bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid screening for specific glycosylation and pathogen interactions on a 78 species avian egg white glycoprotein microarray
Authors: Utratna Marta , Annuk Heidi , Gerlach Jared Q. , Lee Yuan C. , Kane Marian , Kilcoyne Michelle , Joshi Lokesh 
Published: July 2017

AbstractThere is an urgent need for discovery of novel antimicrobials and carbohydrate-based anti-adhesive strategies are desirable as they may not promote resistance. Discovery of novel anti-adhesive molecules from natural product libraries will require the use of a high throughput screening platform. Avian egg white (EW) provides nutrition for the embryo and protects against infection, with glycosylation responsible for binding certain pathogens. In this study, a microarray platform of 78 species of avian EWs was developed and profiled for glycosylation using a lectin panel with a wide range of carbohydrate specificities. The dominating linkages of sialic acid in EWs were determined for the first time using the lectins MAA and SNA-I. EW glycosylation similarity among the different orders of birds did not strictly depend on phylogenetic relationship. The interactions of five strains of bacterial pathogens, including Escherichia coli, Staphylococcus aureus and Vibrio cholera, identified a number of EWs as potential anti-adhesives, with some as strain- or species-specific. Of the two bacterial toxins examined, shiga-like toxin 1 subunit B bound to ten EWs with similar glycosylation more intensely than pigeon EW. This study provides a unique platform for high throughput screening of natural products for specific glycosylation and pathogen interactions. This platform may provide a useful platform in the future for discovery of anti-adhesives targeted for strain and species specificity.
Bimanual grasping does not adhere to Weber’s law
Authors: Ganel Tzvi , Namdar Gal , Mirsky Avigail 
Published: July 2017

AbstractAccording to Weber’s law, a fundamental principle of perception, visual resolution decreases in a linear fashion with an increase in object size. Previous studies have shown, however, that unlike for perception, grasping does not adhere to Weber’s law. Yet, this research was limited by the fact that perception and grasping were examined for a restricted range of stimulus sizes bounded by the maximum fingers span. The purpose of the current study was to test the generality of the dissociation between perception and action across a different type of visuomotor task, that of bimanual grasping. Bimanual grasping also allows to effectively measure visual resolution during perception and action across a wide range of stimulus sizes compared to unimanual grasps. Participants grasped or estimated the sizes of large objects using both their hands. The results showed that bimanual grasps violated Weber’s law throughout the entire movement trajectory. In contrast, Just Noticeable Differences (JNDs) for perceptual estimations of the objects increased linearly with size, in agreement with Weber’s law. The findings suggest that visuomotor control, across different types of actions and for a large range of size, is based on absolute rather than on relative representation of object size.
Full-length cloning, sequence analysis and expression detection of the β-tubulin gene from the Chinese gall aphid (Schlechtendalia chinensis)
Authors: Liu Ping , Yang Zi-Xiang , Chen Xiao-Ming , Chen Hang 
Published: July 2017

AbstractSome insect galls are formed on sumac plants by certain aphid species and have been used for medicinal and chemical purposes as they are rich in tannins. The most prominent species among gall aphids in China is Schlechtendalia chinensis, which formed horn-shaped galls on the winged rachis of Rhus chinensis. S. chinensis has a complex life cycle, with a switch of hosts between R. chinensis and certain mosses, and a switch of sexual and asexual reproduction (cyclical parthenogenesis). We have cloned a full-length cDNA of the β-tubulin gene from S. chinensis, using qPCR and RACE. This cDNA has 1606 base pairs with a 251 bp 5′-untranslated region (5′-UTR) and a 15 bp 3′-untranslated region (3′-UTR). The gene encodes a protein with 376 amino acids residues. The expression levels of the β-tubulin gene in S. chinensis were investigated among fundatrigeniae and overwintering larvae rearing under either natural conditions, or at 7.5 °C and 18 °C. No significant differences (P > 0.01) in gene expression levels were found in insects under these conditions. It is indicates that the β-tubulin gene is highly conserved and then it may be used as a reference for further research in gene expression and reproduction determination in this important aphid.
YY1’s role in the Peg3 imprinted domain
Authors: He Hongzhi , Ye An , Perera Bambarendage P. U. , Kim Joomyeong 
Published: July 2017

AbstractThe ICR (Imprinting Control Region) of the Peg3 (Paternally Expressed Gene 3) domain contains an unusual cluster of YY1 binding sites. In the current study, these YY1 binding sites were mutated to characterize the unknown roles in the mouse Peg3 domain. According to the results, paternal and maternal transmission of the mutant allele did not cause any major effect on the survival of the pups. In the mutants, the maternal-specific DNA methylation on the ICR was properly established and maintained, causing no major effect on the imprinting of the domain. In contrast, the paternal transmission resulted in changes in the expression levels of several genes: down-regulation of Peg3 and Usp29 and up-regulation of Zim1. These changes were more pronounced during the neonatal stage than during the adult stage. In the case of Peg3 and Zim1, the levels of the observed changes were also different between males and females, suggesting the different degrees of YY1 involvement between two sexes. Overall, the results indicated that YY1 is mainly involved in controlling the transcriptional levels, but not the DNA methylation, of the Peg3 domain.
Sexual pair-formation in a cicada mediated by acoustic behaviour of females and positive phonotaxis of males
Authors: Hou Zehai , Luo Changqing , Roberts J. Dale , Wei Cong 
Published: July 2017

AbstractThe functions of female song found in a few cicadas have rarely been studied. In the cicada Subpsaltria yangi we investigated the acoustic behaviour and signal structure of songs produced by females, the phonotaxis of males, and mate choice, as well as the selective pressure imposed on this species by predators. Pair-formation in S. yangi occurs when males signal, females respond, then males move to signaling females, which is opposite to that in most other cicadas where females move to calling males. Females only mate once and are sexually unreceptive after copulation. Most males mate once, but ~25% mate multiply. Females display little direct evidence of mate preference or choice of males, and all mate encounters led to a successful mating. Only males are attacked by a robber fly, Philonicus albiceps, while flying to females. This imposes strong selection on males – only males who can evade predators mate. Males are also attracted to human simulations of female calls. This behaviour exposes the mating system to impacts from anthropogenic noise systems which could disrupt mating activity of this species. Our results improve the understanding of mate choice/competition in cicadas, and are valuable for future studies of the evolution of sound communication in the Cicadoidea.
Relationship between obesity and development of erosive reflux disease: A mediation analysis of the role of cardiometabolic risk factors
Authors: Lee Hyuk , Lim Yaeji , Chi Sangah , Min Yang Won , Min Byung-Hoon , Lee Jun Haeng , Rhee Poong-Lyul , Kim Jae J. 
Published: July 2017

AbstractThis study aimed to evaluate whether the relationship between obesity and erosive reflux disease (ERD) is mediated by cardiometabolic risk factors. This cohort study included subjects who underwent repeated endoscopy. To assess whether the association between body mass index (BMI) and ERD development was mediated by cardiometabolic parameters, multivariate Cox proportional hazard models were fitted for mediation analysis. Of 15,154 subjects with negative index endoscopy findings during health check-up, 11,686 subjects who underwent repeated endoscopy were included. During follow-up, 1,367 incident ERD events (11.7%) were observed. Without mediation effect, the multivariate adjusted hazard ratio of BMI was 1.21 (95% CI, 1.03–1.42) in overweight and 1.39 (95% CI, 1.19–1.62) in obese individuals compared to normal weight individuals. When the metabolic syndrome was included as a mediator, the hazard ratio became 1.19 (95% CI, 1.00–1.40) in overweight and 1.29 (95% CI, 1.10–1.52) in obese individuals. Both systolic blood pressure and triglyceride level were found to fully mediate the effect of BMI on ERD. Fasting glucose level was a partial mediator. The estimated percentage of total effect mediated by cardiometabolic risk factors was 35.4%. Cardiometabolic parameters partially or fully mediate the association between overweight and obesity and incident ERD.
The Rice Phytochrome Genes, PHYA and PHYB, Have Synergistic Effects on Anther Development and Pollen Viability
Authors: Sun Wei , Hui Xu Xiao , Lu Xingbo , Xie Lixia , Bai Bo , Zheng Chongke , Sun Hongwei , He Yanan , Xie Xian-zhi 
Published: July 2017

AbstractPhytochromes are the main plant photoreceptors regulating multiple developmental processes. However, the regulatory network of phytochrome-mediated plant reproduction has remained largely unexplored. There are three phytochromes in rice, phyA, phyB and phyC. No changes in fertility are observed in the single mutants, whereas the seed-setting rate of thephyA phyBdouble mutant is significantly reduced. Histological and cytological analyses showed that the reduced fertility of thephyA phyBmutant was due to defects in both anther and pollen development. The four anther lobes in thephyA phyBmutant were developed at different stages with fewer pollen grains, most of which were aborted. At the mature stage, more than one lobe in the double mutant was just consisted of several cell layers. To identify genes involved in phytochrome-mediated anther development, anther transcriptomes ofphyA,phyBandphyA phyBmutants were compared to that of wild-type rice respectively. Analysis of 2,241 double-mutant-specific differentially expressed transcripts revealed that the metabolic profiles, especially carbohydrate metabolism, were altered greatly, and heat-shock responses were activated in the double mutant. This study firstly provides valuable insight into the complex regulatory networks underlying phytochrome-mediated anther and pollen development in plants, and offers novel clues for hybrid rice breeding.
Nanocrystalline diamond protects Zr cladding surface against oxygen and hydrogen uptake: Nuclear fuel durability enhancement
Authors: Škarohlíd Jan , Ashcheulov Petr , Škoda Radek , Taylor Andrew , Čtvrtlík Radim , Tomáštík Jan , Fendrych František , Kopeček Jaromír , Cháb Vladimír , Cichoň Stanislav , Sajdl Petr , Macák Jan , Xu Peng , Partezana Jonna M. , Lorinčík Jan , Prehradná Jana , Steinbrück Martin , Kratochvílová Irena 
Published: July 2017

AbstractIn this work, we demonstrate and describe an effective method of protecting zirconium fuel cladding against oxygen and hydrogen uptake at both accident and working temperatures in water-cooled nuclear reactor environments. Zr alloy samples were coated with nanocrystalline diamond (NCD) layers of different thicknesses, grown in a microwave plasma chemical vapor deposition apparatus. In addition to showing that such an NCD layer prevents the Zr alloy from directly interacting with water, we show that carbon released from the NCD film enters the underlying Zr material and changes its properties, such that uptake of oxygen and hydrogen is significantly decreased. After 100–170 days of exposure to hot water at 360 °C, the oxidation of the NCD-coated Zr plates was typically decreased by 40%. Protective NCD layers may prolong the lifetime of nuclear cladding and consequently enhance nuclear fuel burnup. NCD may also serve as a passive element for nuclear safety. NCD-coated ZIRLO claddings have been selected as a candidate for Accident Tolerant Fuel in commercially operated reactors in 2020.
A Cryosectioning Technique for the Observation of Intracellular Structures and Immunocytochemistry of Tissues in Atomic Force Microscopy (AFM)
Authors: Usukura Eiji , Narita Akihiro , Yagi Akira , Sakai Nobuaki , Uekusa Yoshitsugu , Imaoka Yuka , Ito Shuichi , Usukura Jiro 
Published: July 2017

AbstractThe use of cryosectioning facilitates the morphological analysis and immunocytochemistry of cells in tissues in atomic force microscopy (AFM). The cantilever can access all parts of a tissue sample in cryosections after the embedding medium (sucrose) has been replaced with phosphate-buffered saline (PBS), and this approach has enabled the production of a type of high-resolution image. The images resembled those obtained from freeze-etching replica electron microscopy (EM) rather than from thin-section EM. The AFM images showed disks stacked and enveloped by the cell membrane in rod photoreceptor outer segments (ROS) at EM resolution. In addition, ciliary necklaces on the surface of connecting cilium, three-dimensional architecture of synaptic ribbons, and the surface of the post-synaptic membrane facing the active site were revealed, which were not apparent using thin-section EM. AFM could depict the molecular binding of anti-opsin antibodies conjugated to a secondary fluorescent antibody bound to the disk membrane. The specific localization of the anti-opsin binding sites was verified through correlation with immunofluorescence signals in AFM combined with confocal fluorescence microscope. To prove reproducibility in other tissues besides retina, cryosectioning-AFM was also applied to elucidate molecular organization of sarcomere in a rabbit psoas muscle.
Strain Balanced AlGaN/GaN/AlGaN nanomembrane HEMTs
Authors: Chang Tzu-Hsuan , Xiong Kanglin , Park Sung Hyun , Yuan Ge , Ma Zhenqiang , Han Jung 
Published: July 2017

AbstractSingle crystal semiconductor nanomembranes (NM) are important in various applications such as heterogeneous integration and flexible devices. This paper reports the fabrication of AlGaN/GaN NMs and NM high electron mobility transistors (HEMT). Electrochemical etching is used to slice off single-crystalline AlGaN/GaN layers while preserving their microstructural quality. A double heterostructure design with a symmetric strain profile is employed to ensure minimal residual strain in freestanding NMs after release. The mobility of the two-dimensional electron gas (2DEG), formed by the AlGaN/GaN heterostructure, is noticeably superior to previously reported values of many other NMs. AlGaN/GaN nanomembrane HEMTs are fabricated on SiO2 and flexible polymeric substrates. Excellent electrical characteristics, including a high ON/OFF ratio and transconductance, suggest that III-Nitrides nanomembranes are capable of supporting high performance applications.
Permeability Barrier and Microstructure of Skin Lipid Membrane Models of Impaired Glucosylceramide Processing
Authors: Sochorová Michaela , Staňková Klára , Pullmannová Petra , Kováčik Andrej , Zbytovská Jarmila , Vávrová Kateřina 
Published: July 2017

AbstractCeramide (Cer) release from glucosylceramides (GlcCer) is critical for the formation of the skin permeability barrier. Changes in β-glucocerebrosidase (GlcCer’ase) activity lead to diminished Cer, GlcCer accumulation and structural defects in SC lipid lamellae; however, the molecular basis for this impairment is not clear. We investigated impaired GlcCer-to-Cer processing in human Cer membranes to determine the physicochemical properties responsible for the barrier defects. Minor impairment (5–25%) of the Cer generation from GlcCer decreased the permeability of the model membrane to four markers and altered the membrane microstructure (studied by X-ray powder diffraction and infrared spectroscopy), in agreement with the effects of topical GlcCer in human skin. At these concentrations, the accumulation of GlcCer was a stronger contributor to this disturbance than the lack of human Cer. However, replacement of 50–100% human Cer by GlcCer led to the formation of a new lamellar phase and the maintenance of a rather good barrier to the four studied permeability markers. These findings suggest that the major cause of the impaired water permeability barrier in complete GlcCer’ase deficiency is not the accumulation of free GlcCer but other factors, possibly the retention of GlcCer bound in the corneocyte lipid envelope.
Iron-Catalyzed Cross-Coupling: Mechanistic Insight for Rational Applications in Synthesis
Authors: Parchomyk Tobias , Koszinowski Konrad 
Published: July 2017

Iron-catalyzed cross-coupling reactions provide a promising way to form new carbon–carbon bonds and build up molecular complexity. This short review presents recent advances in the synthetic application of these reactions as well as in the elucidation of their mechanism. It also highlights remaining problems and aims at pointing out ways toward possible remedies.1	Introduction2	Synthesis: Recent Accomplishments and Unsolved Problems2.1	Substrate Scope: Electrophiles2.2	Substrate Scope: Nucleophiles2.3	Catalyst Activity and Chemoselectivity2.4	Stereoselectivity2.5	Practical Aspects3	Mechanism: Recent Insights and Open Questions3.1	Transmetallation and Activation of the Iron Precatalyst3.2	Coupling via Oxidative Addition and Reductive Elimination3.3	Coupling via C–X Bond Homolysis and Radical Rebound3.4	Coupling via Bimolecular C–X Bond Homolysis3.5	Other Reactions of Organoiron Species with Electrophiles4	Toward Rational Reaction Improvement5	Conclusion
A Case of Succinyl-CoA:3-Oxoacid CoA Transferase Deficiency Presenting with Severe Acidosis in a 14-Month-Old Female: Evidence for Pathogenicity of a Point Mutation in the OXCT1 Gene
Authors: Zheng Daniel , Hooper Michael , Spencer-Manzon Michele , Pierce Richard 
Published: July 2017

AbstractWe describe a case of succinyl-CoA:3-oxoacid CoA transferase (SCOT) deficiency in an otherwise healthy 14 month-old female. She presented with lethargy, tachypnea, and hyperpnea with hypoglycemia and a severe anion gap metabolic acidosis. Early management included correction of the acidosis and metabolic support with dextrose and insulin. Inborn errors of metabolism are rare outside the neonatal period. However, SCOT deficiency may present at older ages. Maintaining a high index of suspicion, immediate transfer to a pediatric intensive care unit, and prompt metabolic support are key to achieving a favorable outcome.
Neuroimaging in Neonatal Nonketotic Hyperglycinemia
Authors: Hattiholi Virupaxi , Kamate Mahesh 
Published: July 2017

AbstractNonketotic hyperglycinemia is a fatal disorder of glycine metabolism presenting with intractable epilepsy, hypotonia, and developmental delay in infancy. Diagnostic tests,such as cerebrospinal fluid glycine estimation and genetic diagnostic methods, are not widely available in developing countries and hence many cases are missed or wrongly diagnosed. The magnetic resonance imaging features, such as abnormal signal intensity in the dorsal pons, midbrain, central tegmental tract, cerebral peduncle, and posterior limb of the internal capsule indicate an important clue to the possibility of the disease and help in guiding the treating neonatologist.
Intrinsically disordered chromatin protein NUPR1 binds to the C-terminal region of Polycomb RING1B
Authors: Santofimia-Castaño Patricia , Rizzuti Bruno , Pey Ángel L. , Soubeyran Philippe , Vidal Miguel , Urrutia Raúl , Iovanna Juan L. , Neira José L. 
Published: July 2017

SignificanceWe describe the interaction between an intrinsically disordered protein (IDP), NUPR1, and the well-folded C-terminal region of RING1B protein of the Polycomb complex, involving residues Ala33 and Thr68 of the IDP. These observations are significant because they raise the possibility that NUPR1 aids the function of the members of the Polycomb complex, playing an active role in carcinogenesis.
Identification of a vesicular ATP release inhibitor for the treatment of neuropathic and inflammatory pain
Authors: Kato Yuri , Hiasa Miki , Ichikawa Reiko , Hasuzawa Nao , Kadowaki Atsushi , Iwatsuki Ken , Shima Kazuhiro , Endo Yasuo , Kitahara Yoshiro , Inoue Tsuyoshi , Nomura Masatoshi , Omote Hiroshi , Moriyama Yoshinori , Miyaji Takaaki 
Published: July 2017

Significance
Although the incidence of chronic pain is estimated at 20–25% worldwide, optimal drug treatment regimens with few side effects have yet to be developed. In this study, we demonstrated that clodronate is a potent and selective inhibitor of vesicular ATP release that attenuates neuropathic and inflammatory pain unrelated to bone abnormalities. Clodronate was more effective and associated with comparatively fewer side effects than existing drugs. Thus, the nonopioid agent clodronate may represent a unique treatment strategy for chronic pain via inhibition of vesicular ATP release, suggesting that clodronate may be effective in the treatment of several diseases involving purinergic chemical transmission, including inflammatory diseases, diabetes, and neurological disorders. Our study identifies a transporter-targeted analgesic drug.
FOLD: a method to optimize power in meta-analysis of genetic association studies with overlapping subjects
Authors: Kim Emma E , Lee Seunghoon , Lee Cue Hyunkyu , Oh Hyunjung , Song Kyuyoung , Han Buhm 
Published: July 2017

Abstract

Motivation
In genetic association studies, meta-analyses are widely used to increase the statistical power by aggregating information from multiple studies. In meta-analyses, participating studies often share the same individuals due to the shared use of publicly available control data or accidental recruiting of the same subjects. As such overlapping can inflate false positive rate, overlapping subjects are traditionally split in the studies prior to meta-analysis, which requires access to genotype data and is not always possible. Fortunately, recently developed meta-analysis methods can systematically account for overlapping subjects at the summary statistics level.

Results
We identify and report a phenomenon that these methods for overlapping subjects can yield low power. For instance, in our simulation involving a meta-analysis of five studies that share 20% of individuals, whereas the traditional splitting method achieved 80% power, none of the new methods exceeded 32% power. We found that this low power resulted from the unaccounted differences between shared and unshared individuals in terms of their contributions towards the final statistic. Here, we propose an optimal summary-statistic-based method termed as FOLD that increases the power of meta-analysis involving studies with overlapping subjects.

Availability and implementation
Our method is available at http://software.buhmhan.com/FOLD.

Supplementary information
Supplementary data are available at Bioinformatics online.