bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phanto-IDP: compact model for precise intrinsically disordered protein backbone generation and enhanced sampling
Authors: Zhu Junjie , Li Zhengxin , Tong Haowei , Lu Zhouyu , Zhang Ningjie , Wei Ting , Chen Hai-Feng 
Published: November 2023

Abstract
The biological function of proteins is determined not only by their static structures but also by the dynamic properties of their conformational ensembles. Numerous high-accuracy static structure prediction tools have been recently developed based on deep learning; however, there remains a lack of efficient and accurate methods for exploring protein dynamic conformations. Traditionally, studies concerning protein dynamics have relied on molecular dynamics (MD) simulations, which incur significant computational costs for all-atom precision and struggle to adequately sample conformational spaces with high energy barriers. To overcome these limitations, various enhanced sampling techniques have been developed to accelerate sampling in MD. Traditional enhanced sampling approaches like replica exchange molecular dynamics (REMD) and frontier expansion sampling (FEXS) often follow the MD simulation approach and still cost a lot of computational resources and time. Variational autoencoders (VAEs), as a classic deep generative model, are not restricted by potential energy landscapes and can explore conformational spaces more efficiently than traditional methods. However, VAEs often face challenges in generating reasonable conformations for complex proteins, especially intrinsically disordered proteins (IDPs), which limits their application as an enhanced sampling method. In this study, we presented a novel deep learning model (named Phanto-IDP) that utilizes a graph-based encoder to extract protein features and a transformer-based decoder combined with variational sampling to generate highly accurate protein backbones. Ten IDPs and four structured proteins were used to evaluate the sampling ability of Phanto-IDP. The results demonstrate that Phanto-IDP has high fidelity and diversity in the generated conformation ensembles, making it a suitable tool for enhancing the efficiency of MD simulation, generating broader protein conformational space and a continuous protein transition path.
Possible ‘silver-spoon’ effect on adult terrestrial jumping in the mangrove rivulus fish (Kryptolebias marmoratus) (Cyprinodontiformes: Rivulidae)
Authors: Styga Joseph M , Brown Isobel G , McMullen Margaret V 
Published: November 2023

Abstract
Survival in complex environments is dependent on whole-animal performance, a target of natural and sexual selection. Variation in whole-animal performance among mature individuals can become broadened by phenotypic plasticity driven by early life experiences. Thus, detailing the environmental factors that contribute to phenotypic plasticity, and the associated phenotypic responses governed by those environmental factors, is essential if we are to understand the evolution of whole-animal performance. Here, using isogenic lines established from the hermaphroditic mangrove rivulus fish (Kryptolebias marmoratus) housed in a ‘common garden’, we investigate the link between variation in adult terrestrial jumping performance and early life experience (i.e. egg density). First, we hypothesize that individuals from different isogenic lineages should vary in jumping performance independent of egg density, suggesting a strict genetic source of variation. Second, we hypothesize that phenotypic plasticity should also introduce variation in adult jumping performance. Specifically, we expect that hatchlings incubated at higher egg densities in early development should adopt better jumping performances as adults, because higher egg density might be a cue for greater intraspecific competition upon hatching.
Genetic and morphological differentiation within Euphorbia japygica (Euphorbiaceae) suggests divergence of populations from the south-eastern Apennine Peninsula
Authors: Boschin Micol , Schönswetter Peter , Frajman Božo 
Published: November 2023

Abstract
The Mediterranean Basin is a hotspot of animal and plant diversity. Contrary to the Balkan and Iberian Peninsulas that were subject of many phylogeographic studies in past decades, the Apennine Peninsula and, in particular, the diversification of its flora has been neglected in contemporary phylogenetic studies. The few available studies showed a complex pattern of north–south differentiation of genetic diversity in Italy, both among the Alps, the Apuan Alps, and the Apennines, as well as within the Apennines. Here, we explore phylogeographic patterns within recently described Euphorbia adriatica, distributed in the central and northern Apennine Peninsula, the southern margin of the Eastern Alps and the north-western Balkan Peninsula, and its relationship to the southern Italian E. japygica. Our integrative approach using nuclear ITS sequences, amplified fragment length polymorphisms, relative genome size estimation combined with chromosome counting, as well as multivariate morphometrics inferred a weak genetic differentiation that only partly corresponds to the morphological differentiation. Whereas all southern populations have hairy capsules characteristic for E. japygica, only those in south-eastern Italy (Puglia and Basilicata) are genetically divergent. There are, however, additional morphological characters that differentiate them from other populations. Our data are thus in favour of recognizing a single species, E. japygica, which includes E. adriatica that should be treated as a subspecies, named E. japygica subsp. prostrata. We provide a revised taxonomic treatment for E. japygica, including the typification. Our study shows the necessity of further in-depth investigations of diversification of Italian biota.
Does prehabilitation before esophagectomy improve postoperative outcomes? A systematic review and meta-analysis
Authors: An Kevin R , Seijas Vanessa , Xu Michael S , Grüßer Linda , Humar Sapna , Moreno Amabelle A , Turk Marvee , Kasanagottu Koushik , Alzghari Talal , Dimagli Arnaldo , Ko Michael A , Villena-Vargas Jonathan , Papatheodorou Stefania , Gaudino Mario F L 
Published: November 2023

Summary
Esophagectomy for esophageal cancer is associated with high morbidity. It remains unclear whether prehabilitation, a strategy aimed at optimizing patients’ physical and mental functioning prior to surgery, improves postoperative outcomes. A systematic review and meta-analysis was conducted to evaluate the effect of prehabilitation on post-operative outcomes after esophagectomy. Data sources included Cochrane Central Register of Controlled Trials, MEDLINE, EMBASE, CINAHL, and PEDro, with information from 1 January 2000 to 5 August 2023. The analysis included randomized controlled trials and observational studies that compared prehabilitation interventions to standard care prior to esophagectomy. A random effects model was used to generate a pooled estimate for pairwise meta-analysis, meta-analysis of proportions, and meta-analysis of means. A total of 1803 patients were included with 584 in randomized controlled trials (RCTs) and 1219 in observational studies. In the randomized evidence, there were no significant differences between prehabilitation and control in the odds of postoperative pneumonia (15.0 vs. 18.9%, odds ratio (OR) 1.06 [95% confidence interval (CI): 0.66;1.72]) or pulmonary complications (14 vs. 25.6%, OR 0.68 [95% CI: 0.32;1.45]). In the observational data, there was a reduction in both postoperative pneumonia (22.5 vs. 32.9%, OR 0.48 [95% CI: 0.28;0.83]) and pulmonary complications (26.1 vs. 52.3%, OR 0.35 [95% CI: 0.17;0.75]) with prehabilitation. Hospital and intensive care unit length of stay (days), operative mortality, and severe complications (Clavien-Dindo ≥ 3) did not differ between groups in both the randomized data and observational data. Prehabilitation demonstrated reductions in postoperative pneumonia and pulmonary complications in observational studies, but not RCTs. The overall certainty of these findings is limited by the low quality of the available evidence.
Comprehensive characterization and detection of nut allergens in bakery foods using Q-TOF mass spectrometry and bioinformatics
Authors: Xu Daokun , Huang Haolun , Liu Zhen , Wang Yumei , Liu Qinan , Jiang Xing , Yang Jun , Ling Rui 
Published: November 2023

Abstract
Food allergy is a growing health issue worldwide and the demand for sensitive, robust and high-throughput analytical methods is rising. In recent years, mass spectrometry-based methods have been established for multiple food allergen detection. In the present study, a novel method was developed for the simultaneous detection of almond, cashew, peanut, and walnut allergens in bakery foods using liquid chromatography–mass spectrometry. Proteins unique to these four ingredients were extracted, followed by trypsin digestion, quadrupole time-of-flight (Q-TOF) mass spectrometry and bioinformatics analysis. The raw data were processed by de-novo sequencing module plus PEAKS DB (database search) module of the PEAKS software to screen peptides specific to each nut species. The thermal stability and uniqueness of these candidate peptides were further verified using triple quadrupole mass spectrometry (QQQ-MS) in multiple reaction monitoring (MRM) mode. Each nut species was represented by four peptides, all of which were validated for label-free quantification (LFQ). Calibration curves were constructed with good linearity and correlation coefficient (r2) greater than 0.99. The limits of detection (LODs) were determined to range from 0.11 to 0.31 mg/kg, and were compared with the reference doses proposed by Voluntary Incidental Trace Allergen Labelling (VITAL). The recoveries of the developed method in incurred bakery food matrices ranged from 72.5% to 92.1% with relative standard deviations (RSD) of &lt;5.2%. The detection of undeclared allergens in commercial bakery food samples confirmed the presence of these allergens. In conclusion, this method provides insight into the qualitative and quantitative detection of trace levels of nut allergens in bakery foods.
HPA axis differential flatness and Liouvillian study for higher resiliency investigations
Authors: Nicolau Florentina , Mounier Hugues , Androulakis Ioannis P 
Published: November 2023

Abstract
In this paper, we study several existing quantitative models of the hypothalamic–pituitary–adrenal (HPA) axis from a control systems theory viewpoint, that is, we suppose that we can act on the dynamics of the HPA axis throughout some parameters, which are the system inputs. In particular, we will focus on flatness and Liouvillian properties of the considered control systems of the HPA axis. We first study the minimal three-dimensional model of Bangsgaard and Ottesen (2017, Math. Biosci., 287:24–35) and the semi-mechanistic four-dimensional model of Gupta et al. (2007, Theor. Biol. Medical Model., 4(1):8) which are shown to be flat, and then, we consider the more involved and important model proposed in Rao & Androulakis (2019, Sci. Rep., 9(1):11212; 2020, IFAC-PapersOnLine, 53(2):15858–15863), with seven states, for which we prove that for the nominal values of the parameters involved in the model, flatness no longer holds. The more involved model satisfies however a similar but weaker property than flatness: it is a Liouvillian system.
Asymptotic Stability of 2-Domain Walls for the Landau–Lifshitz–Gilbert Equation in a Nanowire With Dzyaloshinskii–Moriya Interaction
Authors: Côte Raphaël , Ferriere Guillaume 
Published: November 2023

Abstract
We consider a ferromagnetic nanowire, with an energy functional $E$ with easy-axis in the direction $e_{1}$, and which takes into account the Dzyaloshinskii–Moriya interaction. We consider configurations of the magnetization that are perturbations of two well-separated domain wall and study their evolution under the Landau–Lifshitz–Gilbert flow associated to $E$. Our main result is that, if the two walls have opposite speed, these configurations are asymptotically stable, up to gauges intrinsic to the invariances of the energy $E$. Our analysis builds on the framework developed in [4], taking advantage that it is amenable to space localisation.
Differences in Rotavirus Shedding and Duration by Infant Oral Rotavirus Vaccination Status in Dhaka, Bangladesh, 2011–2014
Authors: Ciszewski Jenna , Taniuchi Mami , Lee Benjamin , Colgate E Ross , Platts-Mills James A , Haque Rashidul , Zaman K , Lopman Benjamin , Petri William A , Kirkpatrick Beth D , Rogawski McQuade Elizabeth T 
Published: November 2023

Abstract
To evaluate how breakthrough rotavirus disease contributes to transmission, we examined the impact of rotavirus vaccination on fecal shedding and duration of illness. We used multivariable linear regression to analyze rotavirus quantity by RT-qPCR and duration among 184 episodes of rotavirus diarrhea positive by ELISA in the PROVIDE study. Vaccinated children had less fecal viral shedding compared to unvaccinated children (mean difference = −0.59 log copies per gram of stool; 95% confidence interval [CI], −.99 to −.19). Duration of illness was on average 0.47 days (95% CI, −.23 to 1.17 days) shorter among vaccinated children. Rotarix vaccination reduces shedding burden among breakthrough cases of rotavirus gastroenteritis.
Clinical Trials Registration . NCT01375647.
Prolonged Mpox Disease in People With Advanced HIV: Characterization of Mpox Skin Lesions
Authors: O’Shea Jesse , Zucker Jason , Stampfer Samuel , Cash-Goldwasser Shama , Minhaj Faisal S , Dretler Alexandra , Cheeley Justin , Chaudhuri Shaoli , Gallitano Stephanie M , Gunaratne Shauna , Parkinson Melissa , Epling Brian , Morcock David R , Sereti Irini , Deleage Claire 
Published: November 2023

Abstract
We report 3 complicated and prolonged cases of mpox in people with advanced human immunodeficiency virus (HIV) not on antiretroviral therapy (ART) at mpox diagnosis. Multiple medical countermeasures were used, including prolonged tecovirimat treatment and immune optimization with ART initiation. Immunofluorescence of skin biopsies demonstrated a dense immune infiltrate of predominantly myeloid and CD8+ T cells, with a strong type I interferon local response. RNAscope detected abundant replication of monkeypox virus (MPXV) in epithelial cells and dendritic cells. These data suggest that prolonged mpox in people with advanced HIV may be due to ongoing MPXV replication, warranting aggressive medical countermeasures and immune optimization.
Epitope Mapping of SARS-CoV-2 Spike Antibodies in Vaccinated Kidney Transplant Recipients Reveals Poor Spike Coverage Compared to Healthy Controls
Authors: Karaba Andrew H , Morgenlander William R , Johnston Trevor S , Hage Camille , Pekosz Andrew , Durand Christine M , Segev Dorry L , Robien Mark A , Heeger Peter S , Larsen Christian P , Blankson Joel N , Werbel William A , Larman H Benjamin , Tobian Aaron A R 
Published: November 2023

Abstract
Kidney transplant recipients (KTRs) develop decreased antibody titers to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination compared to healthy controls (HCs), but whether KTRs generate antibodies against key epitopes associated with neutralization is unknown. Plasma from 78 KTRs from a clinical trial of third doses of SARS-CoV-2 vaccines and 12 HCs underwent phage display immunoprecipitation and sequencing (PhIP-Seq) to map antibody responses against SARS-CoV-2. KTRs had lower antibody reactivity to SARS-CoV-2 than HCs, but KTRs and HCs recognized similar epitopes associated with neutralization. Thus, epitope gaps in antibody breadth of KTRs are unlikely responsible for decreased efficacy of SARS-CoV-2 vaccines in this immunosuppressed population.
Clinical Trials Registration.  NCT04969263.
Tenofovir Douche as HIV Preexposure Prophylaxis for Receptive Anal Intercourse: Safety, Acceptability, Pharmacokinetics, and Pharmacodynamics (DREAM 01)
Authors: Weld Ethel D , McGowan Ian , Anton Peter , Fuchs Edward J , Ho Ken , Carballo-Dieguez Alex , Rohan Lisa C , Giguere Rebecca , Brand Rhonda , Edick Stacey , Bakshi Rahul P , Parsons Teresa , Manohar Madhuri , Seigel Aaron , Engstrom Jared , Elliott Julie , Jacobson Cindy , Bagia Christina , Wang Lin , Al-khouja Amer , Hartman Douglas J , Bumpus Namandje N , Spiegel Hans M L , Marzinke Mark A , Hendrix Craig W 
Published: November 2023

Abstract

Background
Despite highly effective HIV preexposure prophylaxis (PrEP) options, no options provide on-demand, nonsystemic, behaviorally congruent PrEP that many desire. A tenofovir-medicated rectal douche before receptive anal intercourse may provide this option.

Methods
Three tenofovir rectal douches—220 mg iso-osmolar product A, 660 mg iso-osmolar product B, and 660 mg hypo-osmolar product C—were studied in 21 HIV-negative men who have sex with men. We sampled blood and colorectal tissue to assess safety, acceptability, pharmacokinetics, and pharmacodynamics.

Results
The douches had high acceptability without toxicity. Median plasma tenofovir peak concentrations for all products were several-fold below trough concentrations associated with oral tenofovir disoproxil fumarate (TDF). Median colon tissue mucosal mononuclear cell (MMC) tenofovir-diphosphate concentrations exceeded target concentrations from 1 hour through 3 to 7 days after dosing. For 6–7 days after a single product C dose, MMC tenofovir-diphosphate exceeded concentrations expected with steady-state oral TDF 300 mg on-demand 2-1-1 dosing. Compared to predrug baseline, HIV replication after ex vivo colon tissue HIV challenge demonstrated a concentration-response relationship with 1.9 log10 maximal effect.

Conclusions
All 3 tenofovir douches achieved tissue tenofovir-diphosphate concentrations and colorectal antiviral effect exceeding oral TDF and with lower systemic tenofovir. Tenofovir douches may provide a single-dose, on-demand, behaviorally congruent PrEP option, and warrant continued development.
Clinical Trials Registration . NCT02750540.
Development and Evaluation of “The Delta Plus-Minus Even Distribution Check”: A Novel Patient-Based Real-Time Quality Control Method for Laboratory Tests
Authors: Hatanaka Noriko , Yamamoto Yoshikazu , Shiozaki Yuya , Kuramura Eiji , Nagai Naoharu , Kondo Akira , Kamioka Mikio 
Published: November 2023

Abstract

Background
Laboratory testing of large sample numbers necessitates high-volume rapid processing, and these test results require immediate validation and a high level of quality assurance. Therefore, real-time quality control including delta checking is an important issue. Delta checking is a process of identifying errors in individual patient results by reviewing differences from previous results of the same patient (Δ value). Under stable analytical conditions, Δ values are equally positively and negatively distributed.

Methods
The previous 20 Δ values from 3 tests (cholesterol, albumin, and urea nitrogen) were analyzed by calculating the R-value: “the positive Δ value ratio minus 0.5.” This method of monitoring optimized R-values is referred to as the even-check method (ECM) and was compared with quality control (QC) testing in terms of error detection.

Results
Bias was observed on 4 of the 120 days for the 3 analytes measured. When QC detected errors, the ECM captured the same systematic errors and more rapidly. In contrast, the ECM did not generate an alarm for the one random error that occurred in QC. While QC did not detect any errors, the percentage of R-values exceeding the acceptable range was under 2%, the number of days generating alarms was between 16 and 21 days, with short alarm periods, and a median number of samples per alarm period between 7 and 9 samples.

Conclusions
The ECM is a practical real-time QC method, controlled by setting R-value conditions, that quickly detects bias values.
Performance assessment of an iterative ensemble smoother with local analysis to assimilate big 4D seismic datasets applied to a complex pre-salt-like benchmark case
Authors: Maschio Célio , Silva Neto Gilson Moura , Davolio Alessandra , Rios Vinicius de Souza , Schiozer Denis José 
Published: November 2023

Abstract
The use of 4D seismic (4DS) (or time-lapse seismic, TLS) in data assimilation (DA) makes the process more complex due to the higher amount of data to be assimilated, requiring more robust methods and better computational resources (processing capacity and memory). The development and application of permanent seismic monitoring technologies have increased in recent years, improving the overall 4D seismic quality in terms of signal resolution and repeatability. However, a massive amount of data is generated from the multiple monitors, making the incorporation of 4DS data in the DA process more complex. Therefore, robust DA methods capable of dealing with huge amount of data effectively and efficiently are essential. This paper aims to assess the performance of an iterative ensemble smoother method, named subspace ensemble randomized maximum likelihood with a local analysis, to assimilate a big dataset. The method was applied in a challenging pre-salt-like benchmark case with eight seismic surveys, one base, and seven monitors. The 4DS data are the impedance ratios (between two consecutive monitors) in 15 seismic horizons, totaling 105 maps to be assimilated. To our best knowledge, this is state of the art in terms of practical applications in DA. It was possible to assimilate all the data simultaneously: the 105 horizons for the 4DS data and the wells’ production and pressure data. The DA was successful in terms of results quality and method performance. We also ran a case assimilating only well data for comparison purposes.
Multiwavelength variability and broad-band SED modelling of BL Lac during a bright flaring period MJD 59000–59943
Authors: Shah Zahir 
Published: November 2023

ABSTRACT
We carried out a detailed temporal and spectral study of the BL Lacertae (BL Lac) by using the long-term Fermi-Large Area Telescope (LAT) and Swift-X-ray Telescope (XRT)/Ultraviolet Optical Telescope (UVOT) observations, during the period MJD 59000–59943. The daily-binned γ-ray light curve displays a maximum flux of $1.74\pm 0.09\times 10^{-5} \,\rm photons\, cm^{-2}\, s^{-1}$ on MJD 59868, which is the highest daily γ-ray flux observed from BL Lac. The γ-ray variability is characterized by power spectral density (PSD), rms–flux relation, and flux distribution study. We find that the power-law model fits the PSD with index ∼1, which suggests a long-memory process at work. The observed rms–flux relation exhibits a linear trend, which indicates that the γ-ray flux distribution follows a lognormal distribution. The skewness/Anderson–Darling test and histogram fit reject the normality of flux distribution, and instead suggest that the flux distribution is a lognormal distribution. The fractional variability amplitude shows that the source is more variable in the X-ray band than in optical/ultraviolet/γ-ray bands. In order to obtain an insight into the underlying physical process, we extracted broad-band spectra from different time periods of the light curve. The broad-band spectra are statistically fitted with the convolved one-zone leptonic model with different forms of the particle energy distribution. We found that spectral energy distribution during different flux states can be reproduced well with the synchrotron, synchrotron self-Compton, and external Compton emissions from a broken power-law electron distribution, ensuring equipartition condition. A comparison between the best-fitting physical parameters shows that the variation in different flux states is mostly related to an increase in the bulk Lorentz factor and spectral hardening of the particle distribution.