bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of cerebrospinal fluid biomarkers for parkinsonism using a proteomics approach
Authors: Marques Tainá M. , van Rumund Anouke , Kersten Iris , Bruinsma Ilona B. , Wessels Hans J.C.T. , Gloerich Jolein , Kaffa Charlotte , Esselink Rianne A. J. , Bloem Bastiaan R. , Kuiperij H. Bea , Verbeek Marcel M. 
Published: November 2021

AbstractThe aim of our study was to investigate cerebrospinal fluid (CSF) tryptic peptide profiles as potential diagnostic biomarkers for the discrimination of parkinsonian disorders. CSF samples were collected from individuals with parkinsonism, who had an uncertain diagnosis at the time of inclusion and who were followed for up to 12 years in a longitudinal study. We performed shotgun proteomics to identify tryptic peptides in CSF of Parkinson’s disease (PD, n = 10), multiple system atrophy patients (MSA, n = 5) and non-neurological controls (n = 10). We validated tryptic peptides with differential levels between PD and MSA using a newly developed selected reaction monitoring (SRM) assay in CSF of PD (n = 46), atypical parkinsonism patients (AP; MSA, n = 17; Progressive supranuclear palsy; n = 8) and non-neurological controls (n = 39). We identified 191 tryptic peptides that differed significantly between PD and MSA, of which 34 met our criteria for SRM development. For 14/34 peptides we confirmed differences between PD and AP. These tryptic peptides discriminated PD from AP with moderate-to-high accuracy. Random forest modelling including tryptic peptides plus either clinical assessments or other CSF parameters (neurofilament light chain, phosphorylated tau protein) and age improved the discrimination of PD vs. AP. Our results show that the discovery of tryptic peptides by untargeted and subsequent validation by targeted proteomics is a suitable strategy to identify potential CSF biomarkers for PD versus AP. Furthermore, the tryptic peptides, and corresponding proteins, that we identified as differential biomarkers may increase our current knowledge about the disease-specific pathophysiological mechanisms of parkinsonism.
Modeling a primate technological niche
Authors: Reeves Jonathan S. , Proffitt Tomos , Luncz Lydia V. 
Published: November 2021

AbstractThe ability to modify the environment through the transport of tools has been instrumental in shaping the evolutionary success of humans. Understanding the cause-and-effect relationships between hominin behavior and the environment ultimately requires understanding of how the archaeological record forms. Observations of living primates can shed light on these interactions by investigating how tool-use behaviors produce a material record within specific environmental contexts. However, this requires reconciling data derived from primate behavioral observations with the time-averaged nature of the Plio-Pleistocene archaeological record. Here, we use an agent-based model to investigate how repeated short-distance transport events, characteristic for primate tool use, can result in significant landscape-scale patterning of material culture over time. Our results illustrate the conditions under which accumulated short-distance transport bouts can displace stone tools over long distances. We show that this widespread redistribution of tools can also increase access to tool require resources over time. As such, these results elucidate the niche construction processes associated with this pattern of tool transport. Finally, the structure of the subsequent material record largely depends on the interaction between tool transport and environmental conditions over time. Though these results have implications for inferring hominin tool transports from hominin archaeological assemblages. Furthermore, they highlight the difficulties with connecting specific behavioral processes with the patterning in the archaeological record.
Optimising metameric spectra for integrative lighting to modulate the circadian system without affecting visual appearance
Authors: Zandi Babak , Stefani Oliver , Herzog Alexander , Schlangen Luc J. M. , Trinh Quang Vinh , Khanh Tran Quoc 
Published: November 2021

AbstractSmart integrative lighting systems aim to support human health and wellbeing by capitalising on the light-induced effects on circadian rhythms, sleep, and cognitive functions, while optimising the light’s visual aspects like colour fidelity, visual comfort, visual preference, and visibility. Metameric spectral tuning could be an instrument to solve potential conflicts between the visual preferences of users with respect to illuminance and chromaticity and the circadian consequences of the light exposure, as metamers can selectively modulate melanopsin-based photoreception without affecting visual properties such as chromaticity or illuminance. This work uses a 6-, 8- and 11-channel LED luminaire with fixed illuminance of 250 lx to systematically investigate the metameric tuning range in melanopic equivalent daylight illuminance (EDI) and melanopic daylight efficacy ratio (melanopic DER) for 561 chromaticity coordinates as optimisation targets (2700 K to 7443 K ± Duv 0 to 0.048), while applying colour fidelity index Rf criteria from the TM-30-20 Annex E recommendations (i.e. Rf$$\ge$$
≥
85, Rf,h1$$\ge$$
≥
85). Our results reveal that the melanopic tuning range increases with rising CCT to a maximum tuning range in melanopic DER of 0.24 (CCT: 6702 K, Duv: 0.003), 0.29 (CCT: 7443 K, Duv: 0) and 0.30 (CCT: 6702, Duv: 0.006), depending on the luminaire’s channel number of 6, 8 or 11, respectively. This allows to vary the melanopic EDI from 212.5–227.5 lx up to 275–300 lx without changes in the photopic illuminance (250 lx) or chromaticity ($$\Delta u'v'$$

Δ

u
′

v
′

$$\le$$
≤
0.0014). The highest metameric melanopic Michelson contrast for the 6-, 8- and 11-channel luminaire is 0.16, 0.18 and 0.18, which is accomplished at a CCT of 3017 K (Duv: − 0.018), 3456 K (Duv: 0.009) and 3456 K (Duv: 0.009), respectively. By optimising ~ 490,000 multi-channel LED spectra, we identified chromaticity regions in the CIExy colour space that are of particular interest to control the melanopic efficacy with metameric spectral tuning.
Clinical strategy of repeat biopsy in patients with atypical small acinar proliferation (ASAP)
Authors: Kim Hwanik , Kim Jung Kwon , Choe Gheeyoung , Hong Sung Kyu 
Published: November 2021

AbstractAtypical small acinar proliferation (ASAP) occurs in approximately 5% of prostate biopsies. Approximately 30–40% of patients with ASAP have biopsy detectable prostate cancer (PCa) within 5 years. Current guidelines recommend a repeat biopsy within 3–6 months after the initial diagnosis. The aim of the present study was to examine the association between ASAP and subsequent diagnosis of clinically significant PCa (csPCa). The need for immediate repeat biopsy was also evaluated. We identified 212 patients with an ASAP diagnosis on their first biopsy at our institution between February 2006 and March 2018. Of these patients, 102 (48.1%) had at least one follow-up biopsy. Clinicopathologic features including rates of subsequent PCa and csPCa were assessed. Thirty-five patients subsequently underwent radical prostatectomy (RP). Their pathologic results were reviewed. csPCa was defined as the presence of Gleason score (GS) ≥ 3 + 4 in ≥ 1 biopsy core. Adverse pathology (AP) was defined as high-grade (primary Gleason pattern ≥ 4) or non-organ-confined disease (pT3/N1) after RP. Of 102 patients, 87 (85.3%), 13 (12.7%), and 2 (2.0%) had one, two, and three follow-up biopsies, respectively. Median time from the initial ASAP diagnosis to the 2nd follow-up biopsy and the last follow-up biopsy were 21.9 months (range 1–129 months) and 27.7 months (range 1–129 months), respectively. Of these patients, 46 (45.1%) were subsequently diagnosed with PCa, including 20 (19.6%) with csPCa. Only 2 (2.0%) patients had GS ≥ 8 disease. Five (4.9%) patients had number of positive cores > 3. Of 35 patients who subsequently underwent RP, seven (20%) had AP after RP and 17 (48.6%) showed GS upgrading. Of these 17 patients, the vast majority (16/17, 94.1%) had GS upgrading from 3 + 3 to 3 + 4. 45.1% of patients with an initial diagnosis of ASAP who had repeat prostate biopsy were subsequently diagnosed with PCa and 19.6% were found to have csPCa. Our findings add further evidence that after a diagnosis of ASAP, a repeat biopsy is warranted and that the repeat biopsy should not be postponed.
Seasonal and spatial patterns of eukaryotic phytoplankton communities in an urban river based on marker gene
Authors: Yang Jing , Lv Junping , Liu Qi , Nan Fangru , Li Bo , Xie Shulian , Feng Jia 
Published: November 2021

AbstractThe seasonal and spatial eukaryotic phytoplankton composition in the Fenhe River was investigated based on the 18S rDNA V4 region. The relationship between phytoplankton functional groups and environmental factors was explored to effectively capture the responses of these taxa to environmental gradients and their effects on ecosystem function. Our results indicated that the Chlorophyta and Bacillariophyta had higher relative abundance than other taxa, and their diversity and richness indices in spring were higher than those in other seasons. The linear discriminant analysis effect size (LEfSe) analyses detected that the potential seasonal biomarkers included Desmodesmus, Cyclotella, Pseudoschroederia, Discostella, Scenedesmus, Monoraphidium, and Nannochloropsis; the spatial biomarkers included Amphora, Neochloris, Hindakia, Pseudomuriella, Coccomyxa, Chloroidium, Scherffelia, Chromochloris, and Scotinosphaera. The systemic evolution and distribution characteristics of the first 50 representative sequences showed that the dominant genus included Desmodesmus in spring, Pseudopediastrum in summer, Mychonastes in autumn, and Monoraphidium in winter. Main seasonal variation of phytoplankton functional groups was as follows: spring (J + F + C + X1) → summer (J + F + X1 + X2) → autumn (J + F + X1 + C) → winter (X1 + J + B + X2). Pearson correlation, redundancy analysis, and variance partitioning analysis showed temperature and phosphate were the determining factors causing the changes of phytoplankton functional groups and community composition in the Fenhe River.
A hydrated 2,3-diaminophenazinium chloride as a promising building block against SARS-CoV-2
Authors: Mahato Rajani Kanta , Mahanty Ayan Kumar , Kotakonda Muddukrishnaiah , Prasad Sunnapu , Bhattacharyya Subires , Biswas Bhaskar 
Published: November 2021

AbstractPhenazine scaffolds are the versatile secondary metabolites of bacterial origin. It functions in the biological control of plant pathogens and contributes to the producing strains ecological fitness and pathogenicity. In the light of the excellent therapeutic properties of phenazine, we have synthesized a hydrated 2,3-diaminophenazinium chloride (DAPH+Cl−·3H2O) through direct catalytic oxidation of o-phenylenediamine with an iron(III) complex, [Fe(1,10-phenanthroline)2Cl2]NO3 in ethanol under aerobic condition. The crystal structure, molecular complexity and supramolecular aspects of DAPH+Cl− were confirmed and elucidated with different spectroscopic methods and single crystal X-ray structural analysis. Crystal engineering study on DAPH+Cl− exhibits a fascinating formation of (H2O)2…Cl−…(H2O) cluster and energy framework analysis of defines the role of chloride ions in the stabilization of DAPH+Cl−. The bactericidal efficiency of the compound has been testified against few clinical bacteria like Streptococcus pneumoniae, Escherichia coli, K. pneumoniae using the disc diffusion method and the results of high inhibition zone suggest its excellent antibacterial properties. The phenazinium chloride exhibits a significant percentage of cell viability and a considerable inhibition property against SARS-CoV-2 at non-cytotoxic concentration compared to remdesivir. Molecular docking studies estimate a good binding propensity of DAPH+Cl− with non-structural proteins (nsp2 and nsp7-nsp-8) and the main protease (Mpro) of SARS-CoV-2. The molecular dynamics simulation studies attribute the conformationally stable structures of the DAPH+Cl− bound Mpro and nsp2, nsp7-nsp8 complexes as evident from the considerable binding energy values, − 19.2 ± 0.3, − 25.7 ± 0.1, and − 24.5 ± 0.7 kcal/mol, respectively.
Comparison of optical coherence tomography angiography metrics in primary angle-closure glaucoma and normal-tension glaucoma
Authors: Shen Ruyue , Wang Yu Meng , Cheung Carol Y. , Chan Poemen P. , Tham Clement C. 
Published: November 2021

AbstractTo investigate the peripapillary vascular metrics in early normal tension glaucoma (NTG) and early primary angle closure glaucoma (PACG) eyes using optical coherence tomography angiography (OCT-A). One or both eyes of each subject were imaged for a 3 × 3 mm peripapillary region by swept-source OCT-A (DRI-OCT Triton, Topcon, Japan) and assessed by an automated MATLAB program. OCT-A metrics including circumpapillary vessel density (cpVD) and fractal dimension (cpFD) were compared. Their association with visual field (VF) parameters and retinal nerve fiber layer (RNFL) thickness were determined. Sixty-eight eyes of 51 PACG, 68 eyes of 48 NTG, and 68 eyes of 49 control subjects were cross-sectionally analyzed. NTG eyes had significantly lower global cpVD (52.369 ± 0.781%) compared with PACG eyes (55.389 ± 0.721%, P = 0.004) that had comparable disease severity and average RNFL thickness. Multivariable analysis revealed that, for PACG and NTG eyes, decreased cpVD ([PACG] β = −4.242; CI: −8.120, −0.363 vs [NTG] β = −5.531; CI: −9.472, −1.590) and cpFD ([PACG] β = −8.894;CI: −11.925, −5.864 vs [NTG] β = −12.064; CI: −17.095, −6.932) were associated with decreased RNFL thickness (all P ≤ 0.032); with a stronger association between decrease cpFD and decreased RNFL thickness in NTG eyes (P = 0.028). Decreased cpVD was associated with decrease mean deviation (MD) in NTG eyes (β = −0.707; CI: −1.090, −0.324; P ≤ 0.001) and not associated with the visual field parameters in PACG eyes. Early NTG had lower global cpVD compared with early PACG, despite similar disease severity and average RNFL thickness.
Predicting sensitivity of recently harvested tomatoes and tomato sepals to future fungal infections
Authors: Brdar Sanja , Panić Marko , Hogeveen-van Echtelt Esther , Mensink Manon , Grbović Željana , Woltering Ernst , Chauhan Aneesh 
Published: November 2021

AbstractTomato is an important commercial product which is perishable by nature and highly susceptible to fungal incidence once it is harvested. Not all tomatoes are equally vulnerable to pathogenic fungi, and an early detection of the vulnerable ones can help in taking timely preventive actions, ranging from isolating tomato batches to adjusting storage conditions, but also in making right business decisions like dynamic pricing based on quality or better shelf life estimate. More importantly, early detection of vulnerable produce can help in taking timely actions to minimize potential post-harvest losses. This paper investigates Near-infrared (NIR) hyperspectral imaging (1000–1700 nm) and machine learning to build models to automatically predict the susceptibility of sepals of recently harvested tomatoes to future fungal infections. Hyperspectral images of newly harvested tomatoes (cultivar Brioso) from 5 different growers were acquired before the onset of any visible fungal infection. After imaging, the tomatoes were placed under controlled conditions suited for fungal germination and growth for a 4-day period, and then imaged using normal color cameras. All sepals in the color images were ranked for fungal severity using crowdsourcing, and the final severity of each sepal was fused using principal component analysis. A novel hyperspectral data processing pipeline is presented which was used to automatically segment the tomato sepals from spectral images with multiple tomatoes connected via a truss. The key modelling question addressed in this research is whether there is a correlation between the hyperspectral data captured at harvest and the fungal infection observed 4 days later. Using 10-fold and group k-fold cross-validation, XG-Boost and Random Forest based regression models were trained on the features derived from the hyperspectral data corresponding to each sepal in the training set and tested on hold out test set. The best model found a Pearson correlation of 0.837, showing that there is strong linear correlation between the NIR spectra and the future fungal severity of the sepal. The sepal specific predictions were aggregated to predict the susceptibility of individual tomatoes, and a correlation of 0.92 was found. Besides modelling, focus is also on model interpretation, particularly to understand which spectral features are most relevant to model prediction. Two approaches to model interpretation were explored, feature importance and SHAP (SHapley Additive exPlanations), resulting in similar conclusions that the NIR range between 1390–1420 nm contributes most to the model’s final decision.
The meta-gut: community coalescence of animal gut and environmental microbiomes
Authors: Dutton Christopher L. , Subalusky Amanda L. , Sanchez Alvaro , Estrela Sylvie , Lu Nanxi , Hamilton Stephen K. , Njoroge Laban , Rosi Emma J. , Post David M. 
Published: November 2021

AbstractAll animals carry specialized microbiomes, and their gut microbiota are continuously released into the environment through excretion of waste. Here we propose the meta-gut as a novel conceptual framework that addresses the ability of the gut microbiome released from an animal to function outside the host and alter biogeochemical processes mediated by microbes. We demonstrate this dynamic in the hippopotamus (hippo) and the pools they inhabit. We used natural field gradients and experimental approaches to examine fecal and pool water microbial communities and aquatic biogeochemistry across a range of hippo inputs. Sequencing using 16S RNA methods revealed community coalescence between hippo gut microbiomes and the active microbial communities in hippo pools that received high inputs of hippo feces. The shared microbiome between the hippo gut and the waters into which they excrete constitutes a meta-gut system that could influence the biogeochemistry of recipient ecosystems and provide a reservoir of gut microbiomes that could influence other hosts. We propose that meta-gut dynamics may also occur where other animal species congregate in high densities, particularly in aquatic environments.
Distinct microbiome profiles and biofilms in Leishmania donovani-driven cutaneous leishmaniasis wounds
Authors: Jayasena Kaluarachchi T. D. , Campbell Paul M. , Wickremasinghe Rajitha , Ranasinghe Shalindra , Wickremasinghe Renu , Yasawardene Surangi , De Silva Hiromel , Menike Chandrani , Jayarathne M. C. K. , Jayathilake Subodha , Dilhari Ayomi , McBain Andrew J. , Weerasekera Manjula M. 
Published: November 2021

AbstractThe endemic strain of Leishmania donovani in Sri Lanka causes cutaneous leishmaniasis (CL) rather than more common visceral form. We have visualized biofilms and profiled the microbiome of lesions and unaffected skin in thirty-nine CL patients. Twenty-four lesions (61.5%) were biofilm-positive according to fluorescence in situ hybridization. Biopsies of biofilm-positive lesions were dominated by Pseudomonas, class Bacilli and Enterobacteriaceae and distinguished by significantly lower community evenness. Higher relative abundance of a class Bacilli OTU was detected in wound swabs versus contralateral skin. Wound swabs and biopsies had significantly distinct microbiome profiles and lower diversity compared to unaffected skin. Greater abundances of potentially pathogenic organisms were observed in wet ulcers, lesions with high parasite loads and large wounds. In summary, more than half of L. donovani associated CL wounds harboured biofilms and the wounds exhibited a distinct, less diverse, microbiome than unaffected skin.
HIV indirectly accelerates coronary artery disease by promoting the effects of risk factors: longitudinal observational study
Authors: Kolossváry Márton , Celentano David , Gerstenblith Gary , Bluemke David A. , Mandler Raul N. , Fishman Elliot K. , Bhatia Sandeepan , Chen Shaoguang , Lai Shenghan , Lai Hong 
Published: November 2021

AbstractOur objective was to assess whether human immunodeficiency virus (HIV)-infection directly or indirectly promotes the progression of clinical characteristics of coronary artery disease (CAD). 300 African Americans with asymptomatic CAD (210 male; age: 48.0 ± 7.2 years; 226 HIV-infected) who underwent coronary CT angiography at two time points (mean follow-up: 4.0 ± 2.3 years) were randomly selected from 1429 participants of a prospective epidemiological study between May 2004 and August 2015. We calculated Agatston-scores, number of coronary plaques and segment stenosis score (SSS). Linear mixed models were used to assess the effects of HIV-infection, atherosclerotic cardiovascular disease (ASCVD) risk, years of cocaine use on CAD. There was no significant difference in annual progression rates between HIV-infected and—uninfected regarding Agatston-scores (10.8 ± 25.1/year vs. 7.2 ± 17.8/year, p = 0.17), the number of plaques (0.2 ± 0.3/year vs. 0.3 ± 0.5/year, p = 0.11) or SSS (0.5 ± 0.8/year vs. 0.5 ± 1.3/year, p = 0.96). Multivariately, HIV-infection was not associated with Agatston-scores (8.3, CI: [− 37.2–53.7], p = 0.72), the number of coronary plaques (− 0.1, CI: [− 0.5–0.4], p = 0.73) or SSS (− 0.1, CI: [− 1.0–0.8], p = 0.84). ASCVD risk scores and years of cocaine-use significantly increased all CAD outcomes among HIV-infected individuals, but not among HIV-uninfected. Importantly, none of the HIV-medications were associated with any of the CAD outcomes. HIV-infection is not directly associated with CAD and therefore HIV-infected are not destined to have worse CAD profiles. However, HIV-infection may indirectly promote CAD progression as risk factors may have a more prominent role in the acceleration of CAD in these patients.
A single baroreceptor unit consists of multiple sensors
Authors: Liu Jun , Song Nana , Wang Yufang , Walker Jerome , Yu Jerry 
Published: November 2021

AbstractArterial baroreceptors (BRs) play a vital role in the regulation of the cardiopulmonary system. What is known about how these sensors operate at the subcellular level is limited, however. Until recently, one afferent axon was considered to be connected to a single baroreceptor (one-sensor theory). However, in the lung, a single airway mechanosensory unit is now known to house many sensors (multiple-sensor theory). Here we tested the hypothesis that multiple-sensor theory also operates in BR units, using both morphological and electrophysiological approaches in rabbit aortic arch (in whole mount) labeled with Na+/K+-ATPase, as well as myelin basic protein antibodies, and examined microscopically. Sensory structures presented in compact clusters, similar to bunches of grapes. Sensory terminals, like those in the airways, formed leaf-like or knob-like expansions. That is, a single myelinated axon connected with multiple sensors forming a network. We also recorded single-unit activities from aortic baroreceptors in the depressor nerve in anesthetized rabbits and examined the unit response to a bolus intravenous injection of phenylephrine. Unit activity increased progressively as blood pressure (BP) increased. Five of eleven units abruptly changed their discharge pattern to a lower activity level after BP attained a plateau for a minute or two (when BP was maintained at the high level). These findings clearly show that the high discharge baroreceptor deactivates after over-excitation and unit activity falls to a low discharge sensor. In conclusion, our morphological and physiological data support the hypothesis that multiple-sensory theory can be applied to BR units.