bluuebunny/crossref_metadata_2025_split huggingface dataset:
The LUMIERE dataset: Longitudinal Glioblastoma MRI with expert RANO evaluation
Authors: Suter Yannick , Knecht Urspeter , Valenzuela Waldo , Notter Michelle , Hewer Ekkehard , Schucht Philippe , Wiest Roland , Reyes Mauricio 
Published: December 2022

AbstractPublicly available Glioblastoma (GBM) datasets predominantly include pre-operative Magnetic Resonance Imaging (MRI) or contain few follow-up images for each patient. Access to fully longitudinal datasets is critical to advance the refinement of treatment response assessment. We release a single-center longitudinal GBM MRI dataset with expert ratings of selected follow-up studies according to the response assessment in neuro-oncology criteria (RANO). The expert rating includes details about the rationale of the ratings. For a subset of patients, we provide pathology information regarding methylation of the O6-methylguanine-DNA methyltransferase (MGMT) promoter status and isocitrate dehydrogenase 1 (IDH1), as well as the overall survival time. The data includes T1-weighted pre- and post-contrast, T2-weighted, and fluid-attenuated inversion recovery (FLAIR) MRI. Segmentations from state-of-the-art automated segmentation tools, as well as radiomic features, complement the data. Possible applications of this dataset are radiomics research, the development and validation of automated segmentation methods, and studies on response assessment. This collection includes MRI data of 91 GBM patients with a total of 638 study dates and 2487 images.
A Brazilian classified data set for prognosis of tuberculosis, between January 2001 and April 2020
Authors: Lino Ferreira da Silva Barros Maicon Herverton , Santos Guto Leoni , de Almeida Rodrigues Maria Gabriela , Sampaio Vanderson , Lynn Theo , Endo Patricia Takako 
Published: December 2022

AbstractAfter COVID-19, tuberculosis (TB) is the leading cause of death by an infectious disease in the world. This work presents a data set based on data collected from the Brazilian Information System for Notifiable Diseases (SINAN) for the period from January 2001 to April 2020 relating to patients diagnosed with tuberculosis in Brazil. The data from SINAN was pre-processed to generate a new data set with two distinct treatment outcome classes: CURED and DIED. The data set comprises 37 categorical attributes (including socio-demographic, clinical, and laboratory data) as well as the target class. There are 927,909 records of patients classified as CURED and 36,190 classified as DIED, totaling 964,099 records.
Chloroplast genome assemblies and comparative analyses of commercially important Vaccinium berry crops
Authors: Fahrenkrog Annette M. , Matsumoto Gabriel O. , Toth Katalin , Jokipii-Lukkari Soile , Salo Heikki M. , Häggman Hely , Benevenuto Juliana , Munoz Patricio R. 
Published: December 2022

AbstractVaccinium is a large genus of shrubs that includes a handful of economically important berry crops. Given the numerous hybridizations and polyploidization events, the taxonomy of this genus has remained the subject of long debate. In addition, berries and berry-based products are liable to adulteration, either fraudulent or unintentional due to misidentification of species. The availability of more genomic information could help achieve higher phylogenetic resolution for the genus, provide molecular markers for berry crops identification, and a framework for efficient genetic engineering of chloroplasts. Therefore, in this study we assembled five Vaccinium chloroplast sequences representing the economically relevant berry types: northern highbush blueberry (V. corymbosum), southern highbush blueberry (V. corymbosum hybrids), rabbiteye blueberry (V. virgatum), lowbush blueberry (V. angustifolium), and bilberry (V. myrtillus). Comparative analyses showed that the Vaccinium chloroplast genomes exhibited an overall highly conserved synteny and sequence identity among them. Polymorphic regions included the expansion/contraction of inverted repeats, gene copy number variation, simple sequence repeats, indels, and single nucleotide polymorphisms. Based on their in silico discrimination power, we suggested variants that could be developed into molecular markers for berry crops identification. Phylogenetic analysis revealed multiple origins of highbush blueberry plastomes, likely due to the hybridization events that occurred during northern and southern highbush blueberry domestication.
Effect of weekend catch-up sleep on high-sensitivity C-reactive protein levels according to bedtime inconsistency: a population-based cross-sectional study
Authors: Park Soyoung , Kang Dong Yoon , Ahn Hyungwoo , Kim Namwoo , Yoon Jeong-Hwa , Yang Bo Ram 
Published: December 2022

AbstractTo investigate the associations of weekend catch-up sleep (WCS) and high-sensitivity C-reactive protein (hs-CRP) levels according to bedtime inconsistency in the Korean population. In this cross-sectional study using the Korea National Health and Nutrition Examination Survey (2016–2018) with 17,665 participants, four groups were defined: no-WCS (WCS within ± 1 h of weekday sleep time), moderate WCS (1 ≤ , < 3 h), severe WCS (≥ 3 h), and inverse WCS (≤ − 1 h). An inconsistent bedtime was defined as a > 2 h difference between weekend and weekday bedtimes. Outcomes were divided into quartiles based on the hs-CRP level: Lowest (< 0.34), Middle-low (≥ 0.34, < 0.55), Middle-high (≥ 0.55, < 1.10), Highest (≥ 1.10). Adjusted odds ratios (aORs) with 95% confidence intervals (CIs) were calculated using multinomial logistic regression, controlling for relevant covariates. Moderate WCS was associated with a lower risk for the highest hs-CRP levels than no WCS (aOR = 0.87, 95% CI 0.78–0.97), and a similar association was observed only in participants with consistent bedtimes (aOR = 0.88, 95% CI 0.78–0.99). Significant interactions of those associations of WCS and hs-CRP levels with bedtime inconsistency were found. These findings provide evidence that people with inconsistent bedtimes would have limited protective effect of WCS on hs-CRP.
Visual outcomes, spectacle independence, and patient satisfaction of pseudophakic mini-monovision using a new monofocal intraocular lens
Authors: Park Ella SeoYeon , Ahn Hyunmin , Han Sung Uk , Jun Ikhyun , Seo Kyoung Yul , Kim Eung Kweon , Kim Tae-im 
Published: December 2022

AbstractModified monovision—or “mini-monovision”—is an alternative method to multifocal intraocular lenses (IOLs) for treating presbyopia. This study aimed to evaluate the clinical outcomes of patients bilaterally implanted with the new enhanced monofocal Tecnis Eyhance (ICB00) IOLs with the mini-monovision technique to improve near vision. In this retrospective case series, the medical records of 50 patients (100 eyes) who underwent bilateral cataract surgery were reviewed. Patients were divided into the Emmetropia and Mini-monovision groups based on the postoperative spherical equivalent and residual myopia. The binocular visual acuity for far (4 m), intermediate (66 cm), and near (40 cm) distances, binocular defocus curves, contrast sensitivity, visual symptoms, spectacle independence, and patient satisfaction rates were evaluated at 3 months postoperatively. The binocular uncorrected distance and intermediate visual acuities, contrast sensitivity, incidence of photic phenomena, and patient satisfaction were not significantly different between the two groups (p > 0.05). However, the binocular uncorrected near visual acuities and spectacle independence rates were significantly better in the Mini-monovision group (p < 0.001). Conclusively, the pseudophakic mini-monovision technique using enhanced monofocal IOLs may be a promising option for presbyopia correction in patients unsuitable for multifocal IOLs.
Baseline gene expression profiling determines long-term benefit to programmed cell death protein 1 axis blockade
Authors: Vathiotis Ioannis A. , Salichos Leonidas , Martinez-Morilla Sandra , Gavrielatou Niki , Aung Thazin Nwe , Shafi Saba , Wong Pok Fai , Jessel Shlomit , Kluger Harriet M. , Syrigos Konstantinos N. , Warren Sarah , Gerstein Mark , Rimm David L. 
Published: December 2022

AbstractTreatment with immune checkpoint inhibitors has altered the course of malignant melanoma, with approximately half of the patients with advanced disease surviving for more than 5 years after diagnosis. Currently, there are no biomarker methods for predicting outcome from immunotherapy. Here, we obtained transcriptomic information from a total of 105 baseline tumor samples comprising two cohorts of patients with advanced melanoma treated with programmed cell death protein 1 (PD-1)-based immunotherapies. Gene expression profiles were correlated with progression-free survival (PFS) within consecutive clinical benefit intervals (i.e., 6, 12, 18, and 24 months). Elastic net binomial regression models with cross validation were utilized to compare the predictive value of distinct genes across time. Lasso regression was used to generate a signature predicting long-term benefit (LTB), defined as patients who remain alive and free of disease progression at 24 months post treatment initiation. We show that baseline gene expression profiles were consistently able to predict long-term immunotherapy outcomes with high accuracy. The predictive value of different genes fluctuated across consecutive clinical benefit intervals, with a distinct set of genes defining benefit at 24 months compared to earlier outcomes. A 12-gene signature was able to predict LTB following anti-PD-1 therapy with an area under the curve (AUC) equal to 0.92 and 0.74 in the training and validation set, respectively. Evaluation of LTB, via a unique signature may complement objective response classification and characterize the logistics of sustained antitumor immune responses.
Smartphone accelerometer data as a proxy for clinical data in modeling of bipolar disorder symptom trajectory
Authors: Bennett Casey C. , Ross Mindy K. , Baek EuGene , Kim Dohyeon , Leow Alex D. 
Published: December 2022

AbstractBeing able to track and predict fluctuations in symptoms of mental health disorders such as bipolar disorder outside the clinic walls is critical for expanding access to care for the global population. To that end, we analyze a dataset of 291 individuals from a smartphone app targeted at bipolar disorder, which contains rich details about their smartphone interactions (including typing dynamics and accelerometer motion) collected everyday over several months, along with more traditional clinical features. The aim is to evaluate whether smartphone accelerometer data could serve as a proxy for traditional clinical data, either by itself or in combination with typing dynamics. Results show that accelerometer data improves the predictive performance of machine learning models by nearly 5% over those previously reported in the literature based only on clinical data and typing dynamics. This suggests it is possible to elicit essentially the same “information” about bipolar symptomology using different data sources, in a variety of settings.
Self-assembled endogenous DNA nanoparticles for auto-release and expression of the eGFP gene in Bacillus subtilis
Authors: Cao Linfeng , Meng Ziwen , Tan Junjie , Ying Ming , Bi Meiying , Liu Yanjun , Tong Xinrui , Wei Jiaxun , Huang Lei 
Published: December 2022

AbstractThe development of DNA delivery techniques is critical to promote the wider use of deoxyribonucleic acids as cellular transporters. The present study aimed to develop a type of DNA nanoparticle (citZ-box) to automatically load and release cargo. The restriction enzyme can cleave citZ-boxes at pro-designed sites, and the enhanced green fluorescent protein gene (eGFP) can be delivered into the B. subtilis protoplasts by them. The process of eGFP expression is recorded using a confocal microscope over 4 h. Here, multiscaffold and multimodular designs are used for citZ-box assembly with a DAEDALUS module, DX_cage_design and rem (edge_length, 21), to ensure the structure was predicted as B-type DNA. Finally the citZ-box is estimated to be a 50.7 nm cube. The 3D structure of the citZ-box particle is detected to be approximately 50.3 ± 0.3 nm. DNA nanoparticles prepared as citZ-boxes have great potential as drug carriers with automatic loading and releasing abilities.
CryoEM structures of anion exchanger 1 capture multiple states of inward- and outward-facing conformations
Authors: Zhekova Hristina R. , Jiang Jiansen , Wang Weiguang , Tsirulnikov Kirill , Kayık Gülru , Khan Hanif Muhammad , Azimov Rustam , Abuladze Natalia , Kao Liyo , Newman Debbie , Noskov Sergei Yu. , Tieleman D. Peter , Hong Zhou Z. , Pushkin Alexander , Kurtz Ira 
Published: December 2022

AbstractAnion exchanger 1 (AE1, band 3) is a major membrane protein of red blood cells and plays a key role in acid-base homeostasis, urine acidification, red blood cell shape regulation, and removal of carbon dioxide during respiration. Though structures of the transmembrane domain (TMD) of three SLC4 transporters, including AE1, have been resolved previously in their outward-facing (OF) state, no mammalian SLC4 structure has been reported in the inward-facing (IF) conformation. Here we present the cryoEM structures of full-length bovine AE1 with its TMD captured in both IF and OF conformations. Remarkably, both IF-IF homodimers and IF-OF heterodimers were detected. The IF structures feature downward movement in the core domain with significant unexpected elongation of TM11. Molecular modeling and structure guided mutagenesis confirmed the functional significance of residues involved in TM11 elongation. Our data provide direct evidence for an elevator-like mechanism of ion transport by an SLC4 family member.
Neural complexity is a common denominator of human consciousness across diverse regimes of cortical dynamics
Authors: Frohlich Joel , Chiang Jeffrey N. , Mediano Pedro A. M. , Nespeca Mark , Saravanapandian Vidya , Toker Daniel , Dell’Italia John , Hipp Joerg F. , Jeste Shafali S. , Chu Catherine J. , Bird Lynne M. , Monti Martin M. 
Published: December 2022

AbstractWhat is the common denominator of consciousness across divergent regimes of cortical dynamics? Does consciousness show itself in decibels or in bits? To address these questions, we introduce a testbed for evaluating electroencephalogram (EEG) biomarkers of consciousness using dissociations between neural oscillations and consciousness caused by rare genetic disorders. Children with Angelman syndrome (AS) exhibit sleep-like neural dynamics during wakefulness. Conversely, children with duplication 15q11.2-13.1 syndrome (Dup15q) exhibit wake-like neural dynamics during non-rapid eye movement (NREM) sleep. To identify highly generalizable biomarkers of consciousness, we trained regularized logistic regression classifiers on EEG data from wakefulness and NREM sleep in children with AS using both entropy measures of neural complexity and spectral (i.e., neural oscillatory) EEG features. For each set of features, we then validated these classifiers using EEG from neurotypical (NT) children and abnormal EEGs from children with Dup15q. Our results show that the classification performance of entropy-based EEG biomarkers of conscious state is not upper-bounded by that of spectral EEG features, which are outperformed by entropy features. Entropy-based biomarkers of consciousness may thus be highly adaptable and should be investigated further in situations where spectral EEG features have shown limited success, such as detecting covert consciousness or anesthesia awareness.
Spatial analysis of aquatic food access can inform nutrition-sensitive policy
Authors: Bennett Abigail , Rice Emma , Muhonda Park , Kaunda Emmanuel , Katengeza Sam , Liverpool-Tasie Lenis Saweda O. , Belton Ben , Infante Dana M. , Ross Jared , Virdin John , Gondwe Edith 
Published: December 2022

AbstractAquatic foods are critical for food and nutrition security in Malawi, but it is unclear which populations benefit from different aquatic foods and what factors shape food access. Spatial analysis of food flows across value chains from Lake Malawi to domestic consumers shows that usipa (Engraulicypris sardella) reaches more consumers than chambo (Oreochromis karongae) across all Malawi districts, particularly rural populations. Higher number of markets, nutrient content, and overall supply coupled with lower retail prices and volumes make usipa more accessible to consumers than chambo. Spatial analysis of food flows can guide policymakers towards supporting fisheries that reach vulnerable populations and designing interventions that enhance physical and economic access to fish.
Theory of holey twistsonic media
Authors: López María Rosendo , Zhang Zhiwang , Torrent Daniel , Christensen Johan 
Published: December 2022

AbstractRotating two overlapping lattices relative to each other produces the well known moiré interference patterns and has surprisingly led to strongly correlated superconductivity in twisted bilayer graphene. This seminal effect that is associated with electrons occupying flat dispersion bands has stimulated a surge of activities in classical wave physics such as acoustics to explore equivalent scenarios. Here, we mimic twisted bilayer physics by employing a rigorous sound wave expansion technique to conduct band engineering in holey bilayer plates, i.e., twistsonic media. Our numerical findings show how one flexibly is able to design moiré sound interference characteristics that alone are controlled by the twist angle and the interlayer air separation. More specifically, our numerical approach provides a significant advantage in both computational speed and storage size in comparison with widely used commercial finite-element-method solvers. We foresee that our findings should stimulate further studies in terms of band engineering and exotic topological twisted phases.
Robust estimates for the decadal evolution of Agulhas leakage from the 1960s to the 2010s
Authors: Rühs Siren , Schmidt Christina , Schubert René , Schulzki Tobias G. , Schwarzkopf Franziska U. , Le Bars Dewi , Biastoch Arne 
Published: December 2022

AbstractAgulhas leakage, the transport of warm and salty waters from the Indian Ocean into the South Atlantic, has been suggested to increase under anthropogenic climate change, due to strengthening Southern Hemisphere westerly winds. The resulting enhanced salt transport into the South Atlantic may counteract the projected weakening of the Atlantic overturning circulation through warming and ice melting. Here we combine existing and new observation- and model-based Agulhas leakage estimates to robustly quantify its decadal evolution since the 1960s. We find that Agulhas leakage very likely increased between the mid-1960s and mid-1980s, in agreement with strengthening winds. Our models further suggest that increased leakage was related to enhanced transport outside eddies and coincided with strengthened Atlantic overturning circulation. Yet, it appears unlikely that Agulhas leakage substantially increased since the 1990s, despite continuously strengthening winds. Our results stress the need to better understand decadal leakage variability to detect and predict anthropogenic trends.
Fast multi-source nanophotonic simulations using augmented partial factorization
Authors: Lin Ho-Chun , Wang Zeyu , Hsu Chia Wei 
Published: December 2022

AbstractNumerical solutions of Maxwell’s equations are indispensable for nanophotonics and electromagnetics but are constrained when it comes to large systems, especially multi-channel ones such as disordered media, aperiodic metasurfaces and densely packed photonic circuits where the many inputs require many large-scale simulations. Conventionally, before extracting the quantities of interest, Maxwell’s equations are first solved on every element of a discretization basis set that contains much more information than is typically needed. Furthermore, such simulations are often performed one input at a time, which can be slow and repetitive. Here we propose to bypass the full-basis solutions and directly compute the quantities of interest while also eliminating the repetition over inputs. We do so by augmenting the Maxwell operator with all the input source profiles and all the output projection profiles, followed by a single partial factorization that yields the entire generalized scattering matrix via the Schur complement, with no approximation beyond discretization. This method applies to any linear partial differential equation. Benchmarks show that this approach is 1,000–30,000,000 times faster than existing methods for two-dimensional systems with about 10,000,000 variables. As examples, we demonstrate simulations of entangled photon backscattering from disorder and high-numerical-aperture metalenses that are thousands of wavelengths wide.
Evaluating Research Transparency and Openness in Communication Sciences and Disorders Journals
Authors: Schroeder Scott R. , Gaeta Laura , El Amin Mariam , Chow Jason C. , Borders James C. 
Published: December 2022

Purpose:
To improve the credibility, reproducibility, and clinical utility of research findings, many scientific fields are implementing transparent and open research practices. Such open science practices include researchers making their data publicly available and preregistering their hypotheses and analyses. A way to enhance the adoption of open science practices is for journals to encourage or require submitting authors to participate in such practices. Accordingly, the American Speech-Language-Hearing Association's Journals Program has recently announced their intention to promote open science practices. Here, we quantitatively assess the extent to which several journals in communication sciences and disorders (CSD) encourage or require participation in several open science practices by using the Transparency and Openness Promotion (TOP) Factor metric.

Method:
TOP Factors were assessed for 34 CSD journals, as well as several journals in related fields. TOP Factors measure the level of implementation across 10 open science–related practices (e.g., data transparency, analysis plan preregistration, and replication) for a total possible score of 29 points.

Results:

Collectively, CSD journals had very low TOP Factors (
M
= 1.4, range: 0–8). The related fields of Psychology (
M
= 4.0), Rehabilitation (
M
= 3.2), Linguistics (
M
= 1.7), and Education (
M
= 1.6) also had low scores, though Psychology and Rehabilitation had higher scores than CSD.

Conclusion:
CSD journals currently have low levels of encouraging or requiring participation in open science practices, which may impede adoption.

Open Science Form:

https://doi.org/10.23641/asha.21699458
Air–ground trajectory tracking for autonomous mobile robot based on model predictive hybrid tracking control and multiple harmonics time‐varying disturbance observer
Authors: Xiong Shixun , Chen Mengting , Wei ZiQiang , Jiang Linghai 
Published: December 2022

AbstractThis paper studies a model predictive hybrid tracking control scheme under a multiple harmonics time‐varying disturbance observer for a discrete‐time dynamics nonholonomic autonomous mobile robot (AMR) with disturbance. To solve the robust tracking control problem of the AMR and unmanned aerial vehicle (UAV) air–ground cooperative, a hybrid tracking control strategy combined with improved model predictive control (MPC) method is presented. First, a time‐varying air‐ground cooperative tracking control model based on the nonholonomic constraints AMR and UAV is established by polar coordinate transformation. Second, to estimate disturbances of the time‐varying model, a multiple harmonics disturbance observer with time‐varying gains is designed. A hybrid tracking control scheme for the AMR based on the estimated states and MPC method with relaxing factor and kinematics constraints is proposed. Finally, experimental results show the effectiveness of the proposed control strategy.