bluuebunny/crossref_metadata_2025_split huggingface dataset:
Attosecond electronic and nuclear quantum photodynamics of ozone monitored with time and angle resolved photoelectron spectra
Authors: Decleva Piero , Quadri Nicola , Perveaux Aurelie , Lauvergnat David , Gatti Fabien , Lasorne Benjamin , Halász Gábor J. , Vibók Ágnes 
Published: November 2016

AbstractRecently we reported a series of numerical simulations proving that it is possible in principle to create an electronic wave packet and subsequent electronic motion in a neutral molecule photoexcited by a UV pump pulse within a few femtoseconds. We considered the ozone molecule: for this system the electronic wave packet leads to a dissociation process. In the present work, we investigate more specifically the time-resolved photoelectron angular distribution of the ozone molecule that provides a much more detailed description of the evolution of the electronic wave packet. We thus show that this experimental technique should be able to give access to observing in real time the creation of an electronic wave packet in a neutral molecule and its impact on a chemical process.
PEPlife: A Repository of the Half-life of Peptides
Authors: Mathur Deepika , Prakash Satya , Anand Priya , Kaur Harpreet , Agrawal Piyush , Mehta Ayesha , Kumar Rajesh , Singh Sandeep , Raghava Gajendra P. S. 
Published: November 2016

AbstractShort half-life is one of the key challenges in the field of therapeutic peptides. Various studies have reported enhancement in the stability of peptides using methods like chemical modifications, D-amino acid substitution, cyclization, replacement of labile aminos acids, etc. In order to study this scattered data, there is a pressing need for a repository dedicated to the half-life of peptides. To fill this lacuna, we have developed PEPlife (http://crdd.osdd.net/raghava/peplife), a manually curated resource of experimentally determined half-life of peptides. PEPlife contains 2229 entries covering 1193 unique peptides. Each entry provides detailed information of the peptide, like its name, sequence, half-life, modifications, the experimental assay for determining half-life, biological nature and activity of the peptide. We also maintain SMILES and structures of peptides. We have incorporated web-based modules to offer user-friendly data searching and browsing in the database. PEPlife integrates numerous tools to perform various types of analysis such as BLAST, Smith-Waterman algorithm, GGSEARCH, Jalview and MUSTANG. PEPlife would augment the understanding of different factors that affect the half-life of peptides like modifications, sequence, length, route of delivery of the peptide, etc. We anticipate that PEPlife will be useful for the researchers working in the area of peptide-based therapeutics.
Structural evolution of nanoscale metallic glasses during high-pressure torsion: A molecular dynamics analysis
Authors: Feng S. D. , Jiao W. , Jing Q. , Qi L. , Pan S. P. , Li G. , Ma M. Z. , Wang W. H. , Liu R. P. 
Published: November 2016

AbstractStructural evolution in nanoscale Cu50Zr50metallic glasses during high-pressure torsion is investigated using molecular dynamics simulations. Results show that the strong cooperation of shear transformations can be realized by high-pressure torsion in nanoscale Cu50Zr50metallic glasses at room temperature. It is further shown that high-pressure torsion could prompt atoms to possess lower five-fold symmetries and higher potential energies, making them more likely to participate in shear transformations. Meanwhile, a higher torsion period leads to a greater degree of forced cooperative flow. And the pronounced forced cooperative flow at room temperature under high-pressure torsion permits the study of the shear transformation, its activation and characteristics, and its relationship to the deformations behaviors. This research not only provides an important platform for probing the atomic-level understanding of the fundamental mechanisms of high-pressure torsion in metallic glasses, but also leads to higher stresses and homogeneous flow near lower temperatures which is impossible previously.
On the behaviour of lung tissue under tension and compression
Authors: Andrikakou Pinelopi , Vickraman Karthik , Arora Hari 
Published: November 2016

AbstractLung injuries are common among those who suffer an impact or trauma. The relative severity of injuries up to physical tearing of tissue have been documented in clinical studies. However, the specific details of energy required to cause visible damage to the lung parenchyma are lacking. Furthermore, the limitations of lung tissue under simple mechanical loading are also not well documented. This study aimed to collect mechanical test data from freshly excised lung, obtained from both Sprague-Dawley rats and New Zealand White rabbits. Compression and tension tests were conducted at three different strain rates: 0.25, 2.5 and 25 min−1. This study aimed to characterise the quasi-static behaviour of the bulk tissue prior to extending to higher rates. A nonlinear viscoelastic analytical model was applied to the data to describe their behaviour. Results exhibited asymmetry in terms of differences between tension and compression. The rabbit tissue also appeared to exhibit stronger viscous behaviour than the rat tissue. As a narrow strain rate band is explored here, no conclusions are being drawn currently regarding the rate sensitivity of rat tissue. However, this study does highlight both the clear differences between the two tissue types and the important role that composition and microstructure can play in mechanical response.
α-MSH and Foxc2 promote fatty acid oxidation through C/EBPβ negative transcription in mice adipose tissue
Authors: Gan Lu , Liu Zhenjiang , Chen Yizhe , Dan Luo  , Feng Fei , Liu Guannv , Sun Chao 
Published: November 2016

AbstractAlpha melanocyte stimulating hormone (α-MSH) and Forkhead box C2 protein (Foxc2) enhance lipolysis in multiple tissues. However, their relationship in adipose fatty acid oxidation (FAO) remains unclear. Here, we demonstrated that α-MSH and Foxc2 increased palmitate oxidation to CO2 in white (WAT) and brown adipose tissue (BAT). C/EBPβ expression was reduced by α-MSH and Foxc2. FFA level was elevated by α-MSH and pc-Foxc2 treatment along with increased FAO in white and brown adipocytes. The expression of FAO key enzymes, medium-chain acyl-CoA dehydrogenase (MCAD) and long-chain acyl-CoA dehydrogenase (LCAD) were increased in α-MSH and pc-Foxc2 group. Combination of α-MSH and Foxc2 treatment synergistically promoted FAO through increasing the activity of CPT-1 and phosphorylation of ACC. We found C/EBPβ bind to MC5R and Foxc2 promoter regions and inhibited FAO. cAMP level was increased by α-MSH and Foxc2 individually treated or combined treatment. Furthermore, cAMP/PKA pathway-specific inhibitor (H89) blocked the FAO, despite in α-MSH and Foxc2 both added group. While forskolin, the cAMP agonist, promoted FAO and enhanced the effect of α-MSH and Foxc2. Collectively, α-MSH and Foxc2 mutual promote FAO in WAT and BAT via cAMP/PKA signal pathway. And C/EBPβ as a transcription suppressor inhibits α-MSH and Foxc2 expression and FAO.
Power-law rheology controls aftershock triggering and decay
Authors: Zhang Xiaoming , Shcherbakov Robert 
Published: November 2016

AbstractThe occurrence of aftershocks is a signature of physical systems exhibiting relaxation phenomena. They are observed in various natural or experimental systems and usually obey several non-trivial empirical laws. Here we consider a cellular automaton realization of a nonlinear viscoelastic slider-block model in order to infer the physical mechanisms of triggering responsible for the occurrence of aftershocks. We show that nonlinear viscoelasticity plays a critical role in the occurrence of aftershocks. The model reproduces several empirical laws describing the statistics of aftershocks. In case of earthquakes, the proposed model suggests that the power-law rheology of the fault gauge, underlying lower crust, and upper mantle controls the decay rate of aftershocks. This is verified by analysing several prominent aftershock sequences for which the rheological properties of the underlying crust and upper mantle were established.
Protective effect of Cl-amidine against CLP-induced lethal septic shock in mice
Authors: Zhao Ting , Pan Baihong , Alam Hasan B. , Liu Baoling , Bronson Roderick T. , Deng Qiufang , Wu Erxi , Li Yongqing 
Published: November 2016

AbstractProduction of innate and adaptive immune cells from hematopoietic stem cells, and maturation of T lymphocytes are effective immune responses to fight severe microbial infection. In sepsis, this emergency myelopoiesis is damaged, leading to failure of bacterial clearance, and excessive stress-induced steroids cause immature T-lymphocyte apoptosis in thymus. We recently found that Cl-amidine, a peptidylarginine deiminase (PAD) inhibitor, improves survival in a mouse model of cecal ligation and puncture (CLP)-induced septic shock. In the present study we investigated how Cl-amidine promotes survival, focusing on protective effects of Cl-amidine on immune response. We confirmed survival-improving effect of Cl-amidine and are the first to explore the role of Cl-amidine in immune response. CLP caused bone marrow (BM) and thymus atrophy, decreased innate immune cells in BM. CLP increased levels of cytokines (IL-1β, IL-6, and TNF-α) and bacteria load in blood/liver. In primary splenocyte culture, lipopolysaccharide increased TNF-α production. In contrast, Cl-amidine attenuated these CLP and lipopolysaccharide-induced alterations. Moreover, Cl-amidine increased circulating monocytes. Collectively, our results demonstrate Cl-amidine plays protective roles by significantly decreasing BM and thymus atrophy, restoring innate immune cells in BM, increasing blood monocytes and blood/liver bacteria clearance, and attenuating pro-inflammatory cytokine production in a murine model of lethal sepsis.
Descriptive epidemiology of prenatal and perinatal risk factors in a Chinese population with reading disorder
Authors: Liu Lingfei , Wang Jia , Shao Shanshan , Luo Xiu , Kong Rui , Zhang Xiaohui , Song Ranran 
Published: November 2016

AbstractSeveral prenatal and perinatal factors have been found to be associated with developmental dyslexia (reading disorder) in alphabetic language. Given the absence of relevant studies of Chinese children, the present study tries to investigate these risk factors. A total of 45,850 students were recruited from grades three to six, from seven cities of Hubei province. Dyslexia in Chinese was diagnosed based on children’s clinical symptoms. The clinical symptoms of children’s reading performance were assessed by Dyslexia Checklist for Chinese Children (DCCC) and Pupil Rating Scale Revised Screening for Learning Disabilities (PRS) which were completed by parent/guardian and header teacher respectively. Chinese language exam was used to screen children with poor reading capacity. Questionnaires about prenatal and perinatal factors were completed by parent or guardian. Among the 34,748 eligible participants, 1,200 (3.45%) were diagnosed with dyslexia in Chinese. More boys suffered from dyslexia than the girls and the gender ratio was 3:1. Family history of neuropsychiatric diseases, maternal infectious diseases, difficult vaginal delivery, preterm birth, and neonatal asphyxia were found to increase the risk of developmental dyslexia in China. Closer longitudinal developmental monitoring and preventive measures should be taken for high risk children.
Circulating neuregulin 4 levels are inversely associated with subclinical cardiovascular disease in obese adults
Authors: Jiang Jie , Lin Mingzhu , Xu Yanfang , Shao Jin , Li Xuejun , Zhang Huijie , Yang Shuyu 
Published: November 2016

AbstractNeuregulin 4 (Nrg4) has been identified as a new secreted adipokine that may protect against development of obesity and metabolic disorders. However, information is not available regarding the association between circulating Nrg4 and subclinical atherosclerosis in humans. We measured serum Nrg4 in 485 obese adult subjects (aged 40 years or older) who had the measurement of carotid intima-media thickness (CIMT) recruited from the community. Individuals with increased CIMT and carotid plaque had lower levels of circulating Nrg4 than controls (p < 0.05). The risks of increased CIMT and atherosclerotic plaque were significantly decreased by 28% and 31% [OR (95% CI): 0.72 (0.53–0.98) and 0.69 (0.50–0.96), respectively], adjusting for age, sex, current smoking, alcohol consumption, physical activity, BMI, systolic BP, fasting glucose, total cholesterol, HDL-c, HOMA-IR, and body fat. Importantly, individuals in the lowest quartile of serum Nrg4 were 3.70 times (p < 0.001) more likely to have increased CIMT and 2.06 times (p < 0.05) more likely to have atherosclerotic plaque than those in the highest quartile in multivariable logistic regression analyses. These findings suggest that circulating Nrg4 concentrations are inversely associated with subclinical atherosclerosis in obese adults, and indicating that circulating Nrg4 might play a role in identifying patients at high risk for CVD.
Circadian rhythms of European and African-Americans after a large delay of sleep as in jet lag and night work
Authors: Eastman Charmane I. , Tomaka Victoria A. , Crowley Stephanie J. 
Published: November 2016

AbstractJet travel and night shift work produce large changes in when people sleep, work and eat; a challenge that was not encountered during most of our evolution. Successful adaptation would require the internal, master, circadian clock to make large phase shifts to reduce the circadian misalignment between circadian rhythms and the times for sleep, work and meals. We compared African-Americans and non-Hispanic European-Americans in how much their circadian clocks shifted after a 9 hour phase delay of the light/dark, sleep/wake and meal schedule, which has similarities to flying west or sleeping in the daytime after night shifts. We also measured their free-running circadian periods using a forced desynchrony protocol with a 5-h day. European-Americans had longer free-running periods and larger phase delays than African-Americans. Correlations (among all subjects, just African-Americans and just European-Americans) showed that longer circadian periods were associated with larger phase delays. Larger phase delays, facilitated by longer circadian periods, reduce jet lag after westward travel and make it easier to work night shifts and sleep during the daytime after night work. On the other hand, a shorter circadian period, which makes one more of a morning-type person, is better for most people given our early-bird dominated society.
Serum neurofilament light protein predicts clinical outcome in traumatic brain injury
Authors: Shahim Pashtun , Gren Magnus , Liman Victor , Andreasson Ulf , Norgren Niklas , Tegner Yelverton , Mattsson Niklas , Andreasen Niels , Öst Martin , Zetterberg Henrik , Nellgård Bengt , Blennow Kaj 
Published: November 2016

AbstractAxonal white matter injury is believed to be a major determinant of adverse outcomes following traumatic brain injury (TBI). We hypothesized that measurement of neurofilament light protein (NF-L), a protein found in long white-matter axons, in blood samples, may serve as a suitable biomarker for neuronal damage in TBI patients. To test our hypotheses, we designed a study in two parts: i) we developed an immunoassay based on Single molecule array technology for quantification of NF-L in blood, and ii) in a proof-of-concept study, we tested our newly developed method on serial serum samples from severe TBI (sTBI) patients (n = 72) and controls (n = 35). We also compared the diagnostic and prognostic utility of NF-L with the established blood biomarker S100B. NF-L levels were markedly increased in sTBI patients compared with controls. NF-L at admission yielded an AUC of 0.99 to detect TBI versus controls (AUC 0.96 for S100B), and increased to 1.00 at day 12 (0.65 for S100B). Importantly, initial NF-L levels predicted poor 12-month clinical outcome. In contrast, S100B was not related to outcome. Taken together, our data suggests that measurement of serum NF-L may be useful to assess the severity of neuronal injury following sTBI.
Response of Imperiled Okaloosa Darters to Stream Restoration
Authors: Reeves David B. , Tate William B. , Jelks Howard L. , Jordan Frank 
Published: November 2016

Abstract
The Okaloosa Darter Etheostoma okaloosae is a small percid endemic to six stream drainages in northwestern Florida. The U.S. Fish and Wildlife Service listed Okaloosa Darters as endangered in 1973 and downlisted them to threatened in 2011 because of habitat improvements and increasing abundance across much of their geographic range. Delisting is possible if remaining recovery criteria are met, including restoration of degraded stream reaches. Impounded reaches of Anderson Branch, Mill Creek, and Toms Creek were restored by removing impediments to water flow, draining impoundments, and reconstructing stream reaches. Restorations of Anderson Branch and Mill Creek were designed to rehabilitate populations of Okaloosa Darters without significantly affecting popular recreational activities at these locations. Restorations were evaluated from 2007 to 2013 by comparing counts of Okaloosa Darters and the composition of microhabitats in restored and nearby undisturbed reference sites. Okaloosa Darters were absent from degraded stream reaches at the beginning of the study, but they rapidly colonized once restorations were completed. Counts of Okaloosa Darters in reference and restoration sites in Anderson Branch were similar by the end of the study, whereas counts in restoration sites were significantly lower than nearby reference sites in Mill and Toms creeks. Restoration sites tended to have lower coverage of sand and root and higher coverage of macrophytes. As riparian vegetation surrounding restoration sites matures to a closed canopy that reduces excessive growth of macrophytes, stream microhabitats and numbers of darters will probably become similar to reference sites. Restoration of degraded stream sites increased abundance and distribution of Okaloosa Darters and reconnected formerly isolated upstream and downstream populations. These projects demonstrated that restoration is a useful conservation tool for imperiled fishes such as Okaloosa Darters and can be undertaken without interfering with popular recreational activities.
Received March 9, 2016; accepted August 15, 2016 Published online November 7, 2016
Survival of and Tag Retention in Southern Redbelly Dace Injected with Two Sizes of PIT Tags
Authors: Pennock Casey A. , Frenette Bryan D. , Waters Micah J. , Gido Keith B. 
Published: November 2016

Abstract
Passive integrated transponder tags are a common method used in fish ecology research, and their feasibility for use has been well studied in salmonids. Several studies suggest that effects of PIT tagging may be species dependent and these effects should be addressed prior to conducting large-scale tagging studies. In a series of laboratory experiments, we tested factors influencing survival and tag retention in Southern Redbelly Dace Chrosomus erythrogaster. In the first experiment, we tested the effects of tagger and fish length on survival and retention over 30 d for dace tagged with 9-mm PIT tags. Survival was high (84%) while retention of tags was low (30%). We detected no significant effect of tagger experience on survival or tag retention. Logistic regression determined that tag retention increased with fish length. A second experiment showed similar trends for survival (80%) and retention of 9-mm tags (25%) as observed in experiment 1, but retention (86%) was significantly higher for dace tagged with 8-mm tags over the same period. All dace in our sham-injection treatment (needle puncture of the peritoneal cavity) survived, eliminating needle puncture as a source of mortality. Our study, combined with a literature review of PIT-tagging studies, suggests that dace and other cyprinids greater than 60 mm can be tagged reliably with 9-mm tags and individuals greater than 50 mm can be tagged with 8-mm tags.
Received March 16, 2016; accepted August 15, 2016Published online November 8, 2016
KODAMA: an R package for knowledge discovery and data mining
Authors: Cacciatore Stefano , Tenori Leonardo , Luchinat Claudio , Bennett Phillip R , MacIntyre David A 
Published: November 2016

Abstract

Summary
KODAMA, a novel learning algorithm for unsupervised feature extraction, is specifically designed for analysing noisy and high-dimensional datasets. Here we present an R package of the algorithm with additional functions that allow improved interpretation of high-dimensional data. The package requires no additional software and runs on all major platforms.

Availability and Implementation
KODAMA is freely available from the R archive CRAN (http://cran.r-project.org). The software is distributed under the GNU General Public License (version 3 or later).

Supplementary information
Supplementary data are available at Bioinformatics online.
Synergistic drug combinations from electronic health records and gene expression
Authors: Low Yen S , Daugherty Aaron C , Schroeder Elizabeth A , Chen William , Seto Tina , Weber Susan , Lim Michael , Hastie Trevor , Mathur Maya , Desai Manisha , Farrington Carl , Radin Andrew A , Sirota Marina , Kenkare Pragati , Thompson Caroline A , Yu Peter P , Gomez Scarlett L , Sledge George W , Kurian Allison W , Shah Nigam H 
Published: November 2016

ABSTRACTObjective: Using electronic health records (EHRs) and biomolecular data, we sought to discover drug pairs with synergistic repurposing potential. EHRs provide real-world treatment and outcome patterns, while complementary biomolecular data, including disease-specific gene expression and drug-protein interactions, provide mechanistic understanding.Method: We applied Group Lasso INTERaction NETwork (glinternet), an overlap group lasso penalty on a logistic regression model, with pairwise interactions to identify variables and interacting drug pairs associated with reduced 5-year mortality using EHRs of 9945 breast cancer patients. We identified differentially expressed genes from 14 case-control human breast cancer gene expression datasets and integrated them with drug-protein networks. Drugs in the network were scored according to their association with breast cancer individually or in pairs. Lastly, we determined whether synergistic drug pairs found in the EHRs were enriched among synergistic drug pairs from gene-expression data using a method similar to gene set enrichment analysis.Results: From EHRs, we discovered 3 drug-class pairs associated with lower mortality: anti-inflammatories and hormone antagonists, anti-inflammatories and lipid modifiers, and lipid modifiers and obstructive airway drugs. The first 2 pairs were also enriched among pairs discovered using gene expression data and are supported by molecular interactions in drug-protein networks and preclinical and epidemiologic evidence.Conclusions: This is a proof-of-concept study demonstrating that a combination of complementary data sources, such as EHRs and gene expression, can corroborate discoveries and provide mechanistic insight into drug synergism for repurposing.