bluuebunny/crossref_metadata_2025_split huggingface dataset:
The First Zagreb Index of the Zero Divisor Graph for the Ring of Integers Modulo Power of Primes
Authors: Semil @ Ismail Ghazali , Sarmin Nor Haniza , Alimon Nur Idayu , Maulana Fariz 
Published: October 2023

Let be a simple graph with the set of vertices and edges. The first Zagreb index of a graph is defined as the sum of the degree of each vertex to the power of two. Meanwhile, the zero divisor graph of a ring , denoted by , is defined as a graph with its vertex set contains the nonzero zero divisors in which two distinct vertices and are adjacent if . In this paper, the general formula of the first Zagreb index of the zero divisor graph for the commutative ring of integers modulo , where a prime number and a positive integer is determined. A few examples are given to illustrate the main results.
Transient Performance Simulation of Gas Turbine Engine Based on Through-Flow Method and Experimental Verification
Authors: Yuchen Dai , Manxiang Song , Donghai Jin , Xingmin Gui , Xiaoheng Liu 
Published: October 2023

Abstract
Current research on engine transient performance primarily focuses on the variation of key aerothermodynamic parameters in specific sections, neglecting the comprehensive understanding of the engine's inner flow field during transient operations. To address this gap, this paper proposes a two-dimensional transient simulation method that effectively captures the evolution of the flow field in the meridional plane. The approach involves deriving circumferential averaging equations in a rotating coordinate system with variable angular velocity, considering angular acceleration source terms. The engine components, including the compressor, combustion chamber, turbine, and rotating shaft, are individually modeled. The newly derived governing equations are solved using a dual-time-step approach, where an inner-iteration ensures mass flow conservation, and an outer-iteration updates the rotational speed. Using a real turbojet engine as a case study, transient examinations comprising acceleration and deceleration are performed. A comparative analysis of experimental and simulation results is conducted, revealing an average error of 0.9% in shaft speed, 7.8% in engine thrust, 1.7% in engine exhaust temperature, and 5.1% in compressor outlet pressure. Additionally, the study analyzes and compares the internal flow fields during the transient process, contributing to a deeper understanding of the engine's dynamic behavior. The research effort establishes a practical methodology and technology for conducting comprehensive two-dimensional engine transient cycle analyses within reasonable computational resources and timeframes.
Insights Into the Flow Field and Performance of a Boundary Layer Pump
Authors: Rajendran David John , Palaveev Kyril , Anselmi Eduardo , Santhanakrishnan Mani , Pachidis Vassilios 
Published: October 2023

Abstract
A flow field analysis of a realistic, integrated, multidisk boundary layer pump as is necessary for investigating the reasons for typically quoted low efficiencies in such pumps is described. The study focuses on the three-dimensional RANS solutions of a water boundary layer pump model created to replicate a design by Morris, 1973, which consists of 170 disks and a volute channel. A baseline study is performed to investigate the rotor-only performance after which a volute alone is separately simulated to identify the performance and losses in each as separate systems. Thereafter, an integrated model is characterized across mass flow rates and rotational speeds. The flow fields of all three models are discussed and the results of the integrated model are compared to the experimental data. The results from the model with the rotor only confirm the typically made claim that the efficiency of the rotor in a boundary layer pump possesses relatively high values which in this case is ∼87% at the design point, reinforcing results from previous studies that the rotor assembly is not the cause of inefficiency. The volute on its own indicated a hydraulic efficiency of around 97%. However, the integrated model yielded a rotor efficiency of around 74\% and an overall pump efficiency of 51% at the design point, clearly outlining the fact that the effect of the volute integrated with the rotor is the reason for both the rotor and pump efficiency degradation. The reason for this drop in efficiency is discussed in detail by highlighting the change in the flow topologies. The insights into the flow field and the identification of the reason for inefficiencies using a separated component analysis approach provide directions for avenues in which design improvements would need to be attempted.
Load–Velocity Profile and Active Drag in Young Female Swimmers: An Age-Group Comparison
Authors: Wettengl Christina , Karlsson Rebecca , Olstad Bjørn H. , Gonjo Tomohiro 
Published: October 2023

Purpose: The present study aimed to establish differences in load–velocity profiling, active drag (AD), and drag coefficient (Cd) between 3 age groups of female swimmers. Methods: Thirty-three swimmers (11, 13, or 16 y old) were recruited. The individual load–velocity profile was determined for the 4 competitive swimming strokes. The maximal velocity (V0), maximal load (L0), L0 normalized to the body mass, AD, and Cd were compared between the groups. A 2-way analysis of variance and correlation analysis were conducted. Results: Compared with their younger counterparts, 16-year-old swimmers generally had larger V0, L0, and AD, which was particularly evident when comparing them with 11-year-old swimmers (P ≤ .052). The exception was breaststroke, where no differences were observed in L0 and AD and Cd was smaller in the 16-year-old group than the 11-year-old group (P = .03). There was a negative correlation between Cd and V0 for all groups in backstroke (P ≤ .038) and for the 11-year-old group and 13-year-old group in breaststroke (P ≤ .022) and front crawl (P ≤ .010). For the 16-year-old group, large correlations with V0 were observed for L0, L0 normalized to the body mass, and AD (P ≤ .010) in breaststroke and for L0 and AD with V0 in front crawl (P ≤ .042). In butterfly, large negative correlations with V0 were observed in the 13-year-old group for all parameters (P ≤ .027). Conclusions: Greater propulsive force is likely the factor that differentiates the oldest age group from the younger groups, except for breaststroke, where a lower Cd (implying a better technique) is evident in the oldest group.
Structural basis for broad neutralization of human antibody against Omicron sublineages and evasion by XBB variant
Authors: Sun Hui , Wang Yizhen , Chen Xiuting , Jiang Yanan , Wang Siling , Huang Yang , Liu Liqin , Li Yu , Lan Miaolin , Guo Huilin , Yuan Quan , Zhang Yali , Li Tingting , Yu Hai , Gu Ying , Zhang Jun , Li Shaowei , Zheng Zizheng , Zheng Qingbing , Xia Ningshao 
Published: October 2023

ABSTRACT
The continuous emergence of SARS-CoV-2 variants, particularly the newly circulating Omicron XBB subvariants, has led to a significant reduction in the neutralizing potency and breadth of antibodies. In this study, we report a SARS-CoV-2 human neutralizing antibody, 1G11, which potently and broadly neutralizes diverse variants, including Omicron subvariants BA.4/5 and BF.7, but is evaded by the recently emerged BQ.1.1 and XBBs. Cryo-electron microscopy structure analysis of the 1G11 in complex with the BA.4/5 spike trimer reveals that 1G11, a Class 3 nAb, recognizes an epitope similar to those of S309 and LY-CoV1404. Structurally, the mutations K444T and V445P in BQ.1.1 and XBB subvariants are found to disrupt the interface between 1G11 and the spike protein, resulting in antibody evasion. 1G11 is further demonstrated to mediate neutralization through multiple mechanisms, including receptor binding blockage, interspike cross-linking, Fc-mediated ADCC and ADCP. Collectively, these findings provide insights into a better understanding of neutralizing antibody evasion and highlight the potential for broad neutralization by structure-based modification of available antibodies.

IMPORTANCE
The ongoing COVID-19 pandemic has been characterized by the emergence of new SARS-CoV-2 variants including the highly transmissible Omicron XBB sublineages, which have shown significant resistance to neutralizing antibodies (nAbs). This resistance has led to decreased vaccine effectiveness and therefore result in breakthrough infections and reinfections, which continuously threaten public health. To date, almost all available therapeutic nAbs, including those authorized under Emergency Use Authorization nAbs that were previously clinically useful against early strains, have recently been found to be ineffective against newly emerging variants. In this study, we provide a comprehensive structural basis about how the Class 3 nAbs, including 1G11 in this study and noted LY-CoV1404, are evaded by the newly emerged SARS-CoV-2 variants.
Integration of molecular and computational approaches paints a holistic portrait of obscure metabolisms
Authors: Reyes-Umana Victor , Ewens Sophia D. , Meier David A. O. , Coates John D. 
Published: October 2023

ABSTRACT
Microorganisms are essential drivers of earth’s geochemical cycles. However, the significance of elemental redox cycling mediated by microorganisms is often underestimated beyond the most well-studied nutrient cycles. Phosphite, (per)chlorate, and iodate are each considered esoteric substrates metabolized by microorganisms. However, recent investigations have indicated that these metabolisms are widespread and ubiquitous, affirming a need to continue studying the underlying microbiology to understand their biogeochemical effects and their interface with each other and our biosphere. This review focuses on combining canonical techniques of culturing microorganisms with modern omic approaches to further our understanding of obscure metabolic pathways and elucidate their importance in global biogeochemical cycles. Using these approaches, marker genes of interest have already been identified for phosphite, (per)chlorate, and iodate using traditional microbial physiology and genetics. Subsequently, their presence was queried to reveal the distribution of metabolic pathways in the environment using publicly available databases. In conjunction with each other, computational and experimental techniques provide a more comprehensive understanding of the location of these microorganisms, their underlying biochemistry and genetics, and how they tie into our planet’s geochemical cycles.
Nitrogen fixation and transcriptome of a new diazotrophic
Geomonas
from paddy soils
Authors: Liu Guo-Hong , Yang Shang , Han Shuang , Xie Cheng-Jie , Liu Xing , Rensing Christopher , Zhou Shun-Gui 
Published: October 2023

ABSTRACT

Nitrogen gas (N
2
) fixation driven by diazotrophs is a crucial process for supplying nitrogen to paddy soil ecosystems. The genus
Geomonas
has been considered to be an important potential diazotroph in paddy soils, but direct experimental evidence of the nitrogen-fixing ability of
Geomonas
in pure culture is still lacking. Hence, we aimed to demonstrate this nitrogen-fixing capability and shed light on how this process was regulated in response to ammonium (NH
4
+
) in
Geomonas
. In this study, we determined that a key nitrogenase gene (
nifH
) was present in 50 isolates from paddy soils. Members of
Geomonas
contained the minimum nitrogen fixation gene cluster (
nifBHDKEN
) based on genomic analysis, implying
Geomonas
species had the potential to fix nitrogen. Acetylene reduction assay (ARA),
15
N
2
isotope labeling, and total nitrogen accumulation assays validated that
Geomonas
was, indeed, able to fix nitrogen in pure culture. Under nitrogen-fixing conditions, the cell morphology of
Geomonas
changed from short rod-shaped (with NH
4
+
) to long rod-shaped and flagella became longer and thicker. The expression of genes correlated to nitrogen fixation in the
Geomonas
transcriptome was quantified in response to NH
4
+
. Expression of genes associated with nitrogenase, flavin-based electron bifurcation complexes (such as the FixAB system), NH
4
+
uptake, and transformation (e.g., glutamine and glutamate synthetases) were significantly upregulated under nitrogen-fixing conditions, suggesting these mechanisms might be involved in N
2
fixation in
Geomonas
. These results were verified by RT-qPCR. Taken together, our results demonstrate that
Geomonas
species possess the ability to fix N
2
and expand our understanding on the ecological significance and potential applications of
Geomonas
in paddy soil ecosystems.

IMPORTANCE

The ability of
Geomonas
species to fix nitrogen gas (N
2
) is an important metabolic feature for its application as a plant growth-promoting rhizobacterium. This research is of great importance as it provides the first comprehensive direct experimental evidence of nitrogen fixation by the genus
Geomonas
in pure culture. We isolated a number of
Geomonas
strains from paddy soils and determined that
nifH
was present in these strains. This study demonstrated that these
Geomonas
species harbored genes encoding nitrogenase, as do
Geobacter
and
Anaeromyxobacter
in the same class of
Deltaproteobacteria
. We demonstrated N
2
-dependent growth of
Geomonas
and determined regulation of gene expression associated with nitrogen fixation. The research establishes and advances our understanding of nitrogen fixation in
Geomonas
.
Complete genome sequence of
Vibrio parahaemolyticus
strain PH1273, isolated from aquacultured shrimp in the Philippines
Authors: Salazar John Raymond B. , Santos Mary Nia M. , Palaad Jeremy L. , Yen Hsi-Ching , Castellano Jose Louis A. , dela Peña Leobert D. , Amar Edgar C. , Lai Erh-Min , Kuo Chih-Horng 
Published: October 2023

ABSTRACT

We announce the complete genome sequence of
Vibrio parahaemolyticus
strain PH1273. This strain was collected from a
Penaeus vannamei
pond in the Philippines in 2015. Genome analysis revealed that it lacks the gene
pirAB
responsible for causing acute hepatopancreatic necrosis disease but encode multiple secretion systems and the associated effectors.
Conserved, yet disruption-prone, gut microbiomes in neotropical bumblebees
Authors: Villabona Nickole , Moran Nancy , Hammer Tobin , Reyes Alejandro 
Published: October 2023

ABSTRACT

Bumblebees are important pollinators in natural ecosystems and agriculture, but many species are declining. Temperate-zone bumblebees have host-specific and beneficial gut microbiomes, which may have a role in mediating the effects of stressors. However, there is almost no published information on the gut microbiomes of tropical bumblebees. As temperate and tropical bumblebees encounter different floral resources and environmental conditions, their microbiomes could differ. Here, we characterized the gut microbiomes of four neotropical
Bombus
species and, for comparison, co-occurring solitary bees (genus
Thygater
). We collected wild-foraging bees from multiple sites in central Colombia and used 16S rRNA gene sequencing to characterize their gut microbiomes. DNA barcoding and morphology were used to identify bumblebee species. We found that the microbiomes of neotropical bumblebees cluster with those of closely related temperate-zone species, in agreement with a model of bumblebee-symbiont codiversification. There was no evidence of geographic differences in microbiome composition between neotropical and temperate-zone bumblebees. These results suggest that the microbiome was conserved during bumblebee dispersal from North America, despite major shifts in ecology and life history. As previously observed in temperate-zone species, some neotropical bumblebees have highly disrupted microbiomes, in which conserved gut bacterial symbionts are replaced by environmental microbes. In these individuals, the gut microbial profile is more like that of solitary bees than of conspecifics. The gut parasites
Nosema
and
Crithidia
are also prevalent and associated with microbiome disruption. Our findings provide insights into the biogeography of bee microbiomes and a foundation for studying bee-microbe-stressor interactions in the neotropics.

IMPORTANCE
Social bees are an important model for the ecology and evolution of gut microbiomes. These bees harbor ancient, specific, and beneficial gut microbiomes and are crucial pollinators. However, most of the research has concentrated on managed honeybees and bumblebees in the temperate zone. Here we used 16S rRNA gene sequencing to characterize gut microbiomes in wild neotropical bumblebee communities from Colombia. We also analyzed drivers of microbiome structure across our data and previously published data from temperate bumblebees. Our results show that lineages of neotropical bumblebees not only retained their ancient gut bacterial symbionts during dispersal from North America but also are prone to major disruption, a shift that is strongly associated with parasite infection. Finally, we also found that microbiomes are much more strongly structured by host phylogeny than by geography, despite the very different environmental conditions and plant communities in the two regions.
Metabolic modeling predicts unique drug targets in
Borrelia burgdorferi
Authors: Gwynne Peter J. , Stocks Kee-Lee K. , Karozichian Elysse S. , Pandit Aarya , Hu Linden T. 
Published: October 2023

ABSTRACT

The Lyme disease bacterium
Borrelia burgdorferi
is extremely host dependent, with a small genome and correspondingly limited metabolism. As such, it is an excellent candidate for the development of targeted, narrow-spectrum antimicrobials. To accelerate drug discovery in this fastidious bacterium,
in silico
genome-scale metabolic modeling was used to construct a map of
B. burgdorferi
’s metabolism. This map was used to predict essential genes and enzymes; experimental data validated these predicted hits as viable drug targets. Repurposing existing small-molecule inhibitors, it is shown that inhibition of two predicted essential enzymes (pyridoxal kinase and serine hydroxymethyltransferase) selectively kills
B. burgdorferi
in culture. Thus, the essential processes identified here represent targets for the development of narrow-spectrum antimicrobials. This pipeline, pairing
in silico
discovery with validation in culture, may be useful for other genetically intractable pathogens.

IMPORTANCE

Lyme disease is often treated using long courses of antibiotics, which can cause side effects for patients and risks the evolution of antimicrobial resistance. Narrow-spectrum antimicrobials would reduce these risks, but their development has been slow because the Lyme disease bacterium,
Borrelia burgdorferi
, is difficult to work with in the laboratory. To accelerate the drug discovery pipeline, we developed a computational model of
B. burgdorferi
’s metabolism and used it to predict essential enzymatic reactions whose inhibition prevented growth
in silico
. These predictions were validated using small-molecule enzyme inhibitors, several of which were shown to have specific activity against
B. burgdorferi
. Although the specific compounds used are not suitable for clinical use, we aim to use them as lead compounds to develop optimized drugs targeting the pathways discovered here.
Clinical presentation of childhood soft tissue sarcomas: a systematic review and meta-analysis
Authors: Ni Cheallaigh Lorna , Liu Jo-Fen , Fern Lorna , Winyard Paul , Walker David , Ball-Gamble Ashley , Shanmugavadivel Dhurgshaarna 
Published: October 2023

BackgroundTime to diagnosis (TTD) of childhood soft tissue sarcoma (STS) is significantly associated with survival. This review aims to identify pre-diagnostic symptoms/signs to inform earlier diagnosis interventions.MethodsMedline, Embase, Cochrane and Web-of-Science were searched between January 2010 and February 2021 for studies including children (<18 years) diagnosed with STS, with no language restrictions. Pooled proportions of symptoms/signs were calculated and subanalysed by tumour location and age.ResultsFifty-nine eligible studies were identified, totalling 2462 cases. The most frequent symptoms were lump/swelling (38%, 95% CI 27% to 51%), pain (6%, 95% CI 3% to 10%), cutaneous changes (4%, 95% CI 0 to 9%), localised eye swelling (3%, 95% CI 0 to 7%), cranial nerve deficits (2%, 95% CI 0 to 5%) and constitutional symptoms (2%, 95% CI 0 to 5%).Symptoms varied by location and age. Localised eye swelling (20%, 95% CI 3% to 45%), cranial nerve deficits (14%, 95% CI 4% to 28%) and impaired visual function (6%, 95% CI 0 to 17%) were frequent in head and neck tumours. For abdomen/pelvic tumours, urinary symptoms (24%, 95% CI 5% to 15%), abdominal distension/discomfort (22%, 95% CI 4% to 47%), genital lump/swelling (16%, 95% CI 1% to 42%), constitutional symptoms (9%, 95% CI 0%] to 23%), vaginal bleeding (7%, 95%C I 0 to 21%) and bowel habit changes (6%, 95% CI 0 to 17%) were frequent.In <5 years, consumptive coagulopathy (16%, 95% CI 0 to 48%), cutaneous changes (5%, 95% CI 0 to 40%), genital lump/swelling (4%, 95% CI 0 to 14%), reduced mobility (3%, 95% CI 0 to 11%), vaginal bleeding (2%, 95% CI 0 to 11%) and bleeding/bruising/petechiae (2%, 95% CI 0 to 20%) were frequent compared with lump/swelling, constitutional symptoms, pain and headaches which were frequent among >11 years.ConclusionsFor STS, pre-diagnostic symptoms differ by age and location, highlighting the need to tailor early diagnosis interventions.
Towards the validation of quantitative contrast sensitivity as a clinical endpoint: correlations with vision-related quality of life in bilateral AMD
Authors: Vingopoulos Filippos , Bannerman Augustine , Zhou Paul , Koch Thomas , Wescott Hannah E , Kim Leo , Vavvas Demetrios , Miller Joan W , Miller John B 
Published: October 2023

AimTo investigate if active learning of contrast sensitivity (CS) in bilateral age-related macular degeneration (AMD) correlates better than visual acuity (VA) with vision-related quality of life (VRQoL) using factor analysis-calibrated National Eye Institute Visual Function Questionnaire-25 (NEI VFQ-25).MethodsProspective cross-sectional observational study in 93 patients (186 eyes) with bilateral AMD. CS was measured in one eye at a time with the quantitative CS function (qCSF) method (Adaptive Sensory Technology). Same-day VRQoL was assessed with factor analysis-calibrated NEI VFQ-25 visual function and socioemotional scales. Mixed-effects multiple linear regression analyses evaluated the associations of the qCSF outcomes and VA with the NEI VFQ-25 scales. A subgroup analysis on patients with AMD with VA more than 20/25 in both eyes was performed.ResultsCompared with VA, CS outcomes were associated with larger effect on both visual function scale (standardised beta coefficients (β*) for area under the logarithm of CSF (AULCSF) curve and CS thresholds at 1.5, 3 and 6 cycles per degree (cpd): β*=0.50, 0.48, 0.52, 0.46, all p<0.001, respectively, vs β*=−0.45 for VA, all p<0.001) and socioemotional scale (β* for AULCSF and CS threshold at 6 cpd: β*=0.44, 0.44 vs β*=−0.42 for VA, all p<0.001). In patients with AMD with VA more than 20/25 in both eyes (N=20), both VFQ-25 scales and all CS outcomes were significantly reduced.ConclusionsqCSF-measured CS strongly correlates with patient-reported VRQoL in bilateral AMD, even stronger than VA does. This study further validates qCSF-measured CS as a promising functional endpoint for future clinical trials in AMD.