bluuebunny/crossref_metadata_2025_split huggingface dataset:
Errors in the implementation, analysis, and reporting of randomization within obesity and nutrition research: a guide to their avoidance
Authors: Vorland Colby J. , Brown Andrew W. , Dawson John A. , Dickinson Stephanie L. , Golzarri-Arroyo Lilian , Hannon Bridget A. , Heo Moonseong , Heymsfield Steven B. , Jayawardene Wasantha P. , Kahathuduwa Chanaka N. , Keith Scott W. , Oakes J. Michael , Tekwe Carmen D. , Thabane Lehana , Allison David B. 
Published: July 2021

AbstractRandomization is an important tool used to establish causal inferences in studies designed to further our understanding of questions related to obesity and nutrition. To take advantage of the inferences afforded by randomization, scientific standards must be upheld during the planning, execution, analysis, and reporting of such studies. We discuss ten errors in randomized experiments from real-world examples from the literature and outline best practices for their avoidance. These ten errors include: representing nonrandom allocation as random, failing to adequately conceal allocation, not accounting for changing allocation ratios, replacing subjects in nonrandom ways, failing to account for non-independence, drawing inferences by comparing statistical significance from within-group comparisons instead of between-groups, pooling data and breaking the randomized design, failing to account for missing data, failing to report sufficient information to understand study methods, and failing to frame the causal question as testing the randomized assignment per se. We hope that these examples will aid researchers, reviewers, journal editors, and other readers to endeavor to a high standard of scientific rigor in randomized experiments within obesity and nutrition research.
A comprehensive review on biomarkers associated with painful temporomandibular disorders
Authors: Shrivastava Mayank , Battaglino Ricardo , Ye Liang 
Published: July 2021

AbstractPain of the orofacial region is the primary complaint for which patients seek treatment. Of all the orofacial pain conditions, one condition that possess a significant global health problem is temporomandibular disorder (TMD). Patients with TMD typically frequently complaints of pain as a symptom. TMD can occur due to complex interplay between peripheral and central sensitization, endogenous modulatory pathways, and cortical processing. For diagnosis of TMD pain a descriptive history, clinical assessment, and imaging is needed. However, due to the complex nature of pain an additional step is needed to render a definitive TMD diagnosis. In this review we explicate the role of different biomarkers involved in painful TMD. In painful TMD conditions, the role of biomarkers is still elusive. We believe that the identification of biomarkers associated with painful TMD may stimulate researchers and clinician to understand the mechanism underlying the pathogenesis of TMD and help them in developing newer methods for the diagnosis and management of TMD. Therefore, to understand the potential relationship of biomarkers, and painful TMD we categorize the biomarkers as molecular biomarkers, neuroimaging biomarkers and sensory biomarkers. In addition, we will briefly discuss pain genetics and the role of potential microRNA (miRNA) involved in TMD pain.
Differential immune responses in pregnant patients recovered from COVID-19
Authors: Chen Ge , Zhang Yiming , Zhang Yaoyao , Ai Jihui , Yang Bin , Cui Mengge , Liao Qiuyue , Chen Hanxiao , Bai Hualin , Shang Dashing , Chen Jing , Sun ChaoYang , Liu Haiyi , Liu Fengyuan , Mao Bin , Sun Guoqiang , Chen Lu , Lin Jing-wen , Li Kezhen 
Published: July 2021

AbstractPregnant women are generally more susceptible to viral infection. Although the impact of SARS-CoV-2 in pregnancy remains to be determined, evidence indicates that the risk factors for severe COVID-19 are similar in pregnancy to the general population. Here we systemically analyzed the clinical characteristics of pregnant and non-pregnant female COVID-19 patients who were hospitalized during the same period and found that pregnant patients developed marked lymphopenia and higher inflammation evident by higher C-reactive protein and IL-6. To elucidate the pathways that might contribute to immunopathology or protective immunity against COVID-19 during pregnancy, we applied single-cell mRNA sequencing to profile peripheral blood mononuclear cells from four pregnant and six non-pregnant female patients after recovery along with four pregnant and three non-pregnant healthy donors. We found normal clonal expansion of T cells in the pregnant patients, heightened activation and chemotaxis in NK, NKT, and MAIT cells, and differential interferon responses in the monocyte compartment. Our data present a unique feature in both innate and adaptive immune responses in pregnant patients recovered from COVID-19.
Tubulointerstitial nephritis and uveitis in Northern Ireland
Authors: Heaney A. , McLoone E. , Williams M. , Silvestri G. , Courtney A. E. , O’Rourke D. , McAvoy C. E. 
Published: July 2021

Abstract
Objectives
This paper looks at patients with a diagnosis of tubulointerstitial nephritis and uveitis (TINU) presenting to the Northern Ireland regional adult and paediatric uveitis service in the Belfast Health and Social Care Trust. The demographic distribution, treatment required and the visual and renal outcomes of these patients are documented.

Methods
Data were collected retrospectively on 24 patients with TINU using the Northern Ireland Electronic Care Record, central pathology records alongside the adult and paediatric uveitis databases from 2011 to 2021. Patients were categorised into two groups using the Mandeville classification system. Standard Uveitis Nomenclature (SUN) was used to classify the uveitis.

Results
The population prevalence is at least 12.6 cases per million based on a population of 1.9 million. Nineteen of 24 cases were definite TINU and five of 24 probable. Seventeen out of 24 had biopsy-positive TIN, all of which met all of the Mandeville clinical diagnostic features required for a definite diagnosis. All but one presented with acute bilateral anterior uveitis. The paediatric cases ranged from age 12 to 18 at age of onset with a mean age of 14. Of the 18 adult onset cases, the age ranged from 20 to 76 years. The mean age of onset for the adult cases was 53 years. Of these patients 71% were female; 42% required second-line immunosuppression for ocular disease. Visual acuity was maintained. Follow-up time ranged from 3 months to 16 years. No patient developed long-term renal impairment.

Conclusions
TINU is a cause of uveitis in both the paediatric and adult populations. In Northern Ireland average age with TINU was older than much of the published literature. Long-term immunosuppression for uveitis may be required as ongoing ocular, rather than renal inflammation seemed to require treatment.
Clustering and control for adaptation uncovers time-warped spike time patterns in cortical networks in vivo
Authors: Isbister James B. , Reyes-Puerta Vicente , Sun Jyh-Jang , Horenko Illia , Luhmann Heiko J. 
Published: July 2021

AbstractHow information in the nervous system is encoded by patterns of action potentials (i.e. spikes) remains an open question. Multi-neuron patterns of single spikes are a prime candidate for spike time encoding but their temporal variability requires further characterisation. Here we show how known sources of spike count variability affect stimulus-evoked spike time patterns between neurons separated over multiple layers and columns of adult rat somatosensory cortex in vivo. On subsets of trials (clusters) and after controlling for stimulus-response adaptation, spike time differences between pairs of neurons are “time-warped” (compressed/stretched) by trial-to-trial changes in shared excitability, explaining why fixed spike time patterns and noise correlations are seldom reported. We show that predicted cortical state is correlated between groups of 4 neurons, introducing the possibility of spike time pattern modulation by population-wide trial-to-trial changes in excitability (i.e. cortical state). Under the assumption of state-dependent coding, we propose an improved potential encoding capacity.
Discovery of a tsunami deposit from the Bronze Age Santorini eruption at Malia (Crete): impact, chronology, extension
Authors: Lespez Laurent , Lescure Séverine , Saulnier-Copard Ségolène , Glais Arthur , Berger Jean-François , Lavigne Franck , Pearson Charlotte , Virmoux Clément , Müller Celka Sylvie , Pomadère Maia 
Published: July 2021

AbstractA geomorphological survey immediately west of the Minoan town of Malia (Crete) shows that a tsunami resulting from the Bronze Age Santorini eruption reached the outskirts of the Palatial center. Sediment cores testify a unique erosional event during the Late Minoan period, followed locally by a high energy sand unit comprising marine fauna. This confirms that a tsunami impacted northern Crete and caused an inundation up to 400 m inland at Malia. We obtained a radiocarbon range of 1744–1544 BCE for the secure pre-tsunami context and an interval 1509–1430 BCE for the post-event layer. Examination of tsunami deposits was used to constrain run-up not exceeding 8 m asl. The results open the field for new research on the Bronze Age Santorini tsunami regarding both impact and consequences for the Minoan civilization.
Dialysis adequacy predictions using a machine learning method
Authors: Kim Hyung Woo , Heo Seok-Jae , Kim Jae Young , Kim Annie , Nam Chung-Mo , Kim Beom Seok 
Published: July 2021

AbstractDialysis adequacy is an important survival indicator in patients with chronic hemodialysis. However, there are inconveniences and disadvantages to measuring dialysis adequacy by blood samples. This study used machine learning models to predict dialysis adequacy in chronic hemodialysis patients using repeatedly measured data during hemodialysis. This study included 1333 hemodialysis sessions corresponding to the monthly examination dates of 61 patients. Patient demographics and clinical parameters were continuously measured from the hemodialysis machine; 240 measurements were collected from each hemodialysis session. Machine learning models (random forest and extreme gradient boosting [XGBoost]) and deep learning models (convolutional neural network and gated recurrent unit) were compared with multivariable linear regression models. The mean absolute percentage error (MAPE), root mean square error (RMSE), and Spearman’s rank correlation coefficient (Corr) for each model using fivefold cross-validation were calculated as performance measurements. The XGBoost model had the best performance among all methods (MAPE = 2.500; RMSE = 2.906; Corr = 0.873). The deep learning models with convolutional neural network (MAPE = 2.835; RMSE = 3.125; Corr = 0.833) and gated recurrent unit (MAPE = 2.974; RMSE = 3.230; Corr = 0.824) had similar performances. The linear regression models had the lowest performance (MAPE = 3.284; RMSE = 3.586; Corr = 0.770) compared with other models. Machine learning methods can accurately infer hemodialysis adequacy using continuously measured data from hemodialysis machines.
Effects of different returning method combined with decomposer on decomposition of organic components of straw and soil fertility
Authors: Wang Xiao , Wang Xuexin , Geng Peng , Yang Qian , Chen Kun , Liu Ning , Fan Yueling , Zhan Xiumei , Han Xiaori 
Published: July 2021

AbstractIn view of the problems of low straw decomposition rates and reduced soil fertility in southern Liaoning, China, we investigated the effects of no-tillage mode (NT), deep loosening + deep rotary tillage mode (PT), rotary tillage mode (RT) and the addition of decomposing agent (the next is called a decomposer) (NT + S, PT + S, RT + S) on the decomposition proportion of straw, respectively, by using the nylon net bag method in combination with 365-day field plot experiments. The decomposition rules of cellulose, hemicellulose and lignin as well as the dynamics of soil organic carbon (SOC), soil microbial biomass carbon (MBC) and soil dissolved organic carbon (DOC) in straw returned to the field for 15, 35, 55, 75, 95, 145 and 365 days were analyzed. The results showed that in the short term, the decomposition of straw was better in both the rotray tillage and deep loosening + deep rotary modes than in the no-tillage mode, and the addition of decomposer significantly promoted the decomposition of straw and the release of carbon from straw, among them, the RT + S treatment had the highest straw decomposition proportion and carbon release proportion in all sampling periods. After a one year experimental cycle, the RT + S treatment showed the highest proportion of cellulose, hemicellulose and lignin decomposition with 35.49%, 84.23% and 85.50%, respectively, and soil SOC, MBC and DOC contents were also higher than the other treatments with an increase of 2.30 g kg−1, 14.22 mg kg−1 and 25.10 mg kg−1, respectively, compared to the pre-experimental soil. Our results show that in the short term, to accelerate the decomposition rate of returned straw and increase the content of various forms of carbon in soil, rotary tillage can be used to return the straw to the field, while also spraying straw decomposer on its surface. This experiment used a new straw decomposer rich in a variety of microorganisms, combined with the comparison of a variety of straw return modes, and in-depth study of straw decomposition effects of cellulose, hemicellulose and lignin. Thus, a scheme that can effectively improve the decomposition rate of straw and the content of various forms of organic carbon in soil within a short period of time was explored to provide theoretical support for the southern Liaoning.
Citizens and scientists collect comparable oceanographic data: measurements of ocean transparency from the Secchi Disk study and science programmes
Authors: Kirby Richard R. , Beaugrand Gregory , Kleparski Loick , Goodall Susie , Lavender Samantha 
Published: July 2021

AbstractMarine phytoplankton accounts for approximately 50% of all photosynthesis on Earth, underpins the marine food chain and plays a central role in the Earth’s biogeochemical cycles and climate. In situ measurements of ocean transparency can be used to estimate phytoplankton biomass. The scale and challenging conditions of the ocean make it a difficult environment for in situ studies, however. Here, we show that citizen scientists (seafarers) using a simple white Secchi Disk can collect ocean transparency data to complement formal scientific efforts using similar equipment. Citizen scientist data can therefore help understand current climate-driven changes in phytoplankton biomass at a global scale.
Sensitive assay design for detection of anti-drug antibodies to biotherapeutics that lack an immunoglobulin Fc domain
Authors: Johnson Derrick , Simmons Erica , Abdeen Sanofar , Kinne Adam , Parmer Elijah , Rinker Sherri , Thystrup Jennifer , Ramaswamy Swarna , Bowsher Ronald R. 
Published: July 2021

AbstractToday the evaluation of unwanted immunogenicity is a key component in the clinical safety evaluation of new biotherapeutic drugs and macromolecular delivery strategies. However, the evolving structural complexity in contemporary biotherapeutics creates a need for on-going innovation in assay designs for reliable detection of anti-drug antibodies, especially for biotherapeutics that may not be well-suited for testing by a bridging assay. We, therefore, initiated systematic optimization of the direct binding assay to adapt it for routine use in regulatory-compliant assays of serum anti-drug antibodies. Accordingly, we first prepared a SULFO-TAG labeled conjugate of recombinant Protein-A/G to create a sensitive electrochemiluminescent secondary detection reagent with broad reactivity to antibodies across many species. Secondly, we evaluated candidate blocker-diluents to identify ones producing the highest signal-to-noise response ratios. Lastly, we introduced use of the ratio of signal responses in biotherapeutic-coated and uncoated wells as a data transformation strategy to identify biological outliers. This alternative data normalization approach improved normality, reduced skewness, and facilitated application of a parametric screening cut point. We believe the optimized direct binding assay design employing SULFO-TAG labeled Protein-A/G represents a useful analytical design for detecting serum ADA to biotherapeutics that lack an immunoglobulin Fc domain.
Anisotropy in mechanical unfolding of protein upon partner-assisted pulling and handle-assisted pulling
Authors: Arora Nisha , Hazra Jagadish Prasad , Rakshit Sabyasachi 
Published: July 2021

AbstractProteins as force-sensors respond to mechanical cues and regulate signaling in physiology. Proteins commonly connect the source and response points of mechanical cues in two conformations, independent proteins in end-to-end geometry and protein complexes in handshake geometry. The force-responsive property of independent proteins in end-to-end geometry is studied extensively using single-molecule force spectroscopy (SMFS). The physiological significance of the complex conformations in force-sensing is often disregarded as mere surge protectors. However, with the potential of force-steering, protein complexes possess a distinct mechano-responsive property over individual force-sensors. To decipher, we choose a force-sensing protein, cadherin-23, from tip-link complex and perform SMFS using end-to-end geometry and handshake complex geometry. We measure higher force-resilience of cadherin-23 with preferential shorter extensions in handshake mode of pulling over the direct mode. The handshake geometry drives the force-response of cadherin-23 through different potential-energy landscapes than direct pulling. Analysis of the dynamic network structure of cadherin-23 under tension indicates narrow force-distributions among residues in cadherin-23 in direct pulling, resulting in low force-dissipation paths and low resilience to force. Overall, the distinct and superior mechanical responses of cadherin-23 in handshake geometry than single protein geometry highlight a probable evolutionary drive of protein-protein complexes as force-conveyors over independent ones.
FIP200 restricts RNA virus infection by facilitating RIG-I activation
Authors: Wang Lingyan , Song Kun , Hao Wenzhuo , Wu Yakun , Patil Girish , Hua Fang , Sun Yiwen , Huang Chaoqun , Ritchey Jerry , Jones Clinton , Liu Lin , Guan Jun-Lin , Li Shitao 
Published: July 2021

AbstractRetinoic acid-inducible gene I (RIG-I) senses viral RNA and instigates an innate immune signaling cascade to induce type I interferon expression. Currently, the regulatory mechanisms controlling RIG-I activation remain to be fully elucidated. Here we show that the FAK family kinase-interacting protein of 200 kDa (FIP200) facilitates RIG-I activation. FIP200 deficiency impaired RIG-I signaling and increased host susceptibility to RNA virus infection. In vivo studies further demonstrated FIP200 knockout mice were more susceptible to RNA virus infection due to the reduced innate immune response. Mechanistic studies revealed that FIP200 competed with the helicase domain of RIG-I for interaction with the two tandem caspase activation and recruitment domains (2CARD), thereby facilitating the release of 2CARD from the suppression status. Furthermore, FIP200 formed a dimer and facilitated 2CARD oligomerization, thereby promoting RIG-I activation. Taken together, our study defines FIP200 as an innate immune signaling molecule that positively regulates RIG-I activation.
Self-branched Nb2O5 nanoarrays as “electron-ion reservoirs” to enhance the conversion of polysulfides in flexible Li–S batteries
Authors: Li Huanhuan , Chen Huiqin , Chen Yuxin , Bai Guangyue , Zhang Mengjie , Xie Shanshan , Zhuo Kelei 
Published: July 2021

A novel sulfur matrix integrating self-branched Nb2O5 nanoarrays and flexible carbon cloth (NBCC) is designed. Intriguingly, the selected Nb2O5 nanoarrays can work as “electron-ion reservoirs” to accelerate the conversion reaction of LiPSs.
Deriving physical parameters of unresolved star clusters
Authors: Naujalis Rokas , Stonkutė Rima , Vansevičius Vladas 
Published: July 2021

Context. This study is the sixth of a series that investigates degeneracy and stochasticity problems present in the determination of the age, mass, extinction, and metallicity of partially resolved or unresolved star clusters in external galaxies when using Hubble Space Telescope broadband photometry. In the fifth publication, it was noticed that inconsistencies in cluster colour indices, which arise due to projected foreground and background stars on the apertures, enhance age-metallicity-extinction degeneracies.
Aims. In this work we aim to present new aperture photometry results for a sample of star clusters from the M 31 Panchromatic Hubble Andromeda Treasury (PHAT) survey.
Methods. We employed two methods of aperture photometry. The first method is ordinary aperture photometry to measure total cluster fluxes. The second method was introduced to avoid the brightest foreground and background stars that project onto large apertures. This method employs smaller apertures, adapted to cover a central part of clusters, and applies an aperture correction, derived for the F475W passband, to other passbands. We note that this procedure is valid only for clusters without prominent systematic gradients of colour indices beyond half-light radii.
Results. We present two catalogues of star cluster aperture photometry (produced by applying ordinary aperture photometry and adaptive aperture photometry methods) with estimated uncertainties for a sample of 1181 star clusters from the M 31 PHAT survey. Compared to the M 31 PHAT fundamental star cluster aperture photometry catalogue published by Johnson et al., there are changes made in the following: cluster centre coordinates, aperture sizes, and sky background estimates.
MeerKAT 21-cm H I imaging of Abell 2626 and beyond
Authors: Healy J. , Deb T. , Verheijen M. A. W. , Blyth S.-L. , Serra P. , Ramatsoku M. , Vulcani B. 
Published: July 2021

Context. The morphology-density relation manifests the environmental dependence of the formation and evolution of galaxies as they continuously migrate through the cosmic web to ever denser environments. As gas-rich galaxies traverse the outskirts and inner regions of galaxy clusters, they experience sudden and radical changes in their gas content and star formation activity.
Aims. The goal of this work is to gain an H I perspective on gas depletion mechanisms acting on galaxies and galaxy groups that are being accreted by a moderately massive galaxy cluster. We aim to study the relative importance and efficiency of processes such as ram-pressure stripping and tidal interactions as well as their dependency on the local and global environment of galaxies in the cluster core and in its surroundings.
Methods. We have conducted a blind radio continuum and H I spectral line imaging survey with the MeerKAT radio telescope of a 2° × 2° area centred on the galaxy cluster Abell 2626. We have used the CARAcal pipeline to reduce the data, SoFiA to detect sources within the H I data cube, and GIPSY to construct spatially resolved information on the H I morphologies and kinematics of the H I detected galaxies.
Results. We have detected H I in 219 galaxies with optical counterparts within the entire surveyed volume. We present the H I properties of each of the detected galaxies as a data catalogue and as an atlas page for each galaxy, including H I column-density maps, velocity fields, position-velocity diagrams, and global H I profiles. These data will also be used for case studies of identified ‘jellyfish’ galaxies and galaxy population studies by means of morphological classification of the direct H I detections as well as using the H I stacking technique.