bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome sequence of
Gordonia alkaliphila
strain WW102, isolated from influent wastewater at a research center with multiple-species research animal facilities
Authors: Kim Sung Guk , Reyna Mariela , Park Miseon , Wang Sharon X. , Foley Steven L. 
Published: September 2023

ABSTRACT

Gordonia alkaliphila
is a little known mesophilic Gram-positive rod-shaped bacterium. We report the 3.85-Mbp genome sequence of
G. alkaliphila
strain WW102, isolated from wastewater at a research center with multiple-species laboratory animal facilities. The genome predicted FadD32 gene clusters that are involved in the biosynthesis of mycolic acids as found in
Mycobacterium tuberculosis
.
Draft genomes of
Aeromonas caviae
from patients with cholera-like illness during the 2022–2023 cholera outbreak in Malawi
Authors: Jere Khuzwayo C. , Chibwe Innocent , Chaima David , Kasambala Watipaso , Mhango Chimwemwe , Bitilinyu-Bangoh Joseph , Mvula Bernard , Kipandula Wakisa , Kamng'ona Arox W. , Steele A. Duncan , Chauma-Mwale Annie , Hungerford Daniel , Kagoli Matthew , Nyaga Martin M. , Dube Queen , French Neil , Cunliffe Nigel A. , Msefula Chisomo L. , Chaguza Chrispin 
Published: September 2023

ABSTRACT

Aeromonas caviae
is an increasingly recognized etiological agent of acute gastroenteritis. Here, we report five draft genomes of
A. caviae
isolated from suspected cholera cases during the 2022–2023 cholera outbreak in Malawi.
Closed genome sequences of two
Listeria monocytogenes
ST121 strains
Authors: Tibbs-Cortes Bienvenido W. , Schultz Dylan L. , Schmitz-Esser Stephan 
Published: September 2023

ABSTRACT

We performed Oxford Nanopore and Illumina sequencing to generate accurate, closed genomes for the
Listeria monocytogenes
strains 6179 and L58-55. The new assemblies were generally similar to the previous Illumina-based assemblies, but additional rRNA operons and repeat regions were identified in the new assembly for strain 6179.
Ammonium “nutrient capacitor” model for δ15N signatures associated with marine anoxic events
Authors: Uveges Benjamin T. , Pearson Ann 
Published: September 2023

Abstract
Geochemical records of ancient periods of warm climate can be useful to help understand the looming effects of modern anthropogenic warming, including changes to biogeochemical nutrient cycles. Stable nitrogen isotope compositions of marine sediments archive the balance of processes in the global nitrogen cycle. However, the unusual isotopic signals of Mesozoic oceanic anoxic events (OAEs) remain enigmatic, thus hindering our understanding of nitrogen cycle processes and dynamics under conditions of ocean deoxygenation. Here, we present an ammonium “nutrient capacitor” model of the water-column nitrogen cycle to explain the anomalously negative isotopic compositions seen in Mesozoic OAE sediments. Our model applies isotopic inferences derived from high-resolution records of Lake Kivu sediments to show how periodic chemocline overturning of redox-stratified water columns during Mesozoic OAEs may have delivered ammonium to the photic zone in excess of primary producer requirements. Smoothed, stochastic sampling of the changing fluxes within the nitrogen cycle across these events can simulate OAE nitrogen isotope records.
Toxic leukoencephalopathy versus delayed post-hypoxic leukoencephalopathy after oral morphine sulphate overdose
Authors: Rossi Nicholas P , Sathyanarayanan Goutham , Mahmood MdSakir , Shakespeare David 
Published: September 2023

Toxic leukoencephalopathy (TLE) is a rare pathology caused by various substances including opioids (notably heroin), immunosuppressants, chemotherapy agents, cocaine, alcohol and carbon monoxide. However, although heroin is metabolised by the body into morphine, there is a striking paucity in cases of primary oral morphine-induced TLE, especially in the adult population. We present the case of a man in his 40s admitted to hospital in respiratory depression with a Glasgow Coma Scale (GCS) score of 6 after taking an overdose of oral morphine sulphate. Following a complete recovery to baseline, he was then readmitted with an acute deterioration in his neurobehavioural condition. Initial investigations returned normal but MRI showed changes characteristic for TLE.In cases of opioid toxicity such as ours, TLE is difficult to differentiate from delayed post-hypoxic leukoencephalopathy, due to their similar clinical presentation, disease progression and radiological manifestation. We explore how clinicians can approach this diagnostic uncertainty.
Radiographic pneumonia in young febrile infants presenting to the emergency department: secondary analysis of a prospective cohort study
Authors: Florin Todd A , Ramilo Octavio , Banks Russell K , Schnadower David , Quayle Kimberly S , Powell Elizabeth C , Pickett Michelle L , Nigrovic Lise E , Mistry Rakesh , Leetch Aaron N , Hickey Robert W , Glissmeyer Eric W , Dayan Peter S , Cruz Andrea T , Cohen Daniel M , Bogie Amanda , Balamuth Fran , Atabaki Shireen M , VanBuren John M , Mahajan Prashant , Kuppermann Nathan 
Published: September 2023

ObjectiveThe lack of evidence-based criteria to guide chest radiograph (CXR) use in young febrile infants results in variation in its use with resultant suboptimal quality of care. We sought to describe the features associated with radiographic pneumonias in young febrile infants.Study designSecondary analysis of a prospective cohort study in 18 emergency departments (EDs) in the Pediatric Emergency Care Applied Research Network from 2016 to 2019. Febrile (≥38°C) infants aged ≤60 days who received CXRs were included. CXR reports were categorised as ‘no’, ‘possible’ or ‘definite’ pneumonia. We compared demographics, clinical signs and laboratory tests among infants with and without pneumonias.ResultsOf 2612 infants, 568 (21.7%) had CXRs performed; 19 (3.3%) had definite and 34 (6%) had possible pneumonias. Patients with definite (4/19, 21.1%) or possible (11/34, 32.4%) pneumonias more frequently presented with respiratory distress compared with those without (77/515, 15.0%) pneumonias (adjusted OR 2.17; 95% CI 1.04 to 4.51). There were no differences in temperature or HR in infants with and without radiographic pneumonias. The median serum procalcitonin (PCT) level was higher in the definite (0.7 ng/mL (IQR 0.1, 1.5)) vs no pneumonia (0.1 ng/mL (IQR 0.1, 0.3)) groups, as was the median absolute neutrophil count (ANC) (definite, 5.8 K/mcL (IQR 3.9, 6.9) vs no pneumonia, 3.1 K/mcL (IQR 1.9, 5.3)). No infants with pneumonia had bacteraemia. Viral detection was frequent (no pneumonia (309/422, 73.2%), definite pneumonia (11/16, 68.8%), possible pneumonia (25/29, 86.2%)). Respiratory syncytial virus was the predominant pathogen in the pneumonia groups and rhinovirus in infants without pneumonias.ConclusionsRadiographic pneumonias were uncommon in febrile infants. Viral detection was common. Pneumonia was associated with respiratory distress, but few other factors. Although ANC and PCT levels were elevated in infants with definite pneumonias, further work is necessary to evaluate the role of blood biomarkers in infant pneumonias.
Commuting and sick leave: a retrospective longitudinal study among a Belgian military population
Authors: Hinderijckx Peter , Collée Audrey , Godderis Lode , Dhondt Erwin , Goorts Kaat 
Published: September 2023

ObjectivesIn a military context, people often have to deal with long commuting distance. The aim of the current study is to investigate to what extent commuting distances predict sickness absence among a military population.MethodsThe present study is based on a dynamic cohort of active-duty military personnel of the Belgian Defence. A proportional hazard Andersen-Gill model was used to determine the effect of commuting distance on the recurrence of sickness absence, considering relevant covariates. In a second model, an interaction term for commuting and traffic congestion was introduced.ResultsHigher commuting distances led to higher risk of recurring sickness absence, which was 9%, 15%, 8% and 11% higher, respectively, for distances of 5–14 km, 15–29 km, 30–59 km or >60 km compared with a distance of <5 km.A commuting distance of 30–59 km increased the risk with 47%, 33%, 35% and 76% if the reported traffic congestion was, respectively, 5–20%, 20–40%, 40–70% and 70–100% compared with a commuting distance of <5 km and a reported traffic congestion of 0–5%. A commuting distance of >60 km increased the risk with 25% and 76%, respectively, for a reported traffic congestion of 5–20% and 70–100% compared with a commuting distance of <5 km and a reported traffic congestion of 0–5%.ConclusionsThese findings support measures to reduce the distance and frequency of commuting in order to reduce sickness absence, considering for example remote working, a more responsible geographical distribution of the offices or a revision of the employees’ job-changing policies.
Field observations of the movements of locally adapted Atlantic cod (Gadus morhua) living in zero and sub-zero centigrade temperatures for half the year
Authors: Green John M. , Schornagel Dustin , Nguyen Khanh Q. , Pennell Curtis , Morris Corey J. 
Published: September 2023

Atlantic cod ( Gadus morhua Linnaeus, 1758) can experience mortality at sub-zero (<0 °C) temperatures in ice-infested waters, and many populations migrate to deeper and warmer areas during winter. An exception is the resident population in Gilbert Bay, Labrador, which annually experiences 6 months of sub-zero temperatures. We used the VEMCO Positioning System to estimate fish locations to determine depth utilization and seasonal movements of tagged Gilbert Bay cod ranging in size from 43 to 75 cm. This is the first study to directly monitor the movements of adult Atlantic cod for extended periods (months) in sub-zero temperatures. Gilbert Bay cod remained active under an ice-covered surface during the 6 months of sub-zero temperatures. During both warm (>0 °C) and cold (≤0 °C) periods, fish spent similar amounts of time not moving, moving slowly, and moving at medium and fast rates. They tended to utilize shallow depths, <10 m, beneath surface ice during winter, while utilizing deeper depths as well during other times of the year. Surprisingly, fish that resided within our tracking array year-round had greater cumulative swimming distances during sub-zero periods compared to warmer periods. No tracked fish died during winter, further highlighting the cold adaptiveness of this population and its importance to biodiversity conservation.
Cosmogenesis as symmetry transformation
Authors: Balcerzak Adam , Lisaj Mateusz 
Published: September 2023

AbstractWe consider the quantized bi-scalar gravity, which may serve as a locally Lorentz invariant cosmological model with varying speed of light and varying gravitational constant. The equation governing the quantum regime for the case of homogeneous and isotropic cosmological setup is a Dirac-like equation which replaces the standard Wheeler–DeWitt equation. We show that particular cosmogenesis may occur as a result of the action of the symmetry transformation which due to Wigner’s theorem can either be unitary or antiunitary. We demonstrate that the transition from the pre-big-bang contraction to the post-big-bang expansion – a scenario that also occurs in string quantum cosmologies – can be attributed to the action of charge conjugation, which belongs to the class of antiunitary transformations. We also demonstrate that the emergence of the two classical expanding post-big-bang universe–antiuniverse pairs, each with opposite spin projections, can be understood as being triggered by the action of a unitary transformation resembling the Hadamard gate.
China’s 21st Century Maritime Strategy
Authors: Zhao Pieter W.G. 
Published: September 2023

Abstract
In less than three decades, the People’s Liberation Army Navy developed from a minor coastal-defence force into the largest naval force in the world. China’s rapid rise in seapower has gained significant attention from established naval circles, academia, and the public. In their efforts to explain this development, analysts have often referred to 19th-century naval history, seeking to connect China’s maritime developments to the ideas of influential naval strategists like Alfred Thayer Mahan and Julian Corbett. However, in doing so, these naval thinkers are often used to make a case about long-term developments or strategic implications regarding China’s alleged grand strategy. This paper seeks to turn this methodology around by solely focusing on the reflection of those naval theories—in their own right—against China’s maritime strategy. In doing so, it aims to historicise China’s 21st-century maritime strategy by testing to what extent it is reflected by the ideas of the navalists that are often presumed to influence Chinese strategic circles. It is argued that while on a grand-strategic level, Chinese strategic thinking seems to reflect the essence of Mahan’s seapower argument regarding its focus on the interconnectedness of maritime commerce and national power, a closer analysis reveals significant discrepancies in terms of both implementation and the broader strategic mindset regarding China’s geostrategic situation.
A Kinematic Modeling Study of the Reorganization of Snowfall between Cloud-Top Generating Cells and Low-Level Snowbands in Midlatitude Winter Storms
Authors: Janiszeski Andrew , Rauber Robert M. , Jewett Brian F. , McFarquhar Greg M. , Zaremba Troy J. , Yorks John E. 
Published: September 2023

Abstract
This paper explores whether particles within uniformly spaced generating cells falling at terminal velocity within observed 2D wind fields and idealized deformation flow beneath cloud top can be reorganized consistent with the presence of single and multibanded structures present on WSR-88D radars. In the first experiment, two-dimensional wind fields, calculated along cross sections normal to the long axis of snowbands observed during three northeast U.S. winter storms, were taken from the initialization of the High-Resolution Rapid Refresh model. This experiment demonstrated that the greater the residence time of the particles in each of the three storms, the greater particle reorganization occurred. For experiments with longer residence times, increases in particle concentrations were nearly or directly collocated with reflectivity bands. For experiments with shorter residence times, particle reorganization still conformed to the band features but with less concentration enhancement. This experiment demonstrates that the combination of long particle residence time and net convergent cross-sectional flow through the cloud depth is sufficient to reorganize particles into locations consistent with precipitation bands. Increased concentrations of ice particles can then contribute, along with any dynamic forcing, to the low-level reflectivity bands seen on WSR-88D radars. In a second experiment, the impact of flow deformation on the reorganization of falling ice particles was investigated using an idealized kinematic model with stretching deformation flow of different depths and magnitudes. These experiments showed that deformation flow provides for little particle reorganization given typical deformation layer depths and magnitudes within the comma head of such storms.

Significance Statement
Past research with vertically pointing and scanning radars presents two different perspectives regarding snowfall organization in winter storms. Vertically pointing radars often observe cloud-top generating cells with precipitation fallstreaks descending into a broad stratiform echo at lower altitudes. In contrast, scanning radars often observe snowfall organized in quasi-linear bands. This work attempts to provide a connection between these two perspectives by examining how two-dimensional convergent and deformation flow occurring in winter storms can contribute to the reorganization of snowfall between cloud top and the ground.
Towards genetic improvement of social behaviours in livestock using large-scale sensor data: data simulation and genetic analysis
Authors: Wang Zhuoshi , Doekes Harmen , Bijma Piter 
Published: September 2023

Abstract
Background
Harmful social behaviours, such as injurious feather pecking in poultry and tail biting in swine, reduce animal welfare and production efficiency. While these behaviours are heritable, selective breeding is still limited due to a lack of individual phenotyping methods for large groups and proper genetic models. In the near future, large-scale longitudinal data on social behaviours will become available, e.g. through computer vision techniques, and appropriate genetic models will be needed to analyse such data. In this paper, we investigated prospects for genetic improvement of social traits recorded in large groups by (1) developing models to simulate and analyse large-scale longitudinal data on social behaviours, and (2) investigating required sample sizes to obtain reasonable accuracies of estimated genetic parameters and breeding values (EBV).

Results
Latent traits were defined as representing tendencies of individuals to be engaged in social interactions by distinguishing between performer and recipient effects. Animal movement was assumed random and without genetic variation, and performer and recipient interaction effects were assumed constant over time. Based on the literature, observed-scale heritabilities ($${h}_{o}^{2}$$

h

o

2

) of performer and recipient effects were both set to 0.05, 0.1, or 0.2, and the genetic correlation ($${r}_{A}$$

r
A

) between those effects was set to – 0.5, 0, or 0.5. Using agent-based modelling, we simulated ~ 200,000 interactions for 2000 animals (~ 1000 interactions per animal) with a half-sib family structure. Variance components and breeding values were estimated with a general linear mixed model. The estimated genetic parameters did not differ significantly from the true values. When all individuals and interactions were included in the analysis, the accuracy of EBV was 0.61, 0.70, and 0.76 for $${h}_{o}^{2}$$

h

o

2

= 0.05, 0.1, and 0.2, respectively (for $${r}_{A}$$

r
A

= 0). Including 2000 individuals each with only ~ 100 interactions, already yielded promising accuracies of 0.47, 0.60, and 0.71 for $${h}_{o}^{2}$$

h

o

2

= 0.05, 0.1, and 0.2, respectively (with $${r}_{A}$$

r
A

= 0). Similar results were found with $${r}_{A}$$

r
A

of – 0.5 or 0.5.

Conclusions
We developed models to simulate and genetically analyse social behaviours for animals that are kept in large groups, anticipating the availability of large-scale longitudinal data in the near future. We obtained promising accuracies of EBV with ~ 100 interactions per individual, which would correspond to a few weeks of recording. Therefore, we conclude that animal breeding can be a promising strategy to improve social behaviours in livestock.
Highly sensitive and rapid determination of Mycobacterium leprae based on real-time multiple cross displacement amplification
Authors: Huang Junfei , Tong Yi , Chen Yijiang , Yang Xinggui , Wei Xiaoyu , Chen Xu , Li Jinlan , Li Shijun 
Published: September 2023

Abstract
Background
Mycobacterium leprae (ML) is the pathogen that causes leprosy, which has a long history and still exists today. ML is an intracellular mycobacterium that dominantly induces leprosy by causing permanent damage to the skin, nerves, limbs and eyes as well as deformities and disabilities. Moreover, ML grows slowly and is nonculturable in vitro. Given the prevalence of leprosy, a highly sensitive and rapid method for the early diagnosis of leprosy is urgently needed.

Results
In this study, we devised a novel tool for the diagnosis of leprosy by combining restriction endonuclease, real-time fluorescence analysis and multiple cross displacement amplification (E-RT-MCDA). To establish the system, primers for the target gene RLEP were designed, and the optimal conditions for E-RT-MCDA at 67 °C for 36 min were determined. Genomic DNA from ML, various pathogens and clinical samples was used to evaluate and optimize the E-RT-MCDA assay. The limit of detection (LoD) was 48.6 fg per vessel for pure ML genomic DNA, and the specificity of detection was as high as 100%. In addition, the detection process could be completed in 36 min by using a real-time monitor.

Conclusion
The E-RT-MCDA method devised in the current study is a reliable, sensitive and rapid technique for leprosy diagnosis and could be used as a potential tool in clinical settings.
Accessory hepatic vein recanalization for Budd-Chiari syndrome: a systematic review and meta-analysis
Authors: Lv Lu-Lu , Xu Han-Bo , Li Sheng-Li , Xu Peng 
Published: October 2023

Abstract
Background
Budd-Chiari syndrome (BCS) results when the outflow of the hepatic vein (HV) is obstructed. BCS patients exhibiting an accessory HV (AHV) that is dilated but obstructed can achieve significant alleviation of liver congestion after undergoing AHV recanalization. This meta-analysis was developed to explore the clinical efficacy of AHV recanalization in patients with BCS.

Materials and methods
PubMed, Embase, and Wanfang databases were searched for relevant studies published as of November 2022, and RevMan 5.3 and Stata 12.0 were used for pooled endpoint analyses.

Results
Twelve total studies were identified for analysis. Pooled primary clinical success, re-stenosis, 1- and 5-year primary patency, 1- and 5-year secondary patency, 1-year overall survival (OS), and 5-year OS rates of patients in these studies following AHV recanalization were 96%, 17%, 91%, 75%, 98%, 91%, 97%, and 96%, respectively. Patients also exhibited a significant reduction in AHV pressure after recanalization relative to preoperative levels (P < 0.00001). Endpoints exhibiting significant heterogeneity among these studies included, AHV pressure (I2 = 95%), 1-year primary patency (I2 = 51.2%), and 5-year primary patency (I2 = 62.4%). Relative to HV recanalization, AHV recanalization was related to a lower rate of re-stenosis (P = 0.002) and longer primary patency (P < 0.00001), but was not associated with any improvements in clinical success (P = 0.88) or OS (P = 0.29) relative to HV recanalization.

Conclusions
The present meta-analysis highlights AHV recanalization as an effective means of achieving positive long-term outcomes in patients affected by BCS, potentially achieving better long-term results than those associated with HV recanalization.