bluuebunny/crossref_metadata_2025_split huggingface dataset:
Image-encoded biological and non-biological variables may be used as shortcuts in deep learning models trained on multisite neuroimaging data
Authors: Souza Raissa , Wilms Matthias , Camacho Milton , Pike G Bruce , Camicioli Richard , Monchi Oury , Forkert Nils D 
Published: September 2023

Abstract

Objective
This work investigates if deep learning (DL) models can classify originating site locations directly from magnetic resonance imaging (MRI) scans with and without correction for intensity differences.

Material and Methods
A large database of 1880 T1-weighted MRI scans collected across 41 sites originally for Parkinson’s disease (PD) classification was used to classify sites in this study. Forty-six percent of the datasets are from PD patients, while 54% are from healthy participants. After preprocessing the T1-weighted scans, 2 additional data types were generated: intensity-harmonized T1-weighted scans and log-Jacobian deformation maps resulting from nonlinear atlas registration. Corresponding DL models were trained to classify sites for each data type. Additionally, logistic regression models were used to investigate the contribution of biological (age, sex, disease status) and non-biological (scanner type) variables to the models’ decision.

Results
A comparison of the 3 different types of data revealed that DL models trained using T1-weighted and intensity-harmonized T1-weighted scans can classify sites with an accuracy of 85%, while the model using log-Jacobian deformation maps achieved a site classification accuracy of 54%. Disease status and scanner type were found to be significant confounders.

Discussion
Our results demonstrate that MRI scans encode relevant site-specific information that models could use as shortcuts that cannot be removed using simple intensity harmonization methods.

Conclusion
The ability of DL models to exploit site-specific biases as shortcuts raises concerns about their reliability, generalization, and deployability in clinical settings.
A framework for understanding label leakage in machine learning for health care
Authors: Davis Sharon E , Matheny Michael E , Balu Suresh , Sendak Mark P 
Published: September 2023

Abstract

Introduction
The pitfalls of label leakage, contamination of model input features with outcome information, are well established. Unfortunately, avoiding label leakage in clinical prediction models requires more nuance than the common advice of applying “no time machine rule.”

Framework
We provide a framework for contemplating whether and when model features pose leakage concerns by considering the cadence, perspective, and applicability of predictions. To ground these concepts, we use real-world clinical models to highlight examples of appropriate and inappropriate label leakage in practice.

Recommendations
Finally, we provide recommendations to support clinical and technical stakeholders as they evaluate the leakage tradeoffs associated with model design, development, and implementation decisions. By providing common language and dimensions to consider when designing models, we hope the clinical prediction community will be better prepared to develop statistically valid and clinically useful machine learning models.
Dietary lysolecithin supplementation improves growth performance of weaned piglets via improving nutrients absorption, lipid metabolism, and redox status
Authors: Liu Yang , Wu Aimin , Mo Ruixia , Zhou Qiang , Song Lianghui , Li Zheng , Zhao Hua , Fang Zhengfeng , Lin Yan , Xu Shengyu , Feng Bin , Zhuo Yong , Wu De , Che Lianqiang 
Published: September 2023

AbstractLysolecithin is widely used as emulsifier to improve the digestibility and retention of fat. The current study aimed to investigate the effects of dietary lysolecithin supplementation on growth performance, nutrients absorption, lipid metabolism, and redox status of weaned pigs. A total of 60 weaned piglets were assigned into 2 dietary treatments in a randomized complete block design, receiving basal diet with 0 or 1,000 mg/kg lysolecithin for a period of 28 d. Each dietary treatment had 10 replicates with 3 piglets per replicate. Growth performance and fecal score were monitored during trial. Samples of blood, ileum, and liver tissues were collected and analyzed for serology, intestinal histomorphology, and lipid metabolism-related gene and protein expressions. Dietary lysolecithin supplementation increased average daily gain (+15%, P &lt; 0.05) and tended to increase average daily feed intake (+14%, P = 0.08) in overall experimental period. At final, the average body weight of piglets in lysolecithin group was 10% greater than that of control group (P = 0.09). In addition, dietary lysolecithin supplementation improved the ability of nutrients absorption as indicated by the higher d-xylose level in plasma (P &lt; 0.05). Moreover, piglets from lysolecithin group had higher concentration of high-density lipoprotein (P &lt; 0.05), but lower triglyceride (P &lt; 0.05) in plasma. The inclusion of lysolecithin in diet increased the level of reduced glutathione (GSH) and GSH to oxidized glutathione (GSSG) ratio in plasma and liver (P &lt; 0.05), but attenuated the levels of malondialdehyde and GSSG in ileum (P &lt; 0.05). The upregulation of lipogenesis-related genes (FAS and ACC), downregulation of lipolysis (PNPLA2 and PABP1), and lipid mobilization (PGC-1α and SRIT1) genes were observed in lysolecithin relative to control piglets. Compared with control group, dietary lysolecithin supplementation upregulated protein expressions of GPX4, SREBP1, and LPL in liver and LPL in ileum (P &lt; 0.05). Collectively, our study indicates that dietary lysolecithin supplementation improved growth performance of weaned piglets, which may be associated with the improved nutrients absorption, redox status, and lipid metabolism.
Racism, public pedagogy, and the construction of a United States values infrastructure, 1661–2023: a critical reflection
Authors: Becnel Barbara 
Published: September 2023

ABSTRACT
This paper argues that public pedagogy—an educational activity that takes place outside of the traditional classroom setting—has had a potent impact on the history of racism in the United States of America (USA). Yet this paper questions why the education academy’s scholarship has not shown a commensurate focus on the subdiscipline of public pedagogy, particularly racialized public pedagogy. I explore these topics by first examining a fateful confluence of historical circumstances involving slave codes and indentured servant laws governing low-income white workers, laws passed by the Barbados Assembly in 1661, that made their way across the Atlantic to be lifted, word for word, by leaders of colonial territories that became the USA. These laws ended up regulating not only the legal status of black slaves and white indentured servants in the USA, but also regulating social relations between those same black and white people. The resulting black–white social relations led to the evolution of racialized customs in what eventually became the USA, inspiring practices that undergirded black inferiority and white superiority for hundreds of years. Those customs contributed to the construction of what I have labelled a United States (US) values infrastructure dominated by racism, which I contend is a racialized values infrastructure that exists to this day. To gain more insight into this phenomenon, this paper considers the question: how might the complexity of racialized public pedagogy be addressed in the scholarship of education literature and be imagined in a way to fit into an anti-racist curriculum?
Measuring Social Inclusion in Europe: a non-additive approach with the expert-preferences of public policy planners
Authors: Carrino Ludovico , Farnia Luca , Giove Silvio 
Published: September 2023

Abstract
This paper introduces a normative, expert-informed, time-dependent index of Social Inclusion for European administrative regions in five countries, using longitudinal data from Eurostat. Our contribution is twofold: first, our indicator is based on a non-additive aggregation operator (the Choquet Integral), which allows us to model many preferences’ structures and to overcome the limitations embedded in other approaches. Second, we elicit the parameters of the aggregation operator from an expert panel of Italian policymakers in Social Policy, and Economics scholars. Our results highlight that Mediterranean countries exhibit lower Inclusion levels than Northern/Central countries, and that this disparity has grown in the last decade. Our results complement and partially challenge existing evidence from data-driven aggregation methods.
13C-labeling reveals non-conventional pathways providing carbon for hydroxy fatty acid synthesis in Physaria fendleri
Authors: Cocuron Jean-Christophe , Alonso Ana Paula 
Published: September 2023

Abstract
Physaria fendleri is a member of the Brassicaceae that produces in its embryos hydroxy fatty acids, constituents of oils that are very valuable and widely used by industry for cosmetics, lubricants, biofuels, etc. Free of toxins and rich in hydroxy fatty acids, Physaria provides a promising alternative to imported castor oil and is on the verge of being commercialized. This study aims to identify important biochemical step(s) for oil synthesis in Physaria, which may serve as target(s) for future crop improvement. To advance towards this goal, the endosperm composition was analysed by LC-MS/MS to develop and validate culture conditions that mimic the development of the embryos in planta. Using developing Physaria embryos in culture and 13C-labeling, our studies revealed that: (i) Physaria embryos metabolize carbon into biomass with an efficiency significantly lower than other photosynthetic embryos; (ii) the plastidic malic enzyme provides 42% of the pyruvate used for de novo fatty acid synthesis, which is the highest measured so far in developing ‘green’ oilseed embryos; and (iii) Physaria uses non-conventional pathways to channel carbon into oil, namely the Rubisco shunt, which fixes CO2 released in the plastid, and the reversibility of isocitrate dehydrogenase, which provides additional carbon for fatty acid elongation.
Aggregated gene co-expression networks predict transcription factor regulatory landscapes in grapevine
Authors: Orduña Luis , Santiago Antonio , Navarro-Payá David , Zhang Chen , Wong Darren C J , Matus José Tomás 
Published: September 2023

Abstract
Gene co-expression networks (GCNs) have not been extensively studied in non-model plants. However, the rapid accumulation of transcriptome datasets in certain species represents an opportunity to explore underutilized network aggregation approaches. In fact, aggregated GCNs (aggGCNs) highlight robust co-expression interactions and improve functional connectivity. We applied and evaluated two different aggregation methods on public grapevine RNA-Seq datasets from three different tissues (leaf, berry, and ‘all organs’). Our results show that co-occurrence-based aggregation generally yielded the best-performing networks. We applied aggGCNs to study several transcription factor gene families, showing their capacity for detecting both already-described and novel regulatory relationships between R2R3-MYBs, bHLH/MYC, and multiple specialized metabolic pathways. Specifically, transcription factor gene- and pathway-centered network analyses successfully ascertained the previously established role of VviMYBPA1 in controlling the accumulation of proanthocyanidins while providing insights into its novel role as a regulator of p-coumaroyl-CoA biosynthesis as well as the shikimate and aromatic amino acid pathways. This network was validated using DNA affinity purification sequencing data, demonstrating that co-expression networks of transcriptional activators can serve as a proxy of gene regulatory networks. This study presents an open repository to reproduce networks in other crops and a GCN application within the Vitviz platform, a user-friendly tool for exploring co-expression relationships.
FertileCryptococcus neoformansvar.neoformans(C. deneoformans) isolates from natural environment in Kosovo
Authors: Pllana-Hajdari Donjeta , Chidebelu Ekene P , Cogliati Massimo 
Published: September 2023

AbstractA total of 300 tree-associated samples were collected from green areas in three towns in Kosovo, and cultured to isolate Cryptococcus species. One soil sample from Prizren tested positive, yielding three isolates identified as C. neoformans var. neoformans (C. deneoformans), molecular type VNIV, two MATα, and one MATa. Mating experiments revealed that they were fertile when crossed together, and multilocus sequence typing analysis showed unique sequence types not found in the global database. The study reports the presence of C. neoformans strains in the environment in Kosovo and highlights the importance of monitoring pathogen distribution and the potential impacts of climate change.
Enhanced symmetry energy may bear universality of r-process abundances
Authors: Orce José Nicolás , Dey Balaram , Ngwetsheni Cebo , Bhattacharya Srijit , Pandit Deepak , Lesch Brenden , Zulu Andile 
Published: September 2023

ABSTRACT
The abundances of about half of the elements heavier than iron are subtly attuned by the rapid neutron capture process or r-process, which is intimately related to the competition between neutron capture, photo-disintegration, and β-decay rates, and ultimately depends on the binding energy of neutron-rich nuclei. The well-known Bethe–Weizsäcker semi-empirical mass formula describes the binding energy of ground states – i.e. nuclei with temperatures of T = 0 MeV – with the symmetry energy parameter converging between 23 and 27 MeV for heavy nuclei. We find an unexpected enhancement of the symmetry energy well above the ground state – at higher temperatures of T ≈ 0.7–1.0 MeV – from the available data of giant dipole resonances built on excited states. Although these are likely the temperatures where seed nuclei are created – during the cooling down of the ejecta following neutron-star mergers or collapsars – the fact that the symmetry energy remains constant between T ≈ 0.7 and 1.0 MeV, may suggest an enhanced symmetry energy at lower temperatures, where neutron-capture may start occurring. Calculations using this relatively larger symmetry energy yield a reduction of the binding energy per nucleon for heavy neutron-rich nuclei and inhibits radiative neutron-capture rates. This results in a substantial close in of the neutron drip line which may elucidate the long sought universality of heavy-element abundances through the r-process; as inferred from the similar abundances found in extremely metal-poor stars and the Sun. Sensitivity studies of r-process network calculations have been performed using more sophisticated mass models.
The spectroscopic orbit of HD 168112 A,B in NGC 6604: another massive binary target for interferometry
Authors: Putkuri C , Gamen R , Morrell N I , Maíz Apellániz J , Arias J I , Simón-Díaz S , Ferrero G A , Rodríguez C N , Sota A , Benvenuto O G , Barbá R H 
Published: September 2023

ABSTRACT
We present the first spectroscopic orbit of the O-type double-lined star HD 168112 A,B. We analyse 101 high-resolution optical spectra identifying the absorption lines of both components. The orbital solution presents a relatively long period, P = 513.52 ± 0.01 d, and a high eccentricity, e = 0.743 ± 0.005. The binary system consists of two very similar stars of minimum masses of ∼25 M⊙, effective temperatures of ∼40 000 K, and surface gravities of ∼3.7 dex. The system has a minimum semimajor axis a sin i ∼ 1000 R⊙. We confirm that the A and B visual components identified via interferometry do correspond to the spectroscopic ones. We also analyse the underlying stellar groups using Gaia DR3 data and ground-based spectroscopy as part of the Villafranca project, determining that NGC 6604 is at a distance of $1942^{+38}_{-36}$ pc and giving spectral classifications for 23 massive stellar systems in Villafranca O-035 and the surrounding Ser OB2 association, for which we provide the most complete census of massive stars to date.
Precessing binary black holes as better dark sirens
Authors: Yun Qianyun , Han Wen-Biao , Hu Qian , Xu Haiguang 
Published: September 2023

ABSTRACT
Gravitational waves (GWs) from binary black hole mergers provide unique opportunities for cosmological inference such as standard sirens. However, the accurate determination of the luminosity distance of the event is limited by the correlation between the distance and the angle between the binary’s orbital angular momentum and the observer’s line of sight. In the letter, we investigate the effect of precession on the distance estimation of binary black hole events for the third-generation (3G) GW detectors. We find that the precession can enhance the precision of distance inference by one order of magnitude compared to the scenario where precession is absent. The constraint on the host galaxies can be improved due to the improved distance measurement, therefore the Hubble constant can be measured with higher precision and accuracy. These findings underscore the noteworthy impact of precession on the precision of distance estimation for 3G ground-based GW detectors, which can serve as highly accurate probes of the Universe.
Assessing in vivo the impact of gene context on transcription through DNA supercoiling
Authors: Boulas Ihab , Bruno Lisa , Rimsky Sylvie , Espeli Olivier , Junier Ivan , Rivoire Olivier 
Published: September 2023

Abstract
Gene context can have significant impact on gene expression but is currently not integrated in quantitative models of gene regulation despite known biophysical principles and quantitative in vitro measurements. Conceptually, the simplest gene context consists of a single gene framed by two topological barriers, known as the twin transcriptional-loop model, which illustrates the interplay between transcription and DNA supercoiling. In vivo, DNA supercoiling is additionally modulated by topoisomerases, whose modus operandi remains to be quantified. Here, we bridge the gap between theory and in vivo properties by realizing in Escherichia coli the twin transcriptional-loop model and by measuring how gene expression varies with promoters and distances to the topological barriers. We find that gene expression depends on the distance to the upstream barrier but not to the downstream barrier, with a promoter-dependent intensity. We rationalize these findings with a first-principle biophysical model of DNA transcription. Our results are explained if TopoI and gyrase both act specifically, respectively upstream and downstream of the gene, with antagonistic effects of TopoI, which can repress initiation while facilitating elongation. Altogether, our work sets the foundations for a systematic and quantitative description of the impact of gene context on gene regulation.
Trends in epidemiology and risk factors of opportunistic infections in kidney transplant recipients between 2004 and 2017
Authors: Pfirmann Pierre , Garrigue Isabelle , Chauveau Bertrand , Rondeau Virginie , Tumiotto Camille , Weinmann Laurent , Dubois Véronique , Couzi Lionel , Merville Pierre , Kaminski Hannah , Taton Benjamin 
Published: September 2023

ABSTRACTBackgroundWhile opportunistic infections are a frequent and challenging problem in kidney transplant recipients, their long-term epidemiology remains hardly known.MethodsOpportunistic infections were recorded in 1144 recipients transplanted in our center between 2004 and 2015. Incidence rates and baseline risk factors were determined using joint frailty models.ResultsAfter a median follow-up of 5.6 years, 544 opportunistic infections occurred in 373/1144 (33%) patients, dominated by viral infections (396/544, 72%), especially cytomegalovirus (CMV) syndromes and diseases (213/544, 39%). One-third of the infected patients experienced at least two opportunistic infections. The incidence of opportunistic infections was 10 times higher during the first year post-transplantation than after that (34.7 infections for 100 patient-years vs 3.64). Opportunistic infections associated with the age of the donor (P = .032), the age of the recipient (P = .049), the CMV serostatus (P &lt; 10−6), a higher class II HLA mismatch (P = .032) and an induction treatment including rabbit anti-thymocyte globulins (P = .026). Repeated opportunistic infections associated with each other (P &lt; 10−6) and with renal death (P &lt; 10−6).ConclusionOpportunistic infections occur with a two-period incidence pattern and many susceptible patients suffer from repeated episodes. This knowledge may help tailor new prevention and follow-up strategies to reduce the burden of opportunistic infections and their impact on transplantation outcome.
Deep Learning of Multimodal Ultrasound: Stratifying the Response to Neoadjuvant Chemotherapy in Breast Cancer Before Treatment
Authors: Gu Jionghui , Zhong Xian , Fang Chengyu , Lou Wenjing , Fu Peifen , Woodruff Henry C , Wang Baohua , Jiang Tianan , Lambin Philippe 
Published: September 2023

Abstract

Background
Not only should resistance to neoadjuvant chemotherapy (NAC) be considered in patients with breast cancer but also the possibility of achieving a pathologic complete response (PCR) after NAC. Our study aims to develop 2 multimodal ultrasound deep learning (DL) models to noninvasively predict resistance and PCR to NAC before treatment.

Methods
From January 2017 to July 2022, a total of 170 patients with breast cancer were prospectively enrolled. All patients underwent multimodal ultrasound examination (grayscale 2D ultrasound and ultrasound elastography) before NAC. We combined clinicopathological information to develop 2 DL models, DL_Clinical_resistance and DL_Clinical_PCR, for predicting resistance and PCR to NAC, respectively. In addition, these 2 models were combined to stratify the prediction of response to NAC.

Results
In the test cohort, DL_Clinical_resistance had an AUC of 0.911 (95%CI, 0.814-0.979) with a sensitivity of 0.905 (95%CI, 0.765-1.000) and an NPV of 0.882 (95%CI, 0.708-1.000). Meanwhile, DL_Clinical_PCR achieved an AUC of 0.880 (95%CI, 0.751-0.973) and sensitivity and NPV of 0.875 (95%CI, 0.688-1.000) and 0.895 (95%CI, 0.739-1.000), respectively. By combining DL_Clinical_resistance and DL_Clinical_PCR, 37.1% of patients with resistance and 25.7% of patients with PCR were successfully identified by the combined model, suggesting that these patients could benefit by an early change of treatment strategy or by implementing an organ preservation strategy after NAC.

Conclusions
The proposed DL_Clinical_resistance and DL_Clinical_PCR models and combined strategy have the potential to predict resistance and PCR to NAC before treatment and allow stratified prediction of NAC response.