bluuebunny/crossref_metadata_2025 huggingface dataset:
Validation of non-equilibrium kinetics in CO2–N2plasmas
Authors: Fromentin C , Silva T , Dias T C , Baratte E , Guaitella O , Guerra V
Published: April 2023

This work explores the effect of N2addition on CO2dissociation and on the vibrational kinetics of CO2and CO under various non-equilibrium plasma conditions. A self-consistent kinetic model, previously validated for pure CO2and CO2–O2discharges, is further extended by adding the kinetics of N2. The vibrational kinetics considered include levels up tov= 10 for CO,v= 59 for N2and up tov1= 2 andv2=v3= 5, respectively for the symmetric stretch, bending and asymmetric stretch modes of CO2, and account for electron-impact excitation and de-excitation (e–V), vibration-to-translation (V–T) and vibration-to-vibration energy exchange (V–V) processes. The kinetic scheme is validated by comparing the model predictions with recent experimental data measured in a DC glow discharge operating in pure CO2and in CO2–N2mixtures, at pressures in the range 0.6–4 Torr (80.00–533.33 Pa) and a current of 50 mA. The experimental results show a higher vibrational temperature of the different modes of CO2and CO and an increased dissociation fraction of CO2, that can reach values as high as 70%, when N2is added to the plasma. On the one hand, the simulations suggest that the former effect is the result of the CO2–N2and CO–N2V–V transfers and the reduction of quenching due to the decrease of atomic oxygen concentration; on the other hand, the dilution of CO2and dissociation products, CO and O2, reduces the importance of back reactions and contributes to the higher CO2dissociation fraction with increased N2content in the mixture, while the N2(B3Πg) electronically excited state further enhances the CO2dissociation.
Characterization of a superconducting microstrip single-photon detector shunted with an external resistor
Authors: Wang Yu-Ze , Zhang Wei-Jun , Xu Guang-Zhao , Xiong Jia-Min , Fan Dong-Hui , Chen Zhi-Gang , Zhang Xing-Yu , Wang Zhen , You Li-Xing
Published: April 2023

A superconducting microstrip single-photon detector (SMSPD) generally requires a shunt resistor to avoid latching, caused by its high current-carrying capacity and low kinetic inductance. Here, the effect of the shunt resistor on the behaviors of microbridge SMSPDs was investigated. We analyzed the change in equivalent switching current at different shunt resistances in two ways and determined the operating current range using intrinsic dark count rate (iDCR) curves. We observed that the reduction in shunt resistance can increase the operating current range, which helps to improve the internal detection efficiency (IDE) and reduce the iDCR. However, the reduction in the shunt resistance can reduce the pulse amplitude and increase the pulse decay time, which can degrade the timing jitter and count rate performance of the SMSPD. The trends of the experimental results can be qualitatively reproduced using a circuit model for an SMSPD with a shunt resistor, which provides useful information for the selection of shunt resistors. Furthermore, we report the improved detection performance of a helium-ion-irradiated SMSPD shunted with a small resistance of 5.2 Ω. We observed a weak IDE saturation with a bias current at a wavelength up to 2000 nm and a nonlinear relation between detection current and photon energy.
Global dynamics and Impact of Gaussian noise intensity on the stochastic epidemic model with local fractional derivative
Authors: Khan Najeeb Alam , Razzaq Oyoon Abdul , Bajwa Areeba Azam , Ayaz Muhammad
Published: April 2023

Society must understand, model, and forecast infectious disease transmission patterns in order to prevent pandemics. Mathematical models and computer technology may help us better understand the pandemic and create more systematic and effective infection management strategies. This study offers a novel perspective through a compartmental model that incorporates fractional calculus. The first scenario is based on proportional fractional definitions, considering compartmental individuals of susceptible, moving susceptible, exposed, infected, hospitalized, and recovered. Through an extension of this derivative, they decimated the model to integer order. We extended the deterministic model to a stochastic extension to capture the uncertainty or variance in disease transmission. It can develop an appropriate Lyapunov function to detect the presence and uniqueness of positive global solutions. Next, we discuss how the epidemic model might have become extinct. In our theoretical study, we demonstrated that a sufficiently outrageous amount of noise can cause a disease to become extinct. A modest level of noise, on the other hand, promotes the persistence of diseases and their stationary distribution. The Khasminskii method was used to determine the stationary distribution and ergodicity of the model.
Interactions between amphiphilic nanoparticles coated with striped hydrophilic/hydrophobic ligands and a lipid bilayer
Authors: Sun Lijuan , Cao Yu , Chen Xiaojie , Liang Qing
Published: April 2023

Due to their unique physicochemical properties, nanoparticles play an important role in the fields of nanomedicine and so on. In this paper, the interactions between the nanoparticles coated with striped hydrophilic and hydrophobic ligands and a lipid bilayer are investigated by using the coarse-grained molecular dynamics simulation. This study focuses on the effects of the density of the ligands, the ratio of the hydrophilic ligands to the hydrophobic ligands, and the rigidity of the ligands on the interactions of the nanoparticles with the lipid bilayer. The results show that the nanoparticles interact with the lipid bilayer in two different ways. The nanoparticle with a small size, a large ratio of hydrophilic ligands to the hydrophobic ligands, and flexible ligands can readily be inserted into the lipid bilayer, and the nanoparticle rotation is very crucial to the insertion of the nanoparticle into the bilayer. However, the nanoparticle with a large size, a small ratio of hydrophilic ligands to hydrophobic ligands, and rigid ligands can only be adsorbed on the surface of the lipid bilayer. This work provides an effective method to modulate the interactions of the amphiphilic nanoparticles with the lipid bilayers and some insights into the applications of the nanoparticles in drug delivery, cell imaging, etc.
Finding optimal basis states for variation after projection nuclear wave functions*
Authors: Lu Xiao , Lian Zhan-Jiang , Li Xue-Wei , Gao Zao-Chun , Chen Yong-Shou
Published: April 2023

The variation after projection (VAP) method is expected to be an efficient way of obtaining the optimized nuclear wave functions, which can be as close as possible to the exact shell model ones. However, we found that there are two additional problems that may seriously affect the convergence of the VAP iteration. The first problem is the existence of irrelevant projected basis states. At a VAP iteration, the Hill-Wheeler (HW) equation is composed of all updated projected basis states. If one of these projected basis states does not mix with a calculated wave function of interest, which is obtained by solving this HW equation, it is likely that this basis state will never mix with this wave function even after the VAP iteration converges. The other problem is the poor orthonormality among the projected basis states, which seriously affects the accuracy of the calculated VAP wave function. In the present work, solutions for these two problems are proposed, and examples are presented to test the validity. With the present solutions, the most important projected basis states can be reliably obtained, and the fully optimized VAP wave functions can be accurately and efficiently calculated.
Restoring continuous finger function with temporarily paralyzed nonhuman primates using brain–machine interfaces
Authors: Nason-Tomaszewski Samuel R , Mender Matthew J , Kennedy Eric , Lambrecht Joris M , Kilgore Kevin L , Chiravuri Srinivas , Ganesh Kumar Nishant , Kung Theodore A , Willsey Matthew S , Chestek Cynthia A , Patil Parag G
Published: April 2023

Objective. Brain–machine interfaces (BMIs) have shown promise in extracting upper extremity movement intention from the thoughts of nonhuman primates and people with tetraplegia. Attempts to restore a user’s own hand and arm function have employed functional electrical stimulation (FES), but most work has restored discrete grasps. Little is known about how well FES can control continuous finger movements. Here, we use a low-power brain-controlled functional electrical stimulation (BCFES) system to restore continuous volitional control of finger positions to a monkey with a temporarily paralyzed hand. Approach. We delivered a nerve block to the median, radial, and ulnar nerves just proximal to the elbow to simulate finger paralysis, then used a closed-loop BMI to predict finger movements the monkey was attempting to make in two tasks. The BCFES task was one-dimensional in which all fingers moved together, and we used the BMI’s predictions to control FES of the monkey’s finger muscles. The virtual two-finger task was two-dimensional in which the index finger moved simultaneously and independently from the middle, ring, and small fingers, and we used the BMI’s predictions to control movements of virtual fingers, with no FES. Main results. In the BCFES task, the monkey improved his success rate to 83% (1.5 s median acquisition time) when using the BCFES system during temporary paralysis from 8.8% (9.5 s median acquisition time, equal to the trial timeout) when attempting to use his temporarily paralyzed hand. In one monkey performing the virtual two-finger task with no FES, we found BMI performance (task success rate and completion time) could be completely recovered following temporary paralysis by executing recalibrated feedback-intention training one time. Significance. These results suggest that BCFES can restore continuous finger function during temporary paralysis using existing low-power technologies and brain-control may not be the limiting factor in a BCFES neuroprosthesis.
Double scaling limit of the prismatic tensor model
Authors: Krajewski T , Muller T , Tanasa A
Published: April 2023

In Giombi et al (2018 Phys. Rev. D 98 105005), a prismatic tensor model was introduced. We study here the diagrammatics and the double scaling limit of this model, using the intermediate field method. We explicitly exhibit the next-to-leading order Feynman graphs in the

1

/

N

expansion. Using appropriate combinatorial tools, we further study the general term of the

1

/

N

expansion and we compute the two-point function in the double scaling limit. We find that the double scaling limit mechanism implemented here is similar to the one implemented for various quartic tensor models.
Effect of Spraying with Amino Acids (Tryptophan and Glycine) and Nano-Potassium on some Vegetative Growth Characteristics of Stevia Plant (Stevia rebaudiana Bertoni)
Authors: Mahdi Amal Najeh , Abdullah Kadum Mohammed , Almyali Ali Ahmed Hussein
Published: April 2023

Researchers from the College of Agriculture at the University of Kerbala in the Karbala province of Iraq used a greenhouse to examine the effects of nano-potassium and the amino acids tryptophan and glycine on the development of the stevia plant and the concentration of its active substances in the local climate. The experiment had three replicates and was carried out using a factorial trial design within a randomized complete block design (R.C.B.D). The study had three variables. The first component was tryptophan, with three concentrations (0, 25, and 50 mg. L-1), the second factor was glycine, with three concentrations (0, 500, and 1000 mg. L-1), and the third factor was nano-potassium, with two values (0, and 100 nmol L-1) (0, 2 g. L-1). The findings demonstrated that the variables under study, whether acting separately or in combination, significantly improved all characteristics of vegetative development. The triple interaction treatment (50 mg. L-1 tryptophan + 1000 mg. L-1 glycine + 2 g. L-1 potassium) gave the highest percentages for plant height, number of main branches, leaf dry weight, number of total leaves, and total chlorophyll content, where recorded (89.68 cm, 12.67 main branches. plant-1, 48.43 g. plant-1, 189.09 leaves. plant-1, 12,609 mg. 100 g-1 fresh weight, respectively). It may be concluded that the application of an integrated fertilization program can sustain or enhance stevia production in both quantity and quality under challenging environmental circumstances.
Effects of growth temperature on structural and electrical properties of in-rich InAlN–GaN heterostructures by radio-frequency metal–organic molecular beam epitaxy
Authors: Chen Wei-Chun , Chiu Kun-An , Chen Hung-Pin , Lin Yu-Wei , Chen Che-Chin , Chen Fong-Zhi
Published: April 2023

In-rich InAlN is a promising nitride semiconductor alloy for high-efficiency solar cells and wide-range light-emitting diodes due to its tunable bandgap from 0.7 to 6.2 eV. However, incomplete characterization has led to inconsistent fundamental properties in some studies. The aim of this study was to comprehensively investigate the structural, optical, and electrical properties of In-rich InAlN films grown on GaN/Al2O3 templates by RF-MOMBE at various temperatures. The methodology involved state-of-the-art metrology techniques, such as high-resolution x-ray diffraction (HRXRD), scanning electron microscopy (FE-SEM), Hall effect measurements, and transmission electron microscopy (TEM). The results showed that all InxAl1-xN films were epitaxially grown on the GaN/Al2O3 template, with the indium composition (x) decreasing with increasing growth temperature. Furthermore, phase separation of the In-rich InAlN films occurred at high growth temperatures(>550 °C), resulting in a relatively smooth surface. The optical absorption method measured the band-gap of the InxAl1-xN films, which ranged from 1.7 to 1.9 eV for x values between 0.77 and 0.91. The mobility and carrier concentrations of all In-rich InAlN films were measured at ∼60−277 cm2 V−1-s−1 and 2–7 × 1019 cm3 in the growth temperature of range 450 °C–610 °C, respectively. In conclusion, our comprehensive characterization using advanced metrology methods provides valuable insights into the properties of In-rich InAlN films, which can inform future optimization of these materials for various applications.
Inexact restoration for minimization with inexact evaluation both of the objective function and the constraints
Authors: Bueno L. , Larreal F. , Martínez J.
Published: April 2023

In a recent paper an Inexact Restoration method for solving continuous constrained optimization problems was analyzed from the point of view of worst-case functional complexity and convergence. On the other hand, the Inexact Restoration methodology was employed, in a different research, to handle minimization problems with inexact evaluation and simple constraints. These two methodologies are combined in the present report, for constrained minimization problems in which both the objective function and the constraints, as well as their derivatives, are subject to evaluation errors. Together with a complete description of the method, complexity and convergence results will be proved.
The positive mass theorem and distance estimates in the spin setting
Authors: Cecchini Simone , Zeidler Rudolf
Published: April 2023

Let

E

\mathcal {E}

be an asymptotically Euclidean end in an otherwise arbitrary connected Riemannian spin manifold

(
M
,
g
)

(M,g)

. We show that if

E

\mathcal {E}

has negative ADM-mass, then there exists a constant

R
>
0

R > 0

, depending only on

E

\mathcal {E}

, such that

M
M

must become incomplete or have a point of negative scalar curvature in the

R
R

-neighborhood around

E

\mathcal {E}

in

M
M

. This gives a quantitative answer to Schoen and Yau’s question on the positive mass theorem with arbitrary ends for spin manifolds. Similar results have recently been obtained by Lesourd, Unger and Yau [Positive scalar curvature on noncompact manifolds and the liouville theorem, 2020; The positive mass theorem with arbitrary ends, 2021] without the spin condition in dimensions

≤
7

\leq 7

assuming Schwarzschild asymptotics on the end

E

\mathcal {E}

. We also derive explicit quantitative distance estimates in case the scalar curvature is uniformly positive in some region of the chosen end

E

\mathcal {E}

. Here we obtain refined constants reminiscent of Gromov’s metric inequalities with scalar curvature.
Progression of Hodgkin lymphoma and plasma cell neoplasms: Report from the 2021 SH/EAHP Workshop
Authors: Nejati Reza , Amador Catalina , Czader Magdalena , Thacker Elizabeth , Thakkar Devang , Dave Sandeep S , Dogan Ahmet , Duffield Amy , Goodlad John R , Ott German , Wasik Mariusz A , Xiao Wenbin , Cook James R
Published: April 2023

Objectives

To summarize cases submitted to the 2021 Society for Hematopathology/European Association for Haematopathology Workshop under the categories of progression of Hodgkin lymphoma, plasmablastic myeloma, and plasma cell myeloma.

Methods

The workshop panel reviewed 20 cases covered in this session. In addition, whole-exome sequencing (WES) and whole-genome RNA expression analysis were performed on 10 submitted cases, including 6 Hodgkin lymphoma and 4 plasma neoplasm cases.

Results

The cases of Hodgkin lymphoma included transformed cases to or from various types of B-cell lymphoma with 1 exception, which had T-cell differentiation. The cases of plasma cell neoplasms included cases with plasmablastic progression, progression to plasma cell leukemia, and secondary B-lymphoblastic leukemia. Gene variants identified by WES included some known to be recurrent in Hodgkin lymphoma and plasma cell neoplasm. All submitted Hodgkin lymphoma samples showed 1 or more of these mutations: SOCS1, FGFR2, KMT2D, RIT1, SPEN, STAT6, TET2, TNFAIP3, and ZNF217.

Conclusions

Better molecular characterization of both of these neoplasms and mechanisms of progression will help us to better understand mechanisms of progression and perhaps develop better prognostic models, as well as identifying novel therapeutic targets.
Longitudinal Associations Between Neighborhood Child Opportunity and Physical Fitness for New York City Public School Youth
Authors: Zewdie Hiwot Y , Zhao Amy Y , Ogletree S Scott , Messiah Sarah E , Armstrong Sarah C , Skinner Asheley C , Neshteruk Cody D , Hipp J Aaron , Day Sophia E , Konty Kevin J , D’Agostino Emily M
Published: April 2023

Neighborhood environments can support fitness-promoting behavior, yet little is known about their influence on youth physical fitness outcomes over time. We examined longitudinal associations between neighborhood opportunity and youth physical fitness among New York City (NYC) public school youth. The Child Opportunity Index (COI), a composite index of 29 indicators measuring neighborhood opportunity at the census-tract level, along with scores on 4 selected COI indicators were linked to NYC FITNESSGRAM youth data at baseline. Fitness outcomes (measured annually, 2011–2018) included body mass index, curl-ups, push-ups, and Progressive Aerobic Cardiovascular Endurance Run (PACER) laps. Unstratified and age-stratified, adjusted, 3-level generalized linear mixed models, nested by census tract and time, estimated the association between COI and fitness outcomes. The analytical sample (n = 204,939) lived in very low (41%) or low (30%) opportunity neighborhoods. Unstratified models indicated that overall COI is modestly associated with improved youth physical fitness outcomes. The strongest opportunity-fitness associations were observed for PACER. Stratified models show differences in associations across younger vs. older youth. We find that neighborhood factors are associated with youth fitness outcomes over time, with the strength of the associations dependent on age. Future implications include better informed place-based interventions tailored to specific life stages to promote youth health.
Graph deep learning enabled spatial domains identification for spatial transcriptomics
Authors: Liu Teng , Fang Zhao-Yu , Li Xin , Zhang Li-Ning , Cao Dong-Sheng , Yin Ming-Zhu
Published: April 2023

Advancing spatially resolved transcriptomics (ST) technologies help biologists comprehensively understand organ function and tissue microenvironment. Accurate spatial domain identification is the foundation for delineating genome heterogeneity and cellular interaction. Motivated by this perspective, a graph deep learning (GDL) based spatial clustering approach is constructed in this paper. First, the deep graph infomax module embedded with residual gated graph convolutional neural network is leveraged to address the gene expression profiles and spatial positions in ST. Then, the Bayesian Gaussian mixture model is applied to handle the latent embeddings to generate spatial domains. Designed experiments certify that the presented method is superior to other state-of-the-art GDL-enabled techniques on multiple ST datasets. The codes and dataset used in this manuscript are summarized at https://github.com/narutoten520/SCGDL.
DEGGs: an R package with shiny app for the identification of differentially expressed gene–gene interactions in high-throughput sequencing data
Authors: Sciacca Elisabetta , Alaimo Salvatore , Silluzio Gianmarco , Ferro Alfredo , Latora Vito , Pitzalis Costantino , Pulvirenti Alfredo , Lewis Myles J
Published: April 2023

The discovery of differential gene–gene correlations across phenotypical groups can help identify the activation/deactivation of critical biological processes underlying specific conditions. The presented R package, provided with a count and design matrix, extract networks of group-specific interactions that can be interactively explored through a shiny user-friendly interface. For each gene–gene link, differential statistical significance is provided through robust linear regression with an interaction term.

Availability and implementation

DEGGs is implemented in R and available on GitHub at https://github.com/elisabettasciacca/DEGGs. The package is also under submission on Bioconductor.
matchRanges: generating null hypothesis genomic ranges via covariate-matched sampling
Authors: Davis Eric S , Mu Wancen , Lee Stuart , Dozmorov Mikhail G , Love Michael I , Phanstiel Douglas H
Published: April 2023

Motivation

Deriving biological insights from genomic data commonly requires comparing attributes of selected genomic loci to a null set of loci. The selection of this null set is non-trivial, as it requires careful consideration of potential covariates, a problem that is exacerbated by the non-uniform distribution of genomic features including genes, enhancers, and transcription factor binding sites. Propensity score-based covariate matching methods allow the selection of null sets from a pool of possible items while controlling for multiple covariates; however, existing packages do not operate on genomic data classes and can be slow for large data sets making them difficult to integrate into genomic workflows.

Results

To address this, we developed matchRanges, a propensity score-based covariate matching method for the efficient and convenient generation of matched null ranges from a set of background ranges within the Bioconductor framework.

Availability and implementation

Package: https://bioconductor.org/packages/nullranges, Code: https://github.com/nullranges, Documentation: https://nullranges.github.io/nullranges.
FAS: assessing the similarity between proteins using multi-layered feature architectures
Authors: Dosch Julian , Bergmann Holger , Tran Vinh , Ebersberger Ingo
Published: April 2023

Motivation

Protein sequence comparison is a fundamental element in the bioinformatics toolkit. When sequences are annotated with features such as functional domains, transmembrane domains, low complexity regions or secondary structure elements, the resulting feature architectures allow better informed comparisons. However, many existing schemes for scoring architecture similarities cannot cope with features arising from multiple annotation sources. Those that do fall short in the resolution of overlapping and redundant feature annotations.

Results

Here, we introduce FAS, a scoring method that integrates features from multiple annotation sources in a directed acyclic architecture graph. Redundancies are resolved as part of the architecture comparison by finding the paths through the graphs that maximize the pair-wise architecture similarity. In a large-scale evaluation on more than 10 000 human-yeast ortholog pairs, architecture similarities assessed with FAS are consistently more plausible than those obtained using e-values to resolve overlaps or leaving overlaps unresolved. Three case studies demonstrate the utility of FAS on architecture comparison tasks: benchmarking of orthology assignment software, identification of functionally diverged orthologs, and diagnosing protein architecture changes stemming from faulty gene predictions. With the help of FAS, feature architecture comparisons can now be routinely integrated into these and many other applications.

Availability and implementation

FAS is available as python package: https://pypi.org/project/greedyFAS/.
AcrNET: predicting anti-CRISPR with deep learning
Authors: Li Yunxiang , Wei Yumeng , Xu Sheng , Tan Qingxiong , Zong Licheng , Wang Jiuming , Wang Yixuan , Chen Jiayang , Hong Liang , Li Yu
Published: April 2023

Motivation

As an important group of proteins discovered in phages, anti-CRISPR inhibits the activity of the immune system of bacteria (i.e. CRISPR-Cas), offering promise for gene editing and phage therapy. However, the prediction and discovery of anti-CRISPR are challenging due to their high variability and fast evolution. Existing biological studies rely on known CRISPR and anti-CRISPR pairs, which may not be practical considering the huge number. Computational methods struggle with prediction performance. To address these issues, we propose a novel deep neural network for anti-CRISPR analysis (AcrNET), which achieves significant performance.

Results

On both the cross-fold and cross-dataset validation, our method outperforms the state-of-the-art methods. Notably, AcrNET improves the prediction performance by at least 15% regarding the F1 score for the cross-dataset test problem comparing with state-of-art Deep Learning method. Moreover, AcrNET is the first computational method to predict the detailed anti-CRISPR classes, which may help illustrate the anti-CRISPR mechanism. Taking advantage of a Transformer protein language model ESM-1b, which was pre-trained on 250 million protein sequences, AcrNET overcomes the data scarcity problem. Extensive experiments and analysis suggest that the Transformer model feature, evolutionary feature, and local structure feature complement each other, which indicates the critical properties of anti-CRISPR proteins. AlphaFold prediction, further motif analysis, and docking experiments further demonstrate that AcrNET can capture the evolutionarily conserved pattern and the interaction between anti-CRISPR and the target implicitly.

Availability and implementation

Web server: https://proj.cse.cuhk.edu.hk/aihlab/AcrNET/. Training code and pre-trained model are available at.
Predicting the pathogenicity of missense variants using features derived from AlphaFold2
Authors: Schmidt Axel , Röner Sebastian , Mai Karola , Klinkhammer Hannah , Kircher Martin , Ludwig Kerstin U
Published: April 2023

Motivation

Missense variants are a frequent class of variation within the coding genome, and some of them cause Mendelian diseases. Despite advances in computational prediction, classifying missense variants into pathogenic or benign remains a major challenge in the context of personalized medicine. Recently, the structure of the human proteome was derived with unprecedented accuracy using the artificial intelligence system AlphaFold2. This raises the question of whether AlphaFold2 wild-type structures can improve the accuracy of computational pathogenicity prediction for missense variants.

Results

To address this, we first engineered a set of features for each amino acid from these structures. We then trained a random forest to distinguish between relatively common (proxy-benign) and singleton (proxy-pathogenic) missense variants from gnomAD v3.1. This yielded a novel AlphaFold2-based pathogenicity prediction score, termed AlphScore. Important feature classes used by AlphScore are solvent accessibility, amino acid network related features, features describing the physicochemical environment, and AlphaFold2’s quality parameter (predicted local distance difference test). AlphScore alone showed lower performance than existing in silico scores used for missense prediction, such as CADD or REVEL. However, when AlphScore was added to those scores, the performance increased, as measured by the approximation of deep mutational scan data, as well as the prediction of expert-curated missense variants from the ClinVar database. Overall, our data indicate that the integration of AlphaFold2-predicted structures can improve pathogenicity prediction of missense variants.

Availability and implementation

AlphScore, combinations of AlphScore with existing scores, as well as variants used for training and testing are publicly available.
A functional analysis of omic network embedding spaces reveals key altered functions in cancer
Authors: Doria-Belenguer Sergio , Xenos Alexandros , Ceddia Gaia , Malod-Dognin Noël , Pržulj Nataša
Published: April 2023

Motivation

Advances in omics technologies have revolutionized cancer research by producing massive datasets. Common approaches to deciphering these complex data are by embedding algorithms of molecular interaction networks. These algorithms find a low-dimensional space in which similarities between the network nodes are best preserved. Currently available embedding approaches mine the gene embeddings directly to uncover new cancer-related knowledge. However, these gene-centric approaches produce incomplete knowledge, since they do not account for the functional implications of genomic alterations. We propose a new, function-centric perspective and approach, to complement the knowledge obtained from omic data.

Results

We introduce our Functional Mapping Matrix (FMM) to explore the functional organization of different tissue-specific and species-specific embedding spaces generated by a Non-negative Matrix Tri-Factorization algorithm. Also, we use our FMM to define the optimal dimensionality of these molecular interaction network embedding spaces. For this optimal dimensionality, we compare the FMMs of the most prevalent cancers in human to FMMs of their corresponding control tissues. We find that cancer alters the positions in the embedding space of cancer-related functions, while it keeps the positions of the noncancer-related ones. We exploit this spacial ‘movement’ to predict novel cancer-related functions. Finally, we predict novel cancer-related genes that the currently available methods for gene-centric analyses cannot identify; we validate these predictions by literature curation and retrospective analyses of patient survival data.

Availability and implementation

Data and source code can be accessed at https://github.com/gaiac/FMM.
Did the Prison Industrial Complex Deliver on Its Promise? Prison Proliferation and Employment in Rural America
Authors: Zhang Yiwen
Published: April 2023

Two concurrent phenomena emerged in rural America in the 1970s: job losses due to deindustrialization and prison proliferation relating to mass incarceration. While supporters of the prison industrial complex promised an economic lifeline for rural America, opponents questioned the economic benefits of prison openings. Using county fixed-effects models and data covering 1960–2000, this study reveals a null association between prison openings and total rural employment. While prison proliferation marginally increased government employment, it simultaneously had a negative impact on private employment. Specifically, prison openings were associated with decreased employment in manufacturing, finance and recreational services; and had no impact on jobs in construction, wholesale, and local retail sales. Thus, the promises of employment growth relating to prisons were, overall, not kept.
Moderate-to-Severe Diarrhea and Stunting Among Children Younger Than 5 Years: Findings From the Vaccine Impact on Diarrhea in Africa (VIDA) Study
Authors: Nasrin Dilruba , Liang Yuanyuan , Powell Helen , Casanova Ines Gonzalez , Sow Samba O , Hossain M Jahangir , Omore Richard , Sanogo Doh , Tamboura Boubou , Zaman Syed M A , Antonio Martin , Jones Joquina Chiquita M , Awuor Alex O , Kasumba Irene N , Ochieng John B , Badji Henry , Verani Jennifer R , Widdowson Marc-Alain , Roose Anna , Jamka Leslie P , Tennant Sharon M , Ramakrishnan Usha , Kotloff Karen L
Published: April 2023

Background

Stunting affects >20% of children <5 years old worldwide and disproportionately impacts underserved communities. The Vaccine Impact on Diarrhea in Africa (VIDA) Study examined the association between an episode of moderate-to-severe diarrhea (MSD) and the risk of subsequent stunting in children <5 years living in 3 sub-Saharan African countries.

Methods

In this prospective, matched, case-control study among children <5 years, data were collected over 36 months from 2 groups. “Children with MSD” visited a health center within 7 days of illness onset experiencing ≥3 loose stools/day plus sunken eyes, poor skin turgor, dysentery, intravenous rehydration, or hospitalization. “Children without MSD” were enrolled from the community within 14 days of the index MSD child; they were diarrhea-free during the previous 7 days and were matched to the index case by age, sex, and residence. Using generalized linear mixed-effects models, we estimated the effect of an MSD episode on odds of being stunted, defined as height-for-age z-scores <−2, at a follow-up visit 2–3 months post-enrollment.

Results

The proportion of stunting at enrollment was similar when 4603 children with MSD and 5976 children without MSD were compared (21.8% vs 21.3%; P = .504). Among children not stunted at enrollment, those with MSD had 30% higher odds of being stunted at follow-up than children without MSD after controlling for age, sex, study site, and socioeconomic status (adjusted OR: 1.30; 95% CI: 1.05–1.62: P = .018).

Conclusions

Children <5 years in sub-Saharan Africa without stunting experienced an increased likelihood of stunting during 2–3 months following an episode of MSD. Strategies for control of early childhood diarrhea should be integrated into programs intended to reduce childhood stunting.
Stunting Following Moderate-to-Severe Diarrhea Among Children Aged <5 Years in Africa Before and After Rotavirus Vaccine Introduction: A Comparison of the Global Enteric Multicenter Study and the Vaccine Impact on Diarrhea in Africa (VIDA) Study
Authors: Nasrin Dilruba , Liang Yuanyuan , Verani Jennifer R , Powell Helen , Sow Samba O , Omore Richard , Hossain M Jahangir , Doh Sanogo , Zaman Syed M A , Jones Joquina Chiquita M , Awuor Alex O , Kasumba Irene N , Tennant Sharon M , Ramakrishnan Usha , Kotloff Karen L
Published: April 2023

Background

Studies conducted before rotavirus vaccine introduction found that moderate-to-severe diarrhea (MSD) in children aged <5 years was associated with stunting at follow-up. It is unknown whether the reduction in rotavirus-associated MSD following vaccine introduction decreased the risk of stunting.

Methods

The Global Enteric Multicenter Study (GEMS) and the Vaccine Impact on Diarrhea in Africa (VIDA) study, two comparable matched case-control studies, were conducted during 2007–2011 and 2015–2018, respectively. We analyzed data from 3 African sites where rotavirus vaccine was introduced after GEMS and before starting VIDA. Children with acute MSD (<7 days onset) were enrolled from a health center and children without MSD (diarrhea-free for ≥7 days) were enrolled at home within 14 days of the index MSD case. The odds of being stunted at a follow-up visit 2–3 months after enrollment for an episode of MSD was compared between GEMS and VIDA using mixed-effects logistic regression models controlling for age, sex, study site, and socioeconomic status.

Results

We analyzed data from 8808 children from GEMS and 10 579 from VIDA. Among those who were not stunted at enrollment in GEMS, 8.6% with MSD and 6.4% without MSD became stunted during the follow-up period. In VIDA, 8.0% with MSD and 5.5% children without MSD developed stunting. An episode of MSD was associated with higher odds of being stunted at follow-up compared with children without MSD in both studies (adjusted odds ratio [aOR], 1.31; 95% confidence interval [CI]: 1.04–1.64 in GEMS and aOR, 1.30; 95% CI: 1.04–1.61 in VIDA). However, the magnitude of association was not significantly different between GEMS and VIDA (P = .965).

Conclusions

The association of MSD with subsequent stunting among children aged <5 years in sub-Saharan Africa did not change after rotavirus vaccine introduction. Focused strategies are needed for prevention of specific diarrheal pathogens that cause childhood stunting.
Antibiotic-Prescribing Practices for Management of Childhood Diarrhea in 3 Sub-Saharan African Countries: Findings From the Vaccine Impact on Diarrhea in Africa (VIDA) Study, 2015–2018
Authors: Awuor Alex O , Ogwel Billy , Powell Helen , Verani Jennifer R , Sow Samba O , Hossain M Jahangir , Ochieng John B , Juma Jane , Jamka Leslie P , Roose Anna , Doh Sanogo , Deichsel Emily L , Onwuchekwa Uma , Keita Adama Mamby , Antonio Martin , Jones Joquina Chiquita M , Zaman Syed M A , Badji Henry , Kasumba Irene N , Nasrin Dilruba , Platts-Mills James A , Houpt Eric R , Berendes David M , Sugerman Ciara E , Widdowson Marc-Alain , Tennant Sharon M , Mintz Eric D , Omore Richard , Kotloff Karen L
Published: April 2023

Background

Despite antibiotic prescription being recommended for dysentery and suspected cholera only, diarrhea still triggers unwarranted antibiotic prescription. We evaluated antibiotic-prescribing practices and their predictors among children aged 2–59 months in the Vaccine Impact on Diarrhea in Africa (VIDA) Study performed in The Gambia, Mali, and Kenya.

Methods

VIDA was a prospective case-control study (May 2015–July 2018) among children presenting for care with moderate-to-severe diarrhea (MSD). We defined inappropriate antibiotic use as prescription or use of antibiotics when not indicated by World Health Organization (WHO) guidelines. We used logistic regression to assess factors associated with antibiotic prescription for MSD cases who had no indication for an antibiotic, at each site.

Results

VIDA enrolled 4840 cases. Among 1757 (36.3%) who had no apparent indication for antibiotic treatment, 1358 (77.3%) were prescribed antibiotics. In The Gambia, children who presented with a cough (adjusted odds ratio [aOR]: 2.05; 95% confidence interval [95% CI]: 1.21–3.48) were more likely to be prescribed an antibiotic. In Mali, those who presented with dry mouth (aOR: 3.16; 95% CI: 1.02–9.73) were more likely to be prescribed antibiotics. In Kenya, those who presented with a cough (aOR: 2.18; 95% CI: 1.01–4.70), decreased skin turgor (aOR: 2.06; 95% CI: 1.02–4.16), and were very thirsty (aOR: 4.15; 95% CI: 1.78–9.68) were more likely to be prescribed antibiotics.

Conclusions

Antibiotic prescription was associated with signs and symptoms inconsistent with WHO guidelines, suggesting the need for antibiotic stewardship and clinician awareness of diarrhea case-management recommendations in these settings.
Epidemiology of Enteroaggregative, Enteropathogenic, and Shiga Toxin–ProducingEscherichia coliAmong Children Aged <5 Years in 3 Countries in Africa, 2015–2018: Vaccine Impact on Diarrhea in Africa (VIDA) Study
Authors: Ochieng John B , Powell Helen , Sugerman Ciara E , Omore Richard , Ogwel Billy , Juma Jane , Awuor Alex O , Sow Samba O , Sanogo Doh , Onwuchekwa Uma , Keita Adama Mamby , Traoré Awa , Badji Henry , Hossain M Jahangir , Jones Joquina Chiquita M , Kasumba Irene N , Nasrin Dilruba , Roose Anna , Liang Yuanyuan , Jamka Leslie P , Antonio Martin , Platts-Mills James A , Liu Jie , Houpt Eric R , Mintz Eric D , Hunsperger Elizabeth , Onyango Clayton O , Strockbine Nancy , Widdowson Marc-Alain , Verani Jennifer R , Tennant Sharon M , Kotloff Karen L
Published: April 2023

Background

To address knowledge gaps regarding diarrheagenic Escherichia coli (DEC) in Africa, we assessed the clinical and epidemiological features of enteroaggregative E. coli (EAEC), enteropathogenic E. coli (EPEC), and Shiga toxin–producing E. coli (STEC) positive children with moderate-to-severe diarrhea (MSD) in Mali, The Gambia, and Kenya.

Methods

Between May 2015 and July 2018, children aged 0–59 months with medically attended MSD and matched controls without diarrhea were enrolled. Stools were tested conventionally using culture and multiplex polymerase chain reaction (PCR), and by quantitative PCR (qPCR). We assessed DEC detection by site, age, clinical characteristics, and enteric coinfection.

Results

Among 4840 children with MSD and 6213 matched controls enrolled, 4836 cases and 1 control per case were tested using qPCR. Of the DEC detected with TAC, 61.1% were EAEC, 25.3% atypical EPEC (aEPEC), 22.4% typical EPEC (tEPEC), and 7.2% STEC. Detection was higher in controls than in MSD cases for EAEC (63.9% vs 58.3%, P < .01), aEPEC (27.3% vs 23.3%, P < .01), and STEC (9.3% vs 5.1%, P < .01). EAEC and tEPEC were more frequent in children aged <23 months, aEPEC was similar across age strata, and STEC increased with age. No association between nutritional status at follow-up and DEC pathotypes was found. DEC coinfection with Shigella/enteroinvasive E. coli was more common among cases (P < .01).

Conclusions

No significant association was detected between EAEC, tEPEC, aEPEC, or STEC and MSD using either conventional assay or TAC. Genomic analysis may provide a better definition of the virulence factors associated with diarrheal disease.
Clinical and Epidemiologic Features of Cryptosporidium-Associated Diarrheal Disease Among Young Children Living in Sub-Saharan Africa: The Vaccine Impact on Diarrhea in Africa (VIDA) Study
Authors: Hossain M Jahangir , Powell Helen , Sow Samba O , Omore Richard , Roose Anna , Jones Joquina Chiquita M , Zaman Syed M A , Badji Henry , Sarwar Golam , Kasumba Irene N , Onwuchekwa Uma , Doh Sanogo , Awuor Alex O , Ochieng John B , Verani Jennifer R , Liu Jie , Tennant Sharon M , Nasrin Dilruba , Jamka Leslie P , Liang Yuanyuan , Howie Stephen R C , Antonio Martin , Houpt Eric R , Kotloff Karen L
Published: April 2023

Background

As part of the Vaccine Impact on Diarrhea in Africa (VIDA) Study, we examined the prevalence, clinical presentation, and seasonality of Cryptosporidium in children to understand its relative burden after the introduction of rotavirus vaccine.

Methods

VIDA was a 3-year, age-stratified, matched case-control study of medically attended acute moderate-to-severe diarrhea (MSD) in children aged 0–59 months residing in censused populations at sites in Kenya, Mali, and The Gambia. Clinical and epidemiologic data were collected at enrollment, and a stool sample was tested for enteropathogens by quantitative PCR. An algorithm was created based on the organism's cycle threshold (Ct) and association with MSD to identify the subset of Cryptosporidium PCR-positive (Ct <35) cases most likely to be attributed to MSD. Clinical outcomes were assessed at 2–3 months after enrollment.

Results

One thousand one hundred six (22.9%) cases of MSD and 873 controls (18.1%) were PCR positive for Cryptosporidium; 465 cases (42.0%) were considered attributable to Cryptosporidium, mostly among children 6–23 months. Cryptosporidium infections peaked in The Gambia and Mali during the rainy season, while in Kenya they did not have clear seasonality. Compared with cases with watery MSD who had a negative PCR for Cryptosporidium, cases with watery MSD attributed to Cryptosporidium were less frequently dehydrated but appeared more severely ill using a modified Vesikari scale (38.1% vs 27.0%; P < 0.001), likely due to higher rates of hospitalization and intravenous fluid administration, higher prevalence of being wasted or very thin very thin (23.4% vs 14.7%; P < 0.001), and having severe acute malnutrition (midupper arm circumference <115 mm, 7.7% vs 2.5%; P < 0.001). On follow-up, Cryptosporidium-attributed cases had more prolonged and persistent episodes (43.2% vs 32.7%; P <0 .001) and linear growth faltering (change in height-for-age z score between enrollment and follow-up: −0.29 vs −0.17; P < 0.001).

Conclusions

The burden of Cryptosporidium remains high among young children in sub-Saharan Africa. Its propensity to cause illness and further impact children longer term by compromising nutritional status early in life calls for special attention to enable appropriate management of clinical and nutritional consequences.
Health Communication Research Informs Inflammatory Bowel Disease Practice and Research: A Narrative Review
Authors: Karimi Neda , Moore Alison Rotha , Lukin Annabelle , Connor Susan J
Published: April 2023

Background

In the absence of targeted empirical evidence on effective clinical communication in inflammatory bowel disease (IBD), a broad overview of existing evidence on effective communication in healthcare and available recommendations for communication in telehealth is provided and mapped onto IBD research and practice.

Methods

A narrative literature review was conducted using Pubmed and Scopus databases and snowballing literature search.

Results

Evidence-based relationship building strategies include communicating emotions, acknowledging and addressing patients’ hesitancy, and ensuring continued support. A particular recommendation regarding telehealth interaction is to avoid long stretches of talk. Effective informational strategies include facilitating and supporting information exchange and considering patients’ preferences in decision-making. In teleconsultations, clinicians should ask direct questions about patients’ emotional state, clarify their understanding of patients’ concerns and check patients’ understanding, address at least one patient-reported outcome when discussing the recommended treatment, and shorten the consultation where possible. Strategies for maximizing effective clinical communication in the spoken communicative mode include using infographics and simple language, and assessing adherence at the beginning of the consultation. For teleconsultations, clinicians are advised to allow patients to explain the reason for their call at the beginning of the teleconsultation, probe additional concerns early and before ending the teleconsultation, and be mindful of technical issues such as voice delays.

Conclusions

Use of question prompt lists, decision aids, micro-lessons, and communication training interventions for clinicians could be beneficial in IBD care. Further research into the implementation of such interventions as well as clinical communication concerns specific to IBD is warranted.