bluuebunny/crossref_metadata_2025_split huggingface dataset:
Experimental demonstration of novel beam characterization using a polarizable X-band transverse deflection structure
Authors: Marchetti B. , Grudiev A. , Craievich P. , Assmann R. , Braun H.-H. , Catalan Lasheras N. , Christie F. , D’Arcy R. , Fortunati R. , Ganter R. , González Caminal P. , Hoffmann M. , Huening M. , Jaster-Merz S. M. , Jonas R. , Marcellini F. , Marx D. , McMonagle G. , Osterhoff J. , Pedrozzi M. , Prat Costa E. , Reiche S. , Reukauff M. , Schreiber S. , Tews G. , Vogt M. , Wesch S. , Wuensch W. 
Published: February 2021

AbstractThe PolariX TDS (Polarizable X-Band Transverse Deflection Structure) is an innovative TDS-design operating in the X-band frequency-range. The design gives full control of the streaking plane, which can be tuned in order to characterize the projections of the beam distribution onto arbitrary transverse axes. This novel feature opens up new opportunities for detailed characterization of the electron beam. In this paper we present first measurements of the Polarix TDS at the FLASHForward beamline at DESY, including three-dimensional reconstruction of the charge-density distribution of the bunch and slice emittance measurements in both transverse directions. The experimental results open the path toward novel and more extensive beam characterization in the direction of multi-dimensional-beam-phase-space reconstruction.
Evaluation of the number of undiagnosed infected in an outbreak using source of infection measurements
Authors: Melka Akiva Bruno , Louzoun Yoram 
Published: February 2021

AbstractIn times of outbreaks, an essential requirement for better monitoring is the evaluation of the number of undiagnosed infected individuals. An accurate estimate of this fraction is crucial for the assessment of the situation and the establishment of protective measures. In most current studies using epidemics models, the total number of infected is either approximated by the number of diagnosed individuals or is dependent on the model parameters and assumptions, which are often debated. We here study the relationship between the fraction of diagnosed infected out of all infected, and the fraction of infected with known contaminator out of all diagnosed infected. We show that those two are approximately the same in exponential models and across most models currently used in the study of epidemics, independently of the model parameters. As an application, we compute an estimate of the effective number of infected by the SARS-CoV-2 virus in various countries.
Silver nanowires as plasmonic compensators of luminescence quenching in single up-converting nanocrystals deposited on graphene
Authors: Prymaczek A. , Cwierzona M. , Antoniak M. A. , Nyk M. , Mackowski S. , Piatkowski D. 
Published: February 2021

AbstractSingle nanocrystal spectroscopy is employed to demonstrate metal-enhanced optical response of Er3+/Yb3+ doped up-conversion nanocrystals deposited on graphene upon coupling with silver nanowires. Direct interaction between nanocrystals and graphene results in quenching of up-conversion emission and shortening of luminescence decay times, due to the energy transfer to graphene. The amount of the energy absorbed by graphene can be enhanced by coupling Er3+/Yb3+ doped up-conversion nanocrystals with silver nanowires. Microscopy studies with high spatial resolution together with time-resolved analysis of nanocrystal luminescence show increase of the emission rates with fourfold enhancement of the intensity for nanocrystals placed in the vicinity of silver nanowires. This strong enhancement emerges despite simultaneous interaction with graphene. The hybrid nanostructure provides thus a way to combine optical activity of up-conversion nanocrystals and enhancement provided by metallic nanowires with excellent electrical and mechanical properties of graphene.
Hydrodynamic assisted multiparametric particle spectrometry
Authors: Martín-Pérez Alberto , Ramos Daniel , Yubero Marina L. , García-López Sergio , Kosaka Priscila M. , Tamayo Javier , Calleja Montserrat 
Published: February 2021

AbstractThe real-time analysis of single analytes in flow is becoming increasingly relevant in cell biology. In this work, we theoretically predict and experimentally demonstrate hydrodynamic focusing with hollow nanomechanical resonators by using an interferometric system which allows the optical probing of flowing particles and tracking of the fundamental mechanical mode of the resonator. We have characterized the hydrodynamic forces acting on the particles, which will determine their velocity depending on their diameter. By using the parameters simultaneously acquired: frequency shift, velocity and reflectivity, we can unambiguously classify flowing particles in real-time, allowing the measurement of the mass density: 1.35 ± 0.07 g·mL-1 for PMMA and 1.7 ± 0.2 g·mL-1 for silica particles, which perfectly agrees with the nominal values. Once we have tested our technique, MCF-7 human breast adenocarcinoma cells are characterized (1.11 ± 0.08 g·mL-1) with high throughput (300 cells/minute) observing a dependency with their size, opening the door for individual cell cycle studies.
Exposure to perfluoroalkyl substances in early pregnancy and risk of sporadic first trimester miscarriage
Authors: Wikström Sverre , Hussein Ghada , Lingroth Karlsson Annika , Lindh Christian H. , Bornehag Carl-Gustaf 
Published: February 2021

AbstractMany first trimester sporadic miscarriages are unexplained and the role of environmental exposures is unknown. The present aim was to study if levels of Perfluoroalkyl substances (PFASs) in early pregnancy are associated with unexplained, sporadic first trimester miscarriage. The study was performed within the Swedish SELMA pregnancy cohort. Seventy-eight women with non-recurrent first trimester miscarriage were included and 1449 women were available as live birth controls. Eight PFASs were measured in first trimester serum. A doubling of perfluorooctanoic acid (PFOA) exposure, corresponding to an inter-quartile increase, was associated with an odds ratio (95%CI) for miscarriage of 1.48 (1.09–2.01) when adjusting for parity, age and smoking. Analyses per quartiles of PFOA exposure indicated a monotonic dose response association with miscarriage. A similar, but not significant, pattern was observed for perfluorononanoic acid (PFNA). For other PFAS, there were no associations with miscarriage. We have previously shown associations between early pregnancy PFAS exposures and preeclampsia, as well as lower birth weight. Now we report an association between PFOA and miscarriage within the same cohort, which may suggest shared but unknown mechanisms. The study can only represent a period of early placentation and clinical pregnancy loss during the second half of the first trimester.
Visual working memory and sensory processing in autistic children
Authors: Stevenson Ryan A. , Ruppel Justin , Sun Sol Z. , Segers Magali , Zapparoli Busisiwe L. , Bebko James M. , Barense Morgan D. , Ferber Susanne 
Published: February 2021

AbstractWhile atypical sensory processing is one of the more ubiquitous symptoms in autism spectrum disorder, the exact nature of these sensory issues remains unclear, with different studies showing either enhanced or deficient sensory processing. Using a well-established continuous cued-recall task that assesses visual working memory, the current study provides novel evidence reconciling these apparently discrepant findings. Autistic children exhibited perceptual advantages in both likelihood of recall and recall precision relative to their typically-developed peers. When autistic children did make errors, however, they showed a higher probability of erroneously binding a given colour with the incorrect spatial location. These data align with neural-architecture models for feature binding in visual working memory, suggesting that atypical population-level neural noise in the report dimension (colour) and cue dimension (spatial location) may drive both the increase in probability of recall and precision of colour recall as well as the increase in proportion of binding errors when making an error, respectively. These changes are likely to impact core symptomatology associated with autism, as perceptual binding and working memory play significant roles in higher-order tasks, such as communication.
Development of event-specific detection method for identification of insect resistant NIBGE-1601 cotton harboring double gene Cry1Ac-Cry2Ab construct
Authors: Asif Muhammad , Siddiqui Hamid Anees , Naqvi Rubab Zahra , Amin Imran , Asad Shaheen , Mukhtar Zahid , Bashir Aftab , Mansoor Shahid 
Published: February 2021

AbstractBt cotton expressing Cry1Ac is being cultivated in Pakistan. It has been observed that pink bollworm may have developed resistance against single Bt gene (Cry1Ac). For durable resistance, insect resistant NIBGE-1601 cotton harboring double gene Cry1Ac-Cry2Ab construct was developed. There was a need to characterize NIBGE-1601 event for intellectual property rights protection. The Presence of NIBGE Cry1Ac and NIBGE Cry2Ab genes was checked in NIBGE-1601 cotton plants through PCR, while there was no amplification using primers specific for Monsanto events (MON531, MON15985, MON1445). Using genome walking technology, NIBGE-601 event has been characterized. Event-specific primers of NIBGE-1601 were designed and evaluated to differentiate it from other cotton events mentioned above. NIBGE-1601 event detection primers are highly specific, therefore, can detect NIBGE 1601 event at different conditions using single or multiplex PCR. In the qualitative PCR, using NIBGE-1601 event specific primers, 0.05 ng was the limit of detection for NIBGE-1601double gene cotton genomic DNA. Thus event characterization and development of event-specific diagnostics will help in breeding new cotton varieties resistant to cotton bollworms.
Morpho-molecular identification and first report of Fusarium equiseti in causing chilli wilt from Kashmir (Northern Himalayas)
Authors: Hami Ammarah , Rasool Rovidha S. , Khan Nisar A. , Mansoor Sheikh , Mir Mudasir A. , Ahmed Nazeer , Masoodi Khalid Z. 
Published: February 2021

AbstractChilli (Capsicum annuum L.) is one of the most significant vegetable and spice crop. Wilt caused by Fusarium Sp. has emerged as a serious problem in chilli production. Internal transcribed spacer (ITS) region is widely used as a DNA barcoding marker to characterize the diversity and composition of Fusarium communities. ITS regions are heavily used in both molecular methods and ecological studies of fungi, because of its high degree of interspecific variability, conserved primer sites and multiple copy nature in the genome. In the present study we focused on morphological and molecular characterization of pathogen causing chilli wilt. Chilli plants were collected from four districts of Kashmir valley of Himalayan region. Pathogens were isolated from infected root and stem of the plants. Isolated pathogens were subjected to DNA extraction and PCR amplification. The amplified product was sequenced and three different wilt causing fungal isolates were obtained which are reported in the current investigation. In addition to Fusarium oxysporum and Fusarium solani, a new fungal species was found in association with the chilli wilt in Kashmir valley viz., Fusarium equiseti that has never been reported before from this region. The studies were confirmed by pathogenicity test and re-confirmation by DNA barcoding.
Generation of Werner-like states via a two-qubit system plunged in a thermal reservoir and their application in solving binary classification problems
Authors: Ghasemian E. , Tavassoly M. K. 
Published: February 2021

AbstractWe present a theoretical scheme for the generation of stationary entangled states. To achieve the purpose we consider an open quantum system consisting of a two-qubit plunged in a thermal bath, as the source of dissipation, and then analytically solve the corresponding quantum master equation. We generate two classes of stationary entangled states including the Werner-like and maximally entangled mixed states. In this regard, since the solution of the system depends on its initial state, we can manipulate it and construct robust Bell-like state. In the continuation, we analytically obtain the population and coherence of the considered two-qubit system and show that the residual coherence can be maintained even in the equilibrium condition. Finally, we successfully encode our two-qubit system to solve a binary classification problem. We demonstrate that, the introduced classifiers present high accuracy without requiring any iterative method. In addition, we show that the quantum based classifiers beat the classical ones.
Direct reprogramming of oligodendrocyte precursor cells into GABAergic inhibitory neurons by a single homeodomain transcription factor Dlx2
Authors: Boshans Linda L. , Soh Heun , Wood William M. , Nolan Timothy M. , Mandoiu Ion I. , Yanagawa Yuchio , Tzingounis Anastasios V. , Nishiyama Akiko 
Published: February 2021

AbstractOligodendrocyte precursor cells (NG2 glia) are uniformly distributed proliferative cells in the mammalian central nervous system and generate myelinating oligodendrocytes throughout life. A subpopulation of OPCs in the neocortex arises from progenitor cells in the embryonic ganglionic eminences that also produce inhibitory neurons. The neuronal fate of some progenitor cells is sealed before birth as they become committed to the oligodendrocyte lineage, marked by sustained expression of the oligodendrocyte transcription factor Olig2, which represses the interneuron transcription factor Dlx2. Here we show that misexpression of Dlx2 alone in postnatal mouse OPCs caused them to switch their fate to GABAergic neurons within 2 days by downregulating Olig2 and upregulating a network of inhibitory neuron transcripts. After two weeks, some OPC-derived neurons generated trains of action potentials and formed clusters of GABAergic synaptic proteins. Our study revealed that the developmental molecular logic can be applied to promote neuronal reprogramming from OPCs.
Smad4 regulates the nuclear translocation of Nkx2-5 in cardiac differentiation
Authors: Hu Wenyu , Dong Anqi , Karasaki Kohei , Sogabe Shota , Okamoto Daiki , Saigo Masato , Ishida Mari , Yoshizumi Masao , Kokubo Hiroki 
Published: February 2021

AbstractBmp plays an important role in cardiomyocyte differentiation, but the function of Smad4 in Bmp signaling remains elusive. Here, we show that disruption of the Smad4 gene in cardiac progenitors expressing Sfrp5 led to embryonic lethality with hypoplastic heart formation. Although the expression of Nkx2-5 is regulated by Bmp signaling, expression of Nkx2-5 was weakly detected in the mutant heart. However, the nuclear translocation of Nkx2-5 was impaired. Expression of CK2 or PP1, which could alter the phosphorylation status of the NLS of Nkx2-5, was not affected, but Nkx2-5 was found to bind to Smad4 by co-immunoprecipitation experiments. Introduction of Smad4 into cells derived from Smad4 conditional knockout embryonic hearts restored the nuclear localization of Nkx2-5, and exogenous Nkx2-5 failed to translocate into the nucleus of Smad4-depleted fibroblasts. These results suggest that Smad4 plays an essential role in cardiomyocyte differentiation by controlling not only transcription but also the nuclear localization of Nkx2-5.
Grading system utilising the total score of Oxford classification for predicting renal prognosis in IgA nephropathy
Authors: Miyabe Yoei , Karasawa Kazunori , Akiyama Kenichi , Ogura Shota , Takabe Tomo , Sugiura Naoko , Seki Momoko , Iwabuchi Yuko , Hanafusa Norio , Uchida Keiko , Nitta Kosaku , Moriyama Takahito 
Published: February 2021

AbstractThe Oxford classification of IgA nephropathy (IgAN) can evaluate each MEST-C score individually. We analysed a new grading system that utilised the total MEST-C score in predicting renal prognosis. Altogether, 871 IgAN patients were classified into three groups using the new Oxford classification system (O-grade) that utilised the total MEST-C score (O-grade I: 0–1, II: 2–4, and III: 5–7 points), and the 10-year renal prognosis was analysed. The clinical findings became significantly severer with increasing O-grades, and the renal survival rate by the Kaplan–Meier method was 94.1%, 86.9%, and 74.1% for O-grades I, II, and III, respectively. The hazard ratios (HRs) for O-grades II and III with reference to O-grade I were 2.8 (95% confidence interval [CI] 1.3–6.0) and 6.3 (95% CI 2.7–14.5), respectively. In the multivariate analysis, mean arterial pressure and eGFR, proteinuria at the time of biopsy, treatment of corticosteroids/immunosuppressors, and O-grade (HR 1.63; 95% CI 1.11–2.38) were the independent factors predicting renal prognosis. Among the nine groups classified using the O-grade and Japanese clinical-grade, the renal prognosis had an HR of 15.2 (95% CI 3.5–67) in the severest group. The O-grade classified by the total score of the Oxford classification was associated with renal prognosis.
Semantic segmentation of reflectance confocal microscopy mosaics of pigmented lesions using weak labels
Authors: D’Alonzo Marissa , Bozkurt Alican , Alessi-Fox Christi , Gill Melissa , Brooks Dana H. , Rajadhyaksha Milind , Kose Kivanc , Dy Jennifer G. 
Published: February 2021

AbstractReflectance confocal microscopy (RCM) is a non-invasive imaging tool that reduces the need for invasive histopathology for skin cancer diagnoses by providing high-resolution mosaics showing the architectural patterns of skin, which are used to identify malignancies in-vivo. RCM mosaics are similar to dermatopathology sections, both requiring extensive training to interpret. However, these modalities differ in orientation, as RCM mosaics are horizontal (parallel to the skin surface) while histopathology sections are vertical, and contrast mechanism, RCM with a single (reflectance) mechanism resulting in grayscale images and histopathology with multi-factor color-stained contrast. Image analysis and machine learning methods can potentially provide a diagnostic aid to clinicians to interpret RCM mosaics, eventually helping to ease the adoption and more efficiently utilizing RCM in routine clinical practice. However standard supervised machine learning may require a prohibitive volume of hand-labeled training data. In this paper, we present a weakly supervised machine learning model to perform semantic segmentation of architectural patterns encountered in RCM mosaics. Unlike more widely used fully supervised segmentation models that require pixel-level annotations, which are very labor-demanding and error-prone to obtain, here we focus on training models using only patch-level labels (e.g. a single field of view within an entire mosaic). We segment RCM mosaics into “benign” and “aspecific (nonspecific)” regions, where aspecific regions represent the loss of regular architecture due to injury and/or inflammation, pre-malignancy, or malignancy. We adopt Efficientnet, a deep neural network (DNN) proven to accurately accomplish classification tasks, to generate class activation maps, and use a Gaussian weighting kernel to stitch smaller images back into larger fields of view. The trained DNN achieved an average area under the curve of 0.969, and Dice coefficient of 0.778 showing the feasibility of spatial localization of aspecific regions in RCM images, and making the diagnostics decision model more interpretable to the clinicians.
Transcriptome analysis of arterial and venous circulating miRNAs during hypertension
Authors: Jin Ling , Li Min , Wang Hao , Yin Zhongnan , Chen Li , Zhou Yang , Han Yongzheng , Cui Qinghua , Zhou Yuan , Xue Lixiang 
Published: February 2021

AbstractMost current circulating miRNA biomarkers are derived from peripheral venous blood, whereas miRNA deregulation in arterial blood in disease conditions has been largely ignored. To explore whether peripheral venous blood miRNAs could represent a bona fide specific miRNA deregulation pattern, we selected hypertension, a disease that is particularly associated with vessels, as the model. Circulating miRNA profiles of arterial and venous blood from spontaneously hypertensive (SHR) rats and their corresponding controls (i.e., WKY rats) were investigated by next-generation miRNA sequencing. Little miRNAs were observed between arterial and venous circulating miRNAs in WKY rats. Interestingly, this number was enhanced in SHR hypertensive rats. Bioinformatical analysis of disease association, enriched target genes and the regulatory transcription factors of these differentially expressed miRNAs implied a potential functional link with cardiovascular disease-related functions. Comparisons between arterial and venous miRNAs in hypertension-versus-control conditions also revealed prominent disease association of circulating miRNAs and their target genes in arteries but not in veins. Moreover, a young non-hypertensive animal model in SHR background (i.e. JSHR) was used as a second control for SHR. Additional transcriptomic analysis and droplet digital PCR validation of arterial and venous deregulated miRNAs among SHR and its two controls (WKY, JSHR) revealed a noticeable consensus of artery-deregulated miRNAs in hypertension and two novel arterial circulating signatures (miR-455-3p and miR-140-3p) of hypertension. These results suggest the necessity of re-evaluating the efficacy of certain venous miRNAs identified in previous studies as potential biomarkers in cardiovascular diseases or a wider disease spectrum.
Changes in the large carnivore community structure of the Judean Desert in connection to Holocene human settlement dynamics
Authors: Lazagabaster Ignacio A. , Ullman Micka , Porat Roi , Halevi Romi , Porat Naomi , Davidovich Uri , Marom Nimrod 
Published: February 2021

AbstractInvestigating historical anthropogenic impacts on faunal communities is key to understanding present patterns of biodiversity and holds important implications for conservation biology. While several studies have demonstrated the human role in the extinction of large herbivores, effective methods to study human interference on large carnivores in the past are limited by the small number of carnivoran remains in the paleozoological record. Here, we integrate a systematic paleozoological survey of biogenic cave assemblages with the archaeological and paleoenvironmental records of the Judean Desert, to reveal historical changes in the large carnivore community. Our results show a late Holocene (~ 3400 years ago) faunal reassembly characterized by the diminishment of the dominant large carnivoran, the Arabian leopard (Panthera pardus sbsp. nimr), and the spread of the Syrian striped hyena (Hyaena hyaena sbsp. syriaca). We suggest that increased hunting pressure in combination with regional aridification were responsible for the decrease in the number of leopards, while the introduction of domestic animals and settlement refuse brought new scavenging opportunities for hyenas. The recent extirpation of leopards from the region has been a final note to the Holocene human impact on the ecosystem.