bluuebunny/crossref_metadata_2025_split huggingface dataset:
Digging into the low molecular weight peptidome with the OligoNet web server
Authors: Liu Youzhong , Forcisi Sara , Lucio Marianna , Harir Mourad , Bahut Florian , Deleris-Bou Magali , Krieger-Weber Sibylle , Gougeon Régis D. , Alexandre Hervé , Schmitt-Kopplin Philippe 
Published: September 2017

AbstractBioactive peptides play critical roles in regulating many biological processes. Recently, natural short peptides biomarkers are drawing significant attention and are considered as “hidden treasure” of drug candidates. High resolution and high mass accuracy provided by mass spectrometry (MS)-based untargeted metabolomics would enable the rapid detection and wide coverage of the low-molecular-weight peptidome. However, translating unknown masses (<1 500 Da) into putative peptides is often limited due to the lack of automatic data processing tools and to the limit of peptide databases. The web server OligoNet responds to this challenge by attempting to decompose each individual mass into a combination of amino acids out of metabolomics datasets. It provides an additional network-based data interpretation named “Peptide degradation network” (PDN), which unravels interesting relations between annotated peptides and generates potential functional patterns. The ab initio PDN built from yeast metabolic profiling data shows a great similarity with well-known metabolic networks, and could aid biological interpretation. OligoNet allows also an easy evaluation and interpretation of annotated peptides in systems biology, and is freely accessible at https://daniellyz200608105.shinyapps.io/OligoNet/.
Evaluation of therapeutic potential of the silver/silver chloride nanoparticles synthesized with the aqueous leaf extract of Rumex acetosa
Authors: Kota Sobha , Dumpala Pradeep , Anantha Ratna Kumari , Verma Mahendra Kumar , Kandepu Surendranath 
Published: September 2017

AbstractSilver nanoparticles were green synthesized with the aqueous leaf extract of the widely consumed green leafy vegetable, Rumex acetosa (sorrel) and the obtained silver nanoparticles (Ag NPs) were tested for their in vitro antioxidant potential, cytotoxicity against human osteosarcoma (HOS) cell lines and antibacterial effects against sixteen human pathogenic clinical isolates. Different analytical techniques viz. UV-vis, FTIR, XRD, SEM-EDX and TEM were employed to characterize the synthesized Ag NPs. Surface Plasmon spectra for the Ag NPs with brownish black color were centered approximately at 448 nm. FTIR analysis revealed the presence of reactive N-H and O-H groups that are effective in reducing Ag(I) ions to Ag(0) which then reacted with the contents of the extract to AgCl/Ag2C2O4. From SEM and TEM analyses, the particles were found to be predominantly spherical in shape and ranged in size from 5 nm to 80 nm, but were largely in the range of 15 nm to 20 nm. Ag NPs showed considerable antioxidant activity, and all the sixteen clinical isolates of human pathogens tested were significantly inhibited. Also, HOS cell lines were significantly (p < 0.05) inhibited at 25% concentration of the Ag NPs extract, while showing a marginal revival at 50% and 100% concentrations.
Malignancy risk stratification of thyroid nodules: comparisons of four ultrasound Thyroid Imaging Reporting and Data Systems in surgically resected nodules
Authors: Wang Ying , Lei Kai-Rong , He Ya-Ping , Li Xiao-Long , Ren Wei-Wei , Zhao Chong-Ke , Bo Xiao-Wan , Wang Dan , Sun Cheng-Yu , Xu Hui-Xiong 
Published: September 2017

AbstractTo compare the efficiency of four different ultrasound (US) Thyroid Imaging Reporting and Data Systems (TI-RADS) in malignancy risk stratification in surgically resected thyroid nodules (TNs). The study included 547 benign TNs and 464 malignant TNs. US images of the TNs were retrospectively reviewed and categorized according to the TI-RADSs published by Horvath Eet al. (TI-RADS H), Parket al. (TI-RADS P), Kwaket al. (TI-RADS K) and Russet al. (TI-RADS R). The diagnostic performances for the four TI-RADSs were then compared. At multivariate analysis, among the suspicious US features, marked hypoechogenicity was the most significant independent predictor for malignancy (OR: 15.344, 95% CI: 5.313-44.313) (P < 0.05). Higher sensitivity was seen in TI-RADS H, TI-RADS K, TI-RADS R comparing with TI-RADS P (P < 0.05 for all), whereas the specificity, accuracy and area under the ROC curve (Az) of TI-RADS P were the highest (all P < 0.05). Higher specificity, accuracy and Az were seen in TI-RADS K compared with TI-RADS R (P = 0.003). With its higher sensitivity, TI-RADS K, a simple predictive model, is practical and convenient for the management of TNs in clinical practice. The study indicates that there is a good concordance between TI-RADS categories and histopathology.
RNAi-mediated silencing of a pyruvate dehydrogenase kinase enhances triacylglycerol biosynthesis in the oleaginous marine alga Nannochloropsis salina
Authors: Ma Xiaonian , Yao Lina , Yang Bo , Lee Yuan Kun , Chen Feng , Liu Jin 
Published: September 2017

AbstractOleaginous microalgae have been emerging as the third-generation feedstocks for biofuel production. Genetic manipulation for improving triacylglycerol (TAG) accumulation represents a promising approach towards the economics of microalgal biofuels. Acetyl-CoA, the essential carbon precursor for de novo fatty acid biosynthesis, can be derived from pyruvate catalyzed by pyruvate dehydrogenase, which is negatively regulated by pyruvate dehydrogenase kinase (PDK). In the present study, we characterized a PDK gene (NsPDK) from Nannochloropsis salina. Subcellular localization assay assisted by green fluorescence protein (GFP) fusion indicated the localization of NsPDK in mitochondria of N. salina cells. NsPDK knockdown via RNA interference strategy attenuated NsPDK expression at the mRNA level and its enzymatic activity in vivo, leading to faster TAG accumulation without compromising cell growth under high light stress conditions. Interestingly, the TAG increase was accompanied by a decline in membrane polar lipids. NsPDK knockdown also altered fatty acid profile in N. salina. Furthermore, transcriptional analysis suggested that the carbon metabolic pathways might be influenced by NsPDK knockdown leading to diverted carbon flux towards TAG synthesis. Taken together, our results demonstrate the role of NsPDK in regulating TAG accumulation and provide valuable insights into future manipulation of oleaginous microalgae for improving biofuel production.
The Homologous Recombination Machinery Orchestrates Post-replication DNA Repair During Self-renewal of Mouse Embryonic Stem Cells
Authors: Choi Eui-Hwan , Yoon Seobin , Park Kyung-Soon , Kim Keun P. 
Published: September 2017

AbstractEmbryonic stem (ES) cells require homologous recombination (HR) to cope with genomic instability caused during self-renewal. Here, we report expression dynamics and localization of endogenous HR factors in DNA break repair of ES cells. In addition, we analyzed gene expression patterns of HR-related factors at the transcript level with RNA-sequencing experiments. We showed that ES cells constitutively expressed diverse HR proteins throughout the cell cycle and that HR protein expression was not significantly changed even in the DNA damaging conditions. We further analyzed that depleting Rad51 resulted in the accumulation of larger single-stranded DNA (ssDNA) gaps, but did not perturb DNA replication, indicating that ES cells were able to enter the G2-phase in the presence of unrepaired DNA gaps, consistent with the possibility that post-replication repair helps avoid stalling at the G2/M checkpoint. Interestingly, caffeine treatment inhibited the formation of Rad51 or Rad54 foci, but not the formation of γH2AX and Exo1 foci, which led to incomplete HR in ssDNA, thus increasing DNA damage sensitivity. Our results suggested that ES cells possess conserved HR-promoting machinery to ensure effective recruitment of the HR proteins to DNA breaks, thereby driving proper chromosome duplication and cell cycle progression in ES cells.
Matrisome Profiling During Intervertebral Disc Development And Ageing
Authors: Caldeira Joana , Santa Cátia , Osório Hugo , Molinos Maria , Manadas Bruno , Gonçalves Raquel , Barbosa Mário 
Published: September 2017

AbstractIntervertebral disc (IVD) degeneration is often the cause of low back pain. Degeneration occurs with age and is accompanied by extracellular matrix (ECM) depletion, culminating in nucleus pulpous (NP) extrusion and IVD destruction. The changes that occur in the disc with age have been under investigation. However, a thorough study of ECM profiling is needed, to better understand IVD development and age-associated degeneration. As so, iTRAQ LC-MS/MS analysis of foetus, young and old bovine NPs, was performed to define the NP matrisome. The enrichment of Collagen XII and XIV in foetus, Fibronectin and Prolargin in elder NPs and Collagen XI in young ones was independently validated. This study provides the first matrisome database of healthy discs during development and ageing, which is key to determine the pathways and processes that maintain disc homeostasis. The factors identified may help to explain age-associated IVD degeneration or constitute putative effectors for disc regeneration.
Synthesis of enhanced phosphonic functional groups mesoporous silica for uranium selective adsorption from aqueous solutions
Authors: Sarafraz H. , Minuchehr A. , Alahyarizadeh Gh. , Rahimi Z. 
Published: September 2017

AbstractEnhanced phosphonic functional group (PFG)-based mesoporous silicas (MSs) were synthesized by hydrothermal method for uranium [U(VI)] selective adsorption from aqueous solutions. Considering that PFGs are directly related to U(VI) adsorption, the main idea of this research was to synthesize enhanced PFG-MSs and consequently enhance U(VI) adsorption. We synthesized two kinds of MSs based on acetic and phosphoric acids at weakly acidic pH, which allows high-loading phosphonic functionality. The main sodium and phosphonic functionality sources were sodium metasilicate and diethylphosphatoethyltriethoxysilane (DPTS). Adsorption experiment results exhibit enhanced U(VI) adsorption capacity from 55.75 mg/g to 207.6 mg/g for acetic and phosphoric acids, respectively. This finding was due to the enhancement of PFGs by phosphoric acids. The highest adsorption selectivity was 79.82% for U(VI) among the six different elements, including Pb, As, Cu, Mo, Ni, and K. Structural characterization of the samples was performed by Fourier transform infrared, X-ray diffraction, scanning electron microscopy, energy-dispersive X-ray spectroscopy, and Brunauer–Emmett–Teller analysis methods. Element concentrations were measured by inductively coupled plasma optical emission spectrometry. Several parameters affecting adsorption capacity, including pH, contact time, initial U(VI) concentration and solution volume, and adsorbent concentration, were also investigated.
Performance-based ability emotional intelligence benefits working memory capacity during performance on hot tasks
Authors: Gutiérrez-Cobo María José , Cabello Rosario , Fernández-Berrocal Pablo 
Published: September 2017

AbstractEmotional intelligence (EI) is the ability to perceive, use, understand, and regulate emotions. Higher scores on this ability measured through performance tests (but no through self-reports) appears to be related to better performance on “hot” (emotionally laden) cognitive tasks. However, there are relatively few studies concerning how EI may benefit the working memory capacity (WMC). Thus, the objective of this study is to analyse the relationship between EI (as measured through a performance-based ability test, a self-report mixed test, and a self-report ability test) and the WMC during the performance of hot and “cool” (i.e., non-emotionally laden) “2-back” tasks. 203 participants completed three EI tests as well as two 2-back tasks. The results provide evidence for better performance of higher EI participants (specifically in the managing branch) measured through the performance-based ability test, but only on the hot task. For the self-report mixed model, incongruent results were found, and no correlations were obtained using the self-report ability model. The implications of these findings are discussed in terms of the validity of the various EI models.
Highly chromophoric Cy5-methionine for N-terminal fluorescent tagging of proteins in eukaryotic translation systems
Authors: Kim Jung Min , Seong Baik Lin 
Published: September 2017

AbstractDespite significant advances on fluorescent labeling of target proteins to study their structural dynamics and function, there has been need for labeling with high quantum yield ensuring high sensitivity and selectivity without sacrificing the biological function of the protein. Here as a technical advancement over non-canonical amino acid incorporation, we provided a conceptual design of the N-terminal fluorescent tagging of proteins. Cy5-labeled methionine (Cy5-Met) was chemically synthesized, and then the purified Cy5-Met was coupled with synthetic human initiator tRNA by methionine tRNA synthetase. Cy5-Met-initiator tRNA (Cy5-Met-tRNAi) was purified and transfected into HeLa cells with HIV-Tat plasmid, resulting in an efficient production of Cy5-labeled HIV-Tat protein. Based on the universal requirement in translational initiation, the approach provides co-translational incorporation of N-terminal probe to a repertoire of proteins in the eukaryote system. This methodology has potential utility in the single molecule analysis of human proteins in vitro and in vivo for addressing to their complex biological structural and functional dynamics.
Trans Male Voice in the First Year of Testosterone Therapy: Make No Assumptions
Authors: Hancock Adrienne B. , Childs Kayla D. , Irwig Michael S. 
Published: September 2017

Purpose
The purpose of this study was to prospectively examine changes in gender-related voice domain of pitch measured by fundamental frequency, function-related domains of vocal quality, range, and habitual pitch level and the self-perceptions of transmasculine people during their first year of testosterone treatment.

Method
Seven trans men received 2 voice assessments at baseline and 1 assessment at 3, 6, 9, and 12 months after starting treatment.

Results
Vocal quality measures varied between and within participants but were generally within normal limits throughout the year. Mean fundamental frequency (MF0) during reading decreased, although to variable extents and rates. Phonation frequency range shifted down the scale, although it increased in some participants and decreased in others. Considering MF0 and phonation frequency range together in a measure of habitual pitch level revealed that the majority of participants spoke using an MF0 that was low within their range compared with cisgender norms. Although the trans men generally self-reported voice masculinization, it was not correlated with MF0, frequency range, or habitual pitch level at any time point or with MF0 note change from baseline to 1 year of testosterone treatment, but correlations should be interpreted with caution due to the heterogeneous responses of the 7 participants.

Conclusion
In trans men, consideration of voice deepening in the context of objective and subjective measures of voice can reveal unique profiles and inform patient care.
The Islamic State’s information warfare
Authors: Siegel Alexandra A. , Tucker Joshua A. 
Published: September 2017

Abstract
How successful is the Islamic State’s online strategy? To what extent does the organization achieve its goals of attracting a global audience, broadcasting its military successes, and marketing the Caliphate? Using Twitter and YouTube search data, collected throughout 2015 and early 2016, we assess how suspected ISIS accounts, sympathizers, and opponents behave across two social media platforms, offering key insights into the successes and limitations of ISIS’s information warfare strategy. Analyzing the tweet content and metadata from 16,364 suspected ISIS accounts, we find that a core network of ISIS Twitter users are producing linguistically diverse narratives, touting battlefield victories and depicting utopian life in the Caliphate. Furthermore, a dataset of over 70 million tweets, as well as analysis YouTube search data, indicates that although pro-ISIS content spreads globally and remains on message, it is far less prolific than anti-ISIS content. However, this anti-ISIS content is not necessarily anti-extremist or aligned with Western policy goals.
Covert co-activation of bilinguals’ non-target language
Authors: Shook Anthony , Marian Viorica 
Published: September 2017

Abstract
When listening to spoken language, bilinguals access words in both of their languages at the same time; this co-activation is often driven by phonological input mapping to candidates in multiple languages during online comprehension. Here, we examined whether cross-linguistic activation could occur covertly when the input does not overtly cue words in the non-target language. When asked in English to click an image of a duck, English-Spanish bilinguals looked more to an image of a shovel than to unrelated distractors, because the Spanish translations of the words duck and shovel (pato and pala, respectively) overlap phonologically in the non-target language. Our results suggest that bilinguals access their unused language, even in the absence of phonologically overlapping input. We conclude that during bilingual speech comprehension, words presented in a single language activate translation equivalents, with further spreading activation to unheard phonological competitors. These findings support highly interactive theories of language processing.
Winners and losers as mangrove, coral and seagrass ecosystems respond to sea-level rise in Solomon Islands
Authors: Albert Simon , Saunders Megan I , Roelfsema Chris M , Leon Javier X , Johnstone Elizabeth , Mackenzie Jock R , Hoegh-Guldberg Ove , Grinham Alistair R , Phinn Stuart R , Duke Norman C , Mumby Peter J , Kovacs Eva , Woodroffe Colin D 
Published: September 2017

Abstract
A 2007 earthquake in the western Solomon Islands resulted in a localised subsidence event in which sea level (relative to the previous coastal settings) rose approximately 30–70 cm, providing insight into impacts of future rapid changes to sea level on coastal ecosystems. Here, we show that increasing sea level by 30–70 cm can have contrasting impacts on mangrove, seagrass and coral reef ecosystems. Coral reef habitats were the clear winners with a steady lateral growth from 2006–2014, yielding a 157% increase in areal coverage over seven years. Mangrove ecosystems, on the other hand, suffered the largest impact through a rapid dieback of 35% (130 ha) of mangrove forest in the study area after subsidence. These forests, however, had partially recovered seven years after the earthquake albeit with a different community structure. The shallow seagrass ecosystems demonstrated the most dynamic response to relative shifts in sea level with both losses and gains in areal extent at small scales of 10–100 m. The results of this study emphasize the importance of considering the impacts of sea-level rise within a complex landscape in which winners and losers may vary over time and space.
Reply to Comment on ‘High-income does not protect against hurricane losses’
Authors: Geiger Tobias , Frieler Katja , Levermann Anders 
Published: September 2017

Abstract
Recently a multitude of empirically derived damage models have been applied to project future tropical cyclone (TC) losses for the United States. In their study (Geiger et al 2016 Environ. Res. Lett.
11 084012) compared two approaches that differ in the scaling of losses with socio-economic drivers: the commonly-used approach resulting in a sub-linear scaling of historical TC losses with a nation’s affected gross domestic product (GDP), and the disentangled approach that shows a sub-linear increase with affected population and a super-linear scaling of relative losses with per capita income. Statistics cannot determine which approach is preferable but since process understanding demands that there is a dependence of the loss on both GDP per capita and population, an approach that accounts for both separately is preferable to one which assumes a specific relation between the two dependencies. In the accompanying comment, Rybski et al argued that there is no rigorous evidence to reach the conclusion that high-income does not protect against hurricane losses. Here we affirm that our conclusion is drawn correctly and reply to further remarks raised in the comment, highlighting the adequateness of our approach but also the potential for future extension of our research.
Facilitated Extinction Training to Improve Pharmacotherapy for Smoking Cessation: A Pilot Feasibility Trial
Authors: Brandon Thomas H , Unrod Marina , Drobes David J , Sutton Steven K , Hawk Larry W , Simmons Vani N , Brandon Karen O , Roetzheim Richard G , Meltzer Lauren R , Miller Ralph R , Cahill Shawn P 
Published: September 2017

Abstract

Introduction
Varenicline reduces smoking satisfaction during the pre-cessation run-in period, which may contribute to extinction of cravings and smoking behavior. Research indicates that efficacy is enhanced when the run-in period is increased from 1 to 4 weeks, providing a longer extinction opportunity. We hypothesized that efficacy could be further enhanced by harnessing basic and applied research on extinction. We developed a pre-cessation extinction-facilitating intervention and tested its feasibility in a pilot trial.

Methods
The facilitated extinction (FE) intervention comprised brief counseling and workbook-recommending strategies to maximize extinction processes during the run-in, including instructions to smoke at a normal rate across contexts and cues, and use of an extinction cue to enhance generalization. Participants were randomly assigned to one of three varenicline interventions: standard (1-week run-in), extended (4-week run-in), and extended + FE. Interventions were delivered prior to the target quit date (TQD). Assessments were conducted in weeks 1 and 4 pre-TQD and 1 and 3 months post-TQD, with focus on feasibility indices.

Results
Recruitment and retention goals were met (N = 58). Treatment satisfaction was high across groups. The majority of FE participants adhered to instructions and maintained their usual smoking rate during the run-in period. Greater decreases in craving and smoking satisfaction were observed among participants in both extended groups versus the standard group (p &lt; .005).

Conclusions
Feasibility was demonstrated. Participants adhered to the FE intervention, thereby optimizing the number and variety of extinction trials. Findings support testing the novel FE smoking cessation intervention in a fully powered trial.

Implications
This study expands the research on the clinical benefits of extending the pre-cessation run-in period of varenicline. It introduces the hypothesis that further benefit might be achieved by translating basic behavioral research, as well as cue-exposure research and therapy for other disorders, to improve the extinction and generalization processes thought to underlie much of varenicline’s effect. A FE intervention was developed and found acceptable to smokers and feasible to implement in a research setting. The study sets the stage for a subsequent randomized controlled trial.