bluuebunny/crossref_metadata_2025_split huggingface dataset:
Difference of binding modes among three ligands to a receptor mSin3B corresponding to their inhibitory activities
Authors: Hayami Tomonori , Kamiya Narutoshi , Kasahara Kota , Kawabata Takeshi , Kurita Jun-ichi , Fukunishi Yoshifumi , Nishimura Yoshifumi , Nakamura Haruki , Higo Junichi 
Published: March 2021

AbstractA preceding experiment suggested that a compound, which inhibits binding of the REST/NRSF segment to the cleft of a receptor protein mSin3B, can be a potential drug candidate to ameliorate many neuropathies. We have recently developed an enhanced conformational sampling method, genetic-algorithm-guided multi-dimensional virtual-system-coupled canonical molecular dynamics, and in the present study, applied it to three systems consisting of mSin3B and one of three compounds, sertraline, YN3, and acitretin. Other preceding experiments showed that only sertraline inhibits the binding of REST/NRSF to mSin3B. The current simulation study produced the spatial distribution of the compounds around mSin3B, and showed that sertraline and YN3 bound to the cleft of mSin3B with a high propensity, although acitretin did not. Further analyses of the simulation data indicated that only the sertraline–mSin3B complex produced a hydrophobic core similar to that observed in the molecular interface of the REST/NRSF-mSin3B complex: An aromatic ring of sertraline sunk deeply in the mSin3B’s cleft forming a hydrophobic core contacting to hydrophobic amino-acid residues located at the bottom of the cleft. The present study proposes a step to design a compound that inhibits competitively the binding of a ligand to its receptor.
Enhancing the compost maturation of swine manure and rice straw by applying bioaugmentation
Authors: Wang Wei-Kuang , Liang Chih-Ming 
Published: March 2021

AbstractMicroorganisms capable of decomposing cellulose, xylan, starch and protein were individually isolated from swine manure compost and soil in this study. The correlations with pH, carbon source concentration, C/N ratio and enzyme activity among these isolated microorganisms were also investigated. Furthermore, the effect of additional inoculation in the compost was studied by measuring variations in the C/N ratio, enzyme activity and compost maturation rate. The inoculated microorganisms used in this study included four bacterial isolates and one commercial microorganism Phanerochaete chrysosporium. The results indicated that the isolated Kitasatospora phosalacinea strain C1, which is a cellulose-degraded microorganism, presented the highest enzyme activity at 31 ℃ and pH 5.5, while the C/N ratio was 0.8%. The isolated xylan-degraded microorganism Paenibacillus glycanilyticus X1 had the highest enzyme activity at 45 ℃ and pH 7.5, while the C/N ratio was 0.5%. The starch-degraded microorganism was identified as Bacillus licheniformis S3, and its highest enzyme activities were estimated to be 31 ℃ and pH 7.5 while the C/N ratio was 0.8%. The highest enzyme activity of the protein-degraded microorganism Brevinacillus agri E4 was obtained at 45 ℃ and pH 8.5, while the C/N ratio was 1.0%. The rate of temperature increase in the compost inoculated with P. chrysosporium was only higher than that of the compost without inoculation, and its compost maturation level was also lower than that of other composts with additional inoculation. The optimal initial C/N ratio of the compost was 27.5 and the final C/N ratio was 18.9. The composting results also indicated that the secondary inoculation would benefit compost maturation, and the lowest final C/N ratio of 17.0 was obtained.
Antibodies against EGF-like domains in Ixodes scapularis BM86 orthologs impact tick feeding and survival of Borrelia burgdorferi
Authors: Koči Juraj , Bista Sandhya , Chirania Payal , Yang Xiuli , Kitsou Chrysoula , Rana Vipin Singh , Yas Ozlem Buyuktanir , Sonenshine Daniel E. , Pal Utpal 
Published: March 2021

AbstractIxodes scapularisticks transmit multiple pathogens, includingBorrelia burgdorferisensu stricto, and encode many proteins harboring epidermal growth factor (EGF)-like domains. We show thatI. scapularisproduces multiple orthologs for Bm86, a widely studied tick gut protein considered as a target of an anti-tick vaccine, herein termed as Is86. We show that Is86 antigens feature at least three identifiable regions harboring EGF-like domains (termed as EGF-1, EGF-2, and EGF-3) and are differentially upregulated duringB. burgdorferiinfection. Although the RNA interference-mediated knockdown ofIs86genes did not show any influences on tick engorgement orB. burgdorferisensu stricto persistence, the immunization of murine hosts with specific recombinant EGF antigens marginally reduced spirochete loads in the skin, in addition to affecting tick blood meal engorgement and molting. However, given the borderline impact of EGF immunization on tick engorgement and pathogen survival in the vector, it is unlikely that these antigens, at least in their current forms, could be developed as potential vaccines. Further investigations of the biological significance of Is86 (and other tick antigens) would enrich our knowledge of the intricate biology of ticks, including their interactions with resident pathogens, and contribute to the development of anti-tick measures to combat tick-borne illnesses.
Cryogenic cave carbonate and implications for thawing permafrost at Winter Wonderland Cave, Utah, USA
Authors: Munroe Jeffrey , Kimble Kristin , Spötl Christoph , Marks Gabriela Serrato , McGee David , Herron David 
Published: March 2021

AbstractWinter Wonderland Cave contains perennial ice associated with two types of cryogenic cave carbonate (CCC) formed during the freezing of water. CCCfine is characterized by relatively high δ13C values, whereas CCCcoarse exhibits notably low δ18O values indicating precipitation under (semi)closed-system conditions in a pool of residual water beneath an ice lid. Previous work has concluded that CCCcoarse forms during permafrost thaw, making the presence of this precipitate a valuable indicator of past cryospheric change. Available geochronologic evidence indicates that CCC formation in this cave is a Late Holocene or contemporary process, and field observations suggest that the cave thermal regime recently changed in a manner that permits the ingress of liquid water. This is the first documented occurence of CCCcoarse in the Western Hemisphere and one of only a few locations where these minerals have been found in association with ice. Winter Wonderland Cave is a natural laboratory for studying CCC genesis.
Practical lineshape of a laser operating near an exceptional point
Authors: Kim Jinuk , Kim Juman , Seo Jisung , Park Kyu-Won , Moon Songky , An Kyungwon 
Published: March 2021

AbstractWe present a practical laser linewidth broadening phenomenon in the viewpoint of high sensitivity of an exceptional point (EP). A stochastic simulation model is implemented to describe the fluctuations in the cavity resonance frequencies. The linewidth originated from external noises are maximized at the EP. The linewidth enhancement factor behaves similarly to the Petermann factor although the Petermann effect is not considered. In the long coherence time limit, the power spectral density of the laser exhibits a splitting in the vicinity of the EP although the cavity eigenfrequencies coalesce at the EP.
Self-rated health in individuals with and without disease is associated with multiple biomarkers representing multiple biological domains
Authors: Kananen L. , Enroth L. , Raitanen J. , Jylhävä J. , Bürkle A. , Moreno-Villanueva M. , Bernhardt J. , Toussaint O. , Grubeck-Loebenstein B. , Malavolta M. , Basso A. , Piacenza F. , Collino S. , Gonos E. S. , Sikora E. , Gradinaru D. , Jansen E. H. J. M. , Dollé M. E. T. , Salmon M. , Stuetz W. , Weber D. , Grune T. , Breusing N. , Simm A. , Capri M. , Franceschi C. , Slagboom P. E. , Talbot D. C. S. , Libert C. , Koskinen S. , Bruunsgaard H. , Hansen ÅM. , Lund R. , Hurme M. , Jylhä M. 
Published: March 2021

AbstractSelf-rated health (SRH) is one of the most frequently used indicators in health and social research. Its robust association with mortality in very different populations implies that it is a comprehensive measure of health status and may even reflect the condition of the human organism beyond clinical diagnoses. Yet the biological basis of SRH is poorly understood. We used data from three independent European population samples (N approx. 15,000) to investigate the associations of SRH with 150 biomolecules in blood or urine (biomarkers). Altogether 57 biomarkers representing different organ systems were associated with SRH. In almost half of the cases the association was independent of disease and physical functioning. Biomarkers weakened but did not remove the association between SRH and mortality. We propose three potential pathways through which biomarkers may be incorporated into an individual’s subjective health assessment, including (1) their role in clinical diseases; (2) their association with health-related lifestyles; and (3) their potential to stimulate physical sensations through interoceptive mechanisms. Our findings indicate that SRH has a solid biological basis and it is a valid but non-specific indicator of the biological condition of the human organism.
Distant metastasis time to event analysis with CNNs in independent head and neck cancer cohorts
Authors: Lombardo Elia , Kurz Christopher , Marschner Sebastian , Avanzo Michele , Gagliardi Vito , Fanetti Giuseppe , Franchin Giovanni , Stancanello Joseph , Corradini Stefanie , Niyazi Maximilian , Belka Claus , Parodi Katia , Riboldi Marco , Landry Guillaume 
Published: March 2021

AbstractDeep learning models based on medical images play an increasingly important role for cancer outcome prediction. The standard approach involves usage of convolutional neural networks (CNNs) to automatically extract relevant features from the patient’s image and perform a binary classification of the occurrence of a given clinical endpoint. In this work, a 2D-CNN and a 3D-CNN for the binary classification of distant metastasis (DM) occurrence in head and neck cancer patients were extended to perform time-to-event analysis. The newly built CNNs incorporate censoring information and output DM-free probability curves as a function of time for every patient. In total, 1037 patients were used to build and assess the performance of the time-to-event model. Training and validation was based on 294 patients also used in a previous benchmark classification study while for testing 743 patients from three independent cohorts were used. The best network could reproduce the good results from 3-fold cross validation [Harrell’s concordance indices (HCIs) of 0.78, 0.74 and 0.80] in two out of three testing cohorts (HCIs of 0.88, 0.67 and 0.77). Additionally, the capability of the models for patient stratification into high and low-risk groups was investigated, the CNNs being able to significantly stratify all three testing cohorts. Results suggest that image-based deep learning models show good reliability for DM time-to-event analysis and could be used for treatment personalisation.
Social signaling via bioluminescent blinks determines nearest neighbor distance in schools of flashlight fish Anomalops katoptron
Authors: Jägers Peter , Wagner Louisa , Schütz Robin , Mucke Maximilian , Senen Budiono , Limmon Gino V. , Herlitze Stefan , Hellinger Jens 
Published: March 2021

AbstractThe schooling flashlight fish Anomalops katoptron can be found at dark nights at the water surface in the Indo-Pacific. Schools are characterized by bioluminescent blink patterns of sub-ocular light organs densely-packed with bioluminescent, symbiotic bacteria. Here we analyzed how blink patterns of A. katoptron are used in social interactions. We demonstrate that isolated specimen of A. katoptron showed a high motivation to align with fixed or moving artificial light organs in an experimental tank. This intraspecific recognition of A. katoptron is mediated by blinking light and not the body shape. In addition, A. katoptron adjusts its blinking frequencies according to the light intensities. LED pulse frequencies determine the swimming speed and the blink frequency response of A. katoptron, which is modified by light organ occlusion and not exposure. In the natural environment A. katoptron is changing its blink frequencies and nearest neighbor distance in a context specific manner. Blink frequencies are also modified by changes in the occlusion time and are increased from day to night and during avoidance behavior, while group cohesion is higher with increasing blink frequencies. Our results suggest that specific blink patterns in schooling flashlight fish A. katoptron define nearest neighbor distance and determine intraspecific communication.
Malaria transmission in landscapes with varying deforestation levels and timelines in the Amazon: a longitudinal spatiotemporal study
Authors: Laporta Gabriel Z. , Ilacqua Roberto C. , Bergo Eduardo S. , Chaves Leonardo S. M. , Rodovalho Sheila R. , Moresco Gilberto G. , Figueira Elder A. G. , Massad Eduardo , de Oliveira Tatiane M. P. , Bickersmith Sara A. , Conn Jan E. , Sallum Maria Anice M. 
Published: March 2021

AbstractThe relationship between deforestation and malaria is a spatiotemporal process of variation in Plasmodium incidence in human-dominated Amazonian rural environments. The present study aimed to assess the underlying mechanisms of malarial exposure risk at a fine scale in 5-km2 sites across the Brazilian Amazon, using field-collected data with a longitudinal spatiotemporally structured approach. Anopheline mosquitoes were sampled from 80 sites to investigate the Plasmodium infection rate in mosquito communities and to estimate the malaria exposure risk in rural landscapes. The remaining amount of forest cover (accumulated deforestation) and the deforestation timeline were estimated in each site to represent the main parameters of both the frontier malaria hypothesis and an alternate scenario, the deforestation-malaria hypothesis, proposed herein. The maximum frequency of pathogenic sites occurred at the intermediate forest cover level (50% of accumulated deforestation) at two temporal deforestation peaks, e.g., 10 and 35 years after the beginning of the organization of a settlement. The incidence density of infected anophelines in sites where the original forest cover decreased by more than 50% in the first 25 years of settlement development was at least twice as high as the incidence density calculated for the other sites studied (adjusted incidence density ratio = 2.25; 95% CI, 1.38–3.68; p = 0.001). The results of this study support the frontier malaria as a unifying hypothesis for explaining malaria emergence and for designing specific control interventions in the Brazilian Amazon.
Syringeal vocal folds do not have a voice in zebra finch vocal development
Authors: Maxwell Alyssa , Adam Iris , Larsen Pernille S. , Sørensen Peter G. , Elemans Coen P. H. 
Published: March 2021

AbstractVocal behavior can be dramatically changed by both neural circuit development and postnatal maturation of the body. During song learning in songbirds, both the song system and syringeal muscles are functionally changing, but it is unknown if maturation of sound generators within the syrinx contributes to vocal development. Here we densely sample the respiratory pressure control space of the zebra finch syrinx in vitro. We show that the syrinx produces sound very efficiently and that key acoustic parameters, minimal fundamental frequency, entropy and source level, do not change over development in both sexes. Thus, our data suggest that the observed acoustic changes in vocal development must be attributed to changes in the motor control pathway, from song system circuitry to muscle force, and not by material property changes in the avian analog of the vocal folds. We propose that in songbirds, muscle use and training driven by the sexually dimorphic song system are the crucial drivers that lead to sexual dimorphism of the syringeal skeleton and musculature. The size and properties of the instrument are thus not changing, while its player is.
Regional environmental controllers influence continental scale soil carbon stocks and future carbon dynamics
Authors: Gonçalves Daniel Ruiz Potma , Mishra Umakant , Wills Skye , Gautam Sagar 
Published: March 2021

AbstractUnderstanding the influence of environmental factors on soil organic carbon (SOC) is critical for quantifying and reducing the uncertainty in carbon climate feedback projections under changing environmental conditions. We explored the effect of climatic variables, land cover types, topographic attributes, soil types and bedrock geology on SOC stocks of top 1 m depth across conterminous United States (US) ecoregions. Using 4559 soil profile observations and high-resolution data of environmental factors, we identified dominant environmental controllers of SOC stocks in 21 US ecoregions using geographically weighted regression. We used projected climatic data of SSP126 and SSP585 scenarios from GFDL-ESM 4 Earth System Model of Coupled Model Intercomparison Project phase 6 to predict SOC stock changes across continental US between 2030 and 2100. Both baseline and predicted changes in SOC stocks were compared with SOC stocks represented in GFDL-ESM4 projections. Among 56 environmental predictors, we found 12 as dominant controllers across all ecoregions. The adjusted geospatial model with the 12 environmental controllers showed an R2 of 0.48 in testing dataset. Higher precipitation and lower temperatures were associated with higher levels of SOC stocks in majority of ecoregions. Changes in land cover types (vegetation properties) was important in drier ecosystem as North American deserts, whereas soil types and topography were more important in American prairies. Wetlands of the Everglades was highly sensitive to projected temperature changes. The SOC stocks did not change under SSP126 until 2100, however SOC stocks decreased up to 21% under SSP585. Our results, based on environmental controllers of SOC stocks, help to predict impacts of changing environmental conditions on SOC stocks more reliably and may reduce uncertainties found in both, geospatial and Earth System Models. In addition, the description of different environmental controllers for US ecoregions can help to describe the scope and importance of global and local models.
Association between smoking status and outcomes in myocardial infarction patients undergoing percutaneous coronary intervention
Authors: Sia Ching-Hui , Ko Junsuk , Zheng Huili , Ho Andrew Fu-Wah , Foo David , Foo Ling-Li , Lim Patrick Zhan-Yun , Liew Boon Wah , Chai Ping , Yeo Tiong-Cheng , Tan Huay-Cheem , Chua Terrance , Chan Mark Yan-Yee , Tan Jack Wei Chieh , Bulluck Heerajnarain , Hausenloy Derek J. 
Published: March 2021

AbstractSmoking is one of the leading risk factors for cardiovascular diseases, including ischemic heart disease and hypertension. However, in acute myocardial infarction (AMI) patients, smoking has been associated with better clinical outcomes, a phenomenon termed the “smoker’s paradox.” Given the known detrimental effects of smoking on the cardiovascular system, it has been proposed that the beneficial effect of smoking on outcomes is due to age differences between smokers and non-smokers and is therefore a smoker’s pseudoparadox. The aim of this study was to evaluate the association between smoking status and clinical outcomes in ST-segment elevation (STEMI) and non-STEMI (NSTEMI) patients treated by percutaneous coronary intervention (PCI), using a national multi-ethnic Asian registry. In unadjusted analyses, current smokers had better clinical outcomes following STEMI and NSTEMI. However, after adjusting for age, the protective effect of smoking was lost, confirming a smoker’s pseudoparadox. Interestingly, although current smokers had increased risk for recurrent MI within 1 year after PCI in both STEMI and NSTEMI patients, there was no increase in mortality. In summary, we confirm the existence of a smoker’s pseudoparadox in a multi-ethnic Asian cohort of STEMI and NSTEMI patients and report increased risk of recurrent MI, but not mortality, in smokers.
Complete response to PD-1 blockade following EBV-specific T-cell therapy in metastatic nasopharyngeal carcinoma
Authors: Smith Corey , McGrath Margaret , Neller Michelle A. , Matthews Katherine K. , Crooks Pauline , Le Texier Laetitia , Panizza Benedict , Porceddu Sandro , Khanna Rajiv 
Published: March 2021

AbstractNasopharyngeal carcinoma (NPC) is an Epstein–Barr virus (EBV)-associated heterogeneous disease and is characterized by peritumoral immune infiltrate. Adoptive T-cell therapy (ACT) has emerged as a potential therapeutic strategy for NPC. However, the tumor microenvironment remains a major roadblock for the successful implementation of ACT in clinical settings. Expression of checkpoint molecules by malignant cells can inhibit the effector function of adoptively transferred EBV-specific T cells. Here we present a novel case report of a patient with metastatic NPC who was successfully treated with a combination of EBV-specific ACT and programmed cell death-1 blockade therapy. Following combination immunotherapy, the patient showed complete resolution of metastatic disease with no evidence of disease relapse for 22 months. Follow-up immunological analysis revealed dramatic restructuring of the global T-cell repertoire that was coincident with the clinical response. This case report provides an important platform for translating these findings to a larger cohort of NPC patients.
Crowdsourcing digital health measures to predict Parkinson’s disease severity: the Parkinson’s Disease Digital Biomarker DREAM Challenge
Authors: Sieberts Solveig K. , Schaff Jennifer , Duda Marlena , Pataki Bálint Ármin , Sun Ming , Snyder Phil , Daneault Jean-Francois , Parisi Federico , Costante Gianluca , Rubin Udi , Banda Peter , Chae Yooree , Chaibub Neto Elias , Dorsey E. Ray , Aydın Zafer , Chen Aipeng , Elo Laura L. , Espino Carlos , Glaab Enrico , Goan Ethan , Golabchi Fatemeh Noushin , Görmez Yasin , Jaakkola Maria K. , Jonnagaddala Jitendra , Klén Riku , Li Dongmei , McDaniel Christian , Perrin Dimitri , Perumal Thanneer M. , Rad Nastaran Mohammadian , Rainaldi Erin , Sapienza Stefano , Schwab Patrick , Shokhirev Nikolai , Venäläinen Mikko S. , Vergara-Diaz Gloria , Zhang Yuqian ,   the Parkinson’s Disease Digital Biomarker Challenge Consortium, Abrami Avner , Adhikary Aditya , Agurto Carla , Bhalla Sherry , Bilgin Halil , Caggiano Vittorio , Cheng Jun , Deng Eden , Gan Qiwei , Girsa Rajan , Han Zhi , Heisig Stephen , Huang Kun , Jahandideh Samad , Kopp Wolfgang , Kurz Christoph F. , Lichtner Gregor , Norel Raquel , Raghava G. P. S. , Sethi Tavpritesh , Shawen Nicholas , Tripathi Vaibhav , Tsai Matthew , Wang Tongxin , Wu Yi , Zhang Jie , Zhang Xinyu , Wang Yuanjia , Guan Yuanfang , Brunner Daniela , Bonato Paolo , Mangravite Lara M. , Omberg Larsson 
Published: March 2021

AbstractConsumer wearables and sensors are a rich source of data about patients’ daily disease and symptom burden, particularly in the case of movement disorders like Parkinson’s disease (PD). However, interpreting these complex data into so-called digital biomarkers requires complicated analytical approaches, and validating these biomarkers requires sufficient data and unbiased evaluation methods. Here we describe the use of crowdsourcing to specifically evaluate and benchmark features derived from accelerometer and gyroscope data in two different datasets to predict the presence of PD and severity of three PD symptoms: tremor, dyskinesia, and bradykinesia. Forty teams from around the world submitted features, and achieved drastically improved predictive performance for PD status (best AUROC = 0.87), as well as tremor- (best AUPR = 0.75), dyskinesia- (best AUPR = 0.48) and bradykinesia-severity (best AUPR = 0.95).