bluuebunny/crossref_metadata_2025_split huggingface dataset:
The PKA-C3 catalytic subunit is required in two pairs of interneurons for successful mating of Drosophila
Authors: Cassar Marlène , Sunderhaus Elizabeth , Wentzell Jill S. , Kuntz Sara , Strauss Roland , Kretzschmar Doris 
Published: January 2018

AbstractProtein kinase A (PKA) has been shown to play a role in a plethora of cellular processes ranging from development to memory formation. Its activity is mediated by the catalytic subunits whereby many species express several paralogs. Drosophila encodes three catalytic subunits (PKA-C1–3) and whereas PKA-C1 has been well studied, the functions of the other two subunits were unknown. PKA-C3 is the orthologue of mammalian PRKX/Pkare and they are structurally more closely related to each other than to other catalytic subunits within their species. PRKX is expressed in the nervous system in mice but its function is also unknown. We now show that the loss of PKA-C3 in Drosophila causes copulation defects, though the flies are active and show no defects in other courtship behaviours. This phenotype is specifically due to the loss of PKA-C3 because PKA-C1 cannot replace PKA-C3. PKA-C3 is expressed in two pairs of interneurons that send projections to the ventro-lateral protocerebrum and the mushroom bodies and that synapse onto motor neurons in the ventral nerve cord. Rescue experiments show that expression of PKA-C3 in these interneurons is sufficient for copulation, suggesting a role in relaying information from the sensory system to motor neurons to initiate copulation.
Heterologous Expression of a Novel Drug Transporter from the Malaria Parasite Alters Resistance to Quinoline Antimalarials
Authors: Tindall Sarah M. , Vallières Cindy , Lakhani Dev H. , Islahudin Farida , Ting Kang-Nee , Avery Simon V. 
Published: January 2018

AbstractAntimalarial drug resistance hampers effective malaria treatment. Critical SNPs in a particular, putative amino acid transporter were recently linked to chloroquine (CQ) resistance in malaria parasites. Here, we show that this conserved protein (PF3D7_0629500 in Plasmodium falciparum; AAT1 in P. chabaudi) is a structural homologue of the yeast amino acid transporter Tat2p, which is known to mediate quinine uptake and toxicity. Heterologous expression of PF3D7_0629500 in yeast produced CQ hypersensitivity, coincident with increased CQ uptake. PF3D7_0629500-expressing cultures were also sensitized to related antimalarials; amodiaquine, mefloquine and particularly quinine. Drug sensitivity was reversed by introducing a SNP linked to CQ resistance in the parasite. Like Tat2p, PF3D7_0629500-dependent quinine hypersensitivity was suppressible with tryptophan, consistent with a common transport mechanism. A four-fold increase in quinine uptake by PF3D7_0629500 expressing cells was abolished by the resistance SNP. The parasite protein localised primarily to the yeast plasma membrane. Its expression varied between cells and this heterogeneity was used to show that high-expressing cell subpopulations were the most drug sensitive. The results reveal that the PF3D7_0629500 protein can determine the level of sensitivity to several major quinine-related antimalarials through an amino acid-inhibitable drug transport function. The potential clinical relevance is discussed.
OPA1 gene therapy prevents retinal ganglion cell loss in a Dominant Optic Atrophy mouse model
Authors: Sarzi Emmanuelle , Seveno Marie , Piro-Mégy Camille , Elzière Lucie , Quilès Mélanie , Péquignot Marie , Müller Agnès , Hamel Christian P. , Lenaers Guy , Delettre Cécile 
Published: January 2018

AbstractDominant optic atrophy (DOA) is a rare progressive and irreversible blinding disease which is one of the most frequent forms of hereditary optic neuropathy. DOA is mainly caused by dominant mutation in the OPA1 gene encoding a large mitochondrial GTPase with crucial roles in membrane dynamics and cell survival. Hereditary optic neuropathies are commonly characterized by the degeneration of retinal ganglion cells, leading to the optic nerve atrophy and the progressive loss of visual acuity. Up to now, despite increasing advances in the understanding of the pathological mechanisms, DOA remains intractable. Here, we tested the efficiency of gene therapy on a genetically-modified mouse model reproducing DOA vision loss. We performed intravitreal injections of an Adeno-Associated Virus carrying the human OPA1 cDNA under the control of the cytomegalovirus promotor. Our results provide the first evidence that gene therapy is efficient on a mouse model of DOA as the wild-type OPA1 expression is able to alleviate the OPA1-induced retinal ganglion cell degeneration, the hallmark of the disease. These results displayed encouraging effects of gene therapy for Dominant Optic Atrophy, fostering future investigations aiming at clinical trials in patients.
Attention Gates the Selective Encoding of Duration
Authors: Maarseveen Jim , Hogendoorn Hinze , Verstraten Frans A. J. , Paffen Chris L. E. 
Published: January 2018

AbstractThe abundance of temporal information in our environment calls for the effective selection and utilization of temporal information that is relevant for our behavior. Here we investigated whether visual attention gates the selective encoding of relevant duration information when multiple sources of duration information are present. We probed the encoding of duration by using a duration-adaptation paradigm. Participants adapted to two concurrently presented streams of stimuli with different durations, while detecting oddballs in one of the streams. We measured the resulting duration after-effect (DAE) and found that the DAE reflects stronger relative adaptation to attended durations, compared to unattended durations. Additionally, we demonstrate that unattended durations do not contribute to the measured DAE. These results suggest that attention plays a crucial role in the selective encoding of duration: attended durations are encoded, while encoding of unattended durations is either weak or absent.
Ischemia augments alloimmune injury through IL-6-driven CD4+ alloreactivity
Authors: Uehara Mayuko , Solhjou Zhabiz , Banouni Naima , Kasinath Vivek , Xiaqun Ye , Dai Li , Yilmam Osman , Yilmaz Mine , Ichimura Takaharu , Fiorina Paolo , Martins Paulo N. , Ohori Shunsuke , Guleria Indira , Maarouf Omar H. , Tullius Stefan G. , McGrath Martina M. , Abdi Reza 
Published: January 2018

AbstractIschemia reperfusion injuries (IRI) are unavoidable in solid organ transplantation. IRI augments alloimmunity but the mechanisms involved are poorly understood. Herein, we examined the effect of IRI on antigen specific alloimmunity. We demonstrate that ischemia promotes alloimmune activation, leading to more severe histological features of rejection, and increased CD4+ and CD8+ T cell graft infiltration, with a predominantly CD8+ IFNγ+ infiltrate. This process is dependent on the presence of alloreactive CD4+ T cells, where depletion prevented infiltration of ischemic grafts by CD8+ IFNγ+ T cells. IL-6 is a known driver of ischemia-induced rejection. Herein, depletion of donor antigen-presenting cells reduced ischemia-induced CD8+ IFNγ+ allograft infiltration, and improved allograft outcomes. Following prolonged ischemia, accelerated rejection was observed despite treatment with CTLA4Ig, indicating that T cell costimulatory blockade failed to overcome the immune activating effect of IRI. However, despite severe ischemic injury, treatment with anti-IL-6 and CTLA4Ig blocked IRI-induced alloimmune injury and markedly improved allograft survival. We describe a novel pathway where IRI activates innate immunity, leading to upregulation of antigen specific alloimmunity, resulting in chronic allograft injury. Based on these findings, we describe a clinically relevant treatment strategy to overcome the deleterious effect of IRI, and provide superior long-term allograft outcomes.
High dietary salt intake correlates with modulated Th17-Treg cell balance resulting in enhanced bone loss and impaired bone-microarchitecture in male mice
Authors: Dar Hamid Y. , Singh Anjali , Shukla Prashant , Anupam Rajaneesh , Mondal Rajesh K. , Mishra Pradyumna K. , Srivastava Rupesh K. 
Published: January 2018

AbstractOsteoporosis is associated with reduced density and quality of bone leading to weakened skeleton thereby increasing the risk of fractures responsible for increased morbidity and mortality. Due to preference for western food style the consumption of salt intake in our diets has increased many folds. High dietary salt intake has recently been linked with induction of Th17 cells along with impairment of Treg cells. Also, Th17 cells have been one of major players in the pathophysiology of various bone pathologies including osteoporosis. We thus hypothesized that high salt diet (HSD) intake would lead to enhanced bone loss by modulating Th17-Treg cell balance. In the present study, we report for the first time that HSD intake in male mice impairs both trabecular and cortical bone microarchitecture along with decreasing the mineral density and heterogeneity of bones. The HSD modulates host immune system and skews Treg-Th17 balance by promoting osteoclastogenic Th17 cells and inhibiting development of anti-osteoclastogenic Treg cells in mice. HSD also enhanced expression of proinflammatory cytokines (IL-6, TNF-α, RANKL and IL-17) and decreased the expression of anti-inflammatory cytokines (IL-10, IFN-γ). Taken together the present study for the first time establishes a strong correlation between high dietary salt intake and bone health via interplay between Th17-Treg cells.
Visible to near-IR fluorescence from single-digit detonation nanodiamonds: excitation wavelength and pH dependence
Authors: Reineck Philipp , Lau Desmond W. M. , Wilson Emma R. , Nunn Nicholas , Shenderova Olga A. , Gibson Brant C. 
Published: January 2018

AbstractDetonation nanodiamonds are of vital significance to many areas of science and technology. However, their fluorescence properties have rarely been explored for applications and remain poorly understood. We demonstrate significant fluorescence from the visible to near-infrared spectral regions from deaggregated, single-digit detonation nanodiamonds dispersed in water produced via post-synthesis oxidation. The excitation wavelength dependence of this fluorescence is analyzed in the spectral region from 400 nm to 700 nm as well as the particles’ absorption characteristics. We report a strong pH dependence of the fluorescence and compare our results to the pH dependent fluorescence of aromatic hydrocarbons. Our results significantly contribute to the current understanding of the fluorescence of carbon-based nanomaterials in general and detonation nanodiamonds in particular.
The Neuroprotective Effect of Thalidomide against Ischemia through the Cereblon-mediated Repression of AMPK Activity
Authors: Sawamura Naoya , Yamada Mariko , Fujiwara Miku , Yamada Haruka , Hayashi Hideki , Takagi Norio , Asahi Toru 
Published: January 2018

AbstractThalidomide was originally used as a sedative and found to be a teratogen, but now thalidomide and its derivatives are widely used to treat haematologic malignancies. Accumulated evidence suggests that thalidomide suppresses nerve cell death in neurologic model mice. However, detailed molecular mechanisms are unknown. Here we examined the molecular mechanism of thalidomide’s neuroprotective effects, focusing on its target protein, cereblon (CRBN), and its binding protein, AMP-activated protein kinase (AMPK), which plays an important role in maintaining intracellular energy homeostasis in the brain. We used a cerebral ischemia rat model of middle cerebral artery occlusion/reperfusion (MCAO/R). Thalidomide treatment significantly decreased the infarct volume and neurological deficits of MCAO/R rats. AMPK was the key signalling protein in this mechanism. Furthermore, we considered that the AMPK–CRBN interaction was altered when neuroprotective action by thalidomide occurred in cells under ischemic conditions. Binding was strong between AMPK and CRBN in normal SH-SY5Y cells, but was weakened by the addition of H2O2. However, when thalidomide was administered at the same time as H2O2, the binding of AMPK and CRBN was partly restored. These results suggest that thalidomide inhibits the activity of AMPK via CRBN under oxidative stress and suppresses nerve cell death.
Theoretical Study of Sesterfisherol Biosynthesis: Computational Prediction of Key Amino Acid Residue in Terpene Synthase
Authors: Sato Hajime , Narita Koji , Minami Atsushi , Yamazaki Mami , Wang Chao , Suemune Hironori , Nagano Shingo , Tomita Takeo , Oikawa Hideaki , Uchiyama Masanobu 
Published: January 2018

AbstractThe cyclization mechanisms involved in the biosynthesis of sesterterpenes are not fully understood. For example, there are two plausible reaction pathways for sesterfisherol biosynthesis, which differ in the order of ring cyclization: A-D-B/C (Path a) and A-B-C/D (Path b). It is difficult to capture intermediates of terpene cyclization, which is a complex, domino-type reaction, and so here we employed a combination of experimental and computational methods. Density functional theory calculations revealed unexpected intermediates and transition states, and implied that C–H···π interaction between a carbocation intermediate and an aromatic residue of sesterfisherol synthase (NfSS) plays a critical role, serving to accelerate the 1,2-H shift (thereby preventing triquinane carbocation formation) and to protect reactive carbocation intermediates from bases such as pyrophosphate or water in the active site. Site-directed mutagenesis of NfSS guided by docking simulations confirmed that phenylalanine F191 is a critical amino acid residue for sesterfisherol synthase, as the F191A mutant of NfSS produces novel sesterterpenes, but not sesterfisherol. Although both pathways are energetically viable, on the basis of our computational and experimental results, NfSS-mediated sesterfisherol biosynthesis appears to proceed via Path a. These findings may also provide new insight into the cyclization mechanisms in related sesterterpene synthases.
Buccal mucosa cell damage in individuals following dental X-ray examinations
Authors: Li Gang , Yang Pan , Hao Shuai , Hu Wei , Liang Cheng , Zou Bing-shuang , Ma Xu-chen 
Published: January 2018

AbstractThe aim of the present study was to monitor genotoxic and cytotoxic effect of X-ray on exfoliated buccal mucosa cells and investigate the association between the effects and the accumulated absorbed doses of oral mucosa. 98 participants’ buccal mucosa cells were collected before and 10 days after different series of dental radiographs performed. Cytological preparations were successively dyed with the methods of Feulgen and fast-green, and analyzed under a light microscope. Micronuclei (MN)and other cells were scored. Accumulated absorbed dose of buccal mucosa was estimated with the method of anthropomorphic phantom and dosimeter chips. The dose rang was 0.18–3.54 mGy. A significant difference in the rate of MN cell was found before and after X-ray examinations (P = 0.008) as well as in the rates of Pyknotic (p < 0.001) and Karyolytic cell (p = 0.0021). When only the patients whose mucosa absorbed dose is lower than 1 mGy was analyzed, significant differences were not found except for Karyolytic cells (p = 0.0313). There was a correlation between the accumulated does and the change rate (ρ = 0.25, p = 0.0118). The frequency of micronuclei cells in buccal mucosa may be increased when a series of dental radiographs including a CBCT examination was performed.
Diversity and metabolic potential of the microbiota associated with a soil arthropod
Authors: Bahrndorff Simon , de Jonge Nadieh , Hansen Jacob Kjerulf , Lauritzen Jannik Mørk Skovgaard , Spanggaard Lasse Holt , Sørensen Mathias Hamann , Yde Morten , Nielsen Jeppe Lund 
Published: January 2018

AbstractSpringtails are important members of the soil fauna and play a key role in plant litter decomposition, for example through stimulation of the microbial activity. However, their interaction with soil microorganisms remains poorly understood and it is unclear which microorganisms are associated to the springtail (endo) microbiota. Therefore, we assessed the structure of the microbiota of the springtailOrchesella cincta(L.) using 16S rRNA gene amplicon sequencing. Individuals were sampled across sites in the field and the microbiota and in particular the endomicrobiota were investigated. The microbiota was dominated by the families ofRickettsiaceae,EnterobacteriaceaeandComamonadaceaeand at the genus level the most abundant genera includedRickettsia,Chryseobacterium,Pseudomonas, andStenotrophomonas. Microbial communities were distinct for the interior of the springtails for measures of community diversity and exhibited structure according to collection sites. Functional analysis of the springtail bacterial community suggests that abundant members of the microbiota may be associated with metabolism including decomposition processes. Together these results add to the understanding of the microbiota of springtails and interaction with soil microorganisms including their putative functional roles.
Knowledge, Confidence, and Practice Patterns of Speech-Language Pathologists Working With Adults With Traumatic Brain Injury
Authors: Riedeman Sarah , Turkstra Lyn 
Published: January 2018

Purpose
Although speech-language pathologists (SLPs) are important members of the health care team serving adults with traumatic brain injury (TBI) with cognitive–communication disorders, little is known about services SLPs deliver and how they rate their own knowledge and skills. The aims of this study were to identify practice patterns, knowledge, and confidence levels of SLPs working with adults with TBI with cognitive–communication disorders.

Method
We surveyed 100 SLPs from rural and urban hospitals, skilled nursing facilities, and outpatient clinics in Wisconsin and analyzed data descriptively.

Results
SLPs in this sample had a combination of accurate and inaccurate knowledge related to TBI. Although all participants reported working with individuals with TBI, many participants rated themselves as lacking confidence or knowledge in this practice area. SLPs reported variable use of evidence-based procedures and training related to TBI.

Conclusion
Results confirmed the high prevalence of TBI-related practice among SLPs in medical settings, but there was variable knowledge, confidence, and use of current evidence in practice. SLP graduate training programs, individual providers, health care administrators, and the American Speech-Language-Hearing Association can use results from this study to advance and improve SLP clinical services for adults with TBI.
Using raster and vector data to identify objects for classify in flood risk. A case study: Raciborz
Authors: Porczek Mariusz , Rucińska Dorota , Lewiński Stanisław 
Published: January 2018

The severe flood of 1997, which seriously affected Polish, Czech and German territories, gave impetus to research into the management of flood-prone areas. The material losses caused by the “Flood of the Millennium” totalled billions of Polish zloty. The extent of the disaster and of infrastructure repair costs changed the attitude of many branches of the economy, and of science. This is the direct result of consideration of the introduction of changes into spatial management and crisis management. At the same time, it focused the interest of many who were trained in analysing the vulnerability of land-use features to natural disasters such as floods. Research into the spatial distribution of geographic environmental features susceptible to flood in the Odra valley was conducted at the Faculty of Geography and Regional Studies of the University of Warsaw using Geographic Information Systems (GIS).This study seeks to examine the possibility of adapting vector and raster data and using them for land-use classification in the context of risk of flood and inundation damage. The analysed area of the city and surrounding area of Raciborz, on the upper Odra River, is a case study for identifying objects and lands susceptible to natural hazards based on publicly available satellite databases of the highest resolution, which is a very important factor in the quality of further risk analyses for applied use.The objective of the research was to create a 10×10-m-pixel raster network using raster data made available by ESA (Copernicus Land Monitoring Service) and vector data from Open Street Map.
Prediction for driving behaviour in connection with socio – demographic characteristics and individual value system
Authors: Lazdins K.J. , Martinsone K. 
Published: January 2018

The aim of research „prediction for driving behaviour in connection with socio – demographic characteristics and individual value system” was to examine characteristics of individual value system prediction for driving behavior. It raised fundamental question for the research: 1. which of the individual value system characteristics predict driving behavior controlling gender and age.
In the study 108 respondentsparticipated, 40 (37.0%) men and 68 (63.0%) women who filled the questionnaire on the Internet. Two questionnaires were used – „Latvian driving behavior survey” [1], the value and levels of availability relations in different spheres of life” [2, 3].
The results showed that the value system integrity / disintegrity indicator predicts distracted driving, explains 18% of variation and is statistically significantly. Internal vacuum and age statistically significantly negatively predicts risky driving explaining 17% of variation. Age statistically significantly predicts safe and courteous driving, explains 12% of variation. Value system integrity / disintegrity indicator and gender, statistically significantly negatively predicts summary indicator of dangerous driving explain 22% of variation. Age statistically significantly negatively predicts distracted driving, explains 30% of variation.
The results can serve as the basis to create new driving behavior interventions and also applicable to psychologist's professional work, when counseling individuals of this group, as well as can be used in the future development of the field, science and research.
AbDesigner3D: a structure-guided tool for peptide-based antibody production
Authors: Saethang Thammakorn , Hodge Kenneth , Kimkong Ingorn , Payne D Michael , Knepper Mark A , Pisitkun Trairak 
Published: January 2018

Abstract

Summary
We present AbDesigner3D, a new tool for identification of optimal immunizing peptides for antibody production using a peptide-based strategy. AbDesigner3D integrates 3D structural data from the Protein Data Bank (PDB) with UniProt data, which includes basic sequence data, post-translational modification sites, SNP occurrences and more. Other features, such as uniqueness and conservation scores, are calculated based on sequences from UniProt. The 3D visualization capabilities allow an intuitive interface, while an abundance of quantitative output simplifies the process of comparing immunogen peptides. Important quantitative features added in this tool include calculation and display of accessible surface area (ASA) and protein-protein interacting residues (PPIR). The specialized data visualization features of AbDesigner3D will greatly assist users to optimize their choice of immunizing peptides.

Availability and implementation
AbDesigner3D is freely available at http://sysbio.chula.ac.th/AbDesigner3D or https://hpcwebapps.cit.nih.gov/AbDesigner3D/.

Supplementary information
Supplementary data are available at Bioinformatics online.