bluuebunny/crossref_metadata_2025_split huggingface dataset:
Towards conceptualizing patients as partners in health systems: a systematic review and descriptive synthesis
Authors: Vanstone Meredith , Canfield Carolyn , Evans Cara , Leslie Myles , Levasseur Mary Anne , MacNeil Maggie , Pahwa Manisha , Panday Janelle , Rowland Paula , Taneja Shipra , Tripp Laura , You Jeonghwa , Abelson Julia 
Published: January 2023

Abstract
Background
With the sharp increase in the involvement of patients (including family and informal caregivers) as active participants, collaborators, advisors and decision-makers in health systems, a new role has emerged: the patient partner. The role of patient partner differs from other forms of patient engagement in its longitudinal and bidirectional nature. This systematic review describes extant work on how patient partners are conceptualized and engaged in health systems. In doing so, it furthers the understanding of the role and activities of patient partners, and best practices for future patient partnership activities.

Methods
A systematic review was conducted of peer-reviewed literature published in English or French that describes patient partner roles between 2000 and 2021 in any country or sector of the health system. We used a broad search strategy to capture descriptions of longitudinal patient engagement that may not have used words such as “partner” or “advisor”.

Results
A total of 506 eligible papers were identified, representing patient partnership activities in mostly high-income countries. These studies overwhelmingly described patient partnership in health research. We identified clusters of literature about patient partnership in cancer and mental health. The literature is saturated with single-site descriptive studies of patient partnership on individual projects or initiatives. There is a lack of work synthesizing impacts, facilitating factors and outcomes of patient partnership in healthcare.

Conclusions
There is not yet a consolidated understanding of the role, activities or impacts of patient partners. Advancement of the literature has been stymied by a lack of consistently used terminology. The literature is ready to move beyond single-site descriptions, and synthesis of existing pockets of high-quality theoretical work will be essential to this evolution.
Low expression of the dynamic network markers FOS/JUN in pre-deteriorated epithelial cells is associated with the progression of colorectal adenoma to carcinoma
Authors: Huang Xiaoqi , Han Chongyin , Zhong Jiayuan , Hu Jiaqi , Jin Yabin , Zhang Qinqin , Luo Wei , Liu Rui , Ling Fei 
Published: January 2023

Abstract
Background
Deterioration of normal intestinal epithelial cells is crucial for colorectal tumorigenesis. However, the process of epithelial cell deterioration and molecular networks that contribute to this process remain unclear.

Methods
Single-cell data and clinical information were downloaded from the Gene Expression Omnibus (GEO) database. We used the recently proposed dynamic network biomarker (DNB) method to identify the critical stage of epithelial cell deterioration. Data analysis and visualization were performed using R and Cytoscape software. In addition, Single-Cell rEgulatory Network Inference and Clustering (SCENIC) analysis was used to identify potential transcription factors, and CellChat analysis was conducted to evaluate possible interactions among cell populations. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene set variation analysis (GSVA) analyses were also performed.

Results
The trajectory of epithelial cell deterioration in adenoma to carcinoma progression was delineated, and the subpopulation of pre-deteriorated epithelial cells during colorectal cancer (CRC) initialization was identified at the single-cell level. Additionally, FOS/JUN were identified as biomarkers for pre-deteriorated epithelial cell subpopulations in CRC. Notably, FOS/JUN triggered low expression of P53-regulated downstream pro-apoptotic genes and high expression of anti-apoptotic genes through suppression of P53 expression, which in turn inhibited P53-induced apoptosis. Furthermore, malignant epithelial cells contributed to the progression of pre-deteriorated epithelial cells through the GDF signaling pathway.

Conclusions
We demonstrated the trajectory of epithelial cell deterioration and used DNB to characterize pre-deteriorated epithelial cells at the single-cell level. The expression of DNB-neighboring genes and cellular communication were triggered by DNB genes, which may be involved in epithelial cell deterioration. The DNB genes FOS/JUN provide new insights into early intervention in CRC.
High titers of neutralizing SARS-CoV-2 antibodies six months after symptom onset are associated with increased severity in COVID-19 hospitalized patients
Authors: Sejdic Adin , Frische Anders , Jørgensen Charlotte Sværke , Rasmussen Lasse Dam , Trebbien Ramona , Dungu Arnold , Holler Jon G. , Ostrowski Sisse Rye , Eriksson Robert , Søborg Christian , Nielsen Thyge L. , Fischer Thea K. , Lindegaard Birgitte , Franck Kristina Træholt , Harboe Zitta Barrella 
Published: January 2023

AbstractBackgroundViral shedding and neutralizing antibody (NAb) dynamics among patients hospitalized with severe coronavirus disease 2019 (COVID-19) and immune correlates of protection have been key questions throughout the pandemic. We investigated the duration of reverse transcriptase-polymerase chain reaction (RT-PCR) positivity, infectious viral shedding and NAb titers as well as the association between NAb titers and disease severity in hospitalized COVID-19 patients in Denmark 2020–2021.Materials and methodsProspective single-center observational cohort study of 47 hospitalized COVID-19 patients. Oropharyngeal swabs were collected at eight time points during the initial 30 days of inclusion. Serum samples were collected after a median time of 7 (IQR 5 – 10), 37 (IQR 35 – 38), 97 (IQR 95 – 100), and 187 (IQR 185 – 190) days after symptom onset. NAb titers were determined by an in-house live virus microneutralization assay. Viral culturing was performed in Vero E6 cells.ResultsPatients with high disease severity had higher mean log2NAb titers at day 37 (1.58, 95% CI [0.34 –2.81]), 97 (2.07, 95% CI [0.53–3.62]) and 187 (2.49, 95% CI [0.20– 4.78]) after symptom onset, compared to patients with low disease severity. Peak viral load (0.072, 95% CI [− 0.627 – 0.728]), expressed as log10SARS-CoV-2 copies/ml, was not associated with disease severity. Virus cultivation attempts were unsuccessful in almost all (60/61) oropharyngeal samples collected shortly after hospital admission.ConclusionsWe document an association between high disease severity and high mean NAb titers at days 37, 97 and 187 after symptom onset. However, peak viral load during admission was not associated with disease severity.Trial registration. The study is registered athttps://clinicaltrials.gov/(NCT05274373).
Image augmentation and automated measurement of endotracheal-tube-to-carina distance on chest radiographs in intensive care unit using a deep learning model with external validation
Authors: Oliver Matthieu , Renou Amélie , Allou Nicolas , Moscatelli Lucas , Ferdynus Cyril , Allyn Jerôme 
Published: January 2023

Abstract
Background
Chest radiographs are routinely performed in intensive care unit (ICU) to confirm the correct position of an endotracheal tube (ETT) relative to the carina. However, their interpretation is often challenging and requires substantial time and expertise. The aim of this study was to propose an externally validated deep learning model with uncertainty quantification and image segmentation for the automated assessment of ETT placement on ICU chest radiographs.

Methods
The CarinaNet model was constructed by applying transfer learning to the RetinaNet model using an internal dataset of ICU chest radiographs. The accuracy of the model in predicting the position of the ETT tip and carina was externally validated using a dataset of 200 images extracted from the MIMIC-CXR database. Uncertainty quantification was performed using the level of confidence in the ETT–carina distance prediction. Segmentation of the ETT was carried out using edge detection and pixel clustering.

Results
The interrater agreement was 0.18 cm for the ETT tip position, 0.58 cm for the carina position, and 0.60 cm for the ETT–carina distance. The mean absolute error of the model on the external test set was 0.51 cm for the ETT tip position prediction, 0.61 cm for the carina position prediction, and 0.89 cm for the ETT–carina distance prediction. The assessment of ETT placement was improved by complementing the human interpretation of chest radiographs with the CarinaNet model.

Conclusions
The CarinaNet model is an efficient and generalizable deep learning algorithm for the automated assessment of ETT placement on ICU chest radiographs. Uncertainty quantification can bring the attention of intensivists to chest radiographs that require an experienced human interpretation. Image segmentation provides intensivists with chest radiographs that are quickly interpretable and allows them to immediately assess the validity of model predictions. The CarinaNet model is ready to be evaluated in clinical studies.

Graphical Abstract
Pregnancy outcomes in patients receiving assisted reproductive therapy with systemic lupus erythematosus: a multi-center retrospective study
Authors: Lao Minxi , Dai Peiyin , Luo Guangxi , Yang Xing , Peng Miaoguan , Chen Yuyi , Zhan Yanfeng , Zhan Zhongping , Chen Dongying 
Published: January 2023

Abstract

Objectives
To evaluate the safety, efficacy, and maternal and fetal outcomes of assisted reproductive therapy (ART) in systemic lupus erythematosus (SLE).

Methods
Patients from three tertiary hospitals from Guangzhou, China followed-up from 2013 to 2022 were included retrospectively. Patients with planned or unplanned natural pregnancy were chosen as controls. ART procedure and pregnancy outcomes were recorded and compared.

Results
A total of 322 ART cycles in 142 women were analyzed. Sixty-six intrauterine pregnancies out of 72 clinical pregnancies yielded 65 live infants, including 5 pairs of twins. The clinical pregnancy rate was 46.5% (66/142). The mean age at the first clinical pregnancy was 34.0 ± 3.8 years. The median (interquartile range, IQR) disease course was 42.5 (25, 84.8) months. Twenty-seven (40.9%) of them had a history of adverse pregnancy. Primary infertility occurred in 20 (30.3%) patients. Obstruction of fallopian tubes (17/66, 25.8%) and premature ovarian failure (9/66, 13.6%) were the leading causes for infertility. Ovulation induction therapy (OIT) were conducted in 60 (83.3%) pregnancies, and no ovarian hyperstimulation syndrome (OHSS) or thrombosis was observed. The leading maternal adverse pregnancy outcomes (APOs) included premature delivery (21/66, 31.8%), gestational diabetes mellitus (GDM) (15/66, 22.7%), and disease flares (10/66, 15.2%). Spontaneous premature delivery (9/21, 42.9%) and preterm premature rupture of membranes (PPROM) (6/21, 28.6%) were the leading causes for premature delivery. Preeclampsia (19.0% vs 0%, P = 0.012) increased in premature delivery. Infants delivered prematurely were likely to be low-birth-weight (LBW)/very-low-birth-weight (VLBW) (81.0% vs 7.7%, P < 0.001). Disease flares were mild (4/10, 40.0%) or moderate (5/10, 50.0%), and developed during the second (3/10, 30.0%) or third (6/10, 60.0%) trimester with favorable outcomes. Fetal loss in ART (6/66, 9.1%) was primarily attributed to early spontaneous abortion (n = 5). The average delivery time was 36.8 ± 2.1 weeks of gestation. The average birth weight was 2653.5 ± 578.6 g. LBW infants accounted for 30.8% (20/65). No neonatal death or neonatal lupus occurred. The incidence of adverse pregnancy outcomes did not increase in patients with ART compared with planned pregnancy and reduced significantly compared with an unplanned pregnancy.

Conclusion
The safety and efficacy of ART is assured in lupus patients with stable disease. Maternal and fetal APOs are comparable with planned pregnancy, with a relatively high incidence of premature delivery, GDM, and LBW infants.
Prevalence of vitamin B complex deficiencies in women in reproductive age, pregnant, or lactating woman in Brazil: a systematic review and meta-analysis protocol
Authors: Mocellin Michel Carlos , Curioni Cintia Chaves , da Silva Pereira Alessandra , Ribas Simone Augusta , Teixeira Michelle Teixeira , de Macedo Tatiane Salgado Galvão , Palermo Gabriel Mantolvão 
Published: January 2023

AbstractBackgroundVitamin B deficiencies are involved with several outcomes in fertility and pregnancy. In Brazil, the national prevalence rates of these micronutrient deficiencies in women of reproductive age were not known. This study aims to systematically identify, select, evaluate, analyze, and report the prevalence rates of vitamin B complex deficiencies in women of reproductive age in Brazil and identify variables that may modify the outcome rates.MethodsA systematic review will be conducted guided by the following question: “What is the prevalence of vitamin B deficiencies in women of reproductive age in Brazil?”. The studies will be identified and selected from a literature search using electronic databases, consultation with researchers/specialists, and reference lists of eligible studies and reviews on the topic. Major eligibility criteria include observational cross-sectional and cohort studies carried out in Brazil and performed in women 10–49 years old, or pregnant and lactating mothers, and investigated the deficiency of vitamin B complex by laboratory test. Two reviewers independently will perform the screening and selection of the studies, data extraction, and risk of bias assessment. For the data report, a narrative approach will be used to present the characteristics of the included studies and individual findings. A random meta-analysis model will be implemented to summarize the individual prevalence rates in a global value if the studies are sufficiently homogeneous.DiscussionThis study aims to identify the national and regional prevalence rates of vitamin B complex deficiencies in women of reproductive age; allow the policymakers discuss, plan, and implement public policies to screen; and prevent and/or treat these malnutrition conditions. This also aims to know the rates of nutritional deficiencies over the years, serving as an indirect indicator of the socioeconomic and dietary patterns of the population. Specifically for folate, this study allows to compare the prevalence rates of deficiency of this vitamin before and after the mandatory fortification of wheat and corn flours implemented since 2004 in Brazil, in this specific population. The evidence gathered may highlight the need for population-based studies to investigate the deficiency of these vitamins.Systematic review registrationPROSPERO CRD42020188474
Variable impact of geochemical gradients on the functional potential of bacteria, archaea, and phages from the permanently stratified Lac Pavin
Authors: Jaffe Alexander L. , Bardot Corinne , Le Jeune Anne-Hélène , Liu Jett , Colombet Jonathan , Perrière Fanny , Billard Hermine , Castelle Cindy J. , Lehours Anne-Catherine , Banfield Jillian F. 
Published: January 2023

Abstract
Background
Permanently stratified lakes contain diverse microbial communities that vary with depth and so serve as useful models for studying the relationships between microbial community structure and geochemistry. Recent work has shown that these lakes can also harbor numerous bacteria and archaea from novel lineages, including those from the Candidate Phyla Radiation (CPR). However, the extent to which geochemical stratification differentially impacts carbon metabolism and overall genetic potential in CPR bacteria compared to other organisms is not well defined.

Results
Here, we determine the distribution of microbial lineages along an oxygen gradient in Lac Pavin, a deep, stratified lake in central France, and examine the influence of this gradient on their metabolism. Genome-based analyses revealed an enrichment of distinct C1 and CO2 fixation pathways in the oxic lake interface and anoxic zone/sediments, suggesting that oxygen likely plays a role in structuring metabolic strategies in non-CPR bacteria and archaea. Notably, we find that the oxidation of methane and its byproducts is largely spatially separated from methane production, which is mediated by diverse communities of sediment methanogens that vary on the centimeter scale. In contrast, we detected evidence for RuBisCO throughout the water column and sediments, including form II/III and form III-related enzymes encoded by CPR bacteria in the water column and DPANN archaea in the sediments. On the whole, though, CPR bacteria and phages did not show strong signals of gene content differentiation by depth, despite the fact that distinct species groups populate different lake and sediment compartments.

Conclusions
Overall, our analyses suggest that environmental gradients in Lac Pavin select for capacities of CPR bacteria and phages to a lesser extent than for other bacteria and archaea. This may be due to the fact that selection in the former groups is indirect and depends primarily on host characteristics.
Deep learning based identification of bone scintigraphies containing metastatic bone disease foci
Authors: Ibrahim Abdalla , Vaidyanathan Akshayaa , Primakov Sergey , Belmans Flore , Bottari Fabio , Refaee Turkey , Lovinfosse Pierre , Jadoul Alexandre , Derwael Celine , Hertel Fabian , Woodruff Henry C. , Zacho Helle D. , Walsh Sean , Vos Wim , Occhipinti Mariaelena , Hanin François-Xavier , Lambin Philippe , Mottaghy Felix M. , Hustinx Roland 
Published: January 2023

Abstract
Purpose
Metastatic bone disease (MBD) is the most common form of metastases, most frequently deriving from prostate cancer. MBD is screened with bone scintigraphy (BS), which have high sensitivity but low specificity for the diagnosis of MBD, often requiring further investigations. Deep learning (DL) - a machine learning technique designed to mimic human neuronal interactions- has shown promise in the field of medical imaging analysis for different purposes, including segmentation and classification of lesions. In this study, we aim to develop a DL algorithm that can classify areas of increased uptake on bone scintigraphy scans.

Methods
We collected 2365 BS from three European medical centres. The model was trained and validated on 1203 and 164 BS scans respectively. Furthermore we evaluated its performance on an external testing set composed of 998 BS scans. We further aimed to enhance the explainability of our developed algorithm, using activation maps. We compared the performance of our algorithm to that of 6 nuclear medicine physicians.

Results
The developed DL based algorithm is able to detect MBD on BSs, with high specificity and sensitivity (0.80 and 0.82 respectively on the external test set), in a shorter time compared to the nuclear medicine physicians (2.5 min for AI and 30 min for nuclear medicine physicians to classify 134 BSs). Further prospective validation is required before the algorithm can be used in the clinic.
New Gnadenhutten, Moravian Missionaries, and Ojibwe Land Tenure on the Clinton River, 1781–1787
Authors: Quint Jonathan 
Published: January 2023

AbstractThis article reveals how Lake St. Clair Ojibwe communities limited newcomer encroachment and maintained territorial sovereignty by strategically absorbing and then expelling a community of Moravian missionaries and Christian Lenape. In 1782 the Ojibwe allowed Moravians to settle in a liminal Ojibwe hunting territory on the Clinton River. Over five years the settlement expanded, with conflict and cooperation defining Moravian engagement with Ojibwe land tenure and interactions with surrounding communities. Through oratory and formal and informal social practices like verbal warnings, threats, and intimidation, the Ojibwe mediated disputes, regulated Moravian use of land and resources, and attempted to curtail environmental destruction. This article reveals how the Moravian community encountered and experienced Ojibwe land tenure practices, the consequences of transgressing Ojibwe law, and how Ojibwe communities resisted encroachment on traditional lands and territories.
Desk and Derrick: The Women's Petroleum Industry Club That Envisioned Oil's Technocratic Future
Authors: Stanford-McIntyre Sarah 
Published: January 2023

AbstractThis article uncovers the hidden history of Desk and Derrick, a female-only petroleum industry employees’ club, to emphasize the importance of clerical work and support staff to oil industry development. In doing so, it demonstrates that despite the oil industry's mythology of individual inventors and lucky wildcatters, oil was remarkably similar to other large-scale scientific and engineering enterprises during the middle decades of the twentieth century. Throughout the 1950s and 1960s, oil's white-collar and administrative jobs expanded rapidly. And in this industry as in others, women were fundamental to oil industry technological development and labor conflicts. Desk and Derrick's was a haven for working women, providing community, training, and leadership opportunities in an industry deeply hostile to female employees. The club provided numerous outreach and educational campaigns included seminars, workshops, fieldtrips, and conventions. These events showcased female competence and technical knowledge, clashing with union derision and corporate dismissal. The club's vocal emphasis on scientific education and credentialization represented a bid for female inclusion within an increasingly technically complex professional world. However, entrenched workplace sexism and union hostility to changing labor structures limited member opportunities. Ultimately, Desk and Derrick's middle-class aspirations allied the club with industry rebranding efforts and helped support industry automation and union-busting. Desk and Derrick valorized industry engineers and scientific professionals, spreading narratives of prosperity through technology that coincided with industry-wide efforts to repair oil companies’ reputations as greedy, wasteful, and exploitative. In turn, midcentury oil companies promoted Desk and Derrick as a convenient, grassroots way to spread their message.
The Ghost and the Censor
Authors: Ng Emily 
Published: January 2023

Abstract
The history of modern China has been filled with loss in many senses. From certain angles of vision, loss, remembrance, and forgetting orbit around figures of political repression in the People's Republic of China (PRC), particularly that of censorship. These approaches posit a link between the Chinese state, national public amnesia, and international transparency that may occlude other configurations of knowing, speaking, and mourning—those of public secrecy, for instance, including stagings of the unspeakable through aesthetic and literary forms. This essay explores such configurations through Mo Yan's Life and Death Are Wearing Me Out (2008). In the novel, narrated largely by the reincarnated specter of an executed landlord, desire and loss travel between historical, carnal, and cosmic registers while operations of violence, politics, and memory both evoke and depart from common liberalist accounts of the PRC. On a world stage of global reading communities, the tethering of the village ghost to coordinates of apparently knowable historical time pairs with the author's ambiguous position vis-à-vis the formal sign of unknowability—censorship. The text, the (partially) censored author, and their circulations together point to productions of loss in parallax, at once hosting and abstracting loss.