julilili42/papers huggingface dataset:
Untangling the relationship between smoking and systemic sclerosis: an analysis of the EUSTAR cohort
2024-05-01

Objectives To untangle the association between smoking and systemic sclerosis (SSc). Methods In the European Scleroderma Trials and Research cohort, the autoantibody status was compared between ever-smokers and never-smokers. Time until disease progression was assessed using Kaplan-Meier curves. Cox models were built to investigate the influence of smoking over 15 years of follow-up. All analyses were performed for the total cohort and stratified for sex and for positivity of anti-centromere (ACA) and anti-topoisomerase antibodies (ATA). Results Overall, 12 314 patients were included in the study. Of these, 10 393 were women (84%), 4637 were ACA-positive (38%), 3919 were ATA-positive (32%) and 4271 (35%) were ever-smokers. In men, but not in women, smoking was associated with mortality (HR 1.63, 95% CI 1.23 to 2.16, p=0.001). Ever-smoking women were at higher risk for skin progression (HR 1.10, 95% CI 1.00 to 1.22, p=0.046) and for ‘any organ progression’ (HR 1.07, 95% CI 1.00 to 1.13, p=0.036). In women, 34% of never-smokers were ATA-positive compared with 21% of ever-smokers (p&lt;0.001). In the group of ever-smokers, higher exposure rates, reflected by the number of pack-years (OR 0.98, 95% CI 0.97 to 0.99, p&lt;0.001) and by smoking duration (OR 0.96, 95% CI 0.95 to 0.97, p&lt;0.001), were associated with lower frequency of ATA. In ACA-positive patients, the risk of mortality (HR 1.29, 95% CI 1.02 to 1.63, p=0.033), cardiac involvement (HR 1.25, 95% CI 1.03 to 1.43, p=0.001), skin progression (HR 1.21, 95% CI 1.03 to 1.42, p=0.018) and ‘any organ progression’ (HR 1.14, 95% CI 1.05 to 1.24, p=0.002) was increased among smokers. In ATA-positive smoking patients, mortality (HR 1.40, 95% CI 1.10 to 1.78, p=0.006), skin progression (HR 1.19, 95% CI 1.03 to 1.37, p=0.020) digital ulcers (HR 1.17, 95% CI 1.02 to 1.34, p=0.029) and ‘any organ progression’ (HR 1.11, 95% CI 1.00 to 1.22, p=0.048) occurred more frequently. Conclusions Our stratified analysis demonstrates that smoking is associated with an increased risk for mortality in male SSc patients but not in women. Strikingly, smoking is associated with lower prevalence of ATA positivity, in particular in women. In both ATA-positive and ACA-positive patients, smoking is a risk factor for mortality, skin progression and ‘any organ progression’.
OPC-Pod: A New Sensor Payload to Measure Aerosol Particles for Small Uncrewed Aircraft Systems
2024-05-01

Abstract Atmospheric aerosols affect human health and influence atmospheric and biological processes. Dust can be transported long distances in the atmosphere, and the mechanisms that influence dust transport are not fully understood. To improve the database for numerical models that simulate dust transport, measurements are needed that cover both the vertical distribution of the dust and its size distribution. In addition to measurements with crewed aircraft, uncrewed aircraft systems (UASs) provide a particularly suitable platform for this purpose. In this paper, we present a payload for the small fixed-wing UAS of the type Multiple-Purpose Airborne Sensor Carrier 3 (MASC-3) for aerosol particle measurements that is based on the optical particle counter (OPC) OPC-N3 (Alphasense, United Kingdom), modified by the addition of a dryer and a passive aspiration system (OPC-Pod). Based on field tests with a reference instrument in Mannheim, Germany, wind tunnel tests, and a comparison measurement with the UAS-mounted aerosol particle measurement Universal Cloud and Aerosol Sounding System (UCASS) during a dust event over Cyprus, we show that the OPC-Pod can measure particle number concentrations in the range of 0.66–31 μ m as well as particle size distributions. The agreement of the OPC-Pod with UCASS is good. Both instruments resolve a vertical profile of the Saharan dust event, with a prominent dust layer between 1500 and 2800 m MSL, with particle number concentrations up to 35 cm −3 for particles between 0.66 and 31 μ m.
Detection of Vancomycin Resistant Genes in Intrinsically Antibiotic Resistant Bacteria from the Gut Microbiota of Indonesian Individuals.
2024-05-01

The presence of multiple vancomycin resistance genes in intrinsically resistant Gram-negative bacterial strains demonstrated the importance of the gut microbiota as a reservoir and hub for the horizontal transfer of antibiotic resistant genes.
Deployment of Water-based Liquid Scintillator in the Accelerator Neutrino Neutron Interaction Experiment
2024-05-01

Abstract The Accelerator Neutrino Neutron Interaction Experiment (ANNIE) is a 26-ton water Cherenkov neutrino detector installed on the Booster Neutrino Beam (BNB) at Fermilab. Its main physics goals are to perform a measurement of the neutron yield from neutrino-nucleus interactions, as well as a measurement of the charged-current cross section of muon neutrinos. An equally important focus is the research and development of new detector technologies and target media. Specifically, water-based liquid scintillator (WbLS) is of interest as a novel detector medium, as it allows for the simultaneous detection of Cherenkov light and scintillation. This paper presents the deployment of a 366 L WbLS vessel in ANNIE in March 2023 and the subsequent detection of both Cherenkov light and scintillation from the WbLS. This proof-of-concept allows for the future development of reconstruction and particle identification algorithms in ANNIE, as well as dedicated analyses within the WbLS volume, such as the search for neutral-current events and the hadronic scintillation component.
Fate of synthetic chemicals in the agronomic insect pest Spodoptera littoralis: experimental feeding-contact assay and toxicokinetic model
2024-05-01

Abstract Insecticides prevent or reduce insect crop damage, maintaining crop quality and quantity. Physiological traits, such as an insect’s feeding behavior, influence the way insecticides are absorbed and processed in the body (toxicokinetics), which can be exploited to improve species selectivity. To fully understand the uptake of insecticides, it is essential to study their total uptake and toxicokinetics independent of their toxic effects on insects. We studied the toxicokinetics (TK) of insecticidally inactive test compounds incorporating agro-like structural motifs in larvae of the Egyptian cotton leafworm (Spodoptera littoralis, Lepidoptera), and their distribution across all biological matrices, using laboratory experiments and modeling. We measured Spodoptera larval behavior and temporal changes of whole-body concentrations of test compounds during feeding on treated soybean leaf disks and throughout a subsequent depuration period. Differences in the distribution of the total quantities of compounds were found between the biological matrices leaf, larva, and feces. Rate constants for uptake and elimination of test compounds were derived by calibrating a toxicokinetic model to the whole-body concentrations. Uptake and elimination rate constants depended on the physicochemical properties of the test compounds. Increasing hydrophobicity increased the bioaccumulation potential of test compounds. Incomplete quantities in larval matrices indicated that some compounds may undergo biotransformation. As fecal excretion was a major elimination pathway, the variable time of release and number of feces pellets led to a high variability in the body burden. We provide quantitative models to predict the toxicokinetics and bioaccumulation potential of inactive insecticide analogs (parent compounds) in Spodoptera.
Self-generating autocatalytic networks: structural results, algorithms and their relevance to early biochemistry
2024-05-01

The concept of an autocatalytic network of reactions that can form and persist, starting from just an available food source, has been formalized by the notion of a reflexively autocatalytic and food-generated (RAF) set. The theory and algorithmic results concerning RAFs have been applied to a range of settings, from metabolic questions arising at the origin of life, to ecological networks, and cognitive models in cultural evolution. In this article, we present new structural and algorithmic results concerning RAF sets, by studying more complex modes of catalysis that allow certain reactions to require multiple catalysts (or to not require catalysis at all), and discuss the differing ways catalysis has been viewed in the literature. We also focus on the structure and analysis of minimal RAFs and derive structural results and polynomial-time algorithms. We then apply these new methods to a large metabolic network to gain insights into possible biochemical scenarios near the origin of life.
Reconstruction Techniques and Associated Morbidity after Minimally Invasive Gastrectomy for Cancer – Insights from the GastroBenchmark and GASTRODATA databases
2024-05-01

Abstract Background Various anastomotic and reconstruction techniques are used to restore intestinal continuity after minimally invasive total (TG) and subtotal distal gastrectomy (DG). Aims Their effects on anastomotic leakage and postoperative morbidity have not been extensively studied. Methods Patients after minimally invasive TG and DG were selected from a cohort of 9356 oncological gastrectomies performed between 2017-2021 in 44 specialized centers. Results Three anastomotic techniques (circular stapled (CS, 3.7%); linear stapled (LS, 93.8%); hand sewn (HS, 2.5%)) and three types of bowel reconstruction (Roux (RX, 51.5%); Billroth I (BI, 23.1%); Billroth II (BII, 25.4%)) were identified after TG (n=878) and DG (n=3334). Postoperative morbidity was higher after TG compared to DG (AL 5.2% vs. 1.1%, p≤0.001; 90-day mortality 1.6% vs. 0.4%, p≤0.001; overall morbidity 28.6% vs. 16.3%, p≤0.001; major morbidity 15.4% vs. 8.0%, p≤0.001). Anastomotic leakage rate in the TG cohort was higher after CS (13.1%) and HS (7.9%) than after LS anastomoses (1.9%, p&amp;lt;0.001). Similarly, overall (CS: 43.9%, HS: 28.6%, LS: 23.1%) and major complications rates (CS: 25.2%, HS: 11.1%, LS: 12.0%) as well as mortality (CS: 4.7%, HS: 2.2%, LS: 0.8%) were higher after CS. Multivariate analysis confirmed anastomotic technique as a predictive factor for anastomotic leakage (Fig. 1), but not for occurrence of mortality, overall and major complications. In the DG cohort, most (98.7%), outcomes were similar for all types of bowel reconstruction: Anastomotic leakage (BI: 1.4%, BII 0.8%, RX 1.2%, p=0.440), 90-day mortality (BI: 0%, BII 0.1%, RY: 1.1%%, p=0.109), overall (BI: 14.5%, BII: 15.0%, RX: 18.7%, p=0.208) and major morbidity (BI: 7.9%, BII: 9.1%, RX: 7.2%, p=0.219). Conclusion In suitable situations, DG should be preferred to TG, as postoperative morbidity is significantly lower. In addition, LS should be the preferred method of anastomosis after TG. Conversely, the techniques for bowel reconstruction can be chosen according to the surgeon's preference.
Two-year safety and effectiveness of hybrid ablation versus catheter ablation in patients with non-paroxysmal AF: mid-term results of the CEASE-AF trial
2024-05-01

Abstract Background Hybrid Ablation for atrial fibrillation (AF) combines epicardial and endocardial ablation through a Heart Team approach to target durable, transmural isolation of the pulmonary veins (PV) and left atrial posterior wall (LAPW). While the primary efficacy endpoint at 12 months was met with a significant benefit increase for hybrid ablation, we now report the midterm durability of those results. Purpose To evaluate 24-months safety and effectiveness of Hybrid Ablation with left atrial appendage exclusion (LAAE) versus Catheter Ablation in patients with persistent AF/enlarged left atrium and longstanding persistent AF (LSPAF). Methods CEASE-AF is a prospective, multi-center, 2:1 randomized controlled trial. Eligible patients were 18-75 years of age, had symptomatic, drug-refractory persistent AF and enlarged left atrium (&amp;gt;4 cm) or LSPAF, and were undergoing a first ablation. Hybrid Ablation consisted of two stages: thoracoscopic epicardial radiofrequency (RF) ablation for PV and LAPW isolation and epicardial LAAE followed by endocardial ablation 91-180 days later. Catheter Ablation consisted of minimum PV isolation by endocardial RF ablation, and repeat ablation was allowed between 91-180 days. In both arms, additional lesions were permitted according to institutional practices. Effectiveness was freedom from AF/atrial flutter (AFL)/atrial tachycardia (AT) off anti-arrhythmic drugs (AAD) (except AADs not exceeding doses which previously failed) and was assessed through 48-h Holter monitoring reviewed by an independent core laboratory blinded to the study. Safety was major adverse events throughout the study, adjudicated by an independent Clinical Events Committee. Results There were 102 Hybrid Ablation and 52 Catheter Ablation patients; 26% were female, mean age was 60.7±7.9 years, mean LAD was 4.7±0.4 cm, and 19% had LSPAF with no differences between arms. The 12- and 24-month results are shown for comparison (Table). Through 24-months, effectiveness was 66.3% (63/95) in the Hybrid Arm and 33.3% (17/51) in the Catheter Arm (absolute difference 33.0% [95% CI 14.3%, 48.3%; p&amp;lt;0.001]). Major adverse event rates through 24-months were statistically similar at 10.8% (11/102) in the Hybrid Arm and 9.6% (5/52) in the Catheter Arm (p=1.0). Through 24-months, repeat ablations were performed in 7.4% (7/95) of the Hybrid Arm versus 37.3% (19/51) of the Catheter Arm (p&amp;lt;0.001), and cardioversions were performed in 14.7% (14/95) of the Hybrid Arm versus 29.4% (15/51) of the Catheter Arm (p=0.034) Conclusions: CEASE-AF demonstrated that superior effectiveness of Hybrid Ablation including LAAE versus Catheter Ablation was durable through 24-month follow-up, with 33% absolute improvement in freedom from AF/AFL/AT. Safety rates continued to be similar between arms. Three-year follow-up is ongoing.
Attrition in the First Three Therapy Lines in Patients with Advanced Breast Cancer in the German Real-World PRAEGNANT Registry
2024-05-01

Abstract Background With more effective therapies for patients with advanced breast cancer (aBC), therapy sequences are becoming increasingly important. However, some patients might drop out of the treatment sequence due to deterioration of their life status. Since little is known about attrition in the real-world setting, this study assessed attrition in the first three therapy lines using a real-world registry. Methods Patients with information available on the first three therapy lines were selected from the German PRAEGNANT registry (NCT02338167). Attrition was determined for each therapy line using competing risk analyses, with the start of the next therapy line or death as endpoints. Additionally, a simple attrition rate was calculated based on the proportion of patients who completed therapy but did not start the next therapy line. Results Competitive risk analyses were performed on 3988 1st line, 2651 2nd line and 1866 3rd line patients. The probabilities of not starting the next therapy line within 5 years after initiation of 1st, 2nd and 3rd line therapy were 30%, 24% and 24% respectively. Patients with HER2-positive disease had the highest risk for attrition, while patients with HRpos/HER2neg disease had the lowest risk. Attrition rates remained similar across molecular subgroups in the different therapy lines. Conclusion Attrition affects a large proportion of patients with aBC, which should be considered when planning novel therapy concepts that specifically address the sequencing of therapies. Taking attrition into account could help understand treatment effects resulting from sequential therapies and might help develop treatment strategies that specifically aim at maintaining quality of life.
Optimized Predictive Coverage by Averaging Time‐Windowed Bayesian Distributions
2024-05-01

Abstract Hydrogeological models require reliable uncertainty intervals that honestly reflect the total uncertainties of model predictions. The operation of a conventional Bayesian framework only produces realistic (interpretable in the context of the natural system) inference results if the model structure matches the data‐generating process, that is, applying Bayes' theorem implicitly assumes the underlying model to be true. With an imperfect model, we may obtain a too‐narrow‐for‐its‐bias uncertainty interval when conditioning on a long time‐series of calibration data, because the assumption of a quasi‐true model becomes too strict. To overcome the problem of overconfident posteriors, we propose a non‐parametric Bayesian method, called Tau‐averaging method: it applies Bayesian analysis on sliding time windows along the data time series for calibration. Thus, it obtains so‐called transitional posteriors per time window. Then, we average these into a wider predictive posterior. With the proposed routine, we explicitly capture the time‐varying impact of model error on prediction uncertainty. The length of the calibration window is optimized to maximize goal‐oriented statistical skill scores for predictive coverage. Our method loosens the perfect‐model‐assumption by conditioning only on small windows of the data set at a time, that is, it assumes that “the model is sufficient to follow the system dynamics for a smaller duration.” We test our method on two cases of soil moisture modeling and show how it improves predictive coverage as compared to the conventional Bayesian approach. Our findings demonstrate that the proposed method convincingly overcomes the overconfidence drawback of Bayesian inference under model misspecification and long calibration time‐series.
Refocusing the Debate: Our Original Critiques of Koops et al. (2022) Still Stand
2024-05-01

Koops et al. (2022, 2023) claim that an experimental field study (Koops et al., 2022) provided valid evidence against a latent solution explanation for chimpanzee (Pan troglodytes verus) nut cracking know-how in the wild. In our previous response (Tennie &amp; Call, 2023) we identified two major problems with this interpretation. First, Koops et al. (2022) study subjects were clearly unmotivated to access the intended food reward (nut kernels) – rendering the secondary question of whether they would use tools to crack the provided nuts to access these kernels a moot point. Second, only one of the subjects who came into contact with the experimental setup was within the chimpanzee most sensitive learning bracket to develop nut cracking (identified in previous field studies; Matsuzawa, 1994, 1996; Biro et al., 2003). We concluded that Koops et al.’s (2022) study failed to provide valid evidence against the zone of latent solution hypothesis as applied to chimpanzee nut cracking in the wild. In their reply, Koops et al. (2023) argued against both our critiques. Here, we refocus the debate, reiterate our arguments and provide further evidence that invalidate Koops et al. (2022) conclusion that “nut cracking falls outside” the zone of latent solutions of wild chimpanzees. We end with a call for more data.
Prosodic Rephrasing and Violations of the Phase Impenetrability Condition
2024-05-01

According to the Phase Impenetrability Condition (PIC), phasal domains are opaque to further syntactic operations. Some researchers claim that the PIC applies in the phonological component of grammar (i.e., at PF). Others, however, claim that there is no PIC at PF. I use data from Turkish to provide new arguments against the PIC-at-PF view and conclude that the PIC can only possibly hold in syntax. I show that the PIC-at-PF view is too restrictive, as it makes incorrect predictions about variable prosodic domain formation and optional prosodic variation in Turkish.
#2237 Preliminary results of Protection of Renal Function after Conversion of fast IR-Tac Metabolizers to Envarsus® study (The Protect RENvarsus study)
2024-05-01

Abstract Background and Aims As shown in a proof-of-concept study, renal function of fast immediate-release tacrolimus (IR-Tac) metabolizers can recover after conversion to prolonged-release tacrolimus (LCP-Tac), whereas slow Tac metabolizers showed no benefit over a 3-year follow-up [1]. The aim of this study is to test this hypothesis in a multi-center trial. Method In a multicenter European trial, we aim to enroll 300 renal transplant (RTx) recipients who were switched from IR-Tac to LCP-Tac one month or later after RTx. Metabolizer groups will be defined by calculation of the C/D ratio at one month after RTx: fast IR-Tac metabolizers (&amp;lt;1 ng/mL*1/mg) and slow (≥1) [2]. The development of renal function, acute rejections, infections, and the development of diabetes mellitus will be observed in a 5-year follow-up. Results A total of 265 patients have been included in this study to date. Preliminary data confirm that fast metabolizers who were switched to LCP-Tac at a median time of 2.0 months (range: 1.0-253.1 months) showed a recovery of renal function. In contrast, slow metabolizers showed a stable eGFR after switching to LCP-Tac at a median time of 13.2 months (range: 1.2-172.8 months) following RTx. The incidence of complications was low and comparable in both groups. Conclusion Preliminary data confirm that early conversion of fast IR-Tac metabolizers to LCP-Tac can improve renal function after RTx. The 5-year follow-up data will provide additional insight.