bluuebunny/crossref_metadata_2025_split huggingface dataset:
Local Josephson vortex generation and manipulation with a Magnetic Force Microscope
Authors: Dremov Viacheslav V. , Grebenchuk Sergey Yu. , Shishkin Andrey G. , Baranov Denis S. , Hovhannisyan Razmik A. , Skryabina Olga V. , Lebedev Nickolay , Golovchanskiy Igor A. , Chichkov Vladimir I. , Brun Christophe , Cren Tristan , Krasnov Vladimir M. , Golubov Alexander A. , Roditchev Dimitri , Stolyarov Vasily S. 
Published: September 2019

AbstractJosephson vortices play an essential role in superconducting quantum electronics devices. Often seen as purely conceptual topological objects, 2π-phase singularities, their observation and manipulation are challenging. Here we show that in Superconductor—Normal metal—Superconductor lateral junctions Josephson vortices have a peculiar magnetic fingerprint that we reveal in Magnetic Force Microscopy (MFM) experiments. Based on this discovery, we demonstrate the possibility of the Josephson vortex generation and manipulation by the magnetic tip of a MFM, thus paving a way for the remote inspection and control of individual nano-components of superconducting quantum circuits.
Tuning high-Q nonlinear dynamics in a disordered quantum magnet
Authors: Silevitch D. M. , Tang C. , Aeppli G. , Rosenbaum T. F. 
Published: September 2019

AbstractQuantum states cohere and interfere. Atoms arranged imperfectly in a solid rarely display these properties. Here we demonstrate an exception in a disordered quantum magnet that divides itself into nearly isolated subsystems. We probe these coherent spin clusters by driving the system nonlinearly and measuring the resulting hole in the linear spectral response. The Fano shape of the hole encodes the incoherent lifetime as well as coherent mixing of the localized excitations. For the Ising magnet LiHo0.045Y0.955F4, the quality factor Q for spectral holes can be as high as 100,000. We tune the dynamics by sweeping the Fano mixing parameter q through zero via the ac pump amplitude as well as a dc transverse field. The zero crossing of q is associated with a dissipationless response at the drive frequency. Identifying localized two-level systems in a dense and disordered magnet advances the search for qubit platforms emerging from strongly interacting, many-body systems.
PCP and Wnt pathway components act in parallel during zebrafish mechanosensory hair cell orientation
Authors: Navajas Acedo Joaquin , Voas Matthew G. , Alexander Richard , Woolley Thomas , Unruh Jay R. , Li Hua , Moens Cecilia , Piotrowski Tatjana 
Published: September 2019

AbstractPlanar cell polarity (PCP) plays crucial roles in developmental processes such as gastrulation, neural tube closure and hearing. Wnt pathway mutants are often classified as PCP mutants due to similarities between their phenotypes. Here, we show that in the zebrafish lateral line, disruptions of the PCP and Wnt pathways have differential effects on hair cell orientations. While mutations in the PCP genes vangl2 and scrib cause random orientations of hair cells, mutations in wnt11f1, gpc4 and fzd7a/b induce hair cells to adopt a concentric pattern. This concentric pattern is not caused by defects in PCP but is due to misaligned support cells. The molecular basis of the support cell defect is unknown but we demonstrate that the PCP and Wnt pathways work in parallel to establish proper hair cell orientation. Consequently, hair cell orientation defects are not solely explained by defects in PCP signaling, and some hair cell phenotypes warrant re-evaluation.
A high-performance oxygen evolution catalyst in neutral-pH for sunlight-driven CO2 reduction
Authors: Zhou Li Qin , Ling Chen , Zhou Hui , Wang Xiang , Liao Joseph , Reddy Gunugunuri K. , Deng Liangzi , Peck Torin C. , Zhang Ruigang , Whittingham M. Stanley , Wang Chongmin , Chu Ching-Wu , Yao Yan , Jia Hongfei 
Published: September 2019

AbstractThe efficiency of sunlight-driven reduction of carbon dioxide (CO2), a process mimicking the photosynthesis in nature that integrates the light harvester and electrolysis cell to convert CO2 into valuable chemicals, is greatly limited by the sluggish kinetics of oxygen evolution in pH-neutral conditions. Current non-noble metal oxide catalysts developed to drive oxygen evolution in alkaline solution have poor performance in neutral solutions. Here we report a highly active and stable oxygen evolution catalyst in neutral pH, Brownmillerite Sr2GaCoO5, with the specific activity about one order of magnitude higher than that of widely used iridium oxide catalyst. Using Sr2GaCoO5 to catalyze oxygen evolution, the integrated CO2 reduction achieves the average solar-to-CO efficiency of 13.9% with no appreciable performance degradation in 19 h of operation. Our results not only set a record for the efficiency in sunlight-driven CO2 reduction, but open new opportunities towards the realization of practical CO2 reduction systems.
Structural basis for activation of a diguanylate cyclase required for bacterial predation in Bdellovibrio
Authors: Meek Richard W. , Cadby Ian T. , Moynihan Patrick J. , Lovering Andrew L. 
Published: September 2019

AbstractThe bacterial second messenger cyclic-di-GMP is a widespread, prominent effector of lifestyle change. An example of this occurs in the predatory bacterium Bdellovibrio bacteriovorus, which cycles between free-living and intraperiplasmic phases after entering (and killing) another bacterium. The initiation of prey invasion is governed by DgcB (GGDEF enzyme) that produces cyclic-di-GMP in response to an unknown stimulus. Here, we report the structure of DgcB, and demonstrate that the GGDEF and sensory forkhead-associated (FHA) domains form an asymmetric dimer. Our structures indicate that the FHA domain is a consensus phosphopeptide sensor, and that the ligand for activation is surprisingly derived from the N-terminal region of DgcB itself. We confirm this hypothesis by determining the structure of a FHA:phosphopeptide complex, from which we design a constitutively-active mutant (confirmed via enzyme assays). Our results provide an understanding of the stimulus driving DgcB-mediated prey invasion and detail a unique mechanism of GGDEF enzyme regulation.
Neonicotinoid seed treatments of soybean provide negligible benefits to US farmers
Authors: Mourtzinis Spyridon , Krupke Christian H. , Esker Paul D. , Varenhorst Adam , Arneson Nicholas J. , Bradley Carl A. , Byrne Adam M. , Chilvers Martin I. , Giesler Loren J. , Herbert Ames , Kandel Yuba R. , Kazula Maciej J. , Hunt Catherine , Lindsey Laura E. , Malone Sean , Mueller Daren S. , Naeve Seth , Nafziger Emerson , Reisig Dominic D. , Ross William J. , Rossman Devon R. , Taylor Sally , Conley Shawn P. 
Published: September 2019

AbstractNeonicotinoids are the most widely used insecticides worldwide and are typically deployed as seed treatments (hereafter NST) in many grain and oilseed crops, including soybeans. However, there is a surprising dearth of information regarding NST effectiveness in increasing soybean seed yield, and most published data suggest weak, or inconsistent yield benefit. The US is the key soybean-producing nation worldwide and this work includes soybean yield data from 194 randomized and replicated field studies conducted specifically to evaluate the effect of NSTs on soybean seed yield at sites within 14 states from 2006 through 2017. Here we show that across the principal soybean-growing region of the country, there are negligible and management-specific yield benefits attributed to NSTs. Across the entire region, the maximum observed yield benefits due to fungicide (FST = fungicide seed treatment) + neonicotinoid use (FST + NST) reached 0.13 Mg/ha. Across the entire region, combinations of management practices affected the effectiveness of FST + NST to increase yield but benefits were minimal ranging between 0.01 to 0.22 Mg/ha. Despite widespread use, this practice appears to have little benefit for most of soybean producers; across the entire region, a partial economic analysis further showed inconsistent evidence of a break-even cost of FST or FST + NST. These results demonstrate that the current widespread prophylactic use of NST in the key soybean-producing areas of the US should be re-evaluated by producers and regulators alike.
Critical Transitions in Intensive Care Units: A Sepsis Case Study
Authors: Ghalati Pejman F. , Samal Satya S. , Bhat Jayesh S. , Deisz Robert , Marx Gernot , Schuppert Andreas 
Published: September 2019

AbstractThe progression of complex human diseases is associated with critical transitions across dynamical regimes. These transitions often spawn early-warning signals and provide insights into the underlying disease-driving mechanisms. In this paper, we propose a computational method based on surprise loss (SL) to discover data-driven indicators of such transitions in a multivariate time series dataset of septic shock and non-sepsis patient cohorts (MIMIC-III database). The core idea of SL is to train a mathematical model on time series in an unsupervised fashion and to quantify the deterioration of the model’s forecast (out-of-sample) performance relative to its past (in-sample) performance. Considering the highest value of the moving average of SL as a critical transition, our retrospective analysis revealed that critical transitions occurred at a median of over 35 hours before the onset of septic shock, which suggests the applicability of our method as an early-warning indicator. Furthermore, we show that clinical variables at critical-transition regions are significantly different between septic shock and non-sepsis cohorts. Therefore, our paper contributes a critical-transition-based data-sampling strategy that can be utilized for further analysis, such as patient classification. Moreover, our method outperformed other indicators of critical transition in complex systems, such as temporal autocorrelation and variance.
Unveiling the multi-step solubilization mechanism of sub-micron size vesicles by detergents
Authors: Dalgarno Paul A. , Juan-Colás José , Hedley Gordon J. , Piñeiro Lucas , Novo Mercedes , Perez-Gonzalez Cibran , Samuel Ifor D. W. , Leake Mark C. , Johnson Steven , Al-Soufi Wajih , Penedo J. Carlos , Quinn Steven D. 
Published: September 2019

AbstractThe solubilization of membranes by detergents is critical for many technological applications and has become widely used in biochemistry research to induce cell rupture, extract cell constituents, and to purify, reconstitute and crystallize membrane proteins. The thermodynamic details of solubilization have been extensively investigated, but the kinetic aspects remain poorly understood. Here we used a combination of single-vesicle Förster resonance energy transfer (svFRET), fluorescence correlation spectroscopy and quartz-crystal microbalance with dissipation monitoring to access the real-time kinetics and elementary solubilization steps of sub-micron sized vesicles, which are inaccessible by conventional diffraction-limited optical methods. Real-time injection of a non-ionic detergent, Triton X, induced biphasic solubilization kinetics of surface-immobilized vesicles labelled with the Dil/DiD FRET pair. The nanoscale sensitivity accessible by svFRET allowed us to unambiguously assign each kinetic step to distortions of the vesicle structure comprising an initial fast vesicle-swelling event followed by slow lipid loss and micellization. We expect the svFRET platform to be applicable beyond the sub-micron sizes studied here and become a unique tool to unravel the complex kinetics of detergent-lipid interactions.
Clinical, pathophysiologic, and genomic analysis of the outcomes of primary head and neck malignancy after pulmonary metastasectomy
Authors: Lu Hsueh-Ju , Hsieh Chih-Cheng , Yeh Chi-Chun , Yeh Yi-Chen , Wu Chun-Chi , Wang Feng-Sheng , Lai Jin-Mei , Yang Muh-Hwa , Wang Cheng-Hsu , Huang Chi-Ying F. , Chang Peter Mu-Hsin 
Published: September 2019

AbstractThe median overall survival (OS) of some head and neck malignancies, such as head and neck squamous cell carcinoma (HNSCC), with metastatic lesions was only 12 months. Whether aggressive pulmonary metastasectomy (PM) improves survival is controversial. Patients with primary head and neck malignancy undergoing PM were enrolled. Clinical outcomes were compared among different histological types. Whole-exome sequencing was used for matched pulmonary metastatic samples. The genes where genetic variants have been identified were sent for analysis by DAVID, IPA, and STRING. Forty-nine patients with primary head and neck malignancies were enrolled. Two-year postmetastasectomy survival (PMS) rates of adenoid cystic carcinoma, thyroid carcinoma, nasopharyngeal carcinoma, and HNSCC were 100%, 88.2%, 71.4%, and 59.2%, respectively (P = 0.024). In HNSCC, the time to distant metastasis was an independent predictive factor of the efficacy of PM. Several pathways, such as branched-chain amino acid (BCAA) consumption, were significantly associated with the progression of HNSCC [P < 0.001, fold enrichment (FE) = 5.45]. Moreover, metabolism-associated signaling pathways also seemed to be involved in cancer metastasis. Histological types and time to distant metastasis were important factors influencing the clinical outcomes of PM. For HNSCC, metabolic-associated signaling pathways were significantly associated with tumor progression and distant metastasis. Future validations are warranted.
Disorder-aided pulse stabilization in dissipative synthetic photonic lattices
Authors: Derevyanko Stanislav 
Published: September 2019

AbstractWe consider a discrete time evolution of light in dissipative and disordered photonic lattice presenting a generalization of two popular non-Hermitian models in mathematical literature: Hatano-Nelson and random clock model and suggest a possible experimental implementation using coupled fiber loops. We show that if the model is treated as non-unitary Floquet operator rather than the effective Hamiltonian the combination of controlled photon loss and static phase disorder leads to pulse stabilization in the ring topology. We have also studied the topological invariant associated with the system and found additional evidence for the absence of Anderson transition.
Revealing biogeochemical signatures of Arctic landscapes with river chemistry
Authors: Shogren Arial J. , Zarnetske Jay P. , Abbott Benjamin W. , Iannucci Frances , Frei Rebecca J. , Griffin Natasha A. , Bowden William B. 
Published: September 2019

AbstractRiverine fluxes of carbon and inorganic nutrients are increasing in virtually all large permafrost-affected rivers, indicating major shifts in Arctic landscapes. However, it is currently difficult to identify what is causing these changes in nutrient processing and flux because most long-term records of Arctic river chemistry are from small, headwater catchments draining <200 km2 or from large rivers draining >100,000 km2. The interactions of nutrient sources and sinks across these scales are what ultimately control solute flux to the Arctic Ocean. In this context, we performed spatially-distributed sampling of 120 subcatchments nested within three Arctic watersheds spanning alpine, tundra, and glacial-lake landscapes in Alaska. We found that the dominant spatial scales controlling organic carbon and major nutrient concentrations was 3–30 km2, indicating a continuum of diffuse and discrete sourcing and processing dynamics. These patterns were consistent seasonally, suggesting that relatively fine-scale landscape patches drive solute generation in this region of the Arctic. These network-scale empirical frameworks could guide and benchmark future Earth system models seeking to represent lateral and longitudinal solute transport in rapidly changing Arctic landscapes.
White matter microstructure mediates the association between physical fitness and cognition in healthy, young adults
Authors: Opel Nils , Martin Stella , Meinert Susanne , Redlich Ronny , Enneking Verena , Richter Maike , Goltermann Janik , Johnen Andreas , Dannlowski Udo , Repple Jonathan 
Published: September 2019

AbstractWe aimed to extend our knowledge on the relationship between physical fitness (PF) and both white matter microstructure and cognition through in-depth investigation of various cognitive domains while accounting for potentially relevant nuisance covariates in a well-powered sample. To this end, associations between walking endurance, diffusion-tensor-imaging (DTI) based measures of fractional anisotropy (FA) within brain white matter and cognitive measures included in the NIH Toolbox Cognition Battery were investigated in a sample of n = 1206 healthy, young adults (mean age = 28.8; 45.5% male) as part of the human connectome project. Higher levels of endurance were associated with widespread higher FA (pFWE < 0.05) as well as with enhanced global cognitive function (p < 0.001). Significant positive relationships between endurance and cognitive performance were similarly found for almost all cognitive domains. Higher FA was significantly associated with enhanced global cognitive function (p < 0.001) and FA was shown to significantly mediate the association between walking endurance and cognitive performance. Inclusion of potentially relevant nuisance covariates including gender, age, education, BMI, HBA1c, and arterial blood pressure did not change the overall pattern of results. These findings support the notion of a beneficial and potentially protective effect of PF on brain structure and cognition.
Mosaicism of XX and XXY cells accounts for high copy number of Toll like Receptor 7 and 8 genes in peripheral blood of men with Rheumatoid Arthritis
Authors: Martin Gabriel V. , Kanaan Sami B. , Hemon Marie F. , Azzouz Doua F. , El Haddad Marina , Balandraud Nathalie , Mignon-Ravix Cécile , Picard Christophe , Arnoux Fanny , Martin Marielle , Roudier Jean , Auger Isabelle , Lambert Nathalie C. 
Published: September 2019

AbstractThe X chromosome, hemizygous in males, contains numerous genes important to immunological and hormonal function. Alterations in X-linked gene dosage are suspected to contribute to female predominance in autoimmunity. A powerful example of X-linked dosage involvement comes from theBXSBmurine lupus model, where the duplication of the X-linkedToll-Like Receptor 7(Tlr7)gene aggravates autoimmunity in male mice. Such alterations are possible in men with autoimmune diseases. Here we showed that a quarter to a third of men with rheumatoid arthritis (RA) had significantly increased copy numbers (CN) ofTLR7gene and its paralogTLR8. Patients with high CN had an upregulated pro-inflammatory JNK/p38 signaling pathway. By fluorescencein situhybridization, we further demonstrated that the increase in X-linked genes CN was due to the presence of an extra X chromosome in some cells. Men with RA had a significant cellular mosaicism of female (46,XX) and/or Klinefelter (47,XXY) cells among male (46,XY) cells, reaching up to 1.4% in peripheral blood. Our results present a new potential trigger for RA in men and opens a new field of investigation particularly relevant for gender-biased autoimmune diseases.
Survival rate and Outcome of extracorporeal life support (ECLS) for treatment of acute cardiorespiratory failure in trauma patients
Authors: Lang Nikolaus W. , Schwihla Ines , Weihs Valerie , Kasparek Maximilian , Joestl Julian , Hajdu Stefan , Sarahrudi Kambiz 
Published: September 2019

AbstractExtracorporeal life support (ECLS) remains the last option for cardiorespiratory stabilization of severe traumatic injured patients. Currently limited data are available and therefore, the current study assessed the survival rate and outcome of ECLS in a Level I trauma center. Between 2002 and 2016, 18 patients (7 females, 11 males) with an median age of 29.5 IQR 23.5 (range 1–64) years were treated with ECLS due to acute traumatic cardiorespiratory failure. Trauma mechanism, survival rate, ISS, SOFA, GCS, GOS, CPC, time to ECLS, hospital- and ICU stay, surgical interventions, complications and infections were retrospectively assessed. Veno-arterial ECLS was applied in 15 cases (83.3%) and veno-venous ECLS in 3 cases (16.6%). Survivors were significant younger than non-survivors (p = 0.0289) and had a lower ISS (23.5 (IQR 22.75) vs 38.5 (IQR 16.5), p = n.s.). The median time to ECLS cannulation was 2 (IQR 0,25) hours in survivors 2 (IQR 4) in non-survivors. Average GCS was 3 (IQR 9.25) at admission. Six patients (33.3%) survived and had a satisfying neurological outcome with a mean GOS of 5 (IQR 0.25) (p = n.s.). ECLS is a valuable treatment in severe injured patients with traumatic cardiorespiratory failure and improves survival with good neurological outcome. Younger patients and patients with a lower ISS are associated with a higher survival rate. Consideration of earlier cannulation in traumatic cardiorespiratory failure might be beneficial to improve survival.
Impact of Intermittent Hypoxia on Sepsis Outcomes in a Murine Model
Authors: Chou Kun-Ta , Cheng Shih-Chin , Huang Shiang-Fen , Perng Diahn-Warng , Chang Shi-Chuan , Chen Yuh-Min , Hsu Han-Shui , Hung Shih-Chieh 
Published: September 2019

AbstractSleep apnea has been associated with a variety of diseases, but its impact on sepsis outcome remains unclear. This study investigated the effect of intermittent hypoxia [IH]–the principal feature of sleep apnea–on murine sepsis. 5-week-old male C57BL6 mice were assigned to groups receiving severe IH (O2 fluctuating from room air to an O2 nadir of 5.7% with a cycle length of 90 seconds), mild IH (room air to 12%, 4 minutes/cycle), or room air for 3 weeks. Sepsis was induced by cecal ligation and puncture and survival was monitored. Sepsis severity was evaluated by murine sepsis scores, blood bacterial load, plasma tumor necrosis factor-α [TNF-α]/interleukin-6 [IL-6] levels and histopathology of vital organs. Compared with normoxic controls, mice subjected to severe IH had earlier mortality, a lower leukocyte count, higher blood bacterial load, higher plasma TNF-α and IL-6 levels, more severe inflammatory changes in the lung, spleen and small intestine. Mice subjected to mild IH did not differ from normoxic controls, except a higher IL-6 level after sepsis induced. The adverse impact of severe IH was reversed following a 10-day normoxic recovery. In conclusion, severe IH, not mild IH, contributed to poorer outcomes in a murine sepsis model.