bluuebunny/crossref_metadata_2025_split huggingface dataset:
Immunoinformatics design of a novel epitope-based vaccine candidate against dengue virus
Authors: Fadaka Adewale Oluwaseun , Sibuyi Nicole Remaliah Samantha , Martin Darius Riziki , Goboza Mediline , Klein Ashwil , Madiehe Abram Madimabe , Meyer Mervin 
Published: October 2021

AbstractDengue poses a global health threat, which will persist without therapeutic intervention. Immunity induced by exposure to one serotype does not confer long-term protection against secondary infection with other serotypes and is potentially capable of enhancing this infection. Although vaccination is believed to induce durable and protective responses against all the dengue virus (DENV) serotypes in order to reduce the burden posed by this virus, the development of a safe and efficacious vaccine remains a challenge. Immunoinformatics and computational vaccinology have been utilized in studies of infectious diseases to provide insight into the host–pathogen interactions thus justifying their use in vaccine development. Since vaccination is the best bet to reduce the burden posed by DENV, this study is aimed at developing a multi-epitope based vaccines for dengue control. Combined approaches of reverse vaccinology and immunoinformatics were utilized to design multi-epitope based vaccine from the sequence of DENV. Specifically, BCPreds and IEDB servers were used to predict the B-cell and T-cell epitopes, respectively. Molecular docking was carried out using Schrödinger, PATCHDOCK and FIREDOCK. Codon optimization and in silico cloning were done using JCAT and SnapGene respectively. Finally, the efficiency and stability of the designed vaccines were assessed by an in silico immune simulation and molecular dynamic simulation, respectively. The predicted epitopes were prioritized using in-house criteria. Four candidate vaccines (DV-1–4) were designed using suitable adjuvant and linkers in addition to the shortlisted epitopes. The binding interactions of these vaccines against the receptors TLR-2, TLR-4, MHC-1 and MHC-2 show that these candidate vaccines perfectly fit into the binding domains of the receptors. In addition, DV-1 has a better binding energies of − 60.07, − 63.40, − 69.89 kcal/mol against MHC-1, TLR-2, and TLR-4, with respect to the other vaccines. All the designed vaccines were highly antigenic, soluble, non-allergenic, non-toxic, flexible, and topologically assessable. The immune simulation analysis showed that DV-1 may elicit specific immune response against dengue virus. Moreover, codon optimization and in silico cloning validated the expressions of all the designed vaccines in E. coli. Finally, the molecular dynamic study shows that DV-1 is stable with minimum RMSF against TLR4. Immunoinformatics tools are now applied to screen genomes of interest for possible vaccine target. The designed vaccine candidates may be further experimentally investigated as potential vaccines capable of providing definitive preventive measure against dengue virus infection.
Association between plasma homocysteine levels and cognitive deficits in Han Chinese patients with schizophrenia across age groups
Authors: Zhou Sumiao , Huang Yuanyuan , Feng Yangdong , Li Hehua , Wu Kai , Yang Mingzhe , Wu Fengchun , Huang Xingbing 
Published: October 2021

AbstractIt was still unclear how homocysteine (Hcy) levels and cognitive deficits change in patients with schizophrenia of various ages. The present article attempts to assess the relationship between Hcy levels and cognitive deficits in patients with schizophrenia across age groups, especially in young people. Totals of 103 patients and 122 healthy controls were included. All participants were stratified into four groups according to their age: 18–29 years, 30–39 years, 40–49 years, and 50–59 years. Clinical data, plasma Hcy levels, and cognitive function score were collected. Cognitive function was evaluated using the MATRICS Consensus Cognitive Battery of tests assessing speed of processing, verbal learning and memory, visual learning and memory, working memory, and attention/vigilance. Compared with the healthy group, Hcy levels increased significantly, and all the measured cognitive function score were significantly lower in all age groups of patients with schizophrenia (p < 0.001). Hcy levels were negatively associated with speed of processing (SoP), working memory (WM), and visual learning and memory (Vis Lrng) score in 18–29 years. Further multiple regression analysis showed that SoP were independently associated with Hcy levels in patients with schizophrenia aged 18–29 years (B = 0.74, t = 3.12, p = 0.008). Based on our results, patients with schizophrenia performed worse on cognitive assessments and Hcy levels were more closely related to cognition in young patients.
Reactivation of latent tuberculosis through modulation of resuscitation promoting factors by diabetes
Authors: Verma Arpana , Kaur Maninder , Singh Lakshya Veer , Aggarwal Divya , Verma Indu , Radotra Bishan D. , Sharma Sadhna 
Published: October 2021

AbstractThe evidence of an association between diabetes and latent tuberculosis infection (LTBI) remains limited and inconsistent. Thus, the study aims to delineate the role of diabetes in activation of latent tuberculosis infection. Murine model of latent tuberculosis and diabetes was developed, bacillary load and gene expression of resuscitation promoting factors (rpfA-E) along with histopathological changes in the lungs and spleen were studied. Treatment for LTBI [Rifampicin (RIF) + Isoniazid (INH)] was also given to latently infected mice with or without diabetes for 4 weeks. Diabetes was found to activate latent tuberculosis as the colony forming unit (CFU) counts were observed to be > 104in lungs and spleen. The gene expression ofhspXwas downregulated and that ofrpfBandrpfDwas observed to be upregulated in latently infected mice with diabetes compared to those without diabetes. However, no significant reduction in the CFU counts was observed after 4 weeks of treatment with RIF and INH. Diabetes helps in the progression of LTBI to active disease mainly through altered expression of resuscitation promoting factorsrpfBandrpfD, which can serve as important targets to reduce the shared burden of tuberculosis and diabetes.
Second primary malignancy among malignant solid tumor survivors aged 85 years and older
Authors: Zhang Zhijia , Liu Fei , Qu Yanlin , Qiu Liqian , Zhang Liqun , Yang Qiao 
Published: October 2021

AbstractThe cancer burden in the oldest old has increased rapidly. This study aimed to investigate the epidemiology of second primary malignancy (SPM) in malignant solid tumor survivors aged 85 years and older utilizing the Surveillance, Epidemiology, and End Results (SEER) database. A total of 128,466 malignant solid tumor patients had been identified between 2000 and 2011, including 6774 patients who developed a SPM. The overall crude incidence of developing a SPM was 5.3%. Considering death as a competing event, the 3, 5, and 10-year cumulative incidence was 1.9%, 3.2%, and 5.4%, respectively. Relative younger age, male gender, surgery history, local stage and first primary malignancy (FPM) site located in the urinary system were related to higher cumulative incidence. A median time interval of 24.0 months was found between diagnosis of FPM and SPM. The most common SPM site was digestive system, whereas the least common was oral cavity and pharynx. The median overall survival (OS) was 49.0 months, and the median survival after SPM was 13.0 months. Relative older age, male gender and black race were associated with worse OS and survival after SPM, as well as higher hazard ratios of death. In conclusions, this study performed a comprehensive analysis of SPM among malignant solid tumor survivors aged 85 years and older. Additional studies are needed to characterize the specific cancer type of interest.
Concentration of Na+-taurocholate-cotransporting polypeptide expressed after in vitro-transcribed mRNA transfection determines susceptibility of hepatoma cells for hepatitis B virus
Authors: Oswald Andreas , Chakraborty Anindita , Ni Yi , Wettengel Jochen M. , Urban Stephan , Protzer Ulrike 
Published: October 2021

AbstractInfection of hepatocytes by hepatitis B virus (HBV) depends on surface expression of its receptor Na+-taurocholate-cotransporting polypeptide (NTCP), but sufficient NTCP expression is lacking in most cell lines. NTCP can be introduced by plasmid transfection or transduction by viral vectors to render cells permissive for HBV. However, transient transfection of hepatocyte-derived cell lines is inefficient, resulting in inhomogeneous protein expression and does not allow to adapt the level of NTCP expression. We therefore utilized in vitro transcribed mRNA to introduce NTCP into cells. Optimization using alternative cap structures and nucleotide modifications rendered mRNA transfection into different non-hepatic and hepatic cell lines very efficient. After transfection of mRNA, surface expression and functionality of NTCP was demonstrated by staining with an N-terminal HBV-preS peptide and bile acid uptake. Introduction of NTCP by mRNA transfection increased susceptibility of hepatoma cells to HBV in a dose-dependent manner. Transfection of NTCP mRNA into non-liver cells, in contrast, supported bile acid uptake but did still not render the cells permissive for HBV, demonstrating the requirement for additional host factors. Introduction of candidate host factors by mRNA transfection will allow for fast and convenient analysis of the viral life cycle using a transient, but reliable expression system.
Surface plasmon induced spot and line formation at interfaces of ITO coated LiNbO3 slabs and gigantic nonlinearity
Authors: Xiong Zuoren , Ma Xinyan , Pei Yanbo , Zhang Yingbin , Zhao Hua 
Published: October 2021

AbstractRemarkable spots and lines were clearly observed at the two interfaces of indium-tin-oxide coated Z-cut Fe-doped lithium noibate plates under illumination by milliwatt continuous-wave laser light; this occurred because of the visible surface plasmons (SPs) supported by the promising non-metal plasmonic system. The intriguing observations are here explained via the SP-strengthened nonlinear effect, through consideration of the electrostatic field (which is comparable to the atomic field) and its large gradient; this hints at a promising, highly sensitive plasmonic system. The gigantic nonlinear effect discussed in this paper should be ubiquitously existed in many oxide ferroelectric/semiconductor combinations and is promising for visible plasmonic applications.
An automated and combinative method for the predictive ranking of candidate effector proteins of fungal plant pathogens
Authors: Jones Darcy A. B. , Rozano Lina , Debler Johannes W. , Mancera Ricardo L. , Moolhuijzen Paula M. , Hane James K. 
Published: October 2021

AbstractFungal plant-pathogens promote infection of their hosts through the release of ‘effectors’—a broad class of cytotoxic or virulence-promoting molecules. Effectors may be recognised by resistance or sensitivity receptors in the host, which can determine disease outcomes. Accurate prediction of effectors remains a major challenge in plant pathology, but if achieved will facilitate rapid improvements to host disease resistance. This study presents a novel tool and pipeline for the ranking of predicted effector candidates—Predector—which interfaces with multiple software tools and methods, aggregates disparate features that are relevant to fungal effector proteins, and applies a pairwise learning to rank approach. Predector outperformed a typical combination of secretion and effector prediction methods in terms of ranking performance when applied to a curated set of confirmed effectors derived from multiple species. We present Predector (https://github.com/ccdmb/predector) as a useful tool for the ranking of predicted effector candidates, which also aggregates and reports additional supporting information relevant to effector and secretome prediction in a simple, efficient, and reproducible manner.
Right frontal anxiolytic-sensitive EEG ‘theta’ rhythm in the stop-signal task is a theory-based anxiety disorder biomarker
Authors: Shadli Shabah M. , Ando Lynne C. , McIntosh Julia , Lodhia Veema , Russell Bruce R. , Kirk Ian J. , Glue Paul , McNaughton Neil 
Published: October 2021

AbstractPsychiatric diagnoses currently rely on a patient’s presenting symptoms or signs, lacking much-needed theory-based biomarkers. Our neuropsychological theory of anxiety, recently supported by human imaging, is founded on a longstanding, reliable, rodent ‘theta’ brain rhythm model of human clinical anxiolytic drug action. We have now developed a human scalp EEG homolog—goal-conflict-specific rhythmicity (GCSR), i.e., EEG rhythmicity specific to a balanced conflict between goals (e.g., approach-avoidance). Critically, GCSR is consistently reduced by different classes of anxiolytic drug and correlates with clinically-relevant trait anxiety scores (STAI-T). Here we show elevated GCSR in student volunteers divided, after testing, on their STAI-T scores into low, medium, and high (typical of clinical anxiety) groups. We then tested anxiety disorder patients (meeting diagnostic criteria) and similar controls recruited separately from the community. The patient group had higher average GCSR than their controls—with a mixture of high and low GCSR that varied with, but cut across, conventional disorder diagnosis. Consequently, GCSR scores should provide the first theoretically-based biomarker that could help diagnose, and so redefine, a psychiatric disorder.
Identification of the acetaldehyde oxide Criegee intermediate reaction network in the ozone-assisted low-temperature oxidation of trans-2-butene
Authors: Conrad Alan R. , Hansen Nils , Jasper Ahren W. , Thomason Natasha K. , Hidaldo-Rodrigues Laura , Treshock Sean P. , Popolan-Vaida Denisia M. 
Published: October 2021

Jet stirred reactor investigation of ozone-assisted low-temperature oxidation of trans-2-butene reveals an acetaldehyde oxide Criegee intermediate reaction network.
Perspectives on Mental Health Screening in the Audiology Setting: A Focus Group Study Involving Clinical and Nonclinical Staff
Authors: Bennett Rebecca J. , Donaldson Sara , Mansourian Yazdan , Olaithe Michelle , Kelsall-Foreman India , Badcock Johanna C. , Eikelboom Robert H. 
Published: October 2021

Purpose:
Audiology clinical guidelines recommend the use of mental health screening tools; however, they remain underutilized in clinical practice. As such, psychological concerns are frequently undetected in adults with hearing loss. This study aimed to better understand audiology clinic staff's perspectives (including audiologists, audiometrists, reception staff, and clinic managers) on how to improve detection of poor mental health by (a) exploring the role of audiology clinic staff in detecting psychological concerns in adults with hearing loss and (b) investigating the appropriateness, acceptability, and usability of several screening tools in an audiology setting.

Method:

Eleven audiology clinic staff (
M
age
= 33.9 ± 7.3, range: 25–51 years) participated in a semistructured focus group. First, participants discussed the role of audiology clinic staff in detecting psychological difficulties in adults with hearing loss, including current practices and needs for improving practices. Second, participants discussed the appropriateness, acceptability, and usability of nine standardized mental health screening tools commonly used in wider health care settings.

Results:
Audiology clinic staff described their role in being aware of, and detecting, psychological difficulties, as well as their part in promoting an understanding of the link between hearing loss and mental health. Participants described the need to provide support following detection, and highlighted barriers to fulfilling these roles. The use of mental health screening tools was considered to be client and context specific. The language used within the screener was identified as an important factor for its acceptability by audiology clinic staff.

Conclusions:
Audiology clinic staff acknowledged that they have an important role to play in the detection of psychological difficulties and identified the core barriers to using screening tools. Future research may explore the possibility of developing a mental health screening tool specific to the unique experiences of adults with comorbid hearing loss and mental health concerns.

Supplemental Material:

https://doi.org/10.23641/asha.16702501
Mercury’s exospheric He I 58.4 nm emission: Dependence on the orbital phase
Authors: Yoneda M. , Dima G. , Berdyugina S. V. 
Published: October 2021

Aims. Emission from helium atoms in Mercury’s exosphere at 58.4 nm was observed by the Mariner 10 spacecraft in the 1970s. This emission is due to resonant scattering of solar radiation. Since Mercury’s orbit is ellipsoidal, solar radiation and wind fluxes on Mercury vary along its orbit. Furthermore, the flux of the solar He I 58.4 nm emission observed on Mercury varies with Mercury’s radial velocity with the Sun. Using model simulations, we demonstrate how Mercury’s exospheric He I 58.4 nm emission varies due to the periodic changes in solar radiation and wind.
Methods. The simulation is based on our Monte-Carlo model that accounts for changes in fluxes of the solar wind and radiation.
Results. The model results indicate that the He I 58.4 nm brightness varies by between one and three orders of magnitude along the planet’s orbit. These findings are strongly dependent on the intrinsic line width of the solar He I 58.4 nm emission.
Conclusions. Although this variation has never been observed because Mariner 10 only sampled emission near Mercury’s aphelion, we expect this variation to be observable by new missions, such as BepiColombo and Hisaki. Our results are also important for the characterization of exoplanets with ultraviolet space missions.
Simultaneous generation of ultrahigh pressure and temperature to 50 GPa and 3300 K in multi-anvil apparatus
Authors: Xie Longjian , Chanyshev Artem , Ishii Takayuki , Bondar Dmitry , Nishida Keisuke , Chen Zhen , Bhat Shrikant , Farla Robert , Higo Yuji , Tange Yoshinori , Su Xiaowan , Yan BingMin , Ma Shuailin , Katsura Tomoo 
Published: October 2021

We attempted to generate ultrahigh pressure and temperature simultaneously using a multi-anvil apparatus by combining the technologies of ultrahigh-pressure generation using sintered diamond (SD) anvils, which can reach 120 GPa, and ultrahigh-temperature generation using a boron-doped diamond (BDD) heater, which can reach 4000 K. Along with this strategy, we successfully generated a temperature of 3300 K and a pressure of above 50 GPa simultaneously. Although the high hardness of BDD significantly prevents high-pressure generation at low temperatures, its high-temperature softening allows for effective pressure generation at temperatures above 1200 K. High temperature also enhances high-pressure generation because of the thermal pressure. We expect to generate even higher pressure in the future by combining SD anvils and a BDD heater with advanced multi-anvil technology.
Chemical accuracy with σ-functionals for the Kohn–Sham correlation energy optimized for different input orbitals and eigenvalues
Authors: Fauser Steffen , Trushin Egor , Neiss Christian , Görling Andreas 
Published: October 2021

Recently, a new type of orbital-dependent functional for the Kohn–Sham (KS) correlation energy, σ-functionals, was introduced. Technically, σ-functionals are closely related to the well-known direct random phase approximation (dRPA). Within the dRPA, a function of the eigenvalues σ of the frequency-dependent KS response function is integrated over purely imaginary frequencies. In σ-functionals, this function is replaced by one that is optimized with respect to reference sets of atomization, reaction, transition state, and non-covalent interaction energies. The previously introduced σ-functional uses input orbitals and eigenvalues from KS calculations with the generalized gradient approximation (GGA) exchange–correlation functional of Perdew, Burke, and Ernzerhof (PBE). Here, σ-functionals using input orbitals and eigenvalues from the meta-GGA TPSS and the hybrid-functionals PBE0 and B3LYP are presented and tested. The number of reference sets taken into account in the optimization of the σ-functionals is larger than in the first PBE based σ-functional and includes sets with 3d-transition metal compounds. Therefore, also a reparameterized PBE based σ-functional is introduced. The σ-functionals based on PBE0 and B3LYP orbitals and eigenvalues reach chemical accuracy for main group chemistry. For the 10 966 reactions from the highly accurate W4-11RE reference set, the B3LYP based σ-functional exhibits a mean average deviation of 1.03 kcal/mol compared to 1.08 kcal/mol for the coupled cluster singles doubles perturbative triples method if the same valence quadruple zeta basis set is used. For 3d-transition metal chemistry, accuracies of about 2 kcal/mol are reached. The computational effort for the post-self-consistent evaluation of the σ-functional is lower than that of a preceding PBE0 or B3LYP calculation for typical systems.
Omah Cagak Wolu: The Rural Javanese House Architecture In The Cetho Temple Area Of Lawu Mountain, Indonesia
Authors: Ikhsan Fauzan Ali , Setioko Bambang , Suprapti Atiek 
Published: October 2021

Abstract
The architecture of Javanese houses in the Cetho Temple area is a variant of Javanese rural house architecture that has its uniqueness. Cetho Temple is one of the relics of Hinduism during the end of the Majapahit Empire. The climatic conditions of Mount Lawu and the spatial interaction with the Cetho Temple complex affect the concept of thinking and building Javanese houses and their settlement. The adaptation and adjustment processes that take place from generation to generation produce a typology of rural Javanese houses with local characteristics. This study aims to provide an understanding of the architectural characteristics of rural Javanese houses with a Hindu Javanese cultural background in the Cetho Temple area. The research location is in Cetho Hamlet, Gumeng Village, Jenawi District, Karanganyar Regency. The method of selecting the Javanese house research sample was carried out purposively by considering the typology and age of the house to represent the original character of the settlement. The results of the study found that the Javanese rural house in Cetho Hamlet has the characteristics of eight saka (poles). The Cetho people call it Omah Cagak Wolu. Omah Cagak Wolu is one of the typology variants of Javanese houses that are known around the slopes of Mount Lawu. Omah Cagak Wolu shows the interwoven space and function of a rural Javanese house in the Cetho Temple area. The typology of the Omah Cagak Wolu is a response to the mindset of rural Javanese people who are Hindu and the natural conditions on the slopes of Mount Lawu.