bluuebunny/crossref_metadata_2025 huggingface dataset:
A Remote Sensing Driven Soil Moisture Estimator: Uncertain Downscaling With Geostatistically Based Use of Ancillary Data
Authors: Karamouz Mohammad , Alipour Reza Saleh , Roohinia Mahnoor , Fereshtehpour Mohammad
Published: September 2022

In recent years, remote sensing satellites, including Soil Moisture Active Passive (SMAP), continuously monitor SM of the earth. However, the spatial resolution of the remotely sensed SM is insufficient for some hydrological applications. In this paper, a data‐driven model is proposed based on a hybrid approach called artificial neural network kriging (ANNK) to capture the interaction between SM and ancillary data (AD), including normalized difference vegetation index (NDVI), altitude, slope, Antecedent Moisture Condition, AMC (5‐day cumulative precipitation), and daily air temperature (DAT)/land surface temperature (LST). By co‐regionalization of the estimated SM from the ANNK and SMAP 36‐km product, SM in any part of the study area is estimated more accurately and on a finer resolution (1‐km). Finally, through a linear relationship between in‐situ SM with the up‐to‐date AD including AMC (previous 5‐day cumulative precipitation), LST or DAT, slope, NDVI, and the downscaled satellite SM, the soil moisture estimates are adjusted by also adding an error term. Estimation of the final SM product in terms of the Unbiased Root Mean Square Error of less than 0.04 m3/m3 meets the accuracy requirements of the SMAP SM retrieval. Moreover, the results of SM validation show that the proposed technique has a potential for real‐time SM estimations in developing areas.
Giant mid-IR resonant coupling to molecular vibrations in sub-nm gaps of plasmonic multilayer metafilms
Authors: Arul Rakesh , Grys David-Benjamin , Chikkaraddy Rohit , Mueller Niclas S. , Xomalis Angelos , Miele Ermanno , Euser Tijmen G. , Baumberg Jeremy J.
Published: September 2022

Nanomaterials capable of confining light are desirable for enhancing spectroscopies such as Raman scattering, infrared absorption, and nonlinear optical processes. Plasmonic superlattices have shown the ability to host collective resonances in the mid-infrared, but require stringent fabrication processes to create well-ordered structures. Here, we demonstrate how short-range-ordered Au nanoparticle multilayers on a mirror, self-assembled by a sub-nm molecular spacer, support collective plasmon-polariton resonances in the visible and infrared, continuously tunable beyond 11 µm by simply varying the nanoparticle size and number of layers. The resulting molecule-plasmon system approaches vibrational strong coupling, and displays giant Fano dip strengths, SEIRA enhancement factors ~ 106, light-matter coupling strengths g ~ 100 cm−1, Purcell factors ~ 106, and mode volume compression factors ~ 108. The collective plasmon-polariton mode is highly robust to nanoparticle vacancy disorder and is sustained by the consistent gap size defined by the molecular spacer. Structural disorder efficiently couples light into the gaps between the multilayers and mirror, enabling Raman and infrared sensing of sub-picolitre sample volumes.
Optical coherence tomography—in situ and high-speed 3D imaging for laser materials processing
Authors: Wang Xiaodong , Yuan Xin , Shi Liping
Published: September 2022

Exploiting Fourier-domain optical coherence tomography, a high-speed and real-time inspection of multi-photon 3D laser printing has been reported. We expect that this technique can be further extended to single shot compressive 3D imaging for studying the ultrafast dynamics of laser-matter interaction.
Dissecting microbial communities and resistomes for interconnected humans, soil, and livestock
Authors: Maciel-Guerra Alexandre , Baker Michelle , Hu Yue , Wang Wei , Zhang Xibin , Rong Jia , Zhang Yimin , Zhang Jing , Kaler Jasmeet , Renney David , Loose Matthew , Emes Richard D , Liu Longhai , Chen Junshi , Peng Zixin , Li Fengqin , Dottorini Tania
Published: September 2022

A debate is currently ongoing as to whether intensive livestock farms may constitute reservoirs of clinically relevant antimicrobial resistance (AMR), thus posing a threat to surrounding communities. Here, combining shotgun metagenome sequencing, machine learning (ML), and culture-based methods, we focused on a poultry farm and connected slaughterhouse in China, investigating the gut microbiome of livestock, workers and their households, and microbial communities in carcasses and soil. For both the microbiome and resistomes in this study, differences are observed across environments and hosts. However, at a finer scale, several similar clinically relevant antimicrobial resistance genes (ARGs) and similar associated mobile genetic elements were found in both human and broiler chicken samples. Next, we focused on Escherichia coli, an important indicator for the surveillance of AMR on the farm. Strains of E. coli were found intermixed between humans and chickens. We observed that several ARGs present in the chicken faecal resistome showed correlation to resistance/susceptibility profiles of E. coli isolates cultured from the same samples. Finally, by using environmental sensing these ARGs were found to be correlated to variations in environmental temperature and humidity. Our results show the importance of adopting a multi-domain and multi-scale approach when studying microbial communities and AMR in complex, interconnected environments.
Pathological fear, anxiety and negative affect exhibit distinct neurostructural signatures: evidence from psychiatric neuroimaging meta-analysis
Authors: Liu Xiqin , Klugah-Brown Benjamin , Zhang Ran , Chen Huafu , Zhang Jie , Becker Benjamin
Published: September 2022

Internalizing disorders encompass anxiety, fear and depressive disorders, which exhibit overlap at both conceptual and symptom levels. Given that a neurobiological evaluation is lacking, we conducted a Seed-based D-Mapping comparative meta-analysis including coordinates as well as original statistical maps to determine common and disorder-specific gray matter volume alterations in generalized anxiety disorder (GAD), fear-related anxiety disorders (FAD, i.e., social anxiety disorder, specific phobias, panic disorder) and major depressive disorder (MDD). Results showed that GAD exhibited disorder-specific altered volumes relative to FAD including decreased volumes in left insula and lateral/medial prefrontal cortex as well as increased right putamen volume. Both GAD and MDD showed decreased prefrontal volumes compared to controls and FAD. While FAD showed less robust alterations in lingual gyrus compared to controls, this group presented intact frontal integrity. No shared structural abnormalities were found. Our study is the first to provide meta-analytic evidence for distinct neuroanatomical abnormalities underlying the pathophysiology of anxiety-, fear-related and depressive disorders. These findings may have implications for determining promising target regions for disorder-specific neuromodulation interventions (e.g. transcranial magnetic stimulation or neurofeedback).
TIPE1 inhibits osteosarcoma tumorigenesis and progression by regulating PRMT1 mediated STAT3 arginine methylation
Authors: Yang Minghao , Zhang Yuzhu , Liu Guangping , Zhao Ziqian , Li Jigang , Yang Le , Liu Kui , Hu Wei , Lou Yunwei , Jiang Jie , Liu Qing , Zhao Peiqing
Published: September 2022

Osteosarcoma (OS), the most common primary malignancy of the bone, has a poor prognosis due to its high mortality rate and high potential for metastasis. Thus, it is urgently necessary to explore functional molecular targets of therapeutic strategies for osteosarcoma. Here, we reported that TIPE1 expression was decreased in osteosarcoma tissues compared to normal and adjacent nontumor tissues, and its expression was negatively related to tumor stage and tumor size. Functional assays showed that TIPE1 inhibited osteosarcoma carcinogenesis and metastatic potential both in vivo and in vitro. Furthermore, we investigated that the STAT3 signaling pathway was significantly downregulated after TIPE1 overexpression. Mechanistically, TIPE1 bind to the catalytic domain of PRMT1, which deposits an asymmetric dimethylarginine (ADMA) mark on histone/non-histone proteins, and thus inhibited PRMT1 mediated STAT3 methylation at arginine (R) residue 688. This abolished modification decreased STAT3 transactivation and expression, by which subsequently suppressed osteosarcoma malignancy. Taken together, these data showed that TIPE1 inhibits the malignant transformation of osteosarcoma through PRMT1-mediated STAT3 arginine methylation and ultimately decreases the development and metastasis of osteosarcoma. TIPE1 might be a potential molecular therapeutic target and an early biomarker for osteosarcoma diagnosis.
Contactless manipulation of mixed phase fluids in liquid crystal polymer microtubes assisted with light-driven vortex
Authors: Lu Yao , Qin Lang , Liu Quan , Li Zichuan , Zhang Weijia , Zhu Chongyu , Yu Yanlei
Published: September 2022

Smart channels that manipulate liquid motion by anisotropic shape changes represent a promising candidate to construct microfluidics for biochemical analysis. However, the existing systems fail to provide a platform for solid exchange mediums to interact with multiple liquid phases, which is a universal technique to effectively extract, enrich, and precisely detect biomarkers. Herein, a combined photo/magnetic control strategy of mixed phase fluids, which integrates the contactless operations of suspending, depositing, and even separating, is reported for the first time based on a trilayer microtube consisting of a flexible supporting layer, photodeformable liquid crystal polymer, and hydrophilic blocking layer. The asymmetric photodeformation of the liquid crystal polymer generates an internal vortex in the microtube to homogenously disperse solid exchange mediums into various aqueous moving droplets and to enable efficient purification and enrichment of the target biomarkers. A newly constructed homemade portable protein analyzer guided by the combined photo/magnetic control strategy features the advantages of a short detection time (20 min), trace sample consumption (5 μL), and a low detection limit (1 μg mL−1).
Accelerating ice flow at the onset of the Northeast Greenland Ice Stream
Authors: Grinsted Aslak , Hvidberg Christine S. , Lilien David A. , Rathmann Nicholas M. , Karlsson Nanna B. , Gerber Tamara , Kjær Helle Astrid , Vallelonga Paul , Dahl-Jensen Dorthe
Published: September 2022

Mass loss near the ice-sheet margin is evident from remote sensing as frontal retreat and increases in ice velocities. Velocities in the ice sheet interior are orders of magnitude smaller, making it challenging to detect velocity change. Here, we analyze a 35-year record of remotely sensed velocities, and a 6-year record of repeated GPS observations, at the East Greenland Ice-core Project (EastGRIP), located in the middle of the Northeast-Greenland Ice Stream (NEGIS). We find that the shear margins of NEGIS are accelerating, indicating a widening of the ice stream. We demonstrate that the widening of the ice stream is unlikely to be a response to recent changes at the outlets of NEGIS. Modelling indicates that the observed spatial fingerprint of acceleration is more consistent with a softening of the shear margin, e.g. due to evolving fabric or temperature, than a response to external forcing at the surface or bed.
Strain-regulated Gibbs free energy enables reversible redox chemistry of chalcogenides for sodium ion batteries
Authors: Jiang Minxia , Hu Yingjie , Mao Baoguang , Wang Yixin , Yang Zhen , Meng Tao , Wang Xin , Cao Minhua
Published: September 2022

Manipulating the reversible redox chemistry of transition metal dichalcogenides for energy storage often faces great challenges as it is difficult to regulate the discharged products directly. Herein we report that tensile-strained MoSe2 (TS-MoSe2) can act as a host to transfer its strain to corresponding discharged product Mo, thus contributing to the regulation of Gibbs free energy change (ΔG) and enabling a reversible sodium storage mechanism. The inherited strain results in lattice distortion of Mo, which adjusts the d-band center upshifted closer to the Fermi level to enhance the adsorbability of Na2Se, thereby leading to a decreased ΔG of the redox chemistry between Mo/Na2Se and MoSe2. Ex situ and in situ experiments revealed that, unlike the unstrained MoSe2, TS-MoSe2 shows a highly reversible sodium storage, along with an evidently improved reaction kinetics. This work sheds light on the study on electrochemical energy storage mechanism of other electrode materials.
Breakdown of bulk-projected isotropy in surface electronic states of topological Kondo insulator SmB6(001)
Authors: Ohtsubo Yoshiyuki , Nakaya Toru , Nakamura Takuto , Le Fèvre Patrick , Bertran François , Iga Fumitoshi , Kimura Shin-Ichi
Published: September 2022

The topology and spin-orbital polarization of two-dimensional (2D) surface electronic states have been extensively studied in this decade. One major interest in them is their close relationship with the parities of the bulk (3D) electronic states. In this context, the surface is often regarded as a simple truncation of the bulk crystal. Here we show breakdown of the bulk-related in-plane rotation symmetry in the topological surface states (TSSs) of the Kondo insulator SmB6. Angle-resolved photoelectron spectroscopy (ARPES) performed on the vicinal SmB6(001)-p(2 × 2) surface showed that TSSs are anisotropic and that the Fermi contour lacks the fourfold rotation symmetry maintained in the bulk. This result emphasizes the important role of the surface atomic structure even in TSSs. Moreover, it suggests that the engineering of surface atomic structure could provide a new pathway to tailor various properties among TSSs, such as anisotropic surface conductivity, nesting of surface Fermi contours, or the number and position of van Hove singularities in 2D reciprocal space.
ZO-2/Tjp2 suppresses Yap and Wwtr1/Taz-mediated hepatocyte to cholangiocyte transdifferentiation in the mouse liver
Authors: Xu Jianliang , Kausalya P. Jaya , Ong Alicia Ghia Min , Goh Christine Meng Fan , Mohamed Ali Safiah , Hunziker Walter
Published: September 2022

TJP2/ZO-2-inactivating mutations in humans cause progressive cholestatic liver disease. Liver-specific deletion of Tjp2 in the mouse (Tjp2 cKO mice) leads to mild progressive cholestasis without an overt degradation of the bile-blood barrier (BBB). These mice are more susceptible to cholic acid (CA) induced liver injury. Interestingly, while initially also more susceptible, Tjp2 cKO mice develop tolerance to a DDC-supplemented diet. The DDC diet induces an exacerbated ductular reaction in Tjp2 cKO mice, which arises from the transdifferentiation of hepatocytes to cholangiocytes. Consequently, this transdifferentiation is only observed if Tjp2 is inactivated in hepatocytes, but not if deleted in cholangiocytes. The DDC-diet-induced hepatocyte transdifferentiation in Tjp2 cKO mice requires Yap and Wwtr1/Taz, whose protein expression is upregulated in hepatocytes lacking Tjp2, but is independent of Notch2. Although inactivating Tjp2 is sufficient for the upregulation of Yap and Wwtr1/Taz protein, efficient transdifferentiation requires the DDC-diet insult. Thus, Tjp2 negatively regulates Yap/Taz-mediated transdifferentiation of hepatocytes to cholangiocytes in response to DDC-diet-induced liver injury. Furthermore, transdifferentiation is regulated at multiple levels and the type of injury inflicted on the Tjp2 deficient liver plays an important role in the resulting pathophysiology.
A behavioral and brain imaging dataset with focus on emotion regulation of women with fibromyalgia
Authors: Balducci Thania , Rasgado-Toledo Jalil , Valencia Alely , van Tol Marie-José , Aleman André , Garza-Villarreal Eduardo A.
Published: September 2022

Fibromyalgia is a chronic condition characterized by widespread pain, as well as numerous symptoms related to central sensitization such as: fatigue, cognitive disturbances, constipation/diarrhea and sensory hypersensitivity. Furthermore, depression and anxiety are prevalent comorbidities, accompanied by emotion processing and regulation difficulties. Although fibromyalgia physiopathology is still not fully understood, neuroimaging research methods have shown brain structural and functional alterations as well as neuroinflammation abnormalities. We believe that open access to data may help fibromyalgia research advance more. Here, we present an open dataset of 33 fibromyalgia female patients and 33 paired healthy controls recruited from a Mexican population. Dataset includes demographic, clinical, behavioural and magnetic resonance imaging (MRI) data. The MRI data consists of: structural (T1- and T2- weighted) and functional (task-based and resting state) sequences. The task was an emotion processing and regulation task based on visual stimuli. The MRI data contained in the repository are unprocessed, presented in Brain Imaging Data Structure (BIDS) format and available on the OpenNeuro platform for future analysis.
Predicting skin permeability using HuskinDB
Authors: Waters Laura J. , Quah Xin Ling
Published: September 2022

A freely accessible database has recently been released that provides measurements available in the literature on human skin permeation data, known as the ‘Human Skin Database – HuskinDB’. Although this database is extremely useful for sourcing permeation data to help with toxicity and efficacy determination, it cannot be beneficial when wishing to consider unlisted, or novel compounds. This study undertakes analysis of the data from within HuskinDB to create a model that predicts permeation for any compound (within the range of properties used to create the model). Using permeability coefficient (Kp) data from within this resource, several models were established for Kp values for compounds of interest by varying the experimental parameters chosen and using standard physicochemical data. Multiple regression analysis facilitated creation of one particularly successful model to predict Kp through human skin based only on three chemical properties. The model transforms the dataset from simply a resource of information to a more beneficial model that can be used to replace permeation testing for a wide range of compounds.
Passage number affects differentiation of sensory neurons from human induced pluripotent stem cells
Authors: Cantor Erica L. , Shen Fei , Jiang Guanglong , Tan Zhiyong , Cunningham Geneva M. , Wu Xi , Philips Santosh , Schneider Bryan P.
Published: September 2022

Induced pluripotent stem cells (iPSCs) are a valuable resource for neurological disease-modeling and drug discovery due to their ability to differentiate into neurons reflecting the genetics of the patient from which they are derived. iPSC-derived cultures, however, are highly variable due to heterogeneity in culture conditions. We investigated the effect of passage number on iPSC differentiation to optimize the generation of sensory neurons (iPSC-dSNs). Three iPSC lines reprogrammed from the peripheral blood of three donors were differentiated into iPSC-dSNs at passage numbers within each of the following ranges: low (5–10), intermediate (20–26), and high (30–38). Morphology and pluripotency of the parent iPSCs were assessed prior to differentiation. iPSC-dSNs were evaluated based on electrophysiological properties and expression of key neuronal markers. All iPSC lines displayed similar morphology and were similarly pluripotent across passage numbers. However, the expression levels of neuronal markers and sodium channel function analyses indicated that iPSC-dSNs differentiated from low passage numbers better recapitulated the sensory neuron phenotype than those differentiated from intermediate or high passage numbers. Our results demonstrate that lower passage numbers may be better suited for differentiation into peripheral sensory neurons.
Theoretical study of the interaction of fullerenes with the emerging contaminant carbamazepine for detection in aqueous environments
Authors: Lemos Silva Rodrigo A. , Scalabrini Machado Daniel F. , de Oliveira Heibbe C. B. , Ribeiro Luciano , da Silva Filho Demétrio A.
Published: September 2022

The global increase in drug consumption exposes the growing need to develop new systems for the detection, capture, and treatment of bioactive molecules. Carbamazepine is one instance of such contaminants at the top of the ranking commonly found in sewage treatment systems. This work, therefore, presents a theoretical study of fullerene C60and its derivatives with substitutional doping with B, Al, Ga, Si, Ge, N and P, for the detection and capture of carbamazepine is aqueous medium. Solvation effects were included by means of the Polarizable Continuum Solvent method. The results indicate that doped fullerenes are sensitive for the detection of carbamazepine both in gaseous and aquatic environments. Investigation on the intermolecular interactions between the drug and the fullerene molecule were carried out, allowing the characterization of the interactions responsible for stabilizing the adsorption of carbamazepine to the fullerenes. The theoretical survey revealed that fullerenes doped with Al, Ga, Si and Ge chemically adsorb carbamazepine whereas for the case of fullerenes doped with other heteroatoms physisorption is responsible for the molecular recognition. Relying on DFT calculations, the fullerene derivatives C59Al, C59Si and C59Ga are the most suitable to act both as a sensor and to uptake carbamazepine in aquatic environments.
Bioactivity of crude fucoidan extracted from Sargassum ilicifolium (Turner) C. Agardh
Authors: Tsou Min-Hsuan , Lee Cheng-Chang , Wu Zhi-Yuan , Lee Zui-Harng , Lin Hsiu-Mei
Published: September 2022

Fucoidan derived from brown algae has been shown to exhibit antitumor and antioxidant effects, so research on sulfated polysaccharides is increasing. The purpose of this study was to evaluate the characteristics and biological activity of fucoidan that was extracted at two temperatures (65 and 80 °C) from Sargassum ilicifolium (Turner) C. Agardh from five regions of Taiwan. The data show that there are significant differences in the yield, sulfate and total sugar content of Sargassum ilicifolium (Turner) C. Agardh grown in different locations in the same sea area. HPLC was used to determine the monosaccharide compositions of the fucoidan, which contains fucose, mannose, mannose, glucose and galactose and have a low molecular weight of less than 5 kDa, and then we will select the algae collected in Fugang, Taitung, for further biological activity research. The sampled Sargassum ilicifolium (Turner) C. Agardh at all five locations has a good polyphenol content, and it shows great DPPH radical scavenging activity, ABTS radical scavenging activity, Ferrous ion-chelating activity and Reducing power. The Sargassum ilicifolium (Turner) C. Agardh that was collected from Taitung Fugang is not toxic to L929 normal cells, but for A549 cancer cells and HCT116 cancer cells, it is known from the results that it has good cytotoxicity for A549 cancer cells. Thus, this study found that the Sargassum ilicifolium (Turner) C. Agardh that was collected from Taitung Fugang has significant antioxidant and anticancer properties.
Inferring the age of breeders from easily measurable variables
Authors: Genovart Meritxell , Klementisová Katarina , Oro Daniel , Fernández-López Pol , Bertolero Albert , Bartumeus Frederic
Published: September 2022

Age drives differences in fitness components typically due to lower performances of younger and senescent individuals, and changes in breeding age structure influence population dynamics and persistence. However, determining age and age structure is challenging in most species, where distinctive age features are lacking and available methods require substantial efforts or invasive procedures. Here we explore the potential to assess the age of breeders, or at least to identify young and senescent individuals, by measuring some breeding parameters partially driven by age (e.g. egg volume in birds). Taking advantage of a long-term population monitored seabird, we first assessed whether age influenced egg volume, and identified other factors driving this trait by using general linear models. Secondly, we developed and evaluated a machine learning algorithm to assess the age of breeders using measurable variables. We confirmed that both younger and older individuals performed worse (less and smaller eggs) than middle-aged individuals. Our ensemble training algorithm was only able to distinguish young individuals, but not senescent breeders. We propose to test the combined use of field monitoring, classic regression analysis and machine learning methods in other wild populations were measurable breeding parameters are partially driven by age, as a possible tool for assessing age structure in the wild.
Plasma metabolome study reveals metabolic changes induced by pharmacological castration and testosterone supplementation in healthy young men
Authors: de Siqueira Guedes Jéssica , Pla Indira , Sahlin K. Barbara , Monnerat Gustavo , Appelqvist Roger , Marko-Varga György , Giwercman Aleksander , Domont Gilberto Barbosa , Sanchez Aniel , Nogueira Fábio César Sousa , Malm Johan
Published: September 2022

Testosterone is a hormone that plays a key role in carbohydrate, fat, and protein metabolism. Testosterone deficiency is associated with multiple comorbidities, e.g., metabolic syndrome and type 2 diabetes. Despite its importance in many metabolic pathways, the mechanisms by which it controls metabolism are not fully understood. The present study investigated the short-term metabolic changes of pharmacologically induced castration and, subsequently, testosterone supplementation in healthy young males. Thirty subjects were submitted to testosterone depletion (TD) followed by testosterone supplementation (TS). Plasma samples were collected three times corresponding to basal, low, and restored testosterone levels. An untargeted metabolomics study was performed by liquid chromatography–high resolution mass spectrometry (UHPLC–HRMS) to monitor the metabolic changes induced by the altered hormone levels. Our results demonstrated that TD was associated with major metabolic changes partially restored by TS. Carnitine and amino acid metabolism were the metabolic pathways most impacted by variations in testosterone. Furthermore, our results also indicated that LH and FSH might strongly alter the plasma levels of indoles and lipids, especially glycerophospholipids and sphingolipids. Our results demonstrated major metabolic changes induced by low testosterone that may be important for understanding the mechanisms behind the association of testosterone deficiency and its comorbidities.
Femtosecond tunable solitons up to 4.8 µm using soliton self-frequency shift in an InF3 fiber
Authors: Gauthier Jean-Christophe , Olivier Michel , Paradis Pascal , Dumas Marie-Frédérique , Bernier Martin , Vallée Réal
Published: September 2022

A tunable ultrashort soliton pulse source reaching up to 4.8 µm is demonstrated based on a 2.8 µm femtosecond fiber laser coupled to a zirconium fluoride fiber amplifier followed by a small core indium fluoride fiber. This demonstration is extending by 300 nm the long wavelength limit previously reported with soliton self-frequency shift (SSFS) sources based on fluoride fibers. Our experimental and numerical investigation highlighted the spectral dynamics associated with the generation of highly redshifted pulses in the mid-infrared using SSFS enhanced by soliton fission. This study is intended at providing a better understanding of the potential and limitations of SSFS based tunable femtosecond fiber sources in the 3–5  µm spectral range.
STAR sleep recording export software for automatic export and anonymization of sleep studies
Authors: Nikkonen Sami , Korkalainen Henri , Töyräs Juha , Leppänen Timo
Published: September 2022

Sleep research often relies on large retrospective clinical datasets. However, as the data is usually stored in proprietary formats specific for each sleep software, the raw data cannot be easily accessed and analyzed with external tools. While the raw data can usually be exported to more common data formats, this is often a cumbersome and labor-intensive task as it is not required for clinical purposes. Additionally, the recordings often include sensitive patient information which must be removed before the data can be shared or analyzed externally. This anonymization can be difficult to perform manually without the correct tools or knowledge of the file types and how they internally store the data. The STAR sleep recording export software provides a simple tool that can be used to perform the sleep study exports automatically. This allows the user to easily export a batch of sleep studies with minimal effort. In addition, the software can also be used to automatically anonymize the exported sleep recordings allowing researchers to save time and personnel resources as these do not need to be allocated for exporting and anonymizing sleep studies. The software supports Noxturnal, RemLogic, Profusion PSG and Sleepware G3 and it is free and openly available for anyone to download and use.
Surface potential modulation as a tool for mitigating challenges in SERS-based microneedle sensors
Authors: Brasiliense Vitor , Park Ji Eun , Berns Eric J. , Van Duyne Richard P. , Mrksich Milan
Published: September 2022

Raman spectroscopic-based biosensing strategies are often complicated by low signal and the presence of multiple chemical species. While surface-enhanced Raman spectroscopy (SERS) nanostructured platforms are able to deliver high quality signals by focusing the electromagnetic field into a tight plasmonic hot-spot, it is not a generally applicable strategy as it often depends on the specific adsorption of the analyte of interest onto the SERS platform. This paper describes a strategy to address this challenge by using surface potential as a physical binding agent in the context of microneedle sensors. We show that the potential-dependent adsorption of different chemical species allows scrutinization of the contributions of different chemical species to the final spectrum, and that the ability to cyclically adsorb and desorb molecules from the surface enables efficient application of multivariate analysis methods. We demonstrate how the strategy can be used to mitigate potentially confounding phenomena, such as surface reactions, competitive adsorption and the presence of molecules with similar structures. In addition, this decomposition helps evaluate criteria to maximize the signal of one molecule with respect to others, offering new opportunities to enhance the measurement of analytes in the presence of interferants.
Pervasive exposure of wild small mammals to legacy and currently used pesticide mixtures in arable landscapes
Authors: Fritsch Clémentine , Appenzeller Brice , Burkart Louisiane , Coeurdassier Michael , Scheifler Renaud , Raoul Francis , Driget Vincent , Powolny Thibaut , Gagnaison Candice , Rieffel Dominique , Afonso Eve , Goydadin Anne-Claude , Hardy Emilie M. , Palazzi Paul , Schaeffer Charline , Gaba Sabrina , Bretagnolle Vincent , Bertrand Colette , Pelosi Céline
Published: September 2022

Knowledge gaps regarding the potential role of pesticides in the loss of agricultural biodiversity worldwide and mixture-related issues hamper proper risk assessment of unintentional impacts of pesticides, rendering essential the monitoring of wildlife exposure to these compounds. Free-ranging mammal exposure to legacy (Banned and Restricted: BRPs) and currently used (CUPs) pesticides was investigated, testing the hypotheses of: (1) a background bioaccumulation for BRPs whereas a “hot-spot” pattern for CUPs, (2) different contamination profiles between carnivores and granivores/omnivores, and (3) the role of non-treated areas as refuges towards exposure to CUPs. Apodemus mice (omnivore) and Crocidura shrews (insectivore) were sampled over two French agricultural landscapes (n = 93). The concentrations of 140 parent chemicals and metabolites were screened in hair samples. A total of 112 compounds were detected, showing small mammal exposure to fungicides, herbicides and insecticides with 32 to 65 residues detected per individual (13–26 BRPs and 18–41 CUPs). Detection frequencies exceeded 75% of individuals for 13 BRPs and 25 CUPs. Concentrations above 10 ng/g were quantified for 7 BRPs and 29 CUPs (in 46% and 72% of individuals, respectively), and above 100 ng/g for 10 CUPs (in 22% of individuals). Contamination (number of compounds or concentrations) was overall higher in shrews than rodents and higher in animals captured in hedgerows and cereal crops than in grasslands, but did not differ significantly between conventional and organic farming. A general, ubiquitous contamination by legacy and current pesticides was shown, raising issues about exposure pathways and impacts on ecosystems. We propose a concept referred to as “biowidening”, depicting an increase of compound diversity at higher trophic levels. This work suggests that wildlife exposure to pesticide mixtures is a rule rather than an exception, highlighting the need for consideration of the exposome concept and questioning appropriateness of current risk assessment and mitigation processes.
Conformational transition induced in the aspartate:alanine antiporter by l-Ala binding
Authors: Suzuki Satomi , Chiba Fumika , Kimura Takuya , Kon Nanase , Nanatani Kei , Abe Keietsu
Published: September 2022

An aspartate:alanine antiporter (AspT) from the lactic acid bacterium Tetragenococcus halophilus catalyzes the electrogenic aspartate1-:alanine0 exchange reaction. Our previous kinetic analyses of transport reactions mediated by AspT in reconstituted liposomes suggested that, although the substrate transport reactions are physiologically coupled, the putative binding sites of l-aspartate (-Asp) and l-alanine (-Ala) are independently located on AspT. By using the fluorescent probe Oregon Green maleimide (OGM), which reacts specifically with cysteine, we also found that the presence of l-Asp changes the conformation of AspT. In this study, we conducted an OGM labeling assay in the presence of l-Ala. The labeling efficiency of single cysteine mutants (G62C and P79C) in transmembrane helix 3 of the AspT showed novel patterns depending on the presence of l-Ala or analogs. A concentration-dependent shift of AspT from the conformation in the presence of one substrate to that specific to the substrate added subsequently (l-Ala or l-Asp) was observed. Moreover, size-exclusion-chromatography-based thermostability assays indicated that the thermal stability of AspT in the presence of l-Ala differed from that in the presence of l-Asp. From these results, we concluded that l-Ala binding yields a conformation different from the apo or l-Asp binding conformations.
Nondestructive protein sampling with electroporation facilitates profiling of spatial differential protein expression in breast tumors in vivo
Authors: Vitkin Edward , Singh Amrita , Wise Julia , Ben-Elazar Shay , Yakhini Zohar , Golberg Alexander
Published: September 2022

Excision tissue biopsy, while central to cancer treatment and precision medicine, presents risks to the patient and does not provide a sufficiently broad and faithful representation of the heterogeneity of solid tumors. Here we introduce e-biopsy—a novel concept for molecular profiling of solid tumors using molecular sampling with electroporation. As e-biopsy provides access to the molecular composition of a solid tumor by permeabilization of the cell membrane, it facilitates tumor diagnostics without tissue resection. Furthermore, thanks to its non tissue destructive characteristics, e-biopsy enables probing the solid tumor multiple times in several distinct locations in the same procedure, thereby enabling the spatial profiling of tumor molecular heterogeneity.We demonstrate e-biopsy in vivo, using the 4T1 breast cancer model in mice to assess its performance, as well as the inferred spatial differential protein expression. In particular, we show that proteomic profiles obtained via e-biopsy in vivo distinguish the tumors from healthy breast tissue and reflect spatial tumor differential protein expression. E-biopsy provides a completely new molecular sampling modality for solid tumors molecular cartography, providing information that potentially enables more rapid and sensitive detection at lesser risk, as well as more precise personalized medicine.
A novel integrated MADM method for design concept evaluation
Authors: Chen Zhe , Zhong Peisi , Liu Mei , Ma Qing , Si Guangyao
Published: September 2022

Design concept evaluation plays a significant role in new product development. Rough set based methods are regarded as effective evaluation techniques when facing a vague and uncertain environment and are widely used in product research and development. This paper proposed an improved rough-TOPSIS method, which aims to reduce the imprecision of design concept evaluation in two ways. First, the expert group for design concept evaluation is classified into three clusters: designers, manufacturers, and customers. The cluster weight is determined by roles in the assessment using a Multiplicative Analytic Hierarchy Process method. Second, the raw information collection method is improved with a 3-step process, and both design values and expert linguistic preferences are integrated into the rough decision matrix. The alternatives are then ranked with a rough-TOPSIS method with entropy criteria weight. A practical example is shown to demonstrate the method’s viability. The findings suggest that the proposed decision-making process is effective in product concept design evaluation.
Impact of using different-sized touch keyboards on free-text keystroke dynamics authentication in the Arabic language
Authors: Alsuhibany Suliman A. , Almuqbil Afnan S.
Published: September 2022

Authentication using keystroke dynamics (KD) has become an active research area due to its usability and security aspects. Nowadays, the scale of touch keyboard use has expanded to include most modern devices. Although KD typically focuses on a single device at a particular time, authentication systems are adjustable within their environments, as these systems’ users frequently switch between multiple devices. Thus, this paper assesses users’ typing behavior on different tablet devices with varying touch keyboard sizes. In particular, we empirically assess whether the validation results from free-text KD authentication vary depending on the touch keyboard size. The results reveal interesting research directions for future feasibility studies on changing the dynamic keystroke typing-pad effect on user-security and trust-authentication analysis.
Post-disaster building damage assessment based on improved U-Net
Authors: Deng Liwei , Wang Yue
Published: September 2022

When a severe natural disaster occurs, the extraction of post-disaster building damage information is one of the methods to quickly obtain disaster information. The increasingly mature high-resolution remote sensing technology provides a solid foundation for obtaining information about building damage. To address the issues with inaccurate building positioning in existing building damage assessment methods, as well as poor classification due to similar minor and major damage characteristics in building damage classification. Based on U-Net, we designed a two-stage building damage assessment network. The first stage is an independent U-Net focused on building segmentation, followed by a Siamese U-Net focused on building damage classification. The Extra Skip Connection and Asymmetric Convolution Block were used for enhancing the network's ability to segment buildings on different scales; Shuffle Attention directed the network's attention to the correlation of buildings before and after the disaster. The xBD dataset was used for training and testing in the study, and the overall performance was evaluated using a balanced F-score (F1). The improved network had an F1 of 0.8741 for localization and F1 of 0.7536 for classification. When compared to other methods, it achieved better overall performance for building damage assessment and was able to generalize to multiple disasters.
Assessment of risk factors for delayed gastric emptying after distal gastrectomy for gastric cancer
Authors: Mukoyama Tomosuke , Kanaji Shingo , Sawada Ryuichiro , Harada Hitoshi , Urakawa Naoki , Goto Hironobu , Hasegawa Hiroshi , Yamashita Kimihiro , Matsuda Takeru , Oshikiri Taro , Kakeji Yoshihiro
Published: September 2022

The risk factors for delayed gastric emptying (DGE) following gastrectomy are unclear. This study aimed to investigate the risk factors for DGE and the severity of DGE. We retrospectively evaluated 412 patients who underwent gastrectomy for gastric cancer between 2011 and 2019. The cases were classified into the DGE (n = 27) and non-DGE (n = 385) groups; the DGE group was further classified into two subgroups based on nasogastric tube insertion as an indicator of severity. For determining the relationship between resected stomach volume and DGE, we calculated the area of each surgical specimen using the ImageJ software. Female sex (odds ratio [OR] 2.55; 95% confidence interval [CI] 1.09–5.93; P = 0.03), diabetes (OR 2.38; 95% CI 1.02–5.57; P = 0.03), and distal gastric tumors (OR 2.61; 95% CI 1.10–6.19; P = 0.02) were identified as independent risk factors by multivariate analysis. The duration of hospital stay was longer in the DGE group than in the non-DGE group (29 vs. 15 days, P < 0.01). Overall, 24 cases of DGE (89%) were found in more than 1 week following surgery. No correlation was observed between clinical features and the severity of DGE. The resected area in the DGE group was significantly larger than that in the non-DGE group (198.0 vs. 173.9 cm2, P = 0.03). In conclusion, DGE was frequently observed in females and in patients with diabetes and distal gastric tumors. Most of the DGE cases occurred after 7–14 days of surgery, patients who are discharged early should be informed to seek hospitalization if they have symptoms caused by DGE.
Water availability and response of Tarbela Reservoir under the changing climate in the Upper Indus Basin, Pakistan
Authors: Khan Firdos
Published: September 2022

Agriculture is one of the major contributors to the Gross Domestic Product (GDP) of Pakistan which relies on the availability of water. Hydropower contributes approximately 35% to the national electricity gid of Pakistan. Indus River is the main river of the Indus River System (IRS) which provides water for agriculture, hydropower and other purposes. The outputs of the Conformal-Cubic Atmospheric Model (CCAM) are used to force the University of British Columbia Watershed Model (UBCWM) in the Upper Indus Basin (UIB), to investigate future water availability under the two IPCC emission scenarios (RCP4.5 and RCP8.5). Tarbela Reservoir which is the outlet of UIB is used as a measurement tool to assess water availability and response of the reservoir to climate change. The results show that maximum and minimum temperature are increasing in the future in comparison to the reference period. The largest increases in maximum temperature are projected for MAM (March–April–May) and JJA (June–July–August), with increases up to 2 °C in MAM and increases up to 6.4 °C in JJA under the RCP4.5 and RCP8.5, respectively, in the future. Minimum temperature has maximum increase (6.7 °C) in DJF (December–January–February) during 2071–2100 under RCP8.5. Precipitation shows a 5.1% decrease in DJF during 2011–2040 under RCP4.5. The statistics about water availability suggest that there is consistent increase in most of the months in the future, however, under the RCP4.5, there is decline in the river flow during 2071–2100 as compared to the 2041–2070. The findings of this study show that most of the time there will be more water available but in some months, there may be water scarcity under the RCP4.5, however, proper management and optimal utilization can reduce the water scarcity.
HSV-1 0∆NLS vaccine elicits a robust B lymphocyte response and preserves vision without HSV-1 glycoprotein M or thymidine kinase recognition
Authors: Gmyrek Grzegorz B. , Berube Amanda N. , Sjoelund Virginie H. , Carr Daniel J. J.
Published: September 2022

Effective experimental prophylactic vaccines against viral pathogens such as herpes simplex virus type 1 (HSV-1) have been shown to protect the host through T and/or B lymphocyte-driven responses. Previously, we found a live-attenuated HSV-1 mutant, 0ΔNLS used as a prophylactic vaccine, provided significant protection against subsequent ocular HSV-1 challenge aligned with a robust neutralizing antibody response. Yet, how the virus mutant elicited the humoral immune response relative to parental virus was unknown. Herein, we present the characterization of B cell subsets in vaccinated mice at times after primary vaccination and following boost compared to the parental virus, termed GFP105. We found that 0∆NLS-vaccinated mice possessed more CD4+follicular helper T (TFH) cells, germinal B cells and class-switched B cells within the first 7 days post-vaccination. Moreover, 0∆NLS vaccination resulted in an increase in plasmablasts and plasma cells expressing amino-acid transporter CD98 along with an elevated titer of HSV-1-specific antibody compared to GFP105-vaccinated animals. Furthermore, O∆NLS-vaccine-induced CD4+(TFH) cells produced significantly more IL-21 compared to mice immunized with the parental HSV-1 strain. In contrast, there were no differences in the number of regulatory B cells comparing the two groups of immunized mice. In comparing sera recognition of HSV-1-encoded proteins, it was noted antiserum from GFP105-vaccinated mice immunoprecipitated HSV-1 thymidine kinase (TK) and glycoprotein M (gM) whereas sera from 0∆NLS-immunized mice did not even though both groups of vaccinated mice displayed similar neutralizing antibody titers to HSV-1 and were highly resistant to ocular HSV-1 challenge. Collectively, the results suggest (1) the live-attenuated HSV-1 mutant 0∆NLS elicits a robust B cell response that drives select B cell responses greater than the parental HSV-1 and (2) HSV-1 TK and gM are likely expendable components in efficacy of a humoral response to ocular HSV-1 infection.
Changes in the oral status and periodontal pathogens in a Sardinian rural community from pre-industrial to modern time
Authors: Casula Eleonora , Contu Maria Paola , Demontis Cristina , Coghe Ferdinando , Steri Giorgio Carlo , Scano Alessandra , Ferrando Maria Laura , Orrù Germano
Published: September 2022

The oral microbial profile in humans has evolved in response to lifestyle changes over the course of different eras. Here, we investigated tooth lesions and the microbial profile of periodontal bacteria (PB) in dental calculus of a Sardinian pre-industrial rural community. In total, 51 teeth belonging to 12 historical individuals buried in an ossuary in the early 1800s and 26 modern teeth extracted from 26 individuals from the same geographical area were compared to determine the oral health status, bacterial load and amount of most relevant PB. Total caries and bacterial genomes count appeared to be sex-related in historical samples. Historical females presented a higher incidence of caries, PB pathogens and a higher bacterial load than historical males. Furthermore, we compared the PB profile of the historical individuals with the modern ones, revealing a notable increase in modern individuals of PB belonging to “Red complex bacteria” often associated with periodontitis and other chronic diseases of modern life. Our findings could be explained through an analysis of environmental factors such as socioeconomic, hygienic and healthy conditions that can have a great impact on oral health and bacterial composition among individuals of the same and different eras.