bluuebunny/crossref_metadata_2025_split huggingface dataset:
Electrical antimicrobial susceptibility testing based on aptamer-functionalized capacitance sensor array for clinical isolates
Authors: Lee Kyo-Seok , Lee Sun-Mi , Oh Jeseung , Park In Ho , Song Jun Ho , Han Myeonggil , Yong Dongeun , Lim Kook Jin , Shin Jeon-Soo , Yoo Kyung-Hwa 
Published: August 2020

AbstractTo prescribe effective antibiotics to patients with bacterial infections in a timely manner and to avoid the misuse of antibiotics, a rapid antimicrobial susceptibility test (AST) is essential. However, conventional AST methods require more than 16 h to provide results; thus, we developed an electrical AST (e-AST) system, which provides results within 6 h. The proposed e-AST is based on an array of 60 aptamer-functionalized capacitance sensors that are comparable to currently available AST panels and a pattern-matching algorithm. The performance of the e-AST was evaluated in comparison with that of broth microdilution as the reference test for clinical strains isolated from septic patients. A total of 4,554 tests using e-AST showed a categorical agreement of 97% with a minor error of 2.2%, major error of 0.38%, and very major error of 0.38%. We expect that the proposed e-AST could potentially aid antimicrobial stewardship efforts and lead to improved patient outcomes.
Deletion of DJ-1 in rats affects protein abundance and mitochondrial function at the synapse
Authors: Almikhlafi Mohannad A. , Stauch Kelly L. , Villeneuve Lance M. , Purnell Phillip R. , Lamberty Benjamin G. , Fox Howard S. 
Published: August 2020

AbstractDJ-1 is a multifunctional protein affecting different biological and cellular processes. In addition, DJ-1 has roles in regulating mitochondrial function. Loss-of-function mutations in DJ-1 were found to cause an autosomal recessive form of Parkinson’s disease. One of the main pathological features of PD is loss of dopamine neurons in the nigrostriatal pathway. DJ-1 knockout (KO) rats exhibit progressive nigral neurodegeneration with about 50% dopaminergic cell loss at 8 months of age. In order to assess the effects of DJ-1 deficiency on neuronal mitochondria prior to neuron loss, we performed proteomic analysis of synaptic mitochondria isolated from the striatum, the location of nigrostriatal pathway nerve terminals, of 3-month-old DJ-1 KO rats. In total, 371 mitochondrial proteins were quantified, and of these 76 were differentially expressed in DJ-1 KO rats. Proteins perturbed by the loss of DJ-1 were involved in several mitochondrial functional pathways, including the tricarboxylic acid cycle and electron transport chain. Thus, synaptic mitochondrial respiration was measured and showed a significant change due to DJ-1 deficiency. The dataset generated here highlights the role of synaptic mitochondria in PD associated with DJ-1. This study improves our understanding of DJ-1 effects in a complex tissue environment and the synaptic mitochondrial changes that accompany its loss.
New AMS 14C dates track the arrival and spread of broomcorn millet cultivation and agricultural change in prehistoric Europe
Authors: Filipović Dragana , Meadows John , Corso Marta Dal , Kirleis Wiebke , Alsleben Almuth , Akeret Örni , Bittmann Felix , Bosi Giovanna , Ciută Beatrice , Dreslerová Dagmar , Effenberger Henrike , Gyulai Ferenc , Heiss Andreas G. , Hellmund Monika , Jahns Susanne , Jakobitsch Thorsten , Kapcia Magda , Klooß Stefanie , Kohler-Schneider Marianne , Kroll Helmut , Makarowicz Przemysław , Marinova Elena , Märkle Tanja , Medović Aleksandar , Mercuri Anna Maria , Mueller-Bieniek Aldona , Nisbet Renato , Pashkevich Galina , Perego Renata , Pokorný Petr , Pospieszny Łukasz , Przybyła Marcin , Reed Kelly , Rennwanz Joanna , Stika Hans-Peter , Stobbe Astrid , Tolar Tjaša , Wasylikowa Krystyna , Wiethold Julian , Zerl Tanja 
Published: August 2020

AbstractBroomcorn millet (Panicum miliaceum L.) is not one of the founder crops domesticated in Southwest Asia in the early Holocene, but was domesticated in northeast China by 6000 bc. In Europe, millet was reported in Early Neolithic contexts formed by 6000 bc, but recent radiocarbon dating of a dozen 'early' grains cast doubt on these claims. Archaeobotanical evidence reveals that millet was common in Europe from the 2nd millennium bc, when major societal and economic transformations took place in the Bronze Age. We conducted an extensive programme of AMS-dating of charred broomcorn millet grains from 75 prehistoric sites in Europe. Our Bayesian model reveals that millet cultivation began in Europe at the earliest during the sixteenth century bc, and spread rapidly during the fifteenth/fourteenth centuries bc. Broomcorn millet succeeds in exceptionally wide range of growing conditions and completes its lifecycle in less than three summer months. Offering an additional harvest and thus surplus food/fodder, it likely was a transformative innovation in European prehistoric agriculture previously based mainly on (winter) cropping of wheat and barley. We provide a new, high-resolution chronological framework for this key agricultural development that likely contributed to far-reaching changes in lifestyle in late 2nd millennium bc Europe.
Permalloy nanowires/graphene oxide composite with enhanced conductive properties
Authors: Arciniegas Jaimes Diana M. , Márquez Paulina , Ovalle Alexandra , Escrig Juan , Linarez Pérez Omar , Bajales Noelia 
Published: August 2020

AbstractCarbon–metal-based composites arise as advanced materials in the frontiers with nanotechnology, since the properties inherent to each component are multiplexed into a new material with potential applications. In this work, a novel composite consisting of randomly oriented permalloy nanowires (Py NWs) intercalated among the sheets of multi-layered graphene oxide (GO) was performed. Py NWs were synthesized by electrodeposition inside mesoporous alumina templates, while GO sheets were separated by means of sonication. Sequential deposition steps of Py NWs and GO flakes allowed to reach a reproducible and stable graphene oxide-based magnetic assembly. Microscopic and spectroscopic results indicate that Py NWs are anchored on the surface as well as around the edges of the multi-layered GO, promoted by the presence of chemical groups, while magnetic characterization affords additional support to our hypothesis regarding the parallel orientation of the Py NWs with respect to the GO film, and also hints the parallel stacking of GO sheets with respect to the substrate. The most striking result remains on the electrochemical performance achieved by the composite that evidences an enhanced conductive behaviour compared to a standard electrode. Such effect provides an approach to the development of permalloy nanowires/graphene oxide-based electrodes as attractive candidates for molecular sensing devices.
Induction of mitochondria-mediated apoptosis and suppression of tumor growth in zebrafish xenograft model by cyclic dipeptides identified from Exiguobacterium acetylicum
Authors: Jinendiran Sekar , Teng Weilin , Dahms Hans-Uwe , Liu Wangta , Ponnusamy Vinoth Kumar , Chiu Charles Chien-Chih , Kumar B. S. Dileep , Sivakumar Natesan 
Published: August 2020

AbstractColorectal cancer is the most common type of gastrointestinal cancers with poor survival and limited therapeutic options. In this study, four structurally different cyclic dipeptides (or diketopiperazine) were isolated and identified as cyclo (l-Pro-l-Leu), cyclo (l-Pro-l-Val), cyclo (l-Pro-l-Phe) and cyclo (l-Pro-l-Tyr) from the ethyl acetate extract in the cell-free filtrate of Exiguobacterium acetylicum S01. The anticancer potential of identified DKPs on colorectal cancer HT-29 cells in vitro and in vivo zebrafish xenograft model was evaluated. The MTT (3-(4, 5-dimethylthiazol-2yl)-2, 5-diphenyltetrazolium bromide)) assay showed that four DKPs exhibited significant inhibition of HT-29 cells viability in a dose-dependent manner whereas there were no cytotoxic effects on normal mouse fibroblast 3T3 cells. Also, we observed that all DKPs induce early and late apoptotic cell death in HT-29 cells. Moreover, the expression levels of apoptotic (cytochrome-c, caspase-3 and Bid) and anti-apoptotic (Bcl-2) markers were up- and down-regulated in HT-29 cells in response to DKPs treatments. Furthermore, these four DKPs remarkably inhibited the tumor progression in a zebrafish xenograft model within a nonlethal dose range. Overall, our findings suggest that cyclic dipeptides derived from E. acetylicum S01 could be promising chemopreventive/ therapeutic candidates against cancer.
Pit lakes from Southern Sweden: natural radioactivity and elementary characterization
Authors: Mantero J. , Thomas R. , Holm E. , Rääf C. , Vioque I. , Ruiz-Canovas C. , García-Tenorio R. , Forssell-Aronsson E. , Isaksson M. 
Published: August 2020

AbstractNatural radioactivity in the environment is a field gaining more attention in last decades. This work is focused on the study of natural radioactivity complemented with elementary characterization at former non-uraniferous mining areas in Sweden. This aim is addressed through the study of mining lakes, called pit lakes, which are water bodies generated after opencast mining. Environmental matrices (water, sediments and rocks) from 32 Swedish pit lakes, commonly used for recreational purposes were radiometrically characterized via alpha (238U, 234U, 232Th, 230Th, 210Po isotopes) and gamma spectrometry (238U and 232Th series radionuclides). Additionally, ambient dose rate equivalent in the immediate surrounding of each pit lake was quantified. Physico-chemical parameters (pH, specific conductivity, dissolved oxygen, oxidation–reduction potential) and elemental composition (major and trace elements by ICP-MS) were analysed in water samples and elementary composition of sediments/rocks was measured by XRF and SEM–EDX in some specific cases. A non-negligible number of pit lakes (26%) with enhanced U levels in water was found. At some sites, rocks contained up to 4% of U in areas with high degree of interaction with local population. Concerning the elementary perspective, another popular site (due to its turquoise water) was found to have elevated dissolved heavy metal levels. Results obtained in this work prove that measurement of natural radioactivity is another component that should be included in routine analysis of characterization in mining areas, especially if restauration of post-mining sites is intended for human recreational.
Rapid recovery of locomotor performance after leg loss in harvestmen
Authors: Escalante Ignacio , Badger Marc A. , Elias Damian O. 
Published: August 2020

AbstractAnimals have evolved adaptations to deal with environmental challenges. For instance, voluntarily releasing appendages (autotomy) to escape potential predators. Although it may enhance immediate survival, this self-imposed bodily damage may convey long-term consequences. Hence, compensatory strategies for this type of damage might exist. We experimentally induced autotomy in Prionostemma harvestmen. These arachnids are ideal to examine this topic because they show high levels of leg loss in the field but do not regenerate their legs. We video-recorded animals moving on a horizontal track and reconstructed their 3D trajectories with custom software tools to measure locomotor performance. Individuals that lost either three legs total or two legs on the same side of the body showed an immediate and substantial decrease in velocity and acceleration. Surprisingly, harvestmen recovered initial performance after 2 days. This is the quickest locomotor recovery recorded for autotomizing animals. We also found post-autotomy changes in stride and postural kinematics, suggesting a role for kinematic adjustments in recovery. Additionally, following leg loss, some animals changed the gaits used during escape maneuvers, and/or recruited the ‘sensory’ legs for locomotion. Together, these findings suggest that harvestmen are mechanically robust to the bodily damage imposed by leg loss.
Cell death resulted from loss of fumarylacetoacetate hydrolase in Arabidopsis is related to phytohormone jasmonate but not salicylic acid
Authors: Zhou Zhou , Zhi Tiantian , Han Chengyun , Peng Zhihong , Wang Ruozhong , Tong Jianhua , Zhu Qi , Ren Chunmei 
Published: August 2020

AbstractFumarylacetoacetate hydrolase (FAH) catalyzes the final step in Tyr degradation pathway essential to animals but not well understood in plants. Previously, we found that mutation of SSCD1 encoding Arabidopsis FAH causes cell death under short day, which uncovered an important role of Tyr degradation pathway in plants. Since phytohormones salicylic acid (SA) and jasmonate (JA) are involved in programmed cell death, in this study, we investigated whether sscd1 cell death is related to SA and JA, and found that (1) it is accompanied by up-regulation of JA- and SA-inducible genes as well as accumulation of JA but not SA; (2) it is repressed by breakdown of JA signaling but not SA signaling; (3) the up-regulation of reactive oxygen species marker genes in sscd1 is repressed by breakdown of JA signaling; (4) treatment of wild-type Arabidopsis with succinylacetone, an abnormal metabolite caused by loss of FAH, induces expression of JA-inducible genes whereas treatment with JA induces expression of some Tyr degradation genes with dependence of JA signaling. These results demonstrated that cell death resulted from loss of FAH in Arabidopsis is related to JA but not SA, and suggested that JA signaling positively regulates sscd1 cell death by up-regulating Tyr degradation.
Highly accurate determination of heterogeneously stacked Van-der-Waals materials by optical microspectroscopy
Authors: Hutzler Andreas , Fritsch Birk , Matthus Christian D. , Jank Michael P. M. , Rommel Mathias 
Published: August 2020

AbstractThe composition of Van-der-Waals heterostructures is conclusively determined using a hybrid evaluation scheme of data acquired by optical microspectroscopy. This scheme deploys a parameter set comprising both change in reflectance and wavelength shift of distinct extreme values in reflectance spectra. Furthermore, the method is supported by an accurate analytical model describing reflectance of multilayer systems acquired by optical microspectroscopy. This approach allows uniquely for discrimination of 2D materials like graphene and hexagonal boron nitride (hBN) and, thus, quantitative analysis of Van-der-Waals heterostructures containing structurally very similar materials. The physical model features a transfer-matrix method which allows for flexible, modular description of complex optical systems and may easily be extended to individual setups. It accounts for numerical apertures of applied objective lenses and a glass fiber which guides the light into the spectrometer by two individual weighting functions. The scheme is proven by highly accurate quantification of the number of layers of graphene and hBN in Van-der-Waals heterostructures. In this exemplary case, the fingerprint of graphene involves distinct deviations of reflectance accompanied by additional wavelength shifts of extreme values. In contrast to graphene, the fingerprint of hBN reveals a negligible deviation in absolute reflectance causing this material being only detectable by spectral shifts of extreme values.
Detecting ulcerative colitis from colon samples using efficient feature selection and machine learning
Authors: Khorasani Hanieh Marvi , Usefi Hamid , Peña-Castillo Lourdes 
Published: August 2020

AbstractUlcerative colitis (UC) is one of the most common forms of inflammatory bowel disease (IBD) characterized by inflammation of the mucosal layer of the colon. Diagnosis of UC is based on clinical symptoms, and then confirmed based on endoscopic, histologic and laboratory findings. Feature selection and machine learning have been previously used for creating models to facilitate the diagnosis of certain diseases. In this work, we used a recently developed feature selection algorithm (DRPT) combined with a support vector machine (SVM) classifier to generate a model to discriminate between healthy subjects and subjects with UC based on the expression values of 32 genes in colon samples. We validated our model with an independent gene expression dataset of colonic samples from subjects in active and inactive periods of UC. Our model perfectly detected all active cases and had an average precision of 0.62 in the inactive cases. Compared with results reported in previous studies and a model generated by a recently published software for biomarker discovery using machine learning (BioDiscML), our final model for detecting UC shows better performance in terms of average precision.
Land vs. water HIIE effects on muscle oxygenation and physiological parameter responses in postmenopausal women
Authors: Chien Kuei-Yu , Kan Nai-Wen , Liao Yi-Hung , Yang Wen-Ting , Yang Yong 
Published: August 2020

AbstractMuscle oxygenation (MO) status is the dynamic balance between O2 utilization and O2 delivery. Low-impact high-intensity interval exercise MO responses in the exercise and recovery stage are still unclear. We compared the differences in MO and physiological parameters between high-intensity interval water-based exercise (WHIIE) and high-intensity interval land bike ergonomic exercise (LBEHIIE) in postmenopausal women. Eleven postmenopausal women completed WHIIE or LBEHIIE in counter-balanced order. Eight sets were performed and each exercise set included high intensity with 80% heart rate reserve (HRR) in 30 s and dynamic recovery with 50% HRR in 90 s. Muscle tissue oxygen saturation index (TSI), total hemoglobin (tHb), oxy-hemoglobin (O2Hb), and deoxy-hemoglobin (HHb) were recorded. Blood lactate, heart rate and rating of perceived exertion (RPE) were measured at pre and post-exercise. Under similar exercise intensity, RPE in WHIIE was lower than that in LBEHIIE. The heart rate in WHIIE was lower than that in LBEHIIE at 1 and 2 min post-exercise. During the dynamic recovery, TSI, tHb, and O2Hb in water were higher than on land. A negative correlation was found between the change in TSI and lactate concentration (r = − 0.664). WHIIE produced greater muscle oxygenation during dynamic recovery. Muscle TSI% was inversely related to blood lactate concentration during exercise in water.
The methylation status of the chemerin promoter region located from − 252 to + 258 bp regulates constitutive but not acute-phase cytokine-inducible chemerin expression levels
Authors: Kwiecien Kamila , Brzoza Piotr , Bak Maciej , Majewski Pawel , Skulimowska Izabella , Bednarczyk Kamil , Cichy Joanna , Kwitniewski Mateusz 
Published: August 2020

AbstractChemerin is a chemoattractant protein with adipokine properties encoded by the retinoic acid receptor responder 2 (RARRES2) gene. It has gained more attention in the past few years due to its multilevel impact on metabolism and immune responses. However, mechanisms controlling the constitutive and regulated expression of RARRES2 in a variety of cell types remain obscure. To our knowledge, this report is the first to show that DNA methylation plays an important role in the cell-specific expression of RARRES2 in adipocytes, hepatocytes, and B lymphocytes. Using luciferase reporter assays, we determined the proximal fragment of the RARRES2 gene promoter, located from − 252 to + 258 bp, to be a key regulator of transcription. Moreover, we showed that chemerin expression is regulated in murine adipocytes by acute-phase cytokines, interleukin 1β and oncostatin M. In contrast with adipocytes, these cytokines exerted a weak, if any, response in mouse hepatocytes, suggesting that the effects of IL-1β and OSM on chemerin expression is specific to fat tissue. Together, our findings highlight previously uncharacterized mediators and mechanisms that control chemerin expression.
Molecular mapping of QTLs for yield related traits in recombinant inbred line (RIL) population derived from the popular rice hybrid KRH-2 and their validation through SNP genotyping
Authors: Kulkarni Swapnil Ravindra , Balachandran S. M. , Ulaganathan K. , Balakrishnan Divya , Praveen M. , Prasad A. S. Hari , Fiyaz R. A. , Senguttuvel P. , Sinha Pragya , Kale Ravindra R. , Rekha G. , Kousik M. B. V. N. , Harika G. , Anila M. , Punniakoti E. , Dilip T. , Hajira S. K. , Pranathi K. , Das M. Ayyappa , Shaik Mastanbee , Chaitra K. , Rao P. Koteswara , Gangurde Sunil S. , Pandey Manish K. , Sundaram R. M. 
Published: August 2020

AbstractThe study was undertaken to identify the quantitative trait loci (QTLs) governing yield and its related traits using a recombinant inbred line (RIL) population derived from the popular rice hybrid, KRH-2 (IR58025A/KMR3R). A genetic map spanning 294.2 cM was constructed with 126 simple sequence repeats (SSR) loci uniformly distributed across the rice genome. QTL analysis using phenotyping and genotyping information identified a total of 22 QTLs. Of these, five major effect QTLs were identified for the following traits: total grain yield/plant (qYLD3-1), panicle weight (qPW3-1),plant height (qPH12-1),flag leaf width (qFLW4-1)and panicle length (qPL3-1), explaining 20.23–22.76% of the phenotypic variance with LOD scores range of 6.5–10.59. Few genomic regions controlling several traits (QTL hotspot) were identified on chromosome 3 for total grain yield/plant (qYLD3-1)and panicle length (qPL3-1). Significant epistatic interactions were also observed for total grain yield per plant (YLD) and panicle length (PL). While most of these QTLs were observed to be co-localized with the previously reported QTL regions, a novel, major QTL associated with panicle length (qPL3-1) was also identified. SNP genotyping of selected high and low yielding RILs and their QTL mapping with 1,082 SNPs validated most of the QTLs identified through SSR genotyping. This facilitated the identification of novel major effect QTLs with much better resolution and precision. In-silico analysis of novel QTLs revealed the biological functions of the putative candidate gene (s) associated with selected traits. Most of the high-yielding RILs possessing the major yield related QTLs were identified to be complete restorers, indicating their possible utilization in development of superior rice hybrids.
Fano feature induced by a bound state in the continuum via resonant state expansion
Authors: Pankin Pavel S. , Maksimov Dmitrii N. , Chen Kuo-Ping , Timofeev Ivan V. 
Published: August 2020

AbstractWe consider light scattering by an anisotropic defect layer embedded into anisotropic photonic crystal in the spectral vicinity of an optical bound state in the continuum (BIC). Using a resonant state expansion method we derive an analytic solution for reflection and transmission amplitudes. The analytic solution is constructed via a perturbative approach with the BIC as the zeroth order approximation. The solution is found to describe the collapsing Fano feature in the spectral vicinity of the BIC. The findings are confirmed via comparison against direct numerical simulations with the Berreman transfer matrix method.