bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neurofilament Light Chain Is a Novel Biomarker for Major Depression and Related Executive Dysfunction
Authors: Chen Mu-Hong , Liu Yu-Li , Kuo Hsiang-Wei , Tsai Shih-Jen , Hsu Ju-Wei , Huang Kai-Lin , Tu Pei-Chi , Bai Ya-Mei 
Published: October 2021

Abstract

Background
Evidence suggests that major depressive disorder is related to neuroaxonal injury and that neurofilament light chain (NfL) is a biomarker of neuroaxonal injury. In addition, proinflammatory cytokines have been reported to be associated with major depression and neuroaxonal injury.

Methods
Forty patients with major depression and 40 age- and sex-matched healthy control participants were enrolled for the measurement of NfL and proinflammatory cytokines and assessment of executive function. General linear models were used to examine the association between NfL levels, proinflammatory cytokine levels, and executive function.

Results
Patients with major depressive disorder exhibited significantly higher NfL levels (P = .007) than the control participants. NfL levels were positively related to log-transformed levels of tumor necrosis factor-α (P = .004). Higher levels of NfL (P = .002) and tumor necrosis factor-α (P = .013) were associated with greater deficits in executive function.

Discussion
NfL was a novel biomarker for major depressive disorder and related executive dysfunction. Further studies are necessary to elucidate the role of NfL in the pathophysiology of major depression and related cognitive impairment.
Computerized decision support system (CDSS) use for surveillance of antimicrobial resistance in urinary tract infections in primary care
Authors: Delory Tristan , Le Bel Josselin , Lariven Sylvie , Peiffer-Smadja Nathan , Lescure François-Xavier , Bouvet Elisabeth , Jeanmougin Pauline , Tubach Florence , Boëlle Pierre-Yves 
Published: October 2021

Abstract

Background
Hospital-based surveillance of antimicrobial resistance may be irrelevant as a guide to antimicrobial use for urinary tract infections (UTIs) in primary care.

Objectives
To highlight the value of online computerized decision support systems (CDSS) in providing information on the surveillance of antimicrobial resistance in community-acquired UTIs.

Methods
We collected the susceptibility profile for key antibiotics by type of UTI involving Escherichia coli from 2017 to 2020, using queries for UTI (Q-UTI) submitted to a French CDSS. We compared these results with those from the MedQual French surveillance system for community-acquired UTI and the European Antimicrobial Resistance Surveillance Network (EARS-NET) for invasive infections.

Results
We collected 43 591 Q-UTI, of which 10 192 (23%) involved E. coli: 40% cystitis, 32% male-UTI, and 27% pyelonephritis. Resistance was 41.3% (95% CI, 40.3%–42.2%) for amoxicillin, 16.6% (95% CI, 15.9%–17.3%) for fluoroquinolones, 6.6% (95% CI, 6.1%–7.0%) for third-generation cephalosporins (3GC), and 5.7% (95% CI, 5.2%–6.1%) for aminoglycosides. Resistance to amoxicillin was lower than that reported in MedQual (42.7%, P value = 0.004), and in EARS-NET (55.2%, P value &lt; 0.001). For fluoroquinolones, resistance was higher than in MedQual (12.0%, P value &lt; 0.001) and EARS-NET (15.8%, P value = 0.041). In complicated pyelonephritis and male UTI, fluoroquinolone resistance peaked at ∼20%. For 3GC, all UTI had higher resistance than in MedQual (3.5%, P value &lt; 0.001), but lower than in EARS-NET (9.5%, P value &lt; 0.001). Aminoglycoside resistance was not reported by MedQual, and was lower than in EARS-NET (7.1%, P value &lt; 0.001).

Conclusions
CDSS can inform prescribers in real-time about the ecology and surveillance of E. coli resistance in community-acquired UTI. In complicated upper UTIs, they can underline the risk of empirical use of fluoroquinolones and suggest preferential use of 3GC.
Detecting Autoantibodies by Multiparametric Assays: Impact on Prevention, Diagnosis, Monitoring, and Personalized Therapy in Autoimmune Diseases
Authors: Cinquanta Luigi , Infantino Maria , Bizzaro Nicola 
Published: October 2021

Abstract

Background
The introduction of multiparametric autoantibody tests has been proposed to improve the accuracy of the immunological diagnosis of autoimmune diseases (AID) and to accelerate time for completing the diagnostic process. Multiplex tests are capable of detecting many autoantibodies in a single run whereas a traditional immunoassay uses a single antigen to detect only a single specificity of autoantibodies. The reasons why multiplex tests could replace conventional immunoassays lie in the evidence that they allow for more efficient handling of large numbers of samples by the laboratory, while ensuring greater diagnostic sensitivity in AID screening.

Content
This review aims to highlight the important role that multiparametric tests could assume when designed for defined profiles they are used not only for diagnostic purposes but also to predict the onset of AID to identify clinical phenotypes and to define prognosis. Furthermore, differences in the antibody profile could identify which subjects will be responsive or not to a specific pharmacological treatment.

Summary
The use of autoantibody profiles, when specifically requested and performed with clinically validated technologies, can represent a significant step toward personalized medicine in autoimmunology.
The role of invasion and urbanization gradients in shaping avian community composition
Authors: Rogers Andrew M , Griffin Andrea S , Lermite Françoise , van Rensburg Berndt , Archibald Carla , Kark Salit 
Published: October 2021

Abstract
The extent to which native species utilize urban environments depends on species responses to multiple threatening processes. Here, we aimed to quantify changes in bird communities in response to changing habitat structure, invasive species and aggressive native species. We conducted surveys in two independently invaded regions with similar patterns of urban development. The study regions were New South Wales (NSW) and Queensland (QLD), Australia. We observed 127 species in NSW and 144 species in QLD. Most species (NSW 83 and QLD 84) are urban adapters making use of some or all urban sub-environments. Urban avoiders, species only found in remnant vegetation, were the second largest group (urban avoiders: NSW 23 and QLD 31). We found the lowest richness in the most urban sites (urban exploiters: NSW 10 and QLD 15). Using generalized linear mixed models, we found a non-significant relationship between species richness and the abundance of aggressive species like the common myna and noisy miners, Manorina melanocephala, but a significant positive correlation with the percentage of shrub cover at a site. As there is a gradual loss of species with increasing urbanization, retaining higher complexity in vegetation structure in urban areas will support large numbers of species and could help mitigate the potential impacts of aggressive urban-adapted species and habitat loss.
Glucose regulates cotton fiber elongation by interacting with brassinosteroid
Authors: Li Xinyang , Liu Wei , Ren Zhongying , Wang Xingxing , Liu Ji , Yang Zuoren , Zhao Junjie , Pei Xiaoyu , Liu Yangai , He Kunlun , Zhang Fei , Zhang Zhiqiang , Yang Daigang , Ma Xiongfeng , Li Wei 
Published: October 2021

Abstract
In plants, glucose (Glc) plays important roles, as a nutrient and signal molecule, in the regulation of growth and development. However, the function of Glc in fiber development of upland cotton (Gossypium hirsutum) is unclear. Here, using gas chromatography-mass spectrometry (GC-MS), we found that the Glc content in fibers was higher than that in ovules during the fiber elongation stage. In vitro ovule culture revealed that lower Glc concentrations promoted cotton fiber elongation, while higher concentrations had inhibitory effects. The hexokinase inhibitor N-acetylglucosamine (NAG) inhibited cotton fiber elongation in the cultured ovules, indicating that Glc-mediated fiber elongation depends on the Glc signal transduced by hexokinase. RNA sequencing (RNA-seq) analysis and hormone content detection showed that 150mM Glc significantly activated brassinosteroid (BR) biosynthesis, and the expression of signaling-related genes was also increased, which promoted fiber elongation. In vitro ovule culture clarified that BR induced cotton fiber elongation in a dose-dependent manner. In hormone recovery experiments, only BR compensated for the inhibitory effects of NAG on fiber elongation in a Glc-containing medium. However, the ovules cultured with the BR biosynthetic inhibitor brassinazole and from the BR-deficient cotton mutant pag1 had greatly reduced fiber elongation at all the Glc concentrations tested. This demonstrates that Glc does not compensate for the inhibition of fiber elongation caused by BR biosynthetic defects, suggesting that the BR signaling pathway works downstream of Glc during cotton fiber elongation. Altogether, our study showed that Glc plays an important role in cotton fibre elongation, and crosstalk occurs between Glc and BR signaling during modulation of fiber elongation.
The tidal evolution of the Fornax dwarf spheroidal and its globular clusters
Authors: Borukhovetskaya Alexandra , Errani Raphaël , Navarro Julio F , Fattahi Azadeh , Santos-Santos Isabel 
Published: October 2021

ABSTRACT
The dark matter content of the Fornax dwarf spheroidal galaxy inferred from its kinematics is substantially lower than expected from LCDM cosmological simulations. We use N-body simulations to examine whether this may be the result of Galactic tides. We find that, despite improved proper motions from the Gaia mission, the pericentric distance of Fornax remains poorly constrained, mainly because its largest velocity component is roughly antiparallel to the solar motion. Translating Fornax’s proper motion into a Galactocentric velocity is, thus, sensitively dependent on Fornax’s assumed distance: the observed distance uncertainty, $\pm 8\,{{\rm per\,cent}}$, implies pericentric distances that vary between rperi ∼ 50 and ∼150 kpc. Our simulations show that for rperi in the lower range of that estimate, an LCDM subhalo with maximum circular velocity Vmax = 40 km s−1 (or virial mass $M_{200}\approx 10^{10}\, \rm M_\odot$, as expected from LCDM) would be tidally stripped to Vmax ∼ 23 km s−1 over 10 Gyr. This would reduce the dark mass within the Fornax stellar half-mass radius to about half its initial value, bringing it into agreement with observations. Tidal stripping affects mainly Fornax’s dark matter halo; its stellar component is affected little, losing less than $5\,{{\rm per\,cent}}$ of its initial mass in the process. We also explore the effect of Galactic tides on the dynamical friction decay times of Fornax’s population of globular clusters (GCs) and find little evidence for substantial changes, compared with models run in isolation. A population of GCs with initial orbital radii between 1 and 2 kpc is consistent with the present-day spatial distribution of Fornax GCs, despite assuming a cuspy halo. Neither the dark matter content nor the spatial distribution of GCs of Fornax seems inconsistent with a simple model where Fornax inhabits a tidally stripped cuspy cold dark matter halo.
Epoch of reionization power spectrum limits from Murchison Widefield Array data targeted at EoR1 field
Authors: Rahimi M , Pindor B , Line J L B , Barry N , Trott C M , Webster R L , Jordan C H , Wilensky M , Yoshiura S , Beardsley A , Bowman J , Byrne R , Chokshi A , Hazelton B J , Hasegawa K , Howard E , Greig B , Jacobs D , Joseph R , Kolopanis M , Lynch C , McKinley B , Mitchell D A , Murray S , Morales M F , Pober J C , Takahashi K , Tingay S J , Wayth R B , Wyithe J S B , Zheng Q 
Published: October 2021

ABSTRACT
Current attempts to measure the 21 cm power spectrum of neutral hydrogen during the epoch of reionization (EoR) are limited by systematics that produce measured upper limits above both the thermal noise and the expected cosmological signal. These systematics arise from a combination of observational, instrumental, and analysis effects. In order to further understand and mitigate these effects, it is instructive to explore different aspects of existing data sets. One such aspect is the choice of observing field. To date, MWA EoR observations have largely focused on the EoR0 field. In this work, we present a new detailed analysis of the EoR1 field. The EoR1 field is one of the coldest regions of the southern radio sky, but contains the very bright radio galaxy Fornax-A. The presence of this bright extended source in the primary beam of the interferometer makes the calibration and analysis of EoR1 particularly challenging. We demonstrate the effectiveness of a recently developed shapelet model of Fornax-A in improving the results from this field. We also describe and apply a series of data quality metrics that identify and remove systematically contaminated data. With substantially improved source models, upgraded analysis algorithms and enhanced data quality metrics, we determine EoR power spectrum upper limits based on analysis of the best ∼14-h data observed during 2015 and 2014 at redshifts 6.5, 6.8, and 7.1, with the lowest 2σ upper limit at z = 6.5 of Δ2 ≤ (73.78 mK)2 at k = 0.13 h Mpc−1, improving on previous EoR1 measurement results.
AGN orientation through the spectroscopic correlations and model of dusty cone shell
Authors: Lakićević M , Kovačević-Dojčinović J , Popović L Č 
Published: October 2021

ABSTRACT
The differences between Narrow Line Seyfert 1 galaxies (NLS1s) and Broad Line AGNs (BLAGNs) are not completely understood; it is thought that they may have different inclinations and/or physical characteristics. The FWHM(H β)–luminosities correlations are found for NLS1s and their origin is the matter of debate. Here we investigated the spectroscopic parameters and their correlations considering a dusty, cone model of AGN. We apply a simple conical dust distribution (spreading out of broad line region, BLR), assuming that the observed surface of the model is in a good correlation with MIR emission. The dusty cone model in combination with a BLR provides the possibility to estimate luminosity dependence on the cone inclination. The FWHM(H β)–luminosities correlations obtained from model in comparison with observational data show similarities which may indicate the influence of AGN inclination and structure to this correlation. An alternative explanation for FWHM(H β)–luminosities correlations is the selection effect by the black hole mass. These FWHM(H β)–luminosities correlations may be related to the starburst in AGNs, as well. The distinction between spectral properties of the NLS1s and BLAGNs could be caused by multiple effects: beside physical differences between NLS1s and BLAGNs (NLS1s have lighter black hole mass than BLAGNs), inclination of the conical AGN geometry may have important role as well, where NLS1s may be seen in lower inclination angles.
Concordance of multiple methods to define resiliency and vulnerability to sleep loss depends on Psychomotor Vigilance Test metric
Authors: Yamazaki Erika M , Casale Courtney E , Brieva Tess E , Antler Caroline A , Goel Namni 
Published: October 2021

AbstractStudy ObjectivesSleep restriction (SR) and total sleep deprivation (TSD) reveal well-established individual differences in Psychomotor Vigilance Test (PVT) performance. While prior studies have used different methods to categorize such resiliency/vulnerability, none have systematically investigated whether these methods categorize individuals similarly.MethodsForty-one adults participated in a 13-day laboratory study consisting of two baseline, five SR, four recovery, and one 36 h TSD night. The PVT was administered every 2 h during wakefulness. Three approaches (Raw Score [average SR performance], Change from Baseline [average SR minus average baseline performance], and Variance [intraindividual variance of SR performance]), and within each approach, six thresholds (±1 standard deviation and the best/worst performing 12.5%, 20%, 25%, 33%, and 50%) classified Resilient/Vulnerable groups. Kendall’s tau-b correlations examined the concordance of group categorizations of approaches within and between PVT lapses and 1/reaction time (RT). Bias-corrected and accelerated bootstrapped t-tests compared group performance.ResultsCorrelations comparing the approaches ranged from moderate to perfect for lapses and zero to moderate for 1/RT. Defined by all approaches, the Resilient groups had significantly fewer lapses on nearly all study days. Defined by the Raw Score approach only, the Resilient groups had significantly faster 1/RT on all study days. Between-measures comparisons revealed significant correlations between the Raw Score approach for 1/RT and all approaches for lapses.ConclusionThe three approaches defining vigilant attention resiliency/vulnerability to sleep loss resulted in groups comprised of similar individuals for PVT lapses but not for 1/RT. Thus, both method and metric selection for defining vigilant attention resiliency/vulnerability to sleep loss is critical.
An integrative omics approach reveals posttranscriptional mechanisms underlying circadian temperature compensation
Authors: Schmal Christoph , Maier Bert , Ashwal-Fluss Reut , Bartok Osnat , Finger Anna-Marie , Bange Tanja , Koutsouli Stella , Robles Maria S. , Kadener Sebastian , Herzel Hanspeter , Kramer Achim 
Published: October 2021

AbstractA defining property of circadian clocks is temperature compensation, characterized by the resilience of circadian free-running periods against changes in environmental temperature. As an underlying mechanism, the balance or critical reaction hypothesis have been proposed. While the former supposes a temperature-dependent balancing of reactions with opposite effects on circadian period, the latter assumes an insensitivity of certain critical period determining regulations upon temperature changes. Posttranscriptional regulations such as temperature-sensitive alternative splicing or phosphorylation have been described as underlying reactions.Here, we show that knockdown of cleavage and polyadenylation specificity factor subunit 6 (CPSF6), a key regulator of 3’-end cleavage and polyadenylation, abolishes circadian temperature compensation in U-2 OS cells. We apply a combination of 3’-End-RNA-seq and mass spectrometry-based proteomics to globally quantify changes in 3’ UTR length as well as gene and protein expression between wild type and CPSF6 knock-down cells and their dependency on temperature. Analyzing differential responses upon temperature changes in wild type and CPSF6 knockdown cells reveals candidate genes underlying circadian temperature compensation. We identify that eukaryotic translation initiation factor 2 subunit 1 (EIF2S1) is among these candidates. EIF2S1 is known as a master regulator of cellular stress responses that additionally regulates circadian rhythms. We show that knockdown of EIF2S1 furthermore impairs temperature compensation, suggesting that the role of CPSF6 in temperature compensation may be mediated by its regulation of EIF2S1.
A robust receptive field code for optic flow detection and decomposition during self-motion
Authors: Zhang Yue , Huang Ruoyu , Nörenberg Wiebke , Arrenberg Aristides B. 
Published: October 2021

SummaryThe perception of optic flow is essential for any visually guided behaviour of a moving animal. To mechanistically predict behaviour and understand the emergence of self-motion perception in vertebrate brains, it is essential to systematically characterize the motion receptive fields (RFs) of optic flow processing neurons. Here, we present the fine-scale RFs of thousands of motion-sensitive neurons studied in the diencephalon and the midbrain of zebrafish. We found neurons that serve as linear filters and robustly encode directional and speed information of translation-induced optic flow. These neurons are topographically arranged in pretectum according to translation direction. The unambiguous encoding of translation enables the decomposition of translational and rotational self-motion information from mixed optic flow. In behavioural experiments, we successfully demonstrated the predicted decomposition in the optokinetic and optomotor responses. Together, our study reveals the algorithm and the neural implementation for self-motion estimation in a vertebrate visual system.
Phylogenetic analyses for orthogroup-based classification of GDSL-type esterase/lipase (GELP) family in angiosperm representative species
Authors: Alberto Cenci , Mairenys Concepción-Hernández , Angenon Geert , Mathieu Rouard 
Published: October 2021

AbstractGDSL-type esterase/lipase (GELP) enzymes have multiple functions in plants, spanning from developmental processes to the response to biotic and abiotic stresses. Genes encoding GELP belong to a large gene family with several tens to more than hundred members per angiosperm species.Here, we applied iterative phylogenetic analyses to identify 10 main clusters subdivided into 44 expert-curated reference orthogroups (OGs) using three monocot and five dicot genomes. Our results show that some GELP OGs expanded while others were maintained as single copy genes.This semi-automatic approach proves to be effective to characterize large gene families and provides a solid classification framework for the GELP members in angiosperms. The orthogroup-based reference will be useful to perform comparative studies, infer gene functions and better understand the evolutionary history of this gene family.
Application of machine learning methods in clinical trials for precision medicine
Authors: Wang Yizhuo , Carter Bing Z. , Li Ziyi , Huang Xuelin 
Published: October 2021

AbstractObjectiveA key component for precision medicine is a good prediction algorithm for patients’ response to treatments. We aim to implement machine learning (ML) algorithms into the response-adaptive randomization (RAR) design and improve the treatment outcomes.Materials and MethodsWe incorporated nine ML algorithms to model the relationship of patient responses and biomarkers in clinical trial design. Such a model predicted the response rate of each treatment for each new patient and provide guidance for treatment assignment. Realizing that no single method may fit all trials well, we also built an ensemble of these nine methods. We evaluated their performance through quantifying the benefits for trial participants, such as the overall response rate and the percentage of patients who receive their optimal treatments.ResultsSimulation studies showed that the adoption of ML methods resulted in more personalized optimal treatment assignments and higher overall response rates among trial participants. Compared with each individual ML method, the ensemble approach achieved the highest response rate and assigned the largest percentage of patients to their optimal treatments. For the real-world study, we successfully showed the potential improvements if the proposed design had been implemented in the study.ConclusionIn summary, the ML-based RAR design is a promising approach for assigning more patients to their personalized effective treatments, which makes the clinical trial more ethical and appealing. These features are especially desirable for late-stage cancer patients who have failed all the FDA-approved treatment options and only can get new treatments through clinical trials.