bluuebunny/crossref_metadata_2025 huggingface dataset:
Reconfigurable spatially-periodic umbilical defects in nematic liquid crystals enabled by self-organization
Authors: Sasaki Yuji , Araoka Fumito , Orihara Hiroshi
Published: August 2023

Spontaneous formation of ordered structures is observed in many physical systems. Soft materials such as colloids, polymers, and liquid crystals (LCs) are stimuli-responsive and often form various functional self-organized structures that are interesting not only fundamentally but also regarding applications. Nematic LCs (NLCs) consisting of elongated molecules are characterized by anisotropic molecular orientations that are strongly affected by external fields. In particular, the combination of an applied electric field and surface boundary conditions is commonly used for controlling stable configurations and plays a fundamental role in LC devices. Currently, the standard approach to fabricating complex molecular orientations is to use tailored surfaces that mostly rely on top-down lithographic techniques, with relatively few examples of bottom-up systems that produce patterned structures. Moreover, previously known systems such as electroconvection are quite dynamic and not sufficiently controllable, even though they exhibit a variety of patterns. Therefore, exploring the physical mechanism for the formation of a spontaneous pattern could be important in exploiting the further functional properties of NLCs. Here, we briefly review a unique type of self-organization in NLCs induced by an electric field, where the crucial effects of the polymer layer between the NLC and the electrodes lead to the formation of a two-dimensional periodic structure in the sample cell instead of the standard reorientation process. As well as experimental demonstration of the phenomenon, a descriptive theoretical framework is discussed, as are perspectives for optical applications.
Existence of nodal-arc and its evolution into Weyl-nodes in the presence of spin-orbit coupling in TaAs & TaP
Authors: Pandey Vivek , Pandey Sudhir K
Published: August 2023

In this work, we report the existence of nodal-arc, which acts as the building block of all the nodal-rings in TaAs & TaP. This nodal-arc is found to be capable of generating all the nodal-rings in these materials upon the application of space-group symmetry operations including time-reversal symmetry. The arcs are obtained to be dispersive with the energy spread of ∼109 (∼204) meV in TaAs (TaP). Also, the orbitals leading to bands-inversion and thus the formation of nodal-arcs are found to be Ta-5d & As-4p (P-3p) in TaAs (TaP). The area of nodal-rings is found to be highly sensitive to the change in hybridization-strength, where the increase in hybridization-strength leads to the decrease in the area of nodal-rings. In the presence of spin–orbit coupling (SOC), all the points on these arcs get gaped-up and two pairs of Weyl-nodes are found to evolve from them. Out of the two pair, one is found to be situated close to the joining point of the two arcs forming a ring. This causes the evolution of each nodal-ring into three pairs of Weyl-nodes. The coordinates of these Weyl-nodes are found to be robust to the increase in SOC-strength from ∼0.7–3.5 eV. All the results are obtained at the first-principle level. This work provides a clear picture of the existence of nodal-arc due to accidental degeneracy and its evolution into Weyl-nodes under the effect of SOC.
Unsteady Ohmic dissipative flow of ZnO-SAE50 nanofluid past a permeable shrinking cylinder
Authors: Haider Ghulam , Ahmed Naveed
Published: August 2023

The laminar boundary layer flow of a Zinc Oxide-Society of Automotive Engineers 50 alias nano-lubricant (

ZnO
−
SAE
50

) past a permeable shrinking cylinder is investigated. The flow is unsteady, incompressible, and Ohmic dissipative. The present study holds immense significance in different engineering as well as scientific domains. It combines research on nanoparticle effects, unsteady flows, and solid surface interactions. The study claimed that the use of

ZnO
−
SAE
50

nanofluid in the unsteady flow past a permeable shrinking cylinder led to significant heat transfer enhancement. The acquired results from the study would be fruitful in the fields of thermal engineering and heat transfer. The findings of the study can aid in optimizing cooling systems, heat exchangers, and energy-efficient designs. A governing model has been achieved for the flow and heat transfer by using conservation laws related to mass, momentum, and energy. Governing system of partial differential equations is solved to a nonlinear system of ordinary differential equations by using similarity transformation, which is later on solved with the help of the Shooting method and RK-Fehlberg duos. Plots are shown for both velocity and temperature profiles, to display the impacts of involved dimensionless parameters. Additionally, graphs for Nusselt Number have also been represented which shows the local rate of heat transfer. It is examined that the Ohmic dissipation as well as the volumetric ratio of the nanoparticles greatly influence the overall thermal performance of the system.
A machine learning-based approach for RF transfer function modeling of active implantable medical electrodes at 3T MRI
Authors: Yao Aiping , Ma Mingjuan , Shi Hexuan
Published: August 2023

Objective. The objective of this work is to propose a machine learning-based approach to rapidly and efficiently model the radiofrequency (RF) transfer function of active implantable medical (AIM) electrodes, and to overcome the limitations and drawbacks of traditional measurement methods when applied to heterogeneous tissue environments. Approach. AIM electrodes with different geometries and proximate tissue distributions were considered, and their RF transfer functions were modeled numerically. Machine learning algorithms were developed and trained with the simulated transfer function datasets for homogeneous and heterogeneous tissue distributions. The performance of the method was analyzed statistically and validated experimentally and numerically. A comprehensive uncertainty analysis was performed and uncertainty budgets were derived. Main results. The proposed method is able to predict the RF transfer function of AIM electrodes under different tissue distributions, with mean correlation coefficients r of 0.99 and 0.98 for homogeneous and heterogeneous environments, respectively. The results were successfully validated by experimental measurements (e.g. the uncertainty of less than 0.9 dB) and numerical simulation (e.g. transfer function uncertainty <1.6 dB and power deposition uncertainty <1.9 dB). Up to 1.3 dB in vivo power deposition underestimation was observed near generic pacemakers when using a simplified homogeneous tissue model. Significance. Provide an efficient alternative of transfer function modeling, which allows a more realistic tissue distribution and the potential underestimation of in vivo RF-induced power deposition near the AIM electrode can be reduced.
A comparative study of deconvolution techniques for quantum-gas microscope images
Authors: La Rooij A , Ulm C , Haller E , Kuhr S
Published: August 2023

Quantum-gas microscopes are used to study ultracold atoms in optical lattices at the single-particle level. In these systems atoms are localised on lattice sites with separations close to or below the diffraction limit. To determine the lattice occupation with high fidelity, a deconvolution of the images is often required. We compare three different techniques, a local iterative deconvolution algorithm, Wiener deconvolution and the Lucy–Richardson algorithm, using simulated microscope images. We investigate how the reconstruction fidelity scales with varying signal-to-noise ratio, lattice filling fraction, varying fluorescence levels per atom, and imaging resolution. The results of this study identify the limits of singe-atom detection and provide quantitative fidelities which are applicable for different atomic species and quantum-gas microscope setups.
Detecting the driver nodes of temporal networks
Authors: Qin Tingting , Duan Gaopeng , Li Aming
Published: August 2023

Detecting the driver nodes of complex networks has garnered significant attention recently to control complex systems to desired behaviors, where nodes represent system components and edges encode their interactions. Driver nodes, which are directly controlled by external inputs, play a crucial role in controlling all network nodes. While many approaches have been proposed to identify driver nodes of static networks, we still lack an effective algorithm to control ubiquitous temporal networks, where network structures evolve over time. Here we propose an effective online time-accelerated heuristic algorithm (OTaHa) to detect driver nodes of temporal networks. Together with theoretical analysis and numerical simulations on synthetic and empirical temporal networks, we show that OTaHa offers multiple sets of driver nodes, and noticeably outperforms existing methods in terms of accuracy and execution time. We further report that most edges are redundant in controlling temporal networks although the complete instantaneous signal-carrying edges cannot be guaranteed. Moreover, removing edges with high edge betweenness (the number of all-pairs shortest paths passing through the edge) significantly impedes the overall controllability. Our work provides an effective algorithm and paves the way for subsequent explorations on achieving the ultimate control of temporal networks.
Learning to concentrate: multi-tracer forecasts on local primordial non-Gaussianity with machine-learned bias
Authors: Sullivan James M. , Prijon Tijan , Seljak Uroš
Published: August 2023

Local primordial non-Gaussianity (LPNG) is predicted by many non-minimal models of inflation, and creates a scale-dependent contribution to the power spectrum of large-scale structure (LSS) tracers, whose amplitude is characterized by bϕ
.
Knowledge of bϕ
for the observed tracer population is therefore crucial for learning about inflation from LSS.
Recently, it has been shown that the relationship between linear bias b1
and bϕ
for simulated halos exhibits significant secondary dependence on halo concentration.
We leverage this fact to forecast multi-tracer constraints on f
loc
NL.
We train a machine learning model on observable properties of simulated IllustrisTNG galaxies to predict bϕ
for samples constructed to approximate DESI emission line galaxies (ELGs) and luminous red galaxies (LRGs). We find σ(f
loc
NL) = 2.3, and σ(f
loc
NL = 3.7, respectively.
These forecasted errors are roughly factors of 3, and 35% improvements over the single-tracer case for each sample, respectively.
When considering both ELGs and LRGs in their overlap region, we forecast σ(f
loc
NL) = 1.5 is attainable with our learned model, more than a factor of 3 improvement over the
single-tracer case,
while the ideal split by bϕ
could reach σ(f
loc
NL) < 1.
We also perform multi-tracer forecasts for upcoming spectroscopic surveys targeting LPNG (MegaMapper, SPHEREx) and show that splitting tracer samples by bϕ
can lead to an order-of-magnitude reduction in projected σ(f
loc
NL for these surveys.
Towards detecting super-GeV dark matter via annihilation to neutrinos
Authors: Salvador Miranda L. , Basegmez du Pree S. , Ng K.C.Y. , Cheek A. , Arina C.
Published: August 2023

The next generation of neutrino telescopes will feature unprecedented sensitivities in the detection of neutrinos. Here we study the capabilities of a large-scale neutrino telescope, like the fully-operating KM3NeT experiment in the near future, for detecting dark matter annihilation signals from the Galactic Centre.
We consider both ORCA and ARCA detectors, covering dark matter masses from a few GeV to 100 TeV. We obtain the sensitivities with a maximum-likelihood analysis method and present them as upper limits in the thermally averaged annihilation cross-section into Standard Model fermions. Our projections show that the sensitivity of such a neutrino telescope can reach the thermal relic line for mχ
≳ 1 TeV and for mχ
≃ few GeV, for the NFW dark matter density profile. This demonstrates that ORCA- and ARCA-like detectors will be able to perform competitive dark matter searches in a wide range of masses. The implications of these striking projections are investigated in a few selected dark matter particle models, where we show that neutrino telescopes are able to probe new parameter space.
Different elements, same results: time-resolved temperature determination by oxygen and nitrogen elements
Authors: Arjmand S. , Anania M.P. , Biagioni A. , Ferrario M. , Galletti M. , Lollo V. , Pellegrini D. , Pompili R. , Zigler A.
Published: August 2023

The core purpose of this research is to use optical emission spectroscopy to determine the electron temperature (Te
) of a hydrogen plasma generated in a capillary discharge plasma, with a focus on its temporal variation. The plasma density (ne
) is first determined using the Stark broadening technique, which measures the broadening of spectral lines as a result of the electric field in the plasma. Subsequently, a passive spectroscopic technique is employed to estimate the electron plasma temperature by detecting the emitted light from the plasma. This spectral detection is performed using a visible range spectrometer. In this study, two elements, oxygen and nitrogen, are specifically selected based on the chemical composition of the capillary. The electron plasma temperature is estimated using the line ratio method, which involves comparing the intensities of two specific spectral lines emitted by the selected elements. By analyzing these line ratios, the electron plasma temperature can be inferred. The combination of the Stark broadening technique and line ratio method provides valuable insights into the plasma's physical characteristics, specifically its density and temperature.
Experimental studies on the effect of nano silica modified novel concrete CFST columns
Authors: Vasanthi P , Selvan S Senthil , Natrayan L , Thanappan Subash
Published: August 2023

Under axial compression, the present article analyses and compares the behaviour of Plain Concrete filled and Nano Silica modified concrete filled with light gauge steel rectangular columns. In 18 work samples, plain and nano silica-modified concrete was tested on light gauge steel sections. Investigations were conducted into several essential variables, including the geometry of the cross-section, the tubular thickness of light gauge steel, the depth-to-thickness ratio, and the type of concrete infill used. From the experimental results, effects of flat width-to-thickness ratio (w/t), axial load-end shortening, axial load-deflection, axial load-strain characteristics, and failure modes have been studied under the linear stage. To evaluate their confinement effects, this study compared plain and silica-modified nano concrete tube columns with light gauge steel hollow hollow hollow columns. The experimental results are compared using BS5400, EC4, and ACI codes to determine the ultimate sectional capacity. Test outcomes showed that tested nano-silica modified concrete filled steel tubular (CFST) columns exhibited higher strength and outstanding ductility than the plain CFST and hollow light gauge steel columns. The nano silica-modified concrete in-filled columns showed a good yield plateau under the non-linear stage compared with the other columns.
Transfer learning application of self-supervised learning in ARPES
Authors: Ekahana Sandy Adhitia , Winata Genta Indra , Soh Y , Tamai Anna , Milan Radovic , Aeppli Gabriel , Shi Ming
Published: August 2023

There is a growing recognition that electronic band structure is a local property of materials and devices, and there is steep growth in capabilities to collect the relevant data. New photon sources, from small-laboratory-based lasers to free electron lasers, together with focusing beam optics and advanced electron spectrometers, are beginning to enable angle-resolved photoemission spectroscopy (ARPES) in scanning mode with a spatial resolution of near to and below microns, two- to three orders of magnitude smaller than what has been typical for ARPES hitherto. The results are vast data sets inhabiting a five-dimensional subspace of the ten-dimensional space spanned by two scanning dimensions of real space, three of reciprocal space, three of spin-space, time, and energy. In this work, we demonstrate that recent developments in representational learning (self-supervised learning) combined with k-means clustering can help automate the labeling and spatial mapping of dispersion cuts, thus saving precious time relative to manual analysis, albeit with low performance. Finally, we introduce a few-shot learning (k-nearest neighbor) in representational space where we selectively choose one (k = 1) image reference for each known label and subsequently label the rest of the data with respect to the nearest reference image. This last approach demonstrates the strength of self-supervised learning to automate image analysis in ARPES in particular and can be generalized to any scientific image analysis.
Automated visual inspection of CMS HGCAL silicon sensor surface using an ensemble of a deep convolutional autoencoder and classifier
Authors: Grönroos Sonja , Pierini Maurizio , Chernyavskaya Nadezda
Published: August 2023

More than a thousand 8″ silicon sensors will be visually inspected to look for anomalies on their surface during the quality control preceding assembly into the High-Granularity Calorimeter for the CMS experiment at CERN. A deep learning-based algorithm that pre-selects potentially anomalous images of the sensor surface in real time was developed to automate the visual inspection. The anomaly detection is done by an ensemble of independent deep convolutional neural networks: an autoencoder and a classifier. The algorithm was deployed and has been continuously running in production, and data gathered were used to evaluate its performance. The pre-selection reduces the number of images requiring human inspection by 85%, with recall of 97%, and saves 15 person-hours per a batch of a hundred sensors. Data gathered in production can be used for continuous learning to improve the accuracy incrementally.
The emergence of a new wintertime Arctic energy balance regime
Authors: Miyawaki O , Shaw T A , Jansen M F
Published: August 2023

The modern Arctic climate during wintertime is characterized by sea-ice cover, a strong surface temperature inversion, and the absence of convection. Correspondingly, the energy balance in the Arctic atmosphere today is dominated by atmospheric radiative cooling and advective heating, so-called radiative advective equilibrium. Climate change in the Arctic involves sea-ice melt, vanishing of the surface inversion, and emergence of convective precipitation. Here we show climate change in the Arctic involves the emergence of a new energy balance regime characterized by radiative cooling, convective heating, and advective heating, so-called radiative convective advective equilibrium. A time-dependent decomposition of the atmospheric energy balance shows the regime transition is associated with enhanced radiative cooling followed by decreased advective heating. The radiative cooling response consists of a robust clear-sky greenhouse effect and a transient cloud contribution that varies across models. Mechanism-denial experiments in an aquaplanet with and without interactive sea ice highlight the important role of sea-ice melt in both the radiative cooling and advective heating responses. The results show that climate change in the Arctic involves temporally evolving mechanisms, suggesting that an emergent constraint based on historical data or trends may not constrain the long-term response.
The role of the performer in Hanslick’s On the Musically Beautiful
Authors: Sousa Tiago
Published: August 2023

In his On the Musically Beautiful, Hanslick vigorously argued that musical beauty depends neither on the representation nor on the evocation of feelings. However, despite his formalism, Hanslick regards the performance of a musical work as a moment of emotional release. Given the tension between the formalist nature of Hanslick’s general theory and this expressionist drift in his conception of the performer, in this article I pursue two objectives: 1) to argue that there is, in fact, an important internal inconsistency in Hanslick’s theory regarding the nature of performance, and 2) to deepen and render intelligible this perspective of performance. Although internally inconsistent, this perspective, in its search for a synergistic conciliation of the composer’s creativity with the performer’s expressivity, is worthy of analysis.
Evidence of Hematoma Prevention After Facelift
Authors: Stewart Christopher M , Bassiri-Tehrani Brian , Jones Hannah Elizabeth , Nahai Foad
Published: August 2023

Hematoma is a common complication after facelift procedures. Multiple factors have been shown to increase the risk of hematoma formation, such as male gender, anticoagulant medication use, perioperative hypertension, increased intrathoracic pressure, and operative technique. The purpose of this manuscript is to provide an overview of existing literature to provide surgeons with evidence-based recommendations on how to minimize hematoma risk during facelift surgery. A literature search for hematoma and facelift surgery was performed that identified 478 unique manuscripts. Abstracts were reviewed, excluding articles not describing facelift surgery, those written before 1970, studies with a sample size of fewer than 5 patients, non-English studies, and those that did not provide postoperative hematoma rates. Forty-five articles were included in this text, with their recommendations. Measures such as the prophylactic management of pain, nausea, and hypertension, the use of fibrin glue tissue sealants, the use of local anesthesia rather than general anesthesia, and strict blood pressure control of at least <140 mmHg were found to significantly reduce hematoma formation. Quilting sutures has shown benefit in some high-risk patients. Measures such as drains, compression dressings, perioperative use of selective serotonin reuptake inhibitors, and perioperative steroids had no significant effect on hematoma formation. In addition to appropriate patient selection and careful intraoperative hemostasis, many adjunct measures have been shown to reduce postoperative hematoma formation in facelift procedures.

Level of Evidence: 3
Ultrahigh-throughput screening of Trichoderma reesei strains capable of carbon catabolite repression release and cellulase hyperproduction using a microfluidic droplet platform
Authors: Luu Xuan Chinh , Shida Yosuke , Suzuki Yoshiyuki , Kuwahara Daiki , Fujimoto Takeshi , Takahashi Yuka , Sato Naomi , Nakamura Akihiro , Ogasawara Wataru
Published: August 2023

Trichoderma reesei is the most well-known cellulase producer in the biorefinery industry. Its cellulase biosynthesis is repressed by glucose via carbon catabolite repression (CCR), making CCR-releasing strains with cellulase hyperproduction desirable. Here, we employed a microfluidic droplet platform to culture and screen T. reesei mutants capable of CCR release and cellulase overproduction from extensive mutagenesis libraries. With 3 mutagenesis rounds, about 6.20 × 103 droplets were sorted from a population of 1.51 × 106 droplets in a period of 4.4 h; 76 recovery mutants were screened on flask fermentation, and 2 glucose uptake retarded mutants, MG-9-3 and MG-9-3-30, were eventually isolated. We also generated a hypercellulase producer, M-5, with CCR release via a single mutagenesis round. The hyphal morphology and molecular mechanisms in the mutants were analyzed. This versatile approach combined with a comprehensive understanding of CCR release mechanisms will provide innovative and effective strategies for low-cost cellulase production.
Cobind: quantitative analysis of the genomic overlaps
Authors: Ma Tao , Guo Lingyun , Yan Huihuang , Wang Liguo
Published: August 2023

Motivation

Analyzing the overlap between two sets of genomic intervals is a frequent task in the field of bioinformatics. Typically, this is accomplished by counting the number (or proportion) of overlapped regions, which applies an arbitrary threshold to determine if two genomic intervals are overlapped. By making binary calls but disregarding the magnitude of the overlap, such an approach often leads to biased, non-reproducible, and incomparable results.

Results

We developed the cobind package, which incorporates six statistical measures: the Jaccard coefficient, Sørensen–Dice coefficient, Szymkiewicz–Simpson coefficient, collocation coefficient, pointwise mutual information (PMI), and normalized PMI. These measures allow for a quantitative assessment of the collocation strength between two sets of genomic intervals. To demonstrate the effectiveness of these methods, we applied them to analyze CTCF’s binding sites identified from ChIP-seq, cancer-specific open-chromatin regions (OCRs) identified from ATAC-seq of 17 cancer types, and oligodendrocytes-specific OCRs identified from scATAC-seq. Our results indicated that these new approaches effectively re-discover CTCF’s cofactors, as well as cancer-specific and oligodendrocytes-specific master regulators implicated in disease and cell type development.

Availability and implementation

The cobind package is implemented in Python and freely available at https://cobind.readthedocs.io/en/latest/.
Ionmob: a Python package for prediction of peptide collisional cross-section values
Authors: Teschner David , Gomez-Zepeda David , Declercq Arthur , Łącki Mateusz K , Avci Seymen , Bob Konstantin , Distler Ute , Michna Thomas , Martens Lennart , Tenzer Stefan , Hildebrandt Andreas
Published: August 2023

Motivation

Including ion mobility separation (IMS) into mass spectrometry proteomics experiments is useful to improve coverage and throughput. Many IMS devices enable linking experimentally derived mobility of an ion to its collisional cross-section (CCS), a highly reproducible physicochemical property dependent on the ion’s mass, charge and conformation in the gas phase. Thus, known peptide ion mobilities can be used to tailor acquisition methods or to refine database search results. The large space of potential peptide sequences, driven also by posttranslational modifications of amino acids, motivates an in silico predictor for peptide CCS. Recent studies explored the general performance of varying machine-learning techniques, however, the workflow engineering part was of secondary importance. For the sake of applicability, such a tool should be generic, data driven, and offer the possibility to be easily adapted to individual workflows for experimental design and data processing.

Results

We created ionmob, a Python-based framework for data preparation, training, and prediction of collisional cross-section values of peptides. It is easily customizable and includes a set of pretrained, ready-to-use models and preprocessing routines for training and inference. Using a set of ≈21 000 unique phosphorylated peptides and ≈17 000 MHC ligand sequences and charge state pairs, we expand upon the space of peptides that can be integrated into CCS prediction. Lastly, we investigate the applicability of in silico predicted CCS to increase confidence in identified peptides by applying methods of re-scoring and demonstrate that predicted CCS values complement existing predictors for that task.

Availability and implementation

The Python package is available at github: https://github.com/theGreatHerrLebert/ionmob.
SHEPHARD: a modular and extensible software architecture for analyzing and annotating large protein datasets
Authors: Ginell Garrett M , Flynn Aidan J , Holehouse Alex S
Published: August 2023

Motivation

The emergence of high-throughput experiments and high-resolution computational predictions has led to an explosion in the quality and volume of protein sequence annotations at proteomic scales. Unfortunately, sanity checking, integrating, and analyzing complex sequence annotations remains logistically challenging and introduces a major barrier to entry for even superficial integrative bioinformatics.

Results

To address this technical burden, we have developed SHEPHARD, a Python framework that trivializes large-scale integrative protein bioinformatics. SHEPHARD combines an object-oriented hierarchical data structure with database-like features, enabling programmatic annotation, integration, and analysis of complex datatypes. Importantly SHEPHARD is easy to use and enables a Pythonic interrogation of largescale protein datasets with millions of unique annotations. We use SHEPHARD to examine three orthogonal proteome-wide questions relating protein sequence to molecular function, illustrating its ability to uncover novel biology.

Availability and implementation

We provided SHEPHARD as both a stand-alone software package (https://github.com/holehouse-lab/shephard), and as a Google Colab notebook with a collection of precomputed proteome-wide annotations (https://github.com/holehouse-lab/shephard-colab).
Flame (v2.0): advanced integration and interpretation of functional enrichment results from multiple sources
Authors: Karatzas Evangelos , Baltoumas Fotis A , Aplakidou Eleni , Kontou Panagiota I , Stathopoulos Panos , Stefanis Leonidas , Bagos Pantelis G , Pavlopoulos Georgios A
Published: August 2023

Summary: Functional enrichment is the process of identifying implicated functional terms from a given input list of genes or proteins. In this article, we present Flame (v2.0), a web tool which offers a combinatorial approach through merging and visualizing results from widely used functional enrichment applications while also allowing various flexible input options. In this version, Flame utilizes the aGOtool, g: Profiler, WebGestalt, and Enrichr pipelines and presents their outputs separately or in combination following a visual analytics approach. For intuitive representations and easier interpretation, it uses interactive plots such as parameterizable networks, heatmaps, barcharts, and scatter plots. Users can also: (i) handle multiple protein/gene lists and analyse union and intersection sets simultaneously through interactive UpSet plots, (ii) automatically extract genes and proteins from free text through text-mining and Named Entity Recognition (NER) techniques, (iii) upload single nucleotide polymorphisms (SNPs) and extract their relative genes, or (iv) analyse multiple lists of differentially expressed proteins/genes after selecting them interactively from a parameterizable volcano plot. Compared to the previous version of 197 supported organisms, Flame (v2.0) currently allows enrichment for 14 436 organisms.

Availability and implementation

Web Application: http://flame.pavlopouloslab.info. Code: https://github.com/PavlopoulosLab/Flame. Docker: https://hub.docker.com/r/pavlopouloslab/flame.
In search of lost time: tracing the fossil diversity of Podocarpaceae through the ages
Authors: Andruchow-Colombo Ana , Escapa Ignacio H , Aagesen Lone , Matsunaga Kelly K S
Published: August 2023

The Podocarpaceae are a morphologically diverse conifer family that have a cryptic fossil record reported since the Permian. We reviewed the fossil record of Podocarpaceae, tested the affinities of its oldest records using phylogenetic analyses, compiled macrofossil occurrence records, and investigated the diversity, distribution, and morphology of Podocarpaceae through time. We found that Permian, Triassic, and some Jurassic fossils referred to Podocarpaceae should not be placed in the family. Our total-evidence phylogenetic analyses, which sampled all major conifer lineages, recovered the Triassic Rissikia and the Jurassic Nothodacrium as stem-group conifers and the Jurassic Mataia as part of the Araucariales stem group. We further discuss the phylogenetic position of the Mesozoic enigmatic conifers Pararaucaria (Cheirolepidiaceae) and Telemachus (Voltziales), which were recovered most frequently in the conifer stem group. We conclude that the earliest reliable Podocarpaceae occurrences are from the Jurassic of both hemispheres and have scale-like leaves. Most extant genera appear in the fossil record between the Late Cretaceous and the Early Cenozoic. Many extant leaf morphologies appear in the Early Cretaceous, coeval with angiosperm diversification, consistent with the hypothesis that expanded leaves in Podocarpaceae are adaptive responses for light harvesting in angiosperm-dominated environments today.
“Rest as resistance:” Black cyberfeminism, collective healing and liberation on @TheNapMinistry
Authors: Monier Mel
Published: August 2023

Tricia Hersey, founder of The Nap Ministry, uses rest as a “healing mechanism” and a form of resistance. With a vibrant social media following, the Nap Ministry builds upon a strong history of Black feminist activism that centers the lived experiences of Black women. According to Hersey, rest is personal and political, a fight against the commodification and exploitation of laboring Black folks from chattel slavery to contemporary grind and hustle culture. This article explores how Hersey builds upon a lineage of Black women’s activism in digital spaces while also exploring rest, “soul care,” and communal healing as ideologies rooted in Black (cyber)feminism. I argue that Nap Ministry constellates Womanism, Black (cyber)feminism, and Black liberation theory by promoting the power of rest, encouraging resistance against what bell hooks describes as the “imperialist white supremacist capitalist patriarchy” that exploits Black women’s labor and renders their voices invisible.
Long-Read Sequencing with Hierarchical Clustering for Antiretroviral Resistance Profiling of Mixed Human Immunodeficiency Virus Quasispecies
Authors: Ng Timothy Ting-Leung , Su Junhao , Lao Hiu-Yin , Lui Wui-Wang , Chan Chloe Toi-Mei , Leung Amy Wing-Sze , Jim Stephanie Hoi-Ching , Lee Lam-Kwong , Shehzad Sheeba , Tam Kingsley King-Gee , Leung Kenneth Siu-Sing , Tang Forrest , Yam Wing-Cheong , Luo Ruibang , Siu Gilman Kit-Hang
Published: August 2023

Background

HIV infections often develop drug resistance mutations (DRMs), which can increase the risk of virological failure. However, it has been difficult to determine if minor mutations occur in the same genome or in different virions using Sanger sequencing and short-read sequencing methods. Oxford Nanopore Technologies (ONT) sequencing may improve antiretroviral resistance profiling by allowing for long-read clustering.

Methods

A new ONT sequencing-based method for profiling DRMs in HIV quasispecies was developed and validated. The method used hierarchical clustering of long amplicons that cover regions associated with different types of antiretroviral drugs. A gradient series of an HIV plasmid and 2 plasma samples was prepared to validate the clustering performance. The ONT results were compared to those obtained with Sanger sequencing and Illumina sequencing in 77 HIV-positive plasma samples to evaluate the diagnostic performance.

Results

In the validation study, the abundance of detected quasispecies was concordant with the predicted result with the R2 of > 0.99. During the diagnostic evaluation, 59/77 samples were successfully sequenced for DRMs. Among 18 failed samples, 17 were below the limit of detection of 303.9 copies/μL. Based on the receiver operating characteristic analysis, the ONT workflow achieved an F1 score of 0.96 with a cutoff of 0.4 variant allele frequency. Four cases were found to have quasispecies with DRMs, in which 2 harbored quasispecies with more than one class of DRMs. Treatment modifications were recommended for these cases.

Conclusions

Long-read sequencing coupled with hierarchical clustering could differentiate the quasispecies resistance profiles in HIV-infected samples, providing a clearer picture for medical care.
Effect of intraoperative botulinum toxin injection on delayed gastric emptying and need for endoscopic pyloric intervention following esophagectomy: a systematic review, meta-analysis, and meta-regression analysis
Authors: Hajibandeh Shahab , Hajibandeh Shahin , McKenna Matthew , Jones William , Healy Paul , Witherspoon Jolene , Blackshaw Guy , Lewis Wyn , Foliaki Antonio , Abdelrahman Tarig
Published: August 2023

The aim of this study was to evaluate the effect of intraoperative botulinum toxin (BT) injection on delayed gastric emptying (DGE) and need for endoscopic pyloric intervention (NEPI) following esophagectomy. In compliance with Preferred Reporting Items for Systematic reviews and Meta-Analyses statement standards, a systematic review of studies reporting the outcomes of intraoperative BT injection in patients undergoing esophagectomy for esophageal cancer was conducted. Proportion meta-analysis model was constructed to quantify the risk of the outcomes and direct comparison meta-analysis model was constructed to compare the outcomes between BT injection and no BT injection or surgical pyloroplasty. Meta-regression was modeled to evaluate the effect of variations in different covariates among the individual studies on overall summary proportions. Nine studies enrolling 1070 patients were included. Pooled analyses showed that the risks of DGE and NEPI following intraoperative BT injection were 13.3% (95% confidence interval [CI]: 7.9–18.6%) and 15.2% (95% CI: 7.9–22.5%), respectively. There was no difference between BT injection and no BT injection in terms of DGE (odds ratio [OR]: 0.57, 95% CI: 0.20–1.61, P = 0.29) and NEPI (OR: 1.73, 95% CI: 0.42–7.12, P = 0.45). Moreover, BT injection was comparable to pyloroplasty in terms of DGE (OR: 0.85, 95% CI: 0.35–2.08, P = 0.73) and NEPI (OR: 8.20, 95% CI: 0.63–105.90, P = 0.11). Meta-regression suggested that male gender was negatively associated with the risk of DGE (coefficient: −0.007, P = 0.003). In conclusion, level 2 evidence suggests that intraoperative BT injection may not improve the risk of DGE and NEPI in patients undergoing esophagectomy. The risk of DGE seems to be higher in females and in early postoperative period. High quality randomized controlled trials with robust statistical power are required for definite conclusions. The results of the current study can be used for hypothesis synthesis and power analysis in future prospective trials.
Peroral endoscopic myotomy compared to laparoscopic Heller myotomy and pneumatic dilation in the treatment of achalasia: a systematic review
Authors: North Adam , Tewari Nilanjana
Published: August 2023

Peroral endoscopic myotomy (POEM) is an intervention for the treatment of achalasia which has gained popularity over the last decade. It’s efficacy and invasiveness are comparable to laparoscopic Heller myotomy (LHM). The purpose of this systematic review is to compare POEM to existing therapies. The systematic review was performed following the preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines. MEDLINE, EMBASE, Web of Science and Cochrane Libraries were searched using keywords: esophageal achalasia, POEM, LHM, pneumatic dilation (PD), and related terms. The studied outcomes were Eckardt score, clinical success, hospital stay, cost-utility analysis, complications, and post-treatment gastro-esophageal reflux disease. Articles were reviewed by one researcher and uncertainty was resolved by a second researcher. The search strategy retrieved 1948 citations. After removing duplicates and applying the exclusion criteria, 91 studies were selected for full-text review of which a total of 31 studies were considered eligible for further analysis, including two studies which were found through manual searching. POEM has improved efficacy compared to PD with similar cost-effectiveness. POEM results showed comparable patient outcomes when compared with laparoscopic myotomy. Overall, POEM is a feasible first-line treatment for achalasia.
The (Non-)Use of African Law by the International Criminal Court
Authors: Manley Stewart , Tehrani Pardis Moslemzadeh , Rasiah Rajah
Published: August 2023

All defendants before the International Criminal Court (ICC) to date have been African, with their alleged crimes having been committed, at least partly, on African soil. When turning to national laws to resolve issues of interpretation in these cases, should the ICC see whether it can use laws of the African state in which the crime occurred? This article argues that it should, but observes – from a dataset of 16,192 citations containing over 200 citations to national laws – that it rarely does. Instead, it turns much more often to Western European and US laws. This phenomenon, the article suggests, troublingly reflects and perpetuates the marginalization of African and other global South laws from what constitutes international law. The article also argues that the Rome Statute requires the ICC to at least examine for appropriateness the laws of a subset of these neglected systems (‘the national laws of States that would normally exercise jurisdiction over the crime’) when identifying general principles of law. There are several compelling reasons to extend this examination requirement to African and other global South country laws more broadly, and even when not dealing with general principles of law, and few reasons not to.
Gender representation amongst orthodontic editorial boards: trends over time
Authors: Reeves Samuel , Liu Catherine , Mack Gavin
Published: August 2023

Objective

To assess trends in gender representation within editorial boards of European and North American orthodontic journals from 2000 to 2023.

Materials and methods

Retrospective cross-sectional study of editorial boards of orthodontic journals. The first issue of volumes of identified journals from the years 2000, 2010 and 2023 were investigated to demonstrate trends over time.

Results

Eight journals were included. Across the period investigated, a total of 810 editorial board positions were identified with most positions held by men (657/810; 81.1%). The proportion of female editorial board members increased from 14.7% (36/245) in 2000 to 24.5% (73/298) in 2023. The number of female Editor-in-Chief increased from zero in 2000 to two in 2023. Three journals demonstrated a reduction in female representation from 2000 to 2023.

Conclusion

Females remain underrepresented within editorial boards of orthodontic journals which is a key metric of presence and leadership in orthodontic academia.
On the trail of the Willmott and Braikenridge manuscripts
Authors: Burke James
Published: August 2023

The Willmott and Braikenridge manuscripts, once owned by the Norwich merchant John Sadler (d.1592), are all that is known to survive from his second partbook set, dated 1591. This article explores the custodial history of those volumes, tracing their various later owners and the marks they left. It finds that the two surviving volumes may have been apart since 1709—a separation that persisted until they were reunited in 2022—and also that the set’s three missing partbooks may have been lost only since 1885, raising hopes that they may one day be found.
A GFP splicing reporter in a coilin mutant background reveals links between alternative splicing, siRNAs, and coilin function in Arabidopsis thaliana
Authors: Kanno Tatsuo , Chiou Phebe , Wu Ming-Tsung , Lin Wen-Dar , Matzke Antonius , Matzke Marjori
Published: August 2023

Coilin is a scaffold protein essential for the structure of Cajal bodies, which are nucleolar-associated, nonmembranous organelles that coordinate the assembly of nuclear ribonucleoproteins (RNPs) including spliceosomal snRNPs. To study coilin function in plants, we conducted a genetic suppressor screen using a coilin (coi1) mutant in Arabidopsis thaliana and performed an immunoprecipitation-mass spectrometry analysis on coilin protein. The coi1 mutations modify alternative splicing of a GFP reporter gene, resulting in a hyper-GFP phenotype in young coi1 seedlings relative to the intermediate wild-type level. As shown here, this hyper-GFP phenotype is extinguished in older coi1 seedlings by posttranscriptional gene silencing triggered by siRNAs derived from aberrant splice variants of GFP pre-mRNA. In the coi1 suppressor screen, we identified suppressor mutations in WRAP53, a putative coilin–interacting protein; SMU2, a predicted splicing factor; and ZCH1, an incompletely characterized zinc finger protein. These suppressor mutations return the hyper-GFP fluorescence of young coi1 seedlings to the intermediate wild-type level. Additionally, coi1 zch1 mutants display more extensive GFP silencing and elevated levels of GFP siRNAs, suggesting the involvement of wild-type ZCH1 in siRNA biogenesis or stability. The immunoprecipitation-mass spectrometry analysis reinforced the roles of coilin in pre-mRNA splicing, nucleolar chromatin structure, and rRNA processing. The participation of coilin in these processes, at least some of which incorporate small RNAs, supports the hypothesis that coilin provides a chaperone for small RNA trafficking. Our study demonstrates the usefulness of the GFP splicing reporter for investigating alternative splicing, ribosome biogenesis, and siRNA-mediated silencing in the context of coilin function.
Histological Disease Activity as Predictor of Clinical Relapse, Hospitalization, and Surgery in Inflammatory Bowel Disease: Systematic Review and Meta-Analysis
Authors: Shehab Mohammad , Al Akram Sahad , Hassan Amro , Alrashed Fatema , Jairath Vipul , Bessissow Talat
Published: August 2023

Background

The clinical impact of histological remission on short- and long-term clinical outcomes in patients with inflammatory bowel disease (IBD) is not well established. We assessed risk of clinical relapse, hospitalization, and need for surgery in patients achieving histological remission in comparison with active histological disease.

Methods

A systematic review was conducted using MEDLINE, Scopus, Cochrane CENTRAL, EMBASE, and conference abstracts from inception to November 2022. Our main outcome was the rate of clinical relapse in patients with IBD who reached histological remission vs patients with active histological disease. Secondary outcomes were clinical complications of IBD such as hospitalization and need for surgery. The endpoints were investigated at 2 time points, 6 to 12 months (short term) and >12 months (long term).

Results

Short-term outcome analysis showed that the risk of clinical relapse was significantly higher in ulcerative colitis patients with active histological disease in comparison with patients at histological remission (risk ratio [RR], 2.41; 95% confidence interval [CI], 1.69-3.44; P < .01). The risk of hospitalization in ulcerative colitis patients was not significant among the 2 groups (RR, 4.22; 95% CI, 0.91-19.62; P = .07). Long-term outcome analysis demonstrated that the risk of clinical relapse (RR, 2.07; 95% CI, 1.55-2.76; P < .01), need for surgery (RR, 3.14; 95% CI, 1.53-6.45; P < .01), and hospitalization (RR, 2.52; 95% CI, 1.59-4.00; P < .01) was significantly higher in patients with active histological disease.

Conclusions

Histological remission in IBD represents an important therapeutic goal that is not yet routinely pursued in clinical practice. In our study, patients who achieved histological remission have more favorable outcomes than those with active histological disease in ulcerative colitis.