Browse Articles

Logarithmic kinetics and bundling in random packings of elongated 3D physical links

We explore the impact of excluded volume interactions on the local assembly of linear physical networks, where nodes are spheres and links are rigid cylinders with varying length. To focus on the effect of elongated links, we introduce a minimal 3D model that helps us zoom into confined regions of these networks whose distant parts are sequentially connected by the random deposition of physical links with a very large aspect ratio. We show that the nonequilibrium kinetics at which these elongated links, or spaghetti, adhere to the available volume without mutual crossings is logarithmic in time, as opposed to the algebraic growth in lower dimensions for needle-like packings. We attribute this qualitatively different behavior to a delay in the activation of depletion forces caused by the 3D nature of the problem. Equally important, we find that this slow kinetics is metastable, allowing us to analytically predict the kinetic scaling characterizing an algebraic growth due to the nucleation of local bundles. Our findings offer a theoretical benchmark to study the local assembly of physical networks, with implications for the modeling of nest-like packings far from equilibrium.

Building a Synthetic Cell Together

Correction: Machine learning based prediction of cognitive metrics using major biomarkers in SuperAgers

Comparative analysis of differences for pathological upgrade and incomplete resection in endoscopic snare papillectomy for ampullary adenomas: A single-institution retrospective study

Background Inconsistent pathological diagnoses between pre- and post-endoscopic snare papillectomy (ESP) biopsies were frequently observed. We aimed to compare the differences in pathological upgrade and incomplete resection between endoscopic snare papillectomy for ampullary adenomas. Methods The included patients were those referred to Sir Run Run Shaw Hospital and underwent ESP for an ampullary adenoma between 2012 and 2022. The endoscopic and clinicopathological features of ampullary adenomas were obtained using white light endoscopy, narrow-band imaging endoscopy, and endoscopic ultrasound (EUS). Adverse events, histological diagnosis, and follow-up data were also collected. Results Overall, 40 patients underwent ESP of ampullary adenomas and were included in the study. Seventeen patients had inconsistent pre- and post-ESP pathological diagnoses, as they were upgraded from either low-grade dysplasia (LGD) to high-grade dysplasia (HGD) or from HGD to adenocarcinoma. Various characteristics varied between the pathological upgrade and non-upgrade groups, such as alanine transaminase (ALT), alkaline phosphatase levels (ALP), erosion and redness of papilla, a hybrid histological type, procedure time and extended lower bile duct width identified through EUS. Differences were observed between the complete and incomplete resection groups in terms of ALT, Gamma-glutamyl transferase (GGT) levels, tumor extension into the bile duct, and width of lower bile duct extension as determined by EUS. Conclusions Pathological upgrading were relatively common after ESP for ampullary adenomas. Preoperative identification of specific clinical and endoscopic features can enhance diagnostic accuracy and inform treatment strategies.

Influenza A virus NS1 protein mimics oncogenic PI3K resulting in isoform specific cellular redistribution and activation

The nonstructural protein 1 (NS1) of influenza A virus performs a broad variety of proviral activities in the infected cell, primarily mediating evasion from the host innate immune response by being the main viral interferon antagonist. However, there are several interactions whose biological relevance remains obscure, such as the ability of NS1 to bind and activate class IA phosphoinositide 3-kinases (PI3Ks). PI3Ks are highly regulated lipid kinases that act as critical nodes in multiple cell signaling networks and are also important proto-oncogenes. This activation is mediated by NS1 binding specifically to the p85β subunit. To better understand the consequences of this interaction, we developed a bimolecular fluorescence complementation (BiFC) assay to selectively track the different PI3K heterodimers and, using this system, we found that NS1 induces an isoform-specific relocation and activation of the different PI3K heterodimers. We found that clinically relevant oncogenic mutations in both catalytic and regulatory subunits of PI3K could mimic the effect caused by NS1, and partially rescue the loss of viral fitness in a recombinant virus encoding a p85β-binding deficient NS1.

Viral proteins suppress rice defenses by boosting OsTSN1 RNA decay via phase separation and multimerization

Cytoreductive nephroureterectomy for treatment of upper urinary tract urothelial carcinoma initially diagnosed as node-positive

Feeling of self-worth in healthy premenopausal women—relationships with menstrual cycles and ovulation over 1-year in the prospective ovulation cohort

Self-Worth is an over-arching evaluation of a person’s sense of individual value. Self-worth, however, is an underappreciated concept. It has rarely been reported related to physiological data; we found no studies related to the menstrual cycle or ovulation. It is also unclear if Self-Worth is a stable trait or a variable state. We sought to discover if “Feeling of Self-Worth” (as recorded daily) was related to cycle phases and ovulation of spontaneous menstrual cycles (without hormonal contraception) in healthy premenopausal women over one-year in data from the Prospective Ovulation Cohort. Participating women were invited to complete the Menstrual Cycle Diary© (Diary©) daily; it describes cycle-related and other comprehensive everyday life experiences including negative moods as well as changes from each person’s usual Feelings of Self-Worth. Women recorded their Feeling of Self-Worth on a 5-level ordinal scale as a letter translated to a number originally centered on their usual feeling (U = 3) with two higher and two lower (letters) levels. The validated Quantitative Basal Temperature© (QBT©) method was used to assess ovulation and luteal lengths. Fifty-three healthy, community dwelling, normal-weight, non-smoking premenopausal women mean age 33.9 (95% CI 32.4, 35.5) years old were studied. All participants were first required to document two consecutive normal-length (21–36 days) and normally ovulatory (luteal length ≥10 days) cycles before enrolment. Each participant completed the Diary© and QBT© records daily over a mean of 13 cycles (minimum = 8). During the study, cycle lengths were mean 28.04 (95% CI 27.80, 28.28) days with 71% of all cycles being normally ovulatory, 26% having short luteal phases (SLP, LL < 10 days) and 2.6% being anovulatory. Results in all women and all cycles showed that the mean annual Feeling of Self-Worth was 3.01 (95% CI 2.94, 3.09), thus very tightly related to their usual Feeling of Self-Worth. There were only small, inconsistent differences between Feeling of Self-Worth in the follicular versus luteal phases comparing normally ovulatory versus all ovulatory cycles (including those with short luteal phases). Analysis of Self-Worth within the 46 women having both normally ovulatory and ovulatory disturbed cycles (short luteal and anovulatory) showed that it was slightly lower in these women’s normally ovulatory cycles (P = .03). Principal Components Analysis of all Diary© data showed that Feeling of Self-Worth was positively related to Interest in Sex and Feeling of Energy (together explaining 9% of all variance). In addition, Feeling of Self-Worth had a significant, negative loading on the Negative Mood Factor (that explained 14.2% of total variance). These data suggest that Feelings of Self-Worth in this comprehensive menstrual cycle and ovulation dataset in healthy women were not related menstrual phases and ovarian hormone levels.

Structural basis for anaerobic alkane activation by a multisubunit glycyl radical enzyme

X-succinate synthases (XSSs) are glycyl radical enzymes (GREs) that catalyze the addition of hydrocarbons to fumarate via radical chemistry, thereby activating them for microbial metabolism. To date, the only structurally characterized XSS is benzylsuccinate synthase (BSS), which functionalizes toluene. A distinct subclass of XSSs acts on saturated hydrocarbons, which possess much stronger C(sp 3 )–H bonds than toluene, suggesting mechanistic and structural differences from BSS. Here, we use cryogenic electron microscopy to determine the structure of one such enzyme, (1-methylalkyl)succinate synthase (MASS) from Azoarcus strain HxN1, which functionalizes n -alkanes (C6–C8). The structure reveals an asymmetric dimer in which both sides contain a catalytic α-subunit and accessory γ-subunit. One α-subunit also binds two additional subunits, β and δ. The β-subunit binds a [4Fe–4S] cluster and adopts a fold similar to BSSβ. The β-subunit appears to regulate the flexibility of the α-subunit to enable opening of the active site, affording the binding of n -alkane substrates. The δ-subunit, which lacks homology to known GRE subunits, adopts a rubredoxin-like fold that binds a single Fe ion, an architecture not previously reported for GREs. MASSδ occupies the same region of the α-subunit as the activating enzyme (AE) and may regulate the conformational changes required for glycyl radical installation. Structural comparisons between MASS and BSS reveal differences in how fumarate is bound and show amino acid substitutions that could account for the binding of alkanes versus toluene. Together, this structure offers insight into anaerobic alkane activation via fumarate addition.

A hollow-tube-like hydrospongel for multimodal therapy of advanced colorectal cancer

Abstract Preserving anal function in advanced-stage colorectal cancer (CRC) treatment remains a significant challenge. Here we introduce a hollow-tube-like hydrospongel (HTHSG) as an advanced neoadjuvant therapy. Constructed from cellulose nanofibers crosslinked with Fe 3 O 4 @PDA (polydopamine) nanoparticles, the HTHSG combines quick swelling (~10 seconds) with high fracture strength (>250 kPa) for enhanced mechanical stability. The hydrospongel enables precise, localized delivery of the chemotherapeutic agent 5-FU directly to the tumor site. Beyond conventional chemotherapy, HTHSG employs electromagnetic induction to achieve targeted thermal ablation and chemodynamic therapy, minimizing collateral damage to healthy tissues. Comparative studies in orthotopic, cell-derived, and patient-derived xenograft models demonstrate the superior tumor-reduction efficacy of HTHSG over traditional neoadjuvant therapies. Feasibility studies in a beagle model and human-sized dummy model further validate the HTHSG’s potential for clinical application, showing preserved anal function and biocompatibility. These findings establish HTHSG as a promising pre-surgical treatment option for advanced-stage CRC, offering improved therapeutic outcomes and quality of life for patients.

Thermal shock treatment of recyclable bimetallic MOF derived carbon composite for organics oxidation by advanced Fenton-Like technique

Abstract This study offers a bimetallic MIL-88 B Metal–Organic Frameworks (MOF) derived carbon composite Co/Ferrite MOF namely Co/Fe@C that is synthesized through a solvothermal route followed by a simple thermal shock treatment and used as a Fenton-like source. The synthesized Co/Fe@C morphology and elemental analysis are characterized via X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), and field emission scanning electron microscopy (FE-SEM), X-ray photoelectron spectroscopy (XPS), Brunauer–Emmett–Teller (BET) and vibrating sample magnetometer (VSM). Carbon based MOF demonstrated fascinating features as a Fenton source conducted in dark oxidation route. The material exposed a superior efficiency in treating various organic pollutants including basic (Malachite Green, MG) and acidic (Oil Orange SS, OOSS) dyes as a textile simulated effluent and tetracycline (TC) as a model pharmaceutical wastewater. The experimental results exhibited the optimum reaction conditions of 400 mg/L for H2O2 for all contaminants oxidation and ranged from 10 to 40 mg/L for Co/Fe@C catalyst at varied optimal pH values. Under optimal conditions, the Co/Fe@C catalyst achieved removal efficiencies reached to 100% for MG, 83% for OOSS, and 72% for TC within 30 min. Furthermore, for potential full-scale application, the kinetic investigation is highlighted and the reaction is following the second kinetic order. Also, to assure catalyst sustainability, the Co/Fe@C substance is reused after recovery for seven oxidation cycles with a reasonable decline in its activity that reached to 57, 45 and 42% removals for MG, OOSS and TC, respectively. Furthermore, the mechanism exploration indicated the active species involved oxidation process primarily affecting TC and OOSS oxidation is holes (h+) and MG is OH radicals.

Phylogenetic investigation and mitochondrial genome description of ten species in nine genera of Cicadellinae from China (Hemiptera: Cicadellidae)

The Cicadellinae subfamily of the Cicadellidae (Hemiptera: Auchenorrhyncha: Cicadelloidea) is quite large, with about 2400 species across 330 genera worldwide, of which 263 species in 23 genera occur in China. This work involved the sequencing of the mitochondrial genomes of ten species and nine genera within the Cicadellinae family: Anagonalia emeiensis, Anagonalia melichari, Anatkina vespertinula, Erragonalia choui, Gunungidia aurantiifasciata, Kolla paulula, Nanatka castenea, Paratkina nigrifasciana, Seasogonia rosea, and Stenatkina angustata. The acquired mitogenomes displays a significant AT bias, with the AT contents ranging from 76.1% to 81.7%. The lengths of the mitochondrial genomes range from 14,768 bp to 16,194 bp. TAG and a single T are less frequently used as stop codons, whereas TAA is the most frequently used one. Less PCGs begin with T/GTG, and the majority begin with the conventional ATN (ATA/T/G/C) codon. All tRNA genes in Cicadellinae mitogenomes fold into the standard secondary structure of a cloverleaf,except for trnS1, which lacks a stable dihydrouridine (DHU) stem and instead has s simple loop. Six phylogenetic trees constructed by maximum likelihood (ML) and Bayesian inference (BI) for the three mitochondrial datasets, respectively, consistently showed intergeneric and interspecific relationships within the Cicadellinae. Our results in particular shed light on the molecular and phylogenetic evolution of the pronotum in Cicadellinae.

Anisotropic stretch biases the self-organization of actin fibers in multicellular Hydra aggregates

During development, groups of cells generate shape by coordinating their mechanical properties through an interplay of self-organization and prepatterning. Hydra displays a striking planar pattern of actin fibers at the organism scale, and mechanics influence the morphogenesis of biological structures during its prepatterned regeneration. However, how mechanics participate in the formation of an ordered pattern from a totally disordered state remains unknown. To study this, we used cellular aggregates formed from dissociated Hydra cells, which initially lose all actin polarity yet regenerate a long-range actin pattern. We showed quantitatively that the actin meshwork evolves from a disordered symmetric state to an ordered state in which rotational symmetry is broken, and translation symmetry is partially broken, with the nematic and smectic order parameters increasing over days. During the first hours, the actin meshwork displayed spatial heterogeneity in the nematic order parameter, and ordered domains separated by line defects progressively grew and fused. This suggests that local cell–cell interactions drive the transition from disorder to order. To understand the mechanism of ordering, we perturbed the tissue’s physical constraints. We showed that while topology and geometry do not have a direct effect, anisotropic stretch biases the emerging orientation of the actin meshwork within hours. Surprisingly, although a Wnt head organizer is expected to play a role in the actin ordering, the stretch-associated alignment happened without the prior formation of a head organizer. This demonstrates the role of tissue mechanics in the alignment of the actin fibers during the disorder-to-order transition.

Rational design and synthesis of narrow-band emitting Eu(II)-based hybrid halides via alkyl thermal cleavage

Left ventricle strain and T1 mapping evaluation in a mouse model with myocardial infarction

Abstract Myocardial strain and T1 mapping offer precise evaluation of cardiac function and tissue characteristics. The aim of this study is to provide normative myocardial strain and T1 values in mice model along with their changes after myocardial infarction (MI) using a tailored acquisition and analysis protocol. Healthy mice had MRI before and after MI. Imaging was performed to assess cardiac function and left ventricle (LV) strain. A Look-Locker Inversion-Recovery sequence was used for T1 maps reconstruction. Gadolinium doses and timing of image acquisitions were optimized. Radial and circumferential strain measurements were conducted using a custom software based on feature tracking. To address ECG signal interference, adjustments were made for accurate strain calculations. An LV dilation in MI compared to wild-type (WT) with a decrease in LV ejection fraction (p < 0.0001) were reported while stroke volume and cardiac output remained preserved (p > 0.21). Normative strain and T1 mapping data were provided revealing an increase in circumferential strain from base to apex (basal: –14 ± 1%, mid: –15 ± 2%, apical: – 21 ± 3%; p < 0.0001) and notable differences in native and post-contrast T1 values between mid-ventricular and apical LV segments. Circumferential strain differences between MI and WT mice were pronounced, with a significant drop in apical strain (p < 0.0001) in MI. Post-MI mice exhibited higher native T1 and lower post-contrast T1 compared to WT. Our methodological approach not only refines imaging sequences but also offers insights into cardiac function and tissue characteristics in mice. By describing normative values of strain and T1, our findings lay the groundwork for future research, particularly in drug therapy.

Constructing Schwartz values framework using the Rokeach values survey: Human value measurement in the longitudinal internet survey for social sciences

This paper assesses and validates indexes of human values as conceptualized in the Schwartz framework using the Rokeach Value Survey in the publicly available LISS panel data (www.lisspanel.nl), thereby opening an avenue for researchers to relate values to a wide range of attitudes, traits, and behaviors with the most widely used and tested values theory. We start with a theoretical screening of the value items, after which we use multi-dimensional scaling to assess the item’s correlation structure. We developed reliable and valid indexes for 8 of the 10 Schwartz values, of which universalism, achievement, benevolence, and conformity contain 3 or more items, and self-direction, stimulation, hedonism, and security contain 1 or 2 items. We assess the RVS-based indexes by comparing them with other Schwartz indexes in the World Value Survey and the European Social Survey data. Using regressions, all 8 values also show the expected relationships with demographics, political orientation, and personality traits. By tailoring the RVS to align with the Schwartz value structure, researchers can use a well-established framework for assessing human values longitudinally and cross-sectionally, enabling better comparisons and insights across studies and time periods.

Toward a molecular logic of lipid droplet heterogeneity?

Diminished immune cell adhesion in hypoimmune ICAM-1 knockout human pluripotent stem cells

Potential blue carbon in the fringe of Southern European Kelp forests

Abstract Blue Carbon encompasses the organic carbon sequestered and stored by coastal and marine ecosystems, including seaweed forests. This study aims to quantify the potential Blue Carbon storage and sequestration rates of subtidal kelp forests in Northern Portugal, focusing on the most dominant species Laminaria hyperborea and Saccorhiza polyschides. Through in-situ measurements of forest extension, biomass, growth, and carbon content, we determined that these kelp forests store approximately 16.48 Gg of carbon in aboveground biomass, covering an area of 5189 hectares. The estimated carbon sequestration rate is 1903 Mg C year–1, which is lower than the 3717 Mg C year–1 sequestered by saltmarshes and seagrasses in mainland Portugal (available data). However, when normalised by area, kelp forests sequester carbon at rates that equal or exceed those of saltmarshes and seagrasses, underscoring their significance for regional carbon management. Despite this, export assumptions significantly influence total carbon flux estimates, and large portions of the Portuguese coastline remain understudied. Expanding in-situ assessments, combined with regional modelling would improve Blue Carbon estimates and lay the groundwork for a future national-scale assessment. Given their potential role in climate mitigation, conservation and restoration efforts should be prioritized to protect and enhance the Blue Carbon capacity of kelp forests and associated habitats.

Evaluating the use of SPIRIT on participant retention in randomised trials: Challenges in reporting and implications for practice

Objectives To establish whether the use of SPIRIT (Standard Protocol Items: Recommendations for Interventional Trials) item 18b (retention), evidence of planning for retention, has any effect on participant retention rates in randomised controlled trials. Study design and setting A retrospective study of randomised controlled trials between 2014 and 2019. We reviewed 506 trial protocols, 253 protocols that stated the use of SPIRIT guidelines in the protocol, and 253 protocols that did not. Results The reported use of SPIRIT guideline item 18b in the trial protocol has no significant effect on participant retention rates in the corresponding trials. It does not impact the overall retention rate of participants throughout the trial, nor the retention rate of the primary outcome measure. Conclusion SPIRIT item 18b appeared not to contribute to improved participant retention rates in randomised trials. However, the lack of high-certainty evidence for effectiveness of the intervention strategies cited likely impacts this finding. Additionally, inconsistent reporting of retention strategies in trial protocols is evident and needs to be more complete to facilitate evaluation.