bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of Two Clinical Laboratory Assays for Measuring Serum Adalimumab and Antibodies to Adalimumab
Authors: Jain Dharmendra , Pido Mary Therese J , Delgado Julio C , Willrich Maria Alice V , Lázár-Molnár Eszter 
Published: September 2023

Abstract

Background
Adalimumab is a fully human monoclonal antibody developed against tumor necrosis factor (TNF), used for the treatment of autoimmune and chronic inflammatory diseases. Immunogenicity to this drug may lead to therapeutic failure. Various laboratory assays are used for measuring serum adalimumab and anti-drug antibodies (ADA) to adalimumab, for therapeutic monitoring and evaluation of clinical non-responsiveness. This study compared the performance of 2 clinical assays used by different reference laboratories.

Methods
In total, 120 residual clinical samples were tested at both laboratories. A sandwich ELISA for adalimumab detecting free drug and a bridging ELISA capable of detecting both free and bound ADA were performed at the Mayo Clinic. A functional cell-based reporter gene assay (RGA) was used at ARUP Laboratories for measuring bioactive serum drug concentrations, and neutralizing ADA.

Results
Seventy-eight samples had measurable concentrations of adalimumab by both methods and yielded a correlation coefficient r = 0.93, slope = 0.886, and intercept = 0.950. Overall agreement of 92.5% was observed between the assays, with most discrepant drug results being attributed to a higher positivity rate with ELISA (8/9). One outlier positive with RGA and negative with ELISA was confirmed by LC-MS/MS to be attributed to infliximab. Overall agreement of 79.2% was observed between the ADA assays. Differences in ADA results may be due to the bridging ELISA detecting total ADA (free, drug-bound, neutralizing, and non-neutralizing), while RGA detects free, neutralizing ADA only.

Conclusions
Although the assays are fundamentally different, the results show significant concordance between the clinically validated tests performed in different laboratories.
Prediction models using artificial intelligence and longitudinal data from electronic health records: a systematic methodological review
Authors: Carrasco-Ribelles Lucía A , Llanes-Jurado José , Gallego-Moll Carlos , Cabrera-Bean Margarita , Monteagudo-Zaragoza Mònica , Violán Concepción , Zabaleta-del-Olmo Edurne 
Published: September 2023

Abstract

Objective
To describe and appraise the use of artificial intelligence (AI) techniques that can cope with longitudinal data from electronic health records (EHRs) to predict health-related outcomes.

Methods
This review included studies in any language that: EHR was at least one of the data sources, collected longitudinal data, used an AI technique capable of handling longitudinal data, and predicted any health-related outcomes. We searched MEDLINE, Scopus, Web of Science, and IEEE Xplorer from inception to January 3, 2022. Information on the dataset, prediction task, data preprocessing, feature selection, method, validation, performance, and implementation was extracted and summarized using descriptive statistics. Risk of bias and completeness of reporting were assessed using a short form of PROBAST and TRIPOD, respectively.

Results
Eighty-one studies were included. Follow-up time and number of registers per patient varied greatly, and most predicted disease development or next event based on diagnoses and drug treatments. Architectures generally were based on Recurrent Neural Networks-like layers, though in recent years combining different layers or transformers has become more popular. About half of the included studies performed hyperparameter tuning and used attention mechanisms. Most performed a single train-test partition and could not correctly assess the variability of the model’s performance. Reporting quality was poor, and a third of the studies were at high risk of bias.

Conclusions
AI models are increasingly using longitudinal data. However, the heterogeneity in reporting methodology and results, and the lack of public EHR datasets and code sharing, complicate the possibility of replication.

Registration
PROSPERO database (CRD42022331388).
Deep learning algorithms to detect diabetic kidney disease from retinal photographs in multiethnic populations with diabetes
Authors: Betzler Bjorn Kaijun , Chee Evelyn Yi Lyn , He Feng , Lim Cynthia Ciwei , Ho Jinyi , Hamzah Haslina , Tan Ngiap Chuan , Liew Gerald , McKay Gareth J , Hogg Ruth E , Young Ian S , Cheng Ching-Yu , Lim Su Chi , Lee Aaron Y , Wong Tien Yin , Lee Mong Li , Hsu Wynne , Tan Gavin Siew Wei , Sabanayagam Charumathi 
Published: September 2023

Abstract

Objective
To develop a deep learning algorithm (DLA) to detect diabetic kideny disease (DKD) from retinal photographs of patients with diabetes, and evaluate performance in multiethnic populations.

Materials and methods
We trained 3 models: (1) image-only; (2) risk factor (RF)-only multivariable logistic regression (LR) model adjusted for age, sex, ethnicity, diabetes duration, HbA1c, systolic blood pressure; (3) hybrid multivariable LR model combining RF data and standardized z-scores from image-only model. Data from Singapore Integrated Diabetic Retinopathy Program (SiDRP) were used to develop (6066 participants with diabetes, primary-care-based) and internally validate (5-fold cross-validation) the models. External testing on 2 independent datasets: (1) Singapore Epidemiology of Eye Diseases (SEED) study (1885 participants with diabetes, population-based); (2) Singapore Macroangiopathy and Microvascular Reactivity in Type 2 Diabetes (SMART2D) (439 participants with diabetes, cross-sectional) in Singapore. Supplementary external testing on 2 Caucasian cohorts: (3) Australian Eye and Heart Study (AHES) (460 participants with diabetes, cross-sectional) and (4) Northern Ireland Cohort for the Longitudinal Study of Ageing (NICOLA) (265 participants with diabetes, cross-sectional).

Results
In SiDRP validation, area under the curve (AUC) was 0.826(95% CI 0.818-0.833) for image-only, 0.847(0.840-0.854) for RF-only, and 0.866(0.859-0.872) for hybrid. Estimates with SEED were 0.764(0.743-0.785) for image-only, 0.802(0.783-0.822) for RF-only, and 0.828(0.810-0.846) for hybrid. In SMART2D, AUC was 0.726(0.686-0.765) for image-only, 0.701(0.660-0.741) in RF-only, 0.761(0.724-0.797) for hybrid.

Discussion and conclusion
There is potential for DLA using retinal images as a screening adjunct for DKD among individuals with diabetes. This can value-add to existing DLA systems which diagnose diabetic retinopathy from retinal images, facilitating primary screening for DKD.
The leptin receptor gene affects piglet behavior and growth
Authors: Suárez-Mesa Rafael , Ros-Freixedes Roger , Díaz Marta , Marsellés Júlia , Pena Ramona N , Reixach Josep , Estany Joan 
Published: September 2023

Abstract
Piglets with low birth weight present low vitality after farrowing, often leading to impaired weight gain during lactation. A recessive missense variant (C &gt; T) for increased appetite and fatness in the porcine leptin receptor gene (rs709596309) causes a negative maternal effect on the weight of piglets at weaning. However, it is not known whether this variant already exerts an effect on the birth weight and vitality of newborn piglets and on their growing capacity during lactation. An experiment was conducted using 668 purebred Duroc piglets (131 CC, 311 CT, and 226 TT) from 74 multiparous sows (9 CC, 43 CT, and 22 TT) and 14 boars (1 CC, 10 CT, and 3 TT). All piglets were individually weighed at birth and tested for vitality, which was assessed on a scale from 1 (low vitality) to 3 (high vitality) based on behavioral observations, including the status of the piglet immediately before the test. Only non-adopted piglets were considered for piglet performance at weaning. Inferences on the effect of the genotype on birth and weaning traits were done on a Bayesian setting based on 2-trait bivariate models including the effects of the piglet and the litter, as well as the genotype of the sow and the piglet, the sex of the piglet, and the parity number. Vitality and the status of the piglet before the test were analyzed using a liability threshold (probit) model. As compared to other genotypes, TT newborn piglets were 28 g heavier, were more vital (the probability of being scored as highly vital was 6.5% higher) and were more often found suckling before the test (the probability of being suckling at test was 6.5% higher). As a result, they grew more during lactation (153 g) and were heavier at weaning (169 g) than littermates of the two other genotypes, thus partly compensating for the limited maternal capacity of TT sows. Our findings provide evidence that appetite-influencing genes, such as the leptin receptor gene, have developmental implications from very early life stages.
A Qualitative Investigation of Self-Compassion in Music Therapy Group Voicework With Women Coping With Incest
Authors: Riabzev Aviya , Bensimon Moshe 
Published: September 2023

Abstract
Incest occurs worldwide in all socioeconomic classes. To the best of our knowledge, literature on music processes with incest survivors is scarce, and studies focusing on voicework as a main technique for incest survivors in group settings have not been found. The current study aimed to explore incest survivors’ expectations regarding the use of their voice before participating in a vocal group therapy, and their lived experience of using their voice following the therapeutic process. Seventeen women living in an inpatient alternative center, coping with complex posttraumatic stress disorder due to incest, participated in a voicework group led by two music therapists. The women were divided into two groups of eight and nine women each and participated in eight sessions. Data were collected through focus groups before and after the therapeutic experience. Interpretative phenomenological analysis yielded themes indicating that before the therapeutic process, participants’ expectations regarding the use of their voice reflected low self-esteem, self-criticism, loneliness, shame, fear of exposure, and avoidance of singing. Following the therapeutic process, participants experienced their voice in a way that enabled them to feel self-acceptance and courage to sing, togetherness, bonding, belonging, a strengthening of existing relationships and ability to establish new ones, and awareness of body and emotions in the “here and now.” An overall examination of the findings indicates that participants progressed from experiencing lack of self-compassion before the therapeutic experience to enhanced self-compassion at its completion. The findings are interpreted via the self-compassion concept and implications are presented.
Radiation-quality-dependent bystander cellular effects induced by heavy-ion microbeams through different pathways
Authors: Suzuki Masao , Funayama Tomoo , Suzuki Michiyo , Kobayashi Yasuhiko 
Published: September 2023

Abstract
We investigated the radiation-quality-dependent bystander cellular effects using heavy-ion microbeams with different ion species. The heavy-ion microbeams were produced in Takasaki Ion Accelerators for Advanced Radiation Application, National Institutes for Quantum Science and Technology. Carbon (12C5+, 220 MeV), neon (20Ne7+, 260 MeV) and argon (40Ar13+, 460 MeV) ions were used as the microbeams, collimating the beam size with a diameter of 20 μm. After 0.5 and 3 h of irradiation, the surviving fractions (SFs) are significantly lower in cells irradiated with carbon ions without a gap-junction inhibitor than those irradiated with the inhibitor. However, the same SFs with no cell killing were found with and without the inhibitor at 24 h. Conversely, no cell-killing effect was observed in argon-ion-irradiated cells at 0.5 and 3 h; however, significantly low SFs were found at 24 h with and without the inhibitor, and the effect was suppressed using vitamin C and not dimethyl sulfoxide. The mutation frequency (MF) in cells irradiated with carbon ions was 8- to 6-fold higher than that in the unirradiated control at 0.5 and 3 h; however, no mutation was observed in cells treated with the gap-junction inhibitor. At 24 h, the MFs induced by each ion source were 3- to 5-fold higher and the same with and without the inhibitor. These findings suggest that the bystander cellular effects depend on the biological endpoints, ion species and time after microbeam irradiations with different pathways.
A case report of acute appendicitis complicated by pylephlebitis: medical and surgical management
Authors: Patel Krishna , Varre Jaya Sai , Williams Nate , Ruiz Oscar 
Published: September 2023

Abstract
Pylephlebitis is a suppurative thrombus of the portal vein and/or its branches secondary to an intra-abdominal infection. Acute appendicitis is the most common cause of emergency operation in general surgery and is typically treated with antibiotics and timely appendectomy with minimal adverse outcomes (Ferris M, Quan S, Kaplan BS, et al. The global incidence of appendicitis: a systematic review of population-based studies. Ann Surg 2017;266:237–41 and Poon S, Lee J, NG KM, Chiu GWY, et al. The current management of acute uncomplicated appendicitis: should there be a change in paradigm? A systematic review of the literatures and analysis of treatment performance. WJES 2017;12:46). Unfortunately, the identification of pyelephlebitis is difficult to make due to its nonspecific clinical presentation and can result in significant morbidity or mortality if not appropriately treated. Certain laboratory derangements and positive intra-abdominal imaging combined with a high index of suspicion can make the diagnosis. Treatment involves broad-spectrum antibiotics, anticoagulation, and source control of the primary nidus of infection. Our case presentation follows the successful clinical course of a young male diagnosed with acute appendicitis complicated by pylephlebitis. He was treated with antibiotics and anticoagulation followed by interval laparoscopic appendectomy with consequential resolution of thrombus on subsequent cross-sectional imaging.
Photoperiod sensitivity of Ppd-H1 and ppd-H1 isogenic lines of a spring barley cultivar: exploring extreme photoperiods
Authors: Parrado Jorge D , Savin Roxana , Slafer Gustavo A 
Published: September 2023

Abstract
Barley is a long-day plant with a major gene (PPD-H1) that determines its photoperiod sensitivity. Under long days (i.e. 16 h), flowering occurs earlier in sensitive (Ppd-H1) than in insensitive (ppd-H1) genotypes, while under short days (i.e. 12 h) both flower late and more or less simultaneously. We hypothesized that (i) the sensitive line should flower later than the insensitive line under very short days (&lt;12 h), and (ii) both the sensitive and insensitive lines should have similar phenology under very long days (&gt;18 h). When comparing a pair of spring isogenic lines for sensitive and insensitive PPD-H1 alleles (introgressing the PPD-H1 allele into the barley cultivar ‘WI4441’), we found responses fully in line with expectations for the commonly explored range from 12 to 16–18 h. When the responses were extended to very short days, sensitivity increased noticeably, and time to flowering of the sensitive line was longer than that of the insensitive one. Under very long days, the sensitive line did not respond further (it seemed to have reached its minimum time to flowering under a 16 h period), while the insensitive line continued shortening its time to flowering until c. 21 h. Consequently, both lines flowered similarly under very long days, which opens opportunities to easily test for differences in earliness per se, as in wheat.
Rapid leaf xylem acclimation diminishes the chances of embolism in grapevines
Authors: Sorek Yonatan , Netzer Yishai , Cohen Shabtai , Hochberg Uri 
Published: September 2023

Abstract
Under most conditions tight stomatal regulation in grapevines (Vitis vinifera) avoids xylem embolism. The current study evaluated grapevine responses to challenging scenarios that might lead to leaf embolism and consequential leaf damage. We hypothesized that embolism would occur if the vines experienced low xylem water potential (Ψx) shortly after bud break or later in the season under a combination of extreme drought and heat. We subjected vines to two potentially dangerous environments: (i) withholding irrigation from a vineyard grown in a heatwave-prone environment, and (ii) subjecting potted vines to terminal drought 1 month after bud break. In the field experiment, a heatwave at the beginning of August resulted in leaf temperatures over 45 °C. However, effective stomatal response maintained the xylem water potential (Ψx) well above the embolism threshold, and no leaf desiccation was observed. In the pot experiment, leaves of well-watered vines in May were relatively vulnerable to embolism with 50% embolism (P50) at –1.8 MPa. However, when exposed to drought, these leaves acclimated their leaf P50 by 0.65 MPa in less than a week and before reaching embolism values. When dried to embolizing Ψx, the leaf damage proportion matched (percentage-wise) the leaf embolism level. Our findings indicate that embolism and leaf damage are usually avoided by the grapevines’ efficient stomatal regulation and rapid acclimation of their xylem vulnerability.
Utilization of an immunochromatographic lateral flow assay for rapid detection of carbapenemase production in gram negative bacilli
Authors: Sullivan Emily , Macias Jimenez Maria D , Moore Nicholas M 
Published: September 2023

Abstract

Background
Rapid detection of carbapenemase production in gram negative bacilli has important treatment considerations.

Objective
We evaluated a lateral flow assay (LFA) for carbapenemase production compared with molecular detection of 5 (blaKPC, blaNDM, blaVIM, blaIMP, and blaOXA-48) carbapenemase genes.

Methods
A total of 218 carbapenem nonsusceptible strains, including species of Enterobacterales, Pseudomonas aeruginosa isolated from clinical cultures were tested using the Cepheid Xpert Carba-R assay and the NG Biotech Carba-5 lateral flow immunoassay.

Results
Overall agreement with LFA was 98.2% with accuracy for each target &gt;99% compared with polymerase chain reaction. Results were available within 15 minutes compared with 1 hour for molecular detection.

Conclusion
The use of accurate, rapid diagnostics compliments antimicrobial stewardship programs.
Revealing AGNs through TESS variability
Authors: Treiber Helena P , Hinkle Jason T , Fausnaugh Michael M , Shappee Benjamin J , Kochanek Christopher S , Vallely Patrick J , Auchettl Katie , Holoien Thomas W-S , Payne Anna V , Dai Xinyu 
Published: September 2023

ABSTRACT
We used Transiting Exoplanet Survey Satellite (TESS) data to identify 29 candidate active galactic nuclei (AGNs) through their optical variability. The high-cadence, high-precision TESS light curves present an opportunity for the identification of AGNs, including those not selected through other methods. Of the candidates, we found that 18 have either previously been identified as AGNs in the literature or could have been selected based on emission-line diagnostics, mid-IR colours, or X-ray luminosity. AGNs in low-mass galaxies offer a unique window into supermassive black hole and galaxy co-evolution and 8 of the 29 candidates have estimated black hole masses ≲ 106 M⊙. The low-mass galaxies NGC 4395 and NGC 4449 are two of our five ‘high-confidence’ candidates. Since our initial sample largely draws from just nine TESS sectors, we expect to identify at least ∼45 more candidates in the TESS primary and extended mission data sets, of which ∼60 per cent will be new AGNs and ∼20 per cent will be in low-mass galaxies.
Synthetic light-cone catalogues of modern redshift and weak lensing surveys with abacussummit
Authors: Hadzhiyska Boryana , Yuan S , Blake C , Eisenstein D J , Aguilar J , Ahlen S , Brooks D , Claybaugh T , de la Macorra A , Doel P , Emas N , Forero-Romero J E , Garcia-Quintero C , Ishak M , Joudaki S , Jullo E , Kehoe R , Kisner T , Kremin A , Krolewski A , Landriau M , Lange J U , Manera M , Miquel R , Nie Jundan , Poppett C , Porredon A , Rossi G , Ruggeri R , Saulder C , Schubnell M , Tarlé G , Weaver B A , Xhakaj E , Zhou Zhimin 
Published: September 2023

ABSTRACT
The joint analysis of different cosmological probes, such as galaxy clustering and weak lensing, can potentially yield invaluable insights into the nature of the primordial Universe, dark energy, and dark matter. However, the development of high-fidelity theoretical models is a necessary stepping stone. Here, we present public high-resolution weak lensing maps on the light-cone, generated using the N-body simulation suite abacussummit, and accompanying weak lensing mock catalogues, tuned to the Early Data Release small-scale clustering measurements of the Dark Energy Spectroscopic Instrument. Available in this release are maps of the cosmic shear, deflection angle, and convergence fields at source redshifts ranging from z = 0.15 to 2.45 as well as cosmic microwave background convergence maps for each of the 25 base-resolution simulations ($L_{\rm box} = 2000\, h^{-1}\, {\rm Mpc}$ and Npart = 69123) as well as for the two huge simulations ($L_{\rm box} = 7500\, h^{-1}\, {\rm Mpc}$ and Npart = 86403) at the fiducial abacussummit cosmology. The pixel resolution of each map is 0.21 arcmin, corresponding to a healpix Nside of 16 384. The sky coverage of the base simulations is an octant until z ≈ 0.8 (decreasing to about 1800 deg2 at z ≈ 2.4), whereas the huge simulations offer full-sky coverage until z ≈ 2.2. Mock lensing source catalogues are sampled matching the ensemble properties of the Kilo-Degree Survey, Dark Energy Survey, and Hyper Suprime-Cam data sets. The mock catalogues are validated against theoretical predictions for various clustering and lensing statistics, such as correlation multipoles, galaxy–shear, and shear–shear, showing excellent agreement. All products can be downloaded via a Globus endpoint (see Data Availability section).
The morphological transformation of ram pressure stripped galaxies: a pathway from late to early galaxy types
Authors: Marasco A , Poggianti B M , Fritz J , Werle A , Vulcani B , Moretti A , Gullieuszik M , Kulier A 
Published: September 2023

ABSTRACT
We investigate how the ageing of stellar populations can drive a morphological transformation in galaxies whose star formation (SF) activity has been quenched on short time-scales, like in cluster galaxies subject to ram pressure stripping from the intracluster medium. For this purpose, we use a sample of 91 galaxies with MUSE data from the GAs Stripping Phenomena in galaxies with MUSE (GASP) programme and of their spatially resolved SF history derived with the spectral modelling software sinopsis. We simulate the future continuation of the SF activities by exploring two quenching scenarios: an instantaneous truncation of the SF across the whole disc, and an outside-in quenching with typical stripping time-scales of $0.5\,$ and $1\, {\rm Gyr}$. For each scenario, we produce mock MUSE spectroscopic data cubes and optical images for our galaxies during their evolution, and classify their morphology using a new diagnostic tool, calibrated on cluster galaxies from the OmegaWINGS Survey. We find that, in all scenarios considered, the initial galaxy population dominated by blue-cloud spirals ($\sim 90~{{\ \rm per\ cent}}$) evolves into a mixed population mostly composed by red-sequence spirals ($50\!-\!55~{{\ \rm per\ cent}}$) and lenticulars ($\sim 40~{{\ \rm per\ cent}}$). The morphology transformation is completed after just 1.5–3.5 Gyr, proceeding faster in more efficient quenching scenarios. Our results indicate that, even without accounting for dynamical processes, SF quenching caused by the harsh environment of a cluster can significantly affect the morphology of the infalling galaxy population on timescales of a few Gyr.