bluuebunny/crossref_metadata_2025 huggingface dataset:
Unraveling the roles of single transition metal atom anchored on equivalent stoichiometry graphitic carbon nitride (gC6N6) for carbon dioxide reduction: a density functional theory study
Authors: Er Chen-Chen , Putri Lutfi K , Medhekar Nikhil V , Chai Siang-Piao
Published: November 2022

CO2 photoreduction into hydrocarbon fuels is a promising strategy in closing the carbon cycle to realize a sustainable energy economy. Among the many photocatalysts that have been developed thus far, porous graphitic carbon nitride (gC6N6) has emerged as a potential photocatalyst candidate in view of its unique optoelectronic properties, metal-free nature and two-dimensional versatile structure that can be easily modified. In this work, the enhancement of equivalent stoichiometry carbon nitride (gC6N6) through single transition metal atom modification was systematically studied from first principles density functional theory calculations. The formation energy calculations revealed that incorporating single Co, Cu, Ni or Pd atom into gC6N6 is energetically favorable, with the exception of Pt. The computed density of states plot indicates that a greater degree of hybridization of the transition metal atom d-orbitals with the p-orbitals of O atom from CO2 will lead to stronger adsorption interaction. The optical absorption spectra show that Cu, Pd, and Pt promotes greater light absorption by extending the optical absorption to the NIR region. The presence of additional dopant states near the Fermi surface was found to have affected the optical absorption. The band structures of the Co,Cu,Pd,Pt@gC6N6 show bandgap narrowing due to the shifting of conduction band edge closer to the Fermi level. Contrastingly, Ni@gC6N6 exhibits bandgap narrowing through the shifting of the valence band edge to the Fermi level. The band edge positions suggest that anchoring gC6N6 with single Co, Cu, Ni, Pd and Pt atom dopants possesses the capability to reduce CO2 into C1 products. Among all the transition metals studied, Pd@gC6N6 and Cu@gC6N6 are identified as the most promising single-atom photocatalysts for CO2 reduction due to their energetically favorable formation energy, stable CO2 adsorption configuration, narrow bandgap, low charge carrier recombination, extended light absorption range and suitable band edge positions.
Effect of loading orientation on plasticity in nano-laminated CoNiCrFeMn dual-phase high-entropy alloy: a molecular dynamics study
Authors: Shuang Siyao , Liang Yanxiang , Yu Chao , Kan Qianhua , Kang Guozheng , Zhang Xu
Published: November 2022

Dual-phase high-entropy alloys (DP-HEAs) have been proved to be a kind of promising materials that exhibit a combination of excellent strength and ductility. Previous studies have emphasized the effect of interface and phase volume fraction on mechanical performance in DP-HEAs. However, the deformation mechanisms such as interplays between dislocations and the constituent phases have not been fully understood. Particularly, the research concerning plastic anisotropy in DP-HEAs is still lacking. Here, molecular dynamics simulations are performed to probe the effect of loading orientation on plasticity in the nano-laminated face-centered cubic (FCC)/hexagonal close-packed (HCP) CoNiCrFeMn DP-HEA. Results reveal that a switch from strengthening to softening and back to strengthening is closely related to the activation of different slip systems when tailoring the inclination angles of the nanolaminates with respect to the tensile direction from 0° to 90°. Slip transfer across phase boundaries, phase transformation and the nucleation of shear bands dominate the plasticity in the samples with low, medium and high inclination angles, respectively. Furthermore, the evolution of microstructures, such as dislocations, stacking faults, and FCC/HCP phase are analyzed to study the underlying deformation mechanisms. These results can help understand the plastic anisotropy of DP-HEAs and design alloys with excellent mechanical properties for engineering applications.
Corrigendum: Target patterns in a 2D array of oscillators with nonlocal coupling (2018 Nonlinearity

31 4162)
Authors: Jaramillo Gabriela , Venkataramani Shankar C
Published: November 2022

We correct the statement of lemma 3.5 in [Jaramillo et al (2018 Nonlinearity
31 4162)]. The lemma establishes Fredholm properties for a specific radial operator, which in the original paper is incorrectly defined. The error does not alter our main theorem, but does affect the proof of a subsequent result, lemma 4.11, which we fix in this corrigendum.
Characterization of an atmospheric pressure plasma jet producing the auroral transition O(1S) to O(1D)
Authors: Jaiswal S , Aguirre E M , van der Gaag T
Published: November 2022

We present a detailed characterization of an atmospheric pressure plasma jet that produces the metastable oxygen states O(1S) and O

(

1

D) with emission of the ‘auroral’ green line. The device used 99.999

%

pure argon as a working gas for the plasma generation. Optical emission spectroscopy was used to understand the active species present in the plasma jet and to infer the mechanism of O(1S) creation and destruction. The continuum spectrum was used in conjunction with a method based on machine learning for determining the arbitrary electron probability distribution function. Discharge and plasma properties were estimated from Lissajous plots and using calculations with the BOLSIG+ software. The metastable oxygen forms for all operating parameters of the plasma jet system in a linear electrode configuration. The camera images provided information of the overall plasma jet behavior as parameters were altered. While the metastable oxygen was produced for every iteration, the plasma jet behavior changed considerably when the powered and grounded electrodes are switched. Small admixtures of oxygen and nitrogen were introduced in the plasma jet to understand the kinetic processes of metastable oxygen destruction and the 557.7 nm auroral line. This behavior has implications for plasma reactive chemistry in fundamental areas such as auroral physics as well as technological applications of plasmas.
Characterizing physiological high-frequency oscillations using deep learning
Authors: Zhang Yipeng , Chung Hoyoung , Ngo Jacquline P , Monsoor Tonmoy , Hussain Shaun A , Matsumoto Joyce H , Walshaw Patricia D , Fallah Aria , Sim Myung Shin , Asano Eishi , Sankar Raman , Staba Richard J , Engel Jerome , Speier William , Roychowdhury Vwani , Nariai Hiroki
Published: November 2022

Objective. Intracranially-recorded interictal high-frequency oscillations (HFOs) have been proposed as a promising spatial biomarker of the epileptogenic zone. However, HFOs can also be recorded in the healthy brain regions, which complicates the interpretation of HFOs. The present study aimed to characterize salient features of physiological HFOs using deep learning (DL). Approach. We studied children with neocortical epilepsy who underwent intracranial strip/grid evaluation. Time-series EEG data were transformed into DL training inputs. The eloquent cortex (EC) was defined by functional cortical mapping and used as a DL label. Morphological characteristics of HFOs obtained from EC (ecHFOs) were distilled and interpreted through a novel weakly supervised DL model. Main results. A total of 63 379 interictal intracranially-recorded HFOs from 18 children were analyzed. The ecHFOs had lower amplitude throughout the 80–500 Hz frequency band around the HFO onset and also had a lower signal amplitude in the low frequency band throughout a one-second time window than non-ecHFOs, resembling a bell-shaped template in the time–frequency map. A minority of ecHFOs were HFOs with spikes (22.9%). Such morphological characteristics were confirmed to influence DL model prediction via perturbation analyses. Using the resection ratio (removed HFOs/detected HFOs) of non-ecHFOs, the prediction of postoperative seizure outcomes improved compared to using uncorrected HFOs (area under the ROC curve of 0.82, increased from 0.76). Significance. We characterized salient features of physiological HFOs using a DL algorithm. Our results suggested that this DL-based HFO classification, once trained, might help separate physiological from pathological HFOs, and efficiently guide surgical resection using HFOs.
Commissioning of the upgraded RICH system at the LHCb experiment
Authors: Okamura S.
Published: November 2022

The Ring-Imaging Cherenkov (RICH) system is an essential element of the LHCb experiment: it consists of an upstream detector (RICH 1), located close to the interaction point, and a downstream detector (RICH 2), placed after the tracking system and has the task of identifying charged hadrons over the momentum range 2–100 GeV/c. Currently, the LHCb experiment is completing an upgrade phase to allow data collection at a five-fold increase in instantaneous luminosity up to 2 × 1033 cm−2 s−1 and read out data at a rate of 40 MHz. The challenges of the higher luminosity are a significant increase in detector occupancy and a larger radiation dose. To match the new experimental requirements, both RICH detectors have been upgraded with a redesigned opto-electronic chain and new photon detectors. In addition, RICH 1 has a modified layout with new mechanics and spherical mirrors to reduce the maximum occupancy. A summary of the upgrade program and the current status of the commissioning operations will be presented.
Characterization of High-Flux CdZnTe with optimized electrodes for 4th generation synchrotrons
Authors: Baussens O. , Ponchut C. , Ruat M. , Bettelli M. , Zanettini S. , Zappettini A.
Published: November 2022

In this collaboration work between IMEM-CNR and the ESRF, we explore the potential of the Redlen Technologies High-Flux Cadmium Zinc Telluride (HF-CZT) material for direct X-ray detection at fluxes ranging from 10+7 to 10+12 photons mm−2 s−1. HF-CZT single crystals with optimized electroless gold and sputtered platinum electrodes are characterized both under dark conditions and under X-ray irradiation. We report low leakage current under dark conditions (<100 pA/mm2 at 5 kV/cm). We also report good linearity (R
2 > 0.999) under moderate to high incident X-ray flux (10+7 to 10+10 photons mm−2 s−1) as well as good stability and reproducibility for incident X-ray fluxes up to 10+12 photons mm−2 s−1. Finally, we study transient phenomena in the seconds time range and report fast stabilization time (<200 ms) and negligible afterglow in this time range.
Ultra-fast transverse beam orbit control in LCLS copper linac. Part I
Authors: Halavanau A. , Romero A. , Krasnykh A. , Lutman A. , Beukers T. , Hugyik J. , Le A. , Luchini K. , Jongewaard E. , Sy A. , Ibrahimov A. , Benwell A. , Marinelli A. , Decker F.-J.
Published: November 2022

Current and future experiments at LCLS require x-ray pulse trains of variable time separation on the nanosecond scale. For instance, the cavity-based XFEL (CBXFEL) will use up to 4 pulses separated by 218.5 ns, the X-ray Laser Oscillator (XLO) will use 15 to 25 ns spaced pulses, and the Matter under Extreme Conditions (MEC) experiments use pulse trains separated by 5 nanoseconds or less. In this paper, we demonstrate an ultra-fast e-beam trajectory control method based on transverse electro-magnetic (TEM) striplines and state-of-the-art power sources, to enhance LCLS operations in these regimes.
Design of a μSR spectrometer with ultrahigh arrays at China Spallation Neutron Source
Authors: Dong J.Y. , Pan Z.W. , Yang T.Y. , Lin Z.B. , Wang Z. , He Z.Y. , Chen Z. , Jing H.T. , Tang J.Y. , Liu J.D. , Zhang H.J. , Ye B.J.
Published: November 2022

A new muon source has been proposed to conduct muon spin
rotation/relaxation/ resonance (μSR) measurements at China Spallation Neutron Source (CSNS). Only 1 Hz of the CSNS proton beams (25 Hz in total) will be allocated for muon production. To make better use of muons in every pulse, an ultrahigh-array μSR spectrometer (UHAM) with thousands of detector channels is under design. Due to such a high granularity of detectors, multiple counting events generated from particle scattering or spiral motions of positrons in a strong longitudinal field should be carefully considered in the design. Six different structures were modeled and simulated based on two types of angular orientations (parallel arrangement and pointing arrangement) and three kinds of spectrometer geometries (cylinder, cone and sphere). A quality factor, Q, was proposed to evaluate the performance of these structures by integrating their impacts on the overall asymmetry, the counting rate and the percentage of multiple counts. According to the simulation, the conical structure with detectors pointing to the sample has the highest Q in both zero field and longitudinal field. The results also show that all kinds of structures cannot be operated under strong longitudinal fields with a strength over 2 T. The full simulation of a μSR spectrometer can provide good guidance for the construction of the UHAM in the upcoming upgrade of CSNS.
Spatial-temporal variations in green, blue and gray water footprints of crops: how do socioeconomic drivers influence?
Authors: Hu Mengmeng , Wu Wenbin , Yu Qiangyi , Tang Huajun , Wen Yanru , Zhao Fen
Published: November 2022

Nowadays, more than 70% of global freshwater is used for agriculture. The evaluation of the water footprint of crops (CWFs) is an important method to measure the effects of crop production on water resource utilization and water environmental pollution. However, little attention is paid to the impact of socioeconomic development differences on the water footprint of each crop. In this study, the green, blue, and gray water footprints of crop production were quantified, and the socioeconomic drivers of changes in the CWFs were revealed. It is of great significance to provide targeted guidance for agricultural water management in Heilongjiang, a province with the largest crop production in China. Here, we show that the total water footprint of crop production (TWF) increased from 62.2 billion m3 to 101.8 billion m3, and high-value areas were mainly concentrated in the west and south of Heilongjiang Province. Over 95% of the total grain crops sown were covered by maize, rice and soybean, which presented the greatest TWF. The share of green water footprint in TWF has increased, and crop growth is increasingly dependent on rainfall. Furthermore, our results highlight that the effective irrigated quota and crop-planting scale for maize and rice contribute to TWF increase. The TWF and agricultural value-added score were weakly decoupling in most municipalities, indicating the improved efficiency of crop water use; the TWF is growing slower than the economy, which is undesirable. Changes in TWF and agricultural value-added score were the same as the left half of the inverted ‘U of the ‘Environmental Kuznets Curve’, which has not reached the ‘inflection point’. More efforts to control the effective irrigated quota and crop-planting scale while improving effective irrigated efficiency are needed to ensure that economic growth does not come at the expense of consuming enormous quantities of water.
ENSO and QBO modulation of the relationship between Arctic sea ice loss and Eurasian winter climate
Authors: Ma Xuan , Wang Lei , Smith Doug , Hermanson Leon , Eade Rosie , Dunstone Nick , Hardiman Steven , Zhang Jiankai
Published: November 2022

The causality between Arctic sea ice decline and cold boreal winters has been widely debated recently and remains controversial. A major source of uncertainty in the sea ice-cold winter relationship originates from that the stratosphere polar vortex (SPV) is not only affected by Arctic sea ice anomaly but can also be modulated by El Niño-Southern Oscillation (ENSO) and quasi-biennial oscillation (QBO). Using reanalysis data and hindcasts from the decadal prediction system version 4, here we show that both cold and warm winters occur over Eurasia when the Barents–Kara Sea sea ice is abnormally low. Warm winters occur during the La Niña-easterly QBO-low sea ice (LANINA-EQBO-LICE) years and cold winters during the neutral ENSO-neutral QBO (NENSO-NQBO)-LICE and El Niño (ELNINO)-NQBO-LICE years. During the LANINA-EQBO-LICE years, weakened upward-propagating planetary waves from the troposphere to the stratosphere strengthen the Arctic SPV and then weaken the Aleutian low and Siberian high, creating conditions favorable for Eurasian warming. The atmospheric responses are opposite in the NENSO-NQBO-LICE and ELNINO-NQBO-LICE years. This implies that care should be taken in using Arctic sea ice alone as the precursor to predict boreal winter climate.
Divergent runoff impacts of permafrost and seasonally frozen ground at a large river basin of Tibetan Plateau during 1960–2019
Authors: Song Lei , Wang Lei , Zhou Jing , Luo Dongliang , Li Xiuping
Published: November 2022

Since the 20th century, due to global warming, permafrost areas have undergone significant changes. The degradation of permafrost has complicated water cycle processes. Taking the upper Yellow River basin (UYRB) as a demonstration, this study discusses the long-term (1960–2019) changes in frozen ground and their hydrological effects with a cryosphere-hydrology model, in particular a permafrost version of the water and energy budget-based distributed hydrological model. The permafrost at the UYRB, with thickening active layer and lengthening thawing duration, has degraded by 10.8%. The seasonally frozen ground has a more pronounced intra-annual regulation that replenishes surface runoff in the warm season, while the degradation of permafrost leads to a runoff increase. The occurrence of extreme events at the UYRB has gradually decreased with the degradation of frozen ground, but spring droughts and autumn floods become more serious. The results may help better understand the hydrological impacts of permafrost degradation in the Tibetan Plateau.
Keratin intrinsic fluorescence as a mechanism for non-invasive monitoring of its glycation
Authors: Muir Rhona , Forbes Shareen , Birch David J S , Vyshemirsky Vladislav , Rolinski Olaf J
Published: November 2022

We have studied the evolution of keratin intrinsic fluorescence as an indicator of its glycation. Steady-state and time-resolved fluorescence of free keratin and keratin-glucose samples were detected in PBS solutions in vitro. The changes in the fluorescence response demonstrate that the effect of glucose is manifest in the accelerated formation of fluorescent cross-links with an emission peak at 460 nm and formation of new cross-links with emission peaks at 525 nm and 575 nm. The fluorescence kinetics of these structures is studied and their potential application for the detection of long-term complications of diabetes discussed.
Detection and quantification of Pb and Cr in oysters using laser-induced breakdown spectroscopy
Authors: YAN Qingxia , TIAN Ye , LI Ying , LIN Hong , JIA Ziwen , LU Yuan , YU Jin , SUN Chen , BAI Xueshi , DETALLE Vincent
Published: November 2022

The quantitative determination of heavy metals in aquatic products is of great importance for food security issues. Laser-induced breakdown spectroscopy (LIBS) has been used in a variety of foodstuff analysis, but is still limited by its low sensitivity when targeting trace heavy metals. In this work, we compare three sample enrichment methods, namely drying, carbonization, and ashing, for increasing detection sensitivity by LIBS analysis for Pb and Cr in oyster samples. The results demonstrate that carbonization can remove a significant amount of the contributions of organic elements C, H, N and O; meanwhile, the signals of the metallic elements such as Cu, Pb, Sr, Ca, Cr and Mg are enhanced by 3–6 times after carbonization, and further enhanced by 5–9 times after ashing. Such enhancement is not only due to the more concentrated metallic elements in the sample compared to the dried ones, but also the unifying of the matter in carbonized and ashed samples from which higher plasma temperature and electron density are observed. This condition favors the detection of trace elements. According to the calibration curves with univariate and multivariate analysis, the ashing method is considered to be the best choice. The limits of detection of the ashing method are 0.52 mg kg−1 for Pb and 0.08 mg kg−1 for Cr, which can detect the presence of heavy metals in the oysters exceeding the maximum limits of Pb and Cr required by the Chinese national standard. This method provides a promising application for the heavy metal contamination monitoring in the aquatic product industry.
Preprint Highlight: Functional and spatial proteomics profiling reveals intra- and intercellular signaling crosstalk in colorectal cancer
Authors: Lim Grace
Published: November 2022

Standard genomic and proteomic profiling methods for colorectal tumors do not always translate into reliable precision medicine outcomes. Tumor plasticity mechanisms can result in nongenetic responses to targeted therapies, calling for a functional approach using dynamic and physiologically relevant patient models. This study establishes a functional precision medicine workflow by combining the application of kinase inhibitors with quantitative and spatial proteomics to reveal both intrinsic and extrinsic signaling crosstalk in a living biobank of patient-derived colorectal cancer organoid models. The data and methods used here provide a framework for a better understanding of colorectal cancers that accounts for off-target effects of kinase inhibitors and patient-specific plasticity mechanisms that influence downstream cell signaling responses.

This preprint has been assigned the following badges: New Methods, New Materials, Open Data, Open Software.

Read the preprint on bioRxiv ( Plattner et al., 2022 ): https://doi.org/10.1101/2022.09.16.508204 .
Preprint Highlight: Actomyosin cables position cell cohorts during Drosophila germband retraction by entraining their morphodynamic and mechanical properties
Authors: Ríos-Barrera Luis Daniel
Published: November 2022

Midway through embryonic development in Drosophila melanogaster, the germband retracts to relocate the body segments to their final position. This process requires complex cell rearrangements and tissue-scale coordination, but the cellular behaviors and forces that drive it have not been characterized in detail. This work shows that proper tissue retraction requires coordination between distinct supracellular actomyosin cables at the posterior-most segment of the germband: nonconstricting circumferential cables mechanically isolate cell subpopulations within the germband, and constricting cables accelerate overall tissue retraction. Force propagation drives morphogenesis of a wide range of organs and tissues. This work provides a model to understand how forces are coordinated between adjacent tissues but also restrained to specific tissue compartments during development.

This preprint has been assigned the following badges: New Hypothesis, Cross-Validation, Open Data.

Read the preprint on bioRxiv ( Nandi et al., 2022 ): https://doi.org/10.1101/2022.09.23.509113 .
Prescribing and deprescribing in very old age: perceptions of very old adults, caregivers and health professionals
Authors: Ouellet Nicole , Bergeron Anne-Sophie , Gagnon Eric , Cossette Benoit , Labrecque Cory A , Sirois Caroline
Published: November 2022

Background

although they are major consumers of medications, there is little evidence-based data to guide prescribing and deprescribing of medications for very old adults (80+ years).

Objectives

to discover the perceptions of very old adults, caregivers and health professionals in order to further examine the clinical and ethical issues raised by prescribing and deprescribing in very old age.

Methods

individual interviews were conducted with very old adults (n = 10) and caregivers (n = 6), whereas group interviews were conducted with health professionals (n = 11). The themes covered included perceptions of medication use, polypharmacy, deprescribing and patient-health professional relationships. Thematic analysis was used to identify areas of convergence and divergence.

Results

very old adults are satisfied with the medications they are taking, do not see the need to reduce their medication use and consider their doctor as the expert who should make the decisions regarding treatment. The perceptions of caregivers are similar to those of older adults, whereas health professionals believe that very old adults take a lot of inappropriate medications and list multiple barriers to deprescribing. All participants describe a normalisation of medication use with ageing.

Conclusion

there is a dichotomy between the perception of the very old adults/caregivers and that of health professionals regarding the safety of medication in very old age. A cultural change regarding medication use seems essential to optimise therapy and support deprescribing in clinical practice since the potential issues raised by researchers do not resonate with the main stakeholders.
Deep learning-based classifier of diffuse large B-cell lymphoma cell-of-origin with clinical outcome
Authors: Viswanathan Aswathi , Kundal Kavita , Sengupta Avik , Kumar Ambuj , Kumar Keerthana Vinod , Holmes Antony B , Kumar Rahul
Published: November 2022

Diffuse large B-cell lymphoma (DLBCL) is an aggressive form of non-Hodgkin lymphoma with poor response to R-CHOP therapy due to remarkable heterogeneity. Based on gene expression, DLBCL cases were divided into two subtypes, i.e. ABC and GCB, where ABC subtype is associated with poor outcomes. Due to its association with clinical outcome, this classification, also known as cell-of-origin (COO), is an efficient way to predict the response to R-CHOP therapy. Previous COO classification methods have some shortcomings, e.g. limited number of samples in the training dataset. These shortcomings challenge the robustness of methods and make it difficult to implicate these methods at clinical level. To overcome the shortcomings of previous methods, we developed a deep learning-based classifier model on a cohort of 381 DLBCL patients using expression data of 20 genes. We implemented multilayer perceptron (MLP) to train deep learning-based classifier, named MLP-COO. MLP-COO achieved accuracy of 99.70% and 94.70% on training and testing datasets, respectively, with 10-fold cross-validation. We also assessed its performance on an independent dataset of 294 DLBCL patients. On independent dataset, we achieved an accuracy of 95.90% with MCC of 0.917. To show its broader applicability, we used this classifier to predict the clinical outcome using survival data from two large cohorts of DLBCL patients. In survival analysis, MLP-COO recapitulates the survival probabilities of DLBCL patients based on their COO in both cohorts. We anticipate that MLP-COO model developed in this study will benefit in the accurate COO prediction of DLBCL patients and their clinical outcomes.
An end-to-end multi-task system of automatic lesion detection and anatomical localization in whole-body bone scintigraphy by deep learning
Authors: Huang Kaibin , Huang Shengyun , Chen Guojing , Li Xue , Li Shawn , Liang Ying , Gao Yi
Published: November 2022

Limited by spatial resolution and visual contrast, bone scintigraphy interpretation is susceptible to subjective factors, which considerably affects the accuracy and repeatability of lesion detection and anatomical localization. In this work, we design and implement an end-to-end multi-task deep learning model to perform automatic lesion detection and anatomical localization in whole-body bone scintigraphy. A total of 617 whole-body bone scintigraphy cases including anterior and posterior views were retrospectively analyzed. The proposed semi-supervised model consists of two task flows. The first one, the lesion segmentation flow, received image patches and was trained in a supervised way. The other one, skeleton segmentation flow, was trained on as few as five labeled images in conjunction with the multi-atlas approach, in a semi-supervised way. The two flows joint in their encoder layers so each flow can capture more generalized distribution of the sample space and extract more abstract deep features. The experimental results show that the architecture achieved the highest precision in the finest bone segmentation task in both anterior and posterior images of whole-body scintigraphy. Such an end-to-end approach with very few manual annotation requirement would be suitable for algorithm deployment. Moreover, the proposed approach reliably balances unsupervised labels construction and supervised learning, providing useful insight for weakly labeled image analysis.

Supplementary information

Supplementary data are available at Bioinformatics online.
Mixed evidence of a commensal relationship between a rare epiphytic orchid and cohabiting bryophytes
Authors: Crain Benjamin J , Sánchez-Cuervo Ana María , Deren Victoria
Published: November 2022

The co-occurrence of orchids and bryophytes at occupied sites on host trees has been documented on several occasions, particularly in the tropics, and it may represent an important symbiotic relationship that supports epiphytic orchid populations. Despite continuing interest from ecologists, the specific life history traits that are affected by associations of orchids with bryophytes, and how they are affected, remain unclear. Clarifying the nature of the association will improve our understanding of orchid ecology and have practical implications for applied conservation efforts, particularly for rare species in restricted habitats. In this study, we explored the relationship between the abundance of bryophyte cover on host trees and various life history traits related to size, survival and reproduction of a rare tropical epiphytic orchid, Lepanthes caritensis. The results demonstrated that bryophyte abundance on host trees had variable effects on individual aspects of an orchid’s life history. Orchid recruitment was positively correlated with the abundance of bryophyte cover, but survival and flower production were negatively correlated with bryophyte abundance. Our findings revealed that an apparent commensal symbiotic relationship between L. caritensis and bryophytes exists at the recruitment stage, but this is lost during later life stages, when the abundance of bryophytes appears to negatively affect this species.
Testing for quantile sample selection
Authors: Corradi Valentina , Gutknecht Daniel
Published: November 2022

This paper provides distribution free tests for detecting sample selection in conditional quantile functions. The first test is an omitted predictor test with the propensity score as the omitted variable. In the case of rejection we cannot distinguish between rejection due to genuine selection or to misspecification. Thus, we suggest a second test using only individuals with propensity score close to one. The latter relies on an ‘identification at infinity’ argument, but accommodates cases of irregular identification, and neither of the two tests requires a continuous exclusion restriction. We apply our procedure to test for selection in log hourly wages using UK survey data and derive an extension of the tests to the conditional mean.
Evobiopsychosocial medicine
Authors: Hunt Adam D , St-John Smith Paul , Abed Riadh
Published: November 2022

The biopsychosocial model remains the de facto framework of current healthcare, but lacks causational depth, scientific rigour, or any recognition of the importance of evolutionary theory for understanding health and disease. In this article it is updated to integrate Tinbergen’s four questions with the three biopsychosocial levels. This ‘evobiopsychosocial’ schema provides a more complete framework for understanding causation of medical conditions. Its application is exemplified by tabulating depression, rheumatoid arthritis and COVID-19 within its format, which highlights the direct research and practical applications uniquely offered by evolutionary medicine. An evobiopsychosocial framework can serve as a useful tool to introduce evolutionary concepts into mainstream medicine by highlighting the broad and specific contributions of evolutionary analysis to researching, treating and preventing health conditions, providing a suitable next step for the mainstream model of medicine.
Impact of a heart failure nurse practitioner service on rehospitalizations, emergency presentations, and survival in patients hospitalized with acute heart failure
Authors: Driscoll Andrea , Meagher Sharon , Kennedy Rhoda , Hare David L , Johnson Douglas F , Asker Kristina , Farouque Omar , Romaniuk Helena , Orellana Liliana
Published: November 2022

Aims

Heart failure nurse practitioners (HF NPs) are an emerging component of the heart failure (HF) specialist workforce but their impact in an inpatient setting is untested. The aim of this paper is to explore the impact of an inpatient HF NP service on 12-month all-cause rehospitalizations, emergency department (ED) presentations, and mortality in patients hospitalized with HF compared with usual hospital care.

Methods and results

Retrospective, two-group comparative design involving patients (n = 408) admitted via ED with acute HF to a metropolitan quaternary hospital between January 2013 and August 2017. Doubly robust estimation with augmented inverse probability weighting (DR-AIPW) was used to account for the non-random allocation of patients to usual hospital care or the HF NP service in addition to usual in-hospital care. Among 408 patients (186 usual care and 222 HF NP service) admitted with acute HF, the mean age was 76.5 [standard deviation (SD) 12.0] years and 56.4% (n = 230) were male. After IPW adjustment, patients seen by the HF NP service had a lower risk of 12-month rehospitalization (61.3 vs. 78.3% usual care; difference –16.9%, 95% CI: −26.4%, −6.6%) and ED presentations (12.6 vs. 22.0%; difference –9.4%, 95% CI: –17.3%, –1.4%) with no difference in 6- or 12-month mortality. The HF NP service improved referrals to a home visiting programme that was available to HF patients (64.4 vs. 45.4%; difference 19%, 95% CI: 8.8%, 28.8%).

Conclusion

Additional support by an inpatient HF NP service has the potential to significantly reduce rehospitalizations and ED presentations over 12 months. Further evidence from a multicentre randomized control trial is warranted.
Thioredoxin h2 inhibits the MPKK5-MPK3 cascade to regulate the CBF–COR signaling pathway in Citrullus lanatus suffering chilling stress
Authors: Xu Anqi , Wei Nannan , Hu Hao , Zhou Shu , Huang Yuan , Kong Qiusheng , Bie Zhilong , Nie Wen-Feng , Cheng Fei
Published: November 2022

Thioredoxins (TRXs) are ubiquitous oxidoreductases and present as a multigenic family. TRXs determine the thiol redox balance, which is crucial for plants in the response to cold stress. However, limited knowledge is available about the role of TRXs in watermelon (Citrullus lanatus), which is highly sensitive to chilling stress in agricultural practice. Here, we identified 18 genes encoding 14 typical and 4 atypical TRXs from the watermelon genome, and found that ClTRX h2 localized at the plasma membrane was largely induced by chilling. Virus-induced gene silencing of ClTRX h2 resulted in watermelon plants that were more sensitive to chilling stress. We further found that ClTRX h2 physically interacted with mitogen-activated protein kinase kinase 5 (ClMPKK5), which was confirmed to phosphorylate and activate ClMPK3 in vitro, and the activation of ClMPK3 by ClMPKK5 was blocked by a point mutation of the Cys-229 residue to Ser in ClMPKK5. Additionally, ClTRX h2 inhibited the chilling-induced activation of ClMPK3, suggesting that the ClMPKK5–ClMPK3 cascade is regulated in a redox-dependent manner. We showed that ClMPK3-silenced plants had increased tolerance to chilling, as well as enhanced transcript abundances of the C-repeat/DREB binding factor (ClCBF) and cold-responsive (ClCOR) genes. Taken together, our results indicate that redox status mediated by ClTRX h2 inhibits ClMPK3 phosphorylation through the interaction between ClTRX h2 and ClMPKK5, which subsequently regulates the CBF–COR signaling pathway when submitted to chilling stress. Hence, our results provide a link between thiol redox balance and MAPK cascade signaling, revealing a conceptual framework to understand how TRX regulates chilling stress tolerance in watermelon.
Combined effects of temperature and humidity on the interaction between tomato and Botrytis cinerea revealed by integration of histological characteristics and transcriptome sequencing
Authors: Li Tianzhu , Zhou Jie , Li Jianming
Published: November 2022

The environment significantly impacts the interaction between plants and pathogens, thus remarkably affecting crop disease occurrence. However, the detailed combined mechanisms of temperature and humidity influencing this interaction remain unclear. In this study, the interaction between tomato and Botrytis cinerea in various temperature and humidity conditions was analyzed by histological observation and a dual RNA-seq approach. Results showed that low humidity was not favorable for mycelial growth, resulting in infection failure. Both high and low temperatures at high humidity successfully inhibited pathogenic infection and disease incidence in the tomato plants, thus enhancing their resistance to B. cinerea. The high temperature and high humidity (HH) treatment induced the upregulation of light reaction genes, increased the net photosynthetic rate, and expanded the chloroplast morphology of infected tomatoes. The HH treatment also inhibited the expression of cell cycle-related genes of B. cinerea, interfered with conidial germination and mycelial growth, and damaged mycelial cell structure. Low temperature and high humidity (LH) treatment induced the expression of cell wall modification genes and remodeled the cell wall morphology of tomatoes in response to B. cinerea. In addition, the downregulated fungal catabolic genes and the abnormal increase in electron density of mycelial cells under LH treatment subsequently reduced the infection ability of B. cinerea. These results further explain the coupled effects of temperature and humidity on plant defenses and pathogen virulence, and provide a potential means to control gray mold.
Advances in sequencing and key character analysis of mango (Mangifera indica L.)
Authors: Song Miaoyu , Wang Haomiao , Fan Zhiyi , Huang Hantang , Ma Huiqin
Published: November 2022

Mango (Mangifera indica L.) is an important fruit crop in tropical and subtropical countries associated with many agronomic and horticultural problems, such as susceptibility to pathogens, including powdery mildew and anthracnose, poor yield and quality, and short shelf life. Conventional breeding techniques exhibit significant limitations in improving mango quality due to the characteristics of long ripening, self-incompatibility, and high genetic heterozygosity. In recent years, much emphasis has been placed on identification of key genes controlling a certain trait through genomic association analysis and directly breeding new varieties through transgene or genotype selection of offspring. This paper reviews the latest research progress on the genome and transcriptome sequencing of mango fruit. The rapid development of genome sequencing and bioinformatics provides effective strategies for identifying, labeling, cloning, and manipulating many genes related to economically important traits. Preliminary verification of the functions of mango genes has been conducted, including genes related to flowering regulation, fruit development, and polyphenol biosynthesis. Importantly, modern biotechnology can refine existing mango varieties to meet the market demand with high economic benefits.
Model-informed Precision Dosing for Biologics Is Now Available at the Bedside for Patients With Inflammatory Bowel Disease
Authors: Colman Ruben J , Samuels Abigail , Mizuno Tomoyuki , Punt Nieko , Vinks Alexander A , Minar Phillip
Published: November 2022

Lay Summary

It is increasingly recognized that inconsistent biologic therapeutic response is related to pharmacokinetic variability (drug clearance) between patients. This study highlights a multidisciplinary effort to integrate a precision dosing dashboard within the electronic health record to individualize biologic exposure starting and during induction.
Community pharmacists’ attitudes towards, and experiences of, providing medication reviews after hospital discharge: a questionnaire survey
Authors: Veeren Jennifer C , Rogers Philip J , Taylor Andrea D J , Weiss Marjorie C
Published: November 2022

Objectives

To investigate the attitudes and experiences of community pharmacists providing medicines-use review (MUR) and post-discharge medicines-use review (PD-MUR) services.

Methods

An online survey for community pharmacists who had experience providing the MUR service.

Key findings

In total, 495 community pharmacists responded to the survey. A total of 89% (n = 382) of community pharmacists wanted to receive the patient’s full discharge summary and 79% (n = 363) preferred electronic communication. Community pharmacists thought they could build trusted relationships with patients and felt that patients were willing to discuss post-discharge medicines-related issues with them. Less experienced pharmacists conducted more MURs than more experienced pharmacists (P = 0.004), and pharmacists working in large multiples (>50 pharmacies) conducted more MURs than those working in independent pharmacies (<5 pharmacies) (P = 0.001). Community pharmacists working in independent pharmacies conducted more PD-MURs than those working in large multiples (P = 0.004). Community pharmacists working in rural areas also thought they were best placed to provide PD-MURs while those working in urban areas thought that practice pharmacists were best suited to provide this service (P = 0.007).

Conclusions

Community pharmacists believe they have a vital role in supporting patients after hospital discharge. They can build long-lasting, trusted relationships with patients and patients are willing to discuss medication issues with them. By providing community pharmacists in all locations with timely access to accurate discharge information, they could use their knowledge and skills to better support patients after hospital discharge.
Fighting cheapfakes: using a digital media literacy intervention to motivate reverse search of out-of-context visual misinformation
Authors: Qian Sijia , Shen Cuihua , Zhang Jingwen
Published: November 2022

As a significant source of misinformation, out-of-context visual misinformation refers to visuals presented in an unrelated context. This study explores whether a digital media literacy intervention that features reverse image search tools has significant effects on participants’ message credibility judgment, discernment of visual misinformation, and intention of using reverse image search tools. Data were collected from a pre-registered, web-based, between-subjects experiment (N = 905). Results revealed a significant difference on intention of using reverse search tools among three experimental conditions: active intervention that involved both knowledge and behavior, passive intervention that involved knowledge only, and a control condition. Specifically, active intervention significantly increased intention of using reverse search tools, compared to the passive intervention and the control. Neither active nor passive intervention had an effect on credibility judgment or misinformation discernment. We discuss the implications for future digital media intervention designs and journalism practice that aim to combat visual misinformation.
Laparoscopic Ladd’s procedure: a case report and review of the literature on patient selection for an appropriate surgical approach
Authors: Li Jia Xi Julian , Lim Ranah , Muhlmann Mark Damien
Published: November 2022

Intestinal malrotation is a rare condition which is managed surgically with the Ladd’s procedure. We report a case of an adult male presenting with symptomatic intestinal malrotation which was successfully treated with a laparoscopic Ladd’s procedure. While traditionally performed with a laparotomy, the case highlights the emerging evidence in the literature supporting the laparoscopic approach and explores factors affecting patient selection for an appropriate surgical approach.
Tropical cyclones: what are their impacts on phytoplankton ecology?
Authors: Thompson Peter A , Paerl Hans W , Campbell Lisa , Yin Kedong , McDonald Karlie S
Published: November 2022

Following the passage of a tropical cyclone (TC) the changes in temperature, salinity, nutrient concentration, water clarity, pigments and phytoplankton taxa were assessed at 42 stations from eight sites ranging from the open ocean, through the coastal zone and into estuaries. The impacts of the TC were estimated relative to the long-term average (LTA) conditions as well as before and after the TC. Over all sites the most consistent environmental impacts associated with TCs were an average 41% increase in turbidity, a 13% decline in salinity and a 2% decline in temperature relative to the LTA. In the open ocean, the nutrient concentrations, cyanobacteria and picoeukaryote abundances increased at depths between 100 and 150 m for up to 3 months following a TC. While at the riverine end of coastal estuaries, the predominate short-term response was a strong decline in salinity and phytoplankton suggesting these impacts were initially dominated by advection. The more intermediate coastal water-bodies generally experienced declines in salinity, significant reductions in water clarity, plus significant increases in nutrient concentrations and phytoplankton abundance. These intermediate waters typically developed dinoflagellate, diatom or cryptophyte blooms that elevated phytoplankton biomass for 1–3 months following a TC.
Using teledermatology to prevent and diagnose skin cancer in the rural United States
Authors: Benedit Veronica , Aycock Mallory M.
Published: November 2022

In the United States, skin cancer is a prevalent and sometimes preventable form of cancer that causes a significant disease burden in rural and urban communities. Studies have shown, however, that rural residents are less likely to engage in primary prevention behaviors against skin cancer, and rural populations have higher skin cancer incidence and mortality than urban residents. Teledermatology can be used to address disparities in both skin cancer diagnosis and health education to improve dermatology outcomes in rural communities. This article reviews teledermatology formats, barriers, and benefits to encourage integration of teledermatology modalities into clinical practice.
PAs in Myanmar
Authors: Brown Gina R. , Blue Zu Zae Nar
Published: November 2022

Myanmar might be the most recent country to graduate its first class of physician assistants (PAs). The country has a history of medics serving in underserved areas, but graduated its first six PAs in 2020, after a 5-year training program. These clinicians will care for a largely rural population, who live in areas of unreliable infrastructure and security. The PA profession in Myanmar aims to reduce maternal mortality, graduate 75 PAs by 2029, and improve access to healthcare in remote regions.
Dual antiplatelet therapy for minor ischemic stroke and transient ischemic attack
Authors: Miller Blake , Shealy Kayce M.
Published: November 2022

Traditional preventive management of patients suffering from a minor ischemic stroke and/or transient ischemic attack indicated dual antiplatelet agents for 90 days. Newer clinical trial data suggest that therapeutic effectiveness is reached much sooner than previous guideline recommendations. Continued use of dual antiplatelet therapy beyond newly studied durations of efficacy has shown an increased risk in hemorrhagic complications with little to no additional preventive benefit. This article highlights newer trial data and recognizes a significant change in therapeutic management for patients suffering a minor ischemic stroke and/or transient ischemic attack.