bluuebunny/crossref_metadata_2025 huggingface dataset:
Microstructural imaging and transcriptomics of the basal forebrain in first-episode psychosis
Authors: Park Min Tae M. , Jeon Peter , French Leon , Dempster Kara , Chakravarty M. Mallar , MacKinley Michael , Richard Julie , Khan Ali R. , Théberge Jean , Palaniyappan Lena
Published: September 2022

Cholinergic dysfunction has been implicated in the pathophysiology of psychosis and psychiatric disorders such as schizophrenia, depression, and bipolar disorder. The basal forebrain (BF) cholinergic nuclei, defined as cholinergic cell groups Ch1-3 and Ch4 (Nucleus Basalis of Meynert; NBM), provide extensive cholinergic projections to the rest of the brain. Here, we examined microstructural neuroimaging measures of the cholinergic nuclei in patients with untreated psychosis (~31 weeks of psychosis, <2 defined daily dose of antipsychotics) and used magnetic resonance spectroscopy (MRS) and transcriptomic data to support our findings. We used a cytoarchitectonic atlas of the BF to map the nuclei and obtained measures of myelin (quantitative T1, or qT1 as myelin surrogate) and microstructure (axial diffusion; AxD). In a clinical sample (n = 85; 29 healthy controls, 56 first-episode psychosis), we found significant correlations between qT1 of Ch1-3, left NBM and MRS-based dorsal anterior cingulate choline in healthy controls while this relationship was disrupted in FEP (p > 0.05). Case-control differences in qT1 and AxD were observed in the Ch1-3, with increased qT1 (reflecting reduced myelin content) and AxD (reflecting reduced axonal integrity). We found clinical correlates between left NBM qT1 with manic symptom severity, and AxD with negative symptom burden in FEP. Intracortical and subcortical myelin maps were derived and correlated with BF myelin. BF-cortical and BF-subcortical myelin correlations demonstrate known projection patterns from the BF. Using data from the Allen Human Brain Atlas, cholinergic nuclei showed significant enrichment for schizophrenia and depression-related genes. Cell-type specific enrichment indicated enrichment for cholinergic neuron markers as expected. Further relating the neuroimaging correlations to transcriptomics demonstrated links with cholinergic receptor genes and cell type markers of oligodendrocytes and cholinergic neurons, providing biological validity to the measures. These results provide genetic, neuroimaging, and clinical evidence for cholinergic dysfunction in schizophrenia.
Standardised survival probabilities: a useful and informative tool for reporting regression models for survival data
Authors: Syriopoulou Elisavet , Wästerlid Tove , Lambert Paul C. , Andersson Therese M.-L.
Published: September 2022

Background

When interested in studying the effect of a treatment (or other exposure) on a time-to-event outcome, the most popular approach is to estimate survival probabilities using the Kaplan–Meier estimator. In the presence of confounding, regression models are fitted, and results are often summarised as hazard ratios. However, despite their broad use, hazard ratios are frequently misinterpreted as relative risks instead of relative rates.

Methods

We discuss measures for summarising the analysis from a regression model that overcome some of the limitations associated with hazard ratios. Such measures are the standardised survival probabilities for treated and untreated: survival probabilities if everyone in the population received treatment and if everyone did not. The difference between treatment arms can be calculated to provide a measure for the treatment effect.

Results

Using publicly available data on breast cancer, we demonstrated the usefulness of standardised survival probabilities for comparing the experience between treated and untreated after adjusting for confounding. We also showed that additional important research questions can be addressed by standardising among subgroups of the total population.

Discussion

Standardised survival probabilities are a useful way to report the treatment effect while adjusting for confounding and have an informative interpretation in terms of risk.
Mammography radiomics features at diagnosis and progression-free survival among patients with breast cancer
Authors: Luo Chuanxu , Zhao Shuang , Peng Cheng , Wang Chengshi , Hu Kejia , Zhong Xiaorong , Luo Ting , Huang Juan , Lu Donghao
Published: September 2022

Background

The associations between mammographic radiomics and breast cancer clinical endpoints are unclear. We aimed to identify mammographic radiomics features associated with breast cancer prognosis.

Methods

Nested from a large breast cancer cohort in our institution, we conducted an extreme case-control study consisting of 207 cases with any invasive disease-free survival (iDFS) endpoint <5 years and 207 molecular subtype-matched controls with >5-year iDFS. A total of 632 radiomics features in craniocaudal (CC) and mediolateral oblique (MLO) views were extracted from pre-treatment mammography. Logistic regression was used to identify iDFS-associated features with multiple testing corrections (Benjamini–Hochberg method). In a subsample with RNA-seq data (n = 96), gene set enrichment analysis was employed to identify pathways associated with lead features.

Results

We identified 15 iDFS-associated features from CC-view yet none from MLO-view. S(1,−1)SumAverg and WavEnLL_s-6 were the lead ones and associated with favourable (OR 0.64, 95% CI 0.42–0.87, P = 0.01) and poor iDFS (OR 1.53, 95% CI 1.31–1.76, P = 0.01), respectively. Both features were associated with eight pathways (primarily involving cell cycle regulation) in tumour but not adjacent normal tissues.

Conclusion

Our findings suggest mammographic radiomics features are associated with breast cancer iDFS, potentially through pathways involving cell cycle regulation.
A compact cold-atom interferometer with a high data-rate grating magneto-optical trap and a photonic-integrated-circuit-compatible laser system
Authors: Lee Jongmin , Ding Roger , Christensen Justin , Rosenthal Randy R. , Ison Aaron , Gillund Daniel P. , Bossert David , Fuerschbach Kyle H. , Kindel William , Finnegan Patrick S. , Wendt Joel R. , Gehl Michael , Kodigala Ashok , McGuinness Hayden , Walker Charles A. , Kemme Shanalyn A. , Lentine Anthony , Biedermann Grant , Schwindt Peter D. D.
Published: September 2022

The extreme miniaturization of a cold-atom interferometer accelerometer requires the development of novel technologies and architectures for the interferometer subsystems. Here, we describe several component technologies and a laser system architecture to enable a path to such miniaturization. We developed a custom, compact titanium vacuum package containing a microfabricated grating chip for a tetrahedral grating magneto-optical trap (GMOT) using a single cooling beam. In addition, we designed a multi-channel photonic-integrated-circuit-compatible laser system implemented with a single seed laser and single sideband modulators in a time-multiplexed manner, reducing the number of optical channels connected to the sensor head. In a compact sensor head containing the vacuum package, sub-Doppler cooling in the GMOT produces 15 μK temperatures, and the GMOT can operate at a 20 Hz data rate. We validated the atomic coherence with Ramsey interferometry using microwave spectroscopy, then demonstrated a light-pulse atom interferometer in a gravimeter configuration for a 10 Hz measurement data rate and T = 0–4.5 ms interrogation time, resulting in Δg/g = 2.0 × 10−6. This work represents a significant step towards deployable cold-atom inertial sensors under large amplitude motional dynamics.
Decoding the olfactory map through targeted transcriptomics links murine olfactory receptors to glomeruli
Authors: Zhu Kevin W. , Burton Shawn D. , Nagai Maira H. , Silverman Justin D. , de March Claire A. , Wachowiak Matt , Matsunami Hiroaki
Published: September 2022

Sensory processing in olfactory systems is organized across olfactory bulb glomeruli, wherein axons of peripheral sensory neurons expressing the same olfactory receptor co-terminate to transmit receptor-specific activity to central neurons. Understanding how receptors map to glomeruli is therefore critical to understanding olfaction. High-throughput spatial transcriptomics is a rapidly advancing field, but low-abundance olfactory receptor expression within glomeruli has previously precluded high-throughput mapping of receptors to glomeruli in the mouse. Here we combined sequential sectioning along the anteroposterior, dorsoventral, and mediolateral axes with target capture enrichment sequencing to overcome low-abundance target expression. This strategy allowed us to spatially map 86% of olfactory receptors across the olfactory bulb and uncover a relationship between OR sequence and glomerular position.
A functional vulnerability framework for biodiversity conservation
Authors: Auber Arnaud , Waldock Conor , Maire Anthony , Goberville Eric , Albouy Camille , Algar Adam C. , McLean Matthew , Brind’Amour Anik , Green Alison L. , Tupper Mark , Vigliola Laurent , Kaschner Kristin , Kesner-Reyes Kathleen , Beger Maria , Tjiputra Jerry , Toussaint Aurèle , Violle Cyrille , Mouquet Nicolas , Thuiller Wilfried , Mouillot David
Published: September 2022

Setting appropriate conservation strategies in a multi-threat world is a challenging goal, especially because of natural complexity and budget limitations that prevent effective management of all ecosystems. Safeguarding the most threatened ecosystems requires accurate and integrative quantification of their vulnerability and their functioning, particularly the potential loss of species trait diversity which imperils their functioning. However, the magnitude of threats and associated biological responses both have high uncertainties. Additionally, a major difficulty is the recurrent lack of reference conditions for a fair and operational measurement of vulnerability. Here, we present a functional vulnerability framework that incorporates uncertainty and reference conditions into a generalizable tool. Through in silico simulations of disturbances, our framework allows us to quantify the vulnerability of communities to a wide range of threats. We demonstrate the relevance and operationality of our framework, and its global, scalable and quantitative comparability, through three case studies on marine fishes and mammals. We show that functional vulnerability has marked geographic and temporal patterns. We underline contrasting contributions of species richness and functional redundancy to the level of vulnerability among case studies, indicating that our integrative assessment can also identify the drivers of vulnerability in a world where uncertainty is omnipresent.
SARS-CoV-2 vaccination induces mucosal antibody responses in previously infected individuals
Authors: Sano Kaori , Bhavsar Disha , Singh Gagandeep , Floda Daniel , Srivastava Komal , Gleason Charles ,   PARIS Study Group, Amoako Angela A. , Andre Dalles , Beach Katherine F. , Bermúdez-González Maria C. , Cai Gianna , Cognigni Christian , Kawabata Hisaaki , Kleiner Giulio , Lyttle Neko , Mendez Wanni , Mulder Lubbertus C. F. , Oostenink Annika , Raskin Ariel , Rooker Aria , Russo Kayla T. , Salimbangon Ashley Beathrese T. , Saksena Miti , Sominsky Levy A. , Tcheou Johnstone , Wajnberg Ania , Carreño Juan Manuel , Simon Viviana , Krammer Florian
Published: September 2022

Immune responses at the respiratory mucosal interface are critical to prevent respiratory infections but it is unclear to what extent antigen specific mucosal secretory IgA (SIgA) antibodies are induced by mRNA vaccination in humans. Here we analyze paired serum and saliva samples from patients with and without prior coronavirus disease 2019 (COVID-19) at multiple time points pre and post severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mRNA vaccination. Our results suggest mucosal SIgA responses induced by mRNA vaccination are impacted by pre-existing immunity. Indeed, vaccination induced a minimal mucosal SIgA response in individuals without pre-exposure to SARS-CoV-2 while SIgA induction after vaccination was more efficient in patients with a history of COVID-19.
Microspheres from light—a sustainable materials platform
Authors: Delafresnaye Laura , Feist Florian , Hooker Jordan P. , Barner-Kowollik Christopher
Published: September 2022

Driven by the demand for highly specialized polymeric materials via milder, safer, and sustainable processes, we herein introduce a powerful, purely light driven platform for microsphere synthesis – including facile synthesis by sunlight. Our light-induced step-growth precipitation polymerization produces monodisperse particles (0.4–2.4 μm) at ambient temperature without any initiator, surfactant, additive or heating, constituting an unconventional approach compared to the classically thermally driven synthesis of particles. The microspheres are formed via the Diels-Alder cycloaddition of a photoactive monomer (2-methylisophthaldialdehyde, MIA) and a suitable electron deficient dienophile (bismaleimide). The particles are stable in the dry state as well as in solution and their surface can be further functionalized to produce fluorescent particles or alter their hydrophilicity. The simplicity and versatility of our approach introduces a fresh opportunity for particle synthesis, opening access to a yet unknown material class.
Climate and land management accelerate the Brazilian water cycle
Authors: Chagas Vinícius B. P. , Chaffe Pedro L. B. , Blöschl Günter
Published: September 2022

Increasing floods and droughts are raising concerns of an accelerating water cycle, however, the relative contributions to streamflow changes from climate and land management have not been assessed at the continental scale. We analyze streamflow data in major South American tropical river basins and show that water use and deforestation have amplified climate change effects on streamflow extremes over the past four decades. Drying (fewer floods and more droughts) is aligned with decreasing rainfall and increasing water use in agricultural zones and occurs in 42% of the study area. Acceleration (both more severe floods and droughts) is related to more extreme rainfall and deforestation and occurs in 29% of the study area, including southern Amazonia. The regionally accelerating water cycle may have adverse global impacts on carbon sequestration and food security.
WAVY GROWTH Arabidopsis E3 ubiquitin ligases affect apical PIN sorting decisions
Authors: Konstantinova Nataliia , Hoermayer Lukas , Glanc Matouš , Keshkeih Rabab , Tan Shutang , Di Donato Martin , Retzer Katarzyna , Moulinier-Anzola Jeanette , Schwihla Max , Korbei Barbara , Geisler Markus , Friml Jiří , Luschnig Christian
Published: September 2022

Directionality in the intercellular transport of the plant hormone auxin is determined by polar plasma membrane localization of PIN-FORMED (PIN) auxin transport proteins. However, apart from PIN phosphorylation at conserved motifs, no further determinants explicitly controlling polar PIN sorting decisions have been identified. Here we present Arabidopsis WAVY GROWTH 3 (WAV3) and closely related RING-finger E3 ubiquitin ligases, whose loss-of-function mutants show a striking apical-to-basal polarity switch in PIN2 localization in root meristem cells. WAV3 E3 ligases function as essential determinants for PIN polarity, acting independently from PINOID/WAG-dependent PIN phosphorylation. They antagonize ectopic deposition of de novo synthesized PIN proteins already immediately following completion of cell division, presumably via preventing PIN sorting into basal, ARF GEF-mediated trafficking. Our findings reveal an involvement of E3 ligases in the selective targeting of apically localized PINs in higher plants.
Crosstalk between SUMOylation and ubiquitylation controls DNA end resection by maintaining MRE11 homeostasis on chromatin
Authors: Zhang Tao , Yang Han , Zhou Zenan , Bai Yongtai , Wang Jiadong , Wang Weibin
Published: September 2022

DNA end resection is delicately regulated through various types of post-translational modifications to initiate homologous recombination, but the involvement of SUMOylation in this process remains incompletely understood. Here, we show that MRE11 requires SUMOylation to shield it from ubiquitin-mediated degradation when resecting damaged chromatin. Upon DSB induction, PIAS1 promotes MRE11 SUMOylation on chromatin to initiate DNA end resection. Then, MRE11 is deSUMOylated by SENP3 mainly after it has moved away from DSB sites. SENP3 deficiency results in MRE11 degradation failure and accumulation on chromatin, causing genome instability. We further show that cancer-related MRE11 mutants with impaired SUMOylation exhibit compromised DNA repair ability. Thus, we demonstrate that MRE11 SUMOylation in coordination with ubiquitylation is dynamically controlled by PIAS1 and SENP3 to facilitate DNA end resection and maintain genome stability.
Dynamic genome evolution in a model fern
Authors: Marchant D. Blaine , Chen Guang , Cai Shengguan , Chen Fei , Schafran Peter , Jenkins Jerry , Shu Shengqiang , Plott Chris , Webber Jenell , Lovell John T. , He Guifen , Sandor Laura , Williams Melissa , Rajasekar Shanmugam , Healey Adam , Barry Kerrie , Zhang Yinwen , Sessa Emily , Dhakal Rijan R. , Wolf Paul G. , Harkess Alex , Li Fay-Wei , Rössner Clemens , Becker Annette , Gramzow Lydia , Xue Dawei , Wu Yuhuan , Tong Tao , Wang Yuanyuan , Dai Fei , Hua Shuijin , Wang Hua , Xu Shengchun , Xu Fei , Duan Honglang , Theißen Günter , McKain Michael R. , Li Zheng , McKibben Michael T. W. , Barker Michael S. , Schmitz Robert J. , Stevenson Dennis W. , Zumajo-Cardona Cecilia , Ambrose Barbara A. , Leebens-Mack James H. , Grimwood Jane , Schmutz Jeremy , Soltis Pamela S. , Soltis Douglas E. , Chen Zhong-Hua
Published: September 2022

The large size and complexity of most fern genomes have hampered efforts to elucidate fundamental aspects of fern biology and land plant evolution through genome-enabled research. Here we present a chromosomal genome assembly and associated methylome, transcriptome and metabolome analyses for the model fern species Ceratopteris richardii. The assembly reveals a history of remarkably dynamic genome evolution including rapid changes in genome content and structure following the most recent whole-genome duplication approximately 60 million years ago. These changes include massive gene loss, rampant tandem duplications and multiple horizontal gene transfers from bacteria, contributing to the diversification of defence-related gene families. The insertion of transposable elements into introns has led to the large size of the Ceratopteris genome and to exceptionally long genes relative to other plants. Gene family analyses indicate that genes directing seed development were co-opted from those controlling the development of fern sporangia, providing insights into seed plant evolution. Our findings and annotated genome assembly extend the utility of Ceratopteris as a model for investigating and teaching plant biology.
Atmospheric temperature, water vapour and liquid water path from two microwave radiometers during MOSAiC
Authors: Walbröl Andreas , Crewell Susanne , Engelmann Ronny , Orlandi Emiliano , Griesche Hannes , Radenz Martin , Hofer Julian , Althausen Dietrich , Maturilli Marion , Ebell Kerstin
Published: September 2022

The microwave radiometers HATPRO (Humidity and Temperature Profiler) and MiRAC-P (Microwave Radiometer for Arctic Clouds - Passive) continuously measured radiation emitted from the atmosphere throughout the Multidisciplinary drifting Observatory for the Study of the Arctic Climate (MOSAiC) expedition on board the research vessel Polarstern. From the measured brightness temperatures, we have retrieved atmospheric variables using statistical methods in a temporal resolution of 1 s covering October 2019 to October 2020. The integrated water vapour (IWV) is derived individually from both radiometers. In addition, we present the liquid water path (LWP), temperature and absolute humidity profiles from HATPRO. To prove the quality and to estimate uncertainty, the data sets are compared to radiosonde measurements from Polarstern. The comparison shows an extremely good agreement for IWV, with standard deviations of 0.08–0.19 kg m−2 (0.39–1.47 kg m−2) in dry (moist) situations. The derived profiles of temperature and humidity denote uncertainties of 0.7–1.8 K and 0.6–0.45 gm−3 in 0–2 km altitude.
A large EEG dataset for studying cross-session variability in motor imagery brain-computer interface
Authors: Ma Jun , Yang Banghua , Qiu Wenzheng , Li Yunzhe , Gao Shouwei , Xia Xinxing
Published: September 2022

In building a practical and robust brain-computer interface (BCI), the classification of motor imagery (MI) from electroencephalography (EEG) across multiple days is a long-standing challenge due to the large variability of the EEG signals. We collected a large dataset of MI from 5 different days with 25 subjects, the first open-access dataset to address BCI issues across 5 different days with a large number of subjects. The dataset includes 5 session data from 5 different days (2–3 days apart) for each subject. Each session contains 100 trials of left-hand and right-hand MI. In this report, we provide the benchmarking classification accuracy for three conditions, namely, within-session classification (WS), cross-session classification (CS), and cross-session adaptation (CSA), with subject-specific models. WS achieves an average classification accuracy of up to 68.8%, while CS degrades the accuracy to 53.7% due to the cross-session variability. However, by adaptation, CSA improves the accuracy to 78.9%. We anticipate this new dataset will significantly push further progress in MI BCI research in addressing the cross-session and cross-subject challenge.
Ecological and human health risk assessment of heavy metal(loid)s in agricultural soil in hotbed chives hometown of Tangchang, Southwest China
Authors: Gong Cang , Wang Shunxiang , Wang Dewei , Lu Haichuan , Dong Hang , Liu Jiufen , Yan Buqing , Wang Liang
Published: September 2022

To determine the heavy metal(loid)s (HMs) contamination of agricultural soil in hotbed chives hometown of Tangchang, 788 topsoil samples were collected and analyzed for their heavy metal(loid)s concentration. The index of geo-accumulation (Igeo), pollution index (PI) and potential ecological risk index (EIi) were used to assess the degree of pollution. Correlation analysis and principal component analysis (PCA) were used to determine the sources of soil HMs. Human health risks estimated with hazard index (HI) and carcinogenic risk (CR) indices based on ingestion, inhalation and dermal exposure pathways for adults and children. The mean values of Cd, Hg, As, Pb, Cr, Cu, Ni and Zn were 0.221, 0.155, 9.76, 32.2, 91.9, 35.2, 37.1 and 108.8 mg kg−1, respectively, which did not exceed the threshold values of the risk screening value for soil contamination. The potential ecological risk of soil heavy metal(loid)s was low level and there was no significant human health risk. Based on PCA, Pb and Hg may originate from transportation and atmospheric deposition, Zn, Cr and Ni may originate from natural sources and industrial activities, and Cu and Cd may originate from agricultural activities. Overall, from the perspective of HMs content, the soil quality in this study area was at a clean level. This study provides a reference and a basis for formulating effective measures to prevent and control HMs enrichment in agricultural soils.
Ganglion cell inner plexiform layer thickness measured by optical coherence tomography to predict visual outcome in chiasmal compression
Authors: Lee Ga-In , Kim Joonhyoung , Lee Dongyoung , Park Kyung-Ah , Oh Sei Yeul , Kong Doo-Sik , Hong Sang Duk
Published: September 2022

We evaluated the prognostic value of the preoperative macular ganglion cell inner plexiform layer (mGCIPL) thickness along with peripapillary retinal nerve fiber layer (pRNFL) thickness measured by optical coherence tomography (OCT) and estimated an optimal cut-off value to predict postoperative visual field (VF) recovery in adult patients with chiasmal compression after decompression surgery. Two hundred forty eyes of 240 patients aged 20 years or older for which preoperative high-definition Cirrus OCT parameters and pre- and postoperative visual function data were available. The prognostic power of pRNFL and mGCIPL thicknesses for complete postoperative VF recovery or significant VF improvement (improvement ≥ 2 dB in the mean deviation) were assessed. The cut-off values for OCT parameters for VF recovery were estimated. The study found that the higher the preoperative pRNFL and mGCIPL thicknesses, the higher the probability of complete postoperative VF recovery (p = 0.0378 and p = 0.0051, respectively) or significant VF improvement (p = 0.0436 and p = 0.0177, respectively). The area under the receiver operating characteristic analysis of preoperative OCT parameters demonstrated that the mGCIPL thickness showed an area under the curve (AUC) of more than 0.7 for complete VF recovery after decompression surgery (AUC = 0.725, 95% CI: 0.655, 0.795), and the optimal mGCIPL thickness cut-off value for complete VF recovery was 77.25 µm (sensitivity 69% and specificity 69%). Preoperative mGCIPL thickness was a powerful predictor of visual functional outcome after decompression surgery for chiasmal compression.
Breast cancer detection by analyzing the volatile organic compound (VOC) signature in human urine
Authors: Giró Benet Judit , Seo Minjun , Khine Michelle , Gumà Padró Josep , Pardo Martnez Antonio , Kurdahi Fadi
Published: September 2022

A rising number of authors are drawing evidence on the diagnostic capacity of specific volatile organic compounds (VOCs) resulting from some body fluids. While cancer incidence in society is on the rise, it becomes clear that the analysis of these VOCs can yield new strategies to mitigate advanced cancer incidence rates. This paper presents the methodology implemented to test whether a device consisting of an electronic nose inspired by a dog’s olfactory system and olfactory neurons is significantly informative to detect breast cancer (BC). To test this device, 90 human urine samples were collected from control subjects and BC patients at a hospital. To test this system, an artificial intelligence-based classification algorithm was developed. The algorithm was firstly trained and tested with data resulting from gas chromatography-mass spectrometry (GC–MS) urine readings, leading to a classification rate of 92.31%, sensitivity of 100.00%, and specificity of 85.71% (N = 90). Secondly, the same algorithm was trained and tested with data obtained with our eNose prototype hardware, and class prediction was achieved with a classification rate of 75%, sensitivity of 100%, and specificity of 50%.
Remarks on phylogeny and molecular variations of criconematid species (Nematoda: Criconematidae) with case studies from Vietnam
Authors: Nguyen Huu Tien , Nguyen Thi Duyen , Le Thi Mai Linh , Trinh Quang Phap , Bert Wim
Published: September 2022

The family Criconematidae is a remarkable group of nematodes, containing roughly 600 nominal root-ectoparasitic species, of which many species are known to be significant agricultural pests. Strikingly, our phylogenetic analyses based on 18S, D2-D3 of 28S rRNA, and COI mtDNA sequences of criconematid species, supported by tree topology tests (SH and AU tests), revealed that almost all studied genera, including Criconema, Ogma, Crossonema, Discocriconema, Hemicriconemoides, Criconemoides, Mesocriconema, and Lobocriconema, are not monophyletic groups, a finding that is partly contrary to those of previous studies on these groups. Our results suggest that key morphological characters used in the classification of Criconematidae are the consequence of convergent evolution. It is clear from our studies that the species status of at least 40 sequences of criconematid species from GenBank must be either revised or reconsidered, with analyses based on a polyphasic approach that includes different tree- and distance-based molecular species-delimitation methods (bPTP, GMYC, ABGD1, and ABGD2). Our studies found the ABGD2 output of the automatic barcode method to agree remarkably well with established species delimitations, while in general, the four species-delimitation results corresponding to three barcode regions forwarded significantly more putative species compared to those originally considered. This study also characterised for the first time the populations of Criconemoides myungsugae and Discocriconemella hensungica associated with Vietnamese ginseng, one of the most precious and rare ginseng varieties in the world. Although these populations are morphologically in agreement with the original descriptions of C. myungsugae and D. hengsungica, their molecular data display notable variations compared to the sequences deposited in GenBank. These species demonstrate clearly the immense molecular variations that can be observed in several species of the family Criconematidae.
Accurate magnetic field imaging using nanodiamond quantum sensors enhanced by machine learning
Authors: Tsukamoto Moeta , Ito Shuji , Ogawa Kensuke , Ashida Yuto , Sasaki Kento , Kobayashi Kensuke
Published: September 2022

Nanodiamonds can be excellent quantum sensors for local magnetic field measurements. We demonstrate magnetic field imaging with high accuracy of 1.8 $$\upmu $$
μ
T combining nanodiamond ensemble (NDE) and machine learning without any physical models. We discover the dependence of the NDE signal on the field direction, suggesting the application of NDE for vector magnetometry and the improvement of the existing model. Our method enhances the NDE performance sufficiently to visualize nano-magnetism and mesoscopic current and expands the applicability of NDE in arbitrarily shaped materials, including living organisms. This accomplishment bridges machine learning to quantum sensing for accurate measurements.
Effect of a 16-week multi-level classroom standing desk intervention on cognitive performance and academic achievement in adolescents
Authors: Silva Danilo R. , Machado Daniel G. S. , Pinto Fernando , Júdice Pedro B. , Minderico Cláudia S. , Collings Paul J. , Cyrino Edilson S. , Sardinha Luís B.
Published: September 2022

The replacement of traditional classroom desks for active-permissive desks has been tested to reduce sitting time during classes. However, their impact on other domains is still unclear. We aimed to verify the potential effects of a classroom standing desk intervention on cognitive function and academic achievement in 6th-grade students. This was a controlled trial conducted with two classes [intervention (n = 22) and control (n = 27)] from a public school in Lisbon, Portugal. The intervention was carried out for 16 weeks and consisted of multi-level actions (students, parents, and teachers) centered on the implementation of standing desks in the intervention classroom. The control group had traditional classes with no use of standing desks or any other interference/action from the research team. Pre- and post-assessments of executive functions (attention, inhibitory function, memory, and fluid intelligence) and academic achievement were obtained. No differences between groups were found at baseline. Both groups improved (time effect) academic achievement (p < 0.001), memory span (p < 0.001), and inhibitory function (p = 0.008). Group versus time interactions were observed regarding operational memory (intervention: + 18.0% and control: + 41.6%; p = 0.039) and non-verbal fluid intelligence (intervention: − 14.0% and control: + 3.9%; p = 0.017). We concluded that a 16-week classroom standing desk intervention did not improve cognitive performance or academic achievement more than the traditional sitting classes.

Trial registration: ClinicalTrials.gov Identifier (NCT03137836) (date of first registration: 03/05/2017).
High-fat diet causes mechanical allodynia in the absence of injury or diabetic pathology
Authors: Tierney Jessica A. , Uong Calvin D. , Lenert Melissa E. , Williams Marisa , Burton Michael D.
Published: September 2022

Understanding the interactions between diet, obesity, and diabetes is important to tease out mechanisms in painful pathology. Western diet is rich in fats, producing high amounts of circulating bioactive metabolites. However, no research has assessed how a high-fat diet (HFD) alone may sensitize an individual to non-painful stimuli in the absence of obesity or diabetic pathology. To investigate this, we tested the ability of a HFD to stimulate diet-induced hyperalgesic priming, or diet sensitization in male and female mice. Our results revealed that 8 weeks of HFD did not alter baseline pain sensitivity, but both male and female HFD-fed animals exhibited robust mechanical allodynia when exposed to a subthreshold dose of intraplantar Prostaglandin E2 (PGE2) compared to mice on chow diet. Furthermore, calcium imaging in isolated primary sensory neurons of both sexes revealed HFD induced an increased percentage of capsaicin-responsive neurons compared to their chow counterparts. Immunohistochemistry (IHC) showed a HFD-induced upregulation of ATF3, a neuronal marker of injury, in lumbar dorsal root ganglia (DRG). This suggests that a HFD induces allodynia in the absence of a pre-existing condition or injury via dietary components. With this new understanding of how a HFD can contribute to the onset of pain, we can understand the dissociation behind the comorbidities associated with obesity and diabetes to develop pharmacological interventions to treat them more efficiently.
Recognizing the new disorder “idiopathic hypocryoglobulinaemia” in patients with previously unidentified clinical conditions
Authors: Roccatello Dario , Sciascia Savino , Naretto Carla , Barreca Antonella , Solfietti Laura , Battaglia Laura , Viziello Lucia , Fenoglio Roberta , Rossi Daniela
Published: September 2022

A considerable number of patients with high clinical suspicion for cryoglobulinaemic vasculitis either show negative results for the detection of cryoglobulins or show only trace amounts which cannot be characterized for composition. We aimed at establishing whether the failure to detect or the detection of trace amounts of cryoglobulin with conventional methods either identifies a peculiar subset of low level cryoglobulinaemia (from now on hypocryoglobulinaemia) or represents a separate entity. Using a modified precipitation technique in hypo-ionic medium, we prospectively identified between 2008 and 2021 237 patients (median age 60.8 years [22–97], 137 females) having < 0.5% cryocrit and clinical suspicion of autoimmune disorder. Of these 237 patients, only 54 (22.7%) had a history of HCV infection. One hundred and sixty-nine out of 237 patients (71%) had an established underlying disease, while 68 patients (28.6%) (median age 62.9 years [29–93], 35 females) did not show either laboratory markers or clinical symptoms consonant with an underlying aetiology. These 68 cases with only trace amounts of cryoglobulins were defined as having a putatively idiopathic hypocryoglobulinaemia. Nineteen of these 68 patients (27.9%) had a history of HCV infection. Twenty-four patients out of 68 (35.3%) were positive for rheumatoid factor (RF), while 25 (36.7%) patients had signs of complement consumption (i.e., C4 < 15 mg/dl and/or C3 < 80 mg/dl ), and 36 (52.9%) had increased inflammatory indexes. Seven patients only had arthralgia and constitutional symptoms while 61 out of 68 (89.7%) presented with at least one of the three cardinal signs of cryoglobulinaemic vasculitis including skin lesions, peripheral nerve involvement, and glomerulonephritis. Seventy-five percent of the subjects had type III hypocryoglobulins. In patients with hypocryoglobulinaemia the histologic features of glomerulonephritis (also examined by electron microscopy) resembled those of mixed cryoglobulinaemia-associated glomerulonephritis. In conclusion, hypocryoglobulins are often polyclonal and are mainly unrelated to HCV infection. Patients who present high clinical suspicion for vasculitis, especially glomerulonephritis and yet test negative for cryoglobulinaemia detected by standard techniques, could require deeper investigation even in the absence of HCV infection, RF activity or signs of complement consumption.
Synthesis of tolyl guanidine as copper corrosion inhibitor with a complementary study on electrochemical and in silico evaluation
Authors: Abdou Moaz M. , EL-Haddad Mahmoud N.
Published: September 2022

A rapid and new synthetic route forN,N′-di-o-tolyl guanidine (DTG) synthesis from cheap materials is reported. The performance ofDTGas an excellent inhibitor for delaying copper (Cu) corrosion with an efficiency higher than 98% at 20 × 10−6 M in an acidic solution was investigated via electrochemical measurements. These measurements included PDP, EFM, and EIS spectroscopy. The experimental data indicated thatDTGhas an efficient inhibiting effect on the corrosion of Cu in acidic media.TheDTGwas adsorbed on to the Cu surface via chemical adsorption and followed the Langmuir route. The PDP measurements revealed thatDTGacted as a mixed inhibitor. Furthermore, EIS data showed that theDTGadsorbed through the metal/electrolyte interface. This resulted in forming aDTGprotective layer on the Cu surface, thereby impeding the dissolution of Cu in the acidic solution. The corrosive solution containing theDTGinhibitor after immersion of the Cu specimen for 48 h, which promoted the formation of a complex between the Cu cation andDTG, was investigated via ultraviolet/visible spectroscopy. In addition, the formation of aDTGprotective layer on the Cu surface was confirmed via scanning electron microscopy and atomic force microscopy analysis of the Cu surface morphology. Moreover, the active centers for interaction with the Cu surface in an acidic solution were investigated via in silico evaluation ofDTG.
Dynamics of the secreted frizzled related protein Sizzled and potential implications for binding to bone morphogenetic protein-1 (BMP-1)
Authors: Sharma Urvashi , Vadon-Le Goff Sandrine , Harlos Karl , Zhao Yuguang , Mariano Natacha , Bijakowski Cecile , Bourhis Jean-Marie , Moali Catherine , Hulmes David J. S. , Aghajari Nushin
Published: September 2022

Sizzled (Szl) is both a secreted frizzled related protein (sFRP) and a naturally occurring inhibitor of the zinc metalloproteinase bone morphogenetic protein-1 (BMP-1), a key regulator of extracellular matrix assembly and growth factor activation. Here we present a new crystal structure for Szl which differs from that previously reported by a large scale (90°) hinge rotation between its cysteine-rich and netrin-like domains. We also present results of a molecular docking analysis showing interactions likely to be involved in the inhibition of BMP-1 activity by Szl. When compared with known structures of BMP-1 in complex with small molecule inhibitors, this reveals features that may be helpful in the design of new inhibitors to prevent the excessive accumulation of extracellular matrix that is the hallmark of fibrotic diseases.
Hotspot in ferruginous rock may have serious implications in Brazilian conservation policy
Authors: Zeppelini Douglas , Oliveira João Victor L. C. , de Lima Estevam C. Araujo , Brito Roniere A. , Ferreira Aila S. , Stievano Luis C. , Brito Nathan P. , Oliveira-Neto Misael A. , Lopes Bruna C. H.
Published: September 2022

A hotspot of subterranean Collembola in ferruginous rock caves and Mesovoid Shallow Substratum is revealed by the analysis of pseudocryptic diversity. The diversity is accessed by detailed description of chaetotaxy and slight variation in morphology of 11 new species of Trogolaphysa Mills, 1938 (Collembola, Paronellidae, Paronellinae) and the 50 previously recorded species of springtails from caves, using optical and electronic microscopy. When combined with recent subterranean surveys, our results show an important reservoir of cave diversity in the Mesovoid Shallow Substratum. Contrastingly the conservation policy for subterranean fauna in metallogenic areas in Brazil prioritizes the caves instead the cave species, which may be extremely detrimental to the fauna in the shallow subterranean habitats not accessible to humans.
Hepcidin discriminates sepsis from other critical illness at admission to intensive care
Authors: Olinder Jon , Börjesson Alex , Norrman Jakob , West Tobias , Carlström Joakim , Gustafsson Alexander , Annborn Martin , Herwald Heiko , Rydén Cecilia
Published: September 2022

Initial differential diagnosis and prognosis for patients admitted to intensive care with suspected sepsis remain arduous. Hepcidin has emerged as a potential biomarker for sepsis. Here we report data on the relevance of levels of hepcidin versus other biomarkers as a diagnostic and prognostic tool for sepsis. 164 adult patients admitted to the intensive care unit (ICU) within 24 h upon arrival to the hospital were included. Blood samples collected daily for seven consecutive days and hepcidin levels, heparin binding protein (HBP) levels and standard biomarkers were determined. Blood cultures were initiated at inclusion. Clinical scores were evaluated daily and mortality after 28- and 180-days was recorded. One hundred of the patients were found to fulfil the criteria for sepsis whereas 64 did not. Hepcidin levels at admission were significantly higher in the septic than in the non-septic patients. In septic patients hepcidin levels declined significantly already at 24 h followed by a steady decline. A significant negative correlation was observed between hepcidin levels and SAPS 3 in patients with sepsis. Hepcidin levels at inclusion were significantly higher among septic patients that survived 180-days and predicted mortality. Our data show that hepcidin levels are indicative of sepsis in patients admitted to the ICU and has a prognostic value for mortality.
Pla2g2a promotes innate Th2-type immunity lymphocytes to increase B1a cells
Authors: Shinton Susan A. , Brill-Dashoff Joni , Hayakawa Kyoko
Published: September 2022

Newborns require early generation of effective innate immunity as a primary physiological mechanism for survival. The neonatal Lin28+Let7–developmental pathway allows increased generation of Th2-type cells and B1a (B-1 B) cells compared to adult cells and long-term maintenance of these initially generated innate cells. For initial B1a cell growth from the neonatal to adult stage, Th2-type IL-5 production from ILC2s and NKT2 cells is important to increase B1a cells. The Th17 increase is dependent on extracellular bacteria, and increased bacteria leads to lower Th2-type generation. Secreted group IIA-phospholipase A2 (sPLA2-IIA) from the Pla2g2a gene can bind to gram-positive bacteria and degrade bacterial membranes, controlling microbiota in the intestine. BALB/c mice are Pla2g2a+, and express high numbers of Th2-type cells and B1a cells. C57BL/6 mice are Pla2g2a-deficient and distinct from the SLAM family, and exhibit fewer NKT2 cells and fewer B1a cells from the neonatal to adult stage. We found that loss of Pla2g2a in the BALB/c background decreased IL-5 from Th2-type ILC2s and NKT2s but increased bacterial-reactive NKT17 cells and MAIT cells, and decreased the number of early-generated B1a cells and MZ B cells and the CD4/CD8 T cell ratio. Low IL-5 by decreased Th2-type cells in Pla2g2a loss led to low early-generated B1a cell growth from the neonatal to adult stage. In anti-thymocyte/Thy-1 autoreactive μκ transgenic (ATAμκ Tg) Pla2g2a+BALB/c background C.B17 mice generated NKT2 cells that continuously control CD1d+B1 B cells through old aging and lost CD1d in B1 B cells generating strong B1 ATA B cell leukemia/lymphoma. Pla2g2a-deficient ATAμκTg C57BL/6 mice suppressed the initial B1a cell increase, with low/negative spontaneous leukemia/lymphoma generation. These data confirmed that the presence of Pla2g2a to control bacteria is important to allow the neonatal to adult stage. Pla2g2a promotes innate Th2-type immunity lymphocytes to increase early generated B1a cells.
One shot ancient character recognition with siamese similarity network
Authors: Liu Xuxing , Gao Weize , Li Rankang , Xiong Yu , Tang Xiaoqin , Chen Shanxiong
Published: September 2022

Ancient character recognition is not only important for the study and understanding of ancient history but also has a profound impact on the inheritance and development of national culture. In order to reduce the study of difficult professional knowledge of ancient characters, and meanwhile overcome the lack of data, class imbalance, diversification of glyphs, and open set recognition problems in ancient characters, we propose a Siamese similarity network based on a similarity learning method to directly learn input similarity and then apply the trained model to establish one shot classification task for recognition. Multi-scale fusion backbone structure and embedded structure are proposed in the network to improve the model's ability to extract features. We also propose the soft similarity contrast loss function for the first time, which ensures the optimization of similar images with higher similarity and different classes of images with greater differences while reducing the over-optimization of back-propagation leading to model overfitting. Specially, we propose a cumulative class prototype based on our network to solve the deviation problem of the mean class prototype and obtain a good class representation. Since new ancient characters can still be found in reality, our model has the ability to reject unknown categories while identifying new ones. A large number of experiments show that our proposed method has achieved high-efficiency discriminative performance and obtained the best performance over the methods of traditional deep learning and other classic one-shot learning.
Development of a brain wave model based on the quantitative analysis of EEG and EEG biofeedback therapy in patients with panic attacks during the COVID-19 pandemic
Authors: Kopańska Marta , Ochojska Danuta , Mytych Wiktoria , Lis Marcin W. , Banaś-Ząbczyk Agnieszka
Published: September 2022

The current global crisis facing the world is the COVID-19 pandemic. Infection from the SARS-CoV-2 virus leads to serious health complications and even death. As it turns out, COVID-19 not only physically assails the health of those infected, but also leads to serious mental illness regardless of the presence of the disease. Social isolation, fear, concern for oneself and one's loved ones, all of this occurs when a pandemic overloads people. People exhibit numerous neurological disorders that have never happened to them before. Patients are diagnosed with frequent panic attacks, the result of which can be seen in their Quantitative Electroencephalogram results. This test may be one of the main diagnostic tools of the COVID-19 pandemic. From the results obtained, it is possible to compare and draw conclusions. This method of testing effectively allows EEG biofeedback training and observes its effect on brain activity. The feedback received in this way gives us the opportunity to properly tailor a protocol for the patient and their conditions. Numerous studies support the effectiveness of EEG biofeedback for panic attacks and other psychiatric disorders. The purpose of our study was to show the effectiveness of EEG biofeedback with a Quantitative Electroencephalogram of the brainwave pattern after having COVID-19 and what symptoms may result.