bluuebunny/crossref_metadata_2025_split huggingface dataset:
HMGA1P7-pseudogene regulates H19 and Igf2 expression by a competitive endogenous RNA mechanism
Authors: De Martino Marco , Forzati Floriana , Marfella Marianna , Pellecchia Simona , Arra Claudio , Terracciano Luigi , Fusco Alfredo , Esposito Francesco 
Published: November 2016

AbstractRecent studies have revealed that pseudogene transcripts can function as competing endogenous RNAs, and thereby can also contribute to cancer when dysregulated. We have recently identified two pseudogenes, HMGA1P6 and HMGA1P7 for the HMGA1 gene whose overexpression has a critical role in cancer progression. These pseudogenes work as competitive endogenous RNA decoys for HMGA1 and other cancer related genes suggesting their role in carcinogenesis. Looking for new HMGA1 pseudogene ceRNAs, we performed RNA sequencing technology on mouse embryonic fibroblasts deriving from transgenic mice overexpressing HMGA1P7. Here, we report that HMGA1P7 mRNA sustains the H19 and Igf2 overexpression by acting as miRNA decoy. Lastly, the expression of HMGA1P7 was significantly correlated with H19 and IGF2 levels in human breast cancer thereby suggesting a role for HMGA1P7 deregulation in this neoplasia.
Direct observation of electronic-liquid-crystal phase transitions and their microscopic origin in La1/3Ca2/3MnO3
Authors: Tao J. , Sun K. , Yin W.-G. , Wu L. , Xin H. , Wen J. G. , Luo W. , Pennycook S. J. , Tranquada J. M. , Zhu Y. 
Published: November 2016

AbstractThe ground-state electronic order in doped manganites is frequently associated with a lattice modulation, contributing to their many interesting properties. However, measuring the thermal evolution of the lattice superstructure with reciprocal-space probes alone can lead to ambiguous results with competing interpretations. Here we provide direct observations of the evolution of the superstructure in La1/3Ca2/3MnO3 in real space, as well as reciprocal space, using transmission electron microscopic (TEM) techniques. We show that the transitions are the consequence of a proliferation of dislocations plus electronic phase separation. The resulting states are well described by the symmetries associated with electronic-liquid-crystal (ELC) phases. Moreover, our results resolve the long-standing controversy over the origin of the incommensurate superstructure and suggest a new structural model that is consistent with recent theoretical calculations.
Bph32, a novel gene encoding an unknown SCR domain-containing protein, confers resistance against the brown planthopper in rice
Authors: Ren Juansheng , Gao Fangyuan , Wu Xianting , Lu Xianjun , Zeng Lihua , Lv Jianqun , Su Xiangwen , Luo Hong , Ren Guangjun 
Published: November 2016

AbstractAn urgent need exists to identify more brown planthopper (Nilaparvata lugensStål, BPH) resistance genes, which will allow the development of rice varieties with resistance to BPH to counteract the increased incidence of this pest species. Here, using bioinformatics and DNA sequencing approaches, we identified a novel BPH resistance gene, LOC_Os06g03240 (MSU LOCUS ID), from the rice variety Ptb33 in the interval between the markers RM19291 and RM8072 on the short arm of chromosome 6, where a gene for resistance to BPH was mapped by Jirapong Jairinet al.and renamed as “Bph32”. This gene encodes a unique short consensus repeat (SCR) domain protein. Sequence comparison revealed that theBph32gene shares 100% sequence identity with its allele inOryza latifolia. The transgenic introgression ofBph32into a susceptible rice variety significantly improved resistance to BPH. Expression analysis revealed thatBph32was highly expressed in the leaf sheaths, where BPH primarily settles and feeds, at 2 and 24 h after BPH infestation, suggesting thatBph32may inhibit feeding in BPH. Western blotting revealed the presence of Pph (Ptb33) and Tph (TN1) proteins using a Penta-His antibody, and both proteins were insoluble. This study provides information regarding a valuable gene for rice defence against insect pests.
Spatially differentiated trends in urbanization, agricultural land abandonment and reclamation, and woodland recovery in Northern China
Authors: Wang Chao , Gao Qiong , Wang Xian , Yu Mei 
Published: November 2016

AbstractUncovering magnitude, trend, and spatial pattern of land cover/land use changes (LCLUC) is crucial for understanding mechanisms of LCLUC and assisting land use planning and conservation. China has been undergoing unprecedented economic growth, massive rural-to-urban migration, and large-scale policy-driven ecological restoration, and therefore encountering enormous LCLUC in recent decades. However, comprehensive understandings of spatiotemporal LCLUC dynamics and underlying mechanisms are still lacking. Based on classification of annual LCLU maps from MODIS satellite imagery, we proposed a land change detection method to capture significant land change hotspots over Northern China during 2001–2013, and further analyzed temporal trends and spatial patterns of LCLUC. We found rapid decline of agricultural land near urban was predominantly caused by urban expansion. The process was especially strong in North China Plain with 14,057 km2 of urban gain and −21,017 km2 of agricultural land loss. To offset the loss of agricultural land, Northeast China Plain and Xinjiang were reclaimed. Substantial recovery of forests (49,908 km2) and closed shrubland (60,854 km2) occurred in mountainous regions due to abandoned infertile farmland, secondary succession, and governmental conservation policies. The spatial patterns and trends of LCLUC in Northern China provide information to support effective environmental policies towards sustainable development.
Active Brownian particles and run-and-tumble particles separate inside a maze
Authors: Khatami Maryam , Wolff Katrin , Pohl Oliver , Ejtehadi Mohammad Reza , Stark Holger 
Published: November 2016

AbstractA diverse range of natural and artificial self-propelled particles are known and are used nowadays. Among them, active Brownian particles (ABPs) and run-and-tumble particles (RTPs) are two important classes. We numerically study non-interacting ABPs and RTPs strongly confined to different maze geometries in two dimensions. We demonstrate that by means of geometrical confinement alone, ABPs are separable from RTPs. By investigating Matryoshka-like mazes with nested shells, we show that a circular maze has the best filtration efficiency. Results on the mean first-passage time reveal that ABPs escape faster from the center of the maze, while RTPs reach the center from the rim more easily. According to our simulations and a rate theory, which we developed, ABPs in steady state accumulate in the outermost region of the Matryoshka-like mazes, while RTPs occupy all locations within the maze with nearly equal probability. These results suggest a novel technique for separating different types of self-propelled particles by designing appropriate confining geometries without using chemical or biological agents.
Molecular Insight into Affinities of Gallated and Nongallated Proanthocyanidins Dimers to Lipid Bilayers
Authors: Zhu Wei , Xiong Le , Peng Jinming , Deng Xiangyi , Gao Jun , Li Chun-mei 
Published: November 2016

AbstractExperimental studies have proved the beneficial effects of proanthocyanidins (Pas) relating to interaction with the cell membrane. But the detailed mechanisms and structure-function relationship was unclear. In present study, molecular dynamics (MD) simulations were used to study the interactions of four PA dimers with a lipid bilayer composed of 1:1 mixed 1-palmitoyl-2-oleoyl phosphatidylcholine (POPC) and 1-palmitoyl-2-oleoyl phosphatidylethanolamine (POPE). The results showed that the gallated PA dimers had much higher affinities to the bilayer with lower binding free energies compared with nongallated PA dimers. The gallated PA dimers penetrated deeper into the bilayer and formed more hydrogen bonds (H-bonds) with bilayer oxygen atoms, especially the deeper oxygen atoms of the lipids simultaneously, thus inducing stronger lateral expansion of the membrane and lipid tails disorder. The present results provided molecular insights into the interactions between PA dimers and bio-membranes and agreed with our experimental results well. These molecular interactions helped to elucidate the structure-function relationship of the PA dimers and provided a foundation for a better understanding of the underlying mechanisms of the bioactivities of PA oligomers.
Structural and thermal analysis of a hyper-branched exopolysaccharide produced by submerged fermentation of mushroom mycelium
Authors: Chen L. , Cheng W. N. , Zhang B. B. , Cheung P. C. K. 
Published: November 2016

An exopolysaccharide (PTR-EPS1) purified from the culture medium of the mycelial fermentation of Pleurotus tuber-regium had a weight-average molecular mass of 173.6 kDa and a radius of 55.6 nm.
Effectiveness of Low Cut Modified Amplification using Receiver in the Canal Hearing Aid in Individuals with Auditory Neuropathy Spectrum Disorder
Authors: Prabhu Prashanth , Barman Animesh 
Published: November 2016

Introduction The studies on hearing aid benefit in individuals with auditory neuropathy spectrum disorder (ANSD) shows limited benefit. Low cut modified amplification is found to be effective in few individuals with ANSD. With advancement in technology, receiver in the canal (RIC) hearing aids have proven to be more effective than traditional behind the ear (BTE) hearing aids.
Objective Thus, the present study attempts to determine the effectiveness of low cut modified amplification using RIC and BTE.
Method Twenty participants with ANSD were fitted with BTE and RIC using traditional and low cut modified amplification. We divided them into good and poor performers based on unaided speech identification scores (SIS). We then compared aided SIS and aided benefit across conditions in good and poor performers with ANSD across both conditions using BTE and RIC.
Results The results of the study showed that the aided performance improved with low cut modified amplification in both BTE and RIC hearing aids. The improvement noticed with low-cut modified fitting with RIC was significant in more than BTE, especially in good performers with ANSD.
Conclusion The improved clarity and naturalness of sound with RIC may have led to better aided scores and better acceptance of the hearing aid. Thus, low-cut modified amplification, preferably with RIC, needs to be attempted in fitting individuals with ANSD, especially in those with good unaided SIS in quiet.
Total Knee Arthroplasty: What to Expect? A Survey of the Members of the Dutch Knee Society on Long-Term Recovery after Total Knee Arthroplasty
Authors: van der Steen Marieke , Janssen Rob , Reijman Max , Tolk Jaap 
Published: November 2016

AbstractThe rate of satisfaction after total knee arthroplasty (TKA) is consistently reported around 80%, leaving one in five patients unsatisfied to some extent. Fulfillment of expectations is reported as the strongest predictor of treatment satisfaction. In this study, we aimed to evaluate what Dutch orthopedic surgeons assume are realistic expectations for recovery 1 year after TKA. We invited the members of the Dutch Knee Society (DKS) to fill out a web-based questionnaire. For expectation measurement, the validated Dutch version of the Hospital for Special Surgery (HSS) knee replacement expectations survey was used. A total of 150 invitations were successfully sent; 84 orthopedic surgeons responded (56%). The overall HSS knee replacement expectation score was 66.0 (standard deviation, 14.0) on a 0 to 100 scale. Most improvement was predicted for the items “pain relief” and “walking short distances.” Expectations related to patients' ability to kneel or squat after TKA were scored poorly. To the opinion of the members of the DKS, after TKA improvement can be expected in domains of pain, function, activities, and psychological wellbeing. Return to normal is not likely to occur, especially in demanding physical activities.
Retinoic acid signaling determines the fate of uterine stroma in the mouse Müllerian duct
Authors: Nakajima Tadaaki , Iguchi Taisen , Sato Tomomi 
Published: November 2016

SignificanceOviduct, uterus, and vagina are all derived from the Müllerian duct. Epithelial fate of these female reproductive organs in developing mice is determined by factors secreted from the stroma; however, how the preceding stromal differentiation of female reproductive tracts from the Müllerian duct occurs is still unclear. This study showed that retinoic acid (RA) signaling was activated in the proximal Müllerian duct, which develops into oviduct and uterus. Furthermore, RA treatment induced uterine stromal differentiation, whereas inhibition of RA receptor signaling induced vaginal stromal differentiation. Therefore, we concluded that RA establishes a border between the stroma of uterus and vagina.
Disturbance is the key to plant invasions in cold environments
Authors: Lembrechts Jonas J. , Pauchard Aníbal , Lenoir Jonathan , Nuñez Martín A. , Geron Charly , Ven Arne , Bravo-Monasterio Pablo , Teneb Ernesto , Nijs Ivan , Milbau Ann 
Published: November 2016

Significance
This work provides a complete experimental answer to the longstanding question of which local factors determine the success (i.e., establishment, growth, and flowering) of common nonnative plant invaders at their coldest physiological limits. Using a multifactorial seed-addition experiment along repeated elevational gradients in two sub(ant)arctic mountain regions, we pinpoint the relative contribution of all main candidate determinants: temperature, disturbance, nutrient addition, and propagule pressure. We warn that climate change and direct human disturbances will together result in increased plant invasion in cold-climate ecosystems in the near future.
Graphene oxide-based efficient and scalable solar desalination under one sun with a confined 2D water path
Authors: Li Xiuqiang , Xu Weichao , Tang Mingyao , Zhou Lin , Zhu Bin , Zhu Shining , Zhu Jia 
Published: November 2016

Significance
Direct solar desalination, which produces desalinated water directly using solar energy with minimum carbon footprint, is considered a promising technology to address the global water scarcity. Here, we report a solar desalination device, with efficient two-dimensional water supply and suppressed thermal loss, which can enable an efficient (80% under one-sun illumination) and effective (four orders salinity decrement) solar desalination. The energy transfer efficiency of this foldable graphene oxide film-based device fabricated by a scalable process is independent of water quantity and can be achieved without optical or thermal supporting systems, therefore significantly improving the scalability and feasibility of this technology toward a complementary portable and personalized water solution.
The innate immune receptor Dectin-2 mediates the phagocytosis of cancer cells by Kupffer cells for the suppression of liver metastasis
Authors: Kimura Yoshitaka , Inoue Asuka , Hangai Sho , Saijo Shinobu , Negishi Hideo , Nishio Junko , Yamasaki Sho , Iwakura Yoichiro , Yanai Hideyuki , Taniguchi Tadatsugu 
Published: November 2016

SignificanceThe liver is a common site for metastatic disease, and liver metastasis is strongly correlated with poor prognosis. Therefore, an understanding of how liver metastasis is regulated by the immune system is one of the most important issues in cancer immunology. Liver-resident immune cells may either suppress or promote liver metastasis. In this study, we show that Dectin-2 and macrophage C-type lectin, both of which belong to the C-type lectin family of innate receptors, is expressed on resident liver macrophages known as Kupffer cells and play critical roles in the suppression of liver metastasis by enhancing the cells’ phagocytotic activity against cancer cells. Our study sheds light on the protective role of Kupffer cells in liver metastasis with therapeutic implications.
Advanced Boolean modeling of biological networks applied to systems pharmacology
Authors: Irurzun-Arana Itziar , Pastor José Martín , Trocóniz Iñaki F , Gómez-Mantilla José David 
Published: November 2016

AbstractMotivationLiterature on complex diseases is abundant but not always quantitative. Many molecular pathways are qualitatively well described but this information cannot be used in traditional quantitative mathematical models employed in drug development. Tools for analysis of discrete networks are useful to capture the available information in the literature but have not been efficiently integrated by the pharmaceutical industry. We propose an expansion of the usual analysis of discrete networks that facilitates the identification/validation of therapeutic targets.ResultsIn this article, we propose a methodology to perform Boolean modeling of Systems Biology/Pharmacology networks by using SPIDDOR (Systems Pharmacology for effIcient Drug Development On R) R package. The resulting models can be used to analyze the dynamics of signaling networks associated to diseases to predict the pathogenesis mechanisms and identify potential therapeutic targets.Availability and ImplementationThe source code is available at https://github.com/SPIDDOR/SPIDDOR.Supplementary informationSupplementary data are available at Bioinformatics online.
Computational prediction of species-specific malonylation sites via enhanced characteristic strategy
Authors: Wang Li-Na , Shi Shao-Ping , Xu Hao-Dong , Wen Ping-Ping , Qiu Jian-Ding 
Published: November 2016

Abstract

Motivation
Protein malonylation is a novel post-translational modification (PTM) which orchestrates a variety of biological processes. Annotation of malonylation in proteomics is the first-crucial step to decipher its physiological roles which are implicated in the pathological processes. Comparing with the expensive and laborious experimental research, computational prediction can provide an accurate and effective approach to the identification of many types of PTMs sites. However, there is still no online predictor for lysine malonylation.

Results
By searching from literature and database, a well-prepared up-to-data benchmark datasets were collected in multiple organisms. Data analyses demonstrated that different organisms were preferentially involved in different biological processes and pathways. Meanwhile, unique sequence preferences were observed for each organism. Thus, a novel malonylation site online prediction tool, called MaloPred, which can predict malonylation for three species, was developed by integrating various informative features and via an enhanced feature strategy. On the independent test datasets, AUC (area under the receiver operating characteristic curves) scores are obtained as 0.755, 0.827 and 0.871 for Escherichia coli (E.coli), Mus musculus (M.musculus) and Homo sapiens (H.sapiens), respectively. The satisfying results suggest that MaloPred can provide more instructive guidance for further experimental investigation of protein malonylation.

Availability and Implementation
http://bioinfo.ncu.edu.cn/MaloPred.aspx.

Supplementary information
Supplementary data are available at Bioinformatics online.
Intrathecal Amphotericin B: A 60-Year Experience in Treating Coccidioidal Meningitis
Authors: Ho Jackie , Fowler Pete , Heidari Arash , Johnson Royce H 
Published: November 2016

Abstract
Coccidioidal meningitis (CM) is a devastating complication of coccidioidomycosis. Since the late 1950s, intrathecal (IT) amphotericin B deoxycholate (AmBd) has been successfully used to treat and often cure this disease, reducing mortality rates from 100% to approximately 30%. The introduction of azoles further revolutionized the treatment of coccidioidal infections. However, IT AmBd remains the only known curative option in the management of CM. While the use of IT AmBd is well described in many articles, few discuss the actual methods behind preparation, titration, and dosing strategies utilized. The practitioners at Kern Medical (Bakersfield, California) have &gt;60 years of experience in the utilization of IT AmBd and the treatment of CM. This article describes the practice experience in the treatment of CM, preparation of IT AmBd, and the different dosing strategies used in regard to route of administration (ie, cisternal, lumbar, ventricular).
Graphics help patients distinguish between urgent and non-urgent deviations in laboratory test results
Authors: Zikmund-Fisher Brian J , Scherer Aaron M , Witteman Holly O , Solomon Jacob B , Exe Nicole L , Tarini Beth A , Fagerlin Angela 
Published: November 2016

ABSTRACT
Objective: Most electronic health record systems provide laboratory test results to patients in table format. We tested whether presenting such results in visual displays (number lines) could improve understanding.
Materials and Methods: We presented 1620 adults recruited from a demographically diverse Internet panel with hypothetical results from several common laboratory tests, first showing near-normal results and then more extreme values. Participants viewed results in either table format (with a “standard range” provided) or one of 3 number line formats: a simple 2-color format, a format with diagnostic categories such as “borderline high” indicated by colored blocks, and a gradient format that used color gradients to smoothly represent increasing risk as values deviated from standard ranges. We measured respondents’ subjective sense of urgency about each test result, their behavioral intentions, and their perceptions of the display format.
Results: Visual displays reduced respondents’ perceived urgency and desire to contact health care providers immediately for near-normal test results compared to tables but did not affect their perceptions of extreme values. In regression analyses controlling for respondent health literacy, numeracy, and graphical literacy, gradient line displays resulted in the greatest sensitivity to changes in test results.
Discussion: Unlike tables, which only tell patients whether test results are normal or not, visual displays can increase the meaningfulness of test results by clearly defining possible values and leveraging color cues and evaluative labels.
Conclusion: Patient-facing displays of laboratory test results should use visual displays rather than tables to increase people’s sensitivity to variations in their results.