bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simplified ChIP-exo assays
Authors: Rossi Matthew J. , Lai William K. M. , Pugh B. Franklin 
Published: July 2018

AbstractChIP-seq and ChIP-exo identify where proteins bind along any genome in vivo. Although ChIP-seq is widely adopted in academic research, it has inherently high noise. In contrast, ChIP-exo has relatively low noise and achieves near-base pair resolution. Consequently, and unlike other genomic assays, ChIP-exo provides structural information on genome-wide binding proteins. Construction of ChIP-exo libraries is technically difficult. Here we describe greatly simplified ChIP-exo methods, each with use-specific advantages. This is achieved through assay optimization and use of Tn5 tagmentation and/or single-stranded DNA ligation. Greater library yields, lower processing time, and lower costs are achieved. In comparing assays, we reveal substantial limitations in other ChIP-based assays. Importantly, the new ChIP-exo assays allow high-resolution detection of some protein-DNA interactions in organs and in as few as 27,000 cells. It is suitable for high-throughput parallelization. The simplicity of ChIP-exo now makes it a highly appropriate substitute for ChIP-seq, and for broader adoption.
High-throughput discovery of organic cages and catenanes using computational screening fused with robotic synthesis
Authors: Greenaway R. L. , Santolini V. , Bennison M. J. , Alston B. M. , Pugh C. J. , Little M. A. , Miklitz M. , Eden-Rump E. G. B. , Clowes R. , Shakil A. , Cuthbertson H. J. , Armstrong H. , Briggs M. E. , Jelfs K. E. , Cooper A. I. 
Published: July 2018

AbstractSupramolecular synthesis is a powerful strategy for assembling complex molecules, but to do this by targeted design is challenging. This is because multicomponent assembly reactions have the potential to form a wide variety of products. High-throughput screening can explore a broad synthetic space, but this is inefficient and inelegant when applied blindly. Here we fuse computation with robotic synthesis to create a hybrid discovery workflow for discovering new organic cage molecules, and by extension, other supramolecular systems. A total of 78 precursor combinations were investigated by computation and experiment, leading to 33 cages that were formed cleanly in one-pot syntheses. Comparison of calculations with experimental outcomes across this broad library shows that computation has the power to focus experiments, for example by identifying linkers that are less likely to be reliable for cage formation. Screening also led to the unplanned discovery of a new cage topology—doubly bridged, triply interlocked cage catenanes.
Spatial frequency sensitivity in macaque midbrain
Authors: Chen Chih-Yang , Sonnenberg Lukas , Weller Simone , Witschel Thede , Hafed Ziad M. 
Published: July 2018

AbstractVisual brain areas exhibit tuning characteristics well suited for image statistics present in our natural environment. However, visual sensation is an active process, and if there are any brain areas that ought to be particularly in tune with natural scene statistics, it would be sensory-motor areas critical for guiding behavior. Here we found that the rhesus macaque superior colliculus, a structure instrumental for rapid visual exploration with saccades, detects low spatial frequencies, which are the most prevalent in natural scenes, much more rapidly than high spatial frequencies. Importantly, this accelerated detection happens independently of whether a neuron is more or less sensitive to low spatial frequencies to begin with. At the population level, the superior colliculus additionally over-represents low spatial frequencies in neural response sensitivity, even at near-foveal eccentricities. Thus, the superior colliculus possesses both temporal and response gain mechanisms for efficient gaze realignment in low-spatial-frequency-dominated natural environments.
Abrupt high-latitude climate events and decoupled seasonal trends during the Eemian
Authors: Salonen J. Sakari , Helmens Karin F. , Brendryen Jo , Kuosmanen Niina , Väliranta Minna , Goring Simon , Korpela Mikko , Kylander Malin , Philip Annemarie , Plikk Anna , Renssen Hans , Luoto Miska 
Published: July 2018

AbstractThe Eemian (the Last Interglacial; ca. 129–116 thousand years ago) presents a testbed for assessing environmental responses and climate feedbacks under warmer-than-present boundary conditions. However, climate syntheses for the Eemian remain hampered by lack of data from the high-latitude land areas, masking the climate response and feedbacks in the Arctic. Here we present a high-resolution (sub-centennial) record of Eemian palaeoclimate from northern Finland, with multi-model reconstructions for July and January air temperature. In contrast with the mid-latitudes of Europe, our data show decoupled seasonal trends with falling July and rising January temperatures over the Eemian, due to orbital and oceanic forcings. This leads to an oceanic Late-Eemian climate, consistent with an earlier hypothesis of glacial inception in Europe. The interglacial is further intersected by two strong cooling and drying events. These abrupt events parallel shifts in marine proxy data, linked to disturbances in the North Atlantic oceanic circulation regime.
Spin inversion in graphene spin valves by gate-tunable magnetic proximity effect at one-dimensional contacts
Authors: Xu Jinsong , Singh Simranjeet , Katoch Jyoti , Wu Guanzhong , Zhu Tiancong , Žutić Igor , Kawakami Roland K. 
Published: July 2018

AbstractGraphene has remarkable opportunities for spintronics due to its high mobility and long spin diffusion length, especially when encapsulated in hexagonal boron nitride (h-BN). Here, we demonstrate gate-tunable spin transport in such encapsulated graphene-based spin valves with one-dimensional (1D) ferromagnetic edge contacts. An electrostatic backgate tunes the Fermi level of graphene to probe different energy levels of the spin-polarized density of states (DOS) of the 1D ferromagnetic contact, which interact through a magnetic proximity effect (MPE) that induces ferromagnetism in graphene. In contrast to conventional spin valves, where switching between high- and low-resistance configuration requires magnetization reversal by an applied magnetic field or a high-density spin-polarized current, we provide an alternative path with the gate-controlled spin inversion in graphene.
Machine learning hydrogen adsorption on nanoclusters through structural descriptors
Authors: Jäger Marc O. J. , Morooka Eiaki V. , Federici Canova Filippo , Himanen Lauri , Foster Adam S. 
Published: July 2018

AbstractCatalytic activity of the hydrogen evolution reaction on nanoclusters depends on diverse adsorption site structures. Machine learning reduces the cost for modelling those sites with the aid of descriptors. We analysed the performance of state-of-the-art structural descriptors Smooth Overlap of Atomic Positions, Many-Body Tensor Representation and Atom-Centered Symmetry Functions while predicting the hydrogen adsorption (free) energy on the surface of nanoclusters. The 2D-material molybdenum disulphide and the alloy copper–gold functioned as test systems. Potential energy scans of hydrogen on the cluster surfaces were conducted to compare the accuracy of the descriptors in kernel ridge regression. By having recourse to data sets of 91 molybdenum disulphide clusters and 24 copper–gold clusters, we found that the mean absolute error could be reduced by machine learning on different clusters simultaneously rather than separately. The adsorption energy was explained by the local descriptor Smooth Overlap of Atomic Positions, combining it with the global descriptor Many-Body Tensor Representation did not improve the overall accuracy. We concluded that fitting of potential energy surfaces could be reduced significantly by merging data from different nanoclusters.
Recurrent loss of heterozygosity correlates with clinical outcome in pancreatic neuroendocrine cancer
Authors: Lawrence Ben , Blenkiron Cherie , Parker Kate , Tsai Peter , Fitzgerald Sandra , Shields Paula , Robb Tamsin , Yeong Mee Ling , Kramer Nicole , James Sarah , Black Mik , Fan Vicky , Poonawala Nooriyah , Yap Patrick , Coats Esther , Woodhouse Braden , Ramsaroop Reena , Yozu Masato , Robinson Bridget , Henare Kimiora , Koea Jonathan , Johnston Peter , Carroll Richard , Connor Saxon , Morrin Helen , Elston Marianne , Jackson Christopher , Reid Papaarangi , Windsor John , MacCormick Andrew , Babor Richard , Bartlett Adam , Damianovich Dragan , Knowlton Nicholas , Grimmond Sean , Findlay Michael , Print Cristin 
Published: July 2018

AbstractPancreatic neuroendocrine tumors (pNETs) are uncommon cancers arising from pancreatic islet cells. Here we report the analysis of gene mutation, copy number, and RNA expression of 57 sporadic well-differentiated pNETs. pNET genomes are dominated by aneuploidy, leading to concordant changes in RNA expression at the level of whole chromosomes and chromosome segments. We observed two distinct patterns of somatic pNET aneuploidy that are associated with tumor pathology and patient prognosis. Approximately 26% of the patients in this series had pNETs with genomes characterized by recurrent loss of heterozygosity (LoH) of 10 specific chromosomes, accompanied by bi-allelicMEN1inactivation and generally poor clinical outcome. Another ~40% of patients had pNETs that lacked this recurrent LoH pattern but had chromosome 11 LoH, bi-allelicMEN1inactivation, and universally good clinical outcome. The somatic aneuploidy allowed pathogenic germline variants (e.g.,ATM) to be expressed unopposed, with RNA expression patterns showing inactivation of downstream tumor suppressor pathways. No prognostic associations were found with tumor morphology, single gene mutation, or expression of RNAs reflecting the activity of immune, differentiation, proliferative or tumor suppressor pathways. In pNETs, single gene mutations appear to be less important than aneuploidy, withMEN1the only statistically significant recurrently mutated driver gene. In addition, only one pNET in the series had clearly actionable single nucleotide variants (SNVs) (inPTENandFLCN) confirmed by corroborating RNA expression changes. The two clinically relevant patterns of LoH described here define a novel oncogenic mechanism and a plausible route to genomic precision oncology for this tumor type.
Corrosion avoidance in lightweight materials for automotive applications
Authors: Liu Ming , Guo Yang , Wang Jeff , Yergin Mark 
Published: July 2018

AbstractDue to increasing vehicle greenhouse gas emission regulations across the globe, the automotive industry is facing pressure to improving fuel economy. The key to achieving this is reducing vehicle mass and developing alternative energy vehicles, thereby reducing environmental impact. Lightweighting has become one of the most important aspects to consider in the design and manufacture of modern vehicles, while electric vehicles require a different approach to design and build. All the aforementioned factors have a significant impact on materials selection and usage, and corrosion is a vital consideration. In this article, we discuss and summarize some of the challenges and demands of future fuel-efficient vehicles, from the perspective of corrosion avoidance
Temporal intensity correlation of bunched light from a warm atomic vapor with a ladder-type two-photon transition
Authors: Park Jiho , Jeong Taek , Moon Han Seb 
Published: July 2018

AbstractWe report the temporal intensity correlation (TIC) of scattered photons (SPs) generated via a two-photon transition in a Doppler-broadened warm atomic vapor of the 5S1/2 − 5P3/2 − 5D5/2 transition of 87Rb atoms. Through the investigation of the TICs of the SPs obtained via both one- and two-photon transitions, the second-order correlation values g(2)(0) (i.e., at zero time delay) of both SPs were measured as approximately 1.75, respectively. The widths of the g(2)(τ) spectra were measured as 26 ns (corresponding to the natural lifetime of the 5P3/2 state) for the one-photon transition and 1.8 ns (corresponding to the Doppler width of the warm atomic vapor) for the two-photon transition. We confirmed that the coherence time of the SPs can vary in accordance with the photons emitted from the one- or two-photon transitions in the ladder-type atomic system. The correlated SPs obtained via the two-photon transition contributed to almost all the velocity classes of the atoms in the Doppler-broadened atomic ensemble.
Human coelomic fluid investigation: A MS-based analytical approach to prenatal screening
Authors: Aiello Donatella , Giambona Antonino , Leto Filippo , Passarello Cristina , Damiani Gianfranca , Maggio Aurelio , Siciliano Carlo , Napoli Anna 
Published: July 2018

AbstractCoelomic fluid (CF) is the earliest dynamic and complex fluid of the gestational sac. CF contains maternal cells and proteins produced by embryonic cells, tissues and excretions. The biochemical composition of CF is modified throughout the first trimester of pregnancy and its protein profile reflects both physiological/pathological changes affecting the embryo and mother. Identification of variations in the balance of proteins might indicate particular types of pathologies, or ascertain specific genetic disorders. A platform utilizing protein enrichment procedures coupled with shotgun identification and iTRAQ differentiation provided the identification and quantitation of 88 unique embryonic proteins. It is relevant to note that chromosome X protein CXorf23 was found suggesting the embryo sex. Foetal sex was determined by Quantitative Fluorescent Polymerase Chain Reaction (QF-PCR) on coelomic cells, foetal tissues and maternal white blood cells, with a 100% concordance rate between iTRAQ-MS/MS and QF-PCR data. The functional associations among the identified proteins were investigated using STRING database. Open Targets Platform showed as significant the following therapeutic areas: nervous, respiratory, eye and head system disease.
Parenting Stress and Maternal Coherence: Mothers With Deaf or Hard-of-Hearing Children
Authors: Jean Yap Quin , Mazlan Rafidah , Ahmad Mahadir , Maamor Nashrah 
Published: July 2018

PurposeThe aim of this study was to develop a substantive theory that explains parenting stress among mothers of deaf or hard-of-hearing (D/HH) children.MethodFifteen hearing mothers of children with severe-to-profound sensorineural hearing loss were interviewed. Interviews were transcribed verbatim, and a grounded theory approach was used to inductively analyze parental stress in mothers of D/HH children. Theory generation was achieved through triangulation of data sources and systematic organization of data into codes. The coding process identified salient themes that were constantly cross-checked and compared across data to further develop categories, properties, and tentative hypotheses.ResultsIn general, two main themes emerged from the interviews: the contextual stressors and stress-reducing resources. The contextual stressors were labeled as distress over audiology-related needs, pressure to acquire new knowledge and skills, apprehension about the child's future, and demoralizing negative social attitudes. The stress-reducing resources that moderated parenting stress were identified to be the child's progress, mother's characteristics, professional support, and social support. The interaction between the identified stressors and adjustment process uncovered a central theme termed maternal coherence.ConclusionThe substantive theory suggests that mothers of D/HH children can effectively manage parenting stress and increase well-being by capitalizing on relevant stress-reducing resources to achieve maternal coherence.
AgCl/AgIO4 composites as an efficient photocatalyst for visible‐light‐driven degradation of rhodamine B
Authors: Wu Xiang‐Feng , Wang Yi‐Jin , Li Hui , Zhang Chen‐Xu , Zhang Jia‐Rui , Su Jun‐Zhang , Wang Yi‐Wei , Cao Zuo‐Lin , Wang Kai‐Yuan , Zhang Mi 
Published: July 2018

A novel AgCl/AgIO4 composite was fabricated via an in‐suit synthetic method. The as‐prepared samples have been characterised by using X‐ray diffraction, transmission electron microscopy, scanning electron microscopy, UV–vis diffuse reflectance spectroscopy, X‐ray photoelectron spectroscopy and electrochemical impedance spectroscopy. Rhodamine B dilute solution was used to discuss the photocatalytic activities of the as‐prepared composites under the visible light irradiation. Experimental results showed that with increasing the contents of AgIO4 the photocatalytic activity of the as‐prepared hybrids was first increased and then decreased. When the molar ratio of AgCl to AgIO4 was 1:5, in 30 min, the as‐prepared composites with the bandgap of 1.21 eV exhibited the highest photocatalytic activity and possessed 96.3% of degradation efficiency. That was increased by 71.5 and 27.9% compared with AgCl and AgIO4, respectively. Moreover, AgCl was linked with AgIO4 via chemical bonds rather than physical contact at the interfaces of these two semiconductors. In addition, a possible photocatalytic degradation mechanism for the as‐prepared hybrids was also presented.
Accuracy of bone resection in total knee arthroplasty using CT assisted-3D printed patient specific cutting guides
Authors: Nizam Ikram , Batra Ashish V. 
Published: July 2018

Introduction: We conducted this study to determine if the pre-surgical patient specific instrumented planning based on Computed Tomography (CT) scans can accurately predict each of the femoral and tibial resections performed through 3D printed cutting guides. The technique helps in optimization of component positioning determined by accurate bone resection and hence overall alignment thereby reducing errors.
Methods: Prophecy evolution medial pivot patient specific instrumented knee replacement systems were used for end stage arthrosis in all consecutive cases over a period of 20 months by a single surgeon. All resections (4 femoral and 2 tibial) were measured using a vernier callipers intraoperatively. These respective measurements were then compared with the preoperative CT predicted bone resection surgical plan to determine margins of errors that were categorized into 7 groups (0 mm to ≥2.6 mm).
Results: A total of 3618 measurements (averaged to 1206) were performed in 201 knees (105 right and 96 left) in 188 patients (112 females and 76 males) with an average age of 67.72 years (44 to 90 years) and average BMI of 32.3 (25.1 to 42.3). 94% of all collected resection readings were below the error margin of ≤1.5 mm of which 90% showed resection error of ≤1 mm. Mean error of different resections were ≤0.60 mm (P ≤ 0.0001). In 24% of measurements there were no errors or deviations from the templated resection (0.0 mm).
Conclusion: The 3D printed cutting blocks with slots for jigs accurately predict bone resections in patient specific instrumentation total knee arthroplasty which would directly affect component positioning.
Herausforderungen in der Immunonkologie
Authors: Shimabukuro-Vornhagen Alexander , Subklewe Marion , von Bergwelt-Baildon Michael 
Published: July 2018

AbstractImmuno-oncology has undoubtedly started a new era in the treatment of malignant diseases. Within a short time immunotherapeutic therapy concepts have become part of the standard therapy for many tumors. Already, immunotherapy is one of the most potent therapeutic options for the treatment of many malignancies. Despite its impressive achievements, there is still a significant need for improvement and many aspects of the practical application of immunotherapeutic modalities of therapy are unclear. If it succeeds in solving the challenges discussed here, immuno-oncology will certainly be one of the most important pillars of successful tumor therapy in the future. Immunotherapeutic combination therapies offer the opportunity to improve treatment outcomes. The immunological side effects of immunotherapy may sometimes be life-threatening, but if adequately treated they may be associated with a good prognosis. The development of predictive biomarkers is indispensable for effective immunotherapy. The costs of immuno-oncological therapies are sometimes very high. Therefore reasonable solutions must be found.
Das Damon-Bracket – Ein Review
Authors: Madsen Henning 
Published: July 2018

ZusammenfassungUnter den zahlreichen selbstligierenden Brackets auf dem Markt wird besonders das Damon-Bracket mit der Behauptung vermarktet, große Vorteile gegenüber anderen Brackets zu haben. Schnellere Nivellierung, kürzere Behandlungsdauer, weniger Termine, weniger Schmerzen und kürzere Arbeitszeit am Zahnarztstuhl werden als Vorzüge angeführt. Ein Review der Literatur zeigt jedoch, dass allein die kürzere Arbeitszeit belegbar ist, während es keine Evidenz für weitere besondere Vorzüge des Damon-Brackets gibt.
Water Veil Effect to Control Splashing from the Pulsed Water Jet Device: Minimizing the Potential Risk of Dissemination Using Surgical Aspirators
Authors: Nakayashiki Atsushi , Nakagawa Atsuhiro , Sato Motohiko , Mochizuki Fusako , Endo Toshiki , Tominaga Teiji , Kawaguchi Tomohiro 
Published: July 2018

Objective Maximum resection with minimum damage to normal structures is required for a better clinical outcome. Several efficient surgical devices such as the Cavitron ultrasonic surgical aspirator are available. Our group developed the actuator-driven pulsed water jet (ADPJ) to dissect soft tissue with vessel preservation. Although these devices are very effective for resection, tumor seeding is a potential risk. The present study investigated the control of splashing during ADPJ use. We demonstrate the effect of additional water flow around the instrument tip to veil the splashing.
Methods Pulsed water jet was ejected from the tip of the ADPJ nozzle. Effects of ADPJ parameters such as input voltage, suction pressure, and distance between the nozzle and the target (standoff distance) on the amount of splashing were analyzed. Methylene blue solution was ejected on photo paper, gelatin brain phantom, and porcine brain harvested and subsequently immersed into physiologic saline to quantify the amount of splashing.
Results High-input voltage and a long standoff distance had significant correlations with large amounts of splashing (r > 0.5; p < 0.01). However, suction pressure had no correlation (r = 0.23). Additional water flow combined with the ADPJ decreased the amount of splashing. A high-speed camera recording revealed that the additional water flow formed a water veil that prevented droplet dispersion, as confirmed with experiments using the brain phantom and porcine brain, in which the irregularity and elasticity are specific.
Conclusions The veil effect of additional water flow is important to reduce splashing during ADPJ use and can minimize the potential risk of dissemination and enhance the safety of the ADPJ.
Optic Nerve Glioma in Two Sisters with Family History of Neurofibromatosis Type 1
Authors: Nachev Sevdalin , Todorova Lyudmila , Marinov Marin , Surchev Jivko 
Published: July 2018

AbstractOptic nerve glioma (ONG) is associated in 10% of patients with neurofibromatosis (NF) type 1. To date no consensus has been reached regarding the therapeutic approach and prevention of visual impairment in these patients. Reports in the literature vary from a conservative approach (observation) to the use of single treatment modalities or multimodality protocols of surgical removal, radiotherapy, and/or chemotherapy. We present our experience with two siblings with ONG whose mother carries cutaneous stigmata of NF type 1. The younger sister was diagnosed 3 years after the treatment of the older sibling following recommended imaging for screening. Postoperative follow-up for 11 and 15 years, respectively, demonstrated lack of tumor regrowth and preserved vision in the contralateral eye. We discuss the treatment strategy in pediatric patients with orbital ONG associated with NF type 1.