bluuebunny/crossref_metadata_2025_split huggingface dataset:
THz Near-field spectroscopy of metamaterial resonators
Authors: Degl’Innocenti R , Lu Y , Hale L L , Zaman A M , Addamane S J , Brener I , Mitrofanov O 
Published: March 2024

Abstract
Terahertz near-field spectroscopy is a powerful technique for the investigation of metamaterial resonators with subwavelength resolution. Here, we used an a-SNOM THz time domain spectroscopic system for the direct study of all the modes supported by individual D-split ring resonators, their E-field distributions and relative Q factors. A cross-polarized excitation and detection technique is also demonstrated, yielding a modes’ mapping by the resonators with unprecedented resolution and sharpness.
Summer drought weakens land surface cooling of tundra vegetation
Authors: Rietze Nils , Assmann Jakob J , Plekhanova Elena , Naegeli Kathrin , Damm Alexander , Maximov Trofim C , Karsanaev Sergey V , Hensgens Geert , Schaepman-Strub Gabriela 
Published: March 2024

Abstract
Siberia experienced a prolonged heatwave in the spring of 2020, resulting in extreme summer drought and major wildfires in the North-Eastern Siberian lowland tundra. In the Arctic tundra, plants play a key role in regulating the summer land surface energy budget by contributing to land surface cooling through evapotranspiration. Yet we know little about how drought conditions impact land surface cooling by tundra plant communities, potentially contributing to high air temperatures through a positive plant-mediated feedback. Here we used high-resolution land surface temperature and vegetation maps based on drone imagery to determine the impact of an extreme summer drought on land surface cooling in the lowland tundra of North-Eastern Siberia. We found that land surface cooling differed strongly among plant communities between the drought year 2020 and the reference year 2021. Further, we observed a decrease in the normalized land surface cooling (measured as water deficit index) in the drought year 2020 across all plant communities. This indicates a shift towards an energy budget dominated by sensible heat fluxes, contributing to land surface warming. Overall, our findings suggest significant variation in land surface cooling among common Arctic plant communities in the North-Eastern Siberian lowland tundra and a pronounced effect of drought on all community types. Based on our results, we suggest discriminating between functional tundra plant communities when predicting the drought impacts on energy flux related processes such as land surface cooling, permafrost thaw and wildfires.
First principles study of electronic structure and transport in graphene grain boundaries
Authors: Bach Lorentzen Aleksander , Gao Fei , Bøggild Peter , Jauho Antti-Pekka , Brandbyge Mads 
Published: March 2024

Abstract
Grain boundaries play a major role for electron transport in graphene sheets grown by chemical vapor deposition. Here we investigate the electronic structure and transport properties of idealized graphene grain boundaries (GBs) in bi-crystals using first principles density functional theory (DFT) and non-equilibrium Greens functions. We generated 150 different grain boundaries using an automated workflow where their geometry is relaxed with DFT. We find that the GBs generally show a quasi-1D bandstructure along the GB. We group the GBs in four classes based on their conductive properties: transparent, opaque, insulating, and spin-polarizing and show how this is related to angular mismatch, quantum mechanical interference, and out-of-plane buckling. Especially, we find that spin-polarization in the GB correlates with out-of-plane buckling. We further investigate the characteristics of these classes in simulated scanning tunnelling spectroscopy and diffusive transport along the GB which demonstrate how current can be guided along the GB.
Apparent color and Raman vibrational modes of the high-temperature superconductor Bi2Sr2CaCu2O
8+δ
exfoliated flakes
Authors: Figueruelo-Campanero Ignacio , del Campo Adolfo , Nieva Gladys , González Elvira M , Serrano Aida , Menghini Mariela 
Published: March 2024

Abstract
Studying and controlling the properties of individual exfoliated materials is one of the first steps towards the fabrication of complex van der Waals systems. In this work, we present a systematic study of optical properties and micro-Raman spectroscopy on exfoliated flakes of the high-temperature superconductor Bi2Sr2CaCu2O

8
+
δ

(BSCCO-2212). We demonstrate that these are quick and non-invasive techniques for studying air sensitive materials. The apparent color of BSCCO-2212 exfoliated flakes on SiO2/Si has allowed a rough and fast identification of the number of layers. By analyzing the optical contrast of different flakes we determined the complex refractive index in the visible range and found the optimal combination of illumination wavelength and substrate properties for the identification of flakes with different thickness. In addition, we report the hardening of the most characteristic Raman modes as flake thickness decreases, possibly caused by strain in the BiO and CuO2 planes. Moreover, the evolution of the Raman modes establishes a second approach to determine the thickness of BSCCO-2212 thin flakes. As BSCCO-2212 is a challenging material due to its sensitivity to ambient conditions, the present work provides a guide for the fabrication and characterization of complex van der Waals systems paving the way for studying heterostructures based on unconventional superconductors in the 2D limit.
Anomalous redshift in interlayer exciton emission with increasing twist angle in WSe2/MoSe2 heterostructures
Authors: Palekar Chirag Chandrakant , Hagel Joakim , Rosa Barbara , Brem Samuel , Shih Ching-Wen , Limame Imad , von Helversen Martin , Tongay Sefaattin , Malic Ermin , Reitzenstein Stephan 
Published: March 2024

Abstract
Van der Waals heterostructures utilizing semiconducting transition metal dichalcogenide (TMDC) monolayers have surfaced as compelling candidates due to their intriguing optical characteristics, which can be effectively controlled by the manipulation of the stacking twist angle. This study investigates the intricate correlation between twist angle, band offset, and interlayer exciton emission within twisted WSe2/MoSe2 heterostructures. Our findings suggest a crucial influence of monolayer stacking order on the band offset and the dipole orientation in twisted heterostructures that leads to either blueshift or redshift in emission energy. Herein, we fabricate heterobilayers with twist angles varying from 1

∘

to 56

∘

and observe an anomalous redshift energy of 100 meV in the interlayer exciton emission. Additionally, photoluminescence excitation spectroscopy measurements highlight the systematic twist angle dependence of intralayer exciton resonances, indicating significant angle dependent effects on individual monolayer bandgaps and on the interlayer coupling strength. Our fundamental study of exciton resonances provides comprehensive insights into the nuanced interplay between twist angle, dipole orientation, and dielectric asymmetry, providing a deeper understanding of the factors governing the optical properties of layered TMDC heterostructures.
Perfect and Poisonous Dependencies
Authors: Herold-Zanker Katharina 
Published: March 2024

Abstract
Drawing on postcolonial theories of cosmopolitanism and latest developments in decadence Studies, this chapter views Orientalism and decadence as intertwined discourses. It argues that the special relationship between European decadence and Orientalism became particularly visible at the turn of the century when cultural images from Middle Eastern and North African regions were abstracted into decadent images of hybridity—synthesizing Eastern and Western traits in a cosmopolitan yet universalist gesture. The East emerges as a plural and ahistorical concept dominated in the Western fin-de-siècle imaginations by contemporary archaeological finds, the fine arts, literature, and anthropological practices. The introduction provides a historical overview of the triangular relationship between English and German decadent writers communicating through ‘perfect and poisonous’ Eastern codes transmitted from Byzantinism to the Romantic Orient. It charts how English and German decadent writers, otherwise predominantly cherishing a cultural scepticism to the other nation, drew on shared sources such as the work of French decadent authors and the works of Friedrich Nietzsche to establish a sense of their respective cultural progression and definitions of decadence in each cultural context. In their engagement with the East it is revealed how Orientalism functioned as a focal point to bring these two decadent literatures in close proximity.
Evaluating the utility of procalcitonin and a clinical decision support tool to determine duration of antimicrobial therapy for respiratory tract infections
Authors: Pevehouse Rustin , Shah Punit J , Chou Nitha , Oolut Priya , Nair Suneesh , Ahmed Raziuddin 
Published: March 2024

Abstract

Purpose
Procalcitonin (PCT) levels may play a role in decreasing the duration of antimicrobial therapy in institutions that have long durations of therapy for management of community-acquired pneumonia. We assessed the impact of the combination of pharmacist stewardship interventions assisted by a clinical decision support (CDS) tool and PCT assessment on the antimicrobial days of therapy (DOT) prescribed for respiratory tract infections (RTIs).

Methods
We conducted a quasi-experimental study in which patients in the preintervention group were admitted between April and June 2021 and patients in the intervention group were admitted between April and June 2022. In the intervention phase, a CDS tool was utilized to alert clinical pharmacists when patients met specific criteria. This alert was programmed to activate for individual patients when a reported PCT level was less than 0.25 ng/mL and the patient was on antimicrobials prescribed for an RTI as indicated by providers in the electronic health record. Stewardship interventions were made by pharmacists via prospective audit and feedback. The primary endpoint was inpatient antimicrobial DOT for RTIs.

Results
There were 90 patients in the preintervention group and 104 patients in the intervention group. Although baseline characteristics were not well matched between the groups, favoring the preintervention group, the median DOT was lower in the intervention group, at 3 days (interquartile range [IQR], 2-4 days), compared to 4 days (IQR, 2.8-5 days) in the preintervention group (P = 0.001).

Conclusion
The results of our study demonstrate the utility of pharmacist interventions coupled with CDS and PCT in reducing antimicrobial DOT prescribed for RTIs. Antimicrobial stewardship programs may benefit from implementing a PCT bundle.
Group-level workplace interventions to improve mental health in low control, high-demand office-based jobs. A scoping review
Authors: Demou Evangelia , Blake Carolyn , Tan Llorin Charisse , Salanga Maria Guadalupe , Mateo Niño Jose , Lewis Ruth , Mitchell Kirstin R 
Published: March 2024

Abstract

Objectives
Workplace psychosocial risk factors, including low autonomy and high demands, have negative consequences for employee mental health and wellbeing. There is a need to support employees experiencing mental health and well-being problems in these jobs. This scoping review aims to describe group-level workplace interventions and their approaches to improving the mental health and well-being of employees in office-based, low autonomy, and high demands jobs.

Methods
Following PRISMA-ScR guidelines, a search was conducted across 4 databases (Medline, PsycINFO, CINAHL, ASSIA). We explored studies presenting group-level interventions, mode of implementation, facilitators and barriers, and intervention effectiveness. The search was restricted to include office-based, low autonomy, and high-demands jobs. Primary outcome of interest was mental health and secondary outcomes were work-related and other well-being outcomes.

Results
Group-level workplace interventions include an array of organizational, relational, and individual components. Almost all included a training session or workshop for intervention delivery. Several had manuals but theories of change were rare. Most workplace interventions did not use participatory approaches to involve employees in intervention development, implementation and evaluation, and challenges and facilitators were not commonly reported. Key facilitators were shorter intervention duration, flexible delivery modes, and formalized processes (e.g. manuals). A key barrier was the changeable nature of workplace environments. All studies employing behavioural interventions reported significant improvements in mental health outcomes, while no clear pattern of effectiveness was observed for other outcomes or types of interventions employed.

Conclusions
Group-based interventions in low-autonomy office settings can be effective but few studies used participatory approaches or conducted process evaluations limiting our knowledge of the determinants for successful group-based workplace interventions. Involving stakeholders in intervention development, implementation, and evaluation is recommended and can be beneficial for better articulation of the acceptability and barriers and facilitators for delivery and engagement.
metaProbiotics: a tool for mining probiotic from metagenomic binning data based on a language model
Authors: Wu Shufang , Feng Tao , Tang Waijiao , Qi Cancan , Gao Jie , He Xiaolong , Wang Jiaxuan , Zhou Hongwei , Fang Zhencheng 
Published: March 2024

Abstract
Beneficial bacteria remain largely unexplored. Lacking systematic methods, understanding probiotic community traits becomes challenging, leading to various conclusions about their probiotic effects among different publications. We developed language model–based metaProbiotics to rapidly detect probiotic bins from metagenomes, demonstrating superior performance in simulated benchmark datasets. Testing on gut metagenomes from probiotic-treated individuals, it revealed the probioticity of intervention strains–derived bins and other probiotic-associated bins beyond the training data, such as a plasmid-like bin. Analyses of these bins revealed various probiotic mechanisms and bai operon as probiotic Ruminococcaceae’s potential marker. In different health–disease cohorts, these bins were more common in healthy individuals, signifying their probiotic role, but relevant health predictions based on the abundance profiles of these bins faced cross-disease challenges. To better understand the heterogeneous nature of probiotics, we used metaProbiotics to construct a comprehensive probiotic genome set from global gut metagenomic data. Module analysis of this set shows that diseased individuals often lack certain probiotic gene modules, with significant variation of the missing modules across different diseases. Additionally, different gene modules on the same probiotic have heterogeneous effects on various diseases. We thus believe that gene function integrity of the probiotic community is more crucial in maintaining gut homeostasis than merely increasing specific gene abundance, and adding probiotics indiscriminately might not boost health. We expect that the innovative language model–based metaProbiotics tool will promote novel probiotic discovery using large-scale metagenomic data and facilitate systematic research on bacterial probiotic effects. The metaProbiotics program can be freely downloaded at https://github.com/zhenchengfang/metaProbiotics.
MHCpLogics: an interactive machine learning-based tool for unsupervised data visualization and cluster analysis of immunopeptidomes
Authors: Shahbazy Mohammad , Ramarathinam Sri H , Li Chen , Illing Patricia T , Faridi Pouya , Croft Nathan P , Purcell Anthony W 
Published: March 2024

Abstract
The major histocompatibility complex (MHC) encodes a range of immune response genes, including the human leukocyte antigens (HLAs) in humans. These molecules bind peptide antigens and present them on the cell surface for T cell recognition. The repertoires of peptides presented by HLA molecules are termed immunopeptidomes. The highly polymorphic nature of the genres that encode the HLA molecules confers allotype-specific differences in the sequences of bound ligands. Allotype-specific ligand preferences are often defined by peptide-binding motifs. Individuals express up to six classical class I HLA allotypes, which likely present peptides displaying different binding motifs. Such complex datasets make the deconvolution of immunopeptidomic data into allotype-specific contributions and further dissection of binding-specificities challenging. Herein, we developed MHCpLogics as an interactive machine learning-based tool for mining peptide-binding sequence motifs and visualization of immunopeptidome data across complex datasets. We showcase the functionalities of MHCpLogics by analyzing both in-house and published mono- and multi-allelic immunopeptidomics data. The visualization modalities of MHCpLogics allow users to inspect clustered sequences down to individual peptide components and to examine broader sequence patterns within multiple immunopeptidome datasets. MHCpLogics can deconvolute large immunopeptidome datasets enabling the interrogation of clusters for the segregation of allotype-specific peptide sequence motifs, identification of sub-peptidome motifs, and the exportation of clustered peptide sequence lists. The tool facilitates rapid inspection of immunopeptidomes as a resource for the immunology and vaccine communities. MHCpLogics is a standalone application available via an executable installation at: https://github.com/PurcellLab/MHCpLogics.
ICELLNET v2: a versatile method for cell–cell communication analysis from human transcriptomic data
Authors: Massenet-Regad Lucile , Soumelis Vassili 
Published: March 2024

Abstract

Summary
Several methods have been developed in the past years to infer cell–cell communication networks from transcriptomic data based on ligand and receptor expression. Among them, ICELLNET is one of the few approaches to consider the multiple subunits of ligands and receptors complexes to infer and quantify cell communication. In here, we present a major update of ICELLNET. As compared to its original implementation, we (i) drastically expanded the ICELLNET ligand-receptor database from 380 to 1669 biologically curated interactions, (ii) integrated important families of communication molecules involved in immune crosstalk, cell adhesion, and Wnt pathway, (iii) optimized ICELLNET framework for single-cell RNA sequencing data analyses, (iv) provided new visualizations of cell–cell communication results to facilitate prioritization and biological interpretation. This update will broaden the use of ICELLNET by the scientific community in different biological fields.

Availability and implementation
ICELLNET package is implemented in R. Source code, documentation and tutorials are available on GitHub (https://github.com/soumelis-lab/ICELLNET).
vizAPA: visualizing dynamics of alternative polyadenylation from bulk and single-cell data
Authors: Bi Xingyu , Ye Wenbin , Cheng Xin , Yang Ning , Wu Xiaohui 
Published: March 2024

Abstract

Motivation
Alternative polyadenylation (APA) is a widespread post-transcriptional regulatory mechanism across all eukaryotes. With the accumulation of genome-wide APA sites, especially those with single-cell resolution, it is imperative to develop easy-to-use visualization tools to guide APA analysis.

Results
We developed an R package called vizAPA for visualizing APA dynamics from bulk and single-cell data. vizAPA implements unified data structures for APA data and genome annotations. vizAPA also enables identification of genes with differential APA usage across biological samples and/or cell types. vizAPA provides four unique modules for extensively visualizing APA dynamics across biological samples and at the single-cell level. vizAPA could serve as a plugin in many routine APA analysis pipelines to augment studies for APA dynamics.

Availability and implementation
https://github.com/BMILAB/vizAPA.
Acute cement dust poisoning: Rigid bronchoscopy and mechanical insufflation–exsufflation as an effective and novel treatment for its management
Authors: Quiroga Nestor Ivan , Palliser Cristina , Caballeria Estrella , Bello Irene 
Published: March 2024

Abstract
This clinical case shows the repercussions of acute exposure to cement dust in the respiratory tract and other mucous membranes. Following a cement dust pipe explosion, the patient endured a severe inhalation of dust. A combination of rigid bronchoscopy and a mechanical insufflation–exsufflation system was employed to remove cement debris from the airways. Respiratory physiotherapy sessions were implemented for effective secretion clearance, contributing to a successful short-term recovery. While this remains an isolated case, the unconventional techniques employed provide valuable insights for potential similar scenarios in the future.
Phenotypic lags influence rapid evolution throughout a drought cycle
Authors: Branch Haley A , Anstett Daniel N , Angert Amy L 
Published: March 2024

Abstract
Climate anomalies are increasing and posing strong selection, which can lead to rapid evolution. This is occurring on a backdrop of interannual variability that might weaken or even reverse selection. However, the effect of interannual climatic variability on rapid evolution is rarely considered. We study the climatic differences that contribute to rapid evolution throughout a 7-year period, encompassing a severe drought across 12 populations of Mimulus cardinalis (scarlet monkeyflower). Plants were grown in a common greenhouse environment under wet and dry treatments, where specific leaf area and date of flowering were measured. We examine the association between trait values and different climate metrics at different time periods, including the collection year, prior years, and cumulative metrics across sequential years. Of the climatic variables we assessed, we find that anomalies in mean annual precipitation best describe trait differences over our study period. Past climates, of 1–2 years prior, are often related to trait values in a conflicting direction to collection-year climate. Uncovering these complex climatic impacts on evolution is critical to better predict and interpret the impacts of climate change.
Discrimination between icequakes and earthquakes in southern Alaska: an exploration of waveform features using Random Forest algorithm
Authors: Kharita Akash , Denolle Marine A , West Michael E 
Published: March 2024

SUMMARY
This study examines the feature space of seismic waveforms often used in machine learning applications for seismic event detection and classification problems. Our investigation centres on the southern Alaska region, where the seismic record captures diverse seismic activity, notably from the calving of marine-terminating glaciers and tectonic earthquakes along active plate boundaries. While the automated discrimination of earthquakes and glacier quakes is our nominal goal, this data set provides an outstanding opportunity to explore the general feature space of regional seismic phases. That objective has applicability beyond ice quakes and our geographic region of study. We make a noteworthy discovery that features rooted in the spectral content of seismic waveforms consistently outperform statistical and temporal features. Spectral features demonstrate robust performance, exhibiting resilience to class imbalance while being minimally impacted by factors such as epicentral distance and signal-to-noise ratio. We also conduct experiments on the transferability of the model and find that transferability primarily depends on the appearance of the waveforms. Finally, we analyse misclassified events and find examples that are identified incorrectly in the original regional catalogue.