bluuebunny/crossref_metadata_2025 huggingface dataset:
Translating Subphenotypes of Newly Diagnosed Type 2 Diabetes from Cohort Studies to Electronic Health Records in the United States
Authors: Li Zhongyu , Liu Star , Ho Joyce C , Narayan K.M. Venkat , Ali Mohammed K. , Varghese Jithin Sam
Published: October 2024

Novel subphenotypes of type 2 diabetes mellitus (T2DM) are associated with differences in response to treatment and risk of complications. The most widely replicated approach identified four subphenotypes (severe insulin-deficient diabetes [SIDD], severe insulin-resistant diabetes [SIRD], mild obesity-related diabetes [MOD], and mild age-related diabetes [MARD]). However, the widespread clinical application of this model is hindered by the limited availability of fasting insulin and glucose measurements in routine clinical settings. To address this, we pooled data of adults (≥18 years) with newly diagnosed T2DM from six cohort studies (n = 3,377) to perform de novo clustering and developed classification algorithms for each of the four subphenotypes using nine variables routinely collected in electronic health records (EHRs). After operationalizing the classification algorithms on the Epic Cosmos Research Platform, we identified that among the 727,076 newly diagnosed diabetes cases, 21.6% were classified as SIDD, 23.8% as MOD, and 40.9% as MARD. Individuals classified as SIDD were more likely to receive insulin and incretin mimetics treatment and had higher risks for microvascular complications (retinopathy, neuropathy, nephropathy). Our findings underscore the heterogeneity in newly diagnosed T2DM and validated T2DM subphenotypes in routine EHR systems. This offers possibilities for the subsequent development of treatment strategies tailored to subphenotypes.
A hydrodynamic antenna: novel lateral line system in the tail of myliobatid stingrays
Authors: Chaumel Júlia , Lauder George V.
Published: October 2024

Eagle rays, cownose rays, and manta rays (family Myliobatidae) have a slender tail that can be longer than the animal’s body length, but its function and structure are unknown. Using histology, immunohistochemistry, and 3D imaging with micro-CT scans, we describe the anatomy and function of the tail inRhinoptera bonasus, the cownose ray. The tail is an extension of the vertebral column with unique morphological specializations. Along the tail behind the barb, vertebral centra are absent and neural and hemal arches fuse and form a solid mineralized structure that we term the caudal synarcual, which imparts passive stiffness to the tail, reducing bending. Two lateral line canals connected to an extensive tubule network extend along both sides of the tail. Tubules branch from the lateral line canal toward the dorsal and ventral tail surfaces and open to the surrounding water via pores. A continuous neuromast is located within each lateral line canal, maintaining an interrupted structure along the entire tail. The complex lateral line mechanosensory system in the tail ofR. bonasussupports the hypothesis that the tail functions like a hydrodynamic sensory antenna and may play an important role in their behavioral and functional ecology.
The influence of soft tissue volume on estimates of skeletal pneumaticity: implications for fossil archosaurs
Authors: Burton Maria Grace , Benito Juan , Mellor Kirsty , Smith Emily , Martin-Silverstone Elizabeth , O’Connor Patrick , Field Daniel J.
Published: October 2024

Air space proportion (ASP), the volume fraction in bone occupied by air, is frequently applied as a measure for quantifying the extent of skeletal pneumaticity in extant and fossil archosaurs. Nonetheless, ASP estimates rely on a key assumption: that the soft tissue mass within pneumatic bones is negligible, an assumption that has rarely been explicitly acknowledged or tested. Here, we provide the first comparisons between estimated air space proportion (where the internal cavity of a pneumatic bone is assumed to be completely air-filled) and true air space proportion (ASPt, where soft tissues present within the internal cavities of fresh specimens are considered). Using birds as model archosaurs exhibiting postcranial skeletal pneumaticity, we find that estimates of ASPt are significantly lower than estimates of ASP, raising an important consideration that should be acknowledged in investigations of the evolution of skeletal pneumaticity and bulk skeletal density in extinct archosaurs, as well as in volume-based estimates of archosaur body mass. We advocate for the difference between ASP and ASPt to be explicitly acknowledged in studies seeking to quantify the extent of skeletal pneumaticity in extinct archosaurs, to avoid the risk of systematically overestimating the volume fraction of pneumatic bones composed of air.
Investigating the Effects of Synbiotic Intervention on Working Memory performance in Healthy Young Women
Authors: Salimi Yeganeh , Namdarzadeh Behnaz , Dehghani-Arani Fateme , Vahabie Abdol-Hossein , Rezayat Ehsan
Published: October 2024

The gut brain axis (GBA) mediates communication between the gastrointestinal system and the brain, influencing cognitive functions and emotional well being, with gut microbiota playing a crucial role. While synbiotics and probiotics have shown potential to enhance cognitive function, results remain inconsistent. This study examines the effects of synbiotic supplementation on auditory performance metrics threshold, sensitivity, accuracy, and reaction time using a repeated measures design with a control group. Thirty young females (ages 18-32) completed the Positive and Negative Affect Schedule (PANAS) and an auditory working memory task. Although no significant differences were found in auditory thresholds, sensitivity, or accuracy, the synbiotic group exhibited significantly faster reaction times than the control group (p < 0.00001), suggesting enhanced cognitive processing speed. These findings underscore the need for further research into the mechanisms through which synbiotics influence cognitive health.
An oncoembryology approach uncovers SoxC-driven regulation of colon development and cancer
Authors: Dalessi Tosca , Valenta Tomas , Moro Giulia , Brügger Michael David , Meijs Ab , Szczerba Barbara M. , Brunner Tamara , Lampart Simon , Nater Marc , Platt Randall J. , Scharl Michael , van den Broek Maries , Arnold Isabelle C. , Fazilaty Hassan
Published: October 2024

Reactivated embryonic programs are associated with cancer progression, yet their role and regulatory mechanisms remain poorly understood. In this study, we introduce ‘oncoembryology,’ an approach that systematically compares embryonic and cancerous tissues to identify shared molecular programs and assess their functional relevance in disease. Applying this strategy to colorectal cancer, we identified SoxC transcription factors (Sox4, Sox11, Sox12) as critical regulators of both embryonic development and tumorigenesis. SoxC transcription factors regulate diverse downstream targets, including Tead2, Mdk, and Klf4, thereby regulating crucial steps of colon development. Abrogating SoxC function in murine models reduced tumor growth and prevented liver metastasis. Concordantly, a SoxC-driven oncoembryonic gene signature correlated with poor survival in colorectal cancer patients, underscoring the therapeutic potential of targeting SoxC-regulated pathways in cancer treatment.
Geometry of Braided DNA Dictates Supercoiling Partition
Authors: Hong Yifeng , Park Seong ha , Wang Hanjie , Wang Michelle D.
Published: October 2024

During DNA replication, the replisome must rotate relative to the DNA substrate, generating supercoiling that must be partitioned in front of or behind the replisome. Supercoiling partitioned behind the replisome may intertwine (or braid) daughter DNA molecules and restrict chromosome segregation. Supercoiling partitioning and torsional resistance at the replisome should depend on the geometry of the two daughter DNA molecules, determined by their end separations. However, experimental investigation of DNA braiding under well-defined DNA geometry has proven challenging. Here, we present methods to engineer braiding substrates of defined geometry, from minimal to significant end separations. We then directly measured the torque required to braid these substrates using an angular optical trap (AOT) and found that the torque required to initiate the braiding during the first 0.5 turn critically depends on the end separation. Once braiding started, we found that the subsequent effective twist persistence length of DNA braiding is about 20-30 nm, insensitive to the end separations. Our work highlights the crucial role of braiding geometry in dictating supercoiling partitioning and torque build-up during replication. It suggests that dynamic modulation of end separation on the daughter DNA molecules could serve as a mechanism to regulate replication progressionin vivo.
Growth, development, and life history of a mass-reared edible insect,Gryllodes sigillatus(Orthoptera: Gryllidae)
Authors: Kong Jacinta D. , Ritchie Marshall W. , Vadboncoeur Émile , MacMillan Heath A. , Bertram Susan M.
Published: October 2024

Insects provide a potential source of sustainable, alternative protein that can help meet the protein demands of a growing population. Efficient farming of insects to meet this demand depends on an understanding of insect life history. Yet, detailed information and expertise about a single species are not always available for practitioners to make informed decisions about rearing practices or identify arising issues. The cricket (Gryllodes sigillatus) is commonly farmed for human consumption or animal feed, but few studies have characterized the life history of this species throughout ontogeny. Here, we describe the growth and development ofG. sigillatusfrom hatch to adulthood and quantify reproductive traits relevant to mass-rearing and colony management, including egg development. This information provides foundation to start and manage a cricket colony and to conduct research on growth and performance. We highlight ways that a fundamental understanding of cricket biology can be informative for optimizing cricket growth, reducing variability in yield and informing future precision farming practices.
Afadin mediates cadherin-catenin complex clustering on F-actin linked to cooperative binding and filament curvature
Authors: Gong Rui , Reynolds Matthew J. , Sun Xiaoyu , Alushin Gregory M.
Published: October 2024

The E-cadherin–β-catenin–αE-catenin (cadherin-catenin) complex couples the cytoskeletons of neighboring cells at adherens junctions (AJs) to mediate force transmission across epithelia. Mechanical force and auxiliary binding partners converge to stabilize the cadherin-catenin complex’s inherently weak binding to actin filaments (F-actin) through unclear mechanisms. Here we show that afadin’s coiled-coil (CC) domain and vinculin synergistically enhance the cadherin-catenin complex’s F-actin engagement. The cryo-EM structure of an E-cadherin–β-catenin–αE-catenin–vinculin–afadin-CC supra-complex bound to F-actin reveals that afadin-CC bridges adjacent αE-catenin actin-binding domains along the filament, stabilizing flexible αE-catenin segments implicated in mechanical regulation. These cooperative binding contacts promote the formation of supra-complex clusters along F-actin. Additionally, cryo-EM variability analysis links supra-complex binding along individual F-actin strands to nanoscale filament curvature, a deformation mode associated with cytoskeletal forces. Collectively, this work elucidates a mechanistic framework by which vinculin and afadin tune cadherin-catenin complex–cytoskeleton coupling to support AJ function across varying mechanical regimes.
Association Between Major Adverse Cardiac Events and Hormone Therapy Usage in Prostate Cancer Patients of a Diverse Cohort
Authors: Yang Yuanchu J , Zeng Chenjie , Schaffer Kerry R , Tran Tam C , Sauer Peter J , Brown Lincoln A , Park Ben H , Denny Joshua C
Published: October 2024

Importance

Hormone therapy (HT) has led to improved overall survival for prostate cancer patients, but may also increase cardiovascular risk.

Objective

To compare time-to-event for major adverse cardiovascular events (MACE) between those with and without HT use in prostate cancer patients.

Design, Setting, and Participants

This retrospective cohort study examined 5,156 participants from theAll of UsResearch Program who were diagnosed with prostate cancer and either treated or not treated with HT (defined as exposure to a GnRH agonist, GnRH antagonist, and/or anti-androgens). Time to MACE was defined using longitudinal electronic health record data. We evaluated whether HT use affected the risk of MACE using Cox regression adjusted for established cardiovascular risk factors.

Exposures

HT treatment (HT-treated study group), non-HT treatment (control group without HT but with surgery, radiation treatment, and/or non-HT medical therapy), or no treatment (active surveillance control group).

Main Outcomes and Measures

Time-to-event for MACE, which is defined as the interval between the start of treatment (or first prostate cancer diagnosis for the no treatment group) and the date of MACE. Participants who did not develop a MACE were right censored at their last healthcare provider visit.

Results

The final cohort included 5,156 participants; 851 in the HT treatment group, 624 in the non-HT treatment group, and 3,681 in the no treatment group. In participants with pre-treatment dyslipidemia, HT was found to be associated increased risk of MACE (HR, 1.52; 95% CI, 1.19-1.95; P <.001), while in those without pre-existing dyslipidemia, no association were found (HR, 0.96; 95% CI, 0.71-1.30; P = .81). Similar patterns were found across race and ethnicity groups. The combined androgen blockade was statistically significantly associated with MACE in participants with pre-existing dyslipidemia (HR, 1.58; 95% CI, 1.13-2.19; P= .006) and no association in participants without pre-existing dyslipidemia (HR, 0.96; 95% CI, 0.71-1.30; P= .81). We also observed that HT was associated with prolongation of the QTc interval (P= .02).

Conclusions and Relevance

HT treatment was associated with an increased risk for MACE participants with pre-existing dyslipidemia. These results suggest that increased risk stratification can help improve CV outcomes when deciding treatment regimens.
Targeting mutant TNNT2-induced epigenetic perturbation and pathogenic signaling in left ventricular non-compaction cardiomyopathy
Authors: Li You-Yi , Tseng Wei-Chieh , Kao Hua-Ling , Shie Yu-Shin , Chiu Sheunn-Nan , Wu Ya-Ting , Sun Chung-Ming , Tzeng Shiou-Ru , Lai Liang-Chuan , Lin Miao-Hsia , Wu Yen-Wen , Ko Kuan-Yin , Juang Jyh-Ming Jimmy , Hsieh Ryan , Wu Mei-Hwan , Chen Wen-Pin , Ho Hong-Nerng
Published: October 2024

Background

Compound mutations ofTNNT2R141W/+(encoding troponin T) andMYPNS1296T/+(encoding myopalladin) are associated with familial left ventricle non-compaction cardiomyopathy (LVNC). However, it remains unclear in which would be the pathogenic mutation, the underlying mechanism, and the target therapy for LVNC.

Methods

Knock-in C57BL/6J mice harboring mutations in orthologous genes inTnnt2R154Wor/andMypnS1291Tand human cardiomyocytes derived from iPSC of healthy donors and LVNC patients (LVNC-hCM) were employed for disease modeling, omics analysis, mechanistic study, and drug development.

Results

Using knock-in mice for disease modeling, it was clarified that the orthologous mutation inTnnt2, but not inMypn, led to cardiac hypertrabeculation, noncompaction, and heart failure. 3D protein structure modeling by Swiss-model found a loss of slat bridge between TNNT2(R141W) and E-257 in tropomyosin, contributing to the decreased cardiac contraction. Further mechanistic study discovered that troponin T (TNNT2) appears to function as an HDAC1 sponge in cardiomyocyte nuclei. The compromised association between nuclear TNNT2(R141W) and HDAC1 causes cardiac epigenetic perturbation and subsequentially leads to transcriptional dysregulation. The downregulation of cardiac muscular genes was concomitant with the impairment of cardiac contraction, which would be partially rescued by pan HDAC inhibitor. Besides, the upregulation of TGFβ-signaling molecules and EZH2 did contribute to cardiac growth defects, which were mitigated by TGFβR1 inhibitor (A83-01) and EZH2 inhibitor (GSK503), respectively. Simvastatin, a hit drug identified from the repurposed drug screening, can restore nuclear TNNT2(R141W)-HDAC1 association, thereby recovering cardiac epigenetic, translational profiles, growth and function in LVNC-hCMin vitroand cardiac function in LVNC mice harboringTnnt2R154Win vivo. The cardiac function was significantly improved in the proband receiving 5 mg once daily for consecutive two years.

Conclusion

Mutant TNNT2(R141W) diminished its nuclear HDAC1 sponge function in cardiomyocyte to induce LVNC pathogenesis through perturbating cardiac epigenetic and the gene expressions. Targeting to HDAC, TGFβ, EZH2 may rescue part of cardiac pathological signaling. Simvastatin can act as a chemical chaperone to comprehensively recover cardiac epigenetic via restoring nuclear TNNT2(R141W)-HDAC1 association.
Efficacy of a personalised alcohol approach bias modification smartphone app in people accessing outpatient alcohol use disorder treatment: A randomised controlled trial
Authors: Garfield Joshua B. B. , Liu Samuel K. , Piercy Hugh , Rowland Bosco , Bonomo Yvonne , Whelan Danielle , Manning Victoria
Published: October 2024

Background and Aims:Several randomised controlled trials (RCTs) have demonstrated that delivering approach bias modification (ApBM) during residential alcohol use disorder (AUD) treatment reduces likelihood of post-treatment relapse. However, few studies have examined ApBM’s efficacy for AUD in outpatient settings. We trialled a personalised ApBM smartphone app in individuals receiving outpatient treatment for AUD.Design:We conducted a double-blind RCT. Participants were randomised to receive treatment as usual (TAU) + ApBM or TAU + sham training over a 4-week intervention period.Setting:Participants were recruited from alcohol and other drug treatment services in Melbourne, Australia.Participants:79 participants (mean age 46.6 years; 45 male, 34 female) installed the app between May 26, 2022 and January 23, 2024.Intervention and Comparator:In the ApBM condition, the app delivered personalised, gamified ApBM. Participants were prompted by notifications to complete at least 2 sessions of ApBM per week for 4 weeks. The Control version prompted participants to complete a weekly sham-training task for 4 weeks.Measurements:Participants self-reported past-week alcohol use via the app at baseline and 4, 8, and 16 weeks after installing the app. We used these data to derive number of standard drinks (defined as 10 grams pure alcohol) consumed (primary outcome), past-week drinking days, and past-week heavy drinking days (days when>5 standard drinks were consumed). Participants also completed questionnaire measures of AUD severity, quality of life, and alcohol craving.Findings:We found a significant time x group interaction for the primary outcome (coefficient: -1.11, 95% CI: [-2.08, 0-.13]; z(78) = -2.22; p=.03,). Past-week standard drinks declined significantly in ApBM participants (reducing by 55% between baseline and the final follow-up), but not controls (non-significant 11% reduction). Time x group interaction effects were non-significant for all secondary outcomes.Conclusions:Personalised smartphone ApBM may help reduce alcohol consumption in AUD outpatients.
Changing species dynamics and species-specific associations observed betweenAnophelesandPlasmodiumgenera in Diebougou health district, southwest Burkina Faso
Authors: Lado P , Gray LI , Sougué E , Knight AL , Sorensen M , Leon AS , Ring ME , Pugh G , Randall JC , Coffin KL , Hemming-Schroeder E , Goodwin J , Wade M , Sproch H , Ouédraogo COW , Dah SR , Somé AF , Dabiré RK , Parikh S , Foy BD
Published: October 2024

The prevalence of malaria parasite species in parts of Africa is rapidly changing and influenced by detection methods. The natural vector competence and vectorial capacity of African anophelines for humanPlasmodiumspecies has only been well described forP. falciparumand is unclear in the context of mixed and non-falciparum infections. Over the course of two clinical trials (2015 and 2019-2020) testing ivermectin for malaria control in the same region of Burkina Faso, we sampled participants’ blood and their households forAnophelesspp. mosquitoes and tested these samples forPlasmodiumspecies.Plasmodiumprevalence in participants and their blood samples was high in both trials. WhileP. falciparummono-infections comprised most infections in the 1sttrial, mixed and non-falciparum infections comprised 27% of infections in the 2ndtrial, with notable changes in species present within participants over time. Furthermore,An. gambiaes.l. was the main vector captured, butAn. funestusmosquitoes were unexpectedly prevalent in the 2ndtrial, and we found that parasite species prevalence differed in abdominal and head+thorax tissues of these two vector species. Most notably,P. falciparumsporozoites were significantly more prevalent than other parasite species inAn. gambiaes.l. whileP. ovalesporozoites were significantly more prevalent than other parasite species inAn. funestus. Our data suggest differential vector competence forPlasmodiumspecies at the study site, which may significantly impact malaria epidemiology, disease prevalence and control efforts.
Linezolid induced lactic acidosis in tuberculosis: a systematic review of published case reports, case series
Authors: Garg Rajiv , Garg Ravindra Kumar , Garg Pragati , Srivastava Anand , Bajaj Darshan Kumar
Published: October 2024

Background

Linezolid is widely used in the treatment of drug-resistant tuberculosis (TB), but it is associated with severe adverse effects, including lactic acidosis, which remains underreported in the literature and is fatal in many cases.

Methods

This systematic review followed PRISMA guidelines and was registered in PROSPERO (CRD42024552225). We conducted comprehensive searches across PubMed, Scopus, Embase, and Google Scholar, covering case reports and case series without language restrictions. Data were extracted on demographics, clinical presentation, Linezolid dosage, laboratory findings, treatment regimens, and outcomes. Lactic acidosis was defined as a serum pH <7.25 and lactate >4 mmol/L. Quality assessment followed the protocol of Murad MH et al. Data were synthesized narratively and statistically analyzed using Microsoft Excel.

Results

Seven case reports were identified. The average patient age was 49.33 years (range: 20–81 years), with a near-equal distribution between males and females. Most cases were reported from India (3/7). Respiratory symptoms predominated, with gastrointestinal and central nervous system involvement also noted. Linezolid dosing varied between 600 mg and 1200 mg daily. Arterial blood gas analysis showed significant acidosis, with pH values ranging from 6.09 to 7.32. Lactate levels were elevated (range: 10.2–20 mmol/L). Symptoms emerged within 7 days to over 1 month after starting Linezolid, except for one patient who developed symptoms immediately. Four patients died, and three survived after treatment modification.

Conclusion

Linezolid-induced lactic acidosis is a rare but serious complication in drug-resistant TB, emphasizing the need for close monitoring and individualized treatment.
Estrogen Deficiency alters Vascularization and Mineralization dynamics: insight from a novel 3D Humanized and Vascularized Bone Organoid Model
Authors: Bukhari Muhammad M.M. , Khabooshani Mostafa , Naqvi Syeda M. , McNamara Laoise M.
Published: October 2024

Osteoporosis is not merely a disease of bone loss but also involves changes in the mineral composition of the bone that remains.In vitrostudies have investigated these changes and revealed that estrogen deficiency alters osteoblast mineral deposition, osteocyte mechanosensitivity and osteocyte regulation of osteoclastogenesis. During healthy bone development, vascular cells stimulate bone mineralization via endochondral ossification, but estrogen deficiency impairs vascularization. Yet, existingin vitrobone models overlook the role of vascular cells in osteoporosis pathology. Thus, here we (1) develop an advanced 3D vascularized, mineralized and humanized bone model following the endochondral ossification process, and (2) apply this model to mimic postmenopausal estrogen withdrawal and provide a mechanistic understanding of changes in vascularization and bone mineralization in estrogen deficiency. We confirmed the successful development of a vascularized and mineralized human bone model via endochondral ossification, which induced self-organization of vasculature, associated with hypertrophy (collagen X), and promoted mineralization. When the model was applied to study estrogen deficiency, we reported the development of distinct vessel-like structures (CD31+) in the postmenopausal 3D constructs. Moreover, during estrogen withdrawal vascularized bone demonstrated a significant increase in mineral deposition and apoptosis, which did not occur in non-vascularized bone. These findings reveal a potential mechanism for bone mineral heterogeneity in osteoporotic bone, whereby vascularized bone becomes highly mineralized whereas in non-vascularised regions this effect is not observed.

New and Noteworthy

Here we develop anin vitro3D vascularized and humanized bone model following an endochondral ossification approach. We applied the model to recapitulate estrogen deficiency as representative of osteoporotic phenotype. The results of this study reveal that estrogen deficiency exacerbates formation of 3D vessel like structures in vascularized models and thereby drives mineral deposition.
Semi-automated workflow for high-throughputAgrobacterium-mediated plant transformation
Authors: Annese Davide , Romani Facundo , Grandellis Carolina , Ives Lesley , Frangedakis Eftychios , Buson Felipe X. , Molloy Jennifer C. , Haseloff Jim
Published: October 2024

High-throughput experiments in plants are hindered by long generation times and high costs. To address these challenges, we present an optimized pipeline forAgrobacterium tumefacienstransformation and simplified a protocol to obtain stable transgenic lines of the model liverwortMarchantia polymorpha, paving the way for efficient high-throughput experiments for plant synthetic biology and other applications. Our protocol involves freeze-thawAgrobacteriumtransformation method in 6-well plates that can be adapted to robotic automation. Using the Opentrons open-source platform, we implemented a semi-automated protocol showing similar efficiency compared to manual manipulation. Additionally, we have streamlined and simplified the process of stable transformation and selection ofM. polymorpha, reducing cost, time, and manual labour without compromising transformation efficiency. The addition of sucrose in the selection media significantly enhances the production of gemmae, accelerating the generation of isogenic plants. We believe these protocols have the potential to facilitate high-throughput screenings in diverse plant species and represent a significant step towards the full automation of plant transformation pipelines. This approach allows testing ∼100 constructs per month, using conventional plant tissue culture facilities. We recently demonstrated the successful implementation of this protocol for screening hundreds of fluorescent reporters inMarchantiagemmae.
In situ crystalline structure of the human eosinophil major basic protein-1
Authors: Yang Jie E. , Mitchell Joshua M. , Bingman Craig A. , Mosher Deane F. , Wright Elizabeth R.
Published: October 2024

Eosinophils are white blood cells that participate in innate immune responses and have an essential role in the pathogenesis of inflammatory and neoplastic disorders. Upon activation, eosinophils release cytotoxic proteins such as major basic protein-1 (MBP-1) from cytoplasmic secretory granules (SGr) wherein MBP-1 is stored as nanocrystals. How the MBP-1 nanocrystalline core is formed, stabilized, and subsequently mobilized remains unknown. Here, we report thein-situstructure of crystalline MBP-1 within SGrs of human eosinophils. The structure reveals a mechanism for intragranular crystal packing and stabilization of MBP-1 via a structurally conserved loop region that is associated with calcium-dependent carbohydrate binding in other C-type lectin (CTL) proteins. Single-cell and single-SGr profiling correlating real-space three-dimensional information from cellular montage cryo-electron tomography (cryo-ET) and microcrystal electron diffraction (MicroED) data obtained from non-activated and IL33-activated eosinophils revealed activation-dependent crystal expansion and extrusion of expanded crystals from SGr. These results suggest that MBP-1 crystals play a dynamic role in the release of SGr contents. Collectively, this research demonstrates the importance ofin-situmacromolecular structure determination.
Visualization of breast cancer using contrast-enhanced optical coherence elastography based on tissue heterogeneity
Authors: Li Jiayue , Foo Ken Y. , Sanderson Rowan W. , Zilkens Renate , Hardie Mireille , Gale Laura , Yeow Yen L. , Green Celia , Abdul-Aziz Farah , Hamzah Juliana , Stephenson James , Tayaran Ammar , Cid Fernandez Jose , Jackson Lee , Chin Synn Lynn , Hamza Saud , Rijhumal Anmol , Saunders Christobel M. , Kennedy Brendan F.
Published: October 2024

By mapping the mechanical properties of tissue, elastography can improve identification of breast cancer. On the macro-scale, ultrasound elastography and magnetic resonance elastography have emerged as effective clinical methods for the diagnosis of tumors. On the micro-scale, optical coherence elastography (OCE) shows promise for intraoperative tumor margin assessment during breast-conserving surgery. Whilst several OCE studies have demonstrated strong potential, the mechanical models used require the assumption of uniaxial stress throughout the sample. However, breast tissue is heterogeneous and contains compressible features (e.g., ducts and blood vessels) and collagen-rich fibrotic features (e.g., stroma). This heterogeneity can invalidate the assumption of uniaxial stress and reduce the accuracy of OCE, often making it challenging to interpret images. Here, we demonstrate a new variant of OCE based on mapping the Euler angle,i.e., the angle between the principal compression and the loading axis induced by tissue heterogeneity, which removes the assumption of uniaxial deformation. This is enabled by a hybrid three-dimensional (3-D) displacement estimation method that combines phase-sensitive detection and complex cross-correlation, providing access to the 3-D displacement and 3-D strain tensor on the micro-scale. We demonstrate this new OCE technique through experiments on phantoms and 10 fresh human breast specimens. Through close correspondence with histology, our results show that mapping the Euler angle provides additional contrast to both optical coherence tomography and a current OCE technique in identifying cancer. Mapping the Euler angle in breast tissue may provide a new biomarker for intraoperative tumor margin assessment.
Quantitative Insights into Processivity of an Hsp100 Protein Disaggregase on Folded Protein Substrates
Authors: Banwait Jaskamaljot Kaur , Lucius Aaron L.
Published: October 2024

The Hsp100 family of proteins play important roles in maintaining protein homeostasis in cells.E. coliClpB is an Hsp100 protein that remodels misfolded proteins or aggregates. ClpB is proposed to couple the energy from ATP binding and hydrolysis to processively unfold and translocate protein substrates through its axial channel in the hexameric ring structure. However, many of the details of this reaction remain obscure. We have recently developed a transient state kinetics approach to study ClpB catalyzed protein unfolding and translocation. In this work we have used this approach to begin to examine how ATP is coupled to the protein unfolding reaction. Here we show that at saturating [ATP], ClpB induces the cooperative unfolding of a complete TitinI27 domain of 98 amino acids, which is represented by the kinetic step-size m ∼100 amino acids. This unfolding event is followed by rapid and undetected translocation up to the next folded domain. At sub-saturating [ATP], ClpB still induces cooperative unfolding of a complete TitinI27 domain but translocation becomes partially rate-limiting, which leads to an apparent reduced kinetic step-size as small as ∼ 50 amino acids. Further, we show that ClpB exhibits an unfolding processivity of P = (0.74 ± 0.06) independent of [ATP]. These findings advance our understanding of the elementary reactions catalyzed by E. coli ClpB but are broadly applicable to a variety of Hsp100 family members.

Graphical Abstract
Migration strategies of a high-latitude breeding songbird (Setophaga coronata coronata) revealed using multi-sensor geolocators and stable isotopes
Authors: Szarmach Stephanie J , Beam Johanna K , Moore Mads , Van Doren Benjamin M , Brelsford Alan , Toews David P L
Published: October 2024

Seasonal migration allows animals to use habitat where conditions are unfavorable for part of the year but may constrain breeding ranges due to the costs of longer migrations as ranges expand poleward. In species with large ranges, high latitude breeding populations may employ different migratory strategies allowing them to persist far from other core non-breeding areas. The myrtle warbler (Setophaga coronata coronata) has two disjunct non-breeding ranges in North and Central America–one along the Gulf Coast and the other on the Pacific. Previous work indirectly linked birds breeding in Alaska with the Pacific non-breeding area, suggesting that high latitude populations evolved a shorter migration route. We directly tested this hypothesis using geolocators measuring both light and atmospheric pressure to track Alaskan myrtle warbler migration in fine detail and inferred non-breeding areas using hydrogen isotopes for a larger sample of birds breeding in Alaska, British Columbia, and Alberta. We found, contrary to expectations, that all geolocator-tracked birds and most birds with stable isotope data migrated to the southeastern United States, while only a small subset of birds (∼5%) likely wintered on the Pacific Coast. We additionally demonstrate the advantages of pressure geolocation for characterizing migratory behavior at a fine scale.
Sm-site containing mRNAs can accept Sm-rings and are downregulated in Spinal Muscular Atrophy
Authors: Blatnik Anton J. , Sanjeev Manu , Slivka Jacob , Pastore Benjamin , Embree Caleb M. , Tang Wen , Singh Guramrit , Burghes Arthur H. M.
Published: October 2024

Sm-ring assembly is important for the biogenesis, stability, and function of uridine-rich small nuclear RNAs (U snRNAs) involved in pre-mRNA splicing and histone pre-mRNA processing. Sm-ring assembly is cytoplasmic and dependent upon the Sm-site sequence and structural motif, ATP, andSurvival motor neuron(SMN) protein complex. While RNAs other than U snRNAs were previously shown to associate with Sm proteins, whether this association follows Sm-ring assembly requirements is unknown. We systematically identified Sm-sites within the human and mouse transcriptomes and assessed whether these sites can accept Sm-rings. In addition to snRNAs, Sm-sites are highly prevalent in the 3’ untranslated regions of long messenger RNAs. RNA immunoprecipitation experiments confirm that Sm-site containing mRNAs associate with Sm proteins in the cytoplasm. In modified Sm-ring assembly assays, Sm-site containing RNAs, from either bulk polyadenylated RNAs or those transcribedin vitro, specifically associate with Sm proteins in an Sm-site and ATP-dependent manner. In cell and animal models of Spinal Muscular Atrophy (SMA), mRNAs containing Sm-sites are downregulated, suggesting reduced Sm-ring assembly on these mRNAs may contribute to SMA pathogenesis. Together, this study establishes that Sm-site containing mRNAs can accept Sm-rings and identifies a novel mechanism for Sm proteins in regulation of cytoplasmic mRNAs.

GRAPHICAL ABSTRACT
Cargo adaptor identity controls the mechanism and kinetics of dynein activation
Authors: Gillies John P. , Little Saffron R. , Hancock William O. , DeSantis Morgan E.
Published: October 2024

Cytoplasmic dynein-1 (dynein), the primary retrograde motor in most eukaryotes, supports the movement of hundreds of distinct cargos, each with specific trafficking requirements. To achieve this functional diversity, dynein must bind to the multi-subunit complex dynactin and one of a family of cargo adaptors to be converted into an active, processive motor complex. Very little is known about the dynamic processes that promote the formation of this complex. To delineate the kinetic steps that lead to dynein activation, we developed a single-molecule fluorescence assay to visualize the real-time formation of dynein-dynactin-adaptor complexes in vitro. We found that dynactin and adaptors bind dynein independently rather than cooperatively. We also found that different dynein adaptors promote dynein-dynactin-adaptor assembly with dramatically different kinetics, which results in complex formation occurring via different assembly pathways. Despite differences in association rates or mechanism of assembly, all adaptors tested can generate a population of tripartite complexes that are very stable. Our work provides a model for how modulating the kinetics of dynein-dynactin-adaptor binding can be harnessed to promote differential dynein activation and reveals a new facet of the functional diversity of the dynein motor.
Gender- and Age-Based Characterization and Comparison of the Murine Primary Peritoneal Mesothelial Cell Proteome
Authors: Wang Zhikun , Liu Yueying , Safavisohi Reihaneh , Asem Marwa , Hu Daniel D. , Stack Mary Sharon , Champion Matthew M.
Published: October 2024

Organs in the abdominal cavity are covered by a peritoneal membrane, which is comprised of a monolayer of mesothelial cells (MC). Diseases involving the peritoneal membrane include peritonitis, primary cancer (mesothelioma), and metastatic cancers (ovarian, pancreatic, colorectal). These diseases have gender- and/or age-related pathologies; however, the impact of gender and age on the peritoneal MC is not well evaluated. To address this, we identified and characterized gender- and age-related differences in the proteomes of murine primary peritoneal MC. Primary peritoneal MC were isolated from young female (FY) or male (MY) mice (3-6 months) and aged female (FA) or male (MA) mice (20-23 months), lysed, trypsin digested using S-Traps, then subjected to bottom-up proteomics using an LC-Orbitrap mass spectrometer. In each cohort, we identified >1000 protein groups. Proteins were categorized using Gene Ontology and pairwise comparisons between gender and age cohorts were conducted. This study establishes baseline information for studies on peritoneal MC in health and disease at two physiologic age/gender points. Segregation of the data by gender and age could reveal novel factors to specific disease states involving the peritoneum. [Thisin vitroprimary cell model has utility for future studies on the interaction between the mesothelium and foreign materials.]

SUMMARY STATEMENT

Many diseases initiate from or involve peritoneal mesothelial cells including peritonitis, primary cancer (mesothelioma) and metastatic cancers. Progression of these diseases is influenced by many host factors including gender and age; however, the influence of these factors on the peritoneal mesothelial cell proteome has not been evaluated. This study provides novel information and identifies proteins exclusive to both male and female young and aged cohorts. Given the importance of the peritoneal mesothelial cell in abdominal homeostasis, and the impact of gender and age on disease progression, these data will be key for future studies examining mesothelium in both health and disease.
Oncogenicity Variant Interpreter (OncoVI): oncogenicity guidelines implementation to support somatic variants interpretation in precision oncology
Authors: Carta Maria Giulia , Toegel Lars , Hoelsken Annett , Schubart Christoph , Sticht Heinrich , Stoehr Robert , Spoerl Silvia , Meidenbauer Norbert , Hartmann Arndt , Magni Paolo , Haller Florian , Ferrazzi Fulvia
Published: October 2024

Background In precision oncology, the accurate and reproducible classification of variant oncogenicity is fundamental for therapy decision making. In 2022, a set of guidelines for the classification of oncogenicity of somatic variants in cancer were defined by the Clinical Genome Resource, the Cancer Genomics Consortium, and the Variant Interpretation for Cancer Consortium. However, to date an implementation that automates the evaluation of these criteria does not exist. Furthermore, for the majority of the criteria, the interpretation of the criterion-associated textual indication and the choice of publicly available resources to gather criterion-supporting information depends on the user. Thus, the risk of a variant being classified differently by independent laboratories is relevant, with implications for the management of patient care. Methods Here, we developed Oncogenicity Variant Interpreter (OncoVI), a fully-automated Python-based implementation of the oncogenicity guidelines. First, each criterion was interpreted and publicly available resources were identified to be utilised as reference. Then, criteria were implemented in OncoVI and the information reported by the associated resources were integrated. OncoVI is part of a broader Python-framework that, starting from the genomic position of the variant, automatically performs functional annotation, collects the available evidence from the reference resources, and provides a classification of oncogenicity. Results On the set of 93 somatic variants provided by the guidelines OncoVI achieved an overall accuracy of 80%, with a sensitivity of 88% in the classification of Oncogenic/Likely Oncogenic variants. On a real-world data set of 7,802 variants from 557 patients previously evaluated within the Molecular Tumour Board (MTB) Erlangen, an agreement of 79% was observed between the oncogenicity classification of OncoVI and the MTB pathogenicity assessment. In addition, the pathogenicity classification of 135 variants of the MTB data set was re-assessed by expert biologists adhering solely to the oncogenicity guidelines. This re-evaluation confirmed the validity of OncoVI"s interpretation of the resources chosen as reference, but it also underlined the ability of experts in solving conflicting evidence. Conclusions Taken together, OncoVI provides an effective implementation of the oncogenicity guidelines, thus facilitating their adoption and supporting the reproducible and harmonised oncogenicity classification of somatic variants between institutions.
Chikungunya Virus VLP Vaccine: Phase 3 Trial in Adults ≥65 Years of Age
Authors: Tindale Lauren C. , Richardson Jason S. , Anderson Debbie M. , Mendy Jason , Muhammad Sufia , Loreth Tobi , Royalty Tredo Sarah , Ramanathan Roshan , Jenkins Victoria A. , Bedell Lisa , Ajiboye Patrick ,   the EBSI-CV-317-005 Study Group
Published: October 2024

1

Background

Adults ≥65 years of age are at increased risk for atypical presentations of chikungunya disease as well as severe outcomes including death.

Methods

A phase 3, randomized, double-blind, placebo-controlled, parallel-group trial was conducted in adults ≥65 years of age where participants received a single intramuscular dose of chikungunya virus (CHIKV) virus-like particle (VLP) vaccine or placebo on Day 1. Baseline and postvaccination CHIKV serum neutralizing antibody (SNA) titers (NT80) were assessed at selected timepoints. Safety was assessed through Day 183.

Results

A total of 413 participants (206 vaccine, 207 placebo) were randomized. Coprimary endpoints were met including 1) immunologic superiority of CHIKV SNA titers compared to placebo and 2) by geometric mean titer at Day 22. CHIKV VLP vaccine induced a protective seroresponse (SNA NT80≥100; considered the presumptive seroprotective antibody response), in 82% of individuals at Day 15, in 87% of individuals at Day 22, and in 76% of individuals at Day 183. There were no notable differences in AE rates between groups and most AEs were grade 1 or 2 in severity. No vaccine-related serious adverse events or deaths occurred.

Conclusions

We provide robust data from adults ≥65 years of age demonstrating that CHIKV VLP vaccine has a favorable safety profile and can provide a high rate of protection within 2 weeks postvaccination and through 6 months of follow-up. (Funded by Emergent BioSolutions Inc. and Bavarian Nordic A/S [as successor in interest to Emergent BioSolutions Inc.];ClinicalTrials.govnumber,NCT05349617).
Do self-help groups improve sexual and reproductive health and HIV outcomes among female sex workers in sub-Saharan Africa? A scoping review
Authors: Madimutsa Gracious , Machingura Fortunate , Nyamwanza Owen , Cowan Frances M , Mavhu Webster
Published: October 2024

Introduction

Self-help groups (SHGs) have been effective in improving the health and wellbeing of women generally but there is little evidence on whether and how they improve HIV and sexual and reproductive health (SRH) outcomes among female sex workers (FSWs), particularly in sub-Saharan Africa. This scoping review seeks to address this gap by identifying and analysing literature on SHG for FSWs in sub-Saharan Africa.

Materials and methods

This scoping review (1) identified relevant studies; (2) selected the studies; (3) charted the data; and (4) collated, summarised, and reported the results. A search strategy was developed; CINAHL, Medline and Global Health databases were searched.

Results

Eleven studies were identified, two were quantitative, seven were qualitative and two were mixed methods. Studies were from seven countries in sub-Saharan Africa. The studies suggested that SHGs can improve SRH outcomes and reduce HIV vulnerabilities among FSWs by providing emotional and financial support, health education, linkage to care, and social capital (i.e., benefits derived from associations). The studies also highlighted the need for tailored interventions that address the unique needs and challenges faced by FSWs.

Conclusions

The findings of this scoping review underscore the importance of building social cohesion by incorporating SHGs into a range of HIV prevention strategies in sub-Saharan Africa. SHGs have the potential to improve SRH and HIV outcomes among FSWs. Further research is needed to explore the effectiveness of SHGs in different contexts and to identify best practices for implementing and sustaining SHGs for FSWs.