bluuebunny/crossref_metadata_2025_split huggingface dataset:
Suppression of host gene expression is associated with latent TB infection: a possible diagnostic biomarker
Authors: Nakiboneka Ritah , Margaritella Nicolò , Nyirenda Tonney , Chaima David , Walbaum Natasha , Musisi Emmanuel , Tionge Sikwese , Msosa Takondwa , Nliwasa Marriott , Msefula Chisomo L. , Sloan Derek , Sabiiti Wilber 
Published: July 2024

AbstractThe World Health Organization End TB strategy aims for a 90% reduction of tuberculosis (TB) incidence by 2035. Systematic testing and treatment of latent TB infection (LTBI) among contacts of active TB patients is recommended as one of the ways to curtail TB incidence. However, there is a shortage of tools to accurately diagnose LTBI. We assessed the appropriateness of whole blood host transcriptomic markers (TM) to diagnose LTBI among household contacts of bacteriologically confirmed index cases compared to HIV negative healthy controls (HC). QuantiFERON-TB Gold Plus Interferon gamma release assay (IGRA) and reverse-transcriptase quantitative PCR were used to determine LTBI and quantify TM expression respectively. Association between TM expression and LTBI was evaluated by logistic regression modelling. A total of 100 participants, 49 TB exposed (TBEx) household contacts and 51 HC, were enrolled. Twenty-five (51%) TBEx individuals tested positive by IGRA, and were denoted as LTBI individuals, and 37 (72.5%) HC were IGRA-negative. Expression of 11 evaluated TM was significantly suppressed among LTBI compared to HC. Out of the 11 TM, ZNF296 and KLF2 expression were strongly associated with LTBI and successfully differentiated LTBI from HC. Paradoxically, 21 (49%) TBEx participants who tested IGRA negative exhibited the same pattern of suppressed TM expression as IGRA positive (LTBI-confirmed individuals). Results suggest that suppression of gene expression underlies LTBI and may be a more sensitive diagnostic biomarker than standard-of-care IGRA.
Impact of multidrug resistance on outcomes in hematologic cancer patients with bacterial bloodstream infections
Authors: Park Ki-Ho , Jung Ye Ji , Lee Hyun Jung , Kim Hong Jun , Maeng Chi Hoon , Baek Sun Kyung , Han Jae Joon , Jeon Woojae , Kim Dong Youn , Lee Yu-Mi , Lee Mi Suk 
Published: July 2024

AbstractDespite the improved outcomes in patients with hematological malignancies, infections caused by multidrug-resistant organisms (MDROs) pose a new threat to these patients. We retrospectively reviewed the patients with hematological cancer and bacterial bloodstream infections (BSIs) at a tertiary hospital between 2003 and 2022 to assess the impact of MDROs on outcomes. Among 328 BSIs, 81 (24.7%) were caused by MDROs. MDRO rates increased from 10.3% (2003–2007) to 39.7% (2018–2022) (P < 0.001). The 30-day mortality rate was 25.0%, which was significantly higher in MDRO-infected patients than in non-MDRO-infected patients (48.1 vs. 17.4%; P < 0.001). The observed trend was more pronounced in patients with newly diagnosed diseases and relapsed/refractory disease but less prominent in patients in complete remission. Among MDROs, carbapenem-resistant Gram-negative bacteria exhibited the highest mortality, followed by vancomycin-resistant enterococci, methicillin-resistant Staphylococcus aureus, and extended-spectrum β-lactamase-producing Enterobacteriaceae. Multivariate analysis identified independent risk factors for 30-day mortality as age ≥ 65 years, newly diagnosed disease, relapsed/refractory disease, MDROs, polymicrobial infection, CRP ≥ 20 mg/L, and inappropriate initial antibiotic therapy. In conclusion, MDROs contribute to adverse outcomes in patients with hematological cancer and bacterial BSIs, with effects varying based on the underlying disease status and causative pathogens. Appropriate initial antibiotic therapy may improve patient outcomes.
Hydraulic system fault diagnosis decoupling method based on 2D time-series modeling and self-attention fusion
Authors: Wang Haicheng , Zhou Juan , Chen Hu , Xu Bo , Shen Zhengxiang 
Published: July 2024

AbstractHydraulic systems play a pivotal and extensive role in mechanics and energy. However, the performance of intelligent fault diagnosis models for multiple components is often hindered by the complexity, variability, strong hermeticity, intricate structures, and fault concealment in real-world conditions. This study proposes a new approach for hydraulic fault diagnosis that leverages 2D temporal modeling and attention mechanisms for decoupling compound faults and extracting features from multisample rate sensor data. Initially, to address the issue of oversampling in some high-frequency sensors within the dataset, variable frequency data sampling is employed during the data preprocessing stage to resample redundant data. Subsequently, two-dimensional convolution simultaneously captures both the instantaneous and long-term features of the sensor signals for the coupling signals of hydraulic system sensors. Lastly, to address the challenge of feature fusion with multisample rate sensor data, where direct merging of features through maximum or average pooling might dilute crucial information, a feature fusion and decoupling method based on a probabilistic sparse self-attention mechanism is designed, avoiding the issue of long-tail distribution in multisample rate sensor data. Experimental validation showed that the proposed model can effectively utilize samples to achieve accurate fault decoupling and classification for different components, achieving a diagnostic accuracy exceeding 97% and demonstrating robust performance in hydraulic system fault diagnosis under noise conditions.
Identification and validation of a prognostic model based on four genes related to satellite nodules in hepatocellular carcinoma
Authors: Liu Feng , Yan Tinghua , Cui Dan , Jiang Jinhua 
Published: July 2024

AbstractSatellite nodules is a key clinical characteristic which has prognostic value of hepatocellular carcinoma (HCC). Currently, there is no gene-level predictive model for Satellite nodules in liver cancer. For the 377 HCC cases collected from the dataset of Cancer Genome Atlas (TCGA), their original pathological data were analyzed to extract information regarding satellite nodules status as well as other relevant pathological data. Then, this study employed statistical modeling for prognostic model establishment in TCGA, and validation in International Cancer Genome Consortium (ICGC) cohorts and GSE76427. Through rigorous statistical analyses, 253 differential satellite nodules-related genes (SNRGs) were identified, and four key genes related to satellite nodules and prognosis were selected to construct a prognostic model. The high-risk group predicted by our model exhibited an unfavorable overall survival (OS) outlook and demonstrated an association with adverse worse clinical characteristics such as larger tumor size, higher alpha-fetoprotein, microvascular invasion and advanced stage. Moreover, the validation of the model's prognostic value in the ICGC and GSE76427 cohorts mirrored that of the TCGA cohort. Besides, the high-risk group also showed higher levels of resting Dendritic cells, M0 macrophages infiltration, alongside decreased levels of CD8+ T cells and γδT cells infiltration. The prognostic model based on SNRGs can reliability predict the OS of HCC and is likely to have predictive value of immunotherapy for HCC.
Performance analysis of linearization schemes for modelling multi-phase flow in porous media
Authors: Abd Abdul Salam , Asif Ali , Abushaikha Ahmad 
Published: July 2024

AbstractReservoir simulation is crucial for understanding the flow response in underground reservoirs, and it significantly helps reduce uncertainties in geological characterization and optimize methodologies for field development strategies. However, providing efficient and accurate solutions for the strong heterogeneity remains challenging, as most of the discretization methods cannot handle this complexity. In this work, we perform a comprehensive assessment of various numerical linearization techniques employed in reservoir simulation, particularly focusing on the performance of the nonlinear solver for problem dealing with fluid flow in porous media. The primary linearization methods examined are finite difference central (FDC), finite forward difference (FDF), and operator-based linearization (OBL). These methods are rigorously analyzed and compared in terms of their accuracy, computational efficiency, and adaptability to changing reservoir conditions. The results demonstrate that each method has distinct strengths and limitations. The FDC method is more accurate particularly in complex simulations where strong heterogeneity are introduced but is generally slower in convergence. The OBL on the other hand, is more efficient and converges quickly, which makes it suitable for scenarios with limited computational resources and simple physics, while the FDF method provides a balanced combination of precision and computational speed, contingent upon careful step size management of the derivative estimations. This paper aims to guide the selection of appropriate linearization techniques for enhancing nonlinear solvers’ accuracy and efficiency in reservoir simulation .
Changes in the outer nuclear layer and choroidal vascularity during the manifest and quiescent phases of acute central serous chorioretinopathy
Authors: Lim Gyeongsoo , Kim Kyung Tae , Kim Dong Yoon , Chae Ju Byung , Seo Eoi Jong 
Published: July 2024

AbstractTo investigate alteration of outer nuclear layer (ONL) and choroidal vascularity index (CVI) in different status of central serous chorioretinopathy (CSC). A retrospective review of 65 CSC eyes with subretinal fluid (manifest CSC) and 40 control eyes was conducted in a single tertiary university hospital. Differences in best-corrected visual acuity (BCVA), ONL, and CVI were compared. CVI was assessed both in the entire choroid (CVI-EC) and around the 1500 μm leakage area (CVI-1500). Measurements were repeated after the subretinal fluid resorption (quiescent CSC), and compared. CSC eyes showed worse BCVA, thinner ONL and greater CVI than controls. Quiescent CSC showed a recovery of ONL compared to the manifest CSC, along with the BCVA improvement. The resolution of the CSC revealed a decrease across all three choroidal areas (total, stromal and luminal), with a more pronounced reduction in the stromal than in the luminal choroidal area, leading to an increase in the CVI. This phenomenon was shown in both CVI-EC and CVI-1500. Conclusively, ONL thickness can be used as a quantitative biomarker for photoreceptor function in CSC. Increased CVI may reflect a disease activity. The stromal choroidal area is particularly sensitive in illustrating leakage from the choroidal vasculature.
Genomic sequencing reveals convergent adaptation during experimental evolution in two budding yeast species
Authors: Wang Pu , Driscoll William W. , Travisano Michael 
Published: July 2024

AbstractConvergent evolution is central in the origins of multicellularity. Identifying the basis for convergent multicellular evolution is challenging because of the diverse evolutionary origins and environments involved. Haploid Kluyveromyces lactis populations evolve multicellularity during selection for increased settling in liquid media. Strong genomic and phenotypic convergence is observed between K. lactis and previously selected S. cerevisiae populations under similar selection, despite their >100-million-year divergence. We find K. lactis multicellularity is conferred by mutations in genes ACE2 or AIM44, with ACE2 being predominant. They are a subset of the six genes involved in the S. cerevisiae multicellularity. Both ACE2 and AIM44 regulate cell division, indicating that the genetic convergence is likely due to conserved cellular replication mechanisms. Complex population dynamics involving multiple ACE2/AIM44 genotypes are found in most K. lactis lineages. The results show common ancestry and natural selection shape convergence while chance and contingency determine the degree of divergence.
Tracking the hologenome dynamics in aquatic invertebrates by the holo-2bRAD approach
Authors: Ma Cen , Xu Chang , Zhang Tianqi , Mu Qianqian , Lv Jia , Xing Qiang , Yang Zhihui , Xu Zhenyuan , Guan Yalin , Chen Chengqin , Ni Kuo , Dai Xiaoting , Ding Wei , Hu Jingjie , Bao Zhenmin , Wang Shi , Liu Pingping 
Published: July 2024

AbstractThe “hologenome” concept is an increasingly popular way of thinking about microbiome-host for marine organisms. However, it is challenging to track hologenome dynamics because of the large amount of material, with tracking itself usually resulting in damage or death of the research object. Here we show the simple and efficient holo-2bRAD approach for the tracking of hologenome dynamics in marine invertebrates (i.e., scallop and shrimp) from one holo-2bRAD library. The stable performance of our approach was shown with high genotyping accuracy of 99.91% and a high correlation of r > 0.99 for the species-level profiling of microorganisms. To explore the host-microbe association underlying mass mortality events of bivalve larvae, core microbial species changed with the stages were found, and two potentially associated host SNPs were identified. Overall, our research provides a powerful tool with various advantages (e.g., cost-effective, simple, and applicable for challenging samples) in genetic, ecological, and evolutionary studies.
Role of the V2R–βarrestin–Gβγ complex in promoting G protein translocation to endosomes
Authors: Sokrat Badr , Nguyen Anthony H. , Thomsen Alex R. B. , Huang Li-Yin , Kobayashi Hiroyuki , Kahsai Alem W. , Kim Jihee , Ho Bing X. , Ma Symon , Little John , Ehrhart Catherine , Pyne Ian , Hammond Emmery , Bouvier Michel 
Published: July 2024

AbstractClassically, G protein-coupled receptors (GPCRs) promote signaling at the plasma membrane through activation of heterotrimeric Gαβγ proteins, followed by the recruitment of GPCR kinases and βarrestin (βarr) to initiate receptor desensitization and internalization. However, studies demonstrated that some GPCRs continue to signal from internalized compartments, with distinct cellular responses. Both βarr and Gβγ contribute to such non-canonical endosomal G protein signaling, but their specific roles and contributions remain poorly understood. Here, we demonstrate that the vasopressin V2 receptor (V2R)–βarr complex scaffolds Gβγ at the plasma membrane through a direct interaction with βarr, enabling its transport to endosomes. Gβγ subsequently potentiates Gαs endosomal translocation, presumably to regenerate an endosomal pool of heterotrimeric Gs. This work shines light on the mechanism underlying G protein subunits translocation from the plasma membrane to the endosomes and provides a basis for understanding the role of βarr in mediating sustained G protein signaling.
Magnesium hydroxide addition reduces aqueous carbon dioxide in wastewater discharged to the ocean
Authors: Kitidis Vassilis , Rackley Stephen. A. , Burt William. J. , Rau Greg. H. , Fawcett Samuel , Taylor Matthew. , Tarran Glen , Woodward E. Malcolm S. , Harris Carolyn , Fileman Timothy 
Published: July 2024

AbstractOcean alkalinity enhancement (OAE) reduces the concentration of dissolved carbon dioxide (CO2) in seawater, leading to atmospheric carbon dioxide removal (CDR). Here we report laboratory experiments and a field-trial of alkalinity enhancement through addition of magnesium hydroxide to wastewater and its subsequent discharge to the coastal ocean. In wastewater, a 10% increase of average alkalinity (+0.56 mmol/kg) led to a 74% reduction in aqueous CO2 (−0.41 mmol/kg) and pH increase of 0.4 units to 7.78 (efficiency 0.73 molCO2/mol alkalinity). The alkalinization signal was limited to within a few metres of the ocean discharge, evident as 27.2 μatm reduction in CO2 partial pressure and 0.017 unit pH increase, and was consistent with rapid dilution of the alkali-treated wastewater. While this proof of concept field trial did not achieve CDR due to its small scale, it demonstrated the potential of magnesium hydroxide addition to wastewater as a CDR solution.
Unified metagenomic method for rapid detection of microorganisms in clinical samples
Authors: Alcolea-Medina Adela , Alder Christopher , Snell Luke B. , Charalampous Themoula , Aydin Alp , Nebbia Gaia , Williams Tom , Goldenberg Simon , Douthwaite Sam , Batra Rahul , Cliff Penelope R. , Mischo Hannah , Neil Stuart , Wilks Mark , Edgeworth Jonathan D. 
Published: July 2024

Abstract
Background
Clinical metagenomics involves the genomic sequencing of all microorganisms in clinical samples ideally after depletion of human DNA to increase sensitivity and reduce turnaround times. Current human DNA depletion methods preferentially preserve either DNA or RNA containing microbes, but not both simultaneously. Here we describe and present data using a practical and rapid mechanical host-depletion method allowing simultaneous detection of RNA and DNA microorganisms linked with nanopore sequencing.

Methods
The human cells from respiratory samples are lysed mechanically using 1.4 mm zirconium-silicate spheres and the human DNA is depleted using a nonspecific endonuclease. The RNA is converted to dsDNA to allow the simultaneous sequencing of DNA and RNA.

Results
The method decreases human DNA concentration by a median of eight Ct values while detecting a broad range of RNA & DNA viruses, bacteria, including atypical pathogens (Legionella, Chlamydia, Mycoplasma) and fungi (Candida, Pneumocystis, Aspergillus). The first automated reports are generated after 30 min sequencing from a 7 h end-to-end workflow. Sensitivity and specificity for bacterial detection are 90% and 100%, respectively, and viral detection are 92% and 100% after 2 h of sequencing. Prospective validation on 33 consecutive lower respiratory tract samples from ventilated patients with suspected pneumonia shows 60% concordance with routine testing, detection of additional pathogens in 21% of samples and pathogen genomic assembly achieve for 42% of viruses and 33% of bacteria.

Conclusions
Although further workflow refinement and validation on samples containing a broader range of pathogens is required, it holds promise as a clinically deployable workflow suitable for evaluation in routine microbiology laboratories.
Epidemic modelling suggests that in specific circumstances masks may become more effective when fewer contacts wear them
Authors: Klimek Peter , Ledebur Katharina , Thurner Stefan 
Published: July 2024

Abstract
Background
The effectiveness of non-pharmaceutical interventions to control the spread of SARS-CoV-2 depends on many contextual factors, including adherence. Conventional wisdom holds that the effectiveness of protective behaviours, such as wearing masks, increases with the number of people who adopt them. Here we show in a simulation study that this is not always true.

Methods
We use a parsimonious network model based on the well-established empirical facts that adherence to such interventions wanes over time and that individuals tend to align their adoption strategies with their close social ties (homophily).

Results
When these assumptions are combined, a broad dynamic regime emerges in which the individual-level reduction in infection risk for those adopting protective behaviour increases as adherence to protective behaviour decreases. For instance, at 10 % coverage, we find that adopters face nearly a 30 % lower infection risk than at 60 % coverage. Based on surgical mask effectiveness estimates, the relative risk reduction for masked individuals ranges from 5 % to 15 %, or a factor of three. This small coverage effect occurs when the outbreak is over before the pathogen is able to invade small but closely knit groups of individuals who protect themselves.

Conclusions
Our results confirm that lower coverage reduces protection at the population level while contradicting the common belief that masking becomes ineffective at the individual level as more people drop their masks.
Study of construction of Golomb Costas arrays with ideal autocorrelation properties based on extension field
Authors: Yao Jianguo , Liu Ziwei , Wang Xiaoming 
Published: July 2024

AbstractThis paper proposes a specific algebraic structure and demonstrates its nature as an extension field, enabling the construction of Golomb Costas (GC) arrays. It provides detailed instructions and examples for constructing GC arrays using this extension field, along with a corresponding flowchart. Additionally, the paper conducts a thorough analysis, incorporating calculations and comparisons, to evaluate the autocorrelation of a GC array derived from the extension field compared to that of a diagonal frequency hopping array. The analysis reveals the superior autocorrelation properties of GC arrays based on the extension field. Furthermore, the paper establishes a mathematical model for the signal coded by the frequency hopping array and subsequently simulates and compares the ambiguity function of the signal coded by a GC array with that of a signal coded by a diagonal frequency hopping array. This comparison underscores the thumbtack ambiguity function of frequency hopping signal coded by a GC array. Moreover, the paper thoroughly investigates the relationship between the correlation function of GC arrays and the roots of an algebraic equation in a finite field, and strictly proves the ideal autocorrelation properties of Golomb Costas arrays.
A hybrid energy storage array group control strategy for wind power smoothing
Authors: Tong Tong , Wei Le , Chen Yuanye , Fang Fang 
Published: July 2024

AbstractWith the increase of wind power generation, the safety and economy of power system operations are greatly influenced by the intermittency and fluctuation of wind power. To take the advantage of the complementary characteristics between different energy storage devices, a Hybrid Energy Storage System (HESS) consisting of Battery Energy Storage System (BESS) and Flywheel Energy Storage System (FESS) can alleviate the uncertainty of wind power. This article has proposed a coordinated control strategy through group consensus algorithm based on Model Predictive Control (MPC) for Hybrid Energy Storage Array (HESA) to smooth wind power fluctuations. To allocate power commands to the FESS and BESS, the fluctuation of wind power output is extracted with different frequency domain characteristics as instructions by Empirical Mode Decomposition (EMD) technology. Moreover, a group consensus algorithm based on MPC is proposed to complete the adaptive power allocation of energy storage units. Eventually, the actual wind farm data is used for the simulation to verify the effect of control strategy proposed in this paper. It can be seen that the developed group consensus algorithm based on MPC can cope with different frequency power commands, avoid overcharging and discharging of energy storage media, and smooth wind power effectively.
Stereoselective Synthesis of Polyketide Segments of Nemamide A and Euglenatides D–E
Authors: Goswami Rajib Kumar , Sharma Himangshu , Paul Sujan 
Published: July 2024

AbstractA convergent strategy for the stereoselective synthesis of polyketide segments of hybrid natural products nemamide A and euglenatides D–E has been developed for the first time. The salient features of this gram-scale synthesis include Trost–Rychnovsky alkyne rearrangement, HWE olefination, regioselective epoxide ring opening, Prins–Ritter cyclization, and subsequent reductive cleavage of the substituted THP ring. The optimized route is modular and could be tunable to access the other polyketide counterparts of these families of metabolites.