bluuebunny/crossref_metadata_2025_split huggingface dataset:
In Silico Approach on Structural and Functional Characterization of Heat shock protein from Sulfobacillus acidophilus
Authors: Mitra Pritish , Chatterjee Sabyasachi 
Published: November 2024

Abstract

The 70 kDa heat shock proteins (Hsp70s) are highly conserved and ubiquitous molecular chaperones. Hsp70 proteins are intimately involved in different biological activities including maintaining protein homeostasis and resisting environmental stress for survival. Characterizations of eukaryotic Hsp70s with diverse functions are well established but investigations needed for prokaryotes. For better understanding, the sequences of Sulfobacillus acidophilus were retrieved from UniProt. Retrieved Hsp70 proteins were renamed as SaHsp70s and performed an in-silico analysis of Hsp70 proteins to identify sequential, structural properties and functional attributes. The in-silico characterization of Hsp70 proteins revealed that they are acidic, mostly thermostable globular protein with NAD(P)-binding Rossmann-folding. Molecular mass of SaHsp70s ranged from 31.9 to 68.5 kDa and mainly localized in the cytoplasm. Phylogeny revealed the evolutionary distance and relationship among retrieved proteins. Domain analyzed only SaHsp70-1, SaHsp70-3and SaHsp70-14 have actual conserved domain for Hsp70 and share the same clade on phylogenetic tree. Major part of each protein was abundant with α-helix and random coil which make it thermally stable and suitable for interacting with other proteins. SAVES and ProSA server proves the reliability, stability and consistency tertiary structure of SaHsp70s. Functional analysis was done in terms of membrane protein topology, PPI network generation, active and proteolytic cleavage sites prediction, conserved motif and domain detection. Active site predicted Asp, Lys and Glu act as catalytic residue, are important for metal ions binding. Findings suggested that SaHsp70 proteins play central role various complex cellular functions like stress mitigation, thermal stability and related developmental processes.
Transcriptional upregulation of HERV-env genes under simulated microgravity
Authors: Jasemi Somaye , Simula Elena Rita , Pantaleo Antonella , Sechi Leonardo Antonio 
Published: November 2024

Abstract

Background
Human Endogenous retroviruses (HERVs) constitute about 8% of the human genome. Overexpression of HERVs has been detected in in various inflammatory disorders like neuroinflammation and cancer. Interestingly, it has been reported that stress conditions facilitate HERVs expression. Space travel will expose astronauts to microgravity environments (a stress condition), which may result in the activation of HERVs and might influence pathogenic outcomes during and after space flight. This study aimed to elucidate the transcriptional activity of three HERV families (W, K, H) and cytokines genes (IL-1, IL-6, and TNF-α) in different cell lines under microgravity (µg) conditions and compare them with the results obtained under normal gravity (ng; 1g).
Results
We evaluated the expression of HERVs (HERV-K env, HERV-W env, and HERV-H env) and cytokine genes expression (IL-1, IL-6, and TNF-α) in neuroblastoma (SH-SY5Y), HEp-2, and Caco-2 cell lines under simulated microgravity (µg) and normal gravity (1g) conditions. In SH-SY5Y cells, the expression level of IL-1, IL-6, HERV-H env, HERV-K env, and HERV-W env genes was significantly increased when exposed to short-term µg (3 and 6 h). The expression of TNF-α remained unchanged throughout all time points. Additionally, in Caco-2 cells, the expression of HERV-K env and IL-1 genes was significantly higher after 6 hours of incubation in µg conditions compared to 1g. There was no statistically significant difference in the expression levels of HERV-W env, HERV-H env, IL6, and TNF-α genes between µg and 1g conditions. Moreover, in HEp-2 cells, the expression of IL-1, IL6, TNF-α, HERV-H env, HERV-K env, and HERV-W env genes significantly increased following short-term incubation in µg (3 h, 6 h) and, then decreased to levels comparable to those observed in the 1g condition.
Conclusions
Taken together, the dysregulation of cytokines and HERV genes expression was observed under simulated µg condition. The patterns of these dysregulations varied throughout cell lines which demands further investigation for human health protection in space.
Measurement of in-plane thermal diffusivity of thin films using laser periodic heating method with non-research-grade infrared camera and thermocouple detectors
Authors: Lv Maochao , Yang Jie , Zhang Yanhui , Wang Jianli , Zhou Yi 
Published: November 2024

Abstract

The laser periodic heating method is widely used to measure the thermal diffusivity of various thin films. In this technique, surface temperature responses are monitored using either an infrared (IR) camera or a thermocouple (TC) detector. When conducted under air pressure, the effect of air heat loss on these two methods warrants further examination. In this study, we measured the in-plane thermal diffusivity of a polyethylene terephthalate (PET) film under air pressure using both a non-research-grade IR camera and a microscale TC. Results indicate that air heat loss significantly influenced TC measurements, yielding an abnormally large thermal diffusivity. Comparatively, thermal diffusivity measured by the IR camera decreased slightly with increasing modulation frequency. For films with a dimensionless thickness greater than 0.3, values obtained with the IR camera closely matched those under vacuum condition, indicating that the non-contact IR method can effectively suppress the impact of air heat loss.
Gene-Excessive Sleepiness Interactions Suggest Treatment Targets for Obstructive Sleep Apnea Subtype
Authors: Wang Heming , Nagarajan Pavithra , Kurniansyah Nuzulul , Lee Jiwon , Gharib Sina , Xu Yushan , Zhang Yiyan , Spitzer Brian , Faquih Tariq , Zhou Hufeng , Boerwinkle Eric , Chen Han , Gottlieb Daniel , Guo Xiuqing , Heard-Costa Nancy , Hidalgo Bertha , Levy Daniel , Liu Peter , Mei Hao , Montalvan Rebecca , Mukherjee Sutapa , North Kari , O'Connor George , Palmer Lyle , Patel Sanjay , Psaty Bruce , Purcell Shaun , Raffield Laura , Rich Stephen , Rotter Jerome , Saxena Richa , Smith Albert , Stone Katie , Zhu Xiaofeng , Cade Brian , Sofer Tamar , Redline Susan 
Published: November 2024

Abstract

Obstructive sleep apnea (OSA) is a multifactorial sleep disorder characterized by a strong genetic basis. Excessive daytime sleepiness (EDS) is a symptom that is reported by a subset of OSA patients, persisting even after treatment with continuous positive airway pressure (CPAP). It is recognized as a clinical subtype underlying OSA carrying alarming heightened cardiovascular risk. Thus, conceptualizing EDS as an exposure variable, we sought to investigate EDS’s influence on genetic variation linked to apnea-hypopnea index (AHI), a diagnostic measure of OSA severity. This study serves as the first large-scale genome-wide gene x environment interaction analysis for AHI, investigating the interplay between its genetic markers and EDS across and within specific sex. Our work pools together whole genome sequencing data from seven cohorts, enabling a diverse dataset (four population backgrounds) of over 11,500 samples. Among the total 16 discovered genetic targets with interaction evidence with EDS, eight are previously unreported for OSA, including CCDC3, MARCHF1, and MED31 identified in all sexes; TMEM26, CPSF4L, and PI4K2B identified in males; and RAP1GAP and YY1 identified in females. We discuss connections to insulin resistance, thiamine deficiency, and resveratrol use that may be worthy of therapeutic consideration for excessively sleepy OSA patients.
Augmented Multiscale Formulation (AMS) for Incompressible Turbulence
Authors: Ranjan Rakesh , Araya Guillermo 
Published: November 2024

Abstract

We revise the multiscale formulation for incompressible flow computations. In addition to the classical multiscale formulation, we incorporate an iterative penalty approach to ensure the incompressibility condition during the solution of the Navier-Stokes equations. The constraint of incompressibility, enforced by the continuity equation, is approached via an iterative penalty method. The multiscale formulation (MS) of Hughes et al. [1] is reconsidered, introducing a new formulation named Augmented Multiscale Formulation (AMS). We maintain consistency of the formulation by carrying the velocity and pressure variables rather than an L2 projection of the same variables, as previously investigated by researchers in the past. Inexact Newton solvers are utilized to solve discrete problems. In this aspect, the formulation departs from the Multiscale Formulation for incompressible turbulence. In the current formulation, there is no requirement to resort to least squares stabilization as a separate stabilization mechanism, and this departure is intuitive since there are no shock discontinuities when solving incompressible flow. We validated the AMS formulation with the Kovasznay flow problem and standard solutions available. We benchmark the temporal evolution of AMS formulation with the driven cavity solutions provided by the ASUPG/AGLS formulation. Furthermore, the revised formulation is tested on a series of problems such as flow past a series of cylinders, cylinders in rotation, to serve as incompressible flow benchmarks and excellent agreement is reported for all problems, including experimental data from Zdravkovich [2] and Schlichting et al. [3] for the problem of flow past a single cylinder. We report non-linear convergence histories of the formulation, as well which are difficult to provide within the MS formulation. The predictor-corrector scheme that has been utilized for the solutions of incompressible flow computations has been the reason the method has not been able to provide non linear convergence histories for the problems solved. There is departure from the procedure in the present framework: present AMS and MS formulation both recover lower L2 error with analytical solutions of Navier-Stokes equations and the error is found to be lower than the ASUPG formulation of Ranjan [4] for low plevels of 3 and 4. For higher polynomial orders, we report suboptimal convergence of the pressures. This paper provides an insightful look at the non-linear convergence of the incompressible flow Navier-Stokes equations within a stabilized finite element setting.
Comparative metabolomic analysis reveals shared and unique features of COVID-19 cytokine storm and surgical sepsis
Authors: Russkih Iana , Popov Oleg , Klochkova Tatiana , Sushentseva Natalia , Apalko Svetlana , Asinovskaya Anna , Mosenko Sergey , Sarana Andrey , Shcherbak Sergey 
Published: November 2024

Abstract

The clinical manifestations of the cytokine storm (CS) associated with COVID-19 resemble the acute phase of sepsis. Metabolomics may contribute to understanding the specific pathobiology of these two syndromes. The aim of this study was to compare serum metabolomic profiles in CS associated with COVID-19 vs. septic surgery patients. In retrospective cross-sectional study serum samples from patients with CS associated with COVID-19, with and without comorbidity as well as serum samples from patients with surgical sepsis were investigated. A targeted metabolomic analysis was carried out in all samples using LC-MS/MS method. Analysis revealed that similar alterations in serum metabolome of patients with COVID-19 and in surgical septic patients were associated with amino acid metabolism, nitrogen metabolism, inflammatory status, methionine cycle and glycolysis. The most significant difference was identified for the serum levels of metabolites of kynurenine synthesis, tricarboxylic acid cycle, as well as for gamma-aminobutyric acid and niacinamide. The metabolic pathway of cysteine and methionine metabolism was disturbed significantly in COVID-19 and surgical septic patients. For the first time, the similarities and differences between the serum metabolomic profiles of patients with CS associated with COVID-19 and patients with surgical sepsis were investigated for the patients from northwest of Russian Federation.
A Covert, Secure and Energy-Efficient Communication Protocol Based on Statistical Machine Learning in Multi-Domain Communication Applications
Authors: Esmaeili Sobhan , Ghasemi Jamal 
Published: November 2024

Abstract

In recent decades, multi-domain communications (air-water) have garnered significant attention from both scientific and civil communities due to their diverse impacts and applications. However, in addition to security challenges, these types of communications face limitations regarding direct cross-medium communication, transmission capacity, transmission range, and energy consumption due to water properties and reflections occurring at the interface between the two mediums. While various solutions have been proposed to address these challenges, the majority of them are either not energy-efficient or fail to guarantee communication security in specific applications. Therefore, in this research, we propose a secure covert communication protocol with energy efficiency for multi-domain communication applications to address the aforementioned challenges. In this protocol, to enhance security and reduce bandwidth consumption, data is sampled based on its entropy and then simultaneously compressed and encrypted according to its sparsity level. Next, the resulting output is modulated onto amplified spontaneous emission (ASE) noise, hidden, and spread out over time using a chirped fiber Bragg grating (CFBG). The signal is then transmitted through a wide-field optical system. Here, we utilize an array of ultrasonic sensors and a prediction algorithm to calculate the optimal water surface impact point. We also use OOK pulse-based modulation combined with laser diode switching to reduce energy consumption and increase data transmission capacity. Simulation results demonstrate that the proposed model, compared to previous methods, not only enhances security but also reduces energy consumption and increases transmission capacity.
Incorporating Complex Science into Decisions; Lived Experiences of using Genomics Data and Information in Decision-making Processes in Malawi.
Authors: Mijumbi Rhona , Phiri Elias Rejoice , Kalata Olive Mbekwani , Chawani Marlen Stacey , Sakala Melody , Chinkombero Annette , Mitambo Collins , Kasambara Watipaso 
Published: November 2024

Abstract

Policy and decision-makers are increasingly interacting with complex science as the momentum for evidence-informed decision-making grows. Unfortunately, often, the decision-makers have not been equipped optimally for this interaction, and so may not understand, communicate, or use the data and information appropriately, or at all. This leads to missed opportunities for science to improve health and society outcomes, and in the worst case scenarios, may lead to risky decisions, if results are misinterpreted or miscommunicated. In this study, we explored decision-makers' lived experiences interacting with complex science at the mid and grass-roots levels in Malawi, using genomics as a case example of complex science. Decision-makers articulated points at which bottlenecks are present, and how. They identified challenges with knowledge of, interpretation, and application of genomics-related information, not knowing where to find it, the absence of translation of concepts to facilitate local dialogue, and poor evidence-intermediary structures and efforts, among others. They also identified interventions that could facilitate the process including the use of locally established and already-trusted structures for brokering knowledge. It is important that these challenges are addressed to improve the use of complex science in both high and local level decision-making, or it risks continuing to be seen as difficult and elitist and left out of crucial decisions.
Multi-Color Photonic Integrated Circuits Based on Homogeneous Integration of Quantum Cascade Lasers
Authors: Burghart Dominik , Zhang Kevin , Oberhausen Wolfhard , Köninger Anna , Boehm Gerhard , Belkin Mikhail 
Published: November 2024

Abstract

We demonstrate an InP-based mid-infrared photonic integrated circuit processed from a wafer in which two distinct quantum cascade laser active regions are grown in different areas on the same InP crystal. A passive InGaAs waveguiding layer is epitaxially deposited on top of the entire InP substrate prior to the laser active region growth to optically couple the lasers emission and to multiplex their emission wavelengths to a single output waveguide. The method demonstrated in this work enables the creation of monolithic photonic integrated circuits with emission wavelength spanning the entire 3–15 µm spectral range and it is of interest for a wide range of applications.
Metagenomic and bacterial culture studies of human breast milk microbiota: factors influencing its bacterial composition and diversity
Authors: Querin Benjamin , Larsonneur Elise , Caloustian Christophe , Meyer Vincent , Cezard Lauriane , Razafimahefa Hasinirina , Deleuze Jean-François , Lecointe Didier , Segurens Béatrice 
Published: November 2024

Abstract

Background
Human breast milk is used as the optimum feeding regime for newborn infants. In hospitals, it is critical for premature infants, protecting them from illnesses such as necrotizing enterocolitis. It has its own companion microbiota, whose bacterial composition and diversity are affected by several factors linked to the mother and her baby. However, little is known about the breast milk microbiota of mothers who delivered premature infants. The goal of the present study was to examine the breast milk microbiota and determine the factors influencing its composition and diversity over the time.
Results
We analysed 137 breast milk samples collected from 40 women who delivered premature and extremely premature infants. Each sample was both analysed by bacterial culture and the V3-V4 region of the bacterial 16S rRNA gene was sequenced using an Illumina platform to characterize microbial communities. For the samples analysed, a diverse community of breast milk bacteria was found with the most dominant phyla being Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes. At the genus level, Staphylococcus, Acinetobacter and Corynebacterium were the most prevalent. A core milk microbiota has been defined, composed of seven genera. The pregnancy number, lactation stage and mother’s body mass index were shown to influence bacterial diversity. In contrast, no statistically significant differences were observed for maternal age, gestational age, parity, population, mother’s blood group, mode of delivery, infant gender, infant weight, and use of antibiotic prophylaxis during delivery. Most of the bacterial species detected by bacterial culture were also identified to genus taxonomic level by 16S rRNA gene sequencing. Longitudinal analyses showed that bacterial diversity tended to increase over time, while the aerobic bacterial flora was rather stable over time. Moreover, LEfSe analysis allowed us to make associations between bacteria in breast milk with certain maternal conditions or factors.
Conclusions
Our study showed that the bacterial composition and diversity of breast milk are influenced by several maternal factors. We have observed a variability in bacterial diversity and composition during the 3 stages of lactation, which differs between mothers. We have identified bacterial signatures associated with different clinical conditions in the mother and child.
Cerebral Vasculitis in Systemic Lupus Erythematosus (SLE) : Case Report and Literature Review
Authors: AJERTIL Abderrazzak , KABBAJ Najat , QUESSAR Abdeljalil EL 
Published: November 2024

Abstract

Cerebral vasculitis, though rare, represents a serious complication of systemic lupus erythematosus (SLE) and poses numerous challenges in terms of management due to its potential for severe neurological consequences and often poor prognosis. We report the case of a 32-year-old man with SLE who presented with three seizure episodes and cognitive deterioration. Neurological examinations, laboratory analyses, and imaging findings led to a diagnosis of cerebral vasculitis secondary to SLE. Despite intensive immunosuppressive treatment, the patient’s neurological condition deteriorated, resulting in multiorgan failure. Ultimately, the patient died due to multiorgan failure linked to severe central nervous system vasculitis and associated complications. This case highlights the importance of early detection and aggressive treatment of cerebral vasculitis in the context of SLE.
Sequestration of carbon dioxide from a gas sweetening plant in an oilfield via integrated microalgal cultivation with wastewater treatment; A technical appraisal and economic feasibility evaluation.
Authors: Elmezain Ahmed , Abdel-Monem Nabil , Shimi Hassan 
Published: November 2024

Abstract

Carbon capture and storage (CCS) is promoted a promising decarbonization strategy. It is argued to be a potential solution for Egypt’s greenhouse gas emissions which have substantially grown over the past three decades. A widely recognized method of CCS is biological storage via microalgal cultivation. However, most CCS applications in the oil sector are geologic storage and there is no single biological or geologic storage project in Egypt. Additionally, there is a severe lack of research on microalgal applications for CO2 storage in Egypt. That is why this research aims to build a case study for a pure source of CO2 emitted from a gas sweetening plant in Bapetco oil company in the western desert in Egypt. It is a preliminary design for an integrated microalgal cultivation project with wastewater treatment capability for the sake of carbon sequestration and biomass production. To do so, this paper performed a laboratory experiment to examine the tolerability of two microalgal species for being exposed to a CO2 source. Based on the results of this experiment, a technical model was proposed to select the required machinery and infrastructure. Finally, it proposed a financial model of the capital and operating costs, loan repayment, and net present value with sensitivity analysis. The findings showed that selling biomass as a final product was uneconomic enough as it generated negative IRR and NPV. It also showed two strikingly interesting results: species with high CO2tolerability are not recommended, and carbon pricing is of little help in funding microalgal projects compared to biomass productivity. The originality of this research comes from its adoption of biological storage in the oil industry, equipped with technical and financial models.