bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reanalysis of putative ovarian follicles suggests that Early Cretaceous birds were feeding not breeding
Authors: Mayr Gerald , Kaye Thomas G. , Pittman Michael , Saitta Evan T. , Pott Christian 
Published: November 2020

AbstractWe address the identity of putative ovarian follicles in Early Cretaceous bird fossils from the Jehol Biota (China), whose identification has previously been challenged. For the first time, we present a link to the botanical fossil record, showing that the “follicles” of some enantiornithine fossils resemble plant propagules from the Jehol Biota, which belong toCarpolithes multiseminalis. The botanical affinities of this “form-taxon” are currently unresolved, but we note thatC. multiseminalispropagules resemble propagules associated with cone-like organs described asStrobilites taxusoides, which in turn are possibly associated with sterile foliage allocated toLiaoningcladus.Laser-Stimulated Fluorescence imaging furthermore reveals different intensities of fluorescence of “follicles” associated with a skeleton of the confuciusornithidEoconfuciusornis zhengi, with a non-fluorescent circular micro-pattern indicating carbonaceous (or originally carbonaceous) matter. This is inconsistent with the interpretation of these structures as ovarian follicles. We therefore reaffirm that the “follicles” represent ingested food items, and even though the exact nature of theEoconfuciusornisstomach contents remains elusive, at least some enantiornithines ingested plant propagules.
Systems evaluation reveals novel transporter YohJK renders 3-hydroxypropionate tolerance in Escherichia coli
Authors: Nguyen-Vo Thuan Phu , Ko Seyoung , Ryu Huichang , Kim Jung Rae , Kim Donghyuk , Park Sunghoon 
Published: November 2020

AbstractPreviously, we have reported that 3-hydroxypropionate (3-HP) tolerance in Escherichia coli W is improved by deletion of yieP, a less-studied transcription factor. Here, through systems analyses along with physiological and functional studies, we suggest that the yieP deletion improves 3-HP tolerance by upregulation of yohJK, encoding putative 3-HP transporter(s). The tolerance improvement by yieP deletion was highly specific to 3-HP, among various C2–C4 organic acids. Mapping of YieP binding sites (ChIP-exo) coupled with transcriptomic profiling (RNA-seq) advocated seven potential genes/operons for further functional analysis. Among them, the yohJK operon, encoding for novel transmembrane proteins, was the most responsible for the improved 3-HP tolerance; deletion of yohJK reduced 3-HP tolerance regardless of yieP deletion, and their subsequent complementation fully restored the tolerance in both the wild-type and yieP deletion mutant. When determined by 3-HP-responsive biosensor, a drastic reduction of intracellular 3-HP was observed upon yieP deletion or yohJK overexpression, suggesting that yohJK encodes for novel 3-HP exporter(s).
Online quantitative partial discharge monitor based on interferometry
Authors: Xue Liang , Zhu Yueyue , Yang Chuankai , Kumarawadu Sisil 
Published: November 2020

AbstractInterferometry-based online partial discharge (PD) monitor presented in this paper can detect the occurrence of PD sensitively, evaluate the peak value of the discharge inception voltage with random waveform and the damage extent relatively cost effectively. The interferograms affected by the PD are collected online. By extracting the phase information of the interference fringes quantitatively, the peak value of the discharge inception voltage with random waveform can be retrieved real-time. Merits of the proposed method as an online quantitative PD monitor are validated via theoretical analysis as well as experimentations by the use of an artificially localized PD source. Furthermore, the proposed method can capture the light signal emitted by the discharge. Quite in contrast to many commonly used sensor-based methods, our approach avoids the need of amplifying the light signal strength making its practical implantation much convenient. The proposed method promises strong potential for field application.
Alterations of the gut bacterial microbiota in rhesus macaques with SIV infection and on short- or long-term antiretroviral therapy
Authors: Siddiqui Summer , Bao Duran , Doyle-Meyers Lara , Dufour Jason , Wu Yuntao , Liu Yao-Zhong , Ling Binhua 
Published: November 2020

AbstractGut dysbiosis and microbial translocation are associated with chronic systemic immune activation and inflammation in HIV-1 infection. However, the extent of restoration of gut microbiota in HIV-1 patients with short or long-term antiretroviral therapy (ART) is unclear. To understand the impact of ART on the gut microbiota, we used the rhesus macaque model of SIV infection to characterize and compare the gut microbial community upon SIV infection and during ART. We observed altered taxonomic compositions of gut microbiota communities upon SIV infection and at different time points of ART. SIV-infected animals showed decreased diversity of gut microbiome composition, while the ART group appeared to recover towards the diversity level of the healthy control. Animals undergoing ART for various lengths of time were observed to have differential gut bacterial abundance across different time points. In addition, increased blood lipopolysaccharide (LPS) levels during SIV infection were reduced to near normal upon ART, indicating that microbial translocation and immune activation can be improved during therapy. In conclusion, while short ART may be related to transient increase of certain pathogenic bacterial microbiome, ART may promote microbiome diversity compromised by SIV infection, improve the gut microbiota towards the healthy compositions and alleviate immune activation.
Oxidative stress markers in patient-derived non-cancerous cervical tissues and cells
Authors: Katerji Meghri , Filippova Maria , Wongworawat Yan Chen , Siddighi Sam , Bashkirova Sveta , Duerksen-Hughes Penelope J. 
Published: November 2020

AbstractHigh-risk human papillomaviruses (HPV) are the causative agents of cervical cancer. However, not all infected women develop cervical cancer. Cervical tumorigenesis is characterized by a multifactorial etiology, with oxidative stress (OS) likely playing a major role. In addition to exogenous sources, metabolic processes also contribute to OS. In principle, variability in levels of cervical OS has the potential to influence the likelihood of conversion to cervical cancer. To ask whether such variability indeed existed, we assessed the levels of ROS and the oxidative DNA damage biomarker 8-oxodG in normal non-cancerous cervical tissues and cells obtained from women with uterovaginal pelvic organ prolapse following vaginal hysterectomy. We demonstrated five and ten-fold variability between tissues isolated from the transformation zone (TZ) and ectocervix (EC) of different women, respectively. Despite the greater variability (likely due to differences in tissue composition), the overall pattern of ROS levels in EC tissues mirrored those obtained in their corresponding TZ tissues. Our results also show that the levels of ROS in TZ tissues were always higher than or equal to those found in the respective EC tissues, providing a possible explanation for TZ tissue being the primary target for HPV infection and cervical carcinogenesis. Interestingly, primary keratinocytes isolated and cultured from these cervical specimens also displayed high variability in ROS levels, with some strongly mirroring the levels of ROS observed in their corresponding tissues, while others were less closely associated. Finally, we demonstrated that the levels of DNA damage mirrored the levels of ROS in the cultured primary cells. Understanding the factors and mechanisms that dispose certain individuals to develop cervical cancer has the potential to enable the development of approaches that make the conversion of HPV infection to cancer development even more rare.
Observation of nonlinear dynamics in an optical levitation system
Authors: Ma Jinyong , Qin Jiayi , Campbell Geoff T. , Guccione Giovanni , Lecamwasam Ruvi , Buchler Ben C. , Lam Ping Koy 
Published: November 2020

AbstractOptical levitation of mechanical oscillators has been suggested as a promising way to decouple the environmental noise and increase the mechanical quality factor. Here, we investigate the dynamics of a free-standing mirror acting as the top reflector of a vertical optical cavity, designed as a testbed for a tripod cavity optical levitation setup. To reach the regime of levitation for a milligram-scale mirror, the optical intensity of the intracavity optical field approaches 3 MW cm−2. We identify three distinct optomechanical effects: excitation of acoustic vibrations, expansion due to photothermal absorption, and partial lift-off of the mirror due to radiation pressure force. These effects are intercoupled via the intracavity optical field and induce complex system dynamics inclusive of high-order sideband generation, optical bistability, parametric amplification, and the optical spring effect. We modify the response of the mirror with active feedback control to improve the overall stability of the system.
Quantum phase transitions and the role of impurity-substrate hybridization in Yu-Shiba-Rusinov states
Authors: Huang Haonan , Drost Robert , Senkpiel Jacob , Padurariu Ciprian , Kubala Björn , Yeyati Alfredo Levy , Cuevas Juan Carlos , Ankerhold Joachim , Kern Klaus , Ast Christian R. 
Published: November 2020

AbstractSpin-dependent scattering from magnetic impurities inside a superconductor gives rise to Yu-Shiba-Rusinov (YSR) states within the superconducting gap. They can be modeled by the largely equivalent Kondo or Anderson impurity models. The role of the magnetic and nonmagnetic properties of the impurity in relation to the coupling to the substrate is still under debate. Here, we use a scanning tunneling microscope to make a quantitative connection between the energy of a YSR state and the impurity-substrate hybridization. We corroborate the impurity substrate coupling as a key energy scale for surface derived YSR states using the Anderson impurity model. By combining experimental data from YSR state spectra and additional conductance measurements, we can determine on which side of the quantum phase transition the system resides. We thus provide a crucial step towards a more quantitative understanding of the crucial role of impurity substrate coupling utilizing the Anderson model.
Vibrio cholerae FeoB hydrolyzes ATP and GTP in vitro in the absence of stimulatory factors
Authors: Gómez-Garzón Camilo , Payne Shelley M 
Published: November 2020

Abstract
Feo is the most widely conserved system for ferrous iron transport in prokaryotes, and it is important for virulence in some pathogens. However, its mechanism of iron transport is not fully understood. In this study, we used full-length Vibrio cholerae FeoB (VcFeoB) as a model system to study whether its enzymatic activity is affected by regulatory factors commonly associated with FeoB proteins from other species or with G-proteins that have homology to FeoB. VcFeoB showed a higher rate of hydrolysis of both ATP and GTP than its N-terminal domain alone; likewise, ions such as K+ and Fe2+ did not modulate its nucleotide hydrolysis. We also showed that the three V. cholerae Feo proteins (FeoA, FeoB, and FeoC) work in a 1 : 1 : 1 molar ratio in vivo. Although both FeoA and FeoC are required for Feo-mediated iron transport, neither of these proteins affected the VcFeoB NTPase rate. These results are consistent with an active transport mechanism independent of stimulatory factors and highlight the importance of using full-length FeoB proteins as a reliable proxy to study Feo-mediated iron transport in vitro.
Human placental cell line HTR-8/SVneo accumulates cadmium by divalent metal transporters DMT1 and ZIP14
Authors: Widhalm Raimund , Ellinger Isabella , Granitzer Sebastian , Forsthuber Martin , Bajtela Robert , Gelles Katharina , Hartig Pia-Yael , Hengstschläger Markus , Zeisler Harald , Salzer Hans , Gundacker Claudia 
Published: November 2020

Abstract
Cadmium (Cd) is a global pollutant that accumulates in the placenta and can cause placental dysfunction. Although iron transporters have been suggested to participate in placental Cd uptake, it is still unknown which transporters are actually involved in this process. We specifically aimed to study the role of three iron transporters in the uptake of Cd into the placental cell line HTR-8/SVneo. For this purpose, Divalent Metal Transporter (DMT)1 and ZRT/IRT like protein (ZIP)8 and ZIP14 were downregulated and changes in cellular Cd levels analysed in relation to controls. As clearly shown by the reduction of the Cd content by ∼60% in DMT1- and ZIP14-downregulated cells, the two proteins are essential for Cd accumulation in HTR-8/SVneo cells. Using a validated antibody, we show DMT1 to be localised in situ in trophoblast and stromal cells. We further wanted to investigate how placental cells cope with Cd loading and which metallothionein (MT) isoforms they express. Cd-exposed cells accumulate Cd in a dose-dependent manner and upregulate MT2A accordingly (up to 15-fold induction upon 5 μM CdCl2 treatment for 72 h). 5 μM Cd exposure for 72 h decreased cell number to 60%, an effect that was aggravated by MT2A depletion (cell number reduced to 30%) indicating additive effects. In conclusion, our data suggest that DMT1 and ZIP14 are required for Cd uptake into human placental cells that upregulate MT2A to store and detoxify the metal. Cd storage in the placenta reduces Cd transport to the fetus, which, however, could impair placental functions and fetal development.
Euclid: Identification of asteroid streaks in simulated images using StreakDet software
Authors: Pöntinen M. , Granvik M. , Nucita A. A. , Conversi L. , Altieri B. , Auricchio N. , Bodendorf C. , Bonino D. , Brescia M. , Capobianco V. , Carretero J. , Carry B. , Castellano M. , Cledassou R. , Congedo G. , Corcione L. , Cropper M. , Dusini S. , Frailis M. , Franceschi E. , Fumana M. , Garilli B. , Grupp F. , Hormuth F. , Israel H. , Jahnke K. , Kermiche S. , Kitching T. , Kohley R. , Kubik B. , Kunz M. , Laureijs R. , Lilje P. B. , Lloro I. , Maiorano E. , Marggraf O. , Massey R. , Meneghetti M. , Meylan G. , Moscardini L. , Padilla C. , Paltani S. , Pasian F. , Pires S. , Polenta G. , Raison F. , Roncarelli M. , Rossetti E. , Saglia R. , Schneider P. , Secroun A. , Serrano S. , Sirri G. , Taylor A. N. , Tereno I. , Toledo-Moreo R. , Valenziano L. , Wang Y. , Wetzstein M. , Zoubian J. 
Published: November 2020

Context.The ESAEuclidspace telescope could observe up to 150 000 asteroids as a side product of its primary cosmological mission. Asteroids appear as trailed sources, that is streaks, in the images. Owing to the survey area of 15 000 square degrees and the number of sources, automated methods have to be used to find them.Euclidis equipped with a visible camera, VIS (VISual imager), and a near-infrared camera, NISP (Near-Infrared Spectrometer and Photometer), with three filters.Aims.We aim to develop a pipeline to detect fast-moving objects inEuclidimages, with both high completeness and high purity.Methods.We tested theStreakDetsoftware to find asteroids from simulatedEuclidimages. We optimized the parameters ofStreakDetto maximize completeness, and developed a post-processing algorithm to improve the purity of the sample of detected sources by removing false-positive detections.Results.StreakDetfinds 96.9% of the synthetic asteroid streaks with apparent magnitudes brighter than 23rd magnitude and streak lengths longer than 15 pixels (10 arcsec h−1), but this comes at the cost of finding a high number of false positives. The number of false positives can be radically reduced with multi-streak analysis, which utilizes all four dithers obtained byEuclid.Conclusions.StreakDetis a good tool for identifying asteroids inEuclidimages, but there is still room for improvement, in particular, for finding short (less than 13 pixels, corresponding to 8 arcsec h−1) and/or faint streaks (fainter than the apparent magnitude of 23).
Impedance planimetry values for predicting clinical response following peroral endoscopic myotomy
Authors: Moran Robert A. , Brewer Gutierrez Olaya I. , Rahden Burkhard , Chang Kenneth , Ujiki Michael , Yoo In Kyung , Gulati Shraddha , Romanelli John , Al-Nasser Mohammed , Shimizu Toshitaka , Hedberg Mason H. , Cho Joo Young , Hayee Bu , Desilets David , Filser Jörg , Fortinsky Kyle , Haji Amyn , Fayad Lea , Sanaei Omid , Dbouk Mohamad , Kumbhari Vivek , Wolf Bethany J. , Elmunzer B. Joseph , Khashab Mouen A. 
Published: November 2020

Abstract
Background There is growing interest in developing impedance planimetry as a tool to enhance the clinical outcomes for endoscopic and surgical management of achalasia. The primary aim of this study was to determine whether impedance planimetry measurements can predict clinical response and reflux following peroral endoscopic myotomy (POEM).
Methods A multicenter cohort study of patients with achalasia undergoing POEM was established from prospective databases and retrospective chart reviews. Patients who underwent impedance planimetry before and after POEM were included. Clinical response was defined as an Eckardt score of ≤ 3. Tenfold cross-validated area under curve (AUC) values were established for the different impedance planimetry measurements associated with clinical response and reflux development.
Results Of the 290 patients included, 91.7 % (266/290) had a clinical response and 39.4 % (108/274) developed reflux following POEM. The most predictive impedance planimetry measurements for a clinical response were: percent change in cross-sectional area (%ΔCSA) and percent change in distensibility index (%ΔDI), with AUCs of 0.75 and 0.73, respectively. Optimal cutoff values for %ΔCSA and %ΔDI to determine a clinical response were a change of 360 % and 272 %, respectively. Impedance planimetry values were much poorer at predicting post-POEM reflux, with AUCs ranging from 0.40 to 0.62.
Conclusion Percent change in CSA and distensibility index were the most predictive measures of a clinical response, with a moderate predictive ability. Impedance planimetry values for predicting reflux following POEM showed weak predictive capacity.
Study of Additive Effect of Yoga and Physical Therapies to Standard Pharmacologic Treatment in Migraine
Authors: Mehta Jigar N. , Parikh Shweta , Desai Soaham D. , Solanki Rachna C. , G. Pathak Ajay 
Published: November 2020

Abstract
Objective We aimed to evaluate and compare the effectiveness of physical and yoga therapies as an adjuvant therapy along with standard pharmacologic treatment in patients with migraine.
Materials and Methods A total of 61 consenting patients diagnosed to have migraine were randomized into three groups to receive either standard treatment alone, physical therapy along with standard treatment, or yoga therapy along with standard treatment. The respective adjuvant intervention was taught to the respective group of patients and they were advised to perform it daily for 3 months with weekly telephonic reminders and review of their activity logs. Outcome measures assessed were headache frequency, Short-Form McGill Pain Questionnaire (SF-MPQ), and Headache Impact Test-6 (HIT-6) at recruitment and once every month for 3 months.
Statistical Analysis Statistical analysis of the study was done by using Stata 14.1 software. All the descriptive statistics, paired t-test was used to compare the difference between pre and postintervention values of headache frequency, SF-MPQ, and HIT-6 score within all the three groups. Analysis of variance test and post hoc test were used to compare the differences between all groups for outcome measures (p < 0.05).
Results Headache frequency and the visual analog scale before intervention compared during each month intervals for 3 months in all the three groups were significantly decreased in all the three groups (p < 0.005). Yoga or physical therapy as an adjuvant to standard treatment leads to a higher reduction in headache frequency and severity. Sensory and affective pain ratings of SF-MPQ and HIT-6 also showed a significant improvement at 1 to 3 months of treatment compared with baseline in all the three groups.
Conclusion Either physical or yoga therapy as an adjuvant to standard pharmacologic treatment may further improve the quality of life and reduce headache frequency in patients with migraine.
Sacral Giant Cell Tumor-Induced Cauda Equina Syndrome: Case Report with Successful Management
Authors: Singh Saraj K. , Kumar Avinash , Nigam Jitendra 
Published: November 2020

Abstract
Sacral giant cell tumor (GCT) is a rare entity. It often presents late after massive enlargement of tumor. Here we are reporting a case of sacral GCT treated successfully at our institute. A 30-year-old male patient presented with paraplegia, significant sensory disturbance below L2 level, along with severe vesicorectal dysfunction. On imaging, giant mass was seen filling the sacrum with homogenous enhancement and flow voids from L5 level to S4 level. The patient underwent surgical exploration with L4–5 decompressive laminectomy, near-total resection of tumor, and lumboiliac fixation. The patient recovered symptomatically in postoperative period. Sacral GCT is a rare but treatable lesion. Its presentation as sudden cauda equina syndrome is rare, but final management should be aggressive with en bloc resection and fixation.
Leveraging the UMLS As a Data Standard for Rare Disease Data Normalization and Harmonization
Authors: Zhu Qian , Nguyen Dac-Trung , Sid Eric , Pariser Anne 
Published: November 2020

Abstract
Objective In this study, we aimed to evaluate the capability of the Unified Medical Language System (UMLS) as one data standard to support data normalization and harmonization of datasets that have been developed for rare diseases. Through analysis of data mappings between multiple rare disease resources and the UMLS, we propose suggested extensions of the UMLS that will enable its adoption as a global standard in rare disease.
Methods We analyzed data mappings between the UMLS and existing datasets on over 7,000 rare diseases that were retrieved from four publicly accessible resources: Genetic And Rare Diseases Information Center (GARD), Orphanet, Online Mendelian Inheritance in Men (OMIM), and the Monarch Disease Ontology (MONDO). Two types of disease mappings were assessed, (1) curated mappings extracted from those four resources; and (2) established mappings generated by querying the rare disease-based integrative knowledge graph developed in the previous study.
Results We found that 100% of OMIM concepts, and over 50% of concepts from GARD, MONDO, and Orphanet were normalized by the UMLS and accurately categorized into the appropriate UMLS semantic groups. We analyzed 58,636 UMLS mappings, which resulted in 3,876 UMLS concepts across these resources. Manual evaluation of a random set of 500 UMLS mappings demonstrated a high level of accuracy (99%) of developing those mappings, which consisted of 414 mappings of synonyms (82.8%), 76 are subtypes (15.2%), and five are siblings (1%).
Conclusion The mapping results illustrated in this study that the UMLS was able to accurately represent rare disease concepts, and their associated information, such as genes and phenotypes, and can effectively be used to support data harmonization across existing resources developed on collecting rare disease data. We recommend the adoption of the UMLS as a data standard for rare disease to enable the existing rare disease datasets to support future applications in a clinical and community settings.