Bulk Processes Research Articles

Detecting significant expression patterns in single-cell and spatial transcriptomics with a flexible computational approach

Gene expression data holds the potential to shed light on multiple biological processes at once. However, data analysis methods for single cell sequencing mostly focus on finding cell clusters or the principal progression line of the data. Data analysis for spatial transcriptomics mostly addresses clustering and finding spatially variable genes. Existing data analysis methods are effective in finding the main data features, but they might miss less pronounced, albeit significant, processes, possibly involving a subset of the samples. In this work we present SPIRAL: Significant Process InfeRence ALgorithm. SPIRAL is based on Gaussian statistics to detect all statistically significant biological processes in single cell, bulk and spatial transcriptomics data. The algorithm outputs a list of structures, each defined by a set of genes working simultaneously in a specific population of cells. SPIRAL is unique in its flexibility: the structures are constructed by selecting subsets of genes and cells based on statistically significant and consistent differential expression. Every gene and every cell may be part of one structure, more or none. SPIRAL also provides several visual representations of structures and pathway enrichment information. We validated the statistical soundness of SPIRAL on synthetic datasets and applied it to single cell, spatial and bulk RNA-sequencing datasets. SPIRAL is available at https://spiral.technion.ac.il/.

Liquid-phase synthesis of a Li3PS4 solid electrolyte using ethyl isobutyrate as a synthetic medium

A β-Li3PS4 solid electrolyte was prepared via liquid-phase synthesis using ethyl isobutyrate as a synthetic medium. The precursor and solid electrolyte structures were characterized using thermogravimetry–differential thermal analysis and X-ray diffraction techniques. The dielectric relaxation analysis showed two relaxation regions, which revealed a bulk and grain boundary ionic migration process. At a temperature lower than 90°C, the frequency dependence of the dielectric constant of the prepared sample was different from that of glassy Li3PS4, indicating that the motion of the PS4 unit enhances the ionic conductivity of the Li3PS4 solid electrolyte. The ionic conductivities of the cold-pressed and warm-pressed pellets at 25°C were 6.8 × 10−5 Scm−1 and 3.6 × 10−4 Scm−1, respectively.

AnVILWorkflow: A runnable workflow package for Cloud-implemented bioinformatics analysis pipelines

Advancements in sequencing technologies and the development of new data collection methods produce large volumes of biological data. The Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL) provides a cloud-based platform for democratizing access to large-scale genomics data and analysis tools. However, utilizing the full capabilities of AnVIL can be challenging for researchers without extensive bioinformatics expertise, especially for executing complex workflows. We present the AnVILWorkflow R package, which enables the convenient execution of bioinformatics workflows hosted on AnVIL directly from an R environment. AnVILWorkflow simplifies the setup of the cloud computing environment, input data formatting, workflow submission, and retrieval of results through intuitive functions. We demonstrate the utility of AnVILWorkflow for three use cases: bulk RNA-seq analysis with Salmon, metagenomics analysis with bioBakery, and digital pathology image processing with PathML. The key features of AnVILWorkflow include user-friendly browsing of available data and workflows, seamless integration of R and non-R tools within a reproducible analysis pipeline, and accessibility to scalable computing resources without direct management overhead. AnVILWorkflow lowers the barrier to utilizing AnVIL’s resources, especially for exploratory analyses or bulk processing with established workflows. This empowers a broader community of researchers to leverage the latest genomics tools and datasets using familiar R syntax. This package is distributed through the Bioconductor project (https://bioconductor.org/packages/AnVILWorkflow), and the source code is available through GitHub (https://github.com/shbrief/AnVILWorkflow).

Bulk and fracture process zone contribution to the rate-dependent adhesion amplification in viscoelastic broad-band materials

The contact between a rigid Hertzian indenter and an adhesive broad-band viscoelastic substrate is considered. The material behavior is described by a modified power law model, which is characterized by only four parameters, the glassy and rubbery elastic moduli, a characteristic exponent n and a timescale τ0. The maximum adherence force that can be reached while unloading the rigid indenter from a relaxed viscoelastic half-space is studied by means of a numerical implementation based on the boundary element method, as a function of the unloading velocity, preload and by varying the broadness of the viscoelastic material spectrum. Through a comprehensive numerical analysis we have determined the minimum contact radius that is needed to achieve the maximum amplification of the pull-off force at a specified unloading rate and for different material exponents n. The numerical results are then compared with the prediction of Persson and Brener viscoelastic crack propagation theory, providing excellent agreement. However, comparison against experimental tests for a glass lens indenting a PDMS substrate shows data can be fitted with the linear theory only up to an unloading rate of about 100μm/s showing the fracture process zone rate-dependent contribution to the energy enhancement is of the same order of the bulk dissipation contribution. Hence, the limitations of the current numerical and theoretical models for viscoelastic adhesion are discussed in light of the most recent literature results.

Hourglass transistor: An alternative and improved MOS structure robust to total ionization dose radiation

This paper presents a novel MOSFET layout named the “hourglass transistor”, aimed to improve its electrical behavior under Total Ionizing Dose (TID) effects. The new radiation-tolerant device is based on augmenting parasitic channel resistance, alteration of the electric field by the longitudinal corner effect (LCE), and reducing channel resistance within the central gate region. The radiation-robust MOS structure design was implemented in a 130 nm CMOS bulk process and its performance was analyzed through simulations using 3D physical models. The proposed hourglass transistor was compared with rectangular, diamond, dog bone and H-gate devices, showing a reduction in the post-radiation Ioff current of 8.77, 4.6, 1.85 and 13.7 times, respectively; and a pre-radiation normalized saturation current of 2.29, 1.04, 1.58 and 1.52 times greater with an increase of 4.84, 1, 2.47 and 2.03 times the gate area, respectively.

Nf-core/airrflow: An adaptive immune receptor repertoire analysis workflow employing the Immcantation framework.

Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) is a valuable experimental tool to study the immune state in health and following immune challenges such as infectious diseases, (auto)immune diseases, and cancer. Several tools have been developed to reconstruct B cell and T cell receptor sequences from AIRR-seq data and infer B and T cell clonal relationships. However, currently available tools offer limited parallelization across samples, scalability or portability to high-performance computing infrastructures. To address this need, we developed nf-core/airrflow, an end-to-end bulk and single-cell AIRR-seq processing workflow which integrates the Immcantation Framework following BCR and TCR sequencing data analysis best practices. The Immcantation Framework is a comprehensive toolset, which allows the processing of bulk and single-cell AIRR-seq data from raw read processing to clonal inference. nf-core/airrflow is written in Nextflow and is part of the nf-core project, which collects community contributed and curated Nextflow workflows for a wide variety of analysis tasks. We assessed the performance of nf-core/airrflow on simulated sequencing data with sequencing errors and show example results with real datasets. To demonstrate the applicability of nf-core/airrflow to the high-throughput processing of large AIRR-seq datasets, we validated and extended previously reported findings of convergent antibody responses to SARS-CoV-2 by analyzing 97 COVID-19 infected individuals and 99 healthy controls, including a mixture of bulk and single-cell sequencing datasets. Using this dataset, we extended the convergence findings to 20 additional subjects, highlighting the applicability of nf-core/airrflow to validate findings in small in-house cohorts with reanalysis of large publicly available AIRR datasets.

Multiphoton-initiated laser writing of semiconductors using nanosecond mid-infrared pulses

The advent of more powerful mid-infrared nanosecond laser sources allows using them as attractive tools in material laser processing. For semiconductor bulk processing, laser intensities must remain modest to avoid detrimental nonlinear propagation and pre-focal plasma screening effects. Accordingly, nanosecond pulses are usually appropriate to locally initiate energy deposition by multiphoton absorption and subsequent modification, hardly achievable with ultrashort pulses. Employing a 2.8-μm 2.5-ns laser source, we explore the possibility to modify silicon and other semiconductors. With interactions initiated by three-photon absorption, we modify and determine the surface and bulk modification thresholds of Si, GaAs, and InP. For Si, compared to previous studies at telecom wavelengths, we report on a reduction of the energy threshold for volume modification with processing depth, and repeatable rear-surface modifications. Compared to Si, we find for GaAs and InP important fluctuations in the modification responses, which we attribute to an absorption mechanism initially triggered by a greater presence of defects. We also study germanium, as this narrower bandgap semiconductor very interesting for mid-infrared electro-optical applications is transparent at the newly introduced wavelength. Despite the ability to modify the surface, the bulk of Ge remains inaccessible in this two-photon regime, mainly attributed to beam aberrations and nonlinearities. Nonetheless, we demonstrate the ability to process Si chips integrating Ge layers. All these results showcase the potential of mid-infrared wavelengths to offer new degrees of flexibility for 3D laser processing technologies turned to silicon photonics and microelectronics packaging.

Surfactant Partitioning Dynamics in Freshly Generated Aerosol Droplets.

Aerosol droplets are unique microcompartments with relevance to areas as diverse as materials and chemical synthesis, atmospheric chemistry, and cloud formation. Observations of highly accelerated and unusual chemistry taking place in such droplets have challenged our understanding of chemical kinetics in these microscopic systems. Due to their large surface-area-to-volume ratios, interfacial processes can play a dominant role in governing chemical reactivity and other processes in droplets. Quantitative knowledge about droplet surface properties is required to explain reaction mechanisms and product yields. However, our understanding of the compositions and properties of these dynamic, microscopic interfaces is poor compared to our understanding of bulk processes. Here, we measure the dynamic surface tensions of 14-25 μm radius (11-65 pL) droplets containing a strong surfactant (either sodium dodecyl sulfate or octyl-β-D-thioglucopyranoside) using a stroboscopic imaging approach, enabling observation of the dynamics of surfactant partitioning to the droplet-air interface on time scales of 10s to 100s of microseconds after droplet generation. The experimental results are interpreted with a state-of-the-art kinetic model accounting for the unique high surface-area-to-volume ratio inherent to aerosol droplets, providing insights into both the surfactant diffusion and adsorption kinetics as well as the time-dependence of the interfacial surfactant concentration. This study demonstrates that microscopic droplet interfaces can take up to many milliseconds to reach equilibrium. Such time scales should be considered when attempting to explain observations of accelerated chemistry in microcompartments.

AnVILWorkflow: A runnable workflow package for Cloud-implemented bioinformatics analysis pipelines.

Advancements in sequencing technologies and the development of new data collection methods produce large volumes of biological data. The Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL) provides a cloud-based platform for democratizing access to large-scale genomics data and analysis tools. However, utilizing the full capabilities of AnVIL can be challenging for researchers without extensive bioinformatics expertise, especially for executing complex workflows. Here we present the AnVILWorkflow R package, which enables the convenient execution of bioinformatics workflows hosted on AnVIL directly from an R environment. AnVILWorkflowsimplifies the setup of the cloud computing environment, input data formatting, workflow submission, and retrieval of results through intuitive functions. We demonstrate the utility of AnVILWorkflowfor three use cases: bulk RNA-seq analysis with Salmon, metagenomics analysis with bioBakery, and digital pathology image processing with PathML. The key features of AnVILWorkflow include user-friendly browsing of available data and workflows, seamless integration of R and non-R tools within a reproducible analysis pipeline, and accessibility to scalable computing resources without direct management overhead. While some limitations exist around workflow customization, AnVILWorkflowlowers the barrier to taking advantage of AnVIL's resources, especially for exploratory analyses or bulk processing with established workflows. This empowers a broader community of researchers to leverage the latest genomics tools and datasets using familiar R syntax. This package is distributed through the Bioconductor project (https://bioconductor.org/packages/AnVILWorkflow), and the source code is available through GitHub (https://github.com/shbrief/AnVILWorkflow).

Magnetic resonance insights into the heterogeneous, fractal-like kinetics of chemically recyclable polymers.

Moving toward a circular plastics economy is a vital aspect of global resource management. Chemical recycling of plastics ensures that high-value monomers can be recovered from depolymerized plastic waste, thus enabling circular manufacturing. However, to increase chemical recycling throughput in materials recovery facilities, the present understanding of polymer transport, diffusion, swelling, and heterogeneous deconstruction kinetics must be systematized to allow industrial-scale process design, spanning molecular to macroscopic regimes. To develop a framework for designing depolymerization processes, we examined acidolysis of circular polydiketoenamine elastomers. We used magnetic resonance to monitor spatially resolved observables in situ and then evaluated these data with a fractal method that treats nonlinear depolymerization kinetics. This approach delineated the roles played by network architecture and reaction medium on depolymerization outcomes, yielding parameters that facilitate comparisons between bulk processes. These streamlined methods to investigate polymer hydrolysis kinetics portend a general strategy for implementing chemical recycling on an industrial scale.

Dynamics of bulk and surface oxide evolution in copper foams for electrochemical CO2 reduction

Oxide-derived copper (OD-Cu) materials exhibit extraordinary catalytic activities in the electrochemical carbon dioxide reduction reaction (CO2RR), which likely relates to non-metallic material constituents formed in transitions between the oxidized and the reduced material. In time-resolved operando experiment, we track the structural dynamics of copper oxide reduction and its re-formation separately in the bulk of the catalyst material and at its surface using X-ray absorption spectroscopy and surface-enhanced Raman spectroscopy. Surface-species transformations progress within seconds whereas the subsurface (bulk) processes unfold within minutes. Evidence is presented that electroreduction of OD-Cu foams results in kinetic trapping of subsurface (bulk) oxide species, especially for cycling between strongly oxidizing and reducing potentials. Specific reduction-oxidation protocols may optimize formation of bulk-oxide species and thereby catalytic properties. Together with the Raman-detected surface-adsorbed *OH and C-containing species, the oxide species could collectively facilitate *CO adsorption, resulting an enhanced selectivity towards valuable C2+ products during CO2RR.

An 8-way series-parallel combiner based power amplifier for mm-wave 5G communication in 40-nm CMOS

This paper presents a power amplifier (PA) with an 8-way series–parallel power combiner for 5G communication. By theoretical analysis of the S-parameters matrix and the equivalence of the impedance network, the design of the multi-port combiner is transformed into a dual-port on-chip transformer, and the bandwidth expansion is achieved without increasing the in-band gain ripple based on the mismatch-consistent magnetically coupled resonator (MCR) technique. As a validation of the methodology, the 8-way series–parallel power combiner PA is implemented in 40-nm CMOS Bulk process. The large-signal performances of the PA at 31 GHz are 21.36 dBm, 17.1 dBm, and 25.7 % for Psat, OP1dB, and PAEmax, respectively. The proposed PA has a peak S21 of 25.1 dB and a 3-dB bandwidth of 23.5–46.4 GHz, which fully covers the 5G new radio (NR) frequency range2 (FR2) operating band, and the S21 ripple is less than 1-dB in the range of 26.0–42.3 GHz, which achieves a broadband flat frequency response and supports the feasibility of the design.

Norfloxacin adsorption by torrefied coco peat biochar as a novel adsorbent in a circular economy framework

The current study reported torrefied coco-peat biochar treated at 200 °C, as a novel adsorbent exhibiting phenomenal norfloxacin (NFX) adsorption efficiency. The CHNS analysis confirmed the carbon abundance in the biochar (36.45%), however, XRF analysis indicated a significant presence of K2O (27.73%) and chlorine (7.49%). The XRD and Raman spectral analysis confirmed the amorphous structure of the biochar. Multilayer topology was evident in the SEM micrograph of biochar contributing to its large effective surface area. Additionally, the mesoporous structure of the adsorbent was verified by BET. The adsorption mechanism was predicted to be non-ionic since the zeta potential of both adsorbent and adsorbate was found negative. The process parameters were optimized at 30 °C, pH 6.9, dosage 7 g/L, antibiotic load 494.25 mg/L, and time of 89 min for a maximum of 99.52% adsorption of NFX using Central Composite Design, Analysis of Variance, and Response Surface Methodology. The adsorption process was exothermic, and spontaneous obeying the pseudo-second-order kinetics, while the bulk process was confined to surface adsorption. Isotherm study of NFX adsorption revealed the process to be a favorable, monolayer, and homogeneous adsorption. The NFX molecules were desorbed with an efficiency of 89.19% using 80% ethanol and upon recrystallization, 87.76% of the initial NFX was recovered as crude crystal. Moreover, the NFX removal efficiency was consistent across various water systems, tap water (99.02%), seawater (99.56%), river water (98.92%), pond water (98.26%), and distilled water (99.17%). The techno-economic analysis identified bulk expense as the biochar preparation ($0.82/kg) and the process will be profitable having recovered NFX sold at $6/kg instead of the present retail price ($71/kg). Thus, the study successfully demonstrated a zero-waste, self-sustainable, and revenue-generating water treatment process implementing the circular economy framework.

Effect of Mixing Intensity on Electrochemical Performance of Oxide/Sulfide Composite Electrolytes

Despite the variety of solid electrolytes available, no single solid electrolyte has been found that meets all the requirements of the successor technology of lithium-ion batteries in an optimum way. However, composite hybrid electrolytes that combine the desired properties such as high ionic conductivity or stability against lithium are promising. The addition of conductive oxide fillers to sulfide solid electrolytes has been reported to increase ionic conductivity and improve stability relative to the individual electrolytes, but the influence of the mixing process to create composite electrolytes has not been investigated. Here, we investigate Li3PS4 (LPS) and Li7La3Zr2O12 (LLZO) composite electrolytes using electrochemical impedance spectroscopy and distribution of relaxation times. The distinction between sulfide bulk and grain boundary polarization processes is possible with the methods used at temperatures below 10 °C. We propose lithium transport through the space-charge layer within the sulfide electrolyte, which increases the conductivity. With increasing mixing intensities in a high-energy ball mill, we show an overlay of the enhanced lithium-ion transport with the structural change of the sulfide matrix component, which increases the ionic conductivity of LPS from 4.1 × 10−5 S cm−1 to 1.7 × 10−4 S cm−1.

Численное моделирование водородопроницаемости с концентрационной зависимостью коэффициента диффузии

The paper presents a nonlinear mathematical model of alloys hydrogen permeability for membrane technologies of high-purity hydrogen production. Diffusion processes in the material bulk are taken into account as well as physical and chemical phenomena at the surface: adsorption, desorption and relatively fast dissolution. The iterative computational algorithm and software in Scilab have been developed to model the hydrogen permeability with dynamic boundary conditions and concentration-dependent diffusion coefficient.

Cosmological constant as quantum error correction from generalized gauge invariance in double field theory

The holographic principle and its realization as the anti-de Sitter/conformal field theory (AdS/CFT) correspondence leads to the existence of the so-called precursor operators. These are boundary operators that carry nonlocal information regarding events occurring deep inside the bulk and which cannot be causally connected to the boundary. Such nonlocal operators can distinguish nonvacuum-like excitations within the bulk that cannot be observed by any local gauge invariant operators in the boundary. The boundary precursors are expected to become increasingly nonlocal the further the bulk process is from the boundary. Such phenomena are expected to be related to the extended nature of the strings. Standard gauge invariance in the boundary theory equates to quantum error correction which furthermore establishes localization of bulk information. I show that when double field theory quantum error correction prescriptions are considered in the bulk, gauge invariance in the boundary manifests residual effects associated to stringy winding modes. Also, an effect of double field theory quantum error correction is the appearance of positive cosmological constant. The emergence of space–time from the entanglement structure of a dual quantum field theory appears in this context to generalize for de Sitter space–times as well.

Defect-assisted optical breakdown in synthetic diamonds irradiated by IR femtosecond pulses

A comparative study of optical breakdown in several CVD and HPHT single crystals has been performed with IR femtosecond pulses, which are widely used for diamond bulk processing. The breakdown thresholds for the diamond surface and bulk are measured and then compared with the morphology of the laser-modified regions formed during the breakdown process. The highest level of the bulk breakdown threshold is found to be typical for the HPHT crystals, whereas for the CVD crystals breakdown threshold varies greatly. It is assumed that certain defects assembled in microbunches of various sizes may decrease considerably the diamond breakdown threshold. The nature of these defects and the mechanism of the threshold reduction are under study.

ИДЕНТИФИКАЦИЯ ПЕРЕМЕННЫХ ПАРАМЕТРОВ ДИНАМИКИ ХИМИЧЕСКОГО РЕАКТОРА ДЛЯ БЛОЧНОЙ ПОЛИМЕРИЗАЦИИ ИЗОПРЕНА

The dynamics of non-isothermal chemical batch reactor for isoprene polymerization process in bulk, i.e. the object with the distributed, and also the variable parameters, is considered. The identification procedure proposed makes it possible to describe the reactor dynamics with the help of a system of differential equations with constant coefficients in each of partial time intervals. The transfer functions for operating channel obtained are as follows: the reaction mixture temperature – the cold carrier temperature, and also the average conversion – the cold carrier temperature.

Elucidating the redox activity of cobalt-1,2,3,4-cyclopentane-tetracarboxylic acid and 1,2,4,5-benzene-tetracarboxylic acid-based metal-organic frameworks for a hybrid supercapacitor.

The development of electrode materials with extraordinary energy densities or high power densities has experienced a spectacular upsurge because of significant advances in energy storage technology. In recent years, the family of metal-organic frameworks (MOFs) has become an essential contender for electrode materials. Herein, two cobalt-based MOFs are synthesized with distinct linkers named 1,2,4,5-benzene-tetra-carboxylic acid (BTCA) and 1,2,3,4-cyclopentane-tetracarboxylic acid (CPTC). Investigations have been rigorously conducted to fully understand the effect of linkers on the electrochemical properties of Co-based MOFs. The best sample among the MOFs was used with activated carbon to create a battery-supercapacitor hybrid device. Due to its noteworthy results, specific capacity (100.3 C g-1), energy density (23 W h kg-1), power density (3400 W kg-1) and with the lowest ESR value of 0.4 Ω as well as its 95.4% capacity retention, the fabricated hybrid device was discovered to be very appealing for applications demanding energy storage. An approach for evaluating battery-supercapacitors was employed by quantifying the capacitive and diffusive contributions using Dunn's model to reflect the bulk and surface processes occurring during charge storage. This study fills the gap between supercapacitors and batteries, as well as providing a roadmap for creating a new generation of energy storage technologies with improved features.

Radiation-Hardened Flip-Flops in a 65 nm Bulk Process for Terrestrial Applications Coping With Radiation Hardness and Performance Overheads

Radiation-Hardened Flip-Flops in a 65 nm Bulk Process for Terrestrial Applications Coping With Radiation Hardness and Performance Overheads