bluuebunny/crossref_metadata_2025_split huggingface dataset:
Naïve Tests of Basic Local Independence Model’s Invariance
Authors: Chiusole Debora de , Stefanutti Luca , Anselmi Pasquale , Robusto Egidio 
Published: July 2015

AbstractThe basic local independence model (BLIM) is a probabilistic model for knowledge structures, characterized by the property that lucky guess and careless error parameters of the items are independent of the knowledge states of the subjects. When fitting the BLIM to empirical data, a good fit can be obtained even when the invariance assumption is violated. Therefore, statistical tests are needed for detecting violations of this specific assumption. This work provides an extension to theoretical results obtained by de Chiusole, Stefanutti, Anselmi, and Robusto (2013), showing that statistical tests based on the partitioning of the empirical data set into two (or more) groups are not adequate for testing the BLIM’s invariance assumption. A simulation study confirms the theoretical results.
Seipin deficiency increases chromocenter fragmentation and disrupts acrosome formation leading to male infertility
Authors: El Zowalaty A E , Baumann C , Li R , Chen W , De La Fuente R , Ye X 
Published: July 2015

AbstractThe Berardinelli–Seip congenital lipodystrophy type 2 (Bscl2, seipin) gene is involved in adipogenesis. Bscl2−/− males were infertile but had normal mating behavior. Both Bscl2−/− cauda epididymis sperm count and sperm motility were ~20 × less than control. Bscl2−/− seminiferous tubules had relatively normal presence of spermatogonia and spermatocytes but had reduced spermatids and sperm. Spatiotemporal expression analyses in Bscl2+/+ testes demonstrated prominent Bscl2 transcriptional activity in spermatocytes with a plateau reached around postnatal day 28. Seipin protein localization was most abundant in postmeiotic spermatids, suggesting translational repression of Bscl2 mRNA in spermatocytes. In situ end-labeling plus detected increased spermatid apoptosis in Bscl2−/− testis and annexin V detected increased percentage of positive Bscl2−/− round spermatids compared with control. Immunofluorescence of marker proteins synaptonemal complex proteins 3 and 1 (SYCP3 and SYCP1), and H3K9me3 (histone H3 trimethylated at lysine 9) in germ cell spreads detected normal meiotic chromosome pairing and homologous chromosome synapsis in Bscl2−/− spermatocytes, but significantly increased percentages of round spermatids with chromocenter fragmentation and late spermatids and sperm with chromatin vacuoles, indicating defective chromatin condensation in Bscl2−/− spermatids. Bscl2−/− late spermatids were disorganized within the seminiferous epithelium, despite normal appearance of Sertoli cells detected by vimentin immunofluorescence. Peanut agglutinin staining revealed various abnormalities of acrosomes in Bscl2−/− late spermatids, including the absence, irregular-shaped, and fragmented acrosomes, indicating defective acrosome formation in Bscl2−/− late spermatids, which may affect late spermatid orientation in the seminiferous epithelium. Mitotracker strongly stained the midpiece of control sperm but only very weakly labeled the midpiece of Bscl2−/− sperm, indicating defective mitochondrial activity that most likely contributed to reduced Bscl2−/− sperm motility. These data demonstrate novel roles of seipin in spermatid chromatin integrity, acrosome formation, and mitochondrial activity. Increased spermatid apoptosis, increased chromocenter fragmentation, defective chromatin condensation, abnormal acrosome formation, and defective mitochondrial activity contributed to decreased sperm production and defective sperm that resulted in Bscl2−/− male infertility.
Transition of dislocation nucleation induced by local stress concentration in nanotwinned copper
Authors: Lu N. , Du K. , Lu L. , Ye H. Q. 
Published: July 2015

AbstractMetals with a high density of nanometre-scale twins have demonstrated simultaneous high strength and good ductility, attributed to the interaction between lattice dislocations and twin boundaries. Maximum strength was observed at a critical twin lamella spacing (∼15 nm) by mechanical testing; hence, an explanation of how twin lamella spacing influences dislocation behaviours is desired. Here, we report a transition of dislocation nucleation from steps on the twin boundaries to twin boundary/grain boundary junctions at a critical twin lamella spacing (12–37 nm), observed with in situ transmission electron microscopy. The local stress concentrations vary significantly with twin lamella spacing, thus resulting in a critical twin lamella spacing (∼18 nm) for the transition of dislocation nucleation. This agrees quantitatively with the mechanical test. These results demonstrate that by quantitatively analysing local stress concentrations, a direct relationship can be resolved between the microscopic dislocation activities and macroscopic mechanical properties of nanotwinned metals.
Thermodynamic picture of ultrafast charge transport in graphene
Authors: Mics Zoltán , Tielrooij Klaas-Jan , Parvez Khaled , Jensen Søren A. , Ivanov Ivan , Feng Xinliang , Müllen Klaus , Bonn Mischa , Turchinovich Dmitry 
Published: July 2015

AbstractThe outstanding charge transport properties of graphene enable numerous electronic applications of this remarkable material, many of which are expected to operate at ultrahigh speeds. In the regime of ultrafast, sub-picosecond electric fields, however, the very high conduction properties of graphene are not necessarily preserved, with the physical picture explaining this behaviour remaining unclear. Here we show that in graphene, the charge transport on an ultrafast timescale is determined by a simple thermodynamic balance maintained within the graphene electronic system acting as a thermalized electron gas. The energy of ultrafast electric fields applied to graphene is converted into the thermal energy of its entire charge carrier population, near-instantaneously raising the electronic temperature. The dynamic interplay between heating and cooling of the electron gas ultimately defines the ultrafast conductivity of graphene, which in a highly nonlinear manner depends on the dynamics and the strength of the applied electric fields.
Rational design of crystalline supermicroporous covalent organic frameworks with triangular topologies
Authors: Dalapati Sasanka , Addicoat Matthew , Jin Shangbin , Sakurai Tsuneaki , Gao Jia , Xu Hong , Irle Stephan , Seki Shu , Jiang Donglin 
Published: July 2015

AbstractCovalent organic frameworks (COFs) are an emerging class of highly ordered porous polymers with many potential applications. They are currently designed and synthesized through hexagonal and tetragonal topologies, limiting the access to and exploration of new structures and properties. Here, we report that a triangular topology can be developed for the rational design and synthesis of a new class of COFs. The triangular topology features small pore sizes down to 12 Å, which is among the smallest pores for COFs reported to date, and high π-column densities of up to 0.25 nm−2, which exceeds those of supramolecular columnar π-arrays and other COF materials. These crystalline COFs facilitate π-cloud delocalization and are highly conductive, with a hole mobility that is among the highest reported for COFs and polygraphitic ensembles.
Tyrosine glycosylation of Rho by Yersinia toxin impairs blastomere cell behaviour in zebrafish embryos
Authors: Jank Thomas , Eckerle Stephanie , Steinemann Marcus , Trillhaase Christoph , Schimpl Marianne , Wiese Sebastian , van Aalten Daan M. F. , Driever Wolfgang , Aktories Klaus 
Published: July 2015

AbstractYersiniaspecies cause zoonotic infections, including enterocolitis and plague. Here we studiedYersinia ruckeriantifeeding prophage 18 (Afp18), the toxin component of the phage tail-derived protein translocation system Afp, which causes enteric redmouth disease in salmonid fish species. Here we show that microinjection of the glycosyltransferase domain Afp18Ginto zebrafish embryos blocks cytokinesis, actin-dependent motility and cell blebbing, eventually abrogating gastrulation. In zebrafish ZF4 cells, Afp18Gdepolymerizes actin stress fibres by mono-O-GlcNAcylation of RhoA at tyrosine-34; thereby Afp18Ginhibits RhoA activation by guanine nucleotide exchange factors, and blocks RhoA, but not Rac and Cdc42 downstream signalling. The crystal structure of tyrosine-GlcNAcylated RhoA reveals an open conformation of the effector loop distinct from recently described structures of GDP- or GTP-bound RhoA. Unravelling of the molecular mechanism of the toxin component Afp18 as glycosyltransferase opens new perspectives in studies of phage tail-derived protein translocation systems, which are preserved from archaea to human pathogenic prokaryotes.
EGCG reverses human neutrophil elastase-induced migration in A549 cells by directly binding to HNE and by regulating α1-AT
Authors: Xiaokaiti Yilixiati , Wu Haoming , Chen Ya , Yang Haopeng , Duan Jianhui , Li Xin , Pan Yan , Tie Lu , Zhang Liangren , Li Xuejun 
Published: July 2015

AbstractLung carcinogenesis is a complex process that occurs in unregulated inflammatory environment. EGCG has been extensively investigated as a multi-targeting anti-tumor and anti-inflammatory compound. In this study, we demonstrated a novel mechanism by which EGCG reverses the neutrophil elastase-induced migration of A549 cells. We found that neutrophil elastase directly triggered human adenocarcinoma A549 cell migration and that EGCG suppressed the elevation of tumor cell migration induced by neutrophil elastase. We observed that EGCG directly binds to neutrophil elastase and inhibits its enzymatic activity based on the CDOCKER algorithm, MD stimulation by GROMACS, SPR assay and elastase enzymatic activity assay. As the natural inhibitor of neutrophil elastase, α1-antitrypsin is synthesized in tumor cells. We further demonstrated that the expression of α1-antitrypsin was up-regulated after EGCG treatment in neutrophil elastase-treated A549 cells. We preliminarily discovered that the EGCG-mediated induction of α1-antitrypsin expression might be correlated with the regulatory effect of EGCG on the PI3K/Akt pathway. Overall, our results suggest that EGCG ameliorates the neutrophil elastase-induced migration of A549 cells. The mechanism underlying this effect may include two processes: EGCG directly binds to neutrophil elastase and inhibits its enzymatic activity; EGCG enhances the expression of α1-antitrypsin by regulating the PI3K/AKT pathway.
LRP-1-mediated intracellular antibody delivery to the Central Nervous System
Authors: Tian Xiaohe , Nyberg Sophie , Sharp Paul S. , Madsen Jeppe , Daneshpour Nooshin , Armes Steven P. , Berwick Jason , Azzouz Mimoun , Shaw Pamela , Abbott N. Joan , Battaglia Giuseppe 
Published: July 2015

AbstractThe blood-brain barrier (BBB) is by far the most important target in developing new approaches to improve delivery of drugs and diagnostic tools into the Central Nervous System (CNS). Here we report the engineering of pH- sensitive polymersomes (synthetic vesicles formed by amphiphilic copolymers) that exploit endogenous transport mechanisms to traverse the BBB, enabling delivery of large macromolecules into both the CNS parenchyma and CNS cells. We achieve this by targeting the Low Density Lipoprotein Receptor-Related Protein 1 (LRP-1) receptor. We show that LRP-1 is associated with endothelial transcytosis that does not involve acidification of cargo in membrane-trafficking organelles. By contrast, this receptor is also associated with traditional endocytosis in CNS cells, thus aiding the delivery of relevant cargo within their cytosol. We prove this using IgG as a model cargo, thus demonstrating that the combination of appropriate targeting combined with pH-sensitive polymersomes enables the efficient delivery of macromolecules into CNS cells.
Regulation of microtubule dynamics by DIAPH3 influences amoeboid tumor cell mechanics and sensitivity to taxanes
Authors: Morley Samantha , You Sungyong , Pollan Sara , Choi Jiyoung , Zhou Bo , Hager Martin H. , Steadman Kenneth , Spinelli Cristiana , Rajendran Kavitha , Gertych Arkadiusz , Kim Jayoung , Adam Rosalyn M. , Yang Wei , Krishnan Ramaswamy , Knudsen Beatrice S. , Di Vizio Dolores , Freeman Michael R. 
Published: July 2015

AbstractTaxanes are widely employed chemotherapies for patients with metastatic prostate and breast cancer. Here, we show that loss of Diaphanous-related formin-3 (DIAPH3), frequently associated with metastatic breast and prostate cancers, correlates with increased sensitivity to taxanes. DIAPH3 interacted with microtubules (MT) and its loss altered several parameters of MT dynamics as well as decreased polarized force generation, contractility and response to substrate stiffness. Silencing of DIAPH3 increased the cytotoxic response to taxanes in prostate and breast cancer cell lines. Analysis of drug activity for tubulin-targeted agents in the NCI-60 cell line panel revealed a uniform positive correlation between reduced DIAPH3 expression and drug sensitivity. Low DIAPH3 expression correlated with improved relapse-free survival in breast cancer patients treated with chemotherapeutic regimens containing taxanes. Our results suggest that inhibition of MT stability arising from DIAPH3 downregulation enhances susceptibility to MT poisons and that the DIAPH3 network potentially reports taxane sensitivity in human tumors.
The Kallisti Limnes, carbon dioxide-accumulating subsea pools
Authors: Camilli Richard , Nomikou Paraskevi , Escartín Javier , Ridao Pere , Mallios Angelos , Kilias Stephanos P. , Argyraki Ariadne ,   and the Caldera Science Team, Andreani Muriel , Ballu Valerie , Campos Ricard , Deplus Christine , Gabsi Taoufic , Garcia Rafael , Gracias Nuno , Hurtós Natàlia , Magí Lluis , Mével Catherine , Moreira Manuel , Palomeras Narcís , Pot Olivier , Ribas David , Ruzié Lorraine , Sakellariou Dimitris 
Published: July 2015

AbstractNatural CO2 releases from shallow marine hydrothermal vents are assumed to mix into the water column and not accumulate into stratified seafloor pools. We present newly discovered shallow subsea pools located within the Santorini volcanic caldera of the Southern Aegean Sea, Greece, that accumulate CO2 emissions from geologic reservoirs. This type of hydrothermal seafloor pool, containing highly concentrated CO2, provides direct evidence of shallow benthic CO2 accumulations originating from sub-seafloor releases. Samples taken from within these acidic pools are devoid of calcifying organisms and channel structures among the pools indicate gravity driven flow, suggesting that seafloor release of CO2 at this site may preferentially impact benthic ecosystems. These naturally occurring seafloor pools may provide a diagnostic indicator of incipient volcanic activity and can serve as an analog for studying CO2 leakage and benthic accumulations from subsea carbon capture and storage sites.
Biochemical investigations of the mechanism of action of small molecules ZL006 and IC87201 as potential inhibitors of the nNOS-PDZ/PSD-95-PDZ interactions
Authors: Bach Anders , Pedersen Søren W. , Dorr Liam A. , Vallon Gary , Ripoche Isabelle , Ducki Sylvie , Lian Lu-Yun 
Published: July 2015

AbstractZL006 and IC87201 have been presented as efficient inhibitors of the nNOS/PSD-95 protein-protein interaction and shown great promise in cellular experiments and animal models of ischemic stroke and pain. Here, we investigate the proposed mechanism of action of ZL006 and IC87201 using biochemical and biophysical methods, such as fluorescence polarization (FP), isothermal titration calorimetry (ITC) and 1H-15N HSQC NMR. Our data show that under the applied in vitro conditions, ZL006 and IC87201 do not interact with the PDZ domains of nNOS or PSD-95, nor inhibit the nNOS-PDZ/PSD-95-PDZ interface by interacting with the β-finger of nNOS-PDZ. Our findings have implications for further medicinal chemistry efforts of ZL006, IC87201 and analogues and challenge the general and widespread view on their mechanism of action.
Memory-built-in quantum cloning in a hybrid solid-state spin register
Authors: Wang W.-B. , Zu C. , He L. , Zhang W.-G. , Duan L.-M. 
Published: July 2015

AbstractAs a way to circumvent the quantum no-cloning theorem, approximate quantum cloning protocols have received wide attention with remarkable applications. Copying of quantum states to memory qubits provides an important strategy for eavesdropping in quantum cryptography. We report an experiment that realizes cloning of quantum states from an electron spin to a nuclear spin in a hybrid solid-state spin register with near-optimal fidelity. The nuclear spin provides an ideal memory qubit at room temperature, which stores the cloned quantum states for a millisecond under ambient conditions, exceeding the lifetime of the original quantum state carried by the electron spin by orders of magnitude. The realization of a cloning machine with built-in quantum memory provides a key step for application of quantum cloning in quantum information science.
Polyubiquitination of Transforming Growth Factor β-activated Kinase 1 (TAK1) at Lysine 562 Residue Regulates TLR4-mediated JNK and p38 MAPK Activation
Authors: Chen I-Ting , Hsu Pang-Hung , Hsu Wan-Ching , Chen Nien-Jung , Tseng Ping-Hui 
Published: July 2015

AbstractToll-like receptor 4 (TLR4) plays an important role in innate immunity by eliciting inflammation. Upon receptor engagement, transforming growth factor β-activated kinase 1 (TAK1) is an essential mediator that transmits a signal from the receptor to downstream effectors, IκB kinase (IKK) and the mitogen-activated protein kinases (MAPKs), which control the production of inflammatory cytokines. However, the association between phosphorylation and ubiquitination of TAK1 is not yet clear. Here, we examined the crosstalk between phosphorylation and polyubiquitination of TAK1 and further investigated the mechanism of distinct activation of MAPKs and IKK. Inhibition of TAK1 phosphorylation enhanced Lys63-linked polyubiquitination of TAK1. Conversely, ubiquitin modification was counteracted by phospho-mimic TAK1 mutant, T(184,187)D. Moreover, using LC-MS analysis, Lys562 of TAK1 was identified as a novel Lys63-linked ubiquitination site and as the key residue in the feedback regulation. Mutation of Lys562 of TAK1 leads to a decrease in TAK1 phosphorylation and specific inhibition of the MAPK pathway, but has no effect on formation of the TAK1-containing complex. Our findings demonstrate a feedback loop for phosphorylation and ubiquitination of TAK1, indicating a dynamic regulation between TAK1 polyubiquitiantion and phosphorylated activation and the molecular mechanism by which IKK and MAPKs are differentially activated in the TLR4 pathway.
Human rather than ape-like orbital morphology allows much greater lateral visual field expansion with eye abduction
Authors: Denion Eric , Hitier Martin , Levieil Eric , Mouriaux Frédéric 
Published: July 2015

AbstractWhile convergent, the human orbit differs from that of non-human apes in that its lateral orbital margin is significantly more rearward. This rearward position does not obstruct the additional visual field gained through eye motion. This additional visual field is therefore considered to be wider in humans than in non-human apes. A mathematical model was designed to quantify this difference. The mathematical model is based on published computed tomography data in the human neuro-ocular plane (NOP) and on additional anatomical data from 100 human skulls and 120 non-human ape skulls (30 gibbons; 30 chimpanzees / bonobos; 30 orangutans; 30 gorillas). It is used to calculate temporal visual field eccentricity values in the NOP first in the primary position of gaze then for any eyeball rotation value in abduction up to 45° and any lateral orbital margin position between 85° and 115° relative to the sagittal plane. By varying the lateral orbital margin position, the human orbit can be made “non-human ape-like”. In the Pan-like orbit, the orbital margin position (98.7°) was closest to the human orbit (107.1°). This modest 8.4° difference resulted in a large 21.1° difference in maximum lateral visual field eccentricity with eyeball abduction (Pan-like: 115°; human: 136.1°).
The multidrug transporter Pdr5 on the 25th anniversary of its discovery: an important model for the study of asymmetric ABC transporters
Authors: Golin John , Ambudkar Suresh V. 
Published: July 2015

Asymmetric ABC (ATP-binding cassette) transporters make up a significant proportion of this important superfamily of integral membrane proteins. These proteins contain one canonical (catalytic) ATP-binding site and a second atypical site with little enzymatic capability. The baker's yeast (Saccharomyces cerevisiae) Pdr5 multidrug transporter is the founding member of the Pdr subfamily of asymmetric ABC transporters, which exist only in fungi and slime moulds. Because these organisms are of considerable medical and agricultural significance, Pdr5 has been studied extensively, as has its medically important homologue Cdr1 from Candida albicans. Genetic and biochemical analyses of Pdr5 have contributed important observations that are likely to be applicable to mammalian asymmetric ABC multidrug transporter proteins, including the basis of transporter promiscuity, the function of the non-catalytic deviant ATP-binding site, the most complete description of an in vivo transmission interface, and the recent discovery that Pdr5 is a molecular diode (one-way gate). In the present review, we discuss the observations made with Pdr5 and compare them with findings from clinically important asymmetric ABC transporters, such as CFTR (cystic fibrosis transmembrane conductance regulator), Cdr1 and Tap1/Tap2.
Assessing Responses of Fish to Habitat Enhancement in Barrenlands Streams of the Northwest Territories
Authors: Cahill Christopher L. , Erwin Andrea C. , Howland Kimberly L. , Hulsman Mark F. , Lunn Brianne D. , Noddin Fred , Tonn William M. , Baki Abul Basar , Courtice Gregory , Zhu David Z. 
Published: July 2015

Abstract
We examined the effectiveness of three fishpasses (two gabion-style pool–weir fishpasses and one nature-like choke-and-pool fishpass) at enhancing connectivity among three small, headwater lakes as part of a fish habitat compensation project in the Barrenlands region of the Northwest Territories. We quantified fish attraction and passage efficiency of fishpasses using PIT antennae, and compared fish use of fishpasses to reference streams using visual and electrofishing surveys for 1 year before and 2 years after their construction. We did not detect, observe, or capture any fish in either of the gabion-style pool–weir fishpasses during the first year after construction, and these two fishpasses were subsequently retrofitted to improve their hydraulic performance. After retrofits were completed, we still did not detect any tagged fish (≥150 mm) migrating through the two fishpasses using PIT telemetry, but identified some small fish moving downstream through these fishpasses during visual and electrofishing surveys. Conversely, we detected tagged Arctic Grayling Thymallus arcticus migrating upstream and downstream through the nature-like choke-and-pool fishpass during both postenhancement years, and also encountered fish throughout this fishpass during visual and electrofishing surveys. Compared with reference streams, gabion-weir fishpasses limited fish movement and use even after modification, whereas the nature-like fishpass successfully facilitated fish movement and use. We recommend against using gabion-style pool–weir fishpasses in Barrenlands headwater lake–stream systems, particularly when stream flow is limited, and suggest future projects aimed at enhancing lake–stream connectivity explore nature-like fishpass designs in an experimental management framework.