bluuebunny/crossref_metadata_2025_split huggingface dataset:
Overcoming evanescent field decay using 3D-tapered nanocavities for on-chip targeted molecular analysis
Authors: Kumar Shailabh , Park Haeri , Cho Hyunjun , Siddique Radwanul H. , Narasimhan Vinayak , Yang Daejong , Choo Hyuck 
Published: June 2020

AbstractEnhancement of optical emission on plasmonic nanostructures is intrinsically limited by the distance between the emitter and nanostructure surface, owing to a tightly-confined and exponentially-decaying electromagnetic field. This fundamental limitation prevents efficient application of plasmonic fluorescence enhancement for diversely-sized molecular assemblies. We demonstrate a three-dimensionally-tapered gap plasmon nanocavity that overcomes this fundamental limitation through near-homogeneous yet powerful volumetric confinement of electromagnetic field inside an open-access nanotip. The 3D-tapered device provides fluorescence enhancement factors close to 2200 uniformly for various molecular assemblies ranging from few angstroms to 20 nanometers in size. Furthermore, our nanostructure allows detection of low concentration (10 pM) biomarkers as well as specific capture of single antibody molecules at the nanocavity tip for high resolution molecular binding analysis. Overcoming molecule position-derived large variations in plasmonic enhancement can propel widespread application of this technique for sensitive detection and analysis of complex molecular assemblies at or near single molecule resolution.
An iron (II) dependent oxygenase performs the last missing step of plant lysine catabolism
Authors: Thompson Mitchell G. , Blake-Hedges Jacquelyn M. , Pereira Jose Henrique , Hangasky John A. , Belcher Michael S. , Moore William M. , Barajas Jesus F. , Cruz-Morales Pablo , Washington Lorenzo J. , Haushalter Robert W. , Eiben Christopher B. , Liu Yuzhong , Skyrud Will , Benites Veronica T. , Barnum Tyler P. , Baidoo Edward E. K. , Scheller Henrik V. , Marletta Michael A. , Shih Patrick M. , Adams Paul D. , Keasling Jay D. 
Published: June 2020

AbstractDespite intensive study, plant lysine catabolism beyond the 2-oxoadipate (2OA) intermediate remains unvalidated. Recently we described a missing step in the D-lysine catabolism of Pseudomonas putida in which 2OA is converted to D-2-hydroxyglutarate (2HG) via hydroxyglutarate synthase (HglS), a DUF1338 family protein. Here we solve the structure of HglS to 1.1 Å resolution in substrate-free form and in complex with 2OA. We propose a successive decarboxylation and intramolecular hydroxylation mechanism forming 2HG in a Fe(II)- and O2-dependent manner. Specificity is mediated by a single arginine, highly conserved across most DUF1338 proteins. An Arabidopsis thaliana HglS homolog coexpresses with known lysine catabolism enzymes, and mutants show phenotypes consistent with disrupted lysine catabolism. Structural and biochemical analysis of Oryza sativa homolog FLO7 reveals identical activity to HglS despite low sequence identity. Our results suggest DUF1338-containing enzymes catalyze the same biochemical reaction, exerting the same physiological function across bacteria and eukaryotes.
Infrared driven hot electron generation and transfer from non-noble metal plasmonic nanocrystals
Authors: Zhou Dongming , Li Xufeng , Zhou Qiaohui , Zhu Haiming 
Published: June 2020

AbstractNon-noble metal plasmonic materials, e.g. doped semiconductor nanocrystals, compared to their noble metal counterparts, have shown unique advantages, including broadly tunable plasmon frequency (from visible to infrared) and rich surface chemistry. However, the fate and harvesting of hot electrons from these non-noble metal plasmons have been much less explored. Here we report plasmon driven hot electron generation and transfer from plasmonic metal oxide nanocrystals to surface adsorbed molecules by ultrafast transient absorption spectroscopy. We show unambiguously that under infrared light excitation, hot electron transfers in ultrafast timescale (<50 fs) with an efficiency of 1.4%. The excitation wavelength and fluence dependent study indicates that hot electron transfers right after Landau damping before electron thermalization. We revealed the efficiency-limiting factors and provided improvement strategies. This study paves the way for designing efficient infrared light absorption and photochemical conversion applications based on non-noble metal plasmonic materials.
Unconventional valley-dependent optical selection rules and landau level mixing in bilayer graphene
Authors: Ju Long , Wang Lei , Li Xiao , Moon Seongphill , Ozerov Mike , Lu Zhengguang , Taniguchi Takashi , Watanabe Kenji , Mueller Erich , Zhang Fan , Smirnov Dmitry , Rana Farhan , McEuen Paul L. 
Published: June 2020

AbstractSelection rules are of vital importance in determining the basic optical properties of atoms, molecules and semiconductors. They provide general insights into the symmetry of the system and the nature of relevant electronic states. A two-dimensional electron gas in a magnetic field is a model system where optical transitions between Landau levels (LLs) are described by simple selection rules associated with the LL index N. Here we examine the inter-LL optical transitions of high-quality bilayer graphene by photocurrent spectroscopy measurement. We observed valley-dependent optical transitions that violate the conventional selection rules Δ|N| = ± 1. Moreover, we can tune the relative oscillator strength by tuning the bilayer graphene bandgap. Our findings provide insights into the interplay between magnetic field, band structure and many-body interactions in tunable semiconductor systems, and the experimental technique can be generalized to study symmetry-broken states and low energy magneto-optical properties of other nano and quantum materials.
Distinct Functional Requirements for Podocalyxin in Immature and Mature Podocytes Reveal Mechanisms of Human Kidney Disease
Authors: Refaeli Ido , Hughes Michael R. , Wong Alvin Ka-Wai , Bissonnette Mei Lin Z. , Roskelley Calvin D. , Wayne Vogl A. , Barbour Sean J. , Freedman Benjamin S. , McNagny Kelly M. 
Published: June 2020

AbstractDominant and recessive mutations in podocalyxin (PODXL) are associated with human kidney disease. Interestingly, some PODXL mutations manifest as anuria while others are associated with proteinuric kidney disease. PODXL heterozygosity is associated with adult-onset kidney disease and podocalyxin shedding into the urine is a common biomarker of a variety nephrotic syndromes. It is unknown, however, how various lesions in PODXL contribute to these disparate disease pathologies. Here we generated two mouse stains: one that deletes Podxl in developmentally mature podocytes (Podxl∆Pod) and a second that is heterozygous for podocalyxin in all tissues (Podxl+/−). We used histologic and ultrastructural analyses, as well as clinical chemistry assays to evaluate kidney development and function in these strains. In contrast to null knockout mice (Podxl−/−), which die shortly after birth from anuria and hypertension, Podxl∆Pod mice develop an acute congenital nephrotic syndrome characterized by focal segmental glomerulosclerosis (FSGS) and proteinuria. Podxl+/− mice, in contrast, have a normal lifespan, and fail to develop kidney disease under normal conditions. Intriguingly, although wild-type C57Bl/6 mice are resistant to puromycin aminonucleoside (PA)-induced nephrosis (PAN), Podxl+/− mice are highly sensitive and PA induces severe proteinuria and collapsing FSGS. In summary, we find that the developmental timepoint at which podocalyxin is ablated (immature vs. mature podocytes) has a profound effect on the urinary phenotype due to its critical roles in both the formation and the maintenance of podocyte ultrastructure. In addition, Podxl∆Pod and Podxl+/− mice offer powerful new mouse models to evaluate early biomarkers of proteinuric kidney disease and to test novel therapeutics.
A nomogram to predict the risk of hepatic encephalopathy after transjugular intrahepatic portosystemic shunt in Cirrhotic Patients
Authors: Yin Xiaochun , Zhang Feng , Guo Huiwen , Peng Chunyan , Zhang Wei , Xiao Jiangqiang , Wang Yi , Zou Xiaoping , Zhang Ming , Zhuge Yuzheng 
Published: June 2020

AbstractBackground and Aim: Hepatic encephalopathy (HE) is a serious complication of decompensated liver cirrhosis, affecting the prognosis of patients underwent transjugular intrahepatic portosystemic shunts (TIPS). We aim to create a nomogram to predict hepatic encephalopathy- free survivals (HEFS) after TIPS in cirrhotic patients and select appropriate candidates for TIPS. Methods: Cirrhotic patients underwent TIPS from 2015 to 2018 in our department were included. Multivariable Cox regression was conducted to estimate the predictors of overt HE (OHE) after TIPS within one year. A nomogram based on the Cox proportional hazard model using data from a retrospective training cohort (70% of the patients) was developed. Then the prediction model was validated in the remaining 30% patients by Harrell’s C-indexes, ROC curves and calibration plots. Results: Of 373 patients, 117 developed postoperative OHE (31.4%). The training and validation groups comprised 83 (31.4%) and 34 (31.2%) patients, respectively. The cumulative survival rates of patients with HE at 1, 2 and 3 years were 90%, 83% and 76%, respectively. The nomogram included the following variables: age, Child-Turcotte-Pugh class (CTP class), diabetes mellitus (DM), serum creatinine and serum sodium (C-index = 0.772). The C-index for HEFS prediction was 0.773 for the validation cohort. The ROC for predicting HEFS was 0.809 and 0.783, respectively. Conclusions: We created a nomogram of predicting postoperative HEFS in cirrhotic patients received TIPS. This nomogram could be an important tool of HE risk prediction before TIPS to guide the therapeutic strategy in cirrhotic patients.
Sensitivity and noise in THz electro-optic upconversion radiometers
Authors: Santamaría-Botello Gabriel , Popovic Zoya , Abdalmalak Kerlos Atia , Segovia-Vargas Daniel , Brown Elliott R. , García Muñoz Luis Enrique 
Published: June 2020

AbstractThis paper presents a study of noise in room-temperature THz radiometers that use THz-to-optical upconversion followed by optical detection of thermal radiation. Despite some undesired upconverted thermal noise, no noise is intrinsically introduced by efficient electro-optic modulation via a sum-frequency-generation process in high quality factor (Q) whispering-gallery mode (WGM) resonators. However, coherent and incoherent optical detection results in fundamentally different noise characteristics. The analysis shows that the upconversion receiver is quantum limited like conventional amplifiers and mixers, only when optical homodyne or heterodyne detection is performed. However, this type of receiver shows advantages as a THz photon counter, where counting is in the optical domain. Theoretical predictions show that upconversion-based room-temperature receivers can outperform state-of-the-art cooled and room-temperature THz receivers based on low-noise amplifiers and mixers, provided that a photon conversion efficiency greater than 1% is realized. Although the detection bandwidth is naturally narrow due to the highly resonant electro-optic modulator, it is not fundamentally limited and can be broadened by engineering selective optical coupling mechanisms to the resonator.
Faecal DNA to the rescue: Shotgun sequencing of non-invasive samples reveals two subspecies of Southeast Asian primates to be Critically Endangered species
Authors: Ang Andie , Roesma Dewi Imelda , Nijman Vincent , Meier Rudolf , Srivathsan Amrita , Rizaldi  
Published: June 2020

AbstractA significant number of Southeast Asian mammal species described in the 19th and 20th century were subsequently synonymized and are now considered subspecies. Many are affected by rapid habitat loss which creates an urgent need to re-assess the conservation status based on species boundaries established with molecular data. However, such data are lacking and difficult to obtain for many populations and subspecies. We document via a literature survey and empirical study how shotgun sequencing of faecal DNA is a still underutilized but powerful tool for accelerating such evaluations. We obtain 11 mitochondrial genomes for three subspecies in the langur genus Presbytis through shotgun sequencing of faecal DNA (P. femoralis femoralis, P. f. percura, P. siamensis cf. cana). The genomes support the resurrection of all three subspecies to species based on multiple species delimitation algorithms (PTP, ABGD, Objective Clustering) applied to a dataset covering 40 species and 43 subspecies of Asian colobines. For two of the newly recognized species (P. femoralis, P. percura), the results lead to an immediate change in IUCN status to Critically Endangered due to small population sizes and fragmented habitats. We conclude that faecal DNA should be more widely used for clarifying species boundaries in endangered mammals.
Nitric oxide synthase mediates cerebellar dysfunction in mice exposed to repetitive blast-induced mild traumatic brain injury
Authors: Logsdon Aric F. , Schindler Abigail G. , Meabon James S. , Yagi Mayumi , Herbert Melanie J. , Banks William A. , Raskind Murray A. , Marshall Desiree A. , Keene C. Dirk , Perl Daniel P. , Peskind Elaine R. , Cook David G. 
Published: June 2020

AbstractWe investigated the role of nitric oxide synthase (NOS) in mediating blood-brain barrier (BBB) disruption and peripheral immune cell infiltration in the cerebellum following blast exposure. Repetitive, but not single blast exposure, induced delayed-onset BBB disruption (72 hours post-blast) in cerebellum. The NOS inhibitor N(G)-nitro-L-arginine methyl ester (L-NAME) administered after blast blocked BBB disruption and prevented CD4+ T-cell infiltration into cerebellum. L-NAME also blocked blast-induced increases in intercellular adhesion molecule-1 (ICAM-1), a molecule that plays a critical role in regulating blood-to-brain immune cell trafficking. Blocking NOS-mediated BBB dysfunction during this acute/subacute post-blast interval (24–71 hours after the last blast) also prevented sensorimotor impairment on a rotarod task 30 days later, long after L-NAME cleared the body. In postmortem brains from Veterans/military Servicemembers with blast-related TBI, we found marked Purkinje cell dendritic arbor structural abnormalities, which were comparable to neuropathologic findings in the blast-exposed mice. Taken collectively, these results indicate that blast provokes delayed-onset of NOS-dependent pathogenic cascades that can later emerge as behavioral dysfunction. These results also further implicate the cerebellum as a brain region vulnerable to blast-induced mTBI.
Magnetization process of a ferromagnetic nanostrip under the influence of a surface acoustic wave
Authors: Castilla David , Yanes Rocío , Sinusía Miguel , Fuentes Gonzalo , Grandal Javier , Maicas Marco , Álvarez-Arenas Tomás E. G. , Muñoz Manuel , Torres Luis , López Luis , Prieto José L. 
Published: June 2020

AbstractSurface Acoustic Waves (SAW) are one of the possible solutions to target the challenges faced by modern spintronic devices. The stress carried by the SAW can decrease the current required to achieve magnetic switching or domain wall movement by spin transfer torque. Although the last decade has produced very relevant results in this field, it is still important to study the effects of a SAW on the basic unit of many spintronic devices, a ferromagnetic nanostrip. In this work, we perform a complete set of measurements and simulations to characterize the magnetization process of a Ni nanostrip under the influence of a SAW. We find that the SAW increases the mobility and the depinning ability of the magnetic domain walls and consequently, promotes a sharper approach to saturation and substantially decreases coercivity. We have also found other two interesting effects. When the SAW has sufficient energy, is able to trigger irreversible transitions even before switching the direction of the external magnetic field. Additionally, we have found that the magnetization process depends on the direction of the travelling SAW.
Annealing Effect of Glancing Angle Electron Beam Deposited TiO2/In2O3 Nanowires Array on Surface Wettability
Authors: Pooja Pheiroijam , P. Chinnamuthu 
Published: June 2020

AbstractTiO2/In2O3 nanowire (NW) array are prepared using catalyst free glancing angle deposition technique. The wettability of TiO2/In2O3 NW surface are tuned and controlled by the annealing treatment without altering the surface with additional chemical coating. The phase change, surface roughness, change in static and dynamic contact angles due to the heat treatment are studied. Moreover, the surface properties such as frictional force and work of adhesion are calculated for all the samples. The samples annealed at 600 °C shows nearly superhydrophilic with static water contact angle of 12°, frictional force of 85.00748 µN and work of adhesion of 142.3721 mN/m. The surface of TiO2/In2O3 NW is controlled to attain desired water contact angles and sliding angles, which is paramount for designing practical application in self-cleaning, electronic and biomedical fields.
Placental Metabolomics for Assessment of Sex-specific Differences in Fetal Development During Normal Gestation
Authors: Saoi Michelle , Kennedy Katherine M. , Gohir Wajiha , Sloboda Deborah M. , Britz-McKibbin Philip 
Published: June 2020

AbstractThe placenta is a metabolically active interfacial organ that plays crucial roles in fetal nutrient delivery, gas exchange and waste removal reflecting dynamic maternal and fetal interactions during gestation. There is growing evidence that the sex of the placenta influences fetal responses to external stimuli in utero, such as changes in maternal nutrition and exposure to environmental stressors. However, the exact biochemical mechanisms associated with sex-specific metabolic adaptations during pregnancy and its link to placental function and fetal development remain poorly understood. Herein, multisegment injection-capillary electrophoresis-mass spectrometry is used as a high throughput metabolomics platform to characterize lyophilized placental tissue (~2 mg dried weight) from C57BL/6J mice fed a standardized diet. Over 130 authentic metabolites were consistently measured from placental extracts when using a nontargeted metabolomics workflow with stringent quality control and robust batch correction. Our work revealed distinct metabolic phenotype differences that exist between male (n = 14) and female (n = 14) placentae collected at embryonic day E18.5. Intracellular metabolites associated with fatty acid oxidation and purine degradation were found to be elevated in females as compared to male placentae (p < 0.05, effect size >0.40), including uric acid, valerylcarnitine, hexanoylcarnitine, and 3-hydroxyhexanolycarnitine. This murine model sheds new insights into sex-specific differences in placental mitochondrial function and protective mechanisms against deleterious oxidative stress that may impact fetal growth and birth outcomes later in life.
Magmatic overpressures, volatile exsolution and potential explosivity of fissure eruptions inferred via dike aspect ratios
Authors: Geshi Nobuo , Browning John , Kusumoto Shigekazu 
Published: June 2020

AbstractBuoyant magmas abundant in exsolved volatiles (bubbles) drive the rapid upward-propagation of feeder dikes from magma chambers. The consequence of a feeder dike reaching the surface can result in an explosive volcanic eruption depending, partly, on the retention of volatiles. Therefore, timely detection of the vesicularity and overpressure of the magma during feeder dike ascent is critical for the prediction of the explosivity of any future eruption. In this study, we evaluated the explosivity of eruptions based on field investigations of the erupted products and the overpressure of magma in the conduit based on the dimensions of exposed feeder dikes. We found a positive correlation between the explosivity of eruptions and the magma overpressure generated in the conduit during recent fissure eruptions of Miyakejima volcano. Because the buoyancy of low-density magma produces positive overpressure at the dike’s top, feeder dikes with highly-vesiculated magmas possess high amounts of overpressure. An enlargement of the opening width of a feeder dike by magmatic overpressure results in a higher flux of vesiculated magma, which causes vigorous explosive activity. Our results suggest the possibility of forecasting the explosivity of an impending eruption if the width (or opening) of an ascending feeder dike is monitored in real-time through measurements of ground deformation and seismicity induced by the dike.
Prediction of prostate cancer aggressiveness using 18F-Fluciclovine (FACBC) PET and multisequence multiparametric MRI
Authors: Movahedi Parisa , Merisaari Harri , Perez Ileana Montoya , Taimen Pekka , Kemppainen Jukka , Kuisma Anna , Eskola Olli , Teuho Jarmo , Saunavaara Jani , Pesola Marko , Kähkönen Esa , Ettala Otto , Liimatainen Timo , Pahikkala Tapio , Boström Peter , Aronen Hannu , Minn Heikki , Jambor Ivan 
Published: June 2020

AbstractThe aim of this prospective single-institution clinical trial (NCT02002455) was to evaluate the potential of advanced post-processing methods for 18F-Fluciclovine PET and multisequence multiparametric MRI in the prediction of prostate cancer (PCa) aggressiveness, defined by Gleason Grade Group (GGG). 21 patients with PCa underwent PET/CT, PET/MRI and MRI before prostatectomy. DWI was post-processed using kurtosis (ADCk, K), mono- (ADCm), and biexponential functions (f, Dp, Df) while Logan plots were used to calculate volume of distribution (VT). In total, 16 unique PET (VT, SUV) and MRI derived quantitative parameters were evaluated. Univariate and multivariate analysis were carried out to estimate the potential of the quantitative parameters and their combinations to predict GGG 1 vs >1, using logistic regression with a nested leave-pair out cross validation (LPOCV) scheme and recursive feature elimination technique applied for feature selection. The second order rotating frame imaging (RAFF), monoexponential and kurtosis derived parameters had LPOCV AUC in the range of 0.72 to 0.92 while the corresponding value for VT was 0.85. The best performance for GGG prediction was achieved by K parameter of kurtosis function followed by quantitative parameters based on DWI, RAFF and 18F-FACBC PET. No major improvement was achieved using parameter combinations with or without feature selection. Addition of 18F-FACBC PET derived parameters (VT, SUV) to DWI and RAFF derived parameters did not improve LPOCV AUC.