bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systematic characterization of human response to H1N1 influenza vaccination through the construction and integration of personalized transcriptome response profiles
Authors: De Intinis Carlo , Bodini Margherita , Maffione Denise , De Mot Laurane , Coccia Margherita , Medini Duccio , Siena Emilio 
Published: October 2021

AbstractGene expression data is commonly used in vaccine studies to characterize differences between treatment groups or sampling time points. Group-wise comparisons of the transcriptional perturbations induced by vaccination have been applied extensively for investigating the mechanisms of action of vaccines. Such approaches, however, may not be sensitive enough for detecting changes occurring within a minority of the population under investigation or in single individuals. In this study, we developed a data analysis framework to characterize individual subject response profiles in the context of repeated measure experiments, which are typical of vaccine mode of action studies. Following the definition of the methodology, this was applied to the analysis of human transcriptome responses induced by vaccination with a subunit influenza vaccine. Results highlighted a substantial heterogeneity in how different subjects respond to vaccination. Moreover, the extent of transcriptional modulation experienced by each individual subject was found to be associated with the magnitude of vaccine-specific functional antibody response, pointing to a mechanistic link between genes involved in protein production and innate antiviral response. Overall, we propose that the improved characterization of the intersubject heterogeneity, enabled by our approach, can help driving the improvement and optimization of current and next-generation vaccines.
Comparison of bacteria disintegration methods and their influence on data analysis in metabolomics
Authors: Mielko Karolina Anna , Jabłoński Sławomir Jan , Łukaszewicz Marcin , Młynarz Piotr 
Published: October 2021

AbstractMetabolomic experiments usually contain many different steps, each of which can strongly influence the obtained results. In this work, metabolic analyses of six bacterial strains were performed in light of three different bacterial cell disintegration methods. Three strains were gram-negative (Pseudomonas aeruginosa, Escherichia coli, and Klebsiella pneumoniae), and three were gram-positive (Corynebacterium glutamicum, Bacillus cereus, and Enterococcus faecalis). For extraction, the methanol–water extraction method (1:1) was chosen. To compare the efficiency of different cell disintegration methods, sonication, sand mill, and tissue lyser were used. For bacterial extract metabolite analysis, 1H NMR together with univariate and multivariate analyses were applied. The obtained results showed that metabolite concentrations are strongly dependent on the cell lysing methodology used and are different for various bacterial strains. The results clearly show that one of the disruption methods gives the highest concentration for most identified compounds (e. g. sand mill for E. faecalis and tissue lyser for B. cereus). This study indicated that the comparison of samples prepared by different procedures can lead to false or imprecise results, leaving an imprint of the disintegration method. Furthermore, the presented results showed that NMR might be a useful bacterial strain identification and differentiation method. In addition to disintegration method comparison, the metabolic profiles of each elaborated strain were analyzed, and each exhibited its metabolic profile. Some metabolites were identified by the 1H NMR method in only one strain. The results of multivariate data analyses (PCA) show that regardless of the disintegration method used, the strain group can be identified. Presented results can be significant for all types of microbial studies containing the metabolomic targeted and non-targeted analysis.
Two-level modeling approach to identify the regulatory dynamics capturing drug response heterogeneity in single-cells
Authors: Chaves Madalena , Gomes-Pereira Luis C. , Roux Jérémie 
Published: October 2021

AbstractSingle-cell multimodal technologies reveal the scales of cellular heterogeneity impairing cancer treatment, yet cell response dynamics remain largely underused to decipher the mechanisms of drug resistance they take part in. As the phenotypic heterogeneity of a clonal cell population informs on the capacity of each single-cell to recapitulate the whole range of observed behaviors, we developed a modeling approach utilizing single-cell response data to identify regulatory reactions driving population heterogeneity in drug response. Dynamic data of hundreds of HeLa cells treated with TNF-related apoptosis-inducing ligand (TRAIL) were used to characterize the fate-determining kinetic parameters of an apoptosis receptor reaction model. Selected reactions sets were augmented to incorporate a mechanism that leads to the separation of the opposing response phenotypes. Using a positive feedback loop motif to identify the reaction set, we show that caspase-8 is able to encapsulate high levels of heterogeneity by introducing a response delay and amplifying the initial differences arising from natural protein expression variability. Our approach enables the identification of fate-determining reactions that drive the population response heterogeneity, providing regulatory targets to curb the cell dynamics of drug resistance.
Chemical hybridization of sulfasalazine and dihydroartemisinin promotes brain tumor cell death
Authors: Ackermann Annemarie , Çapcı Aysun , Buchfelder Michael , Tsogoeva Svetlana B. , Savaskan Nicolai 
Published: October 2021

AbstractGliomas are primary brain tumors with still poor prognosis for the patients despite a combination of cytoreduction via surgery followed by a radio-chemotherapy. One strategy to find effective treatment is to combine two different compounds in one hybrid molecule via linker to add to or at best potentiate their impact on malignant cells. Here, we report on the effects of a newly synthesized hybrid of sulfasalazine (SAS) and dihydroartemisinin (DHA), called AC254. In previous studies, both SAS and DHA have already proved to have anti-tumor properties themselves and to have sensitizing respectively potentiating effects on other treatments against malignant tumors. We investigated the impact of individual drugs SAS and DHA, their 1:1 combination and a novel SAS-DHA hybrid compound (AC254) on rodent and human glioma cells. In our study SAS alone showed no or only a mild effect on glioma, whereas DHA led to a significant reduction of cell viability in a dose-dependent manner. Next we compared the efficacy of the hybrid AC254 to the combinational treatment of its parent compounds SAS and DHA. The hybrid was highly efficient in combating glioma cells compared to single treatment strategies regarding cell viability and cell death. Interestingly, AC254 showed a remarkable advantage over the combinational treatment with both parent compounds in most used concentrations. In addition to its reduction of tumor cell viability and induction of cell death, the hybrid AC254 displayed changes in cell cycle and reduction of cell migration. Taken together, these results demonstrate that clinically established compounds such as SAS and DHA can be potentiated in their anti-cancer effects by chemical hybridization. Thus, this concept provides the opportunity to devise new effective chemotherapeutic agents.
Electrocorticography reveals thalamic control of cortical dynamics following traumatic brain injury
Authors: Mofakham Sima , Fry Adam , Adachi Joseph , Stefancin Patricia L. , Duong Tim Q. , Saadon Jordan R. , Winans Nathan J. , Sharma Himanshu , Feng Guanchao , Djuric Petar M. , Mikell Charles B. 
Published: October 2021

AbstractThe return of consciousness after traumatic brain injury (TBI) is associated with restoring complex cortical dynamics; however, it is unclear what interactions govern these complex dynamics. Here, we set out to uncover the mechanism underlying the return of consciousness by measuring local field potentials (LFP) using invasive electrophysiological recordings in patients recovering from TBI. We found that injury to the thalamus, and its efferent projections, on MRI were associated with repetitive and low complexity LFP signals from a highly structured phase space, resembling a low-dimensional ring attractor. But why do thalamic injuries in TBI patients result in a cortical attractor? We built a simplified thalamocortical model, which connotes that thalamic input facilitates the formation of cortical ensembles required for the return of cognitive function and the content of consciousness. These observations collectively support the view that thalamic input to the cortex enables rich cortical dynamics associated with consciousness.
Speckles and paraspeckles coordinate to regulate HSV-1 genes transcription
Authors: Li Kun , Wang Ziqiang 
Published: October 2021

AbstractNumbers of nuclear speckles and paraspeckles components have been demonstrated to regulate herpes simplex virus 1 (HSV-1) replication. However, how HSV-1 infection affects the two nuclear bodies, and whether this influence facilitates the expression of viral genes, remains elusive. In the current study, we found that HSV-1 infection leads to a redistribution of speckles and paraspeckles components. Serine/arginine-rich splicing factor 2 (SRSF2), the core component of speckles, was associated with multiple paraspeckles components, including nuclear paraspeckles assembly transcript 1 (NEAT1), PSPC1, and P54nrb, in HSV-1 infected cells. This association coordinates the transcription of viral genes by binding to the promoters of these genes. By association with the enhancer of zeste homolog 2 (EZH2) and P300/CBP complex, NEAT1 and SRSF2 influenced the histone modifications located near viral genes. This study elucidates the interplay between speckles and paraspeckles following HSV-1 infection and provides insight into the mechanisms by which HSV-1 utilizes host cellular nuclear bodies to facilitate its life cycle.
Three-dimensional tracking of the ciliate Tetrahymena reveals the mechanism of ciliary stroke-driven helical swimming
Authors: Marumo Akisato , Yamagishi Masahiko , Yajima Junichiro 
Published: October 2021

AbstractHelical swimming in free-space is a common behavior among microorganisms, such as ciliates that are covered with thousands hair-like motile cilia, and is thought to be essential for cells to orient directly to an external stimulus. However, a direct quantification of their three-dimensional (3D) helical trajectories has not been reported, in part due to difficulty in tracking 3D swimming behavior of ciliates, especially Tetrahymena with a small, transparent cell body. Here, we conducted 3D tracking of fluorescent microbeads within a cell to directly visualize the helical swimming exhibited by Tetrahymena. Our technique showed that Tetrahymena swims along a right-handed helical path with right-handed rolling of its cell body. Using the Tetrahymena cell permeabilized with detergent treatment, we also observed that influx of Ca2+ into cilia changed the 3D-trajectory patterns of Tetrahymena swimming, indicating that the beating pattern of cilia is the determining factor in its swimming behavior.
Cardiac Arrest during Cesarean Section – A Case Report and
Review of the Differential Diagnosis
Authors: Lukac Stefan , Mayer Sebastian , Mühlen Kathrin , Flock Felix 
Published: October 2021

Abstract
Aim According to the World Health Organization, approximately 810 pregnant
women die every day as a consequence of peripartum complications. A large
proportion of deaths happen in developing countries. Peripartum cardiac arrest
is a rare event that must be treated immediately. It is important to consider
the differential diagnoses in order to save lives.
Methods In this review, we discuss a differential diagnosis of cardiac
arrest according to the BEAU-CHOPS scheme of the American Heart Association in
the relation to the case report of our 40-year-old G5/P3 patient who
went into cardiac arrest during cesarean delivery.
Results Typical differentials for cardiac arrest during labor are
bleeding, embolism, anesthetic complications, cardiovascular diseases,
eclampsia, and sepsis. All of them were considered and ruled out in this
patient. In the end, we suspect that physiological cardio-inhibitory reflexes
triggered by sudden profound hypovolemia after placental separation along with
the patientʼs risk factors, especially obesity and maternal age, and the
administration of spinal anesthesia all potentially contributed to the cardiac
arrest.
Conclusions This review highlights that the cardiac arrest during labor
can be triggered by the multifactorial etiology, but firstly the typical
differential diagnosis needs to be excluded.
Rare Report Case of Oral Verruca Vulgaris on Torus Palatinus
Authors: Khoo Lee Kian , Chai Low Eng , Bhattarai Bishwa Prakash , Rokaya Dinesh , Yongvanichakorn Boonaur , Wongsirichat Natthamet 
Published: October 2021

AbstractVerruca vulgaris, also known as common warts, is most often seen on the skin of hands and feet. Human papilloma virus (HPV) plays an aetiological role in the development of this lesion. Oral verruca vulgaris (OVV) may occur on the palate, buccal mucosa, and tongue. Although asymptomatic and benign, HPV has been linked to squamous cell carcinoma in the oral cavity and oropharyngeal areas. Therefore, prompt surgical removal of OVV is warranted. We report a case of a OVV in a 48-year-old male patient on palate. The lesion was a white nonscrapable lesion in the middle of a torus palatinus. Excisional biopsy was done together with surgical removal of torus palatinus. Histopathological analysis confirmed the diagnosis of OVV.
Decreased Cerebral Oxygenation in Premature Infants with Progressive Posthemorrhagic Ventricular Dilatation May Help with Timing of Intervention
Authors: June Angelina , Heck Timothy , Shah Tushar A. , Vazifedan Turaj , Bass William Thomas 
Published: October 2021

Objective The objective of this study was to determine the degree of progressive posthemorrhagic ventricular dilatation (PHVD) that is associated with a significant decrease in regional cerebral oxygen saturation (rScO2) in premature infants at risk for periventricular–intraventricular hemorrhage (PIVH).
Study Design Cranial ultrasound (US) and near-infrared spectroscopy (NIRS) measurements of rScO2 were performed on inborn infants with birth weights less than 1,250 g on admission and at 1, 4, and 8 weeks of age. Infants with severe PIVH were studied weekly. A 1-hour average of rScO2 was compared with the frontal–occipital horn ratio (FOHR) measured the same day. Generalized linear models were used to analyze the relationship between FOHR and rScO2, by severity of PIVH, and adjusted for gestational age. Cut-off points of 0.55 for FOHR and 45% for rScO2 were used to calculate odds ratios (OR) and 95% confidence intervals (CI).
Results The study cohort included 63 infants with normal US, 15 with grade-1 or -2 PIVH (mild group), and 21 with grade-3 or -4 PIVH (severe group). Increases in FOHR in the severe group were associated with decreases in rScO2 at 1 week (p = 0.036), 4 weeks (p = 0.013), and 8 weeks of life (p = 0.001) compared with the normal and mild groups. Infants with FOHR greater than 0.55 were 92% more likely to have rScO2 less than 45% when compared with infants with FOHR less than 0.55 (OR = 0.08, 95% CI: [0.04, 0.13], p < 0.001).
Conclusion Progressive PHVD (FOHR > 0.55) is a strong predictor of compromised cerebral oxygenation. A combination of rScO2 and FOHR measurements may aid in identifying infants with PHVD that would benefit from early intervention.
Key Points
Reticulocyte Count: The Forgotten Factor in Transfusion Decisions for Extremely Low Birth Weight Infants
Authors: Nakhla Daniel , Kushnir Alla , Ahmed Rafat , Bhandari Vineet , Hunter Krystal , Nakhla Tarek 
Published: October 2021

Objective Extremely low birth weight (ELBW) infants often receive transfusions of packed red blood cells (PRBCs). Long-term outcomes of infants treated with liberal versus restricted transfusion criteria have been evaluated with conflicting results. Clinicians incorporate a reticulocyte count (RC) in their transfusion decisions. There is a lack of information on reference ranges for RCs in growing ELBW infants and whether infant's chronologic age or corrected gestational age (GA) generates a specific trend in the RCs. Our aim was to evaluate the levels of RCs obtained from ELBW infants over the course of the initial hospitalization.Study Design A retrospective chart review of ELBW infants treated in the neonatal intensive care unit (NICU) and had RCs performed. We analyzed the RCs to observe trends based on the chronologic age and corrected GA.Results A total of 738 RCs were analyzed. A positive trend in RCs that reached a peak at 32 to 34 weeks' corrected GA and then experienced a downward trend was observed.Conclusion Our report examines a very common hematologic test that is theoretically helpful but is in need of guidelines concerning the appropriate frequency of testing and its utility in making transfusion decisions in ELBW infants.Key Points
Serotonin modulates melatonin synthesis as an autocrine neurotransmitter in the pineal gland
Authors: Lee Bo Hyun , Hille Bertil , Koh Duk-Su 
Published: October 2021

Significance
The pineal gland secretes melatonin at night mainly driven by adrenergic sympathetic inputs. Many other neurotransmitters are found in the pineal gland, suggesting potential fine modulation of melatonin release. Serotonin as a precursor of melatonin synthesis is known to be significantly released by pinealocytes and its receptor also is expressed in pinealocytes. By identifying the release mechanism, cell signaling in the pinealocytes, and its effect on norepinephrine-induced melatonin secretion, our study defines serotonin as an autocrine neurotransmitter in the pineal gland and suggests possible modulatory targets for melatonin secretion.
Analytical and experimental study of the dynamics of a micro-electromechanical resonator based digital-to-analog converter
Authors: Zhao Wen , Ahmed Sally , Fariborzi Hossein , Younis Mohammad I 
Published: October 2021

Abstract
In this paper, an analytical model of a micro-electromechanical (MEM) resonator used as a 4-bit digital-to-analog converter (DAC) is presented. First, we derive the dynamic equation of the 4-bit DAC device, and the nonlinear governing equation is solved by the Galerkin method combined with a shooting technique to simulate the static response, linear eigenvalue problem, and forced vibration response of the device for various electrostatic actuation cases. Also, we optimize the air gaps in the linear domain to ensure enhanced performance of the DAC. Further, to analyze the operation of the DAC in the nonlinear regime, two experimental samples powered by −2 dBm and −12 dBm AC inputs are examined. Forward and backward frequency sweeps are conducted experimentally and analytically. The proposed analytical results are validated by comparison with experimental data. The results indicate that the presented modeling, simulations, and optimization are effective tools for the design of MEM resonator-based circuits.
Vortex formation in a spin–orbit-coupled Bose–Einstein condensates with static quadrupole magnetic field
Authors: Jin Jingjing , Han Wei , Ma Zongmin , Su Ningning 
Published: October 2021

Abstract
The ground-state phases of Rashba spin–orbit (SO)-coupled Bose–Einstein condensates (BECs) in a quadrupole magnetic field are studied. The coupling of quadrupole magnetic field and spin induces local nonzero gauge particle current, accompanied by the generation of equal and opposite canonical particle current, and leads to the spontaneous nucleation of quantized vortices. The condensates exhibit a variety of rich density patterns and vortex arrangements resulting from the competition among quadrupole magnetic field, SO coupling, and interatomic interactions. Novel vortex structures, such as static vortex dipole, three-vortex molecule and the structure of a cross-arranged vortices and anti-vortices surrounded by a density annulus are found in the condensates. These structures greatly enrich the ground-state phases of SO-coupled BECs, and help to understand the superfluid behavior of a BEC and the nonlinear behavior of coherent matter waves.
Multiband tunable thermal camouflage compatible with laser camouflage based on GST plasmonic metamaterial
Authors: Kang Qianlong , Li Dekui , Wang Wei , Guo Kai , Guo Zhongyi 
Published: October 2021

Abstract
In this paper, we propose a simple plasmonic structure based on Ge2Sb2Te5 (GST) to realize tunable multiband camouflage and radiation heat dissipation. In the mid-infrared (MIR) (3–5 μm) range, the proposed structure has average emissivity of 0.18 ∼ 0.76 and can be applied in tunable thermal camouflage as the GST’s crystallization fraction increases from 0 to 1. In the 5–8 μm (safe window) range, radiation heat dissipation of the proposed structure may guarantee thermal stability of the system. In the long-infrared (8–14 μm) range, the designed emitter maintains a relatively stable and low average emissivity of 0.13 ∼ 0.19 when the crystallization fraction of GST changes from 0 to 1. In addition, due to surface lattice resonance of plasmonic metamaterial, our designed emitter can also achieve laser radar camouflage at the wavelength of 10.6 μm. We have also analyzed the dependence of the camouflage performance on the GST’s crystallization fractions, polarization angle and incident angle. Moreover, simulated thermal images demonstrate tunable thermal camouflage for various background temperatures and different ambient backgrounds in the MIR ranges.
Impact of ion beam irradiation on two-dimensional MoS2: a molecular dynamics simulation study
Authors: Wu Xin , Zhu Xiaobao , Lei Bing 
Published: October 2021

Abstract
Two-dimensional (2D) materials such as MoS2 have extraordinary properties and significant application potential in electronics, optoelectronics, energy storage, bioengineering, etc. To realize the numerous application potential, it is needed to modulate the structure and properties of these 2D materials, for which ion beam irradiation has obvious advantages. This research adopted classical molecular dynamics simulations to study the sputtering of atoms in 2D MoS2, defect formation and the control rule under Ar ion beam irradiation, considering the influence of ion irradiation parameters (i.e., ion beam energy, ion dose), layer number of 2D MoS2, substrate. Furthermore, the uniaxial mechanical performance of the ion-irradiated nanostructures was investigated for actual applications loading with mechanical stress/strain. This research could provide important theoretical support for fabricating high-performance 2D MoS2-based nanodevices by ion beam irradiation method.