan K , Basu Sanjib , Alex Gillian C , Liptay Michael J , Geissen Nicole M , Seder Christopher W
Published: November 2024

Background:

It has been proposed that more aggressive tumors trigger a stronger inflammatory response than less aggressive types. We hypothesize that systemic immune inflammatory index (SII) is associated with occult nodal disease (OND) in clinically node negative (cN0) patients undergoing lung resection for non-small cell lung cancer (NSCLC).

Study Design:

The study included patients who underwent lung resection with nodal dissection, according to current guidelines, at a single center between 2010-2021 for NSCLC. Pre-operative SII within three weeks of surgery, was calculated. OND was defined as a clinically node-negative patient found to be pathologically node-positive. Cut-point analysis for SII was performed to identify the level most strongly associated with OND. Univariable and multivariable logistic regressions were used to examine the association between SII, clinical factors, and OND.

Results:

A total of 199 patients met inclusion criteria, of which 51% (102/199) were female. The median number of nodes and nodal stations examined was 13 (IQR 9-17) and 6 (IQR 5-6), respectively. The cut-point was determined to be SII ≥112. On univariable analysis, high SII was associated with OND (OR 15.75, CI 2.09-118.73, p=0.007). On multivariable analysis, after controlling for age, BMI, approach, gender, pack years, FEV1, performance status, comorbidities, histology, lymphovascular invasion, tumor differentiation and tumor size, high SII was associated with OND (OR 34.59, CI 2.69-444.88, p=0.007).

Conclusion:

Increased SII is associated with OND in patients undergoing lung resection for NSCLC.
Uninterpretable graphs at a scientific conference
Authors: Faulkes Zen
Published: November 2024

Comparing averages requires knowing sample variation, which can be shown visually using a bar graph with error bars or a box plot. Because error bars and box plots can show different measures, they must be labelled to be interpretable. Of graphs of averages shown at a scientific conference in 2020, 87.5% of graphs did not contain enough information on the slide to interpret them. The only graphs that were fully interpretable (12.5%) were bar graphs. By comparison, 92% of graphs of averages published in a journal in the same field contained enough information to interpret them. While conferences are not and should not be as stringent about data presentation as journals, that a statistical value as simple as an average are not clearly presented suggests graphs are created by rote.
Rapid and precise quantification of lymphocyte iron content by single cell inductively coupled plasma mass spectrometry
Authors: Holdship Philip , Teh Megan R. , Mazurczyk Michalina , Chuang Huei-Wen , Pironaci Giulia , Hilton Robert G. , Price David , Wade Jon , Drakesmith Hal
Published: November 2024

Metals facilitate catalysis during cellular metabolism, but heterogeneity of metal content at single-cell level within and between cell populations is poorly characterized. This is important because deficiencies of biometals, for example iron, are enormously prevalent worldwide. Here we quantify metal content of single-cells using inductively-coupled plasma mass spectrometry. To develop the method, we used rhodium and iridium-intercalated Jurkat cells, obtaining >0.96% r2cross-analytical correlation with mass cytometry. We quantified iron and calcium mass/cell for murine T-lymphocytes with 3% and 8% 2-sigma intra-precision, respectively, when assessing thousands of cells/minute. T-lymphocytes exposed to a 625-fold difference in extracellular iron concentrations maintained close iron homeostatic control, varying ∼20% in iron content. Nevertheless, this relatively small variation strongly correlated with changes in cellular activation characteristics measured by flow cytometry. We also assessed human B-cell iron content, which was ∼10-fold higher than murine T-lymphocytes. Overall, we demonstrate rapid iron quantification at single-cell level in different cell types and relate cellular iron content to cell function.

Teaser

Precise and rapid iron metallomics of lymphocytes by single cell ICP-MS is a powerful approach for accessing signatures of immunological status.
Communication subspaces align with training in ANNs
Authors: Poggi Peter G. , Mihalas Stefan , Mastrovito Dana
Published: November 2024

Communication subspaces have recently been identified as a promising mechanism for selectively routing information between brain areas. In this study, we explored whether communication sub-spaces develop with training in artificial neural networks (ANNs) and explored differences across connection types. Specifically, we analyzed the subspace angles between activations and weights in ResNet-50 before and after training. We found that activations were more aligned to the weight layers after training, although this effect decreased in deeper layers. We also analyzed the angles between pairs of weight layers. We found that for all branching, direct, and skip connections, weight layer pairs were more geometrically aligned in trained versus untrained models throughout the entire network. These findings indicate that such alignment is essential for the proper functioning of deep networks and highlights the potential to enhance training efficiency through pre-alignment. In biological data, our results motivate further exploration into whether learning induces similar subspace alignment.
Proteome-wide reverse molecular docking reveals folic acid receptor as a mediator of PFAS-induced neurodevelopmental toxicity
Authors: Kong Ally Xinyi , Johnson Maja , Eno Aiden F , Pham Khoa , Zhang Ping , Geng Yijie
Published: November 2024

Per- and polyfluoroalkyl substances (PFAS) are a class of long-lasting chemicals with widespread use and environmental persistence that have been increasingly studied for their detrimental impacts to human and animal health. Several major PFAS species are linked to neurodevelopmental toxicity. For example, epidemiological studies have associated prenatal exposure to perfluorooctanoate (PFOA) and perfluorononanoate (PFNA) with autism risk. However, the neurodevelopmental toxicities of major PFAS species have not been systematically evaluated in an animal model, and the molecular mechanisms underlying these toxicities have remained elusive. Using a high-throughput zebrafish social behavioral model, we screened six major PFAS species currently under regulation by the Environmental Protection Agency (EPA), including PFOA, PFNA, perfluorooctane sulfonate (PFOS), perfluorohexanesulfonic acid (PFHxS), perfluorobutane sulfonate (PFBS), and hexafluoropropylene oxide dimer acid ammonium salt (GenX). We found that embryonic exposure to PFNA, PFOA, and PFOS induced social deficits in zebrafish, recapitulating one of the hallmark behavioral deficits in autistic individuals. To uncover protein targets of the six EPA-regulated PFAS, we screened a virtual library containing predicted binding pockets of over 80% of the 3D human proteome through reverse molecular docking. We found that folate receptor beta (FR-β, encoded by the geneFOLR2) interacts strongly with PFNA, PFOA, and PFOS but to a lesser degree with PFHxS, PFBS, and GenX, correlating positively with theirin vivotoxicity. Embryonic co-exposure to folic acid rescued social deficits induced by PFAS. The folic acid pathway has been implicated in autism, indicating a novel molecular mechanism for PFAS in autism etiology.
ENTPD3-specific CAR Regulatory T cells for Local Immune Control in T1D
Authors: Pieper Tom , Riet Tobias , Saetzler Valerie , Bergerhoff Katharina , McGovern Jenny , Delsing Louise , Atkinson Mark , Lodie Tracey , Jermutus Lutz , Noyan Fatih , Hust Michael , Kusmartseva Irina , Hagedorn Maike , Lieber Maren , Henschel Pierre , Glaser Viktor , Geffers Robert , Yang Mingxing , Polansky-Biskup Julia , Eiz-Vesper Britta , Bonifacius Agnes , Martinez Llordella Marc , Henry Luke , Penston Daniela , Gavriil Artemis , Grothier Thomas , Nikolopoulou Evanthia , Demertzis Nikolaos , Koullourou Victoria , Cox Phillipa , Zarrouki Bader , Sini Marcella , Pfeiff Janice , Matthiesen Isabelle , Hardtke-Wolenski Matthias , Jaeckel Elmar
Published: November 2024

Despite advances in Type 1 Diabetes (T1D) management such a hybrid closed loop systems, patients still face significant morbidity, reduced life expectancy, and impaired glucose regulation compared to healthy individuals or those with pancreas transplants.

Here we developed beta cell-specific Chimeric Antigen Receptors (CAR) targeting the antigen ectonucleoside triphosphate diphosphohydrolase 3 (ENTPD3) using a novel cell-based phage display methodology. ENTPD3 is highly expressed on beta cells of both early and progressed T1D patients. ENTPD3 CAR regulatory T cells (Tregs) homed, expanded and persisted in pancreatic islets in a T1D mouse model (NOD) and completely prevented disease progression. Human ENTPD3 CAR Tregs displayed a stable regulatory phenotype, strong activation, and suppression. Importantly, ENTPD3 CAR T cells recognised and were fully activated by human islets.

This approach holds great promise as a durable treatment option for patients with prediabetes, new-onset diabetes, or those undergoing beta cell replacement therapy.
Vertical sleeve gastrectomy in rodents: impact on metabolic, cardiovascular and hepatic functions of mothers and perinatal consequences
Authors: Payen Cyrielle , Guillot Abigaëlle , Chaigneau Julien , Bichot Lucile , Testa Eugénie , Bourreau Jennifer , Gascoin Géraldine , Vessières Emilie , Proux Carolyne , Moal Valérie , Loufrani Laurent , Schmitt Françoise , Fassot Céline
Published: November 2024

Background

Maternal obesity is a well-known risk factor for obstetrical complications during pregnancy, and cardiovascular and metabolic pathologies in the offspring. In the last two decades, bariatric surgery has emerged as the most effective treatment for severe obesity, and is known to improve fertility, leading to a rise in procedures among women of childbearing age.

Objectives

This study investigates the impact of pre-conceptional sleeve gastrectomy (SG) on metabolic, cardiovascular and hepatic functions of mothers at short and middle terms after surgery, and its perinatal consequences.

Methods

Sprague-Dawley female control rats (CM) received a standard diet, while others were fed a high-fat, high-sugar diet (HFHS). HFHS rats were divided into obese mothers (OM) and sleeve gastrectomy mothers (SM). One month after surgery, all groups underwent gestation and subsequent lactation Metabolic function was assessed at 1 and 4 months after surgery; cardiovascular and hepatic functions were evaluated only 4 months after SG.

Results

From 1 month post-surgery, SM showed normalized leptin and insulin levels compared to OM. Moreover, SG normalized body weight associated with a decreased white adipose tissue weight and adipocyte size at 4 months post-surgery. Interestingly, although steatosis has been detected in HFHS rats, SM exhibited only hepatic fibrosis at 4 months post-surgery. Moreover, SM showed a hypertrophic remodeling of thoracic aorta without effect on its vasoreactivity but along with endothelial dysfunction of mesenteric artery, associated with a stronger involvement of COX/PGI2 pathway. In the offspring, obesity in mothers was associated to a decreased liter size, reversed by sleeve gastrectomy without any effect on the birth weight of pups.

Conclusion

While this study reports an improvement of metabolic function at short- and medium-terms after bariatric surgery, our results highlight an alteration of hepatic and vascular functions by sleeve gastrectomy, with minimal effect on the offspring in the perinatal period.
Unveiling epigenetic regulatory elements associated with breast cancer development
Authors: Jardanowska-Kotuniak Marta , Dramiński Michał , Własnowolski Michał , Łapiński Marcin , Sengupta Kaustav , Agarwal Abhishek , Filip Adam , Ghosh Nimisha , Pancaldi Vera , Grynberg Marcin , Saha Indrajit , Plewczynski Dariusz , Dąbrowski Michał J.
Published: November 2024

Breast cancer is the most common cancer in women and the 2nd most common cancer worldwide, yearly impacting over 2 million females and causing 650 thousand deaths. It has been widely studied, but its epigenetic variation is not entirely unveiled. We aimed to identify epigenetic mechanisms impacting the expression of breast cancer related genes to detect new potential biomarkers and therapeutic targets. We considered The Cancer Genome Atlas database with over 800 samples and several omics datasets such as mRNA, miRNA, DNA methylation, which we used to select 2701 features that were statistically significant to differ between cancer and control samples using the Monte Carlo Feature Selection and Interdependency Discovery algorithm, from an initial total of 417,486. Their biological impact on cancerogenesis was confirmed using: statistical analysis, natural language processing, linear and machine learning models as well as: transcription factors identification, drugs and 3D chromatin structure analyses. Classification of cancer vs control samples on the selected features returned high classification weighted Accuracy from 0.91 to 0.98 depending on feature-type: mRNA, miRNA, DNA methylation, and classification algorithm. In general, cancer samples showed lower expression of differentially expressed genes and increasedβ-values of differentially methylated sites. We identified mRNAs whose expression is well explained by miRNA expression and differentially methylated sitesβ-values. We recognized differentially methylated sites possibly affecting NRF1 and MXI1 transcription factors binding, causing a disturbance inNKAPLandPITX1expression, respectively. Our 3D models showed more loosely packed chromatin in cancer. This study successfully points out numerous possible regulatory dependencies.
Boosting GPT Models for Genomics Analysis: Generating Trusted Genetic Variant Annotations and Interpretations through RAG and fine-tuning
Authors: Lu Shuangjia , Cosgun Erdal
Published: November 2024

Large language models (LLMs) have acquired a remarkable level of knowledge through their initial training. However, they lack expertise in particular domains such as genomics. Variant annotation data, an important component of genomics, is crucial for interpreting and prioritizing disease-related variants among millions of variants identified by genetic sequencing. In our project, we aimed to improve LLM performance in genomics by adding variant annotation data to LLMs by retrieval-augmented generation (RAG) and fine-tuning techniques. Using RAG, we successfully integrated 190 million highly accurate variant annotations, curated from 5 major annotation datasets and tools, into GPT-4o. This integration empowers users to query specific variants and receive accurate variant annotations and interpretations supported by advanced reasoning and language understanding capabilities of LLMs. Additionally, fine-tuning GPT-4 on variant annotation data also improved model performance in some annotation fields, although the accuracy across more fields remains suboptimal. Our model significantly improved the accessibility and efficiency of the variant interpretation process by leveraging LLM capabilities. Our project also revealed that RAG outperforms fine-tuning in factual knowledge injection in terms of data volume, accuracy, and cost-effectiveness. As a pioneering study for adding genomics knowledge to LLMs, our work paves the way for developing more comprehensive and informative genomics AI systems to support clinical diagnosis and research projects, and it demonstrates the potential of LLMs in specialized domains.
Pleistocene sea-level fluctuation shapes archipelago-wide population structure in the Endangered Lord Howe Island cockroachPanesthia lata
Authors: Adams Maxim W.D. , Ewart Kyle M. , Carlile Nicholas , Rose Harley A. , Walker James A. , Hutton Ian , Ho Simon Y.W. , Lo Nathan
Published: November 2024

Studies of biogeographic processes have often centred islands as model systems, yet questions remain about the role of Pleistocene sea-level fluctuations in shaping islands’ biodiversity. One novel, potentially informative model system is the Lord Howe Island Group of Australia. Despite the World Heritage status of this archipelago, almost nothing is known of the biogeographic origins, evolutionary distinctiveness or genetic diversity of the ecological communities across its 28 islands. In this study, we focused on the cockroachPanesthia lata, an ecologically specialized invertebrate with one of the broadest recorded distributions of any LHIG species. To investigate the influence of Pleistocene sea-level fluctuations on LHIG fauna, we explored the phylogeography ofP. latausing single-nucleotide polymorphisms and complete mitochondrial genomes. Our analyses reveal that the lineage on the permanently isolated islet Ball’s Pyramid is highly divergent from the remaining populations, while those on the episodically connected Lord Howe, Roach and Blackburn Islands experienced gene flow during the last glacial period. These results offer the first evidence that Pleistocene land bridges allowed for overland migration across the archipelago. Further, althoughP. latawas believed to have been locally extirpated by rodents on Lord Howe Island, we discovered two surviving, relict populations. We also detected high levels of inbreeding in all populations, emphasizing the need for ongoing conservation management. Finally, the combination of shallow genetic structure and low diversity suggests that genetic rescue from another island may be a viable strategy to conserve the Lord Howe Island population ofP. lata, as well as other species that have been similarly impacted by rodents.
Restoring Synaptic Balance in Schizophrenia: Insights from a thalamo-cortical conductance-based model
Authors: S Berndt Lioba C , Singh Krish D , Shaw Alexander D
Published: November 2024

The dysconnectivity hypothesis of schizophrenia suggests that atypical, aberrant neural communication underlies the disorder’s diverse symptoms. Building on this framework, our study introduces a novel approach to understanding schizophrenia and exploring potential ways to adjust neural activity through synaptic restoration. Using a combination of magnetoencephalography data and dynamic causal modeling, we identified specific synaptic disturbances in schizophrenia patients, including increased NMDA receptor-mediated excitation in superficial pyramidal neurons and reduced GABA-B receptor-mediated inhibition between interneurons and pyramidal cells. These findings reveal a critical imbalance in excitation and inhibition within thalamo-cortical circuits, manifesting as altered gamma and alpha oscillations. The cornerstone of our research is an in silico synaptic restoration analysis, which demonstrates that targeted modifications to AMPA, NMDA, GABA-A, and GABA-B receptor-mediated connections can recalibrate altered neural activity in schizophrenia, aligning it with healthy control patterns. This restoration approach not only highlights the complex nature of synaptic dysfunction in the disorder but also identifies specific pathways as potential therapeutic targets, offering new avenues for investigating schizophrenia’s diverse symptomatology.
Whisker stimulation with different frequencies reveals non-uniform modulation of functional magnetic resonance imaging signal across sensory systems in awake rats
Authors: Paasonen Jaakko , Valjakka Juha S. , Salo Raimo A. , Paasonen Ekaterina , Tanila Heikki , Michaeli Shalom , Mangia Silvia , Gröhn Olli
Published: November 2024

Primary sensory systems are classically considered to be separate units, however there is current evidence that there are notable interactions between them. We examined the cross-sensory interplay by applying a quiet and motion-tolerant zero echo time functional magnetic resonance imaging (fMRI) technique to elucidate the evoked brain-wide responses to whisker pad stimulation in awake and anesthetized rats. Specifically, characterized the brain-wide responses in core and non-core regions to whisker pad stimulation by the varying stimulation-frequency, and determined whether isoflurane-medetomidine anesthesia, traditionally used in preclinical imaging, confounded investigations related to sensory integration. We demonstrated that unilateral whisker pad stimulation not only elicited robust activity along the whisker-mediated tactile system, but also in auditory, visual, high-order, and cerebellar regions, indicative of brain-wide cross-sensory and associative activity. By inspecting the response profiles to different stimulation frequencies and temporal signal characteristics, we observed that the non-core regions responded to stimulation in a very different way compared to the primary sensory system, likely reflecting different encoding modes between the primary sensory, cross-sensory, and integrative processing. Lastly, while the activity evoked in low-order sensory structures could be reliably detected under anesthesia, the activity in high-order processing and the complex differences between primary, cross-sensory, and associative systems were visible only in the awake state. We conclude that our study reveals novel aspects of the cross-sensory interplay of whisker-mediated tactile system, and importantly, that these would be difficult to observe in anesthetized rats.
Wheel running, but not home cage activity in Digital Ventilated Cages® is impaired in a mouse model of breast cancer-induced bone pain
Authors: Hopkins Chelsea , Kanneworff Ida Buur , Kornum Birgitte Rahbek , Heegaard Anne-Marie
Published: November 2024

Introduction

Cancer-induced bone pain (CIBP) due to metastatic breast cancer is common and debilitating. Effective, long-term treatment options have side effects that reduce patients’ quality of life. Preclinical models are a valuable tool to test novel analgesics, but new methods that are translationally and clinically relevant are necessary. This study aimed to assess spontaneous pain-like behaviour of home cage activity and wheel running in Digital Ventilated Cages®.

Method

Twenty BALB/cAnNHsd mice were housed in Digital Ventilated Cages® from Tecniplast® with GYM500 home cage running wheels. Mice were assessed by limb use analysis and static weight bearing to determine the development of CIBP and this was compared to the dark-phase home cage activity and wheel running in the Digital Ventilated Cages®. Ten mice underwent 4T1-Luc2 mammary gland adenocarcinoma cell inoculation into the right femur to establish CIBP and another ten mice underwent a sham surgical procedure.

Results

The 4T1-inoculated mice displayed pain-like behaviour in limb use and weight bearing tests, demonstrating a preference for the contralateral limb. The limb use scores were compared with home cage activity and wheel running. A reduced wheel running distance corresponded to reduced limb use scores, with the shortest wheel running distances corresponding to the lowest limb use scores. However, this behavioural pattern was not observed in home cage activity, which remained consistent over the study period.

Discussion

Reduced wheel running corresponded with reduced limb use scores. This suggests that wheel running behaviour is affected by the development of metastatic breast cancer. However, the home cage activity was not influenced by disease development. Digital Ventilated Cage® wheel running may be a useful behavioural assessment of spontaneous pain-like behaviour of CIBP and may be useful to assess analgesic efficacy.
Vincristine treatment reverses podocyte damage in focal segmental glomerulosclerosis
Authors: Mason William J , Chandler Jennifer C , Pomeranz Gideon , Price Karen L , Antonelou Marilina , Henderson Scott R , Perin Laura , Da Sacco Stefano , Salama Alan D , Long David A , Pepper Ruth J
Published: November 2024

Introduction

Focal segmental glomerulosclerosis (FSGS) is a significant cause of chronic kidney disease and triggered by podocyte damage which can result in cytoskeletal alterations leading to foot process effacement. Vincristine is a chemoprotective drug which alters cytoskeletal microtubules and has been used clinically to reverse FSGS. However, the mechanisms underlying the beneficial effect of vincristine are not understood.

Methods

We exposed immortalised human podocytes to serum obtained from an FSGS patient before, during, and after vincristine treatment. Using RNA-sequencing we determined the effect on the podocyte transcriptome alongside impacts on cytoskeletal structure and filtration barrier integrity using a glomerulus-on-a-chip model.

Results

We describe an adult index FSGS patient successfully treated on multiple occasions by vincristine. Podocytes exposed to serum obtained during or after vincristine treatment contained lower levels of genes associated with microtubule function compared with cells stimulated with serum collected before treatment during disease presentation. Presentation serum altered the patterning of two key podocyte cytoskeletal components, tubulin and F-actin and increased albumin permeability, changes prevented by vincristine treatment. Immunoglobulin depletion experiments revealed that the podocyte damage initiated by the presentation serum was not due to circulating autoantibodies. Defects in tubulin patterning were observed when podocytes were exposed to serum from other FSGS patients, suggestive of a common disease mechanism.

Conclusion

Vincristine therapy produces a milieu that protects against pathological changes induced by FSGS serum, associated with preservation of tubulin and F-actin organisation. The functional role of vincristine warrants further investigation, to advance our understanding of this alternative FSGS therapeutic.
Mechanism-based approach in designing patient-specific combination therapies for nonsense mutation diseases
Authors: Bhat Saleem , Bhattacharya Arpan , Li Hong , Lueck John D. , Goldman Yale E. , Cooperman Barry S
Published: November 2024

Premature termination codon (PTC) diseases, arising as a consequence of nonsense mutations in patient DNA, account for approximately 12% of all human disease mutations. Currently there are no FDA approved treatments for increasing PTC readthrough in nonsense mutation diseases, although one translational readthrough inducing drug, ataluren, has had conditional approval for treatment of Duchenne muscular dystrophy in Europe and elsewhere for 10 years. Ataluren displays consistent low toxicity in clinical trials for treatment of several different PTC diseases, but its therapeutic effects on such diseases are inconsistent. The identity of the stop codon and its sequence context are major determinants of PTC readthrough efficiency in both the absence and presence of nonsense suppressors. Previously we have shown that ataluren stimulates readthrough exclusively by competitively inhibiting release factor complex (RFC, eRF1.eRF3.GTP)-dependent catalysis of translation termination. Here, using an in vitro reconstituted system (PURE-LITE) and both ensemble and single molecule assays, we demonstrate that PTC identity and the immediately adjacent mRNA sequence contexts modulate the catalytic activity of RFC in terminating peptide elongation. Such modulation largely determines the effectiveness of ataluren in stimulating readthrough, whether added alone or in combination with either the aminoglycoside G418 or an anticodon edited aa-tRNA, each of which stimulate readthrough by mechanisms orthogonal to that of ataluren. Our results provide an attractive rationale for the variability of ataluren effectiveness in stimulating readthrough in clinical trials. Patients harboring a PTC mutation with a sequence context promoting strong interaction with RFC are predicted to be resistant to ataluren, whereas ataluren treatment should be more effective for patient sequences conferring weaker interaction with RFC.
Targeted degradation of endogenous condensation-prone proteins improves crop performance
Authors: Luo Ming , Wen Qing , Zhu Sitao , Dang Hua , Niu Ruixia , Long Jiawei , Wang Zhao , Tong Yongjia , Ning Yuese , Yuan Meng , Xu Guoyong
Published: November 2024

Effective methods, such as CRISPR and RNA interference, exist for modulating gene expression at DNA and RNA levels, but approaches for directly modifying endogenous proteins remain lacking in plants. Here, we develop a targeted condensation-prone-protein degradation (TCD) strategy to eliminate endogenous proteins, particularly those prone to condensation. We identify an E3 ligase, E3TCD1, that degrades itself but selectively targets other proteins when fused to them. In rice, transgenic E3TCD1 fusions with Teosinte branched 1 and Early flowering 3 (OsELF3) modulate tiller numbers and flowering times, respectively. The TCD system is also controllable. Using the ProTBF1-uORFsTBF1expression control cassette, we can conditionally degrade the negative defense regulator OsELF3 upon pathogen invasion, enhancing rice resistance without interfering with rice flowering time. This method, unlike animal-targeting strategies, does not rely on small molecules, antibodies, or genetic knock-ins, showing promise as a gene therapeutic avenue for optimizing crop performance and potentially addressing human diseases.
Type I interferon signaling enhances kainic acid-induced seizure severity
Authors: Ma Jeong-Hwa , Eo Jun-Cheol , Lee Changjun , Hwang Inhwa , Choi Jihye , Shin Sung Jae , Kim Chul Hoon , Yu Je-Wook
Published: November 2024

Epilepsy is a chronic neurological disorder characterized by recurrent seizures, yet the role and mechanisms of type I interferon (IFN) signaling in seizure conditions remain elusive. In this study, we demonstrate that type I IFN signaling exacerbates seizure phenotypes in a kainic acid-induced seizure mouse model. We found that the absence of type I IFN signaling inIfnar1-/-mice led to decreased neuronal excitability and microglial activation in response to kainic acid stimulation. Conversely, intracerebroventricular injection of IFN-β heightened the severity of kainic acid-induced seizures.In vitrocalcium imaging revealed that IFN-β treatment amplified both basal and kainic acid-induced neuronal excitability, though no significant difference was observed in basal neuronal excitability between wild-type andIfnar1-/-neurons. Furthermore,Ifnar1-/-mice exhibited reduced mTOR activation in the brain following kainic acid administration. Consistent with this finding, IFN-β treatment induced mTOR activation, as indicated by S6 phosphorylation inin vitromixed glial cultures. Taken together, these results demonstrate the critical role of type I IFN signaling in seizure pathogenesis and suggest that targeting type I IFNs could be a promising therapeutic strategy for reducing seizure severity and mitigating epilepsy.
Exploring large protein sequence space through homology- and representation-based hierarchical clustering
Authors: Chen JZ , Gall B , Tokuriki N , Jackson CJ
Published: November 2024

Exploration of protein sequence space can offer insight into protein sequence-function relationships, benefitting both basic science and industrial applications. The use of sequence similarity networks (SSNs) is a standard method for exploring large sequence datasets, but is currently limited when scaling to very large datasets and when viewing more than one level (hierarchy) of homology. Here, we present a sequence analysis pipeline with a number of innovations that address some limitations of traditional SSNs. First, we develop a hierarchical visualization approach that captures the full range of homologies across protein superfamilies. Second, we leverage representations embedded by protein language models as an alternative homology metric to the basic local alignment search tool (BLAST), showing that they produce comparable results when identifying isofunctional protein families. Finally, we demonstrate that unbiased representative sampling of sequences from genetic neighborhoods can be achieved through the use of hidden Markov models (HMMs) or vector representations. The utility of these methods is exemplified by updating the sequence-function analysis of the FMN/F420-binding split barrel superfamily and improving phylogenetic analyses. We provide our sequence exploration pipeline as publicly available code (ProteinClusterTools) and show it to be scalable to large datasets (∼300k sequences) using desktop computers.
Thanzi La Mawa (TLM) datasets: health worker time and motion, patient exit interview and follow-up, and health facility resources, perceptions and quality in Malawi
Authors: Nkhoma Dominic , Chitsulo Precious , Mulwafu Watipaso , Mnjowe Emmanuel , Tafesse Wiktoria , Mohan Sakshi , Hallet Timothy B , Collins Joseph H , Revill Paul , Chalkley Martin , Mwapasa Victor , Mfutso-Bengo Joseph , Colbourn Tim
Published: November 2024

The Thanzi La Mawa (TLM) study aims to enhance understanding of healthcare delivery and resource allocation in Malawi by capturing real-world data across a range of health facilities. To inform the Thanzi La Onse (TLO) model, which is the first comprehensive health system model developed for any country, this study uses a cross-sectional, mixed-methods approach to collect data on healthcare worker productivity, patient experiences, facility resources, and care quality. The TLM dataset includes information from 29 health facilities sampled across Malawi, covering facility audits, patient exit interviews, follow-ups, time and motion studies, and healthcare worker interviews, conducted from January to May 2024.

Through these data collection tools, the TLM study gathers insights into critical areas such as time allocation of health workers, healthcare resource availability, patient satisfaction, and overall service quality. This data is crucial for enhancing the TLO model’s capacity to answer complex policy questions related to health resource allocation in Malawi. The study also offers a structured framework that other countries in East, Central, and Southern Africa can adopt to improve their healthcare systems.

By documenting methods and protocols, this paper provides valuable guidance for researchers and policymakers interested in healthcare system evaluation and improvement. Given the formal adoption of the TLO model in Malawi, the TLM dataset serves as a foundation for ongoing analyses into quality of care, healthcare workforce efficiency, and patient outcomes. This study seeks to support informed decision-making and future implementation of comprehensive healthcare system models in similar settings.
A Dual Role for the PP2A Phosphatase in Hippo Signalling Regulation
Authors: Sekar Aashika , Rizzo Alberto , Sins Elodie , Fulford Alexander D. , Ribeiro Paulo S.
Published: November 2024

Hippo signalling is an evolutionarily conserved pathway that regulates tissue growth. The FERM domain protein Expanded plays a crucial role in integrating polarity cues to activate the Hippo pathway. Previous work has shown that the apicobasal polarity protein Crumbs can limit Hippo activity by promoting the phosphorylation and degradation of Expanded. Here, we provide evidence that PP2AWrdcan counteract the effects of Crumbs, by dephosphorylating and stabilising Expanded. Indeed, we demonstrate that the PP2AWrdholoenzyme can increase Hippo signalling activity, in contrast to the previously established Hippo pathway inhibitory role of the PP2ACka-containing STRIPAK complex. We also uncover a role for PP2AWrdand PP2ATwsin the regulation of Expanded proteostasis. Remarkably, the upstream Hippo regulator, Kibra interacts with PP2AWrdand prevents Expanded degradation. However, Kibra is unable to antagonise Crumbs-mediated Expanded regulation, in agreement with the previously established role of Crumbs in inhibiting Kibra function. Overall, our work characterises a novel Hippo-activating role for PP2A in the stabilisation of Expanded and provides new insights into how PP2A tightly controls Hippo activity in response to polarity stimuli.