bluuebunny/crossref_metadata_2025_split huggingface dataset:
In vivo mapping of tissue- and subcellular-specific proteomes inCaenorhabditis elegans
Authors: Reinke Aaron W. , Mak Raymond , Troemel Emily R. , Bennett Eric J. 
Published: July 2016

AbstractMulticellular organisms are composed of tissues that have distinct functions requiring specialized proteomes. To define the proteome of a live animal with tissue and subcellular resolution, we adapted a localized proteomics technology for use in the multicellular model organismCaenorhabditis elegans. This approach couples tissue- and location-specific expression of the enzyme ascorbate peroxidase (APX), which facilitates proximity-based protein labeling in vivo, and quantitative proteomics to identify tissue- and subcellular-restricted proteomes. We identified and localized over 3000 proteins from strains ofC. elegansexpressing APX in either the nucleus or cytoplasm of the intestine, epidermis, body wall muscle, or pharyngeal muscle. We also identified several hundred proteins that were specifically localized to one of the four tissues analyzed or specifically localized to the cytoplasm or the nucleus. This approach resulted in the identification of both previously characterized and unknown nuclear and cytoplasmic proteins. Further, we confirmed the tissue- and subcellular-specific localization of a subset of identified proteins using GFP-tagging and fluorescence microscopy, validating our in vivo proximity-based proteomics technique. Together, these results demonstrate a new approach that enables the tissue- and subcellular-specific identification and quantification of proteins within a live animal.
ADRes: a computational pipeline for detecting molecular markers of Anti-malarial Drug Resistance, from Sanger sequencing data
Authors: Amuzu Setor , Ghansah Anita 
Published: July 2016

AbstractBackgroundMalaria control efforts are stifled by the emergence and dispersal of parasite strains resistant to available anti-malarials. Amino acid changes in specific positions of proteins encoded byPlasmodium falciparumgenespfcrt, dhps, dhfr, andpfmdr1are used as molecular markers of resistance to antimalarials such as chloroquine, sulphadoxine-pyrimethamine, as well as artemisinin derivatives. However, a challenge to the detection of single nucleotide polymorphisms (SNPs) in codons responsible for these amino acid changes, in several samples, is the scarcity of automated computational pipelines for molecular biologists to; rapidly analyze ABI (Applied Biosystems) Sanger sequencing data spanning the codons of interest in order to characterize these codons and detect these molecular markers of drug resistance. The pipeline described here is an attempt to address this need.MethodThis pipeline is a combination of existing tools, notably SAMtools and Burrows Wheeler Aligner (BWA), as well as custom Python and BASH scripts. It is designed to run on the UNIX shell, a command line interpreter. To characterize the codons associated with anti-malarial drug resistance (ADR) in a particular gene using this pipeline, the following options are required; a path to reference coding sequence of the gene in FASTA format, gene symbol (pfcrt, pfmdr1, dhps or dhfr), and a path to the directory of ABI sequencing trace files for the samples. With these inputs, the pipeline performs base calling and trimming, sequence alignment, and alignment parsing.ResultsThe output of the pipeline is a CSV (Comma-separated values) file of sample names, codons and their corresponding encoded amino acids. The data generated can be readily analyzed using widely available statistical or spreadsheet software, to determine the frequency of molecular markers of resistance to anti-malarials such as chloroquine, sulphadoxine-pyrimethamine and artemisinin derivatives.ConclusionsADRes is a quick and effective pipeline for detecting common molecular markers of anti-malarial drug resistance, and could be a useful tool for surveillance. The code, description, and instructions for using this pipeline are publicly available athttp://setfelix.github.io/ADRes.
Humans treat unreliable filled-in percepts as more real than veridical ones
Authors: Ehinger Benedikt V. , Häusser Katja , Ossandón José , König Peter 
Published: July 2016

ABSTRACTHumans often evaluate sensory signals according to their reliability for optimal decision-making. However, how do we evaluate percepts generated in the absence of direct input that are, therefore, completely unreliable? Here, we utilize the phenomenon of filling-in occurring at the physiological blind-spots to compare partially inferred and veridical percepts. Subjects chose between stimuli that elicit filling-in, and perceptually equivalent ones presented outside the blind-spots, looking for a Gabor stimulus without a small orthogonal inset. In ambiguous conditions, when the stimuli were physically identical and the inset was absent in both, subjects behaved opposite to optimal, preferring the blind-spot stimulus as the better example of a collinear stimulus, even though no relevant veridical information was available. Thus, a percept that is partially inferred is paradoxically considered more reliable than a percept based on external input. In other words: Humans treat filled-in inferred percepts as more real than veridical ones.
Structure, interaction and post-translational modification study of arsenic reduction system inBifidobacterium longum
Authors: Basharat Zarrin , Yasmin Azra 
Published: July 2016

AbstractMicrobial metabolism contributes to degradation of organoarsenicals, where arsenic reductases (glutaredoxins) play pivotal role in bacterial resistance to arsenic. Ars operon studies have revealed reduction of arsenate As(V) to arsenite As(III) by respiratory-chain-linked reductase enzyme complexes. Although structure of some bacterial arsenate reductases has been solved but not attempted forBifidobacterium longumDJO10A colonizing the human gastrointestinal tract. Here it has been endeavoured to analyze and understand the structure, properties, interaction, evolution and action mechanism of this enzyme (arsC1) and its accessory interactors (arsB1, arsB2 and arsR). A systematic bioinformatic based analysis was carried out using a battery of tools and web servers for this purpose. Arsenic resistance gene cluster of gram-positiveBifidobacteriumobtained from STRING database illustrated contiguous arsC and arsB genes and absence of arsA gene. ArsC1 was determined to be a cytoplasmic small-molecular-mass protein (~15 kDa) related to a class of tyrosine phosphatases mediating the reduction of As(V) to As(III). ArsC1 was found to be involved in dephosphorylation of arsR, arsB1 and arsB2, indicating its role in post translational modification (PTM) of interacting proteins. 3D structure analysis revealed that it was composed of 1 sheet,1 beta alpha beta unit, 4 strands, 5 helices, 3 helix-helix interacs, 13 beta turns and 1 gamma turn. All proteins in the cluster exhibited hydrophobic interactions. Explicit protein-protein hydrogen, ionic, aromatic and cation-pi interactions in arsenate reducing operon ofBifidobacterium longumDJO10A further aided structural understanding of arsenate reduction process.NoteThis research was carried out in 2015. Availability of new information or changes in the algorithm behind software/database used for text mining interaction analysis in the meantime might impact some of the analyzed values. The preprint version may contain grammatical and proofreading mistakes. Errors and omissions excepted.
Sequence based prediction of novel domains in the cellulosome ofRuminiclostridium thermocellum
Authors: Basharat Zarrin , Yasmin Azra 
Published: July 2016

AbstractRuminiclostridium thermocellumstrain ATCC 27405 is valuable with reference to the next generation biofuel production being a degrader of crystalline cellulose. The completion of its genome sequence has revealed that this organism carries 3,376 genes with more than hundred genes encoding for enzymes involved in cellulysis. Novel protein domain discovery in the cellulose degrading enzyme complex of this strain has been attempted to understand this organism at molecular level. Streamlined automated methods were employed to generate possibly unreported or new domains. A set of 12 novel Pfam-B domains was developed after detailed analysis. This finding will enhance our understanding of this bacterium and its molecular processes involved in the degradation of cellulose. This approach ofin silicoanalysis prior to experimentation facilitates in lab study. Previously uncorrelated data has been utilized for rapid generation of new biological information in this study.NoteThis research was conducted in 2014 forClostridium thermocellumATCC 27405. The bacterium was later reannotated asRuminiclostridium thermocellum. See NCBI nonredundant RefSeq protein annotation details athttp://www.ncbi.nlm.nih.gov/refseq/about/prokaryotes/reannotation/. The study utilizes Pfam-B database, which was discontinued with effect from release 28.0 (5/2015). Availability of new information, reannotation/modification in accession numbers might impact some of the analyzed values although effort has been made to provide latest accession numbers and reference strain parameters. The preprint version may contain grammatical and proofreading mistakes. Errors and omissions excepted.
Public service motivation, prosocial behaviours, and career ambitions
Authors: Piatak Jaclyn Schede 
Published: July 2016

Purpose– The purpose of this paper is to examine the behavioural consequences of public service motivation (PSM) and how motivation relates to an individual’s call to serve both inside and outside of the workplace. More specifically, this study examines whether and how PSM relates to prosocial behaviours – volunteering and giving – and career ambitions to work in the government or non-profit sector among public affair graduate students.Design/methodology/approach– Logistic regression is used to examine the PSM link using a composite of the 40-item scale, each of the six dimensions – commitment to the public interest, civic duty, social justice, attraction to policymaking, compassion, and self-sacrifice – and the five-item scale from the Merit Principles Survey. The analyses draw upon data from a unique online survey of 122 graduate students in Master of Public Administration and Master of Public Policy programmes.Findings– The results indicate that people with higher levels of PSM are more likely to want to work in public service and volunteer. However, mixed results were found for the relationship between PSM and giving charitable donations and career ambitions to work in government and no link was found for career ambitions to work in the non-profit sector.Originality/value– This paper answers calls to examine the dimensions of PSM and examines Perry’s (1996) original conception. The results provide practical implications for human resource managers as well as non-profit and public managers in recruiting and retaining employees and volunteers.
Raising the next generation of public servants? Parental influence on volunteering behavior and public service career aspirations
Authors: Stritch Justin M. , Christensen Robert K 
Published: July 2016

Purpose
– While there is a large body of literature examining the effect public service motivation (PSM) has on both an individual’s career and volunteering decisions, the effects of social learning and parental influences on both volunteerism and selection into public service are relatively unexplored. The purpose of this paper is to examine the relationship between parental volunteering and career choice, PSM, and the volunteering behaviors and career choices of their adult children.

Design/methodology/approach
– The authors examine data collected from first-year undergraduate students at a large, public university in the southeastern USA to examine, the impact of parents in the development of public service behaviors like volunteering and career choice.

Findings
– The authors find that parental influence matters in shaping voluntary behavior and career aspirations, but that this social learning is distinct by gender.

Originality/value
– The authors are unaware of work that directly focusses on parents’ volunteering and career choices, after controlling for PSM, on both the volunteering and public service career decisions of their children.
Stepping in the same river twice: Stability amidst change in Eastern European party competition
Authors: ROVNY JAN , POLK JONATHAN 
Published: July 2016

AbstractParty competition in Eastern Europe faces a seeming paradox. On the one hand, research finds increased political volatility in these countries, while, on the other, some authors demonstrate inherent ideological stability in the region. This research note presents a new methodological approach to adjudicating between these two findings, and suggests that while political organisations come and go, the ideological structure of party competition in Eastern Europe is strikingly steady. By developing a number of different measures of the dimensional structure of party competition, the consistency of the measures across countries, as well as their relative stability within countries over time, is demonstrated. The findings speak to current developments in Eastern Europe, and have implications beyond the region. The conclusion that even volatile party systems can be underpinned by stable ideological oppositions points to two different types of party system structure: one related to parties as organisations, and the other related to parties as expressions of political divides.
De novo bone formation underneath the sinus membrane supported by a bone patch: a pilot experiment in rabbit sinus model
Authors: Yoon So‐Ra , Cha Jae‐Kook , Lim Hyun‐Chang , Lee Jung‐Seok , Choi Seong‐Ho , Jung Ui‐Won 
Published: July 2016

AbstractAimsThe objectives of this study were to evaluate bone regeneration beneath a newly devised bone substitute combined with collagen membrane (called a bone patch) lying over a concomitantly placed mini‐implant following sinus floor elevation and verify its usefulness as a carrier system for recombinant human bone morphogenetic protein‐2 (rhBMP‐2) in rabbits.Materials and methodsThe sinus floor elevation procedure was performed bilaterally in five rabbits. Either a plain bone patch (control group) or an rhBMP‐2‐loaded patch (experimental group) was randomly placed beneath the elevated sinus membrane (SM) of both sinuses, where the mini‐implants were concomitantly placed. Micro‐computed tomographic and histologic analyses were performed at 4 weeks post‐surgery.ResultsIn micro‐computed tomography, the median values of the total augmented volume and the mineralized bone volume were significantly higher in the experimental group than in the control group (161 vs. 122 mm3 [P < 0.01] and 48 vs. 42 mm3 [P < 0.05], respectively). Histometric analysis revealed the same outcomes, with new bone areas of 6.41 and 2.97 mm2 in the experimental and control groups, respectively (P < 0.001), and bone‐to‐implant contact ratios of 22.6% and 5.2%, respectively (P < 0.001).ConclusionThe newly devised bone patch in this study can support the elevated SM and facilitate bone regeneration from the basal bone with a reduced amount of biomaterial. The addition of rhBMP‐2 may shorten the healing time for multidirectional bone regeneration toward the implant.
Effects of near‐infrared LED therapy on experimental tooth replantation in rats
Authors: Pigatto Mitihiro Débora , de Paula Ramos Solange , Corazza Montero Janaína , Alves Campos Aline , de Oliveira Toginho Filho Dari , Dezan Garbelini Cassia Cilene 
Published: July 2016

AbstractBackground/AimDental avulsion damages periodontal tissues and may induce dentoalveolar ankylosis and root resorption after replantation. The aim of this work was to evaluate the effects of light‐emitting diode (LED) therapy after tooth replantation.Material and methodsThe upper right incisors of 36 male Wistar rats were extracted and replanted after 15 min. The control group (Co, n = 18) was submitted to replantation and the LED group (n = 18) was submitted to replantation and LED therapy (940 nm, 4 J cm−2) for three consecutive days (0, 24, and 48 h). Six animals from each group were euthanized at 7, 14, and 21 days for histological analysis. The upper left incisors were used as a negative control. Data were compared using the Fisher exact test, considering P < 0.05.ResultsAfter 7 days, the Co (73.3%) and LED (72.2%) groups presented areas of periodontal ligament necrosis. However, periodontal ligament necrosis was more frequent in the LED group at 14 (70%, P < 0.05) and 21 days (43.2%, P < 0.05) in relation to the Co group (33 and 21.6%). Inflammatory cell infiltration was more frequent in the Co group at 7 days (100%) than the LED group (24.4%, P < 0.05), but increased in the LED group after 21 days (83.3%, P < 0.05). Bone necrosis was more frequent in the LED group after 14 (79%, P < 0.05) and 21 days (60%, P < 0.005) than in the Co group (45% and 20%). Bone repair was evident in the Co group at 14 days. All of the replanted teeth had pulp necrosis.ConclusionThe results suggest that the application of LED therapy up to 48 h after tooth replantation may delay periodontal ligament repair.
CTOD‐R Curve Tests of API 5L X90 By SENT Specimen Using a Modified Normalization Method
Authors: Kong L. Z. , Zhou X. Y. , Chen L. Q. , Huang K. , Peng H. T. 
Published: July 2016

AbstractA modified normalization method is presented for obtaining crack tip opening displacement (CTOD) resistance curves of single edge‐notched tension specimens. For the applied load mode, the normalization method should be based on force‐crack mouth opening displacement. A formula is proposed for CLL(i), the core parameter used in the normalization calculation. The modified method is validated using the unloading compliance method. The study of specimen geometry shows that side‐groove depth and crack depth have significant impacts on the obtained CTOD resistance curves, and the shape of the crack front affects the determination accuracy of crack length.
Gingival Retraction Methods: A Systematic Review
Authors: Tabassum Sadia , Adnan Samira , Khan Farhan Raza 
Published: July 2016

AbstractPurposeThe aim of this systematic review was to assess the gingival retraction methods in terms of the amount of gingival retraction achieved and changes observed in various clinical parameters: gingival index (GI), plaque index (PI), probing depth (PD), and attachment loss (AL).MethodsData sources included three major databases, PubMed, CINAHL plus (Ebsco), and Cochrane, along with hand search. Search was made using the key terms in different permutations of gingival retraction* AND displacement method* OR technique* OR agents OR material* OR medicament*.ResultsThe initial search results yielded 145 articles which were narrowed down to 10 articles using a strict eligibility criteria of including clinical trials or experimental studies on gingival retraction methods with the amount of tooth structure gained and assessment of clinical parameters as the outcomes conducted on human permanent teeth only. Gingival retraction was measured in 6/10 studies whereas the clinical parameters were assessed in 5/10 studies.ConclusionsThe total number of teeth assessed in the 10 included studies was 400. The most common method used for gingival retraction was chemomechanical. The results were heterogeneous with regards to the outcome variables. No method seemed to be significantly superior to the other in terms of gingival retraction achieved. Clinical parameters were not significantly affected by the gingival retraction method.
The cardioprotective effect of melatonin and exendin‐4 treatment in a rat model of cardiorenal syndrome
Authors: Chua Sarah , Lee Fan‐Yen , Chiang Hsin‐Ju , Chen Kuan‐Hung , Lu Hung‐I , Chen Yen‐Ta , Yang Chih‐Chao , Lin Kun‐Chen , Chen Yi‐Ling , Kao Gour‐Shenq , Chen Chih‐Hung , Chang Hsueh‐Wen , Yip Hon‐Kan 
Published: July 2016

AbstractWe investigated the cardioprotective effect of melatonin (Mel) and exendin‐4 (Ex4) treatment in a rat model of cardiorenal syndrome (CRS). Adult male SD rats (n=48) were randomly and equally divided into sham control (SC), dilated cardiomyopathy (DCM) (doxorubicin 7 mg/kg i.p. every five days/4 doses), CRS (defined as DCM+CKD) only, CRS‐Mel (20 mg/kg/d), CRS‐Ex4 (10 μg/kg/d), and CRS‐Mel‐Ex4 groups. In vitro results showed protein expressions of oxidative stress (NOX‐1/NOX‐2/oxidized protein), DNA/mitochondrial damage (γ‐H2AX/cytosolic cytochrome c), apoptosis (cleaved caspase‐3/PARP), and senescence (β‐galactosidase cells) biomarkers were upregulated, whereas mitochondrial ATP level was decreased in doxorubicin/p‐cresol‐treated H9c2 cells that were revised by Mel and Ex4 treatments (all P<.001). By day 60, LVEF was highest in the SC and lowest in the CRS, significantly lower in the DCM than in other treatment groups, lower in the CRS‐Mel and CRS‐Ex4 than in the CRS‐Mel‐Ex4, and lower in the CRS‐Mel than in the CRS‐Ex4, whereas LV chamber size and histopathology score showed a pattern opposite to that of LVEF among all groups (all P<.001). Plasma creatinine level was highest in the CRS and lowest in the SC and progressively decreased from the CRS‐Mel, CRS‐Ex4, CRS‐Mel‐Ex4 to DCM (P<.0001). Protein expressions of inflammation (TNF‐α/NF‐κB/MMP‐2/MMP‐9/IL‐1β), apoptosis/DNA damage (Bax/c‐caspase‐3/c‐PARP/γ‐H2AX), fibrosis (Smad3/TGF‐β), oxidative stress (NOX‐1/NOX‐2/NOX‐4/oxidized protein), cardiac hypertrophy/pressure overload (BNP/β‐MHC), and cardiac integrity (Cx43/α‐MHC) biomarkers in LV myocardium showed an opposite pattern compared to that of LVEF among all groups (all P<.001). Fibrotic area, DNA damage (γ‐H2AX+/53BP1+CD90+/XRCC1+CD90+), and inflammation (CD14+/CD68+) biomarkers in LV myocardium displayed a pattern opposite to that of LVEF among all groups (all P<.001). Combined melatonin and exendin‐4 treatment suppressed CRS‐induced deterioration of LVEF and LV remodeling.
The Lilliputian dreams: preliminary observations of nationalism in Okinawa, Taiwan and Hong Kong
Authors: Wu Rwei‐Ren 
Published: July 2016

AbstractThis paper is a preliminary comparative analysis of three polity‐seeking nationalisms that emerged in the contiguous peripheral areas – the overlapping ‘spheres of influence’ of three contending imperial centres: Taiwan, Okinawa and Hong Kong. Specifically, it examines and compares the pattern of nation‐formation and the form, ideology and politics of nationalism in each case, and in doing so it tries to suggest a possible explanatory framework for the rise of these nationalisms. Its tentative conclusion is that the rise of nationalism in Taiwan, Okinawa and Hong Kong should be understood as a macro‐historical sociological phenomenon caused by both the short‐term penetration from centralizing colonial and geopolitical centre(s) that triggered nationalist mobilization in the periphery and the long‐term process of peripheral nation‐formation that created the social basis for mobilization. The three cases also demonstrate some other traits of anti‐centre peripheral nationalism: they all adopted a similar ideological strategy of indigeneity, and all developed a differentiation between radical and pragmatic lines characteristic of minority or peripheral nationalisms. A final observation is that while the geopolitics of states in the region is powerfully shaping the development of the three nationalisms, interactions on the societal level may over time create a counterforce from below.