bluuebunny/crossref_metadata_2025_split huggingface dataset:
The genetic and biochemical determinants of mRNA degradation rates in mammals
Authors: Agarwal Vikram , Kelley David R. 
Published: November 2022

Abstract
Background
Degradation rate is a fundamental aspect of mRNA metabolism, and the factors governing it remain poorly characterized. Understanding the genetic and biochemical determinants of mRNA half-life would enable more precise identification of variants that perturb gene expression through post-transcriptional gene regulatory mechanisms.

Results
We establish a compendium of 39 human and 27 mouse transcriptome-wide mRNA decay rate datasets. A meta-analysis of these data identified a prevalence of technical noise and measurement bias, induced partially by the underlying experimental strategy. Correcting for these biases allowed us to derive more precise, consensus measurements of half-life which exhibit enhanced consistency between species. We trained substantially improved statistical models based upon genetic and biochemical features to better predict half-life and characterize the factors molding it. Our state-of-the-art model, Saluki, is a hybrid convolutional and recurrent deep neural network which relies only upon an mRNA sequence annotated with coding frame and splice sites to predict half-life (r=0.77). The key novel principle learned by Saluki is that the spatial positioning of splice sites, codons, and RNA-binding motifs within an mRNA is strongly associated with mRNA half-life. Saluki predicts the impact of RNA sequences and genetic mutations therein on mRNA stability, in agreement with functional measurements derived from massively parallel reporter assays.

Conclusions
Our work produces a more robust ground truth for transcriptome-wide mRNA half-lives in mammalian cells. Using these revised measurements, we trained Saluki, a model that is over 50% more accurate in predicting half-life from sequence than existing models. Saluki succinctly captures many of the known determinants of mRNA half-life and can be rapidly deployed to predict the functional consequences of arbitrary mutations in the transcriptome.
Overt diabetes imposes a comparable burden on outcomes as pregestational diabetes: a cohort study
Authors: Oppermann Maria Lúcia , Campos Maria Amélia , Hirakata Vânia Naomi , Reichelt Angela Jacob 
Published: November 2022

AbstractBackgroundWomen with diabetes first diagnosed during pregnancy (overt diabetes) may be at the same risk level of adverse outcomes as those with known pregestational diabetes. We compared pregnancy outcomes between these groups.MethodsWe evaluated pregnant women with type 2 diabetes, pregestational or overt diabetes, attending high risk antenatal care in two public hospitals in Southern Brazil, from May 20, 2005 to June 30, 2021. Outcomes were retrieved from electronic medical records. Risk of adverse outcomes, expressed as relative risk (RR) and 95% confidence interval (CI), were calculated using Poisson regression with robust estimates.ResultsOf 618 women, 33% were labelled as having overt diabetes and 67%, pregestational diabetes. Baseline maternal characteristics were similar: there was a slight, non-clinically relevant, difference in maternal age (33 ± 5.7 years in women with pregestational diabetes vs. 32 ± 6.0 years in women with overt diabetes, p = 0.004); and women with overt diabetes reported smoking almost twice compared to those with pregestational diabetes (12.3% vs. 6.5%, p = 0.024). There were no relevant differences between the groups regarding pregnancy outcomes, although there was a trend of higher neonatal intensive care admission in the group of women with pregestational diabetes (45.2% vs. 36.1%, p = 0.051).ConclusionsOvert diabetes was diagnosed in one third of this cohort of pregnant women with hyperglycemia. Their pregnancy outcomes were similar to those of women with pregestational diabetes and were mostly related to maternal demographic characteristics and metabolic control. A call to action should be made to identify women of childbearing age at risk for pre-pregnancy diabetes; to detect hyperglycemia before conception; and to implement timely preconception care to all women with diabetes.
A longitudinal analysis of developing marine science identity in a place-based, undergraduate research experience
Authors: Ambrosino Christine M. , Rivera Malia Ana J. 
Published: November 2022

AbstractBackgroundStudents from historically excluded groups face many pedagogical, societal, and institutional barriers that lead to disproportionately lower levels of entering and higher levels of attrition from Science, Technology, Engineering, and Math (STEM) undergraduate programs. Student experiences within a STEM learning environment play a large role in influencing participation and persistence in science, and place-based education (PBE) is one pedagogical approach that aims to increase student engagement with science. By allowing students to engage with scientific concepts through their own knowledge systems, PBE can develop these students’ science identity and nurture a sense of belonging within the science community. This study examined student science identity in participants of a place-based, early-credit, Hawaiʻi undergraduate research experience, the Research Experiences in Marine Science (REMS) Program.ResultsStudent science identity was measured via responses from pre- and post-program Likert-type surveys before and after participation in the REMS program along the dimensions of Performance/Competence, Interest, and Recognition. The science identities of REMS alumni who returned to participate in the program as near-peer mentors and undergraduate researchers were also measured to explore whether repeated exposure to the program experience continued to promote shifts in identity construct metrics. Results indicate that all student groups who participated in REMS, including alumni, gained confidence in their science content understanding and research skills, increased their interest in science as a subject and as a career pathway, and recognized how science affects their communities. New students demonstrated the largest shifts in their science identity metrics, but alumni also indicated further development of their science identities.ConclusionsThe data from this study suggest that the timing of interventions which aim to influence student science identity and persistence in STEM pathways is an important factor when targeting student groups transitioning to undergraduate programs. Future educational efforts to increase the positive development of student science identity should consider the potential benefits of cumulative research experiences to support students through their early careers as undergraduates in STEM.
The spectrum of cardiovascular complications related to immune-checkpoint inhibitor treatment
Authors: Andres Maria Sol , Ramalingam Sivatharshini , Rosen Stuart D. , Baksi John , Khattar Rajdeep , Kirichenko Yulia , Young Kate , Yousaf Nadia , Okines Alicia , Huddart Robert , Harrington Kevin , Furness Andrew J.S. , Turajlic Samra , Pickering Lisa , Popat Sanjay , Larkin James , Lyon Alexander R. 
Published: November 2022

Abstract
Background
The full range of cardiovascular complications related to the use of Immune checkpoint inhibitors (ICI) is not fully understood. We aim to describe the spectrum of cardiovascular adverse events (cvAEs) by presenting our real-world experience of the diagnosis and management of these complications.

Methods
Two thousand six hundred and forty-seven (2647) patients were started on ICI treatment between 2014 and 2020. Data from 110 patients referred to the cardio-oncology service with a suspected cvAE was collected prospectively and analysed.

Results
Eighty-nine
patients (3.4%) were confirmed to have cvAEs while on ICI therapy.
Myocarditis was the most frequent event (33/89), followed by
tachyarrhythmia (27/89), non-inflammatory left ventricular dysfunction (NILVD)
(15/89) and pericarditis (7/89). Results from myocarditis and non-inflammatory left ventricular
dysfunction cohorts were compared. Myocarditis and NILVD showed significant
differences in respect toof
troponin elevation, cardiac magnetic resonance abnormalities and ventricular
function. Dual ICI therapy and other immune related adverse events were more
frequently associated with myocarditis than NILVD. There was a significant
difference in the median time from starting ICI treatment to presentation with
myocarditis versus NILVD (12 vs 26 weeks p = 0.049). Through early recognition
of myocarditis, prompt treatment with steroids and interruption of ICI, there
were no cardiovascular in-hospital deaths. NILVD did not
require steroid treatment and ICI could be restarted safely.

Conclusions
The full spectrum of cardiovascular complications
in patients with immune checkpoint inhibitors is much broader than initially
described. Myocarditis remains the most frequent cvAE related to ICI treatment.
A novel type of myocardial injury was observed and
defined as Atrial tachyarrhythmias and NILVD
were also frequent in this cohort. NILVD has a This
differs fromdifferent presentation from
ICI-related myocarditis, mainly usually
presenting afterby the lack of
inflammatory features on CMR and biomarkers and
a later presentation in time.
Group Care in the first 1000 days: implementation and process evaluation of contextually adapted antenatal and postnatal group care targeting diverse vulnerable populations in high-, middle- and low-resource settings
Authors: Martens Nele , Crone Mathilde R. , Hindori-Mohangoo Ashna , Hindori Manodj , Reis Ria , Hoxha Ilir S. , Abanga Jedidia , Matthews Shanaaz , Berry Lizette , van der Kleij Rianne M. J. J. , van den Akker-van Marle M. Elske , van Damme Astrid , Talrich Florence , Beeckman Katrien , Court Christine Mc , Rising Sharon Schindler , Billings Deborah L. , Rijnders Marlies 
Published: November 2022

Abstract
Background
Group care (GC) improves the quality of maternity care, stimulates women’s participation in their own care and facilitates growth of women’s social support networks. There is an urgent need to identify and disseminate the best mechanisms for implementing GC in ways that are feasible, context appropriate and sustainable. This protocol presents the aims and methods of an innovative implementation research project entitled Group Care in the first 1000 days (GC_1000), which addresses this need.

Aims
The aim of GC_1000 is to co-create and disseminate evidence-based implementation strategies and tools to support successful implementation and scale-up of GC in health systems throughout the world, with particular attention to the needs of ‘vulnerable’ populations.

Methods
By working through five inter-related work packages, each with specific tasks, objectives and deliverables, the global research team will systematically examine and document the implementation and scale-up processes of antenatal and postnatal GC in seven different countries. The GC_1000 project is grounded theoretically in the consolidated framework for implementation research (CFIR), while the process evaluation is guided by ‘Realistic Evaluation’ principles. Data are gathered across all research phases and analysis at each stage is synthesized to develop Context-Intervention-Mechanism-Outcome configurations.

Discussion
GC_1000 will generate evidence-based knowledge about the integration of complex interventions into diverse health care systems. The 4-year project also will pave the way for sustained implementation of GC, significantly benefitting populations with adverse pregnancy and birthing experiences as well as poor outcomes.
A mixed methods protocol to implement universal firearm injury risk screening and intervention among youth and adults in emergency departments across a large US health system
Authors: Sathya Chethan , Harrison Laura , Dauber Katherine , Kapoor Sandeep 
Published: November 2022

Abstract
Background
Firearm injury is a leading cause of preventable death in the USA. Healthcare providers are uniquely poised to focus on firearm safety and injury prevention from an apolitical harm reduction lens; however, few providers and healthcare settings incorporate firearm injury prevention strategies into usual care. We outline the first protocol to determine how to implement universal Firearm Injury and Mortality Prevention (FIMP) strategies that identify and address firearm access and violence risk in healthcare settings as part of routine care using the Consolidated Framework for Implementation Research (CFIR) to inform implementation and evaluation.

Methods
The components of our FIMP strategy, including universal screening, intervention for patients at risk, and resources, will be developed from existing evidence-based strategies for firearm access and violence risk (intervention characteristics). The implementation process will include components of Screening, Brief Intervention, and Referral to Treatment (SBIRT) for substance use, adapted to FIMP (implementation process). To engage stakeholders, harmonize language, and garner support, an Executive Advisory Board (EAB) will be formed, consisting of the site- and system-level stakeholders (inner setting) and community stakeholders, including influential figures such as local religious and spiritual leaders, individuals with lived experience, and community-based organizations (outer setting). Pre-implementation surveys will identify the characteristics of individuals and guide the development of education prior to implementation. Patient-level screening data will be analyzed to identify the risk factors, implementation will be evaluated using mixed methods, and a limited-efficacy study will evaluate whether strategies were successful in driving behavior change.

Discussion
This study protocol has breakthrough and methodological innovations, by addressing FIMP as part of usual care to directly mitigate firearm injury risk among youth, adults, and household members (e.g., children) and by using rigorous methods to inform healthcare industry implementation of FIMP strategies. The expected outcomes of this study protocol will provide a solid basis for larger-scale dissemination and evaluation of implementation, effectiveness, and usability across broader pediatric and adult healthcare settings. This project will advance the implementation science and have a positive impact on the health of our patients and communities by preventing firearm injury and mortality and shifting the paradigm to view FIMP through a public health lens.
Hydrocarbon generation and expulsion of the Fengcheng Formation in the Mahu sag, Junggar Basin, China: Implications for shale oil resource potential
Authors: Wu Yuping , Liu Chenglin , Jiang Fujie , Hu Tao , Zhang Chenxi , Lv Jiahao , Hu Meiling , Huang Renda , Wu Guanyun , Awan Rizwan Sarwar 
Published: November 2022

The Permian source rocks in the Junggar Basin are widely developed, especially the Fengcheng Formation, which is the most significant source rock in the basin. However, due to insufficient research on the hydrocarbon generation (HG) and hydrocarbon expulsion (HE) characteristics of the source rocks, it is unclear whether a significant amount of retained hydrocarbons remain within shales. In general, the original organic matter abundance and kerogen type control hydrocarbon generation potential (HGP) and HE capacity in lacustrine shales. Therefore, the degradation rate method was used to establish the original organic carbon recovery model for different types of kerogen. Combined with the geologic and geochemical characteristics of the source rock, the HG, HE, and shale oil resource potential of the Fengcheng shale have been evaluated. We have found that the Fengcheng shale is mainly carbonate-type mudstone widely distributed with an average thickness greater than 100 m. The Fengcheng shale is composed of type II kerogen and reached the mature to high-mature thermal maturity stage, with the maximum original organic carbon exceeding 4.0 wt%. Meanwhile, the amount of retained hydrocarbons within shales is abundant according to the HGP model. Monte Carlo simulation finds that the shale oil resources of the Fengcheng shale are 23.30 × 108 t. Free oil resources account for 60%, reaching 13.75 × 108 t, indicating tremendous shale oil exploration potential.
Malnutrition among patients with Type-2 Diabetes Mellitus
Authors: Ahmed Ibrar , Kaifi Hoor Maab , Tahir Hira , Javed Adan 
Published: November 2022

Objectives: The present study aims to evaluate the nutritional status of diabetic patients using Subjective Global Assessment (SGA) tool.
Methods: A prospective cross-sectional study was conducted at Endocrine and Medicine Department of Lady Reading Hospital from September 2019 to March 2020. A total of 359 patients diagnosed with Type-2 Diabetes Mellitus (T2DM) were included in the study. The malnutrition status was assessed using SGA, and clinical parameters including albumin and total leukocyte count (TLC).
Results: We have observed mild to moderate malnutrition among 48.2% patients, and severe malnutrition in 10.6% patients as per the SGA scoring. Among the factors associated with nutritional status were BMI (p<0.01), and presence of CAD (DM complication) (p=0.015). As per the correlation analysis, BMI had a significant negative correlation with nutritional status (r=-0.351; p<0.01).
Conclusion: It is concluded from the study results that there is a high prevalence of malnutrition among the enrolled diabetic patients.
doi: https://doi.org/10.12669/pjms.39.1.5485
How to cite this: Ahmed I, Kaifi HM, Tahir H, Javed A. Malnutrition among patients with Type-2 Diabetes Mellitus. Pak J Med Sci. 2023;39(1):---------. doi: https://doi.org/10.12669/pjms.39.1.5485
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Προσεγγίσεις του χώρου στα λογοτεχνικά κείμενα της Δευτεροβάθμιας εκπαίδευσης με τη χρήση STORYMAP JavaScript (JS)
Authors: Μαργαρίτη Μαρία 
Published: November 2022

Η παρούσα μελέτη εκπονείται στο πλαίσιο της Λογοτεχνικής Γεωγραφίας, ενός πρόσφατα ανεπτυγμένου κλάδου της Ανθρωπογεωγραφίας, που έχει ως ως αντικείμενο την εξέταση του αναπαριστάμενου χώρου στα λογοτεχνικά έργα. Συγκεκριμένα, σκοπός της μελέτης είναι να διερευνήσει το πως μπορεί ο μαθητής να αντιληφθεί καλύτερα τον χώρο που αναπαρίσταται στα επιλεγμένα λογοτεχνικά κείμενα, τα οποία συμπεριλαμβάνονται στα βιβλία της Δευτεροβάθμιας Εκπαίδευσης στην Ελλάδα, με έμφαση στα κείμενα που έχουν ως θέμα την αλληλεπίδραση του ανθρώπου με τη φύση ή κάνουν αναφορά σε περιβαλλοντικά προβλήματα και να συνδέσει στη συνέχεια αυτές τις γνώσεις με τον πραγματικό κόσμο. Για την προσέγγιση του χώρου προτείνεται η χρήση της εφαρμογής STORYMAP JavaScript (JS) για την ανάρτηση ιστοριών στο διαδίκτυο με υλικό που οι μαθητές θα συγκεντρώσουν από τα κείμενα των σχολικών βιβλίων αλλά και από το διαδίκτυο, όπως ιστορικές πληροφορίες και οπτικοακουστικό υλικό, το οποίο θα προσθέσουν στην εφαρμογή τοποθετώντας τα σε γεωγραφικά σημεία στο διαδραστικό χάρτη. Έτσι, με τη συμβολή των νέων τεχνολογιών, η διδασκαλία του μαθήματος της Λογοτεχνίας γίνεται βιωματική και πιο ενδιαφέρουσα.
USING DIGITAL TECHNOLOGIES PROBLEMS IN STUDENT PROJECT TEAMS KNOWLEDGE MANAGEMENT
Authors: Kashtanova YEkatyerina , Lobacheva A. 
Published: November 2022

The article discusses the issues students' ownership of digital technologies and notes the problems associated with the insufficient development of students' digital competencies in the team project work implementation. In contrast to the popular opinion about the negative impact on the use of digital technologies in the educational process of the adaptation difficulties to software products of the university teaching staff, the article authors focus on the primitive possession of digital products and gadgets by students.
One of the main problems the authors highlight is the underdevelopment of students' skills that allow them to immerse themselves in the study of software functionality, the search for possible digital products for consumption and the study of the modern digital services market. This is due to the peculiarities of the social category under consideration, which are presented in the article, as well as the prevailing consuming type of behavior among students and the presence of only superficial knowledge about the technologies functioning.
The authors of the article consider the need for students to develop knowledge management competencies of project teams in a digital environment and using modern digital technologies, describe a few difficulties that arise when trying to establish digital interaction and knowledge management when working with student project teams and analyze the causes of their occurrence.
Trends in SARS-CoV-2 infection prevalence during England’s roadmap out of lockdown, January to July 2021
Authors: Eales Oliver , Wang Haowei , Haw David , Ainslie Kylie E. C. , Walters Caroline E. , Atchison Christina , Cooke Graham , Barclay Wendy , Ward Helen , Darzi Ara , Ashby Deborah , Donnelly Christl A. , Elliott Paul , Riley Steven 
Published: November 2022

Background
Following rapidly rising COVID-19 case numbers, England entered a national lockdown on 6 January 2021, with staged relaxations of restrictions from 8 March 2021 onwards.

Aim
We characterise how the lockdown and subsequent easing of restrictions affected trends in SARS-CoV-2 infection prevalence.

Methods
On average, risk of infection is proportional to infection prevalence. The REal-time Assessment of Community Transmission-1 (REACT-1) study is a repeat cross-sectional study of over 98,000 people every round (rounds approximately monthly) that estimates infection prevalence in England. We used Bayesian P-splines to estimate prevalence and the time-varying reproduction number (Rt) nationally, regionally and by age group from round 8 (beginning 6 January 2021) to round 13 (ending 12 July 2021) of REACT-1. As a comparator, a separate segmented-exponential model was used to quantify the impact on Rt of each relaxation of restrictions.

Results
Following an initial plateau of 1.54% until mid-January, infection prevalence decreased until 13 May when it reached a minimum of 0.09%, before increasing until the end of the study to 0.76%. Following the first easing of restrictions, which included schools reopening, the reproduction number Rt increased by 82% (55%, 108%), but then decreased by 61% (82%, 53%) at the second easing of restrictions, which was timed to match the Easter school holidays. Following further relaxations of restrictions, the observed Rt increased steadily, though the increase due to these restrictions being relaxed was offset by the effects of vaccination and also affected by the rapid rise of Delta. There was a high degree of synchrony in the temporal patterns of prevalence between regions and age groups.

Conclusion
High-resolution prevalence data fitted to P-splines allowed us to show that the lockdown was effective at reducing risk of infection with school holidays/closures playing a significant part.