bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lineage Landscape: a comprehensive database that records lineage commitment across species
Authors: Yan Haoteng , Wang Ronghao , Ma Shuai , Huang Daoran , Wang Si , Ren Jie , Lu Changfa , Chen Xin , Lu Xiaoyong , Zheng Zikai , Zhang Weiqi , Qu Jing , Zhou Yuanchun , Liu Guang-Hui 
Published: October 2022

Abstract
Commitment to specific cell lineages is critical for mammalian embryonic development. Lineage determination, differentiation, maintenance, and organogenesis result in diverse life forms composed of multiple cell types. To understand the formation and maintenance of living individuals, including human beings, a comprehensive database that integrates multi-omic information underlying lineage differentiation across multiple species is urgently needed. Here, we construct Lineage Landscape, a database that compiles, analyzes and visualizes transcriptomic and epigenomic information related to lineage development in a collection of species. This landscape draws together datasets that capture the ongoing changes in cell lineages from classic model organisms to human beings throughout embryonic, fetal, adult, and aged stages, providing comprehensive, open-access information that is useful to researchers of a broad spectrum of life science disciplines. Lineage Landscape contains single-cell gene expression and bulk transcriptomic, DNA methylation, histone modifications, and chromatin accessibility profiles. Using this database, users can explore genes of interest that exhibit dynamic expression patterns at the transcriptional or epigenetic levels at different stages of lineage development. Lineage Landscape currently includes over 6.6 million cells, 15 million differentially expressed genes and 36 million data entries across 10 species and 34 organs. Lineage Landscape is free to access, browse, search, and download at http://data.iscr.ac.cn/lineage/#/home.
A guard protein mediated quality control mechanism monitors 5’-capping of pre-mRNAs
Authors: Klama Sandra , Hirsch Anna G , Schneider Ulla M , Zander Gesa , Seel Anika , Krebber Heike 
Published: October 2022

Abstract
Efficient gene expression requires properly matured mRNAs for functional transcript translation. Several factors including the guard proteins monitor maturation and act as nuclear retention factors for unprocessed pre-mRNAs. Here we show that the guard protein Npl3 monitors 5’-capping. In its absence, uncapped transcripts resist degradation, because the Rat1–Rai1 5’-end degradation factors are not efficiently recruited to these faulty transcripts. Importantly, in npl3Δ, these improperly capped transcripts escape this quality control checkpoint and leak into the cytoplasm. Our data suggest a model in which Npl3 associates with the Rai1 bound pre-mRNAs. In case the transcript was properly capped and is thus CBC (cap binding complex) bound, Rai1 dissociates from Npl3 allowing the export factor Mex67 to interact with this guard protein and support nuclear export. In case Npl3 does not detect proper capping through CBC attachment, Rai1 binding persists and Rat1 can join this 5’-complex to degrade the faulty transcript.
A year of COVID: the evolution of labour market and financial inequalities through the crisis
Authors: Crossley Thomas F , Fisher Paul , Low Hamish , Levell Peter 
Published: October 2022

Abstract
We use high-quality UK panel data to document the extent that pre-existing labour market and financial inequalities were exacerbated by the pandemic between April 2020 and September 2021. Some inequalities worsened, others did not, and in some cases, initial widening of labour market inequalities was subsequently reversed. We find no evidence of an overall divergence in labour market outcomes by gender. Initial changes for ethnic minorities and the young were largely reversed by March 2021. Those in the top third of the long-run income distribution experienced income falls, but also increased saving. Net wealth increased not for only the affluent, but also for middle deciles of the long-run income distribution. These deciles were most protected by the furlough scheme. Those at the bottom of the income distribution were more likely to report a decline in net wealth over the year.
Insight into the control of nodule immunity and senescence during Medicago truncatula symbiosis
Authors: Berrabah Fathi , Bernal Gautier , Elhosseyn Ait-Salem , El Kassis Cyrille , L’Horset Roxane , Benaceur Farouk , Wen Jiangqi , Mysore Kirankumar S , Garmier Marie , Gourion Benjamin , Ratet Pascal , Gruber Véronique 
Published: October 2022

Abstract
Medicago (Medicago truncatula) establishes a symbiosis with the rhizobia Sinorhizobium sp, resulting in the formation of nodules where the bacteria fix atmospheric nitrogen. The loss of immunity repression or early senescence activation compromises symbiont survival and leads to the formation of nonfunctional nodules (fix−). Despite many studies exploring an overlap between immunity and senescence responses outside the nodule context, the relationship between these processes in the nodule remains poorly understood. To investigate this phenomenon, we selected and characterized three Medicago mutants developing fix− nodules and showing senescence responses. Analysis of specific defense (PATHOGENESIS-RELATED PROTEIN) or senescence (CYSTEINE PROTEASE) marker expression demonstrated that senescence and immunity seem to be antagonistic in fix− nodules. The growth of senescence mutants on non-sterile (sand/perlite) substrate instead of sterile in vitro conditions decreased nodule senescence and enhanced defense, indicating that environment can affect the immunity/senescence balance. The application of wounding stress on wild-type (WT) fix+ nodules led to the death of intracellular rhizobia and associated with co-stimulation of defense and senescence markers, indicating that in fix+ nodules the relationship between the two processes switches from opposite to synergistic to control symbiont survival during response to the stress. Our data show that the immune response in stressed WT nodules is linked to the repression of DEFECTIVE IN NITROGEN FIXATION 2 (DNF2), Symbiotic CYSTEINE-RICH RECEPTOR-LIKE KINASE (SymCRK), and REGULATOR OF SYMBIOSOME DIFFERENTIATION (RSD), key genes involved in symbiotic immunity suppression. This study provides insight to understand the links between senescence and immunity in Medicago nodules.
Development of tropoelastin-functionalized anisotropic PCL scaffolds for musculoskeletal tissue engineering
Authors: Zhang Miao , Wang Ziyu , Zhang Anyu , Liu Linyang , Mithieux Suzanne M , Bilek Marcela M M , Weiss Anthony S 
Published: October 2022

Abstract
The highly organized extracellular matrix (ECM) of musculoskeletal tissues, encompassing tendons, ligaments and muscles, is structurally anisotropic, hierarchical and multi-compartmental. These features collectively contribute to their unique function. Previous studies have investigated the effect of tissue-engineered scaffold anisotropy on cell morphology and organization for musculoskeletal tissue repair and regeneration, but the hierarchical arrangement of ECM and compartmentalization are not typically replicated. Here, we present a method for multi-compartmental scaffold design that allows for physical mimicry of the spatial architecture of musculoskeletal tissue in regenerative medicine. This design is based on an ECM-inspired macromolecule scaffold. Polycaprolactone (PCL) scaffolds were fabricated with aligned fibers by electrospinning and mechanical stretching, and then surface-functionalized with the cell-supporting ECM protein molecule, tropoelastin (TE). TE was attached using two alternative methods that allowed for either physisorption or covalent attachment, where the latter was achieved by plasma ion immersion implantation (PIII). Aligned fibers stimulated cell elongation and improved cell alignment, in contrast to randomly oriented fibers. TE coatings bound by physisorption or covalently following 200 s PIII treatment promoted fibroblast proliferation. This represents the first cytocompatibility assessment of novel PIII-treated TE-coated PCL scaffolds. To demonstrate their versatility, these 2D anisotropic PCL scaffolds were assembled into 3D hierarchical constructs with an internally compartmentalized structure to mimic the structure of musculoskeletal tissue.
Deep stratification by transcriptome molecular characters for precision treatment of patients with systemic lupus erythematosus
Authors: Qiao Jun , Zhang Sheng-Xiao , Chang Min-Jing , Zhao Rong , Song Shan , Hao Jia-Wei , Wang Can , Hu Jing-Xi , Gao Chong , Wang Cai-Hong , Li Xiao-Feng 
Published: October 2022

Abstract

Objectives
To leverage the high clinical heterogeneity of systemic lupus erythematosus (SLE), we developed and validated a new stratification scheme by integrating genome-scale transcriptomic profiles to identify patient subtypes sharing similar transcriptomic markers and drug targets.

Methods
A normalized compendium of transcription profiles was created from peripheral blood mononuclear cells (PBMCs) of 1046 SLE patients and 86 healthy controls (HCs), covering an intersection of 13 689 genes from six microarray datasets. Upregulated differentially expressed genes were subjected to functional and network analysis in which samples were grouped using unsupervised clustering to identify patient subtypes. Then, clustering stability was evaluated by the stratification of six integrated RNA-sequencing datasets using the same method. Finally, the Xgboost classifier was applied to the independent datasets to identify factors associated with treatment outcomes.

Results
Based on 278 upregulated DEGs of the transcript profiles, SLE patients were classified into three subtypes (subtype A–C) each with distinct molecular and cellular signatures. Neutrophil activation-related pathways were markedly activated in subtype A (named NE-driving), whereas lymphocyte and IFN-related pathways were more enriched in subtype B (IFN-driving). As the most severe subtype, subtype C [NE-IFN-dual-driving (Dual-driving)] shared functional mechanisms with both NE-driving and IFN-driving, which was closely associated with clinical features and could be used to predict the responses of treatment.

Conclusion
We developed the largest cohesive SLE transcriptomic compendium for deep stratification using the most comprehensive microarray and RNA sequencing datasets to date. This result could guide future design of molecular diagnosis and the development of stratified therapy for SLE patients.
Dementia Caregiver Insights on Use of Assistive Technologies
Authors: Mikula Cynthia M , Perry Casey , Boone Anna E , Benge Jared F , Scullin Michael K , Kiselica Andrew M 
Published: October 2022

Abstract
Concerns about developing memory problems and losing independence constitute a significant source of stress for the aging population. Impairments in cognitive and functional abilities are the hallmark symptoms of dementia, a common age-related condition. The responsibility of caring for older adults with dementia falls disproportionately on family and friends. Technologies, such as smartphone applications, wearable devices, and smart speakers, offer an array of features to support dementia care. However, there is limited information on the current use of technology in caregiving. Thus, we conducted semi-structured interviews with a U.S. sample of 21 caregivers (76.19% female, age 54.76 ± 15.65) to older adults with dementia on the ways they currently use technology for caregiving, as well as concerns about and facilitators of the use of assistive technologies. Participants reported using assistive technologies for a variety of caregiving responsibilities, including facilitating social connectedness, tracking rest and sleep, promoting leisure/activity, managing instrumental activities of daily living, accessing health care, and ensuring patient safety. Several concerns about technology use in caregiving were also identified, including cost, ease of use, and safety and privacy concerns. In addition, caregivers reported that they could be supported in using technology by relying on knowledgeable friends/family members, using simple forms of technology, and receiving assistance for implementing new technology, and helping the person with dementia to use the technology. Results suggest that while technology has the potential to improve many aspects of caregiving and reduce associated caregiver strain, efforts to make these techniques less costly and more familiar are needed.
Pyruvate prevents the onset of the cachectic features and metabolic alterations in myotubes downregulating STAT3 signaling
Authors: Mannelli Michele , Gamberi Tania , Garella Rachele , Magherini Francesca , Squecco Roberta , Fiaschi Tania 
Published: October 2022

AbstractCachexia is a systemic disease associated with several pathologies, including cancer, that leads to excessive weight loss due to enhanced protein degradation. Previously, we showed that cachectic features in myotubes are provoked by a metabolic shift toward lactic fermentation. Our previous results led us to hyphotesise that increasing pyruvate concentration could impede the metabolic modifications responsible for induction of cachexia in myotubes. Here, we demonstrated that the addition of sodium pyruvate in conditioned media from CT26 colon cancer cells (CM CT26) prevents the onset of either phenotypic and metabolic cachectic features. Myotubes treated with CM CT26 containing sodium pyruvate show a phenotype similar to the healthy counterpart and display lactate production, oxygen consumption, and pyruvate dehydrogenase activity as control myotubes. The use of the Mitochondrial Pyruvate Carrier inhibitor UK5099, highlights the importance of mitochondrial pyruvate amount in the prevention of cachexia. Indeed, UK5099‐treated myotubes show cachectic features as those observed in myotubes treated with CM CT26. Finally, we found that sodium pyruvate is able to decrease STAT3 phosphorylation level, a signaling pathway involved in the induction of cachexia in myotubes. Collectively, our results show that cachexia in myotubes could be prevented by the utilization of sodium pyruvate which impedes the metabolic modifications responsible for the acquisition of the cachectic features.
Accelerating to Practice: Defining a Competency-Based Curriculum Framework for Nursing Education Part 1
Authors: Forneris Susan Gross , Tagliareni M. Elaine , Allen Buffy 
Published: October 2022

Abstract

AIM
This study aims to address the transition-to-practice dilemma for novice nurse, define gaps, and lay a foundation for a curriculum framework.

BACKGROUND
The National League for Nursing has challenged and supported nurse educators in developing teaching methodologies that prepare novice nurses for professional practice. Over a decade ago, compelling research fueled a debate that continues today, with nursing education and practice research reporting lack of readiness for practice by novice nurses and the goal of identifying gaps and potential strategies for solutions.

METHOD
The Utstein-style meeting strategy consensus approach was used to refine the data gaps reported in the literature.

RESULTS
The findings from this work generated a strong foundation for a transition-to-practice curriculum framework.

CONCLUSION
The Utstein-style meeting provided for a diverse conversation across multiple perspectives. Participants worked collaboratively in real time to further illuminate and refine the data gaps and inform nursing curricula.
Exploring the Experiences of Doctor of Nursing Practice Students’ Use of Flipgrid to Create a Community of Inquiry in a Predominantly Online Program
Authors: Sebach Aaron M. 
Published: October 2022

Abstract
The purpose of this qualitative descriptive study was to explore the experiences of Doctor of Nursing Practice (DNP) students utilizing Flipgrid, a free, asynchronous online video discussion forum, as an alternative to written journals and discussion boards in a predominately online program. Results suggest greater student engagement, efficiency, and public speaking skills with Flipgrid than with conventional journals and discussion boards. Flipgrid can serve as an active learning strategy to promote a community of inquiry among online DNP students.
Ready, Set, Start: Mentoring Graduating Nursing Students During a Pandemic
Authors: Beauvais Audrey Marie , Vittner Dorothy , Phillips Kathyrn E. , Burrows Karen , Corcoran Karen , Saracino Katherine H. , Kazer Meredith 
Published: October 2022

Abstract
Nurses are graduating from educational programs and entering health care systems at a time of great turmoil because of the COVID-19 pandemic. To support the transition to practice, nursing faculty implemented a postgraduation mentorship program (START). This exploratory study sought to describe the faculty mentor and new graduate mentee experience. Related variables (NCLEX pass rates, perceived stress, and professional quality of life) are provided to contextualize the results. The research is significant given the burden the pandemic places on the health care system, which may limit the resources available to new graduate nurses.
Examining the Impact of Structured, Reflective Prebriefing on Student Performance During Simulation
Authors: Watts Sarah O. , Curtis Amy , Ware Katilya S. , Chidume Tiffani , Jones Meghan C. 
Published: October 2022

Abstract
Little is known about the impact of prebriefing on students’ experiences of learning with simulation. This mixed-methods study evaluated the impact of prebriefing activities on nursing students’ satisfaction, confidence, and performance of nursing skills during a simulation. Findings revealed students who experienced a structured, more robust prebriefing had improved performance during the simulation and reported higher levels of confidence and satisfaction in learning compared to a group that experienced a standard prebriefing. Findings are significant to the profession, they support the incorporation of structured, reflective prebriefing activities in simulation-based experiences.
Health State Utility Values Associated with Cochlear Implants in Adults: A Systematic Review and Network Meta-Analysis
Authors: Dixon Peter R. , Shapiro Justin , Tomlinson George , Cottrell Justin , Lui Justin T. , Falk Lindsey , Chen Joseph M. 
Published: October 2022

Objectives:
The cost-effectiveness of bilateral cochlear implants in adults remains uncertain despite established clinical benefits. In cost-effectiveness studies, benefit is often measured by change in health state utility value (HSUV), a single number summary of health-related quality of life anchored at 0 (state of being dead) and 1 (perfect health). Small differences in bilateral cochlear implant HSUV change conclusions of published models, and invalid estimates can therefore mislead policy and funding decisions. As such, we aimed to review and synthesize published HSUV estimates associated with cochlear implants.

Design:
We included observational or experimental studies reporting HSUV for adult patients (age ≥18 years) with at least moderate-profound sensorineural hearing loss in both ears who received unilateral or bilateral cochlear implants. We searched MEDLINE, EMBASE, PsycINFO, and Cochrane Library databases up to May 1, 2021. Study and participant characteristics and HSUV outcomes were extracted. Narrative synthesis is reported for all studies. A Bayesian network meta-analysis was conducted to generate pooled estimates for the mean difference in HSUV for three comparisons: (1) unilateral cochlear implant versus preimplant, (2) bilateral cochlear implants versus preimplant, (3) bilateral versus unilateral cochlear implants. Our principal measure was pooled mean difference in HSUV.

Results:
Thirty-six studies reporting unique patient cohorts were identified. Health Utilities Index, 3 (HUI-3) was the most common HSUV elicitation method. HSUV from 19 preimplant mean estimates (1402 patients), 19 unilateral cochlear implant mean estimates (1701 patients), and 5 bilateral cochlear implants mean estimates (83 patients) were pooled to estimate mean differences in HUI-3 HSUV by network meta-analysis. Compared with preimplant, a unilateral cochlear implant was associated with a mean change in HSUV of +0.17 (95% credible interval [CrI] +0.12 to +0.23) and bilateral cochlear implants were associated with a mean change of +0.25 (95% CrI +0.12 to +0.37). No significant difference in HSUV was detected for bilateral compared with unilateral cochlear implants (+0.08 [95% CrI −0.06 to +0.21]). Overall study quality was moderate.

Conclusions:
The findings of this review and network meta-analysis comprise the best-available resource for parameterization of cost-utility models of cochlear implantation in adults and highlight the need to critically evaluate the validity of available HSUV instruments for bilateral cochlear implant populations.
Protocol registration: PROSPERO (CRD42018091838)
Review of Autologous Fat Grafting in Postmastectomy Reconstruction Patients: Nonroutine Diagnostics and Oncologic Safety
Authors: Sayyed Adaah A. , Perez-Alvarez Idanis M. , Singh Tanvee , King Caroline A. , Welschmeyer Alexandra F. , Bartholomew Alexander J. , Sher Sarah , Tousimis Eleni A. , Song David H. , Fan Kenneth L. 
Published: October 2022

Background:
Autologous fat grafting (FG) is increasingly used as an adjunctive reconstruction technique to augment volume, achieve symmetry, and improve contour deformities. This study aims to characterize the oncologic and surgical safety of FG in women undergoing autologous breast reconstruction (ABR) or implant-based reconstruction (IBR).

Methods:
A retrospective chart review was performed for all patients undergoing FG at a multi-site single health system between 2015 to 2018. A total of 228 eligible breasts from 155 patients were identified using Current Procedural Terminology codes. Patients were divided by reconstructive technique. Bivariate analyses compared baseline characteristics and post-FG outcomes.

Results:
Mean age for patients undergoing ABR (129 breasts) was 52.8 years compared to 48.6 years for those undergoing IBR (99 breasts; P = 0.002). A heavier volume of fat was grafted per ABR breast (143.8mL) than per IBR breast (102.2mL; P = 0.002). Forty-seven (20.6%) breasts required FG revision, more frequently in ABR breasts (31.0%) than IBR breasts (7.1%; P < 0.001). Following FG, 17.5% of patients experienced a palpable mass, and 18.9% of breasts underwent nonroutine diagnostics or procedures, with no difference between ABR and IBR groups. Most biopsies noted benign findings such as fat necrosis (2.2%) or a benign mass (0.9%), with recurrence only noted in two patients (0.9%). Mean follow-up was 20.4 months.

Conclusion:
FG is a safe, surgically simple procedure more commonly performed in ABR breasts. FG use in ABR and IBR breasts is oncologically safe, with no impairment in breast surveillance and low rates of locoregional recurrence, but possibly increased incidence of nonroutine imaging and biopsies.