bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Radiated Deep-frozen Xenogenic Meniscal Tissue Regenerated the Total Meniscus with Chondroprotection
Authors: Jiang Dong , Zhang Zheng-Zheng , Zhao Feng , Wang Shao-Jie , Qi Yan-Song , Zhao Li-Heng , Zhang Ji-Ying , Yu Jia-Kuo 
Published: June 2018

AbstractMeniscal allograft transplantation yields good and excellent results but is limited by donor availability. The purpose of the study was to evaluate the effectiveness of radiated deep-frozen xenogenic meniscal tissue (RDF-X) as an alternative graft choice in meniscal transplantation. The xenogenic meniscal tissues were harvested from the inner 1/3 part of the porcine meniscus and then irradiated and deeply frozen. The medial menisci of rabbits were replaced by the RDF-X. Meniscal allograft transplantation, meniscectomy and sham operation served as controls. Only a particular kind of rabbit-anti-pig antibody (molecular ranging 60–80 kD) was detected in the blood serum at week 2. The menisci of the group RDF-X grossly resembled the native tissue and the allograft meniscus with fibrocartilage regeneration at postoperative 1 year. Cell incorporation and the extracellular matrix were mostly observed at the surface and the inner 1/3 part of the newly regenerated RDF-X, which was different from the allograft. The biomechanical properties of the group RDF-X were also approximate to those of the native meniscus except for the compressive creep. In addition, chondroprotection was achieved after the RDF-X transplantation although the joint degeneration was not completely prevented. To conclude, the RDF-X could be a promising alternative for meniscal transplantation with similar tissue regeneration capacity to allograft transplantation and superior chondroprotection. The potential minor immunological rejection should be further studied before its clinical application.
Immunome differences between porcine ileal and jejunal Peyer’s patches revealed by global transcriptome sequencing of gut-associated lymphoid tissues
Authors: Maroilley T. , Berri M. , Lemonnier G. , Esquerré D. , Chevaleyre C. , Mélo S. , Meurens F. , Coville J. L. , Leplat J. J. , Rau A. , Bed’hom B. , Vincent-Naulleau S. , Mercat M. J. , Billon Y. , Lepage P. , Rogel-Gaillard C. , Estellé J. 
Published: June 2018

AbstractThe epithelium of the intestinal mucosa and the gut-associated lymphoid tissues (GALT) constitute an essential physical and immunological barrier against pathogens. In order to study the specificities of the GALT transcriptome in pigs, we compared the transcriptome profiles of jejunal and ileal Peyer’s patches (PPs), mesenteric lymph nodes (MLNs) and peripheral blood (PB) of four male piglets by RNA-Seq. We identified 1,103 differentially expressed (DE) genes between ileal PPs (IPPs) and jejunal PPs (JPPs), and six times more DE genes between PPs and MLNs. The master regulator genesFOXP3,GATA3,STAT4,TBX21andRORCwere less expressed in IPPs compared to JPPs, whereas the transcription factorBCL6was found more expressed in IPPs. In comparison between IPPs and JPPs, our analyses revealed predominant differential expression related to the differentiation of T cells into Th1, Th2, Th17 and iTreg in JPPs. Our results were consistent with previous reports regarding a higher T/B cells ratio in JPPs compared to IPPs. We found antisense transcription for respectively 24%, 22% and 14% of the transcripts detected in MLNs, PPs and PB, and significant positive correlations between PB and GALT transcriptomes. Allele-specific expression analyses revealed both shared and tissue-specificcis-genetic control of gene expression.
Dispersion engineering with plasmonic nano structures for enhanced surface plasmon resonance sensing
Authors: Arora Pankaj , Talker Eliran , Mazurski Noa , Levy Uriel 
Published: June 2018

AbstractWe demonstrate numerically and experimentally the enhancement of Surface Plasmon Resonance (SPR) sensing via dispersion engineering of the plasmonic response using plasmonic nanograting. Following their design and optimization, the plasmonic nanograting structures are fabricated using e-beam lithography and lift-off process and integrated into conventional prism based Kretschmann configuration. The presence of absorptive nanograting near the metal film, provides strong field enhancement with localization and allows to control the dispersion relation which was originally dictated by a conventional SPR structure. This contributes to the enhancement in Q factor which is found to be 3–4 times higher as compared to the conventional Kretschmann configuration. The influence of the incident angle on resonance wavelength is also demonstrated both numerically and experimentally, where, only a negligible wavelength shift is observed with increasing the incident angles for plasmonic nanograting configuration. This surprising feature may be helpful for studying and utilizing light-matter interaction between plasmons and narrow linewidth media (e.g. Rb atom or molecule) having nonlocalities in their susceptibility-momentum relation. Finally, we analyze the role of plasmonic nanograting in enhancing the performance of an SPR sensor. Our results indicate that the integrated SPR-nanograting device shows a great promise as a sensor for various types of analytes.
A single cell high content assay detects mitochondrial dysfunction in iPSC-derived neurons with mutations in SNCA
Authors: Little Daniel , Luft Christin , Mosaku Olukunbi , Lorvellec Maëlle , Yao Zhi , Paillusson Sébastien , Kriston-Vizi Janos , Gandhi Sonia , Abramov Andrey Y. , Ketteler Robin , Devine Michael J. , Gissen Paul 
Published: June 2018

AbstractMitochondrial dysfunction is implicated in many neurodegenerative diseases including Parkinson’s disease (PD). Induced pluripotent stem cells (iPSCs) provide a unique cell model for studying neurological diseases. We have established a high-content assay that can simultaneously measure mitochondrial function, morphology and cell viability in iPSC-derived dopaminergic neurons. iPSCs from PD patients with mutations in SNCA and unaffected controls were differentiated into dopaminergic neurons, seeded in 384-well plates and stained with the mitochondrial membrane potential dependent dye TMRM, alongside Hoechst-33342 and Calcein-AM. Images were acquired using an automated confocal screening microscope and single cells were analysed using automated image analysis software. PD neurons displayed reduced mitochondrial membrane potential and altered mitochondrial morphology compared to control neurons. This assay demonstrates that high content screening techniques can be applied to the analysis of mitochondria in iPSC-derived neurons. This technique could form part of a drug discovery platform to test potential new therapeutics for PD and other neurodegenerative diseases.
Year-to-year Variability in Arctic Minimum Sea Ice Extent and its Preconditions in Observations and the CESM Large Ensemble Simulations
Authors: Yang Wenchang , Magnusdottir Gudrun 
Published: June 2018

AbstractArctic sea ice extent (SIE) achieves its minimum in September each year and this value has been observed to decline steeply over the satellite era of the past three decades. Yet large year-to-year fluctuations are also present in the September SIE and the mechanisms for this variability are still not clear. Here we address this issue by examining the preconditions in meteorological fields in the previous spring and summer from observations and a large ensemble of historical climate model simulations. The focus of this study is on the impact of anomalous moisture transport into the Arctic and the associated surface energy fluxes on the September SIE. We find that the below-normal September SIE is associated with enhanced moisture transport into the Arctic in spring, which induces downward thermal radiation at the surface. However, in summer, the anomalous moisture transport over the Arctic is divergent due to an anticyclonic atmospheric flow pattern and the ice albedo feedback plays a leading role in sea ice loss.
Assigning biological function using hidden signatures in cystine-stabilized peptide sequences
Authors: Islam S. M. Ashiqul , Kearney Christopher Michel , Baker Erich J. 
Published: June 2018

AbstractCystine-stabilized peptides have great utility as they naturally block ion channels, inhibit acetylcholine receptors, or inactivate microbes. However, only a tiny fraction of these peptides has been characterized. Exploration for novel peptides most efficiently starts with the identification of candidates from genome sequence data. Unfortunately, though cystine-stabilized peptides have shared structures, they have low DNA sequence similarity, restricting the utility of BLAST and even more powerful sequence alignment-based annotation algorithms, such as PSI-BLAST and HMMER. In contrast, a supervised machine learning approach may improve discovery and function assignment of these peptides. To this end, we employed our previously described m-NGSG algorithm, which utilizes hidden signatures embedded in peptide primary sequences that define and categorize structural or functional classes of peptides. From the generalized m-NGSG framework, we derived five specific models that categorize cystine-stabilized peptide sequences into specific functional classes. When compared with PSI-BLAST, HMMER and existing function-specific models, our novel approach (named CSPred) consistently demonstrates superior performance in discovery and function-assignment. We also report an interactive version of CSPred, available through download (https://bitbucket.org/sm_islam/cystine-stabilized-proteins/src) or web interface (watson.ecs.baylor.edu/cspred), for the discovery of cystine-stabilized peptides of specific function from genomic datasets and for genome annotation. We fully describe, in the Availability section following the Discussion, the quick and simple usage of the CsPred website to automatically deliver function assignments for batch submissions of peptide sequences.
Touch-induced face conditioning is mediated by genetic variation in opioid but not oxytocin receptors
Authors: Fu Yu , Selcuk Emre , Moore Sarah R. , Depue Richard A. 
Published: June 2018

AbstractSoft touch possesses strong prosocial effects that facilitate social bonding and group cohesion in animals. Touch activates opioids (OP) and oxytocin (OXT), two neuromodulators involved in affiliative behaviors and social bonding. We examined whether touch serves as an unconditioned reward in affective conditioning of human faces, a basic process in social bonding, and whether this process is mediated by variation in mu-OP (OPRM1) and OXT (rs53576) receptor genes. Participants viewed affectively-neutral human faces, half of which were paired with a brief soft brushing on the forearm as an unconditioned stimulus (US). Paired and unpaired faces were rated for positive affective and sensory features of touch. Variation inOPRM1but notrs53576significantly modulated strength and development of conditioning, indicating that touch-induced mu-OP but not OXT activity provides rewarding properties of a US in conditioning. Implications for touch-inducedmu-OP activity in normal and disordered conditioned social bonding are discussed.
Super Resolution Network Analysis Defines the Molecular Architecture of Caveolae and Caveolin-1 Scaffolds
Authors: Khater Ismail M. , Meng Fanrui , Wong Timothy H. , Nabi Ivan Robert , Hamarneh Ghassan 
Published: June 2018

AbstractQuantitative approaches to analyze the large data sets generated by single molecule localization super-resolution microscopy (SMLM) are limited. We developed a computational pipeline and applied it to analyzing 3D point clouds of SMLM localizations (event lists) of the caveolar coat protein, caveolin-1 (Cav1), in prostate cancer cells differentially expressing CAVIN1 (also known as PTRF), that is also required for caveolae formation. High degree (strongly-interacting) points were removed by an iterative blink merging algorithm and Cav1 network properties were compared with randomly generated networks to retain a sub-network of geometric structures (or blobs). Machine-learning based classification extracted 28 quantitative features describing the size, shape, topology and network characteristics of ∼80,000 blobs. Unsupervised clustering identified small S1A scaffolds corresponding to SDS-resistant Cav1 oligomers, as yet undescribed larger hemi-spherical S2 scaffolds and, only in CAVIN1-expressing cells, spherical, hollow caveolae. Multi-threshold modularity analysis suggests that S1A scaffolds interact to form larger scaffolds and that S1A dimers group together, in the presence of CAVIN1, to form the caveolae coat.
Triple-negative invasive breast carcinoma: the association between the sonographic appearances with clinicopathological feature
Authors: Li Jia-wei , Zhang Kai , Shi Zhao-ting , Zhang Xun , Xie Juan , Liu Jun-ying , Chang Cai 
Published: June 2018

AbstractIn this study, we aimed to evaluate the clinical and pathological factors that associated with sonographic appearances of triple-negative (TN) invasive breast carcinoma. With the ethical approval, 560 patients who were pathologically confirmed as invasive breast carcinoma were reviewed for ultrasound, clinical, and pathological data. Logistic regression analysis was used to identify the typical sonographic features for TN invasive breast carcinomas. The effect of clinical and pathological factors on the sonographic features of TN invasive breast carcinoma was studied. There were 104 cases of TN invasive breast carcinoma. The independent sonographic features for the TN subgroup included regular shape (odds ratio, OR = 1.73, p = 0.033), no spiculated/angular margin (OR = 2.09, p = 0.01), posterior acoustic enhancement (OR = 2.09, p = 0.004), and no calcifications (OR = 2.11, p = 0.005). Higher pathological grade was significantly associated with regular tumor shape of TN breast cancer (p = 0.012). Higher Ki67 level was significantly associated with regular tumor shape (p = 0.023) and absence of angular/spiculated margin (p = 0.005). Higher human epidermal growth factor receptor 2 (HER2) score was significantly associated with the presence of calcifications (p = 0.033). We conclude that four sonographic features are associated with TN invasive breast carcinoma. Heterogeneity of sonographic features was associated with the pathological grade, Ki67 proliferation level and HER2 score of TN breast cancers.
Glutamine 89 is a key residue in the allosteric modulation of human serine racemase activity by ATP
Authors: Canosa Andrea V. , Faggiano Serena , Marchetti Marialaura , Armao Stefano , Bettati Stefano , Bruno Stefano , Percudani Riccardo , Campanini Barbara , Mozzarelli Andrea 
Published: June 2018

AbstractSerine racemase (SR) catalyses two reactions: the reversible racemisation of L-serine and the irreversible dehydration of L- and D-serine to pyruvate and ammonia. SRs are evolutionarily related to serine dehydratases (SDH) and degradative threonine deaminases (TdcB). Most SRs and TdcBs – but not SDHs – are regulated by nucleotides. SR binds ATP cooperatively and the nucleotide allosterically stimulates the serine dehydratase activity of the enzyme. A H-bond network comprising five residues (T52, N86, Q89, E283 and N316) and water molecules connects the active site with the ATP-binding site. Conservation analysis points to Q89 as a key residue for the allosteric communication, since its mutation to either Met or Ala is linked to the loss of control of activity by nucleotides. We verified this hypothesis by introducing the Q89M and Q89A point mutations in the human SR sequence. The allosteric communication between the active site and the allosteric site in both mutants is almost completely abolished. Indeed, the stimulation of the dehydratase activity by ATP is severely diminished and the binding of the nucleotide is no more cooperative. Ancestral state reconstruction suggests that the allosteric control by nucleotides established early in SR evolution and has been maintained in most eukaryotic lineages.
Preliminary Investigation of Focused Ultrasound-Facilitated Drug Delivery for the Treatment of Leptomeningeal Metastases
Authors: O’Reilly Meaghan A. , Chinnery Tricia , Yee My-Linh , Wu Sheng-Kai , Hynynen Kullervo , Kerbel Robert S. , Czarnota Gregory J. , Pritchard Kathleen I. , Sahgal Arjun 
Published: June 2018

AbstractLeptomeningeal metastases (LM) are a serious complication of cancer in the central nervous system (CNS) and are diagnosed in approximately 5% of patients with solid tumors. Effective treatment using systemically administered therapeutics is hindered by the barriers of the CNS. Ultrasound can mediate delivery of drugs through these barriers. The goal of this study was to test the feasibility of using ultrasound-mediated drug delivery to improve the treatment of LM. LM was induced in the spinal cord of athymic rats by injecting HER2-expressing breast cancer cells into the subarachnoid space of the thoracic spine. Animals were divided into three groups: no treatment (n = 5), trastuzumab only (n = 6) or trastuzumab + focused ultrasound + microbubbles (FUS + MBs) (n = 7). Animals in groups 2 and 3 were treated weekly with intravenous trastuzumab +/− FUS + MBs for three weeks. Suppression in tumor growth was qualitatively observed by MRI in the group receiving ultrasound, and was confirmed by a significant difference in the tumor volume measured from the histology data (25 ± 17 mm3 vs 8 ± 5 mm3, p = 0.04 in the trastuzumab-only vs trastuzumab + FUS + MBs). This pilot study demonstrates the potential of ultrasound-mediated drug delivery as a novel treatment for LM. Future studies will extend this work to larger cohorts and the investigation of LM arising from other cancers.
Avian tail ontogeny, pygostyle formation, and interpretation of juvenile Mesozoic specimens
Authors: Rashid Dana J. , Surya Kevin , Chiappe Luis M. , Carroll Nathan , Garrett Kimball L. , Varghese Bino , Bailleul Alida , O’Connor Jingmai K. , Chapman Susan C. , Horner John R. 
Published: June 2018

AbstractThe avian tail played a critical role in the evolutionary transition from long- to short-tailed birds, yet its ontogeny in extant birds has largely been ignored. This deficit has hampered efforts to effectively identify intermediate species during the Mesozoic transition to short tails. Here we show that fusion of distal vertebrae into the pygostyle structure does not occur in extant birds until near skeletal maturity, and mineralization of vertebral processes also occurs long after hatching. Evidence for post-hatching pygostyle formation is also demonstrated in two Cretaceous specimens, a juvenile enantiornithine and a subadult basal ornithuromorph. These findings call for reinterpretations ofZhongornis haoae, a Cretaceous bird hypothesized to be an intermediate in the long- to short-tailed bird transition, and of the recently discovered coelurosaur tail embedded in amber.Zhongornis, as a juvenile, may not yet have formed a pygostyle, and the amber-embedded tail specimen is reinterpreted as possibly avian. Analyses of relative pygostyle lengths in extant and Cretaceous birds suggests the number of vertebrae incorporated into the pygostyle has varied considerably, further complicating the interpretation of potential transitional species. In addition, this analysis of avian tail development reveals the generation and loss of intervertebral discs in the pygostyle, vertebral bodies derived from different kinds of cartilage, and alternative modes of caudal vertebral process morphogenesis in birds. These findings demonstrate that avian tail ontogeny is a crucial parameter specifically for the interpretation of Mesozoic specimens, and generally for insights into vertebrae formation.
Nano-mechanical properties of Fe-Mn-Al-C lightweight steels
Authors: Rahnama Alireza , Kotadia Hiren , Clark Samuel , Janik Vit , Sridhar Seetharaman 
Published: June 2018

AbstractHigh Al Low-density steels could have a transformative effect on the light-weighting of steel structures for transportation. They can achieve the desired properties with the minimum amount of Ni, and thus are of great interest from an economic perspective. In this study, the mechanical properties of two duplex low-density steels, Fe-15Mn-10Al-0.8C-5Ni and Fe-15Mn-10Al-0.8 C (wt.%) were investigated through nano-indentation and simulation through utilization of ab-initio formalisms in Density Functional Theory (DFT) in order to establish the hardness resulting from two critical structural features (κ-carbides and B2 intermetallic) as a function of annealing temperature (500–1050 °C) and the addition of Ni. In the Ni-free sample, the calculated elastic properties of κ-carbides were compared with those of the B2 intermetallic Fe3Al−L12 and the role of Mn in the κ structure and its elastic properties were studied. The Ni-containing samples were found to have a higher hardness due to the B2 phase composition being NiAl rather than FeAl, with Ni-Al bonds reported to be stronger than the Fe-Al bonds. In both samples, at temperatures of 900 °C and above, the ferrite phase contained nano-sized discs of B2 phase, wherein the Ni-containing samples exhibited higher hardness, attributed again to the stronger Ni-Al bonds in the B2 phase. At 700 °C and below, the nano-sized B2 discs were replaced by micrometre sized needles of κ in the Ni-free sample resulting in a lowering of the hardness. In the Ni-containing sample, the entire α phase was replaced by B2 stringers, which had a lower hardness than the Ni-Al nano-discs due to a lower Ni content in B2 stringer bands formed at 700 °C and below. In addition, the hardness of needle-like κ-carbides formed in α phase was found to be a function of Mn content. Although it was impossible to measure the hardness of cuboid κ particles in γ phase because of their nano-size, the hardness value of composite phases, e.g. γ + κ was measured and reported. All the hardness values were compared and rationalized by bonding energy between different atoms.
Chronic infection with Mycobacterium lepraemurium induces alterations in the hippocampus associated with memory loss
Authors: Becerril-Villanueva Enrique , Ponce-Regalado María Dolores , Pérez-Sánchez Gilberto , Salazar-Juárez Alberto , Arreola Rodrigo , Álvarez-Sánchez María Elizbeth , Juárez-Ortega Mario , Falfán-Valencia Ramcés , Hernández-Pando Rogelio , Morales-Montor Jorge , Pavón Lenin , Rojas-Espinosa Oscar 
Published: June 2018

AbstractMurine leprosy, caused byMycobacterium lepraemurium(MLM), is a chronic disease that closely resembles human leprosy. Even though this disease does not directly involve the nervous system, we investigated a possible effect on working memory during this chronic infection in Balb/c mice. We evaluated alterations in the dorsal region of the hippocampus and measured peripheral levels of cytokines at 40, 80, and 120 days post-infection. To evaluate working memory, we used the T-maze while a morphometric analysis was conducted in the hippocampus regions CA1, CA2, CA3, and dentate gyrus (DG) to measure morphological changes. In addition, a neurochemical analysis was performed by HPLC. Our results show that, at 40 days post-infection, there was an increase in the bacillary load in the liver and spleen associated to increased levels of IL-4, working memory deterioration, and changes in hippocampal morphology, including degeneration in the four subregions analyzed. Also, we found a decrease in neurotransmitter levels at the same time of infection. AlthoughMLMdoes not directly infect the nervous system, these findings suggest a possible functional link between the immune system and the central nervous system.