bluuebunny/crossref_metadata_2025_split huggingface dataset:
Why Mean Potential Vorticity Cannot Be Materially Conserved in the Eddying Southern Ocean
Authors: Stanley Geoffrey J. , Marshall David P. 
Published: April 2022

Abstract
Downstream of Drake Passage, the Antarctic Circumpolar Current (ACC) veers abruptly northward along the continental slope of South America. This spins down the ACC, akin to the western boundary currents of ocean gyres. During this northward excursion, the mean potential vorticity (PV) increases dramatically (decreases in magnitude) by up to a factor of 2 along mean geostrophic streamlines on middepth buoyancy surfaces. This increase is driven by drag near the continental slope, or by breaking eddies further offshore, and is balanced by a remarkably steady, eddy-driven decrease of mean PV along these northern circumpolar streamlines in the open ocean. We show how two related eddy processes that are fundamental to ACC dynamics—poleward buoyancy fluxes and downward fluxes of eastward momentum—are also concomitant with materially forcing PV to increase on the northern flank of a jet at middepth, and decrease on the southern flank. For eddies to drive the required mean PV decrease along northern streamlines, the ACC merges with the subtropical gyres to the north, so these streamlines inhabit the southern flanks of the combined ACC–gyre jets. We support these ideas by analyzing the time-mean PV and its budget along time-mean geostrophic streamlines in the Southern Ocean State Estimate. Our averaging formalism is Eulerian, to match the model’s numerics. The thickness-weighted average is preferable, but its PV budget cannot be balanced using Eulerian 5-day averaged diagnostics, primarily because the z-level buoyancy and continuity equations’ delicate balances are destroyed upon transformation into the buoyancy-coordinate thickness equation.

Significance Statement
The Antarctic Circumpolar Current is the world’s largest ocean current and a key controller of Earth’s climate. As the westerly winds that drive this current shift poleward under global warming, it is vital to know whether the current will follow. To begin addressing this, we study the current’s fundamental dynamics, and constraints, under present-day conditions. By analyzing angular momentum and stratification together, we show that the current is weakened near boundaries and strengthened by eddies elsewhere. The strengthening effects of eddies are isolated to the current by merging the current with oceanic gyres to the north. This gives a new perspective on why the current travels so far northward alongside South America, and may provide dynamical constraints on future changes.
Objective Verification of Clear-Air Turbulence (CAT) Diagnostic Performance in China Using In Situ Aircraft Observation
Authors: Hu Boyan , Ding Jinfeng , Liu Gang , Tang Jianping 
Published: April 2022

Abstract
This study analyzes the spatial and temporal distribution characteristics of the in situ aircraft observations in the middle and higher troposphere in 2019. These aircraft observations are mainly distributed in China, and relatively evenly recorded between 0000 and 1500 UTC in time and 6 and 10 km in height. Based on the 3395 stronger clear-air turbulence (CAT) events and 4038 weaker CAT events selected from the observations in the study region (15°–55°N, 70°–140°E), the performances of 24 CAT diagnostics calculated from the ERA5 data are evaluated. Results show that the diagnostics connected with vertical wind shear (i.e., version 1 of the North Carolina State University index, negative Richardson number, variant 3 and variant 1 of Ellrod’s turbulence index) have the best performances. However, the performances vary greatly from season to season, and overall performances are the best in winter and worst in summer. The annual and seasonal best thresholds for these diagnostics are also listed in this study.
Three-Dimensional Thermodynamic Observations in Supercell Thunderstorms from Swarms of Balloon-Borne Sondes
Authors: Bartos Elissa A. , Markowski Paul M. , Richardson Yvette P. 
Published: March 2022

Abstract
This study analyzes aboveground thermodynamic observations in three tornadic supercells obtained via swarms of small balloon-borne sondes acting as pseudo-Lagrangian drifters; the storm-relative winds draw the sondes through the precipitation, outflow, and baroclinic zones, which are believed to play key roles in tornado formation. Three-dimensional thermodynamic analyses are produced from the in situ observations. The coldest air is found at the lowest analysis levels, where virtual potential temperature deficits of 2–5 K are observed. Air parcels within the forward-flank outflow are inferred from their equivalent potential temperatures to have descended only a few hundred meters or less, whereas parcels within the rear-flank outflow are inferred to have downward excursions of 1–2 km. Additionally, the parcels following paths toward the low-level mesocyclone pass through horizontal buoyancy gradients that are strongest in the lowest 750 m and estimated to be capable of baroclinically generating horizontal vorticity having a magnitude of 6–10 × 10−3 s−1. A substantial component of the baroclinically generated vorticity is initially crosswise, though the vorticity subsequently could become streamwise given the leftward bending of the airstream in which the vorticity is generated. The baroclinically generated vorticity could contribute to tornado formation upon being tilted upward and stretched near the surface beneath a strong, dynamically forced updraft.

Significance Statement
Swarms of balloon-borne probes are used to produce the first-ever, three-dimensional mappings of temperature from in situ observations within supercell storms (rotating storms with high tornado potential). Temperature has a strong influence on the buoyancy of air, and horizontal variations of buoyancy generate spin about a horizontal axis. Buoyancy is one of the primary drivers of upward and downward motions in thunderstorms, and in supercell storms, horizontally oriented spin can be tipped into the vertical and amplified by certain arrangements of upward and downward motions. Unfortunately, the long-standing lack of temperature observations has hampered scientists’ ability to evaluate computer simulations and the tornadogenesis theories derived from them. We find that significant spin could be generated by the horizontal buoyancy variations sampled by the probes.
Optically controlled dual-band quantum dot infrared photodetector
Authors: Vichi Stefano , Bietti Sergio , Basset Francesco Basso , Tuktamyshev Artur , Fedorov Alexey , Sanguinetti Stefano 
Published: March 2022

We present the design for a novel type of dual-band photodetector in the thermal infrared spectral range, the Optically Controlled Dual-band quantum dot Infrared Photodetector (OCDIP). This concept is based on a quantum dot ensemble with a unimodal size distribution, whose absorption spectrum can be controlled by optically injected carriers. An external pumping laser varies the electron density in the QDs, permitting to control the available electronic transitions and thus the absorption spectrum. We grew a test sample which we studied by AFM and photoluminescence. Based on the experimental data, we simulated the infrared absorption spectrum of the sample, which showed two absorption bands at 5.85 μm and 8.98 μm depending on the excitation power.
Local Tumor Behavior Associated With Survival Among Patients With Paraganglioma of the Head and Neck
Authors: Harley Randall J. , Lee Jason H. , Ostrander Benjamin T. , Finegersh Andrey , Pham Tammy B. , Tawfik Kareem O. , Ren Yin , Faraji Farhoud , Friedman Rick A. 
Published: March 2022

ObjectiveThe purpose of this study was to evaluate the utility of ICD‐O‐3–classified local tumor behavior as a prognosticator of head and neck paraganglioma (HNP) outcomes.Study DesignRetrospective cohort study.SettingNational Cancer Database between 2004 and 2016.MethodsThis study included patients aged ≥18 years who were diagnosed with HNP. Clinical outcomes and clinicopathologic features were compared with regard to local tumor behavior.ResultsOur study included 525 patients, of which the majority had HNP classified as locally invasive (45.9%) or borderline (37.9%). The most common anatomic sites involved were the carotid body (33.7%), intracranial regions (29.0%), or cranial nerves (25.5%). Carotid body tumors were exclusively locally invasive, whereas intracranial and cranial nerve HNP were overwhelmingly benign or borderline (94% and 91%, respectively). One‐fourth of patients underwent pathologic analysis of regional lymph nodes, of which the majority were positive for metastasis (80.6%). Metastasis to distant organs was twice as common in patients with locally invasive tumors vs benign (15% vs 7.1). For benign disease, surgery with radiotherapy (adjusted hazard ratio [aHR], 40.45; P =. 006) and active surveillance (aHR, 24.23; P =. 008) were associated with worse survival when compared with surgery alone. For locally invasive tumors, greater age (aHR, 1.07; P <. 0001) and positive surgical margins (aHR, 4.13; P =. 010) were predictors of worse survival, while combined surgery and radiotherapy were predictors of improved survival vs surgery alone (aHR, 0.31; P =. 027).ConclusionWhile criteria for tumor behavior could not be defined, our results suggest that such a classification system could be used to enhance HNP risk stratification and guide clinical management decisions.
ALGAEFUN with MARACAS, microALGAE FUNctional enrichment tool for MicroAlgae RnA-seq and Chip-seq AnalysiS
Authors: Romero-Losada Ana B. , Arvanitidou Christina , de los Reyes Pedro , García-González Mercedes , Romero-Campero Francisco J. 
Published: March 2022

Abstract
Background
Microalgae are emerging as promising sustainable sources for biofuels, biostimulants in agriculture, soil bioremediation, feed and human nutrients. Nonetheless, the molecular mechanisms underpinning microalgae physiology and the biosynthesis of compounds of biotechnological interest are largely uncharacterized. This hinders the development of microalgae full potential as cell-factories. The recent application of omics technologies into microalgae research aims at unraveling these systems. Nevertheless, the lack of specific tools for analysing omics raw data generated from microalgae to provide biological meaningful information are hampering the impact of these technologies. The purpose of ALGAEFUN with MARACAS consists in providing researchers in microalgae with an enabling tool that will allow them to exploit transcriptomic and cistromic high-throughput sequencing data.

Results
ALGAEFUN with MARACAS consists of two different tools. First, MARACAS (MicroAlgae RnA-seq and Chip-seq AnalysiS) implements a fully automatic computational pipeline receiving as input RNA-seq (RNA sequencing) or ChIP-seq (chromatin immunoprecipitation sequencing) raw data from microalgae studies. MARACAS generates sets of differentially expressed genes or lists of genomic loci for RNA-seq and ChIP-seq analysis respectively. Second, ALGAEFUN (microALGAE FUNctional enrichment tool) is a web-based application where gene sets generated from RNA-seq analysis as well as lists of genomic loci from ChIP-seq analysis can be used as input. On the one hand, it can be used to perform Gene Ontology and biological pathways enrichment analysis over gene sets. On the other hand, using the results of ChIP-seq data analysis, it identifies a set of potential target genes and analyses the distribution of the loci over gene features. Graphical representation of the results as well as tables with gene annotations are generated and can be downloaded for further analysis.

Conclusions
ALGAEFUN with MARACAS provides an integrated environment for the microalgae research community that facilitates the process of obtaining relevant biological information from raw RNA-seq and ChIP-seq data. These applications are designed to assist researchers in the interpretation of gene lists and genomic loci based on functional enrichment analysis. ALGAEFUN with MARACAS is publicly available on https://greennetwork.us.es/AlgaeFUN/.
ThPOK inhibits the immune escape of gastric cancer cells by inducing STPG1 to inactivate the ERK pathway
Authors: Chen Ying , Jiang Lili , Xia Lingli , Zhang Gang , Chen Lan 
Published: April 2022

Abstract
Background
Gastric cancer is the second most frequently diagnosed cancer worldwide. Weak immunogenicity helps cancer cells escape from immune elimination and grow into predominant subpopulations. This study aimed to investigate the effect of Zinc finger and BTB domain containing 7B (Zbtb7b, Alias ThPOK) on T cell activation after coculture with gastric cancer cells.

Methods
Cell Counting Kit-8 assay (CCK-8) was performed to explore the viability of gastric cancer cells. Flow cytometry analysis was used to measure CD3+ T cell proliferation and the ratio of activated IFN-γ+ T cells which were co-incubated with gastric cancer cells (HGC-27, SNU-1). The binding between ThPOK and the promoter of its target sperm tail PG-rich repeat containing 1 (STPG1) was explored using ChIP and luciferase reporter assays. Relative gene expression was quantified using RT-qPCR.

Results
ThPOK was expressed at a low level in gastric cancer tissues and cells at mRNA and protein levels. Gastric cancer patients with lower ThPOK expression had poorer prognosis. ThPOK overexpression suppressed gastric cancer cell viability and increased T cell activation. ThPOK served as a transcription factor for STPG1. STPG1 expression was also at a low level in the tissues and cells of gastric cancer. ThPOK positively regulated the mRNA and protein levels of STPG1 in gastric cancer cells. Moreover, ThPOK was demonstrated to bind with STPG1 promoter. STPG1 upregulation also exerted inhibitory effects on gastric cancer cell viability and T cell activation. Additionally, ThPOK and STPG1 were revealed to inactivate the ERK pathway in gastric cancer cells.

Conclusion
ThPOK inhibits gastric cancer cell viability and increases T cell activation by inducing STPG1 to inactivate the ERK pathway.
The gut bacterial microbiome of Nile tilapia (Oreochromis niloticus) from lakes across an altitudinal gradient
Authors: Bereded Negash Kabtimer , Abebe Getachew Beneberu , Fanta Solomon Workneh , Curto Manuel , Waidbacher Herwig , Meimberg Harald , Domig Konrad J. 
Published: April 2022

AbstractBackgroundMicroorganisms inhabiting the gut play a significant role in supporting fundamental physiological processes of the host, which contributes to their survival in varied environments. Several studies have shown that altitude affects the composition and diversity of intestinal microbial communities in terrestrial animals. However, little is known about the impact of altitude on the gut microbiota of aquatic animals. The current study examined the variations in the gut microbiota of Nile tilapia (Oreochromis niloticus) from four lakes along an altitudinal gradient in Ethiopia by using 16S rDNA Illumina MiSeq high-throughput sequencing.ResultsThe results indicated that low-altitude samples typically displayed greater alpha diversity. The results of principal coordinate analysis (PCoA) showed significant differences across samples from different lakes. Firmicutes was the most abundant phylum in the Lake Awassa and Lake Chamo samples whereas Fusobacteriota was the dominant phylum in samples from Lake Hashengie and Lake Tana. The ratio of Firmicutes to Bacteroidota in the high-altitude sample (Lake Hashengie, altitude 2440 m) was much higher than the ratio of Firmicutes to Bacteroidota in the low altitude population (Lake Chamo, altitude 1235 m). We found that the relative abundances of Actinobacteriota, Chloroflexi, Cyanobacteria, and Firmicutes were negatively correlated with altitude, while Fusobacteriota showed a positive association with altitude. Despite variability in the abundance of the gut microbiota across the lakes, some shared bacterial communities were detected.ConclusionsIn summary, this study showed the indirect influence of altitude on gut microbiota. Altitude has the potential to modulate the gut microbiota composition and diversity of Nile tilapia. Future work will be needed to elucidate the functional significance of gut microbiota variations based on the geographical environment.Significance and impact of the studyOur study determined the composition and diversity of the gut microbiota in Nile tilapia collected from lakes across an altitude gradient. Our findings greatly extend the baseline knowledge of fish gut microbiota in Ethiopian lakes that plays an important role in this species sustainable aquaculture activities and conservation.
Association between post-extubation upper airway obstruction symptoms and airway size measured by computed tomography: a single-center observational study
Authors: Shinohara Mafumi , Iwashita Masayuki , Abe Takeru , Takeuchi Ichiro 
Published: March 2022

Abstract
Background
Computed tomography (CT) is often performed to assess patients; however, little is known about how airway size measured by CT scan imaging might influence the occurrence of post-extubation upper airway obstruction.

Methods
This study aimed to evaluate the association between airway size measured by CT and the incidence of post-extubation upper airway obstruction symptoms for each sex. This single-center observational study was conducted at a tertiary emergency medical center/severe trauma center with a 12-bed intensive care unit. We enrolled consecutive adult patients (aged ≥ 20 years), who were intubated in the emergency room, between January 2016 and March 2019. Patients who underwent a CT scan of the glottic region within three hours before and after intubation were included in the analysis. For each sex, we first divided the patients into two groups: those who had post-extubation stridor, hoarseness, or both and those who had no such symptoms. Then, we compared the two groups using the Mann–Whitney U test and Fisher’s exact test. Univariate and multivariate logistic regression analyses were also performed.

Results
During the 39 months, 855 patients were enrolled in this study. A total of 217 patients underwent CT of the glottic region within three hours before and after intubation. Five patients had no records of symptoms after extubation. Thus, we analyzed data from 212 patients. This study included 144 males and 68 females. In female patients, the median [inter-quartile range] (average) of the transverse diameter of the glottis/endotracheal tube outer diameter (OD) ratio was smaller in patients with post-extubation upper airway obstruction symptoms than in patients without the symptoms (1.00 [1.00–1.00] (0.9572) vs. 1.00 [1.00–1.00] (1.00296), respectively; p = .013). Multivariate logistic regression analysis showed that the glottis/tube OD ratio < 1 was associated with the symptoms in females (odds ratio: 95% confidence interval, 5.68: 1.04–30.97). There was no relation between the airway sizes and the symptoms in male patients.

Conclusions
In female patients, no gap between the endotracheal tube and the vocal codes or the glottic transverse diameter being smaller than the endotracheal tube OD on CT scan was associated with post-extubation upper airway obstruction symptoms.
Profile and dynamics of infectious diseases: a population-based observational study using multi-source big data
Authors: Zhao Lin , Wang Hai-Tao , Ye Run-Ze , Li Zhen-Wei , Wang Wen-Jing , Wei Jia-Te , Du Wan-Yu , Yin Chao-Nan , Wang Shan-Shan , Liu Jin-Yue , Ji Xiao-Kang , Wang Yong-Chao , Cui Xiao-Ming , Liu Xue-Yuan , Li Chun-Yu , Qi Chang , Liu Li-Li , Li Xiu-Jun , Xue Fu-Zhong , Cao Wu-Chun 
Published: April 2022

Abstract
Background
The current surveillance system only focuses on notifiable infectious diseases in China. The arrival of the big-data era provides us a chance to elaborate on the full spectrum of infectious diseases.

Methods
In this population-based observational study, we used multiple health-related data extracted from the Shandong Multi-Center Healthcare Big Data Platform from January 2013 to June 2017 to estimate the incidence density and describe the epidemiological characteristics and dynamics of various infectious diseases in a population of 3,987,573 individuals in Shandong province, China.

Results
In total, 106,289 cases of 130 infectious diseases were diagnosed among the population, with an incidence density (ID) of 694.86 per 100,000 person-years. Besides 73,801 cases of 35 notifiable infectious diseases, 32,488 cases of 95 non-notifiable infectious diseases were identified. The overall ID continuously increased from 364.81 per 100,000 person-years in 2013 to 1071.80 per 100,000 person-years in 2017 (χ2 test for trend, P < 0.0001). Urban areas had a significantly higher ID than rural areas, with a relative risk of 1.25 (95% CI 1.23–1.27). Adolescents aged 10–19 years had the highest ID of varicella, women aged 20–39 years had significantly higher IDs of syphilis and trichomoniasis, and people aged ≥ 60 years had significantly higher IDs of zoster and viral conjunctivitis (all P < 0.05).

Conclusions
Infectious diseases remain a substantial public health problem, and non-notifiable diseases should not be neglected. Multi-source-based big data are beneficial to better understand the profile and dynamics of infectious diseases.
Evaluation of the SMARTCHEK Genesystem RT-qPCR assay for the detection of SARS-CoV-2 in clinical samples
Authors: Flores-León Diana , Quino Willi , Cúneo Alejandra E. , Caro-Castro Junior , Cucho-Meza Evans , Gavilan Ronnie G. 
Published: April 2022

Abstract
Background
The COVID-19 pandemic remains the main public health problem, due to the quick and easy dissemination of the causal agent, SARS-CoV-2 virus, around the world. Since the beginning of the pandemic, an opportune laboratory diagnosis has been critical to respond this emergency, and RT-qPCR has been used as reference molecular tests for detection of SARS-CoV-2.

Methods
In this study, we performed the evaluation of a RT-qPCR SMARTCHEK platform (SMARTCHEK, Genesystem) for SARS-CoV-2 detection based on the amplification of RdRp and N gene markers. The platform was evaluated with nasopharyngeal swab samples corresponding to 360 suspected cases of COVID-19 which were remitted to Instituto Nacional de Salud in Peru. This quick method was compared with conventional RT-qPCR as gold standard.

Results
The RT-qPCR SMARTCHEK showed a 98.1% sensitivity (CI: 93.3–99.8%), a 98.8% specificity (CI: 96.6–99.8%), a 97.2% positive predictive value (CI: 92–99.4%) and a 99.2% negative predictive value (CI: 97.2—99.9%). The assay demonstrated a strong agreement between the RT-qPCR SMARTCHEK and conventional RT-qPCR (kappa value ≥ 0.966).

Conclusion
The RT-qPCR SMARTCHEK is a platform that gives reliable and fast results, with high sensitivity and specificity for the detection of SARS-CoV-2, and it will be considered a suitable alternative to COVID-19 diagnosis in low-resource settings.