bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cigarette smoke-induced cell death of a spermatocyte cell line can be prevented by inactivating the Aryl hydrocarbon receptor
Authors: Esakky P , Hansen D A , Drury A M , Cusumano A , Moley K H 
Published: October 2015

AbstractCigarette smoke exposure causes germ cell death during spermatogenesis. Our earlier studies demonstrated that cigarette smoke condensate (CSC) causes spermatocyte cell deathin vivoand growth arrest of the mouse spermatocyte cell line (GC-2spd(ts))in vitrovia the aryl hydrocarbon receptor (AHR). We hypothesize here that inactivation of AHR could prevent the CSC-induced cell death in spermatocytes. We demonstrate that CSC exposure generates oxidative stress, which differentially regulates mitochondrial apoptosis in GC-2spd(ts) and wild type (WT) and AHR knockout (AHR-KO) mouse embryonic fibroblasts (MEFs). SiRNA-mediated silencing ofAhraugments the extent of CSC-mediated cellular damage while complementing the AHR-knockout condition. Pharmacological inhibition using the AHR-antagonist (CH223191) modulates the CSC-altered expression of apoptotic proteins and significantly abrogates DNA fragmentation though the cleavage of PARP appears AHR independent. Pretreatment with CH223191 at concentrations above 50 μM significantly prevents the CSC-induced activation of caspase-3/7 and externalization of phosphatidylserine in the plasma membrane. However, MAPK inhibitors alone or together with CH223191 could not prevent the membrane damage upon CSC addition and the caspase-3/7 activation and membrane damage in AHR-deficient MEF indicates the interplay of multiple cell signaling and cytoprotective ability of AHR. Thus the data obtained on one hand signifies the protective role of AHR in maintaining normal cellular homeostasis and the other, could be a potential prophylactic therapeutic target to promote cell survival and growth under cigarette smoke exposed environment by receptor antagonism via CH223191-like mechanism. Antagonist-mediated inactivation of the aryl hydrocarbon receptor blocks downstream events leading to cigarette smoke-induced cell death of a spermatocyte cell line.
Majorana zero modes and topological quantum computation
Authors: Sarma Sankar Das , Freedman Michael , Nayak Chetan 
Published: October 2015

AbstractWe provide a current perspective on the rapidly developing field of Majorana zero modes (MZMs) in solid-state systems. We emphasise the theoretical prediction, experimental realisation and potential use of MZMs in future information processing devices through braiding-based topological quantum computation (TQC). Well-separated MZMs should manifest non-Abelian braiding statistics suitable for unitary gate operations for TQC. Recent experimental work, following earlier theoretical predictions, has shown specific signatures consistent with the existence of Majorana modes localised at the ends of semiconductor nanowires in the presence of superconducting proximity effect. We discuss the experimental findings and their theoretical analyses, and provide a perspective on the extent to which the observations indicate the existence of anyonic MZMs in solid-state systems. We also discuss fractional quantum Hall systems (the 5/2 state), which have been extensively studied in the context of non-Abelian anyons and TQC. We describe proposed schemes for carrying out braiding with MZMs as well as the necessary steps for implementing TQC.
TIFA, an inflammatory signaling adaptor, is tumor suppressive for liver cancer
Authors: Shen W , Chang A , Wang J , Zhou W , Gao R , Li J , Xu Y , Luo X , Xiang R , Luo N , Stupack D G 
Published: October 2015

AbstractTIFA (TNF receptor associated factor (TRAF)-interacting protein with a Forkhead-associated (FHA) domain), also called T2BP, was first identified using a yeast two-hybrid screening. TIFA contains a FHA domain, which directly binds phosphothreonine and phosphoserine, and a consensus TRAF6-binding motif. TIFA-mediated oligomerization and poly-ubiquitinylation of TRAF6 mediates signaling downstream of the Tumor necrosis factor alpha receptor 1 (TNFaR-I) and interleukin-1/Toll-like receptor 4 (TLR4) pathways. Examining TIFA expression in hepatocellular carcinoma (HCC) tissues microarrays, we noted marked decreases TIFA reactivity in tumor versus control samples. In agreement, we found that HCC cell lines show reduced TIFA expression levels versus normal liver controls. Reconstituting TIFA expression in HCC cell lines promoted two independent apoptosis signaling pathways: the induction of p53 and cell cycle arrest, and the activation of caspase-8 and caspase-3. In contrast, the expression of a non-oligomerizing mutant of TIFA impacted cells minimally, and suppression of TIFA expression protected cells from apoptosis. Mice bearing TIFA overexpression hepatocellular xenografts develop smaller tumors versus TIFA mutant tumors; terminal deoxynucleotidyl transferase dUTP nick end labeling staining demonstrates increased cell apoptosis, and decreased proliferation, reflecting cell cycle arrest. Interestingly, p53 has a greater role in decreased proliferation than cell death, as it appeared dispensable for TIFA-induced cell killing. The findings demonstrate a novel suppressive role of TIFA in HCC progression via promotion of cell death independent of p53.
Australian sea-floor survey data, with images and expert annotations
Authors: Bewley Michael , Friedman Ariell , Ferrari Renata , Hill Nicole , Hovey Renae , Barrett Neville , Marzinelli Ezequiel M. , Pizarro Oscar , Figueira Will , Meyer Lisa , Babcock Russ , Bellchambers Lynda , Byrne Maria , Williams Stefan B. 
Published: October 2015

AbstractThis Australian benthic data set (BENTHOZ-2015) consists of an expert-annotated set of georeferenced benthic images and associated sensor data, captured by an autonomous underwater vehicle (AUV) around Australia. This type of data is of interest to marine scientists studying benthic habitats and organisms. AUVs collect georeferenced images over an area with consistent illumination and altitude, and make it possible to generate broad scale, photo-realistic 3D maps. Marine scientists then typically spend several minutes on each of thousands of images, labeling substratum type and biota at a subset of points. Labels from four Australian research groups were combined using the CATAMI classification scheme, a hierarchical classification scheme based on taxonomy and morphology for scoring marine imagery. This data set consists of 407,968 expert labeled points from around the Australian coast, with associated images, geolocation and other sensor data. The robotic surveys that collected this data form part of Australia's Integrated Marine Observing System (IMOS) ongoing benthic monitoring program. There is reuse potential in marine science, robotics, and computer vision research.
Elucidating temporal resource allocation and diurnal dynamics in phototrophic metabolism using conditional FBA
Authors: Rügen Marco , Bockmayr Alexander , Steuer Ralf 
Published: October 2015

AbstractThe computational analysis of phototrophic growth using constraint-based optimization requires to go beyond current time-invariant implementations of flux-balance analysis (FBA). Phototrophic organisms, such as cyanobacteria, rely on harvesting the sun’s energy for the conversion of atmospheric CO2 into organic carbon, hence their metabolism follows a strongly diurnal lifestyle. We describe the growth of cyanobacteria in a periodic environment using a new method called conditional FBA. Our approach enables us to incorporate the temporal organization and conditional dependencies into a constraint-based description of phototrophic metabolism. Specifically, we take into account that cellular processes require resources that are themselves products of metabolism. Phototrophic growth can therefore be formulated as a time-dependent linear optimization problem, such that optimal growth requires a differential allocation of resources during different times of the day. Conditional FBA then allows us to simulate phototrophic growth of an average cell in an environment with varying light intensity, resulting in dynamic time-courses for all involved reaction fluxes, as well as changes in biomass composition over a diurnal cycle. Our results are in good agreement with several known facts about the temporal organization of phototrophic growth and have implications for further analysis of resource allocation problems in phototrophic metabolism.
Aluminum plasmonic photocatalysis
Authors: Hao Qi , Wang Chenxi , Huang Hao , Li Wan , Du Deyang , Han Di , Qiu Teng , Chu Paul K. 
Published: October 2015

AbstractThe effectiveness of photocatalytic processes is dictated largely by plasmonic materials with the capability to enhance light absorption as well as the energy conversion efficiency. Herein, we demonstrate how to improve the plasmonic photocatalytic properties of TiO2/Al nano-void arrays by overlapping the localized surface plasmon resonance (LSPR) modes with the TiO2 band gap. The plasmonic TiO2/Al arrays exhibit superior photocatalytic activity boasting an enhancement of 7.2 folds. The underlying mechanisms concerning the radiative energy transfer and interface energy transfer processes are discussed. Both processes occur at the TiO2/Al interface and their contributions to photocatalysis are evaluated. The results are important to the optimization of aluminum plasmonic materials in photocatalytic applications.
Mechanical origin of aftershocks
Authors: Lippiello E. , Giacco F. , Marzocchi W. , Godano C. , de Arcangelis L. 
Published: October 2015

AbstractAftershocks are the most striking evidence of earthquake interactions and the physical mechanisms at the origin of their occurrence are still intensively debated. Novel insights stem from recent results on the influence of the faulting style on the aftershock organisation in magnitude and time. Our study shows that the size of the aftershock zone depends on the fault geometry. We find that positive correlations among parameters controlling aftershock occurrence in time, energy and space are a stable feature of seismicity independently of magnitude range and geographic areas. We explain the ensemble of experimental findings by means of a description of the Earth Crust as an heterogeneous elastic medium coupled with a Maxwell viscoelastic asthenosphere. Our results show that heterogeneous stress distribution in an elastic layer combined with a coupling to a viscous flow are sufficient ingredients to describe the physics of aftershock triggering.
High-throughput genotyping of CRISPR/Cas9-mediated mutants using fluorescent PCR-capillary gel electrophoresis
Authors: Ramlee Muhammad Khairul , Yan Tingdong , Cheung Alice M. S. , Chuah Charles T. H. , Li Shang 
Published: October 2015

AbstractRecent advances in the engineering of sequence-specific synthetic nucleases provide enormous opportunities for genetic manipulation of gene expression in order to study their cellular function in vivo. However, current genotyping methods to detect these programmable nuclease-induced insertion/deletion (indel) mutations in targeted human cells are not compatible for high-throughput screening of knockout clones due to inherent limitations and high cost. Here, we describe an efficient method of genotyping clonal CRISPR/Cas9-mediated mutants in a high-throughput manner involving the use of a direct lysis buffer to extract crude genomic DNA straight from cells in culture and fluorescent PCR coupled with capillary gel electrophoresis. This technique also allows for genotyping of multiplexed gene targeting in a single clone. Overall, this time- and cost-saving technique is able to circumvent the limitations of current genotyping methods and support high-throughput screening of nuclease-induced mutants.
No Association Between Time of Onset of Hearing Loss (Childhood Versus Adulthood) and Self-Reported Hearing Handicap in Adults
Authors: Aarhus Lisa , Tambs Kristian , Engdahl Bo 
Published: October 2015

PurposeThis study examined the association between time of onset of hearing loss (childhood vs. adulthood) and self-reported hearing handicap in adults.MethodsThis is a population-based cohort study of 2,024 adults (mean = 48 years) with hearing loss (binaural pure-tone average 0.5–4 kHz ≥ 20 dB HL) who completed a hearing handicap questionnaire. In childhood, the same persons (N= 2,024) underwent audiometry in a school investigation (at ages 7, 10, and 13 years), in which 129 were diagnosed with sensorineural hearing loss (binaural pure-tone average 0.5–4 kHz ≥ 20 dB HL), whereas 1,895 had normal hearing thresholds.ResultsHearing handicap was measured in adulthood as the sum-score of various speech perception and social impairment items (15 items). The sum-score increased with adult hearing threshold level (p< .001). After adjustment for adult hearing threshold level, hearing aid use, adult age, sex, and socioeconomic status, there was no significant difference in hearing handicap sum-score between the group with childhood-onset hearing loss (n= 129) and the group with adult-onset hearing loss (n= 1,895;p= .882).ConclusionSelf-reported hearing handicap in adults increased with hearing threshold level. After adjustment for adult hearing threshold level, this cohort study revealed no significant association between time of onset of hearing loss (childhood vs. adulthood) and self-reported hearing handicap.
Voice Disorder Management Competencies: A Survey of School-Based Speech-Language Pathologists in Nebraska
Authors: Teten Amy F. , DeVeney Shari L. , Friehe Mary J. 
Published: October 2015

Purpose
The purpose of this survey was to determine the self-perceived competence levels in voice disorders of practicing school-based speech-language pathologists (SLPs) and identify correlated variables.

Method
Participants were 153 master's level, school-based SLPs with a Nebraska teaching certificate and/or licensure who completed a survey, including demographic information and a 25-item voice disorders competency checklist.

Results

Findings indicated school-based SLPs did not feel particularly competent in their ability to assess and treat students with voice disorders. Only 1 response mean was higher than a “moderately competent” level. All other item means were at or below this level. Four correlations indicated positive associations with SLPs' overall self-perceived competence levels: number of continuing education activities related to voice disorders, number of clients with voice disorders in the last 3 months, percentage of time spent with clients who have voice disorders, and feelings of preparation in the area of voice disorders immediately after academic program completion. Informal comparisons to medically based SLP respondents (
n
= 22) were included.

Conclusion
School-based SLPs' competence perceptions with voice disorders are consistent with the minimal levels of competence reported for other underserved or low-incidence populations. Pursuing continuing education in voice disorders is recommended at the same time as access to the population becomes available.
Untilted edge‐slot antenna arrays fed by wiggly double‐ridged waveguide
Authors: Moradian M. 
Published: October 2015

A new method is proposed to feed untilted edge slots using a wiggly double‐ridged waveguide. The ridges have constant heights nearby each slot, but the heights of the ridges vary linearly from each slot towards the vicinity of adjacent slots. The heights of the ridges vary alternatively for successive slots whereas gap spacing between the upper and the lower ridges are constant. It is shown that by changing the wiggle depth, the radiated energy of the proposed untilted edge slot can be controlled. An appropriate equivalent circuit is employed for the proposed slot antenna and values of the elements of the equivalent circuit are derived by sweeping slot depths and wiggle depths. A linear array consists of 11 slots are then designed based on the proposed equivalent circuit to achieve −20 dB of side‐lobe level. The designed array is constructed and tested. There is an agreement between the simulation and the measurement results that indicates the effectiveness of the proposed untilted slot.
2.4.1 Carbon Monoxide Insertion into Epoxides and Oxetanes
Authors: Ibrahim H. 
Published: October 2015

AbstractIn this chapter, the most significant developments in the relatively unexplored but industrially relevant area of epoxide and oxetane carbonylation are reviewed. The coverage includes only catalytic procedures and excludes hydroformylation chemistry of the substrates discussed herein. Methods include the ring-expansion carbonylation and ring-opening carbonylation of epoxides and oxetanes, with a full coverage of the underdeveloped asymmetric carbonylation of epoxides. A historic and mechanistic background of the chemistry is presented in the General Introduction. The section on epoxide carbonylation begins with the ring-expansion carbonylation of epoxides to β-lactones and is structured according to the diverse catalytic systems reported thus far. This is followed by other carbonylative epoxide ring-expansion reactions. The ring-opening carbonylation of epoxides covers alkoxy- and aminocarbonylation, leading to β-hydroxy carboxylic acid derivatives. The chapter closes with an overview of the relatively few methods reported for oxetane carbonylation.
2.5.5 Reaction of Formaldehyde with Organometallic Reagents
Authors: Kaposi M. , Witt J. , Cokoja M. , Kühn F. E. 
Published: October 2015

AbstractFormaldehyde is one of the most important single-carbon electrophiles; it is inexpensive and can be used in many organic reactions and thus in natural product synthesis. However, there are scant examples of the application of formaldehyde with organometallic reagents in synthesis. This may be due to the properties of formaldehyde. Monomeric formaldehyde tends to polymerize rapidly to give poorly reactive species such as paraformaldehyde and the trimer trioxane. Paraformaldehyde and trioxane are depolymerized thermally; however, thermal cracking produces highly toxic, gaseous formaldehyde that rapidly repolymerizes. Alternatively, paraformaldehyde and trioxane can be depolymerized with Lewis acids, but this introduces new factors, such as corrosion, toxic waste disposal, and difficult handling. Formaldehyde is also available as an aqueous solution, known as formalin, but this approach is often unsuitable due to the instability of the organometallic compounds in the presence of water. This section discusses all that can be achieved despite these factors.
2.5.7 Formylation and the Vilsmeier Reagent
Authors: Zhang N. , Dong D. 
Published: October 2015

AbstractFormylation, allowing the introduction of a formyl group to an organic molecule, is a useful reaction in organic synthesis. The obtained formyl group can be readily reduced to afford alcohols or oxidized to give acids. Moreover, formylation plays a key role in biological and pharmaceutical fields. This chapter covers formylating reagents that are capable of efficiently introducing a formyl group to various organic molecules. Due to the versatility, ease of operation, and tolerance of many functional groups, the Vilsmeier reaction for the formylation of organic compounds is the main focus of this chapter.
Evolution of chemical diversity by coordinated gene swaps in type II polyketide gene clusters
Authors: Hillenmeyer Maureen E. , Vandova Gergana A. , Berlew Erin E. , Charkoudian Louise K. 
Published: October 2015

Significance
Type II polyketide natural products are powerful antimicrobial agents that are biosynthesized within bacteria by enzyme-encoding clusters of genes. We present a method to elucidate the evolution of these gene clusters as a whole, illuminating how natural selection has led to the chemical diversity of type II polyketides. Our approach can be applied to understand how other natural product gene clusters evolve. This understanding may aid efforts to access novel natural products and to design rational enzyme assemblies that produce chemicals of desired structures and activities.
Repeated Time-to-event Analysis of Consecutive Analgesic Events in Postoperative Pain
Authors: Juul Rasmus Vestergaard , Rasmussen Sten , Kreilgaard Mads , Christrup Lona Louring , Simonsson Ulrika S. H. , Lund Trine Meldgaard 
Published: October 2015

AbstractAbstract
Opioid doses in 63 patients after hip fracture surgery were analyzed by repeated time-to-event approach, more richly demonstrating the lengthening time course of dosing over time and the effect of other variables, including time of day.

Background
Reduction in consumption of opioid rescue medication is often used as an endpoint when investigating analgesic efficacy of drugs by adjunct treatment, but appropriate methods are needed to analyze analgesic consumption in time. Repeated time-to-event (RTTE) modeling is proposed as a way to describe analgesic consumption by analyzing the timing of consecutive analgesic events.

Methods
Retrospective data were obtained from 63 patients receiving standard analgesic treatment including morphine on request after surgery following hip fracture. Times of analgesic events up to 96 h after surgery were extracted from hospital medical records. Parametric RTTE analysis was performed with exponential, Weibull, or Gompertz distribution of analgesic events using NONMEM®, version 7.2 (ICON Development Solutions, USA). The potential influences of night versus day, sex, and age were investigated on the probability.

Results
A Gompertz distribution RTTE model described the data well. The probability of having one or more analgesic events within 24 h was 80% for the first event, 55% for the second event, 31% for the third event, and 18% for fourth or more events for a typical woman of age 80 yr. The probability of analgesic events decreased in time, was reduced to 50% after 3.3 days after surgery, and was significantly lower (32%) during night compared with day.

Conclusions
RTTE modeling described analgesic consumption data well and could account for time-dependent changes in probability of analgesic events. Thus, RTTE modeling of analgesic events is proposed as a valuable tool when investigating new approaches to pain management such as opioid-sparing analgesia.
QPot: An R Package for Stochastic Differential Equation Quasi-Potential Analysis
Authors: Moore Christopher M. , Stieha Christopher R. , Nolting Ben C. , Cameron Maria K. , Abbott Karen C. 
Published: October 2015

AbstractQPot(pronounced) is an R package for analyzing two-dimensional systems of stochastic differential equations. It provides users with a wide range of tools to simulate, analyze, and visualize the dynamics of these systems. One ofQPot’s key features is the computation of the quasi-potential, an important tool for studying stochastic systems. Quasi-potentials are particularly useful for comparing the relative stabilities of equilibria in systems with alternative stable states. This paper describesQPot’s primary functions, and explains how quasi-potentials can yield insights about the dynamics of stochastic systems. Three worked examples guide users through the application ofQPot’s functions.