bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dependence of Aspen Stands on a Subsurface Water Subsidy: Implications for Climate Change Impacts
Authors: Love D. M. , Venturas M. D. , Sperry J. S. , Brooks P. D. , Pettit J. L. , Wang Y. , Anderegg W. R. L. , Tai X. , Mackay D. S. 
Published: December 2018

AbstractThe reliance of 10 Utah (USA) aspen forests on direct infiltration of growing season rain versus an additional subsurface water subsidy was determined from a trait‐ and process‐based model of stomatal control. The model simulated the relationship between water supply to the root zone versus canopy transpiration and assimilation over a growing season. Canopy flux thresholds were identified that distinguished nonstressed, stressed, and dying stands. We found growing season rain and local soil moisture were insufficient for the survival of 5 of 10 stands. Six stands required a substantial subsidy (31–80% of potential seasonal transpiration) to avoid water stress and maximize photosynthetic potential. Subsidy dependence increased with stand hydraulic conductance. Four of the six “subsidized” stands were predicted to be stressed during the survey year owing to a subsidy shortfall. Since winter snowpack is closely related to groundwater recharge in the region, we compared winter precipitation with tree‐ring chronologies. Consistent with model predictions, chronologies were more sensitive to snowpack in subsidized stands than in nonsubsidized ones. The results imply that aspen stand health in the region is more coupled to winter snowpack than to growing season water supply. Winters are predicted to have less precipitation as snow, indicating a stressful future for the region's aspen forests.
Critical Zone Water Balance Over 13 Years in a Semiarid Savanna
Authors: Scott Russell L. , Biederman Joel A. 
Published: December 2018

AbstractQuantifying how much and when precipitation (P) becomes runoff (R), evapotranspiration (ET), and drainage from the root zone (D) is key to understanding how climate and land use impact hydrology of the critical zone. We quantify water balance dynamics of a semiarid savanna with a summer/winter rainfall pattern with 13 years of water fluxes and soil moisture. We find multiyear P is partitioned 96% to ET and 7% to R, while D (−3%) is negligible when considering measurement uncertainty. While weather regulates ET over diurnal time scales, soil water inputs control seasonal to annual ET amounts. Seasonal water availability, estimated by soil moisture inputs, is more closely tracked by ET rather than time‐averaged soil moisture or P. Surprisingly, we find significant, episodic carryover of soil moisture from the summer to spring growing season. Abundant late‐summer P can supply ET in the subsequent spring, even after multimonth dry periods. However, over an annual cycle beginning in early summer, nearly all soil moisture is used by ET. Likewise, D beyond the monitored root zone, assisted by downward hydraulic distribution in plant roots, occurs within a season, but this is counteracted by subsequent ET extraction of deep moisture over the year. Thus, negligible long‐term D occurs, though there is considerable uncertainty in estimation of this small flux as the residual of much larger ones. These comprehensive, long‐term measurements support expectations about the overriding importance of ET in the dryland critical zone water balance and reveal an unexpected degree of interseasonal water storage.
Optoacoustic microscopy at multiple discrete frequencies
Authors: Kellnberger Stephan , Soliman Dominik , Tserevelakis George J. , Seeger Markus , Yang Hong , Karlas Angelos , Prade Ludwig , Omar Murad , Ntziachristos Vasilis 
Published: December 2018

AbstractOptoacoustic (photoacoustic) sensing employs illumination of transient energy and is typically implemented in the time domain using nanosecond photon pulses. However, the generation of high-energy short photon pulses requires complex laser technology that imposes a low pulse repetition frequency (PRF) and limits the number of wavelengths that are concurrently available for spectral imaging. To avoid the limitations of working in the time domain, we have developed frequency-domain optoacoustic microscopy (FDOM), in which light intensity is modulated at multiple discrete frequencies. We integrated FDOM into a hybrid system with multiphoton microscopy, and we examine the relationship between image formation and modulation frequency, showcase high-fidelity images with increasing numbers of modulation frequencies from phantoms and in vivo, and identify a redundancy in optoacoustic measurements performed at multiple frequencies. We demonstrate that due to high repetition rates, FDOM achieves signal-to-noise ratios similar to those obtained by time-domain methods, using commonly available laser diodes. Moreover, we experimentally confirm various advantages of the frequency-domain implementation at discrete modulation frequencies, including concurrent illumination at two wavelengths that are carried out at different modulation frequencies as well as flow measurements in microfluidic chips and in vivo based on the optoacoustic Doppler effect. Furthermore, we discuss how FDOM redefines possibilities for optoacoustic imaging by capitalizing on the advantages of working in the frequency domain.
Loss of Phd2 cooperates with BRAFV600E to drive melanomagenesis
Authors: Liu Shujing , Zhang Gao , Guo Jianping , Chen Xiang , Lei Jingce , Ze Kan , Dong Liyun , Dai Xiangpeng , Gao Yang , Song Daisheng , Ecker Brett L. , Yang Ruifeng , Feltcher Caitlin , Peng Kai , Feng Cheng , Chen Hui , Lee Rebecca X. , Kerestes Heddy , Niu Jingwen , Kumar Suresh , Xu Weiting , Zhang Jie , Wei Zhi , Martin James S. , Liu Xiaoming , Mills Gordon , Lu Yiling , Guo Wei , Sun Lunquan , Zhang Lin , Weeraratna Ashani , Herlyn Meenhard , Wei Wenyi , Lee Frank S. , Xu Xiaowei 
Published: December 2018

AbstractProlyl hydroxylase domain protein 2 (PHD2) is a well-known master oxygen sensor. However, the role of PHD2 in tumor initiation remains controversial. We find that during the transition of human nevi to melanoma, the expression of PHD2 protein is significantly decreased and lower expression PHD2 in melanoma is associated with worse clinical outcome. Knockdown of PHD2 leads to elevated Akt phosphorylation in human melanocytes. Mice with conditional melanocyte-specific expression of Phd2lox/lox (Tyr::CreER;Phd2lox/lox) fail to develop pigmented lesions. However, deletion of Phd2 in combination with expression of BRafV600E in melanocytes (Tyr::CreER;Phd2lox/lox;BRafCA) leads to the development of melanoma with 100% penetrance and frequent lymph node metastasis. Analysis of tumor tissues using reverse phase protein arrays demonstrates that Phd2 deletion activates the AKT-mTOR-S6 signaling axis in the recovered tumors. These data indicate that PHD2 is capable of suppressing tumor initiation largely mediated through inhibiting of the Akt-mTOR signaling pathway in the melanocyte lineage.
Genomic analysis identifies frequent deletions of Dystrophin in olfactory neuroblastoma
Authors: Gallia Gary L. , Zhang Ming , Ning Yi , Haffner Michael C. , Batista Denise , Binder Zev A. , Bishop Justin A. , Hann Christine L. , Hruban Ralph H. , Ishii Masaru , Klein Alison P. , Reh Douglas D. , Rooper Lisa M. , Salmasi Vafi , Tamargo Rafael J. , Wang Qing , Williamson Tara , Zhao Tianna , Zou Ying , Meeker Alan K. , Agrawal Nishant , Vogelstein Bert , Kinzler Kenneth W. , Papadopoulos Nickolas , Bettegowda Chetan 
Published: December 2018

AbstractOlfactory neuroblastoma (ONB) is a rare malignant neoplasm arising in the upper portion of the sinonasal cavity. To better understand the genetic bases for ONB, here we perform whole exome and whole genome sequencing as well as single nucleotide polymorphism array analyses in a series of ONB patient samples. Deletions involving the dystrophin (DMD) locus are found in 12 of 14 (86%) tumors. Interestingly, one of the remaining tumors has a deletion in LAMA2, bringing the number of ONBs with deletions of genes involved in the development of muscular dystrophies to 13 or 93%. This high prevalence implicates an unexpected functional role for genes causing hereditary muscular dystrophies in ONB.
The H/ACA complex disrupts triplex in hTR precursor to permit processing by RRP6 and PARN
Authors: Tseng Chi-Kang , Wang Hui-Fang , Schroeder Morgan R. , Baumann Peter 
Published: December 2018

AbstractHuman telomerase RNA (hTR) is transcribed as a precursor that is then posttranscriptionally modified and processed. A fraction of the transcripts is oligoadenylated by TRAMP and either processed into the mature hTR or degraded by the exosome. Here, we characterize the processing of 3′ extended forms of varying length by PARN and RRP6. We show that tertiary RNA interactions unique to the longer transcripts favor RNA degradation, whereas H/ACA RNP assembly stimulates productive processing. Interestingly, the H/ACA complex actively promotes processing in addition to protecting the mature 3′ end. Processing occurs in two steps with longer forms first being trimmed by RRP6 and shorter forms then being processed by PARN. These results reveal how RNA structure and RNP assembly affect the kinetics of processing and degradation and ultimately determine the amount of functional telomerase produced in cells.
Self-assembled membrane composed of amyloid-like proteins for efficient size-selective molecular separation and dialysis
Authors: Yang Facui , Tao Fei , Li Chen , Gao Lingxiang , Yang Peng 
Published: December 2018

AbstractThe design and scalable construction of robust ultrathin protein membranes with tunable separation properties remain a key challenge in chemistry and materials science. Here, we report a macroscopic ultrathin protein membrane with the potential for scaled-up fabrication and excellent separation efficiency. This membrane, which is formed by fast amyloid-like lysozyme aggregation at air/water interface, has a controllable thickness that can be tuned to 30–250 nm and pores with a mean size that can be tailored from 1.8 to 3.2 nm by the protein concentration. This membrane can retain > 3 nm molecules and particles while permitting the transport of small molecules at a rate that is 1~4 orders of magnitude faster than the rate of existing materials. This membrane further exhibits excellent hemodialysis performance, especially for the removal of middle-molecular-weight uremic toxins, which is 5~6 times higher in the clearance per unit area than the typical literature values reported to date.
Genomic effects of population collapse in a critically endangered ironwood tree Ostrya rehderiana
Authors: Yang Yongzhi , Ma Tao , Wang Zefu , Lu Zhiqiang , Li Ying , Fu Chengxin , Chen Xiaoyong , Zhao Mingshui , Olson Matthew S. , Liu Jianquan 
Published: December 2018

AbstractIncreased human activity and climate change are driving numerous tree species to endangered status, and in the worst cases extinction. Here we examine the genomic signatures of the critically endangered ironwood treeOstrya rehderianaand its widespread congenerO. chinensis. Both species have similar demographic histories prior to the Last Glacial Maximum (LGM); however, the effective population size ofO. rehderianacontinued to decrease through the last 10,000 years, whereasO. chinensisrecovered to Pre-LGM numbers.O. rehderianaaccumulated more deleterious mutations, but purged more severely deleterious recessive variations than inO. chinensis. This purging and the gradually reduced inbreeding depression together may have mitigated extinction and contributed to the possible future survival of the outcrossingO. rehderiana. Our findings provide critical insights into the evolutionary history of population collapse and the potential for future recovery of the endangered trees.
Sustained release of decorin to the surface of the eye enables scarless corneal regeneration
Authors: Hill Lisa J. , Moakes Richard J. A. , Vareechon Chairut , Butt Gibran , Ng Aaron , Brock Kristian , Chouhan Gurpreet , Vincent Rachel C. , Abbondante Serena , Williams Richard L. , Barnes Nicholas M. , Pearlman Eric , Wallace Graham R. , Rauz Saaeha , Logan Ann , Grover Liam M. 
Published: December 2018

AbstractDisorganization of the transparent collagenous matrix in the cornea, as a consequence of a variety of infections and inflammatory conditions, leads to corneal opacity and sight-loss. Such corneal opacities are a leading cause of blindness, according to the WHO. Public health programs target prevention of corneal scarring, but the only curative treatment of established scarring is through transplantation. Although attempts to minimize corneal scarring through aggressive control of infection and inflammation are made, there has been little progress in the development of anti-scarring therapies. This is owing to eye drop formulations using low viscosity or weak gelling materials having short retention times on the ocular surface. In this study, we report an innovative eye drop formulation that has the ability to provide sustained delivery of decorin, an anti-scarring agent. The novelty of this eye drop lies in the method of structuring during manufacture, which creates a material that can transition between solid and liquid states, allowing retention in a dynamic environment being slowly removed through blinking. In a murine model of Pseudomonaskeratitis, applying the eye drop resulted in reductions of corneal opacity within 16 days. More remarkably, the addition of hrDecorin resulted in restoration of corneal epithelial integrity with minimal stromal opacity endorsed by reduced α-smooth muscle actin (αSMA), fibronectin, and laminin levels. We believe that this drug delivery system is an ideal non-invasive anti-fibrotic treatment for patients with microbial keratitis, potentially without recourse to surgery, saving the sight of many in the developing world, where corneal transplantation may not be available.
Non-destructive inspection of food and technical oils by terahertz spectroscopy
Authors: Karaliūnas Mindaugas , Nasser Kinan E. , Urbanowicz Andrzej , Kašalynas Irmantas , Bražinskienė Dalia , Asadauskas Svajus , Valušis Gintaras 
Published: December 2018

AbstractQuality control and non-destructive monitoring are of notable interest of food and pharmaceutical industries. It relies on the ability of non-invasive inspection which can be employed for manufacturing process control. We hereby apply terahertz (THz) time-domain spectroscopy as non-destructive technique to monitor pure and degraded oils as well as hydrocarbon chemicals. Significant differences in the spectra of refractive index (RI) and absorption coefficient arising from the presence of ester linkages in the edible and technical oils were obtained. Explicit increase from 1.38 to 1.5 of the RI in all THz spectrum range was observed in hydrocarbons and mono-functional esters with the increase of molar mass. This fact is in contrast of RI dependence on molar mass in multi-functional esters, such as Adipate or vegetable oils, where it is around 1.54. Degradation products, Oleic Acid (OA) and water in particular, lead only to some changes in absorption coefficient and RI spectra of vegetable oils. We demonstrate that complex colloidal and supramolecular processes, such as dynamics of inverse micelles and oil hydrolysis, take part during oil degradation and are responsible for non-uniform dependence of optical properties on extent of degradation.
Freestanding Three-Dimensional CuO/NiO Core–Shell Nanowire Arrays as High-Performance Lithium-Ion Battery Anode
Authors: Cheng Yin-Wei , Chen Chun-Hung , Yang Shu-Wei , Li Yi-Chang , Peng Bo-Liang , Chang Chia-Chin , Wang Ruey-Chi , Liu Chuan-Pu 
Published: December 2018

AbstractWe demonstrate significant improvement of CuO nanowire arrays as anode materials for lithium ion batteries by coating with thin NiO nanosheets conformally. The NiO nanosheets were designed two kinds of morphologies, which are porous and non-porous. By the NiO nanosheets coating, the major active CuO nanowires were protected from direct contact with the electrolyte to improve the surface chemical stability. Simultaneously, through the observation and comparison of TEM results of crystalline non-porous NiO nanosheets, before and after lithiation process, we clearly prove the effect of expected protection of CuO, and clarify the differences of phase transition, crystallinity change, ionic conduction and the mechanisms of the capacity decay further. Subsequently, the electrochemical performances exhibit lithiation and delithiation differences of the porous and non-porous NiO nanosheets, and confirm that the presence of the non-porous NiO coating can still effectively assist the diffusion of Li+ ions into the CuO nanowires, maintaining the advantage of high surface area, and improves the cycle performance of CuO nanowires, leading to enhanced battery capacity. Optimally, the best structure is validated to be non-porous NiO nanosheets, in contrary to the anticipated porous NiO nanosheets. In addition, considering the low cost and facile fabrication process can be realized further for practical applications.
Expression of the human antimicrobial peptide β-defensin-1 is repressed by the EGFR-ERK-MYC axis in colonic epithelial cells
Authors: Bonamy Clément , Sechet Emmanuel , Amiot Aurélien , Alam Antoine , Mourez Michael , Fraisse Laurent , Sansonetti Philippe J. , Sperandio Brice 
Published: December 2018

AbstractThe human β-defensin-1 (HBD1) is an antimicrobial peptide constitutively expressed by epithelial cells at mucosal surfaces. In addition to its microbicidal properties, the loss of HBD1 expression in several cancers suggests that it may also have an anti-tumor activity. Here, we investigated the link between HBD1 expression and cancer signaling pathways in the human colon cancer cell lines TC7 and HT-29, and in normal human colonic primary cells, using a mini-gut organoid model. Using available datasets from patient cohorts, we found that HBD1 transcription is decreased in colorectal cancer. We demonstrated that inhibiting the Epidermal Growth Factor Receptor (EGFR) increased HBD1 expression, whereas activating EGFR repressed HBD1 expression, through the MEKK1/2-ERK1/2 pathway that ultimately regulates MYC. We finally present evidences supporting a role of MYC, together with the MIZ1 coregulator, in HBD1 regulation. Our work uncovers the role and deciphers the function of the EGFR-ERK-MYC axis as a repressor of HBD1 expression and contributes to the understanding of HBD1 suppression observed in colorectal cancer.
A single-cell micro-trench platform for automatic monitoring of cell division and apoptosis after chemotherapeutic drug administration
Authors: Chatzopoulou E. I. , Raharja-Liu P. , Murschhauser A. , Sekhavati F. , Buggenthin F. , Vollmar A. M. , Marr C. , Rädler J. O. 
Published: December 2018

AbstractCells vary in their dynamic response to external stimuli, due to stochastic fluctuations and non-uniform progression through the cell cycle. Hence, single-cell studies are required to reveal the range of heterogeneity in their responses to defined perturbations, which provides detailed insight into signaling processes. Here, we present a time-lapse study using arrays of micro-trenches to monitor the timing of cell division and apoptosis in non-adherent cells at the single-cell level. By employing automated cell tracking and division detection, we precisely determine cell cycle duration and sister-cell correlations for hundreds of individual cells in parallel. As a model application we study the response of leukemia cells to the chemostatic drug vincristine as a function of cell cycle phase. The time-to-death after drug addition is found to depend both on drug concentration and cell cycle phase. The resulting timing and dose-response distributions were reproduced in control experiments using synchronized cell populations. Interestingly, in non-synchronized cells, the time-to-death intervals for sister cells appear to be correlated. Our study demonstrates the practical benefits of micro-trench arrays as a platform for high-throughput, single-cell time-lapse studies on cell cycle dependence, correlations and cell fate decisions in general.
Toll-Like Receptor-4 Disruption Suppresses Adipose Tissue Remodeling and Increases Survival in Cancer Cachexia Syndrome
Authors: Henriques Felipe , Lopes Magno A. , Franco Felipe O. , Knobl Pamela , Santos Kaltinaitis B. , Bueno Luana L. , Correa Victor A. , Bedard Alexander H. , Guilherme Adilson , Birbrair Alexander , Peres Sidney B. , Farmer Stephen R. , Batista Miguel L. 
Published: December 2018

AbstractCancer-induced cachexia, characterized by systemic inflammation, body weight loss, adipose tissue (AT) remodeling and muscle wasting, is a malignant metabolic syndrome with undefined etiology. Here, we show that both genetic ablation and pharmacological inhibition of TLR4 were able to attenuate the main clinical markers of cachexia in mice bearing Lewis lung carcinoma (LLC). AT remodelling was not found in LLC tumor-bearing (TB) TLR4−/−mice due to reduced macrophage infiltration and adipocyte atrophy. TLR4−/−mice were also resistant to cold-induced browning of subcutaneous AT (scAT). Importantly, pharmacological inhibition of TLR4 (Atorvastatin) reproduced the main protective effect against AT remodeling found in TLR4−/−TB mice. Moreover, the treatment was effective in prolonging survival and attenuating tumor mass growth when compared to non-treated-TB animals. Furthermore, tumor-induced elevation of circulating pro-inflammatory cytokines was similarly abolished in both genetic ablation and pharmacological inhibition of TLR4. These data suggest that TLR4 is a critical mediator and a promising target for novel anti-cachexia therapies.
Identification of specialized pro-resolving mediator clusters from healthy adults after intravenous low-dose endotoxin and omega-3 supplementation: a methodological validation
Authors: Norris Paul C. , Skulas-Ray Ann C. , Riley Ian , Richter Chesney K. , Kris-Etherton Penny M. , Jensen Gordon L. , Serhan Charles N. , Maddipati Krishna Rao 
Published: December 2018

AbstractSpecialized pro-resolving mediator(s) (SPMs) are produced from the endogenous ω-3 polyunsaturated fatty acids (PUFA), eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), and accelerate resolution of acute inflammation. We identified specific clusters of SPM in human plasma and serum using LC-MS/MS based lipid mediator (LM) metabololipidomics in two separate laboratories for inter-laboratory validation. The human plasma cluster consisted of resolvin (Rv)E1, RvD1, lipoxin (LX)B4, 18-HEPE, and 17-HDHA, and the human serum cluster consisted of RvE1, RvD1, AT-LXA4, 18-HEPE, and 17-HDHA. Human plasma and serum SPM clusters were increased after ω-3 supplementation (triglyceride dietary supplements or prescription ethyl esters) and low dose intravenous lipopolysaccharide (LPS) challenge. These results were corroborated by parallel determinations with the same coded samples in a second, separate laboratory using essentially identical metabololipidomic operational parameters. In these healthy subjects, two ω-3 supplementation protocols (Study A and Study B) temporally increased the SPM cluster throughout the endotoxin-challenge time course. Study A and Study B were randomized and Study B also had a crossover design with placebo and endotoxin challenge. Endotoxin challenge temporally regulated lipid mediator production in human serum, where pro-inflammatory eicosanoid (prostaglandins and thromboxane) concentrations peaked by 8 hours post-endotoxin and SPMs such as resolvins and lipoxins initially decreased by 2 h and were then elevated at 24 hours. In healthy adults given ω-3 supplementation, the plasma concentration of the SPM cluster (RvE1, RvD1, LXB4, 18-HEPE, and 17-HDHA) peaked at two hours post endotoxin challenge. These results from two separate laboratories with the same samples provide evidence for temporal production of specific pro-resolving mediators with ω-3 supplementation that together support the role of SPM in vivo in inflammation-resolution in humans.