bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel quantification-driven proteomic strategy identifies an endogenous peptide of pleiotrophin as a new biomarker of Alzheimer’s disease
Authors: Skillbäck Tobias , Mattsson Niklas , Hansson Karl , Mirgorodskaya Ekaterina , Dahlén Rahil , van der Flier Wiesje , Scheltens Philip , Duits Floor , Hansson Oskar , Teunissen Charlotte , Blennow Kaj , Zetterberg Henrik , Gobom Johan 
Published: October 2017

AbstractWe present a new, quantification-driven proteomic approach to identifying biomarkers. In contrast to the identification-driven approach, limited in scope to peptides that are identified by database searching in the first step, all MS data are considered to select biomarker candidates. The endopeptidome of cerebrospinal fluid from 40 Alzheimer’s disease (AD) patients, 40 subjects with mild cognitive impairment, and 40 controls with subjective cognitive decline was analyzed using multiplex isobaric labeling. Spectral clustering was used to match MS/MS spectra. The top biomarker candidate cluster (215% higher in AD compared to controls, area under ROC curve = 0.96) was identified as a fragment of pleiotrophin located near the protein’s C-terminus. Analysis of another cohort (n = 60 over four clinical groups) verified that the biomarker was increased in AD patients while no change in controls, Parkinson’s disease or progressive supranuclear palsy was observed. The identification of the novel biomarker pleiotrophin 151–166 demonstrates that our quantification-driven proteomic approach is a promising method for biomarker discovery, which may be universally applicable in clinical proteomics.
Measuring the Poisson’s Ratio of Fibronectin Using Engineered Nanofibers
Authors: Szymanski John M. , Zhang Kairui , Feinberg Adam W. 
Published: October 2017

AbstractThe extracellular matrix (ECM) is a fibrillar protein-based network, the physical and chemical properties of which can influence a multitude of cellular processes. Despite having an important role in cell and tissue signaling, a complete chemo-mechanical characterization of ECM proteins such as fibronectin (FN) is lacking. In this study, we engineered monodisperse FN nanofibers using a surface-initiated assembly technique in order to provide new insight into the elastic behavior of this material over large deformations. FN nanofibers were patterned on surfaces in a pre-stressed state and when released from the surface underwent rapid contraction. We found that the FN nanofibers underwent 3.3-fold and 9-fold changes in length and width, respectively, and that the nanofiber volume was conserved. Volume was also conserved following uniaxial extension of the FN nanofibers of ~2-fold relative to the patterned state. This data suggests that the FN networks we engineered formed an incompressible material with a Poisson’s ratio of ~0.5. While the Poisson’s ratio of cells and other biological materials are widely estimated as 0.5, our experimental results demonstrate that for FN networks this is a reasonable approximation.
From EST to novel spider silk gene identification for production of spidroin-based biomaterials
Authors: Huang Weidong , Zhang Yan , Chen Yifan , Wang Yin , Yuan Wensu , Zhang Ning , Lam Toong Jin , Gong Zhiyuan , Yang Daiwen , Lin Zhi 
Published: October 2017

AbstractA cDNA library from a pool of all the seven silk glands from a tropical spider species was constructed. More than 1000 expressed sequence tag (EST) clones were created. Almost 65% of the EST clones were identified and around 50% were annotated. The cellular and functional distribution of the EST clones indicated high protein synthesis activity in spider silk glands. Novel clones with repetitive amino acid sequences, which is one of the most important characteristics of spider silk genes, were isolated. One of these clones, namely TuSp2 in current research, contains two almost identical fragments with one short C-terminal domain. Reverse transcription (RT) PCR and expression analysis showed that it is expressed in the tubuliform gland and involved in eggcase silk formation. Furthermore, its single repetitive domain can be induced to form various types of materials, including macroscopic fibers, transparent film and translucent hydrogel. This study implies promising potentials for future identification of novel spidroins and development of new spidroin-based biomaterials.
The potential of liquid biopsies for the early detection of cancer
Authors: Heitzer Ellen , Perakis Samantha , Geigl Jochen B. , Speicher Michael R. 
Published: October 2017

AbstractPrecision medicine refers to the choosing of targeted therapies based on genetic data. Due to the increasing availability of data from large-scale tumor genome sequencing projects, genome-driven oncology may have enormous potential to change the clinical management of patients with cancer. To this end, components of tumors, which are shed into the circulation, i.e., circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), or extracellular vesicles, are increasingly being used for monitoring tumor genomes. A growing number of publications have documented that these “liquid biopsies” are informative regarding response to given therapies, are capable of detecting relapse with lead time compared to standard measures, and reveal mechanisms of resistance. However, the majority of published studies relate to advanced tumor stages and the use of liquid biopsies for detection of very early malignant disease stages is less well documented. In early disease stages, strategies for analysis are in principle relatively similar to advanced stages. However, at these early stages, several factors pose particular difficulties and challenges, including the lower frequency and volume of aberrations, potentially confounding phenomena such as clonal expansions of non-tumorous tissues or the accumulation of cancer-associated mutations with age, and the incomplete insight into driver alterations. Here we discuss biology, technical complexities and clinical significance for early cancer detection and their impact on precision oncology.
Oxidation behavior of silicon nitride fibers obtained from polycarbosilane fibers via electron beam irradiation curing
Authors: Sun X. , Liu H. T. , Cheng H. F. 
Published: October 2017

Near-stoichiometric silicon nitride (Si3N4) fibers, which were successfully prepared from polycarbosilane fibers via electron beam irradiation curing, were heat-treated at elevated temperature for 2 h in the air atmosphere.
Circumstellar ammonia in oxygen-rich evolved stars
Authors: Wong K. T. , Menten K. M. , Kamiński T. , Wyrowski F. , Lacy J. H. , Greathouse T. K. 
Published: October 2017

Context. The circumstellar ammonia (NH3) chemistry in evolved stars is poorly understood. Previous observations and modelling showed that NH3 abundance in oxygen-rich stars is several orders of magnitude above that predicted by equilibrium chemistry.Aims. We would like to characterise the spatial distribution and excitation of NH3 in the oxygen-rich circumstellar envelopes (CSEs) of four diverse targets: IK Tau, VY CMa, OH 231.8+4.2, and IRC +10420.
Methods. We observed NH3 emission from the ground state in the inversion transitions near 1.3 cm with the Very Large Array (VLA) and submillimetre rotational transitions with the Heterodyne Instrument for the Far-Infrared (HIFI) aboard Herschel Space Observatory from all four targets. For IK Tau and VY CMa, we observed NH3 rovibrational absorption lines in the ν2 band near 10.5 μm with the Texas Echelon Cross Echelle Spectrograph (TEXES) at the NASA Infrared Telescope Facility (IRTF). We also attempted to search for the rotational transition within the excited vibrational state (v2 = 1) near 2 mm with the IRAM 30m Telescope. Non-LTE radiative transfer modelling, including radiative pumping to the vibrational state, was carried out to derive the radial distribution of NH3 in the CSEs of these targets.
Results. We detected NH3 inversion and rotational emission in all four targets. IK Tau and VY CMa show blueshifted absorption in the rovibrational spectra. We did not detect vibrationally excited rotational transition from IK Tau. Spatially resolved VLA images of IK Tau and IRC +10420 show clumpy emission structures; unresolved images of VY CMa and OH 231.8+4.2 indicate that the spatial-kinematic distribution of NH3 is similar to that of assorted molecules, such as SO and SO2, that exhibit localised and clumpy emission. Our modelling shows that the NH3 abundance relative to molecular hydrogen is generally of the order of 10−7, which is a few times lower than previous estimates that were made without considering radiative pumping and is at least ten times higher than that in the carbon-rich CSE of IRC +10216. NH3 in OH 231.8+4.2 and IRC +10420 is found to emit in gas denser than the ambient medium. Incidentally, we also derived a new period of IK Tau from its V-band light curve.
Conclusions. NH3 is again detected in very high abundance in evolved stars, especially the oxygen-rich ones. Its emission mainly arises from localised spatial-kinematic structures that are probably denser than the ambient gas. Circumstellar shocks in the accelerated wind may contribute to the production of NH3. Future mid-infrared spectroscopy and radio imaging studies are necessary to constrain the radii and physical conditions of the formation regions of NH3.
Transpancreatic precut papillotomy versus double-guidewire technique in difficult biliary cannulation: prospective randomized study
Authors: Sugiyama Harutoshi , Tsuyuguchi Toshio , Sakai Yuji , Mikata Rintaro , Yasui Shin , Watanabe Yuto , Sakamoto Dai , Nakamura Masato , Nishikawa Takao 
Published: October 2017

Abstract
Background and study aims Difficult biliary cannulation and unintentional pancreatic duct cannulation are thought to be important contributors to pancreatitis occurring after endoscopic retrograde cholangiopancreatography. Our aim was to compare and evaluate the rates of success and complications of transpancreatic precut papillotomy (TPPP) and the double-guidewire technique (DGT), both with prophylactic pancreatic stenting.
Patients and methods From April 2011 to March 2014, patients with difficult biliary cannulation, in whom we planned to first position a guidewire in the pancreatic duct, were enrolled, and 68 patients were prospectively randomly allocated to two groups (TPPP 34, DGT 34). We evaluated the rates of success and complications for each group.
Results TPPP had a significantly higher success rate (94.1 %) than DGT (58.8 %). The rate of post-ERCP pancreatitis was 2.9 % in both groups. There was no significant difference between the two groups in the overall rate of complications related to cannulation.
Conclusion If biliary cannulation cannot be achieved, TPPP should be selected first after unintentional pancreatic duct cannulation.University Hospital Medical Information Network identifier: UMIN000008200
Cold-forceps avulsion with adjuvant snare-tip soft coagulation (CAST) is an effective and safe strategy for the management of non-lifting large laterally spreading colonic lesions
Authors: Tate David , Bahin Farzan , Desomer Lobke , Sidhu Mayenaaz , Gupta Vikas , Bourke Michael 
Published: October 2017

Abstract
Background and aims Non-lifting large laterally spreading colorectal lesions (LSLs) are challenging to resect endoscopically and often necessitate surgery. A safe, simple technique to treat non-lifting LSLs endoscopically with robust long-term outcomes has not been described.
Methods In this single-center prospective observational study of consecutive patients referred for endoscopic mucosal resection (EMR) of LSLs ≥ 20 mm, LSLs not completely resectable by snare because of non-lifting underwent standardized completion of resection with cold-forceps avulsion and adjuvant snare-tip soft coagulation (CAST). Scheduled surveillance colonoscopies were performed at 4 – 6 months (SC1) and 18 months (SC2). Primary outcomes were endoscopic evidence of adenoma clearance and avoidance of surgery. The secondary outcome was safety.
Results From January 2012 to October 2016, 540 lifting LSLs (82.2 %) underwent complete snare excision at EMR. CAST was required for complete removal in 101 non-lifting LSLs (17.8 %): 63 naïve non-lifting lesions (NNLs; 62.7 %) and 38 previously attempted non-lifting lesions (PANLs; 37.3 %). PANLs were smaller (P < 0.001) and more likely to be non-granular (P = 0.001) than the lifting LSLs. NNLs were of similar size (P = 0.77) and morphology (P = 0.10) to the lifting LSLs. CAST was successful in all cases and adverse events were comparable to lifting LSLs resected by complete snare excision. Recurrence at SC1 was comparable for PANLs (15.2 %) and lifting LSLs (15.3 %; P = 0.99), whereas NNLs recurred more frequently (27.5 %; P = 0.049); however, surgery was no more common for either type of non-lifting LSL than for lifting LSLs.
Conclusion CAST is a safe, effective, and surgery-sparing therapy for the majority of non-lifting LSLs. It is easy to use, inexpensive, and does not require additional equipment.Clinicaltrials.gov: NCT 2000141
Fishery and Hatchery Effects on an Endangered Salmon Population with Low Productivity
Authors: Winship1 Arliss J. , O'Farrell Michael R. , Mohr Michael S. 
Published: October 2017

AbstractWe estimated the natural spawner–fry stock–recruitment relationship and juvenile survival rates for Sacramento River winter Chinook Salmon Oncorhynchus tshawytscha in California and used these estimates to examine the expected numbers of spawners and fishing mortality under different fishing mortality rates and levels of hatchery supplementation. A stochastic, age‐structured population dynamics model was fit to fry and female spawner abundance data for the years 1996–2010. Estimated survival rates of fry through the end of the first year in the ocean were generally <0.5%. Estimated survival rates of hatchery‐origin fish from egg to the end of the first year in the ocean were on average about four times greater than the estimated maximum rate for natural‐origin fish. The hatchery program was estimated to increase the number of spawners returning to natural spawning areas and thereby increase the fishing mortality rate that could be sustained. Assessing the past or future net effect of the hatchery on the size of the natural population would require quantifying any potential reduction in the productivity of the natural population as a result of reduced fitness of hatchery‐origin fish spawning in natural spawning areas.Received February 21, 2013; accepted December 14, 2013.
Is Mobility a Fixed Trait? Summer Movement Patterns of Catostomids using PIT Telemetry
Authors: Booth Michael T. , Flecker Alexander S. , Hairston Nelson G. 
Published: October 2017

AbstractFish populations are composed of a mixture of sedentary and mobile individuals, but it is not clear whether movement behavior is plastic or fixed for individuals and what proportion of the population exhibits mobile behavior. To investigate the mobility and movement patterns of two common species of suckers, the Sonora Sucker Catostomus insignis and the Desert Sucker Catostomus clarkii, in the Gila River of western New Mexico, we tracked 449 individuals over three summers using passive integrated transponder (PIT) telemetry. Both species were mobile and the typical linear home ranges for mobile individuals exceeded 150 m, but approximately 25% of individuals were detected only in a single habitat segment. We observed increased movement after spates caused by summer monsoon rains, and fish used areas of the stream differently under high‐ and low‐flow conditions. Fish moved farther between years than within years, but a subset of individuals were found in the same locations from year to year. For the study species, movement behavior does not appear to be a fixed trait for individuals, and many individuals exhibited both stationary and mobile behavior among years. We also investigated whether sample size biased the estimates of movement parameters. We concluded that movement parameters would be underestimated by 20–50% if we had tracked fewer individuals, but the degree to which the parameters were biased varied from year to year.Received August 7, 2013; accepted January 23, 2014
Relationship between Juvenile Fish Condition and Survival to Adulthood in Steelhead
Authors: Evans A. F. , Hostetter N. J. , Collis K. , Roby D. D. , Loge F. J. 
Published: October 2017

AbstractUnderstanding how individual characteristics are associated with survival is important to programs aimed at recovering fish populations of conservation concern. To evaluate whether individual fish characteristics observed during the juvenile life stage were associated with the probability of returning as an adult, juvenile steelhead Oncorhynchus mykiss from two distinct population segments (DPSs; Snake River and upper Columbia River) were captured, photographed to determine external condition (body injuries, descaling, signs of disease, fin damage, and ectoparasites), measured, classified by rearing type (hatchery, wild), marked with a PIT tag, and released to continue out‐migration to the Pacific Ocean during 2007–2010. The PIT tags of returning adults were interrogated in fishways at hydroelectric dams on the lower Columbia River 1–3 years following release as juveniles. Juvenile‐to‐adult survival models were investigated independently for each DPS and indicated that similar individual fish characteristics were important predictors of survival to adulthood for both steelhead populations. The data analysis provided strong support for survival models that included explanatory variables for fish length, rearing type, and external condition, in addition to out‐migration year and timing. The probability of a juvenile surviving to adulthood was positively related to length and was higher for wild fish compared with hatchery fish. Survival was lower for juveniles with body injuries, fin damage, and external signs of disease. Models that included variables for descaling and ectoparasite infestation, however, had less support than those that incorporated measures of body injuries, fin damage, and disease. Overall, results indicated that individual fish characteristics recorded during the juvenile life stage can be used to predict adult survivorship in multiple steelhead populations.Received August 20, 2013; accepted February 14, 2014
Fine‐Scale Movements and Home Ranges of Red Snapper around Artificial Reefs in the Northern Gulf of Mexico
Authors: Piraino Maria N. , Szedlmayer Stephen T. 
Published: October 2017

AbstractRed Snapper Lutjanus campechanus are generally associated with artificial reef habitats in the northern Gulf of Mexico, but whether this association results in fish production is still controversial. Information on fine‐scale habitat use patterns would be helpful in evaluating this. Little is known about the fine‐scale movement patterns of Red Snapper around artificial reefs. The present study examined fine‐scale (∼1‐m accuracy) movements of Red Snapper with the Vemco VR2W Positioning System. This system enabled continuous monitoring of tagged fish from 100 to 694 d. Locations of individual fish were recorded approximately every 10 min and totaled over 1.9 million accurate locations of Red Snapper from August 2010 through May 2012. Red Snapper showed close association with the reef structure (mean ± SD distance = 26.3 ± 35.4 m) but differential habitat use in relation to both diel and seasonal periods. Home range areas (95% kernel density estimates [KDE]) were significantly larger during day than night periods and showed the lowest area use at dawn and dusk. Monthly home ranges (95% KDE) and core areas (50% KDE) were significantly larger in spring, summer, and fall than in winter and were significantly correlated with water temperature, suggesting colder winter temperatures reduced Red Snapper movement. Home range area was significantly correlated with fish size (407–590 mm standard length), and the fish in this study showed the highest site fidelity (88% still present after >10 months) of any Red Snapper in other previous studies. Red Snapper also showed use of multiple reefs within the monitoring area, as home ranges (95% KDE) showed a second peak around other artificial reefs. The high site fidelity, long‐term use, and concentrated use of multiple artificial reefs confirm the importance of structured habitat for Red Snapper.Received September 1, 2013; accepted February 27, 2014
Sampling Little Fish in Big Rivers: Larval Fish Detection Probabilities in Two Lake Erie Tributaries and Implications for Sampling Effort and Abundance Indices
Authors: Pritt Jeremy J. , DuFour Mark R. , Mayer Christine M. , Roseman Edward F. , DeBruyne Robin L. 
Published: October 2017

AbstractLarval fish are frequently sampled in coastal tributaries to determine factors affecting recruitment, evaluate spawning success, and estimate production from spawning habitats. Imperfect detection of larvae is common, because larval fish are small and unevenly distributed in space and time, and coastal tributaries are often large and heterogeneous. We estimated detection probabilities of larval fish from several taxa in the Maumee and Detroit rivers, the two largest tributaries of Lake Erie. We then demonstrated how accounting for imperfect detection influenced (1) the probability of observing taxa as present relative to sampling effort and (2) abundance indices for larval fish of two Detroit River species. We found that detection probabilities ranged from 0.09 to 0.91 but were always less than 1.0, indicating that imperfect detection is common among taxa and between systems. In general, taxa with high fecundities, small larval length at hatching, and no nesting behaviors had the highest detection probabilities. Also, detection probabilities were higher in the Maumee River than in the Detroit River. Accounting for imperfect detection produced up to fourfold increases in abundance indices for Lake Whitefish Coregonus clupeaformis and Gizzard Shad Dorosoma cepedianum. The effect of accounting for imperfect detection in abundance indices was greatest during periods of low abundance for both species. Detection information can be used to determine the appropriate level of sampling effort for larval fishes and may improve management and conservation decisions based on larval fish data.Received August 12, 2013; accepted March 7, 2014
Fishway Bottleneck Relief Models: a Case Study using Radio‐Tagged Pacific Lampreys
Authors: Keefer Matthew L. , Caudill Christopher C. , Moser Mary L. 
Published: October 2017

AbstractStructural or operational changes to fishways can improve fish passage efficiency, but there is often uncertainty regarding which improvements will be most effective. We developed a “bottleneck relief” model using Kaplan–Meier methods to help managers assess where remediation efforts are likely to provide the largest increases in fishway passage. The simulation model uses a matrix of observed efficiency estimates from fishway subsections and incorporates multiple passage attempts by individual tagged fish. In a case study application to test the model, we used radiotelemetry data from 2,170 adult Pacific Lampreys Entosphenus tridentatus at Bonneville Dam (Columbia River, Washington–Oregon), which features multiple fishways and low lamprey passage success (mean fishway passage efficiency ∼0.50; n = 10 years). The model was run iteratively to test potential dam passage benefits from improving efficiency in 20 individual fishway segments. The highest benefits were for improvements at top‐of‐fishway segments and at sites where passage routes converged. Benefits were lower for segments used by fewer fish, segments located downstream from serious bottlenecks, and segments with a limited scope for improvement (i.e., efficiency was already high). The model provides a flexible and objective method for assessing complex fish passage problems and informing remediation decision making.Received December 19, 2013; accepted March 11, 2014