bluuebunny/crossref_metadata_2025_split huggingface dataset:
Network inference from perturbation time course data
Authors: Sarmah Deepraj , Smith Gregory R. , Bouhaddou Mehdi , Stern Alan D. , Erskine James , Birtwistle Marc R. 
Published: November 2022

AbstractNetworks underlie much of biology from subcellular to ecological scales. Yet, understanding what experimental data are needed and how to use them for unambiguously identifying the structure of even small networks remains a broad challenge. Here, we integrate a dynamic least squares framework into established modular response analysis (DL-MRA), that specifies sufficient experimental perturbation time course data to robustly infer arbitrary two and three node networks. DL-MRA considers important network properties that current methods often struggle to capture: (i) edge sign and directionality; (ii) cycles with feedback or feedforward loops including self-regulation; (iii) dynamic network behavior; (iv) edges external to the network; and (v) robust performance with experimental noise. We evaluate the performance of and the extent to which the approach applies to cell state transition networks, intracellular signaling networks, and gene regulatory networks. Although signaling networks are often an application of network reconstruction methods, the results suggest that only under quite restricted conditions can they be robustly inferred. For gene regulatory networks, the results suggest that incomplete knockdown is often more informative than full knockout perturbation, which may change experimental strategies for gene regulatory network reconstruction. Overall, the results give a rational basis to experimental data requirements for network reconstruction and can be applied to any such problem where perturbation time course experiments are possible.
Fabrication and examination of polyorganophosphazene/polycaprolactone-based scaffold with degradation, in vitro and in vivo behaviors suitable for tissue engineering applications
Authors: Gholivand Khodayar , Mohammadpour Mahnaz , Alavinasab Ardebili Seyed Alireza , Eshaghi Malekshah Rahime , Samadian Hadi 
Published: November 2022

AbstractThe present study aimed to synthesis a proper scaffold consisting of hydroxylated polyphosphazene and polycaprolactone (PCL), focusing on its potential use in tissue engineering applications. The first grafting of PCL to poly(propylene glycol)phosphazene (PPGP) was performed via ROP of ε-caprolactone, whereas PPGP act as a multisite macroinitiator. The prepared poly(propylene glycol phosphazene)-graft-polycaprolactone (PPGP-g-PCL) were evaluated by essential tests, including NMR, FTIR, FESEM-EDS, TGA, DSC and contact angle measurement. The quantum calculations were performed to investigate molecular geometry and its energy, and HOMO and LUMO of PPGP-g-PCL in Materials Studio2017. MD simulations were applied to describe the interaction of the polymer on phospholipid membrane (POPC128b) in Material Studio2017. The C2C12 and L929 cells were used to probe the cell–surface interactions on synthetic polymers surfaces. Cells adhesion and proliferation onto scaffolds were evaluated using FESEM and MTT assay. In vitro analysis indicated enhanced cell adhesion, high proliferation rate, and excellent viability on scaffolds for both cell types. The polymer was further tested via intraperitoneal implantation in mice that showed no evidence of adverse inflammation and necrosis at the site of the scaffold implantation; in return, osteogenesis, new-formed bone and in vivo degradation of the scaffold were observed. Herein, in vitro and in vivo assessments confirm PPGP-g-PCL, as an appropriate scaffold for tissue engineering applications.
Influence of mating strategies on seminal material investment in crabs
Authors: Pretterebner Katrin , Pardo Luis Miguel , Paschke Kurt , Riveros Marcela Paz 
Published: November 2022

AbstractReproduction involves high energetic costs which are related to behaviour and gamete production. In females energy allocation to gamete production has been well documented. However, estimations of male investment in seminal material are scarce. The present study aims to assess and compare male investment in four brachyuran species by determining biochemical substrates present in the vasa deferentia to subsequently estimate energetic investment during the reproductive cycle. We identified two groups with contrasting energy investments. Two species, Homalaspis plana and Romaleon setosum, showed high investment due to significant quantities of proteins and lipids. Both species are characterised by large and complex vasa deferentia, and the formation of a remarkably large sperm plug deposited to the female after copulation as a sperm competition avoidance strategy. In contrast, Metacarcinus edwardsii and Taliepus dentatus invested little energy in their smaller-sized and simpler vasa deferentia. Morpho-functional traits may play a key role in determining the investment, which may also be influenced by mechanisms (i.e. mating tactics) to prevent sperm competition and the intensity of polygyny. This study emphasises the high amount of energy males invest in seminal material and highlights the diversity of mating strategies in Brachyura, which are reflected even on the physiological level.
Optoelectronic refractometric sensing device for gases based on dielectric bow-ties and amorphous silicon solar cells
Authors: Elshorbagy Mahmoud H. , Esteban Óscar , Cuadrado Alexander , Alda Javier 
Published: November 2022

AbstractThe transformation of an hydrogenated amorphous silicon solar cell (aSiH) into an optoelectronic refratometric sensor has been possible through the addition of dielectric bow-tie resonant structures. The indium transparent oxide top electrode is replaced by a thin metallic layer to selectively prevent the direct transmission of light to the active layer of the cell. Then, an array of dielectric bow-tie structures is placed on top of this electrode, to activate the optical absorption through surface plasmon resonance (SPR). The whole device is exposed to the analyte under measure, which is the surrounding medium. Three different dielectric materials with low, medium, and high refractive index were selected for the bow-ties, namely magnesium fluoride (MgF$$_2$$

2

), silicon dioxide (SiO$$_2$$

2

), and aluminum nitride (AlN) have been tested as coupling structure for SPR excitation. The maximization of the readout/short circuit current has been achieved through the geometrical parameters of such structure. We have selected the geometrical parameters to maximize the short circuit current delivered by the a-Si cell at a given selected wavelength. The design has been customized to gas measurements application, where the index of refraction is slightly above 1 around 10$$^{-4}$$

-
4

. Our analysis reveals ultra-high sensitivity of $$2.4 \times 10^4$$

2.4
×

10
4

(mA/W)/RIU, and a figure of merit FOM= 107 RIU$$^{-1}$$

-
1

, when the bow-tie is made of SiO$$_2$$

2

. A performance rally competitive with those previously reported in literature, with the additional advantage of circunventing both moving parts and spectral interrogation elements.
Revealing low-temperature plasma efficacy through a dose-rate assessment by DNA damage detection combined with machine learning models
Authors: Sebastian Amal , Spulber Diana , Lisouskaya Aliaksandra , Ptasinska Sylwia 
Published: November 2022

AbstractLow-temperature plasmas have quickly emerged as alternative and unconventional types of radiation that offer great promise for various clinical modalities. As with other types of radiation, the therapeutic efficacy and safety of low-temperature plasmas are ubiquitous concerns, and assessing their dose rates is crucial in clinical settings. Unfortunately, assessing the dose rates by standard dosimetric techniques has been challenging. To overcome this difficulty, we proposed a dose-rate assessment framework that combined the predictive modeling of plasma-induced damage in DNA by machine learning with existing radiation dose-DNA damage correlations. Our results indicated that low-temperature plasmas have a remarkably high dose rate that can be tuned by various process parameters. This attribute is beneficial for inducing radiobiological effects in a more controllable manner.
Validation of days alive and out of hospital as a new patient-centered outcome to quantify life impact after heart transplantation
Authors: M’Pembele René , Roth Sebastian , Stroda Alexandra , Reier Tilman , Lurati Buse Giovanna , Sixt Stephan U. , Westenfeld Ralf , Rellecke Philipp , Tudorache Igor , Hollmann Markus W. , Aubin Hug , Akhyari Payam , Lichtenberg Artur , Huhn Ragnar , Boeken Udo 
Published: November 2022

AbstractThe number of patients waiting for heart transplantation (HTX) is increasing. Thus, identification of outcome-relevant factors is crucial. This study aimed to identify perioperative factors associated with days alive and out of hospital (DAOH)—a patient-centered outcome to quantify life impact—after HTX. This retrospective cohort study screened 187 patients who underwent HTX at university hospital Duesseldorf, Germany from September 2010 to December 2020. The primary endpoint was DAOH at 1 year. Risk factors for mortality after HTX were assessed in univariate analysis. Variables with significant association were entered into multivariable quantile regression. In total, 175 patients were included into analysis. Median DAOH at 1 year was 295 (223–322) days. In univariate analysis the following variables were associated with reduced DAOH: recipient or donor diabetes pre-HTX, renal replacement therapy (RRT), VA-ECMO therapy, recipient body mass index, recipient estimated glomerular filtration rate (eGFR) and postoperative duration of mechanical ventilation. After adjustment, mechanical ventilation, RRT, eGFR and recipient diabetes showed significant independent association with DAOH. This study identified risk factors associated with reduced DAOH at 1-year after HTX. These findings might complement existing data for outcome of patients undergoing HTX.
Gap-filling of ocean color over the tropical Indian Ocean using Monte-Carlo method
Authors: Modi Aditi , Roxy M. K. , Ghosh Subimal 
Published: November 2022

AbstractContinuous remote-sensed daily fields of ocean color now span over two decades; however, it still remains a challenge to examine the ocean ecosystem processes, e.g., phenology, at temporal frequencies of less than a month. This is due to the presence of significantly large gaps in satellite data caused by clouds, sun-glint, and hardware failure; thus, making gap-filling a prerequisite. Commonly used techniques of gap-filling are limited to single value imputation, thus ignoring the error estimates. Though convenient for datasets with fewer missing pixels, these techniques introduce potential biases in datasets having a higher percentage of gaps, such as in the tropical Indian Ocean during the summer monsoon, the satellite coverage is reduced up to 40% due to the seasonally varying cloud cover. In this study, we fill the missing values in the tropical Indian Ocean with a set of plausible values (here, 10,000) using the classical Monte-Carlo method and prepare 10,000 gap-filled datasets of ocean color. Using the Monte-Carlo method for gap-filling provides the advantage to estimate the phenological indicators with an uncertainty range, to indicate the likelihood of estimates. Quantification of uncertainty arising due to missing values is critical to address the importance of underlying datasets and hence, motivating future observations.
Tuning phononic and electronic contributions of thermoelectric in defected S-shape graphene nanoribbons
Authors: Bazrafshan M. Amir , Khoeini Farhad 
Published: November 2022

AbstractThermoelectrics as a way to use waste heat, is essential in electronic industries, but its low performance at operational temperatures makes it inappropriate in practical applications. Tailoring graphene can change its properties. In this work, we are interested in studying the transport properties of S-shape graphene structures with the single vacancy (SV) and double vacancy (DV) models. The structures are composed of a chiral part, which is an armchair graphene nanoribbon, and two zigzag graphene ribbons. We investigate the changes in the figure of merit by means of the Seebeck coefficient, electronic conductance, and electronic and phononic conductances with the vacancies in different device sizes. The transport properties of the system are studied by using the non-equilibrium Green’s function method, so that the related Hamiltonians (dynamical matrices) are obtained from the tight-binding (force constant) model. The maximum figure of merit (ZT) obtains for the DVs in all lengths. Physical properties of such a system can be tuned by controlling various parameters such as the location and the type of the defects, and the device size. Our findings show that lengthening the structure can reduce phononic contribution, and single vacancies than double vacancies can better distinguish between electronic thermal conductance behavior and electronic conductance one. Namely, vacancy engineering can significantly increase thermoelectric performance. In the large devices, the SVs can increase the ZT up to 2.5 times.
An electrocardiography score predicts heart failure hospitalization or death beyond that of cardiovascular magnetic resonance imaging
Authors: Maanja Maren , Schlegel Todd T. , Fröjdh Fredrika , Niklasson Louise , Wieslander Björn , Bacharova Ljuba , Schelbert Erik B. , Ugander Martin 
Published: November 2022

AbstractThe electrocardiogram (ECG) and cardiovascular magnetic resonance imaging (CMR) provide powerful prognostic information. The aim was to determine their relative prognostic value. Patients (n = 783) undergoing CMR and 12-lead ECG with a QRS duration < 120 ms were included. Prognosis scores for one-year event-free survival from hospitalization for heart failure or death were derived using continuous ECG or CMR measures, and multivariable logistic regression, and compared. Patients (median [interquartile range] age 55 [43–64] years, 44% female) had 155 events during 5.7 [4.4–6.6] years. The ECG prognosis score included (1) frontal plane QRS-T angle, and (2) heart rate corrected QT duration (QTc) (log-rank 55). The CMR prognosis score included (1) global longitudinal strain, and (2) extracellular volume fraction (log-rank 85). The combination of positive scores for both ECG and CMR yielded the highest prognostic value (log-rank 105). Multivariable analysis showed an association with outcomes for both the ECG prognosis score (log-rank 8.4, hazard ratio [95% confidence interval] 1.29 [1.09–1.54]) and the CMR prognosis score (log-rank 47, hazard ratio 1.90 [1.58–2.28]). An ECG prognosis score predicted outcomes independently of CMR. Combining the results of ECG and CMR using both prognosis scores improved the overall prognostic performance.
Production of mouse offspring from zygotes fertilized with freeze-dried spermatids
Authors: Wakayama Sayaka , Ito Daiyu , Ooga Masatoshi , Wakayama Teruhiko 
Published: November 2022

AbstractMouse cloning by nuclear transfer using freeze-drying (FD) somatic cells is now possible, but the success rate is significantly lower than that of FD spermatozoa. Because spermatozoa, unlike somatic cells, are haploid cells with hardened nuclei due to protamine, the factors responsible for their tolerance to FD treatment remain unclear. In this study, we attempt to produce offspring from FD spermatid, a haploid sperm progenitor cell whose nuclei, like somatic cells, have not yet been replaced by protamine. We developed a method for collecting FD spermatids from testicular suspension. Despite the significantly lower success rate than that of FD spermatozoa, healthy offspring were obtained when FD spermatids were injected into oocytes. Offspring were also obtained from FD spermatids derived from immature male mice that had not yet produced spermatozoa. These results suggest that nuclear protaminization, rather than haploid nuclei, is one of the key processes responsible for tolerance to FD treatment.
Task demand and load carriage experience affect gait variability among military cadets
Authors: Ulman Sophia , Srinivasan Divya , Nussbaum Maury A. 
Published: November 2022

AbstractLoad carriage is an inevitable daily task for soldiers. The purposes of this study were to explore the extent to which gait variability (GV) is affected by load carriage and experience among military cadets, and whether experience-related differences in GV are dependent on task demand. Two groups of cadets (30 experienced, 30 less experienced) completed a load carriage task in each of three load conditions (no load, 16 kg, 32 kg). Three categories of GV measures were obtained: spatiotemporal variability, joint kinematic variability, and Lyapunov exponents. Compared to traditional mean gait measures, GV measures were more discriminative of experience: although both groups showed similar mean gait measures, the experienced participants had reduced variability in spatiotemporal measures (p ≤ 0.008) and joint kinematics (p ≤ 0.004), as well as lower levels of long-term local dynamic stability at the ankle (p = 0.040). In both groups, heavier loads were also caused increased GV (p ≤ 0.018) and enhanced short-term local dynamic stability at the knee (p = 0.014). These results emphasize the importance of GV measures, which may provide a more complete description of adaptability, stability, and control; highlight alternate movement strategies during more difficult load carriage; and capture experience-related differences in load carriage strategies.
Utility of synovial calprotectin lateral flow test to exclude chronic prosthetic joint infection in periprosthetic fractures: a prospective cohort study
Authors: Lazic Igor , Burdach Alexander , Pohlig Florian , von Eisenhart-Rothe Rüdiger , Suren Christian 
Published: November 2022

AbstractThe diagnosis of periprosthetic joint infection (PJI) requires a combination of various clinical, laboratory, microbiological and histopathological parameters. A concomitant periprosthetic fracture (PPF) further complicates the diagnosis as it causes a confounding local inflammatory response. Synovial calprotectin has been demonstrated as a promising biomarker of PJI. The purpose of the present study was to evaluate the reliability of synovial calprotectin for the pre- or intraoperative diagnosis of PJI in PFF. 30 patients with PPF and implant loosening were included in this prospective study. Synovial fluid with white blood cells and percentage of polymorphonuclear neutrophils, serum C-reactive protein, and synovial calprotectin using a lateral-flow assay were tested against the EBJIS definition with adjusted thresholds to account for the local inflammation. 14 patients were postoperatively classified as confirmed infections (ten total hip arthroplasties and fourtotal knee arthroplasties). The calprotectin assay yielded a sensitivity of 0.71 [0.48; 0.95], a specificity of 0.69 [0.46; 0.91], a positive predictive value of 0.67 [0.43; 0.91] and a negative predictive value of 0.73 [0.51; 0.96]. Calprotectin is a promising diagnostic parameter for the detection of a PJI in a PPF. The lateral flow assay offers prompt results, which may further assist the surgeon in addition to already existing parameters of PJI diagnostics to diagnose concomitant PJI in PPF during surgery.
Overnight dynamics in scale-free and oscillatory spectral parameters of NREM sleep EEG
Authors: G. Horváth Csenge , Szalárdy Orsolya , Ujma Péter P. , Simor Péter , Gombos Ferenc , Kovács Ilona , Dresler Martin , Bódizs Róbert 
Published: November 2022

AbstractUnfolding the overnight dynamics in human sleep features plays a pivotal role in understanding sleep regulation. Studies revealed the complex reorganization of the frequency composition of sleep electroencephalogram (EEG) during the course of sleep, however the scale-free and the oscillatory measures remained undistinguished and improperly characterized before. By focusing on the first four non-rapid eye movement (NREM) periods of night sleep records of 251 healthy human subjects (4–69 years), here we reveal the flattening of spectral slopes and decrease in several measures of the spectral intercepts during consecutive sleep cycles. Slopes and intercepts are significant predictors of slow wave activity (SWA), the gold standard measure of sleep intensity. The overnight increase in spectral peak sizes (amplitudes relative to scale-free spectra) in the broad sigma range is paralleled by a U-shaped time course of peak frequencies in frontopolar regions. Although, the set of spectral indices analyzed herein reproduce known age- and sex-effects, the interindividual variability in spectral slope steepness is lower as compared to the variability in SWA. Findings indicate that distinct scale-free and oscillatory measures of sleep EEG could provide composite measures of sleep dynamics with low redundancy, potentially affording new insights into sleep regulatory processes in future studies.
Serum extracellular traps associate with the activation of myeloid cells in SLE patients with the low level of anti-DNA antibodies
Authors: Hanata Norio , Ota Mineto , Tsuchida Yumi , Nagafuchi Yasuo , Okamura Tomohisa , Shoda Hirofumi , Fujio Keishi 
Published: November 2022

AbstractNeutrophil extracellular traps (NETs) are involved in systemic lupus erythematosus (SLE). We sought to cluster SLE patients based on serum NET levels. Serum NET levels were higher in SLE patients than healthy controls. Frequencies of pleuritis and myositis were increased in patients with high serum NET levels. Serum NET levels negatively correlated with anti–double stranded DNA (anti-dsDNA) antibody titers and C1q-binding immune complexes, but positively correlated with C-reactive protein (CRP) and monocyte counts. Neutrophil transcriptome analysis demonstrated no difference in NET-associated signatures, irrespective of serum NET levels, suggesting anti-dsDNA antibody-mediated clearance of NETs. In serum, NET levels were significantly correlated with myeloid cell-derived inflammatory molecules. Serum NET-based cluster analysis revealed 3 groups of patients based on serum NET and CRP levels, anti-dsDNA antibody titers, and monocyte count. Monocytes were consistently activated following NET-containing immune complex (NET-IC) stimulation. In conclusion, SLE patients with high serum NET levels had lower anti-dsDNA antibody titers and higher inflammatory responses. NET-IC-stimulated monocytes might associate with an inflammatory response characterized by elevated CRP levels. These findings can apply to precision medicine, as inflammatory processes, rather than antibody-dependent processes, can be targeted in specific subpopulations of SLE patients.