Optimization of FFPE preparation and identification of gene attributes associated with RNA degradation.

Formalin-fixed paraffin-embedded (FFPE) tissues are widely available specimens for clinical studies. However, RNA degradation in FFPE tissues often restricts their utility. In this study, we determined optimal FFPE preparation conditions, including tissue ischemia at 4°C (<48 h) or 25°C for a short time (0.5 h), 48-h fixation at 25°C and sampling from FFPE scrolls instead of sections. Notably, we observed an increase in intronic reads and a significant change in gene rank based on expression level in the FFPE as opposed to fresh-frozen (FF) samples. Additionally, we found that more reads were mapped to genes associated with chemical stimulus in FFPE samples. Furthermore, we demonstrated that more degraded genes in FFPE samples were enriched in genes with short transcripts and high free energy. Besides, we found 40 housekeeping genes exhibited stable expression in FF and FFPE samples across various tissues. Moreover, our study showed that FFPE samples yielded comparable results to FF samples in dimensionality reduction and pathway analyses between case and control samples. Our study established the optimal conditions for FFPE preparation and identified gene attributes associated with degradation, which would provide useful clues for the utility of FFPE tissues in clinical practice and research.

Ductile adhesive elastomers with force-triggered ultra-high adhesion strength.

Elastomers play a vital role in many forthcoming advanced technologies in which their adhesive properties determine materials' interface performance. Despite great success in improving the adhesive properties of elastomers, permanent adhesives tend to stick to the surfaces prematurely or result in poor contact depending on the installation method. Thus, elastomers with on-demand adhesion that is not limited to being triggered by UV light or heat, which may not be practical for scenarios that do not allow an additional external source, provide a solution to various challenges in conventional adhesive elastomers. Herein, we report a novel, ready-to-use, ultra high-strength, ductile adhesive elastomer with an on-demand adhesion feature that can be easily triggered by a compression force. The precursor is mainly composed of a capsule-separated, two-component curing system. After a force-trigger and curing process, the ductile adhesive elastomer exhibits a peel strength and a lap shear strength of 1.2 × 104 N m-1 and 7.8 × 103 kPa, respectively, which exceed the reported values for advanced ductile adhesive elastomers. The ultra-high adhesion force is attributed to the excellent surface contact of the liquid-like precursor and to the high elastic modulus of the cured elastomer that is reinforced by a two-phase design. Incorporation of such on-demand adhesion into an elastomer enables a controlled delay between installation and curing so that these can take place under their individual ideal conditions, effectively reducing the energy cost, preventing failures, and improving installation processes.

PWSC: a novel clustering method based on polynomial weight-adjusted sparse clustering for sparse biomedical data and its application in cancer subtyping.

BACKGROUND: Clustering analysis is widely used to interpret biomedical data and uncover new knowledge and patterns. However, conventional clustering methods are not effective when dealing with sparse biomedical data. To overcome this limitation, we propose a hierarchical clustering method called polynomial weight-adjusted sparse clustering (PWSC). RESULTS: The PWSC algorithm adjusts feature weights using a polynomial function, redefines the distances between samples, and performs hierarchical clustering analysis based on these adjusted distances. Additionally, we incorporate a consensus clustering approach to determine the optimal number of classifications. This consensus approach utilizes relative change in the cumulative distribution function to identify the best number of clusters, resulting in more stable clustering results. Leveraging the PWSC algorithm, we successfully classified a cohort of gastric cancer patients, enabling categorization of patients carrying different types of altered genes. Further evaluation using Entropy showed a significant improvement (p = 2.905e-05), while using the Calinski-Harabasz index demonstrates a remarkable 100% improvement in the quality of the best classification compared to conventional algorithms. Similarly, significantly increased entropy (p = 0.0336) and comparable CHI, were observed when classifying another colorectal cancer cohort with microbial abundance. The above attempts in cancer subtyping demonstrate that PWSC is highly applicable to different types of biomedical data. To facilitate its application, we have developed a user-friendly tool that implements the PWSC algorithm, which canbe accessed at http://pwsc.aiyimed.com/ . CONCLUSIONS: PWSC addresses the limitations of conventional approaches when clustering sparse biomedical data. By adjusting feature weights and employing consensus clustering, we achieve improved clustering results compared to conventional methods. The PWSC algorithm provides a valuable tool for researchers in the field, enabling more accurate and stable clustering analysis. Its application can enhance our understanding of complex biological systems and contribute to advancements in various biomedical disciplines.

Highly Recyclable and Tough Elastic Vitrimers from a Defined Polydimethylsiloxane Network.

Despite intensive research on sustainable elastomers, achieving elastic vitrimers with significantly improved mechanical properties and recyclability remains a scientific challenge. Herein, inspired by the classical elasticity theory, we present a design principle for ultra-tough and highly recyclable elastic vitrimers with a defined network constructed by chemically crosslinking the pre-synthesized disulfide-containing polydimethylsiloxane (PDMS) chains with tetra-arm polyethylene glycol (PEG). The defined network is achieved by the reduced dangling short chains and the relatively uniform molecular weight of network strands. Such elastic vitrimers with the defined network, i.e., PDMS-disulfide-D, exhibit significantly improved mechanical performance than random analogous, previously reported PDMS vitrimers, and even commercial silicone-based thermosets. Moreover, unlike the vitrimers with random network that show obvious loss in mechanical properties after recycling, those with the defined network enable excellent thermal recyclability. The PDMS-disulfide-D also deliver comparable electrochemical signals if utilized as substrates for electromyography sensors after the recycling. The multiple relaxation processes are revealed via a unique physical approach. Multiple techniques are also applied to unravel the microscopic mechanism of the excellent mechanical performance and recyclability of such defined network.

Molecular Geometry-Directed Self-Recognition in the Self-Assembly of Giant Amphiphiles.

Three sets of polyoxometalate (POM)-based amphiphilic hybrid macromolecules with different rigidity in their organic tails are used as models to understand the effect of molecular rigidity on their possible self-recognition feature during self-assembly processes. Self-recognition is achieved in the mixed solution of two structurally similar, sphere-rigid T-shape-linked oligofluorene(TOF4 ) rod amphiphiles, with the hydrophilic clusters being Anderson (Anderson-TOF4 ) and Dawson (Dawson-TOF4 ), respectively. Anderson-TOF4 is observed to self-assemble into onion-like multilayer structures and Dawson-TOF4 forms multilayer vesicles. The self-assembly is controlled by the interdigitation of hydrophobic rods and the counterion-mediated attraction among charged hydrophilic inorganic clusters. When the hydrophobic blocks are less rigid, e.g., partially rigid polystyrene and fully flexible alkyl chains, self-recognition is not observed, attributing to the flexible conformation of hydrophobic molecules in the solvophobic domain. This study reveals that the self-recognition among amphiphiles can be achieved by the geometrical limitation of the supramolecular structure due to the rigidity of solvophobic domains.

Chinese expert consensus on the diagnosis and treatment of HER2-altered non-small cell lung cancer.

Human epidermal growth factor receptor 2 (HER2) possesses tyrosine kinase activity and participates in cell growth, differentiation and migration, and survival. Its alterations, mainly including mutations, amplifications, and overexpression are associated with poor prognosis and are one of the major drivers in non-small cell lung cancer (NSCLC). Several clinical trials had been investigating on the treatments of HER2-altered NSCLC, including conventional chemotherapy, programmed death 1 (PD-1) inhibitors, tyrosine kinase inhibitors (TKIs) and antibody-drug conjugates (ADCs), however, the results were either disappointing or encouraging, but inconsistent. Trastuzumab deruxtecan (T-DXd) was recently approved by the Food and Drug Administration as the first targeted agent for treating HER2-mutant NSCLC. Effective screening of patients is the key to the clinical application of HER2-targeted agents such as TKIs and ADCs. Various testing methods are nowadays available, including polymerase chain reaction (PCR), next-generation sequencing (NGS), fluorescence in situ hybridization (FISH), immunohistochemistry (IHC), etc. Each method has its pros and cons and should be reasonably assigned to appropriate patients for diagnosis and guiding treatment decisions. To help standardize the clinical workflow, our expert group reached a consensus on the clinical management of HER2-altered NSCLC, focusing on the diagnosis and treatment strategies.

IGFBP1hiWNT3Alo Subtype in Esophageal Cancer Predicts Response and Prolonged Survival with PD-(L)1 Inhibitor.

PD-(L)1 inhibitor could improve the survival of locally advanced esophageal cancer (ESCA) patients, but we cannot tailor the treatment to common biomarkers. WNT signaling activation was associated with primary resistance to immunotherapy. In this study, we used our two clinical cohorts (BJCH n = 95, BJIM n = 21) and three public cohorts to evaluate and verify a new immunotherapeutic biomarker based on WNT signaling in ESCA patients. Our findings showed that WNT signaling-related genes stratified TCGA patients into Cluster 1, 2, and 3, among which, Cluster 3 had the worst prognosis. The most up- and down-regulated genes in Cluster 3 were IGFBP1 and WNT3A. Further analysis validated that IGFBP1hiWNT3Alo ESCA patients had significantly poor RFS and OS in the TCGA and BJCH cohorts. Interestingly, IGFBP1hiWNT3Alo patients had a good response and prognosis with immunotherapy in three independent cohorts, exhibiting better predictive value than PD-L1 expression (signature AUC = 0.750; PD-L1 AUC = 0.571). Moreover, IGFBP1hiWNT3Alo patients may benefit more from immunotherapy than standard treatment (p = 0.026). Immune cell infiltration analysis revealed a significant increase in DC infiltration in IGFBP1hiWNT3Alo patients post-immunotherapy (p = 0.022), which may enhance immune response. The IGFBP1hiWNT3Alo signature could predict patients who benefited from PD-(L)1 inhibitor treatment and may serve as a biomarker in ESCA.

Self-Healable, Highly Stretchable, Ionic Conducting Polymers as Efficient Protecting Layers for Stable Lithium-Metal Electrodes.

Although numerous studies on polymeric protective films to stabilize lithium (Li)-metal electrodes have been reported, the construction of self-healing polymers that enables the long-term operation of Li-metal batteries (LMBs) at relatively low temperatures has rarely been demonstrated. Herein, a highly stretchable, autonomous self-healable, and ionic-conducting polymer network (SHIPN) is synthesized as an efficient protective film for LMBs. The network backbone, synthesized from copolymerization of poly(ethylene glycol)-mono-methacrylate (PEGMMA) and 2-[[(butylamino)carbonyl]oxy]ethyl acrylate (BCOE), is chemically cross-linked via diisocyanate. With SHIPN-modified electrodes, enhanced electrochemical performance can be achieved in Li/Cu, Li/Li, and Li/LiFePO4 (Li/LFP) cells. The SHIPN@Li/LFP cell delivers a capacity retention of 85.6% after 500 cycles at 5 °C, resulting from the low-temperature self-healability of SHIPN. In full cells with a high-mass-loading LFP cathode (∼17 mg cm-2), the capacity retention is at least 300% higher than that with a bare Li electrode. Further physical characterizations of electrodes confirm the effect of SHIPN in enhancing the interfacial stability and suppressing Li dendrite growth. Our results will provide insights into rationally designing soft and hybrid materials toward stable LMBs at different temperatures.

Case Report: Osimertinib Followed by Osimertinib Plus Bevacizumab, Personalized Treatment Strategy for a Lung Cancer Patient With a Novel EGFR Exon 20 Insertion D770_N771insGT and Multiple Brain Metastases.

Epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (EGFR-TKIs) are the standard of care for non-small cell lung cancer (NSCLC) patients with EGFR exon 19 deletion and L858R mutations. However, no EGFR TKI has been approved for NSCLC patients harboring insertion mutations in EGFR exon 20 (EGFRex20ins), a subgroup of uncommon EGFR mutations resistant to first-generation EGFR TKIs. This unmet clinical challenge is further complicated by disease progression due to brain metastases (BMs), which limits the use of EGFR TKIs with low intracranial activity. Osimertinib, a third-generation EGFR TKI with high CNS activity, has demonstrated superior efficacy as a first-line treatment for EGFR-mutant NSCLC with or without BM. The VEGF pathway is a key mediator of cancer metastasis and resistance to EGFR TKIs. Accumulating evidence has demonstrated that the addition of anti-VEGF agents to EGFR TKIs provides an alternative treatment option for the clinical management of EGFR-mutant NSCLC. We herein report an NSCLC case with a novel EGFRex20ins mutation D770_N771insGT and multiple brain metastases who briefly responded to first-line osimertinib treatment and subsequently achieved prolonged disease control with osimertinib plus bevacizumab as second-line treatment. Our case suggests that osimertinib in combination with bevacizumab may be an effective option for NSCLC patients with specific EGFRex20ins mutations and brain metastases.

Evaluation of Walking Comfort in Children's School Travel at Street Scale: A Case Study in Tianjin (China).

(1) Background: school travel is an important part of a child's daily activities. A comfortable walking environment can encourage children to walk to school. The existing methods of evaluating walking environments are not specific to children's walks to school. (2) Methods: this study proposes a method of evaluating walking comfort in children traveling to school at street scale. Related indexes were selected that reflect children's school travel behavior and their needs in street environments based on walking environment audit tools. Factor analysis was then used to calculate the relative weight of each index. (3) Results: the new evaluation method was tested in the neighborhoods around the First Central Primary School in Hedong District, Tianjin, China. The walking comfort for children's school travel was evaluated in eight indexes: effective street width; street flatness; street cleanliness; interface diversity; buffer; shade coverage; green looking ratio; and sound decibels. Different classes and types of streets were found to have various vulnerabilities. (4) Conclusions: this evaluation method can accurately locate the weak spots in streets to improve the local policymakers' perception of street environments, which can greatly facilitate the implementation of precise measures to promote children walking to school.

Screw dislocation-induced pyramidal crystallization of dendron-like macromolecules featuring asymmetric geometry.

We report herein that dendron-shaped macromolecules AB n crystallize into well-ordered pyramid-like structures from mixed solvents, instead of spherical motifs with curved structures, as found in the bulk. The design of the asymmetric molecular architecture and the choice of mixed solvents are applied as strategies to manipulate the crystallization process. In mixed solvents, the solvent selection for the Janus macromolecule and the existence of dominant crystalline clusters contribute to the formation of flat nanosheets. Whereas during solvent evaporation, the bulkiness of the asymmetric macromolecules easily creates defects within 2D nanosheets which lead to their spiral growth through screw dislocation. The size of the nanosheets and the growth into 2D nanosheets or 3D pyramidal structures can be regulated by the solvent ratio and solvent compositions. Moreover, macromolecules of higher asymmetry generate polycrystals of lower orderliness, probably due to higher localized stress.

Evaluation and Optimization of Walkability of Children's School Travel Road for Accessibility and Safety Improvement.

(1) Background: In the context of a children friendly city, accessibility and safety are the basic needs of children's pedestrian school travel. This study proposes a comprehensive evaluation method of pedestrian accessibility and safety for children's school travel. (2) Methods: Firstly, the school travel network was constructed by simulating the path of children walking to school. Secondly, from the meso and micro dimensions, the impact factors of pedestrian accessibility and safety were combed out, and an evaluation index system was constructed. Finally, pedestrian accessibility and safety were evaluated based on the Space Syntax analysis and ArcGIS spatial analysis, and the results were superimposed and spatially differentiated. The new evaluation method was tested in the Jintang Road area in Hedong District, Tianjin, China. (3) Results: The pedestrian accessibility and safety of children's school travel road in the study area needed to be improved. It was found that the main impact factors were the effective walking width, the spatial connectivity, the visual integration, the obstruction of pedestrian safety, the completeness of crossing facilities and the influence of traffic flow and put forward optimization strategies. After optimized simulation verification, the overall improvement was achieved. (4) Conclusion: The evaluation method is helpful to calculate the pedestrian accessibility and safety of children's school travel, and help decision makers determine the design and management strategies of child-friendly streets.

Accurate Determination of the Quantity and Spatial Distribution of Counterions around a Spherical Macroion.

The accurate distribution of countercations (Rb+ and Sr2+ ) around a rigid, spherical, 2.9-nm size polyoxometalate cluster, {Mo132 }42- , is determined by anomalous small-angle X-ray scattering. Both Rb+ and Sr2+ ions lead to shorter diffuse lengths for {Mo132 } than prediction. Most Rb+ ions are closely associated with {Mo132 } by staying near the skeleton of {Mo132 } or in the Stern layer, whereas more Sr2+ ions loosely associate with {Mo132 } in the diffuse layer. The stronger affinity of Rb+ ions towards {Mo132 } than that of Sr2+ ions explains the anomalous lower critical coagulation concentration of {Mo132 } with Rb+ compared to Sr2+ . The anomalous behavior of {Mo132 } can be attributed to majority of negative charges being located at the inner surface of its cavity. The longer anion-cation distance weakens the Coulomb interaction, making the enthalpy change owing to the breakage of hydration layers of cations more important in regulating the counterion-{Mo132 } interaction.

The complete chloroplast genome sequence of Populus davidiana (Salicaceae).

The complete chloroplast genome sequence of Populus davidiana was characterized from Illumina pair-end sequencing. The chloroplast genome of P. davidiana was 156,868 bp in length, containing a large single-copy region (LSC) of 84,976 bp, a small single-copy region (SSC) of 16,606 bp, and two inverted repeat (IR) regions of 27,643 bp. The overall GC content is 30.70%, while the correponding values of the LSC, SSC, and IR regions are 64.6%, 69.2%, and 60.1%, respectively. The genome contains 131 complete genes, including 86 protein-coding genes (62 protein-coding gene species), 37 tRNA genes (29 tRNA species) and 8 rRNA genes (4 rRNA species). The Neighbour-joining phylogenetic analysis showed that P. davidiana and Populus rotundifolia clustered together as sisters to other Populus species.

Dual-site catalysis for sustainable polymers to replace current commodity polymers - carbonylative copolymerization of ethylene, ethylene oxide, and tetrahydrofuran.

Zwitterionic Ni(ii)-catalyzed carbonylative copolymerization of ethylene and cyclic ethers for the synthesis of photolytically and hydrolytically degradable polymers is reported. The segmented tetrapolymer products are composed of polyketone segments from alternating enchainments of CO and ethylene and poly(ether-co-ester) segments from non-alternating enchainments of CO, ethylene oxide, and tetrahydrofuran. Plastic and elastic products can be obtained via the general synthetic platform with the appropriate choice of catalyst and polymerization conditions.

Rational Control of Self-Recognition of Macroionic γ-Cyclodextrin by Host-Guest Interaction with Super-Chaotropic Borate Cluster Ions.

We report a feasible method to control self-recognition during the self-assembly of a hydrophilic macroion, phosphate-functionalized γ-cyclodextrin (γ-CD-P), though host-guest interactions. We confirmed that γ-CD-P can form a host-guest complex with a super-chaotropic anion, namely the B12 F122- borate cluster, by using NMR spectroscopy and isothermal titration calorimetry. The loaded γ-CD-P, which has a higher charge density, can be distinguished from the uncomplexed γ-CD-P, leading to self-sorting behavior during the self-assembly process, confirmed by the formation of two types of individual supramolecular structures (Rh of ca. 57 nm and 18 nm, determined by light scattering) instead of hybrid structures in mixed dilute solution. This self-recognition behavior is accounted for by the difference in intermolecular electrostatic interactions arising from the loading.

Strong Enantiomeric Preference on the Macroion-Counterion Interaction Induced by Weakly Associated Chiral Counterions.

The role of chiral counterions on the attraction and self-assembly of chiral Pd12L24 metal organic cages (MOCs) with NO3- being the original counterion is studied by laser light scattering and isothermal titration calorimetry. Nitrates can trigger the self-assembly of macrocationic Pd12L24 into hollow spherical blackberry-type supramolecular structures via counterion-mediated attraction. Although chiral counteranions, such as N-(tert-butoxycarbonyl)-alanine (Boc-Ala), have weaker interaction with the MOCs compared to NO3-, they can induce different assembly behaviors between two enantiomeric MOCs by inhibiting the MOC-nitrate binding and weakening the interaction between them. The d-counterions are capable of selectively suppressing and slowing down the assembly of l-MOCs and also considerably decreasing their assembly size due to the much weaker MOC-nitrate interaction. The same scenario is observed for l-counterions when interacting with the d-MOCs. This study unveils the role of weakly associated chiral counterions on the central chiral macroions, especially their supramolecular structure formation, and provides additional evidence on the mechanism of the homochirality phenomenon.

Synthesis, Assembly, and Sizing of Neutral, Lanthanide Substituted Molybdenum Blue Wheels {Mo90Ln10}.

Polyoxometalate molybdenum blue (MB) complexes typically exist as discrete multianionic clusters and are composed of repeating Mo building units. MB wheels such as {Mo176} and {Mo154} are made from pentagon-centered {Mo8} building blocks joined by equal number of {Mo1} units as loin, and {Mo2} dimer units as skirt along the ring edge, with the ring sizes of the MB wheels modulated by the {Mo2} units. Herein we report a new class of contracted lanthanide-doped MB structures that have replaced all the {Mo2} units with lanthanide ions on the inner rim, giving the general formula {Mo90Ln10}. We show three examples of this new decameric {Mo90Ln10} (Ln = La, Ce, and Pr) framework synthesized by high temperature reduction and demonstrate that later Ln ions result in {Mo92Ln9} (Ln = Nd, Sm), conserving one {Mo2} linker unit in its structure, as a consequence of the lanthanide contraction. Remarkably the {Mo90Ln10} compounds are the first examples of charge-neutral molybdate wheels as confirmed by BVS, solubility experiments, and redox titrations. We detail our full synthetic optimization for the isolation of these clusters and complete characterization by X-ray, TGA, UV-vis, and ICP studies. Finally, we show that this fine-tuned self-assembly process can be utilized to selectively enrich Ln-MB wheels for effective separation of lanthanides.

Enhanced Macroanion Recognition of Superchaotropic Keggin Clusters Achieved by Synergy of Anion-π and Anion-Cation Interactions.

Keggin clusters are the most widely used polyoxometalate building blocks for the construction advanced materials, but effective methods for precisely recognizing the isostructural analogues of Keggins are still limited. In this study we employed the zwitterionic molecule 4,4'-dipyridyl N,N'-dioxide as a recognition receptor to specifically bind to the three Keggin analogues PW12 O40 3- , PMo12 O40 3- , and SiW12 O40 4- , which separately co-assembled into three different types of spherical charged colloids of different sizes. The recognition phenomena were confirmed by electrochemical methods and their crystallization behavior. Compared with solely anion-cation interaction-driven systems, the synergism with the anion-π interactions between the superchaotropic Keggins and the electron-deficient pyridine rings is believed to enhance the recognition. This observation is intriguing as the long-range solution assembly of Keggins is mainly driven by short-range anion-π interactions. Our results show that the little-noticed hydration shell of Keggins is significantly influenced by the superchaotropic effect, leading to differentiated binding affinity to the receptors and more obvious recognition phenomena between tungsten/molybdenum Keggin analogues.

Co-ion Effects in the Self-Assembly of Macroions: From Co-ions to Co-macroions and to the Unique Feature of Self-Recognition.

Macroions, as soluble ions with a size on the nanometer scale, show unique solution behavior different from those of simple ions and large colloidal suspensions. In macroionic solutions, the counterions are known to be important and well-explored. However, the role of co-ions (ions carrying the same type of charge as the macroions) is often ignored. Here, through experimental and simulation studies, we demonstrate the role of co-ions as a function of co-ion size on their interaction with the macroions (using {Mo72Fe30} and {SrPd12} as models) and the related self-assembly into blackberry-type structures in dilute solutions. Several regimes of unique co-ion effects are clearly identified: small ions (halides, oxoacid ions), subnanometer-scaled bulky ions (lacunary Keggin and dodecaborate ions), and those with sizes comparable to the macroions. Small co-ions have no observable effect on the self-assembly of fully hydrophilic {Mo72Fe30}, while due to hydrophobic interaction and intermolecular hydrogen bonds, the small co-ions show influences on the self-assembly of hydrophobic {SrPd12}. Subnanometer ions, a.k.a. "superchaotropic ions", are still too small to assemble into a blackberry by themselves, but they can coassemble with the macroions, showing a strong interaction with the macroionic system. When the co-ion size is comparable to that of the macroions, they assemble independently instead of assembling with the macroions, leading to the previously reported unique self-recognition phenomenon for macroions.