bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluating automated electronic case report form data entry from electronic health records
Authors: Cheng Alex C. , Banasiewicz Mary K. , Johnson Jakea D. , Sulieman Lina , Kennedy Nan , Delacqua Francesco , Lewis Adam A. , Joly Meghan M. , Bistran-Hall Amanda J. , Collins Sean , Self Wesley H. , Shotwell Matthew S. , Lindsell Christopher J. , Harris Paul A. 
Published: December 2022

Abstract

Background:
Many clinical trials leverage real-world data. Typically, these data are manually abstracted from electronic health records (EHRs) and entered into electronic case report forms (CRFs), a time and labor-intensive process that is also error-prone and may miss information. Automated transfer of data from EHRs to eCRFs has the potential to reduce data abstraction and entry burden as well as improve data quality and safety.

Methods:
We conducted a test of automated EHR-to-CRF data transfer for 40 participants in a clinical trial of hospitalized COVID-19 patients. We determined which coordinator-entered data could be automated from the EHR (coverage), and the frequency with which the values from the automated EHR feed and values entered by study personnel for the actual study matched exactly (concordance).

Results:
The automated EHR feed populated 10,081/11,952 (84%) coordinator-completed values. For fields where both the automation and study personnel provided data, the values matched exactly 89% of the time. Highest concordance was for daily lab results (94%), which also required the most personnel resources (30 minutes per participant). In a detailed analysis of 196 instances where personnel and automation entered values differed, both a study coordinator and a data analyst agreed that 152 (78%) instances were a result of data entry error.

Conclusions:
An automated EHR feed has the potential to significantly decrease study personnel effort while improving the accuracy of CRF data.
Insect trace fossils as indicators of climatic conditions during the uppermost Pleistocene deposits in southern Brazilian Atlantic coast
Authors: Ramos Kimberly Silva , Netto Renata Guimarães , Sedorko Daniel , Nascimento Diego Luciano 
Published: December 2022

AbstractThe Rio Grande do Sul Coastal Plain records sea-level oscillations driven by climatic changes during Quaternary glaciations, represented as four lagoon-barrier systems, the last one forming after the last glacial maximum and still active. Marine trace fossils are reported in the Pleistocene deposits, but terrestrial burrows also occur in the eolian deposits. The insect trace fossil assemblages from the uppermost Pleistocene deposits of the lagoon-barrier system III are used as relative proxies to infer the climate regimes that controlled sedimentation prior to the last glacial maximum. Two suites occur in the eolian deposits: the Vondrichnus suite, dominated by structures produced by termites, in the basal eolian beds; and the Celliforma suite, dominated by hymenopteran (bees and wasps) structures, in the upper eolian beds. The dominance of termite nests indicates humid conditions. The shift upward to the Celliforma suite signals a change in the humidity regime and the prevalence of drier conditions. The stratigraphic position of the ichnoassemblage, above the uppermost Pleistocene marine transgressive beds that formed during the last interglacial and below the record of the last glacial maximum in this coastal plain, suggests that the last glacial interval controlled this humid-dry fluctuation.
Ultra-processed foods: a fit-for-purpose concept for nutrition policy activities to tackle unhealthy and unsustainable diets
Authors: Lawrence Mark 
Published: December 2022

AbstractModern nutrition science began approximately 100 years ago in the context of nutrient deficiency diseases. Nutrition research and policy activities were framed mostly within a reductionist paradigm in which foods were analysed as being a collection of their constituent nutrients. Today, nutrition problems extend to all forms of malnutrition as well as environmental sustainability considerations and are associated with food and dietary pattern exposures. In 2009, researchers investigating the nutrition transition in Brazil proposed that industrial food processing was a key determinant of nutrition problems. The NOVA food classification system which is based on the nature, extent and purposes of food processing was developed to operationalise this proposition. The ultra-processed food (UPF) concept within NOVA is receiving much attention in relation to nutrition research and policy activities. This commentary describes the UPF concept as being fit-for-purpose in providing guidance to inform policy activities to tackle unhealthy and unsustainable diets. There is now a substantial body of evidence linking UPF exposure with adverse population and planetary health outcomes. The UPF concept is increasingly being used in the development of food-based dietary guidelines and nutrition policy actions. It challenges many conventional nutrition research and policy activities as well as the political economy of the industrial food system. Inevitably, there are politicised debates associated with UPF and it is apparent a disproportionate number of articles claiming the concept is controversial originate from a small number of researchers with declared associations with UPF manufacturers. Prominent examples of these claims are assessed.
Dear Virginia
Authors: S.C.  
Published: December 2022

Congratulations on your admission and fellowship for graduate work at ………. It should be the beginning of a very promising career and I'll be glad to give you whatever advice I can on the subject.In answer to your question, there is probably less overt discrimination against women now. Graduate admissions and fellowships look fairly good on the record. And although departments are still lagging in professorial positions and salaries for women, some of them are making an effort to catch up. It shouldn't be too long before most departments have their “quota” of assistant professors. The problem now is with the subtler forms of discrimination — “Phase II” of whatever it is we are involved in. (Phase II, like Phase I, uses sex as a basis for choice, but its arguments are more sophisticated. Phase I says “A woman's place is in the home.” Phase II says “We'd like to hire a woman, but …”)
A Rank Order of Eateries: A Chicago Stochastic Model
Authors: Haider Donald H. 
Published: December 2022

.... The hands of men took hold and tugged And the breaths of men went into the junk And the junk stood up into skyscrapers and asked Who am I? Am I a city?Carl Sandburg-“The Windy City”Robert Merriam, picking up where his father left off, once indicated that it would take 50 years for an aroused citizenry to root out corruption in Chicago. It has taken at least that long to upgrade Chicago's restaurants. Several decades ago, top gourmet societies labelled Chicago a “gastronomic wasteland.” Among the many old clichés and modern prejudices that the Windy City is constantly seeking to outlive is the quality of its restaurants. New Yorkers, of course, will not let old myths die. Gail Green, New York Magazine galloping gourmet, recently went away from Chicago dubbing its restaurants the “Big Potato” — homely and solid, mealy and bland. Chicago epicureans responded by a whirlwind tour of the Gotham Town's “Best and Most Delectable,” writing devastating critiques of New York's much overrated eating places. If one can transcend these diatribes and gastronomic polemics, you will find Chicago to be as good a dining town as there is in the U.S.A. — variety, service, and prices.
The complexities of suicide: a multilevel survival analysis examining individual, familial and neighbourhood determinants of suicide risk using Danish register-based data
Authors: Davies Megan , Horsdal Henriette Thisted , Antonsen Sussie , Sigsgaard Torben , Fan Chun Chieh , Thompson Wesley K. , Pedersen Carsten Bøcker , Sabel Clive E. 
Published: December 2022

AbstractBackgroundSuicide risk is complex and nuanced, and how place impacts suicide risk when considered alongside detailed individual risk factors remains uncertain. We aimed to examine suicide risk in Denmark with both individual and neighbourhood level risk factors.MethodsWe used Danish register-based data to identify individuals born in Denmark from 1972, with full parental information and psychiatric diagnosis history. We fitted a two-level survival model to estimate individual and neighbourhood determinants on suicide risk.ResultsWe identified 1723 cases of suicide in Denmark during the follow-up period from 1982 to 2015. Suicide risk was explained mainly by individual determinants. Parental comorbidities, particularly maternal schizophrenia [incidence rate ratio (IRR): 2.29, 95% CI 1.56–3.16] and paternal death (2.29, 95% CI 1.31–3.72) partly explained suicide risk when adjusted for all other determinants. The general contextual effect of suicide risk across neighbourhoods showed a median incidence rate ratio (MRR) of 1.13 (1.01–1.28), which was further reduced with full adjustment. Suicide risk increased in neighbourhoods with a higher proportion of manual workers (IRR: 1.08; 1.03–1.14), and decreased with a higher population density (IRR: 0.89; 0.83–0.96).ConclusionSuicide risk varies mainly between individuals, with parental comorbidities having the largest effect on suicide risk. Suicide risk was less impacted by neighbourhood, though, albeit to a lesser extent than individual determinants, some characteristics were associated with suicide risk. Suicide prevention policies might consider targeting interventions towards individuals more vulnerable due to particular parental comorbidities, whilst taking into account that some neighbourhood characteristics might exacerbate this risk further.
Correlation between non-invasive to invasive right-heart data in paediatric heart transplant patients
Authors: McGill Mark , Raja Kishore R. , Evans Michael , Hiremath Gurumurthy , Ameduri Rebecca , Narasimhan Shanti 
Published: December 2022

AbstractBackground:Paediatric studies have shown serum N-terminal pro b-type natriuretic peptide levels to be a valuable tool in the surveillance of myocardial function and an early biomarker for rejection in transplant patients. The correlation between low mean right atrial pressure and increased inferior vena cava collapsibility index is well studied in adults. Our study aims to assess correlation between non-invasive measurements (serum N-terminal pro b-type natriuretic peptide, inferior vena cava dimensions collapsibility, tricuspid regurgitation, and left ventricular remodelling index to invasive mean right atrial pressure in paediatric heart transplant patients).Methods:A single centre, retrospective chart review of the paediatric transplant patients from 0 to 21 years of age was performed between 2015 and 2017. Thirty-nine patients had complete data which includes cardiac catheterisation, transthoracic echocardiogram, and serum N-terminal pro b-type natriuretic peptide levels done within a two weeks of interval.Results:A higher inferior vena cava collapsibility index correlated with a lower mean right atrial pressure (r = −0.21, p = 0.04) and a larger inferior vena cava diameter in expiration indexed to body surface area (IVCmax/BSA0.5) correlated with a higher mean right atrial pressure (r = 0.29, p = 0.01). There was a correlation between elevated N-terminal pro b-type natriuretic peptide and inferior vena cava collapsibility index (r = −0.38, p = 0.0001), IVCmax/BSA0.5 (r = 0.25, p = 0.0002), and mean right atrial pressure (r = 0.6, p = 0.0001).Conclusion:Serum N-terminal pro b-type natriuretic peptide levels correlated to non-invasive measurements (inferior vena cava collapsibility index and IVCmax/BSA0.5) and to the invasive mean right atrial pressure. Non-invasive (IVC-CI IVCmax/BSA0.5) correlates with elevated mean right atrial pressure in this population. Together, these may serve as a reliable surveillance tool in assessing right heart filling pressures and cardiac function within the paediatric heart transplant patient.
Off-label use of a vena caval filter in the SVC in an adolescent with upper deep vein thrombosis
Authors: Dias João , Marinho Joana , Silva Patrícia Vaz , Simões Sofia , Silva Sónia , Pires António 
Published: December 2022

AbstractVena caval filters remain as a useful tool in patients with deep vein thrombosis and contraindications to anticoagulation. Although they are rarely used in paediatric patients, they have been shown to be safe and effective when used in the inferior vena cava.In this case report, we describe the off-label use of a retrievable vena caval filter in the superior vena cava in an adolescent with acute lymphoblastic leukaemia with extensive thrombosis of the right upper neck veins as a means to reduce the risk of pulmonary embolism.
Ultra-processed foods in public health nutrition: the unanswered questions
Authors: Gibney Michael J 
Published: December 2022

AbstractThere is a growing interest in the study of the degree of food processing and both health and nutritional outcomes. To that end, several definitions of the degree of processing have been proposed. However, when each of these is used on a common database of nutritional, clinical and anthropometric variables, the observed effect of high intakes of highly processed food, varies considerably.. Moreover, assigning a given food by nutritional experts, to its appropriate level of processing, has been shown to be variable. Thus, the subjective definitions of the degree of food processing and the coding of foods according to these classifications is prone to error is prone to error. Another issue that need resolution is the relative importance of the degree of food processing and the formulation of a processed food. Although correlational studies linking processed food and obesity abound, there is a need for more investigative studies.
Enhanced Mixing of Heat in the Arctic Ocean Halocline in Weakly Turbulent Conditions
Authors: Carpenter Jeffrey R. , Waterman Stephanie , Scheifele Benjamin 
Published: December 2022

AbstractIn the low‐energy mixing environment of the Arctic Ocean halocline, a unique mixing mechanism of temperature is present. It consists of the formation of small‐vertical‐scale (∼1 m) intrusive features, with temperature anomalies up to ∼0.1°C, that create mean‐square vertical temperature gradients that are orders of magnitude greater than the background. This finescale temperature structure results in enhanced heat fluxes in conditions of extremely weak turbulence and is responsible for an irreversible mixing of heat into cold halocline waters. The rates of thermal variance dissipation and heat transport are comparable to turbulent mechanisms in the Arctic Ocean, such as internal wave‐driven mixing and double diffusive convection. We propose that in conditions of low turbulence, and in the presence of lateral thermal variability, the temperature field displays a self‐regulating mechanism by which it is able to enhance its finescale structure to generate enhanced mixing, thus compensating for the lack of turbulent fluxes.
CMIP6 Models Trend Toward Less Persistent European Blocking Regimes in a Warming Climate
Authors: Dorrington Josh , Strommen Kristian , Fabiano Federico , Molteni Franco 
Published: December 2022

AbstractThe response of the Euro‐Atlantic wintertime circulation to climate change is deeply uncertain. The Atlantic jet is caught in a “tug‐of‐war” between rapid warming trends in both the tropics and the Arctic leading to debate over the changing “waviness” of the jet, which is subject to strong non‐linearity and internal variability. From the complementary perspective of weather regimes, there is considerable uncertainty in how atmospheric blocking will alter under climate change. By applying the hybrid approach of geopotential‐jet regimes to 6th phase of the coupled model inter‐comparison project projections, we show that the centers of action of anticyclonic regimes hardly alter even under severe warming. Instead, regimes are expected to become less persistent, with zonal flow conditions becoming more prevalent, although models disagree on the details of regime changes. Finally, we show the regime response can be captured qualitatively in a simple Lorenz‐like model, emphasizing the conceptual link between observed regimes and those in basic mathematical systems.
Earlier Onset and Shortened Meiyu Season During the Last Interglacial Based on Dynamical Downscaling Simulations
Authors: Jiang Nanxuan , Yan Qing , Wang Huijun , Li Hua 
Published: December 2022

AbstractDeciphering the Meiyu behavior during the Last Interglacial (∼127 ka; LIG) may deepen our understanding of drought and flooding events over East Asia in a warmer‐than‐present world induced by Earth's orbit. Based on dynamical downscaling simulations, we suggested a 15‐ and 30‐day earlier onset and retreat of the Meiyu during the LIG relative to preindustrial, respectively, leading to a shortened Meiyu season. Meantime, extreme precipitation in the Meiyu season became stronger and occurred more frequently. Intensified monsoonal circulation, poleward‐located western North Pacific subtropical high, and poleward shift of East Asian westerly jet during the LIG provided favorable moisture conditions for earlier onset and retreat of the Meiyu. The variations of atmospheric circulations were further regulated by the joint effect of the three oceans and diabatic heating over Tibetan Plateau. Our results highlight an important role of Earth's orbit in the Meiyu and imply more flooding events in a warmer world.
Fog Detection and Estimation Using CALIPSO Lidar Observations
Authors: Qiao Na , Wang Lixin , Marais Eugene , Li Feng 
Published: December 2022

AbstractMost fog detection from space cannot differentiate fog and low stratus clouds, and cannot estimate fog deposition. This study assessed the feasibility of using spaceborne lidar observations from the Cloud‐Aerosol Lidar and Infrared Pathfinder Satellite Observation (CALIPSO) in fog detection and estimation. We tested the method in the central Namib Desert, Namibia, where frequent fog events occur and fog observations are available. Results showed the CALIPSO backscatter signal at 532 nm can differentiate low clouds and fog due to its high‐resolution vertical profiles. Backscatter signals during fog events were significantly higher than those during non‐fog periods. The R2 between backscatter signals and fog observations was 0.85. Moreover, the backscatter signal was also sensitive to relative humidity variation (R2 = 0.66). These results indicate that the CALIPSO data are feasible to estimate fog occurrence and deposition, providing a new perspective for space‐based fog studies.
Riparian Microtopography Affects Event‐Driven Stream DOC Concentrations and DOM Quality in a Forested Headwater Catchment
Authors: Blaurock Katharina , Garthen Phil , da Silva Maria P. , Beudert Burkhard , Gilfedder Benjamin S. , Fleckenstein Jan H. , Peiffer Stefan , Lechtenfeld Oliver J. , Hopp Luisa 
Published: December 2022

AbstractThe transport of dissolved organic carbon (DOC) from the soils to inland waters plays an important role in the global carbon cycle. Widespread increases in DOC concentrations have been observed in surface waters over the last few decades, affecting carbon balances, ecosystem functioning and drinking water treatment. However, the primary hydrological controls on DOC mobilization are still uncertain. The aim of this study was to investigate the role of microtopography in the riparian zone for DOC export and DOM quality. DOC concentration and DOM quality in the shallow groundwater of a riparian zone and in streamflow in a forested headwater catchment was investigated using fluorescence and absorbance characteristics. We found higher DOC concentrations with a higher aromaticity in the microtopographical depressions, which were influenced by highly dynamic shallow groundwater levels, than in the flat forest soil. As a result of the frequent wet‐dry cycles in the upper soil layers, aromatic DOC accumulated in the shallow groundwater within and below the microtopographical depressions. Rising groundwater levels during precipitation events led to the connection of the microtopographical depressions to the stream, resulting in a change toward more aromatic DOC in the stream. Increasing stream DOC concentrations were accompanied by increasing concentrations of iron and aluminum, suggesting the coupled release of these metals with DOC from the riparian zone. Our results highlight the importance of the interplay between microtopography and groundwater level dynamics in the riparian zone for DOC export from headwater catchments.
Recurrent repeat expansions in human cancer genomes
Authors: Erwin Graham S. , Gürsoy Gamze , Al-Abri Rashid , Suriyaprakash Ashwini , Dolzhenko Egor , Zhu Kevin , Hoerner Christian R. , White Shannon M. , Ramirez Lucia , Vadlakonda Ananya , Vadlakonda Alekhya , von Kraut Konor , Park Julia , Brannon Charlotte M. , Sumano Daniel A. , Kirtikar Raushun A. , Erwin Alicia A. , Metzner Thomas J. , Yuen Ryan K. C. , Fan Alice C. , Leppert John T. , Eberle Michael A. , Gerstein Mark , Snyder Michael P. 
Published: December 2022

AbstractExpansion of a single repetitive DNA sequence, termed a tandem repeat (TR), is known to cause more than 50 diseases1,2. However, repeat expansions are often not explored beyond neurological and neurodegenerative disorders. In some cancers, mutations accumulate in short tracts of TRs, a phenomenon termed microsatellite instability; however, larger repeat expansions have not been systematically analysed in cancer3–8. Here we identified TR expansions in 2,622 cancer genomes spanning 29 cancer types. In seven cancer types, we found 160 recurrent repeat expansions (rREs), most of which (155/160) were subtype specific. We found that rREs were non-uniformly distributed in the genome with enrichment near candidate cis-regulatory elements, suggesting a potential role in gene regulation. One rRE, a GAAA-repeat expansion, located near a regulatory element in the first intron of UGT2B7 was detected in 34% of renal cell carcinoma samples and was validated by long-read DNA sequencing. Moreover, in preliminary experiments, treating cells that harbour this rRE with a GAAA-targeting molecule led to a dose-dependent decrease in cell proliferation. Overall, our results suggest that rREs may be an important but unexplored source of genetic variation in human cancer, and we provide a comprehensive catalogue for further study.