bluuebunny/crossref_metadata_2025_split huggingface dataset:
A new ensemble-based targeted observational method and its application in the TPOS 2020
Authors: Rao Weixun , Tang Youmin , Wu Yanling , Shen Zheqi , Song Xiangzhou , Li Xiaojing , Lian Tao , Chen Dake , Zhou Feng 
Published: September 2023

ABSTRACT
Ensemble Kalman filter-based targeted observation is one of the best methods for determining the optimal observational array for oceanic buoy deployment. This study proposes a new algorithm suitable for a ‘cross-region and cross-variable’ approach by introducing a projection operator into the optimization process. A targeted observational analysis was conducted for El Niño–Southern Oscillation (ENSO) events in the tropical western Pacific for the Tropical Pacific Observation System (TPOS) 2020. The prediction target was at the Niño 3.4 region and the first 10 optimal observational sites detected reduced initial uncertainties by 70%, with the best observational array located where the Rossby wave signal dominates. At the vertical level, the most significant contribution was derived from observations near the thermocline. This study provides insights into understanding ENSO-related variability and offers a practical approach to designing an optimal mooring array. It serves as a scientific guidance for designing a TPOS observation network.
Species-specific ecological traits, phylogeny, and geography underpin vulnerability to population declines for North American birds
Authors: Stevens Henry C , Smith Adam C , Buechley Evan R , Şekercioğlu Çağan H , Shirey Vaughn , Rosenberg Kenneth V , La Sorte Frank A , Tallamy Douglas , Marra Peter P 
Published: September 2023

Abstract
Species declines and extinctions characterize the Anthropocene. Determining species vulnerability to decline, and where and how to mitigate threats, are paramount for effective conservation. We hypothesized that species with shared ecological traits also share threats, and therefore may experience similar population trends. Here, we used a Bayesian modeling framework to test whether phylogeny, geography, and 22 ecological traits predict regional population trends for 380 North American bird species. Groups like blackbirds, warblers, and shorebirds, as well as species occupying Bird Conservation Regions at more extreme latitudes in North America, exhibited negative population trends; whereas groups such as ducks, raptors, and waders, as well as species occupying more inland Bird Conservation Regions, exhibited positive trends. Specifically, we found that in addition to phylogeny and breeding geography, multiple ecological traits contributed to explaining variation in regional population trends for North American birds. Furthermore, we found that regional trends and the relative effects of migration distance, phylogeny, and geography differ between shorebirds, songbirds, and waterbirds. Our work provides evidence that multiple ecological traits correlate with North American bird population trends, but that the individual effects of these ecological traits in predicting population trends often vary between different groups of birds. Moreover, our results reinforce the notion that variation in avian population trends is controlled by more than phylogeny and geography, where closely related species within one region can show unique population trends due to differences in their ecological traits. We recommend that regional conservation plans, i.e. one-size-fits-all plans, be implemented only for bird groups with population trends under strong phylogenetic or geographic controls. We underscore the need to develop species-specific research and management strategies for other groups, like songbirds, that exhibit high variation in their population trends and are influenced by multiple ecological traits.
Impact of apolipoprotein A1 on tumor immune microenvironment, clinical prognosis and genomic landscape in hepatocellular carcinoma
Authors: Wang Ying , Chen Shipeng , Xiao Xiao , Yang Fan , Wang Jinhan , Zong Hui , Gao Yuzhen , Huang Chenjun , Xu Xuewen , Fang Meng , Zhang Xiaoyan , Gao Chunfang 
Published: September 2023

Abstract

Background
Current knowledge on apolipoprotein A1 (APOA1) in hepatocellular carcinoma (HCC) is fragmented and even contradictory. Multi-dimensional analyses are required to comprehensively elucidate its value and underlying mechanism.

Methods
We collected 49 RNA-seq datasets, 40 cell line types data and 70 scRNA pan-cancer datasets public available, including 17 HCC datasets (1754 tumor samples), and enrolled 73 pairs of HCC tissue and 516 blood samples independently from our clinics. APOA1 impacting on the HCC tumor microenvironment (TME) was analyzed using intensive data mining. Methylation sequencing, flow cytometry, quantitative PCR, western blot, immunohistochemistry and clinical chemistry assays were conducted for wet experimental investigation.

Results
The APOA1 ontology fingerprint indicated that it played various crucial biological roles in HCC, primarily involved in cholesterol efflux. Consistent findings at histology, serology, and clinical follow-up revealed that high APOA1 was a good prognosis indicator of HCC. Hypermethylation in the APOA1 promoter region was found in clinical samples which is in accordance with the reduction of APOA1 in HCC. The cell cycle, DNA replication, mismatch repair pathways, and tumor cell proliferation were less observed in the HCC APOA1high subgroup. The favorable immunoregulatory abilities of APOA1 showed interesting findings: a positive correlation between APOA1 and anti-tumor immune cells (NK, CD8+ T cells) and a negative association with immune cells exerting immunosuppressive effects, including M2 macrophages.

Conclusion
This is an integrative multidimensional exploration of APOA1 using bioinformatics and experiments. Both the prognostic value and anti-tumor effects based on APOA1 panoramic exploration in the HCC TME demonstrate a new potential clinical target for HCC assessment and intervention in the future.
Finding the Optimal Resistance Training Intensity for Your Bones: Protocol for a Randomized Controlled Trial
Authors: Giangregorio Lora M , Bleakney Robert R , Brien Sheila , Butcher Scotty J , Chan Brian C F , Chilibeck Philip D , Devries Michaela C , Funnell Larry , Jain Ravi , Keller Heather H , Milligan James , Mourtzakis Marina , O’Hare Bonny S , Thabane Lehana , Cheung Angela M 
Published: September 2023

Abstract

Objective
The purpose of this trial is to evaluate the effect of twice-weekly, moderate-to-high intensity progressive resistance training (PRT) for 1 year on lumbar spine bone mineral density (BMD) in individuals with low BMD, compared to attention control. Secondary analyses will examine if resistance training improves other health outcomes; if high intensity is more effective than moderate intensity resistance training for all outcomes; the cost of intervention versus benefit; the willingness to pay; and harms.

Methods
For this study, 324 men or postmenopausal women aged ≥50 years with a femoral neck, total hip, or lumbar spine BMD T-score of ≤−1, or a Fracture Risk Assessment Tool probability of ≥20% for major osteoporotic fracture or ≥ 3% for hip fracture are being recruited to participate in a randomized controlled trial with 1:1:1 randomization. Participants will be stratified by site (3 centers) to twice-weekly, supervised PRT at moderate intensity (about 10 repetitions maximum), to high intensity PRT (≤6 repetitions maximum), or to a home posture and balance exercise program (attention control) for 1 year (resistance training to comparator allocation ratio of 2:1). The primary outcome is lumbar spine BMD via dual-energy X-ray absorptiometry. Secondary outcomes include trabecular bone score, proximal femur and total hip BMD and structure, bone-free and appendicular lean mass, physical functioning, falls, fractures, glucose metabolism, cost per life-year gained, adverse events, and quality of life. Between-group differences will be tested in intention-to-treat and per-protocol analyses using analysis of covariance, chi-square tests, or negative binomial or logistic regression, adjusting for site and baseline values.

Impact
The Finding the Optimal Resistance Training Intensity For Your Bones trial will support decision making on resistance training for people at risk of fracture.
A reduction procedure and pipeline for the detection of trans-Neptunian objects using occultations
Authors: Nir Guy , Ofek Eran O , Zackay Barak 
Published: September 2023

Abstract
Kuiper belt objects smaller than a few kilometres are difficult to observe directly. They can be detected when they randomly occult a background star. Close to the ecliptic plane, each star is occulted once every tens of thousands of hours, and occultations typically last for less than a second. We present an algorithm, and companion pipeline, for detection of diffractive occultation events. Our approach includes: cleaning the data; an efficient and optimal matched filtering of the light curves with a template bank of diffractive occultations; treating the red-noise in the light curves; injection of simulated events for efficiency estimation; and applying data quality cuts. We discuss human vetting of the candidate events in a blinded way to reduce bias caused by the human-in-the-loop. We present Markov Chain Monte Carlo tools to estimate the parameters of candidate occultations, and test them on simulated events. This pipeline is used by the W-FAST. The methods discussed here can be applied to searches for other Trans-Neptunian objects, albeit with larger radii that correspond to a larger diffraction length scale.
Association of interpregnancy interval and risk of adverse pregnancy outcomes in woman by different previous gestational ages
Authors: Chen Peiran , Mu Yi , Liu Zheng , Wang Yanping , Li Xiaohong , Dai Li , Li Qi , Li Mingrong , Xie Yanxia , Liang Juan , Zhu Jun 
Published: September 2023

Abstract

Background:
With an increasing proportion of multiparas, proper interpregnancy intervals (IPIs) are urgently needed. However, the association between IPIs and adverse perinatal outcomes has always been debated. This study aimed to explore the association between IPIs and adverse outcomes in different fertility policy periods and for different previous gestational ages.

Methods:
We used individual data from China's National Maternal Near Miss Surveillance System between 2014 and 2019. Multivariable Poisson models with restricted cubic splines were used. Each adverse outcome was analyzed separately in the overall model and stratified models. The stratified models included different categories of fertility policy periods (2014–2015, 2016–2017, and 2018–2019) and infant gestational age in previous pregnancy (<28 weeks, 28–36 weeks, and ≥37 weeks).

Results:
There were 781,731 pregnancies enrolled in this study. A short IPI (≤6 months) was associated with an increased risk of preterm birth (OR [95% CI]: 1.63 [1.55, 1.71] for vaginal delivery [VD] and 1.10 [1.03, 1.19] for cesarean section [CS]), low Apgar scores and small for gestational age (SGA), and a decreased risk of diabetes mellitus in pregnancy, preeclampsia or eclampsia, and gestational hypertension. A long IPI (≥60 months) was associated with an increased risk of preterm birth (OR [95% CI]: 1.18 [1.11, 1.26] for VD and 1.39 [1.32, 1.47] for CS), placenta previa, postpartum hemorrhage, diabetes mellitus in pregnancy, preeclampsia or eclampsia, and gestational hypertension. Fertility policy changes had little effect on the association of IPIs and adverse maternal and neonatal outcomes. The estimated risk of preterm birth, low Apgar scores, SGA, diabetes mellitus in pregnancy, and gestational hypertension was more profound among women with previous term births than among those with preterm births or pregnancy loss.

Conclusion:
For pregnant women with shorter or longer IPIs, more targeted health care measures during pregnancy should be formulated according to infant gestational age in previous pregnancy.
Quercetin enhances decidualization through AKT-ERK-p53 signaling and supports a role for senescence in endometriosis
Authors: Delenko Julia , Xue Xiangying , Chatterjee Prodyot K , Hyman Nathaniel , Shih Andrew J , Adelson Robert P , Safaric-Tepes Polona , Gregersen Peter K , Metz Christine N 
Published: September 2023

AbstractQuercetin, a flavonoid with senolytic activity, has attracted great interest as a therapy for fibrotic diseases such as pulmonary fibrosis, a disorder attributed to senescent pulmonary fibroblasts. Interestingly, quercetin has shown some benefit in pre-clinical models of endometriosis, an inflammatory condition characterized by senescent endometrial stromal cells and in severe cases, intraperitoneal fibrotic lesions and infertility. Quercetin exerts multiple biological activities but the signaling pathways underlying quercetin’s effects are not well-defined. In this report, we have analyzed the signaling pathways underlying quercetin’s action using menstrual effluent-derived endometrial stromal cells. We found that quercetin promotes decidualization, a well-defined differentiation process known to be defective in patients with endometriosis using cells obtained from endometriosis patients and unaffected controls. We show that quercetin substantially reduces the phosphorylation of multiple signaling molecules in the AKT and ERK1/2 pathways. In contrast, we observed striking phosphorylation of p53 and increased p53 protein expression. Furthermore, p53 inhibition blocks decidualization while p53 activation promotes decidualization. Finally, we provide evidence that quercetin increases apoptosis of endometrial stromal cells with a senescence phenotype. These data provide insight into mechanisms of action of quercetin in the setting of endometriosis and support studies to test senolytics for treating endometriosis.
Self-Focused Brain Predictors of Cognitive Behavioral Therapy Response in a Transdiagnostic Sample
Authors: Fang Angela , Baran Bengi , Feusner Jamie D. , Phan K. Luan , Beatty Clare C. , Crane Jessica , Jacoby Ryan J. , Manoach Dara S. , Wilhelm Sabine 
Published: September 2023

AbstractBackgroundEffective biomarkers of cognitive behavioral therapy (CBT) response provide information beyond available behavioral or self-report measures and may optimize treatment selection for patients based on likelihood of benefit. No single biomarker reliably predicts CBT response. In this study, we evaluated patterns of brain connectivity associated with self-focused attention (SFA) as biomarkers of CBT response for anxiety and obsessive-compulsive disorders. We hypothesized that pre-treatment as well as pre- to post-treatment changes in functional connectivity would be associated with improvement during CBT in a transdiagnostic sample.MethodsTwenty-seven patients with primary social anxiety disorder (n=14) and primary body dysmorphic disorder (n=13) were scanned before and after 12 sessions of CBT targeting their primary disorder. Eligibility was based on elevated trait SFA scores on the Public Self-Consciousness Scale. Seed-based resting state functional connectivity associated with symptom improvement was computed using a seed in the posterior cingulate cortex/precuneus that delineated a self-other functional network.ResultsAt pre-treatment, stronger positive connectivity of the seed with the cerebellum, insula, middle occipital gyrus, postcentral gyrus, and precuneus/superior parietal lobule, and stronger negative connectivity with the putamen, were associated with greater clinical improvement. Between pre- to post-treatment, greater anticorrelation between the seed and precuneus/superior parietal lobule was associated with clinical improvement, although this did not survive thresholding.ConclusionsPre-treatment functional connectivity between regions involved in attentional salience, self-generated thoughts, and external attention predicted greater CBT response. Behavioral and self-report measures of SFA did not contribute to predictions, thus highlighting the value of neuroimaging-based measures of SFA.Clinical Trials RegistrationClinicalTrials.gov Identifier:NCT02808702https://clinicaltrials.gov/ct2/show/NCT02808702
COVID-19-related school closures, United States, July 27, 2020 – June 30, 2022
Authors: Zviedrite Nicole , Jahan Ferdous , Moreland Sarah , Ahmed Faruque , Uzicanin Amra 
Published: September 2023

AbstractAs part of a multi-year project that monitored illness-related school closures, we conducted systematic daily online searches from July 27, 2020–June 30, 2022, to identify public announcements of COVID-19-related school closures (COVID-SCs) in the US lasting ≥1 day. We explored the temporospatial patterns of COVID-SCs and analyzed associations between COVID-SCs and national COVID-19 surveillance data. COVID-SCs reflected national surveillance data: correlation was highest between COVID-SCs and both new PCR test positivity (correlation coefficient, r = 0·73, CI: 0·56, 0·84) and new cases (r = 0·72, CI: 0·54, 0·83) in school year (SY) 2020-21, and with hospitalization rates among all ages (rs = 0·81, CI: [0·67, 0·89]) in SY 2021-22. The number of reactive COVID-SCs during SYs 2020-21 and 2021-22 greatly exceeded previously observed numbers of illness-related reactive school closures in the US, notably being nearly 5-fold greater than reactive closures observed during the 2009 H1N1 Pandemic (H1N1pdm09 virus).Article summary lineCOVID-19-related school closures occurred annually in the US and their temporal patterns mirror the general patterns of COVID-19 activity at the national level as observed through routine COVID-19 epidemiological surveillance.
Contrast sensitivity: a fundamental limit to vision restoration after V1 damage
Authors: Yang Jingyi , Saionz Elizabeth L. , Cavanaugh Matthew R. , Fahrenthold Berkeley K. , Melnick Michael D. , Tadin Duje , Briggs Farran , Carrasco Marisa , Huxlin Krystel R. 
Published: September 2023

AbstractStroke damage to the primary visual cortex (V1) causes severe visual deficits, which benefit from perceptual retraining. However, whereas training with high-contrast stimuli can locally restore orientation and direction discrimination abilities at trained locations, it only partially restores luminance contrast sensitivity (CS). Recent work revealed that high-contrast discrimination abilities may be preserved in the blind field of some patients early after stroke. Here, we asked if CS for orientation and direction discrimination is similarly preserved inside the blind field, to what extent, and whether it could benefit from a visual training intervention. Thirteen subacute (<3 months post-V1-stroke) and 12 chronic (>6 months post-V1-stroke) participants were pre-tested, then trained to discriminate either orientation or motion direction of Gabor patches of progressively lower contrasts. At baseline, more subacute than chronic participants could correctly discriminate the orientation of high-contrast Gabors in their blind field, but all failed to perform this task at lower contrasts, even when 10Hz flicker or motion direction were added. Training improved CS in a greater portion of subacute than chronic participants, but no-one attained normal CS, even when stimuli contained flicker or motion. We conclude that, unlike the near-complete training-induced restoration of high-contrast orientation and direction discrimination, there is limited capacity for restoring CS after V1 damage in adulthood. Our results suggest that CS involves different neural substrates and computations than those required for orientation and direction discrimination in V1-damaged visual systems.Significance statementStroke-induced V1 damage in adult humans induces a rapid and severe impairment of contrast sensitivity for orientation and direction discrimination in the affected hemifield, although discrimination of high-contrast stimuli can persist for months. Adaptive training with Gabor patches of progressively lower contrasts improves contrast sensitivity for these discriminations in the blind-field of both subacute (<3 months post-stroke) and chronic (>6 months post-stroke) participants, although it fails to restore fully-normal contrast sensitivity. Nonetheless, more subacute than chronic stroke participants benefit from such training, particularly when discriminating the orientation of static, non-flickering targets. Thus, contrast sensitivity appears critically dependent on processing within V1, with perceptual training displaying limited potential to fully restore it after V1 damage.
Validating risk prediction models for multiple primaries and competing cancer outcomes in families with Li-Fraumeni syndrome using clinically ascertained data at a single institute
Authors: Nguyen Nam H. , Dodd-Eaton Elissa B. , Corredor Jessica L. , Woodman-Ross Jacynda , Green Sierra , Hernandez Nathaniel D. , Gutierrez Barrera Angelica M. , Arun Banu K. , Wang Wenyi 
Published: September 2023

AbstractPurposeThere exists a barrier between developing and disseminating risk prediction models in clinical settings. We hypothesize this barrier may be lifted by demonstrating the utility of these models using incomplete data that are collected in real clinical sessions, as compared to the commonly used research cohorts that are meticulously collected.Patients and methodsGenetic counselors (GCs) collect family history when patients (i.e., probands) come to MD Anderson Cancer Center for risk assessment of Li-Fraumeni syndrome, a genetic disorder characterized by deleterious germline mutations in theTP53gene. Our clinical counseling-based (CCB) cohort consists of 3,297 individuals across 124 families (522 cases of single primary cancer and 125 cases of multiple primary cancers). We applied our software suite LFSPRO to make risk predictions and assessed performance in discrimination using area under the curve (AUC), and in calibration using observed/expected (O/E) ratio.ResultsFor prediction of deleteriousTP53mutations, we achieved an AUC of 0.81 (95% CI, 0.70 – 0.91) and an O/E ratio of 0.96 (95% CI, 0.70 – 1.21). Using the LFSPRO.MPC model to predict the onset of the second cancer, we obtained an AUC of 0.70 (95% CI, 0.58 – 0.82). Using the LFSPRO.CS model to predict the onset of different cancer types as the first primary, we achieved AUCs between 0.70 and 0.83 for sarcoma, breast cancer, or other cancers combined.ConclusionWe describe a study that fills in the critical gap in knowledge for the utility of risk prediction models. Using a CCB cohort, our previously validated models have demonstrated good performance and outperformed the standard clinical criteria. Our study suggests better risk counseling may be achieved by GCs using these already-developed mathematical models.
Supervised Learning for CT Denoising and Deconvolution Without High-Resolution Reference Images
Authors: Missert Andrew D. , Hsieh Scott S. , Ferrero Andrea , McCollough Cynthia H. 
Published: September 2023

AbstractPurposeConvolutional neural networks (CNNs) have been proposed for super-resolution in CT, but training of CNNs requires high-resolution reference data. Higher spatial resolution can also be achieved using deconvolution, but conventional deconvolution approaches amplify noise. We develop a CNN that mitigates increasing noise and that does not require higher-resolution reference images.MethodsOur model includes a noise reduction CNN and a deconvolution CNN that are separately trained. The noise reduction CNN is a U-Net, similar to other noise reduction CNNs found in the literature. The deconvolution CNN uses an autoencoder, where the decoder is fixed and provided as a hyperparameter that represents the system point spread function. The encoder is trained to provide a deconvolution that does not amplify noise. Ringing can occur from deconvolution but is controlled with a difference of gradients loss function term. Our technique was demonstrated on a variety of patient images and on ex vivo kidney stones.ResultsThe noise reduction and deconvolution CNNs produced visually sharper images at low noise. In ex vivo mixed kidney stones, better visual delineation of the kidney stone components could be seen.ConclusionsA noise reduction and deconvolution CNN improves spatial resolution and reduces noise without requiring higher-resolution reference images.