bluuebunny/crossref_metadata_2025 huggingface dataset:
Minimising multi-centre radiomics variability through image normalisation: a pilot study
Authors: Campello Víctor M. , Martín-Isla Carlos , Izquierdo Cristian , Guala Andrea , Palomares José F. Rodríguez , Viladés David , Descalzo Martín L. , Karakas Mahir , Çavuş Ersin , Raisi-Estabragh Zahra , Petersen Steffen E. , Escalera Sergio , Seguí Santi , Lekadir Karim
Published: July 2022

Radiomics is an emerging technique for the quantification of imaging data that has recently shown great promise for deeper phenotyping of cardiovascular disease. Thus far, the technique has been mostly applied in single-centre studies. However, one of the main difficulties in multi-centre imaging studies is the inherent variability of image characteristics due to centre differences. In this paper, a comprehensive analysis of radiomics variability under several image- and feature-based normalisation techniques was conducted using a multi-centre cardiovascular magnetic resonance dataset. 218 subjects divided into healthy (n = 112) and hypertrophic cardiomyopathy (n = 106, HCM) groups from five different centres were considered. First and second order texture radiomic features were extracted from three regions of interest, namely the left and right ventricular cavities and the left ventricular myocardium. Two methods were used to assess features’ variability. First, feature distributions were compared across centres to obtain a distribution similarity index. Second, two classification tasks were proposed to assess: (1) the amount of centre-related information encoded in normalised features (centre identification) and (2) the generalisation ability for a classification model when trained on these features (healthy versus HCM classification). The results showed that the feature-based harmonisation technique ComBat is able to remove the variability introduced by centre information from radiomic features, at the expense of slightly degrading classification performance. Piecewise linear histogram matching normalisation gave features with greater generalisation ability for classification ( balanced accuracy in between 0.78 ± 0.08 and 0.79 ± 0.09). Models trained with features from images without normalisation showed the worst performance overall ( balanced accuracy in between 0.45 ± 0.28 and 0.60 ± 0.22). In conclusion, centre-related information removal did not imply good generalisation ability for classification.
Root exudate composition reflects drought severity gradient in blue grama (Bouteloua gracilis)
Authors: Ulrich Danielle E. M. , Clendinen Chaevien S. , Alongi Franklin , Mueller Rebecca C. , Chu Rosalie K. , Toyoda Jason , Gallegos-Graves La Verne , Goemann Hannah M. , Peyton Brent , Sevanto Sanna , Dunbar John
Published: July 2022

Plant survival during environmental stress greatly affects ecosystem carbon (C) cycling, and plant–microbe interactions are central to plant stress survival. The release of C-rich root exudates is a key mechanism plants use to manage their microbiome, attracting beneficial microbes and/or suppressing harmful microbes to help plants withstand environmental stress. However, a critical knowledge gap is how plants alter root exudate concentration and composition under varying stress levels. In a greenhouse study, we imposed three drought treatments (control, mild, severe) on blue grama (Bouteloua gracilisKunth Lag. Ex Griffiths), and measured plant physiology and root exudate concentration and composition using GC–MS, NMR, and FTICR. With increasing drought severity, root exudate total C and organic C increased concurrently with declining predawn leaf water potential and photosynthesis. Root exudate composition mirrored the physiological gradient of drought severity treatments. Specific compounds that are known to alter plant drought responses and the rhizosphere microbiome mirrored the drought severity-induced root exudate compositional gradient. Despite reducing C uptake, these plants actively invested C to root exudates with increasing drought severity. Patterns of plant physiology and root exudate concentration and composition co-varied along a gradient of drought severity.
Glutathione improves low temperature stress tolerance in pusa sheetal cultivar of Solanum lycopersicum
Authors: Gul Nadia , Ahmad Parvaiz , Wani Tanveer A. , Tyagi Anshika , Aslam Saima
Published: July 2022

To investigate the impact of Glutathione (GSH) in mitigating low-temperature stress in Pusa Sheetal cv. of Solanum lycopersicum and imparting low-temperature tolerance by evaluating the different physiological responses. The plant under research was also being studied for its growth and stress tolerance. Low temperatures (LT) stress was applied to seedlings with or without GSH application 12 h before LT stress (prophylactic dose), after 12 h-LT (preemptive dose), and post 12-h recovery (curative dose). Different concentrations of GSH [0, G1 (0.5 mM), G2 (1 mM) and G3 (2 mM)] against LT stress were used. Antioxidant activities, photosynthesis, growth, and stress tolerance indices were quantified. LT stress caused an oxidative burst in S. lycopersicum seedlings of the Pusa Sheetal cv. as indicated by increased peroxidation of lipids and H2O2 concentration. Glutathione reductase (GR), superoxide dismutase (SOD), catalase (CAT), and ascorbate peroxidase (APX) activities were enhanced. The best concentration was G2 (1 mM), which resulted in a rise in antioxidant activity. Moreover, a decline in lipid peroxidation and H2O2 levels was also seen. The purpose of this study is to identify the role of GSH in reducing LT stress and to find the best dose concentration. This is the first report to assess the GSH-mediated LT stress tolerance in S. lycopersicum (Pusa Sheetal cv.). Therefore, exogenous GSH application of optimal concentration of GSH to LT stressed S. lycopersicum can be an effective approach for augmenting the plant detoxification system and promoting its growth and development.
Thermodynamic basis for the demarcation of Arctic and alpine treelines
Authors: Martin Meredith Richardson , Kumar Praveen , Sonnentag Oliver , Marsh Philip
Published: July 2022

At the edge of alpine and Arctic ecosystems all over the world, a transition zone exists beyond which it is either infeasible or unfavorable for trees to exist, colloquially identified as the treeline. We explore the possibility of a thermodynamic basis behind this demarcation in vegetation by considering ecosystems as open systems driven by thermodynamic advantage—defined by vegetation’s ability to dissipate heat from the earth’s surface to the air above the canopy. To deduce whether forests would be more thermodynamically advantageous than existing ecosystems beyond treelines, we construct and examine counterfactual scenarios in which trees exist beyond a treeline instead of the existing alpine meadow or Arctic tundra. Meteorological data from the Italian Alps, United States Rocky Mountains, and Western Canadian Taiga-Tundra are used as forcing for model computation of ecosystem work and temperature gradients at sites on both sides of each treeline with and without trees. Model results indicate that the alpine sites do not support trees beyond the treeline, as their presence would result in excessive CO$$_2$$

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loss and extended periods of snowpack due to temperature inversions (i.e., positive temperature gradient from the earth surface to the atmosphere). Further, both Arctic and alpine sites exhibit negative work resulting in positive feedback between vegetation heat dissipation and temperature gradient, thereby extending the duration of temperature inversions. These conditions demonstrate thermodynamic infeasibility associated with the counterfactual scenario of trees existing beyond a treeline. Thus, we conclude that, in addition to resource constraints, a treeline is an outcome of an ecosystem’s ability to self-organize towards the most advantageous vegetation structure facilitated by thermodynamic feasibility.
Structure-based prediction of BRAF mutation classes using machine-learning approaches
Authors: Krebs Fanny S. , Britschgi Christian , Pradervand Sylvain , Achermann Rita , Tsantoulis Petros , Haefliger Simon , Wicki Andreas , Michielin Olivier , Zoete Vincent
Published: July 2022

The BRAF kinase is attracting a lot of attention in oncology as alterations of its amino acid sequence can constitutively activate the MAP kinase signaling pathway, potentially contributing to the malignant transformation of the cell but at the same time rendering it sensitive to targeted therapy. Several pathologic BRAF variants were grouped in three different classes (I, II and III) based on their effects on the protein activity and pathway. Discerning the class of a BRAF mutation permits to adapt the treatment proposed to the patient. However, this information is lacking new and experimentally uncharacterized BRAF mutations detected in a patient biopsy. To overcome this issue, we developed a new in silico tool based on machine learning approaches to predict the potential class of a BRAF missense variant. As class I only involves missense mutations of Val600, we focused on the mutations of classes II and III, which are more diverse and challenging to predict. Using a logistic regression model and features including structural information, we were able to predict the classes of known mutations with an accuracy of 90%. This new and fast predictive tool will help oncologists to tackle potential pathogenic BRAF mutations and to propose the most appropriate treatment for their patients.
Detection of NO3− introduced in plasma-irradiated dry lettuce seeds using liquid chromatography-electrospray ionization quantum mass spectrometry (LC-ESI QMS)
Authors: Okumura Takamasa , Attri Pankaj , Kamataki Kunihiro , Yamashita Naoto , Tsukada Yuichi , Itagaki Naho , Shiratani Masaharu , Ishibashi Yushi , Kuchitsu Kazuyuki , Koga Kazunori
Published: July 2022

Discharge plasma irradiates seeds with reactive oxygen and nitrogen species (RONS). However, RONS introduced in seeds by plasma irradiation have not been successfully detected thus far. This study provides experimental evidence that nitrate ion NO3− is introduced in lettuce seeds as RONS upon irradiation with atmospheric-pressure air dielectric barrier discharge plasma. Plasma irradiation for 5 min promotes seed germination. The components of the plasma-irradiated seeds were examined using electrospray ionization quantum mass spectrometry (ESI QMS), which revealed that the plasma irradiation introduced an ion with a mass of 62 m/z in detectable amounts. This ion was identified as NO3− by liquid chromatography (LC), multiple wavelength detector (MWD), and LC-ESI QMS. A one-dimensional simulation at electron temperature Te = 1 eV, electron density Ne = 1013/m3, and gas temperature Tg = 300 K indicated the introduction of NO3−, involving nitric oxide NO. NO3− is one of the most important ions that trigger signal transduction for germination when introduced in seeds. The scanning electron microscopy (SEM) images revealed that there was no change on the surface of the seeds after plasma irradiation. Plasma irradiation is an effective method of introducing NO3− in seeds in a dry process without causing damage.
Coronamoeba villafranca gen. nov. sp. nov. (Amoebozoa, Dermamoebida) challenges the correlation of morphology and phylogeny in Amoebozoa
Authors: Kudryavtsev Alexander , Voytinsky Fyodor , Volkova Ekaterina
Published: July 2022

Coronamoeba villafranca gen. nov. sp. nov. is a small amoeba isolated from the surface planktonic biotope in the Bay of Villefranche (Mediterranean Sea). It has a confusing set of morphological and molecular characters. Its locomotive form is subcylindrical and monopodial with monoaxial cytoplasmic flow and occasional hyaline bulging at the anterior edge (a monotactic morphotype). Based on this set of characters, this amoeba is most similar to members of the genus Nolandella (Tubulinea, Euamoebida). However, molecular phylogenetic analysis based on only the small subunit ribosomal RNA (SSU rRNA) gene and on two concatenated markers (SSU rRNA gene and actin) robustly places this species in the Discosea, specifically, in a clade with Dermamoeba and Paradermamoeba (Dermamoebida) as the closest described relatives, and several SSU rRNA clones from environmental DNA. A unique glycocalyx of the studied amoeba consisting of complex separate units with pentameric symmetry may be considered a unifying character of this species with other dermamoebids. The monotactic morphotype demonstrated by these amoebae primarily occurs in Tubulinea but was recently confirmed in other clades of Amoebozoa (e.g. Dactylopodida and Variosea). This morphotype may be the plesiomorphic mode of cell organization in Amoebozoa that might have evolved in the last amoebozoan common ancestor (LACA) and conserved in several lineages of this group. It may reflect basic characteristics of the cytoskeletal structure and functions in Amoebozoa.
Skull variation in Afro-Eurasian monkeys results from both adaptive and non-adaptive evolutionary processes
Authors: Schroeder Lauren , Elton Sarah , Ackermann Rebecca Rogers
Published: July 2022

Afro-Eurasian monkeys originated in the Miocene and are the most species-rich modern primate family. Molecular and fossil data have provided considerable insight into their evolutionary divergence, but we know considerably less about the evolutionary processes that underlie these differences. Here, we apply tests developed from quantitative genetics theory to a large (n > 3000) cranio-mandibular morphometric dataset, investigating the relative importance of adaptation (natural selection) and neutral processes (genetic drift) in shaping diversity at different taxonomic levels, an approach applied previously to monkeys of the Americas, apes, hominins, and other vertebrate taxa. Results indicate that natural selection, particularly for differences in size, plays a significant role in diversifying Afro-Eurasian monkeys as a whole. However, drift appears to better explain skull divergence within the subfamily Colobinae, and in particular the African colobine clade, likely due to habitat fragmentation. Small and declining population sizes make it likely that drift will continue in this taxon, with potentially dire implications for genetic diversity and future resilience in the face of environmental change. For the other taxa, many of whom also have decreasing populations and are threatened, understanding adaptive pressures similarly helps identify relative vulnerability and may assist with prioritising scarce conservation resources.
The effect of supporting carbons on the gas phase synthesis of octahedral Pt3Ni electrocatalysts with various H2:CO ratios
Authors: Payattikul L. , Intakhuen L. , Kiatsiriroat T. , Punyawudho K.
Published: July 2022

The gas phase synthesis of octahedral Pt3Ni/C electrocatalysts using several carbon substrates (Ketjen black, Graphene, and Vulcan XC-72R) was investigated. Different carbon substrates altered the morphology and alloy of Pt3Ni nanoparticles, with octahedral morphology and alloy metal preferentially developing on Ketjen black and Graphene, while spherical shape and bimetallic metal preferentially developing on Vulcan. Furthermore, the shape was shown to be regulated throughout the reduction process, with the H2:CO ratio playing a crucial role in controlling octahedral morphology and carrying out the ORR activity. At a 1:3 H2:CO ratio, the Pt3Ni/Ketjen black exhibited the highest ORR activity for both mass activity (1.02 A mgPt−1) and specific activity (5.09 mA cm−2) that were 16.5 and 66.1 times larger than commercial Pt/C catalysts, respectively (0.062 A mgPt−1 and 0.077 mA cm−2). The best ORR activity of Pt3Ni onto Graphene and Vulcan XC-72R was exhibited with a 1:1 H2:CO mixture. The catalysts were tested using a 4000-voltage-cycle accelerated durability test, and the Pt3Ni/Ketjen catalyst fared the best in terms of ORR stability and durability.
Blockade of CD47 enhances the antitumor effect of macrophages in renal cell carcinoma through trogocytosis
Authors: Park Ha-Ram , Kim Seong-Eun , Keam Bhumsuk , Chung Hyewon , Seok Seung Hyeok , Kim Soyeon , Kim Miso , Kim Tae Min , Doh Junsang , Kim Dong-Wan , Heo Dae Seog
Published: July 2022

Immune checkpoint inhibitors and vascular endothelial growth factor receptor tyrosine kinase inhibitors (VEGFR TKIs) are mainstream treatments for renal cell carcinoma (RCC). Both T cells and macrophages infiltrate the tumor microenvironment of RCC. CD47, an immune checkpoint of macrophages, transmits the “don’t eat me” signal to macrophages. We propose a novel therapeutic strategy that activates the antitumor effect of macrophages. We found that CD47 was expressed in patients with RCC, and high CD47 expression was indicative of worse overall survival in datasets from The Cancer Genome Atlas. We observed that CD47-blocking antibodies enhanced the antitumor effect of macrophages against human RCC cell lines. Trogocytosis, rather than phagocytosis, occurred and was promoted by increased cell-to-cell contact between macrophages and RCC cells. Trogocytosis induced by CD47 blockade occurred in the presence of CD11b integrin signaling in macrophages and was augmented when RCC cells were exposed to VEGFR TKIs, except for sunitinib. In conclusion, this study presents evidence that anti-CD47 blocking antibodies improve the antitumor effect of macrophages in RCC. In combination with VEGFR TKIs, CD47 blockade is a potential therapeutic strategy for patients with RCC.
Amyotrophic lateral sclerosis and cerebellum
Authors: Kabiljo Renata , Iacoangeli Alfredo , Al-Chalabi Ammar , Rosenzweig Ivana
Published: July 2022

Amyotrophic lateral sclerosis (ALS) is a devastating, heterogeneous neurodegenerative neuromuscular disease that leads to a fatal outcome within 2–5 years, and yet, a precise nature of the association between its major phenotypes and the cerebellar role in ALS pathology remains unknown. Recently, repeat expansions in several genes in which variants appreciably contribute to cerebellar pathology, including C9orf72, NIPA1, ATXN2 and ATXN1, have been found to confer a significant risk for ALS. To better define this relationship, we performed MAGMA gene-based analysis and tissue enrichment analysis using genome-wide association study summary statistics based on a study of 27,205 people with ALS and 110,881 controls. Our preliminary results imply a striking cerebellar tissue specificity and further support increasing calls for re-evaluation of the cerebellar role in the ALS pathology.
Robust osteogenic efficacy of 2α-heteroarylalkyl vitamin D analogue AH-1 in VDR (R270L) hereditary vitamin D-dependent rickets model rats
Authors: Nishikawa Miyu , Murose Naruhiro , Mano Hiroki , Yasuda Kaori , Isogai Yasuhiro , Kittaka Atsushi , Takano Masashi , Ikushiro Shinichi , Sakaki Toshiyuki
Published: July 2022

Active vitamin D form 1α,25-dihydroxtvitamin D3 (1,25(OH)2D3) plays pivotal roles in calcium homeostasis and osteogenesis via its transcription regulation effect via binding to vitamin D receptor (VDR). Mutated VDR often causes hereditary vitamin D-dependent rickets (VDDR) type II, and patients with VDDR-II are hardly responsive to physiological doses of 1,25(OH)D3. Current therapeutic approaches, including high doses of oral calcium and supraphysiologic doses of 1,25(OH)2D3, have limited success and fail to improve the quality of life of affected patients. Thus, various vitamin D analogues have been developed as therapeutic options. In our previous study, we generated genetically modified rats with mutated Vdr(R270L), an ortholog of human VDR(R274L) isolated from the patients with VDDR-II. The significant reduced affinity toward 1,25(OH)2D3 of rat Vdr(R270L) enabled us to evaluate biological activities of exogenous VDR ligand without 1α-hydroxy group such as 25(OH)D3. In this study, 2α-[2-(tetrazol-2-yl)ethyl]-1α,25(OH)2D3 (AH-1) exerted much higher affinity for Vdr(R270L) in in vitro ligand binding assay than both 25(OH)D3 and 1,25(OH)2D3. A robust osteogenic activity of AH-1 was observed in Vdr(R270L) rats. Only a 40-fold lower dose of AH-1 than that of 25(OH)D3 was effective in ameliorating rickets symptoms in Vdr(R270L) rats. Therefore, AH-1 may be promising for the therapy of VDDR-II with VDR(R274L).
Antibody CDR amino acids underlying the functionality of antibody repertoires in recognizing diverse protein antigens
Authors: Peng Hung-Pin , Hsu Hung-Ju , Yu Chung-Ming , Hung Fei-Hung , Tung Chao-Ping , Huang Yu-Chuan , Chen Chi-Yung , Tsai Pei-Hsun , Yang An-Suei
Published: July 2022

Antibodies recognize protein antigens with exquisite specificity in a complex aqueous environment, where interfacial waters are an integral part of the antibody–protein complex interfaces. In this work, we elucidate, with computational analyses, the principles governing the antibodies’ specificity and affinity towards their cognate protein antigens in the presence of explicit interfacial waters. Experimentally, in four model antibody–protein complexes, we compared the contributions of the interaction types in antibody–protein antigen complex interfaces with the antibody variants selected from phage-displayed synthetic antibody libraries. Evidently, the specific interactions involving a subset of aromatic CDR (complementarity determining region) residues largely form the predominant determinant underlying the specificity of the antibody–protein complexes in nature. The interfacial direct/water-mediated hydrogen bonds accompanying the CDR aromatic interactions are optimized locally but contribute little in determining the epitope location. The results provide insights into the phenomenon that natural antibodies with limited sequence and structural variations in an antibody repertoire can recognize seemingly unlimited protein antigens. Our work suggests guidelines in designing functional artificial antibody repertoires with practical applications in developing novel antibody-based therapeutics and diagnostics for treating and preventing human diseases.
Network analysis of preictal iEEG reveals changes in network structure preceding seizure onset
Authors: Sumsky Stefan , Greenfield L. John
Published: July 2022

Seizures likely result from aberrant network activity and synchronization. Changes in brain network connectivity may underlie seizure onset. We used a novel method of rapid network model estimation from intracranial electroencephalography (iEEG) data to characterize pre-ictal changes in network structure prior to seizure onset. We analyzed iEEG data from 20 patients from the iEEG.org database. Using 10 s epochs sliding by 1 s intervals, a multiple input, single output (MISO) state space model was estimated for each output channel and time point with all other channels as inputs, generating sequential directed network graphs of channel connectivity. These networks were assessed using degree and betweenness centrality. Both degree and betweenness increased at seizure onset zone (SOZ) channels 37.0 ± 2.8 s before seizure onset. Degree rose in all channels 8.2 ± 2.2 s prior to seizure onset, with increasing connections between the SOZ and surrounding channels. Interictal networks showed low and stable connectivity. A novel MISO model-based network estimation method identified changes in brain network structure just prior to seizure onset. Increased connectivity was initially isolated within the SOZ and spread to non-SOZ channels before electrographic seizure onset. Such models could help confirm localization of SOZ regions.
Synthesis of diverse spiro-imidazo pyridine-indene derivatives via acid-promoted annulation reaction of bindone and heterocyclic ketene aminals
Authors: Nasri Shima , Bayat Mohammad , Miankooshki Fatemeh Rostami
Published: July 2022

A new multi-component reaction for the synthesis of novel and diverse spiro-imidazo pyridine-indene derivatives named spiro[imidazo[1,2-a]indeno[2,1-e]pyridine-5,1′-indene and indenylidene-1H-spiro[imidazo[1,2-a]pyridine-7,1′-indene was successfully developed by the reaction between heterocyclic ketene aminals (generated from 1,1-bis(methylthio)-2-nitro ethylene and diamine) and [1,2′-biindenylidene]-1′,3,3′-trione (bindone) (in situ generated from self-condensation of 1,3-indandion) by using malononitrile as a promoter or as one of the precursors respectively in the presence of p-TSA as the acid catalyst in EtOH as reaction medium under reflux conditions. Depending on whether the reaction is single-step or two-step, malononitrile can act as a promoter or reactant. The convenient one-pot operation, straightforward isolation without using additional purification methods, and the use of a variety of diamines and cysteamine hydrochloride causing a variety of structural products are attractive aspects of the present approach. The synthesized bindone and final product contains active methylene and this active site can be involved in further reactions to synthesize more complex heterocycles.
Age estimation from sleep studies using deep learning predicts life expectancy
Authors: Brink-Kjaer Andreas , Leary Eileen B. , Sun Haoqi , Westover M. Brandon , Stone Katie L. , Peppard Paul E. , Lane Nancy E. , Cawthon Peggy M. , Redline Susan , Jennum Poul , Sorensen Helge B. D. , Mignot Emmanuel
Published: July 2022

Sleep disturbances increase with age and are predictors of mortality. Here, we present deep neural networks that estimate age and mortality risk through polysomnograms (PSGs). Aging was modeled using 2500 PSGs and tested in 10,699 PSGs from men and women in seven different cohorts aged between 20 and 90. Ages were estimated with a mean absolute error of 5.8 ± 1.6 years, while basic sleep scoring measures had an error of 14.9 ± 6.29 years. After controlling for demographics, sleep, and health covariates, each 10-year increment in age estimate error (AEE) was associated with increased all-cause mortality rate of 29% (95% confidence interval: 20–39%). An increase from −10 to +10 years in AEE translates to an estimated decreased life expectancy of 8.7 years (95% confidence interval: 6.1–11.4 years). Greater AEE was mostly reflected in increased sleep fragmentation, suggesting this is an important biomarker of future health independent of sleep apnea.
Unleashing the potential of digital pathology data by training computer-aided diagnosis models without human annotations
Authors: Marini Niccolò , Marchesin Stefano , Otálora Sebastian , Wodzinski Marek , Caputo Alessandro , van Rijthoven Mart , Aswolinskiy Witali , Bokhorst John-Melle , Podareanu Damian , Petters Edyta , Boytcheva Svetla , Buttafuoco Genziana , Vatrano Simona , Fraggetta Filippo , van der Laak Jeroen , Agosti Maristella , Ciompi Francesco , Silvello Gianmaria , Muller Henning , Atzori Manfredo
Published: July 2022

The digitalization of clinical workflows and the increasing performance of deep learning algorithms are paving the way towards new methods for tackling cancer diagnosis. However, the availability of medical specialists to annotate digitized images and free-text diagnostic reports does not scale with the need for large datasets required to train robust computer-aided diagnosis methods that can target the high variability of clinical cases and data produced. This work proposes and evaluates an approach to eliminate the need for manual annotations to train computer-aided diagnosis tools in digital pathology. The approach includes two components, to automatically extract semantically meaningful concepts from diagnostic reports and use them as weak labels to train convolutional neural networks (CNNs) for histopathology diagnosis. The approach is trained (through 10-fold cross-validation) on 3’769 clinical images and reports, provided by two hospitals and tested on over 11’000 images from private and publicly available datasets. The CNN, trained with automatically generated labels, is compared with the same architecture trained with manual labels. Results show that combining text analysis and end-to-end deep neural networks allows building computer-aided diagnosis tools that reach solid performance (micro-accuracy = 0.908 at image-level) based only on existing clinical data without the need for manual annotations.
Visuo-thermal congruency modulates the sense of body ownership
Authors: Crucianelli Laura , Ehrsson H. Henrik
Published: July 2022

Thermosensation has been redefined as an interoceptive modality that provides information about the homeostatic state of the body. However, the contribution of thermosensory signals to the sense of body ownership remains unclear. Across two rubber hand illusion (RHI) experiments (N = 73), we manipulated the visuo-thermal congruency between the felt and seen temperature, on the real and rubber hand respectively. We measured the subjectively experienced RHI, the perceived hand location and temperature of touch, and monitored skin temperature. We found that visuo-thermal incongruencies between the seen and felt touch reduced the subjective and behavioural RHI experience (Experiment 1). Visuo-thermal incongruencies also gave rise to a visuo-thermal illusion effect, but only when the rubber hand was placed in a plausible position (Experiment 2) and when considering individual differences in interoceptive sensibility. Thus, thermosensation contributes to the sense of body ownership by a mechanism of dynamic integration of visual and thermosensory signals.
Immunometabolic and potential tumor-promoting changes in 3D cervical cell models infected with bacterial vaginosis-associated bacteria
Authors: Maarsingh Jason D. , Łaniewski Paweł , Herbst-Kralovetz Melissa M.
Published: July 2022

Specific bacteria of the human microbiome influence carcinogenesis at diverse anatomical sites. Bacterial vaginosis (BV) is the most common vaginal disorder in premenopausal women that is associated with gynecologic sequelae, including cervical cancer. BV-associated microorganisms, such as Fusobacterium, Lancefieldella, Peptoniphilus, and Porphyromonas have been associated with gynecologic and other cancers, though the pro-oncogenic mechanisms employed by these bacteria are poorly understood. Here, we integrated a multi-omics approach with our three-dimensional (3-D) cervical epithelial cell culture model to investigate how understudied BV-associated bacteria linked to gynecologic neoplasia influence hallmarks of cancer in vitro. Lancefieldella parvulum and Peptoniphilus lacrimalis elicited robust proinflammatory responses in 3-D cervical cells. Fusobacterium nucleatum and Fusobacterium gonidiaformans modulated metabolic hallmarks of cancer corresponding to accumulation of 2-hydroxyglutarate, pro-inflammatory lipids, and signs of oxidative stress and genotoxic hydrogen sulfide. This study provides mechanistic insights into how gynecologic cancer-associated bacteria might facilitate a tumor-promoting microenvironment in the human cervix.
NUPR1 protects against hyperPARylation-dependent cell death
Authors: Santofimia-Castaño Patricia , Huang Can , Liu Xi , Xia Yi , Audebert Stephane , Camoin Luc , Peng Ling , Lomberk Gwen , Urrutia Raul , Soubeyran Philippe , Neira Jose Luis , Iovanna Juan
Published: July 2022

Proteomic, cellular and biochemical analysis of the stress protein NUPR1 reveals that it binds to PARP1 into the nucleus and inhibits PARP1 activity in vitro. Mutations on residues Ala33 or Thr68 of NUPR1 or treatment with its inhibitor ZZW-115 inhibits this effect. PARylation induced by 5-fluorouracil (5-FU) treatment is strongly enhanced by ZZW-115 and associated with a decrease of NAD+/NADH ratio and rescued by the PARP inhibitor olaparib. Cell death induced by ZZW-115 treatment of pancreas cancer-derived cells is rescued by olaparib and improved with PARG inhibitor PDD00017273. The mitochondrial catastrophe induced by ZZW-115 treatment or by genetic inactivation of NUPR1 is associated to a hyperPARylation of the mitochondria, disorganization of the mitochondrial network, mitochondrial membrane potential decrease, and with increase of superoxide production, intracellular level of reactive oxygen species (ROS) and cytosolic levels of Ca2+. These features are rescued by olaparib or NAD+ precursor nicotinamide mononucleotide in a dose-dependent manner and partially by antioxidants treatments. In conclusion, inactivation of NUPR1 induces a hyperPARylation, which in turn, induces a mitochondrial catastrophe and consequently a cell death through a non-canonical Parthanatos, since apoptosis inducing-factor (AIF) is not translocated out of the mitochondria.
Upregulation of OASIS/CREB3L1 in podocytes contributes to the disturbance of kidney homeostasis
Authors: Miyake Yoshiaki , Obana Masanori , Yamamoto Ayaha , Noda Shunsuke , Tanaka Koki , Sakai Hibiki , Tatsumoto Narihito , Makino Chihiro , Kanemoto Soshi , Shioi Go , Tanaka Shota , Maeda Makiko , Okada Yoshiaki , Imaizumi Kazunori , Asanuma Katsuhiko , Fujio Yasushi
Published: July 2022

Podocyte injury is involved in the onset and progression of various kidney diseases. We previously demonstrated that the transcription factor, old astrocyte specifically induced substance (OASIS) in myofibroblasts, contributes to kidney fibrosis, as a novel role of OASIS in the kidneys. Importantly, we found that OASIS is also expressed in podocytes; however, the pathophysiological significance of OASIS in podocytes remains unknown. Upon lipopolysaccharide (LPS) treatment, there is an increase in OASIS in murine podocytes. Enhanced serum creatinine levels and tubular injury, but not albuminuria and podocyte injury, are attenuated upon podocyte-restricted OASIS knockout in LPS-treated mice, as well as diabetic mice. The protective effects of podocyte-specific OASIS deficiency on tubular injury are mediated by protein kinase C iota (PRKCI/PKCι), which is negatively regulated by OASIS in podocytes. Furthermore, podocyte-restricted OASIS transgenic mice show tubular injury and tubulointerstitial fibrosis, with severe albuminuria and podocyte degeneration. Finally, there is an increase in OASIS-positive podocytes in the glomeruli of patients with minimal change nephrotic syndrome and diabetic nephropathy. Taken together, OASIS in podocytes contributes to podocyte and/or tubular injury, in part through decreased PRKCI. The induction of OASIS in podocytes is a critical event for the disturbance of kidney homeostasis.
Topological surface superconductivity in FeSe0.45Te0.55
Authors: Mascot Eric , Cocklin Sagen , Graham Martin , Mashkoori Mahdi , Rachel Stephan , Morr Dirk K.
Published: July 2022

The engineering of Majorana zero modes in topological superconductors, a paradigm for the realization of topological quantum computing and topology-based devices, has been hampered by the absence of materials with sufficiently large superconducting gaps. Recent experiments, however, have provided enthralling evidence for the existence of topological surface superconductivity in the iron-based superconductor FeSe0.45Te0.55 possessing a full s±-wave gap of a few meV. Here, we propose a mechanism for the emergence of topological superconductivity on the surface of FeSe0.45Te0.55 by demonstrating that the interplay between the s±-wave symmetry of the superconducting gap, surface magnetism, and a Rashba spin–orbit interaction gives rise to robust topological superconducting phases. Moreover, the proposed mechanism explains a series of experimentally observed hallmarks of topological superconductivity, such as the emergence of Majorana zero modes in the center of vortex cores and at the end of line defects, as well as of chiral Majorana edge modes along domain walls. We also propose that the spatial distribution of supercurrents near a domain wall is a characteristic signature measurable via a scanning superconducting quantum interference device that can distinguish between chiral Majorana edge modes and trivial in-gap states.
Probabilistic framework for optimal experimental campaigns in the presence of operational constraints
Authors: Kusumo Kennedy Putra , Kuriyan Kamal , Vaidyaraman Shankarraman , García Muñoz Salvador , Shah Nilay , Chachuat Benoît
Published: July 2022

Methodology for designing optimal experiment campaigns under hard constraints and model uncertainty. A tractable solution technique using a synergistic combination of sampling and convex optimization.
Dual-strategy biosensing of glucose based on multifunctional CuWO4 nanoparticles
Authors: Zhang Yu , Li Shuang , Liu Hongyuan , Shi Feng , Li Juan , Hu Xiaoya , Yang Zhanjun
Published: July 2022

The multifunctional CuWO4 NPs were prepared and exhibit large specific surface area, good conductivity and excellent peroxidase-like activity, which was exploited for electrochemical and colorimetric dual-strategy biosensing of glucose.
Core–shell polycationic polyurea pharmadendrimers: new-generation of sustainable broad-spectrum antibiotics and antifungals
Authors: Pinto Sandra N. , Mil-Homens Dalila , Pires Rita F. , Alves Marta M. , Serafim Gabriel , Martinho Nuno , Melo Manuel , Fialho Arsénio M. , Bonifácio Vasco D. B.
Published: July 2022

A novel class of antimicrobial engineered nanoparticles that mimic natural peptides but exclude their adverse cytotoxicity and hemotoxicity.
Antibody dual-functionalisation enabled through a modular divinylpyrimidine disulfide rebridging strategy
Authors: Hanby Abigail R. , Walsh Stephen J. , Counsell Andrew J. , Ashman Nicola , Mortensen Kim T. , Carroll Jason S. , Spring David R.
Published: July 2022

A modular and metal-free chemical methodology for the synthesis of dual-functionalised antibody-drug conjugates.
Fabrication of antimicrobial polymeric films by compression molding of peptide assemblies and polyethylene
Authors: Kaganovich Michaela , Shlosman Koranit , Goldman Evgeniya , Benchis Marina , Eitan Tamar , Shemesh Rotem , Gamliel Abraham , Reches Meital
Published: July 2022

This paper presents compression molding of peptide assemblies with low-density polyethylene (LDPE) for the robust production of antimicrobial polymeric films.
Up-conversion luminescence properties and temperature sensitivity of AgBi(MoO4)2:Yb3+/Er3+/Ho3+/Tm3+ phosphors
Authors: Wu Heyan , Liang Yunhao , Ma Yue , Yang Jun , Hu Shanshan
Published: July 2022

A series of AgBi(MoO4)2:Ln3+ luminous phosphors emitting green, yellow, blue and white light were obtained. And the AgBi(MoO4)2:Yb3+/Er3+ phosphors show good temperature sensitivity with an absolute sensitivity maximum value of 1.32% K−1 at 463 K.
Expanding the solid-state landscape of dexamethasone: a specific sandwich structure in facilitating the formation of kinetically stable cocrystals from mechanochemistry
Authors: Wong Si Nga , Low Kam-Hung , Weng Jingwen , Chan Ho Wan , Chow Shing Fung
Published: July 2022

We herein report the successful synthesis of the first two dexamethasone cocrystals from mechanochemistry.
Recognition between CD147 and cyclophilin A deciphered by accelerated molecular dynamics simulations
Authors: Yang Zhiwei , Zang Yongjian , Wang He , Kang Ying , Zhang Jianwen , Li Xuhua , Zhang Lei , Zhang Shengli
Published: July 2022

The active site of extracellular cyclosporin A (CypA) binds to a groove formed by the Ig1 and Ig2 domains of CD147, and this binding is regulated by residues Pro180-Gly181 but not Pro211.
Theoretical study of macrocyclic host molecules: from supramolecular recognition to self-assembly
Authors: Wang Hui , Zheng Xiaoyan
Published: July 2022

In this review, we take heteroatom-bridged heteroaromatic calixarene, cucurbituril and cyclodextrin as examples, and summarize the recent progress in the molecular recognition and self-assembly of macrocyclic host molecules by multiscale modelling.
Combined fragment-based machine learning force field with classical force field and its application in the NMR calculations of macromolecules in solutions
Authors: Liao Kang , Dong Shiyu , Cheng Zheng , Li Wei , Li Shuhua
Published: July 2022

We combine fragment-based machine learning force field and molecular mechanics force field, and employ it to predict the NMR chemical shifts of macromolecules in solutions.
Metal organic framework-based antibacterial agents and their underlying mechanisms
Authors: Han Donglin , Liu Xiangmei , Wu Shuilin
Published: July 2022

MOFs can kill the bacteria efficiently by multiple mechanisms, such as releasing metal ions and/or antibacterial micro-molecules; performing as catalytically active site; acting as photosensitizers; mimicking enzymes; based on gas therapy and so on.
Single-molecule magnet behaviour and catalytic properties of tetrahedral Co(ii) complexes bearing chloride and 1,2-disubstituted benzimidazole as ligands
Authors: Milani Jorge Luiz Sônego , da Mata Álvaro Farias Arruda , Oliveira Igor Santos , Valdo Ana Karoline Silva Mendanha , Martins Felipe Terra , Rabelo Renato , Cangussu Danielle , Cano Joan , Lloret Francesc , Julve Miguel , das Chagas Rafael Pavão
Published: July 2022

Field-induced SMM behaviour in a series of tetrahedral 1,2-disubstituted benzimidazole cobalt(ii) complexes and their catalytic properties for an eco-friendly cycloaddition of CO2 with epoxides.
Atomic-level engineering Fe1N2O2 interfacial structure derived from oxygen-abundant metal–organic frameworks to promote electrochemical CO2 reduction
Authors: Zhao Di , Yu Ke , Song Pengyu , Feng Wuyi , Hu Botao , Cheong Weng-Chon (Max) , Zhuang Zewen , Liu Shoujie , Sun Kaian , Zhang Jiatao , Chen Chen
Published: July 2022

Fe1N2O2@NC single-atomic site electrocatalysts were derived from oxygen-abundant metal–organic-frameworks for promoting electrochemical CO2 reduction.
Direct recovery of scrapped LiFePO4 by a green and low-cost electrochemical re-lithiation method
Authors: Zhou Shiyu , Du Jingzhen , Xiong Xiaosong , Liu Lili , Wang Jing , Fu Lijun , Ye Jilei , Chen Yuhui , Wu Yuping
Published: July 2022

This study proposes a novel electrochemical method for recycling LFP based on a Zn//S-LFP double-electrode system, providing green and low-cost recycling technology for future industrial applications.
Ultrafast N-arylation of sulfoximines enabled by micellar catalysis in water
Authors: Song Mingyu , Zhang Lei , Wei Diandian , He Yu , Jia Jiajia , Li Heng , Yuan Bingxin
Published: July 2022

Sustainable and ultrafast N-arylation of sulfoximines in water enabled by micellar catalysis.
19F chemical library and 19F-NMR for a weakly bound complex structure
Authors: Shinya Shoko , Katahira Ritsuko , Furuita Kyoko , Sugiki Toshihiko , Lee Young-Ho , Hattori Yoshikazu , Takeshita Kohei , Nakagawa Atsushi , Kokago Aoi , Akagi Ken-ichi , Oouchi Muneki , Hayashi Fumiaki , Kigawa Takanori , Takimoto-Kamimura Midori , Fujiwara Toshimichi , Kojima Chojiro
Published: July 2022

19F-NMR analysis using the optimized 19F chemical library enables the modeling of the structure of the weakly bound protein–compound complex, overcoming the difficulty in fragment-based drug discovery.
A novel S-scheme heterojunction based on 0D/3D CeO2/Bi2O2CO3 for the photocatalytic degradation of organic pollutants
Authors: Wang Chuantao , Dang Yuechen , Pang Xiangxiang , Zhang Le , Bian Yujie , Duan Wen , Yang Chunming , Zhen Yanzhong , Fu Feng
Published: July 2022

Electron directional transfer driven by a built-in electric field and band bending formed a step-scheme heterostructure.
Effect of ZSM-5 zeolite porosity on catalytic cracking ofn-heptane
Authors: Nakhaei Pour Ali , Mohammadi Ali
Published: July 2022

The selectivity of ethylene and propylene in cracking ofn-heptane is connected to the micropore to mesopore ratioof ZSM-5 structure.
A review on TiO2−x-based materials for photocatalytic CO2 reduction
Authors: Wang Juan , Guo Rui-tang , Bi Zhe-xu , Chen Xin , Hu Xing , Pan Wei-guo
Published: July 2022

Photocatalytic CO2 reduction using TiO2−x-based materials.
Hierarchical MXene/transition metal oxide heterostructures for rechargeable batteries, capacitors, and capacitive deionization
Authors: Xi Wen , Jin Jun , Zhang Youfang , Wang Rui , Gong Yansheng , He Beibei , Wang Huanwen
Published: July 2022

This review introduces and discusses the recent research progress in MXene/TMO heterostructures, focusing on synthetic strategies, heterointerface engineering, and applications in rechargeable batteries, capacitors, and capacitive deionization.
Support stabilized PtCu single-atom alloys for propane dehydrogenation
Authors: Liu Xiaohe , Wang Xianhui , Zhen Shiyu , Sun Guodong , Pei Chunlei , Zhao Zhi-Jian , Gong Jinlong
Published: July 2022

This paper describes PtCu single-atom alloys supported on copper phyllosilicate via Cu+–O–Si. The catalyst exhibits sintering resistance in propane dehydrogenation reaction without sacrificing activity and selectivity.
MOF-derived MoP nanorods decorated with a N-doped thin carbon layer as a robust lithiophilic and sulfiphilic nanoreactor for high-performance Li–S batteries
Authors: Wang Xiaoxiao , Meng Lingshuai , Liu Xueqiang , Deng Nanping , Yan Zirui , Wang Gang , Wei Liying , Zhang Lugang , Cheng Bowen , Kang Weimin
Published: July 2022

A MoP@NC/PCNFs-modified Celgard separator was designed for use in lithium–sulfur batteries.
A ratiometric fluorescent probe based on two-isophorone fluorophore for detecting cysteine
Authors: Li Zhongguo , Zhang Yue , Jiang Youhong , Li Huiwen , Chen Chunyang , Liu Weisheng
Published: July 2022

In this study, a new ratiometric fluorescent probe, TIFC, was proposed to detect Cys. TIFC has high selectivity and quantitative response to cysteine. And it has high biocompatibility to achieve ratiometric fluorescence imaging of living cells.
Controlled growth of 3D assemblies of edge enriched multilayer MoS2 nanosheets for dually selective NH3 and NO2 gas sensors
Authors: Annanouch Fatima Ezahra , Alagh Aanchal , Umek Polona , Casanova-Chafer Juan , Bittencourt Carla , Llobet Eduard
Published: July 2022

The successful controlled growth of edge enriched 3D assemblies of MoS2 nanosheets for the fabrication of dually selective NH3 and NO2 gas sensors using a single step atmospheric pressure CVD method.
MXene reinforced organohydrogels with ultra-stability, high sensitivity and anti-freezing ability for flexible strain sensors
Authors: Wang Sheng-Ji , Chen Zhuo , Hu Xiangshu , Zou Jian , Xie Zhihui , Mi Hao-Yang , Liu Zi-Hao , Zhang Zhi , Shang Yinghui , Jing Xin
Published: July 2022

Hydrogels combining good biocompatibility and super flexibility have attracted tremendous interest in flexible sensors.
Afterglow-intensity-ratio-based temperature sensing using a persistent phosphor
Authors: Liao Chuan , Chen Feng , Wu Hao , Wu Huajun , Zhang Liangliang , Pan Guo-hui , Liu Feng , Wang Xiao-jun , Zhang Jiahua
Published: July 2022

We realized a high relative sensitivity (4.12% °C−1) thermometer based on the afterglow intensity ratio (AIR) in a persistent phosphor using afterglow and thermal quenching models.
Dynamics and coherence of photoexcited states in polyfluorene films with ordered chain phases
Authors: Quintero-Jaime Andrés Felipe , Hafed-Khatiri Salma , Huerta Francisco , Quijada César , Montilla Francisco
Published: July 2022

Understanding the optical and electronic excitations in conjugated polymers, their delocalization, and dynamics is of paramount importance for improving the performance of optoelectronic devices.