bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of plasma screening on electron impact excitation and ionization of Fe16+ in a dense environment
Authors: Zeng Jiaolong , Li Yongjun , Yuan Jianmin 
Published: April 2021

ABSTRACTElectron impact excitation and ionization with atoms and ions within a dense plasma are fundamental microscopic processes that determine the ionization balance, physical properties (such as electron conductive opacity and thermal conductivity) and plasma formation and dynamics. While collision cross-sections and rates are well studied in dilute systems, similar investigations are scarce for dense plasmas under stellar interior conditions using an appropriate plasma-screening potential. Here we investigate the plasma-screening effect on the electron impact excitation and ionization cross-sections, effective collision strengths, and rate coefficients within plasmas under stellar interior conditions in a mass density range of 1–15.748 g cm−3 and a temperature range of 200–1000 eV. These investigations were carried out using our recently developed plasma-screening model, taking Fe16+ as an example. The results show that the cross-sections of the electron impact excitation are generally decreased, whereas they are always significantly increased for the collision ionization due to the plasma screening. In a plasma at a temperature of 200 eV and density of 15.748 g cm−3, the plasma screening causes a decrease in the excitation cross-section of 36 per cent for the dipole-allowed transition $2\mathrm{ s}^22\mathrm{ p}^6~^1\mathrm{ S}_0 \rightarrow 2\mathrm{ s}^22\mathrm{ p}^53\mathrm{ d}~^1\mathrm{ P}^o_1$ and of 50 per cent for the dipole-forbidden transition $2\mathrm{ s}^22\mathrm{ p}^6~^1\mathrm{ S}_0 \rightarrow 2\mathrm{ s}^22\mathrm{ p}^53\mathrm{ d}~^3\mathrm{ D}^o_1$. However, the collision ionization cross-section of a 2p electron from the ground level of Fe16+ is increased by 500 per cent and 100 per cent under an incident electron energy of 1500 and 10 000 eV, respectively. This results in the rate coefficient increasing by a factor of 18.5 at a temperature of 200 eV and density of 15.748 g cm−3.
Simultaneous estimation of segmented telescope phasing errors and non-common path aberrations from adaptive-optics-corrected images
Authors: Lamb Masen P , Correia Carlos , Sivanandam Suresh , Swanson Robin , Zavyalova Polina 
Published: April 2021

ABSTRACT
We investigate the focal plane wavefront sensing technique, known as Phase Diversity, at the scientific focal plane of a segmented mirror telescope with an adaptive optics (AO) system. We specifically consider an optical system imaging a point source in the context of (i) an artificial source within the telescope structure and (ii) from AO-corrected images of a bright star. From our simulations, we reliably disentangle segmented telescope phasing errors from non-common path aberrations (NCPA) for both a theoretical source and on-sky, AO-corrected images where we have simulated the Keck/NIRC2 system. This quantification from on-sky images is appealing, as it is sensitive to the cumulative wavefront perturbations of the entire optical train; disentanglement of phasing errors and NCPA is therefore critical, where any potential correction to the primary mirror from an estimate must contain minimal NCPA contributions. Our estimates require a 1-min sequence of short-exposure, AO-corrected images; by exploiting a slight modification to the AO-loop, we find that 75 defocused images produce reliable estimates. We demonstrate a correction from our estimates to the primary and deformable mirror results in a wavefront error reduction of up to 67 per cent and 65 per cent for phasing errors and NCPA, respectively. If the segment phasing errors on the Keck primary are of the order of ∼130 nm RMS, we show we can improve the H-band Strehl ratio by up to 10 per cent by using our algorithm. We conclude our technique works well to estimate NCPA alone from on-sky images, suggesting it is a promising method for any AO-system.
Towards wide-scale adoption of open science practices: The role of open science communities
Authors: Armeni Kristijan , Brinkman Loek , Carlsson Rickard , Eerland Anita , Fijten Rianne , Fondberg Robin , Heininga Vera E , Heunis Stephan , Koh Wei Qi , Masselink Maurits , Moran Niall , Baoill Andrew Ó , Sarafoglou Alexandra , Schettino Antonio , Schwamm Hardy , Sjoerds Zsuzsika , Teperek Marta , van den Akker Olmo R , van't Veer Anna , Zurita-Milla Raul 
Published: April 2021

Abstract
Despite the increasing availability of Open Science (OS) infrastructure and the rise in policies to change behaviour, OS practices are not yet the norm. While pioneering researchers are developing OS practices, the majority sticks to status quo. To transition to common practice, we must engage a critical proportion of the academic community. In this transition, OS Communities (OSCs) play a key role. OSCs are bottom-up learning groups of scholars that discuss OS within and across disciplines. They make OS knowledge more accessible and facilitate communication among scholars and policymakers. Over the past two years, eleven OSCs were founded at several Dutch university cities. In other countries, similar OSCs are starting up. In this article, we discuss the pivotal role OSCs play in the large-scale transition to OS. We emphasize that, despite the grassroot character of OSCs, support from universities is critical for OSCs to be viable, effective, and sustainable.
Maternal Antibody Response, Neutralizing Potency, and Placental Antibody Transfer After Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection
Authors: Joseph Naima T. , Dude Carolynn M. , Verkerke Hans P. , Irby Les’Shon S. , Dunlop Anne L. , Patel Ravi M. , Easley Kirk A. , Smith Alicia K. , Stowell Sean R. , Jamieson Denise J. , Velu Vijayakumar , Badell Martina L. 
Published: April 2021

OBJECTIVE:
To characterize maternal immune response after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection during pregnancy and quantify the efficiency of transplacental antibody transfer.

METHODS:
We conducted a prospective cohort study of pregnant patients who tested positive for SARS CoV-2 infection at any point in pregnancy and collected paired maternal and cord blood samples at the time of delivery. An enzyme-linked immunosorbent assay (ELISA) and neutralization assays were performed to measure maternal plasma and cord blood concentrations and neutralizing potency of immunoglobulin (Ig)G, IgA, and IgM antibodies directed against the SARS-CoV-2 spike protein. Differences in concentrations according to symptomatic compared with asymptomatic infection and time from positive polymerase chain reaction (PCR) test result to delivery were analyzed using nonparametric tests of significance. The ratio of cord to maternal anti–receptor-binding domain IgG titers was analyzed to assess transplacental transfer efficiency.

RESULTS:
Thirty-two paired samples were analyzed. Detectable anti–receptor-binding domain IgG was detected in 100% (n=32) of maternal and 91% (n=29) of cord blood samples. Functional neutralizing antibody was present in 94% (n=30) of the maternal and 25% (n=8) of cord blood samples. Symptomatic infection was associated with a significant difference in median (interquartile range) maternal anti–receptor-binding domain IgG titers compared with asymptomatic infection (log 3.2 [3.5–2.4] vs log 2.7 [2.9–1.4], P=.03). Median (interquartile range) maternal anti–receptor-binding domain IgG titers were not significantly higher in patients who delivered more than 14 days after a positive PCR test result compared with those who delivered within 14 days (log 3.3 [3.5–2.4] vs log 2.67 [2.8–1.6], P=.05). Median (range) cord/maternal antibody ratio was 0.81 (0.67–0.88).

CONCLUSIONS:
These results demonstrate robust maternal neutralizing and anti–receptor-binding domain IgG response after SARS-CoV-2 infection, yet a lower-than-expected efficiency of transplacental antibody transfer and a significant reduction in neutralization between maternal blood and cord blood. Maternal infection does confer some degree of neonatal antibody protection, but the robustness and durability of protection require further study.
The Coronavirus (COVID-19) Effect on Public Sentiments Regarding Elective Plastic Surgery in the United States
Authors: Chen Jiaxi , Ray Edward C. 
Published: April 2021

Background:
The SARS-CoV-2 coronavirus (COVID-19) has challenged the US's healthcare systems to adapt and innovate on multiple fronts. As the course of the COVID-19 pandemic changes, we explore the US public sentiments on resuming previously postponed elective plastic surgery procedures.

Methods:
A prospective national survey of one thousand US adults was conducted to study public perception of elective plastic surgery procedures during the COVID-19 pandemic. Binomial logarithmic multivariable regression modeling was employed to study the response data.

Results:
Nine hundred seventy-three participants were included in study. The majority (86.6%) believed elective plastic surgery should continue during the COVID-19 pandemic. Most (79.6%) would not delay obtaining plastic surgery more than 6 months. Participants expressed concerns of contracting COVID-19 at elective surgery centers (67.5%) or at hospitals (68.5%). Participants who reside in the Midwest (odds ratio [OR] 2.3, P < 0.05) and participants between the ages of 41 and 60 years old (OR 2.8, P < 0.03) were more likely to resume elective plastic surgery. Participants who had undergone a COVID-19 test (OR 0.13, P < 0.04), contracted the COVID-19 infection (OR 0.26, P < 0.03), or were older than 60 years (OR 0.41, P < 0.02) were less likely to resume elective plastic surgery.

Conclusion:
The majority of the US adult participants (1) agree with resuming elective plastic surgery services, (2) but harbor some concerns of contracting COVID-19 during their procedures, and (3) agree with the majority of safety protocols taken to prevent the spread of COVID-19.
A State of the Science on HIV Prevention Over 40 Years Among Black and Hispanic/Latinx Communities
Authors: Ramos S. Raquel , Nelson LaRon E. , Jones Sandra Gracia , Ni Zhao , Turpin Rodman E. , Portillo Carmen J. 
Published: April 2021

Abstract
We present a state of the science on HIV behavioral prevention interventions in Black and Hispanic/Latinx communities. The purpose of this article is threefold: (a) highlight the early documented underlying social and political barriers that constrained interventions to prevent new HIV infections; (b) address the structural inequities in HIV prevention and treatment; and (c) describe the need for increasing HIV multilevel prevention interventions that support greater HIV testing and pre-exposure prophylaxis uptake. To address HIV prevention, multilevel interventions that address individual, structural, and social level components have demonstrated more sustainable outcomes. Implications for research and clinical practice include (a) updating antiquated curricula in nursing, medicine, and public health that perpetuate racial, structural-level inequities and (b) increasing the pipeline for Black and Hispanic/Latinx persons to pursue research or clinical-focused doctorate degrees.
Probiotics alleviate depressive behavior in chronic unpredictable mild stress rat models by remodeling intestinal flora
Authors: Li Qiufeng , Li Li , Niu Xueqin , Tang Chunling , Wang Huaizhi , Gao Jing , Hu Jian 
Published: April 2021

Objective
To explore the effects of probiotics on depressive behavior in a chronic unpredictable mild stress (CUMS) rat model by remodeling intestinal flora.

Methods
Twenty-four male SD rats aged 6–8 weeks were randomly divided into four groups: control group, depression group (CUMS), depression+paroxetine group (Paro) and depression+probiotics group (Pro). Sucrose preference, open field and forced swimming tests were used to assess depression-like behavior in rats. ELISA was used to detect the levels of adrenocorticotropic hormone (ACTH), and corticosterone, norepinephrine and 5-hydroxytryptamine in rat serum. Real-time PCR was used to determine the changes of Lactobacillus, Bifidobacterium, Enterococcus faecalis and Escherichia coli in rat cecum.

Results
Compared with the control group, CUMS led to significant decreases of body weight, total traveled distance, duration in central area, immobility time, norepinephrine and 5-hydroxytryptamine contents in hippocampal tissues, as well as Lactobacillus and Bifidobacterium in the cecum. It also resulted in marked increases of the contents of E. faecalis and E. coli in the cecum, ACTH and corticosterone contents in the serum of rats. Paroxetine and probiotic treatment each diminished or prevented these changes.

Conclusion
By remodeling intestinal flora, probiotics can reduce the CUMS-induced depressive behavior of rats, increase the levels of norepinephrine and 5-hydroxytryptamine, and inhibit the expression of ACTH and corticosterone. Significantly, the effect of both paroxetine and probiotic on microorganisms is similar.
The herbal combination of Sugarcane, Black Myrobalan, and mastic as a supplementary treatment for COVID-19: a randomized clinical trial
Authors: Shiri Alireza Hashemi , Raiatdoost Esmaeil , Afkhami Hamid , Ravanshad Ruhollah , Hosseini Seyed Ehsan , Kalani Navid , Raoufi Rahim 
Published: April 2021

AbstractBackgroundGiven the COVID-19 pandemic’s, researchers are beseeched for effective treatments. Herbal medicine is also queried for potential supplementary treatments for COVID-19. We aimed to evaluate the effects of Sugarcane, Black Myrobalan, and Mastic herbal medications for COVID-19 patients.MethodsThis was a double-blinded randomized clinical trial study conducted over three months from May to July 2020 in patients admitted with a diagnosis of COVID-19 in Peymaniyeh Hospital in Jahrom, Iran. The intervention group received the treatment protocol approved by the Ministry of Health of Iran during the period of hospitalization and the herbal supplement obtained from the combination of black myrobalan and mastic and sugarcane, twice a day (3g of herbal supplements). All patients were compared in terms of demographic variables, vital signs, clinical and laboratory variables.Results72 patients with COVID-19, divided into intervention (n=37) and control (n=35) groups. intervention and control groups had not any significant difference in terms of baseline characteristics. The time-to-event analysis revealed a significant difference in 4 symptoms of cough, fever, dyspnea, and myalgia (P<0.05). The Control group had a significantly lower decrease in C-reactive protein during 7 days (P<0.05). Patients in the herbal supplement group were hospitalized for 4.12 days and in the control group were hospitalized for 8.37 days (P=0.001). ICU admission and death only happened in 3 (8.6%) patients of the control group.ConclusionWhile advanced studies with more sample size are needed; the proposed combination seems to be effective in the symptom treatment and reducing the length of hospitalization.
A Novel Family of RNA-Binding Proteins Regulate Polysaccharide Metabolism inBacteroides thetaiotaomicron
Authors: Adams Amanda N.D. , Azam Muhammad S. , Costliow Zachary A. , Ma Xiangqian , Degnan Patrick H. , Vanderpool Carin K. 
Published: April 2021

AbstractHuman gut microbiome composition is constantly changing, and diet is a major driver of these changes. Gut microbial species that persist in mammalian hosts for long periods of time must possess mechanisms for sensing and adapting to nutrient shifts to avoid being outcompeted. Global regulatory mechanisms mediated by RNA-binding proteins (RBPs) that govern responses to nutrient shifts have been characterized in Proteobacteria and Firmicutes but remain undiscovered in the Bacteroidetes. Here we report the identification of RBPs that are broadly distributed across the Bacteroidetes, with many genomes encoding multiple copies. Genes encoding these RBPs are highly expressed in manyBacteroidesspecies. A purified RBP, RbpB, fromBacteroides thetaiotaomicronbinds to single-stranded RNAin vitrowith an affinity similar to other characterized regulatory RBPs.B. thetaiotaomicronmutants lacking RBPs show dramatic shifts in expression of polysaccharide utilization and capsular polysaccharide loci, suggesting that these RBPs may act as global regulators of polysaccharide metabolism. AB. thetaiotaomicronΔrbpBmutant shows a growth defect on dietary sugars belonging to the raffinose family of oligosaccharides (RFOs). The ΔrbpBmutant had reduced expression ofBT1871, encoding a predicted RFO-degrading melibiase, compared to the wild-type strain. Mutation ofBT1871confirmed that the enzyme it encodes is essential for growth on melibiose and promotes growth on the RFOs raffinose and stachyose. Our data reveal that RbpB is required for optimal expression ofBT1871and other polysaccharide-related genes, suggesting that we have identified an important new family of global regulatory proteins in the Bacteroidetes.ImportanceThe human colon houses hundreds of bacterial species, including many belonging to the genusBacteroides,that aid in breaking down our food to keep us healthy.Bacteroideshave many genes responsible for breaking down different dietary carbohydrates and complex regulatory mechanisms ensure that specific genes are only expressed when the right carbohydrates are available. In this study, we discovered thatBacteroidesuse a family of RNA-binding proteins as global regulators to coordinate expression of carbohydrate utilization genes. The ability to turn different carbohydrate utilization genes on and off in response to changing nutrient conditions is critical forBacteroidesto live successfully in the gut, and thus the new regulators we have identified may be important for life in the host.
Nucleic acid delivery of immune-focused SARS-CoV-2 nanoparticles drive rapid and potent immunogenicity capable of single-dose protection
Authors: Konrath Kylie M. , Liaw Kevin , Wu Yuanhan , Zhu Xizhou , Walker Susanne N. , Xu Ziyang , Schultheis Katherine , Chokkalingam Neethu , Du Jianqiu , Tursi Nicholas J. , Moore Alan , Purwar Mansi , Reuschel Emma L. , Frase Drew , Sullivan Matthew , Maricic Igor , Andrade Viviane M. , Iffland Christel , Broderick Kate E. , Humeau Laurent M. P. F. , Smith Trevor R.F. , Pallesen Jesper , Weiner David B. , Kulp Daniel W. 
Published: April 2021

AbstractAntibodies from SARS-CoV-2 vaccines may target epitopes which reduce durability or increase the potential for escape from vaccine-induced immunity. Using a novel synthetic vaccinology pipeline, we developed rationally immune focused SARS-CoV-2 Spike-based vaccines. N-linked glycans can be employed to alter antibody responses to infection and vaccines. Utilizing computational modeling and comprehensive in vitro screening, we incorporated glycans into the Spike Receptor-Binding Domain (RBD) and assessed antigenic profiles. We developed glycan coated RBD immunogens and engineered seven multivalent configurations. Advanced DNA delivery of engineered nanoparticle vaccines rapidly elicited potent neutralizing antibodies in guinea pigs, hamsters and multiple mouse models, including human ACE2 and human B cell repertoire transgenics. RBD nanoparticles encoding wild-type and the P.1 SARS-CoV-2 variant induced high levels of cross-neutralizing antibodies. Single, low dose immunization protected against a lethal SARS-CoV-2 challenge. Single-dose coronavirus vaccines via DNA-launched nanoparticles provide a platform for rapid clinical translation of novel, potent coronavirus vaccines.
Mechanistic Insights on ATP’s role as Hydrotrope
Authors: Sarkar Susmita , Mondal Jagannath 
Published: April 2021

AbstractHydrotropes are small amphiphilic molecules which help in solubilizing hydrophobic entities in aqueous medium. Recent experimental investigation has provided convincing evidences that, adenosine triphosphate (ATP), besides being anenergy currency of cell, also can act ashydrotropeto inhibit the formation of protein condensates. In this work, we have designed computer simulations of prototypical macromolecules in aqueous ATP solution to dissect the molecular mechanism underlying ATP’s newly discovered role as a hydrotrope. The simulation demonstrates that ATP can unfold a single-chain of hydrophobic macromolecule as well as can disrupt the aggregation process of a hydrophobic assembly. Moreover, the introduction of charges in the macromolecule is found to reinforce ATP’s disaggregation effects in a synergistic fashion, a behaviour reminiscent of recent experimental observation of pronounced hydrotropic action of ATP in intrinsically disordered proteins. A molecular analysis indicates that this new-found ability of ATP are ingrained in its propensity of preferential binding to the polymer surface, which gets fortified in presence of charges. The investigation also renders evidence that the key to the ATP’s superior hydrotropic role over chemical hydrotrope (Sodium xylene sulfonate, NaXS) may lie in its inherent self-aggregation propensity. Overall, via employing a bottom-up approach the current investigation provides fresh mechanistic insights into the dual solubilizing and denaturing abilities of ATP.
Distortion Discovery: A Framework to Model, Spot and Explain Tumor Heterogeneity and Mitigate its Negative Impact on Cancer Risk Assessment
Authors: Elmansy Dalia 
Published: April 2021

ABSTRACTIn a complex system of inter-genome interactions, false negatives remain an overwhelming problem when using omics data for disease risk prediction. This is especially clear when dealing with complex diseases like cancer in which the infiltration of stromal and immune cells into the tumor tissue can affect the degree of its tumor purity and hence its cancer signal. Previous work was done to estimate the degree of cancer purity in a tissue. In this work, we introduce a data and biomarker selection independent, information theoretic, approach to tackle this problem. We model distortion as a source of false negatives and introduce a mechanism to detect and remove its impact on the accuracy of disease risk prediction.
Micrarchaeota are covered by a proteinaceous S-Layer
Authors: Gfrerer Sabrina , Winkler Dennis , Ducassou Julia Novion , Couté Yohann , Rachel Reinhard , Gescher Johannes 
Published: April 2021

AbstractIn previous publications, it was hypothesized that Micrarchaeota cells are covered by two individual membrane systems. This study proofs that at least the recently cultivated “CandidatusMicrarchaeum harzensis A_DKE” possesses an S-layer covering its cytoplasmic membrane. The potential S-layer protein was found to be among the proteins with the highest abundance in A_DKE andin silicocharacterization of its primary structure indicated homologies to other known S-layer proteins. Homologs of this protein were found in other Micrarchaeota genomes, which raises the question, whether the ability to form an S-layer is a common trait within this phylum. The S-layer protein seems to be glycosylated and the Micrarchaeum expresses genes for N-glycosylation under cultivation conditions, despite not being able to synthesize carbohydrates. Electron micrographs of freeze-etched samples of a previously described co-culture, containing Micrarchaeum A_DKE and a Thermoplasmatales member as its host organism, verified the hypothesis of an S-layer on the surface of A_DKE. Both organisms are clearly distinguishable by cell size, shape and surface structure.