bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Novel Biocontainment Strategy Makes Bacterial Growth and Survival Dependent on Phosphite
Authors: Hirota Ryuichi , Abe Kenji , Katsuura Zen-ichiro , Noguchi Reiji , Moribe Shigeaki , Motomura Kei , Ishida Takenori , Alexandrov Maxym , Funabashi Hisakage , Ikeda Takeshi , Kuroda Akio 
Published: March 2017

AbstractThere is a growing demand to develop biocontainment strategies that prevent unintended proliferation of genetically modified organisms in the open environment. We found that the hypophosphite (H3PO2, HPt) transporter HtxBCDE from Pseudomonas stutzeri WM88 was also capable of transporting phosphite (H3PO3, Pt) but not phosphate (H3PO4, Pi), suggesting the potential for engineering a Pt/HPt-dependent bacterial strain as a biocontainment strategy. We disrupted all Pi and organic Pi transporters in an Escherichia coli strain expressing HtxABCDE and a Pt dehydrogenase, leaving Pt/HPt uptake and oxidation as the only means to obtain Pi. Challenge on non-permissive growth medium revealed that no escape mutants appeared for at least 21 days with a detection limit of 1.94 × 10−13 per colony forming unit. This represents, to the best of our knowledge, the lowest escape frequency among reported strategies. Since Pt/HPt are ecologically rare and not available in amounts sufficient for the growth of the Pt/HPt-dependent bacteria, this strategy offers a reliable and practical method for biocontainment.
A Stronger Multi-observable Uncertainty Relation
Authors: Song Qiu-Cheng , Li Jun-Li , Peng Guang-Xiong , Qiao Cong-Feng 
Published: March 2017

AbstractUncertainty relation lies at the heart of quantum mechanics, characterizing the incompatibility of non-commuting observables in the preparation of quantum states. An important question is how to improve the lower bound of uncertainty relation. Here we present a variance-based sum uncertainty relation for N incompatible observables stronger than the simple generalization of an existing uncertainty relation for two observables. Further comparisons of our uncertainty relation with other related ones for spin-"Equation missing" and spin-1 particles indicate that the obtained uncertainty relation gives a better lower bound.
Direct measurement of the propagation of the phase-transition region of liquid crystals
Authors: Sato Takahiro , Katayama Kenji 
Published: March 2017

AbstractMany types of active matter, such as biological cells, have liquid-crystalline membranes, which are soft and flexible in their interactions with their surroundings and sometimes allow molecular-structural or -orientational changes to extend for long distances, owing to long-range molecular interactions. Despite the technological and fundamental importance of these long-range changes, there is no good physical property with which to express them for the liquid crystal. Here, we show direct measurements of the propagation of structural or orientational changes due to long-range molecular interactions in liquid crystals. We induced a patterned phase transition in a liquid crystal via illumination with a fringe pattern and observed the propagation of the phase-transition region. We determined that the propagation occurred in a ballistic manner with a velocity of 80–110 m/s and that two types of propagation—side-by-side and head-to-tail molecular interactions—were found.
Effect of defects on reaction of NiO surface with Pb-contained solution
Authors: Kim Jongjin , Hou Binyang , Park Changyong , Bahn Chi Bum , Hoffman Jason , Black Jennifer , Bhattacharya Anand , Balke Nina , Hong Hawoong , Kim Ji Hyun , Hong Seungbum 
Published: March 2017

AbstractIn order to understand the role of defects in chemical reactions, we used two types of samples, which are molecular beam epitaxy (MBE) grown NiO(001) film on Mg(001) substrate as the defect free NiO prototype and NiO grown on Ni(110) single crystal as the one with defects. In-situ observations for oxide-liquid interfacial structure and surface morphology were performed for both samples in water and Pb-contained solution using high-resolution X-ray reflectivity and atomic force microscopy. For the MBE grown NiO, no significant changes were detected in the high-resolution X-ray reflectivity data with monotonic increase in roughness. Meanwhile, in the case of native grown NiO on Ni(110), significant changes in both the morphology and atomistic structure at the interface were observed when immersed in water and Pb-contained solution. Our results provide simple and direct experimental evidence of the role of the defects in chemical reaction of oxide surfaces with both water and Pb-contained solution.
Determination of Low Loss in Isotopically Pure Single Crystal 28Si at Low Temperatures and Single Microwave Photon Energy
Authors: Kostylev Nikita , Goryachev Maxim , Bulanov Andrey D. , Gavva Vladimir A. , Tobar Michael E. 
Published: March 2017

AbstractThe low dielectric losses of an isotopically pure single crystal 28Si sample were determined at a temperature of 20 mK and at powers equivalent to that of a single photon. Whispering Gallery Mode (WGM) analysis revealed large Quality Factors of order 2 × 106 (dielectric loss ~5 × 10−7) at high powers, degrading to 7 × 105 (dielectric loss ~1.4 × 10−6) at single photon energy. A very low-loss narrow line width paramagnetic spin flip transition was detected with extreme sensitivity in 28Si, with very small concentration below 1011 cm−3 (less than 10 parts per trillion) and g-factor of 1.995 ± 0.008. Such determination was only possible due to the low dielectric photonic losses combined with the long lifetime of the spin transition (low magnetic loss), which enhances the magnetic AC susceptibility. Such low photonic loss at single photon energy combined with the narrow line width of the spin ensemble, indicate that single crystal 28Si could be an important crystal for future cavity QED experiments.
Priming of transcriptional memory responses via the chromatin accessibility landscape in T cells
Authors: Tu Wen Juan , Hardy Kristine , Sutton Christopher R. , McCuaig Robert , Li Jasmine , Dunn Jenny , Tan Abel , Brezar Vedran , Morris Melanie , Denyer Gareth , Lee Sau Kuen , Turner Stephen J. , Seddiki Nabila , Smith Corey , Khanna Rajiv , Rao Sudha 
Published: March 2017

AbstractMemory T cells exhibit transcriptional memory and “remember” their previous pathogenic encounter to increase transcription on re-infection. However, how this transcriptional priming response is regulated is unknown. Here we performed global FAIRE-seq profiling of chromatin accessibility in a human T cell transcriptional memory model. Primary activation induced persistent accessibility changes, and secondary activation induced secondary-specific opening of previously less accessible regions associated with enhanced expression of memory-responsive genes. Increased accessibility occurred largely in distal regulatory regions and was associated with increased histone acetylation and relative H3.3 deposition. The enhanced re-stimulation response was linked to the strength of initial PKC-induced signalling, and PKC-sensitive increases in accessibility upon initial stimulation showed higher accessibility on re-stimulation. While accessibility maintenance was associated with ETS-1, accessibility at re-stimulation-specific regions was linked to NFAT, especially in combination with ETS-1, EGR, GATA, NFκB, and NR4A. Furthermore, NFATC1 was directly regulated by ETS-1 at an enhancer region. In contrast to the factors that increased accessibility, signalling from bHLH and ZEB family members enhanced decreased accessibility upon re-stimulation. Interplay between distal regulatory elements, accessibility, and the combined action of sequence-specific transcription factors allows transcriptional memory-responsive genes to “remember” their initial environmental encounter.
Targeted deletion of Crif1 in mouse epidermis impairs skin homeostasis and hair morphogenesis
Authors: Shin Jung-Min , Choi Dae-Kyoung , Sohn Kyung-Cheol , Kim Ji-Young , Im Myung , Lee Young , Seo Young-Joon , Shong Minho , Lee Jeung-Hoon , Kim Chang Deok 
Published: March 2017

AbstractThe epidermis, which consists mainly of keratinocytes, acts as a physical barrier to infections by regulating keratinocyte proliferation and differentiation. Hair follicles undergo continuous cycling to produce new one. Therefore, optimum supply of energy from the mitochondria is essential for maintaining skin homeostasis and hair growth. CRIF1 is a mitochondrial protein that regulates mitoribosome-mediated synthesis and insertion of mitochondrial oxidative phosphorylation polypeptides into the mitochondrial membrane in mammals. Recent studies reveal that conditional knockout (cKO) of Crif1 in specific tissues of mice induced mitochondrial dysfunction. To determine whether the mitochondrial function of keratinocytes affects skin homeostasis and hair morphogenesis, we generated epidermis-specific Crif1 cKO mice. Deletion of Crif1 in epidermis resulted in impaired mitochondrial function and Crif1 cKO mice died within a week. Keratinocyte proliferation and differentiation were markedly inhibited in Crif1 cKO mice. Furthermore, hair follicle morphogenesis of Crif1 cKO mice was disrupted by down-regulation of Wnt/β-catenin signaling. These results demonstrate that mitochondrial function in keratinocytes is essential for maintaining epidermal homeostasis and hair follicle morphogenesis.
Efficacy of alginate-based reflux suppressant and magnesium-aluminium antacid gel for treatment of heartburn in pregnancy: a randomized double-blind controlled trial
Authors: Meteerattanapipat Pontip , Phupong Vorapong 
Published: March 2017

AbstractThe aim of this study was to compare the therapeutic efficacy of alginate-based reflux suppressant and magnesium-aluminium antacid gel for treatment of heartburn in pregnancy. A double-blinded, randomized, controlled trial was conducted. One hundred pregnant women at less than 36 weeks gestation with heartburn at least twice per week were randomized to either alginate-based reflux suppressant or to magnesium-aluminium antacid gel. Details of heartburn were recorded before beginning the treatment and the second week of study. Primary outcome measure was the improvement of heartburn frequency after treatment and secondary outcome were the improvement of heartburn intensity, quality of life, maternal satisfaction, maternal side effects, pregnancy and neonatal outcomes. There was no difference between treatment and control groups in improvement of heartburn frequency (80% vs 88%, p = 0.275), 50% reduction of frequency of heartburn (56% vs 52%, p = 0.688), improvement of heartburn intensity (92% vs 92%, p = 1.000) and 50% reduction of heartburn intensity (68% vs 80% cases, p = 0.075). There were also no significant differences in quality of life, maternal satisfaction, maternal side effects, pregnancy and neonatal outcomes. Alginate-based reflux suppressant was not different from magnesium-aluminium antacid gel in the treatment of heartburn in pregnancy.
Analysis of spatial heterogeneity in normal epithelium and preneoplastic alterations in mouse prostate tumor models
Authors: Valkonen Mira , Ruusuvuori Pekka , Kartasalo Kimmo , Nykter Matti , Visakorpi Tapio , Latonen Leena 
Published: March 2017

AbstractCancer involves histological changes in tissue, which is of primary importance in pathological diagnosis and research. Automated histological analysis requires ability to computationally separate pathological alterations from normal tissue with all its variables. On the other hand, understanding connections between genetic alterations and histological attributes requires development of enhanced analysis methods suitable also for small sample sizes. Here, we set out to develop computational methods for early detection and distinction of prostate cancer-related pathological alterations. We use analysis of features from HE stained histological images of normal mouse prostate epithelium, distinguishing the descriptors for variability between ventral, lateral, and dorsal lobes. In addition, we use two common prostate cancer models, Hi-Myc and Pten+/− mice, to build a feature-based machine learning model separating the early pathological lesions provoked by these genetic alterations. This work offers a set of computational methods for separation of early neoplastic lesions in the prostates of model mice, and provides proof-of-principle for linking specific tumor genotypes to quantitative histological characteristics. The results obtained show that separation between different spatial locations within the organ, as well as classification between histologies linked to different genetic backgrounds, can be performed with very high specificity and sensitivity.
Structural and functional studies of a noncanonical Dicer from Entamoeba histolytica
Authors: Yu Xiang , Li Xuhang , Zheng Lina , Ma Jinbiao , Gan Jianhua 
Published: March 2017

AbstractRNaseIII proteins are dsRNA-specific endonucleases involved in many important biological processes, such as small RNA processing and maturation in eukaryotes. Various small RNAs have been identified in a protozoan parasite Entamoeba histolytica. EhRNaseIII is the only RNaseIII endonuclease domain (RIIID)-containing protein in E. histolytica. Here, we present three crystal structures that reveal several unique structural features of EhRNaseIII, especially the interactions between the two helixes (α1 and α7) flanking the RIIID core domain. Structure and sequence analysis indicate that EhRNaseIII is a noncanonical Dicer and it lacks a dsRBD in the C-terminal region (CTR). In vitro studies suggest that EhRNaseIII prefers to bind and cleave longer dsRNAs, generating products around 25 nucleotides in length. Truncation of the CTR or attaching the dsRBD of Aquifex aeolicus RNaseIII can enhance the binding and cleavage activities of EhRNaseIII. In combination with in vitro crosslinking assay, our results suggested that EhRNaseIII functions in a cooperative mode. We speculate that some partner proteins may exist in E. histolytica and regulates the activity of EhRNaseIII through interaction with its CTR. Our studies support that EhRNaseIII plays an important role in producing small RNAs in E. histolytica.
Predicting siRNA efficacy based on multiple selective siRNA representations and their combination at score level
Authors: He Fei , Han Ye , Gong Jianting , Song Jiazhi , Wang Han , Li Yanwen 
Published: March 2017

AbstractSmall interfering RNAs (siRNAs) may induce to targeted gene knockdown, and the gene silencing effectiveness relies on the efficacy of the siRNA. Therefore, the task of this paper is to construct an effective siRNA prediction method. In our work, we try to describe siRNA from both quantitative and qualitative aspects. For quantitative analyses, we form four groups of effective features, including nucleotide frequencies, thermodynamic stability profile, thermodynamic of siRNA-mRNA interaction, and mRNA related features, as a new mixed representation, in which thermodynamic of siRNA-mRNA interaction is introduced to siRNA efficacy prediction for the first time to our best knowledge. And then an F-score based feature selection is employed to investigate the contribution of each feature and remove the weak relevant features. Meanwhile, we encode the siRNA sequence and existed empirical design rules as a qualitative siRNA representation. These two kinds of siRNA representations are combined to predict siRNA efficacy by supported Vector Regression (SVR) at score level. The experimental results indicate that our method may select the features with powerful discriminative ability and make the two kinds of siRNA representations work at full capacity. The prediction results also demonstrate that our method can outperform other popular siRNA efficacy prediction algorithms.
Rectifying the output of vibrational piezoelectric energy harvester using quantum dots
Authors: Li Lijie 
Published: March 2017

AbstractPiezoelectric energy harvester scavenges mechanical vibrations and generates electricity. Researchers have strived to optimize the electromechanical structures and to design necessary external power management circuits, aiming to deliver high power and rectified outputs ready for serving as batteries. Complex deformation of the mechanical structure results in charges with opposite polarities appearing on same surface, leading to current loss in the attached metal electrode. External power management circuits such as rectifiers comprise diodes that consume power and have undesirable forward bias. To address the above issues, we devise a novel integrated piezoelectric energy harvesting device that is structured by stacking a layer of quantum dots (QDs) and a layer of piezoelectric material. We find that the QD can rectify electrical charges generated from the piezoelectric material because of its adaptable conductance to the electrochemical potentials of both sides of the QDs layer, so that electrical current causing energy loss on the same surface of the piezoelectric material can be minimized. The QDs layer has the potential to replace external rectification circuits providing a much more compact and less power-consumption solution.
BDE-99 impairs differentiation of human and mouse NPCs into the oligodendroglial lineage by species-specific modes of action
Authors: Dach Katharina , Bendt Farina , Huebenthal Ulrike , Giersiefer Susanne , Lein Pamela J. , Heuer Heike , Fritsche Ellen 
Published: March 2017

AbstractPolybrominated diphenyl ethers (PBDEs) are bioaccumulating flame retardants causing developmental neurotoxicity (DNT) in humans and rodents. Their DNT effects are suspected to involve thyroid hormone (TH) signaling disruption. Here, we tested the hypothesis whether disturbance of neural progenitor cell (NPC) differentiation into the oligodendrocyte lineage (O4+cells) by BDE-99 involves disruption of TH action in human and mouse (h,m)NPCs. Therefore, we quantified differentiation of NPCs into O4+cells and measured their maturation via expression of myelin-associated genes (hMBP, mMog) in presence and absence of TH and/or BDE-99. T3 promoted O4+cell differentiation in mouse, but not hNPCs, and induced hMBP/mMoggene expression in both species. BDE-99 reduced generation of human and mouse O4+cells, but there is no indication for BDE-99 interfering with cellular TH signaling during O4+cell formation. BDE-99 reduced hMBPexpression due to oligodendrocyte reduction, but concentrations that did not affect the number of mouse O4+cells inhibited TH-induced mMogtranscription by a yet unknown mechanism. In addition, ascorbic acid antagonized only the BDE-99-dependent loss of human, not mouse, O4+cells by a mechanism probably independent of reactive oxygen species. These data point to species-specific modes of action of BDE-99 on h/mNPC development into the oligodendrocyte lineage.
KUS121, a VCP modulator, attenuates ischemic retinal cell death via suppressing endoplasmic reticulum stress
Authors: Hata Masayuki , Ikeda Hanako O. , Kikkawa Chinami , Iwai Sachiko , Muraoka Yuki , Hasegawa Tomoko , Kakizuka Akira , Yoshimura Nagahisa 
Published: March 2017

AbstractIschemic neural damages cause several devastating diseases, including brain stroke and ischemic retinopathies, and endoplasmic reticulum (ER) stress has been proposed to be the underlying mechanism of the neuronal cell death of these conditions. We previously synthesized Kyoto University substances (KUSs) as modulators of valosin-containing protein (VCP); KUSs inhibit VCP ATPase activity and protect cells from different cell death-inducing insults. Here, we examined the efficacy of KUS121 in a rat model of retinal ischemic injury. Systemic administration of KUS121 to rats with ischemic retinal injury significantly suppressed inner retinal thinning and death of retinal ganglion and amacrine cells, with a significant functional maintenance of visual functions, as judged by electroretinography. Furthermore, intravitreal injection of KUS121, which is the clinically preferred route of drug administration for retinal diseases, appeared to show an equal or better neuroprotective efficacy in the ischemic retina compared with systemic administration. Indeed, induction of the ER stress marker C/EBP homologous protein (CHOP) after the ischemic insult was significantly suppressed by KUS121 administration. Our study suggests VCP modulation by KUS as a promising novel therapeutic strategy for ischemic neuronal diseases.
Hypertension and breast cancer risk: a systematic review and meta-analysis
Authors: Han Hedong , Guo Wei , Shi Wentao , Yu Yamei , Zhang Yunshuo , Ye Xiaofei , He Jia 
Published: March 2017

AbstractObservational studies examining the relationship between hypertension and breast cancer risk have reported conflicting findings. We conducted this systematic review and meta-analysis to summarize the evidence regarding the association between hypertension and risk of breast cancer. Eligible studies were identified through a comprehensive literature search of PubMed, EMBASE, and the Cochrane library until August 2016. We included observational studies that reported relative risks (RR) with corresponding 95% confidence intervals (CIs). Results from individual studies were pooled by using a random-effects model. 29 articles of 30 studies, with totally 11643 cases of breast cancer, were eligible for inclusion in the meta-analysis. We observed a statistically significant association between hypertension and increased breast cancer risk (RR: 1.15; 95% CI: 1.08, 1.22). In the subgroup analysis, we found a positive association between hypertension and breast cancer incidence among postmenopausal women (RR: 1.20; 95% CI: 1.09, 1.31). In contrast, hypertension was not associated with risk of breast cancer among premenopausal women (RR: 0.97; 95% CI: 0.84, 1.12) and Asian population (RR: 1.07; 95% CI: 0.94, 1.22).This meta-analysis collectively suggests a significantly association between hypertension and breast cancer risk, specifically for postmenopausal hypertensive women.
Functional conservation and coherence of HIV-1 subtype A Vpu alleles
Authors: Romani Bizhan , Kavyanifard Amirarsalan , Allahbakhshi Elham 
Published: March 2017

AbstractFunctional studies of HIV-1 proteins are normally conducted using lab adapted strains of HIV-1. The extent of those functions in clinical strains is sometimes unknown. In this study, we amplified and sequenced HIV-1 Vpu from 10 Iranian patients infected with HIV-1. Phylogenetic analysis indicated that the Vpu alleles were closely related to the CRF35_AD from Iran and subtype A Vpu. We addressed some of the well-established functions of the HIV-1 Vpu, as well as some of its recently reported functions. Ability of the clinical strains of subtype A Vpu alleles for downregulation of CD4 was similar to that of the lab adapted NL4.3 Vpu. Majority of the subtype A Vpu alleles performed stronger than NL4.3 Vpu for downregulation of SNAT1. The Vpu alleles differentially induced downregulation of HLA-C, ranging from no effect to 88% downregulation of surface HLA-C. Downregulation of tetherin and enhancement of virus release was similar for the subtype A Vpu alleles and NL4.3. Subtype A Vpu alleles were more potent when compared with NL4.3 for inhibition of NF-κB activation. Our study shows that subtype A Vpu alleles exert the classical functions of HIV-1 Vpu.