bluuebunny/crossref_metadata_2025 huggingface dataset:
Cause-specific mortality among patients with cirrhosis in a population-based cohort study in Ontario (2000–2017)
Authors: Wang Peter L. , Djerboua Maya , Flemming Jennifer A.
Published: June 2023

Background:

Although patients with cirrhosis are at increased risk of death, the exact causes of death have not been reported in the contemporary era. This study aimed to describe cause-specific mortality in patients with cirrhosis in the general population.

Methods:

Retrospective cohort study using administrative health care data from Ontario, Canada. Adult patients with cirrhosis from 2000–2017 were identified. Cirrhosis etiologies were defined as HCV, HBV, alcohol-associated liver disease (ALD), NAFLD, or autoimmune liver disease/other with validated algorithms. Patients were followed until death, liver transplant, or end of study. Primary outcome was the cause of death as liver-related, cardiovascular disease, non-hepatic malignancy, and external causes (accident/self-harm/suicide/homicide). Nonparametric analyses were used to describe the cumulative incidence of cause-specific death by cirrhosis etiology, sex, and compensation status.

Results:

Overall, 202,022 patients with cirrhosis were identified (60% male, median age 56 y (IQR 46–67), 52% NAFLD, 26% alcohol-associated liver disease, 11% HCV). After a median follow-up of 5 years (IQR 2–12), 81,428 patients died, and 3024 (2%) received liver transplant . Patients with compensated cirrhosis mostly died from non-hepatic malignancies and cardiovascular disease (30% and 27%, respectively, in NAFLD). The 10-year cumulative incidence of liver-related deaths was the highest among those with viral hepatitis (11%–18%) and alcohol-associated liver disease (25%), those with decompensation (37%) and/or HCC (50%–53%). Liver transplant occurred at low rates (< 5%), and in men more than women.

Conclusions:

Cardiovascular disease and cancer-related mortality exceed liver-related mortality in patients with compensated cirrhosis.
A randomized, controlled, prehabilitation intervention to maximize early recovery (PRIMER) in liver transplantation
Authors: Serper Marina , Jones Lauren S. , Clement Thomas , Reddy Rajender K. , Reese Peter P.
Published: June 2023

Frailty and impaired functional status are associated with adverse outcomes on the liver transplant (LT) waitlist and after transplantation. Prehabilitation prior to LT has rarely been tested. We conducted a 2-arm patient-randomized pilot trial to evaluate the feasibility and efficacy of a 14-week behavioral intervention to promote physical activity prior to LT. Thirty patients were randomized 2:1 to intervention (n = 20) versus control (n = 10). The intervention arm received financial incentives and text-based reminders linked to wearable fitness trackers. Daily step goals were increased by 15% in 2-week intervals. Weekly check-ins with study staff assessed barriers to physical activity. The primary outcomes were feasibility and acceptability. Secondary outcomes included mean end-of-study step counts, short physical performance battery, grip strength, and body composition by phase angle. We fit regression models for secondary outcomes with the arm as the exposure adjusting for baseline performance. The mean age was 61, 47% were female, and the median Model for End-stage Liver Disease sodium (MELD-Na) was 13. One-third were frail or prefrail by the liver frailty index, 40% had impaired mobility by short physical performance battery, nearly 40% had sarcopenia by bioimpedance phase angle, 23% had prior falls, and 53% had diabetes. Study retention was 27/30 (90%; 2 unenrolled from intervention, 1 lost to follow-up in control arm). Self-reported adherence to exercise during weekly check-ins was about 50%; the most common barriers were fatigue, weather, and liver-related symptoms. End-of-study step counts were nearly 1000 steps higher for intervention versus control: adjusted difference 997, 95% CI, 147–1847; p = 0.02. On average, the intervention group achieved daily step targets 51% of the time. A home-based intervention with financial incentives and text-based nudges was feasible, highly accepted, and increased daily steps in LT candidates with functional impairment and malnutrition.
Clinical and Histopathologic Analyses of Nasopharyngeal Hyalinizing Clear Cell Carcinoma
Authors: Zhai Changwen , Yuan Cuncun , Sun Ji , Song Wanjing , Wang Shuyi , Lin Lan
Published: June 2023

The aim of this study was to evaluate the clinicopathologic features, molecular characteristics, treatment strategy, and prognosis of nasopharyngeal hyalinizing clear cell carcinoma (HCCC). Retrospective observational case series. Institutional pathology records between 2006 and 2022 were searched for all cases of nasopharyngeal HCCC. We included 10 male and 16 female patients aged 30 to 82 years (median: 60.5 y, mean: 54.6 y). The most common symptoms were blood-stained rhinorrhea and nasal obstruction. Tumors most often involved the lateral wall of the nasopharynx, followed by the superior posterior wall. Microscopically, all tumor cells were arranged in sheets, nests, cords, and single cells in a hyaline/myxoid/fibrous stroma. The tumor cells were polygonal, with or without distinct cell borders, and displayed abundant clear-to-eosinophilic cytoplasm. All 26 cases were positive for pancytokeratin, CK7, p40, and p63 but negative for myoepithelial differentiation markers. Ki-67 labeling was low and ranged from 1% to 10%. All 26 cases demonstrated EWSR1 and EWSR1-ATF1 rearrangements, and no case demonstrated MAML2 rearrangement. Complete follow-up data were available for 23 patients: 14 patients underwent endoscopic surgery alone, 5 underwent radiation therapy followed by endoscopic surgery, 3 underwent radiation therapy followed by biopsy, and 1 underwent cisplatin chemotherapy before endoscopic surgery. Clinical follow-up ranged from 6 to 195 months; 13 patients (56.5%) were alive without tumor, 5 patients (21.7%) died of disease, 5 patients (21.7%) survived with tumor. HCCCs of the nasopharynx are rare tumors. The definitive diagnosis depends on histopathology, immunohistochemistry, and molecular studies. The optimal treatment for patients with nasopharyngeal HCCC is wide local excision. Radiation and chemotherapy might be good options for managing locally advanced cases. Nasopharyngeal HCCC is less indolent than previously thought. Tumor stage and the choice of treatment are key factors affecting the prognosis of nasopharyngeal HCCC patients.
Stability and change in male fertility patterns by cognitive ability across 32 birth cohorts
Authors: Bratsberg Bernt , Rogeberg Ole
Published: June 2023

The relationship between cognitive ability (CA) and childbearing remains unsettled. Using Norwegian administrative registers with population coverage, we study how male lifetime fertility patterns differ across cognitive score groups, and how these changed across the 1950–1981 birth cohorts, covering a period characterized by rapid social and economic change. The analyses reveal systematic differences in fertility and fertility timing across CA groups, with high scoring males having delayed but ultimately higher fertility than lower scoring males. This pattern remains stable over time despite strong trends towards delayed and reduced fertility. The overall positive relationship between CA and fertility is primarily driven by high rates of childlessness in the lowest scoring group, with low-scoring males showing higher rates of parity progression at higher parities.
Dispersal-induced social stress prolongs gestation in wild meerkats
Authors: Maag Nino , Cozzi Gabriele , Seager David , Manser Marta , Sickmüller Anna , Hildebrandt Thomas B. , Clutton-Brock Tim , Ozgul Arpat
Published: June 2023

In the majority of mammals, gestation length is relatively consistent and seldom varies by more than 3%. In a few species, females can adjust gestation length by delaying the development of the embryo after implantation. Delays in embryonic development allow females to defer the rising energetic costs of gestation when conditions are unfavourable, reducing the risk of embryo loss. Dispersal in mammals that breed cooperatively is a period when food intake is likely to be suppressed and stress levels are likely to be high. Here, we show that pregnant dispersing meerkats (
Suricata suricatta
), which have been aggressively evicted from their natal group and experience weight loss and extended periods of social stress, prolong their gestation by means of delayed embryonic development. Repeated ultrasound scans of wild, unanaesthetized females throughout their pregnancies showed that pregnancies of dispersers were on average 6.3% longer and more variable in length (52–65 days) than those of residents (54–56 days). The variation in dispersers shows that, unlike most mammals, meerkats can adapt to stress by adjusting their pregnancy length by up to 25%. By doing so, they potentially rearrange the costs of gestation during adverse conditions of dispersal and enhance offspring survival.
Complexity of spatio-temporal plantar pressure patterns during everyday behaviours
Authors: Cleland Luke D. , Rowland Holly M. , Mazzà Claudia , Saal Hannes P.
Published: June 2023

The human foot sole is the primary interface with the external world during balance and walking, and also provides important tactile information on the state of contact. However, prior studies on plantar pressure have focused mostly on summary metrics such as overall force or centre of pressure under limited conditions. Here, we recorded spatio-temporal plantar pressure patterns with high spatial resolution while participants completed a wide range of daily activities, including balancing, locomotion and jumping tasks. Contact area differed across task categories, but was only moderately correlated with the overall force experienced by the foot sole. The centre of pressure was often located outside the contact area or in locations experiencing relatively low pressure, and therefore a result of disparate contact regions spread widely across the foot. Non-negative matrix factorization revealed low-dimensional spatial complexity that increased during interaction with unstable surfaces. Additionally, pressure patterns at the heel and metatarsals decomposed into separately located and robustly identifiable components, jointly capturing most variance in the signal. These results suggest optimal sensor placements to capture task-relevant spatial information and provide insight into how pressure varies spatially on the foot sole during a wide variety of natural behaviours.
Stochastic switching of delayed feedback suppresses oscillations in genetic regulatory systems
Authors: Karamched Bhargav R. , Miles Christopher E.
Published: June 2023

Delays and stochasticity have both served as crucially valuable ingredients in mathematical descriptions of control, physical and biological systems. In this work, we investigate how explicitly dynamical stochasticity in delays modulates the effect of delayed feedback. To do so, we consider a hybrid model where stochastic delays evolve by a continuous-time Markov chain, and between switching events, the system of interest evolves via a deterministic delay equation. Our main contribution is the calculation of an effective delay equation in the fast switching limit. This effective equation maintains the influence of all subsystem delays and cannot be replaced with a single effective delay. To illustrate the relevance of this calculation, we investigate a simple model of stochastically switching delayed feedback motivated by gene regulation. We show that sufficiently fast switching between two oscillatory subsystems can yield stable dynamics.
Photoelectrochemical performance of BiOI/TiO
2
nanotube arrays (TNAs) p-n heterojunction synthesized by SILAR-ultrasonication-assisted methods
Authors: Kasuma Warda Ningsih Sherly , Wibowo Rahmat , Gunlazuardi Jarnuzi
Published: June 2023

In order to extend the visible region activity of titania nanotube array (TNAs) films, the successive ionic layer adsorption and reaction (SILAR)-ultrasonication-assisted method has been used to prepare BiOI-modified TiO
2
nanotube arrays (BiOI/TNAs). The band gap of BiOI/TNAs for all the variations reveals absorption in the visible absorption. The surface morphology of BiOI/TNAs is shown in the nanoplate, nanoflake and nanosheet forms with a vertical orientation perpendicular to TiO
2
. The crystalline structure of BiOI did not change the structure of the anatase TNAs, with the band gap energy of the BiOI/TNAs semiconductor in the visible region. The photocurrent density of the BiOI/TNAs extends to the visible-light range. BiOI/TNAs prepared with 1 mM Bi and 1 mM KI on TNAs 40 V 1 h, 50 V 30 min show the optimum photocurrent density. A tandem dye-sensitized solar cell (DSSC)-photoelectrochemical (PEC) was used for hydrogen production in salty water. BiOI/TNAs optimum was used as the photoanode of the PEC cell. The solar to hydrogen conversion efficiency (STH) of tandem DSSC-PEC reaches 1.34% in salty water.
Episodic, compression-driven fluid venting in layered sedimentary basins
Authors: Kearney Luke M. , MacMinn Christopher W. , Katz Richard F. , Kirkham Chris , Cartwright Joe
Published: June 2023

Fluid venting phenomena are prevalent in sedimentary basins globally. Offshore, these localized fluid-expulsion events are archived in the geologic record by the resulting pockmarks at the sea-floor. Venting is widely interpreted to occur via hydraulic fracturing, which requires near-lithostatic pore pressures for initiation. One common driver for these extreme pressures is horizontal tectonic compression, which pressurizes the entire sedimentary column over a wide region. Fluid expulsion leads to a sudden, local relief of this pressure, which then gradually recharges through continued compression, leading to episodic venting. Pressure recharge will also occur through pressure diffusion from neighbouring regions that remain pressurized, but the combined role of compression and pressure diffusion in episodic venting has not previously been considered. Here, we develop a novel poroelastic model for episodic, compression-driven venting. We show that compression and pressure diffusion together set the resulting venting period. We derive a simple analytical expression for this venting period, demonstrating that pressure diffusion can significantly reduce the venting period associated with a given rate of compression. Our expression allows this rate of compression to be inferred from observations of episodic venting. We conclude that pressure diffusion is a major contributor to episodic fluid venting in mudstone-dominated basins.
On the dual advantage of placing observations through forward sensitivity analysis
Authors: Ahmed S. E. , San O. , Lakshmivarahan S. , Lewis J. M.
Published: June 2023

The four-dimensional variational data assimilation methodology for assimilating noisy observations into a deterministic model has been the workhorse in forecasting centres for over three decades. While this method provides a computationally efficient framework for dynamic data assimilation, it is largely silent on the important question concerning the minimum number and placement of observations. To answer this question, we demonstrate the dual advantage of placing the observations where the square of the sensitivity of the model solution with respect to the unknown control variables, called forward sensitivities, attains its maximum. By following this approach, we can force the observability Gramian to be of full rank, which in turn guarantees efficient recovery of the optimal values of the control variables, which is the first of the two advantages of this strategy. We further show that the proposed strategy of placing observations has another inherent optimality: the square of the sensitivity of the optimal estimates of the control with respect to the observations (used to obtain these estimates) attains its minimum value, a second advantage that is a direct consequence of the above strategy for placing observations. Our analytical framework and numerical experiments on linear and nonlinear systems confirm the effectiveness of our proposed strategy.
Two-dimensional interfacial diffusion model of inhibitory synaptic receptor dynamics
Authors: Bressloff Paul C.
Published: June 2023

The diffusion-trapping of protein receptors in post-synaptic regions of a neuron’s plasma membrane plays a key role in determining the strength of synaptic connections and their regulation during learning and memory. In this paper, we construct and analyse a two-dimensional interfacial diffusion model of inhibitory synaptic receptor dynamics. The model involves three major components. First, the boundary of each synapse is treated as a semi-permeable interface due to the effects of cytoskeletal structures. Second, the effective diffusivity within a synapse is taken to be smaller than the extrasynaptic diffusivity due to the temporary binding to scaffold protein buffers within the synapse. Third, receptors from intracellular pools are inserted into the membrane extrasynaptically and internalized extrasynaptically and synaptically. We first solve the model equations for a single synapse in an unbounded domain and explore how the non-equilibrium steady-state number of synaptic receptors depends on model parameters including synaptic radius and the permeability of the synaptic interface. We then use matched asymptotic analysis to solve the corresponding problem of multiple synapses in a large, bounded domain. In particular, we show how diffusion mediates pairwise synaptic interactions that could provide a substrate for heterosynaptic plasticity. Finally, we indicate how to apply the model to the stochastic dynamics of single receptors.
Droplet motion with contact-line friction: long-time asymptotics in complete wetting
Authors: Giacomelli Lorenzo , Gnann Manuel V. , Peschka Dirk
Published: June 2023

We consider the thin-film equation for a class of free boundary conditions modelling friction at the contact line, as introduced by E and Ren. Our analysis focuses on formal long-time asymptotics of solutions in the perfect wetting regime. In particular, through the analysis of quasi-self-similar solutions, we characterize the profile and the spreading rate of solutions depending on the strength of friction at the contact line, as well as their (global or local) corrections, which are due to the dynamical nature of the free boundary conditions. These results are complemented with full transient numerical solutions of the free boundary problem.
Metabolic perturbations and key pathways associated with the bacteriostatic activity of Clitoria ternatea flower anthocyanin fraction against Escherichia coli
Authors: Jeyaraj Ethel Jeyaseela , Han Mei-Ling , Li Jian , Choo Wee Sim
Published: June 2023

Clitoria ternatea flowers are rich in anthocyanins and possess various biological activities. Specifically, the antibacterial mechanism of action of C. ternatea anthocyanins remains unknown and was investigated in

Escherichia coli

. A time–kill assay was used to assess the antibacterial activity and the metabolic perturbations in

E. coli

were investigated utilizing liquid chromatography–mass spectrometry (LC-MS)-based metabolomics. Pathway analyses were carried out for metabolites showing ≥2-fold changes. The anthocyanin fraction remarkably reduced the growth of

E. coli

at 4 h by 95.8 and 99.9 % at minimum inhibitory concentration (MIC) and 2× MIC, respectively. The anthocyanin fraction (MIC) had a bacteriostatic effect and was shown to have perturbed glycerophospholipids (1-acyl-sn-glycero-3-phosphoethanolamine, phosphatidylglycerol, diacylglycerol and cardiolipin), amino acids (valine, tyrosine and isoleucine) and energy (ubiquinone and NAD) metabolites at 1 and 4 h. This study demonstrated significant metabolic perturbations of the glycerophospholipid, amino acid and energy metabolism, with these being the key pathways involved in the bacteriostatic activity of anthocyanins from C. ternatea, which may have promise as bacteriostatic agents for

E. coli

-related infections.
Metagenome-assembled genomes from mineral tundra soils in Rásttigáisá, northern Norway
Authors: Pessi Igor S , Rutanen Aino , Hultman Jenni
Published: June 2023

We report 59 non-redundant metagenome-assembled genomes (MAGs) recovered from mineral tundra soils in Rásttigáisá, Northern Norway. Most MAGs were assigned to the bacterial phyla Candidatus Dormibacterota (n=12), Verrucomicrobiota (n=10), and Acidobacteriota (n=9). All archaeal MAGs (n=4) belong to the genus Candidatus Nitrosopolaris (phylum Thermoproteota).
Quorum Sensing and Biofilms in Entrobacteriaceae
Authors: Rathore Rohit , Chipurupalli alikya , Karumidze Natia
Published: June 2023

Several bacterial species participate in two confirmable behaviours. Irreversible attachment to the surface (biofilm) and to regulate certain phenotypes expression which will synchronize their behaviour (quorum sensing). This sophisticated intercellular communication mechanism called quorum sensing (QS). QS play a major role in the formation of the biofilm & biofilm helps the bacteria in adhesion/ cohesion potentiality, metabolite interchange, cellular connection, defence, nutritious and resistance to medication. Since biofilm is resistant to antibiotics so targeting biofilm is the main therapeutic approach. Biofilm formation is one of the major reason of catheter associated urinary tract infections (CAUTI). E. coli and K. pneumoniae cause Urinary Tract Infection which cost about $1.6 billion in medical expenses every year. Both of them have ability to form biofilms. Exopolysaccharide matrix of biofilm is a double barrier for antibiotics and other antimicrobial substances, therefore makes bacteria more resistant. In many species QS mediated biofilm formation is present, targeting the QS system (anti-QS) are attracting attention in the drug development field. Another treatment strategy is using of bacteriophages. So the aim of our research was to find out bacterial strains able to form biofilms and check the activity of phages able to inhibit formation or eradication of biofilms. We used two species of strains, E. coli and four K. pneumoniae, out of which only E. coli #5 formed biofilm. Bacteriophage specific for E. coli#5 showed that this phage was able to impede the growth of biofilm and also help to eliminate already formed biofilm.
Propofol Mediated Unconsciousness Disrupts Progression of Sensory Signals through the Cortical Hierarchy
Authors: Tauber John M. , Brincat Scott L. , Stephen Emily P. , Donaghue Jacob A. , Kozachkov Leo , Brown Emery N. , Miller Earl K.
Published: June 2023

A critical component of anesthesia is the loss sensory perception. Propofol is the most widely used drug for general anesthesia, but the neural mechanisms of how and when it disrupts sensory processing are not fully understood. We analyzed local field potential (LFP) and spiking recorded from Utah arrays in auditory cortex, associative cortex, and cognitive cortex of non-human primates before and during propofol mediated unconsciousness. Sensory stimuli elicited robust and decodable stimulus responses and triggered periods of stimulus-induced coherence between brain areas in the LFP of awake animals. By contrast, propofol mediated unconsciousness eliminated stimulus-induced coherence and drastically weakened stimulus responses and information in all brain areas except for auditory cortex, where responses and information persisted. However, we found stimuli occurring during spiking Up states triggered weaker spiking responses than in awake animals in auditory cortex, and little or no spiking responses in higher order areas. These results suggest that propofol’s effect on sensory processing is not just due to asynchronous down states. Rather, both Down states and Up states reflect disrupted dynamics.
Demographic disequilibrium and growth-mortality asymmetry of forests across climate gradients
Authors: Zhou Jian
Published: June 2023

Forests are commonly believed to adapt themselves to environment and ultimately converge to demographic equilibrium characterized by a fixed size-structure. The expectation, however, has been lacking in mathematical rigor and been debating for evidential solidity. Here, by giving a general time-dynamic solution to the forest demographic model and verifying the prediction with worldwide forest inventory data, we show the inherent disequilibrium of forest demography with oscillations of forest-size-structure. Forests adapt to environment in a way of asymmetric growth-mortality tradeoff along climate gradients, which generates divergence to convergence oscillations of size-structure with rising temperature and precipitation. The demographic disequilibrium framework can provide a general basis for elucidating the variability of forest-size-structure with implications on intrinsic ecosystem instability, and for improving the Earth system modeling.
Late reproduction is associated with extended female survival but not with familial longevity
Authors: de Kat Annelien C , Roelofs Femke , Slagboom P. Eline , Broekmans Frank JM , Beekman Marian , van den Berg Niels
Published: June 2023

Objective

Female reproductive health comprises adequate oocyte quality and quantity, normal fecundability, a normal course of pregnancy, and the delivery of healthy offspring. General aging patterns and the maintenance of somatic health have been associated with female reproductive health. However, it is unknown whether better long-term somatic maintenance is directly related to reproductive outcomes, and whether there is a shared genetic predisposition underlying both somatic and reproductive aging. Here we investigate whether reproductive health is related to female lifespan or familial longevity.

Design

Observational study

Subjects

10,255 female members of a multigenerational historical cohort (1812-1910), the LINKing System for historical family reconstruction (LINKS) and 1,258 females from 651 long-lived families in the Leiden Longevity Study.

Main outcome measures

The association between reproductive characteristics and longevity was studied both on an individual and familial level. Individual survival was studied in relation to age at last childbirth and total number of children. Familial longevity was studied through parental survival and related to age at last childbirth, total number of children and a polygenic risk score (PRS) for age at menopause.

Results

Females giving birth to their last child at a higher age lived longer: for each year increase in the age of the birth of the last child, a woman’s lifespan increased with 0.06 years (22 days) (p<0.005). Females who lived to be in the top 10% survivors of their birth cohort (n=2,241, 21.9%) on average gave birth to their last child at a 1% later age than the remaining cohort (IRR=1.01, p<0.005).

Females with 1 or 2 long-lived parents did not have a higher mean age of last childbirth. There was neither a significant association between an increasing number of long-lived ancestral family members (familial longevity), nor the PRS.

Conclusion

Female reproductive health associates with a longer lifespan and with survival to more extreme ages (longevity). The heritable component in familial longevity, however, does not associate to extended reproductive health and the PRS underlying age at menopause does not explain familial longevity. Other factors in somatic maintenance that support a longer lifespan are likely to have an impact on reproductive health.
EPIC-TRACE: predicting TCR binding to unseen epitopes using attention and contextualized embeddings
Authors: Korpela Dani , Jokinen Emmi , Dumitrescu Alexandru , Huuhtanen Jani , Mustjoki Satu , Lähdesmäki Harri
Published: June 2023

T cells play an essential role in adaptive immune system to fight pathogens and cancer but may also give rise to autoimmune diseases. The recognition of a peptide-MHC (pMHC) complex by a T cell receptor (TCR) is required to elicit an immune response. Many machine learning models have been developed to predict the binding, but generalizing predictions to pMHCs outside the training data remains challenging.

We have developed a new machine learning model that utilizes information about the TCR from bothαandβchains, epitope sequence, and MHC. Our method uses ProtBERT embeddings for the amino acid sequences of both chains and the epitope, as well as convolution and multi-head attention architectures. We show the importance of each input feature as well as the benefit of including epitopes with only a few TCRs to the training data. We evaluate our model on existing databases and show that it compares favorably against other state-of-the-art models.
Freeze dehydration vs. supercooling in tree stems: physical and physiological modelling
Authors: Bozonnet Cyril , Saudreau Marc , Badel Eric , Améglio Thierry , Charrier Guillaume
Published: June 2023

Frost resistance is the major factor affecting the distribution of plant species at high latitude and elevation. The main effects of freeze-thaw cycles are damage to living cells and formation of gas embolism in tree xylem vessels. Lethal intracellular freezing can be prevented in living cells by two mechanisms: dehydration and deep supercooling. We developed a multiphysics numerical model coupling water flow, heat transfer, and phase change, considering different cell types in plant tissues, to study the dynamics and extent of cell dehydration, xylem pressure changes, and stem diameter changes in response to freezing and thawing. Results were validated using experimental data for stem diameter changes of walnut trees. The effect of cell mechanical properties was found to be negligible as long as the intracellular tension developed during dehydration was sufficiently low compared to the ice induced cryostatic suction. The model was finally used to explore the coupled effects of relevant physiological parameters (initial water and sugar content) and environmental conditions (air temperature variations) on the dynamics and extent of dehydration. It revealed configurations where cell dehydration could be sufficient to protect cells from intracellular freezing, and situations where supercooling was necessary. This model, freely available with this paper, could easily be extended to explore different anatomical structures, different species and more complex physical processes.
Oligomerization-dependent and synergistic regulation of Cdc42 GTPase cycling by a GEF and a GAP
Authors: Tschirpke Sophie , Daalman Werner K-G. , van Opstal Frank , Laan Liedewij
Published: June 2023

Cell polarity is a crucial biological process essential for cell division, directed growth, and motility. InSaccharomyces cerevisiae, polarity establishment centers around the small Rho-type GTPase Cdc42, which cycles between GTP-bound and GDP-bound states, regulated by GEFs like Cdc24 and GAPs such as Rga2. To dissect the dynamic regulation of Cdc42, we employedin vitroGTPase assays, revealing inverse concentration-dependent profiles for Cdc24 and Rga2: with increasing concentration, Cdc24’s GEF activity is non-linear and oligomerization-dependent, which is possibly linked to the relief of its self-inhibition. In contrast, Rga2’s GAP activity saturates, likely due to self-inhibition upon oligomerization. Together, Cdc24 and Rga2 exhibit a strong synergy driven by weak Cdc24-Rga2 binding. We propose that the synergy stems from Cdc24 alleviating the self-inhibition of oligomeric Rga2. We believe this synergy contributes to efficient regulation of Cdc42’s GTPase cycle over a wide range of cycling rates, enabling cells to resourcefully establish polarity. As Cdc42 is highly conserved among eukaryotes, we propose the GEF-GAP synergy to be a general regulatory property in other eukaryotes.
Zero-mode waveguide nanowells for single-molecule detection in living cells
Authors: Yang Sora , Klughammer Nils , Barth Anders , Tanenbaum Marvin E. , Dekker Cees
Published: June 2023

Single-molecule fluorescence imaging experiments generally require sub-nanomolar protein concentrations to isolate single protein molecules, which makes such experiments challenging in live cells due to high intracellular protein concentrations. Here, we show that single-molecule observations can be achieved in live cells through a drastic reduction in the observation volume using overmilled zero-mode waveguides (ZMWs - subwavelength-size holes in a metal film). Overmilling of the ZMW in a palladium film creates a nanowell of tunable size in the glass layer below the aperture, which cells can penetrate. We present a thorough theoretical and experimental characterization of the optical properties of these nanowells over a wide range of ZMW diameters and overmilling depths, showing an excellent signal confinement and a five-fold fluorescence enhancement of fluorescent molecules inside nanowells. ZMW nanowells facilitate live-cell imaging, as cells form stable protrusions into the nanowells. Importantly, the nanowells greatly reduce cytoplasmic background fluorescence, enabling detection of individual membrane-bound fluorophores in the presence of high cytoplasmic expression levels, which could not be achieved with TIRF microscopy. Zero-mode waveguide nanowells thus provide great potential to study individual proteins in living cells.

Graphical abstract
Proteomic profiling identifies Serpin B9 as mediator of resistance to CAR T-cell and bispecific antibody treatment in B-cell lymphoma
Authors: Brinkmann Berit J. , Capraz Tümay , Roider Tobias , Knoll Mareike , Kolb Carolin , Liu Yi , Angeli-Terzidou Antonia-Eugenia , Paramasivam Nagarajan , Chapuy Björn , Eckstein Volker , Sauer Tim , Schmitt Michael , Rosenwald Andreas , Müller-Tidow Carsten , Huber Wolfgang , Dietrich Sascha
Published: June 2023

Although T-cell-engaging therapies are highly effective in patients with relapsed and/or refractory B-cell non-Hodgkin lymphoma (B-NHL), responses are often not durable. To identify tumor-intrinsic drivers of resistance, we quantifiedin-vitroresponse to CD19-directed chimeric antigen receptor T-cells (CD19-CAR) and bispecific antibodies (BsAb) across 46 B-NHL cell lines and measured their proteomic profiles at baseline. Among the proteins associated with poorin-vitroresponse was Serpin B9, an endogenous granzyme B inhibitor. Knock-out ofSERPINB9in cell lines with high intrinsic expression rendered them more susceptible to CD19-CAR and CD19-BsAb. Overexpression in cell lines with low intrinsic expression attenuated responses. Polatuzumab, vorinostat, lenalidomide, or checkpoint inhibitors improved response to CD19-CAR, although independently of Serpin B9 expression. Besides providing an important resource of therapy response and proteomic profiles, this study refines our understanding of resistance in T-cell engaging therapies, and suggests clinically relevant combination regimes.
Engineeringin vitromodels of cystic fibrosis lung disease using neutrophil extracellular trap inspired biomaterials
Authors: Boboltz Allison M. , Yang Sydney , Duncan Gregg A.
Published: June 2023

Cystic fibrosis (CF) is a muco-obstructive lung disease where inflammatory responses due to chronic infection result in the accumulation of neutrophil extracellular traps (NETs) in the airways. NETs are web-like complexes comprised mainly of decondensed chromatin that function to capture and kill bacteria. Prior studies have established excess release of NETs in CF airways increases viscoelasticity of mucus secretions and reduces mucociliary clearance. Despite the pivotal role of NETs in CF disease pathogenesis, currentin vitromodels of this disease do not account for their contribution. Motivated by this, we developed a new approach to study the pathobiological effects of NETs in CF by combining synthetic NET-like biomaterials, composed of DNA and histones, with anin vitrohuman airway epithelial cell culture model. To determine the impact of synthetic NETs on airway clearance function, we incorporated synthetic NETs into mucin hydrogels and cell culture derived airway mucus to assess their rheological and transport properties. We found that the addition of synthetic NETs significantly increases mucin hydrogel and native mucus viscoelasticity. As a result, mucociliary transportin vitrowas significantly reduced with the addition of mucus containing synthetic NETs. Given the prevalence of bacterial infection in the CF lung, we also evaluated the growth ofPseudomonas aeruginosain mucus with or without synthetic NETs. We found mucus containing synthetic NETs promoted microcolony growth and prolonged bacterial survival. Together, this work establishes a new biomaterial enabled approach to study innate immunity mediated airway dysfunction in CF.
Piroplasm parasites (Apicomplexa: Piroplasmida) in northeastern populations of the invasive Asian longhorned tick,Haemaphysalis longicornisNeumann (Ixodida: Ixodidae), in the United States
Authors: Herb H , Ferreira FC , Gonzalez J , Fonseca DM
Published: June 2023

Piroplasms, which include the agents of cattle fever and human and dog babesiosis, are a diverse group of blood parasites of significant veterinary and medical importance. The invasive Asian longhorned tick,Haemaphysalis longicornis, is a known vector of piroplasms in its native range in east Asia and invasive range in Australasia. In the US state of Virginia,H. longicornishas been associated withTheileria orientalisIkeda outbreaks that caused cattle mortality. We examined 667H. longicorniscollected in 2021 from three sites in New Brunswick, New Jersey, the US state where established populations of this species were first detected in 2017. We used primers targeting the 18S small subunit rRNA and the cytochrome b oxidase loci and unveiled the presence of DNA from an unidentifiedTheileriaspecies (in 1 nymph) andTheileria cervitype F (1 adult, 5 nymphs). In addition, we sequenced a 130 bp fragment of the cytochrome oxidase b locus fromOdocoileus virginianus, the white-tailed deer, in a partially engorged questingH. longicornis, supporting the association of this tick species with deer. We also detected DNA from an undescribedBabesiasensu stricto (‘true’Babesia, 2 adults, 2 nymphs) as well asBabesiasp. Coco (1 adult, 1 nymph). Finally, we detected DNA fromBabesia microtiS837 (1 adult, 4 nymphs).Babesia microtiS837 has been sequenced from striped skunks,Mephitis mephitis, and is closely related to the human pathogenB. microtiUS-type. The five parasites we are associating withH. longicornisrepresent a diverse assemblage spanning three clades in the piroplasm phylogeny, two undescribed, raising concerns of transmission amplification of veterinary pathogens as well as spillover of pathogens from wildlife to humans.
Metabolic reprogramming of cancer cells by JMJD6-mediated pre-mRNA splicing is associated with therapeutic response to splicing inhibitor
Authors: Jablonowski Carolyn , Quarni Waise , Singh Shivendra , Tan Haiyan , Bostanthirige Dhanushka Hewa , Jin Hongjian , Fang Jie , Chang Ti-Cheng , Finkelstein David , Cho Ji-Hoon , Hu Dongli , Pagala Vishwajeeth , Sakurada Sadie Miki , Pruett-Miller Shondra M. , Wang Ruoning , Murphy Andrew , Freeman Kevin , Peng Junmin , Davidoff Andrew M , Wu Gang , Yang Jun
Published: June 2023

Dysregulated pre-mRNA splicing and metabolism are two hallmarks of MYC-driven cancers. Pharmacological inhibition of both processes has been extensively investigated as potential therapeutic avenues in preclinical and clinical studies. However, how pre-mRNA splicing and metabolism are orchestrated in response to oncogenic stress and therapies is poorly understood. Here, we demonstrate that Jumonji Domain Containing 6, Arginine Demethylase and Lysine Hydroxylase, JMJD6, acts as a hub connecting splicing and metabolism in MYC-driven neuroblastoma. JMJD6 cooperates with MYC in cellular transformation by physically interacting with RNA binding proteins involved in pre-mRNA splicing and protein homeostasis. Notably, JMJD6 controls the alternative splicing of two isoforms of glutaminase (GLS), namely kidney-type glutaminase (KGA) and glutaminase C (GAC), which are rate-limiting enzymes of glutaminolysis in the central carbon metabolism in neuroblastoma. Further, we show that JMJD6 is correlated with the anti-cancer activity of indisulam, a “molecular glue” that degrades splicing factor RBM39, which complexes with JMJD6. The indisulam-mediated cancer cell killing is at least partly dependent on the glutamine-related metabolic pathway mediated by JMJD6. Our findings reveal a cancer-promoting metabolic program is associated with alternative pre-mRNA splicing through JMJD6, providing a rationale to target JMJD6 as a therapeutic avenue for treating MYC-driven cancers.
Influence of DNA extraction methods on microbiome and resistome analysis in activated sludge
Authors: Calderón-Franco David , Kok Dana , Dukker Renzo , Abbas Ben , Abreu-Silva Joana , Rocha Jaqueline , Lopez Marin Marco Antonio , Vega Rebeca Pallarés , Gajdos Stanislav , Ananth Mythili , Apoorva Seeram , Karpisek Ivan , Solcova Milada , Leal Lucia Hernández , Bartacek Jan , Manaia Célia , Purkrtova Sabina , Weissbrodt David G.
Published: June 2023

Amplicon sequencing, metagenomics, and quantitative polymerase chain reaction (qPCR) are commonly used techniques to analyse microorganisms and antibiotic resistance genes (ARGs) in activated sludge from wastewater treatment plants (WWTPs). However, the lack of workflow harmonisation poses challenges in comparing measurements across studies and research groups. To address this issue, we examined the impact of DNA extraction procedures on 16S rRNA gene amplicon sequencing, shotgun metagenomics, and qPCR analyses of activated sludge by combining two widely used DNA extraction kits (PowerSoil and FastDNA) and two commonly employed disruption instruments (bead-beater and vortex) through a 2×2 factorial experimental design involving four groups of three analysts performing DNA extractions in triplicates. Our findings revealed significant differences in DNA yield, purity, and reproducibility of amplicon sequencing profiles among the extraction kits. Operator variability also influenced the results. We compared microbiome profiles obtained by amplicon sequencing and metagenomics and observed that bead-beating introduced more variability among triplicates compared to vortexing. The combinations of extraction kits and disruption instruments impacted the relative abundances of specific phyla such asActinobacteriota,Bacteroidota, andNitrospirota. For resistome analysis, we employed metagenomics for high-resolution profiling and qPCR for high-sensitivity detection of ARGs. The compositions and diversities of resistome datasets were not significantly affected by the choice of extraction kits and disruption instruments. Although using the same method is ideal for accurate comparisons, our results suggest that acceptable reproducibility can still be achieved when using different methods. This finding encourages the implementation of ARG monitoring in wastewater treatment processes. However, it is important to consider biases introduced by DNA extraction workflows when designing analytical studies, interpreting their results, and comparing their findings. Striving for more harmonised molecular workflows is crucial in the field of wastewater microbiology and engineering.

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Graphical abstract
Critical Role for 24-Hydroxylation in Homeostatic Regulation of Vitamin D Metabolism
Authors: Yazdi Zhinous Shahidzadeh , Streeten Elizabeth A. , Whitlatch Hilary B. , Montasser May E. , Beitelshees Amber L. , Taylor Simeon I.
Published: June 2023

Context

The body has evolved homeostatic mechanisms to maintain free levels of Ca+2and 1,25-dihydroxyvitamin D [1,25(OH)2D] within narrow physiological ranges. Clinical guidelines emphasize important contributions of PTH in maintaining this homeostasis.

Objective

To investigate mechanisms of homeostatic regulation of vitamin D (VitD) metabolism and to apply mechanistic insights to improve clinical assessment of VitD status.

Design

Crossover clinical trial studying participants before and after VitD3-supplementation.

Setting

Community.

Participants

11 otherwise healthy individuals with VitD-deficiency (25-hydroxyvitamin D [25(OH)D] ≤20 ng/mL).

Interventions

VitD3-supplements (50,000 IU once or twice a week depending on BMI, for 4-6 weeks) were administered to achieve 25(OH)D≥30 ng/mL.

Results

VitD3-supplementation significantly increased mean 25(OH)D by 2.7-fold and 24,25-dihydroxyvitamin D [24,25(OH)2D] by 4.3-fold. In contrast, mean levels of PTH, FGF23, and 1,25(OH)2D did not change. Mathematical modeling suggested that 24-hydroxylase activity was maximal for 25(OH)D≥50 ng/mL and achieved a minimum (∼90% suppression) with 25(OH)D<10-20 ng/mL. The 1,25(OH)2D/24,25(OH)2D ratio better predicted modeled 24-hydroxylase activity (h) (ρ=-0.85; p=0.001) compared to total plasma 25(OH)D (ρ=0.51; p=0.01) and the 24,25(OH)2D/25(OH)D ratio (ρ=0.37; p=0.3).

Conclusions

Suppression of 24-hydroxylase provides a first line of defense against symptomatic VitD-deficiency by decreasing metabolic clearance of 1,25(OH)2D. The 1,25(OH)2D/24,25(OH)2D ratio provides a useful index of VitD status since it incorporates 24,25(OH)2D levels and therefore, provides insight into 24-hydroxylase activity. When VitD availability is limited, this suppresses 24-hydroxylase activity – thereby decreasing the level of 24,25(OH)2D and increasing the 1,25(OH)2D/24,25(OH)2D ratio. Thus, an increased 1,25(OH)2D/24,25(OH)2D ratio signifies triggering of homeostatic regulation, which occurs at early stages of VitD-deficiency.
Examining the inter-relationships between social isolation and loneliness and their correlates among older British adults before and during the COVID-19 lockdown: evidence from four British longitudinal studies
Authors: Mansfield Rosie , Di Gessa Giorgio , Patel Kishan , McElroy Eoin , Wels Jaques , Henderson Morag , Maddock Jane , Stafford Jean , Steptoe Andrew , Richards Marcus , Patalay Praveetha
Published: June 2023

Background and Objectives

Unprecedented social restrictions during the COVID-19 pandemic have provided a new lens for considering the inter-relationship between social isolation and loneliness in later life. We present these inter-relationships before and during the COVID-19 restrictions and investigate to what extent demographic, socio-economic, and health factors associated with such experiences differed during the pandemic.

Research Design and Method

We used data from four British longitudinal population-based studies (1946 MRC NSHD, 1958 NCDS, 1970 BCS, and ELSA). Rates, co-occurrences, and correlates of social isolation and loneliness are presented prior to and during the early stage of the COVID-19 pandemic and the inter-relationships between these experiences are elucidated in both periods.

Results

Across the four studies, pre-pandemic proportions reporting social isolation ranged from 15 to 54%, with higher rates in older ages (e.g., 32% of 70-79 and 54% of those over 80). During the pandemic, the percentage of older people reporting both social isolation and loneliness and isolation only slightly increased. The inter-relationship between social isolation and loneliness did not change. Associations between socio-demographic and health characteristics and social isolation and loneliness also remained consistent, with greater burden among those with greater economic precarity (females, non-homeowners, unemployed, illness and greater financial stress).

Discussion and Implications

There were already large inequalities in experiences of social isolation and loneliness and the pandemic had a small impact on worsening these inequalities. The concepts of loneliness and social isolation are not transferable and clarity is needed in how they are conceptualised, operationalised, and interpreted.