bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selective conformal inference with false coverage-statement rate control
Authors: Bao Yajie , Huo Yuyang , Ren Haojie , Zou Changliang 
Published: February 2024

SUMMARY
Conformal inference is a popular tool for constructing prediction intervals. We consider here the scenario of post-selection/selective conformal inference, that is, prediction intervals are reported only for individuals selected from unlabelled test data. To account for multiplicity, we develop a general split conformal framework to construct selective prediction intervals with the false coverage-statement rate control. We first investigate the false coverage rate–adjusted method of Benjamini & Yekutieli (2005) in the present setting, and show that it is able to achieve false coverage-statement rate control, but yields uniformly inflated prediction intervals. We then propose a novel solution to the problem called selective conditional conformal prediction. Our method performs selection procedures on both the calibration set and test set, and then constructs conformal prediction intervals for the selected test candidates with the aid of the conditional empirical distribution obtained by the post-selection calibration set. When the selection rule is exchangeable, we show that our proposed method can exactly control the false coverage-statement rate in a model-free and distribution-free guarantee. For nonexchangeable selection procedures involving the calibration set, we provide non-asymptotic bounds for the false coverage-statement rate under mild distributional assumptions. Numerical results confirm the effectiveness and robustness of our method under false coverage-statement rate control and show that it achieves more narrowed prediction intervals over existing methods across various settings.
Resting-state electroencephalography microstates as a marker of photosensitivity in juvenile myoclonic epilepsy
Authors: Mazzeo Adolfo , Cerulli Irelli Emanuele , Leodori Giorgio , Mancuso Marco , Morano Alessandra , Giallonardo Anna Teresa , Di Bonaventura Carlo 
Published: February 2024

Abstract
Juvenile myoclonic epilepsy is an idiopathic generalized epilepsy syndrome associated with photosensitivity in approximately 30–40% of cases. Microstates consist of a brief period of time during which the topography of the whole resting-state electroencephalography (EEG) signal is characterized by a specific configuration. Previous neurophysiological and neuroimaging studies have suggested that Microstate B may represent activity within the visual network. In this case-control study, we aimed to investigate whether anatomical and functional alterations in the visual network observed in individuals with photosensitivity could lead to changes in Microstate B dynamics in photosensitive patients with juvenile myoclonic epilepsy. Resting-state electroencephalography microstate analysis was performed on 28 patients with juvenile myoclonic epilepsy. Of these, 15 patients exhibited photosensitivity, while the remaining 13 served as non-photosensitive controls. The two groups were carefully matched in terms of age, sex, seizure control and anti-seizure medications. Multivariate analysis of variance and repeated-measures analysis of variance were performed to assess significant differences in microstate metrics and syntax between the photosensitive and the non-photosensitive group. Post hoc false discovery rate adjusted unpaired t-tests were used to determine differences in specific microstate classes between the two groups. The four classical microstates (Classes A, B, C and D) accounted for 72.8% of the total electroencephalography signal variance in the photosensitive group and 75.64% in the non-photosensitive group. Multivariate analysis of variance revealed a statistically significant class–group interaction on microstate temporal metrics (P = 0.021). False discovery rate adjusted univariate analyses of variance indicated a significant class–group interaction for both mean occurrence (P = 0.002) and coverage (P = 0.03), but not for mean duration (P = 0.14). Post hoc false discovery rate adjusted unpaired t-tests showed significantly higher coverage (P = 0.02) and occurrence (P = 0.04) of Microstate B in photosensitive patients compared with non-photosensitive participants, along with an increased probability of transitioning from Microstates C (P = 0.04) and D (P = 0.02) to Microstate B. No significant differences were found concerning the other microstate classes between the two groups. Our study provides novel insights on resting-state electroencephalography microstate dynamics underlying photosensitivity in patients with juvenile myoclonic epilepsy. The increased representation of Microstate B in these patients might reflect the resting-state overactivation of the visual system underlying photosensitivity. Further research is warranted to investigate microstate dynamics in other photosensitive epilepsy syndromes.
A visual, rapid, and sensitive detection platform for Vibrio parahaemolyticus based on RPA-CRISPR/Cas12a and an immunochromatographic test strip
Authors: Wang Jinbin , Xu Danhong , Liu Hua , Liu Juan , Zhu Lemei , Zeng Haijuan , Wu Wenhui 
Published: February 2024

Abstract

Objectives
Vibrio parahaemolyticus is the primary species that causes vibriosis. In this study, a point-of-care detection method was developed for V. parahaemolyticus.

Materials and Methods
The detection platform targeted the thermolabile haemolysin (tlh) gene of V. parahaemolyticus based on recombinant polymerase amplification (RPA) and clustered regularly spaced short palindromic repeat (CRISPR/Cas) systems. The platform was combined with an immunochromatographic test strip (ICS) that enables low-cost, simple, visual detection of V. parahaemolyticus.

Results
The detection limit was 2.5×102 fg/µL for plasmids and 1.4×102 CFU/mL for V. parahaemolyticus. In addition, V. parahaemolyticus in salmon sashimi could be detected at a concentration of 154 CFU/g without enrichment, and the entire detection time was around 30 min. After enrichment for 6 h, 2 CFU/g V. parahaemolyticus could be detected.

Conclusions
Consequently, the proposed RPA-CRISPR/Cas12a-ICS platform could detect V. parahaemolyticus in seafood intuitively, quickly, and sensitively, leading to high practical application value.
An Emerging 21st-Century Midlife Sleep Crisis? Cohort Differences in Sleeping Patterns Among Americans in Midlife and Older Adulthood
Authors: Sheehan Connor M , Infurna Frank J 
Published: February 2024

Abstract

Objectives
To descriptively document birth cohort differences in sleeping patterns, self-reported age-specific sleep duration, and insomnia symptoms among adults aged 50+ from the National Health Interview Survey (NHIS) and the Health and Retirement Study (HRS).

Methods
We analyzed respondents aged 50+ (born 1920–1969) from the 2006–2018 NHIS (n = 162,400) and HRS (n = 28,918). We fit multinomial models among the NHIS sample predicting age-specific optimal sleep duration (optimal for age vs short for age, and optimal for age vs long for age). For the HRS sample, we fit growth curve models predicting age-based insomnia symptom trajectories. The models for both samples adjusted for age, gender, race/ethnicity, and educational attainment.

Results
Results regarding sleep duration in the NHIS, suggested that cohorts born in the 1950s and 1960s had significantly higher odds of reporting short sleep duration than cohorts before them. Results from the HRS similarly illustrated that cohorts born in the 1950s and 1960s had significantly higher levels of insomnia symptoms than those born before them. The worsening sleep among cohorts entering midlife was consistent regardless of alternative cohort specification, when age groups or periods were analyzed, and when more extensive covariates were modeled.

Discussion
We observe a pronounced decline in healthy sleeping patterns among American cohorts in midlife, with consistent and striking results across data sets, methods, and measures. These findings have important implications for the well-being and longevity of Americans who have entered midlife in the 21st century.
A framework for multidisciplinary science observations from commercial ships
Authors: Macdonald Alison M , Hiron Luna , McRaven Leah , Stolp Laura , Strom Kerry , Hudak Rebecca , Smith Shawn R , Hummon Julia , Andres Magdalena 
Published: February 2024

Abstract
Science Research on Commercial Ships (Science RoCS) is a grassroots multi-institution group of scientists, engineers, data managers, and administrators seeking to further research opportunities by equipping commercial vessels with suites of maritime appropriate scientific sensors operated autonomously on regular ship routes with minimal crew intervention. Science RoCS aims to foster cooperation between the shipping industry and scientific community at a level that will be transformative for societally relevant ocean science, promote cross-disciplinary ocean science through simultaneous observation of the air/sea interface and water column, and spur a technological revolution in observational oceanography by developing new turnkey, maritime-industry-appropriate scientific equipment whose data streams can be used to stimulate innovations in oceanic (physical, chemical, and biological) understanding and forecasting. We envision a future where scientific data collection on commercial ships is the new industry standard, providing repeat measurements in undersampled, remote regions, on scales not otherwise accessible to the scientific community.
Shark and odontocete depredation on the catch of the tuna longline fishery in New Caledonia (South Pacific Ocean)
Authors: Mollier Margaux , Mazé Camille , Prioul François , Hamer Paul , Hosken Malo , McKechnie Sam , Tixier Paul 
Published: February 2024

Abstract
Large marine predators feeding on fish caught on fishing gear, referred to as ‘depredation’, occur in a wide range of fisheries worldwide. Depredation can result in negative ecological and socio-economic impacts, leading to conflict between fishers and depredating species. However, depredation remains understudied in many fisheries, and this hampers the development of effective mitigation solutions. In this study, 21 years of fishing data (2002–2022) were used to assess shark and odontocete depredation in the pelagic tuna longline fishery of New Caledonia. Using generalized linear models, the year, season, effort, soaking time, and vessel were identified as variables significantly influencing the probability of depredation to occur. Results showed that while shark depredation occurred more frequently than odontocete depredation (58.5% vs. 9.2% of the longline sets), they damaged a lower proportion of fish (3.9% vs. 12.3%) over the study period. Unlike sharks, odontocetes selectively depredate tuna, with their highest occurrence during periods of high tuna catch rates, suggesting a co-occurrence with fishing activities. Together, these results indicate that depredation in the New Caledonian fishery is high compared to other regions and provide essential information on the dynamics and impacts of the issue as a basis for considering management and mitigation options.
Tangential tensor fields on deformable surfaces—how to derive consistent L2-gradient flows
Authors: Nitschke Ingo , Sadik Souhayl , Voigt Axel 
Published: February 2024

Abstract
We consider gradient flows of surface energies that depend on the surface by a parameterization and on a tangential tensor field. The flow allows for dissipation by evolving the parameterization and the tensor field simultaneously. This requires the choice of a notation for independence. We introduce different gauges of surface independence and show their consequences for the evolution. In order to guarantee a decrease in energy, the gauge of surface independence and the time derivative have to be chosen consistently. We demonstrate the results for a surface Frank–Oseen–Helfrich energy.
One Man, Two Guvnors: Revisiting the Principle Against Two Employers
Authors: Wynn-Evans Charles 
Published: February 2024

Abstract
This case note reviews the detail of, rationale for, and issues arising in relation to the longstanding principle that in general terms an employee cannot simultaneously have two employers in the context of its impact on the scope and application of labour law protections and its recent consideration by the Employment Appeal Tribunal in its Embery and United Taxis decisions. It is argued that this principle is ripe for reconsideration and restatement, not least in the light of the arguments in favour of the adoption of a joint employment model in order, where appropriate, to ensure the effective application of labour standards.
A5 DEVELOPMENT OF A PRE-CLINICAL MOUSE MODEL TO INVESTIGATE ADVERSE FOOD REACTIONS IN INTESTINAL INFLAMMATION
Authors: Barbosa da Luz B , Rondeau L , Dang R , Caminero A 
Published: February 2024

Abstract

Background
Patients with chronic intestinal conditions, including inflammatory bowel disease (IBD), experience diverse food-related adverse reactions. However,, the precise mechanisms of food intolerances in IBD remains unclear. Emerging evidence suggests that altered diet-microbiota interactions can contribute to the development of IBD. Previously we shown that intestinal microbiota plays an important role in the development of food intolerances. We hypothesize that microbial alterations in IBD patients facilitate adverse reactions to foods.

Aims
To establish a preclinical mouse model to study adverse food reactions in intestinal inflammation.

Methods
Eight-week-old C57BL/6 mice were treated with 3% dextran sodium sulfate (DSS) for 5 days, then divided into three groups. The first group was sensitized to dairy protein (3% casein and 3% whey), using 4 oral administrations of cholera toxin over 2 weeks, without any further diet intervention. The second group was also sensitized to casein and whey, then after 1 week of recovery, the mice were subsequently place on a chow containing casein and whey. Finally, the third group was subjected to diet intervention without sensitization. The same experiment was repeated in a different subset of C57BL/6 mice which included a second cycle of DSS (1.5%) during the dietary interventions. Markers of intestinal inflammation (disease activity index (DAI), histological damage, cell infiltration and pro-inflammatory genes expression (NanoString)) and intestinal microbiota were analysed after 1 week of the diet intervention.

Results
Mice previously sensitized on the dairy diet exhibited an enhanced activation of immune cells after intestinal inflammation. While the histological damage score did not reveal significant differences among experimental groups, the sensitized group under dairy intervention exhibited an elevated level of immune cell infiltration, increasing the polymorphonuclear, CD3+ and mast cells. Gene expression also revealed that dairy induced the expression of inflammatory genes, such as C6, Arg1, Tnf, Il6, Cxcl9 and Cxcl10. When animals are subjected to a second DSS-cycle, dairy worsen colitis in mice previously sensitized, as shown by higher DAI compared to group with control diet and dairy diet without sensitization.

Conclusions
In the context of intestinal inflammation, dairy protein leads to immune activation characterized by an increase in polymorphonuclear cells, mast cells and lymphocytes, as well as worsening colitis. Future studies using this model will provide valuable insights into the role of intestinal microbiota in food intolerances associated with intestinal inflammation.

Funding Agencies
CCC
A7 CANNABINOID 1 AND 2 RECEPTOR AGONISTS AND MU-OPIOID RECEPTOR AGONISTS SYNERGISTICALLY INHIBIT COLONIC NOCICEPTION DURING ACUTE COLITIS
Authors: Tsang Q K , Lomax A E , Vanner S , Reed D E 
Published: February 2024

Abstract

Background
Abdominal pain is a debilitating symptom in patients with inflammatory bowel disease. Previously we have shown that combining sub-analgesic doses of cannabinoid 1 receptor (CB1R), but not cannabinoid 2 receptor (CB2R), and mu-opioid receptor (MOR) agonists synergistically inhibits colonic nociception in healthy mice. However, it is unknown whether this combination has analgesic efficacy in a pre-clinical model of colitis.

Aims
To determine the effects of combining sub-analgesic doses of CBR and MOR agonists on colonic nociception during acute colitis.

Methods
Colitis was induced in male and female C57BL/6 mice with 2.5% dextran sulfate sodium in drinking water. Extracellular afferent nerve recordings were obtained from ex vivo flat sheet preparations of mouse distal colon. Mechanosensitivity of single afferent axons was assessed via probing of the colon with a 1g von Frey hair before and after superfusion of agonists of CB1R or CB2R plus MOR. To examine effects in vivo, visceromotor response (VMR) to colorectal distention (volume range 20-80 µL) was measured via electromyography. Mice were injected intraperitoneally with vehicle, or a combination of CB1R or CB2R agonist plus morphine 30-minutes prior to VMR experiment. Data were analyzed using a one or two-way ANOVA with Bonferroni test. N denotes number of mice; n denotes number of single afferent axons.

Results
In afferent nerve recordings, in contrast to healthy mice, the CB2R agonist HU-308 (1 µM and 3 µM) inhibited colonic mechanosensitivity in mice with colitis (1 µM: p&lt;0.01, N=5, n=12; 3 µM: p&lt;0.01, N=7, n=10); a lower concentration (300 nM) had no effect (p=0.52, N=6, n=10). The CB1R agonist ACEA (10 µM) reduced mechanosensitivity during acute colitis (p&lt;0.05, n=11, N=6), whereas 100 nM (p&gt;0.99, n=7, N=5) and 1 µM (p=0.25, n=10, N=6) had no effect. A combination of sub-analgesic concentrations of ACEA (100 nM) and DAMGO (MOR agonist, 1 nM) inhibited colonic mechanosensitivity in healthy mice (p&lt;0.01, N=4, n=8) and during acute colitis (p&lt;0.05, N=6, n=8). While a combination of sub-analgesic concentrations of HU-308 (300 nM) and DAMGO (1 nM) had no effect in healthy mice (p=0.70, N=4, n=8), it inhibited colonic mechanosensitivity during acute colitis (p&lt;0.01, N=8, n=15). In VMR experiments, a combination of a sub-analgesic dose of ACEA (0.3 mg/kg) with morphine (0.3 mg/kg) reduced VMR (p&lt;0.01, N=7) during acute colitis. Similarly, a combination of a sub-analgesic dose of HU-308 (1 mg/kg) and morphine (0.3 mg/kg) reduced VMR (p&lt;0.01, N=6) during acute colitis.

Conclusions
A CB2R agonist inhibits colonic nociception during acute colitis, but not in healthy mice. A sub-analgesic combination of CB1R and MOR agonists can inhibit pain in healthy and inflamed mice, while combining sub-analgesic CB2R and MOR agonists is only inhibitory during acute colitis.

Funding Agencies
NRC
A11 TELOCYTES-FOXL1+ REGULATES THE EXTRACELLULAR MATRIX NETWORK IN COLITIS-ASSOCIATED CANCER
Authors: Reyes Nicolas V , Alfonso A B , Raisch J , Boisvert F , Lauzon M A , Perreault N 
Published: February 2024

Abstract
NOT PUBLISHED AT AUTHOR’S REQUEST
Please acknowledge all funding agencies listed below
Funding Agencies
CIHRDoctoral Scholarship Fonds de recherche du Québec (FRQS)
A15 LEVERAGING CULTURE-DEPENDENT AND -INDEPENDENT METAGENOMICS TO IDENTIFY ENTEROBACTERIACEAE GENES ASSOCIATED WITH ACTIVE ULCERATIVE COLITIS
Authors: Tertigas D , Rinawi F , Moayyedi P , Griffiths A , Surette M 
Published: February 2024

Abstract

Background
Ulcerative colitis (UC) is a type of inflammatory bowel disease (IBD) that is restricted to the large intestine and is characterized by mucosal inflammation. There is evidence that pathogenic bacteria contribute to UC pathogenesis in at least some patients and the bacterial family Enterobacteriaceae are prime suspects. Some strains of Enterobacteriaceae carry virulence genes important for colonizing the gut (e.g. fimH) and disrupting the intestinal epithelium (e.g. hemolysins). We hypothesize that key virulence genes carried by strains of many Enterobacteriaceae species contribute to disease activity in some UC patients. As we predict virulence genes are strain-specific, the detection of the species alone (e.g. Escherichia coli) is insufficient to predict pathogenic potential and this has confounded previous studies to identify infectious agents in UC.

Aims
We aim to use culture-dependent and -independent sequencing approaches to identify Enterobacteriaceae genes in the UC gut microbiome associated with active disease.

Methods
UC patient stool samples collected throughout enrolment in randomized control trials of fecal microbiota transplantation (FMT) for adult UC (n=10) and microbiome studies in early-onset pediatric UC (n=25) were cultured on MacConkey (MAC) agar to enrich for Enterobacteriaceae. Strains were isolated from baseline stool samples cultured on MAC agar for whole genome sequencing and virulence gene characterization. Baseline and post-treatment stool samples cultured on MAC agar were sent for metagenomic sequencing. Using a subset of 11 pediatric patients, I developed a metagenomic pipeline to identify Enterobacteriaceae genes enriched during active UC compared to periods of remission or milder disease.

Results
Known virulence genes, including fimH and hemolysins, were present in some strains across multiple Enterobacteriaceae species. Using an unbiased metagenomic approach with the pediatric cohort, we identified 42 genes enriched at baseline with the criteria they must be elevated in at least three of the 11 patients. The majority of the 42 genes were distributed into six gene clusters, including a small plasmid.

Conclusions
Our approach allows us to identify genes enriched in active UC that have not been previously described in the literature and our analysis will be repeated with our adult cohort. Genes that are enriched in active UC in the pediatric and/or adult cohort will be validated in publicly available metagenomic datasets that consist of both IBD patients and healthy controls. Furthermore, culture-dependent approaches allow us to test mechanisms in vivo that are informed by our bioinformatics. Leveraging microbiome and clinical data provides a unique window to guide future diagnostics and treatments to improve outcomes for UC patients.

Funding Agencies
CIHROGS