TY  - JOUR
AB  - Deep-learning-based classification of pollen grains has been a major driver towards automatic monitoring of airborne pollen. Yet, despite an abundance of available datasets, little effort has been spent to investigate which aspects pose the biggest challenges to the (often black-box- resembling) pollen classification approaches. To shed some light on this issue, we conducted a sample-level difficulty analysis based on the likelihood for one of the largest automatically-generated datasets of pollen grains on microscopy images and investigated the reason for which certain airborne samples and specific pollen taxa pose particular problems to deep learning algorithms. It is here concluded that the main challenges lie in A) the (partly) co-occurring of multiple pollen grains in a single image, B) the occlusion of specific markers through the 2D capturing of microscopy images, and C) for some taxa, a general lack of salient, unique features. Our code is publicly available under https://github.com/millinma/SDPollen
AU  - Milling, M.*
AU  - Rampp, S.D.N.*
AU  - Triantafyllopoulos, A.*
AU  - Plaza, M.P.
AU  - Brunner, J.O.*
AU  - Traidl-Hoffmann, C.
AU  - Schuller, B.W.*
AU  - Damialis, A.*
C1  - 73106
C2  - 56913
TI  - Automating airborne pollen classification: Identifying and interpreting hard samples for classifiers.
JO  - Heliyon
VL  - 11
IS  - 2
PY  - 2025
SN  - 2405-8440
ER  - 

TY  - JOUR
AB  - Bioaerosols, such as pollen and fungal spores, are routinely monitored for agricultural, medical or urban greening practices, but sampling methodology is largely relying on techniques more than half a century old. Moreover, biomonitoring campaigns often take place in urban environments, although sources can be located outside cities’ borders with ampler vegetation. Therefore, the question arises whether we are accurately picturing the biodiversity and abundance of regional bioaerosols and whether those locally detected might derive from long-distance transport, horizontally or vertically. To answer the above, we used novel, mobile monitoring devices, and aerial measurement units, like aircrafts, so as to explore bioaerosol concentrations at a variety of altitudes. An ultralight aircraft was equipped with a sampling device for bioaerosols. The device consisted of duplicate isokinetic impactors that match the physical functioning and the microscopic quantification method of the widely used ground-based Hirst-type impactors. Isokinetic airflow was realized by adjusting the air flux at the impactors’ inlet to the airspeed of the aircraft. Three campaigns were made, where the comparability, efficiency and accuracy of different sampling devices were determined, namely of the abovementioned impactor, and of the mobile conventional Hirst-type pollen sampler. The campaigns involved measurements from ground level (0 m altitude) up to 900 m (above ground level (agl)) via flights. Our results showed that aircraft-based airborne pollen concentration measurements were consistently higher than those of all other devices, regardless of the altitude and sampling time. It is noteworthy that the pollen concentration exceeded 500 pollen grains/m3 at >900 m of altitude, this concentration being 1.77 times higher than that simultaneously measured at ground level. Likewise, the diversity of pollen was also higher at higher altitude. Our results indicate the usability and superiority of small aircraft and high-flow impactors for research, achieving higher biodiversity and abundance over a shorter sampling interval compared to conventional volumetric techniques. Higher pollen amounts at higher altitudes also point at the necessity to monitor bioaerosols across the vertical dimension, especially in densely populated areas and high-traffic air space.
AU  - Plaza, M.P.
AU  - Charalampopoulos, A.*
AU  - Leier-Wirtz, V.*
AU  - Ørby, P.V.*
AU  - Kloster, M.*
AU  - Christiansen, M.D.*
AU  - Traidl-Hoffmann, C.
AU  - Damialis, A.*
AU  - Gosewinkel, U.*
C1  - 72061
C2  - 56359
TI  - Optimisation of bioaerosol sampling using an ultralight aircraft: A novel approach in determining the 3-D atmospheric biodiversity.
JO  - Heliyon
VL  - 10
IS  - 20
PY  - 2024
SN  - 2405-8440
ER  - 

TY  - JOUR
AB  - Growing crops on marginal lands is a promising solution to alleviate the increasing pressure on agricultural land in Europe. Such crops will however be at the same time exposed to increased drought and pathogen prevalence, on already challenging soil conditions. Some sustainable practices, such as Silicon (Si) foliar fertilization, have been proposed to alleviate these two stress factors, but have not been tested under controlled, future climate conditions. We hypothesized that Si foliar fertilization would be beneficial for crops under future climate, and would have cascading beneficial effects on ecosystem processes, as many of them are directly dependent on plant health. We tested this hypothesis by exposing spring barley growing on marginal soil macrocosms (three with, three without Si treatment) to 2070 climate projections in an ecotron facility. Using the high-capacity monitoring of the ecotron, we estimated C, water, and N budgets of every macrocosm. Additionally, we measured crop yield, the biomass of each plant organ, and characterized bacterial communities using metabarcoding. Despite being exposed to water stress conditions, plants did not produce more biomass with the foliar Si fertilization, whatever the organ considered. Evapotranspiration (ET) was unaffected, as well as water quality and bacterial communities. However, in the 10-day period following two of the three Si applications, we measured a significant increase in C sequestration, when climate conditions where significantly drier, while ET remained the same. We interpreted these results as a less significant effect of Si treatment than expected as compared with literature, which could be explained by the high CO2 levels under future climate, that reduces need for stomata opening, and therefore sensitivity to drought. We conclude that making marginal soils climate proof using foliar Si treatments may not be a sufficient strategy, at least in this type of nutrient-poor, dry, sandy soil.
AU  - Rineau, F.*
AU  - Groh, J.*
AU  - Claes, J.*
AU  - Grosjean, K.*
AU  - Mench, M.*
AU  - Moreno-Druet, M.*
AU  - Povilaitis, V.*
AU  - Pütz, T.*
AU  - Rutkowska, B.*
AU  - Schröder, P.
AU  - Soudzilovskaia, N.A.*
AU  - Swinnen, X.*
AU  - Szulc, W.*
AU  - Thijs, S.*
AU  - Vandenborght, J.*
AU  - Vangronsveld, J.*
AU  - Vereecken, H.*
AU  - Verhaege, K.*
AU  - Žydelis, R.*
AU  - Loit, E.*
C1  - 69072
C2  - 53845
CY  - 50 Hampshire St, Floor 5, Cambridge, Ma 02139 Usa
TI  - Limited effects of crop foliar Si fertilization on a marginal soil under a future climate scenario.
JO  - Heliyon
VL  - 10
IS  - 1
PB  - Cell Press
PY  - 2024
SN  - 2405-8440
ER  - 

TY  - JOUR
AB  - Extrachromosomal circular DNA (eccDNA), a pervasive yet enigmatic component of the eukaryotic genome, exists autonomously from its chromosomal counterparts. Ubiquitous in eukaryotes, eccDNA plays a critical role in the orchestration of cellular processes and the etiology of diseases, particularly cancers. However, the full scope of its influence on health and disease remains elusive, presenting a rich vein of research yet to be mined. Unraveling the complexities of eccDNA necessitates a distillation of methodologies — from biogenesis to functional analysis — a landscape we overview in this study with precision and clarity. Here, we systematically outline cutting-edge methodologies from high-throughput sequencing and bioinformatics to experimental validations, showcasing the intricate world of eccDNAs. We combed through a treasure trove of auxiliary research resources and analytical tools. Moreover, we chart a course for future inquiry, illuminating the horizon with potential groundbreaking strategies for designing eccDNA research projects and pioneering new methodological frontiers.
AU  - Yuan, X.Q.*
AU  - Zhou, N.*
AU  - Song, S.J.*
AU  - Xie, Y.X.*
AU  - Chen, S.Q.*
AU  - Yang, T.F.*
AU  - Peng, X.*
AU  - Zhang, C.-Y.
AU  - Zhu, Y.H.*
AU  - Peng, L.*
C1  - 71534
C2  - 56126
CY  - 50 Hampshire St, Floor 5, Cambridge, Ma 02139 Usa
TI  - Decoding the genomic enigma: Approaches to studying extrachromosomal circular DNA.
JO  - Heliyon
VL  - 10
IS  - 17
PB  - Cell Press
PY  - 2024
SN  - 2405-8440
ER  - 

TY  - JOUR
AB  - Prostate cancer (PCa) is one of the two solid malignancies in which a higher T cell infiltration in the tumor microenvironment (TME) corresponds with a worse prognosis for the tumor. The inability of T cells to eliminate tumor cells despite an increase in their number reinforces the possibility of impaired antigen presentation. In this study, we investigated the TME at single-cell resolution to understand the molecular function and communication of dendritic cells (DCs) (as professional antigen-presenting cells). According to our data, tumor cells stimulate the migration of immature DCs to the tumor site by inducing inflammatory chemokines. Many signaling pathways such as TNF-α/NF-κB, IL2/STAT5, and E2F up-regulated after DCs enter the tumor location. In addition, some molecules such as GPR34 and SLCO2B1 decreased on the surface of DCs. The analysis of molecular and signaling alterations in DCs revealed some suppression mechanisms of tumors, such as removing mature DCs, reducing the DC's survival, inducing anergy or exhaustion in the effector T cells, and enhancing the differentiation of T cells to Th2 and Tregs. In addition, we investigated the cellular and molecular communication between DCs and macrophages in the tumor site and found three molecular pairs including CCR5/CCL5, CD52/SIGLEC10, and HLA-DPB1/TNFSF13B. These molecular pairs are involved in the migration of immature DCs to the TME and disrupt the antigen-presenting function of DCs. Furthermore, we presented new therapeutic targets by the construction of a gene co-expression network. These data increase our knowledge of the heterogeneity and the role of DCs in PCa TME.
AU  - Feriz, A.M.*
AU  - Khosrojerdi, A.*
AU  - Lotfollahi, M.
AU  - Shamsaki, N.*
AU  - GhasemiGol, M.*
AU  - HosseiniGol, E.*
AU  - Fereidouni, M.*
AU  - Rohban, M.H.*
AU  - Sebzari, A.R.*
AU  - Saghafi, S.*
AU  - Leone, P.*
AU  - Silvestris, N.*
AU  - Safarpour, H.*
AU  - Racanelli, V.*
C1  - 67772
C2  - 54250
TI  - Single-cell RNA sequencing uncovers heterogeneous transcriptional signatures in tumor-infiltrated dendritic cells in prostate cancer.
JO  - Heliyon
VL  - 9
IS  - 5
PY  - 2023
SN  - 2405-8440
ER  - 

TY  - JOUR
AB  - Parkinson's disease (PD), a neurodegenerative disease characterized by both motor neuron and non-motor neuron symptoms, is the most frequent neurodegenerative disease after Alzheimer's disease. Both genetic and environmental factors take part in disease etiology. Most cases are considered complex multifactorial diseases. About 15% of PD appear in the familial form, and about 5% of all cases arise from a single gene mutation. Among Mendelian causes of PD, PARK7 is one of the autosomal recessive forms due to loss-of-function mutations in both gene alleles. Both single nucleotide variants (SNVs) and copy number variations (CNVs) are observed in PARK7. This study presents an Iranian family with familial PD where some relatives had psychiatric disorders. A homozygous 1617 bp deletion in a female with early-onset PD was detected through copy-number analysis from whole-exome sequencing (WES) data in this consanguineous family. Further investigation by surveying microhomology revealed that the actual size of the deletion is 3,625 bp. This novel CNV that was in the PARK7gene is supposed to co-relation with early-onset PD and infertility in this family.
AU  - Seyedtaghia, M.R.*
AU  - Soudyab, M.*
AU  - Shariati, M.*
AU  - Esfehani, R.J.*
AU  - Vafadar, S.*
AU  - Shalaei, N.*
AU  - Nouri, V.*
AU  - Zech, M.
AU  - Winkelmann, J.
AU  - Shoeibi, A.*
AU  - Sadr-Nabavi, A.
C1  - 67668
C2  - 53975
CY  - 50 Hampshire St, Floor 5, Cambridge, Ma 02139 Usa
TI  - Copy number analysis from whole-exome sequencing data revealed a novel homozygous deletion in PARK7 leads to severe early-onset Parkinson's disease.
JO  - Heliyon
VL  - 9
IS  - 4
PB  - Cell Press
PY  - 2023
SN  - 2405-8440
ER  - 

TY  - JOUR
AB  - In this work, the adsorption-desorption dynamics of diuron in three typical Kenyan agricultural soils, Nzoia (NZ), Thika (TH) and Machakos (MK) was investigated. The equilibrium adsorption data, tested against three classical nonlinear adsorption isotherms, was best described by the Freundlich model. The Freundlich adsorption constant, (KF), increased in the order MK > TH > NZ soil. Additionally, the negative Gibb's free energy values indicate the adsorption processes were thermodynamically spontaneous and physical. Multiple linear regression analysis indicated that the adsorption-desorption behavior was controlled by the clay and phosphorus contents of the soil. Phosphorus negatively affected the adsorption of diuron and promoted desorption. The groundwater ubiquity score (GUS) indicated that diuron movement rating in MK soil was ‘moderate’ while the movement in TH and NZ soils was ‘high’.
AU  - Muendo, B.M.*
AU  - Shikuku, V.O.*
AU  - Getenga, Z.M.*
AU  - Lalah, J.O.*
AU  - Wandiga, S.O.*
AU  - Rothballer, M.
C1  - 61297
C2  - 50113
TI  - Adsorption-desorption and leaching behavior of diuron on selected Kenyan agricultural soils.
JO  - Heliyon
VL  - 7
IS  - 2
PY  - 2021
SN  - 2405-8440
ER  - 

TY  - JOUR
AB  - Background: Molecular MRI is becoming increasingly important for preclinical research. Validation of targeted gadolinium probes in tissue however has been cumbersome up to now. Novel methodology to assess gadolinium distribution in tissue after in vivo application is therefore needed. Purpose: To establish combined Magnetic Resonance Imaging (MRI) and Mass Spectrometry Imaging (MSI) for improved detection and quantification of Gadofluorine P deposition in scar formation and myocardial remodeling. Materials and methods: Animal studies were performed according to institutionally approved protocols. Myocardial infarction was induced by permanent ligation of the left ascending artery (LAD) in C57BL/6J mice. MRI was performed at 7T at 1 week and 6 weeks after myocardial infarction. Gadofluorine P was used for dynamic T1mapping of extracellular matrix synthesis during myocardial healing and compared to Gd-DTPA. After in vivo imaging contrast agent concentration as well as distribution in tissue were validated and quantified by spatially resolved Matrix-Assisted Laser Desorption Ionization (MALDI) MSI and Laser Ablation – Inductively Coupled Plasma – Mass Spectrometry (LA-ICP-MS) imaging. Results: Both Gadofluorine P enhancement as well as local tissue content in the myocardial scar were highest at 15 minutes post injection. R1values increased from 1 to 6 weeks after MI (1.62 s−1vs 2.68 s−1, p = 0.059) paralleled by an increase in Gadofluorine P concentration in the infarct from 0.019 mM at 1 week to 0.028 mM at 6 weeks (p = 0.048), whereas Gd-DTPA enhancement showed no differences (3.95 s−1vs 3.47 s−1, p = 0.701). MALDI-MSI results were corroborated by elemental LA-ICP-MS of Gadolinium in healthy and infarcted myocardium. Histology confirmed increased extracellular matrix synthesis at 6 weeks compared to 1 week. Conclusion: Adding quantitative MSI to MR imaging enables a quantitative validation of Gadofluorine P distribution in the heart after MI for molecular imaging.
AU  - Lohöfer, F.*
AU  - Hoffmann, L.*
AU  - Buchholz, R.*
AU  - Huber, K.
AU  - Glinzer, A.*
AU  - Kosanke, K.*
AU  - Feuchtinger, A.
AU  - Aichler, M.
AU  - Feuerecker, B.*
AU  - Kaissis, G.*
AU  - Rummeny, E.J.*
AU  - Höltke, C.*
AU  - Faber, C.*
AU  - Schilling, F.*
AU  - Botnar, R.M.*
AU  - Walch, A.K.
AU  - Karst, U.*
AU  - Wildgruber, M.*
C1  - 53602
C2  - 44759
TI  - Molecular imaging of myocardial infarction with Gadofluorine P – A combined magnetic resonance and mass spectrometry imaging approach.
JO  - Heliyon
VL  - 4
IS  - 4
PY  - 2018
SN  - 2405-8440
ER  -